title: ACLR2

city: Guangzhou

first: Xue-Ming

last: Ruan

address: College of Life Sciences, Sun Yat-sen University, 135 Xingang West Road, Guangzhou

department: School Of Life Sciences

country: China

institute: Sun Yat-sen University

data_processing:
The raw reads were further processed with a bioinformatic pipeline tool, BMKCloud(www.biocloud.net) online platform.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing.
These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Hisat2 tools soft were used to map with reference genome.
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.
Assembly: SL 4.0
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Solanum lycopersicum

source_name: Mature green mesocarp

growth_protocol: Guangzhou, China, 3 months

extract_protocol:
Tomato tissue were ground in liquid nitrogen into tissue powder. Total RNA was extracted from tissue powder using 1 ml RNAiso Plus reagent (TAKARA, Japan) according to the manufacturer’s instructions.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H . Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Mature green mesocarp

value: AC

value: tissue

tag: cultivar

value: cv. Alisa Craig


title: ACHR2

status: Public on Jun 20 2023

type: SRA

library_source: transcriptomic

molecule: total RNA

source_name: Red ripe mesocarp

tag: tissue

value: Red ripe mesocarp

tag: cell line

tag: cell type


title: ACHR1


title: ACLR1


title: ACHP1

source_name: Red ripe exocarp

value: Red ripe exocarp


title: ACHP2


title: ACY1

source_name: Leaf

value: Leaf


title: ACY2


title: iBMDM, shControl, LPS 4 hours 2

city: Sunnyvale

first: Young

middle: Jun

last: Kang

state: CA

address: 428 Oakmead Pkwy

country: USA

institute: Molecular Medicine Research Institute

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data.
At the same time, Q20, Q30andGCcontent the clean data were calculated. All the downstream analyses were based on the clean data with high quality
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 2 reads were aligned to the reference genome using Hisat2 v2.0.5.
We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes FPKM for each sample

organism: Mus musculus

source_name: Bone marrow-derived macrophage

growth_protocol: DMEM (high glucose) supplemented with 10% FBS, pyruvate, glutamine and antibiotics.

extract_protocol:
Rneasy mini-prep from Qiagen
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

treatment_protocol: 5x10^5 cells per ml, LPS treatment 100 ng/ml for 4 hours

value: Bone marrow-derived macrophage

tag: genotype

value: Control

tag: treatment

value: LPS


title: iBMDM, shControl, LPS 4 hours 1


title: ACLP2

source_name: Mature green exocarp

value: Mature green exocarp


title: genomic DNA of sample F178_CD14

type: genomic

city: Research Triangle Park

first: Xuting

last: Wang

state: NC

address: 111 TW Alexander Dr

institute: NIEHS/NIH

description: Smoker CD14 genomic DNA

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 and MethylationEPIC Beadchips using standard Illumina protocol

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

data_processing: The raw IDAT files of 450K and EPIC methylation arrays were read into R with the minfi package separately; the combineArrays function in minfi was utilized to combine the two arrays’ data together based on their common CpG sites. Then, the data was preprocessed with background and dye bias correction using the preprocess Noob method. The ChAMP package was used to do BMIQ normalization. The combat function in sva package was used to do batch (“Sample_Plate”) correction on methylation array data. Prior to normalization, DNA methylation data were filtered based on these criteria: any samples having more than 5% probes that failed array QC standards, all CpG probes on the X and Y chromosomes, probes containing SNPs with a minor allele frequency ≥ 1% (in EUR or AFR populations of the 1000 Genomes Project) within 5 nucleotides to the CpG site, and probes failing QC standards. We also removed 43,254 probes reported to hybridize to one or more non-target sites in the genome.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

label_protocol: 500 ng of DNA was bisulfite converted using the EZ-DNA Methylation kit (Zymo Research)

extract_protocol: Nucleated DNA from cells was collected after sucrose-induced osmotic lysis of cells followed by phenol-chloroform extraction and DNA was stored in Tris-EDTA buffer at -20°C.

value: SM


title: iBMDM, shPGAM5, LPS 4 hours 3

value: PGAM5 KD


title: iBMDM, shPGAM5, LPS 4 hours 1


title: iBMDM, shControl, LPS 4 hours 3


title: ACLP1


title: 5301, SI-GA-E2

city: Boston

first: Gayani

last: Perera

state: MA

address: 800 Washington Street

department: MCRI

institute: Tufts Medical Center

description: 10x Genomics, S4 Flow Cell

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcode processing, gene counting were done using Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files, and matrix files

molecule: nuclear RNA

source_name: Whole Heart

extract_protocol:
Cryopreserved tissue was thawed in a 37°C water bath for 75 seconds. Nuclei were released from the tissue via dounce homogenization using a buffer containing Triton X-100 (0.1 v/v). The homogenate was filtered through a 10µM cell strainer and nuclei were pelleted (500 x g for 5 minutes at 4°C) and washed before being resuspended in 1% w/v BSA, 1X PBS, and  0.2 U/µL RNase inhibitor
Library was constructed according to manufacturers instructions (single cell 3' v3.1, 10x Genomics).

value: Whole Heart

value: Heart Cells

value: KO


title: 5355, SI-GA-E5

description: 10x Genomics, S4 Flow Cell

value: WT


title: YTN16 cells, shGas6

city: Suwon

first: Tae Hoon

last: Kim

address: 206, World cup-ro, Yeongtong-gu

department: surgery

country: South Korea

institute: Ajou university

data_processing:
Microsoft excel softwere
GraphPad Prism 9 software
Trimmomatic program
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic program (base quality<30)
Trimmed sequence reads were mapped to GrCM38/mm19 using Trimmomatic program (window size=4, mean quality=15, min length=36bp)
Assembly: mm10
Supplementary files format and content: tab-delimited Excel file includes read counts for sample
Supplementary files format and content: tab-delimited Excel file includes FPKM and TPM values for sample

growth_protocol: YTN16 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 0.1% MITO+ serum extender and antibiotics in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 1ug of total RNA was used for the construction of sequencing libraries.
TruSeq Stranded mRNA Library Prep Kit

value: Mouse gastric cancer cells

value: Gas6 knockdown


title: Akita-20wks

city: PHILADELPHIA

first: XING`

last: JI

state: PA

address: 3401 Civic Center Blvd

institute: Children's hospital of Philadelphia

data_processing:
Single-cell RNA-seq data were demultiplexed by processing with cell ranger, then aligned to mouse genome (mm10)
Clustering and gene expression analysis - Seurat v3
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Long bone

extract_protocol:
Tibias and femurs from three mice per group were harvested with the epiphysis surgically removed. The central bone marrow was flushed out with media (M-199 with 10% FBS and 1% P/S) and discarded, followed by scraping clean the periosteum with a scalpel. The metaphysis and mid-shafts were cut into small pieces with scissor. Bone pieces were digested with the STEMxyme1 (1 mg/ml, Worthington, LS004106) and Dispase II (1 mg/ml, ThermoFisher Scientific, 17105041) for 25 minutes at 37 °C in a cell culture shaker (ThermoFisher Scientific, MAXQ 4450). The digested cells were centrifuged at 300g for 3 mins and then suspended in 200 ul staining buffer (HBSS+2%FBS). Samples were stained and FACS sorted for CD45-(Invitrogen, 12-0451-82), CD3 (Biolegend, 100205), CD45R/B220 (Biolegend, 103207), CD19-(Biolegend, 115507), Gr1- (Biolegend, 108407), CD11b-(Biolegend, 101207),Ter119--( Invitrogen, 17-5921-82), CD71-(Biolegend, 113811), 7-AAD+-( Invitrogen, 00-6993), and calcium AM+( Invitrogen, C1430) with MoFlo Astrios Sorter (Beckman coulter ).
They were used to construct barcoded scRNA-seq libraries by using the Chromium single cell 3’ v2 reagent kit (CG000204_ChromiumNextGEMSingleCell3'v3.1, 10x Genomics).

value: Long bone

value: endosteal cells

value: Akita

tag: age

value: 20 weeks


title: 5356, SI-GA-E1

description: 10x Genomics, S4 Flow Cell


title: CF2

city: Berlin

first: Karsten

last: Jürchott

address: Luisenstraße

department: Rahel Hirsch Center

country: Germany

institute: BIH at Charité

data_processing:
HiSeq Control Software 2.2.58, Base-calling: RTA 1.18.64.0.
Sequence reads were demultiplexed using bcl2fastq2 (version 2.18, Illumina) and fastq file quality was assessed using fastqc (version 0.11.7, Bioinformatics Group at the Babraham Institute). Residual adapter sequences and low-quality reads were trimmed using AdapterRemoval (2.2.2).
Reads were aligned to the mm10 (GRCm38.82) version of the mouse genome using tophat (version 2.1.0) and bowtie2 (version 2.2.5). Counts per gene were calculated as the sum of all mapped reads within a gene region. Raw counts of protein-coding genes were normalised and variance stabilizing transformed using DESeq2 (1.28.1) in R (A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/; 4.0.2).
Genome_build: mm10
Supplementary_files_format_and_content: raw_counts - tab-deliminated file with reads summerized per gene.
Supplementary_files_format_and_content: normalized_data - tab-deliminated file with normalized data of protein-coding genes
Supplementary_files_format_and_content: vst_data - tab-deliminated file with variancestabilising transformed data of protein-coding genes

source_name: Neonatal cardiac fibroblasts

growth_protocol: CFs were purchased from PELOBIOTECH (cat. no. PB-C57-6049). For expansion, CFs were plated into gelatin-coated vessels and cultured in high glucose Dulbecco's modified eagle medium (DMEM) supplemented with 10 % heat-inactivated fetal bovine serum (FBS) and 1 % penicillin/streptomycin (P/S, standard medium) at 37 °C and 5 % CO2 in a humified incubator. All experiments were performed with passage 2–5 cells.

extract_protocol: Total RNA was isolated using the Qiagen RNeasy Mini Kit. Genomic DNA was removed with DNAse I. RNA quality and quantity were assessed on a 2100 Bioanalyzer System using the RNA 6000 Nano Kit. For RNA-seq, poly-(A)-selection was performed with 500 ng total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module.

treatment_protocol: CFs were plated in standard medium into gelatin-coated vessels. The next day, CFs were infected with Gata4, Mef2c, Tbx5, and Mef2c lentiviruses at an MOI of 5 each. After 24 h, standard medium was replaced with cardiac reprogramming medium, composed of low glucose DMEM and M199 (3:1) and supplemented with 10 % FBS and 1 % P/S. On day 3 after lentivirus infection, cells were sub-cultured. From day 4 onwards, cells were subjected to G418 selection. Thereafter, reprogramming medium was changed every other day until day 14. Before RNA isolation and RNA sequencing, iCMPs were purified by fluorescence-activated cell sorting based on Myh6/7 mRNA expression using Cy-5–labeled molecular beacons.

value: heart

tag: strain


title: 5300, SI-GA-E7

description: 10x Genomics, S4 Flow Cell


title: 4910, SI-GA-E8

description: 10x Genomics, S4 Flow Cell


title: 4909, SI-GA-E3

description: 10x Genomics, S4 Flow Cell


title: 4686, SI-GA-E4

description: 10x Genomics, S4 Flow Cell


title: 4685, SI-GA-E6

description: 10x Genomics, S4 Flow Cell


title: WT-20wks


title: YTN16 cells, shControl


title: WT-8wks

value: 8 weeks


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i729_i513]

city: Cambridge

first: Bertie

last: Gottgens

address: Jeffrey Cheah Biomedical Centre

country: United Kingdom

institute: University of Cambridge

description:
SLX.17005.i729_i513
NexteraXT_SetD

data_processing:
Smart-Seq2 sequencing reads were aligned to the mouse genome (mm10) using the STAR aligner (version 2.7.3a) with default parameters. Reads mapping to exons were counted with featureCounts (version 2.0.0) using the ENSEMBL v93 annotation.
Assembly: mm10
Supplementary files format and content: Smart-Seq2 data: count matrices for each fastq file as produced by feature counts  10x Genomics data: annotated, filtered (default cellranger setting) cell x gene matrices in .h5 format (cellranger output file)

source_name: STHSC

extract_protocol:
All steps in this section (unless otherwise indicated) were performed on ice, and centrifugation steps performed at 500g, 4°C for 5 min. 8-12 weeks old mice carrying the Hoxb5-mKO2 reporter were sacrificed and cells were isolated from bone marrow (femurs and tibia) by grinding with mortar and pestle in PBS supplemented with 2% Fetal Bovine Serum (cell buffer). The suspension was filtered through a 50µm filter, centrifuged and resuspended in 50ul of FC block, incubated for 5 min and 50ul of antibody cocktail was added. The antibody cocktail contained DAPI and the following antibodies: CD48-APC, CD34-FITC, CD135-PE/Cy5, CD150-PE/Cy7, Lin-biotin, Sca1-APC/Cy7, cKit-BV711. ml of cell buffer. The suspension was incubated for 20min on ice, washed with 1ml of cell bufffer, centrifuged and resuspended in 100ul of Streptavidin-PB, incubated for 15 min on ice, washed with 1ml cell buffer, centrifuged and resuspended in 300ul of cell buffer with addition of DAPI. Cell suspension was filtered as above and sorted with BD influx sorter into 96-well plates containing 2.3 µl lysis buffer (for the Smart-Seq2 protocol). The Smart-Seq2 plates were vortexed, centrifuged at 800g for 2 min and stored at -80°C.
Smart-Seq2  When cell numbers were limiting single cells were profiled with a modified version of the Smart-Seq2 protocol rather than 10x Genomics kit. Single cells were sorted into 96-well plates with 2.3 µl lysis buffer containing 0.115 µl of SUPERase-In RNase Inhibitor at 20 U/µl concentration (ThermoFisher AM2694) and 0.23 µl of 10% Triton X-100 solution (Sigma 93443), plates were vortexed and stored at -80°C. After thawing 2 µl of the annealing solution (0.1 µl of ERCC RNA Spike-In solution (1:300,000 dilution) Thermo-Fisher 4456740), 0.02 µl of the oligo-dT primer (100 µM stock concentration) and 1 µl of dNTP (10 mM stock concentration)) was added. The plate was incubated at 72°C for 3 min, cooled down on ice and reverse transcription was performed by adding 5.7 µl of RT buffer (0.1 µl of Maxima H minus reverse transcriptase at 200 U/µl concentration (ThermoFischer EP0752), 0.25 µl of SUPERase-In RNAse Inhibitor at 20 U/µl concentration, 2 µl of the Maxima enzyme buffer, 0.2 µl of TSO oligo at 100 µM concentration, 1.875 µl of PEG 8000 solution (Sigma P1458) at 40% v/v concentration and 1.275 µl water) and incubation at 42°C for 90 min followed by incubation at 70°C for 15 min. Immediately after, cDNA was amplified by PCR by adding 1 µl of the Terra PCR Direct Polymerase (1.25 U/µl, Takara 639270), 25 µl of the Terra PCR Direct buffer and 1 µl of the ISPCR primer (10 µM stock concentration) to a total volume of 50 µl using the following PCR conditions: 98°C for 3 min, 98°C for 15 s, 65°C for 30 s, 68°C for 4 min (21 cycles), 72°C for 10 min. The amplified cDNA was purified using AMPure XP beads (Beckman A63882), quantified using the PicoGreen assay (ThermoFischer P7589) and used for Nextera library preparation. The libraries were generated using either a standard protocol (batch 7d) or modified protocol (batches 3d7d, 2w4w and 3dr2), see the corresponding metadata) described below. No obvious batch effects were observed among cells analysed with either of the protocols.  The standard Nextera protocol: cDNA was diluted to approximately 50-150 pg/µl and 1.25 µl of the solution was used, 2.5 µl of Tagment DNA buffer 1.25 µl of Amplicon Tagment Mix (Nextera XT kit, Illumina FC-131-1096) were added, samples were incubated at 55°C for 10 min, and the reaction was stopped by addition of 1.25 µl of NT buffer. Tagmentation products were amplified by PCR by adding 1.25 µl of each N and S primers (Illumina Nextera XT 96-index kit FC-131-1002) and 3.75 µl of NPM solution and using the following thermocycler settings: 72°C 3 min, 95°C 30 s, 12 cycles of 95°C 30s, 55°C 30s, 72°C 60s and a final extension at 72°C for 5 min.  The modified Nextera protocol follows the same principle as the standard Nextera protocol and includes the following steps: cDNA was diluted to approximately 50-150 pg/µl and 1.03 µl of the solution was used, 1.63 µl of Tagment DNA buffer and 0.6 µl Amplicon Tagment Mix was added, samples were incubated at 55°C for 10 min, the reaction was stopped by adding 0.82 µl of NT buffer. Tagmentation products were amplified by adding 1.23 µl of each N and S primers (as above but diluted 5 times), 2.3 µl of Phusion HF buffer (ThermoFischer F530L), 0.1 µl of dNTP (25 mM stock concentration), 0.07 µl of Phusion polymerase and 2.5 µl of water and using the following thermocycler settings: 72°C 3 min, 98°C 3 min s, 12 cycles of 98°C 10s, 55°C 30s, 72°C 30s and a final extension at 72°C for 5 min.  Libraries were sequenced using the Illumina Hiseq4000 or NovaSeq instruments, obtaining approximately 100-200 mln reads per 96 cells.  10X genomics  For the 10x Genomics scRNA-Seq protocol up to 20,000 cells were pooled in pairs corresponding to male and female animals, centrifuged and resuspended in a volume of droplet buffer optimal for recovery of up to 10,000 cells and immediately processed with the 10x Genomics Single Cell 3' v3 protocol following the manufacturer's instructions.  Libraries were sequenced using the Illumina NovaSeq instrument, obtaining at least 20,000 reads per cells.

value: STHSC

value: mKOneg


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i729_i521]

description:
SLX.17005.i729_i521
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i728_i516]

description:
SLX.17005.i728_i516
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i727_i521]

description:
SLX.17005.i727_i521
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i729_i515]

description:
SLX.17005.i729_i515
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i729_i517]

description:
SLX.17005.i729_i517
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i729_i520]

description:
SLX.17005.i729_i520
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i728_i517]

description:
SLX.17005.i728_i517
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i729_i522]

description:
SLX.17005.i729_i522
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i729_i518]

description:
SLX.17005.i729_i518
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i728_i521]

description:
SLX.17005.i728_i521
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i727_i522]

description:
SLX.17005.i727_i522
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i728_i520]

description:
SLX.17005.i728_i520
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i728_i513]

description:
SLX.17005.i728_i513
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i727_i518]

description:
SLX.17005.i727_i518
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i729_i516]

description:
SLX.17005.i729_i516
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i727_i515]

description:
SLX.17005.i727_i515
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i727_i516]

description:
SLX.17005.i727_i516
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i727_i513]

description:
SLX.17005.i727_i513
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i727_i520]

description:
SLX.17005.i727_i520
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i728_i518]

description:
SLX.17005.i728_i518
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i728_i522]

description:
SLX.17005.i728_i522
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i726_i522]

description:
SLX.17005.i726_i522
NexteraXT_SetD

value: mKOpos


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i726_i521]

description:
SLX.17005.i726_i521
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i727_i517]

description:
SLX.17005.i727_i517
NexteraXT_SetD


title: Akita-8wks


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i726_i520]

description:
SLX.17005.i726_i520
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i728_i515]

description:
SLX.17005.i728_i515
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i724_i518]

description:
SLX.17005.i724_i518
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i726_i513]

description:
SLX.17005.i726_i513
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i724_i522]

description:
SLX.17005.i724_i522
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i724_i521]

description:
SLX.17005.i724_i521
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i723_i522]

description:
SLX.17005.i723_i522
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i726_i516]

description:
SLX.17005.i726_i516
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i726_i515]

description:
SLX.17005.i726_i515
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i724_i520]

description:
SLX.17005.i724_i520
NexteraXT_SetD


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i722_i522]

description:
SLX.17005.i722_i522
NexteraXT_SetD

source_name: LTHSC

value: LTHSC


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i726_i517]

description:
SLX.17005.i726_i517
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i723_i515]

description:
SLX.17005.i723_i515
NexteraXT_SetD


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i722_i520]

description:
SLX.17005.i722_i520
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i726_i518]

description:
SLX.17005.i726_i518
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i723_i513]

description:
SLX.17005.i723_i513
NexteraXT_SetD


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i722_i518]

description:
SLX.17005.i722_i518
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i724_i517]

description:
SLX.17005.i724_i517
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i723_i516]

description:
SLX.17005.i723_i516
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i723_i518]

description:
SLX.17005.i723_i518
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i723_i520]

description:
SLX.17005.i723_i520
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i724_i515]

description:
SLX.17005.i724_i515
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i723_i517]

description:
SLX.17005.i723_i517
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i723_i521]

description:
SLX.17005.i723_i521
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i724_i513]

description:
SLX.17005.i724_i513
NexteraXT_SetD


title: WTEE-16

city: coventry

first: daniel

last: hebenstreit

address: gibbet hill rd

institute: university of warwick

data_processing:
Raw fastq files for each sample were initially quality checked using FastQC (v0.11.3)
Adaptor contamination removal was performed with Skewer (v0.2.2) using Illumina TruSeq v2 adapter lists and confirmed with FastQC. Skewer parameters adjusted to trim quality below 10 and discard reads with any multiple alignment or length <50bp. (-Q 10 -t 4 -l 50 -z --compress)
Paired fastq files for each sample (forward and reverse) were aligned to the mouse genome (GRCm38) using STAR aligner (v2.5) and annotated (GRCm38.87). The maximum number of mismatches alignment parameter (outFilterMismatchNmax)  was set at 10 per paired-end read.
IGV (v2.3.65)  was used to inspect read alignment and verify the presence of the point mutation (D194A) at the MSK1 gene locus in samples belonging to MSK1 KD group.
Read alignment within individual genes was then quantified using HtSeq (v0.6.1p1): Default minimum alignment score used (10). Other parameters: -r pos -f bam -s no -a 10 -t exon -i gene_name -m union
Assembly: GRCm38
Supplementary_files_format_and_content: Tab-delimited text file which includes gene ID and raw count value by row.

source_name: hippocampus

extract_protocol:
Trizol (Invitrogen, #15596018)
TruSeqv2 (Illumina) LS protocol was used to prepare libraries

treatment_protocol: mice were raised in either standard housing or moved to enriched housing at the age of 18 months where they remained until hippocampal RNA was prepared from both groups at 21 - 23 months of age

value: hippocampus

value: 21-23 months

value: Wild-type

value: enriched housing


title: WTEE-21


title: WTEE-17


title: WTEE-13


title: WTEE-11


title: WTEE-10


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i722_i516]

description:
SLX.17005.i722_i516
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i724_i516]

description:
SLX.17005.i724_i516
NexteraXT_SetD


title: WTSH-7

value: standard housing


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i722_i517]

description:
SLX.17005.i722_i517
NexteraXT_SetD


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i722_i521]

description:
SLX.17005.i722_i521
NexteraXT_SetD


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i721_i521]

description:
SLX.17005.i721_i521
NexteraXT_SetD


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i721_i522]

description:
SLX.17005.i721_i522
NexteraXT_SetD


title: WTSH-4


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i722_i515]

description:
SLX.17005.i722_i515
NexteraXT_SetD


title: WTSH-23


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i722_i513]

description:
SLX.17005.i722_i513
NexteraXT_SetD


title: WTSH-19


title: WTSH-5


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i721_i518]

description:
SLX.17005.i721_i518
NexteraXT_SetD


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i721_i520]

description:
SLX.17005.i721_i520
NexteraXT_SetD


title: KDEE-22

value: MSK1 KD


title: WTSH-2


title: KDEE-20


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i721_i513]

description:
SLX.17005.i721_i513
NexteraXT_SetD


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i721_i516]

description:
SLX.17005.i721_i516
NexteraXT_SetD


title: KDEE-15


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i721_i515]

description:
SLX.17005.i721_i515
NexteraXT_SetD


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i720_i522]

description:
SLX.17005.i720_i522
NexteraXT_SetD


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i720_i521]

description:
SLX.17005.i720_i521
NexteraXT_SetD


title: KDEE-9


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i720_i520]

description:
SLX.17005.i720_i520
NexteraXT_SetD


title: KDEE-14


title: genomic DNA of sample F172_CD4

description: Smoker CD4 genomic DNA

value: SM


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i720_i518]

description:
SLX.17005.i720_i518
NexteraXT_SetD


title: KDSH-24


title: KDSH-18


title: KDSH-8


title: KDSH-6


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i720_i517]

description:
SLX.17005.i720_i517
NexteraXT_SetD


title: KDSH-3


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i721_i517]

description:
SLX.17005.i721_i517
NexteraXT_SetD


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i720_i515]

description:
SLX.17005.i720_i515
NexteraXT_SetD


title: KDSH-1


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i719_i522]

description:
SLX.17005.i719_i522
NexteraXT_SetD


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i719_i521]

description:
SLX.17005.i719_i521
NexteraXT_SetD


title: KDEE-12


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i719_i520]

description:
SLX.17005.i719_i520
NexteraXT_SetD


title: NSPCs, Ash2l-iKO-rep3

city: beijing

first: Peipei

last: liu

address: No. 25-1 West Beisihuan Rd, Haidian District, Beijing

department: State Key Laboratory of Stem cells and Reproductive Biology

institute: institute of zoology,Chinese academy of sciences

data_processing:
Global transcriptome sequencing was conducted by Annoroad Gene Technology Co., Ltd.
To minimize the effect of library construction bias and sequencing depth, we performed pseudo-replicates of FASTQ files according to a uniform processing pipeline
Assembly: gencode.vM24 for mouse
Supplementary files format and content: KO_WT-Diff.txt, TPM.txt

source_name: Brain

extract_protocol:
RNA was extracted from the FACS-sorted NSPC and the quantity and quality of total RNA were assessed using a Nanodrop spectrophotometer (Thermo Scientific).
RNA was amplified by the Smart-Seq2 method. The cDNA production was checked by Qubit 3.0 Fluorometer and Agilent 2100 Bioanalyzer to ensure the expected production, then the cDNA was sheared randomly by ultrasonic waves for Illumina library preparation protocol. After library preparation, PerkinElmer LabChip GX Touch and Step OnePlus Real-Time PCR System were introduced for library quality inspection. Qualified libraries were then loaded on the Illumina HiSeq platform for PE150 sequencing.

value: Brain

value: NSPCs

value: iKO


title: NSPCs, Ash2l-iKO-rep4


title: NSPCs, Ash2l-iKO-rep1


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i719_i517]

description:
SLX.17005.i719_i517
NexteraXT_SetD


title: NSPCs, WT-rep3

value: WT


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i719_i518]

description:
SLX.17005.i719_i518
NexteraXT_SetD


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i719_i515]

description:
SLX.17005.i719_i515
NexteraXT_SetD


title: NSPCs, Ash2l-iKO-rep2


title: NSPCs, WT-rep4


title: NSPCs, WT-rep1


title: Akita-20wks-4

data_processing:
The samples were sequenced using a 2x150bp Paired End (PE) configuration.
Image analysis and base calling were conducted by the HiSeq Control Software (HCS)
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software
Assembly: mm10
Supplementary files format and content: The processed data files contain normalized gene expression values obtained from DESeq2 analysis

extract_protocol:
The bone diaphysis was cleanly dissected and immediately frozen in the liquid nitrogen in grinding tubes (Precellys, P000922-LYK0-A). The samples were homogenized (6000 rpm, 3x 10 sec) in 1 ml TRIzol (Ambion, 15596018) in a Precellys Evolution Homogenizer (Bertin Instruments).  The homogenized samples were mixed with 1 mL RLT buffer with 2-mercaptoethanol and 2mL 70% ethanol, and then extracted for RNA according to the RNeasy mini kit protocol (Qiagen, #74106)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Long bone

value: Akita

value: 20 weeks


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i720_i513]

description:
SLX.17005.i720_i513
NexteraXT_SetD

value: mKOneg


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i719_i513]

description:
SLX.17005.i719_i513
NexteraXT_SetD

value: mKOpos


title: Akita-20wks-2


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i718_i522]

description:
SLX.17005.i718_i522
NexteraXT_SetD

value: LTHSC


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i720_i516]

description:
SLX.17005.i720_i516
NexteraXT_SetD


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i718_i521]

description:
SLX.17005.i718_i521
NexteraXT_SetD


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i718_i520]

description:
SLX.17005.i718_i520
NexteraXT_SetD


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i718_i518]

description:
SLX.17005.i718_i518
NexteraXT_SetD


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i718_i516]

description:
SLX.17005.i718_i516
NexteraXT_SetD


title: WT-20wks-4


title: WT-20wks-3


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i718_i515]

description:
SLX.17005.i718_i515
NexteraXT_SetD


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i718_i517]

description:
SLX.17005.i718_i517
NexteraXT_SetD


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i719_i516]

description:
SLX.17005.i719_i516
NexteraXT_SetD


title: WT-20wks-2


title: NSPCs, WT-rep2


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i718_i513]

description:
SLX.17005.i718_i513
NexteraXT_SetD


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i716_i522]

description:
SLX.17005.i716_i522
NexteraXT_SetD


title: WT-20wks-1


title: Akita-20wks-3


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i716_i518]

description:
SLX.17005.i716_i518
NexteraXT_SetD


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i716_i521]

description:
SLX.17005.i716_i521
NexteraXT_SetD


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i716_i520]

description:
SLX.17005.i716_i520
NexteraXT_SetD


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i716_i517]

description:
SLX.17005.i716_i517
NexteraXT_SetD


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i716_i516]

description:
SLX.17005.i716_i516
NexteraXT_SetD


title: Akita-20wks-1


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i716_i515]

description:
SLX.17005.i716_i515
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i715_i522]

description:
SLX.17005.i715_i522
NexteraXT_SetC

value: STHSC


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i716_i513]

description:
SLX.17005.i716_i513
NexteraXT_SetD


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i715_i521]

description:
SLX.17005.i715_i521
NexteraXT_SetC


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i715_i520]

description:
SLX.17005.i715_i520
NexteraXT_SetC


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i715_i518]

description:
SLX.17005.i715_i518
NexteraXT_SetC


title: 3d7d_SS2_146814.46f [SLX-19982.i729_i522]

description:
Smart-Seq2 scRNA-Seq, see metadata for details
SLX19981_SLX19982_scB5Tom_3d7d_ss2_fcounts.txt

data_processing:
library strategy: Smart-Seq2 or 10x Genomics
Smart-Seq2 sequencing reads were aligned to the mouse genome (mm10) using the STAR aligner (version 2.7.3a) with default parameters. Reads mapping to exons were counted with featureCounts (version 2.0.0) using the ENSEMBL v93 annotation. For consistency only a single read was processed for each sample. 10x genomics reads were pre-processed using cellranger (version 3.1.0, reference genome and annotation version 3.0.0) with default settings
Assembly: mm10
Supplementary files format and content: Smart-Seq2 data: count matrices for each fastq file as produced by feature counts  10x Genomics data: annotated, filtered (default cellranger setting) cell x gene matrices in .h5 format (cellranger output file)

source_name: bone marrow

extract_protocol:
All steps in this section (unless otherwise indicated) were performed on ice, and centrifugation steps performed at 300g, 4°C for 5 min. 8-12 weeks old mice carrying the Hoxb5-Cre and the Rosa26-LoxP-STOP-LoxP-tdTomato constructs were treated with 7 daily injections of tamoxifen and sacrificed at indicated time points. Bone marrow cells were extracted from ilia, tibiae and femura by grinding with mortar and pestle in PBS supplemented with 2% Fetal Bovine Serum (cell buffer). The suspension was filtered through a 50µm filter, centrifuged and resuspended in 3 ml of cell buffer. Red blood cells were removed using the ammonium chloride solution: 5 ml of 0.8% Ammonium Chloride (StemCell Tech. 07800) was added to the suspension and incubated for 10 min with intermittent mixing. Afterwards cells were diluted with 7 ml of cell buffer, centrifuged and resuspended in 1 ml of cell buffer. Subsequently, lineage depletion was performed as follows: added 20 µl of the EasySep mouse haematopoietic progenitor cell isolation cocktail (Stem Cell Technologies 19856), incubated for 15 min, added 30 µl magnetic particles, incubated for 10 min, added 1.5 ml of cell buffer and placed tubes in a magnet, incubated for 3 min at room temperature and eluted cells twice (with additional 2.5 ml of cell buffer). Afterwards, cells were centrifuged, resuspended in 200 µl of cell buffer and stained with the antibody panel as follows: antibody mix was added, cells were incubated for 30 min, washed with 2 ml of cell buffer, centrifuged, reuspended in 200 µl cell buffer. For the secondary staining Streptavidin-BV510 was added, cells were washed with 2 ml of cell buffer, centrifuged and resuspended in 1000 µl of cell buffer supplemented with 7AAD. Afterwards cells were sorted with BD influx sorter into either 96 well plates containing 2.3 µl lysis buffer (for the Smart-Seq2 protocol) or 100 µl of PBS with 0.04% BSA in eppendorf tubes ('droplet buffer') when used for the 10x Genomics scRNA-Seq protocol. The Smart-Seq2 plates were vortexed, centrifuged at 800g for 2 min and stored at -80°C. Antibodies and fluorochromes used: Mouse haematopoietic progenitor cell isolation cocktail (Stem Cell Technologies 19856), CD48-APC (Thermo-Fischer 17-0481-82), c-Kit-APC/Cy7 (Biolegend 105826), Sca1-BV421 (Biolegend 108133) and CD150-PE/Cy7 (Biolegend 115914), Streptavidin-BV510 (Biolegend 405234), 7AAD (Thermo Fischer A1310).
Smart-Seq2:
When cell numbers were limiting single cells were profiled with a modified version of the Smart-Seq2 protocol rather than 10x Genomics kit. Single cells were sorted into 96-well plates with 2.3 µl lysis buffer containing 0.115 µl of SUPERase-In RNase Inhibitor at 20 U/µl concentration (ThermoFisher AM2694) and 0.23 µl of 10% Triton X-100 solution (Sigma 93443), plates were vortexed and stored at -80°C. After thawing 2 µl of the annealing solution (0.1 µl of ERCC RNA Spike-In solution (1:300,000 dilution) Thermo-Fisher 4456740), 0.02 µl of the oligo-dT primer (100 µM stock concentration) and 1 µl of dNTP (10 mM stock concentration)) was added. The plate was incubated at 72°C for 3 min, cooled down on ice and reverse transcription was performed by adding 5.7 µl of RT buffer (0.1 µl of Maxima H minus reverse transcriptase at 200 U/µl concentration (ThermoFischer EP0752), 0.25 µl of SUPERase-In RNAse Inhibitor at 20 U/µl concentration, 2 µl of the Maxima enzyme buffer, 0.2 µl of TSO oligo at 100 µM concentration, 1.875 µl of PEG 8000 solution (Sigma P1458) at 40% v/v concentration and 1.275 µl water) and incubation at 42°C for 90 min followed by incubation at 70°C for 15 min. Immediately after, cDNA was amplified by PCR by adding 1 µl of the Terra PCR Direct Polymerase (1.25 U/µl, Takara 639270), 25 µl of the Terra PCR Direct buffer and 1 µl of the ISPCR primer (10 µM stock concentration) to a total volume of 50 µl using the following PCR conditions: 98°C for 3 min, 98°C for 15 s, 65°C for 30 s, 68°C for 4 min (21 cycles), 72°C for 10 min. The amplified cDNA was purified using AMPure XP beads (Beckman A63882), quantified using the PicoGreen assay (ThermoFischer P7589) and used for Nextera library preparation. The libraries were generated using either a standard protocol (batch 7d) or modified protocol (batches 3d7d, 2w4w and 3dr2), see the corresponding metadata) described below. No obvious batch effects were observed among cells analysed with either of the protocols.
The standard Nextera protocol: cDNA was diluted to approximately 50-150 pg/µl and 1.25 µl of the solution was used, 2.5 µl of Tagment DNA buffer 1.25 µl of Amplicon Tagment Mix (Nextera XT kit, Illumina FC-131-1096) were added, samples were incubated at 55°C for 10 min, and the reaction was stopped by addition of 1.25 µl of NT buffer. Tagmentation products were amplified by PCR by adding 1.25 µl of each N and S primers (Illumina Nextera XT 96-index kit FC-131-1002) and 3.75 µl of NPM solution and using the following thermocycler settings: 72°C 3 min, 95°C 30 s, 12 cycles of 95°C 30s, 55°C 30s, 72°C 60s and a final extension at 72°C for 5 min.
The modified Nextera protocol follows the same principle as the standard Nextera protocol and includes the following steps: cDNA was diluted to approximately 50-150 pg/µl and 1.03 µl of the solution was used, 1.63 µl of Tagment DNA buffer and 0.6 µl Amplicon Tagment Mix was added, samples were incubated at 55°C for 10 min, the reaction was stopped by adding 0.82 µl of NT buffer. Tagmentation products were amplified by adding 1.23 µl of each N and S primers (as above but diluted 5 times), 2.3 µl of Phusion HF buffer (ThermoFischer F530L), 0.1 µl of dNTP (25 mM stock concentration), 0.07 µl of Phusion polymerase and 2.5 µl of water and using the following thermocycler settings: 72°C 3 min, 98°C 3 min s, 12 cycles of 98°C 10s, 55°C 30s, 72°C 30s and a final extension at 72°C for 5 min.
Libraries were sequenced using the Illumina Hiseq4000 or NovaSeq instruments, obtaining approximately 100-200 mln reads per 96 cells.
10X genomics:
For the 10x Genomics scRNA-Seq protocol up to 20,000 cells were pooled in pairs corresponding to male and female animals, centrifuged and resuspended in a volume of droplet buffer optimal for recovery of up to 10,000 cells and immediately processed with the 10x Genomics Single Cell 3' v3 protocol following the manufacturer's instructions.
Libraries were sequenced using the Illumina NovaSeq instrument, obtaining at least 20,000 reads per cells.

treatment_protocol: Mice were treated with tamoxifen to induce a persistent fluorescent label, cells were harvested at indicated time intervals

value: bone marrow

value: Lin-negative, (cKit OR Sca1)-positive


title: 3d7d_SS2_146814.46f [SLX-19982.i722_i522]


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i715_i517]

description:
SLX.17005.i715_i517
NexteraXT_SetC


title: 3d7d_SS2_146814.46f [SLX-19982.i716_i522]


title: 3d7d_SS2_146814.46f [SLX-19982.i718_i522]


title: 3d7d_SS2_146814.46f [SLX-19982.i728_i522]


title: 3d7d_SS2_146814.46f [SLX-19982.i727_i522]


title: 3d7d_SS2_146814.46f [SLX-19982.i726_i522]


title: 3d7d_SS2_146814.46f [SLX-19982.i719_i522]


title: 3d7d_SS2_146814.46f [SLX-19982.i724_i522]


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i715_i516]

description:
SLX.17005.i715_i516
NexteraXT_SetC


title: 3d7d_SS2_146814.46f [SLX-19982.i729_i521]


title: 3d7d_SS2_146814.46f [SLX-19982.i723_i522]


title: 3d7d_SS2_146814.46f [SLX-19982.i721_i522]


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i715_i515]

description:
SLX.17005.i715_i515
NexteraXT_SetC


title: 3d7d_SS2_146814.46f [SLX-19982.i728_i521]


title: 3d7d_SS2_146814.46f [SLX-19982.i720_i522]


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i715_i513]

description:
SLX.17005.i715_i513
NexteraXT_SetC


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i714_i522]

description:
SLX.17005.i714_i522
NexteraXT_SetC


title: 3d7d_SS2_146814.46f [SLX-19982.i724_i521]


title: 3d7d_SS2_146814.46f [SLX-19982.i726_i521]


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i714_i521]

description:
SLX.17005.i714_i521
NexteraXT_SetC


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i714_i518]

description:
SLX.17005.i714_i518
NexteraXT_SetC


title: 3d7d_SS2_146814.46f [SLX-19982.i722_i521]


title: 3d7d_SS2_146814.46f [SLX-19982.i721_i521]


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i714_i517]

description:
SLX.17005.i714_i517
NexteraXT_SetC


title: 3d7d_SS2_146814.46f [SLX-19982.i720_i521]


title: 3d7d_SS2_146814.46f [SLX-19982.i719_i521]


title: 3d7d_SS2_146814.46f [SLX-19982.i727_i521]


title: 3d7d_SS2_146814.46f [SLX-19982.i718_i521]


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i714_i515]

description:
SLX.17005.i714_i515
NexteraXT_SetC


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i712_i522]

description:
SLX.17005.i712_i522
NexteraXT_SetC


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i714_i516]

description:
SLX.17005.i714_i516
NexteraXT_SetC


title: 3d7d_SS2_146814.46f [SLX-19982.i716_i521]


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i714_i513]

description:
SLX.17005.i714_i513
NexteraXT_SetC


title: 3d7d_SS2_146814.46f [SLX-19982.i728_i520]


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i712_i521]

description:
SLX.17005.i712_i521
NexteraXT_SetC


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i712_i520]

description:
SLX.17005.i712_i520
NexteraXT_SetC


title: 3d7d_SS2_146814.46f [SLX-19982.i729_i520]


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i712_i518]

description:
SLX.17005.i712_i518
NexteraXT_SetC


title: 3d7d_SS2_146814.46f [SLX-19982.i724_i520]


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i714_i520]

description:
SLX.17005.i714_i520
NexteraXT_SetC


title: 3d7d_SS2_146814.46f [SLX-19982.i726_i520]


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i712_i516]

description:
SLX.17005.i712_i516
NexteraXT_SetC


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i712_i517]

description:
SLX.17005.i712_i517
NexteraXT_SetC


title: 3d7d_SS2_146814.46f [SLX-19982.i723_i520]


title: 3d7d_SS2_146814.46f [SLX-19982.i727_i520]


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i712_i515]

description:
SLX.17005.i712_i515
NexteraXT_SetC


title: Mouse2_STHSCs_Hoxb5_mKOpos [SLX.17005.i712_i513]

description:
SLX.17005.i712_i513
NexteraXT_SetC


title: 3d7d_SS2_146814.46f [SLX-19982.i720_i520]


title: 3d7d_SS2_146814.46f [SLX-19982.i721_i520]


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i711_i522]

description:
SLX.17005.i711_i522
NexteraXT_SetC


title: 3d7d_SS2_146814.46f [SLX-19982.i719_i520]


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i711_i520]

description:
SLX.17005.i711_i520
NexteraXT_SetC


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i711_i518]

description:
SLX.17005.i711_i518
NexteraXT_SetC


title: 3d7d_SS2_146814.46f [SLX-19982.i716_i520]


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i711_i517]

description:
SLX.17005.i711_i517
NexteraXT_SetC


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i711_i521]

description:
SLX.17005.i711_i521
NexteraXT_SetC


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i711_i516]

description:
SLX.17005.i711_i516
NexteraXT_SetC


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i711_i515]

description:
SLX.17005.i711_i515
NexteraXT_SetC


title: 3d7d_SS2_146814.46f [SLX-19982.i722_i520]


title: 3d7d_SS2_146814.46f [SLX-19982.i729_i518]


title: 3d7d_SS2_146814.46f [SLX-19982.i718_i520]


title: 3d7d_SS2_146814.46f [SLX-19982.i727_i518]


title: 3d7d_SS2_146814.46f [SLX-19982.i728_i518]


title: 3d7d_SS2_146814.46f [SLX-19982.i726_i518]


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i711_i513]

description:
SLX.17005.i711_i513
NexteraXT_SetC


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i710_i522]

description:
SLX.17005.i710_i522
NexteraXT_SetC


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i710_i521]

description:
SLX.17005.i710_i521
NexteraXT_SetC


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i710_i520]

description:
SLX.17005.i710_i520
NexteraXT_SetC


title: 3d7d_SS2_146814.46f [SLX-19982.i723_i518]


title: 3d7d_SS2_146814.46f [SLX-19982.i721_i518]


title: 3d7d_SS2_146814.46f [SLX-19982.i720_i518]


title: 3d7d_SS2_146814.46f [SLX-19982.i722_i518]


title: 3d7d_SS2_146814.46f [SLX-19982.i724_i518]


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i710_i517]

description:
SLX.17005.i710_i517
NexteraXT_SetC


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i710_i518]

description:
SLX.17005.i710_i518
NexteraXT_SetC


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i710_i516]

description:
SLX.17005.i710_i516
NexteraXT_SetC


title: 3d7d_SS2_146814.46f [SLX-19982.i718_i518]


title: 3d7d_SS2_146814.46f [SLX-19982.i719_i518]


title: 3d7d_SS2_146814.46f [SLX-19982.i716_i518]


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i710_i515]

description:
SLX.17005.i710_i515
NexteraXT_SetC


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i707_i522]

description:
SLX.17005.i707_i522
NexteraXT_SetC


title: 3d7d_SS2_146814.46f [SLX-19982.i729_i517]


title: 3d7d_SS2_146814.46f [SLX-19982.i728_i517]


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i707_i521]

description:
SLX.17005.i707_i521
NexteraXT_SetC


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i707_i518]

description:
SLX.17005.i707_i518
NexteraXT_SetC


title: 3d7d_SS2_146814.46f [SLX-19982.i727_i517]


title: 3d7d_SS2_146814.46f [SLX-19982.i726_i517]


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i707_i520]

description:
SLX.17005.i707_i520
NexteraXT_SetC


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i707_i517]

description:
SLX.17005.i707_i517
NexteraXT_SetC


title: 3d7d_SS2_146814.46f [SLX-19982.i722_i517]


title: 3d7d_SS2_146814.46f [SLX-19982.i723_i517]


title: 3d7d_SS2_146814.46f [SLX-19982.i724_i517]


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i707_i515]

description:
SLX.17005.i707_i515
NexteraXT_SetC


title: 3d7d_SS2_146814.46f [SLX-19982.i721_i517]


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i706_i520]

description:
SLX.17005.i706_i520
NexteraXT_SetC


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i706_i518]

description:
SLX.17005.i706_i518
NexteraXT_SetC


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i706_i521]

description:
SLX.17005.i706_i521
NexteraXT_SetC


title: 3d7d_SS2_146814.46f [SLX-19982.i719_i517]


title: 3d7d_SS2_146814.46f [SLX-19982.i716_i517]


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i706_i517]

description:
SLX.17005.i706_i517
NexteraXT_SetC


title: 3d7d_SS2_146814.46f [SLX-19982.i718_i517]


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i710_i513]

description:
SLX.17005.i710_i513
NexteraXT_SetC


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i706_i516]

description:
SLX.17005.i706_i516
NexteraXT_SetC


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i706_i522]

description:
SLX.17005.i706_i522
NexteraXT_SetC


title: 3d7d_SS2_146814.46f [SLX-19982.i729_i516]


title: 3d7d_SS2_146814.46f [SLX-19982.i728_i516]


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i706_i515]

description:
SLX.17005.i706_i515
NexteraXT_SetC


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i706_i513]

description:
SLX.17005.i706_i513
NexteraXT_SetC


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i707_i516]

description:
SLX.17005.i707_i516
NexteraXT_SetC


title: 3d7d_SS2_146814.46f [SLX-19982.i727_i516]


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i705_i522]

description:
SLX.17005.i705_i522
NexteraXT_SetC


title: 3d7d_SS2_146814.46f [SLX-19982.i726_i516]


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i705_i520]

description:
SLX.17005.i705_i520
NexteraXT_SetC


title: 3d7d_SS2_146814.46f [SLX-19982.i723_i516]


title: 3d7d_SS2_146814.46f [SLX-19982.i724_i516]


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i705_i521]

description:
SLX.17005.i705_i521
NexteraXT_SetC


title: Mouse2_LTHSCs_Hoxb5_mKOneg [SLX.17005.i707_i513]

description:
SLX.17005.i707_i513
NexteraXT_SetC


title: 3d7d_SS2_146814.46f [SLX-19982.i720_i517]


title: 3d7d_SS2_146814.46f [SLX-19982.i721_i516]


title: 3d7d_SS2_146814.46f [SLX-19982.i722_i516]


title: 3d7d_SS2_146814.46f [SLX-19982.i719_i516]


title: 3d7d_SS2_146814.46f [SLX-19982.i720_i516]


title: 3d7d_SS2_146814.46f [SLX-19982.i729_i515]


title: 3d7d_SS2_146814.46f [SLX-19982.i716_i516]


title: 3d7d_SS2_146814.46f [SLX-19982.i718_i516]


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i705_i515]

description:
SLX.17005.i705_i515
NexteraXT_SetC


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i705_i516]

description:
SLX.17005.i705_i516
NexteraXT_SetC


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i705_i513]

description:
SLX.17005.i705_i513
NexteraXT_SetC


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i704_i522]

description:
SLX.17005.i704_i522
NexteraXT_SetC


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i704_i521]

description:
SLX.17005.i704_i521
NexteraXT_SetC


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i704_i520]

description:
SLX.17005.i704_i520
NexteraXT_SetC


title: 3d7d_SS2_146814.46f [SLX-19982.i728_i515]


title: 3d7d_SS2_146814.46f [SLX-19982.i727_i515]


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i704_i517]

description:
SLX.17005.i704_i517
NexteraXT_SetC


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i704_i518]

description:
SLX.17005.i704_i518
NexteraXT_SetC


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i705_i518]

description:
SLX.17005.i705_i518
NexteraXT_SetC


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i704_i515]

description:
SLX.17005.i704_i515
NexteraXT_SetC


title: 3d7d_SS2_146814.46f [SLX-19982.i723_i515]


title: 3d7d_SS2_146814.46f [SLX-19982.i724_i515]


title: 3d7d_SS2_146814.46f [SLX-19982.i722_i515]


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i704_i516]

description:
SLX.17005.i704_i516
NexteraXT_SetC


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i703_i522]

description:
SLX.17005.i703_i522
NexteraXT_SetC


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i705_i517]

description:
SLX.17005.i705_i517
NexteraXT_SetC


title: 3d7d_SS2_146814.46f [SLX-19982.i721_i515]


title: 3d7d_SS2_146814.46f [SLX-19982.i720_i515]


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i703_i521]

description:
SLX.17005.i703_i521
NexteraXT_SetC


title: 3d7d_SS2_146814.46f [SLX-19982.i718_i515]


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i703_i520]

description:
SLX.17005.i703_i520
NexteraXT_SetC


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i703_i517]

description:
SLX.17005.i703_i517
NexteraXT_SetC


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i703_i518]

description:
SLX.17005.i703_i518
NexteraXT_SetC


title: 3d7d_SS2_146814.46f [SLX-19982.i726_i515]


title: 3d7d_SS2_146814.46f [SLX-19982.i727_i513]


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i703_i513]

description:
SLX.17005.i703_i513
NexteraXT_SetC


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i703_i515]

description:
SLX.17005.i703_i515
NexteraXT_SetC


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i703_i516]

description:
SLX.17005.i703_i516
NexteraXT_SetC


title: 3d7d_SS2_146814.46f [SLX-19982.i716_i515]


title: 3d7d_SS2_146814.46f [SLX-19982.i726_i513]


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i702_i521]

description:
SLX.17005.i702_i521
NexteraXT_SetC


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i702_i522]

description:
SLX.17005.i702_i522
NexteraXT_SetC


title: 3d7d_SS2_146814.46f [SLX-19982.i719_i515]


title: 3d7d_SS2_146814.46f [SLX-19982.i724_i513]


title: Mouse2_LTHSCs_Hoxb5_mKOpos [SLX.17005.i704_i513]

description:
SLX.17005.i704_i513
NexteraXT_SetC


title: 3d7d_SS2_146814.46f [SLX-19982.i723_i513]


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i702_i518]

description:
SLX.17005.i702_i518
NexteraXT_SetC


title: 3d7d_SS2_146814.46f [SLX-19982.i722_i513]


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i702_i516]

description:
SLX.17005.i702_i516
NexteraXT_SetC


title: 3d7d_SS2_146814.46f [SLX-19982.i721_i513]


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i702_i517]

description:
SLX.17005.i702_i517
NexteraXT_SetC


title: 3d7d_SS2_146814.46f [SLX-19982.i720_i513]


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i702_i515]

description:
SLX.17005.i702_i515
NexteraXT_SetC


title: 3d7d_SS2_146814.46f [SLX-19982.i729_i513]


title: 3d7d_SS2_146814.46f [SLX-19982.i719_i513]


title: 3d7d_SS2_146814.46f [SLX-19982.i728_i513]


title: 3d7d_SS2_146814.46f [SLX-19982.i718_i513]


title: 3d7d_SS2_146814.46f [SLX-19982.i723_i521]


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i702_i513]

description:
SLX.17005.i702_i513
NexteraXT_SetC


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i701_i522]

description:
SLX.17005.i701_i522
NexteraXT_SetC


title: 3d7d_SS2_146813.47a [SLX-19982.i715_i517]


title: 3d7d_SS2_146813.47a [SLX-19982.i712_i517]


title: 3d7d_SS2_146813.47a [SLX-19982.i714_i517]


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i702_i520]

description:
SLX.17005.i702_i520
NexteraXT_SetC


title: 3d7d_SS2_146814.46f [SLX-19982.i716_i513]


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i701_i520]

description:
SLX.17005.i701_i520
NexteraXT_SetC


title: 3d7d_SS2_146813.47a [SLX-19982.i710_i517]


title: 3d7d_SS2_146813.47a [SLX-19982.i706_i517]


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i701_i516]

description:
SLX.17005.i701_i516
NexteraXT_SetC


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i701_i517]

description:
SLX.17005.i701_i517
NexteraXT_SetC


title: 3d7d_SS2_146813.47a [SLX-19982.i707_i517]


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i701_i515]

description:
SLX.17005.i701_i515
NexteraXT_SetC


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i701_i513]

description:
SLX.17005.i701_i513
NexteraXT_SetC


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i701_i518]

description:
SLX.17005.i701_i518
NexteraXT_SetC


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i729_i511]

description:
SLX.17004.i729_i511
NexteraXT_SetB


title: Mouse2_STHSCs_Hoxb5_mKOneg [SLX.17005.i701_i521]

description:
SLX.17005.i701_i521
NexteraXT_SetC


title: 3d7d_SS2_146813.47a [SLX-19982.i705_i517]


title: 3d7d_SS2_146813.47a [SLX-19982.i704_i517]


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i729_i510]

description:
SLX.17004.i729_i510
NexteraXT_SetB


title: 3d7d_SS2_146813.47a [SLX-19982.i702_i517]


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i729_i505]

description:
SLX.17004.i729_i505
NexteraXT_SetB


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i729_i507]

description:
SLX.17004.i729_i507
NexteraXT_SetB


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i729_i506]

description:
SLX.17004.i729_i506
NexteraXT_SetB


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i729_i508]

description:
SLX.17004.i729_i508
NexteraXT_SetB


title: 3d7d_SS2_146813.47a [SLX-19982.i714_i516]


title: 3d7d_SS2_146813.47a [SLX-19982.i712_i516]


title: 3d7d_SS2_146813.47a [SLX-19982.i711_i516]


title: 3d7d_SS2_146813.47a [SLX-19982.i710_i516]


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i729_i502]

description:
SLX.17004.i729_i502
NexteraXT_SetB


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i729_i503]

description:
SLX.17004.i729_i503
NexteraXT_SetB


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i728_i511]

description:
SLX.17004.i728_i511
NexteraXT_SetB


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i728_i508]

description:
SLX.17004.i728_i508
NexteraXT_SetB


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i728_i507]

description:
SLX.17004.i728_i507
NexteraXT_SetB


title: 3d7d_SS2_146813.47a [SLX-19982.i704_i516]


title: 3d7d_SS2_146813.47a [SLX-19982.i703_i517]


title: 3d7d_SS2_146813.47a [SLX-19982.i705_i516]


title: 3d7d_SS2_146813.47a [SLX-19982.i706_i516]


title: 3d7d_SS2_146813.47a [SLX-19982.i715_i516]


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i728_i506]

description:
SLX.17004.i728_i506
NexteraXT_SetB


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i728_i505]

description:
SLX.17004.i728_i505
NexteraXT_SetB


title: 3d7d_SS2_146813.47a [SLX-19982.i703_i516]


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i728_i502]

description:
SLX.17004.i728_i502
NexteraXT_SetB


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i728_i503]

description:
SLX.17004.i728_i503
NexteraXT_SetB


title: 3d7d_SS2_146813.47a [SLX-19982.i701_i516]


title: 3d7d_SS2_146813.47a [SLX-19982.i702_i516]


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i727_i511]

description:
SLX.17004.i727_i511
NexteraXT_SetB


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i727_i510]

description:
SLX.17004.i727_i510
NexteraXT_SetB


title: 3d7d_SS2_146813.47a [SLX-19982.i712_i515]


title: 3d7d_SS2_146813.47a [SLX-19982.i714_i515]


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i727_i508]

description:
SLX.17004.i727_i508
NexteraXT_SetB


title: 3d7d_SS2_146813.47a [SLX-19982.i707_i516]


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i728_i510]

description:
SLX.17004.i728_i510
NexteraXT_SetB


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i727_i507]

description:
SLX.17004.i727_i507
NexteraXT_SetB


title: 3d7d_SS2_146813.47a [SLX-19982.i710_i515]


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i727_i505]

description:
SLX.17004.i727_i505
NexteraXT_SetB


title: 3d7d_SS2_146813.47a [SLX-19982.i706_i515]


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i727_i503]

description:
SLX.17004.i727_i503
NexteraXT_SetB


title: 3d7d_SS2_146813.47a [SLX-19982.i707_i515]


title: 3d7d_SS2_146813.47a [SLX-19982.i711_i517]


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i726_i511]

description:
SLX.17004.i726_i511
NexteraXT_SetB


title: 3d7d_SS2_146813.47a [SLX-19982.i705_i515]


title: 3d7d_SS2_146813.47a [SLX-19982.i704_i515]


title: 3d7d_SS2_146813.47a [SLX-19982.i702_i515]


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i726_i510]

description:
SLX.17004.i726_i510
NexteraXT_SetB


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i727_i502]

description:
SLX.17004.i727_i502
NexteraXT_SetB


title: 3d7d_SS2_146813.47a [SLX-19982.i703_i515]


title: 3d7d_SS2_146813.47a [SLX-19982.i715_i515]


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i726_i508]

description:
SLX.17004.i726_i508
NexteraXT_SetB


title: 3d7d_SS2_146813.47a [SLX-19982.i711_i515]


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i726_i507]

description:
SLX.17004.i726_i507
NexteraXT_SetB


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i726_i506]

description:
SLX.17004.i726_i506
NexteraXT_SetB


title: 3d7d_SS2_146813.47a [SLX-19982.i701_i515]


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i726_i505]

description:
SLX.17004.i726_i505
NexteraXT_SetB


title: 3d7d_SS2_146813.47a [SLX-19982.i715_i513]


title: 3d7d_SS2_146813.47a [SLX-19982.i712_i513]


title: 3d7d_SS2_146813.47a [SLX-19982.i711_i513]


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i727_i506]

description:
SLX.17004.i727_i506
NexteraXT_SetB


title: 3d7d_SS2_146813.47a [SLX-19982.i710_i513]


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i724_i511]

description:
SLX.17004.i724_i511
NexteraXT_SetB


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i726_i502]

description:
SLX.17004.i726_i502
NexteraXT_SetB


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i726_i503]

description:
SLX.17004.i726_i503
NexteraXT_SetB


title: 3d7d_SS2_146813.47a [SLX-19982.i706_i513]


title: 3d7d_SS2_146813.47a [SLX-19982.i707_i513]


title: 3d7d_SS2_146813.47a [SLX-19982.i705_i513]


title: 3d7d_SS2_146813.47a [SLX-19982.i714_i513]


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i724_i502]

description:
SLX.17004.i724_i502
NexteraXT_SetB


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i724_i510]

description:
SLX.17004.i724_i510
NexteraXT_SetB


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i724_i508]

description:
SLX.17004.i724_i508
NexteraXT_SetB


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i724_i505]

description:
SLX.17004.i724_i505
NexteraXT_SetB


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i724_i503]

description:
SLX.17004.i724_i503
NexteraXT_SetB


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i724_i507]

description:
SLX.17004.i724_i507
NexteraXT_SetB


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i723_i510]

description:
SLX.17004.i723_i510
NexteraXT_SetB


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i723_i511]

description:
SLX.17004.i723_i511
NexteraXT_SetB


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i723_i508]

description:
SLX.17004.i723_i508
NexteraXT_SetB


title: 3d7d_SS2_146813.47a [SLX-19982.i704_i513]


title: 3d7d_SS2_146813.47a [SLX-19982.i711_i511]


title: 3d7d_SS2_146813.47a [SLX-19982.i714_i511]


title: 3d7d_SS2_146813.47a [SLX-19982.i715_i511]


title: 3d7d_SS2_146813.47a [SLX-19982.i703_i513]


title: 3d7d_SS2_146813.47a [SLX-19982.i702_i513]


title: 3d7d_SS2_146813.47a [SLX-19982.i701_i513]


title: 3d7d_SS2_146813.47a [SLX-19982.i710_i511]


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i723_i506]

description:
SLX.17004.i723_i506
NexteraXT_SetB


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i723_i507]

description:
SLX.17004.i723_i507
NexteraXT_SetB


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i723_i505]

description:
SLX.17004.i723_i505
NexteraXT_SetB


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i724_i506]

description:
SLX.17004.i724_i506
NexteraXT_SetB


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i723_i503]

description:
SLX.17004.i723_i503
NexteraXT_SetB


title: 3d7d_SS2_146813.47a [SLX-19982.i706_i511]


title: 3d7d_SS2_146813.47a [SLX-19982.i705_i511]


title: 3d7d_SS2_146813.47a [SLX-19982.i704_i511]


title: 3d7d_SS2_146813.47a [SLX-19982.i712_i511]


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i723_i502]

description:
SLX.17004.i723_i502
NexteraXT_SetB


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i722_i511]

description:
SLX.17004.i722_i511
NexteraXT_SetB


title: 3d7d_SS2_146813.47a [SLX-19982.i703_i511]


title: 3d7d_SS2_146813.47a [SLX-19982.i701_i511]


title: 3d7d_SS2_146813.47a [SLX-19982.i714_i510]


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i722_i506]

description:
SLX.17004.i722_i506
NexteraXT_SetB


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i722_i507]

description:
SLX.17004.i722_i507
NexteraXT_SetB


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i722_i508]

description:
SLX.17004.i722_i508
NexteraXT_SetB


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i722_i505]

description:
SLX.17004.i722_i505
NexteraXT_SetB


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i722_i503]

description:
SLX.17004.i722_i503
NexteraXT_SetB


title: 3d7d_SS2_146813.47a [SLX-19982.i702_i511]


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i721_i511]

description:
SLX.17004.i721_i511
NexteraXT_SetB


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i722_i502]

description:
SLX.17004.i722_i502
NexteraXT_SetB


title: 3d7d_SS2_146813.47a [SLX-19982.i707_i510]


title: 3d7d_SS2_146813.47a [SLX-19982.i711_i510]


title: 3d7d_SS2_146813.47a [SLX-19982.i710_i510]


title: 3d7d_SS2_146813.47a [SLX-19982.i712_i510]


title: 3d7d_SS2_146813.47a [SLX-19982.i706_i510]


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i721_i510]

description:
SLX.17004.i721_i510
NexteraXT_SetB


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i721_i508]

description:
SLX.17004.i721_i508
NexteraXT_SetB


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i721_i507]

description:
SLX.17004.i721_i507
NexteraXT_SetB


title: 3d7d_SS2_146813.47a [SLX-19982.i705_i510]


title: 3d7d_SS2_146813.47a [SLX-19982.i704_i510]


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i721_i506]

description:
SLX.17004.i721_i506
NexteraXT_SetB


title: 3d7d_SS2_146813.47a [SLX-19982.i707_i511]


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i722_i510]

description:
SLX.17004.i722_i510
NexteraXT_SetB


title: 3d7d_SS2_146813.47a [SLX-19982.i702_i510]


title: 3d7d_SS2_146813.47a [SLX-19982.i701_i510]


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i721_i502]

description:
SLX.17004.i721_i502
NexteraXT_SetB


title: 3d7d_SS2_146813.47a [SLX-19982.i715_i510]


title: 3d7d_SS2_146813.47a [SLX-19982.i703_i510]


title: 3d7d_SS2_146813.47a [SLX-19982.i715_i508]


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i720_i510]

description:
SLX.17004.i720_i510
NexteraXT_SetB


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i720_i508]

description:
SLX.17004.i720_i508
NexteraXT_SetB


title: 3d7d_SS2_146813.47a [SLX-19982.i714_i508]


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i720_i507]

description:
SLX.17004.i720_i507
NexteraXT_SetB


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i721_i505]

description:
SLX.17004.i721_i505
NexteraXT_SetB


title: 3d7d_SS2_146813.47a [SLX-19982.i711_i508]


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i720_i502]

description:
SLX.17004.i720_i502
NexteraXT_SetB


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i720_i506]

description:
SLX.17004.i720_i506
NexteraXT_SetB


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i721_i503]

description:
SLX.17004.i721_i503
NexteraXT_SetB


title: 3d7d_SS2_146813.47a [SLX-19982.i707_i508]


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i719_i511]

description:
SLX.17004.i719_i511
NexteraXT_SetB


title: 3d7d_SS2_146813.47a [SLX-19982.i710_i508]


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i720_i505]

description:
SLX.17004.i720_i505
NexteraXT_SetB


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i719_i510]

description:
SLX.17004.i719_i510
NexteraXT_SetB


title: 3d7d_SS2_146813.47a [SLX-19982.i705_i508]


title: 3d7d_SS2_146813.47a [SLX-19982.i704_i508]


title: 3d7d_SS2_146813.47a [SLX-19982.i703_i508]


title: 3d7d_SS2_146813.47a [SLX-19982.i702_i508]


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i719_i508]

description:
SLX.17004.i719_i508
NexteraXT_SetB


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i720_i511]

description:
SLX.17004.i720_i511
NexteraXT_SetB


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i719_i507]

description:
SLX.17004.i719_i507
NexteraXT_SetB


title: 3d7d_SS2_146813.47a [SLX-19982.i712_i508]


title: 3d7d_SS2_146813.47a [SLX-19982.i706_i508]


title: 3d7d_SS2_146813.47a [SLX-19982.i701_i508]


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i719_i506]

description:
SLX.17004.i719_i506
NexteraXT_SetB


title: 3d7d_SS2_146813.47a [SLX-19982.i715_i507]


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i720_i503]

description:
SLX.17004.i720_i503
NexteraXT_SetB


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i719_i505]

description:
SLX.17004.i719_i505
NexteraXT_SetB


title: 3d7d_SS2_146813.47a [SLX-19982.i712_i507]


title: 3d7d_SS2_146813.47a [SLX-19982.i714_i507]


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i719_i503]

description:
SLX.17004.i719_i503
NexteraXT_SetB


title: 3d7d_SS2_146813.47a [SLX-19982.i711_i507]


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i719_i502]

description:
SLX.17004.i719_i502
NexteraXT_SetB


title: 3d7d_SS2_146813.47a [SLX-19982.i710_i507]


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i718_i511]

description:
SLX.17004.i718_i511
NexteraXT_SetB


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i718_i510]

description:
SLX.17004.i718_i510
NexteraXT_SetB


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i718_i506]

description:
SLX.17004.i718_i506
NexteraXT_SetB


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i718_i507]

description:
SLX.17004.i718_i507
NexteraXT_SetB


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i718_i508]

description:
SLX.17004.i718_i508
NexteraXT_SetB


title: 3d7d_SS2_146813.47a [SLX-19982.i707_i507]


title: 3d7d_SS2_146813.47a [SLX-19982.i706_i507]


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i718_i503]

description:
SLX.17004.i718_i503
NexteraXT_SetB


title: 3d7d_SS2_146813.47a [SLX-19982.i705_i507]


title: 3d7d_SS2_146813.47a [SLX-19982.i704_i507]


title: 3d7d_SS2_146813.47a [SLX-19982.i701_i507]


title: 3d7d_SS2_146813.47a [SLX-19982.i702_i507]


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i718_i505]

description:
SLX.17004.i718_i505
NexteraXT_SetB


title: 3d7d_SS2_146813.47a [SLX-19982.i715_i506]


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i718_i502]

description:
SLX.17004.i718_i502
NexteraXT_SetB


title: 3d7d_SS2_146813.47a [SLX-19982.i703_i507]


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i716_i511]

description:
SLX.17004.i716_i511
NexteraXT_SetB


title: 3d7d_SS2_146813.47a [SLX-19982.i712_i506]


title: 3d7d_SS2_146813.47a [SLX-19982.i714_i506]


title: 3d7d_SS2_146813.47a [SLX-19982.i711_i506]


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i716_i508]

description:
SLX.17004.i716_i508
NexteraXT_SetB


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i716_i507]

description:
SLX.17004.i716_i507
NexteraXT_SetB


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i716_i506]

description:
SLX.17004.i716_i506
NexteraXT_SetB


title: 3d7d_SS2_146813.47a [SLX-19982.i710_i506]


title: 3d7d_SS2_146813.47a [SLX-19982.i706_i506]


title: 3d7d_SS2_146813.47a [SLX-19982.i707_i506]


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i716_i503]

description:
SLX.17004.i716_i503
NexteraXT_SetB


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i716_i505]

description:
SLX.17004.i716_i505
NexteraXT_SetB


title: 3d7d_SS2_146813.47a [SLX-19982.i705_i506]


title: 3d7d_SS2_146813.47a [SLX-19982.i704_i506]


title: 3d7d_SS2_146813.47a [SLX-19982.i703_i506]


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i716_i510]

description:
SLX.17004.i716_i510
NexteraXT_SetB


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i716_i502]

description:
SLX.17004.i716_i502
NexteraXT_SetB


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i715_i511]

description:
SLX.17004.i715_i511
NexteraXT_SetA


title: 3d7d_SS2_146813.47a [SLX-19982.i702_i506]


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i715_i510]

description:
SLX.17004.i715_i510
NexteraXT_SetA


title: 3d7d_SS2_146813.47a [SLX-19982.i715_i505]


title: 3d7d_SS2_146813.47a [SLX-19982.i701_i506]


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i715_i508]

description:
SLX.17004.i715_i508
NexteraXT_SetA


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i715_i507]

description:
SLX.17004.i715_i507
NexteraXT_SetA


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i715_i505]

description:
SLX.17004.i715_i505
NexteraXT_SetA


title: 3d7d_SS2_146813.47a [SLX-19982.i714_i505]


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i715_i506]

description:
SLX.17004.i715_i506
NexteraXT_SetA


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i715_i503]

description:
SLX.17004.i715_i503
NexteraXT_SetA


title: 3d7d_SS2_146813.47a [SLX-19982.i712_i505]


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i714_i511]

description:
SLX.17004.i714_i511
NexteraXT_SetA


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i715_i502]

description:
SLX.17004.i715_i502
NexteraXT_SetA


title: 3d7d_SS2_146813.47a [SLX-19982.i711_i505]


title: 3d7d_SS2_146813.47a [SLX-19982.i710_i505]


title: 3d7d_SS2_146813.47a [SLX-19982.i707_i505]


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i714_i510]

description:
SLX.17004.i714_i510
NexteraXT_SetA


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i714_i507]

description:
SLX.17004.i714_i507
NexteraXT_SetA


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i714_i508]

description:
SLX.17004.i714_i508
NexteraXT_SetA


title: 3d7d_SS2_146813.47a [SLX-19982.i705_i505]


title: 3d7d_SS2_146813.47a [SLX-19982.i706_i505]


title: 3d7d_SS2_146813.47a [SLX-19982.i704_i505]


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i714_i506]

description:
SLX.17004.i714_i506
NexteraXT_SetA


title: 3d7d_SS2_146813.47a [SLX-19982.i703_i505]


title: 3d7d_SS2_146813.47a [SLX-19982.i702_i505]


title: 3d7d_SS2_146813.47a [SLX-19982.i701_i505]


title: 3d7d_SS2_146813.47a [SLX-19982.i715_i503]


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i712_i508]

description:
SLX.17004.i712_i508
NexteraXT_SetA


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i714_i503]

description:
SLX.17004.i714_i503
NexteraXT_SetA


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i712_i506]

description:
SLX.17004.i712_i506
NexteraXT_SetA


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i714_i502]

description:
SLX.17004.i714_i502
NexteraXT_SetA


title: 3d7d_SS2_146813.47a [SLX-19982.i707_i503]


title: 3d7d_SS2_146813.47a [SLX-19982.i712_i503]


title: 3d7d_SS2_146813.47a [SLX-19982.i710_i503]


title: 3d7d_SS2_146813.47a [SLX-19982.i714_i503]


title: 3d7d_SS2_146813.47a [SLX-19982.i711_i503]


title: 3d7d_SS2_146813.47a [SLX-19982.i706_i503]


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i712_i507]

description:
SLX.17004.i712_i507
NexteraXT_SetA


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i712_i502]

description:
SLX.17004.i712_i502
NexteraXT_SetA


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i712_i503]

description:
SLX.17004.i712_i503
NexteraXT_SetA


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i712_i505]

description:
SLX.17004.i712_i505
NexteraXT_SetA


title: 3d7d_SS2_146813.47a [SLX-19982.i704_i503]


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i711_i511]

description:
SLX.17004.i711_i511
NexteraXT_SetA


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i711_i508]

description:
SLX.17004.i711_i508
NexteraXT_SetA


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i711_i510]

description:
SLX.17004.i711_i510
NexteraXT_SetA


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i714_i505]

description:
SLX.17004.i714_i505
NexteraXT_SetA


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i712_i511]

description:
SLX.17004.i712_i511
NexteraXT_SetA


title: Mouse1_STHSCs_Hoxb5_mKOneg [SLX.17004.i712_i510]

description:
SLX.17004.i712_i510
NexteraXT_SetA


title: 3d7d_SS2_146813.47a [SLX-19982.i702_i503]


title: 3d7d_SS2_146813.47a [SLX-19982.i705_i503]


title: 3d7d_SS2_146813.47a [SLX-19982.i701_i503]


title: 3d7d_SS2_146813.47a [SLX-19982.i715_i502]


title: 3d7d_SS2_146813.47a [SLX-19982.i714_i502]


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i711_i506]

description:
SLX.17004.i711_i506
NexteraXT_SetA


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i710_i511]

description:
SLX.17004.i710_i511
NexteraXT_SetA


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i711_i505]

description:
SLX.17004.i711_i505
NexteraXT_SetA


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i711_i502]

description:
SLX.17004.i711_i502
NexteraXT_SetA


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i711_i503]

description:
SLX.17004.i711_i503
NexteraXT_SetA


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i710_i510]

description:
SLX.17004.i710_i510
NexteraXT_SetA


title: 3d7d_SS2_146813.47a [SLX-19982.i703_i503]


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i710_i508]

description:
SLX.17004.i710_i508
NexteraXT_SetA


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i710_i506]

description:
SLX.17004.i710_i506
NexteraXT_SetA


title: 3d7d_SS2_146813.47a [SLX-19982.i707_i502]


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i710_i507]

description:
SLX.17004.i710_i507
NexteraXT_SetA


title: 3d7d_SS2_146813.47a [SLX-19982.i711_i502]


title: 3d7d_SS2_146813.47a [SLX-19982.i710_i502]


title: 3d7d_SS2_146813.47a [SLX-19982.i712_i502]


title: 3d7d_SS2_146813.47a [SLX-19982.i706_i502]


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i710_i505]

description:
SLX.17004.i710_i505
NexteraXT_SetA


title: 3d7d_SS2_146813.47a [SLX-19982.i704_i502]


title: 3d7d_SS2_146813.47a [SLX-19982.i702_i502]


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i710_i503]

description:
SLX.17004.i710_i503
NexteraXT_SetA


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i711_i507]

description:
SLX.17004.i711_i507
NexteraXT_SetA


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i710_i502]

description:
SLX.17004.i710_i502
NexteraXT_SetA


title: 3d7d_SS2_146814.46d [SLX-19981.i729_i521]


title: 3d7d_SS2_146813.47a [SLX-19982.i701_i502]


title: 3d7d_SS2_146814.46d [SLX-19981.i728_i521]


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i707_i511]

description:
SLX.17004.i707_i511
NexteraXT_SetA


title: 3d7d_SS2_146813.47a [SLX-19982.i705_i502]


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i707_i508]

description:
SLX.17004.i707_i508
NexteraXT_SetA


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i707_i510]

description:
SLX.17004.i707_i510
NexteraXT_SetA


title: 3d7d_SS2_146814.46d [SLX-19981.i727_i521]


title: 3d7d_SS2_146814.46d [SLX-19981.i724_i521]


title: 3d7d_SS2_146813.47a [SLX-19982.i703_i502]


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i707_i507]

description:
SLX.17004.i707_i507
NexteraXT_SetA


title: 3d7d_SS2_146814.46d [SLX-19981.i722_i521]


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i707_i505]

description:
SLX.17004.i707_i505
NexteraXT_SetA


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i707_i506]

description:
SLX.17004.i707_i506
NexteraXT_SetA


title: 3d7d_SS2_146814.46d [SLX-19981.i721_i521]


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i707_i503]

description:
SLX.17004.i707_i503
NexteraXT_SetA


title: 3d7d_SS2_146814.46d [SLX-19981.i720_i521]


title: 3d7d_SS2_146814.46d [SLX-19981.i719_i521]


title: 3d7d_SS2_146814.46d [SLX-19981.i723_i521]


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i706_i510]

description:
SLX.17004.i706_i510
NexteraXT_SetA


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i706_i511]

description:
SLX.17004.i706_i511
NexteraXT_SetA


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i706_i508]

description:
SLX.17004.i706_i508
NexteraXT_SetA


title: 3d7d_SS2_146814.46d [SLX-19981.i716_i521]


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i706_i507]

description:
SLX.17004.i706_i507
NexteraXT_SetA


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i706_i506]

description:
SLX.17004.i706_i506
NexteraXT_SetA


title: 3d7d_SS2_146814.46d [SLX-19981.i729_i520]


title: 3d7d_SS2_146814.46d [SLX-19981.i728_i520]


title: 3d7d_SS2_146814.46d [SLX-19981.i727_i520]


title: 3d7d_SS2_146814.46d [SLX-19981.i726_i521]


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i706_i505]

description:
SLX.17004.i706_i505
NexteraXT_SetA


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i706_i503]

description:
SLX.17004.i706_i503
NexteraXT_SetA


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i705_i511]

description:
SLX.17004.i705_i511
NexteraXT_SetA


title: 3d7d_SS2_146814.46d [SLX-19981.i724_i520]


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i706_i502]

description:
SLX.17004.i706_i502
NexteraXT_SetA


title: 3d7d_SS2_146814.46d [SLX-19981.i718_i521]


title: Mouse1_STHSCs_Hoxb5_mKOpos [SLX.17004.i707_i502]

description:
SLX.17004.i707_i502
NexteraXT_SetA


title: 3d7d_SS2_146814.46d [SLX-19981.i722_i520]


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i705_i510]

description:
SLX.17004.i705_i510
NexteraXT_SetA


title: 3d7d_SS2_146814.46d [SLX-19981.i723_i520]


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i705_i507]

description:
SLX.17004.i705_i507
NexteraXT_SetA


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i705_i506]

description:
SLX.17004.i705_i506
NexteraXT_SetA


title: 3d7d_SS2_146814.46d [SLX-19981.i721_i520]


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i705_i508]

description:
SLX.17004.i705_i508
NexteraXT_SetA


title: 3d7d_SS2_146814.46d [SLX-19981.i716_i520]


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i705_i505]

description:
SLX.17004.i705_i505
NexteraXT_SetA


title: 3d7d_SS2_146814.46d [SLX-19981.i720_i520]


title: 3d7d_SS2_146814.46d [SLX-19981.i718_i520]


title: 3d7d_SS2_146814.46d [SLX-19981.i729_i518]


title: 3d7d_SS2_146814.46d [SLX-19981.i728_i518]


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i705_i502]

description:
SLX.17004.i705_i502
NexteraXT_SetA


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i705_i503]

description:
SLX.17004.i705_i503
NexteraXT_SetA


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i704_i511]

description:
SLX.17004.i704_i511
NexteraXT_SetA


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i704_i510]

description:
SLX.17004.i704_i510
NexteraXT_SetA


title: 3d7d_SS2_146814.46d [SLX-19981.i726_i520]


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i704_i508]

description:
SLX.17004.i704_i508
NexteraXT_SetA


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i704_i507]

description:
SLX.17004.i704_i507
NexteraXT_SetA


title: 3d7d_SS2_146814.46d [SLX-19981.i726_i518]


title: 3d7d_SS2_146814.46d [SLX-19981.i724_i518]


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i704_i506]

description:
SLX.17004.i704_i506
NexteraXT_SetA


title: 3d7d_SS2_146814.46d [SLX-19981.i723_i518]


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i704_i505]

description:
SLX.17004.i704_i505
NexteraXT_SetA


title: 3d7d_SS2_146814.46d [SLX-19981.i722_i518]


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i704_i503]

description:
SLX.17004.i704_i503
NexteraXT_SetA


title: 3d7d_SS2_146814.46d [SLX-19981.i721_i518]


title: Mouse1_LTHSCs_Hoxb5_mKOneg [SLX.17004.i704_i502]

description:
SLX.17004.i704_i502
NexteraXT_SetA


title: 3d7d_SS2_146814.46d [SLX-19981.i719_i520]


title: 3d7d_SS2_146814.46d [SLX-19981.i719_i518]


title: 3d7d_SS2_146814.46d [SLX-19981.i718_i518]


title: 3d7d_SS2_146814.46d [SLX-19981.i727_i518]


title: 3d7d_SS2_146814.46d [SLX-19981.i720_i518]


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i703_i510]

description:
SLX.17004.i703_i510
NexteraXT_SetA


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i703_i507]

description:
SLX.17004.i703_i507
NexteraXT_SetA


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i703_i506]

description:
SLX.17004.i703_i506
NexteraXT_SetA


title: 3d7d_SS2_146814.46d [SLX-19981.i716_i518]


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i703_i505]

description:
SLX.17004.i703_i505
NexteraXT_SetA


title: 3d7d_SS2_146814.46d [SLX-19981.i729_i517]


title: 3d7d_SS2_146814.46d [SLX-19981.i728_i517]


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i703_i503]

description:
SLX.17004.i703_i503
NexteraXT_SetA


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i703_i502]

description:
SLX.17004.i703_i502
NexteraXT_SetA


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i702_i511]

description:
SLX.17004.i702_i511
NexteraXT_SetA


title: 3d7d_SS2_146814.46d [SLX-19981.i726_i517]


title: 3d7d_SS2_146814.46d [SLX-19981.i724_i517]


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i702_i508]

description:
SLX.17004.i702_i508
NexteraXT_SetA


title: 3d7d_SS2_146814.46d [SLX-19981.i723_i517]


title: 3d7d_SS2_146814.46d [SLX-19981.i722_i517]


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i702_i507]

description:
SLX.17004.i702_i507
NexteraXT_SetA


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i702_i510]

description:
SLX.17004.i702_i510
NexteraXT_SetA


title: 3d7d_SS2_146814.46d [SLX-19981.i721_i517]


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i703_i511]

description:
SLX.17004.i703_i511
NexteraXT_SetA


title: 3d7d_SS2_146814.46d [SLX-19981.i719_i517]


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i703_i508]

description:
SLX.17004.i703_i508
NexteraXT_SetA


title: 3d7d_SS2_146814.46d [SLX-19981.i718_i517]


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i702_i503]

description:
SLX.17004.i702_i503
NexteraXT_SetA


title: 3d7d_SS2_146814.46d [SLX-19981.i720_i517]


title: 3d7d_SS2_146814.46d [SLX-19981.i716_i517]


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i702_i506]

description:
SLX.17004.i702_i506
NexteraXT_SetA


title: 3d7d_SS2_146814.46d [SLX-19981.i728_i516]


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i701_i511]

description:
SLX.17004.i701_i511
NexteraXT_SetA


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i702_i505]

description:
SLX.17004.i702_i505
NexteraXT_SetA


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i702_i502]

description:
SLX.17004.i702_i502
NexteraXT_SetA


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i701_i510]

description:
SLX.17004.i701_i510
NexteraXT_SetA


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i701_i508]

description:
SLX.17004.i701_i508
NexteraXT_SetA


title: 3d7d_SS2_146814.46d [SLX-19981.i726_i516]


title: 3d7d_SS2_146814.46d [SLX-19981.i727_i517]


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i701_i505]

description:
SLX.17004.i701_i505
NexteraXT_SetA


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i701_i506]

description:
SLX.17004.i701_i506
NexteraXT_SetA


title: 3d7d_SS2_146814.46d [SLX-19981.i723_i516]


title: 3d7d_SS2_146814.46d [SLX-19981.i724_i516]


title: 3d7d_SS2_146814.46d [SLX-19981.i720_i516]


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i701_i503]

description:
SLX.17004.i701_i503
NexteraXT_SetA


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i701_i502]

description:
SLX.17004.i701_i502
NexteraXT_SetA


title: 3d7d_SS2_146814.46d [SLX-19981.i719_i516]


title: 3d7d_SS2_146814.46d [SLX-19981.i721_i516]


title: 3d7d_SS2_146814.46d [SLX-19981.i722_i516]


title: RNA-seq of Akt3 KD-2iL rep2

city: Nanjing

first: Xiaoxu

last: Liu

state: Jiangsu

address: 2 Sipailou

department: Institute of Life Sciences

institute: Southeast University

data_processing:
RNA-seq reads were aligned to the Mus musculus genome (UCSC genome mm9) by HISAT2(v2.1.0) with default parameters. Read counts were calculated by HTSeq (v0.6.1.post1) using mapped reads, and differentially expressed genes were identified by DESeq2 (v1.36.0) (adjusted P-value<0.05, fold-change >0.58 either up- or down-regulation).
Assembly: mm9
Supplementary files format and content: bigWig

growth_protocol: Feeder-free Mouse V6.5 embryonic stem cells were cultured on 0.1% gelatin-coated plates. mESCs were cultured in N2B27 medium (50% DMEM/F12 and 50%Neurobasal medium, 1× N2 supplement, 1× B27 supplement ,1× Penicillin-Streptomycin, 0.1 mM mercaptoethanol, 2 mM L-glutamine) supplemented with Mek inhibitor (PD0325901, 2.5 M),Gsk3 inhibitor (CHIR99021, 7.5 M) and 5 units of LIF. EpiSC cells were cultured on fibronectin-coated plates (5 g/mL/cm2) in N2B27 medium supplemented with Fgf2 (12 ng/mL) and Activin A (20 ng/mL) at 37°C with 5% CO2 in a humidified incubator and routinely passaged 2-3 times a week.

extract_protocol:
RNAs from two independent biological replicates of ESCs and EpiSCs were extracted with QIAGEN RNeasy Mini Kit. Harvest around of 1 x 106 cells, as a cell pellet or by direct lysis in the vessel.Add 350μl of Buffer RLT. Add 1 volume of 70% ethanol to the lysate and mix well by pipetting. Transfer the sample to a spincolumn placed in a 2 ml collection tube and centrifuge for 1min at 10000 x g. Discard the flow-through. Add 700 μl Buffer RW1 to the RNeasy spin column. Close the lid and centrifuge for 15 s at ≥8000 x g. Discard the flow-through. Add 500 μl Buffer RPE to the spin column. Centrifuge for 1min at 10000x g and discard the flow-through. Then wash samples with 500 μl Buffer RPE in the spin column and elute the RNA with 30–50 μl RNase-free water.
For RNA-seq, library preparation were performed with TruSeq Sample prep kit (Illumina) for further next generation sequencing.


title: 3d7d_SS2_146814.46d [SLX-19981.i729_i516]


title: 3d7d_SS2_146814.46d [SLX-19981.i727_i516]


title: RNA-seq of Ctrl-2iL rep2


title: 3d7d_SS2_146814.46d [SLX-19981.i718_i516]


title: RNA-seq of Ctrl-2iL rep1


title: 3d7d_SS2_146814.46d [SLX-19981.i716_i516]


title: Mouse1_LTHSCs_Hoxb5_mKOpos [SLX.17004.i701_i507]

description:
SLX.17004.i701_i507
NexteraXT_SetA


title: 4C-seq in Ell3 KO

library_source: genomic

data_processing:
For read alignment, we found it extremely slow to map the reads to the whole mm10 genome, especially when using multiple mapping mode. To avoid this problem, we employed an alternative method which mapped the reads to a pseudo genome spanning a viewpoint (e.g. promoter of the gene of interest). In brief, the sequence +/- Mb around the viewpoint in mm10 was downloaded from UCSC genome browser and a pseudo genome was built by Bowtie2 software. A pair of fastq files were mapped to the pseudo genome separately by Bowtie2 with default settings if using unique mapping mode. For multiple mapping, the ‘-a’ option was added into the command line. This method enabled much faster alignment and generated a pair of sam files corresponding to ‘Read1’ and ‘Read2’ in read pairs. A custom script was developed to retrieve the viewpoint-related data from the resulting sam files. Briefly, when a read in either ‘Read1’ or ‘Read2’ sam file overlapped the region +/-1 kb around the viewpoint, the corresponding read in the other sam was collected and used for the downstream analysis. To make the bedgraph files, the 2-Mb pseudo genome was segmented into 1-kb windows and the read counts were calculated for each window. The browser plots were made with WashU genome browser.
Assembly: mm10
Supplementary files format and content: bedgraph
Library strategy: 4C-seq

extract_protocol:
4C-seq was performed as previously described with some modifications. Briefly, 1 × 10^7 V6.5 cells were used per 4C assay. Cells are treated with formaldehyde, which cross-links proteins to proteins and DNA. Cross-linked chromatin is subsequently digested with HindⅢ (NEB) to fragment. Next, chromatin is diluted and then religated by T4 ligase (NEB) to fuse the ends of DNA fragments. DNA is further digested by Csp6i (NEB) that digest the fragment into smaller fragments after the removal of cross-links by heating. These fragments are religated under diluted conditions to create much smaller DNA circles using T4 ligase (NEB) again. Inverse PCR primers with Illumina forward and reverse adaptors were designed to anneal to a bait locus HindIII/Csp6i restriction fragment.
4C template was used to amplify each bait using Expand Long Template Polymerase (Roche) system. The PCR program is as follows: 2 min at 94 °C; 10 sec at 94 °C; 1 min at bait specific annealing temperature; 3 min at 68 °C; 29X repeat; 5 min at 68 °C; hold at 4 °C. All PCR tubes were pooled and purified using High Pure PCR Product Purification Kit (Roche) kit. Subsequently, high-throughput sequencing is used to read the captured regions.

value: Ell3 KO


title: 3d7d_SS2_146814.46d [SLX-19981.i728_i515]


title: RNA-seq of Akt3 KD-2iL rep1


title: 3d7d_SS2_146814.46d [SLX-19981.i729_i515]


title: ATAC-seq in  Ell3 KO

data_processing:
For quantification of repetitive genomic regions, we allowed multiple-mapping reads using Bowtie2 parameter ‘–fast -k 1’.
Peak calling was performed with the MACS2 and TE-specific peaks were selected by overlapping with the RepeatMasker from UCSC (mm9.rmsk) using bedtools
Assembly: mm9
Supplementary files format and content: bigWig

source_name: mES

extract_protocol:
The cell pellets were resuspended with 50 μL transposition mix (5X TTBL 10 μl, TTE Mix V50 5 μl, ddH2O 35 μl, Vazyme TD501) and incubated at 37°C for 30 min.
The DNA were collected using VAHTS DNA Clean Beads (Vazyme) and amplified for 15 cycles using TruePrepTM Index Kit V2 for Illumina® (Vazyme TD202).

value: mES

value: mouse embryonic stem cell

value: ELL3 KO

tag: chip antibody


title: 4C-seq in WT


title: ChIP-seq of H3K4me1 in Ell3 KO

extract_protocol:
For ChIP-seq,cells were crosslinked with 1% formaldehyde for 10 min and quenched with glycine for 5 min at the room temperature. Fixed cells were sonicated and immunoprecipitated with the mixture of beads and antibody overnight at 4 ℃. ChIP-DNA was purified using PCR purification kit (Qiagen) and performed for qPCR using iTaq Universal SYBR Green Supermix (Bio-Rad) on CFX96 (Bio-Rad).
ChIP-seq libraries were prepared with Illumina's ChIP-seq sample prep kit (0801-0303). NEBNext® DNA Library Prep Master Mix Set for Illumina.


title: 3d7d_SS2_146814.46d [SLX-19981.i726_i515]


title: 3d7d_SS2_146814.46d [SLX-19981.i727_i515]


title: 3d7d_SS2_146814.46d [SLX-19981.i724_i515]


title: 3d7d_SS2_146814.46d [SLX-19981.i723_i515]


title: 3d7d_SS2_146814.46d [SLX-19981.i722_i515]


title: ChIP-seq of H3K4me3 in WT


title: ChIP-seq of H3K4me3 in Ell3 KO


title: 3d7d_SS2_146814.46d [SLX-19981.i720_i515]


title: 3d7d_SS2_146814.46d [SLX-19981.i719_i515]


title: LIC,YTHDC1,Proteintech

city: Wuhan

first: Haojian

last: Zhang

address: Donghu Rd.

institute: Wuhan University

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
RIP-seq reads were trimmed from 3' end until the final base had a quality score > 20, using Trim_galore, discarding reads left with < 20 bp
RIP-seq reads were aligned to the GRCm38 transcripts using HISAT2. Only uniquely mapping reads with at most two mismatches were retained.
To create RIP-seq coverage plots, the locations of the mapped RIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per kilobase per million , rpkm) and reformatted in the bigWig file format.
Peaks were called uing MACS with the significance cut-off q-value <=0.01
Assembly: narrowPeak files were generated using MACS v2 with default settings.
Supplementary files format and content: GRCm38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

source_name: lin-ckit+

growth_protocol: IMDM, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin,10μg/ml m-IL3,10μg/ml m-IL6,20μg/ml m-SCF.Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were crosslinked by UV (Stratalinker 1800 (254nm),120mJ/cm2 ×3) . After cell lysis, chromatin was sonicated using a ultrasonicator (Bioruptor).
The purified mRNA fragments were used to construct libraries with TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA),1 μg of RNA was used as starting material for input and ip samples. Libraries were amplified using 20 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length.

value: lin-ckit+

value: Bone Marrow

value: YTHDC1 (Proteintech, #29441-1-AP)


title: LIC, input


title: 3d7d_SS2_146814.46d [SLX-19981.i718_i515]

value: WT


title: LIC, YTHDF2, Proteintech

value: YTHDF2 (Proteintceh, #24744-1-AP)


title: LIC, IGF2BP2,Proteintech

value: IGF2BP2 (Proteintceh, #11601-1-AP)


title: 3d7d_SS2_146814.46d [SLX-19981.i716_i515]


title: ATAC-seq in WT