title: D496_002_HTO_CZINY-0136

city: Palo Alto

first: Lattice

last: Data Coordination

address: 3165 Porter Drive

department: Genetics

institute: Stanford University

description:
Library name: D496_002_HTO_CZINY-0136_lib
hashtag of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

data_processing:
raw_matrix_normalized:False; raw_matrix_value_scale:linear; raw_matrix_background_barcodes_included:False
Assembly: GRCh38, GENCODE32
Supplementary files format and content: h5ad, count matrix

molecule: other

extract_protocol:
Tissue was obtained from deceased organ donors at the time of organ acquisition for clinical transplantation through an approved protocol and material transfer agreement via LiveOnNY, the organ procurement organization for the New York metropolitan area and through the Cambridge Biorepository for Translational Medicine. Each tissue was subjected to a tissue-specific protocol to maximize mononuclear cell (MNC) recovery and viability across a diversity of sites. A series of detailed protocols are available on protocols.io (https://dx.doi.org/10.17504/protocols.io.bwrjpd4n, https://dx.doi.org/10.17504/protocols.io.bwr9pd96, https://dx.doi.org/10.17504/protocols.io.bwsapeae, https://dx.doi.org/10.17504/protocols.io.bwq4pdyw, https://dx.doi.org/10.17504/protocols.io.bwq7pdzn, https://dx.doi.org/10.17504/protocols.io.bwr6pd9e, https://dx.doi.org/10.17504/protocols.io.bz4qp8vw). Each individual tissue single cell suspension (500,000 or 1,000,000 cells) was hash tagged to allow pooling of tissue samples. CITE-seq labeling used either a TotalSeq-C cocktail containing 137 protein targets (10x 5’ libraries) or TotalSeq-A cocktail containing 277 protein targets (10x 3’ libraries).
For scRNA-seq experiments, single cells were loaded onto the channels of a Chromium chip (10x Genomics). cDNA synthesis, amplification, and sequencing libraries were generated using either the Single Cell 5′ Reagent (v1 and v2) or 3′ Reagent (v3) Kits. TCRαβ and BCR paired VDJ libraries were prepared from samples made with the 5′ Reagent kit. All libraries were sequenced on either an Illumina NextSeq 500/550 or NovaSeq 6000 instrument.

tag: donor id

value: 56 years

tag: dev stage

value: adult stage

value: male

tag: ethnicity

value: Hispanic or Latin American

tag: source

value: LiveOnNY

tag: suspension cell_depletion_factors

tag: living at_sample_collection

value: FALSE

tag: sample preservation_method

value: fresh

tag: smoking history

value: current, 90 pack-years

tag: death type

value: brain stem death

tag: cause of_death

value: Cerebrovascular/Stroke

tag: body mass_index

tag: height

tag: test results.ebv

value: positive

tag: test results.cmv

tag: test results.blood_sugar

value: 150 mg/dL

tag: library protocol

value: HTO 10x 3' v3 TSA

tag: raw matrix_genome_annotation

tag: raw matrix_value_units

value: UMI

tag: raw matrix_feature_keys

value: gene symbol, antibody target

tag: raw matrix_assays

value: snRNA-seq, CITE-seq

tag: enriched cell_type

value: mononuclear cell

tag: assay type

value: CITE-seq

tag: antibodies/tags


title: Inulin swtiched to SSD, Tm day11 1

status: Public on Jun 06 2025

type: SRA

city: Frederiksberg C

first: Andrew

last: Williams

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

library_source: transcriptomic

data_processing:
Adaptor sequences and low quality reads removed
Mapped to Mus musculus genome (GRCm39)
DEG assessed using DeSeq2
Assembly: GRCm39
Supplementary files format and content: excel file with count data and gene symbol for each sample

molecule: total RNA

organism: Mus musculus

source_name: Caecum

extract_protocol:
Total RNA was extracted using mRNAeasy kits (Qiagen)
Standard Illumina

tag: tissue

value: Caecum


title: Inulin swtiched to SSD, Tm day11 5


title: blood27_baseline

type: RNA

city: Malaga

first: Mora

last: Guardamagna

state: --- Select One ---

address: Severo Ochoa 35

country: Spain

institute: IBIMA

description: barcoded probe hybridization

hyb_protocol: Hybridization was performed using the NanoString nCounter PanCancer Immune Profiling Panel™ according to the manufacturer’s protocol, with 100 ng of total RNA per sample and overnight hybridization at 65°C.

scan_protocol: Hybridized samples were processed and scanned using the NanoString nCounter® Digital Analyzer following the manufacturer's instructions.

data_processing: Raw data (RCC files) were processed using NanoString nSolver™ and the NanoTube R package. Normalization was performed using the RUVg method (Remove Unwanted Variation using control genes). Differential expression analysis was performed using Limma™. Genes with log2 fold change > 1 and adjusted p-value < 0.05 were considered significant.

organism: Homo sapiens

label_protocol: Not applicable. NanoString technology uses fluorescent barcoded probe pairs for direct hybridization and does not require labeling of RNA samples.

growth_protocol: Not applicable. Peripheral blood samples were collected directly from human patients without in vitro culture.

extract_protocol: RNA was extracted from peripheral blood samples using the RNAEasy Plus Universal Mini Kit™ (for frozen samples) or the QIAamp RNA Blood Mini Kit™ (for fresh samples) according to the manufacturer’s instructions. RNA quality and quantity were assessed using NanoDrop™ spectrophotometry.

treatment_protocol: atients were treated with first-line BRAF/MEK inhibitors for BRAF V600-mutated metastatic melanoma. Blood samples were collected at baseline (T0) and at the first radiological evaluation (T1).

tag: Sex

value: female

tag: responder

value: yes

tag: timepoint

value: BASELINE


title: D496_002_HTO_CZINY-0134

state: CA

country: USA

description:
Library name: D496_002_HTO_CZINY-0134_lib
hashtag of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

library_source: other

tag: donor id

tag: age

value: 56 years

tag: dev stage

value: adult stage

value: male

tag: ethnicity

value: Hispanic or Latin American

tag: source

value: LiveOnNY

tag: suspension cell_depletion_factors

tag: living at_sample_collection

value: FALSE

tag: sample preservation_method

tag: smoking history

tag: death type

tag: cause of_death

tag: body mass_index


title: Hippocampus infected control virus, Ctrl1

city: Hefei

first: d

last: z

address: shushan

country: China

institute: University of Science and Technology of China

data_processing:
DEGSeq
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files includes RPKM values for each Sample

source_name: hippocampus

extract_protocol:
RNA was harvested using MagZol Reagent (Magen). 1.5 ug of total RNA was used for the construction of sequencing libraries.
(1) Total RNA samples were tested and then enriched for eukaryotic mRNA by Oligo(dT) magnetic beads; (2) Add Fragmentation Buffer for mRNA fragmentation; (3) One strand of cDNA was synthesised using a six-base random primer using mRNA as a template, followed by the synthesis of the second strand of cDNA using buffer, dNTPs, DNA polymerase I and RNase H, and cDNA purification; (4) Purified double-stranded cDNA was subjected to end repair, base A was added, sequencing junctions were added, and fragments were screened to recover cDNA around 350 bp; (5) PCR enrichment was performed to obtain cDNA libraries.

value: hippocampus


title: blood26_T1

description: barcoded probe hybridization


title: SSD switched to Inulin, Tm day11 4


title: D496_002_HTO_CZINY-0135

description:
Library name: D496_002_HTO_CZINY-0135_lib
hashtag of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

value: fresh

value: current, 90 pack-years

value: brain stem death

value: Cerebrovascular/Stroke

tag: height

tag: test results.ebv

value: positive

tag: test results.cmv

tag: test results.blood_sugar

value: 150 mg/dL

tag: library protocol

value: HTO 10x 3' v3 TSA

tag: raw matrix_genome_annotation

tag: raw matrix_value_units

tag: raw matrix_feature_keys

tag: raw matrix_assays

tag: enriched cell_type

tag: assay type

tag: antibodies/tags


title: SSD switched to Inulin, Tm day11 3

tag: tissue

value: Caecum


title: Cerebellum, Cxcr4+/+

city: Rozzano

first: Simona

last: Lodato

address: via Manzoni 56

country: Italy

institute: IRCCS Humanitas Research Hospital

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexing has been performed using bcl2fastq v2.20.0.4222 (Illumina)
Barcode processing and gene counting were made using the Cellranger software v7.2 (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: Cerebellum

extract_protocol:
Freshly microdissected lobule III-IV regiond form Cxcr4+/- and control mice cerebella at P1 in ice cold HBSS solution (Mg2+/Ca2+ free supplemented with 10mM HEPES, pH 7.2). The tissues were dissociated to single cell suspension using Papain Dissociation System kit (Worthington-Biochemical, #LK003150).
Library was performed according to the manufacture's instruction of Chromium Next GEM Single Cell 3' kit  v3.1 (10X Genomics, #1000269).
3' gene expression scRNA-seq

value: Cerebellum

tag: genotype

tag: strain

tag: age


title: SSD switched to Inulin, Tm day11 5


title: Inulin swtiched to SSD, Tm day11 3


title: Cerebellum, Cxcr4+/1013

description: 10X Genomics


title: FACS sorted tumor cells from combination (IR + AZD1390) treated tumors biological replicate 6

city: Cambridge

first: Amir

last: Jassim

address: Robinson Way

country: United Kingdom

institute: Cancer Research UK Cambridge Institute

description: 10x Genomics

data_processing:
FASTQ files were processed using Cellranger version 3.1.0 and aligned to the Mus Musculus (mm10-3.0.0) assembly generating barcoded matrices
Assembly: mm10
Supplementary files format and content: Cellranger filtered_feature_bc_matrix output

source_name: Brain

extract_protocol:
Sorted cells were submitted for 10X sequencing and libraries were prepared using the Chromium Single Cell 3’ Reagents kits v.3. Samples were resuspended in PBS with 0.04% BSA and loaded onto the Chromium microfluidic chip (10x genomics) to generate single-cell bead emulsions with individual 10x barcodes.
RNA from barcoded cells was reverse transcribed in a C1000 Touch Thermal Cycler (Bio-Rad) and libraries were prepared according to manufacturers protocols (12 cycles for cDNA amplification). cDNA quantity and quality was measured using an Agilent TapeStation 4200 and about 375ng of material was used for library preparation. Libraries were normalized to equal molar concentrations (10nM) and pooled before being sequenced on a NovaSeq 6000.

value: Brain

tag: cell line

tag: cell type

value: Dual RFP/YFP +ve FACS sorted tumor cells

tag: treatment

value: combination treatment AZD1390 + IR

value: Trp53-/-;Rb-/-; Pten-/- ;ROSAYFP


title: blood26_baseline

description: barcoded probe hybridization

tag: Sex

value: male

tag: responder

value: yes

tag: timepoint

value: BASELINE


title: D496_002_HTO_CZINY-0133

description:
Library name: D496_002_HTO_CZINY-0133_lib
hashtag of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

tag: donor id

value: 56 years

tag: dev stage

value: adult stage

tag: ethnicity

value: Hispanic or Latin American

tag: source

value: LiveOnNY

tag: suspension cell_depletion_factors

tag: living at_sample_collection

value: FALSE

tag: sample preservation_method

tag: smoking history

tag: death type

tag: cause of_death

tag: body mass_index

tag: height

tag: test results.ebv

tag: test results.cmv

tag: test results.blood_sugar

tag: library protocol

tag: raw matrix_genome_annotation

value: UMI

value: gene symbol, antibody target

value: snRNA-seq, CITE-seq

value: mononuclear cell

value: CITE-seq


title: SSD switched to Inulin, Tm day11 2

tag: tissue

value: Caecum


title: blood25_baseline

description: barcoded probe hybridization

tag: Sex

value: female

tag: responder

value: no

tag: timepoint


title: FACS sorted tumor cells from untreated CPC tumors biological replicate 2

description: 10x Genomics

value: Brain

tag: cell line

tag: cell type

value: Dual RFP/YFP +ve FACS sorted tumor cells

tag: treatment

value: untreated CPC

tag: genotype

value: Trp53-/-;Rb-/-; Pten-/- ;ROSAYFP


title: blood25_T1

description: barcoded probe hybridization


title: blood23_T1

description: barcoded probe hybridization

value: male

value: yes


title: D496_002_HTO_CZINY-0130

description:
Library name: D496_002_HTO_CZINY-0130_lib
hashtag of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

tag: donor id

tag: age

value: 56 years

tag: dev stage

value: adult stage

tag: ethnicity

value: Hispanic or Latin American

tag: source

tag: suspension cell_depletion_factors

tag: living at_sample_collection

tag: sample preservation_method

value: fresh

tag: smoking history

value: current, 90 pack-years

tag: death type

value: brain stem death

value: Cerebrovascular/Stroke

value: positive

value: 150 mg/dL

value: HTO 10x 3' v3 TSA

tag: raw matrix_value_units

tag: raw matrix_feature_keys

tag: raw matrix_assays

tag: enriched cell_type

tag: assay type

tag: antibodies/tags


title: Inulin, Tm day11 3

tag: tissue

value: Caecum


title: D496_002_HTO_CZINY-0131

description:
Library name: D496_002_HTO_CZINY-0131_lib
hashtag of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

tag: donor id

tag: Sex

value: LiveOnNY

value: FALSE

tag: cause of_death

tag: body mass_index

tag: height

tag: test results.ebv

tag: test results.cmv

tag: test results.blood_sugar

tag: library protocol

tag: raw matrix_genome_annotation

value: UMI

value: gene symbol, antibody target

value: snRNA-seq, CITE-seq

value: mononuclear cell

value: CITE-seq


title: D496_002_HTO_CZINY-0129

description:
Library name: D496_002_HTO_CZINY-0129_lib
hashtag of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

tag: age

value: 56 years

tag: dev stage

value: adult stage

value: male

tag: ethnicity

tag: source

tag: suspension cell_depletion_factors

tag: living at_sample_collection

tag: sample preservation_method

tag: smoking history

tag: death type

tag: raw matrix_value_units


title: SSD switched to Inulin, Tm day11 1

tag: tissue


title: FACS sorted tumor cells from AZD1390 treated CPC tumors biological replicate 3

description: 10x Genomics

value: Brain

tag: cell line

tag: cell type

value: Dual RFP/YFP +ve FACS sorted tumor cells

tag: treatment

value: AZD1390 treated

tag: genotype

value: Trp53-/-;Rb-/-; Pten-/- ;ROSAYFP


title: Inulin, Tm day11 2


title: FACS sorted tumor cells from IR treated CPC tumors biological replicate 3

description: 10x Genomics

value: IR treated


title: blood22_T1

description: barcoded probe hybridization

tag: Sex

value: female

tag: responder

value: yes

tag: timepoint


title: blood23_baseline

description: barcoded probe hybridization

value: BASELINE


title: Inulin, Tm day11 1

value: Caecum


title: FACS sorted tumor cells from combination (IR + AZD1390) treated tumors biological replicate 5

description: 10x Genomics

value: combination treatment AZD1390 + IR


title: blood22_baseline

description: barcoded probe hybridization


title: D496_002_HTO_CZINY-0120

description:
Library name: D496_002_HTO_CZINY-0120_lib
hashtag of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

tag: donor id

tag: age

tag: dev stage

value: Hispanic or Latin American

value: LiveOnNY

value: FALSE

value: fresh

value: current, 90 pack-years

value: brain stem death

tag: cause of_death

value: Cerebrovascular/Stroke

tag: body mass_index

tag: height

tag: test results.ebv

value: positive

tag: test results.cmv

tag: test results.blood_sugar

value: 150 mg/dL

tag: library protocol

value: HTO 10x 3' v3 TSA

tag: raw matrix_genome_annotation

value: UMI

tag: raw matrix_feature_keys

value: gene symbol, antibody target

tag: raw matrix_assays

tag: enriched cell_type

tag: assay type

tag: antibodies/tags


title: D496_002_HTO_CZINY-0132

description:
Library name: D496_002_HTO_CZINY-0132_lib
hashtag of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

value: 56 years

value: adult stage

tag: Sex

value: male

tag: ethnicity

tag: tissue

tag: source

tag: suspension cell_depletion_factors

tag: living at_sample_collection

tag: sample preservation_method

tag: smoking history

tag: death type

tag: raw matrix_value_units

value: snRNA-seq, CITE-seq

value: mononuclear cell

value: CITE-seq


title: FACS sorted tumor cells from untreated CPC tumors biological replicate 1

description: 10x Genomics

value: Brain

tag: cell line

tag: cell type

value: Dual RFP/YFP +ve FACS sorted tumor cells

tag: treatment

value: untreated CPC

tag: genotype

value: Trp53-/-;Rb-/-; Pten-/- ;ROSAYFP


title: SSD, Tm day11 3

value: Caecum


title: D496_002_HTO_CZINY-0119

description:
Library name: D496_002_HTO_CZINY-0119_lib
hashtag of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

tag: donor id

tag: age

tag: dev stage

value: Hispanic or Latin American

value: LiveOnNY

value: FALSE

value: fresh

value: current, 90 pack-years

value: brain stem death

tag: cause of_death

value: Cerebrovascular/Stroke

tag: body mass_index

tag: height

tag: test results.ebv

tag: test results.cmv

tag: test results.blood_sugar

tag: library protocol

tag: raw matrix_genome_annotation

tag: raw matrix_feature_keys

tag: raw matrix_assays

tag: enriched cell_type


title: blood21_T1

description: barcoded probe hybridization

tag: Sex

value: female

tag: responder

value: yes

tag: timepoint


title: SSD, Tm day11 2

tag: tissue


title: FACS sorted tumor cells from AZD1390 treated CPC tumors biological replicate 2

description: 10x Genomics

tag: cell line

tag: cell type

tag: treatment

value: AZD1390 treated

tag: genotype


title: D496_002_HTO_CZINY-0118

description:
Library name: D496_002_HTO_CZINY-0118_lib
hashtag of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

tag: donor id

tag: age

value: 56 years

tag: dev stage

value: adult stage

value: male

tag: ethnicity

tag: source

tag: suspension cell_depletion_factors

tag: living at_sample_collection

tag: sample preservation_method

tag: smoking history

tag: death type

tag: cause of_death

tag: body mass_index

tag: height

value: positive

value: 150 mg/dL

value: HTO 10x 3' v3 TSA

tag: raw matrix_value_units

value: UMI

value: gene symbol, antibody target

value: snRNA-seq, CITE-seq

value: mononuclear cell

tag: assay type

tag: antibodies/tags


title: D496_002_HTO_CZINY-0117

description:
Library name: D496_002_HTO_CZINY-0117_lib
hashtag of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

tag: Sex

value: Hispanic or Latin American

tag: tissue

value: LiveOnNY

value: FALSE

value: fresh

tag: test results.ebv

tag: test results.cmv

tag: test results.blood_sugar

tag: library protocol

tag: raw matrix_genome_annotation

tag: raw matrix_feature_keys

tag: raw matrix_assays

tag: enriched cell_type

value: CITE-seq


title: FACS sorted tumor cells from IR treated CPC tumors biological replicate 2

description: 10x Genomics

value: Brain

tag: cell line

tag: cell type

value: Dual RFP/YFP +ve FACS sorted tumor cells

tag: treatment

value: IR treated

tag: genotype

value: Trp53-/-;Rb-/-; Pten-/- ;ROSAYFP


title: SSD, Tm day11 1

value: Caecum


title: FACS sorted tumor cells from AZD1390 treated CPC tumors biological replicate 1

description: 10x Genomics

value: AZD1390 treated


title: D496_002_HTO_CZINY-0116

description:
Library name: D496_002_HTO_CZINY-0116_lib
hashtag of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

tag: donor id

tag: age

value: 56 years

tag: dev stage

value: adult stage

value: male

tag: ethnicity

tag: source

tag: suspension cell_depletion_factors

tag: living at_sample_collection

tag: sample preservation_method

tag: smoking history

value: current, 90 pack-years

tag: death type

value: brain stem death

tag: cause of_death

value: Cerebrovascular/Stroke

tag: body mass_index

tag: height

value: positive

value: 150 mg/dL

tag: raw matrix_value_units


title: KO_5

city: Beijing

first: Yuandong

last: Tao

address: Beijing

institute: Chinese PLA General Hospital

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: Hisat2 v2.0.5
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample

source_name: Kidney

extract_protocol:
RNA was extracted using TRIzol (Thermo Fisher). 1.5 μg RNA was used for the construction of sequencing libraries.
RNA libraries were prepared using mRNA-seq Library Prep Kit following manufacture’s protocols.

tag: tissue

value: Kidney

value: UUO


title: blood21_baseline

description: barcoded probe hybridization

tag: Sex

value: female

tag: responder

value: yes

tag: timepoint

value: BASELINE


title: D496_002_HTO_CZINY-0115

description:
Library name: D496_002_HTO_CZINY-0115_lib
hashtag of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

tag: donor id

tag: age

value: Hispanic or Latin American

value: LiveOnNY

value: FALSE

value: fresh

tag: test results.ebv

tag: test results.cmv

tag: test results.blood_sugar

tag: library protocol

value: HTO 10x 3' v3 TSA

tag: raw matrix_genome_annotation

value: UMI

tag: raw matrix_feature_keys

value: gene symbol, antibody target

tag: raw matrix_assays

value: snRNA-seq, CITE-seq

tag: enriched cell_type

value: mononuclear cell

tag: assay type

value: CITE-seq

tag: antibodies/tags


title: KO_4

tag: genotype

tag: treatment


title: FACS sorted tumor cells from IR treated CPC tumors biological replicate 1

description: 10x Genomics

tag: tissue

value: Brain

tag: cell line

tag: cell type

value: Dual RFP/YFP +ve FACS sorted tumor cells

value: IR treated

value: Trp53-/-;Rb-/-; Pten-/- ;ROSAYFP


title: blood20_T1

description: barcoded probe hybridization

tag: Sex

value: male

tag: responder

tag: timepoint


title: D496_002_HTO_CZINY-0114

description:
Library name: D496_002_HTO_CZINY-0114_lib
hashtag of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

tag: donor id

tag: age

value: 56 years

tag: dev stage

value: adult stage

tag: ethnicity

tag: source

tag: suspension cell_depletion_factors

tag: living at_sample_collection

tag: sample preservation_method

tag: smoking history

value: current, 90 pack-years

tag: death type

value: brain stem death

tag: cause of_death

value: Cerebrovascular/Stroke

tag: body mass_index

tag: height

tag: test results.ebv

value: positive

tag: test results.cmv

value: 150 mg/dL

tag: raw matrix_value_units


title: FACS sorted tumor cells from combination (IR + AZD1390) treated tumors biological replicate 4

description: 10x Genomics

tag: tissue

tag: cell line

tag: cell type

tag: treatment

value: combination treatment AZD1390 + IR

tag: genotype


title: blood20_baseline

description: barcoded probe hybridization

tag: Sex

tag: responder

value: yes

tag: timepoint

value: BASELINE


title: blood18_T1

description: barcoded probe hybridization

value: female

value: no


title: KO_2

value: Kidney

value: UUO


title: blood17_baseline

description: barcoded probe hybridization


title: FACS sorted tumor cells from combination (IR + AZD1390) treated tumors biological replicate 3

description: 10x Genomics

value: Brain

value: Dual RFP/YFP +ve FACS sorted tumor cells


title: D496_002_HTO_CZINY-0113

description:
Library name: D496_002_HTO_CZINY-0113_lib
hashtag of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

tag: donor id

tag: age

tag: dev stage

value: male

tag: ethnicity

value: Hispanic or Latin American

tag: source

value: LiveOnNY

tag: suspension cell_depletion_factors

tag: living at_sample_collection

value: FALSE

tag: sample preservation_method

value: fresh

tag: test results.blood_sugar

tag: library protocol

value: HTO 10x 3' v3 TSA

tag: raw matrix_genome_annotation

value: UMI

tag: raw matrix_feature_keys

value: gene symbol, antibody target

tag: raw matrix_assays

value: snRNA-seq, CITE-seq

tag: enriched cell_type

value: mononuclear cell

tag: assay type

value: CITE-seq

tag: antibodies/tags


title: FACS sorted tumor cells from combination (IR + AZD1390) treated tumors biological replicate 2

description: 10x Genomics

tag: tissue

tag: cell line

tag: cell type

tag: treatment

value: combination treatment AZD1390 + IR

tag: genotype

value: Trp53-/-;Rb-/-; Pten-/- ;ROSAYFP


title: D496_002_ADT_CZINY-0144

description:
Library name: D496_002_ADT_CZINY-0144_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

tag: donor id

tag: age

value: 56 years

tag: dev stage

value: adult stage

tag: Sex

tag: ethnicity

tag: source

tag: smoking history

value: current, 90 pack-years

tag: death type

value: brain stem death

tag: cause of_death

value: Cerebrovascular/Stroke

tag: body mass_index

tag: height

tag: test results.ebv

value: positive

tag: test results.cmv

value: 150 mg/dL

value: CITE 10x 3' v3 TSA

tag: raw matrix_value_units

value: TotalSeq-A Human Universal Cocktail


title: KO_1

tag: tissue

value: Kidney

value: UUO


title: blood16_T1

description: barcoded probe hybridization

value: female

tag: responder

value: yes

tag: timepoint


title: D496_002_ADT_CZINY-0143

description:
Library name: D496_002_ADT_CZINY-0143_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

tag: donor id

value: male

value: Hispanic or Latin American

value: LiveOnNY

tag: suspension cell_depletion_factors

tag: living at_sample_collection

value: FALSE

tag: sample preservation_method

value: fresh

tag: test results.blood_sugar

tag: library protocol

tag: raw matrix_genome_annotation

value: UMI

tag: raw matrix_feature_keys

value: gene symbol, antibody target

tag: raw matrix_assays

value: snRNA-seq, CITE-seq

tag: enriched cell_type

value: mononuclear cell

tag: assay type

tag: antibodies/tags


title: FACS sorted tumor cells from combination (IR + AZD1390) treated tumors biological replicate 1

description: 10x Genomics

value: Brain

tag: cell line

tag: cell type

value: Dual RFP/YFP +ve FACS sorted tumor cells

tag: treatment

value: combination treatment AZD1390 + IR

tag: genotype

value: Trp53-/-;Rb-/-; Pten-/- ;ROSAYFP


title: blood16_baseline

description: barcoded probe hybridization

tag: Sex

tag: responder

tag: timepoint

value: BASELINE


title: TAA_miR_7

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

institute: Tigem

description:
EXP1
Transcriptome profile of mice treated with TAA and injected with AAV8 TBG miR34b/c, biological rep7

data_processing:
Sequence reads were trimmed using bbduk software(https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/usage-guide/) (bbmap suite 37.31) to remove adapter sequences, poly-A tails and low-quality end bases (regions with average quality below 6) and then aligned on mm10 reference sequence using STAR
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: Liver of C57BL6J mice

growth_protocol: All mice received humane care according to the criteria outlined in the Guide for the Care and Use of Laboratory Animals. Male 6- to 8-week-old C57BL/6 (Charles River Laboratories) mice were used for this study

extract_protocol:
RNA was quantified and mixed at 10ng/µl
Total RNA (100 ng) from each sample was prepared using QuantSeq 3'mRNA-Seq Library prep kit  (Lexogen, Vienna, Austria) according to manufacturer's instructions
The amplified fragmented cDNA of 300 bp in size were sequenced in single-end mode using the Illumina NovaSeq 6000 with a read length of 100 bp

treatment_protocol: Mice were treated for 12 weeks with increasing doses of TAA in order to induce advanced fibrosis/cirrhosis.  After 10 weeks of TAA, mice were injected with a combination of both AAV8 TBG miR-34b and AAV8 TBG mir-34c), or an AAV expressing green fluorescent protein (GFP) as control and sacrificed after 4 weeks and we extracted the RNA from liver.

tag: agent

value: TAA and injected with AAV8 TBG miR34b/c

tag: strain


title: WT_5

tag: tissue

value: Kidney

value: WT

value: UUO


title: D496_002_ADT_CZINY-0142

description:
Library name: D496_002_ADT_CZINY-0142_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

tag: donor id

tag: age

value: 56 years

tag: dev stage

value: adult stage

value: male

tag: ethnicity

value: Hispanic or Latin American

tag: source

tag: suspension cell_depletion_factors

tag: living at_sample_collection

tag: sample preservation_method

tag: smoking history

value: current, 90 pack-years

tag: death type

value: brain stem death

tag: cause of_death

value: Cerebrovascular/Stroke

tag: body mass_index

tag: height

tag: test results.ebv

value: positive

tag: test results.cmv

tag: test results.blood_sugar

value: 150 mg/dL

tag: library protocol

value: CITE 10x 3' v3 TSA

tag: raw matrix_value_units

value: CITE-seq

value: TotalSeq-A Human Universal Cocktail


title: blood15_T1

description: barcoded probe hybridization

tag: Sex

value: female

tag: responder

value: yes

tag: timepoint


title: WT_4

tag: tissue

value: Kidney

tag: genotype

tag: treatment


title: TAA_miR_6

description:
EXP1
Transcriptome profile of mice treated with TAA and injected with AAV8 TBG miR34b/c, biological rep6

tag: agent

value: TAA and injected with AAV8 TBG miR34b/c

tag: strain


title: blood18_baseline

description: barcoded probe hybridization

value: no

value: BASELINE


title: blood15_baseline

description: barcoded probe hybridization


title: TAA_miR_5

description:
EXP1
Transcriptome profile of mice treated with TAA and injected with AAV8 TBG miR34b/c, biological rep5


title: D496_002_ADT_CZINY-0141

description:
Library name: D496_002_ADT_CZINY-0141_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

tag: donor id

tag: age

value: 56 years

tag: dev stage

value: adult stage

tag: ethnicity

tag: source

value: LiveOnNY

tag: suspension cell_depletion_factors

tag: living at_sample_collection

value: FALSE

tag: sample preservation_method

value: fresh

tag: smoking history

tag: death type

tag: raw matrix_genome_annotation

value: UMI

tag: raw matrix_feature_keys

value: gene symbol, antibody target

tag: raw matrix_assays

value: snRNA-seq, CITE-seq

tag: enriched cell_type

value: mononuclear cell

tag: assay type

tag: antibodies/tags


title: WT_3

tag: tissue

tag: genotype

value: WT

tag: treatment

value: UUO


title: KO_3


title: TAA_miR_4

description:
EXP1
Transcriptome profile of mice treated with TAA and injected with AAV8 TBG miR34b/c, biological rep4

tag: agent

tag: strain


title: D496_002_ADT_CZINY-0140

description:
Library name: D496_002_ADT_CZINY-0140_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

tag: donor id

tag: age

tag: dev stage

tag: Sex

value: male

tag: ethnicity

value: Hispanic or Latin American

tag: source

value: current, 90 pack-years

value: brain stem death

tag: cause of_death

value: Cerebrovascular/Stroke

tag: body mass_index

tag: height

tag: test results.ebv

value: positive

tag: test results.cmv

tag: test results.blood_sugar

value: 150 mg/dL

tag: library protocol

value: CITE 10x 3' v3 TSA

tag: raw matrix_value_units

value: CITE-seq

value: TotalSeq-A Human Universal Cocktail


title: WT_2

tag: tissue

value: Kidney

tag: genotype

tag: treatment


title: D496_002_ADT_CZINY-0138

description:
Library name: D496_002_ADT_CZINY-0138_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

tag: donor id

value: 56 years

value: adult stage

value: LiveOnNY

tag: suspension cell_depletion_factors

tag: living at_sample_collection

value: FALSE

tag: sample preservation_method

value: fresh

tag: smoking history

tag: death type

tag: raw matrix_genome_annotation

value: UMI

tag: raw matrix_feature_keys

tag: raw matrix_assays

tag: enriched cell_type

tag: assay type

tag: antibodies/tags


title: blood11_T1

description: barcoded probe hybridization

tag: Sex

value: male

tag: responder

value: yes

tag: timepoint


title: CD4 T cells, ASO3

city: Baltimore

first: Wesley

last: Godfrey

state: MD

address: 600 N Wolfe, Pathology 508, pathology 508

institute: Johns Hopkins University

data_processing:
FASTQ files were demultiplexed and aligned to the mouse reference genome and quantification was performed with Kallisto.
Assembly: The mouse reference genome GRCm38 was used.
Supplementary files format and content: raw counts

source_name: Splenocytes

extract_protocol:
RNA was extracted via Rneasy kit.
Library construction was performed in collaboration with Novogene according to standard operating protocols.

tag: cell line

value: primary cells

tag: cell type

value: CD4 T cells

tag: genotype

value: WT

value: ASO


title: D496_002_ADT_CZINY-0137

description:
Library name: D496_002_ADT_CZINY-0137_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

tag: donor id

tag: age

tag: dev stage

tag: ethnicity

value: Hispanic or Latin American

tag: tissue

tag: source

tag: suspension cell_depletion_factors

value: current, 90 pack-years

value: brain stem death

tag: cause of_death

value: Cerebrovascular/Stroke

tag: body mass_index

tag: height

tag: test results.ebv

value: positive

tag: test results.cmv

tag: test results.blood_sugar

value: 150 mg/dL

tag: library protocol

tag: raw matrix_value_units

value: gene symbol, antibody target

value: snRNA-seq, CITE-seq

value: mononuclear cell


title: TAA_miR_2

description:
EXP1
Transcriptome profile of mice treated with TAA and injected with AAV8 TBG miR34b/c, biological rep2

tag: agent

value: TAA and injected with AAV8 TBG miR34b/c

tag: strain


title: D496_002_ADT_CZINY-0139

description:
Library name: D496_002_ADT_CZINY-0139_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

tag: donor id

value: 56 years

value: adult stage

tag: Sex

value: LiveOnNY

tag: living at_sample_collection

value: FALSE

tag: sample preservation_method

value: fresh

tag: smoking history

tag: death type

value: CITE 10x 3' v3 TSA

tag: raw matrix_genome_annotation

value: UMI

tag: raw matrix_feature_keys

tag: raw matrix_assays

tag: enriched cell_type

tag: assay type

value: CITE-seq

tag: antibodies/tags

value: TotalSeq-A Human Universal Cocktail


title: blood14_baseline

description: barcoded probe hybridization

value: male

tag: responder

value: no

tag: timepoint

value: BASELINE


title: WT_1

tag: tissue

value: Kidney

tag: genotype

value: WT

tag: treatment

value: UUO


title: blood11_baseline

description: barcoded probe hybridization

value: yes


title: TAA_miR_1

description:
EXP1
Transcriptome profile of mice treated with TAA and injected with AAV8 TBG miR34b/c, biological rep1

tag: agent

value: TAA and injected with AAV8 TBG miR34b/c

tag: strain


title: CD4 T cells, ASO2

tag: cell line

value: primary cells

tag: cell type

value: CD4 T cells

value: ASO


title: TAA_GFP_7

description:
CTR2
Transcriptome profile of mice treated with TAA and injected with AAV8 TBG eGFP, biological rep7

value: TAA and injected with AAV8 TBG eGFP


title: D496_002_ADT_CZINY-0128

description:
Library name: D496_002_ADT_CZINY-0128_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

tag: donor id

tag: age

value: 56 years

tag: dev stage

value: adult stage

tag: Sex

tag: ethnicity

value: Hispanic or Latin American

tag: source

value: LiveOnNY

tag: suspension cell_depletion_factors

tag: living at_sample_collection

value: FALSE

tag: sample preservation_method

value: fresh

tag: smoking history

value: current, 90 pack-years

value: brain stem death

tag: cause of_death

value: Cerebrovascular/Stroke

tag: body mass_index

tag: height

tag: test results.ebv

value: positive

tag: test results.cmv

tag: test results.blood_sugar

value: 150 mg/dL

tag: library protocol

tag: raw matrix_value_units

value: gene symbol, antibody target

value: snRNA-seq, CITE-seq

value: mononuclear cell


title: blood10_T1

description: barcoded probe hybridization

value: male

tag: responder

value: no

tag: timepoint


title: blood10_baseline

description: barcoded probe hybridization

tag: Sex

value: BASELINE


title: D496_002_ADT_CZINY-0126

description:
Library name: D496_002_ADT_CZINY-0126_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

tag: donor id

tag: age

value: 56 years

tag: dev stage

tag: ethnicity

tag: tissue

tag: death type

value: CITE 10x 3' v3 TSA

tag: raw matrix_genome_annotation

value: UMI

tag: raw matrix_feature_keys

tag: raw matrix_assays

tag: enriched cell_type

tag: assay type

value: CITE-seq

tag: antibodies/tags

value: TotalSeq-A Human Universal Cocktail


title: CD4 T cells, ASO1

tag: cell line

value: primary cells

tag: cell type

value: CD4 T cells

tag: genotype

value: WT

tag: treatment

value: ASO


title: CD4 T cells, Scramble3

value: Scramble


title: D496_002_ADT_CZINY-0125

description:
Library name: D496_002_ADT_CZINY-0125_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

value: adult stage

tag: Sex

value: Hispanic or Latin American

tag: source

value: LiveOnNY

tag: suspension cell_depletion_factors

tag: living at_sample_collection

value: FALSE

tag: sample preservation_method

value: fresh

tag: smoking history

value: current, 90 pack-years

value: brain stem death

tag: cause of_death

value: Cerebrovascular/Stroke

tag: body mass_index

tag: height

tag: test results.ebv

value: positive

tag: test results.cmv

tag: test results.blood_sugar

value: 150 mg/dL

tag: library protocol

tag: raw matrix_value_units


title: TAA_miR_3

description:
EXP1
Transcriptome profile of mice treated with TAA and injected with AAV8 TBG miR34b/c, biological rep3

tag: agent

value: TAA and injected with AAV8 TBG miR34b/c

tag: strain


title: blood08_T1

description: barcoded probe hybridization

value: female

tag: responder

value: yes

tag: timepoint


title: blood09_T1

description: barcoded probe hybridization

tag: Sex

value: male


title: blood09_baseline

description: barcoded probe hybridization

value: BASELINE


title: TAA_GFP_5

description:
CTR2
Transcriptome profile of mice treated with TAA and injected with AAV8 TBG eGFP, biological rep5

value: TAA and injected with AAV8 TBG eGFP


title: CD4 T cells, Scramble2

tag: cell line

value: primary cells

tag: cell type

value: CD4 T cells

tag: genotype

value: WT

tag: treatment

value: Scramble


title: TAA_GFP_6

description:
CTR2
Transcriptome profile of mice treated with TAA and injected with AAV8 TBG eGFP, biological rep6


title: CD4 T cells, Scramble1


title: NCI-H660 FOXA2 DiMeLo-seq

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

library_source: genomic

data_processing:
base calling and alignment: guppy/6.2.1_cpu
config file: res_dna_r941_min_modbases-all-context_v001.cfg
Assembly: hg38
Library strategy: DiMeLo-seq

molecule: genomic DNA

source_name: Prostate

growth_protocol: 1.Prostate cancer cell lines LNCaP cells were maintained in RPMI1640 with 10% fetal bovine serum (FBS), 1% penicillin and streptomycin  2. LuCaP PDX were maintained in NOD SCID male mice which were purchased from Charles River Laboratories.

extract_protocol:
The genomic DNA of LuCaP PDX  and LNCaP+FOXA2 cells was extracted with Quick-DNA Miniprep Plus Kit (Zymo, D4068) and fragmented to average size at 8 kb with g-TUBE™ (Covaris, 520079).
The DNA libraries were prepared using Ligation Sequencing Kit (ON SQK-LSK110) per manufacturer’s protocol.
Sequencing was performed on an Oxford Nanopore GridiON sequencer with R9.4.1 flow cells (FLO-MIN106D) from Oxford Nanopore. Adaptive sampling (AS) method was used for targeted sequencing of regions of interest (ROI).

treatment_protocol: LNCaP cells were infected with FOXA2 overexpression virus and fallowed up by 28 days, cells were collected at D2, D14 and D28 for FOXA2 DiMeLo-seq.

tag: tissue

value: Prostate

value: Prostate cancer cell

tag: antibody

value: FOXA2 (Abcam, Cat#ab108422)


title: blood07_T1

description: barcoded probe hybridization


title: D496_002_ADT_CZINY-0127

description:
Library name: D496_002_ADT_CZINY-0127_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

tag: donor id

tag: age

value: 56 years

tag: dev stage

value: adult stage

tag: ethnicity

value: Hispanic or Latin American

tag: source

value: LiveOnNY

tag: suspension cell_depletion_factors

tag: living at_sample_collection

value: FALSE

tag: sample preservation_method

value: fresh

tag: smoking history

value: current, 90 pack-years

tag: death type

value: brain stem death

tag: cause of_death

tag: body mass_index

tag: height

value: CITE 10x 3' v3 TSA

tag: raw matrix_genome_annotation

value: UMI

tag: raw matrix_feature_keys

value: gene symbol, antibody target

tag: raw matrix_assays

value: snRNA-seq, CITE-seq

tag: enriched cell_type

value: mononuclear cell

tag: assay type

value: CITE-seq

tag: antibodies/tags

value: TotalSeq-A Human Universal Cocktail


title: TAA_GFP_4

description:
CTR2
Transcriptome profile of mice treated with TAA and injected with AAV8 TBG eGFP, biological rep4

tag: agent

value: TAA and injected with AAV8 TBG eGFP

tag: strain


title: D496_002_ADT_CZINY-0122

description:
Library name: D496_002_ADT_CZINY-0122_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

tag: donor id

tag: age

tag: dev stage

tag: Sex

value: male

tag: ethnicity

tag: tissue

tag: source

value: Cerebrovascular/Stroke

tag: test results.ebv

value: positive

tag: test results.cmv

tag: test results.blood_sugar

value: 150 mg/dL

tag: library protocol

tag: raw matrix_value_units


title: LuCaP145.1 FOXA2 DiMeLo-seq

value: Prostate

tag: cell line

value: LuCaP145.1 PDX

tag: cell type

value: Prostate cancer cell

tag: genotype

value: WT

tag: antibody

value: FOXA2 (Abcam, Cat#ab108422)

tag: treatment


title: TAA_GFP_3

description:
CTR2
Transcriptome profile of mice treated with TAA and injected with AAV8 TBG eGFP, biological rep3

tag: agent

tag: strain


title: D496_002_ADT_CZINY-0121

description:
Library name: D496_002_ADT_CZINY-0121_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

tag: donor id

tag: age

value: 56 years

tag: dev stage

value: adult stage

value: Hispanic or Latin American

value: LiveOnNY

tag: suspension cell_depletion_factors

tag: living at_sample_collection

value: FALSE

tag: sample preservation_method

value: fresh

tag: smoking history

value: current, 90 pack-years

tag: death type

value: brain stem death

tag: cause of_death

tag: body mass_index

tag: height

value: CITE 10x 3' v3 TSA

tag: raw matrix_genome_annotation

tag: raw matrix_feature_keys

tag: raw matrix_assays

tag: enriched cell_type

tag: assay type

tag: antibodies/tags


title: D496_002_ADT_CZINY-0123

description:
Library name: D496_002_ADT_CZINY-0123_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

tag: donor id

tag: Sex

value: male

tag: ethnicity

tag: tissue

tag: source

value: Cerebrovascular/Stroke

tag: test results.ebv

tag: test results.cmv

tag: test results.blood_sugar

tag: library protocol

tag: raw matrix_value_units

value: UMI

value: gene symbol, antibody target

value: snRNA-seq, CITE-seq

value: mononuclear cell

value: CITE-seq

value: TotalSeq-A Human Universal Cocktail


title: D496_002_ADT_CZINY-0124

description:
Library name: D496_002_ADT_CZINY-0124_lib
CITE-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

tag: age

value: 56 years

tag: dev stage

tag: suspension cell_depletion_factors

tag: living at_sample_collection

tag: sample preservation_method

tag: smoking history

tag: death type

tag: cause of_death

tag: body mass_index

tag: height

value: positive

value: 150 mg/dL


title: TAA_GFP_2

description:
CTR2
Transcriptome profile of mice treated with TAA and injected with AAV8 TBG eGFP, biological rep2

tag: agent

value: TAA and injected with AAV8 TBG eGFP

tag: strain


title: TAA_GFP_1

description:
CTR2
Transcriptome profile of mice treated with TAA and injected with AAV8 TBG eGFP, biological rep1


title: LuCaP145.2 FOXA2 DiMeLo-seq

tag: tissue

value: Prostate

tag: cell line

value: LuCaP145.2 PDX

tag: cell type

value: Prostate cancer cell

tag: genotype

value: WT

tag: antibody

value: FOXA2 (Abcam, Cat#ab108422)

tag: treatment


title: PBS_5

description:
CTR1
Transcriptome profile of mice treated with PBS , biological rep5

value: PBS


title: LNCaP, FOXA2-D14, FOXA2 DiMeLo-seq

data_processing:
base calling and alignment: guppy/6.2.1_cpu
config file: res_dna_r941_min_modbases-all-context_v001.cfg
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: DiMeLo-seq

value: LNCaP


title: PBS_4

description:
CTR1
Transcriptome profile of mice treated with PBS , biological rep4


title: Bci, IAV, rep 4

city: Southampton

first: Karl

last: Staples

address: MP810 Southampton General Hospital, Tremona Road

institute: University of Southampton Faculty of Medicine

description:
Library name: Sample 9
Column name in processed data file: IAV-infected-009 - Total counts

data_processing:
Raw BCL data files were converted to FASTQ file format using bcl2fastq conversion software v2.20 (illumina). Sequencing quality was confirmed using FastQC. Read processing was carried out using CLC Genomics Server 21.0.4. Reads were trimmed by the common sequence, UMI and adapters, keeping reads with lengths of 15 to 55nt.
Reads were mapped to human miRBase version 22 using the workflow “QIAseq miRNA Quantification” of CLC Genomics Server with standard parameters.
Assembly: miRBase version 22
Supplementary files format and content: tab-deliminated text file containing raw read counts for each sample

source_name: Extracellular Vesicles

growth_protocol: BCI-NS1.1 ALI cultures were generated using transwell membrane inserts and pneumacult culture media according to the manufacturers instructions. Cultures were maintained at 37°C, 5% CO2. Differentiation was confirmed by the appearance of motile cillia and transepithelial conductance measurements.

extract_protocol:
EVs were isolated  from the apical surface wash of ALI cultures by filtration and size exclusion chromatography.
RNA was isolated using the miRNeasy Mini Kit (Qiagen)
miRNA sequencing libraries were constructed and processed by Qiagen using the QIAseq miRNA Library Kit (Qiagen) and sequenced on a NextSeq500 (Illumina Inc.), according to the manufacturer instructions with the following parameters: Single-end read, read length 75 nucleotides, average 12 million reads/sample.

treatment_protocol: ALI cultures were exposed to either IAV at 3,600,000 IU/ml (n=5) or uninfected HBSS (n=5) via the apical surface for 2h followed by 22 hour incubation at 37°C, 5% CO2.

value: Extracellular Vesicles

value: Respiratory epithelial cells

value: Infected IAV


title: blood07_baseline

description: barcoded probe hybridization

tag: Sex

value: male

tag: responder

value: yes

tag: timepoint

value: BASELINE


title: blood06_baseline

description: barcoded probe hybridization


title: blood06_T1

description: barcoded probe hybridization


title: blood05_T1

description: barcoded probe hybridization


title: Bci, IAV, rep 5

description:
Library name: Sample 10
Column name in processed data file: IAV-infected-010 - Total counts


title: LuCaP70CR, RRMS

data_processing:
base calling and alignment: guppy/6.2.1_cpu
config file: res_dna_r941_min_modbases-all-context_v001.cfg
Assembly: hg38
Library strategy: RRMS

value: LuCaP70CR PDX


title: LuCaP173.1, RRMS

data_processing:
base calling and alignment: guppy/6.2.1_cpu
config file: res_dna_r941_min_modbases-all-context_v001.cfg
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: RRMS

value: LuCaP173.1 PDX


title: blood08_baseline

description: barcoded probe hybridization

value: female


title: WU005

city: St. Louis

first: Ramon

last: Jin

address: 600 S Euclid

institute: Washington University School of Medicine

description: human BE WU005

hyb_protocol: Following fragmentation with NuGen Encore Biotin Module, 2.5 ug of cDNA were hybridized onto Gene 2.0 ST Array in the GeneChip Hybridization Oven 640 for 18 hr at 45C. GeneChip were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: An Affymetrix GeneChip Scanner 7G 3000 was used to scan the probe arrays. Gene expression intensities were calculated using Affymetrix AGCC software.

data_processing:
Data were processed using the Affymetrix Transcriptome Analysis Console (TAC; Thermo Fisher).
HuGene-2_0-st-v1.r4.pgf
HuGene-2_0-st-v1.r4.mps

label: biotin

source_name: human BE WU005

label_protocol: Biotinylated cDNA were prepared according to the standard NuGen WT-Ovation Pico RNA Amplification system. Per RNA labeling, 50 nanograms of total RNA was used in conjunction with the Affymetrix recommended protocol for the GeneChip 2.0 ST chips.

growth_protocol: Barrett’s esophagus or normal adjacent esophageal squamous organoids were derived from de-identified tissue from patients undergoing Barrett’s esophagus surveillance EGD

extract_protocol: Human Barrett’s esophagus organoids were pelleted, and RNA was extracted using the AllPrep DNA/RNA/Protein Mini Kit (Qiagen) per manufacturer’s protocol.

value: BE


title: PBS_1

description:
CTR1
Transcriptome profile of mice treated with PBS , biological rep1


title: PBS_3

description:
CTR1
Transcriptome profile of mice treated with PBS , biological rep3


title: blood03_T1

description: barcoded probe hybridization


title: PBS_2

description:
CTR1
Transcriptome profile of mice treated with PBS , biological rep2


title: blood05_baseline

description: barcoded probe hybridization


title: ATRβKO (HFD)

city: shanghai

first: Yiruo

last: Ma

state: shanghai

address: 320 Yueyang Road, Shanghai

institute: Shanghai Institute of Nutrition and Health Chinese Academy of Sciences, CAS

description: ATRβKO-HFDexpdetail

data_processing:
Libraries were prepared according to the Illumina TruSeq protocol
Sequenced reads pooled for deep sequencing by using Illumina Nova seq 6000 (2 x150bp read length) platforms.
The raw paired end reads were trimmed and quality controlled by SeqPrep (https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default  parameters.
Then clean reads were separately aligned to reference genome with orientation mode  using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml)[1] software
The mapped reads of  each sample were assembled by StringTie(https://ccb.jhu.edu/software/stringtie/index.shtml?  t=example) in a reference-based approach
Assembly: GRCm39
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Inguinal white adipose tissue

growth_protocol: All mice were maintained at a temperature of 23±3℃ and a humidity of 35±5 % under a 12 h light/dark cycle in a specific pathogen free animal facility

extract_protocol:
Total RNA was isolated by using Trizol reagent from Inguinal white adipose tissue,One sample in each group was collected from 3 pooled iWAT of mice with Vehicle or T3
Libraries were prepared according to the Illumina TruSeq protocol and pooled for deep sequencing by using Illumina Nova seq 6000 (2 x150bp read length) platforms.

treatment_protocol: Floxed and ATRβKO mice received 7 daily T3/PBS injection were euthanized 24 hours after last T3/ PBS injection with normal food. Or Floxed and ATRβKO mice received 2-3 months HFD feeding.

value: Inguinal white adipose tissue

value: ATR{beta}KO

value: HFD


title: Bci, IAV, rep 3

description:
Library name: Sample 8
Column name in processed data file: IAV-infected-008 - Total counts


title: LuCaP147, RRMS

value: Prostate

value: LuCaP147 PDX

value: Prostate cancer cell

value: WT


title: Bci, IAV, rep 2

description:
Library name: Sample 7
Column name in processed data file: IAV-infected-007 - Total counts

value: Extracellular Vesicles


title: LuCaP93, RRMS

value: LuCaP93 PDX


title: Bci, Control, rep 5

description:
Library name: Sample 5
Column name in processed data file: Uninfected-004 - Total counts

value: Respiratory epithelial cells

value: Non- infected


title: Bci, Control, rep 4

description:
Library name: Sample 4
Column name in processed data file: Uninfected-005 - Total counts


title: LuCaP 35CR, RRMS

value: LuCaP 35CR PDX


title: Bci, IAV, rep 1

description:
Library name: Sample 6
Column name in processed data file: IAV-infected-006 - Total counts

value: Infected IAV


title: blood02_baseline

description: barcoded probe hybridization

value: male

value: yes

value: BASELINE


title: Bci, Control, rep 3

description:
Library name: Sample 3
Column name in processed data file: Uninfected-003 - Total counts


title: LuCaP145.2, RRMS

value: LuCaP145.2 PDX


title: LuCaP77CR, RRMS

value: LuCaP 77CR PDX


title: blood03_baseline

description: barcoded probe hybridization

value: female


title: blood02_T1

description: barcoded probe hybridization


title: LNCaP, FOXA2-D28, FOXA2 DiMeLo-seq

value: LNCaP

value: FOXA2 (Abcam, Cat#ab108422)


title: ATRβKO (T3)

description: ATRβKO -T3expdetail

value: Inguinal white adipose tissue

value: ATR{beta}KO


title: blood04_baseline

description: barcoded probe hybridization

value: no


title: Floxed (T3)

description: ATRβKO -T3expdetail

value: Floxed


title: Bci, Control, rep 2

description:
Library name: Sample 2
Column name in processed data file: Uninfected-002 - Total counts

value: Extracellular Vesicles


title: blood01_T1

description: barcoded probe hybridization


title: LNCaP, FOXA2-D2, FOXA2 DiMeLo-seq

value: Prostate

value: Prostate cancer cell

value: WT


title: CX/CX Mouse Sample 6

status: Public on Jun 05 2025

city: Pozzilli

first: Daniela

last: Carnevale

address: Via dell'Elettronica

institute: IRCCS Neuromed and "Sapienza" University of Rome

hyb_protocol: Not Applicable

scan_protocol: Not Applicable

data_processing:
The Normalizaton and all the data were performed according to manufacturer instruction and manufacturer provided excel sheet.
normalized signal against housekeeping genes (Act)

label: SYBR Green

source_name: CD8 T Cells

label_protocol: PCR assays were performed CD8 T Cells and the Mouse Cytokines & Chemokines PCR Array panel (Qiagen) following the manufacturer’s instructions. cDNA was synthesized utilizing RT² First Strand kit (Qiagen) . Quantitative real-time PCR were performed using the 7500 RT systems(Applied Biosystems) thermocycler, the qPCR cycling conditions were 95°C for 10 minutes for 1 cycle, followed by 40 cycles of 95°C for 15 seconds and 60°C for 1 minute.

extract_protocol: Total RNA was obtained by disrupting CD8 T Cells samples in Trizol (Invitrogen, 15596026). Following phenol chloroform extraction, RNA integrity was quantified on Nanodrop 2000 Spectrophotometers (Thermofisher Scientific)

value: CX/CX


title: Bci, Control, rep 1

description:
Library name: Sample 1
Column name in processed data file: Uninfected-001 - Total counts

value: Respiratory epithelial cells

value: Non- infected


title: Floxed (Veh)

description: ATRβKO -T3expdetail

value: PBS


title: CX/CX Mouse Sample 4


title: blood_01_baseline

description: barcoded probe hybridization

value: yes

value: BASELINE


title: CX/CX Mouse Sample 5


title: CX/CX Mouse Sample 2


title: WT Mouse Sample 5


title: Floxed (HFD)

description: ATRβKO-HFDexpdetail

value: HFD


title: CX/CX Mouse Sample 3


title: CX/CX Mouse Sample 1


title: WT Mouse Sample 1


title: WT Mouse Sample 2


title: WT Mouse Sample 3


title: WT Mouse Sample 4


title: Patient32_36h _1.75g/kg/d

city: Montréal

first: Alex

last: Gregorieff

state: QC

address: 1001 Decarie Boulevard

department: Department of Pathology

country: Canada

institute: RI-MUHC

description:
Library name: Patient32_36h
Patient32_36h _1.75g/kg/d

data_processing:
RNA-seq alignment and analysis of FastQ files was performed using GenPipes “RNAseq". Raw reads were trimmed and filtered for quality using Trimmomatic and then mapped to the human reference genome (Homo_sapiens.GRCh38) by STAR. Mapped reads were further refined using GATK and Picard suite. Gene level counts were quantified using HT-seq Count. Genes with read counts below 5 were removed.
Assembly: Homo_sapiens:GRCh38
Supplementary files format and content: Excel file includes read count values for each sample.

source_name: Blood

extract_protocol:
Qiagen, PAXgene blood RNA kit.
Illumina stranded mRNA prep kit for Illumina NovaSeq 6000 S4 PE100 (25M reads).

treatment_protocol: Study subjects were exposed to 0.8, 1.75, or 2.5 g/kg/day protein for 48 hours. Samples for blood transcriptome were obtained before the beginning the intervention (0 hour) or at 12, 24, 36, or 48 hours after, and stored in Qiagen PAXgene tubes.

value: Blood

value: Amino Acid 1.75 g/kg/d for 36 h

tag: batch


title: Patient31_48h _2.5g/kg/d

description:
Library name: Patient31_48h
Patient31_48h _2.5g/kg/d

value: Amino Acid 2.5 g/kg/d for 48 h


title: Patient31_36h _2.5g/kg/d

description:
Library name: Patient31_36h
Patient31_36h _2.5g/kg/d

value: Amino Acid 2.5 g/kg/d for 36 h


title: Patient32_0h _1.75g/kg/d

description:
Library name: Patient32_0h
Patient32_0h _1.75g/kg/d

value: Amino Acid 1.75 g/kg/d for 0 h


title: Patient32_12h _1.75g/kg/d

description:
Library name: Patient32_12h
Patient32_12h _1.75g/kg/d

value: Amino Acid 1.75 g/kg/d for 12 h


title: Patient31_12h _2.5g/kg/d

description:
Library name: Patient31_12h
Patient31_12h _2.5g/kg/d

value: Amino Acid 2.5 g/kg/d for 12 h


title: Patient31_24h _2.5g/kg/d

description:
Library name: Patient31_24h
Patient31_24h _2.5g/kg/d

value: Amino Acid 2.5 g/kg/d for 24 h


title: Patient29_48h _0.8g/kg/d

description:
Library name: Patient29_48h
Patient29_48h _0.8g/kg/d

value: Amino Acid 0.7 g/kg/d for 48 h


title: Patient29_36h _0.8g/kg/d

description:
Library name: Patient29_36h
Patient29_36h _0.8g/kg/d

value: Amino Acid 0.7 g/kg/d for 36 h


title: Patient31_0h _2.5g/kg/d

description:
Library name: Patient31_0h
Patient31_0h _2.5g/kg/d

value: Amino Acid 2.5 g/kg/d for 0 h


title: Patient29_24h _0.8g/kg/d

description:
Library name: Patient29_24h
Patient29_24h _0.8g/kg/d

value: Amino Acid 0.7 g/kg/d for 24 h


title: Patient29_12h _0.8g/kg/d

description:
Library name: Patient29_12h
Patient29_12h _0.8g/kg/d

value: Amino Acid 0.7 g/kg/d for 12 h


title: Patient29_0h _0.8g/kg/d

description:
Library name: Patient29_0h
Patient29_0h _0.8g/kg/d

value: Amino Acid 0.7 g/kg/d for 0 h


title: Patient28_36h _2.5g/kg/d

description:
Library name: Patient28_36h
Patient28_36h _2.5g/kg/d


title: Patient28_12h _2.5g/kg/d

description:
Library name: Patient28_12h
Patient28_12h _2.5g/kg/d


title: Patient28_0h _2.5g/kg/d

description:
Library name: Patient28_0h
Patient28_0h _2.5g/kg/d


title: Patient27_24h _1.75g/kg/d

description:
Library name: Patient27_24h
Patient27_24h _1.75g/kg/d

value: Amino Acid 1.75 g/kg/d for 24 h


title: Patient27_36h _1.75g/kg/d

description:
Library name: Patient27_36h
Patient27_36h _1.75g/kg/d


title: Patient27_48h _1.75g/kg/d

description:
Library name: Patient27_48h
Patient27_48h _1.75g/kg/d

value: Amino Acid 1.75 g/kg/d for 48 h


title: Patient27_0h _1.75g/kg/d

description:
Library name: Patient27_0h
Patient27_0h _1.75g/kg/d


title: Patient26_48h _0.8g/kg/d

description:
Library name: Patient26_48h
Patient26_48h _0.8g/kg/d


title: Patient32_48h _1.75g/kg/d

description:
Library name: Patient32_48h
Patient32_48h _1.75g/kg/d


title: Patient26_36h _0.8g/kg/d

description:
Library name: Patient26_36h
Patient26_36h _0.8g/kg/d


title: Patient26_24h _0.8g/kg/d

description:
Library name: Patient26_24h
Patient26_24h _0.8g/kg/d


title: Patient26_12h _0.8g/kg/d

description:
Library name: Patient26_12h
Patient26_12h _0.8g/kg/d


title: Patient26_0h _0.8g/kg/d

description:
Library name: Patient26_0h
Patient26_0h _0.8g/kg/d


title: Patient32_24h _1.75g/kg/d

description:
Library name: Patient32_24h
Patient32_24h _1.75g/kg/d


title: Patient24_48h _1.75g/kg/d

description:
Library name: Patient24_48h
Patient24_48h _1.75g/kg/d


title: Patient20_48h _1.75g/kg/d

description:
Library name: Patient20_48h
Patient20_48h _1.75g/kg/d


title: Patient20_36h _1.75g/kg/d

description:
Library name: Patient20_36h
Patient20_36h _1.75g/kg/d


title: Patient24_24h _1.75g/kg/d

description:
Library name: Patient24_24h
Patient24_24h _1.75g/kg/d


title: Patient24_36h _1.75g/kg/d

description:
Library name: Patient24_36h
Patient24_36h _1.75g/kg/d


title: Patient24_0h _1.75g/kg/d

description:
Library name: Patient24_0h
Patient24_0h _1.75g/kg/d


title: Patient20_24h _1.75g/kg/d

description:
Library name: Patient20_24h
Patient20_24h _1.75g/kg/d


title: Patient20_0h _1.75g/kg/d

description:
Library name: Patient20_0h
Patient20_0h _1.75g/kg/d


title: Patient20_12h _1.75g/kg/d

description:
Library name: Patient20_12h
Patient20_12h _1.75g/kg/d


title: Patient18_24h _0.8g/kg/d

description:
Library name: Patient18_24h
Patient18_24h _0.8g/kg/d


title: Patient28_24h _2.5g/kg/d

description:
Library name: Patient28_24h
Patient28_24h _2.5g/kg/d


title: Patient18_48h _0.8g/kg/d

description:
Library name: Patient18_48h
Patient18_48h _0.8g/kg/d


title: Patient18_0h _0.8g/kg/d

description:
Library name: Patient18_0h
Patient18_0h _0.8g/kg/d


title: Patient27_12h _1.75g/kg/d

description:
Library name: Patient27_12h
Patient27_12h _1.75g/kg/d


title: Patient15_36h _2.5g/kg/d

description:
Library name: Patient15_36h
Patient15_36h _2.5g/kg/d


title: Patient15_12h _2.5g/kg/d

description:
Library name: Patient15_12h
Patient15_12h _2.5g/kg/d


title: Patient15_24h _2.5g/kg/d

description:
Library name: Patient15_24h
Patient15_24h _2.5g/kg/d


title: Patient15_0h _2.5g/kg/d

description:
Library name: Patient15_0h
Patient15_0h _2.5g/kg/d


title: Patient14_48h _0.8g/kg/d

description:
Library name: Patient14_48h
Patient14_48h _0.8g/kg/d


title: Patient15_48h _2.5g/kg/d

description:
Library name: Patient15_48h
Patient15_48h _2.5g/kg/d


title: Patient14_24h _0.8g/kg/d

description:
Library name: Patient14_24h
Patient14_24h _0.8g/kg/d


title: Patient14_36h _0.8g/kg/d

description:
Library name: Patient14_36h
Patient14_36h _0.8g/kg/d


title: Patient14_12h _0.8g/kg/d

description:
Library name: Patient14_12h
Patient14_12h _0.8g/kg/d


title: Patient14_0h _0.8g/kg/d

description:
Library name: Patient14_0h
Patient14_0h _0.8g/kg/d


title: Patient13_36h _1.75g/kg/d

description:
Library name: Patient13_36h
Patient13_36h _1.75g/kg/d


title: Patient13_12h _1.75g/kg/d

description:
Library name: Patient13_12h
Patient13_12h _1.75g/kg/d


title: Patient13_48h _1.75g/kg/d

description:
Library name: Patient13_48h
Patient13_48h _1.75g/kg/d


title: Patient13_0h _1.75g/kg/d

description:
Library name: Patient13_0h
Patient13_0h _1.75g/kg/d


title: Patient10_48h _1.75g/kg/d

description:
Library name: Patient10_48h
Patient10_48h_1.75g/kg/d


title: Patient18_36h _0.8g/kg/d

description:
Library name: Patient18_36h
Patient18_36h _0.8g/kg/d


title: Patient9_48h _1.75g/kg/d

description:
Library name: Patient9_48h
Patient9_48h_1.75g/kg/d


title: Patient10_36h _1.75g/kg/d

description:
Library name: Patient10_36h
Patient10_36h_1.75g/kg/d


title: Patient18_12h _0.8g/kg/d

description:
Library name: Patient18_12h
Patient18_12h _0.8g/kg/d


title: Patient10_24h _1.75g/kg/d

description:
Library name: Patient10_24h
Patient10_24h_1.75g/kg/d


title: Patient9_24h _1.75g/kg/d

description:
Library name: Patient9_24h
Patient9_24h_1.75g/kg/d


title: Patient9_0h _1.75g/kg/d

description:
Library name: Patient9_0h
Patient9_0h_1.75g/kg/d


title: Patient10_12h _1.75g/kg/d

description:
Library name: Patient10_12h
Patient10_12h_1.75g/kg/d


title: Patient9_36h _1.75g/kg/d

description:
Library name: Patient9_36h
Patient9_36h_1.75g/kg/d


title: Patient9_12h _1.75g/kg/d

description:
Library name: Patient9_12h
Patient9_12h_1.75g/kg/d


title: Patient8_36h _2.5g/kg/d

description:
Library name: Patient8_36h
Patient8_36h_2.5g/kg/d


title: Patient8_24h _2.5g/kg/d

description:
Library name: Patient8_24h
Patient8_24h_2.5g/kg/d


title: Patient8_0h _2.5g/kg/d

description:
Library name: Patient8_0h
Patient8_0h_2.5g/kg/d


title: Patient8_48h _2.5g/kg/d

description:
Library name: Patient8_48h
Patient8_48h_2.5g/kg/d


title: Patient7_48h _2.5g/kg/d

description:
Library name: Patient7_48h
Patient7_48h _2.5g/kg/d


title: Patient7_36h _2.5g/kg/d

description:
Library name: Patient7_36h
Patient7_36h _2.5g/kg/d


title: Patient7_12h _2.5g/kg/d

description:
Library name: Patient7_12h
Patient7_12h _2.5g/kg/d


title: Patient7_24h _2.5g/kg/d

description:
Library name: Patient7_24h
Patient7_24h _2.5g/kg/d


title: Patient13_24h _1.75g/kg/d

description:
Library name: Patient13_24h
Patient13_24h _1.75g/kg/d


title: Patient6_36h _0.8g/kg/d

description:
Library name: Patient6_36h
Patient6_36h _0.8g/kg/d


title: Patient6_12h _0.8g/kg/d

description:
Library name: Patient6_12h
Patient6_12h _0.8g/kg/d


title: Patient6_0h _0.8g/kg/d

description:
Library name: Patient6_0h
Patient6_0h _0.8g/kg/d


title: Patient5_48h _0.8g/kg/d

description:
Library name: Patient5_48h
Patient5_48h _0.8g/kg/d


title: Patient5_36h _0.8g/kg/d

description:
Library name: Patient5_36h
Patient5_36h _0.8g/kg/d


title: Patient5_24h _0.8g/kg/d

description:
Library name: Patient5_24h
Patient5_24h _0.8g/kg/d


title: Patient3_36h _0.8g/kg/d

description:
Library name: Patient3_36h
Patient3_36h _0.8g/kg/d


title: Patient4_24h _1.75g/kg/d

description:
Library name: Patient4_24h
Patient4_24h _1.75g/kg/d


title: Patient3_12h _0.8g/kg/d

description:
Library name: Patient3_12h
Patient3_12h _0.8g/kg/d


title: Patient10_0h _1.75g/kg/d

description:
Library name: Patient10_0h
Patient10_0h_1.75g/kg/d


title: Patient4_36h _1.75g/kg/d

description:
Library name: Patient4_36h
Patient4_36h _1.75g/kg/d


title: Patient5_12h _0.8g/kg/d

description:
Library name: Patient5_12h
Patient5_12h _0.8g/kg/d


title: Patient5_0h _0.8g/kg/d

description:
Library name: Patient5_0h
Patient5_0h _0.8g/kg/d


title: Patient4_12h _1.75g/kg/d

description:
Library name: Patient4_12h
Patient4_12h _1.75g/kg/d


title: Patient3_24h _0.8g/kg/d

description:
Library name: Patient3_24h
Patient3_24h _0.8g/kg/d


title: Patient4_48h _1.75g/kg/d

description:
Library name: Patient4_48h
Patient4_48h _1.75g/kg/d


title: NHDF, M1+HA4-3, 6h

city: Kizugawa

first: Eiko

last: Uno

state: Kyoto

address: 6-5-4 Kunimidai

country: Japan

institute: Rohto Pharmaceutical Co., Ltd.

description: Library name: Sample 9

data_processing:
The resulting reads were analyzed using CLC Genomics Workbench software (ver. 8.01, Qiagen, Venlo, The Netherlands).
Using the RNA-Seq Analysis tool in CLC Genomics Workbench, read counts were obtained for each gene ID and transcript ID. The counts were then normalized by gene length and read depth to calculate TPM (Transcripts Per Million) values. In the processed data file, the expression values represent TPM values.
Statistical differences were analyzed by multiple unpaired t-tests using Prism (version 10.0; GraphPad Software, Boston, MA, USA).
Gene pathway analysis was performed using Ingenuity Pathway Analysis (Qiagen, Venlo, The Netherlands).
The heat map displayed log2(TPM+1) values for each gene from the RNA-seq data created with Prism.
A volcano plot was produced with log2(fold change) on the x-axis and -log10(p-value) on the y-axis using Origin Pro 2023 (Northampton, MA).
Principal component analysis (PCA) was conducted using JMP Pro 18 (SAS Institute Cary, CA) to validate intragroup variance.
Assembly: Homo sapiens GRCh38 (hg38) release-110
Supplementary files format and content: xlsx file include TPM values for each sample

source_name: skin

growth_protocol: Normal Human Dermal Fibroblasts (NHDF) were sourced from KURABO in Osaka, Japan. These NHDF were cultured in Dulbecco’s modified Eagle’s medium enriched with 10% fetal bovine serum (FBS), penicillin (100 IU/mL), and streptomycin (100 μg/mL) and incubated at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted from macrophages and NHDF utilizing the Maxwell® RSC Instrument (Promega, Madison, WI, USA).
The mRNA was then purified using oligo dT beads (NEBNext Poly (A) mRNA Magnet Isolation Module, New England Biolabs, NEB, Ipswich, MA). Complementary DNA (cDNA) library preparation was performed using the NEBNext Ultra II RNA Library Prep Kit (NEB) along with NEBNextplex Oligos for Illumina according to a previously established method (9). Index sequences were incorporated into the fragments through PCR amplification. The cDNA libraries were combined in equal molecular amounts and sequenced on an Illumina NovaSeq 6000 sequencer, employing a 50-bp paired-end cycle sequencing kit (S1 Reagent Kit V1.5) (Illumina, San Diego, CA).

treatment_protocol: Before use, M1-CMs cultured with or without HA4 for NHDF coculture were diluted in a fibroblast culture medium. The CM was diluted 1:64 for RNA-seq.

value: skin

value: NHDF

value: normal human dermal fibroblasts

value: WT

value: cells treated with supernatant from M1 macrophages differentiated in the presence of HA4

tag: time


title: NHDF, M1+HA4-2, 6h

description: Library name: Sample 8


title: NHDF, M1-3, 6h

description: Library name: Sample 6

value: cells treated with supernatant from M1 macrophages


title: Patient3_0h _0.8g/kg/d

description:
Library name: Patient3_0h
Patient3_0h _0.8g/kg/d

value: Blood


title: NHDF, Control-2, 6h

description: Library name: Sample 2

value: untreated control


title: NHDF, Control-1, 6h

description: Library name: Sample 1


title: iPSC neurones, mutation at aa P95L, rep3

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

institute: University of Cambridge

description:
Library name: P95L_3
iPSC derived hypothalamic neurones P95L_3

data_processing:
NovaSeq 6000
Reads were mapped to GRCh38 using STAR 2.5.0a
Differential gene expression performed with EdgeR's Quasi-likelihood f-test with FDR of <0.05
Assembly: GRCh38
Supplementary files format and content: Gene-level read counts in tab-delimited format

source_name: iPSC derived hypothalamic neurones

growth_protocol: KOLF2.1J maintained in supplemented StemFlex media on Geltrex. Following gene editing, clone of interested were differentiated into  hypothalamic neurones with a chemically defined medium and maintained in Synaptojuice 2 until day 28. Differentiated mature neurones were enriched with FACS utilising cell surface markers.

extract_protocol:
Qiagen RNAeasy plus micro kit
Takara Clontech SMARTer Standed Total RNAseq Kit Pico Input V2

value: iPSC derived hypothalamic neurones

value: neurones

value: P95L mutant

value: CRISPER KnockIn

tag: barcode


title: NHDF, M1-2, 6h

description: Library name: Sample 5


title: iPSC neurones, mutation at aa P95L, rep2

description:
Library name: P95L_2
iPSC derived hypothalamic neurones P95L_2


title: Patient8_12h _2.5g/kg/d

description:
Library name: Patient8_12h
Patient8_12h_2.5g/kg/d

value: Amino Acid 2.5 g/kg/d for 12 h


title: iPSC neurones, mutation at aa T194M, rep2

description:
Library name: T194M_2
iPSC derived hypothalamic neurones T194M_2

value: T194M mutant


title: Patient7_0h _2.5g/kg/d

description:
Library name: Patient7_0h
Patient7_0h _2.5g/kg/d

value: Amino Acid 2.5 g/kg/d for 0 h


title: iPSC neurones, mutation at aa T194M, rep1

description:
Library name: T194M_1
iPSC derived hypothalamic neurones T194M_1


title: iPSC neurones, mutation at aa E601K, rep3

description:
Library name: E601K_3
iPSC derived hypothalamic neurones E601K_3

value: E601K mutant


title: Patient3_48h _0.8g/kg/d

description:
Library name: Patient3_48h
Patient3_48h _0.8g/kg/d

value: Amino Acid 0.7 g/kg/d for 48 h


title: Patient4_0h _1.75g/kg/d

description:
Library name: Patient4_0h
Patient4_0h _1.75g/kg/d

value: Amino Acid 1.75 g/kg/d for 0 h


title: NHDF, M1+HA4-1, 6h

description: Library name: Sample 7

value: skin

value: NHDF


title: NHDF, M1-1, 6h

description: Library name: Sample 4

value: normal human dermal fibroblasts

value: WT


title: NHDF, Control-3, 6h

description: Library name: Sample 3


title: iPSC neurones, WT, rep3

description:
Library name: WT_3
iPSC derived hypothalamic neurones WT_3


title: iPSC neurones, WT, rep2

description:
Library name: WT_2
iPSC derived hypothalamic neurones WT_2


title: iPSC neurones, mutation at aa E601K, rep2

description:
Library name: E601K_2
iPSC derived hypothalamic neurones E601K_2


title: iPSC neurones, mutation at aa P95L, rep1

description:
Library name: P95L_1
iPSC derived hypothalamic neurones P95L_1


title: HCT116 p53-/- ORC2 deletion, Input

city: Birmingham

first: Zhangli

last: Su

state: Alabama

address: 720 20th Street South

department: Department of Genetics

institute: University of Alabama

description: Library name: Sample14

data_processing:
Raw sequence data in fastq format were processed as follows: FastQC (v0.11.5) (Andrews, 2010) was used for quality control and sequence data were then mapped to human genome (hg38) using bowtie2 (v2.2.9) (Langdon, 2015). Sam files were converted into bam files using samtools (v1.12) (Li et al., 2009) and only high-quality reads (q-score ≥30) were retained for subsequent analyses. Bam files were then converted to bed files using samtools. Peak calling was performed with MACS2 (callpeak -g hs -B --SPMR -q 0.05 --keep-dup 1 -f BAMPE).
Assembly: hg38
Supplementary files format and content: BigWig files with pileup signals are generated by bdg2bw.
Supplementary files format and content: Bed files for peak summits are generated by MACS2 peak calling. H3K9me3-up are H3K9me3 peaks that are up-regulated in ORC2 KO samples and rescued, H3K9me3-down are H3K9me3 peaks that are down-regulated in ORC2 KO samples and rescued.

growth_protocol: HCT116 p53-/- cell (referred to as wild-type, RRID: CVCL_S744) was a generous gift from Fred Bunz (Johns Hopkins) (Bunz et al., 1998). ORC2B2 (referred to as ORC2-/-) was a clonal cell line that was established by CRISPR/Cas9 technology in the HCT116 p53-/- background (Shibata et al., 2016). ORC2 rescue cells were established by pLHCXORC2 cloning ORC2 with 3’UTR and 5’UTR and clonal selection. ORC1 or ORC5KO clones were established in HCT116 p53-/- cells using CRISPR/Cas9 technology (Shibata and Dutta, 2020; Shibata et al., 2016). All cell lines were maintained in McCoy’s 5A-modified medium (Corning, no. 10-050-CV) supplemented with 10% fetal bovine serum.

extract_protocol: ChIP was performed using SimpleChIP® Enzymatic Chromatin IP Kit (Magnetic Beads) (cell signaling technology, no. 9003) according to the manufacturer’s instruction. Antibodies used were Anti-H3K9ME3 (cell signaling technology, no. 13969) and Anti-H3K27ME3 (cell signaling technology, no. 9733). Sequencing libraries was prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, no. E7645S) according to manufacturer’s instructions.

value: ORC2 deletion

value: input


title: HCT116 p53-/- WT, Input

description: Library name: Sample13

value: wild-type


title: HCT116 p53-/- WT, a-H3K27me3, rep2

description: Library name: Sample8


title: HCT116 p53-/- ORC2 deletion, a-H3K27me3, rep1

description: Library name: Sample9


title: HCT116 p53-/- ORC2 rescue, Input

description: Library name: Sample15

value: ORC2 rescue


title: HCT116 p53-/- ORC2 deletion, a-H3K27me3, rep2

description: Library name: Sample10


title: HCT116 p53-/- ORC2 rescue, a-H3K27me3, rep1

description: Library name: Sample11


title: HCT116 p53-/- ORC2 deletion, a-H3K9me3, rep2

description: Library name: Sample4


title: HCT116 p53-/- ORC2 rescue, a-H3K9me3, rep2

description: Library name: Sample6


title: MN-ORC5 cloneA14 10min Rep3 [ORC5 ChECseq]

description: Library name: Sample18

data_processing:
Raw sequence data in fastq format were processed as follows: FastQC (v0.11.5) (Andrews, 2010) was used for quality control and sequence data were then mapped to human genome (hg38) using bowtie2 (v2.2.9) (Langdon, 2015). Sam files were converted into bam files using samtools (v1.12) (Li et al., 2009) and only high-quality reads (q-score ≥30) were retained for subsequent analyses. Bam files were then converted to bed files using samtools. Peak calling for CTCF was performed with MACS2 (callpeak -g hs -B --SPMR -q 0.05 --keep-dup 1 -f BAMPE).
Assembly: hg38
Supplementary files format and content: BigWig files with pileup signals are generated by bdg2bw.
Supplementary files format and content: Bed files for peak summits are generated by MACS2 peak calling. ORC5_ChEC_shared_peaks.bed represent peaks that are shared in clone3 and clone4 cells.
Library strategy: ChECseq

growth_protocol: HCT116 p53-/- cell (referred to as wild-type, RRID: CVCL_S744) was a generous gift from Fred Bunz (Johns Hopkins) (Bunz et al., 1998). ORC2B2 (referred to as ORC2-/-) was a clonal cell line that was established by CRISPR/Cas9 technology in the HCT116 p53-/- background (Shibata et al., 2016). ORC1 or ORC5KO clones were established in HCT116 p53-/- cells using CRISPR/Cas9 technology (Shibata and Dutta, 2020; Shibata et al., 2016). All cell lines were maintained in McCoy’s 5A-modified medium (Corning, no. 10-050-CV) supplemented with 10% fetal bovine serum.

extract_protocol: For each ChEC experiment, cells were grown in five 10-cm plates. Cells were pelleted at 600 × g at 4 °C for 3 min and washed three times with Washing Buffer (20 mM HEPES-NaOH pH 7.5, 150 mM NaCl, 0.1 mM EGTA, 0.5 mM spermidine, 0.1% BSA, 1 × Roche cOmplete EDTA-free mini protease inhibitors, 1 mM PMSF), centrifuging as above between washes. Cells were resuspended in NE Buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 0.1 mM EGTA, 0.5 mM Spermidine, 0.1% Triton X-100, 20% Glycerol, 1 × Roche cOmplete EDTA-free mini protease inhibitors) and rotated at 4 °C for 10 min. After centrifugation, cells were washed once each with Washing Buffer and Wash Buffer without protease inhibitor and resuspended in Wash Buffer without protease inhibitor. CaCl2 was added to 2 mM and ChEC digests were performed at 25 °C. At each time point, a 150-μl aliquot of the digest was transferred to a tube containing 150 μl 2 × stop buffer (200 mM NaCl, 20 mM EDTA, 4 mM EGTA, 50 µg/mL RNase A, 20 µg /mL Glycogen) and incubated at 37 °C for 30 min. After adding 0.1% SDS, protein was digested with 100 μg proteinase K at 55 °C for 30 min. DNA was extracted one each with an equal volume of phenol and phenol/chloroform/isoamyl alcohol. DNA in aqueous phase was size-selected with 0.45x vol SPRIselect beads and then precipitated with 200 mM NaCl and 2.5 volumes 100% ethanol. Pellets were washed once with 1 ml 70% ethanol, dried, and resuspended in 30 μl 0.1 × TE buffer, pH 8.0. Sequencing libraries was prepared by NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645S).

treatment_protocol: ChEC cell lines expressing MNase-tagged ORC subunits were made with lentivirus by co-transfection of psPAX2, pMD2.G and pCW-nMN-ORC1 (or ORC2 or ORC5) plasmids in the background of ORC1KO-B14, ORC2KOB2 or ORC5KO-24 cells and selected by puromycin. Monoclonal cell population was obtained by limiting dilution. MNase-FusionRed was constructed as a negative control.

value: ORC5 deletion + MN-ORC5 cloneA14

value: 10 min CaCl2 treatment


title: MN-ORC5 cloneA14 10min Rep2 [ORC5 ChECseq]

description: Library name: Sample17


title: HCT116 p53-/- WT, a-H3K9me3, rep1

description: Library name: Sample1


title: HCT116 p53-/- WT, a-H3K9me3, rep2

description: Library name: Sample2


title: HCT116 p53-/- ORC2 rescue, a-H3K9me3, rep1

description: Library name: Sample5


title: MN-ORC5 cloneA14 10min Rep1 [ORC5 ChECseq]

description: Library name: Sample16


title: MN-ORC5 cloneA14 0min Rep3 [ORC5 ChECseq]

description: Library name: Sample15

value: 0 min CaCl2 treatment


title: MN-ORC5 cloneA14 0min Rep1 [ORC5 ChECseq]

description: Library name: Sample13


title: MN-ORC5 cloneA14 0min Rep2 [ORC5 ChECseq]

description: Library name: Sample14


title: iPSC neurones, mutation at aa E601K, rep1

description:
Library name: E601K_1
iPSC derived hypothalamic neurones E601K_1

value: iPSC derived hypothalamic neurones

value: neurones

value: CRISPER KnockIn


title: MN-ORC5 cloneA13 10min Rep3 [ORC5 ChECseq]

description: Library name: Sample12

value: ORC5 deletion + MN-ORC5 cloneA13


title: MN-ORC5 cloneA13 10min Rep1 [ORC5 ChECseq]

description: Library name: Sample10


title: HCT116 p53-/- ORC2 rescue, a-H3K27me3, rep2

description: Library name: Sample12


title: MN-ORC5 cloneA13 10min Rep2 [ORC5 ChECseq]

description: Library name: Sample11


title: iPSC neurones, WT, rep1

description:
Library name: WT_1
iPSC derived hypothalamic neurones WT_1


title: MN-ORC5 cloneA13 0min Rep1 [ORC5 ChECseq]

description: Library name: Sample7


title: HCT116 p53-/- WT, a-H3K27me3, rep1

description: Library name: Sample7


title: MN-ORC5 cloneA13 0min Rep3 [ORC5 ChECseq]

description: Library name: Sample9


title: MN-FusionRed 0min Rep3 [ORC5 ChECseq]

description: Library name: Sample3

value: ORC5 deletion + MN-FusionRed


title: MN-FusionRed 0min Rep2 [ORC5 ChECseq]

description: Library name: Sample2


title: MN-FusionRed 10min Rep3 [ORC5 ChECseq]

description: Library name: Sample6


title: MN-ORC1 clone4 10min Rep3 [ORC1 ChECseq]

description: Library name: Sample18

data_processing:
Raw sequence data in fastq format were processed as follows: FastQC (v0.11.5) (Andrews, 2010) was used for quality control and sequence data were then mapped to human genome (hg38) using bowtie2 (v2.2.9) (Langdon, 2015). Sam files were converted into bam files using samtools (v1.12) (Li et al., 2009) and only high-quality reads (q-score ≥30) were retained for subsequent analyses. Bam files were then converted to bed files using samtools. Peak calling for CTCF was performed with MACS2 (callpeak -g hs -B --SPMR -q 0.05 --keep-dup 1 -f BAMPE).
Assembly: hg38
Supplementary files format and content: BigWig files with pileup signals are generated by bdg2bw.
Supplementary files format and content: Bed files for peak summits are generated by MACS2 peak calling. ORC1_ChEC_shared_peaks.bed represent peaks that are shared in clone3 and clone4 cells.
Library strategy: ChEC-seq

value: ORC1 deletion + MN-ORC1 clone4


title: MN-ORC1 clone4 10min Rep1 [ORC1 ChECseq]

description: Library name: Sample16


title: MN-ORC1 clone4 10min Rep2 [ORC1 ChECseq]

description: Library name: Sample17


title: MN-FusionRed 10min Rep2 [ORC5 ChECseq]

description: Library name: Sample5


title: MN-FusionRed 10min Rep1 [ORC5 ChECseq]

description: Library name: Sample4


title: HCT116 p53-/- ORC2 deletion, a-H3K9me3, rep1

description: Library name: Sample3


title: MN-ORC1 clone4 0min Rep3 [ORC1 ChECseq]

description: Library name: Sample15


title: MN-ORC1 clone4 0min Rep1 [ORC1 ChECseq]

description: Library name: Sample13


title: MN-FusionRed 0min Rep1 [ORC5 ChECseq]

description: Library name: Sample1


title: MN-ORC1 clone3 0min Rep3 [ORC1 ChECseq]

description: Library name: Sample9

value: ORC1 deletion + MN-ORC1 clone3


title: MN-ORC1 clone3 10min Rep3 [ORC1 ChECseq]

description: Library name: Sample12


title: MN-ORC1 clone3 10min Rep2 [ORC1 ChECseq]

description: Library name: Sample11


title: MN-ORC1 clone3 10min Rep1 [ORC1 ChECseq]

description: Library name: Sample10


title: MN-ORC1 clone3 0min Rep2 [ORC1 ChECseq]

description: Library name: Sample8


title: MN-ORC1 clone3 0min Rep1 [ORC1 ChECseq]

description: Library name: Sample7


title: MN-FusionRed 10min Rep3 [ORC1 ChECseq]

description: Library name: Sample6

value: ORC1 deletion + MN-FusionRed


title: MN-FusionRed 0min Rep3 [ORC1 ChECseq]

description: Library name: Sample3


title: MN-FusionRed 10min Rep1 [ORC1 ChECseq]

description: Library name: Sample4


title: MN-ORC2 clone4 10min Rep2 [ChECseq]

data_processing:
Raw sequence data in fastq format were processed as follows: FastQC (v0.11.5) (Andrews, 2010) was used for quality control and sequence data were then mapped to human genome (hg38) using bowtie2 (v2.2.9) (Langdon, 2015). Sam files were converted into bam files using samtools (v1.12) (Li et al., 2009) and only high-quality reads (q-score ≥30) were retained for subsequent analyses. Bam files were then converted to bed files using samtools. Peak calling for CTCF was performed with MACS2 (callpeak -g hs -B --SPMR -q 0.05 --keep-dup 1 -f BAMPE).
Assembly: hg38
Supplementary files format and content: BigWig files with pileup signals are generated by bdg2bw.
Supplementary files format and content: Bed files for peak summits are generated by MACS2 peak calling. ORC2_ChEC_shared_peaks.bed represent peaks that are shared in clone3 and clone4 cells.
Library strategy: ChEC-seq

value: ORC2 deletion + MN-ORC2 clone4


title: MN-FusionRed 10min Rep2 [ORC1 ChECseq]

description: Library name: Sample5


title: MN-FusionRed 0min Rep1 [ORC1 ChECseq]

description: Library name: Sample1


title: MN-FusionRed 0min Rep2 [ORC1 ChECseq]

description: Library name: Sample2


title: MN-ORC2 clone4 0min Rep2 [ChECseq]


title: MN-ORC2 clone4 0min Rep1 [ChECseq]


title: MN-ORC2 clone4 0min Rep3 [ChECseq]


title: MN-ORC2 clone3 10min Rep3 [ChECseq]

value: ORC2 deletion + MN-ORC2 clone3


title: MN-ORC1 clone4 0min Rep2 [ORC1 ChECseq]

description: Library name: Sample14


title: MN-ORC2 clone3 10min Rep2 [ChECseq]


title: MN-ORC2 clone4 10min Rep1 [ChECseq]


title: MN-ORC2 clone3 0min Rep3 [ChECseq]


title: MN-ORC2 clone3 0min Rep2 [ChECseq]


title: MN-ORC2 clone3 10min Rep1 [ChECseq]


title: MN-ORC2 clone3 0min Rep1 [ChECseq]


title: MN-FusionRed 10min Rep3 [ChECseq]

value: ORC2 deletion + MN-FusionRed


title: MN-FusionRed 0min Rep3 [ChECseq]


title: MN-FusionRed 10min Rep1 [ChECseq]


title: MN-FusionRed 0min Rep2 [ChECseq]


title: MN-FusionRed 0min Rep1 [ChECseq]


title: MN-FusionRed 10min Rep2 [ChECseq]


title: HCT116 p53-/- ORC2 rescue [HiC]

data_processing:
The paired-end FASTQ data was trimmed to 36bp from 5’ end and then align to the hg19 reference genome using Bowtie for R1 and R2 separately. Then the two mapped SAM files were merged, and the PCR duplication was removed. The reads were then processed following the HiCorr pipeline (Lu et al., 2020). All the reads were assigned to the DPNII-digested fragments and reads that within the same fragment was removed. Next, all reads were characterized as ‘inward’, ‘outward’, or ‘same-strand’ based on the strand of R1 and R2. All ‘inward’ reads that had <1kb distance or ‘outward’ reads that had <5kb distance are removed. The remaining ‘inward’ and ‘outward’ reads, together with the ‘same-strand’ reads were merged together as the cis reads. The interchromosomal reads were considered as trans reads. The fragments were then assigned to 5kb anchors to do the following bias correction steps. Next, the data was enhanced with DeepLoop universal model and is ready for the downstream analysis (Zhang et al., 2022). All the data were lifted over to hg38 assembly to incorporate with other data analysis. The specific loops called were using the criteria that the |Fold Change| > 2 for the loop strength after DeepLoop enhancement in the top 300k loops. PC1 was picked for the principal component analysis of Hi-C data at 250kb resolution.
Assembly: hg38
Supplementary files format and content: Compartment status (A/B) and pc1 value are summarized across all samples in txt format.
Supplementary files format and content: Altered loops are shown in bed format.

extract_protocol: HiC-seq for cell lines was performed based on HiC2.0 protocol (Belaghzal et al., 2017) with slight modifications. Briefly, cells were crosslinked with 1% formaldehyde for 10 minutes and quenched with 140 mM glycine. Five million crosslinked cells were lysed with 10 mM Tris-HCl, pH 8.0, 10 mM NaCl, 0.2% NP-40. Pelleted nuclei were lysed in 0.1% SDS and quenched by 1% Triton X-100, followed by digestion with DpnII (NEB, no. R0543) at 37 C overnight in ThermoMixer with constant mixing at 600 RPM. Digested DNA ends were then labeled with biotin-14-dATP (Invitrogen, no. 19524016) by DNA polymerase I, large (Klenow) fragment (NEB, no. M0210) at 37 C, 1 hour. Labeled DNA was ligated by T4 DNA ligase (Invitrogen, no. 15224017) and incubated with Proteinase K (Invitrogen, no. 25530015) to reverse crosslinking. Resulting DNA was purified and sonicated by Covaris to produce DNA fragments ~100-400bp. The biotin-labeled DNA fragments were then enriched by MyOne Streptavidin C1 beads (Invitrogen, no. 65001). DNA fragments while on beads were end repaired and made with NEBNext UltraII DNA library prep kit (NEB, no. E7645) with NEBNext Adaptor and Index (PCR amplified 9 cycles). Lastly the libraries were size selected by AMpure XP beads and sequenced on Illumina NovaSeq S4 lane at Novogene. Quality check at various steps was performed according to the HiC2.0 protocol.


title: MN-ORC5 cloneA13 0min Rep2 [ORC5 ChECseq]

description: Library name: Sample8


title: HCT116 p53-/- ORC2 deletion [HiC]

value: ORC2 deletion


title: Single TERT-immortalized fibroblast 7H9S4, PDL = 191

city: Grand Rapids

first: Peter

middle: W

last: Laird

state: MI

address: 333 Bostwick Ave NE

department: Epigenetics

institute: Van Andel Institute

data_processing:
Supplementary files format and content: CSV format with columns chr (chromosome), pos (1-based position of C on reference strand), strand (aligned strand), allele (assigned local microhaplotype), beta (beta value), coverage (number of reads covering C), phase_set (local microhaplotype ID), which_all_has_cg (which allele has a CpG, if this CpG is created or destroyed by a SNP used to distinguish between alleles), twosnp_cpg (is this CpG composed of two SNPs which are used to distinguish between alleles?)
Supplementary files format and content: BED format (no-header TSV, with columns chr [chromosome], start [0-based bin start], end [bin end], and n_reads [number of aligned reads in bin])
Supplementary files format and content: Biscuit BED (no-header TSV with columns chr [chromosome], start [0-based location of C], end [1-based location of G], beta, coverage, and support)
Adapter trimming with Cutadapt; alignment with Biscuit; deduplication with Dupsifter; quality control and filtering with Biscuit and Samtools; methylation calling with Biscuit; allele-resolved methylation analysis with custom tools (see publication methods).
Assembly: hg38

extract_protocol:
Lysis in sodium bisulfite
sc-DEEP-mC

value: TERT-immortalized


title: Single TERT-immortalized fibroblast 7H3S4, PDL = 191


title: HCT116 p53-/- WT [HiC]

value: wild-type


title: MN-ORC2 clone4 10min Rep3 [ChECseq]


title: Single TERT-immortalized fibroblast 7H7S4, PDL = 191


title: Single TERT-immortalized fibroblast 7H8S4, PDL = 191


title: Single TERT-immortalized fibroblast 7G8S4, PDL = 191


title: Single TERT-immortalized fibroblast 7H6S4, PDL = 191


title: Single TERT-immortalized fibroblast 7H2S4, PDL = 191


title: Single TERT-immortalized fibroblast 7H4S4, PDL = 191


title: Single TERT-immortalized fibroblast 7H5S4, PDL = 191


title: Single TERT-immortalized fibroblast 7G6S4, PDL = 191


title: Single TERT-immortalized fibroblast 7G3S4, PDL = 191


title: Single TERT-immortalized fibroblast 7H10S4, PDL = 191


title: Single TERT-immortalized fibroblast 7H1S4, PDL = 191


title: Single TERT-immortalized fibroblast 7G9S4, PDL = 191


title: Single TERT-immortalized fibroblast 7G11S4, PDL = 191


title: Single TERT-immortalized fibroblast 7G5S4, PDL = 191


title: Single TERT-immortalized fibroblast 7G4S4, PDL = 191


title: Single TERT-immortalized fibroblast 7F9S4, PDL = 191


title: Single TERT-immortalized fibroblast 7G12S4, PDL = 191


title: Single TERT-immortalized fibroblast 7F6S4, PDL = 191


title: Single TERT-immortalized fibroblast 7G10S4, PDL = 191


title: Single TERT-immortalized fibroblast 7G2S4, PDL = 191


title: Single TERT-immortalized fibroblast 7H11S4, PDL = 191


title: Single TERT-immortalized fibroblast 7F5S4, PDL = 191


title: Single TERT-immortalized fibroblast 7F3S4, PDL = 191


title: Single TERT-immortalized fibroblast 7F4S4, PDL = 191


title: Single TERT-immortalized fibroblast 7F7S4, PDL = 191


title: Single TERT-immortalized fibroblast 7F12S4, PDL = 191


title: Single TERT-immortalized fibroblast 7G7S4, PDL = 191


title: Single TERT-immortalized fibroblast 7E4S4, PDL = 191


title: Single TERT-immortalized fibroblast 7F10S4, PDL = 191


title: Single TERT-immortalized fibroblast 7E8S4, PDL = 191


title: Single TERT-immortalized fibroblast 7E7S4, PDL = 191


title: Single TERT-immortalized fibroblast 7E6S4, PDL = 191


title: Single TERT-immortalized fibroblast 7F1S4, PDL = 191


title: Single TERT-immortalized fibroblast 7F11S4, PDL = 191


title: Single TERT-immortalized fibroblast 7E2S4, PDL = 191


title: Single TERT-immortalized fibroblast 7E3S4, PDL = 191


title: Single TERT-immortalized fibroblast 7F8S4, PDL = 191


title: Single TERT-immortalized fibroblast 7E10S4, PDL = 191


title: Single TERT-immortalized fibroblast 7E12S4, PDL = 191


title: Single TERT-immortalized fibroblast 7E11S4, PDL = 191


title: Single TERT-immortalized fibroblast 7E9S4, PDL = 191


title: Single TERT-immortalized fibroblast 7E1S4, PDL = 191


title: Single TERT-immortalized fibroblast 7D9S4, PDL = 191


title: Single TERT-immortalized fibroblast 7D6S4, PDL = 191


title: Single TERT-immortalized fibroblast 7D8S4, PDL = 191


title: Single TERT-immortalized fibroblast 7F2S4, PDL = 191


title: Single TERT-immortalized fibroblast 7D4S4, PDL = 191


title: Single TERT-immortalized fibroblast 7D5S4, PDL = 191


title: Single TERT-immortalized fibroblast 7D3S4, PDL = 191


title: Single TERT-immortalized fibroblast 7D7S4, PDL = 191


title: Single TERT-immortalized fibroblast 7D10S4, PDL = 191


title: Single TERT-immortalized fibroblast 7D2S4, PDL = 191


title: Single TERT-immortalized fibroblast 7D1S4, PDL = 191


title: Single TERT-immortalized fibroblast 7D11S4, PDL = 191


title: Single TERT-immortalized fibroblast 7C9S4, PDL = 191


title: Single TERT-immortalized fibroblast 7C7S4, PDL = 191


title: Single TERT-immortalized fibroblast 7C6S4, PDL = 191


title: Single TERT-immortalized fibroblast 7C5S4, PDL = 191


title: Single TERT-immortalized fibroblast 7C3S4, PDL = 191


title: Single TERT-immortalized fibroblast 7C8S4, PDL = 191


title: Single TERT-immortalized fibroblast 7C2S4, PDL = 191


title: Single TERT-immortalized fibroblast 7C1S4, PDL = 191


title: Single TERT-immortalized fibroblast 7C10S4, PDL = 191


title: Single TERT-immortalized fibroblast 7C11S4, PDL = 191


title: Single TERT-immortalized fibroblast 7C4S4, PDL = 191


title: Single TERT-immortalized fibroblast 7B4S4, PDL = 191


title: Single TERT-immortalized fibroblast 7B8S4, PDL = 191


title: Single TERT-immortalized fibroblast 7B7S4, PDL = 191


title: Single TERT-immortalized fibroblast 7B3S4, PDL = 191


title: Single TERT-immortalized fibroblast 7B5S4, PDL = 191


title: Single TERT-immortalized fibroblast 7B6S4, PDL = 191


title: Single TERT-immortalized fibroblast 7G1S4, PDL = 191


title: Single TERT-immortalized fibroblast 7B1S4, PDL = 191


title: Single TERT-immortalized fibroblast 7B10S4, PDL = 191


title: Single TERT-immortalized fibroblast 7B11S4, PDL = 191


title: Single TERT-immortalized fibroblast 7B12S4, PDL = 191


title: Single TERT-immortalized fibroblast 7A7S4, PDL = 191


title: Single TERT-immortalized fibroblast 7B2S4, PDL = 191


title: Single TERT-immortalized fibroblast 7A5S4, PDL = 191


title: Single TERT-immortalized fibroblast 7A6S4, PDL = 191


title: Single TERT-immortalized fibroblast 7A8S4, PDL = 191


title: Single TERT-immortalized fibroblast 7A9S4, PDL = 191


title: Single TERT-immortalized fibroblast 7A10S4, PDL = 191


title: Single TERT-immortalized fibroblast 7A12S4, PDL = 191


title: Single TERT-immortalized fibroblast 7A1S4, PDL = 191


title: Single TERT-immortalized fibroblast 7B9S4, PDL = 191


title: Single TERT-immortalized fibroblast 7A3S4, PDL = 191


title: Single fibroblast 5H7S3, PDL = 56


title: Single fibroblast 5H6S3, PDL = 56


title: Single TERT-immortalized fibroblast 7A2S4, PDL = 191


title: Single TERT-immortalized fibroblast 7A11S4, PDL = 191


title: Single fibroblast 5H9S3, PDL = 56


title: Single fibroblast 5H3S3, PDL = 56


title: Single fibroblast 5H2S3, PDL = 56


title: Single fibroblast 5H12S3, PDL = 56


title: Single fibroblast 5H1S3, PDL = 56


title: Single fibroblast 5G8S3, PDL = 56


title: Single fibroblast 5H11S3, PDL = 56


title: Single TERT-immortalized fibroblast 7D12S4, PDL = 191


title: Single TERT-immortalized fibroblast 7A4S4, PDL = 191


title: Single fibroblast 5H10S3, PDL = 56


title: Single fibroblast 5G7S3, PDL = 56


title: Single fibroblast 5G6S3, PDL = 56