title: T2385_PS50: Saliva - Smoker (96)

city: Columbus

first: Peter

last: Shields

state: OH

address: 420 West 12th Ave

institute: The Ohio State University

data_processing:
FASTQC was used for basecalling.
Sequences were trimmed for adaptor sequences by cutadapt and aligned to human genome (hg19) by TopHat version 2.1.0 with parameteres -p 8 --no-coverage-search --library-type fr-firststrand hg19.genome Read1.fastq.gz Read2.fastq.gz
Reads that were not mapped to the human genome were aligned to complete genomes of microbes downloaded from the NCBI Refseq database (dated March 2018). Kraken v. 1 was used for alignment with the parameters: kraken --preload –Kraken_Database --fastq-input --gzip-compressed --paired Microbiome_Read1.fastq.gz Microbiome_Read2.fastq.gz --output Microbial_alignment. Resulting alignment files were then converted into a read count table: kraken-report -Kraken_Database Microbial_alignment.
Aligned reads by Kraken were then provided to Bracken v.1 to align to bacterial species using the following parameters: python est_abundance.py -i BAL_Samples_Full_Kraken_subanalysis -k KMER_DISTR.txt
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited files include raw bacterial counts for each subject
Supplementary_files_format_and_content: Matrix table with raw gene counts with aligned bacteria species for every sample. One matrix table for saliva samples. One matrix table for BAL samples.

organism: human saliva metagenome

source_name: Saliva

extract_protocol:
BAL and Saliva was stored in RNAlater solution at -80°C. Samples were thawed and spun to pellet cells, and supernatants were removed. RNA was extracted using QIAzol lysis reagent and miRNeasy Mini kit (Cat. # 217004). 200 ng total RNA was used to construct sequencing libraries
Total RNA was treated with Illumina TruSeq Stranded Total RNA Gold to remove rRNA, and libraries were prepared using Illumina TruSeq kit.

tag: smoking status

value: Smoker

value: Cell from saliva


title: T2391_PS56: Saliva - Never-Smoker (53)

status: Public on Jul 13 2022

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

value: Never-Smoker

tag: cell type


title: Viewpoint PGJB2, replicate 2

city: Lausanne

first: Anaïs

last: LE NABEC

address: Station 19

country: Switzerland

institute: EPFL

library_source: genomic

data_processing:
library strategy: 4C-seq
base-calling, alignment, filtering, peak-calling, ouput files are generated with pipe4C pipeline
Assembly: hg19
Supplementary files format and content: rds and wig.gz files

molecule: genomic DNA

organism: Homo sapiens

source_name: SAEC

growth_protocol: Airway epithelial cell medium (PromoCell).Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1,5% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was digested with DpnII, then with NlaIII
200 ng of 4C libraries was used fo inverse PCR with primers and Illumina adapters (P5 and P7) for different viewpoints, with Expand™ Long Template PCR System (Roche) (as described in Krijger et al, 2020). The second inverse PCR were realized with 8-nt index sequence. Inverse PCR for each step were purified by using Nucleomag PCR beads, with a ratio 1.  Sequencing were realized on MiniSeq of Illumina, as single-end reads with 75-bp read length and generated FastQ files.

tag: cell line

value: SAEC

value: small airway epithelial cells


title: Viewpoint PGJB2, replicate 3


title: T2388_PS53: Saliva - Never-Smoker (89)


title: T2382_PS47: Saliva - E-cig User (101)

value: E-cig User


title: Mm_AMB_N200

city: Boston

first: NORC

last: Boston

state: MA

address: 3 Blackfan Circle, CLS0733

institute: Beth Israel Deaconess Medical Center

description: mAMB rep./nucleus #200

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads were demultiplexed to FASTQ format files using bcl2fastq (Illumina; version 2.20.0).
Reads from were aligned with STAR (version 2.6.1) against the GENCODE M16 mouse genome annotation for the GRCm38 assembly, supplemented with the Cre and mCherry sequences. Duplicate alignments were removed using Picard Tools (version 2.18.21). Digital expression matrices were generated from the deduplicated alignments using the Drop-Seq tools <https://github.com/broadinstitute/Drop-seq> software suite (version 2.3.0), specifically the `DigitalExpression` program, counting all unique alignments to both exons and introns.
Assembly: GRCm38
Supplementary files format and content: Digital gene expression matrices (“dge.tsv.gz” files): gene-by-cell counts.

molecule: nuclear RNA

organism: Mus musculus

source_name: single neuron nucleus

extract_protocol:
On the next day, nAmb tissue was homogenized and purified by density-gradient centrifugation into a single-nuclei suspension as previously described (Habib et al., 2016; Todd et al., 2020). The single-nuclei suspension was sorted by FACS to isolate one H2b-mCherry+ nucleus per well of three 96-well plates, which were then centrifuged at 2,500rcf, frozen on dry ice, and stored at -80°C until use.
After purifying the RNA by RNA-clean SPRI reagents (1.5x ratio of SPRI to sample), cDNA libraries were generated from polyadenylated mRNA of each sample using Smart-Seq2 (Picelli et al., 2014), modified as previously described (Tao et al., 2021). Illumina sequencing libraries were prepared from single-nuclei cDNA samples as described previously (Tao et al., 2021) and then sequenced by Illumina Next-Seq 500.

treatment_protocol: The ventrolateral medulla of five male Chat-Cre mice was injected with a Cre-dependent reporter virus, AAV-DIO-H2b-mCherry. Four weeks later, at the age of 27 weeks, mice were rapidly decapitated for brain extraction to avoid stress related changes in nuclear mRNA. Following immediate brain extraction, 1 mm thick coronal sections of hindbrain through the nAmb’s full rostral-caudal extent (Bregma -6.5 mm to -8.0 mm) were cut and immersed in ice-cold RNA-later (Qiagen catalog # 76106). After at least 30 minutes in ice-cold RNA-later, the nAmb was visualized under a fluorescence stereomicroscope (Zeiss Discovery V8) and dissected, then stored in RNA-later overnight at 4°C.

tag: strain

tag: tissue

value: brain

tag: brain region

value: nucleus ambiguus


title: SD_677_H3K4me3

city: PADOVA

first: GIUSEPPE

last: PERSICO

state: PD

address: VIA UGO BASSI 58/B

country: Italy

institute: UNIVERSITA' DI PADOVA

data_processing:
Reads were aligned to the mm10 reference genome using ”bwa aln” (v0.6.2-r126).
Unmapped reads (reads with a MAPQ smaller than 1), reads that mapped outside of chr1-19 and chrX, as well as duplicate reads were removed using samtools (v0.1.18).
Merged BAM files of each group were binarized using the “BinarizeBam” command. Then, the chromatin state model was trained using the “LearnModel” command for 8 outcome states.
Genome_build: mm10
Supplementary_files_format_and_content: Bed file of genomic bins coordinate and their relative associated 'chromatin state' flag, obtained as described in metadata information

source_name: Liver 3m SD rep6

growth_protocol: Inbred C57BL/6 female mice of 3, 6 and 12 months of age were fed with standard diet (SD). The fourth C57BL/6 female group were fed  30% caloric restriction (CR) diet.

extract_protocol:
Chromatin was extracted using a PAT-ChIP protocol
Library were prepared in according to HT-ChIP-Seq Library Preparation protocol

treatment_protocol: Mice were sacrificed by cervical dislocation and livers were washed in phosphate buffer (PBS) and incubated overnight at room temperature (RT) in 4% formalin solution. Formalin-fixed samples were then dehydrated by increasing concentration of ethanol (from 70% to 100%) and subsequently included in paraffin.

value: liver

tag: chip antibody

tag: treatment

value: Standard diet

tag: age

value: 3 months

tag: Sex

value: female


title: Mm_AMB_N201

description: mAMB rep./nucleus #201


title: Mm_AMB_N208

description: mAMB rep./nucleus #208


title: Mm_AMB_N199

description: mAMB rep./nucleus #199


title: T2375_PS40: Saliva - Never-Smoker (64)


title: T2377_PS42: Saliva - Smoker (97)


title: T2381_PS46: Saliva - E-cig User (77)


title: Mm_AMB_N198

description: mAMB rep./nucleus #198


title: Mm_AMB_N197

description: mAMB rep./nucleus #197


title: T2370_PS35: Saliva - Smoker (62)


title: T2372_PS37: Saliva - E-cig User (88)


title: T2369_PS34: Saliva - Never-Smoker (73)


title: T2367_PS32: Saliva - E-cig User (79)


title: Mm_AMB_N196

description: mAMB rep./nucleus #196


title: T2363_PS28: Saliva - Smoker (100)


title: T2361_PS26: Saliva - Smoker (67)


title: Mm_AMB_N195

description: mAMB rep./nucleus #195


title: Mm_AMB_N194

description: mAMB rep./nucleus #194


title: T2357_PS22: Saliva - E-cig User (98)


title: T2358_PS23: Saliva - Never-Smoker (60)


title: T2353_PS18: Saliva - Never-Smoker (63)


title: T2355_PS20: Saliva - E-cig User (87)


title: T2349_PS14: Saliva Never-Smoker (70)


title: T2350_PS15: Saliva - Smoker (102)


title: T2347_PS12: Saliva - E-cig User (55)


title: T2345_PS10: Saliva - E-cig User (58)


title: Mm_AMB_N192

description: mAMB rep./nucleus #192


title: T2365_PS30: Saliva - Never-Smoker (59)


title: T2340_PS5: Saliva - E-cig User (81)


title: Mm_AMB_N190

description: mAMB rep./nucleus #190


title: Mm_AMB_N189

description: mAMB rep./nucleus #189


title: U87MG_LMO2_2

city: Seoul

first: Sang-Hun

last: Choi

address: Anamro 145

department: Biotechnology

country: South Korea

institute: Korea University

data_processing:
Data were processed using Complete Genomics sequencing instrument.
Briefly, raw reads were filtered through several steps; removing reads with adaptors, removing reads when unknown bases are more than 10%, and have low quality. After filtering, the remaining reads are stored as FASTQ format.
Reads mapping were processed by using Bowtie2 and BWA softwares.
Gene expression was calculated by FPKM method to eliminate the influence of different gene length and sequencing discrepancy.
Finally, a probability value (PA) was calculated to screen differentially expressed genes.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Tab-delimited text file which includes contents; 1) NCBI gene accession ID, 2) Gene length, 3) Means of FPKM values for each experimental sets, 4) Log2 ratio of gene expression, 5) Probability value (PA), 6) Gene symbol, 7) Gene description, 8) KEGG orthology, 9) GO component, 10) GO function, 11) GO process, 12) Blast nr

source_name: Glioblastoma cells

growth_protocol: U87MG cells were grown in DMEM supplemented with 10% FBS, 1% penicillin-streptomycin, 1% L-glutamine, and gentamicin sulfate (50µg/ml).

extract_protocol:
Total RNA was isolated from U87MG cells using TRIzol reagent (3 prime) according to the manufacturer's instructions.
Libraries were prepared for RNA-seq by using CG RNA-seq platform. All procedures were proceeded by Beijing Genomics Institute (BGI) coporation.

value: Malignant glioma-derived cells

value: Brain

value: treated with LMO2 lentivirus for 24 hours


title: Mm_AMB_N193

description: mAMB rep./nucleus #193


title: U87MG_LMO2_1


title: Mm_AMB_N188

description: mAMB rep./nucleus #188


title: U87MG_LMO2_3


title: Mm_AMB_N191

description: mAMB rep./nucleus #191


title: Striatum,Saline,rep4

city: Shanghai

first: Weifang

last: TONG

address: 1239 Siping Road, Yangpu District

country: China

institute: Tongji university

data_processing:
Reads were mapped to a mouse genome (mm9) by using hisat2(v2.1). Gene counts were estimated by HTSeq (0.11).
Assembly: mm9

organism: Mus

source_name: striatum

extract_protocol:
Total RNA was extracted from cultured cells using Trizol reagent (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: striatum

value: Saline


title: T2343_PS8: Saliva - Never-Smoker (44)


title: Cerebellum,Saline,rep4

source_name: cerebellum

value: cerebellum


title: U87MG_con_2

value: treated with control lentivirus for 24 hours


title: nigra,Saline,rep4

source_name: nigra

value: nigra


title: Mm_AMB_N186

description: mAMB rep./nucleus #186


title: Cortex,Saline,rep4

source_name: cortex

value: cortex


title: T2338_PS3: Saliva - Never-Smoker (78)

value: Never-Smoker

value: Cell from saliva


title: nigra,Saline,rep3


title: U87MG_con_1


title: Replacement.eST.rep5

city: Guangzhou

first: Yumei

last: Huang

state: Guangdong

address: Haizhu District Xingangxi Road No. 135

institute: Sun Yat-sen University

data_processing:
After removing adapters by Trimmomatic (version 0.36, used parameters 2:30:10:1:true MINLEN:75), short reads were mapped to the corresponding reference genomes of D. melanogaster (r6.36) and D. simulans (r2.02), respectively, using HISAT (version 2.2.0, --dta and other default parameters).
Expression abundance of each gene was calculated as FPKM and TPM with StringTie (version 2.1.4, used -e and other default parameters). The annotation files of dmel-all-r6.36.gtf and dsim-all-r2.02.gtf were downloaded from FlyBase (http://flybase.org/) in October 2020.
HTSeq (version 0.6.0, used parameters -f bam -r name -s no -t exon -m union) was applied to count mapped reads for each gene.
Genome_build: D. melanogaster (r6.36) and D. simulans (r2.02)
Supplementary_files_format_and_content: Tab-delimited text files include FPKM and TPM values for each gene
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Drosophila melanogaster

source_name: Elongating spermatid cyst

growth_protocol: All the flies were raised using cornmeal-sucrose-yeast medium at 25°C with a 12-h light-dark cycle throughout this study.

extract_protocol:
1) For testis samples, adult flies 3-5 days after eclosion were allowed to mate and then testes were dissected in drops of 1× phosphate-buffered saline (PBS) with two pairs of Dumont #5 forceps. For the extraction of total RNA, 20-25 pairs of testes were pooled as a sample. RNeasy Micro Kit (QIAGEN, German) was used for RNA extraction following the manufacturer’s instructions. 2) For single-cyst samples, testes from mated male flies 2-3 days after eclosion were dissected. Two tungsten micro-needles (World Precision Instruments, USA) were used to tear the muscle sheath layer, resulting in germ cell cysts spilling into a drop of 1× phosphate-buffered saline (PBS). The cysts were viewed using an inverted microscope (Leica DMI4000 microscope), and were picked using a glass capillary (BJ-40, Beijing Zhengtian Yi Science and Trade Co. LTD) pulled by a Sutter instrument P-30 with the following parameters: heat#1 = 930; pull = 909. The cysts were staged using the criteria as follows: spermatogonia (SG), 16-cell cysts with cells of <10 μm in diameter for D. melanogaster and < 8 μm in diameter for D. simulans; late primary spermatocytes (pSC), 16-cell cysts with cells of 22-25 μm in diameter; round spermatids (rST), cysts with much more than 32 round or nearly round cells of 14-16 μm in diameter; and elongating spermatids (eST), bundles of 250-350 μm in length. The staged single cyst was transferred into PCR tube by pushing the syringe which was connected with the glass capillary by an infusion tube. Cell lysis, reverse transcription, PCR preamplification and purification of PCR products were conducted using Discover-sc™ WTA Kit V2 (Vazyme Biotech, China) according to the user’s guides.
1) For testis samples, RNA libraries were prepared for sequencing using standard Illumina protocols. 2) For single-cyst samples, RNA-seq libraries were constructed using TruePrep™ DNA Library Prep Kit V2 for Illumina® (Vazyme Biotech, China) and an input of 1 ng amplified cDNAs.

tag: genotype

value: Replacement

value: 2-3 days after eclosion


title: Cortex,Saline,rep3


title: Striatum,Saline,rep2


title: Mm_AMB_N184

description: mAMB rep./nucleus #184

value: brain

value: nucleus ambiguus


title: Striatum,Saline,rep3


title: nigra,Saline,rep2


title: Cortex,Saline,rep2


title: Cerebellum,Saline,rep3


title: Cerebellum,Saline,rep2


title: T2337_PS2: Saliva - Smoker (84)

value: Smoker


title: U87MG_con_3


title: Striatum,Saline,rep1


title: Mm_AMB_N183

description: mAMB rep./nucleus #183


title: Mm_AMB_N182

description: mAMB rep./nucleus #182


title: nigra,Saline,rep1


title: Cortex,Saline,rep1


title: Mm_AMB_N185

description: mAMB rep./nucleus #185


title: Replacement.eST.rep2


title: Cerebellum,Saline,rep1


title: Mm_AMB_N181

description: mAMB rep./nucleus #181


title: Mm_AMB_N179

description: mAMB rep./nucleus #179


title: Mm_AMB_N180

description: mAMB rep./nucleus #180


title: Replacement.rST.rep5

source_name: Round spermatid cyst


title: LVS, rep24

city: LINCOLN

first: Robert

middle: Bristow

last: Moore

state: NE

address: 1901 vine street

department: Biochemistry

institute: University of Nebraska - Lincoln

data_processing:
Trimmomatic was utilized to remove low-quality reads obtained by FastQC, and reads with less than 35 bp were removed from the analysis.
FastQC was applied again and alignments were obtained by using the TopHat2.
Bowtie 2 was utilized for indexing the genes.
Cufflink identified expressed genes and calculated transcript levels in the aligned reads within the TopHat2 generated Sequence Alignment/Map (SAM) formatted files.
Genes transcribed were measured using fragments per kilobase of exon per million (FPKM) reads.
Assembly: Francisella tularensis genome sequences were obtained from NCBI microbial genome database and had the following accession numbers: SCHU S4 (NC_006570.2), MA00-2987 (NZ_CP012372.1), WY96-3418 (NC_009257.1), and LVS (NC_07880.1).
Supplementary files format and content: Cufflinks FPKM data

organism: Francisella tularensis subsp. holarctica

source_name: LVS

growth_protocol: Bacterial strains were cultured in BHI broth to mid-log growth phase.

extract_protocol:
Total RNA was extracted using the FastRNA Pro Blue Kit (MP Biomedicals), and then RNA was treated with DNase I and column purified, as recommended by the respective manufacturer.
To produce the the RNA-Seq libraries, ScriptSeq v2 Complete Library Preparation Kit for Bacteria (Epicentre) was utilized according to the manufacturer's instructions and included Ribo-Zero Ribosomal RNA (rRNA) Reagents for Bacteria to remove rRNA.

treatment_protocol: To preserve RNA integrity, bacterial cultures were added to RNAprotect Bacteria Reagent (Qiagen), as recommended by the manufacturer.

tag: clade

value: Francisella tularensis subspecies holarctica (also referred to as type B)

value: LVS


title: Replacement.eST.rep4


title: LVS, rep22


title: Mm_AMB_N177

description: mAMB rep./nucleus #177


title: Cortex,MPTP,rep4

value: MPTP


title: Replacement.rST.rep4


title: Replacement.rST.rep3


title: LVS, rep21


title: LVS, rep23


title: Replacement.eST.rep3


title: Replacement.rST.rep2


title: Striatum,MPTP,rep3


title: Cerebellum,MPTP,rep4


title: Mm_AMB_N176

description: mAMB rep./nucleus #176


title: LVS, rep20


title: Mm_AMB_N178

description: mAMB rep./nucleus #178


title: Replacement.rST.rep1


title: nigra,MPTP,rep3


title: Replacement.eST.rep1


title: nigra,MPTP,rep4


title: LVS, rep19


title: Mm_AMB_N175

description: mAMB rep./nucleus #175


title: Replacement.pSC.rep5

source_name: Late primary spermatocyte cyst


title: Mm_AMB_N174

description: mAMB rep./nucleus #174


title: Cortex,MPTP,rep3


title: Striatum,MPTP,rep4


title: LVS, rep18


title: Cerebellum,MPTP,rep3


title: Replacement.pSC.rep4


title: Mm_AMB_N173

description: mAMB rep./nucleus #173


title: LVS, rep17


title: Replacement.pSC.rep3


title: Striatum,MPTP,rep2


title: Cortex,MPTP,rep2


title: LVS, rep16


title: Replacement.pSC.rep1


title: LVS, rep15


title: Replacement.pSC.rep2


title: LVS, rep14


title: Mm_AMB_N171

description: mAMB rep./nucleus #171


title: Mm_AMB_N170

description: mAMB rep./nucleus #170


title: Mm_AMB_N169

description: mAMB rep./nucleus #169


title: LVS, rep13


title: nigra,MPTP,rep2


title: Mm_AMB_N172

description: mAMB rep./nucleus #172


title: Replacement.SG.rep6

source_name: Spermatogonion cyst


title: Replacement.SG.rep5


title: Cerebellum,MPTP,rep2


title: Striatum,MPTP,rep1


title: Replacement.SG.rep4


title: Mm_AMB_N168

description: mAMB rep./nucleus #168


title: LVS, rep12


title: Mm_AMB_N167

description: mAMB rep./nucleus #167


title: nigra,MPTP,rep1


title: LVS, rep11


title: Mm_AMB_N187

description: mAMB rep./nucleus #187


title: Mm_AMB_N166

description: mAMB rep./nucleus #166


title: Replacement.SG.rep2


title: Cortex,MPTP,rep1


title: Cerebellum,MPTP,rep1


title: Mm_AMB_N165

description: mAMB rep./nucleus #165


title: LVS, rep9


title: Replacement.SG.rep1


title: Striatum,MPTP+exercise,rep4

value: MPTP+exercise


title: Mm_AMB_N164

description: mAMB rep./nucleus #164


title: dme.KO.eST.rep5


title: Mm_AMB_N163

description: mAMB rep./nucleus #163


title: dme.KO.eST.rep4


title: Cortex,MPTP+exercise,rep4


title: nigra,MPTP+exercise,rep4


title: LVS, rep7


title: LVS, rep8


title: LVS, rep6


title: Mm_AMB_N162

description: mAMB rep./nucleus #162


title: LVS, rep5


title: Mm_AMB_N161

description: mAMB rep./nucleus #161


title: dme.KO.eST.rep2


title: dme.KO.eST.rep3


title: LVS, rep10


title: Mm_AMB_N160

description: mAMB rep./nucleus #160


title: dme.KO.eST.rep1


title: LVS, rep4


title: Striatum,MPTP+exercise,rep3

value: striatum


title: dme.KO.eST.rep6


title: nigra,MPTP+exercise,rep3


title: Mm_AMB_N159

description: mAMB rep./nucleus #159


title: LVS, rep3


title: LVS, rep2


title: Mm_AMB_N158

description: mAMB rep./nucleus #158


title: Mm_AMB_N157

description: mAMB rep./nucleus #157


title: Cerebellum,MPTP+exercise,rep3


title: dme.KO.rST.rep5


title: Striatum,MPTP+exercise,rep2


title: LVS, rep1


title: Mm_AMB_N156

description: mAMB rep./nucleus #156


title: Cerebellum,MPTP+exercise,rep4


title: dme.KO.rST.rep4


title: nigra,MPTP+exercise,rep2


title: Cortex,MPTP+exercise,rep2


title: Mm_AMB_N155

description: mAMB rep./nucleus #155


title: dme.KO.rST.rep2


title: Mm_AMB_N154

description: mAMB rep./nucleus #154


title: Cerebellum,MPTP+exercise,rep2


title: dme.KO.rST.rep6


title: Cortex,MPTP+exercise,rep3


title: dme.KO.rST.rep1


title: Mm_AMB_N153

description: mAMB rep./nucleus #153


title: dme.KO.pSC.rep5


title: dme.KO.rST.rep3


title: Mm_AMB_N152

description: mAMB rep./nucleus #152


title: Mm_AMB_N151

description: mAMB rep./nucleus #151


title: Striatum,MPTP+exercise,rep1


title: dme.KO.pSC.rep3


title: Cerebellum,MPTP+exercise,rep1


title: dme.KO.pSC.rep4


title: Cortex,MPTP+exercise,rep1


title: dme.KO.pSC.rep2


title: KC-KO-Act-3 vs KC-WT-Act-3

type: RNA

city: Cincinnati

first: Mario

last: Medvedovic

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

hyb_protocol: Each mRNA sample was reverse transcribed and tagged with Cy3 or Cy5. Samples labeled with Cy3 or Cy5 were hybridized. After hybridization, slides were washed. Hybridization reactions were performed by the University of Cincinnati Functional Genomics Core (Cincinnati, OH).

scan_protocol: GenePix 4000B (Axon Instruments, Inc., Union City, CA)

data_processing:
Data initially were processed with GenePix 4000B
The file processed_data.txt includes:
*f635_b = Channel 1 median intensity (Background and negative control value subtracted)
*f532_b = Channel 2 median intensity (Background and negative control value subtracted)
*l2r = log2ratio of f635/f532

source_name: Primary keratinocytes (Map3k1 KO-Act)

label_protocol: Labeling of cDNAs and hybridization reactions

growth_protocol: Wild-type and Map3k1ko primary mouse keratinocytes were isolated from the skin of mice at postnatal day 1 and cultured in defined keratinocyte serum free media (DK-SFM, Gibco, Waltham, MA).

extract_protocol: Total RNA was isolated using RNeasy kit (QIAGEN, Valencia, CA) according to the manufacturer’s instructions.

treatment_protocol: When reached 80% confluence, the wild-type and Map3k1ko primary mouse keratinocytes were starved in growth factor-free DK-SFM for 16 hours followed by treatment with 10 ng/ml ActB for 12 hours.

value: Postnatal day 1

value: Skin

value: Map3k1 KO-Act

source_name: Primary keratinocytes (Map3k1 WT-Act)

value: Map3k1 WT-Act


title: Mm_AMB_N150

description: mAMB rep./nucleus #150


title: shMETTL3#2 rep2

first: Yan

last: Xu

address: No. 600 Tianhe Road

institute: The Third Affiliated Hospital of Sun Yat-Sen University

data_processing:
RNA-seq reads were mapped to the human Ensemble genome hg19.
Mapped counts were GC-normalized using EDASeq (v2.0.0)
Differentially expressed genes (DEGs) were calculated by DESeq2 under the following criteria: |log2FC| > 1 and P value < 0.05
Gene set enrichment analysis (GSEA) was conducted using the GSEA software (https://www.broadinstitute.org/gsea/)
Assembly: hg19
Supplementary files format and content: xlsx files containing ensembl gene accession number, gene name and gene counts for each transcript

source_name: shMETTL3-2 LX2 cells-replication 2

growth_protocol: LX2 cells were maintained in DMEM-high glucose medium supplemented with 10% fetal bovine serum (FBS) (PAN, P30-3302). Cells were incubated at 37 ℃ in a humidified atmosphere of 5% CO2.

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction.
Total RNA was extracted and libraries of cDNA were constructed and sequenced by Berry Genomics (Beijing, China). Sequence reads were mapped to the human genome version hg19. GSEA was conducted using the Gene set enrichment analysis (GSEA) software (https://www.broadinstitute.org/gsea/). Sequencing data will be available in the Gene Expression Omnibus database.

treatment_protocol: LX2 was infected with lentivirus-containing supernatants generated in HEK293T supplemented with 1 μg/ml polybrene (Sigma, H9268) for 10 h. Cells were then selected with 1 μg/ml puromycin (Thermo Scientific, A1113803).

value: human hepatic stellate cell line)


title: KC-WT-Ctl-1 vs KC-WT-Act-1

source_name: Primary keratinocytes (Map3k1 WT)

value: Map3k1 WT


title: KC-WT-Ctl-2 vs KC-WT-Act-2


title: Mm_AMB_N148

description: mAMB rep./nucleus #148


title: Mm_AMB_N149

description: mAMB rep./nucleus #149


title: KC-WT-Act-3 vs KC-WT-Ctl-3


title: dme.KO.pSC.rep1


title: nigra,MPTP+exercise,rep1

value: nigra


title: shMETTL3#2 rep1

source_name: shMETTL3-2 LX2 cells-replication 1


title: dme.KO.SG.rep4


title: KC-KO-Act-3 vs KC-KO-Ctl-3

source_name: Primary keratinocytes (Map3k1 KO)

value: Map3k1 KO


title: KC-KO-Ctl-2 vs KC-KO-Act-2


title: Mm_AMB_N147

description: mAMB rep./nucleus #147

source_name: single neuron nucleus


title: dme.KO.SG.rep3

value: 2-3 days after eclosion


title: KC-KO-Ctl-1 vs KC-KO-Act-1


title: dme.KO.SG.rep2


title: Mm_AMB_N145

description: mAMB rep./nucleus #145

value: brain


title: KC-WT-Act-2 vs KC-KO-Act-2


title: shMETTL3#1 rep1

source_name: shMETTL3-1 LX2 cells-replication 1


title: shLuc rep2

source_name: shLuc LX2 cells-replication 2

value: shLuc


title: KUGBM8-40Gy-3

city: Istanbul

first: Nareg

last: Pinarbasi-Degirmenci

address: Rumelifeneri Yolu

country: Turkey

institute: Koç University

description: Samples treated with 40 Gy of ionizing radiation for 4 weeks

data_processing:
Base calling was performed with BGISEQ-500 platforms (BGI)
Sequenced data were converted to FASTQ files using BGISEQ-500 platform at BGI Genome Sequencing Company (Beijing, China).
RNA-seq data were processed and interpreted using Genialis Expressions software (https://www.genialis.com).

source_name: primary glioblastoma cells

growth_protocol: U373,KUGBM8 cells were cultured in DMEM supplemented with 10% fetal bovine serum and %1 Penicillin/Streptomycin.

extract_protocol: For RNA isolation, MN Nucleospin RNA isolation kit was used according to manufacturer's instructions.

treatment_protocol: Cells were exposed to 2 Gy ionizing radiation every day to 4- 6 weeks until total dose reaches 40-60 GY

value: 40 Gy of IR Treatment for 4 weeks


title: Mm_AMB_N143

description: mAMB rep./nucleus #143

value: nucleus ambiguus


title: dme.WT.eST.rep4


title: Mm_AMB_N144

description: mAMB rep./nucleus #144


title: dme.WT.eST.rep5


title: KUGBM8-40Gy-2


title: shLuc rep1

source_name: shLuc LX2 cells-replication 1


title: KC-WT-Act-1 vs KC-KO-Act-1


title: Mm_AMB_N146

description: mAMB rep./nucleus #146


title: shMETTL3#1 rep2

source_name: shMETTL3-1 LX2 cells-replication 2


title: Mm_AMB_N142

description: mAMB rep./nucleus #142


title: KC-WT-Ctl-1 vs KC-KO-Ctl-1


title: KC-WT-Ctl-2 vs KC-KO-Ctl-2


title: dme.WT.eST.rep3

source_name: Elongating spermatid cyst


title: KUGBM8-3

description: Control Sample

value: Control


title: RA patient 3 + PBS [R11]

city: Hannover

first: Maximilian

last: Fuchs

address: Carl-Neuberg-Str. 1

department: IMTTS

country: Germany

institute: Hanover Medical School

data_processing:
Read mapping using Rsubread
Read quantification using Rsubread
Assembly: Homo sapiens GRCh38 dna primary assembly
Supplementary files format and content: csv file containing raw read counts

source_name: from blood

growth_protocol: 3x10^5 cells derived from LRSCs were plated in 100 μl adherence medium (αMEM + GlutaMAX-I (Gibco) + 1 %FCS/1 %PS) per well of a flat-bottom 96 well plate for 90 min (5,5 % CO2 and 37°C). Non-adherent cells were removed by flushing and residual cells were cultured in 200 μl of OC medium (αMEM + GlutaMAX-I (Gibco) + 10 %FCS/1 %PS) supplemented with 30ng/ml hu M-CSF (Peprotech), 10ng/ml hu RANKL (Peprotech) and 1ng/ml hu TGFβ (BioLegend) at 5,5 % CO2 and 37°C. OC medium was replaced on day 3 and 6.

extract_protocol: Total RNA was isolated using RNeasy Plus Mini Kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries by Novogene.

treatment_protocol: 25 μg/ml sCD83 or the corresponding volume of PBS were added on day 0,3,4,5 and 6.

value: from blood

value: monocyte-derived osteoclasts

value: Diseased

value: Mock


title: dme.WT.eST.rep2


title: RA patient 2 + sCD83 [R10]


title: dme.WT.eST.rep1


title: Mm_AMB_N140

description: mAMB rep./nucleus #140


title: KC-KO-Ctl-3 vs KC-WT-Ctl-3

value: Postnatal day 1

value: Skin


title: KUGBM8-2

description: Control Sample


title: RA patient 2 + PBS [R9]


title: Mm_AMB_N139

description: mAMB rep./nucleus #139


title: RA patient 3 + sCD83 [R12]


title: KUGBM8-1

description: Control Sample


title: dme.WT.rST.rep5

source_name: Round spermatid cyst


title: RA patient 1 + PBS [R7]


title: Mm_AMB_N141

description: mAMB rep./nucleus #141


title: dme.WT.rST.rep3


title: U373-60Gy-3

description: Samples treated with 60 Gy of ionizing radiation for 6 weeks

source_name: glioblastoma cells

value: 60 Gy of IR Treatment for 6 weeks


title: RA patient 1 + sCD83 [R8]


title: healthy donor 3 +sCD83 [R6]

value: WT


title: Mm_AMB_N136

description: mAMB rep./nucleus #136


title: healthy donor 3 + PBS [R5]


title: Mm_AMB_N135

description: mAMB rep./nucleus #135


title: dme.WT.rST.rep2


title: dme.WT.rST.rep1


title: healthy donor 2 + sCD83 [R4]


title: Mm_AMB_N134

description: mAMB rep./nucleus #134


title: U373-60Gy-2


title: U373-1

description: Control Sample


title: Mm_AMB_N133

description: mAMB rep./nucleus #133


title: healthy donor 2 + PBS [R3]


title: dme.WT.rST.rep4


title: dme.WT.pSC.rep5

source_name: Late primary spermatocyte cyst


title: Mm_AMB_N138

description: mAMB rep./nucleus #138


title: healthy donor 1 + sCD83 [R2]


title: Mm_AMB_N137

description: mAMB rep./nucleus #137


title: dme.WT.pSC.rep3


title: Mm_AMB_N131

description: mAMB rep./nucleus #131


title: Mm_AMB_N132

description: mAMB rep./nucleus #132


title: healthy donor 1 + PBS [R1]


title: U373-3

description: Control Sample


title: dme.WT.pSC.rep2


title: Mm_AMB_N130

description: mAMB rep./nucleus #130


title: RAI16 KO NIH3T3 cells rep3

first: wen

last: Wang

address: 36 Yunxin Rd.

institute: Tongji University

data_processing:
Raw data were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat2.
FPKM value of each gene was calculated using cufflinks.
Read counts of each gene were obtained by htseq-count.
DEGs were identified using the DESeq (2012) R package functions estimate Size Factors and nbinomTest.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include normalized FPKM values for each Sample

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol. RNA  purity and quantification were evaluated using the NanoDrop2000 spectrophotometer (Thermo   Scientific, USA). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s  instructions.

value: Rai16 KO

value: serum starvation


title: RAI16 KO NIH3T3 cells rep2


title: replicate 1 of colony 2 knocking down DDX18 in cells

city: Tianjin

first: Xiukun

last: Hou

address: Huanhu Road

institute: Tianjin Cancer Institute and Hospital

data_processing:
Illumina RTA software used for image identification and basecalling.
Adaptor sequence and low-quality sequence were trimmed by Trim Galore, then sequence reads were mapped to mm10 genome using Hisat2 with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38
Supplementary files format and content: Processed data files.xlsx includes Normalized count values for each Sample.

source_name: MDA-MB-231 cells

extract_protocol:
Total RNA was extracted with Trizon Reagen (CWBIO) and was subjected to DNase Ｉ(Thermo Scientific) for 30min
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol (VAHTS mRNA-seq V2 Library Prep Kit for Illumina). The mRNA fragmentation and priming was performed using VAHTSFirst Strand Synthesis Reaction Buffer and VAHTS Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double-stranded cDNA（byAxyPrep Mag PCR Clean-up (Axygen)was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using AxyPrep Mag PCR Clean-up (Axygen), and fragments of ~360 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean-up (Axygen), validated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).

value: MDA-MB-231 cells

value: triple negative breast cancer cells

value: DDX18 knockdown (colony 2)


title: RAI16 KO NIH3T3 cells rep1


title: dme.KO.SG.rep1

source_name: Spermatogonion cyst

value: 2-3 days after eclosion


title: U373-2

description: Control Sample


title: dme.WT.pSC.rep1


title: dme.WT.SG.rep7


title: Mm_AMB_N129

description: mAMB rep./nucleus #129

value: brain


title: dme.WT.pSC.rep4


title: U373-60Gy-1


title: Mm_AMB_N128

description: mAMB rep./nucleus #128

value: nucleus ambiguus


title: replicate 2 of colony 1 knocking down DDX18 in cells

value: DDX18 knockdown (colony 1)


title: Wild Type-NIH3T3 cells rep2


title: replicate 1 of colony 1 knocking down DDX18 in cells


title: replicate 2 of colony 2 knocking down DDX18 in cells


title: dme.WT.SG.rep6


title: Mm_AMB_N127

description: mAMB rep./nucleus #127


title: dme.WT.SG.rep5


title: m6A_RIP_cKO_2XY

data_processing:
RNA-seq reads were aligned to the mouse genome version mm10 with HISAT2.1.0.
Differential m6A-modified peaks between RIP and input samples were identified using exomePeak
The longest isoform was retained if a gene has more than one isoform
Motif search was conducted with HOMER
Assembly: mm10
Supplementary files format and content: xlsx files containing ensembl gene accession number, gene name, and m6A peak analysis of indicated genes.

source_name: mouse primary hepatic stellate cells mRNA

growth_protocol: C57BL/6J mice were housed under specific pathogen free conditions. Experiments were performed with animals under ethical conditions approved by the Institutional Animal Care and Use Committee of The Third Affiliated Hospital of Sun Yat-sen University.

extract_protocol:
Total RNA was extracted from HSCs using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction.
The concentration of total RNA was measured by Qubit RNA HS assay kit (Invitrogen, Q32852). 100 μg total RNA was fragmented into 100-200 nt RNA fragments using 10X RNA Fragmentation Buffer (100 mM Tris-HCl, 100 mM ZnCl2 in nuclease-free H2O). The reaction was stopped by adding 10X EDTA (0.5M EDTA). Methylated RNA immunoprecipitation was performed using EpiTM m6A immunoprecipitation kit (Epibiotek, R1804). Briefly, the fragmented RNA was incubated with anti-m6A monoclonal antibody (abcam,ab208577) for 3 h at 4℃ and then with protein A/G magnetic beads (Invitrogen, 8880210002D/10004D) at 4 ℃ for an additional 2 h to obtain immunoprecipitated RNA fragments. The m6A-enriched RNA was purified using TRIzol™ Reagent (Invitrogen, 15596018). The library was prepared by smart-seq method. Both the input samples without IP and the m6A IP samples were subjected to 150-bp, paired-end sequencing on an Illumina NovaSeq 6000 sequencer.  MeRIP-seq data processing

treatment_protocol: Mouse primary HSCs were isolated and cultured for 7 days in vitro for spontaneous activation.

value: primary hepatic stellate cell

value: HSC-specific Mettl3-knockout

tag: rip antibody

value: anti-m6A (Epibiotek, R1804)


title: Control replicate 2

value: Control


title: Wild Type-NIH3T3 cells rep1


title: dme.WT.SG.rep4


title: Wild Type-NIH3T3 cells rep3


title: Control replicate 1


title: m6A_input_cKO_2XY

value: none (input)


title: dme.WT.SG.rep2


title: Mm_AMB_N125

description: mAMB rep./nucleus #125


title: m6A_RIP_cKO_1XY


title: Hu56

city: Houston

first: Humam

last: Kadara

state: TX

address: 2130 W. Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

description: RNA from bronchial airway epithelial brushings from cancer-free waterpipe smokers and non-smokers undergoing diagnostic bronchoscopy

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data.
Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software.
FeatureCounts was used to count the read numbers mapped to each gene. RPKM values for each gene were calculated based on the length of the gene and mapped read counts.
Gene features with positive counts in at least 50% of samples were retained for differential analysis.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file with RPKM values for each sample. Data from all 9 samples are in one file

source_name: Bronchial airway epithelial brushings

extract_protocol:
Total RNA was isolated from homogenized tissues (bronchial airway epithelia) using Qiagen RNeasy mini kit (Qiagen) according to manufacturer’s recommendations. Qubit 4 Fluorometer (Thermo Fisher Scientific, Waltham, MA) was used for measurement of RNA yield, and RNA quality was assessed using the Agilent RNA 6000 Pico Kit (Agilent, Santa Clara, CA).
Library construction was performed based on manufacturer’s recommendation for SMARTer® Stranded Total RNA-Seq Kit v3 – Pico Input RNA Kit (Takara Bio USA Inc., California, USA). Final library quantity was measured by KAPA SYBR® FAST qPCR and library quality evaluated by TapeStation D1000 ScreenTape (Agilent Technologies, CA, USA). Final library size ranged from 300-400 bp with 8-nt dual-indices being used. Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® NovaSeq 6000 instrument (Illumina, California, USA) with a read length configuration of 150 PE for 80 M PE reads per sample (40M in each direction).

value: Bronchial airway epithelial cells

tag: donor

value: Patient 8

tag: waterpipe smoking history

value: No

tag: cigarette smokeing history


title: Mm_AMB_N124

description: mAMB rep./nucleus #124


title: Hu63

value: Patient 9


title: dme.WT.SG.rep1


title: Mm_AMB_N123

description: mAMB rep./nucleus #123


title: m6A_input_cKO_1XY


title: m6A_RIP_Control_2XY

value: WT


title: Hu53

value: Patient 7

value: Yes


title: Mm_AMB_N126

description: mAMB rep./nucleus #126


title: Mm_AMB_N122

description: mAMB rep./nucleus #122


title: Replacement.tes.rep2

source_name: Testis

value: Replacement

value: 3-5 days after eclosion


title: Mm_AMB_N121

description: mAMB rep./nucleus #121

value: brain


title: Hu52

value: Patient 6


title: Replacement.tes.rep1


title: Mm_AMB_N120

description: mAMB rep./nucleus #120

value: nucleus ambiguus


title: Hu51

value: Patient 5


title: m6A_input_Control_2XY

value: primary hepatic stellate cell


title: dme.KO.tes.rep3


title: Mm_AMB_N119

description: mAMB rep./nucleus #119


title: dme.KO.tes.rep2


title: Lung, Rio, 10

first: Junhao

last: Hu

address: Build 13, No.100 Kaike Road, Pudong District

institute: Interdisciplinary Research Center of Biology and Chemistry

data_processing:
Reads cleaning: raw FASTQ files were quality checked using FASTQC . Then fastp was used to quality trim FASTQ files by both read quality and length (Q30 > 20, length > 36).
Alignment: clean reads were processed to pseudo-align to mouse transcriptome GRCm38 using salmon.
Quantification: transcriptional level expression was aggregated to gene level expression using tximport. Ensembl release 95 was used to annotate genes.
Quality check: sample clustering was performed with principle component analysis analysis and sample to sample distance correlation analysis.
DEGs analysis: differential expressed genes were defined by DESeq2 with foldchange > 1.5 and adjusted p-value < 0.05. DEGs based hypergeometric test and gene set enrichment analysis were produced by clusterProfiler.
Assembly: GRCm38
Supplementary files format and content: gene expression raw counts

source_name: Lung lysate

extract_protocol:
Sangon RNA extraction kit (Order NO. B511321)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were given PBS (Vehicle) or Riociguat (i.g.).  Mice were sacrificed after 24 hours.

value: Riociguat

value: lung


title: Replacement.tes.rep3


title: Hu40

value: Patient 3

value: Former, 50 pack-years, stopped 8 years ago


title: Hu44

value: Bronchial airway epithelial cells

value: Patient 4


title: Hu35

value: Patient 2

value: No

value: Former, 2 pack-years, stopped 30 years ago


title: Mm_AMB_N117

description: mAMB rep./nucleus #117

source_name: single neuron nucleus


title: m6A_input_Control_1XY

value: WT

value: none (input)


title: Hu28

value: Patient 1

value: Yes


title: Mm_AMB_N118

description: mAMB rep./nucleus #118

value: brain


title: Mm_AMB_N116

description: mAMB rep./nucleus #116

value: nucleus ambiguus


title: Lung, Rio, 8


title: dme.KO.tes.rep1

value: 3-5 days after eclosion


title: dme.WT.tes.rep3


title: KUGBM8-40Gy-1

value: 40 Gy of IR Treatment for 4 weeks


title: Mm_AMB_N115

description: mAMB rep./nucleus #115


title: m6A_RIP_Control_1XY

value: primary hepatic stellate cell

value: anti-m6A (Epibiotek, R1804)


title: Lung, Rio, 7

value: Riociguat

value: lung


title: Patient32-D7

city: CAMBRIDGE

first: Nicholas

last: Haradhvala

address: 75 Ames St

institute: Broad Institute

data_processing:
Alignment and transcript counting: cellranger v6.0.1
Ambient contamination removal: cellbender v0.2.0
SNP-based demultiplexing: souporcell v2020.7
Genome_build: hg38
Supplementary_files_format_and_content: 10x format single cell gene expression matrices

source_name: Peripheral blood

extract_protocol: Viable cells were resuspended in PBS with 0.04% BSA at a cell concentration of 1000 cells/μL. 40,000 cells were loaded onto a 10x Genomics Chromium™ instrument (10x Genomics) according to the manufacturer’s instructions. The scRNA-seq libraries were processed using Chromium™ single cell 5’ library & gel bead kit and coupled scTCR-seq libraries were obtained using Chromium™ single cell V(D)J enrichment kit (human T cell) (10x Genomics). Quality control for amplified cDNA libraries and final sequencing libraries were performed using Bioanalyzer High Sensitivity DNA Kit (Agilent). Both scRNA-seq and scTCR-seq libraries were normalized to 4nM concentration and pooled in a volume ratio of 4:1. The pooled libraries were sequenced on Illumina NovaSeq S4 platform. The sequencing parameters were: Read 1 of 150bp, Read 2 of 150bp and Index 1 of 8bp.

value: Tisa-cel

tag: sorting

value: CAR-neg

tag: timepoint

value: Day +7


title: Patient32-D7-CART

value: CAR-pos


title: Lung, Veh, 4

value: PBS


title: Mm_AMB_N114

description: mAMB rep./nucleus #114


title: Patient32-Infusion

source_name: Infusion product

value: Day 0


title: Lung, Rio, 9


title: Mm_AMB_N113

description: mAMB rep./nucleus #113


title: Lung, Veh, 2


title: Mm_AMB_N112

description: mAMB rep./nucleus #112


title: Mm_AMB_N111

description: mAMB rep./nucleus #111


title: Low dose sample 9

city: Stanford

first: Meena

last: Easwaran

state: California

address: 240 Pasteur Dr, BMI 1400

institute: Stanford University

description:
LD9
1h CS

hyb_protocol: 250ng of total RNA from all target samples were hybridized to biotinylated capture probe and reporter probe with unique target gene specific fluorochromes present in the NanoString nCounter mouse inflammation v2 panel (Catalog no. XT-CSO-MIN2-12) as per the manufacturer's protocol. Hybridized complexes in solution were immobilized onto catridges for digital count analysis.

scan_protocol: Post hybridization, digital count analysis was performed by nCounter instrument. The number of occurrences of unique bar-coded specific to each target gene was counted by this instrument for every sample. Raw data counts were obtained for further analysis.

data_processing: NanoString’s data analysis application software, nSolver version 4.0 was utilized for the analysis of raw data counts.

label: NanoString bar-coded probes

source_name: Low dose (LD)

label_protocol: As per the manufacturer's protocol

extract_protocol: Total RNA was isolated from control, LD and HD laryngeal samples using the RNeasy Mini Kit (Qiagen, Germantown, MD, USA). RNA quantity and quality (A260/A280) were estimated using the Nanodrop 2000 spectrophotometer (Thermo Fisher Scientific, Rockford, IL, USA).

treatment_protocol: Control mice were room air-exposed for a total of 4 weeks. LD and HD mice were exposed 1h/day and 4h/day to CS respectively for a total of 4 weeks, M-F only.

tag: gender

value: male

value: Larynx

value: 1h/day cigarette smoke exposed


title: Patient31-D7


title: Lung, Veh, 3


title: dme.WT.tes.rep2


title: Low dose sample 8

description:
LD8
1h CS


title: Lung, Veh, 1


title: Patient31-Infusion


title: Low dose sample 10

description:
LD10
1h CS


title: Patient31-Baseline

value: Day -30


title: 90 week old mouse, replicate 2-2, snRNA-seq

city: Cambridge

first: William

middle: Edward

last: Allen

address: Naito 034, Zhuang Group, 12 Oxford St.

department: Chemistry and Chemical Biology

institute: Harvard University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: h5 Matrix files

molecule: polyA RNA

source_name: Brain

extract_protocol:
Female mice aged 4 weeks old or 90 weeks old were anesthetized with isofluorane and then acutely decapitated. Their brains were quickly harvested and cut into hemispheres and each hemisphere was frozen immediately on dry ice Optimal Cutting Temperature Compound (Fisher HealthCare) and then stored at –80oC until sectioning. Brains were taken from storage at –80oC and warmed to –18oC in a cryostat (Leica) for 20 minutes before sectioning.  Sections were discarded until the beginning of frontal cortex was apparent. Brains were then blocked on the cryostat using a razor blade to a region containing frontal cortex and striatum. 100 µm coronal sections were then collected approximately from A/P +2 mm to A/P +1 mm, relative to bregma. The resulting sections were collected in an Eppendorft tube and stored at –80oC until snRNA-seq library preparation.   For snRNA-seq library preparation, nuclei were dounced in Nuclei EZ Prep nuclei extraction buffer (Sigma) + 1% RNase Inhibitor. Nuclei were then spun down, filtered through a 70 µm filter, stained with DAPI, and sorted on a FACS machine (BD FacsAria) to separate nuclei from debris. The resulting clean nuclei preparation were then counted and encapsulated on a 10X Genomics Chromium machine, using the 3’ Transcriptome V3.1 kit (10X Genomics).
After encapsulation, the resulting libraries were reverse transcribed, amplified as cDNA, fragmented, and amplified as a final library following the manufacturer’s instructions. The resulting libraries were sequenced on a NovaSeq S4 flowcell (Illumina) to a target depth of ~50,000 reads per nucleus.
snRNA-seq

tag: cell type

value: Neurons, glia, immune, vascular

value: Brain

value: 90 weeks old


title: dme.WT.tes.rep1

value: 3-5 days after eclosion


title: 90 week old mouse, replicate 2-1, snRNA-seq

description: 10x Genomics

tag: strain


title: Low dose sample 7

description:
LD7
1h CS

tag: tissue


title: High dose sample 9

description:
HD9
4h CS

source_name: High Dose (HD)

value: 4h/day cigarette smoke exposed


title: Patient30-Baseline

value: Day -5


title: Mm_AMB_N107

first: NORC

last: Boston

address: 3 Blackfan Circle, CLS0733

institute: Beth Israel Deaconess Medical Center

description: mAMB rep./nucleus #107

data_processing:
Raw sequencing reads were demultiplexed to FASTQ format files using bcl2fastq (Illumina; version 2.20.0).
Reads from were aligned with STAR (version 2.6.1) against the GENCODE M16 mouse genome annotation for the GRCm38 assembly, supplemented with the Cre and mCherry sequences. Duplicate alignments were removed using Picard Tools (version 2.18.21). Digital expression matrices were generated from the deduplicated alignments using the Drop-Seq tools <https://github.com/broadinstitute/Drop-seq> software suite (version 2.3.0), specifically the `DigitalExpression` program, counting all unique alignments to both exons and introns.
Assembly: GRCm38
Supplementary files format and content: Digital gene expression matrices (“dge.tsv.gz” files): gene-by-cell counts.

extract_protocol:
On the next day, nAmb tissue was homogenized and purified by density-gradient centrifugation into a single-nuclei suspension as previously described (Habib et al., 2016; Todd et al., 2020). The single-nuclei suspension was sorted by FACS to isolate one H2b-mCherry+ nucleus per well of three 96-well plates, which were then centrifuged at 2,500rcf, frozen on dry ice, and stored at -80°C until use.
After purifying the RNA by RNA-clean SPRI reagents (1.5x ratio of SPRI to sample), cDNA libraries were generated from polyadenylated mRNA of each sample using Smart-Seq2 (Picelli et al., 2014), modified as previously described (Tao et al., 2021). Illumina sequencing libraries were prepared from single-nuclei cDNA samples as described previously (Tao et al., 2021) and then sequenced by Illumina Next-Seq 500.

value: brain

tag: brain region

value: nucleus ambiguus


title: Mm_AMB_N109

description: mAMB rep./nucleus #109


title: Mm_AMB_N108

description: mAMB rep./nucleus #108


title: 90 week old mouse, replicate 1-1, snRNA-seq

description: 10x Genomics


title: High dose sample 7

description:
HD7
4h CS


title: Patient31-D7-CART

value: Tisa-cel


title: Patient30-Infusion


title: 90 week old mouse, replicate 1-2, snRNA-seq

description: 10x Genomics


title: Mm_AMB_N110

description: mAMB rep./nucleus #110


title: Mm_AMB_N106

description: mAMB rep./nucleus #106


title: Patient30-D7

value: CAR-neg

value: Day +7


title: High dose sample 10

description:
HD10
4h CS


title: 4 week old mouse, replicate 2-2, snRNA-seq

description: 10x Genomics

value: 4 weeks old


title: Mm_AMB_N105

description: mAMB rep./nucleus #105


title: Control sample 7

description:
C7
Control

source_name: Control

value: Room air exposed


title: Patient29-D7-CART-retreatment

value: CAR-pos


title: 4 week old mouse, replicate 2-1, snRNA-seq

description: 10x Genomics


title: 4 week old mouse, replicate 1-2, snRNA-seq

description: 10x Genomics


title: Control sample 9

description:
C9
Control

value: male

value: Larynx


title: Patient29-D7-CART


title: 92Young

city: New Haven

first: Pramod

last: Mistry

address: 300 Cedar St

institute: Yale University

data_processing:
The pre-processed digital gene expression matrices as obtained from cellranger. These matrices were processed using Seurat (Satija et al., 2015). The clusters were determined using Louvain algorithm for community detection (Vincent D Blondel, 2008). Differential gene expression between the clusters was carried out using the MAST method (Finak et al., 2015). The visualizations and analysis were carried out in R (R Core Team). The data is visualized as tSNE (Hinton, 2002). From 14day pups we sequenced total of 4895 CD45+ cells. For GZ161 treatment experiments we sequenced total of 40763 CD45+ cells that consists of 4 groups of mice with 3 mice/ each group.
Assembly: mm10
Supplementary files format and content: cellranger filtered_feature_bc_matrix

source_name: Microglia

extract_protocol:
Brain was harevested and cells were isolated by enzymatic digestion followed by gradient centrifugation. Isolated cells were then flow sorted using anti-CD45 antibody.
10X Genomics V3 3’ Gene Expression kit and sequenced on NovaSeq flow cells to achieve high read depth

value: Gbaloxp/loxp Cx3cr1Cre/+

value: 6 weeks


title: Mm_AMB_N103

description: mAMB rep./nucleus #103


title: Mm_AMB_N104

description: mAMB rep./nucleus #104


title: Control sample 11

description:
C11
Control


title: Control sample 13

description:
C13
Control


title: 4 week old mouse, replicate 1-1, snRNA-seq

description: 10x Genomics

value: Neurons, glia, immune, vascular

value: Brain


title: AvrM14 E82Q 72h - 4

city: Acton

first: Julian

last: Greenwood

state: ACT

address: Linnaeus Way

country: Australia

institute: Australian National University

description:
JAC_32
Agrobacterium infiltration AvrM14 E82Q 72h
total RNA with rRNA depletion

data_processing:
Reads were aligned to the flax reference genome (Lusitatissimum_200_BGIv1.0.fa) using Hisat2. Sequence alignment map files (.sam) were sorted and converted to binary format (.bam) using samtools.
Transcripts were assembled using Scallop2. Reference annotations in General Feature Format (.gff3) were converted to General Transfer Format (.gtf) using gffread and were merged with the Scallop2 annotations for all samples using stringtie. Unique transcripts that were not present in the reference annotation were identified using gff compare and were separated into a new .gtf file (JAC_scallop2_mod.gtf) using gtfcuff.
The sequences of unique transcripts were extracted from the reference genome using gffread and then merged with the reference transcript file to create transcript fasta file: JAC_transcripts.fasta.
Count data was generated using featurecounts and differential gene expression was determined using DESeq2, or using Salmon with Scallop2 annotation file JAC_scallop2_mod.gtf for reference based analysis.
Assembly: Lusitatissimum_200_BGIv1.0.fa - https://phytozome-next.jgi.doe.gov/info/Lusitatissimum_v1_0
Supplementary files format and content: Count data generated by feature counts - count data includes read counts for all samples, including all reads overlapping features but not multimapping reads : featureCounts -T 12 -p -O -t exon -g gene_id -a JAC_scallop2.gtf -o JAC_5.overlapcount all-JAC_5_sorted.bam
Supplementary files format and content: Count data generated by Salmon - Salmon format tab-delimited text files with TPM and read counts for each Sample

organism: Linum usitatissimum

source_name: Leaf

growth_protocol: Flax plants of the variety Bison were grown in greenhouse conditions for 6 weeks

extract_protocol:
20 treated leaves (~100 mg) were snap frozen and ground to fine powder in 2ml tubes using ball bearings. RNA was extracted fusing PureLink™ RNA Mini Kit (Invitrogen™) using TRIzol Reagent.
Ribosomal RNA was deleted from total RNA using Ribo-Zero Magnetic Kit (for rRNA removal) and Library was prepared using the NEBNext® Ultra  Directional RNA Library Prep Kit for Illumina®
150bp paired end reads using the Illumina NovaSeq 6000 - 10 gigabases of raw data per sample

treatment_protocol: Agrobacterium containing expression constructs for different flax rust effectors, or an empty vector control, were infiltrated into flax leaves of six week old plants. Infiltrated leaves were harvested at either 24 or 72 hours after infiltration.

value: Leaf

value: Bison

value: Agrobacterium infiltration AvrM14 E82Q 72h - 4


title: Mm_AMB_N101

description: mAMB rep./nucleus #101

value: brain


title: AvrM14 E82Q 72h - 3

description:
JAC_31
Agrobacterium infiltration AvrM14 E82Q 72h
total RNA with rRNA depletion

value: Agrobacterium infiltration AvrM14 E82Q 72h - 3


title: High dose sample 12

description:
HD12
4h CS

value: 4h/day cigarette smoke exposed


title: 3CX3-E36

source_name: Brain CD45+ cells

value: 10 months

value: GZ-161 diet


title: Mm_AMB_N100

description: mAMB rep./nucleus #100

value: nucleus ambiguus


title: 75Aged

value: 12 months


title: Patient29-Infusion

value: Tisa-cel

value: Day 0


title: Mm_AMB_N099

description: mAMB rep./nucleus #099


title: AvrM14 E82Q 72h - 2

description:
JAC_30
Agrobacterium infiltration AvrM14 E82Q 72h
total RNA with rRNA depletion

value: Agrobacterium infiltration AvrM14 E82Q 72h - 2


title: Patient29-D7-retreatment

value: CAR-neg

value: Day +7


title: 3CX3-65

value: Gbaloxp/loxp Cx3cr1Cre/+

value: Control diet


title: Patient28-D7


title: AvrM14 E82Q 72h - 1

description:
JAC_29
Agrobacterium infiltration AvrM14 E82Q 72h
total RNA with rRNA depletion

value: Leaf

value: Agrobacterium infiltration AvrM14 E82Q 72h - 1


title: Patient29-Infusion-retreatment


title: Mm_AMB_N098

description: mAMB rep./nucleus #098


title: 3CX3-55

value: Brain

value: Gbaloxp/loxp


title: Mm_AMB_N097

description: mAMB rep./nucleus #097

value: brain


title: Patient30-D7-CART

value: CAR-pos


title: Patient28-D7-CART


title: Patient28-Infusion


title: AvrM14 72h -3

description:
JAC_27
Agrobacterium infiltration AvrM14 72h -3
total RNA with rRNA depletion

value: Bison


title: 190702-775-KO-KOH

city: Göteborg

first: Anders R.

last: Clausen

address: Box 440

country: Sweden

institute: University of Gothenburg

data_processing:
Library strategy: HydEn-seq
Purified libraries were then sequenced using the Illumina NextSeq500 instrument for 2*75 paired end reads. Reads were trimmed for quality and adapter sequence with cutadapt (-m 15 –q 10match-reas-wildcards). Pairs with one or both reads shorter than 15 nts were discarded. Mate 1 of the remaining pairs was aligned to an index containing the sequence of all oligos used in the preparation of these libraries with bowtie sing bowtie 0.12.8 (-m1 -v2), and all pairs with successful alignments were discarded. Pairs passing this filter were subsequently aligned to the mitochondrial genome of mm10 M. musculus reference genome. Single-end alignments were then performed using mate 1 of all unaligned pairs (-v2). The count of ends of paired-end and single-end alignments were determined and these counts were converted to bedGraph format for visualization.
Assembly: mm10
Supplementary files format and content: bedgraph

source_name: heart

extract_protocol:
Genomic DNA was isolated from mouse heart tissue with Gentra Puregene Tissue Kit without RNase A treatment.
HydEn-seq was performed by hydrolysis of 1 mg of genomic DNA with 0.3 M KOH for 2 h at 55°C. After hydrolysis DNA was denatured for 3 min at 85°C, cooled on ice and treated with 10 U T4 Polynucleotide Kinase (3´ phosphatase minus) in 1 mM ATP for 20 min at 37°C and then treated for 20 min at 65°C. DNA was purified using 1.8 volumes of CleanNGS beads and eluted in 14 ml EB. 13 ml DNA was denatured for 3 min at 85 °C and ligated to 1 mM ARC140 using 10 U T4 RNA ligase in 25% PEG3350, 1 mM CoCl3(NH3)6 and 20 mM ATP overnight at room temperature. The day after, two washes was performed using 0.8 volumes of CleanNGS beads and eluted with 20 ml EB in the first step and 13.8 ml EB in the second step. DNA was denatured for 3 min at 85°C and incubated for 5 min with 1xBF for T7 DNA polymerase, 0.2 mM dNTPs, 40 mg/ml BSA, and 1 mM of the adapter consisting of ARC76/ARC77. Reaction was then treated with 4 U of T7 DNA polymerase for 5 min. Product was purified with 0.8 volumes of CleanNGS beads and amplified using primers ARC78-ARC84 and ARC160. All oligos are from IDT. Sequences are provided in table S1. * indicates a phosphorothioate bond. ARC140 contains a 5´-amino group instead of a 5´-OH group, in combination with a C6 linker.

tag: agent

value: 0.3 M KOH

value: deficient in Rnase H1

value: heart


title: 3CX3-11

value: 10 months

tag: treatment

value: GZ-161 diet


title: Islets_6wks_wildType_3 [SVC0011800001]

city: Grand Rapids

first: Luca

last: Fagnocchi

state: MI

address: 333 Bostwick AVE NE

institute: VAI

data_processing:
reads were quality controlled with fastQC
raw sequences were aligned to mouse reference genome GRCm38.p6 with the snakePipes2 RNA-seq pipeline75
data were batch corrected using Combat
differential expression of the raw counts was performed using DESeq2
Gene Set Enrichment Analysis (GSEA) of DE results was performed with fgsea
Assembly: GRCm38/mm10
Supplementary files format and content: 3wks_allSamples_counts.txt: tab-delimited text counts on genomic features (transcripts) for all 3 weeks old samples
Supplementary files format and content: 6wks_allSamples_counts.txt: tab-delimited text counts on genomic features (transcripts) for all 6 weeks old samples

source_name: Pancreatic islet

extract_protocol:
Total RNA was extracted from isolated islets using the Qiagen RNeasy Micro Kit (Cat. No. 74004).
Libraries were prepared from 10 ng of total RNA. Total RNA material was converted to dsDNA using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing, v. 091817 (Takara Bio USA, Mountain View, CA, U.S.A.). We then used the Illumina Nextera DNA Flex kit (Illumina Inc, San Diego, CA, U.S.A.) to convert the cDNA into Illumina-compatible sequencing libraries.

value: Pancreatic islet

value: male

value: wild type

tag: age

value: 6 weeks

tag: phenotype

value: light


title: Patient27-Infusion

value: Tisa-cel

value: Day 0


title: AvrM14 72h -2

description:
JAC_26
Agrobacterium infiltration AvrM14 72h -2
total RNA with rRNA depletion

value: Leaf

tag: genotype


title: Patient29-D7

value: CAR-neg

value: Day +7


title: Patient27-D7-CART

value: CAR-pos


title: 190702-774-KO-KOH


title: 190702-772-WT-KOH-R3

value: WT


title: Islets_6wks_wildType_2 [SVC0011790001]

tag: Sex


title: AvrM14 72h -4

description:
JAC_28
Agrobacterium infiltration AvrM14 72h -4
total RNA with rRNA depletion

value: Bison


title: AvrM14 72h -1

description:
JAC_25
Agrobacterium infiltration AvrM14 72h -1
total RNA with rRNA depletion


title: Islets_6wks_wildType_1 [SVC0011780001]


title: Patient27-D7


title: AvrL8 72h -3

description:
JAC_24
Agrobacterium infiltration AvrL8 72h -3
total RNA with rRNA depletion

value: Agrobacterium infiltration AvrL8 72h -3


title: Patient26-D7-CART


title: AvrL8 72h -2

description:
JAC_23
Agrobacterium infiltration AvrL8 72h -2
total RNA with rRNA depletion

value: Agrobacterium infiltration AvrL8 72h -2


title: Islets_6wks_Nnat-Heavy_3 [SVC0011770001]

value: Nnat+/-p

value: heavy


title: Islets_6wks_Nnat-Heavy_2 [SVC0011760001]

value: Pancreatic islet


title: 190702-772-WT-KOH-R2

value: 0.3 M KOH

value: heart


title: AvrL8 72h -1

description:
JAC_22
Agrobacterium infiltration AvrL8 72h -1
total RNA with rRNA depletion

value: Agrobacterium infiltration AvrL8 72h -1


title: 190702-772-WT-KOH-R1


title: Patient26-Infusion


title: Mm_AMB_N102

city: Boston

description: mAMB rep./nucleus #102

value: brain

value: nucleus ambiguus


title: Patient26-D7

value: Tisa-cel


title: Islets_6wks_Nnat-Light_3 [SVC0011740001]

value: male

value: 6 weeks

value: light


title: Islets_6wks_Nnat-Heavy_1 [SVC0011750001]


title: 44

city: Changsha

first: Xi

middle: Yu

last: Zhou

state: Hunan Province

address: No. 72 Xiangya Road, Changsha City, Hunan Province

institute: Xiangya Stomatological Hospital

data_processing:
Use the total RNA of each sample to prepare a miRNA sequencing library, including the following steps:1）3'connector connection;2）5'connector connection;3)cDNA synthesis;4)PCR amplification;4)Select 135~155bp PCR amplified fragments
The library was denatured into single-stranded DNA molecules, captured on an Illumina flow cell, amplified into clusters in situ, and performed 51 cycles of sequencing on the Illumina NextSeq 500 sequencer according to the supplier’s instructions
The Illumina sequencer generates the original sequence in FASTQ format.  To evaluate the quality of sequencing, the original sequence of each sample will be counted Q30:Q30=-10log10(P)
After sequencing quality control, the original data QC is preprocessed (using cutadapt to remove the 3'linker sequence and filtering out short fragments ≤ 15bp) to obtain trimmed reads, which are compared to the reference genome using bowtie.
Assembly: mmp9
Supplementary files format and content: The xlsx format file contains the CPM value of gene in every sample

source_name: hippocampus

extract_protocol:
Briefly, using TRIzol reagent to extract the total RNA from the hippocampus in accordance with the manufacturer’s instructions.
The NEB Next Ultra Directional RNA Library Prep Kit for Illumina (NEB, MA, USA) was used to establish an RNA library and assessed the RNA library quality and quantity via Agilent 2100 Bioanalyzer. The RNA library was used for sequence analysis. The sequence analysis was conducted by a NextSeq 500 platform (Illumina, CA, USA). The clean reads were filtered out from raw reads by FastQC and selected for further bioinformatics analysis.

value: hippocampus

tag: time

value: post XFZYD treatment day 14

value: XFZYD


title: AvrL2 72h - 2

description:
JAC_20
Agrobacterium infiltration AvrL2 72h
total RNA with rRNA depletion

value: Leaf

value: Bison

value: Agrobacterium infiltration AvrL2 72h - 2


title: 43


title: AvrL2 72h - 1

description:
JAC_19
Agrobacterium infiltration AvrL2 72h
total RNA with rRNA depletion

value: Agrobacterium infiltration AvrL2 72h - 1


title: Islets_6wks_Nnat-Light_2 [SVC0011730001]

value: Pancreatic islet

value: Nnat+/-p


title: AvrL1 72h - 3

description:
JAC_15
Agrobacterium infiltration AvrL1 72h
total RNA with rRNA depletion

value: Agrobacterium infiltration AvrL1 72h - 3


title: Patient25-D7-CART

value: CAR-pos

value: Day +7


title: Islets_6wks_Nnat-Light_1 [SVC0011720001]


title: Islets_3wks_Nnat-Heavy_3 [SVC0012550001]

value: 3 weeks

value: heavy


title: Patient25-Infusion

value: Tisa-cel

value: Day 0


title: 35

value: TBI


title: 36

value: hippocampus


title: Patient25-Baseline

value: Day -5


title: Patient25-D7

value: CAR-neg


title: AvrL1 72h - 2

description:
JAC_14
Agrobacterium infiltration AvrL1 72h
total RNA with rRNA depletion

value: Leaf

value: Agrobacterium infiltration AvrL1 72h - 2


title: 190702-770-KO-KOH

value: 0.3 M KOH

value: deficient in Rnase H1

value: heart


title: Islets_3wks_Nnat-Heavy_1 [SVC0012510001]

value: Pancreatic islet

value: female

value: Nnat+/-p


title: Patient24-D7-CART

value: CAR-pos

value: Day +7


title: 33

value: post XFZYD treatment day 14


title: 28

value: XFZYD


title: Islets_3wks_Nnat-Heavy_2 [SVC0012520001]

value: 3 weeks

value: heavy


title: AvrP 72h - 3

description:
JAC_12
Agrobacterium infiltration AvrP 72h
total RNA with rRNA depletion

value: Bison

value: Agrobacterium infiltration AvrP 72h - 3


title: AvrL2 72h - 3

description:
JAC_21
Agrobacterium infiltration AvrL2 72h
total RNA with rRNA depletion

value: Agrobacterium infiltration AvrL2 72h - 3


title: AvrL1 72h - 1

description:
JAC_13
Agrobacterium infiltration AvrL1 72h
total RNA with rRNA depletion

value: Leaf

value: Agrobacterium infiltration AvrL1 72h - 1


title: Islets_3wks_wildType_4 [SVC0012500001]

value: wild type

value: light


title: Patient24-Baseline

value: Tisa-cel

value: Day -30


title: Patient24-D7

value: CAR-neg


title: AvrP 72h - 1

description:
JAC_10
Agrobacterium infiltration AvrP 72h
total RNA with rRNA depletion

value: Agrobacterium infiltration AvrP 72h - 1


title: 27

value: hippocampus


title: Patient24-Infusion

value: Day 0


title: Patient23-D7

value: Day +7


title: 20

value: post XFZYD treatment day 14

value: TBI


title: Islets_3wks_wildType_3 [SVC0012490001]

value: Pancreatic islet

value: male

value: 3 weeks


title: EV 72h - 2

description:
JAC_8
Agrobacterium infiltration EV 72h
total RNA with rRNA depletion

value: Bison

value: Agrobacterium infiltration EV 72h - 2


title: Islets_3wks_Nnat-Light_3 [SVC0012460001]

value: Nnat+/-p


title: EV 72h - 1

description:
JAC_7
Agrobacterium infiltration EV 72h
total RNA with rRNA depletion

value: Leaf

value: Agrobacterium infiltration EV 72h - 1


title: Islets_3wks_wildType_2 [SVC0012480001]

value: wild type

value: light


title: Islets_3wks_Nnat-Light_2 [SVC0012450001]


title: AvrP 72h - 2

description:
JAC_11
Agrobacterium infiltration AvrP 72h
total RNA with rRNA depletion

value: Agrobacterium infiltration AvrP 72h - 2


title: Islets_3wks_wildType_1 [SVC0012470001]


title: Patient22-Infusion

value: Tisa-cel


title: 21

value: hippocampus


title: Patient23-Infusion

value: Day 0


title: AvrP 24h - 2

description:
JAC_5
Agrobacterium infiltration AvrP 24h
total RNA with rRNA depletion

value: Agrobacterium infiltration AvrP 24h - 2


title: satellite cells, lactoferrin knockout-3, Day4

city: Beijing

first: Xiong

address: No. 17, Qinghua East Road, Haidian District, Beijing

department: College of Food Science and Nutritional Engineering

institute: China Agricultural University

data_processing:
The 3' end of eukaryotic mRNA has a structure of a ployA tail. Using magnetic beads with Oligo (dT) to perform A-T base pairing with ployA, mRNA can be isolated from total RNA for analysis of transcriptome information.
The Illumina Novaseq 6000 platform is used to sequence short sequence fragments. The enriched mRNA is a complete RNA sequence with an average length of several kb, so it needs to be randomly interrupted. Fragmentation buffer can be added to randomly fragment mRNA, and small fragments of about 300bp can be isolated by magnetic bead screening.
Under the action of reverse transcriptase, random hexamers are added to reversely synthesize one-strand cDNA using mRNA as a template, followed by two-strand synthesis to form a stable double-strand structure
The double-stranded cDNA structure is a sticky end, which is filled with End Repair Mix to make a blunt end, and then an "A" base is added to the 3' end for connecting a Y-shaped linker.
On-board sequencing on the Illumina platform.
Assembly: GRCm39, http://asia.ensembl.org/Mus_musculus/Info/Index
Supplementary files format and content: Tab-delimited text file includes TPM values for each Sample

source_name: muscle

growth_protocol: Satellite cells in sterile tubes with 500 μL of DMEM supplemented with with 20% fetal bovine serum, 1% chick embryo extract, 10 ng/ml basic fibroblast growth factor and 1% penicillin-streptomycin at 4 °C. For growth, sorted cells were placed on 10% Matrigel-precoated (BD Biosciences) cell culture plates at 37 °C in a 5% CO2 atmosphere.

extract_protocol:
SCs obtained by flow sorting were seeded into 6-well cell culture plates at a density of 2.5x10^5. After 4 days of growth, cells were harvested, added with 1 ml Trizol, snap-frozen in liquid nitrogen, and transported to GeneDenovo Biotechnology Co. Data were extracted and normalized according to the manufacturer’s standard protocol.
Total RNA was extracted from the collected satellite cell samples, the concentration and purity of the extracted RNA were detected by Nanodrop2000, RNA integrity was detected by agarose gel electrophoresis, and RIN value was determined by Agilent2100. A single library construction requires that the total amount of RNA is ≥1ug, the concentration is ≥35ng/μL, OD260/280≥1.8, and OD260/230≥1.0.

treatment_protocol: Satellite cells were cultured in growth medium for 4 days without any treatment.

value: muscle

value: muscle satellite cells

value: lactoferrin KO

value: growth culture

value: Day 4


title: satellite cells, lactoferrin knockout-2, Day4


title: AvrP 24h - 1

description:
JAC_4
Agrobacterium infiltration AvrP 24h
total RNA with rRNA depletion

value: Bison

value: Agrobacterium infiltration AvrP 24h - 1


title: Patient23-D7-CART

value: CAR-pos

value: Day +7


title: 26

value: post XFZYD treatment day 14

value: XFZYD


title: VSX2 EN1 KO at E14.5 Rep4

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

data_processing:
Low-quality reads and adapter sequences were filtered out by tool Trimmomatic (version 0.38)
Reads were aligned to mouse reference genome mm10 by STAR aligner
Gene counts were quantified by htseq-count (version 0.11.2)
Genome_build: mm10
Supplementary_files_format_and_content: Gene counts file

source_name: E14.5 mouse retina

extract_protocol:
Fresh retinae were placed in TRIReagent (Zymo Research R2050-1-50), and RNA was extracted according to Direct-zol RNA MiniPrep kit protocol (Zymo Research R2050)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: retina

value: VSX2 EN1 KO

tag: model

value: VSX2 EN1 KO at E14.5


title: VSX2 EN1 KO at E14.5 Rep3


title: VSX2 EN1 KO at E14.5 Rep2


title: Islets_3wks_Nnat-Light_1 [SVC0012440001]

value: Pancreatic islet

value: male

value: Nnat+/-p

value: 3 weeks

value: light


title: Patient22-Baseline

value: Tisa-cel

value: Day -30


title: EV 72h - 3

description:
JAC_9
Agrobacterium infiltration EV 72h
total RNA with rRNA depletion

value: Leaf

value: Agrobacterium infiltration EV 72h - 3


title: AvrP 24h - 3

description:
JAC_6
Agrobacterium infiltration AvrP 24h
total RNA with rRNA depletion

value: Bison

value: Agrobacterium infiltration AvrP 24h - 3


title: VSX2 EN1 WT at E14.5 Rep3

value: VSX2 EN1 WT

value: VSX2 EN1 WT at E14.5


title: satellite cells, lactoferrin knockout-1, Day4

value: muscle

value: muscle satellite cells

value: lactoferrin KO

value: growth culture

value: Day 4


title: Patient23-Baseline


title: VSX2 EN1 KO at E14.5 Rep1

value: retina

value: VSX2 EN1 KO

value: VSX2 EN1 KO at E14.5


title: EV 24h - 2

description:
JAC_2
Agrobacterium infiltration EV 24h
total RNA with rRNA depletion

value: Agrobacterium infiltration EV 24h - 2


title: satellite cells, wild type-3, Day4

value: WT


title: Patient21-Baseline

value: Tisa-cel

value: Day 0


title: EV 24h - 1

description:
JAC_1
Agrobacterium infiltration EV 24h
total RNA with rRNA depletion

value: Leaf

value: Agrobacterium infiltration EV 24h - 1


title: VSX2 EN1 WT at E14.5 Rep4


title: VSX2 EN1 WT at E14.5 Rep1


title: Patient21-Infusion


title: Patient21-D14

value: Day +14


title: EU18_SL_3

first: Jun

last: Yang

address: No.35, Tsinghua East Rd.

institute: Beijing Forestry University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9. Perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Eucalyptus urophylla

source_name: Senescent leaf

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Senescent leaf

value: Diploid


title: EV 24h - 3

description:
JAC_3
Agrobacterium infiltration EV 24h
total RNA with rRNA depletion

value: Bison

value: Agrobacterium infiltration EV 24h - 3


title: Patient21-D7

value: Day +7


title: VSX2 SE KO at E14.5 Rep3

value: VSX2 SE KO

value: VSX2 SE KO at E14.5


title: Patient20-D14


title: EU18_SL_1


title: Patient20-Baseline


title: EU18_ML_3

source_name: Mature leaf

value: Mature leaf


title: VSX2 SE WT at E14.5 Rep2

value: retina

value: VSX2 SE WT

value: VSX2 SE WT at E14.5


title: HWPS_104

description: RNA from frozen mouse lungs exposed to heavy WPS

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data.
Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software.
150 PE for 80 M PE reads per sample (40M in each direction)
FeatureCounts was used to count the read numbers mapped to each gene. RPKM values for each gene were calculated based on the length of the gene and mapped read counts.
Gene features with positive counts in at least 50% of samples were retained for differential analysis.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file with RPKM values for each sample. Data from all 20 samples are in one file

source_name: Lungs

extract_protocol:
Total RNA was isolated from homogenized tissues (mouse lungs) using Qiagen RNeasy mini kit (Qiagen) according to manufacturer’s recommendations. Qubit 4 Fluorometer (Thermo Fisher Scientific, Waltham, MA) was used for measurement of RNA yield, and RNA quality was assessed using the Agilent RNA 6000 Pico Kit (Agilent, Santa Clara, CA).
RNA sample quality was assessed by High Sensitivity RNA Tapestation (Agilent Technologies Inc., California, USA) and quantified by Qubit 2.0 RNA HS assay (ThermoFisher, Massachusetts, USA). Library construction is performed based on manufacturer’s recommendation for SMARTer® Stranded Total RNA-Seq Kit v3 – Pico Input RNA Kit (Takara Bio USA Inc., California, USA). Final library quantity was measured by KAPA SYBR® FAST qPCR and library quality evaluated by TapeStation D1000 ScreenTape (Agilent Technologies, CA, USA). Final library size ranges from 300-400 bp with Illumina® 8-nt dual-indices were used. Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® Novaseq S4 (Illumina, California, USA) with a read length configuration of 150 PE for 80 M PE reads per sample (40M in each direction).

value: Lung cells

tag: exposure

value: Waterpipe smoke


title: Patient22-D7-CART

source_name: Peripheral blood

value: Tisa-cel

tag: sorting

value: CAR-pos


title: EU18_ML_1


title: satellite cells, wild type-2, Day4

value: muscle

value: muscle satellite cells

value: WT

value: growth culture

value: Day 4


title: VSX2 SE WT at E14.5 Rep1


title: Patient22-D7

value: CAR-neg

tag: timepoint


title: satellite cells, wild type-1, Day4


title: VSX2 EN1 WT at E14.5 Rep2

value: VSX2 EN1 WT

value: VSX2 EN1 WT at E14.5


title: VSX2-Adult mouse ChIP-Seq Treatment, Rep2

data_processing:
Low-quality reads and adapter sequences trimming by Trimmomatic (version 0.38)
Read alignment to mouse reference genome mm10 by BWA (version 0.7.17)
Aligned reads filtering by Samtools (version 1.9)
Mark duplicate by Picard tool (version 2.18.12)
Peak calling by MACS2 (version 2.1.1.20160309)
Genome_build: mm10
Supplementary_files_format_and_content: WIG

source_name: Adult mouse retina

extract_protocol:
Retinae were fixed, lysed and sheared to an average length of 300-500 bp. After incubation with antibody, beads were washed and DNA was extracted with phenol chroloform and precipitated with ethanol.
Libraries were prepared according to Illumina's instructions

treatment_protocol: untreated

value: Adult

tag: chip antibody

value: VSX2 (Exalpha, Cat No. X1180P, Lot No 14166)

value: untreated


title: EU18_SL_2

value: Senescent leaf

value: Diploid


title: neu_3

first: Shawn

address: 455 MAIN STREET

institute: Whitehead Institute for Biomedical Research

data_processing:
The first 40 bp of the reads were mapped to mouse genome (mm10) using STAR, which was indexed with Ensembl GRCm38.91 gene annotation. The read counts were obtained using featureCounts function from Subread package with unstranded option.
Assembly: mm10
Supplementary files format and content: tab delimited text file with raw gene counts for every gene

growth_protocol: Five-week old male mice labeled with ChR2-YFP transgene1 after conditioning were euthanized by isoflurane. Mouse brains were rapidly extracted, and the hippocampal regions were isolated by microdissection.

extract_protocol:
Clontech's SMARTerUltra-lowPOLYA-V4: Up to 10 ng of sample was prepared using Takara’s SMART-Seq v4 Ultra Low Input RNA protocol per manufacturer’s guidelines. Briefly, RNA underwent reverse transcription via template switching and amplification, resulting in double stranded cDNA. The amount of cDNA between 100-3000 bp was calculated by Fragment Analyzer and Qubit. 150pg of the sample in range was then added to Illumina’s Nextera XT and processed according to manufacturer’s guidelines. Briefly, the cDNA underwent tagmentation, using Nextera XT’s transposase, and unique dual indexes were added by PCR amplification. Final libraries went through QC with the Fragment Analyzer and qPCR on a Roche Light Cycler 480 II. All libraries were then pooled and sequenced at single-end 40 base-pair using the Illumina HiSeq 2500.   Clontech’s SMART-seq v4 Ultra Low Input RNA Kit: Sequencing libraries were prepared using Takara’s SMART-Seq v4 Ultra Low Input RNA protocol per manufacturer’s guidelines, followed by Illumina NexteraXT. Briefly, RNA underwent reverse transcription via template switching and amplification, resulting in double stranded cDNA. cDNA quality and quantity was assessed by Agilent TapeStation 2200 and Qubit. cDNA was converted to sequencing libraries by Illumina Nextera XT. Briefly, the cDNA underwent tagmentation, using Nextera XT’s transposase, and dual indexes were added by PCR amplification. Final libraries went through QC with the TapeStation and Qubit. All libraries were then pooled and sequenced at paired-end 100bp using the Illumina NovaSeq 6000.
Clontech's SMARTerUltra-lowPOLYA-V4 was used except neutral samples, which were prepared with Clontech’s SMART-seq v4 Ultra Low Input RNA Kit

treatment_protocol: Eight mice were pooled by each experimental condition. Single cell suspension was prepared according to the guideline of Adult Brain Dissociation Kit (Miltenyi Botec, Cat No: 13-107-677). Briefly, the hippocampal samples were incubated with digestion enzymes in the C Tube placed on the gentleMACS Octo Dissociator with Heaters with gentleMACS Program: 37C_ABDK_01. After termination of the program, the samples were applied through a MACS SmartStrainer (70 μm). Then a debris removal step and a red blood cell removal step were applied to obtain single cell suspension. The single cell suspension was subject to a BD FACSAria cell sorter according to the manufacturer’s protocol to isolate EYFP-single cell population.

value: The mice were exposured to the same conditioning cage without positive or negative stimuli

value: brain


title: EU18_JL_2

source_name: Juvenile leaf

value: Juvenile leaf


title: neu_2

source_name: Five-week old male mice labeled with ChR2-YFP transgene1 after conditioning were euthanized by isoflurane


title: VSX2 SE WT at E14.5 Rep3

value: retina

value: VSX2 SE WT

value: VSX2 SE WT at E14.5


title: Patient20-D7

value: Tisa-cel

value: Day +7


title: EU18_ML_2

value: Mature leaf


title: HWPS_120

tag: cell type

value: Lung cells

value: Waterpipe smoke


title: VSX2-Adult mouse ChIP-Seq Input, Rep2

tag: strain


title: Patient20-Infusion

source_name: Infusion product

value: Day 0


title: neu_1

tag: tissue


title: EU18_JL_3


title: HWPS_231


title: VSX2 SE KO at E14.5 Rep2

value: VSX2 SE KO

value: VSX2 SE KO at E14.5


title: Patient19-Infusion

value: Axi-cel


title: VSX2-Adult mouse ChIP-Seq Input, Rep1

value: Adult

value: untreated


title: HWPS_121


title: VSX2-Adult mouse ChIP-Seq Treatment, Rep1

value: VSX2 (Exalpha, Cat No. X1180P, Lot No 14166)


title: VSX2 SE KO at E14.5 Rep1


title: HWPS_228


title: EU18_JL_1

value: Diploid


title: HWPS_119


title: EU18_TB_3

source_name: Terminal bud

value: Terminal bud


title: Patient19-D7-CART

value: CAR-pos


title: Patient19-Baseline

value: Day -30


title: Patient19-D7

value: CAR-neg


title: HWPS_229


title: VSX2-E14.5 ChIP-Seq Input, Rep2

value: retina


title: VSX2-E14.5 ChIP-Seq Treatment, Rep1


title: EU17_SL_3

value: Senescent leaf

value: Triploid


title: HWPS_143

value: Lung cells


title: EU17_SL_2


title: EU18_TB_2


title: Patient18-Infusion


title: Patient18-D7-CART

value: Day +7


title: VSX2-E14.5 ChIP-Seq Treatment, Rep2


title: Patient18-Baseline


title: VSX2-E14.5 ChIP-Seq Input, Rep1


title: Patient18-D7


title: HWPS_145

value: Waterpipe smoke


title: EU18_TB_1


title: EU17_SL_1


title: Lung E-&T+

city: Gyeongsan

first: Hyunseok

last: Jee

state: Gyeongbuk

address: 280, Daehak-ro, Gyeongsan, Gyeongbuk, 38541, Republic of Korea

institute: Yeungnam University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: Lung

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: post natal date 28

value: Lung


title: Lung E-&T-


title: FA_242

description: RNA from frozen mouse lungs exposed to fresh air

value: Control air


title: FA_244


title: EU17_ML_3

value: Mature leaf


title: Patient17-D7

value: Axi-cel


title: FA_241


title: Patient17-D7-CART


title: EU17_ML_2


title: EU17_JL_3

value: Juvenile leaf


title: Lung E+&T-


title: Patient17-Infusion

value: Day 0


title: HWPS_141


title: FA_246


title: Lung E+&T+


title: Heart E-&T+

source_name: Heart

value: Heart


title: Patient16-D7


title: Patient17-Baseline


title: Heart E-&T-


title: Heart E+&T-


title: EU17_JL_1


title: FA_263


title: Patient16-Infusion


title: Heart E+&T+


title: EU17_JL_2


title: EU17_ML_1


title: FA_260


title: Patient16-D7-CART

value: CAR-pos


title: FA_258


title: Patient15-Infusion


title: Gastrocnemius E-&T+

source_name: gastrocnemius muscle

value: gastrocnemius muscle


title: EU17_TB_3

value: Terminal bud


title: FA_262


title: FA_245


title: Gastrocnemius E-&T-


title: EU17_TB_1


title: Patient15-D7-CART


title: Patient15-D7

value: CAR-neg


title: WY96-3418, rep24

city: LINCOLN

first: Robert

last: Moore

address: 1901 vine street

institute: University of Nebraska - Lincoln

data_processing:
Trimmomatic was utilized to remove low-quality reads obtained by FastQC, and reads with less than 35 bp were removed from the analysis.
FastQC was applied again and alignments were obtained by using the TopHat2.
Bowtie 2 was utilized for indexing the genes.
Cufflink identified expressed genes and calculated transcript levels in the aligned reads within the TopHat2 generated Sequence Alignment/Map (SAM) formatted files.
Genes transcribed were measured using fragments per kilobase of exon per million (FPKM) reads.
Assembly: Francisella tularensis genome sequences were obtained from NCBI microbial genome database and had the following accession numbers: SCHU S4 (NC_006570.2), MA00-2987 (NZ_CP012372.1), WY96-3418 (NC_009257.1), and LVS (NC_07880.1).
Supplementary files format and content: Cufflinks FPKM data

organism: Francisella tularensis subsp. tularensis

extract_protocol:
Total RNA was extracted using the FastRNA Pro Blue Kit (MP Biomedicals), and then RNA was treated with DNase I and column purified, as recommended by the respective manufacturer.
To produce the the RNA-Seq libraries, ScriptSeq v2 Complete Library Preparation Kit for Bacteria (Epicentre) was utilized according to the manufacturer's instructions and included Ribo-Zero Ribosomal RNA (rRNA) Reagents for Bacteria to remove rRNA.

tag: clade

value: Francisella tularensis subspecies tularensis subtype A.II


title: Gastrocnemius E+&T-


title: Patient15-Baseline

data_processing:
Alignment and transcript counting: cellranger v6.0.1
Ambient contamination removal: cellbender v0.2.0
SNP-based demultiplexing: souporcell v2020.7
Genome_build: hg38
Supplementary_files_format_and_content: 10x format single cell gene expression matrices

extract_protocol: Viable cells were resuspended in PBS with 0.04% BSA at a cell concentration of 1000 cells/μL. 40,000 cells were loaded onto a 10x Genomics Chromium™ instrument (10x Genomics) according to the manufacturer’s instructions. The scRNA-seq libraries were processed using Chromium™ single cell 5’ library & gel bead kit and coupled scTCR-seq libraries were obtained using Chromium™ single cell V(D)J enrichment kit (human T cell) (10x Genomics). Quality control for amplified cDNA libraries and final sequencing libraries were performed using Bioanalyzer High Sensitivity DNA Kit (Agilent). Both scRNA-seq and scTCR-seq libraries were normalized to 4nM concentration and pooled in a volume ratio of 4:1. The pooled libraries were sequenced on Illumina NovaSeq S4 platform. The sequencing parameters were: Read 1 of 150bp, Read 2 of 150bp and Index 1 of 8bp.

value: Day -30


title: WY96-3418, rep23


title: CApM8

city: Boise

first: Matthew

last: Goelzer

state: Idaho

address: 1910 University Drive

department: Materials Science and Engineering

institute: Boise State University

data_processing:
Base calling was performed with the Illumina bcl2fastq
QC was performed on FASTQ files using FastQC
Paired end reads were aligned by STAR
Gene counts generated by DESEQ2
Genome_build: mm10
Supplementary_files_format_and_content: CSV files include raw counts and RPKM log2Fold Change for each gene per sample. Log2Fold for specific sample comparisons.

source_name: Bone marrow derived MSC

extract_protocol:
TRIzol reagent (Invitrogen), extracted using Qiagen RNAeasy Kit.
mRNA version 2 library prep kit (Illumina)

value: MSC

tag: passage

value: Passage 12

tag: media

value: Adipogneic Media

tag: sirna

tag: doxycyline


title: DNam10

value: Growth Media

value: Doxycycline


title: Gastrocnemius E+&T+

tag: age

value: post natal date 28


title: Patient14-Baseline

tag: treatment


title: WY96-3418, rep22


title: WY96-3418, rep21


title: DApM8

value: Doxyxycline


title: WY96-3418, rep20


title: Patient14-Infusion

value: Axi-cel


title: EU17_TB_2

tag: genotype

value: Triploid


title: CNam10


title: DxApM9


title: FA_259

first: Humam

address: 2130 W. Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

value: Lung cells

value: Control air


title: Patient14-D14

first: Nicholas

address: 75 Ames St

institute: Broad Institute

value: Day +14


title: spinal cord - DKO - H3K27Ac rep1

first: Wanjin

last: Li

state: Massachusetts

address: 240 longwood Ave

department: Cell Biology

institute: Harvard Medical School

description:
DKO_1_2_phR_on_Ac_vs_KD_1_vs_KD_2_vs_WT_2_phR_on_Ac_peaks_on_DKO-2_phR.bed
Tbk1+/-; Tak1ΔM/+

data_processing:
Library strategy: CUT&Tag
For ATAC-seq, paired-end 41x41 bp sequencing were performed on the barcoded libraries following the manufacturer’s instructions of NextSeq500 to access open vs closed chromatin regions. Data was processed following ATAC-seq guidelines by Harvard FAS informatics. Paired-end reads were aligned using Bowtie2 version 2.3.4.3 with parameters: --very-sensitive -k 10.
For RNA-seq, libraries were sequenced on an Illumina NextSeq500 instrument with paired 38bp reads. Reads were aligned to the mm9 UCSC mouse transcriptome with Salmon and expression values were determined with DESeq2.
For CUT&Tag,paired-end 41x41bp sequencing were performed on the barcoded libraries following the manufacturer’s instructions of NextSeq500. Paired-end reads were aligned using Bowtie2 version 2.3.4.3 with parameters: --local --very-sensitive --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700.
Genome_build: mm9 for mouse, hg19 for human
Supplementary_files_format_and_content: bigWig files were generated by deeptools version 3.0.2

source_name: spinal cord

extract_protocol:
ATAC-seq was performed according to the standard protocol.
For RNA-seq, RNA was extracted from wildtype or Ripk1D325A/D325A;Ripk3-/- MEFs using Quick-RNA MiniPrep kit (Zymo Research) with the in-column DNase treatment. Libraries were prepared and sequenced by the Bauer Core facility at Harvard University.
For CUT&Tag, the nuclei were isolated and the protein enriched DNA regions were obtained using standard CUT&Tag protocol.
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Ripk1D325A/D325A;Ripk3-/- MEFs treated with vehicle or TNFα with or without Nec-1s

value: Tbk1+/-; Tak1deltaM/+

tag: cut&tag antibody


title: DxNaM9


title: Patient13-D7

value: Day +7


title: Patient14-D7


title: WY96-3418, rep18


title: Patient13-Infusion

value: Day 0


title: WY96-3418, rep19

value: Francisella tularensis subspecies tularensis subtype A.II


title: spinal cord - WT - H3K27Ac

description:
GEN00197591 mm_WT-2_Ac
DKO_1_2_phR_on_Ac_vs_KD_1_vs_KD_2_vs_WT_2_phR_on_Ac_peaks_on_DKO-2_phR.bed
Tbk1+/+; Tak1ΔM/+

value: Tbk1+/+; Tak1deltaM/+


title: spinal cord - KD - p-S166-RIPK1 rep1

description:
DKO_1_2_phR_on_Ac_vs_KD_1_vs_KD_2_vs_WT_2_phR_on_Ac_peaks_on_DKO-2_phR.bed
Tbk1+/-; Tak1ΔM/+; Ripk1D138N/+

value: Tbk1+/-; Tak1deltaM/+; Ripk1D138N/+


title: WY96-3418, rep17


title: spinal cord - KD - p-S166-RIPK1 rep2


title: CnNaM9

value: MSC

value: Passage 12


title: spinal cord - KD - H3K27Ac rep2


title: Patient12-D14


title: CApM7

value: Adipogneic Media


title: spinal cord - KD - H3K27Ac rep1


title: spinal cord - DKO - p-S166-RIPK1 rep2


title: spinal cord - DKO - H3K27Ac rep2


title: WY96-3418, rep15


title: Patient13-Baseline

value: Day -30


title: DNam6

value: Growth Media

value: Doxycycline


title: WY96-3418, rep16


title: Patient12-Infusion

value: Axi-cel


title: DApM7

value: Doxyxycline


title: WY96-3418, rep14


title: CnApM9


title: spinal cord - DKO - p-S166-RIPK1 rep1


title: Patient12-Baseline


title: WY96-3418, rep13


title: Patient12-D7


title: WY96-3418, rep11


title: CNaM6


title: WY96-3418, rep12


title: SNaM15

value: Passage 8

value: Sun1/2 siRNA


title: CNaM15

value: Control siRNA


title: Patient11-Baseline


title: D325A MEFs - TNF+Nec-1s 4h - SMARCC2

source_name: D325A MEFs - TNF+Nec-1s 4h - SMARCC2

tag: cell line

value: MEFs

tag: time


title: D325A MEFs - TNF 4h - SMARCC2

source_name: D325A MEFs - TNF 4h - SMARCC2

value: TNF


title: Patient11-Infusion

tag: sorting

value: Day 0


title: SAp13


title: D325A MEFs - TNF+Nec-1s 2h - SMARCC2

source_name: D325A MEFs - TNF+Nec-1s 2h - SMARCC2


title: Patient11-D7-CART

value: CAR-pos

tag: timepoint

value: Day +7