title: ID87, Gemcitabine/Nab-Paclitaxel plus Placebo, pre-treatment, Center, 4, Slide 1

description:
Library name: Sample 88
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID87, Gemcitabine/Nab-Paclitaxel plus Placebo, pre-treatment, ring2, 4, Slide 1

status: Public on Dec 21 2025

type: SRA

city: Boston

first: Jonathan

middle: Andrew

last: Nowak

state: MA

address: 75 Francis St.

department: Pathology

country: USA

institute: Brigham and Women's Hospital

description:
Library name: Sample 90
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.

library_source: transcriptomic

data_processing:
GeoMx DSP data were pre-processed using the GeoMxTools package (version 3.8.0) in R. DCC files containing raw count data from NGS, the PKC file pertaining to the GeoMx Human WTA, and a custom-made annotation file derived from the FASTQ lab worksheet files were condensed into an object of the GeoMxSetObject class. The GeoMxSetObject contained a total of 716 areas of illumination (AOIs) prior to quality control. AOIs were excluded from further analysis based on read metrics, sequencing saturation, and nuclei count. Probes were excluded from further analysis based on count distribution across AOIs and an outlier test and were then condensed into a gene-level count matrix. Next, all AOIs with at least 1% of genes detected and all genes detected in at least 1% of AOIs were retained in the dataset. After these quality control steps, a total of 676 AOIs remained in the dataset. Batch correction was then performed using the ComBat-Seq algorithm as implemented in the sva R package (3.52.0). Finally, count data were normalized to the third quantile and log2-transformed for downstream analysis.
AOIs were excluded from further analysis based on read metrics, sequencing saturation, and nuclei count.
Probes were excluded from further analysis based on count distribution across AOIs and an outlier test and were then condensed into a gene-level count matrix.
Next, all AOIs with at least 1% of genes detected and all genes detected in at least 1% of AOIs were retained in the dataset.
Batch correction was then performed using the ComBat-Seq algorithm as implemented in the sva R package (3.52.0).
Finally, count data were normalized to the third quantile and log2-transformed for downstream analysis.
Assembly: hg38
Supplementary files format and content: DCC files: Contains target probe counts linked to one area of illumination per file with quality control metadata.
Supplementary files format and content: PKC file: Contains information regarding the Geomx Whole Transcriptome Atlas gene panel.
Supplementary files format and content: annotation_file.xlsx: Derived from lab worksheets produced from each individual run and contains relevant metadata required for analysis as published, including de-identified patient characteristics, anatomic site of origin, and time of biopsy in relation to treatment.
Supplementary files format and content: GeoMxSetObject_postQC.RDS: Third-quartile normalized and batch-corrected data object used in all downstream analysis.
Library strategy: Spatial Transcriptomics

molecule: total RNA

organism: Homo sapiens

source_name: metastatic pancreatic adenocarcinoma

extract_protocol:
Two tumor biopsies were performed on most patients. One biopsy was performed during screening and one was performed after 4-6 weeks of treatment from the same metastatic site to acquire cores for formalin-fixed, paraffin-embedded (FFPE) blocks, frozen OCT blocks, and fresh tissue studies. Slides from FFPE tissue were hematoxylin and eosin (H&E)-stained, followed by review by a pathologist. If no viable tumor was identified in FFPE cores, OCT cores were converted to FFPE blocks if available.
The GeoMx DSP libraries were prepared according to the manufacturer's instructions for the GeoMx Human Whole Transcriptome Atlas (WTA) assay.

treatment_protocol: Each treatment cycle consisted of 28 days. All patients whose samples are represented in this study received albumin-bound paclitaxel followed by gemcitabine (GA). Albumin-bound paclitaxel was administered as a 30-minute infusion at a dose of 125 mg/m2 (maximum infusion time not to exceed 40 minutes) followed by 1000 mg/m2 gemcitabine as a 30-minute infusion for three consecutive weeks followed by a week of rest (treatment on days 1, 8, and 15, during a 28-day cycle). Patients assigned to the GA plus oral placebo arm received an oral placebo taken once daily that could not be physically distinguished from the oral paricalcitol pill. Patients assigned to the GA plus intravenous (IV) paricalcitol arm were initially scheduled to receive 25 mcg of IV paricalcitol three times weekly. However, due to clinical care restrictions imposed during the COVID pandemic, the dose was reduced to 75 mcg of IV paricalcitol weekly. Only one patient received thrice weekly dosing prior to the dosing change. Patients assigned to the GA plus PO paricalcitol arm received 16 mcg of oral paricalcitol daily, which was thought to be analogous to a cumulative weekly dose as 75 mcg of IV paricalcitol based upon the bioavailability of PO paricalcitol.

tag: tissue

value: metastatic pancreatic adenocarcinoma

tag: biopsy site

value: liver

tag: segment

tag: region of_interest_number

tag: patient id

tag: treatment

value: Gemcitabine/Nab-Paclitaxel plus Placebo

tag: biopsy timepoint

value: pre-treatment

tag: Sex

value: M

tag: race

value: White

tag: ethnicity

value: Non-Hispanic

tag: age

tag: batch


title: ID87, Gemcitabine/Nab-Paclitaxel plus Placebo, pre-treatment, ring2, 2, Slide 1

description:
Library name: Sample 84
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID87, Gemcitabine/Nab-Paclitaxel plus Placebo, pre-treatment, ring2, 3, Slide 1

description:
Library name: Sample 87
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID87, Gemcitabine/Nab-Paclitaxel plus Placebo, pre-treatment, ring1, 1, Slide 1

description:
Library name: Sample 81
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID82, Gemcitabine/Nab-Paclitaxel plus IV Paricalcitol, pre-treatment, ring2, 4

description:
Library name: Sample 108
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.

value: F


title: ID87, Gemcitabine/Nab-Paclitaxel plus Placebo, pre-treatment, ring1, 3, Slide 1

description:
Library name: Sample 86
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID94, Gemcitabine/Nab-Paclitaxel plus Oral Paricalcitol, pre-treatment, ring1, 4

description:
Library name: Sample 79
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID82, Gemcitabine/Nab-Paclitaxel plus IV Paricalcitol, pre-treatment, ring1, 3

description:
Library name: Sample 104
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID87, Gemcitabine/Nab-Paclitaxel plus Placebo, pre-treatment, ring1, 4, Slide 1

description:
Library name: Sample 89
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID94, Gemcitabine/Nab-Paclitaxel plus Oral Paricalcitol, pre-treatment, Center, 4

description:
Library name: Sample 78
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.

value: Center


title: ID94, Gemcitabine/Nab-Paclitaxel plus Oral Paricalcitol, pre-treatment, ring1, 3

description:
Library name: Sample 77
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID94, Gemcitabine/Nab-Paclitaxel plus Oral Paricalcitol, pre-treatment, Center, 3

description:
Library name: Sample 76
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID82, Gemcitabine/Nab-Paclitaxel plus IV Paricalcitol, pre-treatment, Center, 3

description:
Library name: Sample 103
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID87, Gemcitabine/Nab-Paclitaxel plus Placebo, pre-treatment, Center, 1, Slide 1

description:
Library name: Sample 80
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID94, Gemcitabine/Nab-Paclitaxel plus Oral Paricalcitol, pre-treatment, ring1, 2

description:
Library name: Sample 75
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID87, Gemcitabine/Nab-Paclitaxel plus Placebo, pre-treatment, Center, 2, Slide 1

description:
Library name: Sample 82
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID94, Gemcitabine/Nab-Paclitaxel plus Oral Paricalcitol, pre-treatment, Center, 1

description:
Library name: Sample 72
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID94, Gemcitabine/Nab-Paclitaxel plus Oral Paricalcitol, pre-treatment, ring1, 1

description:
Library name: Sample 73
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID87, Gemcitabine/Nab-Paclitaxel plus Placebo, pre-treatment, ring1, 2, Slide 1

description:
Library name: Sample 83
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID71, Gemcitabine/Nab-Paclitaxel plus Placebo, pre-treatment, ring2, 4

description:
Library name: Sample 71
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.

value: adrenal


title: ID94, Gemcitabine/Nab-Paclitaxel plus Oral Paricalcitol, pre-treatment, Center, 2

description:
Library name: Sample 74
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID71, Gemcitabine/Nab-Paclitaxel plus Placebo, pre-treatment, ring1, 4

description:
Library name: Sample 70
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID71, Gemcitabine/Nab-Paclitaxel plus Placebo, pre-treatment, ring2, 3

description:
Library name: Sample 68
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID71, Gemcitabine/Nab-Paclitaxel plus Placebo, pre-treatment, Center, 4

description:
Library name: Sample 69
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID71, Gemcitabine/Nab-Paclitaxel plus Placebo, pre-treatment, Center, 3

description:
Library name: Sample 66
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID71, Gemcitabine/Nab-Paclitaxel plus Placebo, pre-treatment, ring1, 3

description:
Library name: Sample 67
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID71, Gemcitabine/Nab-Paclitaxel plus Placebo, pre-treatment, ring2, 2

description:
Library name: Sample 65
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID71, Gemcitabine/Nab-Paclitaxel plus Placebo, pre-treatment, ring1, 2

description:
Library name: Sample 64
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID71, Gemcitabine/Nab-Paclitaxel plus Placebo, pre-treatment, Center, 2

description:
Library name: Sample 63
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID87, Gemcitabine/Nab-Paclitaxel plus Placebo, pre-treatment, Center, 5, Slide 1

description:
Library name: Sample 91
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID71, Gemcitabine/Nab-Paclitaxel plus Placebo, pre-treatment, ring2, 1

description:
Library name: Sample 62
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID71, Gemcitabine/Nab-Paclitaxel plus Placebo, pre-treatment, ring1, 1

description:
Library name: Sample 61
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID75, Gemcitabine/Nab-Paclitaxel plus Oral Paricalcitol, pre-treatment, ring1, 2, Slide 1

description:
Library name: Sample 59
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID75, Gemcitabine/Nab-Paclitaxel plus Oral Paricalcitol, pre-treatment, Center, 1, Slide 1

description:
Library name: Sample 56
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID83, Gemcitabine/Nab-Paclitaxel plus Oral Paricalcitol, pre-treatment, Center, 6

description:
Library name: Sample 54
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.

value: lung


title: ID83, Gemcitabine/Nab-Paclitaxel plus Oral Paricalcitol, pre-treatment, ring2, 4

description:
Library name: Sample 50
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID83, Gemcitabine/Nab-Paclitaxel plus Oral Paricalcitol, pre-treatment, ring2, 5

description:
Library name: Sample 53
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID83, Gemcitabine/Nab-Paclitaxel plus Oral Paricalcitol, pre-treatment, ring1, 6

description:
Library name: Sample 55
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID83, Gemcitabine/Nab-Paclitaxel plus Oral Paricalcitol, pre-treatment, ring1, 5

description:
Library name: Sample 52
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID83, Gemcitabine/Nab-Paclitaxel plus Oral Paricalcitol, pre-treatment, Center, 5

description:
Library name: Sample 51
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID83, Gemcitabine/Nab-Paclitaxel plus Oral Paricalcitol, pre-treatment, ring1, 3

description:
Library name: Sample 47
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID83, Gemcitabine/Nab-Paclitaxel plus Oral Paricalcitol, pre-treatment, ring1, 4

description:
Library name: Sample 49
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID71, Gemcitabine/Nab-Paclitaxel plus Placebo, pre-treatment, Center, 1

description:
Library name: Sample 60
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID83, Gemcitabine/Nab-Paclitaxel plus Oral Paricalcitol, pre-treatment, Center, 3

description:
Library name: Sample 46
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID83, Gemcitabine/Nab-Paclitaxel plus Oral Paricalcitol, pre-treatment, ring1, 2

description:
Library name: Sample 45
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID83, Gemcitabine/Nab-Paclitaxel plus Oral Paricalcitol, pre-treatment, Center, 4

description:
Library name: Sample 48
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID83, Gemcitabine/Nab-Paclitaxel plus Oral Paricalcitol, pre-treatment, ring2, 1

description:
Library name: Sample 43
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID75, Gemcitabine/Nab-Paclitaxel plus Oral Paricalcitol, pre-treatment, Center, 2, Slide 1

description:
Library name: Sample 58
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID83, Gemcitabine/Nab-Paclitaxel plus Oral Paricalcitol, pre-treatment, Center, 1

description:
Library name: Sample 41
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID83, Gemcitabine/Nab-Paclitaxel plus Oral Paricalcitol, pre-treatment, Center, 2

description:
Library name: Sample 44
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID83, Gemcitabine/Nab-Paclitaxel plus Oral Paricalcitol, pre-treatment, ring1, 1

description:
Library name: Sample 42
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID84, Gemcitabine/Nab-Paclitaxel plus IV Paricalcitol, pre-treatment, Center, 8

description:
Library name: Sample 39
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.

value: Other


title: ID84, Gemcitabine/Nab-Paclitaxel plus IV Paricalcitol, pre-treatment, ring1, 8

description:
Library name: Sample 40
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID84, Gemcitabine/Nab-Paclitaxel plus IV Paricalcitol, pre-treatment, ring2, 7

description:
Library name: Sample 38
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID84, Gemcitabine/Nab-Paclitaxel plus IV Paricalcitol, pre-treatment, ring1, 7

description:
Library name: Sample 37
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: AngII3

city: Jilin City

first: Mengyang

last: Wang

state: Jilin

address: No. 3999, Huashan Road, Fengman District, Jilin City, Jilin Province

country: China

institute: Beihua university

description: Library name: Sample 6

data_processing:
Illumina novaseq 6000 software used for basecalling. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100 Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9 perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals. Assembly: GRCm39 Supplementary files format and content: Excel file includes FPKM values for each Sample
Assembly: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary files format and content: tab-delimited text file include raw counts for each Sample

organism: Mus musculus

source_name: heart

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For AngII-induced cardiac hypertrophy model, wild-type C57BL/6J mice were injected with Ang II (1 μg/kg/min) or normal saline via an osmotic pump for four weeks to induce cardiac hypertrophy based on our previous research. An osmotic pump was subcutaneously implanted in the back of each mouse. In the first week after the operation, the incision of the mice was observed daily, while the blood pressure and body weight were measured and recorded every three days. The mice were sacrificed to collect serum and heart tissue samples at four weeks.

value: heart

tag: cell type

value: mouse heart tissue


title: AngII2

description: Library name: Sample 5


title: ID75, Gemcitabine/Nab-Paclitaxel plus Oral Paricalcitol, pre-treatment, ring1, 1, Slide 1

description:
Library name: Sample 57
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID84, Gemcitabine/Nab-Paclitaxel plus IV Paricalcitol, pre-treatment, Center, 7

description:
Library name: Sample 36
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: AngII1

description: Library name: Sample 4


title: ID84, Gemcitabine/Nab-Paclitaxel plus IV Paricalcitol, pre-treatment, ring1, 6

description:
Library name: Sample 35
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID84, Gemcitabine/Nab-Paclitaxel plus IV Paricalcitol, pre-treatment, Center, 6

description:
Library name: Sample 34
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: CON3

description: Library name: Sample 3


title: CON1

description: Library name: Sample 1


title: ID84, Gemcitabine/Nab-Paclitaxel plus IV Paricalcitol, pre-treatment, ring1, 5

description:
Library name: Sample 33
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID84, Gemcitabine/Nab-Paclitaxel plus IV Paricalcitol, pre-treatment, ring2, 4

description:
Library name: Sample 31
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID84, Gemcitabine/Nab-Paclitaxel plus IV Paricalcitol, pre-treatment, Center, 4

description:
Library name: Sample 29
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: CON2

description: Library name: Sample 2


title: NOD mouse, non-progressor to hyperglycemia, 108 days post implant, mouse 2 (biol rep 2)

city: Ann Arbor

first: Lonnie

middle: D

last: Shea

state: MI

address: 1600 Huron Parkway

department: Biomedical Engineering

institute: University of Michigan

description:
Library name: 6872-JK-76
column name in og_gene_expected_count.annot.csv matches library name

data_processing:
Data processing methods provided by the Advanced Genomics Core at the University of Michigan.
Sequence reads were trimmed using Cutadapt  (Martin, 2011). FastQC (Andrews, 2010) was used to ensure the quality of data and Fastq Screen  (Wingett and Andrews, 2018) was used to screen for various types of contamination.
Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR (Dobin et al., 2013) and assigned count estimates to genes with RSEM (Li and Dewey, 2011). Alignment options followed ENCODE standards for RNA-seq.
Multiqc compiled the results from several of these tools and provided a detailed and comprehensive quality control report (Ewels et al., 2016).
Assembly: GRCm38
Supplementary files format and content: og_gene_expected_count.annot.csv: csv file including gene expected counts for all samples run in the first batch
Supplementary files format and content: vc_gene_expected_count.annot.csv: csv file including gene expected counts for all samples run in the ssecond batch

source_name: scaffold immunological niche

extract_protocol:
Scaffolds were lysed in 800µl TRIzol reagent (Fisher Scientific)) and homogenized at 15000 RPM. The homogenized scaffold solution was centrifuged to pellet any remaining scaffold debris, and the supernatant was taken for RNA isolation. RNA isolation was performed using the Zymo Direct-zol RNA miniprep kit (Fisher Scientific).
RNA libraries were prepared by the Advanced Genomics Core at the University of Michigan using the Illumina ribo depletion assay.

value: scaffold immunological niche

tag: strain

value: NOD/ShiLtJ

tag: time

value: 108 days post implant


title: ID84, Gemcitabine/Nab-Paclitaxel plus IV Paricalcitol, pre-treatment, ring1, 4

description:
Library name: Sample 30
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.

value: metastatic pancreatic adenocarcinoma


title: NOD mouse, progressor to hyperglycemia, 6 weeks of age, mouse 5 (biol rep 5)

description:
Library name: 6872-JK-77
column name in og_gene_expected_count.annot.csv matches library name

value: 6 weeks of age


title: ID84, Gemcitabine/Nab-Paclitaxel plus IV Paricalcitol, pre-treatment, Center, 3

description:
Library name: Sample 27
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.

value: liver


title: NOD mouse, non-progressor to hyperglycemia, 108 days post implant, mouse 1 (biol rep 1)

description:
Library name: 6872-JK-75
column name in og_gene_expected_count.annot.csv matches library name


title: ID84, Gemcitabine/Nab-Paclitaxel plus IV Paricalcitol, pre-treatment, ring1, 3

description:
Library name: Sample 28
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.

value: pre-treatment


title: NOD mouse, non-progressor to hyperglycemia, 31 days post implant, mouse 2 (biol rep 2)

description:
Library name: 6872-JK-72
column name in og_gene_expected_count.annot.csv matches library name

value: 31 days post implant


title: NOD mouse, non-progressor to hyperglycemia, 38 days post implant, mouse 1 (biol rep 1)

description:
Library name: 6872-JK-73
column name in og_gene_expected_count.annot.csv matches library name

value: 38 days post implant


title: ID84, Gemcitabine/Nab-Paclitaxel plus IV Paricalcitol, pre-treatment, ring2, 2

description:
Library name: Sample 26
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.

value: M

value: Non-Hispanic


title: NOD mouse, non-progressor to hyperglycemia, 31 days post implant, mouse 1 (biol rep 1)

description:
Library name: 6872-JK-71
column name in og_gene_expected_count.annot.csv matches library name


title: ID85, Gemcitabine/Nab-Paclitaxel plus Placebo, on-treatment, ring2, 8

description:
Library name: Sample 24
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.

value: Gemcitabine/Nab-Paclitaxel plus Placebo

value: on-treatment

value: White


title: NOD mouse, non-progressor to hyperglycemia, 22 weeks of age, mouse 4 (biol rep 4)

description:
Library name: 6872-JK-70
column name in og_gene_expected_count.annot.csv matches library name

value: 22 weeks of age


title: ID84, Gemcitabine/Nab-Paclitaxel plus IV Paricalcitol, pre-treatment, ring1, 2

description:
Library name: Sample 25
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.

value: Other


title: ID85, Gemcitabine/Nab-Paclitaxel plus Placebo, on-treatment, ring1, 8

description:
Library name: Sample 23
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID87, Gemcitabine/Nab-Paclitaxel plus Placebo, pre-treatment, Center, 3, Slide 1

description:
Library name: Sample 85
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.

value: Center


title: NOD mouse, non-progressor to hyperglycemia, 22 weeks of age, mouse 2 (biol rep 2)

description:
Library name: 6872-JK-68
column name in og_gene_expected_count.annot.csv matches library name

value: scaffold immunological niche


title: ID85, Gemcitabine/Nab-Paclitaxel plus Placebo, on-treatment, Center, 8

description:
Library name: Sample 22
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID85, Gemcitabine/Nab-Paclitaxel plus Placebo, on-treatment, ring2, 7

description:
Library name: Sample 21
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: NOD mouse, non-progressor to hyperglycemia, 22 weeks of age, mouse 1 (biol rep 1)

description:
Library name: 6872-JK-67
column name in og_gene_expected_count.annot.csv matches library name

value: NOD/ShiLtJ


title: ID84, Gemcitabine/Nab-Paclitaxel plus IV Paricalcitol, pre-treatment, Center, 5

description:
Library name: Sample 32
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID85, Gemcitabine/Nab-Paclitaxel plus Placebo, on-treatment, ring1, 7

description:
Library name: Sample 20
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: NOD mouse, non-progressor to hyperglycemia, 18 weeks of age, mouse 4 (biol rep 4)

description:
Library name: 6872-JK-66
column name in og_gene_expected_count.annot.csv matches library name

value: 18 weeks of age


title: NOD mouse, non-progressor to hyperglycemia, 18 weeks of age, mouse 3 (biol rep 3)

description:
Library name: 6872-JK-65
column name in og_gene_expected_count.annot.csv matches library name


title: NOD mouse, non-progressor to hyperglycemia, 38 days post implant, mouse 2 (biol rep 2)

description:
Library name: 6872-JK-74
column name in og_gene_expected_count.annot.csv matches library name


title: ID85, Gemcitabine/Nab-Paclitaxel plus Placebo, on-treatment, Center, 7

description:
Library name: Sample 19
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.

value: metastatic pancreatic adenocarcinoma


title: ID85, Gemcitabine/Nab-Paclitaxel plus Placebo, on-treatment, ring2, 6

description:
Library name: Sample 18
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: NOD mouse, non-progressor to hyperglycemia, 18 weeks of age, mouse 1 (biol rep 1)

description:
Library name: 6872-JK-63
column name in og_gene_expected_count.annot.csv matches library name


title: NOD mouse, non-progressor to hyperglycemia, 14 weeks of age, mouse 4 (biol rep 4)

description:
Library name: 6872-JK-62
column name in og_gene_expected_count.annot.csv matches library name

value: 14 weeks of age


title: ID85, Gemcitabine/Nab-Paclitaxel plus Placebo, on-treatment, ring1, 6

description:
Library name: Sample 17
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.

value: liver


title: ID85, Gemcitabine/Nab-Paclitaxel plus Placebo, on-treatment, ring1, 5

description:
Library name: Sample 15
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: NOD mouse, non-progressor to hyperglycemia, 14 weeks of age, mouse 3 (biol rep 3)

description:
Library name: 6872-JK-61
column name in og_gene_expected_count.annot.csv matches library name


title: NOD mouse, non-progressor to hyperglycemia, 18 weeks of age, mouse 2 (biol rep 2)

description:
Library name: 6872-JK-64
column name in og_gene_expected_count.annot.csv matches library name


title: ID85, Gemcitabine/Nab-Paclitaxel plus Placebo, on-treatment, Center, 6

description:
Library name: Sample 16
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID85, Gemcitabine/Nab-Paclitaxel plus Placebo, on-treatment, Center, 5

description:
Library name: Sample 14
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: NOD mouse, non-progressor to hyperglycemia, 14 weeks of age, mouse 2 (biol rep 2)

description:
Library name: 6872-JK-60
column name in og_gene_expected_count.annot.csv matches library name


title: NOD mouse, non-progressor to hyperglycemia, 14 weeks of age, mouse 1 (biol rep 1)

description:
Library name: 6872-JK-59
column name in og_gene_expected_count.annot.csv matches library name


title: ID85, Gemcitabine/Nab-Paclitaxel plus Placebo, on-treatment, ring1, 4

description:
Library name: Sample 12
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID85, Gemcitabine/Nab-Paclitaxel plus Placebo, on-treatment, Center, 4

description:
Library name: Sample 11
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: NOD mouse, non-progressor to hyperglycemia, 10 weeks of age, mouse 3 (biol rep 3)

description:
Library name: 6872-JK-57
column name in og_gene_expected_count.annot.csv matches library name

value: 10 weeks of age


title: ID85, Gemcitabine/Nab-Paclitaxel plus Placebo, on-treatment, ring2, 3

description:
Library name: Sample 10
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: NOD mouse, non-progressor to hyperglycemia, 22 weeks of age, mouse 3 (biol rep 3)

description:
Library name: 6872-JK-69
column name in og_gene_expected_count.annot.csv matches library name


title: NOD mouse, non-progressor to hyperglycemia, 10 weeks of age, mouse 2 (biol rep 2)

description:
Library name: 6872-JK-56
column name in og_gene_expected_count.annot.csv matches library name


title: NOD mouse, non-progressor to hyperglycemia, 10 weeks of age, mouse 4 (biol rep 4)

description:
Library name: 6872-JK-58
column name in og_gene_expected_count.annot.csv matches library name


title: NOD mouse, non-progressor to hyperglycemia, 10 weeks of age, mouse 1 (biol rep 1)

description:
Library name: 6872-JK-55
column name in og_gene_expected_count.annot.csv matches library name


title: ID85, Gemcitabine/Nab-Paclitaxel plus Placebo, on-treatment, Center, 3

description:
Library name: Sample 8
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: NOD mouse, non-progressor to hyperglycemia, 6 weeks of age, mouse 4 (biol rep 4)

description:
Library name: 6872-JK-54
column name in og_gene_expected_count.annot.csv matches library name

value: 6 weeks of age


title: NOD mouse, non-progressor to hyperglycemia, 6 weeks of age, mouse 3 (biol rep 3)

description:
Library name: 6872-JK-53
column name in og_gene_expected_count.annot.csv matches library name


title: ID85, Gemcitabine/Nab-Paclitaxel plus Placebo, on-treatment, ring1, 2

description:
Library name: Sample 6
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID85, Gemcitabine/Nab-Paclitaxel plus Placebo, on-treatment, ring1, 3

description:
Library name: Sample 9
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: NOD mouse, non-progressor to hyperglycemia, 6 weeks of age, mouse 2 (biol rep 2)

description:
Library name: 6872-JK-52-REPREP
column name in og_gene_expected_count.annot.csv matches library name


title: NOD mouse, non-progressor to hyperglycemia, 6 weeks of age, mouse 1 (biol rep 1)

description:
Library name: 6872-JK-51
column name in og_gene_expected_count.annot.csv matches library name


title: ID85, Gemcitabine/Nab-Paclitaxel plus Placebo, on-treatment, ring2, 1

description:
Library name: Sample 4
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID85, Gemcitabine/Nab-Paclitaxel plus Placebo, on-treatment, ring2, 4

description:
Library name: Sample 13
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: NOR mouse, 22 weeks of age, mouse 5 (biol rep 5)

description:
Library name: 6872-JK-50
column name in og_gene_expected_count.annot.csv matches library name

value: NOR/LtJ


title: ID85, Gemcitabine/Nab-Paclitaxel plus Placebo, on-treatment, ring1, 1

description:
Library name: Sample 3
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.

value: M


title: NOR mouse, 22 weeks of age, mouse 4 (biol rep 4)

description:
Library name: 6872-JK-49
column name in og_gene_expected_count.annot.csv matches library name


title: No Template Control 1

description:
Library name: Sample 1
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.


title: ID85, Gemcitabine/Nab-Paclitaxel plus Placebo, on-treatment, Center, 1

description:
Library name: Sample 2
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.

value: Non-Hispanic


title: NOR mouse, 22 weeks of age, mouse 2 (biol rep 2)

description:
Library name: 6872-JK-47
column name in og_gene_expected_count.annot.csv matches library name


title: NOR mouse, 22 weeks of age, mouse 3 (biol rep 3)

description:
Library name: 6872-JK-48
column name in og_gene_expected_count.annot.csv matches library name


title: NOR mouse, 22 weeks of age, mouse 1 (biol rep 1)

description:
Library name: 6872-JK-46
column name in og_gene_expected_count.annot.csv matches library name


title: Gomesin_Selected_B

city: Camperdown

first: G.

middle: Greg

last: Neely

state: NSW

address: Charles Perkins Centre, D17.

country: Australia

institute: University of Sydney

description:
Library name: Gomesin_SelB
Performed next-generation sequencing on PCR amplicons containing sgRNA sequences from gomesin-selected sample, replicate B

library_source: genomic

data_processing:
Data was analyzed using the MAGeCK (v05.9.5) pipeline
Assembly: GRCh37.p13
Supplementary files format and content: .txt file containing counts of individual sgRNAs
Supplementary files format and content: .txt file containing robust rank aggregation scores at gene-level
Supplementary files format and content: .txt file containing robust rank aggregation scores of inidividual sgRNAs
Library strategy: CRISPR Screen

molecule: genomic DNA

extract_protocol:
Genomic DNA was extracted from cell pellets with the ISOLATE II Genomic DNA Kit (Bioline). Samples of gDNA (25 μg for controls and 5 μg for selected samples) were added to NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs) along with the following primers to amplify the integrated sgRNA-containing sequence: NGSCRISPRv2F1 5’-GGACAGCAGAGATCCAGTTTGGT-3’; NGSCRISPRv2R1 5’-GAGCCAATTCCCACTCCTTTCAA-3’. A second PCR reaction with a staggered primer mix of P5 and P7 indexing primers unique to each sample was prepared. Reactions were isolated by gel electrophoresis and excision.
Samples were sequenced with Novogene

tag: cell line

value: 4 rounds of 72 h selection with 25 uM gomesin, Replicate B


title: NOR mouse, 18 weeks of age, mouse 5 (biol rep 4)

description:
Library name: 6872-JK-45
column name in og_gene_expected_count.annot.csv matches library name


title: Gomesin_Selected_A

description:
Library name: Gomesin_SelA
Performed next-generation sequencing on PCR amplicons containing sgRNA sequences from gomesin-selected sample, replicate A

value: 4 rounds of 72 h selection with 25 uM gomesin, Replicate A


title: NOR mouse, 18 weeks of age, mouse 4 (biol rep 3)

description:
Library name: 6872-JK-44
column name in og_gene_expected_count.annot.csv matches library name


title: Gomesin_Control_A

description:
Library name: Gomesin_CTLA
Performed next-generation sequencing on PCR amplicons containing sgRNA sequences from diversity control, replicate A

value: Untreated, Replicate A


title: Gomesin_Control_B

description:
Library name: Gomesin_CTLB
Performed next-generation sequencing on PCR amplicons containing sgRNA sequences from diversity control, replicate B

value: Untreated, Replicate B


title: NOR mouse, 18 weeks of age, mouse 3 (biol rep 2)

description:
Library name: 6872-JK-43
column name in og_gene_expected_count.annot.csv matches library name


title: Input_in_NONO-KO_Day2_rep2

city: Shanghai

first: Feizhen

last: Wu

state: Shanghai

address: Zhangheng Road 825, Pudong

department: Intelligent Medicine Institute

institute: Fudan Univ, Shanghai, China

description: Library name: Sample 10

data_processing:
Sequencing reads underwent trimming with Trim_galore (v0.6.4_dev).
ChIP seq data were aligned to human genomes using Bowtie2 (v2.2.5)
PCR duplicate reads were eliminated using the rmdup command of samtools (v1.7)
To visualize ChIP signals in the UCSC Genome Browser, genomic coverage bedGraph fileswere generated using the bamCoverage in deeptools (v3.0.2)
Peak identification was performed using the callpeak in macs2
Assembly: hg38
Supplementary files format and content: narrowPeak

source_name: WT-iPSC

growth_protocol: the hiPSCs were dissociated using Accutase and were cultured on Matrigel-coated plates in mTeSRTM Plus medium.

extract_protocol:
7-8 x 10^6 Day 2 differentiated cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature, then quenched with 0.125 M glycine for 5 minutes. Cells were washed three times with cold PBS and harvested in DNA LoBind Tubes (Eppendorf, 0030108035/0030108051). Sonication was performed using a Bioruptor (Diagenode, B01020001) on high setting (30 sec on, 30 sec off) for 30 minutes in high salt lysis buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 0.05% SDS, 1% Triton X-100) containing a protease inhibitor cocktail. Chromatin samples were precleared with 15 μL each of Dynabeads Protein G and Protein A, and rotated at 4°C for 1 hour. Precleared samples were then incubated with 6 µg of specific antibody at 4°C for 16 hours. After antibody binding, 15 μL each of Dynabeads Protein G and Protein A were added and incubated for an additional 2 hours at 4°C. The chromatin-antibody complexes underwent four washes with high salt buffer, two washes with low salt buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and one wash with TE buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 50 mM NaCl).Complexes were eluted in elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS) on a Thermal Mixer (Thermo, 13687712) at 65°C for 4 hours, followed by treatment with 10 µg RNase and 10 µg Proteinase K at 55°C for 1 hour on the Thermal Mixer. DNA was purified using a QIAquick PCR Purification Kit (QIAGEN, 28006).
The purified DNA library preparation was constructed using VAHTS Universal Plus DNA Library Prep Kit for Illumina (Vazyme, ND617) in accordance with the manufacturer’s instruction.

treatment_protocol: the hiPSCs Upon reaching approximately 80% confluence, the cells were split at a ratio of 1:5 using Accutase (Sigma, A6964). We utilized a previously established protocol involving WNT activation and inhibition to differentiate hiPSCs into cardiomyocytes38. Briefly, hiPSCs were seeded and, at 80% confluence, treated with B27 minus insulin (Thermo, A1895601)/RPMI1640 (Thermo, 11875119) plus 7μM CHIR-99021 (Selleck, S1263). Following two days of CHIR99021 treatment, the medium was switched to B27 minus insulin/RPMI1640. After 24 hours, the medium was replaced with B27 minus insulin/RPMI1640 containing 5 μM IWR1 (Selleck, S7086) for two days. Subsequently, IWR1 was removed, and differentiation continued in CDM3 medium containing RPMI640, 50mg/ml BSA (Sigma, A1933), and 213mg/ml ascorbic acid (Sigma, A4544).

value: WT-iPSC

value: hiPSCs-derived cardiomyocytes

tag: genotype

value: NONO-KO

tag: chip antibody


title: NOR mouse, 18 weeks of age, mouse 1 (biol rep 1)

description:
Library name: 6872-JK-41
column name in og_gene_expected_count.annot.csv matches library name

tag: tissue

value: scaffold immunological niche


title: ID85, Gemcitabine/Nab-Paclitaxel plus Placebo, on-treatment, ring2, 2

description:
Library name: Sample 7
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.

tag: biopsy site

tag: segment

value: Gemcitabine/Nab-Paclitaxel plus Placebo

value: on-treatment

value: White


title: Input_in_NONO-KO_Day2_rep1

description: Library name: Sample 9


title: NOR mouse, 14 weeks of age, mouse 5 (biol rep 5)

description:
Library name: 6872-JK-40
column name in og_gene_expected_count.annot.csv matches library name

value: 14 weeks of age


title: NOR mouse, 14 weeks of age, mouse 4 (biol rep 4)

description:
Library name: 6872-JK-39
column name in og_gene_expected_count.annot.csv matches library name


title: Input_in_WT_Day2_rep2

description: Library name: Sample 8

value: WT


title: ID85, Gemcitabine/Nab-Paclitaxel plus Placebo, on-treatment, Center, 2

description:
Library name: Sample 5
A total of 716 areas of illumination were profiled and sequenced, represented by one .DCC file for each area. A total of 8 negative control probes were used, corresponding to each 96-well plate. After quality control and normalization, 676 areas of illumination were represented in the dataset for downstream analysis.

value: metastatic pancreatic adenocarcinoma

value: liver

value: Center

tag: region of_interest_number

tag: patient id


title: Input_in_WT_Day2_rep1

description: Library name: Sample 7

tag: treatment


title: HOXA1-HA_ChIP_in_NONO-KO_Day2_rep2

description: Library name: Sample 6

value: NONO-KO Dox induced HOXA1-HA hiPSCs-derived cardiomyocytes

value: Dox induced HOXA1_NONO-KO

value: HA (Abcam, #ab9110)

value: Dox


title: NOR mouse, 14 weeks of age, mouse 3 (biol rep 3)

description:
Library name: 6872-JK-38
column name in og_gene_expected_count.annot.csv matches library name

value: NOR/LtJ


title: NOR mouse, 14 weeks of age, mouse 2 (biol rep 2)

description:
Library name: 6872-JK-37
column name in og_gene_expected_count.annot.csv matches library name


title: HOXA1-HA_ChIP_in_NONO-KO_Day2_rep1

description: Library name: Sample 5

value: WT-iPSC


title: NOR mouse, 14 weeks of age, mouse 1 (biol rep 1)

description:
Library name: 6872-JK-36
column name in og_gene_expected_count.annot.csv matches library name


title: HOXA1-HA_ChIP_in_WT_Day2_rep2

description: Library name: Sample 4

value: Dox induced HOXA1-HA hiPSCs-derived cardiomyocytes

value: Dox induced HOXA1_WT


title: HOXA1-HA_ChIP_in_WT_Day2_rep1

description: Library name: Sample 3


title: NONO_ChIP_in_WT_Day2_rep2

description: Library name: Sample 2

value: hiPSCs-derived cardiomyocytes

value: NONO (Abcam, ab#70335)


title: NOR mouse, 10 weeks of age, mouse 5 (biol rep 5)

description:
Library name: 6872-JK-35
column name in og_gene_expected_count.annot.csv matches library name

value: scaffold immunological niche

value: 10 weeks of age


title: NOR mouse, 10 weeks of age, mouse 3 (biol rep 3)

description:
Library name: 6872-JK-33
column name in og_gene_expected_count.annot.csv matches library name


title: NOR mouse, 10 weeks of age, mouse 2 (biol rep 2)

description:
Library name: 6872-JK-32
column name in og_gene_expected_count.annot.csv matches library name


title: NONO_ChIP_in_WT_Day2_rep1

description: Library name: Sample 1


title: NOR mouse, 6 weeks of age, mouse 5 (biol rep 4)

description:
Library name: 6872-JK-30
column name in og_gene_expected_count.annot.csv matches library name

value: 6 weeks of age


title: MCF7_gH2AX_input

city: Jerusalem

first: Rami

last: Aqeilan

address: Ein Kerem

country: Israel

institute: Hebrew University of Jerusalem

description: Library name: MCF7_gH2AX_input

data_processing:
Reads are trimmed and filtered with trim_galore and quality is tested with fastqc.
Reads are mapped to the genome with hisat2.
Bam files are de-duplicated with umi_tools dedup (breakome files).
Deduplicated bam files are converted to bed and bedgraph fies with bedtools bamtobed and custom R scripts. Bedgraph files are converetd to bigwig files with UCSC bedGraphToBigWig tool.
Count tables and downstream analysis are performed wih custom R scripts.
ChIP-Seq bigwig file is create with deeptools bamCompare tool.
Assembly: hg38
Supplementary files format and content: tab-delemited text file including raw and density counts per sample, Density is raw divided by gene size multiplied by 1E5.
Supplementary files format and content: Bigwig file including ratio between ChIP-Seq and input.

source_name: cell line

growth_protocol: MCF7 (HTB-22) and T-47D (HTB-133) cells were grown in RPMI supplemented with 10% (vol/vol) fetal bovine serum FBS (GIBCO), glutamine, and penicillin/streptomycin. HEK-293 (CRL-1573), MDA-MB-468 (HTB-132), MDA-MB-231 (HTB-26), and HeLa cells (CCL-2) were grown in DMEM supplemented with 10% (vol/vol) FBS, glutamine, and penicillin/streptomycin. A-4098 cells (HTB-44) were grown in. EMEM supplemented with 10% FBS, glutamine, and penicillin/streptomycin. SH-SY5Y (CRL-2266) were grown in DMEM/F12 supplemented with 10% FBS, glutamine, and penicillin/streptomycin. HMLE cells were grown in Promocell mammary epithelial cell basal media (C-21010) with added supplements (c-93110) whereas MCF10A were grown on DMEM/F12 supplemented with 5% Horse serum, 20 ng/ml EGF, 0.5 mg/ml Hydrocortisone, 100 ng/ml Cholera toxin, 10 mg/ml Insulin and Pen/Strep. MCF-7 cells were synchronized in the G1 cell cycle stage by culturing in serum-free media for 72 hours followed by replacing the media with 5% FBS media for 5 hours. Cells were grown at 37°C under a humidified atmosphere with 5% CO2. Cells were routinely authenticated by STR profiling, and tested for mycoplasma, and cell aliquots from early passages were used.

extract_protocol:
sBLISS was conducted as previously described33,60. In summary, 106 cells were fixed in 2% paraformaldehyde in 10% FCS/PBS for 10 minutes at room temperature. The fixation was quenched with 125 mM glycine for 5 minutes at room temperature, followed by another 5 minutes on ice and two washes in ice-cold PBS. Cells were lysed for 60 minutes on ice, and their nuclei were permeabilized for 60 minutes at 37°C. Next, nuclei were rinsed twice with CutSmart Buffer containing 0.1% Triton X-100 (CS/TX100), and double-strand break (DSB) ends were blunted in situ using NEB’s Quick Blunting Kit for 60 minutes at room temperature. The blunted nuclei were then washed twice with 1x CS/TX100 before in situ ligation of the sBLISS adapters to the DSB ends. Adaptor ligation was carried out with T4 DNA Ligase for 20-24 hours at 16°C, with BSA and ATP added. Following ligation, the nuclei underwent two washes with 1x CS/TX100, and genomic DNA was extracted using Proteinase K at 55°C for 14-18 hours while shaking at 800 rpm. Proteinase K was then heat-inactivated for 10 minutes at 95°C, followed by extraction using Phenol:Chloroform:Isoamyl Alcohol, Chloroform, and ethanol precipitation. The purified DNA was sonicated in 100 μL of ultra-pure water using Covaris M220 for 60 seconds. Sonicated samples were concentrated with AMPure XP beads (Beckman Coulter), and fragment sizes were evaluated using a BioAnalyzer 2100 (Agilent Technologies), targeting a range of 300 bp to 800 bp with a peak around 400-600 bp. The sonicated DNA was then in vitro transcribed using the MEGAscript T7 Kit for 14 hours at 37°C. After RNA purification and ligation of the 3’-Illumina adaptors, the RNA underwent reverse transcription. The final library indexing and amplification step was performed with NEBNext® Ultra™ II Q5® Master Mix.MCF7 cells (~106) were crosslinked with 1% formaldehyde (methanol free, Thermo Scientific 28906) for 10 min at room temperature and quenched with glycine, 125 mM final concentration. Fixed cells were washed twice in PBS and incubated in sonication buffer (0.5M NaCl, 0.5%SDS RIPA buffer containing PMSF, protease and phosphatase inhibitors) for 30min on ice. Cells were sonicated using Covaris M220 for 10min to produce chromatin fragments of ~200-300 bp. The sheared chromatin was centrifuged 10min at maximum speed. From the supernatant, 50ul were saved as input DNA and the rest was diluted in RIPA buffer without NaCl and SDS. The chromatin was immunoprecipitated by incubation with 5 μg of gamma-H2AX (phospho S139; Abcam, AB2893) antibody pre mixed with 100ul Dynabeads Protein G (ThermoFisher, 10004D) and incubated over-night at 4°C with rotation. Immunoprecipitates were washed twice with RIPA buffer + 150mM NaCl, twice with RIPA buffer + 300 mM NaCl, and twice with TE buffer. The chromatin was eluted from the beads with 200ul of direct elution buffer (10mM Tris pH 8, 0.3M NaCl, 5mM EDTA, 0.5% SDS) and incubated overnight at 65°C to reverse the cross-linking. Samples were treated with RNAse for 1h at 37 °C and with proteinase K at 55 °C for 2 h. DNA was cleaned up by QIAquick PCR purification column (Qiagen), according to the manufacturer’s instructions, and eluted in 30 μl of elution buffer. The ChIPed and the Input DNA were used for real-time PCR or to prepare libraries by Truseq (Ilumina) and sequenced in Nextseq (Illumina).
sBLISS fastq files are initially de-multiplexed using sample barcodes. Quality control is performed with trim galore to eliminate residual adapters, trim reads to a base quality of at least 20, and filter out short reads smaller than 20 bp. Initial and final sample qualities are assessed with fastqc. Quality-processed fastq files are aligned to the GRCh38 assembly with hisat2, then sorted and indexed using samtools. The resulting bam files are de-duplicated with umi-tools, utilizing genomic coordinates and Unique Molecular Identifiers (UMI). Custom Python and R scripts are employed to identify read start positions and convert bam files to bigwig format for downstream analysis. An additional custom R script is used to discard a blacklist of positions, primarily within centromeres.

treatment_protocol: Cells were treated with DMSO (Sigma-Aldrich), dBET6 (Sigma-Aldrich, SML2638), or CDK9i (NVP-2) (MCE, Cat# Y-12214A) 100 nM for 4 hours. Cells were then treated with DMSO or ATMi (20 uM, KU-55933, Sigma) for 5 hours. Transient transfection of siXRCC4 (Dharmacon; SMARTpool siRNA, Catalog ID: L-004494-00-0005) and siSc (Dharmacon; D-00181010) was carried out using Lipofectamine (ThermoFisher). On the day of transfection, cells were seeded to achieve a confluency of 60-70%. The transfection solution was prepared by mixing 1.5 ml of serum and antibiotic-free RPMI with 30 µL of Lipofectamine and incubating for 5 minutes before adding a mixture of 1.5 ml RPMI and 0.6 nmoles of siRNA, followed by a 20-minute incubation at room temperature. This mixture was then added to cells in a 10 cm plate cultured in antibiotic and serum-free media. The media was replaced with fully supplemented media after 5-6 hours, and the cells were incubated in the incubator for 48 hours.

value: cell line


title: MCF7_gH2AX_ChIP

description: Library name: MCF7_gH2AX_ChIP


title: T47D_rep1

description: Library name: T47D_rep1


title: T47D_rep3

description: Library name: T47D_rep3


title: NOR mouse, 6 weeks of age, mouse 1 (biol rep 1)

description:
Library name: 6872-JK-26
column name in og_gene_expected_count.annot.csv matches library name


title: SHSY5Y_rep3

description: Library name: SHSY5Y_rep3


title: MDA_MB_468_rep3

description: Library name: MDA_MB_468_rep3


title: NOD mouse, progressor to hyperglycemia, onset, mouse 1 (biol rep 1)

description:
Library name: 6872-JK-21
column name in og_gene_expected_count.annot.csv matches library name

value: NOD/ShiLtJ

value: hyperglycemia onset


title: NSCs

description: Library name: NSCs


title: NOR mouse, 10 weeks of age, mouse 4 (biol rep 4)

description:
Library name: 6872-JK-34
column name in og_gene_expected_count.annot.csv matches library name


title: primary tumor cell line from KPC mice, Arpc4 KO-3

city: Heidelberg

first: Yina

last: Qiao

country: Germany

institute: Heidelberg University Hospital

description:
Library name: R254ko13
R254ko13

data_processing:
Counts per million normalization and Log2 transformation
Assembly: mm9
Supplementary files format and content: .xlsx
Supplementary files format and content: Count matrix (2D), Log2CPM normalized (3D)

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin, and 100 µg/mL streptomycin. Cells were maintained at 37°C in a humidified incubator with 5% CO₂.

extract_protocol:
Total RNA was extracted using the Monarch Total RNA Miniprep Kit in accordance with the manufacturer’s protocol. RNA sequencing was performed at the Core Unit Bioinformatics, Medical Faculty, Ulm University.Ex vivo microtumor models were constructed using organoids, mouse primary pancreatic stellate cells (PSCs), and bone marrow-derived macrophages embedded in a matrix consisting of 75% Matrigel, 25% Type I collagen, 5 μg/mL fibronectin, and 2.5 μg/mL vitronectin. Total RNA was extracted by adding TRIzol reagent (Thermo Fisher, USA) to the gel after removing the supernatant and dissolving the gel by thorough mixing. Chloroform (Thermo Fisher, USA) was then added, followed by vigorous vortexing for 15 seconds. After incubation at room temperature for 3 minutes, the mixture was centrifuged at 12,000×g for 15 minutes at 4°C. The upper aqueous phase was carefully transferred to a fresh tube, mixed with an equal volume of ≥95% ethanol, and purified using the Monarch Total RNA Miniprep Kit (New England Biolabs, Germany) according to the manufacturer’s protocol.
200ng of total RNA, measured by Qubit® analysis, was used as input material for library construction using TruSeq RNA Sample Preparation Kit v2 (Illumina). Correct size distribution of the libraries was determined on a DNA1000 ScreenTape® using a Tape Station 4200 (Agilent)

treatment_protocol: Transfections were carried out using Lipofectamine 3000 (Thermo Fisher, USA) according to the manufacturer’s protocol. Forty-eight hours post-transfection, green fluorescent cells were sorted via fluorescence-activated cell sorting (FACS) and selected using puromycin (InvivoGen, Toulouse, France) at concentrations of 0.7 mg/mL for 8025 cells and 1.2 mg/mL for R254 cells. After 5–7 days of puromycin selection, cells were seeded into 96-well plates for clonal expansion. Arpc4 knockout (Arpc4ko) clones were validated via Western blot analysis.

value: primary tumor cell line from KPC mice

value: p48Cre/+; LSL-KrasG12D/+; p53flox/flox

value: Arpc4 knockout


title: NOR mouse, 10 weeks of age, mouse 1 (biol rep 1)

description:
Library name: 6872-JK-31
column name in og_gene_expected_count.annot.csv matches library name


title: primary tumor cell line from KPC mice, Arpc4 KO-2

description:
Library name: R254ko12
R254ko12


title: primary tumor cell line from KPC mice, control-3

description:
Library name: R254ctrl3
R254ctrl3

value: control


title: NOR mouse, 6 weeks of age, mouse 4 (biol rep 3)

description:
Library name: 6872-JK-29
column name in og_gene_expected_count.annot.csv matches library name


title: NOD mouse, progressor to hyperglycemia, 1 week before onset, mouse 4 (biol rep 4)

description:
Library name: 6872-JK-19
column name in og_gene_expected_count.annot.csv matches library name

value: 1 week before onset


title: NOD mouse, progressor to hyperglycemia, onset, mouse 5 (biol rep 5)

description:
Library name: 6872-JK-25
column name in og_gene_expected_count.annot.csv matches library name


title: primary tumor cell line from KPC mice, control-2

description:
Library name: R254ctrl2
R254ctrl2


title: NOD mouse, progressor to hyperglycemia, 1 week before onset, mouse 3 (biol rep 3)

description:
Library name: 6872-JK-18
column name in og_gene_expected_count.annot.csv matches library name


title: SHSY5Y_rep2

description: Library name: SHSY5Y_rep2


title: SHSY5Y_rep1

description: Library name: SHSY5Y_rep1


title: MDA_MB_436_rep2

description: Library name: MDA_MB_436_rep2


title: NOD mouse, progressor to hyperglycemia, onset, mouse 3 (biol rep 3)

description:
Library name: 6872-JK-23
column name in og_gene_expected_count.annot.csv matches library name


title: NOD mouse, progressor to hyperglycemia, onset, mouse 2 (biol rep 2)

description:
Library name: 6872-JK-22
column name in og_gene_expected_count.annot.csv matches library name


title: primary tumor cell line from KC mice, Arpc4 KO-2

description:
Library name: 8025ko12
8025ko12

value: primary tumor cell line from KP mice

value: p48Cre/+; LSL-KrasG12D/+


title: MDA_MB_436_rep1

description: Library name: MDA_MB_436_rep1


title: NOD mouse, progressor to hyperglycemia, 1 week before onset, mouse 1 (biol rep 1)

description:
Library name: 6872-JK-16
column name in og_gene_expected_count.annot.csv matches library name


title: MDA_MB_468_rep2

description: Library name: MDA_MB_468_rep2


title: NOD mouse, progressor to hyperglycemia, 1 week before onset, mouse 5 (biol rep 5)

description:
Library name: 6872-JK-20
column name in og_gene_expected_count.annot.csv matches library name


title: primary tumor cell line from KPC mice, Arpc4 KO-1

description:
Library name: R254ko11
R254ko11


title: T47D_rep2

description: Library name: T47D_rep2


title: MDA_MB_468_rep1

description: Library name: MDA_MB_468_rep1


title: NOD mouse, progressor to hyperglycemia, 3 weeks before onset, mouse 4 (biol rep 4)

description:
Library name: 6872-JK-14
column name in og_gene_expected_count.annot.csv matches library name

value: 3 weeks before onset


title: primary tumor cell line from KPC mice, control-1

description:
Library name: R254ctrl1
R254ctrl1


title: MDA_MB_436_rep3

description: Library name: MDA_MB_436_rep3


title: primary tumor cell line from KC mice, Arpc4 KO-3

description:
Library name: 8025ko13
8025ko13


title: NOD mouse, progressor to hyperglycemia, 1 week before onset, mouse 2 (biol rep 2)

description:
Library name: 6872-JK-17
column name in og_gene_expected_count.annot.csv matches library name


title: 5xFAD rep1

city: nanjing

first: Weixi

last: Feng

address: hanzhong road

institute: Nanjing Medical University

data_processing:
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome (UCSC mm10) with hisat2 software (v2.0.4). Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified. GO and Pathway enrichment analysis were performed based on the differentially expressed mRNAs.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: mRNA_Expression_Profiling.xlsx: Matrix table with raw gene counts and FPKM values for every gene and every sample.

source_name: pulmonary B cells

extract_protocol:
Pulmonary B cells of WT and 5xFAD mice were obtained using MACS. The cells were flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).

value: lung

value: pulmonary B cells

value: 3 months


title: NOD mouse, progressor to hyperglycemia, onset, mouse 4 (biol rep 4)

description:
Library name: 6872-JK-24
column name in og_gene_expected_count.annot.csv matches library name

value: scaffold immunological niche


title: WT rep3

value: WT


title: primary tumor cell line from KC mice, Arpc4 KO-1

description:
Library name: 8025ko11
8025ko11


title: NOD mouse, progressor to hyperglycemia, 3 weeks before onset, mouse 2 (biol rep 2)

description:
Library name: 6872-JK-12
column name in og_gene_expected_count.annot.csv matches library name


title: NOR mouse, 6 weeks of age, mouse 2 (biol rep 2)

description:
Library name: 6872-JK-27
column name in og_gene_expected_count.annot.csv matches library name

value: NOR/LtJ

value: 6 weeks of age


title: primary tumor cell line from KC mice, control-3

description:
Library name: 8025ctrl3
8025ctrl3

source_name: pancreas


title: NOD mouse, progressor to hyperglycemia, 3 weeks before onset, mouse 1 (biol rep 1)

description:
Library name: 6872-JK-11
column name in og_gene_expected_count.annot.csv matches library name

value: NOD/ShiLtJ


title: WT rep1


title: MCF7_rep3

description: Library name: MCF7_rep3

value: cell line


title: primary tumor cell line from KC mice, control-2

description:
Library name: 8025ctrl2
8025ctrl2


title: NOD mouse, progressor to hyperglycemia, 3 weeks before onset, mouse 5 (biol rep 5)

description:
Library name: 6872-JK-15
column name in og_gene_expected_count.annot.csv matches library name


title: primary tumor cell line from KC mice, control-1

description:
Library name: 8025ctrl1
8025ctrl1


title: MCF7_rep2

description: Library name: MCF7_rep2


title: 5xFAD rep3


title: 5xFAD rep2


title: MCF7_DMSO_rep2

description: Library name: MCF7_DMSO_rep2

value: DMSO


title: MCF7_G1_sync_rep2

description: Library name: MCF7_G1_sync_rep2


title: NOD mouse, progressor to hyperglycemia, 3 weeks before onset, mouse 3 (biol rep 3)

description:
Library name: 6872-JK-13
column name in og_gene_expected_count.annot.csv matches library name


title: MCF7_DMSO_rep1

description: Library name: MCF7_DMSO_rep1


title: WT rep2


title: MCF7_G1_sync_rep1

description: Library name: MCF7_G1_sync_rep1


title: Control-4hippo

city: Taichung

first: Ro-Lin

middle: Ro-Lin

last: Chang

state: --- Select One ---

address: 145 Xingda Road, South District.

department: Department of Life Sciences

country: Taiwan

institute: National Chung Hsing University

description: Library name: Control-4hippo

data_processing:
The bases with low quality and sequences from adapters in raw data were removed using program fastp (version 0.20.0). The filtered reads were aligned to the reference genomes using HISAT2 (version 2.1.0). The software featureCounts (version 2.0.1) in Subread package was applied for the quantification of the gene abundance.
Assembly: The filtered reads were aligned to the reference genomes using HISAT2 (version 2.1.0)
Supplementary files format and content: csv file includes normalized counts for each sample

organism: Rattus norvegicus

source_name: brain hippocampus

growth_protocol: All rats were housed in an air-conditioned room (22 ± 2°C, 50 ± 10% humidity) with an automatic 12-h light-dark cycle and were allowed free access to a regular rodent diet and water.

extract_protocol:
50 mg of tissue samples were utilized for total RNA extraction using TRIzol reagent. The quality of RNA samples was examined by Fragment Analyzer 5200, and their concentrations were determined by NanoDrop.
The RNA samples were subjected to the construction of the sequencing library using TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: Twelve 4-week-old male SD rats were used in this study. Following a two-week acclimation period with average weights approximating 200 g, eight rats were assigned to undergo HH exposure in a specialized hypobaric chamber, while the remaining rats, designated as the control (Ctrl) group (n=4), were maintained in a normoxic environment. The HH exposure initiated at ground level, ascending to a simulated altitude of 10,000 feet (ft) at 2,000 ft/min, followed by a 1-min maintenance period, thereafter ascending to a simulated altitude of 28,000 ft at 5,000 ft/min, maintaining this altitude for 5 min, and subsequently descending back to ground level at 5,000 ft/min. The aforementioned protocol was conducted at three-day intervals, culminating in a total of six cycles. One rat succumbed during HH exposure, while the other rats were sacrificed at 24 h (HH-24h group, n = 4) and 48 h (HH-48h group, n = 3) post-final HH exposure.

value: brain hippocampus

value: SD

tag: Sex

value: male

value: no treatment


title: Hypo-24h-2hippo

description: Library name: Hypo-24h-2hippo

value: HH exposure


title: NOD mouse, progressor to hyperglycemia, 5 weeks before onset, mouse 3 (biol rep 3)

description:
Library name: 6872-JK-8
column name in og_gene_expected_count.annot.csv matches library name

value: 5 weeks before onset


title: Control-2hippo

description: Library name: Control-2hippo


title: Hypo-48h-2hippo

description: Library name: Hypo-48h-2hippo


title: Hypo-48h-3hippo

description: Library name: Hypo-48h-3hippo


title: MCF7_DMSO_rep3

description: Library name: MCF7_DMSO_rep3


title: NOD mouse, progressor to hyperglycemia, 5 weeks before onset, mouse 5 (biol rep 5)

description:
Library name: 6872-JK-10
column name in og_gene_expected_count.annot.csv matches library name


title: Hypo-48h-1hippo

description: Library name: Hypo-48h-1hippo


title: Hypo-48h-3cortex

description: Library name: Hypo-48h-3cortex

source_name: brain cortex

value: brain cortex


title: NOD mouse, progressor to hyperglycemia, 5 weeks before onset, mouse 1 (biol rep 1)

description:
Library name: 6872-JK-6
column name in og_gene_expected_count.annot.csv matches library name


title: Hypo-48h-2cortex

description: Library name: Hypo-48h-2cortex


title: Hypo-24h-4hippo

description: Library name: Hypo-24h-4hippo


title: MCF7_rep1

description: Library name: MCF7_rep1


title: Hypo-48h-1cortex

description: Library name: Hypo-48h-1cortex


title: Hypo-24h-3hippo

description: Library name: Hypo-24h-3hippo


title: NOD mouse, progressor to hyperglycemia, 5 weeks before onset, mouse 4 (biol rep 4)

description:
Library name: 6872-JK-9
column name in og_gene_expected_count.annot.csv matches library name


title: Control-3hippo

description: Library name: Control-3hippo


title: NOD mouse, progressor to hyperglycemia, 5 weeks before onset, mouse 2 (biol rep 2)

description:
Library name: 6872-JK-7
column name in og_gene_expected_count.annot.csv matches library name


title: MCF7_DMSO_ATMi_rep3

description: Library name: MCF7_DMSO_ATMi_rep3


title: Control-1hippo

description: Library name: Control-1hippo


title: MCF7_dBET6_rep3

description: Library name: MCF7_dBET6_rep3


title: NOD mouse, progressor to hyperglycemia, 6 weeks of age, mouse 3 (biol rep 3)

description:
Library name: 6872-JK-3
column name in og_gene_expected_count.annot.csv matches library name


title: MCF7_DMSO_ATMi_rep2

description: Library name: MCF7_DMSO_ATMi_rep2


title: Hypo-24h-3cortex

description: Library name: Hypo-24h-3cortex


title: Hypo-24h-2cortex

description: Library name: Hypo-24h-2cortex


title: Control-3cortex

description: Library name: Control-3cortex


title: MCF7_dBET6_rep1

description: Library name: MCF7_dBET6_rep1


title: Control-2cortex

description: Library name: Control-2cortex


title: Control-1cortex

description: Library name: Control-1cortex


title: MCF7_dBET6_rep2

description: Library name: MCF7_dBET6_rep2


title: Hypo-24h-1hippo

description: Library name: Hypo-24h-1hippo


title: NOD mouse, progressor to hyperglycemia, 6 weeks of age, mouse 2 (biol rep 2)

description:
Library name: 6872-JK-2
column name in og_gene_expected_count.annot.csv matches library name


title: MCF7_DMSO_ATMi_rep1

description: Library name: MCF7_DMSO_ATMi_rep1


title: Control-4cortex

description: Library name: Control-4cortex


title: Fgfr3Ach KI mice

city: Suita

first: Noriyuki

last: Tsumaki

state: Select One

address: 2-2 Yamadaoka

department: Department of Biochemistry and Molecular Biology

country: Japan

institute: Osaka University, Graduate School of Medicine

library_source: transcriptomic single cell

data_processing:
Library preparation and the first processing of paired-end FASTQ files were performed according to the workflow outlined in the previously reported TAS-seq method (Shichino S, Ueha S, Hashimoto S, Ogawa T, Aoki H, Wu B, et al. TAS-Seq is a robust and sensitive amplification method for bead-based scRNA-seq. Communications biology. 2022;5(1):602.). Single-cell suspensions were subjected to cDNA synthesis using the BD Rhapsody Express Single-Cell Analysis System (BD Biosciences) and a BD Rhapsody Targeted & Abseq Reagent Kit (BD Biosciences). After reverse transcription, the resulting BD Rhapsody beads were treated with exonuclease I at 37°C for 60 min at 1,200 rpm on a Thermomixer C with Thermotop. The beads were then chilled on ice, whereafter the supernatant was removed. The beads were washed, resuspended, and stored at 4°C. During the washing step, bead-containing DNA LoBind tubes were replaced twice. cDNAs were amplified via the TAS-seq method at Immunogeneteqs Inc. (Noda City, Chiba, Japan) and sequenced with an Illumina Novaseq 6000 sequencer (Illumina, San Diego, CA, USA) using a Novaseq 6000 S4 Reagent Kit v1.0 or v1.5.  To assign cDNA reads to each transcript, bowtie2-indexes built from reference RNA sequences (cDNA and ncRNA fasta files from the Ensembl database; GRCm38.p6 Ensembl release 102) were used. The inflection point in the knee plot (total read count versus rank of the read count) was detected using the DropletUtils package in R 3.6.3 (https://cran.r-project.org/) from the resulting single-cell gene expression matrix files. Cells whose total read count exceeded the inflection point were considered valid. Demultiplexing of single cells via expression of TotalSeq streptavidin/anti-biotin was performed.
Assembly: GRCm38.p6 Ensembl release 102
Supplementary files format and content: tab-delimited text files include raw tag-count values for each sample
Supplementary files format and content: cell name description, each cell was named as follows: [hashtag ID]_[experiment ID]_[cell barcode].bam

molecule: polyA RNA

organism: Mus

source_name: Growth plate cartilage

extract_protocol:
The mice were sacrificed, and tissues around the growth plate cartilage in the proximal tibia were dissected. Samples were cut into small pieces (1~2 mm) and incubated in digestion medium (preparation medium with 0.2 mg/ml LiberaseTM [Roche, Basel, Switzerland] and 2 kU/ml DNase Ⅰ [Merck, Rahway, NJ, USA]) for 4 h. The samples were then filtered using a 70 μm cell strainer (BD Biosciences, Franklin Lakes, NJ, USA). For cell surface labeling, cell surface proteins were biotinylated as previously described36. Cells were resuspended in 1 ml of PBS supplemented with 1% fetal bovine serum (FBS) and 1 ng EZ-Link Sulfo-NHS-Biotin (Thermo Fisher Scientific, Waltham, MA, USA) for 10 min at 4°C and washed. Next, the cells were stained with 0.6 μg/ml of TotalSeq (A0951-A0954 [BioLegend, San Diego, CA, USA]) for 20 min at 4°C, washed, and resuspended in PBS supplemented with 10% FBS and 1 μM Sytox Blue Dead Cell Stain (Invitrogen, Waltham, MA, USA) for 5 min at room temperature.  PE-positive and Sytox blue-negative cells were sorted using a FACS Aria II flow cytometer (BD Bioscience) with BD FACS Diva 9.0.1 (BD Biosciences) and suspended in PBS supplemented with 20% FBS.
Library preparation and the first processing of paired-end fastq files were performed according to the workflow in the previously reported TAS-seq method (Shichino S, Ueha S, Hashimoto S, Ogawa T, Aoki H, Wu B, et al. TAS-Seq is a robust and sensitive amplification method for bead-based scRNA-seq. Communications biology. 2022;5(1):602.). In brief, sorted cells were used to synthesize cDNA with BD Rhapsody Express Single-Cell Analysis System (BD Biosciences). cDNAs were amplified by the TAS-seq method at Immunogeneteqs Inc. (Noda city, Chiba, Japan) and sequenced with an Illumina Novaseq 6000 sequencer (Illumina, San Diego, CA, USA), using a Novaseq 6000 S4 reagent kit v1.0 or v1.5.

value: Growth plate cartilage

value: 19- and 22-days old

value: wild type and Fgfr3Ach KI


title: NOD mouse, progressor to hyperglycemia, 6 weeks of age, mouse 1 (biol rep 1)

description:
Library name: 6872-JK-1
column name in og_gene_expected_count.annot.csv matches library name

value: scaffold immunological niche


title: primary tumor cell line from KC mice, with mPSC and macrophages, Arpc4 KO-2

description:
Library name: X2_8025_K
X2_8025_K

value: primary tumor cell line from KP mice

value: p48Cre/+; LSL-KrasG12D/+

value: Arpc4 knockout


title: Hypo-24h-4cortex

description: Library name: Hypo-24h-4cortex

value: WT


title: MCF7_CDK9i_rep3

description: Library name: MCF7_CDK9i_rep3

value: cell line