title: Whole blood, 68-1 Δpp71 RhCMV gag/rtn/pol, day 448, 35926

city: Minneapolis

first: Michael

last: Gale

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

description: Library name: G411_O06_ABL2_B_35926_D448

data_processing:
Trimgalorev0.6.4 used to remove low quality reads and bases
Filtered out globin and rRNA reads using bowtie2v2.1.0
Aligned reads with STARv2.7.3
quantified read counts with  htseqv0.11.2
Assembly: Rhesus macaques version 10 Ensembl annoation v98
Supplementary files format and content: ount matrix

organism: Macaca mulatta

source_name: Whole blood

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

treatment_protocol: A prime and boost of one of the 4 modified RhCMV/SIV vectors were given to Rhesus macaques

value: Whole blood

value: 68-1 Δpp71 RhCMV gag/rtn/pol

tag: time

value: day 448

tag: animal id

tag: Sex

value: male

tag: dose

tag: treatment outcome

value: notprotected


title: Whole blood, 68-1 Δpp71 RhCMV gag/rtn/pol, day 448, 35924

status: Public on Aug 01 2025

type: SRA

state: Minnesota

country: USA

description: Library name: G409_O06_ABL2_B_35924_D448

library_source: transcriptomic

molecule: total RNA

tag: tissue

tag: treatment

value: protected


title: RAW264.7 cells, control 4

city: shenyang

first: mengjie

last: kang

state: 辽宁省

address: 辽宁省沈阳市于洪区黄河北大街沈阳医学院

country: China

institute: Shenyang Medical College

description:
Library name: Sample4
C-4_tpm

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp (version 0.18.0).
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
The mapped reads of each sample were assembled by using StringTie v1.3.1[4][5] in a referencebased approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Assembly: GRCm39/mm39
Supplementary files format and content: processed data.xlsx

organism: Mus musculus

growth_protocol: Murine macrophage RAW264.7 cells were cultured in high-glucose DEME medium supplemented with 10% fetal bovine serum and the 1% penicillin-streptomycin antibiotics at 37 °C and 5% CO2.

extract_protocol:
Total RNA was extracted from the macrophages using Trizol reagent kit following the manufacturer’s protocols.
The extracted mRNA is enriched using mRNA Capture Beads. After purification with beads, the mRNA is fragmented using high temperatures. The fragmented mRNA is then used as a template to synthesize the first strand of cDNA in a reverse transcription enzyme mixture system. While synthesizing the second strand of cDNA, end repair and A-tailing are completed. Next, adapters are ligated, and Hieff NGS® DNA Selection Beads are used for purification to select target fragments. PCR library amplification is then performed, and finally, detection is carried out using the Illumina Novaseq X Plus.

treatment_protocol: For macrophage phenotype studies, cells were treated with vehicle (culture medium), oxLDL (50 μg/ml), Tirzepatide (100 nmol/ml) or a combination of oxLDL and Tirzepatide

tag: cell line

tag: cell type

value: mononuclear macrophage leukemia cells

tag: genotype

value: vehicle


title: Whole blood, 68-1 Δpp71 RhCMV gag/rtn/pol, day 448, 35923

description: Library name: G408_O06_ABL2_B_35923_D448


title: Day 3 cells cultured in TSCM with Dox (oligo)

city: Ithaca

first: Weiyu

last: Zhang

state: NY

address: 215 Tower Rd, Biotechnology Building

department: MBG

institute: Cornell University

library_source: transcriptomic single cell

data_processing:
DNBC4tools (v2.1.3) was employed to align the reads from the scRNA-seq data and quantify gene counts. Seurat (5.1.0) was then utilized for downstream analysis, with cells displaying low gene counts and high mitochondrial expression excluded from the dataset. Gene expression was normalized using scran (v1.28.1), and DoubletFinder (v2.0.4) was applied to identify and filter out potential doublets. For further analysis, up to 30 principal components (PCs) were selected, and a clustering resolution of 0.2 was used. Outlier clusters were filtered out to optimize downstream analysis.
Assembly: hg38
Supplementary files format and content: RDS file containing a Seurat object.

molecule: polyA RNA

organism: Homo sapiens

extract_protocol:
Total RNA was extracted with TRIzol reagent.
scRNA-seq libraries were prepared using a DNBelab C Series High-throughput Single-cell RNA Library Preparation set (MGI).

value: Expanded Potential Stem Cells

value: WT

value: DOX


title: RAW264.7 cells, oxLDL and tirzepatide 2

address: 辽宁省沈阳市于洪区黄河北大街沈阳医学院

description:
Library name: Sample14
OandT-2_tpm

value: O and T-2

value: oxLDL and Tirzepatide


title: Day 3 cells cultured in TSCM without Dox (cDNA)

value: METTL3 iKO


title: Day 3 cells cultured in TSCM without Dox (oligo)


title: Whole blood, 68-1 Δpp71 RhCMV gag/rtn/pol, day 448, 35922

description: Library name: G407_O06_ABL2_B_35922_D448


title: P2 hEPSC without DOX (oligo)


title: Whole blood, 68-1 Δpp71 RhCMV gag/rtn/pol, day 448, 35920

description: Library name: G406_O06_ABL2_B_35920_D448


title: RAW264.7 cells, control 1

address: 辽宁省沈阳市于洪区黄河北大街沈阳医学院

description:
Library name: Sample1
C-1_tpm


title: Whole blood, 68-1 Δpp71 RhCMV gag/rtn/pol, day 448, 35919

description: Library name: G405_O06_ABL2_B_35919_D448


title: H93PG

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

description: Library name: H93PG

data_processing:
Raw sequencing data were processed using 10x Genomics SpaceRanger (v2.0.0)
Assembly: GRCm38
Supplementary files format and content: HDF5 file containing per-molecule information for all molecules
Library strategy: Spatial Transcriptomics

source_name: Brain

extract_protocol:
Fresh-frozen mouse brain tissue sections dissected from mice of all groups at endpoint analysis were prepared at a thickness of 10 µm and placed on a Superfrost Plus slide. The Visium slides were processed according to the 10x Genomics Visium CytAssist Spatial Gene Expression for Fresh Frozen.
The libraries were constructed using CytAssist Spatial Gene Expression Reagent Kits according to the manufacturer’s instructions.

value: Brain

value: LRRK2 G2019S

value: Parabacteroides goldsteinii MTS01


title: RAW264.7 cells, tirzepatide 2

address: 辽宁省沈阳市于洪区黄河北大街沈阳医学院

description:
Library name: Sample10
T-2_tpm

value: Tirzepatide


title: P0 hEPSC (oligo)


title: Whole blood, 68-1 Δpp71 RhCMV gag/rtn/pol, day 448, 35929

description: Library name: G414_O06_ABL2_B_35929_D448

value: Whole blood

value: 68-1 Δpp71 RhCMV gag/rtn/pol


title: Whole blood, 68-1 Δpp71 RhCMV gag/rtn/pol, day 434, 35928

description: Library name: G403_O06_ABL2_B_35928_D434

value: day 434

value: male


title: RAW264.7 cells, oxLDL 1

address: 辽宁省沈阳市于洪区黄河北大街沈阳医学院

description:
Library name: Sample5
O-1_tpm

value: oxLDL


title: N71GF

description: Library name: N71GF

value: germ-free


title: Whole blood, 68-1 Δpp71 RhCMV gag/rtn/pol, day 448, 35928

description: Library name: G413_O06_ABL2_B_35928_D448

value: day 448

value: protected


title: RAW264.7 cells, control 3

address: 辽宁省沈阳市于洪区黄河北大街沈阳医学院

description:
Library name: Sample3
C-3_tpm

value: mononuclear macrophage leukemia cells

value: vehicle


title: RAW264.7 cells, tirzepatide 1

address: 辽宁省沈阳市于洪区黄河北大街沈阳医学院

description:
Library name: Sample9
T-1_tpm


title: Whole blood, 68-1 Δpp71 RhCMV gag/rtn/pol, day 434, 35927

description: Library name: G402_O06_ABL2_B_35927_D434

value: notprotected


title: Whole blood, 68-1 Δpp71 RhCMV gag/rtn/pol, day 434, 35924

description: Library name: G399_O06_ABL2_B_35924_D434


title: RAW264.7 cells, control 2

address: 辽宁省沈阳市于洪区黄河北大街沈阳医学院

description:
Library name: Sample2
C-2_tpm


title: Whole blood, 68-1 Δpp71 RhCMV gag/rtn/pol, day 434, 35926

description: Library name: G401_O06_ABL2_B_35926_D434


title: RAW264.7 cells, oxLDL 2

address: 辽宁省沈阳市于洪区黄河北大街沈阳医学院

description:
Library name: Sample6
O-2_tpm


title: Whole blood, 68-1 Δpp71 RhCMV gag/rtn/pol, day 448, 35927

description: Library name: G412_O06_ABL2_B_35927_D448


title: Whole blood, 68-1 Δpp71 RhCMV gag/rtn/pol, day 448, 35925

description: Library name: G410_O06_ABL2_B_35925_D448


title: Whole blood, 68-1 Δpp71 RhCMV gag/rtn/pol, day 434, 35919

description: Library name: G395_O06_ABL2_B_35919_D434


title: C-3-2

city: kunming

first: le

last: yang

state: yunnan

address: cuihubeilu

institute: yunnan university

description:
Library name: Sample 20
B_lipDay3_2

data_processing:
The data from high-throughput sequencing were analyzed using the Majorbio tools, a free online platform for data analysis (www.majorbio.com).
HiSat2 and StringTie
cufflinks
Assembly: NOT PROVIDED
Supplementary files format and content: Expression analysis table include TPM values for each WT and mutant sample

organism: Aspergillus niger

source_name: Fungal hyphae cells

growth_protocol: The wild-type and  mutant strains were cultured on potato dextrose agar (PDA) medium at 28°C.

extract_protocol:
Total RNA was extracted from tissue samples, the concentration and purity of the extracted RNA were detected by Nanodrop2000, RNA integrity was detected by agarose gel electrophoresis, and RIN value was determined by Agilent2100. A single library construction requires that the total amount of RNA is ≥1ug, the concentration is ≥35ng/μL, OD260/280 is 1.8 - 2.2, and OD260/230≥1.0.
The libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

value: Fungal hyphae cells

value: TLL expressing strains


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 462, 35914

description: Library name: G394_O06_ABL2_A3_35914_D462

value: day 462


title: C-2-1

description:
Library name: Sample 16
B_lipDay2_1


title: C-1-3

description:
Library name: Sample 15
B_lipDay1_3


title: C-1-2

description:
Library name: Sample 14
B_lipDay1_2


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 462, 35886

description: Library name: G390_O06_ABL2_A3_35886_D462


title: B-4-3

description:
Library name: Sample 12
BDay4_3

value: wild type


title: Whole blood, 68-1 Δpp71 RhCMV gag/rtn/pol, day 434, 35922

description: Library name: G397_O06_ABL2_B_35922_D434


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 462, 33878

description: Library name: G387_O06_ABL2_A3_33878_D462


title: H129GF

description: Library name: H129GF

value: Brain

value: LRRK2 G2019S


title: Whole blood, 68-1 Δpp71 RhCMV gag/rtn/pol, day 434, 35929

description: Library name: G404_O06_ABL2_B_35929_D434

value: Whole blood


title: N85PG

description: Library name: N85PG

value: WT

value: Parabacteroides goldsteinii MTS01


title: B-4-1

description:
Library name: Sample 10
BDay4_1


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 462, 35913

description: Library name: G393_O06_ABL2_A3_35913_D462

value: male


title: C-4-3

description:
Library name: Sample 24
B_lipDay4_3


title: B-3-2

description:
Library name: Sample 8
BDay3_2


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 462, 32707

description: Library name: G384_O06_ABL2_A3_32707_D462


title: Whole blood, 68-1 Δpp71 RhCMV gag/rtn/pol, day 434, 35925

description: Library name: G400_O06_ABL2_B_35925_D434

value: 68-1 Δpp71 RhCMV gag/rtn/pol

value: day 434


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 462, 32689

description: Library name: G383_O06_ABL2_A3_32689_D462


title: B-4-2

description:
Library name: Sample 11
BDay4_2


title: B-2-3

description:
Library name: Sample 6
BDay2_3


title: C-4-1

description:
Library name: Sample 22
B_lipDay4_1


title: C-4-2

description:
Library name: Sample 23
B_lipDay4_2


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 462, 35915

description: Library name: G382_O06_ABL2_A2_35915_D462


title: C-3-3

description:
Library name: Sample 21
B_lipDay3_3


title: Whole blood, 68-1 Δpp71 RhCMV gag/rtn/pol, day 434, 35923

description: Library name: G398_O06_ABL2_B_35923_D434


title: B-2-1

description:
Library name: Sample 4
BDay2_1


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 462, 33543

description: Library name: G379_O06_ABL2_A2_33543_D462


title: C-2-3

description:
Library name: Sample 18
B_lipDay2_3


title: C-3-1

description:
Library name: Sample 19
B_lipDay3_1


title: #12(NdhF1-F124L&EF-G2-R461C), strong high light,rep3

city: Planegg

first: Weiyang

last: Chen

address: Großhaderner Straße 2

department: Biologie I, Botanik

country: Germany

institute: Ludwig-Maximilians-Universität München

data_processing:
RNA-Seq reads were trimmed for adaptor sequences using Trimmomatic and sequencing quality was assessed using FastQC.
Paired-end reads were mapped to the Synechocystis sp. PCC6803 genome (GCF_000009725.1) using HISAT2. Read counts were quantified using featureCounts.
Assembly: GCF_000009725.1
Supplementary files format and content: tab-delimited text file includes FPKM values for all samples

organism: Synechocystis sp. PCC 6803

source_name: Whole cell

extract_protocol:
RNA was extracted with phenol-chloroform from cells in the TRIzol, and finally precipitated with isopropanol. The RNA was treated with the TURBO DNA-freeTM kit to remove genomic DNA, and then purified using Direct-zol™ RNA MiniPrep Plus columns.
Firstly, ribosomal RNA was removed from total RNA, followed by ethanol precipitation. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. During the second strand cDNA synthesis, dUTPs were replaced with dTTPs in the reaction buffer. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

value: Whole cell

value: strong high light


title: C-2-2

description:
Library name: Sample 17
B_lipDay2_2


title: Whole blood, 68-1 Δpp71 RhCMV gag/rtn/pol, day 434, 35920

description: Library name: G396_O06_ABL2_B_35920_D434

value: protected


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 462, 35883

description: Library name: G377_O06_ABL2_A2_35883_D462


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 462, 35910

description: Library name: G392_O06_ABL2_A3_35910_D462


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 462, 35889

description: Library name: G391_O06_ABL2_A3_35889_D462


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 462, 35820

description: Library name: G375_O06_ABL2_A2_35820_D462


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 462, 35885

description: Library name: G389_O06_ABL2_A3_35885_D462


title: #12(NdhF1-F124L&EF-G2-R461C), intermediate high light,rep3

value: intermediate high light


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 462, 35822

description: Library name: G388_O06_ABL2_A3_35822_D462

value: notprotected


title: B-3-1

description:
Library name: Sample 7
BDay3_1

value: Fungal hyphae cells


title: C-1-1

description:
Library name: Sample 13
B_lipDay1_1

value: TLL expressing strains


title: B-3-3

description:
Library name: Sample 9
BDay3_3


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 462, 33877

description: Library name: G386_O06_ABL2_A3_33877_D462

value: day 462


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 462, 33700

description: Library name: G385_O06_ABL2_A3_33700_D462


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 462, 35911

description: Library name: G380_O06_ABL2_A2_35911_D462


title: B-1-3

description:
Library name: Sample 3
BDay1_3

value: wild type


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 462, 35912

description: Library name: G381_O06_ABL2_A2_35912_D462


title: #12(NdhF1-F124L&EF-G2-R461C), normal light,rep2

value: control light


title: B-1-2

description:
Library name: Sample 2
BDay1_2


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 462, 35884

description: Library name: G378_O06_ABL2_A2_35884_D462


title: #12(NdhF1-F124L&EF-G2-R461C), normal light,rep1


title: #12(NdhF1-F124L&EF-G2-R461C), strong high light,rep2


title: B-2-2

description:
Library name: Sample 5
BDay2_2


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 462, 33864

description: Library name: G374_O06_ABL2_A2_33864_D462


title: B-1-1

description:
Library name: Sample 1
BDay1_1


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 462, 35827

description: Library name: G376_O06_ABL2_A2_35827_D462


title: #12(NdhF1-F124L&EF-G2-R461C), strong high light,rep1


title: #12(NdhF1-F124L&EF-G2-R461C), intermediate high light,rep1


title: #2(EF-G2-R461C), intermediate high light,rep3

value: EF-G2-R461C(point mutant)


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 462, 33900

description: Library name: G366_O06_ABL2_A1_33900_D462

value: Whole blood


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 462, 32119

description: Library name: G372_O06_ABL2_A2_32119_D462


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 462, 35916

description: Library name: G370_O06_ABL2_A1_35916_D462


title: #12(NdhF1-F124L&EF-G2-R461C), normal light,rep3


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 462, 32814

description: Library name: G364_O06_ABL2_A1_32814_D462


title: #12(NdhF1-F124L&EF-G2-R461C), intermediate high light,rep2


title: #2(EF-G2-R461C), strong high light,rep3


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 462, 32509

description: Library name: G373_O06_ABL2_A2_32509_D462


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 462, 35815

description: Library name: G368_O06_ABL2_A1_35815_D462


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 462, 35890

description: Library name: G369_O06_ABL2_A1_35890_D462


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 462, 32017

description: Library name: G371_O06_ABL2_A2_32017_D462


title: #2(EF-G2-R461C), intermediate high light,rep1


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 462, 35808

description: Library name: G367_O06_ABL2_A1_35808_D462


title: #2(EF-G2-R461C), intermediate high light,rep2


title: #2(EF-G2-R461C), normal light,rep3


title: #2(EF-G2-R461C), strong high light,rep1


title: #2(EF-G2-R461C), normal light,rep2


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 462, 33879

description: Library name: G365_O06_ABL2_A1_33879_D462


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 462, 32215

description: Library name: G360_O06_ABL2_A1_32215_D462


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 462, 32485

description: Library name: G362_O06_ABL2_A1_32485_D462


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 462, 32321

description: Library name: G361_O06_ABL2_A1_32321_D462


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 462, 32778

description: Library name: G363_O06_ABL2_A1_32778_D462


title: #2(EF-G2-R461C), normal light,rep1


title: #1(NdhF1-F124L), strong high light,rep3

value: NdhF1-F124L (point mutant)


title: #2(EF-G2-R461C), strong high light,rep2


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 448, 35910

description: Library name: G356_O06_ABL2_A3_35910_D448

value: day 448


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 462, 32019

description: Library name: G359_O06_ABL2_A1_32019_D462

value: male


title: #1(NdhF1-F124L), strong high light,rep1


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 448, 35914

description: Library name: G358_O06_ABL2_A3_35914_D448


title: #1(NdhF1-F124L), intermediate high light,rep2


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 448, 35913

description: Library name: G357_O06_ABL2_A3_35913_D448


title: #1(NdhF1-F124L), intermediate high light,rep1


title: #1(NdhF1-F124L), strong high light,rep2


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 448, 35889

description: Library name: G355_O06_ABL2_A3_35889_D448


title: #1(NdhF1-F124L), normal light,rep3


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 448, 35886

description: Library name: G354_O06_ABL2_A3_35886_D448


title: #1(NdhF1-F124L), normal light,rep1


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 448, 33878

description: Library name: G351_O06_ABL2_A3_33878_D448


title: #1(NdhF1-F124L), intermediate high light,rep3


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 448, 35885

description: Library name: G353_O06_ABL2_A3_35885_D448


title: UMMM2, strong high light,rep3

value: UMMM2 (evolved strain)


title: #1(NdhF1-F124L), normal light,rep2


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 448, 35822

description: Library name: G352_O06_ABL2_A3_35822_D448


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 448, 33700

description: Library name: G349_O06_ABL2_A3_33700_D448


title: UMMM2, strong high light,rep2


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 448, 33877

description: Library name: G350_O06_ABL2_A3_33877_D448


title: UMMM2, strong high light,rep1


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 448, 32707

description: Library name: G348_O06_ABL2_A3_32707_D448


title: UMMM2, intermediate high light,rep3


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 448, 35915

description: Library name: G346_O06_ABL2_A2_35915_D448


title: UMMM2, intermediate high light,rep2


title: UMMM2, intermediate high light,rep1


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 448, 35912

description: Library name: G345_O06_ABL2_A2_35912_D448


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 448, 32689

description: Library name: G347_O06_ABL2_A3_32689_D448


title: UMMM2, normal light,rep3


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 448, 33543

description: Library name: G343_O06_ABL2_A2_33543_D448


title: LT(lab type), strong high light,rep2

value: LT(lab type)


title: UMMM2, normal light,rep2

value: Whole cell


title: UMMM2, normal light,rep1


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 448, 35884

description: Library name: G342_O06_ABL2_A2_35884_D448


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 448, 35827

description: Library name: G340_O06_ABL2_A2_35827_D448


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 448, 35911

description: Library name: G344_O06_ABL2_A2_35911_D448


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 448, 35883

description: Library name: G341_O06_ABL2_A2_35883_D448


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 448, 35820

description: Library name: G339_O06_ABL2_A2_35820_D448


title: LT(lab type), strong high light,rep1

value: strong high light


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 448, 33864

description: Library name: G338_O06_ABL2_A2_33864_D448

value: protected


title: LT(lab type), intermediate high light,rep3

value: intermediate high light


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 448, 32509

description: Library name: G337_O06_ABL2_A2_32509_D448


title: LT(lab type), intermediate high light,rep2


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 448, 32119

description: Library name: G336_O06_ABL2_A2_32119_D448


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 448, 32017

description: Library name: G335_O06_ABL2_A2_32017_D448

value: notprotected


title: LT(lab type), intermediate high light,rep1


title: LT(lab type), normal light,rep2


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 448, 35916

description: Library name: G334_O06_ABL2_A1_35916_D448


title: LT(lab type), normal light,rep1


title: LT(lab type), strong high light,rep3


title: WT(original WT), strong high light,rep3

value: Original WT


title: WT(original WT), strong high light,rep2


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 448, 35815

description: Library name: G332_O06_ABL2_A1_35815_D448


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 448, 35890

description: Library name: G333_O06_ABL2_A1_35890_D448


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 448, 35808

description: Library name: G331_O06_ABL2_A1_35808_D448


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 448, 33879

description: Library name: G329_O06_ABL2_A1_33879_D448


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 448, 33900

description: Library name: G330_O06_ABL2_A1_33900_D448


title: WT(original WT), intermediate high light,rep3


title: WT(original WT), strong high light,rep1


title: WT(original WT), intermediate high light,rep2


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 448, 32778

description: Library name: G327_O06_ABL2_A1_32778_D448


title: WT(original WT), normal light, rep2


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 448, 32814

description: Library name: G328_O06_ABL2_A1_32814_D448


title: WT(original WT), intermediate high light,rep1


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 448, 32215

description: Library name: G324_O06_ABL2_A1_32215_D448


title: WT(original WT), normal light, rep3


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 448, 32321

description: Library name: G325_O06_ABL2_A1_32321_D448


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 448, 32019

description: Library name: G323_O06_ABL2_A1_32019_D448


title: WT(original WT), normal light, rep1


title: LT(lab type), normal light,rep3


title: Whole blood, 68-1 Δpp71 RhCMV gag/rtn/pol, day 378, 35928

description: Library name: G321_O06_ABL2_B_35928_D378

value: 68-1 Δpp71 RhCMV gag/rtn/pol

value: day 378


title: Whole blood, 68-1 Δpp71 RhCMV gag/rtn/pol, day 378, 35929

description: Library name: G322_O06_ABL2_B_35929_D378


title: Whole blood, 68-1 Δpp71 RhCMV gag/rtn/pol, day 378, 35927

description: Library name: G320_O06_ABL2_B_35927_D378


title: Whole blood, 68-1 Δpp71 RhCMV gag/rtn/pol, day 378, 35926

description: Library name: G319_O06_ABL2_B_35926_D378


title: Whole blood, 68-1 Δpp71 RhCMV gag/rtn/pol, day 378, 35925

description: Library name: G318_O06_ABL2_B_35925_D378


title: Whole blood, 68-1 Δpp71 RhCMV gag/rtn/pol, day 378, 35923

description: Library name: G316_O06_ABL2_B_35923_D378


title: Whole blood, 68-1 Δpp71 RhCMV gag/rtn/pol, day 378, 35922

description: Library name: G315_O06_ABL2_B_35922_D378


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 448, 32485

description: Library name: G326_O06_ABL2_A1_32485_D448


title: W10_2

city: Wuhan

first: qingqing

last: li

address: No. 238 Jiefang Road, Wuchang District

department: Department of Respiratory and Critical Care Medicine

institute: Renmin Hospital of Wuhan University

description: replicate biosample 2

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to gossypium hirsutum 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: Gossypium hirsutum
Supplementary files format and content: tab-delimited text file includes differential expression genes between FPF1 and W10

organism: Gossypium hirsutum

source_name: leaf

extract_protocol:
RNA was harvested using Trizol reagent.NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB #E7775L) was used with 0.4 ug of total RNA for the construction of sequencing libraries.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNextR UltraTM Directional RNA Library Prep Kit for IlluminaR (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H . Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: leaf

value: wild type


title: Whole blood, 68-1 Δpp71 RhCMV gag/rtn/pol, day 378, 35919

description: Library name: G313_O06_ABL2_B_35919_D378


title: brain(Hippocampus), not exposed to 3% sevoflurane, 0h N2

type: RNA

city: wuhan

first: yikang

last: yuan

address: Luoyu Road, Hongshan District

institute: Wuhan University Stomatological Hospital

description: Expression of circular RNA without exposure to sevoflurane

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Mouse circRNA Arrays v2  (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: A series of data processing including quantile normalization were performed using the R software limma package. The circRNAs that at least 3 out of 6 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses.Differentially expressed circRNAs with statistical significance between two samples or two groups were identified using fold change cutoff or through Volcano Plot filtering respectively.

label_protocol: •Total RNA from each sample was treated with Rnase R to enrich circular RNA. The enriched circular RNA was then amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.).

extract_protocol: The purity and concentration of total RNA samples were determined with NanoDrop ND-1000. Results were provided in Sample QC report.

treatment_protocol: S1-3:Administer continuous 3% sevoflurane exposure for 4 hours on the 7th day postpartum in mice; N1-3：No exposure to sevoflurane

tag: development stage

value: postpartum 7 days


title: W10_1

description: replicate biosample 1


title: FPF1_1

description: replicate biosample 1

value: transgenic lines


title: FPF1_2

description: replicate biosample 2


title: brain(Hippocampus), not exposed to 3% sevoflurane, 0h N3


title: brain(Hippocampus), exposure to 3% sevoflurane, 4h S3

description: Expression of circular RNA after exposure to 3% sevoflurane


title: FPF1_3

description: replicate biosample 3


title: brain(Hippocampus), exposure to 3% sevoflurane, 4h S1


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 385, 35914

description: Library name: G312_O06_ABL2_A3_35914_D385

value: Whole blood

value: day 385


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 385, 35913

description: Library name: G311_O06_ABL2_A3_35913_D385

value: male


title: VeroE6_mock_biological_replicate_3_technical_replicate2

city: Singapore

first: Roland

middle: G

last: Huber

address: 30 Biopolis Street

country: Singapore

institute: Agency for Science, Technology and Research (A*STAR)

description: Library name: RHX1198

data_processing:
The A-to-I editing analysis pipeline was referred to previous study26 with some modifications. Raw reads were cleaned using FASTP47. Ten bases of 5’ and 3’ were trimmed and reads with more than 20% of unqualified bases were removed. The mean quality per base was fixed at a phred-score of 25. The reads that were shorter than 100 nt were discarded. The cleaned reads were mapped to the reference sequence using BWA48 aln (bwa aln -t 20) and mem (bwa mem -M -t 20 -k 50). The unmapped reads were extracted for editing site calling as described in the published study26. Editing site calling was performed by subsampled each library to the same reads’ depth. To identify edited reads, read was specially required to have a minimum number of edited sites >= 4 (with either A-to-G or T-to-C sites in a read). The putative misaligned reads matching any of the criteria as shown in the study26 were also excluded. Only reads with the number of mismatch and low-quality A-to-G/T-to-C sites <=2 were considered as edited reads. For each sample, the editing index was defined as number of editing sites from edited viral reads divided by the total number of viral reads in our study. The editing level was quantified by calculating the percentage of editing counts out of total reads at each position.
Assembly: EPI_ISL_407987 (SARS-CoV-2 WT);ChlSab1.1.102
Supplementary files format and content: SUPPORTING_TABLE_01_SEQUENCING_STATS.csv: Sequencing alignment statistics

organism: Chlorocebus

source_name: E6 TMPRSS2 Vero cell

growth_protocol: Vero E6 TMPRSS2 cells were infected with/without SARS-CoV viruses at an multiplicity of infection (MOI) = 0.01 for 48 h.

extract_protocol: The total RNA was then extracted from the cells using E.Z.N.A. Total RNA Kit I (Omega bio-tek) The A-to-I editing analysis pipeline was referred to previous study26 with some modifications. Raw reads were cleaned using FASTP47. Ten bases of 5’ and 3’ were trimmed and reads with more than 20% of unqualified bases were removed. The mean quality per base was fixed at a phred-score of 25. The reads that were shorter than 100 nt were discarded. The cleaned reads were mapped to the reference sequence using BWA48 aln (bwa aln -t 20) and mem (bwa mem -M -t 20 -k 50). The unmapped reads were extracted for editing site calling as described in the published study26. Editing site calling was performed by subsampled each library to the same reads’ depth. To identify edited reads, read was specially required to have a minimum number of edited sites >= 4 (with either A-to-G or T-to-C sites in a read). The putative misaligned reads matching any of the criteria as shown in the study26 were also excluded. Only reads with the number of mismatch and low-quality A-to-G/T-to-C sites <=2 were considered as edited reads. For each sample, the editing index was defined as number of editing sites from edited viral reads divided by the total number of viral reads in our study. The editing level was quantified by calculating the percentage of editing counts out of total reads at each position.

value: E6 TMPRSS2 Vero cell

value: E6 TMPRSS2

value: Vero cell


title: brain(Hippocampus), exposure to 3% sevoflurane, 4h S2


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 385, 35910

description: Library name: G310_O06_ABL2_A3_35910_D385


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 385, 35889

description: Library name: G309_O06_ABL2_A3_35889_D385


title: VeroE6_mock_biological_replicate_3_technical_replicate1

description: Library name: RHX1197


title: LR1-AB_biological_replicate_3_technical_replicate2

description: Library name: RHX1196


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 385, 35886

description: Library name: G308_O06_ABL2_A3_35886_D385


title: W10_3

description: replicate biosample 3


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 385, 35885

description: Library name: G307_O06_ABL2_A3_35885_D385


title: Whole blood, 68-1 Δpp71 RhCMV gag/rtn/pol, day 378, 35924

description: Library name: G317_O06_ABL2_B_35924_D378


title: brain(Hippocampus), not exposed to 3% sevoflurane, 0h N1


title: LR1-B_biological_replicate_3_technical_replicate2

description: Library name: RHX1194


title: LR1-AB_biological_replicate_3_technical_replicate1

description: Library name: RHX1195


title: LR1-A_biological_replicate_3_technical_replicate2

description: Library name: RHX1192


title: LR1-WT_biological_replicate_3_technical_replicate1

description: Library name: RHX1189


title: VeroE6_mock_biological_replicate_2_technical_replicate1

description: Library name: RHX1187


title: LR1-B_biological_replicate_3_technical_replicate1

description: Library name: RHX1193


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 385, 35915

description: Library name: G300_O06_ABL2_A2_35915_D385


title: Whole blood, 68-1 Δpp71 RhCMV gag/rtn/pol, day 378, 35920

description: Library name: G314_O06_ABL2_B_35920_D378


title: LR1-AB_biological_replicate_2_technical_replicate2

description: Library name: RHX1186


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 385, 35911

description: Library name: G298_O06_ABL2_A2_35911_D385


title: LR1-AB_biological_replicate_2_technical_replicate1

description: Library name: RHX1185


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 385, 33543

description: Library name: G297_O06_ABL2_A2_33543_D385


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 385, 33878

description: Library name: G305_O06_ABL2_A3_33878_D385


title: LR1-B_biological_replicate_2_technical_replicate2

description: Library name: RHX1184


title: LR1-A_biological_replicate_3_technical_replicate1

description: Library name: RHX1191


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 385, 33700

description: Library name: G303_O06_ABL2_A3_33700_D385


title: LR1-WT_biological_replicate_3_technical_replicate2

description: Library name: RHX1190


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 385, 32707

description: Library name: G302_O06_ABL2_A3_32707_D385


title: VeroE6_mock_biological_replicate_2_technical_replicate2

description: Library name: RHX1188


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 385, 32689

description: Library name: G301_O06_ABL2_A3_32689_D385


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 385, 35884

description: Library name: G296_O06_ABL2_A2_35884_D385


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 385, 35912

description: Library name: G299_O06_ABL2_A2_35912_D385


title: LR1-B_biological_replicate_2_technical_replicate1

description: Library name: RHX1183


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 385, 33877

description: Library name: G304_O06_ABL2_A3_33877_D385


title: LR1-A_biological_replicate_2_technical_replicate2

description: Library name: RHX1182


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 385, 33864

description: Library name: G292_O06_ABL2_A2_33864_D385


title: LR1-WT_biological_replicate_2_technical_replicate2

description: Library name: RHX1180


title: LR1-WT_biological_replicate_2_technical_replicate1

description: Library name: RHX1179


title: VeroE6_mock_biological_replicate_1_technical_replicate1

description: Library name: RHX1177


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 385, 32509

description: Library name: G291_O06_ABL2_A2_32509_D385


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 385, 32017

description: Library name: G289_O06_ABL2_A2_32017_D385


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 385, 35883

description: Library name: G295_O06_ABL2_A2_35883_D385


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 385, 35916

description: Library name: G288_O06_ABL2_A1_35916_D385


title: VeroE6_mock_biological_replicate_1_technical_replicate2

description: Library name: RHX1178


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 385, 35890

description: Library name: G287_O06_ABL2_A1_35890_D385


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 385, 35815

description: Library name: G286_O06_ABL2_A1_35815_D385


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 385, 35808

description: Library name: G285_O06_ABL2_A1_35808_D385


title: LR1-B_biological_replicate_1_technical_replicate1

description: Library name: RHX1173


title: LR1-A__biological_replicate_1_technical_replicate1

description: Library name: RHX1171


title: LR1-WT_biological_replicate_1_technical_replicate1

description: Library name: RHX1169


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 385, 35827

description: Library name: G294_O06_ABL2_A2_35827_D385


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 385, 35820

description: Library name: G293_O06_ABL2_A2_35820_D385


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 385, 33879

description: Library name: G283_O06_ABL2_A1_33879_D385


title: LR1-A_biological_replicate_2_technical_replicate1

description: Library name: RHX1181


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 385, 32019

description: Library name: G277_O06_ABL2_A1_32019_D385


title: NTC+virus_biological_replicate2_technical_replicate_1

description: Library name: RHX842


title: LR1-AB_biological_replicate_1_technical_replicate2

description: Library name: RHX1176


title: ASO_CN1_biological_replicate2_technical_replicate_1

description: Library name: RHX840


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 105, 35928

description: Library name: G275_O06_ABL2_B_35928_D105

value: 68-1 Δpp71 RhCMV/SIVgag/RTN/pol

value: day 105


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 105, 35927

description: Library name: G274_O06_ABL2_B_35927_D105


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 385, 32119

description: Library name: G290_O06_ABL2_A2_32119_D385

value: protected


title: LR1-AB_biological_replicate_1_technical_replicate1

description: Library name: RHX1175


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 385, 32814

description: Library name: G282_O06_ABL2_A1_32814_D385


title: LR1-B_biological_replicate_1_technical_replicate2

description: Library name: RHX1174


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 385, 33900

description: Library name: G284_O06_ABL2_A1_33900_D385

value: notprotected


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 105, 35925

description: Library name: G272_O06_ABL2_B_35925_D105


title: LR1-A_biological_replicate_1_technical_replicate2

description: Library name: RHX1172


title: LR1-WT_biological_replicate_1_technical_replicate2

description: Library name: RHX1170


title: ASO_LR1_biological_replicate2_technical_replicate_1

description: Library name: RHX838


title: NTC-virus_biological_replicate2_technical_replicate_2

description: Library name: RHX845


title: NTC+virus_biological_replicate2_technical_replicate_2

description: Library name: RHX843


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 385, 32778

description: Library name: G281_O06_ABL2_A1_32778_D385


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 385, 32485

description: Library name: G280_O06_ABL2_A1_32485_D385


title: NTC-virus_biological_replicate2_technical_replicate_1

description: Library name: RHX844


title: ASO_LR1_biological_replicate2_technical_replicate_2

description: Library name: RHX839


title: NTC-virus_biological_replicate1_technical_replicate_2

description: Library name: RHX835


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 385, 32321

description: Library name: G279_O06_ABL2_A1_32321_D385


title: ASO_CN1_biological_replicate2_technical_replicate_2

description: Library name: RHX841


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 105, 35929

description: Library name: G276_O06_ABL2_B_35929_D105


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 385, 32215

description: Library name: G278_O06_ABL2_A1_32215_D385


title: NTC-virus_biological_replicate1_technical_replicate_1

description: Library name: RHX834


title: ASO_CTRL_biological_replicate2_technical_replicate_2

description: Library name: RHX837


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 105, 35924

description: Library name: G271_O06_ABL2_B_35924_D105


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 105, 35926

description: Library name: G273_O06_ABL2_B_35926_D105


title: ASO_CTRL_biological_replicate2_technical_replicate_1

description: Library name: RHX836


title: ASO_CN1_biological_replicate1_technical_replicate_2

description: Library name: RHX831


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 105, 35923

description: Library name: G270_O06_ABL2_B_35923_D105


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 101, 35928

description: Library name: G265_O06_ABL2_B_35928_D101

value: day 101


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 101, 35926

description: Library name: G263_O06_ABL2_B_35926_D101


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 101, 35925

description: Library name: G262_O06_ABL2_B_35925_D101


title: ASO_CTRL_biological_replicate1_technical_replicate_1

description: Library name: RHX826


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 105, 35920

description: Library name: G268_O06_ABL2_B_35920_D105


title: NTC+virus_biological_replicate1_technical_replicate_1

description: Library name: RHX832


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 101, 35923

description: Library name: G260_O06_ABL2_B_35923_D101


title: SHAPE_OMICRON_NAI_replicate2

data_processing:
SHAPE-MaP samples were processed using Bowtie2 and ShapeMapper 2.1.5
Assembly: EPI_ISL_407987 (SARS-CoV-2 WT); EPI_ISL_754083 (SARS-CoV-2 Alpha); EPI_ISL_1173248 (SARS-CoV-2 Beta); EPI_ISL_2621925 (SARS-CoV-2 Delta); EPI_ISL_14917728 (SARS-CoV-2 Omicron) ;ChlSab1.1.102
Supplementary files format and content: SUPPORTING_TABLE_01_SEQUENCING_STATS.csv: Sequencing alignment statistics
Supplementary files format and content: SUPPORTING_TABLE_02_SHAPE_DATA.csv: SHAPE reactivity data WT, Alpha, Beta, Delta, and Omicron
Library strategy: SHAPE-MaP

extract_protocol:
The total RNA was then extracted from the cells using E.Z.N.A. Total RNA Kit I (Omega bio-tek) SHAPE-MaP libraries were made similar to the published protocol Smola et al. (2015)
SHAPE-MaP structure probing

treatment_protocol: SHAPE-MaP Structure probing was performed by using 1:20 the volume of 1M NAI (03-310, Merck, 25 µl of NAI in 500 µl of infected cells) and incubated the reaction for 15 min at 37 °C for structure probing; we added 1:20 volume of dimethyl sulfoxide (DMSO) as negative control; aside a third portion of the virus as for the denaturing control in the downstream library preparation process.


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 105, 35919

description: Library name: G267_O06_ABL2_B_35919_D105


title: SHAPE_OMICRON_DMSO_replicate1


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 101, 35920

description: Library name: G258_O06_ABL2_B_35920_D101


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 101, 35929

description: Library name: G266_O06_ABL2_B_35929_D101


title: ASO_CN1_biological_replicate1_technical_replicate_1

description: Library name: RHX830


title: SHAPE_OMICRON_unmodified_replicate2


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 98, 35929

description: Library name: G256_O06_ABL2_B_35929_D98

value: day 98


title: ASO_LR1_biological_replicate1_technical_replicate_2

description: Library name: RHX829


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 101, 35927

description: Library name: G264_O06_ABL2_B_35927_D101


title: SHAPE_DELTA_DMSO_replicate2


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 98, 35927

description: Library name: G254_O06_ABL2_B_35927_D98


title: ASO_LR1_biological_replicate1_technical_replicate_1

description: Library name: RHX828


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 101, 35924

description: Library name: G261_O06_ABL2_B_35924_D101


title: SHAPE_OMICRON_DMSO_replicate2


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 105, 35922

description: Library name: G269_O06_ABL2_B_35922_D105


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 98, 35926

description: Library name: G253_O06_ABL2_B_35926_D98


title: NTC+virus_biological_replicate1_technical_replicate_2

description: Library name: RHX833


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 98, 35928

description: Library name: G255_O06_ABL2_B_35928_D98


title: SHAPE_OMICRON_unmodified_replicate1


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 101, 35922

description: Library name: G259_O06_ABL2_B_35922_D101


title: SHAPE_DELTA_NAI_replicate2


title: SHAPE_OMICRON_NAI_replicate1


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 101, 35919

description: Library name: G257_O06_ABL2_B_35919_D101


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 98, 35920

description: Library name: G248_O06_ABL2_B_35920_D98


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 98, 35922

description: Library name: G249_O06_ABL2_B_35922_D98


title: SHAPE_DELTA_DMSO_replicate1


title: SHAPE_DELTA_NAI_replicate1


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 98, 35924

description: Library name: G251_O06_ABL2_B_35924_D98


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 98, 35925

description: Library name: G252_O06_ABL2_B_35925_D98


title: SHAPE_BETA_DMSO_replicate1


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 98, 35923

description: Library name: G250_O06_ABL2_B_35923_D98


title: SHAPE_DELTA_unmodified_replicate1


title: SHAPE_BETA_NAI_replicate1


title: SHAPE_BETA_NAI_replicate2


title: SHAPE_BETA_DMSO_replicate2


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 7, 35929

description: Library name: G246_O06_ABL2_B_35929_D7

value: day 7


title: ASO_CTRL_biological_replicate1_technical_replicate_2

description: Library name: RHX827


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 98, 35919

description: Library name: G247_O06_ABL2_B_35919_D98


title: SHAPE_ALPHA_DMSO_replicate1


title: SHAPE_ALPHA_NAI_replicate2


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 7, 35928

description: Library name: G245_O06_ABL2_B_35928_D7


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 7, 35924

description: Library name: G241_O06_ABL2_B_35924_D7


title: SHAPE_DELTA_unmodified_replicate2


title: SHAPE_BETA_unmodified_replicate2


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 7, 35927

description: Library name: G244_O06_ABL2_B_35927_D7


title: SHAPE_BETA_unmodified_replicate1


title: SHAPE_ALPHA_DMSO_replicate2


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 7, 35926

description: Library name: G243_O06_ABL2_B_35926_D7


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 7, 35925

description: Library name: G242_O06_ABL2_B_35925_D7


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 7, 35923

description: Library name: G240_O06_ABL2_B_35923_D7


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 7, 35922

description: Library name: G239_O06_ABL2_B_35922_D7


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 7, 35920

description: Library name: G238_O06_ABL2_B_35920_D7


title: SHAPE_ALPHA_NAI_replicate1


title: SHAPE_WT_DMSO_replicate2


title: SHAPE_ALPHA_unmodified_replicate1


title: SHAPE_WT_DMSO_replicate1


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 7, 35919

description: Library name: G237_O06_ABL2_B_35919_D7


title: SHAPE_WT_NAI_replicate2


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 3, 35927

description: Library name: G234_O06_ABL2_B_35927_D3

value: day 3


title: SHAPE_WT_unmodified_replicate1


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 3, 35928

description: Library name: G235_O06_ABL2_B_35928_D3


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 3, 35925

description: Library name: G232_O06_ABL2_B_35925_D3


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 3, 35929

description: Library name: G236_O06_ABL2_B_35929_D3


title: SHAPE_WT_NAI_replicate1


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 3, 35923

description: Library name: G230_O06_ABL2_B_35923_D3


title: SHAPE_WT_unmodified_replicate2


title: SHAPE_ALPHA_unmodified_replicate2


title: Tcells_CD3E-EpiE_3

city: Dresden

first: Frank

last: Buchholz

address: Tatzberg 47/49

department: UCC / Medical Faculty and University Hospital Carl Gustav Carus

institute: Technische Universität Dresden

description:
Library name: EpiE3
Column name: EpiE3

data_processing:
Aligned to the human genome GRCh38/hg38 using STAR v2.7.3a for paired-end reads.
Aligned reads fed through featureCounts v2.0.6 of the subread package to generate the count matrix.
Assembly: GRCh38
Supplementary files format and content: Count matrix with sample IDs for columns and gene names for rows.

source_name: blood

growth_protocol: T cells were activated with TransAct CD3/CD28 4 days before electroporation. After electroporation, T cells were recovered in TexMACS Medium supplemented with IL-2,7,15 for 3 days. Subsequently, T cells were rested in RPMI without cytokines for 24h before RNA isolation.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads following Novogene NGS RNA Library Prep Set protocol. Briefly, after fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP for non-directional library. The non-directional library was complete following end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount. The clustering of the index-coded samples was performed according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.

treatment_protocol: T cells were electroporated with mRNA of mCherry (mock) Cas9 (TCR-KO) or epigenetic editor (CD3E-EpiE) and synthetic sgRNA (TCR-KO and CD3E-EpiE) and RNA was isolated 4 days after.

value: blood

value: primary cells

value: T cells

value: TCR+

value: untreated


title: animal 06 SLC KO tissue type cerebellum

city: Miami

first: Tomas

middle: R

last: Guilarte

state: FL

address: 11200 SW 8th Street

department: Environmental Health Sciences

institute: Florida International University

description:
Library name: A6KOCb
A6KOCb_count

data_processing:
Alignments were done with HISAT2 and DESeq2 was used for differential analysis and differential gene screening.
Assembly: ensembl_mus_musculus_grcm38_p6_gca_000001635_8
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Brain tissue

extract_protocol:
RNA was extracted using a standard TRIZOL protocol
Total RNA isolations were QC'd for purity and sent to Novogene for library prep and QC. An in-house protocol was used.

value: Brain tissue

value: Slc39a14 knock-out


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 3, 35924

description: Library name: G231_O06_ABL2_B_35924_D3

value: Whole blood

value: male


title: K562 cells, ChIP INPUT, replicate 1

city: Boston

first: Stephen

last: Gisselbrecht

state: MA

address: 77 Avenue Louis Pasteur, Rm 468

department: Division of Genetics, Department of Medicine

institute: Brigham and Women's Hospital

description: Library name: K562-Input-R1

library_source: genomic

data_processing:
bcl2fastq is used for base calling.
Trim galore (v. 0.6.6) was used to remove adaptor sequences and bases with sequencing quality below 30.
Reads were then mapped to hg19 using bowtie2 (v. 2.5.1) with the settings “--sensitive-local --no-discordant --no-mixed”. PCR duplicates were called using Picard MarkDuplicates. Libraries were filtered for alignments above mapq 30.
Peak calling was performed using MACS2 (v. 2.1.1.20160309) with the corresponding input reads as control and the settings “--broad -g dm -f BAMPE”.
Bigwigs were generated from deduplicated BAM files using Deeptools bamCoverage with CPM normalization. Bigwigs for replicate samples were combined using Deeptools bigwigAverage.
Following ENCODE guidelines, we used the irreproducible discovery rate (IDR) framework to identify peaks that are consistent between the two replicate samples that used the same antibody. For calling peaks found to be reproducible by IDR analysis, a more relaxed threshold of “-p 1e3” was used to call peaks in each library before running IDR (v. 2.0.2).
Assembly: hg19
Supplementary files format and content: bigWig for K562 samples
Supplementary files format and content: bedfiles of consistent peaks between replicates called by IDR (except for input samples)

molecule: genomic DNA

extract_protocol:
Cells were fixed for 10 minutes in 1% formaldehyde, quenched, and frozen. Chromatin was sonicated with a Bioruptor Plus (Diagenode) at high power for 30 seconds on and 30 seconds off. Sixty cycles was chosen to fragment DNA with a peak of fragments ~200 - 600 bp.
100 µg chromatin as measured from the decrosslinked sample was aliquoted to each ChIP reaction. Eluted DNA was decrosslinked and purified using Monarch PCR and DNA Cleanup Kit (New England Biolab T1030S). DNA was quantified using Qubit HS dsDNA and High Sensitivity D5000 DNA ScreenTape assays (Agilent). Sequencing libraries were generated using NEBNext Ultra II (E7645S) with NEBNext multiplex oligos for Illumina (E7335S). The number of PCR cycles was selected according to manufacturer’s recommendations for the mass of DNA in each library. Input libraries were amplified with 3 cycles of PCR, while H4K20me1 libraries using the Active Motif or Thermo antibodies required 6 cycles of PCR. QC of sequencing libraries was performed using Qubit High Sensitivity dsDNA assays for DNA concentration and High Sensitivity D1000 and D5000 DNA ScreenTape assays (Agilent)  for fragment length distributions. Libraries generated using the Active Motif or Thermo H4K20me1 antibodies were size-selected them with SPRISelect beads (Beckman Coulter B23317) prior to sequencing, using a right-side size selection with 0.4x bead ratio to remove large fragments.

tag: chip antibody

tag: batch


title: animal 05 SLC WT tissue type cerebellum

description:
Library name: A5WTCb
A5WTCb_count

value: Slc39a14 wildtype


title: K562 cells, H4K20me1 ChIP with Active Motif AB_2615074 antibody, replicate 2

description: Library name: K562-H4K20me1-AM-R1_R2

value: Active Motif AB_2615074


title: K562 cells, H4K20me1 ChIP with Thermo Fisher MA5-18067 antibody, replicate 2

description: Library name: K562-H4K20me1-Thermo_R2

value: Thermo Fisher MA5-18067


title: K562 cells, H4K20me1 ChIP with Thermo Fisher MA5-18067 antibody, replicate 1

description: Library name: K562-H4K20me1-Thermo_R1


title: K562 cells, H4K20me1 ChIP with Active Motif AB_2615074 antibody, replicate 1

description: Library name: K562-H4K20me1-AM-R1_R1


title: K562 cells, ChIP INPUT, replicate 2

description: Library name: K562-Input-R2


title: Tcells_CD3E-EpiE_1

description:
Library name: EpiE1
Column name: EpiE1


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 385, 35822

description: Library name: G306_O06_ABL2_A3_35822_D385

value: day 385

value: notprotected


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 3, 35926

description: Library name: G233_O06_ABL2_B_35926_D3

value: 68-1 Δpp71 RhCMV/SIVgag/RTN/pol


title: animal 04 SLC KO tissue type cerebellum

description:
Library name: A4KOCb
A4KOCb_count


title: Tcells_TCR-KO_2

description:
Library name: KO2
Column name: KO2


title: Tcells_TCR-KO_3

description:
Library name: KO3
Column name: KO3


title: Tcells_CD3E-EpiE_2

description:
Library name: EpiE2
Column name: EpiE2


title: animal 03 SLC WT tissue type cerebellum

description:
Library name: A3WTCb
A3WTCb_count


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 3, 35920

description: Library name: G228_O06_ABL2_B_35920_D3

value: protected


title: Tcells_mCherry_electroporated_3

description:
Library name: mCh3
Column name: mCh3


title: Tcells_mCherry_electroporated_2

description:
Library name: mCh2
Column name: mCh2


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 3, 35919

description: Library name: G227_O06_ABL2_B_35919_D3

value: day 3


title: animal 02 SLC KO tissue type cerebellum

description:
Library name: A2KOCb
A2KOCb_count


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 0, 35929

description: Library name: G226_O06_ABL2_B_35929_D0

value: day 0


title: Tcells_untreated_3

description:
Library name: WT3
Column name: WT3

value: blood

value: primary cells


title: Tcells_untreated_2

description:
Library name: WT2
Column name: WT2

value: T cells

value: TCR+


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 0, 35928

description: Library name: G225_O06_ABL2_B_35928_D0


title: Tcells_untreated_1

description:
Library name: WT1
Column name: WT1

value: untreated


title: animal 01 SLC WT tissue type cerebellum

description:
Library name: A1WTCb
A1WTCb_count

value: Brain tissue


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 3, 35922

description: Library name: G229_O06_ABL2_B_35922_D3

value: Whole blood


title: siHells_Day2_rep1

city: seoul

first: Jueng Soo

last: You

address: 120 Neungdong-ro

country: South Korea

institute: Konkuk University

description: Library name: siHells_Day2_rep1

data_processing:
Raw reads were quality-checked using FastQC and trimmed with Trimmomatic (v0.38) to remove adapters and low-quality bases.
Cleaned reads were aligned to the mouse genome (mm10, NCBI_108) using HISAT2 (v2.1.0).
Transcript assembly and quantification were performed with StringTie (v2.1.3b) to obtain read counts, FPKM, and TPM values for known genes.
Differential gene expression was analyzed using edgeR with TMM normalization.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts

source_name: Bone marrow-derevied macrophage

extract_protocol:
RNA for RNA-seq was extracted as described by the manufacturer using miRNeasy Mini Kit (217004, Qiagen), and DNase (79254, Qiagen) was treated. RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
RNA libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer's instructions.

value: Bone marrow-derevied macrophage

value: Primary cell

value: siHells

value: Bone marrow-derived macrophages treated with RANKL for 2 days, with or without siHELLS knockdown.


title: mTORi X

city: Evanston

first: Stephenie

last: Droll

state: IL

address: Hogan 2-100 2205 Tech Drive

department: Molecular Biosciences

institute: Northwestern University

data_processing:
Read quality control by FastQC
Adaptor trimming by Trimgalore
Aligned to hg38 with BWA-MEM, default parameters
Peak calling by MACS2, narrowPeak, q 0.001
Assembly: hg38
Supplementary files format and content: MACS2 called peaks in .csv format

source_name: foreskin epidermis

growth_protocol: differentiated to day 4

extract_protocol:
Keratinocytes were fixed with 1% formaldehyde for 10 minutes and quenched with 0.125 M glycine. Nuclei were extracted, lysed in RIPA buffer, and sonicated with a Bioruptor Pico. After H2A.Z IP, DNA was purified with the ChIP DNA Clean & Concentrator Kit from Zymo Research.
NEBNext Ultra II DNA Library Prep Kit

treatment_protocol: Keratinocytes were centrifuged for one hour at 1250 RMP at 32 degrees Celsius with control- or shRNA- lentivirus. Cells were selected for 24 hours with puromycin; DNA was harvested ~72 hours after transduction. To induce differentiation, keratinocytes were seeded at 100% confluency with 1.2 mM CaCl2 for four days. Small molecule inhibitors were added to cell culture media for 48 hours.

value: foreskin epidermis

value: primary keratinocyte


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 0, 35927

description: Library name: G224_O06_ABL2_B_35927_D0

value: 68-1 Δpp71 RhCMV/SIVgag/RTN/pol

value: male

value: notprotected


title: Tcells_TCR-KO_1

description:
Library name: KO1
Column name: KO1


title: AKTi Y

value: 15 uM ARQ 092


title: siControl_Day2_rep2

description: Library name: siControl_Day2_rep2

value: siControl


title: siControl_Day2_rep1

description: Library name: siControl_Day2_rep1


title: DMSO Y


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 0, 35925

description: Library name: G222_O06_ABL2_B_35925_D0

value: day 0


title: Tcells_mCherry_electroporated_1

description:
Library name: mCh1
Column name: mCh1

value: blood

value: primary cells

value: T cells


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 0, 35924

description: Library name: G221_O06_ABL2_B_35924_D0

value: protected


title: PI3Ki X


title: PI3Ki Y

value: 2 uM ZSTK474


title: DMSO X


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 0, 35926

description: Library name: G223_O06_ABL2_B_35926_D0

value: Whole blood


title: five_prime_dex+iberdomide

city: Broomfield

first: Caleb

middle: Karl

last: Stein

state: CO

address: 12735 Yates Street

institute: Mayo Clinic

description:
Library name: 45367
10x Genomics

data_processing:
Gene counts were determined with CellRanger version 7.1 or newer (10x Genomics).
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: bone marrow

extract_protocol:
23 hours post treatment, mice were euthanized and BM cells collected. After ACK lysis, 8,000 mononuclear cells/sample were processed using the 10XGenomicsChromium single cell 3’V2 kit. For a subsequent repeat, we performed ACK lysis of samples from one mouse per treatment to obtain 5,000 mononuclear cells
Library preparation was performed to the manufacturer's protocol (single cell 3'v2 and 5' protocol, 10x Genomics). Illumina libraries were sequenced on a partial Novaseq S4 lane to obatin 50,000 reads per cell.

treatment_protocol: Age matched de novo Vk*MYChCRBN mice with MM received vehicle, dexamethasone at 10 mg/kg, IBER at 10 mg/kg or combination.

value: bone marrow

value: dex + iberdomide


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 0, 35923

description: Library name: G220_O06_ABL2_B_35923_D0


title: hiPSC-CM, MYH7 G256E HOM & HET & WT; MYH7 H251N HET & WT, Day 30, FB-Expression, replicate 3

city: STANFORD

first: Paul

last: Heinrich

address: 265 CAMPUS DRIVE

department: Cardiovascular Insititute

institute: Stanford University

description:
GE FASTQ-files contain Gene Expression Library data, FB FASTQ-files contain Feature Barcode Library (R2;5P(BC)); Demultiplexing Instructions (Clone/Corresponding_oligo); (113/ATGAGGAATTCCTGC), (174/CATGCCAATAGAGCG), (102/CCGTCGTCCAAGCAT), (141/AACGTTAATCACTCA), (157/AAGCTCGTTGGAAGA), (15/CGGATTCCACATCAT), (17/GTTGATCTATAACAG), (4/GCAGGAGGTATCAAT), (3/GAATCGTGATTCTTC), (85/ACATGGTCAACGCTG)
D30CM_MYH7_G256E_H251N_G256EIso.rds

data_processing:
scRNA seq data underwent sample demultiplexing, alignment, filtering, barcode processing, and gene counting using cellranger (10X). Seurat-Object was genererated and single cells were filtered for QC markers such as gene- and feature count as well as mitochnodrial gene ratio. Details can be found in the methods of the manuscript
Assembly: GRCh38-3.0.0
Supplementary files format and content: RDS (Seurat object)

source_name: G256E Clone 113, G256E Clone 174, G256E Clone 102, G256E Clone 157, G256E Clone 141, G256E Clone 15, G256E Clone 17, H251N Clone 3, H251N Clone 4, H251N Clone 85

growth_protocol: hiPSCs were maintained and directed for cardiac differentiation using Wnt-modulating small-molecule-based protocol. Full protocol can be found in the Method section of the manuscript.

extract_protocol:
Detailed protocol can be found in the Method section of the manuscript. Briefly, differentiated cardiomyocytes on differentiation day 30 were harvested and labeled with sample-specific hashtag oligonucleotides according to the manufacturer's protocol (10X Single Cell 3' v3.1 chemistry with CellPlex feature barcoding technology, CG000388 Rev A).
The labeled hiPSC-CMs underwent emulsion-based single cell encapsulation process using 10X Chromium machine, followed by single cell mRNA library construction. The library was constructed using the manufacturer's protocol (10X Single Cell 3' v3.1 chemistry with feature barcoding technology,  CG000388 Rev A). Briefly, the labeled hiPSC-CMs 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 reversetranscribed to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriate sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. Sample 1 has single index, samples 2-7 have dual index.

treatment_protocol: Samples 2 and 3 were treated with 1uM Isoproterenol for 5 days

value: iPSC-Cardiomyocytes


title: hiPSC-CM, MYH7 G256E HOM & HET & WT; MYH7 H251N HET & WT, Day 30, Gene-Expression, replicate 3

value: G256E Clone 113, G256E Clone 174, G256E Clone 102, G256E Clone 157, G256E Clone 141, G256E Clone 15, G256E Clone 17, H251N Clone 3, H251N Clone 4, H251N Clone 85


title: mTORi Y

value: foreskin epidermis

value: primary keratinocyte

value: 10 uM Rapamycin


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 0, 35922

description: Library name: G219_O06_ABL2_B_35922_D0

data_processing:
Trimgalorev0.6.4 used to remove low quality reads and bases
Filtered out globin and rRNA reads using bowtie2v2.1.0
Aligned reads with STARv2.7.3
quantified read counts with  htseqv0.11.2
Assembly: Rhesus macaques version 10 Ensembl annoation v98
Supplementary files format and content: ount matrix

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

value: 68-1 Δpp71 RhCMV/SIVgag/RTN/pol

value: male


title: hiPSC-CM, MYH7 G256E HOM & HET & WT, Day 30, Gene-Expression, replicate 2

description:
GE FASTQ-files contain Gene Expression Library data, FB FASTQ-files contain Feature Barcode Library (R2;5P(BC)); Demultiplexing Instructions (Clone/Corresponding_oligo); (113/AAGATGAGGTCTGTG), (174/GTTGATCTATAACAG), (102/CGCGATATGGTCGGA), (141/AAGCTCGTTGGAAGA), (157/CGGATTCCACATCAT), (15/GCAGGAGGTATCAAT), (17.1/GAATCGTGATTCTTC), (17.2/ACATGGTCAACGCTG)
D30CM_MYH7_G256E_H251N_G256EIso.rds

source_name: G256E Clone 113, G256E Clone 174, G256E Clone 102, G256E Clone 157, G256E Clone 141, G256E Clone 15, G256E Clone 17


title: siHells_Day2_rep2

description: Library name: siHells_Day2_rep2

value: Bone marrow-derevied macrophage

value: Primary cell

value: siHells

value: Bone marrow-derived macrophages treated with RANKL for 2 days, with or without siHELLS knockdown.


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 0, 35920

description: Library name: G218_O06_ABL2_B_35920_D0

value: day 0


title: five_prime_untreated

description:
Library name: 45364
10x Genomics


title: iPSC (Control)

first: Huzefa

last: Husain

state: MN

address: 312 Church St., Nils Hasselmo Hall 7-256

department: Biomedical Engineering

description: 10x Genomics

data_processing:
Data was then analyzed using the Cellranger package from 10X Genomics.
Libraries were individually quality controlled. The matrix of filtered counts per cell barcode was analyzed using Seurat (v 4.3.0.1). Empty droplets were filtered out with a minimum total RNA and Feature counts per barcode based on their count distribution on a per sample basis. The presence of multiplets was assessed using the scDblFinder (v 1.8.0) package, followed by manual filtering of multiplets of the same cell type using an upper RNA count limit.
Assembly: GRCh38.p14
Supplementary files format and content: CellRanger filtered TSV files for import into Seurat. Cell barcode counts, feature names, and counts matrices.

extract_protocol:
Cells from three organoid batches cultured for 14 weeks were thawed at 37°C and resuspended in HBSS to maintain singularization. The resulting cell suspension for each batch was passed through a dead cell removal kit (Miltenyi Biotec #130-090-10).
Details on the specific kit components and protocols could be found on the 10x Genomics website. Following incubation within the GEMs, polyadenylated messenger RNA (mRNA) was reverse transcribed into full-length, barcoded cDNA. This cDNA was then amplified via PCR to achieve sufficient mass for library construction. The quality and quantity of the generated cDNA from each cell suspension were assessed using a fluorometric PicoGreen assay and capillary electrophoresis on an Agilent BioAnalyzer 2100. The cDNA generated from the cell suspensions was then converted into dual index libraries compatible with Illumina sequencers. This conversion utilized 10X Genomics 3' Gene Expression Library Construction kits (PN-1000190). The process involves a series of enzymatic steps: fragmentation of the cDNA, repair of the ends, addition of a poly-A tail, ligation of sequencing adapters, and finally, PCR amplification to generate sufficient library material. The final size distribution of the libraries was validated using capillary electrophoresis, and both the quantity (via fluorimetry with PicoGreen) and quality (via Q-PCR) were assessed.

value: Human Induced Pluripotent Stem Cell


title: B27 (MTO 3)

description: 10x Genomics


title: Whole blood, 68-1 Δpp71 RhCMV/SIVgag/RTN/pol, day 0, 35919

first: Michael

last: Gale

description: Library name: G217_O06_ABL2_B_35919_D0

value: notprotected


title: B25 (MTO 1)

description: 10x Genomics


title: three_prime_iberdomide

description:
Library name: 31881
10x Genomics

value: iberdomide


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 105, 35914

description: Library name: G216_O06_ABL2_A3_35914_D105

value: Whole blood

value: day 105


title: three_prime_dex+iberdomide

description:
Library name: 31882
10x Genomics

value: bone marrow

value: dex + iberdomide


title: B26 (MTO 2)

description: 10x Genomics


title: three_prime_dex

description:
Library name: 31880
10x Genomics

value: dex


title: three_prime_untreated

description:
Library name: 31879
10x Genomics


title: hiPSC-CM, MYH7 G256E HOM & HET & WT, Day 30, FB-Expression, replicate 2

value: G256E Clone 113, G256E Clone 174, G256E Clone 102, G256E Clone 157, G256E Clone 141, G256E Clone 15, G256E Clone 17

value: iPSC-Cardiomyocytes


title: Cyp2b-null male gastrocnemius, 10 mg/kg/day PFOS treatment for 21 days via oral gavage rep 3

city: Clemson

first: William

last: Baldwin

state: SC

address: 132 Long Hall

institute: Clemson University

description: Library name: mnul_203_10

data_processing:
PE150 strategy by Novogene. HISAT2 was used to map clean reads.
Assembly: GRCm39
Supplementary files format and content: Excel file containing raw counts performed by Novogene named "gene_count_all.xls"

source_name: gastrocnemius muscle

extract_protocol:
RNA extractions were performed on approximately 15 mg of liver tissue previously stored at -80C. RNA was extracted with TRIzol (Life Technology, Carlsbad, CA USA) and chloroform. Quality was checked via Nanodrop
Library construction was performed by Novogene (Sacramento, CA USA) using messenger RNA purified from total RNA. Quality was checked with Qubit (Thermo Fisher Scientific, Walkham, MA USA).

value: gastrocnemius muscle


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 105, 35889

city: Minneapolis

address: 689 23rd Ave SE

institute: University of Minnesota

description: Library name: G213_O06_ABL2_A3_35889_D105

value: male


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 105, 35913

description: Library name: G215_O06_ABL2_A3_35913_D105


title: five_prime_dex

description:
Library name: 45365
10x Genomics


title: Carbo-Taxol OKN Tumor 24

city: Oklahoma city

first: Bethany

last: Hannafon

state: OK

address: 975 NE 10th Street

department: Obstetrics and Gynecology

institute: University of Oklahoma Health Sciences Center

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Raw data were normalized and log2 transformed using the geNorm algorithm, differential expression (DE) was determined using the Generalized Linear Model (GLM), and Gene Set Analysis (GSA) was used to summarize the directed global significance score by calculating the change in regulation within each defined gene set relative to the baseline.  Pathway enrichment was also calculated for gene sets as defined in multiple databases, including WikiPathways, REACTOME, MSigDB, and Gene Ontology, and FDR adjustment and p-Elim pruning scores were calculated when appropriate. DE, GSA, and other pathway enrichment were conducted using ROSALIND software (v. 3.38.5.1).

label: not provided

source_name: Carbo-Taxol-OKN

label_protocol: not provided

growth_protocol: Tumors were established by intraperitoneal injection of CS99 cells (1x10^6 /100 μL).

extract_protocol: RNA was extracted using the mirVana PARIS kit (Invitrogen).

treatment_protocol: Mice were randomized into four groups: 1. Untreated Control (UT) (regular drinking water), 2. OKN-007 (150 mg/kg daily in drinking water), and 3.Carboplatin/paclitaxel C-T (50 mg/kg and 15 mg/kg, respectively, once weekly, intraperitoneally), 4. OKN-007/Carboplatin/paclitaxel (150 mg/kg, 50 mg/kg, and 15 mg/kg, intraperitoneal  C-T administered once weekly; OKN-007 was administered daily in drinking water).

value: uterine carcinosarcoma cell line

tag: host strain

value: 4-6-week-old female athymic Nude-Foxn1 nu mice (Envigo)

value: Carbo-Taxol-OKN


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 105, 35910

description: Library name: G214_O06_ABL2_A3_35910_D105

value: protected


title: Carbo-Taxol Tumor 33

source_name: Carbo-Taxol

value: Carbo-Taxol


title: Carbo-Taxol Tumor 24


title: Carbo-Taxol-OKN Tumor 25


title: Carbo-Taxol OKN Tumor 22


title: OKN Tumor 17


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 105, 35886

description: Library name: G212_O06_ABL2_A3_35886_D105


title: Cyp2b-null male gastrocnemius, 10 mg/kg/day PFOS treatment for 21 days via oral gavage rep 1

description: Library name: mnul_199_10


title: OKN Tumor 3


title: Cyp2b-null male gastrocnemius, 10 mg/kg/day PFOS treatment for 21 days via oral gavage rep 2

description: Library name: mnul_201_10


title: OKN Tumor 1


title: Carbo-Taxol Tumor 32


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 105, 35885

description: Library name: G211_O06_ABL2_A3_35885_D105


title: Control Tumor 14

source_name: Control

value: Control


title: Control Tumor 5


title: Cyp2b-null male gastrocnemius, 1 mg/kg/day PFOS treatment for 21 days via oral gavage rep 4

description: Library name: mnul_198_1


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 105, 35822

description: Library name: G210_O06_ABL2_A3_35822_D105

source_name: Whole blood

value: notprotected


title: BANAL-20-236_R.Si_Ada_10_WELL-3

city: Minato-ku

first: Kei

last: Sato

state: Tokyo

address: 4-6-1 Shiroganedai

department: Department of Microbiology and Immunology

country: Japan

institute: The Institute of Medical Science, The University of Tokyo

description: Library name: Sample 9

data_processing:
Sequencing reads were trimmed using fastp (ver. 0.23.4).
Sequencing reads were mapped to the viral genome sequence of BANAL-20-236 (GISAID ID: EPI_ISL_4302647 and GenBank accession: MZ937004) using BWA-MEM (v0.7.17-r1188).
Variant calling and filtering were performed using SAMtools v1.20
Variant annotation was performed using snpEff (v5.0e.48).
Assembly: BANAL-20-236 (GISAID ID: EPI_ISL_4302647 and GenBank accession: MZ937004)
Assembly: BANAL-20-236 (MZ937003.2)
Supplementary files format and content: Variant information (txt)

organism: Bat coronavirus

source_name: fibroblast and epithelial-like

extract_protocol:
Total RNA was extracted using QIAamp viral RNA mini kit (Qiagen, Cat# 52906)
RNA libraries for RNA-seq were prepared using NEB Next Ultra RNA Library Prep Kit for Illumina (New England Biolabs, Cat# E7530) following manufacturer's protocols.

tag: host

value: human

value: fibroblast and epithelial-like

value: HOS

tag: expressing

value: R. sinicus ACE2

tag: infection

value: BANAL-20-236 infection of HOS cells


title: Cyp2b-null male gastrocnemius, 1 mg/kg/day PFOS treatment for 21 days via oral gavage rep 3

description: Library name: mnul_195_1


title: BANAL-20-236_R.Si_Ada_10_WELL-2

description: Library name: Sample 8


title: Control Tumor 15


title: BANAL-20-236_R.Si_Ada_10_WELL-1

description: Library name: Sample 7


title: Cyp2b-null male gastrocnemius, 1 mg/kg/day PFOS treatment for 21 days via oral gavage rep 2

description: Library name: mnul_184_1


title: BANAL-20-236_R.Sh_Ada_10_WELL-3

description: Library name: Sample 6

value: R. shameli ACE2


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 105, 33877

description: Library name: G208_O06_ABL2_A3_33877_D105

value: Whole blood

tag: time

value: day 105

tag: animal id


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 105, 33878

description: Library name: G209_O06_ABL2_A3_33878_D105

tag: Sex

tag: dose


title: Cyp2b-null male gastrocnemius, 0 mg/kg/day PFOS treatment for 21 days via oral gavage rep 4

description: Library name: mnul_179_0

tag: tissue

value: gastrocnemius muscle


title: BANAL-20-236_R.Sh_Ada_10_WELL-1

description: Library name: Sample 4


title: Cyp2b-null male gastrocnemius, 1 mg/kg/day PFOS treatment for 21 days via oral gavage rep 1

description: Library name: mnul_181_1


title: SARS-CoV-2_Omicron(XBB)_biological_replicate2_technical_replicate_3

description: Library name: RHX1612

data_processing:
SPLASH samples were processed according with Aw et. al 2016.
Assembly: EPI_ISL_407987 (SARS-CoV-2 WT); EPI_ISL_754083 (SARS-CoV-2 Alpha); EPI_ISL_1173248 (SARS-CoV-2 Beta); EPI_ISL_2621925 (SARS-CoV-2 Delta); EPI_ISL_14917728 (SARS-CoV-2 Omicron) ;ChlSab1.1.102
Supplementary files format and content: SUPPORTING_TABLE_01_SEQUENCING_STATS.csv: Sequencing alignment statistics
Library strategy: SPLASH, proximity ligation sequencing

organism: Chlorocebus sabaeus

extract_protocol: The total RNA was then extracted from the cells using E.Z.N.A. Total RNA Kit I (Omega bio-tek) SPLASH libraries were made similar to the published protocol (Aw et al. 2016)

treatment_protocol: Vero E6/TMPRSS2 cells were seeded in 15cm cell-culture dish (Corning, NY, USA) at a seeding density of 2.5 x 105 cells/mL and incubated overnight. Cells were then infected with SARS-CoV-2 WT or Omicron XBB at a MOI of 0.01. At 48 hpi, cells were washed once with PBS and incubated with biotinylated psoralen (BioPso; final concentration of 200µM) and 0.01% digitonin in PBS at 37°C for 5 min. The BioPso-treated cells were then irradiated at 365nm on ice for 20 min using a CL-1000 ultraviolet crosslinker (UVP Inc.). Total cellular RNA was extracted using TRIzol LS reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s recommendations, followed by heat-inactivation at 65°C for 10 min before transferring it to BSL-2 laboratory for preparation of SPLASH libraries following the published protocol (Aw et. al 2016).

value: E6 TMPRSS2 Vero cell

value: E6 TMPRSS2

value: Vero cell


title: BANAL-20-236_R.Sh_Ada_10_WELL-2

description: Library name: Sample 5


title: BANAL-20-236_R.Fe_Ada_10_WELL-1

description: Library name: Sample 1

value: R. ferrumequinum ACE2


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 105, 33700

description: Library name: G207_O06_ABL2_A3_33700_D105

tag: treatment

value: male

tag: treatment outcome

value: protected


title: Cyp2b-null male gastrocnemius, 0 mg/kg/day PFOS treatment for 21 days via oral gavage rep 3

description: Library name: mnul_167_0


title: BANAL-20-236_R.Fe_Ada_10_WELL-2

description: Library name: Sample 2

tag: cell line

tag: cell type


title: BANAL-20-236_R.Fe_Ada_10_WELL-3

description: Library name: Sample 3


title: Cyp2b-null male gastrocnemius, 0 mg/kg/day PFOS treatment for 21 days via oral gavage rep 2

description: Library name: mnul_129_0

tag: genotype


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 105, 32689

description: Library name: G205_O06_ABL2_A3_32689_D105


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 105, 32707

description: Library name: G206_O06_ABL2_A3_32707_D105


title: SARS-CoV-2_Wild_type(WT_Wuhan-Hu-1)_biological_replicate2_technical_replicate_4

description: Library name: RHX1610


title: SARS-CoV-2_Omicron(XBB)_biological_replicate2_technical_replicate_2

description: Library name: RHX1611


title: SARS-CoV-2_Wild_type(WT_Wuhan-Hu-1)_biological_replicate2_technical_replicate_3

description: Library name: RHX1609


title: SARS-CoV-2_Omicron(XBB)_biological_replicate2_technical_replicate_1

description: Library name: RHX1606


title: Cyp2b-null male gastrocnemius, 0 mg/kg/day PFOS treatment for 21 days via oral gavage rep 1

description: Library name: mnul_102_0


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 105, 35912

description: Library name: G203_O06_ABL2_A2_35912_D105


title: SARS-CoV-2_Wild_type(WT_Wuhan-Hu-1)_biological_replicate2_technical_replicate_2

description: Library name: RHX1605


title: SARS-CoV-2_Wild_type(WT_Wuhan-Hu-1)_biological_replicate2_technical_replicate_1

description: Library name: RHX1604


title: hCYP2B6-Tg male gastrocnemius, 10 mg/kg/day PFOS treatment for 21 days via oral gavage rep 4

description: Library name: m2B6_163_10


title: SARS-CoV-2_Omicron(XBB)_biological_replicate1_technical_replicate_2

description: Library name: RHX1573


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 105, 35915

description: Library name: G204_O06_ABL2_A2_35915_D105


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 105, 35911

description: Library name: G202_O06_ABL2_A2_35911_D105


title: SARS-CoV-2_Wild_type(WT_Wuhan-Hu-1)_biological_replicate1_technical_replicate_2

description: Library name: RHX1571


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 105, 33543

description: Library name: G201_O06_ABL2_A2_33543_D105


title: hCYP2B6-Tg male gastrocnemius, 10 mg/kg/day PFOS treatment for 21 days via oral gavage rep 2

description: Library name: m2B6_160_10


title: hCYP2B6-Tg male gastrocnemius, 10 mg/kg/day PFOS treatment for 21 days via oral gavage rep 3

description: Library name: m2B6_161_10


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 105, 35884

description: Library name: G200_O06_ABL2_A2_35884_D105


title: hCYP2B6-Tg male gastrocnemius, 10 mg/kg/day PFOS treatment for 21 days via oral gavage rep 1

description: Library name: m2B6_159_10


title: SM-91, PSC, rep1 [SM_91_PSC_1_S1]

first: Eric

last: Liao

address: CRMT, Simches Research Center, CPZN 4400, 185 Cambridge Street

institute: MGH

data_processing:
2x75bp (paired-end; PE) strandspecific Illumina Reads were trimmed to remove Illumina adapter sequences and low-quality sequence with Trimmomatic (v. 0.36) (Bolger et al., 2014). Reads were aligned to GRCh38 genome using STAR (v 2.7.1a) (Dobin et al., 2013) with custom built index based on Ensembl v91 gene annotations
Assembly: GRCh38
Supplementary files format and content: featurecounts

extract_protocol:
RNA was extracted using RNeasy Plus Mini Kit (Qiagen) and genomic DNA contamination was removed using the DNase Max Kit (Qiagen).
libraries were prepared using the NEBNext® Ultra™ II Directional RNA Library Prep with NEBNext® Poly(A) mRNA Magnetic Isolation Module

value: pluripotent stem cell

value: wild-type


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 105, 35883

description: Library name: G199_O06_ABL2_A2_35883_D105

value: notprotected


title: SM-91, PSC, rep2 [SM_91_PSC_2_S9]


title: SM-91, NCC, rep1 [SM_91_D11_1_S7]

value: neural crest cell

value: neural crest differentiation


title: SM-48, NCC, rep1 [SM_48_D11_1_S17]


title: hCYP2B6-Tg male gastrocnemius, 1 mg/kg/day PFOS treatment for 21 days via oral gavage rep 4

description: Library name: m2B6_143_1


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 105, 35827

description: Library name: G198_O06_ABL2_A2_35827_D105


title: hCYP2B6-Tg male gastrocnemius, 1 mg/kg/day PFOS treatment for 21 days via oral gavage rep 2

description: Library name: m2B6_136_1


title: SM-48, PSC, rep2 [SM_48_PSC_2_S10]


title: KO-33, PSC, rep1 [KO_33_PSC_1_S4]

value: kncok-out


title: SARS-CoV-2_Omicron(XBB)_biological_replicate1_technical_replicate_1

description: Library name: RHX1572


title: hCYP2B6-Tg male gastrocnemius, 1 mg/kg/day PFOS treatment for 21 days via oral gavage rep 3

description: Library name: m2B6_141_1


title: SARS-CoV-2_Wild_type(WT_Wuhan-Hu-1)_biological_replicate1_technical_replicate_1

description: Library name: RHX1570


title: SM-48, NCC, rep2 [SM_48_D11_2_S18]


title: SM-91, NCC, rep2 [SM_91_D11_2_S21]


title: KO-33, NCC, rep1 [KO_33_D11_1_S15]


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 105, 35820

description: Library name: G197_O06_ABL2_A2_35820_D105


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 105, 32119

description: Library name: G194_O06_ABL2_A2_32119_D105


title: hCYP2B6-Tg male gastrocnemius, 1 mg/kg/day PFOS treatment for 21 days via oral gavage rep 1

description: Library name: m2B6_127_1


title: KO-33, NCC, rep2 [KO_33_D11_2_S24]


title: SM-48, PSC, rep1 [SM_48_PSC_1_S2]


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 105, 32509

description: Library name: G195_O06_ABL2_A2_32509_D105


title: hCYP2B6-Tg male gastrocnemius, 0 mg/kg/day PFOS treatment for 21 days via oral gavage rep 5

description: Library name: m2B6_122_0


title: KO-27, NCC, rep2 [KO_27_D11_2_S22]


title: KO-27, PSC, rep2 [KO_27_PSC_2_S11]


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 105, 32017

description: Library name: G193_O06_ABL2_A2_32017_D105


title: hCYP2B6-Tg male gastrocnemius, 0 mg/kg/day PFOS treatment for 21 days via oral gavage rep 4

description: Library name: m2B6_120_0


title: KO-27, PSC, rep1 [KO_27_PSC_1_S3]


title: KO-33, PSC, rep2 [KO_33_PSC_2_S12]


title: hCYP2B6-Tg male gastrocnemius, 0 mg/kg/day PFOS treatment for 21 days via oral gavage rep 3

description: Library name: m2B6_118_0


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 105, 33864

description: Library name: G196_O06_ABL2_A2_33864_D105


title: KI-59, NCC, rep1 [KI_59_D11_1_S19]

value: knock-in


title: KI-59, PSC, rep1 [KI_59_PSC_1_S6]


title: hCYP2B6-Tg male gastrocnemius, 0 mg/kg/day PFOS treatment for 21 days via oral gavage rep 2

description: Library name: m2B6_109_0


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 105, 35916

description: Library name: G192_O06_ABL2_A1_35916_D105


title: KI-59, NCC, rep3 [KI_59_D11_3_S23]


title: KI-59, NCC, rep2 [KI_59_D11_2_S20]


title: KI-55, PSC, rep2 [KI_55_PSC_2_S13]


title: AKTi X

value: foreskin epidermis

value: primary keratinocyte


title: hCYP2B6-Tg male gastrocnemius, 0 mg/kg/day PFOS treatment for 21 days via oral gavage rep 1

description: Library name: m2B6_107_0


title: KI-55, PSC, rep1 [KI_55_PSC_1_S5]


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 105, 35815

description: Library name: G190_O06_ABL2_A1_35815_D105

value: Whole blood

value: day 105


title: KO-27, NCC, rep1 [KO_27_D11_1_S8]


title: Cyp2b-null female gastrocnemius, 10 mg/kg/day PFOS treatment for 21 days via oral gavage rep 4

description: Library name: fnul_168_10

value: gastrocnemius muscle


title: KI-55, NCC, rep1 [KI_55_D11_1_S16]


title: Cyp2b-null female gastrocnemius, 10 mg/kg/day PFOS treatment for 21 days via oral gavage rep 2

description: Library name: fnul_137_10


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 105, 35890

description: Library name: G191_O06_ABL2_A1_35890_D105


title: KI-59, PSC, rep2 [KI_59_PSC_2_S14]


title: Cyp2b-null female gastrocnemius, 10 mg/kg/day PFOS treatment for 21 days via oral gavage rep 1

description: Library name: fnul_134_10


title: Cyp2b-null female gastrocnemius, 10 mg/kg/day PFOS treatment for 21 days via oral gavage rep 3

description: Library name: fnul_138_10


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 105, 33900

description: Library name: G188_O06_ABL2_A1_33900_D105


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 105, 35808

description: Library name: G189_O06_ABL2_A1_35808_D105


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 105, 33879

description: Library name: G187_O06_ABL2_A1_33879_D105


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 105, 32814

description: Library name: G186_O06_ABL2_A1_32814_D105