title: Whole blood CSAA+CGA Rat5

city: Vancouver

first: Barbara

last: Stefanska

state: BC

address: 2205 East Mall, FNH 248

department: Faculty of Land and Food Systems

country: Canada

institute: The University of British Columbia

description: 024566_CSAA CGA-24_S19_R1

data_processing:
Raw sequencing reads were pre-processed by standard quality trimming and adapter removal with Trimmomatic v 0.32 and FastX-Toolkit v 0.0.13.2; setting trimscore to 30, trim length of 30, and maximum length set to 51 bp. The final quality score was evaluated with FastQC v 0.11 and FastX. On average, 95% of reads per sample were aligned to the reference genome Rnor version 6.0 using TopHat2 v 2.1 using the lowest tolerance for mismatches, segment-mismatch set to 1 instead of 2.  Finally, aligned reads were annotated to gene features using the R package Rsubread v 2.8, and ENSEMBL IDs were converted to Gene Symbols using biomaRt v 2.46. Genes with fewer than two reads in five or more samples were classified as lowly expressed and removed from the analysis. Lastly, expression values for genes with duplicated ENSEMBL IDs or Gene Symbols were averaged, resulting in a gene expression table with 16,067 genes.
We used DESeq2 v 1.30 for all differential expression (DE) analysis with default parameters. We used two different experimental designs ~ diet for regular DE, and ~ diet + TCell + Bcell + Macrophage to incorporate cell scores determined by CIBERSORTx. Note that the neutrophils fraction was not included in the design since it is linearly dependent on all other cell fractions. We defined differentially expressed genes (DEGs) using an FDR threshold less or equal to 0.05 (FDR ≤ 0.05), and an absolute fold change greater than 2 (|log2(FC)| > 1).
Assembly: rn6
Supplementary files format and content: Excel file Rat_Polyphenols_CountTable

source_name: Whole blood

extract_protocol:
Mouse RiboPure™-Blood RNA Isolation Kit (Invitrogen) was used to extract RNA from rat whole blood samples as recommended by the manufacturer.
RNA libraries were prepared for sequencing using standard Illumina protocols. Quality check was performed using an Agilent Bioanalyzer prior to library preparation from five rats per group, namely, CSAA, CSAA+RSV, CSAA+PTS, and CSAA+CGA. The TruSeq Stranded kit (Illumina, San Diego, CA, USA) was used to prepare libraries followed by sequencing of four rats per lane using the HiSeq2500 on high-throughput mode (1x50 bp reads).

treatment_protocol: Compounds incorporated into the diet

value: Whole blood

value: Fischer 344 (F344)

value: 8 weeks

tag: Sex

value: wild type

value: Diet supplemented with chlorogenic acid (CGA)


title: Whole blood CSAA+CGA Rat3

status: Public on Jan 02 2025

type: SRA

description: 024564_CSAA CGA-12_S17_R1

library_source: transcriptomic

molecule: total RNA

organism: Rattus norvegicus

tag: tissue

tag: strain

tag: age

value: male

tag: genotype

tag: treatment


title: Whole blood CSAA+CGA Rat1

description: 024562_CSAA CGA-4_S15_R1


title: Whole blood CSAA+CGA Rat2

description: 024563_CSAA CGA-8_S16_R1


title: Whole blood CSAA+PTS Rat5

value: Diet supplemented with pterostilbene (PTS)


title: Whole blood CSAA+PTS Rat3


title: Whole blood CSAA+PTS Rat1


title: ALS_8

city: FUJISAWA

first: Yuumi

last: Okuzono

state: KANAGAWA

address: 26-Muraoka-higashi 2-chome

country: Japan

institute: Takeda Pharmaceutical Company Limited

library_source: transcriptomic single cell

data_processing:
Base calling and making fastq files were performed using software provided with the 10X Genomics Cell Ranger (cellranger mkfastq v3.0).
Count data were calculated from fastq files using software provided with the 10X Genomics Cell Ranger (cellranger count v3.0).
Count data were normalized to compare across samples using software provided with the 10X Genomics Cell Ranger (cellranger aggr v3.0).
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include gene symbol and gene expression (read count) for each cell.

organism: Homo sapiens

source_name: PBMC

extract_protocol: A single-cell RNA-seq library was prepared from PBMC using Chromium Single Cell 3' Library Kit v2 (10x Genomics) following the manufacturer’s instructions.

tag: cell type

value: PBMC

tag: disease state

value: Non-rapid ALS


title: Whole blood CSAA+RSV Rat2

value: Diet supplemented with resveratrol (RSV)


title: Whole blood CSAA+RSV Rat5


title: Whole blood CSAA+RSV Rat1


title: Whole blood CSAA+RSV Rat4


title: Whole blood CSAA Rat5

value: Control diet


title: Whole blood CSAA Rat3


title: Whole blood CSAA Rat2


title: Whole blood CSAA Rat1


title: M3

city: Guang zhou

first: Shuquan

last: Zhao

state: Guangdong

address: zhongshan second road 74

country: China

institute: Sun Yat-sen University

description: 20mg/kg  xylazine

data_processing:
Filtered the data with SOAPnuke as previous published and used Dr. Tom Multi-omics Data mining system to conduct data analysis(16). Used Bowtie2 to unite the reads to the gene database, applied RSEM to calculate the gene expression level(17,18). The DESeq2 was used to conduct the differential expression analysis and Q value less than 0.05 or FDR less than 0.001 was identified as differential expression, and Pheatmap was used to draw heatmap (19). To take insight to the change of phenotype, we used Phyper to perform GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis. Q value less than 0.05 was considered significant changes.
Assembly: Rattus_norvegicus 大鼠/NCBI/GCF_015227675.2_mRatBN7.2

source_name: Liver

growth_protocol: Forty male SD rats ranged from 160 to 200 g were obtained from ZhuHai Bestest Biotechnology Co., Ltd. (Zhuhai, China; License: SYXK, Guangdong, 2020-0107). They were feed in the environment for 7 days.

extract_protocol:
Four liver tissues in each group were sampled and then frozen in liquid nitroge and then Bangkok Genomics Innovation Co., Ltd., Wuhan, China performed RNA sequencing. 50mg liver tissue were used to extracted the RNA according to the Extraction of Animal RNA BGI-NGS-TQ-RNA-004 A0
Then isolated and fragmentated the mRNA, synthesis cDNA, conducted PCR and selected the corresponding library based on the product requirements

treatment_protocol: They were randomly divided into were randomly dived into four groups, control (saline), low dose (10mg/kg xylazine), median dose (20mg/kg xylazine) and high dose (40mg/kg xylazine). And the rats were injected the drug intraperitoneal and weighted continuous 28 days

value: Liver

value: 20mg/kg  xylazine


title: M2

description: 20mg/kg  xylazine


title: M4

description: 20mg/kg  xylazine


title: M1

description: 20mg/kg  xylazine


title: Whole blood CSAA+CGA Rat4

description: 024565_CSAA CGA-16_S18_R1


title: H4

description: 40mg/kg xylazine

value: 40mg/kg xylazine


title: Oln93 del Sox10, biological replicate 1

city: Erlangen

first: Michael

last: Wegner

state: Bavaria

address: Fahrstr. 17

department: Institut of Biochemistry

country: Germany

data_processing:
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina
Sequencing libraries were validated using the NGS Kit on an Agilent 5300 Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified using the Qubit 4.0 Fluorometer (Invitrogen, Carlsbad, CA).
The sequencing libraries were multiplexed and loaded on the flow cell on the Illumina HiSeq2500 instrument according to the manufacturer’s instructions. The samples were sequenced using a 2x100 bp single-end configuration.
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using cutadapt v1.9.1. The trimmed reads were mapped to the Rattus norvegicus reference genome available on ENSEMBL (Rnor5) using the STAR aligner v.2.52.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
DESeq2 v.1.16.1 was used for differential gene expression analysis and normalization
Assembly: Rn5
Supplementary files format and content: tab-delimited text files containing counts and DESeq results

source_name: Oln93 cell line

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit according to QIAGEN protocol.
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina

treatment_protocol: Genome-edited Oln93 cells that lack Sox10 were transduced with lentiviruses containing mouse coding sequences  of Sox8, Sox9 and Sox10

tag: cell line

value: Oln93 cell line

value: Sox10 Deletion


title: H3

description: 40mg/kg xylazine


title: H2

description: 40mg/kg xylazine


title: C3

description: normal saline

value: normal saline


title: Whole blood CSAA+PTS Rat4

value: Whole blood


title: Oln93 del Sox10, biological replicate 2


title: C4

description: normal saline


title: C1

description: normal saline


title: Whole blood CSAA+PTS Rat2

value: Fischer 344 (F344)


title: H1

description: 40mg/kg xylazine


title: C2

description: normal saline


title: Whole blood CSAA+RSV Rat3

value: 8 weeks


title: Whole blood CSAA Rat4

value: wild type


title: A2

description: 10mg/kg xylazine

value: 10mg/kg xylazine


title: A3

description: 10mg/kg xylazine


title: brm-3_dog1-4_2

city: Warsaw

first: Michal

last: Krzyszton

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics, Polish Academy of Sciences

data_processing:
In our sequencing strategy read R1 contains UMI, barcode and first nucleotide of oligo(dT). We trim read R1 to keep only UMI and barcode. Our oligo(dT) primers has two parts of UMI splited by barcode sequence - we move UMI sequences to be next to each other. For all of this we use single awk command: awk 'NR%2==1 {print $0} NR%2==0 {print substr($1,16,5) substr($1,1,15)}'
Fastq files for read R2 from the pools was demultiplexed into separate fastq files for each replica using BRBseqTools (v 1.6) Demultiplex with parameters -p UB -UMI 14 -n 1. Read R2 of each library was trimmed to remove potential contamination with poly(A) tail using BRBseqTools (v 1.6) Trim and parameters -polyA 10 -minLength 30. Then mapped using STAR (v 2.7.8a) with parameters --sjdbOverhang 99 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 1. Finally, the deduplicated counts for each gene were obtained using BRBseqTools (v 1.6) CreateDGEMatrix with parameters -p UB -UMI 14 -s yes. Counts were used for differential gene expression analysis using DESeq2 R package.
Assembly: TAIR10
Supplementary files format and content: count text files

organism: Arabidopsis thaliana

source_name: dry seeds

growth_protocol: Plants were grown in pots with soil in a greenhouse with a long-day photoperiod (16-h light/8-h dark) at 22°C/18°C. After harvest seeds were stored in paper bags at room temperature.

extract_protocol:
RNA extraction from seeds was performed by using the phenol–chloroform protocol. The frozen seeds were ground to a powder with using an electric drill and then mixed in 600µL of RNA extraction buffer (100 mM Tris pH 8.5, 5 mM EDTA ph 8.0, 100 mM NaCl, 0.5% SDS, 1% beta-mercaptoethanol). Afterward, samples were centrifuged for 5 min at 14,000 g at 4°C. The supernatant was transferred to new eppendorf tubes and 250µl of chloroform was added and samples were shaken at room temperature for 15 min. Then 250µl of phenol was added and samples were shaken for a further 15 min and centrifuged for 10 min at 14,000 g at 4°C. Then, 550µL of the aqueous layer was transferred to new tubes and mixed with 550µL of phenol–chloroform–isoamyl alcohol 25:24:1. Samples were shaken for 10 min at RT and centrifuged for 10 min at 14,000 g at 4°C. Then, 500µL of supernatant after transferring to new tubes was mixed with 10% of the volume of 3 M sodium acetate and 80% of the volume of pure ice-cold isopropanol and incubated for 15 min at RT. After the incubation, samples were centrifuged for 30 min at 14,000 g at 4°C. Finally, the RNA pellet was washed in 1mL of 80% ethanol, dried and resuspended in Milli-Q water. DNase treatment of RNA samples was performed with using TURBO DNA-freeTM Kit (Life Technologies), according to the manufacturer’s protocol.
500 ng of RNA was used in reverse transcription with 50 mM different barcoded oligo(dT) primers and SuperScript III. 0.25 of each reaction was pooled and pools were purified with Ampure beads (1.2x beads to sample volumes) and eluted in 17 ul of water. 15 ul of recovered cDNA pool was mixed by pipetting with 15 ul of second-strand synthesis mix (2x NEBNext Second Strand Synthesis (dNTP-free) Reaction Buffer (NEB), 1 U RNaseH (NEB), 1 U E. coli DNA ligase I (NEB), 5 U E. coli DNA polymerase (NEB), 30 uM dNTPs) and incubated overnight at 16°C. Reactions were purified with Ampure beads (1.2x beads to sample volumes) and eluted in 4 ul of water. 3 ul of recovered dsDNA sample was used for tagmentation using 3 ul 5x diluted B-loaded Tn5 enzyme (homemade) and 6 ul freshly prepared 2x buffer (20 mM Tris-HCl pH 7.5, 20 mM MgCl2, 50% DMF). Reactions were mixed by pipetting and incubated for 7 min at 55°C followed by 5 min at 80°C. Water was added up to 30 ul, samples were purified with Ampure beads (1.2x beads to sample volumes) and eluted with 11 ul of water. Illumina indexing PCR was performed using 10 ul tagmented DNA in 50 ul reactions with Q5 2× PCR Master Mix (NEB) and 0.5 uM final concentration of primers. Libraries were Illumina Next-seq sequenced to obtain two reads: 21 nt R1 (contain barcode and UMI) and 55 nt R2 (contain mRNA sequence).

value: dry seeds

value: brm-3 dog1-4 double mutant


title: brm-3_dog1-4_3


title: brm-3_dog1-4_4


title: brm-3_4

value: brm-3 mutant


title: brm-3_dog1-4_1


title: brm-3_3


title: brm-3_2


title: brm-3_1


title: dog1-4_4

value: dog1-4 mutant


title: dog1-4_2


title: dog1-4_3


title: Col0_4


title: dog1-4_1


title: Col0_2


title: Col0_3


title: SUCSUL_br2

city: Riverside

first: Ye

last: Xu

state: CA

address: 900 University Ave

country: USA

institute: University of California, Riverside

data_processing:
Raw reads were analyzed by a homemade pipeline pRNASeqTools v0.8 (https://github.com/grubbybio/pRNASeqTools).
Raw reads were subjected to adapter trimming using cutadapt. Reads without an adapter or shorter than 18-nt after trimming were discarded from further processing.
Trimmed reads were aligned to the Arabidopsis genome using ShortStack v3.8 with parameters (--mismatches 0 --mmap u --bowtie_m 1000 --ranmax 50).
Mapped reads were separated by size and normalization was performed by calculating the RPM (Reads per million of (total-rRNA) reads), and comparison was conducted by DESeq2 v1.30.0.
Assembly: TAIR10
Supplementary files format and content: bigwig (.bw) file containing CPM-normalized 18-42nt small RNA read counts along the whole genome

source_name: SUCSUL transgenic line

growth_protocol: 16 hr light and 8 hr dark at 22 ˚C on 1/2 MS medium

extract_protocol:
Total RNAs (30 μg) from wild type (Col-0), SS, and SS amp1 lamp1 were resolved on a 15% urea-PAGE gel with 8 M urea, and the sRNA fractions (15-40 nt) were recovered
sRNA libraries were constructed using the NEB Next Small RNA Library Prep Set for Illumina (NEB, E7300S) according to the manufacturer’s instructions.

tag: ecotype

value: WT

tag: transgene

value: 13-d-old scion


title: Col0_1


title: A4

description: 10mg/kg xylazine

value: Liver


title: SS amp1lamp1_br1

source_name: SUCSUL amp1lamp1 transgenic line


title: Col_br2

value: 13-d-old seedling


title: Col_br1


title: SS amp1lamp1_br2


title: A1

description: 10mg/kg xylazine


title: Rabbit_5 [SP3309D2]

city: Cambridge

first: wenzhong

last: xiao

state: ma

address: 38 sidney st, suite 161

institute: massachusetts general hospital

data_processing:
Sequencing quality was assessed additionally using FASTQC (v0.11.9). Transcriptome annotations of each species were downloaded from Ensembl (https://www.ensembl.org, v90). For each sample, firstly, reads were aligned to human genome hg38 using STAR in the established bulk-RNA sequencing workflow of Bcbio (v1.2.1).  Secondly, the abundance of the annotated genes of the species was estimated from the RNA-seq reads as Transcripts per Million (TPM) using Sailfish. Thirdly, to compare the gene expression between species, the abundance of the genes in each species was then translated to that of the corresponding human orthologues. Here, only genes in a non-human species that had known orthologous human genes (Ensembl v90) were considered in further analysis. When m genes in a non-human species had n orthologous genes in human (m>=0, n>=1), the abundance of each of the human orthologues is assumed to be the sum of the abundance of the m genes divided by n.
Assembly: hg38 Ensembl v90
Supplementary files format and content: TPM matrix

organism: Oryctolagus cuniculus

source_name: blood

extract_protocol:
After incubation, blood in TruCulture tubes was separated according to the manufacturer’s instructions with additional centrifugation at 800 ×g for 10 minutes.  Supernatants were saved and frozen at −80 °C for cytokine analysis.  The cell pellets were lysed using red blood cell lysis solution for 10 min followed by centrifugation at 2,000 ×g for 3 minutes, and remaining white blood cells were lysed in Qiazol and frozen at −80 °C until library construction (Qiagen).
RNA isolated from white blood cells (Qiazol, Qiagen) was quality controlled using A260/A280 ratio, 28S/18S rRNA ratio, and an RNA integrity summary score (Agilent RIN). Total RNA samples (250ngs, RIN>=7.0) were enriched for mRNA, fragmented, and converted into indexed cDNA libraries according to Illumina TruSeq Stranded mRNA protocol and quantity controlled using Agilent TapeStation. Samples were sequenced to at least 25M of 2 x 50bp paired-end reads and assessed using in-house QA/QC metric (Q2Solutions Expression Analysis).

treatment_protocol: Blood was collected into heparin tubes using meticulous pyrogen-free conditions. TruCulture tubes (Myriad RBM) containing either cell culture media only (“control”) or cell culture media plus 10 ng, 100 ng, or 1 μg/mL E. coli0113 US national reference strain LPS were prepared in advance, stored at -20 °C or below, and thawed at room temperature immediately prior to use. 1 mL blood was added to each tube and samples were incubated for 2, 6 and 24 h at 37 °C with 5% CO2.

value: blood

tag: subject

value: LPS

tag: time

tag: timeunit

value: Hour

tag: dose

tag: doseunit

value: ng/mL

tag: group

value: S (sensitive)


title: Rabbit_5 [SPC23708]

value: NC


title: Rabbit_5 [SP55CAEC]


title: Rabbit_5 [SP5CD06D]


title: Rabbit_5 [SPEA0809]


title: Rabbit_4 [SPCDE54A]


title: Rabbit_5 [SPB01875]


title: Rabbit_5 [SP731789]


title: Rabbit_5 [SPC0C71E]


title: Rabbit_5 [SP0E6B20]


title: Rabbit_4 [SPC84853]


title: Rabbit_5 [SP05899E]


title: Rabbit_4 [SPE77618]


title: Rabbit_4 [SPCADF33]


title: Rabbit_4 [SPE5AB16]


title: Rabbit_4 [SP6C93D9]


title: SUCSUL_br1


title: Rabbit_4 [SP480654]


title: Rabbit_4 [SP7C2410]


title: Rabbit_4 [SP97FB83]


title: Rabbit_3 [SP8C097F]


title: Rabbit_5 [SPF00D52]


title: Rabbit_4 [SPD00501]


title: Rabbit_3 [SPCC898A]


title: Rabbit_4 [SPF4FF35]


title: Rabbit_3 [SP84349F]


title: Rabbit_5 [SP40C226]


title: Rabbit_3 [SP0A1100]


title: Rabbit_3 [SP6C813A]


title: Rabbit_3 [SPD5D8D6]


title: Rabbit_3 [SP0CBC78]


title: Rabbit_3 [SP0D0BAD]


title: Rabbit_4 [SPD309F5]


title: Rabbit_2 [SPCCB9AA]


title: Rabbit_3 [SPFABEC3]


title: Rabbit_2 [SPD09FE0]


title: Rabbit_3 [SPCDD38E]


title: Rabbit_2 [SP511604]


title: Rabbit_2 [SP0ADA9D]


title: Rabbit_2 [SP043A6F]


title: Rabbit_3 [SP8845F6]


title: Rabbit_2 [SP62CFC7]


title: Rabbit_3 [SPDB6B51]


title: Rabbit_2 [SP16468C]


title: Rabbit_1 [SPE86D7F]


title: Rabbit_2 [SP52D021]


title: Rabbit_2 [SP9556C2]


title: Rabbit_1 [SP4BFD8F]


title: Rabbit_1 [SPA99F57]


title: Rabbit_1 [SPFE0C20]


title: Rabbit_1 [SP2FF2D4]


title: Rabbit_1 [SPFC88C5]


title: Rabbit_1 [SP1AC679]


title: Rabbit_1 [SP3D0219]


title: Rabbit_1 [SPE256B4]


title: Rabbit_1 [SP8D6A7D]


title: Sheep_4 [SPF88DBD]

organism: Ovis aries


title: Rabbit_1 [SPED433B]


title: Sheep_4 [SP6F735B]


title: Sheep_4 [SPA949B0]


title: Rabbit_2 [SP1AEBDE]


title: Sheep_4 [SP84276E]


title: Sheep_4 [SPF3C576]


title: Sheep_4 [SPB62BBE]


title: Sheep_4 [SPED2CD6]


title: Sheep_4 [SP0F07C2]


title: Sheep_4 [SP1BBBF3]


title: Sheep_4 [SP3F06B9]


title: Sheep_3 [SP29096C]


title: Sheep_3 [SP8091A6]


title: Sheep_3 [SP630836]


title: Rabbit_1 [SPBDF4CC]


title: Sheep_4 [SPBAEAAA]


title: Sheep_3 [SPB5227B]


title: Sheep_3 [SP3321E1]


title: Sheep_3 [SPDCEBE1]


title: Sheep_3 [SP4D1305]


title: Sheep_3 [SPCB745E]


title: Sheep_3 [SP1C9AA4]


title: Sheep_3 [SP966038]


title: Sheep_3 [SP28AB52]


title: Sheep_2 [SP5D824F]


title: Sheep_2 [SPEC6BC8]


title: Sheep_2 [SPF198F4]


title: Sheep_2 [SPE6DFAE]


title: Sheep_2 [SP8F68A4]


title: Sheep_2 [SP49B37F]


title: Sheep_4 [SPC810BE]


title: Sheep_2 [SP92174E]


title: Sheep_2 [SP8AA09D]


title: Sheep_2 [SPD446FE]


title: Sheep_2 [SP0F8692]


title: Sheep_1 [SPCB0256]


title: Sheep_1 [SPC26774]


title: Sheep_2 [SP256847]


title: Sheep_2 [SP0530F6]


title: Sheep_1 [SP85DB81]


title: Sheep_1 [SP5754E5]


title: Sheep_3 [SP65CD8F]


title: Sheep_1 [SPEC6B8B]


title: Sheep_1 [SPB1B061]


title: Sheep_1 [SP23FC6F]


title: Sheep_1 [SPF8F38A]


title: Sheep_1 [SPA8D38D]


title: Sheep_1 [SP468C13]


title: Sheep_1 [SPCAB40D]


title: Sheep_1 [SP16A0BB]


title: imCC_SDH2

city: Rochester

first: Cristina

last: Correia

state: Minnesota

address: Kellen Bld 3 th Floor, 200 1st street SW

institute: Mayo Clinic

data_processing:
Fastq files of pair-end RNA-Seq reads were aligned with STAR to the reference genome mm10 with default parameters.
Reads that aligned to the mouse genome.
Gene level counts were obtained using featureCounts 1.4.6 from the subRead package with gene models from corresponding UCSC annotation packages.
Assembly: mm10
Supplementary files format and content: raw counts in tab-delimited text file

molecule: polyA RNA

organism: Mus musculus

source_name: chromaffin cells/adrenal tissues

growth_protocol: Cells were harvested at 24h, 72h or 84h from initial seeding point to account for three replicates per cell line. For growth conditions, cells were grown in 6 well plates at 37°C, 95% humidity in room air (21% O2) with 5% CO2. Culture media consisted of high-glucose DMEM with GlutaMAX™ (Gibco #10566016), 10% heat-inactivated FBS (Gibco #10082147) and a 0.5 mg/mL final concentration of penicillin/streptomycin antibiotics (Gibco # 15140122). Additional supplements included 1 mM sodium pyruvate (Gibco # 11140035), 10 mM HEPES buffer (Gibco # 15630130) and nonessential amino acids [100 μM final concentration each of glycine, alanine, asparagine, aspartic acid, glutamic acid, proline, and serine (Gibco # 11140035)].

extract_protocol:
RNA was column-extracted using Rneasy Mini kit (qiagen)
RNA-seq libraries were prepared from 100-200 ng high-quality RNA using TruSeq RNA Library Prep Kit v2 (Illumina)

treatment_protocol: For imCC lines, ES cells from 129S2/SvPas mice were transfected through electroporation with a targeting vector that included Sdhb exon 2 surrounded by LoxP sites, along with a neomycin (neo) selection cassette bordered by FRT sites. Two positive embryonic stem clones were selected to be injected into C57BL/6J blastocysts and create chimeras for germline transmission. Male transmitters were bred into a Flipase-expressing background to allow excision of the neo cassette. Derived Sdhb+/fl mice were bred to generate Sdhbfl/fl animals, allowing isolation of mouse chromaffin cells (mCC) from the adrenal medullae of these Sdhbfl/fl mice followed previously described methods. Cells were maintained in a standard culture environment at 37°C with 5% CO2, using Dulbecco’s modified Eagle’s medium with glutamine and high glucose concentration (Gibco #10566016). The medium was supplemented with 10% fetal bovine serum (Gibco # 10437028) and 1% penicillin-streptomycin (Gibco # 15140122). Remaining quiescent for 6 months, some cultures spontaneously initiated growth as immortalized clusters (imCCs). Immortalized cells were isolated and subjected to infection with 107 plaque-forming units (pfu)/mL of an Ad-CMV-iCre adenovirus expressing Cre recombinase (Cell BioLabs #1045). Cloning was used to produce the used SDH-loss clone used in RNAseq, refrenced as clone 8 and its niave WT control. for iMEFs, Sdhcfl/fl mice were introduced to the R26M2rtTA/M2rtTA background to create mice in which Sdhc rearrangement could be induced by doxycycline-dependent expression of Cre recombinase via a tet-inducible promoter. After inducing rearrangement of the Sdhc gene by doxycycline treatment of Sdhcfl/fl and Sdhc+/fl iMEF lines for 5 d, cells were diluted into DMEM supplemented with 0.5 mg/mL penicillin/streptomycin antibiotics, MEM NEAA (containing glycine, alanine, asparagine, aspartic acid, glutamic acid, proline, and serine at a concentration of 100 μM), sodium pyruvate (1 mM), and HEPES buffer (10 mM). Cloning was achieved by limited dilution. Incubation was at 37°C for 2 weeks before screening for colonies. Recovered clones were then expanded gradually from 12-well plates to T25 flasks in growth medium of the same composition. A small number of cells from each clone underwent DNA extraction and PCR analysis to determine the Sdhc gene rearrangement status. Clones exhibiting homogeneous Sdhc rearrangement were selected for expansion and establishing stocks of Sdhc+/- and Sdhc-/- iMEFs refenced as clones 3 (SDH-loss) or clone 1 (heterozygous control).

value: chromaffin cells/adrenal tissues

value: imCC

value: SDH loss

value: Clones were enginneered with CRISP/CAS for SDHB. Knock out was confirmed before RNA collection


title: imCC_WT1

value: Parental


title: imCC_SDH1


title: imCC_WT2


title: imCC_WT3


title: iMEF_SDH3

source_name: fibroblasts/connective-tissue

value: fibroblasts/connective-tissue

value: iMEF

value: Clones were enginneered with CRISP/CAS for SDHC. Knock out was confirmed before RNA collection


title: iMEF_SDH1


title: iMEF_WT3

value: WT


title: iMEF_SDH2


title: iMEF_WT2


title: iMEF_WT1


title: Mouse_8 [SPAA4295]

value: R (resilient)


title: Mouse_8 [SP80EADE]


title: Mouse_8 [SP2D53FF]


title: Mouse_8 [SPE20138]


title: Mouse_8 [SPD18496]


title: Mouse_8 [SPAED881]


title: Mouse_8 [SP7D4B06]


title: Mouse_8 [SPE7E5BD]


title: Mouse_8 [SP346999]


title: Mouse_5 [SP214136]


title: Mouse_8 [SP2BEB55]


title: Mouse_5 [SP3CD195]


title: imCC_SDH3


title: Mouse_5 [SP03942F]


title: Mouse_5 [SPB8A0FB]


title: Mouse_5 [SP2F5647]


title: Mouse_5 [SP3337F9]


title: Mouse_5 [SP488A4B]


title: Mouse_5 [SPBA70C4]


title: Mouse_5 [SPE6A55E]


title: Mouse_4 [SP45B926]


title: Mouse_4 [SPC93091]


title: Mouse_4 [SPC8D314]


title: Mouse_8 [SP8E9296]


title: Mouse_4 [SPEA8C96]


title: Mouse_8 [SPEC068B]


title: Mouse_4 [SPD25A58]


title: Mouse_4 [SP04AB6B]


title: Mouse_5 [SP1E6529]


title: Mouse_4 [SP217267]


title: Mouse_4 [SP18A5A8]


title: Mouse_4 [SP6DAF3E]


title: Mouse_3 [SP62C21B]


title: Mouse_4 [SPE25543]


title: Mouse_3 [SPC22A6F]


title: Mouse_4 [SPD6EC9B]


title: Mouse_3 [SP7C88C2]


title: Mouse_3 [SP0B61EA]


title: Mouse_3 [SPF60CB2]


title: Mouse_3 [SP3C4C8F]


title: Mouse_5 [SP6884C1]


title: Mouse_3 [SP2C2B41]


title: Mouse_5 [SPC6550B]


title: Mouse_3 [SPC17519]


title: Mouse_3 [SPB363A4]


title: Mouse_3 [SP2AA393]


title: Rhesus_5 [SP9884C8]

organism: Macaca


title: Rhesus_5 [SPFBECF1]


title: Rhesus_5 [SP94A087]


title: Mouse_3 [SPE2898F]


title: Rhesus_5 [SP0DF96B]


title: Rhesus_5 [SP9C53CF]


title: Rhesus_5 [SP08E696]


title: Rhesus_5 [SP37601D]


title: Rhesus_5 [SP0CB699]


title: Mouse_4 [SPF9D2B9]


title: Rhesus_5 [SPFB5195]


title: Rhesus_5 [SPC002CE]


title: Rhesus_4 [SP608FE7]


title: Rhesus_5 [SP0999F6]


title: Rhesus_4 [SPE4703B]


title: Rhesus_4 [SP741B94]


title: Rhesus_4 [SP1FE1A6]


title: Rhesus_4 [SP962492]


title: Mouse_3 [SP12D3CB]


title: Rhesus_4 [SP7FDEA2]


title: Rhesus_4 [SP7DB787]


title: Rhesus_4 [SP1AC654]


title: Rhesus_4 [SP3FC07A]


title: Rhesus_5 [SP7363BD]


title: Rhesus_4 [SP7D2325]


title: Rhesus_4 [SPF23403]


title: Rhesus_3 [SP831BB9]


title: Rhesus_3 [SP467257]


title: Rhesus_3 [SP282057]


title: Rhesus_3 [SPFB77B7]


title: Rhesus_3 [SPD54603]


title: Rhesus_3 [SP9F8223]


title: Rhesus_4 [SPDDC56F]


title: Rhesus_3 [SPE794E3]


title: Rhesus_3 [SP0EE605]


title: Rhesus_3 [SPAC59BC]


title: Rhesus_3 [SP229955]


title: Rhesus_2 [SP4ABEEE]


title: Rhesus_2 [SP92F296]


title: Rhesus_2 [SP1C1593]


title: Rhesus_1 [SPDAECDD]


title: FACS sorted Neurons from CTRL 2 [Ctrl2_NeuN]

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

institute: LMU Munich

data_processing:
sequencing reads were aligned to the mouse reference genome (version GRCh38.100) and  gene read counts were calculated with STAR (version 2.7.3a).
Assembly: GRCh38, Ensembl annotation version 100
Supplementary files format and content: count_matrix.txt

molecule: nuclear RNA

source_name: cerebral organois

growth_protocol: hCOs were kept in neural differentiation medium in 10-cm dishes on an orbital shaker at 37°C, 5% CO2 and ambient oxygen level.

extract_protocol:
To isolate nuclei, hCOs were dissociated by Dounce homogenization and filtered with BD Falcon tubes with a cell strainer cap (Corning, 352235) to get single cells. RNase inhibitor (NEB, M0314) (0.4 U/ µl) and DNase I (NEB, M0303) (1 U/ µl) were added to the homogenization buffer. RNase inhibitor (0.2 U/ µl) was added to the blocking solution. Primary antibodies against Pax6 (Biolegend, PRB-278p) and NeuN (Millipore, MAB377) were used at 1:2,500 dilution and 1:1,000, respectively. FACS analysis was performed with a FACS Melody TM cell sorter (BD) in BD FACS Flow TM medium, with a nozzle diameter of 100 lm. Debris and aggregated cells were gated out by forward scatter, sideward scatter; single cells were gated out by FSC-W/FSC-A. RNA was extracted using RNA Clean & Concentrator Kit (Zymo Research, R1015)  according to the manufacturer’s protocol.
The integrity of the extracted RNA was analyzed at the Bioanalyzer by using the RNA 6000 pico kit (Agilent) following the manufacturer’s protocol. First-Strand cDNA synthesis and cDNA amplification were done with the SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Takara Bio USA) following the manufacturer´s protocol. For the cDNA amplification, we performed a range of PCR cycles. The amplified cDNA was purified with AMPure XP beads (Beckman Coulter) following the manufacturer's protocol. The purified sample was collected and its concentration was measured with the Qubit DNA HS kit following the manufacturer´s protocol. The concentration was ranging between 0.5-2 ng/μl. The cDNA shearing was performed using the S220 Covaris with AFA technology (Covaris) .
The library was prepared with Microplex Library preparation kit v2 (Diagenode) following the manufacturer’s protocol. After the Covaris treatment, the resulting cDNA was in 200–500 bp size range. The concentration, measured with the Qubit DNA HS kit, was 0,5-2 ng/ul (10-20 ng in total). After the library amplification steps with the Microplex Library preparation kit v2 (Diagenode) the DNA concentration was measured again with the Qubit DNA HS Kit. The concentration of the DNA was between 5-6 ng/μl. The library was purified using the AMPure XP beads (Beckman Coulter) and the concentration was checked with Qubit HS DNA kit again, revealing a final concentration between 2-6 ng. Finally, the quality and molarity of the library were also analyzed with the DNA 1000 kit (Agilent).

value: cerebral organois

value: Neurons


title: CD133+PD-L1+, rep3

city: 上海

first: Xu

last: Jiaojiao

state: 上海Shanghai

address: Zhangheng Road

institute: Fudan university

description: Library name: CD133_pos_PDL1_pos_rep3

data_processing:
Clean-tags were mapped to the GRCH38 human or the mm10 mouse reference genome dependent on the experiment setup.
For gene expression analysis, the matched reads were calculated and then normalized to fragments per kilobase of exon model per million mapped reads (FPKM) by Expectation Maximization (RSEM) software or StringTie (v1.3.1c).
The significance of the differential expression genes was determined based on a combination of the absolute value of log2 (fold-change) (|log2FC|) ≥1 and false discovery rates (FDR) ≤ 0.001.
The enrichment degrees of differentially expressed genes (DEGs) were analyzed using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database.
The software Cluster and Java Treeview were used for hierarchical cluster analysis of gene expression patterns.
Assembly: GRCH38/mm10
Supplementary files format and content: tab-delimited text files include fpkm values for each Sample

extract_protocol:
Total RNA was extracted using RNeasy Micro kit (Qiagen) or RNAmini kit (Qiagen) according to manufacturer’s instructions.
For the sorted CD133+ and CD133- B16F10 cancer cells, libraries were constructed using the TruSeq RNA sample preparation kit (Illumina), and sequencing was performed on Illumina Novaseq 6000 instrument with 150 bp paired-end reads by Genergy BIO-technology (Shanghai, China). For the other samples, the library construction and sequencing were performed by Beijing Genomics Institute (BGI, Shenzhen, China) using BGISEQ-500 platform. Single end 50 bases reads were used for the cultured macrophages or the tumor tissue samples, and pair end 100 bases reads for sorted GFP+CD133+PD-L1+ and GFP+CD133-PD-L1- cancer cells from the relapsed B16F10 tumors.

value: mouse melanoma model

value: cancer cell

value: adoptively transferred engineered macrophage-based therapy


title: Rhesus_3 [SPFA6DE5]

value: blood

value: LPS

value: Hour

value: ng/mL


title: Rhesus_2 [SP8AB15D]

value: NC


title: Rhesus_3 [SP7F3076]


title: Rhesus_2 [SP5627FD]


title: CD133-PD-L1-, rep2

description: Library name: CD133_neg_PDL1_neg_rep2


title: Rhesus_2 [SPB9E3C7]


title: Rhesus_2 [SPA54850]


title: Rhesus_2 [SPDC2802]


title: Rhesus_2 [SPECD9B6]


title: Rhesus_2 [SPDA7569]


title: Rhesus_2 [SP40232B]


title: CD133+PD-L1+, rep2

description: Library name: CD133_pos_PDL1_pos_rep2


title: CD133+PD-L1+, rep1

description: Library name: CD133_pos_PDL1_pos_rep1


title: Rhesus_2 [SPB1EB1A]


title: Rhesus_1 [SPEF63B3]


title: Rhesus_1 [SP1F602B]


title: Rhesus_1 [SPB572E9]


title: NPs-MΦ1 day 35, rep3

description: Library name: NPs_M_1_day35_rep3


title: Rhesus_1 [SP26A2D0]


title: Rhesus_1 [SP08E1BA]


title: NPs-MΦ1 day 16, rep1

description: Library name: NPs_M_1_day16_rep1


title: Untreated day 8, rep1

description: Library name: Untreated_day8_rep1


title: liver E2

city: Beijing

first: Ting

last: Zhang

address: Dongcheng District

institute: Beijing Municipal Key Laboratory of Child Development and Nutriomics

data_processing:
quality control with MultiQC
adapter and quality trimming with Cutadapt
transcript quantification with featureCounts
differential expression analysis (p value <0.05 and |log2foldchange| >1)
Assembly: grcm38.p6

source_name: liver

extract_protocol:
The mice in the EX group were euthanized and killed by cervical dislocation 24 h after the last training. We used phosphate buffered saline (PBS) for transcardial perfusion and cadavers disinfected with 70% ethanol and placed the dissection table with the abdomen facing up. The tissue samples were packaged and stored according to the requirements of each omics sequence: the size of soybean grains was required for transcription, the amount of tissue was required to reach 50-100 mg for metabolomics, >200 mg for proteomics and >500 mg for modified proteomics. The collected tissue samples were quickly frozen in liquid nitrogen and finally transferred to -80 °C for subsequent trials.
First, TRIzol reagent was used to extract total RNA from liver samples and purify it to ensure that the quality and concentration of RNA samples met the requirements of subsequent sequencing. Library was constructed and sequenced based on DNBseq platform (PE150 strategy). Low-quality sequences, such as head sequence, sequence with mass score <20, original reads with N-base ratio >10% and sequence less than 25bp, were removed from the RNA sequencing results.

value: liver

value: the running distance of each mouse is 22 kilometers


title: Untreated day 8, rep3

description: Library name: Untreated_day8_rep3


title: liver E1


title: CD133-PD-L1-, rep1

description: Library name: CD133_neg_PDL1_neg_rep1


title: LHCN-M2 cells, AICAR, mRNA rep 4

city: Ann Arbor

first: Adelaide

middle: Erin

last: Tovar

state: Michigan

address: 100 Washtenaw Ave

department: Computational Medicine & Bioinformatics

institute: University of Michigan

description:
Library name: ATS0274_mRNA
ATS0274_mRNA

data_processing:
We mapped reads to hg38 using STAR (v2.7.9a) (Dobin et al. 2013). We used SAMtools to filter high-quality read pairs (-q 255 -F 4 -F 256 -F 2048; v. 1.9 using htslib v. 1.9) (Li et al. 2009). We used FastQC to assess the quality of raw sequence data (v. 0.11.5) and MultiQC to summarize quality results (v. 1.11) (Andrews 2010; Ewels et al. 2016). To perform quality control on aligned reads, we used QoRTs (Quality of RNA-seq Tool-Set) (v. 1.3.6) (Hartley and Mullikin 2015).
We used DEseq2 v.1.34.0 (Love, Huber, and Anders 2014) to import raw counts, apply a variance stabilizing transformation, and perform differential expression analysis.
Assembly: hg38
Supplementary files format and content: File "tovar-nishino_rnaseq_raw_counts.txt" is a tab-delimited text file containing raw RNA-seq counts. File "tovar-nishino_rnaseq_vst_counts.txt" is a tab-delimited text file containing VST-transformed RNA-seq counts.

extract_protocol:
We isolated RNA and gDNA from each replicate using the Qiagen AllPrep DNA/RNA mini kit.
We used the NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA) to enrich poly(A)+ RNA transcripts from total RNA for RNA library preparation and sequencing. Afterward, we used the NEBNext® Ultra™ II Directional RNA Library Prep kit (New England BioLabs, Ipswich, MA) to prepare sequencing libraries following manufacturer’s instructions. At this stage, we excluded one sample (ATS0272, AICAR replicate 2) due to low library concentration. We sequenced libraries on an Illumina NovaSeqX and received paired-end 150bp reads.

value: skeletal muscle myocytes


title: LHCN-M2 cells, palmitate, mRNA rep 1

description:
Library name: ATS0275_mRNA
ATS0275_mRNA


title: NPs-MΦ1 day 35, rep1

description: Library name: NPs_M_1_day35_rep1


title: Untreated day 8, rep2

description: Library name: Untreated_day8_rep2


title: Rhesus_1 [SPFA7071]


title: Rhesus_1 [SP86B852]


title: Rhesus_1 [SPD67104]


title: NPs-MΦ1 day 16, rep2

description: Library name: NPs_M_1_day16_rep2


title: LHCN-M2 cells, palmitate, mRNA rep 2

description:
Library name: ATS0276_mRNA
ATS0276_mRNA


title: NPs-MΦ1 day 16, rep3

description: Library name: NPs_M_1_day16_rep3


title: liver E3


title: Rhesus_1 [SP8DAE74]


title: LHCN-M2 cells, palmitate, mRNA rep 4

description:
Library name: ATS0278_mRNA
ATS0278_mRNA


title: NPs-MΦ1 day 35, rep2

description: Library name: NPs_M_1_day35_rep2


title: Rhesus_1 [SP7F3325]


title: Rhesus_1 [SP2FAD26]


title: LHCN-M2 cells, palmitate, mRNA rep 3

description:
Library name: ATS0277_mRNA
ATS0277_mRNA


title: livliver Er C3

value: Con mice did not use treadmill training for hours.


title: livliver Er C2


title: livliver Er C1


title: LHCN-M2 cells, AICAR, mRNA rep 3

description:
Library name: ATS0273_mRNA
ATS0273_mRNA


title: LHCN-M2 cells, AICAR, mRNA rep 1

description:
Library name: ATS0271_mRNA
ATS0271_mRNA


title: Male_LongRead_Cortex_HD_4

city: Irvine

first: Ricardo

last: Miramontes

address: 845 Health Sciences Rd

institute: UC Irvine

description: unfiltered transcript abundances obtained using the talon_abundance module.

data_processing:
analyzed using SMRT Analysis software (v9.0) (Pacific Biosciences). Consensus reads were generated using ccs 4.2.0 with options --skip-polish --minLength 10 --minPasses 3 --min-rq 0.9 --min-snr 2.5. Adapters were removed with lima 1.11.0 with options --isoseq --min-score 0 --min-end-score 0 --min-signal-increase 10 --min-score-lead 0. Full-length non-chimeric reads were extracted, were oriented to the correct strand, and had poly-A tails clipped using isoseq3 refine 3.3.0 with options --min-polya-length 20 --require-polya.
The resulting full-length non-chimeric reads were mapped to mm10 reference genome using minimap2 (2.17-r941)[108] with options -ax splice:hq -uf -MD .  TranscriptClean (v2.0.2) (https://github.com/mortazavilab/TranscriptClean) was used for error correction with option --canonOnly
Assembly: Ensembl 87 annotations
Supplementary files format and content: Filtered transcript lists, which are limited to known and consistently observed transcripts, were generated using talon_filter_transcripts. Filtered and unfiltered transcript abundances were obtained using the talon_abundance module.

source_name: Brain

extract_protocol:
RNA was extracted using Trizol and 10ug of total RNA per sample was treated with Terminator 5’-Phosphate dependent exonuclease (Lucigen TER51020) according to manufacturer’s protocol. 300ng of polyA RNA was used for library construction.
RNA libraries were prepared using the SMRTbell Template Express Prep Kit 2.0 (Pacific Biosciences) using 300 ng cDNA input per sample according to the manufacturer’s protocol.
Pacbio ISO-seq

value: Brain

tag: tissue region

value: Cortex


title: LHCN-M2 cells, diff, mRNA rep 1

description:
Library name: ATS0267_mRNA
ATS0267_mRNA

tag: tissue


title: LHCN-M2 cells, undiff, mRNA rep 2

description:
Library name: ATS0264_mRNA
ATS0264_mRNA


title: LHCN-M2 cells, undiff, mRNA rep 4

description:
Library name: ATS0266_mRNA
ATS0266_mRNA


title: Male_LongRead_Cortex_NT_3

value: Non-transgenic


title: LHCN-M2 cells, diff, mRNA rep 2

description:
Library name: ATS0268_mRNA
ATS0268_mRNA


title: Male_LongRead_Striatum_HD_4

value: Striatum


title: LHCN-M2 cells, undiff, mRNA rep 1

description:
Library name: ATS0263_mRNA
ATS0263_mRNA


title: Male_LongRead_Striatum_HD_2

description:
unfiltered transcript abundances obtained using the talon_abundance module.
Note: The SRR contains raw data for two replicates.


title: Male_LongRead_Cortex_HD_1


title: Male_LongRead_Cortex_HD_3


title: LHCN-M2 cells, undiff, mRNA rep 3

description:
Library name: ATS0265_mRNA
ATS0265_mRNA


title: Male_LongRead_Cortex_NT_1


title: 511S1PB1

city: Guelph

first: Isabelle

last: Aicklen

address: 50 Stone Road East

institute: University of Guelph

data_processing:
fastp was used to trim adapters and remove low quality reads.
Indexing and read alignment for the reference genome alignment was completed using STAR. Annotation and gene ontology was completed using blastp, the Amaranthus hybridus reference genome was aligned to the UniProt Swiss-Prot database and the most appropriate match was selected based on lowest E-value.
Indexing and read alignment for the de novo transcriptome alignment was completed using Bowtie 2. SAM files were converted to BAM files using samtools, read summarization was quantified using featureCounts. Annotation of the transcriptome was done using TransDecoder. Protein sequences were aligned to UniProt Swiss-Prot database using blastp, GO terms were added using InterProScan.
Assembly: Reference sequence (Amaranthus hybridus) and assembled de novo transcriptome.
Supplementary files format and content: Comma delimited file contains raw counts for each sample.

organism: Amaranthus powellii

source_name: Leaf tissue from 4th true leaf sampled when plants were 8 to 10 cm tall

extract_protocol:
Total RNA was extracted using the Direct-zol RNA Miniprep kit by Zymo Research. Libraries were generated using 250 ng of total RNA.
Enrichment of mRNA and library preparation were performed using Illumina Stranded mRNA Prep kit (Illumina) following manufacturer's instructions. A single sample of RNA extracted from susceptible tissue was used for PacBio sequencing. cDNA libraries were prepared using Pacific Biosciences Preparing Iso-Seq libraries using SMRTbell prep kit 3.0 protocol.

value: Mix of treated and untreated tissue


title: TPC-1 cell line, sh-NC2

city: BeiJing

first: yanan

last: zhou

address: No.56 Nanlishi Road, Xicheng District

institute: Beijing Children's Hospital, Capital Medical University

description: Library name: sample5

data_processing:
The image data of the sequencing fragments measured by the high-throughput sequencer is converted into sequence data (reads) through CASAVA base recognition. The file is in fastq format, which mainly contains the sequence information of the sequencing fragments and its corresponding sequencing quality information.
Assembly: NCBI gene symbol
Supplementary files format and content: raw counts for each Sample

source_name: thyroid

extract_protocol:
Total RNA was extracted using NucleoSpin® RNA Plus (Takara Bio, Shiga, Japan)
RNA libraries were prepared for sequencing using standard Illumina protocols.
First use Qubit2.0 Fluorometer for preliminary quantification, dilute the library to 1.5ng/ul, and then use Agilent 2100 bioanalyzer to detect the insert size of the library. After the insert size meets expectations, qRT-PCR accurately quantifies the effective concentration of the library (the library is effective Concentration higher than 1.5nM) to ensure library quality
After passing the library inspection, different libraries are pooled according to the requirements of effective concentration and target off-machine data volume, and then Illumina sequencing is performed.

value: thyroid

value: papillary thyroid carcinoma


title: Male_LongRead_Cortex_NT_4


title: TPC-1 cell line, sh-NC1

description: Library name: sample4


title: Male_LongRead_Striatum_NT_4


title: LHCN-M2 cells, diff, mRNA rep 4

description:
Library name: ATS0270_mRNA
ATS0270_mRNA


title: TPC-1 cell line, sh-NC3

description: Library name: sample6


title: Male_LongRead_Striatum_HD_1


title: Male_LongRead_Striatum_NT_3


title: Male_LongRead_Striatum_HD_3


title: Male_LongRead_Cortex_HD_2


title: TPC-1 cell line, sh-CHI3L1_KD3

description: Library name: sample3


title: Male_LongRead_Cortex_NT_2


title: TPC-1 cell line, sh-CHI3L1_KD2

description: Library name: sample2


title: Male_LongRead_Striatum_NT_2


title: NPs-hMΦ, rep4

description: Library name: NPs_hM_rep4

source_name: Primary cell

value: Primary cell

value: macrophage

value: CuS nanoparticle


title: PBMCs, Caucasian, B012_L002, LONZA3038099

city: Singapore

first: Boxiang

last: Liu

address: 12 Science Drive 2, MD1 - Tahir Foundation Building, Level 5

country: Singapore

institute: National University of Singapore

description: Library name: KR_SGI_B012_L002_5GEX_LONZA3038099

data_processing:
The DRAGEN Single-Cell RNA pipeline in the Illumina DRAGEN v3.8.4 software (version 07.021.602.3.8.4-20-g74395e76) was used for pre-processing of paired-end FASTQ files from each individual scRNA-seq gene expression library. Reads from each pool were mapped to GENCODE Release 32 (GRCh38, Ensembl 98, date 2019-09-05).  The count data was processed and analyzed in R. Within each pool, every cell (barcode) and read was assigned to an individual within that pool using Genotype Data (provided) in DRAGEN v3.8.4.
Assembly: GRCh38/hg38
Supplementary files format and content: Raw data were processed from fatsq files, which contain cDNA sequences. Single-cell expression data were processed using *rds file containing single cell expression and metadata matrix.

extract_protocol:
Eight ml of blood was drawn from each donor using CPT tubes with sodium heparin (BD Vacutainer CPT, cat. no. 362753). PBMC isolation followed a standardized protocol across sites, using FBS (Sigma-Aldrich cat. no. F2442, lot 19G014 and 20A363) for cell isolation, pooling, and washing. Blood samples were processed within 2 hours at room temperature via density-gradient centrifugation (1,500 x g, 30 min, 20°C, with soft acceleration/deceleration). Plasma was aspirated, and PBMCs were pelleted at 300 x g for 15 min, then resuspended in ACK lysing buffer (Thermo Fisher, cat. no. A10492). Cells were washed twice (PBS pH 7.4, 1% FBS, 1 mM EDTA) and cryopreserved in CryoStor CS10 (STEMCELL Technologies, cat. no. 079555). Cryovials were stored at -80°C before transfer to liquid nitrogen. The full protocol is available on Protocols.io: https://www.protocols.io/view/pbmcs-isolation-from-cpt-tube-b8r9rv96.
Both AIDA and LONZA individuals were sequenced in pools of 16 individuals, including 15 AIDA samples and 1 LONZA control sample (chosen from 5 LONZA PBMC samples). Chromium Next GEM Single Cell 5’ Kit v2 was used for library construction

value: blood

value: PBMCs


title: Male_LongRead_Striatum_NT_1


title: PBMCs, Korean cohort, B012_L002, H163

description: Library name: KR_SGI_B012_L002_5GEX_H163


title: PBMCs, Korean cohort, B012_L002, H160

description: Library name: KR_SGI_B012_L002_5GEX_H160


title: PBMCs, Korean cohort, B012_L002, H165

description: Library name: KR_SGI_B012_L002_5GEX_H165


title: PBMCs, Korean cohort, B012_L002, H164

description: Library name: KR_SGI_B012_L002_5GEX_H164


title: MRC5_CoH196_2

city: Changchun

first: Yuanhua

last: Lu

state: Jilin

address: No.1066, Jinhu Road, Guigu Street

institute: Jilin Cancer Hospital

data_processing:
Raw data were filtered using SOAPnuke (v1.5.6) and clean reads were aligned to the reference genome (GCF_000001405.39_GRCh38.p13) by HISAT. Then Bowtie2 was used to align clean reads to the reference gene sequence and obtained alignment results.  Software Parameters References Sources SOAPnuke (v1.5.6) -l 15 -q 0.2 -n 0.05 [1] https://github.com/BGI-flexlab/SOAPnuke; HISAT2(v2.1.0) --sensitive --no-discordant --no-mixed -I 1 -X 1000 -p 8 --rna-strandness RF [2] http://www.ccb.jhu.edu/software/hisat/index.shtml; Bowtie2 (v2.3.4.3) -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 1 -k 200 [3] http://bowtiebio.sourceforge.net/ Bowtie2 /index.shtml RSEM (v1.3.1) --forward-prob 0
Assembly: NCBI GCF_000001405.39_GRCh38.p13
Supplementary files format and content: txt file includes FPKM and TPM values for each sample

extract_protocol:
Total RNA was extracted using TRIzol reagent
mRNAs were enriched by oligo(dT) magnetic beads, enriched mRNAs were fragmented and synthesized to cDNA. cDNA fragments were end repaired and adenylated at 3′ ends, then universal adapters were ligated to cDNA fragments, followed by PCR amplification.

value: Fibroblast

value: Co-culture


title: MRC5_CoH196_1


title: PBMCs, Korean cohort, B012_L002, H157

description: Library name: KR_SGI_B012_L002_5GEX_H157


title: PBMCs, Korean cohort, B012_L002, H158

description: Library name: KR_SGI_B012_L002_5GEX_H158


title: Un-hMΦ, rep3

description: Library name: Un_hM_rep3


title: Un-hMΦ, rep4

description: Library name: Un_hM_rep4


title: NPs-hMΦ, rep1

description: Library name: NPs_hM_rep1


title: NPs-hMΦ, rep3

description: Library name: NPs_hM_rep3


title: TPC-1 cell line, sh-CHI3L1_KD1

description: Library name: sample1


title: Un-hMΦ, rep1

description: Library name: Un_hM_rep1


title: PBMCs, Korean cohort, B012_L002, H156

description: Library name: KR_SGI_B012_L002_5GEX_H156


title: NPs-hMΦ, rep2

description: Library name: NPs_hM_rep2


title: PBMCs, Korean cohort, B012_L002, H159

description: Library name: KR_SGI_B012_L002_5GEX_H159


title: MRC5_CoH69_3


title: PBMCs, Korean cohort, B012_L002, H162

description: Library name: KR_SGI_B012_L002_5GEX_H162


title: PBMCs, Korean cohort, B012_L002, H161

description: Library name: KR_SGI_B012_L002_5GEX_H161


title: PBMCs, Korean cohort, B012_L002, H155

description: Library name: KR_SGI_B012_L002_5GEX_H155


title: Un-hMΦ, rep2

description: Library name: Un_hM_rep2


title: MRC5_CoH196_3


title: MRC5_CoH69_2


title: PBMCs, Korean cohort, B012_L002, H154

description: Library name: KR_SGI_B012_L002_5GEX_H154


title: MRC5_Mo_3

value: Culture separately


title: PBMCs, Korean cohort, B012_L002, H151

description: Library name: KR_SGI_B012_L002_5GEX_H151


title: MRC5_CoH69_1


title: LHCN-M2 cells, diff, mRNA rep 3

description:
Library name: ATS0269_mRNA
ATS0269_mRNA

value: skeletal muscle myocytes


title: MRC5_Mo_1


title: H196_Co_3

value: Small cell lung cancer cell


title: PBMCs, Korean cohort, B012_L001, H163

description: Library name: KR_SGI_B012_L001_5GEX_H163


title: PBMCs, Caucasian, B012_L001, LONZA3038099

description: Library name: KR_SGI_B012_L001_5GEX_LONZA3038099


title: MRC5_Mo_2


title: H196_Co_1


title: PBMCs, Korean cohort, B012_L001, H161

description: Library name: KR_SGI_B012_L001_5GEX_H161


title: PBMCs, Korean cohort, B012_L001, H158

description: Library name: KR_SGI_B012_L001_5GEX_H158


title: PBMCs, Korean cohort, B012_L001, H159

description: Library name: KR_SGI_B012_L001_5GEX_H159


title: PBMCs, Korean cohort, B012_L001, H165

description: Library name: KR_SGI_B012_L001_5GEX_H165


title: PBMCs, Korean cohort, B012_L001, H162

description: Library name: KR_SGI_B012_L001_5GEX_H162


title: PC-3_Deci_SAM_RNA_seq_r3

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

data_processing:
trimmed with trim_galore version 0.6.4. Parameters: --length 26 --phred33
Get raw counts with kallisto quant version 0.4.6.
CPM estimates, generated with cpm function from edgeR version 3.17
Assembly: GRCh38.p13
Supplementary files format and content: raw counts with kallisto quant version 0.4.6.
Supplementary files format and content: CPM estimates, generated with cpm function from edgeR version 3.17

growth_protocol: PC-3 cells were grown in RPMI1640 medium

extract_protocol:
5 days after starting the treatment (Medium was changed every other day) genomic DNA was extracted. DNA was treated with Bisulphite.
RNA libraries were prepared for sequencing using standard BGISeq-500 protocols

treatment_protocol: PC-3 cells were treated with Decitabine or a combination of Decitabine and SAM

value: Prostate cancer


title: PBMCs, Korean cohort, B012_L001, H164

description: Library name: KR_SGI_B012_L001_5GEX_H164


title: PBMCs, Korean cohort, B012_L001, H160

description: Library name: KR_SGI_B012_L001_5GEX_H160


title: PBMCs, Korean cohort, B012_L001, H157

description: Library name: KR_SGI_B012_L001_5GEX_H157


title: PC-3_Deci_SAM_RNA_seq_r1


title: PBMCs, Korean cohort, B012_L001, H156

description: Library name: KR_SGI_B012_L001_5GEX_H156


title: H196_Mo_3


title: H196_Mo_2


title: PC-3_Deci_SAM_RNA_seq_R2


title: PC-3_Deci_RNA_seq_r3

value: Dec


title: H196_Mo_1


title: PBMCs, Korean cohort, B012_L001, H155

description: Library name: KR_SGI_B012_L001_5GEX_H155


title: PBMCs, Korean cohort, B012_L002, H153

description: Library name: KR_SGI_B012_L002_5GEX_H153


title: PBMCs, Korean cohort, B012_L002, H152

description: Library name: KR_SGI_B012_L002_5GEX_H152


title: H196_Co_2


title: PBMCs, Korean cohort, B012_L001, H153

description: Library name: KR_SGI_B012_L001_5GEX_H153


title: PC-3_Ctr_RNA_seq_r2

value: Ctrl


title: PBMCs, Korean cohort, B012_L001, H151

description: Library name: KR_SGI_B012_L001_5GEX_H151


title: PC-3_Ctr_RNA_seq_r3


title: PBMCs, Korean cohort, B012_L001, H152

description: Library name: KR_SGI_B012_L001_5GEX_H152


title: PC-3_Deci_RNA_seq_r1


title: PBMCs, Korean cohort, B012_L001, H154

description: Library name: KR_SGI_B012_L001_5GEX_H154


title: 6 month WT,replicate 3,IgG

city: shanghai

first: danhong

last: wu

address: 3rd Floor, Building 2, 801 Heqing Road, Shanghai

department: Department of Neurology

institute: Shanghai Fifth People’s Hospital, Fudan University

description:
Library name: sample18
acetylated_RNA_sites.mRNA.xlsx

library_source: other

data_processing:
library strategy: acRIP-seq
acRIP enrichment control and library quality control, raw reads were quality controlled using Q30 aacRIP enrichment control and library quality control, raw reads were quality controlled using Q30 and FastQC. Adapter trimming of 3' sequences and removal of low quality reads were performed using Cutadapt software (v1.9.3) to generate clean reads. A post-alignment filter was applied to exclude alignments to mitochondrial DNA (chrM) and mismatched mating pairsnd FastQC
Clean reads were then aligned to the mouse genome (mm10) using Hisat2 software (v2.04).
To identify acetylated sites, we evaluated the enrichment of clean reads in acRIP, input and IgG control samples. MACS software (v1.4.2) was used to detect regions of significant read enrichment in the acRIP samples, with adjustments made to optimize the analysis of transcript-mapped reads (e.g., disabling the shift model and local lambda, and setting the sequencing read length to 150 bp).Input samples were used as controls during peak calling. The enriched regions were identified as acetylated sites and ac4C peaks were generated in bed or bam format for further analysis.
only peaks located on protein-coding exons were selected for further analysis. Additional filters were applied, including an adjusted p-value threshold of <0.05 and a fold enrichment (FE) greater than 1. Peaks with a false discovery rate (FDR)-adjusted p-value <0.05 were considered statistically significant. For IgG control peaks, a calibration step was performed to exclude non-specific IgG binding peaks, retaining only those with no coordinate overlap. Fold enrichment (FE) was calculated by dividing the difference between the acRIP and IgG peaks by the input peak.
Assembly: mm10
Supplementary files format and content: The table contains information about the mRNA acetylation modification peaks identified for each sample
Supplementary files format and content: Column A ~ F: the coordinates of the acetylated RNA sites in bed format, please ref http://genome.ucsc.edu/FAQ/FAQformat.html#format1.
Supplementary files format and content: Column G: the length of the acetylated RNA sites
Supplementary files format and content: Column H ~ I: the transcript id and gene symbol of acetylated RNA.
Supplementary files format and content: Column J ~ L: the enrichment results calculated by MACS.
Supplementary files format and content: Column M ~ U: the annotation of the acetylated gene.

molecule: other

source_name: Hippocampus

extract_protocol:
A total of 10 to 50 micrograms of RNA was subjected to immunoprecipitation using the GenSeq acRIP Kit (GenSeq Inc.) in accordance with the manufacturer's instructions. In summary, total RNA was randomly fragmented to a length of approximately 200 nt using RNA fragmentation reagents. The anti-ac4C antibody or control IgG (sc-2027, Santa Cruz) was conjugated to Protein A/G Dynabeads (Share-Bio, SB-PR001) in PBS and incubated for one hour at room temperature. Subsequently, the RNA fragments were incubated with the bead-conjugated antibodies, which were rotated at 4°C for four hours. Subsequently, the RNA/antibody complexes were subjected to multiple rounds of washing in order to remove any unbound materials. The captured RNA was subsequently eluted from the complexes and purified to ensure its suitability for subsequent analysis. Ribosomal RNA (rRNA) depletion was performed on the RNA samples using the NEBNext rRNA Depletion Kit (New England Biolabs, Inc.).
RNA libraries for immunoprecipitation (IP) and input samples were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc.) in accordance with the standard protocol. The quality of the libraries was evaluated using the Agilent 2100 Bioanalyzer (Agilent), and sequencing was conducted on the NovaSeq platform (Illumina).

value: Hippocampus

value: 6 month

value: WT

tag: antibody

value: IgG


title: 6 month WT,replicate 3,IP

description:
Library name: sample17
acetylated_RNA_sites.mRNA.xlsx

tag: age

value: IP


title: PC-3_Ctr_RNA_seq_r1

tag: genotype


title: 6 month WT,replicate 2,IgG

description:
Library name: sample15
acetylated_RNA_sites.mRNA.xlsx


title: PBMCs, Korean cohort, B011_L002, H149

description: Library name: KR_SGI_B011_L002_5GEX_H149


title: PBMCs, Caucasian, B011_L002, LONZA3030004

description: Library name: KR_SGI_B011_L002_5GEX_LONZA3030004


title: PBMCs, Korean cohort, B011_L002, H147

description: Library name: KR_SGI_B011_L002_5GEX_H147


title: PBMCs, Korean cohort, B011_L002, H148

description: Library name: KR_SGI_B011_L002_5GEX_H148


title: 6 month WT,replicate 2,Input

description:
Library name: sample13
acetylated_RNA_sites.mRNA.xlsx

value: Input


title: 6 month WT,replicate 2,IP

description:
Library name: sample14
acetylated_RNA_sites.mRNA.xlsx


title: 6 month WT,replicate 3,Input

description:
Library name: sample16
acetylated_RNA_sites.mRNA.xlsx


title: PBMCs, Korean cohort, B011_L002, H150

description: Library name: KR_SGI_B011_L002_5GEX_H150


title: PBMCs, Korean cohort, B011_L002, H143

description: Library name: KR_SGI_B011_L002_5GEX_H143


title: 6 month WT,replicate 1,Input

description:
Library name: sample10
acetylated_RNA_sites.mRNA.xlsx


title: PBMCs, Korean cohort, B011_L002, H145

description: Library name: KR_SGI_B011_L002_5GEX_H145


title: PBMCs, Korean cohort, B011_L002, H142

description: Library name: KR_SGI_B011_L002_5GEX_H142


title: PBMCs, Korean cohort, B011_L002, H144

description: Library name: KR_SGI_B011_L002_5GEX_H144


title: 6 month WT,replicate 1,IP

description:
Library name: sample11
acetylated_RNA_sites.mRNA.xlsx


title: PC-3_Deci_RNA_seq_r2

tag: treatment


title: 6 month 5xFAD,replicate 3,IgG

description:
Library name: sample9
acetylated_RNA_sites.mRNA.xlsx


title: PBMCs, Korean cohort, B011_L002, H141

description: Library name: KR_SGI_B011_L002_5GEX_H141

tag: cell type


title: 6 month 5xFAD,replicate 3,Input

description:
Library name: sample7
acetylated_RNA_sites.mRNA.xlsx


title: 6 month 5xFAD,replicate 3,IP

description:
Library name: sample8
acetylated_RNA_sites.mRNA.xlsx


title: PBMCs, Korean cohort, B011_L002, H140

description: Library name: KR_SGI_B011_L002_5GEX_H140


title: PBMCs, Korean cohort, B011_L002, H138

description: Library name: KR_SGI_B011_L002_5GEX_H138


title: PBMCs, Korean cohort, B011_L002, H139

description: Library name: KR_SGI_B011_L002_5GEX_H139


title: 6 month 5xFAD,replicate 2,IP

description:
Library name: sample5
acetylated_RNA_sites.mRNA.xlsx


title: PBMCs, Korean cohort, B011_L002, H146

description: Library name: KR_SGI_B011_L002_5GEX_H146


title: PBMCs, Korean cohort, B011_L002, H136

description: Library name: KR_SGI_B011_L002_5GEX_H136


title: 6 month 5xFAD,replicate 1,IgG

description:
Library name: sample3
acetylated_RNA_sites.mRNA.xlsx


title: PBMCs, Korean cohort, B011_L001, H150

description: Library name: KR_SGI_B011_L001_5GEX_H150


title: 6 month 5xFAD,replicate 2,Input

description:
Library name: sample4
acetylated_RNA_sites.mRNA.xlsx


title: 6 month 5xFAD,replicate 1,Input

description:
Library name: sample1
acetylated_RNA_sites.mRNA.xlsx


title: PBMCs, Korean cohort, B011_L001, H149

description: Library name: KR_SGI_B011_L001_5GEX_H149


title: PBMCs, Korean cohort, B011_L002, H137

description: Library name: KR_SGI_B011_L002_5GEX_H137


title: 6 month 5xFAD,replicate 1,IP

description:
Library name: sample2
acetylated_RNA_sites.mRNA.xlsx


title: E14.5 cKO scRNA-seq

first: Haoyang

last: Yu

state: Beijing

address: 9 Dongdan Santiao, Dongcheng District, Beijing

institute: Peking Union Medical College

description: Library name: E14.5_scRNAseq_cKO

data_processing:
Adapter trimming: Cutadapt was used to remove adapter sequences (for LACE-seq, scRNA-seq, and RNA-seq as needed). Alignment: LACE-seq reads were first mapped to mouse pre‐rRNA (Bowtie) to remove rRNA, then aligned to mm10 allowing up to two mismatches (Bowtie). RNA‐seq reads were mapped to mm10 using HISAT2 (default parameters). scRNA‐seq data were processed with the 10x Genomics pipeline (cellranger) or equivalent for barcode demultiplexing and mm10 alignment. Peak calling (LACE-seq): Piranha (parameters: -s -b 20 -p 0.01) identified enrichment peaks; IgG background signals were removed. Differential expression (RNA-seq): DESeq2 was used to compare WT vs. cKO. Single-cell analysis (scRNA-seq): Clustering, cell-type identification, and differential expression were performed using standard pipelines (e.g., Seurat).
Assembly: All alignments used mm10
Supplementary files format and content: LACE‐seq: The processed files include bigWig (.bw) tracks, representing per-base coverage of captured RNAs after immunoprecipitation. RNA‐seq: Count matrices (.txt/.csv) derived from aligned reads are provided, containing gene-level read counts for each sample. scRNA‐seq: Three files—matrix.mtx, barcodes.tsv, and features.tsv—are included. matrix.mtx holds the raw or filtered gene expression matrix in Matrix Market format, barcodes.tsv lists unique cell barcodes, features.tsv (or genes.tsv) lists gene identifiers or features.

source_name: E14.5 dorsal telencephalon

extract_protocol:
LACE-seq: RNA immunoprecipitation (IP) was performed using anti‐Syncrip or mouse IgG; captured RNA was fragmented by MNase, then dephosphorylated and adapter‐ligated. RNA-seq: Total RNA was extracted using TRIzol (Invitrogen) from cultured NPCs. scRNA-seq: Single-cell suspensions were generated from dissected dorsal cortex, with no separate “extraction” step beyond cell dissociation.
LACE‐seq: After reverse transcription, the first‐strand cDNA was barcoded and linearly amplified prior to high‐throughput sequencing. RNA‐seq: Libraries were prepared with NEBNext Ultra RNA Library Prep (paired-end, 2×150 bp). scRNA‐seq: Single‐cell libraries were generated using the 10x Genomics Chromium Single Cell 3′ Kit (v3.1), capturing ~6000 cells per channel.

value: E14.5 dorsal telencephalon

value: cKO


title: 6 month WT,replicate 1,IgG

description:
Library name: sample12
acetylated_RNA_sites.mRNA.xlsx


title: E14.5 WT scRNA-seq

description: Library name: E14.5_scRNAseq_WT


title: PBMCs, Korean cohort, B011_L001, H148

description: Library name: KR_SGI_B011_L001_5GEX_H148

value: blood

value: PBMCs


title: PBMCs, Caucasian, B011_L001, LONZA3030004

description: Library name: KR_SGI_B011_L001_5GEX_LONZA3030004


title: PBMCs, Korean cohort, B011_L001, H145

description: Library name: KR_SGI_B011_L001_5GEX_H145


title: E14.5 NPCs cKO RNA-seq (Rep2)

description: Library name: E14.5_NPCs_cKO_2

value: primary cells

value: Neural progenitor cells


title: E14.5 NPCs cKO RNA-seq (Rep3)

description: Library name: E14.5_NPCs_cKO_3


title: E14.5 NPCs WT RNA-seq (Rep3)

description: Library name: E14.5_NPCs_WT_3


title: PBMCs, Korean cohort, B011_L001, H147

description: Library name: KR_SGI_B011_L001_5GEX_H147


title: PBMCs, Korean cohort, B011_L001, H146

description: Library name: KR_SGI_B011_L001_5GEX_H146


title: PBMCs, Korean cohort, B011_L001, H143

description: Library name: KR_SGI_B011_L001_5GEX_H143


title: 6 month 5xFAD,replicate 2,IgG

description:
Library name: sample6
acetylated_RNA_sites.mRNA.xlsx


title: E14.5 NPCs WT RNA-seq (Rep2)

description: Library name: E14.5_NPCs_WT_2


title: E14.5 NPCs WT RNA-seq (Rep1)

description: Library name: E14.5_NPCs_WT_1


title: PBMCs, Korean cohort, B011_L001, H142

description: Library name: KR_SGI_B011_L001_5GEX_H142


title: PBMCs, Korean cohort, B011_L001, H144

description: Library name: KR_SGI_B011_L001_5GEX_H144


title: PBMCs, Korean cohort, B011_L001, H140

description: Library name: KR_SGI_B011_L001_5GEX_H140


title: PBMCs, Korean cohort, B011_L001, H141

description: Library name: KR_SGI_B011_L001_5GEX_H141


title: CD133+, rep3

description: Library name: CD133_pos_rep3_S50_L001

value: cancer cell


title: PBMCs, Korean cohort, B011_L001, H138

description: Library name: KR_SGI_B011_L001_5GEX_H138


title: CD133-, rep2

description: Library name: CD133_neg_rep2_S50_L001


title: CD133+, rep2

description: Library name: CD133_pos_rep2_S50_L001


title: CD133+, rep1

description: Library name: CD133_pos_rep1_S50_L001


title: PBMCs, Caucasian, B010_L002, LONZA3038097

description: Library name: KR_SGI_B010_L002_5GEX_LONZA3038097


title: PBMCs, Korean cohort, B011_L001, H139

description: Library name: KR_SGI_B011_L001_5GEX_H139


title: PBMCs, Korean cohort, B011_L001, H137

description: Library name: KR_SGI_B011_L001_5GEX_H137


title: PBMCs, Korean cohort, B011_L001, H136

description: Library name: KR_SGI_B011_L001_5GEX_H136


title: PBMCs, Korean cohort, B010_L002, H135

description: Library name: KR_SGI_B010_L002_5GEX_H135


title: PBMCs, Korean cohort, B010_L002, H133

description: Library name: KR_SGI_B010_L002_5GEX_H133


title: CD133-, rep1

description: Library name: CD133_neg_rep1_S50_L001


title: RA051, Ventral midbrain nuclei, C57BL/6 mice, 16wks

city: Seattle

first: Akira

last: Fushiki

state: WA

address: 615 Westlake Avenue North

institute: Allen Institute

description:
Library name: RA051
10x Genomics

data_processing:
Sequencing data were aligned and quantified using the Cell Ranger Single-Cell Software Suite (v.6.1.2) with default parameters against the ENSEMBL GRCh38 reference genome.
Assembly: Mouse mm10
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: Ventral midbrain

extract_protocol:
For nuclei isolation, frozen tissues were placed into a homogenization buffer that consisted of 10mM Tris pH 8.0, 250mM Sucrose, 25mM KCl, 5mM MgCl2, 0.1% Triton-X 100, 1X Protease inhibitor, 0.5% RNasin Plus RNase inhibitor and 0.1mM DTT. Tissues were placed into a 2ml dounce homogenizer and homogenized using 10 strokes of the loose dounce pestle followed by 10 strokes of the tight pestle to liberate nuclei. Homogenate was strained through a 30μm cell strainer and centrifuged at 900xg for 10 minutes to pellet nuclei. Nuclei were then resuspended in blocking buffer containing 1X PBS supplemented with 0.8% nuclease-free BSA and 0.5% RNasin Plus RNase inhibitor. Prior to fluorescence-activated nuclei sorting (FACS), DAPI was applied to nuclei suspensions at a final concentration of 0.1μg/ml and nuclei suspensions were filtered through a 30μm nylon mesh to remove aggregates.
Libraries were prepared according to the manufacturer’s protocol (10x Genomics Chromium Single Cell 3’ Reagent Kit v3).

value: All nuclei

value: Ventral midbrain

value: C57BL/6 mice

value: 16 weeks old

tag: Sex

value: Male

tag: sample

value: two animals are sampled


title: PBMCs, Korean cohort, B010_L002, H132

description: Library name: KR_SGI_B010_L002_5GEX_H132


title: E14.5 NPCs cKO RNA-seq (Rep1)

description: Library name: E14.5_NPCs_cKO_1

tag: cell line


title: RA050, Ventral midbrain nuclei, MitoPark littermate control, 24wks

description:
Library name: RA050
10x Genomics

value: MitoPark littermate controls

value: 24 weeks old


title: PBMCs, Korean cohort, B010_L002, H130

description: Library name: KR_SGI_B010_L002_5GEX_H130


title: RA049, Ventral midbrain nuclei, MitoPark littermate control, 8wks

description:
Library name: RA049
10x Genomics

value: 8 weeks old


title: RA048, Ventral midbrain nuclei, MitoPark littermate control, 16wks

description:
Library name: RA048
10x Genomics

value: Female


title: PBMCs, Korean cohort, B010_L002, H131

description: Library name: KR_SGI_B010_L002_5GEX_H131


title: PBMCs, Korean cohort, B010_L002, H129

description: Library name: KR_SGI_B010_L002_5GEX_H129


title: RA047, Ventral midbrain nuclei, MitoPark littermate control, 8wks

description:
Library name: RA047
10x Genomics


title: PBMCs, Korean cohort, B010_L002, H128

description: Library name: KR_SGI_B010_L002_5GEX_H128


title: RA046, Ventral midbrain nuclei, C57BL/6 mice, 16wks

description:
Library name: RA046
10x Genomics


title: CD133-, rep3

description: Library name: CD133_neg_rep3_S50_L001


title: CD133+, rep4

description: Library name: CD133_pos_rep4_S50_L001


title: RA044, Ventral midbrain nuclei, MitoPark littermate control, 24wks

description:
Library name: RA044
10x Genomics


title: PBMCs, Korean cohort, B010_L002, H126

description: Library name: KR_SGI_B010_L002_5GEX_H126


title: RA043, Ventral midbrain nuclei, MitoPark littermate control, 16wks

description:
Library name: RA043
10x Genomics


title: PBMCs, Korean cohort, B010_L002, H125

description: Library name: KR_SGI_B010_L002_5GEX_H125


title: PBMCs, Korean cohort, B010_L002, H124

description: Library name: KR_SGI_B010_L002_5GEX_H124


title: RA040, Ventral midbrain nuclei, MitoPark littermate control, 16wks

description:
Library name: RA040
10x Genomics


title: PBMCs, Korean cohort, B010_L002, H122

description: Library name: KR_SGI_B010_L002_5GEX_H122


title: RA041, Ventral midbrain nuclei, MitoPark littermate control, 16wks

description:
Library name: RA041
10x Genomics


title: RA039, Ventral midbrain nuclei, MitoPark littermate control, 8wks

description:
Library name: RA039
10x Genomics


title: PBMCs, Korean cohort, B010_L002, H123

description: Library name: KR_SGI_B010_L002_5GEX_H123


title: RA036, Ventral midbrain nuclei, MitoPark littermate control, 24wks

description:
Library name: RA036
10x Genomics


title: RA034, Ventral midbrain nuclei, MitoPark littermate control, 8wks

description:
Library name: RA034
10x Genomics


title: RA035, Ventral midbrain nuclei, MitoPark littermate control, 24wks

description:
Library name: RA035
10x Genomics


title: PBMCs, Korean cohort, B010_L002, H121

description: Library name: KR_SGI_B010_L002_5GEX_H121


title: PBMCs, Korean cohort, B010_L001, H135

description: Library name: KR_SGI_B010_L001_5GEX_H135


title: PBMCs, Caucasian, B010_L001, LONZA3038097

description: Library name: KR_SGI_B010_L001_5GEX_LONZA3038097


title: CD133-, rep4

description: Library name: CD133_neg_rep4_S50_L001


title: PBMCs, Korean cohort, B010_L001, H134

description: Library name: KR_SGI_B010_L001_5GEX_H134


title: RA031, Ventral midbrain nuclei, C57BL/6 8wks

description:
Library name: RA031
10x Genomics


title: PBMCs, Korean cohort, B010_L002, H127

description: Library name: KR_SGI_B010_L002_5GEX_H127


title: RA032, Ventral midbrain nuclei, C57BL/6 16wks

description:
Library name: RA032
10x Genomics


title: PBMCs, Korean cohort, B010_L001, H133

description: Library name: KR_SGI_B010_L001_5GEX_H133


title: PBMCs, Korean cohort, B010_L001, H131

description: Library name: KR_SGI_B010_L001_5GEX_H131


title: RA027, Ventral midbrain nuclei, C57BL/6 8wks

description:
Library name: RA027
10x Genomics


title: RA030, Ventral midbrain nuclei, C57BL/6 8wks

description:
Library name: RA030
10x Genomics


title: RA029, Ventral midbrain nuclei, C57BL/6 24wks

description:
Library name: RA029
10x Genomics


title: PBMCs, Korean cohort, B010_L001, H130

description: Library name: KR_SGI_B010_L001_5GEX_H130


title: RA028, Ventral midbrain nuclei, C57BL/6 24wks

description:
Library name: RA028
10x Genomics


title: PBMCs, Korean cohort, B010_L001, H129

description: Library name: KR_SGI_B010_L001_5GEX_H129


title: PBMCs, Korean cohort, B010_L001, H132

description: Library name: KR_SGI_B010_L001_5GEX_H132


title: RA026, Ventral midbrain nuclei, C57BL/6 8wks

description:
Library name: RA026
10x Genomics


title: RA025, Ventral midbrain nuclei, C57BL/6 16wks

description:
Library name: RA025
10x Genomics


title: PBMCs, Korean cohort, B010_L001, H126

description: Library name: KR_SGI_B010_L001_5GEX_H126


title: RA023, Ventral midbrain nuclei, C57BL/6 24wks

description:
Library name: RA023
10x Genomics


title: PBMCs, Korean cohort, B010_L001, H128

description: Library name: KR_SGI_B010_L001_5GEX_H128


title: PBMCs, Korean cohort, B010_L001, H124

description: Library name: KR_SGI_B010_L001_5GEX_H124


title: RA021, Ventral midbrain nuclei, MitoPark 16wks

description:
Library name: RA021
10x Genomics

value: MitoPark mice


title: RA022, Ventral midbrain nuclei, C57BL/6 24wks

description:
Library name: RA022
10x Genomics


title: RA020, Ventral midbrain nuclei, MitoPark 24wks

description:
Library name: RA020
10x Genomics


title: RA019, Ventral midbrain nuclei, MitoPark 24wks

description:
Library name: RA019
10x Genomics


title: RA017, Ventral midbrain nuclei, MitoPark 8wks

description:
Library name: RA017
10x Genomics


title: PBMCs, Korean cohort, B010_L001, H121

description: Library name: KR_SGI_B010_L001_5GEX_H121


title: PBMCs, Korean cohort, B010_L001, H122

description: Library name: KR_SGI_B010_L001_5GEX_H122


title: PBMCs, Korean cohort, B010_L002, H134

description: Library name: KR_SGI_B010_L002_5GEX_H134


title: PBMCs, Korean cohort, B010_L001, H123

description: Library name: KR_SGI_B010_L001_5GEX_H123


title: RA015, Ventral midbrain nuclei, MitoPark 24wks

description:
Library name: RA015
10x Genomics


title: RA016, Ventral midbrain nuclei, MitoPark 24wks

description:
Library name: RA016
10x Genomics


title: PBMCs, Korean cohort, B010_L001, H125

description: Library name: KR_SGI_B010_L001_5GEX_H125


title: PBMCs, Korean cohort, B009_L002, H119

description: Library name: KR_SGI_B009_L002_5GEX_H119


title: RA012, Ventral midbrain nuclei, MitoPark 8wks

description:
Library name: RA012
10x Genomics


title: PBMCs, Caucasian, B009_L002, LONZA3038016

description: Library name: KR_SGI_B009_L002_5GEX_LONZA3038016


title: PBMCs, Korean cohort, B009_L002, H120

description: Library name: KR_SGI_B009_L002_5GEX_H120


title: PBMCs, Korean cohort, B009_L002, H117

description: Library name: KR_SGI_B009_L002_5GEX_H117


title: PBMCs, Korean cohort, B009_L002, H118

description: Library name: KR_SGI_B009_L002_5GEX_H118


title: RA005, Ventral midbrain nuclei, MitoPark 16wks

description:
Library name: RA005
10x Genomics


title: RA013, Ventral midbrain nuclei, MitoPark 16wks

description:
Library name: RA013
10x Genomics


title: PBMCs, Korean cohort, B009_L002, H115

description: Library name: KR_SGI_B009_L002_5GEX_H115


title: PBMCs, Korean cohort, B009_L002, H114

description: Library name: KR_SGI_B009_L002_5GEX_H114


title: RA018, Ventral midbrain nuclei, MitoPark 8wks

description:
Library name: RA018
10x Genomics


title: PBMCs, Korean cohort, B009_L002, H113

description: Library name: KR_SGI_B009_L002_5GEX_H113


title: PBMCs, Korean cohort, B009_L002, H112

description: Library name: KR_SGI_B009_L002_5GEX_H112


title: scRNA-seq of S1Tr brain region in acute stress

city: qingdao

first: zhixin

address: ningxia road 308

institute: qingdao university

description: Library name: S1Tr-SC-sample 1

data_processing:
barcodes.tsv: list of spatial barcodes
features.tsv: list of gene lDs
matrix.mtx: gene expresion count data in Matrix Market Exchange Format
Assembly: mouse mm10
Supplementary files format and content: barcodes.tsv, features.tsv and matrix.mtx

source_name: brain S1TR region

extract_protocol:
Bilateral S1Tr were rapidly dissected according to anatomical landmarks.  We snap-frozen the fresh tissues in liquid nitrogen and stored at −80 °C to preserve the samples.
Single cell sequencing was performed using the 10 X Genomics, and Libraries were sequenced on the Illumina NovaSeq 6000 System

treatment_protocol: Mice received forced swimming test, followed 30 min later by rapidly extracting the whole brains and placed on a precooled metal plate.

value: brain S1TR region

value: neurons


title: Susceptible, PFC, sample 47

city: New York

first: Molly

middle: S

last: Estill

state: NY

address: 1 Gustave L. Levy Place

department: Neuroscience

institute: Mount Sinai School of Medicine

description: Library name: PFC_sus_6

data_processing:
Raw sequencing reads were mapped to the mm10 genome using the NGS-Data-Charmer pipeline.  In brief, reads were trimmed to remove adaptor and low-quality sequences, then the reads were aligned to the reference genome. Duplicate alignments were removed prior to gene counting and downstream analysis. Counts of mapped reads were obtained using featureCounts against the GENCODE m25 annotation.
Assembly: mm10
Supplementary files format and content: counts_genic_matrix.txt: Tab-delimited text file containing the raw read counts for annotated genes, with individual samples present as columns. fpkm_genic_matrix.txt: Tab-delimited text file containing the normalized read counts (in fragments per kilobase per million) for annotated genes, with individual samples present as columns.

source_name: PFC

extract_protocol:
RNA was extracted using Zymo’s Directzol RNA MicroPrep kit following manufacturer’s instructions. RNA quality and quantity was assessed using a Bioanalyzer (Agilent).
500 pg of RNA was used as input in Takara’s SMARTer® Stranded Total RNA-Seq Kit v2 – Pico according to manufacturer’s instructions.

treatment_protocol: Astrocytes (n = 7–8/group) were isolated using Miltenyi BioTech’s ACSA-2 MicroBead Kit from freshly micropunched (bilateral, 14G) NAc tissue

value: PFC

tag: mouse id

value: Susceptible


title: Susceptible, NAC, sample 48

description: Library name: NAC_sus_8

source_name: NAC

value: NAC


title: PBMCs, Korean cohort, B009_L002, H111

description: Library name: KR_SGI_B009_L002_5GEX_H111

value: blood

value: PBMCs


title: Resilient, PFC, sample 43

description: Library name: PFC_res_5

value: Resilient


title: Susceptible, NAC, sample 42

description: Library name: NAC_sus_7


title: PBMCs, Korean cohort, B009_L002, H110

description: Library name: KR_SGI_B009_L002_5GEX_H110


title: PBMCs, Korean cohort, B009_L002, H109

description: Library name: KR_SGI_B009_L002_5GEX_H109


title: RA006, Ventral midbrain nuclei, MitoPark 16wks

description:
Library name: RA006
10x Genomics

value: All nuclei

value: Ventral midbrain


title: RA004, Ventral midbrain nuclei, MitoPark 8wks

description:
Library name: RA004
10x Genomics

value: Male


title: Susceptible, PFC, sample 41

description: Library name: PFC_sus_5


title: PBMCs, Korean cohort, B009_L002, H116

description: Library name: KR_SGI_B009_L002_5GEX_H116


title: PBMCs, Korean cohort, B009_L002, H108

description: Library name: KR_SGI_B009_L002_5GEX_H108


title: Control, NAC, sample 40

description: Library name: NAC_ctrl_7

value: Control


title: PBMCs, Korean cohort, B009_L002, H107

description: Library name: KR_SGI_B009_L002_5GEX_H107


title: PBMCs, Korean cohort, B009_L002, H106

description: Library name: KR_SGI_B009_L002_5GEX_H106


title: Resilient, NAC, sample 38

description: Library name: NAC_res_6


title: PBMCs, Caucasian, B009_L001, LONZA3038016

description: Library name: KR_SGI_B009_L001_5GEX_LONZA3038016


title: Susceptible, PFC, sample 35

description: Library name: PFC_sus_4


title: Susceptible, NAC, sample 36

description: Library name: NAC_sus_6


title: Control, NAC, sample 34

description: Library name: NAC_ctrl_6


title: PBMCs, Korean cohort, B009_L001, H119

description: Library name: KR_SGI_B009_L001_5GEX_H119


title: Control, PFC, sample 39

description: Library name: PFC_ctrl_6


title: PBMCs, Korean cohort, B010_L001, H127

description: Library name: KR_SGI_B010_L001_5GEX_H127


title: Control, PFC, sample 33

description: Library name: PFC_ctrl_5


title: PBMCs, Korean cohort, B009_L001, H116

description: Library name: KR_SGI_B009_L001_5GEX_H116


title: Resilient, PFC, sample 31

description: Library name: PFC_res_4


title: PBMCs, Korean cohort, B009_L001, H117

description: Library name: KR_SGI_B009_L001_5GEX_H117


title: PBMCs, Korean cohort, B009_L001, H115

description: Library name: KR_SGI_B009_L001_5GEX_H115


title: Susceptible, NAC, sample 30

description: Library name: NAC_sus_5


title: PBMCs, Korean cohort, B009_L001, H114

description: Library name: KR_SGI_B009_L001_5GEX_H114


title: Susceptible, PFC, sample 29

description: Library name: PFC_sus_3


title: Resilient, NAC, sample 44

description: Library name: NAC_res_7


title: Control, NAC, sample 28

description: Library name: NAC_ctrl_5


title: PBMCs, Korean cohort, B009_L001, H120

description: Library name: KR_SGI_B009_L001_5GEX_H120


title: Control, PFC, sample 27

description: Library name: PFC_ctrl_4


title: Susceptible, NAC, sample 24

description: Library name: NAC_sus_4


title: PBMCs, Korean cohort, B009_L001, H110

description: Library name: KR_SGI_B009_L001_5GEX_H110


title: Resilient, NAC, sample 26

description: Library name: NAC_res_4


title: Resilient, NAC, sample 22

description: Library name: NAC_res_3


title: PBMCs, Korean cohort, B009_L001, H111

description: Library name: KR_SGI_B009_L001_5GEX_H111


title: PBMCs, Korean cohort, B009_L001, H109

description: Library name: KR_SGI_B009_L001_5GEX_H109


title: PBMCs, Korean cohort, B009_L001, H112

description: Library name: KR_SGI_B009_L001_5GEX_H112


title: PBMCs, Korean cohort, B009_L001, H118

description: Library name: KR_SGI_B009_L001_5GEX_H118


title: Resilient, NAC, sample 32

description: Library name: NAC_res_5


title: PBMCs, Korean cohort, B009_L001, H107

description: Library name: KR_SGI_B009_L001_5GEX_H107


title: Control, PFC, sample 17

description: Library name: PFC_ctrl_3


title: Susceptible, NAC, sample 20

description: Library name: NAC_sus_3


title: PBMCs, Korean cohort, B009_L001, H108

description: Library name: KR_SGI_B009_L001_5GEX_H108


title: Control, NAC, sample 18

description: Library name: NAC_ctrl_4


title: PBMCs, Korean cohort, B008_L002, H105

description: Library name: KR_SGI_B008_L002_5GEX_H105


title: PBMCs, Caucasian, B008_L002, LONZA3038099

description: Library name: KR_SGI_B008_L002_5GEX_LONZA3038099


title: Resilient, PFC, sample 15

description: Library name: PFC_res_3


title: PBMCs, Korean cohort, B009_L001, H106

description: Library name: KR_SGI_B009_L001_5GEX_H106


title: Resilient, NAC, sample 12

description: Library name: NAC_res_1


title: Control, NAC, sample 14

description: Library name: NAC_ctrl_3


title: PBMCs, Korean cohort, B009_L001, H113

description: Library name: KR_SGI_B009_L001_5GEX_H113


title: PBMCs, Korean cohort, B008_L002, H102

description: Library name: KR_SGI_B008_L002_5GEX_H102


title: Resilient, PFC, sample 11

description: Library name: PFC_res_2


title: PBMCs, Korean cohort, B008_L002, H101

description: Library name: KR_SGI_B008_L002_5GEX_H101


title: Susceptible, NAC, sample 10

description: Library name: NAC_sus_2


title: Susceptible, PFC, sample 9

description: Library name: PFC_sus_2


title: PBMCs, Korean cohort, B008_L002, H100

description: Library name: KR_SGI_B008_L002_5GEX_H100


title: Control, NAC, sample 8

description: Library name: NAC_ctrl_2


title: Resilient, PFC, sample 5

description: Library name: PFC_res_1


title: PBMCs, Korean cohort, B008_L002, H099

description: Library name: KR_SGI_B008_L002_5GEX_H099


title: PBMCs, Korean cohort, B008_L002, H098

description: Library name: KR_SGI_B008_L002_5GEX_H098


title: Control, PFC, sample 7

description: Library name: PFC_ctrl_2


title: Resilient, NAC, sample 16

description: Library name: NAC_res_2


title: PBMCs, Korean cohort, B008_L002, H096

description: Library name: KR_SGI_B008_L002_5GEX_H096


title: PBMCs, Korean cohort, B008_L002, H095

description: Library name: KR_SGI_B008_L002_5GEX_H095


title: Control, NAC, sample 2

description: Library name: NAC_ctrl_1


title: PBMCs, Korean cohort, B008_L002, H103

description: Library name: KR_SGI_B008_L002_5GEX_H103


title: Susceptible, NAC, sample 4

description: Library name: NAC_sus_1


title: PBMCs, Korean cohort, B008_L002, H104

description: Library name: KR_SGI_B008_L002_5GEX_H104


title: Control, PFC, sample 1

description: Library name: PFC_ctrl_1


title: PBMCs, Korean cohort, B008_L002, H094

description: Library name: KR_SGI_B008_L002_5GEX_H094


title: BV2 cells,NLC1

city: Jinan

first: Weiyue

last: Si

address: wenhuaxi road #107

institute: Qilu hospital of Shandong University

description: Library name: SAMPLE 6

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: count, fpkm values for each Sample

growth_protocol: Mouse BV2 microglia were cultured in Dulbecco's modified Eagle’s medium supplemented with 10% fetal bovine serum and 1% penicillin‒streptomycin. The cells were incubated in 5% CO2 at 37 °C.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacture's protocols.

value: Brain

value: BV2 cells

value: Microglia

value: WT


title: PBMCs, Korean cohort, B008_L002, H092

description: Library name: KR_SGI_B008_L002_5GEX_H092


title: PBMCs, Korean cohort, B008_L002, H091

description: Library name: KR_SGI_B008_L002_5GEX_H091


title: PBMCs, Caucasian, B008_L001, LONZA3038099

description: Library name: KR_SGI_B008_L001_5GEX_LONZA3038099


title: PBMCs, Korean cohort, B008_L002, H093

description: Library name: KR_SGI_B008_L002_5GEX_H093


title: BV2 cells,NLA1

description: Library name: SAMPLE 4


title: BV2 cells,NLB1

description: Library name: SAMPLE 5


title: PBMCs, Korean cohort, B008_L001, H105

description: Library name: KR_SGI_B008_L001_5GEX_H105


title: BV2 cells,LVC1

description: Library name: SAMPLE 3

value: SMEK1 knockdown


title: BV2 cells,LVB1

description: Library name: SAMPLE 2


title: PBMCs, Korean cohort, B008_L001, H104

description: Library name: KR_SGI_B008_L001_5GEX_H104


title: PBMCs, Korean cohort, B008_L002, H097

description: Library name: KR_SGI_B008_L002_5GEX_H097


title: BV2 cells,LVA1

description: Library name: SAMPLE 1


title: PBMCs, Korean cohort, B008_L001, H102

description: Library name: KR_SGI_B008_L001_5GEX_H102


title: PBMCs, Korean cohort, B008_L001, H103

description: Library name: KR_SGI_B008_L001_5GEX_H103


title: Female 3mos Cortex R62 4 IP TDP43-eCLIPseq

description: Female_TDP43eCLIPseq_3mos_CTX_R62_4.clusters.bed

data_processing:
*library strategy: eCLIP-seq
Illumina software used for basecalling
Fastq files were softtrimmed for adaptor sequence and low-quality sequenced dropped, then aligned to mm10
Peak calling was done by normalizing IP samples to input
Assembly: mm10
Supplementary files format and content: bed files containing IP reads normalized to input. Locations of input normalized read clusters (“peaks”) called using the CLIPper algorithm (https://github.com/YeoLab/clipper). The BED file contains the following tab-separated columns: Column 1: Chromosome Column 2: Start position Column 3: Stop position Column 4: -Log10(p-value) Column 5: Log2 fold enrichment in eCLIP vs. input Column 6: Strand (+ or -)

growth_protocol: All mice were housed on a 12/12-hr light/dark schedule with ad libitum access to food and water.

extract_protocol:
lysate was lysed in eCLIP-seq lysis buffer according to manufacturer protocol.
m6A-eCLIP seq (Eclipse Bioinnovation protocol v1.01R) & TDP43-eCLIP seq (Eclipse Bioinnovation protocol v2.01R) // based on Van Nostrand et al., 2016 Nature Methods

treatment_protocol: C57Bl/6 males were dosed at 5 weeks old with PBS control or ASO targeting TDP-43 at 500ug by Intracerebroventricular (ICV) bolus injection. Following 2 weeks post-dose, striatum were collected for downstream analysis.

value: Cortex

value: No Treatment


title: PBMCs, Korean cohort, B008_L001, H101

description: Library name: KR_SGI_B008_L001_5GEX_H101


title: Female 3mos Cortex R62 3 IP TDP43-eCLIPseq

description: Female_TDP43eCLIPseq_3mos_CTX_R62_3.clusters.bed


title: PBMCs, Korean cohort, B008_L001, H100

description: Library name: KR_SGI_B008_L001_5GEX_H100


title: Susceptible, PFC, sample 3

description: Library name: PFC_sus_1

value: PFC


title: Female 3mos Cortex R62 1 IP TDP43-eCLIPseq

description: Female_TDP43eCLIPseq_3mos_CTX_R62_1.clusters.bed


title: PBMCs, Korean cohort, B008_L001, H097

description: Library name: KR_SGI_B008_L001_5GEX_H097


title: Female 3mos Cortex NT 4 IP TDP43-eCLIPseq

description: Female_TDP43eCLIPseq_3mos_CTX_NT_4.clusters.bed

value: Non-transgenic


title: PBMCs, Korean cohort, B008_L001, H096

description: Library name: KR_SGI_B008_L001_5GEX_H096


title: Female 3mos Cortex NT 2 IP TDP43-eCLIPseq

description: Female_TDP43eCLIPseq_3mos_CTX_NT_2.clusters.bed


title: PBMCs, Korean cohort, B008_L001, H098

description: Library name: KR_SGI_B008_L001_5GEX_H098


title: Female 3mos Cortex NT 1 IP TDP43-eCLIPseq

description: Female_TDP43eCLIPseq_3mos_CTX_NT_1.clusters.bed


title: Female 3mos Cortex R62 2 IP TDP43-eCLIPseq

description: Female_TDP43eCLIPseq_3mos_CTX_R62_2.clusters.bed


title: PBMCs, Korean cohort, B008_L001, H093

description: Library name: KR_SGI_B008_L001_5GEX_H093


title: Female 3mos Striatum R62 3 IP TDP43-eCLIPseq

description: Female_TDP43eCLIPseq_3mos_STR_R62_3.clusters.bed

value: Striatum


title: PBMCs, Korean cohort, B008_L001, H095

description: Library name: KR_SGI_B008_L001_5GEX_H095

value: blood


title: Female 3mos Striatum R62 4 IP TDP43-eCLIPseq

description: Female_TDP43eCLIPseq_3mos_STR_R62_4.clusters.bed


title: PBMCs, Korean cohort, B008_L001, H091

description: Library name: KR_SGI_B008_L001_5GEX_H091

value: PBMCs


title: Female 3mos Cortex NT 3 IP TDP43-eCLIPseq

description: Female_TDP43eCLIPseq_3mos_CTX_NT_3.clusters.bed


title: PBMCs, Korean cohort, B008_L001, H094

description: Library name: KR_SGI_B008_L001_5GEX_H094


title: PBMCs, Korean cohort, B008_L001, H099

description: Library name: KR_SGI_B008_L001_5GEX_H099


title: Female 3mos Striatum R62 2 IP TDP43-eCLIPseq

description: Female_TDP43eCLIPseq_3mos_STR_R62_2.clusters.bed


title: PBMCs, Caucasian, B007_L002, LONZA3038306_2

description: Library name: KR_SGI_B007_L002_5GEX_LONZA3038306


title: Female 3mos Striatum NT 4 IP TDP43-eCLIPseq

description: Female_TDP43eCLIPseq_3mos_STR_NT_4.clusters.bed


title: PBMCs, Korean cohort, B007_L002, H090

description: Library name: KR_SGI_B007_L002_5GEX_H090


title: PBMCs, Korean cohort, B007_L002, H089

description: Library name: KR_SGI_B007_L002_5GEX_H089


title: Female 3mos Striatum NT 2 IP TDP43-eCLIPseq

description: Female_TDP43eCLIPseq_3mos_STR_NT_2.clusters.bed


title: Female 3mos Striatum NT 3 IP TDP43-eCLIPseq

description: Female_TDP43eCLIPseq_3mos_STR_NT_3.clusters.bed


title: PBMCs, Korean cohort, B007_L002, H088

description: Library name: KR_SGI_B007_L002_5GEX_H088


title: PBMCs, Korean cohort, B007_L002, H087

description: Library name: KR_SGI_B007_L002_5GEX_H087


title: Female 3mos Striatum NT 1 IP TDP43-eCLIPseq

description: Female_TDP43eCLIPseq_3mos_STR_NT_1.clusters.bed


title: Female 3mos Cortex R62 4 input TDP43-eCLIPseq

description: Female_TDP43eCLIPseq_3mos_CTX_R62_4.clusters.bed


title: Female 3mos Cortex R62 3 input TDP43-eCLIPseq

description: Female_TDP43eCLIPseq_3mos_CTX_R62_3.clusters.bed


title: PBMCs, Korean cohort, B007_L002, H086

description: Library name: KR_SGI_B007_L002_5GEX_H086


title: PBMCs, Korean cohort, B007_L002, H085

description: Library name: KR_SGI_B007_L002_5GEX_H085


title: Female 3mos Cortex R62 1 input TDP43-eCLIPseq

description: Female_TDP43eCLIPseq_3mos_CTX_R62_1.clusters.bed


title: PBMCs, Korean cohort, B008_L001, H092

description: Library name: KR_SGI_B008_L001_5GEX_H092


title: PBMCs, Korean cohort, B007_L002, H083

description: Library name: KR_SGI_B007_L002_5GEX_H083


title: PBMCs, Korean cohort, B007_L002, H082

description: Library name: KR_SGI_B007_L002_5GEX_H082


title: Female 3mos Cortex NT 4 input TDP43-eCLIPseq

description: Female_TDP43eCLIPseq_3mos_CTX_NT_4.clusters.bed


title: PBMCs, Korean cohort, B007_L002, H080

description: Library name: KR_SGI_B007_L002_5GEX_H080


title: PBMCs, Korean cohort, B007_L002, H081

description: Library name: KR_SGI_B007_L002_5GEX_H081


title: Female 3mos Striatum R62 1 IP TDP43-eCLIPseq

description: Female_TDP43eCLIPseq_3mos_STR_R62_1.clusters.bed


title: Female 3mos Cortex NT 1 input TDP43-eCLIPseq

description: Female_TDP43eCLIPseq_3mos_CTX_NT_1.clusters.bed


title: Female 3mos Striatum R62 3 input TDP43-eCLIPseq

description: Female_TDP43eCLIPseq_3mos_STR_R62_3.clusters.bed


title: Female 3mos Striatum R62 4 input TDP43-eCLIPseq

description: Female_TDP43eCLIPseq_3mos_STR_R62_4.clusters.bed


title: PBMCs, Korean cohort, B007_L002, H078

description: Library name: KR_SGI_B007_L002_5GEX_H078


title: PBMCs, Korean cohort, B007_L002, H079

description: Library name: KR_SGI_B007_L002_5GEX_H079


title: PBMCs, Korean cohort, B007_L002, H084

description: Library name: KR_SGI_B007_L002_5GEX_H084


title: PBMCs, Korean cohort, B007_L002, H076

description: Library name: KR_SGI_B007_L002_5GEX_H076


title: Female 3mos Striatum R62 1 input TDP43-eCLIPseq


title: Female 3mos Striatum NT 4 input TDP43-eCLIPseq

description: Female_TDP43eCLIPseq_3mos_STR_NT_4.clusters.bed


title: Female 3mos Striatum NT 2 input TDP43-eCLIPseq

description: Female_TDP43eCLIPseq_3mos_STR_NT_2.clusters.bed


title: Female 3mos Striatum NT 3 input TDP43-eCLIPseq

description: Female_TDP43eCLIPseq_3mos_STR_NT_3.clusters.bed


title: Female 3mos Cortex R62 2 input TDP43-eCLIPseq

description: Female_TDP43eCLIPseq_3mos_CTX_R62_2.clusters.bed


title: PBMCs, Korean cohort, B007_L001, H089

description: Library name: KR_SGI_B007_L001_5GEX_H089


title: PBMCs, Korean cohort, B007_L001, H088

description: Library name: KR_SGI_B007_L001_5GEX_H088


title: PBMCs, Korean cohort, B007_L001, H090

description: Library name: KR_SGI_B007_L001_5GEX_H090


title: Female 3mos Striatum NT 1 input TDP43-eCLIPseq

description: Female_TDP43eCLIPseq_3mos_STR_NT_1.clusters.bed


title: Female 3mos Cortex NT 3 input TDP43-eCLIPseq

description: Female_TDP43eCLIPseq_3mos_CTX_NT_3.clusters.bed


title: PBMCs, Korean cohort, B007_L001, H086

description: Library name: KR_SGI_B007_L001_5GEX_H086


title: Male 3mos Cortex R62 4 IP TDP43-eCLIPseq

description: Male_TDP43eCLIPseq_3mos_CTX_R62_4.clusters.bed


title: Female 3mos Cortex NT 2 input TDP43-eCLIPseq

description: Female_TDP43eCLIPseq_3mos_CTX_NT_2.clusters.bed


title: Male 3mos Cortex R62 3 IP TDP43-eCLIPseq

description: Male_TDP43eCLIPseq_3mos_CTX_R62_3.clusters.bed


title: Male 3mos Cortex R62 2 IP TDP43-eCLIPseq

description: Male_TDP43eCLIPseq_3mos_CTX_R62_2.clusters.bed


title: Male 3mos Cortex R62 1 IP TDP43-eCLIPseq

description: Male_TDP43eCLIPseq_3mos_CTX_R62_1.clusters.bed


title: PBMCs, Korean cohort, B007_L001, H087

description: Library name: KR_SGI_B007_L001_5GEX_H087


title: Female 3mos Striatum R62 2 input TDP43-eCLIPseq

description: Female_TDP43eCLIPseq_3mos_STR_R62_2.clusters.bed