title: B/T HO site

city: Dallas

first: Sneha

last: Korlakunta

state: TX

address: 6000 Harry Hines Blvd

department: Surgery

institute: UT Southwestern Medical Center

description: Day 7 post-B/T, 10X Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting, and aggregation were completed using the Cell Ranger (v5) pipeline.
Assembly: mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: tendon injury

extract_protocol:
Tenotomy injury site was harvested from Day 7 post-tenotomy mice. Tissue samples were digested for 45 minutes in 750U/ml Type 1 Collagenase and 7U/ml Dispase II (Gibco) in Roswell Park Memorial Institute (RPMI) medium at 37°C under constant agitation of 160rpm. Digestions were subsequently quenched with 2% FBS in PBS and filtered through 40μm sterile strainers. Cells were then washed in 2% FBS in PBS, counted and resuspended at a concentration of 1000-1200 cells/ul. Cell viability was assessed with Trypan blue exclusion on a Countess II (Thermo Fisher Scientific) automated counter and only samples with >85% viability were used for scRNA sequencing.
Library construction was performed according to the manufacturer’s instructions (single cell 3’ v3 protocol, 10x Genomics).

treatment_protocol: C57BL/6J male mice, aged 8-10 weeks, underwent a 30% total body surface area dorsal burn with concurrent Achilles tendon transection of the left hindlimb as described previously 14. Prior to BT of the left hindlimb, mice were anesthetized with 2.5% isoflurane and treated with subcutaneous sustained-release buprenorphine analgesia. The uninjured right hindlimb served as an internal control. Mice were randomized into various treatment groups, and subsequent analyses were conducted by experienced researchers blinded to treatment assignments. Mice were randomly allocated to receive either no RT (control), RT on POD1, or RT on POD3 (N=10 each). All mice were anesthetized with 2.5% isoflurane prior to RT. X-RAD 320 (Precision X-ray) was used to deliver a single dose of 7Gy. The irradiation was delivered with the gantry directly facing the injury site while the irradiation beam was controlled by a 2 cm diameter collimator. No bolus was applied.

value: tendon injury

value: male

value: unsorted

tag: strain

tag: age

value: 8-10 weeks

tag: treatment

value: burn/tenotomy


title: patient 139

status: Public on Jun 07 2024

type: RNA

city: Tampa

first: Eric

last: Welsh

state: FL

address: 12902 Magnolia Dr

department: Biostatistics and Bioinformatics

country: USA

institute: H Lee Moffitt Cancer Center

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques. Arrays are hybridized for 18 hours at 45C with vigorous mixing. Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed. Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: IRON normalization was performed on the dataset, batch corrected for RNA quality using PLS

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: macrodissected primary breast tumor

label_protocol: Samples were amplified and labeled using a custom automated version of the NuGEN Ovation v2 with WB (whole blood) reagents protocol (using Ribo-SPIA amplification). The labeled molecules are biotinylated-cRNA. Sample amplification and labeling were performed by LabCorp Clinical Trials-Genomic Services in Seattle, Washington.

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation. Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification. Isolated total RNA samples were assayed for quality (Agilent Bioanalyzer) and yield (Ribogreen) metrics prior to amplification.

tag: tissue

value: macrodissected primary breast tumor

tag: subject

tag: type of surgery

value: Mastectomy

tag: histology

value: Other

tag: er status

value: Positive

tag: pr status

value: Negative

tag: her2 status

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

value: No

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

value: White

tag: chemotherapy

tag: locoregional recurrence

tag: death

value: Dead

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: D1 Lymph Node Protein

type: SRA

city: Chicago

first: David

last: Gate

state: IL

address: 745 N Fairbanks Ct

department: Neurology

institute: Northwestern University

description:
D1_LN_Protein
D1LN_aligned_fiducials.jpg
D1LN_detected_tissue_image.jpg
D1LN_features.tsv.gz
D1LN_matrix.mtx.gz
D1LN_tissue_hires_image.png
D1LN_tissue_lowres_image.png
D1LN_tissue_positions.csv

library_source: other

data_processing:
*library strategy: spatial multi-omics
FASTQs were processed using 10X SpaceRanger v2.1.0
We filtered genes with minimum 10 cells within a spot
In the transcriptomics data, the gene expression counts are log-transformed, normalized by library size and scaling is performed using SCANPY package.
The top 3,000 highly variable genes (HVGs) are selected as input of PCA for dimension reduction.
In the protein data, the first k (number of proteins) principal components are retained and used as the input of the model.
The protein expresssion counts are normalized using CLR (Centered Log Ratio) and then scaling is performed using SCANPY package.
All principal components after PCA dimension reduction are used as the input of the model.
Assembly: GrCh38-2020-A
Supplementary files format and content: Each .h5ad file is a single-sample AnnData object
Supplementary files format and content: the SpaceRanger output files for each sample: isotype normalization factors for protein, aligned fiducials, hires image, lowres image, detected tissue image, tissue positions list, and barcode fluorescence intensity from the spatial output folder, and the features and matrix matrices from the filtered_feature_bc_matrix output folder

molecule: protein

source_name: Lymph Node

extract_protocol:
Formalin-fixed, paraffin-embedded samples were processed according to the Visium CytAssist Spatial Gene and Protein Expression for FFPE – Deparaffinization, H&E Staining, Imaging & Decrosslinking (CG000658, Rev A, 10x Genomics) protocol
Libraries were constructed according to the user guide for Visium CytAssist Spatial Gene and Protein Expression Reagent Kits (CG000494; Rev B; 10x Genomics).

tag: tissue

value: Lymph Node


title: patient 140

tag: subject

tag: type of surgery

tag: histology

tag: er status

tag: pr status

value: Alive


title: B/T RTx HO site

description: Day 7 post-B/T, 7 Gy Radiation, 10X Genomics

organism: Mus musculus

tag: Sex

tag: cell type

tag: strain

tag: age

tag: treatment

value: burn/tenotomy, radiation therapy


title: Sin3a KO Treg, male, biol rep 2

city: Philadelphia

first: Lanette

middle: M

last: Christensen

state: PA

address: 3615 Civic Center Blvd.

department: Pathology and Laboratory Medicine

institute: Children's Hospital of Philadelphia

library_source: transcriptomic

data_processing:
Hisat2 v2.0.5 and featureCounts v1.5.0-p3
Sequence reads were trimmed for adaptor sequence, reads containing N>10%, and reads in which more than 50% of the bases had a Qscore≤5.
Trimmed reads were aligned to the GRCm38/mm10 reference genome using Hisat2 v2.0.5.
Read counts and normalizations were performed using featureCounts v1.5.0-p3.
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text file containing gene counts for each sample
Supplementary files format and content: tab-delimited text file containing gene FPKM values for each sample

source_name: Secondary Lymphoid Organs

extract_protocol:
RNA was isolated from ex vivo CD25+FoxP3+ T-regulatory cells using standard TRIzol/chloroform extraction followed by the Zymo Research RNA Clean and Concentrator Kit. 0.35µg RNA was used for construction of each library.
RNA libraries were prepared by performing polyA enrichment using magnetic bead-linked polyT oligos followed by fragmentation and cDNA synthesis.

treatment_protocol: T-regulatory cells were collected from dissociated secondary lymphiod organs (spleens and lymph nodes). Following dissociation and red blood cell lysis, cells were enriched for CD4+CD25+ using magnetic bead isolation (Miltenyi) then purified by FACS sorting for CD25+FoxP3+ (FACSJazz).

value: Secondary Lymphoid Organs

value: CD25+FoxP3+ T-regulatory cells

tag: genotype

value: Male


title: A1 Tonsil Protein

description:
A1_TNSL_Protein
A1TNSL_aligned_fiducials.jpg
A1TNSL_detected_tissue_image.jpg
A1TNSL_features.tsv.gz
A1TNSL_matrix.mtx.gz
A1TNSL_tissue_hires_image.png
A1TNSL_tissue_lowres_image.png
A1TNSL_tissue_positions.csv

source_name: Tonsil

value: Tonsil


title: A1 Lymph Node Protein

description:
A1_LN_Protein
A1LN_aligned_fiducials.jpg
A1LN_detected_tissue_image.jpg
A1LN_features.tsv.gz
A1LN_matrix.mtx.gz
A1LN_tissue_hires_image.png
A1LN_tissue_lowres_image.png
A1LN_tissue_positions.csv


title: patient 138

value: Lumpectomy

value: IDC

tag: her2 status

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

value: Yes

tag: type of radiotherapy

value: Partial breast irradiation

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: locoregional recurrence


title: patient 136

tag: tissue

value: macrodissected primary breast tumor

tag: subject

tag: type of surgery

value: Mastectomy

tag: histology

tag: er status

tag: pr status

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: patient 137

value: Negative

tag: her2 status

value: Positive

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy


title: patient 134

value: Other

value: No

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

value: White

tag: chemotherapy


title: patient 131

tag: tissue

tag: subject

tag: type of surgery

tag: histology

tag: locoregional recurrence

value: Alive


title: patient 142

tag: er status

tag: pr status

value: External beam radiation

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: patient 132

tag: her2 status

tag: pt

tag: pn

tag: ptnm

tag: bioanalyzer rin (rna integrity number)


title: Sin3a KO Treg, female, biol rep 3

value: Secondary Lymphoid Organs

tag: cell type

tag: genotype

tag: Sex

value: Female


title: patient 135

tag: tissue

tag: subject

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy


title: D1 Tonsil


title: Sin3a KO Treg, female, biol rep 2

value: CD25+FoxP3+ T-regulatory cells


title: Sin3a KO Treg, female, biol rep 1


title: D1 Lymph Node

value: Lymph Node


title: A1 Lymph Node


title: Sin3a KO Treg, male, biol rep 1

value: Male


title: A1 Tonsil

value: Tonsil


title: patient 128

tag: type of surgery

tag: histology

value: IDC

tag: er status

tag: pr status

value: Yes

tag: locoregional recurrence

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: patient 130

value: macrodissected primary breast tumor

tag: her2 status

tag: pt

tag: pn

tag: ptnm

tag: bioanalyzer rin (rna integrity number)


title: patient 133

tag: tissue

tag: subject

value: Lumpectomy

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis


title: patient 129

tag: type of surgery

tag: histology

value: Negative

value: Partial breast irradiation

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy


title: patient 123

value: Mastectomy

value: ILC

tag: er status

value: Positive

tag: pr status

tag: locoregional recurrence

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 122

tag: her2 status

tag: pt

tag: pn

tag: ptnm

value: No

value: White

value: Alive

tag: time to death or censor from date of diagnosis (years)


title: patient 127

tag: tissue

tag: subject

tag: radiotherapy

tag: type of radiotherapy

value: External beam radiation

tag: bioanalyzer rin (rna integrity number)


title: patient 125

tag: type of surgery

tag: histology

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

value: Dead


title: patient 124

tag: er status

tag: pr status

tag: chemotherapy

tag: locoregional recurrence

tag: death


title: patient 126

tag: her2 status

tag: pt

tag: pn

tag: ptnm

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 121

tag: tissue

tag: subject

tag: radiotherapy

tag: type of radiotherapy

tag: time to death or censor from date of diagnosis (years)


title: Control Treg, male, biol rep 2

value: Secondary Lymphoid Organs

tag: cell type

value: CD25+FoxP3+ T-regulatory cells

tag: genotype

tag: Sex


title: patient 120

tag: type of surgery

tag: histology

tag: er status

tag: pr status

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: bioanalyzer rin (rna integrity number)


title: Control Treg, male, biol rep 1

value: Male


title: 2424365_TTC709_RNA_shPHF6_NA_2

city: Memphis

first: Jacquelyn

middle: A

last: Myers

state: TN

address: 262 Danny Thomas Pl

institute: St. Jude Children’s Research Hospital

data_processing:
trim_galore v0.6.3 remove adapter sequences
alignment with STAR2.7.3a --twopassMode Basic
read counts quantified by RSEMv1.3.1
Assembly: GRCh37 hg19
Supplementary files format and content: quantified read counts are provided in the txt format for every sample for gencode v19
Supplementary files format and content: TPM normalized expressed data for every samples in the txt format for every sample for gencode v19

molecule: polyA RNA

source_name: cell line

growth_protocol: All cells were cultured at 37°C with 5% humidity and 5% CO2.

extract_protocol:
Trizol and theDirectZolMini Prep Plus kit (ZymoResearch, R2070)
TruSeq Stranded mRNA Library Prep kit

treatment_protocol: G401 cells were cultured in McCoy’s media with 10% FBS (Sigma Aldrich) and 1% Glutamax (GIBCO). TTC549 and TTC709 cells were cultured in RPMI with 10%FBS(Sigma Aldrich) and 1% Glutamax (GIBCO)

value: cell line

tag: cell line


title: Control Treg, male, biol rep 3

tag: tissue


title: 2424363_TTC709_RNA_shCTRL_NA_3

value: shCTRL


title: patient 119

value: macrodissected primary breast tumor

tag: subject

value: IDC

tag: her2 status

tag: pt

tag: pn

tag: ptnm

tag: chemotherapy

value: Unknown

tag: locoregional recurrence

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)


title: Control Treg, female, biol rep 2

tag: cell type

tag: genotype

tag: Sex

value: Female


title: 2424366_TTC709_RNA_shPHF6_NA_3


title: Control Treg, female, biol rep 3


title: 2424364_TTC709_RNA_shPHF6_NA_1


title: Control Treg, female, biol rep 1


title: 2424362_TTC709_RNA_shCTRL_NA_2


title: 2424361_TTC709_RNA_shCTRL_NA_1


title: patient 118

tag: type of surgery

value: Mastectomy

tag: histology

tag: er status

tag: pr status

value: Negative

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

value: Hispanic, Asian & other

tag: time to death or censor from date of diagnosis (years)


title: patient 117

tag: tissue

tag: subject

value: Other

value: Positive

tag: her2 status

tag: pt

tag: pn

tag: ptnm

value: No

tag: race

value: Yes

tag: bioanalyzer rin (rna integrity number)


title: patient 116

tag: type of surgery

value: ILC

value: White

tag: chemotherapy

tag: locoregional recurrence

tag: death

value: Alive

tag: time to locoregional recurrence from date of diagnosis (years)


title: 2424360_TTC549_RNA_shPHF6_NA_3

tag: cell line

tag: genotype


title: 2424359_TTC549_RNA_shPHF6_NA_2


title: patient 115

tag: histology

tag: er status

tag: pr status

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)


title: patient 114

tag: tissue

tag: subject

value: Lumpectomy

tag: her2 status

tag: pt

tag: pn

tag: ptnm

value: External beam radiation

value: Dead

tag: time to death or censor from date of diagnosis (years)


title: patient 111

value: macrodissected primary breast tumor

tag: type of surgery

tag: race

tag: chemotherapy

tag: locoregional recurrence

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: patient 112

tag: histology

tag: er status

tag: pr status

tag: radiotherapy

tag: type of radiotherapy


title: patient 110

tag: tissue

tag: subject

tag: her2 status

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

value: AA


title: patient 113

tag: type of surgery

value: IDC

tag: pt

tag: pn

tag: ptnm

tag: time to death or censor from date of diagnosis (years)


title: SPNORM8M-3093351_G401shCTRL_PHF6ActiveMotif61807_NA_2_PM

description: ChIP-Seq of PHF6 in shCTRL rep2

library_source: genomic

data_processing:
trim_galore v0.6.3 remove adapter sequences
align quality reads using bwa mem v0.7.17 to a hybrid reference genome
bamsormadup v2.0.87
samtools used to split bam file for hg19 and dm6 reads base on chromosome names
samtools -F 1024 -q 1 to define quality reads
estimate fragment size using spp R package
slopBed -r fragment size estimation determined by spp
Normalized using dm6 spike in scaling factor normalized to 8M reads
Assembly: hg19+dm6 (Gencode GRCh37 and Ensembl r97)
Supplementary files format and content: normalized coverage in the bigwig file format, macs2 narrow peaks

molecule: genomic DNA

extract_protocol:
G401 cells were grown in McCoy's 5A media supplemented with 10% fetal bovine serum and 1% Glutamax (Gibco) at 37°C and 5% CO2.
In brief, cells were cross-linked directly on the plate using 1% paraformaldehyde for 10 min at room temperature and quenched with glycine. Nuclei were isolated using the Covaris TruCHIP kit and Chromatin extracts were sonicated for 8 min using a Covaris E220 focused ultrasonicator at a peak power of 140, a duty factor of 5 and 200 cycles per burst. Chromatin immunoprecipitation was carried overnight with antibodies bound to dynabeads. Chromatin was de-crosslinked, digested with RNase and Proteinase K and DNA was purified using a Qiagen DNA kit. For MNase ChIP, CST kit guidelines were followed. KAPA HyperPrep Kit (Kapa Biosystems, Cat# 7962363001).

treatment_protocol: G401 cells were infected with either control (shCTRL) or PHF6 (shPHF6) targeting shRNAs. 48hrs post infection, cells were selected with 1ug/mL puromycin for 72h and subsequently harvested.

tag: cell type

tag: shRNA

value: shCTRL


title: patient 108

value: Mastectomy

tag: histology

tag: race

tag: chemotherapy

tag: locoregional recurrence

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: 2424357_TTC549_RNA_shCTRL_NA_3

tag: tissue

value: cell line

tag: cell line

tag: genotype


title: patient 109

tag: subject

tag: type of surgery

tag: er status

tag: pr status

tag: her2 status

value: Negative

tag: radiotherapy

tag: type of radiotherapy

value: Partial breast irradiation

tag: age at diagnosis

tag: age at diagnosis (dichotomized)


title: 2424356_TTC549_RNA_shCTRL_NA_2


title: patient 107

tag: histology

value: Positive

tag: pt

tag: pn

tag: ptnm

tag: race

tag: chemotherapy

tag: time to death or censor from date of diagnosis (years)


title: patient 105

tag: tissue

value: No

tag: locoregional recurrence

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: 2424358_TTC549_RNA_shPHF6_NA_1

tag: cell line

tag: genotype


title: KAS-seq_MII_biol rep2

city: Nanjing

first: huiqing

last: an

address: 101 Longmian Rd, Nanjing, Jiangsu, China

country: China

institute: Nanjing Medical University

data_processing:
Paired-end reads of 150-bp were generated on the Illumina novaseq 6000 platform in this study (sequenced by Annoroad). For KAS-seq data, raw reads were trimmed using trim galore (v0.6.10) (parameters: --quality 20 --phred33 –length 30 –stringency 3 --paired) and mapped to mouse reference genome (GRcm38) using Bowtie2 (v2.5.1) (parameters: -X 2000 -I 10). All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed. The signal tracks and heatmap were both generated by deeptools (v3.5.2). The MACS2 (macs2 2.2.7.1) were used for peak calling (parameters: --broad). HOMER (v4.10) was used for motif enrichment analysis. Annotation of peaks was performed using ChIPseeker (v1.36.0).
Assembly: GRcm38
Supplementary files format and content: bigwig
Library strategy: KAS-Seq

source_name: oocyte

extract_protocol:
Oocytes were labeled with N3-Kethxal (5 mM), and labeled genomic DNA (gDNA 9.5 µL) was subsequently extracted using the Quick-DNA Microprep Plus Kit (Zymo D4074)
After labeling, gDNA was fragmented using Tn5 transposase (Vazyme TD501).Following fragmentation, biotinylation labeling was performed using DBCO-PEG4-biotin (20 mM, DMSO solution, Sigma 760749). The biotinylated DNA was then cleaned up using DNA Clean & Concentrator-5 kit (Zymo, D4013), and 5 µL of labeled DNA was retained as input, while the remaining 50 µL of DNA was used for enrichment.The Dynabeads™ MyOne™ Streptavidin C1 (Thermo 65001) were mixed with the 50 µL fragmented DNA obtained from the previous steps and rotated slowly at room temperature for 15 min.DNA-conjugated beads and their corresponding inputs were used for library PCR using i5 and i7 index primers (Vazyme TD205) and VAHTS HiFi Amplification Mix (Vazyme N616). The PCR reactions were initiated with a 5-min incubation at 72°C, followed by 10 min at 95°C, and then amplified for 17 cycles (10 s at 98°C, 30 s at 60°C, 1 min at 72°C). Finally, the libraries were cleaned up by using DNA Clean & Concentrator-5 kit (Zymo, D4013).

tag: cell type

value: oocyte

tag: developmental stage

value: MII


title: KAS-seq_MII_biol rep2_input


title: 2374649_G401_RNA_shBRD9_3


title: KAS-seq_MII_biol rep1_input


title: 2374648_G401_RNA_shBRD9_2


title: patient 99

tag: subject

tag: type of surgery

tag: er status

tag: pr status

tag: her2 status

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

value: White

value: Yes


title: patient 102

tag: tissue

tag: histology

tag: pt

tag: pn

tag: ptnm

tag: race

tag: chemotherapy

tag: locoregional recurrence

value: Alive

tag: time to death or censor from date of diagnosis (years)


title: patient 100

tag: subject

tag: type of surgery

value: Lumpectomy

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: patient 103

tag: er status

tag: pr status

tag: her2 status

tag: radiotherapy

tag: type of radiotherapy


title: 2424355_TTC549_RNA_shCTRL_NA_1

tag: tissue

tag: cell line

tag: genotype


title: KAS-seq_GVBD_biol rep2_input

tag: cell type

tag: developmental stage

value: GVBD


title: patient 98

value: macrodissected primary breast tumor

tag: histology

tag: pt

tag: pn

tag: ptnm

value: External beam radiation

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: locoregional recurrence


title: patient 97

tag: subject

tag: type of surgery

value: Other

tag: er status

tag: pr status

tag: her2 status

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: 2374647_G401_RNA_shBRD9_1

tag: tissue

tag: cell line

tag: genotype


title: patient 106

tag: histology

value: IDC

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis


title: patient 94

tag: subject

tag: type of surgery

tag: er status

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: locoregional recurrence


title: patient 104

tag: tissue

tag: pr status

tag: her2 status

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: patient 95

tag: histology

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

value: Hispanic, Asian & other


title: KAS-seq_GVBD_biol rep2

tag: cell type

tag: developmental stage


title: 2374643_G401_RNA_PGIPZ_3

value: cell line

tag: cell line

tag: genotype

value: PGIPZ


title: KAS-seq_GVBD_biol rep1_input


title: patient 93

tag: subject

tag: type of surgery

tag: er status

value: Negative

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: locoregional recurrence


title: 2374642_G401_RNA_PGIPZ_2

tag: tissue


title: KAS-seq_MII_biol rep1


title: patient 92

value: Mastectomy

tag: histology

value: Positive

tag: pr status

tag: her2 status

tag: pt

tag: pn

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: KAS-seq_GVBD_biol rep1

tag: cell type

value: oocyte

tag: developmental stage


title: 2374641_G401_RNA_PGIPZ_1

tag: cell line

tag: genotype


title: patient 101

tag: subject

tag: type of surgery

tag: er status

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

value: No

value: Dead


title: patient 96

tag: tissue

tag: histology

value: ILC

tag: pr status

tag: her2 status

tag: pt

tag: pn

value: Yes

value: White

tag: chemotherapy

tag: locoregional recurrence

tag: death


title: patient 90

tag: subject

tag: type of surgery

value: Alive

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: patient 88

value: macrodissected primary breast tumor

tag: er status

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis


title: ATAC_shPHF6_3

data_processing:
trim_galore v0.6.3 remove adapter sequences
pbrun fq2bam v3.0.0.6 --bwa-options -K 10000000 -Y -M --num-gpus 2
samtools view -F 1804 -b -q 1 and bamsort
bamToBed -bedpe; grep -v chrM
coverage normalized to 20million reads for all fragment sizes less than 2kb
Assembly: GRCh37.p13 hg19
Supplementary files format and content: bigWig of normalized coverage
Supplementary files format and content: MACS2 narrowPeaks

growth_protocol: G401 cells were grown in McCoy's 5A media supplemented with 10% fetal bovine serum and 1%Glutamax(Gibco) at 37°C and 5% CO2. 50k cells were plated per well in a 6-well dish.

extract_protocol:
Nuclei from 100K cells were isolated usingActive Motif ATAC-seq kit (kit #53150)protocol.
Libraries were prepared using the Active Motif ATAC-Seq kit (kit #53150). Briefly, nuclei were isolated and submitted to tagmentation at 37C for 30’ shaking at 800RPM. Tagmented DNA was purified using the provided columns

tag: tissue

tag: cell line

tag: genotype


title: patient 87

value: Lumpectomy

tag: histology

tag: pr status

tag: her2 status

tag: pt

tag: pn

value: External beam radiation

tag: age at diagnosis (dichotomized)

tag: race


title: ATAC_shPHF6_2

treatment_protocol: G401 cells were grown in McCoy's 5A media supplemented with 10% fetal bovine serum and 1%Glutamax(Gibco) at 37°C and 5% CO2. 50k cells were plated per well in a 6-well dish.


title: KAS-seq_GV SN_biol rep2

tag: cell type

tag: developmental stage

value: GV-SN


title: patient 86

tag: subject

tag: type of surgery

value: IDC

tag: er status

tag: chemotherapy

tag: locoregional recurrence

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: KAS-seq_GV SN_biol rep2_input


title: KAS-seq_GV SN_biol rep1_input


title: KAS-seq_GV SN_biol rep1


title: patient 84

tag: tissue

tag: histology

tag: pr status

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

value: Partial breast irradiation

tag: age at diagnosis


title: KAS-seq_GV NSN_biol rep2_input

tag: cell type

tag: developmental stage

value: GV-NSN


title: patient 83

tag: subject

tag: type of surgery

value: Negative

tag: her2 status

tag: pt

tag: pn

tag: age at diagnosis (dichotomized)

tag: race


title: patient 82

value: Mastectomy

tag: er status

tag: chemotherapy

tag: locoregional recurrence

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: patient 89

tag: tissue

tag: histology

value: Positive

tag: pr status

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis


title: ATAC_shPHF6_1

value: cell line

tag: cell line

tag: genotype


title: patient 81

tag: subject

tag: type of surgery

tag: her2 status

tag: pt

tag: pn

tag: age at diagnosis (dichotomized)

tag: race

value: No


title: patient 91

tag: er status

tag: chemotherapy

tag: locoregional recurrence

tag: death

value: Dead

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: KAS-seq_GV NSN_biol rep2

tag: cell type

value: oocyte

tag: developmental stage


title: patient 80

tag: tissue

tag: histology

tag: pr status

tag: ptnm

tag: radiotherapy

value: Yes

tag: type of radiotherapy

tag: age at diagnosis


title: ATAC_shCTRL_3

tag: cell line

tag: genotype

value: shCTRL


title: ATAC_shCTRL_2


title: KAS-seq_GV NSN_biol rep1_input


title: ATAC_shCTRL_1


title: KAS-seq_GV NSN_biol rep1


title: patient 76

tag: subject

tag: type of surgery

tag: er status

tag: her2 status

tag: pt

tag: pn

tag: age at diagnosis (dichotomized)

tag: race

value: White

tag: chemotherapy

value: Alive


title: patient 79

tag: tissue

value: macrodissected primary breast tumor

tag: histology

tag: locoregional recurrence

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: patient 78

tag: pr status

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis


title: 2415545_G401_input_shCTRL

data_processing:
trim_galore v0.6.3 remove adapter sequences
align quality reads using bwa mem v0.7.17 to a hybrid reference genome
bamsormadup v2.0.87
samtools used to split bam file for hg19 and dm6 reads base on chromosome names
samtools -F 1024 -q 1 to define quality reads; estimate fragment size using spp R package; slopBed -r fragment size estimation determined by spp; Normalize to 15M reads
Assembly: hg19+dm6 (Gencode GRCh37 and Ensembl r97)
Supplementary files format and content: normalized coverage in the bigwig file format, macs2 narrow peaks

growth_protocol: G401 cells were grown in McCoy's 5A media supplemented with 10% fetal bovine serum and 1%Glutamax(Gibco) at 37°C and 5% CO2.

extract_protocol:
In brief, cells were cross-linked directly on the plate using 1% paraformaldehyde for 10 min at room temperature and quenched with glycine. Nuclei were isolated using the Covaris TruCHIP kit and Chromatin extracts were sonicated for 8 min using a Covaris E220 focused ultrasonicator at a peak power of 140, a duty factor of 5 and 200 cycles per burst. Chromatin immunoprecipitation was carried overnight with antibodies bound to dynabeads. Chromatin was de-crosslinked, digested with RNase and Proteinase K and DNA was purified using a Qiagen DNA kit.
KAPA HyperPrep Kit (Kapa Biosystems, Cat# 7962363001)

tag: cell line

tag: antibody

value: input

tag: genotype


title: patient 75

tag: subject

tag: type of surgery

tag: er status

tag: her2 status

tag: pt

tag: pn

tag: age at diagnosis (dichotomized)

tag: race


title: patient 77

tag: tissue

tag: histology

value: ILC

tag: chemotherapy

tag: locoregional recurrence

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: patient 74

value: IDC

tag: pr status

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis


title: 2415546_G401_input_shPHF6

tag: cell line

tag: antibody

tag: genotype


title: Brain, Normal diet, No stim, D23-4372_S32_L004

city: Boston

first: Daniela

middle: Rodrigues

last: Amorim

state: MA

address: 43 Vassar Street, Bldg.46-1303 Cambridge

department: Picower Institute for Learning and Memory

institute: Massachusetts Institute of Technology

data_processing:
Sn-RNA-seq FASTQ files were downloaded and raw files (features, barcodes, and matrix) generated by Cell Ranger v3.0.1 (10X Genomics) were processed, analyzed and visualized using the Cellenics® community instance (https://scp.biomage.net/) hosted by Biomage (https://biomage.net/).
Count matrices were pre-filtered by removing all barcodes with more than 20000 UMIs and using the Cellranger Empty Drops method67 with a false discovery rate (FDR) threshold of 0.1. Barcodes with less than 100 and more than 5000 features were removed.
Pre-filtered count matrices were uploaded to Cellenics®. Barcodes were then filtered in a series of two sequentially applied steps. First, dead and dying cells were removed by filtering out barcodes with a percentage of mitochondrial reads above 10%. Secondly, droplets outside the upper and lower boundaries of the prediction interval were filtered out. Lastly, the probability of droplets containing more than one cell was calculated using the scDblFinder R package (v. 1.11.3).
After filtering, each sample contained between 1255 and 4556 high-quality barcodes, totaling 37001 cells, which were input to the integration pipeline. In the first integration step, data was log-normalized, and the top 2000 highly variable genes were selected based on the variance stabilizing transformation (VST) method. Principal-component analysis (PCA) was performed, and the top 30 principal components, explaining 85.23% of the total variance, were used for batch correction with the Harmony R package
Clustering was performed using Seurat’s implementation of the Louvain method and a total of 18 clusters were identified. To visualize results, a Uniform Manifold Approximation and Projection (UMAP) embedding was calculated, using Seurat’s wrapper around the Uniform Manifold Approximation and Projection (UMAP) package
Assembly: mm10
Supplementary files format and content: Tab-separated values include raw barcodes and features files for each sample
Supplementary files format and content: Matrix market file includes raw matrix for each sample

molecule: nuclear RNA

source_name: Brain

extract_protocol:
The tubes containing frozen tissue (CC) were transferred from the -80ºC freezer to ice, along with the necessary solutions for isolating the nuclei. The isolation of CC nuclei was performed using a commercial kit (Minute™ Single Nucleus Isolation Kit for Neuronal Tissues/Cells, BN-020, Invent Biotechnologies, Inc.).
cDNA libraries were prepared using the Chromium Next GEM Single Cell 3′ Kit v3.1 (10X Genomics), according to manufacture protocol.

treatment_protocol: The mice were assigned to different dietary interventions, involving either a diet consisting of 0.3% CPZ-containing pellets or ND for a duration of 3 weeks. In the first cohort, after 3 weeks of CPZ feeding, the therapeutic group was subjected to GENUS for 3 weeks, while the control group received CPZ without any stimulation (no stim group), maintaining the diet intervention until week 6. In the second cohort, mice were fed with ND and were also exposed to GENUS stimulation or received no stimulation, following the same timeline as the CPZ cohort.

tag: strain

value: Brain

tag: region

value: Corpus callosum

value: WT

tag: Sex

value: Male

tag: age

value: 12 weeks

tag: diet intervention

value: Normal diet

tag: stimulation

value: No stim


title: patient 73

tag: tissue

tag: subject

tag: type of surgery

value: Lumpectomy

tag: histology

tag: er status

value: Positive

tag: her2 status

value: Negative

tag: pt

tag: pn

value: External beam radiation

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

value: No

tag: locoregional recurrence

tag: death

value: Dead

tag: time to locoregional recurrence from date of diagnosis (years)


title: 2415543_G401_EP300_shPHF6_rep3

value: cell line

tag: cell line

tag: antibody

tag: genotype


title: Brain, Normal diet, No stim, D23-4371_S31_L004

tag: strain

tag: tissue

tag: region

tag: Sex

tag: age

tag: diet intervention

tag: stimulation


title: 2415542_G401_EP300_shPHF6_rep2


title: patient 72

value: macrodissected primary breast tumor

tag: subject

tag: type of surgery

value: Mastectomy

tag: histology

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

value: White

value: Yes

value: Alive

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: patient 71

tag: tissue

value: IDC

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: locoregional recurrence

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)


title: Brain, Normal diet, No stim, D23-4370_S30_L004

tag: strain

value: Brain

tag: region

value: Corpus callosum

tag: genotype

value: WT

tag: Sex

value: Male

tag: age

tag: diet intervention

tag: stimulation


title: patient 69

tag: subject

tag: type of surgery

value: Lumpectomy

tag: histology

value: Other

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis


title: Brain, Normal diet, No stim, D23-4369_S29_L004

tag: strain

tag: tissue

tag: region

tag: genotype

value: 12 weeks

value: Normal diet

value: No stim


title: patient 85

value: Negative

value: No

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: locoregional recurrence

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: 2415540_G401_EP300_shCTRL_rep3

value: cell line

tag: cell line

tag: antibody

value: shCTRL


title: patient 66

value: macrodissected primary breast tumor

tag: subject

tag: type of surgery

tag: histology

value: ILC

tag: er status

value: Positive

tag: pr status

tag: her2 status

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

value: External beam radiation

value: White


title: patient 67

tag: tissue

value: Mastectomy

value: IDC

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: locoregional recurrence

value: Alive


title: patient 70

tag: subject

value: Yes

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: Brain, Normal diet, GENUS, D23-4368_S28_L004

tag: strain

value: Brain

tag: region

value: Corpus callosum

tag: genotype

value: WT

tag: Sex

value: Male

tag: age

tag: diet intervention

tag: stimulation

value: GENUS


title: 2410027_G401_input_shPHF6

tag: tissue

tag: cell line

tag: antibody

value: input


title: patient 65

tag: type of surgery

tag: histology

tag: er status

tag: pr status

value: Negative

tag: her2 status

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

value: No


title: 2410026_G401_input_shCTRL

tag: tissue

value: cell line

tag: genotype

value: shCTRL


title: Brain, Normal diet, GENUS, D23-4367_S27_L004

tag: strain

tag: region

tag: Sex

tag: age

value: 12 weeks

tag: diet intervention

value: Normal diet

tag: stimulation


title: patient 64

value: macrodissected primary breast tumor

tag: subject

tag: type of surgery

value: Lumpectomy

tag: histology

value: ILC

tag: er status

value: Positive

tag: pr status

tag: her2 status

tag: pt

value: External beam radiation

value: White

tag: locoregional recurrence

tag: death

value: Dead

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: patient 68

tag: tissue

value: IDC

tag: pn

tag: ptnm

tag: radiotherapy

value: Yes

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy


title: 2410025_G401_BRD9_shPHF6_rep3

tag: cell line

tag: antibody

tag: genotype


title: Brain, Normal diet, GENUS, D23-4366_S26_L004

tag: strain

value: Brain

tag: region

value: Corpus callosum

value: WT

tag: Sex

value: Male

tag: age

tag: diet intervention

tag: stimulation

value: GENUS


title: 2410024_G401_BRD9_shPHF6_rep2

tag: tissue

value: cell line


title: patient 63

tag: subject

tag: type of surgery

tag: histology

tag: er status

value: Negative

tag: pr status

tag: her2 status

tag: pt

tag: pn

tag: ptnm

tag: locoregional recurrence

value: No

tag: death

value: Alive

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: Brain, Normal diet, GENUS, D23-4365_S25_L004

tag: strain

tag: region

tag: genotype

tag: Sex

tag: age

value: 12 weeks

tag: diet intervention

value: Normal diet


title: 2410023_G401_SMARCA4_shPHF6_rep3

tag: tissue

tag: cell line

tag: antibody


title: Brain, CPZ, No stim, D23-4364_S24_L004

value: 0.3% Cuprizone

tag: stimulation

value: No stim


title: 2410022_G401_SMARCA4_shPHF6_rep2


title: Brain, CPZ, No stim, D23-4363_S23_L004


title: patient 61

value: macrodissected primary breast tumor

tag: subject

tag: type of surgery

value: Lumpectomy

tag: histology

value: ILC

tag: er status

value: Positive

tag: pr status

tag: her2 status

tag: pt

tag: pn

tag: radiotherapy

tag: type of radiotherapy

value: External beam radiation

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

value: White

tag: chemotherapy


title: patient 57

tag: tissue

value: Mastectomy

value: IDC

tag: ptnm

tag: locoregional recurrence

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: patient 59

tag: subject

tag: type of surgery

tag: histology

tag: er status

tag: pr status

value: Yes

value: Dead


title: patient 56

tag: her2 status

value: Negative

tag: pt

tag: pn

tag: radiotherapy

tag: type of radiotherapy


title: Brain, CPZ, No stim, D23-4362_S22_L004

tag: strain

tag: tissue

value: Brain

tag: region

value: Corpus callosum

tag: genotype

value: WT

tag: Sex

value: Male

tag: age

tag: diet intervention

tag: stimulation


title: patient 60

tag: subject

tag: type of surgery

tag: ptnm

value: Partial breast irradiation

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: locoregional recurrence

value: No

tag: death

value: Alive

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: patient 62

tag: tissue

value: macrodissected primary breast tumor

tag: histology

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: pn

tag: radiotherapy

tag: type of radiotherapy


title: patient 53

tag: subject

tag: type of surgery

value: Lumpectomy

tag: ptnm

tag: age at diagnosis

tag: age at diagnosis (dichotomized)


title: 2410020_G401_PBRM1_shPHF6_rep2

value: cell line

tag: cell line

tag: antibody

tag: genotype


title: Brain, CPZ, No stim, D23-4361_S21_L004

tag: strain

tag: tissue

tag: region

tag: Sex

tag: age

value: 12 weeks

tag: diet intervention

value: 0.3% Cuprizone

tag: stimulation

value: No stim


title: patient 58

tag: histology

value: ILC

tag: er status

value: Positive

tag: pr status

tag: her2 status

tag: pt

tag: pn

tag: radiotherapy

tag: race

value: White

tag: chemotherapy

tag: locoregional recurrence

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: 2410019_G401_BRD9_shCTRL_rep3

tag: tissue

tag: cell line

tag: antibody

tag: genotype

value: shCTRL


title: patient 54

tag: subject

tag: type of surgery

tag: histology

value: IDC

tag: er status

value: Negative

tag: ptnm

value: Yes

tag: type of radiotherapy

value: External beam radiation

tag: age at diagnosis

tag: age at diagnosis (dichotomized)


title: Brain, CPZ, GENUS, D23-4360_S20_L004

tag: strain

value: Brain

tag: region

value: Corpus callosum

value: WT

tag: Sex

value: Male

tag: age

tag: diet intervention

tag: stimulation

value: GENUS


title: patient 55

tag: tissue

value: macrodissected primary breast tumor

value: Mastectomy

tag: pr status

tag: her2 status

tag: pt

tag: pn

tag: radiotherapy

value: No

tag: race

tag: chemotherapy

tag: locoregional recurrence

tag: death

value: Alive

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: patient 50

tag: subject

tag: type of surgery

tag: histology

tag: er status

tag: ptnm

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)


title: patient 48

tag: tissue

value: Lumpectomy

tag: pr status

tag: her2 status

tag: pt

tag: pn


title: patient 51

value: Positive

tag: radiotherapy

tag: race

tag: chemotherapy

tag: locoregional recurrence

tag: death


title: 2410018_G401_BRD9_shCTRL_rep2

value: cell line

tag: cell line

tag: antibody

tag: genotype


title: 2410021_G401_PBRM1_shPHF6_rep3


title: Brain, CPZ, GENUS, D23-4359_S19_L004

tag: strain

tag: region

tag: Sex

tag: age

value: 12 weeks

tag: diet intervention

value: 0.3% Cuprizone

tag: stimulation


title: patient 52

tag: tissue

tag: subject

tag: type of surgery

tag: histology

value: IDC

tag: er status

tag: pr status

value: Negative

tag: her2 status

tag: ptnm

tag: type of radiotherapy

value: Partial breast irradiation

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

value: White

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: patient 49

tag: pt

tag: pn

tag: radiotherapy

value: Yes

value: External beam radiation

tag: race

tag: chemotherapy

tag: locoregional recurrence

tag: death


title: patient 44

tag: tissue

tag: subject

tag: type of surgery

tag: histology

tag: er status


title: patient 47

tag: pr status

tag: her2 status

tag: ptnm

tag: type of radiotherapy

tag: age at diagnosis


title: 2410017_G401_SMARCA4_shCTRL_rep3

tag: cell line

tag: antibody

tag: genotype

value: shCTRL


title: Brain, CPZ, GENUS, D23-4358_S18_L004

tag: strain

value: Brain

tag: region

value: Corpus callosum

value: WT

tag: Sex

value: Male

tag: age

tag: diet intervention

tag: stimulation

value: GENUS


title: 2410016_G401_SMARCA4_shCTRL_rep2

tag: tissue


title: patient 42

value: macrodissected primary breast tumor

tag: subject

tag: type of surgery

value: Mastectomy

tag: histology

tag: pt

tag: pn

tag: radiotherapy

value: No

tag: age at diagnosis (dichotomized)

tag: race

value: Hispanic, Asian & other

tag: chemotherapy

tag: locoregional recurrence

tag: death

value: Alive

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: Brain, CPZ, GENUS, D23-4357_S17_L004

tag: strain

tag: region

tag: genotype

tag: Sex

tag: age

value: 12 weeks

tag: diet intervention

value: 0.3% Cuprizone


title: 2410015_G401_PBRM1_shCTRL_rep3

tag: tissue

value: cell line

tag: cell line

tag: antibody


title: patient 43

tag: subject

tag: type of surgery

tag: histology

value: IDC

tag: er status

value: Positive

tag: pr status

tag: her2 status

value: Negative

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

value: White


title: D3D_SI_CD8_scTCR_scRNA

city: Shanghai

first: duan

middle: cai

last: wen

address: 1678 dongfang road

institute: Shanghai Children's Medical Center

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using SOAPnuke v1.5.2 with parameters -l 15 -q 0.2 -n 0.05
Sequenced reads were mapped to GRCm38 whole genome using STAR 2.7.6a  with parameters  --runMode alignReads --runThreadN 5  --genomeLoad NoSharedMemory  --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts
The gene expression level (TPM) was calculated according to the Sequencing depth and gene length, and remove batch effect by R package ComBat
Align ATAC-seq reads: STAR v2.5.0c [disable splicing alignment]
Remove ATAC-seq duplicated reads: Picard v1.141
Call ATAC-seq peaks: MACS2 v2.1.1
scRNA-seq and scTCR-seq data processing: cellranger v6.1.2
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: small intestine

extract_protocol:
Use Chromium Next GEM Automated 5' cDNA Generation Kit v2 to generate cDNA
Chromium Next GEM Single Cell 5ʹ Kit v2 & Chromium Single Cell Mouse TCR Amplification Kit

treatment_protocol: CD8 cells were stained with antibodies CD44 and CD62L and sorted by flow cytometry.

tag: strain

value: small intestine

tag: treatment

value: 3 days post DNR chemotherapy of AF9 AML mice


title: 2410014_G401_PBRM1_shCTRL_rep2

tag: tissue

tag: cell line

tag: genotype

value: shCTRL


title: D3D_BM_CD8_scTCR_scRNA

source_name: bone marrow

value: bone marrow


title: AF9_SI_CD8_scTCR_scRNA

value: AF9 AML mice


title: 2396766_G401_HBO1_shPHF6_rep1

tag: antibody


title: patient 40

value: macrodissected primary breast tumor

tag: subject

tag: type of surgery

tag: histology

tag: race

tag: chemotherapy

value: Yes

tag: locoregional recurrence

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: patient 41

value: Lumpectomy

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

value: External beam radiation

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

value: No


title: patient 46

tag: tissue

tag: subject

tag: type of surgery

value: Mastectomy

tag: histology

tag: race

value: Alive


title: patient 38

tag: chemotherapy

tag: locoregional recurrence

tag: death

value: Dead

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: patient 39

value: IDC

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: bioanalyzer rin (rna integrity number)


title: patient 37

value: Positive

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis


title: patient 36

tag: tissue

tag: subject

tag: type of surgery

tag: histology

value: Negative

tag: age at diagnosis (dichotomized)


title: 2396764_G401_input_shPHF6

value: cell line

tag: cell line

tag: antibody

value: input

tag: genotype


title: patient 35

tag: er status

tag: pr status

tag: race

value: White

tag: chemotherapy

tag: locoregional recurrence

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: patient 34

tag: her2 status

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: bioanalyzer rin (rna integrity number)


title: AF9_BM_CD8_scTCR_scRNA

tag: strain

tag: tissue

tag: treatment


title: bmdm, mast cell supernatant treated, rep5

city: Freiburg

first: Michael

last: Mihlan

address: Stuebeweg 51

country: Germany

institute: MPI Immunobiology & Epigenetics

data_processing:
snakePipes 2.5.1 was used to generate the count matrix
Assembly: GRCm38
Supplementary files format and content: tsv file read counts generated by featureCounts (v2.0.0)

source_name: Bone marrow derived macrophages

extract_protocol:
Qiagen Rneasy Plus Micro Kit
Illumina stranded mRNA prep

tag: cell type

value: Bone marrow derived macrophages

tag: genotype

value: WT

value: mast cell supernatant treated


title: patient 32

value: macrodissected primary breast tumor

tag: subject

tag: type of surgery

tag: histology

tag: er status

tag: pr status

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: locoregional recurrence


title: patient 33

value: ILC

tag: her2 status

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: 2396762_G401_HBO1_shCTRL_rep1

tag: tissue

tag: cell line

tag: antibody

tag: genotype

value: shCTRL


title: 2396763_G401_HBO1_shCTRL_rep2


title: bmdm, mast cell supernatant treated, rep4

tag: cell type

tag: treatment


title: 2396767_G401_HBO1_shPHF6_rep2


title: bmdm, mast cell supernatant treated, rep2


title: bmdm, mast cell supernatant treated, rep3


title: patient 31

tag: subject

tag: type of surgery

value: Lumpectomy

tag: histology

tag: er status

tag: pr status

value: Yes

value: External beam radiation

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: bioanalyzer rin (rna integrity number)


title: 2396760_G401_input_shCTRL


title: patient 26

value: Other

tag: her2 status

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

value: No

tag: type of radiotherapy

tag: locoregional recurrence

tag: death

value: Alive

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: patient 28

tag: tissue

tag: subject

tag: type of surgery

tag: histology

value: IDC

tag: er status


title: patient 24

value: Negative

tag: pr status

value: Positive

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy


title: patient 30

tag: her2 status

tag: pt

tag: pn

tag: ptnm

tag: bioanalyzer rin (rna integrity number)


title: patient 25

value: Mastectomy

tag: radiotherapy

tag: type of radiotherapy

tag: locoregional recurrence

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 21

tag: tissue

tag: subject

tag: type of surgery

tag: histology

value: White

tag: time to death or censor from date of diagnosis (years)


title: bmdm, mast cell intracellular trap supernatant treatment, rep3

tag: cell type

value: Bone marrow derived macrophages

tag: genotype

tag: treatment


title: patient 27

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy


title: bmdm, mast cell supernatant treated, rep1

value: WT


title: patient 29

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

value: Partial breast irradiation

tag: locoregional recurrence

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: 2393638_G401_BRD9_shPHF6_rep1

tag: tissue

value: cell line

tag: cell line

tag: antibody

tag: genotype


title: patient 20

value: macrodissected primary breast tumor

tag: subject

tag: type of surgery

tag: histology

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: time to death or censor from date of diagnosis (years)


title: bmdm, mast cell intracellular trap supernatant treatment, rep2

tag: cell type

tag: treatment


title: patient 23

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: locoregional recurrence

tag: death


title: 2396761_G401_EP300_shCTRL_rep1

tag: tissue

tag: cell line

tag: antibody

tag: genotype

value: shCTRL


title: bmdm, mast cell intracellular trap supernatant treatment, rep1


title: 2393640_G401_input_shPHF6

value: input


title: bmdm, untreated, rep6

value: untreated


title: 2393639_G401_input_shCTRL_pair3


title: 2393635_G401_BRD9_shCTRL_rep1


title: bmdm, untreated, rep5


title: SC380

city: Pittsburgh

first: Yuechen

last: Zhou

address: 200 Lothrop Street

department: Department of Medicine

institute: University of Pittsburgh

data_processing:
FASTQ generation, demultiplexing, barcode assignment, gene counting and antibody counting were performed using 10X Genomics' Cell Ranger software v6 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: raw_feature_bc_matrix.h5

source_name: Lung

extract_protocol:
Explanted lungs were finely diced and digested for 1 hour in a mix of either Collagenase A/DNase I or Liberase DL/DNase I.  A single cell suspension was generated by filtering lungs through 70 micron filters and resuspending cells in PBS containing 0.04% BSA.  For some lungs, certain cell populations were partially depleted with Miltenyi magnetic bead separation. Two samples (SC401female81 and SC401male95) were labelled with HTO1 and HTO2 respectively. Cells were loaded into the 10X Genomics Chromium instrument per manufacturer's directions.
Libraries were constructed per the manufacturer’s instructions (Single Cell 3' v1, 3' v2, 3' v3, 5' v1, 5' v2). In short, lung cells were added to the master mix and loaded into the chip; subsequently, gel beads and partitioning oil were added into the chip which was then loaded into the Chromium instrument, generating the gel bead-in-emulsion (GEM). Once emulsified, cells were lysed and poly-A RNA transcribed to cDNA, adding an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and 10x Barcode. Silane DynaBeads were then used to clean up the pooled and barcoded cDNA which was then amplified by PCR.  SPRIselect reagent was used to select the appropriately sized fragments for library construction. Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added during the library construction protocol.

value: Lung

tag: age

tag: disease state

value: systemic sclerosis

tag: Sex

value: Female

tag: core code

tag: protocol

value: 10X Genomics 5PrimeV2

tag: depletion

value: 50% CD163 depleted


title: SC368

value: 50% CD45 depleted


title: patient 15

tag: subject

tag: type of surgery

tag: histology

value: IDC

tag: er status

value: Negative

tag: pr status

tag: her2 status

value: Positive

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

value: No

tag: type of radiotherapy

value: Alive

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: patient 17

tag: tissue

value: Lumpectomy

value: Yes

value: External beam radiation

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

value: White

tag: chemotherapy

tag: locoregional recurrence

tag: death


title: patient 14

value: macrodissected primary breast tumor

tag: subject

tag: type of surgery

value: Mastectomy

tag: histology

tag: er status

tag: pr status


title: SC335

value: Lung

tag: age

tag: disease state

tag: Sex

tag: core code

tag: protocol

value: 10X Genomics 5PrimeV1

tag: depletion

value: 50% CD45, EPCAM depleted


title: patient 9

tag: tissue

tag: her2 status

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

value: Partial breast irradiation

tag: age at diagnosis

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: patient 12

tag: subject

tag: type of surgery

tag: histology

tag: er status

tag: pr status

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: locoregional recurrence

tag: death


title: patient 13

tag: tissue

tag: her2 status

tag: pt

tag: pn

tag: ptnm

value: Dead


title: bmdm, untreated, rep3

tag: cell type

value: Bone marrow derived macrophages

tag: genotype

value: WT

tag: treatment

value: untreated


title: patient 22

tag: subject

tag: type of surgery

value: IDC

value: Positive

value: Negative

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: patient 8

value: Lumpectomy

tag: histology

tag: er status

tag: pr status

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

value: No

tag: locoregional recurrence

tag: death

value: Alive


title: patient 19

tag: tissue

value: ILC

tag: her2 status

tag: pt

tag: pn

tag: ptnm

value: White

value: Yes


title: SC293

value: Lung

tag: age

tag: disease state

value: systemic sclerosis

tag: Sex

value: Female

tag: core code

tag: protocol

value: 10X Genomics 3PrimeV3


title: bmdm, untreated, rep2

tag: cell type

tag: genotype

tag: treatment


title: patient 18

value: macrodissected primary breast tumor

tag: subject

tag: type of surgery

value: Mastectomy

tag: histology

tag: er status

tag: pr status

tag: radiotherapy

tag: type of radiotherapy

value: External beam radiation

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

value: Dead

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: patient 7

tag: tissue

value: IDC

tag: her2 status

tag: pt

tag: pn

tag: ptnm

tag: chemotherapy

tag: locoregional recurrence

tag: death


title: SC286

tag: age

tag: disease state

tag: Sex

tag: core code

tag: protocol


title: bmdm, untreated, rep1

tag: cell type

value: Bone marrow derived macrophages

tag: genotype

value: WT

tag: treatment

value: untreated


title: patient 6

tag: subject

tag: type of surgery

tag: histology

tag: er status

value: Negative

tag: pr status

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

value: No

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: patient 11

tag: tissue

tag: her2 status

tag: pt

tag: pn

tag: ptnm

tag: chemotherapy

tag: locoregional recurrence

tag: death

value: Alive


title: SC284

tag: age

tag: disease state

tag: Sex

value: Male

tag: core code

tag: protocol


title: patient 4

tag: subject

tag: type of surgery

value: Lumpectomy

tag: histology

tag: er status

tag: pr status

value: Positive

tag: radiotherapy

value: Yes

tag: type of radiotherapy

value: Partial breast irradiation

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

value: White


title: bmdm, untreated, rep4

tag: cell type

tag: genotype

tag: treatment


title: patient 10

tag: tissue

value: macrodissected primary breast tumor

tag: her2 status

tag: pt

tag: pn

tag: ptnm

tag: chemotherapy

tag: locoregional recurrence

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: H1876_H3K27ac_HiChIP_Rep1

city: Salt Lake City

first: Xiaoyang

last: Zhang

state: Utah

address: 1950 Circle of Hope Drive

department: Oncological Sciences

institute: University of Utah

data_processing:
Library strategy: HiChIP
HiC-Pro to align sequencing reads
hichipper to identify chromatin loops connecting H3K27ac anchors
Assembly: hg19
Supplementary files format and content: intra-chromosomal interaction counts text file in bedpe format. Rows are interactions (loops). Columns are chromosome1, start1, end1, chromosome2, start2, end2, FDR (blank), PETs
Supplementary files format and content: inter-chromosomal interaction counts text file in bedpe format. Rows are interactions (loops). Columns are chromosome1, start1, end1, chromosome2, start2, end2, FDR (blank), PETs

extract_protocol:
HiChIP protocol (Mumbach et al., 2016, Nature Methods) to enrich DNA fragments that are in proximity with each other
Illumina Tagment DNA Enzyme and Buffer Kit (Illumina 20034197)

tag: cell line

value: Lung squamous cancer cell line

tag: hichip antibody

value: H3K27ac (Abcam ab4729)


title: Day 5, Kras, Fra1WT,RNA, rep 3

city: New York

first: Anil

middle: K.

last: Rustgi

state: New York

address: 1130 St. Nicholas Avenue

institute: Columbia University

data_processing:
Fastq files quality control was assessed with RSeQC v5.0.1
STAR v2.7.10 alignment
featureCounts v2.0.3 generated count tables
Assembly: mm10/GENCODE vM23
Supplementary files format and content: tab-delimited count files for each sample

source_name: Pancreas

extract_protocol:
Acinar-lineage cells were sorted for YFP+/DAPI- signal into Trizol LS and total RNA was extracted using Qiagen RNeasy Plus Micro Kit
Stranded RNA libraries were prepared with NEBNext II Directional RNA Library Preparation Kit

treatment_protocol: 7-8 week old mice were gavaged with tamoxifen. One week later, the mice were treated with 150ug/kg of caerulein eight times hourly for two days. Mice were sacrificed five days after and pancreata were dissociated.

value: Pancreas

value: Primary cell

value: Acinar lineage

value: Acute pancreatitis - Day 5


title: H1876_H3K27ac_HiChIP_Rep2


title: H446_H3K27ac_HiChIP_Rep2


title: patient 2

tag: subject

tag: type of surgery

value: Mastectomy

tag: histology

value: IDC

tag: er status

tag: pr status

tag: radiotherapy

tag: type of radiotherapy

value: External beam radiation

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race


title: patient 3

tag: tissue

value: Negative

tag: her2 status

tag: pt

tag: pn

tag: ptnm

tag: chemotherapy

tag: locoregional recurrence

value: No

value: Alive


title: SC281

value: Lung

tag: age

tag: disease state

value: systemic sclerosis

tag: Sex

value: Female

tag: core code

tag: protocol

value: 10X Genomics 3PrimeV3


title: patient 5

value: macrodissected primary breast tumor

tag: subject

tag: type of surgery

tag: histology

value: Other

tag: er status

value: Positive

tag: pr status

tag: radiotherapy

value: Yes

value: White

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: Day 5, Kras, Fra1WT,RNA, rep 2

tag: tissue

value: Pancreas

tag: cell line

value: Primary cell

tag: cell type

value: Acinar lineage

tag: genotype

tag: treatment


title: H2170_H3K27ac_HiChIP_Rep2

value: Lung squamous cancer cell line

tag: hichip antibody

value: H3K27ac (Abcam ab4729)


title: patient 1

value: Mastectomy

value: IDC

tag: her2 status

value: Negative

tag: pt

tag: pn

tag: ptnm

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: locoregional recurrence


title: SC136

value: Lung

tag: age

tag: disease state

tag: Sex

value: Male

tag: core code

tag: lung section

value: Upper lobe

tag: protocol

value: 10X Genomics 3PrimeV2


title: patient 45

tag: tissue

value: macrodissected primary breast tumor

tag: subject

tag: type of surgery

value: Lumpectomy

tag: histology

tag: er status

tag: pr status

tag: radiotherapy

value: External beam radiation

value: No

tag: death

value: Alive

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: Day 5, Kras, Fra1WT,RNA, rep 1

value: Pancreas

tag: cell line

tag: cell type

tag: genotype

tag: treatment

value: Acute pancreatitis - Day 5


title: SC109

tag: age

tag: disease state

value: systemic sclerosis

tag: Sex

tag: core code

tag: lung section


title: Day 5, Kras, Fra1KO,RNA, rep 3

tag: tissue

value: Primary cell

value: Acinar lineage

value: Ptf1aCreERT;KrasG12D; Fosl1-/-; YFP


title: SC135

value: Lower lobe

tag: protocol


title: SC108


title: Day 5, Kras, Fra1KO,RNA, rep 2


title: SC187

value: Female


title: SC64

value: Lung


title: SC63

value: Male


title: SC401female81 and SC401male95

description: female - HTO1, age 81, ; male - HTO2, age 95

value: normal control

value: 10X Genomics 5PrimeV2


title: Day 5, Kras, Fra1KO,RNA, rep 1


title: SC334

value: 10X Genomics 5PrimeV1


title: SC323

tag: depletion

value: 50% CD45, EPCAM depleted


title: SC333


title: Day 5, Kras, IgG, CUT&RUN, rep 3

data_processing:
Fastq files were trimmed with cutadapt v1.18
Sequencing quality assessed with fastQC v0.12.0
Trimmed files aligned to mm10 using bowtie2 v2.4.5 and converted to bam using samtools v1.6
Reads were filtered for ENCODE blacklist regions and duplicates were removed using picard v2.27.4
macs2 v2.2.7.1 used for peak calling against corresponding IgG control and deeptools v3.5.1 bamCoverage was used to generate bigwigs using CPM normalization
Assembly: mm10
Supplementary files format and content: bigwig files of each sample
Library strategy: CUT&RUN

extract_protocol:
Acinar-lineage cells were sorted for YFP+/DAPI- signal and  were fixed in 0.1% formaldehyde for 2 minutes before quenching with 125mM glycine. Afterwards, cells were washed in wash buffer (20mM HEPES-KOH, pH 7.9, 150mM NaCl, 1% Triton X-100, 0.05% SDS) and proceeded to Concanavalin-coated magnetic bead binding as described previously using 0.01% digitonin for all buffers. H3K27ac (Cell Signaling Technology, 8173S, 1:100) was incubated overnight followed by incubation with secondary antibody, guinea pig anti-rabbit IgG (Antibodies-Online, ABIN101961, 1:100). Rabbit IgG was used as a control (Epicypher, 13-0042). mNase (Epicypher, 15-1016) digestion was carried out following manufacturer’s instructions. Chromatin was precipitated and released following the Henikoff protocol
Libraries were prepared with NEBNext Ultra II Library Preparation Kit

tag: antibody

value: IgG


title: SC51

value: 10X Genomics 3PrimeV2


title: SC17

value: idiopathic pulmonary arterial hypertension

value: 10X Genomics 3PrimeV1


title: SC156

value: Upper lobe


title: SC315


title: Day 5, Kras, IgG, CUT&RUN, rep 2

value: Pancreas

value: Acute pancreatitis - Day 5


title: Day 5, Kras, IgG, CUT&RUN, rep 1

value: Primary cell

value: Acinar lineage


title: SC313


title: SC277

value: 10X Genomics 3PrimeV3


title: SC59


title: SC56

value: Female


title: SC161

value: Lung


title: Day 5, Kras, H3K27ac, CUT&RUN, rep 3


title: Patient3,CCRT,scRNAseq

first: Yifei

last: Pei

address: Yueyang 320

department: Laboratory of Inflammation and Molecular Immunology

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

description: 10x Genomics

data_processing:
Cell Ranger software was used to process Chromium single cell data to align reads, generate feature-barcode matrices, make gene counting and aggregation.
Assembly: hg38
Supplementary files format and content: Compressed tab-separated values files and matrix files.

source_name: Cervical cancer tissue

extract_protocol:
Tumor samples collected by biopsy were immediately transported to the laboratory for digestion. After washing with PBS, each sample was cut into pieces of ~1 mm3 and digested with 5 ml digestion buffer containing collagenase IV and DNase I in a 37 °C incubator for 30 min. Next, the sample was mixed with 3 ml 1% BSA PBS and ﬁltered through a 70-µm mesh size cell strainer. After centrifugation, the supernatant was discarded, and the cell pellet was resuspended.
The Single-Cell 3’ Library Kit (10x Genomics) was used for single-cell transcriptome amplification and library preparation according to the manufacturer’s instructions.

value: Cervical cancer tissue

value: CCRT


title: SC52

value: systemic sclerosis


title: Day 5, Kras, H3K27ac, CUT&RUN, rep 1


title: SC14

value: normal control

value: male


title: SC31


title: Patient3,TN,scRNAseq

description: 10x Genomics

value: TN


title: patient 16

value: macrodissected primary breast tumor

tag: subject

tag: type of surgery

value: Mastectomy

tag: histology

value: IDC

tag: er status

value: Positive

tag: pr status

tag: her2 status

value: Negative

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

value: Yes

tag: type of radiotherapy

value: External beam radiation

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

value: White

tag: chemotherapy

tag: locoregional recurrence

value: No

tag: death

value: Alive


title: SC45

tag: tissue

value: Lung

tag: age

tag: disease state

tag: Sex

tag: core code

tag: protocol

value: 10X Genomics 3PrimeV2


title: SC155

value: Female

tag: lung section

value: Lower lobe


title: Day 5, Kras, H3K27ac, CUT&RUN, rep 2

value: Pancreas

tag: cell line

value: Primary cell

tag: cell type

value: Acinar lineage

tag: genotype

tag: treatment

value: Acute pancreatitis - Day 5

tag: antibody


title: L10_168NULLnpcd05

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

data_processing:
Reads were assigned to transcripts from GENCODE release 27 using Salmon (Patro et al., 2017) and differentially expressed genes were identified using DESeq2 v1.20.0 (Love et al., 2014). DESeq2 analysis modelled fold change between time points using the cell line as an independent factor (using the model '~cell_line + condition'), and fold changes were calculated using lfcShrink function, applying the apeglm method (v 1.2.1) (Zhu et al., 2018).
Time course gene expression clustering was performed using Dirichlet process Gaussian process mixture model using the DP_GP_Cluster Python package (McDowell et al., 2018) to cluster TPM values for genes that show a significant expression difference (using a 5% FDR threshold) between sequential timepoints. Separate gene lists were calculated for NPC and NCC time courses, and expression patterns were clustered separately for WT and TSC2-/- cells within each protocol.
Genome_build: GRCh38
Supplementary_files_format_and_content: fold change and feature counts files

source_name: NPC-Monolayer

growth_protocol: Human pluripotent stem cell lines were differentiated towards neuroectodermal lineages utilizing dual SMAD inhibition. Two differentiation protocols were utilized to enrich for neural progenitor cells and neural crest cells as described in: Delaney, S. P., L. M. Julian, A. Pietrobon, J. Yockell-Lelièvre, C. Doré, T. T. Wang, V. C. Doyon, A. Raymond, D. A. Patten, M.-E. Harper, H. Sun and W. L. Stanford (2019). "TSC2-deficiency potentiates a catabolic signaling switch that differentiates neural and neural crest lineage development and progressive disease manifestations." bioRxiv: 683359.

extract_protocol:
Total RNA was isolated using TRIZOL reagent, followed by DNase digestion and ethanol precipitation of RNA. ERCC Spike-in was added normalizing to cell number.
Total RNA H9 WT and TSC2-/- NCC sample libraries were prepared with ribosome depletion (Illumina # 20020598), all other sample libraries were prepared using the TruSeq Stranded mRNA kit (Illumina #RS-122-2101).

treatment_protocol: Genotype-based treatment groups. WT (control) cultures were compared to TSC2 knockout (treatment) cultures.

value: NPC-Monolayer

tag: time point


title: L12_168NULLnpcd12


title: Patient2,CCRT,scRNAseq

description: 10x Genomics

value: Cervical cancer tissue

value: CCRT


title: L09b_168NULLnpcd03


title: L11_168NULLnpcd08


title: GAN Liver, Cre, c

city: Ann Arbor

first: Shanshan

last: Liu

state: Michigan

address: 210 Washtenaw Avenue

institute: University of Michigan

data_processing:
The reads were trimmed using Cutadapt v2.3 (Martin, 2011).
FastQC v0.11.8 was used to ensure the quality of data (Andrews, 2010).
Fastq Screen v was used to screen for various types of contamination (Wingett and Andrews, 2018).
Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR v2.7.8a (Dobin et  al., 2013) and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, 2011). Alignment  options followed ENCODE standards for RNA-seq.
Multiqc v1.7 compiled the results from several of these tools and provided a detailed and comprehensive  quality control report (Ewels et al., 2016)
Assembly: GRCm38 (ENSEMBL)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Liver

extract_protocol:
Total RNA was extracted using GenElute™ Mammalian Total RNA Miniprep Kit, according to the provided instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were fed Gubra-Amylin NASH diet for 18 weeks.

value: Liver

value: Gubra-Amylin diet


title: L08b_168NULLnpcd01


title: L07_168NULLnpcd00


title: GAN Liver, Cre, b


title: Patient2,TN,scRNAseq

description: 10x Genomics

value: TN


title: GAN Liver, Cre, a


title: L06_168WTnpcd12

value: WT


title: L04_168WTnpcd05


title: L05_168WTnpcd08


title: Patient1,TN,scRNAseq

description: 10x Genomics


title: Patient1,CCRT,scRNAseq

description: 10x Genomics


title: GAN Liver, flox, d


title: GAN Liver, flox, c


title: P13Elafibranor

city: Clichy

first: Adel

last: Hammoutene

address: 100 Boulevard du Général Leclerc, Hôpital Beaujon, Secteur Jaune, Bât Abrami, Porte 4

department: Reasearch Center on Inflammation

country: France

institute: INSERM U1149

data_processing:
Raw sequences were aligned to the human genome (GRCh38, ensembl v107)
Alignement was performed using STAR
Raw read count were obtained using FeatureCount
Raw read count were normalized with the Upper-quartile normalization method after removing genes coded by sex chromosomes
Assembly: GRCh38
Supplementary files format and content: tab-delimited file includes raw count for each Sample.
Supplementary files format and content: tab-delimited file include normalized genes expression  for each Sample.

growth_protocol: PCLS were maintained in culture on 8 µm PET-tissue culture inserts in 6 wells plates containing 2 mL William’s E Medium supplemented with 100 IU/mL penicillin and 100 μg/mL streptomycin, 1 μg/mL amphotericin B and 25 mM D-Glucose, under continuous orbital agitation, in a humidified atmosphere 5% CO2 at 37°C.

extract_protocol:
mRNA from PCLS were extracted in TRIzol reagent using standard procedure according to manufacturers’ instructions.
RNA library was prepared using the SMARTer® Stranded Total RNA-Seq Kit v3 (Pico Input Mammalian) according to manufacturer’s recommendations (634873, Takara). Samples were sequenced on ILLUMINA Novaseq 6000 with S1-200 cartridge

treatment_protocol: PCLS were treated eitheir with Elafibranor (10µM, dissolved in DMSO), or with S217879 (3µM, dissolved in DMSO), or with vehicle (DMSO, final concentration 0.1%)

tag: patient

value: F

tag: bmi

tag: ast

tag: alt

value: YES

value: Elafibranor


title: P13S217879

tag: tissue


title: L02_168WTnpcd01


title: GAN Liver, flox, b


title: L01_168WTnpcd00


title: L22_H1NULLnpcd05


title: L23_H1NULLnpcd08


title: GAN Liver, flox, a


title: L19_H1NULLnpcd00


title: Ear, FM-S1, bulk RNA-seq, Replicate2

city: Wuhan

first: liang

last: dong

address: No.1,Shizishan Street

institute: Huazhong Agricultural University

description:
FM-S1 rep2
raw_counts.txt

data_processing:
For bulk RNA-seq, the quality of raw sequencing data was controlled using Trimmomatic with parameters “LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:20”. For scRNA-seq, the adaptor sequence and the low-quality reads were filtered by fastp with the default parameters.
For bulk RNA-seq, clean data from all samples were mapped to the B73 AGPv4 reference genome using HISAT2 with default parameters. For scRNA-seq, the UMI-based clean data were mapped to the maize genome (B73 RefGen_v4) utilizing STAR mapping with customized parameters to obtain the UMI counts of each sample.
For bulk RNA-seq, we used featureCounts (v.1.6.3) to measure the abundance of RNA with the parameter (-p). “bamCoverage” in deeptools (v3.3.0) were used for bw files.
Assembly: B73 RefGen_v4
Supplementary files format and content: tab-delimited text files includes raw counts for each Sample
Supplementary files format and content: matrix files

organism: Zea mays

source_name: Ear FM-S1

growth_protocol: All samples were harvested from maize plants growing in the field

extract_protocol:
For bulk RNA-seq, RNA was extracted  using direct-zol RNA Miniprep (Zymo Research).For scRNA-seq, protoplasts were prepared as previously described (Satterlee et al., 2020). For each replicate, the freshly dissected FM-S2 or FM-S3 tissues from 15-20 ear or tassel were digested in protoplast lysis buffer for 2 hours at room temperature in the dark with gentle shaking. The mixture was then filtered twice through a 30 μm cell strainer (sysmex, 04-0042-2316) and the protoplasts were collected by horizontal centrifugation at 300 g for 3 min at room temperature. The supernatant was gently removed without disturbing the protoplast pellet. Next, the pellet was resuspended and washed two times using protoplast washing buffer (lysis buffer without enzyme) by the same centrifugation condition as before. After washing, the pellet was resuspended into 600 μl washing buffer and then filtered through the 30 μm cell strainer to remove adherent multicellular mass.
Bulk RNA-seq librarys were constructed using NEBNext Ultra Directional RNA Library Prep Kit or MGIEasy RNA Library Prep Kit according to the instructions. scRNA-seq librarys were constructed using BD Rhapsody™ Whole Transcriptome Analysis Amplification Kit.

value: Ear FM-S1


title: L21_H1NULLnpcd03


title: P11Elafibranor

tag: age

value: NO


title: L20_H1NULLnpcd01


title: P11S217879


title: Ear, FM-S1, bulk RNA-seq, Replicate1

description:
FM-S1 rep1
raw_counts.txt


title: L16_H1WTnpcd05


title: L17_H1WTnpcd08


title: P10S217879

value: M


title: L15_H1WTnpcd03


title: L03_168WTnpcd03


title: Ear, SM, bulk RNA-seq, Replicate3

description:
SM rep3
raw_counts.txt

source_name: Ear SM

value: Ear SM


title: L14_H1WTnpcd01


title: L24_H1NULLnpcd12


title: L36_H7MUTnpcd12


title: P13DMSO

value: DMSO


title: P10Elafibranor


title: Ear, SM, bulk RNA-seq, Replicate1

description:
SM rep1
raw_counts.txt


title: L34_H7MUTnpcd05


title: P10DMSO


title: L35_H7MUTnpcd08


title: L33_H7MUTnpcd03


title: P9S217879


title: Ear, SPM, bulk RNA-seq, Replicate2

description:
SPM rep2
raw_counts.txt

source_name: Ear SPM

value: Ear SPM


title: L30_H7WTnpcd12


title: P9Elafibranor


title: L18_H1WTnpcd12


title: P11DMSO


title: L13_H1WTnpcd00


title: L31_H7MUTnpcd00


title: Ear, SPM, bulk RNA-seq, Replicate1

description:
SPM rep1
raw_counts.txt


title: L29_H7WTnpcd08


title: Ear, SM, bulk RNA-seq, Replicate2

description:
SM rep2
raw_counts.txt


title: P9DMSO


title: L27_H7WTnpcd03


title: Ear, IM, bulk RNA-seq, Replicate3

description:
IM1 rep3
raw_counts.txt

source_name: Ear IM

value: Ear IM


title: Ear, SPM, bulk RNA-seq, Replicate3

description:
SPM rep3
raw_counts.txt


title: L26_H7WTnpcd01

value: NPC-Monolayer


title: L48_H9MUTnpcd12


title: P8S217879


title: P8Elafibranor


title: L28_H7WTnpcd05


title: Ear, IM, bulk RNA-seq, Replicate2

description:
IM1 rep2
raw_counts.txt


title: Ear, IM, bulk RNA-seq, Replicate1

description:
IM1 rep1
raw_counts.txt


title: L25_H7WTnpcd00


title: L47_H9MUTnpcd08


title: L46_H9MUTnpcd05


title: L32_H7MUTnpcd01


title: P8DMSO


title: L44_H9MUTnpcd01


title: L43_H9MUTnpcd00


title: L40_H9WTnpcd05


title: P7S217879


title: P7Elafibranor


title: L42_H9WTnpcd12


title: 227N_normal

type: genomic

city: Sao Paulo

first: Fabio

middle: Albuquerque

last: Marchi

address: Av Dr Arnaldo

department: CTO

country: Brazil

institute: ICESP

description:
Normal tissue
CP227N

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using the Illumina HiScan system.

data_processing:
DNA methylation data, described as beta values of continuous variables between 0 and 1, were recorded for each locus in each sample. The quality control parameters were followed, probes were filtered, normalized, and adjusted using the ChAMP package (v.2.24.0). Cross-reactive probes (≥49 bases), SNPs (Minor Allele Frequency >5%), gender-associated probes, low quality probes (p>0.05), and low bead count (<3) in at least 5% of samples were removed. Data were normalized using the BMIQ method and the annotation was performed according to the Illumina manifest (hg19) and HUGO Gene Nomenclature Committee. The sample groups were compared, and DMPs were identified using the limma package (v.3.50.3) considering a Bonferroni-adjusted p-value < 0.05 and a mean delta-beta (Δβ) ≥0.2 or ≤-0.2.
BMIQ-Normalized Average Beta

label: Cy5 and Cy3

source_name: Normal adjacent tissue

label_protocol: Standard Illumina Protocol

growth_protocol: Not applicable

extract_protocol: Genomic DNA from tumor and normal tissues was extracted using phenol-chloroform method and quantified by Qubit® dsDNA BR Assay (Qubit® 2.0 Fluorometer, Life Technologies - Carlsbad, CA, USA).

treatment_protocol: Not applicable

tag: gender

value: Female

tag: hpv status

value: Negative


title: 214T_tumor

description:
Tumor tissue
CP214T

source_name: Oral cavity squamous cell carcinoma

value: Male


title: L41_H9WTnpcd08


title: 289T_tumor

description:
Tumor tissue
CP289T


title: L37_H9WTnpcd00


title: P7DMSO

value: Liver

tag: Sex


title: 83T_tumor

description:
Tumor tissue
CP83T

value: Positive


title: L39_H9WTnpcd03

value: WT

tag: protocol


title: 207N_normal

description:
Normal tissue
CP207N


title: 35_168KOd07

source_name: NCC-EB

value: NCC-EB


title: P6Elafibranor

value: YES


title: 34_168KOd04


title: P6S217879


title: 207T_tumor

description:
Tumor tissue
CP207T


title: 32_168KOd01


title: L38_H9WTnpcd01


title: 33_168KOd02


title: 31_168KOd00


title: L45_H9MUTnpcd03


title: 227T_tumor

description:
Tumor tissue
CP227T


title: P5S217879


title: P6DMSO


title: 30_168WTd10


title: 83N_normal

description:
Normal tissue
CP83N


title: 214N_normal

description:
Normal tissue
CP214N


title: 29_168WTd07


title: 28_168WTd04


title: P5DMSO


title: 289N_normal

description:
Normal tissue
CP289N


title: 36_168KOd10


title: P5Elafibranor

value: Elafibranor


title: 27_168WTd02


title: 26_168WTd01


title: 223N_normal

description:
Normal tissue
CP223N


title: 238N_normal

description:
Normal tissue
CP238N.2


title: P4S217879

value: F


title: 24_H1KOd10


title: 22_H1KOd04


title: 23_H1KOd07


title: 238T_tumor

description:
Tumor tissue
CP238T


title: 25_168WTd00


title: 21_H1KOd02


title: 19_H1KOd00


title: P4DMSO

value: NO


title: P4Elafibranor


title: 70T_tumor

description:
Tumor tissue
CP70T


title: P3S217879

value: M


title: 18_H1WTd10


title: 20_H1KOd01


title: P3Elafibranor


title: 16_H1WTd04


title: 17_H1WTd07


title: 210T_tumor

description:
Tumor tissue
CP210T


title: P3DMSO


title: 15_H1WTd02


title: 210N_normal

description:
Normal tissue
CP210N


title: 14_H1WTd01


title: 218N_normal

description:
Normal tissue
CP218N


title: 12_H7KOd10


title: P2S217879


title: 13_H1WTd00


title: 11_H7KOd07


title: 70N_normal

description:
Normal tissue
CP70N


title: 08_H7KOd01


title: 223T_tumor

description:
Tumor tissue
CP223T


title: 07_H7KOd00


title: P1S217879


title: P2Elafibranor


title: 218T_tumor

description:
Tumor tissue
CP218T


title: P2DMSO


title: P1Elafibranor


title: 06_H7WTd10


title: G401_ATAC_GFP_1

data_processing:
trim_galore v0.6.3 remove adapter sequences.
pbrun fq2bam v3.0.0.6 --bwa-options -K 10000000 -Y -M --num-gpus 2
samtools view -F 1804 -b -q 1 and bamsort
bamToBed -bedpe; grep -v chrM
Coverage normalized to 20million reads for all fragment sizes less than 2kb.
Genome_build: GRCh37.p13, hg19
Supplementary_files_format_and_content: bigWig of normalized coverage.

growth_protocol: G401 cells were grown in McCoy's 5A media supplemented with 10% fetal bovine serum and 1% Glutamax (Gibco) at 37°C and 5% CO2. 50k cells were plated per well in a 6-well dish.

extract_protocol:
Nuclei from 100K cells were isolated using Active Motif ATAC-seq kit (kit #53150) protocol.
Libraries were prepared using the Active Motif ATAC-Seq kit (kit #53150). Briefly, nuclei were isolated and submitted to tagmentation at 37C for 30’ shaking at 800RPM. Tagmented DNA was purified using the provided columns.

treatment_protocol: G401 cells were engineered to express either GFP under 1µg/µl doxycycline treatment for 24hrs.

tag: expression

value: GFP


title: 76T_tumor

description:
Tumor tissue
CO76T


title: 01_H7WTd00

tag: cell line


title: 02_H7WTd01


title: 184N_normal

description:
Normal tissue
CP184N


title: 03_H7WRd02


title: P1DMSO

value: DMSO


title: 05_H7WTd07


title: 04_H7WTd04


title: G401_input_phf6_2

description:
SJMRT050486_C43
input control for PHF6

data_processing:
trim_galore v0.6.3 remove adapter sequences.
Align quality reads using bwa mem v0.7.17 to a hybrid reference genome.
bamsormadup v2.0.87
samtools used to split bam file for hg19 and dm6 reads base on chromosome names.
samtools -F 1024 -q 1 to define quality reads.
Estimate fragment size using spp R package.
slopBed -r fragment size estimation determined by spp.
Normalize to 15M reads.
Genome_build: hg19+dm6 (Gencode GRCh37 and Ensembl r97)
Supplementary_files_format_and_content: Normalized coverage in the bigwig file format, macs2 narrow peaks.

source_name: G401 cell line

growth_protocol: G401 cells were grown in McCoy's 5A media supplemented with 10% fetal bovine serum and 1% Glutamax (Gibco) at 37°C and 5% CO2.

extract_protocol:
In brief, cells were cross-linked directly on the plate using 1% paraformaldehyde for 10 min at room temperature and quenched with glycine. Nuclei were isolated using the Covaris TruCHIP kit and Chromatin extracts were sonicated for 8 min using a Covaris E220 focused ultrasonicator at a peak power of 140, a duty factor of 5 and 200 cycles per burst. Chromatin immunoprecipitation was carried overnight with antibodies bound to dynabeads. Chromatin was de-crosslinked, digested with RNase and Proteinase K and DNA was purified using a Qiagen DNA kit. For MNase ChIP, CST kit guidelines were followed.
KAPA HyperPrep Kit (Kapa Biosystems, Cat# 7962363001).

tag: chip antibody


title: A32_78_17_NCCd10

tag: genotype


title: 10_H7KOd04


title: 09_H7KOd02


title: 111T_tumor

description:
Tumor tissue
CP111T.A


title: A30_78_17_NCCd07


title: A26_78_17_NCCd02


title: G401_PHF6_2

description:
SJMRT050486_C42
PHF6


title: 190N_normal

description:
Normal tissue
CP190N


title: A28_78_17_NCCd04


title: 58T_tumor

description:
Tumor tissue
CO58T


title: G401_input_phf6_1

description:
SJMRT050486_C40
input control for PHF6


title: A22_78_17_NCCd00


title: A29_H9_10mC_NCCd07


title: 111N_normal

description:
Normal tissue
CP111N


title: A31_H9_10mC_NCCd10


title: 182N_normal

description:
Normal tissue
CP182N.A


title: A24_78_17_NCCd01


title: 56T_tumor

description:
Tumor tissue
CO56T


title: A23_H9_10mC_NCCd01


title: A27_H9_10mC_NCCd04


title: A25_H9_10mC_NCCd02


title: G401_shPHF6_input_hm_1

description:
INPUT-SJMRT050486_C64-PM75_G401_shphf6
input control from all histone marks

tag: shRNA


title: 193N_normal

description:
Normal tissue
CP193N


title: A21_H9_10mC_NCCd00


title: Day 5, Kras, Fra1KO,snATAC, rep 2

description: 10X Genomics

data_processing:
Demultiplexing, barcode processing, fragment counting and transcription factor activity assessment was made using Cell Ranger atac v2.1
Assembly: mm10/GENCODE vM23
Supplementary files format and content: fragment file for each sample in tab-separated value format
Supplementary files format and content: motif file from filtered_tf_bc_matrix output in tab-separated value format
Supplementary files format and content: filtered_tf_matrix file from filtered_tf_bc_matrix output in tab-separated value format
Supplementary files format and content: barcode file from filtered_tf_bc_matrix output in tab-separated value format

extract_protocol:
Nuclei were extracted from an adapted protocol. 2x salt-Tris solution (ST Buffer) containing 292mM NaCl ( 20 mM Tris-HCl pH 7.5, 2 mM CaCl2  and 42 mM MgCl2in Ultrapure water was mixed in a 1:1 ratio with 2x Tween-based lysis buffer to make TST (1 ml of 2× ST buffer, 60 µl of 1% Tween-20 (Promega, H5152), 10 µl of 2% BSA and 930 µl of nuclease-free water) or with a 2x salt BSA buffer to make ST-SB (1 ml of 2× ST buffer, 133ul of 30% BSA , 40ul of 1% Tween-20, 827ul PBS).
Library construction was performed with the Chromium Single Cell ATAC kit

treatment_protocol: 7-8 week old mice were gavaged with tamoxifen. One week later, the mice were treated with 150ug/kg of caerulein eight times hourly for two days. Mice were sacrificed five days after and pancreata were flash frozen in liquid nitrogen.

value: Pancreas

value: Primary cell

tag: cell type

value: Acinar lineage

value: Ptf1aCreERT;KrasG12D; Fosl1-/-; YFP

tag: treatment

value: Acute pancreatitis - Day 5


title: 77T_tumor

description:
Tumor tissue
CO77T

value: Male

value: Negative


title: 47T_tumor

description:
Tumor tissue
CO47T

value: Female


title: Day 5, Kras, Fra1WT,snATAC, rep 2

description: 10X Genomics


title: G401_shCTRL_H3K9me3_1

description:
H3K9me3-AB3-SJMRT050486_C65-PM76_G401_shctrl_1
shCTRL H3K9me3

value: shCTRL


title: G401_PHF6_1

description:
SJMRT050486_C41
PHF6


title: Ms_pdgfrb_14d, scRNAseq

city: Beijing

first: Xianming

last: Wu

state: Chaoyang District

address: Unit 2, No.1 West Beichen Road

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

description: 10x Genomics

data_processing:
cellranger used for analysis
Assembly: mm10_genome with tdTomato gene
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: spinal cord

extract_protocol:
PDGFRβ-CreER::R26-TdT mice received transection SCI as described above. A 4-mm spinal cord segments centered at the lesion core were isolated and chopped into small pieces with sharp scissors. The pieces were digested with papain (Worthington Biochemical, LK003176) containing DNase (Worthington Biochemical, LK003170) for 1h at 37°C with slow rotation. Then add 1.0 mg/ml collagenase type II (Worthington Biochemical, LS004176) and 0.4 mg/ml neutral protease (Worthington Biochemical, LS02104) to incubate for 30 min at at 37°C with slow rotation. The cell pellets were resuspended with 25% percoll and centrifuged at 400 g for 10min to remove myelin debris. By using BD FACSAria Fusion cell sorter, cells were FACS sorted into DPBS buffer depending on tdtomato fluorescence.
Library was constructed depending on  the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: Fibroblasts and pericytes/vSMCs

value: spinal cord

tag: strain

value: (C57BL/6J x 129S6/SvEvTac)F1

value: 2-4 months old

tag: time


title: 189N_normal

description:
Normal tissue
CP189N


title: Ms_pdgfrb_5d, scRNAseq

description: 10x Genomics


title: Day 5, Kras, Fra1WT,snATAC, rep 1

description: 10X Genomics


title: G401_shCTRL_input_hm_1

description:
INPUT-SJMRT050486_C63-PM74_G401_shctrl
input control from all histone marks


title: 174N_normal

description:
Normal tissue
CP174N.B


title: Ms_pdgfrb_0d, scRNAseq

description: 10x Genomics


title: M83

city: Ube-shi

first: Kensuke

last: Shibata

state: Yamaguchi

address: 1-1 Minami-Kogushi 1-chome

country: Japan

institute: Yamaguchi univeristy

description: Sample 4

data_processing:
Illumina RTA3 software used for basecalling.
Quality trimming, mapping onto the genome, and tag counting were performed using CLC Genomics Workbench v12.0.2.
Genome_build: GRCm38 release-95
Supplementary_files_format_and_content: tab-delimited text file includes raw count values for each sample.

source_name: tumor

growth_protocol: Tumor cells were cultured in RPMI medium.

extract_protocol:
After the culture , total RNA was prepared using RNeasy Micro Kit (QIAGEN).
RNA libraries were NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) and NEBNext Ultra Ⅱ RNA Library Prep Kit for Illumina (NEB).

value: colon

tag: genotype/variation

value: ENU mutant


title: Day 5, Kras, Fra1KO,snATAC, rep 1

description: 10X Genomics


title: G401_shCTRL_H3K9me3_2

description:
H3K9me3-AB3-SJMRT050486_C66-PM77_G401_shctrl_2
shCTRL H3K9me3


title: 187N_normal

description:
Normal tissue
CP187N

value: Positive


title: 36T_tumor

description:
Tumor tissue
CO36T


title: 177N_normal

description:
Normal tissue
CP177N