title: Pat.5_PRE_ROI.002_CD68+

data_processing:
The sequencing data was demultiplexed and converted into FASTQ files with bcl2fastq2 Conversion Software (Illumina, v2.2.0).
Raw FASTQ files were subjected to adapter removal, merging of paired-end reads, read alignment to barcode IDs and PCR duplicate removal with GeoMx NGS Pipeline software (NanoString), and resulting DCC files were uploaded into GeoMx DSP Control Center (Nanostring, v.2.4).
For QC, negative probes identified as outliers by Grubbs test were excluded in each segment.
Signal-to-noise ratio [Q3 / geoMean(Negative probes)] was calculated for each segment and segments with signal-to-noise ratio < 1 were excluded from further analyses.
Genes exceeding both the limit of quantitation calculated based on negative probe counts and value 2 in at least 15% of segments were defined as confidently expressed and used in further analyses. For analyses not directly comparing different segment types (differential gene expression and pathway analyses), this gene filtering was performed separately for CD68+, CD31+ and CD68-CD31- segments.
Filtered data were normalized by Q3 values calculated based on all genes passing the aforementioned filters.
Assembly: NanoString's GeoMx Human Whole Transcriptome Atlas, cat. GMX-RNA-NGS-HuWTA; GRCh38.p13
Supplementary files format and content: DCC files that were imported into GeoMx DSP Control Center
Supplementary files format and content: .xlsx file containing Initial Dataset (unnormalized and unfiltered) exported from GeoMx DSP Control Center
Supplementary files format and content: .xlsx files containing Q3 normalized count data (four sheets of data: all segments, CD68+, CD31+ and CD68-CD31- segments)
Library strategy: Spatial Transcriptomics

extract_protocol:
FFPE biopsies were cut into 5μm sections and each patient’s pre- and post-treatment samples were placed on the same slide for subsequent simultaneous analysis. Biopsies were hybridized with RNA probes and stained for CD68, CD31, pan-cytokeratin and nuclei. Using the GeoMx DSP instrument, selected regions of interest (ROIs) were segmented into following areas: 1.) CD68+pan-cytokeratin- area, 2.) CD31+ area and 3.) remaining DNA+ area, and the hybridized RNA probes were collected separately from these three areas.
Spatial transcriptome libraries were prepared using NanoString's GeoMx Human Whole Transcriptome Atlas kit and GeoMx Digital Spatial Prolifer instrument according to manufacturer's instructions.

tag: cancer

tag: biopsy type

tag: patient response_to_bex

tag: segment


title: Pat.5_PRE_ROI.001_CD68-CD31-

status: Public on Oct 26 2023

type: SRA

city: Turku

first: Maija

last: Hollmén

address: Tykistökatu 6A 4th floor

country: Finland

institute: University of Turku

description:
Initial_dataset.xlsx
Q3_normalized_dataset.xlsx

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

source_name: FFPE BRCA biopsy

growth_protocol: FFPE biopsy

treatment_protocol: Patients from ER+ breast cancer (BRCA) and biliary tract cancer (BTC) cohorts of the phase I/II first-in-human MATINS trial (https://clinicaltrials.gov/ct2/show/NCT03733990) were treated with bexmarilimab (FP-1305). FFPE biopsies were collected from target lesions before (PRE) and after (POST) bexmarilimab therapy.

value: BRCA

value: PRE

value: nDC

tag: roi

tag: patient

tag: geomx batch

tag: roi exclusion

value: No

tag: q3 normalized_data_sheets

tag: tissue

value: FFPE BRCA biopsy


title: BLA_FearRecall_fr1_M4_S140

city: Stanford

first: Wenfei

last: Sun

address: 318 Campus Dr.

country: USA

institute: Stanford University

description: Smartseq

library_source: transcriptomic single cell

data_processing:
Fastq reads were mapped with STAR(2.7.9a)
Assembly: mm10
Supplementary files format and content: Cell by gene matrix format

molecule: polyA RNA

organism: Mus musculus

extract_protocol:
OligodT primers were used to enrich mRNA
Brain tissues were dissociated with Worthington Papain Digestion Kit RNA libraries were prepared using smart seq 3
Novaseq 6000 was used for sequencing with standard Illumina protocols

treatment_protocol: Fear conditioning paradigm

tag: genotype

value: TRAP2 Ai14

tag: treatment

value: Fear recall


title: BLA_FearRecall_fr1_M3_S139

description: Smartseq


title: Pat.5_PRE_ROI.001_CD31+


title: T9-CR08-35

city: Beijing

first: Zongcheng

last: Li

address: No. 8 East Street, Fengtai District

country: China

institute: Fifth Medical Center of Chinese PLA General Hospital

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
For modified STRT-seq data, raw reads were first split for each cell by specific barcode sequence attached in Read 2. The TSO sequence and polyA tail sequence were trimmed for the corresponding Read 1 after UMI information was aligned to it. Reads with adapter contaminants or low-quality bases (N > 10%) were discarded. Subsequently, we aligned the stripped Read 1 sequences to hg19 transcriptome (UCSC) using tophat2 (version 2.0.12). Uniquely mapped reads were counted by HTSeq package and grouped by the cell-specific barcodes. Duplicated transcripts were removed based on the UMI information for each gene. Finally, for each individual cell, the copy number of transcripts of a given gene was the number of the distinct UMIs of that gene.
Genome_build: hg19
Supplementary_files_format_and_content: comma-delimited text file includes UMI values for each cell

source_name: Peripheral blood

extract_protocol:
modified STRT-seq
A modified STRT-seq protocol was applied for single-cell RNA-seq. Briefly, sorted single cells in good condition were picked into lysis by mouth pipetting, and the scRNA-seq libraries were constructed based on STRT-seq with some modifications. cDNAs were synthesized using sample-specific 25-nt oligo-dT primer containing 8-nt barcode (TCAGACGTGTGCTCTTCCGATCT-XXXXXXXX-DDDDDDDD-T25, X representing sample-specific barcode while D standing for unique molecular identifiers (UMI).  After reverse transcription and second-strand cDNA synthesis, the cDNAs were amplified by 16 cycles of PCR using ISPCR primer and 3’ Anchor primer. Samples were pooled and purified using Agencourt AMPure XP beads . 4 cycles of PCR were performed to introduce index sequence  and subsequently, 400 ng cDNAs were fragmented to around 300 bp by Covaris S2. After being incubated with Dynabeads MyOneTM Streptavidin C1 beads (Thermo Fisher, 65002) for 1 hour at room temperature, cDNA Libraries were generated using KAPA Hyper Prep Kit (Kapa Biosystems, kk8505). After adaptor ligation, the libraries were amplified by 8 cycles of PCR using QP2 primer and short universal primer. The libraries were sequenced on Illumina Hiseq X Ten platform in 150 bp pair-ended manner

tag: cell type

value: CAR-T cells

tag: cells enriched from

value: Peripheral blood

tag: disease state

value: B-ALL

tag: sampling stage

tag: individual

tag: responses

value: Complete Remission


title: T9-CR08-4


title: T9-CR08-1


title: Pat.5_PRE_ROI.001_CD68+

tag: cancer

tag: biopsy type


title: BLA_FearRecall_fr1_M2_S138

description: Smartseq


title: T9-CR08-2


title: BLA_FearRecall_fr1_M10_S146

description: Smartseq


title: T9-CR07-4


title: Pat.1_POST_ROI.014_CD68-CD31-

value: POST

tag: patient response_to_bex

value: DC

tag: segment


title: BLA_FearRecall_fr1_M1_S137

description: Smartseq


title: T9-CR07-3


title: T9-CR06-1


title: T9-CR02-4


title: Pat.1_POST_ROI.014_CD31+

tag: roi

tag: patient


title: T9-CR02-2


title: BLA_FearRecall_fr1_L9_S122

description: Smartseq


title: T9-CR02-3


title: T9-CR10-3


title: T9-CR02-1


title: T9-CR06-4


title: BLA_FearRecall_fr1_L8_S121

description: Smartseq


title: Pat.1_POST_ROI.014_CD68+

tag: geomx batch

tag: roi exclusion


title: Pat.1_POST_ROI.013_CD68-CD31-

tag: q3 normalized_data_sheets

tag: tissue


title: Pat.1_POST_ROI.013_CD31+


title: BLA_FearRecall_fr1_L6_S119

description: Smartseq

tag: genotype

tag: treatment


title: T6-RE02-4

tag: cell type

tag: cells enriched from


title: T6-RE02-5

tag: disease state

tag: sampling stage


title: BLA_FearRecall_fr1_L7_S120

description: Smartseq


title: T6-RE02-6

tag: individual

tag: responses


title: Pat.1_POST_ROI.013_CD68+

tag: cancer

tag: biopsy type


title: BLA_FearRecall_fr1_L4_S117

description: Smartseq


title: BLA_FearRecall_fr1_L5_S118

description: Smartseq


title: Pat.1_POST_ROI.012_CD68-CD31-

tag: patient response_to_bex

tag: segment


title: T6-RE02-1


title: T6-RE02-2


title: T6-OT04-4


title: T6-RE02-3


title: T6-OT04-3


title: Pat.1_POST_ROI.011_CD68-CD31-

tag: roi

tag: patient


title: BLA_FearRecall_fr1_L3_S116

description: Smartseq


title: BLA_FearRecall_fr1_L2_S115

description: Smartseq


title: Pat.1_POST_ROI.012_CD68+

tag: geomx batch

tag: roi exclusion


title: T6-OT03-4


title: T6-OT03-2


title: T6-OT03-3


title: BLA_FearRecall_fr1_L10_S123

description: Smartseq

tag: tissue


title: T6-OT04-2


title: BLA_FearRecall_fr1_L1_S114

description: Smartseq

tag: genotype


title: Pat.1_POST_ROI.011_CD31+

tag: q3 normalized_data_sheets


title: Pat.1_POST_ROI.011_CD68+


title: BLA_FearRecall_fr1_K9_S99

description: Smartseq

tag: treatment


title: T6-OT02-3

tag: cell type

tag: cells enriched from


title: T6-OT02-4

tag: disease state

tag: sampling stage


title: T6-CR11-3

tag: individual

tag: responses


title: T6-CR11-5


title: Pat.1_POST_ROI.010_CD68-CD31-

tag: cancer

tag: biopsy type


title: T6-CR11-4


title: Pat.1_POST_ROI.012_CD31+

tag: patient response_to_bex

tag: segment


title: T6-CR10-22


title: BLA_FearRecall_fr1_K7_S97

description: Smartseq


title: T6-CR10-2


title: T6-CR10-1


title: Pat.1_POST_ROI.010_CD31+

tag: roi

tag: patient


title: Pat.1_POST_ROI.010_CD68+

tag: geomx batch

tag: roi exclusion


title: T6-OT04-1


title: BLA_FearRecall_fr1_K6_S96

description: Smartseq

tag: tissue

tag: genotype


title: T6-OT02-2


title: T6-CR08-1


title: Pat.1_POST_ROI.009_CD68-CD31-

tag: q3 normalized_data_sheets


title: BLA_FearRecall_fr1_K5_S95

description: Smartseq

tag: treatment


title: T6-CR05-4

tag: cell type

tag: cells enriched from


title: T6-CR05-2

tag: disease state

tag: sampling stage


title: BLA_FearRecall_fr1_K3_S93

description: Smartseq


title: BLA_FearRecall_fr1_K8_S98

description: Smartseq


title: Pat.1_POST_ROI.009_CD68+


title: T3-RE05-1

tag: individual

tag: responses

value: Relapse


title: BLA_FearRecall_fr1_K2_S92

description: Smartseq


title: T6-CR05-1


title: T3-RE03-4


title: Pat.1_POST_ROI.008_CD31+

tag: cancer

tag: biopsy type


title: T3-RE05-2


title: T3-RE03-2


title: BLA_FearRecall_fr1_K1_S91

description: Smartseq


title: BLA_FearRecall_fr1_J9_S76

description: Smartseq


title: Pat.1_POST_ROI.008_CD68-CD31-

tag: patient response_to_bex

tag: segment


title: T3-RE02-4


title: T3-RE02-2


title: Pat.1_POST_ROI.007_CD68-CD31-

tag: roi

tag: patient


title: T3-RE02-1


title: BLA_FearRecall_fr1_J6_S73

description: Smartseq


title: BLA_FearRecall_fr1_J7_S74

description: Smartseq


title: T6-CR05-3


title: T3-OT03-3


title: Pat.1_POST_ROI.009_CD31+

tag: geomx batch

tag: roi exclusion


title: T3-OT03-4


title: BLA_FearRecall_fr1_J5_S72

description: Smartseq

tag: tissue

tag: genotype


title: Pat.1_POST_ROI.007_CD31+

tag: q3 normalized_data_sheets


title: T3-OT03-1

tag: cell type


title: T3-OT03-2

tag: cells enriched from


title: Pat.1_POST_ROI.008_CD68+


title: T3-CR12-2

tag: disease state


title: T3-OT02-12

tag: sampling stage


title: T3-RE03-1

tag: individual


title: T3-RE02-3

tag: responses


title: Pat.1_PRE_ROI.006_CD68-CD31-

tag: cancer


title: BLA_FearRecall_fr1_J10_S77

description: Smartseq

tag: treatment


title: BLA_FearRecall_fr1_J3_S70

description: Smartseq


title: T3-OT02-34


title: Pat.1_PRE_ROI.006_CD31+

tag: biopsy type

tag: patient response_to_bex


title: T3-CR12-3


title: BLA_FearRecall_fr1_J1_S68

description: Smartseq


title: T3-CR11-4


title: T3-CR11-3


title: T3-CR12-1


title: Pat.1_PRE_ROI.005_CD68-CD31-

tag: segment

tag: roi


title: Pat.1_PRE_ROI.006_CD68+

tag: patient

tag: geomx batch


title: BLA_FearRecall_fr1_I9_S53

description: Smartseq

tag: tissue


title: T3-CR11-2


title: BLA_FearRecall_fr1_I8_S52

description: Smartseq

tag: genotype


title: Pat.1_POST_ROI.007_CD68+

tag: roi exclusion

tag: q3 normalized_data_sheets


title: T3-CR10-2

tag: cell type

tag: cells enriched from


title: T3-CR10-3

tag: disease state

tag: sampling stage


title: BLA_FearRecall_fr1_I7_S51

description: Smartseq


title: T3-CR09-4

tag: individual

tag: responses


title: Pat.1_PRE_ROI.005_CD68+

tag: cancer


title: T3-CR09-3


title: T3-CR09-1


title: BLA_FearRecall_fr1_I6_S50

description: Smartseq

tag: treatment


title: BLA_FearRecall_fr1_I3_S47

description: Smartseq


title: Pat.1_PRE_ROI.003_CD31+

tag: biopsy type

tag: patient response_to_bex

value: Yes, low signal-to-noise ratio


title: Pat.1_PRE_ROI.003_CD68-CD31-

tag: segment

tag: roi


title: BLA_FearRecall_fr1_I10_S54

description: Smartseq


title: Pat.1_PRE_ROI.003_CD68+

tag: patient

tag: geomx batch


title: T3-CR08-1


title: BLA_FearRecall_fr1_H9_S30

description: Smartseq

tag: tissue

tag: genotype


title: Pat.1_PRE_ROI.005_CD31+

tag: roi exclusion


title: Pat.1_PRE_ROI.002_CD68-CD31-

tag: q3 normalized_data_sheets


title: Pat.1_PRE_ROI.002_CD31+


title: T14-CR08-5

tag: cell type

tag: cells enriched from


title: T16-CR01-1

tag: disease state

tag: sampling stage


title: T3-CR06-4

tag: individual

tag: responses


title: T3-CR08-3


title: T16-CR01-4


title: T14-CR08-2


title: Pat.1_PRE_ROI.002_CD68+

tag: cancer


title: BLA_FearRecall_fr1_H8_S29

description: Smartseq

tag: treatment


title: Pat.1_PRE_ROI.001_CD68-CD31-

tag: biopsy type

tag: patient response_to_bex


title: T12-RE02-123


title: T12-RE01-7


title: T14-CR08-1


title: T3-CR08-2


title: T12-RE01-6


title: BLA_FearRecall_fr1_I4_S48

description: Smartseq


title: T3-CR06-3


title: T16-CR01-2


title: Pat.1_PRE_ROI.001_CD31+

tag: segment

tag: roi


title: BLA_FearRecall_fr1_H6_S27

description: Smartseq


title: BLA_FearRecall_fr1_I2_S46

description: Smartseq


title: T12-RE01-5


title: Pat.1_PRE_ROI.001_CD68+

tag: patient

tag: geomx batch


title: BLA_FearRecall_fr1_H5_S26

description: Smartseq

tag: tissue

tag: genotype


title: T12-RE01-3


title: T12-OT01-3

value: Extramedullary relapse


title: BLA_FearRecall_fr1_H4_S25

description: Smartseq


title: BLA_FearRecall_fr1_H3_S24

description: Smartseq


title: T12-RE01-4


title: T12-RE01-2


title: T12-CR07-4


title: T12-RE01-1


title: T12-OT01-2


title: T12-OT01-1


title: Pat.2_PRE_ROI.019_CD68-CD31-

value: BTC

tag: roi exclusion

tag: q3 normalized_data_sheets


title: Pat.2_PRE_ROI.019_CD68+


title: T12-CR07-3

tag: cell type

tag: cells enriched from


title: BLA_FearRecall_fr1_H7_S28

description: Smartseq


title: Pat.2_PRE_ROI.018_CD68-CD31-


title: BLA_FearRecall_fr1_H10_S31

description: Smartseq


title: T12-CR05-3

tag: disease state

tag: sampling stage


title: Pat.2_PRE_ROI.018_CD31+


title: T12-CR05-2

tag: individual

tag: responses


title: BLA_FearRecall_fr1_H1_S22

description: Smartseq

tag: treatment


title: T12-CR05-1


title: T12-CR04-4


title: BLA_FearRecall_fr1_G9_S7

description: Smartseq


title: T12-CR04-3


title: Pat.2_PRE_ROI.018_CD68+

tag: cancer

tag: biopsy type


title: Pat.2_PRE_ROI.019_CD31+

tag: patient response_to_bex

tag: segment


title: T12-CR04-2


title: BLA_FearRecall_fr1_G8_S6

description: Smartseq


title: BLA_FearRecall_fr1_G7_S5

description: Smartseq


title: Pat.2_PRE_ROI.017_CD31+

tag: roi

tag: patient


title: BLA_FearRecall_fr1_H2_S23

description: Smartseq

tag: tissue


title: WT-N-3

city: Jeddah

first: Haroon

last: Butt

state: Makkah

address: King Abdullah University of Science and Technology (KAUST) Thuwal, 23955-6900

department: BESE

country: Saudi Arabia

institute: KAUST

description: High-quality RNA samples with RNA integrity number (RIN) 7.0 were selected for library construction. The RNA-seq libraries were constructed using TruSeq mRNA stranded kit following the standard protocol.

data_processing:
Basecalls performed using CASAVA version 1.4
Trimming library adapters and quality controls with Trimmomatic using the following arguments; TrimmomaticPE - LEADING:25 TRAILING:25 CROP:120 MINLEN:120. Illumina adapters were removed and read pairs were trimmed to the same length
Alignement with STAR.

organism: Oryza sativa Japonica Group

source_name: Seedlings

growth_protocol: 7-day-old seedlings

extract_protocol:
Direct-zol RNA MiniPrep Plus (Zymo Research) according to the manufacturer’s instructions
The RNA-seq libraries were constructed using TruSeq mRNA stranded kit following the standard protocol and sequenced on the NovaSeq platform to generate high-quality paired-end reads.

treatment_protocol: Seeds are germinated on 125 mM NaCl, and mock.

tag: cultivar

value: Nipponbare

value: Seedlings

tag: genotype

value: WT

value: 125 mM NaCl


title: T12-CR07-2


title: Pat.2_PRE_ROI.017_CD68+

value: PRE

tag: geomx batch

tag: roi exclusion

value: No

tag: q3 normalized_data_sheets

value: FFPE BRCA biopsy


title: T1-RE04-4

tag: cell type

value: CAR-T cells

tag: cells enriched from

tag: disease state


title: T1-RE04-3

value: Peripheral blood

tag: sampling stage

tag: individual

tag: responses


title: WT-N-2

tag: treatment


title: Pat.2_PRE_ROI.016_CD68-CD31-

tag: cancer

tag: biopsy type

tag: patient response_to_bex


title: BLA_FearRecall_fr1_G6_S4

description: Smartseq

value: TRAP2 Ai14

value: Fear recall


title: Pat.2_PRE_ROI.016_CD31+

tag: segment

tag: roi

tag: patient


title: WT-C-3

tag: cultivar

tag: tissue

tag: genotype

value: Mock


title: T1-RE04-1

value: B-ALL

value: Complete Remission


title: BLA_FearRecall_fr1_G5_S3

description: Smartseq


title: BLA_FearRecall_fr1_G4_S2

description: Smartseq


title: T1-RE04-2


title: Pat.2_PRE_ROI.016_CD68+

value: DC

tag: geomx batch

tag: roi exclusion

tag: q3 normalized_data_sheets


title: WT-C-2

tag: cell type


title: T1-RE03-4

tag: cells enriched from

tag: disease state

tag: sampling stage


title: Pat.2_PRE_ROI.017_CD68-CD31-


title: BLA_FearRecall_fr1_G2_S300

description: Smartseq

tag: treatment


title: WT-C-1


title: BLA_FearRecall_fr1_G10_S8

description: Smartseq


title: Pat.2_POST_ROI.009_CD68-CD31-

tag: cancer

value: POST

value: Yes, necrosis


title: T12-CR03-1

tag: individual

tag: responses


title: T1-RE03-3


title: Pat.2_POST_ROI.009_CD31+

value: BTC

tag: biopsy type

tag: patient response_to_bex

tag: segment


title: SR-N-3

tag: cultivar

value: Nipponbare

value: Seedlings


title: BLA_FearRecall_fr1_G1_S299

description: Smartseq

tag: tissue


title: Pat.2_POST_ROI.009_CD68+

tag: roi

tag: patient


title: T1-RE03-2


title: SR-N-2

tag: genotype

value: 125 mM NaCl


title: BLA_FearRecall_fr1_F8_S283

description: Smartseq


title: BLA_FearRecall_fr1_F9_S284

description: Smartseq


title: Pat.2_POST_ROI.008_CD68-CD31-

tag: geomx batch

tag: roi exclusion

tag: q3 normalized_data_sheets


title: T1-RE03-1

tag: cell type

tag: cells enriched from

tag: disease state


title: WT-N-1

value: WT

tag: treatment


title: Pat.2_POST_ROI.008_CD31+

tag: cancer

value: No


title: SR-C-3


title: T1-OT06-1

tag: sampling stage

tag: individual

tag: responses

value: Infection


title: BLA_FearRecall_fr1_F7_S282

description: Smartseq


title: T1-OT06-2

value: CAR-T cells


title: Pat.2_POST_ROI.008_CD68+

tag: biopsy type

tag: patient response_to_bex

tag: segment

value: FFPE BRCA biopsy


title: SR-C-2

tag: cultivar

tag: tissue


title: BLA_FearRecall_fr1_F6_S281

description: Smartseq

tag: genotype

value: TRAP2 Ai14


title: Pat.2_POST_ROI.007_CD68-CD31-

tag: roi

tag: patient

tag: geomx batch


title: SR-C-1

tag: cell type


title: T1-OT03-4

tag: cells enriched from

value: Peripheral blood


title: O54-P2-Aged_Small intestinal epithelium_Aged-rep3

city: Heidelberg

first: Erica

last: Valentini

address: Im Neuenheimer Feld 580

country: Germany

institute: DKFZ

description:
SEQ360_A3_O52P2Aged
genomic DNA of small intestinal organoids, subjected to transposase reaction for adapter insertion in open chromatin regions

library_source: genomic

data_processing:
nf-core/atacseq  v1.2.1
Nextflow  v20.04.1
FastQC  v0.11.9
Trim Galore! v0.6.4_dev
BWA v0.7.17-r1188
Samtools v1.10
BEDTools v2.29.2
BamTools v2.1.0
deepTools v3.4.3
Picard v2.23.1
R v3.6.2
Pysam v0.15.3
MACS2 v2.2.7.1
ataqv v1.1.1
featureCounts v2.0.1
Preseq v2.0.3
MultiQC v1.9
Genome_build: GRCm38
Supplementary_files_format_and_content: annotatePeaks
Supplementary_files_format_and_content: eatureCounts

molecule: genomic DNA

source_name: Small intestinal epithelium

growth_protocol: small intestinal organoids were cultured for 3-5 weeks (passage 2, 3 & 4) and passaged every week

extract_protocol:
single cell solution of organoids was generated by 5min incubation at 37C with TrypLE and filtered through a 20uM cell strainer. 100.000 single cells were incubated for 3min on ice in lysis buffer to allow for nuclei isolation
Illumina sequencing libraries were prepared using Tn5 Transposase to fragment chromatin and insert sequencing adapters at regions of open chromatin. 10ul of isolated DNA was used for library PCR (20 cycles total), using index i5 and index i7 primer (Illumine Nextera). Libraries were size selected and purified via AMPure XP beads

treatment_protocol: no treatment

value: small intestinal epithelial cells

tag: strain

tag: aged

value: Aged

tag: organoid culture passage


title: BLA_FearRecall_fr1_F4_S279

description: Smartseq

tag: treatment

value: Fear recall


title: Pat.2_POST_ROI.007_CD31+

tag: cancer

value: DC

tag: roi exclusion


title: T1-OT05-1

tag: disease state

value: B-ALL

tag: sampling stage

tag: individual

tag: responses


title: T1-OT03-2

value: Complete Remission


title: Pat.2_POST_ROI.007_CD68+

value: BTC

tag: biopsy type

value: POST

tag: patient response_to_bex

tag: segment

value: Yes, necrosis

tag: tissue


title: BLA_FearRecall_fr1_F5_S280

description: Smartseq

tag: genotype


title: BLA_FearRecall_fr1_F3_S278

description: Smartseq


title: Pat.2_POST_ROI.006_CD68-CD31-

tag: roi

tag: patient

tag: geomx batch


title: O53-P3-Aged_Small intestinal epithelium_Aged-rep2

description:
SEQ360_A2_O52P3Aged
genomic DNA of small intestinal organoids, subjected to transposase reaction for adapter insertion in open chromatin regions

tag: cell type

tag: strain

tag: aged


title: T1-OT03-1

tag: cells enriched from


title: T1-OT02-1


title: BLA_FearRecall_fr1_F10_S285

description: Smartseq

tag: treatment


title: Pat.2_POST_ROI.006_CD31+

tag: cancer

tag: roi exclusion


title: O53-P3-Young_Small intestinal epithelium_Young-rep2

description:
SEQ360_Y2_O52P3Young
genomic DNA of small intestinal organoids, subjected to transposase reaction for adapter insertion in open chromatin regions

value: Young

tag: organoid culture passage


title: BLA_FearRecall_fr1_F2_S277

description: Smartseq


title: O52-P4-Aged_Small intestinal epithelium_Aged-rep1

description:
SEQ360_A1_O52P4Aged
genomic DNA of small intestinal organoids, subjected to transposase reaction for adapter insertion in open chromatin regions


title: T1-OT02-4

tag: disease state

tag: sampling stage

tag: individual

tag: responses


title: Pat.2_POST_ROI.005_CD68-CD31-

tag: biopsy type

tag: patient response_to_bex

tag: segment

tag: tissue


title: T1-OT02-3


title: Pat.2_POST_ROI.006_CD68+

tag: roi

tag: patient

tag: geomx batch


title: BLA_FearRecall_fr1_E9_S261

description: Smartseq

tag: genotype


title: Pat.2_POST_ROI.005_CD31+


title: T1-NR03-2

tag: cell type

tag: cells enriched from

value: No Remission


title: Pat.2_POST_ROI.005_CD68+

tag: cancer


title: BLA_FearRecall_fr1_F1_S276

description: Smartseq

tag: treatment


title: O54-P2-Young_Small intestinal epithelium_Young-rep3

description:
SEQ360_Y3_O52P2Young
genomic DNA of small intestinal organoids, subjected to transposase reaction for adapter insertion in open chromatin regions

tag: strain

tag: aged

tag: organoid culture passage


title: T1-OT02-2

tag: disease state

tag: sampling stage

tag: individual


title: EE_Dam_5

city: Gif-sur-Yvette

first: Katarzyna

last: Siudeja

address: 1, Avenue de la Terrasse

country: France

institute: Institute for Integrative Biology of the Cell (I2BC), INSERM U1280, CEA, CNRS, Université Paris-Saclay

data_processing:
damidseq_pipeline script was used to align the reads in fastq files to Drosophila melanogaster reference genome 6.
Each replicate were normalized to its associated Dam alone replicate (log2 ratio of Dam-fusion/Dam alone)
Assembly: Flybase, release 6.13
Supplementary files format and content: bedgraph, gff

organism: Drosophila melanogaster

source_name: EE

growth_protocol: Flies were kept at 18°C for crosses and during beginning of adulthood. At 3 day old flies were shifted to 29°C for 1 day to induce Dam transgen expression

extract_protocol:
For each replicate, DNA was extracted from 60 dissected guts via Qiagen QIAmp DNA Micro Kit following manufacturers' instructions,
Extracted DNA was digested with DpnI, ligated with DamID adaptors, digested with DpnII before PCR amplification. DNA was sonicated to 300bp, adaptors were removed with AlwI and end-repaired and A-tailed. Sequencing adaptors were ligated to the fragments before PCR amplification.

tag: cell line

value: EE

value: Intestinal cells

value: prosGal4ts_ UAS_Dam

tag: time

value: 24h  induction at 29°C


title: T1-NR03-1

value: CAR-T cells

tag: responses


title: BLA_FearRecall_fr1_E7_S259

description: Smartseq

tag: tissue

value: TRAP2 Ai14


title: EE_Pol_II_2

value: prosGal4ts_ UAS_DamPolII


title: EE_Pol_II_1


title: Pat.2_POST_ROI.004_CD31+

tag: biopsy type

tag: patient response_to_bex

tag: segment

tag: roi

tag: patient

tag: roi exclusion

value: FFPE BRCA biopsy


title: Pat.2_POST_ROI.004_CD68-CD31-

tag: cancer

tag: geomx batch


title: T1-NR03-3

tag: cell type

tag: cells enriched from

value: Peripheral blood


title: BLA_FearRecall_fr1_E8_S260

description: Smartseq

tag: genotype

tag: treatment

value: Fear recall


title: EE_Brm_3

value: prosGal4ts_ UAS_DamBrm


title: BLA_FearRecall_fr1_E4_S256

description: Smartseq


title: T1-NR02-4

tag: disease state

value: B-ALL

tag: sampling stage

tag: individual


title: BLA_FearRecall_fr1_E5_S257

description: Smartseq


title: T1-NR02-3

tag: responses


title: O52-P4-Young_Small intestinal epithelium_Young-rep1

description:
SEQ360_Y1_O52P4Young
genomic DNA of small intestinal organoids, subjected to transposase reaction for adapter insertion in open chromatin regions

value: small intestinal epithelial cells

tag: strain

tag: aged

tag: organoid culture passage


title: Pat.2_POST_ROI.003_CD68-CD31-

value: BTC

tag: biopsy type

value: POST

tag: patient response_to_bex

value: DC

tag: segment

value: No

tag: q3 normalized_data_sheets

tag: tissue


title: T1-NR02-2

value: No Remission


title: Pat.2_POST_ROI.004_CD68+

tag: cancer

tag: roi

tag: patient

tag: geomx batch

tag: roi exclusion

value: Yes, necrosis


title: Pat.2_POST_ROI.003_CD31+


title: EE_Dam_4

tag: cell line

value: EE

tag: cell type

value: Intestinal cells

tag: genotype

value: prosGal4ts_ UAS_Dam

tag: time


title: EE_HP1_3

value: prosGal4ts_ UAS_DamHP1

value: 24h  induction at 29°C


title: EE_H1_2

value: prosGal4ts_ UAS_DamH1


title: BLA_FearRecall_fr1_E2_S254

description: Smartseq

value: TRAP2 Ai14

tag: treatment


title: T1-NR02-1

value: CAR-T cells

tag: cells enriched from

value: Peripheral blood

tag: disease state

tag: sampling stage

tag: individual

tag: responses


title: EE_Dam_3


title: BLA_FearRecall_fr1_E10_S262

description: Smartseq

value: Fear recall


title: EE_Brm_2

value: prosGal4ts_ UAS_DamBrm


title: Pat.2_POST_ROI.003_CD68+

value: BTC

tag: biopsy type

tag: patient response_to_bex

tag: segment

tag: q3 normalized_data_sheets

value: FFPE BRCA biopsy


title: BLA_FearRecall_fr1_E6_S258

description: Smartseq

tag: tissue


title: Pat.2_POST_ROI.002_CD68-CD31-

tag: cancer

value: POST

value: DC

tag: roi

tag: patient

tag: geomx batch


title: BLA_FearRecall_fr1_E1_S253

description: Smartseq

tag: genotype


title: Pat.2_POST_ROI.002_CD31+

tag: roi exclusion

value: Yes, low signal-to-noise ratio


title: EE_HP1_2

tag: cell line

tag: cell type

tag: time


title: T1-NR01-1

tag: cells enriched from

tag: disease state

value: B-ALL

tag: sampling stage

value: No Remission


title: BLA_FearRecall_fr1_D9_S238

description: Smartseq

tag: treatment


title: BLA_FearRecall_fr1_D8_S237

description: Smartseq


title: T1-CR11-4

tag: individual

tag: responses

value: Complete Remission


title: BLA_FearRecall_fr1_E3_S255

description: Smartseq


title: Pat.2_POST_ROI.001_CD31+

tag: biopsy type

tag: patient response_to_bex

tag: segment

value: Yes, necrosis


title: Pat.2_POST_ROI.002_CD68+

tag: cancer

tag: roi

value: No

tag: q3 normalized_data_sheets

tag: tissue


title: T1-CR11-2


title: Pat.2_POST_ROI.001_CD68-CD31-

tag: patient

tag: geomx batch

tag: roi exclusion


title: BLA_FearRecall_fr1_D7_S236

description: Smartseq

tag: genotype


title: BLA_FearRecall_fr1_D6_S235

description: Smartseq


title: EE_Dam_2

tag: cell line

value: EE

tag: cell type

value: Intestinal cells

value: prosGal4ts_ UAS_Dam

tag: time

value: 24h  induction at 29°C


title: T1-CR10-4

value: CAR-T cells

tag: cells enriched from

value: Peripheral blood

tag: disease state

tag: sampling stage


title: EE_Pc_1

value: prosGal4ts_ UAS_DamPc


title: T1-NR01-34

tag: individual

tag: responses


title: BLA_FearRecall_fr1_D5_S234

description: Smartseq

value: TRAP2 Ai14

tag: treatment

value: Fear recall


title: EE_Pc_2


title: Pat.2_POST_ROI.001_CD68+

tag: cancer

value: BTC

tag: biopsy type

value: POST

tag: patient response_to_bex

tag: segment

value: FFPE BRCA biopsy


title: T1-CR10-3

value: B-ALL


title: BLA_FearRecall_fr1_D4_S233

description: Smartseq

tag: tissue


title: T1-CR10-2


title: Pat.4_PRE_ROI.009_CD68-CD31-

value: BRCA

value: PRE

value: nDC

tag: roi

tag: patient

tag: geomx batch

value: Yes, healthy tissue


title: EE_H1_1

tag: cell line

value: EE

tag: genotype

value: prosGal4ts_ UAS_DamH1


title: EE_HP1_1

tag: cell type

value: Intestinal cells

value: prosGal4ts_ UAS_DamHP1

tag: time


title: Pat.4_PRE_ROI.009_CD31+

tag: roi exclusion


title: T1-CR11-3

value: CAR-T cells

tag: cells enriched from

tag: disease state

tag: sampling stage

value: Complete Remission


title: BLA_FearRecall_fr1_D3_S232

description: Smartseq

tag: treatment


title: EE_Dam_1

value: prosGal4ts_ UAS_Dam

value: 24h  induction at 29°C


title: T1-CR10-1

value: Peripheral blood

tag: individual

tag: responses


title: BLA_FearRecall_fr1_D2_S231

description: Smartseq

value: TRAP2 Ai14

value: Fear recall


title: Pat.4_PRE_ROI.009_CD68+

tag: cancer

tag: biopsy type

tag: patient response_to_bex

value: FFPE BRCA biopsy


title: Pat.4_PRE_ROI.008_CD68-CD31-

tag: segment

tag: roi

tag: tissue


title: EE_Brm_1

tag: cell line

value: prosGal4ts_ UAS_DamBrm


title: EB_H1_2

source_name: EB

value: EB

tag: genotype

value: NREGal4ts_ UAS_DamH1


title: BLA_FearRecall_fr1_C9_S215

description: Smartseq


title: T1-CR09-3

tag: cell type

value: B-ALL


title: BLA_FearRecall_fr1_D10_S239

description: Smartseq


title: T1-CR09-2


title: Pat.4_PRE_ROI.008_CD68+

value: BRCA

value: PRE

value: nDC

tag: patient

tag: geomx batch

value: Yes, healthy tissue


title: EB_Pc_3

value: Intestinal cells

value: NREGal4ts_ UAS_DamPc

tag: time


title: T1-CR09-4

value: CAR-T cells

tag: cells enriched from

tag: disease state

value: Complete Remission


title: T1-CR09-1

tag: sampling stage


title: Pat.4_PRE_ROI.007_CD68-CD31-

tag: roi exclusion

value: No

tag: q3 normalized_data_sheets


title: EB_Dam_7

value: NREGal4ts_ UAS_Dam

value: 24h  induction at 29°C


title: Pat.4_PRE_ROI.008_CD31+

tag: cancer


title: T1-CR08-4

value: Peripheral blood

tag: individual

tag: responses


title: BLA_FearRecall_fr1_C8_S214

description: Smartseq

value: TRAP2 Ai14

tag: treatment

value: Fear recall


title: BLA_FearRecall_fr1_C7_S213

description: Smartseq


title: Pat.4_PRE_ROI.007_CD31+

tag: biopsy type

tag: patient response_to_bex

tag: segment

tag: roi

value: FFPE BRCA biopsy


title: EB_HP1_3

tag: cell line

value: EB

tag: cell type

tag: genotype

value: NREGal4ts_ UAS_DamHP1


title: BLA_FearRecall_fr1_C6_S212

description: Smartseq

tag: tissue


title: T1-CR08-3

tag: cells enriched from

value: B-ALL


title: Pat.4_PRE_ROI.007_CD68+

value: BRCA

value: PRE

tag: patient

tag: geomx batch


title: SR-N-1

tag: cultivar

value: Nipponbare

value: Seedlings

value: 125 mM NaCl


title: EB_Pc_2

value: Intestinal cells

value: NREGal4ts_ UAS_DamPc

tag: time


title: EB_Brm_2

value: NREGal4ts_ UAS_DamBrm


title: Pat.4_PRE_ROI.006_CD68-CD31-

tag: cancer

value: nDC

tag: roi exclusion

value: No

tag: q3 normalized_data_sheets


title: T1-CR08-2

value: CAR-T cells

value: Peripheral blood

tag: disease state

tag: sampling stage

tag: individual

tag: responses

value: Complete Remission


title: EB_HP1_2

value: 24h  induction at 29°C


title: BLA_FearRecall_fr1_C4_S210

description: Smartseq

value: TRAP2 Ai14

tag: treatment

value: Fear recall


title: T1-CR08-1

value: B-ALL


title: EB_Dam_6

tag: cell line

value: EB

value: NREGal4ts_ UAS_Dam


title: BLA_FearRecall_fr1_C3_S209

description: Smartseq


title: Pat.4_PRE_ROI.006_CD31+

value: BRCA

tag: biopsy type

value: PRE

tag: patient response_to_bex

tag: segment

tag: roi

value: FFPE BRCA biopsy


title: T1-CR07-4

tag: cell type

tag: cells enriched from


title: BLA_FearRecall_fr1_C2_S208

description: Smartseq

tag: tissue

tag: genotype


title: EB_Brm_1

value: Intestinal cells

tag: time


title: Pat.4_POST_ROI.005_CD68-CD31-

tag: cancer

value: POST

tag: patient

tag: geomx batch

tag: roi exclusion


title: T1-CR07-3

tag: disease state

tag: sampling stage

tag: individual


title: EB_Dam_5

tag: cell line


title: BLA_FearRecall_fr1_C10_S216

description: Smartseq

tag: treatment


title: BLA_FearRecall_fr1_C1_S207

description: Smartseq


title: T1-CR07-2

tag: responses


title: Pat.4_POST_ROI.005_CD31+

tag: biopsy type

tag: patient response_to_bex

tag: segment

tag: q3 normalized_data_sheets


title: T1-CR07-1

tag: cell type

tag: cells enriched from


title: EB_Pc_1

tag: genotype

value: NREGal4ts_ UAS_DamPc

tag: time


title: Pat.4_POST_ROI.005_CD68+

tag: cancer

value: nDC

tag: roi

tag: patient

tag: tissue


title: T0-RE04-4

source_name: Infusion products

value: Infusion products

tag: disease state

tag: sampling stage

value: Cultured


title: BLA_FearRecall_fr1_B9_S192

description: Smartseq


title: EB_H1_1

tag: cell line

value: NREGal4ts_ UAS_DamH1


title: BLA_FearRecall_fr1_C5_S211

description: Smartseq

tag: treatment


title: T0-RE04-3

value: CAR-T cells

tag: individual

tag: responses


title: EB_HP1_1

value: NREGal4ts_ UAS_DamHP1

value: 24h  induction at 29°C


title: Pat.4_POST_ROI.004_CD31+

tag: biopsy type

tag: patient response_to_bex

tag: geomx batch

tag: roi exclusion

value: No


title: BLA_FearRecall_fr1_B7_S190

description: Smartseq

value: TRAP2 Ai14

value: Fear recall


title: Pat.4_POST_ROI.004_CD68-CD31-

tag: segment

tag: q3 normalized_data_sheets


title: EB_Dam_4

value: EB

tag: cell type

tag: genotype

value: NREGal4ts_ UAS_Dam

tag: time


title: Pat.4_PRE_ROI.006_CD68+

tag: cancer

value: BRCA

value: PRE

tag: roi

tag: patient


title: T0-RE04-2

tag: cells enriched from

tag: disease state

value: B-ALL

tag: sampling stage


title: Pat.4_POST_ROI.004_CD68+

value: POST

tag: tissue

value: FFPE BRCA biopsy


title: BLA_FearRecall_fr1_B6_S189

description: Smartseq

tag: treatment


title: T0-RE04-1

tag: individual

tag: responses


title: EB_Pol_II_3

tag: cell line

value: Intestinal cells

value: NREGal4ts_ UAS_DamPolII


title: BLA_FearRecall_fr1_B5_S188

description: Smartseq


title: BLA_FearRecall_fr1_B8_S191

description: Smartseq


title: T0-RE03-4

value: Infusion products

value: Cultured


title: EB_Dam_3


title: Pat.4_POST_ROI.003_CD31+

tag: biopsy type

tag: patient response_to_bex

value: nDC

tag: geomx batch

tag: roi exclusion


title: Pat.4_POST_ROI.003_CD68+

tag: segment

tag: q3 normalized_data_sheets


title: T0-RE03-3

tag: cell type

value: CAR-T cells


title: EB_Pol_II_2

tag: genotype

tag: time

value: 24h  induction at 29°C


title: Pat.4_POST_ROI.002_CD68-CD31-

tag: cancer

tag: roi

tag: patient

value: No


title: T0-RE03-2

tag: cells enriched from

tag: disease state

tag: sampling stage


title: Pat.4_POST_ROI.002_CD31+

tag: tissue


title: BLA_FearRecall_fr1_B4_S187

description: Smartseq

value: TRAP2 Ai14

tag: treatment


title: T0-RE03-1

tag: individual

tag: responses


title: EB_Dam_1

tag: cell line


title: BLA_FearRecall_fr1_B3_S186

description: Smartseq

value: Fear recall


title: T0-OT06-4


title: BLA_FearRecall_fr1_B2_S185

description: Smartseq


title: EC_Brm_2

source_name: EC

value: EC

value: MyoIAGal4ts_ UAS_DamBrm


title: BLA_FearRecall_fr1_B10_S193

description: Smartseq


title: BLA_FearRecall_fr1_B1_S184

description: Smartseq


title: T0-OT06-3


title: EC_H1_2

value: MyoIAGal4ts_ UAS_DamH1


title: Pat.4_POST_ROI.001_CD68-CD31-

value: BRCA

tag: biopsy type

tag: patient response_to_bex

tag: geomx batch

tag: roi exclusion


title: Pat.4_POST_ROI.003_CD68-CD31-

tag: segment

tag: q3 normalized_data_sheets


title: T0-OT06-2

tag: cell type

value: B-ALL


title: Pat.4_POST_ROI.001_CD31+

tag: cancer

value: POST

tag: roi


title: EB_Dam_2

value: EB

tag: genotype

value: NREGal4ts_ UAS_Dam

tag: time


title: EB_Pol_II_1

value: Intestinal cells

value: NREGal4ts_ UAS_DamPolII


title: T0-OT06-1

tag: cells enriched from

value: Infusion products

tag: disease state

tag: sampling stage

value: Cultured


title: BLA_FearRecall_fr1_A8_S168

description: Smartseq

tag: tissue

tag: treatment


title: Pat.4_POST_ROI.002_CD68+

value: nDC

tag: patient

value: FFPE BRCA biopsy


title: EC_Pol_II_3

tag: cell line

value: MyoIAGal4ts_ UAS_DamPolII

value: 24h  induction at 29°C


title: T0-OT05-4

value: CAR-T cells

tag: individual

tag: responses


title: Pat.4_POST_ROI.001_CD68+

tag: biopsy type

tag: patient response_to_bex

tag: geomx batch

tag: roi exclusion

value: No


title: BLA_FearRecall_fr1_A6_S166

description: Smartseq

value: TRAP2 Ai14

value: Fear recall


title: T0-OT05-3

tag: cell type


title: ACD; Timepoint-2; 22-P-1149 [22_P_1149_2_t]

city: Santiago de Compostela

first: Alberto

last: Gómez-Carballa

state: A coruña

address: Choupana sn

department: Pediatrics

country: Spain

institute: GENVIP research group

description:
raw_counts.txt
Norm_corrected_exp_ACD.txt
Norm_corrected_exp_CONTROLS.txt

data_processing:
Quality control (QC) of the RNA-Seq data obtained was performed using the FastQC and MultiQC.
After the QC step, problematic 3' end and adapters were removed with the Trimmomatic package
Reads mapped against the human reference genome using ultrafast universal RNA-Seq aligner STAR
Secondary and low-quality alignments were removed using SAMtools
DESeq2 R package was used to normalize counts and carry out the differential expression (DE) analysis after removing lowly expressed genes
Assembly: (GCh38,v.104)
Supplementary files format and content: Tab-delimited raw counts file
Supplementary files format and content: Tab-delimited Normalized and corrected data (paired-samples design accounting for patient-to-patient differences with respect to TP1) for ACD samples
Supplementary files format and content: Tab-delimited Normalized and corrected data (paired-samples design accounting for patient-to-patient differences with respect to TP1) for control samples

source_name: Capillary blood

extract_protocol:
We collected blood samples using a procedure of capillary puncture before (Time Point 1) and after (Time Point 2) exposure to music, including 16 ACD patients, and 14 healthy donors. Sample was collected in a tube containing the proper volume of PAXgene additive. RNA was isolated using the PAXgene blood miRNA extraction kit (Qiagen). On-column DNase I treatment was carried out during the extraction process. RNA concentration step and an additional DNase treatment were undertaken using an RNA clean & concentrator kit (Zymo Research) prior to sequencing
Strand specific library preparation was completed using the SMARTer Ultra low input RNA library (Poly-A). Sequencing was performed using a NovaSeq 6000 System at 100 paired end configuration to finally obtain 70M reads per sample

value: Capillary blood

tag: gender

value: Female

tag: age

tag: timepoint

tag: group

value: ACD

tag: subject id


title: EC_Brm_1

value: EC

tag: genotype

value: MyoIAGal4ts_ UAS_DamBrm

tag: time


title: T0-OT05-2

tag: cells enriched from

tag: disease state

value: B-ALL

tag: sampling stage


title: EC_Dam_3

tag: cell line

value: Intestinal cells

value: MyoIAGal4ts_ UAS_Dam


title: ACD; Timepoint-2; 22-P-1139 [22_P_1139_2_t]

tag: tissue


title: EC_H1_1

value: MyoIAGal4ts_ UAS_DamH1


title: ACD; Timepoint-1; 22-P-1149 [22_P_1149_1_t]


title: T0-OT05-1

value: Infusion products

tag: individual

tag: responses

value: Cultured


title: BLA_FearRecall_fr1_A5_S165

description: Smartseq

tag: treatment


title: ACD; Timepoint-1; 22-P-1139 [22_P_1139_1_t]


title: BLA_FearRecall_fr1_A4_S164

description: Smartseq


title: BLA_FearRecall_fr1_A3_S163

description: Smartseq


title: T0-OT03-4


title: EC_HP1_2

value: MyoIAGal4ts_ UAS_DamHP1


title: EC_Pc_2

value: MyoIAGal4ts_ UAS_DamPc

value: 24h  induction at 29°C


title: ACD; Timepoint-2; 22-P-1137 [22_P_1137_2_t]


title: BLA_FearRecall_fr1_A9_S169

description: Smartseq


title: EC_Pol_II_2

value: MyoIAGal4ts_ UAS_DamPolII


title: ACD; Timepoint-1; 22-P-1137 [22_P_1137_1_t]


title: BLA_FearRecall_fr1_A2_S162

description: Smartseq

value: TRAP2 Ai14


title: EC_Dam_2


title: T0-OT03-3

value: CAR-T cells


title: BLA_FearRecall_fr1_A10_S170

description: Smartseq

value: Fear recall


title: BLA_FearRecall_fr1_A7_S167

description: Smartseq


title: T0-OT03-2


title: T0-OT03-1


title: T0-OT02-4


title: EC_Pol_II_1


title: EC_HP1_1


title: T0-OT02-2


title: ACD; Timepoint-2; 22-P-1111 [22_P_1111_2_t]

value: Capillary blood

value: Male


title: Control; Timepoint-1; 22-P-1020 [22_P_1020_1_t]

value: Female

value: Control


title: EC_Dam_1

value: EC


title: Control; Timepoint-2; 22-P-1020 [22_P_1020_2_t]


title: T0-OT02-1

value: B-ALL


title: Monocytes, SPF, steadystate, rep3

city: Minneapolis

first: Thomas

last: Griffith

state: MN

address: 2231 6th Street SE

department: Department of Urology

institute: University of Minnesota

data_processing:
The reads count matrices were organized corresponding to experimental design and used for subsequent statistical analysis using the bioconductor package edgeR (version 3.24.3) (McCarthy et al., 2012; Robinson et al., 2010)
The raw reads count table were normalized by using default method in the package prior to generating statistics.
Multidimensional scaling was performed with edgeR using the top 500 differentially expressed genes across samples
The regression model in the edgeR package was used for statistical analysis to select the corresponding significant genes
Clustering and gene ontology analysis was performed by using ComplexHeatmap and clusterProfiler (5,6), respectively on genes with an adjusted p value <0.01
Assembly: Reads were assigned to Ensembl gene models (Mus_musculus.GRCm38.87.gtf) with featureCounts of the Subread software package (version 1.5.1) (Liao et al., 2014)
Supplementary files format and content: Excel file includes raw reads for all genes for each sample
Supplementary files format and content: Excel file includes logFC, LogCPM, Pvalue, and FDR for each gene analyzing two groups (SPF vs CoH)

source_name: Spleen

growth_protocol: Co-housed group was SPF animals co-housed with petstore mice for 60 days. The SPF group were littermate controls that did not undergo co-housing

extract_protocol:
For sorting of CD115+ monocytes, SPF and CoH spleens were collected from uninfected mice. Tissue was homogenized into a single-cell suspension using a gentleMACS dissociator, red blood cells were lysed with ACK, and cells were re-suspended in 1mL of FACS buffer. CD3+ cells were depleted from samples using an EasySep Mouse T cell Isolation kit (STEMCELL Technologies). Flow through cells were then stained with the following mAb: ghost dye 510 (live/dead), CD3, Ly6G, CD11b, and CD115. Cells were run and collected on a FACSDiva (BD) (see Supplemental Fig. 4 for sorting gating strategy). The sorted cells were re-suspended in Trizol, RNA was purified, and libraries were prepared and sequenced using Illumina NovSeq platforms (Genewiz, Azenta Life Sciences)
Raw data was trimmed and mapped, and differential gene expression was determined (Institute for Health Informatics, University of Minnesota), where additional biostatistical data analysis was also performed. The sequencing reads were mapped to the mouse genome (GRCm38) using Bowtie aligner (bowtie2 version 2.3.4.1) with local mode, -L 22 and -N 1 parameters (Langmead and Salzberg, 2012). Reads were assigned to Ensembl gene models (Mus_musculus.GRCm38.87.gtf) with featureCounts of the Subread software package (version 1.5.1) (Liao et al., 2014)

treatment_protocol: Spleens were harvested from the steady state, without additional treatment besides co-housing

value: Spleen

tag: Sex

value: female

value: CD11b+ CD115+ monocytes

value: SPF

value: steady state


title: Monocytes, SPF, steadystate, rep1

tag: cell type


title: DMKG_10mM_rep2

city: Cheongju

first: Kyunghwan

last: Kim

address: Rm #202a, Bldg. S1-5, 1 chungdae-ro

country: South Korea

institute: Chungbuk National University

data_processing:
mRNA-Seq reads were mapped to reference human genome (hg38 assembly) using HISAT2 with default parameters.
RNA expression was quantified using analyzeRepeats.pl command in HOMER.
DEGs were assessed with DESeq2 using getDiffExpression.pl in HOMER.
Assembly: hg38
Supplementary files format and content: fpkm_DMKG.txt: Tab-delimited text file includes FPKM values for each sample.

growth_protocol: SF8628 cells were cultured in DMEM supplemented with 10% FBS and antibiotics in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total RNA was isolated using the TRIzol reagent according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: SF8628c cells were treated with or without 10 mM DMKG for 48h.

value: brain cancer (DIPG) cell line

value: DMKG, 10nM


title: ACD; Timepoint-1; 22-P-1009 [22_P_1009_1_t]

tag: gender

value: ACD


title: T0-NR03-4

value: Infusion products

value: Cultured


title: Monocytes, 60d CoH, steadystate, rep4

value: 60 day co-housed


title: ACD; Timepoint-2; 22-P-1009 [22_P_1009_2_t]

value: Capillary blood

tag: age


title: DMKG_10mM_rep1


title: Monocytes, 60d CoH, steadystate, rep3


title: ACD; Timepoint-1; 22-P-1006 [22_P_1006_1_t]

tag: timepoint


title: T0-NR03-3

value: CAR-T cells


title: BLA_FearRecall_fr1_A1_S161

description: Smartseq

value: TRAP2 Ai14

value: Fear recall


title: ACD; Timepoint-1; 22-P-1111 [22_P_1111_1_t]

value: Male

tag: group


title: EC_Pc_1

value: EC

value: Intestinal cells

value: MyoIAGal4ts_ UAS_DamPc

value: 24h  induction at 29°C


title: T0-NR03-2

value: B-ALL


title: ACD; Timepoint-2; 22-P-1006 [22_P_1006_2_t]

value: Female

tag: subject id


title: Monocytes, 60d CoH, steadystate, rep2

value: Spleen

value: female

value: CD11b+ CD115+ monocytes

value: steady state


title: DMKG_0mM_rep1

value: brain cancer (DIPG) cell line


title: T0-NR03-1

value: Infusion products

value: Cultured


title: Monocytes, SPF, steadystate, rep2

value: SPF


title: T0-CR10-4

value: CAR-T cells


title: Control; Timepoint-1; 22-P-1004-M [22_P_1004_1_M]

value: Capillary blood

value: Control


title: intact, P18856_3012

city: Stockholm

first: Behzad

last: Yaghmaeian Salmani

state: Solna, Stockholm

address: Department of Cell and Molecular Biology (CMB) Karolinska Institute,, Biomedicum, Solnavägen 9, Solna, Stockholm, P.O. Box 285 SE-171 77 Stockholm, Sweden

department: CMB

country: Sweden

institute: Karolinska Institute

description:
10x Genomics
lesion_intact_counts.csv

data_processing:
reads were demultiplexed and aligned to Transcriptome mm10-3.0.0_premrna, using Cell Ranger Pipeline Version 3.1.0 (default settings).
Assembly: mm10-3.0.0_premrna
Supplementary files format and content: two csv files of UMI counts of mapped reads for all samples

source_name: Adult mouse midbrain

extract_protocol:
single nuclei isolation and FANS
Single nucleus libraries were made using Single Cell 3' v3 on Chromium platform (10X Genomics & SciLifeLab, Stockholm) in accordance with the manufacturer’s protocols

treatment_protocol: unilaterally injected, over 2 min, with 0.7 or 1.5 μg of 6-OHDA in 0.01% ascorbate (Sigma–Aldrich) into the medial forebrain bundle (MFB) of the right hemisphere.

value: mDA, non-mDA

value: Adult mouse midbrain

tag: strain

tag: genotype

value: DatCre TrapC fl/fl

tag: sample group

value: intact


title: T0-CR10-2

tag: cells enriched from

tag: disease state

value: B-ALL


title: lesioned, P18856_3011

description:
10x Genomics
lesion_intact_counts.csv

value: lesioned


title: HDM-treated B6.IL31RAKO dorsal skin, replicate 1, scRNA-seq

city: San Francisco

first: Marlys

last: Fassett

state: CA

address: 35 Medical Center Way Rm 1026

department: Dermatology

institute: UCSF-Parnassus

description: 10X genomics

data_processing:
Initial post-processing and quality control including single-cell transcript alignment to mouse genome GRC38/mm10 were also performed by the UCSF Genomics Core Facility, using the 10X Cell Ranger package (Cell Ranger Version 3.1, 10X Genomics).
R package Seurat (version 3.2.2, Satija Lab) was used for single cell transcriptome analysis. Expression matrices for WT and IL31RA were combine using the Seurat merge command. The SCTransform normalization method was used to control for between-sample sequencing depth variation.
Cells were removed according to the following thresholds: <500 genes/cell or >5000 genes per cell, >20000 UMIs/cell, 10% mitochondrial content, <0.01% hemoglobin content. Among the cells retained, the effects of mitochondrial and ribosomal content were regressed out prior to clustering.
Clustering was performed using the default Seurat parameters: clusters are identified using Shared Nearest Neighbors method then optimized using the original Louvain algorithm. Genes were excluded from the final dataset if they were expressed in fewer than 3 cells, resulting in a total of 15,592 genes.
For differential expression (DEG) analysis between clusters, genes were detected if they are expressed in at least 10% of cells in a cluster with a log fold change of at least 0.25. For DEG analysis between comparison groups, genes were detected if expressed in at least 5% of cells in the group with a log fold change of at least 0.25.
Assembly: GRC38/mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: skin

extract_protocol:
HDM-treated dorsal neck skin from 4 pooled Il31RAKO and 4 pooled WT C57Bl/6 mice was defatted, minced, digested (2 hours at 37*C in RPMI supplemented with Liberase TM, Hyaluronidase and DNAse), dissociated (GentleMACS (program C, Miltenyi), and filtered through 70 um metal mesh in preparation for flow cytometry. The live (DAPI-) CD45+ cell fraction of each sample (pooled B6 or pooled B6.IL31RAKO) was sorted using a Moflo XDP (Beckman Coulter) directly into ice-cold 0.5% BSA in PBS.
30,000 cells per sample were immediately processed through the Chromium Single Cell 3′ v2 Library Kit (10X Genomics) per the manufacturer’s protocol by the UCSF Genomics Core Facility of the UCSF Institute for Human Genetics
Single Cell 3′ libraries used standard Illumina sequencing primers for both sequencing and index reads and were run using paired-end sequencing with single indexing where Read1 is 26 cycles and Read 2 is 98 cycles.

treatment_protocol: Biostir ointment (containing D. farinae HDM; obtained from Biostir Inc) was applied epicutaneously to shave dorsal mouse skin twice weekly x3 weeks. Two hours prior to each application of Biostir ointment, skin was treated with a 2% SDS solution.

value: skin

value: Biostir HDM ointment


title: HDM-treated B6 dorsal skin, replicate 1, scRNA-seq

description: 10X genomics

value: WT


title: ACD; Timepoint-2; 22-P-1003 [22_P_1003_2_t]

value: Male

value: ACD


title: ACD; Timepoint-1; 22-P-1003 [22_P_1003_1_t]


title: lesioned, P18856_3009

description:
10x Genomics
lesion_intact_counts.csv

value: female


title: T0-CR10-1

value: Infusion products

tag: sampling stage

value: Cultured


title: intact, P18856_3010

description:
10x Genomics
lesion_intact_counts.csv

tag: tissue


title: T0-CR10-3

value: CAR-T cells

tag: individual


title: ESC_CRISPRa_Nfatc3_CapHiC_rep1

city: Illkirch

first: Tom

last: Sexton

address: 1 rue Laurent Fries

institute: IGBMC (Institute of Genetics and Molecular and Cellular Biology)

description:
Replicate-specific and pooled mat files are provided
ESC_CRISPRa_Nfatc3_CapHiC_pooled.mat

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq.
Individual 4C-seq experiments were demultiplexed according to bait primer sequence using sabre, with two mismatches permitted (-m 2).
Reads were aligned using Bowtie (v1.0.0) with the settings -a -m 1 --best --strata.
Mapped reads were filtered and mapped to restriction fragments, essentially as described in van de Werken, H.J. et al. Robust 4C-seq data analysis to screen for regulatory DNA interactions. Nature Methods 910: 969-972.
Assembly: mm10
Supplementary files format and content: Hi-C contact maps are given as cool files, able to be visualized in HiGlass.
Supplementary files format and content: 4C data are represented as .cis files, containing a header and two columns (restriction fragment midpoint coordinate, counts), the input format for 4See.
Supplementary files format and content: The captured regions from the Capture Hi-C data are represented as text (.mat) files, consisting of headed columns: chr, ID (of capture region), coord_bin1, coord_bin2, from1, to1 (coordinates of first region), to1, to2 (coordinates of second region), and a final column with the normalized interaction score.

source_name: J1 embryonic stem cell

growth_protocol: J1 mouse ES cells were grown on gamma-irradiated mouse embryonic fibroblast cells under standard conditions (4.5 g/L glucose-DMEN, 15% FCS, 0.1 mM non-essential amino acids, 0.1 mM beta-mercaptoethanol, 1 mM glutamine, 500 U/mL LIF, gentamicin), then passaged onto feeder-free 0.2% gelatin-coated plates for at least two passages to remove feeder cells.

extract_protocol:
Five million aliquots of cells were fixed in 2% formaldehyde for 10 min, quenched with 125 mM cold glycine, then collected by centrifugation and washed with PBS. Cells were lysed in lysis buffer (10 mM Tris-HCl pH 8, 100 mM NaCl, 0.2% NP-40, protease inhibitor cocktail) on ice for 30 min and nuclei collected by centrifugation and resuspended in DpnII restriction buffer. ESCs were permeabilized by treatment with 0.4% SDS for 1 h at 37°C, followed by 1.6% Triton X-100 for 1 h at 37°C. Nuclei aliquots were digested overnight at 37°C with 1500 U DpnII, then cohesive ends were filled in with biotin tags by incubating for 90 min at 37°C with 15 μM dATP, 15 μM dTTP, 15 μM dGTP, 15 μM biotin-14-dCTP and 25 U DNA polymerase I Klenow fragment. Nuclei were collected by centrifugation and in situ ligation was performed overnight at 16°C in 500 μL volumes of 1X ligase buffer (NEB) with 20,000 U T4 DNA ligase, before de-crosslinking overnight at 65°C with 0.75 mg/mL proteinase K. DNA was purified by RNase A treatment, phenol/chloroform extraction and isopropanol precipitation. Five microgram aliquots of DNA were sonicated to a fragment size of ~100-400 bp in a Covaris sonicator E220 and bound to Steptavidin MyOne T1 beads, following the manufacturer’s instructions. The DNA was then end-repaired by incubating for 1 h at 20°C with 0.8 mM dNTPs, 0.3 U/μL T4 DNA polymerase, 1 U/μL T4 polynucleotide kinase and 0.1 U/μL DNA polymerase I Klenow fragment in ligase buffer, then A-tailed by incubating for 1 h at 37°C with 200 μM dATP and 0.2 U/μL Klenow fragment (3’-5’ exo-) in NEBuffer 2 (NEB), then Illumina PE adapter was added by incubating overnight at 20°C with 15 μM PE adapter and 2000 U T4 DNA ligase in ligase buffer, washing the beads with appropriate buffers in between each treatment. Hi-C material was then amplified from the beads with 7-9 cycles of PCR using Herculase II Fusion DNA polymerase (Agilent) according to the manufacturer’s instructions. Material at this stage was quantified on a BioAnalyzer (Agilent) and DpnII and HindIII Hi-C material was sequenced (2x50 nt) on a HiSeq 4000 (Illumina) following the manufacturer’s instructions). 750 ng of this DpnII Hi-C material was concentrated in a SpeedVac vacuum concentrator and then target capture was performed using the SureSelect XT Target Enrichment system (Agilent) with the custom-designed library, following the manufacturer’s instructions
Products resulting from extract protocol are immediately ready for cluster generation on Illumina HiSeq 4000, following manufacturer's instructions.

treatment_protocol: Twenty million cell batches of J1 ESCs were transfected each with 20 μg dCas9-VPR vector (Addgene #63798) and 20 μg plasmid constructed by the IGBMC molecular biology platform, containing optimized scaffold for 4 gRNAs alongside a puromycin resistance gene and mCherry reporter, with Lipofectamine 2000 according to the manufacturer’s instructions. After 24 h, transfected cells were treated with 3 μg/mL puromycin and 1 mg/mL G418, and after another 24 h, mCherry-positive cells were sorted by FACS before immediate processing.

tag: cell line

value: J1 embryonic stem cell

value: CRISPRa induction of Nfatc3

tag: restriction enzyme

value: DpnII


title: DMKG_0mM_rep2

value: brain cancer (DIPG) cell line

tag: treatment


title: Monocytes, 60d CoH, steadystate, rep1

value: Spleen

tag: Sex

tag: cell type

value: CD11b+ CD115+ monocytes

value: 60 day co-housed

value: steady state


title: T0-CR09-3

value: B-ALL

tag: responses


title: Control; Timepoint-2; 22-P-1001-M [22_P_1001_2_M]

value: Capillary blood

tag: gender

tag: age

tag: timepoint

value: Control


title: intact, P18856_3008

description:
10x Genomics
lesion_intact_counts.csv

value: mDA, non-mDA

value: Adult mouse midbrain

tag: strain

value: DatCre TrapC fl/fl

value: intact


title: Control; Timepoint-1; 22-P-1001-M [22_P_1001_1_M]

value: Male

tag: group

tag: subject id


title: T0-CR09-4

value: CAR-T cells

tag: cells enriched from

value: Infusion products

value: Cultured


title: lesioned, P18856_3007

description:
10x Genomics
lesion_intact_counts.csv

tag: genotype

value: female

tag: sample group

value: lesioned


title: ESC_CRISPRa_Bcl6_CapHiC_rep1

description:
Replicate-specific and pooled mat files are provided
ESC_CRISPRa_Bcl6_CapHiC_pooled.mat

value: J1 embryonic stem cell

value: WT

value: CRISPRa induction of Bcl6

value: DpnII


title: Control; Timepoint-2; 22-P-1004-M [22_P_1004_2_M]

tag: tissue

value: Female


title: ESC_dCTCF_Bcl6_CapHiC_rep2

description:
Replicate-specific and pooled mat files are provided
ESC_dCTCF_Bcl6_CapHiC_pooled.mat

value: Homozygous deletion of CTCF site at Bcl6 promoter


title: intact, P18856_3006

description:
10x Genomics
lesion_intact_counts.csv


title: ESC_CRISPRa_Nfatc3_CapHiC_rep2

value: CRISPRa induction of Nfatc3


title: ACD; Timepoint-1; 22_P_1119 [22_P_1119_1_t]

value: Capillary blood

value: ACD


title: ACD; Timepoint-2; 22_P_1119 [22_P_1119_2_t]


title: ESC_dCTCF_Bcl6_CapHiC_rep1


title: T0-CR09-2

tag: disease state

value: B-ALL

tag: sampling stage

tag: individual


title: lesioned, P18856_3005

description:
10x Genomics
lesion_intact_counts.csv

value: mDA, non-mDA

value: Adult mouse midbrain

value: DatCre TrapC fl/fl


title: Control; Timepoint-2; 22-P-1103 [22_P_1103_2_t]

value: Control


title: Control; Timepoint-1; 22-P-1103 [22_P_1103_1_t]


title: ESC_CapHiC_rep2

description:
Replicate-specific and pooled mat files are provided
ESC_CapHiC_pooled.mat

tag: cell line

tag: restriction enzyme


title: ESC_CapHiC_rep1


title: intact, P18856_3004

description:
10x Genomics
lesion_intact_counts.csv

tag: cell type

tag: Sex

value: intact


title: lesioned, P18856_3003

description:
10x Genomics
lesion_intact_counts.csv

value: female


title: Control; Timepoint-1; 22-P-1060 [22_P_1060_1_t]

tag: gender


title: ESC_CRISPRa_Bcl6_CapHiC_rep2

tag: treatment


title: T0-CR08-4

value: CAR-T cells

value: Infusion products

tag: responses

value: Cultured


title: intact, P18856_3002

description:
10x Genomics
lesion_intact_counts.csv

tag: strain

tag: age


title: T0-CR08-1


title: lesioned, P18856_3001

description:
10x Genomics
lesion_intact_counts.csv

value: lesioned


title: Control; Timepoint-2; 22-P-1056 [22_P_1056_2_t]

tag: timepoint

tag: group

tag: subject id


title: T0-CR08-2

tag: cells enriched from


title: Control; Timepoint-2; 22-P-1060 [22_P_1060_2_t]

tag: tissue


title: DN3_CapHiC_rep2

description:
Replicate-specific and pooled mat files are provided
DN3_CapHiC_pooled.mat

source_name: CD4-CD8-CD44-CD25+ DN3 thymocyte

extract_protocol:
Five million aliquots of cells were fixed in 2% formaldehyde for 10 min, quenched with 125 mM cold glycine, then collected by centrifugation and washed with PBS. Cells were lysed in lysis buffer (10 mM Tris-HCl pH 8, 100 mM NaCl, 0.2% NP-40, protease inhibitor cocktail) on ice for 30 min and nuclei collected by centrifugation and resuspended in DpnII restriction buffer. Thymocytes were permeabilized by treatment with 0.8% SDS for 20 min at 65°C, followed by 40 min at 37°C, then with 3.3% Triton X-100 for 1 h at 37°C. Nuclei aliquots were digested overnight at 37°C with 1500 U DpnII, then cohesive ends were filled in with biotin tags by incubating for 90 min at 37°C with 15 μM dATP, 15 μM dTTP, 15 μM dGTP, 15 μM biotin-14-dCTP and 25 U DNA polymerase I Klenow fragment. Nuclei were collected by centrifugation and in situ ligation was performed overnight at 16°C in 500 μL volumes of 1X ligase buffer (NEB) with 20,000 U T4 DNA ligase, before de-crosslinking overnight at 65°C with 0.75 mg/mL proteinase K. DNA was purified by RNase A treatment, phenol/chloroform extraction and isopropanol precipitation. Five microgram aliquots of DNA were sonicated to a fragment size of ~100-400 bp in a Covaris sonicator E220 and bound to Steptavidin MyOne T1 beads, following the manufacturer’s instructions. The DNA was then end-repaired by incubating for 1 h at 20°C with 0.8 mM dNTPs, 0.3 U/μL T4 DNA polymerase, 1 U/μL T4 polynucleotide kinase and 0.1 U/μL DNA polymerase I Klenow fragment in ligase buffer, then A-tailed by incubating for 1 h at 37°C with 200 μM dATP and 0.2 U/μL Klenow fragment (3’-5’ exo-) in NEBuffer 2 (NEB), then Illumina PE adapter was added by incubating overnight at 20°C with 15 μM PE adapter and 2000 U T4 DNA ligase in ligase buffer, washing the beads with appropriate buffers in between each treatment. Hi-C material was then amplified from the beads with 7-9 cycles of PCR using Herculase II Fusion DNA polymerase (Agilent) according to the manufacturer’s instructions. 750 ng of this DpnII Hi-C material was concentrated in a SpeedVac vacuum concentrator and then target capture was performed using the SureSelect XT Target Enrichment system (Agilent) with the custom-designed library, following the manufacturer’s instructions.
Products resulting from extract protocol are immediately ready for cluster generation on Illumina HiSeq 4000, following manufacturer's instructions.

treatment_protocol: Thymocytes were obtained from 4-week-old c57/Bl6 mouse (Charles River; equal numbers of males and females) thymus by FACS. Thymuses were dissected, gently homogenized and filtered through a 70 μm strainer in cold PBE (0.5% BSA and 2 mM EDTA in 1X PBS). To purify DN3 cells, ~4 billion cells were first depleted of DP cells by incubating with rat anti-CD4 and rat anti-CD8 anti-sera (kind gift of Susan Chan), washing with cold PBE and binding the DP cells to Dynabeads-sheep anti-rat IgG (Invitrogen). The supernatant was centrifuged to harvest the cells, which were then incubated with anti-mouse CD4-FITC, anti-mouse CD8a-FITC, anti-mouse CD3e-FITC, anti-mouse B220-FITC, anti-mouse CD11b-FITC, anti-mouse Ly-6G(Gr-1)-FITC, anti-mouse NK1.1-FITC, anti-mouse CD44-APC and anti-mouse CD25-PE antibodies (eBioScience) and washed with PBE. DAPI was added and viable PE+APC-FITC- cells were purified by FACS.

value: CD4-CD8-CD44-CD25+ DN3 thymocyte

tag: genotype

value: WT

value: DpnII


title: untreated, 10X_19_011

description:
10x Genomics
untreated_counts.csv

tag: sample group

value: untreated


title: Control; Timepoint-1; 22-P-1056 [22_P_1056_1_t]

value: Capillary blood

value: Female


title: DN3_4C_Rag1

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq.
Individual 4C-seq experiments were demultiplexed according to bait primer sequence using sabre, with two mismatches permitted (-m 2).
Reads were aligned using Bowtie (v1.0.0) with the settings -a -m 1 --best --strata.
Mapped reads were filtered and mapped to restriction fragments, essentially as described in van de Werken, H.J. et al. Robust 4C-seq data analysis to screen for regulatory DNA interactions. Nature Methods 910: 969-972.
Assembly: mm10
Supplementary files format and content: Hi-C contact maps are given as cool files, able to be visualized in HiGlass.
Supplementary files format and content: 4C data are represented as .cis files, containing a header and two columns (restriction fragment midpoint coordinate, counts), the input format for 4See.
Supplementary files format and content: The captured regions from the Capture Hi-C data are represented as text (.mat) files, consisting of headed columns: chr, ID (of capture region), coord_bin1, coord_bin2, from1, to1 (coordinates of first region), to1, to2 (coordinates of second region), and a final column with the normalized interaction score.
Library strategy: 4C

extract_protocol:
Cells were fixed in 2% formaldehyde for 10 min at 23°C. The fixation was quenched with cold glycine at a final concentration of 125 mM, then cells were washed with PBS and permeabilized on ice for 1 h with 10 mM Tris-HCl, pH 8, 100 mM NaCl, 0.1% NP-40 and protease inhibitors. Nuclei were resuspended in DpnII restriction buffer at 10 million nuclei/mL concentration, and 5 million nuclei aliquots were further permeabilized by treatment for 1 h with 0.4% SDS at 37°C, then a further 1h with 2.6% Triton-X100 at 37°C. Nuclei were digested overnight with 1000 U DpnII at 37°C, then washed twice by centrifuging and resuspending in T4 DNA ligase buffer. In situ ligation was performed in 400 μL T4 DNA ligase buffer with 20,000 U T4 DNA ligase overnight at 16°C. DNA was purified by reverse cross-linking with an overnight incubation at 65°C with proteinase K, followed by RNase A digestion, phenol/chloroform extraction and isopropanol precipitation. The DNA was digested with 5 U/μg Csp6I at 37°C overnight, then re-purified by phenol/chloroform extraction and isopropanol precipitation. The DNA was then circularized by ligation with 200 U/μg T4 DNA ligase under dilute conditions (5 ng/μL DNA), and purified by phenol/chloroform extraction and isopropanol precipitation. 50 ng aliquots of this DNA were used as template for PCR with bait-specific primers containing Illumina adapter termini. PCR reactions were pooled and primers were removed by washing with 1.8x AMPure XP beads.
Products resulting from extract protocol are immediately ready for cluster generation on Illumina HiSeq 4000, following manufacturer's instructions.

value: DpnII - Csp6I


title: ACD; Timepoint-1; 22-P-1066 [22_P_1066_1_t]

value: ACD


title: T0-CR09-1

tag: disease state

value: B-ALL

tag: sampling stage

tag: individual


title: T0-CR07-4

tag: cell type


title: DN3_HindIII_HiC_rep2

description:
All DN3 Hi-C datasets are combined to the final processed data file
DN3_HiC.cool

extract_protocol:
Five million aliquots of cells were fixed in 2% formaldehyde for 10 min, quenched with 125 mM cold glycine, then collected by centrifugation and washed with PBS. Cells were lysed in lysis buffer (10 mM Tris-HCl pH 8, 100 mM NaCl, 0.2% NP-40, protease inhibitor cocktail) on ice for 30 min and nuclei collected by centrifugation and resuspended in NEBuffer 2. Thymocytes were permeabilized by treatment with 0.8% SDS for 20 min at 65°C, followed by 40 min at 37°C, then with 3.3% Triton X-100 for 1 h at 37°C. Nuclei aliquots were digested overnight at 37°C with 2000 U HindIII, then cohesive ends were filled in with biotin tags by incubating for 90 min at 37°C with 15 μM dATP, 15 μM dTTP, 15 μM dGTP, 15 μM biotin-14-dCTP and 25 U DNA polymerase I Klenow fragment. Nuclei were collected by centrifugation and in situ ligation was performed overnight at 16°C in 500 μL volumes of 1X ligase buffer (NEB) with 20,000 U T4 DNA ligase, before de-crosslinking overnight at 65°C with 0.75 mg/mL proteinase K. DNA was purified by RNase A treatment, phenol/chloroform extraction and isopropanol precipitation. Five microgram aliquots of DNA were sonicated to a fragment size of ~100-400 bp in a Covaris sonicator E220 and bound to Steptavidin MyOne T1 beads, following the manufacturer’s instructions. The DNA was then end-repaired by incubating for 1 h at 20°C with 0.8 mM dNTPs, 0.3 U/μL T4 DNA polymerase, 1 U/μL T4 polynucleotide kinase and 0.1 U/μL DNA polymerase I Klenow fragment in ligase buffer, then A-tailed by incubating for 1 h at 37°C with 200 μM dATP and 0.2 U/μL Klenow fragment (3’-5’ exo-) in NEBuffer 2 (NEB), then Illumina PE adapter was added by incubating overnight at 20°C with 15 μM PE adapter and 2000 U T4 DNA ligase in ligase buffer, washing the beads with appropriate buffers in between each treatment. Hi-C material was then amplified from the beads with 7-9 cycles of PCR using Herculase II Fusion DNA polymerase (Agilent) according to the manufacturer’s instructions.
Products resulting from extract protocol are immediately ready for cluster generation on Illumina HiSeq 4000, following manufacturer's instructions.

tag: restriction enzyme

value: HindIII


title: DN3_CapHiC_rep1


title: T0-CR07-3


title: T0-CR08-3


title: DN3_HindIII_HiC_rep1


title: T0-CR07-2


title: untreated, 10X_19_010

description:
10x Genomics
untreated_counts.csv

value: mDA, non-mDA

value: Adult mouse midbrain

value: DatCre TrapC fl/fl

tag: Sex


title: DN3_DpnII_HiC_rep2

extract_protocol:
Five million aliquots of cells were fixed in 2% formaldehyde for 10 min, quenched with 125 mM cold glycine, then collected by centrifugation and washed with PBS. Cells were lysed in lysis buffer (10 mM Tris-HCl pH 8, 100 mM NaCl, 0.2% NP-40, protease inhibitor cocktail) on ice for 30 min and nuclei collected by centrifugation and resuspended in DpnII restriction buffer. Thymocytes were permeabilized by treatment with 0.8% SDS for 20 min at 65°C, followed by 40 min at 37°C, then with 3.3% Triton X-100 for 1 h at 37°C. Nuclei aliquots were digested overnight at 37°C with 1500 U DpnII, then cohesive ends were filled in with biotin tags by incubating for 90 min at 37°C with 15 μM dATP, 15 μM dTTP, 15 μM dGTP, 15 μM biotin-14-dCTP and 25 U DNA polymerase I Klenow fragment. Nuclei were collected by centrifugation and in situ ligation was performed overnight at 16°C in 500 μL volumes of 1X ligase buffer (NEB) with 20,000 U T4 DNA ligase, before de-crosslinking overnight at 65°C with 0.75 mg/mL proteinase K. DNA was purified by RNase A treatment, phenol/chloroform extraction and isopropanol precipitation. Five microgram aliquots of DNA were sonicated to a fragment size of ~100-400 bp in a Covaris sonicator E220 and bound to Steptavidin MyOne T1 beads, following the manufacturer’s instructions. The DNA was then end-repaired by incubating for 1 h at 20°C with 0.8 mM dNTPs, 0.3 U/μL T4 DNA polymerase, 1 U/μL T4 polynucleotide kinase and 0.1 U/μL DNA polymerase I Klenow fragment in ligase buffer, then A-tailed by incubating for 1 h at 37°C with 200 μM dATP and 0.2 U/μL Klenow fragment (3’-5’ exo-) in NEBuffer 2 (NEB), then Illumina PE adapter was added by incubating overnight at 20°C with 15 μM PE adapter and 2000 U T4 DNA ligase in ligase buffer, washing the beads with appropriate buffers in between each treatment. Hi-C material was then amplified from the beads with 7-9 cycles of PCR using Herculase II Fusion DNA polymerase (Agilent) according to the manufacturer’s instructions.
Products resulting from extract protocol are immediately ready for cluster generation on Illumina HiSeq 4000, following manufacturer's instructions.


title: untreated, 10X_19_009

description:
10x Genomics
untreated_counts.csv

value: female


title: untreated, 10X_19_008

description:
10x Genomics
untreated_counts.csv


title: T0-CR07-1

value: CAR-T cells

value: Infusion products


title: Control; Timepoint-2; 22-P-1022 [22_P_1022_2_t]

tag: gender

value: Control


title: untreated, 10X_19_007

description:
10x Genomics
untreated_counts.csv


title: Control; Timepoint-1; 22-P-1022 [22_P_1022_1_t]


title: DN3_DpnII_HiC_rep1

value: CD4-CD8-CD44-CD25+ DN3 thymocyte


title: BRC1 induced Input 3 ChIPseq

city: Wageningen

first: Sam

middle: Wijnand

last: van Es

address: Droevendaalsesteeg

department: Plant Developmental Systems

country: Netherlands

institute: Wageningen University and Research

data_processing:
RNA-seq: Bowtie-Tophat-Cuffdiff pipeline
ChIP-seq: Bowtie2 to map reads, MACS2 for peak calling
Genome_build: Arabidopsis TAIR10
Supplementary_files_format_and_content: txt(FPKMs), bedgraph
Supplementary_files_format_and_content: brc1_peaks_intersect_sample1_and_sample2.bed: Bed file in which the raw data from sample 1 and sample 2 were combined.

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings

extract_protocol:
Seedlings were picked from plate and flash frozen in liquid nitrogen. For RNA-seq, InviTrap Spin plant RNA mini Kit was used to extract RNA. For the ChIP-seq experiment as described in Mourik et al. (2015)
For RNA-seq, Illumina Truseq Library preparation kit. For ChIP-seq, NEBNext ChIPseq Library Preparation Kit (NEB)

tag: treatment

value: 10uM estradiol

value: seedlings

tag: chip antibody


title: untreated, 10X_19_006

description:
10x Genomics
untreated_counts.csv

tag: strain

tag: age

value: untreated


title: BRC1 induced Input 2 ChIPseq


title: DP_4C_Bcl6

source_name: CD4+CD8+ DP thymocyte

treatment_protocol: Thymocytes were obtained from 4-week-old c57/Bl6 mouse (Charles River; equal numbers of males and females) thymus by FACS. Thymuses were dissected, gently homogenized and filtered through a 70 μm strainer in cold PBE (0.5% BSA and 2 mM EDTA in 1X PBS). To purify DP cells, ~600 million cells were incubated with anti-mouse CD4-PE, anti-mouse CD8a-FITC and anti-mouse CD3e-APC antibodies (eBioScience), before washing with cold PBE, adding DAPI and purifying viable (DAPI-) PE+ FITC+ APC+ cells by FACS.

value: CD4+CD8+ DP thymocyte

value: WT


title: ACD; Timepoint-1; 22-P-1081 [22_P_1081_1_t]

value: Capillary blood

value: Male

tag: timepoint

tag: group


title: ACD; Timepoint-2; 22-P-1066 [22_P_1066_2_t]

value: Female

value: ACD

tag: subject id


title: ACD; Timepoint-2; 22-P-1081 [22_P_1081_2_t]

tag: tissue


title: ACD; Timepoint-1; 22-P-1145 [22_P_1145_2_t]


title: DP_4C_Rag1

tag: genotype

value: DpnII - Csp6I


title: BRC1 induced sample 2 ChIPseq

value: µMACS Anti-GFP - Miltenyi - 130-091-288


title: ACD; Timepoint-2; 22-P-1145 [22_P_1145_1_t]


title: Infected-2

city: Manchester

first: Juan

middle: Fernando

last: Quintana

address: 2.18c CTF, Grafton Street

department: Lydia Becker Institute of Immunology and Inflammation

country: United Kingdom

institute: University of Manchester

data_processing:
For FASTQ generation and alignments, illumina basecall files (*.bcl) were converted to FASTQs using bcl2fastq
Gene counts were generated using CellRanger for single cell RNAseq (v.6.0.0) or SpaceRanger for spatial transcriptomics (v.1.2.2)
Mapping strategy was conducted on CellRanger or SpaceRanger against a combined Mus musculus (mm10) and Trypanosoma brucei (TREU927) transcriptome reference
After alignment, reads were grouped based on barcode sequences and demultiplexed using the Unique Molecular Identifiers (UMIs)
Assembly: mm10 + TREU927
Supplementary files format and content: .h5 files were generated as outputs from CellRanger or SpaceRanger.

source_name: CNS meninges

growth_protocol: 6-8 weeks old mice were infected (i.p.) with 2,000 Trypanosoma brucei brucei strain Antat 1.1E. Mouse CNS meninges from naïve and infected mice were harvested for scRNAseq analysis using 10X Genomics

extract_protocol:
Single cell suspensions were obtained from murine meninges using enzymatic dissociation, followed by library preparation using the 10X Chromium platform.
Illumina compatible, RNA libraries were prepared with the 10X Chromium technolgy

treatment_protocol: Two biological replicates per time point (naïve and 30 days post-infection) for single cell transcriptomics (n = 3 pooled mice/sample).

value: CNS meninges

value: 6-8 weeks old

tag: library type

value: single cell RNA


title: BRC1 induced Input 1 ChIPseq


title: BRC1 induced sample 3 ChIPseq


title: ACD; Timepoint-2; 22-P-1132 [22_P_1132_2_t]


title: DP_HindIII_HiC_rep2

description:
All DP Hi-C datasets are combined to the final processed data file
DP_HiC.cool

value: HindIII


title: DP_DpnII_HiC_rep2

value: DpnII


title: Infected-1


title: DP_CapHiC_rep1

description:
Replicate-specific and pooled mat files are provided
DP_CapHiC_pooled.mat


title: BRC1 induced sample 1 ChIPseq


title: DP_CapHiC_rep2


title: DP_HindIII_HiC_rep1


title: in_vivo-aged-rep3

description: FACS-sorted small intestinal epithelial cells

data_processing:
cellranger, v3.0.1, --expect-cells=5000
Genome_build: mm10-1.2.0
Supplementary_files_format_and_content: cellranger_output: the filtered countmatrix that is part of the cellranger output: given as .tar archive of the gzipped "out/filtered/" files, i.e. a Market Exchange Format (MEX) for sparse matrices file (matrix.mtx.gz) and tab separated values files giving row and column names (barcodes.tsv.gz and features.tsv.gz)

source_name: epithelial cells, freshly isolated from the small intestine of an aged mouse

extract_protocol:
cells were isolated from the small intestine by EDTA & Trypsin-based digestion and then FACS sorted (EpCam+ ; CD45-)
Illumina sequencing libraries were prepared using the 10x Genomics Single Cell 3' v3 kit

tag: organ

value: small intestine

value: small intestinal epithelium

value: 20-22 months

tag: batch


title: brc1-2 control sample 1 RNAseq

value: 10uM estradiol

value: seedlings


title: Naive-1


title: brc1-2 control sample 3 RNAseq


title: ACD; Timepoint-1; 22-P-1144 [22_P_1144_1_t]


title: brc1-2 control sample 2 RNAseq


title: ACD; Timepoint-1; 22-P-1132 [22_P_1132_1_t]


title: in_vivo-young-rep2

source_name: epithelial cells, freshly isolated from the small intestine of a young mouse

value: 2-3 months


title: BRC1 induced sample 3 RNAseq


title: in_vivo-young-rep3


title: in_vivo-aged-rep1


title: ACD; Timepoint-2; 22-P-1144 [22_P_1144_2_t]

value: Capillary blood


title: Small intestinal organoids_Young-rep6

data_processing:
nf-core/rnaseq  v1.4.2
Nextflow  v20.04.1
FastQC  v0.11.8
Cutadapt v2.5
Trim Galore! v0.6.4
SortMeRNA v2.1b
STAR vSTAR_2.6.1d
HISAT2 v2.1.0
Picard MarkDuplicates v2.21.1
Samtools v1.9
featureCounts v1.6.4
StringTie v2.0
Preseq v2.0.3
deepTools v3.3.1
RSeQC v3.0.1
dupRadar v1.14.0
Qualimap v.2.2.2-dev
MultiQC v1.7
Genome_build: GRCm38
bam files generated using STAR aligner
Supplementary_files_format_and_content: count text files gernerated using R/DESeq2 v1.28.1

source_name: Small intestinal organoids

growth_protocol: small intestinal organoids were culture for 4-5 weeks (passage 3 & 4) and passaged every week

extract_protocol:
RNA was isolated from organoids via QIAGEN RNAeasy kit, including on column DNase digest
Illumina sequencing libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer's protocol. Briefly, poly(A)+ RNA was purified from 500ng of total RNA using oligo(dT) beads, fragmented to a median insert length of 155 bp and converted to cDNA. The ds cDNA fragments were then end-repaired, adenylated on the 3′ end, adapter ligated and amplified with 15 cycles of PCR.

value: small intestinal epithelial cells

value: Young

tag: organoid culture passage

tag: cell line


title: DP_DpnII_HiC_rep1

tag: cell type

value: CD4+CD8+ DP thymocyte

value: WT

tag: restriction enzyme


title: in_vivo-aged-rep2


title: Small intestinal organoids_Aged-rep6

value: Aged


title: ACD; Timepoint-2; 22-P-1134 [22_P_1134_2_t]

tag: gender

value: Female

value: ACD


title: Control; Timepoint-2; 22-P-1069 [22_P_1069_2_t]

value: Control


title: BRC1 induced sample 1 RNAseq

tag: treatment


title: ACD; Timepoint-1; 22-P-1134 [22_P_1134_1_t]


title: Naive-2

value: CNS meninges

tag: Sex

value: 6-8 weeks old

value: single cell RNA


title: in_vivo-young-rep1

description: FACS-sorted small intestinal epithelial cells, sequenced with 10X Genomics Chromium v3.1

tag: strain

value: small intestine

value: small intestinal epithelium


title: Small intestinal organoids_Young-rep5

tag: age


title: RRBS_pESC-PGCLC

city: Munich

first: Chenglei

last: Tian

address: Ingolstädter Landstraße 1

institute: Helmholtz Munich

data_processing:
Bismark software (version 0.16.3) was used to perform alignments of bisulfite-treated reads to a reference genome.
The reference genome was firstly transformed into bisulfite-converted version (C-to-T and G-to-A converted) and then indexed using bowtie2.
Sequence reads were also transformed into fully bisulfite-converted versions (C-to-T and G-to-A converted) before they are aligned to similarly converted versions of the genome in a directional manner.
Sequence reads that produce a unique best alignment from the two alignment processes (original top and bottom strand) are then compared to the normal genomic sequence and the methylation state of all cytosine positions in the read is inferred.
Genome_build: mm10
Supplementary_files_format_and_content: ESC.txt; pESC.txt; ESC-PGCLC.txt; pESC-PGCLC.txt; PGC.txt. The values in column 2 of processed data is Ratio of methylation (methylated sites/ unmethylated sites)

growth_protocol: Female ESC and pESCs were maintained by dissociating cells with 0.25% TE (Invitrogen) every 2~3 days and re-plated onto feeder cells with S/L medium. S/L medium (ESC culture medium) contains knockout DMEM supplemented with 15% FBS (ES quality, Hyclone), 1 mM L-glutamine, 1% nonessential amino acid stock, 50 units/ml penicillin and 50 μg/ml streptomycin, 0.1 mM β-mercaptoethanol, and 1000 IU/ml mLIF. PGCs are isolated for E12.5 fetal gonad with MACS of SSEA1 beads.

extract_protocol:
Cells were collected and isolated their genomic DNA by QIAamp DNA Micro Kit (QIAGEN). DNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) and DNA concentration was measured using Qubit® DNA Assay Kit in Qubit® 2.0 Flurometer (Life Technologies, CA, USA).
A total amount of 1.5 μg DNA were spiked with moderate lambda DNA were handled by MspI, followed by end repair and adenylation. Cytosine-methylated barcodes were ligated to sonicated DNA as per manufacturer’s instructions. Then these DNA fragments were treated twice with bisulfite using EZ DNA Methylation-GoldTM Kit (Zymo Research), before the resulting single-strand DNA fragments were PCR amplificated using KAPA HiFi HotStart Uracil and ReadyMix (2X). Library concentration was quantified by Qubit® 2.0 Flurometer and quantitative PCR, and the insert size was assayed on Agilent Bioanalyzer 2100 system.
The library preparations were sequenced on an Illumina Novaseq platform and 125bp/150bp paired-end reads were generated. Image analysis and base calling were performed with Illumina CASAVA pipeline, and finally 125bp/150bp paired-end reads were generated.

treatment_protocol: Induction of ESC-PGCLC and pESC-PGCLC: ESCs and pESCs were maintained in t2iL medium (in 2iL medium, the concentration of PD0325901 was reduced from 1 μM to 0.4 μM) for 3-5 passages. EpiLCs were induced by plating 1.0×105 pESCs/ESCs on the wells of a 12-well plate coated with human plasma fibronectin (FN, 16.7 μg/ml, Millipore) in N2B27 medium containing activin A (20 ng/ml, PeproTech), bFGF (12 ng/ml), and 1% KSR for 46 h. The medium was changed every day. The PGCLCs were induced for 4 days under floating conditions by plating 3.0×103 EpiLCs in the wells of a low-cell-binding U-bottom 96-well Lipidure-Coat plate (Corning) in GK15 medium (GK15 medium contains GMEM (Invitrogen) added with 15% KSR, 100 μM NEAA, 1 mM sodium pyruvate, 1 mM L-glutamine, 1% nonessential amino acid stock, 50 units/ml penicillin and 50 μg/ml streptomycin, 0.1 mM β-mercaptoethanol) in the presence of the cytokines BMP4 (500 ng/ml, PeproTech), 1000 IU/ml mLIF, SCF (100 ng/ml, PeproTech) and EGF (50 ng/ml, PeproTech). Integrin-β3- (CD61) and SSEA1-double positive PGCLCs were sorted by flow cytometer. Dissociated cells were incubated with anti-integrin-β3 (CD61) antibody and anti-SSEA1 antibody conjugated with PE (Phycoerythrin) and Alexa Fluor 647, respectively. After being washed in PBS supplemented with 0.1% BSA, the cells were sorted and analyzed on a flow cytometer (Aria III; BD Biosciences).

value: Parthenogenetic ES cell line derived PGC-like cell


title: RRBS_ESC-PGCLC

value: Female ES cell line derived PGC-like cell


title: BRC1 induced sample 2 RNAseq

value: 10uM estradiol

value: seedlings


title: 03SAM_3 H3K27me3

last: Schmidt

address: Grabengasse 1

institute: Heidelberg University

data_processing:
The raw ChIP-seq reads were trimmed using fastp (doi 10.1093/bioinformatics/bty560) version 0.23.2, followed by alignment to the GENCODE human reference genome hg38 using the STAR aligner version 2.7.8a (doi 10.1093/bioinformatics/bts635). Subsequently, Samtools version 1.14 (doi 10.1093/gigascience/giab008) was used to sort and merge the aligned reads by experimental condition and methylation marker. The merged alignments were used as input for genome coverage analysis, experimental quality controland peak calling.
Peak calling was performed, using MACS2 version 2.2.7.1 (doi 10.1186/gb-2008-9-9-r137) in broad peak mode, for each condition and histone marker. Consensus peaks were then constructed using bedtools version 2.30.0 (doi 10.1002/0471250953.bi1112s47) by intersecting the called peaks for the respective histone marker from the control and SAM conditions (minimum overlap 50%). Featurecounts version 2.0.1 (doi 10.1093/bioinformatics/btt656) was used to count the number of reads aligning to the consensus peaks. Next, we conducted differential peak calling using DESeq2 version 1.34.0 (doi 10.1186/s13059-014-0550-8). For ChIP-seq experimental quality control, genome coverage analysis was performed to enable visual inspection of called peaks by means of bamCoverage module of deeptools version 3.5.1 (doi 10.1093/nar/gkw257). The R-package DESeq2 version1.36.0 was used to create PCA plots based on the read counts of all consensus peaks found for each sample group (control vs SAM), across the investigated methylation markers. The R-package Pheatmap version 1.0.12 was used to generate clustered Heatmaps for each investigated methylation marker, to visualize the read counts of differentially methylated regions, shared between control and SAM samples (consensus peaks).
Supplementary files format and content: "metadata.xlsx" contains metadata sheet, bigWig files contain genome-wide signal data

growth_protocol: PC-3 cells were seeded in cell culture flasks in RPMI 1640 with 10% fetal calf serum and 1,2% penicillin/streptomycin.

extract_protocol: Nuclei of PC-3 cells were disrupted and sonicated to yield fragment size ranging from 200-500bp. Lysates were incubated with H3K4me3 and H3K27me3 antibody (Rabbit polyclonal) and bound DNA after washes was extracted using Qiagen PCR cleanup kit.

treatment_protocol: They were treated either with vehicle ((0.005M H2SO4) or 200 µMol of SAM. Medium was changed every other day.

value: prostate cancer cells

tag: antibody

value: H3K27me3 Cell Signalling


title: Small intestinal organoids_Aged-rep5

value: small intestinal epithelial cells


title: ACD; Timepoint-1; 22-P-1052 [22_P_1052_1_t]

value: Capillary blood

value: Male

tag: timepoint

tag: group


title: ACD; Timepoint-2; 22-P-1052 [22_P_1052_2_t]

tag: tissue

tag: subject id


title: Small intestinal organoids_Aged-rep3

value: Aged


title: Small intestinal organoids_Aged-rep4


title: 03Ctr_3 H3K27me3


title: 03SAM_2 H3K27me3


title: 03SAM_1 H3K27me3


title: RRBS_pESC

value: Parthenogenetic ES cell line


title: RRBS_PGC

value: Primordial germ cell


title: Control; Timepoint-2; 22-P-1021 [22_P_1021_2_t]

value: Female

value: Control


title: Small intestinal organoids_Young-rep3

value: Young


title: Control; Timepoint-1; 22-P-1069 [22_P_1069_1_t]


title: Control; Timepoint-2; 22-P-1079 [22_P_1079_2_t]


title: 03Ctr_2 H3K27me3


title: Control; Timepoint-1; 22-P-1021 [22_P_1021_1_t]


title: Control; Timepoint-1; 22-P-1079 [22_P_1079_1_t]


title: 02SAM_3 H3K4me3

value: H3K4me3 abcam


title: Small intestinal organoids_Aged-rep2


title: Small intestinal organoids_Aged-rep1


title: Control; Timepoint-1; 22-P-1120 [22_P_1120_1_t]


title: 02SAM_2 H3K4me3


title: Small intestinal organoids_Young-rep2


title: 03Ctr_1 H3K27me3


title: Small intestinal epithelium_Aged [AS-520699-LR-53526]

description:
FACS-sorted small intestinal epithelial cells
AS-520699-LR-53526

data_processing:
nf-core/rnaseq  v1.4.2
Nextflow  v20.04.1
FastQC  v0.11.8
Cutadapt v2.5
Trim Galore! v0.6.4
SortMeRNA v2.1b
STAR vSTAR_2.6.1d
HISAT2 v2.1.0
Picard MarkDuplicates v2.21.1
Samtools v1.9
featureCounts v1.6.4
StringTie v2.0
Preseq v2.0.3
deepTools v3.3.1
RSeQC v3.0.1
dupRadar v1.14.0
Qualimap v.2.2.2-dev
MultiQC v1.7
Genome_build: GRCm38
bam files generated using STAR aligner
Supplementary_files_format_and_content: count text files generated using R/DESeq2 v1.28.1

source_name: Small intestinal epithelium

growth_protocol: cells were directly isolated from in vivo small intestine

extract_protocol:
cells were isolated from the small intestine by EDTA & Trypsin-based digestion and then FACS sorted (EpCam+ ; CD45-)
Illumina sequencing libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer's protocol. Briefly, poly(A)+ RNA was purified from 500ng of total RNA using oligo(dT) beads, fragmented to a median insert length of 155 bp and converted to cDNA. The ds cDNA fragments were then end-repaired, adenylated on the 3′ end, adapter ligated and amplified with 15 cycles of PCR.

value: aged

value: untreated


title: RRBS_Female ESC

source_name: RRBS_Female ESC

value: Female ES cell line


title: ACD; Timepoint-2; 22-P-1055 [22_P_1055_2_t]

extract_protocol:
We collected blood samples using a procedure of capillary puncture before (Time Point 1) and after (Time Point 2) exposure to music, including 16 ACD patients, and 14 healthy donors. Sample was collected in a tube containing the proper volume of PAXgene additive. RNA was isolated using the PAXgene blood miRNA extraction kit (Qiagen). On-column DNase I treatment was carried out during the extraction process. RNA concentration step and an additional DNase treatment were undertaken using an RNA clean & concentrator kit (Zymo Research) prior to sequencing
Strand specific library preparation was completed using the SMARTer Ultra low input RNA library (Poly-A). Sequencing was performed using a NovaSeq 6000 System at 100 paired end configuration to finally obtain 70M reads per sample

value: ACD


title: 01Ctr_3 H3K4me3


title: 02SAM_1 H3K4me3


title: ACD; Timepoint-1; 22-P-1055 [22_P_1055_1_t]


title: Small intestinal epithelium_Young [AS-520698-LR-53526]

description:
FACS-sorted small intestinal epithelial cells
AS-520698-LR-53526

value: young


title: Small intestinal organoids_Young-rep4


title: Small intestinal epithelium_Aged [AS-520697-LR-53526]

description:
FACS-sorted small intestinal epithelial cells
AS-520697-LR-53526


title: Control; Timepoint-1; 22-P-1065 [22_P_1065_1_t]


title: In_SAM_3

value: prostate cancer cells


title: Small intestinal epithelium_Young [AS-520696-LR-53526]

description:
FACS-sorted small intestinal epithelial cells
AS-520696-LR-53526


title: In_SAM_2


title: Hgfac WT day2 wound_3

city: Cambridge

first: Ramnik

last: Xavier

state: MA

address: 415 Main Street

institute: Broad Institute of MIT and Harvard

description: 10x Genomics

data_processing:
Single-cell RNA-seq data was processed using Cell Ranger (version 5.0.1) via the cumulus workflow
Assembly: mm10
Supplementary files format and content: Cell Ranger output files

source_name: distal colon

extract_protocol:
Day2 colonic wounds or intact tissue samples from Hgfac WT and Hgfac KO mice were used. Endoscopic wounds were created by the biopsy forceps on day0 and excised by a 2 mm skin biopsy punch tool under the dissecting microscope on day2. Three wounds per mouse were pooled as a sample. Intact tissues excised by a 2 mm skin biopsy punch tool were also collected and used as an unwounded sample. Epithelial and IEL fractions were isolated from wound biopsies or intact colons via mechanical disruption. Briefly, tissues were disrupted via centrifugal force generated by a small magnet in a flask at 1,100 rpm for 45 min at 37°C in 4 ml of RPMI 1640 medium supplemented with 2 mM EDTA. The supernatant was used for epithelial and IEL fractions and the remaining tissues were used for the lamina proprial fraction. For epithelial and IEL fractions, the supernatant was collected and was centrifuged at 16,000 rpm for 8 min. The pellet was suspended with Advanced DMEM/F12 containing 10% FBS medium once and was centrifuged at 16,000 rpm for 8 min. After removing the supernatant, the pellets were suspended with 1 ml of TripLE at 37°C for 10 min. After washing with Advanced DMEM/F12 containing 10% FBS, the pellet was suspended with FACS buffer and kept on ice during lamina proprial isolation. For the lamina proprial (LP) fraction, the tissues were digested in media containing 20% FBS in RPMI 1640 with 0.5 mg/ml of Collagenase VIII (Sigma) for 60 min. The supernatant was collected, filtered, and centrifuged at 16,000 rpm for 8 min. After washing with FACS buffer (2% FBS in PBS) once, cells were used for the analysis. Finally, both epithelial and IEL fraction and LP fraction were combined and used for scRNA-seq.
Library was performed according to the manufacturer's instructions (single cell3' v3 protocol, 10x Genomics)

value: distal colon

value: Epithelial/fibroblast/immune cells

tag: genotype

value: Hgfac WT

value: wound


title: Small intestinal epithelium_Aged [AS-520695-LR-53526]

description:
FACS-sorted small intestinal epithelial cells
AS-520695-LR-53526

value: small intestinal epithelial cells


title: 01Ctr_2 H3K4me3


title: Small intestinal epithelium_Young [AS-520694-LR-53526]

description:
FACS-sorted small intestinal epithelial cells
AS-520694-LR-53526


title: Control; Timepoint-2; 22-P-1062 [22_P_1062_2_t]

description:
raw_counts.txt
Norm_corrected_exp_ACD.txt
Norm_corrected_exp_CONTROLS.txt

value: Capillary blood

value: Male


title: In Ctr_3


title: Control; Timepoint-1; 22-P-1062 [22_P_1062_1_t]


title: Control; Timepoint-2; 22-P-1120 [22_P_1120_2_t]

value: Female


title: Control; Timepoint-2; 22-P-1013 [22_P_1013_2_t]

value: Control


title: Hgfac WT intact tissue_3

description: 10x Genomics

value: no wound


title: Hgfac WT day2 wound_2

description: 10x Genomics


title: THP-1 cells, Ctrl2

city: Illkirch-Graffenstaden

first: Zhirong

last: ZHANG

address: 1 Rue Laurent fries

department: Stem celll and development

institute: IGBMC

data_processing:
Image analysis and base calling were performed using RTA version 2.7.7 and bcl2fastq version 2.20.0.422.
Sequencing reads were trimmed, aligned and counted using PinAPL-Py and guide RNAs (Brunello library). The Matching Threshold for bowtie2 alignment was defined as 35.
Data were statistically analyzed using Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout (MAGeCK v0.5.9.3). The method ranks sgRNAs based on p-values calculated from the negative binomial model, and uses a modified robust ranking aggregation (RRA) algorithm to identify positively or negatively selected genes. Read counts were normalized by total number of reads. Enrichment testing of paired samples was performed using the test function in MAGeCK with --paired option. Volcano plot was generated using ggplot package in R and significance was defined as FDR < 0.05.
Assembly: hg38
Supplementary files format and content: tab-delimited text file for sgRNA raw counts

source_name: THP-1 cells

growth_protocol: THP-1 cells were grown in RPMI 1640 supplement with 10 mM HEPES, 10% fetal calf serum (FCS), 2.5 g/l glucose, 1 mM sodium pyruvate, gentamycin and 50 µM β-mercaptoethanol at 37°C with 5% CO2.

extract_protocol:
Genomic DNA from both control- and treated groups was isolated using the phenol/chloroform extraction method.
Fragments containing sgRNA were amplified from genomic DNA by PCR referring to the protocol from Broad Institute GPP Web Protal (https://portals.broadinstitute.org/gpp/public/resources/protocols).

treatment_protocol: THP-1 cells stably expressing Cas9 protein were infected with the pooled Brunello lentivirus library at ROI of 0.2. After puromycin selection for 3 days, cells were further expanded. To ensure a representation of minimal 500 cells per sgRNA, at least 4.0×107 cells were used in each group. An adequate number of cells were primed with LPS in suspension for 3 hours and treated with vehicle (control group) or R837 plus Yoda1 (treated group). When pyroptotic cell death reached ~85% in the treated group, R837 and Yoda1 were washed out and the survivals were expanded. When cell number reached 4.0 × 107 cells, these cells were repeatedly treated with R837 plus Yoda1 to reach reached ~85% of pyroptotic cell death. R837 and Yoda1 were washed out and the survivals were further expanded to reach 4.0 × 107 cells.

value: THP-1 cells

value: Monocytes

value: wild type

value: DMSO


title: Control; Timepoint-2; 22-P-1065 [22_P_1065_2_t]