title: FT-CGC-Rep1

source_name: Rat-brain-CGC

value: CGC

value: Treatment with Fluoxetine

value: H3K27ac active motif cat#39133 Lot no.16612005


title: FT-ILC-Rep1

status: Public on Sep 04 2022

type: SRA

city: Singapore

first: Nirmala

last: Arul Rayan

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

library_source: genomic

data_processing:
BWA aligner was used to align raw fastq file to rat genome (rn5)
Dfilter (Kumar et al., Nature Biotechnology, 2013) was used to call peaks using region-specific ChIP-seq files and whole brain control input.
Union of peaks from different brain regions was made and the read-count on those peaks were taken in different brain region
Genome_build: rn5
Supplementary_files_format_and_content: The processed file contain peaks call from Dfilter

molecule: genomic DNA

organism: Rattus norvegicus

source_name: Rat-brain-ILC

growth_protocol: Brains were removed and frozen immediately on dry ice. Frozen brains were cryosectioned at 250um thickness onto poly-lysine coated slides. The anatomical regions subject to punching were verified using Nissl-staining of slide sections and the rat brain atlas of Paxinos and Watson

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K27ac antibody.
Libraries were prepared according to Quail et al. 2008-https://doi.org/10.1038/nmeth.1270. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR-amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: 2-months old Charles River rats were treated with 18 mg/kg body weight of fluoxetine (FT group) or water (Sham group), ad libitum for 6 weeks

tag: age

value: 2 months

tag: tissue

value: brain

tag: brain region

value: ILC

tag: treatment

tag: chip-antibody


title: FT-MS-Rep1

source_name: Rat-brain-MS

value: MS


title: AD patient,  PBMCs treated with HFn-Cur 2

city: Pavia

first: Maria

last: Garofalo

address: Via Mondino 2

country: Italy

institute: IRCCS Mondino Foundation

library_source: transcriptomic

data_processing:
FastQ files were generated via llumina bcl2fastq2 Version 2.17.1.14
Gene and transcript intensities were computed using STAR/RSEM software using Gencode Release m24 (GRCm38) as a reference, using the “-strandness forward” option. Differental expression analysis for mRNA and lncRNA was performed using R package DESeq2
Assembly: HG19
Supplementary files format and content: counts, FPKMs, TPMs

molecule: total RNA

organism: Homo sapiens

source_name: M79, HFn, CUR

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were prepared by centrifugation. Peripheral blood was layered (density=1.077) and centrifuged at 950g for 30 min. After isolation on a Ficoll-Histopaque layer (Sigma, Italy), cell viability was assayed by a trypan blue exclusion test and the cells were used for RNA extraction.

extract_protocol:
Samples were homogenized and total RNA was isolated by Trizol® reagent(Life Science Technologies, Italy) following the manufacturer’s specifications. RNAs were quntified using a Nanodrop ND-100 Spectrophotometer (Nanodrop Technologies, Wilmington, USA) and a 2100 Bioanalyzer (Agilent RNA 6000 Nano Kit, Waldbronn, Germany); RNAs with a 260:280 ratio of ≥1.5 and an RNA ntegrity number of ≥8 were subjected to deep sequencing.
Sequencing libraries were prepared by the Illumina TruSeq Stranded Total RNA kit (Illumina) using 500-ng total RNA (Illumina) and by the Lexogen SENSE Total RNA-Seq Library Prep Kit using 500-ng total RNA (Lexogen). Qualities of sequencing libraries were assessed with 4200 TapeStation with the DNA1000 reagnt kit. RNA processing has been carried out using Illumina NextSeq 500 Sequencing.

treatment_protocol: PBMCs were independently treated for 48 h with Hfn-BDC (10 μM). The experiment is composed by 4 different condition: AD not treated (AD NT), Controls not treated (CTR NT), AD treated with HfnBDC (AD HfnBDC) and controls treated with HfnBDC (CTR HfnBDC). After treatment, cell viability was assayed by a trypan blue exclusion test.

tag: individual

tag: disease state

value: AD

value: Blood

tag: cell type

value: PBMC

value: HFn-Cur


title: RRB1463

description:
10x Genomics Gene Expression*3'v2
dorDG2021_countmatrix.csv.gz

data_processing:
RNA-seq data were aligned to the Rattus norvegicus rn5 genome (Rn5 ENSEMBL) and processed using Cell Ranger (10x Genomics) pipeline
Seurat v3 pipeline
Genome_build: Rn5
Supplementary_files_format_and_content: fastq and count matrix

growth_protocol: Tissue single-cell RNA-seq. Brains were removed and transported on ice in ice cold PBS. The brain was placed on brain slicer moulds and sectioned closer to the hippocampal planes. Dorsal dentate gyrus and ventral dentate gyrus regions were micropunched across 5-6 planes. The anatomical regions subject to punching were verified using the rat brain atlas of Paxinos and Watson.

extract_protocol:
10x Genomics Chromium snRNA-seq was performed on nuclei extracted from dorsal dentate gyrus (dorDG) and ventral dentate gyrus (venDG) regions of control and fluoxetine-treated rats (6 weeks of fluoxetine treatment). All rats were male. Cell-types were identified by unsupervised clustering and differential gene expression was performed between cases and controls for each cell-type cluster. The library preparation was performed with the Chromium Single Cell 3’ Reagent Kits v2. Paired-end sequencing with single-indexing was performed on the HiSeq Illumina 4000. FastQ files were produced with Cellranger v2.1.0 mkfastq. Alignments and gene counts were generated with Cellranger v2.1.0 count.
10x Chromium Single Cell 3’ Reagent Kit v2

treatment_protocol: 2 month old Charles River rats were treated with 18mg/kg body weight of fluoxetine (FT group) or water (Sham group), ad libitum for 6 weeks

tag: sample name

tag: single cell library id

tag: brain region_replicate

tag: treatmeant

value: FT


title: Bulk RNA-seq E3_Young_Bulk RNA-seq rep3

city: Lexington

first: Lance

middle: A

last: Johnson

state: KY

address: 760 Press Ave, HKRB 135

department: Physiology/Sanders-Brown Center on Aging

country: USA

institute: University of Kentucky

data_processing:
Raw FASTQ data and H&E images were processed by the Space Ranger v1.3.0 (10X Genomics) pipeline. Illumina base call (BCL) files from the sequencing instrument were converted to FASTQ format for each sample using the mkfastq. Visium spatial expression libraries were analyzed with the count command. Image alignment to predefined spots was performed by the fiducial alignment grid of the tissue image to determine the orientation and position of the input image. Sequencing reads were aligned to the mm10 reference genome using STAR (v2.5.1b) aligner. Gene expression profiling in each spot was performed with UMI and 10X barcode information.
Assembly: mm10
Supplementary files format and content: Count txt files

organism: Mus musculus

source_name: Brain

extract_protocol:
The mirroring hemisphere (right) from brains processed for scRNAseq were immediately placed in OCT compound (Fisher HealthCare Tissue Plus O.C.T. Compound Clear 4585) and gently lowered into isopentane (Sigma Aldrich 2-Methylbutane M32631) in a beaker surrounded by dry ice (isopentane chilled to approximately -70°C). Brains were submerged for 60 seconds, placed on dry ice, wrapped in aluminum foil, and stored at -80°C until sectioning. Prepared brain hemispheres were cryosectioned to 10 μm thick coronal sections at approximately Bregma -2.00 mm. Serial 10 μm sections immediately rostral and caudal to the section mounted on the Visium Spatial Gene Expression slide (10X Genomics) were collected for immunohistochemistry. Optimal tissue permeabilization time was determined using the manufacturer’s optimization protocols (10X Genomics, Visium Spatial Tissue Optimization), and accordingly, experimental tissues were permeabilized for 18 min for Visium Spatial Gene Expression analysis. Prior to library preparation, tissue sections were methanol-fixed, stained with hematoxylin and eosin (H&E), and imaged on a Nikon NiU microscope with Fi3 color camera. Sections were then permeabilized and processed to obtain cDNA libraries, which were subsequently prepared according to the manufacturer’s protocol (https://support.10xgenomics.com/spatial-gene-expression/libraryprep).
Sample libraries were constructed using Next GEM automated 3’ reagents (10X Genomics, v3.1) following manufacturer’s suggested protocol (#CG000286 Rev B). Final library quantification and quality check was performed using BioAnalyzer (Agilent), and sequencing performed on a NovaSeq 6000 S4 flow cell, 150 bp Paired-End sequencing (Novogene).

value: Brain

value: Brain cells

tag: genotype


title: RRB1457

description:
10x Genomics Gene Expression*3'v2
venDG2021_countmatrix.csv.gz

value: Sham


title: Sham-Snt-Rep1

source_name: Rat-brain-Snt

value: Snt

value: untreated


title: AD patient,  PBMCs treated with HFn-Cur 1

source_name: F75, HFn, CUR


title: Control,  PBMCs treated with HFn-BDC 2

source_name: M70, HFn, BDC

value: Control

value: HFn-BDC


title: E3_middle

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The barcoded processing, gene counting, and aggregation were made using the Cell Ranger software v7.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38 and mm10 combined
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Pooled brain tissue (n=3 per experimental group) was processed for ‘glia-enriched’ single cell suspensions as previously described. Briefly, mice were anesthetized via 5.0% isoflurane before exsanguination and transcardial perfusion with ice-cold Dulbecco’s phosphate buffered saline (DPBS; Gibco #14040133). Following perfusion, brains were quickly removed, pooled, and whole left hemispheres sans brainstem and cerebellum were quickly minced using forceps on top of an ice-chilled petri dish. Minced tissue from the 3 pooled hemispheres per group were immediately transferred into gentleMACS C-tube (Miltenyi #130–093-237) containing Adult Brain Dissociation Kit (ADBK) enzymatic digest reagents (Miltenyi #130–107-677) prepared according to manufacturer’s protocol. Tissues were dissociated using the “37C_ABDK” protocol on the gentleMACS Octo Dissociator instrument (Miltenyi #130–095-937) with heaters attached. After tissue digestion, cell suspensions were filtered through 70 μm mesh cell filters to remove debris following the manufacturer’s suggested ABDK protocol. The resultant suspension was sequentially filtered (x2) using fresh 30 μm mesh filters. Cell viability was checked using AO/PI viability kit (Logos Biosystems # LGBD10012). All cell suspensions were determined to have > 90% viable cells. Following viability and counting, cells were diluted to achieve a concentration of ~ 1700 cells/μL in a 10μL total reaction volume. The diluted cell suspensions were loaded onto the 10X Chromium Connect automated cell portioning system.
Sample libraries were constructed using Next GEM automated 3’ reagents (10X Genomics, v3.1) following manufacturer’s suggested protocol (#CG000286 Rev B). Final library quantification and quality check was performed using BioAnalyzer (Agilent), and sequencing performed on a NovaSeq 6000 S4 flow cell, 150 bp Paired-End sequencing (Novogene).

tag: cell line

value: non-neuronal brain cells

value: Middle


title: E4_aged

description: 10x Genomics

value: Aged


title: RRB1456


title: E4_young

description: 10x Genomics

value: Young


title: E3_aged

description: 10x Genomics


title: E4_middle

description: 10x Genomics


title: Sham-Raphe-Rep1

source_name: Rat-brain-Raphe

value: 2 months

value: brain

value: Raphe

value: H3K27ac active motif cat#39133 Lot no.16612005


title: RRB1455


title: E3_young

description: 10x Genomics


title: AD patient,  PBMCs treated with HFn-BDC 4

source_name: F76, HFn, BDC

value: AD

value: Blood

value: PBMC


title: RRB1458


title: Sham-VTA-Rep1

source_name: Rat-brain-VTA

value: VTA


title: AD patient,  PBMCs treated with HFn-BDC 3

source_name: F59, HFn, BDC


title: RRB1454

value: Sham


title: Sham-PAG-Rep1

source_name: Rat-brain-PAG

value: PAG


title: Sham-LC-Rep1

source_name: Rat-brain-LC

value: LC

value: untreated


title: Sham-arc-Rep1

source_name: Rat-brain-arc

value: arc


title: AD patient,  PBMCs treated with HFn-BDC 1

source_name: F75, HFn, BDC

value: HFn-BDC


title: RRB1453


title: Sham-venCA1-Rep1


title: Control,  PBMCs treated with HFn-BDC 1

source_name: F53, HFn, BDC

value: Control


title: AD patient,  PBMCs treated with HFn-BDC 2

source_name: M79, HFn, BDC


title: Control,  PBMCs untreated 4

source_name: M69, NT


title: Sham-venDG-Rep1

source_name: Rat-brain-venDG

value: venDG


title: RRB1452


title: CT26_CTLA4_3v3mm

city: Cincinnati

first: vishnu

last: modur

state: OH

address: 3333 Burnet Avenue, R7509

institute: Cincinnati Children's Hospital

description: scRNAseq

data_processing:
NovaSeq 6000 Sequencer was used with the sequencing read parameters designated in the user guide.
Chromium Single Cell 3ʹ Reagent Kits v3” by 10x Genomics. Protocol by 10x Genomics
Cell Ranger 1.3 (https://support.10xgenomics.com/) was used to perform sample demultiplexing, barcode processing, and UMI counting. Because four different samples were used to generate single-cell data, BEER (PMID: 31636959 and BBKNN (PMID: 31400197) were used to remove batch effect.
UMAP was used to visualize all cells in a two-dimensional plot. Quality control revealed a clean distribution and low mitochondrial DNA (UMI %), indicative of very low percentage of cell lysis and dropout enabling meaningful comparison across the samples
Assembly: Louvain modularity optimization in Seurat; clusters (unsupervised) at several resolution values, ranging from 0 to 1
Supplementary files format and content: format:h5

source_name: CT26 control cells challenged with Anti-CTLA4

extract_protocol:
CT26 WT cells and CT26 Flavopiridol-treated cells at 25nM for 7 days, injected subcutaneously to mice were sorted for CD45+ TILs by FACS using mouse anti-CD45 antibody (BD Pharmingen, 561018).
A 3ʹ Gene Expression Library was prepared for scRNA-seq by the DNA Genotyping and Sequencing Core of the Cincinnati Children’s Hospital Medical Center, using “Chromium Single Cell 3ʹ Reagent Kits v3” by 10x Genomics.


title: CT26_Flavo_CTLA4_3v3mm

description: scRNAseq

source_name: CT26 flavopiridol treated cells challenged with Anti-CTLA4

value: Test


title: RRB1451

value: FT


title: Mouse Fanca+/+ Engraftment 11 Replicate 4 Keratinocytes

city: New York

first: Andrew

last: Webster

state: NY

address: 1230 York Ave

institute: The Rockefeller University

data_processing:
Transcript expressions were calculated using Salmon (v0.8.2) against mm10.
Gene expression levels as TPMs retrieved using Tximport (v1.8.0).
Genome_build: mm10
Supplementary_files_format_and_content: Excel matrix table displaying gene-level transcript TPM counts for each sample.

molecule: polyA RNA

source_name: Intradermal SCC

growth_protocol: Fanca+/- 129S mice (gift of Markus Grompe) and Trp53+/- B6/129S mice (B6.129S2-Trp53tm1Tyj/J – Jackson Labs) were crossbred to produce Fanca+/+ x Tp53-/- and Fanca-/- x Tp53-/- offspring. At post-natal day 4, a neonate from both genotypes was humanely euthanized and keratinocytes harvested from back-skin tissue via dispase-seperation. Primary keratinocytes were plated on 3T3-J2 feeder cells until colony formation. On day 5 post-plating, keratinocytes of both genotypes were transduced with pZIP-mCMV-Ccnd1-IRES-mCherry vector was applied to immortalize them. Cells were subsequently FACS-sorted for integrin a6hi x integrin b1hi x mCherry+ markers, producing basal (a6hi x b1hi) Ccnd1OE immortalized keratinocyte lines. HRASG12V-puro retrovirus (Addgene plasmid #1768) was then transduced into the keratinocyte lines and infected cells were puromycin selected, to allow for tumor generation upon engraftment.

extract_protocol:
At the first, second, sixth, and eleventh engraftment cycles, Fanca+/+;Tp53-/-;Ccnd1OE;HRASG12V and Fanca-/-;Tp53-/-;Ccnd1OE;HRASG12V tumor cells from each replicate were harvested. Cells were FACS-sorted for mCherry+ cells directly into RNA-stabilizing cell lysis buffer (Qiagen Buffer RLT). Homogenization was performed on QiaShredder columns, followed by RNA isolation using the Qiagen RNAeasy Plus kit. RNA was simultaneously extracted from pre-engraftment keratinocytes.
Total RNA was processed by Novogene for polyA-capture, cDNA synthesis, and 2x150bp paired-end Illumina sequencing to >30 million reads/sample.

treatment_protocol: Fanca+/+;Trp53-/-;Ccnd1OE;HRASG12V and Fanca-/-;Trp53-/-;Ccnd1OE;HRASG12V mouse keratinocytes were serially intradermally allografted into backs of 7 weeks old female Nude/J mice (Jackson Labs) over 11 engraftment cycles (approx. 17 weeks). Four replicates were created for both Fanca+/+ and Fanca-/- genotypes, with each replicate carried forward independently through the engraftment cycles. Each replicate consisted of 4 intradermal engraftment sites on the same mouse, which were combined after harvesting at the end of each cycle. The starting sample size was set at the outset with n=4 independent biological replicates for the intended purpose of comparative SV analysis and RNAseq, but tumor growth analysis was also simultaneously performed as a secondary analysis.  At the first engraftment cycle, each engraftment site received 150,000 cells suspended in a 1:1 ratio of DPBS & Matrigel (Corning). Resulting tumors were grown for a maximum of two weeks. As per IACUC protocol, euthaniasa was performed when tumor size exceeded 2 cm. Host mice were humanely euthanized, and tumors were dissected, minced, dissociated, and strained to a single-cell mixture using collagenase and Trypsin. Resulting tumor cells were plated at 5% CO2 / 3% O2 at 37C, and allowed to recover for 48 hours in low-calcium keratinocyte media (E-Low Media). This ensured consistent cell viability between replicates and permitted in vitro analysis of post-transplant cells. The number of engrafted cells was lowered to 100K for both genotypes for engraftments two to five, further lowered to 70K cells for cycles six to nine and reduced to 35K for the 10-11th cycles. One Fanca-/- replicate was lost at the fifth cycle due to host death, which resulted in removal of this replicate from the sixth engraftment cycle onwards.

tag: strain

value: BL6/129S Hybrid

value: Fanca+/+ x Trp53-/- x Ccnd1(OE) x HRAS(G12V)

value: Keratinocytes


title: Control,  PBMCs untreated 3

source_name: F67, NT


title: Sham-HB-Rep1

source_name: Rat-brain-HB

value: 2 months

value: brain

value: HB

value: H3K27ac active motif cat#39133 Lot no.16612005


title: Control,  PBMCs untreated 1

source_name: F53, NT

value: Blood

value: PBMC


title: RRB1450


title: CT26_IgG_3v3mm

description: scRNAseq

source_name: CT26 control cells challenged with Anti-IgG


title: Sham-dorCA1-Rep1


title: Mouse Fanca+/+ Engraftment 11 Replicate 3 Keratinocytes


title: Sham-DorDG-Rep1

source_name: Rat-brain-DorDG

value: DorDG


title: CT26_Flavo_IgG_3v3mm

description: scRNAseq

source_name: CT26 flavopiridol treated cells challenged with Anti-IgG


title: RRB1449


title: RRB1448


title: Mouse Fanca+/+ Engraftment 11 Replicate 1 Keratinocytes


title: AD patient,  PBMCs untreated 4

source_name: F76, NT

value: AD

value: untreated


title: Mouse Fanca-/- Engraftment 11 Replicate 3 Keratinocytes

value: Fanca-/- x Trp53-/- x Ccnd1(OE) x HRAS(G12V)


title: RRB1447


title: Mouse Fanca+/+ Engraftment 11 Replicate 2 Keratinocytes


title: AD patient,  PBMCs untreated 2

source_name: M79, NT


title: RRB1446


title: Sham-BLA-Rep1

source_name: Rat-brain-BLA

value: BLA


title: Mouse Fanca-/- Engraftment 11 Replicate 2 Keratinocytes


title: RRB1445


title: AD patient,  PBMCs untreated 1

source_name: F75, NT


title: Sham-VMH-Rep1

source_name: Rat-brain-VMH

value: VMH


title: Sham-CMA-Rep1

source_name: Rat-brain-CMA

value: CMA


title: Sham-LH-Rep1

source_name: Rat-brain-LH

value: LH


title: Mouse Fanca-/- Engraftment 11 Replicate 1 Keratinocytes

value: BL6/129S Hybrid


title: Mouse Fanca+/+ Engraftment 6 Replicate 4 Keratinocytes

value: Fanca+/+ x Trp53-/- x Ccnd1(OE) x HRAS(G12V)


title: RRB1444

value: FT


title: RRB1443

value: Sham


title: Sham-PVN-Rep1

source_name: Rat-brain-PVN

value: 2 months

value: brain

value: PVN


title: Stage 40 Pronephros

first: Mark

middle: E.

last: Corkins

address: 1468 Madison Ave, Annenburg 25-86

department: CDRB

institute: Mount Sinai

description: Run at MDAnderson ATGC Genomics Core

data_processing:
10x Genomics CellRanger v6.1.1
genome build: Pre-release Xenopus laevis 9.2 genome available at the Xenbase FTP server < https://ftp.xenbase.org/pub/Genomics/JGI/Xenla9.2/pre-release/>
Supplementary files format and content: filtered Matrix and h5 files

organism: Xenopus laevis

source_name: Pronephros (Embryonic Kidney)

growth_protocol: 1/3x MMR at 23C

extract_protocol:
Manual dissection fallowed by Papain and TryplE disassociation.  Viable cells isolated by optiprep.
10x Genomics Platform

value: Pronephros (Embryonic Kidney)

tag: developmental stage

value: NF 40

value: Primary

value: Wildtype


title: AD patient,  PBMCs untreated 3

source_name: F59, NT

value: AD

value: Blood

value: PBMC

value: untreated


title: Sham-MPOA-Rep1

source_name: Rat-brain-MPOA

value: MPOA

value: H3K27ac active motif cat#39133 Lot no.16612005


title: Nanopore_ONTcDNA Undiff replicate 2

city: Rehovot

first: Bareket

last: Dassa

address: 234 Herzl st.

department: Life Sciences Core Facilities

country: Israel

institute: Weizmann Institute of Science

data_processing:
Bioinformatics data analysis of ONT direct RNA sequences: Raw reads were acquired using the MinION software from Oxford Nanopore Technologies (ONT), and were based called using either ONT albacore (MinKNOW) or Guppy software. Fast5 reads from direct RNA sequencing were processed using Poreplex, trimmed to remove any 3′ adapter sequences, and to filter chimera (remove unsplit reads fused of two or more RNAs in output), with the paremeters --trim-adapter --basecall --filter-chimera.
Bioinformatics data analysis of ONT cDNA sequences: Raw read from cDNA sequencing which were saved in the “skip” folder were based called using Guppy (--flowcell FLO-MIN106  --kit  SQK-PCS108) and processed using porechop (v0.2.3) to remove adaptors. Reads which passed the adapter trimming were merged from the skip and pass folders.
Alignment of reads to the Mus musculus genome (mm10, UCSC) was done using minimap2 adjusted for long-reads spliced alignment (-x splice, --secondary=no).
Counting reads on genes was done using htseq-count using mm10 Gencode annotation (downloaded from iGenomes UCSC), and considering the strandedness of the samples (direct RNA samples were run as strand-specific).
Genome_build: mm10
Supplementary_files_format_and_content: htseq gene counts

source_name: embryonic stem cells

growth_protocol: Embryoid bodies (Ebs) where generated by 4 days incubation of single cell suspension (35000 cells/ml) of R1 mouse embryonic stem (mES) cells in 5 ml mES growth medium (DMEM, 15% FBS, L-Glutamine, Non-Essential Amino Acids) and named sample undiff,  then for 4 days, 2-beta-Mercaptoethanol, without Lif in 6 cm low cell binding dishes.

extract_protocol:
RNA was extracted with an RNeasy Mini kit (Qiagen).
For cDNA-PCR library preparation, a total of 50 ng of poly(A) RNA was used as an input. Libraries were prepared according to manufacturer’s protocols using the cDNA-PCR Sequencing kit (SQK-PCS108, ONT, Oxford, United Kingdom). For the Direct RNA library preparation kit (SQK-RNA002, ONT, Oxford, United Kingdom), an input of 500ng of poly(A) RNA was used. Libraries were prepared according to manufacturer’s protocol.

treatment_protocol: Four-day-old Ebs where treated for 4 days with 2mM Retinoic Acid (RA) (Retinoic Acid, Sigma R2625). The day of RA addition corresponds to the sample name day 0. Day 4 corresponds to the sample that had been treated for 4 days with RA.

value: Embryoid bodies


title: Nanopore_ONTcDNA Day4 replicate 1


title: RRB1442


title: Mouse Fanca+/+ Engraftment 6 Replicate 2 Keratinocytes

source_name: Intradermal SCC

value: BL6/129S Hybrid

value: Fanca+/+ x Trp53-/- x Ccnd1(OE) x HRAS(G12V)

value: Keratinocytes


title: RRB1441

value: Sham


title: Mouse Fanca-/- Engraftment 6 Replicate 3 Keratinocytes

value: Fanca-/- x Trp53-/- x Ccnd1(OE) x HRAS(G12V)


title: Mouse Fanca+/+ Engraftment 6 Replicate 1 Keratinocytes


title: Sham-BNST-Rep1

source_name: Rat-brain-BNST

value: 2 months

value: brain

value: BNST


title: Nanopore_ONTcDNA Undiff replicate 1


title: RRB1440


title: Nanopore_ONTDirect Day4 replicate 2


title: RRB1438


title: Sham-MS-Rep1

source_name: Rat-brain-MS

value: MS


title: RRB1439


title: Sham-NaCcore-Rep1

source_name: Rat-brain-NaCcore

value: NaCcore


title: Sham-LS-Rep1

source_name: Rat-brain-LS

value: LS


title: Nanopore_ONTcDNA Day4 replicate 2


title: Sham-MDT-Rep1

source_name: Rat-brain-MDT

value: MDT


title: Nanopore_ONTDirect Day4 replicate 1


title: Mouse Fanca-/- Engraftment 6 Replicate 2 Keratinocytes


title: Mouse Fanca+/+ Engraftment 6 Replicate 3 Keratinocytes


title: Mouse Fanca-/- Engraftment 6 Replicate 1 Keratinocytes


title: Nanopore_ONTDirect Undiff replicate 2


title: Nanopore_ONTDirect Undiff replicate 1


title: RRB1436


title: Sham-InsularCortex-Rep1

source_name: Rat-brain-InsularCortex

value: InsularCortex


title: Mouse Fanca+/+ Engraftment 2 Replicate 2 Keratinocytes


title: Mouse Fanca+/+ Engraftment 2 Replicate 3 Keratinocytes


title: RRB1435

value: FT


title: Sham-CGC-Rep1

source_name: Rat-brain-CGC

value: CGC

value: untreated


title: KO_Angel-/-_rep2

city: Perth

first: Stefan

middle: J

last: Siira

state: Western Australia

address: 15 Hospital Ave, Nedlands

department: Precision Health

country: Australia

institute: The Kids Research Institute Australia

description: RNAse T1-digested RNA from monosome fraction of 10%-30% sucrose gradient of mitochondrial lysate

data_processing:
Library strategy: Ribosome profiling
Initially, sequenced read pairs were merged with BBMerge (useoverlap=t pfilter=1 mininsert=18 mininsert0=18 trimnonoverlapping=t) (Bshnell et al., 2017, PloS One) to remove non-overlapping sequences and trimmed of remaining linker sequence (AACTGTAGGCACCATCAAT) with BBDuk (ktrim=r mink=4 k=18 hdist=1 tpe tbo) from the BBTools suite v38.79.
Subtractive alignment was performed against Drosophila ncRNA sequences downloaded from Ensembl, including nuclear rRNA and tRNAs, with Bowtie2 (--fr) (Langmead et al., 2021, Nat Methods).
Unmapped reads were mapped to the Drosophila Ensembl v99 transcriptome sequences with Bowtie2 (--very-sensitive --norc), with mitochondrial sequences modified to more accurately reflect the mature RNA transcripts present within the mitochondrion. In short, the singular annotations for bicistronic transcripts were merged (mt:ATP8/mt:ATP6 and mt:ND4/mt:ND4L); 5' and 3' UTRs were added to select transcripts based on the observed positions of 5' ends and polyA tails in RNASeq data (mt:ND1, mt:ND3, mt:ND5, mt:CO3, mt:CYTB); 30 nt polyA tails were added to the 3' end of each mRNA and the large mitochondrial rRNA; a 5' G was added to mt:tRNA:His-GTG and 3' CCA added to all tRNAs to reflect the non-templated additions added post-transcriptionally. This modified mitochondrial annotation is similar to the one used for RNA-Seq, with the addition of post-transcriptional additions present in the mature transcripts.
Mitochondrial mRNA coverage bedgraph files were generated with BEDTools (Quinlan et al., 2010, Bioinformatics) and normalised to total reads mapped to mitochondrial transcripts.
Genome_build: BDGP6.28
Supplementary_files_format_and_content: txt files containing mapped counts per transcript, per sample
Supplementary_files_format_and_content: bedgraph files containing normalised coverage across mitochondrial transcripts, per sample

organism: Drosophila melanogaster

source_name: Third-instar larvae

growth_protocol: The generation of the DmAngel knock-out lines (DmAngelKO#1 and DmAngelKO#2) was performed as previously described (Port et al., 2014, Proc Nat Acad Sci). The sequence of the DmAngel gene, obtained from sequencing genomic DNA from the fly line nos-Cas9 (Bloomington Stock #54591), was entered into CRISPR Optimal Target Finder (http://targetfinder.flycrispr.neuro.brown.edu) and the target sites with the lowest off-target score were selected (GCAGATTTCTTTCCTCCACTCGG and GGTTGTCTCATATAACATCCTGG). The gRNAs were cloned into BbsI digested pCFD4 (Addgene plasmid #49411) by Gibson assembly, as detailed in (Port et al., 2014, Proc Nat Acad Sci). Primers used to generate the constructs are detailed in table S2. The pCFD4 plasmid containing the gRNAs was used to generate a gRNA expressing fly line, using BestGene Inc (California, USA).  To induce germline specific expression of the gRNAs, males carrying the gRNAs were crossed to virgin nos-Cas9 females. Individual offspring flies were crossed to CyO/Gla, Bc balancer flies and the progeny was individually screened for deletions in the DmAngel gene using PCR as detailed. The wings of candidate flies were incubated at 37°C for 45 minutes in freshly prepared adult fly homogenisation buffer (10 mM Tris-HCl, pH 8.2, 25 mM NaCl, 1 mM EDTA, 0,2 μg/μl proteinase K) and the homogenate was used for the subsequent PCR screening and sequencing (Gratz et al., in press, Curr Prot Mol Biol). The DmAngelKO lines that were generated were backcrossed for 6 generations to a w;; background to remove possible off-target effects.

extract_protocol:
The monosome fractions were pooled and RNA was extracted using Direct-zol RNA micro prep kit (Zymo Research) following manufacturer’s instructions and incorporating an on-column RNase-free DNase digestion to remove DNA.
RNA was dephosphorylated and phosphorylated with T4 PNK. RNA sequencing libraries for ribosome profiling were prepared using the Illumina Small RNA Sample Prep Kit, with a size selection step for 15-90 nt RNAs.

treatment_protocol: Isolation of mitochondria from larvae was performed as previously described (Bratic et al., 2011, PloS Genet). Third-instar larvae were washed and homogenized in 250 mM sucrose, 2 mM EGTA and 5 mM Tris pH 7.4 with 1% BSA, nuclei and cell debris were pelleted by centrifugation at 1000 g for 5 minutes at 4°. The supernatant was centrifuged at 7000 g for 10 minutes at 4° to obtain the crude mitochondrial fraction. For ribosome profiling experiments, mitochondrial lysates were treated with 200U of RNAse T1 for 30 minutes at room temperature, centrifuged and loaded onto a 10-30% sucrose gradient in 10 mM MgCl2, 100 mM NH4Cl, 30 mM Tris pH 7.4 with protease inhibitor cocktail and RNase inhibitors. Gradients were centrifuged in a SWTi55 rotor at 39000 g for 3 h at 4°C.

value: RNAse T1

value: Angel-/-


title: Mouse Fanca+/+ Engraftment 2 Replicate 1 Keratinocytes

value: BL6/129S Hybrid

value: Fanca+/+ x Trp53-/- x Ccnd1(OE) x HRAS(G12V)


title: RRB1434


title: WT_Angel+/+_rep2

value: Angel+/+


title: Sham-ILC-Rep1

source_name: Rat-brain-ILC

value: ILC

value: H3K27ac active motif cat#39133 Lot no.16612005


title: Sham-PLC-Rep1

source_name: Rat-brain-PLC

value: 2 months

value: brain

value: PLC


title: KO_Angel-/-_rep1


title: RRB1433


title: Mouse Fanca-/- Engraftment 2 Replicate 2 Keratinocytes

value: Fanca-/- x Trp53-/- x Ccnd1(OE) x HRAS(G12V)

value: Keratinocytes


title: RRB1483


title: WT_Angel+/+_rep1


title: RRB1437

value: Sham


title: Mouse Fanca-/- Engraftment 2 Replicate 3 Keratinocytes


title: Mouse Fanca+/+ Engraftment 2 Replicate 4 Keratinocytes


title: RRB1432


title: Sham-NaCshell-Rep1

source_name: Rat-brain-NaCshell

value: NaCshell


title: Mouse Fanca-/- Engraftment 2 Replicate 1 Keratinocytes


title: Mouse Fanca-/- Engraftment 2 Replicate 4 Keratinocytes


title: RRB1430

value: FT


title: RRB1481


title: nextseq_replicate2, scRNAseq

city: Eugene

first: Cristopher

last: Niell

state: Oregon

institute: University of Oregon

description:
used scRNAseq to determine the cell types of the octopus visual system. Used nextseq to sequence our second biological replicate
2_barcodes.tsv.gz
2_genes.tsv.gz
2_matrix.mtx.gz

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: o_bimaculoides_hifi_v1.0.0
Supplementary files format and content: Tab-separated values files and matrix files

organism: Octopus bimaculoides

source_name: optic lobe

extract_protocol:
O. bimaculoides optic lobes were dissected on ice in Leibovitz-15 medium (Gibco) supplemented with 400mM NaCl, 10mM KCl, 15mM Hepes, 200 U/mL penicillin, and 0.2 mg/mL streptomycin. Single cell dissociation was performed by incubating tissue in papain (1 mg/ml; Worthington Biochemical Co) plus 1% DNase (10mg/ml in HBSS) in supplemented L-15 medium for 10 min at RT. The cells/tissue were gently pipetted up and down several times to dissociate large chunks. The cells/tissue were incubated for another 10 min at RT, pipetted up and down several times, and quenched in wash solution containing 2.5M glucose, 5mM Hepes, and 5% FBS in CMFSS (12mM Hepes, 435mM NaCl, 10.7mM KCl, 21mM Na2HPO4, 16.6mM glucose). Dissociated cells were passed through a 40 μM cell strainer (Fisherbrand), washed again, and resuspended in L-15 medium. A final sample cell concentration of 2000 cells per microliter, as determined on a BioRad TC20 cell counter, was used for cDNA library preparation. Dissociated samples were prepared in tandem, on the same day.
Sample preparation for two biological replicates was performed by the University of Oregon Genomics and Cell Characterization core facility (https://gc3f.uoregon.edu/). Dissociated cells were run on a 10X Chromium platform using 10x v.3 chemistry targeting 10,000 cells. The resulting cDNA libraries were amplified with 11 cycles of PCR and sequenced on either an Illumina Hi-seq or an Illumina Next-seq.

value: optic lobe


title: nextseq_replicate1, scRNAseq

description:
used scRNAseq to determine the cell types of the octopus visual system. Used nextseq to sequence our first biological replicate
1_barcodes.tsv.gz
1_genes.tsv.gz
1_matrix.mtx.gz


title: Mouse Fanca+/+ Engraftment 1 Replicate 4 Keratinocytes


title: RRB1482


title: mutant 6

city: Cambridge

first: Vincent

last: Butty

state: MA

address: 77 Massachusetts Avenue Bldg 68-317A

department: Biology / Koch Institute / Bioengineering / CEHS

institute: Massachusetts Institute of Technology

description:
processed data header: D17-5785
Akerberg_ZF_expression_data.txt

data_processing:
IlluminaNextSeq Control Software v. 2.1.0.31 and RTA v. 2.4.11 used for basecalling.
Quality control: Reads were aligned against GRCz10/danRer10 (Sept. 2014) using bwa mem v. 0.7.12-r1039 with flags –t 16 –f and mapping rates, fraction of multiply-mapping reads, number of unique 20-mers at the 5’ end of the reads, insert size distributions and fraction of ribosomal RNAs were calculated using dedicated perl scripts and bedtools v. 2.25.0.64 In addition, each resulting bam file was randomly down-sampled to a million reads, which were aligned against  GRCz10/danRer10 and read density across genomic features were estimated for RNA-Seq-specific quality control metrics.
RNA-Seq mapping and quantitation: Reads were aligned against  GRCz10 / ENSEMBL 89 annotation using STAR v. 2.5.3a with flags -runThreadN 8 --runMode alignReads  --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM with --genomeDir pointing to a 75nt-junction  GRCz10/danRer10 STAR suffix array.
Gene expression was quantitated using RSEM v. 1.3.0 with the following flags for all libraries: rsem-calculate-expression --calc-pme --alignments -p 8  --forward-prob 0 against an annotation matching the STAR SA reference. Posterior mean estimates (pme) of counts and estimated RPKM were retrieved.
Genome_build: GRCz10/danRer10
Supplementary_files_format_and_content: Tab-delimited text file containing log2-transformed RPKM values and raw counts for all GRCz10/danRer10 annotated genes (ENSEMBL 89) in each sample (RSEM counts and pme_RPKM output).

organism: Danio rerio

source_name: embryos

extract_protocol:
Trizol homogenization followed by column-based RNA purification (Zymo Direct-zol Kit).
For RNAseq, RNA integrity and concentration were checked on a Fragment Analyzer (Advanced Analytical) and libraries were prepared using the Illumina NeoPrep RNAseq kit. Blue Pippin size selection was performed, selecting for 350 nt fragments. Libraries were quantified using the Fragment Analyzer (Advanced Analytical) and qPCR before being loaded for paired-end sequencing 2x75 nucleotides using the Illumina NextSeq 500 in High Output mode.
polyA-based mRNA capture using Neoprep with TruSeq strand-specific strategy.

tag: genotype/variation

value: mutant

value: 33 hours post-fertilization


title: RRB1429


title: RRB1428


title: mutant 3

description:
processed data header: D17-5783
Akerberg_ZF_expression_data.txt

tag: age


title: RRB1480


title: Mouse Fanca+/+ Engraftment 1 Replicate 2 Keratinocytes


title: RRB1431


title: RRB1427


title: ZsYellow negative cells - replicate 2

description:
D13-185
Count_TPMs.txt

data_processing:
Illumina Offline BaseCaller1.9.3 software used for basecalling.
Quality control: Reads were aligned against Zv9/danRer7 using bwa mem v. 0.7.12-r1039 with flags –t 16 –f and mapping rates, fraction of multiply-mapping reads, number of unique 20-mers at the 5’ end of the reads, insert size distributions and fraction of ribosomal RNAs were calculated using dedicated perl scripts and bedtools v. 2.25.0.64 In addition, each resulting bam file was randomly down-sampled to a million reads, which were aligned against Zv9/danRer7 and read density across genomic features were estimated for RNA-Seq-specific quality control metrics.
Read mapping and quantification: Salmon v. 1.2.1  was used with the following flags:   quant  -l IU   --validateMappings in paired-end mode against the GRCz11/danRer11 genome assembly and ENSEMBL 100 annotation, using all GRCz11 sequences as decoys.
Quantification files were processed in R using the TxImport function and per-gene counts and TPM estimates were retrieved.
Genome_build: Zv11/danRer11
Supplementary_files_format_and_content: Matrix table with counts and log2 TPM values for every gene and every sample

source_name: 14-16 somites stage Tg(nkx2.5:ZsYellow) zebrafish embryos

extract_protocol:
Trizol lysis, chloroform extraction and column-based purification (Qiagen RNeasy Kit).
RNA sample quality was evaluated using a 2100 Bioanalyzer Instrument (Agilent Technologies). Approximately 50ng of RNA per sample were used to prepare sequencing libraries with the Clontech low-input RNA library preparation kit. Libraries were sequenced as paired-end 2x50nt on an Illumina HiSeq2500 instrument.
polyA-based RT-priming followed by tagmentation-based RNA-Seq protcol

value: laboratory strain

tag: tissue

value: ZsYellow negative cells from same embryos

value: 14-16 somites stage


title: ZsYellow positive cardiopharyngeal progenitors and cardiomyocytes - replicate 2

description:
D13-183
Count_TPMs.txt


title: ZsYellow negative cells - replicate 1

description:
D13-184
Count_TPMs.txt


title: Mouse Fanca+/+ Engraftment 1 Replicate 1 Keratinocytes

value: BL6/129S Hybrid

value: Fanca+/+ x Trp53-/- x Ccnd1(OE) x HRAS(G12V)


title: RRB1425


title: Mouse Fanca-/- Engraftment 1 Replicate 4 Keratinocytes


title: mutant 2

description:
processed data header: D17-5782
Akerberg_ZF_expression_data.txt


title: ZsYellow positive cardiopharyngeal progenitors and cardiomyocytes - replicate 1

description:
D13-182
Count_TPMs.txt


title: RRB1426


title: mutant 1

description:
processed data header: D17-5781
Akerberg_ZF_expression_data.txt


title: mutant 4

description:
processed data header: D17-5784
Akerberg_ZF_expression_data.txt


title: Mouse Fanca-/- Engraftment 1 Replicate 3 Keratinocytes


title: Mouse Fanca+/+ Engraftment 1 Replicate 3 Keratinocytes

treatment_protocol: Fanca+/+;Tp53-/-;Ccnd1OE;HRASG12V and Fanca-/-;Tp53-/-;Ccnd1OE;HRASG12V mouse keratinocytes were serially intradermally allografted into backs of Nude/J mice (Jackson Labs) over 11 engraftment cycles (approx. 17 weeks). Four replicates were created for both Fanca+/+ and Fanca-/- genotypes, with each replicate carried forward independently through the engraftment cycles. Each replicate consisted of 4 intradermal engraftment sites on the same mouse, which were combined after harvesting at the end of each cycle. At the first engraftment cycle, each engraftment site received 150,000 cells suspended in a 1:1 ratio of DPBS & Corning Matrigel. Resulting tumors were grown for a maximum of two weeks or until tumor size reached ~1.5 cm3, whichever occurred sooner. Host mice were humanely euthanized, and tumors were dissected, minced, dissociated, and strained to a single-cell mixture using collagenase and Trypsin. Resulting tumor cells were plated at 5% CO2 / 3% O2 at 37°C, and allowed to recover for 48 hours in low-calcium keratinocyte media (E-Low Media)58. This ensured consistent cell viability between replicates and permitted in vitro analysis of post-transplant cells. The number of engrafted cells was lowered to 100K for both genotypes for engraftments two to five, further lowered to 70K cells for cycles six to nine and reduced to 35K for the 10-11th cycles. One Fanca-/- replicate was lost at the fifth cycle due to host death, which resulted in removal of this replicate from the sixth engraftment cycle onwards.


title: wt 6

description:
processed data header: D17-5780
Akerberg_ZF_expression_data.txt

value: wt


title: wt 4

description:
processed data header: D17-5779
Akerberg_ZF_expression_data.txt


title: RRB1423


title: hiseq_replicate2, scRNAseq

description:
used scRNAseq to determine the cell types of the octopus visual system. Used hiseq to sequence our second biological replicate
2_barcodes.tsv.gz
2_genes.tsv.gz
2_matrix.mtx.gz


title: hiseq_replicate1, scRNAseq

description:
used scRNAseq to determine the cell types of the octopus visual system. Used hiseq to sequence our first biological replicate
1_barcodes.tsv.gz
1_genes.tsv.gz
1_matrix.mtx.gz


title: RRB1422


title: Mouse Fanca-/- Engraftment 1 Replicate 1 Keratinocytes


title: Mouse Fanca-/- Engraftment 1 Replicate 2 Keratinocytes


title: wt 3

description:
processed data header: D17-5778
Akerberg_ZF_expression_data.txt


title: wt 2

description:
processed data header: D17-5777
Akerberg_ZF_expression_data.txt


title: RRB1421


title: wt 1

description:
processed data header: D17-5776
Akerberg_ZF_expression_data.txt


title: Mouse Fanca+/+ Pre-Engraftment Keratinocytes

source_name: Pre-Engraftment Cells


title: Mouse Fanca-/- Pre-Engraftment Keratinocytes


title: RRB1420

description:
10x Genomics Gene Expression*3'v2
dorDG2021_countmatrix.csv.gz


title: HCT116_SMARCA4-WT

city: Nanjing

first: Xiangwei

last: Zeng

state: Jiangsu

address: Xianlin avenue

country: China

institute: Nanjing university

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
Sequencing reads were aligned to the mm10 reference genome with Bowtie2
CUT&Tag libraries were sequenced with the Illumina Nova6000 sequencer.
MACS2 (version 2.2.7.1) was used to call peaks
Peak annotation was performed by R package ChIPseeker
Assembly: hg19
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: colon

growth_protocol: McCoy's 5 A,10% fetal bovine serum. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Approximately 10,000 cell nuclei were prepared and treated with concanavalin A-coated magnetic beads.
After combining the primary and secondary antibodies, the pA-Tn5 transposome was used to bind and label DNA. Then, the library was established by purifying and amplifying DNA.

value: colon

value: Human eukaryotic cells

tag: chip antibody


title: HCT116_SMARCA4-R1157W

value: SMARCA4-R1157W mutant


title: RRB1424

description:
10x Genomics Gene Expression*3'v2
venDG2021_countmatrix.csv.gz


title: NGP shEED-1 day10 rep 3

status: Public on Sep 03 2022

type: RNA

city: Kitaadachi-gun

first: Hisanori

last: Takenobu

state: Saitama

address: 818, Komuro, Ina-machi

department: Research Institute for Clinical Oncology

country: Japan

institute: Saitama Cancer Center

hyb_protocol: One-color mixes of labelled cRNA pairs were hybridized to 8x60K whole human genome oligonucleotide microarray (Agilent G4851B), at 65°C for 17 hours using Agilent’s Gene Expression Hybridization Kit.

scan_protocol: Purified labeled total RNA was hybridized to the expression microarray. Hybridization, the scanning of microarrays (SureScan G4900DA Microarray Scanner), and data extraction from scanned images were conducted according to Agilent protocol version 6.9.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: NGP shEED-1 day10

label_protocol: Two hundred nanograms of total RNA was labeled with Cyanine3 using a Low Input Quick-Amp Labeling Kit (one color, Agilent Technologies) according to the manufacturer’s instructions.

growth_protocol: Human NB cell line NGP were cultured in RPMI1640 (Wako) supplemented with 10% heat-inactivated fetal bovine serum (Invitrogen) and 50 μg/ml penicillin/streptomycin (Wako) in an incubator with humidified air at 37 °C with 5% CO2

extract_protocol: Total cellular RNA for preparing RT–PCR templates was extracted using ISOGEN II (Nippon Gene KK). RNA was extracted at 10 days after shEED-expressing lentiviral infection.

treatment_protocol: shCont (pLKO.1) control, shEED-1 (TRCN0000021205) or  shEED-2 (TRCN0000021206) vectors shRNA contained plasmids,  were purchased from the MISSION(TM) shRNA Library (Sigma-Aldrich). In the preparation of the shRNA/lentivirus, the packaging cell line HEK 293T (4 × 10^6) was plated on a 10-cm dish and co-transfected the next day with 1.5 μg of each of the shRNA plasmids and 2.0 μg of the packaging vectors (Sigma-Aldrich) using the Fugene HD transfection reagent (Promega) according to the manufacturer’s protocol. Medium was changed the next day and cells were cultured for another 24 h. Conditioned medium was collected and cleared of debris by filtering through a filter with 0.45-μm pores.  Thereafter, 1 × 105 NB cells were seeded on each well of a 6-well plate, and infected by lentiviral-conditioned media with 4 μg/mL polybrene.

value: NGP

value: Human neuroblastoma cell line


title: NGP shEED-1 day10 rep 1


title: NGP shEED-2 day10 rep 3

source_name: NGP shEED-2 day10


title: NGP shEED-2 day10 rep 1


title: NGP pLKO.1 day10 rep 4

source_name: NGP pLKO.1 day10

value: shCont


title: NGP pLKO.1 day10 rep 3


title: NGP pLKO.1 day10 rep 1


title: NGP shEED-2 day10 rep 2


title: NGP shEED-1 day10 rep 2


title: NGP pLKO.1 day10 rep 2


title: Reference Standard CSF UH3119, Sample 13

city: Portland

first: Julie

last: Saugstad

address: 3181 SW Sam Jackson Park Road

department: Anesthesiology & Perioperative Medicine

institute: Oregon Health & Science University

description:
EXR-JSAUG1UH3119-BS-13
total cell-free biofluid RNA
Assay Port: p5_8

data_processing:
miRNAs hsa-miR-1293-002905, hsa-miR-217-002337, hsa-miR-409-5p-002331, and hsa-miR-647-001600 were preselected as negative control probes and not expected to amplify at Ct < 34 in any well; this was fulfilled in the data.
miRNAs hsa-miR-1290-002863, hsa-miR-19b-1*-002425, hsa-miR-204-000508, hsa-miR-30c-000419, hsa-miR-30e-3p-000422, hsa-miR-574-3p-002349, hsa-miR-638-001582, hsa-miR-645-001597, and hsa-miR-92a-000431 were preselected as positive control probes and for inclusion were required to amplify at Ct < 34 in at least 2 out of the 3 replicate wells for at least 90% of samples, with AmpScore > 1.0 and CqConf > 0.8; miRNAs hsa-miR-19b-1*-002425, hsa-miR-30c-000419, and hsa-miR-645-001597 failed to meet this standard and were excluded.
miRNAs with low (< 20%) detection rates in samples, or median well amplification count < 2/3, or median Ct > 34, or mean AmpScore < 1.0 among amplifications with Ct < 34 in at least 2 of 3 wells, or mean CqConf < 0.8 among amplifications with Ct < 34 in at least 2 of 3 wells, were excluded in order to restrict focus to targets with adequate biomarker potential; miRNAs hsa-miR-1291-002838, hsa-miR-145*-002149, hsa-miR-202-002363, hsa-miR-26b-000407, hsa-miR-27b-000409, hsa-miR-30d-000420, hsa-miR-340-002258, hsa-miR-519b-3p-002384, hsa-miR-520b-001116, hsa-miR-590-5p-001984, and hsa-miR-603-001566 were excluded on this basis.
Triplicate wells were summarized by median value for each sample for each miRNA.
miRNAs with median Ct > 34 or less than 2 of 3 wells with Ct < 34 meeting AmpScore > 1.0 and CqConf > 0.8 were marked as censored and viewed as miRNA below the lower limit of detection.
Sample EXR-JSAUG1UH3060-BS was excluded due to complete lack of miRNA expression.
Plates were aligned by median value across common reference samples (EXR-JSAUG1UH3119-BS) using nonlinear spline-based interpolation, and post-aligned Ct values were normalized to a model-based average of expressed but nonchanging (positive control miRNA) samples using BLUPs from a random-effects regression model (see https://pubmed.ncbi.nlm.nih.gov/30689565/ for further details); miRNAs whose median raw Ct value appear as 34 in the non-normalized data matrix should be considered censored measurements in the normalized data matrix, regardless of the normalized value.

label: FAM

source_name: Cerebrospinal fluid

label_protocol: Concentrated RNA samples were reverse transcribed using a custom MiRNA RT pool (4459652, Thermo Fisher Scientific) and TaqMan® MicroRNA Reverse Transcription Kit (4366596, TFS), then pre-amplified using a custom MiRNA PreAmp pool (4459660, TFS) and TaqMan® PreAmp Master Mix w/QRC (4391128, TFS). The pre-amplification products were diluted 1:4 in RNase/DNase-free water, then 18 µL of diluted samples were mixed with TaqMan® Universal PCR Master Mix II, no UNG (4440040, TFS) and RNase/DNase-free water to a final volume of 450 µL, loaded onto a custom TaqMan® Array Card (4449140, TFS) and amplified on a QuantStudio™ 12K Flex Real-Time PCR instrument (4471089, TFS).

extract_protocol: Total RNA was isolated from 0.5 ml CSF using the mirVana PARIS kit (Life Technologies/Ambion AM1556) without enrichment for small RNAs. Isolated RNAs from each sample were concentrated using Zymo RNA Clean & Concentrator-5 (Zymo Research, Irvine CA) spin columns. RNA concentrations were measured using Quant-iT RiboGreen RNA Assay Kit (Life Technologies/Invitrogen). RNA quality was assessed using an Agilent 2100 Bioanalyzer and RNA 6000 Pico chips (Agilent Technologies).

tag: diagnosis

value: Healthy Control

tag: Sex

value: Female

value: 0 y

value: Cerebrospinal fluid

tag: anatomical location

value: Structure of nervous tissue

tag: sample collection method

value: Lumbar puncture

tag: starting amount

tag: holding temperature


title: Reference Standard CSF UH3119, Sample 12

description:
EXR-JSAUG1UH3119-BS-12
total cell-free biofluid RNA
Assay Port: p1_4


title: CGGR 16S-13

type: protein

city: Seoul

first: Jung Hyun

last: Jo

state: --- Select ---

address: 50-1 Yonsei-ro

country: South Korea

institute: Yonsei University Health System

hyb_protocol: protein sample was detected with Cy3-streptavidin (GE Healthcare, Chalfont St. Giles, UK).

scan_protocol: The slide was rinsed scanned using the GenePix 4100A scanner (Axon Instrument, USA) at 10 um resolution, optimal laser power and PMT.

data_processing:
Following image scanning, they were gridded and quantified with GenePix 7.0 Software (Axon Instrument, USA).
Normalized signal is calculated from average intensity of replicate spots / median signal.

molecule: protein

source_name: Pancreatic cancer

label_protocol: 50ug of protein sample was labeled and incubated with coupling mixture on the antibody microarray slide (Fullmoon Biosystems).

extract_protocol: Protein was extracted from plasma using a protein extraction buffer (Fullmoon Biosystems, Sunnyvale, CA) and protein expression was analyzed using antibody microarray analysis (Fullmoon Biosystems) according to the manufacturer’s protocol.

tag: sample group

value: CGGR

value: Blood


title: CGGR 01S-03

description: 01S-03-Visit 1


title: Reference Standard CSF UH3119, Sample 11

description:
EXR-JSAUG1UH3119-BS-11
total cell-free biofluid RNA
Assay Port: p1_4


title: CGGR 01S-13

description: 01S-13-Visit 1


title: BM, CD34+HSPCs, HC, 4, 10X

city: Jinan

first: Yan

last: Liu

state: Shandong

address: 107 West Wenhua Rd, Lixia

department: Department of Hematology

institute: Qilu Hospital, Cheeloo College of Medicine, Shandong University

description: BM_HSPCs_gene_counts.csv, HC_4

data_processing:
Cell Ranger (version 3.0.0) software from 10X Genomics (http://www.10xgenomics.com)  were used to the basecalling.
Raw files were processed with Cell Ranger 3.0.0 pipeline (10X Genomics) using default mapping arguments. Reads were mapped to the human genome (GRCh38-1.2.0).
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: BM, CD34+HSPCs, HC

extract_protocol:
BM samples were obtained by iliac crest aspiration, and removed erythrocytes. BM CD34+ HSPCs were puriﬁed using fluorescence-activated cell sorting (FACS) and the cellular suspensions were loaded onto a Chromium Single Cell Chip (10X Genomics) with barcoded gel beads at a target capture rate of ~6,000 individual cells per sample.
The scRNA-seq dataset of each sample were produced with a Chromium system (10X Genomics, PN1000073) following the manufacturer’s instructions.

value: bone marrow (BM)

tag: cell type

value: BM CD34+ HSPCs

tag: disease state

value: control

tag: individual

value: Healthy control 4

value: 40 years old

tag: treatment

value: untreated


title: CGGR 16S_70


title: Reference Standard CSF UH3119, Sample 09

description:
EXR-JSAUG1UH3119-BS-09
total cell-free biofluid RNA
Assay Port: p5_8


title: Reference Standard CSF UH3119, Sample 10

description:
EXR-JSAUG1UH3119-BS-10
total cell-free biofluid RNA
Assay Port: p5_8


title: BM, CD34+HSPCs, HC, 2, 10X

description: BM_HSPCs_gene_counts.csv, HC_2

value: Healthy control 2

value: Male


title: BM, CD34+HSPCs, HC, 1, 10X

description: BM_HSPCs_gene_counts.csv, HC_1

value: Healthy control 1

value: 48 years old


title: Reference Standard CSF UH3119, Sample 07

description:
EXR-JSAUG1UH3119-BS-07
total cell-free biofluid RNA
Assay Port: p5_8

value: Healthy Control

value: Female


title: Reference Standard CSF UH3119, Sample 06

description:
EXR-JSAUG1UH3119-BS-06
total cell-free biofluid RNA
Assay Port: p5_8

value: 0 y

value: Cerebrospinal fluid


title: CGGR 16S-07


title: Genomic DNA from placental tissue [SC14]

type: genomic

city: Campinas

first: Pedro

last: Cruz

address: Av Candido Rondon 400

country: Brazil

institute: UNICAMP

description: HbSC placental tissue sample

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

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: placental tissue

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from placental tissue samples using QIAamp DNA Mini kit according to standard instructions.

tag: gender

value: Placental Tissue

value: HbSC


title: BM, CD34+HSPCs, HC, 3, 10X

description: BM_HSPCs_gene_counts.csv, HC_3

value: Healthy control 3

value: 35 years old


title: Genomic DNA from placental tissue [CTL24]

description: Normal placental tissue sample

value: Normal


title: BM, CD34+HSPCs, ITP, 4, 10X

description: BM_HSPCs_gene_counts.csv, ITP_4

source_name: BM, CD34+HSPCs, ITP

value: bone marrow (BM)

value: BM CD34+ HSPCs

value: Immune thrombocytopenia (ITP)

value: ITP patient 4

value: 54 years old


title: Reference Standard CSF UH3119, Sample 05

description:
EXR-JSAUG1UH3119-BS-05
total cell-free biofluid RNA
Assay Port: p1_4

value: Structure of nervous tissue

value: Lumbar puncture


title: Genomic DNA from placental tissue [CTL23]

description: Normal placental tissue sample


title: Genomic DNA from placental tissue [SC16]

description: HbSC placental tissue sample


title: Genomic DNA from placental tissue [SC9]

description: HbSC placental tissue sample


title: Genomic DNA from placental tissue [SS7]

description: HbSS placental tissue sample

value: Male

value: HbSS


title: Reference Standard CSF UH3119, Sample 03

description:
EXR-JSAUG1UH3119-BS-03
total cell-free biofluid RNA
Assay Port: p1_4

value: Healthy Control

value: Female


title: Genomic DNA from placental tissue [CTL20]

description: Normal placental tissue sample


title: Genomic DNA from placental tissue [CTL19]

description: Normal placental tissue sample


title: Genomic DNA from placental tissue [SC13]

description: HbSC placental tissue sample


title: Reference Standard CSF UH3119, Sample 02

description:
EXR-JSAUG1UH3119-BS-02
total cell-free biofluid RNA
Assay Port: p5_8

value: 0 y

value: Cerebrospinal fluid


title: Genomic DNA from placental tissue [CTL22]

description: Normal placental tissue sample

value: Placental Tissue


title: Genomic DNA from placental tissue [CTL21]

description: Normal placental tissue sample


title: Genomic DNA from placental tissue [SC15]

description: HbSC placental tissue sample

value: HbSC


title: Genomic DNA from placental tissue [SS2]

description: HbSS placental tissue sample


title: Genomic DNA from placental tissue [SS8]

description: HbSS placental tissue sample


title: Genomic DNA from placental tissue [SS3]

description: HbSS placental tissue sample


title: BM, CD34+HSPCs, ITP, 2, 10X

description: BM_HSPCs_gene_counts.csv, ITP_2

value: ITP patient 2

value: 19 years old

value: untreated


title: Reference Standard CSF UH3119, Sample 01

description:
EXR-JSAUG1UH3119-BS-01
total cell-free biofluid RNA
Assay Port: p1_4


title: Genomic DNA from placental tissue [CTL18]

description: Normal placental tissue sample

value: Normal


title: Genomic DNA from placental tissue [SC11]

description: HbSC placental tissue sample


title: Genomic DNA from placental tissue [SS5]

description: HbSS placental tissue sample


title: Healthy CSF UH3118

description:
EXR-JSAUG1UH3118-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: Genomic DNA from placental tissue [SC12]

description: HbSC placental tissue sample


title: Reference Standard CSF UH3119, Sample 08

description:
EXR-JSAUG1UH3119-BS-08
total cell-free biofluid RNA
Assay Port: p5_8


title: Genomic DNA from placental tissue [SC10]

description: HbSC placental tissue sample


title: Reference Standard CSF UH3119, Sample 04

description:
EXR-JSAUG1UH3119-BS-04
total cell-free biofluid RNA
Assay Port: p1_4


title: Genomic DNA from placental tissue [SS1]

description: HbSS placental tissue sample


title: CGGR 07S-10

value: CGGR

value: Blood


title: BM, CD34+HSPCs, ITP, 1, 10X

description: BM_HSPCs_gene_counts.csv, ITP_1

value: bone marrow (BM)

value: BM CD34+ HSPCs

value: Immune thrombocytopenia (ITP)

value: ITP patient 1

value: 23 years old


title: CGGR 16S-11


title: CGGR 14S-01


title: Genomic DNA from placental tissue [SS4]

description: HbSS placental tissue sample

value: Male

value: HbSS


title: Healthy CSF UH3117

description:
EXR-JSAUG1UH3117-BS
total cell-free biofluid RNA
Assay Port: p5_8

value: Healthy Control

value: Female

value: Structure of nervous tissue

value: Lumbar puncture


title: Genomic DNA from placental tissue [SS6]

description: HbSS placental tissue sample

value: Placental Tissue


title: ADT data from human PBMC (batch 2, ADT 8-fold dilution)

city: Pittsburgh

first: Wei

last: Chen

address: 4401 Penn Ave, Rangos Research Building 9125

institute: UPMC Children's Hospital of Pittsburgh

description: single cell protein data from human PBMC (batch 2)

data_processing:
Standard 10X Genomics CellRanger pipeline
Match RNA data and ADT data with common cell barcodes
Genome_build: GRCh38
Supplementary_files_format_and_content: For each sample, the raw UMI count matrix is stored in a csv file with features as row names and cell barcodes as column names.

source_name: Blood

extract_protocol:
Sorted cells were loaded into the Single Cell Chip and processed through the 10X controller for droplet generation, resulting in droplets containing a single cell and bead per droplet
Chromium Single Cell 3' RNA-seq libraries were prepared for sequencing using standard 10X Genomics protocols

tag: sample type

value: single cell surface protein


title: AD CSF UH3116

description:
EXR-JSAUG1UH3116-BS
total cell-free biofluid RNA
Assay Port: p1_4

value: Alzheimer's Disease

value: Cerebrospinal fluid


title: CGGR 10S-02

value: CGGR


title: AD CSF UH3115

description:
EXR-JSAUG1UH3115-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: CGGR 04S-20

value: Blood


title: Healthy CSF UH3114

description:
EXR-JSAUG1UH3114-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: ADT data from human PBMC (batch 1, ADT 2-fold dilution)

description: single cell protein data from human PBMC (batch 1)


title: Healthy CSF UH3113

description:
EXR-JSAUG1UH3113-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: Healthy CSF UH3112

description:
EXR-JSAUG1UH3112-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: RNA data from human PBMC (batch 2, ADT 8-fold dilution)

description: scRNA data from human PBMC (batch 2)

value: single cell RNA


title: AD CSF UH3110

description:
EXR-JSAUG1UH3110-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: Healthy CSF UH3111

description:
EXR-JSAUG1UH3111-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: RNA data from human PBMC (batch 1, ADT 2-fold dilution)

description: scRNA data from human PBMC (batch 1)


title: Healthy CSF UH3107

description:
EXR-JSAUG1UH3107-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: Healthy CSF UH3108

description:
EXR-JSAUG1UH3108-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: Healthy CSF UH3109

description:
EXR-JSAUG1UH3109-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: AD CSF UH3105

description:
EXR-JSAUG1UH3105-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: Healthy CSF UH3106

description:
EXR-JSAUG1UH3106-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: CGPR 01S-21

description: 01S-21-Visit 1

value: CGPR


title: Healthy CSF UH3104

description:
EXR-JSAUG1UH3104-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: CGPR 11S-08


title: Healthy CSF UH3103

description:
EXR-JSAUG1UH3103-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: Healthy CSF UH3102

description:
EXR-JSAUG1UH3102-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: Alzheimer's Disease CSF148

description:
EXR-JSAUG1UH2148-BS
total cell-free biofluid RNA

data_processing:
miRNAs with low (<~20%) detection rates in samples or less than that number of adequately quantified Ct values were excluded in order to restrict focus to targets with adequate biomarker potential; 617 miRNAs were excluded for these reasons.
miRNAs with raw Ct values at a threshold of 36 and higher were marked as censored, and viewed as miRNA below the lower limit of detection.
Ct values were normalized by subtracting the mean of the 4 same-plate U6 snRNA reference values for the sample for each plate, and recentered by subsequently adding the globally maximum (across all samples) U6 value; miRNAs whose raw Ct value appear as 36 in the non-normalized data matrix should be considered censored measurements in the normalized data matrix, regardless of the normalized value.

label_protocol: As per Life Technologies Human miRNA Megaplex Pool (A + B) protocol. Concentrated RNA samples were reverse transcribed using a custom MiRNA RT pool (4459652, Thermo Fisher Scientific) and TaqMan® MicroRNA Reverse Transcription Kit (4366596, TFS), then pre-amplified using a custom MiRNA PreAmp pool (4459660, TFS) and TaqMan® PreAmp Master Mix w/QRC (4391128, TFS). The pre-amplification products were diluted 1:4 in RNase/DNase-free water, then 18 µL of diluted samples were mixed with TaqMan® Universal PCR Master Mix II, no UNG (4440040, TFS) and RNase/DNase-free water to a final volume of 450 µL, loaded onto a custom TaqMan® Array Card (4449140, TFS) and amplified on a QuantStudio™ 12K Flex Real-Time PCR instrument (4471089, TFS).

extract_protocol: Total RNA was isolated from 0.5 ml CSF using the mirVana PARIS kit (Life Technologies/Ambion) without enrichment for small RNAs. Isolated RNAs from each sample were concentrated using Zymo RNA Clean & Concentrator-5 (Zymo Research, Irvine CA) spin columns. RNA concentrations were measured using Quant-iT RiboGreen RNA Assay Kit (Life Technologies/Invitrogen). RNA quality was assessed using an Agilent 2100 Bioanalyzer and RNA 6000 Pico chips (Agilent Technologies).


title: Alzheimer's Disease CSF149

description:
EXR-JSAUG1UH2149-BS
total cell-free biofluid RNA


title: CGGR 07S-01


title: CGGR 04S-14


title: CGPR 11S-05


title: Healthy CSF UH3100

description:
EXR-JSAUG1UH3100-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: Healthy CSF UH3101

description:
EXR-JSAUG1UH3101-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: CGGR 02S-05


title: Alzheimer's Disease CSF147

description:
EXR-JSAUG1UH2147-BS
total cell-free biofluid RNA


title: Healthy CSF UH3099

description:
EXR-JSAUG1UH3099-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: Alzheimer's Disease CSF122

description:
EXR-JSAUG1UH2122-BS
total cell-free biofluid RNA


title: CGPR 02S-04


title: Healthy CSF UH3098

description:
EXR-JSAUG1UH3098-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: CGPR 01S-11

description: 01S-11-Visit 1


title: Alzheimer's Disease CSF150

description:
EXR-JSAUG1UH2150-BS
total cell-free biofluid RNA


title: Healthy CSF UH3097

description:
EXR-JSAUG1UH3097-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: CGPR 14S-29


title: Alzheimer's Disease CSF095

description:
EXR-JSAUG1UH2095-BS
total cell-free biofluid RNA


title: AD CSF UH3096

description:
EXR-JSAUG1UH3096-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: Alzheimer's Disease CSF094

description:
EXR-JSAUG1UH2094-BS
total cell-free biofluid RNA


title: CGPR 14S-15


title: CGPR 14S-03


title: Alzheimer's Disease CSF093

description:
EXR-JSAUG1UH2093-BS
total cell-free biofluid RNA


title: Healthy CSF UH3092

description:
EXR-JSAUG1UH3092-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: AD CSF UH3093

description:
EXR-JSAUG1UH3093-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: Healthy CSF UH3091

description:
EXR-JSAUG1UH3091-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: CGPR 16S-02


title: AD CSF UH3094

description:
EXR-JSAUG1UH3094-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: CGPR 16S-03


title: Healthy CSF UH3090

description:
EXR-JSAUG1UH3090-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: Alzheimer's Disease CSF091

description:
EXR-JSAUG1UH2091-BS
total cell-free biofluid RNA


title: Alzheimer's Disease CSF090

description:
EXR-JSAUG1UH2090-BS
total cell-free biofluid RNA


title: GGGR 01S-126

description: 01S-126-Visit 1

value: GGGR


title: Alzheimer's Disease CSF089

description:
EXR-JSAUG1UH2089-BS
total cell-free biofluid RNA


title: Healthy CSF UH3095

description:
EXR-JSAUG1UH3095-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: Alzheimer's Disease CSF088

description:
EXR-JSAUG1UH2088-BS
total cell-free biofluid RNA


title: GGGR 01S-73

description: 01S-73-Visit 1


title: Healthy CSF UH3083

description:
EXR-JSAUG1UH3083-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: Healthy CSF UH3084

description:
EXR-JSAUG1UH3084-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: BM, CD34+HSPCs, ITP, 3, 10X

description: BM_HSPCs_gene_counts.csv, ITP_3

value: bone marrow (BM)

value: BM CD34+ HSPCs

value: Immune thrombocytopenia (ITP)

value: ITP patient 3

value: 46 years old

value: untreated


title: GGGR 01S-07

description: 01S-07-Visit 1


title: AD CSF UH3088

description:
EXR-JSAUG1UH3088-BS
total cell-free biofluid RNA
Assay Port: p5_8

value: Female

value: Structure of nervous tissue


title: Healthy CSF UH3089

description:
EXR-JSAUG1UH3089-BS
total cell-free biofluid RNA
Assay Port: p1_4

value: Healthy Control

value: Lumbar puncture


title: AD CSF UH3081

description:
EXR-JSAUG1UH3081-BS
total cell-free biofluid RNA
Assay Port: p1_4

value: Alzheimer's Disease


title: AD CSF UH3086

description:
EXR-JSAUG1UH3086-BS
total cell-free biofluid RNA
Assay Port: p5_8

value: Cerebrospinal fluid


title: Alzheimer's Disease CSF092

description:
EXR-JSAUG1UH2092-BS
total cell-free biofluid RNA


title: AD CSF UH3082

description:
EXR-JSAUG1UH3082-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: Healthy CSF UH3087

description:
EXR-JSAUG1UH3087-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: Healthy CSF UH3080

description:
EXR-JSAUG1UH3080-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: CGPR 11S-06


title: Alzheimer's Disease CSF087

description:
EXR-JSAUG1UH2087-BS
total cell-free biofluid RNA

value: Male


title: Healthy CSF UH3079

description:
EXR-JSAUG1UH3079-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: GGGR 16S-58

value: Blood


title: Alzheimer's Disease CSF086

description:
EXR-JSAUG1UH2086-BS
total cell-free biofluid RNA


title: Healthy CSF UH3085

description:
EXR-JSAUG1UH3085-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: Healthy CSF UH3077

description:
EXR-JSAUG1UH3077-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: Healthy CSF UH3078

description:
EXR-JSAUG1UH3078-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: Alzheimer's Disease CSF085

description:
EXR-JSAUG1UH2085-BS
total cell-free biofluid RNA


title: GGGR 16S-06


title: Healthy CSF UH3075

description:
EXR-JSAUG1UH3075-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: GGGR 01S-54


title: Alzheimer's Disease CSF084

description:
EXR-JSAUG1UH2084-BS
total cell-free biofluid RNA


title: AD CSF UH3074

description:
EXR-JSAUG1UH3074-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: Healthy CSF UH3072

description:
EXR-JSAUG1UH3072-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: Alzheimer's Disease CSF083

description:
EXR-JSAUG1UH2083-BS
total cell-free biofluid RNA


title: GGGR 08S-12


title: GGGR 01S-28


title: Healthy CSF UH3071

description:
EXR-JSAUG1UH3071-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: GGGR 05S-20


title: GGGR 05S-03


title: GGGR 01S-123


title: Healthy CSF UH3076

description:
EXR-JSAUG1UH3076-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: GGGR 07S-06


title: AD CSF UH3073

description:
EXR-JSAUG1UH3073-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: Healthy CSF UH3057

description:
EXR-JSAUG1UH3057-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: AD CSF UH3058

description:
EXR-JSAUG1UH3058-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: AD CSF UH3056

description:
EXR-JSAUG1UH3056-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: Healthy CSF UH3055

description:
EXR-JSAUG1UH3055-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: Alzheimer's Disease CSF079

description:
EXR-JSAUG1UH2079-BS
total cell-free biofluid RNA


title: Alzheimer's Disease CSF078

description:
EXR-JSAUG1UH2078-BS
total cell-free biofluid RNA


title: Alzheimer's Disease CSF076

description:
EXR-JSAUG1UH2076-BS
total cell-free biofluid RNA


title: Alzheimer's Disease CSF077

description:
EXR-JSAUG1UH2077-BS
total cell-free biofluid RNA


title: Alzheimer's Disease CSF075

description:
EXR-JSAUG1UH2075-BS
total cell-free biofluid RNA


title: Alzheimer's Disease CSF082

description:
EXR-JSAUG1UH2082-BS
total cell-free biofluid RNA


title: Alzheimer's Disease CSF080

description:
EXR-JSAUG1UH2080-BS
total cell-free biofluid RNA


title: Alzheimer's Disease CSF081

description:
EXR-JSAUG1UH2081-BS
total cell-free biofluid RNA


title: Healthy CSF UH3069

description:
EXR-JSAUG1UH3069-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: Healthy CSF UH3061

description:
EXR-JSAUG1UH3061-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: AD CSF UH3059

description:
EXR-JSAUG1UH3059-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: Healthy CSF UH3070

description:
EXR-JSAUG1UH3070-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: Alzheimer's Disease CSF074

description:
EXR-JSAUG1UH2074-BS
total cell-free biofluid RNA


title: AD CSF UH3053

description:
EXR-JSAUG1UH3053-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: AD CSF UH3054

description:
EXR-JSAUG1UH3054-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: GGGR 10S-12


title: AD CSF UH3065

description:
EXR-JSAUG1UH3065-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: GGGR 01S-49


title: GGGR 16S-95


title: Healthy CSF UH3068

description:
EXR-JSAUG1UH3068-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: Healthy CSF UH3066

description:
EXR-JSAUG1UH3066-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: AD CSF UH3067

description:
EXR-JSAUG1UH3067-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: GGGR 02S-40


title: AD CSF UH3052

description:
EXR-JSAUG1UH3052-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: Alzheimer's Disease CSF073

description:
EXR-JSAUG1UH2073-BS
total cell-free biofluid RNA


title: AD CSF UH3051

description:
EXR-JSAUG1UH3051-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: Healthy CSF UH3062

description:
EXR-JSAUG1UH3062-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: AD CSF UH3064

description:
EXR-JSAUG1UH3064-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: Healthy CSF UH3063

description:
EXR-JSAUG1UH3063-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: Healthy CSF UH3050

description:
EXR-JSAUG1UH3050-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: Alzheimer's Disease CSF072

description:
EXR-JSAUG1UH2072-BS
total cell-free biofluid RNA


title: AD CSF UH3049

description:
EXR-JSAUG1UH3049-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: Healthy CSF UH3048

description:
EXR-JSAUG1UH3048-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: GGGR 01S-118


title: Healthy CSF UH3044

description:
EXR-JSAUG1UH3044-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: AD CSF UH3045

description:
EXR-JSAUG1UH3045-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: GGGR 01S-129


title: GGGR 01S-25


title: GGGR 03S-01


title: GGGR 16S-67


title: Alzheimer's Disease CSF070

description:
EXR-JSAUG1UH2070-BS
total cell-free biofluid RNA


title: Alzheimer's Disease CSF069

description:
EXR-JSAUG1UH2069-BS
total cell-free biofluid RNA


title: Healthy CSF UH3043

description:
EXR-JSAUG1UH3043-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: GGGR 02S-32


title: GGPR 01S-132

description: 01S-132-Visit 1

value: GGPR


title: AD CSF UH3042

description:
EXR-JSAUG1UH3042-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: Healthy CSF UH3041

description:
EXR-JSAUG1UH3041-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: Healthy CSF UH3040

description:
EXR-JSAUG1UH3040-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: Alzheimer's Disease CSF068

description:
EXR-JSAUG1UH2068-BS
total cell-free biofluid RNA


title: Alzheimer's Disease CSF067

description:
EXR-JSAUG1UH2067-BS
total cell-free biofluid RNA


title: AD CSF UH3039

description:
EXR-JSAUG1UH3039-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: Healthy CSF UH3046

description:
EXR-JSAUG1UH3046-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: GGPR 01S-124

description: 01S-124-Visit 1


title: AD CSF UH3038

description:
EXR-JSAUG1UH3038-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: Healthy CSF UH3047

description:
EXR-JSAUG1UH3047-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: Alzheimer's Disease CSF071

description:
EXR-JSAUG1UH2071-BS
total cell-free biofluid RNA


title: GGPR 01S-111

description: 01S-111-Visit 1


title: Alzheimer's Disease CSF065

description:
EXR-JSAUG1UH2065-BS
total cell-free biofluid RNA


title: Alzheimer's Disease CSF066

description:
EXR-JSAUG1UH2066-BS
total cell-free biofluid RNA


title: Healthy CSF UH3036

description:
EXR-JSAUG1UH3036-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: GGPR 01S-10

description: 01S-10-Visit 1


title: AD CSF UH3035

description:
EXR-JSAUG1UH3035-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: AD CSF UH3033

description:
EXR-JSAUG1UH3033-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: AD CSF UH3032

description:
EXR-JSAUG1UH3032-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: GGPR 01S-57

description: 01S-57-Visit 1


title: AD CSF UH3034

description:
EXR-JSAUG1UH3034-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: Healthy CSF UH3037

description:
EXR-JSAUG1UH3037-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: Healthy CSF UH3031

description:
EXR-JSAUG1UH3031-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: Alzheimer's Disease CSF064

description:
EXR-JSAUG1UH2064-BS
total cell-free biofluid RNA


title: Alzheimer's Disease CSF063

description:
EXR-JSAUG1UH2063-BS
total cell-free biofluid RNA


title: AD CSF UH3029

description:
EXR-JSAUG1UH3029-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: Healthy CSF UH3030

description:
EXR-JSAUG1UH3030-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: GGPR 16S-108


title: Alzheimer's Disease CSF062

description:
EXR-JSAUG1UH2062-BS
total cell-free biofluid RNA


title: AD CSF UH3028

description:
EXR-JSAUG1UH3028-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: GGPR 05S-19


title: Alzheimer's Disease CSF061

description:
EXR-JSAUG1UH2061-BS
total cell-free biofluid RNA


title: AD CSF UH3026

description:
EXR-JSAUG1UH3026-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: AD CSF UH3027

description:
EXR-JSAUG1UH3027-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: GGPR 01S-78

description: 01S-78-Visit 1


title: Healthy CSF UH3025

description:
EXR-JSAUG1UH3025-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: GGPR 08S-06


title: Healthy CSF UH3023

description:
EXR-JSAUG1UH3023-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: AD CSF UH3024

description:
EXR-JSAUG1UH3024-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: Alzheimer's Disease CSF059

description:
EXR-JSAUG1UH2059-BS
total cell-free biofluid RNA


title: GGPR 09S-01


title: AD CSF UH3020

description:
EXR-JSAUG1UH3020-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: Alzheimer's Disease CSF057

description:
EXR-JSAUG1UH2057-BS
total cell-free biofluid RNA


title: GGPR 16S-48


title: Healthy CSF UH3018

description:
EXR-JSAUG1UH3018-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: AD CSF UH3017

description:
EXR-JSAUG1UH3017-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: Healthy CSF UH3019

description:
EXR-JSAUG1UH3019-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: Alzheimer's Disease CSF055

description:
EXR-JSAUG1UH2055-BS
total cell-free biofluid RNA


title: Alzheimer's Disease CSF056

description:
EXR-JSAUG1UH2056-BS
total cell-free biofluid RNA


title: GGPR 06S-01


title: Healthy CSF UH3022

description:
EXR-JSAUG1UH3022-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: GGPR 16S-01


title: Alzheimer's Disease CSF060

description:
EXR-JSAUG1UH2060-BS
total cell-free biofluid RNA


title: Alzheimer's Disease CSF053

description:
EXR-JSAUG1UH2053-BS
total cell-free biofluid RNA


title: Alzheimer's Disease CSF054

description:
EXR-JSAUG1UH2054-BS
total cell-free biofluid RNA


title: GGPR 04S-07


title: Healthy CSF UH3015

description:
EXR-JSAUG1UH3015-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: Healthy CSF UH3016

description:
EXR-JSAUG1UH3016-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: GGPR 11S-17


title: Healthy CSF UH3012

description:
EXR-JSAUG1UH3012-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: Alzheimer's Disease CSF052

description:
EXR-JSAUG1UH2052-BS
total cell-free biofluid RNA


title: GGPR 02S-20


title: AD CSF UH3021

description:
EXR-JSAUG1UH3021-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: AD CSF UH3011

description:
EXR-JSAUG1UH3011-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: AD CSF UH3013

description:
EXR-JSAUG1UH3013-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: Healthy CSF UH3010

description:
EXR-JSAUG1UH3010-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: Alzheimer's Disease CSF050

description:
EXR-JSAUG1UH2050-BS
total cell-free biofluid RNA


title: Alzheimer's Disease CSF051

description:
EXR-JSAUG1UH2051-BS
total cell-free biofluid RNA


title: Healthy CSF UH3007

description:
EXR-JSAUG1UH3007-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: GGPR 14S-13


title: Healthy CSF UH3014

description:
EXR-JSAUG1UH3014-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: Healthy CSF UH3008

description:
EXR-JSAUG1UH3008-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: Alzheimer's Disease CSF049

description:
EXR-JSAUG1UH2049-BS
total cell-free biofluid RNA


title: GGPR 04S-34


title: Alzheimer's Disease CSF048

description:
EXR-JSAUG1UH2048-BS
total cell-free biofluid RNA


title: GGPR 16S-101


title: Healthy CSF UH3001

description:
EXR-JSAUG1UH3001-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: Healthy CSF UH3002

description:
EXR-JSAUG1UH3002-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: AD CSF UH3003

description:
EXR-JSAUG1UH3003-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: AD CSF UH3004

description:
EXR-JSAUG1UH3004-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: GGPR 04S-09


title: AD CSF UH3005

description:
EXR-JSAUG1UH3005-BS
total cell-free biofluid RNA
Assay Port: p1_4


title: AD CSF UH3006

description:
EXR-JSAUG1UH3006-BS
total cell-free biofluid RNA
Assay Port: p5_8


title: GGPR 04S-35


title: Alzheimer's Disease CSF047

description:
EXR-JSAUG1UH2047-BS
total cell-free biofluid RNA


title: GGPR 04S-05


title: GGPR 2S-03


title: wildtype_vehicle_4

city: Nagoya

first: Koji

last: Sakamoto

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

department: Respiratory medicine

institute: Nagoya University

description: lung fibroblast isolated from wt mouse, treated with vehicle for 48hr

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to the Agilent expression microarray according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Agilent Technologies G4900DA SG12494263

data_processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1

source_name: lung fibroblast, 48hr, 0ng/mL, replicate 4

label_protocol: labeled cRNA were prepared from 1~5 ug total RNA using the Agilent’s Quick Amp Labeling Kit

extract_protocol: Total RNA from cell lysates was isolated and purified with RNeasy Mini kit (Qiagen, Germany; Catalog 217004) according to a manufacture instruction. The yields and the quality of extracted RNA were assessed using the NanoDrop ND-1000 (Thermo Fischer Scientific, USA).

treatment_protocol: Primary lung fibroblasts were isolated from WT and meflin-KO mice by enzymatic digestion, and treated with recombinant TGF-β1 (rTGF-β, 5ng/ml, 48hr) (PeproTech Inc, USA).

tag: genotype

value: wild type C57BL/6J

value: vehicle

value: female

value: primary lung fibroblasts


title: AD CSF UH3009

description:
EXR-JSAUG1UH3009-BS
total cell-free biofluid RNA
Assay Port: p5_8

tag: age


title: Alzheimer's Disease CSF045

description:
EXR-JSAUG1UH2045-BS
total cell-free biofluid RNA

tag: tissue


title: Alzheimer's Disease CSF046

description:
EXR-JSAUG1UH2046-BS
total cell-free biofluid RNA


title: wildtype_vehicle_3

source_name: lung fibroblast, 48hr, 0ng/mL, replicate 3


title: wildtype_vehicle_2

source_name: lung fibroblast, 48hr, 0ng/mL, replicate 2


title: wildtype_vehicle_1

source_name: lung fibroblast, 48hr, 0ng/mL, replicate 1


title: Alzheimer's Disease CSF044

description:
EXR-JSAUG1UH2044-BS
total cell-free biofluid RNA


title: Alzheimer's Disease CSF043

description:
EXR-JSAUG1UH2043-BS
total cell-free biofluid RNA


title: GGPR 04S-04


title: GGPR 16S-75


title: Alzheimer's Disease CSF042

description:
EXR-JSAUG1UH2042-BS
total cell-free biofluid RNA


title: wildtype_TGFb_1

description: lung fibroblast isolated from wt mouse, treated with recombinant TGF-b (5ng/mL) for 48hr

source_name: lung fibroblast, 48hr, 5ng/mL, replicate 1

value: TGFb


title: wildtype_TGFb_2

source_name: lung fibroblast, 48hr, 5ng/mL, replicate 2


title: GGPR 16S-89


title: wildtype_TGFb_3

source_name: lung fibroblast, 48hr, 5ng/mL, replicate 3


title: Alzheimer's Disease CSF040

description:
EXR-JSAUG1UH2040-BS
total cell-free biofluid RNA


title: Alzheimer's Disease CSF041

description:
EXR-JSAUG1UH2041-BS
total cell-free biofluid RNA


title: male, testis, rep4

city: Hangzhou

first: Jindong

last: Ren

address: No.198, Shiqiao Road

institute: Zhejiang Academy of Agricultural Sciences

data_processing:
The libraries were sequenced on an Illumina Hiseq 4000 platform (Illumina, San Diego, CA, USA) and 150 bp paired-end reads were generated.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to M. rosenbergii transcriptome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.10.1)  with an adjusted P-value <0.05 found by DESeq were assigned  as differentially expressed.
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.
Assembly: No reference
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Macrobrachium rosenbergii

source_name: Testis

extract_protocol:
Each shrimp was put on ice 1 min for anesthetizing, firstly. After anesthetizing, samples of ovaries (Ov), testicles (Tt) and hepatopancreas (Hp) were collected separately and dissected. Each fresh sample was washed in phosphate-buffered saline (PBS; Gibco, Fisher Scientific, Waltham, MA, USA) and immediately frozen in liquid nitrogen. Total RNA was extracted from each sample using an RNeasy Plus Micro Kit (QIGEN Group, Germany)
Total RNA was used to generate sequencing libraries with varied index label using a NEBNextUltra™ Directional RNA Library Prep Kit for Illumina (New England BioLabs, Ipswich, MA, USA) according to the manufacturer’s instructions

value: Testis

tag: strain

value: male

tag: developmental stage

value: adult

tag: weight gain


title: male, testis, rep5

tag: Sex


title: GGPR 11S-22


title: Alzheimer's Disease CSF039

description:
EXR-JSAUG1UH2039-BS
total cell-free biofluid RNA

tag: diagnosis

tag: anatomical location

tag: sample collection method


title: male, testis, rep3


title: Alzheimer's Disease CSF038

description:
EXR-JSAUG1UH2038-BS
total cell-free biofluid RNA

tag: starting amount

tag: holding temperature


title: meflinKO_vehicle_4

description: lung fibroblast isolated from meflin-KO mouse, treated with vehicle for 48hr

value: Meflin knockout

tag: cell type


title: meflinKO_TGFb_4

description: lung fibroblast isolated from meflin-KO mouse, treated with recombinant TGF-b (5ng/mL) for 48hr

source_name: lung fibroblast, 48hr, 5ng/mL, replicate 4


title: meflinKO_TGFb_3


title: meflinKO_vehicle_1


title: meflinKO_vehicle_2


title: meflinKO_TGFb_2


title: meflinKO_vehicle_3


title: PR8_aCD3

city: OMAHA

first: Meng

last: Niu

state: NE

address: 42nd and Emile

department: Department of Neurological sciences

institute: University of Nebraska Medical Center

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: matrix files in h5 format

source_name: Bronchoalveolar

extract_protocol:
BALF were collected by making an incision in the trachea and lavaging the lung twice with 0.8 ml PBS, pH 7.4. Cells were washed and re-suspended in PBS and stained with a Viability Dye.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, immune cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Immune cells

value: Bronchoalveolar

value: 6-10 weeks old


title: PR8_WT

description: 10x Genomics


title: wildtype_TGFb_4


title: male, testis, rep2


title: meflinKO_TGFb_1


title: Alzheimer's Disease CSF037

description:
EXR-JSAUG1UH2037-BS
total cell-free biofluid RNA

value: Healthy Control

value: Structure of nervous tissue

value: Lumbar puncture


title: male, testis, rep1


title: CrAT12MLFD345

city: Baton Rouge

first: Krisztian

last: Stadler

state: LA

address: 6400 Perkins Rd

institute: Pennington Biomedical Research Center

data_processing:
Lexogen Quantseq pipeline V1.8.8 on the Bluebee platform, quality control, mapping, and read count tables
Annotation and preparation for analysis, R V3.4.3, Rstudio V1.1.423 and biomaRt V2.24.1
DESeq2  V1.18.1 differential gene expression
JMP Genomics V9 quality control, principal components, ANOVA, hierarchical clustering
Assembly: mouse- GRCm38.84
Supplementary files format and content: tab-delimited text containing DESeq2 normalized counts

source_name: kidney cortex

extract_protocol:
RNA was isolated by the TRIzol method.
Lexogen - QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina

tag: cre promoter

value: Ggt

tag: genotype/variation

value: Pt-CrAT

tag: time point

value: 12 months


title: Wt12MLFD327

value: fl/fl


title: Wt12MLFD326


title: Wt12MLFD368


title: CrAT12MLFD328


title: Alzheimer's Disease CSF036

description:
EXR-JSAUG1UH2036-BS
total cell-free biofluid RNA

source_name: Cerebrospinal fluid

value: Alzheimer's Disease

value: Male

value: Cerebrospinal fluid


title: male, hepatopancreas, rep4

source_name: Hepatopancreas

value: Hepatopancreas


title: male, hepatopancreas, rep5

value: male


title: Wt24Mchow165

value: 24 months


title: Wt24Mchow164


title: Alzheimer's Disease CSF035

description:
EXR-JSAUG1UH2035-BS
total cell-free biofluid RNA


title: Wt24Mchow154


title: Alzheimer's Disease CSF034

description:
EXR-JSAUG1UH2034-BS
total cell-free biofluid RNA


title: Wt24Mchow168


title: male, hepatopancreas, rep3

value: adult


title: Wt24Mchow145


title: Alzheimer's Disease CSF033

description:
EXR-JSAUG1UH2033-BS
total cell-free biofluid RNA


title: CrAT24Mchow146


title: CrAT24Mchow136


title: male, hepatopancreas, rep1


title: CrAT24Mchow124


title: CrAT24Mchow123


title: CrAT24Mchow135


title: female, ovary, rep5

source_name: Ovary

value: Ovary

value: female


title: Alzheimer's Disease CSF032

description:
EXR-JSAUG1UH2032-BS
total cell-free biofluid RNA

value: Female


title: CrAT12MLFD337


title: Alzheimer's Disease CSF030

description:
EXR-JSAUG1UH2030-BS
total cell-free biofluid RNA

value: Healthy Control


title: Alzheimer's Disease CSF031

description:
EXR-JSAUG1UH2031-BS
total cell-free biofluid RNA

value: Structure of nervous tissue


title: Wt15Mchow227

value: 15 months


title: female, ovary, rep4


title: Wt15Mchow225


title: Wt15Mchow205


title: CrAT15Mchow185

value: Ggt


title: female, ovary, rep2


title: Alzheimer's Disease CSF028

description:
EXR-JSAUG1UH2028-BS
total cell-free biofluid RNA

value: Lumbar puncture


title: CrAT15Mchow183

value: Pt-CrAT


title: Alzheimer's Disease CSF029

description:
EXR-JSAUG1UH2029-BS
total cell-free biofluid RNA


title: Csf2_flaA_rep2

city: philadelphia

first: Sunny

last: Shin

state: Pennsylvania

address: 3610 Hamilton Walk, Johnson Pavilion

department: Microbiology

institute: University of Pennsylvania

description: infected with Lp02∆flaA

data_processing:
Raw sequencing reads generated from Illumina were pseudo-aligned to mouse genome GRCm38 version 79 using Kallisto with 60 bootstraps and 250 bp expected read length per sample
Transcript abundance was summarized to gene-level using the tximport package in R programming language
Expression data was normalized using the VOOM function in the limma package.
Differentially expressed genes (fold change≥1.5 and false discovery rate ≤0.05) were identified by linear modeling and Bayesian statistics using the limma package.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include log2 counts per million (CPM) values for each Sample …

source_name: Csf2-/- BMDM

growth_protocol: The WT and Csf2-/- BMDMs were replated in 6-well TC plate with a density of 106 cells and incubated at 37°C overnight in a 5% CO2 incubator.

extract_protocol:
The cell plates were centrifuged 5 min at 300 g. The supernatants were aspirated out. The total RNA was isolated using RNeasy Mini Kit.
The RNA libraries were prepared using TruSeq Stranded mRNA Library Preparation Kit Set A (Illumina, RS-122-2101) according to the manufacturer’s instructions. All RNA samples were quantified on Agilent Tape Station for Quality Control before, during and after libraries preparation.

treatment_protocol: The BMDMs were infected with or without Lp02∆flaA strain (MOI=5) for 12 hours.

value: Bone marrow-derived macrophages

tag: agent


title: male, hepatopancreas, rep2


title: female, ovary, rep1


title: Alzheimer's Disease CSF027

description:
EXR-JSAUG1UH2027-BS
total cell-free biofluid RNA

value: Alzheimer's Disease


title: Csf2_flaA_rep3

description: infected with Lp02∆flaA

tag: genotype


title: Csf2_PBS_rep3

description: uninfected


title: Csf2_flaA_rep1

description: infected with Lp02∆flaA


title: female, hepatopancreas, rep5


title: Csf2_PBS_rep2

description: uninfected


title: female, hepatopancreas, rep4


title: Alzheimer's Disease CSF026

description:
EXR-JSAUG1UH2026-BS
total cell-free biofluid RNA

tag: age


title: Csf2_PBS_rep1

description: uninfected


title: Alzheimer's Disease CSF025

description:
EXR-JSAUG1UH2025-BS
total cell-free biofluid RNA

tag: tissue


title: Alzheimer's Disease CSF024

description:
EXR-JSAUG1UH2024-BS
total cell-free biofluid RNA


title: WT_flaA_rep2

description: infected with Lp02∆flaA

source_name: WT BMDM

tag: strain

value: wild type


title: CrAT15Mchow204


title: female, hepatopancreas, rep3

tag: developmental stage


title: WT_flaA_rep1

description: infected with Lp02∆flaA


title: WT_PBS_rep3

description: uninfected


title: WT_flaA_rep3

description: infected with Lp02∆flaA


title: female, ovary, rep3

tag: weight gain


title: WT_PBS_rep2

description: uninfected


title: WT_PBS_rep1

description: uninfected


title: Alzheimer's Disease CSF022

description:
EXR-JSAUG1UH2022-BS
total cell-free biofluid RNA

tag: Sex

value: Cerebrospinal fluid


title: Alzheimer's Disease CSF023

description:
EXR-JSAUG1UH2023-BS
total cell-free biofluid RNA

tag: diagnosis


title: female, hepatopancreas, rep1

value: Hepatopancreas