title: Liver, PI4KB F0 crispant-4 (5 dpi)

city: wuhan

first: wu

middle: xiao

last: man

address: Donghu South Road

institute: Institute of Hydrobiology, Chinese Academy of Sciences

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v4-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: GCGD:Grass Carp Genome Database http://bioinfo.ihb.ac.cn/gcgd/php/index.php?page=download
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Ctenopharyngodon idella

source_name: Liver

extract_protocol:
Livers were removed, flash-frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. RNA concentration and purity was measured using NanoDrop 2000(Thermo Fisher Scientific, Wilmington, DE). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）.First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H . Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Liver

value: PI4KB F0 crispant

tag: developmental stage

value: injected with II-GCRV

tag: sample receiving_time

value: 5 days post injection with II-GCRV


title: InsB12-20(C19S):I-Ag7 tetramer-binding CD4 T cells, RNA

status: Public on Sep 30 2025

type: SRA

city: St Louis

first: Tiandao

last: Li

state: MO

address: 4444 Forest Park Ave

country: USA

institute: Washington University

description:
Library name: TS_gex
10x genomics
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
C19S-combined-barcodes.csv

library_source: transcriptomic single cell

data_processing:
Libraries were processed using Cell Ranger (v7.1.0). Low-quality barcodes and UMIs were filtered and mapped to the mouse genome (mm10). Both datasets were further aggregated using the Cell Ranger aggr pipeline (v7.1.0). The Cell Ranger aggr pipeline automatically equalizes the average read depth between samples. The gene expression from both datasets were filtered, normalized, and clustered, and the resulting Cloupe file was created and imported into the Loupe Browser for further analyses and visualization. To further define the unique molecular features of the cell population in the study, the feature barcode approach was employed to quantify each feature in each cell. The Cell Ranger (v7.1.0) pipeline outputs the feature barcode counts for each cell barcode. Specific antibody detection and filtering were performed as follows: the log2 count of target ≥10, while the other log2 counts ≤6. PCA was performed to reduce the dimensionality of the dataset to its most important features, and the principal components were visualized by UMAP plots.
Assembly: mm10
Supplementary files format and content: barcodes.tsv, features.tsv, matrix.mtx, csv
Supplementary files format and content: barcode.tsv.gz: barcode-1/TC-2, barcode-2/TS-2, barcode-3/TP-2, barcode-4/TS-1, barcode-5/TP-1, barcode-6/TC-1. C19S-combined-barcodes.csv: the 2nd column is cell types

molecule: total RNA

organism: Mus musculus

source_name: Pooled spleens and lymph nodes

extract_protocol:
For scRNA-seq experiments, spleen and lymph node cells were pooled from 8-week-old female NOD mice (n=6-10). After red blood cell lysis, cells were washed with MACS buffer, and the CD19+ B cells and CD11b+ myeloid cells were depleted using CD19 beads (Miltenyi Biotec, Cat #: 130-050-301) and CD11b beads (Miltenyi Biotec, Cat#: 130-097-142). Cells were then stained with fluorochrome-conjugated tetramers followed by magnetic enrichment using anti-PE and anti-APC beads. Surface staining was performed as described above and tetramer-positive and polyclonal cells were sorted using the BD FACS Aria II sorter (BD Biosciences).
cDNA was prepared after the GEM generation and barcoding, followed by the GEM-RT reaction and bead cleanup steps. Purified cDNA was amplified for 11-16 cycles before being cleaned up using SPRI Select beads. Samples were then run on a Bioanalyzer to determine the cDNA concentration. V(D)J target enrichment (TCR) was performed on the full-length cDNA. Gene Expression, Enriched TCR, and Feature libraries were prepared according to the recommended protocols from the 10× Genomics Chromium Single Cell 5′ Reagent Kits User Guide (v2 Chemistry Dual Index) with Feature Barcoding technology for Cell Surface Protein and Immune Receptor Mapping, with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10× Genomics platform, the following kits were used: Chromium Next GEM Single Cell 5′ Kit v2, 16 rxns (Cat #: PN-1000263), Chromium Next GEMChip K Single Cell Kit, 48 rxns (Cat #: PN-1000286), Chromium Single Cell Human TCR Amplification Kit (Cat #: PN-1000252), Dual Index Kit TT Set A, 96 rxns(Cat #: PN-1000215), 5’ Feature Barcode Kit, 16 rxns (Cat #: PN-1000256), and Dual Index Kit TN Set A, 96 rxns (Cat #: PN-1000250).The concentration of each library was accurately determined through qPCR using the KAPA library Quantification Kit according to the manufacturer’s protocol (KAPA Biosystems/Roche) to achieve the desired cluster counts for the Illumina NovaSeq6000 instrument. Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 151×10×10×151 sequencing recipe according to the manufacturer’s protocol. A median sequencing depth of 50,000 reads/cell was targeted for each Gene Expression library, and 5000 reads/cell for each V(D)J and Feature library.

tag: tissue

value: Pooled spleens and lymph nodes

tag: cell type

value: CD4+ T cells

tag: genotype

value: WT NOD mice


title: Tetramer-negative CD4+ T cells, TCR

description:
Library name: TP_tcr
10x genomics
clonotypes.csv.gz
filtered_contig_annotations.csv.gz
C19S-combined-barcodes.csv

library_source: transcriptomic

data_processing:
Libraries were processed using Cell Ranger (v7.1.0). Low-quality barcodes and UMIs were filtered and mapped to the mouse genome (mm10). Both datasets were further aggregated using the Cell Ranger aggr pipeline (v7.1.0). The Cell Ranger aggr pipeline automatically equalizes the average read depth between samples. The gene expression from both datasets were filtered, normalized, and clustered, and the resulting Cloupe file was created and imported into the Loupe Browser for further analyses and visualization. To further define the unique molecular features of the cell population in the study, the feature barcode approach was employed to quantify each feature in each cell. The Cell Ranger (v7.1.0) pipeline outputs the feature barcode counts for each cell barcode. Specific antibody detection and filtering were performed as follows: the log2 count of target ≥10, while the other log2 counts ≤6. PCA was performed to reduce the dimensionality of the dataset to its most important features, and the principal components were visualized by UMAP plots.
Assembly: mm10
Supplementary files format and content: barcodes.tsv, features.tsv, matrix.mtx, csv
Supplementary files format and content: barcode.tsv.gz: barcode-1/TC-2, barcode-2/TS-2, barcode-3/TP-2, barcode-4/TS-1, barcode-5/TP-1, barcode-6/TC-1. C19S-combined-barcodes.csv: the 2nd column is cell types
Library strategy: scTCR-seq


title: InsB12-20:I-Ag7 tetramer-binding CD4 T cells, TCR

description:
Library name: TC_tcr
10x genomics
clonotypes.csv.gz
filtered_contig_annotations.csv.gz
C19S-combined-barcodes.csv


title: Tetramer-negative CD4+ T cells, RNA

description:
Library name: TP_gex
10x genomics
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
C19S-combined-barcodes.csv


title: Liver, PI4KB F0 crispant-3 (5 dpi)

country: China

tag: treatment


title: recombinant inbred line (RIL) JY006

city: Beijing

first: Xin

last: Lu

address: Zhongguancun South Street,Haidian District

institute: Chinese Academy of Agricultural Sciences

library_source: genomic

data_processing:
To identify SNPs in the RIL population, Burrows-Wheeler Aligner (Li and Durbin 2009) and GATK(McKenna et al. 2010) were used for alignment and SNP identification
The SNPs of the RILs were supported by a minimum of 1 base. ANNOVAR was employed to determine the physical position of each SNP based on the B73 RefGen_V4 sequence.
Assembly: B73
Library strategy: genotyping-by-sequencin(GBS)

molecule: genomic DNA

organism: Zea mays

source_name: leaf

growth_protocol: Maize plants were planted in the field and hybrids were removed prior to sampling

extract_protocol:
DNA isolation and extraction using the CTAB protocol (Murray and Thompson 1980)
DNA from 275 RILs was processed according to the previously published GBS method (Zhou et al. 2016), in which NlaⅢ (NEB) and EcoRI (NEB) were used for genomic DNA digestion with a TAA site that can be recognized by the restriction enzyme MseⅠ. Universal primers and index primers were employed to purify PCR products using Agencourt AMPure XP (Beckman). Fragments that were 350–400 bp (including adaptors and indexes) were isolated and purified for sequencing

treatment_protocol: Leaf tissues were collected during the tasseling vegetative stage and freeze-dried at −80 °C or genomic DNA isolation

value: leaf


title: Mock infected_2

city: Jackson

first: Jorge

middle: Eugenio

last: Vidal

state: MS

address: 2500 North State Street, Jackson MS 39216

department: Cell and Molecular Biology

institute: University of Mississippi Medical Center

description:
Library name: Sample 5
column name in P1600_Normalized_counts_STAR.cvs:

data_processing:
fastqc version v0.11.9, STAR version 2.7.10a_alpha_220818, featureCounts version 2.0.6 and R version 4.4.2; Fastq files were mapped using STAR and generated raw read using featureCounts. Normalization was performed on raw read counts using DESeq2
Assembly: Homo sapiens: Ensembl/Hg38 (GRCh38)
Supplementary files format and content: CSV file containing normalized expression values for each gene and sample.

organism: Homo sapiens

source_name: Lung

extract_protocol:
RNA was extracted using the Pure Link RNA Mini Kit from archived samples (Invitrogen) according to manufacturer instructions and assessed for quality control parameters of minimum concentration and fidelity (i.e. 18S and 28S bands, RIS >8) through the UMMC Molecular and Genomics Core Facility (MGCF).
Libraries were prepared for RNA sequencing per detailed protocols from Illumina mRNA stranded kit. Briefly, a pooled library was prepared from using n=12-24 samples per group using TruSeq mRNA Stranded Library Prep Kit (Set-A-indexes),
Libraries were assessed for quality and size Qiagen QIAxcel Advanced System or Agilent TapeStation. The library was sequenced using the NextSeq 2000 using P3 (200 cycles, paired end 100bp) on the Illumina NextSeq 2000 platform.

value: Lung

tag: cell line

value: Epithelial cells

value: Mock infected 4 h


title: InsB12-20:I-Ag7 tetramer-binding CD4 T cells, RNA

description:
Library name: TC_gex
10x genomics
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
C19S-combined-barcodes.csv


title: Liver, PI4KB F0 crispant-2 (5 dpi)


title: InsB12-20(C19S):I-Ag7 tetramer-binding CD4 T cells, TCR

description:
Library name: TS_tcr
10x genomics
clonotypes.csv.gz
filtered_contig_annotations.csv.gz
C19S-combined-barcodes.csv


title: recombinant inbred line (RIL) JY005


title: Liver, WT3 (5 dpi)

value: WT


title: InsB12-20(C19S):I-Ag7 tetramer-binding CD4 T cells, FBC

description:
Library name: TS_fbc
10x genomics
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
C19S-combined-barcodes.csv
feature_reference.csv

library_source: other

molecule: protein


title: TIGR4∆lctO_1

description:
Library name: Sample 4
column name in P1600_Normalized_counts_STAR.cvs:

tag: s. pneumoniae_strain

value: Spn-infected 4 h


title: recombinant inbred line (RIL) JY004


title: TIGR4∆spxB_1

description:
Library name: Sample 3
column name in P1600_Normalized_counts_STAR.cvs:


title: Tetramer-negative CD4+ T cells, FBC

description:
Library name: TP_fbc
10x genomics
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
C19S-combined-barcodes.csv
feature_reference.csv


title: Liver, WT2 (5 dpi)


title: Liver, WT1 (5 dpi)


title: InsB12-20:I-Ag7 tetramer-binding CD4 T cells, FBC

description:
Library name: TC_fbc
10x genomics
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
C19S-combined-barcodes.csv
feature_reference.csv


title: recombinant inbred line (RIL) JY003


title: TIGR4_1

description:
Library name: Sample 2
column name in P1600_Normalized_counts_STAR.cvs:


title: Mock infected_1

description:
Library name: Sample 1
column name in P1600_Normalized_counts_STAR.cvs: P1600_1_H11101_Mock


title: recombinant inbred line (RIL) JY001


title: recombinant inbred line (RIL) JY002


title: Liver, PI4KB F0 crispant-6 (uninfected)

value: injected with PBS

value: 5 days post injection with PBS


title: Liver, PI4KB F0 crispant-3 (uninfected)


title: colon paracancerous tissue O-glycoRNA

city: 苏州市

first: Jianbo

last: Deng

state: 江苏省

address: 江苏省苏州市姑苏区三香路1055号

institute: Second Affiliated Hospital of Soochow University

data_processing:
The sequencing outcome analysis executed on Ubuntu 20.04.6
Removes adapter sequences and low-quality reads by trimmomatic software v 0.30 (parameter:  LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:17).
Download the Rfam database (version 14) and Homo_sapiens.GRCh38.ncrna.fa file to construct a non-coding RNA database (parameter:  makeblastdb -dbtype nucl).
Align the clean sequencing data (after quality control) to the non-coding RNA reference database using BLASTN v 2.2.28+  (parameter:  -outfmt '10 qseqid sseqid pident length qcovs qcovhsp qcovus mismatch gapopen qstart qend sstart send evalue bitscore' -evalue 0.01 -num_threads 4)
Use miRDeep2 V 2_0_0_8 to identified microRNA and their expression data.
Assembly: hg38
Supplementary files format and content: Comma-separated values files include raw counts and TPM for each Sample

molecule: other

source_name: colon

extract_protocol:
We used TRIzol to extract total RNA from the tissues, and then 20 µg of RNA was taken to enrich for N- and O-glycoRNAs using the optimized SPCgRNA and TnORNA techniques. Subsequently, 20 µL of the enriched glycoRNA was utilized for the construction of sequencing libraries.
RNA libraries for small RNA sequencing were prepared using Illumina HiSeq  /Novaseq or MGI2000

value: colon

value: paracancerous


title: Sample tag library associated with mouse NAT and tumor isotype and anti-IL5 treated AKPS CD45 negative, ST, scRNAseq

city: Zürich

first: Kristina

last: Handler

address: Winterthurerstrasse

department: Institute of Experimental Immunology

country: Switzerland

institute: University of Zürich

description: Library name: NAT_tumor_Iso_anti_IL5_Mm_ST

data_processing:
Demultiplexing of BCL files with Bcl2fastq (v2.20.0433, Illumina)
Count matrix generation using the BD Rhapsody™ WTA analysis pipeline (v1.12.1) on the SevenBridges Genomics platform
Assembly: STAR index generation using STAR (v2.5.2b) with gene code GRCm38 v25 for mouse and GRCh38 v43 for human data
Supplementary files format and content: Text file showing the input data for the WTA Analysis pipeline at the beginning of the file. Followed by a matrix (first column: “Cell_index”, cell IDs; second column: “Bioproduct”, Gene Symbols; third column: “RSEC_Reads”, Number of UMI reads per cell ID and bioproduct; forth column: “Raw_Molecules”, Reads with the same cell ID, same UMI sequence and same bioproduct collapsed into single molecules; fifth column: “RSEC_Adjusted_Molecules”, Number of molecules detected after RSEC molecular identifier adjustment algorithm, this is the counts used for downstream analysis;

molecule: polyA RNA

source_name: Colon and tumor

extract_protocol:
BD Rhapsody Express Single-Cell Analysis System (BD Bioscience)
mRNA Whole Transcriptome Analysis (WTA) and Sample Tag Library Preparation Protocol (BD Biosciences)

treatment_protocol: Cell hasing unsing BD Rhapsody Mouse and Human Single-Cell Multiplexing kit

value: Colon and tumor

tag: strain

tag: cell line_injected

value: AKPS organoids (Apc-LOF, p53-LOF, Kras-GOF, Smad4-LOF)

value: Isotype and Anti-IL5 antibody

tag: cellular enrichment

value: CD45 negative

tag: bd rhapsody_capture_bead_version

value: enhanced beads

tag: sample tag_(cell_hashing)_version

value: Single-Cell Multiplex Kit - Mouse custom against MHC-H2 Class I

tag: sample tag_(cell_hashing)


title: low-PC male Ye3189


title: Mouse colon Citrobacter rodentium CD45 pos, WTA, scRNAseq

description: Library name: Colon_Crod_Mm_WTA

source_name: Colon

value: Colon

value: C57BL/6J Cre

value: Citrobacter rodentium infection

value: CD45 positive

value: Single-Cell Multiplex Kit - Mouse


title: high-PC female Ji846

value: leaf


title: Liver, WT3 (uninfected)

value: Liver

value: WT


title: colon paracancerous tissue N-glycoRNA

address: 江苏省苏州市姑苏区三香路1055号


title: colon cancerous O-glycoRNA

address: 江苏省苏州市姑苏区三香路1055号

value: cancerous


title: Liver, WT2 (uninfected)

value: injected with PBS

value: 5 days post injection with PBS


title: Mouse NAT and tumor isotype and anti-IL5 treated AKPS CD45 negative, WTA, scRNAseq

description: Library name: NAT_tumor_Iso_anti_IL5_Mm_WTA

value: Colon and tumor


title: chicken_ES_cyto_2

city: Boulder

first: Mika

last: Nevo

state: Colorado

address: 2315 Walnut St

institute: CU Boulder

description: Cytoplasm

data_processing:
Mapping using hisat2
Annotating using featureCounts
Assembly: gal6
Supplementary files format and content: Matrix of Raw Counts

organism: Gallus gallus

source_name: ES cells

extract_protocol: none provided

value: ES cells


title: colon cancerous N-glycoRNA

address: 江苏省苏州市姑苏区三香路1055号

value: colon


title: Liver, WT1 (uninfected)


title: sh-circFTO-3

city: Hefei

first: Qidong

state: Anhui

address: 443 Huangshan Road, Shushan district

institute: Lianxin Liu Lab

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: hg18
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: HepG2 mesenchymal cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

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 manufacturer's protocols.

treatment_protocol: HepG2 cells were infected with sh-ctrl and sh-circFTO lentivirus

value: epithelial

value: circFTO KD


title: chicken_ES_pbody_1

description: Pbody


title: sh-circFTO-1


title: Testis, KO, bio rep3

city: New Brunswick

first: Tracy

middle: G

last: Anthony

state: NJ

address: 59 Dudley Rd

department: Nutritional Sciences

institute: Rutgers University

description:
Library name: Testis, KO, bio rep3
Testis_KO_r3

data_processing:
De-multiplexed sequencing reads were trimmed using fastp v0.23.4 with default arguments. Trimmed reads were then aligned with HISAT2 v2.1.0 to the HISAT2 transcriptome index using the Mus musculus GRCm38.p4 reference genome assembly plus a putative spliced transcript sequence for the Bckdk gene trap and a NeoR cassette sequence. Output SAM files were converted to BAM files using picard tools v1.119 with option 'VALIDATION_STRINGENCY=LENIENT'. Individual gene counts were generated using htseq-count v0.11.2 with options '-m intersection-nonempty -s yes'. Counts were filtered to include only expressed transcripts using DESeq2 v1.46.0 ‘(rowSums(DESeqDataSetFromHTSeqCount) > = 10)’, which were subsequently normalized using ’counts(., normalized = TRUE) and log-transformed using ‘rlog(., blind – TRUE)’ in DESeq2.
Assembly: GRCm38.p4
Supplementary files format and content: TXT of DESeq2-normalized counts
Supplementary files format and content: TXT of rlog-transformed counts

source_name: Testis

extract_protocol:
Frozen tissues were ground into a fine powder using a mortar and pestle, and RNA was extracted from approximately 20 mg of powdered tissue via the miRNeasy Mini Kit (Qiagen, 217004) per manufacturer’s instructions. In brief, tissues were lysed using QiAzol. Chloroform extraction was performed followed by centrifugation at 12,000 x g for 15 minutes at 4oC. The resulting aqueous solution was isolated, and 1.5 volumes of 100% ethanol was added to each sample and transferred to a RNeasy Mini for on-column DNase treatment. Final elution was by 30 uL of RNase-free water.
RNA quality was assessed by Agilent TapeStation; samples with RQN > 7.2 were selected for library preparation and sequencing. Libraries were generated from polyA-selected RNA using manufacturer’s recommendations for Illumina 2 x 150 basepair sequencing. All samples were sequenced to a minimum depth of 35 million per sample.

treatment_protocol: Mice were euthanized by decapitation and skeletal muscle (gastrocnemius and plantaris combined) and testis tissues were collected between ZT6 –ZT7 (12-1 PM local time). Muscle and testis from Bckdk+/+ and BckdkM/M were collected and flash frozen in liquid nitrogen.

value: Testis

tag: replicate

value: BckdkM/M

tag: Sex

value: Male


title: Testis, KO, bio rep2

description:
Library name: Testis, KO, bio rep2
Testis_KO_r2


title: Testis, KO, bio rep1

description:
Library name: Testis, KO, bio rep1
Testis_KO_r1


title: Sample tag library associated with mouse colon Citrobacter rodentium CD45 pos, ST, scRNAseq

description: Library name: Colon_Crod_Mm_ST

value: Colon

value: C57BL/6J Cre

value: Citrobacter rodentium infection

value: enhanced beads


title: Testis, WT, bio rep3

description:
Library name: Testis, WT, bio rep3
Testis_WT_r3

value: Bckdk+/+


title: sh-circFTO-2

value: Liver

value: WT


title: ChIP-WT-Igg-1

first: Ruifeng

address: haidian

institute: Tsinghua University

data_processing:
1) The ChIP-seq reads were mapped to reference genome by using bowtie2 with the “-p 5 -t -q -N 1 -L 25 -X 2000 --no-mixed --no-discordant” options, followed by removing low mapped quality reads, mitochondrial reads, duplications. PCR duplicates were removed using picard MarkDuplicates. Macs272 was used for peak calling with the setting of “-f BAM -B --nomodel --keep-dup all”. 2) ChIP-seq and CUT&Tag Differential Peak Analysis. The differential peak was analyzed by R package DiffBind73  with the FDR ≤ 0.01 and FC ≥ 1.5.
Assembly: mm10
Supplementary files format and content: bigwig

source_name: spleens and lymph nodes

extract_protocol:
ChIP assay was performed using Active Motif’s ChIP assay kit (53035) according to manufacturer’s instructions with slight modifications
ChIP samples were prepared according to the Active Motif protocol. In brief, CD8+ T cells were activated with anti-CD3/CD28 for 48 h, after 24 h of infection with Irf8-HA, infected CD8+ T cells were purified and cultured in the presence of IL-2 (10U/mL) for another 48 h, then re-stimulated with PMA/Ionomycin for 2 h and fixed with 1% formaldehyde at a concentration of 1 million cells/mL. ChIP assay was performed using Active Motif’s ChIP assay kit (53035) according to manufacturer’s instructions with slight modifications. A total of 1 x 107 cells were lysed and digested with shearing enzyme followed by sonication. Antibodies against HA tag (3724, clone C29F4; Cell Signaling Technology) and anti-CTCF (CST, catalog 3418) was added to supernatant followed by Dynabeads Protein A (LifeTechnologies) pulling down target fragment.

value: spleens and lymph nodes

value: cd8+ T cell


title: sh-control-3

value: ctrl


title: Testis, WT, bio rep2

description:
Library name: Testis, WT, bio rep2
Testis_WT_r2


title: ChIP-WT_CTCF-rep2


title: sh-control-2


title: Testis, WT, bio rep1

description:
Library name: Testis, WT, bio rep1
Testis_WT_r1


title: ChIP-WT-CTCF-rep1


title: sh-control-1


title: Muscle, KO, bio rep3

description:
Library name: Muscle, KO, bio rep3
Muscle_KO_r3

source_name: Muscle

value: Muscle


title: ChIP-KO-Igg-1

value: Irf8 knockout


title: chicken_ES_cyto_1

description: Cytoplasm

value: ES cells


title: chicken_ES_pbody_2

description: Pbody


title: Muscle, KO, bio rep2

description:
Library name: Muscle, KO, bio rep2
Muscle_KO_r2


title: eds1_2_flg22_24_3

type: RNA

city: Meguro

first: Kei

last: Hiruma

state: Tokyo

address: 3-8-1 Komaba,

department: Life Sciences

country: Japan

institute: The University of Tokyo

description: Gene expression data from plant leaves

hyb_protocol: After amplification and fragmentation, 12.5 μg cRNA was hybridized for 16 h at 45°C on a GeneChip ATH1-121501 Genome Array.

scan_protocol: GeneChips were washed and stained with Fluidics Script FS450-004 in an Affymetrix Fluidics Station 450 and scanned using GeneChip Operating Software version 1.4 with Affymetrix default analysis settings and global scaling for signal normalization.

data_processing: Probe signal values were subjected to quantile normalization (Bolstad et al., 2003) and summarization using the GeneChip robust multiarray average algorithm (Wu et al., 2004), and then the expression values of the genes were determined.

label: biotin

organism: Arabidopsis thaliana

source_name: eds1 plant treated with flg22 at 24h, replicate 3

label_protocol: Biotinylated cRNA was prepared according to a standard Ambion protocol from 1 μg total RNA.

extract_protocol: Total RNA was isolated with the RNeasy Mini Kit supplied with RNase-Free DNase (Qiagen) according to the manufacturer’s instructions. RNA quality was assessed with RNA Nanochips on a Bioanalyzer (Agilent).

tag: ecotype

value: leaf


title: eds1_2_flg22_24_2

description: Gene expression data from plant leaves

source_name: eds1 plant treated with flg22 at 24h, replicate 2


title: Col_0_flg22_24_3

description: Gene expression data from plant leaves

source_name: Col-0 plant treated with flg22 at 24h, replicate 3


title: Col_0_flg22_24_2

description: Gene expression data from plant leaves

source_name: Col-0 plant treated with flg22 at 24h, replicate 2


title: ChIP-KO_CTCF-rep2


title: Muscle, KO, bio rep1

description:
Library name: Muscle, KO, bio rep1
Muscle_KO_r1


title: ChIP-KO-CTCF-rep1


title: sEVs, replicate 2

city: Nantes Cedex 1

first: Laura

last: ENTZ

address: Faculté d'Odontologie 1 place Alexis Ricordeau

country: France

institute: INSERM UMR 1229 - RMeS

data_processing:
miRge3.0 -s ${samplename}.fastq -lib ./miRge3_Lib -a illumina -on mouse -db mirbase --adapter AACTGTAGGCACCATCAAT --front GTTCAGAGTTCTACAGTCCGACGATC --qiagenumi -umi 0,12 -cpu 5 -udd -o  {samplename}_results
R version 4.2.2 (Ubuntu 18.04.6 LTS)
DESeq2_1.38.2
Assembly: miRBase v22, GRCm38, https://sourceforge.net/projects/mirge3/files/miRge3_Lib/
Supplementary files format and content: miR.Counts.csv (miRNA raw read counts across samples)

source_name: bone

extract_protocol:
EVs were collected from tibias and femurs of  8-week-old male mice. After carefully removing all surrounding soft tissue and cutting the epiphyses, bones were centrifuged at 14 000 x g for 3 sec to eliminate bone marrow. Then the bones were crushed at 5000 rpm for 10 sec. The supernatant was collected and centrifuged at 700 x g for 10 min to remove bone debris and subsequently a centrifugation at 2000 x g was performed for 10 min to eliminate cells. The supernatant corresponding to the total fraction was ultracentrifuged at 100 000 x g for 70 min to separate the total vesicular fraction (pellet) (EVtot) from the soluble protein fraction (residual supernatant). The total fraction was centrifuged at 10 000 x g for 30 min, the pellet was washed with PBS at 10 000 x g for 30 min to collect a sub-population of large EVs (lEVs). Next, the supernatant was ultracentrifuged on a 30 % PBS-sucrose cushion at 100 000 x g for 70 min. The interface between the supernatant and the PBS-sucrose cushion was collected and washed in PBS at 100 000 x g for 70 min to obtain a population of small EVs (sEVs). All centrifugations were performed at 4°C. All the purified EVs-fractions were resuspended in PBS, aliquoted and stored at 4°, -20° or -80°C before use. Total RNA from three replicate of lEVs and sEVs was extracted using miRNeasy Mini Kit (QUIAGEN).
To construct the libraries, 1-5 ng of the small RNA fraction were processed using Qiaseq mir RNA library prep kit (Qiagen) according to manufacturer instructions.
Libraries are sequenced on an Illumina MiSeq instrument using 75 base-lengths read in a single read mode.

value: bone

tag: group

value: sEVs

value: no treatment


title: Muscle, WT, bio rep3

description:
Library name: Muscle, WT, bio rep3
Muscle_WT_r3

value: Male


title: eds1_2_flg22_24_1

description: Gene expression data from plant leaves

source_name: eds1 plant treated with flg22 at 24h, replicate 1


title: Irf8


title: Muscle, WT, bio rep2

description:
Library name: Muscle, WT, bio rep2
Muscle_WT_r2


title: sEVs, replicate 1


title: Muscle, WT, bio rep1

description:
Library name: Muscle, WT, bio rep1
Muscle_WT_r1


title: RNA-seq_ko2

data_processing:
1) Raw data processing. Raw sequencing reads were first adapter-trimmed by Trim Galore v0.4.4 with the “--paired” option, and aligned to mm10 reference genome with HISAT2 (version 2.2.1) with “-X 600 --rg-id --rg --known-splicesite-infile --novel-splicesite-outfile -p 25 --reorder” options. StringTie (v2.1.4) was used for transcript quantification with GENCODE vM12 annotation and “-e -B -p 10 -G -o” options. “prepDE.py” script was used to extract the read count information directly from the gtf files generated by StringTie with “-i -g -t” options. The reads count per gene was regarded as the gene expression. 2) Differential Genes Analysis. The gene expression matrix was normalized and analyzed by DESeq2 as the software recommended.
Assembly: mm10
Supplementary files format and content: CSV  file includes normalized counts for each Sample

extract_protocol:
Total RNA from CD8+ T cells was extracted by TRIzol (Invitrogen) according to manufacturer’s instruction.
total RNA was sent to BGI Genomics for cDNA library preparation and sequencing. Every sample has two replicates.


title: lEVs, replicate 3

value: lEVs


title: CD-1 LV Saline treatment Biological replicate 4

city: Boston

first: Maria

last: Lehtinen

state: MA

address: 300 Longwood Ave, Mailcode Bch3400

institute: Boston Children's Hospital

description: Library name: Saline4

data_processing:
cutadapt v2.5
STAR 2.6.1b
featureCounts v.2.0.6
Assembly: GRCm39
Supplementary files format and content: txt featurecount output of raw read counts

source_name: choroid plexus

extract_protocol:
Qiagen RNAEasy Microprep kit
Directional mRNA library preparation (poly A enrichment)

treatment_protocol: Whole blood was collected from an E14.5 donor litter into an Eppendorf with 3 µL of 0.8% sodium citrate for anticoagulation. Blood was then centrifuged for 10 minutes at 500g at 4ºC, and supernatant removed. This volume was measured and then 3 µL was subtracted to account for the anticoagulant volume. Approximately 1 mL of sterile saline was added to the tube and the blood resuspended before being centrifuged again. Supernatant was removed, and the wash step repeated at least once, or until supernatant was clear. Replacement of sterile saline to original volume was then added, and cells resuspended.

value: choroid plexus

value: Saline

tag: batch


title: sEVs, replicate 3

tag: tissue


title: Col_0_flg22_24_1

description: Gene expression data from plant leaves

source_name: Col-0 plant treated with flg22 at 24h, replicate 1


title: RNA-seq_ko1

tag: cell type


title: CD-1 LV Saline treatment Biological replicate 3

description: Library name: Saline3

tag: genotype


title: eds1_elf18_24h_3

description: Gene expression data from plant leaves

source_name: eds1 plant treated with elf18 at 24h, replicate 3


title: lEVs, replicate 2

tag: treatment


title: rsw3_elf18_24h_2

description: Gene expression data from plant leaves

source_name: rsw3 plant treated with elf18 at 24h, replicate 2


title: eds1_elf18_24h_2

description: Gene expression data from plant leaves

source_name: eds1 plant treated with elf18 at 24h, replicate 2


title: RNA-seq_wt2


title: eds1_elf18_24h_1

description: Gene expression data from plant leaves

source_name: eds1 plant treated with elf18 at 24h, replicate 1


title: lEVs, replicate 1


title: Input


title: MEL01-B2M

city: Chiba city

first: Yuka

last: Saeki

state: Chiba

address: 1-8-1, Inohana, Chuo-ku

institute: Chiba university

description: Melanoma_B2M-introduced cell line

hyb_protocol: cRNA was hybridized to GeneChip™ Human Gene 2.0 ST Array, washed and stained according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The data were analyzed with median polish summarization and quantile normalization by Affymetrix® Expression Console™ 1.1 software, and obtained normalized intensity values.

source_name: Melanoma_B2M-introduced cell line

label_protocol: The cRNA was amplified, labeled using GeneChip WT Terminal Labeling and Control Kit according to the manufacturer's instructions.

growth_protocol: MEL01-B2M and MEL01-B2M-R were maintained in RPMI1640 10% FCS.

extract_protocol: not provided

value: melanoma

tag: cell line


title: MEL01-B2M-R

description: Melanoma_resistant B2M-induced cell line


title: CD-1 LV Saline treatment Biological replicate 2

description: Library name: Saline2


title: rsw3_elf18_24h_3

description: Gene expression data from plant leaves

source_name: rsw3 plant treated with elf18 at 24h, replicate 3


title: NSC_Batch4

city: Newark

first: Rebecca

last: Zaritsky

address: 205 South Orange Ave

institute: NJMS - - Newark, NJ

description: Library name: Sample20

data_processing:
Data were processed using nf-core/rnaseq v3.10. Raw transcriptome reads were assessed for quality control (FASTQC v0.11.9) and trimmed for quality and adapter contaminants using cutadapt v3.4.
Trimmed reads were aligned to the Mus musculus genome GRCm38 using STAR (v2.6.1), followed by transcript abundance calculation via Salmon (v1.9.0).
Hit count normalization and differential gene expression group cross-comparisons were performed using DESeq2 (v1.26.0).
Assembly: GRCm38
Supplementary files format and content: CSV including RPKM for each sample

source_name: Neural Stem Cell (NSC)

extract_protocol:
RNA was isolated from SVZ neural progenitors (NP) using NucleoSpin® RNA XS according to the manufacturer's instructions. PolyA plus RNAs were amplified and enriched using Ambion’s messageAmp II aRNA amplification kit. The quality of amplified aRNA was verified using the Bioanalyzer.
A cDNA library was constructed using the Illumina TrueSeq protocol. The barcoded cDNA library was purified with AmpureXP beads and quantified using Qubit High sensitivity DNA kit and the quality of the library was determined by analyzing on Agilent bioanalyzer. Libraries mixed at equimolar ratios were sequenced on a NextSeq500 (Illumina, San Diego, CA) for 75 cycles.

treatment_protocol: Pups were euthanised via decapitation at P5. The periventricular tissue was dissected and dissociated using liberase and manual trituration. Cells were stained for 4 surface antigens (CD15, CD133, CD140a, NG2) and isolated based on expression using FACS.

value: Neural Stem Cell (NSC)


title: CD-1 LV Saline treatment Biological replicate 1

description: Library name: Saline1

value: WT


title: Fiko, replicate 3,CTCF

city: Guangzhou

first: Xiaoling

last: Wang

state: Guangdong

address: No. 195, West Dongfeng Road

institute: Guangzhou Medical University

data_processing:
the quality of the raw data was assessed using FastQC (v0.12.1). The adaptor sequences were trimmed, and low-quality bases were removed using Trim Galore (v0.6.10). Subsequently, the reads were aligned to the mouse reference genome (UCSC mm10) and only uniquely mapped reads (MAPQ > 10) were retained using HISAT2 (v2.2.1). SAMtools v1.7 was used to convert the SAM files to BAM files and to sort the BAM files. PicardMarkDuplicates 2.21.6 was used to remove duplicate reads in the bam files. MACS v.2.1.1 was used for ATAC-seq, CTCF and H3K27ac peak calling. BAM files were then converted to Bigwig files using deepTools (v3.5.4). Motif enrichment analysis was conducted using HOMER. Visualization of signal tracks was performed using IGV and WashU Epigenome Browser.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak,matrix files
Library strategy: CUT&Tag

source_name: the spleen and lymph nodes

extract_protocol:
FACS-sorted live Treg cells
A total of 200 ng of RNA was used as input for the SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Clontech), following the manufacturer’s protocol. libraries for ATAC-seq CUT&Tag were following manufacturer's protocols

value: the spleen and lymph nodes

value: Treg cells from the spleen and lymph nodes

value: CtcfiKO


title: NSC_Batch3

description: Library name: Sample19


title: Fiko, replicate 2,CTCF


title: CD-1 LV RBC treatment Biological replicate 3

description: Library name: RBC3

value: red blood cells


title: Col_elf18_24h_3

description: Gene expression data from plant leaves

source_name: Col-0 plant treated with elf18 at 24h, replicate 3


title: rsw3_elf18_24h_1

description: Gene expression data from plant leaves

source_name: rsw3 plant treated with elf18 at 24h, replicate 1


title: Col_elf18_24h_2

description: Gene expression data from plant leaves

source_name: Col-0 plant treated with elf18 at 24h, replicate 2


title: NSC_Batch2

description: Library name: Sample18


title: Fiko, replicate 1,CTCF


title: RNA-seq_wt1

source_name: spleens and lymph nodes

value: spleens and lymph nodes

value: cd8+ T cell


title: CD-1 LV RBC treatment Biological replicate 1

description: Library name: RBC1


title: PFMP_Batch4

description: Library name: Sample16

source_name: Neural Progenitor (PFMP)

value: Neural Progenitor (PFMP)


title: Fctr, replicate 3,CTCF

value: Control


title: CD-1 LV RBC treatment Biological replicate 2

description: Library name: RBC2


title: NSC_Batch1

description: Library name: Sample17


title: rsw3_elf18_10h_2

description: Gene expression data from plant leaves

source_name: rsw3 plant treated with elf18 at 10h, replicate 2

value: leaf


title: PFMP_Batch3

description: Library name: Sample15


title: Fctr, replicate 1,CTCF


title: rsw3_elf18_10h_3

description: Gene expression data from plant leaves

source_name: rsw3 plant treated with elf18 at 10h, replicate 3


title: Multiplexed Pool 3 – Day 7 (BC001–BC004)

city: Schlieren

first: Florence

last: Vallelian

address: Wagistrasse 12

department: Department of Internal Medicine

institute: University Hospital and University of Zurich

description:
Library name: pool3_day7
Samples: IL4_Day_7 (BC001), IL10_Day_7 (BC002), TGFb_Day_7 (BC003), TNFa_Day_7 (BC004)

data_processing:
Demultiplexing and read alignment using CellRangerMulti (cellranger version 9.0.0)
Downstream analysis using scanpy 1.11
Assembly: Mus_musculus/GENCODE/GRCm39/Annotation/Release_M31-2023-01-30
Supplementary files format and content: .h5 output of CellRangerMulti (9.0.0)

source_name: BMDC

extract_protocol:
BM cells were isolated by flushing the femurs and tibias of 7- to 12-week-old C57BL/6J mice and then passed through a 70-μm filter. The BM cells were plated at a density of 3 x 105 cells/ml on tissue culture-treated 60 mm UpCell dishes (Nunc™ UpCell™, ThermoFisher) in complete RPMI-1640 medium (10% fetal calf serum (FCS), 1% L-glutamine and 1% P/S) supplemented with 100 ng/ml recombinant mouse M-CSF (PeproTech) or 20 ng/ml recombinant GM-CSF (PeproTech) as previously described (Vallelian et al. 2022). On day 3, half of the medium was replaced. Cultures were treated on day 3 or 4  with IL-4 (20 ng/ml, PeproTech), IL-10 (100 ng/ml), TGF-β (100 ng/ml), or IFNγ (20 ng/ml, PeproTech). The BM cells were harvested for analysis on day 7 from the temperature-responsive cell culture plates after cooling to room temperature. Cells were washed twice in PBS and centrifuged (300g, 10 min) before processing.
Single-cell suspensions were fixed following the demonstrated protocol Fixation of cells & Nuclei for Chromium Fixed RNA Profiling (10X Genomics, CG000478) and processed for long-term storage at -80°C. After storage, up to 2 Mio cells per sample were hybridized with unique single Mouse WTA probes using BC001-004 according to the User Guide Chromium Fixed RNA Profiling Reagent Kits for Multiplexed Samples (10X Genomics, CG000527).

value: BMDC


title: Col_elf18_24h_1

description: Gene expression data from plant leaves

source_name: Col-0 plant treated with elf18 at 24h, replicate 1


title: PFMP_Batch1

description: Library name: Sample13


title: Multiplexed Pool 2 – Day 5/7 (BC001–BC004)

description:
Library name: pool2_day5_7
Samples: TGFb_Day_5 (BC001), TNFa_Day_5 (BC002), Control_Day_7 (BC003), IFNy_Day_7 (BC004)


title: PFMP_Batch2

description: Library name: Sample14


title: Fiko, replicate 3, H3k27ac


title: rsw3_elf18_10h_1

description: Gene expression data from plant leaves

source_name: rsw3 plant treated with elf18 at 10h, replicate 1


title: Multiplexed Pool 3 – Day 5 (BC001–BC004)

description: Library name: pool3_day5

source_name: MC-38 tumor cells and BMDM

growth_protocol: Tumor cell line culture GFP-MC38 were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin, 1% nonessential amino acids and 1% sodium pyruvate. A cell line with homogeneous GFP expression was obtained by FACS sorting. Cell line authentication was performed before and after cell sorting by Short Tandem Repeat (STR) DNA genotype analysis. Cell cultures were maintained at 37°C and 5% CO2 in a humidified incubator. All cells used in this study were confirmed to be negative for mycoplasma.

extract_protocol:
Spheroids were dissociated in 2 ml digestion medium + 25 µg/ml Liberase ™ + 40 µg/ml DNase I and incubated for 30-45 min in a water bath at 37°C with gentle shaking every 5 min. Then, 4 ml PBS + 0.04% BSA was added to stop the digestion. Digested spheroids were used immediately.
Single-cell suspensions were fixed following the demonstrated protocol Fixation of cells & Nuclei for GEM-X Flex Gene Expression (10X Genomics, CG000782) and processed for long-term storage at -80°C. After storage, a maximum of 0.5 Mio cells per sample were hybridized with unique single Mouse WTA probes using BC001-004 according to the User Guide GEM-X Flex Gene Expression Reagent Kits for Multiplexed Samples (10X Genomics, CG000787).

treatment_protocol: BM cells were isolated by flushing the femurs and tibias of 7- to 12-week-old C57BL/6J mice and then passed through a 70-μm filter. The BM cells were plated at a density of 3 x 105 cells/ml on tissue culture-treated 60 mm UpCell dishes in complete RPMI-1640 medium supplemented with 100 ng/ml recombinant mouse M-CSF or 20 ng/ml recombinant GM-CSF. On day 3, half of the medium was replaced. Cultures were treated on day 3 or 4  with IL-4 (20 ng/ml, PeproTech), IL-10 (100 ng/ml), TGF-β (100 ng/ml) , or IFNγ (20 ng/ml, PeproTech) (100 ng/ml) . The BM cells were harvested for analysis on day 7 from the temperature-responsive cell culture plates after cooling to room temperature. Cells were washed twice in PBS and centrifuged (300g, 10 min) before processing.

value: MC-38 tumor cells and BMDM

tag: pooled samples


title: Multiplexed Pool 1 – Day 5 (BC001–BC004)

description:
Library name: pool1_day5
Samples: Control_Day_5 (BC001), IFNy_Day_5 (BC002), IL4_Day_5 (BC003), IL10_Day_5 (BC004)


title: Fiko, replicate 2, H3k27ac


title: eds1_elf18_10h_3

description: Gene expression data from plant leaves

source_name: eds1 plant treated with elf18 at 10h, replicate 3


title: GRP3_Batch4

description: Library name: Sample12

source_name: Neural Progenitor (GRP3)

value: Neural Progenitor (GRP3)


title: Col_elf18_10h_3

description: Gene expression data from plant leaves

source_name: Col-0 plant treated with elf18 at 10h, replicate 3


title: eds1_elf18_10h_2

description: Gene expression data from plant leaves

source_name: eds1 plant treated with elf18 at 10h, replicate 2


title: Fctr, replicate 2,CTCF


title: eds1_elf18_10h_1

description: Gene expression data from plant leaves

source_name: eds1 plant treated with elf18 at 10h, replicate 1


title: Fctr, replicate 3, H3k27ac

source_name: the spleen and lymph nodes


title: GRP3_Batch3

description: Library name: Sample11


title: Multiplexed Pool 1 – Day 1 (BC001–BC004)

description: Library name: pool1_day1


title: GRP3_Batch2

description: Library name: Sample10


title: Fctr, replicate 2, H3k27ac


title: Multiplexed Pool 2 – Day 1/5 (BC001–BC004)

description: Library name: pool2_day1_5


title: GRP3_Batch1

description: Library name: Sample9


title: Fctr, replicate 1,H3k27ac


title: GRP2MP3_Batch4

description: Library name: Sample8

source_name: Neural Progenitor (GRP2/MP3)

value: Neural Progenitor (GRP2/MP3)


title: Visual cortex, P7-P9, replicate 4

city: Los Angeles

first: Kathie

last: Eagleson

state: CA

address: 4650 Sunset Blvd.

institute: Children's Hospital Los Angeles

description:
VC_processed_all_cell_types.rds
VC_processed_excitatory_neuron_subset.rds

data_processing:
FASTQ files were processed through the complete Cell Ranger pipeline with default settings for sequence alignment and expression quantification.
Assembly: mm10
Supplementary files format and content: Raw and filtered tab separated files and matrix files from Cell Ranger. Clustered, qc'd, and annotated rds files from Seurat.

source_name: visual cortex

extract_protocol:
Brains were removed and placed in Hibernate media on ice. FC and VC were dissected, cut into 0.5mm pieces and transferred to fresh HABG at 37oC for 10 min. The tissue was then incubated in papain in Hibernate A without calcium for 30 min at 30C. The papain was replaced with 2 ml of HABG media, and cells were dissociated by trituration. The trituration step was repeated twice and the final cell suspension was passed through a Falcon 40-micron cell strainer, followed by centrifugation at 200g for 10 min. The cells were resuspended in HABG to yield a final concentration of 800-1000 cells/mL and >80% viability (trypan blue exclusion).
Library preparation was performed in the Spatial Biology and Genomics Core at the Saban Research Institute, CHLA. Each replicate was processed through Chromium Next GEM Automated Single Cell 3′ Library and Gel Bead Kit v3.1, using the manufacturer’s protocol, with an output target of 10,000 cells.

value: visual cortex

value: pooled male and female

tag: ratio

value: 1:1 male to female

tag: age


title: Visual cortex, P7-P9, replicate 5


title: GRP2MP3_Batch3

description: Library name: Sample7


title: Visual cortex, P7-P9, replicate 3

value: 0:2 male to female


title: C32, Infant, 12 weeks old, Week 4

city: Pittsburgh

first: Greg

last: Delgoffe

state: PA

address: 5051 Centre Avenue, 4051

department: Microbiology and Immunology

institute: University of Pittsburgh

description: Library name: C32

data_processing:
The quality of the reads was checked using fastQC, and summarized using MultiQC
After initial quality control, the sequence data were quantified using Kallisto, to obtain transcript level abundances and counts using Mmul_10 (Ensembl) as reference
Assembly: Mmul_10
Supplementary files format and content: csv format and normalized counts
Supplementary files format and content: csv format and TPM

organism: Macaca mulatta

source_name: Peripheral Blood

extract_protocol:
Following collection of peripheral blood (~0.5 mL per time point) in BD PAXgene tubes, the tubes were gently inverted 8-10 times and stored vertically at room temperature for a minimum of 2 hr. The tubes were then transferred to a −80 °C freezer where they were stored until the time of the RNA extraction. Total RNA was extracted using a Paxgene Blood miRNA kit (Qiagen cat# 763134), following the manufacturer’s 775  instructions. The purified RNA was eluted in buffer BR5 (supplied in the kit), incubated at 65 °C for 5 minutes for RNA denaturation, and stored immediately at −80 °C. RNA samples were shipped on dry ice to Novogene Inc. for RNA quality control, library preparation and RNA sequencing.
cDNA libraries were prepared at Novogene Inc. from total RNA using the NEBNext UltraTM II RNA Library Prep Kit for Illumina (NEB Cat# E7770L). Sequencing was performed on a Novaseq 6000 instrument (Illumina, Inc.).

value: Peripheral Blood

tag: time

value: Day 24

value: 3BNC117 (AAV vectored)


title: C29, Infant, 12 weeks old, Day 0

description: Library name: C29

value: Day 0


title: Visual cortex, P7-P9, replicate 2


title: Col_elf18_10h_2

description: Gene expression data from plant leaves

source_name: Col-0 plant treated with elf18 at 10h, replicate 2


title: Fiko, replicate 1,H3k27ac

value: the spleen and lymph nodes

value: Treg cells from the spleen and lymph nodes

value: CtcfiKO


title: GRP2MP3_Batch2

description: Library name: Sample6


title: GRP2MP3_Batch1

description: Library name: Sample5


title: C28, Infant, 12 weeks old, Week 4

description: Library name: C28


title: Visual cortex, P7-P9, replicate 1


title: Frontal cortex, P7-P9, replicate 7

description:
FC_processed_all_cell_types.rds
FC_processed_excitatory_neuron_subset.rds

source_name: frontal cortex

value: frontal cortex

value: 4:3 male to female


title: Col_elf18_10h_1

description: Gene expression data from plant leaves

source_name: Col-0 plant treated with elf18 at 10h, replicate 1

value: leaf


title: rsw3_elf18_02h_3

description: Gene expression data from plant leaves

source_name: rsw3 plant treated with elf18 at 2h, replicate 3


title: rsw3_elf18_02h_2

description: Gene expression data from plant leaves

source_name: rsw3 plant treated with elf18 at 2h, replicate 2


title: C24, Infant, 8 weeks old, Week 4

description: Library name: C24


title: Frontal cortex, P7-P9, replicate 6

value: 3:4 male to female


title: eds1_elf18_02h_3

description: Gene expression data from plant leaves

source_name: eds1 plant treated with elf18 at 2h, replicate 3


title: rsw3_elf18_02h_1

description: Gene expression data from plant leaves

source_name: rsw3 plant treated with elf18 at 2h, replicate 1


title: C21, Infant, 8 weeks old, Day 0

description: Library name: C21


title: eds1_elf18_02h_1

description: Gene expression data from plant leaves

source_name: eds1 plant treated with elf18 at 2h, replicate 1


title: eds1_elf18_02h_2

description: Gene expression data from plant leaves

source_name: eds1 plant treated with elf18 at 2h, replicate 2


title: Frontal cortex, P7-P9, replicate 5

value: 2:4 male to female


title: BNAPGRP1_Batch2

description: Library name: Sample2

source_name: Neural Progenitor (BNAP/GRP1)

value: Neural Progenitor (BNAP/GRP1)


title: C20, Infant, 8 weeks old, Week 4

description: Library name: C20


title: BNAPGRP1_Batch1

description: Library name: Sample1


title: Col_elf18_02h_3

description: Gene expression data from plant leaves

source_name: Col-0 plant treated with elf18 at 2h, replicate 3


title: C17, Infant, 8 weeks old, Day 0

description: Library name: C17


title: BNAPGRP1_Batch4

description: Library name: Sample4


title: C25, Infant, 12 weeks old, Day 0

description: Library name: C25


title: Col_elf18_02h_2

description: Gene expression data from plant leaves

source_name: Col-0 plant treated with elf18 at 2h, replicate 2


title: Frontal cortex, P7-P9, replicate 2

value: 5:2 male to female


title: C16, Infant, 8 weeks old, Week 4

description: Library name: C16


title: Col_elf18_02h_1

description: Gene expression data from plant leaves

source_name: Col-0 plant treated with elf18 at 2h, replicate 1


title: primary spermatogonial cultures, postnatal day 7 mouse testis EVs (PND7) treated, biol rep 2

city: Shenzh

first: Tingting

last: ZHENG

address: Bulan Road

institute: Shenzhen Third People's Hospital

description: Library name: PND7, biol rep 2

data_processing:
A set of analysis pipelines that perform sample demultiplexing, barcode processing, single cell 3' and 5' gene counting, and Feature Barcode analysis from single cell data were perforned using Cell Ranger v7.0.1
Assembly: 2020-A Mouse reference, mm10 (GENCODE vM23/Ensembl 98)
Supplementary files format and content: matrix file, barcodes file and feature file

source_name: primary spermatogonial cultures

extract_protocol:
Primary spermatogonial culture was established from three postnatal day 6 male mice. Briefly, the decapsulated testes were placed in 1 mg/ml Collagenase Type IV, for 10 minutes at 37°C and tissues and cells were collected by brief centrifuge at 300g for 15s, followed by incubation in 0.25% Trypsin and 0.5 ml 5 mg/ml DNase for 10 minutes at 37°C, then stopped by the addition of 10% FBS. Tissue debris was removed by filtering through a 40-um strainer and testicular cells were collected by centrifugation at 300g for 5 min. Spermatogonia were isolated by magnetic activated cell sorting (MACS) against Thy1. 1x107 cells were resuspended in 200 μl of DMEM medium supplemented with 2% FBS and incubated with 20 μl of biotinylated Thy1.2 CD90.2 primary antibody on ice for 15 min on a slow-rocking platform. Cells were washed with PBS and resuspended with 500 μl of DMEM medium supplemented with 2% FBS before being loaded into the pre-calibrated MS column to capture Thy1+ cells. Columns were washed twice with 500 μl of DMEM medium supplemented with 2% FBS and the Thy1+ cells were eluted with 1ml of DMEM medium supplemented with 2% FBS. Then, the Thy1+ cells were cultured on the STO feeder cells in culture medium. The spermatogonial culture were treated with 1ug/ml PND7 tEVs or PBS (vehicle control) for 3 days. a.Obtain the cells of interest in suspension. b. Using a wide-bore pipette tip, gently and thoroughly mix the cells. c. Determine the cell concentration using an automated cell counter or a hemocytometer. d. Calculate the cell resuspension volume required for the desired target concentration.  To calculate cell resuspension volume, assume ~50% cell loss.  e. If significant amounts of cell clumps or debris are observed, gently mix cells by pipetting up and down 10–15x and filter cells using an appropriate cell strainer.f. Centrifuge cells at 300 rcf for 5 min at room temperature and nuclei at 500 rcf for 5–10 min at 4°C.
Step 1. GEMs are generated by combining barcoded Gel Beads, a Master Mix containing  cells, and Partitioning Oil B onto  GEM-X 3' Chip.  Immediately following GEM generation, the Gel Bead is dissolved, primers are released, and any copartitioned cell is lysed. Primers containing an Illumina TruSeq Read 1 (read 1 sequencing primer, Read 1T), 16 nt 10x Barcode, 12 nt unique molecular identifier (UMI), and 30 nt poly(dT) sequence are mixed with both the cell lysate and a Master Mix containing  reverse transcription (RT) reagents. Incubation of the GEMs produces barcoded, full-length cDNA from polyadenylated mRNA.Step 2.  After incubation, GEMs are broken and pooled fractions are recovered. Silane magnetic beads are used to purify the first-strand cDNA from the post GEM-RT reaction mixture, which includes leftover biochemical reagents and primers. Barcoded, full-length cDNA is amplified via PCR to generate sufficient mass for library construction.Step 3.  Enzymatic fragmentation and size selection are used to optimize the cDNA amplicon size. P5 and P7 adaptors, i7 and i5 sample indexes, and TruSeq Read 2 (read 2 primer sequence) are added via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina  amplification.

value: primary spermatogonial cultures

value: coculture with PND7 testis EVs


title: rsw3_control_00h_3

description: Gene expression data from plant leaves

source_name: rsw3 plant treated with mock at 0h, replicate 3


title: BNAPGRP1_Batch3

description: Library name: Sample3


title: C13, Infant, 8 weeks old, Day 0

description: Library name: C13


title: primary spermatogonial cultures, PBS treated (vehicle control), biol rep 2

description: Library name: Ctrl, biol rep 2

value: coculture with PBS


title: Frontal cortex, P7-P9, replicate 4

value: pooled male and female

value: 4:2 male to female


title: Brain, Treatment, 20

city: Norwich

first: Justin

last: Abi Assaf

address: Research Park

department: School of Biological Sciences

country: United Kingdom

institute: University of East Anglia

data_processing:
The bioinformatics pipeline “nf-core/rnaseq” version: 3.11.1 (Ewels et al., 2020) was used to analyse the RNA sequencing data obtained from the zebrafish brain samples using the Ensemble reference genome file (Danio_rerio.GRCz11.109).
Assembly: Ensemble reference genome file (Danio_rerio.GRCz11.109).
Supplementary files format and content: A csv file that includes the location of the raw files on the HPC cluster (ADA)

organism: Danio rerio

source_name: Brain

extract_protocol:
Brain samples were harvested from euthanised fish as per establishment protocol and flash frozen in liquid nitrogen before storage at -80 °C. In this study, the differential expression analysis was performed on a total sample size of n=40 (20 fish from the control diet group and the other 20 fish from the 60% GA experimental group). Samples were first homogenised then kept on ice before nucleic acid extraction. RNA extraction was performed using Quick-RNA™ Miniprep Plus Kit with Zymo-Spin™ IIICG Columns (Capped) & Spin-Away™ Filters (Zymo Research, product code: R1057, Cambridge Bioscience, UK) according to manufacturer’s recommendations
Extracted RNA samples were sent to Novogene for mRNA library preparation (poly A enrichment) then  for Illumina Sequencing (6G of raw data per sample)

value: Brain

value: Male

value: WT


title: primary spermatogonial cultures, PBS treated (vehicle control), biol rep 1

description: Library name: Ctrl, biol rep 1


title: C9, Infant, 4 weeks old, Day 0

description: Library name: C9

source_name: Peripheral Blood

value: Peripheral Blood

value: Day 0

value: 3BNC117 (AAV vectored)


title: Brain, Treatment, 19


title: Flt3L-iKO-BMDC2, rep3

city: SUWON-SI

first: Jinjoo

last: Lee

state: - Select -

address: SEOBU-RO, JANGAN-GU

department: Biology

country: South Korea

institute: SUNGKYUNKWAN UNIVERSIT

description: Library name: SAMPLES 9

data_processing:
QuantSeq 3’ mRNA-Seq reads were aligned using Bowtie2 (Langmead and Salzberg, 2012).
The alignment file was used for assembling transcripts, estimating their abundances and detecting differential expression of genes.
Differentially expressed gene were determined based on counts from unique and multiple alignments using coverage in Bedtools (Quinlan AR, 2010).
The RC (Read Count) data were processed   based on TMM+CPM normalization method using EdgeR within R (R development Core Team, 2020) using Bioconductor (Gentleman et al.,2004)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include Read count values for each Sample

source_name: Bone marrow

growth_protocol: The mouse bone marrow cells were suspended at 2 x 10^6/ml in complete RPMI containing 10% fetal bovine serum (FBS) and 100 U/ml penicillin/streptomycin and supplemented with 100ng/ml recombinant human Flt3L, 10 mM HEPES, and 55 μM β-mercaptoethanol. The cells were plated at 2 ml/well on 6-well plates and incubated at 37°C with 5% CO2 for 9 days.

extract_protocol:
Cell lysis was performed using RNAiso Plus reagent (Takara) and RNA was harvested using PicoPure RNA Isolation Kit (Applied Biosystems)
RNA libraries for RNA-seq were prepared using QuantSeq 3' mRNA-seq Library Prep Kit (Lexogen, Inc. Austria) according to the manufacturer's instructions.

value: Bone marrow

value: Flt3L-cultured bone marrow cells

value: A20fl/fl x CD11ccre


title: Frontal cortex, P7-P9, replicate 3

source_name: frontal cortex

value: frontal cortex

value: 6:0 male to female


title: Brain, Treatment, 18

value: Female


title: rsw3_control_00h_1

description: Gene expression data from plant leaves

source_name: rsw3 plant treated with mock at 0h, replicate 1

value: leaf


title: Flt3L-iKO-BMDC2, rep2

description: Library name: SAMPLES 8


title: C8, Infant, 4 weeks old, Week 4

description: Library name: C8

value: Day 24


title: primary spermatogonial cultures, postnatal day 7 mouse testis EVs (PND7) treated, biol rep 1

description: Library name: PND7, biol rep 1

value: primary spermatogonial cultures

value: coculture with PND7 testis EVs


title: Brain, Control, 20


title: rsw3_control_00h_2

description: Gene expression data from plant leaves

source_name: rsw3 plant treated with mock at 0h, replicate 2


title: C5, Infant, 4 weeks old, Day 0

description: Library name: C5


title: eds1_control_00h_1

description: Gene expression data from plant leaves

source_name: eds1 plant treated with mock at 0h, replicate 1


title: eds1_control_00h_2

description: Gene expression data from plant leaves

source_name: eds1 plant treated with mock at 0h, replicate 2


title: eds1_control_00h_3

description: Gene expression data from plant leaves

source_name: eds1 plant treated with mock at 0h, replicate 3


title: Frontal cortex, P7-P9, replicate 1

value: pooled male and female

value: 5:1 male to female


title: Brain, Treatment, 17

value: Brain

value: Male


title: Flt3L-WT-BMDC2, rep3

description: Library name: SAMPLES 6

value: WT


title: C12, Infant, 4 weeks old, Week 4

description: Library name: C12

value: Peripheral Blood


title: C4, Infant, 4 weeks old, Week 4

description: Library name: C4

value: 3BNC117 (AAV vectored)


title: Brain, Treatment, 16


title: C1, Infant, 4 weeks old, Day 0

description: Library name: C1

value: Day 0


title: Brain, Treatment, 15


title: Flt3L-WT-BMDC2, rep2

description: Library name: SAMPLES 5

value: Bone marrow

value: Flt3L-cultured bone marrow cells


title: Flt3L-WT-BMDC2, rep1

description: Library name: SAMPLES 4


title: Brain, Control, 19


title: ooplasm_biopsy_D29-CL

city: Pirassununga

first: Flavio

middle: Vieira

last: Meirelles

state: Sao Paulo

address: Duque de caxias

department: Veterinary Medicine

country: Brazil

institute: University of Sao Paulo

description:
Single-Oocyte-biopsy RNA-Seq
biopsy_count_table.txt
biopsy_count_table.txt

data_processing:
Trimgalore / cutadapt
STAR/Bismark
featurecounts
DEESEQ2/methylKit
PCIT / CETF
Assembly: ARS-UCD 1.2
Supplementary files format and content: Raw counts for each sample in .txt file
Supplementary files format and content: NDA

organism: Bos taurus

source_name: Ooplasm-biopsy

extract_protocol:
The SMART-Seq®HT kit (Takara Bio, USA) / EpiTect Fast Bisulfite
NextEra XT Stranded mRNA Sample Prep kit following manufacturer instructions/NEBNext Ultra II DNA library

value: Ooplasm-biopsy

value: Diploid


title: Col_control_00h_3

description: Gene expression data from plant leaves

source_name: Col-0 plant treated with mock at 0h, replicate 3


title: Flt3L-WT-BMDC1, rep3

description: Library name: SAMPLES 3


title: GC_D27-BL

description:
Granulosa cells transcriptome
GC_count_table.txt
GC_count_table.txt

source_name: Granulosa cell

value: Granulosa cell

value: Granulosa cell_Diploid


title: Brain, Treatment, 14

value: Female


title: Col_control_00h_1

description: Gene expression data from plant leaves

source_name: Col-0 plant treated with mock at 0h, replicate 1

value: leaf


title: Col_control_00h_2

description: Gene expression data from plant leaves

source_name: Col-0 plant treated with mock at 0h, replicate 2


title: B21, Juvenile, Day 0

description: Library name: B21


title: Flt3L-iKO-BMDC2, rep1

description: Library name: SAMPLES 7

value: A20fl/fl x CD11ccre


title: Flt3L-WT-BMDC1, rep2

description: Library name: SAMPLES 2


title: A12R027-Grp4-Wk24-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

city: Rahway

first: Yuhyun

last: Ji

address: 126 E Lincoln Ave

institute: Merck & Co., Inc.

description: Library name: G04_sample02_time05

data_processing:
RNA sequencing data was normalized to provide consistent and comparable measures of gene expression (mRNA expression) that can be used for performing expression analysis. Log 10-transformation was applied to fragments per kilobase of transcript per million mapped reads (FPKM) with a smoothing addon, pseudo count, of 0.01 for easier visualization and analysis. This small pseudo count (0.01) was to avoid division by zero, and the value was set small enough not to affect the results. Also, we used log10 to symmetrize up/down regulation. We filtered out transformed FPKM values (log(FPKM + 0.01)+0.01) that are below -1 to remove low-intensity data. Among a total number of 35,398 RNA sequencing data, 22,413 data showing low intensity were removed, and 12,985 data were left. 1,663 NHP genes that do not have human equivalents were ignored, and 11,322 gene data were left. We manually selected 1,184 immune-related genes from the remaining gene data for this study. Representative genes and cytokines related to immune-related pathways, including toll-like receptors (TLRs), cytosolic pattern recognition receptors, and C-type lectin receptors, are selected to show RNA expression patterns induced by different adjuvant types.
Assembly: Gene IDs of remaining RNA sequencing data were converted to the human equivalent using the BioMart-Ensemble database (https://mart.ensembl.org).
Supplementary files format and content: We provide fastq files, raw files from the sequencing machine and FPKM values after the polishing steps that we used for the research.

source_name: Blood

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were collected to profile mRNA and compare adjuvant effects on immune gene expression. Blood draws occurred at six time points: pre-dose, 1 day after each dose, and 7 days after each dose. Whole blood was preserved in PAXgene Blood RNA tubes, and total RNA was isolated using the PAXgene Blood RNA kit (PreAnalytix) following the manufacturer's instructions. RNA quantity and integrity were evaluated on an Agilent Bioanalyzer using the RNA6000 Nano Lab Chip (Agilent Technologies). For samples collected in PAXgene tubes, cells were pelleted by centrifugation at 10,000 g for 6 minutes, the supernatant was discarded, and pellets were washed in 1 mL of dimethylpyrocarbonate (DMPC)-treated water before a second centrifugation at 10,000 g for 6 minutes. For samples from other media, cells were pelleted at 2,000 g for 30 minutes and the supernatant removed. All cell pellets were disrupted by vortexing in the appropriate lysis buffer for the chosen extraction method.
Total RNA was extracted from samples using standard extraction methods ensuring high RNA integrity. RNA sequencing libraries were prepared using the TruSeq Stranded Total RNA Ribo-Zero kit (Illumina) according to the manufacturer's instructions. This kit depletes ribosomal RNA to enrich for coding and non-coding transcripts, preserving strand specificity. Following RNA extraction and library preparation, the libraries were sequenced on an Illumina platform using a paired-end 50 base pair read format. Sequencing depth and multiplexing were adjusted according to experimental design to ensure sufficient coverage for downstream transcriptomic analyses.

value: Blood

value: Day 1 after boost dose


title: ooplasm_biopsy_D27-BL


title: Brain, Treatment, 13

value: Brain


title: GC_D24-BL


title: Brain, Treatment, 12


title: B19, Juvenile, Day 3

description: Library name: B19

value: Day 3


title: ooplasm_biopsy_D24-BL


title: GC_D29-CL


title: Brain, Control, 18

value: Male

value: WT


title: B24, Juvenile, Week 4

description: Library name: B24

value: Peripheral Blood

value: Day 24

value: 3BNC117 (AAV vectored)


title: B17, Juvenile, Day 0

description: Library name: B17

value: Day 0


title: GC_D10-CL


title: B23, Juvenile, Day 3

description: Library name: B23


title: Brain, Control, 17


title: MC38-Vector

city: ShenZhen

first: Menghan

last: Wu

address: Guangqiao Road

department: Institute of Molecular Physiology

institute: ShenZhen Bay laboratory

description:
Library name: Sample1
10x Genomics

data_processing:
R1 (read 1 primer sequence) were added to the molecules during GEM incubation. P5, P7, a sample index, and R2 (read 2 primer sequence) were added during library construction via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contained the P5 and P7 primers used in Illumina bridge amplification. Perform high-throughput sequencing on the final libraries using Illumina NovaSeq X Plus. A Single Cell 3’ Library comprised standard Illumina paired-end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI were encoded in Read 1, while Read 2 was used to sequence the cDNA fragment. Sample index sequences were incorporated as the i7 index read. Read 1 and Read 2 were standard Illumina® sequencing primer sites used in paired-end sequencing.
Assembly: mouse mm10
Supplementary files format and content: The cell by gene matrices for each sample were individually imported to Seurat  version 3.1.1 for downstream analysis. Cells with unusually high number of UMIs (≥8000) or mitochondrial gene percent (≥10%) were filtered out. We also excluded cells with less than 500 or more than 4000 genes detected. Additionally, doublet GEMs also should be filtered out. It was achieved by using the tool DoubletFinder (v2.0.3) by the generation of artificial doublets, using the PC distance to find each cell’s proportion of artificial k nearest neighbors (pANN) and ranking them according to the expected number of doublets. After removing unwanted cells from the dataset, we employed a global-scaling normalization method “LogNormalize” that normalizes the gene expression measurements for each cell by the total Integrated expression matrix is then scaled and performed on principal component analysis for dimensional reduction. Then we implemented a resampling test inspired by the jackStraw procedure. We randomly permuted a subset of the data (1% by default) and rerun PCA, constructing a ‘null distribution’ of expression, multiplies this by a scale factor (10,000 by default), and log-transforms the results. To minimize the effects of batch effect and behavioral conditions on clustering, we used Harmony, gene scores, and repeated this procedure. We identified ‘significant’ PCs as those who have a strong enrichment of low p-value genes for downstream clustering and dimensional reduction. an algorithm that projects cells into a shared embedding in which cells group by cell type rather than dataset-specific conditions, to aggregate all samples.[4] The Harmony algorithm inputs a PCA embedding of cells, along with their batch assignments, and returns a batch corrected embedding.

source_name: tumor tissue

growth_protocol: All mice were housed under specific pathogen-free (SPF) conditions with a 12-hour light/dark cycle and provided ad libitum access to standard chow and water.

extract_protocol:
Homogenize Tissue: Remove any adherent tissue and homogenize the sample. Wash with PBS: Rinse the tissue with 5-10 ml of pre-cooled 1x PBS to remove blood stains. Weigh and Cut Tissue: Take approximately 0.05-0.1 g of tissue (about the size of a soybean) and cut it into small pieces that can fit into a centrifuge tube. Transfer to Tube: Place the small tissue pieces into a 1.5 ml centrifuge tube. Add Protectant: Add 1.3 ml of pre-cooled Metheni Tissue Protectant to ensure the tissue is fully saturated with the solution. Seal and Label: Seal the centrifuge tube with a sealing film and clearly mark the sample number on the tube. It's advisable to keep a backup sample. Storage and Shipping: Store the sealed centrifuge tube at 4°C and arrange for prompt shipment to the cold chain logistics company to maintain sample integrity.
Cellular suspensions were loaded on a 10X Genomics GemCode Single-cell instrument that generates single-cell Gel Bead-In-EMlusion (GEMs). Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3’ Reagent Kits v3.1.Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full-length, barcoded cDNAs were then amplified by PCR to generate sufficient mass for library construction. Upon dissolution of the Gel Bead in a GEM, primers containing (i) an Illumina® R1 sequence (read 1 sequencing primer), (ii) a 16 nt 10x Barcode, (iii) a 10 nt Unique Molecular Identifier (UMI), and (iv) a poly-dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded, full-length cDNAs were then reverse-transcribed from poly-adenylated mRNA.

treatment_protocol: Mice untreated

value: tumor tissue

value: vector control

value: no


title: B16, Juvenile, Week 4

description: Library name: B16


title: SrfKO4, GD3.5, uterus

city: Research Triangle Park

first: Francesco

middle: John

last: DeMayo

state: North Carolina

address: 111 T W Alexander Dr

department: DIR

institute: NIEHS

description: Library name: SrfKO4

data_processing:
Raw reads were trimmed to a minimum quality score of 20 using Trimmomatic v0.39.
Paired-end alignment to the mouse mm10 reference genome from the Genome Reference Consortium was performed using HISAT2 v2.2.1.
Alignment files were indexed by Samtools v1.18.
Count matrices were generated using Subread’s featureCounts tool.
Normalization and differential expression analysis was performed using DESeq2 v1.42.0 in R v4.3.1.
Assembly: mm10
Supplementary files format and content: SrfBulk35_RawCounts.csv contains raw counts for each sample
Supplementary files format and content: SrfBulk35_NormCounts.csv contains DESeq2-normalized counts for each sample

source_name: uterus

extract_protocol:
Homogenization was first performed in TRIzol (Invitrogen #15596026) followed by stepwise phase separation in 1-Bromo-3-chloropropane (Sigma-Aldrich #B9673) and chloroform (Sigma-Aldrich #C2432) before cleanup with RNeasy mini kit columns (Qiagen #74106) and treatment with RNase-free DNase (Qiagen #79254).
Libraries were prepared by the NIEHS Epigenomics and DNA Sequencing Core Facility with an Illumina Tru-seq stranded mRNA library prep kit.

value: uterus

value: PgrCre/+Srfflox/flox


title: ooplasm_biopsy_D10-CL

value: Ooplasm-biopsy

value: Diploid


title: Brain, Control, 16

source_name: Brain


title: Brain, Control, 15

value: Female


title: SrfKO3, GD3.5, uterus

description: Library name: SrfKO3


title: Flt3L-WT-BMDC1, rep1

description: Library name: SAMPLES 1

value: Bone marrow

value: Flt3L-cultured bone marrow cells


title: B20, Juvenile, Week 4

description: Library name: B20

source_name: Peripheral Blood


title: B13, Juvenile, Day 0

description: Library name: B13


title: SrfKO2, GD3.5, uterus

description:
Library name: SrfKO2
Additional reads sequenced using NovaSeq 6000


title: Brain, Control, 14

value: Brain


title: B12, Infant, Week 4

description: Library name: B12


title: MC38-TMEM16F KO

description:
Library name: Sample 2
10x Genomics

value: TMEM16F KO


title: GC_B21-BL

value: Granulosa cell

value: Granulosa cell_Diploid


title: Brain, Control, 13

value: Male

value: WT


title: ooplasm_biopsy_B23-CL


title: GC_B23-CL


title: SrfKO1, GD3.5, uterus

description:
Library name: SrfKO1
Additional reads sequenced using NovaSeq 6000


title: ooplasm_biopsy_B21-BL


title: Ctrl3, GD3.5, uterus

description:
Library name: Ctrl3
Additional reads sequenced using NovaSeq 6000

value: Srfflox/flox


title: GC_B20-BL


title: B11, Infant, Day 3

description: Library name: B11

value: Peripheral Blood

value: Day 3

value: 3BNC117 (AAV vectored)


title: Brain, Treatment, 11


title: B8, Infant, Week 4

description: Library name: B8

value: Day 24


title: Ctrl2, GD3.5, uterus

description:
Library name: Ctrl2
Additional reads sequenced using NovaSeq 6000

value: uterus


title: B5, Infant, Day 0

description: Library name: B5

value: Day 0


title: B15, Juvenile, Day 3

description: Library name: B15


title: Brain, Control, 11


title: Ctrl1, GD3.5, uterus

description:
Library name: Ctrl1
Additional reads sequenced using NovaSeq 6000


title: ooplasm_biopsy_B20-BL

value: Ooplasm-biopsy

value: Diploid


title: GC_B14-CL


title: Brain, Control, 12

value: Female


title: ooplasm_biopsy_B14-CL


title: TAC_heart_1

city: Rouen

first: Ebba

last: Brakenhielm

address: Inserm U1096

institute: Inserm

description:
Library name: TAC01_BALB
10xGenomics

data_processing:
Raw FASTQ files were generated and demultiplexed from BCL data using bcl2fastq (v2.20.0). Quality control with FastQC (v0.11.9) indicated >98% perfect index and 86% of bases >= Q30, requiring no treatment. Reads were aligned to the mouse reference genome (GRCm39.111) using STARsolo RNA-seq aligner (v2.7) to produce raw UMI count matrix. Data filtering, normalization, integration, principal component-based unsupervised clustering, and differential analysis were performed using the Seurat package (version 5.0.2) in R (version 4.1.2). Functional enrichment analysis was performed with the R package clusterProfiler (v3.2). In BALB/c mice, among 3908 total sequenced cells, 3436 cardiac cells remained post-filtering, including 1932 cells from sham-operated BALB/c controls and 1504 from post-TAC mice.
Assembly: mouse reference genome (GRCm38)
Supplementary files format and content: expression_data_value.xlsx
Supplementary files format and content: Balb_scRNAseq_ref_README.txt
Supplementary files format and content: all_LEC_barcodes.cvs

source_name: Cardiac

extract_protocol:
Hearts were digested and cardiac endothelial cells sorted by FACS to generate cells for inclusion in scRNAseq experiment
The 10X Genomics Chromium Next Gem Single Cell 3' library kit v.3.1 was used to prepare barcoded mRNA following the guidelines from the supplier. Single Index kit T Set A was used to label each reaction. Samples were loaded onto 3 separate Illumina kit High-throughput 2x75 (<400 million reads) flow-cells and sequenced using Illumina Nextseq, using the settings of: Read1: 28 cycles; Read2: 8 cycles; Read3 (i7): 114 cycles

treatment_protocol: pressure-overload or sham surgery was performed in adult female Balbc

value: Cardiac

value: female

value: Endothelial cells

value: Balb/c

value: TAC-operated


title: Brain, Treatment, 9

value: Brain


title: B3, Infant, Day 3

description: Library name: B3


title: B4, Infant, Week 4

description: Library name: B4


title: Oocyte-3

description:
Single-oocyte RNA-Seq
oocyteXbiopsy_count_table.txt
oocyteXbiopsy_count_table.txt

source_name: Oocyte

value: Oocyte


title: Brain, Treatment, 8

value: Male

value: WT


title: B1, Infant, Day 0

description: Library name: B1

value: Peripheral Blood


title: Sham_heart_2

description:
Library name: SHAM02_BALB
10xGenomics

value: sham-operated


title: A24, Juvenile, Week 4

description: Library name: A24

value: Day 24

value: 3BNC117 (AAV vectored)


title: Sham_heart_1

description:
Library name: SHAM01_BALB
10xGenomics


title: B9, Infant, Day 0

description: Library name: B9

value: Day 0


title: Ctrl4, GD3.5, uterus

description:
Library name: Ctrl4
Additional reads sequenced using NovaSeq 6000

value: uterus

value: Srfflox/flox


title: AAV2.CrAT.NCd8_AAV2.CrAT.NCd8.02

city: Sendai

first: Kota

last: Sato

state: Miyagi

address: 1-1, Seiryo-machi, Aoba-ku

department: Ophthalmology

institute: Tohoku University

description: Library name: Sample 4

data_processing:
RNA-seq libraries were sequenced using paired end reads (50 nt for read 1 and 25 nt for read 2) .
Assembly: The obtained reads were mapped to the mouse GRCm38.p6 (mm10) genome with STAR software (version 2.7.2b).
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tsv files include FPKM values for each Sample

source_name: retina

extract_protocol:
total RNA were extracted with Qiamp RNA micro kit (Qiagen, #217084)
Double-strand cDNA libraries (RNA-seq libraries) were prepared with the SMART-seq v4 Ultra Low Input RNA Kit for Sequencing (Takara, #634888).

value: retina

value: RGC

value: optic nerve crush


title: Brain, Treatment, 10


title: Oocyte-2

value: Diploid


title: AAV2.CrAT.NCd8_AAV2.CrAT.NCd8.01

description: Library name: Sample 3


title: Ooplasm_biopsy-2

description:
Single-Oocyte-biopsy RNA-Seq
oocyteXbiopsy_count_table.txt
oocyteXbiopsy_count_table.txt

value: Ooplasm-biopsy


title: A23, Juvenile, Day 3

description: Library name: A23

value: Day 3


title: Brain, Control, 9

value: Brain

value: Female


title: A20, Juvenile, Week 4

description: Library name: A20


title: AAV2.MCS.NCd8_AAV2.MCS.NCd8.02

description: Library name: Sample 2


title: Oocyte-16

value: Oocyte


title: Ooplasm_biopsy-16


title: Brain, Treatment, 6

value: Male

value: WT


title: A21, Juvenile, Day 0

description: Library name: A21

value: Peripheral Blood


title: AAV2.MCS.NCd8_AAV2.MCS.NCd8.01

description: Library name: Sample 1


title: Ooplasm_biopsy-3


title: Brain, Treatment, 5


title: A19, Juvenile, Day 3

description: Library name: A19


title: Oocyte-6


title: Brain, Treatment, 7


title: A17, Juvenile, Day 0

description: Library name: A17


title: Brain, Control, 7


title: Ooplasm_biopsy-6


title: Brain, Control, 10


title: A16, Juvenile, Week 4

description: Library name: A16

value: Day 24


title: mmem_ctl_sl049

city: Santa Cruz

first: Upasna

last: Sharma

state: California

address: 1156 High St

department: MCD Biology

institute: UCSC

data_processing:
151 x 151 paired end reads. Sequencing libraries were not strand-specific.
Reads were trimmed by 31 bases from the 3' end to 120x120bp
Reads were mapped with Bowtie2 to the RepeatMasker library of mouse repeat elements.
After removing reads with both ends mapped to repeat elements, the remaining reads were mapped to the mm10 genome assembly using STAR.
Potential PCR duplicates were removed with samtools rmdup.
The coverage for each gene was extracted, then divided by 240 (based on 120x120bp mappings) for input as mapping counts to DESeq2
The DESeq2 sizeFactors were used to compute normalized read counts per gene for each sample
Assembly: mm10
Supplementary files format and content: DESeq2 normalized read counts per gene for each sample in tab-separated format
Supplementary files format and content: DESeq2 sizeFactors for each sample in text format

source_name: preimplantation embryo

extract_protocol:
To prepare cell lysates, we first create a 1% solution of 2-mercaptoethanol in TCL buffer. We distribute 5 μl of this solution into each well of a skirted-side 96-well PCR plate, placing a single embryo in each well. The plate is then centrifuged for 1 minute at 800 × g at room temperature. Next, we add 10 μl of RNase-free H₂O to each lysate, followed by 2.2 volumes of RNA-SPRI beads. The lysates are incubated for 10 minutes on the bench to allow for RNA binding, and then the plate is placed on a 96-well plate magnet and incubated for 5 minutes to separate the beads. After carefully removing the supernatant, the beads are washed by adding 75 μl of 80% ethanol to each well. The plate is left to air dry at room temperature for 10 minutes. Finally, the RNA is eluted by adding 4 μl of RNase-free H₂O to each well.
To reverse transcribe mRNA, prepare the workspace, then elute RNA with a primer and dNTP mix. After initial incubation and centrifugation, add a mastermix with SuperScriptII buffer, DTT, betaine, MgCl₂, a template-switching oligo, RNase inhibitor, and reverse transcriptase. Reverse transcribe with a thermal cycler protocol (42°C for 90 mins, cycles at 50°C/42°C, then 70°C). For amplification, add KAPA HiFi mix and PCR primer, then amplify with 20 PCR cycles and store overnight at 4°C. Clean up with DNA SPRI beads, washing with ethanol, then elute in TE buffer. Measure size and concentration, then proceed with Nextera XT library prep: perform tagmentation, add NT Buffer, indexed primers, and amplify. Pool samples, perform SPRI bead cleanup, and measure for sequencing readiness.
single embryo mRNA-seq

treatment_protocol: Embryos were microinjected with either H3.3-GFP mRNA with LNA-containing scramble oligo (Ctrl_LNA) (control group) or H3.3-GFP mRNA plus tRFValCAC antisense LNA oligo (Val_LNA) (experimental group).

value: preimplantation embryo

value: 2-cell stage embryonic cells

value: wild type


title: Brain, Control,8


title: Brain, Control, 6


title: mmem_ctl_sl048


title: A15, Juvenile, Day 3

description: Library name: A15

value: 3BNC117 (AAV vectored)


title: scRNA-Seq of Spodoptera exigua hemocytes (immune-challenged)

city: Andong-si

first: Niayesh

last: Shahmohammadi

state: Gyeongsangbuk-do

address: Songcheon 3-gil

department: Plant Medicals

institute: Gyeongkuk National University

description:
Library name: TRT
10x Genomics

data_processing:
Raw sequencing reads were first processed using Cell Ranger (10x Genomics, v3.1.0) to demultiplex, align, and quantify the unique molecular identifiers (UMIs). Reads were aligned either to the S. exigua de novo transcriptome assembly (generated using Trinity and TransDecoder version 3.0.1 (https://github.com/TransDecoder/TransDecoder/wiki)) or, where applicable, to reference genomes using STAR version 2.7.10a (https://github.com/alexdobin/STAR) or Bowtie2 version 2.4.5 (http://bowtie-bio.sourceforge.net/bowtie2). Cell barcodes and UMIs were filtered based on quality, and only cells expressing over 200 genes with fewer than 10% mitochondrial content were retained for further analysis.
Gene expression matrices were imported into Seurat v4.0 in R for downstream analysis. The data were log-normalized, and the top 5000 highly variable genes were identified using the variance-stabilizing transformation (VST) method. Principal component analysis (PCA) was performed to reduce dimensionality, followed by clustering using the Louvain algorithm. Clusters were visualized via UMAP embedding.
Assembly: Spodoptera exigua, PGI_SPEXI_v6 (GCA_902829305.4)
Supplementary files format and content: Tab-seperated values files and matrix files

organism: Spodoptera exigua

source_name: Hemocyte

growth_protocol: TheSpodoptera exigua larvae were reared on artificial diet under controlled conditions (25 ± 2 °C, 60 ± 5% RH, 16:8 h light:dark), progressing through five larval instars (L1–L5). Adults were supplied with 10% sucrose to promote oviposition.

extract_protocol:
three mL of hemolymph was collected from challenged and control larvae on ice and centrifuged at 500 × g for 2 min at 4°C. The hemocyte pellet was washed twice using one mL of cold TC-100 medium (Welgene, Gyeongsan, Korea) supplemented with 10% heat-inactivated (55oC for 30 min) fetal bovine serum (Welgene, Gyeongsan, Korea), which was followed by filtering through a 40 μm cell strainer (Biosharp, China) and centrifugation at 500 × g for 2 min at 4°C. The hemocyte pellet was resuspended using 1x filtered PBS supplemented with 0.04% bovine serum albumin (BSA) (Sigma Aldrich Korea, Seoul, Korea). The number of hemocytes were counted using a hemocytometer. Cell viabilities were assessed by the intensity of the blue fluorescent signal stained by 0.4% trypan blue. Cell suspension samples with viability (>70%) and quantity (>5×10⁵) were subjected to single cell encapsulation.
primary data processing were performed by Macrogen Inc. (Seoul, South Korea). Cells were partitioned into Gel Bead-in-Emulsions (GEMs) on the 10x Genomics Chromium Controller using Single Cell 3′ Chemistry v2 kit (10X Genomics, Pleasanton, CA) following the manufacturer’s protocol. Within each GEM, a barcoded gel bead bearing a poly(dT) primer captured poly-adenylated mRNA, yielding cell-indexed, UMI-tagged cDNA anchored at the 3′ end. Libraries were prepared according to the Chromium Single Cell 3′ workflow and sequenced on an Illumina NovaSeq 6000 with paired end reads.

treatment_protocol: Newly molted fifth-instar (L5) larvae were immune-challenged by injecting heat-killed Escherichia coli TOP10 (1.4 × 105 cells per larva) into a proleg; naive larvae received phosphate-buffered saline (PBS). Injected larvae were maintained at room temperature for 8 h prior to sampling.

value: Hemocyte

tag: development stage

value: fifth instar larvae


title: scRNA-Seq of Spodoptera exigua hemocytes (naive)

description:
Library name: CON
10x Genomics


title: mmem_ctl_sl047


title: Brain, Treatment, 4


title: A13, Juvenile, Day 0

description: Library name: A13

value: Day 0


title: A12, Infant, Week 4

description: Library name: A12


title: mmem_ctl_sl046


title: Hu1234, 500x cytokines

city: Duarte

first: Hsun

middle: Teresa

last: Ku

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

description: Library name: Hu1234_500x

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 with a single read mode of 51 cycles. HiSeq Real-Time Analysis (RTA) 2.2.38 software was used to process the image analysis.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Pancreatic exocrine tissue

extract_protocol:
RNA was extracted from KG-1A cells by using the Rneasey Mini Kit (QIAGEN, 74104)
RNA sequencing libraries were prepared with the Kapa mRNA HyperPrep Kit (Kapa Biosystems, KR1352) according to the manufacturer's protocol, and the final libraries were validated using the Agilent Bioanalyzer DNA High Sensitivity Kit (Agilent, 5067-4626) and quantified with a Qubit Fluorometer (Thermo Fisher)

value: Pancreatic exocrine tissue

value: Pancreatic ductal cells

value: "500x" cytokines, 48h


title: mmem_ctl_sl045


title: Hu1234, vehicle control

description: Library name: Hu1234_CTRL

value: Vehicle, 48h


title: Hu1234, 250x cytokines

description: Library name: Hu1234_250x

value: "250x" cytokines,48h


title: Brain, Control, 4

value: Brain

value: Female


title: Brain, Treatment, 3

value: WT


title: A11, Infant, Day 3

description: Library name: A11

value: Peripheral Blood

value: Day 3


title: A8, Infant, Week 4

description: Library name: A8

value: Day 24


title: Brain, Control, 5


title: A9, Infant, Day 0

description: Library name: A9


title: Hu1167, 500x cytokines

description: Library name: Hu1167_500x


title: mmem_ctl_sl044

value: preimplantation embryo

value: 2-cell stage embryonic cells


title: Brain, Control, 2

value: Male


title: mmem_ctl_sl035

value: wild type


title: Brain, Control, 3


title: mmem_ctl_sl043


title: mmem_ctl_sl038


title: A5, Infant, Day 0

description: Library name: A5

value: 3BNC117 (AAV vectored)


title: Brain, Treatment, 2


title: mmem_ctl_sl033


title: A7, Infant, Day 3

description: Library name: A7


title: mmem_ctl_sl050


title: mmem_ctl_sl034


title: Hu1167, vehicle control

description: Library name: Hu1167_CTRL


title: mmem_ctl_sl037


title: Hu1167, 250x cytokines

description: Library name: Hu1167_250x


title: Hu1145, 500x cytokines

description: Library name: Hu1145_500x


title: mmem_ctl_sl036


title: Brain, Treatment, 1


title: Hu1108, 500x cytokines

description: Library name: Hu1108_500x


title: A3, Infant, Day 3

description: Library name: A3


title: A4, Infant, Week 4

description: Library name: A4


title: Brain, Control,1


title: Hu1145, vehicle control

description: Library name: Hu1145_CTRL


title: Hu1145, 250x cytokines

description: Library name: Hu1145_250x


title: Hu1108, 250x cytokines

description: Library name: Hu1108_250x


title: mmem_ctl_sl032


title: rh-16, E2, week 23

city: Lund

first: Joan

last: Escrivà-Font

state: Skåne

address: Sölvegatan 19

department: Department of Laboratory Medicine, Faculty of Medicine

country: Sweden

institute: Lund University

description: Library name: H28

data_processing:
Raw sequencing data was processed using the nf-core/rnaseq pipeline v3.9 (https://nf-co.re/rnaseq/3.9).
Reads were trimmed with Trim Galore
Reads were pseudo-aligned to the transcriptome using Salmon, with reference prepared from Macaca_mulatta.Mmul_10 genome and GTF (v110).
Salmon output files were imported with tximport into R.
More info on https://github.com/ConsiglioLab/Hahn_et_al_FHT.
Assembly: Mmul_10
Supplementary files format and content: quant_sf_all.tar.gz: contains all salmon quant.sf output files from the nf-core pipeline.
Supplementary files format and content: counts_lengthScaledTPM_allSamples.csv: tximport lengthScaledTPM
Supplementary files format and content: counts_TPM_allSamples.csv: tximport TPM

source_name: Whole blood

extract_protocol:
Whole blood from the study animals was collected in PAXgene Blood RNA tubes. RNA was extracted according to kit manufacturer instructions (PreAnalytiX, 762174).
cDNA libraries were prepared at Novogene Inc. from total RNA using the NEBNext Ultra™ II RNA Library Prep Kit for Illumina (NEB, E7770L).

treatment_protocol: Exogenous E2 or placebo were delivered via slow-release pellets on study weeks 0, 4, 7, 10, 13, 16, 19, 22, and 25. The 0.3 mg/kg E2 or placebo pellets were administered subcutaneously. For the mRNA vaccinations, four individual syringes per animal were prepared containing 15 μg of mRNA encoding 16055-ConM_SOSIPv8ds. Macaques in both groups A and B received first and second vaccinations at study weeks 18 and 22 respectively.

value: Whole blood

value: E2, LNP/mRNA

tag: weeks post_fht

tag: treatment group

tag: animal id

value: male

tag: sequencing batch


title: mmem_ctl_sl031


title: A1, Infant, Day 0

description: Library name: A1

value: Day 0


title: Hu1108, vehicle control

description: Library name: Hu1108_CTRL

value: Pancreatic exocrine tissue

value: Pancreatic ductal cells

value: Vehicle, 48h


title: AD 3

city: Changsha

first: Liang

last: Tang

address: No 1501, Leifeng road

institute: Changsha Medical University

description: Gene expression in AD group

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4*180k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software version10.7.1.1 (Agilent) using default parameters

source_name: hippocampus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: hippocampus was obatained form Aβ25-35 induced AD model mice and control mice

value: hippocampus

tag: gender

value: day 28


title: mmem_val_sl020