title: A06


title: Fish 3

status: Public on Feb 01 2023

type: SRA

city: Bodø

first: Pål

middle: A.

last: Olsvik

address: Universitetsalléen 11

department: Faculty of Biosciences and Aquaculture

country: Norway

institute: Nord University

library_source: transcriptomic

data_processing:
The library preparations were sequenced on an Illumina platform and 150 bp paired-end reads were generated.
Clean reads were obtained by removing adapter and poly-N sequences and reads with low quality from the raw data. Paired-end clean reads were mapped to the Atlantic salmon reference genome (https://salmobase.org) using HISAT2 software. The Cufflinks Reference Annotation Based Transcript (RABT) assembly method was used to assemble the set of transcript isoforms of each bam file obtained in the mapping step. HTSeq was used to calculate the number of mapped reads to each gene.
RPKM (reads per kilobase of transcript per million reads mapped) was calculated based on gene length and reads mapped to each gene. Differential expression between controls and exposed fish at day 8 and 14 was performed using DESeq2 R package.
Assembly: Atlanitc salmon genome deposited in Ensembl (2020 version).
Supplementary files format and content: Excel file with each line consisting of Salmo salar sequence name (Gene ID), readcount per sample, and annotation (top blast hits) are provided in the Excel file.

molecule: total RNA

organism: Salmo salar

source_name: Liver

extract_protocol:
Homogenization of liver tissue was conducted with a Precellys 24 homogenizer (Bertin Technologies, Montigny-le-Bretonneux, France). Total RNA was extracted and treated with DNase using the BioRobot EZ1 and RNA Tissue Mini Kit (Qiagen, Hilden, Germany). Characterization of total RNA was done with the Agilent 2100 Bioanalyzer using the 6000 Nano LabChip kit (Agilent Technologies, Palo Alto, CA, USA). The RNA integrity number (RIN), which is a measure of degradation in RNA samples, was 9.5 ± 0.2 (n=40) in liver (mean ± st.dev).
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions.

treatment_protocol: No specific treatment except sorting fish according to sampling day and exposure

tag: time point

value: day 8

tag: agent

value: Control

tag: body weight (g)

tag: length (cm)

tag: dose


title: eH3CF2MetO-4_S8

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

country: United Kingdom

institute: University of Oxford

data_processing:
Analysis of the data was performed using CGAT tools and pipelines (https://github.com/cgat-developers)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.1.0 with parameters --score-min L,0.0,-0.2
Genome_build: Hg38
Supplementary_files_format_and_content: comma-delimited text files of read counts for each sample

organism: Homo sapiens

source_name: HeLa

extract_protocol:
RNA from cells was harvested using Trizol reagent. Libraries were constructed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina®
RNA libraries were prepared for sequencing using standard NEB protocols

tag: modification

tag: repeat


title: eH3K18me3-2_S38


title: A04

type: RNA

city: Sengnam

first: Sohyun

last: Hwang

address: 59, Yatap-ro, Bundang-gu

department: Pathology

country: South Korea

institute: Cha University

hyb_protocol: The capture probeSet (2 μL) of the nCounter PanCancer Immune Profiling Panel was added after which the samples were placed in a 65℃ thermocycler (Bio-Rad Laboratories Inc., Hercules, California, USA) for 16 hours. The samples were transferred to the preparation station (NanoString Technologies) with prepared nCounter Master Kit and a cartridge. The preparation station runs for approximately 2.5 to 3 hours.

scan_protocol: The cartridges were transferred to the Digital Analyzer (NanoString Technologies) and were scanned on the Digital Analyzer at 555 fields of view.

data_processing: nSolverTM Analysis Software version 4.0 and NanoString QCPro version 1.14.0 were used to perform a quality check of the NanoString nCounter data. For data normalization for quantifying gene expression values, we used geNorm algorithm in nCounter Advanced Analysis version 2.0.115.

label: Nanostring

source_name: recurred glioblastoma multiforme tissue

label_protocol: The extracted RNAs were run on the NanoString nCounter Analysis System (NanoString Technologies, Inc., WA, USA) according to the manufacturer's instructions. Each RNA (5 μL, 100–300 ng) was mixed with 8 μL of Master Mix (reporter codeSet and hybridization buffer).

extract_protocol: For RNA extraction, 2-10 sections of 5 μm-thick formalin-fixed paraffin-embedded (FFPE) tissue were prepared after selection of one representative block which contained tumor and tumor microenvironment. The FFPE tissues were deparaffinized and homogenized using the Covaris Focused-ultrasonicator (Covaris, Mannheim, Germany). The truXTRAC FFPE total NA Ultra Kit (Covaris, Mannheim, Germany) was used for efficient and sequential extraction of RNA from FFPE tissue samples using Adaptive Focused Acoustics (AFA) according to manufacturer’s instructions.

tag: Sex

value: female

tag: age

tag: response

value: Non-responder

tag: survival


title: A05


title: Fish 2


title: eH3CF2MetO-3_S7


title: eH3K18me3-1_S37


title: SS-Grp-XIII-L07

city: Baltimore

first: Michael

middle: T

last: McCoy

state: Maryland

address: Molecular Neuropsychiatry Branch, 251 Bayview Blvd. Suite 200, 251 Bayview Blvd. Suite 200, 251 Bayview Blvd. Suite 200

country: USA

institute: NIDA

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Rattus norvegicus reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
After extraction of gene hit counts, the gene hit counts were added to the table
Assembly: Rattus norvegicus Rnor6.0

organism: Rattus norvegicus

source_name: Dorsal striatum

extract_protocol:
RNA was extracted using the protocol from RNeasy Mini Handbook (Qiagen)
RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA).  RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).  The sequencing libraries were clustered on two flowcell lanes. After clustering, the flowcells were loaded on the Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration.

treatment_protocol: Rats self-administered (SA) METH for 21 days followed by footshocks for 8 days. The drug-naïve control rats (CT) will be the same as the METH-trained rats except sterile saline is infused after the active lever press. The control animals for footshock also received saline but were yoked to the METH-trained rats that receive contingent shocks. There were separate groups of rats that were yoked (Y) to the corresponding METH shock-resistant (SR) and shock-sensitive (SS) rats. They are termed YSR and YSS, respectively. The animals were euthanized 2 hours the last day of SA, the hippocampal brain region was dissected, snap frozen on dry ice and then stored in the -70C freezer.

tag: strain

value: Sprague Dawley

tag: tissue

value: Dorsal striatum

value: adult

tag: genotype

value: wild type

tag: treatment

value: METH Shock Sensitive


title: eH3K18me3-4_S40


title: SS-GrpXIII-R03


title: A03


title: Fish 1


title: SS-GrpXIII-L05


title: eH3CF2MetO-2_S6


title: BaM_seq_BC16

city: Cambridge

first: Gene-Wei

last: Li

state: MA

address: 77 Massachusetts Ave.

department: Biology

institute: Massachusetts Institute of Technology

data_processing:
RNA sequencing reads were processed by removing poly(A) tails with cutadapt (options -a AAAAAAAAAAAAAAAAAAAA;min_overlap=10)
mapped using Bowtie (options -v 2 -k 1 --best)
Assembly: NC_000964.3, NC_000913.3
Supplementary files format and content: wig files generated using custom scripts

organism: Escherichia coli

source_name: bacteria

extract_protocol:
RNA was extracted and gDNA depleted using RNeasy Plus mini kit (Qiagen) following manufacturer’s instructions
Libraries were generated using custom BaM-seq protocol described herein.

tag: growth condition

value: LB


title: eH3CF2MetO2-4_S16


title: AB control 6h

city: Hamilton

first: Gary

last: Liu

state: ON

address: 1280 Main Street West

department: Institute for Infectious Disease Research

country: Canada

institute: McMaster University

description: Rep 1 and 2 were performed on adjacent wells, denoted in the raw file names. Forward and reverse reads are denoted by R1 and R2.

data_processing:
mRNA abundances were then quantified as transcripts per million using the kallisto (version 0.46.2) “quant” function, and the parameter “-b 100” with paired-end reads
Expression differences between abacin-treated samples and non-treated controls were quantified using the DESeq2 pipeline (version 1.34.0)
Assembly: NCBI CP053098.1 (A. baumannii ATCC 17978 chromosome), CP053099.1 (A. baumannii ATCC 17978 plasmid 1), and CP053100.1 (A. baumannii ATCC 17978 plasmid 2)
Supplementary files format and content: RNA-seq abundances: TPM
Supplementary files format and content: Differential expression analysis between 0x MIC and 5x MIC: log2 fold change, adjusted P-value

organism: Acinetobacter baumannii ATCC 17978

source_name: Clinical bacterial isolate

growth_protocol: A. baumannii ATCC 17978 was grown in 2 ml LB medium overnight at 37°C with shaking

extract_protocol:
After the required durations of incubation post-treatment, 2 ml samples were harvested and flash-frozen on liquid nitrogen. Extractions were performed on fresh frozen cell pellets using Qiagen Rneasy Plus Universal mini kit following manufacturer's instructions (Qiagen, Hilden, Germany).
rRNA depletion sequencing library was prepared by using QIAGEN FastSelect rRNA HMR Kit (Qiagen, Hilden, Germany). RNA sequencing library preparation uses NEBNext Ultra II RNA Library Preparation Kit for Illumina by following the manufacturer’s recommendations (NEB, Ipswich, MA, USA). Briefly, enriched RNAs are fragmented for 15 minutes at 94 °C. First strand and second strand cDNA are subsequently synthesized. cDNA fragments are end repaired and adenylated at 3’ends, and universal adapters are ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated using the Agilent Tapestation 4200 (Agilent Technologies, Palo Alto, CA, USA), and quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

treatment_protocol: Cells were diluted 1/10,000 into 50 ml fresh LB and grown to mid-log at 37°C with shaking, at which time cultures were supplemented with 5x MIC (10 µg/ml) abacin or no drug and grown for an additional 3 hr, 4.5 hr, or 6 hr

tag: cell type

value: Clinical bacterial isolate

value: No treatment, grown for an additional 6 hours post mid-log


title: BaM_seq_BC15


title: A02

value: male


title: SS-GrpXIII-L03


title: A01

value: Responder


title: eH3CF2MetO2-3_S15


title: SR-GrpXII-R07

value: METH Shock Resistant


title: Fish 4

tag: time point


title: AB control 4.5h

value: No treatment, grown for an additional 4.5 hours post mid-log


title: SS-GrpXII-L03


title: AB control 3h

value: No treatment, grown for an additional 3 hours post mid-log


title: BaM_seq_BC14


title: eH3CF2MetO2-2_S14


title: BaM_seq_BC13


title: eH3CF2MetO2-1_S13


title: SR-GrpXII-R05


title: eH3CF2MetO-1_S5


title: SR-GrpXII-L07


title: SR-GrpXII-L05


title: eH3CF2Met-4_S44


title: BaM_seq_BC11


title: eH3CF2Met-3_S43


title: AB Abaucin treated 6h

value: Treated by abaucin at mid-log at a concentration of 10 ug/ml and grown for an additional 6 hours


title: BaM_seq_BC10


title: AB Abaucin treated 4.5h

value: Treated by abaucin at mid-log at a concentration of 10 ug/ml and grown for an additional 4.5 hours


title: SR-GrpXIII-R07


title: SR-GrpXIII-R09


title: AB Abaucin treated 3h

value: Treated by abaucin at mid-log at a concentration of 10 ug/ml and grown for an additional 3 hours


title: BaM_seq_BC9


title: DF1501-2

city: tianjin

first: Defei

state: 天津

address: xiqidao 32

country: China

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with SOAPnuke.
The clean reads were mapped to the predicted transcripts for the M. thermophila ATCC 42464 genome (7) with < 2-base mismatching, using TopHat (v2.0.12)
Raw counts of reads that uniquely mapped to only one gene were calculated for each gene by HTSeq-count (v0.13.5) and used for normalizing transcript abundance (Reads Per Kilobase per Million mapped reads, RPKM)
Assembly: Myceliophthora thermophila ATCC 42464(https://genome.jgi.doe.gov/Spoth2/Spoth2.home.html)
Supplementary files format and content: tab-delimited text files including Reads count for each sample.

organism: Thermothelomyces thermophilus ATCC 42464

source_name: Myceliophthora thermophila ATCC 42464

growth_protocol: Strains were pre-grown in 50 mL shake flasks containing 50 mL1 × Vogel’s minimal medium (VMM) supplemented with 2% (w/v) glucose  at 45 °C and 150 rpm for 24 h. Then mycelia were filtered through a Whatman glass microfiber filter on a Buchner funnel and washed 3 times with VMM. The filtered mycelia were transferred into shake flasks containing 50 ml VMM with 1% (w/v) D-xylose and cultured for an additional 4 h. After that, mycelia for RNA isolation were harvested using vacuum filtration.

extract_protocol:
The mycelia of each strain were harvested by vacuum filtration and immediately homogenized in liquid nitrogen before extraction of total RNA with Trizol reagent (Invitrogen). Total RNA samples from each strain were purified with a Qiagen RNeasy Mini kit
RNA libraries were prepared for sequencing using standard DNBSEQ protocols

value: cell


title: eH3CF2Met-1_S41


title: SR-GrpXIII-L09

value: Sprague Dawley


title: DF1501-1


title: BaM_seq_BC7


title: BaM_seq_BC6


title: CT-Grp-XII-R11

value: Dorsal striatum

value: Control


title: H3.m6A: HeLa Wild-type HeLa m6A-IP rep 3

city: Chicago

first: Philip

middle: Cody

last: He

state: IL

address: 929 E 57th Street

institute: University of Chicago

description:
m6A-IP from m6A-seq
hela_m6a_peaks.bed

data_processing:
Library strategy: m6A-seq
For m6A-seq and RNA-seq: HISAT2 (version 2.1.0) was used to align the sequence reads to reference genome (hg38) with options -k 1 and --known-splicesite-infile generated by the hisat2_extract_splice_sites.py script with the UCSC hg38 GTF. samtools (version 1.7) was used to generate, sort and index bam files.
For MPm6A: Reads were mapped back to a reference genome containing the designed sequences with HISAT27 (version 2.1.0),  with option -k 1. Counts for each sequence were calculated with samtools (version 1.7) idxstats and sequences with at least 10 counts for all barcoded experimental and mutant sequences were retained.
For m6A-seq: The callPeakBinomial function and reportJointPeak from the MeRIPtools R package (version 0.1.0) was used to call m6A peaks with options min_counts = 15, peak_cutoff_fdr = 0.05, peak_cutoff_oddRatio = 1.5, and joint_threshold = 2.  RADAR R/Bioconductor package (version 0.2.1)8 was used to perform differential methylation analysis with options fragmentLength = 150, binSize =5 0, minCountsCutOff = 10, FDR cutoff = .1, log2FC cutoff = 1. Significantly differentially methylated regions were annotated to the RefSeq database (hg38). Bedgraph files for the forward and reverse strand were created using deeptools (version 3.1.3) bamCoverage with options --binSize 10, --normalizeUsing CPM, --exactScaling, --filterRNAstrand forward/reverse.
For RNA-seq: DESeq2 (version 1.18.1 ) was used to detect differentially expressed genes using a significance threshold of adjusted p-value <.05.12 To identify genes that have a significant change in response to EJC KD in WT vs. METTL3mut cells, the design formula ~ genotype + treatment + genotype:treatment was used.
Genome_build: hg38
Supplementary_files_format_and_content: bedgraph

growth_protocol: DMEM, high glucose, pyruvate (Gibco 11995040), 9.1% FBS, Penicillin Streptomycin (100 U/mL), 47C 5% CO2

extract_protocol:
Trizol extraction of RNA
For m6A-seq and RNA-seq: Illumina Stranded Truseq. MPm6A: Custom library construction as described in methods.

tag: cell line

value: HeLa

tag: input or ip

value: WT


title: DF1406-2


title: BaM_seq_BC12

value: LB


title: CT-GrpXIII-R12

value: adult

value: wild type


title: BaM_seq_BC5


title: H2.m6A: HeLa Wild-type HeLa m6A-IP rep 2

description:
m6A-IP from m6A-seq
hela_m6a_peaks.bed


title: DF1406-1


title: AB control 0h

value: Clinical bacterial isolate

value: No treatment, taken at mid-log


title: BaM_seq_BC4


title: CT-Grp-XIII-R11


title: DF1102-2


title: H1.m6A: HeLa Wild-type HeLa m6A-IP rep 1

description:
m6A-IP from m6A-seq
hela_m6a_peaks.bed


title: BaM_seq_BC3


title: DF1102-1


title: eH3CF2Met-2_S42


title: JG207-2


title: BaM_seq_BC1


title: H2.IN: HeLa Wild-type HeLa input rep 2

description:
input for m6A-seq
hela_m6a_peaks.bed

value: input


title: H1.IN: HeLa Wild-type HeLa input rep 1

description:
input for m6A-seq
hela_m6a_peaks.bed


title: CT-GrpXIII-L12


title: CT-GrpXIII-L11


title: CT-GrpXIII-R06


title: CT-GrpXIII-R05


title: H3.IN: HeLa Wild-type HeLa input rep 3

description:
input for m6A-seq
hela_m6a_peaks.bed


title: BaM_seq_BC2


title: JG207-1


title: BT95-SPS

status: Public on Jan 31 2023

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

scan_protocol: After hybridization, excess probes are washed away using a two step magnetic bead- based puri cation on the nCounter Prep Station. Magnetic beads derivatized with short nucleic acid sequences that are complementary to the Capture Probe and the Reporter Probes are used sequentially. First, the hybridization mixture containing target/probe complexes is allowed to bind to magnetic beads complementary to sequences on the Capture Probe. Wash steps are performed to remove excess Reporter Probes and non-target cellular transcripts. After washing, the Capture Probes and target/probe complexes are eluted o the beads and are hybridized to magnetic beads complementary to sequences on the Reporter Probe. An additional wash is performed to remove excess Capture Probes. Finally, the puried target/probe complexes are eluted o the beads and immobilized on the cartridge for data collection. After hybridization, excess probes are washed away using a two step magnetic bead- based puri cation on the nCounter Prep Station. Magnetic beads derivatized with short nucleic acid sequences that are complementary to the Capture Probe and the Reporter Probes are used sequentially. First, the hybridization mixture containing target/probe complexes is allowed to bind to magnetic beads complementary to sequences on the Capture Probe. Wash steps are performed to remove excess Reporter Probes and non-target cellular transcripts. After washing, the Capture Probes and target/probe complexes are eluted o the beads and are hybridized to magnetic beads complementary to sequences on the Reporter Probe. An additional wash is performed to remove excess Capture Probes. Finally, the purified target/probe complexes are eluted out the beads and immobilized on the cartridge for data collection.

data_processing: The raw code counts were normalized by the trimmed mean of M-values normalization method (TMM).

source_name: Breast carcinoma

extract_protocol: Total RNA was extracted from the formalin-fixed paraffin-embedded (FFPE) specimens of primary tumors by using Qiagen’s miRNeasy FFPE Kit (Qiagen, Valencia, CA, USA).

tag: sample

value: SPS


title: BT95-NST

value: NST


title: BT100-NST


title: BT95-MAT

value: MAT


title: BT100-MAT


title: BT91-SPS


title: BT91-NST


title: BT137-MUC

value: MUC


title: BT137-NST


title: BT3-SQC

value: SQC


title: BT3-NST


title: BT64-NST


title: BT61-SPS


title: BT127-SPS


title: BT64-MAT


title: BT118-NST


title: BT118-SPS


title: BT118-MAT


title: BT131-SQC


title: BT122-NST


title: BT122-SPS


title: BT137-RHA

value: RHA


title: BT130-NST


title: BT127-SQC


title: BT127-NST


title: BT118-OGS

value: OGS


title: BT131-NST


title: BT130-MAT


title: BT61-NST


title: BT85-NST


title: BT85-MAT


title: BT79-NST


title: BT83-SQC


title: BT83-NST


title: BT71-MAT


title: BT71-NST


title: BT57-NST


title: BT57-RHA


title: BT46-SPS


title: BT69-NST


title: BT46-NST


title: BT65-SPS


title: BT69-RHA


title: BT65-NST


title: BT44-MAT


title: BT44-NST


title: BT42-NST


title: BT42-SPS


title: BT34-SPS


title: BT79-RHA


title: BT6-MAT


title: BT23-RHA


title: BT23-NST


title: BT15-NST


title: BT15-RHA


title: BT15-SPS


title: BT5-NST


title: BT5-SPS


title: BT34-NST


title: BT6-NST


title: Donor 6 - TPA + RGRN-305

city: Aarhus

first: Hakim

last: Ben Abdallah

state: Denmark

address: Palle Juul-Jensens Boulevard 45

department: Dermatology and Venerology

country: Denmark

institute: Aarhus University Hospital

description: Treated with TPA + RGRN-305

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Raw data were normalized using nSOLVER 4.0 by performing  background subtraction (geom. mean of neg. CTRLs excluding neg. probes NEG_G and _H), positive control normalization (geom. mean of pos. CTRLs besides POS_F), and normalization to housekeeping genes (EEF1G, GAPDH, GUSB, OAZ1, and RPL19)

source_name: Healthy tissue

label_protocol: not provided

extract_protocol: 100 ng of total RNA from keratinocytes was hybridized for 19.5 hours with probes from the nCounter Human Immunology V2 Panel  (579 target genes and 15 reference genes). nCounter SPRINT profiler were used according to the manufacturer’s instructions.

tag: subject

value: Donor 6

value: Healthy tissue

value: TPA + RGRN-305


title: Donor 6 - TPA

description: Treated with TPA

value: TPA


title: Donor 5 - TPA

description: Treated with TPA

value: Donor 5


title: Donor 5 - TPA + RGRN-305

description: Treated with TPA + RGRN-305


title: Donor 5 - Vehicle

description: Treated with Vehicle

value: Vehicle


title: Donor 6 - Vehicle

description: Treated with Vehicle


title: Donor 5 - RGRN-305

description: Treated with RGRN-305


title: Donor 4 - TPA + RGRN-305

description: Treated with TPA + RGRN-305

value: Donor 4


title: Donor 4 - TPA

description: Treated with TPA


title: Donor 4 - RGRN-305

description: Treated with RGRN-305


title: Donor 3 - TPA + RGRN-305

description: Treated with TPA + RGRN-305

value: Donor 3


title: Donor 4 - Vehicle

description: Treated with Vehicle


title: Donor 6 - RGRN-305

description: Treated with RGRN-305


title: Donor 3 - RGRN-305

description: Treated with RGRN-305


title: Donor 3 - TPA

description: Treated with TPA


title: Donor 1 - TPA

description: Treated with TPA

value: Donor 1


title: Donor 1 - RGRN-305

description: Treated with RGRN-305


title: Donor 1 - TPA + RGRN-305

description: Treated with TPA + RGRN-305


title: Donor 2 - TPA

description: Treated with TPA

value: Donor 2


title: Sample18_Donor43

city: New York

first: Vilas

last: Menon

state: NY

department: Neurology

institute: Columbia University Medical Center

data_processing:
fastq files were run through 10x Genomics Spaceranger v2.0.0
output bam files from spaceranger were processed using BAMboozle for anonymization
Assembly: hg38
Supplementary files format and content: Counts tables for all spot barcodes in standard hdf5 output from Spaceranger, along with the tissue position list for each spot (csv format) and a high resolution image of the tissue section on the slide

molecule: polyA RNA

source_name: Lumbar spinal cord

extract_protocol:
Frozen human tissue sections were processed on 10x Genomics Visium slides, as described in the publication. (Yadav, Matson, et al. 2023)
10x Genomics Visium chemistry

value: Lumbar spinal cord (L3/L4)


title: Sample19_Donor47

value: Lumbar spinal cord (L5/S1)


title: Donor 1 - Vehicle

description: Treated with Vehicle


title: Sample20_Donor47


title: Donor 2 - Vehicle

description: Treated with Vehicle


title: peripheral blood exosomes, ISS_1

city: Nanchang

first: xijuan

last: liu

state: Jiangxi

address: No. 1 Minde Road

institute: The Second Affiliated Hospital of Nanchang University

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 12.0 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: ISS, peripheral blood exosomes

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free Dnase.

treatment_protocol: All specimens were obtained from patients who received anterior cervical discectomy and fusion. Cartilage endplate in cervical disc were collected , about 1×1×0.2cm3 size, and preserved in 600μl RNA Stabilization Solution (Cat#AM7020, Ambion, Austin, TX, US)under -80℃.

tag: condition

value: idiopathic short stature (ISS)

value: peripheral blood exosomes


title: Donor 3 - Vehicle

description: Treated with Vehicle


title: peripheral blood exosomes, NC_2

source_name: NC, peripheral blood exosomes

value: control


title: peripheral blood exosomes, NC_3


title: peripheral blood exosomes, NC_1


title: Donor 2 - TPA + RGRN-305

description: Treated with TPA + RGRN-305


title: Sample9_Donor43


title: Sample16_Donor45


title: Sample15_Donor45


title: Sample12_Donor47


title: Sample13_Donor45


title: Sample11_Donor47


title: Sample14_Donor45


title: peripheral blood exosomes, ISS_3


title: Sample17_Donor43


title: peripheral blood exosomes, ISS_2


title: Sample8_Donor47


title: Sample7_Donor47


title: Sample6_Donor43


title: Sample5_Donor43


title: Sample3_Donor19


title: Sample2_Donor19


title: Sample4_Donor19


title: Donor5

data_processing:
fastq files were run through 10x Genomics Cellranger v3.0.2
output bam files from cellranger were processed using BAMboozle for anonymization
Genome_build: hg38
Supplementary_files_format_and_content: Counts tables for all barcodes in standard hdf5 output from Cellranger

extract_protocol:
Nuclei were isolated from frozen human tissue using a triton-based protocol, as described in the publication. (Yadav, Matson, et al. 2022)
10x Genomics Chromium 3' v3 chemistry

tag: subject id

value: Lumbar spinal cord


title: Sample1_Donor19


title: Donor4


title: Donor7


title: Donor3


title: Donor1


title: Donor2


title: Donor6


title: Mouse, brains, cell-ValbB8w1182

city: Beijing

first: Menghan

address: Yiheyuan Road

institute: Peking University

library_source: genomic

data_processing:
For in silico isolation of RNA from DNA reads, we used Cutadapt (version 3.5) to identify  and extract RNA reads which contained a specific sequence  (GGTTGAGGTAGTATTGCGCAATG) within the GAT5-RT primer from the 5-prime end of  5 Read 2. The RNA reads and DNA reads were then processed separately as two files.
We preprocessed Hi-C part of HiRES data as previously described with custom scripts. Briefly, reads were mapped to the GRCm38 reference genome with BWA-mem2 in “5SP” mode. Contacts and 3D genome structures were generated with Hickit software using default parameters. To remove potential contamination from RNA reads, we cleaned contacts between 10 two exons from the same transcript, which counted for ~0.04% of all contacts. For quality control of reconstructed 3D genome structures, five replicates were generated with random seeds, and median RMSD for each combination of 3 replicates was calculated. The first replicate in the combination with the minimum median RMSD value (if < 1.5) were used for downstream analysis. 3D proximity and 3D distance maps were generated as previously descried with custom codes.
For RNA data, we first removed reads containing no poly-A sequence following GAT5-RT primer sequence. We then aligned Read 1 to the GRCm38 reference genome using STAR. Duplications were removed based on UMIs with UMI-tools. RNA count matrix was generated by FeatureCounts with parameters “-O -M --fraction”. We used RNAsnpSplit for phasing of  allele-specific RNA counts.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: genomic DNA

organism: Mus musculus

source_name: Brains

extract_protocol:
All animal maintenance and experimental procedures were carried out in accordance with the guidelines of the Institutional Animal Care and Use Committee (IACUC) of Peking University. Cast/Eij male and C57BL/6J female mice were purchased from Jackson Laboratory and raised under 12h brightness and 12h darkness. 8-week-old mice were naturally mated and females were transferred on the next morning (considered as E0.5). Post-implantation embryos were collected in PBS containing 10%FBS between E7.0 and E11.5. For brain tissues, left cortex was dissected from 8 to 9-week-old F1 hybrid mice in ice-cold PBS.
Mouse Embryos. For E7.0 - E8.5 embryos, all embryos from one mouse were collected and dissociated in 100 μL TrypLE™ Express (Gibco 12604013) for 5 min. For E9.5 - E11.5 embryos, one or two embryos from one mouse were collected and dissociated in 200 μL TrypLE™ Express for 10 min. TrypLE™ Express was inactivated by adding 5-fold volume of  PBS. The cell suspension was then filtered with a 40 μm cell strainer (Falcon 352340) and centrifuged at 100 g fro 5 min at 4 C. The pellet was washed once with 500 μL PBS and the cell number was adjusted to ~100 k in 200 μL PBS.
Mouse Brains. Cortex was dissected in ice-cold PBS and transferred to a 1 mL Dounce homogenizer (Wheaton 357538) containing 1mL ice-cold Homogenization Buffer (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM HEPES pH 8.0, 1 μM DTT, 0.1% Igepal CA 630) with 10 μL Recombinant RNase Inhibitor (TaKaRa 2313B), 10 μL SUPERaseIn (Invitrogen AM2694) and 100 μL protease inhibitor (Sigma P8340). Dissected tissues were homogenized with five strokes of the loose pestle, followed by 15 strokes of the tight pestle. The homogenate was filtered through a 40 μm cell strainer and centrifuged at 300 g for 5 min at 4 C. The pellet was washed in 500 μL Nuclei Storage Buffer (166.5 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM HEPES pH 8.0) with 5 μL Recombinant RNase Inhibitor and 50 μL protease inhibitor and centrifuged at 300 g for 5 min at 4 °C. The pellet was resuspended with 500 μL of Nuclei Storage Buffer to estimate the number of intact nuclei. Then the number of nuclei was adjusted to ~250 k in 500 μL Nuclei Storage Buffer.
The single-cell preamplification product was diluted for 15 folds and 2 μL of each diluted sample was transposed by the addition of 3 μL Transposition Mixture (1 μL 5 X TTBL, 0.25 μL TTE Mix V50 (Vayme TD501), 1.75 μL water) and incubated at 55 °C for 10 min. Transposition was stopped by adding 1.25 μL 0.2% SDS and then the plate 40 was incubated at room temperature for 10 min. For a slight enrichment of cDNA reads, 2 μL 5 μM i5 unique dual (UD) index and 11.75 ul PCR mixture (4 μL 5X KAPA HiFi GC Buffer, 0.6 μL 10 mM dNTP, 0.2 μL 50 μM RNA-P7 primer, 0.4 μL KAPA HiFi DNA Polymerase (KAPA KK2102) and 6.55 μL water) were added to each well and incubated with the following program: Step 1: 72 °C × 3 min; Step 2: 98 °C × 30 s; Step 3: 98 °C × 15 s, 60 °C × 30 s, 72 °C × 2 min 45 and repeat Step 3 for an additional 5 times; Step 4: 4 °C hold on. Then 2 μL 5 μM i7 UD index was added and incubated with: Step 1: 4 °C × 3 min; Step 2: 98 °C × 30 s; Step 3: 98 °C × 15 s, 60 °C × 30 s, 72 °C × 2 min and repeat Step 3 for an additional 5 times; Step 4: 72 °C × 5 min. The sequence of RNA-P7 primer was GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGGTTGAGGTAGTATTGCGCAATG. The barcoded single-cell libraries were then pooled and purified with 0.6 × and 0.15 × AMPure XP Beads (Beckman, A63881). The final libraries were sequenced with paired end 150-bp reads on a NovaSeq 6000 (Illumina) platform according to the manufacturer’s instructions.

value: Brains

value: C57BI6/J(female)x CAST/EiJ(male)


title: Mouse, brains, cell-ValbB8w1192


title: Mouse, brains, cell-ValbB8w1185


title: Mouse, brains, cell-ValbB8w1183


title: Mouse, brains, cell-ValbB8w1188


title: Mouse, brains, cell-ValbB8w1184


title: Mouse, brains, cell-ValbB8w1180


title: Mouse, brains, cell-ValbB8w1191


title: Mouse, brains, cell-ValbB8w1190


title: Mouse, brains, cell-ValbB8w1179


title: Mouse, brains, cell-ValbB8w1187


title: Mouse, brains, cell-ValbB8w1189


title: Mouse, brains, cell-ValbB8w1178


title: Mouse, brains, cell-ValbB8w1176


title: Mouse, brains, cell-ValbB8w1175


title: Mouse, brains, cell-ValbB8w1174


title: Mouse, brains, cell-ValbB8w1177


title: Mouse, brains, cell-ValbB8w1173


title: Mouse, brains, cell-ValbB8w1171


title: Mouse, brains, cell-ValbB8w1167


title: Mouse, brains, cell-ValbB8w1165


title: Mouse, brains, cell-ValbB8w1166


title: Mouse, brains, cell-ValbB8w1169


title: Mouse, brains, cell-ValbB8w1170


title: Mouse, brains, cell-ValbB8w1168


title: Mouse, brains, cell-ValbB8w1186


title: Mouse, brains, cell-ValbB8w1181


title: Mouse, brains, cell-ValbB8w1172


title: Mouse, brains, cell-ValbB8w1155


title: Mouse, brains, cell-ValbB8w1153


title: Mouse, brains, cell-ValbB8w1157


title: Mouse, brains, cell-ValbB8w1154


title: Mouse, brains, cell-ValbB8w1164


title: Mouse, brains, cell-ValbB8w1150


title: Mouse, brains, cell-ValbB8w1149


title: Mouse, brains, cell-ValbB8w1148


title: Mouse, brains, cell-ValbB8w1156


title: Mouse, brains, cell-ValbB8w1158


title: Mouse, brains, cell-ValbB8w1163


title: Mouse, brains, cell-ValbB8w1147


title: Mouse, brains, cell-ValbB8w1152


title: Mouse, brains, cell-ValbB8w1159


title: Mouse, brains, cell-ValbB8w1146


title: Mouse, brains, cell-ValbB8w1145


title: Mouse, brains, cell-ValbB8w1144


title: Mouse, brains, cell-ValbB8w1160


title: Mouse, brains, cell-ValbB8w1151


title: Mouse, brains, cell-ValbB8w1143


title: Mouse, brains, cell-ValbB8w1142


title: Mouse, brains, cell-ValbB8w1136


title: Mouse, brains, cell-ValbB8w1141


title: Mouse, brains, cell-ValbB8w1139


title: Mouse, brains, cell-ValbB8w1140


title: Mouse, brains, cell-ValbB8w1135


title: Mouse, brains, cell-ValbB8w1134


title: Mouse, brains, cell-ValbB8w1130


title: Mouse, brains, cell-ValbB8w1128


title: Mouse, brains, cell-ValbB8w1133


title: Mouse, brains, cell-ValbB8w1132


title: Mouse, brains, cell-ValbB8w1119


title: Mouse, brains, cell-ValbB8w1131


title: Mouse, brains, cell-ValbB8w1122


title: Mouse, brains, cell-ValbB8w1129


title: Mouse, brains, cell-ValbB8w1118


title: Mouse, brains, cell-ValbB8w1124


title: Mouse, brains, cell-ValbB8w1123


title: Mouse, brains, cell-ValbB8w1126


title: Mouse, brains, cell-ValbB8w1120


title: Mouse, brains, cell-ValbB8w1125


title: Mouse, brains, cell-ValbB8w1127


title: Mouse, brains, cell-ValbB8w1138


title: Mouse, brains, cell-ValbB8w1114


title: Mouse, brains, cell-ValbB8w1112


title: Mouse, brains, cell-ValbB8w1111


title: Mouse, brains, cell-ValbB8w1117


title: Mouse, brains, cell-ValbB8w1115


title: Mouse, brains, cell-ValbB8w1110


title: Mouse, brains, cell-ValbB8w1109


title: Mouse, brains, cell-ValbB8w1108


title: Mouse, brains, cell-ValbB8w1107


title: Mouse, brains, cell-ValbB8w1106


title: Mouse, brains, cell-ValbB8w1116


title: Mouse, brains, cell-ValbB8w1121


title: Mouse, brains, cell-ValbB8w1105


title: Mouse, brains, cell-ValbB8w1104


title: Mouse, brains, cell-ValbB8w1103


title: Mouse, brains, cell-ValbB8w1099


title: Mouse, brains, cell-ValbB8w1100


title: Mouse, brains, cell-ValbB8w1101


title: Mouse, brains, cell-ValbB8w1102


title: Mouse, brains, cell-ValbB8w1098


title: Mouse, brains, cell-ValbB8w1097


title: Mouse, brains, cell-ValbB8w1095


title: Mouse, brains, cell-ValbB8w1089


title: Mouse, brains, cell-ValbB8w1092


title: Mouse, brains, cell-ValbB8w1090


title: Mouse, brains, cell-ValbB8w1094


title: Mouse, brains, cell-ValbB8w1088


title: Mouse, brains, cell-ValbB8w1087


title: Mouse, brains, cell-ValbB8w1091


title: Mouse, brains, cell-ValbB8w1083


title: Mouse, brains, cell-ValbB8w1086


title: Mouse, brains, cell-ValbB8w1085


title: Mouse, brains, cell-ValbB8w1081


title: Mouse, brains, cell-ValbB8w1082


title: Mouse, brains, cell-ValbB8w1084


title: Mouse, brains, cell-ValbB8w1080


title: Mouse, brains, cell-ValbB8w1079


title: Mouse, brains, cell-ValbB8w1096


title: Mouse, brains, cell-ValbB8w1078


title: Mouse, brains, cell-ValbB8w1077


title: Mouse, brains, cell-ValbB8w1093


title: Mouse, brains, cell-ValbB8w1076


title: Mouse, brains, cell-ValbB8w1075


title: Mouse, brains, cell-ValbB8w1074


title: Mouse, brains, cell-ValbB8w1072


title: Mouse, brains, cell-ValbB8w1071


title: Mouse, brains, cell-ValbB8w1070


title: Mouse, brains, cell-ValbB8w1073


title: Mouse, brains, cell-ValbB8w1067


title: Mouse, brains, cell-ValbB8w1068


title: Mouse, brains, cell-ValbB8w1063


title: Mouse, brains, cell-ValbB8w1066


title: Mouse, brains, cell-ValbB8w1065


title: Mouse, brains, cell-ValbB8w1060


title: Mouse, brains, cell-ValbB8w1064


title: Mouse, brains, cell-ValbB8w1059


title: Mouse, brains, cell-ValbB8w1057


title: Mouse, brains, cell-ValbB8w1058


title: Mouse, brains, cell-ValbB8w1062


title: Mouse, brains, cell-ValbB8w1061


title: Sample10_Donor43


title: Mouse, brains, cell-ValbB8w1055


title: Mouse, brains, cell-ValbB8w1054


title: Mouse, brains, cell-ValbB8w1053


title: Mouse, brains, cell-ValbB8w1069


title: Mouse, brains, cell-ValbB8w1052


title: Donor 2 - RGRN-305

description: Treated with RGRN-305

value: Healthy tissue


title: Mouse, brains, cell-ValbB8w1050


title: Mouse, brains, cell-ValbB8w1048


title: Mouse, brains, cell-ValbB8w1047


title: Mouse, brains, cell-ValbB8w1056


title: Mouse, brains, cell-ValbB8w1046


title: Mouse, brains, cell-ValbB8w1045


title: Mouse, brains, cell-ValbB8w1049


title: Mouse, brains, cell-ValbB8w1044


title: Mouse, brains, cell-ValbB8w1043


title: Mouse, brains, cell-ValbB8w1051


title: Mouse, brains, cell-ValbB8w1042


title: Mouse, brains, cell-ValbB8w1041


title: Mouse, brains, cell-ValbB8w1040


title: Mouse, brains, cell-ValbB8w1038


title: Mouse, brains, cell-ValbB8w1033


title: Mouse, brains, cell-ValbB8w1035


title: Mouse, brains, cell-ValbB8w1037


title: Mouse, brains, cell-ValbB8w1031


title: Mouse, brains, cell-ValbB8w1032


title: Mouse, brains, cell-ValbB8w1039


title: Mouse, brains, cell-ValbB8w1036


title: Mouse, brains, cell-ValbB8w1029


title: Mouse, brains, cell-ValbB8w1028


title: Mouse, brains, cell-ValbB8w1026


title: Mouse, brains, cell-ValbB8w1027


title: Mouse, brains, cell-ValbB8w1025


title: Mouse, brains, cell-ValbB8w1024


title: Mouse, brains, cell-ValbB8w1023


title: Mouse, brains, cell-ValbB8w1022


title: Mouse, brains, cell-ValbB8w1018


title: Mouse, brains, cell-ValbB8w1034


title: Mouse, brains, cell-ValbB8w1021


title: Mouse, brains, cell-ValbB8w1019


title: Mouse, brains, cell-ValbB8w1020


title: Mouse, brains, cell-ValbB8w1016


title: Mouse, brains, cell-ValbB8w1017


title: Mouse, brains, cell-ValbB8w1014


title: Mouse, brains, cell-ValbB8w1013


title: Mouse, brains, cell-ValbB8w1030


title: Mouse, brains, cell-ValbB8w1009


title: Mouse, brains, cell-ValbB8w1008


title: Mouse, brains, cell-ValbB8w1015


title: Mouse, brains, cell-ValbB8w1010


title: Mouse, brains, cell-ValbB8w1005


title: Mouse, brains, cell-ValbB8w1006


title: Mouse, brains, cell-ValaB8w4192


title: Mouse, brains, cell-ValbB8w1002


title: Mouse, brains, cell-ValbB8w1001


title: Mouse, brains, cell-ValbB8w1003


title: Mouse, brains, cell-ValaB8w4191


title: Mouse, brains, cell-ValaB8w4190


title: Mouse, brains, cell-ValaB8w4189


title: Mouse, brains, cell-ValbB8w1012


title: Mouse, brains, cell-ValbB8w1011


title: Mouse, brains, cell-ValaB8w4188


title: Mouse, brains, cell-ValaB8w4187


title: Mouse, brains, cell-ValaB8w4186


title: Mouse, brains, cell-ValbB8w1007


title: Mouse, brains, cell-ValaB8w4181


title: Mouse, brains, cell-ValaB8w4183


title: Mouse, brains, cell-ValbB8w1004


title: Mouse, brains, cell-ValaB8w4178


title: Mouse, brains, cell-ValaB8w4179


title: Mouse, brains, cell-ValaB8w4174


title: Mouse, brains, cell-ValaB8w4176


title: Mouse, brains, cell-ValaB8w4175


title: Mouse, brains, cell-ValaB8w4172


title: Mouse, brains, cell-ValaB8w4173


title: Mouse, brains, cell-ValaB8w4170


title: Mouse, brains, cell-ValaB8w4169


title: Mouse, brains, cell-ValaB8w4168


title: Mouse, brains, cell-ValaB8w4164


title: Mouse, brains, cell-ValaB8w4166


title: Mouse, brains, cell-ValaB8w4184


title: Mouse, brains, cell-ValaB8w4162


title: Mouse, brains, cell-ValaB8w4163


title: Mouse, brains, cell-ValaB8w4167


title: Mouse, brains, cell-ValaB8w4180


title: Mouse, brains, cell-ValaB8w4177


title: Mouse, brains, cell-ValaB8w4165


title: Mouse, brains, cell-ValaB8w4182


title: Mouse, brains, cell-ValaB8w4160


title: Mouse, brains, cell-ValaB8w4159


title: Mouse, brains, cell-ValaB8w4156


title: Mouse, brains, cell-ValaB8w4158


title: Mouse, brains, cell-ValaB8w4161


title: Mouse, brains, cell-ValaB8w4155


title: Mouse, brains, cell-ValaB8w4154


title: Mouse, brains, cell-ValaB8w4153


title: Mouse, brains, cell-ValaB8w4171


title: Mouse, brains, cell-ValaB8w4150


title: Mouse, brains, cell-ValaB8w4151


title: Mouse, brains, cell-ValaB8w4146


title: Mouse, brains, cell-ValaB8w4149


title: Mouse, brains, cell-ValaB8w4147


title: Mouse, brains, cell-ValaB8w4145


title: Mouse, brains, cell-ValaB8w4144


title: Mouse, brains, cell-ValaB8w4148


title: Mouse, brains, cell-ValaB8w4143


title: Mouse, brains, cell-ValaB8w4142


title: Mouse, brains, cell-ValaB8w4139


title: Mouse, brains, cell-ValaB8w4140


title: Mouse, brains, cell-ValaB8w4157


title: Mouse, brains, cell-ValaB8w4138


title: Mouse, brains, cell-ValaB8w4137


title: Mouse, brains, cell-ValaB8w4136


title: Mouse, brains, cell-ValaB8w4152


title: Mouse, brains, cell-ValaB8w4132


title: Mouse, brains, cell-ValaB8w4130


title: Mouse, brains, cell-ValaB8w4131


title: Mouse, brains, cell-ValaB8w4135


title: Mouse, brains, cell-ValaB8w4124


title: Mouse, brains, cell-ValaB8w4129


title: Mouse, brains, cell-ValaB8w4125


title: Mouse, brains, cell-ValaB8w4127


title: Mouse, brains, cell-ValaB8w4133


title: Mouse, brains, cell-ValaB8w4126


title: Mouse, brains, cell-ValaB8w4128


title: Mouse, brains, cell-ValaB8w4123


title: Mouse, brains, cell-ValaB8w4141


title: Mouse, brains, cell-ValaB8w4122


title: Mouse, brains, cell-ValaB8w4120


title: Mouse, brains, cell-ValaB8w4121


title: Mouse, brains, cell-ValaB8w4118


title: Mouse, brains, cell-ValaB8w4116


title: Mouse, brains, cell-ValaB8w4117


title: Mouse, brains, cell-ValaB8w4114


title: Mouse, brains, cell-ValaB8w4134


title: Mouse, brains, cell-ValaB8w4113


title: Mouse, brains, cell-ValaB8w4112


title: Mouse, brains, cell-ValaB8w4110


title: Mouse, brains, cell-ValaB8w4111


title: Mouse, brains, cell-ValaB8w4107


title: Mouse, brains, cell-ValaB8w4104


title: Mouse, brains, cell-ValaB8w4108


title: Mouse, brains, cell-ValaB8w4105


title: Mouse, brains, cell-ValaB8w4106


title: Mouse, brains, cell-ValaB8w4102


title: Mouse, brains, cell-ValaB8w4101


title: Mouse, brains, cell-ValaB8w4103


title: Mouse, brains, cell-ValaB8w4100


title: Mouse, brains, cell-ValaB8w4097


title: Mouse, brains, cell-ValaB8w4096


title: Mouse, brains, cell-ValaB8w4099


title: Mouse, brains, cell-ValaB8w4119


title: Mouse, brains, cell-ValaB8w4098


title: Mouse, brains, cell-ValaB8w4115


title: Mouse, brains, cell-ValaB8w4094


title: Mouse, brains, cell-ValaB8w4092


title: Mouse, brains, cell-ValaB8w4093


title: Mouse, brains, cell-ValaB8w4090


title: Mouse, brains, cell-ValaB8w4091


title: Mouse, brains, cell-ValaB8w4109


title: Mouse, brains, cell-ValaB8w4088


title: Mouse, brains, cell-ValaB8w4089


title: Mouse, brains, cell-ValaB8w4086


title: Mouse, brains, cell-ValaB8w4085


title: Mouse, brains, cell-ValaB8w4084


title: Mouse, brains, cell-ValaB8w4087


title: Mouse, brains, cell-ValaB8w4082


title: Mouse, brains, cell-ValaB8w4083


title: Mouse, brains, cell-ValaB8w4095


title: Mouse, brains, cell-ValaB8w4079


title: Mouse, brains, cell-ValaB8w4081


title: Mouse, brains, cell-ValaB8w4078


title: Mouse, brains, cell-ValaB8w4080


title: Mouse, brains, cell-ValaB8w4074


title: Mouse, brains, cell-ValaB8w4075


title: Mouse, brains, cell-ValaB8w4077


title: Mouse, brains, cell-ValaB8w4076


title: Mouse, brains, cell-ValaB8w4072


title: Mouse, brains, cell-ValaB8w4073


title: Mouse, brains, cell-ValaB8w4071


title: Mouse, brains, cell-ValaB8w4070


title: Mouse, brains, cell-ValaB8w4069


title: Mouse, brains, cell-ValaB8w4068


title: Mouse, brains, cell-ValaB8w4066


title: Mouse, brains, cell-ValaB8w4067


title: Mouse, brains, cell-ValaB8w4065


title: Mouse, brains, cell-ValaB8w4064


title: Mouse, brains, cell-ValaB8w4060


title: Mouse, brains, cell-ValaB8w4061


title: Mouse, brains, cell-ValaB8w4058


title: Mouse, brains, cell-ValaB8w4059


title: Mouse, brains, cell-ValaB8w4057


title: Mouse, brains, cell-ValaB8w4056


title: Mouse, brains, cell-ValaB8w4055


title: Mouse, brains, cell-ValaB8w4054


title: Mouse, brains, cell-ValaB8w4052


title: Mouse, brains, cell-ValaB8w4050


title: Mouse, brains, cell-ValaB8w4048


title: Mouse, brains, cell-ValaB8w4049


title: Mouse, brains, cell-ValaB8w4044


title: Mouse, brains, cell-ValaB8w4051


title: Mouse, brains, cell-ValaB8w4047


title: Mouse, brains, cell-ValaB8w4041


title: Mouse, brains, cell-ValaB8w4040


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