title: Donor T-HDR-0

description:
Cells were brought to the exposure chamber, but never exposed.
SP0254-T-HDR-0

value: 0 Gy

value: Donor T

value: male


title: Donor T-HDR-0.05

status: Public on Feb 28 2025

type: SRA

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

description:
Cells were exposed according to the dose and dose rate
SP0254-T-HDR-1

library_source: transcriptomic

data_processing:
Initial quality assessment was performed using negative controls (water only) and reference standards (human universal reference RNA and human brain total RNA) included on every TempO-Seq plate. We confirmed very little signal (< 0.3%) from samples with no cells/RNA. The BCL files were converted to FASTQ files and the reads were demultiplexed using bcl2fastq v. 2.20.0.42. The FASTQ files were processed using the “pete. star. Script_v3.0” (BioSpyder). The script uses star v.2.5 and the qCount function from QuasR to align the reads and to extract the feature counts specified in a Gene Transfer Format (GTF) file from the aligned reads, respectively. Using R 3.4.1, the read counts of all samples were normalized as counts per million (CPM) (Law et al. 2014).
Assembly: hg38
Supplementary files format and content: Comma-delimited table containing read counts per TempO-Seq probe
Library strategy: TempO-Seq

molecule: total RNA

organism: Homo sapiens

source_name: Blood

growth_protocol: Lymphocytes were maintained in RPMI culture medium supplemented with antibiotics and FBS

extract_protocol:
Cells were lysed and RNA were extracted according to BioSpyder's protocol
Total RNA input of 100 ng was used to build whole transcriptome Templated Oligo-Sequencing libraries (BioSpyder, Carlsbad, CA); RNA was diluted to 50 ng/ul in 1 x TempO-Seq lysis buffer and 2 ul of this mixture was used as input. Briefly, detector oligos (DO) targeting whole transcriptome were annealed to mRNA. Each transcript is targeted by a pair of DOs. Bound DOs were ligated to form one contiguous sequence, while unbound DOs were eliminated by nuclease digestion. The ligated DOs were indexed and amplified by PCR, after which 96 individual libraries were pooled to create a single pool for sequencing on the NextSeq 500 (Illumina).
A 96-sample Human Whole Transcriptome Template Oligo-Sequencing (TempO-Seq) kit, which contains 50 nt detector oligos that target mRNA transcripts, was used to generate sequencing libraries.

treatment_protocol: Isolated white blood cells (mainly lymphocytes and NK) were exposed

tag: tissue

value: Blood

tag: cell line

value: Primary Cell

tag: cell type

value: Lymphocyte

tag: treatment

value: HDR

tag: dose rate

value: 1 Gy/min

tag: dose

tag: individual

tag: Sex

tag: age


title: YD087

city: Yangzhou

first: Bo

last: Pan

state: Jiangsu

address: No.136, JiangYangZhongLu

department: Department of Pharmacy

country: China

institute: Yangzhou University Medical College

data_processing:
Raw data (raw reads) of fastq format were firstly processed with ‘Trim Galore!’ (Version 0.6.7) to remove reads containing adapter and low-quality reads.
The clean reads were aligned to the genome using the software ‘HISAT2’ (Version 2.2.1) and ‘SAMtools’ (Version 1.15.1) with the gene annotation file from Ensembl (GRCh38, Release 105).
FeatureCounts (Subread package Version 2.0.1) was employed to count the reads and then to create the expression matrix.
Assembly: GRCh38, Release 105
Supplementary files format and content: A tab-delimited text file includes raw counts for each sample.

source_name: PBMC

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing library.
The RNA-seq library for sequencing was prepared by Novogene following the standard Illumina protocols.

value: PBMC

tag: subject

tag: disease state

value: healthy control


title: YD081


title: AtWT1

city: Columbia

first: Jose Roberto

last: Da Silva Nascimento

state: MO

address: 1201 Rollins Street

department: Life Sciences Center

country: USA

institute: University of MIssouri

data_processing:
raw Illumina sequencing data was passed through the protocol of Cufflinks suite tools in Linux
The raw paired reads were mapped to the reference genome (TAIR10) by using Tophat
Gene expression was compared by Cuffdiff
Log2 fold change of FPKM for all identified genes was calculated
Assembly: TAIR10
Supplementary files format and content: .txt files containing the number of normalyzed read counts mapped for each gene per sample

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: Developing seed

growth_protocol: Arabidopsis thaliana WT and badc1/3 T-DNA insertion mutant crosses were grown in a growth chamber under 16 h day length with 100-150 µmol photons m-2 sec-1 white light measured at the soil surface. Temperatures ranged from 21-23°C during the day and 18-20°C at night.

extract_protocol:
Total RNA was purified using the NucleoSpin® RNA Plant kit (MACHEREY-NAGEL), as recommended by the manufacturer
mRNA Stranded Library Preparation (Poly A)

treatment_protocol: Arabidopsis thaliana WT and badc1/3 T-DNA insertion.

value: Developing seed

tag: genotype

value: WT


title: AtWTtr3


title: Donor S-LDR-6

description:
Cells were exposed according to the dose and dose rate
SP0254-S-LDR-8

value: LDR

value: 0.05 Gy/min

value: Donor S

value: female


title: YD085


title: AtWTtr2


title: Donor S-HDR-4

description:
Cells were exposed according to the dose and dose rate
SP0254-S-HDR-7


title: Donor S-LDR-4

description:
Cells were exposed according to the dose and dose rate
SP0254-S-LDR-7


title: Donor S-HDR-2

description:
Cells were exposed according to the dose and dose rate
SP0254-S-HDR-6


title: Donor S-LDR-1

description:
Cells were exposed according to the dose and dose rate
SP0254-S-LDR-5


title: YD079


title: YD093


title: Donor S-LDR-0.25

description:
Cells were exposed according to the dose and dose rate
SP0254-S-LDR-3


title: YD082


title: YD083


title: Donor S-HDR-0.50

description:
Cells were exposed according to the dose and dose rate
SP0254-S-HDR-4


title: Donor S-LDR-0.10

description:
Cells were exposed according to the dose and dose rate
SP0254-S-LDR-2


title: Donor S-LDR-0.05

description:
Cells were exposed according to the dose and dose rate
SP0254-S-LDR-1


title: AtWT2


title: Donor S-LDR-0

description:
Cells were brought to the exposure chamber, but never exposed.
SP0254-S-LDR-0


title: Donor S-HDR-0.10

description:
Cells were exposed according to the dose and dose rate
SP0254-S-HDR-2


title: Donor S-HDR-6

description:
Cells were exposed according to the dose and dose rate
SP0254-S-HDR-8


title: YD080


title: Donor S-HDR-1

description:
Cells were exposed according to the dose and dose rate
SP0254-S-HDR-5


title: AtBDtr3

value: badc1/badc3 double knock out


title: Donor S-Control-0b

description:
Cells were in incubator the whole time
SP0254-S-CON-0b

value: CON


title: Donor S-HDR-0.05

description:
Cells were exposed according to the dose and dose rate
SP0254-S-HDR-1


title: Donor S-Control-0a

description:
Cells were in incubator the whole time
SP0254-S-CON-0a


title: YD074


title: AtBD3


title: AtBDtr2


title: Donor S-HDR-0

description:
Cells were brought to the exposure chamber, but never exposed.
SP0254-S-HDR-0

value: 0 Gy


title: AtBD2


title: YD076


title: YD075


title: Donor R-LDR-0.10

description:
Cells were exposed according to the dose and dose rate
SP0254-R-LDR-2

value: Donor R

value: male


title: EaR2 LS1 R3

city: Prosser

first: Ricardo

last: Delgado Santander

address: 24106 N Bunn Rd

institute: Washington State University

description: Library name: SA48

data_processing:
Fastp (Chen et al., 2018) was used for adapter/quality trimming. FasQC was used for quality control. HISAT2 (D. Kim et al., 2015) was used to map the clean reads to E. amylovora CFBP 1430 genome (assembly GCF_000091565.1). StringTie (Pertea et al., 2015) was used for transcript assembly. Individual transcript assemblies from multiple samples were merged into a unified set of transcripts with StringTie merge and the merged file was used as reference in a new run of StringTie, providingthe gene count files for differential expression analysis, functional annotation, and data visualization. For differential expression analysis, voom-transformed data was used for linear modeling in limma (Law et al., 2014; Ritchie et al., 2015), with significance at |log2FC| ≥ 1.5 andfalse discovery rate (FDR) ≤ 0.05.
Assembly: not apply
Supplementary files format and content: tab-delimited text file with normalized gene counts for each sample
Supplementary files format and content: tab-delimited text file with filtered gene counts for each sample

organism: Erwinia amylovora

source_name: Liquid culture

growth_protocol: LB or LB+1-3 mM CuSO4, 28ºC, 180 rpm

extract_protocol:
Cells were pelleted (10,000 xg, 2.5 min), rinsed with PBS, and cell pellets treated with RNAprotect Bacteria Reagent (Qiagen, Valencia, CA) diluted in PBS according to manufacturer’s instructions. Treated cell pellets were stored at -80 ºC until use. RNA was extracted according to Rivas et al (2001), and cleaned and concentrated according to Kharadi et al (2022). RNA yield and quality was measured via spectrophotometry and agarose-gel electrophoresis.
RNA libraries were prepared at Cornell’s TREx facility, using NEBNext rRNA Depletion Kit (Bacteria) (New England Biolabs, USA) and NEB Next Ultra II directional Library Prep kit(New England Biolabs, USA) for Illumina (1000 ng total RNA) and sequenced on Illumina NovaSeq Sequencer, producing 2 x150 nucleotide paired-end reads.

treatment_protocol: Copper-shock response was assessed by exposing mid-log cultures in LB to 1 mM CuSO4 for 5 minutes. Copper adaptation responses were studied in cells grown in LB with 1 mM CuSO4 (sampled at mid-exponential and after 20-hour growth, in stationary phase) and with 3 mM CuSO4 (sampled after 20h, in stationary phase). Control samples without copper were collected for each condition. All treatments were performed in three independent assays.

value: Liquid culture

tag: strain

value: Bacteria

value: Mid log-phase, copper shock with 1 mM CuSO4 (LS1)

tag: batch

value: BIOL. REPEAT 3


title: Donor R-LDR-0.50

description:
Cells were exposed according to the dose and dose rate
SP0254-R-LDR-4

value: Blood

value: Primary Cell

value: Lymphocyte


title: AtBDtr1

value: Developing seed


title: Donor S-HDR-0.25

description:
Cells were exposed according to the dose and dose rate
SP0254-S-HDR-3

value: HDR

value: 1 Gy/min


title: AtBD1


title: YD069

value: PBMC

value: healthy control


title: Donor R-LDR-6

description:
Cells were exposed according to the dose and dose rate
SP0254-R-LDR-8

value: LDR

value: 0.05 Gy/min


title: Donor R-LDR-4

description:
Cells were exposed according to the dose and dose rate
SP0254-R-LDR-7


title: Donor R-HDR-6

description:
Cells were exposed according to the dose and dose rate
SP0254-R-HDR-8


title: YD068


title: Donor R-HDR-1

description:
Cells were exposed according to the dose and dose rate
SP0254-R-HDR-5


title: Donor R-HDR-0

description:
Cells were brought to the exposure chamber, but never exposed.
SP0254-R-HDR-0

value: 0 Gy


title: YD066


title: Donor P-LDR-6

description:
Cells were exposed according to the dose and dose rate
SP0254-P-LDR-8

value: Donor P


title: Donor R-LDR-2

description:
Cells were exposed according to the dose and dose rate
SP0254-R-LDR-6

value: Donor R

value: male


title: Donor P-LDR-4

description:
Cells were exposed according to the dose and dose rate
SP0254-P-LDR-7


title: Donor R-LDR-1

description:
Cells were exposed according to the dose and dose rate
SP0254-R-LDR-5


title: YD073


title: YD078


title: YD077


title: EaR2 LA1 R3

description: Library name: SA47

value: Liquid culture

value: Bacteria

value: Mid log-phase, copper adaptation with 1 mM CuSO4 (LA!)


title: Donor R-LDR-0.25

description:
Cells were exposed according to the dose and dose rate
SP0254-R-LDR-3

value: Blood


title: Donor R-LDR-0.05

description:
Cells were exposed according to the dose and dose rate
SP0254-R-LDR-1

value: Primary Cell


title: YD071


title: Donor R-LDR-0

description:
Cells were brought to the exposure chamber, but never exposed.
SP0254-R-LDR-0

value: Lymphocyte


title: EaR2 SA3 R3

description: Library name: SA43

value: Stationary phase, copper adaptation with 3 mM CuSO4 (SA3)

value: BIOL. REPEAT 3


title: YD070


title: Donor R-HDR-4

description:
Cells were exposed according to the dose and dose rate
SP0254-R-HDR-7

value: HDR

value: 1 Gy/min


title: YD072

value: PBMC

value: healthy control


title: EaR2 SA1 R3

description: Library name: SA42

value: Stationary phase, copper adaptation with 1 mM CuSO4 (SA1)


title: Donor R-HDR-2

description:
Cells were exposed according to the dose and dose rate
SP0254-R-HDR-6


title: EaR2 L R3

description: Library name: SA46

value: Mid log-phase (L)


title: EaR2 S R3

description: Library name: SA41

value: Stationary phase (S)


title: EaR2 LS1 R2

description: Library name: SA40

value: Mid log-phase, copper shock with 1 mM CuSO4 (LS1)

value: BIOL. REPEAT 2


title: Donor R-HDR-0.50

description:
Cells were exposed according to the dose and dose rate
SP0254-R-HDR-4

value: Donor R

value: male


title: YD067


title: Donor R-Control-0b

description:
Cells were in incubator the whole time
SP0254-R-CON-0b

value: CON


title: EaR2 LA1 R2

description: Library name: SA39

value: Liquid culture

value: Bacteria

value: Mid log-phase, copper adaptation with 1 mM CuSO4 (LA!)


title: Donor R-HDR-0.25

description:
Cells were exposed according to the dose and dose rate
SP0254-R-HDR-3

value: Blood

value: Primary Cell

value: Lymphocyte


title: EaR2 L R2

description: Library name: SA38


title: Donor R-HDR-0.10

description:
Cells were exposed according to the dose and dose rate
SP0254-R-HDR-2

value: HDR

value: 1 Gy/min


title: Donor R-HDR-0.05

description:
Cells were exposed according to the dose and dose rate
SP0254-R-HDR-1


title: Donor R-Control-0a

description:
Cells were in incubator the whole time
SP0254-R-CON-0a

value: 0.05 Gy/min


title: EaR2 SA3 R2

description: Library name: SA35

value: Stationary phase, copper adaptation with 3 mM CuSO4 (SA3)


title: YD065

value: PBMC

value: healthy control


title: YD064


title: Donor P-LDR-2

description:
Cells were exposed according to the dose and dose rate
SP0254-P-LDR-6

value: LDR

value: Donor P


title: EaR2 SA1 R2

description: Library name: SA34

value: Stationary phase, copper adaptation with 1 mM CuSO4 (SA1)

value: BIOL. REPEAT 2


title: YD063


title: Donor P-LDR-0.50

description:
Cells were exposed according to the dose and dose rate
SP0254-P-LDR-4

value: male


title: EaR2 S R2

description: Library name: SA33

value: Liquid culture

value: Stationary phase (S)


title: Donor P-LDR-0.10

description:
Cells were exposed according to the dose and dose rate
SP0254-P-LDR-2


title: Donor P-LDR-0.25

description:
Cells were exposed according to the dose and dose rate
SP0254-P-LDR-3


title: EaR2 LS1 R1

description: Library name: SA32

value: Bacteria

value: Mid log-phase, copper shock with 1 mM CuSO4 (LS1)

value: BIOL. REPEAT 1


title: Donor P-LDR-1

description:
Cells were exposed according to the dose and dose rate
SP0254-P-LDR-5

value: Blood

value: Primary Cell

value: Lymphocyte


title: Donor P-LDR-0

description:
Cells were brought to the exposure chamber, but never exposed.
SP0254-P-LDR-0

value: 0.05 Gy/min

value: 0 Gy


title: YD062

value: PBMC


title: Donor P-LDR-0.05

description:
Cells were exposed according to the dose and dose rate
SP0254-P-LDR-1


title: EaR2 LA1 R1

description: Library name: SA31

value: Mid log-phase, copper adaptation with 1 mM CuSO4 (LA!)


title: Donor P-HDR-6

description:
Cells were exposed according to the dose and dose rate
SP0254-P-HDR-8

value: HDR

value: 1 Gy/min


title: YD059

value: healthy control


title: YD061


title: EaR2 L R1

description: Library name: SA30

value: Mid log-phase (L)


title: Donor P-HDR-4

description:
Cells were exposed according to the dose and dose rate
SP0254-P-HDR-7

value: Donor P

value: male


title: Donor P-HDR-2

description:
Cells were exposed according to the dose and dose rate
SP0254-P-HDR-6


title: YD057


title: Donor P-HDR-0.25

description:
Cells were exposed according to the dose and dose rate
SP0254-P-HDR-3


title: EaR2 SA1 R1

description: Library name: SA26

value: Liquid culture

value: Stationary phase, copper adaptation with 1 mM CuSO4 (SA1)


title: Donor P-HDR-0.05

description:
Cells were exposed according to the dose and dose rate
SP0254-P-HDR-1


title: Donor P-HDR-0.10

description:
Cells were exposed according to the dose and dose rate
SP0254-P-HDR-2


title: EaR2 SA3 R1

description: Library name: SA27

value: Bacteria

value: Stationary phase, copper adaptation with 3 mM CuSO4 (SA3)


title: YD056


title: Donor P-HDR-0

description:
Cells were brought to the exposure chamber, but never exposed.
SP0254-P-HDR-0

value: Blood


title: YD055


title: Donor P-Control-0b

description:
Cells were in incubator the whole time
SP0254-P-CON-0b

value: Primary Cell

value: CON


title: YD053


title: Donor N-LDR-1

description:
Cells were exposed according to the dose and dose rate
SP0254-N-LDR-5

value: Lymphocyte

value: LDR

value: 0.05 Gy/min

value: Donor N


title: YD052

value: PBMC


title: Donor N-LDR-2

description:
Cells were exposed according to the dose and dose rate
SP0254-N-LDR-6


title: Donor N-LDR-0.25

description:
Cells were exposed according to the dose and dose rate
SP0254-N-LDR-3


title: Donor N-LDR-0.10

description:
Cells were exposed according to the dose and dose rate
SP0254-N-LDR-2


title: YD051


title: Ea273 SA1 R3

description: Library name: SA18

value: BIOL. REPEAT 3


title: YD058

value: healthy control


title: Donor P-HDR-1

description:
Cells were exposed according to the dose and dose rate
SP0254-P-HDR-5

value: HDR

value: 1 Gy/min


title: Donor N-LDR-0

description:
Cells were brought to the exposure chamber, but never exposed.
SP0254-N-LDR-0

value: 0 Gy

value: male


title: Donor N-HDR-2

description:
Cells were exposed according to the dose and dose rate
SP0254-N-HDR-6


title: Donor P-HDR-0.50

description:
Cells were exposed according to the dose and dose rate
SP0254-P-HDR-4

value: Donor P


title: Ea273 LS1 R2

description: Library name: SA16

value: Liquid culture

value: Bacteria

value: Mid log-phase, copper shock with 1 mM CuSO4 (LS1)

value: BIOL. REPEAT 2


title: Ea273 LA1 R2

description: Library name: SA15

value: Mid log-phase, copper adaptation with 1 mM CuSO4 (LA!)


title: EaR2 S R1

description: Library name: SA25

value: Stationary phase (S)

value: BIOL. REPEAT 1


title: Donor N-HDR-0.50

description:
Cells were exposed according to the dose and dose rate
SP0254-N-HDR-4

value: Blood

value: Primary Cell

value: Lymphocyte


title: Ea273 LS1 R3

description: Library name: SA24

value: BIOL. REPEAT 3


title: Donor P-Control-0a

description:
Cells were in incubator the whole time
SP0254-P-CON-0a

value: CON

value: 0.05 Gy/min


title: Donor N-HDR-0.10

description:
Cells were exposed according to the dose and dose rate
SP0254-N-HDR-2

value: HDR

value: 1 Gy/min

value: Donor N


title: YD054

value: PBMC

value: healthy control


title: Donor N-LDR-6

description:
Cells were exposed according to the dose and dose rate
SP0254-N-LDR-8

value: LDR

value: male


title: Donor N-LDR-4

description:
Cells were exposed according to the dose and dose rate
SP0254-N-LDR-7


title: Ea273 LA1 R3

description: Library name: SA23

value: Liquid culture

value: Bacteria


title: Donor N-LDR-0.50

description:
Cells were exposed according to the dose and dose rate
SP0254-N-LDR-4


title: Ea273 SA3 R3

description: Library name: SA19

value: Stationary phase, copper adaptation with 3 mM CuSO4 (SA3)


title: Ea273 L R3

description: Library name: SA22

value: Mid log-phase (L)


title: YD050


title: Donor N-LDR-0.05

description:
Cells were exposed according to the dose and dose rate
SP0254-N-LDR-1

value: Blood


title: Ea273 S R2

description: Library name: SA9

value: Stationary phase (S)

value: BIOL. REPEAT 2


title: Donor M-LDR-6

description:
Cells were exposed according to the dose and dose rate
SP0254-M-LDR-8

value: Primary Cell

value: Lymphocyte

value: Donor M

value: female


title: Ea273 S R3

description: Library name: SA17

value: BIOL. REPEAT 3


title: Donor N-HDR-6

description:
Cells were exposed according to the dose and dose rate
SP0254-N-HDR-8

value: HDR

value: 1 Gy/min

value: Donor N


title: YD040

value: PBMC

value: healthy control


title: Ea273 LS1 R1

description: Library name: SA8

value: Liquid culture

value: Mid log-phase, copper shock with 1 mM CuSO4 (LS1)

value: BIOL. REPEAT 1


title: YD049


title: Donor M-LDR-1

description:
Cells were exposed according to the dose and dose rate
SP0254-M-LDR-5

value: LDR

value: 0.05 Gy/min


title: Donor N-HDR-4

description:
Cells were exposed according to the dose and dose rate
SP0254-N-HDR-7

value: Blood

value: male


title: Donor N-HDR-1

description:
Cells were exposed according to the dose and dose rate
SP0254-N-HDR-5

value: Primary Cell


title: YD039


title: Ea273 LA1 R1

description: Library name: SA7

value: Bacteria

value: Mid log-phase, copper adaptation with 1 mM CuSO4 (LA!)


title: YD038


title: Ea273 L R2

description: Library name: SA14

value: Mid log-phase (L)

value: BIOL. REPEAT 2


title: YD048


title: YD045


title: YD044


title: Donor N-HDR-0.05

description:
Cells were exposed according to the dose and dose rate
SP0254-N-HDR-1

value: Lymphocyte

value: HDR


title: Donor M-LDR-0.10

description:
Cells were exposed according to the dose and dose rate
SP0254-M-LDR-2

value: Donor M

value: female


title: YD037

value: PBMC

value: healthy control


title: Donor M-LDR-0

description:
Cells were brought to the exposure chamber, but never exposed.
SP0254-M-LDR-0

value: 0 Gy


title: Ea273 SA3 R1

description: Library name: SA3

value: Liquid culture

value: Stationary phase, copper adaptation with 3 mM CuSO4 (SA3)

value: BIOL. REPEAT 1


title: Ea273 SA3 R2

description: Library name: SA11


title: Donor M-HDR-6

description:
Cells were exposed according to the dose and dose rate
SP0254-M-HDR-8

value: Blood

value: 1 Gy/min


title: YD043


title: Donor N-HDR-0

description:
Cells were brought to the exposure chamber, but never exposed.
SP0254-N-HDR-0

value: Primary Cell

value: Donor N

value: male


title: Donor N-Control-0b

description:
Cells were in incubator the whole time
SP0254-N-CON-0b

value: CON


title: Donor N-HDR-0.25

description:
Cells were exposed according to the dose and dose rate
SP0254-N-HDR-3


title: Donor N-Control-0a

description:
Cells were in incubator the whole time
SP0254-N-CON-0a

value: 0.05 Gy/min


title: Ea273 SA1 R2

description: Library name: SA10

value: Bacteria

value: Stationary phase, copper adaptation with 1 mM CuSO4 (SA1)

value: BIOL. REPEAT 2


title: YD042


title: Ea273 L R1

description: Library name: SA6

value: Mid log-phase (L)


title: Ea273 SA1 R1

description: Library name: SA2


title: YD035

value: PBMC


title: Donor M-HDR-2

description:
Cells were exposed according to the dose and dose rate
SP0254-M-HDR-6

value: Lymphocyte

value: HDR

value: Donor M

value: female


title: Ea273 S R1

description: Library name: SA1

value: Liquid culture

value: Stationary phase (S)

value: BIOL. REPEAT 1


title: Donor M-LDR-4

description:
Cells were exposed according to the dose and dose rate
SP0254-M-LDR-7

value: Blood

value: Primary Cell

value: LDR


title: Donor M-LDR-2

description:
Cells were exposed according to the dose and dose rate
SP0254-M-LDR-6


title: visi_B03_P12

city: Bethesda

first: Daniel

middle: S

last: Reich

state: Maryland

address: 10 Center Drive Bldg 10 Rm 5C103

department: NINDS

institute: NIH

data_processing:
*library strategy: spatial transcriptomes
Spatial transcriptomic (ST) data analysis pipeline
Alignment, data preprocessing, and image correction. The raw ST reads were aligned to the same reference package as for the snRNA-seq dataset using SpaceRanger (version 1.2.2, 10x Genomics) software to generate spot barcode-to-gene feature matrix for downstream analysis. Individual ST objects were created by Load10X_Spatial() function with Seurat (v3.2.2) package (146) and normalized with SCTransform() function (147). The merge() function was used to aggregate 16 slices into one ST object (Visi) containing images, and the Visi@assays$SCT@counts was pulled to create a separate ST object (VisiDot) by CreateSeuratObject() function to get aggregated spots without images. A processing pipeline similar to that of snRNA-seq was employed for the VisiDot object; specifically, Harmony() was applied over “IL01_uniqueID” variable to integrate 16 samples. To match the terminal MRI images, the orientation of the Visium images was corrected by transforming the image array stored at Visi@images$slice1@image, and the spot information stored at Visi@images$slice1$@coordinates was swapped accordingly (See GitHub post for detail). The microenvironment (ME) cluster annotated in the VisiDot object was transferred back to the Visi object for spatial visualization.
ST Gene module analysis and gene ontology (GO) analysis. As described in (42), Monocle3 (148) was used to group genes in the Visi object (Visi@assays$Spatial@counts[rownames(Visi), ]) into modules by their similarity along the learned neighbor (Knn) or principal (PG) graph. The score of the gene list was then calculated and added to VisiDot object by AddModuleScore() function and visualized in Seurat (FigS8). For each gene module, GO analysis was performed by the gost() function with gprofiler2 (v0.2.1) package using “cjacchus” database, including electronic GO annotations (IEA), and applying g:SCS for multiple testing correction. Terms that passed a significance cutoff (p=0.05) after correction were kept, and the fold enrichment was calculated as follows: (intersection_size/query_size)/(term_size/effective_domain_size).
Lesion rim assignment and subregion analysis with ST image processing pipeline. To annotate Visium spots by their histological and lesional features, several masks were created (FigS4B). Specifically, the myelinated WM area (SB+) was extracted (Colour_3 channel) from the SB/NFR image of Visium slide by “Colour Deconvolution” function in Fiji software (v2.9.0/1.53t, ImageJ2) with the default "H DAB" setting. The Colour_3 channel was then thresholded to create SB+ WM binary mask. After reorientating the SB+ WM mask to match the corrected Seurat object as stated above, the coordinates of the mask were exported and transferred to the 10x Visium hexagon coordinate system (Visi@images$slice1$@coordinates) by dilating each SB+ pixel using 8-neighbor model 5 times (resulting in ~10 µm expansion in diameter). To further distinguish SB--gray matter (GM) from SB--demyelinated WM area, GM and lesion gene module scores were calculated and filtered to create GM and lesion masks accordingly. Specifically, EAE200 object was used to find DEG over the coarse tissue category (IL06_tissue.1 label, “WM,” “other,” and “GM”) with Seurat using the Wilcoxon Rank Sum test. Significantly (adjusted p-value < 0.05) enriched (average log fold change > 0.25) DEGs detected in less than 10% (pct.2 < 0.1) of the other population were kept for enrichment score calculation. Filtered DEG gene lists for “GM” and “other” were combined and added to the Visi object with AddModuleScore() function and termed as “ModuleScore_EAE.otherGM;” similarly, filtered “WM” DEG module scores were added and termed “ModuleScore_EAE.WM” (See TableS8 for gene list). The ModuleScore_EAE.otherGM and ModuleScore_EAE.WM scores >0.01 and >0.1 were filtered to create the GM and Lesion masks, respectively (FigS4B). Next, spots that exhibited both SB- and Lesion+ signals were identified as the lesion core, and 10 concentric rims (SB+WM_rims) extending outward from the lesion core (coordinates [x±1, y±1] and [x, y±2]) were assigned to mark the adjacent lesional neighborhoods. The normal-appearing (NA) WM area was annotated by subtracting the lesional neighborhoods from the SB+ WM mask in animals with EAE, and this region was labeled as “SB+WM_NA.Ctrl.” Additionally, lesional neighborhoods that overlapped with the GM mask were labeled as “SB-notWM_rims,” while the supplemental area was labeled as “SB-notWM_EAE” in animals with EAE. Furthermore, the subregions within the lesion core were further divided based on centripetal rim assignments (SB-WM_-rims) with the same strategy as stated above. For healthy animals, “SB+WM_He.Ctrl” and “SB-notWM_He” labels were used to annotate tissue with or without SB staining, respectively. Regional differentially expressed genes (rDEG) across assigned subregions are calculated with Seurat.
ST resolution enhancement. To facilitate ST data exploration, several strategies were employed to increase the spatial resolution aiding the recognition of patterns and the deconvolution of cell types. First, the BayesSpace (v 1.10.1) package (40) was utilized to infer an enhanced transcription expression map to near single-cell level per subspot. Specifically, readVisium() function was applied to create SingleCellExperiment (Sce) object for each sample from the output of SpaceRanger. The Sce object was preprocessed with the sptialPreprocess() function to log-normalize the counts, followed by PCA analysis on 2000 variable genes and retention of the top 7 PCs. After applying qTune() function, parameters (q=9, d=7, model="t", gamma=2, nrep=1000, burn.in=100, jitter_prior=0.3, jitter_scale=3.5) were used for spatialEnhance(), and the enhanceFeatures() function was used to predict expression for all genes to create enhanced Sce object (Bayes). The inferred expression matrix was then retrieved by the logcounts(Bayes) function to create an enhanced Seurat Spatial object (Bayes2Seurat) for visualization, which was rescaled to 1 for downstream processing. Specifically, “Bayes2Seurat@images” was swapped with a reconstituted object containing the original tissue image (“Seurat@images$slice1@image”) and enhanced indexes were pulled from “colData(Bayes).” The image and indexes of Bayes2Seurat object were further reoriented as described above to match the terminal MRI. To annotate the subspot, scores of rescaled values were averaged and compared for selected genes among lists and assigned to each subspot by similarity (FigS4C).
Assembly: ASM275486v1
Supplementary files format and content: SpaceRanger (version 1.2.2, 10x Genomics) for individual sample
Supplementary files format and content: Rdata for merged data

organism: Callithrix jacchus

source_name: oWM

extract_protocol:
Tissue block and library preparation for spatial transcriptomic (ST) analysis
RNAlater-preserved tissue blocks were thawed at room temperature (RT), retrieved from the cryomold with a pair of RNase AWAY (surface decontaminant, 7000TS1, ThermoFisher) treated forceps, dabbed with clean Kimwipes to remove excess liquid, and incubated in a new cryomold filled with OCT at RT for 10 min to further remove RNAlater residual. At the end of incubation, tissue blocks were transferred to a new cryomold filled with OCT, positioned to desired orientation without creating bubbles, and left frozen at −20°C before trimming. Frozen OCT blocks were trimmed to desired size (~8 mm on each side) to reduce the chances of tissue folding during serial sectioning. To increase the precision of tissue capture, a cryo-resistant plastic grid with matching capture areas was attached to the back of each Visium Spatial Gene Expression Slide (2000233, 10x Genomics) and 12 microslides (Superfrost+ and ColorFrost+, EF15978Z, Daigger Scientific). Gird-attached slides and tissue blocks were left equilibrated inside the cryostat chamber for 30 min prior to a serial tissue scan, which was performed to ensure the capture of the desired ROI with matching morphology to the terminal MRI. Specifically, tissue blocks were sectioned at 10 µm, captured with microslides, and stained every 120 µm with 3% Sudan black (199664-25G, Sigma-Aldrich) in ethylene glycol (BDH1125-1LP, VWR) solution at 56˚C for 30 sec in a water bath to color myelin. After Sudan black (SB) stain, microslide was rinsed with running tap water for 1 min, transferred to hematoxylin (100% Surgipath SelecTech Hematoxylin 560MX, 3801575, Leica) at 56˚C for 30 sec to color gray matter and white matter lesions. After hematoxylin staining, the microslide was rinsed with running tap water again for 1 min, coverslipped (Premium Cover Glasses, EF15972L, Daigger Scientific) with UltraPureTM glycerol (15514-011, Invitrogen), and visualized with a brightfield microscope (Leitz Laborlux S Wild GMBH). When the morphology of the tissue section meets the desired target, the adjacent section is captured and mounted onto the Visium Spatial Gene Expression Slide without covering the fiducial frame to facilitate image alignment in the downstream data analysis. In parallel, pre- and post-Visium captured tissue sections were made and kept at −20°C for long-term storage.
At the end of tissue scans, Visium Spatial Transcriptomics slides containing the tissue sections of interest were transported on dry ice and kept at −80°C for long-term storage or immediately proceeded to staining and library preparation. Slides were thawed on a pre-warmed Thermocycler Adapter (3000380, 10x Genomics) at 37˚C for 1 min to minimize tissue damage caused by condensation. To stain myelin, 1 mL of filtered 1% SB/ethylene glycol was pipetted directly onto the leveled tissue slide and incubated for 5 minutes at RT. After removing excess SB solution, stained slide was dipped in 50 mL of ddH2O (351-029-131CS, Quality Biological) in a Falcon tube 5 times, dipped in 800 mL of ddH2O 15 times, and then another 15 times in a separate glass beaker containing 800 mL of ddH2O. To get an optimal contrast between myelin and gray matter, tissue was dried for 1 min (the time was extended if the tissue section was not dry) before being stained with 1 mL Nuclear Fast Red (NFR, ab246831, Abcam) for 10 min at RT on a level surface and rinsed again as described for SB staining. To avoid bubbles, slides were first saturated with 5 mL of ddH2O on a leveled surface and gradually replaced with 80% glycerol solution containing 5% RNase inhibitor (AM2684, Thermo Fisher Scientific) through steady vacuuming off ddH2O from one end of the slide and adding glycerol with a pipette at the opposite end simultaneously. At the end of solution swapping, the homogenous mounting media was coverslipped and proceeded immediately to 4X tiling imaging with a Nikon Eclipse Ci microscope. After imaging, the coverslip was rinsed off by submerging the slide in 3X SSC buffer (46-020-CM, Corning) diluted in ddH2O, then rinsed briefly in 1X SSC buffer to remove excess mounting media.
After imaging and coverslip removal, the slide was enzymatically permeabilized with Visium Spatial Gene Expression Reagent Kit (PN-1000184, Spatial 3’ v1, 10x Genomics) at 37 ˚C for 20 min, which was determined by Tissue Optimization protocol (PN-1000193, 10x Genomics). The cDNA library was then prepared following the manufacturer’s protocol (Visium Spatial Gene Expression Reagents Kits User Guide, Rev D). The cycle number for cDNA amplification for each library (TableS2) was determined using the Cq value obtained from the qPCR steps detailed in the manufacturer’s protocol. All libraries were sequenced using the Illumina Novaseq S2 platform. Library quantity and quality were assessed using Qubit™ dsDNA HS Assay Kit (Q32854, Invitrogen™) with a Qubit™ 4 Fluorometer (Q33226, Thermo Fisher Scientific) and High Sensitivity DNA Kit (5067-4626, Agilent Technologies) with a 2100 Bioanalyzer instrument (G2939BA, Agilent Technologies), respectively.

value: oWM

value: tissue

tag: il01 uniqueid

tag: il02 species

value: cjacchus

tag: il03 source

tag: il04 sex

value: F

tag: il05 agedays

tag: il06 tissue

tag: il07 location

tag: il08 condition

tag: il09 illumina

tag: il10 chemistry

tag: il10 chemistry.slidecode

tag: il10 chemistry.sn

tag: il11 batch

tag: il14 dataset

tag: cycle number


title: Donor M-LDR-0.25

description:
Cells were exposed according to the dose and dose rate
SP0254-M-LDR-3

tag: tissue

tag: cell line

tag: cell type

tag: treatment

tag: dose rate

value: 0.05 Gy/min

tag: dose

tag: individual

tag: Sex

tag: age


title: Donor M-LDR-0.50

description:
Cells were exposed according to the dose and dose rate
SP0254-M-LDR-4


title: Donor M-LDR-0.05

description:
Cells were exposed according to the dose and dose rate
SP0254-M-LDR-1


title: Donor M-HDR-4

description:
Cells were exposed according to the dose and dose rate
SP0254-M-HDR-7

value: 1 Gy/min


title: Donor M-HDR-0.50

description:
Cells were exposed according to the dose and dose rate
SP0254-M-HDR-4


title: Donor M-HDR-0.25

description:
Cells were exposed according to the dose and dose rate
SP0254-M-HDR-3


title: YD031

value: PBMC

tag: subject

tag: disease state

value: healthy control


title: YD034


title: Donor M-HDR-1

description:
Cells were exposed according to the dose and dose rate
SP0254-M-HDR-5

value: Lymphocyte

value: HDR


title: Donor M-Control-0b

description:
Cells were in incubator the whole time
SP0254-M-CON-0b

value: CON

value: Donor M

value: female


title: Donor M-Control-0a

description:
Cells were in incubator the whole time
SP0254-M-CON-0a


title: Donor M-HDR-0

description:
Cells were brought to the exposure chamber, but never exposed.
SP0254-M-HDR-0

value: 0 Gy


title: YD032


title: visi_B03_P10

source_name: tWM

value: tWM

tag: il01 uniqueid

tag: il02 species

tag: il03 source

tag: il04 sex

tag: il05 agedays

tag: il06 tissue

tag: il07 location

tag: il08 condition

tag: il09 illumina

tag: il10 chemistry


title: Donor J-LDR-4

description:
Cells were exposed according to the dose and dose rate
SP0254-J-LDR-7

tag: tissue

value: Blood

tag: cell line

value: Primary Cell

tag: cell type

tag: treatment

tag: dose rate

value: Donor J


title: visi_B03_P09

source_name: pWM/pCC

value: pWM/pCC

value: tissue

tag: il10 chemistry.slidecode

tag: il10 chemistry.sn

tag: il11 batch

tag: il14 dataset

tag: cycle number


title: Donor J-LDR-1

description:
Cells were exposed according to the dose and dose rate
SP0254-J-LDR-5

value: LDR

tag: dose

tag: individual

tag: Sex

tag: age


title: Donor J-LDR-0.25

description:
Cells were exposed according to the dose and dose rate
SP0254-J-LDR-3

value: 0.05 Gy/min


title: YD027

tag: subject

tag: disease state


title: YD030


title: visi_B03_P06

tag: il01 uniqueid

tag: il02 species

value: cjacchus

tag: il03 source

tag: il04 sex

value: F

tag: il05 agedays

tag: il06 tissue

tag: il07 location

tag: il08 condition

tag: il09 illumina

tag: il10 chemistry


title: Donor M-HDR-0.10

description:
Cells were exposed according to the dose and dose rate
SP0254-M-HDR-2

tag: tissue

tag: cell line

tag: cell type

tag: treatment

tag: dose rate

value: 1 Gy/min


title: Donor J-LDR-0.10

description:
Cells were exposed according to the dose and dose rate
SP0254-J-LDR-2

value: Lymphocyte

tag: dose

tag: individual

tag: Sex

tag: age


title: visi_B03_P08

value: oWM

tag: il01 uniqueid

tag: il02 species

tag: il03 source

tag: il10 chemistry.slidecode

tag: il10 chemistry.sn

tag: il11 batch

tag: il14 dataset

tag: cycle number


title: YD029

tag: tissue

value: PBMC

tag: subject

tag: disease state

value: healthy control


title: Donor J-LDR-6

description:
Cells were exposed according to the dose and dose rate
SP0254-J-LDR-8

tag: cell line

tag: cell type

tag: treatment

value: female


title: Donor J-LDR-2

description:
Cells were exposed according to the dose and dose rate
SP0254-J-LDR-6

tag: dose rate

tag: dose

tag: individual


title: visi_B03_P07

tag: il01 uniqueid

tag: il04 sex

value: M

tag: il05 agedays

tag: il06 tissue

tag: il07 location

tag: il08 condition

tag: il09 illumina

tag: il10 chemistry


title: YD026

tag: tissue


title: Donor M-HDR-0.05

description:
Cells were exposed according to the dose and dose rate
SP0254-M-HDR-1

value: HDR

value: Donor M

tag: Sex

tag: age


title: Donor J-HDR-4

description:
Cells were exposed according to the dose and dose rate
SP0254-J-HDR-7

value: Blood

tag: cell line

value: Primary Cell


title: visi_B03_P05

value: pWM/pCC

tag: cell type

tag: il02 species

tag: il03 source

tag: il10 chemistry.slidecode

tag: il10 chemistry.sn

tag: il11 batch

tag: il14 dataset

tag: cycle number


title: visi_B02_P16

value: tissue

tag: il01 uniqueid

tag: il04 sex

tag: il05 agedays

tag: il06 tissue


title: Donor J-HDR-1

description:
Cells were exposed according to the dose and dose rate
SP0254-J-HDR-5

tag: treatment

tag: dose rate

tag: dose

tag: individual

value: Donor J


title: Donor J-LDR-0.05

description:
Cells were exposed according to the dose and dose rate
SP0254-J-LDR-1

tag: tissue

tag: cell line

value: LDR

value: 0.05 Gy/min

tag: Sex

tag: age


title: Donor J-HDR-0.50

description:
Cells were exposed according to the dose and dose rate
SP0254-J-HDR-4

tag: cell type


title: Donor J-LDR-0.50

description:
Cells were exposed according to the dose and dose rate
SP0254-J-LDR-4


title: YD028

tag: subject

tag: disease state


title: visi_B02_P14

tag: il02 species

value: cjacchus

tag: il03 source

tag: il07 location

tag: il08 condition

tag: il09 illumina

tag: il10 chemistry

tag: il10 chemistry.slidecode

tag: il10 chemistry.sn

tag: il11 batch

tag: il14 dataset


title: Donor J-LDR-0

description:
Cells were brought to the exposure chamber, but never exposed.
SP0254-J-LDR-0

tag: tissue

tag: treatment

tag: dose rate

tag: dose

value: 0 Gy

tag: individual


title: YD020

tag: subject


title: Donor J-HDR-6

description:
Cells were exposed according to the dose and dose rate
SP0254-J-HDR-8

tag: cell line

tag: cell type

value: Lymphocyte

value: 1 Gy/min

tag: Sex

tag: age


title: Donor J-HDR-2

description:
Cells were exposed according to the dose and dose rate
SP0254-J-HDR-6


title: Donor H-LDR-4

description:
Cells were exposed according to the dose and dose rate
SP0254-H-LDR-7

value: Donor H


title: YD025

value: PBMC

tag: disease state

value: healthy control


title: visi_B01_P03

source_name: OpT

value: OpT

tag: il01 uniqueid

tag: il02 species

tag: il03 source

tag: il04 sex

value: F

tag: il05 agedays

tag: il06 tissue

tag: il07 location

tag: il08 condition

tag: il09 illumina

tag: cycle number


title: YD018

tag: tissue


title: Donor H-LDR-2

description:
Cells were exposed according to the dose and dose rate
SP0254-H-LDR-6

tag: treatment

tag: dose rate

tag: dose

tag: individual

value: female


title: YD024

tag: subject


title: visi_B02_P15

value: tWM

tag: cell line

tag: cell type

tag: il10 chemistry

tag: il10 chemistry.slidecode

tag: il10 chemistry.sn

tag: il11 batch

tag: il14 dataset


title: YD023

tag: disease state


title: YD022


title: Donor J-HDR-0.10

description:
Cells were exposed according to the dose and dose rate
SP0254-J-HDR-2

value: Blood

value: Primary Cell

value: HDR

tag: Sex

tag: age


title: Donor J-HDR-0.25

description:
Cells were exposed according to the dose and dose rate
SP0254-J-HDR-3

value: Donor J


title: Donor J-HDR-0.05

description:
Cells were exposed according to the dose and dose rate
SP0254-J-HDR-1


title: visi_B02_P13

value: pWM/pCC

value: tissue

tag: il01 uniqueid

tag: il02 species

tag: il03 source

tag: il04 sex

tag: il05 agedays

tag: il06 tissue

tag: il07 location

tag: il08 condition

tag: il09 illumina

tag: cycle number


title: Donor J-HDR-0

description:
Cells were brought to the exposure chamber, but never exposed.
SP0254-J-HDR-0

tag: tissue

tag: cell line

tag: cell type

tag: treatment

tag: dose rate

tag: dose

tag: individual


title: Donor J-Control-0b

description:
Cells were in incubator the whole time
SP0254-J-CON-0b

value: CON

tag: Sex

tag: age


title: YD016

tag: subject

tag: disease state


title: visi_B01_P04

tag: il01 uniqueid

tag: il02 species

value: cjacchus

tag: il03 source

tag: il04 sex

value: M

tag: il05 agedays

tag: il10 chemistry

tag: il10 chemistry.slidecode

tag: il10 chemistry.sn

tag: il11 batch

tag: il14 dataset


title: Donor H-LDR-0.25

description:
Cells were exposed according to the dose and dose rate
SP0254-H-LDR-3

tag: tissue

tag: cell line

tag: cell type

value: Lymphocyte

tag: treatment

value: LDR

tag: dose rate

value: 0.05 Gy/min


title: Donor J-Control-0a

description:
Cells were in incubator the whole time
SP0254-J-CON-0a

tag: dose

tag: individual

tag: Sex

tag: age


title: YD019

value: PBMC

tag: subject

tag: disease state

value: healthy control


title: Donor H-LDR-6

description:
Cells were exposed according to the dose and dose rate
SP0254-H-LDR-8

value: Donor H


title: visi_B01_P01

source_name: fWM/aCC

value: fWM/aCC

tag: il01 uniqueid

tag: il02 species

tag: il03 source

tag: il04 sex

value: F

tag: il05 agedays

tag: il06 tissue

tag: il07 location

tag: il08 condition

tag: il09 illumina

tag: cycle number


title: Donor H-LDR-1

description:
Cells were exposed according to the dose and dose rate
SP0254-H-LDR-5

tag: tissue

value: Blood

tag: cell line

tag: cell type

tag: treatment

tag: dose rate

value: female


title: visi_B01_P02

tag: il10 chemistry

tag: il10 chemistry.slidecode

tag: il10 chemistry.sn

tag: il11 batch

tag: il14 dataset


title: Donor H-HDR-6

description:
Cells were exposed according to the dose and dose rate
SP0254-H-HDR-8

value: Primary Cell

value: HDR

value: 1 Gy/min

tag: dose

tag: individual

tag: Sex

tag: age


title: RRBS conditional knockout kidney-2

city: BOSTON

first: Satya keerthi

last: Kota

state: MA

address: 188 LONGWOOD AVE HSDM REB 406

institute: HARVARD UNIV

description: Library name: KKO-2 RRBS

library_source: genomic

data_processing:
Sequencing adapters and low-quality data of the sequencing data are removed by Trimmomatic (v0.36). The BSMAP software is used to map the bisulfite sequence to the reference genome with parameters ‘-n 0 -g 0 -v 0.08 -m 50 -x 1000.
The software metilene (v0.2-7) was used to identify DMR (differentially methylated regions) by a binary segmentation algorithm combined with a two-dimensional statistical test (parameters: -M 300 -m 5 -d 0.1 -t 1 -f 1 -v 0.7).
Assembly: MM10
Supplementary files format and content: bedgraph

molecule: genomic DNA

organism: Mus musculus

source_name: Kidney

extract_protocol:
Genomic DNA from control and Kdm1a conditional knockout frozen kidney tissues was isolated and quantified using the Qubit (Life Technologies).
RRBS library preparation was performed using the Premium RRBS kit (Diagenode)

value: Kidney


title: Donor H-LDR-0

description:
Cells were brought to the exposure chamber, but never exposed.
SP0254-H-LDR-0

value: 0 Gy


title: YD015

tag: subject

tag: disease state


title: Donor H-HDR-4

description:
Cells were exposed according to the dose and dose rate
SP0254-H-HDR-7


title: Donor H-LDR-0.50

description:
Cells were exposed according to the dose and dose rate
SP0254-H-LDR-4


title: RRBS control kidney-1

description: Library name: KWT-1 RRBS


title: Donor H-HDR-0.25

description:
Cells were exposed according to the dose and dose rate
SP0254-H-HDR-3


title: Donor H-LDR-0.05

description:
Cells were exposed according to the dose and dose rate
SP0254-H-LDR-1


title: RRBS conditional knockout kidney-1

description: Library name: KKO-1 RRBS


title: YD036


title: YD017


title: control group C_3.

city: chongqing

first: Wanli

last: Yu

address: 118 Xingguang Avenue, Liangjiang New District, Chongqing

institute: chongqing medical university

description: Library name: sample9

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Brain

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Brain


title: Donor H-HDR-0

description:
Cells were brought to the exposure chamber, but never exposed.
SP0254-H-HDR-0


title: YD014


title: YD010


title: RRBS control kidney-2

description: Library name: KWT-2 RRBS


title: control group C_1.

description: Library name: sample7


title: Donor H-Control-0b

description:
Cells were in incubator the whole time
SP0254-H-CON-0b

value: CON


title: YD009


title: Donor G-LDR-6

description:
Cells were exposed according to the dose and dose rate
SP0254-G-LDR-8

value: Lymphocyte

value: Donor G


title: Donor H-LDR-0.10

description:
Cells were exposed according to the dose and dose rate
SP0254-H-LDR-2

value: LDR

value: 0.05 Gy/min


title: Donor H-HDR-2

description:
Cells were exposed according to the dose and dose rate
SP0254-H-HDR-6


title: Donor H-HDR-1

description:
Cells were exposed according to the dose and dose rate
SP0254-H-HDR-5


title: YD013

value: PBMC

value: healthy control


title: Donor H-HDR-0.50

description:
Cells were exposed according to the dose and dose rate
SP0254-H-HDR-4

value: Donor H


title: YD011


title: Donor H-HDR-0.05

description:
Cells were exposed according to the dose and dose rate
SP0254-H-HDR-1


title: intervention group P_3

description: Library name: sample6


title: Donor G-LDR-2

description:
Cells were exposed according to the dose and dose rate
SP0254-G-LDR-6


title: Donor H-HDR-0.10

description:
Cells were exposed according to the dose and dose rate
SP0254-H-HDR-2


title: YD012


title: YD007


title: Donor G-LDR-1

description:
Cells were exposed according to the dose and dose rate
SP0254-G-LDR-5


title: Donor G-LDR-4

description:
Cells were exposed according to the dose and dose rate
SP0254-G-LDR-7


title: Donor H-Control-0a

description:
Cells were in incubator the whole time
SP0254-H-CON-0a


title: control group C_2.

description: Library name: sample8


title: Donor G-LDR-0.50

description:
Cells were exposed according to the dose and dose rate
SP0254-G-LDR-4


title: intervention group P_1

description: Library name: sample4


title: YD008


title: intervention group P_2

description: Library name: sample5


title: Donor G-LDR-0.10

description:
Cells were exposed according to the dose and dose rate
SP0254-G-LDR-2


title: Donor G-LDR-0.25

description:
Cells were exposed according to the dose and dose rate
SP0254-G-LDR-3


title: Donor G-LDR-0.05

description:
Cells were exposed according to the dose and dose rate
SP0254-G-LDR-1


title: experimental group M_3

description: Library name: sample3


title: YD005


title: YD006


title: Donor G-HDR-6

description:
Cells were exposed according to the dose and dose rate
SP0254-G-HDR-8


title: Donor G-LDR-0

description:
Cells were brought to the exposure chamber, but never exposed.
SP0254-G-LDR-0


title: experimental group M_2

description: Library name: sample2


title: YD004


title: Donor G-HDR-4

description:
Cells were exposed according to the dose and dose rate
SP0254-G-HDR-7


title: experimental group M_1

description: Library name: sample1


title: Donor G-HDR-2

description:
Cells were exposed according to the dose and dose rate
SP0254-G-HDR-6


title: YD003


title: Donor G-HDR-1

description:
Cells were exposed according to the dose and dose rate
SP0254-G-HDR-5


title: conditional knockout kidney

description: Library name: KKO input

data_processing:
ChIP sequencing reads were processed with Trimmomatic (v0.36)40 to filter out low-quality reads and trim adaptor sequences. Reads were aligned to the reference genome using STAR software (v2.5.3a)41 with default parameters. Distribution of reads was analyzed using RSeQC (v2.6)
H3K9 trimethylation peak calling was performed with MACS2 (v2.1.1)
Assembly: MM10
Supplementary files format and content: bigWig

extract_protocol:
Frozen kidney tissue cells were fixed with 1% formaldehyde for 10 min and quenched with 125 mM of glycine for 5 minutes at room temperature, after washes sheared chromatin was obtained by sonication
Library preparation was performed using KAPA Hyper Prep kit (Roche, Basel, Switzerland) per manufacturer’s recommendations.

tag: chip antibody


title: Donor G-HDR-0.50

description:
Cells were exposed according to the dose and dose rate
SP0254-G-HDR-4

tag: tissue


title: YD002


title: Donor G-HDR-0.10

description:
Cells were exposed according to the dose and dose rate
SP0254-G-HDR-2

tag: cell line


title: Donor G-HDR-0

description:
Cells were brought to the exposure chamber, but never exposed.
SP0254-G-HDR-0

tag: cell type


title: Donor G-HDR-0.05

description:
Cells were exposed according to the dose and dose rate
SP0254-G-HDR-1

tag: treatment


title: Donor G-HDR-0.25

description:
Cells were exposed according to the dose and dose rate
SP0254-G-HDR-3

tag: dose rate


title: conditional knockout kidney-2

description: Library name: KKO-2 H3K9me3IP


title: Donor G-Control-0b

description:
Cells were in incubator the whole time
SP0254-G-CON-0b


title: Control kidney

description: Library name: KWT input


title: YD001


title: Donor G-Control-0a

description:
Cells were in incubator the whole time
SP0254-G-CON-0a


title: The normal aganglionic of HSCR (2N)

city: xuzhou

first: jianjun

last: zhang

state: jiangsu

address: 18 Su Di North Road, Quanshan District

department: Department of Neonatal Surgery

institute: Xuzhou Children’s Hospital

description: The normal aganglionic of HSCR

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).
We aligned reads of all samples to the Homo sapiens reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Tissue of colon

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp.

value: male

value: normal aganglionic of Hirschsprung's disease (HSCR)


title: conditional knockout kidney-1

description: Library name: KKO-1 H3K9me3 IP


title: Donor F-LDR-6

description:
Cells were exposed according to the dose and dose rate
SP0254-F-LDR-8

value: Blood

value: Donor F


title: Control kidney-2

description: Library name: KWT-2 H3K9me3 IP


title: The normal aganglionic of HSCR (1N)

description: The normal aganglionic of HSCR

value: female


title: Donor F-LDR-4

description:
Cells were exposed according to the dose and dose rate
SP0254-F-LDR-7

value: Primary Cell


title: Donor F-LDR-2

description:
Cells were exposed according to the dose and dose rate
SP0254-F-LDR-6


title: Donor F-LDR-0.50

description:
Cells were exposed according to the dose and dose rate
SP0254-F-LDR-4


title: The normal aganglionic of HSCR (3N)

description: The normal aganglionic of HSCR


title: Control kidney-1

description: Library name: KWT-1 H3K9me3 IP

value: Kidney


title: The aganglionic of HSCR (3A)

description: The aganglionic of HSCR

value: aganglionic of Hirschsprung's disease (HSCR)


title: Donor F-LDR-0.25

description:
Cells were exposed according to the dose and dose rate
SP0254-F-LDR-3


title: MASH-fibrosis NPCs

city: MIlano

first: Paola

last: Dongiovanni

address: Via Pace 9

country: Italy

institute: Fondazione IRCCS Cà Granda ospedale Policlinico

description:
Library name: L8
10x Genomics

library_source: transcriptomic single cell

data_processing:
Base calling, demultiplexing and adapter masking with Illumina BCL Convert v3.9.3. Alignment, filtering, barcode counting, and UMI counting was performed using 10x Genomics Cell Ranger v4.0.6 and "refdata-gex-mm10-2020-A" transcriptome reference.
Assembly: mm10 (GENCODE vM23/Ensembl98)
Supplementary files format and content: tab-separated files and matrix files

source_name: Liver

extract_protocol:
In n=2 mice/group for each time point primary mouse hepatocytes and non-parenchymal cells (NPCs) were isolated by a multi-step ethylene glycol tetra-acetic acid (EGTA)/collagenase perfusion technique, through microcannulation of portal vein to ensure efficient perfusion of tissues. Cells were centrifuged at 50g x 3 minutes for three times to separate hepatocytes (on bottom) and NPCs (on top). Next, cell suspensions were FACS sorted by using FACSanto to remove dead cells and cellular debris, exploiting 7-Aminoactinomycin D (7-AAD) staining, thus allowing viable cell enrichment. CD45+positive cells were depleted by hepatocyte fractions. Hepatocytes and NPCs live cells were separately loaded on a Chromium Single Cell Instrument (10x Genomics) to generate single-cell gel beads in emulsion. RNA-seq libraries were prepared with the Chromium Single Cell Library protocol (10x Genomics) according to manufacturer’s instructions, and sequencing was performed on the Novaseq machine using paired-end sequencing runs (3200 million paired-end 150bp) for gene expression analysis.
Final libraries were checked with both Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and Agilent Bioanalyzer DNA assay or Caliper (PerkinElmer, Waltham, MA). Libraries were then prepared for sequencing and sequenced on paired-end 150 bp mode on NovaSeq 6000 (Illumina, San Diego, CA).

value: Liver

value: NPCs

value: Hepatic cells

tag: genotype

value: wild-type

value: AMLN diet


title: Donor F-LDR-0.10

description:
Cells were exposed according to the dose and dose rate
SP0254-F-LDR-2

value: Lymphocyte

value: LDR

value: 0.05 Gy/min


title: The aganglionic of HSCR (2A)

description: The aganglionic of HSCR


title: Donor F-LDR-0.05

description:
Cells were exposed according to the dose and dose rate
SP0254-F-LDR-1


title: MASH-fibrosis Heps

description:
Library name: L7
10x Genomics

value: Hepatocytes


title: Donor F-LDR-0

description:
Cells were brought to the exposure chamber, but never exposed.
SP0254-F-LDR-0

value: 0 Gy

value: male


title: Donor F-LDR-1

description:
Cells were exposed according to the dose and dose rate
SP0254-F-LDR-5

value: Blood


title: Donor F-HDR-4

description:
Cells were exposed according to the dose and dose rate
SP0254-F-HDR-7

value: HDR

value: 1 Gy/min

value: Donor F


title: Donor F-HDR-6

description:
Cells were exposed according to the dose and dose rate
SP0254-F-HDR-8

value: Primary Cell


title: MASH NPCs

description:
Library name: L6
10x Genomics


title: dnFGFR, Opposite, Sample 5

city: Boulder

first: Pei-San

last: Tsai

state: CO

address: 354 UCB

department: Integrative Physiology

institute: University of Colorado Boulder

description:
Library name: PN320DO5
Colum name in Rsub_less_id.coverage.csv: PN320DO5.bam

data_processing:
DESeq2 (v1.36.0) for R.
Results of sequencing were received in the form of .bam files representing raw reads preprocessed and aligned (HISAT2) to the mouse genome (NCBI GRCm38) by Novogene using their in-house bioinformatics pipeline.
Counts were generated from aligned reads using Rsubread (v2.0.1) for R, and annotated with the NCBI refSeq annotation.
Sample outlier detection and removal were performed using robust principal component analysis (PCA) on all raw gene counts using RRcov (v1.7-3) for R.
. DESeq2 (v1.36.0) for R was used as a means to generate normalized counts, perform differential expression analysis, and prepare a ranked order gene list for gene set enrichment analysis (GSEA).
Assembly: NCBI GRCm38
Supplementary files format and content: csv file includes raw counts for each sample.
Supplementary files format and content: bam files include aligned reads for each sample generated by Novogene using an in-house bionformatics pipeline.

source_name: Brain (mPOA)

extract_protocol:
Total RNA was isolated from the POA samples using the RNeasy Mini kit (Qiagen) according to the manufacturer’s instructions.
Sequencing libraries were generated using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA), following the manufacturer’s protocol (Novogene, USA).

treatment_protocol: Male control or dnFGFR mice were paired at PND20 with a same or opposite sex partner, and allowed to age until tissue collection at PND320.

value: Brain (mPOA)

value: whole-brain

value: dnFGFR

value: opposite sex-housed


title: dnFGFR, Opposite, Sample 4

description:
Library name: PN320DO4
Colum name in Rsub_less_id.coverage.csv: PN320DO4.bam


title: The aganglionic of HSCR (1A)

description: The aganglionic of HSCR

value: aganglionic of Hirschsprung's disease (HSCR)


title: Donor F-HDR-1

description:
Cells were exposed according to the dose and dose rate
SP0254-F-HDR-5


title: Donor F-HDR-2

description:
Cells were exposed according to the dose and dose rate
SP0254-F-HDR-6


title: Steatosis NPCs

description:
Library name: L4
10x Genomics

value: Liver

value: NPCs

value: Hepatic cells

value: wild-type

value: AMLN diet


title: Donor F-HDR-0.50

description:
Cells were exposed according to the dose and dose rate
SP0254-F-HDR-4

value: Lymphocyte


title: visi_B03_P11

value: tWM

value: tissue

tag: il01 uniqueid

tag: il02 species

value: cjacchus

tag: il03 source

tag: il04 sex

value: M

tag: il05 agedays

tag: il06 tissue

tag: il07 location

tag: il08 condition

tag: il09 illumina

tag: il10 chemistry

tag: il10 chemistry.slidecode

tag: cycle number


title: Steatosis Heps

description:
Library name: L3
10x Genomics

tag: tissue

tag: cell line

value: Hepatocytes


title: Donor F-HDR-0.25

description:
Cells were exposed according to the dose and dose rate
SP0254-F-HDR-3

value: Blood

value: Primary Cell

tag: cell type

tag: treatment

value: HDR

value: 1 Gy/min

tag: dose

tag: individual

value: Donor F

tag: Sex

value: male

tag: age


title: Donor F-HDR-0.10

description:
Cells were exposed according to the dose and dose rate
SP0254-F-HDR-2

tag: dose rate


title: dnFGFR, Opposite, Sample 3

description:
Library name: PN320DO3
Colum name in Rsub_less_id.coverage.csv: PN320DO3.bam

value: Brain (mPOA)

value: whole-brain

tag: genotype

value: dnFGFR

value: opposite sex-housed


title: dnFGFR, Opposite, Sample 2

description:
Library name: PN320DO2
Colum name in Rsub_less_id.coverage.csv: PN320DO2.bam


title: Donor F-HDR-0.05

description:
Cells were exposed according to the dose and dose rate
SP0254-F-HDR-1


title: Donor F-Control-0b

description:
Cells were in incubator the whole time
SP0254-F-CON-0b

value: CON


title: dnFGFR, Opposite, Sample 1

description:
Library name: PN320DO1
Colum name in Rsub_less_id.coverage.csv: PN320DO1.bam


title: Control NPCs

description:
Library name: L2
10x Genomics

value: Liver

value: NPCs

value: Hepatic cells

value: wild-type

value: SD


title: Donor F-HDR-0

description:
Cells were brought to the exposure chamber, but never exposed.
SP0254-F-HDR-0

value: Lymphocyte

value: 0 Gy


title: Donor F-Control-0a

description:
Cells were in incubator the whole time
SP0254-F-CON-0a

value: Blood

value: Primary Cell

value: 0.05 Gy/min


title: MASH Heps

description:
Library name: L5
10x Genomics

value: Hepatocytes

value: AMLN diet


title: dnFGFR, Same, Sample 5

description:
Library name: PN320DS5
Colum name in Rsub_less_id.coverage.csv: PN320DS5.bam

value: Brain (mPOA)

value: same sex-housed


title: Donor E-LDR-6

description:
Cells were exposed according to the dose and dose rate
SP0254-E-LDR-8

value: LDR

value: Donor E

value: female


title: Donor E-LDR-4

description:
Cells were exposed according to the dose and dose rate
SP0254-E-LDR-7


title: Donor E-LDR-2

description:
Cells were exposed according to the dose and dose rate
SP0254-E-LDR-6


title: Donor E-LDR-1

description:
Cells were exposed according to the dose and dose rate
SP0254-E-LDR-5


title: Control Heps

description:
Library name: L1
10x Genomics

value: Liver


title: dnFGFR, Same, Sample 3

description:
Library name: PN320DS3
Colum name in Rsub_less_id.coverage.csv: PN320DS3.bam

value: whole-brain

value: dnFGFR


title: Heart, IR,ML264, 2hrs, rep3

city: Cincinnati

first: Georgios

last: Siokatas

state: OH

address: 231 ALBERT SABIN WAY

department: Pharmacology and Systems Physiology

institute: University of Cincinnati

data_processing:
A quality control check on the fastq files was performed using FastQC. Upon passing basic quality metrics, the reads were trimmed to remove adapters and low-quality reads using default parameters in Trimmomatic1 [Version 0.33]. The trimmed reads were then mapped to a reference genome using default parameters with strandness (R for single-end and RF for paired-end) option in Hisat22 [Version 2.0.5]. In the next step, transcript/gene abundance was determined using kallisto3 [Version 0.43.1]. We first created a transcriptome index in kallisto using Ensembl cDNA sequences for the reference genome. This index was then used to quantify transcript abundance in raw counts and transcript per million (TPM).
Assembly: GRCm38/mm10
Supplementary files format and content: Csv file containing: transcript IDs, Gene IDs and Counts of each sample.

source_name: Heart

extract_protocol:
Total RNA extraction from frozen heart tissue was performed using TRIzol reagent according to the manufacturer's instructions
Libraries were created for all samples using 1 ng of cDNA. Specifically, the Illumina protocol, the Nextera XT DNA Sample Preparation Kit, was used to create DNA library templates from the double stranded cDNA. The concentrations were measured using the Qubit dsDNA HS assay. The size of the libraries for each sample was measured using the Agilent HS DNA chip. Samples were pooled and run on the NovaSeq X Plus sequencer using one lane of the 10B flow cell. The sequencing parameters included 100 bp Paired End Reads. Based on the size of the lane (1 billion reads) we expected a minimum of 77 million read pairs per sample. Libraries were sequenced on the Illumina NovaSeq 6000 system following the manufacturer's protocol.

value: Heart

value: IR,ML264, 2hrs


title: Heart, IR,ML264, 2hrs, rep2


title: Donor E-LDR-0.50

description:
Cells were exposed according to the dose and dose rate
SP0254-E-LDR-4

value: Lymphocyte


title: dnFGFR, Same, Sample 2

description:
Library name: PN320DS2
Colum name in Rsub_less_id.coverage.csv: PN320DS2.bam


title: Donor E-LDR-0.10

description:
Cells were exposed according to the dose and dose rate
SP0254-E-LDR-2


title: dnFGFR, Same, Sample 4

description:
Library name: PN320DS4
Colum name in Rsub_less_id.coverage.csv: PN320DS4.bam


title: Donor E-LDR-0.25

description:
Cells were exposed according to the dose and dose rate
SP0254-E-LDR-3


title: Heart, IR,ML264, 2hrs, rep1


title: Donor E-LDR-0.05

description:
Cells were exposed according to the dose and dose rate
SP0254-E-LDR-1


title: dnFGFR, Same, Sample 1

description:
Library name: PN320DS1
Colum name in Rsub_less_id.coverage.csv: PN320DS1.bam


title: Donor E-HDR-6

description:
Cells were exposed according to the dose and dose rate
SP0254-E-HDR-8

value: HDR

value: 1 Gy/min


title: Control, Opposite, Sample 5

description:
Library name: PN320CO5
Colum name in Rsub_less_id.coverage.csv: PN320CO5.bam

value: Control

value: opposite sex-housed


title: Heart, IR, 2hrs, rep4

value: IR, 2hrs


title: Donor E-HDR-2

description:
Cells were exposed according to the dose and dose rate
SP0254-E-HDR-6

value: Blood

value: Primary Cell


title: Heart, IR, 2hrs, rep3


title: Heart, IR, 2hrs, rep2


title: Control, Opposite, Sample 3

description:
Library name: PN320CO3
Colum name in Rsub_less_id.coverage.csv: PN320CO3.bam

value: Brain (mPOA)


title: Donor E-HDR-0.25

description:
Cells were exposed according to the dose and dose rate
SP0254-E-HDR-3


title: Heart, IR, 2hrs, rep1


title: Donor E-HDR-0.10

description:
Cells were exposed according to the dose and dose rate
SP0254-E-HDR-2


title: Control, Opposite, Sample 2

description:
Library name: PN320CO2
Colum name in Rsub_less_id.coverage.csv: PN320CO2.bam


title: Donor E-HDR-0

description:
Cells were brought to the exposure chamber, but never exposed.
SP0254-E-HDR-0

value: 0 Gy


title: Control, Opposite, Sample 1

description:
Library name: PN320CO1
Colum name in Rsub_less_id.coverage.csv: PN320CO1.bam


title: Heart, Sham, 2hrs, rep3

value: Sham, 2hrs


title: Donor E-Control-0b

description:
Cells were in incubator the whole time
SP0254-E-CON-0b

value: CON

value: Donor E

value: female


title: Donor D-LDR-6

description:
Cells were exposed according to the dose and dose rate
SP0254-D-LDR-8

value: LDR

value: 0.05 Gy/min

value: Donor D

value: male


title: Donor E-LDR-0

description:
Cells were brought to the exposure chamber, but never exposed.
SP0254-E-LDR-0

value: Lymphocyte


title: Control, Same sex, Sample 5

description:
Library name: PN320CS5
Colum name in Rsub_less_id.coverage.csv: PN320CS5.bam

value: whole-brain

value: same sex-housed


title: Donor D-LDR-2

description:
Cells were exposed according to the dose and dose rate
SP0254-D-LDR-6


title: Donor D-LDR-4

description:
Cells were exposed according to the dose and dose rate
SP0254-D-LDR-7


title: Donor E-HDR-4

description:
Cells were exposed according to the dose and dose rate
SP0254-E-HDR-7

value: HDR

value: 1 Gy/min


title: Donor D-LDR-1

description:
Cells were exposed according to the dose and dose rate
SP0254-D-LDR-5

value: Blood


title: Control, Opposite, Sample 4

description:
Library name: PN320CO4
Colum name in Rsub_less_id.coverage.csv: PN320CO4.bam

value: Control

value: opposite sex-housed


title: Control, Same sex, Sample 4

description:
Library name: PN320CS4
Colum name in Rsub_less_id.coverage.csv: PN320CS4.bam

value: Brain (mPOA)


title: Donor E-HDR-1

description:
Cells were exposed according to the dose and dose rate
SP0254-E-HDR-5

value: Primary Cell


title: Control, Same sex, Sample 3

description:
Library name: PN320CS3
Colum name in Rsub_less_id.coverage.csv: PN320CS3.bam


title: Donor D-LDR-0.50

description:
Cells were exposed according to the dose and dose rate
SP0254-D-LDR-4


title: Donor E-HDR-0.50

description:
Cells were exposed according to the dose and dose rate
SP0254-E-HDR-4


title: Lung,B6,mouse32,ADT

city: Worcester

first: Christopher

last: Sassetti

address: 368 Plantation Street

institute: UMass Chan Medical School

data_processing:
FASTQ files were uploaded to the 10x Genomics Cloud Analysis application for alignment, filtering, barcode counting and UMI counting using CellRanger count pipeline (cellranger-6.1.2). C57BL/6 was aligned to the GRCm38 reference. Custom references and annotations for PWK/PhJ, CC011, and CC024 were built using cellranger mkref from pseudogenomes generated by g2gtools (v0.2.7). References for the pseudogenomes were the GRCm38 primary assembly, GENCODE vM25 annotations, and variant calls from Srivastava et al (PMID  28592495).
The resulting feature-barcode matrices were imported to Seurat (v5.0.3) using R (v4.2.2) and Rstudio (2022.12.0+353).  Cells were filtered for high mitochondrial content (<10%), empty cells (nFeature_RNA>200) and high feature counts (nFeature_RNA<4000). Doublets were called by DoubletFinderv2 (v2.0.3) and excluded. Gene expression data was normalized using SCTransform followed by dimensionality reduction for the top 30 PCs and clustering via UMAP (resolution=0.5). The antibody derived tag library (ADT) was normalized using the centered log-ratio (CLR) method followed by centering and scaling.Datasets were then integrated and dimensionality reduction and clustering were re-run. Clusters were annotated using SingleR, existing scRNAseq datasets, and expression of canonical markers in the ADT dataset.
Assembly: GRCm38
Supplementary files format and content: an RDS file of the integrated Seurat object containing all GEX and ADT data
Supplementary files format and content: a csv file containing the antibodies and barcodes in the ADT pool
Library strategy: CITE-seq

source_name: Lung

extract_protocol:
C57BL/6, CC011, PWK/PhJ, and CC024 mice were infected by low-dose aerosol with Mtb. At 4wks post-infection, 4 mice per strain were humanely euthanized and lungs were perfused with DMEM (Gibco) containing 10% FBS. The right Lung lobes were harvested into R10 media (RPMI 1640 plus L-glutamine (Gibco), 10% FBS (Sigma), HEPES (Gibco), and penicillin-streptomycin (Gibco)), treated with collagenase (Gibco) and dissociated using a GentleMacs (Miltenyi). After incubation at 37C for 30 minutes, tissues were subject to another dissociation and passed through a 70um filter. Red blood cells were then lysed (eBioscience RBC Lysis buffer, Thermo Fisher), then cells were washed, and passed through a 40um filter. Dead cells were removed using the Dead Cell Removal Kit (Milentyi Biotec) according to manufacturer’s instructions. Cell suspensions were counted and 1.25x105 cells/sample were transferred to round-bottom polystyrene tubes, treated with TruStain FcX PLUS (Biolegend) to block non-specific antibody binding, and stained with TotalSeq-A universal mouse antibody panel, (Biolegend, pre-catalog version #99833) according to the manufacturer’s instructions. Cells were counted and 10,000 cells/sample were run through the 10x Genomics Chromium Controller using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 as indicated by the manufacturer.
Gene expression (GEX) and antibody derived (ADT) libraries were constructed following the 10x Genomics User Guide #206 and Biolegend TotalSeq-A manufacturer instructions. Libraries were pooled at a ratio of 80% GEX to 20% ADT and sequenced on a NovaSeq6000 sequencer (Illumina) targeting 50,000 paired-end reads/cell.

value: Lung

value: primary

value: lung cells

tag: library type

value: antibody derived tag

value: 4wks post-infection


title: Donor D-LDR-0.25

description:
Cells were exposed according to the dose and dose rate
SP0254-D-LDR-3

value: LDR

value: 0.05 Gy/min

value: Donor D


title: Heart, Sham, 2hrs, rep4

value: Heart

value: Sham, 2hrs


title: Donor E-HDR-0.05

description:
Cells were exposed according to the dose and dose rate
SP0254-E-HDR-1

value: Lymphocyte

value: HDR

value: Donor E

value: female


title: Lung,B6,mouse31,ADT


title: Donor D-LDR-0.05

description:
Cells were exposed according to the dose and dose rate
SP0254-D-LDR-1

value: Blood

value: male


title: Control, Same sex, Sample 1

description:
Library name: PN320CS1
Colum name in Rsub_less_id.coverage.csv: PN320CS1.bam

value: Brain (mPOA)

value: whole-brain

value: Control

value: same sex-housed


title: Control, Same sex, Sample 2

description:
Library name: PN320CS2
Colum name in Rsub_less_id.coverage.csv: PN320CS2.bam


title: Donor D-LDR-0.10

description:
Cells were exposed according to the dose and dose rate
SP0254-D-LDR-2

value: Primary Cell


title: Heart, Sham, 2hrs, rep2


title: Donor E-Control-0a

description:
Cells were in incubator the whole time
SP0254-E-CON-0a

value: CON


title: Lung,CC024,mouse30,ADT

value: Lung

value: primary

value: lung cells

value: antibody derived tag

value: 4wks post-infection


title: Heart, Sham, 2hrs, rep1

value: Heart

value: Sham, 2hrs


title: Donor D-HDR-4

description:
Cells were exposed according to the dose and dose rate
SP0254-D-HDR-7

value: Lymphocyte

value: HDR

value: 1 Gy/min

value: Donor D


title: SalContrl_3

city: Uvalde

first: Vijay

last: Joshi

state: Texas

address: 1619 Garner Field Road

department: Department of Horticultural Sciences

institute: Texas A&M AgriLife Research

description: Control

data_processing:
Sequencing on DNBSEQ (DNBSEQ Technology) platform. The reads with low quality, adapter contamination, and highly unknown N bases were filtered. The clean reads were aligned to GenBank assembly GCA_027235085.1 sequenced by the FDA Center for Food Safety and Applied Nutrition. and the transcriptions assembly. The read count for every transcript was determined from the findings of the mapping process.
Sequenced reads were trimmed for adaptor sequence by fastp, and masked for low-complexity or low-quality sequence, then mapped to Allium cepa genome using  the chain-specific patterns of HISAT2 and StringTie for mapping and assembly, For the assembly results of individual transcripts,  each transcript  was confirmed to meet FPKM >= 0.5, Coverage > 1 and Length> 200
Cuffmerge (one tool of Cufflinks) was used to merge the results of assembly, and the merged transcripts were used as final results and subsequent analysis.We used Bowtie2 to align clean reads to the reference sequence, and then use RSEM to calculate the expression of genes and transcripts. To compare the expression levels between samples, ithe standardized method  by RSEM was FPKM. We use the difference analysis software DEseq2 for intergroup difference analysis. Filtration conditions of gene with significant differences: DEseq2 : abs(log2FC) >= 0 and Qvalue <= 0.050000
The expression levels were calculated and normalized to Fragments Per Kilobase of transcript sequence per million base pairs sequenced (FPKM) using RSEM (Li & Dewey, 2011).
The DESeq2 R package (1.20.0) was used for the differential expression analysis. The P-values obtained were adjusted using Benjamini and Hochberg's method to control the false discovery rate. Genes identified as differentially expressed genes (DEGs) had an adjusted P-value <0.05 and an absolute log2FC ≥0, as determined by DESeq2.
Assembly: GCA_027235085.1
Supplementary files format and content: raw read counts and RPKM for each sample

organism: Salmonella enterica subsp. enterica serovar Newport

source_name: onion bulb

growth_protocol: Transcriptomic analysis of  Salmonella strains recovered from inoculated onion bulbs was performed 1 day and 7 days post-inoculation and controlled Salmonella culture. Salmonella enterica subsp. enterica ser. Newport, isolated from clinical cases affected by the onion-linked outbreak in 2020 (CDC, 2020), was used for the onion bulb inoculation. The samples were collected as 3 replicates for both time points and flash-frozen in liquid nitrogen before storing at -80℃ for further processing.

extract_protocol:
Total RNA was extracted from each sample using the RNeasy® Mini Kit and rRNA removal . The mRNA was isolated from the total RNA was fragmented into short segments using a fragmentation buffer. cDNA was synthesized via reverse transcription (Superscript III, Invitrogen).
The fragmented mRNA was used to first-strand cDNA using random primers, and the second-strand cDNA was synthesized with dUTP instead of dTTP. The synthesized cDNA was subjected to end-repair and 3' adenylation. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments. The U-labeled second-strand template was digested with Uracil-DNA-Glycosylase (UDG) before PCR amplification. The library was amplified to make DNA nanoball (DNB), and the sequencing was performed on the DNBSEQ (DNBSEQ Technology) platform.

treatment_protocol: Onion bulbs inoculated with Salmonella enterica were flash-frozen in liquid nitrogen from three independent bulbs 1 and 7 days after injection. The samples were used for total RNA extractions. Salmonella samples recovered from inoculated bulbs from Day 1 (ONtreatedlD1_1, ONtreatedlD1_2, ONtreatedlD1_3) and Day 7 (ONtreatedlD7_1, ONtreatedlD7_2, ONtreatedlD7_3) were compared with control cultures of Salmonella (SalContrl_1, 2 and 3).

value: onion bulb

value: Salmonella cocktail of outbreak strains

value: Uninoculated Control


title: Lung,CC024,mouse29,ADT


title: Donor D-HDR-1

description:
Cells were exposed according to the dose and dose rate
SP0254-D-HDR-5

source_name: Blood

value: Blood

value: male


title: Donor D-HDR-2

description:
Cells were exposed according to the dose and dose rate
SP0254-D-HDR-6

value: Primary Cell


title: Donor D-HDR-0.50

description:
Cells were exposed according to the dose and dose rate
SP0254-D-HDR-4


title: Lung,CC011,mouse27,ADT

value: Lung


title: Heart, IR,ML264, 2hrs, rep4

value: IR,ML264, 2hrs


title: Lung,CC011,mouse28,ADT

value: primary

value: lung cells


title: SalContrl_2

description: Control


title: SalContrl_1

description: Control


title: Donor D-HDR-0.10

description:
Cells were exposed according to the dose and dose rate
SP0254-D-HDR-2


title: Donor D-HDR-0.05

description:
Cells were exposed according to the dose and dose rate
SP0254-D-HDR-1


title: Lung,PWK,mouse26,ADT

value: PWK

value: antibody derived tag

value: 4wks post-infection


title: Donor D-HDR-0

description:
Cells were brought to the exposure chamber, but never exposed.
SP0254-D-HDR-0

value: Lymphocyte

value: 0 Gy


title: SaltreatedlD7_3

description: Day 7 inoculated

value: Salmonella inoculation


title: Lung,PWK,mouse25,ADT


title: Donor D-Control-0b

description:
Cells were in incubator the whole time
SP0254-D-CON-0b

value: CON

value: 1 Gy/min

value: Donor D


title: Donor D-LDR-0

description:
Cells were brought to the exposure chamber, but never exposed.
SP0254-D-LDR-0

value: LDR

value: 0.05 Gy/min


title: SaltreatedlD7_2

description: Day 7 inoculated

value: onion bulb

value: Salmonella cocktail of outbreak strains


title: SaltreatedlD7_1

description: Day 7 inoculated


title: Donor C-LDR-6

description:
Cells were exposed according to the dose and dose rate
SP0254-C-LDR-8

value: Blood

value: Primary Cell

value: Donor C

value: male


title: Donor D-HDR-6

description:
Cells were exposed according to the dose and dose rate
SP0254-D-HDR-8

value: HDR


title: Donor D-Control-0a

description:
Cells were in incubator the whole time
SP0254-D-CON-0a


title: Donor C-LDR-2

description:
Cells were exposed according to the dose and dose rate
SP0254-C-LDR-6


title: Lung,B6,mouse23,ADT

value: Lung

value: primary

value: lung cells

value: antibody derived tag


title: Donor C-LDR-1

description:
Cells were exposed according to the dose and dose rate
SP0254-C-LDR-5

value: Lymphocyte


title: Donor C-LDR-0.25

description:
Cells were exposed according to the dose and dose rate
SP0254-C-LDR-3


title: Donor D-HDR-0.25

description:
Cells were exposed according to the dose and dose rate
SP0254-D-HDR-3


title: Lung,CC024,mouse21,ADT

value: 4wks post-infection


title: ONtreatedlD7_3

description: Day 7 Inoculated

data_processing:
Sequencing on DNBSEQ (DNBSEQ Technology) platform. The reads with low quality, adapter contamination, and highly unknown N bases were filtered. The clean reads were aligned to the reference genome (a doubled haploid onion line DHCU066619 (https://www.oniongenome.wur.nl/)  and the transcriptions assembly. The read count for every transcript was determined from the findings of the mapping process.
Sequenced reads were trimmed for adaptor sequence by fastp, and masked for low-complexity or low-quality sequence, then mapped to Allium cepa genome using  the chain-specific patterns of HISAT2 and StringTie for mapping and assembly, For the assembly results of individual transcripts,  each transcript  was confirmed to meet FPKM >= 0.5, Coverage > 1 and Length> 200
Cuffmerge (one tool of Cufflinks) was used to merge the results of assembly, and the merged transcripts were used as final results and subsequent analysis.We used Bowtie2 to align clean reads to the reference sequence, and then use RSEM to calculate the expression of genes and transcripts. To compare the expression levels between samples, ithe standardized method  by RSEM was FPKM. We use the difference analysis software DEseq2 for intergroup difference analysis. Filtration conditions of gene with significant differences: DEseq2 : abs(log2FC) >= 0 and Qvalue <= 0.050000
The expression levels were calculated and normalized to Fragments Per Kilobase of transcript sequence per million base pairs sequenced (FPKM) using RSEM (Li & Dewey, 2011).
The DESeq2 R package (1.20.0) was used for the differential expression analysis. The P-values obtained were adjusted using Benjamini and Hochberg's method to control the false discovery rate. Genes identified as differentially expressed genes (DEGs) had an adjusted P-value <0.05 and an absolute log2FC ≥0, as determined by DESeq2.
Assembly: a doubled haploid onion line DHCU066619 (https://www.oniongenome.wur.nl/)
Supplementary files format and content: raw read counts and RPKM for each sample

organism: Allium cepa

source_name: Bulb

growth_protocol: Transcriptomic analysis of onion bulbs inoculated with Salmonella strain was performed 1 day and 7 days post-inoculation. Salmonella enterica subsp. enterica ser. Newport, isolated from clinical cases affected by the onion-linked outbreak in 2020 (CDC, 2020), was used for the onion bulb inoculation. The bulb tissue samples were collected as 3 replicates for both time points and flash-frozen in liquid nitrogen before storing at -80℃ for further processing.

extract_protocol:
Total RNA was extracted from each sample using the QIAseq fastSelect rRNA kits. The mRNA was isolated from the total RNA using magnetic beads with Oligo (dT) and fragmented into short segments using a fragmentation buffer. cDNA was synthesized via reverse transcription (Superscript III, Invitrogen).
Oligo dT beads were used to enrich mRNA with poly A tail from total RNA, and mRNA molecules were fragmented into small pieces. The fragmented mRNA was used to first-strand cDNA using random primers, and the second-strand cDNA was synthesized with dUTP instead of dTTP. The synthesized cDNA was subjected to end-repair and 3' adenylation. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments. The U-labeled second-strand template was digested with Uracil-DNA-Glycosylase (UDG) before PCR amplification. The library was amplified to make DNA nanoball (DNB), and the sequencing was performed on the DNBSEQ (DNBSEQ Technology) platform.

treatment_protocol: Onion bulbs inoculated with Salmonella enterica were flash-frozen in liquid nitrogen from three independent bulbs at 1 and 7 days after injection. The samples were used for RNA extractions. For the Day 1 set of samples, uninoculated samples (ONControlD1_1, ONControlD1_2, ONControlD1_3) were compared to inoculated samples (ONtreatedlD1_1, ONtreatedlD1_2, ONtreatedlD1_3). For Day 7, samples (ONControlD7_1, ONControlD7_2, ONControlD7_3) were compared to inoculated samples (ONtreatedlD7_1, ONtreatedlD7_2, ONtreatedlD7_3).

value: Bulb

value: Bulb cells

value: Outer and inner scales

value: Don Victor

value: Salmonella inoculation


title: Donor C-HDR-6

description:
Cells were exposed according to the dose and dose rate
SP0254-C-HDR-8

value: 1 Gy/min


title: Donor C-LDR-0.05

description:
Cells were exposed according to the dose and dose rate
SP0254-C-LDR-1

value: Blood

value: LDR

value: 0.05 Gy/min


title: Donor C-LDR-0.10

description:
Cells were exposed according to the dose and dose rate
SP0254-C-LDR-2

value: Primary Cell

value: Donor C

value: male


title: SaltreatedlD1_3

description: Day 1 Inoculated

value: onion bulb

value: Salmonella cocktail of outbreak strains


title: Donor C-LDR-0

description:
Cells were brought to the exposure chamber, but never exposed.
SP0254-C-LDR-0

value: 0 Gy


title: Donor C-HDR-4

description:
Cells were exposed according to the dose and dose rate
SP0254-C-HDR-7

value: Lymphocyte

value: HDR


title: Lung,B6,mouse24,ADT

value: Lung

value: primary

value: lung cells

value: antibody derived tag

value: 4wks post-infection


title: Donor C-HDR-2

description:
Cells were exposed according to the dose and dose rate
SP0254-C-HDR-6

value: 1 Gy/min


title: SaltreatedlD1_1

description: Day 1 Inoculated

value: Salmonella inoculation


title: Donor C-HDR-1

description:
Cells were exposed according to the dose and dose rate
SP0254-C-HDR-5

value: Blood


title: ONtreatedlD7_1

description: Day 7 Inoculated

value: Bulb

value: Bulb cells

value: Outer and inner scales

value: Don Victor


title: ONtreatedlD7_2

description: Day 7 Inoculated


title: Lung,PWK,mouse18,ADT

value: PWK


title: Donor C-LDR-4

description:
Cells were exposed according to the dose and dose rate
SP0254-C-LDR-7

value: Primary Cell

value: LDR

value: 0.05 Gy/min

value: Donor C

value: male


title: Donor C-HDR-0.50

description:
Cells were exposed according to the dose and dose rate
SP0254-C-HDR-4

value: Lymphocyte

value: HDR


title: Lung,CC011,mouse19,ADT

value: Lung

value: primary

value: lung cells

value: antibody derived tag


title: Donor C-HDR-0.25

description:
Cells were exposed according to the dose and dose rate
SP0254-C-HDR-3

value: Blood

value: 1 Gy/min


title: SaltreatedlD1_2

description: Day 1 Inoculated

value: onion bulb

value: Salmonella cocktail of outbreak strains

value: Salmonella inoculation


title: ONControlD7_3

description: Day 7 uninoculated

value: Bulb

value: Bulb cells

value: Outer and inner scales

value: Don Victor

value: Uninoculated Control


title: Donor C-HDR-0.10

description:
Cells were exposed according to the dose and dose rate
SP0254-C-HDR-2

value: Primary Cell

value: Donor C

value: male


title: Lung,CC024,mouse22,ADT

value: Lung

value: 4wks post-infection


title: Lung,CC011,mouse20,ADT

value: primary

value: lung cells


title: Lung,PWK,mouse17,ADT

value: PWK

value: antibody derived tag


title: ONControlD7_2

description: Day 7 uninoculated


title: Lung,B6,mouse32,GEX

value: gene expression


title: ONtreatedlD1_3

description: Day 1 Inoculated


title: Lung,CC024,mouse30,GEX


title: Donor C-HDR-0

description:
Cells were brought to the exposure chamber, but never exposed.
SP0254-C-HDR-0

value: Blood

value: Lymphocyte

value: HDR

value: 1 Gy/min

value: 0 Gy


title: Donor C-Control-0a

description:
Cells were in incubator the whole time
SP0254-C-CON-0a

value: CON

value: 0.05 Gy/min


title: ONControlD7_1

description: Day 7 uninoculated

value: Bulb

value: Bulb cells

value: Outer and inner scales

value: Don Victor

value: Uninoculated Control


title: Lung,CC024,mouse29,GEX

value: Lung

value: primary

value: 4wks post-infection


title: Donor B-LDR-1

description:
Cells were exposed according to the dose and dose rate
SP0254-B-LDR-5

value: Primary Cell

value: LDR

value: Donor B

value: male


title: Donor B-LDR-4

description:
Cells were exposed according to the dose and dose rate
SP0254-B-LDR-7

value: Blood

value: Lymphocyte


title: Donor C-Control-0b

description:
Cells were in incubator the whole time
SP0254-C-CON-0b

value: 1 Gy/min

value: Donor C


title: Donor B-LDR-2

description:
Cells were exposed according to the dose and dose rate
SP0254-B-LDR-6

value: 0.05 Gy/min


title: Donor B-LDR-0.25

description:
Cells were exposed according to the dose and dose rate
SP0254-B-LDR-3


title: Donor B-LDR-0.10

description:
Cells were exposed according to the dose and dose rate
SP0254-B-LDR-2


title: Donor B-LDR-6

description:
Cells were exposed according to the dose and dose rate
SP0254-B-LDR-8


title: ONtreatedlD1_2

description: Day 1 Inoculated

value: Bulb

value: Salmonella inoculation


title: Lung,CC011,mouse28,GEX

value: lung cells

value: gene expression


title: Donor C-HDR-0.05

description:
Cells were exposed according to the dose and dose rate
SP0254-C-HDR-1

value: HDR


title: ONControlD1_3

description: Day 1 uninoculated

value: Bulb cells

value: Outer and inner scales

value: Don Victor

value: Uninoculated Control


title: Donor B-LDR-0.05

description:
Cells were exposed according to the dose and dose rate
SP0254-B-LDR-1

value: Primary Cell

value: LDR


title: Lung,CC011,mouse27,GEX

value: Lung

value: primary

value: 4wks post-infection


title: Donor B-LDR-0

description:
Cells were brought to the exposure chamber, but never exposed.
SP0254-B-LDR-0

value: Blood

value: Lymphocyte

value: 0 Gy

value: Donor B

value: male


title: ONControlD1_2

description: Day 1 uninoculated

value: Bulb


title: Donor B-HDR-6

description:
Cells were exposed according to the dose and dose rate
SP0254-B-HDR-8

value: 1 Gy/min


title: Lung,PWK,mouse26,GEX

value: lung cells

value: PWK

value: gene expression


title: Donor B-HDR-4

description:
Cells were exposed according to the dose and dose rate
SP0254-B-HDR-7

value: HDR


title: Lung,B6,mouse31,GEX


title: Donor B-HDR-2

description:
Cells were exposed according to the dose and dose rate
SP0254-B-HDR-6


title: ONControlD1_1

description: Day 1 uninoculated

value: Bulb cells

value: Outer and inner scales

value: Don Victor

value: Uninoculated Control


title: Lung,PWK,mouse25,GEX

value: Lung

value: primary


title: Donor B-LDR-0.50

description:
Cells were exposed according to the dose and dose rate
SP0254-B-LDR-4

value: Blood

value: Primary Cell

value: LDR

value: 0.05 Gy/min


title: Donor B-HDR-1

description:
Cells were exposed according to the dose and dose rate
SP0254-B-HDR-5

value: Lymphocyte

value: Donor B

value: male


title: ONtreatedlD1_1

description: Day 1 Inoculated

value: Bulb

value: Salmonella inoculation


title: Donor B-HDR-0.05

description:
Cells were exposed according to the dose and dose rate
SP0254-B-HDR-1

value: 1 Gy/min


title: MFC_DL1_rep2

city: Mexico

first: Leticia

last: Vega

state: Mexico

address: Circuito Ext s/n

country: Mexico

institute: Universidad Nacional Autonoma de Mexico

description: Library name: Sample 8

data_processing:
Illumina bcl2fastq software were used for basecalling
Reads were aligned to the GCF_000007985.2/ASM798v2 genome assembly using smalt
The number of reads falling in the genes  were counted using coveragebed software and normalized with edgeR software
Assembly: GCF_000007985.2
Supplementary files format and content: tab-delimited text file include the differential expression results of edgeR and raw and normalized counts  for each sample.

organism: Geobacter sulfurreducens

growth_protocol: G. sulfurreducens biofilms grown on glass supports were grown in NBAF medium at 25 oC for 48 hours. The planktonic cells were separated from the biofilm that grew at the bottom of the culture tube. On the other hand, biofilms of G. sulfurreducens grown on graphite electrodes were separated from microbial fuel cells poised  operated for 2 weeks. In the MFC, to grow G. sulfurreducens, FWAF medium was used.

extract_protocol:
RNA was extracted using the RNeasy mini kit (Qiagen) following the manufacturer's instructions, and residual DNA was removed by DNaseI treatment (Thermo Scientific). RNA samples were quantified using the NanoDrop 200c (Thermo Scientific) and examined with an Agilent 2100 Bioanalyzer.
cDNA libraries were constructed using the TruSeq Stranded mRNA kit (Illumina) following the manufacturer´s protocol. The cDNA libraries were purified with the Zymoclean Gel DNA Recovery Kit (Zymo Research).

treatment_protocol: The cells present in the biofilms were resuspended in 1 mL of NBAF and incubated with 100 uL of RNAlater. Cells were pelleted by centrifugation and frozen at -70 oC until use.

value: DL1 wild type strain

value: Biofilm grown on graphite electrode in microbial fuel cell operated for 2 weeks


title: MFC_DL1_rep1

description: Library name: Sample 7


title: Lung,B6,mouse23,GEX

value: lung cells

value: gene expression

value: 4wks post-infection


title: MFC_csrA_rep2

description: Library name: Sample 6

value: DL1 with csrA-deletion


title: MFC_csrA_rep1

description: Library name: Sample 5


title: Lung,CC024,mouse22,GEX

value: Lung

value: primary


title: Donor B-Control

description:
Cells were in incubator the whole time
SP0254-B-CON-0

value: Blood

value: Primary Cell

value: CON