title: TC71_doxy_3

data_processing:
Samples were barcoded, pooled, and sequenced on an Illumina NovaSeq 6000 to obtain a minimum of 30 million, paired-end, 100 bp reads per sample.
FastQC was used to assess the quality of the sequencing reads. Reads were then mapped against the human reference genome (GRCh38) using the STAR aligner and summarized at the exon level using featureCounts. Alignment quality was assessed using MultiQC.
Raw counts were transformed using the cpm function in EdgeR for sample clustering and principal components analysis (PCA). No outlier samples were identified or removed from the analysis.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for each gene and sample

treatment_protocol: Two Ewing sarcoma cell lines (EW8, TC71) expressing a doxycycline-inducible, lentiviral system to simultaneously overexpress both c-Jun and c-Fos were treated with either vehicle (DMSO) or doxycycline (2000ng/ml) for 72 hours.

value: doxycycline 72h


title: H10-KTB42-NP-AA

status: Public on Sep 30 2024

type: SRA

city: Indianapolis

first: Harikrishna

last: Nakshatri

state: IN

address: 980 W. Walnut St. R3C218C

department: General Surgery

country: USA

institute: Indiana University School of Medicine

library_source: transcriptomic

data_processing:
Adapters and low quality bases were trimmed using Trimmomatic (version 0.32) with following specific parameters ILLUMINACLIP:<adapters.fa>:2:20:5 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:17. Custom perl scripts  were used to truncate poly-G tails and then reduce fastq files to a non-redundant set of reads to decrease mapping computational load.
Reads were mapped against GRCh38 using TopHat2 version 2.1.0 with parameters “--b2-very-sensitive --read-edit-dist 2 --max-multihits 100 --library-type fr-secondstrand”
Read counts for each gene were created using custom perl scripts and Gencode v23 as the annotation
Differential expression analysis was performed using the DESeq2 package (version 1.10.1) in R/Bioconductor (R version 3.2.1).
Assembly: GRCh38
Supplementary files format and content: tab-delimited file includes raw gene count values for each sample

molecule: polyA RNA

organism: Homo sapiens

source_name: African American

extract_protocol:
RNA was harvested using the RNAEasy kit (Qiagen)
Poly-A RNA libraries were constructed using mRNA Stranded TruSeq protocol (Illumina, San Diego, CA). Small RNA library construction was performed using the TruSeq Small RNA kit (Illumina). Purified libraries were visualized and quantified using a TapeStation HSD1000 (Agilent, Santa Clara, CA).

tag: tissue

value: breast

tag: cell type

value: Primary Mature luminal cells (CD49F-/EpCAM+) grown from breast tissues


title: H9-KTB42-PP-AA

value: Primary Luminal progenitor cells (CD49F+/EpCAM+) grown from breast tissues


title: Chondrocyte-dKO-1

city: Rochester

first: Alexandra

last: Krivonos

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

data_processing:
The samples were sequencing using a 2 x 150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the Control software.
Raw sequence data (.bcl files) generated by the sequencer were converted into fastq files and de-multiplexed using Illumina’s bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality. The trimmed reads were mapped to the reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Assembly: mm10
Supplementary files format and content: tab-delimited text file contains raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: Chondrocytes

extract_protocol:
Primary epiphyseal chondrocytes were harvested from five-day-old female WT, Phlpp1-/-, Phlpp2-/-, and Phlpp1/2-/- mice. Chondrocytes were digested for one hour in 0.5mg/mL collagenase II in DMEM culture medium, then digested overnight in 3mg/mL collagenase II in DMEM culture media. Cells were then cryopreserved until a sufficient n was reached for each genotype. At that point, cells were thawed, plated in DMEM+10% FBS+1% antibiotic/antimycotic overnight. The next day, chondrocytes washed in ice-cold PBS three times, then resuspended in Trizol for RNA extraction. Total RNA was extracted using phenol-chloroform.
RNA Sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina per the manufacturer’s instructions (NEB, Ipswich, MA).

value: Chondrocytes

tag: strain

tag: Sex

value: Female

tag: genotype

value: Phlpp1/2 KO

tag: age

value: 5 days old


title: TC71_doxy_2

city: Iowa City

first: Emma

last: Croushore

state: Iowa

address: 25 S Grand Ave

department: Pediatric Hematology/Oncology

institute: University of Iowa

growth_protocol: The cell lines were cultured in DMEM with 10% FBS.

extract_protocol:
RNA was isolated from cell lines using RNeasy Plus Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina TruSeq Stranded mRNA protocols.

tag: cell line

value: Ewing sarcoma cell line

tag: treatment


title: B2002_D15_10.7Gy_Male

city: Bethesda

first: Uma

middle: T

last: Shankavaram

state: MD

address: 9000 Rockville Pike

department: NCI

institute: NIH

description:
B2002_D15_S84
B2002_D15_10.7Gy

data_processing:
The FASTQ sequences were trimmed using CutAdapt v. 2.10 [https://doi.org/10.14806/ej.17.1.200] with the following settings: “--nextseq-trim=2 --trim-n -n 5 -O 5 -q 10,10 -m 15 -j 0” and aligned using STAR v. 2.7.6a [https://doi.org/10.1093/bioinformatics/bts635] with parameters set as recommended by ENCODE3 consortium (https://www.encodeproject.org/pipelines/ENCPL444CYA/). Macaca mulatta (Rhesus monkey) genome assembly Mmul_10 (release date: Feb. 2019) with RefSeq annotation (accession number GCF_003339765.1) was used as a reference. Counting was performed with the help of Subread package v. 2.0.1 [10.1093/bioinformatics/btt656]. The count matrix was processed in R (1) for further analysis.
Assembly: Macaca mulatta (Rhesus monkey) genome assembly Mmul_10 (release date: Feb. 2019).
Supplementary files format and content: *.txt: Tab-delimited text files include raw counts and normalized counts for each Sample.

organism: Macaca mulatta

source_name: Whole blood

extract_protocol: Blood samples were procured from each of the animals (n = 28) two days before irradiation as control, every three days post-irradiation for the initial 30 days, on days 40, 50, and 60, and approximately every 30 days until the euthanization of all surviving animals at day 270 post-irradiation.

value: Whole blood

value: Male

value: 10.7Gy thoracic radiation

tag: time point

value: 15 days

tag: animal id


title: H8-KTB41-NP-AA


title: Alveolar macrophage from co-culture with early lesion cells,  biological replicate 2

city: The Bronx

first: Michael

last: Papanicolaou

state: New York

address: 1300 Morris Park Avenue

department: Cell Biology

institute: Albert Einstein College of Medicine

description:
RNAseq EL AM_Raw read counts.xlsx
RNAseq EL AM_Raw read counts.xlsx

data_processing:
Illumina HiSeq, 2x150bp configuration, single index, per lane
Assembly: mm10
The sequencing libraries were pooled and clustered on lane.  After clustering, the flowcell was loaded on the Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions.  The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
Supplementary files format and content: Extensible Markup Language file with raw counts for each sample

source_name: AM from co-culture with EL 2

growth_protocol: DMEM/F12, 5% horse serum, 500ng/ml Hydrocortisone (Lonza CC-403), 40 mg/ml Insulin (Gibco 12585-014), 20 ng/ml EGF (Pepro- tech AF-100-15-A), 100 units/ml penicillin and 100ug/ml streptomycin (Corning) in wells coated with 100% matrigel that has gellated

extract_protocol:
Total RNA was extracted from fresh frozen cell pellets using Qiagen RNeasy Plus Universal mini kit following manufacturer’s instructions (Qiagen, Hilden, Germany). Extracted RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA).
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). mRNAs were enriched with Oligo(dT) beads

treatment_protocol: Mammary early lesion cells or mammary primary tumor cells were isolated from the MMTV-HER2 mouse model and lung alveolar macrophages were isolated from congenic wildtype mice. Early lesion or primary tumor cells were co-culture with alveolar macrophages, and were FACS-sorted and bulk RNA-sequencing was performed. Mono-culture controls of each cell type were also sequenced. Cells were co-cultured for 7 days before being sorted and processed for RNA-seq.

value: lung

value: primary cells

value: primary alveolar macrophage

value: wildtype FVB

value: co-cultured with early lesion cells


title: EW8_siControl_3

data_processing:
Samples were barcoded, pooled, and sequenced on an Illumina NovaSeq 6000 to obtain a minimum of 30 million, paired-end, 100 bp reads per sample.
FastQC was used to assess the quality of the sequencing reads. Since each paired-end sample was split over two flow cells, each of the 12 samples output 4 fastq files. For each sample, forward reads from lanes 1 and 2 were merged into one fastq file, and reverse reads from lanes 1 and 2 were combined into one fastq file.
Reads were then mapped against the human reference genome (hg38) using the STAR aligner and summarized at the exon level using featureCounts. Alignment quality was assessed using MultiQC.
Raw counts were transformed using the cpm function in EdgeR for sample clustering and principal components analysis (PCA). No outlier samples were identified or removed from the analysis.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for each gene and sample

treatment_protocol: Two parential Ewing sarcoma cell lines (EW8, TC71) were treated with siControl or siEWS-FLI1 for 48 hours.

value: WT

value: siControl 48h


title: B2002_Ctl_0Gy_Male

description:
B2002_Ctl_S27
B2002_Ctl_0Gy

value: control

value: -2 days


title: TC71_doxy_1

value: doxycycline 72h


title: B2001_D90_10.7Gy_Male

description:
B2001_D90_S0
B2001_D90_10.7Gy

value: 90 days


title: B2002_D6_10.7Gy_Male

description:
B2002_D6_S115
B2002_D6_10.7Gy

value: 6 days


title: Chondrocyte-Phlpp2-3

value: Chondrocytes

value: Female

value: Phlpp2 KO

value: 5 days old


title: H7-KTB41-PP-AA

value: breast

value: Primary Luminal progenitor cells (CD49F+/EpCAM+) grown from breast tissues


title: TC71_3

value: Ewing sarcoma cell line

value: no doxycycline 72h


title: B2001_D60_10.7Gy_Male

description:
B2001_D60_S0
B2001_D60_10.7Gy

value: Whole blood

value: Male

value: 10.7Gy thoracic radiation

value: 60 days


title: B2001_D30_10.7Gy_Male

description:
B2001_D30_S0
B2001_D30_10.7Gy

value: 30 days


title: H5-KTB40-PP-AA


title: TC71_2

value: WT


title: TC71_1


title: H4-KTB39-NP-AA

value: Primary Mature luminal cells (CD49F-/EpCAM+) grown from breast tissues


title: Chondrocyte-Phlpp1-3

value: Phlpp1 KO


title: Chondrocyte-Phlpp2-1


title: H3-KTB39-PP-AA


title: EW8_doxy_2

value: doxycycline 72h


title: H2-KTB8-NP-AA


title: Chondrocyte-Phlpp1-1

value: Chondrocytes


title: Chondrocyte-Phlpp1-2

value: Female


title: B2001_D6_10.7Gy_Male

description:
B2001_D6_S114
B2001_D6_10.7Gy

value: 6 days


title: B2001_D9_10.7Gy_Male

description:
B2001_D9_S62
B2001_D9_10.7Gy

value: 9 days


title: EW8_doxy_3


title: EW8_doxy_1


title: Chondrocyte-WT-3

value: 5 days old


title: Chondrocyte-Phlpp2-2

value: Phlpp2 KO


title: EW8_3

value: Ewing sarcoma cell line


title: B2001_D3_10.7Gy_Male

description:
B2001_D3_S38
B2001_D3_10.7Gy

value: 3 days


title: H6-KTB40-NP-AA

value: breast


title: H1-KTB8-PP-AA

value: Breast

value: Primary Luminal progenitor cells (CD49F+/EpCAM+) grown from breast tissues


title: Chondrocyte-WT-2


title: B2001_D21_10.7Gy_Male

description:
B2001_D21_S193
B2001_D21_10.7Gy

value: Whole blood

value: Male

value: 10.7Gy thoracic radiation

value: 21 days


title: 1ko-cc

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw Data was processed with Perl scripts to ensure the quality of data used in further analysis. The adopted filtering criteria are as follows：1) Remove the adaptor-polluted reads. (Reads containing more than 5 adapter-polluted bases were regarded as adaptor-polluted reads and would be filtered out; 2) Remove the low-quality reads. Reads with the number of low quality bases (phred Quality value less than 19) accounting for more than 15% of total bases are regarded as low-quality reads; 3) Remove reads with number of N bases accounting for more than 5 %.
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was mapped to the reference genome using TopHat v2.0.12.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and RPKM (Reads Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Cerebral corpus callosum

extract_protocol:
Total RNA was harvested by Trizol reagent.2 ug of total RNA was used to construct sequencing libraries.
RNA libraries sequencing  was performed using standard Illumina protocols

value: Cerebral corpus callosum

value: ko


title: 2ko-cc


title: 2wt-cc

value: wt


title: EW8_1

value: WT

value: no doxycycline 72h


title: Chondrocyte-WT-1

value: Chondrocytes

value: Female


title: Bone-KO-4

source_name: Bone

extract_protocol:
Femurs were isolated from 24-week-old male WT (n=4) and Girk3-/- (n=4) mice. The epiphyses were removed, then the diaphyseal bone was flushed with PBS three times to remove all bone marrow. Bone tissue was then placed in 1 mL trizol, homogenized, and total RNA was extracted using the Zymo Direct-zol RNA Miniprep Kit.
RNA Sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina per the manufacturer’s instructions (NEB, Ipswich, MA).

value: Bone

value: male

value: Girk3 KO

value: 24 weeks old


title: EW8_2

value: Ewing sarcoma cell line


title: B2001_Ctl_0Gy_Male

description:
B2001_Ctl_S26
B2001_Ctl_0Gy

value: control

value: -2 days


title: B2001_D15_10.7Gy_Male

description:
B2001_D15_S136
B2001_D15_10.7Gy

value: Whole blood

value: Male

value: 15 days


title: AML cells_9

city: Boston

first: Grant

last: Rowe

state: MA

address: 1 Blackfan Circle

institute: Boston Children's Hospital

description:
expected_count_9
genes_counts.txt

data_processing:
FastQC
CUT&RUNTools
CUT&RUN.  Raw data were processed using FastQC and CUT&RUNTools and mapped to hg19.  Parameters of individual software called by CUT&RUNTools, including Bowtie2, Trimmomatic, Picard (http://broadinstitute.github.io/picard/), Samtools were left unchanged. E. coli spike-in DNA was used for normalization.  We mapped the sequencing reads to E. coli genome using Bowtie2 (–end-to-end –very-sensitive –no-overlap –nodovetail–no-mixed –no-discordant) and calculated the "spike_in_ratio" in each sample as ‘‘Ecoli_reads/Total_reads’’. The bigwig tracks were generated using bamCoverage from deeptools package with "scale_factor" calculated as 1/(spike_in_ratio * cell_number_factor), where "cell_number_factor" to balance signal based on cell input and pooled from the triplicate samples.
RNA-seq.  For the trimming and quality improvement of RNA-seq reads, we utilized Trimmomatic (version 0.39). Paired reads were processed with the following parameters: adapter removal (TruSeq3-PE.fa), trimming of low-quality bases at the beginning and end (minimum score of 3), application of a 4-base sliding window to maintain an average quality above 15, and exclusion of reads shorter than 36 bases. The reads were processed generating files of both paired and unpaired processed reads. For mapping the processed RNA-seq reads, we employed the STAR software (version 2.7.10b). The paired reads, after trimming, were aligned to the reference genome (Homo_sapiens. GRCh38.86). To ensure the quality of mapping, the basic two-pass mode was activated, allowing only unique alignments. For the quantification of gene expression from the RNA-seq alignments, we used RSEM (version 1.3.1).
Assembly: hg19
Supplementary files format and content: CUT&RUN .bw
Supplementary files format and content: RNA-seq raw counts

source_name: AML cells

growth_protocol: IMDM/20% FCS, 100 ng/ml hSCF, 50 ng/ml hTPO, 10 ng/ml hFLT3L, 10 ng/ml hIL-3, 10 ng/ml hIL-6

extract_protocol:
RNA: RNAeasy; CUT&RUN: Epizyme
NEB

value: AML cells

tag: cell subset

value: AML


title: B1506_D30_9.8Gy_Female

description:
B1506_D30_S0
B1506_D30_9.8Gy

value: 9.8Gy thoracic radiation

value: 30 days


title: AML cells_7

description:
expected_count_7
genes_counts.txt


title: Bone-KO-2


title: AML cells_8

description:
expected_count_8
genes_counts.txt


title: 1wt-cc

value: Cerebral corpus callosum

value: wt


title: AML cells_6

description:
expected_count_6
genes_counts.txt


title: B1506_D172_9.8Gy_Female

description:
B1506_D172_S0
B1506_D172_9.8Gy

value: Female

value: 172 days


title: B2001_D40_10.7Gy_Male

description:
B2001_D40_S223
B2001_D40_10.7Gy

value: 10.7Gy thoracic radiation

value: 40 days


title: B1506_D150_9.8Gy_Female

description:
B1506_D150_S0
B1506_D150_9.8Gy

value: 150 days


title: Bone-KO-1

value: Bone

value: male

value: Girk3 KO

value: 24 weeks old


title: B1506_D90_9.8Gy_Female

description:
B1506_D90_S232
B1506_D90_9.8Gy

value: Whole blood

value: 90 days


title: Bone-WT-4

value: WT


title: Bone-WT-3


title: AML cells_4

description:
expected_count_4
genes_counts.txt

value: AML cells

value: AML


title: B1506_D9_9.8Gy_Female

description:
B1506_D9_S61
B1506_D9_9.8Gy

value: 9.8Gy thoracic radiation

value: 9 days


title: Bone-WT-2


title: Bone-KO-3


title: SKO_1

city: New Haven

first: Vijayakumar

middle: R

last: Kakade

state: Connecticut

address: 300 Cedar St Room S240

department: Internal Medicine/Section of Nephrology

institute: Yale Univeristy

data_processing:
Illumina’s bcl2fastq
Supplementary files format and content: tab-delimited text file include FPKM values for each sample
Assembly: UCSC mm10

source_name: Kidney

extract_protocol:
Total RNA was extracted from whole kidneys using TRIzol reagent. 1ug of RNA was used for the construction of library.
RNA libraries were prepared using mRNA-seq sample prep kit (Illumina) following manufacturer's protocols.

value: Kidney

value: Pkd1 knockout

value: 8 weeks


title: B1506_D60_9.8Gy_Female

description:
B1506_D60_S230
B1506_D60_9.8Gy

value: Female

value: 60 days


title: AML cells_3

description:
expected_count_3
genes_counts.txt


title: B1506_D6_9.8Gy_Female

description:
B1506_D6_S48
B1506_D6_9.8Gy

value: 6 days


title: SKO_0


title: KO BMDM, 5h LPS, rep3

city: Santa Cruz

first: Susan

last: Carpenter

state: CA

address: Red Hill Rd, Biomedical Sciences

department: MCD

institute: UC Santa Cruz

description:
Cre-249-LPS-Pool-2
kolps012
Deseq.results.wtlps.kolps.txt
IUTA_estimates.txt
IUTA_pvalues.txt

data_processing:
All samples were sequenced together on an Illumina HiSeq system (paired-end 150bp), and sequencing reads were mapped to mm10 using STAR. For analysis of differential genes, STAR outputs were processed using DESeq2.
Differential Isoform usage was determined from alignemnt files using IUTA with default settings.
Assembly: mm10
Supplementary files format and content: Deseq normalized gene counts for fl/fl and KO unstimulated BMDMs
Supplementary files format and content: Deseq normalized gene counts for fl/fl and KO BMDMs stimulated with LPS
Supplementary files format and content: IUTA isoform abundace estimates from fl/fl and KO BMDMs stimulated with LPS
Supplementary files format and content: IUTA p-values for differential isofrom usage between fl/fl and KO BMDMs stimulated with LPS

source_name: Bone Marrow

growth_protocol: BMDMs were generated by culturing erythrocyte-depleted BM cells in DMEM supplemented with 10% FCS, 5 mL pen/strep (100×), 500 μL ciprofloxacin (10 mg/mL), and 10% L929 supernatant for 7 to 14 d, with the replacement of culture medium every 2 to 3 d.

extract_protocol:
Total RNA was purified from cells or tissues using Direct-zol RNA MiniPrep Kit (Zymo Research, R2072) and TRIzol reagent (Ambion, T9424) according to the manufacturer’s instructions. RNA was quantified and assessed for purity using a nanodrop spectrometer (Thermo Fisher)
RNA-Seq libraries were generated from total RNA (1 μg) using the Bioo kit.

treatment_protocol: Bone marrow derived macrophage cells were stimulated with Lipopolysaccharide (LPS) at 200ng/ml (TLR4) for 5hrs.

value: Bone Marrow

value: Bone Marrow Derived Macrophages

value: KO


title: AML cells_2

description:
expected_count_2
genes_counts.txt


title: Control_2

value: Uninduced control


title: KO BMDM, 5h LPS, rep2

description:
Cre-245-LPS-Pool-2
kolps011
Deseq.results.wtlps.kolps.txt
IUTA_estimates.txt
IUTA_pvalues.txt


title: AML cells_1

description:
expected_count_1
genes_counts.txt


title: B1506_D3_9.8Gy_Female

description:
B1506_D3_S104
B1506_D3_9.8Gy

value: Whole blood

value: 3 days


title: B1506_D21_9.8Gy_Female

description:
B1506_D21_S95
B1506_D21_9.8Gy

value: 21 days


title: Control_1


title: AML cells_5

description:
expected_count_5
genes_counts.txt

value: AML cells


title: KO BMDM, 5h LPS, rep1

description:
Cre-244-LPS-Pool-2
kolps010
Deseq.results.wtlps.kolps.txt
IUTA_estimates.txt
IUTA_pvalues.txt


title: TPC-1 cells, treated with selpercatinib for 48 h #2

city: Kyoto

first: Yuki

last: Katayama

address: 465, Kajii-cho, Kamigyo-ku

country: Japan

institute: Kyoto prefectural university of medicine

description:
tpmsTPC1.tsv
TPC1-S02

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
The FASTQ files are pre-processed with the Fastp tool (Chen et al., 2018), and expression quantification is performed with Salmon (Patro et al., 2017).
Assembly: GRCh38
Supplementary files format and content: TPMs

source_name: thyroid

growth_protocol: LC-2/ad cells were cultured in RPMI-1640/F-12 medium (1:1 mixture) plus 10% fetal bovine serum (FBS). TPC1 cells were cultured in RPMI-1640 plus 10% FBS.

extract_protocol:
Total RNA was extracted using NucleoSpin® RNA Plus (Takara Bio, Shiga, Japan)
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were treated with 100 nM selpercatinib for 48 h.

value: thyroid

value: papillary thyroid cancer

value: selpercatinib


title: KO BMDM, 0h LPS, rep3

description:
Cre-249-Pool-1
kontr006
Deseq.results.wtntr.kontr.txt


title: Control_0

value: Kidney


title: TPC-1 cells, treated with selpercatinib for 48 h #3

description:
tpmsTPC1.tsv
TPC1-S03


title: B1506_D15_9.8Gy_Female

description:
B1506_D15_S83
B1506_D15_9.8Gy

value: 9.8Gy thoracic radiation

value: 15 days


title: TPC-1 cells, treated with selpercatinib for 48 h #1

description:
tpmsTPC1.tsv
TPC1-S01


title: Bone-WT-1

value: Bone

value: male

value: WT

value: 24 weeks old


title: KO BMDM, 0h LPS, rep1

description:
Cre-244-Pool-1
kontr004
Deseq.results.wtntr.kontr.txt

value: Bone Marrow

value: Bone Marrow Derived Macrophages


title: TPC-1 cells, parent cells #2

description:
tpmsTPC1.tsv
TPC1-C02


title: TPC-1 cells, parent cells #3

description:
tpmsTPC1.tsv
TPC1-C03


title: Cortex; miR-33 WT rep 3

first: Jungsu

last: Kim

address: 320 W. 15th Street

description: Sex of animal: Female

data_processing:
Base calling done by Illumina Real-Time Analysis v2
Adapters and polyA tails removed by bbduk from bbtools/38.72 using references files polyA/polyT (poly(A) sequence of 18 As, and a poly(T) sequence of 18 Ts) & truseq_rna.fa (from the BBTools suite: https://sourceforge.net/projects/bbmap/) and parameters k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20
Alignment done by STAR/2.7.3a using parameters: --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.6 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD
Gene counts done by htseq-count from htseq/0.9.1-py13 using parameters htseq-count -m intersection-nonempty -s yes -f bam -r pos
Assembly: GRCm39
Supplementary files format and content: Matrix table of raw gene counts for each gene and each sample in experimental design

source_name: Brain cortex

extract_protocol:
Total RNA was extracted from mouse cortical tissues using phenol/chloroform & TRI reagent® (Molecular Research Center, Inc) and was quantified using the NanoDrop 2000 spectrophotometer (Thermo Scientific).
Isolated RNA was shipped to Lexogen for library preparation and sequencing. Libraries were prepared manually according to the manufacturer’s instructions using QuantSeq 3' mRNA-Seq FWD Library Prep Kit (Lexogen, UG Version 015UG009V0252). Briefly, 50 ng total RNA was denatured for 3 minutes at 85°C with oligo(dT) primers containing an Illumina-compatible sequence at its 5’ end followed by reverse transcription at 42°C for 15 minutes. After RNA removal, the second strand of the cDNA was synthesized by a random primer containing an Illumina-compatible linker sequence at its 5’ end, and the end product was purified by a magnetic bead-based method to remove all reaction components. Finally, individual sample barcodes (dual indexing) for multiplexing were introduced via PCR (cycle number determined by qPCR) and the leftover reaction components were removed by a magnetic bead-based purification method. All libraries were analyzed for adapter dimers, size distribution and concentration on a Fragment Analyzer System using the DNF-474 HS NGS Fragment kit (1-6,000 bp) (Agilent). After pooling the libraries in an equimolar ratio, the concentration and the size distribution of the lane mix was analyzed by QubitdsDNA HS assay(Thermo Fisher Scientific) and by 2100 Bioanalyzerdevice using the HS-DNA assay(Agilent), respectively. A 2 nM dilution of the lane mix was denatured and diluted to loading concentration for sequencing on a NextSeq 500 instrumentwith SR75 High Output Kit(Illumina). Seventy-six-base-pair single-end reads were generated at Lexogen Services.

value: Brain cortex

value: miR-33 WT


title: KO BMDM, 0h LPS, rep2

description:
Cre-245-Pool-1
kontr005
Deseq.results.wtntr.kontr.txt

value: KO


title: Cortex; miR-33 WT rep 2

description: Sex of animal: Female


title: Fl/Fl BMDM, 5h LPS, rep3

description:
Fl-231-LPS-Pool-1
wtlps009
Deseq.results.wtlps.kolps.txt
IUTA_estimates.txt
IUTA_pvalues.txt

value: Fl/FL


title: Cortex; miR-33 WT rep 4

description: Sex of animal: Female


title: Cortex; miR-33 WT rep 1

description: Sex of animal: Female


title: B1506_Ctl_0Gy_Female

description:
B1506_Ctl_S25
B1506_Ctl_0Gy

value: Whole blood

value: Female

value: control

value: -2 days


title: Fl/Fl BMDM, 5h LPS, rep2

description:
Fl-230-LPS-Pool-1
wtlps008
Deseq.results.wtlps.kolps.txt
IUTA_estimates.txt
IUTA_pvalues.txt


title: B1505_D30_9.8Gy_Female

description:
B1505_D30_S0
B1505_D30_9.8Gy

value: 30 days


title: TPC-1 cells, parent cells #1

description:
tpmsTPC1.tsv
TPC1-C01

value: thyroid

value: papillary thyroid cancer


title: B1506_D40_9.8Gy_Female

description:
B1506_D40_S0
B1506_D40_9.8Gy

value: 9.8Gy thoracic radiation

value: 40 days


title: Cortex; miR-33 KO rep 4

description: Sex of animal: Female

value: miR-33 KO


title: Fl/Fl BMDM, 0h LPS, rep3

description:
Fl-231-Pool-1
wtntr003
Deseq.results.wtntr.kontr.txt


title: Cortex; miR-33 KO rep 3

description: Sex of animal: Female


title: Cortex; miR-33 KO rep 2

description: Sex of animal: Female


title: LC-2/ad cells, treated with selpercatinib for 48 h #1

description:
tpmsLC2ad.tsv
Lc2ad-Sel1

source_name: lung

value: lung

value: lung cancer

value: selpercatinib


title: LC-2/ad cells, treated with selpercatinib for 48 h #2

description:
tpmsLC2ad.tsv
Lc2ad-Sel2


title: Fl/Fl BMDM, 5h LPS, rep1

description:
Fl-229-LPS-Pool-1
wtlps007
Deseq.results.wtlps.kolps.txt
IUTA_estimates.txt
IUTA_pvalues.txt

value: Bone Marrow

value: Bone Marrow Derived Macrophages


title: Fl/Fl BMDM, 0h LPS, rep2

description:
Fl-230-Pool-1
wtntr002
Deseq.results.wtntr.kontr.txt


title: B1505_D150_9.8Gy_Female

description:
B1505_D150_S0
B1505_D150_9.8Gy

value: 150 days


title: Cortex; miR-33 KO rep 1

description: Sex of animal: Female

value: Brain cortex


title: B1506_D120_9.8Gy_Female

description:
B1506_D120_S236
B1506_D120_9.8Gy

value: Whole blood

value: 120 days


title: B1505_D9_9.8Gy_Female

description:
B1505_D9_S60
B1505_D9_9.8Gy

value: Female

value: 9 days


title: Fl/Fl BMDM, 0h LPS, rep1

description:
Fl-229-Pool-1
wtntr001
Deseq.results.wtntr.kontr.txt

value: Fl/FL


title: LC-2/ad cells, parent cells #2

description:
tpmsLC2ad.tsv
Lc2ad-cont2


title: B1505_D90_9.8Gy_Female

description:
B1505_D90_S207
B1505_D90_9.8Gy

value: 90 days


title: Input_B

city: Nice

first: Filippo

last: Massa

state: Provence-Alpes-Cote d'Azur

address: 28, Avenue de Valombrose

country: France

institute: CNRS

library_source: genomic

data_processing:
Basecalls were performed using bcl2fastq v2.17
ChIP-seq reads were trimmed using Trimmomatic trim-galore (Version 0.6.7) and groomed with FASTQ Groomer available on use.galaxy.com
ChIP-seq reads were aligned to the UCSC mm10 genome using Bowtie version 2.5.1. Only uniquely mapped reads with at most two mismatches were retained.
Broad Peaks were called usinbg bdgbroadcall utility from the MACS2 Package, with the significance cut-off q-value <=0.01. Only overlapping regions from the two replicates were maintained
Assembly: GRCm38/mm10
Supplementary files format and content: .bigwig files, consistent broadPeaks file between replictates (except for Input sample)

molecule: genomic DNA

source_name: primary podocytes

extract_protocol:
Kidneys from Dynabeads perfused mice were dissociated with Pronase/Collagenase supplemented medium for 20 minutes, the glomeruli isolated by magnetic field and further dissociated for 45 minutes with the same conditions. Single cells suspension was fixed with 1% methanol free formaldehyde, permabilized and stained with Podocin antibody before purification by FACS. Isolated podocytes were  Podocytes were then sonicated using a S220 focused-ultrasonicator (Covaris).
MicroPlex Library Preparation Kit v2 (Diagenode, C05010013)

value: primary podocytes

tag: chip antibody


title: Healthy_spleen_rep4

city: Hamburg

first: Jan Broder

last: Engler

address: Falkenried 94

department: Institut für Neuroimmunologie und Multiple Sklerose

country: Germany

institute: Universitätsklinikum Hamburg-Eppendorf

data_processing:
Alignment with STAR (v2.5.2b)
Counting by featureCounts (v1.5.1)
Analysis with DESeq2 (v1.36.0)
Assembly: ensemble.mouse.GRCm38r79
Supplementary files format and content: Rows represent genes, columns represent samples

source_name: Spleen

extract_protocol:
Qiagen RNeasy micro kit
NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs)

value: Spleen

value: Sorted MAIT cells

tag: mouse strain

tag: disease state

value: Healthy


title: LC-2/ad cells, treated with selpercatinib for 48 h #3

description:
tpmsLC2ad.tsv
Lc2ad-Sel3

value: lung


title: LC-2/ad cells, parent cells #3

description:
tpmsLC2ad.tsv
Lc2ad-cont3

value: lung cancer


title: B1505_D210_9.8Gy_Female

description:
B1505_D210_S0
B1505_D210_9.8Gy

value: 9.8Gy thoracic radiation

value: 210 days


title: Healthy_spleen_rep3


title: LC-2/ad cells, parent cells #1

description:
tpmsLC2ad.tsv
Lc2ad-cont1


title: B1505_D6_9.8Gy_Female

description:
B1505_D6_S113
B1505_D6_9.8Gy

value: 6 days


title: B1505_D60_9.8Gy_Female

description:
B1505_D60_S205
B1505_D60_9.8Gy

value: 60 days


title: H3K27me3_B


title: B1505_D180_9.8Gy_Female

description:
B1505_D180_S0
B1505_D180_9.8Gy

value: 180 days


title: Healthy_spleen_rep2


title: Input_A


title: A431, sgRNA_DUSP1_rep3

city: Madrid

first: Ana

last: Sastre-Perona

state: Madrid

address: Calle Paseo de la Castellana 261, INGEMM, Laboratorio de Epigenética, Hospital Universitario La Paz

country: Spain

institute: IdiPAZ

description:
s18_RNACL2_3
A431_RNAseq_Counts.txt

data_processing:
Mapping was done using HISAT2
StringTie was used for transcriptome assembly
Deseq was used to identify differentially expressed genes
Assembly: hg38 or mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Skin

growth_protocol:
A431 control or knock-out cells were grown in DMEM supplemented with 10% FBS and humidified atmosphenre at 5% CO2 at 37C. 100,000 cells were injected intradermically, and tumors grew for 3 weeks. Tumors were disected and cancer epithelial cells isolated using the Mouse cell Depletion kit (130-104-694, Miltenyi).
Full sections OCT from WT skin, WT SCC, Dusp1KO papilloma, Dusp1KO SCC were used to extract RNA

extract_protocol:
total RNA was extracted using Trizol and the microprep RNA extraction kit, Zymo
RNA libraries for RNA-seq were prepared using  the llumina® Stranded mRNA Prep and following the manufacture's instructions

value: Skin

value: Keratinocytes

value: DUSP1 KO

tag: group


title: H3K27me3_A


title: Healthy_spleen_rep1

value: Female


title: B1505_D40_9.8Gy_Female

description:
B1505_D40_S0
B1505_D40_9.8Gy

value: Whole blood

value: 40 days


title: A431, sgRNA_DUSP1_rep2

description:
s17_RNACL2_3
A431_RNAseq_Counts.txt


title: B1505_D3_9.8Gy_Female

description:
B1505_D3_S138
B1505_D3_9.8Gy

value: 3 days


title: H3K4me3_B

value: primary podocytes

value: H3K4me3 (Diagenode, C15410030)


title: EAE_spleen_rep4

value: Spleen

value: Sorted MAIT cells

value: EAE day 14


title: A431, sgRNA_DUSP1_rep1

description:
s16_RNACL2_1
A431_RNAseq_Counts.txt


title: H3K4me3_A


title: B1505_D21_9.8Gy_Female

description:
B1505_D21_S94
B1505_D21_9.8Gy

value: 9.8Gy thoracic radiation

value: 21 days


title: EAE_spleen_rep3


title: B1505_D15_9.8Gy_Female

description:
B1505_D15_S135
B1505_D15_9.8Gy

value: 15 days


title: H3K4me1_B

value: H3K4me1 (Diagenode, C15410037)


title: A431, sgRNA_Tomato_rep3

description:
s15_RNAAtom3
A431_RNAseq_Counts.txt

value: WT


title: IPF, rep2

city: London

first: Marco

last: Mura

state: Ontario

address: 800 Commissioners Road E

department: Medicine, Respirology

country: Canada

institute: Western University

data_processing:
Demultiplexed reads were aligned to hg38/GENCODE (v21) comprehensive annotation with STAR/2.7.9a (parameters: --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical)
Duplicate reads were removed with ‘-F 1024’ option in samtools/1.17
A count table was generated using HTSeq/2.0.2
Normalization and differential gene expression analysis were performed with edgeR/3.40.2
Nextflow pipeline and R script are available online (https://github.com/kimsjune/ILD_DSP_2023/tree/main/bulk).
Assembly: hg38
Supplementary files format and content: csv file includes raw counts for each sample

extract_protocol:
RNA was harvested using Monarch Total RNA Miniprep kit (NEB). Residual DNA was digested using DNaseI following the manufacturer's recommendation. 1-5 ug of total RNA was submitted to the McGill Genomics Centre for library preparation and sequencing.
Libraries were prepared using TruSeq ribodepleted mRNA, stranded kit by the McGill Genomics Centre.

value: lung

tag: condition

value: IPF

tag: replicate


title: EAE_spleen_rep2

tag: tissue


title: EAE_CNS_rep4

source_name: Brain and spinal cord

value: Brain and spinal cord

tag: cell type


title: B1505_Ctl_0Gy_Female

description:
B1505_Ctl_S24
B1505_Ctl_0Gy

value: Female

value: control

value: -2 days


title: B1505_D240_9.8Gy_Female

description:
B1505_D240_S238
B1505_D240_9.8Gy

value: Whole blood

value: 240 days


title: B1505_D270_9.8Gy_Female

description:
B1505_D270_S0
B1505_D270_9.8Gy

value: 270 days


title: A431, sgRNA_Tomato_rep2

description:
s14_RNAAtom2
A431_RNAseq_Counts.txt

value: Skin

value: Keratinocytes


title: A431, sgRNA_Tomato_rep1

description:
s13_RNAAtom1
A431_RNAseq_Counts.txt


title: INPUT-B

data_processing:
Basecalls were performed using bcl2fastq v2.17
ChIP-seq reads were trimmed using Trimmomatic trim-galore (Version 0.6.7) and groomed with FASTQ Groomer available on use.galaxy.com
ChIP-seq reads were aligned to the UCSC mm10 genome using Bowtie version 2.5.1. Only uniquely mapped reads with at most two mismatches were retained.
NarrowPeaks were called using MACS2 Package, with the significance cut-off q-value FDR<0.05. IDR analysis retained the constant peaks of WT1 (IDR<0.001) and MAFB (IDR<0.05) fbetween replicates.
Assembly: GRCm38/mm10
Supplementary files format and content: bamcoverage files (.bigwig), NarrowPeaks list (IDR analysis, except for Input sample)

source_name: isolated mouse podocytes

extract_protocol:
Kidneys from Dynabeads perfused mice were dissociated with Pronase/Collagenase supplemented medium for 20 minutes and the glomeruli isolated by magnetic field before crosslink with 1% methanol free formaldehyde. The reaction was quenched with 0.125M Glycerin and the glomeruli sonicated using a S220 focused-ultrasonicator (Covaris).
MicroPlex Library Preparation Kit v2 (Diagenode, C05010013)

value: isolated mouse podocytes


title: B1505_D120_9.8Gy_Female

description:
B1505_D120_S235
B1505_D120_9.8Gy

value: 9.8Gy thoracic radiation

value: 120 days


title: INPUT-A


title: EAE_CNS_rep3

value: Sorted MAIT cells

value: EAE day 14


title: EAE_spleen_rep1

value: Spleen


title: EAE_CNS_rep2


title: MAFB-B

value: anti-MAFB (SIGMA, ref. HPA005653)


title: MAFB-A


title: EAE_CNS_rep1


title: B1504_D90_9.8Gy_Female

description:
B1504_D90_S0
B1504_D90_9.8Gy

value: 90 days


title: NSIP, rep3

value: lung

value: NSIP


title: B1504_D60_9.8Gy_Female

description:
B1504_D60_S0
B1504_D60_9.8Gy

value: Female

value: 60 days


title: WT1-B

value: anti-WT1 (SantaCruz, ref. sc192)


title: CHP, rep1

value: CHP


title: CHP, rep2


title: B1504_D30_9.8Gy_Female

description:
B1504_D30_S0
B1504_D30_9.8Gy

value: Whole blood

value: 30 days


title: WT1-A


title: Ast16495

city: Charlottesville

first: Robert

last: Cornelison

state: VA

address: 345 Crispell Drive Carter-Harrison Research Building MR6 B710 Carter-Harrison Research Building MR6 B710

department: pathology

institute: UVA School of Medicine

description: 150bp seq

data_processing:
adaptor trimmed
Assembly: hg38
Supplementary files format and content: kallisto abundances

source_name: astrocytes

growth_protocol: 5% co2 37 degrees C | RPMI 10% FBS

extract_protocol:
trizol or BLADE-R\
poly-a

treatment_protocol: advillin overexpression vs control

value: astrocytes

value: astrocytes tert immortalized

value: control overexpression plasmid


title: NSIP, rep1


title: H3K4me1_A

value: primary podocytes

value: H3K4me1 (Diagenode, C15410037)


title: B1504_D102_9.8Gy_Female

description:
B1504_D102_S0
B1504_D102_9.8Gy

value: 9.8Gy thoracic radiation

value: 102 days


title: IPF, rep1

value: IPF


title: Ast16596

description: 150bp seq


title: B1504_D6_9.8Gy_Female

description:
B1504_D6_S112
B1504_D6_9.8Gy

value: 6 days


title: DLBCL_27, DE

city: Seoul

first: Yoon Kyung

last: Jeon

address: 101 Daehak-ro, Jongno-gu

department: Pathology

country: South Korea

institute: Seoul National University College of Medicine

data_processing:
The library was sequenced using an Illumina HiSeq2500 sequencer (Illumina, CA).
Low quality reads were filtered according to the following criteria; reads contain more than 10% of skipped bases (marked as ‘N’s), reads contain more than 40% of bases whose quality scores are less than 20 and reads whose average quality scores of each read is less than 20.
Filtered reads were mapped to the human reference genome (Ensembl release 77, Flicek P. et al., 2013) using the aligner Tophat
Gene expression level was measured with Cufflinks v2.1.1 (Trapnell C. et al, 2012) using the gene annotation database of Ensembl release 77
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) was calculated as the expression value.
Assembly: GRCh37
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: DLBCL

extract_protocol:
Total RNA was extracted using RNeasy with QIAshredders (Qiagen) and the RNA quality was assessed an Agilent RNA 6000 Nano kit (Agilent Technologies). 1 μg of total RNA was used for the construction of sequencing libraries.
RNA library was constructed by using the TruSeq Access RNA(Illumina, CA) according to the manufacturer’s protocol

value: DLBCL

tag: de status

value: DE

tag: cell of_origin_by_hans

value: nonGCB

tag: age at_diagnosis

tag: serum ldh

value: Elevated


title: High_Plate3.H4

city: Sendai

first: Kota

last: Sato

state: Miyagi

address: 1-1, Seiryo-machi, Aoba-ku

department: Ophthalmology

institute: Tohoku University

library_source: transcriptomic single cell

data_processing:
Obtained raw reads were trimmed and quality-filtered using the Trim Galore! (version 0.4.4), Trimmomatic (version 0.36), and cutadapt (version 1.16) software. Trimmed reads were then mapped to the mouse GRCm38.p6 (mm10) genome with STAR software (version 2.7.2b). Reads on annotated genes were counted using featureCounts (version 1.6.1). FPKM values were calculated from mapped reads by normalizing to total counts and transcript.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include FPKM values for each sample.

source_name: retina

extract_protocol:
Total RNA were directly extracted with lysis buffer inculding Rnase inhibitor from single cell sorted with FACS.
RNA sequence library preparation, sequencing, mapping, gene expression, and gene ontology (GO) enrichment analysis were performed by DNAFORM (Yokohama, Kanagawa, Japan). cDNA synthesis and amplification of RNA derived from lysed cell was sequentially conducted in a same PCR tube. After purification, amplified cDNA was validated and quantified. Following tagmentation of cDNA, adapter addition and PCR amplification were conducted using Nextera XT DNA Library Prep Kit (Illumina).

value: microglia

value: retina

tag: strain

tag: age

value: 12 weeks old

value: 10mg/kg ripasudil treatment


title: B1504_D40_9.8Gy_Female

description:
B1504_D40_S221
B1504_D40_9.8Gy

data_processing:
The FASTQ sequences were trimmed using CutAdapt v. 2.10 [https://doi.org/10.14806/ej.17.1.200] with the following settings: “--nextseq-trim=2 --trim-n -n 5 -O 5 -q 10,10 -m 15 -j 0” and aligned using STAR v. 2.7.6a [https://doi.org/10.1093/bioinformatics/bts635] with parameters set as recommended by ENCODE3 consortium (https://www.encodeproject.org/pipelines/ENCPL444CYA/). Macaca mulatta (Rhesus monkey) genome assembly Mmul_10 (release date: Feb. 2019) with RefSeq annotation (accession number GCF_003339765.1) was used as a reference. Counting was performed with the help of Subread package v. 2.0.1 [10.1093/bioinformatics/btt656]. The count matrix was processed in R (1) for further analysis.
Assembly: Macaca mulatta (Rhesus monkey) genome assembly Mmul_10 (release date: Feb. 2019).
Supplementary files format and content: *.txt: Tab-delimited text files include raw counts and normalized counts for each Sample.

source_name: Whole blood

extract_protocol: Blood samples were procured from each of the animals (n = 28) two days before irradiation as control, every three days post-irradiation for the initial 30 days, on days 40, 50, and 60, and approximately every 30 days until the euthanization of all surviving animals at day 270 post-irradiation.

value: Whole blood

tag: Sex

value: Female

tag: treatment

tag: time point

value: 40 days


title: High_Plate3.H3


title: GCTB, scRNAseq

city: Guangzhou

first: Wei

last: Luo

address: No.396, Tongfu Middle Road, Haizhu District, Guangzhou city

institute: Guangzhou Red Cross Hospital

description: BD Rhapsody

data_processing:
Basecalls performed using CASAVA version 1.8
Umi-tools was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:  MT% < 30%;   Cell Gene Number < Median Gene Number * 2;  Cell Gene Number > 200. PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Assembly: GRCh38_Ensembl
Supplementary files format and content: Single cell matrix files

source_name: giant cell tumor of bone

extract_protocol:
Pulmonary artery tissues were placed in DMEM/F12(Gibco), and cut into small fragments and digested them with collagenase II (Invitrogen) for 2h at 37℃. After digestion, the obtained cells were filtered through a 70μm filter and collect it into a collection tube.
Sequencing libraries were conducted using the BD Rhapsody Single-Cell Analysis System (BD Biosciences), following the manufacture's protocol.

value: giant cell tumor of bone

value: Excision of giant cell tumor of left distal femur


title: High_Plate3.H6


title: DLBCL_25, DE


title: ast435a astrocytes

description: 150bp seq

value: astrocytes

tag: cell line

value: astrocytes tert immortalized

tag: genotype

value: control overexpression plasmid


title: High_Plate3.H5


title: B1504_D9_9.8Gy_Female

description:
B1504_D9_S59
B1504_D9_9.8Gy

value: 9.8Gy thoracic radiation

value: 9 days

tag: animal id


title: Human embryonic stem cells (WA09) at Day 0 of vagal neural crest differentation

city: Vienna

first: Igor

last: Adameyko

address: Spitalgass 4

department: Neuroimmunology Department

country: Austria

institute: Medical University of Vienna

description: 10x Genomics

data_processing:
The demultiplexing, barcoded pprocessing, gene counting and aggregationg were made in Cell Ranger software version 7.0.1 (https://www.10xgenomics.com/support/software/cell-ranger/release-notes/cr-release-notes)
Assembly: GRCh38-2020-A
Supplementary files format and content: adata.h5ad
Supplementary files format and content: The file contains preprocessed, normalized count data of all experiments in the h5ad-file format.

source_name: WA09 embryonic stem cells

extract_protocol:
Cells were dissociated into single cells at specific time points using TrypLE (5min at 37oC). Cells were resuspended in DMEM:F12 and centrifuged to remove dissociation reagent. To crypreserve, cells were resuspended in STEMCELL-BANKER and stored at -80oC. Cells were shipped to Single Cell discoveries for scRNAsequencing analysis using 10x genomics
Library preparation was carried out using the 10x Genomics 3' v3.1 kit followed by sequencing on an Illumina Novaseq 6000.

value: WA09 embryonic stem cells

value: Embryonic stem cells

value: wild type


title: DLBCL_24, nonDE

value: DLBCL

value: nonDE

value: GCB

value: Male

value: Elevated


title: DLBCL_28, nonDE

value: Female


title: B1504_D21_9.8Gy_Female

first: Uma

last: Shankavaram

address: 9000 Rockville Pike

description:
B1504_D21_S130
B1504_D21_9.8Gy

value: Whole blood

value: 21 days


title: B1504_D15_9.8Gy_Female

description:
B1504_D15_S82
B1504_D15_9.8Gy

value: 15 days


title: DLBCL_23, DE

value: DE

value: nonGCB


title: High_Plate3.G5

value: microglia

value: retina

value: 12 weeks old

value: 10mg/kg ripasudil treatment


title: DLBCL_21, nonDE


title: Patient 17 survived more than 5 year

city: Rotterdam

first: Jie

last: Ju

address: Dr. Molewaterplein 40

country: Netherlands

institute: Erasmus University Medical Center

data_processing:
Quality check were performed using FastQC v0.11.9 and FastQA v3.1.25 QC tools
Quality trimming and adapter removal of the raw sequencing reads were performed using fastp v0.20.1 (default settings)
The short reads were mapped to the indexed human (GRCh38.p13) from Ensembl using the splice junction-aware mapper STAR v2.5.4b4
The aligned reads are stored in a sorted BAM format and indexed with the samtools v1.10 package.
Feature counting based on the mapped locations in the alignment file the frequency of how often a read was mapped on a transcript was determined with HTSeq v0.11.0.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: Primary PDAC tumor tissue

growth_protocol: Surgical specimens were formalin-fixed paraffin-embedded (FFPE)

extract_protocol:
rRNA was depleted from total RNA using the Qiagen fast select kit (#334376 and #335927).
The sample preparation was performed according to the protocol "NEBNext Ultra II Directional RNA Library Prep Kit for Illumina"

treatment_protocol: treatment naïve

value: Primary PDAC tumor tissue

value: treatment naive


title: High_Plate3.G4


title: B1503_D90_9.8Gy_Female

city: Bethesda

institute: NIH

description:
B1503_D90_S0
B1503_D90_9.8Gy

value: 9.8Gy thoracic radiation

value: 90 days


title: B1504_D3_9.8Gy_Female

description:
B1504_D3_S103
B1504_D3_9.8Gy

value: 3 days


title: Human embryonic stem cells (WA09) at Day 6 of vagal neural crest differentation

description: 10x Genomics

value: WA09 embryonic stem cells

value: Day 6 Vagal neural crest

value: wild type


title: Patient 15 survived more than 5 year


title: DLBCL_26, DE

value: DLBCL

value: GCB

value: Male

value: Elevated


title: High_Plate3.H1


title: High_Plate3.G2


title: Human embryonic stem cells (WA09) at Day 4 of vagal neural crest differentation

description: 10x Genomics

value: Day 4 Anterior neural crest


title: High_Plate3.H2

value: microglia


title: DLBCL_18, nonDE

value: nonDE

value: nonGCB


title: NSIP, rep2

value: lung

value: NSIP


title: Patient 19 survived more than 5 year

value: Primary PDAC tumor tissue

value: treatment naive


title: High_Plate3.G6

value: retina

value: 12 weeks old

value: 10mg/kg ripasudil treatment


title: B1503_D240_9.8Gy_Female

description:
B1503_D240_S0
B1503_D240_9.8Gy

value: Whole blood

value: Female

value: 9.8Gy thoracic radiation

value: 240 days


title: High_Plate3.F5


title: DLBCL_17, DE

value: DLBCL

value: DE

value: Male


title: DLBCL_16, nonDE

value: Elevated


title: Patient 11 survived more than 5 year


title: High_Plate3.F4

value: microglia


title: B1503_D30_9.8Gy_Female

description:
B1503_D30_S0
B1503_D30_9.8Gy

value: 30 days


title: Patient 18 survived more than 5 year


title: DLBCL_22, DE

value: nonGCB


title: DLBCL_15, nonDE

value: nonDE

value: GCB


title: B1503_D180_9.8Gy_Female

description:
B1503_D180_S0
B1503_D180_9.8Gy

value: 180 days


title: High_Plate3.G3

value: retina


title: High_Plate3.F3

value: 12 weeks old


title: B1503_D60_9.8Gy_Female

description:
B1503_D60_S0
B1503_D60_9.8Gy

value: 60 days


title: High_Plate2.H6

value: 10mg/kg ripasudil treatment


title: High_Plate2.H5


title: Patient 14 survived more than 5 year

value: Primary PDAC tumor tissue

value: treatment naive


title: DLBCL_20, nonDE

value: Normal


title: B1503_D9_9.8Gy_Female

description:
B1503_D9_S58
B1503_D9_9.8Gy

value: Whole blood

value: Female

value: 9.8Gy thoracic radiation

value: 9 days


title: Patient 13 survived more than 5 year


title: DLBCL_19, nonDE

value: DLBCL

value: Male

value: Elevated


title: High_Plate3.G1

value: microglia


title: Patient 15 survived less than 6 months


title: Patient 12 survived more than 5 year


title: Patient 16 survived less than 6 months


title: DLBCL_12, DE

value: DE

value: nonGCB


title: B1503_D270_9.8Gy_Female

description:
B1503_D270_S0
B1503_D270_9.8Gy

value: 270 days


title: High_Plate2.H3

value: retina

value: 12 weeks old


title: B1503_D40_9.8Gy_Female

description:
B1503_D40_S220
B1503_D40_9.8Gy

value: 40 days


title: High_Plate3.F6

value: 10mg/kg ripasudil treatment


title: B1503_D210_9.8Gy_Female

description:
B1503_D210_S0
B1503_D210_9.8Gy

value: 210 days


title: Patient 7 survived more than 5 year

value: Primary PDAC tumor tissue

value: treatment naive


title: Patient 1 survived more than 5 year


title: B1503_D150_9.8Gy_Female

description:
B1503_D150_S0
B1503_D150_9.8Gy

value: Whole blood

value: Female

value: 150 days


title: DLBCL_14, DE

value: DLBCL

value: Normal


title: Patient 2 survived more than 5 year


title: B1503_D3_9.8Gy_Female

description:
B1503_D3_S102
B1503_D3_9.8Gy

value: 9.8Gy thoracic radiation

value: 3 days


title: B1503_D120_9.8Gy_Female

description:
B1503_D120_S0
B1503_D120_9.8Gy

value: 120 days


title: DLBCL_13, nonDE

value: nonDE

value: nonGCB

value: Male

value: Elevated


title: Patient 6 survived more than 5 year


title: DLBCL_08, nonDE


title: High_Plate2.H4

value: microglia

value: retina

value: 12 weeks old


title: DLBCL_11, nonDE

value: GCB


title: B1503_D15_9.8Gy_Female

description:
B1503_D15_S81
B1503_D15_9.8Gy

value: 15 days


title: B1503_D6_9.8Gy_Female

description:
B1503_D6_S47
B1503_D6_9.8Gy

value: Whole blood

value: 6 days


title: DLBCL_10, nonDE

value: Female


title: Patient 10 survived less than 6 months

value: Primary PDAC tumor tissue

value: treatment naive


title: Patient 14 survived less than 6 months


title: Patient 9 survived less than 6 months


title: High_Plate2.H2

value: 10mg/kg ripasudil treatment


title: DLBCL_05, DE

value: DLBCL

value: DE


title: DLBCL_09, DE


title: High_Plate2.H1


title: Patient 12 survived less than 6 months


title: Patient 8 survived less than 6 months


title: High_Plate2.G3


title: B1503_D21_9.8Gy_Female

description:
B1503_D21_S93
B1503_D21_9.8Gy

value: 9.8Gy thoracic radiation

value: 21 days


title: High_Plate2.G6


title: Patient 11 survived less than 6 months


title: DLBCL_07, DE

value: nonGCB


title: DLBCL_04, DE

value: Normal


title: High_Plate2.G5

value: microglia


title: DLBCL_03, DE

value: Elevated


title: B1504_Ctl_0Gy_Female

description:
B1504_Ctl_S133
B1504_Ctl_0Gy

value: control

value: -2 days


title: High_Plate2.G4

value: retina

value: 12 weeks old


title: B1502_D90_9.8Gy_Female

description:
B1502_D90_S0
B1502_D90_9.8Gy

value: Whole blood

value: 90 days


title: B1502_D240_9.8Gy_Female

description:
B1502_D240_S0
B1502_D240_9.8Gy

value: Female

value: 240 days


title: B1503_Ctl_0Gy_Female

description:
B1503_Ctl_S97
B1503_Ctl_0Gy


title: Patient 7 survived less than 6 months

value: Primary PDAC tumor tissue

value: treatment naive


title: DLBCL_01, DE

value: DLBCL

value: DE


title: Patient 4 survived less than 6 months


title: Patient 2 survived less than 6 months


title: High_Plate2.G1

value: 10mg/kg ripasudil treatment


title: Subj_169, liver, middle aged, early MASLD [104538-001-025]

city: Leiden

last: Kleemann

address: Sylviusweg 71

institute: The Netherlands Organisation for Applied Scientific Research

data_processing:
Quality filtering and adapter-trimming of the Illumina NovaSeq6000 fastq files was performed by TRIMMOMATIC software
Trimmed Fastq files were merged (in case of Paired-end reads) and aligned to the reference genome using the STAR 2.5 algorithm with default settings (https://github.com/alexdobin/STAR).
Based on the mapped read locations and the gene annotation, Htseq-count 0.6.1p1 was used to count the read mapping frequency/gene (transcript region) resulting in count.files.
Assembly: Homo_sapiens.GRCh38.gencode.v29
Supplementary files format and content: The count files contain the # reads mapped per gene (not normalised per sample). These counts serve as input for the statistical analysis using DEseq2 package.

source_name: liver

extract_protocol:
RNA was extracted from ~10 mg snap-frozen liver tissue using a total-RNA isolation kit (Bio-connect, Huissen, the Netherlands) as described  previously.25,26 RNA concentrations were determined using Nanodrop 1000 (Isogen Life Science, De Meern, the Netherlands) and RNA integrity was assessed using RNA 6000 Nano LabChip 669 kit and a bioanalyzer 2100 (Agilent Technologies, Amstelveen, the Netherlands). NGS (NovaSeq6000) was performed at GenomeScan (Leiden, the Netherlands).
Ribosomal RNA (rRNA) was depleted from total RNA (rRNA depletion kit NEB# E6310, Biolabs), the total RNA was processed into tagged random sequence libraries (NEBNext Ultra II Directional RNA Library Prep Kit, NEB #E7760S/L for Illumina, Biolabs) and sample quality was checked for proper size distribution (300-500 bp peak, Fragment Analyzer). The mixed (multiplex) sample libraries were sequenced on an Illumina NovaSeq6000 sequencer with a paired-read 150-cycle sequencing protocol at GenomeScan BV (Leiden, the Netherlands), resulting in ~45 million read counts per sample (median=41, avg=49, min=30, max=208).
Clustering and DNA sequencing using the NovaSeq6000 was performed according to manufacturer's protocols. A concentration of 1.1 nM of DNA was used yielding paired end reads (2x 150bp). NovaSeq control software NCS v1.6 was used. Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA3.4.4 and Bcl2fastq v2.20.

value: liver

tag: subject id

value: middle aged

tag: subject status

value: early MASLD

value: x

tag: brainparameters

value: ContactAuthor


title: HTR8_siYTHDC1-2_rep1

city: Shanghai

last: Li

address: 910# Hengshan Road, Shanghai, China.

institute: International Peace Maternity and Child Health Hospital

description:
RNA_H8-seq.count
H8-siY-3

data_processing:
PCR duplicates were marked with the Picard “Mark Duplicates” utility and removed from further analysis.
Gene annotated in NCBI were quantified using featureCounts
Peaks were called using MACS2 with the significance cut-off q-value <=0.01
Sequenced reads were trimmed for adaptor sequence and low-quality bases, then mapped to hg38 whole genome using Bowtie with standard alignment parameters.
Bam files were converted to BigWig files using deepTools.
Assembly: hg38
Supplementary files format and content: bigWig, MeRIP-seq peak (except for Input sample)
Supplementary files format and content: txt, counts for each RIP-seq sample

source_name: placenta

growth_protocol: The HTR-8/SVneo cells were cultured in DMEM/F12 (Gibco, Thermo Fisher Scientific-CN),medium was routinely supplemented with 10% fetal bovine serum (Hyclone, Thermo Fisher Scientific-CN) and 1% antibiotic solution (Gibco).

extract_protocol:
Total RNA from HTR-8/SVneo cells were extracted using TRIzol reagent (Invitrogen, CA, USA) following the manufacturer's instructions.
For the RNA-seq, the sequencing library was prepared using an Illumina mRNA-seq sample preparation kit and was then subjected to paired-end sequencing on the Illumina HiSeq platform.                                                      For the RIP-seq, the sequencing library was prepared deploying NEBNext Ultra Directional RNA Library Prep kit (New England Biolabs, USA) and sequenced on the Illumina HiSeq 3000 platform. For the MeRIP-seq, the library was prepared by smart-seq method. Both the input samples without IP and the m6A IP samples were subjected to 150-bp, paired-end sequencing on an Illumina NovaSeq 6000 sequencer.                                                                                For the ChIPseq, input amounts of DNA was converted into high quality libraries for next-generation sequencing on the Illumina platform using the NEBNext Ultra II DNA Library Prep Kit. Bead based size selection was performed for final library size selection to obtain ChIP-seq libraries containing fragments of 250 bp to 500 bp.

treatment_protocol: Before siRNA transfection, around 0.4 million HTR-8/SVneo cells  were seeded in to 6 well plate per

tag: tissue

value: placenta

value: trophoblast cells


title: DLBCL_02, nonDE

value: nonDE

value: nonGCB

value: Male

value: Normal


title: HTR8_siNC2_rep2

description:
RNA_H8-seq.count
H8-siNC4

tag: cell type

value: siNC


title: DLBCL_06, nonDE

tag: de status

value: Elevated


title: Patient 3 survived less than 6 months

value: Primary PDAC tumor tissue

value: treatment naive


title: High_Plate1.H6

value: microglia

value: retina

value: 12 weeks old


title: High_Plate2.F6

value: 10mg/kg ripasudil treatment


title: B1502_D60_9.8Gy_Female

description:
B1502_D60_S0
B1502_D60_9.8Gy

value: Whole blood

value: Female

value: 9.8Gy thoracic radiation

value: 60 days


title: High_Plate2.F5


title: HTR8_siNC2_rep1

description:
RNA_H8-seq.count
H8-siNC3

value: placenta

value: trophoblast cells


title: B1502_D210_9.8Gy_Female

description:
B1502_D210_S0
B1502_D210_9.8Gy

value: 210 days


title: Subj_166, liver, middle aged, early MASLD [104538-001-022]

value: liver

value: middle aged

value: early MASLD

value: x

value: ContactAuthor


title: B1502_D30_9.8Gy_Female

description:
B1502_D30_S0
B1502_D30_9.8Gy

value: 30 days


title: High_Plate2.F4

value: microglia


title: High_Plate2.F3

value: retina


title: B1502_D6_9.8Gy_Female

description:
B1502_D6_S111
B1502_D6_9.8Gy

value: 6 days


title: Subj_168, liver, middle aged, early MASLD [104538-001-024]


title: High_Plate1.H3

value: 12 weeks old

value: 10mg/kg ripasudil treatment


title: B1502_D270_9.8Gy_Female

description:
B1502_D270_S0
B1502_D270_9.8Gy

value: Whole blood

value: Female

value: 270 days


title: B1502_D150_9.8Gy_Female

description:
B1502_D150_S0
B1502_D150_9.8Gy

value: 9.8Gy thoracic radiation

value: 150 days


title: Subj_167, liver, middle aged, early MASLD [104538-001-023]


title: Subj_163, liver, middle aged, early MASLD [104538-001-019]


title: High_Plate1.H2


title: B1502_D120_9.8Gy_Female

description:
B1502_D120_S0
B1502_D120_9.8Gy

value: 120 days


title: HTR8_siYTHDC1-2_rep2

description:
RNA_H8-seq.count
H8-siY1-R3

value: placenta

value: trophoblast cells


title: Subj_161, liver, middle aged, early MASLD [104538-001-017]

value: liver

value: middle aged

value: early MASLD


title: High_Plate1.H5


title: B1502_D21_9.8Gy_Female

description:
B1502_D21_S92
B1502_D21_9.8Gy

value: 21 days


title: B1502_D180_9.8Gy_Female

description:
B1502_D180_S0
B1502_D180_9.8Gy

value: 180 days


title: HTR8_siNC1_rep1

description:
RNA_H8-seq.count
H8-siNC1

value: siNC


title: B1502_D9_9.8Gy_Female

description:
B1502_D9_S57
B1502_D9_9.8Gy

value: 9 days


title: HTR8_siYTHDC1-1_rep2

description:
RNA_H8-seq.count
H8-siY-1-R1


title: High_Plate1.H4

value: microglia

value: retina

value: 12 weeks old


title: Subj_160, liver, middle aged, early MASLD [104538-001-016]

value: ContactAuthor


title: High_Plate1.G6

value: 10mg/kg ripasudil treatment


title: Subj_159, liver, middle aged, early MASLD [104538-001-015]

value: x


title: B1502_D15_9.8Gy_Female

description:
B1502_D15_S134
B1502_D15_9.8Gy

value: Whole blood

value: Female

value: 9.8Gy thoracic radiation

value: 15 days


title: HTR8_siYTHDC1-1_rep1

description:
RNA_H8-seq.count
H8-siY-1

value: placenta

value: trophoblast cells


title: Subj_164, liver, middle aged, early MASLD [104538-001-020]

value: liver

value: middle aged

value: early MASLD


title: MS_20_Treg_Exvivo

first: Tomokazu

middle: S

last: Sumida

state: CT

address: 300 George St,, 3rd floor room349

department: Neurology

institute: Neurology, Yale School of Medicine

data_processing:
After sequencing, adapter sequences and poor-quality bases (quality score < 3) were trimmed with Trimmomatic. Remaining bases were trimmed if their average quality score in a 4 bp sliding window fell below 5. FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to obtain quality control metrics before and after trimming. Remaining reads were aligned to the GRCh38 human genome assembly with STAR 2.5.2. We used Picard (https://github.com/broadinstitute/picard) to remove optical duplicates and to compile alignment summary statistics and RNA-seq summary statistics. After alignment, reads were quantitated to gene level with RSEM using the GENCODE annotation.
Assembly: hg38
Supplementary files format and content: txt

source_name: primary T cells

extract_protocol: cDNAs were directly generated from lysed cells by using SMART-Seq v4 Ultra Low Input RNA Kit for sequencing (Takara/Clontech). Barcoded libraries were generated by the Nextera XT DNA Library Preparation kit (Illumina) and sequenced with a 2x100 bp paired-end protocol on the HiSeq 2500 Sequencing System (Illumina).

value: Treg

tag: disease

value: MS


title: B1502_D3_9.8Gy_Female

description:
B1502_D3_S37
B1502_D3_9.8Gy

value: 3 days


title: High_Plate1.G5

value: microglia

value: retina


title: High_Plate1.G3

value: 12 weeks old


title: B1501_D60_9.8Gy_Female

description:
B1501_D60_S0
B1501_D60_9.8Gy

value: 60 days


title: High_Plate1.H1

value: 10mg/kg ripasudil treatment


title: MS_19_Teff_Exvivo

value: Teff


title: MS_21_Teff_Exvivo


title: B1501_D30_9.8Gy_Female

description:
B1501_D30_S0
B1501_D30_9.8Gy

value: Whole blood

value: Female

value: 30 days


title: B1502_Ctl_0Gy_Female

description:
B1502_Ctl_S96
B1502_Ctl_0Gy

value: control

value: -2 days


title: Subj_156, liver, middle aged, early MASLD [104538-001-012]

value: liver

value: x

value: ContactAuthor


title: Subj_165, liver, middle aged, early MASLD [104538-001-021]

value: middle aged

value: early MASLD


title: Subj_157, liver, middle aged, early MASLD [104538-001-013]


title: HTR8_siNC1_rep2

description:
RNA_H8-seq.count
H8-siNC2

value: placenta

value: trophoblast cells

value: siNC


title: MS_19_Treg_Exvivo

value: Treg

value: MS


title: High_Plate1.G1

value: microglia

value: retina

value: 12 weeks old

value: 10mg/kg ripasudil treatment


title: MS_18_Teff_Exvivo

value: Teff


title: B1502_D40_9.8Gy_Female

description:
B1502_D40_S219
B1502_D40_9.8Gy

value: Whole blood

value: Female

value: 9.8Gy thoracic radiation

value: 40 days


title: MS_21_Treg_Exvivo


title: MS_20_Teff_Exvivo


title: High_Plate1.G4


title: Subj_158, liver, middle aged, early MASLD [104538-001-014]

value: liver

value: x

value: ContactAuthor


title: B1501_D90_9.8Gy_Female

description:
B1501_D90_S0
B1501_D90_9.8Gy

value: 90 days


title: MS_17_Teff_Exvivo


title: High_Plate1.F4


title: Subj_151, liver, middle aged, early MASLD [104538-001-007]

value: middle aged

value: early MASLD


title: B1501_D6_9.8Gy_Female

description:
B1501_D6_S46
B1501_D6_9.8Gy

value: 6 days


title: Subj_149, liver, middle aged, early MASLD [104538-001-006]


title: High_Plate1.F3


title: Subj_148, liver, middle aged, early MASLD [104538-001-005]


title: High_Plate1.G2


title: Subj_155, liver, middle aged, early MASLD [104538-001-011]


title: B1501_D150_9.8Gy_Female

description:
B1501_D150_S0
B1501_D150_9.8Gy

value: 150 days


title: High_Plate1.F6

value: microglia


title: Subj_154, liver, middle aged, early MASLD [104538-001-010]


title: MS_16_Treg_Exvivo

value: Treg

value: MS


title: B1501_D3_9.8Gy_Female

description:
B1501_D3_S101
B1501_D3_9.8Gy

value: 3 days


title: MS_18_Treg_Exvivo


title: Low_Plate3.F1

value: retina

value: 14 weeks old

value: 1mg/kg ripasudil treatment


title: Subj_147, liver, middle aged, early MASLD [104538-001-004]


title: B1501_D120_9.8Gy_Female

description:
B1501_D120_S0
B1501_D120_9.8Gy

value: Whole blood

value: Female

value: 9.8Gy thoracic radiation

value: 120 days


title: Subj_152, liver, middle aged, early MASLD [104538-001-008]

value: liver

value: x

value: ContactAuthor


title: High_Plate1.F5

value: 12 weeks old

value: 10mg/kg ripasudil treatment


title: MS_17_Treg_Exvivo


title: B1501_D9_9.8Gy_Female

description:
B1501_D9_S56
B1501_D9_9.8Gy

value: 9 days


title: MS_16_Teff_Exvivo

value: Teff


title: B1501_Ctl_0Gy_Female

description:
B1501_Ctl_S132
B1501_Ctl_0Gy

value: control

value: -2 days


title: B1501_D15_9.8Gy_Female

description:
B1501_D15_S80
B1501_D15_9.8Gy

value: 15 days


title: B1501_D40_9.8Gy_Female

description:
B1501_D40_S0
B1501_D40_9.8Gy

value: 40 days


title: Subj_133, liver, middle aged, early MASLD [104259-001-009]

value: middle aged

value: early MASLD


title: Subj_41, liver, middle aged, early MASLD [104259-001-003]


title: MS_13_Teff_Exvivo

value: MS


title: Low_Plate3.F2

value: microglia

value: retina

value: 14 weeks old

value: 1mg/kg ripasudil treatment


title: Low_Plate3.E4


title: Subj_89, liver, middle aged, early MASLD [104019-002-023]

value: liver

value: x


title: B1006_D90_9.8Gy_Male

description:
B1006_D90_S0
B1006_D90_9.8Gy

value: Whole blood

value: Male

value: 9.8Gy thoracic radiation

value: 90 days


title: MS_11_Teff_Exvivo

value: Teff


title: B1501_D21_9.8Gy_Female

description:
B1501_D21_S129
B1501_D21_9.8Gy

value: Female

value: 21 days


title: MS_15_Teff_Exvivo


title: Subj_146, liver, middle aged, early MASLD [104538-001-003]

value: ContactAuthor


title: Low_Plate3.E6


title: MS_14_Teff_Exvivo


title: B1006_D120_9.8Gy_Male

description:
B1006_D120_S0
B1006_D120_9.8Gy

value: 120 days


title: Low_Plate3.E5


title: MS_10_Teff_Exvivo


title: Low_Plate3.D5


title: Subj_72, liver, middle aged, early MASLD [104019-002-019]

value: middle aged

value: early MASLD


title: MS_12_Teff_Exvivo

value: MS


title: B1006_D60_9.8Gy_Male

description:
B1006_D60_S0
B1006_D60_9.8Gy

value: 60 days


title: MS_12_Treg_Exvivo

value: Treg


title: Subj_5, liver, middle aged, early MASLD [104259-001-001R]


title: MS_10_Treg_Exvivo


title: Subj_67, liver, middle aged, early MASLD [104019-002-017]


title: Low_Plate3.E2

value: microglia

value: retina

value: 14 weeks old

value: 1mg/kg ripasudil treatment


title: High_Plate2.G2

value: 12 weeks old

value: 10mg/kg ripasudil treatment


title: B1006_D30_9.8Gy_Male

description:
B1006_D30_S0
B1006_D30_9.8Gy

value: Whole blood

value: Male

value: 9.8Gy thoracic radiation

value: 30 days


title: Subj_85, liver, middle aged, early MASLD [104019-002-022]

value: liver

value: x

value: ContactAuthor


title: Low_Plate3.E1


title: Low_Plate3.D3


title: MS_11_Treg_Exvivo


title: Subj_76, liver, middle aged, early MASLD [104019-002-021]

value: middle aged

value: early MASLD


title: Low_Plate3.D6


title: Low_Plate3.E3


title: B1006_D9_9.8Gy_Male

description:
B1006_D9_S55
B1006_D9_9.8Gy

value: 9 days


title: Subj_20, liver, middle aged, early MASLD [104019-002-007]


title: B1006_D6_9.8Gy_Male

description:
B1006_D6_S110
B1006_D6_9.8Gy

value: 6 days


title: Low_Plate3.D4

value: microglia


title: B1006_D40_9.8Gy_Male

description:
B1006_D40_S0
B1006_D40_9.8Gy

value: 40 days


title: Subj_12, liver, middle aged, early MASLD [104019-002-004]


title: MS_9_Teff_Exvivo

value: Teff

value: MS


title: MS_7_Teff_Exvivo


title: Low_Plate3.D1

value: retina

value: 14 weeks old

value: 1mg/kg ripasudil treatment


title: Subj_114, liver, middle aged, early MASLD [104019-001-090]


title: B1006_D3_9.8Gy_Male

description:
B1006_D3_S100
B1006_D3_9.8Gy

value: Whole blood

value: Male

value: 3 days


title: B1005_D90_9.8Gy_Male

description:
B1005_D90_S0
B1005_D90_9.8Gy

value: 9.8Gy thoracic radiation

value: 90 days


title: B1006_D21_9.8Gy_Male

description:
B1006_D21_S128
B1006_D21_9.8Gy

value: 21 days


title: MS_8_Treg_Exvivo

value: Treg


title: Subj_4, liver, middle aged, early MASLD [104019-002-001]

value: liver

value: middle aged

value: early MASLD

value: x

value: ContactAuthor


title: MS_7_Treg_Exvivo


title: Low_Plate3.C6

value: microglia


title: Subj_34, liver, middle aged, early MASLD [104019-002-010]


title: Low_Plate3.C5


title: B1005_D60_9.8Gy_Male

description:
B1005_D60_S0
B1005_D60_9.8Gy

value: 60 days


title: MS_8_Teff_Exvivo

value: Teff

value: MS


title: MS_6_Treg_Exvivo


title: MS_5_Teff_Exvivo


title: MS_6_Teff_Exvivo


title: Subj_122, liver, middle aged, early MASLD [104019-001-082]


title: B1005_D120_9.8Gy_Male

description:
B1005_D120_S0
B1005_D120_9.8Gy

value: 120 days


title: Low_Plate2.E5

value: retina

value: 14 weeks old

value: 1mg/kg ripasudil treatment


title: Subj_113, liver, middle aged, early MASLD [104019-001-089]


title: Low_Plate2.F2


title: MS_4_Teff_Exvivo


title: B1005_D9_9.8Gy_Male

description:
B1005_D9_S54
B1005_D9_9.8Gy

value: Whole blood

value: Male

value: 9.8Gy thoracic radiation

value: 9 days


title: Low_Plate3.D2


title: Low_Plate2.F1


title: Subj_126, liver, middle aged, early MASLD [104019-001-085]

value: liver


title: Subj_116, liver, middle aged, early MASLD [104019-001-076]

value: middle aged


title: B1005_D30_9.8Gy_Male

description:
B1005_D30_S0
B1005_D30_9.8Gy

value: 30 days


title: MS_4_Treg_Exvivo

value: Treg


title: Low_Plate2.E4


title: B1006_D15_9.8Gy_Male

description:
B1006_D15_S79
B1006_D15_9.8Gy

value: 15 days


title: Subj_115, liver, middle aged, early MASLD [104019-001-075]

value: early MASLD

value: x

value: ContactAuthor


title: B1005_D40_9.8Gy_Male

description:
B1005_D40_S0
B1005_D40_9.8Gy

value: 40 days


title: MS_3_Teff_Exvivo

value: Teff

value: MS


title: B1006_Ctl_0Gy_Male

description:
B1006_Ctl_S23
B1006_Ctl_0Gy

value: control

value: -2 days


title: MS_3_Treg_Exvivo


title: MS_5_Treg_Exvivo


title: Low_Plate2.E6

value: microglia

value: retina

value: 14 weeks old

value: 1mg/kg ripasudil treatment


title: Subj_112, liver, middle aged, early MASLD [104019-001-072]

value: liver


title: B1005_D6_9.8Gy_Male

description:
B1005_D6_S109
B1005_D6_9.8Gy

value: Whole blood

value: Male

value: 9.8Gy thoracic radiation

value: 6 days


title: Low_Plate2.D6


title: Low_Plate2.E3


title: MS_2_Treg_Exvivo

value: Treg


title: Low_Plate2.D5


title: Low_Plate2.E2


title: B1005_Ctl_0Gy_Male

description:
B1005_Ctl_S131
B1005_Ctl_0Gy


title: Subj_99, liver, middle aged, early MASLD [104019-001-061]

value: middle aged

value: early MASLD

value: x


title: B1005_D3_9.8Gy_Male

description:
B1005_D3_S36
B1005_D3_9.8Gy

value: 3 days


title: HC_21_Teff_Exvivo

value: Teff

value: HC


title: Low_Plate2.E1


title: B1004_D90_9.8Gy_Male

description:
B1004_D90_S0
B1004_D90_9.8Gy

value: 90 days


title: B1005_D21_9.8Gy_Male

description:
B1005_D21_S137
B1005_D21_9.8Gy

value: 21 days


title: Subj_117, liver, middle aged, early MASLD [104019-001-077]

value: ContactAuthor


title: Subj_97, liver, middle aged, early MASLD [104019-001-059]


title: Low_Plate2.D3

value: microglia

value: retina

value: 14 weeks old


title: HC_20_Teff_Exvivo


title: Subj_83, liver, middle aged, early MASLD [104019-001-049]

value: liver


title: MS_2_Teff_Exvivo

value: MS


title: Low_Plate2.D2

value: 1mg/kg ripasudil treatment


title: B1005_D15_9.8Gy_Male

description:
B1005_D15_S78
B1005_D15_9.8Gy

value: Whole blood

value: Male

value: 9.8Gy thoracic radiation

value: 15 days


title: Subj_103, liver, middle aged, early MASLD [104019-001-065]

value: middle aged

value: early MASLD


title: Low_Plate2.D4


title: Subj_105, liver, middle aged, early MASLD [104019-001-066]

value: x


title: Subj_82, liver, middle aged, early MASLD [104019-001-048]


title: HC_21_Treg_Exvivo

value: Treg

value: HC


title: B1004_D270_9.8Gy_Male

description:
B1004_D270_S0
B1004_D270_9.8Gy

value: 270 days


title: Subj_106, liver, middle aged, early MASLD [104019-001-067]

value: ContactAuthor


title: B1004_D60_9.8Gy_Male

description:
B1004_D60_S0
B1004_D60_9.8Gy

value: 60 days


title: HC_19_Treg_Exvivo


title: Low_Plate2.C6

value: microglia

value: retina


title: Subj_80, liver, middle aged, early MASLD [104019-001-046]

value: liver


title: HC_18_Teff_Exvivo

value: Teff


title: Low_Plate2.C5

value: 14 weeks old

value: 1mg/kg ripasudil treatment


title: B1004_D30_9.8Gy_Male

description:
B1004_D30_S0
B1004_D30_9.8Gy

value: Whole blood

value: Male

value: 30 days


title: HC_20_Treg_Exvivo


title: Low_Plate2.D1


title: Subj_78, liver, middle aged, early MASLD [104019-001-044]

value: middle aged


title: HC_19_Teff_Exvivo


title: HC_17_Teff_Exvivo


title: B1004_D240_9.8Gy_Male

description:
B1004_D240_S0
B1004_D240_9.8Gy

value: 9.8Gy thoracic radiation

value: 240 days


title: Low_Plate1.F1


title: Subj_61, liver, middle aged, early MASLD [104019-001-039]

value: early MASLD


title: Low_Plate1.E6


title: B1004_D150_9.8Gy_Male

description:
B1004_D150_S0
B1004_D150_9.8Gy

value: 150 days


title: B1004_D120_9.8Gy_Male

description:
B1004_D120_S0
B1004_D120_9.8Gy

value: 120 days


title: Low_Plate1.F2


title: B1004_D180_9.8Gy_Male

description:
B1004_D180_S0
B1004_D180_9.8Gy

value: 180 days


title: Subj_58, liver, middle aged, early MASLD [104019-001-036]

value: x

value: ContactAuthor


title: Subj_69, liver, middle aged, early MASLD [104019-001-041]


title: B1004_D210_9.8Gy_Male

description:
B1004_D210_S0
B1004_D210_9.8Gy

value: 210 days


title: HC_16_Teff_Exvivo

value: HC


title: Subj_81, liver, middle aged, early MASLD [104019-001-047]

value: liver


title: HC_18_Treg_Exvivo

value: Treg


title: B1004_D6_9.8Gy_Male

description:
B1004_D6_S45
B1004_D6_9.8Gy

value: 6 days


title: Low_Plate1.E5

value: microglia

value: retina

value: 14 weeks old

value: 1mg/kg ripasudil treatment


title: HC_17_Treg_Exvivo


title: B1004_D9_9.8Gy_Male

description:
B1004_D9_S53
B1004_D9_9.8Gy

value: Whole blood

value: Male

value: 9.8Gy thoracic radiation

value: 9 days


title: Low_Plate1.E3


title: B1004_D40_9.8Gy_Male

description:
B1004_D40_S0
B1004_D40_9.8Gy

value: 40 days


title: Subj_55, liver, middle aged, early MASLD [104019-001-034]

value: middle aged

value: early MASLD


title: Low_Plate1.E4


title: HC_16_Treg_Exvivo


title: HC_15_Teff_Exvivo

value: Teff


title: HC_14_Teff_Exvivo


title: Subj_49, liver, middle aged, early MASLD [104019-001-030]

value: x

value: ContactAuthor


title: Low_Plate1.D6


title: Low_Plate1.D4


title: HC_13_Teff_Exvivo

value: HC


title: B1004_Ctl_0Gy_Male

description:
B1004_Ctl_S22
B1004_Ctl_0Gy

value: control

value: -2 days


title: B1004_D3_9.8Gy_Male

description:
B1004_D3_S35
B1004_D3_9.8Gy

value: 3 days


title: HC_15_Treg_Exvivo

value: Treg


title: Subj_47, liver, middle aged, early MASLD [104019-001-028]

value: liver


title: B1004_D21_9.8Gy_Male

description:
B1004_D21_S91
B1004_D21_9.8Gy

value: 21 days


title: Low_Plate1.E1

value: microglia

value: retina

value: 14 weeks old

value: 1mg/kg ripasudil treatment


title: Low_Plate1.D3


title: Subj_45, liver, middle aged, early MASLD [104019-001-027]


title: HC_14_Treg_Exvivo


title: Subj_42, liver, middle aged, early MASLD [104019-001-024]


title: Low_Plate1.D5


title: Subj_40, liver, middle aged, early MASLD [104019-001-023]


title: Subj_19, liver, middle aged, early MASLD [104019-001-012]


title: B1004_D15_9.8Gy_Male

description:
B1004_D15_S77
B1004_D15_9.8Gy

value: Whole blood

value: Male

value: 9.8Gy thoracic radiation

value: 15 days


title: HC_11_Teff_Exvivo

value: Teff


title: Subj_54, liver, middle aged, early MASLD [104019-001-033]

value: middle aged

value: early MASLD

value: x

value: ContactAuthor


title: B1003_D30_9.8Gy_Male

description:
B1003_D30_S0
B1003_D30_9.8Gy

value: 30 days


title: HC_13_Treg_Exvivo

value: Treg

value: HC


title: Subj_29, liver, middle aged, early MASLD [104019-001-018]

value: liver


title: B1003_D210_9.8Gy_Male

description:
B1003_D210_S0
B1003_D210_9.8Gy

value: 210 days


title: HC_12_Teff_Exvivo


title: Subj_17, liver, middle aged, early MASLD [104019-001-011]


title: Low_Plate1.C5

value: microglia

value: retina


title: Subj_9, liver, middle aged, early MASLD [104019-001-006]


title: Low_Plate1.E2

value: 14 weeks old

value: 1mg/kg ripasudil treatment


title: Subj_21, liver, middle aged, early MASLD [104019-001-013]


title: Low_Plate1.D2


title: HC_12_Treg_Exvivo


title: Subj_7, liver, middle aged, early MASLD [104019-001-005]


title: B1003_D60_9.8Gy_Male

description:
B1003_D60_S204
B1003_D60_9.8Gy

value: Whole blood

value: Male

value: 60 days


title: PBS_Plate3.C4

value: 10-14 weeks old

value: PBS treatment


title: HC_9_Teff_Exvivo

value: Teff


title: HC_9_Treg_Exvivo


title: Subj_136, liver, middle aged, early MASLD [104019-001-092]

value: middle aged

value: early MASLD

value: x


title: B1003_D150_9.8Gy_Male

description:
B1003_D150_S0
B1003_D150_9.8Gy

value: 9.8Gy thoracic radiation

value: 150 days


title: Low_Plate1.D1


title: HC_10_Teff_Exvivo

value: HC


title: Low_Plate1.C6


title: HC_11_Treg_Exvivo

value: Treg


title: PBS_Plate3.C1

value: microglia


title: B1003_D9_9.8Gy_Male

description:
B1003_D9_S52
B1003_D9_9.8Gy

value: 9 days


title: B1003_D90_9.8Gy_Male

description:
B1003_D90_S206
B1003_D90_9.8Gy

value: 90 days


title: HC_10_Treg_Exvivo


title: PBS_Plate3.B6

value: retina


title: HC_7_Teff_Exvivo


title: HC_8_Teff_Exvivo


title: Subj_127, liver, middle aged, early MASLD [104019-001-086]

value: liver


title: B1003_D21_9.8Gy_Male

description:
B1003_D21_S127
B1003_D21_9.8Gy

value: Whole blood

value: Male

value: 21 days


title: B1003_D180_9.8Gy_Male

description:
B1003_D180_S0
B1003_D180_9.8Gy

value: 180 days


title: Subj_1, liver, middle aged, early MASLD [104019-001-001]

value: ContactAuthor


title: Subj_109, liver, middle aged, early MASLD [104019-001-069]

value: middle aged


title: PBS_Plate3.B4

value: 10-14 weeks old

value: PBS treatment


title: B1003_D3_9.8Gy_Male

description:
B1003_D3_S99
B1003_D3_9.8Gy

value: 9.8Gy thoracic radiation

value: 3 days


title: PBS_Plate3.C3


title: PBS_Plate3.C2


title: B1003_Ctl_0Gy_Male

description:
B1003_Ctl_S21
B1003_Ctl_0Gy

value: control

value: -2 days


title: B1003_D6_9.8Gy_Male

description:
B1003_D6_S44
B1003_D6_9.8Gy

value: 6 days


title: Subj_128, liver, middle aged, early MASLD [104019-001-087]

value: early MASLD

value: x


title: PBS_Plate3.B5

value: microglia

value: retina


title: Subj_95, liver, middle aged, early MASLD [104019-001-058]

value: liver


title: HC_6_Treg_Exvivo

value: Treg

value: HC


title: HC_7_Treg_Exvivo


title: B1003_D270_9.8Gy_Male

description:
B1003_D270_S239
B1003_D270_9.8Gy

value: Whole blood

value: Male

value: 270 days


title: Subj_44, liver, middle aged, early MASLD [104019-001-026]

value: middle aged


title: Subj_108, liver, middle aged, early MASLD [104019-001-068]


title: Subj_66, liver, middle aged, early MASLD [104019-002-016]


title: B1003_D40_9.8Gy_Male

description:
B1003_D40_S215
B1003_D40_9.8Gy

value: 40 days


title: PBS_Plate3.B2

value: 10-14 weeks old

value: PBS treatment


title: HC_6_Teff_Exvivo

value: Teff


title: HC_5_Treg_Exvivo


title: B1003_D240_9.8Gy_Male

description:
B1003_D240_S237
B1003_D240_9.8Gy

value: 9.8Gy thoracic radiation

value: 240 days


title: B1003_D120_9.8Gy_Male

description:
B1003_D120_S234
B1003_D120_9.8Gy

value: 120 days


title: B1002_D30_9.8Gy_Male

description:
B1002_D30_S0
B1002_D30_9.8Gy

value: 30 days


title: B1003_D15_9.8Gy_Male

description:
B1003_D15_S76
B1003_D15_9.8Gy

value: 15 days


title: Subj_28, liver, middle aged, early MASLD [104019-002-009]

value: early MASLD

value: x


title: D42 SLPI KO pellets rep 3

first: zhijie

last: Lin

address: Baiyun Jingxi road

institute: Southern Medical University

data_processing:
The obtained sequencing data perform quality check through FastQC(v0.11.9)， yielding a set of clean reads which were aligned to a reference genome employing HISAT2 (v2.2.1).
The resulting alignments were further processed with samtools(v1.6)for transcript abundance estimation using featureCounts(v2.0.3).
The obtained expression of genes data import r software to calculate and subsequent analysis.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

source_name: M1 hEPSC

extract_protocol:
Total RNA was isolated from the collected samples using Trizol reagent (Takara) as per the manufacturer’s instructions.
Library preparation and RNA sequencing were performed by Novogene using their paired-end sequencing pipeline.

value: M1 hEPSC

value: chondrocytes

value: knock in and SLPI knock out

value: chondrocytic differentiation


title: PBS_Plate3.A5

value: microglia

value: retina


title: PBS_Plate3.A6


title: HC_3_Teff_Exvivo

value: HC


title: HC_4_Treg_Exvivo

value: Treg


title: PBS_Plate3.A4

value: 10-14 weeks old

value: PBS treatment


title: D42 SLPI KO pellets rep 2


title: HC_5_Teff_Exvivo

value: Teff


title: PBS_Plate3.A3


title: D42 SLPI KO pellets rep 1


title: PBS_Plate3.B1


title: HC_4_Teff_Exvivo


title: D42 control pellets rep 3

value: knock in


title: HC_2_Teff_Exvivo


title: PBS_Plate3.B3


title: PBS_Plate3.A2


title: B1002_D9_9.8Gy_Male

description:
B1002_D9_S51
B1002_D9_9.8Gy

value: Whole blood

value: Male

value: 9.8Gy thoracic radiation

value: 9 days


title: D42 control pellets rep 2


title: PBS_Plate3.A1


title: B1002_D60_9.8Gy_Male

description:
B1002_D60_S229
B1002_D60_9.8Gy

value: 60 days


title: HC_2_Treg_Exvivo


title: HC_1_Treg_Exvivo


title: D42 control pellets rep 1

value: M1 hEPSC


title: PBS_Plate2.C4


title: D42 PM treated pellets rep 3

value: chondrocytes


title: B1002_D40_9.8Gy_Male

description:
B1002_D40_S214
B1002_D40_9.8Gy

value: 40 days


title: MS_1_Treg_Exvivo

value: MS


title: B1002_D150_9.8Gy_Male

description:
B1002_D150_S0
B1002_D150_9.8Gy

value: 150 days


title: B1002_D160_9.8Gy_Male

description:
B1002_D160_S0
B1002_D160_9.8Gy

value: 160 days


title: B1002_D6_9.8Gy_Male

description:
B1002_D6_S43
B1002_D6_9.8Gy

value: 6 days


title: PBS_Plate2.C2

value: microglia

value: retina


title: PBS_Plate2.C3

value: 10-14 weeks old

value: PBS treatment


title: AE2_051820_COPD_7days

city: gaithersburg

first: Xiaotao

last: Qu

state: md

address: 1 medimmune way

institute: Astrazeneca

data_processing:
scRNA-seq Mapping using CellRanger (v3.0.2; 10x Genomics).The scRNA-seq dataset was mapped against GRCh38
Seurat 3.0 was used to QC and filtering individual sample data
Scanpy 1.6.0 was used to integrated data to generate the final normalzed data matrix
Genome_build: GRCh38
Supplementary_files_format_and_content: normalzed data matrix

source_name: human lung cell lung in alveosphere culture

growth_protocol: culture in spheroids

extract_protocol: Use 10x  Genomics' protocol (Chromium Single Cell 3 Reagent Kit, v3 Chemistry) to obtain single cell 3 libraries for Illumina sequencing

value: iAT2 epithelial cells

tag: source subject status

value: COPD

value: lung


title: D42 PM treated pellets rep 1

value: knock in

value: chondrocytic differentiation


title: B1002_D90_9.8Gy_Male

description:
B1002_D90_S231
B1002_D90_9.8Gy

value: Whole blood

value: Male

value: 9.8Gy thoracic radiation

value: 90 days


title: HC_3_Treg_Exvivo

city: New Haven

value: Treg

value: HC


title: B1002_D21_9.8Gy_Male

description:
B1002_D21_S90
B1002_D21_9.8Gy

value: 21 days


title: PBS_Plate2.C1


title: B1002_D3_9.8Gy_Male

description:
B1002_D3_S34
B1002_D3_9.8Gy

value: 3 days


title: AE2_051820_7days


title: D42 vehicle pellets biol rep 3

value: M1 hEPSC

value: chondrocytes


title: D42 vehicle pellets biol rep 2


title: PBS_Plate2.B5

value: microglia

value: retina

value: 10-14 weeks old


title: PBS_Plate2.B6

value: PBS treatment


title: B1002_Ctl_0Gy_Male

description:
B1002_Ctl_S20
B1002_Ctl_0Gy

value: control

value: -2 days


title: D42 vehicle pellets biol rep 1

value: knock in

value: chondrocytic differentiation


title: B1002_D120_9.8Gy_Male

description:
B1002_D120_S233
B1002_D120_9.8Gy

value: Whole blood

value: Male

value: 120 days


title: PBS_Plate2.B4


title: Candida albicans WO1, HaCaT co-culture, 4 hours, replicate 2

city: Szeged

first: Marton

last: Horvath

state: Csongrád

address: Közép fasor 52.

department: Microbiology

country: Hungary

institute: University of Szeged

description:
fungi_raw_counts.csv
WO_HK_2

data_processing:
Human sequenced reads were trimmed for standard Illumina adaptor sequences / low-quality sequences using trim-galore (v0.6.4) (parameters: -q 20 --length 36 --paired --illumina). Fungal sequenced reads were trimmed for specified adaptor sequences using Cutadapt (v2.8) (parameters: (-a CGTATGCCGTCTTCTGCTTG$ -A GCATACGGCAGAAGACGAAC$ -g ^AATGATACGGCGACCACCGAGA -G ^TTACTATGCCGCTGGTGGCTCT).
Processed human- and fungal reads were aligned using Hisat2 (v2.1.0)  (parameter: --phred33 --dta --non-deterministic --rna-strandness "RF")
The resulting alignment files were sorted and indexed via Samtools (v1.15), and fungal reads were quantified with featureCounts (v2.0.1) (parameters: -p --countReadPairs -s 2 -f -O -M).
Assembly: GRCh38 (release 96) from ENSEMBL, C. parapsilosis CDC317 and C. albicans SC5314 (Assembly21) from the Candida Genome Database
Supplementary files format and content: Sorted bam files containing aligned human reads ordered by their alignment positions on the reference genome.
Supplementary files format and content: Sorted bam files containing aligned fungal reads ordered by their alignment positions on the reference genome.

organism: Candida albicans

growth_protocol: HPV-KER cells were maintained in K-SFM medium supplemented with 1% L-glutamine, 1% penicillin-streptomycin, 0.05mg/ml BPE and 0.005 μg/ml rEGF and HaCaT keratinocytes in DMEM medium supplemented with 10% FBS, 1% penicillin-streptomycin and 1% L-glutamine at 37 °C, in the presence of 5% CO2, until 80% confluency.

extract_protocol:
Fungal transcriptome: Total RNA was isolated from C. albicans cells after their coincubation with HaCaT epithelial cells (MOI 10:1) for 4 hours at 37C, in the presence of 5% CO2. MOI = pathogen : host.
Total RNA was isolated from cell lines using the RNeasy® Plus Mini Kit, according to the manufacturer’s suggestions. Total RNA was isolated from yeast cells with the RiboPure Yeast Kit according to the manufacturer’s suggestions.
mRNA sequencing library preparation and mRNA sequencing (Illumina) was performed by specialists at Novogene according to their standard library preparation protocols.

treatment_protocol: Host transcriptome: After reaching 80% confluency, total RNA was isolated from HPV-KER / HaCaT epithelial cells after stimuli with either C. albicans (MOI of 1:25) or C. parapsilosis (MOI of 1:1) cells for 12 hours at 37C, in the presence of 5% CO2. MOI = pathogen : host.

value: budding yeast

tag: time

value: C.albicans MOI1(host):10(patogen)


title: D42 PM treated pellets rep 2


title: PBS_Plate2.B3

tag: strain


title: Candida albicans WO1, HaCaT co-culture, 4 hours, replicate 1

description:
fungi_raw_counts.csv
WO_HK_1


title: COL2+COL10+ biol rep 3


title: PBS_Plate2.B2

tag: age


title: B1001_D60_9.8Gy_Male

description:
B1001_D60_S0
B1001_D60_9.8Gy

tag: Sex

value: 9.8Gy thoracic radiation

value: 60 days


title: B1001_D90_9.8Gy_Male

description:
B1001_D90_S0
B1001_D90_9.8Gy

tag: treatment

value: 90 days


title: COL2+COL10+ biol rep 1

value: M1 hEPSC

value: chondrocytes


title: COL2+COL10+ biol rep 2


title: PBS_Plate2.B1

value: microglia

value: retina


title: Candida albicans WO1, non-treated control, 4 hours, replicate 2

description:
fungi_raw_counts.csv
WO_C_2

value: untreated control


title: Candida albicans WO1, non-treated control, 4 hours, replicate 3

description:
fungi_raw_counts.csv
WO_C_3


title: B1002_D15_9.8Gy_Male

description:
B1002_D15_S75
B1002_D15_9.8Gy

tag: time point

value: 15 days


title: COL2+COL10- biol rep 3

tag: cell line


title: AE2_051820_Healthy_7days

description: single cell RNAseq on 10x platform

value: iAT2 epithelial cells

value: Healthy

value: lung


title: B1001_D30_9.8Gy_Male

description:
B1001_D30_S0
B1001_D30_9.8Gy

value: Whole blood

value: 30 days


title: B1001_D127_9.8Gy_Male

description:
B1001_D127_S0
B1001_D127_9.8Gy

value: Male

value: 127 days


title: Candida albicans SC5314, HaCaT co-culture, 4 hours, replicate 3

description:
fungi_raw_counts.csv
SC5314_HK_3

value: budding yeast

value: C.albicans MOI1(host):10(patogen)


title: PBS_Plate2.A6

value: 10-14 weeks old

value: PBS treatment


title: Candida albicans WO1, non-treated control, 4 hours, replicate 1

description:
fungi_raw_counts.csv
WO_C_1


title: COL2+COL10- biol rep 2

value: M1 hEPSC

tag: genotype

value: knock in

value: chondrocytic differentiation


title: PBS_Plate2.A5

value: microglia

value: retina


title: B1001_D120_9.8Gy_Male

description:
B1001_D120_S0
B1001_D120_9.8Gy

value: 9.8Gy thoracic radiation

value: 120 days

tag: animal id


title: Candida albicans SC5314, HaCaT co-culture, 4 hours, replicate 2

description:
fungi_raw_counts.csv
SC5314_HK_2


title: Candida albicans WO1, HaCaT co-culture, 4 hours, replicate 3

description:
fungi_raw_counts.csv
WO_HK_3


title: COL2+COL10- biol rep 1

value: chondrocytes


title: PBS_Plate2.A4


title: Candida albicans SC5314, HaCaT co-culture, 4 hours, replicate 1

description:
fungi_raw_counts.csv
SC5314_HK_1


title: B1001_D6_9.8Gy_Male

description:
B1001_D6_S108
B1001_D6_9.8Gy

value: 6 days


title: PBS_Plate2.A2


title: HTR8_Input_1

value: placenta

value: trophoblast cells


title: PBS_Plate2.A1


title: PBS_Plate2.A3


title: B1001_D21_9.8Gy_Male

description:
B1001_D21_S89
B1001_D21_9.8Gy

value: Whole blood

value: Male

value: 21 days


title: HTR8_RXRA


title: HTR8_Input_2


title: HJAR_Input

description:
MeRIP_JAR_peak.bed
JAR-Input_L1_1.fq.gz

data_processing:
PCR duplicates were marked with the Picard “Mark Duplicates” utility and removed from further analysis.
Gene annotated in NCBI were quantified using featureCounts
Peaks were called using MACS2 with the significance cut-off q-value <=0.01
Sequenced reads were trimmed for adaptor sequence and low-quality bases, then mapped to hg38 whole genome using Bowtie with standard alignment parameters.
Bam files were converted to BigWig files using deepTools.
Assembly: hg38
Supplementary files format and content: bigWig, MeRIP-seq peak (except for Input sample)
Supplementary files format and content: txt, counts for each RIP-seq sample
Library strategy: MeRIP-seq


title: B1001_D3_9.8Gy_Male

description:
B1001_D3_S98
B1001_D3_9.8Gy

value: 3 days


title: Candida albicans SC5314, non-treated control, 4 hours, replicate 1

description:
fungi_raw_counts.csv
SC5314_C_1

value: budding yeast

value: untreated control


title: B1001_D40_9.8Gy_Male

description:
B1001_D40_S213
B1001_D40_9.8Gy

value: 40 days


title: Candida albicans SC5314, non-treated control, 4 hours, replicate  3

description:
fungi_raw_counts.csv
SC5314_C_3


title: Candida albicans SC5314, non-treated control, 4 hours, replicate 2

description:
fungi_raw_counts.csv
SC5314_C_2


title: PBS_Plate1.C4

value: 10-14 weeks old

value: PBS treatment


title: HTR8_H3K27ac


title: JAR_m6A

description:
MeRIP_JAR_peak.bed
JAR-Ip_L1_1.fq.gz


title: B1001_D15_9.8Gy_Male

description:
B1001_D15_S74
B1001_D15_9.8Gy

value: 15 days


title: B1001_D9_9.8Gy_Male

description:
B1001_D9_S50
B1001_D9_9.8Gy

value: 9 days


title: PBS_Plate1.C3

value: microglia

value: retina


title: HTR8_Input

description:
MeRIP_H8_peak.bed
H8-Input_L1_1.fq.gz


title: PBS_Plate1.B6


title: B1001_Ctl_0Gy_Male

description:
B1001_Ctl_S19
B1001_Ctl_0Gy

value: control

value: -2 days


title: HTR8_m6A

description:
MeRIP_H8_peak.bed
H8-Ip_L1_1.fq.gz

value: placenta


title: PBS_Plate1.C1


title: Rat synovium_Sy inj

city: Bunkyo-ku

first: Kentaro

last: Endo

state: Tokyo

address: 1-5-45 Yushima

institute: Institute of Science Tokyo

data_processing:
SOAPnuke v1.5.2
Remove the reads containing the adaptor, the reads whose N content is greater than 5%, and low-quality reads using SOAPnuke (parameter: -l 15 -q 0.2 -n 0.05).
Trimmed sequence reads were mapped to Rnor_6.0 using HISAT2 v2.0.4 (parameter: --sensitive --no-discordant --no-mixed -I 1 -X 1000 -p 8 --rna-strandness RF).
Read count extraction and normalization were performed using HISAT2.
Assembly: GCF_000001895.5_Rnor_6.0
Supplementary files format and content: Tab-delimited text files include TPM values for each sample

organism: Rattus norvegicus

source_name: Synovium

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (QIAGEN, Hilden, German).
mRNA was isolated using oligo dT beads and fragmented. Single-strand cDNA was generated using random N6-primed reverse transcription, followed by a secondstrand cDNA with dUTP. After PCR amplification and DNA nanoball synthesis, the products were sequenced by BGISEQ-500.

value: Synovium

tag: disease state

value: osteoarthritis

value: Injected with human SyMSCs


title: Rat synovium_Ad mix

value: Injected with PBS


title: patient S M(IL4,CGRP)

city: Calgary

first: Paul

last: Gordon

state: AB

address: 3330 Hospital Drive NW

institute: University of Calgary

data_processing:
Basecalling and demultiplexing using Illumina's bcl2fastq v2.20.0.422
Pseudomapping to human NCBI RefSeq RNA dataset using Kallisto v0.48.0
Supplementary files format and content: tab delimited raw counts from kallisto

source_name: macrophage

extract_protocol:
NEBNext Ultra II Directional RNA Library Prep Kit
polyA tailed RNA capture and sequencing

tag: individual

value: patient S

value: macrophage


title: Rat synovium_Sy mix


title: PBS_Plate1.B5


title: patient S M(IL4)


title: PBS_Plate1.B4


title: patient S M(0)


title: PBS_Plate1.B3


title: PBS_Plate1.C2