title: NR3_melanoma

status: Public on Aug 31 2025

type: SRA

city: Zurich

first: Richard

last: Chahwan

address: Winterthurerstrasse 190

department: Institute of Experimental Immunology

country: Switzerland

institute: University of Zurich

description:
Processed data_Melanoma EVs readcounts.txt
HG18.1201_Melanoma_NTLS

library_source: transcriptomic

data_processing:
BGI GENOMICS
HISAT to align the clean reads to the reference genome
Bowtie2 to align the clean reads to the reference genes
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: tab-delimited text file includign TPM values or readcounts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: slow-frozen patient biopsies

extract_protocol:
total RNA was isolated with RNeasy Mini Kit (qiagen)
Library preparation and sequencing was done with DNBSEQ™ platform (BGI Genomics)

tag: tissue

value: slow-frozen patient biopsies

tag: cell line

value: Patient 11


title: NR2_melanoma

description:
Processed data_Melanoma EVs readcounts.txt
Hg18_3693_Mel

value: Patient 10


title: NR4_melanoma

description:
Processed data_Melanoma EVs readcounts.txt
HG18.924_TLS_3_Mel

value: Patient 12


title: R8_melanoma

description:
Processed data_Melanoma EVs readcounts.txt
Hg20_6327_Mel

value: Patient 8


title: R7_melanoma

description:
Processed data_Melanoma EVs readcounts.txt
Hg20_452_Mel

value: Patient 7


title: R6_melanoma

description:
Processed data_Melanoma EVs readcounts.txt
Hg19_4576_Mel

value: Patient 6


title: R5_melanoma

description:
Processed data_Melanoma EVs readcounts.txt
Hg19_1_Mel

value: Patient 5


title: NR1_melanoma

description:
Processed data_Melanoma EVs readcounts.txt
Hg17_3442_Mel

value: Patient 9


title: NR5_melanoma

description:
Processed data_Melanoma EVs readcounts.txt
Hg19_699_Mel

value: Patient 13


title: R4_melanoma

description:
Processed data_Melanoma EVs readcounts.txt
Hg18_2387_Mel

value: Patient 4


title: NR4_CD19

description:
Processed data_CD19  EVs readcounts.txt
HG18.924_TLS_3_CD19


title: R3_melanoma

description:
Processed data_Melanoma EVs readcounts.txt
Hg17_2590_Mel

value: Patient 3


title: NR5_CD19

description:
Processed data_CD19  EVs readcounts.txt
Hg19_699_CD19


title: NR3_CD19

description:
Processed data_CD19  EVs readcounts.txt
HG18.1201_CD19_NTLS


title: R2_melanoma

description:
Processed data_Melanoma EVs readcounts.txt
Hg16_884_Mel

value: Patient 2


title: NR2_CD19

description:
Processed data_CD19  EVs readcounts.txt
Hg18_3693_CD19


title: NR1_CD19

description:
Processed data_CD19  EVs readcounts.txt
Hg17_3442_CD19


title: R8_CD19

description:
Processed data_CD19  EVs readcounts.txt
Hg20_6327_CD19


title: R6_CD19

description:
Processed data_CD19  EVs readcounts.txt
Hg19_4576_CD19


title: R7_CD19

description:
Processed data_CD19  EVs readcounts.txt
Hg20_452_CD19


title: R5_CD19

description:
Processed data_CD19  EVs readcounts.txt
Hg19_1_CD19


title: R3_CD19

description:
Processed data_CD19  EVs readcounts.txt
Hg17_2590_CD19


title: R4_CD19

description:
Processed data_CD19  EVs readcounts.txt
Hg18_2387_CD19


title: R2_CD19

description:
Processed data_CD19  EVs readcounts.txt
Hg16_884_CD19


title: D02_neg_pull

description:
Processed data_pulldown seq TPM.txt
D02_neg_pull TPM

source_name: PBMCs

value: PBMCs

value: Donor 2

tag: cell type

value: B cells

tag: treatment

value: negative control antagomir


title: D05_neg_pull

description:
Processed data_pulldown seq TPM.txt
D05_neg_pull TPM

value: Donor 5


title: D05_mimic99_pull

description:
Processed data_pulldown seq TPM.txt
D05_mimic99_pull TPM

value: miR99a-5p-biotin mimic


title: R1_CD19

description:
Processed data_CD19  EVs readcounts.txt
Hg16_1263_CD19

value: slow-frozen patient biopsies

value: Patient 1


title: D02_mimic99_pull

description:
Processed data_pulldown seq TPM.txt
D02_mimic99_pull TPM


title: D01_neg_pull

description:
Processed data_pulldown seq TPM.txt
D01_neg_pull TPM

value: Donor 1


title: R1_melanoma

description:
Processed data_Melanoma EVs readcounts.txt
Hg16_1263_Mel


title: D06_T_neg

description:
processed data_antg seq TPM.txt
D06_T_neg TPM

value: Donor 6

value: T cells


title: D01_mimic99_pull

description:
Processed data_pulldown seq TPM.txt
D01_mimic99_pull TPM


title: D05_T_antg99

description:
processed data_antg seq TPM.txt
D05_T_antg99 TPM

value: antagomir against miR99a-5p


title: D06_T_antg99

description:
processed data_antg seq TPM.txt
D06_T_antg99 TPM


title: D06_B_neg

description:
processed data_antg seq TPM.txt
D06_B_neg TPM


title: D06_B_antg99

description:
processed data_antg seq TPM.txt
D06_B_antg99 TPM


title: D05_B_neg

description:
processed data_antg seq TPM.txt
D05_B_neg TPM


title: D05_T_neg

description:
processed data_antg seq TPM.txt
D05_T_neg TPM


title: D05_B_antg99

description:
processed data_antg seq TPM.txt
D05_B_antg99 TPM


title: D02_T_neg

description:
processed data_antg seq TPM.txt
D02_T_neg TPM


title: D02_B_neg

description:
processed data_antg seq TPM.txt
D02_B_neg TPM


title: D02_T_antg99

description:
processed data_antg seq TPM.txt
D02_T_antg99 TPM


title: D01_T_neg

description:
processed data_antg seq TPM.txt
D01_T_neg TPM


title: D02_B_antg99

description:
processed data_antg seq TPM.txt
D02_B_antg99 TPM


title: D01_T_antg99

description:
processed data_antg seq TPM.txt
D01_T_antg99 TPM


title: D01_B_antg99

description:
processed data_antg seq TPM.txt
D01_B_antg99 TPM


title: tph_3_CAM787_1

city: Haifa

first: Nabeel

middle: S.

last: Ganem

address: Stern lab, Faculty of Biology, Technion City, Haifa 3200003, Israel.

department: Biology

country: Israel

institute: Technion - Israel Institute of Technology

description: Library name: tph_3_CAM787_1

data_processing:
Data was generated using Illumina NextSeq platforms: either NextSeq 550 with the High Output Kit v2.5 (75 cycles) or NextSeq 2000 with the P2 100 cycles kit, both with sequencing parameters of Read1-36, Index1-8, Index2-8, and Read2-37.
Assembly: The obtained sequencing read fragments were aligned to the WBPS16 using the STAR aligner  (Dobin et al., 2013) v2.7.9a. Expression levels of single gene were normalized by gene mapped counts per million total reads (RPM).
Supplementary files format and content: text  files for both strains including all samples and time for each sample and RPM value for each gene

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: Single individual

growth_protocol: C. elegans woms (wild-type N2 and tph-1 mutant) were cultured on NGM agar with OP50 E. coli following standard protocols (Brenner, 1974). For behavioral imaging, eggs obtained by bleaching were placed individually in 10 mm circular arenas on custom multi-well plates containing NGM agar with UV-killed OP50 to prevent bacterial growth during experiments (Stern et al., 2017).

extract_protocol:
Fresh working lysis buffer is prepared daily by mixing a stable lysis buffer stock (made of Tris-HCl, Triton-X, Tween-20, EDTA, and water), Proteinase K, and RNase inhibitor. Worms were collected individually, and cut with a needle if larval. After adding lysis buffer, samples are mixed, centrifuged, and incubated in a thermocycler at 65 °C for 10 min, 85 °C for 1 min, then 4 °C before cooling on ice.
Library preparation for each single individual was according to the Illumina Nextera tagmentation protocol (Illumina), with DNA input and reagents adjusted for 20 ng of cDNA. The tagmented DNA was cleaned, and PCR amplification was performed. PCR primers were removed using Ampure XP beads.

treatment_protocol: After the behavioral experiment, each individual was pipetted in 2 μl UltraPure  water onto the side wall of a 0.2 ml PCR tube containing 2 μl Lysis buffer. The tube was laid on its side under a ZEISS Stemi 508 dissecting microscope, and the worm was cut into several fragments with a sterile 25 G 1.5-inch needle, spun down, shock-frozen in liquid nitrogen, and stored at −80 °C until use

value: Single individual

tag: developmental stage

tag: strain

tag: genotype

value: tph-1(mg280) II

tag: time (min_in_l4_stage)


title: tph_2_CAM795_5

description: Library name: tph_2_CAM795_5


title: tph_3_CAM791_2

description: Library name: tph_3_CAM791_2


title: tph_3_CAM788_4

description: Library name: tph_3_CAM788_4


title: tph_3_CAM796_6

description: Library name: tph_3_CAM796_6


title: tph_1_CAM795_2

description: Library name: tph_1_CAM795_2


title: tph_3_CAM788_5

description: Library name: tph_3_CAM788_5


title: tph_3_CAM791_6

description: Library name: tph_3_CAM791_6


title: tph_2_CAM241_3

description: Library name: tph_2_CAM241_3


title: tph_3_CAM791_3

description: Library name: tph_3_CAM791_3


title: tph_3_CAM040_6

description: Library name: tph_3_CAM040_6


title: tph_2_CAM245_4

description: Library name: tph_2_CAM245_4


title: tph_2_CAM788_5

description: Library name: tph_2_CAM788_5


title: tph_2_CAM796_4

description: Library name: tph_2_CAM796_4


title: tph_2_CAM787_2

description: Library name: tph_2_CAM787_2


title: tph_2_CAM795_6

description: Library name: tph_2_CAM795_6


title: tph_2_CAM795_2

description: Library name: tph_2_CAM795_2


title: tph_2_CAM236_1

description: Library name: tph_2_CAM236_1


title: tph_3_CAM787_2

description: Library name: tph_3_CAM787_2


title: D01_B_neg

description:
processed data_antg seq TPM.txt
D01_B_neg TPM


title: tph_3_CAM040_4

description: Library name: tph_3_CAM040_4


title: tph_4_CAM231_2

description: Library name: tph_4_CAM231_2


title: tph_2_CAM796_3

description: Library name: tph_2_CAM796_3


title: tph_3_CAM795_1

description: Library name: tph_3_CAM795_1


title: tph_2_CAM228_5

description: Library name: tph_2_CAM228_5


title: tph_3_CAM795_4

description: Library name: tph_3_CAM795_4


title: tph_3_CAM791_5

description: Library name: tph_3_CAM791_5


title: tph_3_CAM231_2

description: Library name: tph_3_CAM231_2


title: tph_3_CAM795_6

description: Library name: tph_3_CAM795_6


title: tph_2_CAM796_6

description: Library name: tph_2_CAM796_6


title: tph_2_CAM245_5

description: Library name: tph_2_CAM245_5


title: tph_1_CAM787_2

description: Library name: tph_1_CAM787_2


title: tph_2_CAM796_1

description: Library name: tph_2_CAM796_1


title: tph_2_CAM228_4

description: Library name: tph_2_CAM228_4


title: tph_2_CAM796_2

description: Library name: tph_2_CAM796_2


title: tph_1_CAM231_2

description: Library name: tph_1_CAM231_2


title: tph_1_CAM245_1

description: Library name: tph_1_CAM245_1


title: tph_2_CAM228_6

description: Library name: tph_2_CAM228_6


title: tph_2_CAM787_6

description: Library name: tph_2_CAM787_6


title: tph_2_CAM795_1

description: Library name: tph_2_CAM795_1


title: tph_2_CAM229_6

description: Library name: tph_2_CAM229_6


title: tph_1_CAM245_2

description: Library name: tph_1_CAM245_2


title: tph_2_CAM241_2

description: Library name: tph_2_CAM241_2


title: tph_1_CAM796_3

description: Library name: tph_1_CAM796_3


title: tph_3_CAM040_2

description: Library name: tph_3_CAM040_2


title: tph_1_CAM228_4

description: Library name: tph_1_CAM228_4


title: tph_1_CAM791_3

description: Library name: tph_1_CAM791_3


title: tph_2_CAM787_1

description: Library name: tph_2_CAM787_1


title: tph_1_CAM788_4

description: Library name: tph_1_CAM788_4


title: tph_2_CAM228_1

description: Library name: tph_2_CAM228_1


title: tph_3_CAM788_3

description: Library name: tph_3_CAM788_3


title: tph_2_CAM245_3

description: Library name: tph_2_CAM245_3


title: tph_1_CAM795_6

description: Library name: tph_1_CAM795_6


title: tph_1_CAM231_3

description: Library name: tph_1_CAM231_3


title: tph_4_CAM231_4

description: Library name: tph_4_CAM231_4


title: tph_3_CAM040_1

description: Library name: tph_3_CAM040_1


title: tph_1_CAM228_5

description: Library name: tph_1_CAM228_5


title: tph_1_CAM228_2

description: Library name: tph_1_CAM228_2


title: tph_1_CAM040_5

description: Library name: tph_1_CAM040_5


title: tph_2_CAM236_3

description: Library name: tph_2_CAM236_3


title: tph_3_CAM229_4

description: Library name: tph_3_CAM229_4


title: tph_1_CAM787_1

description: Library name: tph_1_CAM787_1


title: tph_3_CAM229_5

description: Library name: tph_3_CAM229_5


title: tph_1_CAM787_5

description: Library name: tph_1_CAM787_5


title: tph_1_CAM796_5

description: Library name: tph_1_CAM796_5


title: tph_2_CAM795_4

description: Library name: tph_2_CAM795_4


title: tph_2_CAM788_1

description: Library name: tph_2_CAM788_1


title: tph_1_CAM228_6

description: Library name: tph_1_CAM228_6


title: tph_1_CAM040_2

description: Library name: tph_1_CAM040_2


title: tph_1_CAM788_5

description: Library name: tph_1_CAM788_5


title: tph_3_CAM245_5

description: Library name: tph_3_CAM245_5


title: tph_2_CAM229_4

description: Library name: tph_2_CAM229_4


title: tph_1_CAM796_2

description: Library name: tph_1_CAM796_2


title: tph_3_CAM241_6

description: Library name: tph_3_CAM241_6


title: tph_1_CAM788_6

description: Library name: tph_1_CAM788_6


title: tph_1_CAM231_4

description: Library name: tph_1_CAM231_4


title: tph_1_CAM228_1

description: Library name: tph_1_CAM228_1


title: tph_1_CAM787_4

description: Library name: tph_1_CAM787_4


title: tph_1_CAM231_5

description: Library name: tph_1_CAM231_5


title: tph_1_CAM040_4

description: Library name: tph_1_CAM040_4


title: tph_3_CAM229_2

description: Library name: tph_3_CAM229_2


title: tph_2_CAM229_1

description: Library name: tph_2_CAM229_1


title: tph_1_CAM787_6

description: Library name: tph_1_CAM787_6


title: tph_3_CAM245_4

description: Library name: tph_3_CAM245_4


title: tph_2_CAM236_5

description: Library name: tph_2_CAM236_5


title: tph_1_CAM228_3

description: Library name: tph_1_CAM228_3


title: tph_4_CAM245_6

description: Library name: tph_4_CAM245_6


title: tph_2_CAM040_3

description: Library name: tph_2_CAM040_3


title: tph_3_CAM245_3

description: Library name: tph_3_CAM245_3


title: tph_1_CAM788_2

description: Library name: tph_1_CAM788_2


title: tph_1_CAM236_4

description: Library name: tph_1_CAM236_4


title: tph_1_CAM229_3

description: Library name: tph_1_CAM229_3


title: tph_1_CAM791_5

description: Library name: tph_1_CAM791_5


title: tph_1_CAM231_6

description: Library name: tph_1_CAM231_6


title: tph_3_CAM241_5

description: Library name: tph_3_CAM241_5


title: tph_1_CAM791_1

description: Library name: tph_1_CAM791_1


title: tph_1_CAM245_4

description: Library name: tph_1_CAM245_4


title: tph_4_CAM229_5

description: Library name: tph_4_CAM229_5


title: tph_2_CAM245_2

description: Library name: tph_2_CAM245_2


title: tph_1_CAM236_1

description: Library name: tph_1_CAM236_1


title: tph_2_CAM040_6

description: Library name: tph_2_CAM040_6


title: tph_4_CAM231_1

description: Library name: tph_4_CAM231_1


title: tph_4_CAM245_1

description: Library name: tph_4_CAM245_1


title: tph_1_CAM795_5

description: Library name: tph_1_CAM795_5


title: tph_3_CAM236_3

description: Library name: tph_3_CAM236_3


title: tph_4_CAM796_5

description: Library name: tph_4_CAM796_5


title: tph_2_CAM791_3

description: Library name: tph_2_CAM791_3


title: tph_1_CAM241_6

description: Library name: tph_1_CAM241_6


title: tph_4_CAM796_1

description: Library name: tph_4_CAM796_1


title: tph_1_CAM791_2

description: Library name: tph_1_CAM791_2


title: tph_1_CAM796_4

description: Library name: tph_1_CAM796_4


title: tph_1_CAM231_1

description: Library name: tph_1_CAM231_1


title: tph_1_CAM229_2

description: Library name: tph_1_CAM229_2


title: tph_3_CAM241_1

description: Library name: tph_3_CAM241_1


title: tph_1_CAM229_6

description: Library name: tph_1_CAM229_6


title: tph_1_CAM229_4

description: Library name: tph_1_CAM229_4


title: tph_1_CAM229_5

description: Library name: tph_1_CAM229_5


title: tph_1_CAM795_4

description: Library name: tph_1_CAM795_4


title: tph_3_CAM245_1

description: Library name: tph_3_CAM245_1


title: tph_3_CAM229_1

description: Library name: tph_3_CAM229_1


title: tph_3_CAM231_5

description: Library name: tph_3_CAM231_5


title: tph_4_CAM787_5

description: Library name: tph_4_CAM787_5


title: tph_1_CAM795_1

description: Library name: tph_1_CAM795_1


title: tph_2_CAM788_6

description: Library name: tph_2_CAM788_6


title: tph_4_CAM795_1

description: Library name: tph_4_CAM795_1


title: tph_4_CAM787_2

description: Library name: tph_4_CAM787_2


title: tph_3_CAM229_3

description: Library name: tph_3_CAM229_3


title: tph_1_CAM236_3

description: Library name: tph_1_CAM236_3


title: tph_4_CAM229_3

description: Library name: tph_4_CAM229_3


title: tph_2_CAM040_2

description: Library name: tph_2_CAM040_2


title: tph_4_CAM791_5

description: Library name: tph_4_CAM791_5


title: tph_4_CAM791_3

description: Library name: tph_4_CAM791_3


title: tph_4_CAM795_2

description: Library name: tph_4_CAM795_2


title: tph_3_CAM229_6

description: Library name: tph_3_CAM229_6


title: tph_1_CAM040_3

description: Library name: tph_1_CAM040_3


title: tph_4_CAM241_3

description: Library name: tph_4_CAM241_3


title: tph_4_CAM795_6

description: Library name: tph_4_CAM795_6


title: tph_1_CAM236_5

description: Library name: tph_1_CAM236_5


title: tph_4_CAM228_1

description: Library name: tph_4_CAM228_1


title: tph_3_CAM245_6

description: Library name: tph_3_CAM245_6


title: tph_4_CAM791_4

description: Library name: tph_4_CAM791_4


title: tph_3_CAM236_2

description: Library name: tph_3_CAM236_2


title: tph_3_CAM236_4

description: Library name: tph_3_CAM236_4


title: tph_4_CAM796_6

description: Library name: tph_4_CAM796_6


title: tph_4_CAM245_4

description: Library name: tph_4_CAM245_4


title: tph_4_CAM229_6

description: Library name: tph_4_CAM229_6


title: tph_4_CAM040_6

description: Library name: tph_4_CAM040_6


title: tph_4_CAM245_3

description: Library name: tph_4_CAM245_3


title: tph_4_CAM231_5

description: Library name: tph_4_CAM231_5


title: tph_1_CAM236_6

description: Library name: tph_1_CAM236_6


title: tph_1_CAM791_6

description: Library name: tph_1_CAM791_6


title: tph_4_CAM236_4

description: Library name: tph_4_CAM236_4


title: tph_1_CAM040_1

description: Library name: tph_1_CAM040_1


title: tph_4_CAM795_5

description: Library name: tph_4_CAM795_5


title: tph_4_CAM040_5

description: Library name: tph_4_CAM040_5


title: tph_4_CAM788_4

description: Library name: tph_4_CAM788_4


title: tph_4_CAM236_2

description: Library name: tph_4_CAM236_2


title: tph_4_CAM228_4

description: Library name: tph_4_CAM228_4


title: tph_4_CAM796_3

description: Library name: tph_4_CAM796_3


title: tph_4_CAM796_4

description: Library name: tph_4_CAM796_4


title: tph_4_CAM791_2

description: Library name: tph_4_CAM791_2


title: COH-B6-1

type: RNA

city: Taipei

first: Linda

last: Yu

address: 1 Jen-Ai Rd. Sec. 1

country: Taiwan

institute: National Taiwan University

description: RMA expression difference analysis by Transcriptome Analysis Console (TAC) software

hyb_protocol: Samples were hybridized with probes of Clariom™ S Assay, mouse Arrays (Affymetrix) and scanned using a gene microarray device (Affymetrix).

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed with  background correction and normalization (Affymetrix).  Data analysis by Transcriptome Analysis Console (TAC) 4.0.

label: biotin

organism: Mus musculus

source_name: Co-housed

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT Amplification  Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Wild-type B6 mice cohousing with MLCKtg mice for four weeks

extract_protocol: Colonic mucosal RNA was isolated using the RNeasy Mini Kit (Qiagen).

value: Wild-type

tag: gender

value: male

value: colonic mucosa


title: COH-B6-2


title: COH-B6-3


title: tph_4_CAM228_6

description: Library name: tph_4_CAM228_6


title: tph_4_CAM245_2

description: Library name: tph_4_CAM245_2


title: SIN-B6-3

source_name: Single-housed


title: DI_rep2

city: STANFORD

first: Jin

middle: Billy

last: Li

state: CA

address: 300 Pasteur Dr.

department: Genetics

country: USA

institute: Stanford University

description:
deaminase inactive without MDA5
DIwoMDA5_rep2

data_processing:
Raw sequencing reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using trim_galore 0.6.4
Preprocessed reads were then mapped to the reference genome (hg38) using STAR v2.5.2a with default parameters for paired-end mapping.
We then extracted reads mapped to the transcriptome from the STAR genome mapping data based on transcripts defined by GENCODE Release 34 and then used RSEM v1.3.2 to quantify the expression level of each transcripts.
Genome_build: hg38
Supplementary_files_format_and_content: Expression data of transcripts is provided in tsv file format for each sample. Expression level is estimated using reads counts (4th column) and TPM (5th column).

extract_protocol:
Approximately 2-5 million HEK293T wild type or mutant cells were collected and the RNA was extracted using the Zymo RNA miniprep kit following the manufacture’s manual. Genomic DNA was removed by on-column digestion of DNase I. Human embryonic stem cells (hESCs) and the differentiated neural progenitor cells (NPCs) were collected and the RNA was extracted using the Trizol method. Briefly, the cells were resuspended in 500ul-1000ul Trizol and incubated at room temperature for 5 minutes and debris was removed after centrifugation. 0.2 volume of chloroform was added to the supernatant. Aqueous phase was collected after centrifugation at 4C and mixed with 1 volume of isopropanol at -20C for more than 30 minutes. RNA was precipitated at 13,000 rpm 4C. 1-2ug RNA was used for cDNA synthesis using the iScript Advanced kit (Bio-Rad) following the manual.
rRNA was depleted from total RNA using RNase H-based protocols adopted from (Adiconis et al., 2013; Morlan et al., 2012). In brief, approximately 100-1000 ng of RNA was annealed with pooled rRNA antisense DNA oligo (gift from J. Salzman lab at Stanford) by heating at 94°C  and slowly cooling down to 45°C. Hybridase Thermostable RNase H (Epicenter, Madison, WI: Lucigen H39500) was added to the mix and incubated at 45°C on a thermocycler for 30 minutes to remove rRNA. rRNA-depleted RNA was then purified using Agencourt RNAClean XP beads (Beckman Coulter: A63987). Excessive DNA oligo was removed by treatment of TURBO DNase (Invitrogen: AM1907). The RNA was then purified with RNAClean XP beads again and was used as RNAseq library prep input using the KAPA HyperPrep RNA-seq Kit (Kapa Biosystems: KK8540).

value: HEK293T cell line


title: WTwoMDA5_rep3

description:
WT without MDA5
WTwoMDA5_rep3

value: WT


title: tph_4_CAM791_6

description: Library name: tph_4_CAM791_6


title: N2_8_CAM245_6

description: Library name: N2_8_CAM245_6


title: DI_rep1

description:
deaminase inactive without MDA5
DIwoMDA5_rep1


title: tph_4_CAM229_4

description: Library name: tph_4_CAM229_4


title: N2_6_CAM040_1

description: Library name: N2_6_CAM040_1


title: N2_8_CAM795_5

description: Library name: N2_8_CAM795_5


title: N2_6_CAM236_4

description: Library name: N2_6_CAM236_4


title: DI_1allele

description:
heterozygot with 1 DI allele
DIhet1


title: N2_8_CAM788_3

description: Library name: N2_8_CAM788_3


title: N2_8_CAM791_5

description: Library name: N2_8_CAM791_5


title: DI_MDA5_MAVSKO_rep2

description:
DI with MAVS ko with MDA5
DI_MDA5_MAVSKO_rep2


title: N2_8_CAM791_6

description: Library name: N2_8_CAM791_6


title: DI_MDA5_MAVSKO_rep1

description:
DI with MAVS ko with MDA5
DI_MDA5_MAVSKO_rep1


title: DI_rep3

description:
deaminase inactive without MDA5
DIwoMDA5_rep3


title: N2_8_CAM787_2

description: Library name: N2_8_CAM787_2


title: DI_2allele

description:
heterozygot with 2 DI allele
DIhet2


title: N2_8_CAM229_1

description: Library name: N2_8_CAM229_1


title: SIN-B6-2


title: WTwoMDA5_rep1

description:
WT without MDA5
WTwoMDA5_rep1


title: WTwoMDA5_rep2

description:
WT without MDA5
WTwoMDA5_rep2


title: untransduced, rep4

city: San Francisco

first: Gokul

middle: Nathan

last: Ramadoss

state: California

address: 1200 Mariposa St

institute: UCSF

description: Library name: Untr-4

data_processing:
Cutadapt, HISAT2, featurecounts
Assembly: hg38
Supplementary files format and content: counts table outputted from featurecounts

source_name: NGN2 neurons

growth_protocol: NGN2 neuron differentiation

extract_protocol:
Zymo Quick RNA Microprep Kit
QuantSeq 3' mRNA-Seq V2 Library Prep Kit FWD with UDI

treatment_protocol: VLPs added to media

value: NGN2 neurons

value: untransduced


title: N2_6_CAM040_2

description: Library name: N2_6_CAM040_2


title: SIN-B6-1


title: N2_6_CAM231_3

description: Library name: N2_6_CAM231_3


title: untransduced, rep2

description: Library name: Untr-2


title: untransduced, rep3

description: Library name: Untr-3


title: untransduced, rep1

description: Library name: Untr-1


title: N2_8_CAM245_2

description: Library name: N2_8_CAM245_2


title: Cas9-NTg1 VLP, rep3

description: Library name: NT-3

value: Cas9-NTg1 VLP


title: N2_8_CAM787_1

description: Library name: N2_8_CAM787_1


title: Cas9-NTg1 VLP, rep4

description: Library name: NT-4


title: N2_8_CAM796_6

description: Library name: N2_8_CAM796_6


title: Cas9-NEFLg1 VLP, rep2

description: Library name: NEFL-2

value: Cas9-NEFLg1 VLP


title: Cas9-NEFLg1 VLP, rep1

description: Library name: NEFL-1


title: N2_7_CAM229_5

description: Library name: N2_7_CAM229_5


title: N2_6_CAM229_3

description: Library name: N2_6_CAM229_3


title: N2_6_CAM241_3

description: Library name: N2_6_CAM241_3


title: HSV2

city: Hangzhou

first: Xiang

last: Yuhang

address: Yuhang Tang street

country: China

description: Library name: Sample 5

data_processing:
Library preparation and sequencing were performed by Beijing Genomics Institute. A BGIseq500 platform was used to generate 150 bp paired-end reads.
Assembly: mm10 and KOS
Supplementary files format and content: gene-read count data.txt

source_name: Brain

extract_protocol:
Neuro-2a cells were infected with HSV-1 virus for 5 h (MOI = 10) before being harvested for RNA extraction using a total RNA extraction kit (Vazyme RC112-01)
DNA libraries were constructed and sequenced by Tianjin Novogene Bioin_x0002_formatic Technology Co., Ltd. Briefly, an NEBNext® Ultra™ II DNA Library Prep kit (catalogue no. E7645L; NEB) was used for library preparation.

treatment_protocol: For infection, cells were infected with HSV-1 (strain KOS) for 5hpi (MOI = 10) before RNAseq

value: Brain

value: Infect cells with HSV-1 virus for five hours


title: Cas9-NTg1 VLP, rep2

description: Library name: NT-2


title: HSV1

description: Library name: Sample 4


title: GFP VLP, rep3

description: Library name: GFP-3

value: GFP VLP


title: Cas9-NEFLg1 VLP, rep4

description: Library name: NEFL-4


title: dCas9-B2Mg1 VLP, rep3

description: Library name: dCas9-3

value: dCas9-B2Mg1 VLP


title: N2_8_CAM245_5

description: Library name: N2_8_CAM245_5


title: GFP VLP, rep4

description: Library name: GFP-4


title: Cas9-NEFLg1 VLP, rep3

description: Library name: NEFL-3


title: HSV3

description: Library name: Sample 6


title: N2_6_CAM236_1

description: Library name: N2_6_CAM236_1


title: N2_8_CAM795_4

description: Library name: N2_8_CAM795_4


title: GFP VLP, rep1

description: Library name: GFP-1


title: GFP VLP, rep2

description: Library name: GFP-2


title: dCas9-B2Mg1 VLP, rep2

description: Library name: dCas9-2


title: N2_6_CAM228_2

description: Library name: N2_6_CAM228_2


title: Mock3

description: Library name: Sample 3

value: Mock


title: N2_8_CAM228_4

description: Library name: N2_8_CAM228_4


title: dCas9-B2Mg1 VLP, rep4

description: Library name: dCas9-4


title: N2_7_CAM236_4

description: Library name: N2_7_CAM236_4


title: Cas9-B2Mg1 VLP, rep4

description: Library name: B2M-4

value: Cas9-B2Mg1 VLP


title: Mock2

description: Library name: Sample 2


title: dCas9-B2Mg1 VLP, rep1

description: Library name: dCas9-1


title: Mock1

description: Library name: Sample 1


title: Cas9-B2Mg1 VLP, rep3

description: Library name: B2M-3


title: N2_6_CAM229_5

description: Library name: N2_6_CAM229_5

value: Single individual


title: cauda sperm, low PFAS, rep 3

city: Philadelphia

first: Natalie

middle: Alyce

last: Trigg

state: Pennsylvania

address: 421 Curie Blvd

institute: Children's Hospital of Philadelphia

library_source: other

data_processing:
For each small RNA library, reads were mapped to rRNAs, miRbase, murine tRNAs, piRNA clusters, to Repeatmasker, and Refseq using Bowtie 2.
genome build: mm10
Supplementary files format and content: Excel spreadsheet with two sheets, the first depicting raw small RNA reads from sperm samples the second illustrating transcript per million (TPM) counts for embryo samples.

molecule: other

source_name: cauda sperm

extract_protocol:
Total RNA was extracted from the tissues and subjected to gel electrophoresis to isolate small RNA (18-40nts).
Illumina Tru-seq Small RNA Library
RNA was isolated using RNA-Clean XP beads for RNA-seq, for small RNA-seq total RNA was extracted from the tissues and subjected to gel electrophoresis to isolate small RNA (18-40nts).
Illumina Nextera XT Kit for RNA-seq and Illumina Tru-seq Small RNA Library for small RNA libraries

value: cauda sperm

value: low PFAS


title: cauda sperm, high PFAS, rep 1

value: high PFAS


title: 4T1_NC

city: Chongqing

first: Si-zhen

last: Yang

state: Chongqing

address: Gaotanyan Street, No.30

institute: Army Medical University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp (version 0.23.4) (parameter arsg: -l 39 --dont_eval_duplication  --qualified_quality_phred 20 --unqualified_percent_limit 8 --adapter_sequence  --adapter_sequence_r2  --fix_mgi_id)
Trimmed reads were mapped to GRCh38 using STAR software (version 2.5.3a) (parameters- --outSAMtype BAM SortedByCoordinate)
Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter -T 10 -d 30 -D 1000 -C -s 1 -t {exon} -g {geneid} --primary -O -a {gff_annotation_file}）
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: 4T1 Breast cancer cell

extract_protocol:
RNA was harvested using TRIzol Reagent (Invitrogen, cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following manufacturer's protocols.

value: 4T1 Breast cancer cell

value: tumor cell

value: vehicle


title: cauda sperm, control, rep 3

value: control


title: cauda sperm, control, rep 2


title: Cas9-B2Mg1 VLP, rep1

description: Library name: B2M-1

value: NGN2 neurons


title: WT Liver, LPS 15mg/kg, 6h, rep3

city: Beijing

first: Weixuan

last: Wang

address: No. 38 Xueyuan Road, Haidian District

institute: Peking University

description:
Library name: WT3
10x Genomics

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Liver

extract_protocol:
Total RNA was extracted with Trizol reagent (Invitrogen) and reverse transcribed into cDNA with GoScriptTM Reverse Transcription System (Promega). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using standard Illumina protocols.

value: Liver

value: WT

value: LPS 15mg/kg


title: N2_6_CAM245_3

description: Library name: N2_6_CAM245_3


title: Cas9-B2Mg1 VLP, rep2

description: Library name: B2M-2


title: WT Liver, LPS 15mg/kg, 6h, rep1

description:
Library name: WT1
10x Genomics


title: cauda sperm, high PFAS, rep 3


title: 4T1_Ast

value: astragalin


title: cauda sperm, control, rep 1


title: cauda sperm, high PFAS, rep 2


title: cauda sperm, low PFAS, rep 1


title: cauda sperm, low PFAS, rep 2


title: N2_8_CAM228_6

description: Library name: N2_8_CAM228_6


title: WT Liver, LPS 15mg/kg, 6h, rep2

description:
Library name: WT2
10x Genomics


title: N2_8_CAM245_1

description: Library name: N2_8_CAM245_1


title: N2_8_CAM796_2

description: Library name: N2_8_CAM796_2


title: N2_7_CAM228_5

description: Library name: N2_7_CAM228_5


title: 4-cell embryo, fertilized by low PFAS exposed sperm, rep 4

data_processing:
Reads were mapped using RSEM and normalized to transcripts per million (tpm).
genome build: mm10
Supplementary files format and content: Excel spreadsheet with two sheets, the first depicting raw small RNA reads from sperm samples the second illustrating transcript per million (TPM) counts for embryo samples.

source_name: preimplantation embryo

extract_protocol:
RNA was isolated using RNA-Clean XP beads
Illumina Nextera XT Kit
RNA was isolated using RNA-Clean XP beads for RNA-seq, for small RNA-seq total RNA was extracted from the tissues and subjected to gel electrophoresis to isolate small RNA (18-40nts).
Illumina Nextera XT Kit for RNA-seq and Illumina Tru-seq Small RNA Library for small RNA libraries

value: preimplantation embryo

value: 4-cell embryo

value: fertilizing sperm exposed to low PFAS


title: N2_8_CAM231_5

description: Library name: N2_8_CAM231_5


title: PTENα-/- Liver, LPS 15mg/kg, 6h, rep3

description:
Library name: KO3
10x Genomics

value: PTENalpha knockout


title: 4-cell embryo, fertilized by low PFAS exposed sperm, rep 2


title: 4-cell embryo, fertilized by low PFAS exposed sperm, rep 3


title: N2_6_CAM245_2

description: Library name: N2_6_CAM245_2

value: Single individual


title: PTENα-/- Liver, LPS 15mg/kg, 6h, rep2

description:
Library name: KO2
10x Genomics


title: 4-cell embryo, fertilized by low PFAS exposed sperm, rep 1


title: 4-cell embryo, fertilized by high PFAS exposed sperm, rep 3

value: fertilizing sperm exposed to high PFAS


title: N2_8_CAM791_2

description: Library name: N2_8_CAM791_2


title: PTENα-/- Liver, LPS 15mg/kg, 6h, rep1

description:
Library name: KO1
10x Genomics


title: 4-cell embryo, fertilized by high PFAS exposed sperm, rep 2


title: 4-cell embryo, fertilized by control sperm, rep 3


title: 4-cell embryo, fertilized by high PFAS exposed sperm, rep 1


title: N2_8_CAM229_5

description: Library name: N2_8_CAM229_5


title: 4-cell embryo, fertilized by control sperm, rep 2


title: black ball 2

city: Jinan

first: Jing

last: Cai

state: Shandong

address: 4 Duanxing West Road

department: Shandong Provincial ENT Hospital

institute: Shandong University

description:
Library name: Sample 2
identify
black_ball_2

data_processing:
mapping: Paired-end sequence files (fastq ) were mapped to the reference genome (GRCm39.111) using Hisat2 (Hierarchical Indexing for Spliced Alignment of Transcripts, version 2.0.5). The output SAM (sequencing alignment/map) files were converted to BAM (binary alignment/map) files and sorted using SAM tools (version1.3.1).Gene abundance was expressed as fragments per kilobase of exon per million reads mapped (FPKM). Stringtie software was used to count the fragment within each gene, and TMM algorithm was used for normalization.Differential expression analysis for gene was performed using R package edgeR. Differentially expressed RNAs with |log2(FC)| value >1 and q value <0.05, considered as significantly modulated, were retained for further analysis. This choice is motivated by the decision to maximize the sensitivity of this analysis, in order to perform a massive screening and identify candidate genes to be validated with a wider sample population with real-time PCR analysisWe performed a Gene Ontology (GO) analysis for biological processes, cellular components and molecular function and a KEGG pathway.Analysis (Kyoto Encyclopedia of Genes and Genomes http://www.genome.ad.jp/kegg) via enrich R package.
Assembly: GRCm39.111.
Supplementary files format and content: Gene abundance was expressed as fragments per kilobase of exon per million reads mapped (FPKM). Stringtie software was used to count the fragment within each gene, and TMM algorithm was used for normalization.

source_name: vestibular cells

extract_protocol:
Single-cell amplification was performed using SMART-Seq® HT Kit (Takara, USA) according to the manufacturer’s instructions. A total of 18 “black ball-like” cells from 9 mice (3 mice/group) were lysed in a buffer containing free dNTP and oligo(dT) oligonucleotides. The RNA fragments were copied into the first strand cDNA using reverse transcriptase and several template-free C nucleotides. The oligonucleotide primers were hybridized with poly(C) to form the second strand cDNA. cDNA was purified and enriched using PCR.
The cDNA libraries were constructed using the KAPA Hyper Prep Kit (KAPA, USA) according to the manufacturer’s instructions. Purified libraries were quantified and validated using a Qubit® 3.0 Fluorometer and an Agilent 2100 bioanalyzer to confirm the insert size and calculate the mole concentration. The RNA fragments were copied into the first strand cDNA using reverse transcriptase and several template-free C nucleotides. The oligonucleotide primers were hybridized with poly(C) to form the second strand cDNA. cDNA was purified and enriched using PCR. The cluster was generated by cBot after the library was diluted to 10 pM and sequenced on the Illumina NovaSeq 6000 platform (Illumina, USA).

value: vestibular cells

value: immune cells

value: macrophages


title: N2_6_CAM231_6

description: Library name: N2_6_CAM231_6


title: black ball 3

description:
Library name: Sample 3
identify
black_ball_3


title: N2_6_CAM228_4

description: Library name: N2_6_CAM228_4


title: black ball 1

description:
Library name: Sample 1
identify
black_ball_1


title: N2_8_CAM788_5

description: Library name: N2_8_CAM788_5


title: HE12Ctrl3

city: Lübeck

first: Kristian

last: Händler

address: Ratzeburger Allee 160

department: Human Genetics

country: Germany

institute: UKSH

data_processing:
bcl2fastq2 v2.20 (Illumina)
kallisto
Assembly: mm10
Supplementary files format and content: comma-separated text file containing the raw pseudo-aligned reads per gene after kallisto alignment to mm10

source_name: bone-marrow

extract_protocol:
Quiagen Rneasy mini following manufacturer's protocol
QuantSeq 3’ mRNA-Seq V2 Library Prep Kit with UDI Lexogen following manufacturer's protocol
3' quantification mRNA-Seq

treatment_protocol: Femurs and tibias of C57BL/6 mice were collected. CD11c+ cells were isolated from murine BM by FACS and loaded with acLDL (or Ctrl) on culture day 6 for 24 hours

value: bone-marrow

value: CD11c positive cells

value: no


title: HCD

library_source: transcriptomic single cell

data_processing:
bcl2fastq2 v2.20 (Illumina)
cellranger 5.0.1 (10X Genomics)
seurat v4
Assembly: mm10
Supplementary files format and content: filtered and merged seurat object (.rds) containing both conditions

source_name: aorta

extract_protocol:
physical disruption of frozen tissue, lysis, filtering through 10um cell strainer, DAPI stain and FACS sort of single nuclei for cleanup
Next GEM Single Cell 3ʹ Kit v3.1 (10X Genomics) following manufacturer's protocol
single-nuclei mRNA 3' counting

treatment_protocol: C57BL/6 mice fed a standard diet or high cholesterol (HC) diet for 6 weeks

value: aorta

value: high cholesterol diet 6w


title: HE12Ctrl2


title: 4-cell embryo, fertilized by control sperm, rep 1

value: control


title: Chow

value: chow diet 6w


title: HE12Ctrl4


title: N2_8_CAM040_5

description: Library name: N2_8_CAM040_5

value: WT


title: HE12Ctrl1


title: Adipose tissue,KO3

city: Shanghai

first: Hui

address: Songhu road

institute: Fudan University

description: Library name: KO3

data_processing:
we performed double-ended sequencing on it using illumina Novaseq 6000 in accordance with standard operations, with the sequencing mode being PE150.
Assembly: GRCm39
Supplementary files format and content: csv files include counts values for each samples

source_name: Adipose tissue

extract_protocol:
The RNA of the total sample was separated and purified using the TransZol Up Plus RNA Kit(Full Gold) according to the operation plan provided by the manufacturer. Then, the quantity and purity of total RNA were controlled using Pono-650 (Porabio). The integrity of RNA was then detected by Qsep100 (BiOptic, Taiwan). The concentration >20ng/μL, the RIN value >7.0, and the total RNA>1μg meet the requirements for downstream experiments.
The PolyA-containing mRNA was specifically captured using oligo(dT) magnetic beads (item No. N403, Vazyme Novozyme) through two rounds of purification. The captured mRNA was fragmented under high-temperature conditions using magnesium ion disruption (all the following are from the same kit, item number NR605, Vazyme Novozyme). cDNA is synthesized from fragmented RNA under the action of reverse transcriptase. Then, two-strand synthesis is carried out, and dUTP is simultaneously incorporated into the two strands to complete the ends of the double-stranded DNA to flat ends. Then add an A base to each end of it to enable it to connect with the connector with a T base at the end, and then use magnetic beads to screen and purify the size of its fragments. Then, through PCR - pre-denaturation at 98 ° C for 45 seconds, denaturation at 98 ° C for 15 seconds, denaturation at 60 ° C for 30 seconds, and denaturation at 72 ° C for 30 seconds, a total of 12 cycles were carried out. Finally, it was extended to 72 ° C for 1 minute to form a library with fragment sizes of 370-470bp.

value: Adipose tissue

value: tissue

value: knocked out of Kindlin-2

value: cold tolerance


title: Adipose tissue,KO4

description: Library name: KO4


title: Adipose tissue,KO2

description: Library name: KO2


title: N2_8_CAM241_2

description: Library name: N2_8_CAM241_2

value: Single individual


title: HE12acLDL3

value: acLDL


title: HE12acLDL4


title: N2_7_CAM229_2

description: Library name: N2_7_CAM229_2


title: HE12acLDL2


title: HE12acLDL1


title: Adipose tissue,KO1

description: Library name: KO1


title: N2_8_CAM796_3

description: Library name: N2_8_CAM796_3


title: Adipose tissue,WT4

description: Library name: WT4


title: N2_6_CAM241_1

description: Library name: N2_6_CAM241_1


title: female nymph, whole body, rep1

city: Kunming

first: Qin

last: Lu

state: Yunnan

address: Bailongsi

institute: Institute of Highland Forest Science, Chinese Academy of Forestry

description: BD Rhapsody

data_processing:
Raw reads with the length of R1 less than 66 bp, the length of R2 less than 64 bp, the average score less than 20, single nucleotide polymorphism (SNF) of R1 ≥ 0.55, SNF of R2 ≥ 0.80 were deleted. Clean data was uploaded to SevenBridge platform and aligned to the reference genome, BD Rhapsody™ WTA Pipeline was used to analysis the data with default settings. The output matrices that contained the information for cell index and gene expression levels were submitted to Seurat (v.4.0.6) for downstream analysis. Quality control was carried out for the four samples respectively, then datasets were integrated by FindIntegrationAnchors function. The integrated dataset was performed dimensionality reduction by principle componenet analysis (PCA). A k-nearest neighbor graph was executed with Euclidean distances in the space of the first 10 significant principal components. The clustering results were visualized by UMAP project (resolution = 0.5).
Assembly: Ericerus pela genome
Supplementary files format and content: Tab-separated values files and matrix files

organism: Ericerus pela

source_name: whole body

extract_protocol:
Samples were homogenized in the PBS, and then filtered through a cellular sieve. The cell viability of the filtrated cell suspension was examined under a fluorescence microscope.
Single-cell suspension was loaded into a BD Rhapsody cartridge, and single-cell mRNA capture was achieved by a cartridge with > 200,000 microwells and magnetic beads with barcoded capture oligos. Then, beads were collected for subsequent cDNA synthesis and library construction following the BD Rhapsody single cell 3’ whole transcriptome amplification (WTA) workflow. Finally, the libraries were quantified using the Agilent 2100 Bioanalyzer and the Qubit 4.0 and were sequenced on Illumina NovaSeq 6000 with 300-bp reads.

tag: Sex

value: female

value: whole body

value: nymph


title: female adult, whole body, rep1

description: BD Rhapsody

value: adult


title: Adipose tissue,WT3

description: Library name: WT3


title: male adult, whole body, rep1

description: BD Rhapsody

value: male


title: N2_8_CAM787_3

description: Library name: N2_8_CAM787_3


title: Adipose tissue,WT2

description: Library name: WT2


title: N2_8_CAM787_6

description: Library name: N2_8_CAM787_6


title: LNT4_3

city: Uvalde

first: Vijay

last: Joshi

state: Texas

address: 1619 Garner Field Road

department: Department of Horticultural Sciences

institute: Texas A&M AgriLife Research

description: Middle of Dark

data_processing:
The reads with low quality, adapter contamination, and highly unknown N bases were filtered. The clean reads were aligned to the reference genome (a doubled haploid onion line DHCU066619 (https://www.oniongenome.wur.nl/)  and the transcriptions assembly. The read count for every transcript was determined from the findings of the mapping process. The expression levels were calculated and normalized to Fragments Per Kilobase of transcript sequence per million base pairs sequenced (FPKM) using RSEM (Li & Dewey, 2011). The DESeq2 R package (1.20.0) was used for the differential expression analysis. The P-values obtained were adjusted using Benjamini and Hochberg's method to control the false discovery rate. Genes identified as differentially expressed genes (DEGs) had an adjusted P-value <0.05 and an absolute log2FC ≥0, as determined by DESeq2. Transcriptomic analysis of onion bulb tissue (Variety Don Victor) in response to Salmonella was performed 24 hours and 7 days post-inoculation to identify Differentially Expressed Genes (DEGs) in onion. Within 24 hours of inoculation, 4259 genes were upregulated while 3393 genes were downregulated. After 7 days, 8213 and 6417 genes were up and down-regulated, respectively, as shown below. (FDR<0.05 and Abs (log 2(Y/X) >0)
RNA libraries were prepared for sequencing using NovaSeq X Plus Series
Sequencing on NovaSeq X Plus Series
Sequenced reads were trimmed for adaptor sequence and low-complexity or low-quality sequences, then mapped to spinach genome using  the chain-specific patterns of HISAT2 for mapping and assembly,
For the assembly results of individual transcripts,  each transcript  was confirmed to meet FPKM >= 0.5, Coverage > 1 and Length> 200
Assembly: Sp75 Genome (http://spinachbase.org/ftp/genome/Sp75/)
Supplementary files format and content: gene_fpkm
Supplementary files format and content: the FPKM list with the annotation of each gene

organism: Spinacia oleracea

source_name: Leaf

growth_protocol: Spinach plants of the variety Space were grown in non-soil turface growing media under 8 hrs of light at 22-23C and 67% humidity and supplemented with diifferent levels on nitrogen. The transcriptomic analysis of spinach leaves was performed using 48-day-old plants. The tissue samples were collected from 3 independent plants at 4-time points in a single day and flash-frozen in liquid nitrogen before storing at -80℃ for further processing.

extract_protocol:
Total RNA was extracted from each sample using using the Zymo Research Quick-RNA Plant Miniprep Kit. The mRNA was was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand of cDNA was synthesized using random hexamer primers, followed by the second strand of cDNA synthesis using dUTP for directional library.
RNA libraries were prepared for sequencing using NovaSeq X Plus Series

treatment_protocol: Plants were fertilized by two levels of nitrogen high (200 ppm) and low (50 ppm) as described by Joshi et al (2022).

value: Leaf

value: Space

value: Low nitrogen


title: Adipose tissue,WT1

description: Library name: WT1


title: LNT4_1

description: Middle of Dark


title: LNT3_3

description: End of Light


title: N2_7_CAM241_5

description: Library name: N2_7_CAM241_5


title: LNT4_2

description: Middle of Dark


title: LNT3_2

description: End of Light


title: LNT2_3

description: Middle of Light


title: N2_8_CAM236_1

description: Library name: N2_8_CAM236_1


title: LNT3_1

description: End of Light


title: EC, cre+, vincristine 3

city: Dresden

first: Tatyana

last: Grinenko

address: Fetscherstraße 74

institute: IKL , Carl Gustav Carus Universitätsklinikum, TU Dresden

description: Library name: Sample30

data_processing:
Low quality nucleotides were removed Illumina fastq filterer/).
Reads were further subjected adaptor trimming using cutadapt.
Alignment of the reads to the Mouse genome was done using STAR Aligner using the parameters: “--runMode alignReads --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat”. Mouse Genome version GRCm38 (release M12 GENCODE)
HTSeq-0.6.1p1 was used to count the reads that map to the genes in the aligned sample files. Read Quantification was performed using the parameters: 'htseq-count -f bam -s reverse -m union -a 20'. The GTF file (gencode.vM12.annotation.gtf) used for read
Assembly: mm10
Supplementary files format and content: Tab-Delimited Gene-Wise Raw read counts text file

source_name: bone marrow

extract_protocol:
Cells were sorted in RLT bufer. RNA was isolated using RNeasy Plus Micro Kit according to the manufacturer’s instructions
SmartSeq2 sequencing method was used for Illumina sequencing

treatment_protocol: Mice were treated witn saline or 0.125mg/kg vincristine. For HSCs, treatment for 6 weeks/twice a week was performed. For ECs and MSCs mice were injected once

value: bone marrow

value: endothelial cells

value: vincrictine once

tag: age (weeks)


title: LNT2_1

description: Middle of Light


title: EC, cre+, vincristine 2

description: Library name: Sample29


title: LNT2_2

description: Middle of Light


title: EC, cre+, vincristine 1

description: Library name: Sample28


title: LNT1_3

description: End of Dark


title: N2_8_CAM795_1

description: Library name: N2_8_CAM795_1

value: WT


title: LNT1_2

description: End of Dark


title: male pupa, whole body, rep1

description: BD Rhapsody

value: pupa


title: EC, cre-, vincristine 3

description: Library name: Sample27


title: N2_6_CAM795_2

description: Library name: N2_6_CAM795_2


title: EC, cre-, vincristine 2

description: Library name: Sample26


title: HNT4_2

description: Middle of Dark

value: High nitrogen


title: HNT4_1

description: Middle of Dark


title: HNT4_3

description: Middle of Dark


title: N2_8_CAM040_4

description: Library name: N2_8_CAM040_4


title: HNT3_3

description: End of Light


title: HNT3_1

description: End of Light


title: N2_8_CAM796_1

description: Library name: N2_8_CAM796_1


title: EC, cre-, vincristine 1

description: Library name: Sample25


title: EC, cre+, control 2

description: Library name: Sample23


title: HNT3_2

description: End of Light


title: N2_6_CAM231_4

description: Library name: N2_6_CAM231_4


title: HNT2_1

description: Middle of Light


title: HNT2_2

description: Middle of Light


title: EC, cre+, control 1

description: Library name: Sample22


title: N2_8_CAM787_5

description: Library name: N2_8_CAM787_5


title: HNT1_2

description: End of Dark


title: N2_6_CAM236_6

description: Library name: N2_6_CAM236_6


title: EC, cre-, control 3

description: Library name: Sample21


title: HNT1_1

description: End of Dark


title: LNT1_1

description: End of Dark


title: HNT1_3

description: End of Dark


title: EC, cre-, control 2

description: Library name: Sample20


title: N2_8_CAM788_1

description: Library name: N2_8_CAM788_1


title: N2_8_CAM231_3

description: Library name: N2_8_CAM231_3


title: EC, cre+, control 3

description: Library name: Sample24


title: N2_7_CAM241_4

description: Library name: N2_7_CAM241_4


title: HNT2_3

description: Middle of Light


title: HSC-2 cells, IFNγ, rep3

city: Mizuho

first: Eisuke

last: Domae

state: Gifu

country: Japan

institute: Asahi university

description: Library name: SAMPLE 6

data_processing:
For bioinformatics analysis, raw reads were processed using the DRAGEN Bio-IT Platform (Illumina), which performs adapter trimming, quality filtering, and alignment to the human reference genome (GRCh38).
Assembly: GRCh38
Supplementary files format and content: Excel files include raw counts for each sample.

growth_protocol: HSC-2 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using the TRIzol Plus RNA Purification Kit (Thermo Fisher Scientific) according to the manufacturer’s protocol, including on-column DNase treatment to remove genomic DNA contamination.
Full-length cDNA was synthesized and amplified from 10 ng of total RNA using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio) following the manufacturer’s instructions. Sequencing libraries were prepared via tagmentation using the Nextera XT DNA Library Prep Kit (Illumina) and uniquely indexed with IDT for Illumina DNA/RNA UD Indexes (Illumina).

treatment_protocol: HSC-2 cells were treated with 10ng/mL IFNγ for 24h.

value: IFNγ


title: EC, cre-, control 1

description: Library name: Sample19


title: HSC-2 cells, IFNγ, rep1

description: Library name: SAMPLE 4


title: HSC-2 cells, control, rep3

description: Library name: SAMPLE 3

value: PBS


title: HSC-2 cells, control, rep2

description: Library name: SAMPLE 2


title: MSC, cre+, vincristine 3

description: Library name: Sample18

value: mesenchymal stromal cells


title: HSC-2 cells, control, rep1

description: Library name: SAMPLE 1


title: N2_8_CAM040_1

description: Library name: N2_8_CAM040_1

data_processing:
Data was generated using Illumina NextSeq platforms: either NextSeq 550 with the High Output Kit v2.5 (75 cycles) or NextSeq 2000 with the P2 100 cycles kit, both with sequencing parameters of Read1-36, Index1-8, Index2-8, and Read2-37.
Assembly: The obtained sequencing read fragments were aligned to the WBPS16 using the STAR aligner  (Dobin et al., 2013) v2.7.9a. Expression levels of single gene were normalized by gene mapped counts per million total reads (RPM).
Supplementary files format and content: text  files for both strains including all samples and time for each sample and RPM value for each gene

extract_protocol:
Fresh working lysis buffer is prepared daily by mixing a stable lysis buffer stock (made of Tris-HCl, Triton-X, Tween-20, EDTA, and water), Proteinase K, and RNase inhibitor. Worms were collected individually, and cut with a needle if larval. After adding lysis buffer, samples are mixed, centrifuged, and incubated in a thermocycler at 65 °C for 10 min, 85 °C for 1 min, then 4 °C before cooling on ice.
Library preparation for each single individual was according to the Illumina Nextera tagmentation protocol (Illumina), with DNA input and reagents adjusted for 20 ng of cDNA. The tagmented DNA was cleaned, and PCR amplification was performed. PCR primers were removed using Ampure XP beads.

value: Single individual


title: MSC, cre+, vincristine 2

description: Library name: Sample17


title: Si-3

city: Shenyang

first: Juan

address: No.44 Xiaoheyan Road

institute: Liaoning Cancer Hospital & Institute

description: Library name: Sample6

data_processing:
The high-throughput sequencing platform was used to sequence the cDNA library, the data of great size and quality from the platform was named Raw data. Most of its base quality scores can reach or exceed Q30. Raw data was normally provided in FASTQ format. Two FASTQ files were obtained for each sample containing sequences measured from both ends.
Reference genome was pre-defined for the analysis. Version information of the reference genome is: Homo_sapiens.GRCh38_release95.genome.fa. HISAT2[2] is a highly efficient system for mapping RNA-seq reads, which is a more advanced version of TopHat2/Bowtie2.HISAT2 uses a Burrows-Wheeler Transform and Ferragina-Manzini（FM）index based search. HISAT2 uses one global graph FM index (GFM) to represent general population, as well as small indexes (local indexes) combined with several alignment strategies in order to achieve more efficient alignment. StringTie[3] was applied to assemble the mapped reads. The algorithm is established based on optimality theory. It utilizes a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantify transcripts representing multiple spliced variants for each gene locus.
To ensure the quality of library, following three quality examinations were performed on RNA library. (1)Fragment randomness and degradation of RNA sample was estimated by checking the distribution of mapped reads on genome (2)Length dispersion was examined by the length distribution of inserts (3)Sufficiency of library Volume (or mapped reads) was examined by generating saturation curve between sampled mapped reads against genes identified within certain expression accuracy.
The number of fragments from a transcript is affected by sequencing data volume (or number of mapped reads), length of the transcript, expression level of transcripts. In order to reveal the expression level of each transcript more accurately, the number of mapped reads needs to be normalized by the length of its transcripts. FPKM(Fragments Per Kilobase of transcript per Million fragments mapped) was applied to measure the expression level of a gene or transcript by StringTie using maximum flow algorithm.
The expression of a gene can be influenced by both external stimuli and internal environment, which is highly temporal-specific and tissue-specific. The genes expressed significantly different under different conditions, such as treatment vs control, wild type vs mutants, different time points, different tissue, etc., are defined as Differentially Expressed Genes (DEG). Similarly, transcripts with significantly different expression level are named Differentially Expressed Transcript (DET). The collection of genes acquired in differential expression analysis is defined as DEG set. In result files, the gene sets were named as "A_VS_B" to specify the comparing pair. Normally, "A" represents control group, wild type or former time point. "B" normally represents corresponding treated group, mutant or later time point. The genes with a higher expression level in B than A are defined as up-regulated genes. The ones with lower expression level in B are defined as down-regulated genes. Therefore, up-reg and down-reg are relative definitions, which relies on the order of A and B. For experiments with biological replicates, differential expression analysis is processed by DESeq2[24]. For projects without biological replicates, edgeR[25] is applied. Criteria for differentially expressed genes was set as Fold Change(FC)≥1.5 and Pvalue<0.01. Fold change(FC) refers to the ratio of gene expression in two samples. False Discovery Rate (FDR) refers to adjusted p-value, which is used to measure significancy of difference.
Assembly: Homo_sapiens.GRCh38_release95.genome.fa
Supplementary files format and content: The processed data is stored in an Excel spreadsheet, containing gene names, group information, normalized gene expression levels, differential expression results, and functional enrichment results.

extract_protocol:
HCT116 cells in the logarithmic growth phase were treated with either negative control siRNA (NC) or siCPT2 for 48 hours. The cells were collected, washed three times with PBS, and lysed with 1 mL of TRIzol for 5 minutes on ice.
(1) mRNA was isolated by Oligo(dT)-attached magnetic beads. (2) mRNA was then randomly fragmented in fragmentation buffer. (3) First-strand cDNA was synthesized with fragmented mRNA as template and random hexamers as primers, followed by second-strand synthesis with addition of PCR buffer, dNTPs, RNase H and DNA polymerase I. Purification of cDNA was processed with AMPure XP beads. (4) Double-strand cDNA was subjected to end repair. Adenosine was added to the end and ligated to adapters. AMPure XP beads were applied here to select fragments within size range of 300-400 bp. (5) cDNA library was obtained by certain rounds of PCR on cDNA fragments generated from step 4.

value: Colorectal cancer

value: CPT2 knockdown


title: Si-1

description: Library name: Sample4


title: MSC, cre+, vincristine 1

description: Library name: Sample16


title: MSC, cre-, vincristine 3

description: Library name: Sample15


title: NC-2

description: Library name: Sample2

value: NC


title: HSC-2 cells, IFNγ, rep2

description: Library name: SAMPLE 5


title: NC-1

description: Library name: Sample1


title: NC-3

description: Library name: Sample3


title: N2_8_CAM791_1

description: Library name: N2_8_CAM791_1


title: N2_6_CAM229_4

description: Library name: N2_6_CAM229_4


title: thymus sample of donor46

city: Chengdu

first: Yujun

last: Deng

address: No. 17, Section 3, Renmin South Road, Chengdu

institute: Sichuan University

description:
Library name: donor46
10x Genomics
3'scRNAseq

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 or v6.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: transcript files :Tab-separated values files and matrix files; TCR files :comma-separated values files

source_name: thymus

extract_protocol:
Human thymus samples were collected and transferred to RPMI1640 medium supplied with 10% FBS on ice, the tissues were cut into small pieces to release thymocytes. After thymocytes were collected, the remaining tissues were washed with RPMI1640 for 2-3 times and subjected to digestion with pre-warmed RPMI1640 containing 0.1g/mL collagenase and 100ug/mL DNase at 37ºC for 30-40 mins. The cell suspension was passed through 70m cell strainer and combined with thymocytes collected previously. The cells were centrifuged at 500g for 6min and suspended with RPMI1640 medium for cell counting, staining and sorting.  PBMCs were isolated from peripheral blood using Lymphocyte Separation Medium (LTS1077, TBD). Briefly, blood was added into 15mL tube containing equal volume of Lymphocyte Separation Medium gently and centrifuged at 2000 rpm for 20 min at room temperature with brake off. The PBMCs layer located at the interface were collected and washed with PBS plus 5% FBS.  For scRNA-seq, fresh cells isolated from human thymus were sorted as 7-AAD-CD235a-CD45+ and 7-AAD-CD235a-CD45- cells and combined with ratio at 6:4, or sorted as CD34+ cells or EpCAM+ cells. The sorted cells were applied for 10X single cell RNA-sequencing, TCR repertoire sequencing or cellular indexing of transcriptomes and epitopes sequencing.
For 10X single cell RNA-sequencing and 5’-TCR repertoire sequencing, 20,000 live sorted thymic cells or PBMCs were loaded on to each of the Chromium Controller (10X Genomics). Single cell cDNA and unique molecular identifier (UMI) tagged scRNA-Seq libraries and TCR repertoire Seq libraries were prepared using 10X Genomics platform.

value: thymus

tag: age

value: 55 years

value: Male


title: MSC, cre-, vincristine 2

description: Library name: Sample14

value: male


title: N2_8_CAM791_4

city: Haifa

first: Nabeel

description: Library name: N2_8_CAM791_4

source_name: Single individual


title: thymus sample of donor47

description:
Library name: donor47
10x Genomics
3'scRNAseq

value: 38 years

value: Female


title: thymus sample of donor45

description:
Library name: donor45
10x Genomics
3'scRNAseq

value: 54 years


title: N2_8_CAM229_4

description: Library name: N2_8_CAM229_4

value: WT


title: MSC, cre-, vincristine 1

description: Library name: Sample13

value: bone marrow

value: vincrictine once


title: thymus sample of donor44

description:
Library name: donor44
10x Genomics
3'scRNAseq


title: thymus sample of donor43

description:
Library name: donor43
10x Genomics
3'scRNAseq


title: N2_8_CAM231_1

description: Library name: N2_8_CAM231_1


title: N2_8_CAM241_1

description: Library name: N2_8_CAM241_1


title: Si-2

description: Library name: Sample5


title: MSC, cre+, control 2

description: Library name: Sample11


title: thymus sample of donor42

description:
Library name: donor42
10x Genomics
3'scRNAseq

value: EpCAM+

value: 61 years


title: N2_8_CAM040_3

description: Library name: N2_8_CAM040_3


title: MSC, cre+, control 1

description: Library name: Sample10

value: mesenchymal stromal cells


title: thymus sample of donor40, sorted CD34+cells, rep1

description:
Library name: donor40-1
10x Genomics
3'scRNAseq

value: 70 years


title: N2_8_CAM231_6

description: Library name: N2_8_CAM231_6

value: Single individual


title: thymus sample of donor38

description:
Library name: donor38
10x Genomics
3'scRNAseq


title: MSC, cre-, control 2

description: Library name: Sample8


title: thymus sample of donor37

description:
Library name: donor37
10x Genomics
3'scRNAseq

value: 35 years


title: N2_8_CAM228_2

description: Library name: N2_8_CAM228_2


title: MSC, cre-, control 3

description: Library name: Sample9


title: N2_8_CAM229_2

description: Library name: N2_8_CAM229_2


title: iMGL_recombinant_tau_monomeric_4

city: Oxford

first: Sam

last: Washer

state: Oxfordshire

address: NDMRB, Roosevelt Drive

department: Centre for Medicines Discovery

country: United Kingdom

institute: University of Oxford

description: Library name: Sample 22

data_processing:
Raw read QC with FastQC (version 0.12.1)
Raw read adapter trimming with TrimGalore (0.6.10) and Cutadapt (4.6), phred cut off 20, adapter sequence Illumina TruSeq.
Trimmed read QC with FastQC (version 0.12.1)
Alignment of trimmed paired reads to GRCh38 transcriptome using Kallisto (0.44.0), with 50 bootstraps
Assembly: GRCh38
Supplementary files format and content: abundance.tsv - transcript abundance file from Kallisto for each sample
Supplementary files format and content: abundance.h5 - transcript abundance file from Kallisto for each sample

growth_protocol: iMGL were differentiated following (Washer et al 2022) from iPSC (SFC 856-03-06)

extract_protocol:
RNeasy - Qiagen
NEBNext Ultra II RNA Library Prep Kit - NEB

treatment_protocol: treated with either vehicle control, labelled recombinant monomeric tau (1ug/mL), labelled recombinant fibrilar tau (1ug/mL), Tau PHF extracted from AD patient brain (Eli Lily, pooled from 5 patients, 0.25ug/mL), HT7 Tau Ab immunodepleted brain sample (Eli Lily, pooled from 5 patients, matched to samples 4,5,6,22), Tau PHF extracted from AD patient brain (Oxford Brain Bank, patient 1, 2 or 3), Tau PHF extracted from healthy patient brain (Oxford Brain Bank, patient 1,2,3), for 24 hours. Cells were then harvested, snap frozen, and sent to Azenta for RNA extraction, QC, library prep, and bulk RNAseq

value: iPSC-derived microglia like cells

value: rTauM

tag: tau source

value: Recombinant

tag: donor


title: N2_8_CAM241_6

address: Stern lab, Faculty of Biology, Technion City, Haifa 3200003, Israel.

institute: Technion - Israel Institute of Technology

description: Library name: N2_8_CAM241_6


title: thymus sample of donor41, sorted EpCAM+cells

description:
Library name: donor41-2
10x Genomics
3'scRNAseq

value: thymus

value: 57 years

value: Male


title: N2_7_CAM236_3

description: Library name: N2_7_CAM236_3


title: iMGL_humanised_tau_Control_Oxford_3

description: Library name: Sample 21

value: hTauConOx

value: Human - Oxford Brain Bank


title: N2_8_CAM241_5

description: Library name: N2_8_CAM241_5

value: WT


title: thymus sample of donor41, sorted CD34+cells

description:
Library name: donor41-1
10x Genomics
3'scRNAseq


title: iMGL_humanised_tau_Control_Oxford_1

description: Library name: Sample 19


title: HSC, cre+, vincristin 3

description: Library name: Sample6

value: bone marrow

value: hematopoietic stem cells

value: vincristine 6 weeks

value: female


title: iMGL_humanised_tau_AD_Oxford_3

description: Library name: Sample 18

value: hTauOx


title: MSC, cre+, control 3

description: Library name: Sample12

value: mesenchymal stromal cells

value: male


title: thymus sample of donor40, sorted CD34+cells, rep2

description:
Library name: donor40-2
10x Genomics
3'scRNAseq

value: 70 years


title: N2_8_CAM229_6

description: Library name: N2_8_CAM229_6

value: Single individual


title: HSC, cre+, vincristin 2

description: Library name: Sample5


title: HSC, cre+, vincristin 1

description: Library name: Sample4


title: N2_7_CAM245_6

description: Library name: N2_7_CAM245_6


title: MSC, cre-, control 1

description: Library name: Sample7


title: iMGL_humanised_tau_depleted_Eli_Lily_2

description: Library name: Sample 14

value: iPSC-derived microglia like cells

value: hdTauEL

value: Human - Eli Lily


title: thymus sample of donor39

description:
Library name: donor39
10x Genomics
3'scRNAseq

value: thymus

value: EpCAM+

value: 61 years


title: HSC, cre-, vincristin 3

description: Library name: Sample3


title: iMGL_humanised_tay_Eli_Lily_4

description: Library name: Sample 24

value: hTauEL


title: iMGL_humanised_tau_Eli_Lily_3

description: Library name: Sample 12


title: iMGL_humanised_tau_Eli_Lily_1

description: Library name: Sample 10


title: N2_8_CAM236_5

description: Library name: N2_8_CAM236_5

value: WT


title: N2_6_CAM229_6

description: Library name: N2_6_CAM229_6


title: iMGL_recombinant_tau_fibrils_2

description: Library name: Sample 8

value: rTauF

value: Recombinant


title: iMGL_humanised_tau_Eli_Lily_2

description: Library name: Sample 11


title: N2_7_CAM241_1

description: Library name: N2_7_CAM241_1


title: iMGL_recombinant_tau_fibrils_4

description: Library name: Sample 23


title: iMGL_recombinant_tau_monomeric_2

description: Library name: Sample 5

value: rTauM


title: iMGL_humanised_tau_Control_Oxford_2

description: Library name: Sample 20

value: hTauConOx

value: Human - Oxford Brain Bank


title: MFN2Col2a1-/-2

city: Suzhou

first: Mingzhuang

last: Hou

address: Pinghai Street 899#

institute: Suzhou University

description: Library name: Sample 5

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: GRCm39
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

source_name: chondrocytes

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: chondrocytes


title: MFN2Col2a1-/-1

description: Library name: Sample 4


title: iMGL_recombinant_tau_fibrils_3

description: Library name: Sample 9


title: MFN2Col2a1-/-3

description: Library name: Sample 6


title: HSC, cre-, vincristin 1

description: Library name: Sample1

value: bone marrow

value: hematopoietic stem cells

value: vincristine 6 weeks

value: female


title: iMGL_recombinant_tau_fibrils_1

description: Library name: Sample 7

value: iPSC-derived microglia like cells


title: iMGL_recombinant_tau_monomeric_1

description: Library name: Sample 4


title: iMGL_recombinant_tau_monomeric_3

description: Library name: Sample 6


title: iMGL_humanised_tau_AD_Oxford_2

description: Library name: Sample 17

value: hTauOx


title: iMGL_humanised_tau_AD_Oxford_1

description: Library name: Sample 16


title: N2_8_CAM231_2

last: Ganem

description: Library name: N2_8_CAM231_2

value: Single individual


title: iMGL_humanised_tau_depleted_Eli_Lily_3

description: Library name: Sample 15

value: hdTauEL

value: Human - Eli Lily


title: iMGL_humanised_tau_depleted_Eli_Lily_1

description: Library name: Sample 13


title: HSC, cre-, vincristin 2

description: Library name: Sample2


title: MFN2wt3

description: Library name: Sample 3


title: iMGL_vehicle_3

description: Library name: Sample 3

value: Vehicle


title: N2_8_CAM241_4

description: Library name: N2_8_CAM241_4

value: WT


title: iMGL_vehicle_2

description: Library name: Sample 2


title: N2_8_CAM236_4

description: Library name: N2_8_CAM236_4


title: MFN2wt2

description: Library name: Sample 2


title: N2_7_CAM241_6

description: Library name: N2_7_CAM241_6


title: MFN2wt1

description: Library name: Sample 1


title: P22 ccRCC, ischaemia, rep1

city: Cambridge

first: Cissy

last: Yong

state: I am not in the U.S. or Canada

address: Hills Road

department: Surgery

institute: University of Cambridge

data_processing:
Sequencing was performed using the NextSeq 500 (Illumina) with the high output 75 cycle kits (Ilumina). Base calling after sequencing was done using the software provided by Illumina, bcl2fastq
QC of the reads was performed using FastQC (v0.11.4, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads were trimmed using TrimGalore (v0.5.0, https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Reads were mapped to the genome using STARmapper (v2.7.1) and Ensembl Homo Sapiens GRCh38 (release 105) reference genome using the annotated transcripts from the ensembl Homo_Sapiens.GRCh38.105.gtf file. The number of reads that map to genomic features was calculated using HTSeq v0.6.1. Reads with a poor mapping quality (< 10), mapping to multiple loci, or to overlapping gene regions were discarded to avoid ambiguity and false positives.
Batch correction was performed using the COMBAT_seq correction method from the SVA package
Normalisation and differential gene expression was performed using EdgeR (v3.26.5)
Assembly: hg38
Supplementary files format and content: text file format files includes raw counts for each sample.

source_name: tumour

extract_protocol:
Tissue RNA was extracted (AllPrep DNA/RNA Mini Kit, Qiagen, Germany) and quantified using the 4150 Tapestation system (Agilent, cat.no. G2992AA).
Library preparation was performed using SMARTseq v4 low-input mRNA (Takara Bioscience, cat.no. 634893). After obtaining cDNA, the Nextera XT workflow (Illumina, cat.no. FC-131-1096) was used to perform the adapter ligation using the tagmentation protocol. The libraries for each sample were then quantified and pooled together using both the Qubit 2.0 (Invitrogen) and qPCR system (Aria MX real time PCR system, Agilent). The KAPA library quantification kit (Roche) was used for qPCR

value: tumour

value: ischaemia


title: P22 kidney, ischaemia, rep2

source_name: kidney

value: kidney


title: N2_8_CAM787_4

description: Library name: N2_8_CAM787_4


title: iMGL_vehicle_1

description: Library name: Sample 1


title: P22 ccRCC, ischaemia, rep2


title: P22 ccRCC, in vivo, rep2

value: in vivo


title: P22 ccRCC, in vivo, rep3


title: N2_6_CAM228_3

description: Library name: N2_6_CAM228_3


title: Hippocampus, 28 Months, Rep16

city: Kiel

first: Lena

last: Best

address: Michaelis-Straße 5

department: Institute of Experimental Medicine

institute: Christian-Albrechts-University Kiel

description:
Library name: 28M.N16
28M_19, J14338

library_source: genomic

data_processing:
Sequence information was converted to fastq format using bcl2fastq v2.20.0.422. From validation samples only those reads were downstream processed, that start with a Tecan/NuGen TrueMethyl diversity adapter (length 0-3, clipped afterwards) followed by a MspI cutting site.
Read quality trimming (cutoff 20) and TruSeq universal adapter clipping was performed using Cutadapt v2.10. Due to MspI cutting site end-repair, R1 adapter was prefixed by NN and in case of paired-end data, unconditional 5' clipping of length 2 was conducted on R2.
Mappings were done via segemehl v0.3.4 (methyl-C mode, accuracy 95%, reference GRCm38) and filtered for unique alignments. Paired-end alignments were further filtered for proper-read pairs and overlaps of R2 with R1 were trimmed using BamUtil clipOverlap v1.0.14.
Validation data alignments were deduplicated for over amplified PCR fragments based on unique molecular identifiers utilizing UMI-tools v1.1.1.
Methylation rates were inferred utilizing haarz v0.3.0. Rates and coverages within a CpG context were compiled using BEDTools v2.30.0.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Tabular delimited text file in bismark cov format of methylated and unmethylated CpG coverage per GRCm38 chromosomal CpG and sample.

molecule: genomic DNA

source_name: Hippocampus

growth_protocol: All the mice were kept solely for aging in a controlled environment and health status.

extract_protocol:
Genomic DNA was isolated with the DNeasy Blood & Tissue Kit (Qiagen).
200 ng of DNA was fragmented via a 5 hour Msp1-digest (New England Biolabs), followed by TrueSeq adapter ligation (Illumina, San Diego, CA, USA) and subsequent bisulfite conversion following the manufacturers protocol (EZ DNA Methylation Gold Kit, Zymo Research). The bisulfite converted DNA was amplified in a 19-cycles PCR with Pfu Turbo Cx Hotstart DNA Polymerase (Agilent Technologies) and the resulting libraries were quality checked using 4200 TapeStation (Agilent Technologies). For sequencing of validation samples, Illumina’s next-generation sequencing methodology 87 was used. In detail, genomic DNA was quality checked and quantified using the 4200 TapeStation instruments in combination with the Genomic DNA ScreenTape (both Agilent Technologies). Libraries were prepared from 100 ng of input material using Ovation RRBS Methyl-Seq with TrueMethyl oxBS (Tecan). In detail, only the bisulfite part of the protocol was followed, oxidation of DNA was not done, and samples were treated as MOCK oxBS samples according to the manufacturer’s instruction. Quantification and quality check of libraries were done using the 4200 TapeStation and D5000 ScreenTapes instruments (both Agilent Technologies).

value: Hippocampus

value: Male

value: 28 Months


title: Hippocampus, 28 Months, Rep12

description:
Library name: 28M.N12
28M_16N, J14306


title: P22 kidney, ischaemia, rep1


title: P22 ccRCC, in vivo, rep1


title: N2_7_CAM236_6

description: Library name: N2_7_CAM236_6


title: P22 kidney, in vivo, rep1


title: Hippocampus, 28 Months, Rep18

description:
Library name: 28M.N18
28M_18, J14370


title: N2_7_CAM245_2

description: Library name: N2_7_CAM245_2


title: N2_7_CAM229_3

description: Library name: N2_7_CAM229_3


title: P22 kidney, in vivo, rep3


title: P19 kidney, ischaemia, rep2


title: P19 ccRCC, ischaemia, rep1


title: P22 kidney, in vivo, rep2


title: P19 ccRCC, in vivo, rep1


title: N2_8_CAM229_3

description: Library name: N2_8_CAM229_3


title: Hippocampus, 28 Months, Rep14

description:
Library name: 28M.N14
28M_17, J14324


title: N2_7_CAM245_5

description: Library name: N2_7_CAM245_5


title: P18 ccRCC, ischaemia, rep1


title: P19 kidney, ischaemia, rep1


title: P19 ccRCC, ischaemia, rep2


title: N2_8_CAM228_5

description: Library name: N2_8_CAM228_5


title: Hippocampus, 28 Months, Rep15

description:
Library name: 28M.N15
28M_15, J14328


title: Hippocampus, 28 Months, Rep13

description:
Library name: 28M.N13
28M_16, J14312


title: Hippocampus, 28 Months, Rep17

description:
Library name: 28M.N17
28M_14, J14362


title: N2_8_CAM231_4

description: Library name: N2_8_CAM231_4


title: P19 kidney, in vivo, rep2


title: N2_8_CAM228_1

description: Library name: N2_8_CAM228_1


title: Hippocampus, 28 Months, Rep2

description:
Library name: 28M.N2
28M_12, J14216


title: P18 kidney, ischaemia, rep1


title: P19 kidney, in vivo, rep1


title: Hippocampus, 28 Months, Rep6

description:
Library name: 28M.N6
28M_10, J14252


title: P18 ccRCC, in vivo, rep2


title: N2_7_CAM228_4

description: Library name: N2_7_CAM228_4


title: P17 ccRCC, ischaemia, rep2


title: N2_8_CAM040_6

description: Library name: N2_8_CAM040_6


title: P18 ccRCC, in vivo, rep1


title: Hippocampus, 28 Months, Rep7

description:
Library name: 28M.N7
28M_9, J14254


title: P18 kidney, in vivo, rep1


title: P18 kidney, in vivo, rep2


title: Hippocampus, 28 Months, Rep1

description:
Library name: 28M.N1
28M_13, J14214


title: P17 kidney, ischaemia, rep2


title: P19 ccRCC, in vivo, rep2


title: N2_7_CAM229_6

description: Library name: N2_7_CAM229_6


title: Hippocampus, 28 Months, Rep8

description:
Library name: 28M.N8
28M_8, J14272


title: P17 ccRCC, ischaemia, rep1


title: P17 ccRCC, in vivo, rep2


title: Hippocampus, 28 Months, Rep4

description:
Library name: 28M.N4
28M_6, J14236


title: Hippocampus, 28 Months, Rep5

description:
Library name: 28M.N5
28M_7, J14238


title: N2_8_CAM241_3

description: Library name: N2_8_CAM241_3


title: P17 kidney, in vivo, rep1


title: P17 kidney, ischaemia, rep1


title: N2_8_CAM245_4

description: Library name: N2_8_CAM245_4


title: P17 ccRCC, in vivo, rep1


title: N2_3_CAM791_6

description: Library name: N2_3_CAM791_6


title: N2_3_CAM791_4

description: Library name: N2_3_CAM791_4


title: P16 ccRCC, ischaemia, rep3


title: P16 ccRCC, ischaemia, rep1


title: Hippocampus, 28 Months, Rep10

description:
Library name: 28M.N10
28M_3, J14290


title: Hippocampus, 28 Months, Rep3

description:
Library name: 28M.N3
28M_4, J14220


title: P16 ccRCC, ischaemia, rep2


title: N2_4_CAM795_5

description: Library name: N2_4_CAM795_5


title: P16 kidney, ischaemia, rep2


title: Hippocampus, 28 Months, Rep11

description:
Library name: 28M.N11
28M_2, J14296


title: P16 kidney, ischaemia, rep3


title: P16 kidney, ischaemia, rep1


title: N2_4_CAM796_1

description: Library name: N2_4_CAM796_1


title: P16 ccRCC, in vivo, rep2


title: Hippocampus, 28 Months, Rep9

description:
Library name: 28M.N9
28M_1, J14286


title: P16 kidney, in vivo, rep3


title: N2_5_CAM795_2

description: Library name: N2_5_CAM795_2


title: P16 ccRCC, in vivo, rep1


title: Hippocampus, 24 Months, Rep11

description:
Library name: 24M.N11
24M_32, J14304

value: 24 Months


title: P16 kidney, in vivo, rep2


title: P16 kidney, in vivo, rep1


title: Hippocampus, 24 Months, Rep13

description:
Library name: 24M.N13
24M_31, J14332


title: N2_4_CAM791_4

description: Library name: N2_4_CAM791_4


title: Hippocampus, 24 Months, Rep12

description:
Library name: 24M.N12
24M_30, J14326


title: N2_1_CAM791_2

description: Library name: N2_1_CAM791_2


title: N2_4_CAM040_5

description: Library name: N2_4_CAM040_5


title: Hippocampus, 24 Months, Rep16

description:
Library name: 24M.N16
24M_14, J14364


title: Hippocampus, 24 Months, Rep15

description:
Library name: 24M.N15
24M_12, J14360


title: N2_4_CAM788_6

description: Library name: N2_4_CAM788_6


title: N2_4_CAM040_4

description: Library name: N2_4_CAM040_4


title: N2_1_CAM787_2

description: Library name: N2_1_CAM787_2


title: N2_4_CAM791_5

description: Library name: N2_4_CAM791_5


title: Hippocampus, 24 Months, Rep14

description:
Library name: 24M.N14
24M_11, J14336


title: Hippocampus, 24 Months, Rep4

description:
Library name: 24M.N4
24M_10, J14250


title: N2_4_CAM795_4

description: Library name: N2_4_CAM795_4


title: Hippocampus, 24 Months, Rep10

description:
Library name: 24M.N10
24M_9, J14302


title: N2_4_CAM796_5

description: Library name: N2_4_CAM796_5


title: Hippocampus, 24 Months, Rep17

description:
Library name: 24M.N17
24M_13, J14344


title: Hippocampus, 24 Months, Rep6

description:
Library name: 24M.N6
24M_7, J14264


title: Hippocampus, 24 Months, Rep2

description:
Library name: 24M.N2
24M_8, J14228


title: N2_3_CAM787_2

description: Library name: N2_3_CAM787_2


title: N2_4_CAM787_3

description: Library name: N2_4_CAM787_3


title: Hippocampus, 24 Months, Rep8

description:
Library name: 24M.N8
24M_5, J14284


title: N2_3_CAM796_2

description: Library name: N2_3_CAM796_2


title: Hippocampus, 24 Months, Rep9

description:
Library name: 24M.N9
24M_4, J14294


title: N2_4_CAM796_4

description: Library name: N2_4_CAM796_4


title: Hippocampus, 24 Months, Rep7

description:
Library name: 24M.N7
24M_3, J14274


title: N2_4_CAM787_2

description: Library name: N2_4_CAM787_2


title: N2_4_CAM795_1

description: Library name: N2_4_CAM795_1


title: N2_3_CAM795_3

description: Library name: N2_3_CAM795_3


title: Hippocampus, 15 Months, Rep16

description:
Library name: 15M.N16
15M_16, J14352

value: 15 Months


title: Hippocampus, 24 Months, Rep3

description:
Library name: 24M.N3
24M_1, J14246


title: Hippocampus, 24 Months, Rep1

description:
Library name: 24M.N1
24M_2, J14212


title: N2_4_CAM787_4

description: Library name: N2_4_CAM787_4


title: Hippocampus, 15 Months, Rep13

description:
Library name: 15M.N13
15M_13, J14322


title: Hippocampus, 15 Months, Rep11

description:
Library name: 15M.N11
15M_12, J14310


title: Hippocampus, 15 Months, Rep15

description:
Library name: 15M.N15
15M_15, J14342


title: N2_3_CAM787_1

description: Library name: N2_3_CAM787_1


title: N2_3_CAM791_2

description: Library name: N2_3_CAM791_2


title: Hippocampus, 15 Months, Rep12

description:
Library name: 15M.N12
15M_11, J14320


title: Hippocampus, 15 Months, Rep10

description:
Library name: 15M.N10
15M_10, J14308


title: N2_3_CAM796_5

description: Library name: N2_3_CAM796_5


title: Hippocampus, 15 Months, Rep3

description:
Library name: 15M.N3
15M_8, J14232


title: N2_4_CAM040_2

description: Library name: N2_4_CAM040_2


title: N2_4_CAM795_6

description: Library name: N2_4_CAM795_6


title: N2_2_CAM791_1

description: Library name: N2_2_CAM791_1


title: N2_4_CAM787_1

description: Library name: N2_4_CAM787_1


title: N2_3_CAM796_3

description: Library name: N2_3_CAM796_3


title: Hippocampus, 15 Months, Rep8

description:
Library name: 15M.N8
15M_7, J14280


title: N2_3_CAM040_5

description: Library name: N2_3_CAM040_5


title: Hippocampus, 24 Months, Rep5

description:
Library name: 24M.N5
24M_6, J14258


title: Hippocampus, 15 Months, Rep4

description:
Library name: 15M.N4
15M_6, J14242


title: N2_4_CAM791_3

description: Library name: N2_4_CAM791_3


title: N2_1_CAM040_5

description: Library name: N2_1_CAM040_5


title: Hippocampus, 15 Months, Rep14

description:
Library name: 15M.N14
15M_14, J14334


title: Hippocampus, 15 Months, Rep1

description:
Library name: 15M.N1
15M_9, J14222


title: Hippocampus, 15 Months, Rep9

description:
Library name: 15M.N9
15M_5, J14288


title: N2_3_CAM796_1

description: Library name: N2_3_CAM796_1


title: Hippocampus, 15 Months, Rep7

description:
Library name: 15M.N7
15M_4, J14278


title: N2_1_CAM787_3

description: Library name: N2_1_CAM787_3


title: N2_3_CAM787_3

description: Library name: N2_3_CAM787_3


title: Hippocampus, 15 Months, Rep6

description:
Library name: 15M.N6
15M_3, J14262


title: N2_7_CAM236_1

description: Library name: N2_7_CAM236_1


title: Hippocampus, 15 Months, Rep2

description:
Library name: 15M.N2
15M_2, J14230


title: Hippocampus, 15 Months, Rep5

description:
Library name: 15M.N5
15M_1, J14244


title: N2_5_CAM788_2

description: Library name: N2_5_CAM788_2


title: Hippocampus, 9 Months, Rep12

description:
Library name: 9M.N12
9M_16, J14348

value: 9 Months


title: Hippocampus, 9 Months, Rep13

description:
Library name: 9M.N13
9M_15, J14356


title: N2_2_CAM788_3

description: Library name: N2_2_CAM788_3


title: N2_4_CAM040_3

description: Library name: N2_4_CAM040_3


title: Hippocampus, 9 Months, Rep14

description:
Library name: 9M.N14
9M_14, J14366


title: N2_3_CAM787_6

description: Library name: N2_3_CAM787_6


title: Hippocampus, 9 Months, Rep10

description:
Library name: 9M.N10
9M_12, J14314


title: N2_3_CAM795_2

description: Library name: N2_3_CAM795_2


title: Hippocampus, 9 Months, Rep16

description:
Library name: 9M.N16
9M_13, J14372


title: N2_3_CAM791_3

description: Library name: N2_3_CAM791_3


title: Hippocampus, 9 Months, Rep11

description:
Library name: 9M.N11
9M_10, J14316


title: Hippocampus, 9 Months, Rep4

description:
Library name: 9M.N4
9M_9, J14260


title: Hippocampus, 9 Months, Rep15

description:
Library name: 9M.N15
9M_11, J14368


title: Hippocampus, 9 Months, Rep5

description:
Library name: 9M.N5
9M_8, J14266


title: N2_5_CAM788_6

description: Library name: N2_5_CAM788_6


title: N2_3_CAM795_4

description: Library name: N2_3_CAM795_4


title: Cel-ccar-1(n2070)_R3

city: Baltimore

first: Nikita

middle: Sudhir

last: Jhaveri

address: 3400 N Charles Street

institute: Johns Hopkins University

description:
Library name: Cel-ccar-1(n2070)_R3
column L

data_processing:
RNA sample quality was vetted for inclusion based on Bioanalyzer RIN scores
MultiQC was used to aggregate multiple results into a single report (Ewels et al. 2016).
Reads were aligned to the genome using RNA STAR, set to paired-end sequences and default settings (Dobin et al. 2013).
To count hits per gene, featureCounts was used with default settings for paired-end reads (Liao, et al. 2014).
Assembly: C. elegans WBcel235, with WS283 for annotation
Supplementary files format and content: Excel file (.xlsx) containing gene read counts, obtained from Featurecounts

source_name: Whole organism (hermaphrodite)

growth_protocol: C. elegans was cultured at 20ºC with Escherichia coli OP50 as described (Brenner 1974). C. elegans animals (Wild-type N2, ccar-1(gk433), and ccar-1(n2070)) were synchronized to mixed stage. Four biological replicates were prepared for each genotype.

extract_protocol:
RNA was isolated using Trizol-reagent (Sigma, USA, Catalog Number T9424), chloroform, and isopropanol (Chomczynski and Sacchi 1987).
cDNA libraries were constructed from 100–200 ng RNA using an Illumina-specific commercial kit (NEBNext® Ultra™ II RNA Library Prep Kit for Illumina (cat # E7770)

value: Whole organism (hermaphrodite)

tag: time

value: Mixed stage


title: Cel-ccar-1(n2070)_R2

description:
Library name: Cel-ccar-1(n2070)_R2
column K


title: N2_5_CAM787_3

description: Library name: N2_5_CAM787_3

value: Single individual


title: Cel-ccar-1(n2070)_R4

description:
Library name: Cel-ccar-1(n2070)_R4
column M


title: Hippocampus, 9 Months, Rep8

description:
Library name: 9M.N8
9M_7, J14282


title: Hippocampus, 9 Months, Rep7

description:
Library name: 9M.N7
9M_6, J14276


title: Hippocampus, 9 Months, Rep2

description:
Library name: 9M.N2
9M_5, J14226


title: N2_5_CAM788_5

description: Library name: N2_5_CAM788_5


title: Cel-ccar-1(gk433)_R3

description:
Library name: Cel-ccar-1(gk433)_R3
column H


title: Hippocampus, 9 Months, Rep1

description:
Library name: 9M.N1
9M_4, J14218


title: Cel-ccar-1(n2070)_R1

description:
Library name: Cel-ccar-1(n2070)_R1
column J


title: Cel-ccar-1(gk433)_R4

description:
Library name: Cel-ccar-1(gk433)_R4
column I


title: N2_5_CAM040_6

description: Library name: N2_5_CAM040_6


title: N2_5_CAM791_4

description: Library name: N2_5_CAM791_4


title: Cel-ccar-1(gk433)_R2

description:
Library name: Cel-ccar-1(gk433)_R2
column G


title: N2_5_CAM796_1

description: Library name: N2_5_CAM796_1


title: Cel-ccar-1(gk433)_R1

description:
Library name: Cel-ccar-1(gk433)_R1
column F


title: Hippocampus, 9 Months, Rep9

description:
Library name: 9M.N9
9M_3, J14300


title: N2_1_CAM788_1

description: Library name: N2_1_CAM788_1


title: N2_5_CAM796_3

description: Library name: N2_5_CAM796_3


title: N2_R4

description:
Library name: N2_R4
column E


title: Hippocampus, 9 Months, Rep6

description:
Library name: 9M.N6
9M_2, J14268


title: Hippocampus, 9 Months, Rep3

description:
Library name: 9M.N3
9M_1, J14240


title: Hippocampus, 3 Months, Rep12

description:
Library name: 3M.N12
3M_16, J14340

value: 3 Months


title: Hippocampus, 3 Months, Rep11

description:
Library name: 3M.N11
3M_15, J14330


title: N2_5_CAM795_4

description: Library name: N2_5_CAM795_4


title: N2_R2

description:
Library name: N2_R2
column C


title: Hippocampus, 3 Months, Rep10

description:
Library name: 3M.N10
3M_14, J14318


title: N2_5_CAM040_3

description: Library name: N2_5_CAM040_3


title: N2_4_CAM040_6

description: Library name: N2_4_CAM040_6


title: N2_R3

description:
Library name: N2_R3
column D


title: N2_R1

description:
Library name: N2_R1
column B


title: Hippocampus, 3 Months, Rep16

description:
Library name: 3M.N16
3M_13, J14358


title: N2_1_CAM795_2

description: Library name: N2_1_CAM795_2


title: 9-EOT

city: PHOENIX

first: Aarthi

last: Talla

state: ARIZONA

address: 2448 W ROWEL RD

institute: IMMUNASYST

description:
Library name: Sample 49
whole blood collected from timepoint EOT

data_processing:
Samples were demutliplexed using 'bcl2fastq.1.8.4' (*Note - Raw Fastqs for some samples are unavailable since they were lost during lab relocation).
The sequencing raw reads were trimmed off adapter sequence contaminants using Trimmomatic 0.32.
The trimmed reads mapped onto the Ensembl version of the human genome (Ensembl - Grch38), using the STAR 2.4.0f1 aligner.
The transcript abundance was then estimated by counting the number of reads mapping to the exons that are unique to the transcripts of a gene using HTSeq. The obtained transcript counts were normalized by TMM (Trimmed Mean of M-values) by correcting for the library size and differential expressed genes were determined using the edgeR Bioconductor package.
Whole blood RNA-sequencing was done in 2 batches and transcript count matrices were corrected using the ComBat package in R.
Assembly: Ensembl - Grch38
Supplementary files format and content: Tab delimited text files of the batch corrected counts per million (CPM) of every transcript per sample are provided.

source_name: whole blood

extract_protocol:
10mL of whole peripheral blood (collected in PAXgene tubes) were collected for each sample and cryopreserved at -80C. The PreAnalytix PAXgene Blood RNA  kit was used to extract RNA and an RNA-integrity number of 8 or above (measured using a bioanalyzer) was ensured prior to library preparation.
The construction of mRNA libraries was performed according to the Illumina TruSeq V2 library preparation kit. The validation of these libraries occurred through microelectrophoresis on a 2100 Bioanalyzer system (Agilent), quantification using Kapa Library Quantification Kits (Roche), and eventual pooling and clustering on Illumina TruSeq V2 flow cells.

value: whole blood

tag: disease state

value: HIV infected

value: EOT

tag: participant id


title: 9-C01D02

description:
Library name: Sample 48
whole blood collected from timepoint C01D02


title: N2_5_CAM796_4

description: Library name: N2_5_CAM796_4

tag: tissue

value: WT


title: N2_3_CAM795_6

description: Library name: N2_3_CAM795_6


title: Hippocampus, 3 Months, Rep13

description:
Library name: 3M.N13
3M_12, J14346


title: N2_3_CAM791_1

description: Library name: N2_3_CAM791_1


title: N2_5_CAM791_5

description: Library name: N2_5_CAM791_5


title: 8-C01D02

description:
Library name: Sample 45
whole blood collected from timepoint C01D02


title: 8-EOT

description:
Library name: Sample 46
whole blood collected from timepoint EOT


title: Hippocampus, 3 Months, Rep14

description:
Library name: 3M.N14
3M_10, J14350


title: N2_5_CAM796_5

description: Library name: N2_5_CAM796_5


title: 8-C01D01

description:
Library name: Sample 44
whole blood collected from timepoint C01D01

value: pre-treatment/baseline


title: N2_1_CAM791_5

description: Library name: N2_1_CAM791_5


title: Hippocampus, 3 Months, Rep6

description:
Library name: 3M.N6
3M_9, J14256


title: N2_4_CAM788_2

description: Library name: N2_4_CAM788_2


title: Hippocampus, 3 Months, Rep5

description:
Library name: 3M.N5
3M_8, J14248


title: 7-C01D02

description:
Library name: Sample 42
whole blood collected from timepoint C01D02


title: Hippocampus, 3 Months, Rep3

description:
Library name: 3M.N3
3M_7, J14224


title: N2_5_CAM796_2

description: Library name: N2_5_CAM796_2


title: N2_1_CAM796_1

description: Library name: N2_1_CAM796_1


title: Hippocampus, 3 Months, Rep2

description:
Library name: 3M.N2
3M_5, J14210


title: N2_2_CAM795_2

description: Library name: N2_2_CAM795_2


title: Hippocampus, 3 Months, Rep1

description:
Library name: 3M.N1
3M_4, J14208


title: 6-C01D01

description:
Library name: Sample 39
whole blood collected from timepoint C01D01


title: N2_5_CAM795_5

description: Library name: N2_5_CAM795_5


title: Hippocampus, 3 Months, Rep9

description:
Library name: 3M.N9
3M_3, J14298


title: 5-C01D02

description:
Library name: Sample 38
whole blood collected from timepoint C01D02


title: N2_5_CAM040_2

description: Library name: N2_5_CAM040_2


title: 9-C01D01

description:
Library name: Sample 47
whole blood collected from timepoint C01D01


title: Hippocampus, 3 Months, Rep15

description:
Library name: 3M.N15
3M_11, J14354


title: Hippocampus, 3 Months, Rep8

description:
Library name: 3M.N8
3M_2, J14292


title: 5-C01D01

description:
Library name: Sample 37
whole blood collected from timepoint C01D01


title: N2_1_CAM795_6

description: Library name: N2_1_CAM795_6


title: Hippocampus, 3 Months, Rep4

description:
Library name: 3M.N4
3M_1, J14234


title: N2_5_CAM787_6

description: Library name: N2_5_CAM787_6


title: 7-EOT

description:
Library name: Sample 43
whole blood collected from timepoint EOT


title: 4-EOT

description:
Library name: Sample 36
whole blood collected from timepoint EOT