title: BSSE_QGF_143471_HN7CFDRXX_1_A06_Plate_B_2007Seq7_CCGGTTCCTA_TATATTCGAG_S137_L001_R1_001.fastq.gz

description:
ID in processed data file:
A6_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410151_R07C01

status: Public on Jul 20 2022

type: genomic

city: Oslo

first: Lasse

last: Pihlstrøm

address: Sognsvannsveien 20

department: Department of Neurology

country: Norway

institute: Oslo University Hospital

description: Human postmortem frontal cortex tissue

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using and Illumina array scanner with standard recommended Illumina settings

data_processing:
Raw signal intensity data were imported into R using the minfi package. CpG sites with a beadcount < 3 in 5% of samples or detection p-value > 0.05 in 1% of samples were filtered out using the pfilter function in the wateRmelon package. Samples failing sex-checks, samples with low median signal intensities as flagged by the minfi getQC function, and outlier samples with low proportions of NeuN positive cells as estimated using the estimateCellCounts algorithm implemented in the mini package were filtered out. The wateRmelon dasen method was used for normalization.
Normalized average Beta using the dasen method implemented in the wateRmelon R package

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: frontal cortex

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted using the Qiagen AllPrep DNA/RNA/miRNA Universal Kit according to the manufacturer’s instructions

tag: slide

value: no

tag: Sex

value: M

tag: dementia

value: yes

value: DLB

value: sparse


title: frontal_cortex_203048410057_R01C01

description: Human postmortem frontal cortex tissue

value: F

value: AD

value: frequent


title: frontal_cortex_203048410151_R06C01

description: Human postmortem frontal cortex tissue

value: control

value: CONTR


title: BSSE_QGF_143469_HN7CFDRXX_1_G05_Plate_B_2007Seq7_TGGCCTCTGT_TGAGACAGCG_S135_L001_R1_001.fastq.gz

type: SRA

city: Basel

first: Tobias

last: Kull

address: Mattenstrasse 26

country: Switzerland

institute: ETH Zurich

description:
ID in processed data file:
G5_Plate2
see PickedGMPs_PassedQC_191029TK20.csv

library_source: transcriptomic

data_processing:
Illumina RTA Version: 2.4.11 used for basecalling.
Sequenced reads were mapped to M21 musmusculus whole genome using star 2.5.3a with --quantMode GeneCounts.
The resulting sam files were converted into bam files with samtools. R
Raw counts were extracted from bam files using  subread version 1.5.0 featureCount with parameters:-t gene -g gene_id
Assembly: M21 (ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M21)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: The file "seq_metadata_column-sample-matching.xlsx" provides the column header ID for each sample in this data set. This information is also available in the 'Description' field above.

molecule: polyA RNA

organism: Mus musculus

source_name: GMP (ganulocyte monocyte progenitor)

extract_protocol:
Single GMP cells were isolated with a micromanipulator and immediately placed into lysis buffer at 4 degree Celsius. Then Smart-Seq2 in adaption from https://www.nature.com/articles/s41467-018-05347-6
Nextera DNA Flex Library Prep

tag: strain

tag: tissue

value: bone marrow

tag: cell type

value: GMP (ganulocyte monocyte progenitor)

tag: age

value: 12 - 19 weeks

tag: genotype

value: GFP-p65 homozygous /H2BmCherry heterozygous


title: frontal_cortex_203048410151_R03C01

description: Human postmortem frontal cortex tissue

value: Atypical


title: BSSE_QGF_143468_HN7CFDRXX_1_F05_Plate_B_2007Seq7_TGGTGTTATG_TCCAATTCTA_S134_L001_R1_001.fastq.gz

description:
ID in processed data file:
F5_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: BSSE_QGF_143470_HN7CFDRXX_1_H05_Plate_B_2007Seq7_CCAGGCACCA_ACGCTAATTA_S136_L001_R1_001.fastq.gz

description:
ID in processed data file:
H5_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203271740112_R01C01

description: Human postmortem frontal cortex tissue

value: PD


title: frontal_cortex_203048410055_R07C01

description: Human postmortem frontal cortex tissue

value: VD

value: PDD


title: BSSE_QGF_143467_HN7CFDRXX_1_E05_Plate_B_2007Seq7_AACGAGGCCG_ATACCTGGAT_S133_L001_R1_001.fastq.gz

description:
ID in processed data file:
E5_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203271740112_R02C01

description: Human postmortem frontal cortex tissue

value: no


title: BSSE_QGF_143466_HN7CFDRXX_1_D05_Plate_B_2007Seq7_ATGTAACGTT_ACGATTGCTG_S132_L001_R1_001.fastq.gz

description:
ID in processed data file:
D5_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410131_R08C01

description: Human postmortem frontal cortex tissue

value: M

value: yes


title: frontal_cortex_203048410055_R03C01

description: Human postmortem frontal cortex tissue

value: DLB


title: frontal_cortex_203048410131_R06C01

description: Human postmortem frontal cortex tissue

value: sparse


title: frontal_cortex_203048410131_R07C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203048410151_R05C01

description: Human postmortem frontal cortex tissue

value: F


title: BSSE_QGF_143465_HN7CFDRXX_1_C05_Plate_B_2007Seq7_TTCGGTGTGA_GAACAAGTAT_S131_L001_R1_001.fastq.gz

description:
ID in processed data file:
C5_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: BSSE_QGF_143475_HN7CFDRXX_1_E06_Plate_B_2007Seq7_CTTATTGGCC_GATAACAAGT_S141_L001_R1_001.fastq.gz

description:
ID in processed data file:
E6_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: BSSE_QGF_143474_HN7CFDRXX_1_D06_Plate_B_2007Seq7_TACGTGAAGG_CGGTTATTAG_S140_L001_R1_001.fastq.gz

description:
ID in processed data file:
D6_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410131_R04C01

description: Human postmortem frontal cortex tissue

value: AD

value: frequent


title: frontal_cortex_203048410131_R05C01

description: Human postmortem frontal cortex tissue


title: BSSE_QGF_143462_HN7CFDRXX_1_H04_Plate_B_2007Seq7_CTAATAACCG_AACCGCATCG_S128_L001_R1_001.fastq.gz

description:
ID in processed data file:
H4_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: BSSE_QGF_143461_HN7CFDRXX_1_G04_Plate_B_2007Seq7_GCTGACGTTG_TGTTCGCATT_S127_L001_R1_001.fastq.gz

description:
ID in processed data file:
G4_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410131_R03C01

description: Human postmortem frontal cortex tissue

value: control

value: CONTR


title: BSSE_QGF_143460_HN7CFDRXX_1_F04_Plate_B_2007Seq7_AGGAGGTATC_CCAGTTGGCA_S126_L001_R1_001.fastq.gz

description:
ID in processed data file:
F4_Plate2
see PickedGMPs_PassedQC_191029TK20.csv

value: bone marrow

value: GMP (ganulocyte monocyte progenitor)


title: BSSE_QGF_143459_HN7CFDRXX_1_E04_Plate_B_2007Seq7_AGGCCGTGGA_CTCGTGCGTT_S125_L001_R1_001.fastq.gz

description:
ID in processed data file:
E4_Plate2
see PickedGMPs_PassedQC_191029TK20.csv

value: 12 - 19 weeks

value: GFP-p65 homozygous /H2BmCherry heterozygous


title: frontal_cortex_203048410130_R08C01

description: Human postmortem frontal cortex tissue

value: iLBD

value: moderate


title: BSSE_QGF_143458_HN7CFDRXX_1_D04_Plate_B_2007Seq7_CTGCGTTACC_TATGGCTCGA_S124_L001_R1_001.fastq.gz

description:
ID in processed data file:
D4_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203253040201_R07C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203048410130_R06C01

description: Human postmortem frontal cortex tissue

value: PDD

value: Atypical


title: frontal_cortex_203048410131_R02C01

description: Human postmortem frontal cortex tissue

value: no

value: M


title: frontal_cortex_203281980108_R08C01

description: Human postmortem frontal cortex tissue

value: DLB

value: yes


title: BSSE_QGF_143464_HN7CFDRXX_1_B05_Plate_B_2007Seq7_ATAGCCAAGA_AGTGCCACTG_S130_L001_R1_001.fastq.gz

description:
ID in processed data file:
B5_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: BSSE_QGF_143454_HN7CFDRXX_1_H03_Plate_B_2007Seq7_AGGACAGGCC_CATTCCAGCT_S120_L001_R1_001.fastq.gz

description:
ID in processed data file:
H3_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410130_R04C01

description: Human postmortem frontal cortex tissue


title: BSSE_QGF_143456_HN7CFDRXX_1_B04_Plate_B_2007Seq7_GATATTGTGT_ACCACACGGT_S122_L001_R1_001.fastq.gz

description:
ID in processed data file:
B4_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410130_R07C01

description: Human postmortem frontal cortex tissue

value: F

value: sparse


title: BSSE_QGF_143453_HN7CFDRXX_1_G03_Plate_B_2007Seq7_TCCGCCAATT_CTCCGTGCTG_S119_L001_R1_001.fastq.gz

description:
ID in processed data file:
G3_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: BSSE_QGF_143455_HN7CFDRXX_1_A04_Plate_B_2007Seq7_AGAGAACCTA_GGTTATGCTA_S121_L001_R1_001.fastq.gz

description:
ID in processed data file:
A4_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: BSSE_QGF_143463_HN7CFDRXX_1_A05_Plate_B_2007Seq7_TCTAGGCGCG_CGAAGGTTAA_S129_L001_R1_001.fastq.gz

description:
ID in processed data file:
A5_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: BSSE_QGF_143452_HN7CFDRXX_1_F03_Plate_B_2007Seq7_ATACTTGTTC_TAACCGCCGA_S118_L001_R1_001.fastq.gz

description:
ID in processed data file:
F3_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410130_R02C01

description: Human postmortem frontal cortex tissue

value: AD


title: BSSE_QGF_143451_HN7CFDRXX_1_E03_Plate_B_2007Seq7_CCGTGACCGA_CCGAACGTTG_S117_L001_R1_001.fastq.gz

description:
ID in processed data file:
E3_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: BSSE_QGF_143450_HN7CFDRXX_1_D03_Plate_B_2007Seq7_ATCGGCGAAG_TCCAAGAATT_S116_L001_R1_001.fastq.gz

description:
ID in processed data file:
D3_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: BSSE_QGF_143449_HN7CFDRXX_1_C03_Plate_B_2007Seq7_AGGCAGCTCT_CGGCTAACGT_S115_L001_R1_001.fastq.gz

description:
ID in processed data file:
C3_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410130_R03C01

description: Human postmortem frontal cortex tissue

value: frequent


title: frontal_cortex_203048410027_R08C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203048410130_R01C01

description: Human postmortem frontal cortex tissue

value: MSA


title: BSSE_QGF_143448_HN7CFDRXX_1_B03_Plate_B_2007Seq7_TAGAATTGGA_GTTAATCTGA_S114_L001_R1_001.fastq.gz

description:
ID in processed data file:
B3_Plate2
see PickedGMPs_PassedQC_191029TK20.csv

value: bone marrow


title: BSSE_QGF_143447_HN7CFDRXX_1_A03_Plate_B_2007Seq7_GAATTACAAG_ACCGGCTCAG_S113_L001_R1_001.fastq.gz

description:
ID in processed data file:
A3_Plate2
see PickedGMPs_PassedQC_191029TK20.csv

value: GMP (ganulocyte monocyte progenitor)


title: frontal_cortex_203048410027_R05C01

description: Human postmortem frontal cortex tissue

value: control

value: CONTR


title: BSSE_QGF_143446_HN7CFDRXX_1_H02_Plate_B_2007Seq7_TGATGGCTAC_CCAACAACAT_S112_L001_R1_001.fastq.gz

description:
ID in processed data file:
H2_Plate2
see PickedGMPs_PassedQC_191029TK20.csv

value: 12 - 19 weeks

value: GFP-p65 homozygous /H2BmCherry heterozygous


title: frontal_cortex_203048410027_R04C01

description: Human postmortem frontal cortex tissue

value: PDD


title: frontal_cortex_203048410027_R06C01

description: Human postmortem frontal cortex tissue

value: moderate


title: frontal_cortex_203048410027_R03C01

description: Human postmortem frontal cortex tissue

value: no


title: BSSE_QGF_143457_HN7CFDRXX_1_C04_Plate_B_2007Seq7_CGTACAGGAA_TAGGTTCTCT_S123_L001_R1_001.fastq.gz

description:
ID in processed data file:
C4_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: BSSE_QGF_143444_HN7CFDRXX_1_F02_Plate_B_2007Seq7_TAATTAGCGT_TGGTTAAGAA_S110_L001_R1_001.fastq.gz

description:
ID in processed data file:
F2_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410027_R02C01

description: Human postmortem frontal cortex tissue


title: BSSE_QGF_143445_HN7CFDRXX_1_G02_Plate_B_2007Seq7_ATTAACAAGG_TGTTGTTCGT_S111_L001_R1_001.fastq.gz

description:
ID in processed data file:
G2_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410026_R08C01

description: Human postmortem frontal cortex tissue

value: VD


title: frontal_cortex_203048410026_R07C01

description: Human postmortem frontal cortex tissue

value: Atypical


title: BSSE_QGF_143442_HN7CFDRXX_1_D02_Plate_B_2007Seq7_AGTACTCATG_ATGTCGTGGT_S108_L001_R1_001.fastq.gz

description:
ID in processed data file:
D2_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: BSSE_QGF_143443_HN7CFDRXX_1_E02_Plate_B_2007Seq7_GGTAGAATTA_GTAGCCATCA_S109_L001_R1_001.fastq.gz

description:
ID in processed data file:
E2_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: BSSE_QGF_143441_HN7CFDRXX_1_C02_Plate_B_2007Seq7_GAACGCAATA_ATCTTACTGT_S107_L001_R1_001.fastq.gz

description:
ID in processed data file:
C2_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410027_R01C01

description: Human postmortem frontal cortex tissue

value: M

value: yes


title: BSSE_QGF_143440_HN7CFDRXX_1_B02_Plate_B_2007Seq7_TTCTGTAGAA_GAGCGCAATA_S106_L001_R1_001.fastq.gz

description:
ID in processed data file:
B2_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410026_R06C01

description: Human postmortem frontal cortex tissue

value: F

value: sparse


title: BSSE_QGF_143439_HN7CFDRXX_1_A02_Plate_B_2007Seq7_CAGCAATCGT_TGTGATGTAT_S105_L001_R1_001.fastq.gz

description:
ID in processed data file:
A2_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410026_R05C01

description: Human postmortem frontal cortex tissue

value: DLB


title: BSSE_QGF_143436_HN7CFDRXX_1_F01_Plate_B_2007Seq7_ATGGCGCCTG_TCCACGGCCT_S102_L001_R1_001.fastq.gz

description:
ID in processed data file:
F1_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410027_R07C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203048410026_R02C01

description: Human postmortem frontal cortex tissue

value: AD

value: frequent


title: BSSE_QGF_143438_HN7CFDRXX_1_H01_Plate_B_2007Seq7_GGTCTATTAA_CCACGACACG_S104_L001_R1_001.fastq.gz

description:
ID in processed data file:
H1_Plate2
see PickedGMPs_PassedQC_191029TK20.csv

value: bone marrow

value: GMP (ganulocyte monocyte progenitor)


title: frontal_cortex_203048410026_R04C01

description: Human postmortem frontal cortex tissue


title: BSSE_QGF_143437_HN7CFDRXX_1_G01_Plate_B_2007Seq7_TCCGTTATGT_TTGTAGTGTA_S103_L001_R1_001.fastq.gz

description:
ID in processed data file:
G1_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410026_R03C01

description: Human postmortem frontal cortex tissue


title: BSSE_QGF_143435_HN7CFDRXX_1_E01_Plate_B_2007Seq7_ATATGCATGT_TGGTGCCTGG_S101_L001_R1_001.fastq.gz

description:
ID in processed data file:
E1_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410018_R05C01

description: Human postmortem frontal cortex tissue


title: BSSE_QGF_143433_HN7CFDRXX_1_C01_Plate_B_2007Seq7_TCTCACACGC_CGGACAGTGA_S99_L001_R1_001.fastq.gz

description:
ID in processed data file:
C1_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410026_R01C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203048410018_R04C01

description: Human postmortem frontal cortex tissue

value: control

value: CONTR


title: frontal_cortex_203045470190_R08C01

description: Human postmortem frontal cortex tissue


title: BSSE_QGF_143431_HN7CFDRXX_1_A01_Plate_B_2007Seq7_TGCCGGTCAG_CCTGATACAA_S97_L001_R1_001.fastq.gz

description:
ID in processed data file:
A1_Plate2
see PickedGMPs_PassedQC_191029TK20.csv

value: 12 - 19 weeks

value: GFP-p65 homozygous /H2BmCherry heterozygous


title: D16, PorcineTrophoblastCells, Control, biorep5

city: Olsztyn

first: Monika

middle: M

last: Kaczmarek

address: Tuwima 10

country: Poland

institute: Institute of Animal Reproduction and Food Research, Polish Academy of Sciences

data_processing:
The raw reads were first quality checked and trimmed using FastQC and Trimmomatic.
The reads were mapped to the Sus scrofa reference genome (Sscrofa11.1) using STAR.
Mapped reads were counted with featureCounts 2.0.3.
Differential gene expression analysis was conducted using DESeq2 1.34.0
Assembly: Sus scrofa reference genome (Sscrofa11.1)
Supplementary files format and content: Raw counts of sequencing reads

molecule: total RNA

organism: Sus scrofa

source_name: trophoblast

growth_protocol: After enzymatic dispersion porcine trophoblast primary cells were cultured in DMEM/F12 supplemented with 10 % (v/v) newborn calf serum (NCS) and 1 % (v/v) penicillin/streptomycin (P/S) at 37°C with 5% CO2 to reach the confluence.

extract_protocol:
Total RNA was isolated using miRVana miRNA isolation kit and stored at -80°C in RNase-free H2O until assayed. Quantity and quality of RNA were assessed using Bioanalyzer 2100 and Qubit 3.0 Fluorometer.
One microgram of total RNA was used to construct cDNA libraries with the TruSeq Stranded Total RNA with Ribo-Zero Gold Human/Mouse/Rat kit following manufacturer's protocols.

treatment_protocol: Cells were treated for 6 h with 2% EVs in free DMEM/F12. Next medium was changed to DMEM/F12 supplemented with 10 % (v/v) NCS and 1 % (v/v) P/S and cells were cultured for another 18 h. Each treatment was performed using EVs and trophoblast cells isolated from the same animal.

value: trophoblast

value: porcine primary trophoblast cells

value: WT

tag: treatment

value: Control


title: frontal_cortex_203048410018_R03C01

description: Human postmortem frontal cortex tissue

value: no

value: M


title: D16, PorcineTrophoblastCells, EVs, biorep6

value: EVs


title: frontal_cortex_203048410018_R06C01

description: Human postmortem frontal cortex tissue

value: yes

value: sparse


title: BSSE_QGF_143432_HN7CFDRXX_1_B01_Plate_B_2007Seq7_CACTCAATTC_TTAAGTTGTG_S98_L001_R1_001.fastq.gz

description:
ID in processed data file:
B1_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: D16, PorcineTrophoblastCells, Control, biorep6


title: frontal_cortex_203048410018_R02C01

description: Human postmortem frontal cortex tissue

value: F

value: DLB

value: moderate


title: BSSE_QGF_143430_HN7CFDRXX_1_H12_Plate_A_2007Seq7_CCTCCGTCCA_CACATCGGTG_S96_L001_R1_001.fastq.gz

description:
ID in processed data file:
H12_Plate1
see PickedGMPs_PassedQC_191029TK20.csv

value: bone marrow

value: GMP (ganulocyte monocyte progenitor)


title: frontal_cortex_203045470190_R07C01

description: Human postmortem frontal cortex tissue

value: PDD


title: frontal_cortex_203048410018_R01C01

description: Human postmortem frontal cortex tissue


title: D16, PorcineTrophoblastCells, EVs, biorep5


title: BSSE_QGF_143429_HN7CFDRXX_1_G12_Plate_A_2007Seq7_GTATTCCACC_ATGTAGACAA_S95_L001_R1_001.fastq.gz

description:
ID in processed data file:
G12_Plate1
see PickedGMPs_PassedQC_191029TK20.csv

value: 12 - 19 weeks


title: D16, PorcineTrophoblastCells, EVs, biorep4


title: frontal_cortex_203045470190_R06C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203045470190_R05C01

description: Human postmortem frontal cortex tissue

value: PD


title: frontal_cortex_203045470190_R04C01

description: Human postmortem frontal cortex tissue

value: AD


title: D16, PorcineTrophoblastCells, Control, biorep4

value: trophoblast

value: porcine primary trophoblast cells


title: frontal_cortex_203045470190_R03C01

description: Human postmortem frontal cortex tissue


title: BSSE_QGF_143427_HN7CFDRXX_1_E12_Plate_A_2007Seq7_ACATATCCAG_TATGTGCAAT_S93_L001_R1_001.fastq.gz

description:
ID in processed data file:
E12_Plate1
see PickedGMPs_PassedQC_191029TK20.csv

value: GFP-p65 homozygous /H2BmCherry heterozygous


title: BSSE_QGF_143428_HN7CFDRXX_1_F12_Plate_A_2007Seq7_TCATAGATTG_GATTAAGGTG_S94_L001_R1_001.fastq.gz

description:
ID in processed data file:
F12_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203045470064_R08C01

description: Human postmortem frontal cortex tissue

value: no

value: FTD


title: frontal_cortex_203045470190_R01C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203045470190_R02C01

description: Human postmortem frontal cortex tissue

value: M


title: D16, PorcineTrophoblastCells, Control, biorep3

value: WT

value: Control


title: frontal_cortex_203045470064_R07C01

description: Human postmortem frontal cortex tissue

value: control

value: iLBD

value: frequent


title: frontal_cortex_203045470064_R06C01

description: Human postmortem frontal cortex tissue

value: F

value: yes

value: moderate

value: Atypical


title: D16, PorcineTrophoblastCells, EVs, biorep2

value: EVs


title: BSSE_QGF_143434_HN7CFDRXX_1_D01_Plate_B_2007Seq7_TCAATGGAGA_GCACTACAAC_S100_L001_R1_001.fastq.gz

description:
ID in processed data file:
D1_Plate2
see PickedGMPs_PassedQC_191029TK20.csv

value: bone marrow

value: GMP (ganulocyte monocyte progenitor)

value: 12 - 19 weeks


title: frontal_cortex_203045470064_R05C01

description: Human postmortem frontal cortex tissue


title: D16, PorcineTrophoblastCells, EVs, biorep3

value: trophoblast

value: porcine primary trophoblast cells


title: frontal_cortex_203045470064_R04C01

description: Human postmortem frontal cortex tissue

value: no

value: DLB

value: sparse


title: frontal_cortex_203045470064_R03C01

description: Human postmortem frontal cortex tissue

value: M


title: BSSE_QGF_143424_HN7CFDRXX_1_B12_Plate_A_2007Seq7_ACTTCAAGCG_GAACCATGAA_S90_L001_R1_001.fastq.gz

description:
ID in processed data file:
B12_Plate1
see PickedGMPs_PassedQC_191029TK20.csv

value: GFP-p65 homozygous /H2BmCherry heterozygous


title: BSSE_QGF_143425_HN7CFDRXX_1_C12_Plate_A_2007Seq7_TCAGAAGGCG_GGCCATCATA_S91_L001_R1_001.fastq.gz

description:
ID in processed data file:
C12_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: BSSE_QGF_143426_HN7CFDRXX_1_D12_Plate_A_2007Seq7_GCGTTGGTAT_ACATACTTCC_S92_L001_R1_001.fastq.gz

description:
ID in processed data file:
D12_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: D16, PorcineTrophoblastCells, Control, biorep2

value: WT

value: Control


title: D16, PorcineTrophoblastCells, EVs, biorep1


title: frontal_cortex_203045470058_R08C01

description: Human postmortem frontal cortex tissue

value: PD


title: D16, PorcineTrophoblastCells, Control, biorep1


title: frontal_cortex_203045470058_R07C01

description: Human postmortem frontal cortex tissue

value: F

value: control

value: iLBD


title: frontal_cortex_203045470064_R02C01

description: Human postmortem frontal cortex tissue

value: AD

value: yes

value: frequent


title: BSSE_QGF_143423_HN7CFDRXX_1_A12_Plate_A_2007Seq7_GTCCGTAAGC_CGTGTATCTT_S89_L001_R1_001.fastq.gz

description:
ID in processed data file:
A12_Plate1
see PickedGMPs_PassedQC_191029TK20.csv

value: bone marrow

value: GMP (ganulocyte monocyte progenitor)

value: 12 - 19 weeks


title: frontal_cortex_203045470064_R01C01

description: Human postmortem frontal cortex tissue

value: no


title: frontal_cortex_203045470058_R06C01

description: Human postmortem frontal cortex tissue

value: moderate


title: R3_HCC827_ONT

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

data_processing:
MinKNOW PromethION Release 19.12.9 (ONT)
Base calling and quality scoring (Illumina): Real-Time Analysis on board software v2.4.6. Base calling (ONT): Guppy 4.2.2, with the PromethION model, in high-accuracy mode.
Circular consensus sequence generation (PacBio): ccs 4.0.0 (commit SL-release-8.0.0).
FASTQ file generation and de-multiplexing (Illumina): bcl2fastw conversion software v2.15.0.4. De-multiplexing (PacBio): lima 1.10.0 (commit SL-release-8.0.0).
Refining and clustering (PacBio): isoseq3 3.2.2 (commit SL-release-8.0.0)
Sequenced reads were mapped to the GRCh38 reference genome and RNA Sequin decoy chromosome combined sequences using the align function in the Rsubread package (version 1.34.7, Liao et al. Nucleic Acids Research, 2013) with default parameters (Illumina),  minimap2 version 2.17 with arguments -ax splice  MD -L (ONT) and pbmm2 1.1.0 (commit SL-release-8.0.0) (PacBio).
Gene-level counts were obtained using the featureCounts function (Liao et al. Bioinformatics, 2014) from the Rsubread package (version 1.34.7) using the GENCODE v33 annotation and RNA sequin annotation 2.4 combined GTF file (Illumina) and the GENCODE v29 annotation and RNA sequin annotation 2.4 combined GTF file (ONT, PacBio) .
Genome_build: GrCh38 and RNA sequin decoy chromosome 2.4 combined sequences
Supplementary_files_format_and_content: Tab-delimited text files with columns representing Ensembl IDs and the number of reads mapping to that gene.

source_name: Human lung cancer cell line HCC827

growth_protocol: The cell lines were retrieved from the ATCC (https://www.atcc.org/) and cultured in Roswell Park Memorial Institute (RPMI) 1640 medium with 10% fetal calf serum and 1% penicillin-streptomycin. The cells were grown independently at 37°C with 5% carbon dioxide until near 100% confluency.

extract_protocol:
The mRNA was extracted using a Qiagen RNA miniprep kit and purified using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490).
3.75ng purified mRNA spiked with sequins were used for the NEBNext Ultra II Directional RNA Library Prep Kit (Illumina). Fragmentation was done for 15 minutes at 94°C, and final amplification with 11 PCR cycles. The libraries were sequenced in 75PE on NextSeq 500. The cRNA-PCR Barcoding (SQK-PCS109 with SQK-PBK004) kit was used with the supplied protocol (ONT). Amplication for 1.5ng purified mRNA spiked with sequins was done with 14 PCR cycles with a 2 minutes and 30 seconds extension step. Pooled barcoded libraries were sequenced on 5 PromethION R9 flow cells. Iso-Seq libraries were prepared and sequenced by Novogene on Sequel II (PacBio). Libraries were prepared according to the manufacturer's specifications from total RNA spiked in with sequins. Size selection was performed for the standard ~2kb target. The total number of PCR cycles is 12.

treatment_protocol: Cells were dissociated into single cell suspensions in FACS buffer, centrifuged and frozen at -80 °C.

value: Human lung cancer cell line

tag: cell line

tag: replicate


title: frontal_cortex_203045470058_R04C01

description: Human postmortem frontal cortex tissue

value: M

value: PDD


title: frontal_cortex_203045470058_R05C01

description: Human postmortem frontal cortex tissue

value: DLB

value: sparse


title: BSSE_QGF_143421_HN7CFDRXX_1_G11_Plate_A_2007Seq7_CCTCTACATG_GATACCTCCT_S87_L001_R1_001.fastq.gz

description:
ID in processed data file:
G11_Plate1
see PickedGMPs_PassedQC_191029TK20.csv

value: GFP-p65 homozygous /H2BmCherry heterozygous


title: R2_HCC827_ONT


title: BSSE_QGF_143420_HN7CFDRXX_1_F11_Plate_A_2007Seq7_TTGGAATTCC_ACGTCAATAC_S86_L001_R1_001.fastq.gz

description:
ID in processed data file:
F11_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203045470058_R03C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203045470155_R08C01

description: Human postmortem frontal cortex tissue

value: PD


title: frontal_cortex_203045470058_R02C01

description: Human postmortem frontal cortex tissue

value: F


title: BSSE_QGF_143418_HN7CFDRXX_1_D11_Plate_A_2007Seq7_ACAAGTGGAC_GCGCGATGTT_S84_L001_R1_001.fastq.gz

description:
ID in processed data file:
D11_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: BSSE_QGF_143419_HN7CFDRXX_1_E11_Plate_A_2007Seq7_TGGTACCTAA_CATGAGTACT_S85_L001_R1_001.fastq.gz

description:
ID in processed data file:
E11_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: R3_H1975_ONT

source_name: Human lung cancer cell line NCI-H1975


title: frontal_cortex_203045470058_R01C01

description: Human postmortem frontal cortex tissue

value: control

value: CONTR


title: frontal_cortex_203045470155_R05C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203045470155_R06C01

description: Human postmortem frontal cortex tissue


title: BSSE_QGF_143417_HN7CFDRXX_1_C11_Plate_A_2007Seq7_TATGCCTTAC_AGACACATTA_S83_L001_R1_001.fastq.gz

description:
ID in processed data file:
C11_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203045470155_R07C01

description: Human postmortem frontal cortex tissue


title: BSSE_QGF_143422_HN7CFDRXX_1_H11_Plate_A_2007Seq7_GGAGCGTGTA_ATCCGTAAGT_S88_L001_R1_001.fastq.gz

description:
ID in processed data file:
H11_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: R2_H1975_ONT


title: frontal_cortex_203045470155_R04C01

description: Human postmortem frontal cortex tissue


title: BSSE_QGF_143416_HN7CFDRXX_1_B11_Plate_A_2007Seq7_ACCGTTACAA_CTCATAGCGA_S82_L001_R1_001.fastq.gz

description:
ID in processed data file:
B11_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203045470155_R02C01

description: Human postmortem frontal cortex tissue

value: AD

value: yes


title: frontal_cortex_203045470155_R01C01

description: Human postmortem frontal cortex tissue


title: BSSE_QGF_143415_HN7CFDRXX_1_A11_Plate_A_2007Seq7_TGTCGCTGGT_TCGTCTGACT_S81_L001_R1_001.fastq.gz

description:
ID in processed data file:
A11_Plate1
see PickedGMPs_PassedQC_191029TK20.csv

value: bone marrow


title: R1_H1975_ONT


title: frontal_cortex_203045470155_R03C01

description: Human postmortem frontal cortex tissue

value: frequent


title: novo_50ng_6

city: Tampere

first: Andre

last: Ribeiro

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

data_processing:
RNA sequencing reads were trimmed to remove possible adapter sequences and nucleotides with poor quality with Trimmomatic v.0.36
Trimmed reads were then mapped to the reference genome, E. coli MG1655 (NC_000913.3), using the STAR aligner v.2.5.2b (for temperature RNA-seq) and Bowtie2 aligner v.2.3.5.1 (for Novobiocin RNA-seq), which outputs BAM files
featureCounts from the Rsubread R package (v.1.34.7) was used to calculate unique gene hit counts. Genes with less than 5 counts in more than 3 samples, and genes whose mean counts are less than 10 were removed from further analysis.
Gene hit counts was then used for the subsequent differential expression analysis. For this, we used the DESeq2 R package (v.1.24.0) to compare gene expression between groups of samples and calculate log2 of fold changes (LFC) of RNA levels between group of samples and calculate p-values using Wald tests (function ‘nbinomWaldTest’).
P-values were adjusted for multiple hypotheses testing (Benjamini–Hochberg, BH procedure)
Genome_build: Escherichia coli str. K-12 substr. MG1655 (NC_000913.3)
Supplementary_files_format_and_content: tab-delimited .csv file containing Deseq normalized raw counts

growth_protocol: From a glycerol stock (at -80°C), cells were streaked on LB agar plates and incubated at 37 °C overnight. The next day, three independent single colonies were picked from the plate, inoculated in fresh LB medium at 30 °C overnight with shaking at 250 RPM. Overnight culture cells were then diluted into fresh M9 media, supplemented with 0.4 % glucose, amino acids, and vitamin solutions, until reaching 0.03 OD and allowed to grow with aeration until reaching the mid-exponential phase of growth (OD of 0.3). At this moment, the temperature was shifted to 15 °C, and cells were collected at OD=0.3 (considered as 0th minute), and after 20 minutes, 80 minutes and 180 minutes at 15 °C. The same was done with 3 colonies not subjected to the temperature shift, for purposes of control.    For RNA-seq measurements under Gyrase inhibition, the antibiotic Novobiocin was added (50 50 ng/μl) upon reaching the OD ~0.3 and the cells were only collected 120 minutes after the treatment. This did not disturb the growth rate.

extract_protocol:
Total RNA was extracted using RNeasy kit (Qiagen).
RNA-seq libraries were constructed according to the Illumina's protocol.
RNA sequencing was conducted at GENEWIZ, Inc. (Leipzig, Germany).

treatment_protocol: Extracted RNA was treated twice with DNase (Turbo DNA-free kit, Ambion, USA) and quantified using Qubit 2.0 Fluorometer RNA assay (Invitrogen, Carlsbad, CA, USA).


title: BSSE_QGF_143414_HN7CFDRXX_1_H10_Plate_A_2007Seq7_GGCAAGCCAG_CAAGCATCCG_S80_L001_R1_001.fastq.gz

description:
ID in processed data file:
H10_Plate1
see PickedGMPs_PassedQC_191029TK20.csv

value: GMP (ganulocyte monocyte progenitor)

value: 12 - 19 weeks


title: R1_HCC827_ONT


title: novo_50ng_5

organism: Escherichia coli str. K-12 substr. MG1655


title: frontal_cortex_203045470154_R08C01

description: Human postmortem frontal cortex tissue

value: no


title: frontal_cortex_203045470154_R05C01

description: Human postmortem frontal cortex tissue


title: novo_50ng_4


title: frontal_cortex_203045470154_R07C01

description: Human postmortem frontal cortex tissue


title: BSSE_QGF_143413_HN7CFDRXX_1_G10_Plate_A_2007Seq7_ACGGTCAGGA_CGGCCTCGTT_S79_L001_R1_001.fastq.gz

description:
ID in processed data file:
G10_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203045470154_R04C01

description: Human postmortem frontal cortex tissue

value: moderate


title: novo_0ng_3


title: frontal_cortex_203045470026_R08C01

description: Human postmortem frontal cortex tissue

value: M


title: frontal_cortex_203045470154_R02C01

description: Human postmortem frontal cortex tissue

value: iLBD


title: frontal_cortex_203045470154_R01C01

description: Human postmortem frontal cortex tissue


title: BSSE_QGF_143411_HN7CFDRXX_1_E10_Plate_A_2007Seq7_TCTGGTATCC_CGTTGCTTAC_S77_L001_R1_001.fastq.gz

description:
ID in processed data file:
E10_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: BSSE_QGF_143412_HN7CFDRXX_1_F10_Plate_A_2007Seq7_CATTAGTGCG_TGACTACATA_S78_L001_R1_001.fastq.gz

description:
ID in processed data file:
F10_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: novo_0ng_2


title: novo_0ng_1


title: frontal_cortex_203045470026_R06C01

description: Human postmortem frontal cortex tissue

value: DLB


title: frontal_cortex_203045470026_R07C01

description: Human postmortem frontal cortex tissue


title: BSSE_QGF_143410_HN7CFDRXX_1_D10_Plate_A_2007Seq7_CTGACTCTAC_ACGGCCGTCA_S76_L001_R1_001.fastq.gz

description:
ID in processed data file:
D10_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: UM-UC-3, PAI-1, biol rep2

city: Los Angeles

first: Hideki

last: Furuya

state: CA

address: 110 N. George Burns Road, Davis 2025

department: Surgery

country: USA

institute: Cedars Sinai Medical Center

library_source: genomic

data_processing:
Quality control check on FASTQ raw files were performed using FastQC and Trimmomatic is a fast, multithreaded command line tool that can be used to trim and crop Illumina (FASTQ) data as well as to remove adapters.
Processed data were mapped to the reference human genome (hg19) using Bowtie (version 1.1.1) with the default parameters.
PCR duplicates were removed from all downstream analyses with Picard (http://broadinstitute.github.io/picard/).
Enriched regions were identified using MACS2 (version 2.1.0.20140616).
Assembly: UCSC.hg19
Supplementary files format and content: bdg
Supplementary files format and content: bed

extract_protocol:
ChIP assay was performed using MAGnify™ Chromatin Immunoprecipitation System (Cat No. 492024, Thermo Fisher Scientific) with anti-PAI-1 antibody (M01, clone 3F2; Abnova, Taipei City, Taiwan) according to manufacturer’s instruction.
Library construction was performed using the Illumina TruSeq Nano DNA library preparation kit (Illumina, San Diego, CA, USA).

value: Human bladder cancer

tag: chip antibody


title: frontal_cortex_203045470026_R05C01

description: Human postmortem frontal cortex tissue

value: sparse


title: BSSE_QGF_143409_HN7CFDRXX_1_C10_Plate_A_2007Seq7_CTCTGCAGCG_GATGGATGTA_S75_L001_R1_001.fastq.gz

description:
ID in processed data file:
C10_Plate1
see PickedGMPs_PassedQC_191029TK20.csv

value: GFP-p65 homozygous /H2BmCherry heterozygous


title: frontal_cortex_203045470026_R03C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203045470026_R04C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203048410019_R01C01

description: Human postmortem frontal cortex tissue


title: UM-UC-3, input


title: frontal_cortex_203045470026_R02C01

description: Human postmortem frontal cortex tissue

value: PDD


title: BSSE_QGF_143407_HN7CFDRXX_1_A10_Plate_A_2007Seq7_CCTGCGGAAC_ATCATAGGCT_S73_L001_R1_001.fastq.gz

description:
ID in processed data file:
A10_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203045470154_R03C01

description: Human postmortem frontal cortex tissue

value: F

value: FTD


title: UM-UC-3, PAI-1, biol rep1


title: BSSE_QGF_143408_HN7CFDRXX_1_B10_Plate_A_2007Seq7_TTCATAAGGT_TGTTAGAAGG_S74_L001_R1_001.fastq.gz

description:
ID in processed data file:
B10_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: BSSE_QGF_143406_HN7CFDRXX_1_H09_Plate_A_2007Seq7_ACACAGGTGG_TGAGCGTTGT_S72_L001_R1_001.fastq.gz

description:
ID in processed data file:
H9_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: RT112, PAI-1, biol rep2


title: RT112, PAI-1, biol rep1


title: BSSE_QGF_143405_HN7CFDRXX_1_G09_Plate_A_2007Seq7_CTTGTACACC_AAGCGCGCTT_S71_L001_R1_001.fastq.gz

description:
ID in processed data file:
G9_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203045470026_R01C01

description: Human postmortem frontal cortex tissue

value: PD


title: frontal_cortex_203045470024_R08C01

description: Human postmortem frontal cortex tissue


title: BSSE_QGF_143404_HN7CFDRXX_1_F09_Plate_A_2007Seq7_GTATTGACGT_GGAATTCCAA_S70_L001_R1_001.fastq.gz

description:
ID in processed data file:
F9_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: HUVEC_607KD3

city: Duarte

first: Zhen

last: Chen

address: 1500 E Duarte Rd

department: DMRI

institute: City of Hope

description: polyA RNA enriched

data_processing:
none provided by the submitter
Genome_build: hg38
Supplementary_files_format_and_content: The processed counts.txt files are tab-delimited tables which includes annotation columns (‘Geneid’) and data columns (i.e. read counts for genes) for each library.

source_name: Human Umbilical Vein Endothelial Cells transfected with LNA targeting LINC00607 and harvested after 48 hours

growth_protocol: HUVECs and HVSMC were grown following the manufacturer's protocol

extract_protocol:
Approximately 1 million cells were used for total RNA extraction and construction of strand-specific mRNA-seq library
The libraries were constructed using the KAPA mRNA stranded Hyper kit following the user manual

treatment_protocol: HUVECs or HVSMC were cultured in complete medium; transfected with either 50 nM scramble LNA (Scr) or LNA targeting LINC00607 (607KD) and then harvested after 48 hours post transfection.

value: HUVEC

tag: assay

value: RNA-seq


title: frontal_cortex_203045470024_R05C01

description: Human postmortem frontal cortex tissue

value: yes


title: frontal_cortex_203045470024_R04C01

description: Human postmortem frontal cortex tissue

value: AD


title: frontal_cortex_203045470024_R06C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203045470024_R07C01

description: Human postmortem frontal cortex tissue


title: RT112, input


title: BSSE_QGF_143403_HN7CFDRXX_1_E09_Plate_A_2007Seq7_TGGAGTACTT_TCTGTGTGGA_S69_L001_R1_001.fastq.gz

description:
ID in processed data file:
E9_Plate1
see PickedGMPs_PassedQC_191029TK20.csv

value: bone marrow

value: GMP (ganulocyte monocyte progenitor)

value: 12 - 19 weeks


title: frontal_cortex_203045470024_R03C01

description: Human postmortem frontal cortex tissue

value: no

value: M


title: frontal_cortex_203045470024_R02C01

description: Human postmortem frontal cortex tissue


title: HUVEC_607KD2

description: polyA RNA enriched


title: BSSE_QGF_143402_HN7CFDRXX_1_D09_Plate_A_2007Seq7_CACGGAACAA_AACCTAGCAC_S68_L001_R1_001.fastq.gz

description:
ID in processed data file:
D9_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203045470023_R08C01

description: Human postmortem frontal cortex tissue

value: moderate


title: HUVEC_607KD1

description: polyA RNA enriched


title: frontal_cortex_203045470023_R07C01

description: Human postmortem frontal cortex tissue


title: HUVEC_Scr3

description: polyA RNA enriched

source_name: Human Umbilical Vein Endothelial Cells transfected with scramble LNA and harvested after 48 hours


title: frontal_cortex_203045470023_R05C01

description: Human postmortem frontal cortex tissue

value: epilepsy

value: iLBD


title: BSSE_QGF_143400_HN7CFDRXX_1_B09_Plate_A_2007Seq7_ATACCAACGC_AATTGCTGCG_S66_L001_R1_001.fastq.gz

description:
ID in processed data file:
B9_Plate1
see PickedGMPs_PassedQC_191029TK20.csv

value: GFP-p65 homozygous /H2BmCherry heterozygous


title: frontal_cortex_203045470023_R04C01

description: Human postmortem frontal cortex tissue

value: control


title: frontal_cortex_203045470023_R06C01

description: Human postmortem frontal cortex tissue

value: F


title: HUVEC_Scr2

description: polyA RNA enriched


title: frontal_cortex_203045470024_R01C01

description: Human postmortem frontal cortex tissue

value: PDD

value: sparse


title: frontal_cortex_203045470023_R02C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203045470022_R08C01

description: Human postmortem frontal cortex tissue

value: VD


title: frontal_cortex_203045470022_R07C01

description: Human postmortem frontal cortex tissue

value: DLB


title: frontal_cortex_203045470023_R01C01

description: Human postmortem frontal cortex tissue

value: yes


title: frontal_cortex_203045470022_R04C01

description: Human postmortem frontal cortex tissue

value: AD

value: frequent


title: M026P8A7M_bis

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

data_processing:
Basecalling was performed by Illumina CASAVA.
Reads were aligned against the Human Genome assembly GRCh38 using STAR with default settings (version 2.5).
HTSeq-count (version 0.9) was used to generate rage gene counts
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table (tab delimited) with raw gene counts for every gene and every sample

source_name: ACM CStC 3 passage 8 adipo + MB3

growth_protocol: Cardiac stromal cells (CStCs) from ACM patients were isolated and characterized as previously reported (PMID: 20833652, PMID: 26590176). Cells were cultured in basal medium (BM) composed of IMDM (Lonza), supplemented with 20% Foetal Bovine Serum (FBS, Hyclone, Italy), Penicillin- Streptomycin 1% (Thermo Fisher Scientific) and 20mM L-Glutamine (Thermo Fisher Scientific).

extract_protocol:
Total RNA was extracted from CStCs using Direct-zol RNA Kit (Zymo Research), according to manufacturer’s instructions. The concentration and purity of the isolated total RNA was assessed by Nanodrop and Qubit, while the integrity was evaluated using the Experion RNA StdSens Analysis Kit (Bio- Rad). High quality RNA, with A260/A280 > 1.8, A260/A230 ranging from 1.8 up to 2.02 and RQI > 9.5, were used for subsequent library preparation.
500 ng of RNA for each sample were used for the preparations of the libraries, using the QuantSeq 3' mRNA-Seq Library Prep FWD (Lexogen). Samples were sequenced using the platform HiSeq2500, following the protocol SR1000.

treatment_protocol: Adipogenic differentiation was performed by culturing the cells for 7 days in adipogenic medium (ADIPO) composed of IMDM, supplemented with 10% FBS (FBS, Gibco), 0.5 mM 3-isobutyl-1-methylxanthine (IBMX, Sigma- Aldrich), 0.1 mM indomethacin (Sigma-Aldrich), 0.1 µM hydrocortisone (Sigma-Aldrich), Penicillin- Streptomycin 1% (Thermo Fisher Scientific), 20 mM L-Glutamine (Thermo Fisher Scientific) (PMID: 26590176). CStCs treatment with the specific GCN5 inhibitor MB-3 (200 µM, Sigma-Aldrich) (PMID: 15274229; PMID: 17154519) was performed in ADIPO medium for 7 days.

value: cardiac stromal cells

tag: individual

value: ACM 3

value: male

value: adipogenic medium + MB3

tag: passage


title: frontal_cortex_203045470022_R06C01

description: Human postmortem frontal cortex tissue

value: no


title: M020P11A7M_bis

source_name: ACM CStC 2 passage 11 adipo + MB3

value: ACM 2


title: frontal_cortex_203045470022_R05C01

description: Human postmortem frontal cortex tissue


title: BSSE_QGF_143397_HN7CFDRXX_1_G08_Plate_A_2007Seq7_ATTGCGCGGT_TTGGCTCCGC_S63_L001_R1_001.fastq.gz

description:
ID in processed data file:
G8_Plate1
see PickedGMPs_PassedQC_191029TK20.csv

value: bone marrow

value: GMP (ganulocyte monocyte progenitor)

value: 12 - 19 weeks


title: BSSE_QGF_143396_HN7CFDRXX_1_F08_Plate_A_2007Seq7_AACACTGTTA_GCAAGTCTCA_S62_L001_R1_001.fastq.gz

description:
ID in processed data file:
F8_Plate1
see PickedGMPs_PassedQC_191029TK20.csv

value: GFP-p65 homozygous /H2BmCherry heterozygous


title: BSSE_QGF_143399_HN7CFDRXX_1_A09_Plate_A_2007Seq7_TAATGTGTCT_GTAAGGCATA_S65_L001_R1_001.fastq.gz

description:
ID in processed data file:
A9_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: M035P10A7M

source_name: ACM CStC 5 passage 8 adipo + MB3

value: ACM 5

value: female


title: frontal_cortex_203045470208_R05C01

description: Human postmortem frontal cortex tissue

value: F


title: BSSE_QGF_143395_HN7CFDRXX_1_E08_Plate_A_2007Seq7_TGGCTAATCA_AGGCATGTAG_S61_L001_R1_001.fastq.gz

description:
ID in processed data file:
E8_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203045470022_R02C01

description: Human postmortem frontal cortex tissue

value: M

value: PDD


title: M020P10A7M

source_name: ACM CStC 2 passage 10 adipo + MB3


title: BSSE_QGF_143394_HN7CFDRXX_1_D08_Plate_A_2007Seq7_TTACCTGGAA_ACAGTTCCAG_S60_L001_R1_001.fastq.gz

description:
ID in processed data file:
D8_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410130_R05C01

description: Human postmortem frontal cortex tissue

value: MSA

value: yes

value: DLB


title: HUVEC_Scr1

description: polyA RNA enriched

value: HUVEC

value: RNA-seq


title: frontal_cortex_203045470023_R03C01

description: Human postmortem frontal cortex tissue

value: sparse


title: frontal_cortex_203048410058_R02C01

description: Human postmortem frontal cortex tissue

value: no


title: frontal_cortex_203045470019_R07C01

description: Human postmortem frontal cortex tissue

value: moderate


title: frontal_cortex_203048410018_R07C01

description: Human postmortem frontal cortex tissue

value: control

value: CONTR


title: M020P11A7M

value: cardiac stromal cells

value: ACM 2

value: male

value: adipogenic medium + MB3


title: BSSE_QGF_143398_HN7CFDRXX_1_H08_Plate_A_2007Seq7_TGGCGCGAAC_AACTGATACT_S64_L001_R1_001.fastq.gz

description:
ID in processed data file:
H8_Plate1
see PickedGMPs_PassedQC_191029TK20.csv

value: bone marrow

value: GMP (ganulocyte monocyte progenitor)

value: 12 - 19 weeks

value: GFP-p65 homozygous /H2BmCherry heterozygous


title: BSSE_QGF_143393_HN7CFDRXX_1_C08_Plate_A_2007Seq7_CTGTTGGTCC_ATAGACCGTT_S59_L001_R1_001.fastq.gz

description:
ID in processed data file:
C8_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410057_R05C01

description: Human postmortem frontal cortex tissue

value: yes

value: F


title: BSSE_QGF_143390_HN7CFDRXX_1_H07_Plate_A_2007Seq7_AACGCACGAG_GCCTCGGATA_S56_L001_R1_001.fastq.gz

description:
ID in processed data file:
H7_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203045470210_R08C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203045470022_R03C01

description: Human postmortem frontal cortex tissue

value: DLB


title: frontal_cortex_203045470210_R06C01

description: Human postmortem frontal cortex tissue


title: M061P8A7M

source_name: ACM CStC 7 passage 8 adipo + MB3

value: ACM 7


title: frontal_cortex_203045470022_R01C01

description: Human postmortem frontal cortex tissue

value: M

value: PD


title: frontal_cortex_203045470019_R01C01

description: Human postmortem frontal cortex tissue

value: no


title: frontal_cortex_203045470019_R08C01

description: Human postmortem frontal cortex tissue


title: BSSE_QGF_143391_HN7CFDRXX_1_A08_Plate_A_2007Seq7_TCTATCCTAA_CGTCGACTGG_S57_L001_R1_001.fastq.gz

description:
ID in processed data file:
A8_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203045470019_R02C01

description: Human postmortem frontal cortex tissue

value: AD

value: sparse


title: M035P10A7

source_name: ACM CStC 5 passage 10 adipo

value: cardiac stromal cells

value: ACM 5

value: female

value: adipogenic medium


title: BSSE_QGF_143392_HN7CFDRXX_1_B08_Plate_A_2007Seq7_CTCGCTTCGG_TACTAGTCAA_S58_L001_R1_001.fastq.gz

description:
ID in processed data file:
B8_Plate1
see PickedGMPs_PassedQC_191029TK20.csv

value: bone marrow


title: frontal_cortex_203045470019_R05C01

description: Human postmortem frontal cortex tissue

value: moderate


title: frontal_cortex_203045470210_R05C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203045470019_R04C01

description: Human postmortem frontal cortex tissue

value: VD


title: M026P8A7_bis

source_name: ACM CStC 3 passage 8 adipo

value: ACM 3

value: male


title: BSSE_QGF_143388_HN7CFDRXX_1_F07_Plate_A_2007Seq7_GCATAAGCTT_TTCCGTCGCA_S54_L001_R1_001.fastq.gz

description:
ID in processed data file:
F7_Plate1
see PickedGMPs_PassedQC_191029TK20.csv

value: GMP (ganulocyte monocyte progenitor)

value: 12 - 19 weeks

value: GFP-p65 homozygous /H2BmCherry heterozygous


title: BSSE_QGF_143387_HN7CFDRXX_1_E07_Plate_A_2007Seq7_GGAATTGTAA_AGCACATCCT_S53_L001_R1_001.fastq.gz

description:
ID in processed data file:
E7_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: M020P11A7_bis

source_name: ACM CStC 2 passage 11 adipo

value: ACM 2


title: M026P8A7M

value: adipogenic medium + MB3


title: M064P9A7M

source_name: ACM CStC 8 passage 9 adipo + MB3

value: ACM 8


title: M020P10A7

source_name: ACM CStC 2 passage 10 adipo


title: frontal_cortex_203045470210_R03C01

description: Human postmortem frontal cortex tissue

source_name: frontal cortex

value: no

value: F

value: AD

value: frequent


title: BSSE_QGF_143386_HN7CFDRXX_1_D07_Plate_A_2007Seq7_TGATGTAAGA_GTGCGTCCTT_S52_L001_R1_001.fastq.gz

description:
ID in processed data file:
D7_Plate1
see PickedGMPs_PassedQC_191029TK20.csv

source_name: GMP (ganulocyte monocyte progenitor)


title: frontal_cortex_203045470019_R03C01

description: Human postmortem frontal cortex tissue

value: M

value: PD

value: sparse


title: frontal_cortex_203045470210_R01C01

description: Human postmortem frontal cortex tissue

value: yes


title: BSSE_QGF_143389_HN7CFDRXX_1_G07_Plate_A_2007Seq7_CTGAGGAATA_CTTAACCACT_S55_L001_R1_001.fastq.gz

description:
ID in processed data file:
G7_Plate1
see PickedGMPs_PassedQC_191029TK20.csv

value: bone marrow


title: BSSE_QGF_143385_HN7CFDRXX_1_C07_Plate_A_2007Seq7_CCTGTCTGTC_ACTGTTGTGA_S51_L001_R1_001.fastq.gz

description:
ID in processed data file:
C7_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203045470210_R07C01

description: Human postmortem frontal cortex tissue

value: PDD


title: M020P11A7

value: cardiac stromal cells

value: male

value: adipogenic medium


title: frontal_cortex_203045470208_R08C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203045470208_R07C01

description: Human postmortem frontal cortex tissue


title: BSSE_QGF_143383_HN7CFDRXX_1_A07_Plate_A_2007Seq7_AGTGTTGCAC_CTGGTACACG_S49_L001_R1_001.fastq.gz

description:
ID in processed data file:
A7_Plate1
see PickedGMPs_PassedQC_191029TK20.csv

value: GMP (ganulocyte monocyte progenitor)

value: 12 - 19 weeks

value: GFP-p65 homozygous /H2BmCherry heterozygous


title: frontal_cortex_203045470208_R06C01

description: Human postmortem frontal cortex tissue

value: MSA


title: frontal_cortex_203045470208_R04C01

description: Human postmortem frontal cortex tissue

value: no


title: BSSE_QGF_143382_HN7CFDRXX_1_H06_Plate_A_2007Seq7_CAGTGGCACT_TAACAATAGG_S48_L001_R1_001.fastq.gz

description:
ID in processed data file:
H6_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203253040201_R06C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203045470208_R02C01

description: Human postmortem frontal cortex tissue

value: F

value: VD

value: moderate


title: frontal_cortex_203045470208_R03C01

description: Human postmortem frontal cortex tissue

value: M


title: M026P8A7

value: ACM 3


title: frontal_cortex_203045470207_R08C01

description: Human postmortem frontal cortex tissue

value: frequent


title: frontal_cortex_203045470208_R01C01

description: Human postmortem frontal cortex tissue

value: yes

value: sparse


title: M064P9A7

source_name: ACM CStC 8 passage 9 adipo

value: ACM 8


title: frontal_cortex_203045470210_R02C01

description: Human postmortem frontal cortex tissue

value: AD

value: DLB


title: BSSE_QGF_143381_HN7CFDRXX_1_G06_Plate_A_2007Seq7_GTCCTGGATA_CGGTGGCGAA_S47_L001_R1_001.fastq.gz

description:
ID in processed data file:
G6_Plate1
see PickedGMPs_PassedQC_191029TK20.csv

value: bone marrow


title: frontal_cortex_203273630201_R02C01

description: Human postmortem frontal cortex tissue


title: Donor111_t2d

city: Stockholm

first: Jens

last: Hjerling-Leffler

address: Solnavägen 9

department: MBB

country: Sweden

institute: Karolinska Institutet

data_processing:
STAR 2.4.2a was used for alignments with the reference genome using 2-pass alignment to have improved performance of de nove splice junction reads, filtered for only uniquely mapping reads and saved in bam files.
Genome_build: hg38
Supplementary_files_format_and_content: The expression values of each RefSeq and Ensembl annotated gene is provided as tab-delimited text format.The expression values were computed as reads per kilobase of gene model and million mappable reads (RPKM), The expression values were computed per gene as described in Ramsköld et al. (2009 PLoS Comp Biol) using uniquely aligned reads and correcting ofr the uniqueiy alignable positions using MULTo (Storvall et al. 2013 PLoS ONE).
Supplementary_files_format_and_content: The count matrix shows the individual counts aligning to each gene per cell
Supplementary_files_format_and_content: Sequenced cells with number of mRNA reads <100000, percent of uniquely mapping reads <50 % or percent of uniquely exonic reads <40 % were removed. The expression of 3383 high-quality single-cell transcriptomes are stored in files Expression_counts_HQ_allsamples.txt and Expression_RPKM_HQ_allsamples.txt

source_name: Pancreatic islets cells

extract_protocol:
Human islets were received in 30 ml HEPES buffered media. Islets were transferred to a 50 ml tube and centrifuged at 150 rcf (g) for 2 min at RT. Supernatant was removed and cells were washed once with 5 ml of Accutase.  Another 5 ml of Accutase was added for incubation at 37 C for 8-10 min with pippeting up and down every other minute. After incubation 5 ml of cold islet media was added and cells were suspended by pipetting. Cells were passed through a 40 um cell strainer and centrifuged at 500 g for 5 min. Cells were washed twice with PBS, 500g and 5 min. Finally, cells were re-suspended in HBSS and keep on ice before FACS. Single-cell were FACS-sorted into 384 well plates.
Smart-seq2 (Picelli et al. Nature Methods 2013)

tag: disease state

value: Pancreatic islets cells


title: Donor110_t2d


title: Donor109_t2d


title: BSSE_QGF_143380_HN7CFDRXX_1_F06_Plate_A_2007Seq7_AGATCCATTA_ATCTCTACCA_S46_L001_R1_001.fastq.gz

description:
ID in processed data file:
F6_Plate1
see PickedGMPs_PassedQC_191029TK20.csv

value: GMP (ganulocyte monocyte progenitor)

value: 12 - 19 weeks


title: BSSE_QGF_143401_HN7CFDRXX_1_C09_Plate_A_2007Seq7_AGGATGTGCT_TTACAATTCC_S67_L001_R1_001.fastq.gz

description:
ID in processed data file:
C9_Plate1
see PickedGMPs_PassedQC_191029TK20.csv

value: GFP-p65 homozygous /H2BmCherry heterozygous


title: frontal_cortex_203271740112_R07C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203253040201_R05C01

description: Human postmortem frontal cortex tissue

value: no

value: PD

value: Atypical


title: BSSE_QGF_143384_HN7CFDRXX_1_B07_Plate_A_2007Seq7_GACACCATGT_TCAACGTGTA_S50_L001_R1_001.fastq.gz

description:
ID in processed data file:
B7_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203045470207_R05C01

description: Human postmortem frontal cortex tissue

value: control

value: iLBD

value: moderate


title: Donor108_t2d


title: M061P8A7

source_name: ACM CStC 7 passage 8 adipo

value: cardiac stromal cells

value: ACM 7

value: male

value: adipogenic medium


title: BSSE_QGF_143379_HN7CFDRXX_1_E06_Plate_A_2007Seq7_CGTTATTCTA_CCATAAGGTT_S45_L001_R1_001.fastq.gz

description:
ID in processed data file:
E6_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: BSSE_QGF_143378_HN7CFDRXX_1_D06_Plate_A_2007Seq7_CTGCGAGCCA_AATCCGGCCA_S44_L001_R1_001.fastq.gz

description:
ID in processed data file:
D6_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410156_R08C01

description: Human postmortem frontal cortex tissue

value: yes

value: M


title: frontal_cortex_203253040201_R04C01

description: Human postmortem frontal cortex tissue

value: F

value: DLB

value: sparse


title: BSSE_QGF_143377_HN7CFDRXX_1_C06_Plate_A_2007Seq7_CCATCTCGCC_TTCTATGGTT_S43_L001_R1_001.fastq.gz

description:
ID in processed data file:
C6_Plate1
see PickedGMPs_PassedQC_191029TK20.csv

value: bone marrow

value: GMP (ganulocyte monocyte progenitor)

value: 12 - 19 weeks


title: frontal_cortex_203271740112_R08C01

description: Human postmortem frontal cortex tissue

value: no


title: frontal_cortex_203045470207_R04C01

description: Human postmortem frontal cortex tissue

value: PDD


title: BSSE_QGF_143376_HN7CFDRXX_1_B06_Plate_A_2007Seq7_GTCTAATGGC_AGTGGTCAGG_S42_L001_R1_001.fastq.gz

description:
ID in processed data file:
B6_Plate1
see PickedGMPs_PassedQC_191029TK20.csv

value: GFP-p65 homozygous /H2BmCherry heterozygous


title: frontal_cortex_203045470207_R02C01

description: Human postmortem frontal cortex tissue

value: AD


title: Donor107_t2d

value: Pancreatic islets cells


title: frontal_cortex_203048410147_R08C01

description: Human postmortem frontal cortex tissue


title: Donor105_control


title: BSSE_QGF_143375_HN7CFDRXX_1_A06_Plate_A_2007Seq7_ACTCGGCAAT_GACAACTGAA_S41_L001_R1_001.fastq.gz

description:
ID in processed data file:
A6_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410146_R08C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203045470207_R01C01

description: Human postmortem frontal cortex tissue

value: frequent


title: Donor104_control


title: BSSE_QGF_143374_HN7CFDRXX_1_H05_Plate_A_2007Seq7_TATGTAGTCA_CGCACTAATG_S40_L001_R1_001.fastq.gz

description:
ID in processed data file:
H5_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: Donor103_control


title: frontal_cortex_203045470206_R07C01

description: Human postmortem frontal cortex tissue


title: BSSE_QGF_143373_HN7CFDRXX_1_G05_Plate_A_2007Seq7_CAATCGGCTG_GCTGTAGGAA_S39_L001_R1_001.fastq.gz

description:
ID in processed data file:
G5_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203038300119_R08C01

description: Human postmortem frontal cortex tissue


title: BSSE_QGF_143372_HN7CFDRXX_1_F05_Plate_A_2007Seq7_GTGCAGACAG_TACCATCCGT_S38_L001_R1_001.fastq.gz

description:
ID in processed data file:
F5_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410088_R04C01

description: Human postmortem frontal cortex tissue

value: PSP


title: frontal_cortex_203045470206_R05C01

description: Human postmortem frontal cortex tissue


title: Donor101_control


title: Donor102_control


title: BSSE_QGF_143371_HN7CFDRXX_1_E05_Plate_A_2007Seq7_TGTAATCGAC_GATCACCGCG_S37_L001_R1_001.fastq.gz

description:
ID in processed data file:
E5_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410152_R08C01

description: Human postmortem frontal cortex tissue


title: Donor106_control


title: frontal_cortex_203253040201_R03C01

description: Human postmortem frontal cortex tissue

value: moderate


title: hsRNH1_WT_Asyn_R2

city: Montpellier

first: Domenico

last: Libri

address: 1919 route de Mende

country: France

institute: IGMM - CNRS

data_processing:
sequencing performed with NextSeq 500 High Output Kit 75 cycles V2.
Samples were demultiplexed using the pyBarcodeFilter script from the pyCRAC utility suite (webb et al). Subsequently, the 3' adaptor was clipped with Cutadapt (-a TGGAATTCTCGGGTGCCAAGGATCTCGTATGCCGTCTTCTGCTTG -m 10) (martin M. embnet.journal, 2011) and the resulting insert  quality trimmed from the 3' end using Trimmomatic rolling mean clipping (bolger et al, 2014) (window size = 5, minimum quality = 25). At this stage the pyCRAC script pyFastqDuplicateRemover is used to collapse PCR duplicates and ensure each insert is represented only once. Each unique insert in our library is associated with a 6 nucleotides random tag within the 5' adaptor. During demultiplexing, pyBarcodeFilter retains this information in the header of each sequence. This information is used at this stage to better discern between entical inserts and PCR duplicates of the same insert. The resulting sequences are reverse complemented with Fastx reverse complement (part of the fastx toolkit, http://hannonlab.cshl.edu/fastx_toolkit/) and mapped to the R64 genome (cherry et al, 2012, nar) with bowtie2 (-N 1 -f) (langmead et al, 2012).
Genome_build: R64
Supplementary_files_format_and_content: Bigwig files providing coverage for all samples. All values are normalized to 10,000,000 reads or to S. pombe spike-in

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae culture

growth_protocol: For all datasets, 2L of yeast cells expressing an HTP-tagged version of target protein were grown at 30°C to OD600=0.6 in conditional media.

extract_protocol:
Cells were broken and extracts were prepared as described in the original publication.
Library construction is described in Candelli et al., EMBO J, 2018 and in the associated manuscript.

treatment_protocol: Cells were crosslinked for 50 seconds using a W5 UV crosslinking unit (UVO3).

value: wild-type

tag: cell cycle phase

value: Asynchronous


title: frontal_cortex_203048410088_R08C01

description: Human postmortem frontal cortex tissue

tag: slide

value: yes


title: BSSE_QGF_143370_HN7CFDRXX_1_D05_Plate_A_2007Seq7_ACCGGCCGTA_TGGCAATATT_S36_L001_R1_001.fastq.gz

description:
ID in processed data file:
D5_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203045470206_R01C01

description: Human postmortem frontal cortex tissue

tag: Sex

value: F

value: PD


title: frontal_cortex_203048410156_R07C01

description: Human postmortem frontal cortex tissue

value: M

value: DLB

tag: dementia


title: BSSE_QGF_143369_HN7CFDRXX_1_C05_Plate_A_2007Seq7_GGTAACTCGC_AAGTTGGTGA_S35_L001_R1_001.fastq.gz

description:
ID in processed data file:
C5_Plate1
see PickedGMPs_PassedQC_191029TK20.csv

tag: strain

value: bone marrow

value: GMP (ganulocyte monocyte progenitor)


title: frontal_cortex_203045470207_R07C01

description: Human postmortem frontal cortex tissue

value: no


title: frontal_cortex_203045470206_R08C01

description: Human postmortem frontal cortex tissue


title: Rnh201_WT+OEhsRNH1_Asyn_R2


title: frontal_cortex_203048410156_R06C01

description: Human postmortem frontal cortex tissue


title: hsRNH1_WT_Asyn_R1


title: BSSE_QGF_143368_HN7CFDRXX_1_B05_Plate_A_2007Seq7_CAGCCGCGTA_ACTAGCCGTG_S34_L001_R1_001.fastq.gz

description:
ID in processed data file:
B5_Plate1
see PickedGMPs_PassedQC_191029TK20.csv

tag: tissue

value: 12 - 19 weeks


title: Rnh201_WT+OEhsRNH1_Asyn_R1


title: frontal_cortex_203045470154_R06C01

description: Human postmortem frontal cortex tissue

value: MSA


title: BSSE_QGF_143367_HN7CFDRXX_1_A05_Plate_A_2007Seq7_TGATTATACG_GTCGATTACA_S33_L001_R1_001.fastq.gz

description:
ID in processed data file:
A5_Plate1
see PickedGMPs_PassedQC_191029TK20.csv

tag: cell type

value: GFP-p65 homozygous /H2BmCherry heterozygous


title: frontal_cortex_203253040201_R01C01

description: Human postmortem frontal cortex tissue

value: AD

value: sparse


title: Rnh201_sen1-3_Asyn_R2


title: BSSE_QGF_143365_HN7CFDRXX_1_G04_Plate_A_2007Seq7_GTGACACGCA_GCTTACGGAC_S31_L001_R1_001.fastq.gz

description:
ID in processed data file:
G4_Plate1
see PickedGMPs_PassedQC_191029TK20.csv

tag: age


title: BSSE_QGF_143366_HN7CFDRXX_1_H04_Plate_A_2007Seq7_ACAGTGTATG_GAACATACGG_S32_L001_R1_001.fastq.gz

description:
ID in processed data file:
H4_Plate1
see PickedGMPs_PassedQC_191029TK20.csv

tag: genotype


title: frontal_cortex_203048410155_R07C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203048410146_R07C01

description: Human postmortem frontal cortex tissue

value: PDD


title: frontal_cortex_203048410156_R05C01

description: Human postmortem frontal cortex tissue

value: frequent


title: frontal_cortex_203048410156_R01C01

description: Human postmortem frontal cortex tissue


title: Rnh201_sen1-3_Asyn_R1


title: frontal_cortex_203048410155_R06C01

description: Human postmortem frontal cortex tissue


title: BSSE_QGF_143364_HN7CFDRXX_1_F04_Plate_A_2007Seq7_CCACCAGGCA_CTTATGGAAT_S30_L001_R1_001.fastq.gz

description:
ID in processed data file:
F4_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410155_R05C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203045470206_R06C01

description: Human postmortem frontal cortex tissue


title: Rnh201_WT_Asyn_R1

value: wild-type


title: frontal_cortex_203048410155_R03C01

description: Human postmortem frontal cortex tissue


title: BSSE_QGF_143363_HN7CFDRXX_1_E04_Plate_A_2007Seq7_GCCGCACTCT_TCCGACCTCG_S29_L001_R1_001.fastq.gz

description:
ID in processed data file:
E4_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: Rnh201_WT_Asyn_R2

value: Asynchronous


title: frontal_cortex_203048410088_R07C01

description: Human postmortem frontal cortex tissue

value: yes


title: BSSE_QGF_143362_HN7CFDRXX_1_D04_Plate_A_2007Seq7_ACCACGACAT_TCGTATGCGG_S28_L001_R1_001.fastq.gz

description:
ID in processed data file:
D4_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203253040201_R02C01

description: Human postmortem frontal cortex tissue

value: moderate


title: frontal_cortex_203048410155_R01C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203048410152_R06C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203273630201_R08C01

description: Human postmortem frontal cortex tissue


title: Rnh1_WT_Asyn_R2


title: frontal_cortex_203048410152_R07C01

description: Human postmortem frontal cortex tissue

value: F


title: Rnh1_sen1-3_Asyn_R1


title: BSSE_QGF_143360_HN7CFDRXX_1_B04_Plate_A_2007Seq7_GGTTGCGAGG_AATAGAGCAA_S26_L001_R1_001.fastq.gz

description:
ID in processed data file:
B4_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410152_R05C01

description: Human postmortem frontal cortex tissue

value: VD


title: BSSE_QGF_143359_HN7CFDRXX_1_A04_Plate_A_2007Seq7_AACCATAGAA_GGCGAGATGG_S25_L001_R1_001.fastq.gz

description:
ID in processed data file:
A4_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410152_R01C01

description: Human postmortem frontal cortex tissue

value: M


title: frontal_cortex_203281980108_R07C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203048410152_R02C01

description: Human postmortem frontal cortex tissue

value: PD


title: BSSE_QGF_143358_HN7CFDRXX_1_H03_Plate_A_2007Seq7_TTCTACATAC_CTAACTGTAA_S24_L001_R1_001.fastq.gz

description:
ID in processed data file:
H3_Plate1
see PickedGMPs_PassedQC_191029TK20.csv

value: bone marrow

value: GMP (ganulocyte monocyte progenitor)


title: frontal_cortex_203281980108_R06C01

description: Human postmortem frontal cortex tissue

value: no

value: DLB


title: Rnh1_WT_Asyn_R1


title: Rpb1_sen1-3+OEhsRNH1_Asyn_R2


title: Rnh1_sen1-3_Asyn_R2


title: frontal_cortex_203048410147_R07C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203048410152_R04C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203048410147_R06C01

description: Human postmortem frontal cortex tissue

value: control

value: iLBD

value: Atypical


title: BSSE_QGF_143357_HN7CFDRXX_1_G03_Plate_A_2007Seq7_ACGCCTTGTT_TAAGGAACGT_S23_L001_R1_001.fastq.gz

description:
ID in processed data file:
G3_Plate1
see PickedGMPs_PassedQC_191029TK20.csv

value: 12 - 19 weeks

value: GFP-p65 homozygous /H2BmCherry heterozygous


title: frontal_cortex_203273630201_R07C01

description: Human postmortem frontal cortex tissue

value: AD

value: frequent


title: BSSE_QGF_143356_HN7CFDRXX_1_F03_Plate_A_2007Seq7_TATTGCGCTC_CTGTGTTAGG_S22_L001_R1_001.fastq.gz

description:
ID in processed data file:
F3_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410147_R04C01

description: Human postmortem frontal cortex tissue

value: yes

value: sparse


title: BSSE_QGF_143361_HN7CFDRXX_1_C04_Plate_A_2007Seq7_TAAGCATCCA_TCAATCCATT_S27_L001_R1_001.fastq.gz

description:
ID in processed data file:
C4_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: BSSE_QGF_143355_HN7CFDRXX_1_E03_Plate_A_2007Seq7_ATGGTTGACT_GGCCTGTCCT_S21_L001_R1_001.fastq.gz

description:
ID in processed data file:
E3_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410147_R03C01

description: Human postmortem frontal cortex tissue

value: F

value: PDD


title: frontal_cortex_203048410132_R05C01

description: Human postmortem frontal cortex tissue

value: M


title: Rpb1_rnhDD_Asyn_R2

value: rnh1-delta rnh201-delta

value: Asynchronous


title: BSSE_QGF_143354_HN7CFDRXX_1_D03_Plate_A_2007Seq7_GATAGGCCGA_CGCACATGGC_S20_L001_R1_001.fastq.gz

description:
ID in processed data file:
D3_Plate1
see PickedGMPs_PassedQC_191029TK20.csv

value: bone marrow

value: GMP (ganulocyte monocyte progenitor)


title: frontal_cortex_203048410147_R01C01

description: Human postmortem frontal cortex tissue

value: no

value: moderate


title: Rpb1_WT+OEhsRNH1_Asyn_R2

value: wild-type


title: Rpb1_rnhDD_Asyn_R1


title: frontal_cortex_203281980108_R04C01

description: Human postmortem frontal cortex tissue

value: VD


title: Rpb1_sen1-3_S45_R2

value: Released in S-phase for 45 min


title: frontal_cortex_203048410146_R06C01

description: Human postmortem frontal cortex tissue

value: control

value: CONTR


title: Rpb1_WT+OEhsRNH1_Asyn_R1


title: Rpb1_sen1-3+OEhsRNH1_Asyn_R1


title: BSSE_QGF_143353_HN7CFDRXX_1_C03_Plate_A_2007Seq7_CCATCATTAG_GGTTGCCTCT_S19_L001_R1_001.fastq.gz

description:
ID in processed data file:
C3_Plate1
see PickedGMPs_PassedQC_191029TK20.csv

value: 12 - 19 weeks

value: GFP-p65 homozygous /H2BmCherry heterozygous


title: Rpb1_sen1-3_S45_R1


title: frontal_cortex_203281980108_R05C01

description: Human postmortem frontal cortex tissue

value: yes

value: sparse


title: frontal_cortex_203048410146_R04C01

description: Human postmortem frontal cortex tissue

value: F

value: PDD


title: BSSE_QGF_143351_HN7CFDRXX_1_A03_Plate_A_2007Seq7_GAGAATGGTT_TCGGCAGCAA_S17_L001_R1_001.fastq.gz

description:
ID in processed data file:
A3_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410156_R04C01

description: Human postmortem frontal cortex tissue

value: M


title: Rpb1_WT_S45_R2


title: frontal_cortex_203048410146_R03C01

description: Human postmortem frontal cortex tissue

value: DLB


title: frontal_cortex_203048410146_R05C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203045470210_R04C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203048410146_R01C01

description: Human postmortem frontal cortex tissue

value: AD


title: Rpb1_WT_S45_R1


title: BSSE_QGF_143352_HN7CFDRXX_1_B03_Plate_A_2007Seq7_AGAGGCAACC_CTAATGATGG_S18_L001_R1_001.fastq.gz

description:
ID in processed data file:
B3_Plate1
see PickedGMPs_PassedQC_191029TK20.csv

value: bone marrow

value: GMP (ganulocyte monocyte progenitor)


title: frontal_cortex_203048410088_R05C01

description: Human postmortem frontal cortex tissue

value: no


title: BSSE_QGF_143349_HN7CFDRXX_1_G02_Plate_A_2007Seq7_TCCATTGCCG_GAATGCACGA_S15_L001_R1_001.fastq.gz

description:
ID in processed data file:
G2_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410132_R08C01

description: Human postmortem frontal cortex tissue

value: iLBD


title: BSSE_QGF_143350_HN7CFDRXX_1_H02_Plate_A_2007Seq7_CGGTTACGGC_AAGACTATAG_S16_L001_R1_001.fastq.gz

description:
ID in processed data file:
H2_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410132_R07C01

description: Human postmortem frontal cortex tissue

value: frequent


title: frontal_cortex_203048410147_R05C01

description: Human postmortem frontal cortex tissue


title: BSSE_QGF_143348_HN7CFDRXX_1_F02_Plate_A_2007Seq7_GAAGCGGCAC_CGGCTCTACT_S14_L001_R1_001.fastq.gz

description:
ID in processed data file:
F2_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410132_R06C01

description: Human postmortem frontal cortex tissue

value: moderate


title: Rpb1_sen1-3_G1_R2

value: Arrested in G1 by alpha-factor


title: frontal_cortex_203281980108_R03C01

description: Human postmortem frontal cortex tissue


title: Rpb1_sen1-3_G1_R1


title: frontal_cortex_203048410089_R04C01

description: Human postmortem frontal cortex tissue


title: BSSE_QGF_143347_HN7CFDRXX_1_E02_Plate_A_2007Seq7_CTTGCCATTA_ATCACGAAGG_S13_L001_R1_001.fastq.gz

description:
ID in processed data file:
E2_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410132_R03C01

description: Human postmortem frontal cortex tissue

value: PD


title: Rpb1_WT_G1_R1

value: wild-type


title: BSSE_QGF_143346_HN7CFDRXX_1_D02_Plate_A_2007Seq7_GAGTCATAGG_GTGTGGCGCT_S12_L001_R1_001.fastq.gz

description:
ID in processed data file:
D2_Plate1
see PickedGMPs_PassedQC_191029TK20.csv

value: 12 - 19 weeks

value: GFP-p65 homozygous /H2BmCherry heterozygous


title: frontal_cortex_203045470207_R03C01

description: Human postmortem frontal cortex tissue

value: yes


title: frontal_cortex_203048410132_R01C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203045470206_R03C01

description: Human postmortem frontal cortex tissue

value: VD


title: frontal_cortex_203048410156_R03C01

description: Human postmortem frontal cortex tissue

value: F

value: control

value: CONTR


title: frontal_cortex_203038300119_R07C01

description: Human postmortem frontal cortex tissue


title: Rpb1_sen1-3_S30_R1

value: Released in S-phase for 30 min


title: BSSE_QGF_143344_HN7CFDRXX_1_B02_Plate_A_2007Seq7_AGTCAGACGA_ACCAGCGACA_S10_L001_R1_001.fastq.gz

description:
ID in processed data file:
B2_Plate1
see PickedGMPs_PassedQC_191029TK20.csv

value: bone marrow


title: BSSE_QGF_143345_HN7CFDRXX_1_C02_Plate_A_2007Seq7_CCGTATGTTC_CATACACTGT_S11_L001_R1_001.fastq.gz

description:
ID in processed data file:
C2_Plate1
see PickedGMPs_PassedQC_191029TK20.csv

value: GMP (ganulocyte monocyte progenitor)


title: Rpb1_WT_S30_R2


title: BSSE_QGF_143343_HN7CFDRXX_1_A02_Plate_A_2007Seq7_GACTGAGTAG_GTTGATAGTG_S9_L001_R1_001.fastq.gz

description:
ID in processed data file:
A2_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203038300119_R05C01

description: Human postmortem frontal cortex tissue

value: no

value: M


title: frontal_cortex_203038300119_R04C01

description: Human postmortem frontal cortex tissue

value: sparse


title: frontal_cortex_203048410152_R03C01

description: Human postmortem frontal cortex tissue

value: DLB


title: BSSE_QGF_143340_HN7CFDRXX_1_F01_Plate_A_2007Seq7_AACATCGCGC_GTCCACTTGT_S6_L001_R1_001.fastq.gz

description:
ID in processed data file:
F1_Plate1
see PickedGMPs_PassedQC_191029TK20.csv


title: Rpb1_sen1-3_S30_R2


title: frontal_cortex_203038300119_R01C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203038300119_R03C01

description: Human postmortem frontal cortex tissue

value: iLBD


title: Rpb1_WT_S30_R1


title: frontal_cortex_203038300119_R02C01

description: Human postmortem frontal cortex tissue

value: FTD

value: AD

value: frequent


title: Rpb1_sen1-3_Asyn_R2

value: Asynchronous


title: Rpb1_sen1-3_Asyn_R1


title: frontal_cortex_203048410110_R08C01

description: Human postmortem frontal cortex tissue

value: yes

value: moderate


title: frontal_cortex_203038300119_R06C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203048410110_R07C01

description: Human postmortem frontal cortex tissue

value: stroke


title: BSSE_QGF_143338_HN7CFDRXX_1_D01_Plate_A_2007Seq7_ATTCCATAAG_TGCCTGGTGG_S4_L001_R1_001.fastq.gz

description:
ID in processed data file:
D1_Plate1
see PickedGMPs_PassedQC_191029TK20.csv

value: 12 - 19 weeks

value: GFP-p65 homozygous /H2BmCherry heterozygous


title: Rpb1_WT_G1_R2

value: wild-type

value: Arrested in G1 by alpha-factor


title: BSSE_QGF_130173_HHJWMBGXC_1_G12_Plate_B_1908Seq6_TTGAATGTTG_CGCAATCTAG_S191_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
G12_Plate2
see PickedGMPs_PassedQC_190729TK20.csv

value: bone marrow

value: GMP (ganulocyte monocyte progenitor)


title: Rpb1_WT_Asyn_R2


title: frontal_cortex_203048410110_R06C01

description: Human postmortem frontal cortex tissue

value: no

value: F


title: frontal_cortex_203045470206_R02C01

description: Human postmortem frontal cortex tissue

value: M

value: DLB


title: frontal_cortex_203048410110_R03C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203048410110_R04C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203048410110_R05C01

description: Human postmortem frontal cortex tissue

value: PDD


title: BSSE_QGF_130170_HHJWMBGXC_1_D12_Plate_B_1908Seq6_TGCTACTGCC_CAACCGGAGG_S188_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
D12_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: frontal_cortex_203048410110_R02C01

description: Human postmortem frontal cortex tissue

value: PD


title: BSSE_QGF_130169_HHJWMBGXC_1_C12_Plate_B_1908Seq6_AGCGCCACAC_CTAATGTCTT_S187_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
C12_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: BSSE_QGF_130172_HHJWMBGXC_1_F12_Plate_B_1908Seq6_CACCTTAATC_TTAGGATAGA_S190_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
F12_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: BSSE_QGF_130174_HHJWMBGXC_1_H12_Plate_B_1908Seq6_CCGGTAACAC_GAGTTGTACT_S192_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
H12_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: Rpb1_WT_Asyn_R1


title: EV from activated SCAP, sample 3

city: Brussels

first: Viridiane

last: Gratpain

address: avenue Emmanuel Mounier 73

department: Louvain Drug Research Institute

country: Belgium

institute: Université Catholique de Louvain

data_processing:
Small RNA sequences were aligned on Homo_sapiens.GRCh38.dna.primary_assembly and quantified using mirdeep2 pipeline and miRNA/precursors sequences from miRBase 21.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes a matrix of raw counts for each sample

source_name: Human apical papilla

growth_protocol: SCAP were maintained in MEM supplemented with 10% fœtal bovin serum (FBS), 1% L-Glutamine and 1% Penicillin/Streptomycin in humidified atmosphere with 5% CO2 at 37C. For the EV isolation, same medium was used but without FBS.

extract_protocol:
RNA was extracted using miRNeasy mini kit (Qiagen). 50 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for small RNA-seq were prepared using a Illumina compatible library preparation kit

treatment_protocol: For the EV from activated-SCAP, SCAP were activated with TNFα (20 ng/ml) and IFNγ (20ng/ml) for 72h, prior to EV isolation.

value: Human apical papilla

value: Mesenchymal stem cells

tag: treatment

value: TNFα (20 ng/ml) + IFNγ (20ng/ml)


title: EV from non-activated SCAP, sample 3

tag: cell line


title: EV from non-activated SCAP, sample 2


title: frontal_cortex_203048410156_R02C01

description: Human postmortem frontal cortex tissue

value: control

value: iLBD


title: frontal_cortex_203048410089_R08C01

description: Human postmortem frontal cortex tissue

value: yes

value: sparse


title: BSSE_QGF_130167_HHJWMBGXC_1_A12_Plate_B_1908Seq6_ACGGTCCAAC_TCTTACATCA_S185_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
A12_Plate2
see PickedGMPs_PassedQC_190729TK20.csv

value: 12 - 19 weeks

value: GFP-p65 homozygous /H2BmCherry heterozygous


title: frontal_cortex_203048410089_R07C01

description: Human postmortem frontal cortex tissue

value: AD

value: frequent


title: EV from non-activated SCAP, sample 1


title: frontal_cortex_203048410110_R01C01

description: Human postmortem frontal cortex tissue

value: no


title: BSSE_QGF_130166_HHJWMBGXC_1_H11_Plate_B_1908Seq6_ATCCAGGTAT_CAACGTCAGC_S184_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
H11_Plate2
see PickedGMPs_PassedQC_190729TK20.csv

value: bone marrow

value: GMP (ganulocyte monocyte progenitor)


title: frontal_cortex_203048410089_R02C01

description: Human postmortem frontal cortex tissue

value: F


title: EV from activated SCAP, sample 1


title: frontal_cortex_203048410089_R03C01

description: Human postmortem frontal cortex tissue

value: M


title: frontal_cortex_203048410089_R06C01

description: Human postmortem frontal cortex tissue

value: PD


title: EV from activated SCAP, sample 2

value: Human apical papilla


title: frontal_cortex_203273630201_R04C01

description: Human postmortem frontal cortex tissue


title: BSSE_QGF_130168_HHJWMBGXC_1_B12_Plate_B_1908Seq6_GTAACTTGGT_CGCCATACCT_S186_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
B12_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: frontal_cortex_203281980108_R01C01

description: Human postmortem frontal cortex tissue

value: PDD

value: moderate


title: frontal_cortex_203273630201_R01C01

description: Human postmortem frontal cortex tissue


title: BSSE_QGF_130162_HHJWMBGXC_1_D11_Plate_B_1908Seq6_CGCTGTCTCA_ATTACTCACC_S180_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
D11_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: frontal_cortex_203048410088_R03C01

description: Human postmortem frontal cortex tissue

value: control

value: CONTR


title: frontal_cortex_203048410089_R01C01

description: Human postmortem frontal cortex tissue


title: BSSE_QGF_130171_HHJWMBGXC_1_E12_Plate_B_1908Seq6_CAACACCGCA_GGCAGTAGCA_S189_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
E12_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: frontal_cortex_203273630201_R05C01

description: Human postmortem frontal cortex tissue

value: yes


title: ATAC PE, replicate B

city: Roma

first: Alessio

last: Colantoni

state: RM

address: Piazzale Aldo Moro, 5

department: Dipartimento di Biologia e Biotecnologie "Charles Darwin"

institute: "Sapienza" University of Rome

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq v2.20 software. One mismatch was allowed for index sequence identification.
Sequencing adapters and low-quality bases were trimmed using the Trimmomatic v0.39 software with parameters ILLUMINACLIP:/path/to/adapter:2:30:10:1:true SLIDINGWINDOW:20:15 MINLEN:36.
Preprocessed reads were then aligned to hg38 genome using Bowtie2 v2.3.4.1 with parameters --wrapper basic-0 --fr -X 2000.
Aligned reads were filtered using SAMtools v1.11 to keep only concordant primary alignments having a minimum mapping quality of 30. PCR or optical duplicates were marked using Picard v2.25.1 tool and removed. Reads mapping to mitochondrial DNA and to unplaced contigs were filtered out. Aligned reads were also shifted using the deepTools v3.5.1 alignmentSieve tool with the --ATACshift parameter. After this shift, reads falling in ENCODE Blacklist regions were removed using BEDTools v2.30.0 pairToBed tool.
deepTools bamCoverage tool was employed to convert BAM files to bigWig files with RPGC normalization and the genomic bin size set to 10 bp.
Assembly: hg38
Supplementary files format and content: Sample-specific read coverage tracks (bigWig format).
Supplementary files format and content: Sample-specific narrowPeak files produced by MACS2.

source_name: Pharyngeal Endoderm (PE)

growth_protocol: H9 hESCs were routinely propagated feeder-free in mTeSR1 on cell culture plates previously coated with Matrigel following the manufacturer instructions. Undifferentiated hESCs were propagated and passed at least 3 times after thawing and plated for the differentiation when at 80% of confluence. Cells were maintained in culture and expanded at high quality with particular care to avoid any spontaneous differentiation, which would confound downstream differentiation. The day before the induction of the differentiation, hESCs were washed twice in PBS, dissociated with Accutase, plated in mTeSR1 + Rock Inhibitor (Y27632, 5uM) to promote cell survival and incubated for 12 hours at 37 °C, 5% CO2 for 12 hours. The day after, 30% confluent hESCs were induced to differentiate into definitive endoderm, by incubation with Medium A (Gibco cat. n. A30621-01) for 24 hours and with Medium B (Gibco cat. n. 30624-01) for the following 24 hours at 37 °C, 5% CO2. The third day DE was patterned into AFG by the addition of CDM2 medium with A-83-01, 1uM and DM3189, 250nM. The composition of CDM2 basal medium was as follows: 50% IMDM (+GlutaMAX, +HEPES, +Sodium Bicarbonate; Gibco, 31980-097) + 50% F12 (+GlutaMAX; Gibco, 31765-092) + 1 mg/mL polyvinyl alcohol (Sigma, P8136-250G) + 1% v/v concentrated lipids (Gibco, 11905-031) + 450 µM monothioglycerol (Sigma, M6145) + 0.7 µg/mL insulin (Roche, 1376497) + 15 µg/mL transferrin (Roche, 652202) and incubated at 37 °C, 5% CO2. From day four to day 5, Retinoic Acid 200 nM was added at the CDM2 medium with A-83-01, 1 uM and DM3189, 250 nM and medium was changed every 24 hours.

extract_protocol:
DE, AFE and PE live cell samples (two biological replicates per cell type) were thawed, washed, and treated with DNAse I (Life Tech, Cat. #EN0521) to remove genomic DNA contamination. Live cell samples were quantified and assessed for viability using a Countess Automated Cell Counter (ThermoFisher Scientific, Waltham, MA, USA). After cell lysis and cytosol removal, nuclei were treated with Tn5 enzyme (Illumina, Cat. #20034197) for 30 minutes at 37°C and purified with Minelute PCR Purification Kit (Qiagen, Cat. #28004) to produce tagmented DNA samples.
Tagmented DNA was barcoded with Nextera Index Kit v2 (Illumina, Cat. #FC-131-2001) and amplified via PCR prior to a SPRI Bead cleanup to yield purified DNA libraries.

value: Pharyngeal Endoderm (PE)

tag: time

value: Day 5 + RA

tag: sequencing run


title: scRNA PE

library_source: transcriptomic single cell

data_processing:
Illumina base call files were converted to FASTQ files using the Cell Ranger v2.0 program.
FASTQ files were then aligned to the hg19 human reference genome using Cell Ranger.
Cell Ranger count function was used to to produce count matrices for both DE and PE cell types.
Assembly: hg19
Supplementary files format and content: Files produced by the Cell Ranger software. barcodes.tsv contains barcodes sequences for cell-associated barcodes, features.tsv contains gene IDs, gene names and the feature type. They are, respectively, column and row indices for matrix.mtx, which contains the UMI counts for each feature and each barcode.

growth_protocol: H9 hESCs were routinely propagated feeder-free in mTeSR1 on cell culture plates previously coated with Matrigel following the manufacturer instructions. Undifferentiated hESCs were propagated and passed at least 3 times after thawing and plated for the differentiation when at 80% of confluence. Cells were maintained in culture and expanded at high quality with particular care to avoid any spontaneous differentiation, which would confound downstream differentiation. The day before the induction of the differentiation, hESCs were washed twice in PBS, dissociated with Accutase, plated in mTeSR1 + Rock Inhibitor (Y27632, 5uM) to promote cell survival and incubated for 12 hours at 37 °C, 5% CO2 for 12 hours. The day after, 30% confluent hESCs were induced to differentiate into definitive endoderm, by incubation with Medium A (Gibco cat. n. A30621-01) for 24 hours and with Medium B (Gibco cat. n. 30624-01) for the following 24 hours at 37 °C, 5% CO2. The third day DE was patterned into AFG by the addition of CDM2 medium with A-83-01, 1uM and DM3189, 250nM. The composition of CDM2 basal medium was as follows: 50% IMDM (+GlutaMAX, +HEPES, +Sodium Bicarbonate; Gibco, 31980-097) + 50% F12 (+GlutaMAX; Gibco, 31765-092) + 1 mg/mL polyvinyl alcohol (Sigma, P8136-250G) + 1% v/v concentrated lipids (Gibco, 11905-031) + 450 µM monothioglycerol (Sigma, M6145) + 0.7 µg/mL insulin (Roche, 1376497) + 15 µg/mL transferrin (Roche, 652202) and incubated at 37 °C, 5% CO2. From day four to day 5, Retinoic Acid 200 nM was added at the CDM2 medium with A-83-01, 1 uM and DM3189, 250 nM and medium was changed every 24 hours.

extract_protocol:
DE and PE differentiated cells were washed twice with CDM2 medium to remove dead cells and detached using Accutase. Cells were collected and counted using Countess® II Automated Cell Counter. 500,000 cells for each condition were collected in a PBS-0.04%BSA buffer and processed according to the 10X Genomics Single Cell Protocols Cell Preparation Guide  (available at https://assets.ctfassets.net/an68im79xiti/56DlUZEsVOWc8sSG42KQis/35cbcf6dcd4b0c0196263ee93815b0ae/CG000053_CellPrepGuide_RevC.pdf). For each cell type, 5000 cells were loaded per lane on the 10x Genomics Chromium platform, with the goal of capturing 2500 cells.
Cells were processed for cDNA synthesis and library preparation using 10X Genomics Chromium Version 2 chemistry (catalog number 120234) as per the manufacturer’s protocol. cDNA libraries were checked for quality on the Agilent 4200 Tape Station platform and their concentration was quantified by KAPA qPCR.


title: BSSE_QGF_130161_HHJWMBGXC_1_C11_Plate_B_1908Seq6_TATCCGAGGC_GGCCAATAAG_S179_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
C11_Plate2
see PickedGMPs_PassedQC_190729TK20.csv

value: 12 - 19 weeks

value: GFP-p65 homozygous /H2BmCherry heterozygous


title: ATAC PE, replicate A


title: frontal_cortex_203273630201_R03C01

description: Human postmortem frontal cortex tissue

value: AD

value: frequent


title: scRNA DE

source_name: Definitive Endoderm (DE)

value: Definitive Endoderm (DE)

value: Day 2


title: frontal_cortex_203281980108_R02C01

description: Human postmortem frontal cortex tissue

value: no

value: sparse


title: frontal_cortex_203048410089_R05C01

description: Human postmortem frontal cortex tissue

value: F


title: BSSE_QGF_130163_HHJWMBGXC_1_E11_Plate_B_1908Seq6_AATGCGAACA_AATTGGCGGA_S181_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
E11_Plate2
see PickedGMPs_PassedQC_190729TK20.csv

value: bone marrow

value: GMP (ganulocyte monocyte progenitor)


title: frontal_cortex_203048410088_R01C01

description: Human postmortem frontal cortex tissue

value: moderate


title: ATAC AFE, replicate B

source_name: Anterior Foregut Endoderm (AFE)

value: Anterior Foregut Endoderm (AFE)

value: Day 5


title: BSSE_QGF_130165_HHJWMBGXC_1_G11_Plate_B_1908Seq6_TTCCTACAGC_GGCGAATTCT_S183_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
G11_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: BSSE_QGF_130160_HHJWMBGXC_1_B11_Plate_B_1908Seq6_GATCGTCGCG_CTGGATATGT_S178_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
B11_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: ATAC DE, replicate B


title: BSSE_QGF_130157_HHJWMBGXC_1_G10_Plate_B_1908Seq6_GGACCAGTGG_CGCGAGCCTA_S175_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
G10_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: BSSE_QGF_130164_HHJWMBGXC_1_F11_Plate_B_1908Seq6_AATTCTTGGA_TTGTCAACTT_S182_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
F11_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: frontal_cortex_203048410088_R02C01

description: Human postmortem frontal cortex tissue

value: yes


title: ATAC AFE, replicate A


title: BSSE_QGF_130155_HHJWMBGXC_1_E10_Plate_B_1908Seq6_GTCCACCGCT_TCCTATTAGC_S173_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
E10_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: ATAC DE, replicate A


title: BulkRNA PE, replicate B

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq v2.17 software. One mismatch was allowed for index sequence identification.
Adapter sequences and poor quality ends were removed using the Trimmomatic v0.39 software with parameters ILLUMINACLIP:/path/to/adapter:2:30:10:1:true  SLIDINGWINDOW:20:15 MINLEN:36.
Salmon v1.3.0 tool was employed to quantify transcript expression, producing isoform-level transcripts per million (TPM) values from a full decoy transcriptome index created using the GENCODE v35 transcriptome and the hg38 genome.
Assembly: hg38
Supplementary files format and content: Sample-specific Salmon quantification files

extract_protocol:
Total RNA from hESCs, DE, AFE, and PE cells was isolated by collecting cells using TRI Reagent (Zymo Research), followed by column purification and DNAse treatment using Direct-zol RNA MiniPrep Kit (Zymo Research), and quantification by Nanodrop (Thermo Scientific).
1 ug of RNA from three biological replicates of hESCs, DE, AFE and PE conditions was quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA).  RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads.  Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end-repaired and adenylated at 3’ ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

value: Pharyngeal Endoderm (PE)


title: BSSE_QGF_130158_HHJWMBGXC_1_H10_Plate_B_1908Seq6_CCTTCTAACA_GATAAGCTCT_S176_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
H10_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: BSSE_QGF_130154_HHJWMBGXC_1_D10_Plate_B_1908Seq6_CCTCCGGTTG_CATAACACCA_S172_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
D10_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: BulkRNA PE, replicate C

value: Day 5 + RA


title: BSSE_QGF_130153_HHJWMBGXC_1_C10_Plate_B_1908Seq6_AGGCGTTCGC_TTCATCCAAC_S171_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
C10_Plate2
see PickedGMPs_PassedQC_190729TK20.csv

value: 12 - 19 weeks


title: BulkRNA PE, replicate A


title: BSSE_QGF_130159_HHJWMBGXC_1_A11_Plate_B_1908Seq6_CTCGAATATA_GAGATGTCGA_S177_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
A11_Plate2
see PickedGMPs_PassedQC_190729TK20.csv

value: GFP-p65 homozygous /H2BmCherry heterozygous


title: BulkRNA AFE, replicate B


title: BSSE_QGF_130156_HHJWMBGXC_1_F10_Plate_B_1908Seq6_ATTGTTCGTC_TCTCTAGATT_S174_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
F10_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: BulkRNA AFE, replicate C


title: BulkRNA AFE, replicate A


title: BSSE_QGF_130151_HHJWMBGXC_1_A10_Plate_B_1908Seq6_ATGTTGTTGG_CAATCTATGA_S169_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
A10_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: BSSE_QGF_130152_HHJWMBGXC_1_B10_Plate_B_1908Seq6_GCACCACCAA_TGGTACTGAT_S170_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
B10_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: BulkRNA DE, replicate C


title: BSSE_QGF_130150_HHJWMBGXC_1_H09_Plate_B_1908Seq6_TATGACAATC_TTGCTTGTAT_S168_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
H9_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: BulkRNA DE, replicate B


title: BSSE_QGF_130149_HHJWMBGXC_1_G09_Plate_B_1908Seq6_AGCCTATGAT_CACCACCTAC_S167_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
G9_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: BSSE_QGF_130148_HHJWMBGXC_1_F09_Plate_B_1908Seq6_CATATGCGAT_CCTTGAACGG_S166_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
F9_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: BulkRNA DE, replicate A