title: HL-Day3-2

description:
Library name: Sample 41
H_3_B_2


title: HL-Day2-NaCl-CMP-3

status: Public on Jun 27 2025

type: SRA

city: Ningbo

first: Bin

last: Hu

address: No.169 Qixing South Road, Meishan Street, Beilun District, Ningbo City, Zhejiang Province, China

country: China

institute: Ningbo university

description:
Library name: Sample 39
H_2_NC_3

library_source: transcriptomic

data_processing:
Fastp Software for Quality Control with Default Parameters
Alignment to the Reference Genome Using HISAT2 v2.2.1
The alignment results were sorted and converted to BAM format using SAMtools
FeatureCounts was used for gene quantification(TPM)
Assembly: Strain: NIES-144GenBank accession: GCA_011766145.1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: The table file includes TPM values for all samples combined into one

molecule: total RNA

organism: Haematococcus lacustris

source_name: Unicellular Alga

extract_protocol:
Total RNA of each sample was extracted using Trizol (Sangon Biotech, China) in accordance with the manufacturer’s instructions. RNA concentration and quality were assessed using a NanoDrop ND1000 spectrophotometer (Thermo Scientific, Waltham, MA, USA) and an Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA). RNA samples meeting the following criteria were used for library preparation and sequencing: concentration > 200 ng/μL, OD260/OD280 > 1.8, OD260/OD230 > 1.8, RIN > 6.5, and 28S/18S ratio > 1.0.
After passing quality control, RNA sequencing libraries were constructed using the MGIEasy™ mRNA Library Preparation Kit (MGI, Shenzhen, China). mRNA was enriched using oligo(dT) magnetic beads, which bind to the polyA tail of mRNA through A-T base pairing. The enriched mRNA was fragmented and reverse transcribed into second-strand cDNA using N6 random primers. The cDNA was then purified using DNA magnetic beads and subjected to PCR amplification. After amplification, the library was purified again using DNA magnetic beads. The quality and size of the libraries were evaluated using a Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and an Agilent 2100 system (Agilent Technologies, Santa Clara, CA, USA). Sequencing was performed by Wuhan BGI (Wuhan, China) on the MGISEQ-2000 platform, generating approximately 20 million clean reads per sample using single-end sequencing.

tag: tissue

value: Unicellular Alga

tag: cell line

tag: cell type

value: Green Motile Cells,Red Non-Motile Cells

tag: genotype

value: WT

tag: light intensity

value: High light

tag: sampling time

value: Day 2

tag: exogenous treatment

value: 0.5 g/L NaCl plus 0.5 mM CMP


title: HL-Day3-1

description:
Library name: Sample 40
H_3_B_1

value: Day 3


title: HL-Day5-1mM-FDP-1

description:
Library name: Sample 59
H_5_1mFDP_1

value: Day 5

value: 1 mM Fructose diphosphate


title: HL-Day2-NaCl-CMP-1

description:
Library name: Sample 37
H_2_NC_1


title: HL-Day2-NaCl-CMP-2

description:
Library name: Sample 38
H_2_NC_2


title: HL-Day2-2

description:
Library name: Sample 35
H_2_B_2


title: HL-Day2-3

description:
Library name: Sample 36
H_2_B_3


title: HL-Day1-NR-2

description:
Library name: Sample 32
H_1_IN_2

value: Day 1

value: Nitrogen-repletion


title: HL-Day1-NR-1

description:
Library name: Sample 31
H_1_IN_1


title: HL-Day1-NR-3

description:
Library name: Sample 33
H_1_IN_3


title: HL-Day2-1

description:
Library name: Sample 34
H_2_B_1


title: HL-Day3-Xan-5

description:
Library name: Sample 56
H_3_H_5

value: 1 mM Xanthosine


title: HL-Day1-ND-3

description:
Library name: Sample 30
H_1_DN_3

value: Nitrogen-deprivation


title: HL-Day3-Tau-3

description:
Library name: Sample 51
H_3_N_3

value: 1 Mm Taurine


title: HL-Day1-ND-2

description:
Library name: Sample 29
H_1_DN_2


title: HL-Day1-ND-1

description:
Library name: Sample 28
H_1_DN_1


title: HL-Day1-6

description:
Library name: Sample 27
H_1_B_6


title: HL-Day1-5mM-FDP-3

description:
Library name: Sample 26
H_1_5mFDP_3

value: 5 mM Fructose diphosphate


title: HL-Day1-5

description:
Library name: Sample 23
H_1_B_5


title: HL-Day1-1mM-KI-3

description:
Library name: Sample 19
H_1_KI_3

value: 1 mM Potassium iodide


title: HL-Day1-5mM-FDP-1

description:
Library name: Sample 24
H_1_5mFDP_1


title: HL-Day1-5mM-FDP-2

description:
Library name: Sample 25
H_1_5mFDP_2


title: HL-Day1-4

description:
Library name: Sample 22
H_1_B_4


title: HL-Day1-2

description:
Library name: Sample 20
H_1_B_2


title: HL-Day1-1mM-FDP-2

description:
Library name: Sample 15
H_1_1mFDP_2


title: HL-Day1-1mM-FDP-3

description:
Library name: Sample 16
H_1_1mFDP_3


title: HL-Day1-1mM-KI-1

description:
Library name: Sample 17
H_1_KI_1


title: HL-Day1-1mM-FDP-1

description:
Library name: Sample 14
H_1_1mFDP_1


title: HL-Day1-1

description:
Library name: Sample 13
H_1_B_1


title: HL-Day10-KI-1

description:
Library name: Sample 10
H_10_KI_1

value: Day 10


title: HL-Day10-KI-2

description:
Library name: Sample 11
H_10_KI_2

value: Unicellular Alga


title: HL-Day10-KI-3

description:
Library name: Sample 12
H_10_KI_3

value: Green Motile Cells,Red Non-Motile Cells


title: HL-Day10-2

description:
Library name: Sample 8
H_10_B_2

value: WT


title: HL-Day10-3

description:
Library name: Sample 9
H_10_B_3

value: High light


title: HL-Day10-1

description:
Library name: Sample 7
H_10_B_1


title: HL-60h-Mutant-1

description:
Library name: Sample 4
H_2.5_M_1

value: MT

value: Mutant


title: HL-60h-Mutant-3

description:
Library name: Sample 6
H_2.5_M_3


title: HL-60h-3

description:
Library name: Sample 3
H_2.5_B_3


title: HL-Day1-3

description:
Library name: Sample 21
H_1_B_3


title: HL-60h-2

description:
Library name: Sample 2
H_2.5_B_2


title: HL-60h-1

description:
Library name: Sample 1
H_2.5_B_1


title: wound_patient_4983

type: genomic

city: Lubbock

first: Khalid

last: Omeir

state: Texas

address: 2901 Main St.

department: Department of Biological Sciences

country: USA

institute: Texas Tech University

description: Genomic DNA extracted from buccal swabs was genotyped using Infinium Global Screening Array-24 v3.0 BeadChip (Illumina)

scan_protocol: The Illumina iScan System with the GenomeStudio Genotyping Module was used to calculate analysis call rates and heterozygosities.

data_processing: The PLINK Input Report Plug-in extension for GenomeStudio was used to export and preasses PLINK files

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: buccal cells

label_protocol: Genotyping was performed according to the Illumina Infinium High-Throughput Screening (HTS) Assay protocol (Illumina, San Diego, CA, USA). In brief, whole-genome amplification was performed at 37°C for 20-24 hours. Post-amplification, DNAs were fragmented and hybridized to Illumina BeadChips with incubation at 48°C for 16-24 hours. Nonspecifically hybridized and unhybridized DNA were removed by washing, biotin or dinitrophenyl labeled nucleotides were added to extend hybridized primers, and BeadChips (Illumina) were coated for genotype calling.

extract_protocol: DNA extraction from buccal swabs was completed using Gentra Puregene Buccal Kits (Qiagen, Gaithersburg, MD, USA), with overnight lysis at 55°C, inclusion of RNase A for RNA-free purified DNA, and a final elution in 50 μL molecular biology grade water (GE Healthcare Life Sciences MA, USA).

tag: diabetes mellitus

value: no

tag: age

tag: gender

value: male


title: wound_patient_4967

hyb_protocol: Post-amplification, DNAs were fragmented and hybridized to Illumina BeadChips with incubation at 48°C for 16-24 hours. Nonspecifically hybridized and unhybridized DNA were removed by washing, biotin or dinitrophenyl labeled nucleotides were added to extend hybridized primers, and BeadChips (Illumina) were coated for genotype calling.


title: wound_patient_4963

value: yes


title: wound_patient_4939


title: HL-Day1-1mM-KI-2

description:
Library name: Sample 18
H_1_KI_2

value: Day 1


title: wound_patient_4770

value: female


title: wound_patient_4907


title: wound_patient_4745


title: wound_patient_4743


title: wound_patient_4724


title: wound_patient_4702


title: wound_patient_4700


title: wound_patient_4687


title: wound_patient_4683


title: HL-60h-Mutant-2

description:
Library name: Sample 5
H_2.5_M_2


title: wound_patient_4673


title: wound_patient_4660


title: wound_patient_4676


title: wound_patient_4655


title: wound_patient_4640


title: wound_patient_4600


title: Melanoma_Pretreatment

type: RNA

city: chiba city

first: Kazuhiro

last: Aoyama

state: Chiba

address: 1-8-1 Inohana, Chuo-ku, Chiba-shi, Chiba 260-8677, Japan

country: Japan

institute: chiba university

hyb_protocol: cRNA was hybridized to Thermo Fisher Clariom S Assay human array, washed and stained according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Affymetrix scanner.

data_processing: The raw data were normalized with SST-RMA algorithm (gene level) using Affymetrix Expression Console 1.4.1 software.

label: biotin

source_name: Melanoma,Pretreatment

label_protocol: The cRNA was amplified, labeled using GeneChip WT PLUS Reagent Kit according to the manufacturer's instructions.

growth_protocol: MEL02-1 and MEL02-2 were maintained in RPMI1640 10% FCS.

extract_protocol: Total RNA was purified from the cells using miRNeasy Mini Kit(QIAGEN cat. #217004) according to the manufacturer's instructions.

value: melanoma


title: wound_patient_4624


title: wound_patient_4593


title: wound_patient_4595


title: wound_patient_4581


title: wound_patient_4585


title: wound_patient_4578


title: wound_patient_4570


title: wound_patient_4577


title: wound_patient_4566


title: Melanoma_Posttreatment

source_name: Melanoma,Posttreatmnt


title: wound_patient_4557


title: wound_patient_4555


title: wound_patient_4552


title: wound_patient_4550


title: wound_patient_4531


title: wound_patient_4544


title: wound_patient_4530


title: wound_patient_4549


title: wound_patient_4528


title: wound_patient_4634


title: wound_patient_4527


title: wound_patient_4520


title: wound_patient_4503


title: wound_patient_3995


title: wound_patient_4504


title: wound_patient_3986


title: wound_patient_4510


title: wound_patient_3979


title: wound_patient_3973


title: wound_patient_3972


title: wound_patient_4560


title: wound_patient_3955


title: wound_patient_3958


title: wound_patient_3954


title: wound_patient_3952


title: wound_patient_4567


title: wound_patient_3950


title: wound_patient_3935


title: wound_patient_3933


title: wound_patient_3931


title: wound_patient_3925


title: wound_patient_3932


title: wound_patient_3908


title: wound_patient_3922


title: wound_patient_3917


title: wound_patient_3997


title: wound_patient_3913


title: wound_patient_3921


title: wound_patient_3903


title: wound_patient_3855


title: wound_patient_3845


title: wound_patient_3959


title: wound_patient_3830


title: wound_patient_3847


title: wound_patient_3825


title: wound_patient_3835


title: wound_patient_3836


title: wound_patient_3804


title: wound_patient_3794


title: wound_patient_3806


title: wound_patient_3792


title: wound_patient_3791


title: wound_patient_3784


title: wound_patient_3948


title: wound_patient_3776


title: wound_patient_3762


title: wound_patient_3760


title: wound_patient_3757


title: wound_patient_3751


title: wound_patient_3756


title: wound_patient_3731


title: wound_patient_3729


title: wound_patient_3728


title: wound_patient_3755


title: wound_patient_3727


title: wound_patient_3707


title: wound_patient_3708


title: wound_patient_3719


title: wound_patient_3703


title: wound_patient_3722


title: wound_patient_3702


title: wound_patient_3718


title: wound_patient_3691


title: HL-Day5-1mM-FDP-2

description:
Library name: Sample 60
H_5_1mFDP_2

value: Day 5

value: 1 mM Fructose diphosphate


title: wound_patient_3802


title: wound_patient_3601


title: wound_patient_3608


title: wound_patient_3683


title: wound_patient_3607


title: wound_patient_3684


title: wound_patient_3674


title: wound_patient_3638


title: wound_patient_3600


title: wound_patient_3766


title: wound_patient_3768


title: wound_patient_3595


title: wound_patient_3590


title: wound_patient_3582


title: wound_patient_3574


title: wound_patient_3575


title: wound_patient_3571


title: wound_patient_3568


title: wound_patient_3565


title: wound_patient_3564


title: wound_patient_3560


title: wound_patient_3542


title: wound_patient_3548


title: wound_patient_3534


title: wound_patient_3537


title: wound_patient_3557


title: wound_patient_3506


title: wound_patient_3502


title: wound_patient_3510


title: wound_patient_3515


title: wound_patient_3517


title: wound_patient_3419


title: wound_patient_3524


title: wound_patient_3535


title: wound_patient_3424


title: wound_patient_3434


title: wound_patient_3454


title: wound_patient_3509


title: wound_patient_3561


title: wound_patient_3400


title: wound_patient_3398


title: wound_patient_3525


title: wound_patient_3390


title: wound_patient_3396


title: wound_patient_3375


title: wound_patient_3371


title: wound_patient_3370


title: wound_patient_3467


title: wound_patient_3365


title: wound_patient_3361


title: wound_patient_3367


title: wound_patient_3357


title: wound_patient_3354


title: wound_patient_3345


title: wound_patient_3347


title: wound_patient_3350


title: wound_patient_3414


title: wound_patient_3340


title: wound_patient_3343


title: wound_patient_3337


title: wound_patient_3335


title: wound_patient_3404


title: CA1 Parental, shBRM, Untreated rep1

city: Rotterdam

first: Mathijs

last: Verhagen

address: Doctor Molewaterplein 40

country: Netherlands

institute: Erasmus Medical Center

data_processing:
Adapter trimming and quality filtering was performed using the SOAPnuke pipeline
Reads were aligned with STAR (v2.7.6a) to the hg19 reference genome with gencode annotations (V35)
A count table was generated with featureCounts (v2.0.0)
Downstream analysis was performed with DESeq2 (v1.42.0)
Counts were normalized with a variance stabilizing transformation (VST)
Assembly: hg19
Supplementary files format and content: tab-delimited text files include Ensemble Gene Id  and read count
Supplementary files format and content: tab-delimited text files include Ensemble Gene Id  and VST normalized values

molecule: polyA RNA

growth_protocol: OSCC cell lines were grown in standard culture conditions

extract_protocol:
RNA was harvested using Trizol reagent.
RNA-Seq was performed at BGI (Shenzhen, China) according to the PE150 DNA Nanoball sequencing (DNBseq) protocol till a depth of 25M reads per sample.

treatment_protocol: Inducible short hairpin RNAs directed against BRG1 (SMARCA4) or BRM (SMARCA2) were used to mutually exclusive ATPase subunits of the SWI/SNF complex

value: OSCC cell line

tag: treatment

value: Control


title: CA1 Parental, shBRM, Untreated rep2


title: wound_patient_3338


title: wound_patient_3326


title: CA1 Parental, shBRM, Dox, rep1

value: shBRM


title: wound_patient_3320


title: wound_patient_3307


title: CA1 Parental, shBRG1, Untreated rep1


title: wound_patient_3315


title: CA1 Parental, shBRG1, Dox, rep2


title: wound_patient_3304


title: LM Parental

data_processing:
Adapter trimming and quality filtering was performed using the SOAPnuke pipeline
Reads were aligned with STAR (v2.7.6a) to the hg19 reference genome with gencode annotations (V35)
A count table was generated with featureCounts (v2.0.0)
Downstream analysis was performed with DESeq2 (v1.36.0)
Counts were normalized with a variance stabilizing transformation (VST)
Assembly: hg19
Supplementary files format and content: tab-delimited text files include Ensemble Gene Id  and read count
Supplementary files format and content: tab-delimited text files include Ensemble Gene Id  and VST normalized values

source_name: LM

treatment_protocol: CRISPR/Cas9 technology was used to generate CDK2AP1 knock outs

value: LM

value: oral squamous cell carcinoma (OSCC) cell line

value: Parental


title: wound_patient_3299


title: wound_patient_3298


title: LM CDK2AP1 KO, Clone H4

value: CDK2AP1 KO


title: wound_patient_3294


title: wound_patient_3293


title: wound_patient_3292


title: CA1 Parental, shBRM, Dox, rep2


title: wound_patient_3324


title: LM CDK2AP1 KO, Clone B4


title: CA1 CDK2AP1 KO, Clone G3


title: CA1 CDK2AP1 KO, Clone B3


title: CA1 Parental


title: wound_patient_3282


title: wound_patient_3278


title: wound_patient_3281


title: CA1 Parental, shBRG1, Untreated rep2


title: CA1 CDK2AP1 KO, Clone A11


title: wound_patient_3305


title: SNU-449 cells, nucleus,siPANAD-1/2,rep1

city: Guangzhou

first: huanhui

last: feng

address: Xin Gang Xi Road 135#

institute: Sun Yat-sen University

description:
Library name: SAMPLE15
Column name in SNU-counts.csv: SNU-siPANADnuclRep1

data_processing:
Trim_Galore(0.6.4), Hisat 2.2.1, Feature Count v2.0.3
Raw paired-end RNA-seq reads were preprocessed using Trim_Galore to remove adapter sequences and low quality bases
High-quality reads were then aligned to to the human genome (hg38) using HISAT2 (2.2.1).
Gene counts were determined with Feature Count(2.0.3)
Assembly: hg38
Supplementary files format and content: csv file including counts for each sample

molecule: nuclear RNA

source_name: liver

growth_protocol: HepG2 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibootics in humidified atmosphere with 5% at 37℃； SNU-449 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibootics in humidified atmosphere with 5% at 37℃

extract_protocol:
RNA was isolated from the cytoplasmic and nuclear extracts using Trizol reagent(Invitrogen). RNA quality was assessed with a NanoDrop ND-1000 spectrophotometer.
Directional RNA-seq libraries were constructed and then sequenced at the Anoroad Genome (Beijing, China) on an Illumina NovaSeq 6000 Platform.

treatment_protocol: HepG2 and SNU-449 cells were transfected with NC or mixtures of siPANAD-1 and siPANAD-2 for 48 h.

value: liver

value: hepatocellular carcinoma cells


title: wound_patient_3275

value: no


title: SNU-449 cells, nucleus,siPANAD-1/2,rep2

description:
Library name: SAMPLE16
Column name in SNU-counts.csv: SNU-siPANADnuclRep2


title: wound_patient_3269


title: wound_patient_3267

value: male


title: CA1 Parental, shBRG1, Dox, rep1


title: SNU-449 cells, nucleus,NC,rep1

description:
Library name: SAMPLE13
Column name in SNU-counts.csv: SNU-NCnuclRep1

value: NC


title: SNU-449 cells, nucleus,NC,rep2

description:
Library name: SAMPLE14
Column name in SNU-counts.csv: SNU-NCnuclRep2


title: SNU-449 cells, cytoplasm,siPANAD-1/2,rep2

description:
Library name: SAMPLE12
Column name in SNU-counts.csv: SNU-siPANADcytoRep2

molecule: cytoplasmic RNA


title: wound_patient_3265

value: yes


title: LM CDK2AP1 KO, Clone B6


title: SNU-449 cells, cytoplasm,siPANAD-1/2,rep1

description:
Library name: SAMPLE11
Column name in SNU-counts.csv: SNU-siPANADcytoRep1


title: wound_patient_3259

value: female


title: wound_patient_3255


title: wound_patient_3254


title: SNU-449 cells, cytoplasm,NC,rep1

description:
Library name: SAMPLE9
Column name in SNU-counts.csv: SNU-NCcytoRep1


title: wound_patient_3246


title: HepG2 cells, nucleus,siPANAD-1/2,rep2

description:
Library name: SAMPLE8
Column name in G2-counts.csv: G2-siPANADnuclRep2


title: OVCAR4 ResB_R3

city: Madison

first: Jessica

last: Lang

state: WI

address: Wisconsin Institutes for Medical Research Room 2766 1111 Highland Avenue

department: Pathology and Laboratory Medicine

institute: UW-Madison

data_processing:
BCL to FASTQ conversion was performed on instrument using Illumina’s DRAGEN DRAGEN BCL Convert v3.8.4 for NextSeq 1000/2000.
FASTQ files were then used as input into the NextFlow (v22.04.5) pipeline nf-core/rnaseq pipeline (v3.8.1) using genome GRCh38 for alignment and annotation.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file containing gene transcripts per million for each sample
Supplementary files format and content: Tab-delimited text file containing gene counts for each sample

source_name: OVCAR4 ResB

extract_protocol:
RNA was extracted using a Quick DNA/RNA Miniprep Plus Kit (Zymo Research) and 300ng of total RNA was used for sequencing library prep.
RNA-sequencing libraries were prepared using a KAPA mRNA HyperPrep Kit (Roche) according to manufacturer's protocol with the following modifications: RNA fragmentation at 94°C for 6 minutes, 10 cycles of PCR amplification

value: OVCAR4 ResB

tag: replicate


title: wound_patient_3244


title: wound_patient_3245


title: wound_patient_3272


title: HepG2 cells, nucleus,siPANAD-1/2,rep1

description:
Library name: SAMPLE7
Column name in G2-counts.csv: G2-siPANADnuclRep1


title: wound_patient_3223


title: wound_patient_3241


title: HepG2 cells, nucleus,NC,rep1

description:
Library name: SAMPLE5
Column name in G2-counts.csv: G2-NCnuclRep1


title: OVCAR4_R3


title: HepG2 cells, nucleus,NC,rep2

description:
Library name: SAMPLE6
Column name in G2-counts.csv: G2-NCnuclRep2


title: wound_patient_3221


title: wound_patient_3220


title: OVCAR3 ResB_R3

source_name: OVCAR3 ResB

value: OVCAR3 ResB


title: wound_patient_3219


title: OVCAR3 ResA_R3

source_name: OVCAR3 ResA

value: OVCAR3 ResA


title: HepG2 cells, cytoplasm,siPANAD-1/2,rep2

description:
Library name: SAMPLE4
Column name in G2-counts.csv: G2-siPANADcytoRep2


title: wound_patient_3218


title: wound_patient_3212


title: OVCAR3_R3


title: HepG2 cells, cytoplasm,siPANAD-1/2,rep1

description:
Library name: SAMPLE3
Column name in G2-counts.csv: G2-siPANADcytoRep1


title: SNU-449 cells, cytoplasm,NC,rep2

description:
Library name: SAMPLE10
Column name in SNU-counts.csv: SNU-NCcytoRep2


title: PEA2_R3


title: wound_patient_3201


title: wound_patient_3195


title: wound_patient_3243


title: HepG2 cells, cytoplasm,NC,rep2

description:
Library name: SAMPLE2
Column name in G2-counts.csv: G2-NCcytoRep2


title: OVCAR4 ResA_R3

source_name: OVCAR4 ResA

value: OVCAR4 ResA


title: wound_patient_3193


title: PEA1_R3


title: HepG2 cells, cytoplasm,NC,rep1

description:
Library name: SAMPLE1
Column name in G2-counts.csv: G2-NCcytoRep1


title: wound_patient_3192

description: Genomic DNA extracted from buccal swabs was genotyped using Infinium Global Screening Array-24 v3.0 BeadChip (Illumina)


title: wound_patient_3190


title: PEO6_R3


title: CG1.ZZ.CAR.LCK cells, Donor 4, day 0

city: Chapel Hill

first: Office of Genomics Research

last: UNC Lineberger Comprehensive Cancer Center

state: NC

address: 125 Mason Farm Road, CB #7599 5105-5106 Marsico Hall

institute: University of North Carolina at Chapel Hill

description: Library name: CG1.ZZ.CAR.LCK.D4_Day0

data_processing:
Alignment: STAR (v.2.7.6a)
Quantification: Salmon (v.1.4.0)
QA: FastQC (v0.11.9)
QA: Picard (v2.22.4) CollectRnaSeqMetrics
Assembly: Assembly: Ensembl release 99, GRCh38
Supplementary files format and content: Salmon count data by Ensembl gene ID

source_name: Expanded T cells from PBMCs

growth_protocol: Buffy coats from HLA-A2⁺ healthy volunteer donors were obtained from the Gulf Coast Regional Blood Center (Houston, TX, USA). Peripheral blood mononuclear cells (PBMCs) were isolated by density gradient centrifugation using Lymphoprep (Accurate Chemical and Scientific Corporation). Isolated PBMCs were activated and transduced as previously described, then cultured for 10 days in the presence of IL-7 and IL-15 prior to use in co-culture experiments. The U937 tumor cell line was purchased from ATCC and maintained in RPMI 1640 medium (Gibco) supplemented with 10% fetal bovine serum (FBS; Sigma), 1% L-glutamine (Gibco), and 1% penicillin-streptomycin (Gibco), in a humidified incubator at 37 °C with 5% CO₂ until use.

extract_protocol:
RNA was immediately extracted from the sorted cells and  purified Qiagen's RNeasy Plus Mini kit (74134). The Qubit 4 Fluorometer was used to quantify  the RNA and Agilent's TapeStation 2200 confirmed RNA integrity.
The RNAseq was performed  using Illumina’s “Stranded mRNA Prep Ligation” kit for library preparation, starting with 100 ng of  total RNA. This method uses oligo(dT) magnetic beads to capture mRNAs with polyA tails. The  average fragment length for these libraries was between 300-400 bp. Paired-end sequencing  was performed using the NextSeq 2000 P2 kit version 3.0 (2X100).

treatment_protocol: Isolated PBMCs were activated using anti-CD3 and anti-CD28 antibody-coated plates, as previously described. After 48 hours, cells were transduced with either CAR.CG1 or CAR.CG1.ζζ.LCK using retroviral supernatants on coated plates. Transduced cells were cultured for 10 additional days in the presence of IL-7 and IL-15 before being used in co-culture experiments. The structures of the CAR constructs and the protocol for generating retroviral supernatants have been previously described. The vector encoding human LCK was also previously reported. The co-expression of CAR and LCK was achieved by incorporating a 2A-TAV self-cleaving peptide sequence, as described in prior work. U937 cells were transduced with a retroviral vector encoding human HLA-A2 to generate the U937/HLA-A2 cell line, which was maintained in complete medium under standard conditions, as previously described.

value: Expanded T cells from PBMCs


title: wound_patient_3189


title: PEO4_R3


title: wound_patient_3182


title: wound_patient_3181


title: CG1.ZZ.CAR.LCK cells, Donor 3, day 0

description: Library name: CG1.ZZ.CAR.LCK.D3_Day0


title: wound_patient_3187


title: PEO1_R3


title: CG1.ZZ.CAR.LCK cells, Donor 4, day 5

description: Library name: CG1.ZZ.CAR.LCK.D4_Day5


title: CG1.ZZ.CAR.LCK cells, Donor 3, day 5

description: Library name: CG1.ZZ.CAR.LCK.D3_Day5


title: wound_patient_3180


title: OVCAR4 ResB_R2


title: wound_patient_3204


title: wound_patient_3174


title: OVCAR4 ResA_R2


title: CG1.ZZ.CAR.LCK cells, Donor 4, day 1

description: Library name: CG1.ZZ.CAR.LCK.D4_Day1


title: wound_patient_3169


title: OVCAR4 _R2


title: wound_patient_3168


title: wound_patient_3166


title: CG1.ZZ.CAR.LCK cells, Donor 3, day 1

description: Library name: CG1.ZZ.CAR.LCK.D3_Day1


title: wound_patient_3162


title: OVCAR3 ResB_R2


title: wound_patient_3161


title: OVCAR3 ResA_R2


title: CG1.CAR cells, Donor 4, day 0

description: Library name: CG1.CAR.D4_Day0

value: CG1 CAR


title: wound_patient_3160


title: CG1.CAR cells, Donor 3, day 0

description: Library name: CG1.CAR.D3_Day0


title: wound_patient_3148


title: CG1.CAR cells, Donor 4, day 5

description: Library name: CG1.CAR.D4_Day5


title: wound_patient_3176


title: wound_patient_3149


title: CG1.CAR cells, Donor 3, day 5

description: Library name: CG1.CAR.D3_Day5


title: PEA2_R2


title: wound_patient_3158


title: OVCAR3_R2


title: wound_patient_3150


title: wound_patient_3138


title: CG1.CAR cells, Donor 4, day 1

description: Library name: CG1.CAR.D4_Day1


title: wound_patient_3139


title: wound_patient_3175


title: PEA1_R2


title: PEO6_R2


title: CG1.CAR cells, Donor 3, day 1

description: Library name: CG1.CAR.D3_Day1


title: wound_patient_3134


title: PEO4_R2


title: wound_patient_3116


title: CG1.ZZ.CAR.LCK, Donor 1, day 5

description: Library name: CG1.ZZ.CAR.LCK.D1_Day5


title: CG1.CAR cells, Donor 1, day 5

description: Library name: CG1.CAR.D1_Day5


title: PEO1_R2


title: wound_patient_3140


title: wound_patient_3108


title: wound_patient_3021


title: wound_patient_3032


title: OVCAR4 ResA_R1


title: OVCAR4_R1


title: wound_patient_3137


title: wound_patient_3120


title: wound_patient_2973


title: wound_patient_2962


title: wound_patient_2975


title: OVCAR3 ResB_R1


title: wound_patient_2967


title: CG1.ZZ.CAR.LCK, Donor 1, day 1

description: Library name: CG1.ZZ.CAR.LCK.D1_Day1


title: CG1.CAR cells, Donor 2, day 5

description: Library name: CG1.CAR.D2_Day5


title: wound_patient_3110


title: wound_patient_2955


title: CG1.ZZ.CAR.LCK, Donor 2, day 1

description: Library name: CG1.ZZ.CAR.LCK.D2_Day1


title: OVCAR4 ResB_R1


title: wound_patient_2956


title: wound_patient_3127


title: CG1.CAR cells, Donor 1, day 1

description: Library name: CG1.CAR.D1_Day1


title: OVCAR3_R1


title: wound_patient_2946


title: CG1.CAR cells, Donor 2, day 1

description: Library name: CG1.CAR.D2_Day1


title: PEA2_R1


title: wound_patient_2940


title: CG1.ZZ.CAR.LCK, Donor 2, day 5

description: Library name: CG1.ZZ.CAR.LCK.D2_Day5


title: CG1.ZZ.CAR.LCK, Donor 1, day 0

description: Library name: CG1.ZZ.CAR.LCK.D1_Day0


title: wound_patient_2928


title: wound_patient_2930


title: OVCAR3 ResA_R1


title: PEA1_R1


title: wound_patient_2911


title: wound_patient_2913


title: CG1.ZZ.CAR.LCK, Donor 2, day 0

description: Library name: CG1.ZZ.CAR.LCK.D2_Day0


title: wound_patient_2899


title: PEO6_R1


title: CG1.CAR cells, Donor 1, day 0

description: Library name: CG1.CAR.D1_Day0


title: PEO4_R1


title: CG1.CAR cells, Donor 2, day 0

description: Library name: CG1.CAR.D2_Day0


title: wound_patient_2924


title: PEO1_R1


title: wound_patient_2892


title: Follicular lymphoma 21, BCR expression, IRF4_high

city: Rochester

first: Emmanuel

last: Contreras Guzman

state: Minnesota

address: 150 3rd St SW

institute: Mayo Clinic

description: Library name: FL21_BCR

data_processing:
*library strategy: BCR-seq
Gene expression libraries were sequenced at a minimum of 50,000 read pairs per cell and BCR libraries at a minimum of 10,000 read pairs per cell. Both library types were pooled and loaded across multiple lanes of a NovaSeq S4 flow cell, following Illumina’s standard protocol for the NovaSeq 6000 (San Diego, CA) and using the NovaSeq XP 4-Lane kit for individual lane loading. The flow cells were sequenced as 100 X 2 paired end reads using NovaSeq Control Software v1.8.0. Base-calling was performed using Illumina’s RTA version 3.4.4.
Assembly: GRCh38
Supplementary files format and content: CellRanger Output files: clonotype.csv, filtered_contig_annotations.csv, sample_filtered_feature_bc_matrix.h5

source_name: lymph nodes

extract_protocol:
The whole live cells were counted and measured for viability using the Vi-Cell XR Cell Viability Analyzer (Beckman Coulter, Indianapolis, IN).  With a desired capture target of 10,000 cells, samples were prepared according to the instructions for the Chromium Next GEM Single Cell 5’ Reagent Kits v2 (10x Genomics, Pleasanton, CA).
For cDNA generation, the resulting GEMs were collected and proceeded to reverse transcription, GEM dissolution, and cDNA clean-up. The resulting cDNA, a pool of uniquely barcoded molecules, was used to generate 5’ gene expression libraries. Enriched B-cell receptor (BCR) libraries were also prepared using the Chromium Single Cell V(D)J Amplification Kit (10x Genomics). During library construction, standard Illumina sequencing primers and a unique i7 Sample index (Dual Index TT Set A; 10x Genomics) were added to each cDNA pool (gene expression and BCR). All cDNA pools and final libraries were measured using Qubit High Sensitivity assays (ThermoFisher Scientific, Waltham, MA) and Agilent Bioanalyzer High Sensitivity chips (Santa Clara, CA).

value: lymph nodes

value: B-cells and Immune cells

tag: group


title: wound_patient_2895


title: OVK18

description: Sample 36

value: ovarian cancer


title: wound_patient_2890


title: Follicular lymphoma 20, BCR expression, IRF4_low

description: Library name: FL20_BCR


title: wound_patient_2884


title: wound_patient_2878


title: PEO6

description: Sample 35


title: wound_patient_2876


title: PEO4

description: Sample 34


title: wound_patient_2875


title: wound_patient_2873


title: Follicular lymphoma 18, BCR expression, IRF4_high

description: Library name: FL18_BCR


title: wound_patient_2898


title: wound_patient_2871


title: PEO1

description: Sample 33


title: Follicular lymphoma 17, BCR expression, IRF4_low

description: Library name: FL17_BCR


title: OVCAR3

description: Sample 32


title: wound_patient_2864


title: wound_patient_2850


title: wound_patient_2865


title: wound_patient_2881


title: Follicular lymphoma 16, BCR expression, IRF4_low

description: Library name: FL16_BCR


title: Follicular lymphoma 15, BCR expression, IRF4_high

description: Library name: FL15_BCR


title: JHOS2

description: Sample 31


title: wound_patient_2843


title: wound_patient_2848


title: wound_patient_2839


title: Follicular lymphoma 13, BCR expression, IRF4_high

description: Library name: FL13_BCR


title: wound_patient_2838


title: BIN67

description: Sample 29


title: wound_patient_2847


title: ES2

description: Sample 28


title: Follicular lymphoma 19, BCR expression, IRF4_low

description: Library name: FL19_BCR


title: wound_patient_2831


title: wound_patient_2830


title: Follicular lymphoma 12, BCR expression, IRF4_low

description: Library name: FL12_BCR


title: wound_patient_2827


title: JHOC5

description: Sample 27


title: RMG1

description: Sample 26


title: wound_patient_2826


title: Follicular lymphoma 11, BCR expression, IRF4_high

description: Library name: FL11_BCR


title: JHOS4

description: Sample 30


title: wound_patient_2825


title: wound_patient_2822


title: wound_patient_2821


title: wound_patient_2807


title: wound_patient_2833


title: Follicular lymphoma 10, BCR expression, IRF4_high

description: Library name: FL10_BCR


title: IGROV1

description: Sample 23


title: wound_patient_2766


title: Follicular lymphoma 9, BCR expression, IRF4_high

description: Library name: FL9_BCR


title: PEA2

description: Sample 24


title: wound_patient_2805


title: wound_patient_2747


title: Follicular lymphoma 5, BCR expression, IRF4_low

description: Library name: FL5_BCR


title: Follicular lymphoma 6, BCR expression, IRF4_low

description: Library name: FL6_BCR


title: wound_patient_2803


title: wound_patient_2802


title: Follicular lymphoma 8, BCR expression, IRF4_low

description: Library name: FL8_BCR


title: Follicular lymphoma 14, BCR expression, IRF4_high

description: Library name: FL14_BCR


title: CAOV4

description: Sample 22


title: COV434

description: Sample 25


title: wound_patient_2817


title: Follicular lymphoma 7, BCR expression, IRF4_low

description: Library name: FL7_BCR


title: COV362

description: Sample 21


title: wound_patient_2741


title: Follicular lymphoma 4, BCR expression, IRF4_low

description: Library name: FL4_BCR


title: wound_patient_2734


title: EFO27

description: Sample 19


title: wound_patient_2770


title: Follicular lymphoma 3, BCR expression, IRF4_high

description: Library name: FL3_BCR


title: wound_patient_2675


title: wound_patient_2640


title: JHOC9

description: Sample 18


title: Follicular lymphoma 2, BCR expression, IRF4_high

description: Library name: FL2_BCR


title: wound_patient_2632


title: KURAMOVHI

description: Sample 17

source_name: KURAMOVHI

value: KURAMOVHI


title: Follicular lymphoma 1, BCR expression, IRF4_low

description: Library name: FL1_BCR


title: wound_patient_2600


title: wound_patient_2614


title: wound_patient_2739


title: wound_patient_2612


title: OAW42

description: Sample 15


title: Follicular lymphoma 21, gene expression, IRF4_high

description: Library name: FL21_GEX

library_source: transcriptomic single cell

data_processing:
Gene expression libraries were sequenced at a minimum of 50,000 read pairs per cell and BCR libraries at a minimum of 10,000 read pairs per cell. Both library types were pooled and loaded across multiple lanes of a NovaSeq S4 flow cell, following Illumina’s standard protocol for the NovaSeq 6000 (San Diego, CA) and using the NovaSeq XP 4-Lane kit for individual lane loading. The flow cells were sequenced as 100 X 2 paired end reads using NovaSeq Control Software v1.8.0. Base-calling was performed using Illumina’s RTA version 3.4.4.
Assembly: GRCh38
Supplementary files format and content: CellRanger Output files: clonotype.csv, filtered_contig_annotations.csv, sample_filtered_feature_bc_matrix.h5


title: wound_patient_2587


title: wound_patient_2554


title: wound_patient_2591


title: 59M

description: Sample 16


title: Follicular lymphoma 20, gene expression, IRF4_low

description: Library name: FL20_GEX


title: wound_patient_2732


title: Follicular lymphoma 19, gene expression, IRF4_low

description: Library name: FL19_GEX


title: wound_patient_2551


title: Follicular lymphoma 18, gene expression, IRF4_high

description: Library name: FL18_GEX


title: CAOV3

description: Sample 14


title: wound_patient_2533


title: OVCAR4

description: Sample 13


title: TOV112D

description: Sample 12


title: wound_patient_2525


title: Follicular lymphoma 17, gene expression, IRF4_low

description: Library name: FL17_GEX


title: wound_patient_2518


title: wound_patient_2527


title: OVISE

description: Sample 11

source_name: OVISE

value: OVISE


title: wound_patient_2516


title: wound_patient_2629


title: Follicular lymphoma 16, gene expression, IRF4_low

description: Library name: FL16_GEX


title: wound_patient_2499


title: Follicular lymphoma 15, gene expression, IRF4_high

description: Library name: FL15_GEX


title: wound_patient_2497


title: wound_patient_2439


title: OVMANA

description: Sample 10

source_name: OVMANA

value: OVMANA


title: Follicular lymphoma 14, gene expression, IRF4_high

description: Library name: FL14_GEX


title: PEA1

description: Sample 9


title: wound_patient_2494


title: Follicular lymphoma 13, gene expression, IRF4_high

description: Library name: FL13_GEX


title: wound_patient_2381

value: no


title: OVTOKO

description: Sample 8

source_name: OVTOKO

value: OVTOKO


title: wound_patient_2351


title: wound_patient_2356

value: male


title: wound_patient_2435


title: wound_patient_2359

value: yes


title: wound_patient_2314


title: Follicular lymphoma 12, gene expression, IRF4_low

description: Library name: FL12_GEX


title: TYK-NY.CPR

description: Sample 7


title: wound_patient_2301


title: Follicular lymphoma 11, gene expression, IRF4_high

description: Library name: FL11_GEX


title: Follicular lymphoma 10, gene expression, IRF4_high

description: Library name: FL10_GEX


title: wound_patient_2298

value: female


title: OVCAR8

description: Sample 6


title: OVSAHO

description: Sample 5

source_name: OVSAHO

value: OVSAHO


title: wound_patient_2266


title: wound_patient_2252


title: wound_patient_2978


title: Follicular lymphoma 9, gene expression, IRF4_high

description: Library name: FL9_GEX


title: TYK-NU

description: Sample 3

source_name: TYK-NU

value: TYK-NU


title: wound_patient_2245

source_name: buccal cells


title: Follicular lymphoma 8, gene expression, IRF4_low

description: Library name: FL8_GEX


title: wound_patient_2229


title: wound_patient_2232


title: Follicular lymphoma 7, gene expression, IRF4_low

description: Library name: FL7_GEX


title: wound_patient_2208


title: wound_patient_2190


title: Follicular lymphoma 6, gene expression, IRF4_low

description: Library name: FL6_GEX


title: wound_patient_2116


title: SKOV3

description: Sample 1


title: wound_patient_2110


title: Ethanol-fed PFOS replicate 6

city: Louisville

first: Jae Yeon

last: Hwang

state: Kentucky

address: 505 S. Hancock Street

department: Division of Medical Oncology & Hematology

institute: University of Louisville

description: Library name: EFP6

data_processing:
Raw sequence data were processed using Illumina's bcl2fastq 2.17 software, and trimmed reads were mapped to the GRCm39 mouse reference genome with the GRCm39.110 transcriptome (Ensembl GTF release 110) using the STAR aligner (v.2.7.10a). Differentially expressed genes were identified using Cuffdiff (v2.2.1)
Assembly: GRCm39
Supplementary files format and content: CSV file and FPKM values

organism: Mus musculus

source_name: Liver

growth_protocol: Nine-week-old male C57BL/6J mice (Jackson Laboratory, Stock# 000664) were maintained under AAALAC-accredited specific pathogen-free conditions with IACUC approval. Mice were group-housed (5/cage) at 23-25°C, 55±10% humidity, 12h light/dark cycle, with ad libitum access to standard rodent chow and water during one-week acclimatization.

extract_protocol:
Total RNA was extracted from liver tissue samples (n=6) using Trizol.
RNA-seq libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB, Ipswich, MA). Sequencing was performed on an Illumina NovaSeq 6000 S4 flow cell using a 2 x 150 bp paired-end configuration.

treatment_protocol: C57BL/6J mice were subjected to a chronic-binge ethanol model with stepwise ethanol concentration increases (0-5%) over 21 days, while pair-fed controls received isocaloric maltose-dextrin diet. Following a 5-day adaptation to 5% ethanol or control diet, mice were orally gavaged with either PFOS (1 mg/kg body weight) or vehicle control (2% Tween-80) daily for 10 days while continuing their respective diets. Diet consumption and body weights were monitored daily, with pair-fed groups receiving equivalent caloric intake as their ethanol-fed counterparts from the previous day.

value: Liver

tag: Sex

tag: strain

value: ethanol-fed + PFOS exposure


title: Follicular lymphoma 5, gene expression, IRF4_low

description: Library name: FL5_GEX


title: Ethanol-fed PFOS replicate 5

description: Library name: EFP5


title: wound_patient_2078


title: Follicular lymphoma 4, gene expression, IRF4_low

description: Library name: FL4_GEX


title: wound_patient_2076


title: TOV21G

description: Sample 4


title: Follicular lymphoma 3, gene expression, IRF4_high

description: Library name: FL3_GEX


title: wound_patient_2099


title: Ethanol-fed PFOS replicate 4

description: Library name: EFP4


title: Ethanol-fed PFOS replicate 3

description: Library name: EFP3


title: Follicular lymphoma 2, gene expression, IRF4_high

description: Library name: FL2_GEX


title: OV90

description: Sample 2


title: wound_patient_1968


title: wound_patient_1961


title: wound_patient_1960


title: wound_patient_2199


title: wound_patient_1959


title: Ethanol-fed PFOS replicate 1

description: Library name: EFP1


title: wound_patient_2107


title: CD19+ B I.1

city: New York

first: Emily

last: Mace

state: NY

institute: Columbia University Irving Medical Center

description: Library name: PBMC_20

data_processing:
The FASTQ files were generated using FastQC (v0.11.7) and trimmed reads (Trimmomatic 0.38) were mapped to UCSC hg38 with HISAT2 (v2.1.0, Bowtie2 2.3.4.1), splice-aware aligner. Transcript is assembled by StringTie (v2.1.3b) and abundance of genes are calculated as FPKM.
Assembly: USCS_hg38
Supplementary files format and content: txt file with RPKM

source_name: PBMC

growth_protocol: Primary PBMC cells

extract_protocol:
2~10 X 10^4 cells were lysed, and RNA was collected with NucleoSpin RNA XS kit (Takara, 740902) according to the manufacturer’s protocol. RNA quality control was performed using the Agilent 2100 Bioanalyzer System.
Libraries were generated with SMARTer stranded RNA-Seq kit (Takara, 634839) according to the manufecturer's protocol.

treatment_protocol: No treatment

value: PBMC

value: GINS4 Q191X/WT

value: sorted


title: wound_patient_1908


title: CD3+ NK I.1

description: Library name: PBMC_19


title: wound_patient_2063


title: Ethanol-fed Vehicle replicate 6

description: Library name: EFV6

value: ethanol-fed + vehicle


title: Ethanol-fed Vehicle replicate 5

description: Library name: EFV5


title: wound_patient_1884


title: wound_patient_1914


title: wound_patient_1984


title: wound_patient_1870


title: CD19+ B I.2

description: Library name: PBMC_16

value: GINS4 V171L/WT


title: Ethanol-fed Vehicle replicate 3

description: Library name: EFV3


title: Ethanol-fed Vehicle replicate 4

description: Library name: EFV4


title: CD3+ NK I.2

description: Library name: PBMC_15


title: wound_patient_1882


title: CD56+ NK I.1

description: Library name: PBMC_18


title: Ethanol-fed PFOS replicate 2

description: Library name: EFP2


title: Follicular lymphoma 1, gene expression, IRF4_low

description: Library name: FL1_GEX

value: lymph nodes

value: B-cells and Immune cells


title: wound_patient_1847


title: wound_patient_1828


title: Ethanol-fed Vehicle replicate 2

description: Library name: EFV2


title: wound_patient_1827


title: wound_patient_1824


title: CD56+ NK I.2

description: Library name: PBMC_14


title: wound_patient_1822


title: CD19+ B II.2

description: Library name: PBMC_12

value: GINS4 V171L/Q191X


title: wound_patient_1889

value: no


title: wound_patient_1906


title: wound_patient_1808


title: wound_patient_1800


title: Pair-fed PFOS replicate 5

description: Library name: PFP5

value: pair-fed + PFOS exposure


title: Pair-fed PFOS replicate 6

description: Library name: PFP6

value: male


title: wound_patient_1805

value: yes


title: wound_patient_1798

value: female


title: CD56+ NK II.2

description: Library name: PBMC_10


title: wound_patient_1792


title: CD3+ NK II.2

description: Library name: PBMC_11


title: wound_patient_1754


title: wound_patient_1751


title: wound_patient_1783


title: CD19+ B II.1

description: Library name: PBMC_8


title: Pair-fed PFOS replicate 3

description: Library name: PFP3


title: wound_patient_1734


title: CD56+ NK II.1

description: Library name: PBMC_6


title: wound_patient_1737


title: Pair-fed PFOS replicate 2

description: Library name: PFP2


title: Ethanol-fed Vehicle replicate 1

description: Library name: EFV1


title: wound_patient_1732


title: wound_patient_1712


title: CD19+ B Con_M

description: Library name: PBMC_4

value: GINS4 WT/WT


title: Pair-fed Vehicle replicate 6

description: Library name: PFV6

value: pair-fed + vehicle


title: Pair-fed PFOS replicate 1

description: Library name: PFP1

value: Liver


title: wound_patient_1687


title: wound_patient_1727


title: CD3+ NK Con_M

description: Library name: PBMC_3


title: wound_patient_1665


title: Pair-fed PFOS replicate 4

description: Library name: PFP4


title: wound_patient_1654


title: wound_patient_1660


title: VCP_3_Cyto_ML240

city: London

first: Christy

last: Hung

address: Gower St, London WC1E 6BT

country: United Kingdom

institute: UCL

data_processing:
Data was processed using nfcore/rnaseq pipeline v 3.9
Adapter removal and quality trimming was performed with Trim Galore.
Read alignment using STAR and gene quantification using RSEM.
Differential Gene expression was carried out using DESEq2 within an R environment ( 4.2.2)
Assembly: Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa release 95 obtained from Ensembl
Supplementary files format and content: RSEM quantification: tab delimited text file containing counts per gene per sample. One file per sample

source_name: neuron

growth_protocol: Dissociated hiPSCs were plated on six-well plates coated with GelTrex (Life Technologies) and neural induction was initiated by changing into culture medium that supports neuronal differentiation and neurogenesis, a 1:1 mixture of N2- and B27-containing media (N2B27) (supplemented with 1 μM dorsomorphin and 10 μM SB431542 to inhibit TGFβ signalling during neural induction). Media was replaced every 24 h. At Day 12, neuroepithelial cells were harvested with dispase and replated in laminin-coated plates with FGF2-containing media for 4 days. FGF2 was then withdrawn and dissociated using Accutase and neural progenitor cells were plated on GelTrex-coated plates. Plated neurons were maintained for up to 120 days with a medium change every 2–3 days.

extract_protocol:
iPSNs underwent subcellular fractionation into nuclear and cytoplasmic compartments using the Ambion PARIS kit cell fractionation buffer, following the manufacturer’s general protocol and an 8M urea nuclear lysis buffer (50mM Tris-HCL (pH8), 100mM NaCl, 0.1% SDS, and 1mM DTT). Paired-end poly(A)+ selected reverse stranded RNA sequencing libraries were prepared from nuclear and cytoplasmic fractions using the NEBNext® Ultra II Directional RNA Library kit for Illumina®, with 500ng of total RNA as input.
RNA libraries for RNA-Seq were prepared using NEBNext Ultra II Directional PolyA mRNA following manufacturer's instructions.

treatment_protocol: For VCP inhibitor treatment, medium was changed to fresh medium containing 1 μM of ML240 (Sigma; SML1071; CAS: 1346527-98-7), or the same percentage of DMSO for 2 h before harvesting.

value: neuron

value: ipsn

value: VCP


title: Pair-fed Vehicle replicate 4

description: Library name: PFV4


title: wound_patient_1633


title: Pair-fed Vehicle replicate 5

description: Library name: PFV5


title: CD3+ NK II.1

description: Library name: PBMC_7

value: PBMC

value: sorted


title: wound_patient_1620


title: wound_patient_1621


title: Pair-fed Vehicle replicate 3

description: Library name: PFV3


title: Pair-fed Vehicle replicate 2

description: Library name: PFV2


title: EFO21

description: Sample 20

value: ovarian cancer


title: wound_patient_1592


title: wound_patient_1618


title: wound_patient_1590


title: Pair-fed Vehicle replicate 1

description: Library name: PFV1


title: wound_patient_1588


title: PSEN1_3_Cyto_ML240


title: VCP_1_Cyto_ML240


title: wound_patient_1587


title: LAG3+ NK cells Day2 replicate 3

first: Marie

last: Marotel

state: ON

address: 2 143 Eccles Street

department: Cancer Research

country: Canada

institute: Ottawa Hospital Research Institute

description:
Library name: Sample 6
Column name in tpm_matrix_LAG3_LAG3pos3

data_processing:
Transcript quantification for each sample was performed using Kallisto (v0.45.0) with the GRCm38 transcriptome reference and the -b 50 bootstrap option.
The R package DESeq2 (v1.44.0) was then used to construct general linear models of each gene across experimental conditions. Wald’s test was used to test for differential expression between groups and the resultant p-values were adjusted using the Benjamini-Hochberg false discovery rate method.
Assembly: Transcript quantification for each sample was performed using Kallisto (v0.45.0) with the GRCm38 transcriptome reference and the -b 50 bootstrap option.
Supplementary files format and content: csv file includ tpm value for each gene for each sample

source_name: spleen

growth_protocol: primary NK cells sorted from the spleen of C57BL/6 mice injected with poly (I:C)

extract_protocol:
RNA was harvested using GenElute™ Mammalian Total RNA Miniprep Kit (Sigma Aldrich)
The entire process of experiments from library preparation to sequencing was performed by DNA Link (DNA Link Inc., Seoul, Republic of Korea). mRNA was purified and fragmented from total RNA using poly-T oligo-attached magnetic beads using two rounds of purification. Cleaved RNA Fragments primed with random hexamers were reverse transcribed into first strand cDNA using reverse transcriptase, random primers, dUTP in place of dTTP. These cDNA fragments then had the addition of a single 'A' base and subsequent ligation of the adapter. The products were purified and enriched with PCR to create the final strand specific cDNA library. The quality of the libraries was verified by Tapestation (Agilent Technologies, Santa Clara, CA, USA). After quantitative PCR (qPCR) using KAPA SYBR FAST qPCR Master Mix (Kapa Biosystems, Wilmington, MA, USA), we combined libraries that index tagged in equimolar amounts in the pool.

treatment_protocol: 200 ug Poly(I:C) injection intra peritoneally

value: spleen

value: primary NK cells

value: innate lymphocytes

value: Poly (I:C)

tag: batch


title: LAG3- NK cells Day2 replicate 3

description:
Library name: Sample 5
Column name in tpm_matrix_LAG3_LAG3neg3


title: PSEN1_2_Cyto_ML240


title: wound_patient_1583


title: wound_patient_1567


title: wound_patient_1651


title: CD56+ NK Con_M

description: Library name: PBMC_2


title: PSEN1_1_Cyto_ML240


title: wound_patient_1565

value: no


title: VCP_2_Cyto_ML240


title: wound_patient_1560

value: male


title: LAG3+ NK cells Day2 replicate 2

description:
Library name: Sample 4
Column name in tpm_matrix_LAG3_LAG3pos2


title: LAG3- NK cells Day2 replicate 2

description:
Library name: Sample 3
Column name in tpm_matrix_LAG3_LAG3neg2


title: APP_2_Cyto_ML240

value: APP


title: wound_patient_1555

value: yes

value: female


title: APP_3_Cyto_ML240


title: LAG3+ NK cells Day2 replicate 1

description:
Library name: Sample 2
Column name in tpm_matrix_LAG3_LAG3pos1


title: wound_patient_1550


title: wound_patient_1531


title: APP_1_Cyto_ML240


title: wound_patient_1507


title: LAG3- NK cells Day2 replicate 1

description:
Library name: Sample 1
Column name in tpm_matrix_LAG3_LAG3neg1


title: wound_patient_1505


title: Ctrl_3_Cyto_ML240

value: WT


title: PG_HET_terminal

city: Taipei

first: Jian-Da

last: Lin

address: No. 1, Sec. 4, Roosevelt Rd., Da'an Dist.

department: Department of Biochemical Science & Technology

country: Taiwan

institute: National Taiwan University

description:
Library name: Sample8
10X Genomics

data_processing:
FASTQ files obtained from sequencing were processed using CellRanger (7.1.0) with default settings.
Demultiplexing of concatenated samples was performed using CellRanger
Raw gene expression matrices were read into R (version 4.3.2) separately and converted to Seurat objects using the Seurat R package (version 5.0.3).
Assembly: mm10
Supplementary files format and content: sv file

source_name: Intestine

extract_protocol:
Large intestine tissue was cut into 2 cm segments and placed in a 50 ml Falcon tube with 10 ml cold 1X HBSS, then shaken by hand and incubated in a bacterial shaker at 37°C and 225 rpm for 15 minutes to separate intraepithelial and lamina propria lymphocytes. The tissue was then transferred to a new tube containing EDTA-only mix and shaken under similar conditions. Next, the contents were moved to a tube with FACS buffer, gently mixed, and transferred to a 6-well plate for mincing. Digestion buffer was added, and the plate was shaken at 37°C until digestion was complete. The digested tissue was filtered, washed with FACS buffer, centrifuged to discard the supernatant, resuspended in FACS buffer, and finally transferred to FACS tubes for analysis. The collected cells were then stained with CD45  (Biolegend, Cat# 103122) and Live/Dead (L/D) Blue markers (Thermo Fisher, Cat# L34962), and the CD45-positive, L/D Blue-negative cells were sorted for single-cell library preparation.
Single cellswere processed through throgh the GemCode Single Cell Platform using the Chromium Next GEM Single cell 3' Kit v3.1 (10X Genonmics, Pleasanton) according to the manufacturer's protocol. In brief, Cell suspensions were loaded onto a Chromium Single-Cell Chip G along with the ereerse transcription (RT) master mix and single cell 3' gel beads. Following generation of single-cell gel bead-in-emulsions (GEMs), reverse transcription was performed using a Applied Biosystems™ Veriti™ 96-Well Thermal Cycler (Thermo Fisher Scientific, US). Amplified cDNA was purified using SPRIselect beads and converted to the sequencing library according to the manufacturer's protocol. Library was sesquenced on an Ilumina NovaSeq platform following read length: 150 bp Read 1 (16bp single cell barcode, 10x barcod; 12bp Unique molecular Identifier, UMI), 150 bp Read 2 (transcipt insert), 10 bp i7 Index (sample index), 10 bp i5 index (sample index)

value: Intestine

value: Immune cells


title: Ctrl_2_Cyto_ML240

value: neuron

value: ipsn


title: wound_patient_1479


title: wound_patient_1457


title: wound_patient_1453


title: VCP_3_Nulceus_ML240

value: VCP


title: wound_patient_1448


title: wound_patient_1559


title: wound_patient_1450


title: wound_patient_1429


title: wound_patient_1461


title: wound_patient_1458


title: wound_patient_1468


title: VCP_2_Nulceus_ML240


title: VCP_1_Nulceus_ML240


title: GF_NTG_terminal

description:
Library name: Sampe5
10X Genomics

value: FVB/NJ


title: wound_patient_1432


title: PG_HET_midterm

description:
Library name: Sample4
10X Genomics


title: wound_patient_1557


title: PSEN1_3_Nulceus_ML240


title: PG_NTG_terminal

description:
Library name: Sample6
10X Genomics


title: wound_patient_1423


title: GF_HET_midterm

description:
Library name: Sample3
10X Genomics


title: wound_patient_1428


title: wound_patient_1408


title: GF_HET_terminal

description:
Library name: Sample7
10X Genomics


title: wound_patient_1404


title: Ctrl_1_Cyto_ML240


title: PSEN1_2_Nulceus_ML240


title: PG_NTG_midterm

description:
Library name: Sample2
10X Genomics


title: GF_NTG_midterm

description:
Library name: Sample1
10X Genomics


title: PSEN1_1_Nulceus_ML240


title: wound_patient_1389


title: wound_patient_1395


title: SC19_ABCD1_KO-100 mg/kg_Animal39

city: Cambridge

first: Jeremy

last: Huang

address: 350 Water Street

department: Research

institute: Sanofi

description: Single-nuclei sequencing of ABCD1 -/y mouse spinal cord with 100mg/kg CPD37 (Elovl1 inhibitor) Treatment

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the CellRanger software v5.0.0
Paired-end sequencing was performed across 3 runs and four lanes and aggregation was performed in CellRanger
Assembly: mm10-2020-A_ARSA
Supplementary files format and content: Cell Ranger Feature Barcode Matrices

source_name: Spinal Cord

extract_protocol:
Tissue samples were stored at -80°C. For tissue lysis and washing of nuclei, sample sections were added to 1 mL Nuclei PURE lysis buffer (Sigma, NUC-201) and thawed on ice. Samples were then Dounce homogenized with PestleAx20 and PestleBx20 before transfer to a new tube, with the addition of additional lysis buffer. Following incubation on ice for 15 minutes, samples were then filtered using a 30 mM MACS strainer (Fisher, NC0642012), centrifuged at 500xg for 5 minutes at 4°C using a swinging bucket rotor (Sorvall Legend RT, Thermo Fisher), and then pellets were washed with an additional 1 mL cold lysis buffer and incubated on ice for an additional 5 minutes.
Library was performed according to the manufacture's instructions (single cell 3' v3.1 kit, 10x Genomics).
snRNA-seq

value: Spinal Cord

tag: animal

value: 100 mg/kg


title: wound_patient_1379


title: APP_3_Nulceus_ML240


title: wound_patient_1372


title: wound_patient_1374


title: SC16_WT-Vehicle_Animal4

description: Single-nuclei sequencing of WT mouse spinal cord with Vehicle Treatment

tag: tissue

value: Vehicle


title: wound_patient_1363


title: APP_2_Nulceus_ML240

tag: cell line


title: SC14_ABCD1_KO-100 mg/kg_Animal38


title: SC17_ABCD1_KO-Vehicle_Animal28

description: Single-nuclei sequencing of ABCD1 -/y mouse spinal cord with Vehicle Treatment


title: wound_patient_1343


title: wound_patient_1341


title: APP_1_Nulceus_ML240

tag: cell type


title: Ctrl_3_Nulceus_ML240

tag: genotype


title: SC12_ABCD1_KO-Vehicle_Animal27


title: wound_patient_1346


title: Ctrl_2_Nulceus_ML240


title: SC9_ABCD1_KO-100 mg/kg_Animal37


title: wound_patient_1327


title: Ctrl_1_Nulceus_ML240


title: wound_patient_1326


title: SC11_WT-Vehicle_Animal3


title: wound_patient_1320


title: wound_patient_1294


title: wound_patient_1299


title: wound_patient_1291


title: SC7_ABCD1_KO-Vehicle_Animal26


title: wound_patient_1286


title: VCP_2_Whole_ML240


title: wound_patient_1270


title: wound_patient_1267


title: SC2_ABCD1_KO-Vehicle_Animal25


title: wound_patient_1281


title: wound_patient_1331


title: wound_patient_1356


title: SC4_ABCD1_KO-100 mg/kg_Animal36


title: SC6_WT-Vehicle_Animal2


title: wound_patient_1231


title: wound_patient_1198


title: PSEN1_3_Whole_ML240


title: wound_patient_1232


title: VCP_1_Whole_ML240


title: PSEN1_1_Whole_ML240


title: wound_patient_1186


title: SC1_WT-Vehicle_Animal1


title: VCP_3_Whole_ML240


title: wound_patient_1182


title: B37_ABCD1_KO-Vehicle_Animal28

description: Single-nuclei sequencing of ABCD1 -/y mouse brain with Vehicle Treatment

source_name: Brain

value: Brain


title: B36_WT-Vehicle_Animal4

description: Single-nuclei sequencing of WT mouse brain with Vehicle Treatment


title: wound_patient_1150


title: APP_2_Whole_ML240


title: wound_patient_1196


title: wound_patient_1179


title: wound_patient_1168


title: APP_3_Whole_ML240


title: wound_patient_1151


title: wound_patient_1145


title: wound_patient_1130


title: PSEN1_2_Whole_ML240


title: B32_ABCD1_KO-Vehicle_Animal27


title: wound_patient_1139


title: Ctrl_3_Whole_ML240


title: B34_ABCD1_KO-100 mg/kg_Animal38

description: Single-nuclei sequencing of ABCD1 -/y mouse brain with 100mg/kg CPD37 (Elovl1 inhibitor) Treatment


title: wound_patient_1093


title: wound_patient_1118


title: wound_patient_1099


title: wound_patient_1107


title: wound_patient_1077


title: wound_patient_1082


title: Ctrl_2_Whole_ML240


title: B39_ABCD1_KO-100 mg/kg_Animal39


title: B31_WT-Vehicle_Animal3


title: APP_1_Whole_ML240


title: Ctrl_1_Whole_ML240


title: wound_patient_1064


title: VCP_3_Cyto

value: untreated


title: wound_patient_1057

value: no


title: B29_ABCD1_KO-100 mg/kg_Animal37


title: VCP_2_Cyto


title: B26_WT-Vehicle_Animal2


title: B27_ABCD1_KO-Vehicle_Animal26


title: wound_patient_1054


title: wound_patient_1043


title: VCP_1_Cyto


title: B24_ABCD1_KO-100 mg/kg_Animal36


title: PSEN1_3_Cyto


title: wound_patient_1041


title: wound_patient_1038


title: B22_ABCD1_KO-Vehicle_Animal25


title: wound_patient_1035


title: PSEN1_2_Cyto


title: wound_patient_1016


title: B21_WT-Vehicle_Animal1


title: Arch, scRNAseq

description: BD Rhapsody

data_processing:
FASTQ files obtained from sequencing were processed using the BD Rhapsody WTA Analysis Pipeline (version 1.11.1) with default settings, provided by Seven Bridges (https://www.sevenbridges.com/).
Demultiplexing of concatenated samples was performed using sample tag calls, with SampleTag01 assigned to WT sample and SampleTag02 assigned to Saa3KO sample.
Raw gene expression matrices were read into R (version 4.3.1) separately and converted to Seurat objects using the Seurat R package (version 4.3.0).
Assembly: mm10
Supplementary files format and content: matrix csv file

source_name: Arotic arch

extract_protocol:
To isolate aortic cells from mice, the procedure involved aorta perfusion using phosphate-buffered saline (PBS). After perfusion, the aortas were stored in FACS buffer. The enzymatic digestion processes involved immersing the aorta in a digestion buffer containing liberase (Roche, Cat# 54001127001), hyaluronidase (Sigma, Cat# H3506), and DNase I (Sigma, Cat# DN25) at specified concentrations, followed by fine mincing. The mixture was incubated at 37°C to facilitate effective digestion, with the process repeated multiple times to ensure complete tissue breakdown. After digestion, the mixture was filtered through a 35µm strainer to obtain a single-cell suspension. The collected cells were then stained with CD45 (Biolegend, Cat# 103122) and Live/Dead (L/D) Blue markers (Thermo Fisher, Cat# L34962), and the CD45-positive, L/D Blue-negative cells were sorted for single-cell library preparation.
Single-cell samples were labeled using the BD™ Mouse Immune Single-Cell Multiplexing Kit (Cat. 633793) for each cartridge run on the BD Rhapsody Express Single Cell Analysis System for single-cell capture, followed by cDNA synthesis with the BD Rhapsody cDNA Kit (Cat. 633773). The mRNA Whole Transcriptome Analysis (WTA) and Sample Tag libraries were prepared using the BD Rhapsody™ WTA Amplification Kit (Cat. 633801), according to the manufacturer's guidelines. The quality and quantity of the libraries were assessed using the Agilent 4200 TapeStation System with Agilent High Sensitivity D1000 ScreenTape (Agilent Technologies, Santa Clara, Cat. 5067-5584) and a Qubit Fluorometer with the Qubit dsDNA HS Assay (Invitrogen, MA, USA). Finally, the libraries were sequenced using the NovaSeq 6000 PE150 sequencer (Illumina, San Diego, CA).

value: Arotic arch

value: Aortic cells

value: FACS sorting (CD45+, Live/Dead-)


title: PSEN1_1_Cyto


title: wound_patient_1011

value: yes

value: male


title: wound_patient_1010

value: female


title: APP_3_Cyto

value: APP


title: LSK cells, Control mouse

city: Tianjin

first: Wenbing

last: Liu

address: No. 288 Nanjing Road

institute: Institute of Hematology and Blood Diseases Hospital

library_source: genomic

data_processing:
CUT&Tag reads were mapped to the mm10 reference genome using Bowtie 2 (v2.4.1).
The mapped reads were processed, including removing PCR duplicates (samtools v1.9) and sorting.
Bigwig files were made using the bam-Coverage function in deepTools.
Assembly: mm10
Supplementary files format and content: Bigwig
Library strategy: CUT&Tag

source_name: bone marrow

extract_protocol:
Cells were captured with Concanavalin A beads and incubated with anti-H3K27me3 antibody (# 9733, Cell Signaling Technology) at 4°C overnight. Mouse Anti-rabbit IgG secondary antibody was added the next day. Cells were then incubated with pA/G-Tnp for 1h and the DNA fragmentation was performed.
Libraries were constructed using Hyperactive Universal CUT&Tag Assay Kit for Illumina (#TD903, Vazyme) and TruePrep Index Kit V2 for Illumina (#TD202, Vazyme) according to the manufacturer’s protocol

value: bone marrow

value: LSK cells

tag: antibody

value: control


title: wound_patient_85

data_processing: The PLINK Input Report Plug-in extension for GenomeStudio was used to export and preasses PLINK files


title: wound_patient_1007


title: wound_patient_81


title: APP_1_Cyto

value: neuron

value: ipsn


title: APP_2_Cyto


title: wound_patient_82


title: LSK cells, Control mouse,rep5

data_processing:
Sequencing reads were mapped to mm10 using hisat2 (v2.0.5)
Read count extraction was performed using featureCounts (v1.5.0-p3)
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: LSK cells were maintained in DMEM with 2% FBS before and after cell sorting.

extract_protocol:
RNA was extracted using RNAiso Plus (Takara) following the manufacturer's protocol.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer's recommendations.

treatment_protocol: Poly[I:C] was injected at a dose of 5 mg/kg every other day for 4 times to the AML1/ETO mouse and control mouse. After 4 weeks, the mice were sacrificed and the Lin-Sca-1+c-Kit+ (LSK) cells were sorted for RNA-seq.

value: WT

tag: library type

value: mRNA


title: LSK cells, AML1/ETO mouse


title: Ctrl_3_Cyto


title: wound_patient_1044


title: wound_patient_76


title: wound_patient_75


title: LSK cells, Control mouse,rep4


title: Ctrl_2_Cyto


title: wound_patient_74


title: LSK cells, Control mouse,rep3


title: wound_patient_1008


title: wound_patient_68


title: LSK cells, Control mouse,rep2


title: wound_patient_71


title: wound_patient_66


title: Ctrl_1_Cyto


title: VCP_3_Nulceus

value: VCP


title: wound_patient_65


title: wound_patient_62


title: LSK cells, Control mouse,rep1


title: wound_patient_77


title: wound_patient_59


title: LSK cells, AML1/ETO mouse, rep2


title: wound_patient_61


title: VCP_1_Nulceus

value: untreated


title: wound_patient_67


title: VCP_2_Nulceus


title: LSK cells, AML1/ETO mouse, rep1


title: wound_patient_60

value: no


title: wound_patient_57


title: wound_patient_63


title: PSEN1_3_Nulceus


title: LSK cells, AML1/ETO mouse, rep3


title: PSEN1_2_Nulceus


title: LSK cells, Control mouse

data_processing:
Sequencing reads were mapped to the mm10 reference genome using Bowtie 2 (v2.4.1).
The mapped reads were processed, including removing PCR duplicates (samtools v1.9) and mitochondrial DNA.
Bigwig files were made using the bam-Coverage function in deepTools.
Assembly: mm10
Supplementary files format and content: Bigwig

extract_protocol:
Cells were lysed in ice-cold lysis buffer (10 mM Tris-HCl, pH 7.4; 10 mM NaCl; 3 mM MgCl2; 0.1% (v/v) Igepal CA-630) for 10 min on ice. The nuclei was washed and then centrifuged at 500 g for 10 min at 4℃.
Libraries were constructed using TruePrep DNA Library Prep Kit V2 for Illumina (#TD501, Vazyme) and TruePrep Index Kit V2 for Illumina (#TD202, Vazyme) according to the manufacturer's protocol.

treatment_protocol: Poly[I:C] was injected at a dose of 5 mg/kg every other day for 4 times to the AML1/ETO mouse and control mouse. After 4 weeks, the mice were sacrificed and the Lin-Sca-1+c-Kit+ (LSK) cells were sorted for ATAC-seq.

value: DNA


title: wound_patient_53

extract_protocol: DNA extraction from buccal swabs was completed using Gentra Puregene Buccal Kits (Qiagen, Gaithersburg, MD, USA), with overnight lysis at 55°C, inclusion of RNase A for RNA-free purified DNA, and a final elution in 50 μL molecular biology grade water (GE Healthcare Life Sciences MA, USA).


title: wound_patient_52


title: APP_3_Nulceus


title: wound_patient_56


title: wound_patient_55


title: APP_2_Nulceus


title: wound_patient_44


title: PSEN1_1_Nulceus


title: LSK cells, AML1/ETO mouse


title: wound_patient_42


title: wound_patient_50


title: wound_patient_41


title: P301S/CAG::Cre+/Nr1d1fl/fl (PS19/RKO)-4

city: St. Louis

first: Eric

last: Tycksen

state: Missouri

address: 4444 Forest Park Avenue

department: McDonnell Genome Institute

institute: Washington University in St. Louis School of Medicine

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.7.9a
Gene counts quantitated with Subread:featureCount 2.0.3 with CPM and RPKM transformations added with custom Rscripting.
Assembly: Ensembl GRCm38.101
Supplementary files format and content: Gene counts with CPM and RPKM in tab-delimitted text format

source_name: Hippocampus

extract_protocol:
Tissues were lyzed with Trisol and RNA was prepared using RNA prep kit (Invitrogen, PureLink RNA kit).
Takara Clontech SMARTer

value: Hippocampus


title: P301S/CAG::Cre+/Nr1d1fl/fl (PS19/RKO)-6


title: P301S/CAG::Cre+/Nr1d1fl/fl (PS19/RKO)-3


title: Ctrl_2_Nulceus


title: wound_patient_47


title: Ctrl_1_Nulceus


title: wound_patient_43


title: wound_patient_36


title: P301S/CAG::Cre+/Nr1d1fl/fl (PS19/RKO)-5


title: APP_1_Nulceus


title: wound_patient_40


title: P301S/CAG::Cre+/Nr1d1fl/fl (PS19/RKO)-2


title: wound_patient_38


title: wound_patient_35


title: wound_patient_34


title: P301S/CAG::Cre+/Nr1d1fl/fl (PS19/RKO)-1


title: wound_patient_31


title: wound_patient_48


title: VCP_1_Whole


title: wound_patient_29


title: wound_patient_26


title: wound_patient_25


title: wound_patient_28


title: P301S/CAG::Cre-/Nr1d1fl/fl (PS19)-4


title: P301S/CAG::Cre-/Nr1d1fl/fl (PS19)-2


title: wound_patient_27


title: Ctrl_3_Nulceus


title: P301S/CAG::Cre-/Nr1d1fl/fl (PS19)-1


title: wound_patient_19


title: PSEN1_1_Whole


title: PSEN1_3_Whole


title: CAG::Cre+/Nr1d1fl/fl (RKO)-4

value: Rev-erb[alpha] KO


title: wound_patient_24


title: wound_patient_23

value: yes


title: wound_patient_21

value: male


title: wound_patient_15


title: VCP_3_Whole


title: P301S/CAG::Cre-/Nr1d1fl/fl (PS19)-5


title: wound_patient_17

value: female


title: wound_patient_12


title: VCP_2_Whole


title: APP_3_Whole

value: APP


title: CAG::Cre+/Nr1d1fl/fl (RKO)-2


title: wound_patient_10


title: PSEN1_2_Whole


title: CAG::Cre+/Nr1d1fl/fl (RKO)-1


title: wound_patient_20


title: Ctrl_3_Whole


title: APP_2_Whole


title: wound_patient_14


title: wound_patient_13


title: P301S/CAG::Cre-/Nr1d1fl/fl (PS19)-3


title: CAG::Cre-/Nr1d1fl/fl (WT)-5


title: wound_patient_9


title: APP_1_Whole


title: wound_patient_5


title: wound_patient_3


title: wound_patient_6


title: Ctrl_1_Whole


title: wound_patient_7


title: wound_patient_2


title: agm09-dpi12

city: Galveston

first: Jacquelyn

last: Turcinovic

state: TX

address: Galveston National Laboratory, 301 University Blvd.

department: Microbiology and Immunology

institute: University of Texas Medical Branch

hyb_protocol: Overnight hybridization according to standard NanoString protocol

scan_protocol: Scanned and quantified via nCounter SPRINT profiler according to standard protocol

data_processing:
Raw RCC files were background-thresholded using the NSolver v4.0 default parameters to generate the sample matrix. Downstream normalization and differential expression analyses were performed via limma.
Background-thresholded mRNA counts

organism: Chlorocebus sabaeus

source_name: African green monkey, whole blood, 12 days postinfection

extract_protocol: Total RNA extracted from AVL spiked with carrier RNA via the QIAgen Viral RNA Kit

tag: nhp

tag: dpi

tag: outcome

value: Succumbed

tag: status

value: Late

tag: qcfilter

value: TRUE


title: CAG::Cre-/Nr1d1fl/fl (WT)-4


title: P12_PE_HiC

city: Amsterdam

first: Wilbert

last: Zwart

state: Noord-Holland

address: Plesmanlaan 121

department: Oncogenomics

institute: Netherlands Cancer Institute

description: NovaSeq6000 PE 61bp

data_processing:
Hi-C reads were  mapped with Open2C distiller-nextflow pipeline v0.3.3 (Abdennur et al., Bioinformatics 2009). Reads were mapped with bwa mem v0.7.17-r1188 (Li et al., Bioinformatics 2009) to the GRCh38/hg38 human reference genome.
Mapped reads were parsed and filtered with pairtools v0.3.064. Only reads with MAPQ>30 were considered for the Hi-C matrix generation.
Cool files were created by cooler v0.8.1165 and balanced via “balance” function with default parameters.
Assembly: hg38/GRCh38
Supplementary files format and content: .mcool, 1-2-5-10-20-50-100-200-500-1000-2000-5000kb resolution

source_name: Pleural Effusion

growth_protocol: Flash-frozen tissue

extract_protocol:
For each sample, a minimum of 10×50µM sections (tissue samples) or ~10×10e6 of cryopreserved cells (pleural effusions) were cross-linked, digested using using MboI (New England Biolabs), and Hi-C library preparation was performed as previously described (Rao et al., Cell 2014; Donaldson Collier, Nat Genet 2019).
Quality and quantification of the Hi-C libraries was assessed using the 2100 Bioanalyzer (Agilent, DNA 7500 kit). Biological replicates were pooled and subjected to sequencing using with paired-end setup using the sequencer indicated in the description field of each sample.

value: Pleural Effusion

tag: genome build

value: Tumor (Metastasis)

tag: restriction enzyme

value: MboI


title: CAG::Cre+/Nr1d1fl/fl (RKO)-3


title: agm09-dpi10

source_name: African green monkey, whole blood, 10 days postinfection


title: agm09-dpi07

source_name: African green monkey, whole blood, 7 days postinfection

value: Middle


title: P11_PE_HiC

description: NovaSeq6000 PE 61bp


title: agm09-dpi04

source_name: African green monkey, whole blood, 4 days postinfection

value: Early


title: agm09-dpi03

source_name: African green monkey, whole blood, 3 days postinfection


title: P10_PE_HiC

description: NovaSeq6000 PE 61bp


title: CAG::Cre-/Nr1d1fl/fl (WT)-1

value: WT


title: agm02-dpi14

source_name: African green monkey, whole blood, 14 days postinfection


title: agm09-dpi00

source_name: African green monkey, whole blood, 0 days postinfection

value: Baseline


title: 2_G1, choroid plexus

city: Bethesda

first: Teruhiko

last: Yoshida

state: Maryland

address: 10 Center Drive, 9N208

department: NIDDK - KDB

institute: National Institutes of Health

data_processing:
The analysis was performed with the Cell Ranger v6.1.2 software using the default parameters with premRNA analysis turned on.
The reference was built from mm10 reference genome and human APOL1 sequence added.
Assembly: mm10 and APOL1
Supplementary files format and content: tar.gz files contain filtered_feature_bc_matrix folder output from CellRanger Count

source_name: Choroid plexus

extract_protocol:
Mouse brain choroid plexus tissue samples were dissected under the microscope immediately after CO2 euthanasia. These tissues were snap-frozen on dry ice. Nuclei from the choroid plexus tissues from ApoE-KO and ApoE-KO/APOL1-G1 mice were prepared as follows. Snap-frozen choroid plexus tissues were lysed in EZlysis buffer (#NUC101-1KT, Sigma-Aldrich, St. Louis, MO) and homogenized 15 times using a loose Dounce homogenizer and 5 times in a tight pestle. After 5 min incubation, the homogenate was passed through a 40 µm filter (43-50040, PluriSelect, El Cajon, CA) and centrifuged at 500 g at 4°C for 5 min. The pellet was washed with EZlysis buffer and again centrifuged at 500g at 4°C for 5 min. The pellet was resuspended with Dulbecco’s phosphate-buffered saline (DPBS) with 1% FBS to make a final nuclear preparation for loading on to a 10x Chromium Chip G (10x Genomics, Pleasanton, CA) formation of gel beads in emulsion (GEM).
10x Genomics Chromium 3’ V3.1 mRNA-seq library protocol

value: Choroid plexus


title: P09_PE_HiC

description: NovaSeq6000 PE 61bp


title: Ctrl_2_Whole

source_name: neuron

value: neuron

value: ipsn

tag: treatment

value: untreated


title: agm02-dpi07


title: P04_PB_ERa

data_processing:
All ChIP-seq samples were processed using the SPACCa pipeline (available at https://github.com/sebastian-gregoricchio/SPACCa) using default parameters.
FASTQ reads were mapped to the reference genome Hg38/GRCh38, using the accelerated version of the Burrows-Wheeler Aligner (BWA-MEM2 v0.5.10)
Reads were filtered based on mapping quality (MAPQ ≥ 20), and duplicated reads were marked  (GATK/Picard).
Peaks were called using MACS2 using the corresponding input of each condition as background/control.
ChIP-seq signal was normalized to 1x coverage (RPGC, Reads Per Genomic Content) and averaged in bins of 10bp using deeptools bamCoverage tool.
Assembly: hg38/GRCh38
Supplementary files format and content: .narrowPeaks, MACS2 peaks
Supplementary files format and content: .bw, RPGC normalized bigWigs (10bp bins)

source_name: Primary Breast Cancer

extract_protocol:
Chromatin immunoprecipitation followed by sequencing (ChIP)-seq was performed as previously described (Schmidt, D. et al. Methods 48, 240–248 (2009). Per each ChIP, 50 µL of magnetic Protein A beads (10008D, Thermo Fisher Scientific) were conjugated to 5µg of ERa antibody (sc-542).
Illumina, Paired-End, 51bp

value: Primary Breast Cancer

value: Tumor

tag: chip antibody

value: sc-542 (Santa Cruz)


title: agm02-dpi10

value: Succumbed


title: 1_WT, choroid plexus

value: ApoE-KO


title: agm02-dpi04

value: TRUE


title: agm02-dpi03


title: P04_LM_ERa

source_name: Liver Metastasis

value: Liver Metastasis


title: R8_CCGTCC_L002

city: Omaha

first: Dhundy

last: Bastola

state: NE

address: 1110 S 67th Street

institute: University of Nebraska at Omaha

data_processing:
Reads were aligned to GRCm38 transcripts using hisat2 and hisat2 provided index files.
The 'featureCounts' tool from 'SubRead' package was used to summarize the read counts for each sample at each gene level
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file that includes feature count values for each replicate from each sample

source_name: colon,colitis-associated colon cancer

extract_protocol: RNA was harvested using a quick-RNA mini prep kit (Zymo Research). 1.3 ug of total RNA was used for the construction of sequencing libraries.

treatment_protocol: single dose of AOM (10 mg/Kg body weight) and 3 cycle of 2.5% DSS (w/v)

value: Colon

value: AOM-DSS


title: P04_PB_HiC

description: NextSeq500 PE 75bp

value: MboI


title: P03_PB_ERa


title: CAG::Cre-/Nr1d1fl/fl (WT)-3

value: Hippocampus


title: P04_LM_HiC

description: NextSeq500 PE 75bp

value: Tumor (Metastasis)


title: agm02-dpi00

value: Baseline


title: agm10-dpi14

value: Late


title: P03_LM_ERa


title: CAG::Cre-/Nr1d1fl/fl (WT)-2

value: WT


title: P03_PB_HiC

description: NextSeq500 PE 75bp


title: P02_RPB_ERa

source_name: Recurrence Primary Breast cancer

value: Recurrence Primary Breast cancer


title: agm10-dpi10


title: P03_LM_HiC

description: NextSeq500 PE 75bp


title: R5_CGATGT_L002


title: P02_PB_ERa


title: agm10-dpi07

value: Middle


title: R9_ATCACG_L002


title: agm10-dpi04

value: Early


title: P05_PB_HiC

description: NextSeq500 PE 75bp + PE 43bp

value: Primary Breast Cancer

value: Tumor


title: P02_LM_ERa

value: sc-542 (Santa Cruz)


title: P02_HB_HiC

description: NextSeq500 PE 75bp + PE 43bp

source_name: Healthy Breast

value: Healthy Breast

value: Healthy


title: P02_HB_ERa


title: R3_CTTGTA_L002

source_name: colon,Control

value: Control


title: P02_PB_HiC

description: NextSeq500 PE 75bp


title: P01_PB_ERa


title: P01_LM_HiC

description: NextSeq500 PE 75bp

value: Liver Metastasis


title: R7_CAGATC_L002

value: Colon

value: AOM-DSS


title: P01_PB_HiC

description: NextSeq500 PE 75bp

value: MboI


title: R2_GCCAAT_L002


title: R1_ACAGTG_L002


title: agm05-dpi11

source_name: African green monkey, whole blood, 11 days postinfection

value: Succumbed

value: TRUE


title: agm10-dpi00

value: Baseline


title: P01_LM_ERa

value: Tumor (Metastasis)


title: P01_HB_HiC

description: NextSeq500 PE 75bp + PE 43bp


title: agm05-dpi10

value: Late


title: R9_ATCACG_L001


title: R6_TGACCA_L002

value: WT


title: P01_HB_ERa


title: R8_CCGTCC_L001


title: agm05-dpi07

value: Middle


title: Non failing control 1

city: Goettingen

first: Tousif

last: Azmain

state: State...

address: Robert Koch Street 40

department: Cardiology and Pneumology

country: Germany

institute: Georg August University

data_processing:
CellRanger by 10XGenomics (standard protocol)
Assembly: grch38
Supplementary files format and content: fastq files for each sample
Supplementary files format and content: CellRanger software output files (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz) for each sample

source_name: Heart left ventricle

growth_protocol: Not applicable

extract_protocol:
Nuclei were processed following 10X Genomics provided protocol
cDNA library were prepared following 10X Genomics provided protocol

treatment_protocol: Biopsie tissues were minced to isolate single nuclei

value: Heart left ventricle

tag: subject status

value: Non failing control


title: agm10-dpi03

value: Early


title: agm05-dpi04


title: MelSTR RNA-seq sheIF2A 1

city: Barcelona

first: Neus

last: Mestre-Farràs

state: Barcelona

address: C/ Doctor AIguader 88

country: Spain

institute: CRG

data_processing:
First, technical replicates were merged.
For Ribo-seq data, reads were trimmed according to the indications from the manufacturer. First, the LACE-seq linker was trimmed from the 3’ with cutadapt v4.1 (Martin 2011). Then, the 5’ and 3’ UMIs were extracted with the function ‘extract’ from UMI-tools (Smith 2017) and finally, cutadapt was used again to cut the thymidine preceding the RPF.  Reads from ribosomal RNA were removed with ribodetector (Deng 2022) and the remaining reads were aligned to the genome hg38 reference with STAR (Dobin 2013) allowing a maximum of 2 mismatches and forcing end-to-end read alignment. Then, the function ‘dedup’ from UMI-tools (Smith 2017) was run to remove duplicated sequences. For gene-centered analysis, read counts were obtained with featureCounts (Liao 2014) taking only the reads aligned to the CDS (specified options -t CDS -g gene_id -O -J).
For RNA-seq data, sequencing adaptors were removed with TrimGalore (Krueger et al 2021), and then the reads were aligned to the genome hg38 reference with STAR (Dobin 2013) using ENCODE standard options. Read counts were obtained with featureCounts (Liao 2014) using the same option as for RPFs
Assembly: hg38
Supplementary files format and content: tab separated values. Each row contains a different gene. Raw counts, TMP and FPKM values are included.
Library strategy: Ribo-Seq

source_name: MelSTR

growth_protocol: cells were cultured in DMEM-Glutamax media (Gibco 31966021) supplemented with 7% FBS (Gibco 10270106) and 1% penicillin-streptomycin (Gibco 15070063) at 37°C and 5% CO2 and grown upon 80% confluency

extract_protocol:
Cells were lysed in ice-cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM MgCl2, 100 mM NaCl, 1 % Triton, 2 mM DTT, 0.25 % Deoxycholate, 100 μg/ml CHX) and cleared for 5 min at 12000 g.
For Ribo-seq, 6 A260 units were digested with 36 U RNAse1/unit (10 min, 22°C, 500 rpm) (Ambion, AM2294) and digestion was stopped by adding RNAsin. 10%-50% sucrose gradients were prepared by underlying 50% sucrose dissolved in polysome buffer 2.0 (20 mM Tris-HCl pH 7.5, 10 mM MgCl2, 100 mM NH4Cl, 0.1 mg/ml CHX) a 10% sucrose solution and mixed using a Gradient Master. Digested lysates were loaded onto the sucrose gradients and centrifuged for 3h at 35000 rpm 4°C in a Beckman SW41 rotor. Monosome peaks were collected and RNA extracted. Ribosome protected fragments (RPFs) were PAGE purified on a 15% TBE-Urea geal using PAGExt (Immagina, #KGE002) and library preparation from these fragments was prepared using LACESeq (Immagina, #LS-001) following the instructions of the manufacturer. RNA-Seq libraries were prepared from 1 ug of total RNA. PolyA-selection and library preparation for Illumina.

treatment_protocol: Cells were incubated 2 min in DMEM containing 0.1 mg/ml CHX

value: MelSTR

value: Ras transformed melanocytes


title: Aortic stenosis patient AS78

value: Aortic stenosis patient


title: MelSTR RNA-seq sheIF2A 2


title: R6_TGACCA_L001


title: agm05-dpi03


title: Aortic stenosis patient AS338


title: MelSTR RNA-seq shCntrl 3


title: agm05-dpi00


title: R5_CGATGT_L001


title: R4_GTGAAA_L001


title: MelSTR RNA-seq shCntrl 2


title: MelSTR RNA-seq shCntrl 1


title: Aortic stenosis patient AS325


title: R3_CTTGTA_L001

value: Control


title: agm06-dpi10

source_name: African green monkey, whole blood, 10 days postinfection


title: Aortic stenosis patient AS312


title: R2_GCCAAT_L001

value: Colon


title: Aortic stenosis patient AS241


title: MelST RNA-seq sheIF2A 3

source_name: MelST

value: MelST

value: Immortalized melanocytes


title: Aortic stenosis patient AS09


title: MelSTR RNA-seq sheIF2A 3


title: agm06-dpi07

source_name: African green monkey, whole blood, 7 days postinfection

value: Succumbed


title: R7_CAGATC_L001

value: AOM-DSS


title: R1_ACAGTG_L001


title: MelST RNA-seq sheIF2A 2


title: iPSC II.1-Cor, day42, CD45-

data_processing:
The FASTQ files were generated using FastQC (v0.11.7) and trimmed reads (Trimmomatic 0.38) were mapped to UCSC hg38 with HISAT2 (v2.1.0, Bowtie2 2.3.4.1), splice-aware aligner. The sequencing depth is between 58 and 80 million mappable reads. Transcript is assembled by StringTie (v2.1.3b) and abundance of genes are calculated as read counts and FPKM.
Assembly: USCS_hg38
Supplementary files format and content: txt file with count and RPKM

source_name: iPSC

growth_protocol: NK cell differentiation from iPSC was performed as described in Knorr et al. (27). Briefly, 9000 cells per well were plated on 96 well polystyrene round bottomed microwell plates (Fisher Scientific, 262162) for EB formation in APEL-2 media (StemCell Technologies, 5275) containing 10μM ROCK inhibitor, 40ng/ml SCF (Peprotech, 300-07), 20ng/ml BMP (R&D, 314-BP), 20ng/ml VEGF (R&D, 293-VE), and 1μM GSK inhibitor (CHIR99021; StemCell Technologies, 72052). EBs were cultured for six days. For autologous stroma supported differentiation, day 6 EBs were transferred to gelatin (Millipore, ES-006-B) coated 24 well plates (4EB/well; Fisher Scientific, 08-772-1C) with NK cell differentiation basal media supplemented with 5ng/ml IL-3 (1st week only; Peprotech, 200-03), 10ng/ml IL-15 (Peprotech, 200-15), 10ng/ml Flt3L (Peprotech, 300-19), 20ng/ml SCF, and 20ng/ml IL-7 (Peprotech, 200-07). NK cell differentiation basal media is made with 55% DMEM (Fisher Scientific, 11965118), 28% Hems F12 (Fisher Scientific, 10-080-CV), 15% human AB serum (GeminiBio, 100-512), 1% L-Glutamax (Fisher Scientific, 35050079), 1% Penicillin/streptomycin (100U/ml), 25μM BME (Fisher Scientific, 21985023), 50 μM Ethanolamine (Sigma, E0135-100ML), 25 μg/mL Ascorbic acid (Sigma, A5960-25G), and 5 ng/mL sodium selenite (Sigma, S5261-25G). After transfer, the cells from EB propagate and differentiate to NK cells in the 24 well plate for 35 days with weekly half media change.

extract_protocol:
2~10 X 10^4 cells were lysed, and RNA was collected with NucleoSpin RNA XS kit (Takara, 740902) according to the manufacturer’s protocol. RNA quality control was performed using the Agilent 2100 Bioanalyzer System.
Libraries were generated with SMARTer stranded RNA-Seq kit (Takara, 634839).

value: iPSC

value: GINS4 WT/WT

value: NK differentiation


title: agm06-dpi04

source_name: African green monkey, whole blood, 4 days postinfection

value: TRUE


title: agm06-dpi03

source_name: African green monkey, whole blood, 3 days postinfection


title: R4_GTGAAA_L002

value: WT


title: MelST RNA-seq sheIF2A 1


title: WT2_S2_L001

data_processing:
Reads were aligned to GRCm38 transcripts using hisat2 and hisat2 provided index files.
The 'featureCounts' tool from 'SubRead' package was used to summarize the read counts for each sample at each gene level
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file that includes feature count values for each replicate from each sample (allCount.tsv)


title: iPSC II.1-Cor, day42, CD45+


title: WT3_S3_L001


title: MelST RNA-seq shCntrl 3


title: agm06-dpi13

source_name: African green monkey, whole blood, 13 days postinfection

value: Late


title: agm06-dpi00

source_name: African green monkey, whole blood, 0 days postinfection

value: Baseline


title: iPSC C.1, day42, CD45-


title: WT1_S1_L001


title: MelST RNA-seq shCntrl 2


title: iPSC C.1, day42, CD45+


title: agm08-dpi12

source_name: African green monkey, whole blood, 12 days postinfection


title: iPSC II.2, day42, CD45-

value: GINS4 V171L/Q191X


title: Riz-19-61_S10_L001

source_name: colon, colitis-associated colon cancer

value: Claudin-2 knockout


title: MelST RNA-seq shCntrl 1


title: agm08-dpi10


title: agm08-dpi07

value: Middle


title: Riz-19-59_S9_L001


title: agm08-dpi04

value: Early


title: iPSC II.2, day42, CD45+


title: iPSC I.1, day42, CD45-

value: GINS4 Q191X/WT


title: MelSTR Ribo-seq sheIF2A 3

library_source: other

molecule: other

value: MelSTR

value: Ras transformed melanocytes


title: Riz-19-58_S8_L001

value: Colon


title: MelSTR Ribo-seq sheIF2A 2


title: MelSTR Ribo-seq sheIF2A 1


title: agm08-dpi03

value: Succumbed


title: Riz-19-57A_S11_L001

value: AOM-DSS


title: agm08-dpi00


title: agm01-dpi10


title: Riz-19-56_S7_L001


title: MelSTR Ribo-seq shCntrl 3


title: iPSC I.2, day42, CD45-

value: iPSC

value: GINS4 V171L/WT


title: iPSC I.2, day42, CD45+

value: NK differentiation


title: MelSTR Ribo-seq shCntrl 2


title: Riz-19-63_S12_L001


title: Riz-19-144_S15_L001

source_name: colon,mucosal repair/recovery

value: DSS-Recovery


title: iPSC II.1, day42, CD45-


title: MelSTR Ribo-seq shCntrl 1


title: Riz-19-143_S14_L001

value: WT


title: agm01-dpi07

value: TRUE


title: iPSC II.1, day42, CD45+


title: iPSC II.1-Cor, day21, CD45-

value: GINS4 WT/WT


title: MelST Ribo-seq sheIF2A 2

value: MelST

value: Immortalized melanocytes


title: Riz-19-137_S18_L001

value: Claudin-2 knockout


title: iPSC I.1, day42, CD45+


title: agm01-dpi04

value: Early


title: agm01-dpi00

value: Baseline


title: iPSC II.1-Cor, day21, CD45+


title: Riz-19-136_S17_L001


title: agm01-dpi03


title: iPSC C.1, day21, CD45-


title: MelST Ribo-seq shCntrl 3


title: agm03-dpi13

value: Late


title: MelST Ribo-seq sheIF2A 1


title: MelST Ribo-seq shCntrl 2


title: CI2KO-3_S6_L001

value: Control


title: agm03-dpi10


title: iPSC C.1, day21, CD45+


title: MelST Ribo-seq shCntrl 1


title: iPSC II.2, day21, CD45-

value: GINS4 V171L/Q191X


title: agm03-dpi07

value: Succumbed

value: Middle


title: agm03-dpi04


title: MelST Ribo-seq sheIF2A 3


title: MelSTR cells, anti-eIF2A 2

data_processing:
RNA-seq data was processed using the nf-core/rnaseq v3.10.1 Nextflow pipeline (Ewels PA et al. 2020, Patel, H. et al. 2020). Reads were mapped with STAR and RSEM was used to quantify read counts
Assembly: hg38
Supplementary files format and content: tab separated values. In "rsem.merged.gene_counts.tsv" all samples are merged: each row contains a different gene and each column a different sample.
Supplementary files format and content: tab separated values. In the genes.results, only data from one sample is included. Raw counts, FPKM and TPM quantification are included.

extract_protocol:
Cells were lysed in hypotonic gentle lysisbuffer (10 mM Tris-Hcl, 10 mM NaCL, 2 mM EDTA and 0.5% triton) and centrifuged for 10 min at maximum speed at 4°C. Supernatant was diluted in 1xNet buffer (50 mM Tris-Hcl, 150 mM NaCl, 0.1% NP40, 1 mM EDTA and RNAse inhibitor (Promega, #N2111) and incubated for 2h at 4°C on a wheel with 50 ul Dynabeads A previously coupled to 3 ug eIF2A or IgG antibody, respectively. Afterwards beads were washed 5 times with 500 ul 1xNet buffer. RNA was extracted from the remaining beads using Trizol. For input samples, RNA was directly extracted with Trizol after extract collection.
RNA immunoprecipitations (RIP) were performed under native conditions using an eIF2A antibody (abcam #ab169528), an IgG rabbit control antibody and Dynabeads A (invitrogen, #10002D).. Libraries were prepared with poly-A selection for 50bp Illumina sequencing

value: MelSTR

value: Ras transformed melanocytes


title: MelSTR cells, anti-eIF2A 3


title: Riz-19-140_S13_L001

value: Colon


title: CI2KO-2_S5_L001


title: iPSC II.2, day21, CD45+

value: iPSC

value: NK differentiation


title: Aged_5w_Sham_OB_5

city: Baltimore

first: Hangnoh

middle: Joseph

last: Lee

state: MD

address: 670 W Baltimore St

institute: University of Maryland School of Medicine

description: Library name: Aged_5w_Sham_OB_5

data_processing:
The sequencing company used CASAVA version 1.8.2 (Illumina, San Diego, CA) was for the base calling
We used STAR 2.7.5c (Dobin et al., 2013, PMID: 23104886) with the default parameters for alignment of the short reads to the reference genome.
We used the GENCODE mouse gene annotation, version M33, for alignment and quantification.
We used RSEM version 1.3.3 (PMID: 21816040) for the gene and RNA-isoform level quantifications.
Assembly: Mouse reference genome GRCm39 (Ensembl release 100)
Supplementary files format and content: These are tab-limited, gzipped text files that contain Ensembl gene IDs and gene expression levels in FPKM (fragments per kilobase of transcript per million mapped reads) and TPM (transcripts per million).

source_name: Olfactory Bulb

extract_protocol:
Following euthanasia 24 hours and 5 weeks after GA/OP, mice were perfused with 50 mL of ice-cold saline. Total RNA was isolated from the OB and hippocampus (HI) of both sham and GA/OP mice using a miRNeasy isolation kit (Cat# 217084, Qiagen). In brief, approximately 600ul of Buffer RLT were added to each sample and disrupted in a Precellys 24 Touch homogenizer. The aqueous phase containing RNA was collected, mixed with ethanol, and applied to a silica membrane spin column. After a series of washes to remove contaminants, RNA was eluted in RNase-free water. A minimum of 100ng was sent to the University of Maryland Institute for Genome Sciences and Novogene for downstream sequencing assays.
Library preparations were performed by the University of Maryland Institute for Genome Sciences (Baltimore, MD) and Novogene (Sacramento, CA) for sequencing on the Illumina platform (paired-end, 150 bp). mRNA was enriched using poly-A pulldown

value: Olfactory Bulb

tag: developmental stage

value: Adult

tag: age

value: 18 to 25 months

tag: Sex

value: male

tag: strain

value: Sham

tag: time point

value: 5 weeks after General Anesthesia and Operation

tag: biological replicate


title: CI2KO-1_S4_L001

tag: tissue

tag: genotype

value: Claudin-2 knockout


title: agm03-dpi03

tag: nhp

tag: dpi

value: Early

value: TRUE


title: agm03-dpi00

tag: outcome

tag: status

value: Baseline


title: iPSC I.1, day21, CD45+

tag: cell line

tag: cell type

value: GINS4 Q191X/WT


title: Aged_5w_Sham_OB_4

description: Library name: Aged_5w_Sham_OB_4

tag: treatment


title: MelST cells, anti-eIF2A 3

value: MelST

value: Immortalized melanocytes


title: MelSTR cells, anti-eIF2A 1

value: MelSTR

value: Ras transformed melanocytes


title: agm04-dpi29

source_name: African green monkey, whole blood, 29 days postinfection

value: Succumbed

value: Late

tag: qcfilter

value: FALSE


title: Riz-19-134_S16_L001

value: Colon

value: DSS-Recovery


title: MelST cells, anti-eIF2A 2


title: Aged_5w_Sham_OB_3

description: Library name: Aged_5w_Sham_OB_3

value: Olfactory Bulb

value: Adult

value: 18 to 25 months

value: male


title: agm04-dpi28

source_name: African green monkey, whole blood, 28 days postinfection

value: Recovered


title: Aged_5w_Sham_OB_2

description: Library name: Aged_5w_Sham_OB_2

value: Sham

value: 5 weeks after General Anesthesia and Operation


title: iPSC II.1, day21, CD45-

value: iPSC

value: GINS4 V171L/Q191X

value: NK differentiation


title: agm04-dpi21

source_name: African green monkey, whole blood, 21 days postinfection


title: iPSC I.2, day21, CD45+

value: GINS4 V171L/WT


title: Aged_5w_Sham_OB_1

description: Library name: Aged_5w_Sham_OB_1


title: MelST cells, anti-eIF2A 1

value: MelST

value: Immortalized melanocytes


title: MelSTR cells, input control 3

value: MelSTR

value: Ras transformed melanocytes


title: iPSC I.1, day21, CD45-

value: GINS4 Q191X/WT


title: agm04-dpi14

source_name: African green monkey, whole blood, 14 days postinfection

value: Succumbed

value: FALSE


title: iPSC II.1-Cor, day14, CD45-

value: GINS4 WT/WT


title: MelSTR cells, input control 2

source_name: MelSTR


title: Aged_5w_Sham_Hi_5

description: Library name: Aged_5w_Sham_Hi_5

source_name: Hippocampus

value: Hippocampus

value: Adult

value: 18 to 25 months


title: agm04-dpi10

source_name: African green monkey, whole blood, 10 days postinfection

value: Late


title: Aged_5w_Sham_Hi_4

description: Library name: Aged_5w_Sham_Hi_4

value: male

value: Sham

value: 5 weeks after General Anesthesia and Operation


title: iPSC II.1, day21, CD45+

value: iPSC

value: GINS4 V171L/Q191X

value: NK differentiation


title: agm04-dpi07

source_name: African green monkey, whole blood, 7 days postinfection

value: Middle


title: iPSC II.1-Cor, day14, CD45+

source_name: iPSC


title: iPSC I.2, day21, CD45-

value: GINS4 V171L/WT


title: Aged_5w_Sham_Hi_3

description: Library name: Aged_5w_Sham_Hi_3


title: MelSTR cells, input control 1

value: MelSTR

value: Ras transformed melanocytes


title: iPSC C.1, day14, CD45-


title: MelST cells, input control 3

source_name: MelST

value: MelST

value: Immortalized melanocytes


title: agm04-dpi03

source_name: African green monkey, whole blood, 3 days postinfection

value: Succumbed

value: Early

value: FALSE


title: agm04-dpi04

source_name: African green monkey, whole blood, 4 days postinfection