title: BT199_The SNP of whole genome

source_name: BT199 SNP of whole genome


title: PT425C

status: Public on Mar 09 2022

type: SRA

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

country: USA

institute: WSU

description: male.child.results.csv.gz

library_source: genomic

data_processing:
Basic read quality was verified using summaries produced by FastQC. Trimmomatic was used to remove low quality reads and bases
The reads for each sample were mapped to the human (GRCh38) genome using Bowtie2
The mapped read files were then converted to sorted BAM files using SAMtools
The MEDIPS R package was used to calculate differential coverage between sample groups. To identify DMR, the reference genome was broken into 1000 bp windows. The edgeR Pvalue was used to determine the relative difference between the two sample groups for each genomic window. Windows with an edgeR P value less than an arbitrarily chosen threshold were considered DMR. The DMR edges were extended until no genomic window with an edgeR P value less than 0.1 remained within 1000 bp of the DMR.
The selected DMR were then summarized and annotated.
In addition to the main analysis, two sets of test samples were collected. A first internal test set was composed of technical replicates of samples from the main analysis. These samples were used to identify potential batch effects. A second external test set was composed of additional samples not included in the main analysis. These samples were used to determine whether the preterm birth status could be predicted from the DMRs identified in the main analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window and other summary values.

molecule: genomic DNA

organism: Homo sapiens

source_name: buccal

growth_protocol: St. Franciscan Hospital and Indiana University School of Medicine. IU Health Hospitals (Riley Hospital for Children, IUH Methodist, IUH North) and Franciscan Health, Indianapolis, Indiana, USA provided samples for the study. Informed consent and HIPAA authorization was obtained from all participants prior to the clinical sample collection. The study protocol was approved by the Indiana University Institutional Review Board (IRB) #1901985132 and the Franciscan Institutional Review Board (IRB), #1489434-5. All research was performed in accordance with relevant guidelines/regulations. Informed consent and HIPAA authorization was obtained from all participants prior to sample collection. For sample collection involving human participants that are minors, informed consent from a parent and/or legal guardian for study participation was obtained prior to sample collection.

extract_protocol:
Frozen human buccal samples were thawed for analysis. Genomic DNA from buccal samples was prepared as follows: The buccal brush was suspended in 750 μl of cell lysis solution and 3.5 µl of Proteinase K (20 mg/ml). This suspension was incubated at 55ºC for 3 hours, then vortexed and centrifuged briefly. The lysis solution was then transferred to a new 1.5 µl microcentrifuge tube. The microcentrifuge tube with the buccal brush was centrifuged again to retain any remaining solution which was combined with the transferred lysis solution. The buccal brush was discarded and 300 µl of protein precipitation solution (Promega, A795A, Madison, WI) was added to the lysis solution. The sample was incubated on ice for 15 minutes, then centrifuged at 4C for 30 minutes. The supernatant was transferred to a fresh 2 mL microcentrifuge tube and 1,000 µl ice cold isopropanol was added along with 2 µL glycoblue. This suspension was mixed thoroughly and incubated at -20 ºC overnight. The suspension was then centrifuged at 4ºC for 20 minutes, the supernatant was discarded, and the pellet was washed with 75% ethanol, then air-dried and resuspended in 100 μl H2O. DNA concentration was measured using the Nanodrop (Thermo Fisher, Waltham, MA). Methylated DNA Immunoprecipitation (MeDIP) with genomic DNA was performed as follows: individual DNA samples (2-4 ug of total DNA) were diluted to 130 μl with 1x Tris-EDTA (TE, 10 mM Tris, 1 mM EDTA) and sonicated with the Covaris M220 using the 300 bp setting. Fragment size was verified on a 2% E-gel agarose gel. The sonicated DNA was transferred from the Covaris tube to a 1.7 ml microfuge tube, and the volume was measured. The sonicated DNA was then diluted with TE buffer (10mM Tris HCl, pH7.5; 1mM EDTA) to 400 μl, heat-denatured for 10 min at 95 C, then immediately cooled on ice for 10 min. Then 100 μl of 5X IP buffer and 5 μg of antibody (monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006) were added to the denatured sonicated DNA. The DNA-antibody mixture was incubated overnight on a rotator at 4 C. The following day magnetic beads (Dynabeads M-280 Sheep anti-Mouse IgG; 11201D) were pre-washed as follows: The beads were resuspended in the vial, then the appropriate volume (50 μl per sample) was transferred to a microfuge tube. The same volume of Washing Buffer (at least 1 mL 1XPBS with 0.1% BSA and 2mM EDTA) was added and the bead sample was resuspended. The tube was then placed into a magnetic rack for 1-2 min and the supernatant was discarded. The tube was removed from the magnetic rack and the beads were washed once. The washed beads were resuspended in the same volume of 1xIP buffer (50 mM sodium phosphate ph7.0, 700 mM NaCl, 0.25% TritonX-100) as the initial volume of beads. 50μl of beads were added to the 500μl of DNA-antibody mixture from the overnight incubation, then incubated for 2 hours on a rotator at 4 C. After the incubation, the bead-antibody-DNA complex was washed three times with 1X IP buffer as follows: The tube was placed into a magnetic rack for 1-2 min and the supernatant was discarded, then the magnetic bead antibody pellet was washed with 1xIP buffer 3 times. The washed bead antibody DNA pellet was then resuspended in 250 μl digestion buffer with 3.5 μl Proteinase K (20mg/ml). The sample was incubated for 2-3 hours on a rotator at 55 C, then 250 μl of buffered Phenol-Chloroform- Isoamylalcohol solution was added to the sample, and the tube was vortexed for 30 sec and then centrifuged at 14,000rpm for 5 min at room temperature. The aqueous supernatant was carefully removed and transferred to a fresh microfuge tube. Then 250 μl chloroform were added to the supernatant from the previous step, vortexed for 30 sec and centrifuged at 14,000rpm for 5 min at room temperature. The aqueous supernatant was removed and transferred to a fresh microfuge tube. To the supernatant 2μl of glycoblue (20mg/ml), 20μl of 5M NaCl and 500μl ethanol were added and mixed well, then precipitated in -20 C freezer for 1 hour to overnight. The precipitate was centrifuged at 14,000rpm for 20 min at 4 C and the supernatant was removed, while not disturbing the pellet. The pellet was washed with 500μl cold 70% ethanol in -20 C freezer for 15 min then centrifuged again at 14,000rpm for 5 min at 4 C and the supernatant was discarded. The tube was spun again briefly to collect residual ethanol to the bottom of the tube and as much liquid as possible was removed with gel loading tip. The pellet was air-dried at RT until it looked dry (about 5 min) then resuspended in 20μl H2O or TE. DNA concentration was measured in Qubit (Life Technologies) with ssDNA kit (Molecular Probes Q10212).
The MeDIP DNA samples (50 ng of each) were used to create libraries for next generation sequencing (NGS) using the NEBNext Ultra RNA Library Prep Kit for Illumina (San Diego, CA) starting at step 1.4 of the manufacturer’s protocol to generate double stranded DNA. After this step the manufacturer’s protocol was followed. Each sample received a separate index primer. NGS was performed at WSU Spokane Genomics Core using the Illumina HiSeq 2500 with a PE50 application, with a read size of approximately 50bp and approximately 5-35 million reads per sample, and 6-7 sample libraries each were run in one lane.

treatment_protocol: Buccal samples were collected from the mother, father, and child in instances where pre-term birth occurred (case), or where term birth occurred (control). Buccal swabs were stored at -80 C until use.

tag: treatment group

value: control

tag: family member

value: male child


title: BT203_The SNP of whole genome

type: genomic

city: Hangzhou

first: Liu-Bin

last: Wang

address: 9 South Meiling road

department: Tea Research Institute

country: China

institute: Chinese Academy of Agricultural Sciences

description: Tea SNP 96-Array Plate detected the SNP of whole genome of tea

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the GeneTitan MC.

data_processing:
The array image was acquired using Affymetrix AxiomTM Tea SNP 96 -Array Plate detected the SNP of whole genome of tea plant
SNP call:G/G,T/G,T/T,C/C,etc.

label: biotin

organism: Camellia sinensis

source_name: BT203 SNP of whole genome

label_protocol: As per manufacturer (Affymetrix).

growth_protocol: Tea plant  were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from young leafs of tea using the TianGen DNA Kit. DNA quality and quantity was assessed using a Nanodrop.

tag: tissue

value: Leaf

tag: cultivar


title: PT426C

description: female.child.results.csv.gz

value: female child


title: BT205_The SNP of whole genome

source_name: BT205 SNP of whole genome


title: BT198_The SNP of whole genome

source_name: BT198 SNP of whole genome


title: UTHT4_ROW02_3

city: Geneva

first: Julien

last: Prados

address: Rue Michel Servet 1

department: SCMU

country: Switzerland

institute: University of Geneva

description:
singlecell_countmatrix.tsv.gz
singlecell_metadata.tsv

library_source: transcriptomic

data_processing:
Single cell only: The 4bp UMI sequence (initially sequenced in read1), are appended at the end of the headers of the reads (here the reads we provide are resulting from this operation)
Reads are mapped with STAR on the mouse genome GRCm38 considering Ensembl 85 as genome annoatations
Single cell only: bam files are processed with umi_tools to deduplicate reads with identical UMI sequence
gene expression are quantifyied using summarizeOverlaps() method of the R package GenomicsAlignments(). Only exonic reads are considered in the quantification (this includes 5' and 3' UTRs), and only reads with a mapping quality >=255 (to exclude those ambiguously mapping at multiple positions).
Genome_build: GRCm38
Supplementary_files_format_and_content: singlecell_countmatrix.tsv.gz: is a count matrix in tab-separated format. It contains the result of the single cell quantification for all genes. The integers values represent the number of exonic reads mapping into each gene after UMI correction. The first columns contains the gene name that is quantified.    bulk_countmatrix.tsv.gz: count matrix for the bulk experiments in tab-separated format.    singlecell_metadata.tsv: is a table containing metadata information for each cell in tab-separated. The content of the columns are: MT=proportion of mithocondrial reads; ngenes=number of expressed gene; epor_age=age at which the mous as been electroporated; collection_age=age at which cells were collected; cond=condition Control/miR-137/miR-122; cell_type, cell_type_pred1, cell_type_pred2: predicted cell types for the cell; tSNE1, tSNE2= coordinate of the cell in the t-SNE space

molecule: polyA RNA

organism: Mus musculus

source_name: cortex

extract_protocol:
Single-cell RNA sequencing    Embryonic cortex: Tissue collection was performed as in Telley et al., Science 2019. Briefly, pregnant females were sacrificed, and embryos were extracted in ice-cold HBSS either at E15.5 and E17.5 after E14.5 in utero electroporation. Three hundred micrometer- acute coronal brain sections were performed after embedding in 4% low melt- agar using a vibratome (Leica, #VT1000S) under RNase-free conditions. The putative primary somatosensory cortex (S1) was microdissected using a Leica Dissecting Microscope (Leica, #M165FC) and incubated in 0.05% trypsin at 37°C for 5 minutes. Following tissue digestion, cells were incubated in fetal bovine serum and cells were manually dissociated via gentle pipetting. Cells were then centrifuged for 5 minutes at 500 rpm, resuspended in 1 mL FACS buffer (2 mg/mL glucose, 0.1% bovine serum albumin, 1/50 citrate phosphate dextrose, 10 units/mL DNaseI, 1 uM MgCl2, in L15 medium) and filtered using a 70 mm- cell strainer (ClearLine, #141379C), before 10 minute- incubation with Hoechst (0.1 mg/mL) at 37°C .    Postnatal cortex: Tissue collection was performed as in Klingler et al., Curr Biol 2019. Briefly, 600 um acute coronal brain sections were cut on a vibratome and S1 was microdissected as described above in ice-cold oxygenated artificial cerebrospinal fluid (ACSF) under RNase-free conditions. Cells were next dissociated by incubating microdissected samples in 0.5 mg/mL pronase (Sigma, #P5147) at 37°C for 10 minutes, followed by a 3 minute- inactivation in 5% bovine serum albumin, washes in ACSF and manual trituration using pulled glass pipettes of decreasing diameters. Cells were then centrifuged for 10 minutes at 500 rpm, resuspended and filtered using a 70 um- cell strainer (ClearLine, #141379C), incubated for 10 minutes with Hoechst (0.1 mg/mL) at 37°C.    Singlet GFP+/Hoechst+ embryonic and postnatal cells were sorted using a Beckman Coulter Moflo Astrios FAC-sorter according to their Forward and Slide scattering properties, and their negativity for Draq7TM (Viability dye, far red DNA intercalating agent, Beckman Coulter, #B25595). Three microliters of C1 Suspension Reagent (Fluidigm) was added to 10 ul of FACsorted cells, which were captured into 800 well- AutoPrep integrated fluidic circuit (IFC) designed for 10 to 17 um diameter-cells (Fluidigm HT800, #100-57-80), and imaged using the ImageXpress Micro Widefield High Content Screening System (Molecular Devices®).        Bulk RNA sequencing    Brains were collected from E14.5 in utero electroporated miR-122 pups at P7. The primary somatosensory cortex was microdissected following the same procedure as described above with further separation of superficial (SL) and deep (DL) layers. SL and DL cells were dissociated and FACsorted as for single-cell RNA sequencing.
Single-cell RNA sequencing  cDNA synthesis and preamplification was processed following the manufacturer’s instructions (C1 system, Fluidigm). cDNA libraries were prepared using Nextera XT DNA library prep kit (Illumina), quality control was done using 2001 Bioanalyzer from Agilent, and sequenced using HiSeq 2500 sequencer for E14.5 electroporated pups, and HiSeq 5000 sequencer for E14 and E15.5 electroporated pups with an expected sequencing depth of 1M reads per single cell, and a final mapping read length of 70bp.    Bulk RNA sequencing  RNA from each sample was extracted and quality control was done using 2001 Bioanalyzer from Agilent. cDNA libraries were obtained using SMARTseq v4 kit (Clontech, # 634888) and sequenced using HiSeq 2500 sequencer.

value: cortex


title: UTHT4_ROW36_9


title: BT209_The SNP of whole genome

source_name: BT209 SNP of whole genome


title: UTHT4_ROW31_7


title: BT196_The SNP of whole genome

source_name: BT196 SNP of whole genome


title: UTHT4_ROW18_15


title: BT206_The SNP of whole genome

source_name: BT206 SNP of whole genome


title: PT424C

description: female.child.results.csv.gz


title: PT424F

description: father.results.csv.gz

value: father


title: PT423M

description: mother.results.csv.gz

value: mother


title: BT197_The SNP of whole genome

source_name: BT197 SNP of whole genome


title: UTHT4_ROW24_16


title: BT195_The SNP of whole genome

source_name: BT195 SNP of whole genome


title: PT424M

description: mother.results.csv.gz


title: BT207_The SNP of whole genome

source_name: BT207 SNP of whole genome


title: BT194_The SNP of whole genome

source_name: BT194 SNP of whole genome


title: PT425M

description: mother.results.csv.gz


title: BT200_The SNP of whole genome

source_name: BT200 SNP of whole genome


title: BT193_The SNP of whole genome

source_name: BT193 SNP of whole genome


title: UTHT4_ROW16_10


title: UTHT4_ROW23_6


title: UTHT4_ROW18_16


title: BT192_The SNP of whole genome

source_name: BT192 SNP of whole genome


title: UTHT4_ROW03_11


title: PT426F

description: father.results.csv.gz


title: BT191_The SNP of whole genome

source_name: BT191 SNP of whole genome


title: PT422F

description: father.results.csv.gz


title: UTHT4_ROW39_18


title: PT422M

description: mother.results.csv.gz


title: BT189_The SNP of whole genome

source_name: BT189 SNP of whole genome


title: BT190_The SNP of whole genome

source_name: BT190 SNP of whole genome


title: BT188_The SNP of whole genome

source_name: BT188 SNP of whole genome


title: PT421F

description: father.results.csv.gz

source_name: buccal


title: UTHT4_ROW37_13


title: PT421M

description: mother.results.csv.gz


title: UTHT4_ROW12_20


title: PT419M

description: mother.results.csv.gz

value: preterm birth


title: PT423C

description: male.child.results.csv.gz


title: PT423F

description: father.results.csv.gz


title: PT422C

description: male.child.results.csv.gz


title: BT187_The SNP of whole genome

source_name: BT187 SNP of whole genome


title: UTHT4_ROW23_1

source_name: cortex


title: BT186_The SNP of whole genome

source_name: BT186 SNP of whole genome


title: UTHT4_ROW13_19


title: UTHT4_ROW34_10


title: PT419C

description: female.child.results.csv.gz


title: BT185_The SNP of whole genome

source_name: BT185 SNP of whole genome


title: UTHT4_ROW21_1


title: UTHT4_ROW15_15


title: UTHT4_ROW12_3


title: PT419F

description: father.results.csv.gz


title: BT182_The SNP of whole genome

source_name: BT182 SNP of whole genome


title: BT183_The SNP of whole genome

source_name: BT183 SNP of whole genome


title: PT418M

description: mother.results.csv.gz


title: PT418F

description: father.results.csv.gz


title: UTHT4_ROW10_2


title: UTHT4_ROW40_1


title: UTHT4_ROW40_2


title: PT421C

description: male.child.results.csv.gz


title: UTHT4_ROW12_1


title: PT418C

description: female.child.results.csv.gz


title: BT180_The SNP of whole genome

source_name: BT180 SNP of whole genome


title: PT417M

description: mother.results.csv.gz


title: BT179_The SNP of whole genome

source_name: BT179 SNP of whole genome


title: UTHT4_ROW29_4


title: UTHT4_ROW06_5


title: PT417C

description: male.child.results.csv.gz


title: BT177_The SNP of whole genome

source_name: BT177 SNP of whole genome


title: BT178_The SNP of whole genome

source_name: BT178 SNP of whole genome


title: BT184_The SNP of whole genome

source_name: BT184 SNP of whole genome


title: UTHT4_ROW26_6


title: BT174_The SNP of whole genome

source_name: BT174 SNP of whole genome


title: UTHT4_ROW29_7


title: BT176_The SNP of whole genome

source_name: BT176 SNP of whole genome


title: UTHT4_ROW03_6


title: PT416M

description: mother.results.csv.gz


title: PT416C

description: female.child.results.csv.gz


title: BT175_The SNP of whole genome

source_name: BT175 SNP of whole genome


title: UTHT4_ROW03_7


title: PT416F

description: father.results.csv.gz


title: BT173_The SNP of whole genome

source_name: BT173 SNP of whole genome


title: BT181_The SNP of whole genome

source_name: BT181 SNP of whole genome


title: PT414M

description: mother.results.csv.gz

source_name: buccal


title: BT172_The SNP of whole genome

source_name: BT172 SNP of whole genome


title: UTHT4_ROW18_3

source_name: cortex


title: PT414F

description: father.results.csv.gz


title: UTHT4_ROW34_3


title: PT414C

description: male.child.results.csv.gz


title: BT171_The SNP of whole genome

source_name: BT171 SNP of whole genome


title: UTHT4_ROW30_9


title: PT417F

description: father.results.csv.gz


title: BT170_The SNP of whole genome

source_name: BT170 SNP of whole genome


title: BT169_The SNP of whole genome

source_name: BT169 SNP of whole genome


title: PT413F

description: father.results.csv.gz


title: UTHT4_ROW15_10


title: UTHT4_ROW30_3


title: BT168_The SNP of whole genome

source_name: BT168 SNP of whole genome


title: UTHT4_ROW34_2


title: PT412M

description: mother.results.csv.gz


title: BT167_The SNP of whole genome

source_name: BT167 SNP of whole genome


title: PT412F

description: father.results.csv.gz


title: BT166_The SNP of whole genome

source_name: BT166 SNP of whole genome


title: BT164_The SNP of whole genome

source_name: BT164 SNP of whole genome


title: PT411M

description: mother.results.csv.gz


title: BT165_The SNP of whole genome

source_name: BT165 SNP of whole genome


title: PT412C

description: female.child.results.csv.gz


title: UTHT4_ROW15_1


title: UTHT4_ROW36_10


title: UTHT4_ROW39_4


title: PT411C

description: female.child.results.csv.gz


title: BT163_The SNP of whole genome

source_name: BT163 SNP of whole genome


title: PT410M

description: mother.results.csv.gz


title: BT161_The SNP of whole genome

source_name: BT161 SNP of whole genome


title: UTHT4_ROW38_9


title: BT162_The SNP of whole genome

source_name: BT162 SNP of whole genome


title: PT411F

description: father.results.csv.gz


title: PT413C

description: female.child.results.csv.gz


title: PT410C

description: male.child.results.csv.gz


title: PT413M

description: mother.results.csv.gz


title: PT409M

description: mother.results.csv.gz


title: BT158_The SNP of whole genome

source_name: BT158 SNP of whole genome


title: UTHT4_ROW13_5


title: NC3

city: Zhengzhou

first: zhuoyu

last: gu

state: China

address: No. 50, Jianshe East Road, Erqi District

institute: First Affiliated Hospital of Zhengzhou University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.

molecule: total RNA

source_name: lung adenocarcinoma

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: lung adenocarcinoma

tag: age

value: Fifth generation

tag: genotype

value: hnRNPK shNC


title: SH2

value: hnRNPK knockdown


title: SH3


title: SH1


title: PT409F

description: father.results.csv.gz


title: NC2


title: BT157_The SNP of whole genome

source_name: BT157 SNP of whole genome


title: PT409C

description: male.child.results.csv.gz

source_name: buccal


title: NC1


title: BT156_The SNP of whole genome

source_name: BT156 SNP of whole genome


title: PT408M

description: mother.results.csv.gz


title: EC-MSI

city: Shanghai

first: Yin

last: Liu

state: Shanghai

address: Building #2, 507 Zhengmin Road

department: Department of Laboratory Medicine

institute: Shanghai Pulmonary Hospital, Tongji University School of Medicine

data_processing:
The Cell Ranger software pipeline (version 2.2.0, https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/2.0) provided by 10xGenomics was used to process reads. Fastq files generated from Illumina sequencing output were mapped to the human reference genome (GRCh37) and transcriptome using the STAR aligner, and then read count matrices were generated by counting unique molecular identifiers (UMIs). Finally, we generate a gene-barcode matrix containing the barcoded cells and gene expression counts.
We imported the count data into the Seurat (version 2.3.4) R package for quality control. We first excluded genes detected in < 3 cells and cells where < 100 genes had nonzero counts. We further discarded low-quality cells that had > 5% mitochondrial genes.
Library size normalization was performed in Seurat on the filtered matrix to obtain the normalized count. Additional cell-cell normalization was performed using the LogNormalize method, and inherent variation caused by mitochondrial gene expression and the number of unique molecular identifiers (UMIs) per cell was regressed out. Gene expression matrices were normalized to total cellular read count and to mitochondrial read count using linear regression as implemented in Seurat’s ScaleData function. Before incorporating a sample into our merged dataset, we individually inspected the cells-by-genes matrix of each as a Seurat object.
Genome_build: GRCh37
Supplementary_files_format_and_content: tsv, mtx

source_name: patient tissue

extract_protocol: Single-cell library preparation was carried out using Chromium Single cell 3’ Reagent v2 Kits (10 × Genomics, USA) according to the manufacturer’s protocol. Cells were loaded on the Chromium Single Cell Controller Instrument to generate single cell gel beads in emulsions (GEMs). Next, reverse transcription was performed, cDNA was cleaned up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific, USA), and was then amplified by PCR with appropriate cycles. Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed, index adaptor-ligated and subjected to library amplification.

value: endometrial carcinomas

tag: subject status

value: MSI-H/MMR-D endometrial carcinomas patient


title: BT154_The SNP of whole genome

source_name: BT154 SNP of whole genome


title: SW480_PCAT2_KI

city: Bethesda

first: Songjoon

last: Baek

state: MD

address: 41 Library Drive

department: CCR

institute: NCI / NIH

data_processing:
Library strategy: DNase-seq
Base-calling with Illumina run time analysis software 1.12.4.2
Alignment to hg38 using Casava Eland extended
DNase hypersensitive sites were identified as hotspots using DNase2Hotspots.
Genome_build: hg38
Supplementary_files_format_and_content: BedGraph

source_name: SW480 colon cancer cells

extract_protocol:
Cells were treated with Proteinase K and 1% SDS overight at 55C and genomic DNA was isolated using PCI method.
Sequencing libraries were generated using Illumina TruSeq V3 protocol and subject to 51 bp single-end sequencing on Illumina HiSeq2000.

tag: cell type

value: SW480 colon cancer cells knocked-in with PCAT2 gene


title: BT155_The SNP of whole genome

source_name: BT155 SNP of whole genome


title: PT410F

description: father.results.csv.gz


title: PT408F

description: father.results.csv.gz


title: BT153_The SNP of whole genome

source_name: BT153 SNP of whole genome


title: SW_KI_CpA_R1

data_processing:
Base-calling with Illumina run time analysis software 1.12.4.2
Alignment to mm9 using Casava Eland extended
ChIP-seq binding sites were identified as hotspots after adjustment using the input DNA control.
Genome_build: hg38
Supplementary_files_format_and_content: BedGraph

extract_protocol:
For CENP-A ChIP, the samples were crosslinked with 1% formaldehyde for 10 minutes at room temperature. After crosslinking, chromatin was extracted overight followed by incubation in CENP-A a/b overnight and a/b bound DNA was captured using Protein A/G tagged magnetic beads (Dynabeads). The DNA was extracted using PCI menthod. Samples were treated with RNase I followed by one more PCI to isolate RNA free DNA. DNA fragments with a size range of 150 to 300 base pairs.
Sequencing libraries were generated using Illumina TruSeq V3 protocol and subject to 51 bp single-end sequencing on Illumina HiSeq2000.

tag: chip antibody

value: CENP-A (Custom)


title: SW_KI_CpA_R2


title: PT407F

description: father.results.csv.gz


title: PT407M

description: mother.results.csv.gz


title: BT160_The SNP of whole genome

source_name: BT160 SNP of whole genome


title: PT407C

description: male.child.results.csv.gz


title: SW_Cntrl_CpA_R1

value: SW480 colon cancer cells


title: BT151_The SNP of whole genome

source_name: BT151 SNP of whole genome


title: BT148_The SNP of whole genome

source_name: BT148 SNP of whole genome


title: BT152_The SNP of whole genome

source_name: BT152 SNP of whole genome


title: BT150_The SNP of whole genome

source_name: BT150 SNP of whole genome


title: PT406F

description: father.results.csv.gz


title: SW_Cntrl_CpA_R2


title: BT159_The SNP of whole genome

source_name: BT159 SNP of whole genome


title: BT149_The SNP of whole genome

source_name: BT149 SNP of whole genome


title: SW_Cntrl_Input_R1


title: PT408C

description: male.child.results.csv.gz


title: SW_KI_Input_R2


title: PT406C

description: female.child.results.csv.gz


title: SW_Cntrl_Input_R2


title: 0h rep2, Control

data_processing:
Base-calling with Illumina run time analysis software 1.12.4.2
Alignment to mm9 using Casava Eland extended
Transcript levels were quantified using Tophat and Cufflinks.
Genome_build: hg38
Supplementary_files_format_and_content: FPKM

extract_protocol:
Total RNA was isolated using TRIzol methods and treated with DNAse.
Sequencing libraries were generated using Illumina TruSeq V3 protocol and subject to 101 bp paired-end sequencing on Illumina HiSeq2000.

tag: cell tyep


title: SW_KI_Input_R1


title: BT147_The SNP of whole genome

source_name: BT147 SNP of whole genome


title: PT405F

description: father.results.csv.gz


title: BT146_The SNP of whole genome

source_name: BT146 SNP of whole genome


title: PT406M

description: mother.results.csv.gz


title: PT405M

description: mother.results.csv.gz


title: BT144_The SNP of whole genome

source_name: BT144 SNP of whole genome


title: 0h rep2, PCAT2 KI

value: SW480 knocked-in with PCAT2 gene


title: BT143_The SNP of whole genome

source_name: BT143 SNP of whole genome


title: PT405C

description: female.child.results.csv.gz

source_name: buccal


title: 0h rep1, PCAT2 KI


title: PT404M

description: mother.results.csv.gz


title: PT404F

description: father.results.csv.gz


title: WT_FLAG_LMW rep2 input

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

description:
eCLIP4_5.WTL-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP4_5.WTL-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw

data_processing:
Sequenced reads were reformatted to include randomers in read headers with umi_tools (1.0.0). Args: --random-seed 1 --bc-pattern NNNNNNNNNN
Reads were then trimmed with cutadapt (1.14). Args: --match-read-wildcards -O 1 --times 1 -e 0.1 --quality-cutoff 6 -m 18 -a InvRNA*.fasta (fasta sequences can be found at: https://github.com/YeoLab/eclip/tree/master/example/inputs/)
Reads were then trimmed once more with cutadapt (1.14) to remove double-ligation events. Args: --match-read-wildcards -O 5 --times 1 -e 0.1 --quality-cutoff 6 -m 18  -a InvRNA*.fasta (fasta sequences can be found at: https://github.com/YeoLab/eclip/tree/master/example/inputs/)
Trimmed reads were then mapped with STAR (2.4.0i) against a repeat element database (RepBase 18.05). Args: --runThreadN 16 \  --genomeDir human_repbase \  --readFilesIn path/to/read1 \  --outFileNamePrefix out_prefix \  --outReadsUnmapped Fastx \  --outSAMtype BAM Unsorted \  --outSAMattributes All \  --outSAMunmapped Within \  --outSAMattrRGline ID:foo \  --outFilterType BySJout \  --outFilterMultimapNmax 30 \  --outFilterMultimapScoreRange 1 \  --outFilterScoreMin 10 \  --alignEndsType EndToEnd
Unmapped reads filtered of repeat elements were then mapped with STAR (2.4.0i) against a human genome (hg19/ChlSab2). Args: --runThreadN 16 \  --genomeDir genomedir \  --readFilesIn /path/to/read1 \  --outFileNamePrefix out_prefix \  --outReadsUnmapped Fastx \  --outSAMtype BAM   Unsorted \  --outSAMattributes All \  --outSAMunmapped Within \  --outSAMattrRGline ID:foo \  --outFilterType BySJout \  --outFilterMultimapNmax 1 \  --outFilterMultimapScoreRange 1 \  --outFilterScoreMin 10 \  --alignEndsType EndToEnd
Aligned reads were sorted with samtools (1.6)
Sorted reads were collapsed with umi_tools (1.0.0). Args: --random-seed 1 --method unique
BAM files were used to identify peak clusters with Clipper (1.2.2). Args: --species (hg19/ChlSab2_Sars) --bam path/to/input.bam --timeout 3600000 --maxgenes 1000000 --save-pickle --outfile path/to/output.bam
Peak clusters were normalized using BAM files for IP against BAM files for INPUT with peaksnormalize.pl (overlap_peakfi_with_bam_PE.pl), included in eclip 0.1.5+.
Overlapping normalized peak regions were merged with compress_l2foldenrpeakfi_for_replicate_overlapping_bedformat.pl, included within eclip-0.1.5+
Normalized peak (compressed.bed) files were ranked by entropy score (make_informationcontent_from_peaks.pl included within the merge_peaks pipeline) and used as inputs to IDR (2.0.2) to determine reproducible peaks.
Reproducible peaks were filtered for those ≥20 bases in length, and not overlapping with WT negative control samples.
Genome_build: hg19
Genome_build: ChlSab2
Genome_build: Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome (MN908947.3)

growth_protocol:
BEAS-2B cells were cultured on Matrigel (Corning) coated plates and maintained in the PneumaCult-Ex Plus Medium (Stem Cell Technologies), supplemented with 33 µg/ml hydrocortisone (Stem Cell Technologies). Growth media was replaced every two days, and the cells were passaged every four days. Vero E6 cells were cultured in DMEM (ThermoFisher) supplemented with 10% FBS (ThermoFisher) and passaged every three days. All cell cultures were incubated at 37ºC and 5% CO2.
Vero E6 cells were cultured in DMEM supplemented with 10% FBS.

extract_protocol:
Biological replicates (according to ENCODE requirements) of 20 million cells were treated with 400mJ of UV using the Stratalinker 2400, harvested by scraping in ice cold PBS and pellets flash frozen in liquid nitrogen and stored in -80 degrees until ready to IP with antibody bound Dynabeads Subsequent protocol exactly as detailed in Van Nostrand et al 2016. Sequencing was performed on Illumina 2000 Hi Seq paired end reads and data processed through Dr. Yeo's eCLIP pipeline.
Libraries were constructed as per the eCLIP protocol using Illumina 50x forward and 70x reverse primers.
eCLIP

treatment_protocol:
Cells were UV cross-linked with 400 mJ/cm^2 and processed through the eCLIP protocol as previously described (van Nostrand et al, 2016). Anti-Strep tag or Anti-FLAG tag antibody was  employed for immunoprecipitation.
Vero E6 cells were infected with SARS-CoV-2 at MOI of 0.02 for 48 hours before UV crosslinking with 400 mJ/cm^2. Anti-N, Anti-NSP8 and Anti-NSP12 antibodies were used for immunoprecipitation.

tag: antibody manufacturer

value: Sigma-Aldrich

tag: antibody catalog #

value: Monoclonal ANTI-FLAG® M2 antibody produced in mouse, Sigma Aldrich, F3165

tag: antibody

value: 3XFLAG tag

tag: adapter


title: 0h rep1, Control


title: BT145_The SNP of whole genome

source_name: BT145 SNP of whole genome

value: Leaf


title: BT141_The SNP of whole genome

source_name: BT141 SNP of whole genome


title: BT142_The SNP of whole genome

source_name: BT142 SNP of whole genome


title: PT404C

description: male.child.results.csv.gz

value: male child


title: WT_FLAG_LMW rep1 input

description:
eCLIP4_5.WTL-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP4_5.WTL-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw


title: PT403M

description: mother.results.csv.gz

value: mother


title: BT140_The SNP of whole genome

source_name: BT140 SNP of whole genome


title: BT139_The SNP of whole genome

source_name: BT139 SNP of whole genome


title: PT403F

description: father.results.csv.gz

value: preterm birth

value: father


title: PT403C

description: female.child.results.csv.gz

value: female child


title: BT138_The SNP of whole genome

source_name: BT138 SNP of whole genome


title: WT_FLAG_HMW rep1 input

description:
eCLIP4_5.WTH-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP4_5.WTH-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw


title: WT_FLAG_HMW rep2 input

description:
eCLIP4_5.WTH-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP4_5.WTH-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw


title: WT_Strep_LMW rep2 input

description:
eCLIP2.WT-low-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP2.WT-low-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw

value: IBA Lifesciences

value: StrepMAB-Immo, iba life sciences, Cat.no:2-1517-001

value: 2xStrep tag


title: BT137_The SNP of whole genome

source_name: BT137 SNP of whole genome


title: PT402M

description: mother.results.csv.gz


title: BT136_The SNP of whole genome

source_name: BT136 SNP of whole genome


title: PT402F

description: father.results.csv.gz


title: PT402C

description: female.child.results.csv.gz


title: BT135_The SNP of whole genome

source_name: BT135 SNP of whole genome


title: WT_Strep_HMW rep2 input

description:
eCLIP2.WT-high-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP2.WT-high-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw


title: WT_Strep_HMW rep1 input

description:
eCLIP2.WT-high-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP2.WT-high-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw


title: BT134_The SNP of whole genome

source_name: BT134 SNP of whole genome


title: PT401M

description: mother.results.csv.gz


title: BT133_The SNP of whole genome

source_name: BT133 SNP of whole genome


title: ORF10 rep2 input

description:
eCLIP4_4.ORF10-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP4_4.ORF10-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw

source_name: BEAS-2B expressing ORF10


title: PT401F

description: father.results.csv.gz


title: ORF10 rep1 input

description:
eCLIP4_4.ORF10-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP4_4.ORF10-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw


title: ORF9c rep2 input

description:
eCLIP5_7.orf9c-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP5_7.orf9c-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw

source_name: BEAS-2B expressing ORF9c


title: BT132_The SNP of whole genome

source_name: BT132 SNP of whole genome


title: PT400M

description: mother.results.csv.gz


title: ORF9c rep1 input

description:
eCLIP5_7.orf9c-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP5_7.orf9c-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw


title: BT130_The SNP of whole genome

source_name: BT130 SNP of whole genome


title: BT129_The SNP of whole genome

source_name: BT129 SNP of whole genome


title: BT128_The SNP of whole genome

source_name: BT128 SNP of whole genome


title: PT400C

description: male.child.results.csv.gz

source_name: buccal


title: N rep2 input

description:
eCLIP2.N-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP2.N-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw

source_name: BEAS-2B expressing N


title: RNAseq PCOS_4 GF

city: orlando

first: Adeline

last: Divoux

state: FL

address: 301 E. Princeton St

department: Translational Research Institute

institute: Adventhealth

description: countData.GF.txt

data_processing:
Raw data were aligned to hg19 genome (GENCODE v19) using STAR v2.7.7a.
SAMtools v1.3.1 was used for indexing and filtering the low-quality reads (MAPQ < 10).
Generate raw read count table, Rsubread’s featureCounts v2.4.0 was used
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw count data for control and PCOS samples

source_name: ASC

growth_protocol: Stromal-vascular fractions were isolated from scWAT abdominal and GF depot, plated and grown in aMEM supplemented with 2.5% bovine serum and with addition of hEGF and hFGF (Life technologies, 10µg/ml and 4µg/ml respectively). Cells were initially purified by depletion of the endothelial cells and macropahges using FACS.

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen) from ABD and GF ASCs of 4 control and 4 PCOS women.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: origin

value: isolated from subcutaneous gluteo-femoral adipose tissue

tag: group

value: PCOS


title: WT_Strep_LMW rep1 input

description:
eCLIP2.WT-low-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP2.WT-low-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw


title: RNAseq PCOS_4 ABD

description: countData.ABD.txt

value: isolated from subcutaneous abdominal adipose tissue


title: BT127_The SNP of whole genome

source_name: BT127 SNP of whole genome


title: ORF8 rep2 input

description:
eCLIP5_6.orf8-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP5_6.orf8-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw

source_name: BEAS-2B expressing ORF8


title: RNAseq PCOS_3 GF

description: countData.GF.txt


title: N rep1 input

description:
eCLIP2.N-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP2.N-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw


title: RNAseq PCOS_3 ABD

description: countData.ABD.txt


title: BT125_The SNP of whole genome

description: Tea SNP 96-Array Plate detected the SNP of whole genome of tea

source_name: BT125 SNP of whole genome


title: RNAseq PCOS_2 GF

description: countData.GF.txt


title: BT124_The SNP of whole genome

source_name: BT124 SNP of whole genome


title: ORF8 rep1 input

description:
eCLIP5_6.orf8-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP5_6.orf8-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw


title: BT123_The SNP of whole genome

source_name: BT123 SNP of whole genome


title: PT401C

description: male.child.results.csv.gz

tag: treatment group


title: RNAseq PCOS_2 ABD

description: countData.ABD.txt


title: ORF7b rep2 input

description:
eCLIP5_5.orf7b-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP5_5.orf7b-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw

source_name: BEAS-2B expressing ORF7b


title: ORF7b rep1 input

description:
eCLIP5_5.orf7b-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP5_5.orf7b-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw


title: BT122_The SNP of whole genome

source_name: BT122 SNP of whole genome


title: ORF7a rep2 input

description:
eCLIP2.ORF7a-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP2.ORF7a-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw

source_name: BEAS-2B expressing ORF7a


title: RNAseq PCOS_1 ABD

description: countData.ABD.txt


title: PT400F

description: father.results.csv.gz

tag: family member


title: RNAseq PCOS_1 GF

description: countData.GF.txt


title: ORF9b rep2 input

description:
eCLIP5_6.orf9b-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP5_6.orf9b-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw

source_name: BEAS-2B expressing ORF9b


title: BT131_The SNP of whole genome

source_name: BT131 SNP of whole genome

tag: tissue


title: RNAseq Control_4 GF

description: countData.GF.txt

value: Control


title: BT121_The SNP of whole genome

source_name: BT121 SNP of whole genome

tag: cultivar


title: ORF9b rep1 input

description:
eCLIP5_6.orf9b-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP5_6.orf9b-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw


title: ORF7a rep1 input

description:
eCLIP2.ORF7a-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP2.ORF7a-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw


title: ORF6 rep2 input

description:
eCLIP2.ORF6-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP2.ORF6-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw

source_name: BEAS-2B expressing ORF6


title: BT120_The SNP of whole genome

source_name: BT120 SNP of whole genome


title: BT119_The SNP of whole genome

source_name: BT119 SNP of whole genome


title: RNAseq Control_4 ABD

description: countData.ABD.txt


title: BT126_The SNP of whole genome

source_name: BT126 SNP of whole genome


title: RNAseq Control_3 GF

description: countData.GF.txt


title: ORF6 rep1 input

description:
eCLIP2.ORF6-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP2.ORF6-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw


title: M rep2 input

description:
eCLIP2.M-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP2.M-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw

source_name: BEAS-2B expressing M


title: RNAseq Control_3 ABD

description: countData.ABD.txt

source_name: ASC


title: M rep1 input

description:
eCLIP2.M-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP2.M-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw


title: RNAseq Control_2 GF

description: countData.GF.txt


title: RNAseq Control_2 ABD

description: countData.ABD.txt


title: RNAseq Control_1 GF

description: countData.GF.txt


title: BT114_The SNP of whole genome

source_name: BT114 SNP of whole genome


title: BT116_The SNP of whole genome

source_name: BT116 SNP of whole genome


title: BT115_The SNP of whole genome

source_name: BT115 SNP of whole genome


title: E rep2 input

description:
eCLIP2.E-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP2.E-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw

source_name: BEAS-2B expressing E


title: BT112_The SNP of whole genome

source_name: BT112 SNP of whole genome


title: E2_12h_run2_RNAseq

city: buenos aires

first: Patricia

last: Saragüeta

state: CABA

address: Vuelta de Obligado 2490

country: Argentina

institute: IByME

data_processing:
Good quality 50bp reads were aligned to the reference human genome (hg19, UCSC) using Tophat software keeping those that mapped uniquely to the reference with up to two mismatches and transcript assembly, abundance quantification and differential expression analyses were performed with the Cufflinks tool.
Genes under 200bp in length or with FPKM values below 0,1 were excluded from downstream analyses. Genes were classified into induced, repressed or non-regulated depending on log2FC value relative to untreated cells (T0). Threshold value was arbitrarily set at log2FC = +/- 0.8 and q<0.05 (FDR).
Genome_build: hg19
Supplementary_files_format_and_content: text file including fpkm values for all samples of two biological replicates (run1 and run2) and fold change versus untreated sample

source_name: endometrial adenocarcinoma

growth_protocol: Ishikawa cells were routinely cultured in DMEM/F12 (1:1) supplemeted with 10% FCS and gentamycin

extract_protocol:
Cells were washed once in PBS and whole cell lysates were prepared using Trizol reagent (Invitrogen). Total RNA (>200bp) was obtain using RNeasy Plus Mini kit (Qiagen) according to manufacturer specifications.
Poly-A-enriched RNA was used to prepare libraries with TruSeq RNA Sample Preparation kit v2 y v4 (ref. RS-122-2001/2, Illumina) according to instructions from manufacturer followed by single-end (run1) and paired-end (run2) sequencing

treatment_protocol: Adequate number of cells were seeded in culture plates using DMEM/F12 (1:1) without phenol red and supplemented with 5% dextran-coated charcoal stripped FCS and gentamycin for 48h, followed by overnight incubation in DMEM/F12 (1:1) without phenol red and without FCS. After overnight incubation, cells were treated or not with R5020 10nM and E2 10nM for 12h.

tag: disease state

value: endometrial adenocarcinoma

tag: cell line

value: Ishikawa

tag: passages

value: epithelial-like

tag: growth mode

value: adherent

tag: treatment

value: 12h E2-treated Ishikawa cells


title: R5020_12h_run2_RNAseq

tag: cell type

value: 12h R5020-treated Ishiakwa cells


title: BT111_The SNP of whole genome

source_name: BT111 SNP of whole genome

value: Leaf


title: E rep1 input

description:
eCLIP2.E-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP2.E-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw


title: SPIKE rep2 input

description:
eCLIP4_4.SPIKE-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP4_4.SPIKE-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw

source_name: BEAS-2B expressing SPIKE

value: Sigma-Aldrich

value: Monoclonal ANTI-FLAG® M2 antibody produced in mouse, Sigma Aldrich, F3165

value: 3XFLAG tag


title: BT110_The SNP of whole genome

source_name: BT110 SNP of whole genome


title: SNIP-TIL

city: Stanford

first: Louai

last: Labanieh

address: 265 Campus Drive, Room G2105

department: Stanford Cancer Institute

institute: Stanford University

data_processing:
BulkRNA: Reads were pseudo-aligned using Salmon
BulkRNA: Differential gene expression analysis performed using DESeq2
scRNA: See Labanieh et al. 2022
scRNA: filtered according to Labanieh et al. then transformed using sctransform using Seurat package
scRNA: barcode suffix "1"=SNIP TIL,  barcode suffix "2"=Const TIL
Genome_build: gencode v33 (bulk RNA)
Supplementary_files_format_and_content: SNIP_BULK_RNAseq_TPM.csv (TPM abundance)
Supplementary_files_format_and_content: Const_vs_SNIP_DESeq.csv (Differentially expressed genes)
Supplementary_files_format_and_content: single_cell_TIL_counts.csv (scRNA-seq count matrix)

source_name: primary  T cells

growth_protocol: scRNA: Buffy coats from healthy donors were purchased from the Stanford Blood Center under an IRB-exempt-protocol. Primary human T cells were purified by negative selection using the RosetteSep Human T cell Enrichment kit (Stem Cell Technologies) and SepMate-50 tubes. T cells were cryopreserved at 1-2x107 cells per mL in CryoStor CS10 cryopreservation media (Stem Cell Technologies) until use. At Day 0, primary human T cells were thawed and activated with anti-CD3/CD28 Human T-Expander Dynabeads (Thermo Fisher) at a 3:1 bead to cell ratio. On Day 2 virus coated culture plates were prepared on non TC-treated 12-well plates that had been pre-coated with RetroNectin (Takara Bio) according to the manufacturer’s instructions, by incubating with 1mL of retroviral supernatant and centrifugation at 3200 RPM, 32 °C for two hours. The supernatant was subsequently aspirated off of the wells and 0.5E6 T cells were added in 1mL of T cell media comprised of: AIM V (Thermo Fisher), 5% fetal bovine serum (FBS), 100 U/mL penicillin (Gibco), 100 mg/mL streptomycin (Gibco), 2 mM L-glutamine (Gibco), 10 mM HEPES (Gibco), and 100 U/mL rhIL-2 (Peprotech). After addition of the T cells, the plates were gently spun down at 1200 RPM for 2 min then incubated for 24hrs at 37°C 5% CO2. This transduction process was repeated at Day 3. Dynabeads were removed on Day 4 by magnetic separation. Cells were maintained between 0.4 - 2x10^6 cells/mL and expanded until Day 10

extract_protocol:
scRNA:  Tumors were harvested at Day 15 post tumor implantation. Tumors were mechanically dissociated using a gentleMACS dissociator (Miltenyi). Single-cell suspensions were made by passing tumors  through a 70μm cell strainer, depleting red blood cells by ACK lysis (Quality Biological Inc.), and further filtration through flow cytometry filter tubes with 35μm cell strainer caps (Falcon). T cells were purified by magnetic separation using the REAlease® CD4/CD8 (TIL) MicroBead Kit (Miltenyi) according to the manufacturer’s instructions
scRNA: Sent to the Stanford Functional Genomics facility for single-cell RNAseq library preparation using the Chromium Single Cell 3' Solution v3 platform (10x GENOMICS). Libraries were sent to Novogene for sequencing on a NovaSeq S4 lane (PE150) with >53,000 reads per cell

treatment_protocol: scRNA: 1E6 143B cells in 100μL DPBS were injected into the tibia periosteum of NSG mice. Four days after tumor implantation and after visual confirmation of tumor formation, mice were treated with 5E6 SNIP or constitutive HER2.BBz CAR-T cells. Mice that received SNIP HER2.BBz CAR-T cells were implanted with osmotic pumps containing 54 mg/mL GPV and 6 mg/mL RTV on Day 4 post-tumor implantation and administered 50 mg/kg GPV and 25mg/kg RTV by oral gavage 2 times per day (SNIP ON).

value: tumor-infiltrating lymphocyte (TIL)

tag: protocol

value: SNIP-TIL


title: ORF3b rep2 input

description:
eCLIP5_5.orf3b-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP5_5.orf3b-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw

source_name: BEAS-2B expressing ORF3b

tag: antibody manufacturer


title: ORF3a rep1 input

description:
eCLIP2.ORF3a-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP2.ORF3a-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw

source_name: BEAS-2B expressing ORF3a

value: IBA Lifesciences

tag: antibody catalog #

value: StrepMAB-Immo, iba life sciences, Cat.no:2-1517-001

value: 2xStrep tag


title: BT117_The SNP of whole genome

description: Tea SNP 96-Array Plate detected the SNP of whole genome of tea

source_name: BT117 SNP of whole genome


title: BT113_The SNP of whole genome

source_name: BT113 SNP of whole genome


title: RNAseq Control_1 ABD

description: countData.ABD.txt

value: isolated from subcutaneous abdominal adipose tissue


title: ORF3b rep1 input

description:
eCLIP5_5.orf3b-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP5_5.orf3b-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw

tag: antibody


title: SNIP CAR-T 2

description:
SNIP_BULK_RNAseq_TPM.csv
Const_vs_SNIP_DESeq.csv

growth_protocol: BULK RNA: Buffy coats from healthy donors were purchased from the Stanford Blood Center under an IRB-exempt-protocol. Primary human T cells were purified by negative selection using the RosetteSep Human T cell Enrichment kit (Stem Cell Technologies) and SepMate-50 tubes. T cells were cryopreserved at 1-2x107 cells per mL in CryoStor CS10 cryopreservation media (Stem Cell Technologies) until use. At Day 0, primary human T cells were thawed and activated with anti-CD3/CD28 Human T-Expander Dynabeads (Thermo Fisher) at a 3:1 bead to cell ratio. On Day 2 virus coated culture plates were prepared on non TC-treated 12-well plates that had been pre-coated with RetroNectin (Takara Bio) according to the manufacturer’s instructions, by incubating with 1mL of retroviral supernatant and centrifugation at 3200 RPM, 32 °C for two hours. The supernatant was subsequently aspirated off of the wells and 0.5E6 T cells were added in 1mL of T cell media comprised of: AIM V (Thermo Fisher), 5% fetal bovine serum (FBS), 100 U/mL penicillin (Gibco), 100 mg/mL streptomycin (Gibco), 2 mM L-glutamine (Gibco), 10 mM HEPES (Gibco), and 100 U/mL rhIL-2 (Peprotech). After addition of the T cells, the plates were gently spun down at 1200 RPM for 2 min then incubated for 24hrs at 37°C 5% CO2. This transduction process was repeated at Day 3. Dynabeads were removed on Day 4 by magnetic separation. Cells were maintained between 0.4 - 2x10^6 cells/mL and expanded until Day 10

extract_protocol:
BULK RNA: SNIP CAR-T cells were cultured in the absence of drug (SNIP OFF). RNA was extracted from Day 10 in vitro T cells using the RNeasy Plus Mini Kit (Qiagen) and send to NovoGene for library preparation
BULK RNA: Sent to NovoGene for library preparation, PE150 sequencing with a minimum of 6G raw output per sample, and demultiplexing.

treatment_protocol: BULK RNA: untreated

value: T cells

value: untreated

value: SNIP CAR-T


title: Const-TIL

value: Const-TIL


title: ORF3a rep2 input

description:
eCLIP2.ORF3a-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP2.ORF3a-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw

tag: adapter


title: Untreated_T0_run2_RNAseq

value: endometrial adenocarcinoma

value: Ishikawa

value: epithelial-like

value: adherent

value: untreated Ishikawa cells


title: NSP16 rep1 input

description:
eCLIP7.NSP16-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP7.NSP16-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw

source_name: BEAS-2B expressing NSP16

value: Sigma-Aldrich

value: Monoclonal ANTI-FLAG® M2 antibody produced in mouse, Sigma Aldrich, F3165


title: BT106_The SNP of whole genome

source_name: BT106 SNP of whole genome

value: Leaf


title: SNIP CAR-T 1


title: BT118_The SNP of whole genome

source_name: BT118 SNP of whole genome


title: BT109_The SNP of whole genome

source_name: BT109 SNP of whole genome


title: BT105_The SNP of whole genome

source_name: BT105 SNP of whole genome


title: Constitutive CAR-T 3

value: Constitutive CAR-T


title: NSP15 rep2 input

description:
eCLIP2.nsp15-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP2.nsp15-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw

source_name: BEAS-2B expressing NSP15

value: IBA Lifesciences


title: SPIKE rep1 input

description:
eCLIP4_4.SPIKE-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP4_4.SPIKE-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw

value: 3XFLAG tag


title: NSP15 rep1 input

description:
eCLIP2.nsp15-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP2.nsp15-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw

value: StrepMAB-Immo, iba life sciences, Cat.no:2-1517-001

value: 2xStrep tag


title: BT103_The SNP of whole genome

source_name: BT103 SNP of whole genome


title: NSP14 rep1 input

description:
eCLIP4_1.NSP14-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP4_1.NSP14-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw

source_name: BEAS-2B expressing NSP14


title: NSP14 rep2 input

description:
eCLIP4_1.NSP14-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP4_1.NSP14-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw


title: BT108_The SNP of whole genome

source_name: BT108 SNP of whole genome


title: BT107_The SNP of whole genome

source_name: BT107 SNP of whole genome


title: BT102_The SNP of whole genome

source_name: BT102 SNP of whole genome


title: BNT_Naive_14_Day48

first: Hye Kyung

last: Lee

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

data_processing:
RNA-seq data were trimmed using trimmomatic (Bolger et al., Bioinformatics, 2014) and subsequently aligned to the reference genome hg19 applying STAR RNA-seq aligner (Dobin et al., Bioinformatics, 2013). HTSeq(Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
HTSeq(Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
Trimmed RNA-seq data were aligned to the human V, D and J genes and obtained immune clonotypes using MiXCR (Bolotin et al., Nat Methods, 2015; Bolotin et al., Nat Biotechnol, 2017).
Genome_build: hg19
Supplementary_files_format_and_content: HTSeq counts from RNA-seq samples
Supplementary_files_format_and_content: clonotypes from RNA-seq samples

source_name: PBMCs

growth_protocol: Blood samples were collected from the convalescnet COVID-19 patients and SARS-CoV-2 naïve individuals both before and after vaccinations.

extract_protocol:
The buffy coat was extracted by centrifuge after blood sample collection and RBC was removed using RBC lysis buffer in the buffy coat. Total RNA was isolated using a Maxwell RSC simply RNA Blood purification kit.
Libraries for sequencing were prepared with TruSeq Stranded mRNA Kit following standard Illumina protocols.

tag: age

tag: gender

value: Male

tag: condition

value: SARS-CoV-2 Naïve


title: NSP13 rep2 input

description:
eCLIP6.NSP13-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP6.NSP13-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw

source_name: BEAS-2B expressing NSP13


title: NSP16 rep2 input

description:
eCLIP7.NSP16-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP7.NSP16-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw


title: Constitutive CAR-T 2

source_name: primary  T cells

value: T cells

value: untreated


title: Constitutive CAR-T 1


title: NSP13 rep1 input

description:
eCLIP4_0.NSP13-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP4_0.NSP13-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw


title: BNT_Naive_14_Day41


title: BT104_The SNP of whole genome

source_name: BT104 SNP of whole genome


title: NSP12 rep1 input

description:
eCLIP5_1.nsp12-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP5_1.nsp12-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw

source_name: BEAS-2B expressing NSP12


title: BNT_Naive_14_Day40


title: SNIP CAR-T 3

value: SNIP CAR-T


title: NSP11 rep1 input

description:
eCLIP6.NSP11-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP6.NSP11-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw

source_name: BEAS-2B expressing NSP11


title: BNT_Naive_13_Day41

value: Female


title: BT099_The SNP of whole genome

source_name: BT099 SNP of whole genome


title: BT096_The SNP of whole genome

source_name: BT096 SNP of whole genome


title: BNT_Naive_14_Day11


title: BT098_The SNP of whole genome

source_name: BT098 SNP of whole genome


title: BT095_The SNP of whole genome

source_name: BT095 SNP of whole genome


title: NSP10 rep1 input

description:
eCLIP2.nsp10-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP2.nsp10-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw

source_name: BEAS-2B expressing NSP10


title: BNT_Naive_13_Day10


title: BT093_The SNP of whole genome

source_name: BT093 SNP of whole genome


title: NSP9 rep2 input

description:
eCLIP3_3.nsp9-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP3_3.nsp9-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw

source_name: BEAS-2B expressing NSP9


title: BT101_The SNP of whole genome

description: Tea SNP 96-Array Plate detected the SNP of whole genome of tea

source_name: BT101 SNP of whole genome


title: BNT_Naive_13_Day34


title: BT097_The SNP of whole genome

source_name: BT097 SNP of whole genome


title: BT092_The SNP of whole genome

source_name: BT092 SNP of whole genome


title: NSP9 rep1 input

description:
eCLIP3_3.nsp9-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP3_3.nsp9-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw


title: NSP8 rep2 input

description:
eCLIP4_3.NSP8-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP4_3.NSP8-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw

source_name: BEAS-2B expressing NSP8


title: BT091_The SNP of whole genome

source_name: BT091 SNP of whole genome


title: BNT_Naive_12_Day41

source_name: PBMCs


title: BNT_Naive_13_Day0


title: BNT_Naive_14_Day0


title: NSP11 rep2 input

description:
eCLIP4_0.NSP11-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP4_0.NSP11-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw


title: BNT_Naive_12_Day35


title: Ly6Chi-derived macrophages [R10145]

city: Singapore

first: Nicholas

last: Ang

address: 8a Biomedical Grove, Singapore 138648

country: Singapore

institute: Singapore Immunology Network (SIgN)

data_processing:
FASTQ files were mapped using STAR to  GRCm38 genome build
Gene counts were obtained using featureCounts on GENCODE vM22 annotations
Genome_build: GRCm38
Supplementary_files_format_and_content: gene_counts

source_name: macrophages

growth_protocol: Sorted TpMos and Mature Ly6Chi monocytes were plated and cultured at 37ºC, 5% CO2 in complete RPMI 1640 medium with 25mM HEPES (Hyclone), 10% Fetal Bovine Serum (FBS) (Serana), 2mM L-Glutamine (Invitrogen), and 100x Penicillin/Streptomycin (Invitrogen) with indicated CSF-1 (Stemcell Technologies) concentrations for 7 days.

extract_protocol:
Cultured macrophages were harvested using cell scrappers. Total RNA was extracted using Arcturus Picopure RNA Isolation kit according to the manufacturer’s protocol. All mouse RNA samples were analysed on Perkin Elmer Labchip GX system for quality assessment with RIN > 7.9.
cDNA libraries preparation utilized 2 ng of total RNA and 1 µl of a 1:50,000 dilution of ERCC RNA Spike in Controls (Ambion) using SMARTSeq v2 protocol, with modifications: (1) 20 µM TSO; and (2) 250 pg of cDNA with 1/5 reaction of Illumina Nextera XT kit. Length distribution of the cDNA libraries was monitored using DNA High Sensitivity Reagent kit on the Perkin Elmer Labchip. Samples were subjected to an indexed PE sequencing run of 2 × 51 cycles on an Illumina HiSeq 2500 Rapid mode (14 samples/lane).

treatment_protocol: Not Applicable

value: Ly6Chi-derived macrophages


title: BT090_The SNP of whole genome

source_name: BT090 SNP of whole genome


title: NSP12 rep2 input

description:
eCLIP5_1.nsp12-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP5_1.nsp12-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw

source_name: BEAS-2B expressing NSP12


title: BNT_Naive_13_Day35


title: NSP8 rep1 input

description:
eCLIP4_3.NSP8-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP4_3.NSP8-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw


title: NSP10 rep2 input

description:
eCLIP2.nsp10-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP2.nsp10-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw


title: BT089_The SNP of whole genome

source_name: BT089 SNP of whole genome


title: BNT_Naive_12_Day34


title: NSP7 rep2 input

description:
eCLIP5_4.nsp7-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP5_4.nsp7-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw

source_name: BEAS-2B expressing NSP7


title: Ly6Chi-derived macrophages [R10143]


title: BT088_The SNP of whole genome

source_name: BT088 SNP of whole genome


title: BNT_Naive_12_Day0


title: NSP7 rep1 input

description:
eCLIP5_4.nsp7-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP5_4.nsp7-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw


title: TpMo-derived macrophages [R10141]

value: TpMo-derived macrophages


title: NSP6 rep1 input

description:
eCLIP5_3.nsp6-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP5_3.nsp6-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw

source_name: BEAS-2B expressing NSP6


title: NSP6 rep2 input

description:
eCLIP5_3.nsp6-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP5_3.nsp6-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw


title: TpMo-derived macrophages [R10142]


title: BNT_Naive_11_Day41


title: BT086_The SNP of whole genome

source_name: BT086 SNP of whole genome


title: BNT_Naive_11_Day35


title: NSP5_C145A rep2 input

description:
eCLIP2.nsp5_C145A-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP2.nsp5_C145A-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw

source_name: BEAS-2B expressing NSP5_C145A


title: BNT_Naive_11_Day34


title: TpMo-derived macrophages [R10140]


title: BT085_The SNP of whole genome

source_name: BT085 SNP of whole genome


title: d6_mid_grade_sepsis_ly6chi_mo [R9494]

data_processing:
FASTQ files were mapped using STAR to  GRCm38 genome build
Gene counts were obtained using featureCounts on GENCODE vM20 annotations
Genome_build: GRCm38
Supplementary_files_format_and_content: gene_counts

source_name: monocytes

growth_protocol: Not Applicable

extract_protocol:
Mice were sacrificed 6 days post-surgery, BM TpMos and mature Ly6Chi monocytes were then sorted. Total RNA was extracted using Arcturus Picopure RNA Isolation kit according to the manufacturer’s protocol. All mouse RNA samples were analysed on Perkin Elmer Labchip GX system for quality assessment with RIN > 7.9.
cDNA libraries preparation utilized 2 ng of total RNA and 1 µl of a 1:50,000 dilution of ERCC RNA Spike in Controls (Ambion) using SMARTSeq v2 protocol, with modifications: (1) 20 µM TSO; and (2) 250 pg of cDNA with 1/5 reaction of Illumina Nextera XT kit. Length distribution of the cDNA libraries was monitored using DNA High Sensitivity Reagent kit on the Perkin Elmer Labchip. Samples were subjected to an indexed PE sequencing run of 2 × 51 cycles on an Illumina HiSeq 2500 Rapid mode (14 samples/lane).

value: Ly6Chi monocytes


title: BT084_The SNP of whole genome

source_name: BT084 SNP of whole genome


title: d6_mid_grade_sepsis_ly6chi_mo [R9493]


title: NSP5_C145A rep1 input

description:
eCLIP2.nsp5-C145A-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP2.nsp5-C145A-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw


title: BNT_Naive_12_Day10


title: BT083_The SNP of whole genome

source_name: BT083 SNP of whole genome


title: BNT_Naive_11_Day11


title: Ly6Chi-derived macrophages [R10144]


title: d6_mid_grade_sepsis_ly6chi_mo [R9492]


title: BNT_Naive_11_Day0


title: NSP5 rep2 input

description:
eCLIP5_3.nsp5-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP5_3.nsp5-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw

source_name: BEAS-2B expressing NSP5

value: Sigma-Aldrich


title: NSP5 rep1 input

description:
eCLIP5_3.nsp5-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP5_3.nsp5-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw

value: Monoclonal ANTI-FLAG® M2 antibody produced in mouse, Sigma Aldrich, F3165


title: BT087_The SNP of whole genome

source_name: BT087 SNP of whole genome

value: Leaf


title: BT082_The SNP of whole genome

source_name: BT082 SNP of whole genome


title: BNT_Naive_10_Day41

source_name: PBMCs


title: BT081_The SNP of whole genome

source_name: BT081 SNP of whole genome


title: d6_mid_grade_sepsis_tpmo [R9491]

value: BM TpMos


title: NSP4 rep2 input

description:
eCLIP4_2.NSP4-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP4_2.NSP4-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw

source_name: BEAS-2B expressing NSP4


title: NSP4 rep1 input

description:
eCLIP6.NSP4-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP6.NSP4-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw


title: d6_mid_grade_sepsis_tpmo [R9490]


title: BT080_The SNP of whole genome

description: Tea SNP 96-Array Plate detected the SNP of whole genome of tea

source_name: BT080 SNP of whole genome


title: d6_mid_grade_sepsis_tpmo [R9489]


title: BNT_Naive_10_Day34


title: BT079_The SNP of whole genome

source_name: BT079 SNP of whole genome


title: BT078_The SNP of whole genome

source_name: BT078 SNP of whole genome


title: BNT_Naive_10_Day10


title: NSP3 rep2 input

description:
eCLIP5_2.nsp3-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP5_2.nsp3-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw

source_name: BEAS-2B expressing NSP3


title: BNT_Naive_10_Day0


title: Normal_ControlSaline_rep3

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

institute: University of Geneva Medical School

data_processing:
Basecalls performed using CASAVA version 1.8.2
Raw reads were all trimmed to 50bp and mapped to the reference genome using STAR 2.4 with --outFilterMultimapNmax 1
Raw count measurements were obtained with featureCounts 1.4.6 keeping only unambiguous reads
Genome_build: GRCm38.96
Supplementary_files_format_and_content: Raw_counts.txt

source_name: Lung

growth_protocol: C57BL/6J mice, obtained from the mice facility of University of Geneva were kept under specific-pathogen-free conditions. Housing conditions were 12 hours day and 12 hours night. Mice had access to food and drinking water ad libitum.

extract_protocol:
Offspring lungs were collected at ped21 and laser dissected and 3-5 mouse lungs were used for each group (C-S, N-S, eC-E, nC-E, eN-E, nN-E). cDNA libraries were constructed by the Genomic platform of the University of Geneva using the Illumina TruSeq RNA Sample Preparation Kit (CA, USA) according to the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-Seq. Smarter + Nextera technology was used due to low initial levels of mRNA.

treatment_protocol: Nicotine (200 mg/L) was started immediately after mating and administered to the females in drinking water supplemented with 2% saccharin for the whole period of gestation and lactation. As a control, we used drinking water with 2% saccharin. Pups born from nicotine-exposed mothers (nicotine group) or the controls (control group) were instilled intranasaly either with elastase or saline at the age of 11 weeks and their lungs were harvested at post-elastase day (ped) 21 for further RNAseq analysis.

tag: strain

value: Lung

tag: group

value: post-elastase day 21

tag: genotype

value: wild type


title: NSP3 rep1 input

description:
eCLIP5_2.nsp3-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP5_2.nsp3-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw

value: 3XFLAG tag


title: Normal_ControlSaline_rep2

tag: tissue


title: NSP2 rep2 input

description:
eCLIP5_2.nsp2-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP5_2.nsp2-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw

source_name: BEAS-2B expressing NSP2

value: IBA Lifesciences

value: StrepMAB-Immo, iba life sciences, Cat.no:2-1517-001

value: 2xStrep tag


title: BNT_Naive_9_Day41

value: Male

value: SARS-CoV-2 Naïve


title: BT076_The SNP of whole genome

source_name: BT076 SNP of whole genome

tag: cultivar


title: Normal_ControlSaline_rep1


title: NSP2 rep1 input

description:
eCLIP5_2.nsp2-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP5_2.nsp2-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw


title: BNT_Naive_9_Day35


title: BT075_The SNP of whole genome

source_name: BT075 SNP of whole genome


title: NSP1 rep1 input

description:
eCLIP7.NSP1-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP7.NSP1-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw

source_name: BEAS-2B expressing NSP1


title: BNT_Naive_10_Day35

value: Female


title: Normal_ControlElastase_rep5


title: BNT_Naive_9_Day34


title: Normal_ControlElastase_rep4


title: WT_FLAG_LMW rep2 IP


title: BT074_The SNP of whole genome

source_name: BT074 SNP of whole genome


title: BNT_Naive_9_Day0


title: BT072_The SNP of whole genome

source_name: BT072 SNP of whole genome


title: WT_FLAG_LMW rep1 IP


title: Normal_ControlElastase_rep1


title: BT077_The SNP of whole genome

source_name: BT077 SNP of whole genome


title: BT100_The SNP of whole genome

source_name: BT100 SNP of whole genome


title: BT071_The SNP of whole genome

source_name: BT071 SNP of whole genome


title: BNT_Naive_8_Day41

source_name: PBMCs


title: BT070_The SNP of whole genome

source_name: BT070 SNP of whole genome


title: WT_FLAG_HMW rep1 IP


title: Normal_NicotineSaline_rep3


title: WT_Strep_LMW rep2 IP


title: Normal_NicotineSaline_rep2


title: WT_FLAG_HMW rep2 IP


title: Normal_NicotineSaline_rep1


title: BNT_Naive_8_Day34


title: BT073_The SNP of whole genome

source_name: BT073 SNP of whole genome


title: Normal_NicotineElastase_rep3


title: BNT_Naive_8_Day10


title: BT068_The SNP of whole genome

source_name: BT068 SNP of whole genome


title: WT_Strep_LMW rep1 IP


title: BNT_Naive_8_Day0


title: WT_Strep_HMW rep2 IP


title: BNT_Naive_9_Day10


title: Normal_NicotineElastase_rep1


title: BT067_The SNP of whole genome

source_name: BT067 SNP of whole genome


title: BNT_Naive_7_Day35


title: WT_Strep_HMW rep1 IP


title: BT066_The SNP of whole genome

source_name: BT066 SNP of whole genome


title: ORF10 rep2 IP

source_name: BEAS-2B expressing ORF10


title: Emphysema_ControlElastase_rep5

source_name: Lung


title: BNT_Naive_7_Day34


title: Emphysema_ControlElastase_rep4


title: Normal_NicotineElastase_rep4


title: BT065_The SNP of whole genome

source_name: BT065 SNP of whole genome


title: ORF10 rep1 IP


title: BNT_Naive_7_Day7


title: Emphysema_ControlElastase_rep3


title: BT064_The SNP of whole genome

source_name: BT064 SNP of whole genome


title: BNT_Naive_7_Day0


title: ORF9c rep2 IP

source_name: BEAS-2B expressing ORF9c


title: BT069_The SNP of whole genome

source_name: BT069 SNP of whole genome


title: Emphysema_ControlElastase_rep2


title: BT063_The SNP of whole genome

source_name: BT063 SNP of whole genome


title: ORF9c rep1 IP


title: BNT_Naive_6_Day41


title: BNT_Naive_7_Day41


title: ORF9b rep2 IP

source_name: BEAS-2B expressing ORF9b


title: Emphysema_ControlElastase_rep1


title: BT062_The SNP of whole genome

source_name: BT062 SNP of whole genome


title: Emphysema_NicotineElastase_rep4


title: BT061_The SNP of whole genome

source_name: BT061 SNP of whole genome


title: BNT_Naive_6_Day34


title: BT060_The SNP of whole genome

source_name: BT060 SNP of whole genome


title: BNT_Naive_6_Day35

source_name: PBMCs


title: ORF9b rep1 IP


title: N rep2 IP

source_name: BEAS-2B expressing N


title: BNT_Naive_6_Day10


title: BT059_The SNP of whole genome

source_name: BT059 SNP of whole genome


title: BNT_Naive_6_Day0


title: N rep1 IP


title: Emphysema_NicotineElastase_rep1


title: BT058_The SNP of whole genome

source_name: BT058 SNP of whole genome


title: ORF8 rep1 IP

source_name: BEAS-2B expressing ORF8


title: BNT_Naive_5_Day41


title: BT057_The SNP of whole genome

source_name: BT057 SNP of whole genome


title: ORF8 rep2 IP


title: BT055_The SNP of whole genome

source_name: BT055 SNP of whole genome


title: BNT_Naive_5_Day35


title: Control_Saline_rep2

source_name: Lung

extract_protocol:
Offspring lungs were collected at ped3 and RNA was isolated and purified using Macherey-Nagel purification kit (Germany). Three to 5 offspring lung were used for each group, namelly control-saline (C-S), control-elastase (C-E), nicotine-saline (N-S) and nicotine-elastase (N-E) group. cDNA libraries were constructed by the Genomic platform of the University of Geneva using the Illumina TruSeq RNA Sample Preparation Kit (CA, USA) according to the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Nicotine (200 mg/L) was started immediately after mating and administered to the females in drinking water supplemented with 2% saccharin for the whole period of gestation and lactation. As a control, we used drinking water with 2% saccharin. Pups born from nicotine-exposed mothers (nicotine group) or the controls (control group) were instilled intranasaly either with elastase or saline at the age of 11 weeks and their lungs were harvested at post-elastase day (ped) 3 for further RNAseq analysis.

value: post-elastase day 3


title: BT054_The SNP of whole genome

source_name: BT054 SNP of whole genome

extract_protocol: Genomic DNA was extracted from young leafs of tea using the TianGen DNA Kit. DNA quality and quantity was assessed using a Nanodrop.


title: ORF7b rep2 IP

source_name: BEAS-2B expressing ORF7b


title: Control_Saline_rep1


title: ORF7b rep1 IP


title: BT053_The SNP of whole genome

source_name: BT053 SNP of whole genome


title: BNT_Naive_5_Day11


title: ORF7a rep2 IP

source_name: BEAS-2B expressing ORF7a


title: Emphysema_NicotineElastase_rep3


title: BNT_Naive_5_Day0


title: Control_Elastase_rep2


title: BT052_The SNP of whole genome

source_name: BT052 SNP of whole genome


title: Control_Elastase_rep3


title: BNT_Naive_4_Day41


title: Emphysema_NicotineElastase_rep2


title: Control_Elastase_rep1


title: ORF7a rep1 IP


title: BNT_Naive_4_Day35


title: ORF6 rep2 IP

source_name: BEAS-2B expressing ORF6


title: BT051_The SNP of whole genome

source_name: BT051 SNP of whole genome


title: BNT_Naive_4_Day34


title: Control_Saline_rep3


title: Nicotine_Saline_rep3


title: BNT_Naive_4_Day7


title: ORF6 rep1 IP


title: BT050_The SNP of whole genome

source_name: BT050 SNP of whole genome


title: BNT_Naive_4_Day0


title: BT049_The SNP of whole genome

source_name: BT049 SNP of whole genome


title: Nicotine_Saline_rep2


title: M rep2 IP

source_name: BEAS-2B expressing M


title: BT048_The SNP of whole genome

source_name: BT048 SNP of whole genome


title: BT047_The SNP of whole genome

source_name: BT047 SNP of whole genome


title: BNT_Naive_3_Day41

source_name: PBMCs


title: M rep1 IP


title: Nicotine_Saline_rep1


title: BT046_The SNP of whole genome

source_name: BT046 SNP of whole genome


title: E rep2 IP

source_name: BEAS-2B expressing E


title: Nicotine_Elastase_rep5


title: BNT_Naive_3_Day35


title: Nicotine_Elastase_rep4


title: BT045_The SNP of whole genome

source_name: BT045 SNP of whole genome


title: Nicotine_Elastase_rep3

source_name: Lung


title: E rep1 IP


title: BNT_Naive_3_Day34


title: BNT_Naive_3_Day10


title: ORF3b rep2 IP

source_name: BEAS-2B expressing ORF3b


title: Nicotine_Elastase_rep2


title: BT044_The SNP of whole genome

source_name: BT044 SNP of whole genome


title: Nicotine_Elastase_rep1


title: BT043_The SNP of whole genome

source_name: BT043 SNP of whole genome


title: ORF3b rep1 IP


title: BNT_Naive_3_Day0


title: ORF3a rep2 IP

source_name: BEAS-2B expressing ORF3a


title: BNT_Naive_2_Day41


title: Z2_WT_Z1_sh1_Exp2

first: Pushkar

last: Dakle

address: 14 Medical Dr

institute: Cancer Science Institute of Singapore

data_processing:
MSI (mis-splicing index) values were calculated for each intron
Only those introns with a coverage of at least one read at each of their junctions and with total coverage of the two junctions being higher than 4 were considered. Also, introns which did not have a coverage of at least 1 for 95% of their length were filtered out.
To identify differentially spliced introns, differences in MSI values (ΔMSI) were calculated as ΔMSI=MSIknockout−MSIwildtype. Significance of this difference was computed using Fisher's test and the obtained p-values were corrected for multiple testing.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited output files – intronwise mis-splicing index

extract_protocol:
Total RNA was extracted from sorted myeloid precursors (common myeloid precursors (CMP), granulocyte monocyte precursors (GMP) and megakaryocyte erythroid precursors (MEP)), MEFs and ex-vivo cultured Lin−Kit+ bone marrow cells using either RNeasy Micro or Mini Kits (Qiagen).
polyA-selected RNA was used to prepare libraries using either TruSeq sample preparation kit (CMP, GMP, MEP and MEF) or NEBNext Ultra RNA Library Prep Kit (Lin−Kit+ bone marrow cells).

tag: strain background

tag: genotype/variation

value: Depletion of Zrsr1


title: Z2_WT_Z1_sh1_Exp1

tag: treatment


title: ORF3a rep1 IP


title: BT042_The SNP of whole genome

source_name: BT042 SNP of whole genome


title: SPIKE rep2 IP

source_name: BEAS-2B expressing SPIKE


title: BNT_Naive_2_Day35


title: BT040_The SNP of whole genome

source_name: BT040 SNP of whole genome


title: Z2_WT_Z1_sh10_Exp2


title: BT039_The SNP of whole genome

source_name: BT039 SNP of whole genome


title: SPIKE rep1 IP


title: BNT_Naive_2_Day10


title: NSP16 rep2 IP

source_name: BEAS-2B expressing NSP16


title: Z2_WT_Con_sh_Exp2


title: BT038_The SNP of whole genome

source_name: BT038 SNP of whole genome


title: Z2_WT_Z1_sh10_Exp1


title: BNT_Naive_2_Day0


title: BNT_Naive_1_Day41


title: Z2_WT_Con_sh_Exp1


title: NSP15 rep2 IP

source_name: BEAS-2B expressing NSP15


title: BT037_The SNP of whole genome

source_name: BT037 SNP of whole genome


title: NSP16 rep1 IP


title: Z2_KO_Z1_sh1_Exp2


title: BT041_The SNP of whole genome

source_name: BT041 SNP of whole genome


title: BT036_The SNP of whole genome

source_name: BT036 SNP of whole genome


title: NSP15 rep1 IP


title: BT035_The SNP of whole genome

source_name: BT035 SNP of whole genome


title: BNT_Naive_2_Day34

source_name: PBMCs


title: Z2_KO_Z1_sh1_Exp1


title: Z2_KO_Z1_sh10_Exp2


title: NSP14 rep2 IP

source_name: BEAS-2B expressing NSP14


title: NSP14 rep1 IP


title: BNT_Naive_1_Day0


title: Z2_KO_Z1_sh10_Exp1


title: NSP13 rep2 IP

source_name: BEAS-2B expressing NSP13


title: Z2_KO_Con_sh_Exp2


title: Z2_KO_Con_sh_Exp1


title: NSP12 rep2 IP

source_name: BEAS-2B expressing NSP12


title: BNT_Convalescent_16_Day1

value: COVID-19 Recovered


title: BT033_The SNP of whole genome

source_name: BT033 SNP of whole genome


title: BNT_Convalescent_16_Day7


title: BT032_The SNP of whole genome

source_name: BT032 SNP of whole genome


title: BNT_Naive_1_Day35


title: BNT_Convalescent_16_Day0


title: BT031_The SNP of whole genome

source_name: BT031 SNP of whole genome


title: WT4_MEF

tag: cell type

value: MEFs


title: NSP12 rep1 IP

value: Sigma-Aldrich

value: Monoclonal ANTI-FLAG® M2 antibody produced in mouse, Sigma Aldrich, F3165


title: BT030_The SNP of whole genome

source_name: BT030 SNP of whole genome

value: Leaf


title: BT034_The SNP of whole genome

source_name: BT034 SNP of whole genome


title: NSP11 rep1 IP

source_name: BEAS-2B expressing NSP11


title: BNT_Naive_1_Day34


title: BNT_Convalescent_15_Day7


title: WT6_MEF


title: BT028_The SNP of whole genome

source_name: BT028 SNP of whole genome


title: BT029_The SNP of whole genome

source_name: BT029 SNP of whole genome


title: NSP10 rep2 IP

source_name: BEAS-2B expressing NSP10


title: BNT_Convalescent_15_Day1


title: WT5_MEF


title: WT3_GMP

value: granulocyte monocyte precursors (GMP)


title: BNT_Naive_1_Day10


title: BT025_The SNP of whole genome

source_name: BT025 SNP of whole genome


title: BT027_The SNP of whole genome

source_name: BT027 SNP of whole genome


title: WT3_MEP

value: megakaryocyte erythroid precursors (MEP)


title: BNT_Convalescent_14_Day7


title: NSP10 rep1 IP


title: BT026_The SNP of whole genome

source_name: BT026 SNP of whole genome


title: WT3_CMP

value: wild type

value: common myeloid precursors (CMP)


title: BNT_Convalescent_14_Day1


title: BT023_The SNP of whole genome

source_name: BT023 SNP of whole genome


title: BNT_Convalescent_15_Day0

source_name: PBMCs


title: NSP9 rep2 IP

source_name: BEAS-2B expressing NSP9

value: IBA Lifesciences


title: BNT_Convalescent_14_Day0


title: NSP8 rep2 IP

source_name: BEAS-2B expressing NSP8

value: 3XFLAG tag


title: NSP11 rep2 IP


title: BT024_The SNP of whole genome

source_name: BT024 SNP of whole genome


title: WT2_GMP


title: WT2_MEP


title: NSP13 rep1 IP

source_name: BEAS-2B expressing NSP13


title: NSP9 rep1 IP

value: StrepMAB-Immo, iba life sciences, Cat.no:2-1517-001

value: 2xStrep tag


title: BNT_Convalescent_13_Day0


title: WT1_MEP


title: BNT_Convalescent_13_Day1


title: BT021_The SNP of whole genome

source_name: BT021 SNP of whole genome


title: BNT_Convalescent_12_Day7


title: WT2_CMP


title: BNT_Convalescent_13_Day7


title: NSP8 rep1 IP


title: BT022_The SNP of whole genome

source_name: BT022 SNP of whole genome


title: WT1_GMP


title: NSP7 rep2 IP

source_name: BEAS-2B expressing NSP7


title: BNT_Convalescent_12_Day1


title: WT1_CMP


title: BT020_The SNP of whole genome

source_name: BT020 SNP of whole genome


title: NSP7 rep1 IP


title: BT017_The SNP of whole genome

source_name: BT017 SNP of whole genome


title: BT019_The SNP of whole genome

source_name: BT019 SNP of whole genome


title: BNT_Convalescent_12_Day0


title: NSP6 rep2 IP

source_name: BEAS-2B expressing NSP6


title: KO4_MEF


title: BNT_Convalescent_11_Day1


title: NSP5_C145A rep2 IP

source_name: BEAS-2B expressing NSP5_C145A


title: NSP6 rep1 IP


title: KO6_MEF


title: BNT_Convalescent_11_Day0


title: KO5_MEF


title: KO3_MEP


title: BT013_The SNP of whole genome

source_name: BT013 SNP of whole genome


title: BNT_Convalescent_10_Day0


title: NSP5 rep2 IP

source_name: BEAS-2B expressing NSP5


title: NSP5 rep1 IP


title: KO3_GMP


title: BNT_Convalescent_11_Day7


title: BT011_The SNP of whole genome

source_name: BT011 SNP of whole genome


title: KO3_CMP


title: BT010_The SNP of whole genome

source_name: BT010 SNP of whole genome


title: NSP4 rep2 IP

source_name: BEAS-2B expressing NSP4


title: BT009_The SNP of whole genome

source_name: BT009 SNP of whole genome


title: BNT_Convalescent_9_Day1

source_name: PBMCs


title: KO2_MEP


title: BNT_Convalescent_9_Day7


title: BNT_Convalescent_9_Day0


title: BT016_The SNP of whole genome

source_name: BT016 SNP of whole genome


title: BT014_The SNP of whole genome

source_name: BT014 SNP of whole genome


title: BT015_The SNP of whole genome

source_name: BT015 SNP of whole genome


title: NSP5_C145A rep1 IP


title: BT007_The SNP of whole genome

source_name: BT007 SNP of whole genome


title: KO2_CMP


title: BNT_Convalescent_8_Day7


title: NSP3 rep1 IP

source_name: BEAS-2B expressing NSP3


title: BT008_The SNP of whole genome

source_name: BT008 SNP of whole genome


title: KO1_MEP


title: BNT_Convalescent_8_Day1


title: NSP2 rep2 IP

source_name: BEAS-2B expressing NSP2


title: BT006_The SNP of whole genome

source_name: BT006 SNP of whole genome


title: KO1_GMP


title: NSP3 rep2 IP


title: NSP4 rep1 IP


title: NSP1 rep2 IP

source_name: BEAS-2B expressing NSP1


title: KO1_CMP


title: KO2_GMP


title: BT005_The SNP of whole genome

source_name: BT005 SNP of whole genome


title: NSP2 rep1 IP


title: BT004_The SNP of whole genome

source_name: BT004 SNP of whole genome


title: BNT_Convalescent_7_Day7


title: NSP1 rep1 IP


title: RNA_Control_rep2

city: seoul

first: Jueng Soo

last: You

address: 120 Neungdong-ro

country: South Korea

institute: Konkuk University

data_processing:
Adators and low-quality reads  were trimmed using Trim galore
The filtered reads were aligned to the human reference genome (hg38 assembly) using STAR
To calculate expression values and perform differentially expressed gene analysis, Cufflinks (cuffnorm and cuffdiff) was used
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files were generated using HOMER (makeTagDirectory and makeUCSCfile) with the –style rnaseq –strand both” options

source_name: neuroblastoma

growth_protocol: Cells were grown in DMEM/10%FBS+antibiotics. Cells were plated ~10% in dishes and the medium was changed do differentiating medium(normal+RA) a day after. The medium was changed every other day.

extract_protocol:
Total RNA was extracted using TRIzol reagent, digested with DNase I and reverse transcribed using a High Capacity cDNA Reverse Transcription Kit (Applied Biosystems, Foster City, CA).
The construction of library was performed using NEBNext® UltraTM DNA Library Prep Kit for Illumina (New England Biolabs, UK) according to the manufacturer’s instructions.

treatment_protocol: After 5 days of differentiation, recombinant adenoviral vector were added at 33 m.o.i. for a day and removed. The new medium was added and grown for 3(?) days and the total RNA was obtained.

value: Differentiated with 50 nM retinoic acid

tag: transduction

value: transduction with recombinant adeno/lacZ virus


title: A2

city: Columbus

first: Amy

last: Hite

state: OH - Ohio

address: 1800 Cannon Drive 250 Lincoln Tower

department: Biomedical Informatics

institute: The Ohio State University

data_processing:
Reads were aligned to Rat genome Rnor6.0 with HISAT2.
counts generated for Rnor 6.0 v101 with featureCounts from the subread package.
Counts were normalized with voom and differential expression tested with limma.
Genome_build: Rnor6.0
Supplementary_files_format_and_content: Text file of voom normalized expression for each gene and each sample

organism: Rattus norvegicus

source_name: Glomerular

growth_protocol: Male Wistar Rats , ~175g

extract_protocol:
On Day 11, rats were sacked, kidneys harvested and glomeruli were isolated by sieve method. Total RNA was extracted.
The mRNA libraries were generated using the following kits and conditions:   • NEBNext® Ultra™ II Directional (stranded) RNA Library Prep Kit for Illumina (NEB #E7760L)   • NEBNext Poly (A) mRNA Magnetic Isolation Module (NEB #E7490)   • NEBNext Multiplex Oligos for Illumina Unique Dual Index Primer Pairs (NEB #6442S/L)   • Library input amount: 200ng total RNA (quantified using Qubit Fluorometer) and total RNA achieved a RIN of >7  • Fragmentation: 10 minutes   • PCR: 12x   • Libraries were sequenced with Illumina NovaSeq 6000 flow cell using paired-end 150-bp format to at least 17 million passed-filter clusters/sample (equivalent to 34 million reads)

treatment_protocol: Male Wistar rats were intravenously (IV) injected with puromycin aminonucleoside (PAN) (Sigma-Aldrich, St. Louis, MO) and treatment groups were treated by oral gavage with Pioglitazone, GQ-16, or a sham vehicle daily.

value: Wistar

tag: Sex

value: Male

value: glomeruli

tag: groups


title: BT002_The SNP of whole genome

data_processing:
The array image was acquired using Affymetrix AxiomTM Tea SNP 96 -Array Plate detected the SNP of whole genome of tea plant
SNP call:G/G,T/G,T/T,C/C,etc.

source_name: BT002 SNP of whole genome


title: RNA_Control_rep1


title: BNT_Convalescent_7_Day0

value: Female

value: COVID-19 Recovered


title: BNT_Convalescent_6_Day7


title: A3


title: BNT_Convalescent_7_Day1


title: A1


title: BT001_The SNP of whole genome

source_name: BT001 SNP of whole genome


title: A34


title: A27


title: BNT_Convalescent_8_Day0


title: RNA_SNCA_rep2

value: transduction with recombinant adeno/a-syn virus


title: BNT_Convalescent_6_Day1


title: RNA_SNCA_rep1


title: SKHS_3A

city: Shenzhen

first: Yan

last: WANG

address: 1068 Xueyuan Ave

institute: Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences

data_processing:
Raw sequencing reads (fastq) were quality checked using SOAPnuke (v1.5.2).
Bowtie2 (v2.2.5) was applied to align the clean reads to the genomes.
The expression level of gene was calculated by RSEM (v1.2.12).
Differential expression analysis was performed using DESeq2 (v1.4.5)
Genome_build: GCF_000001405.39_GRCh38.p13
Supplementary_files_format_and_content: excel

source_name: C28/I2 cell line

growth_protocol: C28/I2 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin–streptomycin.

extract_protocol:
RNAs were extracted from culture tissues. The samples were homogenized in Trizol (Invitrogen) and processed for RNA extraction according to the manufacturer’s instructions.
BGI in-house kit (BGI-Shenzhen, China)

treatment_protocol: C28/I2 cells were treated with or without SDF-1/natural products for 48 h and then collected for bulk RNA sequencing.

value: chondrocyte

value: SDF-1a 50 nM and TCM formula SKHS 1%, 48 h


title: BNT_Convalescent_6_Day0

source_name: PBMCs


title: BNT_Convalescent_5_Day7


title: SKHS_2A


title: A15


title: ChIP_rH2AX_Control

data_processing:
Adators and low-quality reads  were trimmed using Trim galore
The filtered reads were aligned to the human reference genome (hg38 assembly) using bowtie2
Peaks were called using HOMER (findPeaks) to identify specific P53 binding sites and rH2AX histone modification enriched sites corresponding to input samples with a false discovery rate (FDR)-adjusted p value cutoff of 0.001.
The identified peaks were annotated according to the known gene database (Refseq) using HOMER (annotatePeaks.pl)
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files were generated using HOMER (makeTagDirectory and makeUCSCfile)

extract_protocol:
For each assay, 100 μg DNA was precipitated by P53 and rH2A antibodies
The construction of library was performed using NEBNext® UltraTM DNA Library Prep Kit for Illumina (New England Biolabs, UK) according to the manufacturer’s instructions.


title: SKHS_1A


title: HQJG_3A

value: SDF-1a 50 nM and Astragaloside IV 10 μM, 48 h


title: BT003_The SNP of whole genome

source_name: BT003 SNP of whole genome

value: Leaf


title: ChIP_Input (P53 and rH2AX enrichment control)


title: A14


title: A13


title: ChIP_p53_Control


title: A6

value: PAN


title: BNT_Convalescent_4_Day7


title: BNT_Convalescent_5_Day1


title: HQJG_2A


title: BNT_Convalescent_5_Day0


title: ChIP_rH2AX_SNCA


title: A32


title: A31


title: ChIP_p53_SNCA


title: BNT_Convalescent_4_Day1