title: MCF7_FLAG_input

first: Douglas

last: Barrows

address: 1230 York Ave

institute: Rockefeller University

data_processing:
ChIP-seq reads were aligned using Rsubread’s align method and predicted fragment lengths were calculated by the ChIPQC R Bioconductor package. Normalized, fragment extended signal bigWigs were created using the rtracklayer R Bioconductor package. Peak calls were made using the MACS2 software.
Assembly: hg38
Supplementary files format and content: bigwig files
Supplementary files format and content: narrowPeak files from MACS2

extract_protocol:
Post-confluent cells were fixed with 1% formaldehyde for 10 min, followed by quenching with 125mM glycine and washed with cold TBS (20mM Tris-HCl, 150mM NaCl, pH 7.4) twice. Cells were lysed in cell lysis buffer (10mM Tris-HCl, 10mM NaCl, 0.5% NP-40, pH7.5) and then incubated on ice for 10 mins. Lysates spinned down and resuspended in 500 μl MNase digestion buffer (20mM Tris-HCl, 15mM NaCl, 60mM KCl, 1mM CaCl2, pH 7.5) with MNase (New England, M0247S, 0.25U/1000 cells). After 20 minutes of incubation at 37°C with continuous mixing, digestion was stopped by addition of 500 μl of 2X STOP/ChIP buffer (100mM Tris-HCl, 20mM EDTA, 200mM NaCl, 2% Triton X-100, 0.2% sodium deoxycholate, pH8.1). Samples were sonicated for 7 cycles (30 secs on/30 secs off) with 40% amplitude (Branson Digital Sonifier) and then centrifuged at 12,000rpm for 15min at 4°C to remove insoluble debris. Apart from input samples (1% volume for each ChIP reaction) kept for reverse-crosslinking, lysates were incubated with antibodies (antibody information: see table attached) at 4°C overnight. Antibody-bound complexes were then captured by incubation with Protein A sepharose CL-4B beads (Amersham) for rabbit antibodies or Protein G sepharose 4B beads (Invitrogen) for mouse antibodies (both 20μl per 1mL lysate) for 4 hr at 4 °C. The beads were washed sequentially with STOP/ChIP buffer (50mM Tris-HCl, 10mM EDTA, 100mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, pH8.1), high salt buffer (50mM Tris-HCl, 10mM EDTA, 500mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, pH8.1), LiCl2 buffer (10mM Tris-HCl, 0.25M LiCl2, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA, pH8.0), and TE buffer (50mM Tris-HCl, 10mM EDTA, pH 8.0) (twice). Bound DNA was eluted and reverse-crosslinked at 65°C overnight in ChIP elution buffer (10mM Tris-HCl, 150mM NaCl, 10mM EDTA, 5mM DTT, 1% SDS, pH 8.0). After treatment with RNase A (0.2mg/ml, 37°C, 1h) and proteinase K (2mg/ml, 37°C, 2h), DNA used for sequencing was purified using a MiniElute PCR purification kit (Qiagen), and DNA used for qPCR was purified using a QIAquick PCR purification kit (Qiagen). DNA quality was assessed using an Agilent Bioanalyzer, and quantified using a Qubit Fluorometer (Invitrogen).
ChIP-seq libraries were generated using DNA SMART ChIP-seq kits (Takara Bio) according to the manufacturer's instructions. After size selection (for 250-600bp) by AMPure XP beads (Beckman Coulter), the library was quality was evaluated using the Bioanalyzer and sequenced on Illumina NovaSeq SP (100bp two ends) and Illumina NextSeq High (75 bp single end).

value: breast cancer cell line

value: original

tag: chip antibody


title: S2133_00156_R1_S61

status: Public on Aug 01 2025

type: SRA

city: New York

first: James

last: Krueger

state: NY

address: 1230 York Avenue

department: Center for Clinical and Translational Science

country: USA

institute: The Rockefeller University

description: Column 'S2133_00156' in counts.matrix

library_source: transcriptomic

data_processing:
Adapter & low quality reads removal with cutadapt v2.0
Alignment with star v2.4.2a
quantification with featureCount (subread v1.5.0.post3)
Assembly: GRCh37
Supplementary files format and content: counts.matrix contains gene counts of each sample

molecule: total RNA

organism: Homo sapiens

source_name: SKIN

extract_protocol: RNA-Seq

tag: tissue

value: SKIN

tag: disease

value: Psoriasis

tag: treatment

value: Ixekizumab 80mg Q2W

tag: timepoint

value: BL

tag: group

value: LS


title: PBMCs, IL15, day 7, 32062

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

description:
Library name: G011_O16_32062_d7_GEMS1_cDNA1_LIB1
!0x Genomics

library_source: transcriptomic single cell

data_processing:
demuliplexed and aligned data using CellRanger v6.0.1 to the Rhesus macaque genome (Mmul 10)
Assembly: Rhesus macaque genome v10 (Mmul) Ensembl annotation version 100
Supplementary files format and content: barcode, features and matrix files

organism: Macaca mulatta

source_name: PBMCs

extract_protocol:
10x extraction protocol
Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 ; 10X Genomics

treatment_protocol: Rhesus macaques were treated with IL-15/IL-15Rawere collected at 4 time points (baseline, pre IL-15, and days 3, 7 and 10)

value: PBMCs

tag: time

value: day 7

tag: Sex

value: male

tag: animal id

tag: dose

value: 10 ug/kg IL-15/IL-15Ra


title: Whole blood, Control, day 0, 39097

description: Library name: G003_O20_Cy_39097_D0

data_processing:
Trimgalorev0.6.10 used to remove low quality reads and bases
Filtered out globin and rRNA reads using bowtie2v2.4.4
Aligned reads with STARv2.7.10b to both rhesus macaque and cynomolgus macaque genomes
Assembly: Macaca fascicularis version 6 Ensembl annoation v110 and Macaca mulatta version 10 Ensembl annoation v110
Supplementary files format and content: Two count matricies one the macaca fascicularis and macaca mulatta

organism: Macaca fascicularis

source_name: Whole blood

extract_protocol:
Isolation of RNA from Whole Blood Using the RNAdvance Blood Kit
mRNA Library Prep for RNA from Whole Blood using KAPA HyperPrep Reagents

treatment_protocol: Cynomolgus macaques treated  treated with increasing doses of IL-15/IL-15Ra

value: Whole blood

value: Control

value: day 0

value: Female

value: 0 ug/kg IL-15/IL-15Ra


title: PBMCs, IL15, day 3, 31954

description:
Library name: G010_O16_31954_d3_GEMS2_cDNA1_LIB1
!0x Genomics

value: day 3

value: 5 ug/kg IL-15/IL-15Ra


title: Whole blood, Control, day 0, 39098

description: Library name: G004_O20_Cy_39098_D0


title: MCF7_p300

library_source: genomic

molecule: genomic DNA

tag: cell line

tag: cell type

value: breast cancer cell line

tag: genotype

value: original

value: anti p300 (N-15) (Santa Cruz SC-584)


title: S2133_00137_R1_S20

description: Column 'S2133_00137' in counts.matrix

value: SKIN

value: Psoriasis

value: Ixekizumab 80mg Q2W


title: PBMCs, IL15, day 3, 34100

description:
Library name: G009_O16_34100_d3_GEMS2_cDNA1_LIB2
!0x Genomics

value: PBMCs


title: Whole blood, Control, day 0, 39095

description: Library name: G002_O20_Cy_39095_D0


title: S2133_00064_R1_S11

description: Column 'S2133_00064' in counts.matrix

value: LS


title: MCF7_FLAG

value: anti FLAG (M2) (Sigma A2220)


title: MCF7_AceK

value: anti pan-acetyl-lysine (Ac-K-103) (Cell Signaling #9681)


title: PBMCs, IL15, day 3, 34024

description:
Library name: G008_O16_34024_d3_GEMS1_cDNA1_LIB1
!0x Genomics

value: male


title: S2133_00106_R1_S14

description: Column 'S2133_00106' in counts.matrix


title: Whole blood, Control, day 0, 39090

description: Library name: G001_O20_Cy_39090_D0

value: Whole blood

value: Control


title: PBMCs, IL15, 48hr, 38157, 3

description: Library name: G132_O19_38157_IL15_48hr_3

extract_protocol:
Isolation of RNA using Qiagen RNeasy Mini Kit
mRNA Library Prep Using KAPA mRNA HyperPrep Kit

treatment_protocol: Ex-vivo PBMCs from cynomolgus macaques were treated with IL-15/IL-15Ra (40ng/ml)

value: Male

tag: replicate

value: 40 ng/ml


title: PBMCs, IL15, day 3, 33047

description:
Library name: G007_O16_33047_d3_GEMS1_cDNA1_LIB1
!0x Genomics

value: day 3


title: MCF7_MED1KR_HiCAR

description: 10k bin

data_processing:
Fastq files were run through the Nextflow HiCAR pipeline, using default settings (https://nf-co.re/hicar ) (v1.0.0). Cooler files from the Nextflow pipeline were visualized as heatmaps at 2.5Mbp, 50Kbp, and 5Kbp resolution using the HiGlass tool (Kerpedjiev, 2018). To determine quantitative changes of read counts in interactions between WT/KO and 6KR/KO MED1 cells, data from cooler files were extracted at 10K resolution using the ‘cooler dump’ function from the cooler command line interface (v0.9.1) (Abdennur, 2020). The HiCcompare R Bioconductor package was used to read unbalanced count data into R, adjust for sequencing depth, apply loess normalization, and determine fold changes (v1.12.0) (Stansfield 2018).
Assembly: hg38
Supplementary files format and content: mcool files for genomic interaction data
Supplementary files format and content: bedPE files showing significant interactions from MAPS
Library strategy: HiCAR-seq

source_name: MCF7 MED1 6KR

extract_protocol:
About 400,000 post-confluent cells were digested and fixed with 1% formaldehyde for 10 min, followed by quenching with 125mM glycine and washed with cold TBS (20mM Tris-HCl, 150mM NaCl, pH 7.4) once. Cells were lysed by NPB buffer (PBS with 5% BSA, 0.2% NP-40, 1mM DTT) and nuclei were spinned down and re-suspended with TB buffer (33mM Tris-AC, 66mM KAc, 10mM MgAC2, 16% DMF, pH 7.8) where tagmentation by assembled Tn5 (Diagenode) complex was performed. The nuclei were further lysed by 0.5% SDS at 62°C and 1.25% Triton X-100 at 37°C and then digested by CviQI (New England) followed by Tn5 adapter ligation which required help from splint oligo in RCB buffer (50mM Tris-HCl, 50mM NaCl, 0.2% SDS, pH 8.0). Next, cross-links were reversed and DNA was precipitated in glycogen-NaAC-Ethanol solution and re-suspended in Tris-HCl (10mM, pH 8.0) where Nla III digestion was performed.
AMPure XP beads (Beckman Coulter) was used for size selection and DNA at 1 ng/μl was circularized by T4 DNA ligase (New England) in Tris-HCl (10mM, pH 8.0). Final library was amplified by Q5 polymerase (New England). The PCR condition: initial denaturation 98°C for 30 sec, 12 cycles of denaturation 98°C for 10 sec/ annealing 59°C for 30 sec/ extension 72°C for 30 sec, then final extension 72°C for 5 min. The size of library should range from 200bp to 800bp, so the DNA with smaller or larger size was removed by another round of AMPure XP beads purification. The sequencing was performed with Illumina NovaSeq SP (100bp two ends).

value: MCF7 MED1 6KR


title: S2133_00016_R1_S18

description: Column 'S2133_00016' in counts.matrix

value: BL


title: MCF7_MED1WT_HiCAR

description: 10k bin

source_name: MCF7 MED1 WT

value: MCF7 MED1 WT

value: breast cancer cell line


title: PBMCs, IL15, day 3, 32062

description:
Library name: G006_O16_32062_d3_GEMS1_cDNA1_LIB1
!0x Genomics

value: 5 ug/kg IL-15/IL-15Ra


title: PBMCs, IL15, 48hr, 38157, 1

description: Library name: G130_O19_38157_IL15_48hr_1


title: S2133_00167_R1_S7

description: Column 'S2133_00167' in counts.matrix

value: SKIN

value: Psoriasis

value: Guselkumab 100mg


title: MCF7 cells, KR_3

data_processing:
Transcript abundance was computed from FASTQ files using Salmon (v0.8.2) and the GENCODE reference transcript sequences, transcript counts were imported into R with the tximport R Bioconductor package, and differential gene expression was determined with the DESeq2 R Bioconductor package
Assembly: hg38
Supplementary files format and content: raw counts from DESeq2

molecule: polyA RNA

source_name: MCF7 6KR MED1

extract_protocol:
Cells were harvested, washed with PBS, and flash frozen in liquid nitrogen. RNA was isolated using QIAGEN RNeasy kit.
Libraries were generated using mRNA TruSeq stranded 350bp

value: MCF7 6KR MED1

value: ectopic 6KR MED1

value: rep 3


title: PBMCs, IL15, 48hr, 38157, 2

description: Library name: G131_O19_38157_IL15_48hr_2

value: PBMCs


title: PBMCs, control, Baseline, 31954

description:
Library name: G005_O16_31954_BS_GEMS1_cDNA1_LIB1
!0x Genomics

value: control

value: Baseline

value: male

value: 0 ug/kg IL-15/IL-15Ra


title: S2133_00006_R1_S20

description: Column 'S2133_00006' in counts.matrix

value: Ixekizumab 80mg Q2W

value: LS


title: PBMCs, IL15, 24hr, 38157, 3

description: Library name: G129_O19_38157_IL15_24hr_3

value: Male

value: 40 ng/ml


title: PBMCs, control, Baseline, 34100

description:
Library name: G004_O16_34100_BS_GEMS2_cDNA1_LIB2
!0x Genomics


title: MCF7 cells, KR_2

value: breast cancer cell line

value: rep 2


title: PBMCs, control, Baseline, 34024

description:
Library name: G003_O16_34024_BS_GEMS1_cDNA1_LIB1
!0x Genomics


title: S2133_00062_R1_S19

description: Column 'S2133_00062' in counts.matrix

value: SKIN


title: S2133_00119_R1_S26

description: Column 'S2133_00119' in counts.matrix

value: Psoriasis

value: BL


title: PBMCs, IL15, 24hr, 38157, 1

description: Library name: G127_O19_38157_IL15_24hr_1


title: PBMCs, control, Baseline, 33047

description:
Library name: G002_O16_33047_BS_GEMS1_cDNA1_LIB1
!0x Genomics


title: PBMCs, IL15, 12hr, 38157, 3

description: Library name: G126_O19_38157_IL15_12hr_3


title: PBMCs, IL15, 24hr, 38157, 2

description: Library name: G128_O19_38157_IL15_24hr_2


title: PBMCs, control, Baseline, 32062

description:
Library name: G001_O16_32062_BS_GEMS1_cDNA1_LIB1
!0x Genomics


title: MCF7 cells, WT_2

source_name: MCF7 WT MED1

value: MCF7 WT MED1

value: ectopic WT MED1


title: S2133_00019_R1_S33

description: Column 'S2133_00019' in counts.matrix

value: Guselkumab 100mg


title: MCF7 cells, WT_3

value: rep 3


title: PID140, unvaccinated , unvaccinated, SIV infected, 29557

description:
Library name: G131_ABL01_29557_PID140
!0x Genomics

data_processing:
demuliplexed and aligned data using CellRanger v6.0.1 to the Rhesus Macaque genome (Mmul10, Ensembl v100)
Aligned reads from samples collected only during post SIV challenge time points to SIV genome SIV239_M33262_1 using scPathoQuant
Assembly: Rhesus Macaque genome (Mmul10, Ensembl v100)
Supplementary files format and content: Barcodes.tsv, feature.tsv, and matrix.mtx files

treatment_protocol: Adminstration of 68-1 or 68-1.2 RhCMV/SIV vector in  prime and boost regimine

value: PBMCs

value: unvaccinated

tag: treatment outcome

value: unvaccinated, SIV infected


title: MCF7 cells, WT_1

value: rep 1


title: S2133_00080_R1_S26

description: Column 'S2133_00080' in counts.matrix


title: BSLN, unvaccinated , unvaccinated, SIV infected, 29557

description:
Library name: G130_ABL01_29557_BSLN
!0x Genomics

value: BSLN


title: S2133_00047_R1_2_S13

description: Column 'S2133_00047' in counts.matrix

value: LS


title: PBMCs, IL15, 12hr, 38157, 1

description: Library name: G124_O19_38157_IL15_12hr_1

value: Male


title: MCF7 cells, KO3_2

source_name: MCF7 MED1 KO3

value: MCF7 MED1 KO3

value: MED1 KO3 pool


title: BSLN, unvaccinated , unvaccinated, SIV infected, 29358

description:
Library name: G129_ABL01_29358_BSLN
!0x Genomics


title: MCF7 cells, KO3_1

value: breast cancer cell line


title: PBMCs, IL15, 6hr, 38157, 1

description: Library name: G121_O19_38157_IL15_6hr_1

value: 40 ng/ml


title: MCF7 cells, KO2_2

source_name: MCF7 MED1 KO2

value: MCF7 MED1 KO2

value: MED1 KO2 pool

value: rep 2


title: S2133_00020_R1_S8

description: Column 'S2133_00020' in counts.matrix

value: SKIN

value: Psoriasis


title: S2133_00112_R1_S60

description: Column 'S2133_00112' in counts.matrix

value: Guselkumab 100mg


title: MCF7 cells, KR_1

value: MCF7 6KR MED1

value: ectopic 6KR MED1


title: PBMCs, IL15, 6hr, 38157, 2

description: Library name: G122_O19_38157_IL15_6hr_2

value: PBMCs


title: PBMCs, IL15, 12hr, 38157, 2

description: Library name: G125_O19_38157_IL15_12hr_2


title: BSLN, unvaccinated , unvaccinated, SIV infected, 29324

description:
Library name: G127_ABL01_29324_BSLN
!0x Genomics

value: unvaccinated

value: unvaccinated, SIV infected


title: MCF7 cells, KO1_2

source_name: MCF7 MED1 KO1

value: MCF7 MED1 KO1

value: MED1 KO1 pool


title: MCF7 cells, KO2_1

value: rep 1


title: PBMCs, IL15, 6hr, 38157, 3

description: Library name: G123_O19_38157_IL15_6hr_3

value: Male


title: PBMCs, IL15, 2hr, 38157, 2

description: Library name: G119_O19_38157_IL15_2hr_2


title: S2133_00037_R1_S34

description: Column 'S2133_00037' in counts.matrix

value: LS


title: BSLN, unvaccinated , unvaccinated, SIV infected, 29330

description:
Library name: G128_ABL01_29330_BSLN
!0x Genomics

value: BSLN


title: PBMCs, IL15, 2hr, 38157, 3

description: Library name: G120_O19_38157_IL15_2hr_3

value: 40 ng/ml


title: BSLN, unvaccinated , unvaccinated, SIV infected, 29060

description:
Library name: G126_ABL01_29060_BSLN
!0x Genomics


title: S2133_00127_R1_S49

description: Column 'S2133_00127' in counts.matrix


title: PID56, unvaccinated , unvaccinated, SIV infected, 29557

description:
Library name: G125_ABL01_29557_PID56
!0x Genomics


title: MCF7 cells, KO1_1

value: breast cancer cell line


title: S2133_00069_R1_S14

description: Column 'S2133_00069' in counts.matrix

value: BL


title: PID28, unvaccinated , unvaccinated, SIV infected, 29557

description:
Library name: G124_ABL01_29557_PID28
!0x Genomics


title: MCF7 cells, ctrl_2

value: control

value: rep 2


title: PBMCs, IL15, 2hr, 38157, 1

description: Library name: G118_O19_38157_IL15_2hr_1


title: S2133_00053_R1_S57

description: Column 'S2133_00053' in counts.matrix

value: SKIN

value: Psoriasis

value: Guselkumab 100mg


title: PID140, unvaccinated , unvaccinated, SIV infected, 29358

description:
Library name: G123_ABL01_29358_PID140
!0x Genomics

value: PBMCs


title: S2133_00116_R1_S63

description: Column 'S2133_00116' in counts.matrix


title: PBMCs, Control, 48hr, 38157, 3

description: Library name: G117_O19_38157_C_48hr_3

value: Control

value: 0 ng/ml


title: PBMCs, Control, 48hr, 38157, 2

description: Library name: G116_O19_38157_C_48hr_2


title: MCF7 cells, ctrl_1


title: PID84, unvaccinated , unvaccinated, SIV infected, 29358

description:
Library name: G122_ABL01_29358_PID84
!0x Genomics

value: unvaccinated

value: unvaccinated, SIV infected


title: S2133_00105_R1_S40

description: Column 'S2133_00105' in counts.matrix


title: S2133_00087_R1_S51

description: Column 'S2133_00087' in counts.matrix


title: T cells, HTO-derived cDNA

city: Shinjuku-ku

first: Taeko

last: Hayakawa

state: Tokyo

address: 35 Shinanomachi

department: Division of Tumor Immunology, Institute for Advanced Medical Research

country: Japan

institute: Keio University School of Medicine

description: Hashtag-derived oligonucleotide (HTO1,2)

library_source: other

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.2
(https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: filtered_feature_bc_matrix(.h5)
TotalseqC0251 anti-human  Hashtag 1 - GTCAACTCTTTAGCG - cont CAR-T
TotalseqC0252 anti-human  Hashtag 2 - TGATGGCCTATTGGG - KO CAR-T

molecule: protein

source_name: PBMC

extract_protocol:
On day 12, the CD3e+ and CAR+ cells sorted by a cell sorter (Sony) were used as a single cell RNA sequencing sample.
Library was performed according to the manufacter’s instructions (Chromium Next GEM SIngle Cell 5'Reagent Kits v2, 10x Genomics). Briefly, CAR T cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was reversely transcribed to cDNA with Gel Bead primers containingan Illumina TruSeq Read1 sequence, a 10x Barcode, a unique Molecular Identifier (UMI), and template switch oligo (TSO), and poly(dT) primers. Simultaneously in the same partition, the Gel Bead primer captures the cell surface protein Feature Barcode conjugated to HashTag antibodies containing a Nextera Read 2 , a Feature Barcode, and capture sequence, and produces 10x Barcoded DNA with Feature Barcode of Hash Tag antibodies. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R1 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: PBMC

value: T cell

value: CD3+ T cell

value: CAR-T therapy


title: PBMCs, Control, 48hr, 38157, 1

description: Library name: G115_O19_38157_C_48hr_1

value: Male


title: PID56, unvaccinated , unvaccinated, SIV infected, 29358

description:
Library name: G121_ABL01_29358_PID56
!0x Genomics


title: S2133_00018_R1_S62

description: Column 'S2133_00018' in counts.matrix

value: Ixekizumab 80mg Q2W

value: LS


title: PBMCs, Control, 24hr, 38157, 3

description: Library name: G114_O19_38157_C_24hr_3


title: S2133_00166_R1_S64

description: Column 'S2133_00166' in counts.matrix


title: PID28, unvaccinated , unvaccinated, SIV infected, 29358

description:
Library name: G120_ABL01_29358_PID28
!0x Genomics


title: PBMCs, Control, 24hr, 38157, 2

description: Library name: G113_O19_38157_C_24hr_2


title: 231 ACO1KD EV, rep2

city: Wuhan

first: Yan

last: Wei

address: Bayi road 229

country: China

institute: wuhan university

data_processing:
After cluster generation, the library preparations were sequenced on an Illumina platform and 50 bp single-end reads were generated. The raw paired end reads were trimmed and quality controlled by SeqPrep and Sickle with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HIASAT software.
The mapped reads of each sample were assembled by StringTie in a reference-based approach. Low-quality bases (Sanger base quality of < 20) of the 3’ end were trimmed using in-house perl scripts, and then the sequencing adapters were removed with the fastx toolkit software.All identical sequences of sizes ranging from 18 to 32nt were counted and eliminated from the initial data set.The assembled unique sequences were used for a BLAST search of the Rfam database, version 10.1, to remove non-miRNA sequences (rRNA, tRNA, snoRNA etc.). Bowtie2 was used to annotate the chromosomal location against the reference genome data.
Through a BLAST search of the miRbase, version 21.0, the highly matched sequences were used to count and analyze the known miRNA expression profile. The characteristics of hairpin structure of miRNA precursor could be used to predict novel miRNA. Mireap or miRDeep2 were used to predict novel miRNA, and the Dicer cleavage site and the minimum free energy of the small RNA tags were unannotated in the former steps. Meanwhile, in-house scripts were used to obtain the identified miRNA base bias on the first position with certain length and on each position of all identified miRNA.
The expression level of each miRNA was calculated according to the transcripts TPM method.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

growth_protocol: MDA-MB-231 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
RNA was prepared following TruSeq RNA sample preparation Kit from Illumina (San Diego, CA) using 1 μg of total RNA.
Sequencing libraries were generated using NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: The medium from 90% confluent cells grown in EV-free was collected and pre-cleared by centrifugation at 500 × g for 15 min and then at 10,000 × g for 20 min.EVs were pelleted by ultracentrifugation at 110,000 × g for 70 min, and resuspended in PBS.

value: epithelial cell

value: ACO1 knockdown


title: PBMCs, Control, 24hr, 38157, 1

description: Library name: G112_O19_38157_C_24hr_1


title: PID84, unvaccinated , unvaccinated, SIV infected, 29330

description:
Library name: G118_ABL01_29330_PID84
!0x Genomics


title: S2133_00078_R1_S56

description: Column 'S2133_00078' in counts.matrix

value: SKIN

value: BL


title: PID56, unvaccinated , unvaccinated, SIV infected, 29330

description:
Library name: G117_ABL01_29330_PID56
!0x Genomics


title: PBMCs, Control, 12hr, 38157, 3

description: Library name: G111_O19_38157_C_12hr_3


title: 231 EV, rep3

value: WT


title: PBMCs, Control, 12hr, 38157, 2

description: Library name: G110_O19_38157_C_12hr_2

value: PBMCs


title: 231 EV, rep2


title: S2133_00011_R1_S10

description: Column 'S2133_00011' in counts.matrix

value: Psoriasis

value: Guselkumab 100mg


title: S2133_00086_R1_S5

description: Column 'S2133_00086' in counts.matrix


title: 231 EV, rep1


title: PBMCs, Control, 12hr, 38157, 1

description: Library name: G109_O19_38157_C_12hr_1

value: Control

value: 0 ng/ml


title: PID84, unvaccinated , unvaccinated, SIV infected, 29324

description:
Library name: G114_ABL01_29324_PID84
!0x Genomics

value: unvaccinated

value: unvaccinated, SIV infected


title: PID140, unvaccinated , unvaccinated, SIV infected, 29324

description:
Library name: G115_ABL01_29324_PID140
!0x Genomics


title: PBMCs, Control, 6hr, 38157, 3

description: Library name: G108_O19_38157_C_6hr_3


title: CAF, 231 -G EV, rep3

data_processing:
The raw paired end reads were trimmed and quality controlled by SeqPrep  and Sickle with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software.
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
The expression level of each transcript was calculated according to the transcripts per million reads (TPM) method.RSEM was used to quantify gene abundances.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: tumor

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

extract_protocol:
RNA-seq transcriptome library was prepared following TruSeq RNA sample preparation Kit from Illumina (San Diego, CA) using 1 μg of total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 2 μg of EVs (equivalent to those derived from ~5 × 106 producer cells) based on protein measurement using BCA protein assay kit (Thermo Fisher Scientific) was added to 2 × 105 recipient cells in a six-well plate.

value: tumor

value: Cancer-associated fibroblast

value: fibroblast


title: T cells , mRNA-derived cDNA

description: poly A RNA

value: PBMC

value: T cell

value: CD3+ T cell

value: CAR-T therapy


title: S2133_00136_R1_S11

description: Column 'S2133_00136' in counts.matrix

value: SKIN

value: LS


title: 231 ACO1KD EV, rep3

value: epithelial cell

value: ACO1 knockdown


title: PID56, unvaccinated , unvaccinated, SIV infected, 29324

description:
Library name: G113_ABL01_29324_PID56
!0x Genomics

value: PBMCs

value: Male


title: PBMCs, Control, 6hr, 38157, 2

description: Library name: G107_O19_38157_C_6hr_2

value: Control


title: S2133_00118_R1_S36

description: Column 'S2133_00118' in counts.matrix

value: Psoriasis

value: Ixekizumab 80mg Q2W


title: S2133_00128_R1_S63

description: Column 'S2133_00128' in counts.matrix


title: PID140, unvaccinated , unvaccinated, SIV infected, 29330

description:
Library name: G119_ABL01_29330_PID140
!0x Genomics

value: unvaccinated

value: unvaccinated, SIV infected


title: S2133_00056_R1_S4

description: Column 'S2133_00056' in counts.matrix

value: Guselkumab 100mg


title: 231 ACO1KD EV, rep1


title: PID140, unvaccinated , unvaccinated, SIV infected, 29060

description:
Library name: G112_ABL01_29060_PID140
!0x Genomics


title: CAF, 231 -G EV, rep2

value: tumor

value: Cancer-associated fibroblast

value: fibroblast

value: WT


title: PBMCs, Control, 2hr, 38157, 3

description: Library name: G105_O19_38157_C_2hr_3

value: 0 ng/ml


title: PBMCs, Control, 6hr, 38157, 1

description: Library name: G106_O19_38157_C_6hr_1


title: CAF, 231 EV, rep3


title: PID28, unvaccinated , unvaccinated, SIV infected, 29330

description:
Library name: G116_ABL01_29330_PID28
!0x Genomics


title: CAF, 231 -G EV, rep1


title: PID84, unvaccinated , unvaccinated, SIV infected, 29060

description:
Library name: G111_ABL01_29060_PID84
!0x Genomics


title: CAF, 231 EV, rep2


title: S2133_00160_R1_S15

description: Column 'S2133_00160' in counts.matrix

value: SKIN

value: BL


title: S2133_00073_R1_S9

description: Column 'S2133_00073' in counts.matrix

value: LS


title: PID140, 68-1.2 RhCMV/SIV, subcutaneously, Protected, 29522

description:
Library name: G109_ABL01_29522_PID140
!0x Genomics

value: 68-1.2 RhCMV/SIV, subcutaneously

value: Protected


title: S2133_00145_R1_S15

description: Column 'S2133_00145' in counts.matrix


title: PBMCs, Control, 2hr, 38157, 2

description: Library name: G104_O19_38157_C_2hr_2

value: PBMCs

value: Male


title: PBMCs, Control, 0hr, 38157, 3

description: Library name: G102_O19_38157_C_0hr_3

value: Control


title: PID56, unvaccinated , unvaccinated, SIV infected, 29060

description:
Library name: G110_ABL01_29060_PID56
!0x Genomics


title: S2133_00050_R1_S7

description: Column 'S2133_00050' in counts.matrix

value: Psoriasis


title: PBMCs, Control, 2hr, 38157, 1

description: Library name: G103_O19_38157_C_2hr_1


title: S2133_00048_R1_S30

description: Column 'S2133_00048' in counts.matrix


title: CAF, 231 EV, rep1


title: PID28, 68-1.2 RhCMV/SIV, subcutaneously, Protected, 29300

description:
Library name: G107_ABL01_29300_PID28
!0x Genomics


title: PID56, 68-1.2 RhCMV/SIV, subcutaneously, Protected, 29292

description:
Library name: G105_ABL01_29292_PID56
!0x Genomics


title: PID140, 68-1.2 RhCMV/SIV, subcutaneously, Protected, 29300

description:
Library name: G108_ABL01_29300_PID140
!0x Genomics


title: PBMCs, Control, 0hr, 38157, 2

description: Library name: G101_O19_38157_C_0hr_2


title: A549 PFKFB3 overexpression mock 2 [A549mock8-2]

city: Su Zhou

first: Shiyou

last: Wang

state: Jiang Su

address: Chong Wen street

department: Suzhou Institute of Systems Medicine

institute: Peking Union Medical College

data_processing:
CLC Genomics Workbench v 12.0.3
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg19
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

growth_protocol: PFKFB3 plasmid was tranfected into A549 cells to get PFKFB3 stably expressed cells.

extract_protocol:
RNA was harvested using Trizol
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: A549 cells were infected by VSV

value: PFKFB3 overexpression

value: mock


title: A549 PFKFB3 overexpression VSV 1 [A549vsv8-1]

value: VSV


title: A549 PFKFB3 overexpression mock 1 [A549mock8-1]


title: PBMCs, Control, 0hr, 38157, 1

description: Library name: G100_O19_38157_C_0hr_1


title: A549 Ctrl VSV 2 [A549vsv1-2]

value: NC


title: A549 PFKFB3 overexpression VSV 2 [A549vsv8-2]


title: PID84, 68-1.2 RhCMV/SIV, subcutaneously, Protected, 29292

description:
Library name: G106_ABL01_29292_PID84
!0x Genomics


title: S2133_00025_R1_S30

description: Column 'S2133_00025' in counts.matrix

value: Guselkumab 100mg


title: A549 Ctrl mock 2 [A549mock1-2]


title: PBMCs, IL15, 24hr, 38155, 3

description: Library name: G096_O19_38155_IL15_24hr_3

value: Female

value: 40 ng/ml


title: PBMCs, IL15, 48hr, 38155, 3

description: Library name: G099_O19_38155_IL15_48hr_3


title: A549 Ctrl VSV 1 [A549vsv1-1]


title: S2133_00083_R1_S56

description: Column 'S2133_00083' in counts.matrix

value: Ixekizumab 80mg Q2W


title: S2133_00107_R1_S2

description: Column 'S2133_00107' in counts.matrix

value: SKIN


title: PID84, 68-1.2 RhCMV/SIV, subcutaneously, Protected, 28809

description:
Library name: G104_ABL01_28809_PID84
!0x Genomics


title: A549 Ctrl mock 1 [A549mock1-1]


title: S2133_00044_R1_S37

description: Column 'S2133_00044' in counts.matrix


title: PID56, 68-1 RhCMV/SIV, subcutaneously, Protected, 29515

description:
Library name: G100_ABL01_29515_PID56
!0x Genomics

value: 68-1 RhCMV/SIV, subcutaneously


title: PBMCs, IL15, 48hr, 38155, 2

description: Library name: G098_O19_38155_IL15_48hr_2


title: PBMCs, IL15, 24hr, 38155, 1

description: Library name: G094_O19_38155_IL15_24hr_1


title: PID56, 68-1.2 RhCMV/SIV, subcutaneously, Protected, 28809

description:
Library name: G103_ABL01_28809_PID56
!0x Genomics


title: PID28, 68-1 RhCMV/SIV, subcutaneously, Protected, 29515

description:
Library name: G099_ABL01_29515_PID28
!0x Genomics


title: S2133_00077_R1_S31

description: Column 'S2133_00077' in counts.matrix

value: LS


title: S2133_00150_R1_S23

description: Column 'S2133_00150' in counts.matrix

value: BL


title: PBMCs, IL15, 24hr, 38155, 2

description: Library name: G095_O19_38155_IL15_24hr_2


title: S2133_00151_R1_S6

description: Column 'S2133_00151' in counts.matrix


title: S2133_00014_R1_S1

description: Column 'S2133_00014' in counts.matrix


title: ZIKV, 10 days [S3]

data_processing:
CLC Genomics Workbench v 12.0.3
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

value: PBMC

value: WT

value: ZIKV

value: 10 days


title: S2133_00063_R1_S46

description: Column 'S2133_00063' in counts.matrix

value: Psoriasis


title: PBMCs, IL15, 48hr, 38155, 1

description: Library name: G097_O19_38155_IL15_48hr_1

value: PBMCs


title: ZIKV, 3 months [S5]

value: 3 months


title: PID84, 68-1 RhCMV/SIV, subcutaneously, Protected, 29515

description:
Library name: G101_ABL01_29515_PID84
!0x Genomics

value: Protected

value: Male


title: ZIKV, 1 month [S4]

value: 1 month


title: PID56, 68-1 RhCMV/SIV, subcutaneously, Protected, 29299

description:
Library name: G096_ABL01_29299_PID56
!0x Genomics


title: PID140, 68-1 RhCMV/SIV, subcutaneously, Protected, 29299

description:
Library name: G098_ABL01_29299_PID140
!0x Genomics


title: PID84, 68-1 RhCMV/SIV, subcutaneously, Protected, 29299

description:
Library name: G097_ABL01_29299_PID84
!0x Genomics


title: PBMCs, IL15, 12hr, 38155, 1

description: Library name: G091_O19_38155_IL15_12hr_1

value: Female


title: S2133_00017_R1_S49

description: Column 'S2133_00017' in counts.matrix


title: PBMCs, IL15, 6hr, 38155, 3

description: Library name: G090_O19_38155_IL15_6hr_3

value: 40 ng/ml


title: ZIKV, 3 days [S1]

value: 3 days


title: S2133_00010_R1_S55

description: Column 'S2133_00010' in counts.matrix

value: SKIN

value: Ixekizumab 80mg Q2W


title: PBMCs, IL15, 6hr, 38155, 2

description: Library name: G089_O19_38155_IL15_6hr_2


title: ZIKV, 7 days [S2]

value: 7 days


title: S2133_00101_R1_S13

description: Column 'S2133_00101' in counts.matrix

value: Guselkumab 100mg

value: BL

value: LS


title: PID140, 68-1 RhCMV/SIV, subcutaneously, Protected, 29208

description:
Library name: G095_ABL01_29208_PID140
!0x Genomics

value: 68-1 RhCMV/SIV, subcutaneously


title: PBMCs, IL15, 12hr, 38155, 3

description: Library name: G093_O19_38155_IL15_12hr_3


title: PBMCs, IL15, 12hr, 38155, 2

description: Library name: G092_O19_38155_IL15_12hr_2


title: PBMCs, IL15, 6hr, 38155, 1

description: Library name: G088_O19_38155_IL15_6hr_1


title: PID84, 68-1 RhCMV/SIV, subcutaneously, Protected, 29208

description:
Library name: G094_ABL01_29208_PID84
!0x Genomics


title: S2133_00095_R1_S54

description: Column 'S2133_00095' in counts.matrix


title: PBMCs, IL15, 2hr, 38155, 3

description: Library name: G087_O19_38155_IL15_2hr_3


title: S2133_00174_R1_S57

description: Column 'S2133_00174' in counts.matrix


title: S2133_00169_R1_S38

description: Column 'S2133_00169' in counts.matrix


title: PID140, 68-1 RhCMV/SIV, subcutaneously, Protected, 29558

description:
Library name: G092_ABL01_29558_PID140
!0x Genomics


title: PBMCs, Control, 48hr, 38155, 3

description: Library name: G084_O19_38155_C_48hr_3

value: Control

value: 0 ng/ml


title: PBMCs, IL15, 2hr, 38155, 2

description: Library name: G086_O19_38155_IL15_2hr_2

value: PBMCs


title: S2133_00164_R1_S1

description: Column 'S2133_00164' in counts.matrix

value: Psoriasis


title: S2133_00099_R1_S44

description: Column 'S2133_00099' in counts.matrix


title: S2133_00028_R1_S3

description: Column 'S2133_00028' in counts.matrix


title: PID56, 68-1 RhCMV/SIV, subcutaneously, Protected, 29558

description:
Library name: G091_ABL01_29558_PID56
!0x Genomics

value: Protected


title: siCTCFL K562 rep2

type: RNA

city: London

first: Gopuraja

last: Dharmalingam

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

country: United Kingdom

institute: MRC London Institute of Medical Sciences

description: Gene expression analysis of K562 cells transiently transfected with siCTCFL

hyb_protocol: Labelled cDNA from three biological replicates per condition was hybridised to GeneChip Human Gene 1.0 ST (Affymetrix).

scan_protocol: Arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were normalized using the vsnrma function in the vsn R/Bioconductor package.

label: biotin

source_name: K562 cells transfected with siCTCFL

label_protocol: GeneChip WT Terminal Labeling Kit (Affymetrix)  was used for hybridization on GeneChIP Human Gene 1.0 ST according to Affymetrix protocol

growth_protocol: K562 were grown in corresponding published medium. Cells were transfected with 0.4M siNEG or siCTCFL for 48h.

extract_protocol: RNA was extracted using RNeasy Mini Kit, QIAGEN.

treatment_protocol: Cells were transfected with 0.4M siCTCFL for 48h (Dharmafect, Dharmacon)

value: immortalised myelogenous leukaemia cell line (erythroleukaemia type)

tag: gender

value: female


title: siCTCFL K562 rep3


title: S2133_00068_R1_S6

description: Column 'S2133_00068' in counts.matrix


title: PID84, 68-1 RhCMV/SIV, orally, Protected, 29212

description:
Library name: G088_ABL01_29212_PID84
!0x Genomics

value: 68-1 RhCMV/SIV, orally

value: Male


title: siCTCFL K562 rep1


title: S2133_00172_R1_S9

description: Column 'S2133_00172' in counts.matrix


title: PID28, 68-1 RhCMV/SIV, subcutaneously, Protected, 29558

description:
Library name: G090_ABL01_29558_PID28
!0x Genomics


title: PBMCs, Control, 48hr, 38155, 2

description: Library name: G083_O19_38155_C_48hr_2

value: Female


title: FLAG-CTCFL ES rep2

description: Gene expression analysis of ES cells stably transfected with a vector encoding FLAG-CTCFL

hyb_protocol: Labelled cDNA from three biological replicates per condition was hybridised to GeneChip Mouse Gene 1.0 ST (Affymetrix).

organism: Mus musculus

source_name: mESCs transfected with FLAG-mCTCFL

label_protocol: GeneChip WT Terminal Labeling Kit (Affymetrix)  was used for hybridization on GeneChip Mouse Gene 1.0 ST v1 according to Affymetrix protocol

growth_protocol: Cells were grown in 10%-serum containing medium, grown on 0.1%-precoated plates. Cells were either expressing a control Vector or a vector coding for FLAG-mCTCFL.

treatment_protocol: Cells were constantly grown under 1ug/ml puromycin selection to promote FLAG-CTCFL expression.

value: ESCs cloned from 46C cells

value: 46C (Sox1-GFP knock-in) + FLAG-CTCFL Vector

value: male

tag: background strain


title: siNEG K562 rep3

description: Gene expression analysis of K562 cells transiently transfected with siNEG

source_name: K562 cells transfected with siNEG

treatment_protocol: Cells were transfected with 0.4M siNEG for 48h (Dharmafect, Dharmacon)


title: PBMCs, Control, 24hr, 38155, 2

description: Library name: G080_O19_38155_C_24hr_2


title: siNEG K562 rep2


title: PBMCs, Control, 48hr, 38155, 1

description: Library name: G082_O19_38155_C_48hr_1


title: siNEG K562 rep1


title: PBMCs, Control, 24hr, 38155, 3

description: Library name: G081_O19_38155_C_24hr_3


title: PID56, 68-1 RhCMV/SIV, orally, Protected, 29212

description:
Library name: G087_ABL01_29212_PID56
!0x Genomics


title: S2133_00043_R1_S56

description: Column 'S2133_00043' in counts.matrix

value: SKIN

value: Guselkumab 100mg


title: PBMCs, IL15, 2hr, 38155, 1

description: Library name: G085_O19_38155_IL15_2hr_1

value: 40 ng/ml


title: S2133_00088_R1_S61

description: Column 'S2133_00088' in counts.matrix

value: BL

value: LS


title: PBMCs, Control, 12hr, 38155, 3

description: Library name: G078_O19_38155_C_12hr_3

value: Control

value: 0 ng/ml


title: PID28, 68-1 RhCMV/SIV, orally, Protected, 29212

description:
Library name: G086_ABL01_29212_PID28
!0x Genomics

value: PBMCs


title: Drosophila BBB brain, + / TraF biol rep 2

city: Houston

first: Brigitte

last: Dauwalder

state: TX

address: 3455 Cullen Blvd Rm 342

department: Biology and Biochemistry

institute: University of Houston

description:
Library name: 27982
27982s_7_1_sequence_TraF2

data_processing:
Kallisto
DESeq2
Assembly: DESeq2
Supplementary files format and content: raw_counts_per_sample.csv

organism: Drosophila melanogaster

source_name: brain

extract_protocol:
RNeasy mini kit (Qiagen)
Illumina TruSeq RNA v1 library preparation

value: brain

value: +/TraF


title: FLAG-CTCFL ES rep3


title: PID140, 68-1 RhCMV/SIV, orally, Protected, 29212

description:
Library name: G089_ABL01_29212_PID140
!0x Genomics

value: Protected


title: Control Vector ES rep2

description: Gene expression analysis of ES cells stably transfected with a control vector

source_name: mESCs transfected with control vector

value: 46C (Sox1-GFP knock-in) + Control Vector


title: PID140, 68-1 RhCMV/SIV, orally, Protected, 28885

description:
Library name: G085_ABL01_28885_PID140
!0x Genomics

value: 68-1 RhCMV/SIV, orally

value: Male


title: S2133_00111_R1_S53

description: Column 'S2133_00111' in counts.matrix

source_name: SKIN

value: Psoriasis

value: Ixekizumab 80mg Q2W


title: PID56, 68-1 RhCMV/SIV, orally, Protected, 28885

description:
Library name: G084_ABL01_28885_PID56
!0x Genomics

source_name: PBMCs


title: PID28, 68-1 RhCMV/SIV, orally, Protected, 28885

description:
Library name: G083_ABL01_28885_PID28
!0x Genomics


title: S2133_00035_R1_S48

description: Column 'S2133_00035' in counts.matrix


title: Control Vector ES rep3

value: ESCs cloned from 46C cells

value: male


title: Control Vector ES rep1


title: PBMCs, Control, 24hr, 38155, 1

description: Library name: G079_O19_38155_C_24hr_1

value: Female


title: S2133_00076_R1_S22

description: Column 'S2133_00076' in counts.matrix

value: SKIN

value: Guselkumab 100mg


title: PID84, 68-1 RhCMV/SIV, orally, Protected, 29483

description:
Library name: G081_ABL01_29483_PID84
!0x Genomics


title: PBMCs, Control, 6hr, 38155, 3

description: Library name: G075_O19_38155_C_6hr_3


title: PID140, 68-1 RhCMV/SIV, orally, Protected, 29483

description:
Library name: G082_ABL01_29483_PID140
!0x Genomics


title: S2133_00114_R1_S50

description: Column 'S2133_00114' in counts.matrix

value: LS


title: Drosophila brain + / TraF biol rep 1

description:
Library name: 27979
27979s_3_1_sequence_TraF1


title: S2133_00085_R1_S50

description: Column 'S2133_00085' in counts.matrix


title: S2133_00032_R1_S13

description: Column 'S2133_00032' in counts.matrix


title: PBMCs, Control, 12hr, 38155, 1

description: Library name: G076_O19_38155_C_12hr_1

value: Control


title: PBMCs, Control, 6hr, 38155, 2

description: Library name: G074_O19_38155_C_6hr_2

value: 0 ng/ml


title: FLAG-CTCFL ES rep1

value: 46C (Sox1-GFP knock-in) + FLAG-CTCFL Vector


title: PID140, 68-1 RhCMV/SIV, orally, Protected, 29482

description:
Library name: G080_ABL01_29482_PID140
!0x Genomics

value: PBMCs


title: PID84, 68-1 RhCMV/SIV, orally, Protected, 29482

description:
Library name: G079_ABL01_29482_PID84
!0x Genomics


title: Drosophila brain SPG-GAL4/UAS-TraF, biol rep 2

description:
Library name: 27981
27981s_6_1_sequence_SPG_TraF2

value: brain


title: PBMCs, Control, 12hr, 38155, 2

description: Library name: G077_O19_38155_C_12hr_2


title: Drosophila brain  + / SPG-GAL4 biol rep 1

description:
Library name: 27977
27977s_1_1_sequence_SPG1


title: PBMCs, Control, 6hr, 38155, 1

description: Library name: G073_O19_38155_C_6hr_1


title: S2133_00158_R1_S57

description: Column 'S2133_00158' in counts.matrix

value: BL


title: PBMCs, Control, 2hr, 38155, 3

description: Library name: G072_O19_38155_C_2hr_3


title: Drosophila brain SPG-GAL4/UAS-TraF, biol rep 1

description:
Library name: 27978
27978s_2_1_sequence_SPG_TraF1


title: S2133_00144_R1_S5

description: Column 'S2133_00144' in counts.matrix


title: PID56, 68-1 RhCMV/SIV, orally, Protected, 29482

description:
Library name: G078_ABL01_29482_PID56
!0x Genomics

value: Protected


title: S2133_00024_R1_S15

description: Column 'S2133_00024' in counts.matrix


title: PID28, 68-1 RhCMV/SIV, orally, Protected, 29482

description:
Library name: G077_ABL01_29482_PID28
!0x Genomics

value: 68-1 RhCMV/SIV, orally


title: PBMCs, Control, 2hr, 38155, 2

description: Library name: G071_O19_38155_C_2hr_2


title: Drosophila brain  + / SPG-GAL4 biol rep 2

description:
Library name: 27980
27980s_5_1_sequence_SPG2


title: D595, 68-1.2 RhCMV/SIV, subcutaneously, Non-protected, 30434

description:
Library name: G076_ABL01_30434_D595
!0x Genomics

value: 68-1.2 RhCMV/SIV, subcutaneously

value: Non-protected

value: Male


title: S2133_00126_R1_S26

description: Column 'S2133_00126' in counts.matrix

value: Psoriasis


title: BoneAssociated_scRNAseq_1

city: Vancouver

first: Freda

last: Miller

state: BC

address: 2185 East Mall

country: Canada

institute: University of British Columbia

description:
Library name: BoneAssociated_1
10X Genomics

data_processing:
FASTQ reads were processed and aligned to the wild-type mouse genome (mm10) using Cell Ranger v3 software (cellranger count function) with settings as recommended by the manufacturer (10X Genomics).
The data packages contain the filtered digital gene expression for each sample obtained from the Cell Ranger Single Cell Pipeline.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Dura/Skull

extract_protocol:
For single cell isolation the entire dorsal and lateral V-SVZ were microdissected out. Tissues were finely chopped and incubated in Hibernate A minus calcium medium (Brain Bits) supplemented with 2% B27, 20 units/mL papain, and 0.005% DNaseI for 30 minutes at 37°C in the dark. This enzymatic incubation solution also contained DRAQ5, a membrane permeable dye to stain for live cells (at 5 μM or 3000- fold dilution, Thermo Fisher). After enzymatic treatment, the tissue suspension was centrifuged at 300 x g for 5 minutes and resuspended in HBSS/0.025% BSA. A cell suspension was produced via manual trituration using blunt needles of sequentially decreasing diameter. The resultant cell suspension was filtered through a 40 μm strainer and labeled with 1 μg/mL propidium iodide (PI, Abcam). Viable cells were collected using flow cytometry sorting for propidium iodide-negative and DRAQ5-positive cells.
Libraries were prepared according to the manufacturer's instructions (10X Genomics) using the Chromium Single Cell 3' Library and Gel Bead Kit.

value: Dura/Skull


title: BSLN, 68-1.2 RhCMV/SIV, subcutaneously, Non-protected, 30434

description:
Library name: G075_ABL01_30434_BSLN
!0x Genomics

value: BSLN


title: PBMCs, Control, 0hr, 38155, 3

description: Library name: G069_O19_38155_C_0hr_3

value: Female


title: CorticalSurfaceAssociated_scRNAseq_4

description:
Library name: CorticalSurfaceAssociated_4
10X Genomics

source_name: Brain

value: Brain


title: Hl-60 Nuclear Extract S-Phase 1hr Clicked RNA-Seq

city: Boston

first: Annalisa

last: Di Ruscio

address: 3 Blackfan Circle, Center of Life Science, Room 407

institute: Beth Israel Deaconess Medical Center, Harvard Medical School

data_processing:
Raw reads were trimmed using fastp with the flags: “LeadMinTrimQual: 3 TrailMinTrimQual: 3 avgMinQual: 15 minReadLength: 40 palindromeClipTreshold: 30 seedMisMatches: 2 simpleClipThreshold: 10 windowSize: 4”. After cleanup, reads were aligned to hg38  uisng hisat2 (v2.1) with options: --rna-strandness FR –no-mixed –no-discordant”. Bam file sorting and indexing was performed using samtools (v1.12). Reads mapping  to promoter regions were obtained the “intersect” function of bedtools bedtools (v2.30)  Novel transcripts arising from promoter regions were assembled using STRINGTIE (v2.2.1) in mix mode (Nanopore plus Illumina sequencing) using options set to: “-s 3 --fr -p 30”. Output GTF files were merged with the gffCompare utility using the Ensembl GTF (release 100) as a reference  and splitted into two different GTF files describing either promoter RNAs or corresponding genes.  These files  were subsequently converted into BED format using Kent’s utility (gtfToGenePred and genePredToBed) and then converted to the SAF format using a custom awk command (awk -v OFS="\t" 'BEGIN{print "GeneID","Chr","Start","End","Strand"}; {print $4,$1,$2,$3,$6}'). Reads counting was performed using featureCounts (subread-2.0.1). For  promoter RNAs reads were counted  using options set to: “-p -B -O -F 'SAF' -s 1, whereas for corresponding genes the following options were used: “--splitOnly -p -B -s 1 -O -F 'GTF'”.  The resulting count matrix was imported into R and TPMs were calculated using a custom R function.  Only promter RNA and genes expressed at least one TPM were retained for further analyses. Bam coverage maps were generated using bamCoverage from deeptools with options set to: “ --effectiveGenomeSize 2913022398 –normalizeUsing BPM –smoothLength 5 -bs 1 --ignoreDuplicates –exactScaling –filterRNAstrand=[forward|reverse].
Assembly: hg38
Supplementary files format and content: bigWig coverage files

molecule: nuclear RNA

growth_protocol: The human leukemia cell line HL-60 was obtained from ATCC and grown in glutamine containing medium in the absence of antibiotics, at 37 °C in a humidified atmosphere with 5% CO2.

extract_protocol:
Nanopore RNA-Seq - Total nuclera RNA was  isolated after one hour from the release of the S-phase using TRI Reagent (MRC) according to manufacturer’s istructions. RNA sample was  depleted of ribosomal RNA with Ribo-ZeroTM Magnetic Gold Kit. The Polyadenylated RNAs were enriched using oligod(T)25 magnetic beads (NEB S1419S). The remaining polyA minus RNAs wer polyadenylated using TdT (NEB M0315S). The resulting RNA from both fractions, polyA plus and minus were subjected to library preparation using the Direct RNA sequencing kit (SQK-RNA002, Oxford Nanopore Technologies, UK)  according to manufacturer’s istructions. Libraries were sequenced on PromethIon device using R10.4 flow cells.
Nascent RNA/DNA capture was performed using Click-iT® Nascent RNA Capture Kit (ThermoFisher) according to the manufacturer’s instructions with minor modifications. Briefly, 1. Labeling the cells with EU/EdU. 200 mM EU or 30 mM EdU stock solutions were added to the cells, to a final concentration 0.5 mM or 30 uM, respectively. 2. Incubation. The cells were incubated for 1 or 2 hours. 3. RNA/DNA isolation. The cells were harvested and the RNA/DNA were isolated and dissolved in 14 uL of H2O. 4. Biotinylation of RNA/DNA by Click reaction. Click-iT reaction cocktail (50 uL per reaction) was prepared accordingly to manufacturer’s instructions: a mixture containing 1x Click-iT EU buffer; 2 mM CuSO4; 1 mM Biotin azide; 13.25 uL of the isolated RNA; 10 mM Click-iT® reaction buffer additive 1; 12 mM Click-iT reaction buffer additive 2 was prepared. After adding each component, the reaction cocktail was gently mixed by vortexing. The addition of the Click-iT reaction buffer additive 1 stock initiates the click reaction between the EU-RNA/EdU-DNA and biotin azide. Afterwards the Click-iT reaction buffer additive 2 is added and incubated for 30 minutes with gentle vortexing. 5. RNA/DNA precipitation. 1 uL of UltraPure Glycogen, 55 uL of 7 M ammonium acetate, and 750 uL of chilled 100% ethanol were added to the click reaction, incubated at –70°C for at least 30 minutes and after centrifugation the pellet was dissolved in 125 uL of H2O. 6. Binding biotinylated RNA/DNA to Dynabeads MyOne Streptavidin T1 magnetic beads. The RNA/DNA binding reaction mixture included: 125 uL 2xClick-iT RNA binding buffer; 2 uL Ribonuclease Inhibitor or 2 uL of water for DNA; 125 uL of the isolated biotinylated RNA/DNA. The RNA binding reaction mixture was heated at 68–70°C for 5 minutes and 50 uL of bead suspension added into the heated RNA binding reaction mixture. The tube containing the RNA/DNA binding reaction was incubated at r.t. for 30 min while gently vortexing to prevent the beads from settling. The beads were immobilized using the magnet and washed 5 times with 500 uL of Click-iT reaction wash buffer 1 and 5 times with 500 uL of Click-iT reaction wash buffer 2. Finally, the beads were resuspended in 50 uL of Click-iT reaction wash buffer 2 and the captured RNA immediately processed to cDNA synthesis. The captured DNA was released into 50 uL of boiling water and used in qPCR analyses. RIP-Seq - Immunoprecipitated RNA were processed for sequencing as described by Di Ruscio et al.(Di Ruscio et al., 2013) with some modifications. RNAs were depleted of ribosomal RNA with Ribo-ZeroTM Magnetic Gold Kit. Double stranded cDNA libraries were constructed using ScriptSeq v2 RNA-Seq Library Preparation Kit. The libraries were subjected to final size-selection in 3% agarose gels. 250-500 bp fragments were excised and recovered using the Qiaquick Gel Extraction Kit (Qiagen). RNA-Seq - RNA was extracted with TRI Reagent (MRC). RNA samples were treated with DNase I (10 U of DNase I (Roche) per 3 ug of total RNA; 37ºC for one hour; in the presence of RNase A inhibitor).   RIP-Seq - Immunoprecipitated RNA were processed for sequencing as described by Di Ruscio et al.(Di Ruscio et al., 2013) with some modifications. RNAs were depleted of ribosomal RNA with Ribo-ZeroTM Magnetic Gold Kit. Double stranded cDNA libraries were constructed using ScriptSeq v2 RNA-Seq Library Preparation Kit. The libraries were subjected to final size-selection in 3% agarose gels. 250-500 bp fragments were excised and recovered using the Qiaquick Gel Extraction Kit (Qiagen). RNA-Seq - RNA was extracted with TRI Reagent (MRC). RNA samples were treated with DNase I (10 U of DNase I (Roche) per 3 ug of total RNA; 37ºC for one hour; in the presence of RNase A inhibitor). RNAs were depleted of ribosomal RNA with Ribo-Zero Magnetic Gold Kit. Double stranded cDNA libraries were constructed using ScriptSeq v2 RNA-Seq Library Preparation Kit. The libraries were subjected to final size-selection in 3% agarose gel. 250-500 bp fragments were excised and recovered using the Qiaquick Gel Extraction Kit (Qiagen). Libraries were sequenced on a Hi-Seq-2000 Illumina. ChIP-Seq – ChIP libraries’ construction was performed as described (Mikkelsen et al., 2008) and paired-end sequenced on NextSeq500 platform, at a reading length of 36 nucleotides. Nanopore RNA-Seq - Total nuclera RNA was  isolated after one hour from the release of the S-phase using TRI Reagent (MRC) according to manufacturer’s istructions. RNA sample was  depleted of ribosomal RNA with Ribo-ZeroTM Magnetic Gold Kit. The Polyadenylated RNAs were enriched using oligod(T)25 magnetic beads (NEB S1419S). The remaining polyA minus RNAs wer polyadenylated using TdT (NEB M0315S). The resulting RNA from both fractions, polyA plus and minus were subjected to library preparation using the Direct RNA sequencing kit (SQK-RNA002, Oxford Nanopore Technologies, UK)  according to manufacturer’s istructions. Libraries were sequenced on PromethIon device using R10.4 flow cells.

treatment_protocol: Double Thymidine block (early S-phase block) was carried out as described (Di Ruscio et al., 2013). Briefly, HL-60 cells were grown overnight to 70-80% confluence, washed twice with 1xPBS and cultured in DMEM (10% FCS) + 2.5 mM Thymidine for 18 h (first block). Thymidine was washed out with 1xPBS and cells were grown in DMEM (10% FCS). After 8 hrs cells were cultured in the presence of thymidine for 18 h (second block) and then released as described (Di Ruscio et al., 2013). Synchrony was monitored by flow cytometry analysis of propidium iodide-stained cells using a LSRII flow cytometer (BD Biosciences) at the Harvard Stem Cell Institute/Beth Israel Deaconess Center flow cytometry facility. DRB and Actinomycin D treatments were carried out as described (Di Ruscio et al., 2013). Briefly, after release from double thymidine block, HL-60 cells were treated with 100 μM of 5,6-Dichlorobenzimidazole 1-β–D-ribofuranoside (DRB)(Mitchell and Fraser, 2008) (Sigma Aldrich) or 0.8 μM of Actinomycin D (Sigma Aldrich) as indicated at each time point.

value: Human Caucasian promyelocytic leukaemia


title: S2133_00013_R1_S19

description: Column 'S2133_00013' in counts.matrix

value: SKIN

value: Guselkumab 100mg

value: LS


title: PBMCs, Control, 0hr, 38155, 1

description: Library name: G067_O19_38155_C_0hr_1

value: PBMCs

value: Control

value: 0 ng/ml


title: CorticalSurfaceAssociated_scRNAseq_2

description:
Library name: CorticalSurfaceAssociated_2
10X Genomics


title: BSLN, 68-1.2 RhCMV/SIV, subcutaneously, Non-protected, 30025

description:
Library name: G073_ABL01_30025_BSLN
!0x Genomics


title: PBMCs, Control, 0hr, 38155, 2

description: Library name: G068_O19_38155_C_0hr_2


title: D595, 68-1.2 RhCMV/SIV, subcutaneously, Non-protected, 30025

description:
Library name: G074_ABL01_30025_D595
!0x Genomics


title: D595, 68-1.2 RhCMV/SIV, subcutaneously, Non-protected, 29535

description:
Library name: G072_ABL01_29535_D595
!0x Genomics


title: PBMCs, IL15, 48hr, 38147, 3

description: Library name: G066_O19_38147_IL15_48hr_3

value: 40 ng/ml


title: CorticalSurfaceAssociated_scRNAseq_3

description:
Library name: CorticalSurfaceAssociated_3
10X Genomics


title: BoneAssociated_scRNAseq_2

description:
Library name: BoneAssociated_2
10X Genomics


title: Hl-60 Nuclear Extract S-Phase 1hr RNA-Seq


title: Ilf3-KO-3

city: GUANGZHOU

first: Baifu

last: Qin

address: Institute of Molecular and Medical Virology, Key Laboratory of Ministry of Education for Viral Pathogenesis & Infection Prevention and Control, School of Medicine, Jinan University, Guangzhou, Guangdong Province

data_processing:
IIIumina Casava1.4 software used for basecalling.
Data were filtered the low-quality sequence, including adapter sequence and low-quality bases (mass value <=20) using the software FASTP
Reads were reference to the henome using HISAT2 (Hierarchical Indexing for Spliced Alignment of Transcripts) software
Reads were calculated using fragment per kilobase of exon per million fragments mapped (FPKM) software
Assembly: mm10
Supplementary files format and content: tab-delimited text files include Count  values for each Sample

source_name: Large intestine, Colon

extract_protocol:
Tumor tissue were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. 1μg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard IIIumina protocol.

treatment_protocol: AOM (10mg/kg) was injected to the mice, then DSS was administered 3 times in weekly intervals.

value: Large intestine, Colon

value: Colorectal Cancer cell

tag: strain


title: PBMCs, Control, 2hr, 38155, 1

description: Library name: G070_O19_38155_C_2hr_1

tag: tissue


title: PID140, 68-1 RhCMV/SIV, subcutaneously, Protected, 29515

description:
Library name: G102_ABL01_29515_PID140
!0x Genomics

value: 68-1 RhCMV/SIV, subcutaneously

value: Protected


title: Ilf3-KO-4

institute: Institute of Molecular and Medical Virology


title: BSLN, 68-1.2 RhCMV/SIV, subcutaneously, Protected, 29522

description:
Library name: G069_ABL01_29522_BSLN
!0x Genomics

value: 68-1.2 RhCMV/SIV, subcutaneously

value: Male


title: PBMCs, IL15, 24hr, 38147, 3

description: Library name: G063_O19_38147_IL15_24hr_3


title: Ilf3-WT-3


title: D595, 68-1.2 RhCMV/SIV, subcutaneously, Protected, 29300

description:
Library name: G068_ABL01_29300_D595
!0x Genomics


title: PBMCs, IL15, 24hr, 38147, 2

description: Library name: G062_O19_38147_IL15_24hr_2


title: BSLN, 68-1.2 RhCMV/SIV, subcutaneously, Non-protected, 29535

description:
Library name: G071_ABL01_29535_BSLN
!0x Genomics

value: Non-protected

value: BSLN


title: PBMCs, IL15, 48hr, 38147, 2

description: Library name: G065_O19_38147_IL15_48hr_2


title: BSLN, 68-1.2 RhCMV/SIV, subcutaneously, Protected, 29300

description:
Library name: G067_ABL01_29300_BSLN
!0x Genomics


title: PBMCs, IL15, 24hr, 38147, 1

description: Library name: G061_O19_38147_IL15_24hr_1


title: Ilf3-WT-2


title: Hl-60 Nuclear Extract RNA-Seq


title: PRDX2_KO_3.2

city: Strasbourg

first: Frank

last: Jühling

address: 3 Rue Koeberlé

country: France

institute: Université de Strasbourg, Inserm, Institut de Recherche sur Les Maladies Virales et Hépatiques UMR_S1110

data_processing:
Reads were aligned to Mus musculus genome GRCm38 using HISAT2.
Gene counts for GENCODE vM15 genome annotation were compiled using htseq-count.
Reads were further processed and normalized using DESeq2.
Supplementary files format and content: tab-delimited text files include DESeq2 differential expression analysis PRDX2_KO-vs-CTRL
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: liver

growth_protocol: Alb-Cre/Cas9 F1 generation were weaned 21 days after birth and kept in idividually ventilated cages with ad libidum drinking water and chow diet until they were used for treatment protcol.

extract_protocol:
Livers were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: AAV8-U6-sgCtrl and AAV8-U6-sgPrdx2 were delivered through intravenous injection in 4 to 5-week old Alb-Cre/Cas9 mice. Three weeks later, mice were intraperitoneally injected with 100mg/kg diethylnitrosamine (DEN) and after one week they were fed with a choline-deficient amino-acid adapted high-fat diet (CDAHFD) for 6 months. Mice were housed in individually ventilated cages with ad libidum drinking water and diet.

value: Alb-Cre/Cas9 F1 generation

tag: single guide rna

value: liver

tag: age

value: post natal 8 months

value: CDAHFD + DEN


title: BSLN, 68-1.2 RhCMV/SIV, subcutaneously, Protected, 29292

description:
Library name: G065_ABL01_29292_BSLN
!0x Genomics

tag: treatment


title: Ilf3-WT-1


title: PBMCs, IL15, 48hr, 38147, 1

description: Library name: G064_O19_38147_IL15_48hr_1


title: PBMCs, IL15, 12hr, 38147, 3

description: Library name: G060_O19_38147_IL15_12hr_3


title: Ilf3-KO-1


title: PBMCs, IL15, 12hr, 38147, 2

description: Library name: G059_O19_38147_IL15_12hr_2


title: PRDX2_KO_1.1


title: D595, 68-1.2 RhCMV/SIV, subcutaneously, Protected, 29522

description:
Library name: G070_ABL01_29522_D595
!0x Genomics


title: PRDX2_KO_1.3


title: PBMCs, IL15, 12hr, 38147, 1

description: Library name: G058_O19_38147_IL15_12hr_1


title: D595, 68-1.2 RhCMV/SIV, subcutaneously, Non-protected, 29084

description:
Library name: G064_ABL01_29084_D595
!0x Genomics


title: PBMCs, IL15, 6hr, 38147, 2

description: Library name: G056_O19_38147_IL15_6hr_2


title: IMCD cells overexpressing ILK-T173I, biological rep 1

city: Toronto

first: Norman

middle: D

last: Rosenblum

address: 686 Bay Street

institute: The Hospital for Sick Children

hyb_protocol: Extract was hybridized for 16 hours at 45 degrees and washed with FS450_002

scan_protocol: Extracted was scanned using Affymetric GeneChip Scanner 3000

data_processing: Data was prosseced using the oligo r package with version 1.44 using the RMA method with background subtraction, normalization (quantile), and summarization (median-polish)

source_name: inner medullary collecting duct cells

label_protocol: Extract was labelled with Biotin Allonamide Triphosphate

growth_protocol: cells were cultured in DMEM:F12 supplemented with 10% FBS and 1%P/S at 37 degress and 5%CO2.

extract_protocol: Qiagen Mini Kit according to manufacturers instruction and Affymetrix WT PLUS kit

treatment_protocol: cells were transduced with lentivirus expressing wild type ILK and missense variant ILK-T173I to generate cell lines. The cells were stimulated with EGF (20ng/ml) for 15 minutes and incubated for 1 hour prior to extraction

value: IMCD

tag: transduction


title: PBMCs, IL15, 2hr, 38147, 3

description: Library name: G054_O19_38147_IL15_2hr_3

value: PBMCs

tag: time


title: PID56, 68-1 RhCMV/SIV, subcutaneously, Protected, 29208

description:
Library name: G093_ABL01_29208_PID56
!0x Genomics

tag: Sex


title: 13WT1

city: Stanford

first: Marten

middle: CG

last: Winge

address: 269 Campus Dr

institute: Stanford University

description: MiSeq® Reagent Kit v3 (150 cycle)

data_processing:
UMIs were used to deduplicate fastq.gz files
fastq.gzc was used for quality control of sequencing
STAR mapping was used to align reads to mm10 reference genome
featureCounts file was generated as DESeq2 inpout file
DESeq2 comparisons were generated for DMSO vs BZ treated samples
Assembly: mm10
Supplementary files format and content: DESeq2 comparisons for DMSO vs BZ treated samples included in tab separated file format
Supplementary files format and content: featureCoounts file with aligned count data

source_name: ear skin

growth_protocol: 6-8 week old c57/Bl6 mice

extract_protocol:
RNA was extracted using Qiagen RNAeasy prep
500 ng of RNA was used to generate libraries using the lexogen 3'mRNA kit with UMIs

treatment_protocol: mice were treated topically for 6 days

value: ear skin


title: 10BZ502

description: MiSeq® Reagent Kit v3 (150 cycle)

value: benzamil+imq


title: D595, 68-1 RhCMV/SIV, subcutaneously, Protected, 29515

description:
Library name: G060_ABL01_29515_D595
!0x Genomics

extract_protocol:
10x extraction protocol
Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 ; 10X Genomics

tag: animal id


title: BSLN, 68-1.2 RhCMV/SIV, subcutaneously, Non-protected, 29084

description:
Library name: G063_ABL01_29084_BSLN
!0x Genomics


title: IMCD cells overexpressing wild type ILK, biological rep 3

value: wild type ILK


title: IMCD cells overexpressing ILK-T173I, biological rep 2


title: IMCD cells overexpressing wild type ILK, biological rep 1


title: PBMCs, IL15, 6hr, 38147, 3

description: Library name: G057_O19_38147_IL15_6hr_3

data_processing:
Trimgalorev0.6.10 used to remove low quality reads and bases
Filtered out globin and rRNA reads using bowtie2v2.4.4
Aligned reads with STARv2.7.10b to both rhesus macaque and cynomolgus macaque genomes
Assembly: Macaca fascicularis version 6 Ensembl annoation v110 and Macaca mulatta version 10 Ensembl annoation v110
Supplementary files format and content: Two count matricies one the macaca fascicularis and macaca mulatta

tag: dose

value: 40 ng/ml


title: 12BZ504

description: MiSeq® Reagent Kit v3 (150 cycle)


title: CTRL_7.1

value: sgCTRL


title: IMCD cells overexpressing wild type ILK, biological rep 2

tag: cell line


title: D595, 68-1.2 RhCMV/SIV, subcutaneously, Protected, 28809

description:
Library name: G062_ABL01_28809_D574
!0x Genomics


title: 14WT2

description: MiSeq® Reagent Kit v3 (150 cycle)


title: 11BZ503

description: MiSeq® Reagent Kit v3 (150 cycle)


title: BSLN, 68-1.2 RhCMV/SIV, subcutaneously, Protected, 28809

description:
Library name: G061_ABL01_28809_BSLN
!0x Genomics


title: PBMCs, IL15, 6hr, 38147, 1

description: Library name: G055_O19_38147_IL15_6hr_1


title: CTRL_5.1


title: 9BZ501

description: MiSeq® Reagent Kit v3 (150 cycle)


title: BSLN, 68-1 RhCMV/SIV, subcutaneously, Protected, 29515

description:
Library name: G059_ABL01_29515_BSLN
!0x Genomics

value: 68-1 RhCMV/SIV, subcutaneously


title: 3DMSO3

description: MiSeq® Reagent Kit v3 (150 cycle)

value: dmso+imq


title: IMCD cells overexpressing ILK-173I, biological rep 3


title: 4DMSO4

description: MiSeq® Reagent Kit v3 (150 cycle)


title: CTRL_7.2


title: PBMCs, IL15, 2hr, 38147, 2

description: Library name: G053_O19_38147_IL15_2hr_2


title: Tg(mNTCP-C9)-6months-male-rep3

city: Beijing

first: Wenhui

last: Li

address: 7 Science Park Road ZGC Life Science Park

data_processing:
Clean mRNA-seq reads were aligned to the mouse reference genome (GRCm38) using HISAT2 (v2.0.4) with default parameters.
Gene-level read counts were calculated with HTseq (v0.6.1p1) with the union mode.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include gene-level read count for each Sample

source_name: Liver

growth_protocol: All animals were housed and maintained under specific pathogen-free conditions in a temperature- and humidity-controlled animal facility with food and water ad libitum, under a 12-hour light/12-hour dark cycle at the National Institute of Biological Sciences (NIBS), Beijing.

extract_protocol:
Freshly isolated livers were immediately frozen and stored in liquid nitrogen until use. mRNA was extracted using Trizol regent (Invitrogen) following the manufacturer’s instructions. For mRNA-seq analysis, mRNA was isolated with Dynabeads® mRNA Purification Kits (Invitrogen), fragmented in 5x first strand buffer(Invitrogen) at 95°C for 5 min, and reverse-transcribed using SuperScript® II Reverse Transcriptase (Invitrogen). After the first strand was synthesized, Second Strand Buffer (Invitrogen), RNase H (New England Biolabs), dNTPs, and DNA polymerase I (TaKaRa) were added to the second-strand synthesis reaction for 2.5 h at 16°C, and cDNA was purified with Agencourt AMPure XP beads (Beckman). Libraries were constructed with a NEBNext DNA Library Prep Master Mix Set for Illumina (New England Biolabs), PCR products were purified using AMPure XP beads. RNA libraries were quantified by Qubit 1.0 (Invitrogen) and analyzed with an Agilent 2100 bioanalyzer(Agilent) for size distribution, and were sequenced with the Illumina Hiseq-2500 platform.
Libraries were constructed with a NEBNext DNA Library Prep Master Mix Set for Illumina (New England Biolabs), PCR products were purified using AMPure XP beads. RNA libraries were quantified by Qubit 1.0 (Invitrogen) and analyzed with an Agilent 2100 bioanalyzer(Agilent) for size distribution.

value: male

value: 6 months


title: Tg(mNTCP-C9)-6months-male-rep5

institute: National Institute of Biological Sciences


title: D595, 68-1 RhCMV/SIV, subcutaneously, Protected, 29299

description:
Library name: G052_ABL01_29299_D595
!0x Genomics

value: Protected

value: Male


title: Tg(mNTCP-C9)-6months-male-rep4


title: PBMCs, IL15, 2hr, 38147, 1

description: Library name: G052_O19_38147_IL15_2hr_1

extract_protocol:
Isolation of RNA using Qiagen RNeasy Mini Kit
mRNA Library Prep Using KAPA mRNA HyperPrep Kit


title: 1DMSO1

description: MiSeq® Reagent Kit v3 (150 cycle)


title: D595, 68-1 RhCMV/SIV, subcutaneously, Non-protected, 29511

description:
Library name: G058_ABL01_29511_D595
!0x Genomics

value: Non-protected


title: BSLN, 68-1 RhCMV/SIV, subcutaneously, Non-protected, 29511

description:
Library name: G057_ABL01_29511_BSLN
!0x Genomics

value: BSLN


title: PBMCs, Control, 48hr, 38147, 1

description: Library name: G049_O19_38147_C_48hr_1

value: Control

value: 0 ng/ml


title: PBMCs, Control, 48hr, 38147, 3

description: Library name: G051_O19_38147_C_48hr_3


title: WT-6months-male-rep4

value: wild type

value: liver


title: D595, 68-1 RhCMV/SIV, subcutaneously, Protected, 29208

description:
Library name: G048_ABL01_29208_D595
!0x Genomics

value: PBMCs


title: Drosophila intestinal cell line 18 - passage 16

city: Bloomington

first: Arthur

last: Luhur

state: IN

address: 1001 E Third St, DGRC Department of Biology

institute: Indiana University

description:
Library name: L18
10X Genomics

data_processing:
Cell Ranger 7.0.1 was utilized to process the raw sequence data generated. The filtered gene-cell barcodematrices generated by Cell Ranger were used for further analysis
Seurat version 4 was used for datanormalization, data scaling, graph-based clustering, cluster marker genes identification.
Assembly: Drosophila / Ensembl BDGP6.46.111
Supplementary files format and content: 10x HDF5 Output (Cell Ranger software v7.2)

growth_protocol: Cells were grown in 25 cm2 T-flasks at 25°C in M3 + 10% FCS medium and were passaged at between 90% and full confluence using trypsin to release cells from the tissue-culture surface. Trypsin is needed as cells in all the lines are adherent. In some cases, cell scrapers were used to aid dissociation, in addition to trypsin.  Cells were pelleted and sub-cultured at a ratio between 1:4 to 1:5. Cells were checked using an inverted microscope approximately every 2-3 days. The medium was changed on cultures showing signs of poor cell health (extended processes, little growth). This was sometimes necessary for cell types that acidify the medium. Cells were passaged every 5–7 days. Cell freezing (M3 medium with 20% heat inactivated fetal bovine serum and 10% DMSO (Dimethyl sulfoxide)) was used to keep a supply of frozen aliquots so that cells with similar passage numbers were used in experiments

extract_protocol: Libraries were prepared following the v3.1 Next GEM Single Cell 3' reagent kit User Guide (10X Genomics, Inc)

value: CG10116-GAL4, UAS 6XGFP ; UAS-Ras[V12] / P{attP.w[+].attP}JB89B


title: 2DMSO2

description: MiSeq® Reagent Kit v3 (150 cycle)

value: ear skin


title: BSLN, 68-1 RhCMV/SIV, subcutaneously, Protected, 29299

description:
Library name: G051_ABL01_29299_BSLN
!0x Genomics

data_processing:
demuliplexed and aligned data using CellRanger v6.0.1 to the Rhesus Macaque genome (Mmul10, Ensembl v100)
Aligned reads from samples collected only during post SIV challenge time points to SIV genome SIV239_M33262_1 using scPathoQuant
Assembly: Rhesus Macaque genome (Mmul10, Ensembl v100)
Supplementary files format and content: Barcodes.tsv, feature.tsv, and matrix.mtx files


title: Tg(mNTCP-C9)-6months-male-rep1


title: Tg(mNTCP-C9)-6months-male-rep2


title: PBMCs, Control, 24hr, 38147, 3

description: Library name: G048_O19_38147_C_24hr_3


title: PBMCs, Control, 48hr, 38147, 2

description: Library name: G050_O19_38147_C_48hr_2


title: WT-6months-male-rep5


title: WT-6months-male-rep2


title: WT-6months-male-rep1


title: WT-LP2-ip

city: Guangzhou

first: Xiaoyun

state: Guangdong

address: 190 Kaiyuan Avenue, Huangpu

department: Infection and Immunity

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

data_processing:
*library strategy: meRIP-seq
Adaptors and raw reads containing low-quality bases were first removed by applying trim_galore (version 0.6.6) to all RNA-seq raw data including the MeRIP-seq input libraries. The resulting reads of at least 35 bp were mapped to the reference genome (mm39, dm6-FLYBASE).
The obtained comparison results were removed and sorted using samtools (version 1.3.1) for PCR duplicates.
The featureCounts program (43) in the Subread package (version 2.0.1) at SourceForge was used to count the reads that mapped to genes. The genes that showed an average read count of less than 10 in any group or lacked read count in any replicate were primarily filtered.
The R package DESeq2 (version 1.36.0) was used for the identification of differentially expressed genes (DEGs) by setting a false discovery rate-corrected P value < 0.05 and fold change >= 0.5 as the thresholds for significance.
We first processed the raw data of MeRIP-seq IP libraries with the same upstream pipeline employed for RNA-seq. The mapping results of both MeRIP-seq IP and input libraries were used for calling m6A peaks. Differential m6A peaks of the single-factor comparisons between groups were analyzed using the R package exomePeak2 (version 1.8.1) (45), with Poisson's generalized linear model (GLM) used as a quantitative method to call the m6A peaks of individual groups as well as the m6A peaks of single-factor comparative differences between groups. To reduce false positives, the called m6A peaks from each biological replicate were considered significant and retained for subsequent analyses according to the following thresholds: peak width <= 1500 bp, log2FC > 1, FDR < 0.05, Input.RPM>=0.1, IP.RPM>=0.1. Similarly, the called differential m6A peaks between groups were considered significant under the following thresholds: peak width <= 1500 bp, |diff.log2FC|>1, FDR < 0.05, Input.Control.RPM>0.1, IP.Control.RPM>0.1, Input.Treated.RPM>0.1, IP.Treated.RPM>0.1. HOMER (version 3.12) (46) was used for de novo motif searching around peak summit-centered (mouse, peak 300 bp region; Drosophila, peak 250 bp) regions. The R packages ChIPseeker (version 1.32.0) (47) and Guitar (version 2.12.0) (48) were used for annotation and representation of the distribution characteristics of the significant/differential m6A peaks. The bamCoverage script in deeptools (version 3.5.1) was used to perform read-coverage trajectory calculations on the results of mapping IP libraries and Input libraries to the genome. Integrative Genomics Viewer (IGV) software (version 2.14.0) (49) was used to display read coverage tracks of target genes.
Assembly: mm39,dm6-FLYBASE
Supplementary files format and content: bed
Supplementary files format and content: csv

growth_protocol: Drosophila S2 cells were cultured at 28℃ in SIM-SF(Gibco) insect cell medium with 10% fetal calf serum, and the cells were resuspended and sub-cultured every three days.

extract_protocol:
Total RNAs were extracted with Trizol and NanoDrop 2000 spectrophotometer (ThermoFisher) was used to quantify the concentration of total RNA at a wavelength of 260 nm.
About 1.5 µg of purified poly(A)-RNA was fragmented into ~100 nt fragments using RNA fragmentation buffer (AM8740, Thermo Scientific). One-tenth of fragmented RNAs were used for the construction of RNA-seq libraries (Input) and the left RNAs were used for the construction of m6A MeRIP-seq libraries (IP). m6A IP was conducted using an EpiMark® N6-Methyladenosine Enrichment Kit (#E1610S, NEB) following the product manual. The resultant m6A-enriched and untreated poly(A)-RNA fragments were used to construct strand-specific IP and Input libraries, respectively. A VAHTS® Universal V6 RNA-seq Library Prep Kit for Illumina (NR604-02, Vazyme Biotech. Co., Ltd.) and VAHTS® RNA Adapters set3 for Illumina (N809, Vazyme Biotech. Co., Ltd.) provided the necessary reagents for first- and second-strand cDNA synthesis, adaptor ligation, and library amplification. RNA-seq and MeRIP-seq of the prepared libraries were performed in Berry Genomics on the NovaSeq 6000 platform (Illumina, CA, USA) to obtain paired-end reads of 150 bp. Library quality was assessed on an Agilent Bioanalyzer 4200 TapeStation before loading onto the sequencer, ~8G of raw reads was obtained for each library.

treatment_protocol: Folic acid supplementation in Drosophila：The conventional Drosophila melanogaster strain w1118 was reared on yeast-glucose medium (1 L water, 100 g yeast, 100 g glucose, 1.2% agar, 0.1% potassium sorbate) at 25°C, 70% relative humidity, and a photoperiod of 12L: 12D. Folic acid supplementation in mice：Three-week-old C57BL/6J SPF mice (six mice for male and female, respectively) were purchased, and each gender of mice was randomly divided into two groups with three mice in each group. All mice had free access to a sterilized diet and water, and the corn bedding was changed regularly. Each mouse was fed with folic acid via gavage at a volume of 0.1 mL/day and a concentration of 500 μg/kg/day for 14 days. After 14 days, mice organs were dissected and collected, including the brain, heart, liver, kidney, spleen, muscle, thymus, and testis. Mice organ samples were immediately frozen in liquid nitrogen and stored at -80℃ until use. The protocol for an animal experiment in this study was reviewed and approved by the Institutional Animal Care and Use Committee (IACUC) of South China Normal University (protocol code SCNU-SLS-2022-009).


title: PBMCs, Control, 12hr, 38147, 2

description: Library name: G044_O19_38147_C_12hr_2


title: Drosophila intestinal cell line 15 - passage 18

description:
Library name: L15
10X Genomics


title: D595, 68-1 RhCMV/SIV, subcutaneously, Protected, 29558

description:
Library name: G036_ABL01_29558_D595
!0x Genomics


title: WT-6months-male-rep3


title: Slc10a1-KO-8weeks-female-rep5

value: female

value: 8 weeks


title: Drosophila intestinal cell line 10 - passage 4

description:
Library name: L10
10X Genomics


title: D595, 68-1 RhCMV/SIV, subcutaneously, Non-protected, 30412

description:
Library name: G042_ABL01_30412_D595
!0x Genomics

value: 68-1 RhCMV/SIV, subcutaneously


title: BSLN, 68-1 RhCMV/SIV, subcutaneously, Protected, 29208

description:
Library name: G047_ABL01_29208_BSLN
!0x Genomics


title: WT-LP2


title: D595, 68-1 RhCMV/SIV, subcutaneously, Non-protected, 29523

description:
Library name: G034_ABL01_29523_D574
!0x Genomics


title: PBMCs, Control, 12hr, 38147, 1

description: Library name: G043_O19_38147_C_12hr_1


title: PBMCs, Control, 24hr, 38147, 1

description: Library name: G046_O19_38147_C_24hr_1


title: WT-LP1


title: PBMCs, Control, 24hr, 38147, 2

description: Library name: G047_O19_38147_C_24hr_2


title: WT-LP3-ip


title: Slc10a1-KO-8weeks-female-rep3


title: BSLN, 68-1 RhCMV/SIV, subcutaneously, Non-protected, 30412

description:
Library name: G041_ABL01_30412_BSLN
!0x Genomics


title: D595, 68-1 RhCMV/SIV, subcutaneously, Non-protected, 28819

description:
Library name: G032_ABL01_28819_D595
!0x Genomics


title: PBMCs, Control, 12hr, 38147, 3

description: Library name: G045_O19_38147_C_12hr_3


title: PBMCs, Control, 6hr, 38147, 1

description: Library name: G040_O19_38147_C_6hr_1


title: WT-LP1-ip


title: BSLN, 68-1 RhCMV/SIV, subcutaneously, Non-protected, 28819

description:
Library name: G031_ABL01_28819_BSLN
!0x Genomics


title: Slc10a1-KO-8weeks-female-rep6


title: BSLN, 68-1 RhCMV/SIV, subcutaneously, Protected, 29558

description:
Library name: G035_ABL01_29558_BSLN
!0x Genomics


title: WT-LP3


title: PBMCs, Control, 6hr, 38147, 3

description: Library name: G042_O19_38147_C_6hr_3


title: Slc10a1-KO-8weeks-female-rep1


title: Slc10a1-KO-8weeks-female-rep4


title: BSLN, 68-1 RhCMV/SIV, subcutaneously, Non-protected, 29523

description:
Library name: G033_ABL01_29523_BSLN
!0x Genomics


title: PBMCs, Control, 6hr, 38147, 2

description: Library name: G041_O19_38147_C_6hr_2


title: D595, 68-1 RhCMV/SIV, orally, Protected, 28885

description:
Library name: G020_ABL01_28885_D595
!0x Genomics

value: 68-1 RhCMV/SIV, orally


title: WT-8weeks-female-rep1


title: Slc10a1-KO-8weeks-female-rep2


title: WT-Control3-ip


title: PBMCs, Control, 2hr, 38147, 3

description: Library name: G039_O19_38147_C_2hr_3


title: WT-Control2


title: PBMCs, Control, 0hr, 38147, 2

description: Library name: G035_O19_38147_C_0hr_2


title: WT-Control2-ip


title: WT-Control1-ip


title: WT-8weeks-female-rep3


title: S2-Folate3-ip

source_name: S2 (Schneider 2)

value: S2 (Schneider 2)

tag: cell type

value: Drosophila embryo s2 cell


title: PBMCs, IL15, 48hr, 38142, 3

description: Library name: G033_O19_38142_IL15_48hr_3

value: Female

value: 40 ng/ml


title: D595, 68-1 RhCMV/SIV, orally, Protected, 29212

description:
Library name: G028_ABL01_29212_D595
!0x Genomics

value: Protected

value: Male


title: PBMCs, Control, 2hr, 38147, 1

description: Library name: G037_O19_38147_C_2hr_1

value: Control


title: Slc10a1-KO-8weeks-male-rep2

value: male

tag: genotype


title: BSLN, 68-1 RhCMV/SIV, orally, Protected, 29212

description:
Library name: G027_ABL01_29212_BSLN
!0x Genomics

value: BSLN


title: WT-8weeks-female-rep2

value: wild type

value: liver


title: WT-Control3


title: PBMCs, Control, 0hr, 38147, 3

description: Library name: G036_O19_38147_C_0hr_3

value: PBMCs

tag: replicate

value: 0 ng/ml


title: WT-Control1


title: BSLN, 68-1 RhCMV/SIV, orally, Protected, 28885

description:
Library name: G019_ABL01_28885_BSLN
!0x Genomics

tag: treatment outcome


title: PBMCs, Control, 0hr, 38147, 1

description: Library name: G034_O19_38147_C_0hr_1


title: BSLN, 68-1 RhCMV/SIV, orally, Non-protected, 29528

description:
Library name: G009_ABL01_29528_BSLN
!0x Genomics

value: Non-protected


title: S2-Folate3


title: D595, 68-1 RhCMV/SIV, orally, Non-protected, 30400

description:
Library name: G012_ABL01_30400_D595
!0x Genomics


title: D595, 68-1 RhCMV/SIV, orally, Protected, 29483

description:
Library name: G008_ABL01_29483_D595
!0x Genomics


title: Slc10a1-KO-8weeks-male-rep3

tag: gender

value: 8 weeks


title: PBMCs, Control, 2hr, 38147, 2

description: Library name: G038_O19_38147_C_2hr_2


title: BSLN, 68-1 RhCMV/SIV, orally, Non-protected, 30400

description:
Library name: G011_ABL01_30400_BSLN
!0x Genomics


title: PBMCs, IL15, 24hr, 38142, 2

description: Library name: G029_O19_38142_IL15_24hr_2


title: S2-Folate2-ip


title: D595, 68-1 RhCMV/SIV, orally, Non-protected, 29528

description:
Library name: G010_ABL01_29528_D595
!0x Genomics


title: S2-Folate2


title: PBMCs, IL15, 48hr, 38142, 2

description: Library name: G032_O19_38142_IL15_48hr_2


title: S2-Control3-ip


title: Slc10a1-KO-8weeks-male-rep4


title: S2-Folate1-ip


title: WT-8weeks-male-rep2


title: Slc10a1-KO-8weeks-male-rep1


title: PBMCs, IL15, 24hr, 38142, 3

description: Library name: G030_O19_38142_IL15_24hr_3


title: BSLN, 68-1 RhCMV/SIV, orally, Protected, 29482

description:
Library name: G005_ABL01_29482_BSLN
!0x Genomics


title: D595, 68-1.2 RhCMV/SIV, subcutaneously, Protected, 29292

description:
Library name: G066_ABL01_29292_D595
!0x Genomics

value: 68-1.2 RhCMV/SIV, subcutaneously


title: PBMCs, IL15, 48hr, 38142, 1

description: Library name: G031_O19_38142_IL15_48hr_1


title: S2-Control2-ip


title: BSLN, 68-1 RhCMV/SIV, orally, Protected, 29483

description:
Library name: G007_ABL01_29483_BSLN
!0x Genomics

value: 68-1 RhCMV/SIV, orally


title: S2-Folate1

value: S2 (Schneider 2)


title: D595, 68-1 RhCMV/SIV, orally, Protected, 29482

description:
Library name: G006_ABL01_29482_D595
!0x Genomics


title: PBMCs, IL15, 24hr, 38142, 1

description: Library name: G028_O19_38142_IL15_24hr_1


title: D595, 68-1 RhCMV/SIV, orally, Non-protected, 28724

description:
Library name: G002_ABL01_28724_D595
!0x Genomics


title: PBMCs, IL15, 6hr, 38142, 3

description: Library name: G024_O19_38142_IL15_6hr_3


title: S2-Control2

value: Drosophila embryo s2 cell


title: PBMCs, IL15, 12hr, 38142, 3

description: Library name: G027_O19_38142_IL15_12hr_3

value: Female


title: D595, 68-1 RhCMV/SIV, orally, Non-protected, 29306

description:
Library name: G004_ABL01_29306_D595
!0x Genomics


title: PBMCs, IL15, 12hr, 38142, 2

description: Library name: G026_O19_38142_IL15_12hr_2

value: 40 ng/ml


title: p24240.s032_1E9.BN18.D18

first: Dan

last: Barouch

state: MA

address: 3 Blackfan Cir

department: CVVR

institute: Beth Israel Deaconess Medical Center

description: Library name: p24240.s032_1E9.BN18.D18

data_processing:
Alignment was performed using STAR version 2.7.9a to a composite of the Rhesus Mmul10 reference assembly sequence (Ensembl v104 annotation) and the NCBI H5N1 reference assembly (GCF_000864105.1). Transcript abundance estimates were calculated internal to the STAR aligner using the algorithm of htseq-count. DESeq2 was used for normalization, producing a both raw and normalized read count tables and for differential gene expression analysis.
Assembly: Rhesus mmul10
Supplementary files format and content: raw-counts-H5N1.csv, raw read counts
Supplementary files format and content: normalized-counts-H5N1.csv, normalized read counts

source_name: Whole blood

extract_protocol:
Blood was collected into PAXgene Blood RNA tubes (BD Biosciences) and the RNA was extracted using the MagMAX for Stabilized Blood Tubes RNA Isolation Kit, compatible with PAXgene Blood RNA Tubes (ThermoFisher Scientific).
RNA quality was assessed using a Fragment Analyzer (Agilent) and then one microgram of total RNA was subjected to globin transcript depletion using the GLOBINclear Kit, human (ThermoFisher Scientific). Ten nanograms of the globin-depleted RNA was used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to the manufacturer’s instructions. Amplified cDNA was fragmented and appended with dual-indexed bar codes using the Nextera XT DNA Library Preparation kit (Illumina). Libraries were validated by capillary electrophoresis on a TapeStation 4200 (Agilent), pooled at equimolar concentrations, and sequenced with PE100 reads on an Illumina NovaSeq 6000, yielding ~30 million reads per sample on average.

value: Whole blood

tag: route

value: IN+IT

tag: dose (tcid50_h5n1)

tag: timepoint


title: p24240.s033_1E9.CZ29.D18

description: Library name: p24240.s033_1E9.CZ29.D18

tag: tissue


title: ago2c_IR

city: Jeongeup-si

first: Jin-Hong

last: Kim

state: Jeonbuk-do

address: 29 Geumgu-gil

country: South Korea

institute: Korea Atomic Energy Research Institute

description: Gene expression of Arabidopsis whole seedling (ago2c), 24hr, 200Gy, gamma-ray

hyb_protocol: Cy3-labeled cRNA was fragmented for 30 minutes at 60°C in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocker according to the manufacturer's instructions. Upon completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the Agilent Total Arabidopsis Gene Expression Microarray (V4) (021169) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, the microarrays were washed with GE Wash Buffer 1 (Agilent) at room temperature for 1 min and with 37°C GE Wash Buffer 2 (Agilent) for 1 min, and then immediately dried by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10 µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with feature extraction software 9.1 (Agilent) to obtain processed signal intensities that were background-removed and spatially detrended. Features flagged as feature non-uniform outliers were excluded from feature extraction.

organism: Arabidopsis thaliana

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

growth_protocol: Arabidopsis (ecotype Columbia-0) wild-type and ago2 mutant seeds were surface disinfected for 1 min in 70% ethanol, 5 min in 20% bleach solution, and rinsed five times with sterile water. Seeds were cold treated for 3 d in the dark at 4°C and then grown in 1/2 MS medium (pH 5.7) containing 1% sucrose and 0.65% agar at approximately 23°C and 50% relative humidity under a 16-h light, 8-h dark cycle.

extract_protocol: Total RNA was isolated from at least 10 whole seedlings using the RNeasy Plant Mini Kit (Qiagen) and pooled from three independent batches.

treatment_protocol: A Co-60 gamma irradiator (IR-222, MDS Nordion Inc.) was used to expose 14-day-old seedlings to 200 Gy of gamma radiation (dose rate 50 Gy/hr).

value: Whole seedling

tag: developmental stage


title: S2-Control1-ip


title: BSLN, 68-1 RhCMV/SIV, orally, Non-protected, 29306

first: Michael

address: 689 23rd Ave SE

institute: University of Minnesota

description:
Library name: G003_ABL01_29306_BSLN
!0x Genomics

tag: treatment

value: Male


title: WT_IR

description: Gene expression of Arabidopsis whole seedling (wild-type), 24hr, 200Gy, gamma-ray


title: ago2a_con

description: Gene expression of Arabidopsis whole seedling (ago2a), mock


title: ago2a_IR

description: Gene expression of Arabidopsis whole seedling (ago2a), 24hr, 200Gy, gamma-ray


title: ago2c_con

description: Gene expression of Arabidopsis whole seedling (ago2c), mock


title: GF-Folate2-ip

tag: strain


title: WT_con

description: Gene expression of Arabidopsis whole seedling (wild-type), mock


title: S2-Control3


title: PBMCs, IL15, 6hr, 38142, 2

description: Library name: G023_O19_38142_IL15_6hr_2

tag: time