title: ALR-migrated_S11

value: Skin

value: Migrated Langerhans cells (LCs)


title: MCF7 Monoculture Sample 2

status: Public on Jul 21 2022

type: SRA

city: Ann Arbor

first: Gary

last: Luker

state: MI

address: 109 Zina Pitcher Place  A710 Biomedical Sciences Research Building

department: Radiology

country: USA

institute: University of Michigan

description:
285-JB-1
Counts_Raw_285.txt
CPM_285.txt

library_source: transcriptomic

data_processing:
Trimmed using Trim_Galore (v 0.5.0) https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
Aligned using STAR (v 2.6.0) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530905/
UMI collapsed using Lexogen’s supplied collapse_UMI_bam binary.
Counted using Bioconductor R package Rsubread and featureCounts function:
Genome_build: Reference and Annotation: GRCh38 from ENSEMBL

molecule: total RNA

organism: Homo sapiens

source_name: ER+ Breast Cancer Cells

growth_protocol: We grew cells for 24 hours in 10cm polystyrene, cell culture-treated dishes in full medium (DMEM (#11995, Gibco, Thermo Fisher, Grand Island, NY, USA) with 10% FBS (HyClone, ThermoScientific, Waltham, MA, USA), 1% GlutaMAX (#35050, Gibco), and 1% Penicillin-Streptomycin (P/S, #15140, Gibco)). We seeded cells either by themselves (monoculture) or in co-culture at a ratio of 10% cancer cells with 90% MSCs. After 24 hours, we changed medium to low glucose, phenol-red free DMEM (LG/LF, #11054, Gibco) with 1% FBS, 1% GlutaMAX, 1% P/S, and 10 nM β-Estradiol (#E2758, Sigma-Aldrich, Millipore Sigma, Saint Louis, MO, USA). We waited 48 hours after changing media to harvest cells.

extract_protocol:
To separate cancer cells from stromal cells in co-culture conditions, we used human CD326 (EpCAM) Microbeads (#130-061-101, Miltenyi, Auburn, California, USA) and LS columns (#130-042-401, Miltenyi) and followed the manufacturer’s recommendations for separation.
We extracted RNA using the RNeasy Mini Kit following manufacturer’s instructions (#74104, Qiagen, Hilden, Germany)
We prepared RNA libraries for sequencing using standard Illumina protocols

tag: cell line

tag: source condition

value: Mono-Culture

tag: batch

tag: biological replicate

tag: replicate (of biological replicate)

value: A


title: MB011B_scramble_biol_Rep1_control

city: Waltham

first: Leslie

middle: C

last: Griffith

state: MA

address: 415 South St.

department: Volen National Center for Complex Systems/ Neuroscience

institute: Brandeis University

description: Brains diseccted at ZT12-ZT13.5 from female flies that were mated and aged 3-4 days post-eclosion.

data_processing:
Reads were mapped to the dm6 Drosophila genome using STAR (Dobin et al., 2013). PCR duplicates were removed using Picard
HTseq-count was used to generate raw read counts for individual genes. This was used as the input for EdgeR differential gene expression analysis (Robinson et al., 2010), performed on three biological replications.
Assembly: dm6
Supplementary files format and content: Comma-delineated EdgeR output with logFC (fold-change), logCPM(counts per million) and P-Value for each gene, comparing relative change in expression in experimental (MB011B>bantam-spg, GFP) compared to control (MB011B>scramble, GFP) neurons.

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: gamma5Beta'2a/Beta'2mp/Beta'2mp_bilateral Mushroom Body Output Neurons

extract_protocol:
Dynabead mRNA purification kit used on FACS isolated neurons
Smartseq 2 with NEXTERA XT (Illumina)

treatment_protocol: FACS isolation of Drosophila γ5β′2a/β′2mp/β′2mp_bilateral Mushroom Body Output Neurons

tag: age

value: 3-4 days post-eclosion

tag: Sex

value: female

tag: cell type

tag: genotype

tag: treatment

value: FACS isolated neurons


title: HS27a from MCF7+HS27a Co-Culture Sample 1

description:
139621
Counts_Raw_148.txt
CPM_148.txt

source_name: Bone Marrow Stromal/Stem Cells

value: MCF7+HS27a Co-Culture


title: Passage 1 organoid derived from murine salivary glands at 90 days post sham-IR, rep2

city: Groningen

first: Rob

last: Coppes

address: Ant. Deusinglaan 1

department: Biomedical Sciences of Cells and Systems

country: Netherlands

institute: University Medical Center Groningen

data_processing:
Base-calling: bcl2fastq software (Illumina Inc.) version 2.20.0.422.
QuantSeq 3′ mRNA-Seq analysis: Bluebee (Lexogen) version 015UG108V0311
Assembly: GRCm39
Supplementary files format and content: A tab-delimited text file containing read counts

organism: Mus musculus

source_name: salivary gland stem/progenitor cells

growth_protocol: Organoids were cultured in Matrigel, complete growth medium consisting of DMEM-12 (Gibco/Invitrogen, 11320-074), 1x Pen/Strep antibiotics (Gibco), 2mM Glutamax (ThermoFischer Scientific, 35050038), 1x N2 (Gibco, 17502-048), 20 ng/ml EGF (Sigma-Aldrich, E9644), 20 ng/ml FGF2 (PeproTech, 100-18B), 10 μg/ml insulin (Sigma-Aldrich, I6634), 1 μM dexamethasone (Sigma-Aldrich, d4902) and 10 μM Y-27632 (Abcam, ab120129).

extract_protocol:
RNA was isolated with the RNeasy Mini Kit (Qiagen, 74104) according to manufacturer’s instructions including DNase I treatment
QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen)

tag: strain

value: salivary gland stem/progenitor cells

tag: tissue

value: Passage 1 organoid

value: sham-IR

tag: time

value: 90 days


title: ABC-T0-_S6

city: Créteil

first: cecile

last: lefebvre

address: 51 Avenue du Marechal De Lattre de Tassigny

country: France

institute: INSERM U955_VRI

data_processing:
Base calls were performed using Illumina CASAVA 1.8.2
Sequenced reads were trimmed for low-quality sequence, then mapped to hg19 whole genome using Star 2.5.3 with performed using Partek® Flow® software, Copyright ©; 2019 Partek Inc.
Aligned reads were quantified to annotation model hg19 - GENCODE Genes - release 19, with Partek E/M and counts normalized by the counts per million (CPM + 0.0001) method with performed using Partek® Flow® software, Copyright ©; 2019 Partek Inc.
Genome_build: hg19
Supplementary_files_format_and_content: LANGERHANS_MigratedvsSteadyState_Normalized_counts. 12 samples

source_name: Steady state LCs

growth_protocol: RNAseq analysis on primary skin LC. Epidermal LC of 6 healthy donors were isolated either at steady state or after 3 days of migration in culture.

extract_protocol:
Total RNA was purified from normal skin with the RNeasy Plus Micro Kit (Qiagen)
Libraries were prepared with the NEBNext UltraII directional RNA Library Prep kit. Sequencing : Single read of 101 bp, performed on the Illumina HiSeq 2500 at Vaccine Research Institute genomics Platform

value: Steady state Langerhans cells (LCs)


title: MB011B_scramble_biol_Rep2_control

value: gamma5Beta'2a/Beta'2mp/Beta'2mp_bilateral Mushroom Body Output Neurons


title: Passage 2 organoid derived from murine salivary glands at 14 days post IR, rep3

value: Passage 2 organoid

value: IR

value: 14 days


title: Blood, pregnant buffalo 3

city: Hefei

first: Zubing

last: Cao

state: Anhui

address: 130 changjiang west road

department: Animal Science

country: China

institute: Anhui Agricultural University

description:
circle RNA
p-buffalo-3

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp.
We used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference Bubalus bubalis (Version: GRCh38).
Mapped reads of IP and input libraries were provided for R package exomePeak (https://bioconductor.org/packages/exomePeak), which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software (http://www.igv.org).  HOMER (http://homer.ucsd.edu/homer/motif) were used for de novo  motif finding followed by localization of the motif with respect to peak summit. Called peaks were annotated by intersection with gene architecture using R package ChIPseeker (https://bioconductor.org/packages/ChIPseeker).
Then StringTie (https://ccb.jhu.edu/software/stringtie) was used to perform expression level for all mRNAs from input libraries by calculating FPKM (total exon fragments /mapped reads (millions) × exon length (kB)).
The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and p value < 0.05 by R package edgeR (https://bioconductor.org/packages/edgeR).
Assembly: Version GRCh38.p10
Supplementary files format and content: count, srpbm

organism: Bubalus bubalis

source_name: blood

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

value: blood

tag: group

value: pregnant

tag: breed

value: Jianghuai


title: HS5 from MCF7+HS5 Co-Culture Sample 1

description:
139619
Counts_Raw_148.txt
CPM_148.txt

value: MCF7+HS5 Co-Culture

value: A


title: MCF7 from MCF7+HS27a Co-Culture Sample 1

description:
139620
Counts_Raw_148.txt
CPM_148.txt


title: Passage 2 organoid derived from murine salivary glands at 14 days post IR, rep2


title: w.16.4

city: Ithaca

first: Hao

last: Wu

state: NY

address: 236 Tower Rd, Plant Science Building Room #236

institute: Cornell University

data_processing:
Raw reads were quality checked using FastQC and mapped to the maize reference genome using Tophat v2.1.1
Reads mapped to each gene were counted using featureCounts and RPKM values were calculated by Cufflinks v2.2.1
Assembly: N/A
Supplementary files format and content: Excel spreadsheet with the RPKM value of each gene

organism: Zea mays

source_name: 16 DAP whole endosperm

growth_protocol: Field grown plants were self-pollinated

extract_protocol:
Total RNA was extracted by conventional LiCl approach as described (Li et al., 2014) except that GeneJET RNA Cleanup and Concentration Micro Kit (Thermo Fisher Scientific) was used to clean up DNaseI-treated RNA.
Multiplexed sequencing libraries were constructed using the Illumina TruSeq Stranded mRNA Library Preparation Kit with poly(A) selection

treatment_protocol: Whole Endosperms at 16 DAP were collected

tag: cell line_background

value: WT

value: 16 DAP whole endosperm


title: n2.16.4


title: Blood, pregnant buffalo 2

description:
circle RNA
p-buffalo-2


title: Passage 2 organoid derived from murine salivary glands at 14 days post IR, rep1


title: MCF7 from MCF7+HS5 Co-Culture Sample 1

description:
139618
Counts_Raw_148.txt
CPM_148.txt


title: Blood, pregnant buffalo 1

description:
circle RNA
p-buffalo-1


title: n1.16.4


title: HS27a Monoculture Sample 1

description:
139617
Counts_Raw_148.txt
CPM_148.txt

value: Mono-Culture


title: Passage 2 organoid derived from murine salivary glands at 14 days post sham-IR, rep3

value: salivary gland stem/progenitor cells


title: w.16.3


title: Blood, non-pregnant buffalo 3

description:
circle RNA
c-buffalo-3

value: non-pregnant


title: HS5 Monoculture Sample 1

description:
139616
Counts_Raw_148.txt
CPM_148.txt


title: Passage 2 organoid derived from murine salivary glands at 14 days post sham-IR, rep2

value: sham-IR


title: Passage 1 organoid derived from murine salivary glands at 90 days post sham-IR, rep1

value: Passage 1 organoid

value: 90 days


title: n2.16.3


title: ABC-migrated_S5

source_name: Migrated LCs

value: Skin

value: Migrated Langerhans cells (LCs)


title: Blood, non-pregnant buffalo 2

description:
circle RNA
c-buffalo-2


title: w.16.2


title: MCF7 Monoculture Sample 1

description:
139615
Counts_Raw_148.txt
CPM_148.txt


title: n1.16.3


title: FBE6E7_122_Rep3

city: Guadalajara

first: Adriana

middle: Del Carmen

last: Aguilar Lemarroy

state: Jalisco

address: Sierra Mojada 800, Independencia Oriente, 44340 Guadalajara, Jal.

department: División de Inmunología

country: Mexico

institute: Centro de Investigación Biomédica de Occidente

data_processing:
Illumina NovaSeq 6000  was used.
The open source Galaxy platform (https://www.usegalaxy.org) and RStudio software (2021.09.0) were used for bioinformatics analysis of the raw reads.
The quality of the reads was checked through FastQC tool (v0.11.9) and to remove ambiguous nucleotides Trimmomatic tool was used.
Subsequently, all the clean reads were mapped to the human genome reference  (hg38 vs 38) using Rsubread (v3.14) for Rstudio.
Once obtained all the BAM files, the reads were count by featureCounts tool (v2.0.1), and gene expression analysis was conducted by DESeq2 tool (v2.11.40.6).
Genome_build: hg38 vr 38
Supplementary_files_format_and_content: The tab-delimited text files include the FPKM and log2 (Fold Change) values for each sample.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Skin

growth_protocol: Models obtained in fibroblasts were cultivated in Dulbecco’s Modified Eagle Medium (DMEM) with L-glutamine (584 mg/L), sodium pyruvate (110 mg/L), penicillin (100 U/mL), streptomycin (100µg/mL), 10% Fetal Bovine Serum (FBS) on 100 mm plates at 37°C in a 5% CO2 atmosphere using a incubator.

extract_protocol:
Total RNA was extracted from each of the obtained models with Quick-RNA miniprep plus kit (Cat. No. R1058, Zymo Research, Irvine, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols (using the services of Novogene Bioinformatics Technology Company). At least 3 micrograms of RNA were send to Novogene.

treatment_protocol: Cells were selected by adding puromicine (0.3 micrograms/mL) to culture medium during 2 weeks

value: Fibroblast


title: Blood, non-pregnant buffalo 1

description:
circle RNA
c-buffalo-1


title: Passage 1 organoid derived from murine salivary glands at 14 days post IR, rep3

value: IR

value: 14 days


title: FBE6E7_122_Rep1


title: n1.16.2


title: FBE6E7_122_Rep2


title: Passage 1 organoid derived from murine salivary glands at 14 days post IR, rep1


title: Passage 1 organoid derived from murine salivary glands at 14 days post IR, rep2


title: n2.16.2


title: FBE6E7_107_Rep3


title: FBE6E7_107_Rep2


title: Passage 1 organoid derived from murine salivary glands at 14 days post sham-IR, rep3


title: w.16.1


title: Brain, CNTNAP4-KO mice 2

city: Guangzhou

first: Wenlong

last: Zhang

address: Yuexiu

institute: The First Affiliated Hospital of Guangzhou Medical University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

organism: Mus

source_name: brain

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: basolateral amygdala

value: female


title: Brain, Wild type mice 3

value: Wild type


title: Brain, CNTNAP4-KO mice 1


title: Brain, CNTNAP4-KO mice 3


title: Passage 1 organoid derived from murine salivary glands at 14 days post sham-IR, rep1


title: Passage 1 organoid derived from murine salivary glands at 14 days post sham-IR, rep2


title: n2.16.1


title: n1.16.1


title: Brain, Wild type mice 2


title: FBE6E7_107_Rep1


title: Brain, Wild type mice 1


title: FBE6E7_38b_Rep3


title: MB011B_ban_spg_biol_Rep3_exp

value: 3-4 days post-eclosion

value: gamma5Beta'2a/Beta'2mp/Beta'2mp_bilateral Mushroom Body Output Neurons

value: FACS isolated neurons


title: FBE6E7_38b_Rep2


title: KPC female pancreas gemcitabine 3

city: Davis

first: Gerardo

middle: Guillermo

last: Mackenzie

state: California

address: One Shields Ave

department: Nutrition

institute: University of California, Davis

description: CG 3

data_processing:
Raw data was aligned to mm10 genome using HISAT2
read counts and normalized read count were generated using the feature Counts
and the differentially expressed genes were identified using DESeq2.
Assembly: mm10

source_name: pancreas tumor

extract_protocol:
Total RNA was extracted following the manufacturer’s instructions using a RNeasy mini kit (74104, QIAGEN) from frozen pancreas/tumors
RNA-sequencing were performed by Novogene Co., LTD (Beijing, China)

treatment_protocol: KPC mice were treated with or without a ketogenic diet and with or without gemcitabine

value: pancreas tumor

value: gemcitabine


title: MB011B_scramble_biol_Rep3_control


title: KPC female pancreas gemcitabine 2

description: CG 2


title: FBE6E7_38b_Rep1


title: Yap low density

city: New Haven

first: Scott

middle: Dean

last: Pope

state: Connecticut

address: 300 Cedar St

department: Immunobiology

institute: Yale School of Medicine

library_source: genomic

data_processing:
Reads from Illumina paired end fastq files were mapped to the mouse genome (mm9) using Bowtie  with the options “-S -q --best -m 1 -p 20 -v 1 -a -strata” to generate SAM files.  Read duplicates were removed and BAM files were generated with the Picard toolkit.
Bigwig files were generated using Homer software83 using the option “-fsize 1e20” and visualized with UCSC genome browser.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig

molecule: genomic DNA

source_name: Murine embryonic fibroblast

growth_protocol: All cell cultures were in their growth medium as descrbied in a 37° C incubator at 5% CO2. Growth medium is DMEM 10% FBS supplemented with glutamine, pyruvate, Penstrap, and HEPES.

extract_protocol:
MEFs were crosslinked by adding formaldehyde to the medium to a final concentration of 1%  in 15 cm plates with continuous, gentle rocking at RT for 10 minutes. The reaction was quenched by adding 125 mM final concentration of glycine, with continuous, gentle rocking at RT for 5 minutes. The cells were washed 3 times with ice cold PBS, scraped with 10 ml of PBS, and spun down for 5 minutes at 1,500 rpm at 4°C. For Chromatin-immunoprecipitation, for cell pellets of 106 cells, 1 ml cell lysis buffer (10 mM Hepes pH 7.3, 85 mM KCl, 1 mM EDTA, 0.5% IGEPAL CA-630, 1x protease inhibitors (ThermoFisher Halt)) was used to resuspend the pellet and incubated on ice for 5 minutes. The lysate was centrifuged for 5 minutes at 4,000 rpm at 4°C, the supernatant was removed, and the pellet was resuspended in 0.3 ml of nuclear lysis buffer for sonication (10mM Tris pH 8.0, 0.5% N-lauroylsarcosine, 0.1% sodium deoxycholate, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1x protease inhibitors (ThermoFisher Halt)). Cell lysate was transferred to 1.5 ml Bioruptor Plus TPX microtube (Diagenode), and was sonicated for 4 rounds of 15 cycles of 30 seconds on/30 seconds off on high power (Diagenode Biorupter plus). After sonication, the chromatin was centrifuged for 15 minutes at max speed at 4°C and the supernatant was carefully transferred to a new tube and 1% Triton X-100 was added.  0.7 mL of ChIP dilution buffer (20 mM Tris pH 7.5, 0.5% Triton X-100, 100 mM NaCl, 1 mM EDTA, 1x protease inhibitor) was then added to the sonicated chromatin.   10% of the chromatin was taken as “Input”, and the remaining chromatin incubated overnight with anti-YAP1 antibody at 1:50 dilution (CST) overnight on a rotator at 4°C. Protein G Dynabeads (ThermoFisher 10004D) were washed 3 times with PBS + 0.5% BSA and then added to the chromatin and antibody mixture and rotated at 4°C for 3 hours. Protein G dynabeads were washed sequentially with low-salt wash buffer (20 mM Tris pH 7.5, 0.1% SDS, 1 % Triton X-100, 150 mM NaCl, 1 mM EDTA), and LiCl wash buffer (10 mM Tris pH 7.5, 1% sodium deoxycholate, 1% Triton X-100, 250 mM LiCl, 1 mM EDTA) 3 times, and washed once with TE to remove detergents and salts. Bound DNA was eluted twice by resuspending the beads with 125 ul of elution buffer (50 mM NaHCO3, 1% SDS) and incubated for 10 minutes at RT, followed by 3 minutes of vigorous shaking at 37°C. Eluted DNA was digested with proteinase K at 55°C for 2 hours and reverse-crosslinked at 65°C overnight.
DNA was purified using the Qiagen MinElute PCR Purification Kit and ChIPseq libraries were generated using the NEBNext Ultra II DNA Library Prep Kit for Illumina. Sequencing was performed with Illumina NextSeq500 for paired-end 38bp reads.

treatment_protocol: 800K/150mm plate and 8,000K/150mm plate are two density of fibroblasts being examined here. Cells were plated at the indicated densityovernight culture. During collection, 30 plates of 800K/ plate and 3 plates of 8,000K/plate cells were harvest for ChIP, to reach ~ 25M per ChIP experiment.

value: embryonic fibroblast

tag: density

value: low


title: Yap high density

value: high


title: Infected-AT2-Ki67(+)

city: Philadelphia

first: Ying

last: Tian

state: PA

address: 3500 N. Broad Street

department: Pharmacology, Center for Translational Medicine

institute: Lewis Katz School of Medicine at Temple University

data_processing:
The scRNAseq data was processed by Cell Ranger (v.3.0.2, 10X Genomics) followed by Seurat suite (version 4.0.1)
sample demultiplexing was performed based on sample index reads to generate FASTQ files for each sequencing library using Cell Ranger mkfastq mode
STAR aligner was used to map raw reads to the mouse genome (mm10) through the Cell Ranger count mode
the Seurat suite (version 4.0.1) was used to perform filtering, normalization, data scaling, and Principal component analysis (PCA) and Uniform Manifold Approximation and Projection (UMAP) analysis for dimensionality reduction and clustering
Genes differentially expressed across clusters were identified using likelihood ratio test
Genome_build: mm10
Supplementary_files_format_and_content: *differential_expression.csv

source_name: Mouse primary AT2 cells

extract_protocol:
Mouse AT2 cells were isolated using dispase digestion method. Dissociated cells were processed for flow cytometry to obtain GFP+/tdTomato+ cells or GFP+/tdTomato- cells on a BD influx LSRII.
Single cell RNA-seq libraries were generated using Single Cell 3’ Reagent Kits v2 (10xGenomics) according to the manufacturer’s protocol

treatment_protocol: The clinical isolated pneumococcal strain SpT4 was used. Anesthetized mice using ketamine/xylazine mixture were infected intranasally with a dose of approximately 5x106 colony-forming units (CFU) in 30 μL of sterile PBS. Control groups are mice treated with intranasal inhalation of PBS.

value: Primary proliferative alveolar epithelial type 2 cells

value: 6-10 weeks of age

value: 4 days after Streptococcus pneumoniae infection


title: KPC female pancreas gemcitabine 1

description: CG 1


title: FBE6E7_18_Rep2

value: Skin

value: Fibroblast


title: FBE6E7_18_Rep3


title: KPC female pancreas keto diet+gemcitabine 4

description: KG 4

value: keto diet+gemcitabine


title: Passage 2 organoid derived from murine salivary glands at 14 days post sham-IR, rep1

value: salivary gland stem/progenitor cells

value: Passage 2 organoid

value: sham-IR

value: 14 days


title: Naive-AT2-Ki67(+)

value: 4 days after PBS treatment


title: Infected-AT2-Ki67(-)

value: Primary non-proliferative alveolar epithelial type 2 cells


title: KPC female pancreas keto diet+gemcitabine 2

description: KG 2

value: pancreas tumor

value: female


title: FBE6E7_16_Rep3


title: KPC female pancreas keto diet+gemcitabine 3

description: KG 3


title: AT2 cell - Ad Thra_rep3

data_processing:
The Illumina Nextseq 500 system was used to generate raw data at 75 cycles
Fastq files was aligned to the reference genome and DEseq2 was used to analyze the differentially expressed genes
Genome_build: mm10
Supplementary_files_format_and_content: tsv files with FPKM values for each samples

source_name: AT2 cell - Ad Thra

growth_protocol: Mouse AT2 cells were isolated from 5- or 6-week-old mice. Purified AT2 cells were plated at a density of 50000/cm2 to rat tail collagen-coated plates and were maintained in culture medium with 2% fetal bovine serum. Culture medium composition is 0.25% bovine serum albumin, 1 mM L-glutamine, 10 mM HEPES, 0.1 mM nonessential amino acids, 0.05% insulin-transferrin-sodium selenite, 100 U/mL penicillin G, 100 μg/mL streptomycin in DMEM/F12 (1:1)

extract_protocol:
Total RNA was harvested using RNeasy Mini Kit (QIAGEN, Catalog number 74104). RNA libraries were prepared using NEB ULTRA RNA II kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: At 24 hours after cell seeding, AT2 cells were infected with Ad-Cre, Ad-GFP-Atf3 and Ad-Thra at 100 MOI in culture medium for 48 hours.

value: AT2; Primary alveolar epithelial type 2 cells

value: 6 weeks of age

value: Adneovirus-Thra


title: FBE6E7_18_Rep1


title: AT2 cell - Ad Thra_rep1


title: Naive-AT2-Ki67(-)


title: KPC female pancreas keto diet+gemcitabine 1

description: KG 1


title: FBpLVX_Rep6

description: the sample was used as a calibrator

value: Empty-vector


title: FBE6E7_16_Rep2


title: FBE6E7_16_Rep1


title: AT2 cell - Ad Thra_rep2


title: Y6774_K3

city: Columbus

first: Maciej

last: Pietrzak

state: OH

address: 1800 Cannon Drive, 340C Lincoln Tower

department: Department of Biomedical Informatics College of Medicine

institute: Ohio State University

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (v6.0) (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lung

extract_protocol:
Single cells were obtained from asthmatic lung tissues by mechanical and enzymatic dissociation. After enzymatic digestion, the cells were placed in inactivation buffer (RPMI1640 + 10% FBS), filtered to remove any remaining tissue, the filtrate was centrifuged at 300g and the cell pellet was suspended in RBC lysis buffer, resuspended in inactivation buffer and viability is determined to be 85-95% before submitting for approximately 0.75 to 1x10^5  cells for scRNA-seq analysis.
Library preparation was carried out using 10x Genomics Chromium controller (10x Genomics). Chromium 10x Genomics single cell library was sequenced as 150 base pair single-end reads on an Illumina NovaSeq 6000 (Illumina, Inc.), with cells from each of the two microchips sequenced across three flow cell lanes.

value: Lung

value: Mir-155 KO


title: Y7544_K2


title: AT2 cell - Ad Atf3_rep3

source_name: AT2 cell - Ad Atf3


title: Y7543_K1


title: AT2 cell - Ad Atf3_rep2


title: Y6773_W3

value: WT


title: FBpLVX_Rep4

description: the sample was used as a calibrator

value: Skin

value: Fibroblast


title: AT2 cell - Ad Atf3_rep1


title: AT2 cell - Ad Cre_rep3

source_name: AT2 cell - Ad Cre

value: Adneovirus-Cre


title: FBpLVX_Rep3

description: the sample was used as a calibrator


title: Y7541_W1


title: Y7542_W2


title: FBpLVX_Rep2

description: the sample was used as a calibrator


title: AT2 cell - Ad Cre_rep2


title: FBpLVX_Rep1

description: the sample was used as a calibrator


title: FA2

city: Changzhou

first: Xia

last: Yi

address: Gehu Middle Road #21

institute: Changzhou University

description: All_Counts for weak acids.txt

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Clean Reads mapped to Sscrofa10.2  genome using Mapsplice v2.1.8 with  parameters -s 22 -p 15 --ins 6 --del 6 --non-canonical --bam -o
count counting
Assembly: ZN-0.fa
Supplementary files format and content: TXT file contain counts for each sample

organism: Amorphotheca resinae

source_name: mycelia

growth_protocol: A. resinae ZN1 with inoculated with 1 × 108 spores was cultured at 28 °C in PAD (potato-dextrose agar) medium separately amended with 1.0 g/L furfural, 1.0 g/L HMF, 0.1 g/L 4-hydroxybenzaldehyde, 0.1 g/L syringaldehyde, 0.1 g/L vanillin, 2.0 g/L acetic acid, and 4.0 g/L formic acid.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen).
RNA library using standard Ion proton RNA-Seq Kit v2.0 protocol

treatment_protocol: The A. resinae ZN1 mycelia were harvested at 4 h for RNA isolation. All assays were carried in twice.

value: mycelia

value: Amorphotheca resinae ZN1

value: Wild type

value: Formic acid


title: AT2 cell - Ad Cre_rep1


title: FA1

description: All_Counts for weak acids.txt


title: AA1

description: All_Counts for weak acids.txt

value: Acetic acid


title: CEM [RNA-seq]

data_processing:
Illumina NovaSeq 6000 Sequencing System
To remove the adapters from the sequence, the CutAdapt tool was used, after that the quality analysis was carried out with the "FAST QC Read Quality Reports" tool, then the "Trimmomatic" tool was used to make criteria base pair cuts. (evaluation of paired sequences).
The "RNA STAR" tool and the reference genome "GRCh38.p13" were used for the alignment. To perform the differential expression analysis, Deseq2 was used and finally the counting tables were obtained with the values of fragments per million kilobases (FPKM).
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Cell line

extract_protocol:
For RNA extraction, we used the kit RNA isolation Zymo Research (Cat.R1058), and manufacter's instructions were followed.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue/cell line

value: CEM

tag: leukemia type

value: ALL

value: untreated


title: r1-m3_AL_rep3

data_processing:
The raw reads of 18 samples (3 genotypes × 2 compartments × 3 biological replicates) were trimmed by Trimmomatic (v0.39), followed by quality control by FastQC
The trimmed reads were mapped to the maize reference genome via HISAT2
The output SAM files were converted to BAM files and were sorted and indexed by SAMtools
For differential expression analysis, mapped transcripts in sorted BAM files were assembled according to annotation file Zea_mays.B73_RefGen_v4.50.gtf
Read counts were calculated by HTSeq (v0.11.2) and differentially expressed genes (DEGs) were called via DEseq2
Assembly: Zm-B73-REFERENCE-GRAMENE-4.0
Supplementary files format and content: Tab-delimited text files including read counts calculated by HTSeq

source_name: Endosperm

extract_protocol:
Use Arcturus PicoPure RNA Isolation kit following the manufacturers instruction for LCM, and 5 ng of captured RNA was used for cDNA amplification by Ovation RNA-Seq System V2 kit (Nugen Technologies) following the manufacturer’s protocols
The construction of the cDNA paired-end libraries and their quality checking were carried out at the High-Throughput Genomics and Bioinformatic Analysis Shared Resource at HCI at the University of Utah, using a NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) with ~400 ng of amplified cDNA

treatment_protocol: Endosperms AL and SE compartment were laser microdissected at 19 DAP

value: Endosperm

tag: cell line

value: Aleurone

value: Laser Capture Microdissection


title: K2

description: All_Counts for weak acids.txt

value: Control for weak acids


title: R1-sc_AL_rep3


title: FBpLVX_Rep5

description: the sample was used as a calibrator

value: Empty-vector


title: M5 [RNA-seq]

source_name: Bone Marrow

value: Bone Marrow

value: ALL-T


title: K1

description: All_Counts for weak acids.txt


title: AA2

description: All_Counts for weak acids.txt


title: R1-sc_SE_rep3

value: Starchy endosperm


title: Undiff_Basic03-2

city: Yokohama

first: nobuaki

last: shiraki

address: 4259-B-25 Nagatsuta-cho, Midori-ku

department: School of Life Science and Technology

country: Japan

institute: Tokyo Institute of Technology

description: undifferentiated hiPSCS cultured with Basic03 medium with bFGF for 48 hours. One of three samples (#2).

data_processing:
RNA-seq reads were processed with Subio Platform v1.24.5659.
The pipeline composed of fastp v0.20.0, HISAT2 v2.1.0, and StringTie v2.0.6 software and calculated with the GRCh38 genome and Ensembl's gene model of the same genome version.
It output TPM and reverse-calculated count values, which we analyzed with the Subio Platform software afterward.
Genome_build: GRCh38.p13

source_name: Undifferenitiated human iPS cells

growth_protocol: Ff-I01s01 undifferentiated human iPS cells were dissociated and plated at 5×10^5 cells/well on SynthemaxII-coated 6-well plates (Corning) and cultured at 37 °C for 24 h.

extract_protocol:
RNA was extracted using the RNeasy micro-kit (Qiagen, Germany) and DNase I (Qiagen) treatment was performed according to the manufacturer’s instructions.
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations.   Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.   Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.   Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-).   Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H.   Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities.   After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization.   In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA).   Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor- ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR.   Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer.   At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.  The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions.   After cluster generation, the library preparations were sequenced on an Illumina platform (Novaseq 6000PE150) and paired-end reads were generated.

treatment_protocol: The cells were treated with undiff-AKM (IGF1) medium & Zn addition (0, 0.5, 3, and 10 μM) or Basic03 & bFGFand cultured for 48 h.

value: Undifferentiated human iPS cells

value: 48 h days under Basic03 with bFGF condition


title: JURKAT [RNA-seq]

value: JURKAT


title: C2

description: All_Counts for phenolic aldehydes.txt

value: mycelia

value: Amorphotheca resinae ZN1

value: Wild type

value: Control for phenolic aldehydes


title: R1-g_AL_rep3


title: r1-m3_SE_rep2


title: C1

description: All_Counts for phenolic aldehydes.txt


title: Hy2

description: All_Counts for phenolic aldehydes.txt


title: r1-m3_AL_rep2


title: S2

description: All_Counts for phenolic aldehydes.txt

value: Syringaldehyde


title: r1-m3_SE_rep3


title: R1-g_SE_rep3


title: S1

description: All_Counts for phenolic aldehydes.txt


title: Undiff_Zn10-3

description: undifferentiated hiPSCS cultured with a medium containing 10 μM zinc for 48 hours. One of three samples (#3).

value: 48 h days under AKM (IGF1) with 10 μM Zn condition


title: Undiff_Zn3-3

description: undifferentiated hiPSCS cultured with a medium containing 3 μM zinc for 48 hours. One of three samples (#3).

value: 48 h days under AKM (IGF1) with 3 μM Zn condition


title: Undiff_Zn10-2

description: undifferentiated hiPSCS cultured with a medium containing 10 μM zinc for 48 hours. One of three samples (#2).


title: Undiff_Basic03-1

description: undifferentiated hiPSCS cultured with Basic03 medium with bFGF for 48 hours. One of three samples (#1).


title: Undiff_Zn10-1

description: undifferentiated hiPSCS cultured with a medium containing 10 μM zinc for 48 hours. One of three samples (#1).


title: R1-sc_SE_rep2

value: Endosperm


title: Undiff_Basic03-3


title: R1-g_AL_rep2

value: Aleurone

value: Laser Capture Microdissection


title: V1

description: All_Counts for phenolic aldehydes.txt

value: Vanillin


title: R1-sc_AL_rep2


title: Hy1

description: All_Counts for phenolic aldehydes.txt


title: R1-g_SE_rep2


title: Undiff_Zn3-2

description: undifferentiated hiPSCS cultured with a medium containing 3 μM zinc for 48 hours. One of three samples (#2).


title: V2

description: All_Counts for phenolic aldehydes.txt


title: H3

description: All_Counts for furans.txt

value: HMF


title: H4

description: All_Counts for furans.txt


title: r1-m3_SE_rep1


title: r1-m3_AL_rep1


title: Undiff_Zn0-2

description: undifferentiated hiPSCS cultured with zinc-free medium for 48 hours. One of three samples (#2).

value: 48 h days under AKM (IGF1) with 0 μM Zn condition


title: R1-sc_SE_rep1

value: Starchy endosperm


title: R1-sc_AL_rep1


title: Undiff_Zn0-1

description: undifferentiated hiPSCS cultured with zinc-free medium for 48 hours. One of three samples (#1).

value: Undifferentiated human iPS cells


title: R1-g_SE_rep1


title: O1

description: All_Counts for furans.txt

value: Control for furans


title: F1

description: All_Counts for furans.txt

value: Furfural


title: Undiff_Zn0.5-2

description: undifferentiated hiPSCS cultured with a medium containing 0.5 μM zinc for 48 hours. One of three samples (#2).

value: 48 h days under AKM (IGF1) with 0.5 μM Zn condition


title: Undiff_Zn3-1

description: undifferentiated hiPSCS cultured with a medium containing 3 μM zinc for 48 hours. One of three samples (#1).


title: Undiff_Zn0.5-3

description: undifferentiated hiPSCS cultured with a medium containing 0.5 μM zinc for 48 hours. One of three samples (#3).


title: Undiff_Zn0.5-1

description: undifferentiated hiPSCS cultured with a medium containing 0.5 μM zinc for 48 hours. One of three samples (#1).


title: F2

description: All_Counts for furans.txt

value: mycelia

value: Amorphotheca resinae ZN1


title: Undiff_Zn0-3

description: undifferentiated hiPSCS cultured with zinc-free medium for 48 hours. One of three samples (#3).


title: T_cold_80min_I1

status: Public on Jul 20 2022

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: T_cold_180min_J1

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


title: T_cold_180min_J2


title: T_cold_180min_J3


title: T_cold_80min_I2


title: T_cold_80min_I3


title: Tgace2_72h_cellulose_rep1

city: Nanjing

first: Youzhi

last: Miao

address: WeiGang NO.1

institute: Nanjing Agricultural University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to strain NJAU4742 whole genome using Tophat2 software
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated and compared in different samples using Cufflinks, Cuffdiff and Cuffnorm softwares.
Supplementary_files_format_and_content: gene RPKM values

organism: Trichoderma guizhouense

source_name: mycelium

extract_protocol:
RNA was extracted using the RNeasy Plant Mini Kit (Qiagen, German) combined with the RNase-Free DNase set (Qiagen, German)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: incubation substrates

value: cellulose

tag: sampling time


title: Tgace2_72h_cellulose_rep2


title: Tgace2_72h_cellulose_rep3


title: NB4-GNE987-H3K27ac

city: Suzhou

first: Fang

last: Fang

state: Jiangsu

address: 92 Zhongnan street

institute: Children’s Hospital of Soochow University

data_processing:
Raw data of ChIP-Seq was aligned to the reference genome (UCSC hg38) using Bowtie2 (v 2.3.5)
Peaks were identified using MACS2 (v2.0.9)
Genome_build: hg38
Supplementary_files_format_and_content: peak text files

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions

tag: chip antibody

tag: treat


title: O2

description: All_Counts for furans.txt

value: Wild type


title: T_cold_20min_H3


title: T_cold_20min_H1


title: T_cold_20min_H2


title: R1-g_AL_rep1

tag: cell type


title: Tgace2_24h_cellulose_rep3


title: Tgace2_24h_cellulose_rep2


title: Tgace2_24h_cellulose_rep1


title: Tgace2_4h_cellulose_rep3


title: Tgace2_4h_cellulose_rep2


title: Tgace2_4h_cellulose_rep1


title: Tgace2_72h_xylan_rep3

value: xylan


title: Tgace2_72h_xylan_rep2


title: frontal_cortex_203253040201_R08C01

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

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: F

value: control

tag: dementia

value: CONTR

value: sparse


title: frontal_cortex_203265020004_R07C01

description: Human postmortem frontal cortex tissue

value: M

value: PDD

value: yes


title: frontal_cortex_203273630201_R06C01

description: Human postmortem frontal cortex tissue

value: frequent


title: frontal_cortex_203168670039_R01C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203168500030_R01C01

description: Human postmortem frontal cortex tissue


title: Smchd1MD1_Xist1lox_EpiSCs

city: Toyonaka

first: Koji

last: Nagao

state: Osaka

address: 1-1 Machikaneyama

department: Graduate School of Science

institute: Osaka University

data_processing:
Allele-resolved RNA-seq analysis was performed as described by Sakata et al. (2017) with minor modifications: (1) paired-end reads were used as single-end reads; (2) the numbers of allele-specific reads in replicates were summed; (3) genes with more than 10 allele-specific reads were considered to be informative for assessing the expression from the Xi; (4) Cufflinks v2.2.1 cuffdiff (Trapnell et al., 2010) with option ‘--library-type ff- firststrand --multi-read-correct’ was used to estimate gene expression level as the FPKM (fragments per kilobase of exon per million fragments mapped) in a non-allelic manner. RNA-seq data of MEFs were reported previously (Sakakibara et al., 2018). For each gene, the number of maternal (B6 or 129) and paternal (JF1) allele-specific reads were counted and percentages of total expression from the paternal allele were calculated as %Xi for assessing the expression from the Xi.
Assembly: mm9
Supplementary files format and content: tab-delimited text file includes patRatio (the ratio of the number of paternal reads to the number of total allele specific reads), asReads (the total number of allele-specific reads), and FPKM values for each sample.

source_name: EpiSCs

extract_protocol:
Total RNAs were extracted from EpiSCs using TRIzol (Ambion)
Libraries were prepared using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina)

tag: strain

value: C57BL6/J x (JF1 x C57BL6/J F1)

tag: developmental stage

value: EpiSCs

tag: genotype

value: Smchd1^MD1/MD1 Xist^1lox/+

value: female


title: Tgace2_24h_xylan_rep3


title: Smchd1WT_XistdeltaA_EpiSCs

value: Smchd1^+/+ Xist^deltaA/+


title: Tgace2_72h_xylan_rep1


title: frontal_cortex_203048410058_R06C01

description: Human postmortem frontal cortex tissue


title: Tgace2_4h_xylan_rep3


title: frontal_cortex_203048410063_R05C01

description: Human postmortem frontal cortex tissue

value: PD


title: Tgace2_4h_xylan_rep1


title: Smchd1WT_Xist1lox_EpiSCs

value: Smchd1^+/+ Xist^1lox/+


title: frontal_cortex_203048410131_R01C01

description: Human postmortem frontal cortex tissue

value: iLBD


title: frontal_cortex_203049640050_R08C01

description: Human postmortem frontal cortex tissue

value: no


title: frontal_cortex_203265020004_R08C01

description: Human postmortem frontal cortex tissue

value: F


title: frontal_cortex_203048410151_R01C01

description: Human postmortem frontal cortex tissue

value: control


title: frontal_cortex_203168500099_R08C01

description: Human postmortem frontal cortex tissue

value: CONTR

value: moderate


title: Smchd1MD1_XistdeltaA_EpiSCs

value: Smchd1^MD1/MD1 Xist^deltaA/+


title: frontal_cortex_203271740112_R06C01

description: Human postmortem frontal cortex tissue

value: sparse


title: frontal_cortex_203168500099_R07C01

description: Human postmortem frontal cortex tissue

value: M


title: Tgace2_0h_rep1

value: glucose


title: frontal_cortex_203168500099_R05C01

description: Human postmortem frontal cortex tissue

value: MSA

value: yes

value: PDD


title: Tgace2_24h_xylan_rep2

value: xylan


title: Tgace1_72h_cellulose_rep1

value: cellulose


title: Tgace1_72h_cellulose_rep2


title: Tgace2_4h_xylan_rep2


title: frontal_cortex_203168500099_R06C01

description: Human postmortem frontal cortex tissue


title: Tgace2_0h_rep3


title: frontal_cortex_203168500099_R03C01

description: Human postmortem frontal cortex tissue

value: PD


title: Tgace1_24h_cellulose_rep3


title: frontal_cortex_203168500099_R02C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203168500072_R08C01

description: Human postmortem frontal cortex tissue


title: Tgace1_4h_cellulose_rep2


title: Tgace2_0h_rep2


title: frontal_cortex_203168500072_R06C01

description: Human postmortem frontal cortex tissue

value: DLB


title: Tgace1_72h_xylan_rep3


title: frontal_cortex_203168500072_R05C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203168500072_R07C01

description: Human postmortem frontal cortex tissue


title: Tgace1_4h_cellulose_rep3


title: Tgace1_72h_cellulose_rep3


title: Tgace1_72h_xylan_rep2


title: frontal_cortex_203168500099_R04C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203168500072_R03C01

description: Human postmortem frontal cortex tissue


title: Tgace1_72h_xylan_rep1


title: frontal_cortex_203168500072_R02C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203168500072_R01C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203168500099_R01C01

description: Human postmortem frontal cortex tissue


title: Tgace1_24h_xylan_rep2


title: Tgace1_24h_cellulose_rep2


title: Tgace1_4h_xylan_rep3


title: Tgace1_24h_cellulose_rep1


title: frontal_cortex_203168500064_R08C01

description: Human postmortem frontal cortex tissue


title: Tgace1_4h_xylan_rep2


title: frontal_cortex_203168500064_R07C01

description: Human postmortem frontal cortex tissue


title: Tgace1_4h_cellulose_rep1


title: frontal_cortex_203168500064_R05C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203168500059_R04C01

description: Human postmortem frontal cortex tissue

value: iLBD


title: Tgace1_4h_xylan_rep1


title: frontal_cortex_203168500072_R04C01

description: Human postmortem frontal cortex tissue

value: no


title: frontal_cortex_203168500059_R02C01

description: Human postmortem frontal cortex tissue

value: F


title: Tgace1_0h_rep3


title: frontal_cortex_203168500059_R01C01

description: Human postmortem frontal cortex tissue

value: control


title: frontal_cortex_203168500059_R08C01

description: Human postmortem frontal cortex tissue

value: CONTR


title: Tgace2_24h_xylan_rep1


title: Tgxyr1_72h_carbon_starvation_rep2

value: no carbon


title: Tgace1_0h_rep2


title: Tgace1_24h_xylan_rep1


title: Tgxyr1_72h_carbon_starvation_rep3


title: Tgace1_0h_rep1


title: Tgxyr1_72h_carbon_starvation_rep1


title: frontal_cortex_203168500059_R06C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203168500059_R05C01

description: Human postmortem frontal cortex tissue


title: Tgxyr1_24h_carbon_starvation_rep3


title: Tgace1_24h_xylan_rep3


title: frontal_cortex_203168500064_R02C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203168500064_R04C01

description: Human postmortem frontal cortex tissue


title: Tgxyr1_24h_carbon_starvation_rep1


title: frontal_cortex_203168500064_R06C01

description: Human postmortem frontal cortex tissue

value: moderate


title: frontal_cortex_203168500064_R01C01

description: Human postmortem frontal cortex tissue


title: Tgxyr1_24h_carbon_starvation_rep2


title: Tgxyr1_4h_carbon_starvation_rep3


title: frontal_cortex_203163300140_R07C01

description: Human postmortem frontal cortex tissue


title: Tgxyr1_72h_cellulose_rep3


title: Tgxyr1_4h_carbon_starvation_rep1


title: frontal_cortex_203163300140_R06C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203168500059_R07C01

description: Human postmortem frontal cortex tissue

value: sparse


title: frontal_cortex_203163300140_R05C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203163300140_R04C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203163300140_R08C01

description: Human postmortem frontal cortex tissue

value: M


title: frontal_cortex_203163300140_R03C01

description: Human postmortem frontal cortex tissue


title: Tgxyr1_72h_cellulose_rep1


title: frontal_cortex_203163300140_R02C01

description: Human postmortem frontal cortex tissue


title: Tgxyr1_24h_cellulose_rep2


title: Tgxyr1_4h_cellulose_rep2


title: frontal_cortex_203163300140_R01C01

description: Human postmortem frontal cortex tissue


title: Tgxyr1_24h_cellulose_rep1


title: frontal_cortex_203168670039_R08C01

description: Human postmortem frontal cortex tissue


title: Tgxyr1_4h_cellulose_rep3


title: Tgxyr1_72h_xylan_rep2


title: frontal_cortex_203168670039_R07C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203168670039_R05C01

description: Human postmortem frontal cortex tissue

value: AD


title: Tgxyr1_72h_cellulose_rep2


title: frontal_cortex_203168670039_R06C01

description: Human postmortem frontal cortex tissue

value: frequent


title: Tgxyr1_72h_xylan_rep3


title: Tgxyr1_4h_cellulose_rep1


title: Tgxyr1_4h_carbon_starvation_rep2


title: Tgxyr1_24h_cellulose_rep3


title: frontal_cortex_203168670039_R03C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203168670039_R04C01

description: Human postmortem frontal cortex tissue

value: yes


title: Tgxyr1_24h_xylan_rep3


title: frontal_cortex_203168670039_R02C01

description: Human postmortem frontal cortex tissue


title: Tgxyr1_24h_xylan_rep2


title: frontal_cortex_203163300131_R07C01

description: Human postmortem frontal cortex tissue


title: Tgxyr1_4h_xylan_rep3


title: Tgxyr1_4h_xylan_rep2


title: Tgxyr1_24h_xylan_rep1


title: frontal_cortex_203163300131_R06C01

description: Human postmortem frontal cortex tissue

value: PDD


title: frontal_cortex_203163300131_R04C01

description: Human postmortem frontal cortex tissue


title: Tgxyr1_4h_xylan_rep1

value: xylan


title: frontal_cortex_203163300131_R08C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203163300131_R02C01

description: Human postmortem frontal cortex tissue


title: Tgxyr1_0h_rep3

value: glucose


title: frontal_cortex_203163300131_R01C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203168500030_R08C01

description: Human postmortem frontal cortex tissue


title: Tgxyr1_72h_xylan_rep1


title: frontal_cortex_203168500030_R06C01

description: Human postmortem frontal cortex tissue


title: WT_72h_carbon_starvation_rep2


title: frontal_cortex_203168500030_R07C01

description: Human postmortem frontal cortex tissue


title: WT_72h_carbon_starvation_rep1


title: frontal_cortex_203163300131_R05C01

description: Human postmortem frontal cortex tissue


title: WT_24h_carbon_starvation_rep3


title: WT_24h_carbon_starvation_rep2


title: frontal_cortex_203168500030_R04C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203168500030_R05C01

description: Human postmortem frontal cortex tissue


title: WT_24h_carbon_starvation_rep1


title: frontal_cortex_203163300131_R03C01

description: Human postmortem frontal cortex tissue


title: WT_4h_carbon_starvation_rep2


title: frontal_cortex_203168500030_R03C01

description: Human postmortem frontal cortex tissue


title: WT_4h_carbon_starvation_rep1


title: Tgxyr1_0h_rep1


title: frontal_cortex_203168500028_R08C01

description: Human postmortem frontal cortex tissue

value: PD


title: WT_72h_cellulose_rep3

value: cellulose


title: WT_72h_cellulose_rep2


title: WT_72h_cellulose_rep1


title: WT_24h_cellulose_rep3


title: Tgxyr1_0h_rep2


title: frontal_cortex_203168500028_R05C01

description: Human postmortem frontal cortex tissue

value: DLB


title: frontal_cortex_203168500028_R04C01

description: Human postmortem frontal cortex tissue

value: no

value: FTD


title: frontal_cortex_203168500028_R06C01

description: Human postmortem frontal cortex tissue

value: F

value: control


title: frontal_cortex_203168500028_R03C01

description: Human postmortem frontal cortex tissue

value: VD


title: WT_24h_cellulose_rep1


title: frontal_cortex_203168500028_R02C01

description: Human postmortem frontal cortex tissue

value: CONTR


title: frontal_cortex_203168500030_R02C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203168670027_R07C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203168500028_R01C01

description: Human postmortem frontal cortex tissue


title: WT_4h_cellulose_rep2


title: WT_4h_cellulose_rep3


title: frontal_cortex_203168670027_R06C01

description: Human postmortem frontal cortex tissue

value: moderate


title: WT_72h_xylan_rep3


title: WT_4h_cellulose_rep1


title: frontal_cortex_203168670027_R04C01

description: Human postmortem frontal cortex tissue

value: sparse


title: WT_72h_xylan_rep2


title: frontal_cortex_203168670027_R05C01

description: Human postmortem frontal cortex tissue

value: M


title: WT_24h_xylan_rep3


title: frontal_cortex_203168500028_R07C01

description: Human postmortem frontal cortex tissue


title: WT_24h_xylan_rep2


title: WT_24h_cellulose_rep2


title: frontal_cortex_203168670027_R02C01

description: Human postmortem frontal cortex tissue

value: AD


title: WT_72h_xylan_rep1


title: frontal_cortex_203168670108_R08C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203168670108_R07C01

description: Human postmortem frontal cortex tissue

value: yes

value: frequent


title: frontal_cortex_203168670027_R01C01

description: Human postmortem frontal cortex tissue

value: PDD


title: WT_4h_xylan_rep2

value: xylan


title: WT_24h_xylan_rep1


title: WT_4h_xylan_rep3


title: frontal_cortex_203168670108_R04C01

description: Human postmortem frontal cortex tissue

value: PD


title: frontal_cortex_203168670108_R06C01

description: Human postmortem frontal cortex tissue


title: WT_4h_xylan_rep1


title: frontal_cortex_203168670108_R05C01

description: Human postmortem frontal cortex tissue


title: WT_0h_rep2

value: glucose


title: WT_0h_rep1


title: frontal_cortex_203168670108_R02C01

description: Human postmortem frontal cortex tissue

value: Atypical


title: frontal_cortex_203168670106_R07C01

description: Human postmortem frontal cortex tissue

value: no

value: DLB


title: frontal_cortex_203168670106_R03C01

description: Human postmortem frontal cortex tissue

value: F


title: frontal_cortex_203168670106_R04C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203168670106_R06C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203048410095_R07C01

description: Human postmortem frontal cortex tissue

value: control

value: iLBD


title: WT_0h_rep3


title: frontal_cortex_203048410095_R05C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203168670108_R01C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203168670106_R02C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203168670106_R08C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203168670106_R05C01

description: Human postmortem frontal cortex tissue

value: CONTR


title: frontal_cortex_203048410095_R06C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203048410095_R02C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203168670106_R01C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203048410095_R01C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203168670108_R03C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203048410095_R04C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203048410095_R03C01

description: Human postmortem frontal cortex tissue


title: 3SN

type: RNA

city: Homburg

first: Tanja

last: Stachon

address: Kirrergerstr. 100

department: Dr. Rolf  M. Schwiete Center

country: Germany

institute: Saarland University

hyb_protocol: The expression profile of 2549 human miRNAs was determined using SurePrint G3 8x60k miRNA microarrays (Agilent) according to the manufacturers recommendations

scan_protocol: Array´s were scanned with the Agilent Scanner with default settings.

data_processing: Raw expression values were extracted using the Feature Extraction Software of Agilent. Raw signal intensities were quantil-normalized and log2 transformed.

label: using miRNA Complete Labeling and Hyb Kit (Agilent, Cat. No 5190-0456),  Cyanine 3-pcp

source_name: corneal stroma

extract_protocol: Total RNA including miRNAs was isolated using the Qiagen miRNeasy Kit according to manufacturers recommendations.

tag: age

tag: gender

tag: disease

value: healthy control


title: frontal_cortex_203048410165_R07C01

description: Human postmortem frontal cortex tissue

value: sparse


title: 4SN

label_protocol: The expression profile of 2549 human miRNAs was determined using SurePrint G3 8x60k miRNA microarrays (Agilent) according to the manufacturers recommendations

value: M


title: Blastocyst from oocyte exposed to high NEFAs vs control rep3

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

country: Canada

institute: Université Laval

description: Biological replicates 3 of 4

hyb_protocol: Hybridizations were performed according to the microarray manufacturer’s instructions (Agilent Technologies). Briefly, 500 ng of labeled sample (in 22 μL) was mixed with 61 μL of hybridization master mix containing 5 μL of Cot-1 (1 mg/ml) , Applied Genetics Laboratories), 1μL of Agilent 100x Blocking Agent and 55 μL of Agilent 2× HI-RPM Hybridization Buffer (Agilent Technologies). Samples were held at 95°C for 3 min and at 37°C for 30 min followed by addition of 27 μL of Agilent-CGHBlock (final volume 110 μL). The samples were loaded onto the microarray and hybridization was carried out in a hybridization oven (Shel Lab) for 40 h at 65°C and 20 rpm. Washing was carried out according to the microarray manufacturer’s instructions

scan_protocol: Scan on a PowerScanner (Tecan) at 2um using the autogain function. Images were quantified using ArrayPro version 6.3 (MediaCybernetics)

data_processing: The array data analysis methods and downstream analysis pipelines are described in detail in (Saadi et al., 2014). Briefly, after Loess normalization, quantile inter-array scale normalization was performed and fitted to a linear model and thus, Bayesian statistics of differential expression were obtained. Thus, differentially methylated probes were identified using linear models for microarray data (LIMMA).

organism: Sus scrofa

source_name: Blastocysts

label_protocol: For each sample, 1 μg of DNA was labeled using the Universal Linkage System (ULS) labeling kit (Kreatech Biotechnology) according to the manufacturer’s instructions with minor modifications: 1 μL of Cy-ULS dye was added per 1 μg of genomic DNA adjusted with 10× labeling buffer. The labelling mixture was then held for 30 min at 85°C in a thermocycler, followed by 3 min on ice. Non-reacted ULS-Cy3/5 was removed by purification using a QIAquick PCR Purification Kit and samples were eluted in 25 μL 1/10 Buffer EB. A 1.5 μL aliquot was used to determine DNA concentration and dye incorporation using the ND- 1000 NanoDrop.

extract_protocol:
Total RNA and gDNA were extracted using the AllPrep DNA/RNA Micro Kit (Qiagen)
The methodology have been thoroughly describef in (Saadi et al., 2014). Briefly, 10ng of DNA sample and spike-in control were cut in ≈160bp fragment using MSEI restriction enzyme. MseLig 12 and MseLig 21 adapters were added to the fragmented gDNA sites. Sample were the digested using methyl sensitive restriction enzyme HpaII, HinP1I and AciI. Only unmethylated fragment have been targeted by those enzyme, leaving only one adapter on the cleaved fragment. Efficiency of the digestion was confirmed by analyzing the spike-in control added prior to the DNA fragmentation step. For the step, qPCR was performed by preparing a separate mixes containing forward and reverse primer targeting HpaII, HinP1I and AciI site. Undigested spike-in (1/1000 dilution) was used as a positive control and non-template controls were also added as negatives control. The amplification plot and the dissociation curve were evaluated for each primer set separately. The DNA fragmentation was considered successful when the threshold cycle (ct) was greater than 5 when compared to the undigested control.Fragment selection by ligation-mediated PCR After cleavage by methyl sensitive enzyme, the gDNA was purified by ethanol precipitation and dissolve in nuclease free water. Selective amplification of methylated fragments was performed using two rounds of ligation-mediated PCR (LM-PCR). The PCR products were resolved on 0.8% agarose gel to assess the quality. Then the previously added linker were removed.

value: Blastocyst from oocyte in control


title: frontal_cortex_203048410095_R08C01

description: Human postmortem frontal cortex tissue


title: 2SN


title: Blastocyst from oocyte exposed to high NEFAs vs control rep4

description: Biological replicates 4 of 4


title: Blastocyst from oocyte exposed to high NEFAs vs control rep1

description: Biological replicates 1 of 4


title: Blastocyst from oocyte exposed to high NEFAs vs control rep2

description: Biological replicates 2 of 4


description: Biological replicates 4 of 4

value: Blastocyst from oocyte exposed to high NEFAs


title: frontal_cortex_203048410165_R06C01

description: Human postmortem frontal cortex tissue

value: FTD


description: Biological replicates 2 of 4


title: frontal_cortex_203048410165_R04C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203048410165_R05C01

description: Human postmortem frontal cortex tissue

value: yes

value: frequent


description: Biological replicates 3 of 4


title: frontal_cortex_203048410165_R08C01

description: Human postmortem frontal cortex tissue


description: Biological replicates 1 of 4


title: 4SKC

source_name: KC corneal stroma

value: KC

tag: Stage


title: 1SN


title: frontal_cortex_203048410165_R01C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203049640153_R08C01

description: Human postmortem frontal cortex tissue


title: 3SKC


title: frontal_cortex_203048410165_R02C01

description: Human postmortem frontal cortex tissue

value: AD

value: moderate


title: 2SKC


title: 5EN

source_name: corneal epithelium


title: 1SKC


title: 7EN


title: frontal_cortex_203049640153_R07C01

description: Human postmortem frontal cortex tissue

value: no

value: VD


title: 8EN


title: 6EN


title: frontal_cortex_203049640153_R05C01

description: Human postmortem frontal cortex tissue

value: F

value: PDD


title: frontal_cortex_203049640153_R03C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203049640153_R04C01

description: Human postmortem frontal cortex tissue

value: DLB


title: frontal_cortex_203049640153_R01C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203049640152_R08C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203049640152_R06C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203049640153_R02C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203049640152_R04C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203049640152_R07C01

description: Human postmortem frontal cortex tissue

value: control

value: CONTR


title: 1EKC

source_name: KC corneal epithelium


title: 7SKC


title: 7SN

value: healthy control


title: 6SN

value: M


title: 2EKC


title: 6SKC


title: 5SN


title: frontal_cortex_203049640152_R05C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203049640152_R02C01

description: Human postmortem frontal cortex tissue


title: 8SN


title: frontal_cortex_203049640151_R08C01

description: Human postmortem frontal cortex tissue

value: PD


title: frontal_cortex_203049640153_R06C01

description: Human postmortem frontal cortex tissue


title: 4EKC


title: frontal_cortex_203048410165_R03C01

description: Human postmortem frontal cortex tissue

value: sparse


title: 8SKC


title: 5SKC


title: frontal_cortex_203049640152_R03C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203049640151_R07C01

description: Human postmortem frontal cortex tissue


title: 3EKC


title: 3EN


title: frontal_cortex_203049640151_R06C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203049640152_R01C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203049640151_R05C01

description: Human postmortem frontal cortex tissue


title: 4EN


title: 2EN


title: frontal_cortex_203049640151_R01C01

description: Human postmortem frontal cortex tissue


title: HUVEC_Scr_NM_2

city: Duarte

first: Zhen

last: Chen

state: CA

address: 1500 E Duarte Rd

department: DMRI

institute: City of Hope

description: Single-cell RNA sequencing assay

data_processing:
10X Genomics cellranger (v3.0) was used to process sequencing data produced from Chromium Single Cell Gene Expression
Genome_build: hg38
Supplementary_files_format_and_content: Three processed data files per each sample: a matrix file (.mtx format) with UMI counts per each gene (rows) and single cell (columns); genes list (.tsv format) with the list of genes (features) detected; cell barcodes list (.tsv format) with the list of barcodes of the single cells in the sample.

source_name: Human Umbilical Vein Endothelial Cells cultured under osmotic control (25 mM mannitol) for 7 days combined with transfection with scramble LNA on the last 3 days

growth_protocol: HUVECs were grown following the manufacturer's protocol

extract_protocol:
Single-cell suspension was prepared by using the 10XGenomics Chromium Controller
10X Genomics Single Cell 3' v3. gene expression

treatment_protocol: HUVECs were cultured in complete medium with either 25nM Mannitol (NM) or 25mM D-Glucose and 5ng/mL TNF-alpha (HT) for 7 days in total; on the 5th day, the cells were transfected with either scramble LNA (Scr) or LNA targeting LINC00607 (LNA1) and then returned to either NM or HT medium for another 3 days.

value: HUVEC

tag: assay

value: scRNA-seq


title: frontal_cortex_203271740112_R05C01

description: Human postmortem frontal cortex tissue

value: yes


title: frontal_cortex_203049640151_R02C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203049640050_R03C01

description: Human postmortem frontal cortex tissue

value: frequent


title: 7EKC

value: KC


title: 8EKC


title: HVSMC 607KD2

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 Vascular Smooth Muscle 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.

tag: cell line

value: HVSMC

value: RNA-seq


title: frontal_cortex_203049640050_R07C01

description: Human postmortem frontal cortex tissue

value: no


title: HUVEC_Scr_HT_2

description: Single-cell RNA sequencing assay

source_name: Human Umbilical Vein Endothelial Cells exposed to high glucose (HG, to mimic hyperglycemia) and TNFα (to mimic inflammation) for 7 days combined with transfection with scramble LNA on the last 3 days


title: HUVEC_Scr_NM_1

description: Single-cell RNA sequencing assay


title: 6EKC


title: 5EKC

value: F


title: frontal_cortex_203049640050_R05C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203049640050_R06C01

description: Human postmortem frontal cortex tissue


title: HUVEC_Scr_HT_1

description: Single-cell RNA sequencing assay


title: HUVEC_LNA_HT_1

description: Single-cell RNA sequencing assay

source_name: Human Umbilical Vein Endothelial Cells exposed to high glucose (HG, to mimic hyperglycemia) and TNFα (to mimic inflammation) for 7 days combined with transfection with LNA targeting LINC00607 on the last 3 days


title: frontal_cortex_203049640050_R04C01

description: Human postmortem frontal cortex tissue

value: PDD


title: HVSMC Scr1

description: polyA RNA enriched

source_name: Human Vascular Smooth Muscle Cells transfected with scramble LNA and harvested after 48 hours


title: frontal_cortex_203049640050_R02C01

description: Human postmortem frontal cortex tissue

value: DLB

value: moderate


title: 1EN


title: 143B_shMETTL14

first: hongbo

last: li

state: Guangdong

address: No.58, Zhongshan Rd.2

institute: The First Affiliated Hospital of Sun Yat-sen University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: abundance measurements

source_name: osteosarcoma cell line

growth_protocol: All cells were cultured in DMEM medium supplemented with 10% fetal bovine serum, 2mM glutamine, and 1% penicillin/streptomycin

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq SR Cluster Kit v3-cBot-HS (#GD-401-3001, Illumina) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were infected with lentiviral shRNA targeting METTL14

tag: treatment


title: frontal_cortex_203049640046_R07C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203049640050_R01C01

description: Human postmortem frontal cortex tissue


title: HUVEC_LNA_HT_2

description: Single-cell RNA sequencing assay


title: frontal_cortex_203049640046_R05C01

description: Human postmortem frontal cortex tissue


title: HVSMC 607KD1

description: polyA RNA enriched


title: frontal_cortex_203049640046_R06C01

description: Human postmortem frontal cortex tissue


title: U2OS_shMETTL14


title: 143B_shMETTL14_IP

data_processing:
FastQC (V0.11.5) was used to quality the raw data obtained from Illumina sequencing
After the quality control, use Trimmomatic to filter the original data and compare it to the reference genome in the Ensembl database (Hisat2).
ExomePeak was used to detect M6A methylation site (Peaks), and the obtained Peaks were annotated according to the Ensembl database annotation information.
Integrate statistics on the annotated samples of the peaks. If there is peak on the transcript of the sample, mark it as 1, otherwise replace it with blank.
Genome_build: Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: peak files

growth_protocol: All cells were cultured in DMEM medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin

tag: merip antibody

value: anti-m6A antibody (202,003, Synaptic Systems)

tag: fraction

value: IP RNA


title: 143B_shMETTL14_Input

value: Input RNA


title: 143B_NC

value: shNC


title: HVSMC Scr2

description: polyA RNA enriched


title: frontal_cortex_203049640046_R03C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203049640046_R02C01

description: Human postmortem frontal cortex tissue

value: PD

value: Atypical


title: frontal_cortex_203049640046_R04C01

description: Human postmortem frontal cortex tissue

value: CONTR

value: sparse


title: frontal_cortex_203048410037_R07C01

description: Human postmortem frontal cortex tissue

value: M

value: yes


title: frontal_cortex_203049640046_R08C01

description: Human postmortem frontal cortex tissue

value: AD


title: frontal_cortex_203048410037_R06C01

description: Human postmortem frontal cortex tissue


title: U2OS_NC


title: U2OS_shMETTL14_IP


title: U2OS_NC_IP


title: 143B_NC_IP


title: frontal_cortex_203048410037_R05C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203048410037_R04C01

description: Human postmortem frontal cortex tissue

value: control

value: iLBD


title: U2OS_shMETTL14_Input


title: frontal_cortex_203048410037_R08C01

description: Human postmortem frontal cortex tissue

value: no

value: F

value: frequent


title: frontal_cortex_203048410037_R03C01

description: Human postmortem frontal cortex tissue

value: PDD


title: frontal_cortex_203048410037_R02C01

description: Human postmortem frontal cortex tissue


title: U2OS_NC_Input


title: frontal_cortex_203048410019_R07C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203048410037_R01C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203048410019_R06C01

description: Human postmortem frontal cortex tissue

value: moderate


title: frontal_cortex_203048410019_R08C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203049640117_R06C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203049640117_R05C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203048410019_R03C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203049640117_R01C01

description: Human postmortem frontal cortex tissue

value: DLB


title: frontal_cortex_203049640117_R02C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203048410019_R04C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203048410019_R05C01

description: Human postmortem frontal cortex tissue


title: 143B_NC_Input

value: Input RNA


title: frontal_cortex_203049640046_R01C01

description: Human postmortem frontal cortex tissue

value: other


title: frontal_cortex_203049640112_R06C01

description: Human postmortem frontal cortex tissue

value: PD


title: frontal_cortex_203049640117_R04C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203049640112_R08C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203049640117_R03C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203049640112_R07C01

description: Human postmortem frontal cortex tissue

value: FTD


title: frontal_cortex_203049640117_R07C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203049640112_R04C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203049640112_R02C01

description: Human postmortem frontal cortex tissue

value: CONTR


title: frontal_cortex_203049640112_R03C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203049640004_R06C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203049640004_R08C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203048410019_R02C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203049640004_R05C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203049640112_R01C01

description: Human postmortem frontal cortex tissue

value: sparse


title: frontal_cortex_203049640004_R02C01

description: Human postmortem frontal cortex tissue

value: VD


title: BSSE_QGF_143522_HN7CFDRXX_1_D12_Plate_B_2007Seq7_TGCTACTGCC_CAACCGGAGG_S188_L001_R1_001.fastq.gz

city: Basel

first: Tobias

last: Kull

address: Mattenstrasse 26

country: Switzerland

institute: ETH Zurich

description:
ID in processed data file:
D12_Plate2
see PickedGMPs_PassedQC_191029TK20.csv

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.

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: tissue

value: bone marrow

value: GMP (ganulocyte monocyte progenitor)

value: 12 - 19 weeks

value: GFP-p65 homozygous /H2BmCherry heterozygous


title: frontal_cortex_203048410063_R08C01

description: Human postmortem frontal cortex tissue

value: no

value: M

value: yes


title: BSSE_QGF_143521_HN7CFDRXX_1_C12_Plate_B_2007Seq7_AGCGCCACAC_CTAATGTCTT_S187_L001_R1_001.fastq.gz

description:
ID in processed data file:
C12_Plate2
see PickedGMPs_PassedQC_191029TK20.csv

tag: cell type


title: BSSE_QGF_143526_HN7CFDRXX_1_H12_Plate_B_2007Seq7_CCGGTAACAC_GAGTTGTACT_S192_L001_R1_001.fastq.gz

description:
ID in processed data file:
H12_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203049640112_R05C01

description: Human postmortem frontal cortex tissue

tag: slide

value: F

value: control

value: iLBD


title: frontal_cortex_203049640004_R03C01

description: Human postmortem frontal cortex tissue

tag: Sex

value: AD

value: frequent


title: BSSE_QGF_143518_HN7CFDRXX_1_H11_Plate_B_2007Seq7_ATCCAGGTAT_CAACGTCAGC_S184_L001_R1_001.fastq.gz

description:
ID in processed data file:
H11_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: BSSE_QGF_143517_HN7CFDRXX_1_G11_Plate_B_2007Seq7_TTCCTACAGC_GGCGAATTCT_S183_L001_R1_001.fastq.gz

description:
ID in processed data file:
G11_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: BSSE_QGF_143520_HN7CFDRXX_1_B12_Plate_B_2007Seq7_GTAACTTGGT_CGCCATACCT_S186_L001_R1_001.fastq.gz

description:
ID in processed data file:
B12_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203049640004_R01C01

description: Human postmortem frontal cortex tissue

tag: dementia

value: moderate


title: BSSE_QGF_143519_HN7CFDRXX_1_A12_Plate_B_2007Seq7_ACGGTCCAAC_TCTTACATCA_S185_L001_R1_001.fastq.gz

description:
ID in processed data file:
A12_Plate2
see PickedGMPs_PassedQC_191029TK20.csv

tag: strain


title: frontal_cortex_203048410063_R07C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203048410063_R03C01

description: Human postmortem frontal cortex tissue

value: PD


title: BSSE_QGF_143516_HN7CFDRXX_1_F11_Plate_B_2007Seq7_AATTCTTGGA_TTGTCAACTT_S182_L001_R1_001.fastq.gz

description:
ID in processed data file:
F11_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203271740112_R04C01

description: Human postmortem frontal cortex tissue

value: DLB


title: BSSE_QGF_143514_HN7CFDRXX_1_D11_Plate_B_2007Seq7_CGCTGTCTCA_ATTACTCACC_S180_L001_R1_001.fastq.gz

description:
ID in processed data file:
D11_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: BSSE_QGF_143525_HN7CFDRXX_1_G12_Plate_B_2007Seq7_TTGAATGTTG_CGCAATCTAG_S191_L001_R1_001.fastq.gz

description:
ID in processed data file:
G12_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: BSSE_QGF_143513_HN7CFDRXX_1_C11_Plate_B_2007Seq7_TATCCGAGGC_GGCCAATAAG_S179_L001_R1_001.fastq.gz

description:
ID in processed data file:
C11_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: BSSE_QGF_143515_HN7CFDRXX_1_E11_Plate_B_2007Seq7_AATGCGAACA_AATTGGCGGA_S181_L001_R1_001.fastq.gz

description:
ID in processed data file:
E11_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: BSSE_QGF_143511_HN7CFDRXX_1_A11_Plate_B_2007Seq7_CTCGAATATA_GAGATGTCGA_S177_L001_R1_001.fastq.gz

description:
ID in processed data file:
A11_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: BSSE_QGF_143523_HN7CFDRXX_1_E12_Plate_B_2007Seq7_CAACACCGCA_GGCAGTAGCA_S189_L001_R1_001.fastq.gz

description:
ID in processed data file:
E12_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: BSSE_QGF_143524_HN7CFDRXX_1_F12_Plate_B_2007Seq7_CACCTTAATC_TTAGGATAGA_S190_L001_R1_001.fastq.gz

description:
ID in processed data file:
F12_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203049640004_R04C01

description: Human postmortem frontal cortex tissue

value: CONTR


title: frontal_cortex_203048410063_R01C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203048410063_R02C01

description: Human postmortem frontal cortex tissue


title: BSSE_QGF_143512_HN7CFDRXX_1_B11_Plate_B_2007Seq7_GATCGTCGCG_CTGGATATGT_S178_L001_R1_001.fastq.gz

description:
ID in processed data file:
B11_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410063_R06C01

description: Human postmortem frontal cortex tissue


title: BSSE_QGF_143509_HN7CFDRXX_1_G10_Plate_B_2007Seq7_GGACCAGTGG_CGCGAGCCTA_S175_L001_R1_001.fastq.gz

description:
ID in processed data file:
G10_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410062_R06C01

description: Human postmortem frontal cortex tissue

value: sparse


title: frontal_cortex_203048410062_R05C01

description: Human postmortem frontal cortex tissue

value: PDD


title: BSSE_QGF_143508_HN7CFDRXX_1_F10_Plate_B_2007Seq7_ATTGTTCGTC_TCTCTAGATT_S174_L001_R1_001.fastq.gz

description:
ID in processed data file:
F10_Plate2
see PickedGMPs_PassedQC_191029TK20.csv

value: bone marrow

value: GMP (ganulocyte monocyte progenitor)


title: frontal_cortex_203048410062_R07C01

description: Human postmortem frontal cortex tissue


title: BSSE_QGF_143507_HN7CFDRXX_1_E10_Plate_B_2007Seq7_GTCCACCGCT_TCCTATTAGC_S173_L001_R1_001.fastq.gz

description:
ID in processed data file:
E10_Plate2
see PickedGMPs_PassedQC_191029TK20.csv

value: 12 - 19 weeks

value: GFP-p65 homozygous /H2BmCherry heterozygous


title: BSSE_QGF_143505_HN7CFDRXX_1_C10_Plate_B_2007Seq7_AGGCGTTCGC_TTCATCCAAC_S171_L001_R1_001.fastq.gz

description:
ID in processed data file:
C10_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410061_R08C01

description: Human postmortem frontal cortex tissue

value: no


title: BSSE_QGF_143504_HN7CFDRXX_1_B10_Plate_B_2007Seq7_GCACCACCAA_TGGTACTGAT_S170_L001_R1_001.fastq.gz

description:
ID in processed data file:
B10_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410062_R01C01

description: Human postmortem frontal cortex tissue

value: M

value: yes


title: frontal_cortex_203048410061_R05C01

description: Human postmortem frontal cortex tissue

value: F


title: BSSE_QGF_143501_HN7CFDRXX_1_G09_Plate_B_2007Seq7_AGCCTATGAT_CACCACCTAC_S167_L001_R1_001.fastq.gz

description:
ID in processed data file:
G9_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: BSSE_QGF_143500_HN7CFDRXX_1_F09_Plate_B_2007Seq7_CATATGCGAT_CCTTGAACGG_S166_L001_R1_001.fastq.gz

description:
ID in processed data file:
F9_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410061_R07C01

description: Human postmortem frontal cortex tissue

value: control

value: iLBD


title: BSSE_QGF_143503_HN7CFDRXX_1_A10_Plate_B_2007Seq7_ATGTTGTTGG_CAATCTATGA_S169_L001_R1_001.fastq.gz

description:
ID in processed data file:
A10_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: BSSE_QGF_143499_HN7CFDRXX_1_E09_Plate_B_2007Seq7_TTAACCTTCG_AGGCCAGACA_S165_L001_R1_001.fastq.gz

description:
ID in processed data file:
E9_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410062_R08C01

description: Human postmortem frontal cortex tissue


title: BSSE_QGF_143510_HN7CFDRXX_1_H10_Plate_B_2007Seq7_CCTTCTAACA_GATAAGCTCT_S176_L001_R1_001.fastq.gz

description:
ID in processed data file:
H10_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: BSSE_QGF_143498_HN7CFDRXX_1_D09_Plate_B_2007Seq7_CGTGTACCAG_AGGATAAGTT_S164_L001_R1_001.fastq.gz

description:
ID in processed data file:
D9_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: BSSE_QGF_143506_HN7CFDRXX_1_D10_Plate_B_2007Seq7_CCTCCGGTTG_CATAACACCA_S172_L001_R1_001.fastq.gz

description:
ID in processed data file:
D10_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: BSSE_QGF_143497_HN7CFDRXX_1_C09_Plate_B_2007Seq7_ACTTGTTATC_CGCGCCTAGA_S163_L001_R1_001.fastq.gz

description:
ID in processed data file:
C9_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410061_R03C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203048410062_R03C01

description: Human postmortem frontal cortex tissue

value: depression


title: frontal_cortex_203048410062_R02C01

description: Human postmortem frontal cortex tissue

value: moderate


title: frontal_cortex_203048410058_R08C01

description: Human postmortem frontal cortex tissue

value: AD

value: frequent

value: Atypical


title: BSSE_QGF_143496_HN7CFDRXX_1_B09_Plate_B_2007Seq7_TTAACGGTGT_TCCTGACCGT_S162_L001_R1_001.fastq.gz

description:
ID in processed data file:
B9_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410061_R01C01

description: Human postmortem frontal cortex tissue


title: BSSE_QGF_143502_HN7CFDRXX_1_H09_Plate_B_2007Seq7_TATGACAATC_TTGCTTGTAT_S168_L001_R1_001.fastq.gz

description:
ID in processed data file:
H9_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: BSSE_QGF_143495_HN7CFDRXX_1_A09_Plate_B_2007Seq7_AATTCCATCT_CTTCAGTTAC_S161_L001_R1_001.fastq.gz

description:
ID in processed data file:
A9_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410061_R02C01

description: Human postmortem frontal cortex tissue

value: VD


title: frontal_cortex_203048410062_R04C01

description: Human postmortem frontal cortex tissue

value: PDD


title: BSSE_QGF_143493_HN7CFDRXX_1_G08_Plate_B_2007Seq7_TCCGGACTAG_GACGAACAAT_S159_L001_R1_001.fastq.gz

description:
ID in processed data file:
G8_Plate2
see PickedGMPs_PassedQC_191029TK20.csv

value: bone marrow


title: BSSE_QGF_143492_HN7CFDRXX_1_F08_Plate_B_2007Seq7_CGATGCGGTT_CCTGCTTGGT_S158_L001_R1_001.fastq.gz

description:
ID in processed data file:
F8_Plate2
see PickedGMPs_PassedQC_191029TK20.csv

value: GMP (ganulocyte monocyte progenitor)


title: frontal_cortex_203048410063_R04C01

description: Human postmortem frontal cortex tissue


title: BSSE_QGF_143491_HN7CFDRXX_1_E08_Plate_B_2007Seq7_CTAGATTGCG_AGATATGGCG_S157_L001_R1_001.fastq.gz

description:
ID in processed data file:
E8_Plate2
see PickedGMPs_PassedQC_191029TK20.csv

value: 12 - 19 weeks


title: BSSE_QGF_143489_HN7CFDRXX_1_C08_Plate_B_2007Seq7_ATAGCGGAAT_GCGCAGAGTA_S155_L001_R1_001.fastq.gz

description:
ID in processed data file:
C8_Plate2
see PickedGMPs_PassedQC_191029TK20.csv

value: GFP-p65 homozygous /H2BmCherry heterozygous


title: BSSE_QGF_143490_HN7CFDRXX_1_D08_Plate_B_2007Seq7_GCAATATTCA_GGCGCCAATT_S156_L001_R1_001.fastq.gz

description:
ID in processed data file:
D8_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410058_R03C01

description: Human postmortem frontal cortex tissue

value: no

value: sparse


title: frontal_cortex_203048410058_R04C01

description: Human postmortem frontal cortex tissue

value: M

value: yes

value: DLB


title: frontal_cortex_203048410058_R01C01

description: Human postmortem frontal cortex tissue

value: F


title: frontal_cortex_203048410151_R02C01

description: Human postmortem frontal cortex tissue

value: MSA

value: PD


title: frontal_cortex_203048410061_R06C01

description: Human postmortem frontal cortex tissue


title: BSSE_QGF_143488_HN7CFDRXX_1_B08_Plate_B_2007Seq7_GTTCGGAGTT_CGCCTTCTGA_S154_L001_R1_001.fastq.gz

description:
ID in processed data file:
B8_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: BSSE_QGF_143487_HN7CFDRXX_1_A08_Plate_B_2007Seq7_CCACGCTGAA_TATTCCTCAG_S153_L001_R1_001.fastq.gz

description:
ID in processed data file:
A8_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: BSSE_QGF_143486_HN7CFDRXX_1_H07_Plate_B_2007Seq7_CACAGCGGTC_ATTCCTATTG_S152_L001_R1_001.fastq.gz

description:
ID in processed data file:
H7_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410057_R07C01

description: Human postmortem frontal cortex tissue

value: control

value: CONTR


title: BSSE_QGF_143494_HN7CFDRXX_1_H08_Plate_B_2007Seq7_GTGACGGAGC_TGGCGGTCCA_S160_L001_R1_001.fastq.gz

description:
ID in processed data file:
H8_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410061_R04C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203048410058_R07C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203048410057_R08C01

description: Human postmortem frontal cortex tissue


title: BSSE_QGF_143483_HN7CFDRXX_1_E07_Plate_B_2007Seq7_GATTCTGAAT_AGCGGTGGAC_S149_L001_R1_001.fastq.gz

description:
ID in processed data file:
E7_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: BSSE_QGF_143485_HN7CFDRXX_1_G07_Plate_B_2007Seq7_TTGTATCAGG_ACAGAGGCCA_S151_L001_R1_001.fastq.gz

description:
ID in processed data file:
G7_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410057_R03C01

description: Human postmortem frontal cortex tissue


title: BSSE_QGF_143482_HN7CFDRXX_1_D07_Plate_B_2007Seq7_CCGCGTATAG_TAGGAACCGG_S148_L001_R1_001.fastq.gz

description:
ID in processed data file:
D7_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: BSSE_QGF_143484_HN7CFDRXX_1_F07_Plate_B_2007Seq7_TAGAGAATAC_TATAGATTCG_S150_L001_R1_001.fastq.gz

description:
ID in processed data file:
F7_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410057_R02C01

description: Human postmortem frontal cortex tissue


title: frontal_cortex_203048410057_R06C01

description: Human postmortem frontal cortex tissue

value: AD

value: frequent


title: frontal_cortex_203048410057_R04C01

description: Human postmortem frontal cortex tissue

value: depression

value: iLBD

value: Atypical


title: frontal_cortex_203271740112_R03C01

description: Human postmortem frontal cortex tissue


title: BSSE_QGF_143480_HN7CFDRXX_1_B07_Plate_B_2007Seq7_CGCAGCAATT_ATTCCGCTAT_S146_L001_R1_001.fastq.gz

description:
ID in processed data file:
B7_Plate2
see PickedGMPs_PassedQC_191029TK20.csv

value: bone marrow

value: GMP (ganulocyte monocyte progenitor)

value: 12 - 19 weeks


title: BSSE_QGF_143481_HN7CFDRXX_1_C07_Plate_B_2007Seq7_ACGTTCCTTA_GACCGCTGTG_S147_L001_R1_001.fastq.gz

description:
ID in processed data file:
C7_Plate2
see PickedGMPs_PassedQC_191029TK20.csv

value: GFP-p65 homozygous /H2BmCherry heterozygous


title: frontal_cortex_203048410058_R05C01

description: Human postmortem frontal cortex tissue

value: no

value: M


title: frontal_cortex_203048410055_R08C01

description: Human postmortem frontal cortex tissue


title: BSSE_QGF_143479_HN7CFDRXX_1_A07_Plate_B_2007Seq7_TATGATGGCC_GATTGTCATA_S145_L001_R1_001.fastq.gz

description:
ID in processed data file:
A7_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: BSSE_QGF_143478_HN7CFDRXX_1_H06_Plate_B_2007Seq7_AATCCAATTG_CATGTAGAGG_S144_L001_R1_001.fastq.gz

description:
ID in processed data file:
H6_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410055_R06C01

description: Human postmortem frontal cortex tissue

value: PDD

value: yes


title: BSSE_QGF_143477_HN7CFDRXX_1_G06_Plate_B_2007Seq7_GTTGGATGAA_TTCCAGGTAA_S143_L001_R1_001.fastq.gz

description:
ID in processed data file:
G6_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: BSSE_QGF_143476_HN7CFDRXX_1_F06_Plate_B_2007Seq7_ACAACTACTG_AGTTATCACA_S142_L001_R1_001.fastq.gz

description:
ID in processed data file:
F6_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410055_R05C01

description: Human postmortem frontal cortex tissue

value: F

value: sparse


title: frontal_cortex_203048410055_R04C01

description: Human postmortem frontal cortex tissue

value: control


title: frontal_cortex_203048410055_R02C01

description: Human postmortem frontal cortex tissue

value: DLB


title: BSSE_QGF_143473_HN7CFDRXX_1_C06_Plate_B_2007Seq7_GAATACCTAT_ACAATAGAGT_S139_L001_R1_001.fastq.gz

description:
ID in processed data file:
C6_Plate2
see PickedGMPs_PassedQC_191029TK20.csv


title: frontal_cortex_203048410151_R08C01

description: Human postmortem frontal cortex tissue


title: BSSE_QGF_143472_HN7CFDRXX_1_B06_Plate_B_2007Seq7_GGCCAATATT_CGGTCCGATA_S138_L001_R1_001.fastq.gz

description:
ID in processed data file:
B6_Plate2
see PickedGMPs_PassedQC_191029TK20.csv