title: Patient CAN021 ROI  002

description: CAN-021 CAN-022 | 002 | Full ROI

tag: tissue

tag: smoking status

tag: platinum administered

tag: best recist response to treatment

tag: date of first dose of treatment

tag: date of last dose of treatment


title: Patient CAN021 ROI  003

status: Public on Apr 09 2024

type: SRA

city: Madrid

first: Jon

last: Zugazagoitia

address: Avenida de Cordoba s/n

department: Medical Oncology

country: Spain

institute: Hospital Universitario 12 de Octubre

description: CAN-021 CAN-022 | 003 | Full ROI

library_source: transcriptomic

data_processing:
Raw sequencing data FASTQ files were generated using Illumina NextSeq 2000 instrument.
Raw sequencing data FASTQ files were processed using GeoMx NGS Pipeline software version 3.1 to generate DCC files.
DCC files were uploaded on to the GeoMx DSP instrument to obtain gene expression raw count data.
Quality control (QC) and Q3 normalization of mRNA data were performed using the GeoMx Digital Spatial Profiler (DSP) software.
Assembly: GRCh38.p13
Supplementary files format and content: .dcc and .pkc files.
Supplementary files format and content: CANTABRICO_DSP_rawcounts.xlsx: gene expression raw count data.
Supplementary files format and content: CANTABRICO_DSP_normalizedcounts.xlsx: gene expression normalized count data.
Supplementary files format and content: .png: image of tissue and ROIs.
Library strategy: spatial transcriptomics

molecule: total RNA

organism: Homo sapiens

source_name: Lung

extract_protocol:
Formalin-fixed tissue were paraffin embedded (FFPE), 5-mm tissue sections were cut with microtome.
Spatial transcriptome sequencing libraries were prepared according to GeoMx Digital Spatial Profiler (DSP) NGS Readout User manual (MAN-10153-04).

value: Lung

tag: patient id

tag: disease

value: ES-SCLC

tag: age

tag: Sex

value: Female

value: Current smoker

tag: ecog performance status at baseline

tag: cns metastases at baseline

value: No

tag: liver metastases at baseline

tag: bone metastases at baseline

value: Carboplatin

value: Partial response

tag: disease progression or death of disease

value: Yes

tag: disease progression or death

tag: death

tag: death of disease

tag: date of disease progression or death

tag: date of death

tag: date of last follow-up

tag: treatment

value: durvalumab + carboplatin/cisplatin + etoposide


title: Patient CAN020 ROI  013

description: CAN-019 CAN-020 | 013 | Full ROI

source_name: Oral cavity

tag: tissue

value: Oral cavity

value: Male

tag: smoking status

tag: platinum administered

tag: best recist response to treatment

tag: date of first dose of treatment

tag: date of last dose of treatment


title: Patient CAN021 ROI  001

description: CAN-021 CAN-022 | 001 | Full ROI

tag: patient id

tag: disease

tag: age

tag: Sex

tag: ecog performance status at baseline

tag: cns metastases at baseline


title: Patient CAN020 ROI  012

description: CAN-019 CAN-020 | 012 | Full ROI

tag: liver metastases at baseline

tag: bone metastases at baseline

tag: disease progression or death of disease

tag: disease progression or death

tag: death

tag: death of disease


title: Patient CAN020 ROI  010

description: CAN-019 CAN-020 | 010 | Full ROI

tag: tissue

tag: smoking status

tag: date of last follow-up

tag: treatment


title: Patient CAN020 ROI  011

description: CAN-019 CAN-020 | 011 | Full ROI

tag: platinum administered

tag: best recist response to treatment

tag: date of first dose of treatment

tag: date of last dose of treatment


title: Patient CAN020 ROI  009

description: CAN-019 CAN-020 | 009 | Full ROI

tag: patient id

tag: disease

tag: age

tag: Sex


title: Patient CAN019 ROI  008

description: CAN-019 CAN-020 | 008 | Full ROI

tag: ecog performance status at baseline

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: bone metastases at baseline

value: Stable disease

tag: date of disease progression or death

tag: date of death


title: Patient CAN040 ROI  003

description: CAN-040 CAN-041.1 | 003 | Full ROI

tag: tissue

tag: smoking status

value: Former smoker

tag: disease progression or death of disease

tag: disease progression or death

tag: death

tag: death of disease


title: Patient CAN040 ROI  002

description: CAN-040 CAN-041.1 | 002 | Full ROI

tag: platinum administered

tag: best recist response to treatment

tag: date of first dose of treatment

tag: date of last dose of treatment

tag: date of last follow-up

tag: treatment


title: Patient CAN019 ROI  006

description: CAN-019 CAN-020 | 006 | Full ROI

tag: patient id

tag: disease

tag: age

tag: Sex

tag: ecog performance status at baseline

tag: cns metastases at baseline


title: Patient CAN037 ROI  001

description: CAN-037 CAN-039 | 001 | Full ROI

tag: tissue

tag: smoking status

tag: liver metastases at baseline

tag: bone metastases at baseline

tag: date of disease progression or death

tag: date of death


title: Patient CAN029 ROI  003

description: CAN-028 CAN-029 | 003 | Full ROI

tag: platinum administered

value: Cisplatin

tag: best recist response to treatment

value: Progressive disease

tag: disease progression or death of disease

tag: disease progression or death

tag: death

tag: death of disease


title: Patient CAN019 ROI  004

description: CAN-019 CAN-020 | 004 | Full ROI

tag: patient id

tag: disease

tag: date of first dose of treatment

tag: date of last dose of treatment

tag: date of last follow-up

tag: treatment


title: Patient CAN019 ROI  002

description: CAN-019 CAN-020 | 002 | Full ROI

tag: tissue

tag: age

tag: Sex

tag: smoking status

tag: ecog performance status at baseline

tag: cns metastases at baseline


title: Patient CAN019 ROI  001

description: CAN-019 CAN-020 | 001 | Full ROI

tag: liver metastases at baseline

tag: bone metastases at baseline

tag: platinum administered

tag: best recist response to treatment

tag: date of disease progression or death

tag: date of death


title: Patient CAN018 ROI  006

description: CAN-017 CAN-018 | 006 | Full ROI

tag: patient id

tag: disease

tag: disease progression or death of disease

tag: disease progression or death

tag: death

tag: death of disease


title: Patient CAN019 ROI  003

description: CAN-019 CAN-020 | 003 | Full ROI

tag: tissue

tag: age

tag: date of first dose of treatment

tag: date of last dose of treatment

tag: date of last follow-up

tag: treatment


title: Patient CAN017 ROI  004

description: CAN-017 CAN-018 | 004 | Full ROI

source_name: Cervical

value: Cervical

tag: Sex

tag: smoking status

tag: ecog performance status at baseline

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: bone metastases at baseline


title: Patient CAN017 ROI  002

description: CAN-017 CAN-018 | 002 | Full ROI

tag: patient id

tag: disease

tag: platinum administered

tag: best recist response to treatment

tag: date of disease progression or death

tag: date of death


title: Patient CAN008 ROI  011

description: CAN-007 CAN-008 | 011 | Full ROI

tag: tissue

tag: age

tag: disease progression or death of disease

tag: disease progression or death

tag: death

tag: death of disease


title: Patient CAN009 ROI  003

description: CAN-009 CAN-015 | 003 | Full ROI

tag: Sex

tag: smoking status

tag: date of first dose of treatment

tag: date of last dose of treatment

tag: date of last follow-up

tag: treatment


title: Patient CAN015 ROI  004

description: CAN-009 CAN-015 | 004 | Full ROI

tag: patient id

tag: disease

tag: ecog performance status at baseline

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: bone metastases at baseline

value: Complete response


title: Patient CAN008 ROI  010

description: CAN-007 CAN-008 | 010 | Full ROI

tag: tissue

value: Lung

tag: age

tag: platinum administered

tag: best recist response to treatment

tag: date of disease progression or death

tag: date of death


title: Patient CAN017 ROI  001

description: CAN-017 CAN-018 | 001 | Full ROI

value: ES-SCLC

tag: Sex

tag: smoking status

tag: disease progression or death of disease

tag: disease progression or death

tag: death

tag: death of disease


title: Patient CAN017 ROI  003

description: CAN-017 CAN-018 | 003 | Full ROI

tag: patient id

tag: disease

value: Female

tag: date of first dose of treatment

tag: date of last dose of treatment

tag: date of last follow-up

tag: treatment


title: Patient CAN008 ROI  008

description: CAN-007 CAN-008 | 008 | Full ROI

tag: tissue

tag: age

value: Current smoker

tag: ecog performance status at baseline

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: bone metastases at baseline


title: Patient CAN008 ROI  007

description: CAN-007 CAN-008 | 007 | Full ROI

tag: Sex

tag: smoking status

value: No

tag: platinum administered

tag: best recist response to treatment

tag: date of disease progression or death

tag: date of death


title: Patient CAN007 ROI  006

description: CAN-007 CAN-008 | 006 | Full ROI

tag: patient id

tag: disease

value: Carboplatin

tag: disease progression or death of disease

tag: disease progression or death

tag: death

tag: death of disease


title: Patient CAN007 ROI  005

description: CAN-007 CAN-008 | 005 | Full ROI

tag: tissue

tag: age

tag: date of first dose of treatment

tag: date of last dose of treatment

tag: date of last follow-up

tag: treatment


title: Patient CAN019 ROI  007

description: CAN-019 CAN-020 | 007 | Full ROI

tag: Sex

tag: smoking status

tag: ecog performance status at baseline

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: bone metastases at baseline


title: Patient CAN008 ROI  009

description: CAN-007 CAN-008 | 009 | Full ROI

tag: patient id

tag: disease

tag: platinum administered

tag: best recist response to treatment

value: Partial response

tag: date of disease progression or death

tag: date of death


title: Patient CAN005 ROI  011

description: CAN-005 CAN-006 | 011 | Full ROI

tag: tissue

tag: age

value: Yes

tag: disease progression or death of disease

tag: disease progression or death

tag: death

tag: death of disease


title: Patient CAN019 ROI  005

description: CAN-019 CAN-020 | 005 | Full ROI

tag: Sex

tag: smoking status

tag: date of first dose of treatment

tag: date of last dose of treatment

tag: date of last follow-up

tag: treatment

value: durvalumab + carboplatin/cisplatin + etoposide


title: Patient CAN007 ROI  003

description: CAN-007 CAN-008 | 003 | Full ROI

tag: patient id

tag: disease

tag: ecog performance status at baseline

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: bone metastases at baseline


title: Patient CAN007 ROI  002

description: CAN-007 CAN-008 | 002 | Full ROI

tag: tissue

tag: age

tag: platinum administered

tag: best recist response to treatment

tag: date of disease progression or death

tag: date of death


title: Patient CAN018 ROI  005

description: CAN-017 CAN-018 | 005 | Full ROI

tag: Sex

tag: smoking status

tag: disease progression or death of disease

tag: disease progression or death

tag: death

tag: death of disease


title: Patient CAN007 ROI  001

description: CAN-007 CAN-008 | 001 | Full ROI

tag: patient id

tag: disease

tag: date of first dose of treatment

tag: date of last dose of treatment

tag: date of last follow-up

tag: treatment


title: Patient CAN005 ROI  009

description: CAN-005 CAN-006 | 009 | Full ROI

tag: tissue

tag: age

tag: ecog performance status at baseline

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: bone metastases at baseline


title: Patient CAN009 ROI  002

description: CAN-009 CAN-015 | 002 | Full ROI

tag: Sex

tag: smoking status

tag: platinum administered

tag: best recist response to treatment

tag: date of disease progression or death

tag: date of death


title: Patient CAN005 ROI  008

description: CAN-005 CAN-006 | 008 | Full ROI

tag: patient id

tag: disease

tag: disease progression or death of disease

tag: disease progression or death

tag: death

tag: death of disease


title: Patient CAN005 ROI  007

description: CAN-005 CAN-006 | 007 | Full ROI

tag: tissue

tag: age

tag: date of first dose of treatment

tag: date of last dose of treatment

tag: date of last follow-up

tag: treatment


title: Patient CAN005 ROI  010

description: CAN-005 CAN-006 | 010 | Full ROI

tag: Sex

tag: smoking status

tag: ecog performance status at baseline

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: bone metastases at baseline


title: Patient CAN005 ROI  004

description: CAN-005 CAN-006 | 004 | Full ROI

tag: patient id

tag: disease

tag: platinum administered

tag: best recist response to treatment

tag: date of disease progression or death

tag: date of death


title: Patient CAN005 ROI  005

description: CAN-005 CAN-006 | 005 | Full ROI

tag: tissue

tag: age

tag: disease progression or death of disease

tag: disease progression or death

tag: death

tag: death of disease


title: Patient CAN015 ROI  005

description: CAN-009 CAN-015 | 005 | Full ROI

tag: Sex

tag: smoking status

tag: date of first dose of treatment

tag: date of last dose of treatment

tag: date of last follow-up

tag: treatment


title: Patient CAN005 ROI  002

description: CAN-005 CAN-006 | 002 | Full ROI

tag: patient id

tag: disease

tag: ecog performance status at baseline

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: bone metastases at baseline


title: Patient CAN003 ROI  006

description: CAN-003 CAN-004 | 006 | Full ROI

tag: tissue

tag: age

tag: platinum administered

tag: best recist response to treatment

tag: date of disease progression or death

tag: date of death


title: Patient CAN005 ROI  001

description: CAN-005 CAN-006 | 001 | Full ROI

tag: Sex

tag: smoking status

tag: disease progression or death of disease

tag: disease progression or death

tag: death

tag: death of disease


title: Patient CAN003 ROI  003

description: CAN-003 CAN-004 | 003 | Full ROI

tag: patient id

tag: disease

tag: date of first dose of treatment

tag: date of last dose of treatment

tag: date of last follow-up

tag: treatment


title: Patient CAN003 ROI  004

description: CAN-003 CAN-004 | 004 | Full ROI

tag: tissue

tag: age

tag: ecog performance status at baseline

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: bone metastases at baseline


title: Patient CAN003 ROI  002

description: CAN-003 CAN-004 | 002 | Full ROI

tag: Sex

tag: smoking status

tag: platinum administered

tag: best recist response to treatment

tag: date of disease progression or death

tag: date of death


title: Patient CAN009 ROI  001

description: CAN-009 CAN-015 | 001 | Full ROI

tag: patient id

tag: disease

tag: disease progression or death of disease

tag: disease progression or death

tag: death

tag: death of disease


title: Patient CAN003 ROI  005

description: CAN-003 CAN-004 | 005 | Full ROI

tag: tissue

tag: age

tag: date of first dose of treatment

tag: date of last dose of treatment

tag: date of last follow-up

tag: treatment


title: Patient CAN002 ROI  020

description: CAN-001 CAN-002 | 020 | Full ROI

tag: Sex

tag: smoking status

tag: ecog performance status at baseline

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: bone metastases at baseline


title: Patient CAN002 ROI  019

description: CAN-001 CAN-002 | 019 | Full ROI

tag: patient id

tag: disease

tag: platinum administered

tag: best recist response to treatment


title: Patient CAN003 ROI  001

description: CAN-003 CAN-004 | 001 | Full ROI

tag: disease progression or death of disease

tag: disease progression or death

tag: death

tag: death of disease

tag: date of disease progression or death

tag: date of death


title: Patient CAN007 ROI  004

description: CAN-007 CAN-008 | 004 | Full ROI

tag: tissue

tag: age

tag: date of first dose of treatment

tag: date of last dose of treatment

tag: date of last follow-up

tag: treatment


title: Patient CAN002 ROI  018

description: CAN-001 CAN-002 | 018 | Full ROI

tag: Sex

tag: smoking status

tag: ecog performance status at baseline

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: bone metastases at baseline


title: Patient CAN002 ROI  021

description: CAN-001 CAN-002 | 021 | Full ROI

tag: patient id

tag: disease

tag: platinum administered

tag: best recist response to treatment

tag: disease progression or death of disease

tag: disease progression or death


title: Patient CAN002 ROI  015

description: CAN-001 CAN-002 | 015 | Full ROI

tag: tissue

tag: age

tag: death

tag: death of disease


title: Patient CAN002 ROI  016

description: CAN-001 CAN-002 | 016 | Full ROI

tag: date of first dose of treatment

tag: date of last dose of treatment

tag: date of last follow-up

tag: treatment


title: Patient CAN002 ROI  017

description: CAN-001 CAN-002 | 017 | Full ROI

tag: Sex

tag: smoking status

tag: ecog performance status at baseline

tag: cns metastases at baseline


title: Patient CAN002 ROI  014

description: CAN-001 CAN-002 | 014 | Full ROI

tag: patient id

tag: disease

tag: liver metastases at baseline

tag: bone metastases at baseline


title: Patient CAN002 ROI  013

description: CAN-001 CAN-002 | 013 | Full ROI

tag: platinum administered

tag: best recist response to treatment

tag: disease progression or death of disease

tag: disease progression or death


title: Patient CAN005 ROI  006

description: CAN-005 CAN-006 | 006 | Full ROI

tag: tissue

tag: age

tag: death

tag: death of disease

tag: date of disease progression or death

tag: date of death


title: PBMC DNA, young adult, 18

city: Fort Collins

first: Thomas

middle: J

last: LaRocca

state: CO

address: 1582 Campus Delivery

country: USA

institute: Colorado State University

library_source: genomic

data_processing:
Adapters trimmed & file QC by Fastp
RNA-seq: Reads aligned using STAR and counted with TEtranscripts
RNA-seq: Differential expression performed with DESeq2
WGBS: Reads aligned using Abismal program.
WGBS: Bisulfite conversion rates and site- and regional methylation calculated using MethPipe program.
Assembly: hg38
Supplementary files format and content: .xlsx formatted as a counts matrix with rows labeled by gene name and columns labeled by sample ID
Supplementary files format and content: .xlsx with differentially methylated regions

molecule: genomic DNA

source_name: PBMC

extract_protocol:
RNA for RNA-seq extracted using Trizol and Zymo spin columns; DNA for WGBS extracted using Zymo DNA binding buffer and Zymo spin columns.
Total RNA libraries prepared according to manufacturer's instructions using Tarkara Pico kits; DNA bisulfite-converted libraries prepared according to manufacturer's using Zymo EZ-96 methylation library kit.

value: PBMC


title: Patient CAN005 ROI  003

description: CAN-005 CAN-006 | 003 | Full ROI

tag: Sex

value: Male

tag: smoking status

tag: date of first dose of treatment

tag: date of last dose of treatment

tag: date of last follow-up

tag: treatment


title: PBMC DNA, young adult, 15


title: PBMC DNA, young adult, 9


title: PBMC DNA, young adult, 8


title: Patient CAN001 ROI  012

description: CAN-001 CAN-002 | 012 | Full ROI

source_name: Skin

value: Skin

tag: patient id

tag: disease

tag: ecog performance status at baseline

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: bone metastases at baseline


title: Patient CAN001 ROI  011

description: CAN-001 CAN-002 | 011 | Full ROI

tag: tissue

tag: age

tag: platinum administered

tag: best recist response to treatment

tag: disease progression or death of disease

tag: disease progression or death


title: Patient CAN001 ROI  010

description: CAN-001 CAN-002 | 010 | Full ROI

tag: Sex

tag: smoking status

tag: death

tag: death of disease

tag: date of disease progression or death


title: Patient CAN001 ROI  009

description: CAN-001 CAN-002 | 009 | Full ROI

tag: patient id

tag: date of first dose of treatment

tag: date of last dose of treatment

tag: date of last follow-up

tag: treatment


title: Patient CAN001 ROI  008

description: CAN-001 CAN-002 | 008 | Full ROI

tag: disease

tag: ecog performance status at baseline

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: bone metastases at baseline


title: PBMC DNA, young adult, 11

tag: tissue


title: PBMC DNA, young adult, 10


title: PBMC DNA, older adult POST, 9


title: Patient CAN001 ROI  007

description: CAN-001 CAN-002 | 007 | Full ROI

tag: age

tag: platinum administered

tag: best recist response to treatment

tag: disease progression or death of disease

tag: disease progression or death


title: Patient CAN001 ROI  006

description: CAN-001 CAN-002 | 006 | Full ROI

tag: Sex

tag: smoking status

tag: death

tag: death of disease

tag: date of disease progression or death


title: Patient CAN001 ROI  005

description: CAN-001 CAN-002 | 005 | Full ROI

tag: patient id

tag: date of first dose of treatment

tag: date of last dose of treatment

tag: date of last follow-up

tag: treatment


title: PBMC DNA, older adult POST, 8


title: Patient CAN001 ROI  004

description: CAN-001 CAN-002 | 004 | Full ROI

tag: disease

tag: ecog performance status at baseline

tag: cns metastases at baseline

tag: liver metastases at baseline

tag: bone metastases at baseline


title: PBMC DNA, older adult PRE, 9

tag: tissue


title: Patient CAN001 ROI  003

description: CAN-001 CAN-002 | 003 | Full ROI

tag: age

tag: platinum administered

tag: best recist response to treatment

tag: disease progression or death of disease

tag: disease progression or death


title: PBMC DNA, older adult PRE, 8


title: Patient CAN001 ROI  002

description: CAN-001 CAN-002 | 002 | Full ROI

tag: Sex

tag: smoking status

tag: death

tag: death of disease

tag: date of disease progression or death


title: PBMC DNA, older adult POST, 7


title: Patient CAN001 ROI  001

description: CAN-001 CAN-002 | 001 | Full ROI

tag: patient id

tag: date of first dose of treatment

tag: date of last dose of treatment

tag: date of last follow-up

tag: treatment


title: Hela Roxorrubicin (2 µM), 24h, rep4

city: Valencia

first: Francisco

middle: José

last: Iborra

state: Valencia

address: C/ JAIME ROIG, 11

institute: Instituto de Biomedicina de Valencia (CSIC)

data_processing:
In this workflow, reads are aligned to a reference genome using HISAT2. From these alignment, the number of alignments per gene are then quantified.
In essence this workflow contains 3 steps per sample, namely read trimming, alignment ans quantification.
In the trimming Illumina adapter and poly-A sequences are removed from the reads. The trimmed reads are then aligned using HISAT2 (Kim et al, 2019).
After the HISAT2 alignment, quantification is performed using HT-Seq count
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include counts values for each Sample

source_name: Cervix

growth_protocol: HeLa  cells were maintained in DMEM GlutaMAX supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using RNeasy mini kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
We have prepared sequencing libraries from your 16 samples using the Truseq stranded mRNA library preparation method from Illumina
RNAseq. Paire-end. 150 bp

treatment_protocol: TRAIL 24 h treatment (30 ng/ml), Camptothecin 24h treatment (10 µM), or Doxorubicin 24h treatment (2 µM)

value: Cervix

tag: cell line

value: HeLa

tag: cell type

value: epithelial cell

tag: genotype

value: ATCC CCL-2

value: Roxorrubicin 24h


title: PBMC DNA, older adult POST, 5

tag: tissue


title: Hela Roxorrubicin (2 µM), 24h, rep3


title: PBMC DNA, older adult PRE, 7


title: PBMC DNA, older adult PRE, 5


title: PBMC DNA, young adult, 12


title: PBMC DNA, older adult POST, 4


title: Hela Roxorrubicin (2 µM), 24h, rep2


title: PBMC DNA, older adult PRE, 4


title: Hela Camptothecin (10 µM), 24h, rep3

value: Camptothecin 24h


title: PBMC DNA, older adult POST, 3


title: PBMC DNA, young adult, 1


title: Hela Roxorrubicin (2 µM), 24h, rep1


title: Hela Camptothecin (10 µM), 24h, rep4


title: PBMC DNA, older adult PRE, 3


title: PBMC DNA, older adult POST, 2


title: Hela Camptothecin (10 µM), 24h, rep2


title: Hela TRAIL (30 ng/ml), 24h, rep4

value: TRAIL 24h


title: PBMC DNA, older adult PRE, 2


title: PBMC DNA, older adult POST, 13


title: Hela TRAIL (30 ng/ml), 24h, rep3


title: Hela Camptothecin (10 µM), 24h, rep1


title: PBMC DNA, older adult POST, 12


title: PBMC DNA, older adult PRE, 13


title: PBMC DNA, older adult PRE, 12


title: Hela TRAIL (30 ng/ml), 24h, rep2


title: Hela, Control, rep4

value: control


title: Hela TRAIL (30 ng/ml), 24h, rep1


title: Hela, Control, rep3


title: PBMC DNA, older adult POST, 11


title: PBMC DNA, older adult PRE, 11


title: PBMC DNA, older adult POST, 10


title: Hela, Control, rep1


title: Hela, Control, rep2


title: PBMC DNA, older adult POST, 1


title: PBMC DNA, older adult PRE, 10


title: spacer_desaulted_R3

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

country: United Kingdom

institute: University of Oxford

library_source: transcriptomic single cell

data_processing:
We performed basecalling on the raw pod5 data using Derado in GPU mode from Oxford Nanopore Technologies running on four A100 graphics card. For each read we identify the barcode and UMI sequence by searching for the polyA region and flanking regions before and after the barcode/UMI. Accurately sequenced barcodes were identified based on their dual nucleotide complementarity. Unambiguous barcodes were then used as a guide to error correct the ambiguous barcodes in a second pass correction analysis approach. Fastq data was processed using TallyTrin pipelines (https://github.com/cribbslab/TallyTriN). Mapping settings we as follows: -ax splice -uf MD –sam-hit-only –junc-bed and using the reference transcriptome for human hg38 and mouse mm10. The resulting sam file was sorted and indexed using samtools. Mapping settings we as follows: -ax splice -uf MD –sam-hit-only –junc-bed and using the reference transcriptome for human hg38 and mouse mm10. The resulting sam file was sorted and indexed using samtools. The transcript name was then appended to the bam XT flag using the xt_tag_nano script before umi_tools count module was used to count the features using the following settings: --per-gene --gene-tag=XT --per-cell --dual-nucleotide. The umi_tools used to correct for the dimer UMIs is located in the AC-dualoligo in a fork at the repository: https://github.com/Acribbs/UMI-tools.
Assembly: hg38 and mm10
Supplementary files format and content: Tab seperated files and market matrix gz files
Supplementary files format and content: log files: the calculation of polyA positive data that is integral for an up and coming manuscript. The data contained in these files is the output of our analysis workflow.

molecule: polyA RNA

organism:
Homo sapiens
Mus musculus

source_name: 5TGM1 and Jurkat

growth_protocol: Jurkat and 5TGM1 cells were cultured in complete RPMI medium supplemented with 10% Foetal Calf Serum

extract_protocol:
Samples were processed using the Drop-seq DolomiteBio Nadia encapsulator system.
scCOLOR-seq v2 protocol was used.

value: 5TGM1 and Jurkat


title: spacer_desaulted_R2


title: PBMC DNA, older adult PRE, 1


title: PBMC, young adult, 13


title: spacer_desaulted_R1


title: nospacer_desault_R3


title: nospacer_desault_R2


title: PBMC, young adult, 12


title: PBMC, young adult, 11


title: PBMC, young adult, 10


title: nospacer_desault_R1


title: phasic BNST female MR2 203_BNST

city: Mainz

first: Anna

last: Wierczeiko

address: Hanns-Dieter-Hüsch-Weg 15

department: Institute for Human Genetics

country: Germany

institute: University Medical Center, Johannes Gutenberg University Mainz

description: phasic BNST female MR2

data_processing:
Sequence reads were trimmed for adapter sequence and low-quality sequence using BBDuk.
Trimmed sequence reads were mapped to GrCM38/mm10 using the STAR aligner with default parameters.
Read count extraction were performed using FeatureCounts.
Assembly: mm10
Supplementary files format and content: tab-delimited text file of raw gene counts per sample

organism: Mus musculus

source_name: BNST

extract_protocol:
Mouse brains were snap-frozen on dry ice and stored at -80°C. Regions of interest (ACC, BNST, BLA, and CeA) were isolated by a brain punching technique from the whole-mount brain in the cryostat Leica CM3050 S (Leica Biosystems, Nussloch, Germany) at -20°C using biopsy pens EMS Rapid-Core (Electron Microscopy Sciences, Hatfield, USA). To localize the subregions of interest in the brain, punching was carried out by referencing toluidine blue staining of brain slices (Franklin & Paxinos, 2007).  ACC was sampled approximately from 1.34 to 0.5mm (from bregma) using a 1mm pen. BNST (0.5: -0.22)mm, BLA (-0.94: -2.06)mm, and CeA (-0.94: -1.82)mm were sampled bilaterally using a 0.5mm pen. Biopsies were stored at -80°C for further RNA extraction. RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
All steps were carried out on ice. Tissue biopsies were moved to precooled Precellys tubes containing ice-cold ceramic beads for homogenization via Precellys 24 (Peqlab, Erlangen, Germany) (600 g, 20 s). Extraction was performed using RNeasy® mini kit (Qiagen, Hilden, Germany) according to the protocol provided by the manufacturer.

tag: strain

value: BNST

value: female

tag: phenotype

value: phasic

tag: time point


title: phasic CeA female MR2 203_CeA

description: phasic CeA female MR2

source_name: CeA

value: CeA

tag: Sex


title: PBMC, young adult, 9


title: phasic BLA female MR2 203_BLA

description: phasic BLA female MR2

source_name: BLA

value: BLA


title: phasic ACC female MR2 203_ACC

description: phasic ACC female MR2

source_name: ACC

value: ACC


title: PBMC, young adult, 8

value: PBMC


title: sustained BNST female MR2 202_BNST

description: sustained BNST female MR2

value: sustained


title: PBMC, young adult, 5


title: PBMC, young adult, 4


title: sustained ACC female MR2 202_ACC

description: sustained ACC female MR2


title: PBMC, young adult, 3


title: sustained CeA female MR2 201_CeA

description: sustained CeA female MR2


title: sustained BLA female MR2 202_BLA

description: sustained BLA female MR2


title: PBMC, young adult, 1


title: PBMC, older adult POST, 10


title: PBMC, older adult PRE, 10


title: PBMC, young adult, 2


title: sustained ACC female MR2 201_ACC

description: sustained ACC female MR2


title: sustained BNST female MR2 201_BNST

description: sustained BNST female MR2


title: sustained CeA female MR2 194_CeA

description: sustained CeA female MR2


title: PBMC, older adult POST, 9


title: PBMC, older adult PRE, 9


title: sustained BLA female MR2 201_BLA

description: sustained BLA female MR2


title: sustained ACC female MR2 194_ACC

description: sustained ACC female MR2


title: sustained BLA female MR2 194_BLA

description: sustained BLA female MR2


title: sustained BNST female MR2 194_BNST

description: sustained BNST female MR2


title: PBMC, young adult, 7


title: PBMC, young adult, 6


title: PBMC, older adult PRE, 8


title: PBMC, older adult POST, 8


title: sustained CeA female MR2 181_CeA

description: sustained CeA female MR2


title: sustained BNST female MR2 181_BNST

description: sustained BNST female MR2


title: PBMC, older adult PRE, 7


title: sustained ACC female MR2 181_ACC

description: sustained ACC female MR2


title: PBMC, older adult POST, 7


title: PBMC, older adult PRE, 6


title: phasic CeA female MR2 175_CeA

description: phasic CeA female MR2


title: PBMC, older adult PRE, 5


title: PBMC, older adult POST, 5


title: phasic BNST female MR2 175_BNST

description: phasic BNST female MR2


title: phasic BLA female MR2 175_BLA

description: phasic BLA female MR2


title: phasic ACC female MR2 175_ACC

description: phasic ACC female MR2


title: PBMC, older adult PRE, 4


title: phasic CeA female MR2 174_CeA

description: phasic CeA female MR2


title: PBMC, older adult POST, 3


title: PBMC, older adult POST, 2


title: PBMC, older adult PRE, 3


title: phasic BNST female MR2 174_BNST

description: phasic BNST female MR2


title: phasic BLA female MR2 174_BLA

description: phasic BLA female MR2


title: phasic ACC female MR2 174_ACC

description: phasic ACC female MR2


title: PBMC, older adult PRE, 2


title: PBMC, older adult POST, 1


title: PBMC, mid to older adult, data set ONE, 90


title: PBMC, older adult POST, 6


title: phasic ACC female MR2 173_ACC

description: phasic ACC female MR2


title: phasic CeA female MR2 167_CeA

description: phasic CeA female MR2


title: phasic BNST female MR2 173_BNST

description: phasic BNST female MR2


title: sustained BLA female MR2 181_BLA

description: sustained BLA female MR2


title: phasic BLA female MR2 173_BLA

description: phasic BLA female MR2


title: PBMC, mid to older adult, data set ONE, 89


title: PBMC, mid to older adult, data set ONE, 88


title: phasic BNST female MR2 167_BNST

description: phasic BNST female MR2


title: PBMC, older adult PRE, 1


title: phasic BLA female MR2 167_BLA

description: phasic BLA female MR2


title: PBMC, older adult POST, 4


title: PBMC, mid to older adult, data set ONE, 86


title: phasic ACC female MR2 167_ACC

description: phasic ACC female MR2


title: PBMC, mid to older adult, data set ONE, 85


title: sustained CeA female MR2 166_CeA

description: sustained CeA female MR2


title: PBMC, mid to older adult, data set ONE, 87


title: sustained BNST female MR2 166_BNST

description: sustained BNST female MR2


title: PBMC, mid to older adult, data set ONE, 84


title: phasic CeA female MR2 173_CeA

description: phasic CeA female MR2


title: PBMC, mid to older adult, data set ONE, 83


title: sustained BLA female MR2 166_BLA

description: sustained BLA female MR2


title: PBMC, mid to older adult, data set ONE, 82


title: sustained ACC female MR2 166_ACC

description: sustained ACC female MR2


title: PBMC, mid to older adult, data set ONE, 80


title: PBMC, mid to older adult, data set ONE, 81


title: PBMC, mid to older adult, data set ONE, 79


title: sustained BNST female MR2 164_BNST

description: sustained BNST female MR2


title: sustained BLA female MR2 164_BLA

description: sustained BLA female MR2


title: CF3D NO

city: Maynooth

first: Fearon

middle: C

last: Cassidy

address: Kathleen Lonsdale Institute of Human Health

country: Ireland

institute: Maynooth University

data_processing:
Firstly, Cutadapt  and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). We used HISAT2 to map reads to the genome .
The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare.
After the ﬁnal transcriptome was generated, StringTie and Ballgown was used to estimate the expression levels of all transcripts.
StringTie was used to perform expression level for mRNAs by calculating FPKM. The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package Ballgown.
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample

source_name: human bone marrow-derived mesenchymal stromal cells

growth_protocol: MSCs were isolated from the collected marrow as previously described in detail by Cassidy et al. (2020). Briefly, the collected marrow was centrifuged and the pellet resuspended in (PBS, Gibco via Biosciences, Dun Laoghaire, Ireland, 14190094). The number of mononuclear cells (MNCs) were quantified and the cells were plated in tissue culture flasks in expansion medium (α-MEM with GlutaMAX™, Gibco, 32561029) supplemented with 10% fetal bovine serum (FBS, HyClone via ThermoFisher, Ballycollen, Ireland SV30160.03), 1% antibiotic antimycotic solution (Merck, Dublin, Ireland, A5955), and 1 ng/mL recombinant human FGF-basic (Peprotech, London, UK, 100-18B)) at 37 °C with 5% CO2. Following the first passage (P0), the MSCs were lifted from the growth surface with 0.25% trypsin-Ethylenediaminetetraacetic acid (EDTA, Gibco, 25200056), evenly distributed in freezing medium (10% DMSO (Sigma, Arklow, Ireland, D2650), 90% FBS), and cryopreserved in liquid nitrogen.

extract_protocol:
Total RNA was extracted using the QIAGEN RNEasy Plus Mini Kit (Qiagen, Germany) and according to the manufacturer's protocol. RNA quality and quantity was then assessed with Nanodrop (Thermo Fisher, USA) and Agilent Bioanalyser 2100 with RNA 6000 Nano LabChip Kit (Agilent Technologies, USA).
Optimal RNA characteristics for sequencing were set by LC Sciences, USA (RNA amount ≥ 2μg, 260/280 >1.8, 260/230 >1.0, RIN value ≥ 7.0) who were contracted to perform sequencing, quality control, mapping and assembly of reads, and assessment of differential expression of genes and transcripts.

tag: condition

value: No osteoporosis

value: mesenchymal stromal cells


title: PBMC, mid to older adult, data set ONE, 77


title: PBMC, mid to older adult, data set ONE, 76


title: PBMC, mid to older adult, data set ONE, 78


title: PBMC, mid to older adult, data set ONE, 74


title: CF2D NO


title: CF4D NO


title: PBMC, mid to older adult, data set ONE, 75


title: CF1D NO


title: PBMC, mid to older adult, data set ONE, 73


title: CF4 NO


title: PBMC, mid to older adult, data set ONE, 72


title: CF3 NO


title: PBMC, mid to older adult, data set ONE, 71


title: PBMC, mid to older adult, data set ONE, 70


title: CF1 NO


title: CF2 NO


title: PBMC, mid to older adult, data set ONE, 69


title: PBMC, mid to older adult, data set ONE, 68


title: FO3D O

value: With osteoporosis


title: FO2D O


title: sustained CeA female MR2 164_CeA

description: sustained CeA female MR2


title: sustained ACC female MR2 164_ACC

description: sustained ACC female MR2


title: PBMC, mid to older adult, data set ONE, 67


title: PBMC, mid to older adult, data set ONE, 66


title: FO2 O


title: FO3 O


title: PBMC, mid to older adult, data set ONE, 64


title: PBMC, mid to older adult, data set ONE, 65


title: PBMC, mid to older adult, data set ONE, 63


title: PBMC, mid to older adult, data set ONE, 62


title: hPD organoids 2, live sort, rep3, scRNAseq

city: Leiden

first: Françoise

last: Carlotti

address: Albinusdreef 2

country: Netherlands

institute: Leiden University Medical Center

data_processing:
Paired-end reads from automated CEL-seq2 (SORTseq) were aligned to the transcriptome using bwa with default parameters. The transcriptome contained all RefSeq gene models based on the human genome release hg38. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to a sample specific barcode followed by a 4bp unique molecular identifier (UMI). The remainder of the left read contains a polyT stretch followed by a number (<40) of transcript derived bases
Assembly: hg38
Supplementary files format and content: Tab-separated values files containing cell barcodes, read counts and transcript counts

source_name: Pancreatic islet-depleted tissue derived organoids

extract_protocol:
The islet-depleted tissue was mechanically dispersed using a 21G needle (BD Microlance 3), followed by three washes with Hank’s Balanced Salt Solution (Thermo Fisher Scientific) supplemented with 100μg/ml trypsin inhibitor (Merck) at 200g for 4 minutes at 4°C. The tissue was dissociated in TrypLE at 37°C 15-30 minutes depending on the sample. Dissociation was stopped with Advanced DMEM/F12 (Thermo Fisher Scientific) supplemented with 10% Fetal Bovine Serum (FBS; Greiner Bio-One). The cells were centrifuged at 200g for 3 minutes, at 4°C to collect the cell pellet and resuspended in DPBS (no calcium, no magnesium; Thermo Fisher Scientific) supplemented with 2% FBS and 1mM EDTA (Thermo Fisher Scientific) and passed through a 40μm cell-strainer before FACS sorting into 384 well cell capture plates. hPDO's were collected and dissociated for 15 minutes in TrypLE, washed in DPBS, strained and sorted into 384 cell capture plates.
CEL-seq2 (Hashimshony et al 2016)

tag: sort

value: live sort

tag: organoid line

value: line 2


title: PBMC, mid to older adult, data set ONE, 60


title: PBMC, mid to older adult, data set ONE, 61


title: PBMC, mid to older adult, data set ONE, 59


title: hPD organoids 2, live sort, rep1, scRNAseq

value: Pancreatic islet-depleted tissue derived organoids


title: hPD organoids 1, live sort, rep2, scRNAseq

value: line 1


title: hPD organoids 1, live sort, rep3, scRNAseq


title: hPD organoids 2, live sort, rep2, scRNAseq


title: PBMC, mid to older adult, data set ONE, 58


title: PBMC, mid to older adult, data set ONE, 57


title: P578, GP2 sort, rep4, scRNAseq

source_name: Pancreatic islet-depleted tissue

value: Pancreatic islet-depleted tissue

tag: donor

value: GP2 sort


title: hPD organoids 1, live sort, rep1, scRNAseq


title: PBMC, mid to older adult, data set ONE, 55


title: FO1D O


title: P578, GP2 sort, rep3, scRNAseq


title: PBMC, mid to older adult, data set ONE, 56


title: PBMC, mid to older adult, data set ONE, 54


title: P578, GP2 sort, rep2, scRNAseq


title: PBMC, mid to older adult, data set ONE, 52


title: FO1 O


title: P575, GP2 sort, rep3, scRNAseq


title: PBMC, mid to older adult, data set ONE, 53


title: P575, GP2 sort, rep4, scRNAseq


title: PBMC, mid to older adult, data set ONE, 50


title: P575, GP2 sort, rep2, scRNAseq


title: P575, GP2 sort, rep1, scRNAseq


title: PBMC, mid to older adult, data set ONE, 48


title: P587, live sort, rep3, scRNAseq


title: PBMC, mid to older adult, data set ONE, 47


title: P587, live sort, rep2, scRNAseq


title: P570, live sort, rep3, scRNAseq


title: P587, live sort, rep1, scRNAseq


title: PBMC, mid to older adult, data set ONE, 45


title: PBMC, mid to older adult, data set ONE, 46


title: S48h3

city: Hohhot

first: xi

last: zhen

address: Genghis Khan Street

country: China

institute: College of Grassland Resources and Environment, Inner Mongolia Agricultural University

description: Centrifuf (Eppendorf, Centrifuge 5418, Germany); PCR (Bio-rad, MyCycler, Beijing); Ultraviolet spectrophotometer (Thermo, NanoDrop2000, USA); Quantifier (Invitrogen, Qubit2.0, USA); Invitrogen, Magnetic Stand9, USA; Bioanalyzer (Aglient, 2100, USA).

data_processing:
1. Quality control and De novo assembly
2. Functional annotation
3. Unigene quantification, analysis of differentially expressed unigenes (DEGs), cluster analysis, GO and KEGG enrichment
Assembly: No reference genome
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Apocynum venetum

source_name: Leaf tissue

extract_protocol:
A. Add 600 uL Lysis/Binding Buffer to the cell or tissue lysate. Then add 30 uL miRNA Homogenate Additive to homogenate, and mix well by vortexing or inverting the tube several times. Leave the mixture on ice for 10 min. B. Add a volume of Acid-Phenol: Chloroform that is equal to the lysate volume before addition of the miRNA Homogenate Additive. Centrifuge for 5 min at maximum speed (10,000 x g) to separate the aqueous and organic phases. Carefully remove the aqueous (upper) phase without disturbing the lower phase, and transfer it to a fresh tube. C. Add 1.25 volumes of room temperature 100% ethanol to the aqueous phase. D. Pipet the lysate/ethanol mixture (from the previous step) onto the Filter Cartridge (Note: Up to 700 uL can be applied to a Filter Cartridge at a time.). Centrifuge for 30 sec at 13,000 rpm to pass the mixture through the filter. Discard the flow-through.E. Apply 350 uL miRNA Wash Solution 1 to the Filter Cartridge and centrifuge for  30 sec at 13,000 rpm. Discard the flow-through from the Collection Tube, and replace  the Filter Cartridge into the same Collection Tube. F. The 10 uL DNase I and 70 uL Buffer RDD QIAGEN (#79254) were mixed. Then  the mixture was added to the Filter Cartridge. Leave it at the room temperature for 15  min. G. Apply 350 uL miRNA Wash Solution 1 to the Filter Cartridge and centrifuge for  30 sec at 13,000 rpm. Discard the flow-through from the Collection Tube, and replace  the Filter Cartridge into the same Collection Tube. H. Apply 500 uL Wash Solution 2/3 and centrifuge for 30 sec at 13,000 rpm. Draw  it through the Filter Cartridge as in the previous step. Repeat with a second 500 uL aliquot of Wash Solution 2/3. I. Spin the assembly for 1 min to remove residual fluid from the filter. Transfer  the Filter Cartridge into a fresh Collection Tube. Apply 100 uL of pre-heated (95°C)  Elution Solution to the center of the filter. Leave it at the room temperature for 2 min.  Spin for ~20-30 sec at maximum speed to recover the RNA. Collect the eluate (which  contains the RNA) and store it at -70°C.
1. Purify and Fragment mRNA;2.Synthesize First Strand cDNA;3. Synthesize Second Strand cDNA;4. Adenylate 3’Ends;5. Ligate Adapters;6. Enrich DNA Fragments;7.Purification;8.Validate library

value: Leaf tissue

value: wild P. apocinae

value: nutrient solution (containing 300 mmol/L NaCl)


title: P570, live sort, rep1, scRNAseq


title: P578, GP2 sort, rep1,scRNAseq


title: S48h2


title: PBMC, mid to older adult, data set ONE, 43


title: R138, live sort, rep3, scRNAseq


title: R138, live sort, rep2, scRNAseq


title: R138, live sort, rep1, scRNAseq


title: S48h1


title: PBMC, mid to older adult, data set ONE, 51


title: PBMC, mid to older adult, data set ONE, 42


title: S24h3


title: PBMC, mid to older adult, data set ONE, 49


title: PBMC, mid to older adult, data set ONE, 41


title: sci-Plex-EGFRi-PDCLpilot

city: New York

first: José

middle: L

last: McFaline-Figueroa

email: jm5200@columbia.edu, joselmc@uw.edu

state: NY

department: Biomedical Engineering

institute: Columbia University

description: sci-Plex chemical transcriptomic profiling of glioblastoma neurosphere lines exposed to a 6 inhibitor panel targeting EGFR  or dmso vehicle control.

data_processing:
Expression matrices, cell annotations and gene annotations were generated according to the protocol described in our manuscript as well as in Cao et al. 2019 Nature 566(7745) p. 496-502 (three level sci-RNA-seq).
Nuclear barcodes "hash" sequences were extracted from fastq files if the first 10 bp of read 2 match a hash from the appropriate hashSampleSheet.txt (2nd column) within a hamming distance of 1, the last column of the hashSampleSheet.txt file pertains to whether 1 or 2 hashes were used to identify a condition (only single hashes were used in these experiments). Reads were then deduplicated by cell barcode and UMI to create a file of hash UMI counts (hashTable.out.txt files) for each nuclear transcriptome in the experiment. Tab-delimited columns of hashTable.out.txt files correspond to a sample id, the cell barcode identified for that hash, a "_" delimited string with treatment metadata, an axis id for each hash (not used in these experiments), and umi counts for each hash. The first tab-delimited column of the appropriate hashSampleSheet.txt files contains metadata for the experiment divided by underscores. The first "_" delimited string corresponds to the chemical agent, the second corresponds to the dose of the chemical agent in nM, and the third corresponds to the combination of hash plate (e.g. 01, 02) and hash well e.g. (A01, B01). The hash well also corresponds to the orientation of the cells position for drugging. For data related to sci-Plex-EGFRi-ATCCpilot, different hash plates denote technical replicates for a given cell line and the associated CellLine.RT.Plate.csv file contains cell line information based on the RT step of the sci-RNA-seq3 process. For data related to sci-Plex-EGFRi-PDCLpilot, different hash plates denote technical replicates and the associated CellLine.RT.Plate.csv file shows that BT333 was the PDCL used. For data related to sci-Plex-EGFRi-largescreen, hash plates differ in the dose of each chemical agent and the associated CellLine.RT.Plate.csv file contains both PDCL and replicate information. Note that specifically for the large screen, BT228 replicate 2 hash plate 01, the chemical agents for row C and D are in a flipped orientation (i.e., rowD hashes for that sample correspond to rowC treatments and vice-versa.
Assembly: GRCh38
Supplementary files format and content: Expression matrices are output by our pipeline in matrix market exchange format and the cell and gene annotation files that accompany these files are in tsv file format.

source_name: Brain tumor

growth_protocol: Established cell lines were cultured in DMEM supplemented with 10% FBS and 1% penn-strep. Lines were disoociated with Tryp-LE for passaging. Neurosphere cultures were maintained in Neurocult-NS-A proliferation media supplemented with 0.0002% heparin, 20 ng/mL EGFR, 10 ng/mL FGF on low-attachment plates. Neurospheres were dissociated with accutase for passaging and plating.

extract_protocol:
24 hours hours after drug exposure, cells were harvested following the sci-Plex protocols (Srivatsan, McFaline-Figueroa, Ramani et al. 2020 Science) as described in the methods section of our manuscript. Nuclei were isolated in-well and nuclei barcoded by fixation of well-specific barcode containing oligonucleotides. After fixation wells were pooled and nuclei pellets flash frozen until sci-RNA-seq library preparation.
Nuclei were subjected to a modified version of the three-level sci-RNA-seq described in  Cao et al. 2019 Nature 566(7745) p. 496-502 that incorporates random hexamer priming as in Sziraki et al. 2023 Nature Genetics with modifications to allow compatibility with sci-Plex multiples increase yield and decrease cost, see methods.

treatment_protocol: Cells were seeded at 25,000 cells per well in 96 well flat-bottom plates for established lines and v-bottom 96 well plates for neurospheres. 24 hours after seeding, cells were exposed to increasing doses of small molecules or dmso vehicle control.

value: Brain tumor

value: BT333 neurospheres

value: Human glioblastoma brain cancer cells.

value: Cells were treated with increasing doses of the small molecules Afatinib, Brigatinib, CUDC-101, EAI045, Neratinib, Osimertinib or dmso vehicle control.


title: sci-Plex-EGFRi-ATCCpilot

description: sci-Plex chemical transcriptomic profiling of established glioblastoma cell lines exposed to a 6 inhibitor panel targeting EGFR or dmso vehicle control.

value: A172, T98G and U87MG cells


title: sci-Plex-EGFRi-largescreen

description: sci-Plex chemical transcriptomic profiling of glioblastoma neurosphere lines exposed to a 74 inhibitor panel targeting EGFR, controls or dmso vehicle control.

value: BT112, BT228, BT333 neurospheres

value: Cells were treated with increasing doses of 71 EGFR targeting small molecules, 1 EGFR neutralizing antibody, 1 EGFR activator, puromycin or dmso vehicle control.


title: S24h1


title: P570, live sort, rep2, scRNAseq


title: PBMC, mid to older adult, data set ONE, 40

value: PBMC


title: PBMC, mid to older adult, data set ONE, 44


title: S12h3


title: PBMC, mid to older adult, data set ONE, 39


title: PBMC, mid to older adult, data set ONE, 38


title: KO male4

city: Portland

first: Taasin

last: Srivastava

address: 3181 SW Sam Jackson Park Road

department: Pediatrics

institute: Oregon Health & Science University

data_processing:
Tophat2 with default parameters was to align the sequenced reads against the mouse genome using the GRCm38
HTSeq python software with default parameters was used to quantify the transcripts of the aligned reads using the corresponding GRCm38 gene annotation model from Ensembl and the downstream analysis was done in R-studio (v.2023.03.0+386)
Raw read counts were processed and normalized using the median of ratio method. Low abundance genes below a mean count of 5 reads per sample were filtered out.
The count data was used as an input for DEG analysis using DESeq2 (v.1.38.3; R package)
Assembly: mm10
Supplementary files format and content: tab delimited text file includes normalized counts for each sample

source_name: Forebrain

growth_protocol: Forebrain slice cultures were prepared from postnatal day 4 mouse pups.

extract_protocol:
RNA was harvested using RNAeasy kit (Qiagen) and 1ug was used to generate cDNA libraries
The libraries were prepared using Smart Seq V4 chemistry

treatment_protocol: The slices were exposed to 5% Horse serum in DMEM for 24 hours. Both the WT and KO slices were exposed to serum containing DMEM.

value: Forebrain

value: Knock Out

value: 5% horse serum


title: S12h2


title: KO male3


title: S12h1


title: PBMC, mid to older adult, data set ONE, 37


title: PBMC, mid to older adult, data set ONE, 36


title: Het male3

value: Heterozygous


title: L4

type: RNA

city: Genova

first: Sara

last: Stigliani

address: largo R Benzi 10

country: Italy

institute: IRCCS AOU San Martino-IST

description: gene expression analysis

hyb_protocol: Purified-Cye3-labeled cDNA (3μg) were hybridized to Human GE4×44K v2 microarrays (Agilent Technologies) at 65°C, 10 rpm for 17 h.

scan_protocol: Slides were washed and scanned by Agilent G2505C scanner. Data were extracted using Feature Extraction (FE) software (Agilent Technologies).

data_processing: Microarray gene expression data were analysed in R/BioConductor. We used the limma and samr R package to normalise agilent data, performing background correction and quantile normalization between arrays. Array probe annotation was performed with hgug4112a.db R package. Probe with no annotation, low counts or no annotations ones were removed. Differentially expressed genes were identified by Significance Analysis of microarrays applying variance and intensity filters. The paired or unpaired SAM analysis (significance analysis of microarray) was used when appropriate.

source_name: long cryopreserved spermatozoa pool4

label_protocol: Total RNA from each pool (5ng) was amplified using Ovation Pico WTA SystemV2 (NuGEN Technologies, San Carlos, CA, USA). After amplification, cDNA was labeled by Enzymatic Labeling Kit (Agilent Technologies).

extract_protocol: Total RNA was extracted from each sample using the miRNeasy Micro kit (Qiagen, Hilden, Germany), according to the manufacturer’s protocol. Quantification and quality control of RNA were performed by High Sensitivity RNA on 2200 Tape Station system (Agilent Technologies, Santa Clara, CA, USA). For C1-4 and F1-4 13 paired samples were divided in 4 pools (the same patients were used in the fresh and cryopreserved pools). For L1-4 11 samples were divided in 3 pools.

treatment_protocol: For samples C1-4 and F1-4; semen samples were obtained from 13 men, who donated an aliquot of their semen to the study. Each sample was divided in two aliquots, one was diluted in Sydney IVF Gamete Buffer (Cook Medical, Sydney, Australia) and centrifuged at 1400 rpm for 10 min. The total RNA was immediately extracted. The second aliquot was diluted 1:1 by dropwise addition of a glycerol-based cryoprotectant with continuous shaking (Freezing medium test yolk buffer; Irvine Scientific, Santa Ana, CA, USA) and then loaded into High-Security sperm straws (Cryo Bio System, L’Aigle, France) that contained 0.5 mL of fluid each. After 7 days in liquid nitrogen the samples were thawed for 5–10 min at room temperature, washed in Sydney IVF Gamete Buffer (Cook Medical, Sydney, Australia) and centrifuged at 1400 rpm for 10 min and the total RNA was extracted. For samples L1-4 semen samples cryopreserved for a long period (7-10 years) were thawed washed in Sydney IVF Gamete Buffer (Cook Medical, Sydney, Australia) and centrifuged at 1400 rpm for 10 min and the total RNA was extracted.

tag: gender

value: male


title: S6h3


title: S6h2


title: L1

description: gene expression analysis

source_name: long cryopreserved spermatozoa pool1


title: S24h2


title: PBMC, mid to older adult, data set ONE, 35


title: L3

description: gene expression analysis

source_name: long cryopreserved spermatozoa pool3


title: Het male2


title: F4

description: gene expression analysis

source_name: fresh spermatozoa pool4


title: F3

description: gene expression analysis

source_name: fresh spermatozoa pool3


title: KO male2


title: S6h1


title: S2h3


title: KO male1


title: PBMC, mid to older adult, data set ONE, 33

source_name: PBMC


title: PBMC, mid to older adult, data set ONE, 31


title: KO female4


title: PBMC, mid to older adult, data set ONE, 32


title: KO female3


title: C4

description: gene expression analysis

source_name: cryopreserved spermatozoa pool4


title: S2h1


title: KO female2


title: KO female1


title: BAZ2A_iCLIP_mESC_rep3_background

city: Zurich

first: Raffaella

last: Santoro

address: Winterthurerstrasse 190

department: Dep. of Molecular Mechanisms  of Disease

country: Switzerland

institute: University of Zurich

data_processing:
iCLIP data was generated for crosslinked and non-crosslinked background control samples in triplicates (17-29x10^6 reads). iCLIP reads were demultiplexed and trimmed of adaptors using Flexbar (version 3.5). Reads were then mapped to the mouse genome (mm10) using STAR (version 2.6). Mapped reads were deduplicated using UMI-tools (version 0.5.1). Peaks were called using omniCLIP (version 0.1.0) with default parameters.
Assembly: mm10 (GRCm38)
Supplementary files format and content: BAZ2A.omniCLIP.peaks.ensembl.bed: Identified RNAs bound by BAZ2A enriched in crosslinked samples by OmniCLIP.
Library strategy: iCLIP

growth_protocol: Mouse embryonic stem cells (E14) were cultured in N2B27 medium with LIF/2i.

extract_protocol:
About 2.5x10^6 mouse ESCs were subjected to 400 mJ/cm2 UV-C (254 nm) crosslinking energy. Cells were subsequently scraped on ice and pelleted at 500 g. To control for unspecific RNA binding 2.5x10^6 mouse ESCs were also subjected to iCLIP analysis without being subjected to UV-crosslinking. The entire procedure was performed in triplicates for each condition. To isolate nuclei cells were resuspended in hypotonic buffer (10 mM HEPES pH 7.6, 1.5 mM MgC2, 10 mM KCl), incubated 10 min on ice, then TritonX-100 was added to the final concentration of 0.1%. Upon additional 10 min of incubation on ice, nuclei were pelleted by 5 min centrifugation at 1600 g at 4°C. Nuclei were lysed into lysis buffer (50 mM Tris pH 7.4, 100 mM NaCl, 0.1% SDS, 1% NP-40, 0.5% NaDeoxycholate) and treated with TURBO™ DNase and RNase I (ThermoFisher, AM2238 and EN0601) (high RNase condition 1:50; low RNase condition 1:400) for 3 min at 37°C at 1100 rpm. To properly solubilize BAZ2A, lysate was subjected to high salt extraction by adding NaCl to final concentration of 400 mM. Upon 10 min incubation on ice, lysate was then centrifuged 10 min at 21000 g at 4°C. Salt concentration was diluted back to physiological 150 mM NaCl by adding iCLIP lysis buffer lacking NaCl.
Immunoprecipitation was performed by incubating lysate with the Anti-FLAG® M2 Affinity Gel agarose beads overnight at 4°C under rotation. Beads were washed subsequently twice in High-salt wash (50 mM TRIS PH 7.4, 1 M NaCl, 1 mM EDTA, 1% NP-40, 0.1% SDS, 0.5% NaDeoxycholate), twice in 0.8 M Urea wash (0.8 M Urea, 20 mM Tris pH 7.4, 250 mM NaCl, 1 mM EDTA, 1% NP-40, 0.1% SDS, 0.5% NaDeoxycholate), and twice in PNK buffer (20 mM Tris pH 7.4, 10 mM MgCl2, 0.2% Tween-20). All washes were performed by 5 min incubation at 4°C under rotation followed by 3 min centrifugation at 1300 g at 4°C. RNA 3’ end dephosphorylation and L3 adapter ligation steps were performed on beads according to original protocol. 90% of the beads were subjected to RNA 5’ end labeling in a total volume of 20 µl of hot PNK mix 2 µl 10× PNK buffer, 16.5 µl H2O, 1 µl PNK, 0.5 µl of 10µCi/µl γ-32P-ATP). Upon 10 min incubation at 37°C at 1100 rpm, beads were quickly washed in PNK buffer.
Immunoprecipitated BAZ2A-RNA complexes were eluted from beads by adding a mix containing 20 µl PNK buffer, 6 µl of 4× LDS NuPAGE sample buffer and 1 µl of 1 M DTT and incubated 10 min at 70°C at 1100 rpm. Eluted material was then subjected to SDS-PAGE on a 3-8% TrisAcetate pre-casted gel for 1h at 150 V followed by semidry transfer on nitrocellulose membrane using the iBlot™ Gel Transfer Device (Invitrogen). Membrane was then exposed for 1h or overnight to a Fuji film for autoradiography. Isolation of RNA species associated with BAZ2A from nitrocellulose membrane and reverse transcription were performed according to original protocol. Crosslinked samples were reverse transcribed using the RT#Clip primer #1 (5Phos/NNAACCNNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC), whereas the RT#Clip primer #3 (5Phos/NNATTGNNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC) was used for non-crosslinked samples. Upon alkaline hydrolysis, precipitated cDNA was subjected to gel purification on a 6% TBE-UREA pre-casted gel according to original protocol. Bands of 80-120 nt were cut out from the gel using the stained DNA ladder and the plastic marks on the gel support for orientation. Gel pieces were then placed into a 0.5 ml microtube, where a hole on its bottom was previously mate using a 21 g needle. Microtube was placed on a 2 ml tube and subjected to centrifugation for 2 min at max speed at room temperature (RT). Crushed gel pieces were then supplemented with 400 µl TE buffer and incubated 30 min at 50°C at 1100 rpm. Eluted material was then passed into a Costar® Spin-X® Centrifuge Tube Filters (Corning, 8161) with two glass pre-filters by spinning 1 min at max speed at RT, and cDNA was subsequently isolated by Phenol:Chloroform extraction following original protocol’s instructions.
Ligation of the RT#Clip primer to the 5’ end of the cDNA via circularization and re-linearization steps were performed according to the original protocol. PCR optimization was performed as indicated and 28 cycles amplification was selected for preparative PCR. Since quality check on gel clearly showed no amplification products for non-crosslinking samples, each crosslinked replicate was pulled in a 1/1 volume ratio with its corresponding non-crosslinked replicate. Libraries were then size-selected and further purified using the BluePippin system (Sage Science) according to manufacturer’s instructions. Upon quantification and quality check on 4200 TapeStation System (Agilent), samples were subjected to next generation sequencing.

value: Mouse embryonic stem cells (ESCs)

value: BAZ2A endogenously Flag and HA tagged

tag: antibody

value: anti-FLAG


title: Het male1


title: BAZ2A_iCLIP_mESC_rep3_crosslinked


title: PBMC, mid to older adult, data set ONE, 34


title: C1

description: gene expression analysis

source_name: cryopreserved spermatozoa pool1


title: BAZ2A_iCLIP_mESC_rep2_crosslinked


title: C3

description: gene expression analysis

source_name: cryopreserved spermatozoa pool3


title: C2

description: gene expression analysis

source_name: cryopreserved spermatozoa pool2


title: F1

description: gene expression analysis

source_name: fresh spermatozoa pool1


title: PBMC, mid to older adult, data set ONE, 29


title: S0h2

value: Leaf tissue

value: wild P. apocinae

value: nutrient solution (containing 300 mmol/L NaCl)


title: F2

description: gene expression analysis

source_name: fresh spermatozoa pool2


title: Het female3


title: Het female2


title: PBMC, mid to older adult, data set ONE, 28


title: BAZ2A_iCLIP_mESC_rep2_background


title: S0h1


title: S2h2


title: PBMC, mid to older adult, data set ONE, 27


title: Het female1


title: PBMC, mid to older adult, data set ONE, 26


title: serum treated KO forebrain slice 3

treatment_protocol: The slices were exposed to 5% Horse serum in DMEM for 4 hours. Both the WT and KO slices were exposed to serum containing DMEM.

value: KO

value: 5 percent horse serum


title: BAZ2A_iCLIP_mESC_rep1_background


title: serum treated KO forebrain slice 2


title: PBMC, mid to older adult, data set ONE, 30


title: OSKM-CMs_B3

city: SINGAPORE

first: Yike

last: Zhu

state: Singapore

address: 14 Medical Dr, Singapore, MD6 - Centre for Translational Medicine

country: Singapore

institute: National University of Singapore

data_processing:
Well established quality-control tools such as CASAVA version 1.8.2 (Illumina), FASTQC (Babraham Bioinformatics) and Trimmomatic were used to filter raw reads.
Filtered reads were aligned to mouse genome (Mus Musculus) mm9 assembly using mapping software, STAR version 2.5.3 using default settings.
Gene count per sample was computed with htseq-count, using mm9 GENCODE version M1.
Genome_build: mm9
Supplementary_files_format_and_content: abundance measurements

source_name: Adult mouse CMs_OSKM

extract_protocol:
CMs were isolated and purified from adult mice using the protocol published previously (Ackers-Johnson et al., 2016). Total RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: AAV-cTnT-Oct4-His6, AAV-cTnT-Sox2-Flag, AAV-cTnT-Klf4-HA and AAV-cTnT-Myc-V5 were mixed and administered at a titer of 2.5 × 1010 virus genome (vg)/body gram each factor via thoracic cavity injection to 8-week-old male C57BL/6 mice, with AAV-cTnT-BFP administered at a titer of 10 × 1010 vg/body gram as control group.

value: Heart

tag: age

value: 12-14 weeks old

value: cardiomyocytes (CMs)

value: AAV-cTnT-OSKM


title: PBMC, mid to older adult, data set ONE, 24

value: PBMC


title: serum treated KO forebrain slice 1

value: Forebrain


title: OSKM-CMs_B2


title: OSKM-CMs_B1


title: PBMC, mid to older adult, data set ONE, 23


title: PBMC, mid to older adult, data set ONE, 22


title: serum treated WT forebrain slice 1

value: WT


title: serum treated WT forebrain slice 2


title: serum treated WT forebrain slice 3


title: PBMC, mid to older adult, data set ONE, 19


title: Control-CMs_C3

source_name: Adult mouse CMs_control

value: AAV-cTnT-BFP (Control)


title: WNT 10x, SOX2 positive, rep 2

city: Houston

first: Aryeh

last: Warmflash

state: TX

address: 6100 Main St

institute: Rice University

data_processing:
To quantify the abundance of transcripts for each sample, Salmon v1.9.01was used. Reads were aligned to the human transcriptome (GRCh38) index for salmon, with salmon index using the selective alignment method (salmon_sa_index:default in http://refgenomes.databio.org/v3/ genomes/splash/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4). We quantified transcripts with Salmon using the -l A flag to infer the library type (paired-end) automatically and the –validateMappings -o flag to use the mapping-based mode. The resulting datasets were then processed using the tximeta2 package in R, and the counts matrix was exported for downstream analyses.
Assembly: GRCh38
Supplementary files format and content: Excel file with the counts matrix for each replicate in each sample, obtained by processing the Salmon output with the tximeta2 package in R.

source_name: ESI017 SOX2::mCitrine

growth_protocol: SOX2::mCitrine cells were grown in the chemically defined medium mTeSR Plus (STEMCELL Technologies) in Matrigel (Corning, 1:200 with DMEMF12) coated culture dishes and kept at 37C, 5% CO2

extract_protocol:
RNA was collected with the Invitrogen RNAqueous-Micro Total RNA Isolation Kit. Sequencing was performed by Novogene Co. using the Illumina paired-end 150 platform (Novaseq 6000).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: SOX2::mCitrine cells were seeded into 4 separate micropattern glass coverslips CYTOO: (1) Control consisting of colonies in N2B27 medium only, (2) Colonies treated with FGF8 (200 ng/ml) with WNT3a (100 ng/ml), (3) Colonies treated with FGF8 (200 ng/ml) with WNT3a (300 ng/ml), and (4) Colonies treated with FGF8 (200 ng/ml) with WNT3a (1000 ng/ml); all for 3 days. Colonies were dissociated into single-cell suspensions using Accutase at 37ºC for 5 minutes. Cells were collected, centrifuged at 1000 rpm for 4 minutes, and re-suspended in PBS-EDTA (10 mM). Cells were then filtered through a 5ml Polystyrene Round-Bottom tube with cell-strainer mesh 40um cap (FALCON). A Sony SH800S Cell Sorter with a 488 nm laser was used to separate the SOX2 positive cells from the negative ones. Another biological repeat of all conditions except (3) was performed using the same protocol.

value: ESI017 SOX2::mCitrine

value: hPSCs

value: N2B27 + FGF8 (200ng/ml) + WNT3A (1000ng/ml) for 3 days


title: InjATAC1_Y-S+_2

city: Cambridge

first: Helle

last: Jorgensen

address: Papworth Road

department: Cardiorespiratory section

institute: University of Cambridge

description:
ATAC-seq Nextera kit
Illumina HiSeq or HiSeq2500-RapidRun

data_processing:
Raw sequence reads were split based on their Nextera barcodes and sequencing quality was assessed using the FASTQC package (Andrews, 2010). Adaptor sequences and base-calls with Phred score < 20 were removed using Trim Galore v.0.6.1, running Cutadapt v.1.18. Reads trimmed to <20bp were discarded and quality-filtered reads aligned to the GRC38.98 Mus musculus genome using Bowtie2 v.2.3.5, discarding reads with >1% error probability. Reads were shifted to account for Tn5 transposase adaptor sequence insertion (+4/-5bp) using alignmentSieve within deeptools v.3.4.3. BAM files were generated using the view command within samtools v.1.18 and deeptools v.3.4.3 was used for conversion to BigWig format for data visualisation in the IGV browser, removing duplicate reads and normalisation by counts per million.
Peak-calling was done after removing reads mapping to a blocklist with repetitive sequences and other mapability issues (a total of 0.02% of the genome, samtools, v.1.18) or having low confidence (bedtools v.2.27.1) using MACS2 v.2.2.7.1 (paired-end mode with parameters: –f BAMPE –nomodel –nolambda –q 0.05 –broad). Only peaks that overlapped at least 50% between biological replicates were included in condition-specific peak lists. Peaks were associated with genomic features using ChIPseeker v.1.24.0.
Assembly: GRC38.98 Mus musculus genome
Supplementary files format and content: BigWig files for each sample

source_name: carotid

growth_protocol: Cells are from carotid arteries of lineage labelled Myh11-EYFP/Mki67-RFP animals 7 days after carotid ligation surgery and non-ligated littermate controls.

extract_protocol:
The Omni-ATAC protocol was used to process 5,000 cells (Corces et al, 2017) from each sample (two independent replicates), using 10-13 PCR amplification cycles
Libraries were sequenced with a 50 bp paired-end run cycle (Illumina HiSeq or HiSeq2500-RapidRun, 40-60 million reads/sample).

treatment_protocol: Lineage-traced (EYFP+) VSMCs were isolated by cell sorting (BD AriaIII) from non-ligated carotid arteries of control animals. Cells from ligated arteries were stained for SCA1 prior to sorting EYFP+SCA1+, EYFP+SCA1- or EYFP-SCA1+ cells.

value: carotid

value: carotid ligation


title: PBMC, mid to older adult, data set ONE, 20


title: PBMC, mid to older adult, data set ONE, 18


title: WNT 10x, SOX2 negative, rep 2


title: InjATAC1_Y-S+_1


title: InjATAC1_NSY+_2

value: EYFP+ VSMCs

value: non-ligated control


title: WNT 1x, SOX2 positive, rep2

value: N2B27 + FGF8 (200ng/ml) + WNT3A (100ng/ml) for 3 days


title: BAZ2A_iCLIP_mESC_rep1_crosslinked

value: Mouse embryonic stem cells (ESCs)

value: BAZ2A endogenously Flag and HA tagged

value: anti-FLAG


title: PBMC, mid to older adult, data set ONE, 17


title: InjATAC1_NSY+_1


title: PBMC, mid to older adult, data set ONE, 25


title: PBMC, mid to older adult, data set ONE, 16


title: Control, rep 2

value: N2B27 for 3 days


title: InjATAC1_Y+S-_2

value: EYFP+SCA1- VSMCs


title: Control-CMs_C5

value: Heart

value: 12-14 weeks old

value: cardiomyocytes (CMs)


title: PBMC, mid to older adult, data set ONE, 15

value: PBMC


title: PBMC, mid to older adult, data set ONE, 21


title: InjATAC1_Y+S-_1


title: WNT 10x, SOX2 positive, rep 1

value: ESI017 SOX2::mCitrine


title: PBMC, mid to older adult, data set ONE, 14


title: InjATAC1_Y+S+_2

value: EYFP+SCA1+ VSMCs


title: WNT 10x, SOX2 negative, rep 1

value: hPSCs

value: N2B27 + FGF8 (200ng/ml) + WNT3A (1000ng/ml) for 3 days


title: PBMC, mid to older adult, data set ONE, 13


title: InjATAC1_Y+S+_1

value: carotid

value: carotid ligation


title: WNT 3x, SOX2 positive, rep 1

value: N2B27 + FGF8 (200ng/ml) + WNT3A (300ng/ml) for 3 days


title: WNT 3x, SOX2 negative, rep 1


title: PBMC, mid to older adult, data set ONE, 11


title: Oct4C48S#46 Bl/6J ESC_RA_D2_2

city: Salt Lake City

first: Dean

last: Tantin

state: UT

address: N Campus Dr, Salt Lake City, UT 84103

department: Pathology

institute: University of Utah

data_processing:
STAR version 2.7.9a
Differential expression analysis with DESeq2
Assembly: mm39
Supplementary files format and content: tab-delimited text files

source_name: Embryonic stem cell

growth_protocol: Undifferentiated ESCs were cultured as described previously with “2iV” supplementation: the MEK inhibitor PD03259010 (1 μM, LC laboratories) and the glycogen synthase kinase-3b (GSK3b) inhibitor CHIR99021 (3 μM, LC Laboratories). Culture medium was also supplemented with 50 mg/mL ascorbic acid (Sigma).

extract_protocol:
Undifferentiated and RA-differentiated cells were collected, and RNA was prepared using a kit (RNeasy, Qiagen).
RNA libraries for RNA-seq were prepared with NEBNext rRNA Depletion Kit v2 (Human, Mouse, Rat) (E7400) following manufacturer's protocol

treatment_protocol: Differentiated parental and derived Oct4C48S ESC lines were differentiated in media lacking LIF and containing 1.5mg/L RA for 2 days.

value: Embryonic stem cell

value: Oct4 C48S

value: RA Day6


title: Oct4C48S#46 Bl/6J ESC_RA_D2_3

value: RA Day7


title: WNT 1x, SOX2 negative, rep1

value: N2B27 + FGF8 (200ng/ml) + WNT3A (100ng/ml) for 3 days


title: WT Bl/6J ESC_RA_D2_3

value: WT

value: RA Day4


title: WNT 1x, SOX2 positive, rep1


title: WNT 1x, SOX2 negative, rep2


title: WT Bl/6J ESC_RA_D2_2

value: RA Day3


title: PBMC, mid to older adult, data set ONE, 10


title: Oct4C48S#46 Bl/6J ESC_RA_D2_1

value: RA Day5


title: PBMC, mid to older adult, data set ONE, 9

value: PBMC


title: WT Bl/6J ESC_RA_D2_1

value: RA Day2


title: PBMC, mid to older adult, data set ONE, 8


title: Control, rep 1

description: ctrl

value: ESI017 SOX2::mCitrine

value: N2B27 for 3 days


title: PBMC, mid to older adult, data set ONE, 7


title: PBMC, mid to older adult, data set ONE, 6


title: Oct4C48S#46 Bl/6J ESC_NT_3

value: No treatment


title: PBMC, mid to older adult, data set ONE, 5


title: PBMC, mid to older adult, data set ONE, 4


title: Oct4C48S#46 Bl/6J ESC_NT_2


title: PBMC, mid to older adult, data set ONE, 2


title: WT Bl/6J ESC_NT_2


title: PBMC, mid to older adult, data set ONE, 1


title: PBMC, mid to older adult, data set ONE, 12


title: PBMC, mid to older adult, data set ONE, 3


title: TRIP10 96 hpi

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

data_processing:
for sgRNA libraries, MAGeCK v0.5.6 was used to count sgRNA from FASTQ files
for genomic target loci, sequences were aligned to the human genome using STAR v2.5.3a 42 with the following flags: scoreDelBase 0, scoreDelOpen 0, scoreInsOpen 0, scoreInsBase 0, alignIntronMin 300, alignIntronMax 299. The indel rate was calculated as the fraction of reads containing insertions or deletions based on the CIGAR sequence.
Assembly: hg19
Supplementary files format and content: sgRNA_counts.csv is a coma separated file where each line contains an sgRNA name, the gene it targets and the read counts in each of the samples in the paper
Supplementary files format and content: indel_counts.tsv is a tab separated file listing the number of reads containing indels (Indel.reads) and the number of reads without mutations (WT.reads), in each sample. Samples are defined by targeted gene and by time point (tp)
Library strategy: amplicon sequencing

source_name: HFF

extract_protocol:
DNA from cells and virus pellets was extracted using a published protocol (Chen et al. 2015, Cell). The viral and cell pellets resuspended in 300 µl and 6 ml of NK buffer, respectively, and DNA extraction was continued normally with volumes adjusted to the 300 µl start, and GlycoBlue™ (Thermo-Fisher, catalog number AM9516) was added at the stage of DNA precipitation.
the region of interest (sgRNA casette or targeted genomic locus) was PCR amplified with addition of illumina adaptors, followed by SPRI bead size selection and purification of the product.

tag: experiment type

value: host knockout efficiency

tag: time

value: 96 hpi

value: HFF

tag: selection round

tag: replicate

tag: targeted gene


title: RPF_DIMT1.rep1

city: philadelphia

first: Fange

last: Liu

state: PA

address: 415 curie blvd, Clinical Research Building Rm 350

institute: UPENN

description: ribo-minus depletion RNA

data_processing:
The high throughput sequencing reads were adaptor and quality trimmed using Trimmomatic with following command: trimmomatc SE -phred33 ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 MAXINFO:20:0.5 MINLEN:20.
Reads mapping to rRNA, tRNA and mtDNA should be cleaned firstly using bowtie2. The rRNA sequences were download from the genebank. The tRNA seqeunces were downloaded from gtRNA database. The mtDNA seqeunce were diffectly obtained from the whole genome sequence.
Map the clean reads to genome using STAR with following command: STAR --runThreadN 8 --alignSJDBoverhangMin 1 --alignSJoverhangMin 51 --outFilterMismatchNmax 2 --alignEndsType EndToEnd  --readFilesCommand gunzip -c --outFileNamePrefix $sample --quantMode GeneCounts --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 31532137230 --outSAMattributes All.
Count the read for each gene using featureCounts.
Genome_build: GRCh38
Supplementary_files_format_and_content: table with raw gene counts for every gene of every sample

growth_protocol: MOLM-13 cells were cultured using RPMI-1640 medium with  10% CS and 1% Pen/Strep

extract_protocol:
The cells were harvested by cell lifter after being washed with ice-cold PBS supplemented with CHX (100 μg/ml). The cell pellets were resuspended in lysis buffer (10 mM Tris-HCl at pH 7.4, 150 mM Kcl, 5 mM MgCl2, 100 mg/ml CHX, 0.5% Triton X-100, Protease Inhibitor Cocktail, Rnase inhibitor, and 100 μg/ml CHX) and kept on ice for 15 min. The cell lysates were centrifuged at 13,000 rpm for 15 min at 4°C to remove the cell debris. 100 μl of the cell lysis was aliquoted and 10 μl of 10% SDS was added to it. The Zymo Research RNA Clean &  Concentrator-25 kit was used to purify the total RNA. 200 μl of the cell lysis was aliquoted and 1 U/μl Rnase I was added to it and  kept  at RT for 30 min. Further  Rnase  activity was stopped by addition of SUPERase:In (Ambion). A 10 - 50% w/v sucrose gradient was prepared in the lysis buffer without Triton X-100 by the Gradient Master (BioCamp). The digested cell lysis was layered on top of the gradient and centrifuged at 35,000 rpm for 2.5 hrs at 4°C in a SW-40Ti (Beckman) rotor using an Optima XE-100 Ultracentrifuge (Beckman). Then, the gradient was fractionated into 1 mL by a Biocomp piston fractionator with a TRIAX flow cell for continuous UV detection, and the monosome fractions were pooled. The Zymo Research RNA Clean &  Concentrator-25 kit was used to purify the RPF subsequencially. Obtained RNA was depleted of rRNA with Ribo-minus kit (Invitrogen). For RPF, the RNA was further separated in15% TBE-Urea gel and stained with SYBR Gold. Gel slices containing nucleic acid 27-30 nt were excised and purifed using Zymo small RNA gel purication kit.
Libraries were constructed according to NEBNext Small RNA Library Prep kit (NEB) protocol. The concentrations for all the libraries were determined by KAPA Library Quantification Kit (KAPA Biosystems) following the manufacturer’s protocol, and subjected to Next-generation high-throughput sequewncing using an illumina NextSeq 550 with a single-end 75-bp read length.
Ribo-seq

treatment_protocol: 100 μg/ml cycloheximide (CHX) was added to the media and incubated for 7 min to hold ribosome on the mRNA

tag: treatment

value: DIMT1 depletion


title: WT Bl/6J ESC_NT_1

tag: tissue

value: Embryonic stem cell

tag: cell line

tag: cell type

tag: genotype


title: TRIP10 uninfected

value: 0 hpi


title: StC in N-fix+NH3Cl2 biol4

city: Rio de Janeiro

first: Luis

middle: Willian

last: Pacheco Arge

state: Rio de Janeiro

address: Av. Carlos Chagas Filho, 373

department: Genetica

country: Brazil

institute: UFRJ

data_processing:
The library cleaning step was performed using Trimmomatic Ver. 0.39, where possible adapters and low-quality bases were removed from the raw data files.
Reads from each library were mapped against the C. thermoautotrophica StC genome using Bowtie2 Ver. 2.3.4.3 (Li et al., 2023). Mapping text files (SAM) were converted to binary format (BAM) using Samtools Ver. 0.1.20 (Li et al., 2009), and then used to count mapped reads by genes. HTSeq Ver. 2.0.3 (Siddique et al., 2021) was used to perform the step of counting of mapped reads over the genome, and the expression values were normalized to TPM (Transcript Per Million).
Supplementary files format and content: text format of raw counts

organism: Carbonactinospora thermoautotrophica

source_name: bacterial cell

growth_protocol: The cells of StC were grown under three different conditions: i) autotrophically in a N-FIX solid culture medium with a gas atmosphere (CO/CO2/N2/O2); ii) heterotrophically in R2A culture medium (glucose and peptone as carbon and nitrogen source respectively) solidified with Noble Ágar (Sigma-Aldrich); II)N-FIX solid culture medium with a gas atmosphere (CO/CO2) Aand NH4Cl2

extract_protocol:
RNA  were extracted from the same sample using NucleoSpin TriPrep kit (Macherey-Nagel). 100 ug of a total RNA was used for  Total RNA for the construction the sequencing libraries
RNA libraries for RNA-seq were prepered using using the KAPA mRNA HyperPrep Kits (Roche) by following the manufacturer's instructions

treatment_protocol: The cells of StC were grown for four days at 60 °C

tag: strain

value: StC

value: bacterial cell

value: carbon gasses; organic nitrogen NH4Cl3


title: RPF_Rosa.rep2

description: ribo-minus depletion RNA

value: Rosa depletion


title: StC in N-fix+NH3Cl2 biol5


title: RPF_Rosa.rep1

description: ribo-minus depletion RNA


title: TRIP10 48 hpi

value: 48 hpi


title: StC in N-fix+NH3Cl2 biol3


title: StC in N-fix+NH3Cl2 biol2


title: WT Bl/6J ESC_NT_3

value: WT


title: TRIP10 24 hpi

value: 24 hpi


title: Input_DIMT1.rep2

description: ribo-minus depletion RNA


title: TRIP10 10 hpi

value: 10 hpi


title: StC in R2A biol4

value: Heterotrophic condition


title: StC in R2A biol5


title: RRM2 uninfected


title: RRM2 48 hpi


title: Input_Rosa.rep2

description: ribo-minus depletion RNA


title: Input_Rosa.rep1

description: ribo-minus depletion RNA


title: Input_DIMT1.rep1

description: ribo-minus depletion RNA


title: StC in R2A biol2


title: RRM2 96 hpi


title: StC in R2A biol3


title: RPF_DIMT1.rep2

description: ribo-minus depletion RNA


title: StC in R2A biol1


title: RRM2 24 hpi


title: StC in N-fix biol5

value: Autotrophic condition


title: passage 6 spleen untreated, 2

city: Columbus

first: Bradley

middle: Wayne

last: Blaser

state: OH

address: 400 W 12th Ave

department: Comprehensive Cancer Center

institute: Ohio State University

description:
Mus musculus/Homo Sapiens xenograft
10x Genomics

data_processing:
Cell barcode/gene count matrices were generated using Cellranger v 6.1.2.  The reads were aligned to the combined GRCh38/mm10 reference.
Human cells were selected using the sample_barcodes.csv file generated by Cellranger.
Low quality cells were identified by low feature counts (more than 2 median absolute deviations less than the median for the sample) or high percent of mitochondrial reads (more than 2 median absolute deviations greater than the median for the sample) and filtered out.
Doubletfinder was used to predict and remove high-likelihood doublet events.
Dimension reduction was performed using PCA and UMAP algorithms implemented within monocle3.
Clustering was performed using the louvain, leiden and partitioning algorithms as implemented in monocle3.
Assembly: GRCh38/mm10
Supplementary files format and content: XX_barcodes.tsv.gz:  tab delimited file containing filtered cell barcodes generated by Cellranger.
Supplementary files format and content: XX_features.tsv.gz:  tab delimited file containing gene identifiers from the GRCh38/mm10 reference
Supplementary files format and content: XX_matrix.mtx.gz:  Sparse matrix containing gene counts per cell barcode.
Supplementary files format and content: XX_sample_barcodes.csv:  comma delimited file with cell barcodes and genome identified by Cellranger.

source_name: spleen

extract_protocol:
Single splenocytes were isolated using the 10X Genomics 5' Capture Immune Profiling kit.  For samples with less than 75% viability, the Miltenyi dead cell removal kit was used.
Gene expression and immune receptor libraries were constructed according to the manufacturer's protocol.

value: spleen

value: primary human mantle cell lymphoma cells and murine splenocytes

value: untreated


title: progeny 5 dpi rep C

value: VECOS library screen

value: 5 dpi

value: HFF

value: C


title: passage 6 spleen untreated, 1


title: RRM2 10 hpi

value: host knockout efficiency


title: passage 7 spleen PRMT5i


title: StC in N-fix biol4

value: StC

value: bacterial cell


title: progeny 5 dpi rep B

value: B


title: StC in N-fix biol3


title: progeny 5 dpi rep A

value: A


title: StC in N-fix biol2


title: passage 6 spleen PRMT5i, 2


title: passage 6 spleen PRMT5i, 1


title: secreted 5 dpi rep C


title: passage 5 spleen untreated


title: StC in N-fix biol1


title: cells 5 dpi rep C


title: secreted 5 dpi rep A


title: RNAseq_Ca_2

city: Beijing

first: Chuan

last: Ye

address: 38 Xueyuan Road, Haidian District

institute: Peking University

data_processing:
Illumina Casava1.7 software used for basecalling. Trim-galore v0.6.7 was used for adapter trimming and low-quality reads. Clean reads mapping was conducted by Hisat2 v2.2.1, and mm10 was used as mouse reference genome. Gene expression was quantified by featureCounts v2.0.1.
Assembly: mm10
Supplementary files format and content: An Excel file contains count values for each gene of each sample.

source_name: Intestinal epithelia

growth_protocol: 108 CFU C. albicans or PBS was gavaged to  Apoe-/-  mice every 3 days for 2 weeks. Then the intestinal epithelia was collected.

extract_protocol:
The polyA mRNA isolation was performed using Oligo(dT) beads
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Intestinal epithelia

value: Candida albicans


title: RNAseq_Ca_1


title: insc-GAL4>orb2RNAi brains, sample 1

city: Durham

first: Don

last: Fox

state: NC

address: DUMC Box 3813  C315 LSRC  Duke University

institute: Duke University

data_processing:
Galaxy version 24.0.1.dev0
Reads were trimmed by TrimGalore! To Phred quality score 20
Trimmed reads were mapped with HISAT2 to DmBDGP6.32
Read counts made with featurecounts
Normalization and significant changes made with DESeq2
Assembly: DmBDGP6.32
Supplementary files format and content: fastqsanger.gz files include raw data for each sample
Supplementary files format and content: txt files of featurecounts from hisat2 mapped data

organism: Drosophila melanogaster

source_name: brain

growth_protocol: flies were cultured for 1 week until they were wandering L3s

extract_protocol:
dissection in cold 1XPBS in batches of 20, then RNA extracted according to Trizol protocol
libraries made using Illumina TruseqV2 kit

treatment_protocol: RNAi depletion of white or orb2 driven by inscuteable-GAL4

value: brain


title: insc-GAL4>wRNAi brains, sample 2


title: insc-GAL4>orb2RNAi brains, sample 2


title: Oct4C48S#46 Bl/6J ESC_NT_1

value: Embryonic stem cell

value: Oct4 C48S

value: No treatment


title: RNAseq_PBS_3

value: PBS


title: cells 5 dpi rep B


title: insc-GAL4>wRNAi brains, sample 1


title: progeny round 3 rep C

value: 10 dpi


title: RNAseq_PBS_2


title: cells 5 dpi rep A

value: VECOS library screen


title: scRNA-seq HTO library, T cells, lane2

city: Bethesda

first: Verena

last: Link

address: 4 Memorial Drive

department: NIAID

institute: NIH

description:
HTO_features_Tcells.csv
Tcells_lane2_matrix.mtx.gz
Tcells_lane2_features.tsv.gz
Tcells_lane2_barcodes.tsv.gz
Tcells_SeuratObj.rds

data_processing:
Data were filtered and mapped to mm10 reference genome by using Cellranger 6.1.1 (10X Genomics). Data were normalized in Seurat.
Assembly: mm10
Supplementary files format and content: csv files for HTO libraries to run cellranger count
Supplementary files format and content: csv files for features and barcodes - output of cellranger count
Supplementary files format and content: mtx files for count matrix - output of cellranger count
Supplementary files format and content: rds files for Seurat objects

source_name: skin

extract_protocol:
Skin lymphocytes (CD45+ Thy1.2+, exclude γδTCRhi population) or skin dendritic cells (CD45+ Lin- Ly6G- Siglec-F- CD11c+ MHC-II+) from 8-9-week-old female and male mice were sorted from samples labeled with TotalSeqC hashtags antibodies (BioLegend) on a Sony MA900 cell sorter.
10X Genomics 5' kit
All DC and all T cell samples were pooled together in two separate vials, and 45,000 cells were loaded to a Chromium Single Cell Controller (10X Genomics) to encapsulate cells into droplets. Libraries were prepared using a Chromium Single Cell 5’ Reagent Kit (10X Genomics) following manufacturer's instructions and the HTO library was prepared according to a previous publication (M. Stoeckius et al, 2019). Libraries were then sequenced on an Illumina Nextseq500 (Next Seq 500/550 High Output Kit v2, Illumina).

value: skin

value: T cells

value: WT male and female

value: Control and S. epidermidis


title: RNAseq_PBS_1


title: scRNA-seq gene expression, T cells, lane2


title: progeny round 3 rep B

value: HFF


title: progeny round 3 rep A


title: scRNA-seq gene expression, T cells, lane1

description:
HTO_features_Tcells.csv
Tcells_lane1_matrix.mtx.gz
Tcells_lane1_features.tsv.gz
Tcells_lane1_barcodes.tsv.gz
Tcells_SeuratObj.rds


title: secreted round 3 rep C

value: C


title: Ocab mCherry Positive 3

first: Erik

middle: Peter

last: Hughes

state: Utah

address: 2000 Cir of Hope Dr.

source_name: C57BL/6 Primary

extract_protocol:
After 14 days of treatment, lymphnodes (Cervical, Brachial, Axillary, Inguinal) were isolated and Live, CD19-, CD8-, CD4+ T cells were FACS sorted by Ocab mCherry expression. (3 biological relpicates with paired positive and negative samples for each animal). Total RNA was isolated using Zymo Research Quick RNA micro prep kit.
Total RNA samples (5-500 ng) were hybridized with NEBNext rRNA Depletion Kit v2 (Human, Mouse, Rat) (E7400) to substantially diminish rRNA from the samples.  Stranded RNA sequencing libraries were prepared as described using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760L).  Purified libraries were qualified on an Agilent Technologies 4150 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583).  The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824).  Individual libraries were normalized to 5 nM in preparation for Illumina sequence analysis.
NovaSeq 150x150 bp Sequencing:  Sequencing libraries were chemically denatured and applied to an Illumina NovaSeq flow cell using the NovaSeq XP workflow (20043131).  Following transfer of the flowcell to an Illumina NovaSeq 6000 instrument, a 150 x 150 cycle paired end sequence run was performed using a NovaSeq 6000 S4 reagent Kit v1.5 (20028312).

treatment_protocol: Ocab mCherry reporter mice were sub cutaneously injected with 100uL MOG35-55 in CFA (0.5umol/mL).

value: Lymph Node (Cervical, Brachial, Axillary, Inguinal)

value: CD4 T cell

value: Ocab mCherry reporter

value: MOG35-55 in CFA Primed


title: Ocab mCherry Positive 2


title: secreted 5 dpi rep B

value: 5 dpi

value: B


title: RNAseq_Ca_3

value: Intestinal epithelia

value: Candida albicans


title: secreted round 3 rep B


title: secreted round 3 rep A

value: A


title: Ocab mCherry Negative 3


title: scRNA-seq HTO library, DCs, lane1

description:
HTO_features_DCs.csv
DCs_lane1_matrix.mtx.gz
DCs_lane1_features.tsv.gz
DCs_lane1_barcodes.tsv.gz
DC_SeuratObj.rds

value: dendritic cells


title: cells round 3 rep C

value: VECOS library screen

value: 10 dpi


title: scRNA-seq gene expression, DCs, lane1

value: skin


title: Ocab mCherry Negative 2


title: cells round 3 rep B


title: RNAseq_keratinocytes_male_Sepi_rep5

data_processing:
Sequencing reads were mapped to the C57BL/6 mouse genome (GRCm38: mm10) and differential gene expression was calculated by DESeq2
Assembly: mm10
Supplementary files format and content: txt

extract_protocol:
RNA was extracted with the Qiagen microRNA kit following manufactuer's instruction
Sequencing library was prepared using the Ovation SoLo RNA-Seq library preparataion kit (Tecan) following manufacture’s instructions.

value: keratinocytes

value: WT male

value: S. epidermidis


title: Ocab mCherry Negative 1


title: Ocab(fl/fl);CD4-Cre

description: 10X Genomics

data_processing:
Cell Ranger
Assembly: mm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: CNS

extract_protocol:
At remission timepoint, brain and spinal cord cells were FACS sorted for CD3e+ cells.
The Chromium Next GEM Single Cell 5’ Reagent kits v2 (PN-1000265) was used to barcode individual cells with oligonucleotides containing an Illumina R1 sequence, a 16 nt 10x Barcode, a 10 nt Unique Molecular Identifier (UMI), and  a 13 nt template switch oligo (TSO) according to the manufacture.  The following protocol based on 10x Genomics user guide (CG000331) was performed by High-Throughput Genomics Shared Resource at Huntsman Cancer Institute, University of Utah.  Filtered CD3e+ cells  with 10x Gel Beads and reverse transcription reagents were loaded to Chromium Single Cell Chip K (PN-1000287) to form Gel-Bead-In EMulsions (GEMs), the nano-droplets.  Within individual GEMs, barcoded cDNA generated from captured poly-adenylated mRNA was synthesized by reverse transcription (RT) with a master mix containing reverse transcription reagents and poly d(T) RT primer at the setting of 53°C for 45 min followed by 85°C for 5 min.  Subsequent fragmentation, end repair and A-tailing, adaptor ligation and sample indexing with dual index (PN-1000215) were performed in bulk according to the user guide.  The resulting barcoded libraries were qualified using Agilent D1000 ScreenTape on Agilent Technology 4150 TapeStation system and quantified by quantification PCR using KAPA Biosystems Library Quantification Kit for Illumina Platforms (KK4842).  Multiple libraries were then normalized, pooled and sequenced on NovaSeq 6000 with 150x150 paired-end mode

treatment_protocol: NOD Ocab(fl/fl) and Ocab(fl/fl);CD4-Cre mice were induced with EAE

value: CNS

value: NOD Primary

value: EAE Remission


title: RNAseq_keratinocytes_male_Sepi_rep4


title: progeny round 2 rep B

value: HFF


title: Ocab(fl/fl) - 1

description: 10X Genomics

value: Ocab(fl/fl)


title: scRNA-seq HTO library, DCs, lane2

description:
HTO_features_DCs.csv
DCs_lane2_matrix.mtx.gz
DCs_lane2_features.tsv.gz
DCs_lane2_barcodes.tsv.gz
DC_SeuratObj.rds

value: WT male and female

value: Control and S. epidermidis


title: progeny round 2 rep C

value: C


title: Ocab mCherry Positive 1

value: Lymph Node (Cervical, Brachial, Axillary, Inguinal)

value: CD4 T cell

value: Ocab mCherry reporter

value: MOG35-55 in CFA Primed


title: Ocab(fl/fl) - 2

description: 10X Genomics


title: scRNA-seq HTO library, T cells, lane1

value: T cells


title: RNAseq_keratinocytes_male_Sepi_rep1

value: skin


title: progeny round 2 rep A

value: VECOS library screen

value: 10 dpi

value: A


title: RNAseq_keratinocytes_male_Sepi_rep2

value: keratinocytes

value: WT male

value: S. epidermidis


title: Ocab(fl/fl);CD4-Cre

description: 10X Genomics

extract_protocol:
At relapse timepoint, brain and spinal cord cells were FACS sorted for CD3e+ cells.
The Chromium Next GEM Single Cell 5’ Reagent kits v2 (PN-1000265) was used to barcode individual cells with oligonucleotides containing an Illumina R1 sequence, a 16 nt 10x Barcode, a 10 nt Unique Molecular Identifier (UMI), and  a 13 nt template switch oligo (TSO) according to the manufacture.  The following protocol based on 10x Genomics user guide (CG000331) was performed by High-Throughput Genomics Shared Resource at Huntsman Cancer Institute, University of Utah.  Filtered CD3e+ cells  with 10x Gel Beads and reverse transcription reagents were loaded to Chromium Single Cell Chip K (PN-1000287) to form Gel-Bead-In EMulsions (GEMs), the nano-droplets.  Within individual GEMs, barcoded cDNA generated from captured poly-adenylated mRNA was synthesized by reverse transcription (RT) with a master mix containing reverse transcription reagents and poly d(T) RT primer at the setting of 53°C for 45 min followed by 85°C for 5 min.  Subsequent fragmentation, end repair and A-tailing, adaptor ligation and sample indexing with dual index (PN-1000215) were performed in bulk according to the user guide.  The resulting barcoded libraries were qualified using Agilent D1000 ScreenTape on Agilent Technology 4150 TapeStation system and quantified by quantification PCR using KAPA Biosystems Library Quantification Kit for Illumina Platforms (KK4842).  Multiple libraries were then normalized, pooled and sequenced on NovaSeq 6000 with 150x150 paired-end mode

value: CNS

value: NOD Primary

value: EAE Relapse


title: cells round 3 rep A

value: HFF


title: RNAseq_keratinocytes_male_Ctrl_rep2

value: Control