title: Slide2: S-19-17013 A1 & S-19-23239 B3 _02232023 | 008 | PanCK

description: Library name: DSP-1001660006909-E-C08


title: Slide2: S-19-17013 A1 & S-19-23239 B3 _02232023 | 007 | CD45

status: Public on Oct 07 2025

type: SRA

city: Dallas

first: Fabiana

last: Napolitano

state: TX

address: 6000 Harry Hines Blvd.

country: USA

institute: Simmons Comprehensive Cancer Center

description: Library name: DSP-1001660006909-E-C06

library_source: transcriptomic

data_processing:
FASTQ files were processed into digital count conversion files using Nanostring’s GeoMx NGS Pipeline software.
Assembly: hg38
Supplementary files format and content: Normalized count file in csv format
Library strategy: Spatial Transcriptomics

molecule: total RNA

organism: Homo sapiens

source_name: breast cancer

extract_protocol:
FFPE tumor sections (5-µm) were mounted on charged slides
GeoMx NGS libraries were prepared following the manufacturer's protocol.

tag: tissue

value: breast cancer

tag: cell type

value: ED-sensitive

tag: treatment

value: letrozole


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description: Library name: DSP-1001660014850-C-C11

value: ED-resistant


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description: Library name: DSP-1001660014849-B-F03


title: Slide 10 ( SU19-33212 G1 & SU20-06925 C20) | 008 | PanCK

description: Library name: DSP-1001660014849-B-G08


title: Slide 10 ( SU19-33212 G1 & SU20-06925 C20) | 001 | CD45

description: Library name: DSP-1001660014849-B-F01


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 021 | CD45

description: Library name: DSP-1001660014849-B-E10


title: Slide 10 ( SU19-33212 G1 & SU20-06925 C20) | 001 | PanCK

description: Library name: DSP-1001660014849-B-E12


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 021 | PanCK

description: Library name: DSP-1001660014849-B-E09


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 019 | CD45

description: Library name: DSP-1001660014849-B-E04


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 020 | REST

description: Library name: DSP-1001660014849-B-E08


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 020 | PanCK

description: Library name: DSP-1001660014849-B-E06


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 019 | PanCK

description: Library name: DSP-1001660014849-B-E03


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 019 | REST

description: Library name: DSP-1001660014849-B-E05


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 017 | REST

description: Library name: DSP-1001660014849-B-D12


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 017 | PanCK

description: Library name: DSP-1001660014849-B-D10


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 018 | REST

description: Library name: DSP-1001660014849-B-E02


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 016 | REST

description: Library name: DSP-1001660014849-B-D09


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 018 | PanCK

description: Library name: DSP-1001660014849-B-E01


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 017 | CD45

description: Library name: DSP-1001660014849-B-D11


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 016 | PanCK

description: Library name: DSP-1001660014849-B-D08


title: postSens_65

description: Library name: 2101-LF-97

data_processing:
Alignment, quantification, and differential analysis were performed using the QBRC_BulkRnaSeqDE pipeline
Assembly: GRCh38
Supplementary files format and content: csv file includes raw count for each Sample

extract_protocol:
RNA was extracted from 4-8 10-μm FFPE tumor sections using the Promega Maxwell® 16 LEV RNA FFPE Purification Kit and instrument ,according to the manufacturer’s instructions
RNA libraries were prepared using KAPA Library Quantification Kit for Illumina Sequencing platforms, pooled and normalized to 2 nM, and denatured using 0.2 N NaOH prior to sequencing

value: aromatase inhibitor


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 015 | CD45

description: Library name: DSP-1001660014849-B-D06


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 015 | PanCK

description: Library name: DSP-1001660014849-B-D05


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 015 | REST

description: Library name: DSP-1001660014849-B-D07


title: postSens_64

description: Library name: 2101-LF-95


title: preSens_65

description: Library name: 2101-LF-94


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 014 | REST

description: Library name: DSP-1001660014849-B-D04


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 021 | REST

description: Library name: DSP-1001660014849-B-E11


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 020 | CD45

description: Library name: DSP-1001660014849-B-E07


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 014 | CD45

description: Library name: DSP-1001660014849-B-D03


title: preSens_64

description: Library name: 2101-LF-90


title: postSens_62

description: Library name: 2101-LF-89


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 014 | PanCK

description: Library name: DSP-1001660014849-B-D02


title: preSens_63

description: Library name: 2101-LF-88


title: postSens_61

description: Library name: 2101-LF-83


title: preRest_20

description: Library name: 2101-LF-84


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 012 | REST

description: Library name: DSP-1001660014849-B-C11


title: postRest_23

description: Library name: 2101-LF-85


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 013 | CD45

description: Library name: DSP-1001660014849-B-C12


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 012 | PanCK

description: Library name: DSP-1001660014849-B-C09


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 012 | CD45

description: Library name: DSP-1001660014849-B-C10


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 011 | PanCK

description: Library name: DSP-1001660014849-B-C06


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 011 | REST

description: Library name: DSP-1001660014849-B-C08


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 011 | CD45

description: Library name: DSP-1001660014849-B-C07


title: postSens_60

description: Library name: 2101-LF-81


title: preSens_61

description: Library name: 2101-LF-80


title: postRest_22

description: Library name: 2101-LF-8


title: preSens_66

description: Library name: 2101-LF-96


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 010 | REST

description: Library name: DSP-1001660014849-B-C05


title: postSens_63

description: Library name: 2101-LF-91


title: postRest_21

description: Library name: 2101-LF-79


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 010 | CD45

description: Library name: DSP-1001660014849-B-C04


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 009 | REST

description: Library name: DSP-1001660014849-B-C03


title: preSens_60

description: Library name: 2101-LF-76


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 009 | CD45

description: Library name: DSP-1001660014849-B-C02


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 013 | REST

description: Library name: DSP-1001660014849-B-D01


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 009 | PanCK

description: Library name: DSP-1001660014849-B-C01


title: preSens_59

description: Library name: 2101-LF-70


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 008 | REST

description: Library name: DSP-1001660014849-B-B12


title: postRest_20

description: Library name: 2101-LF-7


title: preSens_62

description: Library name: 2101-LF-82


title: postSens_59

description: Library name: 2101-LF-69


title: preSens_58

description: Library name: 2101-LF-68


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 007 | REST

description: Library name: DSP-1001660014849-B-B09


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 008 | PanCK

description: Library name: DSP-1001660014849-B-B10


title: postRest_19

description: Library name: 2101-LF-67


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 007 | CD45

description: Library name: DSP-1001660014849-B-B08


title: postSens_58

description: Library name: 2101-LF-65


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 008 | CD45

description: Library name: DSP-1001660014849-B-B11


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 007 | PanCK

description: Library name: DSP-1001660014849-B-B07


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 006 | REST

description: Library name: DSP-1001660014849-B-B06


title: preRest_19

description: Library name: 2101-LF-78


title: postRest_18

description: Library name: 2101-LF-6


title: preSens_57

description: Library name: 2101-LF-64


title: postSens_57

description: Library name: 2101-LF-59


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 006 | CD45

description: Library name: DSP-1001660014849-B-B05


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 006 | PanCK

description: Library name: DSP-1001660014849-B-B04


title: preSens_56

description: Library name: 2101-LF-58


title: postSens_56

description: Library name: 2101-LF-55


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 005 | REST

description: Library name: DSP-1001660014849-B-B03


title: preSens_55

description: Library name: 2101-LF-54


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 004 | PanCK

description: Library name: DSP-1001660014849-B-A11


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 005 | PanCK

description: Library name: DSP-1001660014849-B-B02


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 004 | REST

description: Library name: DSP-1001660014849-B-B01


title: postSens_54

description: Library name: 2101-LF-51


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 004 | CD45

description: Library name: DSP-1001660014849-B-A12


title: preSens_54

description: Library name: 2101-LF-52


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 003 | REST

description: Library name: DSP-1001660014849-B-A10


title: preSens_53

description: Library name: 2101-LF-50


title: preRest_18

description: Library name: 2101-LF-66


title: postSens_52

description: Library name: 2101-LF-49


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 003 | PanCK

description: Library name: DSP-1001660014849-B-A08


title: postSens_53

description: Library name: 2101-LF-5


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 002 | CD45

description: Library name: DSP-1001660014849-B-A06


title: postSens_55

description: Library name: 2101-LF-53


title: postSens_51

description: Library name: 2101-LF-47


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 002 | PanCK

description: Library name: DSP-1001660014849-B-A05


title: preSens_52

description: Library name: 2101-LF-48


title: preSens_51

description: Library name: 2101-LF-46


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 003 | CD45

description: Library name: DSP-1001660014849-B-A09


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 001 | REST

description: Library name: DSP-1001660014849-B-A04


title: preSens_50

description: Library name: 2101-LF-44


title: postSens_50

description: Library name: 2101-LF-45


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 001 | PanCK

description: Library name: DSP-1001660014849-B-A02


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 001 | CD45

description: Library name: DSP-1001660014849-B-A03


title: postSens_49

description: Library name: 2101-LF-43


title: preSens_49

description: Library name: 2101-LF-42


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 017 | CD45

description: Library name: DSP-1001660014848-A-H03


title: postSens_48

description: Library name: 2101-LF-4


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 017 | PanCK

description: Library name: DSP-1001660014848-A-H02


title: postSens_47

description: Library name: 2101-LF-37


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 016 | CD45

description: Library name: DSP-1001660014848-A-G12


title: Slide 9 ( SU19-03323 D16 & SU20-16111 I3)_R | 002 | REST

description: Library name: DSP-1001660014849-B-A07


title: postSens_46

description: Library name: 2101-LF-35


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 015 | REST

description: Library name: DSP-1001660014848-A-G10


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 016 | PanCK

description: Library name: DSP-1001660014848-A-G11


title: postRest_17

description: Library name: 2101-LF-3


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 015 | CD45

description: Library name: DSP-1001660014848-A-G09


title: preSens_47

description: Library name: 2101-LF-34


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 015 | PanCK

description: Library name: DSP-1001660014848-A-G08


title: postRest_16

description: Library name: 2101-LF-29


title: preRest_17

description: Library name: 2101-LF-28


title: preSens_46

description: Library name: 2101-LF-26


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 014 | CD45

description: Library name: DSP-1001660014848-A-G06


title: postSens_45

description: Library name: 2101-LF-27


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 014 | PanCK

description: Library name: DSP-1001660014848-A-G05


title: postSens_44

description: Library name: 2101-LF-25


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 017 | REST

description: Library name: DSP-1001660014848-A-H04


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 013 | REST

description: Library name: DSP-1001660014848-A-G04


title: postSens_43

description: Library name: 2101-LF-248


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 013 | CD45

description: Library name: DSP-1001660014848-A-G03


title: postRest_15

description: Library name: 2101-LF-249


title: preSens_45

description: Library name: 2101-LF-247


title: preSens_48

description: Library name: 2101-LF-36


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 012 | CD45

description: Library name: DSP-1001660014848-A-F12


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 013 | PanCK

description: Library name: DSP-1001660014848-A-G02


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 012 | REST

description: Library name: DSP-1001660014848-A-G01


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 016 | REST

description: Library name: DSP-1001660014848-A-H01


title: postSens_42

description: Library name: 2101-LF-243


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 012 | PanCK

description: Library name: DSP-1001660014848-A-F11


title: preRest_16

description: Library name: 2101-LF-246


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 014 | REST

description: Library name: DSP-1001660014848-A-G07


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 011 | REST

description: Library name: DSP-1001660014848-A-F10


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 011 | PanCK

description: Library name: DSP-1001660014848-A-F08


title: postSens_40

description: Library name: 2101-LF-241


title: postSens_39

description: Library name: 2101-LF-240


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 011 | CD45

description: Library name: DSP-1001660014848-A-F09


title: preSens_44

description: Library name: 2101-LF-24


title: postSens_41

description: Library name: 2101-LF-242


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 010 | REST

description: Library name: DSP-1001660014848-A-F07


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 010 | CD45

description: Library name: DSP-1001660014848-A-F06


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 010 | PanCK

description: Library name: DSP-1001660014848-A-F05


title: preSens_43

description: Library name: 2101-LF-236


title: preSens_42

description: Library name: 2101-LF-235


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 009 | REST

description: Library name: DSP-1001660014848-A-F04


title: postSens_38

description: Library name: 2101-LF-239


title: preSens_41

description: Library name: 2101-LF-234


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 009 | PanCK

description: Library name: DSP-1001660014848-A-F03


title: preRest_15

description: Library name: 2101-LF-232


title: preSens_40

description: Library name: 2101-LF-233


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 008 | CD45

description: Library name: DSP-1001660014848-A-F01


title: preSens_39

description: Library name: 2101-LF-231


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 008 | REST

description: Library name: DSP-1001660014848-A-F02


title: postRest_14

description: Library name: 2101-LF-23


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 007 | REST

description: Library name: DSP-1001660014848-A-E12


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 006 | REST

description: Library name: DSP-1001660014848-A-E10


title: postSens_37

description: Library name: 2101-LF-227


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 007 | PanCK

description: Library name: DSP-1001660014848-A-E11


title: postRest_13

description: Library name: 2101-LF-229


title: preSens_38

description: Library name: 2101-LF-226


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 006 | PanCK

description: Library name: DSP-1001660014848-A-E08


title: postSens_36

description: Library name: 2101-LF-225


title: preSens_37

description: Library name: 2101-LF-224


title: preSens_36

description: Library name: 2101-LF-223


title: postSens_35

description: Library name: 2101-LF-220


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 006 | CD45

description: Library name: DSP-1001660014848-A-E09


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 005 | CD45

description: Library name: DSP-1001660014848-A-E06


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 005 | REST

description: Library name: DSP-1001660014848-A-E07


title: preRest_14

description: Library name: 2101-LF-22


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 005 | PanCK

description: Library name: DSP-1001660014848-A-E05


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 004 | CD45

description: Library name: DSP-1001660014848-A-E03


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 004 | PanCK

description: Library name: DSP-1001660014848-A-E02


title: preSens_35

description: Library name: 2101-LF-218


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 003 | REST

description: Library name: DSP-1001660014848-A-E01


title: postSens_33

description: Library name: 2101-LF-216


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 003 | CD45

description: Library name: DSP-1001660014848-A-D12


title: Parental LU65, SR-4835, biol rep 2

city: Tampa

first: Eric

last: Haura

state: FL

address: 12902 Magnolia Drive

institute: H. Lee Moffitt Cancer Center and Research Institute, Inc

description: Library name: LU65_SR4835_2

data_processing:
Read adapters were detected using BBMerge (version 37.88) and removed with Cutadapt (version 1.3.1).
Processed reads were aligned to human genome GRCh37 using STAR (version 2.5.3a).
Gene expression was evaluated as read count at gene level by RSEM (version 1.3.0) and GENCODE gene model (v30).
Gene expression data was normalized across all samples, and differential gene expression was evaluated using DEseq2 by pairwise comparison between SR-4835- and DMSO-treated samples within each parental or sotorasib-resistant model, or between DMSO-treated parental and sotorasib-resistant models within each cell line.
Assembly: GRCh37
Supplementary files format and content: read_counts_raw.tsv

source_name: Lung

growth_protocol: Parental NCI-H358 and LU65 cells were maintained in RPMI supplemented with 10% FBS (Gibco) and 1% Antibiotic-Antimycotic (Gibco) (complete RPMI) in a humidified atmosphere with 5% CO2 at 37C. Sotorasib-resistant NCI-H358 cells were maintained in complete media supplemented with 400 nM AMG-510 (Selleck Chemicals). Sotorasib-resistant LU65 cells were maintained in complete media supplemented with 1 µM AMG-510 (Selleck Chemicals).

extract_protocol:
Homogenized lysates from three independent replicates were thawed and extracted using the RNeasy Mini kit (Qiagen) with on-column DNase I digestion (Qiagen) according to the manufacturer's protocol.
RNA content was quantified using a Qubit fluorometer, and 100 ng of total RNA was used to generate cDNA using the NuGEN Universal RNA-Seq Library Preparation Kit (Tecan Genomics). Quality control on prepared libraries was performed by TapeStation size assessment and quantification using the Kapa Library Quantification Kit (Roche).

treatment_protocol: Cells were seeded at approximately 60% confluence and allowed to adhere overnight in drug-free complete RPMI. The following day, fresh complete RPMI supplemented with 0.1% DMSO or 100 nM SR-4835 was added. 24 hours after treatment, cells were washed 1X in PBS, lysed in RLT buffer (Qiagen) and homogenized using a Qiashredder column (Qiagen). Homogenized lysates were stored at -80C prior to extraction.

value: Lung

tag: cell line

value: Parental LU65

value: NSCLC

tag: genotype


title: postSens_34

description: Library name: 2101-LF-219


title: postSens_32

description: Library name: 2101-LF-215


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 003 | PanCK

description: Library name: DSP-1001660014848-A-D11


title: Parental LU65, SR-4835, biol rep 1

description: Library name: LU65_SR4835_1


title: postSens_31

description: Library name: 2101-LF-21


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 002 | REST

description: Library name: DSP-1001660014848-A-D10


title: postSens_30

description: Library name: 2101-LF-208


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 002 | CD45

description: Library name: DSP-1001660014848-A-D09


title: Parental LU65, DMSO control, biol rep 3

description: Library name: LU65_DMSO_3


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 002 | PanCK

description: Library name: DSP-1001660014848-A-D08


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 004 | REST

description: Library name: DSP-1001660014848-A-E04


title: postSens_29

description: Library name: 2101-LF-206


title: Parental LU65, DMSO control, biol rep 2

description: Library name: LU65_DMSO_2


title: Sotorasib-resistant LU65, SR-4835, biol rep 3

description: Library name: LU65-AMGR_SR4835_3

value: Sotorasib-resistant LU65


title: Sotorasib-resistant LU65, SR-4835, biol rep 2

description: Library name: LU65-AMGR_SR4835_2


title: preSens_33

description: Library name: 2101-LF-204


title: postSens_28

description: Library name: 2101-LF-203


title: Slide 4 (SU20-19889 B1 & SU20-26359 G4) | 016 | REST

description: Library name: DSP-1001660014848-A-D05


title: Sotorasib-resistant LU65, SR-4835, biol rep 1

description: Library name: LU65-AMGR_SR4835_1


title: postSens_27

description: Library name: 2101-LF-201


title: Slide 4 (SU20-19889 B1 & SU20-26359 G4) | 016 | PanCK

description: Library name: DSP-1001660014848-A-D04


title: Parental LU65, SR-4835, biol rep 3

description: Library name: LU65_SR4835_3


title: preSens_32

description: Library name: 2101-LF-200


title: Slide 4 (SU20-19889 B1 & SU20-26359 G4) | 015 | REST

description: Library name: DSP-1001660014848-A-D03


title: Slide 4 (SU20-19889 B1 & SU20-26359 G4) | 015 | CD45

description: Library name: DSP-1001660014848-A-D02


title: preSens_31

description: Library name: 2101-LF-20


title: Slide 4 (SU20-19889 B1 & SU20-26359 G4) | 015 | PanCK

description: Library name: DSP-1001660014848-A-D01


title: postSens_26

description: Library name: 2101-LF-2


title: Sotorasib-resistant LU65, DMSO control, biol rep 1

description: Library name: LU65-AMGR_DMSO_1


title: Parental LU65, DMSO control, biol rep 1

description: Library name: LU65_DMSO_1


title: Parental H358, SR-4835, biol rep 3

description: Library name: H358_SR4835_3

value: Parental NCI-H358


title: preSens_34

description: Library name: 2101-LF-207


title: Slide 4 (SU20-19889 B1 & SU20-26359 G4) | 014 | REST

description: Library name: DSP-1001660014848-A-C12


title: Slide 4 (SU20-19889 B1 & SU20-26359 G4) | 014 | CD45

description: Library name: DSP-1001660014848-A-C11


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 001 | REST

description: Library name: DSP-1001660014848-A-D07


title: Slide 6 (SU21-05016 A1 & SU21-10165 G1) | 001 | PanCK

description: Library name: DSP-1001660014848-A-D06


title: preSens_30

description: Library name: 2101-LF-198


title: Parental H358, SR-4835, biol rep 2

description: Library name: H358_SR4835_2


title: Parental H358, SR-4835, biol rep 1

description: Library name: H358_SR4835_1


title: preSens_29

description: Library name: 2101-LF-197


title: Parental H358, DMSO control, biol rep 3

description: Library name: H358_DMSO_3


title: Slide 4 (SU20-19889 B1 & SU20-26359 G4) | 014 | PanCK

description: Library name: DSP-1001660014848-A-C10


title: Slide 4 (SU20-19889 B1 & SU20-26359 G4) | 013 | REST

description: Library name: DSP-1001660014848-A-C09


title: Parental H358, DMSO control, biol rep 2

description: Library name: H358_DMSO_2


title: Sotorasib-resistant LU65, DMSO control, biol rep 3

description: Library name: LU65-AMGR_DMSO_3


title: postSens_24

description: Library name: 2101-LF-196


title: preSens_28

description: Library name: 2101-LF-195


title: postSens_23

description: Library name: 2101-LF-194


title: Slide 4 (SU20-19889 B1 & SU20-26359 G4) | 013 | CD45

description: Library name: DSP-1001660014848-A-C08


title: Parental H358, DMSO control, biol rep 1

description: Library name: H358_DMSO_1


title: Sotorasib-resistant LU65, DMSO control, biol rep 2

description: Library name: LU65-AMGR_DMSO_2


title: Slide 4 (SU20-19889 B1 & SU20-26359 G4) | 013 | PanCK

description: Library name: DSP-1001660014848-A-C07


title: Sotorasib-resistant H358, SR-4835, biol rep 3

description: Library name: H358-AMGR_SR4835_3

value: Sotorasib-resistant NCI-H358


title: Slide 4 (SU20-19889 B1 & SU20-26359 G4) | 012 | REST

description: Library name: DSP-1001660014848-A-C06


title: postRest_12

description: Library name: 2101-LF-192


title: Sotorasib-resistant H358, SR-4835, biol rep 2

description: Library name: H358-AMGR_SR4835_2


title: postSens_25

description: Library name: 2101-LF-199


title: Sotorasib-resistant H358, SR-4835, biol rep 1

description: Library name: H358-AMGR_SR4835_1


title: preRest_13

description: Library name: 2101-LF-191


title: Slide 4 (SU20-19889 B1 & SU20-26359 G4) | 011 | REST

description: Library name: DSP-1001660014848-A-C04


title: Slide 4 (SU20-19889 B1 & SU20-26359 G4) | 011 | PanCK

description: Library name: DSP-1001660014848-A-C03


title: postRest_11

description: Library name: 2101-LF-19


title: postSens_22

description: Library name: 2101-LF-190


title: Sotorasib-resistant H358, DMSO control, biol rep 1

description: Library name: H358-AMGR_DMSO_1


title: preSens_26

description: Library name: 2101-LF-189


title: postSens_21

description: Library name: 2101-LF-188


title: Slide 4 (SU20-19889 B1 & SU20-26359 G4) | 010 | REST

description: Library name: DSP-1001660014848-A-C02


title: preSens_25

description: Library name: 2101-LF-187


title: Sotorasib-resistant H358, DMSO control, biol rep 2

description: Library name: H358-AMGR_DMSO_2


title: Slide 4 (SU20-19889 B1 & SU20-26359 G4) | 009 | REST

description: Library name: DSP-1001660014848-A-B11


title: preSens_24

description: Library name: 2101-LF-185


title: preSens_27

description: Library name: 2101-LF-193


title: Slide 4 (SU20-19889 B1 & SU20-26359 G4) | 009 | CD45

description: Library name: DSP-1001660014848-A-B10


title: Slide 4 (SU20-19889 B1 & SU20-26359 G4) | 009 | PanCK

description: Library name: DSP-1001660014848-A-B09


title: preRest_12

description: Library name: 2101-LF-183


title: preSens_23

description: Library name: 2101-LF-181


title: Sotorasib-resistant H358, DMSO control, biol rep 3

description: Library name: H358-AMGR_DMSO_3


title: Slide 4 (SU20-19889 B1 & SU20-26359 G4) | 008 | REST

description: Library name: DSP-1001660014848-A-B08


title: postSens_20

description: Library name: 2101-LF-180


title: Slide 4 (SU20-19889 B1 & SU20-26359 G4) | 012 | CD45

description: Library name: DSP-1001660014848-A-C05


title: Slide 4 (SU20-19889 B1 & SU20-26359 G4) | 008 | CD45

description: Library name: DSP-1001660014848-A-B07


title: preRest_11

description: Library name: 2101-LF-18


title: Slide 4 (SU20-19889 B1 & SU20-26359 G4) | 010 | PanCK

description: Library name: DSP-1001660014848-A-B12


title: preSens_22

description: Library name: 2101-LF-179


title: Slide 4 (SU20-19889 B1 & SU20-26359 G4) | 007 | REST

description: Library name: DSP-1001660014848-A-B05


title: Slide 4 (SU20-19889 B1 & SU20-26359 G4) | 007 | CD45

description: Library name: DSP-1001660014848-A-B04


title: preSens_21

description: Library name: 2101-LF-177


title: postSens_19

description: Library name: 2101-LF-178


title: Slide 4 (SU20-19889 B1 & SU20-26359 G4) | 010 | CD45

description: Library name: DSP-1001660014848-A-C01


title: postSens_18

description: Library name: 2101-LF-176


title: Slide 4 (SU20-19889 B1 & SU20-26359 G4) | 007 | PanCK

description: Library name: DSP-1001660014848-A-B03


title: Slide 4 (SU20-19889 B1 & SU20-26359 G4) | 006 | REST

description: Library name: DSP-1001660014848-A-B02


title: preSens_20

description: Library name: 2101-LF-175


title: Slide 4 (SU20-19889 B1 & SU20-26359 G4) | 006 | PanCK

description: Library name: DSP-1001660014848-A-B01


title: postSens_17

description: Library name: 2101-LF-174


title: Slide 4 (SU20-19889 B1 & SU20-26359 G4) | 005 | REST

description: Library name: DSP-1001660014848-A-A12


title: Slide 4 (SU20-19889 B1 & SU20-26359 G4) | 004 | REST

description: Library name: DSP-1001660014848-A-A10


title: preSens_18

description: Library name: 2101-LF-171


title: Slide 4 (SU20-19889 B1 & SU20-26359 G4) | 004 | PanCK

description: Library name: DSP-1001660014848-A-A08


title: postSens_15

description: Library name: 2101-LF-17


title: preSens_19

description: Library name: 2101-LF-173


title: Slide 4 (SU20-19889 B1 & SU20-26359 G4) | 005 | PanCK

description: Library name: DSP-1001660014848-A-A11


title: postSens_16

description: Library name: 2101-LF-172


title: Slide 4 (SU20-19889 B1 & SU20-26359 G4) | 003 | REST

description: Library name: DSP-1001660014848-A-A07


title: preRest_10

description: Library name: 2101-LF-168


title: Slide 4 (SU20-19889 B1 & SU20-26359 G4) | 008 | PanCK

description: Library name: DSP-1001660014848-A-B06


title: Slide 4 (SU20-19889 B1 & SU20-26359 G4) | 002 | PanCK

description: Library name: DSP-1001660014848-A-A04


title: postSens_13

description: Library name: 2101-LF-165


title: postRest_10

description: Library name: 2101-LF-169


title: Slide 4 (SU20-19889 B1 & SU20-26359 G4) | 001 | REST

description: Library name: DSP-1001660014848-A-A03


title: Slide 4 (SU20-19889 B1 & SU20-26359 G4) | 003 | PanCK

description: Library name: DSP-1001660014848-A-A06


title: preSens_16

description: Library name: 2101-LF-164


title: Slide 4 (SU20-19889 B1 & SU20-26359 G4) | 001 | PanCK

description: Library name: DSP-1001660014848-A-A02


title: postSens_12

description: Library name: 2101-LF-161


title: preSens_15

description: Library name: 2101-LF-160


title: preSens_14

description: Library name: 2101-LF-16


title: postSens_11

description: Library name: 2101-LF-159


title: postSens_10

description: Library name: 2101-LF-157


title: preSens_13

description: Library name: 2101-LF-158


title: preSens_12

description: Library name: 2101-LF-156


title: postRest_9

description: Library name: 2101-LF-155


title: Slide 4 (SU20-19889 B1 & SU20-26359 G4) | 004 | CD45

description: Library name: DSP-1001660014848-A-A09


title: preSens_17

description: Library name: 2101-LF-170


title: preRest_9

description: Library name: 2101-LF-154


title: preSens_11

description: Library name: 2101-LF-152


title: postSens_9

description: Library name: 2101-LF-153


title: postSens_14

description: Library name: 2101-LF-167


title: Slide 4 (SU20-19889 B1 & SU20-26359 G4) | 002 | REST

description: Library name: DSP-1001660014848-A-A05


title: postSens_8

description: Library name: 2101-LF-147


title: postRest_8

description: Library name: 2101-LF-15


title: postSens_7

description: Library name: 2101-LF-14


title: postRest_6

description: Library name: 2101-LF-135


title: preRest_6

description: Library name: 2101-LF-126


title: postRest_4

description: Library name: 2101-LF-127


title: preRest_8

description: Library name: 2101-LF-134


title: preRest_7

description: Library name: 2101-LF-130


title: preRest_5

description: Library name: 2101-LF-124


title: preSens_10

description: Library name: 2101-LF-146


title: postRest_5

description: Library name: 2101-LF-131


title: preRest_4

description: Library name: 2101-LF-120


title: postRest_3

description: Library name: 2101-LF-121


title: preSens_9

description: Library name: 2101-LF-125


title: postSens_5

description: Library name: 2101-LF-12


title: preSens_8

description: Library name: 2101-LF-119


title: preSens_6

description: Library name: 2101-LF-113


title: preRest_3

description: Library name: 2101-LF-114


title: preSens_7

description: Library name: 2101-LF-115


title: preRest_2

description: Library name: 2101-LF-112


title: preRest_1

description: Library name: 2101-LF-111


title: postSens_4

description: Library name: 2101-LF-110


title: preSens_5

description: Library name: 2101-LF-109


title: postRest_7

description: Library name: 2101-LF-149


title: preSens_4

description: Library name: 2101-LF-108


title: postSens_3

description: Library name: 2101-LF-107


title: preSens_2

description: Library name: 2101-LF-102


title: preSens_3

description: Library name: 2101-LF-106


title: postSens_6

description: Library name: 2101-LF-13


title: preSens_1

description: Library name: 2101-LF-100


title: postSens_1

description: Library name: 2101-LF-101


title: postSens_2

description: Library name: 2101-LF-103


title: postRest_2

description: Library name: 2101-LF-10


title: postRest_1

description: Library name: 2101-LF-1


title: WT Bd21-3 leaf developmental zone, protoplasted, replicate 3

status: Public on Sep 23 2025

city: BERN

first: Michael

middle: T

last: Raissig

address: Altenbergrain 21

department: Institute of Plant Sciences

country: Switzerland

institute: University of Bern

description: Library name: Protoplasted_3

data_processing:
pre-processing of bulk RNASeq data was done on usegalaxy.org
datasets were quality checked with FastQC
transcriptomes were mapped to the Bd21-3 v1.1 genome using bowtie2
read counts were summarized in R using summarizeOverlaps of the GenomicAlignments package, differentially expressed genes were called using DESeq2.
Assembly: Brachypodium distachyon Bd21-3 v1.1
Supplementary files format and content: csv file including raw counts, RPK and TPM values

molecule: polyA RNA

organism: Brachypodium distachyon

source_name: leaf developmental zone

growth_protocol: soil-grown plants

extract_protocol:
RNA extraction was performed with the RNeasy micro kit (Qiagen) following the manufacturer’s instructions
Extracted RNA was quality checked with an Agilent 2100 Bioanalyzer, NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) using NEBNext Multiplex Oligos for Illumina for sample indexing was used to prepare sequencing libraries

treatment_protocol: protoplasts were generated by digesting the tissue with Macerozyme R10 and Cellulase Onozuka RS

value: leaf developmental zone

value: WT Bd21-3

value: non-protoplasted


title: WT Bd21-3 leaf developmental zone, protoplasted, replicate 1

description: Library name: Protoplasted_1


title: WT Bd21-3 leaf developmental zone, protoplasted, replicate 2

description: Library name: Protoplasted_2


title: WT Bd21-3 leaf developmental zone, collected in 2022, 1st sequencing run (merged with WT2022-2 in Cellranger)

description:
Library name: WT2022-1
10X Genomics

library_source: transcriptomic single cell

data_processing:
Pre-processing (de-multiplexing, barcode processing, mapping, gene counting) was done with the Cellranger software (v7.0.1, 10X Genomics, https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: Brachypodium distachyon Bd21-3 v1.2
Supplementary files format and content: Tab-separated values files and matrix files; if merged, the files are linked to the correponding 1st sequencing sample records.

growth_protocol: soil-grown plants, 3 weeks old

extract_protocol:
Tissue was digested with macerozyme R10 and Cellulase Onozuka RS and subsequently washed to obtain protoplasts
GEM wells were prepared to encapsule protoplasts in droplets, cDNA was extracted per protoplast and libraries were prepared according to the guidelines provided by 10X Genomics (single cell 3' version 3)

value: protoplasted


title: sid leaf developmental zone, collected in 2021

description:
Library name: sid2021
10X Genomics


title: WT Bd21-3 vegetative shoot apex and leaf primordia, collected in 2023 (17.05.)

description:
Library name: WT2023-17-05
10X Genomics


title: WT Bd21-3 vegetative shoot apex and leaf primordia, collected in 2023 (16.05.)

description:
Library name: WT2023-16-05
10X Genomics


title: sid leaf developmental zone, collected in 2022, 1st sequencing run (merged with sid2022-2 in Cellranger)

description:
Library name: sid2022-1
10X Genomics


title: WT Bd21-3 leaf developmental zone, non-protoplasted, replicate 3

description: Library name: Non-protoplasted_3


title: WT Bd21-3 leaf developmental zone, non-protoplasted, replicate 2

description: Library name: Non-protoplasted_2


title: WT Bd21-3 leaf developmental zone, non-protoplasted, replicate 1

description: Library name: Non-protoplasted_1


title: WT Bd21-3 leaf developmental zone, collected in 2022, 2nd sequencing run (merged with WT2022-1 in Cellranger)

description:
Library name: WT2022-2
10X Genomics
WT2022_barcodes.tsv
WT2022_matrix.mtx


title: WT Bd21-3 leaf developmental zone, protoplasted, collected in 2024 (18.09.)

description:
Library name: WT2024-3
10X Genomics


title: Cryoablation day 7 Xenium

status: Public on Sep 22 2025

type: RNA

city: Würzburg

first: Andy

middle: Shing Fung

last: Chan

address: Gebäude E6,, Versbacher Str. 9

country: Germany

institute: Institute for Systems Immunology, University of Würzburg

description: formalin-fixed paraffin-embedded tissue sections, in situ sequencing

hyb_protocol: "Gene panel targeting 475 genes was applied to the sample in 10nM, which targeted mRNA molecules of the 475 target genes. In addition to the gene panel, two negative controls were added, to assess non-specific binding and ensure the signals were from binding to RNA but not to genomic DNA. Hybridization was performed at 50°C overnight, followed by a washing step to remove unhybridized probes. Samples were then ligated at 37°C for 2h, for annealing of rolling circle amplification (RCA) primer, followed by circularized probe amplification at 4°C for 1h, and 37°C for 2h, resulting in amplification of the gene-specific barcode for each RNA binding probe, enhancing the signal-to-noise ratio. Background fluorescence was chemically quenched.

scan_protocol: Sections were placed in an imaging cassette and loaded onto the Xenium Analyzer instrument combining a high numerical aperture and a fast area scan camera with a low read noise sensor (achieving a lateral resolution of 200nm per pixel). Images were acquired in sequential hybridization-imaging cycles. In each cycle, unique fluorescently labeled secondary probes targeting RCA-amplified probe-RNA complexes were hybridized, and visualized in combination with 4′,6-diamidino-2-phenylindole (DAPI) staining. Stained samples were imaged, followed by stripping off the secondary probe and starting of another round of hybridization and imaging. Z-stacks were acquired at a 0.75μm step size across the tissue thickness.

data_processing: Images were pre-processed with the built-in pipeline, where low quality signals were filtered out, and the identities of transcripts were decoded using a Xenium codebook. For quality scoring, a Phred-style Q-Score was assigned to each decoded transcript, reflecting confidence in transcript identity. Q-Scores were calibrated using negative control codewords, probes targeting non-biological sequences, and unassigned codewords. Only transcripts with a Q-Score ≥20 were included in downstream analyses.   Multimodal cell segmentation was also performed by the Xenium in-built pipeline where cells were segmented based on nuclear (DAPI), cell boundary and interior RNA signals.

organism: Mus musculus

source_name: heart left ventricles

label_protocol: Barcode oligo-conjugated antibodies (ATP1A1, E-Cadherin, CD45, SMA, Vimentin and 18S rRNA marker) labeling the cell boundaries and interior proteins were added to label cellular structures.

extract_protocol: All experimental steps followed the guideline of the Xenium workflow. Briefly, 5μm formalin-fixed paraffin-embedded tissue sections (transverse plane of the LV) were mounted on a Xenium slide within the desired imaging region. The mRNA was exposed by deparaffinization and permeabilization.

value: Cryoablation


title: WT Bd21-3 leaf developmental zone, collected in 2024 (16.09.)

description:
Library name: WT2024-1
10X Genomics


title: Cryoablation day 28 Xenium

label: secondary probes targeting RCA-amplified probe-RNA complexes


title: Sham day 7 Xenium

value: Sham


title: Treg cells from MDD patient, TCR-seq, replicate 6

status: Public on Sep 20 2025

city: xi'an

first: Yao

last: Gao

address: 277 Yanta West Road

department: Psychiatry

country: China

institute: the first affiliated hospital of Xi'an Jiaotong University

description: Library name: Sample TCR 10

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the 10×Genomics Cell Ranger pipeline (https://support.10×genomics.com/single-cell-geneexpression/software/pipelines/latest/what-is-cell-ranger).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: TCR-Seq

source_name: Blood

extract_protocol:
Tregs (CD4+CD25+CD127dim/-) were isolated from fresh PBMCs using a CD4+CD25+CD127dim/- Regulatory T Cell Isolation Kit for Human (Miltenyi Biotec), in accordance with the manufacturer’s instructions. In brief, total CD4+ T cells were isolated by negative selection using an LD column (Miltenyi Biotec). Subsequently, Tregs were purified from the CD4+ T cell population using an MS column (Miltenyi Biotec).
The magnetic isolated Treg cells were encapsulated on Chromium Next GEM Chip G (10×Genomics, 1000120) using Single Cell 5’ chemistry (v2, PN-1000263), with cellular barcoding performed on a Chromium × controller (10×Genomics). Library preparation using either Chromium Single Cell 5’ v2 Reagent Kit (PN-1000263), or Barcoded cells underwent reverse transcription followed by TCR library preparation using 5’ Kit and Human TCR V(D)J Enrichment Kit (PN-1000255). All steps followed 10×Genomics User Guide CG000331Rev F.

value: Blood

value: Treg cells

tag: subject status

value: Major depressive disorder (MDD)

tag: Sex

value: Female

tag: age

value: 21 yr


title: Treg cells from MDD patient, TCR-seq, replicate 5

description: Library name: Sample TCR 9

value: Male


title: Treg cells from MDD patient, TCR-seq, replicate 4

description: Library name: Sample TCR 8

value: 19 yr


title: WT Bd21-3 leaf developmental zone, collected in 2021

description:
Library name: WT2021
10X Genomics


title: Treg cells from MDD patient, TCR-seq, replicate 1

description: Library name: Sample TCR 5

value: 28 yr


title: Treg cells from healthy control, TCR-seq, replicate 3

description: Library name: Sample TCR 3

value: healthy control

value: 23 yr


title: Treg cells from healthy control, TCR-seq, replicate 2

description: Library name: Sample TCR 2

value: 29 yr


title: Treg cells from MDD patient, TCR-seq, replicate 2

description: Library name: Sample TCR 6

value: 31 yr


title: Treg cells from MDD patient, scRNA-seq, replicate 6

description: Library name: Sample scRNA 10

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the 10×Genomics Cell Ranger pipeline (https://support.10×genomics.com/single-cell-geneexpression/software/pipelines/latest/what-is-cell-ranger).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files


title: Treg cells from MDD patient, scRNA-seq, replicate 5

description: Library name: Sample scRNA 9


title: sid leaf developmental zone, collected in 2022, 2nd sequencing run (merged with sid2022-1 in Cellranger)

description:
Library name: sid2022-2
10X Genomics
sid2022_barcodes.tsv
sid2022_matrix.mtx

value: leaf developmental zone


title: Treg cells from MDD patient, scRNA-seq, replicate 4

description: Library name: Sample scRNA 8


title: Treg cells from MDD patient, scRNA-seq, replicate 3

description: Library name: Sample scRNA 7

value: 20 yr


title: Treg cells from MDD patient, scRNA-seq, replicate 2

description: Library name: Sample scRNA 6


title: Treg cells from healthy control, scRNA-seq, replicate 3

description: Library name: Sample scRNA 3


title: Treg cells from healthy control, scRNA-seq, replicate 2

description: Library name: Sample scRNA 2


title: Treg cells from healthy control, scRNA-seq, replicate 1

description: Library name: Sample scRNA 1


title: WT Bd21-3 leaf developmental zone, protoplasted, collected in 2024 (17.09.)

description:
Library name: WT2024-2
10X Genomics

value: WT Bd21-3

value: protoplasted


title: PEM_3

status: Public on Aug 25 2025

city: Columbus

first: Juhi

last: Bagaitkar

address: 700 Childrens Dr

institute: Nationwide Childrens.org

data_processing:
Pair-end reads coming from bulk RNA-seq were aligned with STAR v2.7.0f. Gene counts were derived by featureCount v2.0.0.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text file with raw counts

source_name: Macrophages

extract_protocol:
RNA was collected from the sorted cell populations using RNeasy mini kit (Qiagen); ~0.5 ug total RNA was used for construction of the sequencing library
NEB Ultra II RNA library prep kit (according to kit instructions)

treatment_protocol: Peritoneal cavities of mice were lavaged twice with cold sterile PBS 4 h after injections; cells collected in lavages were immediately stained for cell sorting (BD Influx) & sorted to obtain pure macrophage populations

value: Macrophages

value: Periodoate injection


title: Treg cells from healthy control, scRNA-seq, replicate 4

description: Library name: Sample scRNA 4

value: Blood

value: Treg cells

value: 25 yr


title: Treg cells from MDD patient, scRNA-seq, replicate 1

description: Library name: Sample scRNA 5

value: Major depressive disorder (MDD)

value: Female


title: PEM_1


title: isoctrl_3

value: Isotype control antibody


title: isoctrl_2


title: PEM_2


title: Treg cells from healthy control, TCR-seq, replicate 4

description: Library name: Sample TCR 4

value: Male


title: Treg cells from MDD patient, TCR-seq, replicate 3

description: Library name: Sample TCR 7


title: isoctrl_1


title: isoctrl_4


title: gLN_4h_4

value: RgpB-treated neutrophils of human origin, 4h


title: gLN_4h_3


title: gLN_24h_4

value: RgpB-treated neutrophils of human origin, 24h


title: gLN_4h_2


title: gLN_24h_2


title: gLN_24h_3


title: gLN_24h_1


title: PEM_4


title: AN_4h_4

value: Apoptotic neutrophils of human origin, 4h


title: AN_4h_2


title: Treg cells from healthy control, TCR-seq, replicate 1

description: Library name: Sample TCR 1

value: healthy control

value: 28 yr


title: AN_4h_1


title: AN_4h_3


title: AN_24h_3

value: Apoptotic neutrophils of human origin, 24h


title: AN_24h_4


title: AN_24h_2


title: rpm_2

data_processing:
Pair-end reads coming from bulk RNA-seq were aligned with STAR v2.7.9a1. Gene counts were derived by featureCount v2.0.32.
Assembly: GRCm38.p6
Supplementary files format and content: Tab-delimited text file with raw counts

extract_protocol:
RNA was collected from the sorted cell populations using RNeasy micro kit (Qiagen) according to kit instructions; ~0.02 ug of total RNA used for construction of the sequencing library
Takara-Clontech SMARTseq mRNA LP (according to kit instructions)

treatment_protocol: Peritoneal cavities of mice were lavaged twice with cold sterile PBS 4 h after injections; cells collected in lavages were immediately stained for cell sorting (BD Influx); cells were sorted to obtain efferocytosing macrophages or non-efferocytosing (control) macrophages

value: Sterile saline injection


title: AN_24h_1


title: rpm_1


title: rpm_3


title: pem_4


title: rpm_4


title: pem_2


title: pem_3


title: pem_1


title: g-BMN_2

value: RgpB-treated neutrophils of mouse origin


title: g-BMN ctr_3

value: Macrophages

value: Control for RgpB-treated neutrophils


title: g-BMN ctr_2


title: g-BMN ctr_1


title: gLN_4h_1


title: a-BMN_4

value: Apoptotic neutrophils of human origin


title: a-BMN ctr_3

value: Control for apoptotic neutrophils treatment


title: a-BMN ctr_4


title: g-BMN_1


title: a-BMN_3

value: Apoptotic neutrophils of mouse origin


title: Per_F_control_2

status: Public on Aug 21 2025

city: Aurora

first: Christian

last: Mosimann

state: Colorado

address: 12801 E. 17th Avenue

department: Department of Pediatrics, Section of Developmental Biology

institute: University of Colorado School of Medicine Anschutz Medical Campus

description:
Library name: Per_F_control_2
salmon.merged.gene_counts.tsv

data_processing:
RNA-seq: 1X150 directional mRNA sequencing was performed using an Illumina NovaSeqX resulting in an average of 40 million mapped reads per sample. Bulk RNA-seq sequencing were mapped to Rnor_6.0 and genes quantified using the nfcore rnaseq v3.12.0 pipeline (https://zenodo.org/records/10171269). Fragments per kilobase of exon per million mapped reads values were calculated using Cufflinks for each sample (n = 5 pericardial tissue, n=7 myocardial tissue (6 males and 1 females). Differentially expressed genes were calculated using the nfcore differentialabundance v1.3.1 pipeline (https://zenodo.org/records/10046399) starting with the raw counts file.
Assembly: RNA-seq: Rnor_6.0
Supplementary files format and content: RNA-seq: tab deliminted text file includes raw counts for each gene for each sample
scRNA-seq: Fastq sequencing files from were processed through Cell Ranger (v5.0.1)with a zebrafish GRCz11 library to obtain UMI gene expression counts and analyzed using the standard methods in the Seurat pipeline.
scRNA-seq: Clustering was performed at a resolution of 0.8 snn and the mesothelium cluster was sub-clustered to separate the mesothelium and pericardium clusters. Clusters were annotated manually using marker gene expression and the differentially expressed genes for each cluster were calculated with the FindAllMarkers function.
Assembly: scRNA-seq: GRCz11
Supplementary files format and content: scRNA-seq: tab separated files and matrix file output from cellranger and R object file of Seurat Object

organism: Rattus norvegicus

source_name: pericardium

extract_protocol:
RNA-seq: RNA was extracted from tissues using the mirVana kit (Ambion) according to manufacturer instructions.
RNA-seq: Libraries were prepped using the iScript cDNA Synthesis Kit (Bio-Rad). Samples with RNA integrity above 9 RIN were considered suitable and high quality for RNA-seq.
scRNA-seq: Around 1000 drl:mCherry;hand2:EGFP double-transgenic embryos were grown at 28.5 °C in E3 medium until tailbud stage (10 hpf) was reached. Embryos were dechorionated by incubating in 1 mg/mL Pronase (Sigma, 53702-50KU) and rinsed with E3 medium. For dissociation, PBS was replaced with 2 mg/mL collagenase IV (Worthington) in DMEM (high glucose (4.5 g/l) and NaHCO3, without L-glutamine and sodium pyruvate, Sigma-Aldrich). Embryos were incubated for 2x 5 min in a water bath at 37°C and carefully pipetted up and down into a single-cell suspension. Cells were filtered through a 35 μm cell-strainer (Falcon, round-bottom tubes with cell-strainer cap) and centrifuged at 400xg for 30 sec. Cells were washed in 1X HBSS (Gibco) containing 2% FBS. After washing, the cells were centrifuged again, and the pellet was resuspended in 1X PBS. Next, cells were sorted to isolate EGFP- and mCherry-expressing cells using the MoFlo XDP100 sorter at the CU-SOM Cancer Center Flow Cytometry shared resources platform at CU Anschutz Medical Campus. Sorted cells were collected in a 1.5 mL FBS-coated microcentrifuge tube.
scRNA-seq: 10X Genomics Chromium technology was used to capture and profile single cell transcriptome 3’ gene expression (Genomics Core at CU Anschutz). Generated libraries were sequenced on the Illumina NovaSeq 6000 instrument at the University of Colorado Cancer center.

value: pericardium

value: WT

tag: timepoint

value: 3 weeks


title: Per_M_control_2

description:
Library name: Per_M_control_2
salmon.merged.gene_counts.tsv


title: Per_M_control_1

description:
Library name: Per_M_control_1
salmon.merged.gene_counts.tsv


title: LV_M_control_6

description:
Library name: LV_M_control_6
salmon.merged.gene_counts.tsv

source_name: left ventricle myocardium

value: left ventricle myocardium


title: Per_F_control_1

description:
Library name: Per_F_control_1
salmon.merged.gene_counts.tsv


title: LV_M_control_4

description:
Library name: LV_M_control_4
salmon.merged.gene_counts.tsv


title: LV_F_control_1

description:
Library name: LV_F_control_1
salmon.merged.gene_counts.tsv


title: g-BMN_3


title: S5_TREGS_FCRL3+

status: Public on Aug 16 2025

city: Bellinzona

first: Cristina

last: Leoni

state: Ticino

address: Via F. Chiesa 5

department: Molecular Immunology

institute: Institute for Research in Biomedicine

data_processing:
We used FastQC v0.11.9 to assess the quality of the reads. Adapters sequences were removed using Trimmomatic v0.39.
Reads were subsequently mapped to the human genome using HISAT2 v2.1.0.
Table of Counts were generated using HTSeq-count v2.0.2
Differential expression analysis was performed using Omics Playground platform v2.7.8
Assembly: GRCh38
Supplementary files format and content: *.counts.txt files contain raw read counts for each samples.

source_name: Memory CD4+ regulatory T lymphocytes

extract_protocol:
Cells were lysed in TRI reagent, and RNA extraction was performed using the Direct-Zol RNA mini Prep kit (Zymo Research).
The mRNA-seq library preparation from 100 ng of total RNA (RIN > 8) was performed following the Smart-seq2 protocol with minor modification and paired-end sequenced on an Illumina NOVASeq 6000 platform.

value: Memory CD4+ regulatory T lymphocytes

value: Male


title: LV_M_control_2

description:
Library name: LV_M_control_2
salmon.merged.gene_counts.tsv


title: LV_M_control_3

description:
Library name: LV_M_control_3
salmon.merged.gene_counts.tsv


title: LPM_scRNAseq

description: Library name: LPM_scRNAseq

organism: Danio rerio

source_name: whole embryo

value: whole embryo

value: lateral plate mesoderm

value: WT/AB


title: LV_M_control_1

description:
Library name: LV_M_control_1
salmon.merged.gene_counts.tsv


title: S4_TREGS_FCRL3-


title: S3_TREGS_FCRL3+


title: S2_TREGS_FCRL3-


title: S4_TREGS_FCRL3+


title: S2_TREGS_FCRL3+


title: S1_TREGS_FCRL3-


title: Per_M_control_3

description:
Library name: Per_M_control_3
salmon.merged.gene_counts.tsv


title: LV_M_control_5

description:
Library name: LV_M_control_5
salmon.merged.gene_counts.tsv


title: S4_CD4_FCRL3+

source_name: Memory CD4+ T lymphocytes

value: Memory CD4+ T lymphocytes


title: S4_CD4_FCRL3-


title: S5_CD4_FCRL3+


title: S5_CD4_FCRL3-


title: S3_TREGS_FCRL3-


title: S3_CD4_FCRL3-


title: S2_CD4_FCRL3+


title: S3_CD4_FCRL3+


title: S5_TREGS_FCRL3-


title: S5_CD8_FCRL3-

source_name: Memory CD8+ T lymphocytes

value: Memory CD8+ T lymphocytes


title: S2_CD4_FCRL3-


title: S4_CD8_FCRL3-


title: S1_CD4_FCRL3-


title: S1_CD4_FCRL3+


title: S5_CD8_FCRL3+


title: S4_CD8_FCRL3+


title: S2_CD8_FCRL3-


title: S3_CD8_FCRL3-


title: S1_CD8_FCRL3+


title: S3_CD8_FCRL3+


title: S2_CD8_FCRL3+


title: S1_CD8_FCRL3-


title: ctrl_panc_scrna

status: Public on Aug 07 2025

city: TORONTO

first: Adrian

middle: Kwan Ho

last: Loe

state: ON

address: 686 Bay Street

country: Canada

institute: The Hospital for Sick Children

data_processing:
basecalling: bcl2fastq v2.17 (ATAC and RNA)
trimming: trimmomatic v0.32 (ATAC and RNA)
alignment: bwa mem v0.7.8 (ATAC); STAR v2.5.1b (RNA)
filtering + peak calling (ATAC): ataqv v0.9.1 + MACS2 v2.1.2
read counting: featurecounts.txt v2.5.0/v2.5.3 (ATAC and RNA)
For scRNA-seq: Data were processed, aligned to the mouse genome (mm10), and converted to gene expression matrices with the Cell Ranger Single-Cell Suite pipeline (v3.1.0) run with default settings
Genome_build: mm10; GENCODEvM4
Supplementary_files_format_and_content: For scRNA-seq: Filtered gene expression matrices generated for each sample by the Cell Ranger pipeline
Supplementary_files_format_and_content: all_merged.counts.txt: Peak-level counts.txt, counted over merged broadPeaks from this study and samples re-analyzed from GSE147418 and also included in this study.
Supplementary_files_format_and_content: ctl_panc_merged_rna.bg and eed_panc_merged_rna.bg contain both strands for washU epigenome browser: https://epigenomegateway.wustl.edu/

source_name: E13.5 Whole Pancreas

extract_protocol:
10X Chromium Single Cell 3' Reagent Kit Version 2
10X Chromium Single Cell 3' Reagent Kit Version 2

treatment_protocol: Pancreata were micro-dissected from E13.5 embryos into PBS containing 2% fetal bovine serum (2% FBS) on ice. Single-cell suspensions were prepared via micropipette mechanical dissociation in a 2:1 solution of TyrpLE Express Enzyme (Gibco):PBS incubated in a 37°C water bath. Digestion was stopped using an equal volume of 2% FBS. Cells were spun down at 400g in a 4°C centrifuge. After washing, cells were re-suspended in 1:5000 SYTOX Blue dead cell stain (Thermo Fisher Scientific) prepared in 2% FBS, and then filtered through a 45 µm cell strainer. Live cells were sorted using the MoFlo XDP (Beckman Coulter) or the Sony SH800 (Sony Biotechnology).

value: Whole Pancrea

tag: strain

tag: developmental stage


title: eed_panc_scrna


title: S1_TREGS_FCRL3+


title: GSM4430329_KO_St_ATAC_rep2_re-analyzed

description:
all_merged.counts.txt
GSM4430329_KO_St_ATAC_rep2

library_source: genomic

molecule: genomic DNA

source_name: E13.5 Stomach Mesenchyme

extract_protocol:
Omni-ATAC
Illumina Tn5 (15027865) + buffer (15027866)

value: Stomach Mesenchyme


title: GSM4430323_WT_Int_ATAC_rep2_re-analyzed

description:
all_merged.counts.txt
GSM4430323_WT_Int_ATAC_rep2

source_name: E13.5 Intestinal Mesenchyme

value: Intestinal Mesenchyme


title: GSM4430324_KO_Int_ATAC_rep1_re-analyzed

description:
all_merged.counts.txt
GSM4430324_KO_Int_ATAC_rep1


title: GSM4430328_KO_St_ATAC_rep1_re-analyzed

description:
all_merged.counts.txt
GSM4430328_KO_St_ATAC_rep1


title: GSM4430327_WT_St_ATAC_rep2_re-analyzed

description:
all_merged.counts.txt
GSM4430327_WT_St_ATAC_rep2


title: ctl_panc_atac_rep1

description:
ctl_panc_merged_atac.bedgraph
ctl_panc_peaks.broadPeak
all_merged.counts.txt

source_name: E13.5 Pancreatic Mesenchyme

value: Pancreatic Mesenchyme


title: ctl_panc_rna_rep2

extract_protocol:
RNeasy Micro Kit (Qiagen, 74004)
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina + SIRV Set 3 Spike-In


title: GSM4430326_WT_St_ATAC_rep1_re-analyzed

description:
all_merged.counts.txt
GSM4430326_WT_St_ATAC_rep1


title: GSM4430322_WT_Int_ATAC_rep1_re-analyzed

description:
all_merged.counts.txt
GSM4430322_WT_Int_ATAC_rep1


title: eed_panc_rna_rep1


title: LAM-39/RBJ

status: Public on Aug 05 2025

city: Nottingham

first: Roya

last: Babaei Jadidi

state: Nottinghamshire

address: Biodiscovery institute

country: United Kingdom

institute: University of Nottingham

description: laser cut (nodules) from biopsy sample

data_processing:
RNA-seq data alignment, QC and normalization was done using the RNA-Seq workflow in Partek Flow software (v7. Partek Inc., St. Louis, MO, USA). Human genome hg38 was used as reference. Gene counts were normalized using the median of ratios (i.e., ratio of read count to its geometric mean across all samples before being subjected to a differential expression analysis44. Differentially expressed genes (DEGs) were identified using DESeq2 in Partek with the combination criteria of a p-value < 0.05 and absolute fold change >1.5. Genes with mean average count across all samples < 10 were removed for further analysis. DESeq2 was used to find differentially expressed genes between the laser capture samples and their corresponding rest of lung samples for each clinical measurement group.
Assembly: Human genome hg38
Supplementary files format and content: tab-delimited text file include normalized values for each Sample

source_name: lung

extract_protocol:
Tissue sections were mounted on PEN Membrane Glass Slides, deparaffinised and stained using Cresyl Violet. LCM was carried out using a Zeiss AxioImager Z1. Microdissected samples were captured by AdhesiveCap 500ul microcentrifuge tubes. RNA extraction was performed by using RNeasy DSP FFPE Kit (QIAGEN, ID: 73604). Genomic DNA was eliminated using, RQ1 RNase-Free DNase (Promega, M6101) and clean-up performed using Monarch® RNA Cleanup Kit (Biolabs, New England, T2030L).
. The library preparation and RNA sequencing was performed by Birmingham Genomic centre using Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD from Illumina. Libraries were quantified using a PicoGreen Quant-iT kit and sized with a D1000 tape
For sequencing, libraries were pooled in equal volumes according to their molarity. These were then quality checked using the Agilent TapeStation DNA 1000 tape and DNA HS Qubit. Pooled libraries was taken into sequencing at 2nM and loaded on the NovaSeq 6000 at 400pM with an SP 100 cycle flowcell.

value: lung

tag: disease

value: LAM  patient


title: LAM-38/RBJ

description: rest of lung(all the lung parafin slide minus nodules) from biopsy sample


title: ctl_panc_atac_rep2


title: eed_panc_atac_rep2

description:
eed_panc_merged_atac.bedgraph
eed_panc_peaks.broadPeak
all_merged.counts.txt


title: eed_panc_atac_rep1


title: eed_panc_rna_rep2


title: LAM-35/RBJ

description: laser cut (nodules) from biopsy sample


title: ctl_panc_rna_rep1


title: LAM-36/RBJ


title: LAM-37/RBJ

description: laser cut (nodules) from biopsy sample


title: LAM-34/RBJ


title: LAM-32/RBJ


title: LAM-28/RBJ

description: transplant lung- whole parafin slide


title: LAM-30/RBJ


title: LAM-19/RBJ


title: LAM-18/RBJ

description: laser cut (nodules) from biopsy sample


title: LAM-25/RBJ

description: laser cut (nodules) from biopsy sample


title: LAM-27/RBJ

description: whole parafin slide


title: LAM-17/RBJ

description: transplant lung- whole parafin slide


title: LAM-24/RBJ


title: GSM4430325_KO_Int_ATAC_rep2_re-analyzed

description:
all_merged.counts.txt
GSM4430325_KO_Int_ATAC_rep2


title: LAM-11/RBJ


title: LAM-23/RBJ

description: laser cut (nodules) from biopsy sample


title: LAM-22/RBJ

description: transplant lung- whole parafin slide


title: LAM-21/RBJ


title: LAM-2/RBJ

description: laser cut (nodules) from biopsy sample


title: LAM-20/RBJ

description: laser cut (nodules) from biopsy sample


title: LAM-16/RBJ

description: whole parafin slide

value: control subject


title: LAM-15/RBJ


title: LAM-14/RBJ

description: laser cut (nodules) from biopsy sample


title: LAM-13/RBJ


title: Kcnj2 KO/+ 13.5 anterior palate

status: Public on Jul 28 2025

first: Emily

middle: Anne

last: Bates

state: CO

institute: University of Colorado Anschutz Medical Campus

description:
Library name: Kcnj2 KO/+
10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Data was normalized using Single Cell Transform v0.3.2 (https://github.com/satijalab/sctransform) and analyzed with Seurat v4.0.4 (https://satijalab.org/seurat/)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: anterior palate

extract_protocol:
In ice-cold PBS, heads were removed from embryos. The top of the head was cut flat, and the head was laid ventral. The secondary palate was exposed by removing the mandible and tongue. The anterior 1/3 of the palate was dissected away from the remainder of the head using forceps. Paired anterior palatal shelves were washed twice in PBS and transferred to 750 uL 0.25% Trypsin-EDTA for 10 minutes at 37C with frequent trituration. Trypsinization was stopped with addition of 750uL DMEM + 10% FBS . Cells were pipetted up and down 20 times to assist in cell dispersion, pelleted at 300 g for 3 min, and resuspended in PBS with 0.1% BSA before being filtered through a Flowmi 40uM cell strainer. Single cell suspensions were confirmed by microscopy and cells were counted on a hemocytometer with trypan blue staining.
Chromium single cell 3’ NextGen V3.1 chemistry (10X Genomics)

value: anterior palate

value: Kcnj2 KO/+

value: Female


title: LAM-12/RBJ

description: laser cut (nodules) from biopsy sample


title: LAM-10/RBJ

description: laser cut (nodules) from biopsy sample


title: LAM-1/RBJ

description: whole parafin slide


title: LAM-26/RBJ


title: LAM-3/RBJ


title: parathyroid, normal, rep1

status: Public on Jul 01 2025

city: Dalian

first: Rulin

last: Hua

state: Liaoning

address: 9 Western Section, Lvshun South Street, Lvshunkou District

institute: Dalian Medical University

description: Library name: PTG

data_processing:
Using the default parameters of Cell Ranger v8.0.1, the 10x single-cell data were processed, including FASTQ file reading, reference genome alignment, cell barcode processing, and single-cell gene counting. The reference genome Rnor6.0 for rats was downloaded from GENCODE. Each sample's FASTQ files were independently processed using the Cell Ranger Count pipeline, which employs STAR to align cDNA sequences from the FASTQ files to the reference genome (Rnor6.0). The pipeline then filters and corrects cell barcodes and UMIs mapped to the reference genome to remove PCR duplicates, ensuring accurate quantification of the number of transcript molecules captured per gene in each cell. The resulting cell-gene count matrix for each sample was generated for downstream analysis.
Assembly: Rat Rnor6.0
Supplementary files format and content: Tab-separated values files and matrix files

source_name: parathyroid tissue

extract_protocol:
The excised glands were minced and enzymatically digested at 37°C for 40 minutes with gentle shaking in a solution containing TL (1 mg/mL, Roche), Dispase (2 mg/mL, Miltenyi Biotec), and DNase I (0.05 mg/mL, Sigma). Every 20 minutes, dissociated cells were collected using a 10 mL plastic pipette containing fetal bovine serum (FBS). The resulting cell suspension was filtered through a 20 μm mesh filter (BD Biosciences), centrifuged at 300 g for 5 min, and incubated in red blood cell lysis buffer (155 mM NH₄Cl, 0.1 mM Na₂EDTA, 10 mM KHCO₃) for 3 minutes. The dissociated parathyroid cells were then resuspended and stored in Dulbecco’s phosphate-buffered saline (DPBS).
Single-cell cDNA library preparation and 3' single-cell RNA sequencing were conducted by CapitalBio Technology (Beijing, China). Libraries were prepared using the 10x Genomics Chromium platform, following the manufacturer’s instructions with the Single Cell 3' Library and Gel Bead Kit V3 (10x Genomics, 1000075) and the Chromium Single Cell B Chip Kit (10x Genomics, 1000074). Cells were suspended in PBS containing 0.04% BSA, and approximately 8,000 cells were loaded onto the Chromium Single Cell Controller (10x Genomics) to generate single-cell gel bead emulsions (GEMs). Captured cells were lysed, and released RNA was barcoded through reverse transcription within individual GEMs. RT-PCR was performed using an S1000™ Touch Thermal Cycler (Bio-Rad) under the following conditions: 53°C for 45 min, 85°C for 5 min, followed by a hold at 4°C. cDNA was recovered, amplified, and quality-assessed using the Agilent 4200 system (conducted by Beijing Cade Biotechnology Co., Ltd.). Single-cell RNA-seq libraries were constructed using the Single Cell 3' Library and Gel Bead Kit V3, following the manufacturer’s protocol. Finally, sequencing was performed on an Illumina NovaSeq 6000 platform, generating paired-end 150 bp (PE150) reads with a minimum sequencing depth of 100,000 reads per cell (conducted by Beijing Cade Biotechnology Co., Ltd.).

value: parathyroid tissue

value: Sprague-Dawley

value: 12 weeks

value: wild-type

value: male


title: Multiome_scATACseq_MCMV D1.5, liver, Stat1-GOF, biol rep 1

status: Public on Jun 13 2025

city: Bethesda

first: Kan

last: Jiang

state: MD

address: 9000 Rockville Pike

institute: NIAMS/NIH

description: Library name: MCMV.D1.5.liver_gof_rep1_ATAC

library_source: genomic single cell

data_processing:
Multiome: Alignment to mm10, filtering, barcode counting, and unique molecular identifier counting were performed using Cell Ranger ARC (v2.0.0).
CITE-seq: Alignment, filtering, barcode counting, and unique molecular identifier counting, and demultiplexing of Hashtags were performed using Cell Ranger (v7.1.0) with mkfastq and multi. The GEX data were aligned to the mm10 reference genome, while ADT and HTO data were processed using a custom feature reference file.
Assembly: mm10
Supplementary files format and content: Multiome: Cell Ranger gene expression and ATAC output files (matrix and fragment).
Supplementary files format and content: CITE-seq: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx) are split by experimental condition according to HTO (e.g., "wt", "gof", etc.) and separated by individual captures (e.g., "capt1" and "capt2"). The Cell Ranger output files contain both GEX and Feature Barcode (ADT).

source_name: liver

extract_protocol:
Immune cells from liver after MCMV infection were FACS sorted prior to capture.  For Multiome, nuclei were isolated by lysing cells for 3 min in 100 µl of freshly made lysis buffer (10 mM Tris-HCl-pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween 20, 0.1% Nonidet P-40 Substitute, 0.01% digitonin, 1% BSA, 1 mM DTT, and 1000 U/ml of RNase inhibitor). Nuclei were washed twice with freshly made Wash Buffer (10 mM Tris-HCl-pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween 20, 1% BSA, 1 mM DTT, and 1 U/µl RNase inhibitor) and resuspended in 1x Nuclei Buffer (10x Genomics) for Tn5 incubation. For CITEseq, cells were stained with TotalSeq Hashtag antibodies and TotalSeq ADT antibodies prior to capture.
We used Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits (10x Genomics) to generate scRNA-Seq and scATAC-Seq libraries according to the manufacturer’s protocol. We used Chromium Next GEM Single Cell 5' HT v2 Kit and 5' Feature Barcode kit (10x Genomics) to generate CITE-seq libraries according to the manufacturer’s protocol.

value: liver

value: Liver, CD45+, Ter119-, Ly6G-

value: MCMV day 1.5

tag: library type

value: ATAC


title: Kcnj2 KO/KO 1 13.5 anterior palate

description:
Library name: Kcnj2 KO/KO 1
10X Genomics

value: Kcnj2 KO/KO

value: Male


title: CITEseq_MCMV D4, liver, surface protein

description:
Library name: MCMV.D4.liver_mixed_surfaceProtein
Feature Barcode (FB) library derived from Hashtag-derived oligonucleotide (HTO) and Antibody-derived oligonucleotide (ADT) antibodies

library_source: other

data_processing:
Multiome: Alignment to mm10, filtering, barcode counting, and unique molecular identifier counting were performed using Cell Ranger ARC (v2.0.0).
CITE-seq: Alignment, filtering, barcode counting, and unique molecular identifier counting, and demultiplexing of Hashtags were performed using Cell Ranger (v7.1.0) with mkfastq and multi. The GEX data were aligned to the mm10 reference genome, while ADT and HTO data were processed using a custom feature reference file.
Assembly: mm10
Supplementary files format and content: Multiome: Cell Ranger gene expression and ATAC output files (matrix and fragment).
Supplementary files format and content: CITE-seq: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx) are split by experimental condition according to HTO (e.g., "wt", "gof", etc.) and separated by individual captures (e.g., "capt1" and "capt2"). The Cell Ranger output files contain both GEX and Feature Barcode (ADT).
Library strategy: CITE-seq

molecule: protein

value: Liver, CD45+, Ter119-

value: mixed (WT, Stat1-T385M/+, WT plus anti-IFN-g, Stat1-T385M/+ plus rec-IFN-g)

value: MCMV day 4

value: Feature protein (HTO, ADT)

tag: hto

value: TotalSeq C0301 anti-mouse Hashtag 1 (WT), TotalSeq C0302 anti-mouse Hashtag 2 (Stat1-T385M/+), TotalSeq C0303 anti-mouse Hashtag 3 (WT plus anti-IFN-g), TotalSeq C0304 anti-mouse Hashtag 4 (Stat1-T385M/+ plus rec-IFN-g)

tag: adt

value: TotalSeq C Mouse Universal Cocktail, V1.0


title: Multiome_scATACseq_MCMV D1.5, liver, WT, biol rep 2

description: Library name: MCMV.D1.5.liver_wt_rep2_ATAC

value: WT


title: Multiome_scRNAseq_MCMV D1.5, liver, WT, biol rep 2

description: Library name: MCMV.D1.5.liver_wt_rep2_RNA

value: mRNA


title: Multiome_scRNAseq_MCMV D1.5, liver, Stat1-GOF, biol rep 2

description: Library name: MCMV.D1.5.liver_gof_rep2_RNA


title: IgG Cut&Tag, Stat1-T385M/+ NK, IFNa plus IL-18, experiment 3

description: Library name: S1gof_NK_IFNa.IL18_IgG_exp3

data_processing:
Paired-end reads were quality controlled with FastQC, aligned to mm10 via Bowtie2, and peaks were called with SEACR returning the top 0.01 fraction of peaks based on the peak of the curve (i.e. stringent mode). Bigwig files were generated with deepTools.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: spleen

extract_protocol:
CUT&Tag was performed with Active Motif’s CUT&Tag-IT Assay Kit (Anti-Rabbit, #53171) per manufacturer’s protocol. IgG negative control was included for each genotype in per experiment.
Libraries were constructed with Active Motif’s CUT&Tag-IT Assay Kit components.

treatment_protocol: Isolated NK cells were stimulated in vitro for 3 hours with 33ng/ml of IFN-a (R&D Systems, #10150-IF-050) and 100ng/ml of IL-18 (R&D Systems #9139-IL-050).

value: spleen

value: Natural Killer cells

value: IFNa plus IL-18

tag: cut&tag antibody

value: IgG (Cell Signaling Technology, #663262)


title: Multiome_scRNAseq_MCMV D1.5, liver, Stat1-GOF, biol rep 1

description: Library name: MCMV.D1.5.liver_gof_rep1_RNA

value: liver

value: Liver, CD45+, Ter119-, Ly6G-


title: Stat1 Cut&Tag, Stat1-T385M/+ NK, IFNa plus IL-18, experiment 3

description: Library name: S1gof_NK_IFNa.IL18_Stat1_exp3

value: Stat1 (Cell Signaling Technology, #14994)


title: CITEseq_MCMV D4, liver, gene expression

description:
Library name: MCMV.D4.liver_mixed_RNA
Gene expression (GEX) (5' HT v2 mRNA) library


title: Stat1 Cut&Tag, WT NK, IFNa plus IL-18, experiment 3

description: Library name: WT_NK_IFNa.IL18_Stat1_exp3


title: Multiome_scATACseq_MCMV D1.5, liver, WT, biol rep 1

description: Library name: MCMV.D1.5.liver_wt_rep1_ATAC

value: MCMV day 1.5

value: ATAC


title: Stat4 Cut&Tag, Stat1-T385M/+ NK, IFNa plus IL-18, experiment 2

description: Library name: S1gof_NK_IFNa.IL18_Stat4_exp2

value: Stat4 (ThermoFisher Scientific, #71-4500


title: IgG Cut&Tag, WT NK, IFNa plus IL-18, experiment 2

description: Library name: WT_NK_IFNa.IL18_IgG_exp2


title: Stat4 Cut&Tag, WT NK, IFNa plus IL-18, experiment 2

description: Library name: WT_NK_IFNa.IL18_Stat4_exp2


title: IgG Cut&Tag, Stat1-T385M/+ NK, IFNa plus IL-18, experiment 2

description: Library name: S1gof_NK_IFNa.IL18_IgG_exp2


title: IgG Cut&Tag, Stat1-T385M/+ NK, IFNa plus IL-18, experiment 1

description: Library name: S1gof_NK_IFNa.IL18_IgG_exp1


title: Stat1 Cut&Tag, Stat1-T385M/+ NK, IFNa plus IL-18, experiment 1

description: Library name: S1gof_NK_IFNa.IL18_Stat1_exp1


title: Stat4 Cut&Tag, Stat1-T385M/+ NK, IFNa plus IL-18, experiment 1

description: Library name: S1gof_NK_IFNa.IL18_Stat4_exp1


title: IgG Cut&Tag, WT NK, IFNa plus IL-18, experiment 1

description: Library name: WT_NK_IFNa.IL18_IgG_exp1


title: Stat1 Cut&Tag, WT NK, IFNa plus IL-18, experiment 1

description: Library name: WT_NK_IFNa.IL18_Stat1_exp1


title: Multiome_scATACseq_MCMV D1.5, liver, Stat1-GOF, biol rep 2

description: Library name: MCMV.D1.5.liver_gof_rep2_ATAC


title: IgG Cut&Tag, WT NK, IFNa plus IL-18, experiment 3

description: Library name: WT_NK_IFNa.IL18_IgG_exp3


title: Stat4 Cut&Tag, WT NK, IFNa plus IL-18, experiment 1

description: Library name: WT_NK_IFNa.IL18_Stat4_exp1


title: Stat1-GOF Splenic NK cells, no cytokine, biol rep 2

description: Library name: gof.NK.nc_rep2

data_processing:
Sequence reads were trimmed with Cutadapt (v2.10), aligned to mouse genome (build mm10) using STAR (v2.5.4a, options: --outFilterType BySJout --outFilterMultimapNmax 200 -alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 -outFilterMismatchNoverLmax 0.6 --alignIntronMin 20 --alignIntronMax 1,000,000 -alignMatesGapMax 1,000,000), bam files were created with SAMtools (v1.10) and transcript abundance quantified using subread (v2.0.2).
Assembly: mm10
Supplementary files format and content: CSV file is count per million (CPM) calculated using calcNormFactors(method = "TMM") and cpm(normalized.lib.sizes = TRUE) from the edgeR package.

extract_protocol:
Cells were harvested and stored in Zymo Trizol Reagent until RNA isolation with Direct-zol RNA MicroPrep kit (Zymo Research, #R2062) per manufacturer’s instructions, with DNase I treatment
library preparation with QuantSeq 3′ mRNA-seq Library Prep kit FWD and SIRV + ERCC Spike-In Controls

treatment_protocol: Splenic NK cells (Live, NK1.1+NKp46+TCRb-B220-) were isolated by FACS on a FACSAria Fusion and then 8 × 104 cells were stimulated with 5000 U/ml of IFN-α in complete media (RPMI + 10% FCS + P/S/Q/NEAA) at 37°C for 2 hours or no cytokine for 30 min

value: no cytokine


title: Kcnj2 KO/KO 2 13.5 anterior palate

description:
Library name: Kcnj2 KO/KO 2
10X Genomics

value: anterior palate

value: Kcnj2 KO/KO

value: Male


title: WT Splenic NK cells, IFN-a, biol rep 2

description: Library name: wt.NK.IFNa_rep2

value: IFN-a


title: Stat1-GOF Splenic NK cells, IFN-a, biol rep 1

description: Library name: gof.NK.IFNa_rep1


title: Multiome_scRNAseq_MCMV D1.5, liver, WT, biol rep 1

description: Library name: MCMV.D1.5.liver_wt_rep1_RNA

value: WT


title: WT Splenic NK cells, IFN-a, biol rep 1

description: Library name: wt.NK.IFNa_rep1


title: WT Splenic NK cells, no cytokine, biol rep 1

description: Library name: wt.NK.nc_rep1


title: 3xTG LiO 9

status: Public on Jun 12 2025

city: Boston

first: Jae Joon

last: Choi

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description: Library name: Sample 18

data_processing:
Reads were aligned to the mouse genome (mm10) using STAR aligner (STAR aligner options: --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --outFilterMultimapNmax 20 --outFilterType BySJout --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --outSAMattributes Standard --limitBAMsortRAM 40000000000).
Reads aligned to each genes were counted using htseq-count (default options, used mm10 gene annotation(.gtf) from NCBI RefSeq).
Assembly: mm10
Supplementary files format and content: htseq-count output file (.htseq). Tab-delimited files containing gene symbols and their supporting read counts.

source_name: Hippocampus

extract_protocol:
Mice were transcardially perfused with cold PBS 1x and the hippocampi were rapidly dissected and snap frozen. The total hippocampal RNA was extracted using Trizol reagent (Ambion 15596018) and purified using the Direct-zol RNA Mini Prep kit (Zymo Research, R2050) according to the manufacturer’s instructions. RNA integrity and concentration were assayed using an Agilent 2100 Bioanalyzer instrument. All RNA samples had a RIN>8.2.
Libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kits from 500 ng of purified total RNA according to the manufacturer’s protocol. The finished dsDNA libraries were quantified using Qubit fluorometer, Agilent TapeStation 2200, and RT–qPCR using the Kapa Biosystems library quantification kit according to the manufacturer’s protocols. Uniquely indexed libraries were pooled and sequenced on an Illumina NextSeq 500 with paired-end 75-bp reads by the Dana-Farber Cancer Institute Molecular Biology Core Facilities. Samples were pooled with multiple samples per lane and sequenced.

treatment_protocol: Control vs Lithium Orotate

value: Hippocampus

value: LiO


title: 3xTG LiO 5

description: Library name: Sample 14


title: 3xTG LiO 7

description: Library name: Sample 16


title: 3xTG LiO 4

description: Library name: Sample 13


title: 3xTG LiO 3

description: Library name: Sample 12


title: 3xTG LiO 2

description: Library name: Sample 11


title: 3xTG LiO 1

description: Library name: Sample 10


title: 3xTG Control 9

description: Library name: Sample 9

value: Control


title: 3xTG Control 8

description: Library name: Sample 8


title: 3xTG Control 7

description: Library name: Sample 7


title: 3xTG Control 5

description: Library name: Sample 5