title: e-miRNA_plasma_ICAD_80

description: Library name: 119202-80

tag: disease

value: Male

tag: history of_diabetes

value: no

tag: history of_hypertension

value: yes

tag: history of_hypercholesterolemia

tag: angiostatin+ (ng/ml)


title: Donor 1237, stimulated with EBNA

status: Public on Dec 17 2025

type: SRA

city: Gif-sur-Yvette

first: Stephane

last: Hua

address: Porte Nord RD36

country: France

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

description:
Library name: 1237_EBNA_POS
VF_1237_EBNA.txt

library_source: other

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

organism: Homo sapiens

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).

tag: tissue

value: blood

tag: subject id

value: Donor 1237

tag: cell type

value: CD4 T cells

tag: treatment

value: stimulated with EBNA


title: replicate 4 citalopram 50ug/L exposed (0-24hpf) total RNA at 48hpf

city: Bozeman

first: Christa

last: Merzdorf

state: Montana

address: 109 Lewis Hall

department: MCB

country: USA

institute: Montana State University

description:
Library name: R4_50
S19

library_source: transcriptomic

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

molecule: total RNA

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.

value: Total embryo (50 embryos)

tag: genotype

value: WT

value: 50 ug/L Citalopram

tag: batch


title: Donor 1239, not stimulated with EBNA

description:
Library name: 1239_EBNA_NEG
VF_1239_EBNA.txt

value: Donor 1239

value: not stimulated with EBNA


title: replicate 1 citalopram 250ug/L exposed (0-24hpf) total RNA at 48hpf

description:
Library name: R1_250
S05

value: 250 ug/L Citalopram


title: replicate 5 citalopram 50ug/L exposed (0-24hpf) total RNA at 48hpf

description:
Library name: R5_50
S24


title: e-miRNA_plasma_ICAD_79

city: Los Angeles

first: Nestor R.

last: Gonzalez

state: California

address: 127 S San Vicente Blvd

department: Neurosurgery

institute: Cedars Sinai Medical Center

description: Library name: 119202-79

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: phenotype

value: Non-Hemodynamic

value: intracranial atherosclerosis

tag: Sex

tag: baseline modified_rankin_scale_(mrs)

tag: vegf 165b+

tag: vegf (pg/ml)

tag: hgf (pg/ml)

tag: endostatin (ng/ml)


title: Donor 1237, not stimulated with EBNA

description:
Library name: 1237_EBNA_NEG
VF_1237_EBNA.txt


title: R16A-FLAG, antiFLAG, 2

city: Bethesda

first: Caroline

last: Esnault

state: md

address: 9000 Rockville Pike,

institute: NICHD NIH

description: Library name: R16A-FLAG_antiFLAG_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.

organism: Escherichia coli

growth_protocol: The strains were grown in LB (Lennox) at 37 °C with agitation. When the OD600 reached 1.0, 40 OD600 of cells were collected by centrifuging at 5000 rpm for 10 min at 4°C.

extract_protocol:
The proteins and RNA molecules were crosslinked in vivo by exposing the cells to 800 mJ of 254 nm UV irradiation. After lysing the cells mechanically, Hfq and its bound RNAs were coimmunoprecipitated using either anti-Flag antibody or Hfq antibody. RNAs were trimmed by RNase A/T1 and then treated by T4 polynucleotide kinase (PNK) to generate fragments with 5’ P and 3’ OH ends that can be subsequently ligated. T4 RNA ligase was then used to ligase the neighboring RNAs. After digesting Hfq protein by proteinase K, the RNAs were isolated and subjected to sequencing library construction.
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 samples or Hfq co-IP RNA samples were used as input. 12 cycles of PCR were performed at the last step to enrich each library.

tag: condition

tag: cell line

tag: antibody

value: antiFLAG


title: replicate 3  citalopram 50ug/L exposed (0-24hpf) total RNA at 48hpf

description:
Library name: R3_50
S14


title: e-miRNA_plasma_ICAD_78

description: Library name: 119202-78

tag: disease

value: Female

tag: history of_diabetes

tag: history of_hypertension

tag: history of_hypercholesterolemia

tag: angiostatin+ (ng/ml)


title: replicate 2 citalopram 50ug/L exposed (0-24hpf) total RNA at 48hpf

description:
Library name: R2_50
S09

tag: tissue

tag: genotype

tag: treatment


title: R16A-FLAG, antiFLAG, 1

description: Library name: R16A-FLAG_antiFLAG_1


title: Donor 1206, not stimulated with HA

description:
Library name: 1206_HA_NEG
VF_1206_HA.txt

tag: subject id

value: Donor 1206

tag: cell type

value: not stimulated with HA


title: e-miRNA_plasma_ICAD_77

description: Library name: 119202-77

tag: phenotype

tag: Sex

value: no

tag: baseline modified_rankin_scale_(mrs)

tag: vegf 165b+


title: e-miRNA_plasma_ICAD_83

description: Library name: 119202-83

value: Hemodynamic

tag: vegf (pg/ml)

tag: hgf (pg/ml)

tag: endostatin (ng/ml)


title: Donor 1206, stimulated with EBNA

description:
Library name: 1206_EBNA_POS
VF_1206_EBNA.txt

value: blood

value: CD4 T cells


title: Donor 1237, stimulated with HA

description:
Library name: 1237_HA_POS
VF_1237_HA.txt

value: Donor 1237

value: stimulated with HA


title: replicate 1 citalopram 50ug/L exposed (0-24hpf) total RNA at 48hpf

description:
Library name: R1_50
S04

value: Total embryo (50 embryos)

value: WT

value: 50 ug/L Citalopram

tag: batch


title: Hfq-FLAG, antiFLAG, 1

description: Library name: Hfq-FLAG_antiFLAG_1

source_name: Hfq-FLAG

tag: condition

tag: cell line

value: Hfq-FLAG

tag: antibody


title: replicate 5 citalopram 0.9ug/L exposed (0-24hpf) total RNA at 48hpf

description:
Library name: R5_0.9
S23

value: 0.9 ug/L Citalopram


title: Donor 1237, not stimulated with HA

description:
Library name: 1237_HA_NEG
VF_1237_HA.txt


title: R16A-FLAG, antiHfq, IP, 2

description: Library name: R16A-FLAG_antiHfq_2

value: antiHfq


title: Donor 1206, not stimulated with EBNA

description:
Library name: 1206_EBNA_NEG
VF_1206_EBNA.txt

value: not stimulated with EBNA


title: e-miRNA_plasma_ICAD_81

description: Library name: 119202-81

value: plasma

value: Non-Hemodynamic

tag: disease

value: intracranial atherosclerosis

tag: history of_diabetes

tag: history of_hypertension

value: yes

tag: history of_hypercholesterolemia

tag: angiostatin+ (ng/ml)


title: e-miRNA_plasma_ICAD_76

description: Library name: 119202-76

tag: tissue

value: Female

value: no


title: replicate 4 citalopram 0.9ug/L exposed (0-24hpf) total RNA at 48hpf

description:
Library name: R4_0.9
S18

tag: genotype

tag: treatment


title: replicate 3 citalopram 0.9ug/L exposed (0-24hpf) total RNA at 48hpf

description:
Library name: R3_0.9
S13


title: Donor 1205, stimulated with HA

description:
Library name: 1205_HA_POS
VF_1205_HA.txt

value: blood

tag: subject id

value: Donor 1205

tag: cell type


title: e-miRNA_plasma_ICAD_74

description: Library name: 119202-74

tag: phenotype

tag: Sex

value: Male

tag: baseline modified_rankin_scale_(mrs)

tag: vegf 165b+

tag: vegf (pg/ml)


title: R16A-FLAG, totalRNA, input, 2

description: Library name: R16A-FLAG_totalRNA_noIP_2

tag: condition

tag: cell line

value: input


title: WT-Hfq, ctrlplasmid, IP, 1

description: Library name: Hfq_ctrlplasmid_IP_1

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

source_name: WT-Hfq

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.

value: WT-Hfq

tag: antibody

tag: plasmid

value: ctrlplasmid


title: R16A-FLAG, antiHfq, IP, 1

description: Library name: R16A-FLAG_antiHfq_1


title: Donor 1206, stimulated with HA

description:
Library name: 1206_HA_POS
VF_1206_HA.txt

value: Donor 1206

value: CD4 T cells

value: stimulated with HA


title: Donor 1205, not stimulated with HA

description:
Library name: 1205_HA_NEG
VF_1205_HA.txt

value: not stimulated with HA


title: e-miRNA_plasma_ICAD_73

description: Library name: 119202-73

tag: disease

tag: history of_diabetes

tag: history of_hypertension

tag: hgf (pg/ml)

tag: endostatin (ng/ml)


title: replicate 2 citalopram 0.9ug/L exposed (0-24hpf) total RNA at 48hpf

description:
Library name: R2_0.9
S08

tag: tissue

value: Total embryo (50 embryos)

tag: genotype

value: WT

tag: treatment

value: 0.9 ug/L Citalopram

tag: batch


title: Donor 1205, stimulated with EBNA

description:
Library name: 1205_EBNA_POS
VF_1205_EBNA.txt

tag: subject id

tag: cell type

value: stimulated with EBNA


title: R16A, antiHfq, IP, 2

description: Library name: R16A_antiHfq_2

value: antiHfq


title: replicate 1 citalopram 0.9ug/L exposed (0-24hpf) total RNA at 48hpf

description:
Library name: R1_0.9
S03


title: e-miRNA_plasma_ICAD_71

description: Library name: 119202-71

value: plasma

tag: phenotype

value: Non-Hemodynamic

value: intracranial atherosclerosis

tag: Sex

value: yes

tag: history of_hypercholesterolemia

tag: baseline modified_rankin_scale_(mrs)

tag: vegf 165b+

tag: angiostatin+ (ng/ml)


title: Donor 1205, not stimulated with EBNA

description:
Library name: 1205_EBNA_NEG
VF_1205_EBNA.txt

value: blood

value: Donor 1205

value: not stimulated with EBNA


title: replicate 5 citalopram 0.03ug/L exposed (0-24hpf) total RNA at 48hpf

description:
Library name: R5_0.03
S22

value: 0.03 ug/L Citalopram


title: Donor 1198, stimulated with HA

description:
Library name: 1198_HA_POS
VF_1198_HA.txt

value: Donor 1198


title: e-miRNA_plasma_ICAD_70

description: Library name: 119202-70

tag: disease

value: Male

value: no

tag: vegf (pg/ml)


title: R16A, totalRNA, input, 2

description: Library name: R16A_totalRNA_noIP_2

tag: condition

tag: cell line

tag: antibody

value: input


title: R16A, antiHfq, IP, 1

description: Library name: R16A_antiHfq_1


title: e-miRNA_plasma_ICAD_69

description: Library name: 119202-69

tag: tissue

tag: history of_diabetes

tag: history of_hypertension

tag: hgf (pg/ml)

tag: endostatin (ng/ml)


title: replicate 3 citalopram 0.03ug/L exposed (0-24hpf) total RNA at 48hpf

description:
Library name: R3_0.03
S12

value: Total embryo (50 embryos)

tag: genotype

tag: treatment

tag: batch


title: Donor 1198, stimulated with EBNA

description:
Library name: 1198_EBNA_POS
VF_1198_EBNA.txt

tag: subject id

tag: cell type

value: CD4 T cells


title: R16A, totalRNA, input, 1

description: Library name: R16A_totalRNA_noIP_1


title: replicate 2 citalopram 0.03ug/L exposed (0-24hpf) total RNA at 48hpf

description:
Library name: R2_0.03
S07

value: WT


title: e-miRNA_plasma_ICAD_75

description: Library name: 119202-75

tag: phenotype

tag: Sex

tag: history of_hypercholesterolemia

tag: baseline modified_rankin_scale_(mrs)

tag: vegf 165b+


title: e-miRNA_plasma_ICAD_67

description: Library name: 119202-67

tag: disease

value: Female

tag: vegf (pg/ml)

tag: angiostatin+ (ng/ml)


title: Hfq-FLAG, antiHfq, IP, 1

description: Library name: Hfq-FLAG-antiHfq_1

tag: condition

value: Hfq-FLAG-antiHfq

tag: cell line

value: Hfq-FLAG

tag: antibody

value: antiHfq


title: R16A-FLAG, totalRNA, input, 1

description: Library name: R16A-FLAG_totalRNA_noIP_1


title: replicate 1 citalopram 0.03ug/L exposed (0-24hpf) total RNA at 48hpf

description:
Library name: R1_0.03
R1_0.03

tag: tissue


title: Donor 1198, not stimulated with EBNA

description:
Library name: 1198_EBNA_NEG
VF_1198_EBNA.txt


title: Donor 1170, stimulated with HA

description:
Library name: 1170_HA_POS
VF_1170_HA.txt

value: Donor 1170

value: stimulated with HA


title: Donor 1170, not stimulated with HA

description:
Library name: 1170_HA_NEG
VF_1170_HA.txt

value: blood

value: not stimulated with HA


title: e-miRNA_plasma_ICAD_68

description: Library name: 119202-68

value: plasma

value: Non-Hemodynamic

value: intracranial atherosclerosis

tag: history of_diabetes

value: yes

tag: history of_hypertension

tag: hgf (pg/ml)

tag: endostatin (ng/ml)


title: Hfq-FLAG, antiHfq, IP, 2

description: Library name: Hfq-FLAG-antiHfq_2


title: e-miRNA_plasma_ICAD_66

description: Library name: 119202-66

value: no


title: Hfq-FLAG, totalRNA, input, 2

description: Library name: Hfq-FLAG_totalRNA_noIP_2

value: input


title: replicate 4 citalopram 0.03ug/L exposed (0-24hpf) total RNA at 48hpf

description:
Library name: R4_0.03
S17

value: Total embryo (50 embryos)

tag: genotype

tag: treatment

value: 0.03 ug/L Citalopram

tag: batch


title: replicate 5 control WT zebrafish total RNA at 48hpf

description:
Library name: R5Control
S21

value: WT


title: replicate 3 control WT zebrafish total RNA at 48hpf

description:
Library name: R3Control
S11


title: Hfq-FLAG, totalRNA, input, 1

description: Library name: Hfq-FLAG_totalRNA_noIP_1


title: Donor 1170, stimulated with EBNA

description:
Library name: 1170_EBNA_POS
VF_1170_EBNA.txt

tag: subject id

tag: cell type

value: CD4 T cells

value: stimulated with EBNA


title: e-miRNA_plasma_ICAD_64

description: Library name: 119202-64

tag: phenotype

tag: Sex

value: Female

tag: history of_hypercholesterolemia

tag: baseline modified_rankin_scale_(mrs)

tag: vegf 165b+


title: Hfq, antiHfq, IP, 2

description: Library name: Hfq_antiHfq_2

tag: condition

tag: cell line

value: antiHfq


title: replicate 2 control WT zebrafish total RNA at 48hpf

description:
Library name: R2Control
S06

tag: tissue


title: Donor 1170, not stimulated with EBNA

description:
Library name: 1170_EBNA_NEG
VF_1170_EBNA.txt

value: Donor 1170

value: not stimulated with EBNA


title: e-miRNA_plasma_ICAD_72

description: Library name: 119202-72

tag: disease

value: Male

tag: history of_diabetes

tag: vegf (pg/ml)

tag: angiostatin+ (ng/ml)


title: Hfq, antiHfq, IP, 1

description: Library name: Hfq_antiHfq_1

tag: antibody


title: Donor 1079, stimulated with HA

description:
Library name: 1079_HA
VF_1079_HA.txt

value: blood

value: Donor 1079

tag: treatment

value: stimulated with HA


title: e-miRNA_plasma_ICAD_61

description: Library name: 119202-61

value: plasma

value: Hemodynamic

value: intracranial atherosclerosis

tag: history of_hypertension

tag: hgf (pg/ml)

tag: endostatin (ng/ml)


title: replicate 1 control WT zebrafish total RNA at 48hpf

description:
Library name: R1Control
R1Control

tag: genotype

tag: batch


title: Hfq, totalRNA, input, 2

description: Library name: Hfq_totalRNA_noIP_2

value: input


title: Donor 1198, not stimulated with HA

description:
Library name: 1198_HA_NEG
VF_1198_HA.txt

tag: subject id

value: Donor 1198

tag: cell type

value: not stimulated with HA


title: Hfq, totalRNA, input, 1

description: Library name: Hfq_totalRNA_noIP_1


title: rhAmpSeq, K562, CHD4 guide 14, ADSS1 singleplex

city: La Jolla

first: Graham

last: McVicker

state: CA

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

description: Library name: DNA_16

library_source: genomic

data_processing:
Reads were analyzed using CRISAltRations.
Assembly: hg38
Supplementary files format and content: Tab-separated text file of summary data

molecule: genomic DNA

growth_protocol: Cells were grown in RPMI-1640. All cell cultures were supplemented with 10% heat-inactivated FBS and pen/strep, and incubated at 37°C, 5% CO2.

extract_protocol:
Genomic DNA was extracted by column purification.
RhAmpSeq libraries were prepared by the rhAmpSeq CRISPR Library Preparation protocol (IDT), using 50 ng of genomic DNA per sample. Pooled <i>ADSS1</i> libraries were combined with pooled multiplex libraries at a 1 to 4 ratio by mass.

treatment_protocol: Cells were edited by electroporation with Cas9-guide ribonucleoprotein (RNP) and Superb-seq T7 promoter.

value: CHD4 g14 RNP + T7 promoter


title: e-miRNA_plasma_ICAD_60

description: Library name: 119202-60

tag: phenotype

value: Non-Hemodynamic

tag: Sex

value: yes

tag: history of_hypercholesterolemia

value: no

tag: baseline modified_rankin_scale_(mrs)

tag: vegf 165b+


title: Donor 1078, stimulated with HA

description:
Library name: 1078_HA_POS
VF_1078_HA.txt

tag: tissue

value: Donor 1078

value: CD4 T cells


title: rhAmpSeq, K562, CHD4 guide 12, ADSS1 singleplex

description: Library name: DNA_15

tag: cell line

value: CHD4 g12 RNP + T7 promoter


title: replicate 4 control WT zebrafish total RNA at 48hpf

description:
Library name: R4Control
S16

value: Total embryo (50 embryos)

value: WT


title: Donor 1079, stimulated with EBNA

description:
Library name: 1079_EBNA
VF_1079_EBNA.txt

value: blood

value: Donor 1079

value: stimulated with EBNA


title: e-miRNA_plasma_ICAD_65

description: Library name: 119202-65

value: plasma

tag: disease

value: Male

tag: history of_diabetes

tag: vegf (pg/ml)

tag: angiostatin+ (ng/ml)


title: rhAmpSeq, K562, CHD3 guide 10, ADSS1 singleplex

description: Library name: DNA_14

tag: treatment

value: CHD3 g10 RNP + T7 promoter


title: Hfq, Y25D-FLAG, input, 2

description: Library name: Hfq_Y25D-FLAG_input_2

tag: condition

tag: antibody

value: input


title: e-miRNA_plasma_ICAD_58

description: Library name: 119202-58

value: intracranial atherosclerosis

value: Female

tag: history of_hypertension

tag: hgf (pg/ml)

tag: endostatin (ng/ml)


title: Donor 1078, not stimulated with HA

description:
Library name: 1078_HA_NEG
VF_1078_HA.txt

tag: subject id

tag: cell type

value: not stimulated with HA


title: rhAmpSeq, K562, SMARCA4 guide 22, ADSS1 singleplex

description: Library name: DNA_13

value: SMARCA4 g22 RNP + T7 promoter


title: e-miRNA_plasma_ICAD_57

description: Library name: 119202-57

tag: phenotype

value: Non-Hemodynamic

tag: Sex

value: no

value: yes

tag: history of_hypercholesterolemia


title: Donor 1078, not stimulated with EBNA

description:
Library name: 1078_EBNA_NEG
VF_1078_EBNA.txt

tag: tissue

value: Donor 1078

value: CD4 T cells

value: not stimulated with EBNA


title: Hfq, Y25D-FLAG, input, 1

description: Library name: Hfq_Y25D-FLAG_input_1

tag: cell line


title: Donor 1078, stimulated with EBNA

description:
Library name: 1078_EBNA_POS
VF_1078_EBNA.txt

value: blood


title: e-miRNA_plasma_ICAD_63

description: Library name: 119202-63

value: Hemodynamic

tag: disease

tag: baseline modified_rankin_scale_(mrs)

tag: vegf 165b+


title: rhAmpSeq, K562, SMARCA4 guide 19, ADSS1 singleplex

description: Library name: DNA_12

value: SMARCA4 g19 RNP + T7 promoter


title: Donor 1073, stimulated with HA

description:
Library name: 1073_HA
VF_1073_HA.txt

value: Donor 1073

value: stimulated with HA


title: e-miRNA_plasma_ICAD_56

description: Library name: 119202-56

value: plasma

value: Male

tag: history of_diabetes

tag: vegf (pg/ml)

tag: angiostatin+ (ng/ml)


title: rhAmpSeq, K562, ARID1A guide 06, ADSS1 singleplex

description: Library name: DNA_11

tag: treatment

value: ARID1A g06 RNP + T7 promoter


title: Hfq, Y25D-FLAG, IP, 2

description: Library name: Hfq_Y25D-FLAG_2

tag: condition

tag: antibody

value: antiFLAG


title: Hfq, R16A-FLAG, input, 2

description: Library name: Hfq_R16A-FLAG_input_2

value: input


title: Hfq, Y25D-FLAG, IP, 1

description: Library name: Hfq_Y25D-FLAG_1


title: rhAmpSeq, K562, ARID1A guide 05, ADSS1 singleplex

description: Library name: DNA_10

value: ARID1A g05 RNP + T7 promoter


title: Donor 1073, stimulated with EBNA

description:
Library name: 1073_EBNA
VF_1073_EBNA.txt

value: stimulated with EBNA


title: e-miRNA_plasma_ICAD_55

description: Library name: 119202-55

value: Non-Hemodynamic

value: intracranial atherosclerosis

value: Female

value: no

tag: history of_hypertension

tag: hgf (pg/ml)

tag: endostatin (ng/ml)


title: e-miRNA_plasma_ICAD_54

description: Library name: 119202-54

tag: phenotype

value: yes


title: e-miRNA_plasma_ICAD_59

description: Library name: 119202-59

tag: Sex


title: rhAmpSeq, K562, Unedited, ADSS1 singleplex

description: Library name: DNA_09

value: Electroporation only


title: Hfq, R16A-FLAG, IP, 2

description: Library name: Hfq_R16A-FLAG_2


title: e-miRNA_plasma_ICAD_53

description: Library name: 119202-53

tag: history of_hypercholesterolemia


title: rhAmpSeq, K562, CHD4 guide 14, 52 multiplex

description: Library name: DNA_08

value: CHD4 g14 RNP + T7 promoter


title: Donor 1072, stimulated with EBNA

description:
Library name: 1072_EBNA
VF_1072_EBNA.txt

tag: tissue

value: blood

tag: subject id

value: Donor 1072

tag: cell type

value: CD4 T cells


title: e-miRNA_plasma_ICAD_52

description: Library name: 119202-52

value: plasma

value: Hemodynamic

tag: disease

tag: baseline modified_rankin_scale_(mrs)


title: rhAmpSeq, K562, CHD4 guide 12, 52 multiplex

description: Library name: DNA_07

tag: cell line

value: CHD4 g12 RNP + T7 promoter


title: Donor 1171, stimulated with EBNA

description:
Library name: 1171_EBNA_POS
VF_1171_EBNA.txt

value: Donor 1171


title: Hfq, R16A-FLAG, IP, 1

description: Library name: Hfq_R16A-FLAG_1

value: antiFLAG


title: e-miRNA_plasma_ICAD_51

description: Library name: 119202-51

value: Male

tag: history of_diabetes

tag: vegf 165b+

tag: vegf (pg/ml)


title: Donor 1171, not stimulated with EBNA

description:
Library name: 1171_EBNA_NEG
VF_1171_EBNA.txt

tag: treatment

value: not stimulated with EBNA


title: rhAmpSeq, K562, CHD3 guide 10, 52 multiplex

description: Library name: DNA_06

value: CHD3 g10 RNP + T7 promoter


title: e-miRNA_plasma_ICAD_50

description: Library name: 119202-50

value: Non-Hemodynamic

value: intracranial atherosclerosis

tag: angiostatin+ (ng/ml)


title: Hfq, K31A-FLAG, input, 2

description: Library name: Hfq_K31A-FLAG_input_2

tag: condition

tag: antibody

value: input


title: Hfq, K31A-FLAG, input, 1

description: Library name: Hfq_K31A-FLAG_input_1


title: Hfq, K31A-FLAG, IP, 2

description: Library name: Hfq_K31A-FLAG_2


title: e-miRNA_plasma_ICAD_49

description: Library name: 119202-49

value: no

tag: history of_hypertension

value: yes

tag: hgf (pg/ml)

tag: endostatin (ng/ml)


title: rhAmpSeq, K562, SMARCA4 guide 19, 52 multiplex

description: Library name: DNA_04

value: SMARCA4 g19 RNP + T7 promoter


title: e-miRNA_plasma_ICAD_48

description: Library name: 119202-48

tag: phenotype

tag: Sex

value: Female

tag: history of_hypercholesterolemia


title: Donor 1059, stimulated with HA

description:
Library name: 1059_HA_POS
VF_1059_HA.txt

tag: tissue

value: blood

tag: subject id

value: Donor 1059

tag: cell type

value: stimulated with HA


title: Hfq, K31A-FLAG, IP, 1

description: Library name: Hfq_K31A-FLAG_1

tag: cell line


title: e-miRNA_plasma_ICAD_47

description: Library name: 119202-47

value: plasma

tag: disease

tag: history of_diabetes

tag: baseline modified_rankin_scale_(mrs)


title: rhAmpSeq, K562, ARID1A guide 06, 52 multiplex

description: Library name: DNA_03

tag: treatment

value: ARID1A g06 RNP + T7 promoter


title: Hfq, R16A-FLAG, input, 1

description: Library name: Hfq_R16A-FLAG_input_1


title: Hfq, D9A-FLAG, input, 2

description: Library name: Hfq_D9A-FLAG_input_2


title: hPSCs, Matrigel

city: Vienna

first: Abdel Rahman

last: Abdel Fattah

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

description:
Library name: sample2
10x Genomics

library_source: transcriptomic single cell

data_processing:
The data generated from sequencing was demultiplexed and mapped against human genome reference using CellRanger v3.0.2.
Assembly: GRCh38
Supplementary files format and content: Comma separated data matrix (processed_data_raw_counts.csv)
Supplementary files format and content: Tab separated metadata file (metadata.txt)

source_name: Human pluripotent stem cells (hPSCs)

growth_protocol: 600,000 cell were plated in a well of a 6-well-plate under pluripotent conditions, E8-Felx medium supplemented with ROCK-inhibitor Y-27632 (10 µM) for 24 h. The mediu was then replaced by ROCK-inhibitor-free medium and the cells cultured for another 24 h. Next, in the Matrigel condition, the medium was replaced by E8-Felx medium sumplemented with 10% Matrigel and incubated for 24 h. Control conditions underwent normal medium change. 3 technical replicates were performed per condition. Cell were dissociated and processed for single cell RNA sequencing

extract_protocol:
Samples were washed with PBS to ensure little to no Matrigel is left, then dissociated into single cells using an incubation period of 3 min in 1 mL TrypLE Express in every well. The 1 mL solutions were neutralized with 9 mL of DMEM medium supplemented with 20% FBS, the control and Matrigel conditions were pooled, then centrifuged for 5 min at 300 RCF. After decanting the supernatant, the cell pellets were resuspended in 200 μL of E8-Flex medium and put on ice.
Library preparations for the scRNAseq was performed using 10X Genomics Chromium Single Cell 3’ Kit, v3 (10X Genomics, Pleasanton, CA, USA). The cell count and the viability of the samples were assessed using LUNA dual fluorescence cell counter (Logos Biosystems) and a targeted cell recovery of 10,000 cells was aimed for all the samples. Post cell count and QC, the samples were immediately loaded onto the HyDrop Hybrid38 platform. Single-cell RNA-seq libraries were prepared using manufacturers recommendations (Single-cell 3’ reagent kits v3 user guide; CG00052 Rev B), and at the different check points, the library quality was assessed using Qubit (ThermoFisher) and Bioanalyzer (Agilent). 10X libraries were sequenced on MGISEQ-2000 sequencing platform and was sequenced at the MGI Hong Kong SAR sequencing facility. Before being able to sequence on the MGI platforms, the 10X libraries need to undergo a conversion step using MGIEasy Universal DNA Library Prep kit. Briefly, the final 10X sequencing libraires were circularized using the splint-ligation step and the circularized libraries were converted to single stranded DNA copies. DNA nanoballs were prepared from the circularized ssDNA using Rolling Circle Amplification (RCA). DNB libraries generated were then flown through the patterned flow cell of the MGISEQ-2000RS High-Throughput Sequencing kit. For a targeted sequencing saturation of 50-60%, sequencing were performed at a depth of 30,000 - 60,000 reads per cell. A custom sequencing recipe of paired end read of 28 bps (read 1), 100 bps (read 2) and 10 bps (index 1) was used for sequencing.

treatment_protocol: To treat cells with Matrigel, E8-Felx medium was supplmented with 10% Matrigel and was subsequently added to the cell and incubated for 24 h.

value: Human pluripotent stem cells (hPSCs)

value: Pluripotent media + 10% Matrigel - 24 h


title: Donor 1072, stimulated with HA

description:
Library name: 1072_HA
VF_1072_HA.txt

value: Donor 1072

value: CD4 T cells


title: rhAmpSeq, K562, ARID1A guide 05, 52 multiplex

description: Library name: DNA_02

value: ARID1A g05 RNP + T7 promoter


title: e-miRNA_plasma_ICAD_46

description: Library name: 119202-46

value: Non-Hemodynamic

value: Male

tag: vegf 165b+

tag: vegf (pg/ml)

tag: angiostatin+ (ng/ml)


title: Hfq, D9A-FLAG, input, 1

description: Library name: Hfq_D9A-FLAG_input_1

tag: condition

tag: antibody

value: input


title: hPSCs, Control

description:
Library name: sample1
10x Genomics

value: Pluripotent media - 24 h


title: rhAmpSeq, K562, Unedited, 52 mutiplex

description: Library name: DNA_01

value: Electroporation only


title: e-miRNA_plasma_ICAD_45

description: Library name: 119202-45

value: Hemodynamic

value: intracranial atherosclerosis

value: no

tag: history of_hypertension

value: yes

tag: hgf (pg/ml)

tag: endostatin (ng/ml)


title: SKOV3 HAQ/- cells, 10 μg/mL of 2’3’-cGAMP

city: Philadelphia

first: Lin

last: Zhang

state: PA

address: 421 Curie Blvd

institute: Univerisity of Pennsylvania

description: Library name: S06

data_processing:
RNA seq reads were aligned using STAR and then quantified with RSEM
Assembly: GRCh38/hg38
Supplementary files format and content: Tab delimited text file includes estimated counts for all samples

source_name: Ovarian cancer

extract_protocol:
cells were harvested immediately after treatment and total RNA was extracted using TRIzol Reagent
Illumina mRNA TruSeq library preparation was employed following manufacturer's protocol

value: Ovarian cancer

value: ovarian cancer cell

tag: genotype

value: HAQ/-


title: Hfq, D9A-FLAG, IP, 2

description: Library name: Hfq_D9A-FLAG_2

value: antiFLAG


title: e-miRNA_plasma_ICAD_44

description: Library name: 119202-44

tag: tissue

value: plasma

tag: phenotype

tag: Sex

value: Female

tag: history of_hypercholesterolemia


title: Hfq, D9A-FLAG, IP, 1

description: Library name: Hfq_D9A-FLAG_1

tag: cell line


title: SKOV3 HAQ/- cells, control

description: Library name: S05

tag: cell type

value: control


title: MAA-22033 QH17C15

type: RNA

city: Setagaya-ku

first: Kazuaki

last: Nakamura

state: Tokyo

department: Department of Pharmacology

country: Japan

institute: National Center for Child Health and Development

hyb_protocol: Hybridization and washing were followed by the protocol supplied by the manufacturer.

scan_protocol: Toray 3D-Gene Scanner was used for scanning.

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots' signal intensities of 95% confidence intervals.

source_name: Primary human hepatocyte

label_protocol: CyeDye coupling and fragmentation were performed according to the protocol supplied by the manufacturer.

growth_protocol: Cells were thawed in the Cryopreserved Hepatocyte Recovery Medium, centrifuged, gently suspended, and seeded in the plating medium, MP100, on collagen I-coated plates.

extract_protocol: RNA samples from each cell sample were extracted using the RNaesy mini kit.

treatment_protocol: Suspension hepatocytes with or without treatment with elastase were collected immediately after elastase treatment or 24 hours after seeding.

value: liver

value: Primary human hepatocyte

value: Without elastase 24-h incubation


title: MAA-22033 QH17C14

value: With elastase 24-h incubation


title: rhAmpSeq, K562, SMARCA4 guide 22, 52 multiplex

description: Library name: DNA_05

value: SMARCA4 g22 RNP + T7 promoter


title: Donor 1059, not stimulated with HA

description:
Library name: 1059_HA_NEG
VF_1059_HA.txt

value: blood

tag: subject id

value: Donor 1059

value: CD4 T cells

value: not stimulated with HA


title: Hfq-FLAG, input, 2

description: Library name: Hfq-FLAG_input_2

value: Hfq-FLAG

value: input


title: MAA-22033 QH17C12

tag: treatment

value: With elastase 0-h incubation


title: e-miRNA_plasma_ICAD_42

description: Library name: 119202-42

value: Non-Hemodynamic

tag: disease

value: intracranial atherosclerosis

tag: history of_diabetes

value: no

value: yes

tag: baseline modified_rankin_scale_(mrs)

tag: vegf 165b+


title: SKOV3 WT/- cells, 10 μg/mL of 2’3’-cGAMP

description: Library name: S04

value: Ovarian cancer

value: ovarian cancer cell

value: WT/-


title: Hfq-FLAG, input, 1

description: Library name: Hfq-FLAG_input_1

tag: condition

tag: antibody


title: SKOV3 WT/- cells, control

description: Library name: S03

value: control


title: e-miRNA_plasma_ICAD_41

description: Library name: 119202-41

value: plasma

value: Male

tag: history of_hypertension

tag: vegf (pg/ml)

tag: hgf (pg/ml)

tag: angiostatin+ (ng/ml)


title: SKOV3 WT/HAQ cells, 10 μg/mL of 2’3’-cGAMP

description: Library name: S02

tag: tissue

tag: genotype

value: WT/HAQ


title: Hfq-FLAG, IP, 2

description: Library name: Hfq-FLAG_2

value: antiFLAG


title: e-miRNA_plasma_ICAD_39

description: Library name: 119202-39

tag: phenotype

tag: Sex

value: Female

tag: history of_hypercholesterolemia

tag: endostatin (ng/ml)


title: Hfq-FLAG, IP, 1

description: Library name: Hfq-FLAG_1

tag: cell line


title: MAA-22032 QH17C08

value: liver

tag: cell type

value: Primary human hepatocyte

tag: treatment

value: Without elastase 24-h incubation


title: MAA-22032 QH17C09

value: With elastase 24-h incubation


title: SKOV3 WT/HAQ cells, control

description: Library name: S01


title: e-miRNA_plasma_ICAD_38

description: Library name: 119202-38

value: Non-Hemodynamic

tag: disease

tag: history of_diabetes

tag: baseline modified_rankin_scale_(mrs)


title: MAA-22033 QH17C11

value: Without elastase 0-h incubation


title: WT, Untagged Hfq, input, 2

description: Library name: WT_Untagged_Hfq_input_2

tag: condition

tag: antibody

value: input


title: MAA-22032 QH17C06

value: With elastase 0-h incubation


title: Donor_8,PBMC,CD4,PMAiIL2,rep1

city: Chapel Hill

first: Edward

middle: Patrick

last: Browne

state: NC

address: 120 Mason Farm Road

institute: UNC-Chapel Hill

description: Library name: Donor8_sample4

data_processing:
Alignment and cell-calling was performed on the UNC high performance computing cluster with cellranger v7.1.0 (10x Genomics) against a custom human-HIV reference genome. Alignment was performed for all files using cellranger count function with default parameters but --jobmode=slurm to run on the UNC high-performance computing cluster.
CITE-seq analysis was performed with cellranger v7.1.0 (10x Genomics) using the human-HIV reference genome and a feature reference .csv. The feature reference file: "TotalSeq_B_Human_Universal_Cocktail_V1_399904_Antibody_reference_UMI_counting_CellRanger_addHTO.csv"  was derived from the manufacturer supplied document with 6 TotalSeq B anti-human hashtag antibodies (TotalSeq B0251-B0256) added as the final 6 entries in the feature reference file. Gene expression (GEX) and CITE-seq surface (ADT) data were split in Seurat from the contents of the cellranger output directories "filtered_feature_barcode_matrix", renamed, and uploaded as separate files for each GEX and ADT library.
The custom human-HIV reference genome was generated from concatenating GRCh38 fasta and .gtf files to an additional contig containing consensus clade B HIV sequence fasta and .gtf files and compiling with the cellranger mkref function.
Assembly: human genome (GRCh38), version 32 (Ensembl 98)
Supplementary files format and content: hdf5 files containing machine readable scRNA seq cell-by-feature matrices
Supplementary files format and content: separate matrix.mtx, barcodes.tsv, and features.tsv files split for GEX and ADT data

molecule: polyA RNA

source_name: PBMC

growth_protocol: After isolation (colon-derived) or thawing (blood-derived), cells were rested overnight at >1M/mL in complete RPMI-1640 (Gibco) containing 10U/mL of IL-2, 10µM ZVAD-FMK caspase inhibitors (Selleck Chem,), and 500nM Raltegravir (Selleck Chem).

extract_protocol:
PBMCs were isolated by Ficoll gradient centrifugation with ammonium-chloride-potassium buffer-based red-blood cell lysis and viably frozen in liquid nitrogen. Intra-epithelial lymphocytes (IEL) and Lamina propria-resident immune cells (LP cells) were isolated in the method of Trapecar et al. DOI:10.1089/aid.2017.0208 and pooled after isolation. Epithelial stripping was performed in an EDTA+DTT buffer with mechanical disruption on a gentleMACS dissociator, with IEL cells liberated to the supernatant. The remaining lamina propria fraction was digested in CLSPA+DNAse buffer and subjected to additional gentleMACS dissociation and mechanical disruption by syringe. LP cells were isolated by filtration of the supernatant through a 70 micron filter. LP and IEL cells were treated with DNAse, filtered through a 40 micron filter, and rinsed in complete RPMI culture media. Cells were then subjected to a dead cell removal protocol (Biolegend) to remove epithelial debris.
scRNAseq libraries were prepared according to manufacturer instructions (10x Genomics scRNAseq v3.1 3’ sequencing, catalog 1000269, protocol ). Gel-bead and cell emulsions (GEMs) were generated using the Chromium controller, subjected to reverse transcription, and first-strand cDNA was extracted from GEMs. Purified cDNA was PCR pre-amplified (12-cycles, 1-minute extension) with primers binding the P7 region and the Template Switching Oligo, cleaned up by solid-phase reversible immobilization (SPRI) beads, analyzed by HS DNA 5000 capillary electrophoresis (Agilent), and concentration calculated by Qubit (ThermoFisher).  From this material, 25% was used for Illumina NGS library construction involving fragmentation, end-repair/A-tailing, adapter TA ligation, and SPRI double-sided size selection to remove adapters and unfragmented products.  Libraries were amplified with Illumina indexing/sequencing i5 and i7 primers (13 cycles), then cleaned with SPRI beads before being quantified by Qubit and the fragment size determined using a Tapestation (Agilent).  Libraries were then pooled at an equimolar concentration and sequencing was performed using NovaSeq or NovaseqX sequencing (Illumina). CITE seq was performed as above, but with the following additional steps. The TotalSeq-B Universal Human antibody panel (Biolegend, catalog 399904) of lyophilized DNA-tagged antibodies was resuspended and spun down according to manufacturer’s instructions.  Meanwhile, cells were treated with Human TruStain FcX (Biolegend, catalog 422301) to prevent antibody binding by human Fc receptors.  Next, cells from each donor were stained with Totalseq-B hash-tag oligonucleotide antibodies (Biolegend, catalog 155831, 155833, and 155835) then added to three pools comprising untreated PBMCs, untreated CD4 cells, and PMA/ionomycin stimulated CD4 T cells. Pooled samples were stained in parallel with the TotalSeq-B Universal Human antibody panel, washed, and prepared for scRNA seq library construction as above but with additional PCR amplification of cell surface feature libraries following manufacturer instructions (10x Genomics protocol #CG000206).

treatment_protocol: Following overnight rest, cultures were split and treatment cultures were stimulated with PMA/ionomycin (16nM/1μM) and IL-2 (100U/mL) for 6 hours

value: PBMC

value: isolated CD4


title: e-miRNA_plasma_ICAD_43

description: Library name: 119202-43

value: intracranial atherosclerosis

value: yes

tag: history of_hypertension

value: no

tag: vegf 165b+

tag: vegf (pg/ml)


title: WT, Untagged Hfq, input, 1

description: Library name: WT_Untagged_Hfq_input_1


title: e-miRNA_plasma_ICAD_37

description: Library name: 119202-37

tag: tissue

value: plasma

tag: hgf (pg/ml)

tag: angiostatin+ (ng/ml)


title: MAA-22032 QH17C05


title: Donor_8,PBMC,CD4,Untreated,rep1

description: Library name: Donor8_sample3

value: Untreated


title: e-miRNA_plasma_ICAD_36

description: Library name: 119202-36

tag: phenotype

value: Hemodynamic

tag: Sex


title: Donor_8,Colon,CD4,PMAiIL2,rep1

description: Library name: Donor8_sample2

source_name: Sigmoid Colon

value: Sigmoid Colon


title: Donor_8,Colon,CD4,Untreated,rep1

description: Library name: Donor8_sample1


title: e-miRNA_plasma_ICAD_35

description: Library name: 119202-35

value: Female

tag: history of_hypercholesterolemia

tag: endostatin (ng/ml)


title: WT, Untagged Hfq, IP, 1

description: Library name: WT_Untagged_Hfq_1

tag: cell line

value: antiFLAG


title: R16A-FLAG, IPRNA, antiHfq

description:
Library name: R16A-FLAG_IPRNA_antiHfq
featurecounts_AX.txt

data_processing:
Samples were processed through lcdb-wf v1.10.2, https://github.com/lcdb/lcdb-wf. Briefly, FASTQ files demultiplexing, adaptor-trimming and quality filtering were carried out with cutadapt v4.3 with the parameters ‘--error-rate=0.2 --overlap=9’, then '--nextseq-trim 20 --overlap 6 --minimum-length 25'. Trimmed FASTQ files were mapped to the E. coli genome GCF_000005845.2 ASM584v2 with bwa v0.7.17 with default parameters. Gene expression was quantified with featureCounts from subreads 2.0.3 with the parameter ‘-O’ to allow counting of reads in overlapping features, using the RILseq-formatted annotation NC_000913-3_all_feature.gff file. Differential expression analysis was carried out with DESeq2 v1.38.0 in R v4.2.2.
Assembly: E. coli GCF_000005845.2 ASM584v2
Supplementary files format and content: TSV file of raw sequence reads per genomic feature, from featurecounts

growth_protocol: The strains were cultured in LB (Lennox) at 37 °C with agitation. When the OD600 reached 1.0, 20 OD600 of cells were collected by centrifuging at 5000 rpm for 10 min 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). The isolation of total RNA and Hfq co-IP RNA was performed as previously described (Kavita, K., et al., 2022, Nucleic Acids Res., 50, 1718-1733) with the following modifications: 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 samples or Hfq co-IP RNA samples were used as input. 7 cycles of PCR were performed at the last step to enrich each library.

value: antiHfq


title: e-miRNA_plasma_ICAD_34

description: Library name: 119202-34


title: MAA-22031 QH17C03

value: liver

tag: cell type

value: Primary human hepatocyte

tag: treatment

value: Without elastase 24-h incubation


title: Donor_7,PBMC,CD4,PMAiIL2,rep1

description: Library name: Donor7_sample7


title: R16A-FLAG, IPRNA, antiHf2

description:
Library name: R16A-FLAG_IPRNA_antiHf2
featurecounts_AX.txt


title: e-miRNA_plasma_ICAD_33

description: Library name: 119202-33

tag: disease

value: Male

tag: history of_diabetes


title: MAA-22031 QH17C01

value: Without elastase 0-h incubation


title: MAA-22031 QH17C02

value: With elastase 0-h incubation


title: Donor_7,PBMC,CD4,Untreated,rep1

description: Library name: Donor7_sample6

value: PBMC

value: isolated CD4


title: R16A, IPRNA, antiHfq, 1

description:
Library name: R16A_IPRNA_antiHfq_1
featurecounts_AX.txt

tag: condition


title: e-miRNA_plasma_ICAD_31

description: Library name: 119202-31

value: Non-Hemodynamic

value: intracranial atherosclerosis

value: yes

tag: baseline modified_rankin_scale_(mrs)


title: Donor_7,Colon,CD4,PMAiIL2,rep4

description: Library name: Donor7_sample5


title: e-miRNA_plasma_ICAD_32

description: Library name: 119202-32

value: plasma

value: no

tag: history of_hypertension


title: R16A, IPRNA, antiHfq, 2

description:
Library name: R16A_IPRNA_antiHfq_2
featurecounts_AX.txt

tag: antibody


title: WT, Untagged Hfq, IP, 2

description: Library name: WT_Untagged_Hfq_2


title: e-miRNA_plasma_ICAD_28

description: Library name: 119202-28

tag: vegf 165b+

tag: vegf (pg/ml)


title: MAA-20229 QH01P41

treatment_protocol: Cells were seeded on collagen I-coated vessels, and after 2 hours, non-adherent and adherent cells were collected separately.

tag: tissue

value: Adhered cells separated from non-adhered cells


title: e-miRNA_plasma_ICAD_29

description: Library name: 119202-29

value: Hemodynamic

tag: hgf (pg/ml)

tag: angiostatin+ (ng/ml)


title: MAA-22031 QH17C04

value: With elastase 24-h incubation


title: R16A-FLAG, totalRNA, noIP, 2

description:
Library name: R16A-FLAG_totalRNA_noIP_2
featurecounts_AX.txt


title: Donor_7,Colon,CD4,PMAiIL2,rep2

description: Library name: Donor7_sample3

value: Sigmoid Colon


title: MAA-20229 QH01P44

value: liver


title: Donor_7,Colon,CD4,PMAiIL2,rep3

description: Library name: Donor7_sample4


title: R16A-FLAG, totalRNA, noIP, 1

description:
Library name: R16A-FLAG_totalRNA_noIP_1
featurecounts_AX.txt


title: Donor_7,Colon,CD4,PMAiIL2,rep1

description: Library name: Donor7_sample2


title: e-miRNA_plasma_ICAD_27

description: Library name: 119202-27

tag: phenotype

tag: Sex


title: MAA-20228 QH01P37

value: Non-adhered cells separated from adhered cells


title: Donor_7,Colon,CD4,Untreated,rep1

description: Library name: Donor7_sample1

value: Untreated


title: e-miRNA_plasma_ICAD_26

description: Library name: 119202-26

value: Female

tag: history of_hypercholesterolemia

tag: endostatin (ng/ml)


title: MAA-20228 QH01P43

tag: cell type


title: MAA-20229 QH01P39


title: MAA-20228 QH01P42


title: R16A, totalRNA, noIP, 2

description:
Library name: R16A_totalRNA_noIP_2
featurecounts_AX.txt

tag: cell line


title: MEKi+RT  rep3

city: jiann

first: Yawen

last: zheng

address: jiefang road No105

country: China

institute: jinan central hospital

description:
Library name: sample12
MEKi+RT3

data_processing:
The raw data contains reads of low quality, reads with adaptor sequences and reads with high levels of N base. Those reads need to be filtered before the data analysis for reliability analysis results.
We used HISAT to align the clean reads to the reference genome.
Assembly: GCF_000001635.27_GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample. csv files include FPKM values for each Sample.

organism: Mus musculus

source_name: Lewis Lung Carcinoma Cells

extract_protocol:
RNA was extracted using a total RNA extraction kit (Fastagen; Cat No. RNAfast200). 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Lewis Lung Carcinoma Cells

tag: genotype

value: WT

tag: treatment

value: trametinib 10 nmol/L  8Gy/1f   24h rep3

tag: batch

value: scan data


title: Donor_6,PBMC,CD4,PMAiIL2,rep1

description: Library name: Donor6_sample5

value: PBMC

value: isolated CD4


title: Hfq-FLAG, IPRNA, antiHfq, 2

description:
Library name: Hfq-FLAG_IPRNA_antiHfq_2
featurecounts_AX.txt

tag: condition

value: Hfq-FLAG

value: antiHfq


title: MEKi+RT  rep2

description:
Library name: sample11
MEKi+RT2

value: trametinib 10 nmol/L  8Gy/1f   24h  rep2


title: e-miRNA_plasma_ICAD_25

description: Library name: 119202-25

value: plasma

tag: disease

value: intracranial atherosclerosis

value: Male

tag: history of_diabetes

value: yes

tag: history of_hypertension

tag: baseline modified_rankin_scale_(mrs)


title: Donor_6,PBMC,CD4,Untreated,rep1

description: Library name: Donor6_sample4

tag: tissue


title: Donor_6,Colon,CD4,PMAiIL2,rep2

description: Library name: Donor6_sample3

value: Sigmoid Colon


title: Hfq, IPRNA, antiHfq, 2

description:
Library name: Hfq_IPRNA_antiHfq_2
featurecounts_AX.txt

tag: antibody


title: Donor_6,Colon,CD4,PMAiIL2,rep1

description: Library name: Donor6_sample2


title: Hfq, IPRNA, antiHfq, 1

description:
Library name: Hfq_IPRNA_antiHfq_1
featurecounts_AX.txt


title: RT rep2

description:
Library name: sample8
RT2

value: 8Gy/1f 24h rep2


title: Hfq-FLAG, IPRNA, antiHfq, 1

description:
Library name: Hfq-FLAG_IPRNA_antiHfq_1
featurecounts_AX.txt


title: Donor_5,PBMC,CD4,PMAiIL2,rep1

description: Library name: Donor5_sample6


title: e-miRNA_plasma_ICAD_22

description: Library name: 119202-22

value: Hemodynamic

tag: vegf 165b+

tag: vegf (pg/ml)

tag: hgf (pg/ml)

tag: angiostatin+ (ng/ml)


title: e-miRNA_plasma_ICAD_23

description: Library name: 119202-23

tag: phenotype

tag: Sex

value: Female

value: no

tag: history of_hypercholesterolemia

tag: endostatin (ng/ml)


title: e-miRNA_plasma_ICAD_24

description: Library name: 119202-24


title: MEKi+RT  rep1

description:
Library name: sample10
MEKi+RT1

tag: cell line

value: Lewis Lung Carcinoma Cells

tag: genotype

value: WT

tag: treatment

value: trametinib 10 nmol/L  8Gy/1f   24h  rep1


title: e-miRNA_plasma_ICAD_20

description: Library name: 119202-20

tag: disease


title: e-miRNA_plasma_ICAD_21

description: Library name: 119202-21

value: Non-Hemodynamic

tag: history of_diabetes


title: Hfq-FLAG, totalRNA, noIP, 1

description:
Library name: Hfq-FLAG_totalRNA_noIP_1
featurecounts_AX.txt

tag: condition


title: Hfq-FLAG, totalRNA, noIP, 2

description:
Library name: Hfq-FLAG_totalRNA_noIP_2
featurecounts_AX.txt


title: RT rep3

description:
Library name: sample9
RT3

value: 8Gy/1f 24h rep3

tag: batch

value: scan data


title: R16A, totalRNA, noIP, 1

description:
Library name: R16A_totalRNA_noIP_1
featurecounts_AX.txt


title: MEKi rep3

description:
Library name: sample6
MRKi3

value: trametinib 10 nmol/L   24h rep3


title: Donor_5,PBMC,CD4,Untreated,rep1

description: Library name: Donor5_sample5

tag: tissue

value: PBMC

tag: cell type

value: isolated CD4

value: Untreated


title: Donor_6,Colon,CD4,Untreated,rep1

description: Library name: Donor6_sample1


title: RT rep1

description:
Library name: sample7
RT1

value: 8Gy/1f 24h rep1


title: e-miRNA_plasma_ICAD_19

description: Library name: 119202-19

value: plasma

value: intracranial atherosclerosis

tag: history of_hypertension

value: yes

tag: baseline modified_rankin_scale_(mrs)

tag: vegf 165b+


title: Hfq, totalRNA, noIP, 2

description:
Library name: Hfq_totalRNA_noIP_2
featurecounts_AX.txt

tag: antibody


title: Donor_5,Colon,CD4,PMAiIL2,rep3

description: Library name: Donor5_sample4

value: Sigmoid Colon


title: Hfq, totalRNA, noIP, 1

description:
Library name: Hfq_totalRNA_noIP_1
featurecounts_AX.txt


title: e-miRNA_plasma_ICAD_18

description: Library name: 119202-18

tag: phenotype

value: Hemodynamic

value: Male

tag: vegf (pg/ml)

tag: hgf (pg/ml)

tag: angiostatin+ (ng/ml)


title: MEKi rep1

description:
Library name: sample4
MRKi1

tag: cell line

value: Lewis Lung Carcinoma Cells

value: trametinib 10 nmol/L 24h rep1


title: Donor_5,Colon,CD4,PMAiIL2,rep2

description: Library name: Donor5_sample3


title: e-miRNA_plasma_ICAD_17

description: Library name: 119202-17

tag: Sex

value: Female

value: no

tag: history of_hypercholesterolemia

tag: endostatin (ng/ml)


title: Control rep3

description:
Library name: sample3
control3

tag: genotype

value: WT

tag: treatment


title: Hfq-Y25D, Hfq-FLAG, 2

description:
Library name: Hfq_Y25D-FLAG_2
featurecounts_FMD.txt

tag: condition


title: Control rep2

description:
Library name: sample2
control2

tag: batch

value: scan data


title: Hfq-Y25D, Hfq-FLAG, 1

description:
Library name: Hfq_Y25D-FLAG_1
featurecounts_FMD.txt


title: Hfq-R16A, Hfq-FLAG, 2

description:
Library name: Hfq_R16A-FLAG_2
featurecounts_FMD.txt


title: Donor_5,Colon,CD4,Untreated,rep1

description: Library name: Donor5_sample1

tag: tissue

tag: cell type


title: Donor_5,Colon,CD4,PMAiIL2,rep1

description: Library name: Donor5_sample2


title: Control rep1

description:
Library name: sample1
control1


title: e-miRNA_plasma_ICAD_15

description: Library name: 119202-15

value: Non-Hemodynamic

tag: disease

tag: history of_diabetes

tag: history of_hypertension

tag: baseline modified_rankin_scale_(mrs)


title: e-miRNA_plasma_ICAD_14

description: Library name: 119202-14

tag: phenotype

tag: vegf 165b+

tag: vegf (pg/ml)


title: d6_NTmimic_3

city: Nuthetal

first: Heike

last: Vogel

state: BRB

address: Arthur-Scheunert-Allee 114-116

department: Department of Experimental Diabetology

country: Germany

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

description: Library name: d6_NTmimic_3

data_processing:
Standard pipeline performed by BGI (Shenzen, China) using soapnuke v1.5.6. Hisat2 v2.2.1, rsem v1.3.1,
Assembly: Mus_musculus_10090.UCSC.mm39.v2201
Supplementary files format and content: xlsx file containing gene counts for each sample

source_name: 3T3-L1 fibroblasts (ATTC CL-17)

growth_protocol: 3T3-L1 fibroblasts (ATTC CL-17)  were cultured in IMDM (Iscove’s Modified Dulbecco’s Medium, PAN-Biotech) containing 10 % NBC (newborn calf serum, PAN-Biotech) at 37°C in 5 % CO2. Fibroblasts were seeded on collagen-coated (Collagen A, Biochrom GmbH, Berlin, Germany) cell culture plates.

extract_protocol:
total RNA was extracted using a miRNeasy kit (Qiagen, Germany) as per the manufacturer’s instructions
done by BGI (Shenzhen, China)

treatment_protocol: Using Lipofectamine 2000 (Invitrogen) transfection reagent, 20 nM miRNA mimic miR-335-5p (YM00473600-ADA, Qiagen) was transfected into these 3T3-L1 fibroblasts for 48 h. The scrambled miRNA (YM00479902-ADA, Qiagen) was used as a control. Differentiation was started using IMDM/10%FBS containing 200 nM insulin (Roche), 0.5 mM 3-isobutyl-1-methylxanthine (SigmaAldrich), 2 mM rosiglitazone (SigmaAldrich) and 250 nM dexamethasone (SigmaAldrich) and cultured for three days. Medium was replaced with IMDM/10%FBS containing 200 nM insulin every day for two days, followed by one day in IMDM/10%FBS and 1% penicillin/streptomycin (P/S). RNA sequencing was conducted at day 3 and day 6 of differentiation.

tag: cell line

value: 3T3-L1 fibroblasts (ATTC CL-17)

value: NT mimic

tag: differentiation stage

value: adipocyte


title: Donor_4,PBMC,CD4,PMAiIL2,rep1

description: Library name: Donor4_sample6

value: PBMC

value: isolated CD4


title: Hfq-R16A, Hfq-FLAG, 1

description:
Library name: Hfq_R16A-FLAG_1
featurecounts_FMD.txt

tag: antibody


title: Donor_4,PBMC,CD4,Untreated,rep2

description: Library name: Donor4_sample5

value: Untreated


title: d6_NTmimic_2

description: Library name: d6_NTmimic_2


title: e-miRNA_plasma_ICAD_13

description: Library name: 119202-13

value: plasma

value: intracranial atherosclerosis

tag: Sex

value: yes

tag: history of_hypercholesterolemia

tag: hgf (pg/ml)

tag: endostatin (ng/ml)

tag: angiostatin+ (ng/ml)


title: Donor_4,PBMC,CD4,Untreated,rep1

description: Library name: Donor4_sample4

tag: tissue

tag: treatment


title: Hfq-K31A, Hfq-FLAG, 2

description:
Library name: Hfq_K31A-FLAG_2
featurecounts_FMD.txt

tag: condition


title: Hfq-K31A, Hfq-FLAG, 1

description:
Library name: Hfq_K31A-FLAG_1
featurecounts_FMD.txt


title: e-miRNA_plasma_ICAD_12

description: Library name: 119202-12

tag: disease

value: Male

tag: history of_diabetes


title: d6_NTmimic_1

description: Library name: d6_NTmimic_1


title: MEKi  rep2

description:
Library name: sample5
MRKi2

value: Lewis Lung Carcinoma Cells

tag: genotype

value: trametinib 10 nmol/L  24h rep2

tag: batch


title: Hfq-D9A, Hfq-FLAG, 2

description:
Library name: Hfq_D9A-FLAG_2
featurecounts_FMD.txt


title: e-miRNA_plasma_ICAD_16

description: Library name: 119202-16

tag: phenotype

tag: history of_hypertension

tag: baseline modified_rankin_scale_(mrs)

tag: vegf 165b+


title: d6_335mimic_3

description: Library name: d6_335mimic_3

tag: cell line

value: miR-335-5p mimic

tag: differentiation stage


title: e-miRNA_plasma_ICAD_11

description: Library name: 119202-11

tag: Sex

tag: history of_hypercholesterolemia

tag: vegf (pg/ml)


title: e-miRNA_plasma_ICAD_10

description: Library name: 119202-10

value: Hemodynamic

value: no

tag: hgf (pg/ml)

tag: endostatin (ng/ml)

tag: angiostatin+ (ng/ml)


title: Donor_4,Colon,CD4,PMAiIL2,rep1

description: Library name: Donor4_sample2

tag: tissue

value: Sigmoid Colon

tag: cell type

tag: treatment


title: Hfq-D9A, Hfq-FLAG, 1

description:
Library name: Hfq_D9A-FLAG_1
featurecounts_FMD.txt

tag: condition

tag: antibody


title: Donor_4,Colon,CD4,Untreated,rep1

description: Library name: Donor4_sample1


title: d6_335mimic_2

description: Library name: d6_335mimic_2


title: WT, Hfq-FLAG, 2

description:
Library name: Hfq-FLAG_2
featurecounts_FMD.txt

value: Hfq-FLAG


title: e-miRNA_plasma_ICAD_09

description: Library name: 119202-9

tag: phenotype

value: Non-Hemodynamic

tag: disease

value: Female

tag: history of_diabetes


title: e-miRNA_plasma_ICAD_08

description: Library name: 119202-8

tag: history of_hypertension

tag: baseline modified_rankin_scale_(mrs)

tag: vegf 165b+


title: SH_LacZ_2

city: New Orleans

first: Kuan-Jui

last: Su

state: LA

address: 1440 Canal St,suite 1619G

department: Center for Biomedical Informatics and Genomics

institute: Tulane University

description: Library name: sample 4

data_processing:
CLC Genomics Workbench v11.0.1
Sequence reads were trimmed for adeptor sequence/low-quality sequence using CLC Genomics Workbench
Trimmed sequence read were mapped to GrCM38/mm10 using CLC genomics benchwork (parameters_mismath cost :2insertion cost:3 deletion cost: 3 lenghth fraction : 08similarity fraction:0.8
Assembly: GRCh38/hg38
Supplementary files format and content: FPKM value of each Sample

growth_protocol: SH-SY-5Y cells were maintained in RPMI1640 supplemented with 10% fetal bovine serum and antibiotics at 5% CO2, 37oC incubators

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen), 1.5µg  total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using SMARTER mRNA Seq Library Prep Kit following manufacturer's protocol

treatment_protocol: INSM1 overexpression was induced by transduction with INSM1 adenoviral vectors

tag: cell line

value: neuroblastoma

tag: genotype

value: WT

value: transduction with LacZ adenoviral vectors


title: d6_335mimic_1

description: Library name: d6_335mimic_1

value: 3T3-L1 fibroblasts (ATTC CL-17)

tag: differentiation stage

value: adipocyte


title: WT, Untagged, Hfq, 2

description:
Library name: WT_Untagged_Hfq_2
featurecounts_FMD.txt


title: WT, Hfq-FLAG, 1

description:
Library name: Hfq-FLAG_1
featurecounts_FMD.txt


title: e-miRNA_plasma_ICAD_06

description: Library name: 119202-6

value: plasma

value: intracranial atherosclerosis

tag: Sex

tag: history of_hypercholesterolemia

tag: vegf (pg/ml)

tag: hgf (pg/ml)


title: WT, Untagged, Hfq, 1

description:
Library name: WT_Untagged_Hfq_1
featurecounts_FMD.txt


title: d3_NTmimic_3

description: Library name: d3_NTmimic_3

value: NT mimic

value: preadipocyte


title: d3_NTmimic_2

description: Library name: d3_NTmimic_2


title: d3_NTmimic_1

description: Library name: d3_NTmimic_1


title: Donor_4,Colon,CD4,PMAiIL2,rep2

description: Library name: Donor4_sample3

tag: tissue

tag: cell type

value: isolated CD4


title: d3_335mimic_3

description: Library name: d3_335mimic_3

tag: treatment

value: miR-335-5p mimic


title: SNU-398 cells, shMRPL37, repeat2

city: yichang

first: Hao

last: Deng

state: hubei

address: DAXUE Road No.8

institute: China Three Gorges University

description: Library name: shMRPL37_rep2

data_processing:
Raw sequencing reads were subjected to quality control using FastQC (v0.11.9)
Adapter sequences and low-quality bases were trimmed using Trimmomatic (v0.39)
Clean reads were aligned to the human reference genome (GRCh38/hg38) using STAR aligner (v2.7.9a)
Gene expression quantification was performed using featureCounts (Subread v2.0.1) based on GENCODE annotation (release 38)
Differential gene expression analysis was conducted using DESeq2 (v1.30.0) in R
Assembly: hg38
Supplementary files format and content: Processed data files include gene-level read count matrices in tab-delimited text format (TXT) and normalized expression data (e.g., TPM or FPKM) in Excel (XLSX) or text (TXT) format. Each file contains gene identifiers in rows and sample names in columns, with values representing gene expression levels.

source_name: Liver

growth_protocol: SNU-398 human hepatocellular carcinoma cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin at 37°C in a humidified atmosphere containing 5% CO₂. Cells were maintained at sub-confluent conditions and routinely passaged using trypsin-EDTA.

extract_protocol:
Total RNA was extracted using TRIzol reagent and purified using phenol-chloroform extraction. rRNA was removed, and mRNA was purified using the Fast RNA-seq Lib Prep Kit V2 (Aibotech, RK20306).
Libraries were prepared and subjected to high-throughput sequencing (PE150) on an Illumina platform.

value: Liver

value: human hepatocellular carcinoma cell line

value: MRPL37 knockdown

value: Transduced with shRNA targeting MRPL37


title: SH_INSM1_1

description: Library name: sample 1

value: INSM1 Overexpression

value: transduction with INSM1 adenoviral vectors


title: e-miRNA_plasma_ICAD_05

description: Library name: 119202-5

value: Hemodynamic

value: Female

value: yes

value: no

tag: endostatin (ng/ml)

tag: angiostatin+ (ng/ml)


title: SH_INSM1_2

description: Library name: sample 2

value: neuroblastoma


title: e-miRNA_plasma_ICAD_04

description: Library name: 119202-4

value: plasma

tag: phenotype

tag: disease


title: SNU-398 cells, shMRPL37, repeat1

description: Library name: shMRPL37_rep1


title: d3_335mimic_2

description: Library name: d3_335mimic_2

value: 3T3-L1 fibroblasts (ATTC CL-17)


title: EO771

city: Seoul

first: Minkyu

last: Shim

address: 103, Daehak-ro, Jongno-gu

country: South Korea

institute: Seoul National University

description: Library name: EO771

library_source: genomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0.
Assembly: hg38, mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: tumor

extract_protocol:
After surgery, TNBC samples were chopped into submilimeter particles manually and incubated for 30 minutes in a 37℃ 5% CO2 incubator with RPMI-160, supplemented with 1mg/mL hyaluronidase, 1mg/mL collagenase type IV, and 0.5mg/mL DNase I. After tissue digestion, cells were filtered with 70um cell strainers. Erythrocytes were lysed with 3ml ACK lysis buffer on ice for 5 min. The reaction was stopped by adding 10ml 1X PBS. After centrifugation, cells were resuspended with 1ml RPMI-1640 supplemented with 10% FBS. CD11b+ cells were isolated with BD Aria III sorter, and then were immediately sent for scRNA-seq.
Library was performed according to the manufacturer's instructions.

value: tumor

value: naïve


title: e-miRNA_plasma_ICAD_07

description: Library name: 119202-7

value: Non-Hemodynamic

value: intracranial atherosclerosis

tag: history of_diabetes

tag: history of_hypertension


title: SNU-398 cells, shControl, repeat2

description: Library name: shCtrl_rep2

value: Liver

value: WT

value: Transduced with non-targeting control shRNA


title: d3_335mimic_1

description: Library name: d3_335mimic_1

value: miR-335-5p mimic

value: preadipocyte


title: SH_LacZ_1

description: Library name: sample 3

value: transduction with LacZ adenoviral vectors


title: SNU-398 cells, shControl, repeat1

description: Library name: shCtrl_rep1

value: human hepatocellular carcinoma cell line


title: e-miRNA_plasma_ICAD_01

description: Library name: 119202-1

value: Female

tag: baseline modified_rankin_scale_(mrs)

tag: vegf 165b+


title: Kidney, HU

city: Shenzhen

first: Donglin

last: Sun

state: None Selected

address: Xinhu Road, Bao'an District

institute: Southern Medical University

description: BD Rhapsody,GEX

data_processing:
Basecalls performed using CASAVA version 1.8
We applied  STARsolo with default parameter to analyze single-cell GEX
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Kidney

extract_protocol:
single cell suspension of kidney cells were prepared for single cell sequencing analysis
BD Rhapsody system  were used to capture the single cells and construct the scRNA-Seq libraries

value: Kidney

value: unilateral ureteral obstruction (UUO) combined with NAFLD through high-fat diet feeding


title: BBN19207, CTR with infection

status: Public on Dec 16 2025

city: Exeter

first: Giulia

last: Pegoraro

address: Barrack Road

country: United Kingdom

institute: University of Exeter

description: Library name: BBN19207

data_processing:
The FASTQ files containing the sequenced data underwent QC analysis using FastQC. Subsequently, FastQ Screen was utilized to assess typical contaminants, and fastp was employed for trimming adapters and removing low-quality reads.
The genes in the count matrix underwent expression level filtration using the filterByExpr function in EdgeR, with a minimum count set to 10 and the minimum proportion of samples where a gene needs to be expressed set to 80%. Data were normalized by taking the log2 of the values obtained from the counts per million (CPM) method. Normalization factors were computed based on library sizes using the trimmed mean of the M-values method (TMM) with the calcNormFactors function.
Assembly: GrCh38
Supplementary files format and content: csv file containing raw counts
Supplementary files format and content: csv file containing log2 CPM normalized counts

source_name: Prefrontal cortex

extract_protocol:
Qiagen AllPrep DNA/RNA/miRNA Universal kit
The library preparation was performed using Illumina Stranded Total RNA Prep protocol using 9ng total RNA with samples organised across plates by RIN score, whilst randomising for other variables.

value: Prefrontal cortex

tag: age

tag: gender

value: F

tag: ad

tag: infection

tag: sequencing plate_number

tag: library size

tag: extraction batch

tag: sample group

value: CTR with infection


title: BBN8918, AD with infection

description: Library name: BBN8918

tag: tissue

value: AD with infection


title: BBN9332, AD with infection

description: Library name: BBN9332


title: BBN00629544, AD with infection

description: Library name: BBN00629544


title: BBN00328775, CTR no infection

description: Library name: BBN00328775

value: M

value: CTR no infection


title: BBN19605, CTR no infection

description: Library name: BBN19605


title: BBN4232, AD no infection

description: Library name: BBN4232

value: AD no infection


title: BBN7477, CTR no infection

description: Library name: BBN7477


title: BBN9262, AD no infection

description: Library name: BBN9262


title: BBN7310, AD no infection

description: Library name: BBN7310


title: BBN7485, AD with infection

description: Library name: BBN7485


title: e-miRNA_plasma_ICAD_03

description: Library name: 119202-3

value: plasma

value: Non-Hemodynamic

value: intracranial atherosclerosis

tag: Sex

value: yes

value: no

tag: history of_hypercholesterolemia

tag: vegf (pg/ml)

tag: hgf (pg/ml)

tag: endostatin (ng/ml)


title: BBN9389, CTR no infection

description: Library name: BBN9389


title: e-miRNA_plasma_ICAD_02

description: Library name: 119202-2

tag: phenotype

value: Hemodynamic

tag: disease

value: Male

tag: history of_diabetes

tag: history of_hypertension

tag: angiostatin+ (ng/ml)


title: BBN9151, AD no infection

description: Library name: BBN9151

tag: age

tag: gender

tag: ad


title: Kidney, WU

description: BD Rhapsody,GEX

tag: treatment

value: unilateral ureteral obstruction (UUO) combined with normal diet


title: BBN9367, AD no infection

description: Library name: BBN9367

tag: infection

tag: sequencing plate_number

tag: library size

tag: extraction batch


title: BBN00329202, CTR no infection

description: Library name: BBN00329202

tag: tissue

tag: sample group


title: BBN7540, AD no infection

description: Library name: BBN7540


title: BBN9263, AD with infection

description: Library name: BBN9263


title: BEAS_2B E6E7 Cy5 rep 2

city: Santiago

first: Ulises

last: Urzua

address: Independencia 1027

department: Basic and Clinical Oncology

country: Chile

institute: University of Chile

hyb_protocol: The labeled cDNA was purified by Minelute columns (QIAGEN). Absorbance readings at 260, 550 and 650 nm were measured to estimate labeling efficiency using a Nanodrop1000 spectrophotometer (Thermo Scientific). 39 uL the labeled cDNA were combined with 45 ul of formamide solution 2X (0.2% SDS, 0.2 ug/mL fish sperm DNA, 10X SSC buffer) and denatured at 95° C for 3 min. The total 90 uL of this mixture were deposited on the microarray, covered with a LifterSlip and incubated in a ArrayIt hybridization cassette for 22 h at 42° C.

scan_protocol: The slides were showing four times with showing solutions for two min and then analyzing into the scan (Perkin Elmer Scan Array Lite).

data_processing: The output Image was analyzed with GenePix pro 6.0 and the normalization of dates was make in the TMEV software. Lowess normalized log2 ratio representing test/reference (Cy5/Cy3) in sample 2 and 4, and dye swap replicates test/reference (Cy3/Cy5) in sample 1 and 3. columns B and D, and dye swap replicates test/reference (Cy3/Cy5) in columns C and E.

source_name: Bronchial lung cell

label_protocol: RNA quality was verified by 0.9% agarose gel electrophoresis. 15 μg of RNA  were labeled by reverse transcription in a 35 uL reaction containing 3 ug of random primers, 3 ug oligo-dT, 10 nmoles of dATP, dGTP and dTCP, 4 nmoles of dTTP, 2.5 nmol of either Cy3 or Cy5-dUTP, 40 U of RNAsin and 800 U of M-MLV Reverse Transcriptase (Promega). After incubation at 37ºC for 2 h, 300 additional U of enzyme and further incubated for 2 h.

growth_protocol: Cells were grown in RPMI-1640 basal medium supplemented with 10% FBS and antibiotics (gentamicin, penicillin and streptomicin) at 37ºC with 5% CO2 atmosphere. For subculture, cells were trypsinized 3-5 min and treated with fresh medium containing FBS. Stably transfected BEAS_2B cells were selected and grown in a culture medium containing 0.1 μg/mL G418.

extract_protocol: Total RNA was obtained using 1 mL of Trizol reagent (Invitrogen) according to the manufacturer's instructions.

treatment_protocol: Cells were cultured to 80% confluence and serum depleted for 24 h. Then, cells were exposed to CSC (Kentucky University) dissolved in RPMI-1640 medium at 10 μg/mL.

tag: cell type

value: BEAS_2B ATCC

tag: transfection

value: empty pLXSN vector

value: E6E7 HPV-16 genes using pLXSN vector


title: BEAS_2B E6E7 Cy3 rep 1


title: BBN15259, AD no infection

description: Library name: BBN15259

value: Prefrontal cortex

value: F


title: BBN7422, CTR no infection

description: Library name: BBN7422


title: BEAS_2B E6E7 Cy3 rep 2


title: BEAS_2B E6E7 Cy5 rep 1


title: BBN00135156, CTR no infection

description: Library name: BBN00135156


title: BBN00332233, AD with infection

description: Library name: BBN00332233

value: AD with infection


title: BBN00627017, AD with infection

description: Library name: BBN00627017


title: BBN4204, AD no infection

description: Library name: BBN4204

value: M


title: BBN00629614, AD with infection

description: Library name: BBN00629614


title: BBN7214, AD no infection

description: Library name: BBN7214


title: BBN14416, CTR with infection

description: Library name: BBN14416

value: CTR with infection


title: BBN9219, AD no infection

description: Library name: BBN9219

value: AD no infection


title: BBN24324, AD no infection

description: Library name: BBN24324


title: BBN8770, CTR with infection

description: Library name: BBN8770


title: BBN22622, AD no infection

description: Library name: BBN22622


title: BBN00328369, CTR no infection

description: Library name: BBN00328369

value: CTR no infection


title: BBN00129135, AD with infection

description: Library name: BBN00129135


title: BBN00332200, AD with infection

description: Library name: BBN00332200


title: BBN00735762, CTR with infection

description: Library name: BBN00735762


title: BBN24895, AD no infection

description: Library name: BBN24895


title: BBN26009, CTR with infection

description: Library name: BBN26009


title: BBN24325, CTR with infection

description: Library name: BBN24325


title: BBN9505, AD no infection

description: Library name: BBN9505


title: BBN24528, CTR no infection

description: Library name: BBN24528


title: BBN7535, AD with infection

description: Library name: BBN7535


title: BBN7462, AD with infection

description: Library name: BBN7462


title: BBN7545, CTR no infection

description: Library name: BBN7545


title: BBN12609, CTR with infection

description: Library name: BBN12609


title: BBN7519, CTR no infection

description: Library name: BBN7519


title: BBN00333724, CTR with infection

description: Library name: BBN00333724


title: BBN7511, AD with infection

description: Library name: BBN7511


title: BBN15810, AD no infection

description: Library name: BBN15810


title: BBN00532843, AD with infection

description: Library name: BBN00532843


title: BBN9420, AD no infection

description: Library name: BBN9420


title: BBN00128771, AD no infection

description: Library name: BBN00128771


title: BBN00631516, CTR with infection

description: Library name: BBN00631516


title: BBN7196, CTR no infection

description: Library name: BBN7196


title: BBN7591, AD with infection

description: Library name: BBN7591


title: BBN00126719, CTR no infection

description: Library name: BBN00126719


title: BBN00130047, CTR with infection

description: Library name: BBN00130047


title: BBN4205, CTR no infection

description: Library name: BBN4205


title: BBN00128799, CTR with infection

description: Library name: BBN00128799


title: BBN3454, CTR no infection

description: Library name: BBN3454


title: BBN00328372, CTR no infection

description: Library name: BBN00328372


title: BBN9377, AD no infection

description: Library name: BBN9377


title: BBN9303, AD no infection

description: Library name: BBN9303


title: BBN00126718, AD with infection

description: Library name: BBN00126718


title: BBN9123, AD with infection

description: Library name: BBN9123


title: BBN9315, AD with infection

description: Library name: BBN9315


title: BBN00329753, CTR with infection

description: Library name: BBN00329753


title: BBN8819, AD with infection

description: Library name: BBN8819


title: BBN7541, AD with infection

description: Library name: BBN7541


title: BBN00726827, AD no infection

description: Library name: BBN00726827


title: BBN9005, AD no infection

description: Library name: BBN9005


title: BBN00326947, CTR no infection

description: Library name: BBN00326947


title: BBN11763, AD no infection

description: Library name: BBN11763


title: BBN7623, CTR no infection

description: Library name: BBN7623


title: BBN00635477, AD no infection

description: Library name: BBN00635477


title: BBN14795, AD with infection

description: Library name: BBN14795


title: BBN9031, AD with infection

description: Library name: BBN9031


title: BBN9408, CTR with infection

description: Library name: BBN9408


title: BBN7569, AD no infection

description: Library name: BBN7569


title: BBN9359, CTR with infection

description: Library name: BBN9359


title: BBN9003, AD no infection

description: Library name: BBN9003


title: BBN9076, AD with infection

description: Library name: BBN9076


title: BBN9435, AD with infection

description: Library name: BBN9435


title: BBN00529822, CTR with infection

description: Library name: BBN00529822


title: BBN00130208, CTR no infection

description: Library name: BBN00130208


title: BBN00126309, CTR no infection

description: Library name: BBN00126309


title: BBN9423, CTR with infection

description: Library name: BBN9423


title: BBN00629018, CTR no infection

description: Library name: BBN00629018


title: BBN00130147, CTR no infection

description: Library name: BBN00130147


title: BBN00332261, CTR no infection

description: Library name: BBN00332261


title: BBN24526, AD no infection

description: Library name: BBN24526


title: BBN19608, CTR with infection

description: Library name: BBN19608


title: BBN9419, AD with infection

description: Library name: BBN9419


title: BBN25739, AD no infection

description: Library name: BBN25739


title: BBN7125, AD with infection

description: Library name: BBN7125


title: BBN7539, AD with infection

description: Library name: BBN7539


title: BBN25060, CTR no infection

description: Library name: BBN25060


title: BBN8846, AD with infection

description: Library name: BBN8846


title: BBN00135381, CTR with infection

description: Library name: BBN00135381


title: BBN00632514, AD no infection

description: Library name: BBN00632514


title: BBN00328342, CTR no infection

description: Library name: BBN00328342


title: BBN9122, AD no infection

description: Library name: BBN9122


title: BBN9113, AD no infection

description: Library name: BBN9113


title: BBN24563, AD with infection

description: Library name: BBN24563


title: BBN00529468, CTR no infection

description: Library name: BBN00529468


title: BBN9371, AD no infection

description: Library name: BBN9371


title: BBN00332218, AD with infection

description: Library name: BBN00332218


title: BBN7494, AD with infection

description: Library name: BBN7494


title: BBN00631488, CTR with infection

description: Library name: BBN00631488


title: BBN00634151, AD no infection

description: Library name: BBN00634151


title: BBN9323, AD with infection

description: Library name: BBN9323


title: BBN4214, AD no infection

description: Library name: BBN4214


title: BBN8833, AD with infection

description: Library name: BBN8833


title: BBN00128416, CTR no infection

description: Library name: BBN00128416


title: BBN00128793, CTR no infection

description: Library name: BBN00128793


title: BBN9354, CTR no infection

description: Library name: BBN9354


title: BBN24322, AD no infection

description: Library name: BBN24322


title: BBN00628766, AD with infection

description: Library name: BBN00628766


title: BBN00129521, AD with infection

description: Library name: BBN00129521


title: BBN00632924, AD no infection

description: Library name: BBN00632924


title: BBN9430, CTR no infection

description: Library name: BBN9430


title: BBN7110, AD with infection

description: Library name: BBN7110


title: BBN00129136, CTR with infection

description: Library name: BBN00129136


title: BBN8997, AD no infection

description: Library name: BBN8997


title: BBN19206, CTR no infection

description: Library name: BBN19206


title: BBN00328560, CTR no infection

description: Library name: BBN00328560


title: BBN8868, AD with infection

description: Library name: BBN8868


title: BBN9342, AD no infection

description: Library name: BBN9342


title: BBN00332278, AD no infection

description: Library name: BBN00332278


title: BBN4240, CTR with infection

description: Library name: BBN4240


title: BBN00130916, CTR no infection

description: Library name: BBN00130916


title: BBN3447, CTR no infection

description: Library name: BBN3447


title: BBN9134, AD no infection

description: Library name: BBN9134


title: BBN22226, CTR no infection

description: Library name: BBN22226


title: BBN7306, AD with infection

description: Library name: BBN7306


title: BBN00628893, CTR no infection

description: Library name: BBN00628893


title: BBN00532822, CTR with infection

description: Library name: BBN00532822


title: BBN00635953, AD no infection

description: Library name: BBN00635953


title: BBN00332222, AD with infection

description: Library name: BBN00332222


title: BBN2602, AD with infection

description: Library name: BBN2602


title: BBN00635895, AD no infection

description: Library name: BBN00635895


title: BBN00531442, CTR with infection

description: Library name: BBN00531442


title: BBN9429, CTR no infection

description: Library name: BBN9429


title: BBN00635513, AD no infection

description: Library name: BBN00635513


title: BBN24312, CTR no infection

description: Library name: BBN24312


title: BBN00126307, AD with infection

description: Library name: BBN00126307


title: BBN9183, AD with infection

description: Library name: BBN9183


title: BBN00335201, AD with infection

description: Library name: BBN00335201


title: BBN9422, CTR with infection

description: Library name: BBN9422


title: BBN24668, AD no infection

description: Library name: BBN24668


title: BBN8719, CTR no infection

description: Library name: BBN8719


title: BBN9016, CTR no infection

description: Library name: BBN9016


title: BBN9413, CTR no infection

description: Library name: BBN9413


title: BBN00328692, CTR no infection

description: Library name: BBN00328692


title: BBN00126722, CTR no infection

description: Library name: BBN00126722


title: BBN00633738, AD no infection

description: Library name: BBN00633738


title: BBN19364, CTR no infection

description: Library name: BBN19364


title: BBN13407, CTR with infection

description: Library name: BBN13407


title: BBN24561, CTR no infection

description: Library name: BBN24561


title: BBN8965, AD with infection

description: Library name: BBN8965


title: BBN8961, CTR no infection

description: Library name: BBN8961


title: BBN2624, AD with infection

description: Library name: BBN2624


title: BBN00128402, CTR with infection

description: Library name: BBN00128402


title: BBN9205, AD no infection

description: Library name: BBN9205


title: BBN9189, AD no infection

description: Library name: BBN9189


title: BBN00632578, CTR no infection

description: Library name: BBN00632578


title: BBN00130142, AD no infection

description: Library name: BBN00130142


title: BBN00135109, AD no infection

description: Library name: BBN00135109


title: BBN3442, CTR no infection

description: Library name: BBN3442


title: BBN8958, AD no infection

description: Library name: BBN8958


title: BBN8857, AD with infection

description: Library name: BBN8857


title: BBN9268, AD with infection

description: Library name: BBN9268


title: BBN9378, AD no infection

description: Library name: BBN9378


title: BBN00529874, CTR no infection

description: Library name: BBN00529874


title: BBN9188, AD with infection

description: Library name: BBN9188


title: BBN7530, AD no infection

description: Library name: BBN7530


title: BBN19597, CTR with infection

description: Library name: BBN19597


title: BBN7517, AD with infection

description: Library name: BBN7517


title: BBN00328355, AD with infection

description: Library name: BBN00328355


title: BBN7465, AD no infection

description: Library name: BBN7465


title: BBN7602, AD with infection

description: Library name: BBN7602


title: BBN00632544, CTR with infection

description: Library name: BBN00632544


title: BBN9341, AD with infection

description: Library name: BBN9341


title: BBN2612, AD with infection

description: Library name: BBN2612


title: BBN00332849, CTR with infection

description: Library name: BBN00332849


title: BBN9421, AD with infection

description: Library name: BBN9421


title: BBN8960, AD no infection

description: Library name: BBN8960


title: BBN00528597, CTR no infection

description: Library name: BBN00528597


title: BBN00328567, CTR with infection

description: Library name: BBN00328567


title: Blood,S29_W16

city: Lubbock

first: Aravindan

last: Kalyanasundaram

state: Texas

address: 3601 4th Street

department: Immunology and Molecular Microbiology

institute: Texas Tech University Health Sciences Center

description:
Library name: S29_W16
S.mansoni Human challenge model

data_processing:
A comprehensive transcriptomic analysis pipeline was implemented, beginning with stringent quality control of raw FASTQ sequencing reads using FastQC, Fastp, SortMeRNA, and Kraken2/Bracken to remove lowquality sequences and contaminants.
Cleaned reads were aligned to the CHM13 human reference genome using STAR, and gene expression was quantified with featureCounts, followed by normalization using edgeR.
Assembly: CHM13
Supplementary files format and content: raw.counts.tsv.gz

source_name: Blood

extract_protocol:
Total RNA was extracted and purified from whole blood collected in PAXgene Blood RNA tubes from 30 participants at six time points, including baseline (prior to exposure, Week 0) and every four weeks thereafter until Week 20 post-exposure (i.e., Weeks 0, 4, 8, 12, 16, and 20 using the Total RNA extraction kit (RNeasy kit, Qiagen).
The Ribo-Zero Gold kit and TruSeq Stranded Total RNA Sample Preparation Kit (Illumina, Inc., San Diego, CA) were used to deplete rRNA from total RNA and to prepare stranded RNA libraries. Paired-end whole-transcriptome sequencing (100 base pairs) was performed on the NovaSeq 6000 platform (Illumina, Inc., San Diego, CA) at the Clinical Genomics Core Facility in Gothenburg, Sweden.

treatment_protocol: The two controlled human Schistosoma infection dose escalation trials at Leiden University Medical Center. A total of 30 volunteers (designated S1 to S30) were recruited. In the first CHI trial (NCT02755324), 17 volunteers were exposed with either 10 (n = 3), 20 (n =11), or 30 (n = 3) male S. mansoni cercariae.  In the second CHI trial (NCT04269915), 13 volunteers (5 male and 8 female adult volunteers) were challenged with 10 (n = 3) or 20 (n = 10) female S. mansoni cercariae. Participants exposed with male cercariae received PZQ at Week 12, while those exposed with female cercariae were treated at both Week 8 and Week 12.

value: Blood

value: Cercarial challenge

tag: time

value: Week 16

tag: Sex

value: female

tag: batch


title: Blood,S28_W20

description:
Library name: S28_W20
S.mansoni Human challenge model

value: Week 20


title: Blood,S30_W16

description:
Library name: S30_W16
S.mansoni Human challenge model

value: male


title: Blood,S30_W0

description:
Library name: S30_W0
S.mansoni Human challenge model

value: Week 0


title: Blood,S28_W8

description:
Library name: S28_W8
S.mansoni Human challenge model

value: Week 8


title: Blood,S28_W4

description:
Library name: S28_W4
S.mansoni Human challenge model

value: Week 4


title: Blood,S29_W8

description:
Library name: S29_W8
S.mansoni Human challenge model


title: Blood,S29_W12

description:
Library name: S29_W12
S.mansoni Human challenge model

value: Week 12


title: Blood,S30_W8

description:
Library name: S30_W8
S.mansoni Human challenge model


title: Blood,S30_W4

description:
Library name: S30_W4
S.mansoni Human challenge model


title: Blood,S29_W0

description:
Library name: S29_W0
S.mansoni Human challenge model


title: Blood,S28_W12

description:
Library name: S28_W12
S.mansoni Human challenge model


title: Blood,S28_W16

description:
Library name: S28_W16
S.mansoni Human challenge model


title: Blood,S27_W8

description:
Library name: S27_W8
S.mansoni Human challenge model


title: Blood,S27_W20

description:
Library name: S27_W20
S.mansoni Human challenge model


title: Blood,S28_W0

description:
Library name: S28_W0
S.mansoni Human challenge model


title: Blood,S27_W12

description:
Library name: S27_W12
S.mansoni Human challenge model


title: Blood,S26_W20

description:
Library name: S26_W20
S.mansoni Human challenge model


title: Blood,S26_W8

description:
Library name: S26_W8
S.mansoni Human challenge model


title: Blood,S26_W16

description:
Library name: S26_W16
S.mansoni Human challenge model


title: Blood,S25_W8

description:
Library name: S25_W8
S.mansoni Human challenge model


title: Blood,S25_W4

description:
Library name: S25_W4
S.mansoni Human challenge model


title: Blood,S25_W20

description:
Library name: S25_W20
S.mansoni Human challenge model


title: Blood,S27_W0

description:
Library name: S27_W0
S.mansoni Human challenge model


title: Blood,S24_W8

description:
Library name: S24_W8
S.mansoni Human challenge model


title: Blood,S25_W0

description:
Library name: S25_W0
S.mansoni Human challenge model


title: Blood,S25_W16

description:
Library name: S25_W16
S.mansoni Human challenge model


title: Blood,S24_W20

description:
Library name: S24_W20
S.mansoni Human challenge model


title: Blood,S24_W0

description:
Library name: S24_W0
S.mansoni Human challenge model


title: Blood,S24_W16

description:
Library name: S24_W16
S.mansoni Human challenge model


title: Blood,S23_W8

description:
Library name: S23_W8
S.mansoni Human challenge model


title: Blood,S25_W12

description:
Library name: S25_W12
S.mansoni Human challenge model


title: Blood,S22_W20

description:
Library name: S22_W20
S.mansoni Human challenge model


title: Blood,S21_W8

description:
Library name: S21_W8
S.mansoni Human challenge model


title: Blood,S24_W4

description:
Library name: S24_W4
S.mansoni Human challenge model


title: Blood,S27_W16

description:
Library name: S27_W16
S.mansoni Human challenge model


title: Blood,S21_W4

description:
Library name: S21_W4
S.mansoni Human challenge model


title: Blood,S23_W0

description:
Library name: S23_W0
S.mansoni Human challenge model


title: Blood,S22_W4

description:
Library name: S22_W4
S.mansoni Human challenge model


title: Blood,S20_W8

description:
Library name: S20_W8
S.mansoni Human challenge model


title: Blood,S21_W12

description:
Library name: S21_W12
S.mansoni Human challenge model


title: Blood,S26_W0

description:
Library name: S26_W0
S.mansoni Human challenge model


title: Blood,S20_W4

description:
Library name: S20_W4
S.mansoni Human challenge model


title: Blood,S20_W0

description:
Library name: S20_W0
S.mansoni Human challenge model


title: Blood,S19_W4

description:
Library name: S19_W4
S.mansoni Human challenge model


title: Blood,S19_W20

description:
Library name: S19_W20
S.mansoni Human challenge model


title: Blood,S19_W0

description:
Library name: S19_W0
S.mansoni Human challenge model


title: Blood,S22_W0

description:
Library name: S22_W0
S.mansoni Human challenge model


title: Blood,S19_W8

description:
Library name: S19_W8
S.mansoni Human challenge model