title: Peripheral whole blood DNA from fILD patient 169

description:
206139120078
206139120078_R01C01

value: UPitt


title: PANC02 cell, shSrebf1-3

status: Public on Feb 28 2025

type: SRA

city: Hangzhou

first: Mengyi

last: Lao

state: Zhejiang

address: Qingchun 79 road

country: China

institute: Zhejiang university

description: Library name: samples12

library_source: transcriptomic

data_processing:
CLC Genomics Workbench v11.0.1
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files includeFPKM values for each Sample

molecule: total RNA

organism: Mus musculus

growth_protocol: KPC and PANC02 pancreatic cancer cells were maintained inDMEM supplemented with10% fetal bovine serum (FBS)and antibiotics in humidified atmosphere with 5%CO2 at 37℃

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.

treatment_protocol: The control group and the treatment group cells were transfected with the vector and the shSrebf1 plasmid, respectively.

tag: cell line

tag: cell type

value: Pancreatic cancer cell

tag: genotype

tag: treatment

value: lipid metabolism


title: Peripheral whole blood DNA from fILD patient 168

type: genomic

city: Vancouver

first: Gillian

middle: Catherine

last: Goobie

state: British Columbia

address: Centre for Heart Lung Innovation, St. Paul's Hospital, 1081 Burrard Street

department: Division of Respiratory Medicine

country: Canada

institute: University of British Columbia

description:
206139120101
206139120101_R08C01

hyb_protocol: Bisulphite converted DNA was amplified, fragmented, and hybridized to human Infinium MethylatioEPIC BeadChip (Illumina) using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and standard recommended Illumina scanner settings

data_processing:
A multi-package approach to processing and analyzing raw DNAm data produced from the Infinium MethylationEPIC array was implemented. First, raw .idat files for each sample underwent pre-processing, quality control, filtering, and analysis using R statistical computing environment (version 4.2.1, www.r-project.org). Using the minfi package, samples with a mean detection p-value >0.05 were excluded (n=2). The detection p-value compares the total unmethylated and methylated signal at each CpG location and compares it to the background signal inferred from negative control probes, such that p-values >0.05 or >0.01 indicate a failed probe where the signal from the probe is not significantly different from the background. All samples are from blood, and thus it was not expected there would be major global differences in methylation patterns between the samples. This enabled normalization using a subset quantile procedure, which helps to mitigate the impacts of artifacts in the data that are the result of differences between Type-I and Type-II methylation probes and other technical sources of variation. Next, for probe filtering, we removed any CpG probes whose detection p-value was >0.01 on one or more samples. We also removed sex chromosome probes given that our study includes patients of male and female sex. Next, we removed probes that had a single nucleotide polymorphism (SNP) at the CpG site, as this can result in impaired hybridization and detection of methylation for individuals with a variant allele at that locus. Subsequently, we removed cross-reactive probes that do not uniquely hybridize to a single CpG site on the MethylationEPIC array.
*processed value definition = Average Beta

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Whole blood DNA

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was isolated from peripheral whole blood samples taken from patients enrolled in the UPitt cohort using the Puregene DNA isolation kit or QiaAmp blood DNA isolation kit (Qiagen) and from the UBC cohort using the DNeasy Blood and Tissue Kit (Qiagen), all according to the manufacturer’s instructions. UBC samples were transferred to UPitt for simultaneous analysis alongside the UPitt samples. Prior to analysis, all DNA samples were stored at -20°C. DNA concentration and purity were assessed using the Infinite M200 Pro NanoQuant Plate Reader. Samples with an A260/A280 absorbance ratio outside of the 1.7-2.0 range were excluded.

tag: cohort

tag: Sex

value: F

tag: smokehx

value: Former

value: IPF

tag: tissue

value: Whole blood DNA


title: KPC cell, shSrebf1-2

description: Library name: samples5

source_name: KPC

value: KPC


title: UM-2

type: RNA

city: Daegu

first: Su Young

last: Oh

address: 2177, Dalgubeol-daero, Jung-gu

country: South Korea

institute: Kyungpook National University

description: OSCC

hyb_protocol: Following fragmentation, 5.5 ug of framented cDNA were hybridized for about 17 hr at 45℃ on Human Gene 2.0 ST array. The hybridized probe arrays were stained and washed with GeneChip® Hybridization, Wash and Stain Kit(900720, Thermo Fisher Scientific) using the Fluidics Station 450(Affymetrix).

scan_protocol: The stained GeneChips were scanned with a GeneChip® Scanner 3000+ 7G(Affymetrix) a 570 nm.

data_processing: The RMA algorithm was used for expression summary and signal calculation of Human Gene 2.0 ST array data. Sketch Quantile normalization was performed for the signal normalization.

label: biotin

source_name: UMSCC1 (UM-2)

label_protocol: The GeneChip® procedure for generation of the biotin-labeled single-stranded cDNA by in vitro transcription were performed according to the manufacturer's instructions from 200ng total RNA. Protocol performed using GeneChip™ WT PLUS Reagent Kit(902280, Thermo Fisher Scientific).

growth_protocol: OSCC cells were cultured in DMEM medium containing 10% FBS and 1% penicillin/streptomycin solution at 37°C in a 5% CO2 humidified atmosphere.

extract_protocol: Total RNA was obtained from UMSCC1 and UM-Cis cells cultured without cisplatin using Trizol reagent (Invitrogen, Carlsbad, CA, USA). RNA quality was assessed by Agilent 2100 bioanalyzer (Agilent Technologies, USA), and the quantity was determined using the ND-1000 spectrophotometer (NanoDrop Technologies, USA).

treatment_protocol: Cisplatin-resistant UM-Cis cells were derived from original UMSCC1 cells by continuous exposure to stepwise increasing concentrations of cisplatin. Initially, the exponentially growing cells were exposed to 1 μg/ml concentration of cisplatin in DMEM medium supplemented with 10% FBS and 1% penicillin/streptomycin, and subcultured upon reaching 70 - 80% confluency. At this point, cisplatin concentration was increased gradually and the above process was repeated. Aliquots of cell sublines were cryopreserved at each incremental concentration. The final concentration of cisplatin treated in UM-Cis cells is 5 μg/ml which is the IC50 of the original UMSCC1 cells. This development period was carried out for approximately 12 months.


title: KPC cell, shSrebf1-1

description: Library name: samples4


title: Sample_23_BCR Memory B Cell Run4

city: Bethesda

first: Sarah

last: Andrews

state: Maryland

address: 9000 Rockville Pike

country: USA

institute: National Institutes of Health

description:
Library name: Sample_23_BCR
Run4

library_source: transcriptomic single cell

data_processing:
CellRanger v6.0.0
GEX and ADT libraries were run through CellRanger count together to produce one matrix file
Assembly: GRCh38 human reference genome 3.0.0
Supplementary files format and content: Sample_GEX_ADT_barcodes.tsv.gz
Supplementary files format and content: Sample_GEX_ADT_features.tsv.gz
Supplementary files format and content: Sample_GEX_ADT_matrix.mtx.gz
Supplementary files format and content: FeatureReferenceFile.csv

source_name: pbmc

extract_protocol:
Single-cells were encapsulated in Gel-beads-in-emulsion using the 10x Genomics Chromium Controller and a Single Cell Immune Profiling Next GEM v2 Chemistry Kit.
10x Genomics Single Cell Immune Profiling Next GEM v2 Chemistry Kit

value: pbmc

value: Memory B Cell

value: H2 Influenza Vaccination

tag: library type

value: BCR


title: KPC cell, shSrebf3-3

description: Library name: samples6


title: HSC_reference_rep1

city: Milano

first: Emanuela

last: Colombo

address: Via Adamello, 16

country: Italy

institute: European Institute of Oncology

description: Gene expression data of LT-HSC purified from a pool of control animals

hyb_protocol: Hybridization was performed using the Affymetrix GeneChip® Hybridization, Wash and Stain Kit, according to the Encore® Biotin Module (NuGEN Technologies, Inc)  recommended protocol for Affymetrix GeneChip® Mouse Gene ST 2.0 Arrays. Briefly, Targets were diluted in hybridization buffer at a concentration of 23 ng/ul, denatured at 99 °C for 2 minutes, incubated at 45 °C for 5 minutes  and centrifuged at maximum speed for 1 minute prior to introduction into the GeneChip cartridge. A single GeneChip® Mouse Gene ST 2.0 was then hybridized with each biotin-labeled target.   Hybridizations were performed for 18 hours at 45°C in a rotisserie oven. GeneChip® cartridges were washed and stained in the Affymetrix Fluidics Station 450 following the FS450_0002 standard protocol, including the following steps: (1) (wash) 10 cycles of 2 mixes/cycle with Wash Buffer A at 30 °C; (2) (wash) 6 cycles of 15 mixes/cycle with Wash Buffer B at 50 °C; (3) stain of the probe array for 5 min in SAPE solution at 35 °C; (4) (wash) 10 cycles of 4 mixes/cycle with Wash Buffer A at 30 °C; (5) stain of the probe array for 5 min in antibody solution at 35 °C; (6) stain of the probe array for 5 min in SAPE solution at 35 °C; (7) (final wash) 15 cycles of 4 mixes/cycle with Wash Buffer A at 35 °C; (8) fill the probe array with Array Holding buffer.

scan_protocol: GeneChip arrays were scanned using an Affymetrix GeneChip® Scanner3000 7G using default parameters. Affymetrix GeneChip® Command Console software (AGCC) was used to acquire GeneChip® images and generate .DAT and .CEL files, which were used for subsequent analysis with proprietary software.  Partek Genomics Suite v 6.6 was used for analysis of microarray data

data_processing: Probes to Import: Interrogating Probes and Control Probes  Probe filtering: skip  Algorithm: RMA  Background Correction: RMA Background Correction  Normalization: Quantile Normalization+batch effect correction  Log Probes using Base: 2 (scaling parameters)  Probeset Summarization: Median Polish

source_name: LT-HSC sorted 4 months post bone marrow transplatation

label_protocol: Bioin-labeled cDNA targets were synthesized starting from  ≈ 5 ng of total RNA. Double stranded cDNA synthesis and related cRNA was performed with Nugen® Pico WTA Systems V2 (NuGEN Technologies, Inc). With the Encore® Biotin Module (NuGEN Technologies, Inc) was synthesized the fragmented and labeled cDNA. All steps of the labeling protocol were performed according to the manufacturer's recommended protocols.

extract_protocol: total RNA have been extacted from freshly isolated HSC using Rneasy mini kit from Qiagen. The quality of total RNA was first assessed using an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA)

value: bone marrow

tag: strain


title: KPC cell, shNC3

description: Library name: samples3

value: shNC


title: Sample_22_BCR Memory B Cell Run4

description:
Library name: Sample_22_BCR
Run4


title: PANC02 cell, shNC3

description: Library name: samples9


title: Peripheral whole blood DNA from fILD patient 167

description:
206139120101
206139120101_R07C01

value: UNCLASSIFIABLE


title: KPC cell, shNC2

description: Library name: samples2


title: KPC cell, shNC1

description: Library name: samples1


title: Peripheral whole blood DNA from fILD patient 166

description:
206139120101
206139120101_R06C01

value: M


title: Nucleus Accumbens Core, Ethanol 3

city: San Juan

first: Mario

middle: Ernesto

last: Lloret

state: Puerto Rico

address: Calle Norzagarai Instituto de Neurobiologia

department: Academic Affairs

institute: Unversity of Puerto Rico Medical Sciences Campus

description:
Library name: Sample6
NAcCore-EtOH-3

data_processing:
Sequencing data is converted into raw data for the analysis (Table 1). The Illumina sequencer generates raw images utilizing sequencing control software for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis). The BCL (base calls) binary is converted into FASTQ utilizing the illumina package bcl2fastq. Adapters are not trimmed away from the reads. The total number of bases, reads, GC (%), Q20 (%), and Q30 (%) are calculated for the 6 samples. For example, in NAcCore-Control-1, 98,998,428 reads are produced, and total read bases are 14.9G bp. The GC content (%) is 51.23% and Q30 is 93.41%. Note: N=3 NAc core control and N=3 experimental.  Each N contains the NAc core tissue punches from 3 mice for a total of 9 tissue punches per N.
Samples were processed for quality control using a Phred quality score that numerically expresses the accuracy of each nucleotide. A higher Q number signifies higher accuracy. For example, if Phred assigns a quality score of 30 to a base, the chances of having base call errors are 1 in 1000. Phred Quality Score Q is calculated with -10log10P, where P is the probability of an erroneous base. These tests were performed using an independent agency and according to strict guidelines (Psomagen, MD).
Assembly: mm10
Supplementary files format and content: The tab delimited text file contains both the raw counts and the FPKM values for each sample

source_name: Nuclues Accumbens Core

extract_protocol:
RNA extraction was done by placing samples into ice-cold TRI reagent, 1 ml per 50–100 mg of tissue of TRIzol reagent (Sigma-Aldrich). Total RNA was extracted following the manufacturer's instructions (mRNeasy Micro Kit; QIAGEN). RNA was quantified by UV spectrometry with a NanoDropTM UV-Vis Spectrophotometer (Thermo Scientific, United States). Total RNA was shipped to Psomagen Laboratories where mRNA was further isolated and processed with the highest standards to determine the quality of samples for subsequent RNA sequencing.
mRNA was extracted from each sample and underwent quality control (QC). Qualified samples proceeded to library construction. The sequencing library was prepared by random fragmentation of the DNA or cDNA sample, followed by 5’ and 3’ adapter ligation. Alternatively, “tagmentation” combines the fragmentation and ligation reactions into a single step increasing the efficiency of the library preparation process. Adapter-ligated fragments are then PCR amplified and gel purified. For cluster generation, the library was loaded into a flow cell where fragments were captured on a lawn of surface-bound oligos complementary to the library adapters. Each fragment is then amplified into distinct, clonal clusters through bridge amplification. When cluster generation is complete, the templates are processed for sequencing. We utilized Illumina SBS technology allowing for a reversible terminator-based method that detects single bases as they are incorporated into DNA template strands. As all 4 reversible, terminator-bound dNTPs are present during each sequencing cycle, natural competition minimizes incorporation bias and greatly reduces raw error rates. The result was highly accurate base-by-base sequencing that virtually eliminates sequence-context-specific errors, even within repetitive sequence regions and homopolymers.

treatment_protocol: After fear conditioning mice received six intraperitoneal injections (i.p.) of 20% EtOH v/v with saline solution using a 26.5-gauge needle evenly spaced over 6 hours. The first injection was at an EtOH concentration of 1.8 g/kg, and the subsequent five injections were at a concentration of 1.2 g/kg. After each injection, mice were placed back in their housing and carefully monitored. Mice then underwhent fear extinction trials and the subsequent every other day drinking paradigm.

value: Nuclues Accumbens Core

value: Mixed

value: WT

value: Ethanol Exposure


title: Sample_21_BCR Memory B Cell Run4

description:
Library name: Sample_21_BCR
Run4


title: Nucleus Accumbens Core, Ethanol 2

description:
Library name: Sample5
NAcCore-EtOH-2


title: Nucleus Accumbens Core, Ethanol 1

description:
Library name: Sample4
NAcCore-EtOH-1


title: Sample_20_BCR Memory B Cell Run4

description:
Library name: Sample_20_BCR
Run4


title: Nucleus Accumbens Core, Control 3

description:
Library name: Sample3
NAcCore-Control-3


title: Peripheral whole blood DNA from fILD patient 165

description:
206139120101
206139120101_R05C01

value: UPitt

value: Always


title: Nucleus Accumbens Core, Control 2

description:
Library name: Sample2
NAcCore-Control-2


title: Sample_19_BCR Memory B Cell Run4

description:
Library name: Sample_19_BCR
Run4


title: Nucleus Accumbens Core, Control 1

description:
Library name: Sample1
NAcCore-Control-1


title: Peripheral whole blood DNA from fILD patient 164

description:
206139120101
206139120101_R04C01

value: Former

value: IPF


title: Peripheral whole blood DNA from fILD patient 163

description:
206139120101
206139120101_R03C01

value: Unknown

value: CTD-ILD

value: Whole blood DNA


title: BMDM cells Olfml3 knockout  LPS 3

city: Shanghai

first: Qijun

last: Yu

state: Shanghai

address: 227 South Chongqing Road

institute: Shanghai Jiaotong University School of Medicine

description: Library name: KL3

data_processing:
The sequencing was performed in a 2×150 paired-end (PE) configuration, following the manufacturer's guidelines.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: BMDM

growth_protocol: RAW264.7 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C. BMDMs were maintained in IMDM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol (Thermofisher). 1 ug of total RNA was used for the construction of sequencing libraries.
Libraries with distinct indices were multiplexed and loaded onto an Illumina HiSeq, Illumina Novaseq, or MGI2000 for sequencing.

treatment_protocol: 100 ng/mL LPS was added to cells for 4h before havest

value: BMDM

value: Primary murine bone marrow derived macrophages

value: Olfml3 knockout

value: LPS


title: Sample_17_BCR Memory B Cell Run4

description:
Library name: Sample_17_BCR
Run4

value: pbmc

value: Memory B Cell

value: H2 Influenza Vaccination

value: BCR


title: BMDM cells Olfml3 knockout  LPS 2

description: Library name: KL2


title: Peripheral whole blood DNA from fILD patient 162

description:
206139120101
206139120101_R02C01

value: F

value: HP


title: Sample_16_BCR Memory B Cell Run3

description:
Library name: Sample_16_BCR
Run3


title: BMDM cells LPS 1

description: Library name: WL1


title: Sample_18_BCR Memory B Cell Run4

description:
Library name: Sample_18_BCR
Run4


title: BMDM cells LPS 3

description: Library name: WL3


title: BMDM cells Olfml3 knockout 3

description: Library name: KO3

value: WT

value: PBS


title: BMDM cells LPS 2

description: Library name: WL2


title: Peripheral whole blood DNA from fILD patient 161

description:
206139120101
206139120101_R01C01

value: UPitt

value: M

value: Former


title: Sample_15_BCR Plasmablast Run3

description:
Library name: Sample_15_BCR
Run3

value: Plasmablast


title: Peripheral whole blood DNA from fILD patient 160

description:
206144080156
206144080156_R08C01

value: IPF

value: Whole blood DNA


title: BMDM cells Olfml3 knockout 2

description: Library name: KO2

value: BMDM

value: Primary murine bone marrow derived macrophages


title: Sample_14_BCR Memory B Cell Run3

description:
Library name: Sample_14_BCR
Run3


title: Peripheral whole blood DNA from fILD patient 158

description:
206144080156
206144080156_R06C01

value: Unknown

value: CTD-ILD


title: Sample_13_BCR Plasmablast Run3

description:
Library name: Sample_13_BCR
Run3

value: pbmc


title: Peripheral whole blood DNA from fILD patient 159

description:
206144080156
206144080156_R07C01


title: BMDM cells control 3

description: Library name: WT3


title: BMDM cells control 1

description: Library name: WT1


title: BMDM cells Olfml3 knockout 1

description: Library name: KO1


title: Sample_12_BCR Memory B Cell Run3

description:
Library name: Sample_12_BCR
Run3

value: Memory B Cell

value: H2 Influenza Vaccination


title: RAW264.7 cells Olfml3 knockout  LPS 3

description: Library name: OL3

value: Murine mononuclear macrophage leukemia cells

value: Olfml3 knockout

value: LPS


title: Sample_11_BCR Memory B Cell Run3

description:
Library name: Sample_11_BCR
Run3

value: BCR


title: Peripheral whole blood DNA from fILD patient 157

description:
206144080156
206144080156_R05C01

value: UPitt

value: F


title: Peripheral whole blood DNA from fILD patient 156

description:
206144080156
206144080156_R04C01

value: M


title: RAW264.7 cells Olfml3 knockout  LPS 1

description: Library name: OL1


title: BMDM cells Olfml3 knockout  LPS 1

description: Library name: KL1


title: Sample_10_BCR Plasmablast Run3

description:
Library name: Sample_10_BCR
Run3

value: Plasmablast


title: RAW264.7 cells LPS 3

description: Library name: dL3


title: RAW264.7 cells LPS 1

description: Library name: dL1


title: Sample_9_BCR Memory B Cell Run3

description:
Library name: Sample_9_BCR
Run3


title: RAW264.7 cells Olfml3 knockout 3

description: Library name: O3

value: WT

value: PBS


title: RAW264.7 cells LPS 2

description: Library name: dL2


title: Peripheral whole blood DNA from fILD patient 154

description:
206144080156
206144080156_R02C01

value: Former

value: IPF

value: Whole blood DNA


title: Peripheral whole blood DNA from fILD patient 155

description:
206144080156
206144080156_R03C01

value: Unknown

value: CTD-ILD


title: Sample_8_BCR Memory B Cell Run3

description:
Library name: Sample_8_BCR
Run3

value: pbmc

value: Memory B Cell


title: RAW264.7 cells control 3

description: Library name: d3

value: Murine mononuclear macrophage leukemia cells


title: RAW264.7 cells Olfml3 knockout 2

description: Library name: O2


title: RAW264.7 cells control 2

description: Library name: d2


title: BMDM cells control 2

description: Library name: WT2

value: BMDM

value: Primary murine bone marrow derived macrophages


title: Sample_6_BCR Memory B Cell Run3

description:
Library name: Sample_6_BCR
Run3

value: H2 Influenza Vaccination

value: BCR


title: Peripheral whole blood DNA from fILD patient 152

description:
206144080095
206144080095_R08C01

value: UPitt


title: RAW264.7 cells Olfml3 knockout  LPS 2

description: Library name: OL2

value: Olfml3 knockout

value: LPS


title: Sample_5_BCR Plasmablast Run3

description:
Library name: Sample_5_BCR
Run3

value: Plasmablast


title: CnB1KO_SD6 biol rep4

city: Beijing

first: Rui

last: Zhou

address: NIBS

institute: NIBS

data_processing:
High quality of the raw fastq files was assessed and confirmed with FastQC (v0.12.1).
Adapter sequences and low-quality reads were removed using Trim Galore (v0.6.10), rRNA contamination was eliminated with SortMeRNA (v4.3.6), and duplicate reads were removed by Picard (v2.18.29).
Gene expression quantification was performed with StringTie (v2.2.1), which calculated Fragments Per Kilobase of transcript per Million mapped reads (FPKM) and Transcripts Per Million (TPM).
SAM and BAM formatted data were managed with Samtools (v1.6).
HTSeq (v2.0.4) was used for final read count determination.
Low-quality samples were detected by calculating pairwise Pearson correlation coefficients of gene expression between replicates. For instance, replicate 1 of LC samples from SD6 ABC-CnB1KO mice was removed as outliers.
Assembly: GRCm38
Supplementary files format and content: CSV file include raw counts values for each sample.
Supplementary files format and content: CSV files include FPKM and TPM values for each sample.

molecule: polyA RNA

source_name: locus coeruleus

extract_protocol:
For RNA-seq analysis, mouse brains were quickly dissected from normal slept (S6) or 6-h sleep-deprived (SD6) ABC-Ctrl (WT) and ABC-CnB1KO (KO) mice, rinsed with PBS, and flash frozen in liquid nitrogen (4 weeks after AAV-hSyn-Cre injection). After equilibration at -20 °C, mouse brains were sectioned at 200 μm on a cryostat microtome (Leica) under the protection of tissue OCT-Freeze medium. Locus coeruleus (LC) was further dissected from related slices and frozen in liquid nitrogen. Total RNA was isolated from LC (four to five biological replicates per group) using Trizol (ambion, 15596018) and precipitated by isopropanol added Sodium Acetate and Dr.GenTLE™ Precipitation Carrier (9094, Takara).
Briefly, poly(A) mRNA was isolated from total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490L, NEB). First-strand cDNA was synthesized with the SuperScript II Reverse Transcriptase (18064014, Invitrogen), and second-strand cDNA was synthesized using Second Strand cDNA Synthesis Kit (A48570, Invitrogen). Libraries were constructed with the NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645L, NEB).
Libraries were sequenced on Illumina HiSeq2500.

value: locus coeruleus


title: CnB1KO_SD6 biol rep3


title: CnB1KO_SD6 biol rep2


title: Peripheral whole blood DNA from fILD patient 149

description:
206144080095
206144080095_R05C01

value: F

value: Former


title: CnB1KO_SD6 biol rep5


title: Sample_4_BCR Memory B Cell Run3

description:
Library name: Sample_4_BCR
Run3


title: CnB1KO_SD6 biol rep1


title: CnB1KO_S6 biol rep5


title: Peripheral whole blood DNA from fILD patient 148

description:
206144080095
206144080095_R04C01

value: Whole blood DNA


title: CnB1KO_S6 biol rep3


title: Peripheral whole blood DNA from fILD patient 153

description:
206144080156
206144080156_R01C01

value: Unknown


title: RAW264.7 cells Olfml3 knockout 1

description: Library name: O1

value: WT

value: PBS


title: CnB1KO_S6 biol rep2


title: Sample_2_BCR Plasmablast Run2

description:
Library name: Sample_2_BCR
Run2

value: pbmc


title: Sample_3_BCR Plasmablast Run3

description:
Library name: Sample_3_BCR
Run3


title: Sample_7_BCR Plasmablast Run3

description:
Library name: Sample_7_BCR
Run3


title: Peripheral whole blood DNA from fILD patient 147

description:
206144080095
206144080095_R03C01

value: M

value: CTD-ILD


title: CnB1KO_S6 biol rep4


title: Sample_1_BCR Memory B Cell Run2

description:
Library name: Sample_1_BCR
Run2

value: Memory B Cell


title: RAW264.7 cells control 1

description: Library name: d1

value: Murine mononuclear macrophage leukemia cells


title: Peripheral whole blood DNA from fILD patient 151

description:
206144080095
206144080095_R07C01

value: Never

value: IPF


title: WT_SD6 biol rep4


title: HPAF-II, JPI-547, 72 h, rep3

city: Seoul

first: Kyoung-Seok

address: 101 Daehak-ro, Jongno-gu

institute: Seoul National University Cancer Research Institute

description: HPAF-II JPI #3

data_processing:
Raw sequence reads underwent meticulous trimming with Trimmomatic 0.38 and subsequent alignment to the Homo sapiens reference genome (GRCh38) employing HISAT v2.1.0.
The assembled transcripts and read counts per gene were generated using StringTie v2.1.3b.
Differentially expressed genes (DEGs) were identified using DESeq2, considering a | fold change | ≥ 1.5 and raw p < 0.05 as significant criteria.
Assembly: GRCh38
Supplementary files format and content: xlsx file includes raw counts, FPKM, TPM values for each sample.

source_name: Pancreas

extract_protocol:
Total RNA was isolated using the TRIzol method, and RNA integrity was assessed using Agilent's TapeStation RNA screentape (Agilent, #5067-5576).
Only samples with a RNA Integrity Number (RIN) exceeding 7.0 were deemed suitable for RNA library construction. RNA-seq libraries were meticulously crafted utilizing the TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc., San Diego, CA, USA, #RS-122-2101). These libraries underwent quantification via KAPA Library Quantification kits and quality assessment using a TapeStation D1000 ScreenTape (Agilent Technologies, #5067-5582).

value: Pancreas

value: HPAF-II

value: human pancreatic ductal adenocarcinoma

value: JPI-547 1µM


title: Peripheral whole blood DNA from fILD patient 150

description:
206144080095
206144080095_R06C01

value: UPitt

value: F


title: Peripheral whole blood DNA from fILD patient 145

description:
206144080095
206144080095_R01C01

value: Former

value: Whole blood DNA


title: WT_SD6 biol rep2

value: locus coeruleus

value: WT


title: WT_SD6 biol rep1


title: HPAF-II, JPI-547, 72 h, rep2

description: HPAF-II JPI #2


title: Peripheral whole blood DNA from fILD patient 144

description:
206144080150
206144080150_R08C01

value: Unknown


title: WT_S6 biol rep4


title: HPAF-II, JPI-547, 72 h, rep1

description: HPAF-II JPI #1


title: WT_S6 biol rep3


title: Peripheral whole blood DNA from fILD patient 143

description:
206144080150
206144080150_R07C01


title: WT_S6 biol rep2


title: HPAF-II, olaparib, 72 h, rep3

description: HPAF-II ola #3

value: Olaparib 1µM


title: cell, (A/R) platelet treated, 24h, rep 3

city: hangzhou

first: Zhaoming

last: Ye

address: 88 jiefang road

institute: The Second Affiliated Hospital, Zhejiang University School of Medicine

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: excel file include FPKM and count values for each Sample

source_name: cell line

growth_protocol: K7M2 osteosarcoma cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini 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.

treatment_protocol: K7M2 osteosarcoma cells were treated with mouse platelets for 24h

value: cell line

value: mouse oseosarcoma cell line

value: treated with mouse (A/R)platelet for 29h


title: CnB1KO_S6 biol rep1


title: Peripheral whole blood DNA from fILD patient 142

description:
206144080150
206144080150_R06C01

value: M

value: CTD-ILD


title: Peripheral whole blood DNA from fILD patient 141

description:
206144080150
206144080150_R05C01


title: HPAF-II, olaparib, 72 h, rep2

description: HPAF-II ola #2

value: Pancreas


title: WT_S6 biol rep1


title: WT_SD6 biol rep5


title: HPAF-II, olaparib, 72 h, rep1

description: HPAF-II ola #1

value: HPAF-II


title: cell, (A/R) platelet treated, 24h, rep 2

value: treated with mouse (A/R)platelet for 28h


title: cell, (A/R) platelet treated, 24h, rep 1

value: treated with mouse (A/R)platelet for 27h


title: Peripheral whole blood DNA from fILD patient 146

description:
206144080095
206144080095_R02C01

value: UPitt

value: IPF


title: Peripheral whole blood DNA from fILD patient 140

description:
206144080150
206144080150_R04C01


title: cell, platelet treated, 24h, rep 1

value: treated with mouse platelet for 24h


title: cell, platelet treated, 24h, rep 2

value: treated with mouse platelet for 25h


title: WT_SD6 biol rep3

value: locus coeruleus


title: HPAF-II, control, rep3

description: HPAF-II cont #3

value: human pancreatic ductal adenocarcinoma

value: untreated


title: Peripheral whole blood DNA from fILD patient 139

description:
206144080150
206144080150_R03C01

value: F

value: Unknown

value: HP

value: Whole blood DNA


title: cell, untreated, 24h, rep 3

value: cell line

value: mouse oseosarcoma cell line

value: WT


title: HPAF-II, control, rep2

description: HPAF-II cont #2

value: Pancreas

value: HPAF-II


title: cell, untreated, 24h, rep 1


title: cell, untreated, 24h, rep 2


title: Peripheral whole blood DNA from fILD patient 138

description:
206144080150
206144080150_R02C01

value: Never


title: HPAF-II, control, rep1

description: HPAF-II cont #1


title: cell, platelet treated, 24h, rep 3

value: treated with mouse platelet for 26h


title: Peripheral whole blood DNA from fILD patient 137

description:
206144080150
206144080150_R01C01

value: UPitt

value: CTD-ILD


title: Peripheral whole blood DNA from fILD patient 136

description:
206144080033
206144080033_R08C01

value: M

value: Former

value: IPF


title: Peripheral whole blood DNA from fILD patient 135

description:
206144080033
206144080033_R07C01


title: Capan-1, JPI-547, 72 h, rep2

description: Capan-1 JPI #2

value: human pancreatic ductal adenocarcinoma

value: JPI-547 1µM


title: Capan-1, olaparib, 72 h, rep3

description: Capan-1 ola #3

value: Olaparib 1µM


title: Peripheral whole blood DNA from fILD patient 134

description:
206144080033
206144080033_R06C01

value: F


title: Capan-1, JPI-547, 72 h, rep1

description: Capan-1 JPI #1


title: M5_Bet

city: Munich

first: Hans

middle: Carlo

last: Maurer

state: Bavaria

address: Ismaninger Str. 22

department: II. Medizinische Klinik

country: Germany

institute: Klinikum rechts der Isar

description:
Library name: Sample 10
R1 fastq file: cDNA; R2 fastq file: barcode/UMI

data_processing:
Dropseq (v1.0) – see Macosko et al., PMID: 26000488.
Assembly: Human GRCh38
Supplementary files format and content: Tab-delimited files contains raw counts for each sample

source_name: colonic organoids

growth_protocol: Minced intestinal, colonic tissue biopsies were digested in 2 mM EDTA in DPBS on ice for 20 min. Next, suspension was flushed with cold 10% (v/v) FBS in PBS and was filtered using a 100 µm cell strainer. Crypt suspensions were pelleted and resuspended in Corning Matrigel Growth Factor Reduced Basement Membrane Matrix. Droplets of 50 µl were plated on 24-well plates (Corning), overlayed with L-WRN medium and incubated at 37 °C, 5% CO2 for 7 days with medium exchange every 2-3 days.

extract_protocol:
Qiagen RNAeasy Mini Kit according to the manufacturer’s instructions.
cDNA was generated with Maxima RT polymerase (Thermo Fisher) and amplified with Terra PCR Direct Polymerase (Takara). Library preparation was carried out with NEBNext® Ultra™ II FS DNA Library Prep Kit (NEB)

treatment_protocol: Established organoid lines (passage 3 or more) were passaged and incubated with standard L-WRN medium overnight. Medium was exchanged with fresh medium supplemented with Bethanechol (250 nM). Medium was replenished daily with fresh Bch-containing medium for 4 days.

value: colonic organoids

tag: gender

value: male

value: bethanechol

tag: biological replicate


title: M7_Con

description:
Library name: Sample 13
R1 fastq file: cDNA; R2 fastq file: barcode/UMI

value: untreated


title: M8_Bet

description:
Library name: Sample 16
R1 fastq file: cDNA; R2 fastq file: barcode/UMI


title: M4_Bet

description:
Library name: Sample 8
R1 fastq file: cDNA; R2 fastq file: barcode/UMI

value: female


title: Peripheral whole blood DNA from fILD patient 133

description:
206144080033
206144080033_R05C01

value: Whole blood DNA


title: M7_Bet

description:
Library name: Sample 14
R1 fastq file: cDNA; R2 fastq file: barcode/UMI


title: M6_Bet

description:
Library name: Sample 12
R1 fastq file: cDNA; R2 fastq file: barcode/UMI


title: Peripheral whole blood DNA from fILD patient 132

description:
206144080033
206144080033_R04C01

value: Never


title: Capan-1, olaparib, 72 h, rep2

description: Capan-1 ola #2

value: Pancreas


title: M4_Con

description:
Library name: Sample 7
R1 fastq file: cDNA; R2 fastq file: barcode/UMI


title: Capan-1, olaparib, 72 h, rep1

description: Capan-1 ola #1


title: M3_Bet

description:
Library name: Sample 6
R1 fastq file: cDNA; R2 fastq file: barcode/UMI


title: M2_Bet

description:
Library name: Sample 4
R1 fastq file: cDNA; R2 fastq file: barcode/UMI


title: Peripheral whole blood DNA from fILD patient 131

description:
206144080033
206144080033_R03C01

value: UPitt


title: M2_Con

description:
Library name: Sample 3
R1 fastq file: cDNA; R2 fastq file: barcode/UMI


title: M8_Con

description:
Library name: Sample 15
R1 fastq file: cDNA; R2 fastq file: barcode/UMI


title: Capan-1, JPI-547, 72 h, rep3

description: Capan-1 JPI #3


title: M6_Con

description:
Library name: Sample 11
R1 fastq file: cDNA; R2 fastq file: barcode/UMI


title: Peripheral whole blood DNA from fILD patient 130

description:
206144080033
206144080033_R02C01


title: M1_Con

description:
Library name: Sample 1
R1 fastq file: cDNA; R2 fastq file: barcode/UMI


title: M5_Con

description:
Library name: Sample 9
R1 fastq file: cDNA; R2 fastq file: barcode/UMI


title: Capan-1, control, rep2

description: Capan-1 cont #2


title: Peripheral whole blood DNA from fILD patient 129

description:
206144080033
206144080033_R01C01


title: Capan-1, control, rep1

description: Capan-1 cont #1


title: Peripheral whole blood DNA from fILD patient 128

description:
206139130084
206139130084_R08C01

value: Unknown

value: CTD-ILD


title: Peripheral whole blood DNA from fILD patient 127

description:
206139130084
206139130084_R07C01

value: M

value: Former


title: Peripheral whole blood DNA from fILD patient 126

description:
206139130084
206139130084_R06C01

value: IPF


title: M3_Con

description:
Library name: Sample 5
R1 fastq file: cDNA; R2 fastq file: barcode/UMI


title: HL-60 cells, OE-CFim25, 6h, replicate 3

city: Boston

first: Srimoyee

last: Mukherjee

state: MA

address: 150 Harrison Ave., Jaharis Bldg., Room #401A

department: Department of Developmental, Molecular & Chemical Biology

institute: Tufts University

data_processing:
The reverse read (read 2) of QuantSeq FWD was used for APA analysis. Briefly, adapter and poly(T) regions were trimmed and trimmed reads were aligned by using STAR-2.7.7a to human genome sequence (hg19).
Only the alignments to PAS regions annotated by the PolyA_DB v3 database (-100 to +25 nt around each PAS) were kept. The last aligned position (LAP) of each mapped read was compared to PolyA_DB-annotated-PASs, allowing ± 24 nt flexibility.
Matched reads were considered PAS-supporting (PASS) reads, which were used for further APA analysis. The abundance of transcripts associated with a given PAS was based on the number of PASS reads normalized to the total number of PASS reads per sample, yielding a reads per million (RPM) value.
Assembly: hg19
Supplementary files format and content: Excel file containing sample information for mapping statistics
Supplementary files format and content: Excel file containing RED values indicating APA shortening or lengthening

source_name: Blood

growth_protocol: Cells were maintained in RPMI 1640 medium supplemented with 2 mM L-glutamine and 10% heat-inactivated fetal bovine serum (FBS) at 37°C in a humidified atmosphere of 5% CO2. Cells were cultured in 6-well plates at a density of 1×106 cells/well.

extract_protocol:
By trizol as per manufacturer's protocol
Library preparation of total RNA was carried out by using the Lexogen 3′ mRNA-Seq QuantSeq FWD or QuantSeq-Pool kit according to manufacturer’s instructions. Library preparation, quality control, and sequencing were carried out by Admera Health (South Plainfield, NJ, USA). cDNA libraries were sequenced on an Illumina HiSeq machine (2 × 150 nt) at Admera Health.
3' end RNA QuantSeq

treatment_protocol: Differentiation of the HL-60 human monocytic cell-lines transfected with OE-control and OE-CFIm25 was performed by treatment with 3 nM phorbol-12-myristate-13-acetate (PMA; Sigma-Aldrich) for 6h.

value: Blood

value: Promyeloblast

value: Macrophage differentiation by PMA


title: Peripheral whole blood DNA from fILD patient 125

description:
206139130084
206139130084_R05C01


title: Capan-1, control, rep3

description: Capan-1 cont #3

value: human pancreatic ductal adenocarcinoma


title: HL-60 cells, OE-CFim25, 6h, replicate 2


title: 611990_inf_P4_ROI-003_Ciliated_S3

city: Kansas City

first: Andrew

last: Godwin

state: Kansas

address: 3901 Rainbow Blvd

department: Pathology

institute: Kansas University Medical Center

description: Library name: DSP-1001660037560-B-H11

data_processing:
FASTQ files downloaded from the NextSeq are converted into the DCC file format using the GeoMxNGSPipeline (version-2.3.3.10).
Initial quality control and data analyses were performed using the GeoMxWorkflows, NanoStringNCTools, and GeoMxTools packages provided on Bioconductor, following the vignette “Analyzing GeoMx-NGS RNA Expression Data with GeoMxTools” provided by NanoString.
Assembly: GRCh38.p13
Supplementary files format and content: .dcc: probe count data
Supplementary files format and content: .pkc: probe metadata linking probe barcodes with target genes IDs
Supplementary files format and content: .xlsx: annotation file containing segment annotation info
Library strategy: Spatial Transcriptomics

extract_protocol:
Formalin-fixed paraffin-embedded (FFPE) slides were prepared following the “RNA Slide Preparation Protocol” in MAN-10150 in the Manual Slide Preparation User Manual, available from NanoString. The RNA probe hybridization solution was prepared using the GeoMx® Cancer Transcriptome Atlas (CTA) RNA probe mix (NanoString), following the recommended dilution (10% probe mix + 10% DEPC water + 80% Buffer R).
Library prep was performed according to instructions provided in NanoString’s NGS Readout Library Prep User Manual (MAN-10117-05), followed by paired-end (27 x 27 cycles) sequencing on the Illumina NextSeq 550 sequencer using a high-output flow cell.

tag: region

value: Infundibulum

tag: patient

tag: roi

tag: segment

value: Ciliated

tag: area


title: 611990_inf_P4_ROI-002_Secretory_S3

description: Library name: DSP-1001660037560-B-H10

value: Secretory


title: 611990_inf_P4_ROI-001_Secretory_S3

description: Library name: DSP-1001660037560-B-H08


title: 611990_isth_P4_ROI-002_Secretory_S4

description: Library name: DSP-1001660037560-B-H06

value: Isthmus


title: 611990_inf_P4_ROI-001_Ciliated_S3

description: Library name: DSP-1001660037560-B-H07


title: M1_Bet

description:
Library name: Sample 2
R1 fastq file: cDNA; R2 fastq file: barcode/UMI

value: colonic organoids

value: female

value: bethanechol


title: 611990_isth_P4_ROI-001_Secretory_S4

description: Library name: DSP-1001660037560-B-H04


title: 611990_isth_P4_ROI-002_Ciliated_S4

description: Library name: DSP-1001660037560-B-H05


title: 611990_inf_P4_ROI-002_Ciliated_S3

description: Library name: DSP-1001660037560-B-H09


title: HL-60 cells, OE-CFim25, 6h, replicate 1

tag: cell line


title: Peripheral whole blood DNA from fILD patient 124

description:
206139130084
206139130084_R04C01

value: UPitt

value: Whole blood DNA


title: 612198_fim_P7_ROI-003_Secretory_S2

description: Library name: DSP-1001660037560-B-H02

value: Fimbria


title: 611990_inf_P4_ROI-003_Secretory_S3

description: Library name: DSP-1001660037560-B-H12


title: Peripheral whole blood DNA from fILD patient 123

description:
206139130084
206139130084_R03C01

value: M


title: 612198_fim_P7_ROI-003_Ciliated_S2

description: Library name: DSP-1001660037560-B-H01


title: HL-60 cells, OE-control, 6h, replicate 2

tag: cell type

value: OE-control


title: 612198_fim_P7_ROI-002_Ciliated_S2

description: Library name: DSP-1001660037560-B-G11


title: HL-60 cells, OE-control, 6h, replicate 1

tag: genotype


title: 612198_fim_P7_ROI-002_Secretory_S2

description: Library name: DSP-1001660037560-B-G12


title: Peripheral whole blood DNA from fILD patient 122

description:
206139130084
206139130084_R02C01

value: F

value: Former

value: IPF

tag: treatment


title: 612198_fim_P7_ROI-001_Secretory_S2

description: Library name: DSP-1001660037560-B-G10


title: 612198_fim_P7_ROI-001_Ciliated_S2

description: Library name: DSP-1001660037560-B-G09


title: HL-60 cells, OE-control, 6h, replicate 3

value: Blood

value: Promyeloblast

value: Macrophage differentiation by PMA


title: Peripheral whole blood DNA from fILD patient 121

description:
206139130084
206139130084_R01C01

tag: cohort


title: 611990_isth_P4_ROI-001_Ciliated_S4

description: Library name: DSP-1001660037560-B-H03

value: Ciliated


title: 612198_inf_P7_ROI-003_Secretory_S2

description: Library name: DSP-1001660037560-B-G08

value: Infundibulum

value: Secretory


title: Trial 9 CTRL R24

city: Liege

first: Ira

middle: Mercedes

last: ESPUNY CAMACHO

state: Liege

address: Avenue de l'Hôpital,11

department: Département des sciences biomédicales et précliniques

country: Belgium

institute: Uliege

data_processing:
Raw reads were processed through nf-core RNAseq pipeline (version 3.0)
Assembly: GRCh38
Supplementary files format and content: tab delimited file, containind the gene ID from ENSEMBL, the gene name, base mean and raw counts for each sample

source_name: Brain organoids

growth_protocol: Cell are differentiated into neuronal fate by WNt and TGFB inhibitors in DMEM F12 and KO 20% serum for 2 weeks and then cultured in a medium suitable for neuron growth and survival (DMEM F12, Neurobasal and B27). Aggregates of cells were formed in 96 U bottom plates for 2 weeks

extract_protocol:
RNA was extracted using the RNeasy mini kit (Qiagen ref: 74104)
Library were generated the polyA RNA-seq libraries using Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus following the manufacturer protocol (Illumina ref: 20040529)

treatment_protocol: Brain organoids were infected by SARS-CoV2 MOI 0.5 for 3h and collected 72h post infection

value: Brain organoids

value: hESC-H9 cell line (WA09)

value: hESC

value: WT

value: CTRL


title: Peripheral whole blood DNA from fILD patient 118

description:
206144080009
206144080009_R06C01

value: UPitt

tag: Sex

value: Whole blood DNA


title: Peripheral whole blood DNA from fILD patient 119

description:
206144080009
206144080009_R07C01

tag: smokehx


title: Trial 9 CTRL R23

tag: tissue


title: 612198_inf_P7_ROI-001_Secretory_S2

description: Library name: DSP-1001660037560-B-G04


title: Trial 9 72h R25

value: SARS COV2 infection


title: 612198_inf_P7_ROI-002_Ciliated_S2

description: Library name: DSP-1001660037560-B-G05


title: 612198_inf_P7_ROI-003_Ciliated_S2

description: Library name: DSP-1001660037560-B-G07


title: Peripheral whole blood DNA from fILD patient 120

description:
206144080009
206144080009_R08C01

value: M


title: 612198_inf_P7_ROI-002_Secretory_S2

description: Library name: DSP-1001660037560-B-G06


title: Trial 9 72h R26


title: Trial 7 CTRL R16


title: 612198_inf_P7_ROI-001_Ciliated_S2

description: Library name: DSP-1001660037560-B-G03


title: 612198_amp_P7_ROI-002_Secretory_S3

description: Library name: DSP-1001660037560-B-F12

value: Ampulla


title: 612198_amp_P7_ROI-004_Secretory_S3

description: Library name: DSP-1001660037560-B-G02


title: Peripheral whole blood DNA from fILD patient 117

description:
206144080009
206144080009_R05C01

value: Former

value: IPF


title: 612198_amp_P7_ROI-004_Ciliated_S3

description: Library name: DSP-1001660037560-B-G01


title: 612198_amp_P7_ROI-002_Ciliated_S3

description: Library name: DSP-1001660037560-B-F11


title: Trial 7 CTRL R15


title: Peripheral whole blood DNA from fILD patient 116

description:
206144080009
206144080009_R04C01

value: Never


title: 612198_amp_P7_ROI-001_Secretory_S3

description: Library name: DSP-1001660037560-B-F10


title: Trial 7 72h R18


title: 612198_amp_P7_ROI-001_Ciliated_S3

description: Library name: DSP-1001660037560-B-F09


title: Peripheral whole blood DNA from fILD patient 115

description:
206144080009
206144080009_R03C01

value: F

value: Unknown

value: CTD-ILD


title: 612198_isth_P7_ROI-002_Secretory_S2

description: Library name: DSP-1001660037560-B-F08

value: Isthmus

value: Secretory


title: 612198_isth_P7_ROI-002_Ciliated_S2

description: Library name: DSP-1001660037560-B-F07

value: Ciliated


title: Peripheral whole blood DNA from fILD patient 114

description:
206144080009
206144080009_R02C01


title: Trial 7 72h R17

value: Brain organoids

value: hESC-H9 cell line (WA09)

value: hESC


title: 612198_isth_P7_ROI-001_Secretory_S2

description: Library name: DSP-1001660037560-B-F06


title: 612198_isth_P7_ROI-001_Ciliated_S2

description: Library name: DSP-1001660037560-B-F05


title: BMMNCs,PRCA patient,relapse(P4)

first: Hu

last: Qi

state: Beijing

address: No.5 Yiheyuan Road,Haidian District

institute: Peking University

description: BD Rhapsody system

data_processing:
BD WTA Rhapsody Analysis Pipeline Version 1 were used for analysis. Raw data were processed using fastQ to filter adaptor sequences and remove low-quality reads.
Cell barcode whitelist was identified by UMI tools.The UMI-based clean data were mapped to human reference genome (Ensemble V.91) using the STAR algorithm.
UMI count matrices were generated for each sample, and imported into the Seurat R toolkit (V. 4.1.3).
Assembly: hg38
Supplementary files format and content: matrix files

source_name: Bone Marrow Mononuclear Cells

extract_protocol:
Bone marrow cells were diluted 1:1 in ice-cold phosphate-buffered saline (PBS). Mononuclear cell separation was performed using density centrifugation media (Ficoll-Paque; GE Healthcare Life Sciences) at a 1:1 ratio with diluted blood or marrow cells. After centrifugation (1200  g, 10 min), mononuclear cells were carefully aspirated to lyse red blood cells. Subsequently, mononuclear cells were either cryopreserved in CryoStor cell cryopreservation media CS10 (Sigma-Aldrich) in liquid nitrogen or immediately subjected to scRNA-Seq.
Whole transcriptome libraries were prepared according to the BD Rhapsody single-cell whole-transcriptome amplification workflow and sequenced using HiSeq Xten (Illumina, San Diego, California, USA) on 150 bp paired-end run

value: Bone Marrow Mononuclear Cells

tag: disease state

value: PRCA relapse


title: 611868_isth_P6_ROI-003_Secretory_S2

description: Library name: DSP-1001660037560-B-F04


title: Peripheral whole blood DNA from fILD patient 113

description:
206144080009
206144080009_R01C01

value: UPitt

value: Whole blood DNA


title: BMMNCs,healthy donor,rep2-4 merge

description: BD Rhapsody system

value: healthy donor


title: 611868_isth_P6_ROI-003_Ciliated_S2

description: Library name: DSP-1001660037560-B-F03


title: Peripheral whole blood DNA from fILD patient 111

description:
206139130079
206139130079_R07C01

value: M

value: UNCLASSIFIABLE


title: 611868_isth_P6_ROI-002_Secretory_S2

description: Library name: DSP-1001660037560-B-F02


title: 611868_isth_P6_ROI-002_Ciliated_S2

description: Library name: DSP-1001660037560-B-F01


title: BMMNCs,healthy donor,rep1

description: BD Rhapsody system


title: BMMNCs,PRCA patient ,partially recover(P3)

description: BD Rhapsody system

value: PRCA partially recover


title: erythroblast,PRCA, lenalidomide,rep2

data_processing:
The raw data of RNA-seq was first checked quality using FastQC.
Hisat2 was used to align the paired-end reads to hg19 version of human reference genome and estimate the reads counts with HTSeq.
Samtools was used to covert files format and generate index files.
Assembly: hg19
Supplementary files format and content: text files includes raw counts for each samples
Supplementary files format and content: text files includes TPM values for each samples

source_name: BMMNCs

extract_protocol:
After treatment with indicated drugs in erythroid differentiation medium for 6 days, erythroid progenitor cells were collected and sorted by fluorescence-activated cell sorting (FACS).
Sequencing libraries were prepared by Novogene, and 150 bp paired-end sequencing of each condition with two biological replicates was obtained in a HiSeq X-Ten (PE150, Illumina)

value: pure red cell aplasia (PRCA)

value: BMMNCs

value: erythroid differentiation for 6 days

value: lenalidomide

tag: developmental stage

value: CD71+ cells sorted by FACS


title: 611868_isth_P6_ROI-001_Secretory_S2

description: Library name: DSP-1001660037560-B-E12

value: Isthmus

value: Secretory


title: 611868_isth_P6_ROI-001_Ciliated_S2

description: Library name: DSP-1001660037560-B-E11

value: Ciliated


title: Peripheral whole blood DNA from fILD patient 109

description:
206139130079
206139130079_R05C01

value: F

value: Unknown

value: CTD-ILD


title: 611868_fim_P6_ROI-002_Secretory_S2

description: Library name: DSP-1001660037560-B-E08

value: Fimbria


title: 611868_fim_P6_ROI-003_Secretory_S2

description: Library name: DSP-1001660037560-B-E10


title: 611868_fim_P6_ROI-001_Secretory_S2

description: Library name: DSP-1001660037560-B-E06


title: 611868_fim_P6_ROI-003_Ciliated_S2

description: Library name: DSP-1001660037560-B-E09


title: Peripheral whole blood DNA from fILD patient 108

description:
206139130079
206139130079_R04C01

value: UPitt

value: Former

value: IPF

value: Whole blood DNA


title: Peripheral whole blood DNA from fILD patient 110

description:
206139130079
206139130079_R06C01

value: M


title: erythroblast,PRCA ,lenalidomide,rep1

value: pure red cell aplasia (PRCA)


title: erythroblast,PRCA ,DMSO,rep2

value: BMMNCs

value: DMSO


title: 611868_fim_P6_ROI-002_Ciliated_S2

description: Library name: DSP-1001660037560-B-E07


title: 611868_amp_P6_ROI-003_Ciliated_S4

description: Library name: DSP-1001660037560-B-E03

value: Ampulla


title: Peripheral whole blood DNA from fILD patient 107

description:
206139130079
206139130079_R03C01

value: Never


title: erythroblast,PRCA,,DMSO,rep1

value: erythroid differentiation for 6 days

value: CD71+ cells sorted by FACS


title: 611868_amp_P6_ROI-003_Secretory_S4

description: Library name: DSP-1001660037560-B-E04

value: Secretory


title: 611868_amp_P6_ROI-002_Secretory_S4

description: Library name: DSP-1001660037560-B-E02


title: Peripheral whole blood DNA from fILD patient 112

description:
206139130079
206139130079_R08C01

value: F


title: Peripheral whole blood DNA from fILD patient 106

description:
206139130079
206139130079_R02C01


title: erythroblast,healthy donor, lenalidomide,rep2

value: healthy donor

value: lenalidomide


title: 611868_amp_P6_ROI-001_Secretory_S4

description: Library name: DSP-1001660037560-B-D12


title: 611868_amp_P6_ROI-001_Ciliated_S4

description: Library name: DSP-1001660037560-B-D11

value: Ciliated


title: 611868_amp_P6_ROI-002_Ciliated_S4

description: Library name: DSP-1001660037560-B-E01


title: 611868_inf_P6_ROI-002_Secretory_S4

description: Library name: DSP-1001660037560-B-D08

value: Infundibulum


title: 611868_inf_P6_ROI-003_Ciliated_S4

description: Library name: DSP-1001660037560-B-D09


title: erythroblast,healthy donor,lenalidomide,rep1


title: erythroblast,healthy donor,DMSO,rep2


title: Peripheral whole blood DNA from fILD patient 105

description:
206139130079
206139130079_R01C01

value: UPitt

value: Former


title: 611868_inf_P6_ROI-001_Secretory_S4

description: Library name: DSP-1001660037560-B-D06


title: Peripheral whole blood DNA from fILD patient 102

description:
206144080003
206144080003_R06C01

value: IPF

value: Whole blood DNA


title: Peripheral whole blood DNA from fILD patient 104

description:
206144080003
206144080003_R08C01

value: M


title: 611868_inf_P6_ROI-003_Secretory_S4

description: Library name: DSP-1001660037560-B-D10


title: 611868_inf_P6_ROI-002_Ciliated_S4

description: Library name: DSP-1001660037560-B-D07


title: 611868_fim_P6_ROI-001_Ciliated_S2

description: Library name: DSP-1001660037560-B-E05

value: Fimbria


title: Peripheral whole blood DNA from fILD patient 103

description:
206144080003
206144080003_R07C01


title: ow99

city: Yangzhou

first: Bo

last: Pan

state: Jiangsu

address: No.136, JiangYangZhongLu

department: Department of Pharmacy

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

value: schizophrenia


title: erythroblast,healthy donor,DMSO,rep1

value: BMMNCs

value: DMSO


title: 611868_inf_P6_ROI-001_Ciliated_S4

description: Library name: DSP-1001660037560-B-D05


title: Peripheral whole blood DNA from fILD patient 101

description:
206144080003
206144080003_R05C01

value: Never

value: UNCLASSIFIABLE


title: 612113_fim_P5_ROI-003_Secretory_S1

description: Library name: DSP-1001660037560-B-D04

value: Secretory


title: 612113_fim_P5_ROI-003_Ciliated_S1

description: Library name: DSP-1001660037560-B-D03


title: 612113_fim_P5_ROI-002_Secretory_S1

description: Library name: DSP-1001660037560-B-D02


title: Peripheral whole blood DNA from fILD patient 100

description:
206144080003
206144080003_R04C01


title: 612113_fim_P5_ROI-002_Ciliated_S1

description: Library name: DSP-1001660037560-B-D01


title: ow97


title: Peripheral whole blood DNA from fILD patient 99

description:
206144080003
206144080003_R03C01


title: ow96


title: 612113_fim_P5_ROI-001_Ciliated_S1

description: Library name: DSP-1001660037560-B-C11


title: 612113_fim_P5_ROI-001_Secretory_S1

description: Library name: DSP-1001660037560-B-C12


title: 612113_inf_P5_ROI-003_Secretory_S1

description: Library name: DSP-1001660037560-B-C10


title: Peripheral whole blood DNA from fILD patient 98

description:
206144080003
206144080003_R02C01


title: ow95


title: 612113_inf_P5_ROI-002_Secretory_S1

description: Library name: DSP-1001660037560-B-C08


title: Peripheral whole blood DNA from fILD patient 97

description:
206144080003
206144080003_R01C01


title: ow91


title: 612113_inf_P5_ROI-001_Secretory_S1

description: Library name: DSP-1001660037560-B-C06


title: 612113_inf_P5_ROI-002_Ciliated_S1

description: Library name: DSP-1001660037560-B-C07


title: 612113_inf_P5_ROI-003_Ciliated_S1

description: Library name: DSP-1001660037560-B-C09


title: 612113_amp_P5_ROI-003_Secretory_S1

description: Library name: DSP-1001660037560-B-C04

value: Ampulla


title: ow92


title: ow98


title: 612113_amp_P5_ROI-002_Secretory_S1

description: Library name: DSP-1001660037560-B-C02


title: ow90


title: 612113_inf_P5_ROI-001_Ciliated_S1

description: Library name: DSP-1001660037560-B-C05


title: Peripheral whole blood DNA from fILD patient 94

description:
206139120058
206139120058_R06C01

value: F


title: 612113_amp_P5_ROI-003_Ciliated_S1

description: Library name: DSP-1001660037560-B-C03

value: Ciliated


title: Peripheral whole blood DNA from fILD patient 93

description:
206139120058
206139120058_R05C01


title: Peripheral whole blood DNA from fILD patient 95

description:
206139120058
206139120058_R07C01


title: 612113_amp_P5_ROI-001_Ciliated_S1

description: Library name: DSP-1001660037560-B-B11


title: ow89


title: ow87


title: 612113_amp_P5_ROI-002_Ciliated_S1

description: Library name: DSP-1001660037560-B-C01


title: Peripheral whole blood DNA from fILD patient 92

description:
206139120058
206139120058_R04C01


title: 612113_amp_P5_ROI-001_Secretory_S1

description: Library name: DSP-1001660037560-B-B12


title: 612113_isth_P5_ROI-002_Secretory_S1

description: Library name: DSP-1001660037560-B-B08

value: Isthmus


title: ow86


title: Peripheral whole blood DNA from fILD patient 91

description:
206139120058
206139120058_R03C01

value: UPitt


title: 612113_isth_P5_ROI-002_Ciliated_S1

description: Library name: DSP-1001660037560-B-B07


title: Peripheral whole blood DNA from fILD patient 96

description:
206139120058
206139120058_R08C01


title: ow84


title: 612113_isth_P5_ROI-001_Secretory_S1

description: Library name: DSP-1001660037560-B-B06


title: Peripheral whole blood DNA from fILD patient 90

description:
206139120058
206139120058_R02C01


title: Peripheral whole blood DNA from fILD patient 89

description:
206139120058
206139120058_R01C01


title: 612113_isth_P5_ROI-001_Ciliated_S1

description: Library name: DSP-1001660037560-B-B05


title: ow83


title: Peripheral whole blood DNA from fILD patient 88

description:
206139120060
206139120060_R08C01

value: Former


title: 611990_amp_P4_ROI-003_Secretory_S1

description: Library name: DSP-1001660037560-B-B01


title: 611990_amp_P4_ROI-003_Ciliated_S1

description: Library name: DSP-1001660037560-B-A12


title: 611990_isth_P4_ROI-001_Secretory_S2

description: Library name: DSP-1001660037560-B-B02


title: ow8


title: 612113_isth_P5_ROI-003_Secretory_S1

description: Library name: DSP-1001660037560-B-B10


title: 611990_isth_P4_ROI-003_Secretory_S2

description: Library name: DSP-1001660037560-B-B04


title: Peripheral whole blood DNA from fILD patient 87

description:
206139120060
206139120060_R07C01

value: IPF


title: 611990_isth_P4_ROI-002_Secretory_S2

description: Library name: DSP-1001660037560-B-B03


title: ow78


title: Peripheral whole blood DNA from fILD patient 86

description:
206139120060
206139120060_R06C01

value: Whole blood DNA


title: 611990_amp_P4_ROI-002_Secretory_S1

description: Library name: DSP-1001660037560-B-A11


title: ow77


title: 611990_amp_P4_ROI-002_Ciliated_S1

description: Library name: DSP-1001660037560-B-A10


title: 611990_amp_P4_ROI-001_Secretory_S1

description: Library name: DSP-1001660037560-B-A09


title: 612113_isth_P5_ROI-003_Ciliated_S1

description: Library name: DSP-1001660037560-B-B09


title: Peripheral whole blood DNA from fILD patient 85

description:
206139120060
206139120060_R05C01

value: M


title: ow76


title: 611990_amp_P4_ROI-001_Ciliated_S1

description: Library name: DSP-1001660037560-B-A08


title: 611990_fim_P4_ROI-003_Ciliated_S4

description: Library name: DSP-1001660037560-B-A06

value: Fimbria


title: ow75

value: PBMC


title: 611990_fim_P4_ROI-002_Secretory_S4

description: Library name: DSP-1001660037560-B-A05


title: Peripheral whole blood DNA from fILD patient 84

description:
206139120060
206139120060_R04C01


title: 611990_fim_P4_ROI-002_Ciliated_S4

description: Library name: DSP-1001660037560-B-A04


title: ow74

value: schizophrenia


title: 611990_fim_P4_ROI-001_Secretory_S4

description: Library name: DSP-1001660037560-B-A03


title: Peripheral whole blood DNA from fILD patient 83

description:
206139120060
206139120060_R03C01


title: 1001660037560_NTC

description: Library name: DSP-1001660037560-B-A01


title: 611990_fim_P4_ROI-001_Ciliated_S4

description: Library name: DSP-1001660037560-B-A02


title: ow73


title: Peripheral whole blood DNA from fILD patient 82

description:
206139120060
206139120060_R02C01


title: ow72


title: 605855_fim_P1_ROI-003_Secretory_S5

description: Library name: DSP-1001660010839-A-B07


title: 605855_fim_P1_ROI-003_Ciliated_S5

description: Library name: DSP-1001660010839-A-B06


title: 605855_fim_P1_ROI-002_Secretory_S5

description: Library name: DSP-1001660010839-A-B05


title: 605855_fim_P1_ROI-002_Ciliated_S5

description: Library name: DSP-1001660010839-A-B04


title: Peripheral whole blood DNA from fILD patient 81

description:
206139120060
206139120060_R01C01


title: ow71


title: Peripheral whole blood DNA from fILD patient 80

description:
206139120098
206139120098_R08C01


title: Peripheral whole blood DNA from fILD patient 79

description:
206139120098
206139120098_R07C01


title: 605855_fim_P1_ROI-001_Ciliated_S5

description: Library name: DSP-1001660010839-A-B02


title: 605855_amp_P1_ROI-003_Secretory_S4

description: Library name: DSP-1001660010839-A-B01


title: ow70


title: 605855_fim_P1_ROI-001_Secretory_S5

description: Library name: DSP-1001660010839-A-B03


title: Peripheral whole blood DNA from fILD patient 78

description:
206139120098
206139120098_R06C01


title: 605855_amp_P1_ROI-003_Ciliated_S4

description: Library name: DSP-1001660010839-A-A12


title: ow69


title: 605855_amp_P1_ROI-002_Ciliated_S4

description: Library name: DSP-1001660010839-A-A10


title: Peripheral whole blood DNA from fILD patient 77

description:
206139120098
206139120098_R05C01


title: ow68


title: 605855_amp_P1_ROI-002_Secretory_S4

description: Library name: DSP-1001660010839-A-A11


title: 605855_amp_P1_ROI-001_Secretory_S4

description: Library name: DSP-1001660010839-A-A09


title: 605855_amp_P1_ROI-001_Ciliated_S4

description: Library name: DSP-1001660010839-A-A08


title: Peripheral whole blood DNA from fILD patient 76

description:
206139120098
206139120098_R04C01


title: 605855_inf_P1_ROI-003_Secretory_S5

description: Library name: DSP-1001660010839-A-A07

value: Infundibulum


title: ow67


title: Peripheral whole blood DNA from fILD patient 75

description:
206139120098
206139120098_R03C01


title: 605855_inf_P1_ROI-003_Ciliated_S5

description: Library name: DSP-1001660010839-A-A06


title: 605855_inf_P1_ROI-002_Ciliated_S5

description: Library name: DSP-1001660010839-A-A04


title: 605855_inf_P1_ROI-001_Secretory_S5

description: Library name: DSP-1001660010839-A-A03


title: Peripheral whole blood DNA from fILD patient 74

description:
206139120098
206139120098_R02C01


title: ow7


title: ow64


title: Peripheral whole blood DNA from fILD patient 73

description:
206139120098
206139120098_R01C01

value: Unknown


title: 1001660010839_NTC

description: Library name: DSP-1001660010839-A-A01


title: 605855_inf_P1_ROI-001_Ciliated_S5

description: Library name: DSP-1001660010839-A-A02


title: Peripheral whole blood DNA from fILD patient 72

description:
206139120135
206139120135_R08C01

value: Never


title: ow63


title: 605856_fim_P2_ROI-004_Secretory_S1

description: Library name: DSP-1001660010692-B-H12


title: 605856_fim_P2_ROI-004_Ciliated_S1

description: Library name: DSP-1001660010692-B-H11


title: Peripheral whole blood DNA from fILD patient 71

description:
206139120135
206139120135_R07C01


title: 605856_fim_P2_ROI-003_Ciliated_S1

description: Library name: DSP-1001660010692-B-H09


title: ow61


title: 605856_fim_P2_ROI-002_Secretory_S1

description: Library name: DSP-1001660010692-B-H08


title: ow66


title: 605856_fim_P2_ROI-002_Ciliated_S1

description: Library name: DSP-1001660010692-B-H07


title: ow60


title: Peripheral whole blood DNA from fILD patient 69

description:
206139120135
206139120135_R05C01


title: 605856_fim_P2_ROI-003_Secretory_S1

description: Library name: DSP-1001660010692-B-H10


title: 605856_inf_P2_ROI-004_Secretory_S5

description: Library name: DSP-1001660010692-B-H04


title: 605856_inf_P2_ROI-004_Ciliated_S5

description: Library name: DSP-1001660010692-B-H03


title: 605855_inf_P1_ROI-002_Secretory_S5

description: Library name: DSP-1001660010839-A-A05


title: 605856_inf_P2_ROI-003_Secretory_S5

description: Library name: DSP-1001660010692-B-H02


title: ow59


title: ow62


title: 605856_inf_P2_ROI-003_Ciliated_S5

description: Library name: DSP-1001660010692-B-H01


title: ow57


title: 605856_inf_P2_ROI-002_Ciliated_S5

description: Library name: DSP-1001660010692-B-G11


title: Peripheral whole blood DNA from fILD patient 65

description:
206139120135
206139120135_R01C01


title: 605856_inf_P2_ROI-002_Secretory_S5

description: Library name: DSP-1001660010692-B-G12


title: ow58


title: 605856_inf_P2_ROI-001_Secretory_S5

description: Library name: DSP-1001660010692-B-G10


title: 605856_amp_P2_ROI-004_Secretory_S5

description: Library name: DSP-1001660010692-B-G08


title: 605856_inf_P2_ROI-001_Ciliated_S5

description: Library name: DSP-1001660010692-B-G09


title: 605856_fim_P2_ROI-001_Ciliated_S1

description: Library name: DSP-1001660010692-B-H05


title: 605856_amp_P2_ROI-004_Ciliated_S5

description: Library name: DSP-1001660010692-B-G07


title: 605856_fim_P2_ROI-001_Secretory_S1

description: Library name: DSP-1001660010692-B-H06


title: ow54


title: ow6


title: Peripheral whole blood DNA from fILD patient 64

description:
206139120063
206139120063_R08C01


title: Peripheral whole blood DNA from fILD patient 63

description:
206139120063
206139120063_R07C01


title: 605856_amp_P2_ROI-003_Ciliated_S5

description: Library name: DSP-1001660010692-B-G05


title: Peripheral whole blood DNA from fILD patient 70

description:
206139120135
206139120135_R06C01


title: ow52


title: Peripheral whole blood DNA from fILD patient 68

description:
206139120135
206139120135_R04C01


title: Peripheral whole blood DNA from fILD patient 67

description:
206139120135
206139120135_R03C01


title: Peripheral whole blood DNA from fILD patient 66

description:
206139120135
206139120135_R02C01

value: UNCLASSIFIABLE


title: 605856_amp_P2_ROI-002_Ciliated_S5

description: Library name: DSP-1001660010692-B-G03


title: Peripheral whole blood DNA from fILD patient 62

description:
206139120063
206139120063_R06C01


title: ow51


title: Peripheral whole blood DNA from fILD patient 61

description:
206139120063
206139120063_R05C01


title: 605856_amp_P2_ROI-001_Secretory_S5

description: Library name: DSP-1001660010692-B-G02

value: Secretory


title: ow55


title: 605856_amp_P2_ROI-001_Ciliated_S5

description: Library name: DSP-1001660010692-B-G01

value: Ampulla


title: ow50


title: Peripheral whole blood DNA from fILD patient 60

description:
206139120063
206139120063_R04C01

value: F


title: ow5


title: 605856_isth_P2_ROI-004_Ciliated_S4

description: Library name: DSP-1001660010692-B-F11

value: Ciliated


title: Peripheral whole blood DNA from fILD patient 59

description:
206139120063
206139120063_R03C01


title: 605856_isth_P2_ROI-004_Secretory_S4

description: Library name: DSP-1001660010692-B-F12

value: Isthmus


title: 605856_isth_P2_ROI-003_Ciliated_S4

description: Library name: DSP-1001660010692-B-F09


title: 605856_isth_P2_ROI-003_Secretory_S4

description: Library name: DSP-1001660010692-B-F10


title: 605856_amp_P2_ROI-003_Secretory_S5

description: Library name: DSP-1001660010692-B-G06


title: ow48


title: 605856_isth_P2_ROI-001_Secretory_S4

description: Library name: DSP-1001660010692-B-F06


title: 605856_isth_P2_ROI-002_Secretory_S4

description: Library name: DSP-1001660010692-B-F08


title: 605856_amp_P2_ROI-002_Secretory_S5

description: Library name: DSP-1001660010692-B-G04


title: ow49


title: 605856_isth_P2_ROI-002_Ciliated_S4

description: Library name: DSP-1001660010692-B-F07


title: Peripheral whole blood DNA from fILD patient 56

description:
206139120114
206139120114_R08C01

value: UPitt


title: 605856_isth_P2_ROI-001_Ciliated_S4

description: Library name: DSP-1001660010692-B-F05


title: Peripheral whole blood DNA from fILD patient 58

description:
206139120063
206139120063_R02C01

value: Former


title: ow47


title: 605937_isth_P3_ROI-004_Secretory_S3

description: Library name: DSP-1001660010693-A-H08


title: 1001660010692_NTC

description: Library name: DSP-1001660010692-B-A01


title: ow46


title: 605937_isth_P3_ROI-004_Ciliated_S3

description: Library name: DSP-1001660010693-A-H07


title: 605937_isth_P3_ROI-003_Secretory_S3

description: Library name: DSP-1001660010693-A-H06


title: 605937_isth_P3_ROI-003_Ciliated_S3

description: Library name: DSP-1001660010693-A-H05


title: Peripheral whole blood DNA from fILD patient 54

description:
206139120114
206139120114_R06C01

value: IPF


title: 605937_isth_P3_ROI-002_Secretory_S3

description: Library name: DSP-1001660010693-A-H04


title: ow45


title: 605937_isth_P3_ROI-002_Ciliated_S3

description: Library name: DSP-1001660010693-A-H03


title: Peripheral whole blood DNA from fILD patient 53

description:
206139120114
206139120114_R05C01

value: Whole blood DNA


title: ow44


title: Peripheral whole blood DNA from fILD patient 57

description:
206139120063
206139120063_R01C01

value: M


title: ow43


title: 605937_isth_P3_ROI-001_Secretory_S3

description: Library name: DSP-1001660010693-A-H02


title: Peripheral whole blood DNA from fILD patient 52

description:
206139120114
206139120114_R04C01

value: HP


title: ow42

value: PBMC


title: Peripheral whole blood DNA from fILD patient 51

description:
206139120114
206139120114_R03C01


title: ow41

value: schizophrenia


title: ow40


title: 605937_amp_P3_ROI-003_Ciliated_S2

description: Library name: DSP-1001660010693-A-G09


title: 605937_amp_P3_ROI-002_Secretory_S2

description: Library name: DSP-1001660010693-A-G08


title: 605937_amp_P3_ROI-002_Ciliated_S2

description: Library name: DSP-1001660010693-A-G07


title: Peripheral whole blood DNA from fILD patient 49

description:
206139120114
206139120114_R01C01


title: Peripheral whole blood DNA from fILD patient 55

description:
206139120114
206139120114_R07C01


title: 605937_amp_P3_ROI-001_Secretory_S2

description: Library name: DSP-1001660010693-A-G06


title: Peripheral whole blood DNA from fILD patient 48

description:
206139120099
206139120099_R08C01


title: 605937_amp_P3_ROI-004_Ciliated_S2

description: Library name: DSP-1001660010693-A-G11


title: 605937_amp_P3_ROI-001_Ciliated_S2

description: Library name: DSP-1001660010693-A-G05


title: 605937_inf_P3_ROI-002_Secretory_S5

description: Library name: DSP-1001660010693-A-G02

value: Infundibulum


title: Peripheral whole blood DNA from fILD patient 47

description:
206139120099
206139120099_R07C01


title: 605937_inf_P3_ROI-003_Secretory_S5

description: Library name: DSP-1001660010693-A-G04


title: ow36


title: 605937_inf_P3_ROI-002_Ciliated_S5

description: Library name: DSP-1001660010693-A-G01


title: 605937_isth_P3_ROI-001_Ciliated_S3

description: Library name: DSP-1001660010693-A-H01


title: 605937_amp_P3_ROI-004_Secretory_S2

description: Library name: DSP-1001660010693-A-G12


title: ow39


title: 605937_inf_P3_ROI-001_Secretory_S5

description: Library name: DSP-1001660010693-A-F12


title: ow34


title: Peripheral whole blood DNA from fILD patient 50

description:
206139120114
206139120114_R02C01


title: 605937_amp_P3_ROI-003_Secretory_S2

description: Library name: DSP-1001660010693-A-G10


title: 605937_fim_P3_ROI-003_Secretory_S1

description: Library name: DSP-1001660010693-A-F10

value: Fimbria


title: ow32


title: 605937_inf_P3_ROI-003_Ciliated_S5

description: Library name: DSP-1001660010693-A-G03


title: 605937_fim_P3_ROI-003_Ciliated_S1

description: Library name: DSP-1001660010693-A-F09


title: Peripheral whole blood DNA from fILD patient 44

description:
206139120099
206139120099_R04C01

value: Never


title: Peripheral whole blood DNA from fILD patient 43

description:
206139120099
206139120099_R03C01

value: Always


title: 605937_fim_P3_ROI-002_Secretory_S1

description: Library name: DSP-1001660010693-A-F08

value: Secretory


title: ow31


title: 605937_fim_P3_ROI-001_Secretory_S1

description: Library name: DSP-1001660010693-A-F06


title: 605937_fim_P3_ROI-002_Ciliated_S1

description: Library name: DSP-1001660010693-A-F07


title: ow30


title: Peripheral whole blood DNA from fILD patient 42

description:
206139120099
206139120099_R02C01


title: ow38


title: 605937_fim_P3_ROI-001_Ciliated_S1

description: Library name: DSP-1001660010693-A-F05


title: Peripheral whole blood DNA from fILD patient 46

description:
206139120099
206139120099_R06C01


title: 605855_isth_P1_ROI-002_Secretory_S4

description: Library name: DSP-1001660010693-A-E09


title: ow29


title: 605855_isth_P1_ROI-002_Ciliated_S4

description: Library name: DSP-1001660010693-A-E08


title: Peripheral whole blood DNA from fILD patient 41

description:
206139120099
206139120099_R01C01


title: Peripheral whole blood DNA from fILD patient 45

description:
206139120099
206139120099_R05C01


title: ow28


title: 605855_isth_P1_ROI-001_Secretory_S4

description: Library name: DSP-1001660010693-A-E07


title: 605855_isth_P1_ROI-001_Ciliated_S4

description: Library name: DSP-1001660010693-A-E06


title: 605937_fim_P3_ROI-007_Ciliated_S10

description: Library name: DSP-1001660006709-D-H12


title: 605937_inf_P3_ROI-001_Ciliated_S5

description: Library name: DSP-1001660010693-A-F11


title: ow26


title: Peripheral whole blood DNA from fILD patient 40

description:
206139120126
206139120126_R08C01


title: ow24


title: Peripheral whole blood DNA from fILD patient 39

description:
206139120126
206139120126_R07C01


title: 605937_fim_P3_ROI-005_Ciliated_S10

description: Library name: DSP-1001660006709-D-H10


title: 605937_fim_P3_ROI-006_Ciliated_S10

description: Library name: DSP-1001660006709-D-H11


title: Peripheral whole blood DNA from fILD patient 38

description:
206139120126
206139120126_R06C01


title: 605937_isth_P3_ROI-004_Secretory_S10

description: Library name: DSP-1001660006709-D-H09


title: 605937_isth_P3_ROI-003_Secretory_S10

description: Library name: DSP-1001660006709-D-H07


title: Peripheral whole blood DNA from fILD patient 36

description:
206139120126
206139120126_R04C01


title: 605937_isth_P3_ROI-004_Ciliated_S10

description: Library name: DSP-1001660006709-D-H08


title: ow21


title: Peripheral whole blood DNA from fILD patient 37

description:
206139120126
206139120126_R05C01


title: Peripheral whole blood DNA from fILD patient 35

description:
206139120126
206139120126_R03C01


title: 605937_isth_P3_ROI-002_Secretory_S10

description: Library name: DSP-1001660006709-D-H05


title: 605937_isth_P3_ROI-001_Secretory_S10

description: Library name: DSP-1001660006709-D-H03


title: ow20


title: 605937_isth_P3_ROI-002_Ciliated_S10

description: Library name: DSP-1001660006709-D-H04


title: Peripheral whole blood DNA from fILD patient 34

description:
206139120126
206139120126_R02C01


title: ow18


title: 605855_isth_P1_ROI-005_Secretory_S9

description: Library name: DSP-1001660006709-D-H01


title: Peripheral whole blood DNA from fILD patient 33

description:
206139120126
206139120126_R01C01


title: ow23


title: 605937_isth_P3_ROI-003_Ciliated_S10

description: Library name: DSP-1001660006709-D-H06


title: 1001660010693_NTC

description: Library name: DSP-1001660010693-A-A01


title: 605855_isth_P1_ROI-003_Secretory_S9

description: Library name: DSP-1001660006709-D-G11


title: 605937_isth_P3_ROI-001_Ciliated_S10

description: Library name: DSP-1001660006709-D-H02


title: 605855_isth_P1_ROI-002_Secretory_S9

description: Library name: DSP-1001660006709-D-G09


title: ow2


title: 605855_isth_P1_ROI-003_Ciliated_S9

description: Library name: DSP-1001660006709-D-G10


title: 605855_isth_P1_ROI-004_Ciliated_S9

description: Library name: DSP-1001660006709-D-G12


title: Peripheral whole blood DNA from fILD patient 32

description:
206139120113
206139120113_R08C01


title: 605855_isth_P1_ROI-001_Ciliated_S9

description: Library name: DSP-1001660006709-D-G06


title: 605856_amp_P2_ROI-003_Ciliated_S4

description: Library name: DSP-1001660006709-D-G05

value: Ampulla


title: Peripheral whole blood DNA from fILD patient 31

description:
206139120113
206139120113_R07C01

value: F


title: 605856_amp_P2_ROI-002_Ciliated_S4

description: Library name: DSP-1001660006709-D-G04

value: Ciliated


title: ow16


title: Peripheral whole blood DNA from fILD patient 30

description:
206139120113
206139120113_R06C01


title: ow12


title: ow110


title: 605855_isth_P1_ROI-001_Secretory_S9

description: Library name: DSP-1001660006709-D-G07

value: Isthmus


title: Peripheral whole blood DNA from fILD patient 27

description:
206139120113
206139120113_R03C01

value: UPitt


title: Peripheral whole blood DNA from fILD patient 29

description:
206139120113
206139120113_R05C01

value: Former


title: ow108


title: 605856_amp_P2_ROI-001_Ciliated_S4

description: Library name: DSP-1001660006709-D-G03


title: 605856_isth_P2_ROI-003_Secretory_S2

description: Library name: DSP-1001660006709-D-G02


title: 605855_isth_P1_ROI-002_Ciliated_S9

description: Library name: DSP-1001660006709-D-G08


title: ow11


title: Peripheral whole blood DNA from fILD patient 28

description:
206139120113
206139120113_R04C01

value: IPF


title: ow107


title: Peripheral whole blood DNA from fILD patient 25

description:
206139120113
206139120113_R01C01

value: Whole blood DNA


title: 605856_isth_P2_ROI-003_Ciliated_S2

description: Library name: DSP-1001660006709-D-G01


title: ow109


title: 605856_isth_P2_ROI-002_Ciliated_S2

description: Library name: DSP-1001660006709-D-F11


title: Peripheral whole blood DNA from fILD patient 26

description:
206139120113
206139120113_R02C01


title: 605856_isth_P2_ROI-002_Secretory_S2

description: Library name: DSP-1001660006709-D-F12


title: 605856_isth_P2_ROI-001_Ciliated_S2

description: Library name: DSP-1001660006709-D-F09


title: SC391

city: Pittsburgh

first: Kathryn

last: Torok

state: PA

address: 4401 Penn Ave

department: Pediatric Rheuamatology

institute: University of Pittsburgh

description:
Library name: Sample 13
10x Genomics

data_processing:
Cell Ranger
Seurat
Harmony
Assembly: GRCh38
Supplementary files format and content: Matrix  table with raw gene counts for every gene and every sample

source_name: Skin

extract_protocol:
Miltenyi Biotec Whole Skin Dissociation Kit Human
10X Genomics Single Cell RNA Seq 3 Prime V2 Libraries

value: Healthy

value: Skin

value: Pediatric


title: 605856_isth_P2_ROI-001_Secretory_S2

description: Library name: DSP-1001660006709-D-F10


title: SC392

description:
Library name: Sample 14
10x Genomics


title: ow104

value: PBMC

value: schizophrenia


title: Peripheral whole blood DNA from fILD patient 23

description:
206139120089
206139120089_R07C01

data_processing:
A multi-package approach to processing and analyzing raw DNAm data produced from the Infinium MethylationEPIC array was implemented. First, raw .idat files for each sample underwent pre-processing, quality control, filtering, and analysis using R statistical computing environment (version 4.2.1, www.r-project.org). Using the minfi package, samples with a mean detection p-value >0.05 were excluded (n=2). The detection p-value compares the total unmethylated and methylated signal at each CpG location and compares it to the background signal inferred from negative control probes, such that p-values >0.05 or >0.01 indicate a failed probe where the signal from the probe is not significantly different from the background. All samples are from blood, and thus it was not expected there would be major global differences in methylation patterns between the samples. This enabled normalization using a subset quantile procedure, which helps to mitigate the impacts of artifacts in the data that are the result of differences between Type-I and Type-II methylation probes and other technical sources of variation. Next, for probe filtering, we removed any CpG probes whose detection p-value was >0.01 on one or more samples. We also removed sex chromosome probes given that our study includes patients of male and female sex. Next, we removed probes that had a single nucleotide polymorphism (SNP) at the CpG site, as this can result in impaired hybridization and detection of methylation for individuals with a variant allele at that locus. Subsequently, we removed cross-reactive probes that do not uniquely hybridize to a single CpG site on the MethylationEPIC array.
*processed value definition = Average Beta

source_name: Whole blood DNA

extract_protocol: Genomic DNA was isolated from peripheral whole blood samples taken from patients enrolled in the UPitt cohort using the Puregene DNA isolation kit or QiaAmp blood DNA isolation kit (Qiagen) and from the UBC cohort using the DNeasy Blood and Tissue Kit (Qiagen), all according to the manufacturer’s instructions. UBC samples were transferred to UPitt for simultaneous analysis alongside the UPitt samples. Prior to analysis, all DNA samples were stored at -20°C. DNA concentration and purity were assessed using the Infinite M200 Pro NanoQuant Plate Reader. Samples with an A260/A280 absorbance ratio outside of the 1.7-2.0 range were excluded.


title: SC457

description:
Library name: Sample 10
10x Genomics

value: LS


title: SC386

description:
Library name: Sample 16
10x Genomics


title: ow106


title: Peripheral whole blood DNA from fILD patient 24

description:
206139120089
206139120089_R08C01

value: Never


title: SC407

description:
Library name: Sample 15
10x Genomics


title: ow105


title: SC388

description:
Library name: Sample 12
10x Genomics


title: SC361

description:
Library name: Sample 11
10x Genomics


title: ow17


title: Peripheral whole blood DNA from fILD patient 22

description:
206139120089
206139120089_R06C01

value: M


title: SC389

description:
Library name: Sample 5
10x Genomics

value: Adult


title: ow102


title: SC455

description:
Library name: Sample 9
10x Genomics


title: SC446

description:
Library name: Sample 4
10x Genomics


title: Peripheral whole blood DNA from fILD patient 19

description:
206139120089
206139120089_R03C01


title: SC443

description:
Library name: Sample 8
10x Genomics


title: SC445

description:
Library name: Sample 3
10x Genomics


title: SC442

description:
Library name: Sample 7
10x Genomics


title: Peripheral whole blood DNA from fILD patient 21

description:
206139120089
206139120089_R05C01


title: ow103


title: SC424

description:
Library name: Sample 6
10x Genomics


title: Peripheral whole blood DNA from fILD patient 20

description:
206139120089
206139120089_R04C01


title: YD102

value: healthy control


title: ow100


title: RNAseq_PLC_HERVE_int_sg244_rep1

city: Hong Kong China

first: Cheuk Yin

last: CHENG

address: The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong

department: Life Science

country: Hong Kong

description: Cells were generated by transducing PLC cells stably expressing dCas9 with the pLKO5.sgRNA.EGFP vector carrying sgRNA targeting HERVE-int (sg244)

data_processing:
Reads were aligned to GRCh38/hg38 and GENCODE v39 with STAR v2.7.6 using ENCODE parameters except where -outFilterMultimapNmax was set to 1 to keep only uniquely mapped reads.
TPM of genes were quantified with RSEM v1.3.3.
Assembly: GRCh38/hg38
Supplementary files format and content: Signal tracks with TPM for piled up genomic alignments were generated using the bamCoverage program in deepTools24 v3.5.1 with parameters –normalizeUsing BPM –exactScaling, and –filterRNAstrand forward/reverse for minus/plus strand, respectively

source_name: PLC

growth_protocol: Cells were maintained in Dulbecco’s modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (Gibco), 1% L-glutamine (Gibco), 1% non-essential amino acids (Gibco), 1% sodium pyruvate (Gibco) and 1% penicillin-streptomycin (Gibco) at 37°C in 5% CO2. Medium was changed every 48 hours and cells were passed once they reach 80% confluency

extract_protocol:
Total RNA was extracted using RNeasy® Mini Kit (Qiagen) following manufacturer's protocol. Extracted Total RNA was subjected to rRNA depletion using Ribo-off rRNA depletion Kit (H/M/R) (Vazyme) before library preparation.
Stranded total RNA-seq libraries were prepared using QIAseq™ Stranded Library Kit (Qiagen).

value: PLC

value: Hepatocellular carcinoma

value: PLC transduced with sgRNA targeting HERVE-int


title: SC409

description:
Library name: Sample 2
10x Genomics


title: Peripheral whole blood DNA from fILD patient 18

first: Gillian

address: Centre for Heart Lung Innovation, St. Paul's Hospital, 1081 Burrard Street

description:
206139120089
206139120089_R02C01

value: UPitt


title: YD101


title: SC408

description:
Library name: Sample 1
10x Genomics


title: RNAseq_PLC_HERVE_int_sg244_rep2

institute: The Hong Kong University of Science and Technology


title: Peripheral whole blood DNA from fILD patient 17

institute: University of British Columbia

description:
206139120089
206139120089_R01C01

value: Former


title: YD100


title: YD103


title: RNAseq_HepG2_THE1D_sg65

description: Cells were generated by transducing HepG2 cells stably expressing dCas9 with the pLKO5.sgRNA.EGFP vector carrying sgRNA targeting THE1D (sg65)

value: HepG2 transduced with sgRNA targeting THE1D


title: Peripheral whole blood DNA from fILD patient 14

description:
206139120083
206139120083_R06C01

value: IPF

value: Whole blood DNA


title: RNAseq_PLC_sgLuci_rep2

description: Cells were generated by transducing PLC cells stably expressing dCas9 with the pLKO5.sgRNA.EGFP vector carrying sgRNA targeting luciferase (sgLuci)

value: PLC transduced with sgRNA targeting luciferase


title: RNAseq_HepG2_sgLuci_rep2

description: Cells were generated by transducing HepG2 cells stably expressing dCas9 with the pLKO5.sgRNA.EGFP vector carrying sgRNA targeting luciferase (sgLuci)

value: HepG2 transduced with sgRNA targeting luciferase


title: Peripheral whole blood DNA from fILD patient 16

description:
206139120083
206139120083_R08C01


title: Peripheral whole blood DNA from fILD patient 12

description:
206139120083
206139120083_R04C01


title: Peripheral whole blood DNA from fILD patient 13

description:
206139120083
206139120083_R05C01

value: F


title: RNAseq_PLC_sgLuci_rep1


title: Peripheral whole blood DNA from fILD patient 15

description:
206139120083
206139120083_R07C01

value: Always


title: RNAseq_PLC

value: Wildtype


title: ow101

value: PBMC

value: schizophrenia


title: ChIPseq_H3K27ac_PLC

library_source: genomic

data_processing:
Reads were aligned to GRCh38/hg38 using ENCODE ChIP-seq pipeline v2.2.1 (https://github.com/ENCODE-DCC/chip-seq-pipeline2).
Assembly: GRCh38/hg38
Supplementary files format and content: Signal tracks with fold enrichment over control were generated using MACS2 v2.2.7.1.

extract_protocol:
Chromaitn was extracted by lysing the cells and digested with MNase (Thermo Fisher Scientific). The histone-DNA complexes were then isolated with antibodies targeting specific histone mark.
ChIP-seq libraries were prepared using HyperPrep DNA Kit (Roche) following manufacturer’s instruction and sequenced on Illumina NextSeq 500

value: Hepatoblastoma


title: ChIPseq_Input_HepG2


title: RNAseq_HepG2_THE1D_sg175

description: Cells were generated by transducing HepG2 cells stably expressing dCas9 with the pLKO5.sgRNA.EGFP vector carrying sgRNA targeting THE1D (sg175)


title: YD098

value: healthy control


title: Donor T-LDR-6

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

institute: Government of Canada

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

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

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

value: Blood

value: Primary Cell

value: Lymphocyte

value: LDR

tag: dose rate

value: 0.05 Gy/min

tag: dose

tag: individual

value: Donor T

value: male

tag: age


title: ChIPseq_Input_PLC

value: PLC


title: YD094


title: RNAseq_HepG2_sgLuci_rep1

value: Hepatocellular carcinoma


title: Donor T-LDR-2

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


title: RNAseq_HepG2


title: ChIPseq_H3K4me3_PLC


title: YD097


title: Peripheral whole blood DNA from fILD patient 8

city: Vancouver

last: Goobie

description:
206139120124
206139120124_R08C01

value: UPitt

value: M

value: Never

value: IPF

value: Whole blood DNA


title: Peripheral whole blood DNA from fILD patient 11

description:
206139120083
206139120083_R03C01

value: F

value: Former


title: ChIPseq_H3K4me3_HepG2

value: Hepatoblastoma

value: Wildtype


title: YD096

value: PBMC

value: healthy control


title: Donor T-LDR-0.10

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

value: Blood

value: Primary Cell

value: Lymphocyte

value: LDR


title: Donor T-LDR-0.05

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

value: 0.05 Gy/min

value: Donor T

value: male


title: Peripheral whole blood DNA from fILD patient 6

description:
206139120124
206139120124_R06C01

value: UPitt

value: M


title: YD092


title: YD091


title: ChIPseq_H3K27ac_HepG2


title: Peripheral whole blood DNA from fILD patient 10

description:
206139120083
206139120083_R02C01

value: Never

value: IPF


title: Peripheral whole blood DNA from fILD patient 9

description:
206139120083
206139120083_R01C01

value: F

value: Whole blood DNA


title: YD099


title: YD095


title: Donor T-LDR-0

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

value: 0 Gy


title: Donor T-LDR-4

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


title: Donor T-LDR-1

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


title: Peripheral whole blood DNA from fILD patient 5

description:
206139120124
206139120124_R05C01

value: Former


title: Peripheral whole blood DNA from fILD patient 4

description:
206139120124
206139120124_R04C01


title: YD089

value: PBMC


title: Donor T-LDR-0.50

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


title: Peripheral whole blood DNA from fILD patient 7

description:
206139120124
206139120124_R07C01


title: Donor T-LDR-0.25

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


title: Donor T-HDR-6

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

value: HDR

value: 1 Gy/min


title: Donor T-HDR-0.10

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

value: Blood

value: Primary Cell


title: Peripheral whole blood DNA from fILD patient 1

description:
206139120124
206139120124_R01C01


title: Donor T-Control-0b

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

value: Lymphocyte

value: CON


title: YD086

value: healthy control


title: YD090


title: Donor T-HDR-4

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

value: Donor T

value: male


title: Donor T-HDR-2

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


title: Donor T-Control-0a

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

value: 0.05 Gy/min


title: Donor T-HDR-1

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


title: Peripheral whole blood DNA from fILD patient 3

description:
206139120124
206139120124_R03C01

value: UPitt

value: Never


title: Donor T-HDR-0.50

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


title: YD084


title: Donor S-LDR-2

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

value: LDR

value: Donor S

value: female


title: YD088


title: AtWTtr1

city: Columbia

first: Jose Roberto

last: Da Silva Nascimento

state: MO

address: 1201 Rollins Street

department: Life Sciences Center

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

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

value: WT


title: Peripheral whole blood DNA from fILD patient 2

description:
206139120124
206139120124_R02C01

value: F

value: Former

value: IPF

value: Whole blood DNA


title: Donor T-HDR-0.25

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

value: Blood

value: Primary Cell

value: Lymphocyte

value: HDR

value: 1 Gy/min


title: AtWT3


title: Donor S-LDR-0.50

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

value: 0.05 Gy/min