title: Infantile Cerebellar-Retinal Degeneration, patient 1, biol rep 2

description:
Library name: ICRD1_B
I19B

value: Skin

value: Fibroblasts

value: female

value: ICCb

tag: batch


title: IL-1R1 eRestore_F_sham_9h_A175

status: Public on Jul 29 2026

type: SRA

city: Lexington

first: Joshua

middle: M

last: Morganti

state: KY

address: 789 S. Limestone St

department: Sanders-Brown Center on Aging

country: USA

institute: University of Kentucky

description:
Library name: A175
Bulk RNA-seq, IL-1R1 eRestore, F, sham, 9h

library_source: transcriptomic

data_processing:
Quality assessment of raw reads with FastQC
Read alignment with STAR to mouse genome
Transcript quantification with Salmon
Gene-level count aggregation with tximeta
Differential expression analysis with DESeq2
Assembly: GRCm39 (mm39)
Supplementary files format and content: Tab-delimited text file with Salmon-quantified gene-level read counts (salmon.merged.gene_counts.tsv). Columns are sample IDs, rows are Ensembl gene IDs with gene names.
Supplementary files format and content: Tab-delimited text file with Salmon-quantified gene-level TPM values (salmon.merged.gene_tpm.tsv). Columns are sample IDs, rows are Ensembl gene IDs with gene names.

molecule: total RNA

organism: Mus musculus

source_name: mouse brain

growth_protocol: 14:10 (light:dark), ad lib food access

extract_protocol:
RNeasy Mini with genomic dna depletion
RNA library preparation was performed by Novogene (Project X202SC24077443-Z01-F001). [Add library prep kit info, e.g., Illumina Stranded mRNA Prep, polyA selection, etc.]

treatment_protocol: Mice underwent closed head injury (CHI) or sham surgery. Brain tissue was collected at 9h, 24h, or 72h post-injury.

tag: tissue

value: mouse brain

tag: strain

value: IL-1R1 eRestore

tag: Sex

value: Female

tag: surgery

value: sham

tag: timepoint

tag: age (months)

value: 4.5 months

tag: animal id

tag: experiment id


title: 203991400160_R07C01_PD142_CNG

type: genomic

city: Exeter

last: Harvey

state: Devon

address: RILD Building, RD&E, Barrack Road

department: Clinical and Biomedical Sciences

country: United Kingdom

institute: University of Exeter

hyb_protocol: 500 ng DNA from each sample was sodium bisulfite-treated using the Zymo EZ 96 DNA methylation kit (Zymo Research) according to the manufacturer’s standard protocol.

scan_protocol: Samples were assessed using the Illumina Infinium HumanMethylationEPIC BeadChip (Illumina) using a Illumina iScan System (Illumina)

data_processing:
Data was imported using the R package methylumi methylumIDAT function. Data was then pre-processed in the R package wateRmelon using the pfilter and dasen functions.
[ukbbn_betas_normalised.Rdata] wateRmelon processed beta values, dasen quantile normalised

label: Cy3 & Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Anterior cingulate

label_protocol: Standard Illumina Protocol

extract_protocol: ~30mg of brain tissue was milled over liquid nitrogen and extracted following the Qiagen AllPrep DNA/RNA/miRNA Universal kit following standard protocol. Samples were pre-checked using nanodrop fluorometer prior to further processing.

value: Anterior cingulate

tag: regiondescription

tag: plate

tag: centre

value: Imperial Brain Bank

value: male

tag: thal

value: FALSE


title: Cortex, 12-week-old, WT, rep2

city: Houston

first: Hamin

last: Lee

state: TX

address: 1 Baylor Plaza, Jan and Dan Duncan Neurological Research institute

institute: Baylor College of Medicine

description: Library name: CTX-WT-2

data_processing:
For each sample, the raw reads from multiple lanes were merged, and then were aligned to the Mus musculus reference transcriptome (GRCm38.p6, GENCODE M18) using STAR v2.7 with "-quantMode GeneCounts" to generate raw read counts
Assembly: GRCm38.p6, GENCODE M18
Supplementary files format and content: tsv file including raw counts of each sample

source_name: Cortex

extract_protocol:
Total RNA was isolated using the miRNeasy Mini Kit (Qiagen) from flash-frozen tissue
RNA libraries were prepared by Azenta Life Science using polyA selection and standard Illumina protocols

value: Cortex

tag: genotype

value: WT

tag: time


title: Infantile Cerebellar-Retinal Degeneration, patient 1, biol rep 1

city: ANGERS CEDEX 01

first: Cléis

last: Beaulieu

address: 40 RUE DE RENNES

country: France

institute: UNIVERSITE D'ANGERS

description:
Library name: ICRD1_A
I19A

data_processing:
An average of 33.4 million paired raw reads per sample were generated. Low quality bases and adapter sequences were trimmed using the fastp tool v.0.24.0. Filtered reads were aligned to the human reference genome GRCh38 using the STAR tool v.2.7.11b with default parameters. The average alignment of uniquely mapped reads was 30.4 million per sample, with 88% corresponding to mRNA. Gene-level counts matrix was generated using featureCounts/subread v.2.0.3
Prior to differentially expressed (DE) genes analysis, only genes annotated as protein-coding in the GTF annotation file (GENCODE v38), and with at least 10 counts in a sufficient number of samples within at least one condition, were retained for downstream analyses. DE genes were determined using DESeq2 v.1.44.0.
Assembly: GRCh38
Supplementary files format and content: .tsv file includes raw counts for each sample

molecule: polyA RNA

source_name: Skin

growth_protocol: All cell lines (4 controls, 4 patients) were synchronized at the same passage and biological triplicates were obtained at 3 consecutive passages to ensure minimal physiological variation. Samples (n=24) were prepared in a randomized order throughout the entire procedure to minimize experimental bias.

extract_protocol:
Total RNA was extracted from all samples using the Rneasy Mini Kit (Qiagen), and residual DNA was removed using the Rnase-Free Dnase Set (Qiagen). mRNA were enriched from 250 ng of total RNA using a PolyA selection.
Library preparation was performed using the Illumina® Stranded mRNA Prep ligation kit (Illumina, 20040532), and samples were barcoded with index adapters from the Illumina® RNA UD Indexes (Illumina, 20091655) according to the manufacturer’s instructions. Libraries were normalized to 4nM, pooled, and sequenced on a NextSeq 550 Sequencing System (Illumina) in a paired-end (75 bp) mode using a High Output Flowcell v2.5 (Illumina, 20024907).

tag: cell type

tag: sample id

value: ICCa

tag: sample id_2

tag: patient id_ctrl

value: Patient

value: Syndromic

value: ICRD


title: IL-1R1 eRestore_F_sham_9h_A098

description:
Library name: A098
Bulk RNA-seq, IL-1R1 eRestore, F, sham, 9h

tag: tissue

tag: strain

value: 4.73 months


title: Cortex, 12-week-old, WT, rep1

description: Library name: CTX-WT-1

tag: batch


title: 203991400160_R04C01_PD016_CNG

tag: Sex

value: female


title: Recessive Optic Atrophy, biol rep 3

description:
Library name: ROA_C
ROAc

value: Skin

value: Fibroblasts


title: Lung, P6, Cic-L-KO, rep8

description: Library name: L-LKO-8

source_name: Lung

value: Lung

value: Cic-L-KO


title: IL-1R1 eRestore_F_sham_9h_A097

description:
Library name: A097
Bulk RNA-seq, IL-1R1 eRestore, F, sham, 9h

value: mouse brain

value: IL-1R1 eRestore

value: Female

tag: surgery

value: sham

tag: timepoint

tag: age (months)


title: 203973690018_R08C01_NP14/075_CNG

value: Anterior cingulate

tag: regiondescription

value: Oxford Brain Bank

value: male

value: FALSE


title: Recessive Optic Atrophy, biol rep 2

description:
Library name: ROA_B
ROAB

value: Patient


title: IL-1R1 eRestore_F_sham_72h_A149

description:
Library name: A149
Bulk RNA-seq, IL-1R1 eRestore, F, sham, 72h

value: 5.87 months

tag: animal id

tag: experiment id


title: Lung, P6, Cic-L-KO, rep7

description: Library name: L-LKO-7


title: 203973690018_R01C01_P10/14_CNG

tag: plate

tag: centre

value: QSBB

tag: thal


title: Recessive Optic Atrophy, biol rep 1

description:
Library name: ROA_A
ROAa

tag: cell type

tag: genotype

value: Syndromic

value: ICRD


title: IL-1R1 eRestore_F_sham_72h_A075

description:
Library name: A075
Bulk RNA-seq, IL-1R1 eRestore, F, sham, 72h

value: 5.63 months


title: Lung, P6, Cic-L-KO, rep6

description: Library name: L-LKO-6

tag: time


title: 203976760050_R08C01_PD800_CNG

value: Imperial Brain Bank

value: female


title: Dominant Optic Atrophy, biol rep 3

description:
Library name: DOA_C
DOAc

value: Skin

value: Fibroblasts

tag: sample id

value: DOAc

tag: sample id_2

tag: patient id_ctrl

value: DOA

value: Non syndromic


title: IL-1R1 eRestore_F_sham_72h_A072

description:
Library name: A072
Bulk RNA-seq, IL-1R1 eRestore, F, sham, 72h

tag: tissue

value: mouse brain

tag: strain

value: IL-1R1 eRestore

value: Female

value: sham

value: 5.8 months


title: Lung, P6, Cic-L-KO, rep5

description: Library name: L-LKO-5

value: Lung

value: Cic-L-KO

tag: batch


title: Dominant Optic Atrophy, biol rep 2

description:
Library name: DOA_B
DOAB

tag: Sex

value: DOAB

value: Patient


title: IL-1R1 eRestore_F_sham_24h_A052

description:
Library name: A052
Bulk RNA-seq, IL-1R1 eRestore, F, sham, 24h

tag: surgery

tag: timepoint

tag: age (months)

value: 4.9 months


title: 203976760050_R07C01_PD784_CNG

value: Anterior cingulate

tag: regiondescription

value: Imperial Brain Bank

value: FALSE


title: Lung, P6, Cic-L-KO, rep4

description: Library name: L-LKO-4


title: 203976760050_R02C01_PD143_CNG

tag: plate

value: male


title: Dominant Optic Atrophy, biol rep 1

description:
Library name: DOA_A
DOAA

value: Skin

value: Fibroblasts

value: female

value: DOAA


title: IL-1R1 eRestore_F_sham_24h_A051

description:
Library name: A051
Bulk RNA-seq, IL-1R1 eRestore, F, sham, 24h

value: mouse brain

value: IL-1R1 eRestore

tag: animal id

tag: experiment id


title: Lung, P6, Cic-L-KO, rep3

description: Library name: L-LKO-3


title: 203976760050_R01C01_20130020_CNG

tag: centre

value: Newcastle Brain Tissue Resource

tag: thal


title: HeLa, U2AF2, 250ug, rep 2

city: Frankfurt am Main

first: Michaela

last: Müller-McNicoll

address: Max-von-Laue-Str. 13

country: Germany

institute: Goethe University Frankfurt

description:
Library name: iCLIP3_U2AF2_250ug_rep2
iCLIP3

data_processing:
Processing pipeline racoon_clip (v2.0.12): experiment_type: "iCLIP3" quality_filter_barcodes: False adapter_cycles: 1madapter_trimming: True The racoon_clip pipeline performed the following steps.
Quality control: FastQC (v0.12.1), MultiQC (v.1.31), FastQ Screen (v0.15.3)
Adapter and 5'UMI trimming: Flexbar (v3.5.0) with non-default parameters: flexbar --zip-output GZ --adapters AGATCGGAAGAGCACACGTC  --adapter-trim-end RIGHT --adapter-error-rate 0.1 --adapter-min-overlap 1 --adapter-cycles 1 --min-read-length 15
3'UMI trimming: Flexbar (v3.5.0) with non-default parameters: flexbar --zip-output GZ -y 3 --min-read-length 15
Mapping: STAR (v2.7.11a) with non-default parameters: STAR --sjdbGTFfile gencode.v49.primary_assembly.annotation.gtf --sjdbOverhang 141 --alignEndsType Extend5pOfRead1 --outFilterMismatchNoverReadLmax 0.04 --outFilterMismatchNmax 999 --outFilterMultimapNmax 1 --outSAMattributes All --outReadsUnmapped Fastx --outSJfilterReads Unique --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate (output: SAMPLE.mapped.bam)
Duplicate removal: UMI-tools (v1.1.6) with non-default parameters: umi_tools dedup -I SAMPLE.bam -S SAMPLE.duprm.bam --extract-umi-method read_id --method unique
Convert bed file format using BEDTools (v2.31.1) bedtools bamtobed. (output: SAMPLE.bed)
Remove reads directly mapped at chromosome ends (their upstream/crosslink position does not exist): awk 'BEGIN{{OFS="\t"}} FNR==NR{{chr_len[$1]=$2; next}} !(($6=="+" && $2==0) || ($6=="-" && $3==chr_len[$1]))' GRCh38.p14.genome.fa.fai SAMPLE.bed > SAMPLE.bed.tmp && mv SAMPLE.bed.tmp SAMPLE.bed
Shifting one base upstream; BEDTools (v2.31.1): bedtools shift -m 1 -p -1 -i stdin -g GRCh38.p14.genome.fa.fai | sort -k1,1 -k2,2n -k3,3n > SAMPLE.shifted1bp.bed
BED to bedGraph considering only 5' end positions;  BEDTools (v2.31.1): bedtools genomecov -bg -strand + -5 -i SAMPLE.shifted1bp.bed -g GRCh38.p14.genome.fa.fai > SAMPLE.duprm.plus.bedgraph | LC_COLLATE=C sort -k1,1 -k2,2n -k3,3n; bedtools genomecov -bg -strand - -5 -i SAMPLE.shifted1bp.bed -g GRCh38.p14.genome.fa.fai | LC_COLLATE=C sort -k1,1 -k2,2n -k3,3n > SAMPLE.duprm.minus.bedgraph
bedGraph to bigWig using bedGraphToBigWig of the UCSC tool suite (v472)
Merge of bam files from replicates; samtools (v1.22.1)
Peakcalling on merged replicates; PureCLIP (v1.3.1)
Definition of binding sites; BindingSiteFinder (Bioconductor R package, v2.8.0) BSFind function: non-default parameters bsSize = 5, cutoff.geneWiseFilter = 0.1, repro.nReps = 2, repro.cutoff = 0.1, overlaps.geneAssignment = “hierarchy”, overlaps.rule.geneAssignment = gene_hierarcy, overlaps.TranscriptRegions = “hierarchy”, overlaps.rule.TranscriptRegions = transcript_region_hierarcy with gene_hierarcy = c( “protein_coding”, “lncRNA”, “snRNA”, “snoRNA”,  “miRNA”, “rRNA”,  “misc_RNA”, “tRNA”, “pseudogene”); transcript_region_hierarcy = c(“INTRON”, “UTR5”, “UTR3”, “CDS”)
Assembly: GRCh38.p14 (Gencode release 49)
Supplementary files format and content: bigWig files containing the genomic coordinates and duplicate removed counts of uniquely mapped crosslinks for each replicate separated by strand.
Supplementary files format and content: bed files containing the defined reproducible binding sites (removed crosslinking background) per U2AF2 concentration (40ug, 100ug, 250ug)
Library strategy: iCLIP

source_name: HeLa

growth_protocol: HeLa cells were cultured in high glucose, pyruvate Dulbecco’s modified Eagle’s medium (DMEM; Gibco) + GlutaMAX supplemented with 10% fetal bovine serum (FBS; heat-inactivated at 56°C for 30 min) and 1% penicillin/streptomycin (P/S) at 37°C in a humidified 5% CO₂ incubator.

extract_protocol:
Cells were lysed and treated with RNase I. U2AF2 was immunoprecipitated with Gamma binding beads coupled to anti-U2AF2 antibody.
iCLIP3 - After stringent washing, RNA was dephosphorylated and 10% were ligated to the pCp-IR750 and 90% to a L7 linker. Protein-RNA complexes were resolved by denaturing gel electrophoresis and transfered to nitrocellulose membrane. A membrane region above the expected size of the protein was cut and RNA was released by Proteinase K treatment. RNA was reverse transcribed using reverse primer and a second adapter containing unique molecular identifiers (UMIs) was ligated to the cDNA 3'-ends. The cDNA was pre-amplified for 5 cycles using short P5 and P7 primers. After a size selection using ProNex beads, a second PCR amplification was performed with long Tru-seq P5 and P7 primers that contain i5 and i7 sequences required for cluster generation on Illumina flow cells, as well as dual 8-nucleotide indices (XXXXXXXX) for sample multiplexing to generate the final iCLIP3 libraries.

treatment_protocol: Cells were washed with PBS and irradiated once with 254 nm UV light to crosslink proteins to nucleic acids.

tag: cell line

value: HeLa

tag: treatment


title: IL-1R1 eRestore_F_CHI_9h_A198

description:
Library name: A198
Bulk RNA-seq, IL-1R1 eRestore, F, CHI, 9h

value: Female

value: CHI

value: 4.7 months


title: Lung, P6, Cic-L-KO, rep2

description: Library name: L-LKO-2

value: Lung

tag: genotype

value: Cic-L-KO

tag: time


title: 203991400062_R08C01_P46/10_CNG

tag: tissue

value: Anterior cingulate

value: QSBB

value: TRUE


title: HeLa, U2AF2, 250ug, rep 1

description:
Library name: iCLIP3_U2AF2_250ug_rep1
iCLIP3


title: IL-1R1 eRestore_F_CHI_9h_A182

description:
Library name: A182
Bulk RNA-seq, IL-1R1 eRestore, F, CHI, 9h

tag: strain


title: Lung, P6, Cic-L-KO, rep1

description: Library name: L-LKO-1

tag: batch


title: 203991400062_R07C01_19970112_CNG

tag: Sex

value: male

value: FALSE


title: IL-1R1 eRestore_F_CHI_9h_A176

description:
Library name: A176
Bulk RNA-seq, IL-1R1 eRestore, F, CHI, 9h

tag: surgery

value: 4.5 months


title: HeLa, U2AF2, 100ug, rep 2

description:
Library name: iCLIP3_U2AF2_100ug_rep2
iCLIP3


title: Lung, P6, Cic-S-KO, rep8

description: Library name: L-SKO-8

value: Cic-S-KO


title: 203991400062_R05C01_PD959_CNG

value: Imperial Brain Bank


title: HeLa, U2AF2, 100ug, rep 1

description:
Library name: iCLIP3_U2AF2_100ug_rep1
iCLIP3


title: IL-1R1 eRestore_F_CHI_9h_A173

description:
Library name: A173
Bulk RNA-seq, IL-1R1 eRestore, F, CHI, 9h

value: mouse brain

tag: timepoint


title: Lung, P6, Cic-S-KO, rep7

description: Library name: L-SKO-7


title: 203991400062_R04C01_20090027_CNG

value: female


title: HeLa, U2AF2, 40ug, rep 2

description:
Library name: iCLIP3_U2AF2_40ug_rep2
iCLIP3

value: 40 µg


title: IL-1R1 eRestore_F_CHI_9h_A172

description:
Library name: A172
Bulk RNA-seq, IL-1R1 eRestore, F, CHI, 9h

value: IL-1R1 eRestore

tag: age (months)


title: Lung, P6, Cic-S-KO, rep6

description: Library name: L-SKO-6


title: 203991400062_R01C01_PD109_CNG

tag: regiondescription


title: HeLa, U2AF2, 40ug, rep 1

description:
Library name: iCLIP3_U2AF2_40ug_rep1
iCLIP3

value: HeLa


title: IL-1R1 eRestore_F_CHI_9h_A096

description:
Library name: A096
Bulk RNA-seq, IL-1R1 eRestore, F, CHI, 9h

value: Female

value: CHI


title: Lung, P6, Cic-S-KO, rep5

description: Library name: L-SKO-5

value: Lung


title: 203991390104_R04C01_P29/12_CNG

tag: plate


title: RPMI-Scr-R3

city: Pamplona

first: Nahia

last: Gomez-Echarte

address: Avenida Pio XII, 55

country: Spain

institute: CIMA

description:
Library name: sample 25
raw_counts_all_samples.txt

data_processing:
The reads were aligned to the human genome hg38 (GRCh38.p13) for all the samples.
RNA-seq: differential gene expression analysis was performed using Limma-voom pipeline and GSEA analyses were conducted using ClusterProfiler.
Assembly: GRCh38.p13
Supplementary files format and content: RNA-seq: one excel file containing the cpm for all the samples (divided cell lines and human samples).

source_name: blood

growth_protocol: MM cell lines were maintained in RPMI-1640 medium containing L-Glutamine supplemented with 1% of penicillin-treptomycin, 2% HEPES Buffer and 20% of Fetal Bovine Serum.

extract_protocol:
RNA was isolated with the MagMAX mirVana total RNA Isolation kit (applied biosystems)
RNA-seq library was prepared using Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit (Illumina).

treatment_protocol: transduction of lentiviral particles containing the empty vector (scramble) or the vector containing the sgRNAs against IRF2 (IRF2-ssg1 and IRF2-ssg2).

value: blood

value: RPMI 8226

tag: cell type

value: Multiple Myeloma

value: modified to express Cas9 protein

value: scramble


title: IL-1R1 eRestore_F_CHI_72h_A143

description:
Library name: A143
Bulk RNA-seq, IL-1R1 eRestore, F, CHI, 72h

value: 5.87 months

tag: animal id

tag: experiment id


title: Lung, P6, Cic-S-KO, rep4

description: Library name: L-SKO-4


title: 203991390104_R03C01_20100742_CNG

value: Anterior cingulate

tag: centre

value: Newcastle Brain Tissue Resource

value: male

tag: thal

value: FALSE


title: RPMI-Scr-R2

description:
Library name: sample 24
raw_counts_all_samples.txt

tag: cell line

tag: treatment


title: Lung, P6, Cic-S-KO, rep3

description: Library name: L-SKO-3

tag: genotype

value: Cic-S-KO

tag: time


title: 203991390104_R01C01_PD1075_CNG

tag: tissue

value: Imperial Brain Bank

value: female


title: IL-1R1 eRestore_F_CHI_72h_A141

description:
Library name: A141
Bulk RNA-seq, IL-1R1 eRestore, F, CHI, 72h

value: mouse brain

tag: strain

value: IL-1R1 eRestore


title: RPMI-Scr-R1

description:
Library name: sample 23
raw_counts_all_samples.txt


title: IL-1R1 eRestore_F_CHI_72h_A078

description:
Library name: A078
Bulk RNA-seq, IL-1R1 eRestore, F, CHI, 72h

tag: Sex

value: Female

value: CHI

value: 5.7 months


title: Lung, P6, Cic-S-KO, rep2

description: Library name: L-SKO-2

value: Lung

tag: batch


title: 203991400061_R08C01_20110310_CNG


title: IL-1R1 eRestore_F_CHI_72h_A076

description:
Library name: A076
Bulk RNA-seq, IL-1R1 eRestore, F, CHI, 72h

tag: surgery

tag: timepoint

value: 5.63 months


title: RMPI-IRF2-G2-R3

description:
Library name: sample 22
raw_counts_all_samples.txt

value: blood

value: RPMI 8226

value: Multiple Myeloma

value: modified to express Cas9 protein


title: Lung, P6, Cic-S-KO, rep1

description: Library name: L-SKO-1


title: RMPI-IRF2-G2-R2

description:
Library name: sample 21
raw_counts_all_samples.txt


title: 203991400061_R05C01_P22/12_CNG

value: Anterior cingulate

tag: regiondescription

value: QSBB


title: Lung, P6, WT, rep8

description: Library name: L-WT-8

value: WT


title: IL-1R1 eRestore_F_CHI_72h_A070

description:
Library name: A070
Bulk RNA-seq, IL-1R1 eRestore, F, CHI, 72h

tag: age (months)

value: 6.17 months


title: 203991400061_R06C01_PD704_CNG

tag: plate

value: Imperial Brain Bank

value: male

value: FALSE


title: RMPI-IRF2-G2-R1

description:
Library name: sample 20
raw_counts_all_samples.txt

tag: cell type


title: 203991400061_R04C01_PDC016_CNG

value: female


title: RPMI-IRF2-G1-R3

description:
Library name: sample 19
raw_counts_all_samples.txt


title: IL-1R1 eRestore_F_CHI_72h_A068

description:
Library name: A068
Bulk RNA-seq, IL-1R1 eRestore, F, CHI, 72h

value: mouse brain

value: IL-1R1 eRestore

value: Female

tag: animal id

tag: experiment id


title: Lung, P6, WT, rep6

description: Library name: L-WT-6

value: Lung


title: Lung, P6, WT, rep7

description: Library name: L-WT-7


title: IL-1R1 eRestore_F_CHI_24h_A049

description:
Library name: A049
Bulk RNA-seq, IL-1R1 eRestore, F, CHI, 24h

value: CHI

value: 5.3 months


title: Lung, P6, WT, rep5

description: Library name: L-WT-5


title: IL-1R1 eRestore_F_CHI_24h_A050

description:
Library name: A050
Bulk RNA-seq, IL-1R1 eRestore, F, CHI, 24h

value: 4.9 months


title: 203990170009_R08C01_19900113_CNG

tag: centre

value: Newcastle Brain Tissue Resource

tag: thal


title: IL-1R1 eRestore_F_CHI_24h_A014

description:
Library name: A014
Bulk RNA-seq, IL-1R1 eRestore, F, CHI, 24h

value: 7.4 months


title: 203991400061_R01C01_20020045_CNG

value: Anterior cingulate


title: mIMCD3 cells, K9me3_DMSO

city: Tianjin

first: xudan

last: dou

state: Tianjin

address: No.22 Qixiangtai Road

country: China

institute: Tianjin Medical University

library_source: genomic

data_processing:
The Bowtie2 algorithm was employed to align paired-end reads obtained from ChIP-seq and ATAC-seq experiments to the mouse reference genome mm10. To eliminate PCR duplicates and reads aligned to mtDNA, the "mark duplicates" command from Picard (http://broadinstitute.github.io/picard/) was utilized. Subsequently, ChIP-seq and ATAC-seq peaks were identified using HOMER's findPeaks algorithm. Bigwig files were generated based on the deepTools output5. Statistical differences in normalized read counts across peaks between sets of ChIP-seq experiments were determined using HOMER's getDifferentialPeaks.pl, which leverages the statistical modeling functions of DESeq2. ChromHMM algorithm was then applied to define chromatin states, while the AnnotatePeaks.pl algorithm was utilized to analyze the distribution of peaks around the transcription start site (TSS). Additionally, the FindMotifsGenome.pl algorithm was employed to assess motif enrichment.
Assembly: mm10
Supplementary files format and content: bigwig

extract_protocol:
mIMCD3 cells were fixed with 1% formaldehyde at room temperature for 10 minutes. Crosslinking was halted by adding 150 mM of glycine for 5 minutes at room temperature.mIMCD3 cells were fixed with 1% formaldehyde at room temperature for 10 minutes. Crosslinking was halted by adding 150 mM of glycine for 5 minutes at room temperature.
Library construction was effected with a VAHTS Universal DNA Library Prep Kit for Illumina V3, and sequencing was carried out on the Illumina platform.

tag: chip antibody

value: H3K9me3 (Abcam, ab3446)

tag: cell line

value: Mouse inner medullary collecting duct

tag: treatment

value: DMSO


title: Endosperm+tegument, 21DPA, biol rep 3

city: Bologna

first: Cristian

last: Forestan

state: BO

address: Viale Fanin 44

department: Dipartimento di Scienze e Tecnologie Agro-alimentari (DISTAL)

country: Italy

institute: University of Bologna

description: Library name: Endosperm_21DPA_R3

data_processing:
Raw reads quality filtering and trimming for adapter contaminants with Trimmomatic v0.39 (Bolger et al., 2014)
High quality reads were mapped to the Triticum durum cv. Svevo Rel 2.0 genome and annotation using STAR 2.7.10b (Dobin et al., 2013).
Read counts and transcripts per million TPM were calculated per gene using RSEM v1.3.3 (Li and Dewey, 2011).
Assembly: Svevo Rel2.0 genome assembly
Supplementary files format and content: tab delimited text file including rawcounts for each sample
Supplementary files format and content: tab delimited text file including TPM values for each sample

organism: Triticum turgidum subsp. durum

source_name: Endosperm+tegument sampled at 21DPA

growth_protocol: Durum wheat seeds (Triticum turgidum L. ssp. durum) cv. Svevo were pre-germinated in Petri dishes with wet filter paper, at 4 °C for 5 days to obtain a synchronous germination. Germinating seeds were then transferred into pots filled with loam-based potting soil, plus 1/3 of sand and perlite (in 1:1 volume ratio) in a controlled environment starting with a 14/10 hours day/night length at 14/8 °C and progressively reaching 16/8 hours day night length at 24/20 °C

extract_protocol:
Total RNA was extracted from 100 mg fresh weight material; the Direct-Zol RNA Miniprep Kits Zymo Research) was used for leaf, root, meristem and ovary samples, while the RNeasy Plant Mini Kit (Qiagen) was used for seed samples. In both protocols genomic DNA contamination was removed using the on-column DNase treatment
Firstly, ribosomal RNA was removed from total RNA, followed by ethanol precipitation. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. During the second strand cDNA synthesis, dUTPs were replaced with dTTPs in the reaction buffer. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification

tag: tissue

value: Endosperm+tegument

tag: Stage

tag: cultivar

value: Svevo


title: RPMI-IRF2-G1-R2

description:
Library name: sample 18
raw_counts_all_samples.txt

value: blood

value: RPMI 8226

value: Multiple Myeloma

tag: genotype

value: modified to express Cas9 protein


title: RPMI-IRF2-G1-R1

description:
Library name: sample 17
raw_counts_all_samples.txt


title: Endosperm+tegument, 21DPA, biol rep 1

description: Library name: Endosperm_21DPA_R1


title: Lung, P6, WT, rep3

description: Library name: L-WT-3

value: WT

tag: time

tag: batch


title: Lung, P6, WT, rep4

description: Library name: L-WT-4

value: Lung


title: MMIS-Scr-R3

description:
Library name: sample 16
raw_counts_all_samples.txt

value: scramble


title: 203990170009_R06C01_20174968_CNG

tag: regiondescription

tag: Sex

value: male

value: FALSE


title: IL-1R1 eRestore_F_CHI_24h_A012

description:
Library name: A012
Bulk RNA-seq, IL-1R1 eRestore, F, CHI, 24h

value: mouse brain

tag: strain

value: IL-1R1 eRestore

value: Female

tag: surgery

value: CHI

tag: timepoint

tag: age (months)


title: 203990170009_R04C01_PD897_CNG

value: Anterior cingulate

tag: plate

tag: centre

value: Imperial Brain Bank


title: Lung, P6, WT, rep2

description: Library name: L-WT-2


title: IL-1R1 eRestore_F_CHI_24h_A010

description:
Library name: A010
Bulk RNA-seq, IL-1R1 eRestore, F, CHI, 24h

value: 7.07 months

tag: animal id

tag: experiment id


title: 203990170009_R03C01_PD737_CNG

tag: thal


title: MMIS-Scr-R2

description:
Library name: sample 15
raw_counts_all_samples.txt

tag: tissue

tag: cell line

tag: cell type

tag: treatment


title: IL-1R1 eRestore_F_CHI_24h_A009

description:
Library name: A009
Bulk RNA-seq, IL-1R1 eRestore, F, CHI, 24h


title: Lung, P6, WT, rep1

description: Library name: L-WT-1

tag: genotype

tag: time


title: 203990170009_R01C01_PD017_CNG

tag: regiondescription


title: MMIS-G2-R2

description:
Library name: sample 13
raw_counts_all_samples.txt


title: MMIS-Scr-R1

description:
Library name: sample 14
raw_counts_all_samples.txt


title: AB20015

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description: Library name: Sample 61

library_source: transcriptomic single cell

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary files format and content: cell_metadata.csv

source_name: Tumor

extract_protocol:
Isolation of tumor cells and tumor-infiltrating immune cells was performed from tumor-bearing brain hemispheres. Briefly mice were perfused with PBS and the tumor-bearing brain hemisphere was collected in Roswell Park Memorial Institute (RPMI) medium containing 0.4 mg/ml Collagenase IV and 0.1 mg/ml DNase I (both Sigma-Aldrich). The tissue was then incubated for 40 min at 37°C and further homogenize using a 18G needle. Myelin was removed using a 30% Percoll centrifugation step (Sigma-Aldrich).
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)

treatment_protocol: Mice were implanted with 2x10^4 GL261 cells intracerebrally. 12 days later mice received lomustine and L19-TNFa. One day later mice were sacrificed and tumors were extracted for single cell processing.

value: Tumor

tag: sorting gate

tag: batch


title: AB20014

description: Library name: Sample 60


title: mIMCD3 cells, K9ac-SFN

tag: chip antibody

value: H3K9ac (Abcam, ab3446)

value: Mouse inner medullary collecting duct

value: SFN


title: AB20016

description: Library name: Sample 62


title: C57BL/6J_M_sham_9h_A193

description:
Library name: A193
Bulk RNA-seq, C57BL/6J, M, sham, 9h

tag: strain

tag: Sex

value: Male

tag: surgery

value: sham

tag: timepoint

value: 4.4 months


title: MMIS-G2-R1

description:
Library name: sample 12
raw_counts_all_samples.txt

value: blood

value: Multiple Myeloma

value: modified to express Cas9 protein


title: MMIS-G1-R2

description:
Library name: sample 10
raw_counts_all_samples.txt


title: 203973690073_R04C01_20174903_CNG

tag: plate

tag: centre

value: Newcastle Brain Tissue Resource

value: male

value: FALSE


title: C57BL/6J_M_sham_9h_A087

description:
Library name: A087
Bulk RNA-seq, C57BL/6J, M, sham, 9h

value: mouse brain

tag: age (months)

value: 4.8 months

tag: animal id

tag: experiment id


title: 203973690073_R08C01_20040063_CNG

tag: tissue

value: Anterior cingulate

tag: thal


title: 203973690073_R05C01_PD207_CNG

value: Imperial Brain Bank


title: C57BL/6J_M_sham_72h_A115

description:
Library name: A115
Bulk RNA-seq, C57BL/6J, M, sham, 72h

value: 6.77 months


title: MMIS-G1-R3

description:
Library name: sample 11
raw_counts_all_samples.txt

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: AB20013

description: Library name: Sample 59

value: Tumor

tag: sorting gate

tag: batch


title: C57BL/6J_M_sham_9h_A194

description:
Library name: A194
Bulk RNA-seq, C57BL/6J, M, sham, 9h

tag: strain


title: MMIS-G1-R1

description:
Library name: sample 9
raw_counts_all_samples.txt


title: AB20012

description: Library name: Sample 58


title: 203973690073_R02C01_NP12/060_CNG

tag: regiondescription

value: Oxford Brain Bank

tag: Sex

value: female


title: C57BL/6J_M_sham_72h_A044

description:
Library name: A044
Bulk RNA-seq, C57BL/6J, M, sham, 72h

value: Male

tag: surgery

tag: timepoint

value: 5.17 months


title: KMS28-Scr-R3

description:
Library name: sample 8
raw_counts_all_samples.txt

value: scramble


title: C57BL/6J_M_sham_72h_A043

description:
Library name: A043
Bulk RNA-seq, C57BL/6J, M, sham, 72h

value: sham


title: 203973690036_R07C01_PD562_CNG

tag: plate

tag: centre


title: KMS28-Scr-R2

description:
Library name: sample 7
raw_counts_all_samples.txt

value: blood

value: Multiple Myeloma


title: 203973690036_R05C01_20174906_CNG

value: Newcastle Brain Tissue Resource


title: AB20010

description: Library name: Sample 56


title: 203973690073_R01C01_P30/14_CNG

value: QSBB

value: male


title: AB20011

description: Library name: Sample 57


title: C57BL/6J_M_sham_24h_A123

description:
Library name: A123
Bulk RNA-seq, C57BL/6J, M, sham, 24h

value: mouse brain

tag: age (months)

tag: animal id


title: 203973690036_R04C01_NP12/064_CNG

tag: tissue

value: FALSE


title: C57BL/6J_M_sham_24h_A031

description:
Library name: A031
Bulk RNA-seq, C57BL/6J, M, sham, 24h

value: 5.2 months

tag: experiment id


title: 203991410125_R05C01_PD079_CNG

value: Anterior cingulate

value: Imperial Brain Bank

tag: thal


title: C57BL/6J_M_sham_24h_A133

description:
Library name: A133
Bulk RNA-seq, C57BL/6J, M, sham, 24h

value: 4.8 months


title: C57BL/6J_M_CHI_9h_A195

description:
Library name: A195
Bulk RNA-seq, C57BL/6J, M, CHI, 9h

value: CHI

value: 4.4 months


title: AB20009

description: Library name: Sample 55

value: Tumor

tag: cell type


title: KMS28-G2-R3

description:
Library name: sample 5
raw_counts_all_samples.txt

tag: cell line

tag: genotype

value: modified to express Cas9 protein


title: C57BL/6J_M_CHI_9h_A192

description:
Library name: A192
Bulk RNA-seq, C57BL/6J, M, CHI, 9h

value: Male


title: KMS28-G2-R1

description:
Library name: sample 4
raw_counts_all_samples.txt

tag: treatment

value: IRF2-sg2 (transduced with lentiviral particles containing sgRNA-2 against IRF2)


title: KMS28-Scr-R1

description:
Library name: sample 6
raw_counts_all_samples.txt

value: blood

value: scramble (transduced with lentiviral particles containing the empty vector)


title: AB20008

description: Library name: Sample 54

tag: sorting gate

tag: batch


title: AB20007

description: Library name: Sample 53


title: AB20006

description: Library name: Sample 52


title: 203991410125_R04C01_PD915_CNG

tag: regiondescription

value: female


title: KMS28-G1-R3

description:
Library name: sample 3
raw_counts_all_samples.txt

value: Multiple Myeloma


title: AB20005

description: Library name: Sample 51


title: AB20004

description: Library name: Sample 50


title: 203991410002_R07C01_20174913_CNG

value: Newcastle Brain Tissue Resource

tag: Sex

value: male


title: 203991410002_R04C01_PD010_CNG

value: FALSE


title: MM_149

description: Library name: sample 231

data_processing:
The reads were aligned to the human genome hg38 (GRCh38.p13) for all the samples.
RNA-seq: differential gene expression analysis was performed using DESeq2 and GSEA analyses were conducted using ClusterProfiler.
Assembly: GRCh38.p13
Supplementary files format and content: RNA-seq: one excel file containing the cpm for all the samples (divided cell lines and human samples).

source_name: bone marrow

treatment_protocol: transduction of lentiviral particles containing the empty vector (scramble) or the vector containing the sgRNAs against IRF2 (IRF2-sg1 and IRF2-sg2).

value: bone marrow

value: Myeloma Plasma Cell


title: 203991410125_R02C01_C085_CNG

value: Anterior cingulate

value: Imperial Brain Bank


title: 203991410002_R02C01_PD827_CNG


title: AB20002

description: Library name: Sample 48


title: MM_148

description: Library name: sample 230


title: C57BL/6J_M_CHI_9h_A103

description:
Library name: A103
Bulk RNA-seq, C57BL/6J, M, CHI, 9h

value: mouse brain

tag: strain

tag: surgery

value: CHI

value: 4.8 months


title: AB20001

description: Library name: Sample 47

value: Tumor


title: KMS28-G1-R2

description:
Library name: sample 2
raw_counts_all_samples.txt

value: modified to express Cas9 protein


title: C57BL/6J_M_CHI_9h_A191

description:
Library name: A191
Bulk RNA-seq, C57BL/6J, M, CHI, 9h

value: Male

tag: timepoint

value: 4.4 months


title: 203991410125_R01C01_PDC029_CNG

tag: plate

tag: centre


title: MM_147

description: Library name: sample 229


title: MM_150

description: Library name: sample 232


title: C57BL/6J_M_CHI_9h_A186

description:
Library name: A186
Bulk RNA-seq, C57BL/6J, M, CHI, 9h

tag: age (months)

tag: animal id


title: KMS28-G1-R1

description:
Library name: sample 1
raw_counts_all_samples.txt

tag: tissue

value: blood

value: IRF2-sg1 (transduced with lentiviral particles containing sgRNA-1 against IRF2)


title: C57BL/6J_M_CHI_9h_A185

description:
Library name: A185
Bulk RNA-seq, C57BL/6J, M, CHI, 9h

tag: experiment id


title: C57BL/6J_M_CHI_9h_A088

description:
Library name: A088
Bulk RNA-seq, C57BL/6J, M, CHI, 9h


title: AB20000

description: Library name: Sample 46

tag: cell type


title: AB20003

description: Library name: Sample 49


title: 203991410001_R05C01_20185937_CNG

value: female

tag: thal


title: C57BL/6J_M_CHI_9h_A104

description:
Library name: A104
Bulk RNA-seq, C57BL/6J, M, CHI, 9h


title: C57BL/6J_M_CHI_72h_A148

description:
Library name: A148
Bulk RNA-seq, C57BL/6J, M, CHI, 72h

value: 5.27 months


title: MM_145

description: Library name: sample 227

tag: cell line

tag: genotype


title: 203991410124_R04C01_20160560_CNG

value: Newcastle Brain Tissue Resource

value: male


title: MM_144

description: Library name: sample 226

value: bone marrow

tag: treatment


title: 203991410001_R01C01_PD874_CNG

value: FALSE


title: AB19998

description: Library name: Sample 44

tag: sorting gate

tag: batch


title: AB19999

description: Library name: Sample 45


title: C57BL/6J_M_CHI_72h_A140

description:
Library name: A140
Bulk RNA-seq, C57BL/6J, M, CHI, 72h

tag: Sex


title: 203991410124_R05C01_PD775_CNG

value: Anterior cingulate

tag: regiondescription


title: MM_146

description: Library name: sample 228

value: Myeloma Plasma Cell


title: MM_143

description: Library name: sample 225


title: 203991410124_R03C01_NP15/013_CNG

value: Oxford Brain Bank


title: C57BL/6J_M_CHI_72h_A114

description:
Library name: A114
Bulk RNA-seq, C57BL/6J, M, CHI, 72h

value: mouse brain

tag: strain

tag: surgery

value: CHI

value: 6.77 months


title: AB19997

description: Library name: Sample 43

value: Tumor


title: C57BL/6J_M_CHI_72h_A067

description:
Library name: A067
Bulk RNA-seq, C57BL/6J, M, CHI, 72h

value: Male

tag: timepoint


title: AB19995

description: Library name: Sample 41


title: AB19996

description: Library name: Sample 42


title: 203991410124_R02C01_PD341_CNG

tag: plate

tag: centre

value: Imperial Brain Bank


title: 203991400131_R03C01_NP12/136_CNG


title: AB19994

description: Library name: Sample 40


title: 203991400131_R04C01_PD002_CNG

value: TRUE


title: C57BL/6J_M_CHI_72h_A066

description:
Library name: A066
Bulk RNA-seq, C57BL/6J, M, CHI, 72h

tag: age (months)

tag: animal id


title: MM_141

description: Library name: sample 223

tag: tissue


title: MM_142

description: Library name: sample 224

tag: cell type


title: MM_140

description: Library name: sample 222


title: C57BL/6J_M_CHI_72h_A065

description:
Library name: A065
Bulk RNA-seq, C57BL/6J, M, CHI, 72h

tag: experiment id


title: C57BL/6J_M_CHI_72h_A042

description:
Library name: A042
Bulk RNA-seq, C57BL/6J, M, CHI, 72h

value: 5.17 months


title: MM_139

description: Library name: sample 221

tag: cell line


title: 203991400166_R06C01_PD1016_CNG

value: female

tag: thal


title: AB19993

description: Library name: Sample 39

tag: treatment


title: C57BL/6J_M_CHI_72h_A041

description:
Library name: A041
Bulk RNA-seq, C57BL/6J, M, CHI, 72h


title: AB19992

description: Library name: Sample 38

tag: sorting gate


title: 203991400166_R03C01_PD822_CNG


title: C57BL/6J_M_CHI_24h_A124

description:
Library name: A124
Bulk RNA-seq, C57BL/6J, M, CHI, 24h

value: 4.8 months


title: MM_138

description: Library name: sample 220

tag: genotype


title: MM_137

description: Library name: sample 219


title: AB19990

description: Library name: Sample 36

tag: batch


title: C57BL/6J_M_CHI_24h_A035

description:
Library name: A035
Bulk RNA-seq, C57BL/6J, M, CHI, 24h

tag: Sex

value: 5.2 months


title: 203991400166_R04C01_C036_CNG

tag: regiondescription

value: male


title: MM_135

description: Library name: sample 217

value: bone marrow


title: C57BL/6J_M_CHI_24h_A034

description:
Library name: A034
Bulk RNA-seq, C57BL/6J, M, CHI, 24h

tag: strain

tag: surgery


title: 203991400142_R03C01_20100979_CNG

tag: plate

value: Newcastle Brain Tissue Resource

value: FALSE


title: MM_134

description: Library name: sample 216

value: Myeloma Plasma Cell


title: C57BL/6J_M_CHI_24h_A132

description:
Library name: A132
Bulk RNA-seq, C57BL/6J, M, CHI, 24h

tag: timepoint


title: 203991400142_R06C01_PD870_CNG

value: Anterior cingulate

tag: centre


title: AB19988

description: Library name: Sample 34


title: AB19989

description: Library name: Sample 35


title: MM_136

description: Library name: sample 218


title: AB19991

description: Library name: Sample 37


title: 203991400142_R04C01_PD761_CNG


title: AB19987

description: Library name: Sample 33


title: C57BL/6J_M_CHI_24h_A033

description:
Library name: A033
Bulk RNA-seq, C57BL/6J, M, CHI, 24h

value: mouse brain

tag: age (months)

tag: animal id


title: MM_133

description: Library name: sample 215

tag: tissue

tag: cell type


title: 203991400142_R02C01_NP12/161_CNG

value: Oxford Brain Bank


title: AB19986

description: Library name: Sample 32


title: C57BL/6J_M_CHI_24h_A032

description:
Library name: A032
Bulk RNA-seq, C57BL/6J, M, CHI, 24h

value: CHI

tag: experiment id


title: 203991400142_R01C01_PD036_CNG

tag: thal


title: MM_132

description: Library name: sample 214

tag: cell line

tag: treatment


title: AB19985

description: Library name: Sample 31

value: Tumor

tag: sorting gate


title: 203991400143_R08C01_RI94/1280_CNG


title: C57BL/6J_F_sham_9h_A178

description:
Library name: A178
Bulk RNA-seq, C57BL/6J, F, sham, 9h

value: Female

value: sham

value: 4.43 months


title: C57BL/6J_F_sham_9h_A180

description:
Library name: A180
Bulk RNA-seq, C57BL/6J, F, sham, 9h


title: MM_131

description: Library name: sample 213

tag: genotype


title: AB19984

description: Library name: Sample 30

tag: batch


title: 203991400143_R07C01_PD755_CNG

tag: regiondescription

value: Imperial Brain Bank

tag: Sex


title: MM_130

description: Library name: sample 212


title: C57BL/6J_F_sham_9h_A093

description:
Library name: A093
Bulk RNA-seq, C57BL/6J, F, sham, 9h

tag: strain

tag: surgery


title: AB19983

description: Library name: Sample 29


title: 203991400143_R05C01_20110715_CNG

tag: plate


title: C57BL/6J_F_sham_72h_A145

description:
Library name: A145
Bulk RNA-seq, C57BL/6J, F, sham, 72h

tag: timepoint

value: 5.27 months


title: AB19982

description: Library name: Sample 28


title: C57BL/6J_F_sham_72h_A084

description:
Library name: A084
Bulk RNA-seq, C57BL/6J, F, sham, 72h

tag: age (months)

value: 6.8 months


title: MM_129

description: Library name: sample 211


title: MM_128

description: Library name: sample 210


title: 203991400143_R04C01_PD730_CNG

tag: centre

value: female


title: 203991400143_R01C01_20131187_CNG

tag: tissue

value: male


title: AB19981

description: Library name: Sample 27

tag: cell type


title: MM_127

description: Library name: sample 209

value: bone marrow


title: C57BL/6J_F_sham_72h_A001

description:
Library name: A001
Bulk RNA-seq, C57BL/6J, F, sham, 72h

value: 5.93 months

tag: animal id

tag: experiment id


title: AB19980

description: Library name: Sample 26


title: 203991390124_R07C01_PD443_CNG

tag: thal

value: FALSE


title: MM_126

description: Library name: sample 208

tag: cell line

value: Myeloma Plasma Cell

tag: treatment


title: 203991400162_R05C01_PD905_CNG

value: Anterior cingulate


title: A2780 cells, Vec-2

city: Shanghai

first: Cuiping

last: Yang

address: No. 168 Wanghe Road, Fengxian District, Shanghai, China Welfare Association International Peace Maternity and Child Health Hospital, Fengxian Campus

department: Central Laboratory

description:
Library name: Sample2
Column name in all_samples_gene_Count.xlsx:  Vec-2

data_processing:
Raw data preprocessing: Raw data (FASTQ format) were first processed through in-house Perl scripts. Adapter sequences were removed, and low-quality reads (where bases with quality value ≤ 25 accounted for >60% of the read) and reads with >5% ambiguous bases ('N') were filtered out to obtain clean reads.
Alignment to reference genome: Clean reads were aligned to the reference genome using HISAT2 software (http://daehwankimlab.github.io/hisat2/) with default parameters.
Quantification of gene expression: FeatureCounts (http://subread.sourceforge.net/) was used to count the number of reads mapped to each gene. Gene expression levels were calculated as FPKM (Fragments Per Kilobase of transcript per Million mapped reads).
Assembly: GRCh38.p13 (Homo sapiens)
Supplementary files format and content: raw read counts for each gene across all samples (generated by FeatureCounts).
Supplementary files format and content: FPKM values for each gene across all samples.

growth_protocol: A2780 cells were maintained in Dulbecco’s Modified Eagle Medium/Nutrient Mixture F-12 (DMEM/F12) supplemented with 10% fetal bovine serum (FBS) supplemented with 1% penicillin-streptomycin (P/S). Cells were kept at 37℃ in a humidified environment with 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol reagent (Magen) according to the manufacturer’s protocol. Chloroform and isopropanol (Sinopharm) were used for phase separation and RNA precipitation.  1.0 ug of total RNA was used for the construction of sequencing libraries.
Libraries were constructed using the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (ABclonal) following the manufacturer’s instructions. Magnetic beads (AMPure XP system, Beckman Coulter) were used for purification and size selection.

value: ovarian cancer cells

tag: genotype

value: WT


title: WT_1

city: London

first: Folkert

last: van Werven

address: 1 Midland Road

institute: Francis Crick Institute

description:
Library name: sample 1
A1

data_processing:
FASTQ files were processed using the nf-core/rnaseq pipeline (version 3.10.1; 10.5281/zenodo.1400710), executed using Nextflow (v23.10.0) (Di Tommaso et al., 2017). Reads were aligned to the Saccharomyces cerevisiae strain SK1 reference genome (SK1_SGD_2018_NCSL00000000) using STAR (2.7.10a)47, and gene-level quantification was performed with RSEM (v1.3.1).  Differential expression analysis was carried out with DESeq2 (1.48.1) using a simple design formula (~ group). Wald tests were used to assess differential expression. Multiple-testing correction was performed using Independent Hypothesis Weighting (IHW)50; genes with an IHW-adjusted p-value below 0.05 were considered significant. ashr 51 was used for effect-size shrinkage.
Assembly: SK1-MvO-V1
Supplementary files format and content: txt and counts per gene

organism: Saccharomyces cerevisiae

source_name: diploid

growth_protocol: Cells were arrested in early meiosis as described previously 9. Briefly, yeast cells were inoculated in yeast extract peptone dextrose (YPD) media [1% weight/volume (w/v) yeast extract, 2% w/v bacto peptone, 2% w/v glucose, uracil (24 mg/l) and adenine (12 mg/l)] for approximately 24 hours, before being diluted to OD600 0.4 in buffered, yeast extract, tryptone, acetate (BYTA, (1.0% w/v yeast extract, 2.0% w/v peptone, 1% potassium acetate, 50 mM potassium phthalate monobasic) and incubated for 16-18 hours. OD600 1.8 of yeast cells were then washed and transferred to SPO (0.3% Potassium acetate, Acetic acid to pH 7.0, 0.02% D-(+)-Raffinose pentahydrate).

extract_protocol:
24 OD units were collected by centrifugation, and snap frozen in liquid nitrogen. Per 10 OD units, RNA was extracted with Tris-EDTA-SDS (TES) buffer (10 mM Tris-HCl pH 7.5, 10 mM EDTA, 0.5% SDS) and Acid Phenol:Chloroform:Isoamyl alcohol (125:24:1, Ambion) at 65°C for 45 minutes. Precipitation was carried out. rDNase (Machery-Nagel) treatment was carried out, before spin column purification (Machery-Nagel).
For degron strains, libraries from 100 ng of RNA were generated using the NEBNext Ultra II Directional PolyA mRNA Kit (modules K0105 and K0078), following the manufacturer’s protocols. Paired-end sequencing (100 bp) was performed on an Illumina NovaSeq X platform, with a minimum depth of 20 million reads per sample.

treatment_protocol: 3 hours after transfer to sporulation medium, copper (II) sulphate (CuSO4, 50 μM) was added. In all steps yeast were grown at 30°C at 300 rpm, and a 1:10 culture volume to flask total volume ratio was maintained.

value: diploid yeast cell

value: MATa/alpha ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG


title: IL-1R1 gKO_M_CHI_9h_A153

description:
Library name: A153
Bulk RNA-seq, IL-1R1 gKO, M, CHI, 9h

value: mouse brain

value: IL-1R1 gKO

value: Male

value: CHI

value: 4.0 months


title: 203991390124_R06C01_20050098_CNG

value: Newcastle Brain Tissue Resource


title: AB19979

description: Library name: Sample 25

value: Tumor

tag: sorting gate

tag: batch


title: C57BL/6J_F_sham_24h_A055

description:
Library name: A055
Bulk RNA-seq, C57BL/6J, F, sham, 24h

tag: Sex

value: Female

value: sham

value: 5.2 months


title: MM_125

description: Library name: sample 207

value: bone marrow


title: C57BL/6J_F_sham_24h_A054

description:
Library name: A054
Bulk RNA-seq, C57BL/6J, F, sham, 24h

tag: strain


title: 203991390124_R03C01_PD590_CNG

tag: regiondescription

value: Imperial Brain Bank

value: female

value: FALSE


title: AB19978

description: Library name: Sample 24


title: MM_124

description: Library name: sample 206

value: Myeloma Plasma Cell


title: AB19977

description: Library name: Sample 23


title: 203991390147_R07C01_PD717_CNG

value: Anterior cingulate

tag: plate


title: C57BL/6J_F_sham_24h_A005

description:
Library name: A005
Bulk RNA-seq, C57BL/6J, F, sham, 24h

tag: surgery

tag: timepoint

value: 5.93 months


title: MM_123

description: Library name: sample 205


title: C57BL/6J_F_CHI_9h_A200

description:
Library name: A200
Bulk RNA-seq, C57BL/6J, F, CHI, 9h

value: mouse brain

tag: age (months)

value: 4.43 months


title: 203991390147_R06C01_PD113_CNG

tag: tissue

tag: centre

value: male


title: AB19975

description: Library name: Sample 21

tag: cell type


title: MM_122

description: Library name: sample 204


title: C57BL/6J_F_CHI_9h_A199

description:
Library name: A199
Bulk RNA-seq, C57BL/6J, F, CHI, 9h

value: CHI

tag: animal id

tag: experiment id


title: C57BL/6J_F_CHI_9h_A184

description:
Library name: A184
Bulk RNA-seq, C57BL/6J, F, CHI, 9h


title: 203991390147_R05C01_20150829_CNG

tag: thal


title: MM_121

description: Library name: sample 203

tag: cell line

tag: treatment


title: AB19976

description: Library name: Sample 22

tag: sorting gate


title: AB19974

description: Library name: Sample 20

tag: batch


title: 203991390147_R04C01_PD900_CNG

tag: Sex


title: MM_120

description: Library name: sample 202

tag: genotype


title: C57BL/6J_F_CHI_9h_A179

description:
Library name: A179
Bulk RNA-seq, C57BL/6J, F, CHI, 9h

tag: strain


title: 203991390147_R03C01_P15/10_CNG

tag: regiondescription

tag: plate

value: QSBB


title: AB19973

description: Library name: Sample 19


title: MM_119

description: Library name: sample 201


title: C57BL/6J_F_CHI_9h_A171

description:
Library name: A171
Bulk RNA-seq, C57BL/6J, F, CHI, 9h

tag: surgery

tag: timepoint


title: 203991390147_R02C01_PD553_CNG

tag: tissue


title: AB19972

description: Library name: Sample 18


title: MM_118

description: Library name: sample 200


title: C57BL/6J_F_CHI_9h_A094

description:
Library name: A094
Bulk RNA-seq, C57BL/6J, F, CHI, 9h

tag: age (months)

value: 4.8 months


title: 203991390147_R01C01_PD028_CNG

tag: centre


title: AB19971

description: Library name: Sample 17

value: Tumor

tag: cell type


title: MM_117

description: Library name: sample 199


title: AB19970

description: Library name: Sample 16


title: MM_116

description: Library name: sample 198


title: 203991410071_R08C01_20174907_CNG

value: Newcastle Brain Tissue Resource


title: C57BL/6J_F_CHI_9h_A092

description:
Library name: A092
Bulk RNA-seq, C57BL/6J, F, CHI, 9h

value: Female

tag: animal id

tag: experiment id


title: 203991410071_R05C01_20080081_CNG

tag: thal


title: AB19969

description: Library name: Sample 15

tag: treatment


title: C57BL/6J_F_CHI_72h_A144

description:
Library name: A144
Bulk RNA-seq, C57BL/6J, F, CHI, 72h

value: 5.27 months


title: MM_115

description: Library name: sample 197

value: bone marrow

tag: cell line


title: C57BL/6J_F_CHI_72h_A085

description:
Library name: A085
Bulk RNA-seq, C57BL/6J, F, CHI, 72h

value: 6.8 months


title: S.cerevisae BY4741_Ty1, Gal12h, Biol Rep1

city: Vancouver

first: Marjan

last: Barazandeh

state: BC

address: 6622-2405 Wesbrook Mall

department: Pharmaceutical Sciences

country: Canada

institute: University of British Columbia

description:
Library name: RP_12h_R1
12h_rep_avg.bw

data_processing:
Adapters and low-quality bases were removed from paired-end reads with Trimmomatic (v0.39).
The reads were then mapped to the S. cerevisiae R64 reference genome using BWA-MEM (v0.7.18).
Only primary alignments with MAPQ ≥30 were retained, and unmapped, secondary, QC-fail, and supplementary reads were excluded.
PCR/optical duplicates were removed to generate de-duplicated, coordinate-sorted BAM files, which were indexed and summarized with SAMtools (v1.19.2).
dyad-centered coverage tracks were generated from de-duplicated BAMs using a 147-bp fragment shift, normalized to the genome-wide mean (excluding zero bins), Gaussian-smoothed (window = 3), and converted to bigWig.
Assembly: R64 (SacCer3)
Supplementary files format and content: bigWig

growth_protocol: overnight in SC-Ura+2% raffinose+ 0.1% dextrose, SC-Ura+2% galactose for 24 hours, SC-Ura+2% glucose for 24 hours, SC-Ura+2% galactose for 6 hours, SC-Ura+2% galactose for 12 hours,  SC-Ura+2% galactose for 24 hours, SC complete+2% glucose for 24 hours

extract_protocol:
Qiagen MinElute column
NEBNext Ultra™ II DNA Library Prep Kit

treatment_protocol: Minimal media with Raffinose, Galactose, glucose

value: MATa his3delta1 leu2delta0 ura3delta0 met15delta0

value: BY4741+ Ty1 vector grown in SC-Ura+2% galactose for 12 hours


title: Static3

city: New Haven

first: Yibing

last: Qyang

address: 300 George St

institute: Yale University

description: Library name: Sample6

data_processing:
RNA-seq reads were aligned to the reference genome with STAR(version= 2.7.11a), gene counts were obtained using Subread/featureCounts(v2.0.3), and differential expression was analyzed in R (v4.4.1-foss-2022b) with DESeq2. GO enrichment was performed with clusterProfiler (org.Hs.eg.db, AnnotationDbi, enrichplot, DOSE), and KEGG pathways were analyzed using pathview. P-value less than 0.05 was considered significant.
Assembly: GRCh38
Supplementary files format and content: txt file including raw counts of each sample and gene IDs

source_name: Endothelial Cell

extract_protocol:
After conditioning, ECs from both flow and static grafts were lysed directly in TRIzol. Each RNA sample represented a pooled lysate from three independent batches derived from one HLHS patients. In total, iPSC-ECs from three HLHS patients were used for both flow and static graft conditions.
mRNA is purified, from a normalized input between 10-1000ng of total RNA, using mRNA capture beads prior to fragmentation (Watchmaker mRNA Library Prep Kit).  Following first-strand synthesis with random primers, second strand synthesis and A-tailing are performed with dUTP for generating strand-specific sequencing libraries. Adapter ligation with 3’ T overhangs are ligated to library insert fragments.  Library amplification amplifies fragments carrying the appropriate adapter sequences at both ends.  Strands marked with dUTP are not amplified. Indexed libraries that meet appropriate cut-offs for both are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution is determined with the LabChip GX or Agilent TapeStation. Samples with a yield of ≥0.5 ng/ul are used for sequencing.

treatment_protocol: iPSC-ECs were then seeded onto decellularized human umbilical arteries (dHUAs) and subjected to two hemodynamic conditions: (1) a shear preconditioning protocol designed to mimic IVC hemodynamics (ramping from 1 to 15 dynes/cm² over 36 h, maintaining 15 dynes/cm² for 48 h, then reducing to 5 dynes/cm² for 12 h), and (2) a static condition followed by abrupt exposure to 5 dynes/cm² for 6 h (static + abrupt flow).

value: Endothelial Cell

value: Static + abrupt flow


title: 203991410071_R03C01_19900133_CNG

value: Anterior cingulate

value: FALSE


title: AB19968

description: Library name: Sample 14

tag: sorting gate

tag: batch


title: MM_114

description: Library name: sample 196

value: Myeloma Plasma Cell

tag: genotype


title: C57BL/6J_F_CHI_72h_A083

description:
Library name: A083
Bulk RNA-seq, C57BL/6J, F, CHI, 72h

value: mouse brain

tag: strain

tag: Sex


title: 203991410071_R01C01_PDC126_CNG

tag: regiondescription

tag: plate

value: Imperial Brain Bank

value: male


title: AB19967

description: Library name: Sample 13


title: MM_113

description: Library name: sample 195


title: AB19966

description: Library name: Sample 12


title: C57BL/6J_F_CHI_72h_A082

description:
Library name: A082
Bulk RNA-seq, C57BL/6J, F, CHI, 72h

tag: surgery

value: CHI

tag: timepoint


title: C57BL/6J_F_CHI_72h_A081

description:
Library name: A081
Bulk RNA-seq, C57BL/6J, F, CHI, 72h

tag: tissue

tag: age (months)


title: MM_112

description: Library name: sample 194

tag: cell type


title: 203991410070_R06C01_PD340_CNG

tag: centre


title: 203991410070_R04C01_20140969_CNG


title: MM_111

description: Library name: sample 193


title: C57BL/6J_F_CHI_72h_A002

description:
Library name: A002
Bulk RNA-seq, C57BL/6J, F, CHI, 72h

value: 5.93 months

tag: animal id

tag: experiment id


title: AB19965

description: Library name: Sample 11

value: Tumor

tag: treatment


title: 203991410070_R02C01_20030113_CNG

value: Newcastle Brain Tissue Resource

tag: thal


title: MM_110

description: Library name: sample 192

tag: cell line


title: 203991410070_R01C01_20141915_CNG


title: C57BL/6J_F_CHI_24h_A057

description:
Library name: A057
Bulk RNA-seq, C57BL/6J, F, CHI, 24h

value: Female

value: 5.2 months


title: AB19963

description: Library name: Sample 9

tag: sorting gate

tag: batch


title: AB19964

description: Library name: Sample 10


title: MM_109

description: Library name: sample 191

value: bone marrow

tag: genotype


title: 203991400127_R07C01_PD801_CNG

tag: Sex

value: female


title: AB19962

description: Library name: Sample 8


title: MM_108

description: Library name: sample 190


title: 203991400127_R06C01_PD233_CNG

tag: regiondescription


title: AB19961

description: Library name: Sample 7


title: C57BL/6J_F_CHI_24h_A053

description:
Library name: A053
Bulk RNA-seq, C57BL/6J, F, CHI, 24h

tag: strain


title: 203991400127_R05C01_P64/11_CNG

tag: plate

value: QSBB


title: AB19960

description: Library name: Sample 6


title: MM_106

description: Library name: sample 188


title: C57BL/6J_F_CHI_24h_A008

description:
Library name: A008
Bulk RNA-seq, C57BL/6J, F, CHI, 24h

tag: surgery

tag: timepoint


title: C57BL/6J_F_CHI_24h_A007

description:
Library name: A007
Bulk RNA-seq, C57BL/6J, F, CHI, 24h

tag: tissue

tag: age (months)


title: MM_105

description: Library name: sample 187

tag: cell type


title: C57BL/6J_F_CHI_24h_A006

description:
Library name: A006
Bulk RNA-seq, C57BL/6J, F, CHI, 24h

tag: animal id


title: AB19958

description: Library name: Sample 4


title: 203991400127_R02C01_PD286_CNG

tag: centre


title: MM_104

description: Library name: sample 186

tag: treatment


title: C57BL/6J_F_CHI_24h_A004

description:
Library name: A004
Bulk RNA-seq, C57BL/6J, F, CHI, 24h

tag: experiment id


title: 203991400128_R04C01_20174934_CNG

tag: thal


title: AB19957

description: Library name: Sample 3

tag: sorting gate


title: C57BL/6J_F_CHI_24h_A003

description:
Library name: A003
Bulk RNA-seq, C57BL/6J, F, CHI, 24h


title: AB19956

description: Library name: Sample 2

tag: batch


title: 203991400128_R01C01_20174960_CNG


title: MM_103

description: Library name: sample 185

tag: cell line

tag: genotype


title: AB19955

description: Library name: Sample 1


title: mPFC_csds_Ketamine20

city: Solna

first: Serena

last: Gasperoni

address: Solnavägen 9

department: Neuroscience

country: Sweden

institute: Karolinska Institutet

description: Library name: P30210_1079_S153

data_processing:
The Bcl to FastQ conversion was performed using bcl2fastq_v2.20.0.422 from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: mPFC

extract_protocol:
miRNeasy Micro Kit (Qiagen), 100 ng of total RNA was used for construction of sequencing libraries
Illumina Stranded mRNA Prep

value: mPFC

tag: group

value: csds

tag: Sex

value: WT

value: Ketamine

tag: ID


title: 203991400153_R04C01_P21/13_CNG

value: Anterior cingulate

tag: regiondescription

tag: plate

value: FALSE


title: vHipp_csds_Ketamine20

description: Library name: P30210_1078_S152

source_name: vHipp

tag: tissue

value: vHipp


title: Cd4-Cre⁺/⁻ Rxra^f/f Rxrb^f/f C57BL/6 female 7weeks, Naïve CD8+ T cells, anti-CD3 / anti-CD28 12h, rep3

city: Ulsan

first: Jun Pyo

last: Jeon

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan, Republic of Korea

country: South Korea

institute: Unist

description: Library name: TDKO3

data_processing:
Adapter sequences and low-quality bases were trimmed using Skewer (v.0.2.2).
Pre-alignment was performed using Bowtie2 (v2.5.4). The filtered reads were then aligned to the mouse reference genome (mm10) using Bowtie2.
PCR duplicates were marked and removed using Picard MarkDuplicates (v2.24.0).
Peaks overlapping blacklisted regions (ENCODE mm10 blacklist) were removed using bedtools intersect (v2.30.0).
For visualization and peak analysis, HOMER (v4.11.1) was used. Tag directories were generated using makeTagDirectory for each sample. Biological replicates from the same condition were pooled using HOMER's mergeTagDirectory. The pooled tag directories were used to generate genome browser tracks (UCSC track files, bedgraph)
Assembly: mm10
Supplementary files format and content: bedgraph file compressed in gzip format

source_name: spleen & lymph-node

extract_protocol:
100,000 cells were washed with PBS and lysed using a cold lysis buffer containing 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin. Cells were incubated on ice for 5 minutes. Nuclei were pelleted by centrifugation at 500 x g for 10 minutes at 4°C, washed with 1ml cold lysis buffer without digitonin and Tween-20, and resuspended in transposition reaction buffer.
Transposition was carried out in a 50 µL reaction containing 25 µL 2× TD buffer, 2.5 µL Tn5 transposase, 16.5 µL PBS, 0.5 µL 1% digitonin, 0.5 µL 10% Tween-20, and 5 µL nuclease-free water. The reaction was incubated at 37°C for 45 minutes with with tapping every 10 minutes. Directly following transposition, each sample was purified using a DNA clean & ConcentratorTM-5. Following purification, transposed fragments were PCR-amplified using Nextera dual-index primers and NEBNext High-Fidelity Master Mix. PCR products were cleaned using AMPure XP beads.

treatment_protocol: Cells were immediately plated onto anti-CD3 (1 μg ml⁻¹) / anti-CD28 (2 μg ml⁻¹)–coated 24-well plates and cultured for 12 hours in complete RPMI-1640 (10 % FBS) in humidified atmosphere with 5% CO2 at 37℃

value: spleen & lymph-node

tag: strain

value: Naive CD8+ T cells

value: Rxra & Rxrb knockout

value: anti-CD3 / anti-CD28 12h


title: 203991400153_R03C01_PD022_CNG

value: Imperial Brain Bank


title: mPFC_csds_Saline18

description: Library name: P30210_1077_S151

value: male

value: Saline


title: MM_99

description: Library name: sample 181

value: bone marrow

tag: cell type

value: Myeloma Plasma Cell


title: vHipp_csds_Saline18

description: Library name: P30210_1076_S150


title: 203991390154_R08C01_PD045_CNG


title: mPFC_ctrl_Ketamine40

description: Library name: P30210_1075_S149

value: ctrl


title: Cd4-Cre⁺/⁻ Rxra^f/f Rxrb^f/f C57BL/6 female 7weeks, Naïve CD8+ T cells, anti-CD3 / anti-CD28 12h, rep1

description: Library name: TDKO1

value: female


title: 203991390154_R05C01_PD690_CNG


title: MM_97

description: Library name: sample 179


title: C57BL/6 female 7weeks, Naïve CD8+ T cells, anti-CD3 / anti-CD28 12h, rep5

description: Library name: WT5


title: 203991390154_R03C01_PD332_CNG


title: MM_96

description: Library name: sample 178


title: mPFC_ctrl_Saline38

description: Library name: P30210_1073_S147

value: mPFC


title: 203991410102_R05C01_PD927_CNG


title: C57BL/6 female 7weeks, Naïve CD8+ T cells, anti-CD3 / anti-CD28 12h, rep3

description: Library name: WT3

value: WT


title: mPFC_csds_Ketamine17

description: Library name: P30210_1071_S145

value: csds

value: Ketamine


title: C57BL/6 female 7weeks, Naïve CD8+ T cells, anti-CD3 / anti-CD28 12h, rep2

description: Library name: WT2


title: MM_93

description: Library name: sample 175


title: vHipp_csds_Ketamine17

description: Library name: P30210_1070_S144


title: C57BL/6 female 7weeks, Naïve CD8+ T cells, anti-CD3 / anti-CD28 12h, rep1

description: Library name: WT1


title: 203991400153_R08C01_P24/14_CNG

value: Anterior cingulate

value: QSBB

value: FALSE


title: Cd4-Cre⁺/⁻ Rxra^f/f Rxrb^f/f C57BL/6 female 7weeks, Naïve CD8+ T cells, anti-CD3 / anti-CD28 12h, rep4

description: Library name: TDKO4

value: spleen & lymph-node

value: Naive CD8+ T cells


title: MM_100

description: Library name: sample 182


title: 203991410102_R01C01_19870884_CNG

value: Newcastle Brain Tissue Resource


title: MM_92

description: Library name: sample 174


title: MM_98

description: Library name: sample 180


title: mPFC_csds_Saline19

description: Library name: P30210_1069_S143


title: Male LSL-Sting1-N153S; Lck-cre N8

city: Dallas

last: Yan

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

data_processing:
HISAT used to  align clean reads to the reference genome and Bowtie2 to align the clean reads to the reference genes
Assembly: m39
Supplementary files format and content: each tab delimited text file contains Gene ID, Gene Name, Reference location, Strand, Start, End, Coverage, FPKM and TPM for each sample.

source_name: thymus

extract_protocol:
RNeasy Mini Kit (QIAGEN, 74104).
BGI Americas

value: thymus

value: Double positive  TCRb-/lo-int thymocytes


title: 203991410115_R08C01_PD1013_CNG

value: Imperial Brain Bank

value: male


title: MM_91

description: Library name: sample 173

value: bone marrow

value: Myeloma Plasma Cell


title: vHipp_csds_Saline19

description: Library name: P30210_1068_S142

value: vHipp

value: Saline


title: Male LSL-Sting1-N153S; Lck-cre N7


title: vHipp_ctrl_Ketamine40

description: Library name: P30210_1074_S148

value: ctrl

value: WT


title: MM_95

description: Library name: sample 177


title: MM_90

description: Library name: sample 172


title: mPFC_ctrl_Ketamine37

description: Library name: P30210_1067_S141

value: mPFC

value: Ketamine


title: 203991410115_R03C01_20070105_CNG

value: Anterior cingulate


title: MM_89

description: Library name: sample 171


title: MM_94

description: Library name: sample 176


title: 203991410115_R02C01_PD726_CNG

value: FALSE


title: vHipp_ctrl_Ketamine37

description: Library name: P30210_1066_S140


title: Female LSL-Sting1-N153S; Lck-cre N5

value: Female


title: MM_88

description: Library name: sample 170


title: mPFC_ctrl_Saline39

description: Library name: P30210_1065_S139


title: Male LSL-Sting1-N153S control N4


title: vHipp_ctrl_Saline39

description: Library name: P30210_1064_S138


title: MM_87

description: Library name: sample 169


title: Male LSL-Sting1-N153S control N3


title: mPFC_csds_Ketamine16

description: Library name: P30210_1063_S137

value: csds


title: MM_86

description: Library name: sample 168


title: 203968030135_R04C01_PD636_CNG


title: Male LSL-Sting1-N153S control N2


title: MM_85

description: Library name: sample 167


title: vHipp_csds_Ketamine16

description: Library name: P30210_1062_S136


title: Female LSL-Sting1-N153S control N1


title: 203968030135_R03C01_PD911_CNG


title: MM_84

description: Library name: sample 166


title: mPFC_csds_Saline15

description: Library name: P30210_1061_S135


title: 203991410115_R06C01_20090067_CNG

value: Newcastle Brain Tissue Resource

value: female


title: T2D_PD_US

city: Chongqing

first: Li

last: houxuan

address: Medical College Road, Yuzhong District,

institute: Chongqing Medical University

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: Maxillary alveolar bone

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: Maxillary alveolar bone


title: 203968030072_R07C01_20150691_CNG

data_processing:
Data was imported using the R package methylumi methylumIDAT function. Data was then pre-processed in the R package wateRmelon using the pfilter and dasen functions.
[ukbbn_betas_normalised.Rdata] wateRmelon processed beta values, dasen quantile normalised


title: MM_83

description: Library name: sample 165


title: vHipp_csds_Saline15

description: Library name: P30210_1060_S134


title: T2D_PD


title: 203968030072_R05C01_PD908_CNG

value: Imperial Brain Bank


title: MM_82

description: Library name: sample 164


title: Male LSL-Sting1-N153S; Lck-cre N6

value: thymus

value: male

value: Double positive  TCRb-/lo-int thymocytes


title: mPFC_ctrl_Ketamine36

description: Library name: P30210_1059_S133


title: PD_US

value: Ligature+LIPUS


title: C57BL/6J_F_CHI_24h_A056

city: Lexington

last: Morganti

address: 789 S. Limestone St

description:
Library name: A056
Bulk RNA-seq, C57BL/6J, F, CHI, 24h

data_processing:
Quality assessment of raw reads with FastQC
Read alignment with STAR to mouse genome
Transcript quantification with Salmon
Gene-level count aggregation with tximeta
Differential expression analysis with DESeq2
Assembly: GRCm39 (mm39)
Supplementary files format and content: Tab-delimited text file with Salmon-quantified gene-level read counts (salmon.merged.gene_counts.tsv). Columns are sample IDs, rows are Ensembl gene IDs with gene names.
Supplementary files format and content: Tab-delimited text file with Salmon-quantified gene-level TPM values (salmon.merged.gene_tpm.tsv). Columns are sample IDs, rows are Ensembl gene IDs with gene names.

source_name: mouse brain

extract_protocol:
RNeasy Mini with genomic dna depletion
RNA library preparation was performed by Novogene (Project X202SC24077443-Z01-F001). [Add library prep kit info, e.g., Illumina Stranded mRNA Prep, polyA selection, etc.]

value: mouse brain

tag: surgery

value: CHI

tag: timepoint

tag: age (months)

value: 5.2 months

tag: animal id


title: MM_81

description: Library name: sample 163

value: bone marrow

value: Myeloma Plasma Cell

tag: treatment


title: 203968030072_R04C01_20010072_CNG

city: Exeter

last: Harvey

address: RILD Building, RD&E, Barrack Road

source_name: Anterior cingulate

extract_protocol: ~30mg of brain tissue was milled over liquid nitrogen and extracted following the Qiagen AllPrep DNA/RNA/miRNA Universal kit following standard protocol. Samples were pre-checked using nanodrop fluorometer prior to further processing.

value: Anterior cingulate

tag: centre

tag: thal


title: PD

value: WT

value: Ligature


title: 203968030072_R01C01_PD880_CNG

value: FALSE


title: vHipp_ctrl_Ketamine36

description: Library name: P30210_1058_S132

value: vHipp

value: ctrl

value: Ketamine


title: MM_80

description: Library name: sample 162

tag: cell line


title: 203968030135_R06C01_P90/17_CNG

value: QSBB

value: female


title: AB19959

description: Library name: Sample 5

value: Tumor

tag: sorting gate

tag: batch


title: MM_107

description: Library name: sample 189

tag: genotype


title: mPFC_ctrl_Saline33

description: Library name: P30210_1057_S131

value: mPFC

tag: group

tag: Sex

value: male

value: Saline

tag: ID


title: 203991400127_R03C01_NP10/083_CNG

tag: tissue

tag: regiondescription

tag: plate

value: Oxford Brain Bank


title: 203968030080_R08C01_19900165_CNG

value: Newcastle Brain Tissue Resource


title: MM_79

description: Library name: sample 161

value: bone marrow

tag: cell type


title: Genetically induced BCC, murine, mouse 1642, tumor 8

city: Kgs Lyngby

first: Martin

last: Wiinberg

state: Hovedstaden

address: Produktionstorvet 423

department: Department of Health Technology

country: Denmark

institute: Technical University of Denmark

description:
Library name: M06_GEM8
Gene.Symbol;M1_GEM1;M2_GEM2;M2_GEM3;M3_GEM4;M4_GEM5;M5_GEM6;M6_GEM7;M6_GEM8;M7_GEM9;M8_TP1;M9_TP2;M10_TP3;M11_TP4

data_processing:
The SOAPnuke package v.1.5.6 (parameters: -l 15 -q 0.2 -n 0.0001 -G) was used to clean raw reads.
Reads were aligned to the NCBI mus musculus genome (Mus_musculus_10090.NCBI.GCF_000001635.27_GRCm39.v2201) using Bowtie v2.3.4.3 (parameters: -q –sensitive –dpad 0 –gbar 99999999 –mp 1,1 –np 1 –score-min L,0,-0.1 -l 1 -X 1000 –no-mixed –no-discordant -p 8 -k 20 -N 1) and quantified using RSEM v1.3.1 (-p 8 –forward-prob 0).
Assembly: Mus_musculus_10090.NCBI.GCF_000001635.27_GRCm39.v2201
Supplementary files format and content: Raw gene counts for each sample presented in a tab-delimited text file

source_name: BCC tumor

growth_protocol:
Transplantable Basal cell carcinoma (TP-BCC) was induced by inoculating 2E+6 isolated GEM-BCC cells subcutaneous in right flank of the recipient mice. All TP-BCC tumors used for the RNA sequecing presented originates from one single GEM-BCC tumor.
Genetically induced basal cell carcinoma (GEM-BCC) was induced in murine skin by administering tamoxifen (three intraperitoneal injections of 300 µg each), followed by a single X-ray irradiation (4 Gy delivered over 2.05 minutes)

extract_protocol:
Tumors were excised, cut into smaller fragments, preserved in RNAlater™ solution (Thermo Fisher Scientific, cat#AM7021), and stored at -20°C until further processing. RNA was isolated using TRIzol (Thermo Fisher Scientific, cat# 15596026), homogenization was performed with the Retsch MM 400 mixer mill (Verder Scientific, Haan, Nordrhein-Westfalen, Germany) and Acid-Phenol:Chloroform (Thermo Fisher scientific, cat#AM9722). RNA was purified with NucleoSpin RNA kit (Düren, Nordrhein-Westfalen, Germany, cat#740955.50).
Library preparation performed using Oligo(dT)-attached magnetic beads for mRNA enrichment before poly(A) tail fragmentation and reverse transcription. cDNA double strands were end-paired and 5’phosphorylated, ligated with bubble-shaped adapter and amplified with PCR.

value: BCC tumor

tag: strain

value: Ptch1+/- K14-CreER2 p53fl/fl

value: Female

tag: disease state

value: Basal cell carcinoma

tag: tumor location

value: Intradermal

tag: condition

value: GEM

tag: tumor induction

value: Tamoxifen (3 i.p. injections with 300 µg tamoxifen) + x-ray (1 irradiation, 4 Gy over 2.05 minutes)


title: 203968030135_R05C01_20150639_CNG

value: Anterior cingulate

tag: centre

tag: thal

value: FALSE


title: vHipp_ctrl_Saline33

description: Library name: P30210_1056_S130

value: vHipp

value: ctrl

value: WT

tag: treatment


title: Genetically induced BCC, murine, mouse 1642, tumor 5

description:
Library name: M06_GEM7
Gene.Symbol;M1_GEM1;M2_GEM2;M2_GEM3;M3_GEM4;M4_GEM5;M5_GEM6;M6_GEM7;M6_GEM8;M7_GEM9;M8_TP1;M9_TP2;M10_TP3;M11_TP4

tag: batch


title: MM_102

description: Library name: sample 184

tag: cell line

value: Myeloma Plasma Cell

tag: genotype


title: MM_78

description: Library name: sample 160


title: mPFC_csds_Ketamine14

description: Library name: P30210_1055_S129

value: mPFC

tag: group

value: csds

tag: Sex

value: male

value: Ketamine


title: 203968030080_R06C01_20100575_CNG

tag: tissue

value: Newcastle Brain Tissue Resource


title: 203968030080_R05C01_PDC084_CNG

tag: regiondescription

value: Imperial Brain Bank


title: Genetically induced BCC, murine, mouse 1452, tumor 9

description:
Library name: M02_GEM3
Gene.Symbol;M1_GEM1;M2_GEM2;M2_GEM3;M3_GEM4;M4_GEM5;M5_GEM6;M6_GEM7;M6_GEM8;M7_GEM9;M8_TP1;M9_TP2;M10_TP3;M11_TP4

value: BCC tumor

value: Ptch1+/- K14-CreER2 p53fl/fl

value: Female


title: MM_101

description: Library name: sample 183

value: bone marrow


title: vHipp_csds_Ketamine14

description: Library name: P30210_1054_S128

tag: ID


title: MM_77

description: Library name: sample 159

tag: cell type


title: Genetically induced BCC, murine, mouse 1452, tumor 4

description:
Library name: M02_GEM2
Gene.Symbol;M1_GEM1;M2_GEM2;M2_GEM3;M3_GEM4;M4_GEM5;M5_GEM6;M6_GEM7;M6_GEM8;M7_GEM9;M8_TP1;M9_TP2;M10_TP3;M11_TP4

tag: strain

value: Basal cell carcinoma

value: Intradermal

value: GEM

value: Tamoxifen (3 i.p. injections with 300 µg tamoxifen) + x-ray (1 irradiation, 4 Gy over 2.05 minutes)


title: 203968030071_R05C01_P67/15_CNG

value: Anterior cingulate

tag: plate

value: QSBB

value: FALSE


title: MM_76

description: Library name: sample 158

value: Myeloma Plasma Cell


title: mPFC_csds_Saline13

description: Library name: P30210_1053_S127

value: mPFC

value: csds

value: WT

value: Saline


title: 203968030071_R03C01_20140182_CNG

value: Newcastle Brain Tissue Resource

value: male


title: Genetically induced BCC, murine, mouse 142, tumor 3

description:
Library name: M01_GEM1
Gene.Symbol;M1_GEM1;M2_GEM2;M2_GEM3;M3_GEM4;M4_GEM5;M5_GEM6;M6_GEM7;M6_GEM8;M7_GEM9;M8_TP1;M9_TP2;M10_TP3;M11_TP4

value: BCC tumor

value: Ptch1+/- K14-CreER2 p53fl/fl

tag: disease state

tag: tumor location


title: MM_75

description: Library name: sample 157

value: bone marrow


title: Cd4-Cre⁺/⁻ Rxra^f/f Rxrb^f/f C57BL/6 female 7weeks, Naïve CD8+ T cells, anti-CD3 / anti-CD28 12h, rep2

description: Library name: TDKO2

value: spleen & lymph-node

value: female

value: Naive CD8+ T cells

value: Rxra & Rxrb knockout

value: anti-CD3 / anti-CD28 12h


title: vHipp_csds_Saline13

description: Library name: P30210_1052_S126

value: vHipp


title: MM_74

description: Library name: sample 156


title: Genetically induced BCC, murine, mouse 140, tumor 1

description:
Library name: M03_GEM4
Gene.Symbol;M1_GEM1;M2_GEM2;M2_GEM3;M3_GEM4;M4_GEM5;M5_GEM6;M6_GEM7;M6_GEM8;M7_GEM9;M8_TP1;M9_TP2;M10_TP3;M11_TP4

value: Female

value: Basal cell carcinoma

value: Intradermal

tag: condition

value: GEM

tag: tumor induction

value: Tamoxifen (3 i.p. injections with 300 µg tamoxifen) + x-ray (1 irradiation, 4 Gy over 2.05 minutes)


title: 203991410033_R08C01_PD687_CNG

value: Anterior cingulate

tag: centre

value: Imperial Brain Bank

tag: thal

value: FALSE


title: 203991410033_R07C01_PD359_CNG

value: male


title: Genetically induced BCC, murine, mouse 1394, tumor 2

description:
Library name: M05_GEM6
Gene.Symbol;M1_GEM1;M2_GEM2;M2_GEM3;M3_GEM4;M4_GEM5;M5_GEM6;M6_GEM7;M6_GEM8;M7_GEM9;M8_TP1;M9_TP2;M10_TP3;M11_TP4

value: BCC tumor

value: Ptch1+/- K14-CreER2 p53fl/fl

tag: batch


title: MM_73

description: Library name: sample 155

value: bone marrow

tag: cell line

value: Myeloma Plasma Cell

tag: treatment


title: mPFC_ctrl_Ketamine34

description: Library name: P30210_1051_S125

value: mPFC

tag: group

value: ctrl

tag: genotype

value: WT

value: Ketamine


title: 203991410077_R01C01_PD061_CNG

tag: tissue

tag: Sex


title: Genetically induced BCC, murine, mouse 1354, tumor 2

description:
Library name: M04_GEM5
Gene.Symbol;M1_GEM1;M2_GEM2;M2_GEM3;M3_GEM4;M4_GEM5;M5_GEM6;M6_GEM7;M6_GEM8;M7_GEM9;M8_TP1;M9_TP2;M10_TP3;M11_TP4

value: Female


title: vHipp_ctrl_Ketamine34

description: Library name: P30210_1050_S124

value: vHipp

tag: ID


title: MM_72

description: Library name: sample 154

tag: cell type


title: mPFC_ctrl_Saline35

description: Library name: P30210_1049_S123

value: Saline


title: Genetically induced BCC, murine, mouse 112, tumor 3

description:
Library name: M07_GEM9
Gene.Symbol;M1_GEM1;M2_GEM2;M2_GEM3;M3_GEM4;M4_GEM5;M5_GEM6;M6_GEM7;M6_GEM8;M7_GEM9;M8_TP1;M9_TP2;M10_TP3;M11_TP4

tag: strain

value: Basal cell carcinoma

value: Intradermal

value: GEM


title: 203977090028_R07C01_PD405_CNG

value: Anterior cingulate

tag: regiondescription

tag: plate

value: Imperial Brain Bank


title: vHipp_ctrl_Saline35

description: Library name: P30210_1048_S122

value: male


title: 203991410102_R08C01_PD772_CNG

value: FALSE


title: MM_71

description: Library name: sample 153


title: MM_70

description: Library name: sample 152


title: 203977090028_R03C01_PDC110_CNG

value: female


title: Transplanted BCC, murine, mouse 674, tumor 1

description:
Library name: M11_TP4
Gene.Symbol;M1_GEM1;M2_GEM2;M2_GEM3;M3_GEM4;M4_GEM5;M5_GEM6;M6_GEM7;M6_GEM8;M7_GEM9;M8_TP1;M9_TP2;M10_TP3;M11_TP4

value: BCC tumor

tag: disease state

tag: tumor location

value: Subcutaneous

value: TP

value: 2M basal cell carcinoma subcutaneous inoculated in right flank


title: mPFC_csds_Ketamine12

description: Library name: P30210_1047_S121

value: mPFC

value: csds

value: WT


title: 203977090028_R02C01_PD309_CNG


title: Transplanted BCC, murine, mouse 672, tumor 1

description:
Library name: M10_TP3
Gene.Symbol;M1_GEM1;M2_GEM2;M2_GEM3;M3_GEM4;M4_GEM5;M5_GEM6;M6_GEM7;M6_GEM8;M7_GEM9;M8_TP1;M9_TP2;M10_TP3;M11_TP4

value: Female

tag: condition

tag: tumor induction


title: MM_69

description: Library name: sample 151

value: bone marrow

value: Myeloma Plasma Cell


title: Transplanted BCC, murine, mouse 662, tumor 1

description:
Library name: M09_TP2
Gene.Symbol;M1_GEM1;M2_GEM2;M2_GEM3;M3_GEM4;M4_GEM5;M5_GEM6;M6_GEM7;M6_GEM8;M7_GEM9;M8_TP1;M9_TP2;M10_TP3;M11_TP4

value: Basal cell carcinoma


title: 203977090014_R08C01_PD1029_CNG

tag: centre

tag: thal


title: vHipp_csds_Ketamine12

description: Library name: P30210_1046_S120

value: vHipp

value: Ketamine


title: mPFC_csds_Saline10

description: Library name: P30210_1045_S119

value: Saline


title: Transplanted BCC, murine, mouse 640, tumor 1

description:
Library name: M08_TP1
Gene.Symbol;M1_GEM1;M2_GEM2;M2_GEM3;M3_GEM4;M4_GEM5;M5_GEM6;M6_GEM7;M6_GEM8;M7_GEM9;M8_TP1;M9_TP2;M10_TP3;M11_TP4

tag: batch


title: 203977090014_R03C01_PD579_CNG

value: Anterior cingulate

value: Imperial Brain Bank

value: male


title: 203977090014_R05C01_P24/17_CNG

value: QSBB

value: female

value: FALSE


title: mPFC_ctrl_Ketamine31

description: Library name: P30210_1043_S117

value: ctrl

tag: treatment


title: vHipp_csds_Saline10

description: Library name: P30210_1044_S118

tag: group


title: MM_67

description: Library name: sample 149

tag: cell line

tag: genotype


title: MM_66

description: Library name: sample 148

tag: tissue


title: 203977090014_R02C01_PD847_CNG

tag: Sex


title: vHipp_ctrl_Ketamine31

description: Library name: P30210_1042_S116

tag: ID


title: 203976760067_R08C01_PD134_CNG


title: Sample 4_2B

city: Fort Collins

first: Ahmed

last: Gad

state: Colorado

address: 3107 Rampart Rd

department: Biomedical Sciences

institute: Colorado State University

description:
Library name: Sample 4
GC_miRNAs_in_Rhino_CPM.xlsx

data_processing:
Raw FASTQ files were first subjected to quality control and adapter trimming using FASTp, with a minimum Phred quality score of 20, a required minimum read length of 15 nucleotides, and a maximum read length of 35 nucleotides. Filtered reads were then processed using the miRDeep2 Mapper module, discarding reads shorter than 15 nucleotides. miRNA quantification was performed with the miRDeep2 Quantifier tool using miRBase release 22.1 as the reference database. Reads were annotated against equine, bovine, and human precursor and mature miRNAs, allowing up to one mismatch.
Differential expression analysis was conducted using DESeq2 within Galaxy.
Assembly: miRBase release 22.1
Supplementary files format and content: xlsx file include CPM values for each sample

organism: Ceratotherium simum simum

source_name: Ovarian Follicule

extract_protocol:
For the GC ampless, total RNA, including miRNA, was isolated using the Qiagen miRNeasy Micro Kit (Qiagen, Germantown, MD) per the manufacturer’s instructions. Briefly, granulosa cells were incubated with Qiazol lysis reagent and vortexed to homogenize the cells. After 5 min, chloroform was added to the sample and centrifuged at 10,000 x g for 15 min to separate RNA and protein. The RNA phase was added to an elution column and eluted in water after multiple washes. For the follicular fluid (FF) samples, FF was centrifuged at 300 x g for 10 min, the supernatant was re-centrifuged at 2000 x g for 10 min, and again at 16,500 x g for 30 min. The final supernatant was passed through a 0.20-μm sterile syringe filter, removing particles larger than 200 nm in diameter. For the EV isolation, 2 ml of pre-centrifuged follicular samples were subjected to an ultracentrifugation procedure at 120,000 xg for 70 min at 4 C using the Beckman SWTi55 rotor. The EVs pellet was washed with sterile PBS and then centrifuged again at 120,000 xg for 70 min. The washed pellets were then resuspended in DPBS.  To precipitate EVs,  Exo-spin™ buffer was added to each sample and incubated overnight at 4°C. The precipitated EVs were purified using Exo-spin™ mini columns according to the manufacturer’s instructions. Final 180 µL EV aliquots were stored at −80°C for subsequent characterization and analysis. Total RNA including miRNAs was isolated from EVs using a Norgen Exosomal RNA Isolation kit (Norgen, Canada), according to the manufacturer’s instructions. On-column DNA digestion was performed to remove genomic DNA contaminants.
For GC samples library preparation kit was SMARTer smRNA-Seq Library Preparation Kit (Takara Bio) per manufacturer’s instructions. For FF-EV samples, Small-RNA libraries were prepared for next-generation sequencing (NGS) using a TruSeq Small RNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.

value: Ovarian Follicule

tag: cell type

value: Granulosa Cells

tag: corresponding oocyte_maturation

value: NoPB


title: MM_64

description: Library name: sample 146


title: mPFC_ctrl_Saline30

description: Library name: P30210_1041_S115

value: mPFC

value: WT


title: Sample 3_2A

description:
Library name: Sample 3
GC_miRNAs_in_Rhino_CPM.xlsx


title: MM_63

description: Library name: sample 145

value: bone marrow

value: Myeloma Plasma Cell


title: vHipp_ctrl_Saline30

description: Library name: P30210_1040_S114

value: vHipp


title: MM_62

description: Library name: sample 144


title: 203976760067_R03C01_20050033_CNG

first: Joshua

institute: University of Exeter

tag: regiondescription

tag: plate

value: Newcastle Brain Tissue Resource


title: mPFC_csds_Ketamine11

description: Library name: P30210_1039_S113

value: csds

value: Ketamine


title: Sample 1_1A

description:
Library name: Sample 1
GC_miRNAs_in_Rhino_CPM.xlsx

value: PB


title: MM_61

description: Library name: sample 143


title: vHipp_csds_Ketamine11

description: Library name: P30210_1038_S112

value: male


title: control_25h_2

city: Boston

first: Carol

middle: A

last: Kumamoto

state: MA

address: 150 Harrison Ave.

department: Department of Molecular Biology and Microbiology

institute: Tufts University

description:
Library name: Sample 4
10x Genomics

data_processing:
Initial data analysis including demultiplexing, barcode processing and aligning reads to the human genome was performed using Cell Ranger.
Assembly: human GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Colonoid line CJ50

growth_protocol: Preparation of colonoid monolayers on transwells. Colonoid line CJ50 was derived from colonic biopsies obtained from a 67 year old Chinese female undergoing routine outpatient colonoscopy for colorectal cancer screening at Tufts Medical Center (IRB #11652, principal investigator: Jatin Roper). The cells were propagated in Matrigel (Corning 356231) as described previously [29]. Medium compo-sition was as described [22] except that L-WRN conditioned medium (L-WRN cells ATCC CRL- 3276 [30]) was used at 65% instead of L-WNT3A, R-Spondin and Noggin conditioned media, Primocin (InvivoGen ant-pm-1) was used instead of pen-strep and 5 uM Y27632 (Rho kinase inhibitor, Sigma Y0503) was added for the first 48 hrs of culturing. For preparation of monolayers on transwells, colonoid spheres were recovered from Matrigel, washed with PBS and digested with TrypLE Express (Gibco 12605-010) for 2.5 min at 37oC. After digestion, cells were diluted with 1 volume advanced DMEM (Invi-trogen 12634-028), 1% Glutamax (Gibco 35050-061), 20% FBS (Fisher 26140079) and filtered through a 40 um cell strainer. Cells were diluted with 0.4% Trypan blue, counted with a Corning CytoSmart counter and diluted to 2.5 x 106 cells/ml with warmed 65% LWRN medium containing Y27632. Matrigel was diluted with CMGF- to 33 or 66 ug protein/mL, 125 ul was applied to each 6.5mm diameter, 0.4 um pore, polycarbonate filter transwell (Costar 3413) and incubated at 37oC for 2 hours. Liquid was removed from the transwell, the basolateral compartment was filled with 0.5 ml 65% medium and 50 ul of medium was added to the apical compartment. Cells (2.5 x 105 cells per 6.5 mm diameter transwell) were added and the seeded transwells were incubated in a tissue culture incubator with 5% CO2 at 37oC. The next day, transwells were given fresh 65% L-WRN medium containing 5 uM Y27632 (Sigma Y0503), replacing the basolateral medium and adding 0.2 ml to the apical compartment. The next day, the medium was changed to 65% without Y27632 (0.4 ml apically and 0.5 ml basolaterally) and was changed again after 2 days when the mono-layer was typically confluent. Confluent monolayers were differentiated by washing with CMGF-, followed by feeding with Differentiation Medium (DM) [22, 31] containing Primocin. Medium was changed the next day with DM containing Primocin. Monolayers were fed 2 days later (day 3) (DM without Primocin) and in the late afternoon of day 4 or in the morning of day 5 (DM without Primocin). Monolayers were inoculated with pre-germinated spores on day 5. For measurement of trans-epithelial electrical resistance (TEER), a Millicell ERS-2 volt/ohm meter was used following manufacturer’s protocol.

extract_protocol:
Monolayers were cultured on 12 mm diameter 0.4 um polycarbonate filters (Millicell PIHP01250) and differentiated as described above. Spores were treated with glycine and sodium cholate, as above, collected by centrifugation (Eppendorf 5415, 13200 rpm, 5 min) resuspended in PBS and 1 x 105 spores in 10 ul or PBS was added to the apical medium. Transwells were incubated as described above. After 4, 15, 20 or 25 hours of incubation, monolayers were washed with 100 ul PBS, EDTA 0.5 mM, pH 8 and incubated with TrypLE Express, 600 ul in the basolateral and 400 ul in the apical compartments at 37oC for 12 min. One hundred ul 50% FBS was added to the apical compartment and the cells were suspended by pipeting up and down several times. Cells were passed through a 40 um cell strainer and recovered in tubes precoated with 0.1% BSA. The transwells were then washed with 400 ul CMGF-, which was passed through the strainer and combined with the previous filtrate. Cells were collected by centrifugation at 300g x 5 min. Most of the supernatant was gently removed. Cells were resuspended in 1 ml of 0.04% BSA, 5 uM Y27632 and collected as above. Using a wide bore tip, the pellet was resuspended in the remaining supernatant by pipetting up and down. Cells were counted with a Corning Cytosmart counter and adjusted to 1 x 106 cells/ml.
The remaining steps were performed following manufacturer’s protocol. Briefly, the cell suspension was loaded along with reagents, barcoded Single Cell 3’ v3.1 Gel Beads and Partitioning Oil onto the Chromium Next GEM Chip G. Cells were partitioned into GEMS using the Chromium Controller. Gel beads were then dissolved, releasing primers, and the cells were lysed. Reverse transcription was performed to generate cDNA tagged with cell specific barcodes and Illumina TruSeq Read 1 sequencing primer. GEMS were broken and first strand cDNA was purified and PCR amplified. After enzymatic fragmentation followed by size selection, the cDNA was PCR amplified, incorporating a sample index and primers P5, P7, and TruSeq Read 2 for Illumina sequencing. Library quality was assessed using an Agilent Bioanalyzer. Paired end sequencing was performed by the Tufts University Genomics Core Facility.

treatment_protocol: Co-culturing C. difficile with colonoid monolayers. Pre-germinated spores (approximately 5 x 107 per ml) were prepared as above and 10ul of the preparation was added gently to the apical medium of the transwell. Control samples were inoculated with 10ul of buffer. The plates were wrapped with Parafilm and incubated in a standard tissue culture incubator (37oC, 5% CO2, room air). At various times, transwells were taken into the anaerobic chamber (2 transwells at a time) to estimate the number of bacteria per transwell. The first 170 ul of apical medium was carefully removed. This medium was not turbid and was discarded. The second approximately 170 ul of medium was collected into the pipet tip and used to wash the monolayer twice, then collected into a pre-weighed tube. For inoculated transwells, this sample was typically turbid. 10 ul of this sample was immediately diluted with 1 ml of pre-reduced PBS to measure CFU. The remainder of the sample was removed from the chamber and weighed to determine the volume recovered from each transwell after correction for the 10 ul removed for CFU. Transwell monolayers were removed from the chamber and fixed with 4% para-formaldehyde for 15 min at room temp, followed by washing 3 times with PBS at room temperature. Transwells were stored at 4oC in PBS. For some experiments, transwells were inoculated with vegetative C. difficile cells. Strains were grown in pre-reduced TY broth and harvested during log phase. A sample of each culture was diluted 1/50 into pre-reduced PBS. DM medium was pre-reduced and 0.4 ml was transferred to a gasketed screw cap tube for each inoculation. 10 ul of bacteria diluted in PBS was added to each tube (or PBS only for mock inoculation). The caps were screwed on tightly and tubes removed from the chamber. The transwells were inoculated by removing their apical medium and replacing it with the bacteria-containing medium. Transwells were inoculated with approximately 5 x 104 CFU.

value: Colonoid line CJ50

value: non-infected

tag: time point


title: MM_60

city: Pamplona

last: Gomez-Echarte

address: Avenida Pio XII, 55

description: Library name: sample 142

extract_protocol:
RNA was isolated with the MagMAX mirVana total RNA Isolation kit (applied biosystems)
RNA-seq library was prepared using Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit (Illumina).


title: mPFC_csds_Saline9

description: Library name: P30210_1037_S111

value: Saline


title: 203977090024_R05C01_PD808_CNG

value: Anterior cingulate

value: Imperial Brain Bank

value: female

value: FALSE


title: control_25h_1

description:
Library name: Sample 3
10x Genomics


title: MM_59

description: Library name: sample 141


title: vHipp_csds_Saline9

description: Library name: P30210_1036_S110


title: 203977090024_R02C01_P32/10_CNG

value: QSBB

value: TRUE


title: control_4h_2

description:
Library name: Sample 2
10x Genomics


title: MM_58

description: Library name: sample 140

value: bone marrow


title: mPFC_ctrl_Ketamine32

description: Library name: P30210_1035_S109

value: mPFC

value: ctrl

value: WT


title: control_4h_1

description:
Library name: Sample 1
10x Genomics


title: vHipp_ctrl_Ketamine32

description: Library name: P30210_1034_S108

value: vHipp


title: MM_57

description: Library name: sample 139

value: Myeloma Plasma Cell


title: H358 SMARCA4 KO clone 3

city: New York

first: Sam

middle: E

last: Tischfield

state: NY

address: 1275 York Ave

department: Center for Molecular Oncology

institute: Memorial Sloan-Kettering Cancer Center

description: Library name: SM4KO-3

data_processing:
Pseudo-mapping with Kallisto v0.50.0
Quantification with Sleuth v0.30.0
Assembly: HG19
Supplementary files format and content: TPM  values for transcripts in tab delimited matrix

growth_protocol: H358 cells were cultured in in RPMI media supplemented with 10% FBS and 1X Penicillin-Streptomycin (PS) and incubated in 5% CO2 at 37° C.

extract_protocol:
Total RNA was extracted using Qiagen Rneasy Plus Universal Mini kit following manufacturer’s instructions.
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions.

value: SMARCA4 KO


title: MM_56

description: Library name: sample 138


title: 203968030133_R06C01_PDC035_CNG


title: mPFC_ctrl_Saline29

description: Library name: P30210_1033_S107

value: male


title: H358 SMARCA4 KO clone 2

description: Library name: SM4KO-2


title: 203968030133_R05C01_NP16/044_CNG

value: Oxford Brain Bank


title: vHipp_ctrl_Saline29

description: Library name: P30210_1032_S106


title: H358 SMARCA4 KO clone 1

description: Library name: SM4KO-1


title: MM_54

description: Library name: sample 136


title: 203968030133_R03C01_PD572_CNG


title: H358 SAFE clone 3

description: Library name: SAFE-3


title: 203968030133_R02C01_PD740_CNG


title: mPFC_csds_Ketamine6

description: Library name: P30210_1031_S105

value: csds

value: Ketamine


title: MM_53

description: Library name: sample 135


title: MM_65

description: Library name: sample 147


title: vHipp_csds_Ketamine6

description: Library name: P30210_1030_S104


title: MM_52

description: Library name: sample 134