title: Blood, AH, Week 24 Day 2, 17U039

description:
Library name: 17U039_AH_W24D2
Column name in TMM_counts.txt:17U039_AH_W24D2


title: Blood, AH, Week 24 Day 2, 15U027

status: Public on Dec 17 2025

type: SRA

city: Silver Spring

first: Rasmi

last: Thomas

state: MD

address: 503 Robert Grant Avenue

department: MHRP

country: USA

institute: Walter Reed Army Institute of Research

description:
Library name: 15U027_AH_W24D2
Column name in TMM_counts.txt:15U027_AH_W24D2

library_source: transcriptomic

data_processing:
Raw sequencing data were converted to FASTQ using bcl2fastq2 v.2.20.0 (Illumina)
Low quality bases were removed using Trimmomatic v0.39 and FastQC v0.11.860.
Reads were mapped to the Rhesus Macaque genome (Mmul_10) using HISAT2 v2.1.061.
Subread featureCounts v1.6.4 was used for gene expression quantification of protein-coding genes, and trimmed mean of M values (TMM)-based normalization was implemented within edgeR v3.36.062.
Genes aligning to highly divergent regions of the genome, deriving from mitochondria, coding for ribosomal proteins and hemoglobin-related genes were excluded from the count matrix. Only genes with counts above 10 in a minimum of 15 samples were retained.
Assembly: Mmul_10
Supplementary files format and content: tab-delimitted text file contains TMM-normalized counts for all samples.

molecule: total RNA

organism: Macaca mulatta

source_name: Blood

extract_protocol:
Total RNA was extracted from 10,000-100,000 or 30,000-6.5 million cryopreserved PBMC using the Single Cell RNA Purification Kit (Norgen Biotek Corp) or the PureLink RNA Mini Kit (ThermoFisher Scientific)
Amplified cDNA was made from 6.66-10ng of RNA using the SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio Inc.), spiked with 5μL of 1:20,000 diluted ERCC Mix 1 or 2 (ThermoFisher Scientific). Sequence-ready libraries were generated using the Illumina DNA Library Prep Kit, quantified on a MiSeq.

tag: tissue

value: Blood

tag: cell type

value: peripheral blood cells

tag: treatment

value: AH

tag: time


title: UOK120 cells, shControl biol rep 3

city: Nanjing

first: Yanwen

last: Lu

state: jiangsu

address: No. 22 Hankou Rd., Gulou District, Nanjing, Jiangsu 210093, P.R.China

country: China

institute: Nanjing University

data_processing:
reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the follwing assembly analysis. Thus, to get high quality clean reads.
We aligned reads of all samples to the research species referencegenome using HISAT2 package.
The mapped reads of each sample were assembled using StringTie with default parameters.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes counts values for each Sample
Supplementary files format and content: tab-delimited text file includes FPKM values counts for each Sample

organism: Homo sapiens

source_name: Kidney

extract_protocol:
RNA was harvested using RNA easy mini plus kit (Qiagen). 1.3 ug RNA was used for the construction of the squencing libraries.
RNA libraries for RNA-seq  were prepared using SMARTER mrna-seq library Prep kit following manufacturer's protocols

value: Kidney

tag: cell line

value: Xp11.2 translocation renal carcinoma cell lines

value: shRNA(nc)


title: SK05-RK10338_S30

city: Ramat Gan

first: Tzipi

last: Braun

address: Derech Sheba 2

country: Israel

institute: Sheba Medical Center at Tel Hashomer

data_processing:
Reads were quantified by kallisto version 42.5, using Gencode v24 as the reference genome
Assembly: Gencode v24
Supplementary files format and content: tab-delimited text files include RPM (reads per million) values for each Sample

source_name: Ileum

extract_protocol:
RNA was isolated from FFPE tissue sections using the Qiagen AllPrep RNA/DNA FFPE Kit.
Lexogen QuantSeq 3' mRNA-Seq libraries and single-end 100-bp sequencing was performed

value: Ileum

tag: average ileal_microvillus_length_(µm)

tag: cd microvillus_length_quartile


title: SK10-RK10620_S19


title: 5040

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

country: Canada

institute: Université Laval

description: Library name: Sample 4

library_source: genomic

data_processing:
Reads were filtered, trimmed, and deduplicated using fastp version 0.23.1 with default parameters
Read conversion, alignment to the Bos taurus reference genome (ARS-UCD1.2.104)
Methyl calling were performed using Bismark. This process was implemented in the DRAGEN Methylation Pipeline, which was run on an Illumina DRAGEN server using default parameters
Methylation calls from Bismark were filtered to retain CpG sites covered by at least six reads in a minimum of five samples per group.
The annotation was performed using the annotatePeak function of the R ChIPseeker (version 1.32.1).
Assembly: ARS-UCD1.2
Supplementary files format and content: A tab-delimited text file contains information about positions correlated with age in the control group (48 samples) along with their annotations; the corresponding positions in diseased cows (48 samples) are also available.
Library strategy: EM-seq

molecule: genomic DNA

organism: Bos taurus

growth_protocol: The cows were raised in the same conditions on the farm

extract_protocol:
One mL of blood was sent to the Génome Québec sequencing platform for DNA extraction, enzymatic methyl-seq (EM-seq) library preparation and whole-genome sequencing
Libraries were pooled at equimolar concentrations and sequenced using Illumina NovaSeq technology, generating approximately 450 million 150-bp paired-end reads per library.During library preparation, there is a DNA conversion step involves in three primary enzymes: TET2 and T4-BGT detect and transform 5mC and 5hmC into a product that cannot be deaminated by the APOBEC3A enzyme. Subsequently, APOBEC3A deaminates unmodified cytosines by converting them to uracils. As a result, unmethylated cytosines are transformed into uracils and then to thymines during PCR amplification, while methylated cytosines remain as cytosines

tag: genotype

value: Low Production


title: Blood, AH, Week 24 Day 2, 15U016

description:
Library name: 15U016_AH_W24D2
Column name in TMM_counts.txt:15U016_AH_W24D2


title: SK10-RK10479_S52


title: UOK109 cells, shControl biol rep 3


title: Blood, AH, Week 24 Day 2, 14U024

description:
Library name: 14U024_AH_W24D2
Column name in TMM_counts.txt:14U024_AH_W24D2


title: UOK109 cells, shNR1D3 biol rep 3


title: 5095

description: Library name: Sample 6

value: Control


title: 5045

description: Library name: Sample 5


title: SK06-RK10152_S40


title: Blood, AH, Week 24 Day 2, 14U055

description:
Library name: 14U055_AH_W24D2
Column name in TMM_counts.txt:14U055_AH_W24D2


title: 5023

description: Library name: Sample 3


title: UOK109 cells, shNR1D1 biol rep 2


title: Blood, AH, Week 24 Day 2, 13U062

description:
Library name: 13U062_AH_W24D2
Column name in TMM_counts.txt:13U062_AH_W24D2


title: SK06-RK10142_S36


title: UOK109 cells, shControl biol rep2


title: 5005

description: Library name: Sample 2


title: 11

description: Library name: Sample 1


title: UOK120 cells, shControl biol rep 1


title: TCGA KIRP, TCGA-A4-8312

city: New York

first: Fengshen

last: Kuo

state: New York

address: 1275 York Ave

institute: Memorial Sloan Kettering Cancer Center

description: Library name: TCGA_2

data_processing:
RNA-seq sequencing reads were aligned against human genome assembly hg19 by STAR 2-pass alignment. Gene level read count values were computed by using the R GenomicAlignments package over aligned reads using UCSC KnownGene in hg19 as the base gene model. The Union Counting mode was used and only mapped paired reads passing alignment quality filtering were considered. Finally, gene (Entrez gene) level FPKM and raw read count values were computed by the R DESeq2 package.
Supplementary files format and content: Comma-separated files including raw count file: MaskID.hg19KnownGene.raw.csv
Supplementary files format and content: Comma-separated files including FPKM count file: MaskID.hg19KnownGene.fpkm.csv

molecule: polyA RNA

source_name: PRNRP

extract_protocol:
20-30mg frozen tissue were homogenized in 1 mL TRIzol Reagent (ThermoFisher catalog # 15596018) and phase separation was induced with 200 µL chloroform. RNA was extracted from 350 µL of the aqueous phase using the miRNeasy Mini Kit (Qiagen catalog # 217004) on the QIAcube Connect (Qiagen) according to the manufacturer’s protocol. Samples were eluted in 25-38 µL RNase-free water
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 500 ng of total RNA with RIN values of 8.1-9.2 underwent polyA selection and library preparation using the TruSeq Stranded mRNA LT Kit (Illumina catalog # RS-122-2102) according to instructions provided by the manufacturer with 8 cycles of PCR. Samples were barcoded and run on a NovaSeq 6000 in a PE100 run, using the NovaSeq 6000 S4 Reagent Kit (200 Cycles) (Illumina).  An average of 72 million paired reads was generated per sample. Ribosomal reads represented 0.04-0.09% of the total reads generated and the percent of mRNA bases averaged 85%

value: renal papillary cell carcinoma (Please refer to TCGA)

tag: histopathology

value: PRNRP

tag: tumor grade


title: UOK109 cells, shNR1D1 biol rep 1


title: Blood, ALFQA, Week 12 Day 2, 15U034

description:
Library name: 15U034_ALFQA_W12D2
Column name in TMM_counts.txt:15U034_ALFQA_W12D2

value: ALFQA


title: SK05-RK10326_S34


title: TCGA KIRP, TCGA-BQ-5883

description: Library name: TCGA_3


title: TCGA KIRP, TCGA-MH-A854

description: Library name: TCGA_5

source_name: KRAS mutant PRCC

value: Papillary RCC


title: UOK109 cells, shControl biol rep 1


title: Blood, ALFQA, Week 12 Day 2, 13U013

description:
Library name: 13U013_ALFQA_W12D2
Column name in TMM_counts.txt:13U013_ALFQA_W12D2


title: SK11-RK10543_S9


title: Blood, ALFQ, Week 12 Day 2, 14U026

description:
Library name: 14U026_ALFQ_W12D2
Column name in TMM_counts.txt:14U026_ALFQ_W12D2

value: ALFQ


title: Blood, ALFQ, Week 12 Day 2, 16U010

description:
Library name: 16U010_ALFQ_W12D2
Column name in TMM_counts.txt:16U010_ALFQ_W12D2


title: hKO

city: Daejeon

first: In Hwan

last: Tae

address: 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

library_source: transcriptomic single cell

data_processing:
Sequencing reads were processed with the Cell Ranger version 7.0.1 (10X Genomics, CA, USA) using the Human reference transcriptome GRch38 from ensembl. From the gene expression matrix, downstream analysis was carried out with R version 4.0.2. Quality control, filtering, data clustering and visualization, and differential expression analysis was carried out using WinSeurat program (Ebiogen Inc, Korea) based on Seurat version 4.2.0. For each individual dataset, genes expressed in cells < 500 UMIs and < 300 genes were removed from the gene expression matrix.
Assembly: GRch38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: human kidney organoid

extract_protocol:
Single-cell suspensions were made from human kidney organoid using TrypLE (Thermo Fisher, 12604013), and then filtered through a 40 uM mesh strainer (Corning, CLS431750) to isolate single cells.
Single-cell RNA-sequencing libraries were then prepared using the Chromium Next GEM Single Cell 3’ reagent kit v3.1 (10X Genomics, Pleasanton, CA) in accordance with the manufacturer’s protocol.
libraries were sequenced in multiplex on the Novaseq 6000 sequencer (Illumina, San Diego, CA) to produce on average a minimum of 60,000 reads per single cell

value: human kidney organoid


title: SK07-RK10211_S11


title: SK13-RK10601_S46


title: TCGA KIRP, TCGA-GL-A9DC

description: Library name: TCGA_4


title: Blood, ALFQ, Week 12 Day 2, 13U037

description:
Library name: 13U037_ALFQ_W12D2
Column name in TMM_counts.txt:13U037_ALFQ_W12D2


title: SK06-RK10176_S45


title: Seedling, YJBT2

city: Shenyang

first: Xiaoxue

last: Wang

state: Liaoning

address: 120 Dongling Road, Shenhe District

department: Rice Research Institute

institute: Shenyang Agricultural University

data_processing:
The clustering of the index-coded samples is performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.
After cluster generation, the library preparations are sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads are generated.
Raw data (raw reads) of fastq format are firstly processed through in-house perl scripts.
Index of the reference genome is built using Bowtie v2.2.3 and paired-end clean reads are aligned to the reference genome using TopHat v2.0.12.
HTSeq v0.6.1 is used to count the reads numbers mapped to each gene.
Assembly: IRGSP-1.0
Supplementary files format and content: xls/readcount
Supplementary files format and content: xls/fpkm

organism: Oryza sativa

source_name: Seedling

growth_protocol: 7-day-old seedling of rice grown under 14 h light-10 h dark at 28oC

extract_protocol:
Total RNA is extracted with Takara RNAiso Plus (Takara, Cat# 9108)
Sequencing libraries are generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes are added to attribute sequences to each sample. The library quality is assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: no treatment; gravity stimulation

value: Seedling

value: gravity stimulation


title: Blood, ALFQA, Week 12 Day 2, 15U011

description:
Library name: 15U011_ALFQA_W12D2
Column name in TMM_counts.txt:15U011_ALFQA_W12D2

value: Blood


title: SK08-RK10227_S1


title: Seedling, YJBT1


title: SK07-RK10198_S2


title: Blood, ALFA, Week 12 Day 2, 15U036

description:
Library name: 15U036_ALFA_W12D2
Column name in TMM_counts.txt:15U036_ALFA_W12D2

value: peripheral blood cells

value: ALFA


title: SK06-RK10167_S30


title: Blood, ALFQ, Week 12 Day 2, 17U011

description:
Library name: 17U011_ALFQ_W12D2
Column name in TMM_counts.txt:17U011_ALFQ_W12D2


title: S24h5

type: RNA

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

description: Gene expression data from  rat  heart with SAP treated for 24 hours

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16 hr at 45℃ on Affymetrix Clariom S Assay, Rat. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Genechips were scanned by GeneChip® Scanner 3000.

data_processing: The data were analyzed with Expression Console™, Version 1.3.1.

label: biotin

organism: Rattus norvegicus

source_name: SD Rats with SAP treated for 24 hours

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-8 ug total RNA

growth_protocol: 8-10weeks-old male SD Rats were kept at least 1 wk at 22°C and 55% relative humidity in a 12-h day/night lighting environment with free access to food and water.

extract_protocol: All mice were euthanized by an overdose of pentobarbital on hours 6, 24 and 72 of  ischemia/reperfusion (I/R) treated. Total RNA was isolated with TRIzol (Invitrogen) from hearts at each time point according to manufacturer's instructions.

treatment_protocol: 8-10weeks-old male SD Rats were subjected to subjected to retrograde infusion of 5% sodium taurocholate into the pancreatic and biliary ducts to induce severe acute pancreatitis (SAP) of 12 and 24 hours.

tag: gender

value: Male

value: Heart


title: SK06-RK10320_S1


title: TCGA KIRP, TCGA-2Z-A9JN

description: Library name: TCGA_1


title: S24h3


title: SK10-RK10650_S40


title: S24h4


title: Blood, ALFA, Week 12 Day 2, 15U018

description:
Library name: 15U018_ALFA_W12D2
Column name in TMM_counts.txt:15U018_ALFA_W12D2


title: Seedling, YJWT1

description: WT

value: WT


title: Seedling, YJWT2

description: WT


title: Blood, ALFA, Week 12 Day 2, 14U043

description:
Library name: 14U043_ALFA_W12D2
Column name in TMM_counts.txt:14U043_ALFA_W12D2


title: S24h2


title: Seedling, YJBC2

value: no


title: SK13-RK10648_S33

value: Ileum


title: SK05-RK10312_S9


title: Seedling, YJBC1


title: Blood, ALFA, Week 12 Day 2, 17U041

description:
Library name: 17U041_ALFA_W12D2
Column name in TMM_counts.txt:17U041_ALFA_W12D2


title: S12h4

description: Gene expression data from  rat  heart with SAP treated for 12 hours

source_name: SD Rats with SAP treated for 12 hours


title: S24h1


title: S12h5


title: SK13-RK10660_S48


title: Seedling, YJWC2

description: WT


title: S12h3


title: Blood, ALFA, Week 12 Day 2, 13U067

description:
Library name: 13U067_ALFA_W12D2
Column name in TMM_counts.txt:13U067_ALFA_W12D2


title: Blood, AH, Week 12 Day 2, 15U027

description:
Library name: 15U027_AH_W12D2
Column name in TMM_counts.txt:15U027_AH_W12D2

value: AH


title: Seedling, YJWC1

description: WT


title: SK08-RK10286_S12


title: Young_G4P_1

city: guangzhou

first: haoxian

last: zhou

address: zhongshan 2nd Road

institute: guangdong people hosptial

data_processing:
For RIP-seq, cutadapt (v2.0.dev0) was used to trim the relevant adapter sequence and remove the low-quality reads as well as filter reads the outside of 24-35 nt range. Reads aligning to rRNA were removed using bowtie (v1.1.2) with default parameters. The remaining reads were then mapped to the human genome(hg38) using Tophat(v2.0.13) with default options.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include expected values for each sample

source_name: cell

extract_protocol:
For G4P-RIP-seq：G4P-stable expressing cells were grown in an appropriate culture medium and induced with DOX. To cross-link the cells, the formaldehyde solution was added to achieve a final concentration of 1% and incubated for 10 minutes at room temperature(RT). The reaction was stopped by adding one-tenth the volume of 2.66 M glycine and incubating for an additional 5 minutes at RT. Then collected cells and centrifugated at 1000 ×g for 5 minutes at 4 °C, and the supernatant was discarded. The cells were washed twice with 1× ice-cold PBS. Next, the cells were resuspended in 4 mL of cell lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 0.5 % NP-40,1 mM DTT, 200 units/ml RNase OUT, and EDTA-free Protease Inhibitor Cocktail) and incubated for 15 minutes on ice. The nuclei were sonicated to obtain DNA fragments within the range of 200 to 1000 bp. After the sonication, 250 units/mL of DNase were added to the chromatin and incubated for 30 minutes at 37 °C. In a separate 1.5 ml tube, 20 μl of Flag magnetic beads were added and washed twice with 0.5 ml of NT-2 buffer(50 mM Tris-HCl pH 7.4, 150 mM NaCl, 1 mM MgCl2, 0.05 % NP-40). Centrifuge the cell lysate at 20,000 ×g for 10 minutes at 4 °C. Remove 975 μl of the supernatant and add it to each Flag beads reaction. Take 10% of the cell lysate supernatant and transfer it to a new tube labeled "Input". Incubate all tubes on a rotating wheel for 6 hours at 4 °C. After the overnight incubation, spin down the tubes, place them on a magnetic support over ice, and discard the supernatant. Resuspend each immunoprecipitate in 150 μl of Proteinase K buffer(50 mM Tris-HCl pH 7.4, 150 mM NaCl, 1 mM MgCl2, 0.05 % NP-40, 1%SDS, 1.2 mg/ml Proteinase K). For each “Input” sample, add 107 μl of NT-2, 15 μl of 10% SDS, and 18 μl of Proteinase K, reaching a total volume of 150 μl. Incubate all tubes at 55 °C for 30 minutes with shaking to digest the proteins. Recover the RNA by phenol:chloroform:isoamyl alcohol (125:24:1) and absolute ethanol precipitation. Resuspend the pellets in 20 μl of RNase-free water and place the tube on ice.
For G4P-RIP-seq: 1 ug of input RNA and 0.2-1ug IP RNA was used for the construction of sequencing libraries. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.The NEBNext Ultra II Directional RNA Library Prep Kit standard protocol (NEB) was employed for library preparation.

value: cell

value: BJ fibroblast

tag: condition

value: young

tag: rip antibody


title: S12h2


title: SK12-RK11014_S19


title: Blood, AH, Week 12 Day 2, 15U016

description:
Library name: 15U016_AH_W12D2
Column name in TMM_counts.txt:15U016_AH_W12D2


title: Blood, ALFA, Week 12 Day 2, 14U018

description:
Library name: 14U018_ALFA_W12D2
Column name in TMM_counts.txt:14U018_ALFA_W12D2


title: SEN_G4P_2

value: senescence


title: Blood, AH, Week 12 Day 2, 14U055

description:
Library name: 14U055_AH_W12D2
Column name in TMM_counts.txt:14U055_AH_W12D2


title: SK14-RK11007_S29


title: SEN_G4P_input_2

description: INPUT, not description

value: none (input)


title: Blood, AH, Week 12 Day 2, 14U024

description:
Library name: 14U024_AH_W12D2
Column name in TMM_counts.txt:14U024_AH_W12D2


title: S12h1


title: SK13-RK10395_S12

value: Ctl


title: Con4

description: Gene expression data from  rat  heart with sham surgery

source_name: SD Rats with sham surgery


title: Con5


title: SEN_G4P_1


title: RK10063


title: Con3


title: SEN_G4P_input_1

description: INPUT, not description


title: Wk18_Group3-4_GEM1_S6-3_HTO

city: La Jolla

first: Shane

last: Crotty

state: California

address: 9420 Athena

institute: La Jolla Institute For Immunology

description:
Library name: Wk18_Group3-4_GEM1_S6-3_HTO
HTO 5' mRNA library

library_source: other

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation were performed using Cell Ranger v7.0 (10X Genomics). VDJ reads were assembled de novo in Cell Ranger, and GEX sequencing libraries were aligned to the Macaca mulatta reference genome.
Assembly: Mmul10
Supplementary files format and content: Fasta files, Tab-separated values files and matrix files
Library strategy: CITE-seq

molecule: protein

source_name: PBMC

extract_protocol:
N332-GT5, Apex-GT6 and 10E8-GT12 -specific B cells were isolated from peripheral blood samples collected from rhesus macaques immunized with N332-GT5, Apex-GT6 and 10E8-GT12 germline targeting immunogens. Groups 1, 2 and 3 were immunized with N332-GT5, 10E8-GT12 24mer or Apex-GT6 respectively. Groups 4 and 5 were immunized with N332-GT5 in combination with Apex-GT6 or 10E8-GT12 24mer, respectively. Finally, Group 6 received all three GT immunogens. Booster immunizations including the same set of immunogens delivered at the prime were given at wk10. Peripheral blood mononuclear cells (PBMCs) were collected at weeks 12 and 18 post immunisation. To identify antigen-specific B cells, samples were stained with tetramerized332-GT5, Apex-GT6 and 10E8-GT12 probes conjugated to fluorescent and TotalSeq-C oligo-tagged streptavidin. Surface staining included a panel of fluorescently labeled antibodies, along with one of ten different TotalSeq-C oligo-tagged antibodies per sample. These oligo-tagged antibodies targeted β2M and CD298 and served as sample-specific hashtags to enable multiplexing across animals. Cells were sorted on a FACSymphony S6 (BD Biosciences). N332-GT5, Apex-GT6 and 10E8-GT12 -specific memory B cells were collected into 1.5 mL tubes containing RPMI 1640 medium supplemented with 50% fetal bovine serum (FBS) and kept on ice for immediate downstream processing.
Libraries were constructed according to the manufacturer's protocol using the Chromium Next GEM Single Cell 5’ Reagent Kit v2.

value: PBMC

value: B cells

value: Protein immunized

tag: library type

value: HTO

tag: hto

value: TotalSeq-C0251 anti-Human Hashtag1 (r19079),TotalSeq-C0253 anti-Human Hashtag3 (r19088),TotalSeq-C0257 anti-Human Hashtag7 (r21022),TotalSeq-C0258 anti-Human Hashtag8 (r20041),TotalSeq-C0259 anti-Human Hashtag9 (r20045),TotalSeq-C0260 anti-Human Hashtag10 (r20082), TotalSeq-C5225 BV421 Streptavidin (Apex), TotalSeq-C5232 BV421 Streptavidin (10E8-GT12), TotalSeq-C0996 AF647 Streptavidin (N332-GT5), TotalSeq-C0997 AF647 Streptavidin (10E8-GT12)


title: HEK293T VSV-infected cells smallRNA-seq replicate 2

city: Strasbourg

first: Sébastien

last: Pfeffer

address: 2 allée Konrad Roentgen

department: UPR 9002 - Architecture et Réactivité de l'ARN

country: France

institute: CNRS - Institut de Biologie Moléculaire et Cellulaire (IBMC)

description: Library name: HEK_VSV2_1

data_processing:
Raw reads were pre-cleanned by the sequencing platform, including adapter, contaminant and low-quality removal (Phred+33). Before alignment, redundant sequences were collapsed to one copy using fastq_collapser from FASTX-Toolkit 0.0.14 and a read-size filter was applied (18-35 bp). HEK293T and M. myotis short reads were then respectively aligned to human genome assembly GRCh38 and M. myotis genome mMyoMyo1.p. Mapping was performed using Bowtie 1.3.1 with parameters ‘-v 1 -a --best --strata’. Unmapped reads were next separately aligned against virus genomes SINV-GFP and VSV-GFP using the following parameters ‘-v 2 -y -m 30 -a --best --strata’. siRNA signature was finally research on 22nt mapped reads by the python tool signature (Antonieski, 2014) with 22 22 1 22 options.
Assembly: GRCh38/hg38 ; mMyoMyo1.p ; FJ478454.1
Supplementary files format and content: Read counts after mapping on different genomes.

source_name: HEK 293T

growth_protocol: All cells were maintened in Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS) in a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted from cell lysates using Trizol Reagent (15586018, InVitrogen) to which 200 µl of chloroform was added before centrifugation for 15 minutes at 12,000 xg at 4°C. For small RNA extraction, supernatants were collected and nucleic acids were precipitated in 3 volumes of 100% ethanol + 10% 1M sodium acetate for 30 minutes at -80°C. RNA was pelleted for 10 min at 12,000 xg at 4°C then washed with 70% ethanol and reconstituted in RNase free water.
Samples were shipped to BGI for library preparation. Sequencing was realized on DNBSEQ technology, for 50bp single-end reads and standard output of 20 million reads per sample.

value: HEK 293T

value: Embryonic kidney cell

tag: infection

value: VSV-GFP


title: Blood, AH, Week 12 Day 2, 17U039

description:
Library name: 17U039_AH_W12D2
Column name in TMM_counts.txt:17U039_AH_W12D2

value: Blood

value: peripheral blood cells


title: SK12-RK11009_S14

value: Ileum


title: Con2

value: Male

value: Heart


title: HEK293T VSV-infected cells smallRNA-seq replicate 1

description: Library name: HEK_VSV1_1


title: RK10065


title: Con1

description: Gene expression data from rat heart with sham surgery


title: Wk18_Group3-4_GEM1_S6-3_GEX

description:
Library name: Wk18_Group3-4_GEM1_S6-3_GEX
GEX 5' mRNA library

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation were performed using Cell Ranger v7.0 (10X Genomics). VDJ reads were assembled de novo in Cell Ranger, and GEX sequencing libraries were aligned to the Macaca mulatta reference genome.
Assembly: Mmul10
Supplementary files format and content: Fasta files, Tab-separated values files and matrix files

value: mRNA


title: Young_G4P_input_2

description: INPUT, not description

value: cell

value: BJ fibroblast

value: young


title: SK09-RK10387_S44

value: Ctl


title: SK09-RK10392_S45


title: Wk18_Group3-4_GEM1_S6-3_VDJ

description:
Library name: Wk18_Group3-4_GEM1_S6-3_VDJ
VDJ 5' mRNA library

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation were performed using Cell Ranger v7.0 (10X Genomics). VDJ reads were assembled de novo in Cell Ranger, and GEX sequencing libraries were aligned to the Macaca mulatta reference genome.
Assembly: Mmul10
Supplementary files format and content: Fasta files, Tab-separated values files and matrix files
Library strategy: BCR-Seq

value: PBMC

value: B cells

value: VDJ


title: HEK293T SINV-infected cells smallRNA-seq replicate 1

description: Library name: HEK_SINV1_1

value: SINV-GFP


title: SK09-RK10386_S43


title: Young_G4P_input_1

description: INPUT, not description

value: none (input)


title: Wk18_Group3-4_GEM1_S6-2_HTO

description:
Library name: Wk18_Group3-4_GEM1_S6-2_HTO
HTO 5' mRNA library

value: Protein immunized

value: HTO

value: TotalSeq-C0251 anti-Human Hashtag1 (r18051),TotalSeq-C0253 anti-Human Hashtag3 (r18103),TotalSeq-C0257 anti-Human Hashtag7 (r19060),TotalSeq-C0258 anti-Human Hashtag8 (r17021),TotalSeq-C0259 anti-Human Hashtag9 (r19038),TotalSeq-C0260 anti-Human Hashtag10 (r19069), TotalSeq-C5225 BV421 Streptavidin (Apex), TotalSeq-C5232 BV421 Streptavidin (10E8-GT12), TotalSeq-C0996 AF647 Streptavidin (N332-GT5), TotalSeq-C0997 AF647 Streptavidin (10E8-GT12)


title: HEK293T mock cells smallRNA-seq replicate 2

description: Library name: HEK_m2_1

value: HEK 293T

value: Embryonic kidney cell

value: mock


title: Young_1

data_processing:
For RNA-seq data, demultiplexed sequencing reads were processed by trimming adapter sequences using Cutadapt (v2.0.dev0). Reads that aligned to the human genome (hg38) were identified using STAR (v2.4.2a) with ENCODE standard options for the long RNA-seq pipeline, employing the GENCODE transcriptome annotation (GENCODE v32) as a reference. Read counts were generated through featureCounts (v1.6.4) with default settings. Significantly differentially expressed (DE) genes were analyzed using DESeq2 and selected based on a p-value threshold of 5%.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include expected values for each sample

extract_protocol:
For RNA-seq: Three micrograms of total RNA were utilized for polyadenylated RNA enrichment with VAHTS mRNA Capture Beads (Vayzme) following the manufacturer’s protocol. The NEBNext Ultra II Directional RNA Library Prep Kit standard protocol (NEB) was employed for library preparation. Subsequently, the libraries were subjected to sequencing on an Illumina HiSeq X Ten platform, generating 150-bp paired-end reads at Annoroad Gene Technology Company.
For RNA-seq: A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: DMSO


title: RK10064

value: Ileum


title: HEK293T mock cells smallRNA-seq replicate 1

description: Library name: HEK_m1_1


title: Blood, AH, Week 12 Day 2, 13U062

description:
Library name: 13U062_AH_W12D2
Column name in TMM_counts.txt:13U062_AH_W12D2

value: Blood

value: peripheral blood cells

value: AH


title: Young_2

value: cell

value: BJ fibroblast

value: young


title: Wk18_Group3-4_GEM1_S6-2_VDJ

description:
Library name: Wk18_Group3-4_GEM1_S6-2_VDJ
VDJ 5' mRNA library

value: PBMC

value: B cells

value: VDJ


title: Wk18_Group3-4_GEM1_S6-2_GEX

description:
Library name: Wk18_Group3-4_GEM1_S6-2_GEX
GEX 5' mRNA library

value: Protein immunized

value: mRNA


title: SK09-RK10393_S46

value: Ctl


title: Young_cPDS-1

value: cPDS (2 μM)


title: PHF23 KO HeLa, Normal media, rep2

city: Seoul

first: Young Suk

last: Yu

address: 1-Gwanak-ro, Gwanak-gu

institute: Seoul National University

description: Library name: KO_CTL_2

data_processing:
Reads were mapped to GRCh38 by STAR (v2.7.10b).
Read counts were generated by featureCounts (v2.0.6).
The differential gene expression analysis was performed using Bioconductor package DESeq2 (v1.44.0).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files, read counts from featureCounts

source_name: HeLa

extract_protocol:
Total RNA extraction was performed using Trizol (Invitrogen)
The DNBseq RNA library construction method and sequencing process are carried out according to the following steps: 1. Take a certain amount of total RNA samples, and use oligo dT beads to enrich mRNA with poly A tail; 2. mRNA molecules were fragmented into small pieces; 3. The fragmented mRNA was synthesized into first strand cDNA using random primers; 4. The second strand cDNA was synthesized with dUTP instead of dTTP; 5. The synthesized cDNA was subjected to end-repair and 3' adenylated. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments; 6. Perform PCR amplification; 7. Library quality control; 8. Library circularization; 9. The library was amplified to make DNA nanoball (DNB); 10. Sequencing on DNBSEQ (DNBSEQ Technology) platform.

value: HeLa

value: epithelial cell

value: PHF23 KO

value: Normal


title: Young_cPDS-2


title: PHF23 KO HeLa, Normal media, rep1

description: Library name: KO_CTL_1


title: Young_G4P_2


title: Wk18_Group2-5_GEM1_S6-3_GEX

description:
Library name: Wk18_Group2-5_GEM1_S6-3_GEX
GEX 5' mRNA library


title: iCARUb

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

description: Library name: Sample5

data_processing:
Briefly, mRNA was isolated and amplified by in vitro transcription. The resulting cRNA was converted to ssDNA by multiplex reverse transcription using a collection of TRAV/TRBV specific primers containing UMI and Illumina adapters. TCR-beta were then amplified by PCR (20 cycles) with a single primer pair binding to the constant region and the Illumina adapter added during the reverse transcription. A second round of PCR (25 cycles) was performed to add the different indexes used for multiplexing. The TCR products were purified, quantified and loaded on MiSeq or NextSeq instruments (Illumina)
The TCR sequences were further processed using ad hoc Perl scripts to: (i) pool all TCR sequences coding for the same protein sequence; (ii) correct for amplification and sequencing errors using 9mers UMI; (iii) filter out all out-frame sequences; (iv) determine the abundance of each distinct TCR sequence. TCR with a single read were removed for the analysis.
Assembly: TCR reference
Supplementary files format and content: tab separated, processed counts
Library strategy: TCR-seq

organism: Mus musculus

extract_protocol:
Tumors (n=8 per cohort) were harvested at the study endpoint, minced, treated with collagenase, and filtered through a 70 μm cell strainer in PBS to generate single-cell suspensions. Live and dead cells from each tumor were counted, and aliquots containing approximately 50,000 live cells per tumor were prepared. Aliquots from mice within the same cohort were pooled together, and live cells were subsequently isolated using a live/dead cell separation kit. The pooled cell samples were centrifuged, resuspended in 300 µl of lysis buffer (catalog number: A33562), and stored at –80°C.
Bulk TCR sequencing analysis was performed as described previously (Cell Reports Methods 2023, Genolet et al)


title: HEK293T SINV-infected cells smallRNA-seq replicate 2

description: Library name: HEK_SINV2_1

value: HEK 293T

value: Embryonic kidney cell

value: SINV-GFP


title: PHF23 WT HeLa, Amino acid starvation media, rep2

description: Library name: WT_AAS_2

value: PHF23 WT

value: Amino acid starvation


title: Wk18_Group2-5_GEM1_S6-3_VDJ

description:
Library name: Wk18_Group2-5_GEM1_S6-3_VDJ
VDJ 5' mRNA library


title: SK13-RK10379_S2

value: Ileum


title: RK10061


title: PHF23 WT HeLa, Amino acid starvation media, rep1

description: Library name: WT_AAS_1


title: iCARUb IL12

description: Library name: Sample4


title: SK09-RK10384_S42


title: SK13-RK10394_S11


title: Tumor lysate

description: Library name: Sample3


title: Wk18_Group2-5_GEM1_S6-2_GEX

description:
Library name: Wk18_Group2-5_GEM1_S6-2_GEX
GEX 5' mRNA library

value: PBMC


title: PHF23 WT HeLa, Normal media, rep1

description: Library name: WT_CTL_1


title: RK10062


title: Wk18_Group2-5_GEM1_S6-2_HTO

description:
Library name: Wk18_Group2-5_GEM1_S6-2_HTO
HTO 5' mRNA library

value: B cells

value: HTO

value: TotalSeq-C0251 anti-Human Hashtag1 (r17011),TotalSeq-C0253 anti-Human Hashtag3 (r17019),TotalSeq-C0257 anti-Human Hashtag7 (r18104),TotalSeq-C0258 anti-Human Hashtag8 (r15050),TotalSeq-C0259 anti-Human Hashtag9 (r18052),TotalSeq-C0260 anti-Human Hashtag10 (r18084), TotalSeq-C5225 BV421 Streptavidin (Apex), TotalSeq-C5232 BV421 Streptavidin (10E8-GT12), TotalSeq-C0996 AF647 Streptavidin (N332-GT5), TotalSeq-C0997 AF647 Streptavidin (10E8-GT12)


title: Wk18_Group2-5_GEM1_S6-2_VDJ

description:
Library name: Wk18_Group2-5_GEM1_S6-2_VDJ
VDJ 5' mRNA library

value: Protein immunized

value: VDJ


title: Ctrl-iCARUb IL12

description: Library name: Sample2


title: Ctrl-iCARUb

description: Library name: Sample1


title: SK10-RK10399_S1

value: Ctl


title: plasmid_ICB sub-library_S23_L004

city: Houston

first: Weiyi

last: Peng

state: TX

address: 3455 Cullen Blvd., Suite 342

department: Department of Biology and Biochemistry

institute: University of Houston

description:
plasmid of  in vivo gRNA sub-library-lane4
220106_WP_PM1608.count.txt

data_processing:
Genome-wide in vitro immune screen analysis: The MAGeCK (v0.5.9.4) count module was used to calculate the read count of individual gRNAs in different samples with the following parameters: “-l Mouse_v2_CRISPR.library --norm-method total --sample-label Ctrl,ET02,ET1 -n Mouse_v2_CRISPR_191205.count.version2.txt --fastq files.fq”. MAGeCK test module was then applied with parameters “-k Mouse_v2_CRISPR_191205.count.version2.txt -c Ctrl,ET02,ET1 --norm-method total --keep-tmp -n Mouse_v2_CRISPR_191205 _ET_Ctrl --gene-lfc-method secondbest”, to identify the genes whose gRNAs were significant differentially presented between the control and T cell treatment groups at the cutoff using |log2(fold-change)| ≥ 0.25 and p< 0.05.
In vivo screen analysis: For the results from the in vivo immune screen, the sequencing reads were mapped to the ICB sub-library using bowtie (1.2.2) with parameters “--best --strata -a --norc -m 1 -5 6 –S”. Samtools (1.9) was used to calculate the read count of each gRNA. The fold change and statistical significance of genes among the between non-responder and IgG control or responder and IgG control groups were calculated as using a modification of the DrugZ algorithm
Assembly: mm10
Supplementary files format and content: gene_summary.txt, sgrna_summary.txt, count.txt

organism: synthetic construct

source_name: Plasmid

growth_protocol: ID8 and related derived cell lines were obtained from the American Type Culture Collection (ATCC, Bethesda, MD). All cell lines and their genetically modified cell lines were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 5% heated-inactivated fetal bovine serum (FBS; #S11150, R&D System, Minneapolis, MN), 5 ug/mL of insulin, transferrin and sodium selenite and 100μg/ml of Normocin (ant-nr-1, InvivoGen, San Diego, CA). Cells were grown at 37 °C with 5% CO2. All cell lines were authenticated by short tandem repeat fingerprinting or the expression of tagged markers used for genetic modification. The mycoplasma detection kit (#13100-01, SouthernBiotech, Birmingham, AL) was used to routinely monitor for mycoplasma contamination of cultured cells. The maximum length of time of in vitro cell culture between thawing and use in the described experiments was two weeks.

extract_protocol:
Genomic DNA from all cell samples was extracted by using TRIzol (#15596026; ThermoFisher) according to the manufacturer’s protocol.
DNA fragments containing gRNA sequences were amplified and barcoded with adaptation by nested polymerase chain reaction (PCR) as previously described. The quality and concentration of all PCR products were determined by the Qubit ssDNA high sensitivity assay kit (#Q10212; ThermoFisher) and the bioanalyzer High Sensitivity DNA Kit (#5067-4626 2100; Agilent, Santa Clara, CA) respectively. Samples were then sequenced by Illumina Next-Generation Sequencing (NSG) at the MD Anderson Cancer Center Advanced Technology Genomics Core.
PCR amplicon of gRNA fragments

treatment_protocol: For in vitro CRISPR screen, the mouse improved genome-wide knockout CRISPR Library version 2 consisting of 90,230 gRNAs targeted 18,424 genes was purchased from Addgene and used to generate lentivirus as described above. 1.5× 108 of ID8/GC cells were transduced with pooled library lentivirus at low multiplicity of infection (MOI; ~0.15-0.2) and cultured with growth medium in present of 2ug/ml puromycin to select gRNA-transduced cells. One week after selection, pooled gRNA-transduced tumor cells were washed and seeded incell culture dishes for overnight. For T cell treated groups, cultured Pmel T cells were added at effector: target (ET) ratio of 0.2:1 and 1:1 for 16 hours. For non-T cell treated groups, equal amount of T cell growth medium was added. After treatment, non-adhesive cells including T cells and dead tumor cells were removed by repeated wash using pre-warmed PBS. Adherent cells were harvested by using 0.25% Trypsin-EDTA and washed three times using PBS. Additionally, tumor cells after 48-hour or 7-day puromycin selection were collected to determine the coverage of the genome-wide library in transduced cells before the functional immune screen. Three replicates were performed for all treatment groups, and each sample includes at least 3×107 of transduced cells for genomic DNA isolation using Blood & Cell Culture DNA MAXI Kit as described by the manufacturer’s protocol.  For in vivo CRISPR screen, After construction of the library, ID8/GC cells were transduced to express the pooled in vivo sub-library. Briefly, to generate lentiviral supernatants, HEK293T cells were seeded 16 hours before transfection and transfected with 9μg of lentiviral vectors encoding gRNAs library, along with lentiviral packaging plasmids (3μg of pCMV-VSV-G and 4.5μg of psPAX2) by the jetPRIME transfection reagent according to the manufacturer’s protocol. Viral supernatants were collected 72 hours post-transfection and filtered by 0.45um Syringe Filter Unit to remove cell debris. 1.2x107 ID8/GC cells were transduced with the pooled lentiviral supernatant at a low MOI (~0.15-0.2) and cultured with completed growth media for 48 hours. Then, transduced ID8/GC cells were under the selection pressure with 2μg/mL of puromycin for seven days. Additionally, 3.0x107 sub-library expressing ID8/GC (ID8/GCSL) cells were collected after 7 days of puromycin selection and served as reference samples (Ref). After 7 days of puromycin selection and expansion, ID8/GCSL cells were collected and subcutaneously inoculated into C57BL/6 and NSG mice at 1.0x107 cells per injection into the posterior-lateral flank of the mice. After 3 days post tumor inoculation, tumor-bearing C57BL/6 mice were randomized into two groups to receive anti-PD-1 treatment (N=10) or control (N=5). Intraperitoneal injection of anti-PD-1 at 100μg/per dose, every other day, were used for the mice in anti-PD-1 group. NSG mice bearing pooled tumor cells served as a control to eliminate the genes with essential role in controlling tumor development independent to endogenous immune responses. Additionally, tumor size of all mice was monitored every other day by recording perpendicular diameters taken by calipers. At the end of the treatment cycle of 12 days, tumors were collected to extract genomic DNA as described above.

value: Plasmid

tag: screen

value: plasmid


title: Wk18_Group2-5_GEM1_S6-3_HTO

description:
Library name: Wk18_Group2-5_GEM1_S6-3_HTO
HTO 5' mRNA library

tag: tissue

value: TotalSeq-C0251 anti-Human Hashtag1 (r19087),TotalSeq-C0253 anti-Human Hashtag3 (r20088),TotalSeq-C0257 anti-Human Hashtag7 (rh3092),TotalSeq-C0258 anti-Human Hashtag8 (r19002),TotalSeq-C0259 anti-Human Hashtag9 (rh3009),TotalSeq-C0260 anti-Human Hashtag10 (rh3018), TotalSeq-C5225 BV421 Streptavidin (Apex), TotalSeq-C5232 BV421 Streptavidin (10E8-GT12), TotalSeq-C0996 AF647 Streptavidin (N332-GT5), TotalSeq-C0997 AF647 Streptavidin (10E8-GT12)


title: Wk18_Group1-6_GEM1_S6-3_HTO

description:
Library name: Wk18_Group1-6_GEM1_S6-3_HTO
HTO 5' mRNA library

tag: cell type

value: TotalSeq-C0251 anti-Human Hashtag1 (r19010),TotalSeq-C0253 anti-Human Hashtag3 (rh3035),TotalSeq-C0257 anti-Human Hashtag7 (rh3078),TotalSeq-C0258 anti-Human Hashtag8 (r20037),TotalSeq-C0259 anti-Human Hashtag9 (r20047),TotalSeq-C0260 anti-Human Hashtag10 (r21035), TotalSeq-C5225 BV421 Streptavidin (Apex), TotalSeq-C5232 BV421 Streptavidin (10E8-GT12), TotalSeq-C0996 AF647 Streptavidin (N332-GT5), TotalSeq-C0997 AF647 Streptavidin (10E8-GT12)


title: PHF23 KO HeLa, H3K27Ac ChIP-seq, rep1

description: Library name: H3K27Ac_KO_1

data_processing:
Seqeuncing adapters were removed with NGmerge (v0.2)
Reads were mapped to GRCm38 by Bowtie2 (v2.5.4).
The chromatin-accessible peaks were called using Macs2 (v2.2.9.1).
bigWig files were generated using bamCoverage (v3.5.5)
Assembly: GRCh38
Supplementary files format and content: bigWig format

extract_protocol:
Crosslinked DNA was fragmented with sonication and IP with H3K27Ac and PHF23 antibody.
The DNBSEQ ChIP-Seq library construction method and sequencing process are carried out according to the following steps:1. Take IPed-DNA and Input DNA for sample qualification; 2. DNA-end repair, 3'-dA overhang and adaptor ligation. 3. PCR amplification and size selection. 4. Library quality control; 5. Library circularization; 6. The library was amplified to make DNA nanoball (DNB); 7. Sequencing on DNBSEQ (DNBSEQ Technology) platform.

value: HeLa

value: epithelial cell

value: PHF23 KO

tag: treatment

value: Normal


title: Wk18_Group1-6_GEM1_S6-3_GEX

description:
Library name: Wk18_Group1-6_GEM1_S6-3_GEX
GEX 5' mRNA library

value: mRNA


title: HMEC16_cell8_kd

city: Malmo

first: Dmytro

last: Kryvokhyzha

address: Jan Waldenströms gata 35

department: Clinical Sciences

country: Sweden

institute: Lund University

description: Library name: HMEC16

data_processing:
reads counting with Salmon 1.3.0 and annotation GENCODE version 34
QC with fastQC 0.10
Assembly: GRCh38
Supplementary files format and content: raw counts for each sample in a tab-delimited file

extract_protocol:
RNeasy Plus Mini Kit (Qiagen).
TruSeq Stranded Total RNA Library Prep Kit (Illumina)

treatment_protocol: CRISPR/Cas9-mediated knockdown

value: mammary epithelial cell

value: kd


title: plasmid_ICB sub-library_S23_L003

description:
plasmid of  in vivo gRNA sub-library-lane3
220106_WP_PM1608.count.txt


title: HMEC15_cell8_control

description: Library name: HMEC15

value: control


title: Wk18_Group1-6_GEM1_S6-3_VDJ

description:
Library name: Wk18_Group1-6_GEM1_S6-3_VDJ
VDJ 5' mRNA library

value: PBMC

value: B cells


title: plasmid_ICB sub-library_S23_L002

description:
plasmid of  in vivo gRNA sub-library-lane2
220106_WP_PM1608.count.txt


title: PHF23 WT HeLa, H3K27Ac ChIP-seq, rep2

description: Library name: H3K27Ac_WT_2

value: PHF23 WT


title: PHF23 WT HeLa, Normal media, rep2

description: Library name: WT_CTL_2


title: PHF23 WT HeLa, H3K27Ac ChIP-seq, rep1

description: Library name: H3K27Ac_WT_1


title: HMEC14_cell7_kd

description: Library name: HMEC14


title: Wk18_Group1-6_GEM1_S6-2_HTO

description:
Library name: Wk18_Group1-6_GEM1_S6-2_HTO
HTO 5' mRNA library

value: Protein immunized

value: HTO

value: TotalSeq-C0251 anti-Human Hashtag1 (r17016),TotalSeq-C0253 anti-Human Hashtag3 (r18027),TotalSeq-C0257 anti-Human Hashtag7 (r18097),TotalSeq-C0258 anti-Human Hashtag8 (r18095),TotalSeq-C0259 anti-Human Hashtag9 (r19020),TotalSeq-C0260 anti-Human Hashtag10 (r19047), TotalSeq-C5225 BV421 Streptavidin (Apex), TotalSeq-C5232 BV421 Streptavidin (10E8-GT12), TotalSeq-C0996 AF647 Streptavidin (N332-GT5), TotalSeq-C0997 AF647 Streptavidin (10E8-GT12)


title: HMEC13_cell7_control

description: Library name: HMEC13


title: Wk18_Group1-6_GEM1_S6-2_GEX

description:
Library name: Wk18_Group1-6_GEM1_S6-2_GEX
GEX 5' mRNA library


title: PHF23 KO HeLa, input, rep2

description: Library name: input_KO_2


title: HMEC12_cell6_kd

description: Library name: HMEC12


title: Wk18_Group1-6_GEM1_S6-2_VDJ

description:
Library name: Wk18_Group1-6_GEM1_S6-2_VDJ
VDJ 5' mRNA library

value: VDJ


title: PHF23 KO HeLa, H3K27Ac ChIP-seq, rep2

description: Library name: H3K27Ac_KO_2


title: PHF23 KO HeLa, input, rep1

description: Library name: input_KO_1


title: Wk12_Group4-6_GEM2_S6-3-HTO

description:
Library name: Wk12_Group4-6_GEM2_S6-3-HTO
HTO 5' mRNA library

value: TotalSeq-C0251 anti-Human Hashtag1 (r18095),TotalSeq-C0253 anti-Human Hashtag3 (r19020),TotalSeq-C0257 anti-Human Hashtag7 (r19047),TotalSeq-C0258 anti-Human Hashtag8 (r20037),TotalSeq-C0259 anti-Human Hashtag9 (r20047),TotalSeq-C0260 anti-Human Hashtag10 (r21035), TotalSeq-C5225 BV421 Streptavidin (Apex), TotalSeq-C5232 BV421 Streptavidin (10E8-GT12), TotalSeq-C0996 AF647 Streptavidin (N332-GT5), TotalSeq-C0997 AF647 Streptavidin (10E8-GT12)


title: X2 PDPN replicate 3

city: Huddinge

first: Jonas

last: Fuxe

address: Alfred Nobels Allé 8

department: Laboratory Medicine

institute: Karolinska Institutet

description:
Library name: X2_PDPN_replicate_3
counts_batch_2.txt
X2_Pp_3

data_processing:
Sequencing was run in two batches: the first batch included X2, CCR7, CCR7-PDPN and the second batch included X2, X2-PDPN, and CCR7-PDPN. All the data was analysed using Python (v.3.11.5). Normalization was performed using Transcripts Per Million by rnanorm (v.1.5.1). Subsequently, PCA was conducted using sklearn (v.1.3.0) to reduce dimensionality and visualize the data, particularly by observing batch effects and sample variations.
Assembly: Mouse reference genome (GRCm38/mm10)
Supplementary files format and content: txt

growth_protocol: Cells were maintained in RPMI-1640 with HEPES (Gibco™), supplemented with 10% fetal bovine serum (FBS, Gibco™), 1% L-glutamine (Gibco™), and 1% penicillin-streptomycin (Gibco™) at 37°C in a humidified incubator with 5% CO₂.

extract_protocol:
Total RNA was extracted from EO771 samples (4 technical replicates), using the RNeasy Mini Kit (Qiagen, Valencia, CA) following the manufacturer’s instructions.
Libraries were generated using the TruSeq Stranded mRNA kit (Illumina) and sequenced on an Illumina NextSeq 550 platform in single-end mode, producing 75 bp reads mapped to the mouse reference genome (GRCm38/mm10).

treatment_protocol: CCR7-expressing EO771 and vector control, EO772 X2, were generated through retroviral transduction. PLNCX2 (Clontech) vectors containing mouse Ccr7 cDNA and the tdTomato reporter gene were transduced into EO771 mouse mammary carcinoma cells (CH3 Biosystems). Retrovirus production and transduction was performed using Phoenix ampho-helper-free cells as described (26). Cells expressing tdTomato and CCR7 were enriched by fluorescence-activated cell sorting (FACS) on a BD FACSAria III (BD Biosciences). CCR7 was detected using anti-CCR7-APC (4B12, Thermo Fisher Scientific) and dead cells were excluded using SYTOX™ Blue dead cell stain (Thermo Fisher Scientific). Further sorting was conducted to isolate cell populations based on spontaneous upregulation of PDPN using anti-PDPN-eFluor™660 (eBio8.1.1, Thermo Fisher Scientific). No clonal selection was performed. Over the course of repeated experiments both CCR7 expression and PDPN expression were controlled for by flow cytometry.

value: mouse mammary tumor cells

value: spontaneous tumor from C57BL/6 mice

value: Vector control sorted for high PDPN expression

tag: batch


title: X2 PDPN replicate 4

description:
Library name: X2_PDPN_replicate_4
counts_batch_2.txt
X2_Pp_4

tag: cell line


title: HMEC11_cell6_control

description: Library name: HMEC11


title: X2 PDPN replicate 2

description:
Library name: X2_PDPN_replicate_2
counts_batch_2.txt
X2_Pp_2


title: HMEC10_cell5_kd

description: Library name: HMEC10


title: Wk12_Group4-6_GEM2_S6-3_GEX

description:
Library name: Wk12_Group4-6_GEM2_S6-3_GEX
GEX 5' mRNA library


title: PHF23 WT HeLa, input, rep1

description: Library name: input_WT_1

value: HeLa

value: epithelial cell


title: X2 PDPN replicate 1

description:
Library name: X2_PDPN_replicate_1
counts_batch_2.txt
X2_Pp_1


title: HMEC9_cell4_control

description: Library name: HMEC9


title: PHF23 ChIP-seq, rep3

description: Library name: PHF23_3

value: Normal


title: CCR7 PDPN batch 2 replicate 4

description:
Library name: CCR7_PDPN_batch_2_replicate_4
counts_batch_2.txt
Pp_4

value: CCR7 overexpression sorted for high PDPN expression


title: plasmid_ICB sub-library_S23_L001

description:
plasmid of  in vivo gRNA sub-library-lane1
220106_WP_PM1608.count.txt

value: Plasmid

value: plasmid


title: Wk12_Group4-6_GEM2_S6-3_VDJ

description:
Library name: Wk12_Group4-6_GEM2_S6-3_VDJ
VDJ 5' mRNA library

value: PBMC


title: Wk12_Group4-6_GEM2_S6-2_HTO

description:
Library name: Wk12_Group4-6_GEM2_S6-2_HTO
HTO 5' mRNA library

value: B cells

value: TotalSeq-C0251 anti-Human Hashtag1 (r17021),TotalSeq-C0253 anti-Human Hashtag3 (r19038),TotalSeq-C0257 anti-Human Hashtag7 (r19069),TotalSeq-C0258 anti-Human Hashtag8 (r20041),TotalSeq-C0259 anti-Human Hashtag9 (r20045),TotalSeq-C0260 anti-Human Hashtag10 (r20082),TotalSeq-C5225 BV421 Streptavidin (Apex), TotalSeq-C5232 BV421 Streptavidin (10E8-GT12), TotalSeq-C0996 AF647 Streptavidin (N332-GT5), TotalSeq-C0997 AF647 Streptavidin (10E8-GT12)


title: PHF23 ChIP-seq, rep2

description: Library name: PHF23_2

value: PHF23 WT


title: HMEC8_cell4_kd

description: Library name: HMEC8

value: mammary epithelial cell

value: kd


title: CCR7 PDPN batch 2 replicate 3

description:
Library name: CCR7_PDPN_batch_2_replicate_3
counts_batch_2.txt
Pp_3


title: HMEC7_cell4_control

description: Library name: HMEC7

value: control


title: PHF23 ChIP-seq, rep1

description: Library name: PHF23_1


title: Wk12_Group4-6_GEM2_S6-2_GEX

description:
Library name: Wk12_Group4-6_GEM2_S6-2_GEX
GEX 5' mRNA library

value: Protein immunized

value: mRNA


title: CCR7 PDPN batch 2 replicate 2

description:
Library name: CCR7_PDPN_batch_2_replicate_2
counts_batch_2.txt
Pp_2

value: mouse mammary tumor cells

value: spontaneous tumor from C57BL/6 mice


title: HMEC6_cell3_kd

description: Library name: HMEC6


title: Wk12_Group4-6_GEM2_S6-2_VDJ

description:
Library name: Wk12_Group4-6_GEM2_S6-2_VDJ
VDJ 5' mRNA library

value: VDJ


title: PHF23 WT HeLa, input, rep2

description: Library name: input_WT_2

value: HeLa

value: epithelial cell


title: CCR7 PDPN batch 2 replicate 1

description:
Library name: CCR7_PDPN_batch_2_replicate_1
counts_batch_2.txt
Pp_1

value: CCR7 overexpression sorted for high PDPN expression


title: input, rep2

description: Library name: Input_2

value: Normal


title: Wk12_Group4-6_GEM1_S6-3_GEX

description:
Library name: Wk12_Group4-6_GEM1_S6-3_GEX
GEX 5' mRNA library


title: HMEC5_cell3_control

description: Library name: HMEC5


title: CCR7 PDPN batch 1 replicate 4

description:
Library name: CCR7_PDPN_batch_1_replicate_4
featureCounts_mm10_ensembl_genes.txt
8_MP_PDPN_Plus_4


title: CCR7 PDPN batch 1 replicate 3

description:
Library name: CCR7_PDPN_batch_1_replicate_3
featureCounts_mm10_ensembl_genes.txt
7_MP_PDPN_Plus_3


title: PHF23 KO HeLa, rep2

description: Library name: KO_2

extract_protocol:
Cells were lysed in ice-cold lysis buffer and the transposition reaction was performed using the Tn5 transposase
The illumina libraries for ATAC-seq were prepared by Illumina Tagment DNA TDE1 Enzyme and Buffer Kits according to the manufacturer’s protocol.

value: PHF23 KO


title: HMEC4_cell2_kd

description: Library name: HMEC4


title: HMEC3_cell2_control

description: Library name: HMEC3


title: Wk12_Group4-6_GEM1_S6-3_VDJ

description:
Library name: Wk12_Group4-6_GEM1_S6-3_VDJ
VDJ 5' mRNA library

value: PBMC


title: CCR7 PDPN batch 1 replicate 2

description:
Library name: CCR7_PDPN_batch_1_replicate_2
featureCounts_mm10_ensembl_genes.txt
6_MP_PDPN_Plus_2


title: CCR7 PDPN batch 1 replicate 1

description:
Library name: CCR7_PDPN_batch_1_replicate_1
featureCounts_mm10_ensembl_genes.txt
5_MP_PDPN_Plus_1


title: PHF23 WT HeLa, rep2

description: Library name: WT_2


title: PHF23 KO HeLa, rep1

description: Library name: KO_1


title: Wk12_Group4-6_GEM1_S6-2_GEX

description:
Library name: Wk12_Group4-6_GEM1_S6-2_GEX
GEX 5' mRNA library

value: B cells


title: HMEC2_cell1_kd

description: Library name: HMEC2


title: Wk12_Group4-6_GEM1_S6-2_HTO

description:
Library name: Wk12_Group4-6_GEM1_S6-2_HTO
HTO 5' mRNA library

value: HTO

value: TotalSeq-C0251 anti-Human Hashtag1 (r17021),TotalSeq-C0253 anti-Human Hashtag3 (r19038),TotalSeq-C0257 anti-Human Hashtag7 (r19069),TotalSeq-C0258 anti-Human Hashtag8 (r20041),TotalSeq-C0259 anti-Human Hashtag9 (r20045),TotalSeq-C0260 anti-Human Hashtag10 (r20082),TotalSeq-C5225 BV421 Streptavidin (Apex), TotalSeq-C5232 BV421 Streptavidin (10E8-GT12), TotalSeq-C0996 AF647 Streptavidin (N332-GT5), TotalSeq-C0997 AF647 Streptavidin (10E8-GT12)


title: PHF23 WT HeLa, rep1

description: Library name: WT_1

value: PHF23 WT


title: CCR7 batch 1 replicate 4

description:
Library name: CCR7_batch_1_replicate_4
featureCounts_mm10_ensembl_genes.txt
12_MP_PDPN_Minus_4

value: CCR7 overexpression


title: HMEC1_cell1_control

description: Library name: HMEC1

value: mammary epithelial cell

value: control


title: CCR7 batch 1 replicate 3

description:
Library name: CCR7_batch_1_replicate_3
featureCounts_mm10_ensembl_genes.txt
11_MP_PDPN_Minus_3


title: input, rep3

description: Library name: Input_3


title: pRS315-EM shuffle, 1.25h Rapamycin, replicate 2

city: Garching

first: Frauke

last: Huth

address: James-Franck Str. 1

department: Department of Biosciences

country: Germany

institute: Technical University Munich

description:
Library name: sample_R36
Rapamycin induced Abf1 Anchor-Away pRS315-EM shuffle, 1.25h Rapamycin, total RNA, replicate 2

data_processing:
The S.cerevisiae reference genome SacCer3 build R64-1-1 was used for alignment with STAR. Expression was quantified using rsem-calculate-expression.
Assembly: SacCer3 R64-1-1
Supplementary files format and content: Each file is a tab separated values file and contains the gene name (gene_id), transcripts per million (tpms) as well as absolute counts (counts).

organism: Saccharomyces cerevisiae

growth_protocol: The Abf1 anchor away strain ABF1-aa-V5 clone A9 was obtained from Wim de Jonge and Frank Holstege (de Jonge et al., Mol Syst Biol. 2020). The strain was transformed with pRS315-based plasmids encoding wildtype Abf1, select Abf1 constructs, or the empty pRS315 plasmid as a control. At least three independent clones were isolated and stored as glycerol cultures after transformation and used for biologically independent replicate experiments. Anchor away strains were grown to log phase, ca. OD600 of 0.4, in YNB –leucine media.

extract_protocol:
Total RNA was prepared with the RNeasy kit (Qiagen). 4 OD600 units of cells were washed with PBS (50 mM phosphate buffer pH 7, 150 mM NaCl) and flash frozen in liquid nitrogen. The cell wall was broken up by incubation with beta-mercaptoethanol and Zirconia bead-beating (6x 3 min 30 Hz with 3 min breaks). The cell lysate was cleared by centrifugation, mixed with ethanol, and bound to a column provided in the kit. The optional DNaseI digestion on the column was carried out. RNA was washed on the resin, eluted, and digested using DNase I in solution.
After ethanol precipitation, the total RNA preparation was converted into sequencing libraries with the NEBNext Ultra II directional RNA library prep kit for Illumina.

treatment_protocol: The strains were incubated for the indicated amount of time with 8 µg/mL rapamycin.

value: ABF1-aa-V5 clone A9

value: RNeasy kit (Qiagen) with DNaseI digestion; NEBNext Ultra II directional RNA library prep kit for Illumina.


title: e-miRNA_plasma_ICAD_120

city: Los Angeles

first: Nestor R.

last: Gonzalez

address: 127 S San Vicente Blvd

department: Neurosurgery

institute: Cedars Sinai Medical Center

description: Library name: 119202-120

data_processing:
Missing data was completed using a Multiple Imputation by Chained Equations (MICE)
All samples were analyzed in duplicate. The mean intra-assay coefficient of variation (CV) was maintained below 20%. Inter-assay CV was assessed using control samples across plates.
Supplementary files format and content: Processed data contains mature mi-RNA counts for each study subject.

source_name: plasma

extract_protocol:
Exosome extraction and purification: Plasma samples were centrifuged at 1500 rpm for 5 min for debris removal. For exosome isolation, a 1.5 ml Eppendorf tube was filled with supernatant. This was later combined with ExoQuick (System Biosciences, Palo Alto, CA) at a 1:4 ratio, incubated (30 min, 4 °C), and centrifuged for an additional 30 min.  Exosome total RNA isolation: The SeraMir Exosome RNA Purification Column kit (Cat #RA808A-1, System Biosciences, Palo Alto, CA) was used to isolate total RNA. Concentration of small RNA was measured with the Small RNA kit for Bioanalyzer 2100 Bioanalyzer Systems (Agilent, Santa Clara, CA). A concentration of 200 pg/ul small RNA was used for subsequent library generation.
The NGS library was generated using the CleanTag Small RNA Library Preparation Kit (TriLink, Cat# L-3206) and quantified using the High Sensitivity DNA Reagents (Agilent, Santa Clara, CA, PO# G2933-85004) and High Sensitivity DNA Chips (Agilent, Santa Clara, CA, PO# 5067–4626). NGS libraries were pooled using the TBE gel (Invitrogen by Life Technologies, Grand Island, NY, Ref# EC6215) and quantified using the High Sensitivity DNA 1000 Screen Tape (Agilent Technologies, Santa Clara, CA, PO # 5067–5584), High Sensitivity D1000 reagents (, Agilent Technologies, Santa Clara, CA, PO# 5067–5585), and the TailorMix HT1 qPCR assay (Cat# TM-505, SeqMatic, Union City, CA), followed by a NextSeq High Output single-end sequencing run at SR75 using NextSeq 500/550 High Output v2 kit (Illumina, San Diego, CA, Cat #FC-404-2005).

treatment_protocol: EDTA tubes were used to obtain blood samples. Following collection, the samples were separated by centrifugation at 3500 rpm for 15 minutes at a temperature of 4 °C. Subsequently, the plasma was carefully stored in 2 cc cryovials at -80 °C for preservation.

value: plasma

tag: disease

value: intracranial atherosclerosis


title: e-miRNA_plasma_ICAD_119

description: Library name: 119202-119


title: Wk12_Group3-5_GEM1_S6-3_HTO

description:
Library name: Wk12_Group3-5_GEM1_S6-3_HTO
HTO 5' mRNA library

value: Protein immunized

value: TotalSeq-C0251 anti-Human Hashtag1 (r18051),TotalSeq-C0253 anti-Human Hashtag3 (r18103),TotalSeq-C0257 anti-Human Hashtag7 (r19060),TotalSeq-C0258 anti-Human Hashtag8 (r15050),TotalSeq-C0259 anti-Human Hashtag9 (r18052),TotalSeq-C0260 anti-Human Hashtag10 (r18084), TotalSeq-C5225 BV421 Streptavidin (Apex), TotalSeq-C5232 BV421 Streptavidin (10E8-GT12), TotalSeq-C0996 AF647 Streptavidin (N332-GT5), TotalSeq-C0997 AF647 Streptavidin (10E8-GT12)


title: CCR7 batch 1 replicate 2

description:
Library name: CCR7_batch_1_replicate_2
featureCounts_mm10_ensembl_genes.txt
10_MP_PDPN_Minus_2

value: mouse mammary tumor cells

value: spontaneous tumor from C57BL/6 mice


title: Wk12_Group4-6_GEM1_S6-2_VDJ

description:
Library name: Wk12_Group4-6_GEM1_S6-2_VDJ
VDJ 5' mRNA library

value: VDJ


title: pRS315-NCS506, 1.25h Rapamycin, replicate 2

description:
Library name: sample_R34
Rapamycin induced Abf1 Anchor-Away pRS315-NCS506, 1.25h Rapamycin, total RNA, replicate 2


title: Wk12_Group4-6_GEM1_S6-3_HTO

description:
Library name: Wk12_Group4-6_GEM1_S6-3_HTO
HTO 5' mRNA library

value: PBMC

value: TotalSeq-C0251 anti-Human Hashtag1 (r18095),TotalSeq-C0253 anti-Human Hashtag3 (r19020),TotalSeq-C0257 anti-Human Hashtag7 (r19047),TotalSeq-C0258 anti-Human Hashtag8 (r20037),TotalSeq-C0259 anti-Human Hashtag9 (r20047),TotalSeq-C0260 anti-Human Hashtag10 (r21035), TotalSeq-C5225 BV421 Streptavidin (Apex), TotalSeq-C5232 BV421 Streptavidin (10E8-GT12), TotalSeq-C0996 AF647 Streptavidin (N332-GT5), TotalSeq-C0997 AF647 Streptavidin (10E8-GT12)


title: input, rep1

description: Library name: Input_1

value: HeLa

value: epithelial cell

value: Normal


title: Wk12_Group3-5_GEM1_S6-3_GEX

description:
Library name: Wk12_Group3-5_GEM1_S6-3_GEX
GEX 5' mRNA library

value: B cells

value: mRNA


title: CCR7 batch 1 replicate 1

description:
Library name: CCR7_batch_1_replicate_1
featureCounts_mm10_ensembl_genes.txt
9_MP_PDPN_Minus_1

value: CCR7 overexpression


title: e-miRNA_plasma_ICAD_118

description: Library name: 119202-118


title: pRS315-FUS(1-163)12E, 1.25h Rapamycin

description:
Library name: sample_R31
Rapamycin induced Abf1 Anchor-Away pRS315-FUS(1-163)12E, 1.25h Rapamycin, total RNA

value: ABF1-aa-V5 clone A9


title: Wk12_Group3-5_GEM1_S6-3_VDJ

description:
Library name: Wk12_Group3-5_GEM1_S6-3_VDJ
VDJ 5' mRNA library


title: X2 batch 2 replicate 4

description:
Library name: X2_batch_2_replicate_4
counts_batch_2.txt
ctrl_4

value: Vector control


title: e-miRNA_plasma_ICAD_117

description: Library name: 119202-117

value: plasma


title: pRS315-EM shuffle, 1.25h Rapamycin, replicate 1

description:
Library name: sample_R30
Rapamycin induced Abf1 Anchor-Away pRS315-EM shuffle, 1.25h Rapamycin, total RNA, replicate 1

value: RNeasy kit (Qiagen) with DNaseI digestion; NEBNext Ultra II directional RNA library prep kit for Illumina.


title: e-miRNA_plasma_ICAD_116

description: Library name: 119202-116

value: intracranial atherosclerosis


title: Wk12_Group3-5_GEM1_S6-2_HTO

description:
Library name: Wk12_Group3-5_GEM1_S6-2_HTO
HTO 5' mRNA library

value: Protein immunized

value: HTO

value: TotalSeq-C0251 anti-Human Hashtag1 (r18051),TotalSeq-C0253 anti-Human Hashtag3 (r18103),TotalSeq-C0257 anti-Human Hashtag7 (r19060),TotalSeq-C0258 anti-Human Hashtag8 (r15050),TotalSeq-C0259 anti-Human Hashtag9 (r18052),TotalSeq-C0260 anti-Human Hashtag10 (r18084), TotalSeq-C5225 BV421 Streptavidin (Apex), TotalSeq-C5232 BV421 Streptavidin (10E8-GT12), TotalSeq-C0996 AF647 Streptavidin (N332-GT5), TotalSeq-C0997 AF647 Streptavidin (10E8-GT12)


title: e-miRNA_plasma_ICAD_115

description: Library name: 119202-115


title: pRS315-NCS506, 1.25h Rapamycin, replicate 1

description:
Library name: sample_R28
Rapamycin induced Abf1 Anchor-Away pRS315-NCS506, 1.25h Rapamycin, total RNA, replicate 1


title: Wk12_Group3-5_GEM1_S6-2_GEX

description:
Library name: Wk12_Group3-5_GEM1_S6-2_GEX
GEX 5' mRNA library


title: pRS315 - no Abf1, 1.25h Rapamycin, replicate 3

description:
Library name: sample_R18
Rapamycin induced Abf1 Anchor-Away pRS315 - no Abf1, 1.25h Rapamycin, total RNA, replicate 3


title: X2 batch 2 replicate 3

description:
Library name: X2_batch_2_replicate_3
counts_batch_2.txt
ctrl_3

value: mouse mammary tumor cells

value: spontaneous tumor from C57BL/6 mice


title: e-miRNA_plasma_ICAD_114

description: Library name: 119202-114


title: Wk12_Group3-5_GEM1_S6-2_VDJ

description:
Library name: Wk12_Group3-5_GEM1_S6-2_VDJ
VDJ 5' mRNA library

value: PBMC

value: VDJ


title: e-miRNA_plasma_ICAD_113

description: Library name: 119202-113


title: pRS315 - no Abf1, 1.25h Rapamycin, replicate 2

description:
Library name: sample_R17
Rapamycin induced Abf1 Anchor-Away pRS315 - no Abf1, 1.25h Rapamycin, total RNA, replicate 2


title: X2 batch 2 replicate 2

description:
Library name: X2_batch_2_replicate_2
counts_batch_2.txt
ctrl_2


title: e-miRNA_plasma_ICAD_112

description: Library name: 119202-112


title: Wk12_Group1-2_GEM2_S6-3_HTO

description:
Library name: Wk12_Group1-2_GEM2_S6-3_HTO
HTO 5' mRNA library

value: TotalSeq-C0251 anti-Human Hashtag1 (r19010),TotalSeq-C0253 anti-Human Hashtag3 (rh3035), TotalSeq-C0257 anti-Human Hashtag7 (rh3078), TotalSeq-C0258 anti-Human Hashtag8 (r19087), TotalSeq-C0259 anti-Human Hashtag9 (r20088), TotalSeq-C0260 anti-Human Hashtag10 (rh3092), TotalSeq-C5225 BV421 Streptavidin (Apex), TotalSeq-C5232 BV421 Streptavidin (10E8-GT12), TotalSeq-C0996 AF647 Streptavidin (N332-GT5), TotalSeq-C0997 AF647 Streptavidin (10E8-GT12)


title: Wk12_Group1-2_GEM2_S6-3_GEX

description:
Library name: Wk12_Group1-2_GEM2_S6-3_GEX
GEX 5' mRNA library


title: X2 batch 1 replicate 4

description:
Library name: X2_batch_1_replicate_4
featureCounts_mm10_ensembl_genes.txt
4_MP_Control_4


title: X2 batch 1 replicate 3

description:
Library name: X2_batch_1_replicate_3
featureCounts_mm10_ensembl_genes.txt
3_MP_Control_3


title: X2 batch 2 replicate 1

description:
Library name: X2_batch_2_replicate_1
counts_batch_2.txt
ctrl_1


title: e-miRNA_plasma_ICAD_111

description: Library name: 119202-111


title: Wk12_Group1-2_GEM2_S6-3_VDJ

description:
Library name: Wk12_Group1-2_GEM2_S6-3_VDJ
VDJ 5' mRNA library


title: X2 batch 1 replicate 2

description:
Library name: X2_batch_1_replicate_2
featureCounts_mm10_ensembl_genes.txt
2_MP_Control_2


title: pRS315-FUS(1-163)12E YM, 1.25h Rapamycin, replicate 1

description:
Library name: sample_R27
Rapamycin induced Abf1 Anchor-Away pRS315-FUS(1-163)12E YM, 1.25h Rapamycin, total RNA, replicate 1


title: X2 batch 1 replicate 1

description:
Library name: X2_batch_1_replicate_1
featureCounts_mm10_ensembl_genes.txt
1_MP_Control_1


title: e-miRNA_plasma_ICAD_108

description: Library name: 119202-108

tag: phenotype

value: Non-Hemodynamic

tag: Sex

value: Male

tag: history of_diabetes

value: yes

tag: history of_hypertension

tag: history of_hypercholesterolemia

tag: baseline modified_rankin_scale_(mrs)

tag: vegf 165b+

tag: vegf (pg/ml)

tag: hgf (pg/ml)

tag: endostatin (ng/ml)

tag: angiostatin+ (ng/ml)


title: e-miRNA_plasma_ICAD_109

description: Library name: 119202-109

tag: tissue

value: Female

value: no


title: pRS315-IDR2, 1.25h Rapamycin

description:
Library name: sample_R26
Rapamycin induced Abf1 Anchor-Away pRS315-IDR2, 1.25h Rapamycin, total RNA

tag: genotype

value: ABF1-aa-V5 clone A9


title: Wk12_Group1-2_GEM2_S6-2_GEX

description:
Library name: Wk12_Group1-2_GEM2_S6-2_GEX
GEX 5' mRNA library

tag: cell type

value: B cells

tag: treatment

tag: library type

value: mRNA


title: pRS315-FUS(1-163)12E aromatic clusters, 1.25h Rapamycin, replicate 2

description:
Library name: sample_R24
Rapamycin induced Abf1 Anchor-Away pRS315-FUS(1-163)12E aromatic clusters, 1.25h Rapamycin, total RNA, replicate 2

tag: cell line

value: RNeasy kit (Qiagen) with DNaseI digestion; NEBNext Ultra II directional RNA library prep kit for Illumina.

tag: batch


title: e-miRNA_plasma_ICAD_107

description: Library name: 119202-107

value: plasma

tag: phenotype

tag: disease

value: intracranial atherosclerosis

tag: Sex


title: pic43_Young_replicate 1-4

city: Suita

first: Daneil

last: Semmy

state: Osaka

address: Yamadaoka 3-1

department: Homeostatic Regulation

country: Japan

institute: Osaka University Research Institute for Microbial Diseases

description:
Library name: pic43_Young
Skin basal layer of the fin

data_processing:
The barcodes and unique-molecular-identifiers in the reads were extracted using UMI-tools (version 1.0.0) with the command: umi_tools extract -I r1.fastq --read2-in=r2.fastq --bc-pattern=NNNNNNCCCCCC --read2-stdout.
The reads were mapped by the aligning software HISAT2 (version 2.1.0) to the reference genome (Nfu_20140520).
Read counts per gene was performed with featureCounts (version 1.6.4) and UMI-tools with the command: umi_tools count --method=directional --per-gene --per-cell --gene-tag=XT.
The duplicates in unique molecular identifiers were discarded.
Using the resulting counts, differentially expressed genes (those with adjusted p-values < 0.1) were extracted by the R library DESeq2 (version 1.20.0).
Assembly: GRZ Assembly (05/2015); https://nfingb.leibniz-fli.de/
Supplementary files format and content: count matrix:CSV
Library strategy: CEL-seq2

organism: Nothobranchius furzeri

source_name: Skin basal layer of the fin

extract_protocol:
Lysis solution(0.1% Tween and 400 ug/ml of ProteinaseK in PBS) were loaded onto the specimens and incubated for 30 min at 55°C cDNA;mRNA hybrids were purified with QIAGEN Mini Elute PCR Purification Kit.
All subsequent steps are according to the CEL-seq2 method as follows: Second strand DNA is synthesized by nick translation method using RNase H, DNA polymerase I, and DNA ligase mix, by which only the cDNAs derived from the photo-irradiated region are filled-in to the 5' end of T7 promoter, thereby allowing the cDNAs to be linearly amplified as RNAs (aRNAs) by IVT reaction. The libraries are further reverse-transcribed, followed by paired-end sequencing on the Illumina platform.

treatment_protocol: Control young and control aged killfish were submerged in DMSO, while aged treated killifish were treated with tunicamycin 1ug/mL for one night.Tissue samples were frozen and sectioned and then permeabilized in TE buffer preheated to 70°C for 1 hour in staining jar and then cooled down in PBS for 3 minutes. Reverse transcription was performed by adding UV-responsive 6-nitropiperonyloxymethyl-caged reverse transcription primers containing T7 promotor, unique molecular identifiers (UMIs), multiple barcodes, and poly T sequence to the trunk and fin sections. Immunofluorescence of p63 were conducted as described above to visualize epidermal basal layer for UV irradiation. p63 positive cells in epidermal basal layer were irradiated with UV light for 3 min with a Digital Micromirror Device (Polygon 1000-G, Mightex) to uncage 6-nitropiperonyloxymethyl moieties from reverse transcription primers.

value: Skin basal layer of the fin

value: Nothobranchius furzeri


title: pic43_Aged_Tnc_replicate 1-3

description:
Library name: pic43_Aged_Tnc
Skin basal layer of the fin


title: pRS315-FUS(1-163)12E aromatic clusters, 1.25h Rapamycin, replicate 1

description:
Library name: sample_R23
Rapamycin induced Abf1 Anchor-Away pRS315-FUS(1-163)12E aromatic clusters, 1.25h Rapamycin, total RNA, replicate 1


title: Wk12_Group1-2_GEM2_S6-2_VDJ

description:
Library name: Wk12_Group1-2_GEM2_S6-2_VDJ
VDJ 5' mRNA library

value: Protein immunized


title: Wk12_Group1-2_GEM1_S6-3_HTO

description:
Library name: Wk12_Group1-2_GEM1_S6-3_HTO
HTO 5' mRNA library

value: PBMC

value: HTO

tag: hto


title: pRS315-LS15, 1.25h Rapamycin, replicate 2

description:
Library name: sample_R22
Rapamycin induced Abf1 Anchor-Away pRS315-LS15, 1.25h Rapamycin, total RNA, replicate 2


title: e-miRNA_plasma_ICAD_106

description: Library name: 119202-106

tag: history of_diabetes

tag: history of_hypertension

tag: history of_hypercholesterolemia

tag: baseline modified_rankin_scale_(mrs)


title: pRS315 - no Abf1, 1.25h Rapamycin, replicate 1

description:
Library name: sample_R16
Rapamycin induced Abf1 Anchor-Away pRS315 - no Abf1, 1.25h Rapamycin, total RNA, replicate 1


title: pic43_Aged_replicate 1-4

description:
Library name: pic43_Aged
Skin basal layer of the fin


title: pRS315-FUS(1-163)12E YM, 1.25h Rapamycin, replicate 2

description:
Library name: sample_R33
Rapamycin induced Abf1 Anchor-Away pRS315-FUS(1-163)12E YM, 1.25h Rapamycin, total RNA, replicate 2


title: e-miRNA_plasma_ICAD_104

description: Library name: 119202-104

tag: vegf 165b+

tag: vegf (pg/ml)

tag: hgf (pg/ml)

tag: endostatin (ng/ml)


title: Wk12_Group1-2_GEM1_S6-3_VDJ

description:
Library name: Wk12_Group1-2_GEM1_S6-3_VDJ
VDJ 5' mRNA library

tag: tissue

tag: cell type

value: VDJ


title: e-miRNA_plasma_ICAD_105

description: Library name: 119202-105

value: Non-Hemodynamic

tag: angiostatin+ (ng/ml)


title: pRS315-Gal4(768-881), 1.25h Rapamycin, replicate 2

description:
Library name: sample_R20
Rapamycin induced Abf1 Anchor-Away pRS315-Gal4(768-881), 1.25h Rapamycin, total RNA, replicate 2

tag: cell line

tag: genotype

tag: treatment


title: Donor 1206 , bulk CD4 T cells

city: Gif-sur-Yvette

first: Stephane

last: Hua

address: Porte Nord RD36

institute: Commissariat à l'Energie Atomique et aux Energies Renouvelables

description:
Library name: 1206_total
1206_Total_Vf.txt

data_processing:
After sequencing quality filtering, the clean data was aligned to against the international ImMunoGeneTics library using the MiXCR v4.2.0 tool. The high-quality reads were further assembled into clonotypes, correctiong for PCR and sequencing errors. The downstream analysis was performed with MIXCR, “immunarch” R package and in house R script
Assembly: IMGT
Supplementary files format and content: text file includes raw counts of clonotypes for each sample, linked to the correponding *'not stimulated' sample records (when generated from both stimulated and not-stimulated samples)
Library strategy: TCR-Seq

molecule: other

source_name: blood

growth_protocol: PBMCs were seeded at 2x10^6 cells/mL in a 6-well plate in the presence of the peptide HA or EBNA peptide in RPMI 1640 medium supplemented with 5% human AB serum, IL-2, IL-4 and anti-CD28. The medium was changed every 2–3 days with the same medium supplemented with IL-2 and IL-4 and at day 8, medium was changed for the same medium without cytokines. At day 10, cells were washed and incubated with and without peptide and 24 hours later cells were stainedand sorted on a FACS ARIA III cytometer

extract_protocol:
RNA was extracted from pellets of expanded CD4 cells and circulating CD4 cells using the RNeasy PLUS microkit (Qiagen)
RNA was reverse transcribed using a TCRB chain constant region reverse primer with Superscript IV First-Strand Synthesis System. cDNA was column purified with the Oligo Clean Concentrator kit. cDNA of TCRB chain was used as template for PCR with KAPA2G Fast Multiplex Mix. Forward TCRB primers were used with a single nested TCRB constant region reverse primer. Samples underwent 20 cycles for NGS library preparation for PCR1. For PCR2, 2 µL of PCR1 was added to 18 µL of PCR2 master mix (0.25 µM each i5 and i7 sample barcoding primers) and underwent 20 cycles with the use of Herculase II fusion DNA Polymerase. PCR2 product was then run on agarose gel (2%) and desired band were purified using a GeneJet PCR Purification kit (ThermoFisher Scientific).

value: blood

tag: subject id

value: Donor 1206

value: bulk CD4 T cells


title: Donor 1078 , bulk CD4 T cells

description:
Library name: 1078_total
1078_Total_Vf.txt

value: Donor 1078


title: Wk12_Group1-2_GEM1_S6-3_GEX

description:
Library name: Wk12_Group1-2_GEM1_S6-3_GEX
GEX 5' mRNA library

tag: library type


title: Wk12_Group1-2_GEM2_S6-2_HTO

description:
Library name: Wk12_Group1-2_GEM2_S6-2_HTO
HTO 5' mRNA library

tag: hto

value: TotalSeq-C0251 anti-Human Hashtag1 (r17016), TotalSeq-C0253 anti-Human Hashtag3 (r18027),TotalSeq-C0257 anti-Human Hashtag7 (r18097), TotalSeq-C0258 anti-Human Hashtag8 (r17011), TotalSeq-C0259 anti-Human Hashtag9 (r17019), TotalSeq-C0260 anti-Human Hashtag10 (r18104), TotalSeq-C5225 BV421 Streptavidin (Apex), TotalSeq-C5232 BV421 Streptavidin (10E8-GT12), TotalSeq-C0996 AF647 Streptavidin (N332-GT5), TotalSeq-C0997 AF647 Streptavidin (10E8-GT12)


title: e-miRNA_plasma_ICAD_103

description: Library name: 119202-103

tag: phenotype

tag: disease

tag: Sex

value: Female

tag: history of_diabetes

value: no

value: yes


title: Wk12_Group1-2_GEM1_S6-2_HTO

description:
Library name: Wk12_Group1-2_GEM1_S6-2_HTO
HTO 5' mRNA library

value: B cells


title: e-miRNA_plasma_ICAD_102

description: Library name: 119202-102

value: plasma

value: intracranial atherosclerosis

value: Male

tag: history of_hypertension

tag: history of_hypercholesterolemia

tag: baseline modified_rankin_scale_(mrs)

tag: vegf 165b+


title: Donor 1239 , bulk CD4 T cells

description:
Library name: 1239_total
1239_Total_Vf.txt

tag: tissue

value: Donor 1239


title: Wk12_Group1-2_GEM1_S6-2_GEX

description:
Library name: Wk12_Group1-2_GEM1_S6-2_GEX
GEX 5' mRNA library

value: PBMC

tag: cell type

value: Protein immunized

value: mRNA


title: pRS315-WT Abf1, 1.25h Rapamycin

description:
Library name: sample_R32
Rapamycin induced Abf1 Anchor-Away pRS315-WT Abf1, 1.25h Rapamycin, total RNA

value: ABF1-aa-V5 clone A9

value: RNeasy kit (Qiagen) with DNaseI digestion; NEBNext Ultra II directional RNA library prep kit for Illumina.

tag: batch


title: pRS315-Gal4(768-881), 1.25h Rapamycin, replicate 1

description:
Library name: sample_R19
Rapamycin induced Abf1 Anchor-Away pRS315-Gal4(768-881), 1.25h Rapamycin, total RNA, replicate 1

tag: cell line


title: e-miRNA_plasma_ICAD_101

description: Library name: 119202-101

value: Non-Hemodynamic

tag: vegf (pg/ml)

tag: hgf (pg/ml)

tag: endostatin (ng/ml)

tag: angiostatin+ (ng/ml)


title: Wk12_Group1-2_GEM1_S6-2_VDJ

description:
Library name: Wk12_Group1-2_GEM1_S6-2_VDJ
VDJ 5' mRNA library

tag: treatment

tag: library type

value: VDJ


title: G_ND53

type: genomic

city: Nuthetal

first: Heike

last: Vogel

state: BRB

address: Arthur-Scheunert-Allee 114-116

department: Department of Experimental Diabetology

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

hyb_protocol: Genomic DNA was bisulfite converted, amplified, fragmented, hybridized onto the Infinium Mouse Methylation BeadChip using standard Illumina protocol

scan_protocol: Standard Illumina Pipeline

data_processing:
sesame package (v 1.14.2) in R environment (v 4.2.0)
Beta values

label: other

source_name: Gonadal white adipise tissue

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was isolated using the ReliaPrep™ gDNA Tissue Miniprep System (Promega) as per the manufacturer’s instructions

value: Gonadal white adipise tissue

tag: strain

value: NZO

tag: disease state

value: diabetes-prone


title: Donor 1237 , bulk CD4 T cells

description:
Library name: 1237_total
1237_Total_Vf.txt

value: blood

tag: subject id

value: Donor 1237

value: bulk CD4 T cells


title: e-miRNA_plasma_ICAD_100

description: Library name: 119202-100

value: plasma

tag: phenotype

value: Hemodynamic

tag: disease

tag: Sex

value: Female

tag: history of_diabetes

value: no

tag: history of_hypertension

value: yes


title: G_ND5

tag: tissue


title: delHfq, t4rnl1, totalRNA, 2

city: Bethesda

first: Caroline

last: Esnault

state: md

address: 9000 Rockville Pike,

institute: NICHD NIH

description: Library name: delHfq_t4rnl1_totalRNA_2

data_processing:
RNA-RNA interactions were determined by identifying chimeric reads in the RIL-seq sequence reads. FASTQ files were processed through a Snakemake RIL-seq analysis pipeline, based on the Github repositories lcdb-wf v1.10.2 https://github.com/lcdb/lcdb-wf and RIL-seq v0.82 https://github.com/asafpr/RIL-seq. Briefly, FASTQ files were demultiplexed using cutadapt v4.3 with the parameters ‘--error-rate=0.2 --overlap=9’, then cutadapt was run a second time for adapter-trimming and quality-filtering with the parameters '--nextseq-trim 20 --overlap 6 --minimum-length 25'. Trimmed FASTQ files mapped to the E. coli genome GCF_000005845.2 ASM584v2 with the RIL-seq command map_single_fragments.py with default parameters besides '--feature exon --create_wig'.  Chimeric reads were characterized with RIL-seq map_chimeric_fragments.py with the parameter '-r' for reverse stranded library. Significant regions were identified with RIL-seq RILseq_significant_regions.py with the parameters '--total_reverse ' (reverse-stranded library), '--ribozero ' (to remove rRNA prior to the statistical analysis) and '--BC_chrlist "chr"' (to only consider chromosome chr). Non-specific chimeras were identified as outside of significant interaction regions and filtered out.
Assembly: E. coli GCF_000005845.2 ASM584v2
Supplementary files format and content: .wig files correspond to the read coverage of all mapped fragments (chimera and single fragments)
Supplementary files format and content: .bed files gives the coordinates of the significant chimeric fragments identified by RILseq.
Supplementary files format and content: .txt file of raw counts, from featurecounts

organism: Escherichia coli

source_name: delHfq

growth_protocol: A single colony of each transformant was picked and inoculated in 10 ml of LB (Lennox) medium supplemented with 100 µg/ml ampicillin, then grown overnight at 37°C with agitation. The overnight cultures were diluted into 80 ml of fresh medium to an OD600 of 0.05 and incubated at 37°C with agitation. When OD600 reached 0.5, 0.2% arabinose was added to induce T4 RNA Ligase I expression. Cultures were further grown until the OD600 reached approximately 1.0, at which point 20 OD600 units of cells were collected by centrifugation at 5000 rpm for 10 minutes at 4°C.

extract_protocol:
The cells were lysed by vortexing with 212-300 mm glass beads (Sigma) in a total volume of 2 ml lysis buffer (20 mM Tris-HCl/pH 8.0, 150 mM KCl, 1 mM MgCl2 and 1 mM DTT). Isolation of total RNA and Hfq co-IP RNA was performed as described previously. 1.9 ml of cell lysate were mixed with 100 µl of Hfq antibody and 120 mg of protein A-Sepharose CL-4B (GE Healthcare). Hfq co-IP RNA was isolated from protein A-Sepharose beads by extraction with phenol:chloroform:isoamyl alcohol (25:24:1), followed by ethanol precipitation. Total RNA was isolated from 100 µl of cell lysate by Trizol (ThermoFisher Scientific) extraction followed by chloroform extraction and isopropanol precipitation. RNA was dissolved in 15 µl of DEPC water.
cDNA libraries were constructed based on a protocol adapted to capture the bacterial sRNAs as well as mRNAs (Melamed et al., 2018, Nat. Protoc., 13, 1-33). 400 ng of total RNA or Hfq co-IP RNA was used as input for cDNA synthesis, with total RNA serving as input for Hi-GRIL-seq and Hfq co-IP RNA for iRIL-seq. Ribosomal RNA was depleted using DASH protocol. 12 cycles of PCR were performed at the last step to enrich each library.

tag: condition

value: delHfq

tag: antibody

value: input

tag: plasmid


title: pRS315-LS15, 1.25h Rapamycin, replicate 1

description:
Library name: sample_R21
Rapamycin induced Abf1 Anchor-Away pRS315-LS15, 1.25h Rapamycin, total RNA, replicate 1

tag: cell line

tag: genotype

value: ABF1-aa-V5 clone A9

tag: batch


title: e-miRNA_plasma_ICAD_99

description: Library name: 119202-99

value: intracranial atherosclerosis

value: Male

tag: history of_hypercholesterolemia

tag: baseline modified_rankin_scale_(mrs)

tag: vegf 165b+

tag: vegf (pg/ml)

tag: hgf (pg/ml)

tag: endostatin (ng/ml)

tag: angiostatin+ (ng/ml)


title: delHfq, t4rnl1, totalRNA, 1

description: Library name: delHfq_t4rnl1_totalRNA_1


title: Donor 1072 , bulk CD4 T cells

description:
Library name: 1072_total
1072_Total_Vf.txt

tag: subject id

value: Donor 1072

tag: cell type


title: e-miRNA_plasma_ICAD_98

description: Library name: 119202-98

tag: phenotype

tag: disease

tag: Sex

tag: history of_diabetes

tag: history of_hypertension


title: G_ND27

tag: tissue

value: Gonadal white adipise tissue

tag: strain

tag: disease state


title: e-miRNA_plasma_ICAD_97

description: Library name: 119202-97

tag: history of_hypercholesterolemia


title: G_ND15

value: NZO


title: delHfq, ctrlplasmid, totalRNA, 1

description: Library name: delHfq_ctrlplasmid_totalRNA_1

tag: condition

tag: cell line

tag: antibody

tag: plasmid

value: ctrlplasmid


title: delHfq, ctrlplasmid, totalRNA, 2

description: Library name: delHfq_ctrlplasmid_totalRNA_2


title: e-miRNA_plasma_ICAD_96

description: Library name: 119202-96

value: Non-Hemodynamic

tag: baseline modified_rankin_scale_(mrs)

tag: vegf 165b+

tag: vegf (pg/ml)

tag: hgf (pg/ml)

tag: endostatin (ng/ml)


title: Donor 1205 , bulk CD4 T cells

description:
Library name: 1205_total
1205_Total_Vf.txt

value: blood

tag: subject id

value: Donor 1205

tag: cell type


title: Donor 1073 , bulk CD4 T cells

description:
Library name: 1073_total
1073_Total_Vf.txt

value: Donor 1073

value: bulk CD4 T cells


title: Hfq-R16A, plasmid t4rnl1, totalRNA, 2

description: Library name: R16A_t4rnl1_totalRNA_2


title: Donor 1059 , bulk CD4 T cells

description:
Library name: 1059_total
1059_Total_Vf.txt

value: Donor 1059


title: G_ND14

tag: Sex

value: Female

value: diabetes-prone


title: Donor 1238 , bulk CD4 T cells

description:
Library name: 1238_total
1238_Total_Vf.txt

value: Donor 1238


title: e-miRNA_plasma_ICAD_95

description: Library name: 119202-95

value: plasma

tag: phenotype

tag: disease

tag: history of_diabetes

value: no

tag: history of_hypertension

value: yes

tag: angiostatin+ (ng/ml)


title: Hfq-R16A, plasmid t4rnl1, totalRNA, 1

description: Library name: R16A_t4rnl1_totalRNA_1

tag: condition

value: input


title: Donor 1171 , bulk CD4 T cells

description:
Library name: 1171_total
1171_Total_Vf.txt

tag: tissue

value: Donor 1171


title: G_ND86

value: Gonadal white adipise tissue

tag: strain

tag: disease state

value: diabetes-resistant


title: e-miRNA_plasma_ICAD_94

description: Library name: 119202-94

value: intracranial atherosclerosis

tag: history of_hypercholesterolemia

tag: baseline modified_rankin_scale_(mrs)


title: G_ND84

value: NZO


title: Hfq-R16A, plasmid t4rnl1, IP, 2

description: Library name: R16A_t4rnl1_IP_2

tag: cell line

tag: antibody

value: antiHfq

tag: plasmid


title: Donor 1079 , bulk CD4 T cells

description:
Library name: 1079_total
1079_Total_Vf.txt

value: blood

tag: subject id

value: Donor 1079


title: Donor 1170 , bulk CD4 T cells

description:
Library name: 1170_total
1170_Total_Vf.txt

value: Donor 1170

tag: cell type

value: bulk CD4 T cells


title: G_ND49

tag: Sex

value: Female


title: Hfq-R16A, plasmid t4rnl1, IP, 1

description: Library name: R16A_t4rnl1_IP_1


title: G_ND78


title: Donor 1198 , bulk CD4 T cells

description:
Library name: 1198_total
1198_Total_Vf.txt

value: Donor 1198


title: e-miRNA_plasma_ICAD_92

description: Library name: 119202-92

tag: phenotype

value: Non-Hemodynamic

value: Male

tag: vegf 165b+

tag: vegf (pg/ml)

tag: hgf (pg/ml)

tag: endostatin (ng/ml)


title: Donor 1239, stimulated with HA

description:
Library name: 1239_HA_POS
VF_1239_HA.txt

value: Donor 1239

value: CD4 T cells

tag: treatment

value: stimulated with HA


title: Hfq-R16A, ctrlplasmid, totalRNA, 2

description: Library name: R16A_ctrlplasmid_totalRNA_2

tag: condition

value: input

value: ctrlplasmid


title: e-miRNA_plasma_ICAD_91

description: Library name: 119202-91

tag: tissue

value: plasma

value: Hemodynamic

tag: disease

tag: history of_diabetes

value: no

tag: history of_hypertension

value: yes

tag: angiostatin+ (ng/ml)


title: G_ND66

value: Gonadal white adipise tissue

tag: strain

value: NZO

tag: disease state

value: diabetes-resistant


title: Donor 1239, not stimulated with HA

description:
Library name: 1239_HA_NEG
VF_1239_HA.txt

value: blood

tag: subject id

value: not stimulated with HA


title: G_ND61

value: Female


title: e-miRNA_plasma_ICAD_90

description: Library name: 119202-90

value: Non-Hemodynamic

value: intracranial atherosclerosis

tag: history of_hypercholesterolemia

tag: baseline modified_rankin_scale_(mrs)


title: Hfq-R16A, ctrlplasmid, totalRNA, 1

description: Library name: R16A_ctrlplasmid_totalRNA_1

tag: cell line

tag: antibody

tag: plasmid


title: Donor 1239, stimulated with EBNA

description:
Library name: 1239_EBNA_POS
VF_1239_EBNA.txt

value: Donor 1239

tag: cell type

value: stimulated with EBNA


title: Hfq-R16A, ctrlplasmid, IP, 2

description: Library name: R16A_ctrlplasmid_IP_2

value: antiHfq


title: WT-Hfq, plasmid t4rnl1, totalRNA, 2

description: Library name: Hfq_t4rnl1_totalRNA_2

source_name: WT-Hfq

value: WT-Hfq

value: input


title: Donor 1238, stimulated with HA

description:
Library name: 1238_HA_POS
VF_1238_HA.txt

value: Donor 1238

value: CD4 T cells

value: stimulated with HA


title: e-miRNA_plasma_ICAD_89

description: Library name: 119202-89

value: plasma

tag: phenotype

tag: Sex

value: Male

value: no

value: yes

tag: vegf 165b+

tag: vegf (pg/ml)

tag: hgf (pg/ml)

tag: endostatin (ng/ml)


title: Hfq-R16A, ctrlplasmid, IP, 1

description: Library name: R16A_ctrlplasmid_IP_1

tag: condition

value: ctrlplasmid


title: replicate 5 citalopram 250ug/L exposed (0-24hpf) total RNA at 48hpf

city: Bozeman

first: Christa

last: Merzdorf

state: Montana

address: 109 Lewis Hall

department: MCB

institute: Montana State University

description:
Library name: R5_250
S25

data_processing:
Sequenced by NovaGene via Novaseq X Plus Platform paired end reads
Raw reads are available as the fq.gz files
Trimmed via trimmomatic, and ran through rCorrector, then mapped to GRCz11 (ensemble) constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files
Assembly: GRCz11
Supplementary files format and content: txt files of aggregated count matrixes

organism: Danio rerio

source_name: Total embryo (50 embryos)

growth_protocol: zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C

extract_protocol:
Trizol Chloroform extraction of total RNA followed by Dnase I treatment, and Monarch RNA cleanup kit (T2030L). All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100
Zymo-Seq RiboFree Total RNA library Kit (R30003)

treatment_protocol: one of the following conditions: fentanyl effluent (FE; 0.629 pg/mL), fentanyl therapeutic (FT; 3.14 ng/mL), oxycodone effluent (OE; 10.6 pg/mL), oxycodone therapeutic (OT; 35.14 ng/mL), Control. Opioid exposed embryos were exposed from 0 to 24 hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.

tag: tissue

value: Total embryo (50 embryos)

tag: genotype

value: WT

tag: treatment

value: 250 ug/L Citalopram

tag: batch


title: e-miRNA_plasma_ICAD_88

description: Library name: 119202-88

value: Non-Hemodynamic

tag: disease

value: intracranial atherosclerosis

tag: history of_diabetes

tag: history of_hypertension

tag: history of_hypercholesterolemia

tag: angiostatin+ (ng/ml)


title: e-miRNA_plasma_ICAD_93

description: Library name: 119202-93

tag: baseline modified_rankin_scale_(mrs)


title: e-miRNA_plasma_ICAD_87

description: Library name: 119202-87

tag: phenotype

value: Female


title: Dissociated granuloma tissue from *AB (WT) zebrafish

city: Durham

first: David

last: Tobin

state: North Carolina

address: 207 Research Drive

institute: Duke University

description:
Library name: WT
10X Genomics

data_processing:
The Molecular Genomics Core’s standard analytical pipeline was used for single cell RNAseq analysis. Briefly, raw compressed base call (CBCL) files generated by an Illumina sequencer were demultiplexed into FASTQ, then aligned to the Ensembl zebrafish genome assembly GRCz11.113. Filtering, barcode and UMI counting were performed using the most current version of 10X’s Cell Ranger software. The R package Seurat was used to perform quality control and linear dimensional reduction. Datasets were integrated using FindIntegrationAnchors() and JoinLayers(). Cells were clustered de novo for unbiased cell type discovery using Seurat’s FindNeighbors() and FindClusters() functions, graph-based clustering approach with visualization of cells being achieved through the use of UMAP plots. Cluster specific markers were generated by FindConservedMarkers() and differentially expressed genes between datasets were generated by FindMarkers(). Expression of canonical gene markers were used to annotate clusters with specific cell types
Assembly: Zebrafish GRCz11.113
Supplementary files format and content: Tab-separated values and matrix files

source_name: Granuloma

extract_protocol:
Granulomas were extracted from infected zebrafish and transferred to a 1.5 mL tube. Cells were dissociated using 1 mL of 0.05% trypsin/EDTA (ThermoFisher Scientific, 25300054) at 30 C for 35 minutes with rocking. Cells were then collected by centrifugation for 5 min at 300 xg, resuspended in 1x DPBS with 10% FBS on ice, and passed through a 40 mm strainer.
Single-cell suspenions were submitted to the Molecular Genomics Core at Duke Molecular Physiology Institute for library preparation using Chromium GEM-X 3' chemistry on the 10X Genomics platform. Libraries were sequenced at the Duke Center for Genomic and Computational Biology.

treatment_protocol: Infection with approximately ~417  fluorescent bodies of wildtype Mycobacterium marinum.

value: Granuloma

tag: cell type

value: immune and stromal cells

value: *AB (WT)


title: WT-Hfq, plasmid t4rnl1, totalRNA, 1

description: Library name: Hfq_t4rnl1_totalRNA_1

tag: cell line

value: WT-Hfq

tag: antibody

value: input

tag: plasmid


title: Donor 1238, not stimulated with HA

description:
Library name: 1238_HA_NEG
VF_1238_HA.txt

value: blood

tag: subject id

value: Donor 1238

value: CD4 T cells

value: not stimulated with HA


title: replicate 4 citalopram 250ug/L exposed (0-24hpf) total RNA at 48hpf

description:
Library name: R4_250
S20


title: e-miRNA_plasma_ICAD_86

description: Library name: 119202-86

value: plasma

tag: Sex

value: Male

value: no

value: yes

tag: vegf 165b+

tag: vegf (pg/ml)

tag: hgf (pg/ml)

tag: endostatin (ng/ml)


title: Donor 1238, stimulated with EBNA

description:
Library name: 1238_EBNA_POS
VF_1238_EBNA.txt

tag: tissue

tag: treatment

value: stimulated with EBNA


title: replicate 3 citalopram 250ug/L exposed (0-24hpf) total RNA at 48hpf

description:
Library name: R3_250
S15

value: Total embryo (50 embryos)

tag: genotype

value: WT

value: 250 ug/L Citalopram

tag: batch


title: e-miRNA_plasma_ICAD_85

description: Library name: 119202-85

value: Non-Hemodynamic

tag: disease

value: intracranial atherosclerosis

tag: history of_diabetes

tag: history of_hypertension

tag: history of_hypercholesterolemia

tag: angiostatin+ (ng/ml)


title: WT-Hfq, plasmid t4rnl1, IP, 1

description: Library name: Hfq_t4rnl1_IP_1

tag: condition

tag: cell line

tag: antibody

value: antiHfq


title: replicate 2 citalopram 250ug/L exposed (0-24hpf) total RNA at 48hpf

description:
Library name: R2_250
S10


title: Donor 1238, not stimulated with EBNA

description:
Library name: 1238_EBNA_NEG
VF_1238_EBNA.txt

tag: subject id

tag: cell type

value: not stimulated with EBNA


title: G_ND25

value: Gonadal white adipise tissue

tag: strain

value: NZO

tag: Sex

value: Female

tag: disease state

value: diabetes-resistant


title: WT-Hfq, ctrlplasmid, totalRNA, 2

description: Library name: Hfq_ctrlplasmid_totalRNA_2

value: WT-Hfq

value: input

tag: plasmid

value: ctrlplasmid


title: e-miRNA_plasma_ICAD_82

description: Library name: 119202-82

tag: tissue

value: plasma

tag: phenotype

tag: baseline modified_rankin_scale_(mrs)

tag: vegf 165b+

tag: vegf (pg/ml)

tag: hgf (pg/ml)

tag: endostatin (ng/ml)


title: WT-Hfq, ctrlplasmid, totalRNA, 1

description: Library name: Hfq_ctrlplasmid_totalRNA_1


title: WT-Hfq, plasmid t4rnl1, IP, 2

description: Library name: Hfq_t4rnl1_IP_2


title: WT-Hfq, ctrlplasmid, IP, 2

description: Library name: Hfq_ctrlplasmid_IP_2