title: amniotic fluid fetal cells 51

description: Hybridized to CytoScan 750K

value: microdeletion of 16p13.11


title: amniotic fluid fetal cells 54

status: Public on Aug 14 2024

type: genomic

city: Fuzhou

first: Yanting

last: Que

address: No. 88, Jiaotong Road, Taijiang District, Fuzhou City, Fujian Province

country: China

institute: Fujian Medical University

description: Hybridized to CytoScan 750K

hyb_protocol: DNA was processed as follows. Restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer`s instructions.

scan_protocol: The arrays were then washed using Affymetrix Fluidics Stations, and scanned using the GeneChip Scanner 750K

data_processing: The array image was acquired using Affymetrix GeneChip® Command Console (AGCC version 4.0.0.1567). Data processing and analysis (CEL file generation, smoothing and segmentation) were used Chromosome Analysis Suite (version 3.3).

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: amniotic fluid fetal cells

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA of fetal cells in amniotic fluid or cord blood sampling was extracted with using the QIAamp DNA extraction kit (Qiagen, Dusseldorf, Germany)

tag: tissue

value: amniotic fluid fetal cells

tag: diagnosis

value: microdeletion of 17q12


title: amniotic fluid fetal cells 53

description: Hybridized to CytoScan 750K

value: microdeletion of Xp22.31


title: Sorted mouse lung cells, tamoxifen-treated biol rep 3

status: Public on Aug 15 2024

type: SRA

city: Pittsburgh

first: John

last: Alcorn

state: Pennsylvania

address: 4401 Penn Avenue

department: Pediatrics

country: USA

institute: University of Pittsburgh

library_source: transcriptomic

data_processing:
STAR v2.7.3a
Sequences were trimmed for unwanted sequences using Bowtie2 v2.5.1, and quality control was performed with RNA-SeQC v1.1.8, RSeQC v3.0.1, and MultiQC v1.7
Paired-end reads were aligned and mapped to reference genome GRCm38 using STAR 2.7.3a
Read count extraction and normalization was performed using DESeq2 and expression was estimated using HTSeq v0.11.2
Assembly: GRCm38.p6
Supplementary files format and content: .xlsx includes raw normalized counts for all samples
Supplementary files format and content: .txt files include splicing annotations for all samples
Supplementary files format and content: .xlsx file includes FPKM values for all samples

molecule: total RNA

organism: Mus musculus

source_name: lung

extract_protocol:
RNA was isolated using the Rneasy Mini Kit (Qiagen) per manufacturer instructions.
RNA libraries for RNAseq were prepared using the Takara SMART-Seq v4 Ultra low Input RNA kit per manufacturer instructions.

treatment_protocol: Mice were treated with 1.5mg Tamoxifen in corn oil or corn oil alone intraperitoneally on d-14, -7, 0, and 5. Mice were infected with 900 PFU PR8 on d0 and sacrificed on d6.

value: lung

tag: genotype

tag: treatment

value: Tamoxifen


title: amniotic fluid fetal cells 49

description: Hybridized to CytoScan 750K


title: amniotic fluid fetal cells 50

description: Hybridized to CytoScan 750K


title: amniotic fluid fetal cells 45

description: Hybridized to CytoScan 750K

value: microdeletion of 16p11.2


title: amniotic fluid fetal cells 46

description: Hybridized to CytoScan 750K


title: amniotic fluid fetal cells 47

description: Hybridized to CytoScan 750K


title: amniotic fluid fetal cells 44

description: Hybridized to CytoScan 750K


title: amniotic fluid fetal cells 43

description: Hybridized to CytoScan 750K


title: amniotic fluid fetal cells 41

description: Hybridized to CytoScan 750K


title: amniotic fluid fetal cells 40

description: Hybridized to CytoScan 750K


title: amniotic fluid fetal cells 42

description: Hybridized to CytoScan 750K


title: amniotic fluid fetal cells 39

description: Hybridized to CytoScan 750K


title: amniotic fluid fetal cells 37

description: Hybridized to CytoScan 750K

value: microdeletion of 15q11.2


title: amniotic fluid fetal cells 38

description: Hybridized to CytoScan 750K


title: amniotic fluid fetal cells 36

description: Hybridized to CytoScan 750K


title: amniotic fluid fetal cells 35

description: Hybridized to CytoScan 750K


title: amniotic fluid fetal cells 33

description: Hybridized to CytoScan 750K


title: amniotic fluid fetal cells 52

description: Hybridized to CytoScan 750K

value: microdeletion of 1q21.1


title: amniotic fluid fetal cells 30

description: Hybridized to CytoScan 750K


title: amniotic fluid fetal cells 31

description: Hybridized to CytoScan 750K


title: amniotic fluid fetal cells 32

description: Hybridized to CytoScan 750K


title: amniotic fluid fetal cells 48

description: Hybridized to CytoScan 750K


title: amniotic fluid fetal cells 29

description: Hybridized to CytoScan 750K


title: amniotic fluid fetal cells 28

description: Hybridized to CytoScan 750K


title: amniotic fluid fetal cells 26

description: Hybridized to CytoScan 750K


title: amniotic fluid fetal cells 27

description: Hybridized to CytoScan 750K


title: amniotic fluid fetal cells 25

description: Hybridized to CytoScan 750K

value: microdeletion of 22q11.21


title: amniotic fluid fetal cells 24

description: Hybridized to CytoScan 750K


title: amniotic fluid fetal cells 21

description: Hybridized to CytoScan 750K


title: amniotic fluid fetal cells 20

description: Hybridized to CytoScan 750K


title: amniotic fluid fetal cells 18

description: Hybridized to CytoScan 750K


title: amniotic fluid fetal cells 12

description: Hybridized to CytoScan 750K


title: amniotic fluid fetal cells 19

description: Hybridized to CytoScan 750K


title: amniotic fluid fetal cells 14

description: Hybridized to CytoScan 750K


title: amniotic fluid fetal cells 22

description: Hybridized to CytoScan 750K


title: amniotic fluid fetal cells 23

description: Hybridized to CytoScan 750K


title: amniotic fluid fetal cells 16

description: Hybridized to CytoScan 750K


title: amniotic fluid fetal cells 15

description: Hybridized to CytoScan 750K


title: amniotic fluid fetal cells 13

description: Hybridized to CytoScan 750K

value: microduplication of 1q21.1


title: amniotic fluid fetal cells 10

description: Hybridized to CytoScan 750K


title: amniotic fluid fetal cells 34

description: Hybridized to CytoScan 750K


title: amniotic fluid fetal cells 9

description: Hybridized to CytoScan 750K


title: cord blood sampling 24

description: Hybridized to CytoScan 750K

source_name: cord blood sampling

value: cord blood sampling


title: cord blood sampling 1

description: Hybridized to CytoScan 750K


title: amniotic fluid fetal cells 7

description: Hybridized to CytoScan 750K


title: cord blood sampling 2

description: Hybridized to CytoScan 750K


title: cord blood sampling 3

description: Hybridized to CytoScan 750K


title: amniotic fluid fetal cells 6

description: Hybridized to CytoScan 750K


title: amniotic fluid fetal cells 17

description: Hybridized to CytoScan 750K


title: amniotic fluid fetal cells 5

description: Hybridized to CytoScan 750K


title: T31C-2b

city: Chengdu

first: guoqiang

last: zhu

address: No. 24, Section 1, South Section 1, First Ring Road

institute: sichuan university

data_processing:
The raw reads obtained from the HiSeq 2500 and BGISEQ-500 were analysed using FastQC (FastQC, RRID:SCR 014583) to compute the quality metrics of the reads, such as base sequence qualities, base sequence content, %GC, and sequence composition.
Once the read qualities were verified using FastQC (FastQC, RRID:SCR 014583), we used the PALEOMIX pipeline (PALEOMIX, RRID:SCR 015057) [18] to trim the adapter sequences, trim Ns and low-quality bases from the ends of reads, estimate ancient DNA damage, and finally map the trimmed reads to the reference genome.
AdapterRemoval (v. 2.1.3) was used to trim the adapter sequences from the ends of the reads using the default mismatch rate of 1/3.
In addition, bases with a quality score of less than 2 and unidentified bases (Ns) at the ends of reads were trimmed.
Finally, only reads that were longer than 25 bases were retained for downstream analyses.
Supplementary files format and content: The trimmed reads were mapped to the chicken reference genome using the mem algorithm in bwa (BWA, RRID:SCR 010910; v. 0.7.10), using the default settings for the mapping algorithm.
Supplementary files format and content: The mapped reads were subsequently processed using the GATK (v. 3.3.0) indel realigner (GATK, RRID:SCR 001876)  to fix the alignment issues arising from the presence of short indels at the beginnings and ends of reads.

organism: Gallus gallus

source_name: late-stage ovarian cancer

extract_protocol:
All samples were predigested at 56◦C for 1 hour, after which the buffer was changed and then a second 12- hour digest was performed. Digests from methods B and C were centrifuged at 6000 ×G for 1 minute, after which 500 μl supernatant was mixed 1:8 with a binding buffer. DNA bound to the columns was washed with 800 μl buffer PE (Qiagen), then eluted using 2 washes in 17 μl buffer EB (Qiagen)—each with an incubation for 5 minutes at 37◦C. Prior to library construction, small aliquots of each extract were analysed on an Agilent 2200 TapeStation HS chip (Agilent Technologies, Palo Alto, CA, USA) for fragment size estimation and molar concentration.
Library blanks and index PCR blanks were also included to evaluate the potential contaminations during the library building process. Adapters were first diluted to 500 μM with ×1 TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8.0, SigmaAldrich). Subsequently, an equimolar concentration of each pair of long and short adapters was mixed together and hybridized through incubation at 95◦C for 1 minute, followed by a decrease in temperature with 0.1◦C/s from 95◦C to 12◦C. After hybridization, adapters AD1 and AD2 were mixed and diluted at a concentration of 10 μM prior to their use in the library construction.
First, the libraries were qPCR-quantified using the CommonprimerBGI forward primer and 1 of the indexed reverse primers. Second, subsequent index PCR amplifications used 8 to 15 cycles with CommonprimerBGI forward primer and the indexed reverse primers. Third, because several of the BGISEQ-500 libraries exhibited residual adapter dimers after the initial purification post-index PCR, each purified BGISEQ-500 library was split to 2 aliquots, and 1 of each aliquot was subject to an extra purification to remove any residual primer dimers. All amplified libraries were subsequently sent to BGI for circularization and sequencing on the BGISEQ-500 platform. For circularization, PCR products with different barcodes were pooled together at equimolar concentration to yield a final amount of 80 ng.

value: late-stage ovarian cancer


title: amniotic fluid fetal cells 3

description: Hybridized to CytoScan 750K


title: T25C-2b


title: amniotic fluid fetal cells 11

description: Hybridized to CytoScan 750K


title: amniotic fluid fetal cells 2

description: Hybridized to CytoScan 750K


title: amniotic fluid fetal cells 1

description: Hybridized to CytoScan 750K


title: T07C-2b


title: T23C-2b


title: N03A-2b

source_name: normal ovary

value: normal ovary


title: N04A-2b


title: amniotic fluid fetal cells 8

description: Hybridized to CytoScan 750K


title: T03C-2b


title: E21B-2b

source_name: early-stage ovarian cancer

value: early-stage ovarian cancer


title: N07A-2b


title: E11B-2b


title: E12B-2b


title: T25C-2


title: T23C-2


title: E09B-2b


title: T07C-2


title: T31C-2


title: N07A-2


title: amniotic fluid fetal cells 4

description: Hybridized to CytoScan 750K


title: N06A-2


title: N04A-2


title: T03C-2


title: E21B-2


title: N06A-2b


title: E11B-2


title: E09B-2


title: fibroblast, NET stimulated, rep1

city: Florence

first: Gabriele

last: Dragoni

address: Viale Pieraccini, 6

country: Italy

institute: University of Florence

description:
read_count_fibro24h_NET1
DEF_PROCESSED_gene_expression_readcounts.xlsx

data_processing:
The sequencing data was filtered with SOAP nuke by removing reads containing sequencing adapter, then removing reads whose low-quality base ratio was more than 20%; finally, reads whose unknown base ('N' base) ratio was more than 5% were also removed to obtain clean reads to be stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
Bowtie2 (http://bowtie-bio.sourceforge.net/index.shtml) was applied to align the clean reads to the gene set, a database built by the service company BGI (Beijing Genomic Institute), in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM (v1.3.1). Differential expression analysis was performed using the DESeq2(v1.4.5) (or DEGseq or PoissonDis) with Q value ≤ 0.05 (or FDR ≤0.001).
GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analyses of DEG (differentially expressed genes) were performed. The significant levels of terms and pathways were corrected by Q value with a threshold ≤ 0.05
Assembly: GCF_000001405.38_GRCh38.p12, GRCh38.
Supplementary files format and content: processed data are presented as readcounts in excel file format

source_name: ileum/small intestine

extract_protocol:
total RNA was extracted using TRIzol reagent (Thermofisher) according to manufacturer's instructions
The quality of libraries was assessed by checking the distribution of the fragment size using the Agilent 2100 bioanalyzer. The double stranded PCR products were then heat-denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) was formatted as the final library.

value: ileum/small intestine

tag: cell type

value: primary intestinal fibroblast

value: NET stimulation


title: fibroblast, unstimulated, rep3

description:
read_count_fibro24h_ctrl4
DEF_PROCESSED_gene_expression_readcounts.xlsx

value: unstimulated


title: fibroblast, unstimulated, rep2

description:
read_count_fibro24h_ctrl3
DEF_PROCESSED_gene_expression_readcounts.xlsx


title: fibroblast, NET stimulated, rep2

description:
read_count_fibro24h_NET3
DEF_PROCESSED_gene_expression_readcounts.xlsx


title: E12B-2


title: fibroblast, unstimulated, rep1

description:
read_count_fibro24h_ctrl1
DEF_PROCESSED_gene_expression_readcounts.xlsx


title: CPVA5

city: Jinan

first: Yinglong

last: Hou

state: ShanDong

address: No. 16766, Jingshi Road, Lixia District, Jinan City, Shandong Province, China

institute: Qianfoshan Hospital of Shandong Province

description: CPVA

data_processing:
The raw image data files obtained by high-throughput sequencing were transformed into the original sequencing sequence by CASAVA Base Calling analysis(Sequenced Reads)
The sequencing quality value Phred.The conversion formula between Quality Score (Q-phred) and Probability of Incorrect Base Call (P) is:Q-phred= -10log10 (P)
The original sequencing sequence contains Low Quality reads with connectors. To ensure the quality of subsequent analysis, it is necessary to remove the connectors and filter out low quality reads. The number of bases with base quality value less than or equal to 25 accounted for more than 60% of the whole reads) and the proportion of N (N means that base information could not be determined) was greater than 5% to obtain clean reads that could be used for subsequent analysis
In this project, the HISAT2 software was used to sequence align CleanReads with the designated genome to obtain information about their position on the reference genome.
The expected number of Fragments PerKilobase of transcript sequence per Millions (FPKM) was calculated for each gene in each sample using featureCounts software base pairs sequenced)
Assembly: canFam3.1
Supplementary files format and content: Include FPKM values for each Sample with xls files.

organism: Canis lupus familiaris

source_name: Atrium

extract_protocol:
For the extraction of total RNA, 1 ml TRIzol (Magen (R4801-02)) was added to the sample ground in liquid nitrogen, and total RNA was extracted by the TRIzol method.  Then, the sample concentration and 260/280, 260/230 ratio were measured and recorded by Nanodrop (ThermoFisher (ND-2000)), and the integrity of RNA was checked by Agilent 4150 (Agilent Technologies Inc).
For the library construction, oligo (DT) beads were used to enrich eukaryotic mRNA, fragmentation buffer was added to randomly interrupt mRNA, mRNA was used as template to synthesize two strands of cDNA, and double-stranded cDNA was purified by AMPure XP beads.  The purified double-stranded cDNAs were end-repaired and A-tailed, and then the fragment size was selected by AMPure XP beads.  Finally, the final cDNA library was obtained by PCR enrichment.

value: Atrium


title: ST2 pLNCX

type: RNA

city: Hamburg

first: Thorsten

last: Schinke

address: Martinistr. 52

department: Department of Osteology and Biomechanics

country: Germany

institute: University Medical Center Hamburg-Eppendorf

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized for 16 h at 45 °C on mouse Clariom D Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: Microarrays were scanned using the Affymetrix GeneChip Scanner 7G.

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC 4.0.1.36) using  default analysis settings (version 2) and Gene + Exon - SST-RMA as summarization and normalization method.

label: biotin

source_name: ST2, 5d 1 µg pLNCX

label_protocol: Proprietary labeled 2nd-cycle ss-cDNA was prepared from 100 ng total RNA using the mouse Clariom D kit according to the GeneChipTM WT PLUS Reagent Kit Manual Target Preparation for GeneChipTM Whole Transcript (WT) Expression Arrays user guide (version 23 January 2017) from ThermoFisher Scientific

growth_protocol: ST2 cells were plated at a density of 10000 cells/cm² in 12-well format cell culture dishes. Cells were cultured in alpha-MEM with 10% FCS at 37 °C, 5 % CO2, 95 % rH until 80-90 % confluency.

extract_protocol: RNA was extraced 5 days after transfection using the Nucleospin RNA kit (Macherey-Nagel) according to the manufacturer's instructions.

treatment_protocol: ST2 cells transfected with 1 µg plasmid/well using Lipofectamine 2000.

tag: cell tylinepe

value: pLNCX


title: CPVA3

description: CPVA


title: CPVA1

description: CPVA


title: CPVA2

description: CPVA


title: Control5

description: control


title: Control4

description: control


title: ST2 pLNCX-Wnt1

source_name: ST2, 5d 1 µg pLNCX-Wnt1


title: WGS_MALT tumor sample

city: New Haven

first: Rong

last: Fan

state: Connecticut

address: 55 Prospect St.

department: Biomedical Engineering

institute: Yale University

description: somatic.snvs.vcf.gz

library_source: genomic

data_processing:
Raw FASTQ files were mapped to the human GRCh38 reference genome using BWA V0.7.17. Duplicate reads were marked by GATK V4.2.0.0 and removed with samtools V1.16.1. De-duplicated BAM files were then used to call somatic mutations with Strelka V2.9.10 in somatic mode.
Assembly: human GRCh38
Supplementary files format and content: Somatic Variant Call Format (VCF) file
Library strategy: whole genome sequencing

source_name: Lymph node

extract_protocol:
FFPE tissue sections were deparaffinized and decrosslinked following the standard procedures. Total DNA was extracted and purified using the Qiagen DNeasy Blood & Tissue Kit according to the manufacturer’s protocol.
Samples underwent quality control via agarose gel electrophoresis. Genomic DNA was randomly sheared into shorter fragments, which were end-repaired, A-tailed, and ligated with Illumina adapters. The adapter-ligated fragments were size-selected, PCR amplified, purified, quantified, and sequenced at 50X depth on an Illumina NovaSeq system with a 150bp paired-end read length.

value: Lymph node

tag: disease

value: Lymphoma


title: WGS_Paired normal tissue sample

description: somatic.snvs.vcf.gz

source_name: Gastric tissue

value: Gastric tissue

value: Normal


title: N03A-2


title: Control2

description: control


title: Control3

description: control


title: fibroblast, NET stimulated, rep3

description:
read_count_fibro24h_NET4
DEF_PROCESSED_gene_expression_readcounts.xlsx


title: PMBC_Day7_8091

first: Dhivyaa

last: Rajasundaram

state: PA

description:
RNAseq
d7_8091_ALC220A166_S11

data_processing:
Quality-controlled RNA sequencing reads were aligned to the human genome (hg38/GRCh38) using STAR aligner (version 2.6.1), and gene-level read counts were calculated using featureCounts based on Ensembl annotation (GRCh38.96). The assembled count values were used as the input for the differential gene expression analysis between the different conditions and time points using DESeq2. The resulting differentially expressed genes between the groups were defined at cut-off criteria of |log2fold-change| ≥ 1.5 andP< .05.
Assembly: hg38/GRCh38
Supplementary files format and content: Count_Data.csv

molecule: polyA RNA

source_name: Blood

growth_protocol: Blood samples were collected using BD Vacutainer serum separator (for antibody titer at day 0 and day 21 postvaccination) and CPT tubes (for PBMC collection at day 0, 7, and 21 postvaccination). Tubes were maintained at room temperature and were delivered for processing within 4 hours of blood draw.

extract_protocol:
The PBMCs were isolated from whole blood, washed, counted, and banked in freezing medium (heat-inactivated fetal bovine serum with 10% dimethyl sulfoxide) in liquid nitrogen until isolation of RNA was performed using a RNeasy Minikit (QIAGEN). Laboratory staff conducting the HAI and MN assays were blinded to vaccine assignment.
Peripheral blood mononuclear cell RNA was assessed for integrity and concentration using an Agilent Tape Station and Qubit Fluorometric Quantification.

value: Blood

value: PBMCs

value: WT

value: Sanofi Pasteur Fluzone (egg-based)


title: PMBC_Day7_8098

description:
RNAseq
d7_8098_ALC220A169_S44


title: PMBC_Day7_8088

description:
RNAseq
d7_8088_ALC220A164_S75


title: PMBC_Day7_8090

description:
RNAseq
d7_8090_ALC220A165_S85

value: Seqirus Flucelvax (cell-based)


title: 174

city: Barretos

first: Rhafaela

middle: Lima

last: Causin

state: SP

address: Antenor Duarte Villela, 1331

department: Molecular Oncology Research Center

country: Brazil

institute: Barretos Cancer Hospital

hyb_protocol: 3 µL of sample containing 100 ng of total RNA were used, a reporter and a capture probe were added and hybridized in the respective genes of interest, according to the manufacturer's instructions (NanoString Technologies).

scan_protocol: the cartridge containing immobilized and aligned reporter complexes were transferred to nCounter® Digital Analyzer (NanoString Technologies), with 280 fields of view. These results were tabulated in RCC (Reporter Code Count) format.

data_processing: Raw data were collected and pre-processed by nSolver™ Analysis Software v4.0 (NanoString Technologies), and further normalization by LoW CV method and differential expression analysis were performed in the R statistical environment (R-project v3.6.3; The R Foundation, Viena, Austria). The data were normalized using the housekeeping method by the NanoStringNorm package (Bioconductor). Normalized data were log2-transformed and used as input for the differential expression analysis.

source_name: Plasma extracellular vesicle

growth_protocol: EVs were isolated from plasma samples by ultracentrifugation (Thermo Fisher Scientific, Inc. Sorvall WX+ Ultracentrifuge Series; TH-660 Swinging Bucket Rotor) following the manufacturer’s instructions and available literature.

extract_protocol: Total RNA was extracted from cervical cancer cells using miRNeasy Mini Kit (Qiagen, Germany) according to the manufacturer’s protocol

tag: group

value: Não recidivou

tag: breast cancer

value: Luminal

tag: origin

value: I live without disease

tag: Sex

value: Female

tag: age

value: 45 years


title: PMBC_Day7_8087

description:
RNAseq
d7_8087_ALC220A163_S65


title: 172


title: 161

value: Recidivou

value: I live with disease

value: 52 years


title: 156

value: Death not related to cancer


title: PMBC_Day7_8072

description:
RNAseq
d7_8072_ALC220A159_S21


title: PMBC_Day7_8084

description:
RNAseq
d7_8084_ALC220A161_S43


title: CPVA4

description: CPVA

value: Atrium


title: Control1

description: control


title: PMBC_Day7_8070

description:
RNAseq
d7_8070_ALC220A158_S10


title: 148

value: Cancer related death

value: 35 years


title: PMBC_Day7_8068

description:
RNAseq
d7_8068_ALC220A156_S74

value: Blood


title: 149

value: 39 years


title: 138


title: PMBC_Day7_8065

description:
RNAseq
d7_8065_ALC220A155_S64

value: PBMCs

value: WT


title: 136

value: 50 years


title: PMBC_Day7_8062

description:
RNAseq
d7_8062_ALC220A152_S31

value: Seqirus Flucelvax (cell-based)


title: 133


title: PMBC_Day7_8053

description:
RNAseq
d7_8053_ALC220A151_S20


title: PMBC_Day7_8044

description:
RNAseq
d7_8044_ALC220A127_S17

value: Sanofi Pasteur Fluzone (egg-based)


title: PMBC_Day7_8042

description:
RNAseq
d7_8042_ALC220A125_S80


title: 129

value: Não recidivou

value: Luminal

value: I live without disease


title: 108

value: Recidivou

value: Female

value: 40 years


title: PMBC_Day7_8041

description:
RNAseq
d7_8041_ALC220A124_S70


title: 100


title: 99

value: 44 years


title: 97

value: 46 years


title: PMBC_Day7_8035

description:
RNAseq
d7_8035_ALC220A121_S38


title: 93

value: 41 years


title: PMBC_Day7_8027

description:
RNAseq
d7_8027_ALC220A119_S16


title: PMBC_Day7_8016

description:
RNAseq
d7_8016_ALC220A116_S69


title: 94

value: 31 years


title: 73

value: Cancer related death


title: PMBC_Day7_7013

description:
RNAseq
d7_7013_ALC220A91_S56

value: Blood


title: PMBC_Day7_7014

description:
RNAseq
d7_7014_ALC220A92_S66

value: PBMCs


title: 50

value: 34 years


title: PMBC_Day7_6032

description:
RNAseq
d7_6032_ALC220A85_S55

value: WT


title: 32

value: 62 years


title: 24

value: follow-up loss

value: 39 years


title: 13

value: Não recidivou

value: Luminal

value: 58 years


title: PMBC_Day7_6023

description:
RNAseq
d7_6023_ALC220A82_S22

value: Seqirus Flucelvax (cell-based)


title: CA

city: London

first: Chi

last: Zhang

address: 15 Cotswold Road

department: Division of Cancer Therapeutics

country: United Kingdom

institute: The Institute of Cancer Research

data_processing:
WGS sequencing reads from WGS was aligned to GRCh38 genome assembly using Burrow-Wheelers aligner. RNA-seq sequencing reads were aligned to GRCh38 genome assembly and GENCODE GRCh38.p13 annotation using STAR programme, followed by processing of the resultant file with SAMtools. Read counting on genomic features was carried out using Rsubread, and the R package DESeq2 was used to perform statistic-based quantification.
Joint variant calling was conducted using GATK 3.8. The aligned WGS or RNA-seq reads, which are stored in .bam format, were first subjected to base quality score recalibration (BQSR). For WGS, the BQSR involves the following steps: read reordering, read group assignment, mark duplicated reads, indel realignment, base score recalibration. For BQSR of RNA-seq reads, and additional step of split ‘N’ bases in reads was performed before indel realignment. SNP sites curated in dbSNP v150 database was used for BQSR. Mutect2 algorithm was used to perform joint variant calling, with WGS reads set as reference control and with germline mutation controls curated in gnomAD database. For variant filtering, the resulting variants were first filtered using GATK (‘FilterMutectCalls’), and SNPs were selected from the results. SNPs within homopolymer runs and repeated elements were further filtered by SNPiR.
Sequence reads were split according to their aligned strands. Sequence read depth of SNP for RNA-seq reads were extracted using ‘mpileup’ module of SAMtools, with a minimum read depth set to 10. The resulting matrix were subjected to log ranking test in the rMATS-DVR programme. For annotation of identified DVRs, the following resources were used to supplement for rMATS-DVR programme: REDIportal, RADAR, RepeatMasker, Gencode v40, and dbSNP v150. To qualify as a DVR, a false discovery rate less than or equal to 5% was required.
Assembly: GRCh38
Supplementary files format and content: Microsoft Excel file,listing the results for differential variants on RNA (DVRs) calling
Library strategy: WGS

source_name: T47D expressing A3B

growth_protocol: T-47D (ATCC HTB-133) cells were obtained from ATCC, and maintained in RPMI-1640 medium supplemented with 10% v/v FBS (PAA), 0.2 Units/ml bovine insulin (Sigma) and 0.5% v/v pen/strep (Gibco). Cells were transduced with lentiviral inducible 3×Flag-A3B-P2A-hUGI-HA cassette, which was maintained with 1 µg/ml puromycin (Gibco

extract_protocol:
Genomic DNA was extracted using Qiagen Genomic-tips 500/G kit following manufacturer’s instructions.Total RNA from T-47D cells were extracted using MagNA pure 96 instrument (Roche), and RNA integrity number was measured by BioAnalyzer 2100 (Agilent).
WGS libraries were constructed by Beijing Genomics Institute Hong Kong, using DNB technology. RNA libraries were constructed and sequenced by BGI using poly-dT enrichment or ribosomal depletion in conjunction with DNB technology on BGISEQ-500 instrument.

value: mammary gland

tag: cell line

value: cell line


title: CM

source_name: T47D expressing inactive mutant A3B

value: A3B (E68/255Q)-inducible


title: 5

value: I live without disease

value: Female

value: 56 years


title: 15

value: 52 years


title: PMBC_Day7_6103

description:
RNAseq
d7_6103_ALC220A88_S23

value: Blood

value: PBMCs

value: Sanofi Pasteur Fluzone (egg-based)


title: M72-lnc-4

data_processing:
WGS sequencing reads from WGS was aligned to GRCh38 genome assembly using Burrow-Wheelers aligner. RNA-seq sequencing reads were aligned to GRCh38 genome assembly and GENCODE GRCh38.p13 annotation using STAR programme, followed by processing of the resultant file with SAMtools. Read counting on genomic features was carried out using Rsubread, and the R package DESeq2 was used to perform statistic-based quantification.
Joint variant calling was conducted using GATK 3.8. The aligned WGS or RNA-seq reads, which are stored in .bam format, were first subjected to base quality score recalibration (BQSR). For WGS, the BQSR involves the following steps: read reordering, read group assignment, mark duplicated reads, indel realignment, base score recalibration. For BQSR of RNA-seq reads, and additional step of split ‘N’ bases in reads was performed before indel realignment. SNP sites curated in dbSNP v150 database was used for BQSR. Mutect2 algorithm was used to perform joint variant calling, with WGS reads set as reference control and with germline mutation controls curated in gnomAD database. For variant filtering, the resulting variants were first filtered using GATK (‘FilterMutectCalls’), and SNPs were selected from the results. SNPs within homopolymer runs and repeated elements were further filtered by SNPiR.
Sequence reads were split according to their aligned strands. Sequence read depth of SNP for RNA-seq reads were extracted using ‘mpileup’ module of SAMtools, with a minimum read depth set to 10. The resulting matrix were subjected to log ranking test in the rMATS-DVR programme. For annotation of identified DVRs, the following resources were used to supplement for rMATS-DVR programme: REDIportal, RADAR, RepeatMasker, Gencode v40, and dbSNP v150. To qualify as a DVR, a false discovery rate less than or equal to 5% was required.
Assembly: GRCh38
Supplementary files format and content: Microsoft Excel file,listing the results for differential variants on RNA (DVRs) calling

source_name: T47D expressing inactive mutant A3B, non-induced, T72

value: 1 ug/ml doxycycline, 72 hours


title: PMBC_Day7_6016

description:
RNAseq
d7_6016_ALC220A81_S11

value: WT


title: M72-lnc-3


title: PMBC_Day7_8036

description:
RNAseq
d7_8036_ALC220A122_S49


title: PMBC_Day7_6007

description:
RNAseq
d7_6007_ALC220A79_S75


title: M72-lnc-2


title: PMBC_Day7_8005

description:
RNAseq
d7_8005_ALC220A115_S59


title: PMBC_Day7_6004

description:
RNAseq
d7_6004_ALC220A76_S43


title: M72-lnc-1


title: M0-lnc-4

source_name: T47D expressing inactive mutant A3B, non-induced, T0


title: PMBC_Day7_6000

description:
RNAseq
d7_6000_ALC220A74_S21


title: PMBC_Day7_5298

description:
RNAseq
d7_5298_ALC220A73_S10


title: M0-lnc-3


title: PMBC_Day7_5297

description:
RNAseq
d7_5297_ALC220A72_S84


title: M0-lnc-2


title: M0-lnc-1

source_name: T47D expressing A3B, non-induced, T0


title: PMBC_Day7_5267

description:
RNAseq
d7_5267_ALC220A69_S53


title: A72-lnc-4

source_name: T47D expressing A3B, non-induced, T72


title: PMBC_Day7_6015

description:
RNAseq
d7_6015_ALC220A80_S85


title: PMBC_Day7_5258

description:
RNAseq
d7_5258_ALC220A42_S17


title: PMBC_Day7_5260

description:
RNAseq
d7_5260_ALC220A43_S28


title: A72-lnc-3


title: PMBC_Day7_5104

description:
RNAseq
d7_5104_ALC220A38_S60


title: A72-lnc-1


title: A72-lnc-2


title: PMBC_Day7_5103

description:
RNAseq
d7_5103_ALC220A37_S49


title: PMBC_Day7_5257

description:
RNAseq
d7_5257_ALC220A41_S6


title: PMBC_Day7_5099

description:
RNAseq
d7_5099_ALC220A36_S38


title: A72-4


title: A0-lnc-1


title: PMBC_Day7_5049

description:
RNAseq
d7_5049_ALC220A34_S16


title: PMBC_Day7_5270

description:
RNAseq
d7_5270_ALC220A71_S74


title: PMBC_Day7_5026

description:
RNAseq
d7_5026_ALC220A28_S37


title: A0-lnc-3


title: PMBC_Day7_5048

description:
RNAseq
d7_5048_ALC220A33_S5


title: A72-1


title: A72-2


title: A24-4

source_name: T47D expressing A3B, non-induced, T24

value: 1 ug/ml doxycycline, 24 hours


title: PMBC_Day7_5019

description:
RNAseq
d7_5019_ALC220A26_S15


title: A0-lnc-2


title: PMBC_Day7_5020

description:
RNAseq
d7_5020_ALC220A27_S26


title: A24-3


title: PMBC_Day7_5001

description:
RNAseq
d7_5001_ALC220A23_S68


title: PMBC_Day7_5009

description:
RNAseq
d7_5009_ALC220A25_S4


title: A24-2


title: A0-lnc-4


title: A72-3


title: PMBC_Day0_8098

description:
RNAseq
d0_8098_ALC220A149_S83

value: Pre-Treatment


title: PMBC_Day7_5085

description:
RNAseq
d7_5085_ALC220A35_S27


title: PMBC_Day0_8097

description:
RNAseq
d0_8097_ALC220A148_S73


title: A0-3


title: A24-1


title: PMBC_Day0_8093

description:
RNAseq
d0_8093_ALC220A147_S63


title: A0-4


title: A0-2


title: PMBC_Day0_8091

description:
RNAseq
d0_8091_ALC220A146_S52


title: PMBC_Day0_5267

description:
RNAseq
d0-5276_ALC220A170_S55


title: A0-1


title: PMBC_Day0_8088

description:
RNAseq
d0_8088_ALC220A144_S30


title: PMBC_Day0_8084

description:
RNAseq
d0_8084_ALC220A141_S82


title: PMBC_Day0_8087

description:
RNAseq
d0_8087_ALC220A143_S19


title: IP_VIRUS_2

city: Wuhan

first: zhu

last: miao

address: jin long street

institute: Wuhan institution of virology

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing. In brief, clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster. Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster. After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-clusters. After these steps, any errors and biases introduced by PCR amplification or sequencing were eliminated.
The de-duplicated consensus sequences were used for m6A site analysis. They were mapped to the reference genome of Homo sapiens from GRCh38 using STAR software (version 2.5.3a) with default parameters.
The exomePeak（Version 3.8）software was used for peak calling,which identifies m6A peaks with bigwig format that can be adapted for visualization on the IGV software (http://www.igv.org).The m6A peaks were annotated using bedtools（Version 2.25.0）.
Assembly: GRCh38
Supplementary files format and content: bigWig

extract_protocol:
Total RNAs were extracted using TRIzol Reagent (Invitrogen, cat. NO 15596026）. DNA digestion was carried out after RNA extraction by DNaseI. The RNA integrity was assessed by Agilent5300 (Agilent) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Qualified RNAs were finally quantified by Qubit4.0 with Qubit™ RNA HS Assay Kit (Life Technologies, Q33224).
50 μg total RNAs were used for polyadenylated RNA enrichment by VAHTS mRNA Capture Beads（VAHTS, cat. NO. N401-01/02）. 20mM ZnCl2 was added to mRNA and incubated at 95℃ for 5min-10min until the RNA fragments were mainly distributed in 100-200 nt. Then 10% RNA fragments was saved as “Input” and the rest was used for m6A immunoprecipitation（IP）.The specific anti-m6A antibody (Synaptic Systems, 202203) was applied for m6A immunoprecipitation. RNA samples of both input and IP were prepared using TRIzol reagent(Invitrogen, cat. NO 15596026). The stranded RNA sequencing library was constructed by KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on DNBSEQ-T7 sequencer (MGI Tech Co., Ltd. China) with PE150 model.

value: Hepatoma cell

value: SARS-CoV-2 infection


title: IP_VIRUS_3


title: IN_VIRUS_2


title: PMBC_Day0_8073

description:
RNAseq
d0_8073_ALC220A140_S72


title: IN_VIRUS_3


title: PMBC_Day0_8070

description:
RNAseq
d0_8070_ALC220A138_S51


title: IN_VIRUS_1


title: PMBC_Day0_8064

description:
RNAseq
d0_8064_ALC220A134_S7


title: PMBC_Day0_8062

description:
RNAseq
d0_8062_ALC220A132_S71


title: IP_MOCK_3

value: Mock


title: IN_MOCK_3


title: PMBC_Day0_8053

description:
RNAseq
d0_8053_ALC220A131_S61


title: PMBC_Day0_8045

description:
RNAseq
d0_8045_ALC220A110_S4


title: IN_MOCK_2


title: IN_MOCK_1


title: PMBC_Day0_8032

description:
RNAseq
d0_8032_ALC220A102_S3


title: PMBC_Day0_8035

description:
RNAseq
d0_8035_ALC220A103_S14


title: PMBC_Day0_8027

description:
RNAseq
d0_8027_ALC220A101_S77


title: IP_MOCK_1


title: PMBC_Day0_8086

description:
RNAseq
d0_8086_ALC220A142_S8


title: IP_VIRUS_1


title: Sfeir002_G3G4_GEX_BlankMPs_IL4MPs

city: Buffalo

first: Lu

last: Li

state: NY

address: 3435 Main Street

institute: University at Buffalo

description:
poly-A RNA
GEX (3' mRNA) library: raw_feature_bc_matrix.h5, Gene Expression matrix contains processed information which was subsequently filtered in R to retain cell barcodes with a minimum of 200 genes
GEX (3' mRNA) library: read 1 FASTQ file contains cell barcode and UMI barcode, read 2 FASTQ file contains transcript

library_source: transcriptomic single cell

data_processing:
CellRanger v4.0.0 count was utilized, aligning gene expression to reference mm10-2020-A to produce gene expression UMI count matrix, input feature_reference.csv was utilized to obtained hashtag oligo  (HTO) counts per cell to be used for demultiplexing
raw_feature_bc_matrix.h5 files were utilized in R with Seurat package filtering to retain only cells that contained at least 200 genes
Seurat HTODemux was utilized to demultiplex samples based on HTO counts
Assembly: mm10-2020-A
Supplementary files format and content: CellRanger output files: raw_feature_bc_matrix.h5, containing both gene expression GEX and hashtag oligo HTO counts
Supplementary files format and content: CellRanger input files: feature_reference.csv, containing antibody hashtag sample assignment

source_name: maxillary gingival tissue

extract_protocol:
Cells from samples were individually tagged utilizing BioLegend TotalSeq-A mouse hashtags then pooled and loaded into the 10X Genomics Chromium Controller where cells were individually encapsulated in an oil droplet with a gel bead, forming Gel-Beads-in emulsion (GEM).  This was perfromed according to the Chromium Single Cell 3' GEM Library and Gel Bead kit protocol.
10X Genomics 3' v3 single-index library prepration protocol for 3' poly-A mRNA capture with sample multiplexing protocol adapted from Stoeckius et al.'s 2017 protocol, as seen: https://cite-seq.com/wp-content/uploads/2019/02/cell_hashing_protocol_190213.pdf
scRNA with HTO sample multiplexing derived from (Stoeckius et al., 2017) protocol

treatment_protocol: At the end of the 7 days disease induction period, mice were sacrificed, and the maxillae were harvested for isolation of gingival immune cells on the ligated side.  Alveolar gingival tissues surrounding the ligated tooth  were dissected and minced in small pieces then digested in 5 ml RPMI with 3.2 mg/ml Collagenase Type IV (Gibco) and 1 mg/ml DNAse for 1 hour (Sigma). Five minutes before the end of digestion, 50 ul of EDTA were added to the digest. Next, 5 ml of RPMI with 1 mg/ml DNAse were added to the collagenase DNAse medium containing digested gingival tissue, and then the mixture was passed through a 70-μm cell strainer to obtain a single cell suspension. The cell suspension was then centrifuged at 1500 xg for 6 minutes in a pre-cooled centrifuge, then the cell pellet was resuspended in PBS with 2% FBS.  The pooled cell suspensions from each treatment group were magnetically labelled with a CD45 microbeads kit (Miltenyi Biotec). The CD45-positive cells were then positively selected by passing the magnetically labelled cell suspension through a MACS column placed in the magnetic field of a MACS separator. The unlabeled (CD45-negative) cells passed through the column, while the labelled (CD45-positive) cells were retained in the column. Next, the column was removed from the magnetic field and the retained CD45-positive cells were eluted into a collection tube by flushing appropriate amount of PBS through the column. The flushed CD45 enriched cell suspensions were counted using AOPI dye using the Nexcelom Cellometer Auto 2000 cell counter (Nexcelom Bioscience)  to determine the number of viable cells. A cell viability of at least 80% was verified before proceeding to the Sc-RNA Seq workflow.

value: maxillary gingival tissue

value: Wild type (Balb/C - 6-8 weeks old)

value: mixed sample (G3:Blank MPs ; G4:IL-4 MPs)

tag: library type

value: mRNA


title: Sfeir002_G3G4_HTO_BlankMPs_IL4MPs

description:
Hashtag-derived oligonucleotide (HTO)
HTO (Antibody Capture for Sample Multiplexing): raw_feature_bc_matrix.h5, Antibody Capture slot contains HTO counts used for sample demultiplexing with Seurat funciton HTODemux
HTO library: read 1 FASTQ file contains cell barcode and UMI barcode, read 2 FASTQ file contains Antibody Hashtag Derived reads

library_source: other

molecule: protein

value: HTO

tag: hto

value: TotalSeq-A0301 anti-mouse Hashtag 1, TotalSeq-A0302 anti-mouse Hashtag 2, TotalSeq-A0303 anti-mouse Hashtag 3, TotalSeq-A0304 anti-mouse Hashtag 4, TotalSeq-A0305 anti-mouse Hashtag 5, TotalSeq-A0306 anti-mouse Hashtag 6, TotalSeq-A0307 anti-mouse Hashtag 7, TotalSeq-A0308 anti-mouse Hashtag 8, TotalSeq-A0309 anti-mouse Hashtag 9, TotalSeq-A0310 anti-mouse Hashtag 10, TotalSeq-A0311 anti-mouse Hashtag 11, TotalSeq-A0312 anti-mouse Hashtag 12, TotalSeq-A0313 anti-mouse Hashtag 13, TotalSeq-A0314 anti-mouse Hashtag 14, TotalSeq-A0315 anti-mouse Hashtag 15


title: Sfeir002_G5_HTO_Ccl2MPs

value: CCL2 MPs

value: TotalSeq-A0308 anti-mouse Hashtag 8, TotalSeq-A0309 anti-mouse Hashtag 9, TotalSeq-A0310 anti-mouse Hashtag 10, TotalSeq-A0311 anti-mouse Hashtag 11, TotalSeq-A0312 anti-mouse Hashtag 12, TotalSeq-A0313 anti-mouse Hashtag 13, TotalSeq-A0314 anti-mouse Hashtag 14, TotalSeq-A0315 anti-mouse Hashtag 15


title: Sfeir002_G1G2_GEX_HealthyControl_Untreated

value: mixed sample (G1:healthy control; G2:untreated)


title: PMBC_Day0_8024

description:
RNAseq
d0_8024_ALC220A100_S67

value: Blood

value: PBMCs


title: PMBC_Day0_8016

description:
RNAseq
d0_8016_ALC220A98_S46

value: WT


title: PMBC_Day0_8005

description:
RNAseq
d0_8005_ALC220A97_S35


title: PMBC_Day0_7100

description:
RNAseq
d0_7100_ALC220A94_S2


title: Sfeir001_G3G4_HTO_BlankMPs_IL4MPs

value: TotalSeq-A0301 anti-mouse Hashtag 1, TotalSeq-A0302 anti-mouse Hashtag 2, TotalSeq-A0303 anti-mouse Hashtag 3, TotalSeq-A0304 anti-mouse Hashtag 4, TotalSeq-A0305 anti-mouse Hashtag 5, TotalSeq-A0306 anti-mouse Hashtag 6, TotalSeq-A0307 anti-mouse Hashtag 7, TotalSeq-A0308 anti-mouse Hashtag 8, TotalSeq-A0309 anti-mouse Hashtag 9, TotalSeq-A0310 anti-mouse Hashtag 10, TotalSeq-A0311 anti-mouse Hashtag 11, TotalSeq-A0312 anti-mouse Hashtag 12, TotalSeq-A0313 anti-mouse Hashtag 13, TotalSeq-A0314 anti-mouse Hashtag 14


title: PMBC_Day0_7015

description:
RNAseq
d0_7015_ALC220A68_S42

value: Pre-Treatment


title: PMBC_Day0_8046

description:
RNAseq
d0_8046_ALC220A111_S15


title: Sfeir001_G5_HTO_Ccl2MPs

value: TotalSeq-A0309 anti-mouse Hashtag 9, TotalSeq-A0310 anti-mouse Hashtag 10, TotalSeq-A0311 anti-mouse Hashtag 11, TotalSeq-A0312 anti-mouse Hashtag 12, TotalSeq-A0313 anti-mouse Hashtag 13, TotalSeq-A0314 anti-mouse Hashtag 14, TotalSeq-A0315 anti-mouse Hashtag 15


title: Sfeir002_G1G2_HTO_HealthyControl_Untreated


title: PMBC_Day0_8041

description:
RNAseq
d0_8041_ALC220A106_S47


title: IP_MOCK_2

value: Hepatoma cell


title: PMBC_Day0_7014

description:
RNAseq
d0_7014_ALC220A67_S31


title: PMBC_Day0_7009

description:
RNAseq
d0_7009_ALC220A65_S9


title: Sfeir001_G1G2_HTO_HealthyControl_Untreated


title: Sfeir002_G5_GEX_Ccl2MPs


title: Sfeir001_G5_GEX_Ccl2MPs


title: PMBC_Day0_6112

description:
RNAseq
d0_6112_ALC220A64_S83


title: Sfeir001_G3G4_GEX_BlankMPs_IL4MPs


title: Sfeir001_G1G2_GEX_HealthyControl_Untreated


title: PMBC_Day0_6101

description:
RNAseq
d0_6101_ALC220A62_S63


title: PMBC_Day0_8023

description:
RNAseq
d0_8023_ALC220A99_S57


title: PMBC_Day0_6032

description:
RNAseq
d0_6032_ALC220A60_S41


title: PMBC_Day0_6037

description:
RNAseq
d0_6037_ALC220A61_S52


title: KO_Stim2

city: Guangdong

first: Shihan

last: Xu

address: North Campus, Sun Yat-Sen University, No. 74, 2nd Yat-Sen Road/Street, Yuexiu District, Guangzhou City

institute: Sun Yat-sen University

data_processing:
Quality control: Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that  Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: mm10
Supplementary files format and content: gene_count.csv

source_name: Bone marrow

growth_protocol: Bone Marrow-Derived Macrophages (BMMs) were isolated from the femurs of euthanized male mice, and cultured in DMEM (Cytiva, USA) containing 50 ng/mL Macrophage Colony-Stimulating Factor (M-CSF, CB34, Novoprotein, China), supplemented with 10% FBS and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen, USA), then enrichment of mRNA with polyA tails was achieved through Oligo(dT) magnetic beads.
First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer.

treatment_protocol: BMMs from two mouse genotypes stimulated with Pg at an MOI of 1:20 for 2 hours

value: Bone marrow

value: Induced primary cells

value: Bone marrow-derived macrophages

value: Pg stimulation


title: KO_Stim1


title: PMBC_Day0_6024

description:
RNAseq
d0_6024_ALC220A58_S19


title: PMBC_Day0_6030

description:
RNAseq
d0_6030_ALC220A59_S30


title: KO_NC2

value: Control


title: KO_NC3


title: PMBC_Day0_6003

description:
RNAseq
d0_6003_ALC220A50_S18


title: HE_NC1


title: HE_Stim1


title: HE_Stim3


title: PMBC_Day0_5099

description:
RNAseq
d0_5099_ALC220A14_S57


title: PMBC_Day0_5298

description:
RNAseq
d0_5298_ALC220A48_S81


title: PMBC_Day0_5214

description:
RNAseq
d0_5214_ALC220A17_S3


title: KO_Stim3


title: PMBC_Day0_5266

description:
RNAseq
d0_5266_ALC220A22_S58


title: PMBC_Day0_6005

description:
RNAseq
d0_6005_ALC220A52_S40


title: PMBC_Day0_5269

description:
RNAseq
d0_5269_ALC220A45_S50


title: HE_NC2


title: PMBC_Day0_6016

description:
RNAseq
d0_6016_ALC220A56_S82


title: PMBC_Day0_6015

description:
RNAseq
d0_6015_ALC220A55_S72


title: KO_NC1


title: PMBC_Day0_5049

description:
RNAseq
d0_5049_ALC220A12_S35


title: HE_NC3


title: PMBC_Day0_5085

description:
RNAseq
d0_5085_ALC220A13_S46


title: PMBC_Day0_5048

description:
RNAseq
d0_5048_ALC220A11_S24


title: HE_Stim2


title: PMBC_Day0_5040

description:
RNAseq
d0_5040_ALC220A10_S13


title: Mouse brain, chronic stress, 4sU, rep4

city: Shanghai

first: Yang

last: Yang

address: 393 Middle Huaxia Road, Pudong, Shanghai

institute: ShanghaiTech University

description:
U5
exon_geneid_chronic_D_PM_CD_U.outs.txt

data_processing:
Raw data from RNA-Seq were preprocessed using Cutadapt v3.1 for adapter sequence/short sequence removal (parameters - minimum length: 15 nucleotides).
Preprocessed data were aligned to the NCBI reference mouse genome (mm10) using Hisat2 v2.1.0
The resulting alignment data in SAM format was converted to BAM format using Samtools v1.9.
The T>C mutation counts for each sample were computed using the software SLAM-DUNK v0.2.4, designed for SLAM-Seq analysis. Annotation data for 3' UTR regions were obtained from the RefSeq and Ensembl databases (parameters - readlength: 150).
Gene expression quantification was performed using FeatureCounts v2.0.1, utilizing the mm10 reference gene GTF file from the UCSC Genome Browser (parameters: Is paired-end, Check for chimeric fragments, Feature type: exon, Attribute type: gene_id).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw T>C mutation values and T coverage for each Sample.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Library strategy: SLAM-seq

source_name: brain

extract_protocol:
RNA was extracted from the bilateral amygdala of mice using the Trizol method, followed by alkylation treatment of the RNA.
RNA libraries for RNA-seq were prepared using VAHTS® Universal V8 RNA-seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: 4sU (100mM desolved in DMSO) or DMSO was injected stereotaxically into mouse amygdala 24h prior to RNA extraction.

value: brain

value: 4-thiouridine injection

tag: stress

value: chronic stress


title: PMBC_Day0_5034

description:
RNAseq
d0_5034_ALC220A8_S76


title: Mouse brain, chronic stress, DMSO, rep2

description:
CD3
exon_geneid_chronic_D_PM_CD_U.outs.txt

value: DMSO injection


title: Mouse brain, chronic stress, DMSO, rep1

description:
CD1
exon_geneid_chronic_D_PM_CD_U.outs.txt


title: Mouse brain, chronic stress, DMSO, rep3

description:
CD5
exon_geneid_chronic_D_PM_CD_U.outs.txt


title: Mouse brain, chronic stress, 4sU, rep3

description:
U4
exon_geneid_chronic_D_PM_CD_U.outs.txt


title: PMBC_Day0_6023

description:
RNAseq
d0_6023_ALC220A57_S8


title: IgG

city: Minato-ku

first: Yuko

last: Shimosato

state: Tokyo

address: 4-6-1 Shirokanedai

department: Molecular Oncology

country: Japan

institute: Tokyo university

data_processing:
Pair-end sequencing FASTQ files were aligned to the murine reference genome (mm10) using Bowtie2on Galaxy platform (https://usegalaxy.org).Peak calling was performed with MACS2 callpeak.Gene list of peak calling was established by using R package CHIPseeker.
Assembly: mm10
Supplementary files format and content: Gene list with FDR =0.1
Library strategy: CUT and RUN

extract_protocol:
1×105 NPM1-CCDC28A cells were collected per sample to perform CUT&RUN assay using CUT&RUN kit (Cell Signaling, #86652)
1×105 NPM1-CCDC28A cells were collected per sample to perform CUT&RUN assay using CUT&RUN kit (Cell Signaling, #86652) with an anti-flag antibody (FUJIFILM catalog 014-22383) and Rabbit (DA1E) mAb IgG XP® Isotype control antibody (Cell Signaling#66362) as negative control.

tag: chip antibody


title: Flag

tag: tissue

value: an anti-flag antibody (FUJIFILM catalog 014-22383)


title: Mouse brain, chronic stress, 4sU, rep1

description:
U2
exon_geneid_chronic_D_PM_CD_U.outs.txt


title: Mouse brain, acute stress, DMSO, rep3

description:
AD5
exon_geneid_acute_D_PM_AD_PP.outs.txt

value: acute stress


title: Mouse brain, chronic stress, 4sU, rep2

description:
U3
exon_geneid_chronic_D_PM_CD_U.outs.txt


title: Mouse brain, acute stress, DMSO, rep1

description:
AD3
exon_geneid_acute_D_PM_AD_PP.outs.txt


title: PMBC_Day0_5030

description:
RNAseq
d0_5030_ALC220A7_S66

value: Blood

value: PBMCs


title: PMBC_Day0_5020

description:
RNAseq
d0_5020_ALC220A5_S45

value: WT


title: Mouse brain, acute stress, DMSO, rep2

description:
AD4
exon_geneid_acute_D_PM_AD_PP.outs.txt


title: PMBC_Day0_5005

description:
RNAseq
d0_5005_ALC220A2_S12

value: Pre-Treatment


title: PMBC_Day0_5019

description:
RNAseq
d0_5019_ALC220A4_S34


title: Mouse brain, acute stress, DMSO, rep4

description:
AD6
exon_geneid_acute_D_PM_AD_PP.outs.txt


title: fetal RPE cells,L-ALKBH3_2

city: Nanjing

first: Ying

last: Wang

address: Guangzhou Road

institute: NanJing Medical University

data_processing:
Raw sequencing data were processed and filtered to produce clean reads, which were aligned to the human genome using the STAR software.
Assembly: hg19
Supplementary files format and content: HTSeq v0.6.0 to calculate the fragments per kilobase per million mapped reads (FPKM) of each gene or transcript.
Supplementary files format and content: The DESeq2 algorithm was applied to identify differentially expressed genes.

source_name: eye

extract_protocol:
Total RNA was extracted from cell lysates and murine tissues using TRIzol reagent (Invitrogen). The quality and quantity of the RNA were assessed with a BioSpec-Nano-2000 spectrophotometer (Nano-Drop Technologies, Wilmington, DE, USA).
Ideal RNA samples were sent for library construction using the Directional RNA Library Prep Kit (GenSeq, Shanghai, China), according to the manufacturer’s instructions. The mRNA is typically fragmented into pieces of ~300 nucleotides in length. cDNA synthesis form the mRNA fragments was then carried out using reverse transcriptase and random hexamer primers. The resulting cDNA fragments were subjected to end-repair and dA-tailing, followed by adapter ligation. These adapter-ligated cDNA samples were subsequently amplified via PCR and purified to yield sequencing libraries. Finally, the libraries were sequenced on an Illumina Novaseq 6000 platform (Illumina) using a paired-end 150 bp mode.

value: eye

value: RPE cells

value: lentivirus transduction


title: PMBC_Day0_5009

description:
RNAseq
d0_5009_ALC220A3_S23


title: fetal RPE cells,L-ALKBH3_3


title: Mouse brain, acute stress, 4sU, rep3

description:
PP14
exon_geneid_acute_D_PM_AD_PP.outs.txt


title: fetal RPE cells,L-ALKBH3_1


title: Mouse brain, acute stress, 4sU, rep4

description:
PP15
exon_geneid_acute_D_PM_AD_PP.outs.txt


title: fetal RPE cells,L-EV_3

value: L-EV


title: Mouse brain, acute stress, 4sU, rep5

description:
PP16
exon_geneid_acute_D_PM_AD_PP.outs.txt


title: fetal RPE cells,L-EV_1


title: Mouse brain, acute stress, 4sU, rep2

description:
PP7
exon_geneid_acute_D_PM_AD_PP.outs.txt


title: fetal RPE cells,L-EV_2


title: PKH26-reduced cells (R6)

city: Shinjuku

first: Tomohiro

last: Tamura

address: Shinanomachi 35

department: Department of Extended Intelligence for Medicine, The Ishii-Ishibashi Laboratory

institute: Keio University School of Medicine

data_processing:
The quality of RNA was assessed using an Agilent 2100 Bioanalyzer, ensuring an RIN value greater than 7 for all samples. The multiplexed library pools were sequenced using 151 bp paired-end reads on the NovaSeq6000 platform (Illumina). Quality control was performed using FastQC.
Assembly: GRCh38
Supplementary files format and content: CSV files include TPM values for each sample

source_name: fallopian tube epithelial organoids

extract_protocol:
Organoids were subjected to RNA extraction using an RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s instructions.
RNA libraries were constructed using the TruSeq Stranded mRNA Library Prep Kit (Illumina).

value: fallopian tube epithelial organoids


title: Mouse brain, acute stress, 4sU, rep1

description:
PP3
exon_geneid_acute_D_PM_AD_PP.outs.txt


title: Mouse brain, baseline, DMSO, rep4

description:
D18
exon_geneid_chronic_D_PM_CD_U.outs.txt
exon_geneid_acute_D_PM_AD_PP.outs.txt

value: baseline


title: Mouse brain, baseline, DMSO, rep3

description:
D17
exon_geneid_chronic_D_PM_CD_U.outs.txt
exon_geneid_acute_D_PM_AD_PP.outs.txt


title: PKH26-retained cells (R3)


title: Mouse brain, baseline, DMSO, rep2

description:
D16
exon_geneid_chronic_D_PM_CD_U.outs.txt
exon_geneid_acute_D_PM_AD_PP.outs.txt


title: OCM_treated4

city: Detroit

first: Grace

middle: Michelle

last: Swanson

state: MI

address: 275 E. Hancock, C.S. Mott Center room 271

institute: Wayne State University

data_processing:
Libraries were quantified on the Qubit and Agilent 2200 Tapestation using the DNA High Sensitivity Screen tape.
Data was demultiplexed using Illumina's CASAVA 1.8.2 software.
Assembly: hg38
Supplementary files format and content: tab-delimited file with raw counts for each sample

extract_protocol:
trizol
Lexogen’s QuantSeq 3’mRNA-seq Library Prep Kit (FWD for Illumina)


title: Mouse brain, acute stress, DMSO, rep5

description:
AD8
exon_geneid_acute_D_PM_AD_PP.outs.txt


title: PMBC_Day0_5026

description:
RNAseq
d0_5026_ALC220A6_S56


title: Mouse brain, baseline, DMSO, rep1

description:
D15
exon_geneid_chronic_D_PM_CD_U.outs.txt
exon_geneid_acute_D_PM_AD_PP.outs.txt


title: Mouse brain, baseline, 4sU, rep5

description:
PM24
exon_geneid_chronic_D_PM_CD_U.outs.txt
exon_geneid_acute_D_PM_AD_PP.outs.txt


title: NT_Control4


title: Mouse brain, baseline, 4sU, rep4

description:
PM23
exon_geneid_chronic_D_PM_CD_U.outs.txt
exon_geneid_acute_D_PM_AD_PP.outs.txt


title: OCM_treated2


title: Mouse brain, baseline, 4sU, rep3

description:
PM22
exon_geneid_chronic_D_PM_CD_U.outs.txt
exon_geneid_acute_D_PM_AD_PP.outs.txt


title: NT_Control3


title: Mouse brain, baseline, 4sU, rep1

description:
PM17
exon_geneid_chronic_D_PM_CD_U.outs.txt
exon_geneid_acute_D_PM_AD_PP.outs.txt


title: NT_Control2


title: Mouse brain, baseline, 4sU, rep2

description:
PM21
exon_geneid_chronic_D_PM_CD_U.outs.txt
exon_geneid_acute_D_PM_AD_PP.outs.txt


title: OCM_treated1


title: P25 neocortex, Chd8 het female, snRNA-seq, rep2

first: James

last: Noonan

state: CT

address: 333 Cedar St

department: Genetics

institute: Yale School of Medicine

description: 10x Genomics, v3 chemistry, dual-indexed

data_processing:
Reads were mapped to the mm10 reference genome using STAR v2.7.9a, using recommended settings to generate genome indices (cellranger reference 2020-A; parameters: --outSAMtype BAM Unsorted --outSAMattributes NH HI AS nM CR CY UR UY GX GN --outSAMprimaryFlag AllBestScore --outSAMmultNmax 10 --outBAMcompression 10 --sjdbOverhang 99 --genomeSAsparseD 3). Reads mapping to more than 10 loci or with more than one best-scoring alignment were discarded. Droplet filtering and generation of nucleus-by-gene count matrices was performed using STARsolo using settings recommended for single-nucleus data (STAR v2.7.9a; parameters: --soloFeatures GeneFull --soloType CB_UMI_Simple  --soloCBwhitelist 3M-february-2018.txt --soloBarcodeReadLength 1 --soloCBmatchWLtype 1MM_multi --soloInputSAMattrBarcodeSeq CR UR --soloInputSAMattrBarcodeQual CY UY  --soloMultiMappers Unique --soloUMIdedup 1MM_CR --soloUMIfiltering - --soloCellFilter EmptyDrops_CR 3000 0.99 10 45000 90000 500 0.01 20000 0.01 10000).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files, which constitute outputs from STARsolo

source_name: cerebral cortex

extract_protocol:
The cerebral cortex was dissected from four litter- and sex-matched pairs of postnatal day (P) 25 wild type and Chd8+/- mice, followed by removal of the medial cortex. These samples were flash-frozen in liquid nitrogen. All 8 samples were processed in parallel for nuclei isolation using the 10x Chromium Nuclei Isolation kit, then loaded onto the 10x Genomics Chromium Controller for single nucleus capture.
Libraries were generated and indexed using the 10x Chromium Next GEM Single-Cell 3' kit with v3 chemistry, then sequenced using standard Illumina protocols on an Illumina NovaSeq 6000, with 28 cycles for read 1 and 90 cycles for read 2.

tag: time point

value: cerebral cortex

value: female

value: Chd8 het

tag: strain


title: P25 neocortex, Chd8 het male, snRNA-seq, rep2

value: male

tag: genotype


title: NT_Control1


title: P25 neocortex, Chd8 het female, snRNA-seq, rep1

description: 10x Genomics, v3 chemistry, single-indexed


title: P25 neocortex, Chd8 het male, snRNA-seq, rep1


title: P25 neocortex, wild type female, snRNA-seq, rep1


title: P25 neocortex, wild type female, snRNA-seq, rep2


title: P25 neocortex, Chd8 het female, bulk RNA-seq, rep3

description:
C34_FH3
Chd8_bulk-RNA-seq_P25-counts.txt

data_processing:
Trimmed reads were mapped to the mm39 reference genome with STAR v2.7.9a (parameters: --outSAMtype SAM --outSAMunmapped Within --outSAMattributes Standard --quantMode GeneCounts) and converted to a sorted BAM file. Gene count matrices were generated using featureCounts from the Subread package (parameters: -p --countReadPairs -s 2 -t exon -g gene_id).
Assembly: mm39
Supplementary files format and content: Tab-separated raw count files, which constitute outputs from featureCounts

extract_protocol:
For embryonic samples, the dorsal telencephalon was dissected from six litter- and sex-matched pairs of wild type and Chd8+/- embryos at two time points: embryonic day (E) 12.5 and E17.5. The medial dorsal telencephalon was removed to avoid capturing the hippocampal primordium and flash-frozen in liquid nitrogen until RNA extraction. For postnatal day (P) 25 samples, the cerebral cortex was dissected from six litter- and sex-matched pairs wild type and Chd8+/- mice, followed by removal of the medial cortex and flash-freezing in liquid nitrogen until RNA extraction. RNA was extracted using either the QIAGEN miRNeasy Micro Kit with on-column DNase digestion (E12.5 samples) or the QIAGEN miRNeasy Mini Kit with on-column DNase digestion (E17.5 and P25 samples).
PolyA-enriched RNA libraries were generated using the Roche Kapa mRNA Hyper Prep Kit, then sequenced (2 x 100bp) using standard Illumina protocols on an Illumina NovaSeq 6000.


title: P25 neocortex, Chd8 het female, bulk RNA-seq, rep2

description:
C31_FH2
Chd8_bulk-RNA-seq_P25-counts.txt


title: P25 neocortex, Chd8 het female, bulk RNA-seq, rep1

description:
C28_FH1
Chd8_bulk-RNA-seq_P25-counts.txt


title: P25 neocortex, wild type female, bulk RNA-seq, rep2

description:
C32_FW2
Chd8_bulk-RNA-seq_P25-counts.txt


title: P25 neocortex, Chd8 het male, bulk RNA-seq, rep3

description:
C35_MH3
Chd8_bulk-RNA-seq_P25-counts.txt


title: P25 neocortex, Chd8 het male, bulk RNA-seq, rep2

description:
C29_MH2
Chd8_bulk-RNA-seq_P25-counts.txt


title: P25 neocortex, Chd8 het male, bulk RNA-seq, rep1

description:
C26_MH1
Chd8_bulk-RNA-seq_P25-counts.txt


title: P25 neocortex, wild type female, bulk RNA-seq, rep1

description:
C27_FW1
Chd8_bulk-RNA-seq_P25-counts.txt


title: P25 neocortex, wild type female, bulk RNA-seq, rep3

description:
C33_FW3
Chd8_bulk-RNA-seq_P25-counts.txt


title: P25 neocortex, wild type male, bulk RNA-seq, rep3

description:
C36_MW3
Chd8_bulk-RNA-seq_P25-counts.txt


title: OCM_treated3


title: P25 neocortex, wild type male, snRNA-seq, rep2


title: E17.5 dorsal telencephalon, Chd8 het female, bulk RNA-seq, rep2

description:
C20_FH3
Chd8_bulk-RNA-seq_E17.5-counts.txt

source_name: dorsal telencephalon

value: dorsal telencephalon


title: E17.5 dorsal telencephalon, Chd8 het female, bulk RNA-seq, rep1

description:
C13_FH2
Chd8_bulk-RNA-seq_E17.5-counts.txt


title: E17.5 dorsal telencephalon, Chd8 het male, bulk RNA-seq, rep1

description:
C14_MH3
Chd8_bulk-RNA-seq_E17.5-counts.txt


title: P25 neocortex, wild type male, snRNA-seq, rep1


title: E17.5 dorsal telencephalon, Chd8 het male, bulk RNA-seq, rep3

description:
C23_MH1
Chd8_bulk-RNA-seq_E17.5-counts.txt


title: E17.5 dorsal telencephalon, Chd8 het female, bulk RNA-seq, rep3

description:
C22_FH2
Chd8_bulk-RNA-seq_E17.5-counts.txt


title: E12.5 dorsal telencephalon, Chd8 het female, bulk RNA-seq, rep2

description:
C9_FH2
Chd8_bulk-RNA-seq_E12.5-counts.txt


title: E17.5 dorsal telencephalon, wild type male, bulk RNA-seq, rep3

description:
C24_MW1
Chd8_bulk-RNA-seq_E17.5-counts.txt


title: E17.5 dorsal telencephalon, wild type female, bulk RNA-seq, rep3

description:
C21_FW1
Chd8_bulk-RNA-seq_E17.5-counts.txt


title: E17.5 dorsal telencephalon, wild type female, bulk RNA-seq, rep2

description:
C17_FW3
Chd8_bulk-RNA-seq_E17.5-counts.txt


title: E12.5 dorsal telencephalon, Chd8 het female, bulk RNA-seq, rep3

description:
C10_FH3
Chd8_bulk-RNA-seq_E12.5-counts.txt


title: E17.5 dorsal telencephalon, wild type female, bulk RNA-seq, rep1

description:
C16_FW2
Chd8_bulk-RNA-seq_E17.5-counts.txt


title: E17.5 dorsal telencephalon, Chd8 het male, bulk RNA-seq, rep2

description:
C19_MH2
Chd8_bulk-RNA-seq_E17.5-counts.txt


title: E17.5 dorsal telencephalon, wild type male, bulk RNA-seq, rep1

description:
C15_MW2
Chd8_bulk-RNA-seq_E17.5-counts.txt


title: E17.5 dorsal telencephalon, wild type male, bulk RNA-seq, rep2

description:
C18_MW3
Chd8_bulk-RNA-seq_E17.5-counts.txt


title: E12.5 dorsal telencephalon, wild type male, bulk RNA-seq, rep3

description:
C12_MW3
Chd8_bulk-RNA-seq_E12.5-counts.txt


title: E12.5 dorsal telencephalon, Chd8 het male, bulk RNA-seq, rep2

description:
C5_MH2
Chd8_bulk-RNA-seq_E12.5-counts.txt


title: E12.5 dorsal telencephalon, Chd8 het female, bulk RNA-seq, rep1

description:
C1_FH1
Chd8_bulk-RNA-seq_E12.5-counts.txt


title: E12.5 dorsal telencephalon, wild type female, bulk RNA-seq, rep3

description:
C11_FW3
Chd8_bulk-RNA-seq_E12.5-counts.txt


title: E12.5 dorsal telencephalon, wild type female, bulk RNA-seq, rep1

description:
C4_FW1
Chd8_bulk-RNA-seq_E12.5-counts.txt


title: P25 neocortex, wild type male, bulk RNA-seq, rep1

description:
C25_MW1
Chd8_bulk-RNA-seq_P25-counts.txt


title: E12.5 dorsal telencephalon, Chd8 het male, bulk RNA-seq, rep1

description:
C2_MH1
Chd8_bulk-RNA-seq_E12.5-counts.txt


title: E12.5 dorsal telencephalon, wild type male, bulk RNA-seq, rep2

description:
C8_MW2
Chd8_bulk-RNA-seq_E12.5-counts.txt


title: P25 neocortex, wild type male, bulk RNA-seq, rep2

description:
C30_MW2
Chd8_bulk-RNA-seq_P25-counts.txt


title: E12.5 dorsal telencephalon, wild type male, bulk RNA-seq, rep1

description:
C3_MW1
Chd8_bulk-RNA-seq_E12.5-counts.txt


title: Cerebellum-Multiplexed-8wk-snRNA-seq

city: Irvine

first: Albert

last: La Spada

state: CA

address: 419 S. Circle View Dr.

department: Neurology

institute: University of California Irvine

data_processing:
Sequencing FASTQ files were demultiplexed before running through the 10X Genomics CellRanger count pipeline (v4.0.0) to generate a feature filtered barcode matrix containing UMI filtered gene counts for each cell barcode. The Seurat R package (v4.2.0) was used to normalize counts, identify variable features, scale data, and cluster nuclei with UMAP dimensional reduction. MULTI-seq barcode FASTQs were run through the deMULTIplex R package to generate sample specific barcode counts for each nucleus, remove doublets and ambiguous nuclei, and classify each nucleus to its animal of origin. Filtered and labeled nuclear clusters were then annotated to their cell type of origin using top cluster specific marker genes with Seurat::FindMarkers, referencing known cell type marker genes and the Mouse Transcriptomic Cerebellar Atlas
Assembly: mm10-3.0.0_premrna
Supplementary files format and content: Seurat R data objects with UMI filtered gene counts, demultiplexed to each animal by MULTIseq barcodes, with animal metadata and cell type annotation

molecule: nuclear RNA

source_name: WT and SCA7-266Q cerebella, two male and two female mice, 8.5-weeks of age, multiplexed with MULTI-seq CMOs

growth_protocol: SCA7-266Q mice (B6.129S7-Atxn7tm1Hzo/J ; JAX#:008682) were maintained on a C57BL/6J background at Duke University DLAR facility in groups of 2-5 per cage with a 12 hour dark-light cycle and free access to food and water. All animal work adhered to NIH guidelines under IACUC approved protocols at Duke University

extract_protocol:
Nuclear isolation with Purkinje nuclei enrichment was performed on snap frozen cerebellum tissue using a modified protocol based closely on Kozareva et.al. 2021 (26), by increasing K2SO4 concentration to 2.8 g / 500 mL Dissociation Buffer which preferentially depletes small, dense nuclei from suspension. The resulting supernatant then contains a nuclear homogenate with elevated Purkinje cell proportions. After nuclei were purified, enriched for PCs, and stained with Hoechst 33342, separate wells representing nuclei from individual animals were labeled with MULTI-seq Cholesterol-Modified Oligos (CMOs) containing unique sample barcodes as described in McGinnis et.al. 2019. Barcoded nuclei from each animal were then sorted into a single collection tube using a BD FACSAria II cell sorter from the Hoechst singlet population before loading onto the 10X Genomics Chromium Controller with the 3’ Gene Expression v3.1 kit.
Sequencing libraries for snRNA and MULTI-seq barcodes were prepared separately from the cDNA as described in McGinnis et.al. 2019

value: cerebellum

value: WT and SCA7-266Q

value: 8.5-weeks of age


title: Cerebellum-Multiplexed-5wk-snRNA-seq

source_name: WT and SCA7-266Q cerebella, two male and two female mice, 5-weeks of age, multiplexed with MULTI-seq CMOs

value: 5-weeks of age


title: M3_IFNg_Hypox

city: South San Francisco

first: Sandra

last: Melo

address: 1 DNA Way

institute: Genentech, Inc.

data_processing:
RNA-seq data were analyzed using HTSeqGenie (https://bioconductor.org/packages/release/bioc/html/HTSeqGenie.html) as follows: first, reads with low nucleotide qualities (70% of bases with quality <23) or matches to ribosomal RNA and adapter sequences were removed. The remaining reads were aligned to the human reference genome (mm10) using GSNAP, allowing a maximum of 2 mismatches per 75-base sequence. Subsequently, the number of fragments was calculated by counting the number of uniquely mapped concordant pairs to the exons of each RefSeq gene using the summarize Overlaps function from the GenomicAlignments package
Assembly: mm10

source_name: BMDMs

extract_protocol:
Total RNA was isolated using the Qiagen RNeasy isolation kit (74104) and quantified with Qubit RNA HS Assay Kit (Thermo Fisher Scientific) and quality was assessed using RNA ScreenTape on 4200 TapeStation (Agilent Technologies).
For sequencinglibrary generation, the Truseq Stranded mRNA kit (Illumina) was used with an input of 100 nanograms of total RNA. Libraries were quantified with Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and the average library size was determined using D1000 ScreenTape on 4200 TapeStation (Agilent Technologies).Libraries were pooled and sequenced on NovaSeq 6000 (Illumina) to generate 30 millions single-end 50-base pairreads for each sample.

value: BMDMs

tag: cell type

value: WT

tag: treatment

tag: treatment time


title: M3_IFNg_TNFa

value: IFNg+TNF


title: M3_IFNg

value: IFNg


title: M3_ctrl

value: ctrl


title: M2_IFNg_IL1b


title: E12.5 dorsal telencephalon, Chd8 het male, bulk RNA-seq, rep3

description:
C6_MH3
Chd8_bulk-RNA-seq_E12.5-counts.txt


title: M2_IFNg_LPS

value: IFNg+LPS


title: E12.5 dorsal telencephalon, wild type female, bulk RNA-seq, rep2

description:
C7_FW2
Chd8_bulk-RNA-seq_E12.5-counts.txt


title: M2_IFNg


title: M2_IFNg_Hypox


title: M1_IFNg_LPS


title: M1_IFNg_Hypox


title: D92_NTC_ctrl

data_processing:
RNA-seq data were analyzed using HTSeqGenie (https://bioconductor.org/packages/release/bioc/html/HTSeqGenie.html) as follows: first, reads with low nucleotide qualities (70% of bases with quality <23) or matches to ribosomal RNA and adapter sequences were removed. The remaining reads were aligned to the human reference genome (hg38) using GSNAP, allowing a maximum of 2 mismatches per 75-base sequence. Subsequently, the number of fragments was calculated by counting the number of uniquely mapped concordant pairs to the exons of each RefSeq gene using the summarize Overlaps function from the GenomicAlignments package
Assembly: hg38

source_name: hMDMs

value: hMDMs


title: M2_IFNg_TNF


title: D91_NTC_IFNg


title: D92_NTC_TNF_IFNg


title: M1_ctrl


title: M1_IFNg


title: M2_ctrl


title: D91_NTC_TNF_IFNg


title: M1_IFNg_IL1b


title: D91_NTC_ctrl


title: S209A_1 fed, light polysome

city: San Francisco

first: Haojun

address: 1450 3rd Street

institute: UCSF

data_processing:
Galaxy server at the University of Manchester (https://centaurus.itservices.manchester.ac.uk/)
Sequence reads were trimmed with Trimmomatic.
Trimmed reads were aligned to the mouse genome (Version mm10) using HISAT2
Counts were calculated using Stringtie and annotated using GENCODE.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Library strategy: polysome-seq

source_name: Liver

growth_protocol: Wild type or eIF4E S209A/S209A C57BL/6 mice were were maintained under pathogen-free conditions and all experiments were performed in compliance with guidelines approved by the Institutional Animal Care and Use Committee of UCSF.

extract_protocol:
Samples were seperated using sucrose gradient, and fractions 2-7, and 8-13 were pulled together, same amout of ERCC was added to each pool, PureLink™ RNA Mini Kit (ThermoFisher). 10ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTer® Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian following manufacturer's protocols.

treatment_protocol: For studying ketogenic diet, mice were fed with either chow or ketogenic diet for 24h. Fed mice were available to food all the time.

value: Liver

value: Male

value: eIF4E S209A/S209A

value: Fed chow

tag: time

tag: group

value: light polysome


title: S209A_1 fed, heavy polysome

value: heavy polysome


title: D92_NTC_IFNg


title: M3_IFNg_IL1b


title: D37_NTC_IFNg_TNF


title: M3_IFNg_LPS


title: WT_3 fed, light polysome


title: D37_NTC_ctrl


title: D37_NTC_IFNg


title: WT_3 fed, heavy polysome


title: WT_2 keto, heavy polysome

value: Fed ketogenic diet


title: M1_IFNg_TNF


title: WT_2 keto, light polysome


title: D7_WTAP_IC

data_processing:
RNA-seq data were analyzed using HTSeqGenie (https://bioconductor.org/packages/release/bioc/html/HTSeqGenie.html) as follows: first, reads with low nucleotide qualities (70% of bases with quality <23) or matches to ribosomal RNA and adapter sequences were removed. The remaining reads were aligned to the human reference genome (mm10) using GSNAP, allowing a maximum of 2 mismatches per 75-base sequence. Subsequently, the number of fragments was calculated by counting the number of uniquely mapped concordant pairs to the exons of each RefSeq gene using the summarize Overlaps function from the GenomicAlignments package
Assembly: hg38

value: WTAP

value: PolyIC


title: D7_WTAP_R848


title: D7_WTAP_LPS

value: LPS


title: WT_1 keto, light polysome


title: D7_ZC3H13_IC


title: WT_2 chow, heavy polysome


title: WT_1 chow, light polysome


title: D7_WTAP_ctrl


title: D7_NTC_IC

value: NTC


title: WT_1 chow, heavy polysome

value: WT


title: PSC, KPC inverse, 72 h control, rep 3

city: Halle (Saale)

first: Anais

last: Zourelidis

state: Sachsen-Anhalt

address: Ernst-Grube-street 40

department: General Surgery

institute: University hospital Halle

data_processing:
Data was processed as per Novogene standard protocols. CASAVA was used for base calling.
Raw reads were processed through fastq, and therefore, reads containing adapters, reads containing > 10 % bases that could not be determined, and low-quality reads (Qscore of over 50% bases of the read <= 5) were removed. CG content distribution and base error rate were determined for a quality check. Subsequent analyses were carried out with the clean data. For mapping the reads to the reference genome, mus musculus (Genom ID ensembl\_mus\_musculus\_grcm38\_p6\_gca\ _000001635\_8), the HISAT2 algorithm v2.0.5 was used. Reads were quantified using FeatureCounts v1.5.0-p3, and fragments per kilobase per million mapped reads (FPKM) of the genes were calculated.
For differential gene expression analysis, the DESeq2 R package v1.20.0 was used. This process involved the calculation of log2FoldChange, p-values, and adjusted p-values (padj), employing the Benjamini and Hochberg method to control the false discovery rate. Enrichment analysis, such as Gene Ontology (GO)- and Kyoto Encyclopedia of Genes and Genomes (KEGG)-analysis, was performed using the ClusterProfiler v3.8.1 R package.
Assembly: mm10
Supplementary files format and content: text file includes FPKM values for each sample

source_name: Pancreatic stellate cell

growth_protocol: PSC were cultured in DMEM low glucose medium (Sigma-Aldrich, Germany) supplemented with 40 % Nutrient mixture F12 (Gibco, UK), 16 % FBS (Sigma-Aldrich, Germany), 1 % Amphotericin B (Sigma-Aldrich, Germany) and 1 % penicillin/streptomycin (Gibco, UK).

extract_protocol:
RNA was harvested using direct-zol RNA Microprep Kit (Zymo Research, Germany). 450 ng (standard) or 120 ng (inverse) of total RNA was used for construction of sequencing libraries.
RNA libraries for RNA Seq were prepared by Novogene (Cambridge, United Kingdom) using Novogene NGS RNA Library Prep Set (PT042).

treatment_protocol: For standard co-culture, 1 x 105 KPC cells were seeded in the bottom of a 6-well dish and 1 x 105 PSC from wild-type C57BL/6J mice were seeded separately on top of the porous membrane of a culture-insert. After 24 h, the culture medium was changed, and the co-culture insert with PSC was transferred into the well with KPC cells. For inverse co-culture, culture inserts were turned around 180 °, and 1 x 105 KPC cells were seeded on the bottom of the membrane. After 24 h at 37 °C in 5 % CO2, the insert was turned around 180 ° again, and the attachment of the cancer cells was controlled via microscopy. Then, 1 x 105 PSC were seeded into the culture insert on top of the membrane. Another 24 hours later, the experiment was started. For all co-cultures, Advanced DMEM/F-12 medium (Gibco, UK) supplemented with 10 % FBS (Sigma-Aldrich, Germany) and 1 % penicillin/streptomycin (Gibco, UK) was used.

value: Pancreatic stellate cell

value: control

value: 72 h control


title: PSC, KPC inverse, 24 h control, rep 3

value: 24 h control


title: PSC, KPC inverse, 24 h treatment, rep 3

value: close paracrine KPC co-culture

value: 24 h treatment


title: D7_NTC_LPS

value: hMDMs


title: D7_NTC_R848


title: PSC, KPC inverse, 72 h treatment, rep 3

value: 72 h treatment


title: PSC, KPC inverse, 72 h control, rep 2


title: D4_WTAP_IC


title: D7_NTC_ctrl

value: ctrl


title: WT_1 keto, heavy polysome

value: Liver

value: Male


title: D7_ZC3H13_LPS


title: PSC, KPC inverse, 24 h control, rep 2


title: D4_WTAP_R848


title: D4_WTAP_LPS


title: PSC, KPC inverse, 72 h control, rep 1


title: D7_ZC3H13_ctrl


title: PSC, KPC inverse, 72 h treatment, rep 2


title: WT_2 chow, light polysome

value: Fed chow

value: light polysome


title: D7_ZC3H13_R848


title: D4_ZC3H13_ctrl


title: PSC, KPC inverse, 72 h treatment, rep 1


title: PSC, KPC inverse, 24 h treatment, rep 2


title: PSC, KPC inverse, 24 h control, rep 1


title: D4_ZC3H13_LPS


title: D4_NTC_IC

value: PolyIC


title: D4_ZC3H13_IC


title: D4_NTC_R848


title: PSC, KPC inverse, 24 h treatment, rep 1


title: PSC, KPC standard, 24 h control, rep 3


title: PSC, KPC standard, 24 h treatment, rep 3

value: distant paracrine KPC co-culture


title: D4_NTC_LPS

value: NTC

value: LPS


title: PSC, KPC standard, 72 h treatment, rep 3

value: Pancreatic stellate cell

value: WT


title: D4_NTC_ctrl


title: PSC, KPC standard, 72 h control, rep 2

value: control

value: 72 h control


title: PSC, KPC standard, 72 h control, rep 3


title: D3_WTAP_IC

value: WTAP


title: PSC, KPC standard, 24 h control, rep 2

value: 24 h control


title: D3_WTAP_R848

value: hMDMs


title: D4_WTAP_ctrl


title: D3_WTAP_LPS


title: D3_WTAP_ctrl


title: PSC, KPC standard, 72 h control, rep 1


title: PSC, KPC standard, 72 h treatment, rep 1

value: 72 h treatment


title: D3_ZC3H13_IC


title: PSC, KPC standard, 72 h treatment, rep 2


title: D3_ZC3H13_R848


title: PSC, KPC standard, 24 h control, rep 1


title: IP RPN11-WT-4

first: Yunchen

last: Luo

address: shanghai hongkou

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
Clean reads of all libraries were aligned to the reference genome (mm10) by Hisat2 software (v2.0.4).
Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA were figured out and chosen by home-made scripts.
Assembly: MM10
Supplementary files format and content: Methylated_RNA_sites.mRNA.xlsx: methylation sites and enrichment information of all samples.

source_name: liver

growth_protocol: All mice were raised under Specific Pathogen Free conditions with a 12-hour dark/light cycle, 20–22 °C and 45–65% humidity with water and food provided ad libitum.

extract_protocol:
Total RNAs were obtained from RPN11 HKO and METTL3 HKO mice with their respective flox/flox mice using TRIzol reagent (catalog T9108, Takara) according to the manufacturer's protocol.
RNA was randomly fragmented to ~200 nt by RNA Fragmentation Reagents. Protein A/G beads were coupled to the m6A antibody by rotating at room temperature for 1 h. The RNA fragments were incubated with the bead-linked antibodies and rotated at 4°C for 4 h. After incubation, the RNA/antibody complexes were washed for several times, and then, captured RNA was eluted from the complexes and purified. RNA libraries for IP and input samples were then constructed with GenSeq® Low Input Whole RNA Library Prep Kit(GenSeq, Inc.) by following the manufacturer’s instructions. Libraries were qualified using Agilent 2100 bioanalyzer and then sequenced in a NovaSeq platform (Illumina).
MeRIP-m6A-mRNA-seq

value: liver

value: male

value: RPN11 flox/flox


title: D3_NTC_R848


title: PSC, KPC standard, 24 h treatment, rep 1

value: 24 h treatment


title: IP RPN11-WT-3


title: D3_NTC_LPS


title: D3_NTC_IC


title: D3_ZC3H13_ctrl

value: ctrl


title: IP RPN11-WT-1


title: IP RPN11-WT-2


title: PSC, KPC standard, 24 h treatment, rep 2


title: IP RPN11-KO-4

value: RPN11 hepatocyte-specific knockout


title: D1_WTAP_R848


title: D3_NTC_ctrl


title: IP RPN11-KO-3


title: D1_WTAP_LPS


title: D1_WTAP_IC

value: PolyIC


title: IP RPN11-KO-2


title: D4_ZC3H13_R848


title: D1_WTAP_ctrl


title: IP METTL3-WT-4

value: METTL3 flox/flox


title: IP RPN11-KO-1


title: D3_ZC3H13_LPS

value: LPS


title: IP METTL3-WT-3


title: D1_ZC3H13_R848


title: IP METTL3-WT-2


title: D1_ZC3H13_LPS


title: IP METTL3-KO-4

value: METTL3 hepatocyte-specific knockout


title: IP METTL3-WT-1


title: D1_ZC3H13_ctrl


title: IP METTL3-KO-3


title: IP METTL3-KO-2


title: RPN11-WT-3


title: D8_METTL3_IFNg

value: METTL3 KO

value: IFNg


title: RPN11-WT-4


title: D1_NTC_LPS

value: NTC


title: RPN11-WT-2


title: D1_NTC_ctrl


title: D1_NTC_R848


title: D6_METTL3_IFNg


title: IP METTL3-KO-1


title: D1_ZC3H13_IC


title: D6_NTC_IFNg

value: WT


title: RPN11-KO-4


title: D8_NTC_IFNg


title: D5_METTL3_IFNg


title: RPN11-KO-2


title: RPN11-WT-1


title: RPN11-KO-3


title: D4_METTL3_IFNg


title: RPN11-KO-1


title: D4_NTC_IFNg


title: METTL3-WT-4


title: D1_NTC_IC


title: D1_NTC_IFNg


title: METTL3-WT-3


title: D1_METTL3_IFNg


title: Keto_eFT508_2 light polysome

source_name: T3M4 tumor from xenograft mouse model

growth_protocol: Female nude mice were were maintained under pathogen-free conditions and sub-Q injected with T3M4 cells. All experiments were performed in compliance with guidelines approved by the Institutional Animal Care and Use Committee of UCSF.

extract_protocol:
Tumors were isolated from mice with different treatment at same time. Then tumors were lysed and lysates were seperated using sucrose gradient, and fractions 2-7, and 8-13 were pulled together, same amout of ERCC was added to each pool, PureLink™ RNA Mini Kit (ThermoFisher). 10ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTer® Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian following manufacturer's protocols.

treatment_protocol: After tumors reached 150 mm3, mice were randomly seperated into different treatment groups, including regular chow with vehicle, ketogenic diet with vehicle, and ketogenic diet with eFT508. Vehicle and eF5508 were orally treated everyday from Monday to Friday. Mice were available to food all the time.

value: T3M4 tumor from xenograft mouse model

value: Male

value: Ketogenic diet and eFT508 treatment

value: light polysome


title: METTL3-WT-2

value: liver

value: male


title: METTL3-KO-4


title: METTL3-KO-3


title: Keto_eFT508_2 heavy polysome

value: heavy polysome


title: D5_NTC_IFNg

value: hMDMs


title: METTL3-KO-2


title: Keto_Veh_2 light polysome

value: Ketogenic diet and vehicle treatment


title: METTL3-KO-1


title: liver, RPN11-WT-3

data_processing:
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome with hisat2 software (v2.0.4).
HTSeq software (v0.9.1) was used to get the raw count, and edgeR was used to perform normalization, then differentially expressed mRNAs were identified by p-value and fold change.
Assembly: MM10
Supplementary files format and content: Gene Expression Profiling.xlsx: raw counts, normalized counts and annotations of all samples of the gene.

extract_protocol:
Total RNAs were obtained from RPN11 HKO and METTL3 HKO mice with their respective flox/flox mice using TRIzol reagent (catalog T9108, Takara) according to the manufacturer's protocol.
Briefly, total RNA was used for removing the rRNAs with GenSeq® rRNA Removal Kit (GenSeq, Inc.). Then, the rRNA-depleted samples were subjected to library construction with GenSeq® Low Input RNA Library Prep Kit (GenSeq, Inc.) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).

value: RPN11 flox/flox


title: Keto_eFT508_1 heavy polysome


title: Chow_Veh_1 light polysome

value: Chow and Vehicle treatment


title: Keto_Veh_1 light polysome


title: Keto_eFT508_1 light polysome


title: Keto_Veh_2 heavy polysome


title: liver, RPN11-WT-4


title: liver, RPN11-WT-1


title: Chow_Veh_2 heavy polysome


title: Keto_Veh_1 heavy polysome


title: liver, RPN11-KO-3

value: RPN11 hepatocyte-specific knockout


title: Chow_Veh_1 heavy polysome


title: liver, RPN11-WT-2


title: METTL3-WT-1

value: METTL3 flox/flox


title: 19278X64 CN01

city: Salt Lake City

first: Dekker

last: Deacon

state: Utah

address: 2000 Circle of Hope Dr #1950

department: Dermatology

institute: University of Utah

data_processing:
The human GRCh38 genome and gene annotation files were downloaded from Ensembl release 104 and a reference database was created using STAR version 2.7.9a
A custom Perl script (smallRNA_pe_umi_extractor.pl from https://github.com/HuntsmanCancerInstitute/UMIScripts) was used to trim adapters and extract the Unique Molecular Index (UMI) from the second read of a paired-end Qiagen small RNA library.
The trimmed reads were aligned to the reference database using STAR options optimized for shorter miRNA reads (>=16 bases matched to the genome, number of mismatches <= 5% of mapped length, splicing switched off).
A second Perl script (bam_umi_dedup.pl) removed duplicates from the aligned BAM file
Mapped reads were assigned to annotated miRNAs in miRbase release 22.1 using featureCounts version 1.6.3.
Assembly: GRCh38
Supplementary files format and content: featureCount output files combined into a single tab-delimited matrix

molecule: other

source_name: Primary human skin, FFPE

extract_protocol:
RNA was extracted from whole unstained sections of FFPE blocks using the RecoverAll Total Nucleic Acid Isolation Kit for FFPE, after CitriSolv de-parrafinization.
small RNA library prep
RNA libraries were constructed using the Qiagen QIAseq miRNA Library Prep

value: Primary human skin, FFPE

tag: sample type

value: Cutaneous Nevus

tag: years in_ffpe

tag: gender

value: M

tag: rna concentration_(ng/ul)

tag: biopsy type

value: SHAVE

tag: % melanocytic_estimate


title: 19278X63 CM18

value: Cutaneous Melanoma


title: liver, RPN11-KO-1

tag: Sex


title: liver, METTL3-WT-4


title: liver, RPN11-KO-4


title: 19278X62 CM14

value: F


title: liver, METTL3-WT-3


title: 19278X61 AN18

value: Acral Nevus


title: liver, METTL3-WT-2


title: liver, METTL3-WT-1


title: Chow_Veh_2 light polysome

value: T3M4 tumor from xenograft mouse model

value: Male

value: WT

value: light polysome


title: 19278X59 AM07

value: Acral Melanoma

value: PUNCH


title: 19278X60 AN2


title: liver, METTL3-KO-3

value: liver

value: male

value: METTL3 hepatocyte-specific knockout


title: liver, METTL3-KO-4


title: liver, RPN11-KO-2

value: RPN11 hepatocyte-specific knockout


title: liver, METTL3-KO-2


title: liver, METTL3-KO-1


title: 19278X56 CN21

value: Primary human skin, FFPE


title: Ileum, male, PFAS, rep9

first: Katherine

last: Gurdziel

address: 275 E. Hancock

data_processing:
Aligned to mm10 with STAR
Tabulated to gene regions using htseq count
ANOVA like analysis in edgeR
Assembly: mm10
Supplementary files format and content: Excel file R results

source_name: Ileum

extract_protocol:
Total RNA was harvested from ileum samples from male mice via the phenol-chloroform method using TRI Reagent. The RNA purity and quantity were measured using a spectrophotometer. 1 ug of total RNA was used for the construction of sequencing libraries.
Lexogen QuantSeq 3' mRNAseq

treatment_protocol: Male and female B6.129S7-Ldlrtm1Her/J mice (Ldlr-/-) mice were fed an atherogenic diet (Clinton/Cybulsky low fat diet, 0.15% cholesterol) for one week prior to the beginning of PFAS exposure, then continued on the atherogenic diet for the remainder of the study. Mice were exposed to either control water or water containging a mixture of 5 PFAS (PFOA, PFOS, PFNA, PFHxS, and GenX) each at a concentration of 2mg/L for 7 weeks.

value: Ileum

value: LDLR KO

value: PFAS Water


title: Ileum, male, PFAS, rep10


title: 19278X52 CN03

value: Cutaneous Nevus

value: M

value: SHAVE


title: 19278X55 CN20

value: F


title: Ileum, male, PFAS, rep8


title: 19278X53 CN12


title: 19278X50 CM21

value: Cutaneous Melanoma


title: Ileum, male, PFAS, rep5


title: 19278X51 CM15


title: Ileum, male, PFAS, rep6


title: 19278X49 CM19


title: Ileum, male, PFAS, rep7


title: Ileum, male, PFAS, rep4


title: Ileum, male PFAS, rep3


title: 19278X48 CM11


title: 19278X58 CN14


title: 19278X57 CN13


title: Ileum, male PFAS, rep2


title: Ileum, male, PFAS, rep1


title: 19278X46 CM07


title: Ileum, male, control, rep10

value: Control Water


title: 19278X44 AN11

value: Acral Nevus


title: 19278X45 CM06


title: 19278X54 CN15


title: 19278X42 AN19


title: Ileum, male, control, rep8


title: 19278X43 AN10


title: Ileum, male, control, rep9


title: Ileum, male, control, rep7


title: 19278X40 AN06


title: 19278X39 AN1


title: 19278X38 AM12

value: Acral Melanoma


title: Ileum, male, control, rep5


title: Ileum, male, control, rep3


title: 19278X36 AM13


title: Ileum, male, control, rep2


title: 19278X37 AM06

value: PUNCH


title: 19278X35 AM01

value: EXCISION


title: 19278X34 AM14

value: EXCISION/AMPUTATION


title: 19278X33 AM04


title: WT-input

data_processing:
The library quality was determined by using Agilent 2100 Bioanalyzer (Agilent), and then, subjected to high-throughput 150 base paired-end sequencing on Illumina NovaSeq sequencer.
Raw data were generated after sequencing, image analysis, base calling and quality filtering on Illumina Novaseq6000 sequencer.
Q30 was used to perform quality control.
After adaptor-trimming and low quality reads removing by cutadapt (v1.9.3) software, high quality clean reads were generated.
Clean reads were aligned to reference genome using bowtie2 software (v2.2.4) with default parameters. Peak calling was performed with MACS software (v2.2.7.1).
Differentially enriched regions were identified by diffReps software (v1.55.4).The enriched peaks were then annotated with the latest UCSC RefSeq database to connect the peak information with the gene annotation.
Assembly: MM10
Supplementary files format and content: H3K23Pr-KO-IP_vs_KO-input_peaks.xls: peak of H3K23Pr-KO-IP
Supplementary files format and content: H3K23Pr-WT-IP_vs_WT-input_peaks.xls: peak of H3K23Pr-WT-IP

extract_protocol:
1% formaldehyde was used to crosslink proteins and DNA for 10min. Cell lysates were sonicated to obtain DNA fragments, then immunoprecipitated with 3 µg anti-H3K23pr at 4 °C for 12-16 hours. The complexes were rotationally incubated with 30 µL ChIP-Grade Protein G Magnetic Beads for 2hr at 4 °C.
Chromatin Immunoprecipitation was performed with GenSeq® Chromatin Immunoprecipitation (ChIP) Kit (GenSeq Inc.) according to the manufacturer’s instructions.The yield of ChIPed DNA was determined via Quant IT fluorescence assay (ThermoFisher), and sequencing libraries were generated with GenSeq® Rapid DNA Library Prep Kit (GenSeq Inc.) by following the manufacturer’s manual.

value: liver

value: male

value: RPN11 flox/flox

tag: chip antibody


title: 19278X32 CN08

tag: tissue

value: Primary human skin, FFPE


title: H3K23Pr-WT-IP

value: H3k23pr(PTM Biolabs, PTM-208)


title: KO-input

value: RPN11 hepatocyte-specific knockout


title: 19278X41 AN08


title: 19278X31 CN06

value: Cutaneous Nevus


title: Ileum, male, control, rep6

value: Ileum

value: LDLR KO


title: H3K23Pr-KO-IP


title: 19278X28 AM18

value: M