title: H3K4me1.D.rep2

city: Shanghai

first: Yuxuan

last: Zheng

address: 825 Zhangheng Rd.

institute: Fudan University

data_processing:
Base-calling was performed using CASAVA.
Firstly, All of the Histone modification ChIP-seq data were send to trim-galore to remove adapter contamination and low quality sequences, Phred score of any bases in a reads under 20 and adapter sequence were removed, reads after trimming shorter than 30 were discarded.
Trimmed sequences were then mapped with Bowtie (v2.2.6) using default parameters. Duplicate reads were removed by samtools rmdup -s. Unique and monoclonal mapped reads were extended to 150-bp based on the average sonicated chromatin DNA length.
Spike-in reads were mapped to drosophila genome (dm6) using same parameters.
GenomeCoverageBed (bedtools) was used to transfer bed files to bedGraph files, then spikein reads was used as a normalization factor that equalizes the signal across samples. Normalized bedGraph files were subsequently transferred to bigwig files.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

growth_protocol: Spermatogenesis was synchronized and validated as previously described.

extract_protocol:
ChIP assay was carried out as previously described. The sorted homogenous synchronous spermatogenic cells were crosslinked with 1% formaldehyde for 10 mins and then stopped by adding 125 mM Glycine. Chromatin samples were lysed with lysis buffer (20 mM Tris-HCl pH8.0, 500 mM NaCl, 1 mM EDTA, 1% TritonX-100 and 0.1% SDS) and sonicated with Qsonica. Histone modification specific antibody was incubated with chromatin samples overnight at 4 ℃.0.5 ug spike-in antibody (Active motif #61686) and 25 ng spike-in chromatin (Active motif #53083) were used in this ChIP assay according to the manufacture’s guidelines.
DNA samples were analyzed using real time PCR and prepared for deep sequencing according to the manufacture’s guidelines (KAPA Biosystems KK8503 and VAHTS Universal DNA Library Prep Kit for Illumina V3 ND607). Finally, libraries were pooled and sequenced on the Illumina HiSeq 2500 sequencer for 150-bp paired-end sequencing.

treatment_protocol: Briefly, 2-dpp mice were pipette fed 100 μg/g body weight WIN 18,446 (MP), suspended in 1% gum tragacanth, for 7 consecutive days. At Day 8 of WIN 18,446 treatments, these animals were received an i.p. injection of RA (Sigma; 30 μg/g body weight) in dimethyl sulfoxide (DMSO), and were then left to recover for sample collections. The undifferentiated spermatogonia was isolated from Lin28-YFP knockin mice. Testes from 3-week-old Lin28-YFP knockin mice were collected and digested by type I collagenase and 0.25% Trypsin as described previously1. After centrifugation, the pellet was resuspended in DMEM containing 2% BSA at a concentration of 1×106 cells/40 μL, followed by incubating with PE-conjugated anti-CD117 antibody (0.1 μg/106 cells; Molecular probes) for 30 min on ice. The undifferentiated spermatogonia (YFP-positive, PE-negative population) was collected using FACS (BD). The type A1 spermatogonia was isolated from synchronous Stra8-GFPCre mice. Testes were collected and digested. The type A1 spermatogonia (GFP-positive population) was collected using FACS. The type B spermatogonia and different stages of spermatocytes were isolated from synchronous Lin28-YFP and Vasa-tdTomato double positive mice. To isolate the type B spermatogonia, testes were digested and the synchronous advanced spermatogenic cells (tdTomato positive population) were collected using FACS. To isolate different stages of spermatocytes, testes were digested and the cell suspensions were stained with Hoechst 33342. The tdTomato positive 4N population were collected using FACS. The identity of sorted spermatocytes were validated using surface spreading and immunofluorescence.

tag: strain

tag: Stage

value: D

tag: genotype

value: wild type

tag: chip antibody

value: Active Motif 39297, lot 19417002


title: H3K4me1.mP.rep2

status: Public on May 26 2020

type: SRA

country: China

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: homogenous synchronous spermatogenic cells

value: mP


title: Human thymus, CD4+CD3+, replicate 1

type: RNA

city: Ghent

first: Tom

last: Taghon

address: Corneel Heymanslaan 10

department: Diagnostic Sciences

country: Belgium

institute: Ghent University

description:
miRNA expression data from ex vivo isolated CD4+CD3+ thymocytes
DONOR2_CD4+CD3+

data_processing:
Normalization of the microRNA expression data was done using the global mean normalization method (Mestdagh P. Genome Biol. 2009).
Cq values above 32 were removed and samples were mean centered. Next, miRNAs expressed in less than two samples were removed and missing values were imputed by the highest value for each miRNA and multiplied by -1.
Matrix normalized worksheet reports global mean normalization.

label: FAM

molecule: total RNA

organism: Homo sapiens

source_name: Human thymus, CD4+CD3+, replicate 1

label_protocol: miRNA profiling was performed using stem-loop reverse transcriptase primers for miRNA complementary DNA (cDNA) synthesis followed by a pre-amplification step and TaqMan PCR analysis (Applied Biosystems).

extract_protocol: Total RNA was harvested using the miRNeasy Mini Kit (Qiagen) with Dnase treatment on-column.

treatment_protocol: Cell suspension from child thymus was stained for specific cell surface markers in order to sort out dinsinct T cell subsets.

tag: tissue

value: thymus

tag: cell type

tag: origin

value: ex vivo isolated


title: Human thymus, CD4+CD8+CD3+, replicate 2

description:
miRNA expression data from ex vivo isolated CD4+CD8+CD3+ thymocytes
DONOR3_CD4+CD8+CD3+

source_name: Human thymus, CD4+CD8+CD3+, replicate 2


title: H3K4me1.Late-Z.rep1

value: Late-Z


title: H3K4me1.L.rep2

value: L


title: Human thymus, CD4+CD8+CD3+, replicate 1

description:
miRNA expression data from ex vivo isolated CD4+CD8+CD3+ thymocytes
DONOR2_CD4+CD8+CD3+

source_name: Human thymus, CD4+CD8+CD3+, replicate 1


title: adipose tissue, AL49

city: Évora

first: André

middle: Filipe Barreto

last: Albuquerque

address: Rua Ramalho Ortigao, 15

country: Portugal

institute: Universidade de Évora

library_source: transcriptomic

data_processing:
Obtained sequence reads were trimmed for three consecutive times for Ilumina adapters, poli-A and poli-T tails using Trim Galore (version 0.5.0) while removing resulting low quality nucleotides (Phred Score, Q<20) and short length reads (<40).
Reads were aligned to the reference pig genome version Sscrofa11.1 (Ensembl release 94) using HISAT2 version 2.1.0
Generated SAM files were then converted to BAM with Samtools version 1.9
HTSeq-count version 0.11.1 was used to count and merge reads based on overlapping paired-end reads
Gcount files were run with the R package DESeq2 with a filtering of a minimum 50 reads per group. Genes were considered as differentially expressed when presenting a false discovery rate (FDR) lower than 0.05
Genome_build: reference pig genome version Sscrofa11.1 (Ensembl release 94)
Supplementary_files_format_and_content: Comma Separated Values (CSV) files that include log2FoldChange and associated p-adjusted values

organism: Sus scrofa

source_name: adipose tissue

extract_protocol:
Adipose tissue samples were collected. Total RNA was obtained through extraction following Ambion RiboPure Kit with Trizol and was stored at -80°C
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Alentejano

value: adipose tissue

tag: carcass weight


title: Human thymus, CD4+CD8+CD3-, replicate 2

description:
miRNA expression data from ex vivo isolated CD4+CD8+CD3- thymocytes
DONOR3_CD4+CD8+CD3-

source_name: Human thymus, CD4+CD8+CD3-, replicate 2


title: Human thymus, CD4+CD8+CD3-, replicate 1

description:
miRNA expression data from ex vivo isolated CD4+CD8+CD3- thymocytes
DONOR2_CD4+CD8+CD3-

source_name: Human thymus, CD4+CD8+CD3-, replicate 1


title: H3K4me1.mPL.rep2

value: mPL


title: Human thymus, CD4+CD3-CD28+, replicate 2

description:
miRNA expression data from ex vivo isolated CD4+CD3-CD28+ thymocytes
DONOR3_CD4+CD3-CD28+


title: Human thymus, CD4+CD3-CD28+, replicate 1

description:
miRNA expression data from ex vivo isolated CD4+CD3-CD28+ thymocytes
DONOR2_CD4+CD3-CD28+


title: hel2∆ [SM024M]

city: Bethesda

first: Nicholas

middle: R

last: Guydosh

state: MD

address: 8 Center Dr, Bldg 8, 220

department: NIDDK

country: USA

institute: National Institutes of Health

description: Biological replicate of SM016M

data_processing:
Base calling and demultiplexing was performed at the NHLBI DNA Sequencing and Genomics Core at the NIH Intramural program, Bethesda, MD.
Files were demultiplexed and then trimmed to the start of the linker sequence.
Reads were aligned to a library of non coding RNA genes and those not matching were retained.
Reads were then aligned to the genome and those not matching to a custom library of splice junctions by using Bowtie (Langmead et al., 2009). For footprints, reads that did not match in these steps were trimmed of consecutive 3' As and realigned. The aligned reads from all alignment rounds were pooled and normalized to units of reads per million (rpm) (by dividing by the total number of million mapped reads in a sample) to generate wig files.
Replicates or multiple sequencing lanes for a given sample were pooled together to create a single wig file for each condition to be used in downstream analysis.
Genome_build: R64-1-1
Supplementary_files_format_and_content: All files are fixedStep wig files (text format, each line representing one position in the genome).

organism: Saccharomyces cerevisiae

source_name: Whole cells

growth_protocol: Cells were generally grown to an OD of ~0.6 and harvested.

extract_protocol:
Ribosome profiling lysates were clarified, treated with RNase I, and run over sucrose gradients to extract either the monosome or the disome peak. RNA was then extracted using SDS/hot phenol/chloroform and footprints of the specified size were retained by gel purification.
Briefly, RNAs were ligated to a universal DNA linker followed by reverse transcription. cDNAs were then circularized and PCR amplified. Ribosome profiling circularized cDNA was subject to ribosomal RNA subtraction using custom biotinylated oligos in some cases. In others, Ribo-Zero was used. RNA-Seq samples were prepared with the Illumina Truseq Stranded ribo-zero kit.

treatment_protocol: Cells were rapidly vacuum filtered and flash frozen. Ribosome profiling samples were lysed in a freezer mill with lysis buffer. Total RNA for mRNA-Seq was extracted from whole cells.


title: Human thymus, CD4+CD3+, replicate 2

description:
miRNA expression data from ex vivo isolated CD4+CD3+ thymocytes
DONOR3_CD4+CD3+

source_name: Human thymus, CD4+CD3+, replicate 2


title: MH-24

city: Indianapolis

first: Xiaocheng

middle: Charlie

last: Dong

state: IN

address: 635 Barnhill Drive, MS1021D

department: Biochemistry and Molecular Biology

institute: Indiana University School of Medicine

data_processing:
Sequencing was done on Illumina HiSeq 2000
The reads were mapped to the mouse genome using STAR (v2.5) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to mm10 genes using featureCounts (from subread v1.5.3) with the following parameters: “-s 2 –p –Q 10”.
The data was filtered using read count per million (CPM) > 0.5 in more than 4 of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using edgeR (v3.20.8).
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts and analysis (excel) from edgeR

source_name: WT liver

extract_protocol:
Mouse livers were dissected and snap frozen in liquid nitrogen. Total RNAs were isolated using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were treated with a diet (Research Diets D12109C) containing 20% kcal protein, 40% kcal fat, 40% kcal carbohydrate, 1.25% cholesterol, and 0.5% sodium cholate for 4 weeks.

value: liver

tag: age

value: 4 months

tag: gender

value: Male

tag: diet

value: high fat diet


title: H3K4me1.Undiff.rep2

value: Undiff


title: WT [SM023M]

description: Biological replicate of SM015M

value: WT


title: H3K4me1.A1.rep2


title: Human thymus, CD4+CD3-CD28-, replicate 2

description:
miRNA expression data from ex vivo isolated CD4+CD3-CD28- thymocytes
DONOR3_CD4+CD3-CD28-


title: hel2∆ [SM016M]


title: MH-23


title: H3K4me1.TypeB.rep2

value: TypeB


title: MCF-7 treated with 100 uMOXY, biological rep3 (passage no. 45)

city: Liverpool

first: Sarayut

last: Radapong

address: 2 Hatton Garden

country: United Kingdom

institute: Liverpool John Moores University

description:
Gene expression data from cell treated with 100 uM OXY rep 3
18159_9_(Clariom_S_Human).sst-rma-gene-full.chp Signal

hyb_protocol: The labeled cDNA product was heated to 99°C and hybridised to each array for 16 h at 45°C. Samples were washed with stain cocktail and the array-holding buffer on the GeneChipTM Fluidics Station 450 (Thermo Fisher Scientific, California, USA).

scan_protocol: A GeneChip 3000G scanner (Affymetrix Inc.) and the Expression Console software (Affymetrix Inc.) were used to obtain fluorescent signals and quality control data of the scanned arrays.

data_processing:
Signal intensities from each array were analyzed using Partek Genomic Suite version 6.4 (Partek, St Louis, Missouri, USA).
The Transcriptome Analysis Console (TAC) Software (Thermo Fisher Scientific, California, USA) was used for the visualization of the expression data in the biological pathways context. The data set was analysed using this tool and a gene expression fold change > 2 or < -2. Ebayes Anova was used for statistical analysis with a p-value < 0.05

label: biotin

source_name: MCF-7 treated with 100 uMOXY

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng of the pooled RNA (GeneChipTM WT PLUS Reagent Kit Manual Target Preparation for GeneChipTM Whole Transcript (WT) Expression Arrays UserGuide, 2017, Affymetrix).

growth_protocol: MCF-7 cells were seeded at 2.5 x 105 cells/well in 6-well plates for 24 h with in Eagle’s minimum essential medium (Thermo Fisher Scientific, New York, USA) supplemented with 10% fetal bovine serum in a 5% CO2 incubator at 37°C

extract_protocol: Total RNA of each sample was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany) pre-treated with on-column DNase digestion with DNase-free DNase set (Qiagen, Hilden, Germany). According to the manufacturer’s protocol, RNA was re-suspended in 30 μL of nuclease-free water and stored at −80°C until further analysis.

treatment_protocol: The seeded cells were treated with OXY at the concentrations of 0, 50, and 100 μM, each concentration was treated in triplicates with different cell passage no. and then incubated for 24 h in the cell incubator.

tag: cell line

value: 100 uM Oxyresveratrol


title: Human thymus, CD4+CD3-CD28-, replicate 1

description:
miRNA expression data from ex vivo isolated CD4+CD3-CD28- thymocytes
DONOR2_CD4+CD3-CD28-


title: MH-22

value: wild type


title: MCF-7 treated with 100 uMOXY, biological rep2 (passage no. 40)

description:
Gene expression data from cell treated with 100 uM OXY rep 2
18159_8_(Clariom_S_Human).sst-rma-gene-full.chp Signal


title: MCF-7 treated with 100 uMOXY, biological rep1(passage no. 35)

description:
Gene expression data from cell treated with 100 uM OXY rep 1
18159_7_(Clariom_S_Human).sst-rma-gene-full.chp Signal


title: MCF-7 treated with 50 uMOXY, biological rep3 (passage no. 45)

description:
Gene expression data from cell treated with 50 uM OXY rep 3
18159_6_(Clariom_S_Human).sst-rma-gene-full.chp Signal

source_name: MCF-7 treated with 50 uMOXY

value: 50 uM Oxyresveratrol


title: MCF-7 treated with 0 uMOXY, biological rep2 (passage no. 40)

description:
Gene expression data from cell control rep 2
18159_2_(Clariom_S_Human).sst-rma-gene-full.chp Signal

source_name: MCF-7 treated with 0 uMOXY

value: 0 uM Oxyresveratrol


title: Human thymus, CD34+CD1+CD4+, replicate 2

description:
miRNA expression data from ex vivo isolated CD34+CD1+CD4+ thymocytes
DONOR3_CD34+CD1+CD4+

value: thymus

value: ex vivo isolated


title: WT [SM015M]


title: MH-21

source_name: Sesn3 KO liver

value: Sesn3 KO


title: MCF-7 treated with 50 uMOXY, biological rep2 (passage no. 40)

description:
Gene expression data from cell treated with 50 uM OXY rep 2
18159_5_(Clariom_S_Human).sst-rma-gene-full.chp Signal


title: MCF-7 treated with 0 uMOXY, biological rep3 (passage no. 45)

description:
Gene expression data from cell control rep 3
18159_3_(Clariom_S_Human).sst-rma-gene-full.chp Signal


title: Ltbr-cKO_rep1

city: Beijing

first: Mingzhao

last: Zhu

address: 15 Da Tun Rd, Chaoyang District

department: Key Laboratory of Infection and Immunity

institute: Institute of Biophysics, Chinese Academy of Sciences

description:
gene_count_matrix_Villin_Ltbr.csv
cpm_Villin_Ltbr.csv

data_processing:
Illumina reads were aligned to the Mus musculus GRCm38 genome build 84 and proceeded by HISAT2 (2.1.0) with parameter --dta, and sorted with samtools with parameters view -uS and sort -O BAM
Aligned bams were annoated by stringtie (1.3.6) with parameters -e -v
Using prepDE.py given by stringtie to generate count matrix for downtream analysis
Using edgeR to do differential expression analysis with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: Comma separated values file include 1. raw count values, 2. library-normalized cpm values for each sample

source_name: Ileum epithelial cells

growth_protocol: All mice were maintained in specific-pathogen-free facilities, co-housed littermates were used as controls.

extract_protocol:
RNA of ileum pieces or cells was extracted by EasyPure RNA Kit (Transgen). cDNA was prepared with cDNA transcript kit (Transgen).
The library was prepared using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB).

treatment_protocol: The isolated ilea were treated with 1.5 mM DTT and 30 mM EDTA in PBS for 20 min on ice and followed by shaking in PBS with 30 mM EDTA for 10 min at 37°C on a shaker. The SIECs were collected from the supernatant by centrifuge.

tag: Sex

value: Female

tag: organ

value: Intestine

tag: genotype/variation

value: Villin<delta>Ltbr (cKO)


title: Ltbr-cKO_rep2


title: WT_rep2


title: Ltbr-cKO_rep3


title: Human thymus, CD34+CD1+CD4+, replicate 1

description:
miRNA expression data from ex vivo isolated CD34+CD1+CD4+ thymocytes
DONOR2_CD34+CD1+CD4+


title: WT_rep1


title: WT, ANS [SM040Fd]

description:
Ribosome-protected RNA 40-68 nt
Cells treated with ANS

data_processing:
Library strategy: Ribo-Seq
Base calling and demultiplexing was performed at the NHLBI DNA Sequencing and Genomics Core at the NIH Intramural program, Bethesda, MD.
Files were demultiplexed and then trimmed to the start of the linker sequence.
Reads were aligned to a library of non coding RNA genes and those not matching were retained.
Reads were then aligned to the genome and those not matching to a custom library of splice junctions by using Bowtie (Langmead et al., 2009). For footprints, reads that did not match in these steps were trimmed of consecutive 3' As and realigned. The aligned reads from all alignment rounds were pooled and normalized to units of reads per million (rpm) (by dividing by the total number of million mapped reads in a sample) to generate wig files.
Replicates or multiple sequencing lanes for a given sample were pooled together to create a single wig file for each condition to be used in downstream analysis.
Genome_build: R64-1-1
Supplementary_files_format_and_content: All files are fixedStep wig files (text format, each line representing one position in the genome).


title: MH-20

value: liver


title: MCF-7 treated with 50 uMOXY, biological rep1(passage no. 35)

description:
Gene expression data from cell treated with 50 uM OXY rep 1
18159_4_(Clariom_S_Human).sst-rma-gene-full.chp Signal


title: WT, 3-AT [SM037Fd]

description:
Ribosome-protected RNA 40-68 nt
Cells treated with 3-AT

value: WT, His3+


title: brown adipose tissue, Beclin1 KO_rep3

city: Seoul

first: Yeonho

last: Son

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

data_processing:
bcl2fastq2-v2.20.0 package was used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence with Trimmomatic0.38. (Trimmomatic option : ILLUMINACLIP:[TruSeq3-PE-2.fa]:2:30:10:5:true ,LEADING:3 , TRAILING:3 , SLIDINGWINDOW:4:15, MINLEN:36)
To estimate expression levels, the RNA-Seq reads were mapped to Mus musculus genome (mm10) using HISAT2 version 2.1.0, which is capable of reporting split-read alignments across splice junctions and determined using StringTie version 1.3.4d software in default options.
The read count data of filtered genes was normalized by RLE (Relative Log Expression) normalization with DESeq2. The nbinomWaldTest function in DESeq2 was used to test for differential expression. The output prints foldChange, p-value and FDR values which corrected by the Benjamin-Hochberg procedure. DEGs was determined by |fold change|>=2 and p-value <0.05. For DEGs, hierarchical clustering analysis was performed with complete linkage method and Euclidean distance as a measure of similarity.
Gene-enrichment analysis and KEGG pathway analysis for DEGs were also performed based on Gene Ontology (http://geneontology.org/) and KEGG pathway (https://www.genome.jp/kegg/) database respectively. All statistical analysis and visualization of differentially expressed genes was conducted using R.3.5.1 (www.r-project.org).
Genome_build: mm10
Supplementary_files_format_and_content: Excel file includes baseMean values for each Comparison

source_name: interscapular brown adipose tissue

growth_protocol: Mice were fed a standard chow diet and were kept on a 12-h light/12-h dark cycle with free access to food and water at 22±1 °C.

extract_protocol:
RNA was isolated using Trizol reagent (Invitrogen) and processed as per manufacturer’s instructions.
libraries were prepared using the TruSeq Stranded mRNA LT Sample Prep Kit, according to the manufacturer’s instructions.

treatment_protocol: For Cre recombination, transgenic mice and wildtype controls were treated with tamoxifen dissolved in sunflower oil (Sigma, 75 mg/kg) by oral gavage on each of 5 consecutive days

tag: background strain

tag: treatment

value: untreated

value: interscapular brown adipose tissue


title: Human thymus, CD34+CD1+CD4-, replicate 2

description:
miRNA expression data from ex vivo isolated CD34+CD1+CD4- thymocytes
DONOR3_CD34+CD1+CD4-


title: MCF-7 treated with 0 uMOXY, biological rep1(passage no. 35)

description:
Gene expression data from cell control rep 1
18159_1_(Clariom_S_Human).sst-rma-gene-full.chp Signal

value: 0 uM  Oxyresveratrol


title: MH-19

tag: strain

value: 4 months

value: Male

value: high fat diet


title: WT, no 3-AT [SM036Fd]

description:
Ribosome-protected RNA 40-68 nt
Mock treated cells

tag: genotype


title: Human thymus, CD34+CD1+CD4-, replicate 1

description:
miRNA expression data from ex vivo isolated CD34+CD1+CD4- thymocytes
DONOR2_CD34+CD1+CD4-


title: rpl11B∆ [SM035Fd]

description:
Ribosome-protected RNA 54-68 nt
Biological replicate of SM034Fd


title: Human thymus, CD34+CD1-CD4-, replicate 2

description:
miRNA expression data from ex vivo isolated CD34+CD1-CD4- thymocytes
DONOR3_CD34+CD1-CD4-


title: DN4 lymphoma T-cell subpopulation, replicate 1

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

description: Gene expression data from aged Wild type mouse

hyb_protocol: Labeled fragments were hybridized to Affymetrix Mouse Gene ST 2.0 arrays for 16h at 45°C with 60 rpm in an Affymetrix Hybridization oven 645.

scan_protocol: After washing and staining, the arrays were scanned with the Affymetrix GeneChip Scanner 3000 7G. CEL-files were produced from the raw data with Affymetrix GeneChip Command Console Software.

data_processing: CEL files were analysed using the oligo R package. RMA method, log2 transformed were used to normalized the probe intensities.

label: Biotin

source_name: Murine lymphoma out of thymus, replicate 1

label_protocol: We used the Affymetrix WT Pico kit for cDNA synthesis, amplification, and second-cycle cDNA synthesis, as well as fragmentation and labeling with Biotin, as described by the manufacturer.

growth_protocol: Sublethally irradiated Lck-Cre transgene mice were transplanted with retroviral infected bone marrow cells. Thereby, NPM-ALK is retroviral and lineage-specific expressed in early T-cells. ALCL developing mice were sacrificed when moribund. Mouse housing was in accordance with national and institutional guidelines for animal care and experiments.

extract_protocol: Extraction of total RNA was performed by RNeasy Micro Kit (Quiagen) according to the manufacturer's instructions.

treatment_protocol: Harvested lymphomas or healthy bone marrow were flushed in DMEM (+10% FCS) followed by lysis of erythrocytes for 5 minutes at room temperature and staining for stem cell and T-cell markers (CD4, CD8, CD25, CD44, IL7Rα, cKIT, SCA1, Lineage markers). Lymphoma subpopulations (DN1, DN2, DN3, DN4, CLP) or LSK cells were sorted using Coulter MoFlo XDP and and cell pelletts were stored at -80°C.

value: lymphoma out of thymus

value: DN4 lymphoma T-cell subpopulation

value: moribund mouse

value: Lck-Cre transgene


title: brown adipose tissue, WT_rep3

value: wild-type


title: Human thymus, CD34+CD1-CD4-, replicate 1

description:
miRNA expression data from ex vivo isolated CD34+CD1-CD4- thymocytes
DONOR2_CD34+CD1-CD4-

value: thymus

value: ex vivo isolated


title: rpl11B∆ [SM034Fd]

description: Ribosome-protected RNA 54-68 nt


title: hcr1∆ [SM033Fd]

description:
Ribosome-protected RNA 54-68 nt
Biological replicate of SM032Fd


title: brown adipose tissue, WT_rep2


title: brown adipose tissue, WT_rep1


title: Tomato_PSTVd_L2

city: Sherbrooke

first: Charith Raj

last: Adkar-Purushothama

state: Quebec

address: 3201 rue Jean-Mignault

department: Biochemistry

country: Canada

institute: Université de Sherbrooke

description:
variant RG1
circular viroid
Plants were inoculated with PSTVd-RG1 strain and library prepared using F2/R2 primers

data_processing:
CASAVA version 1.4 was used for base-calling.
The primers were trimmed
300-bp long sequences were filtered
Workflow was divided in four main steps, specifically steps A to D. Each step was performed independently for both libraries with the exception of step C. Step A consisted of creating the library fragments by aligning the read pair in their overlapping parts. Initially, the adapter sequence were trimmed using the Trimmomatic tools and the resulting fragments were filtered against sequence quality metrics, overlapping ambiguities and length criteria. Step B consisted of removing the sequence parts that were targeted by the PCR primers for amplification in order to mask the PCR primer binding regions before evaluating any redundancy between the two libraries. Step C was the evaluation of the redundancy between the fragments of both libraries. A sequence was retained only if it was present in both libraries. As described in step B above, the PCR primer regions were not considered in step C. Finally, step D included three sub-steps: (i) the extraction; (ii) the occurrence filtering; and, (iii) the rotation. Based on the redundancy set obtained in step C, all of the sequences that were present in both the libraries were extracted. Thus, the extracted repetitive sequences were filtered in order to obtain those sequences that were found at least 10 times in one of the libraries. Then, these sequences were aligned against the master sequence in order to identify the sequence variation.
Genome_build: Data obtained were analysed against PSTVd-RG1 genome (GenBank Acc. No. U23058).
Supplementary_files_format_and_content: Percentage of 10 most abundant PSTVd variant occured for each week was retrieved and presented in .pdf

organism: Potato spindle tuber viroid

source_name: Solanum lycopersicum cv. Rutgers leaf tissue

growth_protocol: Grown at a temperature of 25 ºC with 16 h of light and 8 h of darkness.

extract_protocol:
Total RNA from infected leaf samples was extracted using the mirVana miRNA isolation kit (Ambion) with modifications. Briefly, 150 mg of leaf sample was ground with 600 µL of lysis/binding buffer in the presence of sand. Then, 70 µL of microRNA homogenate was added and the sample was mixed by vortexing followed by incubation on ice for 10 min. Total RNA was isolated by acid phenol-chloroform (5:1) extraction and was precipitated by centrifugation after adding 2.5 volumes (vol.) of absolute ethanol. The RNA was further purified by DNase I (Promega) treatment. RNA integrity was examined in a 2100 Bioanalyzer (Agilent Technologies).
For the viroid library preparation, circular PSTVd molecules were purified from the pooled total RNA of each week by separating 10 µg of total RNA by 5% polyacrylamide-8 M urea denaturating gel electrophoresis (5 %-dPAGE). The circular PSTVd (cPSTVd) molecules were eluted from the gel and precipitated with 2.5 vol. of ethanol. In order to prepare the 2 complementary DNA (cDNA) libraries, 1 µg of purified cPSTVd RNA was separately subjected to reverse transcription (RT) using a primer binding at either position 280- to 269 (L1) or 10 to 354 (L2) of PSTVd-RG1, respectively, for each week. The resulting cDNA libraries were amplified by polymerase chain reaction (PCR) with the primers F1/R1 for L1 and F2/R2 for L2 followed by indexing of each library.

treatment_protocol: Tomato plants were agro-infiltrated with the plasmid containing a dimeric head-to-tail construct of PSTVd-RG1 in Agrobacterium tumefaciens.

tag: variant


title: not4∆ [SM031Fd]

description:
Ribosome-protected RNA 54-68 nt
Biological replicate of SM030Fd


title: Tomato_PSTVd_L1

description:
variant RG1
circular viroid
Plants were inoculated with PSTVd-RG1 strain and library prepared using F1/R1 primers


title: Pneumonia [115_CAP]

city: Marburg

first: Wilhelm

last: Bertrams

address: Hans-Meerwein-Str. 2

department: Institute for Lung Research

institute: Philipps University Marburg

data_processing:
Raw Ct data are shown in Matrix non-normalized. U6 snRNA (average of 4 values) was used for normalization in Matrix normalized, yielding deltaCt values.
Fold changes were calculated with the the ddCt method (2^-ddCt)

label: FAM/NFQ-MGB

label_protocol: RNA was reverse transcribed with the Life Technologies miR RT kit wiith megaplex primers. Reverse transcribed RNA was then run on a TLDA plate with FAM-labelled primers

extract_protocol: Total RNA was isolated by cell lysis in Trizol and subsequent phenol/chloroform precipitation

treatment_protocol: PBMCs were isolated from patients suffering from Community Acquired Pneumonia (CAP) or acute exacerbating chronic obstructive pulmonary disease (AECOPD) or from healthy donors. RNA was extracted from these samples.

tag: subject status

value: Pneumonia patient

tag: tissue

value: PBMC (blood leukocyte)

tag: molecule type

value: microRNA


title: Pneumonia [117_CAP]


title: hcr1∆ [SM032Fd]

description: Ribosome-protected RNA 54-68 nt


title: Pneumonia [97_CAP]


title: WT [SM026Fd]

description:
Ribosome-protected RNA 54-68 nt
Biological replicate of SM015Fd and SM023Fd

value: WT


title: not4∆ [SM030Fd]

description: Ribosome-protected RNA 54-68 nt


title: Pneumonia [96_CAP]


title: Pneumonia [77_CAP]


title: Pneumonia [89_CAP]


title: slh1∆ [SM029Fd]

description:
Ribosome-protected RNA 54-68 nt
Biological replicate of SM025Fd


title: Pneumonia [71_CAP]


title: hel2∆ [SM016Fd]

description: Ribosome-protected RNA 40-80 nt


title: AECOPD [125_AECOPD]

value: AECOPD patient


title: brown adipose tissue, Beclin1 KO_rep2

value: untreated

value: interscapular brown adipose tissue


title: WT [SM015Fd]

description:
Ribosome-protected RNA 40-80 nt
end3SM015Fd23Fd_minus.wig
end3SM015Fd23Fd_plus.wig


title: AECOPD [109_AECOPD]


title: brown adipose tissue, Beclin1 KO_rep1


title: hel2∆ [SM024F]

description:
Ribosome-protected RNA 25-34 nt
Biological replicate of SM016F


title: WT [SM023F]

description:
Ribosome-protected RNA 25-34 nt
Biological replicate of SM015F
end3SM015F23F_minus.wig
end3SM015F23F_plus.wig


title: hel2∆ [SM016F]

description: Ribosome-protected RNA 25-34 nt


title: AECOPD [107_AECOPD]


title: AECOPD [101_AECOPD]


title: AECOPD [100_AECOPD]


title: WT [SM015F]

description:
Ribosome-protected RNA 25-34 nt
end3SM015F23F_minus.wig
end3SM015F23F_plus.wig


title: AECOPD [102_AECOPD]


title: AECOPD [76_AECOPD]


title: wt_eco_pc2

city: Boston

first: Xuemei

last: Xie

state: MA

address: 811 Enders Building, 320 Longwood Ave.

department: Transfusion Medicine

institute: Boston Children's Hospital

description: Single cell RNA-seq

data_processing:
Sequenced reads of mouse were aligned to the mm10 mouse transcriptome, then quantify the expression of transcripts in each cell using Cell Ranger v2.2.0.
Sequenced reads of human were aligned to the hg38 human transcriptome, then quantify the expression of transcripts in each cell using BD™ Rhapsody Whole Transcriptome Assay Analysis Pipeline.
Genome_build: mm10 (mouse) or hg38 (human)
Supplementary_files_format_and_content: *.txt: Text files include UMIs for each Sample.

source_name: peritoneal cavity neutrophil

extract_protocol: 10x Genomics Single Cell 3’ Library Kit V2.

tag: strain/background

tag: cell type

value: Peritoneal cavity neutrophil

tag: condition

value: E. coli challenge (24h)

tag: sorting

value: Sorted by Gr1+


title: healthy [22_H]

value: healthy donor


title: lsd2-ΔC (REP3) RNA-Seq [T12]

city: Winston Salem

first: David

last: de la Cerda

state: NC

address: 1834 Wake Forest Rd

department: Biology

institute: Wake Forest University

description:
T12
lsd2-ΔC

data_processing:
Raw Reads were mapped using STAR v 2.7.2b.
Mapped reads were processed into read profiles using deepTools v 3.2.1.
Genome_build: ASM294v2
Supplementary_files_format_and_content: *bw: BigWig files were generated using deepTools and profile single-base expression RNA-Seq profiles.

organism: Schizosaccharomyces pombe

extract_protocol: Invitrogen PureLink RNA Mini Kit.


title: ASC donor 3 normal glucose

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description:
LA_normal_45
Lipoaspirate derived mesenchymal stromal cells

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner 3000.

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 7, from SAS. Gene expression profiling was performed using arrays of Human Transcriptome Array 2.0-type from Affymetrix. A Custom CDF Version 22 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary.

source_name: Primary cell culture, isolated from human lipoaspirate

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: ASC were cultured in standard medium (DMEM 1g/l glucose + 10% pooled human AB blood serum for ASC), and HRMVPC in pericyte growth medium (PleoBiotech).

extract_protocol: Cell harvest using trypsin; RNA extraction using Qiagen RNeasy Micro kit.

treatment_protocol: Control group was kept in standard medium. For the high glucose condition 3.5 g/l glucose were added to the medium. Cells were harvested after 7 days.

value: ASC

value: Normal glucose


title: lsd2-ΔC (REP2) RNA-Seq [T11]

description:
T11
lsd2-ΔC


title: healthy [17_H]


title: lsd2-ΔC (REP1) RNA-Seq [T10]

description:
T10
lsd2-ΔC


title: ASC donor 3 high glucose

description:
LA_high_46
Lipoaspirate derived mesenchymal stromal cells

value: High glucose


title: ASC donor 1 normal glucose

description:
LA_normal_37
Lipoaspirate derived mesenchymal stromal cells


title: healthy [21_H]


title: HRMVPC donor 2 normal glucose

description:
HRMVPC_normal_39
Human retinal microvascular pericytes

source_name: Pelo Biotech, Planegg, Germany

value: HRMVPC


title: ASC donor 2 high glucose

description:
LA_high_42
Lipoaspirate derived mesenchymal stromal cells


title: ASC donor 2 normal glucose

description:
LA_normal_41
Lipoaspirate derived mesenchymal stromal cells


title: HRMVPC donor 3 normal glucose

description:
HRMVPC_normal_43
Human retinal microvascular pericytes


title: HRMVPC donor 2 high glucose

description:
HRMVPC_high_40
Human retinal microvascular pericytes


title: HRMVPC donor 3 high glucose

description:
HRMVPC_high_44
Human retinal microvascular pericytes


title: ASC donor 1 high glucose

description:
LA_high_38
Lipoaspirate derived mesenchymal stromal cells


title: HRMVPC donor 1 normal glucose

description:
HRMVPC_normal_35
Human retinal microvascular pericytes


title: wt_eco_sp2

description: Single cell RNA-seq

source_name: spleen neutrophil

value: Spleen neutrophil


title: lsd1-ΔHMG (REP 2) RNA-Seq [T8]

description:
T8
lsd1-ΔHMG


title: lsd1-ΔHMG (REP 3) RNA-Seq [T9]

description:
T9
lsd1-ΔHMG


title: wt_eco_pb2

description: Single cell RNA-seq

source_name: peripheral blood neutrophil

value: Peripheral blood neutrophil


title: HRMVPC donor 1 high glucose

description:
HRMVPC_high_36
Human retinal microvascular pericytes


title: healthy [08_H]


title: lsd1-ΔHMG (REP 1) RNA-Seq [T7]

description:
T7
lsd1-ΔHMG


title: wt_eco_lv2

description: Single cell RNA-seq

source_name: liver neutrophil

value: Liver neutrophil


title: wt_eco_bm2

description: Single cell RNA-seq

source_name: bone marrow neutrophil

value: Bone marrow neutrophil


title: 86A_42

city: Durham

first: Jen-Tsan

last: Chi

address: 101 Science Drive, DUMC 3382

department: Molecular Genetics and Microbiology

institute: Duke University

hyb_protocol: Briefly, 100 ng of each total RNA sample was used as input into the nCounter Human miRNA sample preparation. Hybridization was conducted for 16 h at 65°C. Subsequently, the strip tubes were placed into the nCounter Prep Station for automated sample purification and subsequent reporter capture.

scan_protocol: Each sample was scanned for 600 FOV on the nCounter Digital Analyzer. Data was extracted using the nCounter RCC Collector.

data_processing: Raw data was normalized using internal positive spike controls to account for variability in the hybridization process. The data was further normalized to the average counts of all endogenous miRNAs in each lane to account for any variability in the sample input. MiRNA detection was determined using a metric that yields a detection call at a confidence level of 95% (p<0.05). This detection measure identifies all miRNAs in which the count of the miRNA is two standard deviations above the average of negative spike probes.

source_name: RBC stored for 42 days

label_protocol: No RNA labeling were performed prior to the hybridization as a special feature the Nanostring technology.

growth_protocol: All studies were approved by the Institutional Review Board. Following informed consent, whole blood from healthy adults was drawn into CPD-ADSOL [AS-1] collection set, and processed into leukodepleted packed RBC units following standard procedures. Units were stored at 1-6 ºC in a monitored refrigerator for 42 days. 5 mL samples were removed for testing at days 1, 3, 7, 10, 14, 28, 36 or 42 (expiration date). Removal of aliquots was accomplished anaerobically via a sterile-docking device fitted with a valve to ensure there was no re-entry of air, or other contamination, into the RBC unit. RNA was isolated from RBCs using the mirVana™ miRNA Isolation Kit (Thermo Fisher). miRNA expression was normalized using non-human miRNAs exogenously added to each sample during RNA isolation.

extract_protocol: RNA were extracted using Ambion small RNA processing kits

tag: sample type

value: Packed RBC processed in blood bank

tag: ex vivo storage days

value: 42 days


title: wt_eco_bm1

description: Single cell RNA-seq

value: Sorted by cKit+ Gr1+


title: Wild-type cells (REP 3) RNA-Seq [C3]

source_name: Wild-type

value: Wild-type


title: wt_ctl_sp2

description: Single cell RNA-seq

value: Steady state


title: Wild-type cells (REP 2) RNA-Seq [C2]


title: wt_ctl_pb2

description: Single cell RNA-seq


title: healthy [02_H]

value: PBMC (blood leukocyte)

value: microRNA


title: Wild-type cells (REP 1) RNA-Seq [C1]


title: wt_ctl_bm1

description: Single cell RNA-seq


title: H3K4me1.D.rep1

source_name: homogenous synchronous spermatogenic cells

tag: Stage

value: D

value: wild type

tag: chip antibody

value: Active Motif 39297, lot 19417002


title: wt_ctl_bm2

description: Single cell RNA-seq

value: Sorted by Gr1+


title: 86A_36

source_name: RBC stored for 36 days

value: 36 days


title: healthy [05_H]

value: healthy donor


title: 86A_28

source_name: RBC stored for 28 days

value: 28 days


title: 86A_10

source_name: RBC stored for 10 days

value: 10 days


title: 86A_14

source_name: RBC stored for 14 days

value: 14 days


title: H3K4me1.mP.rep1

value: mP


title: hel2∆, no 3-AT [SM038Ft]

data_processing:
Library strategy: ribosome profiling
Base calling and demultiplexing was performed at the NHLBI DNA Sequencing and Genomics Core at the NIH Intramural program, Bethesda, MD.
Files were demultiplexed and then trimmed to the start of the linker sequence.
Reads were aligned to a library of non coding RNA genes and those not matching were retained.
Reads were then aligned to the genome and those not matching to a custom library of splice junctions by using Bowtie (Langmead et al., 2009). For footprints, reads that did not match in these steps were trimmed of consecutive 3' As and realigned. The aligned reads from all alignment rounds were pooled and normalized to units of reads per million (rpm) (by dividing by the total number of million mapped reads in a sample) to generate wig files.
Replicates or multiple sequencing lanes for a given sample were pooled together to create a single wig file for each condition to be used in downstream analysis.
Genome_build: R64-1-1
Supplementary_files_format_and_content: All files are fixedStep wig files (text format, each line representing one position in the genome).

source_name: Whole cells

value: whole cells

tag: genotype/variation

value: hel2<delta> BY4741, His3+

tag: molecule subtype

value: Ribosome-protected RNA 80-100 nt


title: WT, no 3-AT [SM036Ft]

value: WT BY4741, His3+


title: hel2∆ YCplac33-hel2-C64AC67A [SM045Fd]

value: hel2<delta> BY4741

value: Ribosome-protected RNA 54-68 nt


title: H3K4me1.mZ.rep1

data_processing:
Base-calling was performed using CASAVA.
Firstly, All of the Histone modification ChIP-seq data were send to trim-galore to remove adapter contamination and low quality sequences, Phred score of any bases in a reads under 20 and adapter sequence were removed, reads after trimming shorter than 30 were discarded.
Trimmed sequences were then mapped with Bowtie (v2.2.6) using default parameters. Duplicate reads were removed by samtools rmdup -s. Unique and monoclonal mapped reads were extended to 150-bp based on the average sonicated chromatin DNA length.
Spike-in reads were mapped to drosophila genome (dm6) using same parameters.
GenomeCoverageBed (bedtools) was used to transfer bed files to bedGraph files, then spikein reads was used as a normalization factor that equalizes the signal across samples. Normalized bedGraph files were subsequently transferred to bigwig files.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

value: mZ


title: 86A_1

source_name: RBC stored for 1 days

value: Packed RBC processed in blood bank

value: 1 day


title: 86A_7

source_name: RBC stored for 7 days

value: 7 days


title: H3K4me1.L.rep1

value: L

value: wild type

value: Active Motif 39297, lot 19417002


title: healthy [13_H]

value: healthy donor

value: PBMC (blood leukocyte)

value: microRNA


title: H3K4me1.mPL.rep1

value: mPL


title: 85A_42

value: 42 days


title: hel2∆ YCplac33 [SM043Fd]

value: whole cells


title: 86A_3

source_name: RBC stored for 3 days

value: 3 days


title: WT YCplac33 [SM042Fd]

value: WT BY4741


title: 85A_36

value: 36 days


title: hel2∆, no 3-AT [SM038Fd]

value: hel2<delta> BY4741, His3+

value: Ribosome-protected RNA 40-68 nt


title: H3K4me1.TypeB.rep1

value: TypeB


title: 85A_28

value: Packed RBC processed in blood bank

value: 28 days


title: SeV DMSO treatment P13-6

city: new york

first: satoshi

last: ikegame

state: new york

address: 1468 madison avenue, Annenbergbuilding 17-24

department: microbiology

institute: Icahn school of medicine at Mount Sinai

description: replicate 6 of passage 13

data_processing:
Illumina Control software was used for basecalling
BBTools for mergingpaired-end reads
bowtie2 for alignment
IGVtools for exporting wig file.
Genome_build: 10,673bp -13,757bp of KY29509 was used as reference sequence for alignment. virus reference sequence
Supplementary_files_format_and_content: processed data show the coverage of sequenced reads

organism: Respirovirus muris

source_name: Sendai virus

growth_protocol: Sendai virus were amplified in Vero cells with or without anti-virus drug (GHP-88309). Viruses were amplified up to passage 13, then RNA was extracted from virion.

extract_protocol:
Qiagen RNeasy kit
3,085bp amplicon (corresponds to 10,673bp -13,757bp of KY29509) were reverse transcribed and amplified by superscript III one-step. This amplicon was separated into 8 pieces (400-450bps) and re-amplified individually and sequenced by Miseq (2x250bp). The library was prepped by NEBNext Ultra DNA Library Prep kit.

treatment_protocol: Passaging of SeV under increasing concentrations of GHP-88309 (Starting at 1 µM GHP-88309 and increasing gradually until final concentration at 13th passage=200 µM GHP-88309)

value: Vero E6 cells

tag: passages

tag: host cells

value: african green monkey renal cells

value: RNA from the virion


title: H3K4me1.A1.rep1

tag: strain

tag: genotype

value: wild type

value: Active Motif 39297, lot 19417002


title: SeV DMSO treatment P13-4

description: replicate 4 of passage 13


title: RBD00006-T

data_processing:
sequenced reads of human were aligned to the hg38 human transcriptome, then quantify the expression of transcripts in each cell using BD™ Rhapsody Whole Transcriptome Assay Analysis Pipeline
Genome_build: hg38 (human)
Supplementary_files_format_and_content: tab-delimited text files include UMIs for each Sample

extract_protocol: BD Rhapsody Cartridge Reagent Kit

value: peripheral blood neutrophil

value: steady state

value: Sorted by CD33+


title: hel2∆ YCplac33-HEL2 [SM044Fd]

value: whole cells

value: hel2<delta> BY4741

value: Ribosome-protected RNA 54-68 nt


title: H3K4me1.Undiff.rep1

extract_protocol:
ChIP assay was carried out as previously described. The sorted homogenous synchronous spermatogenic cells were crosslinked with 1% formaldehyde for 10 mins and then stopped by adding 125 mM Glycine. Chromatin samples were lysed with lysis buffer (20 mM Tris-HCl pH8.0, 500 mM NaCl, 1 mM EDTA, 1% TritonX-100 and 0.1% SDS) and sonicated with Qsonica. Histone modification specific antibody was incubated with chromatin samples overnight at 4 ℃.0.5 ug spike-in antibody (Active motif #61686) and 25 ng spike-in chromatin (Active motif #53083) were used in this ChIP assay according to the manufacture’s guidelines.
DNA samples were analyzed using real time PCR and prepared for deep sequencing according to the manufacture’s guidelines (KAPA Biosystems KK8503 and VAHTS Universal DNA Library Prep Kit for Illumina V3 ND607). Finally, libraries were pooled and sequenced on the Illumina HiSeq 2500 sequencer for 150-bp paired-end sequencing.

value: Undiff


title: MUT3

city: Guangzhou

first: Guang-Rong

last: Yan

state: Guangdong

address: 63 Duobao Road

institute: Biomedicine Research Center, the Third Affiliated Hospital of Guangzhou Medical University

data_processing:
Illumina Casava1.7 software was used for basecalling.
Data filtering were performed as follows:1 ) Remove reads with adaptor sequences; 2). Remove reads in which the percentage of unknown bases (N) is greater than 10%; 3). Remove low quality reads. If the percentage of the low quality base (base with quality value ≤ 5) is greater than 50% in a read, this read is defined as low quality. No more than 2 mismatches were allowed in the alignment.
Fragments per kilobase of exon per million fragments mapped (FPKM) method is used in calculated expression level (Mortazavi et al., 2008)
Genome_build: GRCh38(hg38)

source_name: colon cancer cell line

growth_protocol: These cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum at 37℃ in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was harvested using Trizol reagent. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell line

value: colon cancer cell line


title: 85A_14

value: 14 days


title: 85A_10

value: 10 days


title: HP1-SKD cDNA, rep 2

city: Stockholm

first: Artem

last: Ilin

address: Svante Arrhenius väg 20C

department: MBW

country: Sweden

institute: Stockholm University

description:
RNA-seq_HP1-SKD_rep2
Poly(A)+ RNA

data_processing:
Library strategy: RNA-seq
Reads were aligned to dm3/R5 genome assembly, counted for genes (BDGP5.78 annotation) and converted to transcripts per million (TPM) values using Salmon (Patro et al. 2017) or mapped on TE consensus sequences using HISAT2 (Pertea et al. 2016). Differential expression was revealed by DESeq2 (Love et al. 2014) package for R with the cutoff parameters P < 0.05 and TPM fold change > 2.
Genome_build: dm3 (BDGP Release 5)
Supplementary_files_format_and_content: bedgraph files were generated using htseq-count software and R via Rstudio, counts represent RPM values per 500-nt bins.
Supplementary_files_format_and_content: sf.txt files are read counts per gene of each RNA-seq replica which were obtained via Salmon software.

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Ovaries

growth_protocol: Flies were grown according to standard protocols.

extract_protocol:
Approximately 100 ovaries from 0-4 day-old control or HP1a-SKD females were manually dissected in the cold PBS. Poly(A)+ RNA purified on the oligo(dT) column was isolated (in two biological replicates) using Trizol reagent (Invitrogen).
Purification of poly(A)+ RNA on the oligo(dT) column, cDNA library preparation with random primers and single-end deep sequencing on Illumina HiSeq 1500 were carried out by the Genoanalytica (https://www.genoanalytica.ru) resulting in the 19-39 million 50 nt single-end reads.

value: F1 from tj-Gal4 x HP1a RNAi

tag: tissue

value: Ovaries

tag: Sex

value: Female

tag: biological replicate


title: SeV DMSO treatment P13-5

description: replicate 5 of passage 13

tag: cell type

value: Vero E6 cells

value: african green monkey renal cells


title: HP1-SKD cDNA, rep 1

description:
RNA-seq_HP1-SKD_rep1
Poly(A)+ RNA


title: SeV DMSO treatment P13-3

description: replicate 3 of passage 13

value: RNA from the virion


title: MUT1


title: MUT2


title: SeV DMSO treatment P13-2

description: replicate 2 of passage 13


title: ORF3

value: ORF


title: Control cDNA, rep 2

description:
RNA-seq_control_rep2
Poly(A)+ RNA

value: F1 from tj-Gal4 x #60000 (VDRC)


title: Control cDNA, rep 1

description:
RNA-seq_control_rep1
Poly(A)+ RNA


title: ORF2


title: SeV DMSO treatment P13-1

description: replicate 1 of passage 13


title: 85A_3

value: Packed RBC processed in blood bank

value: 3 days


title: 75A_42

value: 42 days


title: ORF1


title: 75A_36

value: 36 days


title: 85A_7

value: 7 days


title: SeV Drug treatment P13-4

description: replicate 4 of passage 13


title: 75A_28

value: 28 days


title: NC2

value: colon cancer cell line

value: blank vector


title: NC3


title: SeV Drug treatment P13-3

description: replicate 3 of passage 13


title: 85A_1

value: 1 day


title: 75A_14

value: 14 days


title: NC1


title: 75A_10

value: 10 days


title: SeV Drug treatment P13-2

description: replicate 2 of passage 13


title: SeV Drug treatment P13-1

description: replicate 1 of passage 13


title: NKD181202670

description: Single cell RNA-seq

source_name: peripheral blood neutrophil

extract_protocol: BD Rhapsody Cartridge Reagent Kit.

value: Peripheral blood neutrophil

tag: condition

value: Steady state

value: Sorted by CD33+


title: 75A_7


title: SeV Drug treatment P13-6

description: replicate 6 of passage 13

value: Vero E6 cells

value: african green monkey renal cells

value: RNA from the virion


title: SeV Drug treatment P13-5

description: replicate 5 of passage 13


title: 75A_3

value: Packed RBC processed in blood bank


title: 75A_1


title: SGBS cells, differentiation with differentiation medium, day 10

status: Public on May 25 2020

city: Leipzig

first: Petra

last: Büttner

address: Strümpellstrasse 163

department: Internal medicine/ Cardiology

institute: Heart Center Leipzig

description:
d10
Cells were kept in DMEM/Ham’s F12 containing 33 μM biotin, 17 μM pantothenate, 10 μg/ml apo-transferrin, 20 nM insulin, 10nM hydrocortisone, and 0.2 nM triiodothyroxine. Medium was changed every second day.
t 10 . d 10 . Gr 4  raw

hyb_protocol: Sample processing and labeling were done according to Affymetrix protocols. 5µg RNA were processed.

scan_protocol: Scanning was done using GCOS v1.5.

data_processing: The data was processed using  MAS 5.0.

source_name: preadipocytes from a boy with Simpson-Golabi-Behmel syndrome (SGBS)

growth_protocol: Typically, cells at generation 30–60 (corresponding to passage 10–20) are grown for 3 days to near confluence in DMEM/F12 (optional containing 10% fetal calf serum (FCS)). Differentiation is started (day 0) by washing cells 3 times with phosphate buffered saline (PBS) and then changing to a serum- and albumin-free differentiation medium (DMEM/F12 supplemented with 33 μM biotin, 17 μM pantothenate, 10 μg/ml apo-transferrin, 20 nM insulin, 10nM hydrocortisone, 0.2 nM triiodothyroxine, 25 nM dexamethasone, 500 μM IBMX, and 2 μM rosiglitazone . At day four the medium contains only 33 μM biotin, 17 μM pantothenate, 10 μg/ml apo-transferrin, 20 nM insulin, 10nM hydrocortisone, and 0.2 nM triiodothyroxine.

extract_protocol: Total RNA was extracted from cells using phenol-chloroform extraction procedure in combination with commercially available column cleanup.

treatment_protocol: A set of molecules was added to SGBP preadipocytes to initiate differentiation and to keep differentiation of mature adipocytes (see protocoll).

tag: gender

value: male

tag: disease state

value: SGBS

tag: cell origin

value: lipome

value: preadipocytes

tag: protocol

tag: time

value: day 10


title: P210_P8_WT_C57BL/6J_cerebellum_rep3

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

institute: University Medical Center Freiburg

data_processing:
Individual Fastq files were aligned to the mouse Genome (Gencode M11 / GRCm38) using the STAR aligner version 2.5.2b with parameters STAR --runThreadN <cpu> --genomeDir <index> --genomeLoad LoadAndKeep --limitBAMsortRAM 20000000000 --readFilesIn <fastq> --readFilesCommand zcat --outFileNamePrefix <sampleID> --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outSAMtype BAM SortedByCoordinate
Gene counts were obtained from BAM files using featureCounts v1.5.1 with parameters -a <Gencode_vM11.gtf> -G <GRCm38.primary_assembly.genome.fa> -o counts.txt -F GTF -R -g gene_id -t exon -T 12 --largestOverlap <bamfiles>
single cell RNAseq analysis and clustering was performed using RaceId/StemId2 (Grün, D., L. Kester, and A. van Oudenaarden. 2014. “Validation of noise models for single-cell transcriptomics.” Nat. Methods 11 (6): 637–40.). Cells with less than 500 detected genes, less than 5000 aligned reads or more than 700 000 aligned reads were discarded. Only genes with a count of 5 in at least a single cell were used for analysis.
Genome_build: Gencode M11 / GRCm38
Supplementary_files_format_and_content: comma separated (csv) file with gene counts per sample

source_name: microglia

extract_protocol:
After transcardial perfusion with PBS, brains were roughly minced and homogenized with a potter in HBSS containing 15 mM HEPES buffer and 0.54 % Glucose. Whole-brain homogenate was separated by 70/37/30 % layered Percoll gradient centrifugation at 800 g for 30 min at 4 °C (no brake). The CNS macrophages containing interphase was then collected and washed once with PBS containing 2% FCS and 10mM EDTA before staining. Cells were stained with primary antibodies directed against CD11b (M1/70, BioLegend), CD45 (30-F11, BD Biosciences), Ly6C (AL-21, BD Biosciences) and Ly6G (1A8, BD Biosciences) for 20 min, and CD206 (C068C2, BioLegend) for 45 min at 4 °C. After washing, cells were analyd using a MoFlo Astrios (Beckman Coulter). microglia were FACS-sorted from six different CNS regions of healthy and diseased brains (see gating strategy shown in supplementary Fig.2) into a 384-well plate containing a lysis buffer.
Single cell RNAseq libraries were generated following the published SmartSeq2 protocol (Picelli et al. Nature Metods 2013)

value: cerebellum

value: wildtype


title: P210_P9_WT_C57BL/6J_cerebellum_rep3


title: P210_P7_WT_C57BL/6J_cerebellum_rep3


title: SGBS cells, differentiation with differentiation medium, day 5

description:
d5
Cells were kept in differentiation medium: DMEM/Ham’s F12 containing 33 μM biotin, 17 μM pantothenate, 10 μg/ml apo-transferrin, 20 nM insulin, 10nM hydrocortisone, and 0.2 nM triiodothyroxine. Medium was changed every second day.
t 5 . d 5 . Gr x  raw

label_protocol: Sample processing and labeling were done according to Affymetrix protocols. 5µg RNA were processed.

value: day 5


title: SGBS cells, undifferentiated, in preadipocyte medium, replicate 2, day 0

description:
d0_2pa
Cells were kept in DMEM/Ham’s F12.
t 2pa . d 0 . Gr 1  raw

value: day 0


title: SGBS cells, undifferentiated, in preadipocyte medium, replicate 1, day 0

description:
d0_1pa
Cells were kept in DMEM/Ham’s F12.
t 1pa . d 0 . Gr 1  raw


title: SGBS cells, start of differentiation with quick differentiation medium, day 4

description:
d4
Cells were kept in DMEM/Ham’s F12 containing 33 μM biotin, 17 μM pantothenate, 10 μg/ml apo-transferrin, 20 nM insulin, 10nM hydrocortisone, and 0.2 nM triiodothyroxine, 25 nM dexamethasone, 500 μM IBMX, and 2 μM rosiglitazone.
t 4 . d 4 . Gr 2  raw

value: day 4


title: SGBS cells, start of differentiation with quick differentiation medium, day 1

description:
d1
Cells were kept in quick differentiation medium: DMEM/Ham’s F12 containing 33 μM biotin, 17 μM pantothenate, 10 μg/ml apo-transferrin, 20 nM insulin, 10nM hydrocortisone, and 0.2 nM triiodothyroxine, 25 nM dexamethasone, 500 μM IBMX, and 2 μM rosiglitazone.
t 1qd . d 1 . Gr x  raw

value: day 1


title: SGBS cells, differentiation with differentiation medium, day 12

description:
d12
Cells were kept in DMEM/Ham’s F12 containing 33 μM biotin, 17 μM pantothenate, 10 μg/ml apo-transferrin, 20 nM insulin, 10nM hydrocortisone, and 0.2 nM triiodothyroxine. Medium was changed every second day.
t 12 . d 12 . Gr 4  raw

value: day 12


title: SGBS cells, differentiation with differentiation medium, day 8

description:
d8
Cells were kept in DMEM/Ham’s F12 containing 33 μM biotin, 17 μM pantothenate, 10 μg/ml apo-transferrin, 20 nM insulin, 10nM hydrocortisone, and 0.2 nM triiodothyroxine. Medium was changed every second day.
t 8 . d 8 . Gr 3  raw

value: day 8


title: SGBS cells, undifferentiated, in medium with fetal calf serum, day 0

description:
d0_2fcs
Cells were kept in DMEM/Ham’s F12 with 10% FCS.
t 2fcs . d 0 . Gr 1  raw


title: P210_P5_WT_C57BL/6J_cerebellum_rep2


title: SGBS cells, differentiation with differentiation medium, day 6

description:
d6
Cells were kept in DMEM/Ham’s F12 containing 33 μM biotin, 17 μM pantothenate, 10 μg/ml apo-transferrin, 20 nM insulin, 10nM hydrocortisone, and 0.2 nM triiodothyroxine. Medium was changed every second day.
t 6 . d 6 . Gr 3  raw

value: day 6


title: SGBS cells, start of differentiation with quick differentiation medium, day 3

description:
d3
Cells were kept in DMEM/Ham’s F12 containing 33 μM biotin, 17 μM pantothenate, 10 μg/ml apo-transferrin, 20 nM insulin, 10nM hydrocortisone, and 0.2 nM triiodothyroxine, 25 nM dexamethasone, 500 μM IBMX, and 2 μM rosiglitazone.
t 3 . d 3 . Gr 2  raw

value: day 3


title: HSFB2 with stretch and TA

city: Xi’an

first: Huayu

state: Shaanxi

address: Changle Xilu 15

department: Department of Burns and Cutaneous Surgery, Xijing Hospital

institute: Fourth Military Medical University

description: HSFB2 with stretch and TA

hyb_protocol: 1.5 ug of 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 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: The labeled cRNAs were hybridized onto the microarray. After washing, the arrays were scanned by the Agilent Scanner G2505C (Agilent Technologies).

data_processing: Feature extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data.Genespring (version 14.8,Agilent Technologies) were employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm. The probes that at least 1 conditions out of 2 conditions have flags in “Detected” were chosen for further data analysis. Differentially expressed genes were then identified through fold change as well as P value calculated with t-test. The threshold set for up- and down-regulated genes was a fold change>= 2.0 and a P value<= 0.05.

source_name: HSFB2 with stretch and TA

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.

growth_protocol: Cultured hypertrophic scars fibroblasts (from hypertrophic scar patients) were pelleted and grown in DMEM supplemented with 10% fetal calf serum.

extract_protocol: Total RNA was extracted using TRIZOL Reagentfollowing the manufacturer’s instructions. RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific) and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: Hypertrophic scars fibroblasts treated with glucocorticoid were seeded in the chambers and subjected to mechanical stretch. Paired HSFBs in the control groups were treated with solvent and subjected to mechanical stretch.

value: Hypertrophic scar


title: HSFB3 with stretch and TA

description: HSFB3 with stretch and TA

source_name: HSFB3 with stretch and TA


title: HSFB3 with stretch

description: HSFB3 with stretch

source_name: HSFB3 with stretch


title: HSFB2 with stretch

description: HSFB2 with stretch

source_name: HSFB2 with stretch


title: SGBS cells, differentiation with differentiation medium, day 14

description:
d14
Cells were kept in DMEM/Ham’s F12 containing 33 μM biotin, 17 μM pantothenate, 10 μg/ml apo-transferrin, 20 nM insulin, 10nM hydrocortisone, and 0.2 nM triiodothyroxine. Medium was changed every second day.
t 14 . d 14 . Gr 4  raw

value: day 14


title: P210_P24_blank

description: blank

source_name: blank

value: blank


title: P210_P4_WT_C57BL/6J_cerebellum_rep2


title: P210_P20_5xFAD_C57BL/6J_cortex_rep3

value: cortex


title: P210_P23_5xFAD_C57BL/6J_cortex_rep4


title: HSFB1 with stretch and TA

description: HSFB1 with stretch and TA

source_name: HSFB1 with stretch and TA


title: P210_P21_5xFAD_C57BL/6J_cortex_rep3


title: HSFB1 with stretch

description: HSFB1 with stretch

source_name: HSFB1 with stretch


title: P210_P2_WT_C57BL/6J_cerebellum_rep1


title: P210_P16_5xFAD_C57BL/6J_cortex_rep2


title: P210_P13_5xFAD_C57BL/6J_cortex_rep1


title: P210_P18_5xFAD_C57BL/6J_cortex_rep2


title: P210_P15_5xFAD_C57BL/6J_cortex_rep1


title: P210_O9_WT_C57BL/6J_cerebellum_rep3


title: P210_P1_WT_C57BL/6J_cerebellum_rep1


title: P210_P17_5xFAD_C57BL/6J_cortex_rep2


title: P210_P12_blank

description: blank


title: P210_P11_WT_C57BL/6J_cerebellum_rep4


title: P210_P10_WT_C57BL/6J_cerebellum_rep4


title: SGBS cells, start of differentiation with quick differentiation medium, day 2

description:
d2
Cells were kept in DMEM/Ham’s F12 containing 33 μM biotin, 17 μM pantothenate, 10 μg/ml apo-transferrin, 20 nM insulin, 10nM hydrocortisone, and 0.2 nM triiodothyroxine, 25 nM dexamethasone, 500 μM IBMX, and 2 μM rosiglitazone.
t 2qd . d 2 . Gr 2  raw

value: male

value: SGBS

value: lipome

value: day 2


title: P210_O8_WT_C57BL/6J_cerebellum_rep3

value: cerebellum

value: wildtype


title: P210_P3_WT_C57BL/6J_cerebellum_rep1


title: P210_P19_5xFAD_C57BL/6J_cortex_rep3


title: P210_O7_WT_C57BL/6J_cerebellum_rep3


title: P210_P6_WT_C57BL/6J_cerebellum_rep2


title: P210_O4_WT_C57BL/6J_cerebellum_rep2


title: P210_O24_blank

description: blank


title: P210_O5_WT_C57BL/6J_cerebellum_rep2


title: P210_O3_WT_C57BL/6J_cerebellum_rep1


title: P210_O23_5xFAD_C57BL/6J_cortex_rep4


title: P210_O22_5xFAD_C57BL/6J_cortex_rep4


title: P210_O2_WT_C57BL/6J_cerebellum_rep1


title: P210_O21_5xFAD_C57BL/6J_cortex_rep3


title: P210_O20_5xFAD_C57BL/6J_cortex_rep3


title: P210_O19_5xFAD_C57BL/6J_cortex_rep3


title: P210_O12_blank

description: blank


title: P210_O14_5xFAD_C57BL/6J_cortex_rep1


title: P210_O17_5xFAD_C57BL/6J_cortex_rep2


title: P210_O18_5xFAD_C57BL/6J_cortex_rep2


title: P210_O13_5xFAD_C57BL/6J_cortex_rep1


title: P210_O16_5xFAD_C57BL/6J_cortex_rep2


title: P210_O15_5xFAD_C57BL/6J_cortex_rep1


title: P210_O6_WT_C57BL/6J_cerebellum_rep2


title: P210_N9_WT_C57BL/6J_cerebellum_rep3


title: P210_O1_WT_C57BL/6J_cerebellum_rep1


title: P210_N7_WT_C57BL/6J_cerebellum_rep3


title: P210_N8_WT_C57BL/6J_cerebellum_rep3


title: P210_N6_WT_C57BL/6J_cerebellum_rep2


title: P210_N4_WT_C57BL/6J_cerebellum_rep2


title: P210_N23_5xFAD_C57BL/6J_cortex_rep4


title: P210_N24_5xFAD_C57BL/6J_cortex_rep4


title: P210_N5_WT_C57BL/6J_cerebellum_rep2


title: P210_N3_WT_C57BL/6J_cerebellum_rep1


title: P210_N20_5xFAD_C57BL/6J_cortex_rep3


title: P210_N2_WT_C57BL/6J_cerebellum_rep1


title: P210_N22_5xFAD_C57BL/6J_cortex_rep4


title: P210_N18_5xFAD_C57BL/6J_cortex_rep2


title: P210_P14_5xFAD_C57BL/6J_cortex_rep1


title: P210_N21_5xFAD_C57BL/6J_cortex_rep3


title: P210_N17_5xFAD_C57BL/6J_cortex_rep2


title: P210_N19_5xFAD_C57BL/6J_cortex_rep3


title: P210_O11_WT_C57BL/6J_cerebellum_rep4


title: P210_O10_WT_C57BL/6J_cerebellum_rep4


title: P210_N16_5xFAD_C57BL/6J_cortex_rep2


title: P210_N14_5xFAD_C57BL/6J_cortex_rep1


title: P210_N11_WT_C57BL/6J_cerebellum_rep4


title: P210_N10_WT_C57BL/6J_cerebellum_rep4


title: P210_N12_WT_C57BL/6J_cerebellum_rep4


title: P210_N1_WT_C57BL/6J_cerebellum_rep1


title: P210_M9_WT_C57BL/6J_cerebellum_rep3


title: P210_M6_WT_C57BL/6J_cerebellum_rep2


title: P210_M7_WT_C57BL/6J_cerebellum_rep3


title: P210_M4_WT_C57BL/6J_cerebellum_rep2


title: P210_M5_WT_C57BL/6J_cerebellum_rep2


title: P210_M3_WT_C57BL/6J_cerebellum_rep1


title: P210_M22_5xFAD_C57BL/6J_cortex_rep4


title: P210_M24_5xFAD_C57BL/6J_cortex_rep4


title: P210_M18_5xFAD_C57BL/6J_cortex_rep2


title: P210_M17_5xFAD_C57BL/6J_cortex_rep2


title: P210_M21_5xFAD_C57BL/6J_cortex_rep3


title: P210_N15_5xFAD_C57BL/6J_cortex_rep1


title: P210_N13_5xFAD_C57BL/6J_cortex_rep1


title: P210_M2_WT_C57BL/6J_cerebellum_rep1


title: P210_M20_5xFAD_C57BL/6J_cortex_rep3


title: P210_M13_5xFAD_C57BL/6J_cortex_rep1


title: P210_M15_5xFAD_C57BL/6J_cortex_rep1


title: P210_M11_WT_C57BL/6J_cerebellum_rep4


title: P210_M1_WT_C57BL/6J_cerebellum_rep1


title: P210_L9_WT_C57BL/6J_cerebellum_rep3


title: P210_M14_5xFAD_C57BL/6J_cortex_rep1


title: P210_L7_WT_C57BL/6J_cerebellum_rep3


title: P210_M12_WT_C57BL/6J_cerebellum_rep4


title: P210_M10_WT_C57BL/6J_cerebellum_rep4


title: P210_M8_WT_C57BL/6J_cerebellum_rep3


title: P210_L8_WT_C57BL/6J_cerebellum_rep3


title: P210_L6_WT_C57BL/6J_cerebellum_rep2


title: P210_L5_WT_C57BL/6J_cerebellum_rep2


title: P210_L3_WT_C57BL/6J_cerebellum_rep1


title: P210_M23_5xFAD_C57BL/6J_cortex_rep4


title: P210_L23_5xFAD_C57BL/6J_cortex_rep4


title: P210_M16_5xFAD_C57BL/6J_cortex_rep2


title: P210_L22_5xFAD_C57BL/6J_cortex_rep4


title: P210_M19_5xFAD_C57BL/6J_cortex_rep3


title: P210_L24_5xFAD_C57BL/6J_cortex_rep4


title: P210_L21_5xFAD_C57BL/6J_cortex_rep3


title: P210_L2_WT_C57BL/6J_cerebellum_rep1


title: P210_L4_WT_C57BL/6J_cerebellum_rep2


title: P210_L18_5xFAD_C57BL/6J_cortex_rep2


title: P210_L17_5xFAD_C57BL/6J_cortex_rep2


title: P210_L16_5xFAD_C57BL/6J_cortex_rep2


title: P210_L14_5xFAD_C57BL/6J_cortex_rep1


title: P210_L13_5xFAD_C57BL/6J_cortex_rep1


title: P210_L15_5xFAD_C57BL/6J_cortex_rep1


title: P210_L10_WT_C57BL/6J_cerebellum_rep4


title: P210_L12_WT_C57BL/6J_cerebellum_rep4


title: P210_L19_5xFAD_C57BL/6J_cortex_rep3


title: P210_K8_WT_C57BL/6J_cerebellum_rep3


title: P210_L11_WT_C57BL/6J_cerebellum_rep4


title: P210_K7_WT_C57BL/6J_cerebellum_rep3


title: P210_K9_WT_C57BL/6J_cerebellum_rep3


title: P210_L1_WT_C57BL/6J_cerebellum_rep1


title: P210_K5_WT_C57BL/6J_cerebellum_rep2


title: P210_K6_WT_C57BL/6J_cerebellum_rep2


title: P210_K4_WT_C57BL/6J_cerebellum_rep2


title: P210_K3_WT_C57BL/6J_cerebellum_rep1


title: P210_K24_5xFAD_C57BL/6J_cortex_rep4


title: P210_K23_5xFAD_C57BL/6J_cortex_rep4


title: P210_K21_5xFAD_C57BL/6J_cortex_rep3


title: P210_K22_5xFAD_C57BL/6J_cortex_rep4


title: P210_L20_5xFAD_C57BL/6J_cortex_rep3


title: P210_K20_5xFAD_C57BL/6J_cortex_rep3


title: P210_K2_WT_C57BL/6J_cerebellum_rep1


title: P210_K19_5xFAD_C57BL/6J_cortex_rep3


title: P210_K18_5xFAD_C57BL/6J_cortex_rep2


title: P210_K17_5xFAD_C57BL/6J_cortex_rep2


title: P210_K15_5xFAD_C57BL/6J_cortex_rep1


title: P210_K16_5xFAD_C57BL/6J_cortex_rep2


title: P210_K1_WT_C57BL/6J_cerebellum_rep1


title: P210_K10_WT_C57BL/6J_cerebellum_rep4


title: P210_K12_WT_C57BL/6J_cerebellum_rep4


title: P210_K11_WT_C57BL/6J_cerebellum_rep4


title: P210_J9_WT_C57BL/6J_cerebellum_rep3


title: P210_K13_5xFAD_C57BL/6J_cortex_rep1


title: P210_J6_WT_C57BL/6J_cerebellum_rep2


title: P210_K14_5xFAD_C57BL/6J_cortex_rep1


title: P210_J3_WT_C57BL/6J_cerebellum_rep1


title: P210_J8_WT_C57BL/6J_cerebellum_rep3


title: P210_J5_WT_C57BL/6J_cerebellum_rep2


title: P210_J4_WT_C57BL/6J_cerebellum_rep2


title: P210_J7_WT_C57BL/6J_cerebellum_rep3


title: P210_J24_5xFAD_C57BL/6J_cortex_rep4


title: P210_J19_5xFAD_C57BL/6J_cortex_rep3


title: P210_J20_5xFAD_C57BL/6J_cortex_rep3


title: P210_J23_5xFAD_C57BL/6J_cortex_rep4


title: P210_J22_5xFAD_C57BL/6J_cortex_rep4


title: P210_J21_5xFAD_C57BL/6J_cortex_rep3


title: P210_J18_5xFAD_C57BL/6J_cortex_rep2


title: P210_J17_5xFAD_C57BL/6J_cortex_rep2


title: P210_J12_WT_C57BL/6J_cerebellum_rep4


title: P210_J15_5xFAD_C57BL/6J_cortex_rep1


title: P210_J13_5xFAD_C57BL/6J_cortex_rep1


title: P210_J11_WT_C57BL/6J_cerebellum_rep4


title: P210_J14_5xFAD_C57BL/6J_cortex_rep1


title: P210_P22_5xFAD_C57BL/6J_cortex_rep4


title: P210_J1_WT_C57BL/6J_cerebellum_rep1


title: P210_J10_WT_C57BL/6J_cerebellum_rep4


title: P210_I9_WT_C57BL/6J_cerebellum_rep3


title: P210_I7_WT_C57BL/6J_cerebellum_rep3


title: P210_I8_WT_C57BL/6J_cerebellum_rep3


title: P210_I6_WT_C57BL/6J_cerebellum_rep2


title: P210_I4_WT_C57BL/6J_cerebellum_rep2


title: P210_I5_WT_C57BL/6J_cerebellum_rep2


title: P210_I23_5xFAD_C57BL/6J_cortex_rep4


title: P210_I24_5xFAD_C57BL/6J_cortex_rep4


title: P210_I21_5xFAD_C57BL/6J_cortex_rep3


title: P210_I22_5xFAD_C57BL/6J_cortex_rep4


title: P210_I20_5xFAD_C57BL/6J_cortex_rep3


title: P210_J2_WT_C57BL/6J_cerebellum_rep1


title: P210_I18_5xFAD_C57BL/6J_cortex_rep2


title: P210_I19_5xFAD_C57BL/6J_cortex_rep3


title: P210_J16_5xFAD_C57BL/6J_cortex_rep2


title: P210_I2_WT_C57BL/6J_cerebellum_rep1


title: P210_I17_5xFAD_C57BL/6J_cortex_rep2


title: P210_I15_5xFAD_C57BL/6J_cortex_rep1


title: P210_I11_WT_C57BL/6J_cerebellum_rep4


title: P210_I13_5xFAD_C57BL/6J_cortex_rep1


title: P210_I14_5xFAD_C57BL/6J_cortex_rep1


title: P210_I10_WT_C57BL/6J_cerebellum_rep4


title: P210_I16_5xFAD_C57BL/6J_cortex_rep2


title: P210_I12_WT_C57BL/6J_cerebellum_rep4


title: P210_I3_WT_C57BL/6J_cerebellum_rep1


title: P210_H8_WT_C57BL/6J_cerebellum_rep3


title: P210_H9_WT_C57BL/6J_cerebellum_rep3


title: P210_H3_WT_C57BL/6J_cerebellum_rep1


title: P210_H4_WT_C57BL/6J_cerebellum_rep2


title: P210_H5_WT_C57BL/6J_cerebellum_rep2


title: P210_H22_5xFAD_C57BL/6J_cortex_rep4


title: P210_H24_5xFAD_C57BL/6J_cortex_rep4


title: P210_H23_5xFAD_C57BL/6J_cortex_rep4


title: HDY_PB

value: peripheral blood neutrophil

value: steady state

tag: sorting

value: Sorted by CD33+


title: P210_H19_5xFAD_C57BL/6J_cortex_rep3


title: P210_H20_5xFAD_C57BL/6J_cortex_rep3


title: P210_H18_5xFAD_C57BL/6J_cortex_rep2


title: P210_H2_WT_C57BL/6J_cerebellum_rep1


title: P210_H21_5xFAD_C57BL/6J_cortex_rep3


title: P210_H17_5xFAD_C57BL/6J_cortex_rep2


title: P210_H16_5xFAD_C57BL/6J_cortex_rep2


title: P210_H15_5xFAD_C57BL/6J_cortex_rep1


title: P210_I1_WT_C57BL/6J_cerebellum_rep1


title: P210_H13_5xFAD_C57BL/6J_cortex_rep1


title: P210_H14_5xFAD_C57BL/6J_cortex_rep1


title: P210_H12_WT_C57BL/6J_cerebellum_rep4


title: P210_H11_WT_C57BL/6J_cerebellum_rep4


title: P210_H1_WT_C57BL/6J_cerebellum_rep1


title: P210_G7_WT_C57BL/6J_cerebellum_rep3


title: P210_G9_WT_C57BL/6J_cerebellum_rep3


title: P210_H6_WT_C57BL/6J_cerebellum_rep2


title: P210_H7_WT_C57BL/6J_cerebellum_rep3


title: P210_H10_WT_C57BL/6J_cerebellum_rep4


title: P210_G6_WT_C57BL/6J_cerebellum_rep2


title: P210_G5_WT_C57BL/6J_cerebellum_rep2


title: P210_G4_WT_C57BL/6J_cerebellum_rep2


title: P210_G8_WT_C57BL/6J_cerebellum_rep3


title: P210_G24_5xFAD_C57BL/6J_cortex_rep4


title: P210_G23_5xFAD_C57BL/6J_cortex_rep4


title: P210_G3_WT_C57BL/6J_cerebellum_rep1


title: P210_G22_5xFAD_C57BL/6J_cortex_rep4


title: P210_G20_5xFAD_C57BL/6J_cortex_rep3


title: P210_G2_WT_C57BL/6J_cerebellum_rep1


title: P210_G19_5xFAD_C57BL/6J_cortex_rep3


title: P210_G15_5xFAD_C57BL/6J_cortex_rep1


title: P210_G17_5xFAD_C57BL/6J_cortex_rep2


title: P210_G16_5xFAD_C57BL/6J_cortex_rep2


title: P210_G12_WT_C57BL/6J_cerebellum_rep4


title: P210_G13_5xFAD_C57BL/6J_cortex_rep1


title: P210_G14_5xFAD_C57BL/6J_cortex_rep1


title: P210_G18_5xFAD_C57BL/6J_cortex_rep2


title: P210_G10_WT_C57BL/6J_cerebellum_rep4


title: P210_G1_WT_C57BL/6J_cerebellum_rep1


title: P210_F9_WT_C57BL/6J_cerebellum_rep3


title: P210_G11_WT_C57BL/6J_cerebellum_rep4


title: P210_F8_WT_C57BL/6J_cerebellum_rep3


title: P210_F7_WT_C57BL/6J_cerebellum_rep3


title: P210_F4_WT_C57BL/6J_cerebellum_rep2


title: P210_F6_WT_C57BL/6J_cerebellum_rep2


title: P210_F3_WT_C57BL/6J_cerebellum_rep1


title: P210_F5_WT_C57BL/6J_cerebellum_rep2


title: P210_F20_5xFAD_C57BL/6J_cortex_rep3


title: P210_F24_5xFAD_C57BL/6J_cortex_rep4


title: P210_F22_5xFAD_C57BL/6J_cortex_rep4


title: P210_G21_5xFAD_C57BL/6J_cortex_rep3


title: P210_F23_5xFAD_C57BL/6J_cortex_rep4


title: P210_F18_5xFAD_C57BL/6J_cortex_rep2


title: P210_F21_5xFAD_C57BL/6J_cortex_rep3


title: P210_F2_WT_C57BL/6J_cerebellum_rep1


title: P210_F19_5xFAD_C57BL/6J_cortex_rep3


title: P210_F16_5xFAD_C57BL/6J_cortex_rep2


title: P210_F12_WT_C57BL/6J_cerebellum_rep4


title: P210_F11_WT_C57BL/6J_cerebellum_rep4


title: P210_F14_5xFAD_C57BL/6J_cortex_rep1


title: P210_E9_WT_C57BL/6J_cerebellum_rep3


title: P210_F10_WT_C57BL/6J_cerebellum_rep4


title: P210_E8_WT_C57BL/6J_cerebellum_rep3


title: P210_E7_WT_C57BL/6J_cerebellum_rep3


title: P210_E6_WT_C57BL/6J_cerebellum_rep2


title: P210_E4_WT_C57BL/6J_cerebellum_rep2


title: P210_E5_WT_C57BL/6J_cerebellum_rep2


title: P210_F1_WT_C57BL/6J_cerebellum_rep1


title: P210_E3_WT_C57BL/6J_cerebellum_rep1


title: P210_E24_5xFAD_C57BL/6J_cortex_rep4


title: P210_F17_5xFAD_C57BL/6J_cortex_rep2


title: P210_E2_WT_C57BL/6J_cerebellum_rep1


title: P210_E20_5xFAD_C57BL/6J_cortex_rep3


title: P210_E18_5xFAD_C57BL/6J_cortex_rep2


title: P210_F15_5xFAD_C57BL/6J_cortex_rep1


title: P210_E17_5xFAD_C57BL/6J_cortex_rep2


title: P210_E13_5xFAD_C57BL/6J_cortex_rep1


title: P210_E12_WT_C57BL/6J_cerebellum_rep4


title: P210_E15_5xFAD_C57BL/6J_cortex_rep1


title: P210_E11_WT_C57BL/6J_cerebellum_rep4


title: P210_D9_WT_C57BL/6J_cerebellum_rep3


title: P210_E23_5xFAD_C57BL/6J_cortex_rep4


title: P210_E14_5xFAD_C57BL/6J_cortex_rep1


title: P210_E1_WT_C57BL/6J_cerebellum_rep1


title: P210_F13_5xFAD_C57BL/6J_cortex_rep1


title: P210_D4_WT_C57BL/6J_cerebellum_rep2


title: P210_E10_WT_C57BL/6J_cerebellum_rep4


title: P210_E16_5xFAD_C57BL/6J_cortex_rep2


title: P210_D7_WT_C57BL/6J_cerebellum_rep3


title: P210_E22_5xFAD_C57BL/6J_cortex_rep4


title: P210_D5_WT_C57BL/6J_cerebellum_rep2


title: P210_E21_5xFAD_C57BL/6J_cortex_rep3


title: P210_E19_5xFAD_C57BL/6J_cortex_rep3


title: P210_D3_WT_C57BL/6J_cerebellum_rep1


title: P210_D24_5xFAD_C57BL/6J_cortex_rep4


title: P210_D22_5xFAD_C57BL/6J_cortex_rep4


title: P210_D19_5xFAD_C57BL/6J_cortex_rep3


title: P210_D20_5xFAD_C57BL/6J_cortex_rep3


title: P210_D18_5xFAD_C57BL/6J_cortex_rep2


title: P210_D2_WT_C57BL/6J_cerebellum_rep1


title: P210_D17_5xFAD_C57BL/6J_cortex_rep2


title: P210_D21_5xFAD_C57BL/6J_cortex_rep3


title: P210_D16_5xFAD_C57BL/6J_cortex_rep2


title: P210_D15_5xFAD_C57BL/6J_cortex_rep1


title: P210_D8_WT_C57BL/6J_cerebellum_rep3


title: P210_D14_5xFAD_C57BL/6J_cortex_rep1


title: P210_D6_WT_C57BL/6J_cerebellum_rep2


title: P210_D11_WT_C57BL/6J_cerebellum_rep4


title: P210_D12_WT_C57BL/6J_cerebellum_rep4


title: P210_D23_5xFAD_C57BL/6J_cortex_rep4


title: P210_C7_WT_C57BL/6J_cerebellum_rep3


title: P210_C6_WT_C57BL/6J_cerebellum_rep2


title: P210_C5_WT_C57BL/6J_cerebellum_rep2


title: P210_D1_WT_C57BL/6J_cerebellum_rep1


title: P210_C8_WT_C57BL/6J_cerebellum_rep3


title: P210_C23_5xFAD_C57BL/6J_cortex_rep4


title: P210_C3_WT_C57BL/6J_cerebellum_rep1


title: P210_C4_WT_C57BL/6J_cerebellum_rep2


title: P210_C22_5xFAD_C57BL/6J_cortex_rep4


title: P210_C21_5xFAD_C57BL/6J_cortex_rep3


title: P210_C20_5xFAD_C57BL/6J_cortex_rep3


title: P210_C19_5xFAD_C57BL/6J_cortex_rep3


title: P210_D13_5xFAD_C57BL/6J_cortex_rep1


title: P210_C17_5xFAD_C57BL/6J_cortex_rep2


title: P210_C18_5xFAD_C57BL/6J_cortex_rep2


title: P210_C16_5xFAD_C57BL/6J_cortex_rep2


title: P210_C15_5xFAD_C57BL/6J_cortex_rep1


title: P210_C12_WT_C57BL/6J_cerebellum_rep4


title: P210_C13_5xFAD_C57BL/6J_cortex_rep1


title: P210_C10_WT_C57BL/6J_cerebellum_rep4


title: P210_C11_WT_C57BL/6J_cerebellum_rep4


title: P210_C9_WT_C57BL/6J_cerebellum_rep3


title: P210_C1_WT_C57BL/6J_cerebellum_rep1


title: P210_D10_WT_C57BL/6J_cerebellum_rep4


title: P210_C14_5xFAD_C57BL/6J_cortex_rep1


title: P210_B6_WT_C57BL/6J_cerebellum_rep2


title: P210_B7_WT_C57BL/6J_cerebellum_rep3


title: P210_B4_WT_C57BL/6J_cerebellum_rep2


title: P210_B5_WT_C57BL/6J_cerebellum_rep2


title: P210_B3_WT_C57BL/6J_cerebellum_rep1


title: P210_B8_WT_C57BL/6J_cerebellum_rep3


title: P210_C24_5xFAD_C57BL/6J_cortex_rep4


title: P210_B22_5xFAD_C57BL/6J_cortex_rep4


title: P210_B23_5xFAD_C57BL/6J_cortex_rep4


title: P210_C2_WT_C57BL/6J_cerebellum_rep1


title: P210_B21_5xFAD_C57BL/6J_cortex_rep3


title: P210_B24_5xFAD_C57BL/6J_cortex_rep4


title: P210_B20_5xFAD_C57BL/6J_cortex_rep3


title: P210_B19_5xFAD_C57BL/6J_cortex_rep3


title: P210_B2_WT_C57BL/6J_cerebellum_rep1


title: P210_B17_5xFAD_C57BL/6J_cortex_rep2


title: P210_B15_5xFAD_C57BL/6J_cortex_rep1


title: P210_B13_5xFAD_C57BL/6J_cortex_rep1


title: P210_B14_5xFAD_C57BL/6J_cortex_rep1


title: P210_B9_WT_C57BL/6J_cerebellum_rep3


title: P210_B18_5xFAD_C57BL/6J_cortex_rep2


title: P210_B11_WT_C57BL/6J_cerebellum_rep4


title: P210_B10_WT_C57BL/6J_cerebellum_rep4


title: P210_B1_WT_C57BL/6J_cerebellum_rep1


title: P210_A9_WT_C57BL/6J_cerebellum_rep3


title: P210_A8_WT_C57BL/6J_cerebellum_rep3


title: P210_A6_WT_C57BL/6J_cerebellum_rep2


title: P210_A7_WT_C57BL/6J_cerebellum_rep3


title: P210_A4_WT_C57BL/6J_cerebellum_rep2


title: P210_A5_WT_C57BL/6J_cerebellum_rep2


title: P210_A23_5xFAD_C57BL/6J_cortex_rep4


title: P210_A3_WT_C57BL/6J_cerebellum_rep1


title: P210_A22_5xFAD_C57BL/6J_cortex_rep4


title: P210_A24_5xFAD_C57BL/6J_cortex_rep4


title: P210_A19_5xFAD_C57BL/6J_cortex_rep3


title: P210_A20_5xFAD_C57BL/6J_cortex_rep3


title: P210_A21_5xFAD_C57BL/6J_cortex_rep3


title: P210_A16_5xFAD_C57BL/6J_cortex_rep2


title: P210_A18_5xFAD_C57BL/6J_cortex_rep2


title: P210_A17_5xFAD_C57BL/6J_cortex_rep2


title: P210_A2_WT_C57BL/6J_cerebellum_rep1


title: P210_A15_5xFAD_C57BL/6J_cortex_rep1


title: P210_B16_5xFAD_C57BL/6J_cortex_rep2


title: P210_B12_WT_C57BL/6J_cerebellum_rep4


title: P210_A12_WT_C57BL/6J_cerebellum_rep4


title: P210_A14_5xFAD_C57BL/6J_cortex_rep1


title: P210_A10_WT_C57BL/6J_cerebellum_rep4


title: P210_A11_WT_C57BL/6J_cerebellum_rep4


title: P209_P4_WT_C57BL/6J_cortex_rep2


title: P209_P6_WT_C57BL/6J_cortex_rep2


title: P209_P5_WT_C57BL/6J_cortex_rep2


title: P210_A1_WT_C57BL/6J_cerebellum_rep1


title: P209_P3_WT_C57BL/6J_cortex_rep1


title: P209_P8_WT_C57BL/6J_cortex_rep3


title: P209_P24_blank

description: blank


title: P210_A13_5xFAD_C57BL/6J_cortex_rep1


title: P209_P20_WT_C57BL/6J_hippocampus_rep3

value: hippocampus


title: P209_P19_WT_C57BL/6J_hippocampus_rep3


title: P209_P21_WT_C57BL/6J_hippocampus_rep3


title: P209_P23_WT_C57BL/6J_hippocampus_rep4


title: P209_P17_WT_C57BL/6J_hippocampus_rep2


title: P209_P18_WT_C57BL/6J_hippocampus_rep2


title: P209_P16_WT_C57BL/6J_hippocampus_rep2


title: P209_P12_blank

description: blank


title: P209_P14_WT_C57BL/6J_hippocampus_rep1


title: P209_P15_WT_C57BL/6J_hippocampus_rep1


title: P209_P13_WT_C57BL/6J_hippocampus_rep1


title: P209_P11_WT_C57BL/6J_cortex_rep4


title: P209_P10_WT_C57BL/6J_cortex_rep4


title: P209_P9_WT_C57BL/6J_cortex_rep3


title: P209_P1_WT_C57BL/6J_cortex_rep1


title: P209_O8_WT_C57BL/6J_cortex_rep3


title: P209_O9_WT_C57BL/6J_cortex_rep3


title: P209_P7_WT_C57BL/6J_cortex_rep3


title: P209_O6_WT_C57BL/6J_cortex_rep2


title: P209_O5_WT_C57BL/6J_cortex_rep2


title: P209_O4_WT_C57BL/6J_cortex_rep2


title: P209_O3_WT_C57BL/6J_cortex_rep1


title: P209_P22_WT_C57BL/6J_hippocampus_rep4


title: P209_O22_WT_C57BL/6J_hippocampus_rep4


title: P209_O24_blank

description: blank


title: P209_P2_WT_C57BL/6J_cortex_rep1


title: P209_O21_WT_C57BL/6J_hippocampus_rep3


title: P209_O2_WT_C57BL/6J_cortex_rep1


title: P209_O19_WT_C57BL/6J_hippocampus_rep3


title: P209_O20_WT_C57BL/6J_hippocampus_rep3


title: P209_O17_WT_C57BL/6J_hippocampus_rep2


title: P209_O16_WT_C57BL/6J_hippocampus_rep2


title: P209_O18_WT_C57BL/6J_hippocampus_rep2


title: P209_O15_WT_C57BL/6J_hippocampus_rep1


title: P209_O14_WT_C57BL/6J_hippocampus_rep1


title: P209_O13_WT_C57BL/6J_hippocampus_rep1


title: P209_O12_blank

description: blank


title: P209_O11_WT_C57BL/6J_cortex_rep4


title: P209_N9_WT_C57BL/6J_cortex_rep3


title: P209_O10_WT_C57BL/6J_cortex_rep4


title: P209_N8_WT_C57BL/6J_cortex_rep3


title: P209_N5_WT_C57BL/6J_cortex_rep2


title: P209_O23_WT_C57BL/6J_hippocampus_rep4


title: P209_N7_WT_C57BL/6J_cortex_rep3


title: P209_N3_WT_C57BL/6J_cortex_rep1


title: P209_N6_WT_C57BL/6J_cortex_rep2


title: P209_O7_WT_C57BL/6J_cortex_rep3


title: P209_N24_WT_C57BL/6J_hippocampus_rep4


title: P209_N23_WT_C57BL/6J_hippocampus_rep4


title: P209_N21_WT_C57BL/6J_hippocampus_rep3


title: P209_N4_WT_C57BL/6J_cortex_rep2


title: P209_N2_WT_C57BL/6J_cortex_rep1


title: P209_N20_WT_C57BL/6J_hippocampus_rep3


title: P209_N22_WT_C57BL/6J_hippocampus_rep4


title: P209_N19_WT_C57BL/6J_hippocampus_rep3


title: P209_N16_WT_C57BL/6J_hippocampus_rep2


title: P209_N17_WT_C57BL/6J_hippocampus_rep2


title: P209_N15_WT_C57BL/6J_hippocampus_rep1


title: P209_N14_WT_C57BL/6J_hippocampus_rep1


title: P209_O1_WT_C57BL/6J_cortex_rep1


title: P209_N10_WT_C57BL/6J_cortex_rep4


title: P209_N13_WT_C57BL/6J_hippocampus_rep1


title: P209_N12_WT_C57BL/6J_cortex_rep4


title: P209_M8_WT_C57BL/6J_cortex_rep3


title: P209_M9_WT_C57BL/6J_cortex_rep3


title: P209_N18_WT_C57BL/6J_hippocampus_rep2


title: P209_N11_WT_C57BL/6J_cortex_rep4


title: P209_M6_WT_C57BL/6J_cortex_rep2


title: P209_M7_WT_C57BL/6J_cortex_rep3


title: P209_N1_WT_C57BL/6J_cortex_rep1


title: P209_M4_WT_C57BL/6J_cortex_rep2


title: P209_M23_WT_C57BL/6J_hippocampus_rep4


title: P209_M21_WT_C57BL/6J_hippocampus_rep3


title: P209_M24_WT_C57BL/6J_hippocampus_rep4


title: P209_M5_WT_C57BL/6J_cortex_rep2


title: P209_M2_WT_C57BL/6J_cortex_rep1


title: P209_M17_WT_C57BL/6J_hippocampus_rep2


title: P209_M20_WT_C57BL/6J_hippocampus_rep3


title: P209_M22_WT_C57BL/6J_hippocampus_rep4


title: P209_M3_WT_C57BL/6J_cortex_rep1


title: P209_M15_WT_C57BL/6J_hippocampus_rep1


title: P209_M19_WT_C57BL/6J_hippocampus_rep3


title: P209_M18_WT_C57BL/6J_hippocampus_rep2


title: P209_M16_WT_C57BL/6J_hippocampus_rep2


title: P209_M14_WT_C57BL/6J_hippocampus_rep1


title: P209_M1_WT_C57BL/6J_cortex_rep1


title: P209_M11_WT_C57BL/6J_cortex_rep4


title: P209_M12_WT_C57BL/6J_cortex_rep4


title: P209_M10_WT_C57BL/6J_cortex_rep4


title: P209_L9_WT_C57BL/6J_cortex_rep3


title: P209_L8_WT_C57BL/6J_cortex_rep3


title: P209_L6_WT_C57BL/6J_cortex_rep2


title: P209_L3_WT_C57BL/6J_cortex_rep1


title: P209_L4_WT_C57BL/6J_cortex_rep2


title: P209_L23_WT_C57BL/6J_hippocampus_rep4


title: P209_L24_WT_C57BL/6J_hippocampus_rep4


title: P209_L21_WT_C57BL/6J_hippocampus_rep3


title: P209_L22_WT_C57BL/6J_hippocampus_rep4


title: P209_L20_WT_C57BL/6J_hippocampus_rep3


title: P209_L2_WT_C57BL/6J_cortex_rep1


title: P209_L18_WT_C57BL/6J_hippocampus_rep2


title: P209_L19_WT_C57BL/6J_hippocampus_rep3


title: P209_L15_WT_C57BL/6J_hippocampus_rep1


title: P209_L17_WT_C57BL/6J_hippocampus_rep2


title: P209_L14_WT_C57BL/6J_hippocampus_rep1


title: P209_L11_WT_C57BL/6J_cortex_rep4


title: P209_M13_WT_C57BL/6J_hippocampus_rep1


title: P209_L16_WT_C57BL/6J_hippocampus_rep2


title: P209_L10_WT_C57BL/6J_cortex_rep4


title: P209_L12_WT_C57BL/6J_cortex_rep4


title: P209_L7_WT_C57BL/6J_cortex_rep3


title: P209_K8_WT_C57BL/6J_cortex_rep3


title: P209_L5_WT_C57BL/6J_cortex_rep2


title: P209_L1_WT_C57BL/6J_cortex_rep1


title: P209_K7_WT_C57BL/6J_cortex_rep3


title: P209_K5_WT_C57BL/6J_cortex_rep2


title: P209_K3_WT_C57BL/6J_cortex_rep1


title: P209_K9_WT_C57BL/6J_cortex_rep3


title: P209_K23_WT_C57BL/6J_hippocampus_rep4


title: P209_K4_WT_C57BL/6J_cortex_rep2


title: P209_K22_WT_C57BL/6J_hippocampus_rep4


title: P209_L13_WT_C57BL/6J_hippocampus_rep1


title: P209_K17_WT_C57BL/6J_hippocampus_rep2


title: P209_K20_WT_C57BL/6J_hippocampus_rep3


title: P209_K2_WT_C57BL/6J_cortex_rep1


title: P209_K18_WT_C57BL/6J_hippocampus_rep2


title: P209_K21_WT_C57BL/6J_hippocampus_rep3


title: P209_K16_WT_C57BL/6J_hippocampus_rep2


title: P209_K15_WT_C57BL/6J_hippocampus_rep1


title: P209_K19_WT_C57BL/6J_hippocampus_rep3


title: P209_K14_WT_C57BL/6J_hippocampus_rep1


title: P209_K10_WT_C57BL/6J_cortex_rep4


title: P209_K1_WT_C57BL/6J_cortex_rep1


title: P209_K13_WT_C57BL/6J_hippocampus_rep1


title: P209_K11_WT_C57BL/6J_cortex_rep4


title: P209_J8_WT_C57BL/6J_cortex_rep3


title: P209_J9_WT_C57BL/6J_cortex_rep3


title: P209_J7_WT_C57BL/6J_cortex_rep3


title: P209_K6_WT_C57BL/6J_cortex_rep2


title: P209_J6_WT_C57BL/6J_cortex_rep2


title: P209_J24_WT_C57BL/6J_hippocampus_rep4


title: P209_J3_WT_C57BL/6J_cortex_rep1


title: P209_J5_WT_C57BL/6J_cortex_rep2


title: P209_J4_WT_C57BL/6J_cortex_rep2


title: P209_J20_WT_C57BL/6J_hippocampus_rep3


title: P209_J2_WT_C57BL/6J_cortex_rep1


title: P209_K24_WT_C57BL/6J_hippocampus_rep4


title: P209_J22_WT_C57BL/6J_hippocampus_rep4


title: P209_J21_WT_C57BL/6J_hippocampus_rep3


title: P209_J23_WT_C57BL/6J_hippocampus_rep4


title: P209_K12_WT_C57BL/6J_cortex_rep4


title: P209_J16_WT_C57BL/6J_hippocampus_rep2


title: P209_J19_WT_C57BL/6J_hippocampus_rep3


title: P209_J15_WT_C57BL/6J_hippocampus_rep1


title: P209_J14_WT_C57BL/6J_hippocampus_rep1


title: P209_J18_WT_C57BL/6J_hippocampus_rep2


title: P209_J17_WT_C57BL/6J_hippocampus_rep2


title: P209_I9_WT_C57BL/6J_cortex_rep3


title: P209_I7_WT_C57BL/6J_cortex_rep3


title: P209_I8_WT_C57BL/6J_cortex_rep3


title: P209_J1_WT_C57BL/6J_cortex_rep1


title: P209_J10_WT_C57BL/6J_cortex_rep4


title: P209_J12_WT_C57BL/6J_cortex_rep4


title: P209_I24_WT_C57BL/6J_hippocampus_rep4


title: P209_I6_WT_C57BL/6J_cortex_rep2


title: P209_I3_WT_C57BL/6J_cortex_rep1


title: P209_I4_WT_C57BL/6J_cortex_rep2


title: P209_I22_WT_C57BL/6J_hippocampus_rep4


title: P209_I23_WT_C57BL/6J_hippocampus_rep4


title: P209_J13_WT_C57BL/6J_hippocampus_rep1


title: P209_I21_WT_C57BL/6J_hippocampus_rep3


title: P209_I2_WT_C57BL/6J_cortex_rep1


title: P209_I5_WT_C57BL/6J_cortex_rep2


title: P209_I18_WT_C57BL/6J_hippocampus_rep2


title: P209_I17_WT_C57BL/6J_hippocampus_rep2


title: P209_I15_WT_C57BL/6J_hippocampus_rep1


title: P209_J11_WT_C57BL/6J_cortex_rep4


title: P209_I10_WT_C57BL/6J_cortex_rep4


title: P209_H9_WT_C57BL/6J_cortex_rep3


title: P209_I1_WT_C57BL/6J_cortex_rep1


title: P209_I16_WT_C57BL/6J_hippocampus_rep2


title: P209_I14_WT_C57BL/6J_hippocampus_rep1


title: P209_I12_WT_C57BL/6J_cortex_rep4


title: P209_H8_WT_C57BL/6J_cortex_rep3


title: P209_H5_WT_C57BL/6J_cortex_rep2


title: P209_H6_WT_C57BL/6J_cortex_rep2


title: P209_I20_WT_C57BL/6J_hippocampus_rep3


title: P209_H24_WT_C57BL/6J_hippocampus_rep4


title: P209_H7_WT_C57BL/6J_cortex_rep3


title: P209_H4_WT_C57BL/6J_cortex_rep2


title: P209_H3_WT_C57BL/6J_cortex_rep1


title: P209_H20_WT_C57BL/6J_hippocampus_rep3


title: P209_H23_WT_C57BL/6J_hippocampus_rep4


title: P209_H19_WT_C57BL/6J_hippocampus_rep3


title: P209_I19_WT_C57BL/6J_hippocampus_rep3


title: P209_H22_WT_C57BL/6J_hippocampus_rep4


title: P209_H21_WT_C57BL/6J_hippocampus_rep3


title: P209_H16_WT_C57BL/6J_hippocampus_rep2


title: P209_H2_WT_C57BL/6J_cortex_rep1


title: P209_H18_WT_C57BL/6J_hippocampus_rep2


title: P209_H17_WT_C57BL/6J_hippocampus_rep2


title: P209_H14_WT_C57BL/6J_hippocampus_rep1


title: P209_I11_WT_C57BL/6J_cortex_rep4


title: P209_I13_WT_C57BL/6J_hippocampus_rep1


title: P209_H12_WT_C57BL/6J_cortex_rep4


title: P209_H15_WT_C57BL/6J_hippocampus_rep1


title: P209_H11_WT_C57BL/6J_cortex_rep4


title: P209_G9_WT_C57BL/6J_cortex_rep3


title: P209_G8_WT_C57BL/6J_cortex_rep3


title: P209_G5_WT_C57BL/6J_cortex_rep2


title: P209_G3_WT_C57BL/6J_cortex_rep1


title: P209_G6_WT_C57BL/6J_cortex_rep2


title: P209_G24_WT_C57BL/6J_hippocampus_rep4


title: P209_G2_WT_C57BL/6J_cortex_rep1


title: P209_G19_WT_C57BL/6J_hippocampus_rep3


title: P209_G20_WT_C57BL/6J_hippocampus_rep3


title: P209_G17_WT_C57BL/6J_hippocampus_rep2


title: P209_G16_WT_C57BL/6J_hippocampus_rep2


title: P209_G18_WT_C57BL/6J_hippocampus_rep2


title: P209_G15_WT_C57BL/6J_hippocampus_rep1


title: P209_H1_WT_C57BL/6J_cortex_rep1


title: P209_G12_WT_C57BL/6J_cortex_rep4


title: P209_G13_WT_C57BL/6J_hippocampus_rep1


title: P209_H13_WT_C57BL/6J_hippocampus_rep1


title: P209_G11_WT_C57BL/6J_cortex_rep4


title: P209_G23_WT_C57BL/6J_hippocampus_rep4


title: P209_G10_WT_C57BL/6J_cortex_rep4


title: P209_G1_WT_C57BL/6J_cortex_rep1


title: P209_F9_WT_C57BL/6J_cortex_rep3


title: P209_F7_WT_C57BL/6J_cortex_rep3


title: P209_G4_WT_C57BL/6J_cortex_rep2


title: P209_F6_WT_C57BL/6J_cortex_rep2


title: P209_F5_WT_C57BL/6J_cortex_rep2


title: P209_F3_WT_C57BL/6J_cortex_rep1


title: P209_F4_WT_C57BL/6J_cortex_rep2


title: P209_F23_WT_C57BL/6J_hippocampus_rep4


title: P209_F24_WT_C57BL/6J_hippocampus_rep4


title: P209_H10_WT_C57BL/6J_cortex_rep4


title: P209_G7_WT_C57BL/6J_cortex_rep3


title: P209_F21_WT_C57BL/6J_hippocampus_rep3


title: P209_G14_WT_C57BL/6J_hippocampus_rep1


title: P209_F2_WT_C57BL/6J_cortex_rep1


title: P209_G22_WT_C57BL/6J_hippocampus_rep4


title: P209_F19_WT_C57BL/6J_hippocampus_rep3


title: P209_F12_WT_C57BL/6J_cortex_rep4


title: P209_F16_WT_C57BL/6J_hippocampus_rep2


title: P209_F18_WT_C57BL/6J_hippocampus_rep2


title: P209_F10_WT_C57BL/6J_cortex_rep4


title: P209_F13_WT_C57BL/6J_hippocampus_rep1


title: P209_F14_WT_C57BL/6J_hippocampus_rep1


title: P209_F11_WT_C57BL/6J_cortex_rep4


title: P209_F17_WT_C57BL/6J_hippocampus_rep2


title: P209_F1_WT_C57BL/6J_cortex_rep1


title: P209_F8_WT_C57BL/6J_cortex_rep3


title: P209_E7_WT_C57BL/6J_cortex_rep3


title: P209_E9_WT_C57BL/6J_cortex_rep3


title: P209_E3_WT_C57BL/6J_cortex_rep1


title: P209_E8_WT_C57BL/6J_cortex_rep3


title: P209_F22_WT_C57BL/6J_hippocampus_rep4


title: P209_E22_WT_C57BL/6J_hippocampus_rep4


title: P209_E24_WT_C57BL/6J_hippocampus_rep4


title: P209_E21_WT_C57BL/6J_hippocampus_rep3


title: P209_E5_WT_C57BL/6J_cortex_rep2


title: P209_F20_WT_C57BL/6J_hippocampus_rep3


title: P209_E20_WT_C57BL/6J_hippocampus_rep3


title: P209_F15_WT_C57BL/6J_hippocampus_rep1


title: P209_E4_WT_C57BL/6J_cortex_rep2


title: P209_E19_WT_C57BL/6J_hippocampus_rep3


title: P209_E18_WT_C57BL/6J_hippocampus_rep2


title: P209_E2_WT_C57BL/6J_cortex_rep1


title: P209_E14_WT_C57BL/6J_hippocampus_rep1


title: P209_E11_WT_C57BL/6J_cortex_rep4


title: P209_E15_WT_C57BL/6J_hippocampus_rep1


title: P209_E13_WT_C57BL/6J_hippocampus_rep1


title: P209_E10_WT_C57BL/6J_cortex_rep4


title: P209_E16_WT_C57BL/6J_hippocampus_rep2


title: P209_E12_WT_C57BL/6J_cortex_rep4


title: P209_E17_WT_C57BL/6J_hippocampus_rep2


title: P209_E1_WT_C57BL/6J_cortex_rep1


title: P209_D9_WT_C57BL/6J_cortex_rep3


title: P209_E6_WT_C57BL/6J_cortex_rep2


title: P209_D8_WT_C57BL/6J_cortex_rep3


title: P209_D7_WT_C57BL/6J_cortex_rep3


title: P209_E23_WT_C57BL/6J_hippocampus_rep4


title: P209_D6_WT_C57BL/6J_cortex_rep2


title: P209_D5_WT_C57BL/6J_cortex_rep2


title: P209_D3_WT_C57BL/6J_cortex_rep1


title: P209_D24_WT_C57BL/6J_hippocampus_rep4


title: P209_D23_WT_C57BL/6J_hippocampus_rep4


title: P209_D22_WT_C57BL/6J_hippocampus_rep4


title: P209_D19_WT_C57BL/6J_hippocampus_rep3


title: P209_D21_WT_C57BL/6J_hippocampus_rep3


title: P209_D20_WT_C57BL/6J_hippocampus_rep3


title: P209_D2_WT_C57BL/6J_cortex_rep1


title: P209_D18_WT_C57BL/6J_hippocampus_rep2


title: P209_D17_WT_C57BL/6J_hippocampus_rep2


title: P209_G21_WT_C57BL/6J_hippocampus_rep3


title: P209_D16_WT_C57BL/6J_hippocampus_rep2


title: P209_D10_WT_C57BL/6J_cortex_rep4


title: P209_D13_WT_C57BL/6J_hippocampus_rep1


title: P209_D11_WT_C57BL/6J_cortex_rep4


title: P209_D14_WT_C57BL/6J_hippocampus_rep1


title: P209_D15_WT_C57BL/6J_hippocampus_rep1


title: P209_D12_WT_C57BL/6J_cortex_rep4


title: P209_C8_WT_C57BL/6J_cortex_rep3


title: P209_C9_WT_C57BL/6J_cortex_rep3


title: P209_D1_WT_C57BL/6J_cortex_rep1


title: P209_C5_WT_C57BL/6J_cortex_rep2


title: P209_C7_WT_C57BL/6J_cortex_rep3


title: P209_C6_WT_C57BL/6J_cortex_rep2


title: P209_C4_WT_C57BL/6J_cortex_rep2


title: P209_D4_WT_C57BL/6J_cortex_rep2


title: P209_C3_WT_C57BL/6J_cortex_rep1


title: P209_C23_WT_C57BL/6J_hippocampus_rep4


title: P209_C24_WT_C57BL/6J_hippocampus_rep4


title: P209_C22_WT_C57BL/6J_hippocampus_rep4


title: P209_C20_WT_C57BL/6J_hippocampus_rep3


title: P209_C21_WT_C57BL/6J_hippocampus_rep3


title: P209_C19_WT_C57BL/6J_hippocampus_rep3


title: P209_C2_WT_C57BL/6J_cortex_rep1


title: P209_C16_WT_C57BL/6J_hippocampus_rep2


title: P209_C17_WT_C57BL/6J_hippocampus_rep2


title: P209_C18_WT_C57BL/6J_hippocampus_rep2


title: P209_C14_WT_C57BL/6J_hippocampus_rep1


title: P209_C12_WT_C57BL/6J_cortex_rep4


title: P209_C13_WT_C57BL/6J_hippocampus_rep1


title: P209_C11_WT_C57BL/6J_cortex_rep4


title: P209_B8_WT_C57BL/6J_cortex_rep3


title: P209_B7_WT_C57BL/6J_cortex_rep3


title: P209_B9_WT_C57BL/6J_cortex_rep3


title: P209_B4_WT_C57BL/6J_cortex_rep2


title: P209_C1_WT_C57BL/6J_cortex_rep1


title: P209_B6_WT_C57BL/6J_cortex_rep2


title: P209_B24_WT_C57BL/6J_hippocampus_rep4


title: P209_B22_WT_C57BL/6J_hippocampus_rep4


title: P209_B5_WT_C57BL/6J_cortex_rep2


title: P209_B21_WT_C57BL/6J_hippocampus_rep3


title: P209_B20_WT_C57BL/6J_hippocampus_rep3


title: P209_B2_WT_C57BL/6J_cortex_rep1


title: P209_C15_WT_C57BL/6J_hippocampus_rep1


title: P209_B19_WT_C57BL/6J_hippocampus_rep3