title: PBMC-BCR

description: 10x Genomics

data_processing:
PBMC-scRNA/scVDJ: Sequencing data were processed using the Cell Ranger 6.0.1 pipeline and aligned to GRCh38-1.1.0 reference genome to generate cell-by-gene count matrix (GEX) or filtered contig annotations (scVDJ).
BALF-scRNA: Sequencing data were processed using the Cell Ranger 6.0.1 pipeline and aligned to GRCh38-1.1.0 reference genome to generate cell-by-gene count matrix (scRNA).
PBMC-scATAC: Sequencing reads were processed through the Cell Ranger ATAC 1.1.0 pipeline and aligned to GRCh38-1.1.0 reference genome for mapping, de-duplication, and identification of Tn5 cut sites.
Assembly: GRCh38-1.1.0
Supplementary files format and content: filtered_contig_annotations.csv, consensus_annotations.csv
Supplementary files format and content: Tar archives include barcodes.tsv, features.tsv, matrix.mtx files.
Supplementary files format and content: fragments.tsv
Library strategy: scVDJ-seq

value: Peripheral blood

value: Peripheral blood mononuclear cells


title: Control_Male4

status: Public on Sep 07 2023

type: SRA

city: Montreal

first: Aurèle

last: Besse-Patin

address: 3801 University Street

country: Canada

institute: McGill University

library_source: transcriptomic

data_processing:
Filtering with Trimmomatic to remove adapter sequences, contamination, and low quality reads
Mapping using HISAT2
Counting using featureCounts
Differential expression analysis was done using DeSeq2
Assembly: mm10
Supplementary files format and content: excel sheet, differential expression analysis and data used in manscript graphs

molecule: polyA RNA

organism: Mus musculus

source_name: Liver

growth_protocol: Mice were maintained in a vivarium with controlled temperature and light cycles, and allowed access to food and water ad libitum.

extract_protocol:
RNA was extracted using Trizol-chloroform, followed by purification on RNA-binding column.
Library was prepared using PolyA selection followed by KAPA RNA Hyperprep protocol, using xGen Dual Index UMI Adapters (IDT).

treatment_protocol: MAPL-/- and MAPLwt/wt mice were fasted overnight and refed for 2 hours. Pieces of liver were snap frozen in liquid nitrogen.

tag: tissue

value: Liver

tag: genotype

value: wt/wt


title: VFY3

city: Tianjin

first: Yanjie

last: Lan

address: 288 Nanjing Road

country: China

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2with paremeters
Reads Per Kilobase of exon per Megebase of library size(RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acid Research, 2009. In short, exons from all isoforms
Assembly: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

molecule: total RNA

source_name: Bone marrow

extract_protocol:
RNA was extracted using TRIzol reagent. Illumina Truseq RNA Sample Prep kit was use with  1µg of total RNA  for the construction.
RNA libraries were prepared for sequencing using standard illumina protocols.

value: Bone marrow

tag: cell type

value: LSK

value: Vav1-Cre; Phf6fl-R274X/Y


title: Control_Male3


title: VFY2


title: PBMC-TCR

city: Shenzhen

first: Jiacheng

last: Zhong

address: Longmen north rd

institute: shenzhen people's hospital

description: 10x Genomics

organism: Homo sapiens

source_name: Peripheral blood

extract_protocol:
PBMC sample was collected from the patient and subjected to GEX/V(D)J-seq according to the manufacturer’s protocol.
For PBMC, single cell suspension was loaded into 10x Genomics Chromium system using Chromium Next GEM Single Cell 5' v1.1 to generate TCR/BCR libraries and 5' GEX libraries.

tag: diagnosis

value: Hyper-IgE syndrome (HIES)

tag: Sex

value: Male

tag: age

value: 18 years


title: BVC 5013 (5)

type: RNA

city: Leicester

first: Nicolas

last: Sylvius

address: University Road

department: CBS-Genetics

country: United Kingdom

institute: University of Leicester

hyb_protocol: Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C .  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted on a Promega Maxwell 16 robot using the Maxwell 16 LEV simplyRNA Cells Kit (Reference AS1270). RNA quality and quantity was assessed using the 2100 Bioanalyzer Instrument (Agilent)

treatment_protocol: Thirteen-week-old female VillinCreER/0/BrafV600E-LSL/+ mice received either 10 mg/kg atorvastatin by oral gavage or 5% DMSO/PBS vehicle control daily for 12 days.  A 20 mg/mL atorvastatin (Generon) stock in DMSO was freshly diluted to a 1 mg/mL working solution in PBS. Days 1-7 of the study were a daily pre-treatment period of atorvastatin/vehicle. Days 8-10 consisted of both atorvastatin/vehicle gavage and intraperitoneal tamoxifen injection to induce BrafV600E expression. On the final day of the study at 3-days post- BrafV600E induction, mice received intraperitoneal injections of 200 μL of 20 mM BrdU solution (Sigma) 3 hrs before tissue harvesting.

value: Intestinal tissue

tag: strain


title: STAR_4: Adult Heart

city: Matsumoto

first: Shin

last: Kadota

address: 3-1-1 Asahi

department: Regenerative Science and Medicine

country: Japan

institute: Shinshu University

data_processing:
NovaSeq 6000
Sequenced reads were trimmed by Trimmomatic (v0.39) with parameters of SLIDINGWINDOW:10:30. Only the reads derived from xenograft samples were separated human and rat reads using Xenome (v1.0.0). Reads classified as human were mapped to the hg38 reference with STAR (v2.7.2a) and gene count matrix was generated with featureCounts (v1.6.4).
Raw counts were normalized with transcripts per million (TPM) normalization.
Genome_build: hg38
Supplementary_files_format_and_content: featurecounts_1-4-13-18-19-21.txt is a raw counts file and tpm-normalized_counts_vivo3m.csv is a transcripts per million (TPM) normalized count file

source_name: Heart

growth_protocol: Undifferentiated human induced pluripotent stem cells reached 90% confluency, E8 medium was supplied with 1 uM of Wnt activator CHIR99201 (Sigma-Aldrich). The next day (day 0), E8 medium was changed to the cardiac differentiation medium (RPMI 1640 with B27 supplement minus insulin (Gibco) plus L-glutamine adding activin A (100 ng/mL, R&D) and Matrigel. On day1, bone morphologic protein 4 (BMP4; 10 ng/mL, R&D) and CHIR99201, followed by addition of Wnt inhibitor XAV939 (1 uM Sigma-Aldrich) on day 3-4. After day 7, medium was changed to RPMI 1640 with B27 supplement (Gibco) every other day. The cells were heat-shocked at 43ºC for 30 minutes and cryopreserved on day 28 or 56.

extract_protocol:
For sample 1-2, total RNA was isolated using the RNeasy Mini Kit (Qiagen), in accordance with the manufacturer’s protocol including DNase treatment.  For sample 5-8, rat hearts of each time points were collected and immediately embedded in an OCT-embedding compound and kept in -80℃. Tissues were sectioned at a thickness of 10 µm using a cryostat (Leica). The graft areas were captured using laser microdissection system (Leica) from unstained unfixed specimens attached on the membrane coated slides (Leica 11600289). Total RNA was extracted by Arcturus PicoPure RNA Isolation Kit (Thermo).
cDNA was synthesized by SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (TaKaRa). Library preparations were conducted using Nextera DNA Library Prep Kit

treatment_protocol: 2 x 10^7 human induced pluripotent stem cell-derived cardiomyocytes were directly injected to rat hearts (sample 5-8)

tag: cell line

value: Clontech 636532

value: Heart

tag: dev stage

value: adult heart


title: VCB 5473 (5)


title: VFY1


title: Control_Male2


title: STAR_3: Fetal Heart

value: Clontech 636583

value: fetal heart


title: VCB 5119 (5)


title: Control_Male1


title: FY13


title: VCB 5154 (5)

source_name: Cre control

value: Cre control


title: FY12


title: 10x scATAC-seq on the mouse liver (0d3236)

city: Leuven

first: Carmen

last: Bravo Gonzalez-Blas

address: Herestraat 49

country: Belgium

institute: VIB-KU Leuven Center for Brain & Disease Research

description:
Mouse_7_Fresh
Single-cell ATAC-seq (10X Genomics)

library_source: genomic single cell

data_processing:
The generated fastq files were processed with cellranger ATAC (v1.1.0) count function, with include introns=True option. Reads were aligned to Mus musculus reference genome (refdata-cellranger-atac-mm10-1.1.0).
10x scATAC-seq samples were processed with cisTopic,(v0.3.0) using the cells called by cellRanger (5,628 cells) and mm10 SCREEN regions (1,212,823 regions). For topic modelling, we used warpLDA with default parameters, using 500 iterations and inferring models with 2, 5, 10 to 30 (by a step of 1), 35, 40, 45 and 50. This resulted in a model with 19 topics. After correcting sample effects with harmony (v1.0, applied on the scaled topic distributions), we performed Leiden clustering with resolution 0.6, obtaining 11 clusters. The labelled 10x scATAC-seq and multiome cells (annotated based on the transcriptome labels) and the scATAC-seq fragments were used as input for pycisTopic (v1.0.1.dev75+g3d3b721). Briefly, we first created pseudobulks per cell type and performed peak calling using MACS2 (v2.2.7.1, with –format BEDPE –keep-dup all –shift 73 –ext_size 146 as parameters, as recommended for single-cell ATAC-seq data). To derive a set of consensus peaks, we used the iterative overlap peak merging procedure describe in Corces et al. (2018). This resulted in 486,888 regions. We further filtered the data set based on the scATAC-seq quality as well, keeping cells with at least 1,000 fragments, FRiP > 0.4 and TSS enrichment > 7, resulting in 22,600 high-quality cells.
Assembly: mm10
Supplementary files format and content: MLV__4aa2e0__Mouse_liver_ctrl_fragments.tsv.gz: Tab-separated text file containing chromosome, start, end, cell barcode and counts for each read for the mouse 6 sample.
Supplementary files format and content: MLV__0d3236__liver_fresh_07_07_2020_fragments.tsv.gz: Tab-separated text file containing chromosome, start, end, cell barcode and counts for each read for the mouse 6 sample.
Supplementary files format and content: scatac_counts.tsv.gz: Tab-separated flat text file containing regions as rows, cells as columns and fragment counts in each region for each cell as values.

molecule: genomic DNA

source_name: Liver (P56)

extract_protocol:
For scATAC-seq we used a modified protocol from the Nuclei Isolation for Single Cell ATAC Sequencing (CG000169) from 10x Genomics. In brief, 200 mg of fresh mouse liver tissue was minced and transferred to a Dounce homogenizer cylinder containing 1 mL of ice-cold homogenization buffer (10 mM NaCl, 10 mM Tris-HCl (pH 7.4), 3 mM MgCl2, 0.1% Tween-20, 0.1% IGEPAL CA-63, 0.01% Digitonin, 1% BSA) and incubated for 5 min on ice. Next the tissue was homogenized with 15 strokes of pestle A and 15 strokes of pestle B until a homogeneous nuclei suspension was achieved. The resulting homogenate was filtered through a 70-μm cell strainer (Corning). The tissue material was spun down at 500 x g for 5 min and the supernatant was discarded. The tissue pellet was resuspended in 1 mL wash buffer (20 mM NaCl, 20 mM Tris-HCl (pH 7.4), 6 mM MgCl2, 1% BSA). The wash step was repeated one more time and the resulting final pellet was resuspended in 100 µl Diluted Nuclei Buffer (10x Genomics scATAC kit). 9 μL of sample was mixed with 1 μL of arginine orange/propidium iodide (AO/PI) stain, loaded onto a LUNA-FL slide and visualized with the LUNA-FL Automated cell counter for nuclei yield, morphology, and presence of clumps/debris.
Single-nuclei libraries were generated using the 10x Chromium Single-Cell Instrument and Single Cell ATAC v1 kit (10x Genomics) according to the manufacturer’s protocol. In brief, the single mouse liver nuclei were incubated for 60 min at 37°C with a transposase that fragments the DNA in open regions of the chromatin and adds adapter sequences to the ends of the DNA fragments. After generation of nanolitre-scale gel bead-in-emulsions (GEMs), GEMs were incubated in a C1000 Touch Thermal Cycler (Bio-Rad) under the following program: 72°C for 5 min; 98°C for 3 s; 12 cycles of 98°C for 10 s, 59°C for 30 s, 72°C for 1 min; 72°C for 1 min; and hold at 4°C. Incubation of the GEMs produced 10x barcoded DNA from the transposed DNA. Next, single-cell droplets were dissolved, and the transposed DNA was isolated using Cleanup Mix containing Silane Dynabeads. Illumina P7 sequence and a sample index were added to the single-strand DNA during ATAC library construction via PCR: 98°C for 45 s; 9 cycles of 98°C for 20 s, 67°C for 30 s, 72°C for 20 s; 72°C for 1 min; and hold at 4°C. The sequencing-ready ATAC-seq library was cleaned up with SPRIselect beads (Beckman Coulter). Before sequencing, the fragment size of every library was analyzed using the Bioanalyzer high-sensitivity chip and were sequenced on NextSeq500 instruments (Illumina) with the following sequencing parameters: 50 bp read 1 – 8 bp index 1 (i7) – 16 bp index 2 (i5) - 49 bp read 2.

value: Liver (P56)


title: CFN12, Control participants, control sample, non-IBD mesenteric fat

status: Public on Sep 06 2023

city: Seoul

first: SoJung

last: Park

state: Songpa-gu

address: 88, Olympic-ro 43-gil

country: South Korea

institute: Ulsan medical university

data_processing:
The RNA sequencing reads were trimmed using Cutadapt (v.3.7) in paired-end mode (parameter- Quality : 20 minimum length : 20).
The filtered reads were mapped to the reference genome GRCH38 using STAR software v2.7.9a (parameter- default).
Quantification of the gene expression levels was performed using RNA-SeQC v2.1.2 (parameter- default).
Assembly: GRCH38
Supplementary files format and content: TPM_matrix.txt: Tab-delimited text file includes TPM values for each Sample.

source_name: Mesenteric fat

extract_protocol:
RNA was extracted using RNeasy Plus Mini Kit (Qiagen, Tokyo, Japan).
The sequencing libraries were prepared with the Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Globin (Illumina, San Diego, CA, United States).

value: Mesenteric fat

value: Female

tag: disease

value: Colon cancer


title: FY11

value: Bone marrow


title: CFN06, Control participants, control sample, non-IBD mesenteric fat


title: CFN01, Control participants, control sample, non-IBD mesenteric fat


title: 10x scATAC-seq on the mouse liver (4aa2e0)

description:
Mouse_6_Fresh
Single-cell ATAC-seq (10X Genomics)


title: CFN07, Control participants, control sample, non-IBD mesenteric fat


title: VCB 5475 (5)


title: CFN11, Control participants, control sample, non-IBD mesenteric fat


title: CFN09, Control participants, control sample, non-IBD mesenteric fat


title: CFN05, Control participants, control sample, non-IBD mesenteric fat


title: CFN04, Control participants, control sample, non-IBD mesenteric fat


title: VCB 5474 (5)


title: BVC 5012 (5)


title: CFN02, Control participants, control sample, non-IBD mesenteric fat


title: UC94, Control participants, control sample, UC mesenteric fat

value: Ulcerative colitis


title: FN82, CD participants, pair sample, CD mesenteric fat

value: Crohn's disease


title: STAR_2: Day56-CM

source_name: human induced pluripotent stem cell-derived cardiomyocyte

value: Cardiomyocytes

value: differentiation day 56


title: VCB 5120 (5)


title: FN77, CD participants, pair sample, CD mesenteric fat


title: UC100, Control participants, control sample, UC mesenteric fat


title: FN72, CD participants, pair sample, CD mesenteric fat

value: Male


title: VCB 5486 (5)

value: Intestinal tissue


title: FN69, CD participants, pair sample, CD mesenteric fat


title: FN71, CD participants, pair sample, CD mesenteric fat


title: FN74, CD participants, pair sample, CD mesenteric fat


title: STAR_1: Day28-CM

value: differentiation day 28


title: FN67, CD participants, pair sample, CD mesenteric fat


title: FN65, CD participants, pair sample, CD mesenteric fat


title: FN63, CD participants, pair sample, CD mesenteric fat


title: FN62, CD participants, pair sample, CD mesenteric fat


title: FN61, CD participants, pair sample, CD mesenteric fat


title: FN60, CD participants, pair sample, CD mesenteric fat


title: FN58, CD participants, pair sample, CD mesenteric fat


title: FN57, CD participants, pair sample, CD mesenteric fat


title: FN54, CD participants, pair sample, CD mesenteric fat


title: FN56, CD participants, pair sample, CD mesenteric fat


title: FN52, CD participants, pair sample, CD mesenteric fat


title: FN48, CD participants, pair sample, CD mesenteric fat


title: FN51, CD participants, pair sample, CD mesenteric fat


title: FN50, CD participants, pair sample, CD mesenteric fat


title: UC92, Control participants, control sample, UC mesenteric fat


title: FN45, CD participants, pair sample, CD mesenteric fat


title: FP72, CD participants, pair sample, Creeping fat


title: FN42, CD participants, pair sample, CD mesenteric fat


title: FP71, CD participants, pair sample, Creeping fat


title: FP77, CD participants, pair sample, Creeping fat


title: FN68, CD participants, pair sample, CD mesenteric fat


title: FP74, CD participants, pair sample, Creeping fat


title: FP82, CD participants, pair sample, Creeping fat


title: FP67, CD participants, pair sample, Creeping fat


title: FP69, CD participants, pair sample, Creeping fat


title: FP68, CD participants, pair sample, Creeping fat


title: FP63, CD participants, pair sample, Creeping fat


title: CFN03, Control participants, control sample, non-IBD mesenteric fat


title: FP65, CD participants, pair sample, Creeping fat


title: FP58, CD participants, pair sample, Creeping fat


title: FP60, CD participants, pair sample, Creeping fat


title: FP62, CD participants, pair sample, Creeping fat


title: FP61, CD participants, pair sample, Creeping fat


title: FP52, CD participants, pair sample, Creeping fat


title: FP54, CD participants, pair sample, Creeping fat


title: FP51, CD participants, pair sample, Creeping fat


title: FP50, CD participants, pair sample, Creeping fat


title: FP56, CD participants, pair sample, Creeping fat


title: FP57, CD participants, pair sample, Creeping fat


title: FP45, CD participants, pair sample, Creeping fat


title: FP48, CD participants, pair sample, Creeping fat


title: FP42, CD participants, pair sample, Creeping fat


title: healthy control [NOR5]

city: Shijiazhuang

first: Xiao

last: Bing

address: No.215, Heping West Road, Shijiazhuang, Hebei, China

institute: The Second Hospital of Hebei Medical University

data_processing:
The quality and quantity of RNA were determined on a Nanodrop ND-1000 spectrophotometer. Agilent 2100 Bioanalyzer was used to determine the quality of the sequencing library.
The Illumina HiSeq platform was applied to perform RNA sequencing. The original image data obtained by Illumina sequencing was converted into sequence data (FASTQ format) through Base Calling.
Trimmomatic software was used to preprocess the original data, including removal of adaptor, low quality reads and the low quality bases from the 3' end and 5' end in different ways.
The original sequencing volume, effective sequencing volume, Q30 and GC content were counted and comprehensively evaluated. After quality control, the high-quality sequence was compared with the specified reference genome (GRCh38) by hisat2.
Assembly: hg18
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: venous blood

extract_protocol:
Total RNAs were extracted from peripheral venous blood samples by using the Trizol reagent.
RNA libraries for RNA-seq were prepared using RNeasy Mini Kit. following manufacturer's protocols.

value: venous blood cells

value: venous blood

tag: bmi


title: CAE patient [CAE5]


title: healthy control [NOR2]


title: healthy control [NOR3]


title: healthy control [NOR4]


title: CAE patient [CAE2]


title: CAE patient [CAE3]


title: CAE patient [CAE4]


title: CARNMT1 KO rep 2

city: Hirakata

first: Rei

last: Yoshimoto

state: Osaka

address: 45-1 Nagaotoge-cho

department: Faculty of Agriculture

institute: Setsunan University

data_processing:
RNA-seq reads were aligned to the hg19 genome assembly using HISAT2
bedgraph files were generated using bedtools genomecov
Assembly: hg19
Supplementary files format and content: bedgraph

source_name: HEK293 cells

growth_protocol: HEK293  cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Wako) supplemented  with 10% fetal bovine serum (FBS).

extract_protocol:
Total RNAs were prepared with RNeasy Mini Kit (QIAGEN).
rRNA depletion was performed with NEBNext rRNA Depletion Kit v2 (NEB) The preparation of RNA libraries were performed using NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs).

value: HEK293 cells

value: CARNMT1 KO


title: Control biol rep 3

value: WT


title: CARNMT1 KO rep 1


title: CARNMT1 KO rep 3


title: Control biol rep 2


title: Control biol rep 1


title: Retina, 2W, Glaucoma, Male

city: Baltimore

first: Casey

last: Keuthan

address: 400 N Broadway, Smith Bldg, Rm 3001-N

country: USA

institute: Johns Hopkins University

data_processing:
FastQC was performed to assess sequence quality.
Sequence reads were aligned to GRCm38 using HISAT2 (v2.2.1) with default parameters.
Mapped reads were assembled into transcripts with StringTie (v1.3.0) using gene annotation from GRCm38 M25 from gencode. Expression from both reference and de novo transcripts were reported.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited file includes count matrix for genes for all Samples
Supplementary files format and content: Tab-delimited file includes count matrix for transcripts for all Samples
Supplementary files format and content: Tab-delimited files include assembled transcript structures and their estimated expression levels (FPKM/TPM and base coverage values) for each Sample

source_name: Retina

extract_protocol:
Total RNA from individual tissue samples was isolated using TRIzol® Reagent following the manufacturer's protocol. Purified RNA from sex replicates were pooled in equal amounts for the construction of sequencing libraries.
Pooled RNA samples were shipped to Genewiz where RNA libraries for RNA-seq were prepared using an ultra low-input library prep kit.

value: Retina

tag: time

value: 2 weeks

tag: treatment

value: Glaucoma


title: Retina, 3D, Glaucoma, Female

value: Female

value: 3 days


title: Retina, 6W, Glaucoma, Female

value: 6 weeks


title: Retina, 3D, Crush, Female

value: Crush


title: Retina, 0D, Naïve, Female

value: 0 days

value: Naïve


title: Retina, 6W, Glaucoma, Male

value: Male


title: Retina, 2W, Glaucoma, Female


title: Retina, 3D, Crush, Male


title: Retina, 2W, Crush, Male


title: Retina, 2W, Crush, Female


title: MON, 0D, Naïve, Male

source_name: MON

value: MON


title: healthy control [NOR1]


title: MON, 0D, Naïve, Female


title: CAE patient [CAE1]


title: MON, 6W, Glaucoma, Female


title: MON, 6W, Glaucoma, Male


title: MON, 3D, Crush, Male


title: MON, 3D, Glaucoma, Female


title: MON, 3D, Glaucoma, Male


title: MON, 2W, Glaucoma, Female


title: Retina, 3D, Glaucoma, Male


title: MON, 3D, Crush, Female


title: Retina, 0D, Naïve, Male


title: MON, 2W, Crush, Female


title: UON, 6W, Glaucoma, Male

source_name: UON

value: UON


title: MON, 2W, Crush, Male


title: UON, 0D, Naïve, Male


title: UON, 6W, Glaucoma, Female


title: UON, 3D, Glaucoma, Female


title: UON, 2W, Glaucoma, Male


title: UON, 3D, Glaucoma, Male


title: UON, 3D, Crush, Male


title: UON, 2W, Crush, Female


title: BALB/c Murine Liver CD45+CD3-CD19-Siglec-F-Ly6g- cells, DOL 14, RRV-treated, ADT

city: Chicago

first: Deborah

middle: R

last: Winter

state: IL

address: 240 E. Huron Street, M300

institute: Northwestern University

description: ADT 10x Genomics

library_source: other

data_processing:
CITE-seq libraries were processed using the 10X GenomicsCell Ranger pipeline versions 3.1.0 (healthy and BA) and 6.0.0 (BDL) with mm10 3.0.0 as reference genome.  ADT reads were assigned to proteins using the included ADT_reference.csv.
Assembly: mm10
Supplementary files format and content: Matrix files with all data (raw)
Supplementary files format and content: Matrix files after filtering for cells (filtered)
Library strategy: CITE-seq

molecule: protein

source_name: Whole Liver

extract_protocol:
On DOL 14 (healthy and BA) or 17 (BDL), whole liver tissue from 3 mice per experimental group was processed and pooled into a single-cell suspension. CD45+/CD3-/CD19-/Siglec-F-/Ly6g- immune cells were isolated by fluorescence-activated cell sorting (FACS)
CITE-seq libraries were prepared using the Single Cell 3’ v3 Reagent Kit on the 10x Genomics Chromium Controller.  Cellular mRNA and antibody-derived tag (ADT) oligos

treatment_protocol:
In the murine model of BDL, a midline incision was made to enter the peritoneal cavity and the common bile duct was exposed and separated from the adjacent portal vein and hepatic artery on BALB/c mice DOL 10.  An 8-0 nylon suture was used to tie two surgical knots and ligate the bile duct. The abdomen was then closed in two layers.  Sham surgery was performed on control mice at DOL 10 by creating an abdominal incision and closure without further manipulation.  All surgery was done using isoflurane inhalation for anesthesia, and efforts were made to minimize suffering.
In the murine model of BA, newborn BALB/c mice received intra-peritoneal injections of RRV at DOL 0 and developed sequelae of biliary obstruction by DOL 10-14.

value: female

value: Whole Liver

value: CD45+CD3-CD19-Siglec-F-Ly6g- cells

value: BALB/c

value: RRV injection DOL0


title: UON, 2W, Glaucoma, Female


title: BALB/c Murine Liver CD45+CD3-CD19-Siglec-F-Ly6g- cells, DOL 14, RRV-treated, scRNA

description: 3' 10x Genomics


title: UON, 2W, Crush, Male


title: UON, 3D, Crush, Female


title: BALB/c Murine Liver CD45+CD3-CD19-Siglec-F-Ly6g- cells, DOL14, No treatment,  ADT

description: ADT 10x Genomics


title: denervation gastrocnemius snATAC-seq  3

city: Houston

first: Zhaoyong

last: Hu

state: Texas

address: One Baylor Plaza

department: Nephrology

institute: Baylor college of medicine

description: 10x Genomics

data_processing:
Raw sequencing data were processed using Cell Ranger Single Cell Software Suite (v3.0.2) (10x Genomics). The Mus musculus genome reference (mm10) was used for reads alignment in accordance with 10x Genomics recommendations and all reads were mapped to the reference genome using STAR (Spliced Transcripts Alignment to a Reference) with default setting. The mapped reads with valid barcodes and unique molecular identifiers (UMIs) were used to generate the peak-barcode matrix.
Assembly: mm10
Supplementary files format and content: Matrix table with raw peak counts for every region and every nucleus

source_name: Gastrocnemius muscle

growth_protocol: Animals were maintained on standard chow diet, ad libitum, under a standard 12 hr light-dark cycle

extract_protocol:
We first prepared nuclei isolation media1 (NIM1: 320 mM sucrose, 25mM KCl, 5 mM MgCl2, and 10 mM Tris buffer, pH=8.0) and homogenization buffer [NIM1 buffer containing 1 µM DTT, 0.4 U/μL RNase Inhibitor (NEB Inc, Ipswich, MA), 0.20U/μL SUPERase-In RNase Inhibitor (Thermo Fisher scientific Inc, Waltham, MA), and 0.1% Triton X-100]. Then, Gas muscles (100~150mg) were minced on ice with a razor blade. Muscles were resuspended in 5 mL ice-cold homogenization buffer and homogenized with a dounce grinder for 12 strokes gently on ice. The homogenate was sequentially filtered through 70 mm and 40 mm cell strainers (pluriSelect, El Cajon,CA) and centrifuged (x1000g) for 5 minutes at 4°C to pellet the nuclei. The pellet was resuspended with 1 mL of ice-cold wash buffer (PBS containing 2% bovine serum albumin and 0.2U/μL ribonuclease inhibitor) and then filtered through the 20μm cell strainer before centrifugation (x500g) for 5 minutes at 4°C.  Following centrifugation, the pellet was resuspended in Nuclei Buffer (10 × Genomics, Chromium Single-Cell ATAC kit ) according to the manufacturer’s protocol.
6 snATAC-seq libraries were created with 10X Genomics Chromium Single Cell ATAC v1 chemistry following nuclear dissociation according to the manufacturer's protocol

treatment_protocol: Mice were anesthetized and the left sciatic nerve was removed for a 2-mm piece. Gastrocnemius (Gas) muscles were harvested 2 weeks after denervation. Gas muscles from left hind limb of normal mice served as controls.

value: Gastrocnemius muscle

value: male

value: sciatic denervation


title: BALB/c Murine Liver CD45+CD3-CD19-Siglec-F-Ly6g- cells, DOL14, No treatment, scRNA

description: 3' 10x Genomics


title: MON, 2W, Glaucoma, Male

value: 2 weeks

value: Glaucoma


title: normal gastrocnemius snATAC-seq  3

description: 10x Genomics

value: normal


title: normal gastrocnemius snATAC-seq  1

description: 10x Genomics


title: denervation gastrocnemius snATAC-seq  1

description: 10x Genomics


title: normal gastrocnemius snATAC-seq  2

description: 10x Genomics


title: UON, 0D, Naïve, Female

value: Female


title: 85-OS-sglacZ

city: Munich

first: Elvir

last: Becirovic

address: Butenandtstr. 5-13

department: Department of Pharmacy - Center for Drug Research

country: Germany

institute: LMU Munich

data_processing:
Total RNA was sent to a commercial provider (Genewiz Germany GmbH) to perform RNA sequencing and analysis.
Sequence reads were trimmed for adapter sequences and quality using Trimmomatic v.0.36 and mapped using the STAR aligner v.2.5.2b to the Mus musculus GRCm38 reference genome provided by ENSEMBL.
FeatureCounts from the Subread package v.1.5.2 was used to calculate unique gene hit counts; unique reads that fell outside of exon regions were excluded
The obtained gene hit counts were analyzed using DESeq2.
P-values and log2 fold changes were obtained using the Wald test.
Assembly: Mus musculus GRCm38 reference genome
Supplementary files format and content: comma-separated values file with raw gene counts for every gene and every sample
Supplementary files format and content: comma-separated values file with normalized gene counts for every gene and every sample

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using the Qiagen Rneasy Mini Kit. mRNA was enriched by poly(A) selection
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice heterozygous for the P23H mutation were subretinally injected at post natal day 21 with dual AAV encoding for Cas9-VPR and sgRNAs for either the knockout of Rhodopsin and transactivation of M-opsin (sgRho-3xsgOpn1mw, n = 3) or a control sgRNAs targeting the bacterial lacZ locus (sglacZ, n = 4). Retinas were isolated 4 weeks after subretinal injection.

value: retina

value: post natal day 49

value: sgLacZ


title: 70-OD-sglacZ


title: 1-OS-sglacZ


title: 45-OS-sgLacZ


title: 45-OD-sgRho-3xsgOpn1mw


title: 6-OS-sgRho-3xsgOpn1mw


title: Primary AT2_KOBLM3

first: Soo Yeon

last: Lee

address: yonsei-ro 50-1

institute: Yonsei university

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: Murine primary ATII cells

growth_protocol: The mice were housed in a specific pathogen-free animal facility, with a controlled temperature and humidity under conditions of a 12-h light/12-h dark cycle. To generate a conditional p300 null allele, LoxP sites were inserted into the flanking regions of the p300 gene on exon 9.

extract_protocol:
Mice were sacrificed, and the lungs were perfused and harvested. Dissociated lung cells were stained with CD74 and Ep-CAM antibodies. Primary ATII cells were sorted by using Flow cytometry.  Total RNA was isolated using Trizol reagent. Total RNA was isolated using Trizol reagent (Invitrogen). RNA quality was as sessed by Agilent 2100 bioanaly zer using the RNA 6000 Nano Chip and RNA quantification was performed using ND-2000 Spectrophotometer.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: Before administration of bleomycin, 8-week-old mice were injected with 10 mg/kg tamoxifen to delete p300 gene in ATII cells. Mice were intratracheally injected with PBS or 4 mg/kg bleomycin.

tag: p300 knockout

value: p300 knockout

value: Bleomycin


title: Primary AT2_KOBLM2


title: Primary AT2_KOBLM1


title: Primary AT2_KO2

value: PBS


title: Primary AT2_KO1


title: Primary AT2_BLM1

value: negative control


title: Primary AT2_BLM2


title: Primary AT2_KO3


title: Primary AT2_WT2


title: Primary AT2_WT1


title: denervation gastrocnemius snATAC-seq  2

description: 10x Genomics


title: endometrial biopsy, URS097

city: Parkville

first: Peter

last: Rogers

state: VIC

address: Level 7, University Department, Royal Women's Hospital, Crn Grattan Street and Flemington Rd

department: Department of Obstetrics and Gynaecology

country: Australia

institute: University of Melbourne

description: Sample URS097 from batch 2

data_processing:
Sequence reads were trimmed for adaptor sequences and low quality sequences using Trimmomatic v0.36.
Trimmed reads were aligned against the human reference genome (Ensembl GRCh38 release 84) using HISAT2 v2.0.5.
Transcript quantification was performed using StringTie v1.3.1 and the Ensembl Homo sapiens GRCh8 release 91 reference annotation.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited file containing raw gene counts for all samples.

source_name: Human endometrium

extract_protocol:
Total RNA was isolated from endometrial tissue using the Qiagen Allprep DNA/RNA Mini Kit according to the manufacturer's instructions.
Stranded RNA-seq libraries were prepared using the Illumina TruSeq Stranded Total RNA Gold protocol which includes ribosomal depletion.

value: Human endometrium

tag: cycle stage

tag: pod

tag: batch

value: batch 2


title: endometrial biopsy, URS077

description: Sample URS077 from batch 2

tag: tissue


title: endometrial biopsy, URS093

description: Sample URS093 from batch 2


title: endometrial biopsy, URS083

description: Sample URS083 from batch 2


title: 8-OD-sgRho-3xsgOpn1mw

tag: genotype


title: endometrial biopsy, URS076

description: Sample URS076 from batch 2


title: endometrial biopsy, URS078

description: Sample URS078 from batch 2


title: endometrial biopsy, URS075

description: Sample URS075 from batch 2


title: endometrial biopsy, URS070

description: Sample URS070 from batch 2


title: endometrial biopsy, URS056

description: Sample URS056 from batch 2


title: endometrial biopsy, URS068

description: Sample URS068 from batch 2


title: endometrial biopsy, URS066

description: Sample URS066 from batch 2


title: endometrial biopsy, URS057

description: Sample URS057 from batch 2


title: endometrial biopsy, URS062

description: Sample URS062 from batch 2


title: Primary AT2_BLM3


title: Primary AT2_WT3


title: endometrial biopsy, URS042

description: Sample URS042 from batch 2


title: endometrial biopsy, URS041

description: Sample URS041 from batch 2


title: endometrial biopsy, URS047

description: Sample URS047 from batch 2


title: endometrial biopsy, URS038

description: Sample URS038 from batch 2


title: endometrial biopsy, URS018

description: Sample URS018 from batch 2


title: endometrial biopsy, URS032

description: Sample URS032 from batch 2


title: endometrial biopsy, URS028

description: Sample URS028 from batch 2


title: endometrial biopsy, URS020

description: Sample URS020 from batch 2


title: endometrial biopsy, URS037

description: Sample URS037 from batch 2


title: endometrial biopsy, URS015

description: Sample URS015 from batch 2


title: endometrial biopsy, URS081

description: Sample URS081 from batch 2


title: endometrial biopsy, URS012

description: Sample URS012 from batch 2


title: endometrial biopsy, URS001

description: Sample URS001 from batch 2


title: endometrial biopsy, X210687

description: Sample X210687 from batch 3

value: batch 3


title: endometrial biopsy, URS072

description: Sample URS072 from batch 2


title: endometrial biopsy, X210685

description: Sample X210685 from batch 3


title: endometrial biopsy, X210686

description: Sample X210686 from batch 3


title: endometrial biopsy, URS054

description: Sample URS054 from batch 2


title: endometrial biopsy, X210684

description: Sample X210684 from batch 3


title: endometrial biopsy, URS003

description: Sample URS003 from batch 2


title: endometrial biopsy, X210679

description: Sample X210679 from batch 3


title: endometrial biopsy, X210676

description: Sample X210676 from batch 3


title: endometrial biopsy, X210674

description: Sample X210674 from batch 3


title: endometrial biopsy, X210678

description: Sample X210678 from batch 3


title: endometrial biopsy, X210665_2

description: Sample X210665_2 from batch 3


title: endometrial biopsy, X210673

description: Sample X210673 from batch 3


title: endometrial biopsy, X210663

description: Sample X210663 from batch 3


title: endometrial biopsy, X210665

description: Sample X210665 from batch 3


title: endometrial biopsy, URS026

description: Sample URS026 from batch 2


title: endometrial biopsy, X210662_2

description: Sample X210662_2 from batch 3


title: endometrial biopsy, X210662

description: Sample X210662 from batch 3


title: endometrial biopsy, X210659

description: Sample X210659 from batch 3


title: endometrial biopsy, X210654

description: Sample X210654 from batch 3


title: endometrial biopsy, X210650

description: Sample X210650 from batch 3


title: endometrial biopsy, X210648

description: Sample X210648 from batch 3


title: endometrial biopsy, X210648_2

description: Sample X210648_2 from batch 3


title: endometrial biopsy, X210644

description: Sample X210644 from batch 2


title: endometrial biopsy, X210643

description: Sample X210643 from batch 2


title: endometrial biopsy, X210645

description: Sample X210645 from batch 2


title: endometrial biopsy, X210641

description: Sample X210641 from batch 2


title: endometrial biopsy, X210637

description: Sample X210637 from batch 2


title: endometrial biopsy, X210681

description: Sample X210681 from batch 3


title: endometrial biopsy, X210642

description: Sample X210642 from batch 2


title: endometrial biopsy, X210638

description: Sample X210638 from batch 2


title: endometrial biopsy, X210636

description: Sample X210636 from batch 2


title: endometrial biopsy, X210626

description: Sample X210626 from batch 2


title: endometrial biopsy, X210632

description: Sample X210632 from batch 2


title: endometrial biopsy, X210634

description: Sample X210634 from batch 2


title: endometrial biopsy, X210627

description: Sample X210627 from batch 2


title: endometrial biopsy, X210625

description: Sample X210625 from batch 2


title: endometrial biopsy, X210635

description: Sample X210635 from batch 2


title: endometrial biopsy, X210624

description: Sample X210624 from batch 2


title: endometrial biopsy, X210633

description: Sample X210633 from batch 2


title: endometrial biopsy, X210622

description: Sample X210622 from batch 2


title: endometrial biopsy, X210623

description: Sample X210623 from batch 2


title: endometrial biopsy, X210617

description: Sample X210617 from batch 2


title: endometrial biopsy, X210616

description: Sample X210616 from batch 2


title: endometrial biopsy, X210608

description: Sample X210608 from batch 2


title: endometrial biopsy, X210612

description: Sample X210612 from batch 2


title: endometrial biopsy, X210602

description: Sample X210602 from batch 2


title: endometrial biopsy, X210599

description: Sample X210599 from batch 2


title: endometrial biopsy, X210652

description: Sample X210652 from batch 3


title: endometrial biopsy, X210588

description: Sample X210588 from batch 2


title: endometrial biopsy, X210589

description: Sample X210589 from batch 2


title: endometrial biopsy, X210593

description: Sample X210593 from batch 2


title: endometrial biopsy, X210582

description: Sample X210582 from batch 2


title: endometrial biopsy, X210590

description: Sample X210590 from batch 2


title: endometrial biopsy, X210598

description: Sample X210598 from batch 2


title: endometrial biopsy, X210581

description: Sample X210581 from batch 2


title: endometrial biopsy, X210575

description: Sample X210575 from batch 2


title: endometrial biopsy, X210573

description: Sample X210573 from batch 2


title: endometrial biopsy, X210569

description: Sample X210569 from batch 2


title: endometrial biopsy, X210574

description: Sample X210574 from batch 2


title: endometrial biopsy, X210567

description: Sample X210567 from batch 2


title: endometrial biopsy, X210562

description: Sample X210562 from batch 2


title: endometrial biopsy, X210561

description: Sample X210561 from batch 2


title: endometrial biopsy, X210557

description: Sample X210557 from batch 2


title: endometrial biopsy, X210562_2

description: Sample X210562_2 from batch 3


title: endometrial biopsy, X210552

description: Sample X210552 from batch 2


title: endometrial biopsy, X210566

description: Sample X210566 from batch 2


title: endometrial biopsy, X210563

description: Sample X210563 from batch 2


title: endometrial biopsy, X210555

description: Sample X210555 from batch 2


title: endometrial biopsy, X210550

description: Sample X210550 from batch 2


title: endometrial biopsy, X210560

description: Sample X210560 from batch 2


title: endometrial biopsy, X210554

description: Sample X210554 from batch 2


title: endometrial biopsy, X210547

description: Sample X210547 from batch 2


title: endometrial biopsy, X210544

description: Sample X210544 from batch 2


title: endometrial biopsy, X210610

description: Sample X210610 from batch 2


title: endometrial biopsy, X210540

description: Sample X210540 from batch 2


title: endometrial biopsy, X210546

description: Sample X210546 from batch 2


title: endometrial biopsy, X210549

description: Sample X210549 from batch 2


title: endometrial biopsy, X210537

description: Sample X210537 from batch 2


title: endometrial biopsy, X210533

description: Sample X210533 from batch 2


title: endometrial biopsy, X210538

description: Sample X210538 from batch 2


title: endometrial biopsy, X210527

description: Sample X210527 from batch 2


title: endometrial biopsy, X210530

description: Sample X210530 from batch 2


title: endometrial biopsy, X210534

description: Sample X210534 from batch 2


title: endometrial biopsy, X210524

description: Sample X210524 from batch 2


title: endometrial biopsy, X210522

description: Sample X210522 from batch 2


title: endometrial biopsy, X210525

description: Sample X210525 from batch 2


title: endometrial biopsy, X210516

description: Sample X210516 from batch 2


title: endometrial biopsy, X210512

description: Sample X210512 from batch 2


title: endometrial biopsy, X210510

description: Sample X210510 from batch 2


title: endometrial biopsy, X210507

description: Sample X210507 from batch 2


title: endometrial biopsy, X210543

description: Sample X210543 from batch 2


title: endometrial biopsy, X210505

description: Sample X210505 from batch 2


title: endometrial biopsy, X210504

description: Sample X210504 from batch 2


title: endometrial biopsy, X210501

description: Sample X210501 from batch 2


title: endometrial biopsy, X210496

description: Sample X210496 from batch 2


title: endometrial biopsy, X210506

description: Sample X210506 from batch 2


title: endometrial biopsy, X210511

description: Sample X210511 from batch 2


title: endometrial biopsy, X210494

description: Sample X210494 from batch 2


title: endometrial biopsy, X210492

description: Sample X210492 from batch 2


title: endometrial biopsy, X210491

description: Sample X210491 from batch 2


title: endometrial biopsy, X210487

description: Sample X210487 from batch 2


title: endometrial biopsy, X210499

description: Sample X210499 from batch 2


title: endometrial biopsy, X210495

description: Sample X210495 from batch 2


title: endometrial biopsy, X210532

description: Sample X210532 from batch 2


title: endometrial biopsy, X210475

description: Sample X210475 from batch 2


title: endometrial biopsy, X210536

description: Sample X210536 from batch 2


title: endometrial biopsy, X210473

description: Sample X210473 from batch 2


title: endometrial biopsy, X210526

description: Sample X210526 from batch 2


title: endometrial biopsy, X210474

description: Sample X210474 from batch 2


title: endometrial biopsy, X210468

description: Sample X210468 from batch 2


title: endometrial biopsy, X210464

description: Sample X210464 from batch 2


title: endometrial biopsy, X210470

description: Sample X210470 from batch 2


title: endometrial biopsy, X210456

description: Sample X210456 from batch 2


title: endometrial biopsy, X210447

description: Sample X210447 from batch 2


title: endometrial biopsy, X210444_2

description: Sample X210444_2 from batch 3


title: endometrial biopsy, X210435

description: Sample X210435 from batch 2


title: endometrial biopsy, X210444

description: Sample X210444 from batch 2


title: endometrial biopsy, X210434

description: Sample X210434 from batch 2


title: endometrial biopsy, X210432

description: Sample X210432 from batch 2


title: endometrial biopsy, X210431

description: Sample X210431 from batch 2


title: endometrial biopsy, X210428

description: Sample X210428 from batch 2


title: endometrial biopsy, X210427

description: Sample X210427 from batch 2


title: endometrial biopsy, X210424

description: Sample X210424 from batch 2


title: endometrial biopsy, X210416

description: Sample X210416 from batch 2


title: endometrial biopsy, X210423

description: Sample X210423 from batch 2


title: endometrial biopsy, X210415

description: Sample X210415 from batch 2


title: endometrial biopsy, X210414

description: Sample X210414 from batch 2


title: endometrial biopsy, X210421

description: Sample X210421 from batch 2


title: endometrial biopsy, X210420

description: Sample X210420 from batch 2


title: endometrial biopsy, X210417

description: Sample X210417 from batch 2


title: endometrial biopsy, X210399

description: Sample X210399 from batch 2


title: endometrial biopsy, X210400

description: Sample X210400 from batch 2


title: endometrial biopsy, X210395

description: Sample X210395 from batch 2


title: endometrial biopsy, X210462

description: Sample X210462 from batch 2


title: endometrial biopsy, X210394

description: Sample X210394 from batch 2


title: endometrial biopsy, X210396

description: Sample X210396 from batch 2


title: endometrial biopsy, X210397

description: Sample X210397 from batch 2


title: endometrial biopsy, X210388

description: Sample X210388 from batch 2


title: endometrial biopsy, X210382

description: Sample X210382 from batch 2


title: endometrial biopsy, X210382_2

description: Sample X210382_2 from batch 2


title: endometrial biopsy, X210450

description: Sample X210450 from batch 2


title: endometrial biopsy, X210381

description: Sample X210381 from batch 2


title: endometrial biopsy, X210393

description: Sample X210393 from batch 2


title: endometrial biopsy, X210376_2

description: Sample X210376_2 from batch 3


title: endometrial biopsy, X210376

description: Sample X210376 from batch 2


title: endometrial biopsy, X210369_2

description: Sample X210369_2 from batch 2


title: endometrial biopsy, X210367

description: Sample X210367 from batch 2


title: endometrial biopsy, X210365

description: Sample X210365 from batch 2


title: endometrial biopsy, X210370

description: Sample X210370 from batch 2


title: endometrial biopsy, X210369

description: Sample X210369 from batch 2


title: endometrial biopsy, X210341

description: Sample X210341 from batch 2


title: endometrial biopsy, X210345_2

description: Sample X210345_2 from batch 2


title: endometrial biopsy, X210360

description: Sample X210360 from batch 2


title: endometrial biopsy, X210323_2

description: Sample X210323_2 from batch 2


title: endometrial biopsy, X210323

description: Sample X210323 from batch 2


title: endometrial biopsy, X210345

description: Sample X210345 from batch 2


title: endometrial biopsy, X210335

description: Sample X210335 from batch 2


title: endometrial biopsy, X210331

description: Sample X210331 from batch 2


title: endometrial biopsy, X210322

description: Sample X210322 from batch 2


title: endometrial biopsy, X210311_2

description: Sample X210311_2 from batch 2


title: endometrial biopsy, X210309

description: Sample X210309 from batch 2


title: endometrial biopsy, X210320

description: Sample X210320 from batch 2


title: endometrial biopsy, X210304

description: Sample X210304 from batch 2


title: endometrial biopsy, X210294

description: Sample X210294 from batch 2


title: endometrial biopsy, X210312

description: Sample X210312 from batch 2


title: endometrial biopsy, X210287

description: Sample X210287 from batch 2


title: endometrial biopsy, X210298

description: Sample X210298 from batch 2


title: endometrial biopsy, X210281

description: Sample X210281 from batch 2


title: endometrial biopsy, X210303

description: Sample X210303 from batch 2


title: endometrial biopsy, X210375

description: Sample X210375 from batch 2


title: endometrial biopsy, X210380

description: Sample X210380 from batch 2


title: endometrial biopsy, X210274

description: Sample X210274 from batch 2


title: endometrial biopsy, X210262

description: Sample X210262 from batch 2


title: endometrial biopsy, X210269

description: Sample X210269 from batch 2


title: endometrial biopsy, X210258

description: Sample X210258 from batch 2


title: endometrial biopsy, X210251

description: Sample X210251 from batch 2


title: endometrial biopsy, X210329

description: Sample X210329 from batch 2


title: endometrial biopsy, X210252

description: Sample X210252 from batch 2


title: endometrial biopsy, X210256

description: Sample X210256 from batch 2


title: endometrial biopsy, X210246_2

description: Sample X210246_2 from batch 2


title: endometrial biopsy, X210246

description: Sample X210246 from batch 2


title: endometrial biopsy, X210241

description: Sample X210241 from batch 2


title: endometrial biopsy, X210321

description: Sample X210321 from batch 2


title: endometrial biopsy, X210240

description: Sample X210240 from batch 2


title: endometrial biopsy, X210221_2

description: Sample X210221_2 from batch 2


title: endometrial biopsy, X210226

description: Sample X210226 from batch 2


title: endometrial biopsy, X210209_2

description: Sample X210209_2 from batch 2


title: endometrial biopsy, X210210

description: Sample X210210 from batch 2


title: endometrial biopsy, X210204

description: Sample X210204 from batch 2


title: endometrial biopsy, X210202_2

description: Sample X210202_2 from batch 2


title: endometrial biopsy, X210194

description: Sample X210194 from batch 2


title: endometrial biopsy, X210189

description: Sample X210189 from batch 2


title: endometrial biopsy, X210202

description: Sample X210202 from batch 2


title: endometrial biopsy, X210166

description: Sample X210166 from batch 2


title: endometrial biopsy, X210181

description: Sample X210181 from batch 2


title: endometrial biopsy, X210164

description: Sample X210164 from batch 2


title: endometrial biopsy, X210170_2

description: Sample X210170_2 from batch 2


title: endometrial biopsy, X210165

description: Sample X210165 from batch 2


title: endometrial biopsy, X210163

description: Sample X210163 from batch 2


title: endometrial biopsy, X210244

description: Sample X210244 from batch 2


title: endometrial biopsy, X210141

description: Sample X210141 from batch 2


title: endometrial biopsy, X210152

description: Sample X210152 from batch 2


title: endometrial biopsy, X210149

description: Sample X210149 from batch 2


title: endometrial biopsy, X210161_2

description: Sample X210161_2 from batch 2


title: endometrial biopsy, X210140

description: Sample X210140 from batch 2


title: endometrial biopsy, X210161

description: Sample X210161 from batch 2


title: endometrial biopsy, X210156

description: Sample X210156 from batch 2


title: endometrial biopsy, X210228

description: Sample X210228 from batch 2


title: endometrial biopsy, X210125

description: Sample X210125 from batch 2


title: endometrial biopsy, X210131

description: Sample X210131 from batch 2


title: endometrial biopsy, X210125_2

description: Sample X210125_2 from batch 2


title: endometrial biopsy, X210120

description: Sample X210120 from batch 2


title: endometrial biopsy, X210213

description: Sample X210213 from batch 2


title: endometrial biopsy, X210105_2

description: Sample X210105_2 from batch 2


title: endometrial biopsy, X210102

description: Sample X210102 from batch 2


title: endometrial biopsy, X210105

description: Sample X210105 from batch 2


title: endometrial biopsy, X210099

description: Sample X210099 from batch 2


title: endometrial biopsy, X210096

description: Sample X210096 from batch 2


title: endometrial biopsy, X210091

description: Sample X210091 from batch 2


title: endometrial biopsy, X210075_2

description: Sample X210075_2 from batch 2


title: endometrial biopsy, X210061

description: Sample X210061 from batch 2


title: endometrial biopsy, X210055

description: Sample X210055 from batch 2


title: endometrial biopsy, X210083

description: Sample X210083 from batch 2


title: endometrial biopsy, X210041

description: Sample X210041 from batch 2


title: endometrial biopsy, X210047

description: Sample X210047 from batch 2


title: endometrial biopsy, X210070

description: Sample X210070 from batch 2


title: endometrial biopsy, X210018

description: Sample X210018 from batch 2


title: endometrial biopsy, X210013_2

description: Sample X210013_2 from batch 2


title: endometrial biopsy, X210046

description: Sample X210046 from batch 2


title: GRMut6

city: Sheffield

first: Vincent

middle: Trevor

last: Cunliffe

state: South Yorkshire

address: Western Bank

department: School of Biosciences

institute: University of Sheffield

data_processing:
FastQC software used for quality control (MultiQC for combining individual quality control files)
SortMeRNA version 2.1 (rRNA removal)
Sequence reads were trimmed for adaptor sequence/low-quality sequences using Trimmomatic version 3.9
Trimmed reads were used as an input for STAR alignment (Spliced Transcripts Alignment to a Reference)
Normalisation of the read counts and differential expression analysis was performed using DESeq2 R software
Assembly: Processed reads were aligned to danio rerio genome GRCz11
Supplementary files format and content: Tab-delimited text file for each individual sample: Normalised counts with DESeq2

organism: Danio rerio

source_name: Brain

extract_protocol:
Adult zebrafish brain were dissected (together with pituitary glands) and RNA was extracted via Qiagen RNeasy kit (dissolved in RNAse free water).
Library preparation step was performed with the input of 500ng total RNA (quality was checked on a 1% TAE agarose gel and with Agilent Bioanalyzer), following Illumina Ultra II Directiona RNA Lib Prep protocol (using NEBNext Ultra II RNA Kit). cDNA Library construction procedure included: mRNA inrichment by poly-dT pull down (NEBNext Poly(A) Kit) and 9 PCR cycles during cDNA library preparation with NEB adaptors. mRNA libraries were sequenced using a 375-390bp paired-end method.

value: Brain


title: GRMut5


title: GRMut1


title: GRMut4


title: GRMut3


title: WTTL7


title: GRMut2


title: WTTL5


title: WTTL3


title: WTTL2


title: WTTL4


title: pkr2-2;pkl-10 biol rep 2

city: Galway

first: Charles

last: Spillane

state: Galway

country: Ireland

institute: Plant and Agribioscience Centre

data_processing:
Low quality sequences with a PHRED Quality < 30 were removed using Fastp (Ver. 0.20.1).
Resulting high-quality RNA sequences were mapped to reference genome TAIR10.1 using TopHat (Ver. 2.1.1).
Cufflinks (Ver. 2.2.1.3.) was used to calculate gene relative expression using the Fragment per Kilobase per Million (FPKM) method and Differentially Expressed genes (DEGs) were determined using geometrical method and negative binomial method for dispersion estimation (Poisson law).
Assembly: TAIR10.1
Supplementary files format and content: Tab-delemited .txt files including cufflink output: RPKM and log2fold-change for each dataset comparison

organism: Arabidopsis thaliana

source_name: 4 DAP seeds

extract_protocol:
RNA was extracted from snap frozen seeds from at least 30 siliques per replicate collected at 3 DAP according to the protocol described by Allorent et al. (2010), with some modifications. In particular, seeds were homogenised in 2ml Eppendorf tubes using a plastic reusable pestle and mixed with 1 ml RNA extraction buffer as described by Oñate-Sánchez and Vicente-Carbajosa (2008). The protocol continued as described (Allorent et al. 2010). DNase treatment was performed on 1μg of crude RNA using the DNase I amplification grade kit (Invitrogen, UK), followed by clean-up and concentration for RNAseq using RNA clean and concentrator kit from Zymo Research (Cambridge Bioscience, UK). RNA integrity was assessed by agarose gel electrophoresis, and at least 400 ng of RNA per sample were used for mRNA sequencing (Novogene, Cambridge, UK).
mRNA was enriched using oligo(dT) beads, rRNA was removed using the Ribo-Zero kit. mRNA was fragmented randomly with a fragmentation buffer. cDNA was synthetized by using mRNA template and random hexamers primer, after which an illumina second strand synthesis kit was used with dNTPs, RNase H and DNA polymerase I. Finally, after a series of terminal repair, 3' A ligation followed by sequencing illumina adaptors ligation, the double stranded DNA library was completed through size selection and PCR enrichment.
RNAseq was performed with an Illumina Novaseq 6000 machine on two biological replicates per sample, 20 million reads depth and pair-end read.

treatment_protocol: Arabidopsis thaliana seeds were surface sterilized with Chlorine gas (3:1 bleach:Hydrochloric acid in a bell jar for one hour). Seeds were germinated on 0.5x Murashige and Skoog (MS) medium containing 1% w/v sucrose and 0.8% w/v agar, and grown in a Percival Tissue Culture cabinet under a 16:8 hr light: dark (21 °C/18 °C) regime until they were transferred to soil (five parts Westland compost [Dungannon, N. Ireland]: 1 part perlite: 1 part vermiculite). Plants were grown in chambers under fluorescent lamps at 200 μmol m-2 s-1 with the same photoperiod.

value: 4 DAP seeds


title: endometrial biopsy, X210052

description: Sample X210052 from batch 2


title: pkr2-2 biol rep 1


title: Col-0 biol rep 2

value: WT


title: pkr2-2 biol rep 2


title: pkl-1 biol rep 2


title: WTTL1


title: Col-0 biol rep 1


title: Seq_NC-3

city: Guiyang city

first: xianjun

last: chen

state: 贵州

address: 28 Guiyi Street, Yunyan District, Guiyang city, Guizhou Province, China

department: Critical care medicine

institute: Affiliated Hospital of Guizhou Medical University

data_processing:
Libraries were controlled for quality and quantified using the BioAnalyzer 2100 sys-tem (Agilent Technologies, Inc, USA).
Library sequencing was performed on an Illu-mina Novaseq instrument with 150bp paired end reads.
raw RNA sequencing da-ta required quality control (QC) on the raw reads.
The resulting clean data were aligned to the reference sequence and low-quality reads were discarded after QC.
Af-ter image recognition and base recognition, raw reads were harvested from Illumina NovaSeq 6000 sequencer. Q30 is used as the quality control standard, and Q30 > 80% indicates good sequencing quality.
Assembly: RN5
Supplementary files format and content: excel

organism: Rattus norvegicus

source_name: Rat ATII cells (RLE-6TN) LPS-injured  24h

growth_protocol: Rat ATII cells (RLE-6TN) were cultured in DMEM containing 10% fetal bovine serum (FBS) and 100 IU/mL penicillin-streptomycin in a humidified atmosphere of 5% CO2 and 95% air at 37 °C.

extract_protocol:
total RNA was used for removing the rRNAs with GenSeq® rRNA Removal Kit (Gen-Seq, Inc.). Then, the rRNA-depleted samples were subjected to library construction with GenSeq® Low Input RNA Library Prep Kit (GenSeq, Inc.) according to the manu-facturer’s instructions.
the rRNA-depleted samples were subjected to library construction with GenSeq® Low Input RNA Library Prep Kit (GenSeq, Inc.) according to the manufacturer’s instructions.

treatment_protocol: ATII cells was cultured either with LPS (LPS 5ug/ml, LPS group) or with normal saline (Control group) for 24 hours.

value: Lung

tag: cell type

value: alveolar type II cells

value: LPS- injured 24h


title: Seq_NC-2


title: Seq_NC-1


title: pkl-1 biol rep 1


title: endometrial biopsy, X210000

description: Sample X210000 from batch 2


title: NC-3

source_name: Rat ATII cells (RLE-6TN) normal saline  24h

value: normal saline  24h


title: endometrial biopsy, X210013

description: Sample X210013 from batch 2


title: retina, scRNA-seq

city: Shanghai

first: Li

last: Lin

address: No. 639 manufacturing bureau road, Huangpu District, Shanghai

institute: Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

library_source: transcriptomic single cell

data_processing:
The scRNA-seq data were aligned and quantified by using Cell Ranger(10X Genomics)
The preliminary counts were then used for downstream data analysis by Seurat (v4.1.0) including quality control filtering, data preprocessing, and data visualization.
The DoubletFinder (v2.0.3) was used for doublets finding.
Supplementary files format and content: Tab-separated values and matrix files

organism: Macaca fascicularis

source_name: retina

extract_protocol:
Anesthesia was carried out before operation and the body core temperature was monitored and maintained at the physical level. The eyelids are stretched and the muscles and blood vessels were separated carefully till the posterior part of the eyeball was exposed. The orbital segment of the ophthalmic artery encircles the optic nerve within the optic nerve sheath. Therefore, the optic nerve sheath was cut so as to exposed, isolated and ligated the ophthalmic artery with a tiny string clearly. One macaque was picked up randomly to do the ligation bilaterally. Sham-operated macaque underwent the same operation without ligation. After the ophthalmic artery occlusion and retina ischemia, the eyeballs of two macaques were separated completely. The fresh retina was isolated immediately under the operating microscope and stored in the sterile ice-cold sCelLiveTM Tissue Preservation Solution (Singleron) after the surgery within 30 mins.
Single-cell suspensions at the concentration of 1×105 cells/ml were loaded into microfluidic devices and scRNA-seq was processed through 10X Genomics Chromium platform. After lysing and being marked with specific barcode and UMI, RNA was released and reverse-transcribed into cDNA. Subsequently, the scRNA-seq libraries were constructed based on the processed cDNA.

value: retina

tag: condition

value: normal


title: ischemic retina, scRNA-seq

value: ischemic


title: NC-1


title: OE-6, 200 mM NaCl, 24h, Rep 2

city: Upton

first: Meng

last: Xie

state: NY

address: 50 Bell Ave

institute: Brookhaven National Laboratory

data_processing:
Raw data with adapter sequences or low-quality sequences was filtered using SOAPnuke (v 2.1.7) with parameters: "-n 0.001 -l 20 -q 0.4 --adaMR 0.25 --ada_trim --minReadLen  150"
Clean reads were mapped to TAIR11 using Bowtie2 (v 2.4.5) with default parameters
Transcripts were assembled and quantified using StringTie (v 2.1.7) with default parameters
DEGs were detected using DESeq2 (v 2.11.40.7) with default parameters
Assembly: TAIR11
Supplementary files format and content: tab-delimited tabular.txt files include raw counts for each sample

source_name: seedling

growth_protocol: 14-day-old plants growing hydroponically

extract_protocol:
Total RNAs were extracted using Spectrum Plant Total RNA kit (Sigma) following manufacturer's protocols.
mRNAs with poly A tail were enriched from total RNAs using oligo dT beads. mRNA molecules were fragmented into samll pieces. The fragmented mRNA was synthesized into first strand cDNA using random primers. The second strand cDNA was synthesized with dUTP instead of dTTP. The synthesized cDNA was subjected to end-repair and 3' adenylated. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments. Digest the U-labeled second-strand template with Uracil-DNA-Glycosylase (UDG) and perform PCR amplification. After quality control and circularization, libraries were amplified to make DNA nanoball for sequencing on DNBSEQ platform.

treatment_protocol: 200 mM NaCl treatment

value: seedling

value: atdgcr14l-1 35S:AtDGCR14L

value: 24h 200 mM NaCl


title: atdgcr14l-1, 200 mM NaCl, 24h, Rep 2


title: atdgcr14l-1, 200 mM NaCl, 24h, Rep 3


title: OE-6, 200 mM NaCl, 24h, Rep 1


title: OE-6, 200 mM NaCl, 24h, Rep 3


title: Col-0, 200 mM NaCl, 24h, Rep 2


title: Col-0, 200 mM NaCl, 24h, Rep 3


title: OE-6, 200 mM NaCl, 0h, Rep 3

value: 0h 200 mM NaCl


title: pkr2-2;pkl-10 biol rep 1


title: Col-0, 200 mM NaCl, 24h, Rep 1


title: OE-6, 200 mM NaCl, 0h, Rep 1


title: OE-6, 200 mM NaCl, 0h, Rep 2


title: atdgcr14l-1, 200 mM NaCl, 0h, Rep 3


title: atdgcr14l-1, 200 mM NaCl, 0h, Rep 2


title: Human meningioma, Frozen [QM99]

city: San Francisco

first: William

last: Chen

state: CA

address: 1450 3rd Street, HD 402

institute: UCSF

description: Nanostring nCounter

hyb_protocol: 200 ng of total RNA per sample was hybridized to barcoded reporter probes and biotin-conjugated capture probes from a custom codeset targeting genes of interest at 65C for 16 hours according to manufacturer instruction. Hybridization mixtures were washed and target/probe complexes were purified and bound to streptavidin coated cartridges.

scan_protocol: Cartridges were scanned on the nCounter Digital Analyzer with a FOV setting of 550

data_processing:
Samples here are unique meningiomas included in the study. Counts were positive control normalized using the spike-in positive control probes in the nSolver solftware, as per recommendations from the manufacturer (Nanostring).
Positive control normalized counts

source_name: Human meningioma, Frozen

extract_protocol: Total RNA was extracted from frozen or FFPE meningioma tumor samples using Qiagen AllPrep or Qiagen FFPE RNAeasy kits.

value: meningioma


title: Human meningioma, Frozen [QM98]

description: Nanostring nCounter

label_protocol: 200 ng of total RNA per sample was hybridized to barcoded reporter probes and biotin-conjugated capture probes from a custom codeset targeting genes of interest at 65C for 16 hours according to manufacturer instruction. Hybridization mixtures were washed and target/probe complexes were purified and bound to streptavidin coated cartridges.


title: Human meningioma, Frozen [QM96]

description: Nanostring nCounter


title: Col-0, 200 mM NaCl, 0h, Rep 2


title: NC-2


title: atdgcr14l-1, 200 mM NaCl, 0h, Rep 1


title: Col-0, 200 mM NaCl, 0h, Rep 1


title: Human meningioma, Frozen [QM93]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM92]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM95]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM94]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM91]

description: Nanostring nCounter


title: atdgcr14l-1, 200 mM NaCl, 24h, Rep 1


title: Human meningioma, Frozen [QM86]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM84]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM80]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM83]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM88]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM89]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM87]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM79]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM78]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM8]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM76]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM71]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM67]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM65]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM69]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM66]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM7]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM74]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM63]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM90]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM64]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM62]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM61]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM59]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM77]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM6]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM51]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM9]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM55]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM52]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM53]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM5]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM50]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM73]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM72]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM68]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM49]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM47]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM58]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM421]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM81]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM420]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM85]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM42]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM416]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM48]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM45]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM43]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM44]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM414]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM60]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM411]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM407]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM402]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM405]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM406]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM397]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM408]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM403]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM40]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM46]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM401]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM396]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM392]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM391]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM390]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM395]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM389]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM387]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM384]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM393]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM381]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM380]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM379]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM388]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM400]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM410]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM378]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM377]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM376]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM385]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM375]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM372]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM37]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM369]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM371]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM370]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM366]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM368]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM362]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM39]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM364]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM365]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM361]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM356]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM357]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM36]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM359]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM358]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM355]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM352]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM353]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM350]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM354]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM360]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM35]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM348]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM351]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM373]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM347]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM346]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM344]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM34]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM343]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM341]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM340]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM342]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM339]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM335]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM337]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM336]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM331]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM329]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM333]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM330]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM328]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM327]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM325]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM324]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM326]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM322]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM323]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM321]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM32]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM345]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM320]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM318]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM338]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM317]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM310]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM311]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM316]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM31]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM308]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM314]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM313]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM33]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM332]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM307]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM305]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM302]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM301]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM306]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM303]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM304]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM300]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM30]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM3]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM297]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM298]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM290]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM289]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM286]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM29]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM287]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM285]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM284]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM283]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM28]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM277]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM273]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM276]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM272]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM274]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM282]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM270]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM299]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM271]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM268]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM291]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM27]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM266]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM262]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM261]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM269]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM259]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM267]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM263]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM26]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM256]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM258]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM255]

description: Nanostring nCounter


title: Human meningioma, Frozen [QM257]

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