title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 5, Replicate 2

description:
Library name: Sample_P5_L8_2_270_307
Cerebral cortex of a single offspring, Postnatal Day 5


title: HEK293 , LMNB2 , Rep2 , ATAC

status: Public on Jan 30 2026

type: SRA

city: Urbana

first: Simon

last: Lizarazo

state: IL

address: 505 S Goodwin Ave

department: Molecular and Integrative Physiology

country: USA

institute: University of Illinois Urbana Champaign

description:
Library name: HEK293_LMNB2_2_ATAC
HEK293_LB2_2

library_source: transcriptomic

data_processing:
The processing of ATAC-Seq data was carried out by following and adapting established protocols. Briefly cCounts were extracted over a comprehensive RNAcentral database annotation of noncoding RNAs. For each gene, a total of 150 nucleotides were added to both the upstream and downstream regions to improve mapability. Additionally, counts were extracted from the regions upstream and downstream of the gene of interest. These regions were 500 bp, 5000 bp, and 50000 bp in size with a buffer region of 300 bp allowed between the genes and the additional mapped regions. For smallRNA-Seq counts were extracted over the same comprehensive RNAcentral database annotation of noncoding RNAs. All count matrices were TPM normalized subsequently.
Assembly: GRCh38
Supplementary files format and content: count files for both small RNA seq and ATAC Seq

molecule: total RNA

organism: Homo sapiens

extract_protocol:
HEK293 (ATCC) were cultured in complete Dulbecco’s Modified Eagle’s Medium (DMEM) (Corning) supplemented with 10% fetal bovine serum ( Corning) and 1% Penicillin-Streptomycin. Cells were maintained in 10-cm dishes by seeding 1 x 10^6 cells with complete medium every 2-3 days. Cells were maintained in a humidified atmosphere at 37 C with 5% CO2.
For ATAC-Seq, 100,000 cells were collected following overexpression of eGFP, LMNA, LMNB1, or LMNB2. Libraries were prepared using the ATAC-Seq Kit (Active Motif) according to the manufacturer’s protocol. For small RNA-Seq, cells from the same overexpression conditions (eGFP, LMNA, LMNB1, or LMNB2) were recollected, and total RNA enriched for small RNAs was extracted using the mirVana PARIS Kit (Thermo Fisher Scientific) following the manufacturer’s instructions. All sequencing was performed at the University of Illinois, Roy J. Carver Biotechnology Center.

tag: cell line

tag: genotype

value: Wild Type

tag: treatment

value: LaminB2 Overexpression

tag: batch


title: HEK293 , LMNB1 , Rep1 , smallRNA

description:
Library name: HEK293_LMNB1_1_smallRNA
LMNB11_sRNA

value: LaminB1 Overexpression


title: HEK293 , LMNA , Rep2 , ATAC

description:
Library name: HEK293_LMNA_2_ATAC
HEK293_LA_2

value: LaminA Overexpression


title: HEK293 , LMNB2 , Rep1 , ATAC

description:
Library name: HEK293_LMNB2_1_ATAC
HEK293_LB2_1


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 4, Replicate 6

city: New Haven

first: Matthew

last: Yuen

state: Connecticut

address: 100 College

department: Neuroscience

institute: Yale School of Medicine

description:
Library name: Sample_P5_L7_6_223_354
Cerebral cortex of a single offspring, Postnatal Day 5

data_processing:
Quality control on FASTQ reads was performed using FastQC (version 0.11.9) and a threshold set for 95% of bases meeting Q30 within a given read to ensure high sequencing quality. Paired-end reads were trimmed using Fastp (version 0.23.2) with default arguments. Pseudoalignment to mm39 mouse genome (reference provided by the Yale Center for Genome Analysis) and quantification was performed using Salmon (version 1.4.0) with selective alignment enabled.
Assembly: mm39
Supplementary files format and content: *_quant.sf (Salmon quantification file) A tab-separated text file produced by Salmon that contains transcript-level quantification results. Each row corresponds to one transcript (or gene, if Salmon was run in gene mode). Typical columns include: Name (transcript ID), Length (transcript length in bp), EffectiveLength (bias-corrected length used for quantification), TPM (Transcripts Per Million, normalized expression value), and NumReads (estimated number of reads/fragments assigned to the transcript). This file is the main output used for downstream differential expression and expression profiling analyses.

organism: Mus musculus

source_name: Cerebral cortex

extract_protocol:
For bulk RNA-sequencing of the brain and placenta, pregnant dams were euthanized via cervical dislocation. Embryos were harvested from the dams and stored in ice-cold HBSS over ice as the placentas and embryonic brains were dissected in ice-cold HBSS. The placentas and dorsal cortex of offspring were dissected, placed in RNAProtect overnight, and  transferred to -20°C for later archival storage. To extract the RNA from placenta and dorsal cortices, tissue were homogenized using Lysis Matrix D ceramic beads. After centrifugation of the homogenate, the supernatant was extracted and total RNA was purified via the Qiagen RNeasy Mini kit. RNA samples were submitted to Yale’s Center for Genome Analysis for cDNA library preparation (Kapa mRNA HyperPrep) and sequenced (NovaSeq6000) at 100 million reads per sample.
RNA Seq Library Prep: mRNA is purified from a normalized input between 50-1000ng of total RNA with oligo-dT beads and sheared by incubation at 94C in the presence of Mg (Kapa mRNA Hyper Prep). Following first-strand synthesis with random primers, second strand synthesis and A-tailing are performed with dUTP for generating strand-specific sequencing libraries. Adapter ligation with 3’ dTMP overhangs are ligated to library insert fragments. Library amplification amplifies fragments carrying the appropriate adapter sequences at both ends. Strands marked with dUTP are not amplified. Indexed libraries that meet appropriate cut-offs for both are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX or Agilent TapeStation. Samples with a yield of ≥0.5 ng/ul are used for sequencing.

treatment_protocol: Mock Infection (50 uL of 1x PBS) or SARS-CoV-2 Infection (50μl of SARS-CoV-2 [3 × 107 PFU/ml]) of pregnant dams at embryonic day 11.

tag: tissue

value: Cerebral cortex

tag: cell type

value: Neurons + Glia

value: Wildtype


title: HEK293 , LMNB1 , Rep3 , ATAC

description:
Library name: HEK293_LMNB1_3_ATAC
HEK293_LB1_3


title: HEK293 , LMNB1 , Rep1 , ATAC

description:
Library name: HEK293_LMNB1_1_ATAC
HEK293_LB1_1


title: HEK293 , LMNA , Rep1 , smallRNA

description:
Library name: HEK293_LMNA_1_smallRNA
LMNA1_sRNA


title: HEK293 , GFP , Rep3 , smallRNA

description:
Library name: HEK293_GFP_3_smallRNA
EGFP3_sRNA

value: eGFP Overexpression


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 4, Replicate 5

description:
Library name: Sample_P5_L7_5_235_342
Cerebral cortex of a single offspring, Postnatal Day 5

value: SARS-CoV-2 Infection (50μl of SARS-CoV-2 [3 × 107 PFU/ml])


title: HEK293 , GFP , Rep2 , smallRNA

description:
Library name: HEK293_GFP_2_smallRNA
EGFP2_sRNA


title: Normoxia CD38bright CLL-1bright rep3

city: Brighton

first: Chris

last: Pepper

address: Falmer

country: United Kingdom

institute: University of Sussex

description:
Library name: Npp3
KG1a bright, normoxia

data_processing:
Base calling was performed using Illumina Real-Time Analysis (RTA) software, version used: RTA 3.4.4 (standard for NovaSeq 6000)
Adapter trimming and quality filtering were performed using Trimmomatic v0.39, with the following parameters: ILLUMINACLIP:adapter.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Assembly: Reads were aligned to the GRCh38 (hg38) human genome assembly using STAR aligner (v2.4.2a)
Supplementary files format and content: FASTQ files paired-end 150 bp reads

source_name: KG1a cells

growth_protocol: KG1a cells and primary AML cells were grown in RPMI media with 20% FBS

extract_protocol:
Total RNA was extracted from KG1a cells using Active Motif’s standard RNA extraction workflow. Sequencing was carried out on an Illumina NovaSeq 6000 platform, generating paired-end 150 bp reads.
Library construction was undertaken by Active Motif
mRNA enrichment and RNA-seq library preparation were performed by Active Motif using their validated commercial protocols.

treatment_protocol: Normoxia and hypoxia (3% oxygen)

value: KG1a cells

value: WT


title: ICC CAF cells, shControl, Hypoxic condition, 1

city: HANGZHOU

first: Jianing

last: Fan

address: NO. 3 EAST QINGCHUN ROAD

country: China

institute: Sir Run Run Shaw Hospital

description:
Library name: Sample4
CAFSHNCHYPO_1

data_processing:
FastQC (version 0.12.0) was used to read all the raw data and perform quality control
Use Trim_Galore (version v0.6.10) to remove low-quality reads and adapters
The index and gene annotation files were downloaded, and reads were aligned using HISAT2 (version 2.2.1)
featureCounts (version 2.0.6) was used to count the reads numbers mapped to each gene
Assembly: GRCh38
Supplementary files format and content: CSV file including Reads count for each sample

source_name: Biliary tract tumor tissue

growth_protocol: ICC CAF cells were maintained in DMEM supplemented with 10% fetalbovine serum (FBS) and antibiotics at 37°C with 5% CO2 condition

extract_protocol:
RNA was harvested using Fast Pure Cell / Tissue Total RNA Isolation Kit (Vazyme). The minimum total amount of RNA used for constructing the sequencing library was 3.24 μg
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

value: Biliary tract tumor tissue

value: ICC CAF

value: Fibroblast


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 4, Replicate 4

description:
Library name: Sample_P5_L7_4_247_330
Cerebral cortex of a single offspring, Postnatal Day 5


title: ICC CAF cells, shControl, Control condition, 1

description:
Library name: Sample1
CAFSHNCCTRL_1


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 5, Replicate 3

description:
Library name: Sample_P5_L8_3_258_319
Cerebral cortex of a single offspring, Postnatal Day 5


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 4, Replicate 3

description:
Library name: Sample_P5_L7_3_259_318
Cerebral cortex of a single offspring, Postnatal Day 5


title: Normoxia CD38bright CLL-1bright rep2

description:
Library name: Npp2
KG1a bright, normoxia


title: HEK293 , GFP , Rep1 , ATAC

description:
Library name: HEK293_GFP_1_ATAC
HEK293_GFP_1


title: shNC_2

city: GuangZhou

first: xiaoxia

last: Liang

address: 26 Yuancun Er Heng Road

institute: Sixth Affiliated Hospital of Sun Yat-sen University

description: Library name: Sample5

data_processing:
fastp software (https://github.com/OpenGene/fastp)
Assembly: Homo sapiens, GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
Supplementary files format and content: Files include counts for each sample

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp.

value: co-culturing SW480 shNC cell CM


title: HEK293 , LMNB2 , Rep1 , smallRNA

description:
Library name: HEK293_LMNB2_1_smallRNA
LMNB21_sRNA


title: Normoxia CD38bright CLL-1bright rep1

description:
Library name: Npp1
KG1a bright, normoxia


title: HEK293 , GFP , Rep1 , smallRNA

description:
Library name: HEK293_GFP_1_smallRNA
EGFP1_sRNA


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 5, Replicate 1

description:
Library name: Sample_P5_L8_1_282_295
Cerebral cortex of a single offspring, Postnatal Day 5


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 4, Replicate 8

description:
Library name: Sample_P5_L7_8_199_378
Cerebral cortex of a single offspring, Postnatal Day 5


title: HEK293 , GFP , Rep2 , ATAC

description:
Library name: HEK293_GFP_2_ATAC
HEK293_GFP_2


title: HEK293 , LMNB1 , Rep3 , smallRNA

description:
Library name: HEK293_LMNB1_3_smallRNA
LMNB13_sRNA


title: sh_1

description: Library name: Sample1

value: co-culturing SW480 shOPN  cell CM


title: Rimonabant treated replicate

city: Brookline, MA

first: Timothy

middle: Robert

last: Kunz

state: MA

address: 120 Babcock St, Apt 2

department: Stem Cell and Regenerative Biology

institute: Harvard

description: Library name: Rimonabant_2

data_processing:
Raw Illumina Reads from Admera health
Assembly: GRCh38
Supplementary files format and content: Counts.txt = Tab delimited results for each treatment with counts calculated with the HTSeq Python library

source_name: In vitro derived islets

growth_protocol: Standard SC-Islet differentiation

extract_protocol:
Whole islet cultures were lysed using RLT-buffer then RNA was extracted using the Qiagen Rneasy extraction kit (Cat. No. 74104).
Admera Health received this RNA and performed the following processing and library prep. Library preparation was performed with KAPA RNA HyperPrep Kit with RiboErase (HMR). Sequencing was performed using  for 30M PE reads in each direction. FastQC (version v0.11.8) was applied to check the quality of raw reads. Trimmomatic (version v0.38) was applied to cut adaptors and trim low-quality bases with default setting. STAR Aligner version 2.7.1a was used to align the reads. Picard tools (version 2.20.4) was applied to mark duplicates of mapping. The StringTie version 2.0.4 was used to assemble the RNA-Seq alignments into potential transcripts. The featureCounts (version 1.6.0)/HTSeq was used to count mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations.

treatment_protocol: Compounds used in addition to growth media at stage 5 through 7 days post stage 6

value: In vitro derived islets

value: In vitro differentiated human islets, from embryonic stem cells

value: Rimonabant 125nM


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 4, Replicate 7

description:
Library name: Sample_P5_L7_7_211_366
Cerebral cortex of a single offspring, Postnatal Day 5


title: Hypoxia CD38dim CLL-1dim rep3

description:
Library name: Hmm3
KG1a dim, hypoxia


title: Normoxia CD38dim CLL-1dim rep1

description:
Library name: Nmm1
KG1a dim, normoxia


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 3, Replicate 6

description:
Library name: Sample_P5_L6_6_212_365
Cerebral cortex of a single offspring, Postnatal Day 5


title: Vardenafil treated replicate

description: Library name: Vardenafil_2

value: Vardenafil 125nM


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 4, Replicate 2

description:
Library name: Sample_P5_L7_2_271_306
Cerebral cortex of a single offspring, Postnatal Day 5


title: HEK293 , LMNA , Rep2 , smallRNA

description:
Library name: HEK293_LMNA_2_smallRNA
LMNA2_sRNA

value: Wild Type

value: LaminA Overexpression


title: Hypoxia CD38dim CLL-1dim rep2

description:
Library name: Hmm2
KG1a dim, hypoxia


title: HEK293 , LMNA , Rep3 , smallRNA

description:
Library name: HEK293_LMNA_3_smallRNA
LMNA3_sRNA


title: Hypoxia CD38dim CLL-1dim rep1

description:
Library name: Hmm1
KG1a dim, hypoxia


title: shNC_3

description: Library name: Sample6


title: Ly-294022 treated

description: Library name: Ly-294002_1


title: Epirizole treated replicate

description: Library name: Epirizole_2

value: Epirizole 2.5uM


title: CWR22Rv1, siTRA2A/B 72h, biological replicate 1

city: Newcastle upon Tyne

first: Luke

last: Gaughan

address: Paul O'Gorman Building, Framlington Place

institute: Newcastle University

description:
Library name: Sample 10
AB-1

data_processing:
Quality control performed using FastQC
Illumina adapter sequences were trimmed with Cutadapt
Trimmed reads were aligned to GRCh38 using STAR
SAMtools was used to sort aligned files by genomic coordinate
Raw gene-level counts (Brittain_CWR22Rv1_TRA2_KD_featureCounts.tsv) were generated using featureCounts from the Subread package.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited (.tsv) file containing raw gene-level counts output by featureCounts for each sample. Column name prefixes correspond to raw sequencing file names.

molecule: polyA RNA

growth_protocol: CWR22Rv1 cells were cultured in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and penicillin-streptomycin antibiotic. Cells were cultured in a humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
GenElute™ mammalian total RNA miniprep kit
Strand-specific paired-end RNA-Seq with polyA selection (performed by GENEWIZ)

treatment_protocol: CWR22Rv1 cells were reverse transfected using 0.2% lipofectamine RNAiMAX™ with 25 nM siRNA targeting TRA2A (siTRA2A), TRA2B (siTRA2B), both TRA2A and TRA2B (siTRA2A/TRA2B) or a scrambled/non-targeting siRNA (siScr). 72 hours later, total RNA was extracted for analysis.

value: Castrate resistant prostate cancer


title: shNC_1

description: Library name: Sample4


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 3, Replicate 2

description:
Library name: Sample_P5_L6_2_260_317
Cerebral cortex of a single offspring, Postnatal Day 5

value: Cerebral cortex

value: Neurons + Glia

value: Wildtype


title: Epirizole treated

description: Library name: Epirizole_1

value: WT


title: CWR22Rv1, siTRA2B 72h, biological replicate 3

description:
Library name: Sample 9
B-3


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 3, Replicate 1

description:
Library name: Sample_P5_L6_1_272_305
Cerebral cortex of a single offspring, Postnatal Day 5

value: SARS-CoV-2 Infection (50μl of SARS-CoV-2 [3 × 107 PFU/ml])


title: sh_3

description: Library name: Sample3


title: Colchicine treated

description: Library name: Colchicine_1

value: Colchicine 10nM


title: DMSO control treated replicate

description: Library name: DMSO_2

value: DMSO


title: Normoxia CD38dim CLL-1dim rep3

description:
Library name: Nmm3
KG1a dim, normoxia

value: KG1a cells


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 2, Replicate 9

description:
Library name: Sample_P5_L5_9_284_293
Cerebral cortex of a single offspring, Postnatal Day 5


title: Normoxia CD38dim CLL-1dim rep2

description:
Library name: Nmm2
KG1a dim, normoxia


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 3, Replicate 7

description:
Library name: Sample_P5_L6_7_200_377
Cerebral cortex of a single offspring, Postnatal Day 5


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 4, Replicate 1

description:
Library name: Sample_P5_L7_1_283_294
Cerebral cortex of a single offspring, Postnatal Day 5


title: sh_2

description: Library name: Sample2

value: co-culturing SW480 shOPN  cell CM


title: Rottlerin treated replicate

description: Library name: Rottlerin_2

value: In vitro derived islets

value: Rottlerin 1.23 uM


title: Vardenafil treated

description: Library name: Vardenafil_1

value: In vitro differentiated human islets, from embryonic stem cells


title: CWR22Rv1, siTRA2A 72h, biological replicate 3

description:
Library name: Sample 6
A-3


title: CWR22Rv1, siTRA2B 72h, biological replicate 1

description:
Library name: Sample 7
B-1


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 3, Replicate 5

description:
Library name: Sample_P5_L6_5_224_353
Cerebral cortex of a single offspring, Postnatal Day 5


title: v4 ko CD8T-2

city: Hefei

first: xia

last: zhou

address: huang shan Road 443

institute: university of science and technology of china

description: Library name: Sample-4

data_processing:
MiXCR (v.3.0.13) toolkit.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: TCR-Seq

source_name: liver

extract_protocol:
Liver tissues enriched for metastatic B16F10 melanomas were harvested from WT or Vsig4-/- mice, cut into small pieces and digested with 0.5 mg/mL collagenase IV (Sigma) and 5 U/mL DNase I (Sigma) for 20 mins at 37℃ under shaking. The cell suspension was filtered through a 70 µm cell strainer and centrifugated at 400g for 5 mins at 4℃, followed by lysis of red blood cell inn ACK buffer (Biolegend).DAPI-CD45+CD3+CD8+ T cells  were sorted by FACS and further processed for bulk TCR-seq.
RNA libraries for TCR-seq were prepared using Evo M-MLV Kit Ver.2 AG11728 kit  following manufacture's protocols.

value: liver

value: CD8+ T cells

value: VSIG4 KO

value: liver bearing metastatic B16F10 melanomas


title: Rottlerin treated

description: Library name: Rottlerin_1


title: v4 ko CD8T-1

description: Library name: Sample-3


title: Moxifloxacin treated replicate

description: Library name: Moxifloxacin_2

value: Moxifloxacin 1.1uM


title: Moxifloxacin treated

description: Library name: Moxifloxacin_1


title: Spatial profiling of a solid tumor ROI from ovarian cancer patient BB24-011_3

city: Yokohama

first: Shinichi

last: Onishi

state: Kanagawa

address: 216,Totsuka-cho, Totsuka-ku

country: Japan

institute: Chugai pharmaceutical co., Ltd.

description:
Library name: BB24-011_ST_high_3
Region of Interest (ROI) from a solid tumor area (ST) in a CLDN6-positive area of an FFPE ovarian serous adenocarcinoma tissue section from patient BB24-011. Gene expression was profiled from the Pan-CK positive segmented area.

data_processing:
Sequencing libraries were sequenced on an Illumina NextSeq 500 system (2x38 bp paired-end).
Raw FASTQ files were processed using the GeoMx NGS pipeline software to generate Digital Count Conversion (DCC) files.
DCC files were uploaded to the GeoMx DSP instrument. Data processing and Q3 normalization (normalization to the 75th percentile) were performed using the GeoMx DSP data analysis software.
Assembly: GRCh38
Supplementary files format and content: DCC files containing raw gene expression counts for each Region of Interest (ROI).
Library strategy: Spatial Transcriptomics

source_name: Ovarian serous adenocarcinoma

extract_protocol:
FFPE tissue sections were deparaffinized. Target retrieval was performed by incubating in Tris-EDTA at 99°C for 15 minutes. RNA targets were exposed by incubating with 1 μg/mL proteinase K at 37°C for 15 minutes. Samples were post-fixed and then incubated overnight with NanoString GeoMx Whole Transcriptome Atlas probes.
Following probe hybridization, slides were washed and stained with SYTO83 (nuclear stain), anti-PanCK antibody, and anti-CLDN6 antibody for 100 minutes. Slides were scanned using the GeoMx Digital Spatial Profiler. Regions of interest (ROIs) were selected from CLDN6-positive/Pan-CK-positive areas. Barcoded oligo probes were collected from PanCK-positive segmented regions by UV-cleavage. The collected oligos were then indexed by PCR using the GeoMx Seq Code Pack to generate sequencing libraries.

value: Ovarian serous adenocarcinoma

value: ovarian adenocarcinoma cells


title: Rimonabant treated

description: Library name: Rimonabant_1

value: Rimonabant 125nM


title: CWR22Rv1, siTRA2A/B 72h, biological replicate 2

description:
Library name: Sample 11
AB-2

value: Castrate resistant prostate cancer


title: Ly-294002 treated replicate

description: Library name: Ly-294002_2

value: WT


title: CWR22Rv1, siTRA2A 72h, biological replicate 1

description:
Library name: Sample 4
A-1


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 3, Replicate 3

description:
Library name: Sample_P5_L6_3_248_329
Cerebral cortex of a single offspring, Postnatal Day 5

value: Cerebral cortex

value: Neurons + Glia

value: Wildtype

value: SARS-CoV-2 Infection (50μl of SARS-CoV-2 [3 × 107 PFU/ml])


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 3, Replicate 4

description:
Library name: Sample_P5_L6_4_236_341
Cerebral cortex of a single offspring, Postnatal Day 5


title: Colchicine treated replicate

description: Library name: Colchicine_2

value: In vitro derived islets

value: Colchicine 10nM


title: CWR22Rv1, siTRA2B 72h, biological replicate 2

description:
Library name: Sample 8
B-2


title: CWR22Rv1, siScr 72h, biological replicate 3

description:
Library name: Sample 3
NT-3

value: siScr


title: CWR22Rv1, siTRA2A/B 72h, biological replicate 3

description:
Library name: Sample 12
AB-3


title: Spatial profiling of a small cluster ROI from ovarian cancer patient BB24-011_1

description:
Library name: BB24-011_SC_high_1
Region of Interest (ROI) from a dispersed small tumor cell cluster (SC) in a CLDN6-positive area of an FFPE ovarian serous adenocarcinoma tissue section from patient BB24-011. Gene expression was profiled from the Pan-CK positive segmented area.


title: Spatial profiling of a small cluster ROI from ovarian cancer patient BB24-011_4

description:
Library name: BB24-011_SC_high_4
Region of Interest (ROI) from a dispersed small tumor cell cluster (SC) in a CLDN6-positive area of an FFPE ovarian serous adenocarcinoma tissue section from patient BB24-011. Gene expression was profiled from the Pan-CK positive segmented area.


title: DMSO control treated

description: Library name: DMSO_1

value: In vitro differentiated human islets, from embryonic stem cells

value: DMSO


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 2, Replicate 3

description:
Library name: Sample_P5_L5_3_261_316
Cerebral cortex of a single offspring, Postnatal Day 5


title: CWR22Rv1, siScr 72h, biological replicate 1

description:
Library name: Sample 1
NT-1


title: Spatial profiling of a solid tumor ROI from ovarian cancer patient BB24-009_4

description:
Library name: BB24-009_ST_high_4
Region of Interest (ROI) from a solid tumor area (ST) in a CLDN6-positive area of an FFPE ovarian serous adenocarcinoma tissue section from patient BB24-009. Gene expression was profiled from the Pan-CK positive segmented area.


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 2, Replicate 2

description:
Library name: Sample_P5_L5_2_273_304
Cerebral cortex of a single offspring, Postnatal Day 5


title: Spatial profiling of a solid tumor ROI from ovarian cancer patient BB24-009_2

description:
Library name: BB24-009_ST_high_2
Region of Interest (ROI) from a solid tumor area (ST) in a CLDN6-positive area of an FFPE ovarian serous adenocarcinoma tissue section from patient BB24-009. Gene expression was profiled from the Pan-CK positive segmented area.


title: Spatial profiling of a solid tumor ROI from ovarian cancer patient BB24-009_3

description:
Library name: BB24-009_ST_high_3
Region of Interest (ROI) from a solid tumor area (ST) in a CLDN6-positive area of an FFPE ovarian serous adenocarcinoma tissue section from patient BB24-009. Gene expression was profiled from the Pan-CK positive segmented area.


title: MYC ChIP-seq in CM, replicate 2

first: Ruiying

last: Cheng

address: B520 Chemical & Life Sciences Laboratory

department: School of Molecular & Cellular Biology

institute: The University of Illinois Urbana-Champaign

description:
Library name: CM_MYC_rep2
ChIP-seq of MYC in H1-derived cardiomyocyte using the POLR3A ChIP-seq protocol.

library_source: genomic

data_processing:
Reads were trimmed using TrimGalore and then mapped to the genome (GRCh38) using BowTie2. Counts were extracted over a comprehensive RNACentral database annotation of noncoding RNAs using BEDTools.
BigWig files where processeded from each Bam fil using Deeptools.
Assembly: hg38
Supplementary files format and content: bigwig files

molecule: genomic DNA

source_name: cardiac muscle

extract_protocol:
H1 stem cells and H1-derived cardiomyocytes were harvested (~10 million cells per ChIP experiment) and resuspended in growth media at 1 × 106 cells/mL and cross-linked with rotation at room temperature in 1% formaldehyde for 10 min. Cross-linking was quenched with the addition of 200 mM glycine and an additional 5 min of rotation at room temperature. Cross-linked cells were then spun down and resuspended in 1× RIPA lysis buffer, followed by chromatin shearing via sonication (3 cycles using a Branson sonicator: 30 s on, 60 s off; 20 additional cycles on a Bioruptor sonicator: 30 s on, 30 s off). Individual ChIP experiments were performed on pre-cleared chromatin using antibody-coupled ChIP grade Protein G magnetic beads (Cell Signaling Technology). POLR3A antibody was obtained from ThermoFisher Scientific (PA5-58170). 5 ug of antibody per ChIP was coupled to 18 uL of beads and rotated overnight with sheared chromatin at 4°C. Beads were then washed 5× in ChIP wash buffer (Santa Cruz), 1× in TE, and chromatin eluted in TE + 1% SDS. Cross-linking was then reversed by incubation at 65°C overnight, followed by digestion of RNA (30 min RNase incubation at 37°C) and digestion of protein (30 min proteinase K incubation at 45°C). ChIP DNA was then purified on a minElute column (Qiagen), followed by DNA library preparation (NEBNext Ultra II DNA Library Prep Kit for Illumina) and size selection of 350-550 bp fragments via gel extraction (Qiagen).
Cross-linking was then reversed by incubation at 65°C overnight, followed by digestion of RNA (30 min RNase incubation at 37°C) and digestion of protein (30 min proteinase K incubation at 45°C). ChIP DNA was then purified on a minElute column (Qiagen), followed by DNA library preparation (NEBNext Ultra II DNA Library Prep Kit for Illumina) and size selection of 350-550 bp fragments via gel extraction (Qiagen).

value: cardiac muscle

value: H1-derived cardiomyocyte

value: cardiomyocyte

value: wild type

value: differentiation


title: Spatial profiling of a small cluster ROI from ovarian cancer patient BB24-009_5

description:
Library name: BB24-009_SC_high_5
Region of Interest (ROI) from a dispersed small tumor cell cluster (SC) in a CLDN6-positive area of an FFPE ovarian serous adenocarcinoma tissue section from patient BB24-009. Gene expression was profiled from the Pan-CK positive segmented area.

value: Ovarian serous adenocarcinoma

value: ovarian adenocarcinoma cells


title: Spatial profiling of a small cluster ROI from ovarian cancer patient BB24-009_3

description:
Library name: BB24-009_SC_high_3
Region of Interest (ROI) from a dispersed small tumor cell cluster (SC) in a CLDN6-positive area of an FFPE ovarian serous adenocarcinoma tissue section from patient BB24-009. Gene expression was profiled from the Pan-CK positive segmented area.


title: Cerebral cortex, P5, Mock Infection, Mouse Litter 4, Replicate 7

description:
Library name: Sample_P5_L14_7_137_056
Cerebral cortex of a single offspring, Postnatal Day 5

value: Mock Infection (50 uL of 1x PBS)


title: WT CD8T-2

description: Library name: Sample-2

value: liver

value: CD8+ T cells

value: WT

value: liver bearing metastatic B16F10 melanomas


title: MYC ChIP-seq in hESC, replicate 1

description:
Library name: hESC_MYC_rep1
ChIP-seq of MYC in H1 hESC using the POLR3A ChIP-seq protocol.

source_name: embryonic stem cell

value: embryonic stem cell

value: H1 hESC


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 2, Replicate 8

description:
Library name: Sample_P5_L5_8_201_376
Cerebral cortex of a single offspring, Postnatal Day 5

value: Cerebral cortex

value: Neurons + Glia

value: Wildtype

value: SARS-CoV-2 Infection (50μl of SARS-CoV-2 [3 × 107 PFU/ml])


title: Cerebral cortex, P5, Mock Infection, Mouse Litter 4, Replicate 6

description:
Library name: Sample_P5_L14_6_205_372
Cerebral cortex of a single offspring, Postnatal Day 5


title: human, normal, lung, rep3

city: Chengdu

first: Bisen

last: Ding

address: Renmin South Road

institute: State Key Laboratory of Biotherapy

description:
Library name: Normal_3
10x Genomics

library_source: transcriptomic single cell

data_processing:
The cellranger pipeline (version 3.1.0, 10X Genomics) was used to process raw sequencing output.
Assembly: hg38
Supplementary files format and content: Cell Ranger software output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: lung

extract_protocol:
The homogenized lung tissues were suspended in DMEM medium (C11995500BT, GIBCO) containing 1 mg/mL type I collagenase (C8140，Solarbio), 1 mg/mL type IV collagenase (C8160，Solarbio), 1 mg/mL Dispase II (D6430，Solarbio), and 0.2 mg/mL DNAase (D8071, Solarbio) at 37°C for 30 min. The digested lung tissues were filtered through a 70 μm filter membrane (BS-70-XBS, biosharp), and the filtrate was centrifuged and treated with red blood cell lysis buffer (R1010, Solarbio) for 10 min, centrifuged again under the same conditions, the pellet was washed once with sterile PBS (C10010500BT, GIBCO), and centrifuged again under the same conditions. Cell pellet was resuspended again with MACS mixture (2 mM EDTA, 0.1% BSA, 1% penicillin/streptomycin/antimitotic in DPBS) to obtain lung single cell suspension.
Single-nucleus RNA sequencing (snRNA-seq) was performed using the 10X Chromium 3′ v3 kit (10X Genomics, Pleasanton, CA) according to the manufacturer's instructions.

value: lung


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 2, Replicate 7

description:
Library name: Sample_P5_L5_7_213_364
Cerebral cortex of a single offspring, Postnatal Day 5


title: WT CD8T-1

description: Library name: Sample-1


title: Spatial profiling of a solid tumor ROI from ovarian cancer patient BB24-011_4

description:
Library name: BB24-011_ST_high_4
Region of Interest (ROI) from a solid tumor area (ST) in a CLDN6-positive area of an FFPE ovarian serous adenocarcinoma tissue section from patient BB24-011. Gene expression was profiled from the Pan-CK positive segmented area.


title: CWR22Rv1, siTRA2A 72h, biological replicate 2

description:
Library name: Sample 5
A-2

value: Castrate resistant prostate cancer


title: POLR3GL ChIP-seq in CM, replicate 2

description:
Library name: CM_POLR3GL_rep2
ChIP-seq of POLR3GL in H1-derived cardiomyocyte using the POLR3A ChIP-seq protocol.

value: cardiac muscle

value: H1-derived cardiomyocyte

value: cardiomyocyte

value: wild type


title: human, IPF, lung, rep1

description:
Library name: IPF_1
10x Genomics


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 2, Replicate 6

description:
Library name: Sample_P5_L5_6_225_352
Cerebral cortex of a single offspring, Postnatal Day 5


title: Spatial profiling of a solid tumor ROI from ovarian cancer patient BB24-011_1

description:
Library name: BB24-011_ST_high_1
Region of Interest (ROI) from a solid tumor area (ST) in a CLDN6-positive area of an FFPE ovarian serous adenocarcinoma tissue section from patient BB24-011. Gene expression was profiled from the Pan-CK positive segmented area.

value: Ovarian serous adenocarcinoma

value: ovarian adenocarcinoma cells


title: Spatial profiling of a solid tumor ROI from ovarian cancer patient BB24-011_2

description:
Library name: BB24-011_ST_high_2
Region of Interest (ROI) from a solid tumor area (ST) in a CLDN6-positive area of an FFPE ovarian serous adenocarcinoma tissue section from patient BB24-011. Gene expression was profiled from the Pan-CK positive segmented area.


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 2, Replicate 4

description:
Library name: Sample_P5_L5_4_249_328
Cerebral cortex of a single offspring, Postnatal Day 5


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 2, Replicate 5

description:
Library name: Sample_P5_L5_5_237_340
Cerebral cortex of a single offspring, Postnatal Day 5


title: Patient HNC0183, Human sample

city: Derry

first: Mary-Kate

last: Riley

address: 26 Knightsbridge

institute: Queen's University Belfast

description: Library name: HNC0183PRH00

data_processing:
Sequencing quality was initially assessed using FastQC (v0.11.8) and adapter trimming and quality filtering were performed with Trim Galore (v0.6.10, paired-end mode).
Reads were aligned using STAR (v2.7.3a)
For PDX samples, reads were independently aligned to the mouse and human reference genome, whereas samples derived exclusively from patient material were aligned only to the human reference genome.
Following alignment, XenofilteR (v1.6) (PMID: 30286710) was applied to the resulting BAM files to computationally separate human- and mouse-derived reads in PDX samples.
Gene-level read counts were generated using HTSeq-count
Post-alignment quality control metrics were aggregated and summarized using MultiQC (v1.7)
Assembly: Alignments were performed against the human reference genome GRCh38 with GENCODE v33 annotation and the mouse reference genome GRCm38 with GENCODE vM15 annotation.
Supplementary files format and content: csv files for raw HTSeq counts, normalised DESeq2 counts, and normalised TPM counts. Samples in columns and genes in rows.

source_name: Oral Cavity

extract_protocol:
total RNA was extracted using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA quantity and integrity were assessed using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano Kit (Agilent).
total RNA was processed using the Kapa Hyper Plus with ribo-erase RNA Library Prep Kit (Roche) by the Health and Life Sciences Genomics Core Technology Unit at Queen’s University Belfast and sequenced on a HiSeq-X instrument (Illumina) by BGI Genomics using 150-bp paired-end reads, aiming for 30M+ reads per sample.

value: Oral Cavity

value: Head and Neck Squamous Cell Carcinoma


title: Spatial profiling of a small cluster ROI from ovarian cancer patient BB24-011_3

description:
Library name: BB24-011_SC_high_3
Region of Interest (ROI) from a dispersed small tumor cell cluster (SC) in a CLDN6-positive area of an FFPE ovarian serous adenocarcinoma tissue section from patient BB24-011. Gene expression was profiled from the Pan-CK positive segmented area.


title: Cerebral cortex, P5, Mock Infection, Mouse Litter 4, Replicate 4

description:
Library name: Sample_P5_L14_4_229_348
Cerebral cortex of a single offspring, Postnatal Day 5

value: Mock Infection (50 uL of 1x PBS)


title: human, normal, lung, rep1

description:
Library name: Normal_1
10x Genomics


title: Patient HNC0179, Human sample

description: Library name: HNC0179PRH00


title: CWR22Rv1, siScr 72h, biological replicate 2

description:
Library name: Sample 2
NT-2

value: siScr


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 2, Replicate 1

description:
Library name: Sample_P5_L5_1_285_292
Cerebral cortex of a single offspring, Postnatal Day 5


title: Cerebral cortex, P5, Mock Infection, Mouse Litter 4, Replicate 3

description:
Library name: Sample_P5_L14_3_241_336
Cerebral cortex of a single offspring, Postnatal Day 5


title: Spatial profiling of a small cluster ROI from ovarian cancer patient BB24-011_2

description:
Library name: BB24-011_SC_high_2
Region of Interest (ROI) from a dispersed small tumor cell cluster (SC) in a CLDN6-positive area of an FFPE ovarian serous adenocarcinoma tissue section from patient BB24-011. Gene expression was profiled from the Pan-CK positive segmented area.


title: Patient HNC0157, Human sample

description: Library name: HNC0157PRH00

source_name: Oropharynx

value: Oropharynx


title: Spatial profiling of a solid tumor ROI from ovarian cancer patient BB24-009_1

description:
Library name: BB24-009_ST_high_1
Region of Interest (ROI) from a solid tumor area (ST) in a CLDN6-positive area of an FFPE ovarian serous adenocarcinoma tissue section from patient BB24-009. Gene expression was profiled from the Pan-CK positive segmented area.


title: MYC ChIP-seq in CM, replicate 1

description:
Library name: CM_MYC_rep1
ChIP-seq of MYC in H1-derived cardiomyocyte using the POLR3A ChIP-seq protocol.

value: differentiation


title: Patient HNC0151, Human sample

description: Library name: HNC0151PRH00


title: Patient HNC0148, Human sample

description: Library name: HNC0148PRH00


title: Cerebral cortex, P5, Mock Infection, Mouse Litter 4, Replicate 8

description:
Library name: Sample_P5_L14_8_193_384
Cerebral cortex of a single offspring, Postnatal Day 5

value: Cerebral cortex

value: Neurons + Glia


title: Patient HNC0141, Human sample

description: Library name: HNC0141PRH00


title: Cerebral cortex, P5, Mock Infection, Mouse Litter 3, Replicate 5

description:
Library name: Sample_P5_L13_5_277_300
Cerebral cortex of a single offspring, Postnatal Day 5

value: Wildtype


title: MYC ChIP-seq in hESC, replicate 2

description:
Library name: hESC_MYC_rep2
ChIP-seq of MYC in H1 hESC using the POLR3A ChIP-seq protocol.

value: embryonic stem cell

value: H1 hESC


title: Spatial profiling of a small cluster ROI from ovarian cancer patient BB24-009_2

description:
Library name: BB24-009_SC_high_2
Region of Interest (ROI) from a dispersed small tumor cell cluster (SC) in a CLDN6-positive area of an FFPE ovarian serous adenocarcinoma tissue section from patient BB24-009. Gene expression was profiled from the Pan-CK positive segmented area.


title: Patient HNC0139, Human sample

description: Library name: HNC0139PRH00


title: Cerebral cortex, P5, Mock Infection, Mouse Litter 4, Replicate 5

description:
Library name: Sample_P5_L14_5_217_360
Cerebral cortex of a single offspring, Postnatal Day 5


title: Patient HNC0138, Human sample

description: Library name: HNC0138PRH00


title: Spatial profiling of a small cluster ROI from ovarian cancer patient BB24-009_1

description:
Library name: BB24-009_SC_high_1
Region of Interest (ROI) from a dispersed small tumor cell cluster (SC) in a CLDN6-positive area of an FFPE ovarian serous adenocarcinoma tissue section from patient BB24-009. Gene expression was profiled from the Pan-CK positive segmented area.


title: POLR3G ChIP-seq in hESC, replicate 2

description:
Library name: hESC_POLR3G_rep2
ChIP-seq of POLR3G in H1 hESC using the POLR3A ChIP-seq protocol.


title: Patient HNC0135, Human sample

description: Library name: HNC0135PRH00


title: Cerebral cortex, P5, Mock Infection, Mouse Litter 3, Replicate 3

description:
Library name: Sample_P5_L13_3_206_371
Cerebral cortex of a single offspring, Postnatal Day 5


title: Patient HNC0143, Human sample

description: Library name: HNC0143PRH00


title: Patient HNC0164, Human sample

description: Library name: HNC0164PRH00


title: POLR3GL ChIP-seq in CM, replicate 1

description:
Library name: CM_POLR3GL_rep1
ChIP-seq of POLR3GL in H1-derived cardiomyocyte using the POLR3A ChIP-seq protocol.

value: cardiac muscle


title: Patient HNC0108, Human sample

description: Library name: HNC0108PRH00


title: Patient HNC0172, Human sample

description: Library name: HNC0172PRH00


title: POLR3C ChIP-seq in hESC, replicate 2

description:
Library name: hESC_POLR3C_rep2
ChIP-seq of POLR3C in H1 hESC using the POLR3A ChIP-seq protocol.


title: POLR3GL ChIP-seq in hESC, replicate 2

description:
Library name: hESC_POLR3GL_rep2
ChIP-seq of POLR3GL in H1 hESC using the POLR3A ChIP-seq protocol.


title: Cerebral cortex, P5, Mock Infection, Mouse Litter 3, Replicate 1

description:
Library name: Sample_P5_L13_1_230_347
Cerebral cortex of a single offspring, Postnatal Day 5


title: Patient HNC0104, Human sample

description: Library name: HNC0104PRH00


title: Patient HNC0159, Human sample

description: Library name: HNC0159PRH00


title: Cerebral cortex, P5, Mock Infection, Mouse Litter 4, Replicate 2

description:
Library name: Sample_P5_L14_2_253_324
Cerebral cortex of a single offspring, Postnatal Day 5


title: Cerebral cortex, P5, Mock Infection, Mouse Litter 4, Replicate 1

description:
Library name: Sample_P5_L14_1_265_312
Cerebral cortex of a single offspring, Postnatal Day 5


title: POLR3GL ChIP-seq in hESC, replicate 1

description:
Library name: hESC_POLR3GL_rep1
ChIP-seq of POLR3GL in H1 hESC using the POLR3A ChIP-seq protocol.


title: Patient HNC0089, Human sample

description: Library name: HNC0089PRH00


title: POLR3G ChIP-seq in CM, replicate 2

description:
Library name: CM_POLR3G_rep2
ChIP-seq of POLR3G in H1-derived cardiomyocyte using the POLR3A ChIP-seq protocol.

value: H1-derived cardiomyocyte


title: Patient HNC0087, Human sample

description: Library name: HNC0087PRH00

source_name: Larynx

value: Larynx


title: Patient HNC0147, Human sample

description: Library name: HNC0147PRH00


title: POLR3G ChIP-seq in CM, replicate 1

description:
Library name: CM_POLR3G_rep1
ChIP-seq of POLR3G in H1-derived cardiomyocyte using the POLR3A ChIP-seq protocol.

value: cardiomyocyte

value: wild type


title: Cerebral cortex, P5, Mock Infection, Mouse Litter 3, Replicate 4

description:
Library name: Sample_P5_L13_4_194_383
Cerebral cortex of a single offspring, Postnatal Day 5


title: Cerebral cortex, P5, Mock Infection, Mouse Litter 2, Replicate 5

description:
Library name: Sample_P5_L12_5_278_299
Cerebral cortex of a single offspring, Postnatal Day 5


title: Patient HNC0132, Human sample

description: Library name: HNC0132PRH00

source_name: Oral Cavity + Oropharynx

value: Oral Cavity + Oropharynx


title: Patient HNC0122, Human sample

description: Library name: HNC0122PRH00

value: Oral Cavity


title: Patient HNC0086, Human sample

description: Library name: HNC0086PRH00

value: Head and Neck Squamous Cell Carcinoma


title: POLR3C ChIP-seq in CM, replicate 2

description:
Library name: CM_POLR3C_rep2
ChIP-seq of POLR3C in H1-derived cardiomyocyte using the POLR3A ChIP-seq protocol.


title: Cerebral cortex, P5, Mock Infection, Mouse Litter 3, Replicate 2

description:
Library name: Sample_P5_L13_2_218_359
Cerebral cortex of a single offspring, Postnatal Day 5

value: Mock Infection (50 uL of 1x PBS)


title: POLR3G ChIP-seq in hESC, replicate 1

description:
Library name: hESC_POLR3G_rep1
ChIP-seq of POLR3G in H1 hESC using the POLR3A ChIP-seq protocol.


title: Patient HNC0109, Human sample

description: Library name: HNC0109PRH00


title: POLR3C ChIP-seq in CM, replicate 1

description:
Library name: CM_POLR3C_rep1
ChIP-seq of POLR3C in H1-derived cardiomyocyte using the POLR3A ChIP-seq protocol.


title: Patient HNC0107, Human sample

description: Library name: HNC0107PRH00


title: Patient HNC0115, Human sample

description: Library name: HNC0115PRH00


title: POLR3C ChIP-seq in hESC, replicate 1

description:
Library name: hESC_POLR3C_rep1
ChIP-seq of POLR3C in H1 hESC using the POLR3A ChIP-seq protocol.


title: Cerebral cortex, P5, Mock Infection, Mouse Litter 2, Replicate 7

description:
Library name: Sample_P5_L12_7_254_323
Cerebral cortex of a single offspring, Postnatal Day 5


title: Cerebral cortex, P5, Mock Infection, Mouse Litter 2, Replicate 3

description:
Library name: Sample_P5_L12_3_207_370
Cerebral cortex of a single offspring, Postnatal Day 5


title: Cerebral cortex, P5, Mock Infection, Mouse Litter 2, Replicate 8

description:
Library name: Sample_P5_L12_8_242_335
Cerebral cortex of a single offspring, Postnatal Day 5


title: POLR3A ChIP-seq in CM, replicate 2

description:
Library name: CM_POLR3A_rep2
ChIP-seq of POLR3A in H1-derived cardiomyocyte using the POLR3A ChIP-seq protocol.


title: Patient HNC0063, Human sample

description: Library name: HNC0063PRH00


title: Patient HNC0119, Human sample

description: Library name: HNC0119PRH00


title: Patient HNC0081, Human sample

description: Library name: HNC0081PRH00


title: Cerebral cortex, P5, Mock Infection, Mouse Litter 2, Replicate 2

description:
Library name: Sample_P5_L12_2_219_358
Cerebral cortex of a single offspring, Postnatal Day 5


title: Patient HNC0092, Human sample

description: Library name: HNC0092PRH00


title: Patient HNC0098, Human sample

description: Library name: HNC0098PRH00


title: POLR3B ChIP-seq in CM, replicate 1

description:
Library name: CM_POLR3B_rep1
ChIP-seq of POLR3B in H1-derived cardiomyocyte using the POLR3A ChIP-seq protocol.


title: Cerebral cortex, P5, Mock Infection, Mouse Litter 2, Replicate 6

description:
Library name: Sample_P5_L12_6_266_311
Cerebral cortex of a single offspring, Postnatal Day 5


title: POLR3B ChIP-seq in CM, replicate 2

description:
Library name: CM_POLR3B_rep2
ChIP-seq of POLR3B in H1-derived cardiomyocyte using the POLR3A ChIP-seq protocol.


title: Patient HNC0052, Human sample

description: Library name: HNC0052PRH00


title: Patient HNC0083, Human sample

description: Library name: HNC0083PRH00


title: Patient HNC0041, Human sample

description: Library name: HNC0041PRH00


title: POLR3A ChIP-seq in hESC, replicate 1

description:
Library name: hESC_POLR3A_rep1
ChIP-seq of POLR3A in H1 hESC using the POLR3A ChIP-seq protocol.


title: Patient HNC0039, Human sample

description: Library name: HNC0039PRH00

source_name: Larynx + Oral Cavity

value: Larynx + Oral Cavity


title: Cerebral cortex, P5, Mock Infection, Mouse Litter 1, Replicate 5

description:
Library name: Sample_P5_L11_5_243_334
Cerebral cortex of a single offspring, Postnatal Day 5


title: Patient HNC0035, Human sample

description: Library name: HNC0035PRH00

source_name: Hypopharynx

value: Hypopharynx


title: POLR3B ChIP-seq in hESC, replicate 2

description:
Library name: hESC_POLR3B_rep2
ChIP-seq of POLR3B in H1 hESC using the POLR3A ChIP-seq protocol.


title: POLR3A ChIP-seq in hESC, replicate 2

description:
Library name: hESC_POLR3A_rep2
ChIP-seq of POLR3A in H1 hESC using the POLR3A ChIP-seq protocol.


title: Cerebral cortex, P5, Mock Infection, Mouse Litter 2, Replicate 4

description:
Library name: Sample_P5_L12_4_195_382
Cerebral cortex of a single offspring, Postnatal Day 5


title: D83-siREST

city: Solna

first: Vladimir

middle: S.

last: Shavva

address: Solnavägen 30

department: Department of Medicine, Solna

country: Sweden

institute: Karolinska Institutet

description: Library name: A8

data_processing:
Alignment was performed using Salmon
Data was imported into R using tximport and analyzed using DEseq2
Assembly: hg38
Supplementary files format and content: raw counts are fastq files
Supplementary files format and content: processed files are tab deliminated files, output of Salmon

source_name: Liver

growth_protocol: Cells were cultivated in DMEM + 10% FBS for 6 days, passaged, and cultivated for additional 6 days in DMEM + 10% FBS.

extract_protocol:
RNA was isolated using RNeasy Mini Kit (Qiagene, #74104) with DNA digestion (Qiagene, #79254) according to manufacturers instructions.
RNA pola-A enrichment, preparation and sequencing was performed by Novogene. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Sequencing was perforimed using Illumina NovaSeq platform (HWI-ST1276).

treatment_protocol: Cells were transfected with scrambled siRNA or siRNA targeting REST.

value: Liver

value: Primary human Hepatic Stellate Cells

value: REST siRNA


title: differentiated immortalized human podocyte, 100 nM VCS (replicate 3), 24 hrs

city: New York

first: Evren

middle: U

last: Azeloglu

state: NY

address: 1 Gustave L. Levy Place

department: Nephrology

institute: Icahn School of Medicine at Mount Sinai

description:
Library name: VCS100nM_3
Column name in counts_ControlPlus100nM.csv : VCS-100nM-3

data_processing:
Raw sequencing reads were quantified at the transcript level using Salmon.
A decoy-aware transcriptome index was constructed using GENCODE v44 transcript annotations and the GRCh38 primary assembly genome.
Transcript-level abundances were summarized to gene-level counts for downstream analysis.
Assembly: GRCh38
Supplementary files format and content: Processed data files consist of a comma-separated values (CSV) file containing unnormalized gene-level read counts. Rows correspond to Ensembl gene identifiers and columns correspond to individual samples.

source_name: Moin Saleem human podocytes

growth_protocol: For all experiments we used a conditionally immortalized human podocyte cell line, previously developed by transfection with the temperature-sensitive SV40-T gene(51). Cells were grown in T75 flasks (Thermo Fisher Scientific, Cat. No. 156499) at a concentration of 1,200 cells per cm2 at the permissive temperature (33°C, 5% CO2). We used RPMI 1640 media supplemented with 1% Pen/Strep antibiotic (Gibco, Cat. No. #15140122), 10% fetal bovine serum (FBS, Gibco, Cat. No. 26140079) and 1× insulin-transferin selenium (ITS-G,  Gibco, Cat. No. 41400045). Differentiation was induced after moving the cells to a non-permissive temperature (37°C, 5% CO2) for 7-10 days to inactivate the SV40 T antigen before CNI treatment.

extract_protocol:
Total RNA was isolated from cells using standard RNA extraction procedures.
RNA-seq libraries were prepared from total RNA using a poly(A)-selected Illumina library preparation protocol with ERCC spike-ins and in-line UMIs.

treatment_protocol: Cells were treated with cyclosporine A, tacrolimus, or voclosporin (100 nM), or with DMSO control, for 24 hours.

value: Moin Saleem human podocytes

value: human immortalized and differentiated podocyte

value: Voclosporin 100 nM


title: Patient HNC0032, Human sample

description: Library name: HNC0032PRH00


title: Cerebral cortex, P5, Mock Infection, Mouse Litter 1, Replicate 2

description:
Library name: Sample_P5_L11_2_279_298
Cerebral cortex of a single offspring, Postnatal Day 5

source_name: Cerebral cortex

value: Cerebral cortex

value: Neurons + Glia

value: Wildtype


title: Patient HNC0080, Human sample

description: Library name: HNC0080PRH00


title: POLR3B ChIP-seq in hESC, replicate 1

description:
Library name: hESC_POLR3B_rep1
ChIP-seq of POLR3B in H1 hESC using the POLR3A ChIP-seq protocol.

value: embryonic stem cell

value: H1 hESC


title: Patient HNC0077, Human sample

description: Library name: HNC0077PRH00

value: Oropharynx


title: Patient HNC0027, Human sample

description: Library name: HNC0027PRH00

value: Oral Cavity


title: D62-Scrambled

description: Library name: A5

value: Scrambled siRNA


title: Patient HNC0015, Human sample

description: Library name: HNC0015PRH00

value: Head and Neck Squamous Cell Carcinoma


title: differentiated immortalized human podocyte, 100 nM TAC (replicate 2), 24 hrs

description:
Library name: TAC100nM_2
Column name in counts_ControlPlus100nM.csv : TAC-100nM-2

value: Tacrolimus 100 nM


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 1, Replicate 9

description:
Library name: Sample_P5_L10_9_208_369
Cerebral cortex of a single offspring, Postnatal Day 5

value: SARS-CoV-2 Infection (50μl of SARS-CoV-2 [3 × 107 PFU/ml])


title: POLR3A ChIP-seq in CM, replicate 1

description:
Library name: CM_POLR3A_rep1
ChIP-seq of POLR3A in H1-derived cardiomyocyte using the POLR3A ChIP-seq protocol.

value: cardiac muscle

value: H1-derived cardiomyocyte

value: cardiomyocyte

value: wild type

value: differentiation


title: Patient HNC0012, Human sample

description: Library name: HNC0012PRH00


title: differentiated immortalized human podocyte, 100 nM CSA (replicate 3), 24 hrs

description:
Library name: CSA100nM_3
Column name in counts_ControlPlus100nM.csv : CsA-100nM-3

value: Moin Saleem human podocytes

value: human immortalized and differentiated podocyte

value: Cyclosporine A 100 nM


title: Patient HNC0050, Human sample

description: Library name: HNC0050PRH00

value: Larynx


title: D51-Scrambled

description: Library name: A3

value: Liver

value: Primary human Hepatic Stellate Cells


title: Patient HNC0009, Human sample

description: Library name: HNC0009PRH00


title: differentiated immortalized human podocyte, 100 nM CSA (replicate 2), 24 hrs

description:
Library name: CSA100nM_2
Column name in counts_ControlPlus100nM.csv : CsA-100nM-2


title: Cerebral cortex, P5, Mock Infection, Mouse Litter 2, Replicate 1

description:
Library name: Sample_P5_L12_1_231_346
Cerebral cortex of a single offspring, Postnatal Day 5

value: Cerebral cortex

value: Neurons + Glia

value: Wildtype

value: Mock Infection (50 uL of 1x PBS)


title: Cerebral cortex, P5, Mock Infection, Mouse Litter 1, Replicate 4

description:
Library name: Sample_P5_L11_4_255_322
Cerebral cortex of a single offspring, Postnatal Day 5


title: differentiated immortalized human podocyte, DMSO (replicate 3), 24 hrs

description:
Library name: Control_3
Column name in counts_ControlPlus100nM.csv : Control-3

value: DMSO


title: Patient HNC0005, Human sample

description: Library name: HNC0005PRH00

value: Head and Neck Squamous Cell Carcinoma


title: differentiated immortalized human podocyte, DMSO (replicate 2), 24 hrs

description:
Library name: Control_2
Column name in counts_ControlPlus100nM.csv : Control-2


title: Patient HNC0002, Human sample

description: Library name: HNC0002PRH00

value: Oropharynx


title: differentiated immortalized human podocyte, 100 nM VCS (replicate 2), 24 hrs

description:
Library name: VCS100nM_2
Column name in counts_ControlPlus100nM.csv : VCS-100nM-2

value: Voclosporin 100 nM


title: D83-Scrambled

description: Library name: A7

value: Scrambled siRNA


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 1, Replicate 4

description:
Library name: Sample_P5_L10_4_268_309
Cerebral cortex of a single offspring, Postnatal Day 5

value: SARS-CoV-2 Infection (50μl of SARS-CoV-2 [3 × 107 PFU/ml])


title: Patient HNC0034, Human sample

description: Library name: HNC0034PRH00


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 1, Replicate 5

description:
Library name: Sample_P5_L10_5_256_321
Cerebral cortex of a single offspring, Postnatal Day 5


title: PLG_11

city: Nashville

first: Danielle

middle: L

last: Michell

state: TN

address: 2220 Pierece Ave

department: Department of Medicine

institute: Vanderbilt Univ. Medical Center

data_processing:
TIGER (“Tools for Integrative Genome analysis of Extracellular sRNAs”), an in-house small RNA sequencing analysis pipeline, was used to quantify small RNAs (Allen, R. M., Zhao, S., Ramirez Solano, M. A., Zhu, W., et al., Bioinformatic analysis of endogenous and exogenous small RNAs on lipoproteins. J Extracell Vesicles 2018, 7, 1506198.)
Briefly, Cutadapt (v4.5) was used to trim 3’ adapters for raw reads. All reads with less than 16 nucleotides were designated as “too short” and discarded. Quality control on both raw reads and adaptor-trimmed reads was performed using FastQC (v0.12.1)(www.bioinformatics.babraham.ac.uk/projects/fastqc).
The adaptor-trimmed reads were mapped to the GENCODE GRCh38.p13 genome, addition to rRNA and tRNA reference sequences, by Bowtie1 (v1.3.1) allowing only one mismatch
Significantly differential expressed features with absolute fold change >= 1.5 and p value <= 0.05 were detected by DESeq2 (v1.42.1) using total reads as normalization factor.
The reads with less than 20 nucleotides which were neither annotated as small RNA nor perfectly mapped to human genome were discarded. Remaining unmapped reads were then mapped in parallel to exogenous structural RNA databases and curated microbial genome databases allowing no mismatches. Reads that failed to align to any strategy were categorized as ‘unknown’.
Assembly: Human GRCh38.p13 genome
Supplementary files format and content: csv file containing reads per million of each sample

source_name: plasma

extract_protocol:
Total RNA was purified from using the miRNeasy Mini kit (Qiagen).
Libraries were prepared using the NEXTFlex small RNA sequencing kit v3 with UDIs (Revvity), using 1:8 adatper dilution, 24 PCR cycles and the no size selection bead cleanup.

value: plasma

value: FH


title: PLG_10


title: Cerebral cortex, P5, Mock Infection, Mouse Litter 1, Replicate 3

description:
Library name: Sample_P5_L11_3_267_310
Cerebral cortex of a single offspring, Postnatal Day 5


title: D62-siREST

description: Library name: A6

value: REST siRNA


title: differentiated immortalized human podocyte, 100 nM VCS (replicate 1), 24 hrs

description:
Library name: VCS100nM_1
Column name in counts_ControlPlus100nM.csv : VCS-100nM-1

value: Moin Saleem human podocytes

value: human immortalized and differentiated podocyte


title: Cerebral cortex, P5, Mock Infection, Mouse Litter 1, Replicate 1

description:
Library name: Sample_P5_L11_1_196_381
Cerebral cortex of a single offspring, Postnatal Day 5


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 1, Replicate 2

description:
Library name: Sample_P5_L10_2_197_380
Cerebral cortex of a single offspring, Postnatal Day 5


title: differentiated immortalized human podocyte, 100 nM TAC (replicate 3), 24 hrs

description:
Library name: TAC100nM_3
Column name in counts_ControlPlus100nM.csv : TAC-100nM-3

value: Tacrolimus 100 nM


title: Patient HNC0179, PDX sample

description: Library name: HNC0179PRX0B

value: Oral Cavity


title: HT29-IN-2

city: Hong Kong

first: Jiaxi

last: Li

state: Hong Kong (SAR)

address: FLAT G,8/F,SUN ON BUILDING,490 QUEENS ROAD WEST

department: surgery

country: Hong Kong

institute: The university of Hong Kong

description:
Library name: sample11
piR-37524 inhibited

data_processing:
Illumina’s Real-Time Analysis (RTA) software (version 2.7.7) was used for base-calling, with default parameters to convert raw sequencing signals into FASTQ files.
Fastq files were processed using Cutadapt (version 1.9.1) to remove adapter sequences and low-quality bases. Parameters: --quality-cutoff 20 (phred score threshold), --minimum-length 75 (retaining reads ≥ 75 bp after trimming).
Clean reads were aligned to the human reference genome (GRCh38) using Hisat2 (version 2.2.1). Parameters: --dta-cufflinks (enabling downstream transcript assembly), --max-intronlen 500000 (allowing for large introns in human genes).
Gene expression levels (raw counts) were quantified using HTSeq (version 0.6.1). Parameters: --mode union (handling overlapping reads), --stranded no (non-stranded library), with gene annotations from ENSEMBL (GRCh38.105).
FPKM values were calculated based on raw counts and gene length using custom R scripts. Differential expression analysis was performed using DESeq2 (version 1.30.1) with parameters: padj ≤ 0.05 and |log2FC| > 1 to identify differentially expressed genes.
Assembly: GRCh38
Supplementary files format and content: tab-delimited txt file includes raw counts values and FPKM value for each sample

extract_protocol:
RNA was harvested using TRIzol reagent (Invitrogen). 1 μg total RNA was used for following library preparation.
The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.

value: colorectal cancer cells

value: piR-37524 knockdown


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 1, Replicate 1

description:
Library name: Sample_P5_L10_1_209_368
Cerebral cortex of a single offspring, Postnatal Day 5

value: Cerebral cortex

value: Neurons + Glia

value: Wildtype


title: PLG_8


title: Patient HNC0172, PDX sample

description: Library name: HNC0172PRX0A

value: Head and Neck Squamous Cell Carcinoma


title: D51-siREST

description: Library name: A4

value: Liver

value: Primary human Hepatic Stellate Cells


title: PLG_6

value: Healthy


title: differentiated immortalized human podocyte, 100 nM TAC (replicate 1), 24 hrs

description:
Library name: TAC100nM_1
Column name in counts_ControlPlus100nM.csv : TAC-100nM-1


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 1, Replicate 8

description:
Library name: Sample_P5_L10_8_220_357
Cerebral cortex of a single offspring, Postnatal Day 5

value: SARS-CoV-2 Infection (50μl of SARS-CoV-2 [3 × 107 PFU/ml])


title: Patient HNC0159, PDX sample, Biological Replicate B

description: Library name: HNC0159PRX0B

value: Oropharynx


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 1, Replicate 6

description:
Library name: Sample_P5_L10_6_244_333
Cerebral cortex of a single offspring, Postnatal Day 5


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 1, Replicate 7

description:
Library name: Sample_P5_L10_7_232_345
Cerebral cortex of a single offspring, Postnatal Day 5


title: PLG_12

value: plasma

value: FH


title: Patient HNC0007, Human sample

description: Library name: HNC0007PRH00


title: PLG_5


title: Cerebral cortex, E15, SARS-CoV-2 Infection, Mouse Litter 4, Replicate 6

description:
Library name: Sample_L7_6_351_226
Cerebral cortex of a single offspring, Embryonic Day 15


title: differentiated immortalized human podocyte, 100 nM CSA (replicate 1), 24 hrs

description:
Library name: CSA100nM_1
Column name in counts_ControlPlus100nM.csv : CsA-100nM-1

value: Moin Saleem human podocytes

value: Cyclosporine A 100 nM


title: D24-siREST

description: Library name: A2

value: REST siRNA


title: D24-Scrambled

description: Library name: A1

value: Scrambled siRNA


title: Patient HNC0183, PDX sample

description: Library name: HNC0183PRX0A

value: Oral Cavity


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 1, Replicate 3

description:
Library name: Sample_P5_L10_3_280_297
Cerebral cortex of a single offspring, Postnatal Day 5


title: PLG_9


title: Patient HNC0157, PDX sample

description: Library name: HNC0157PRX0A


title: HT29-IN-1

description:
Library name: sample10
piR-37524 inhibited

value: colorectal cancer cells

value: piR-37524 knockdown


title: Cerebral cortex, E15, SARS-CoV-2 Infection, Mouse Litter 4, Replicate 9

description:
Library name: Sample_L7_9_315_262
Cerebral cortex of a single offspring, Embryonic Day 15

value: Cerebral cortex

value: Neurons + Glia


title: Patient HNC0008, Human sample

description: Library name: HNC0008PRH00

value: Hypopharynx

value: Head and Neck Squamous Cell Carcinoma


title: HCT116-IN-3

description:
Library name: sample6
piR-37524 inhibited


title: Cerebral cortex, E15, SARS-CoV-2 Infection, Mouse Litter 4, Replicate 5

description:
Library name: Sample_L7_5_363_214
Cerebral cortex of a single offspring, Embryonic Day 15

value: Wildtype


title: Patient HNC0151, PDX sample

description: Library name: HNC0151PRX0B


title: Cerebral cortex, E15, SARS-CoV-2 Infection, Mouse Litter 4, Replicate 8

description:
Library name: Sample_L7_8_327_250
Cerebral cortex of a single offspring, Embryonic Day 15


title: PLG_7


title: PLG_3

value: Healthy


title: PLG_2


title: Patient HNC0164, PDX sample

description: Library name: HNC0164PRX0A


title: HT29-IN-3

description:
Library name: sample12
piR-37524 inhibited


title: HCT116-IN-2

description:
Library name: sample5
piR-37524 inhibited


title: Cerebral cortex, E15, SARS-CoV-2 Infection, Mouse Litter 4, Replicate 2

description:
Library name: Sample_L7_2_304_273
Cerebral cortex of a single offspring, Embryonic Day 15

value: SARS-CoV-2 Infection (50μl of SARS-CoV-2 [3 × 107 PFU/ml])


title: differentiated immortalized human podocyte, DMSO (replicate 1), 24 hrs

description:
Library name: Control_1
Column name in counts_ControlPlus100nM.csv : Control-1

value: human immortalized and differentiated podocyte

value: DMSO


title: Patient HNC0159, PDX sample, Biological Replicate A

description: Library name: HNC0159PRX0A

value: Oropharynx


title: Patient HNC0147, PDX sample

description: Library name: HNC0147PRX0A


title: HT29-NC-3

description:
Library name: sample9
Control

value: WT


title: HT29-NC-2

description:
Library name: sample8
Control


title: HCT116-NC-3

description:
Library name: sample2
Control


title: Cerebral cortex, E15, SARS-CoV-2 Infection, Mouse Litter 4, Replicate 1

description:
Library name: Sample_L7_1_316_261
Cerebral cortex of a single offspring, Embryonic Day 15


title: HDL_3

value: plasma


title: Patient HNC0143, PDX sample

description: Library name: HNC0143PRX0B


title: Cerebral cortex, E15, SARS-CoV-2 Infection, Mouse Litter 3, Replicate 7

description:
Library name: Sample_L6_7_328_249
Cerebral cortex of a single offspring, Embryonic Day 15


title: HT29-NC-1

description:
Library name: sample7
Control


title: Patient HNC0139, PDX sample

description: Library name: HNC0139PRX0A


title: Cerebral cortex, E15, SARS-CoV-2 Infection, Mouse Litter 3, Replicate 6

description:
Library name: Sample_L6_6_340_237
Cerebral cortex of a single offspring, Embryonic Day 15


title: Cerebral cortex, E15, SARS-CoV-2 Infection, Mouse Litter 4, Replicate 7

description:
Library name: Sample_L7_7_339_238
Cerebral cortex of a single offspring, Embryonic Day 15


title: BRAFiR 888meltreated with GDC0575, 12h, biological replicate 2

city: Rio de Janeiro

first: Patricia

last: Abrao Possik

state: RJ

address: Rua Andre Cavalcanti 37

country: Brazil

institute: Brazilian National Cancer Institute

description: Library name: R12_2

data_processing:
Sequenced reads were trimmed to remove low-quality bases using Trimmomatic v0.39 (SLIDINGWINDOW:4:20 LEADING:3 TRAILING:3 MINLEN:36).
The default parameters of STAR program version 2.6.0c (https://github.com/alexdobin/STAR/releases) was used to map the clean reads using GRCh38 genome (Ensembl) as reference and to quantify the number of reads per gene, using the "quantMode GeneCounts" option.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes normalized counts for all Samples
Supplementary files format and content: tab-delimited text files with the number of reads per gene for each Sample

growth_protocol: 888mel and 888mel BRAFiR melanoma cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS), 3.7mg/ml NaHCO3, 1% penicillin-streptomycin 100x, 1% sodium pyruvate 100x and 1% L-glutamine 200mM. 888mel BRAFiR melanoma cells were derived from 888mel as described previously (MÜLLER et al., 2014; KEMPER et al., 2016) and maintained in 3 μM PLX4720.

extract_protocol:
RNA was extracted using the RNeasy Plus Mini kit (Qiagen) and quantified with Qubit RNA Broad Range kit and the Qubit 4 (Invitrogen). RNA quality was assessed using the RNA 6000 Nano kit and the 2100 Bioanalyzer (Agilent Technologies).
Library was prepared with TruSeq Stranded mRNA kit (Illumina). Samples were indexed and analyzed by paired-end sequencing of 75 base pairs on the HiSeq 2500 instrument (Illumina).

treatment_protocol: Cells were seeded in 10 cm dishes (1x106 cells/dish) and exposed to 0.3 µM of GDC-0575 for six hours. As a control, cells were harvested before treatment (T0). Experiments were performed in three independent biological replicates.

value: melanoma cell line

value: BRAF V600E


title: HCT116-NC-2-NEW

description:
Library name: sample1
Control


title: Patient HNC0150, PDX sample, Merged Technical Replicate

description: Library name: HNC0150PRX0A


title: Patient HNC0148, PDX sample

description: Library name: HNC0148PRX0A

value: Oral Cavity


title: BRAFiR 888mel treated with GDC0575, 12h, biological replicate 1

description: Library name: R12_1


title: PAD321

city: Gainesville

first: Terence

last: Ryan

address: 1864 Stadium Rd

institute: University of Florida

description: Library name: PAD321

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences.
Assembly: Homo sapiens GRCh38 reference genome
Supplementary files format and content: TPM counts file

source_name: gastrocnemius muscle

extract_protocol:
total RNA isolated using Zymo Direct-Zol RNA isolation kit
Illumina library preparation performed by Azenta Life Sciences

value: gastrocnemius muscle

tag: disease state

value: PAD+CKD


title: PAD320

description: Library name: PAD320

value: PAD


title: PLG_4


title: HCT116-IN-1

description:
Library name: sample4
piR-37524 inhibited

value: colorectal cancer cells

value: piR-37524 knockdown


title: Patient HNC0132, PDX sample

description: Library name: HNC0132PRX0A

value: Oral Cavity + Oropharynx

value: Head and Neck Squamous Cell Carcinoma


title: HDL_2

value: Healthy


title: Cerebral cortex, E15, SARS-CoV-2 Infection, Mouse Litter 4, Replicate 4

first: Matthew

last: Yuen

address: 100 College

institute: Yale School of Medicine

description:
Library name: Sample_L7_4_375_202
Cerebral cortex of a single offspring, Embryonic Day 15

data_processing:
Quality control on FASTQ reads was performed using FastQC (version 0.11.9) and a threshold set for 95% of bases meeting Q30 within a given read to ensure high sequencing quality. Paired-end reads were trimmed using Fastp (version 0.23.2) with default arguments. Pseudoalignment to mm39 mouse genome (reference provided by the Yale Center for Genome Analysis) and quantification was performed using Salmon (version 1.4.0) with selective alignment enabled.
Assembly: mm39
Supplementary files format and content: *_quant.sf (Salmon quantification file) A tab-separated text file produced by Salmon that contains transcript-level quantification results. Each row corresponds to one transcript (or gene, if Salmon was run in gene mode). Typical columns include: Name (transcript ID), Length (transcript length in bp), EffectiveLength (bias-corrected length used for quantification), TPM (Transcripts Per Million, normalized expression value), and NumReads (estimated number of reads/fragments assigned to the transcript). This file is the main output used for downstream differential expression and expression profiling analyses.

extract_protocol:
For bulk RNA-sequencing of the brain and placenta, pregnant dams were euthanized via cervical dislocation. Embryos were harvested from the dams and stored in ice-cold HBSS over ice as the placentas and embryonic brains were dissected in ice-cold HBSS. The placentas and dorsal cortex of offspring were dissected, placed in RNAProtect overnight, and  transferred to -20°C for later archival storage. To extract the RNA from placenta and dorsal cortices, tissue were homogenized using Lysis Matrix D ceramic beads. After centrifugation of the homogenate, the supernatant was extracted and total RNA was purified via the Qiagen RNeasy Mini kit. RNA samples were submitted to Yale’s Center for Genome Analysis for cDNA library preparation (Kapa mRNA HyperPrep) and sequenced (NovaSeq6000) at 100 million reads per sample.
RNA Seq Library Prep: mRNA is purified from a normalized input between 50-1000ng of total RNA with oligo-dT beads and sheared by incubation at 94C in the presence of Mg (Kapa mRNA Hyper Prep). Following first-strand synthesis with random primers, second strand synthesis and A-tailing are performed with dUTP for generating strand-specific sequencing libraries. Adapter ligation with 3’ dTMP overhangs are ligated to library insert fragments. Library amplification amplifies fragments carrying the appropriate adapter sequences at both ends. Strands marked with dUTP are not amplified. Indexed libraries that meet appropriate cut-offs for both are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX or Agilent TapeStation. Samples with a yield of ≥0.5 ng/ul are used for sequencing.

value: Cerebral cortex

value: Neurons + Glia

value: Wildtype

value: SARS-CoV-2 Infection (50μl of SARS-CoV-2 [3 × 107 PFU/ml])


title: PLG_1


title: PAD316

description: Library name: PAD316

value: CKD


title: Patient HNC0125, PDX sample, Biological Replicate B

description: Library name: HNC0125PRX0B


title: HDL_4

value: plasma


title: Patient HNC0141, PDX sample

description: Library name: HNC0141PRX0B

value: Oropharynx


title: Cerebral cortex, E15, SARS-CoV-2 Infection, Mouse Litter 4, Replicate 3

description:
Library name: Sample_L7_3_292_285
Cerebral cortex of a single offspring, Embryonic Day 15


title: Cerebral cortex, E15, SARS-CoV-2 Infection, Mouse Litter 3, Replicate 5

description:
Library name: Sample_L6_5_352_225
Cerebral cortex of a single offspring, Embryonic Day 15


title: BRAFiR 888mel treated with GDC0575, 6h, biological replicate 1

description: Library name: R6_1

value: melanoma cell line

value: BRAF V600E


title: PAD312

description: Library name: PAD312

value: gastrocnemius muscle


title: HCT116-NC-3-NEW

description:
Library name: sample3
Control

value: WT


title: BRAFiR 888mel treated with GDC0575, 6h, biological replicate 3

description: Library name: R6_3


title: Patient HNC0138, PDX sample

description: Library name: HNC0138PRX0A

value: Oral Cavity


title: Patient HNC0135, PDX sample

description: Library name: HNC0135PRX0A


title: Cerebral cortex, E15, SARS-CoV-2 Infection, Mouse Litter 2, Replicate 4

description:
Library name: Sample_L5_4_341_236
Cerebral cortex of a single offspring, Embryonic Day 15


title: HDL_1


title: Patient HNC0124, PDX sample, Biological Replicate A

description: Library name: HNC0124PRX0A


title: Cerebral cortex, E15, SARS-CoV-2 Infection, Mouse Litter 2, Replicate 5

description:
Library name: Sample_L5_5_329_248
Cerebral cortex of a single offspring, Embryonic Day 15


title: Pancreatic ductal adenocarcinoma

city: Anhui

first: 午洋

last: 张

state: State

address: No.17 Lujiang Road, Hefei City, Anhui Province, China

institute: The First Affiliated Hospital of USTC

description: Library name: sameple

data_processing:
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Slides&Reagent kit according to manufacture's construction
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell
Library strategy: Spatial Transcriptomics

source_name: pancreas

extract_protocol:
The study was approved by the Ethics Committee of USTC (Ethics Approval No.: 2024-RE-359). All pancreatic cancer patients who participated in this study at the No. 1 Affliated Hospital of USTC provided consent forms. None of the patients received any neoadjuvant therapy before tissue collection. Fresh tumor specimens and adjacent mucosal specimens were resected intraoperatively and there were no cancer cells remaining at the end of the resected samples as confirmed by the histopathologist. Representative hemoglobin/eosin (H&E)-stained sections of the excised specimens used for scRNA-seq were delineated with the help of a pathologist to delineate the three adjacent subregions (tumor core, tumor margin, and distal paracancerous region), after which each of the three regions was digested into single-cell suspensions and analyzed using droplet-based scRNA-seq.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

value: pancreas

value: Pancreatic ductal cells

value: Pancreatic ductal adenocarcinoma


title: Cerebral cortex, E15, SARS-CoV-2 Infection, Mouse Litter 3, Replicate 1

city: New Haven

description:
Library name: Sample_L6_1_305_272
Cerebral cortex of a single offspring, Embryonic Day 15


title: BRAFiR 888mel treated with GDC0575, 12h, biological replicate 3

description: Library name: R12_3


title: Patient HNC0122, PDX sample, Biological Replicate B

description: Library name: HNC0122PRX0B

value: Head and Neck Squamous Cell Carcinoma


title: BRAFiR 888mel, 0h, biological replicate 2

description: Library name: R0_2


title: Cerebral cortex, E15, SARS-CoV-2 Infection, Mouse Litter 3, Replicate 3

description:
Library name: Sample_L6_3_376_201
Cerebral cortex of a single offspring, Embryonic Day 15


title: BRAFiR 888mel treated with GDC0575, 6h, biological replicate 2

description: Library name: R6_2


title: PAD310

description: Library name: PAD310

value: PAD


title: Cerebral cortex, E15, SARS-CoV-2 Infection, Mouse Litter 3, Replicate 4

description:
Library name: Sample_L6_4_364_213
Cerebral cortex of a single offspring, Embryonic Day 15

value: Cerebral cortex


title: Cerebral cortex, E15, SARS-CoV-2 Infection, Mouse Litter 2, Replicate 2

description:
Library name: Sample_L5_2_365_212
Cerebral cortex of a single offspring, Embryonic Day 15

value: Neurons + Glia


title: Cerebral cortex, E15, SARS-CoV-2 Infection, Mouse Litter 3, Replicate 2

description:
Library name: Sample_L6_2_293_284
Cerebral cortex of a single offspring, Embryonic Day 15

value: Wildtype


title: PAD306

description: Library name: PAD306

value: Control


title: PAD315

description: Library name: PAD315

value: PAD+CKD


title: Patient HNC0119, PDX sample

description: Library name: HNC0119PRX0B


title: Patient HNC0125, PDX sample, Biological Replicate A

description: Library name: HNC0125PRX0A


title: BRAFiR 888mel, 0h, biological replicate 3

description: Library name: R0_3


title: Cerebral cortex, E15, SARS-CoV-2 Infection, Mouse Litter 2, Replicate 6

description:
Library name: Sample_L5_6_317_260
Cerebral cortex of a single offspring, Embryonic Day 15

value: SARS-CoV-2 Infection (50μl of SARS-CoV-2 [3 × 107 PFU/ml])


title: Cerebral cortex, E15, SARS-CoV-2 Infection, Mouse Litter 2, Replicate 1

description:
Library name: Sample_L5_1_377_200
Cerebral cortex of a single offspring, Embryonic Day 15


title: 888mel treated with GDC0575, 12h, biological replicate 3

description: Library name: P12_3


title: Patient HNC0122, PDX sample, Biological Replicate A

description: Library name: HNC0122PRX0A


title: BRAFiR 888mel, 0h, biological replicate 1

description: Library name: R0_1


title: Patient HNC0115, PDX sample

description: Library name: HNC0115PRX0A


title: 888mel treated with GDC0575, 6h, biological replicate 3

description: Library name: P6_3


title: Patient HNC0124, PDX sample, Biological Replicate B

description: Library name: HNC0124PRX0B


title: 888mel treated with GDC0575, 12h, biological replicate 1

description: Library name: P12_1


title: PAD303

description: Library name: PAD303

value: CKD


title: Cerebral cortex, E15, SARS-CoV-2 Infection, Mouse Litter 2, Replicate 3

description:
Library name: Sample_L5_3_353_224
Cerebral cortex of a single offspring, Embryonic Day 15


title: Cerebral cortex, E15, SARS-CoV-2 Infection, Mouse Litter 1, Replicate 5

description:
Library name: Sample_L4_5_306_271
Cerebral cortex of a single offspring, Embryonic Day 15


title: 888mel treated with GDC0575, 12h, biological replicate 2

description: Library name: P12_2

value: melanoma cell line


title: PAD309

description: Library name: PAD309


title: 888mel treated with GDC0575, 6h, biological replicate 2

description: Library name: P6_2

value: BRAF V600E


title: PAD302

description: Library name: PAD302

value: gastrocnemius muscle


title: Patient HNC0108, PDX sample

description: Library name: HNC0108PRX0A


title: Patient HNC0107, PDX sample, Biological Replicate B

description: Library name: HNC0107PRX0B


title: Patient HNC0107, PDX sample, Biological Replicate A

description: Library name: HNC0107PRX0A


title: Cerebral cortex, E15, SARS-CoV-2 Infection, Mouse Litter 1, Replicate 2

description:
Library name: Sample_L4_2_342_235
Cerebral cortex of a single offspring, Embryonic Day 15


title: Cerebral cortex, E15, SARS-CoV-2 Infection, Mouse Litter 1, Replicate 6

description:
Library name: Sample_L4_7_294_283
Cerebral cortex of a single offspring, Embryonic Day 15


title: 888mel treated with GDC0575, 6h, biological replicate 1

description: Library name: P6_1


title: PAD305

description: Library name: PAD305


title: PAD308

description: Library name: PAD308


title: PAD298

description: Library name: PAD298


title: Cerebral cortex, E15, SARS-CoV-2 Infection, Mouse Litter 1, Replicate 1

description:
Library name: Sample_L4_1_354_223
Cerebral cortex of a single offspring, Embryonic Day 15


title: Patient HNC0109, PDX sample

description: Library name: HNC0109PRX0B


title: 888mel, 0h, biological replicate 1

description: Library name: P0_1


title: Cerebral cortex, E15, Mock Infection, Mouse Litter 2, Replicate 7

description:
Library name: Sample_L3_7_378_199
Cerebral cortex of a single offspring, Embryonic Day 15

value: Mock Infection (50 uL of 1x PBS)


title: Patient HNC0104, PDX sample

description: Library name: HNC0104PRX0B

value: Oral Cavity


title: Cerebral cortex, E15, SARS-CoV-2 Infection, Mouse Litter 1, Replicate 4

description:
Library name: Sample_L4_4_318_259
Cerebral cortex of a single offspring, Embryonic Day 15


title: PAD301

description: Library name: PAD301


title: Patient HNC0092, PDX sample, Biological Replicate B

description: Library name: HNC0092PRX0B


title: PAD299

description: Library name: PAD299


title: PAD294

description: Library name: PAD294


title: 888mel, 0h, biological replicate 3

description: Library name: P0_3


title: PAD300

description: Library name: PAD300


title: Tonsil_RT, No40

type: RNA

city: Shinjuku

first: Satomi

last: Kobayashi

state: Tokyo

address: 2-5-1 Nakaochiai

institute: Seibo International Catholic Hospital

description: Gene expression in tonsil from patient with RT

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Ver.3.0 Microarray (Agilent, G4851C) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61×21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters (protocol GE1_1200_Jun14 and Grid 072363_D_F_20200924) to obtain background subtracted and spatially detrended Processed Signal intensities. The 75th percentile shift normalization was performed using Agilent GeneSpring GX 14.9.1.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng Total RNA using Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer’s instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Tonsillar crypt samples were lysed using QIAzol Lysis Reagent (QIAGEN; Hilden, Germany) and homogenized with a TissueRupter (QIAGEN). RNA was extracted using an RNeasy Plus Universal Kit (QIAGEN) according to the manufacturer’s protocol. RNA concentrations and quality were assessed using a NanoDropTM 1000 (Thermo Fisher Scientific) and an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA, USA). RNA quality was confirmed if A260/A280 was ≥1.8, A260/A230 was ≥2.0, and the RNA Integrity Number was ≥7.0.

value: Tonsil


title: PAD297

description: Library name: PAD297


title: Cerebral cortex, E15, Mock Infection, Mouse Litter 2, Replicate 6

description:
Library name: Sample_L3_6_295_282
Cerebral cortex of a single offspring, Embryonic Day 15


title: 888mel, 0h, biological replicate 2

description: Library name: P0_2


title: Patient HNC0092, PDX sample, Biological Replicate A

description: Library name: HNC0092PRX0A


title: Patient HNC0098, PDX sample

description: Library name: HNC0098PRX0A

value: Larynx


title: Patient HNC0087, PDX sample

description: Library name: HNC0087PRX0B


title: Patient HNC0089, PDX sample

description: Library name: HNC0089PRX0B


title: Cerebral cortex, E15, Mock Infection, Mouse Litter 2, Replicate 3

description:
Library name: Sample_L3_3_331_246
Cerebral cortex of a single offspring, Embryonic Day 15


title: Patient HNC0083, PDX sample

description: Library name: HNC0083PRX0A


title: Patient HNC0086, PDX sample

description: Library name: HNC0086PRX0A


title: Tonsil_PPP/PAO, No35

description: Gene expression in tonsil from patient with PPP/PAO


title: Cerebral cortex, E15, SARS-CoV-2 Infection, Mouse Litter 1, Replicate 3

description:
Library name: Sample_L4_3_330_247
Cerebral cortex of a single offspring, Embryonic Day 15


title: Tonsil_RT, No39


title: PAD285

description: Library name: PAD285


title: PAD291

description: Library name: PAD291


title: Patient HNC0080, PDX sample

description: Library name: HNC0080PRX0A


title: Tonsil_RT, No38


title: Tonsil_RT, No36


title: Tonsil_PPP, No33

description: Gene expression in tonsil from patient with PPP


title: PAD293

description: Library name: PAD293


title: PAD288

description: Library name: PAD288


title: Cerebral cortex, E15, Mock Infection, Mouse Litter 1, Replicate 8

description:
Library name: Sample_L1_8_296_281
Cerebral cortex of a single offspring, Embryonic Day 15


title: Cerebral cortex, E15, Mock Infection, Mouse Litter 2, Replicate 8

description:
Library name: Sample_L3_8_366_211
Cerebral cortex of a single offspring, Embryonic Day 15


title: PAD286

description: Library name: PAD286


title: Cerebral cortex, E15, Mock Infection, Mouse Litter 2, Replicate 1

description:
Library name: Sample_L3_1_355_222
Cerebral cortex of a single offspring, Embryonic Day 15


title: Cerebral cortex, E15, Mock Infection, Mouse Litter 1, Replicate 6

description:
Library name: Sample_L1_6_320_257
Cerebral cortex of a single offspring, Embryonic Day 15


title: Patient HNC0063, PDX sample

description: Library name: HNC0063PRX0B


title: Tonsil_PPP/PAO, No30


title: Patient HNC0081, PDX sample

description: Library name: HNC0081PRX0A


title: Cerebral cortex, E15, Mock Infection, Mouse Litter 2, Replicate 5

description:
Library name: Sample_L3_5_307_270
Cerebral cortex of a single offspring, Embryonic Day 15


title: PAD281

description: Library name: PAD281


title: Cerebral cortex, E15, Mock Infection, Mouse Litter 2, Replicate 4

description:
Library name: Sample_L3_4_319_258
Cerebral cortex of a single offspring, Embryonic Day 15


title: Cerebral cortex, E15, Mock Infection, Mouse Litter 1, Replicate 4

description:
Library name: Sample_L1_4_344_233
Cerebral cortex of a single offspring, Embryonic Day 15


title: Patient HNC0052, PDX sample

description: Library name: HNC0052PRX0A


title: Tonsil_PPP/PAO, No29


title: Cerebral cortex, E15, Mock Infection, Mouse Litter 2, Replicate 2

description:
Library name: Sample_L3_2_343_234
Cerebral cortex of a single offspring, Embryonic Day 15


title: PAD280

description: Library name: PAD280


title: PAD284

description: Library name: PAD284


title: PAD289

description: Library name: PAD289


title: Patient HNC0077, PDX sample

description: Library name: HNC0077PRX0A

value: Oropharynx


title: Patient HNC0050, PDX sample

description: Library name: HNC0050PRX0A

value: Head and Neck Squamous Cell Carcinoma


title: Cerebral cortex, E15, Mock Infection, Mouse Litter 1, Replicate 7

description:
Library name: Sample_L1_7_308_269
Cerebral cortex of a single offspring, Embryonic Day 15


title: Tonsil_PPP/PAO, No37


title: Cerebral cortex, E15, Mock Infection, Mouse Litter 1, Replicate 3

description:
Library name: Sample_L1_3_356_221
Cerebral cortex of a single offspring, Embryonic Day 15


title: Patient HNC0070, PDX sample, Biological Replicate A

description: Library name: HNC0070PRX0A


title: Cerebral cortex, E15, Mock Infection, Mouse Litter 1, Replicate 2

description:
Library name: Sample_L1_2_368_209
Cerebral cortex of a single offspring, Embryonic Day 15


title: PAD275

description: Library name: PAD275


title: PAD283

description: Library name: PAD283

value: PAD


title: PAD276

description: Library name: PAD276


title: PAD277

description: Library name: PAD277


title: Tonsil_PPP/PAO, No32


title: Mus musculus,ZEA exposure group_input RNA (Biological Repetition 3)

city: Harbin

first: Lige

last: Bao

state: Heilongjiang

address: 600 Changjiang Road, Xiangfang District, Harbin 150030, P. R. China

institute: Northeast Agricultural University

description: Library name: ZEA40_3_input

data_processing:
Base calling software: BCL convert
Data filter: fastp(0.19.4)，remove adapters, repeat sequences and low quality sequences
reads alignment : HISAT2(2.0.4)
Peak calling diffpeak : R package: exomePeak (1.5.0)
Peak annotation : ANNOVAR
Transcript assembly and quantification : StringTie (2.1.2)
Differential Expression Analysis :R package: edgeR(4.1)
Motif: HOMER(4.10)
Assembly: GRCm39
Supplementary files format and content: Control_IPVSControl_input_peak.xlsx,ZEA40_IPVSZEA40_input_peak.xlsx,which contained methylation site information of m6A
Supplementary files format and content: ControlVSZEA40_diffPeak_result.xlsx, which contained the result  of differential methylation sites
Supplementary files format and content: 4_genes_fpkm_expression.xlsx,which  contained the expression information of various genes in various samples (Expression profile)
Supplementary files format and content: Control_inputVSZEA40_input_Gene_differential_expression.xlsx, which contains the list of differentially expressed genes between control_input and ZEA40_input samples.
Supplementary files format and content: ControlVSZEA40_diffPeak_Gene_differential_expression.xlsx, which contains the integrated analysis of differentially methylated m6A peaks and differentially expressed genes between the Control and ZEA40 groups (genes showing both differential m6A peaks and differential expression).

source_name: testis

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA), and the RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA). Poly (A) RNA was purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) by two rounds of purification.
the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. The cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). The IP RNA was reverse-transcribed to cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which was next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base was added to the blunt ends of each strand, preparing for ligation to the indexed adapters. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. At last, we performed paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 platform(LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol

value: testis

tag: Sex

value: male