title: Chlorella vulgaris treated replicate 1

status: Public on Jul 13 2023

city: Catania

first: Angela Roberta

last: Lo Piero

state: CT

address: Via S. Sofia 98

country: Italy

institute: University of Catania

data_processing:
Base calling, base quality and Phred score relationship performed with the Illumina CASAVA v1.8 software
Raw reads are filtered to remove reads containing adapters or reads of low quality
Clean reads have been assembled using Trinity software (2.6.6 version, minKmerCov= 3, min_glue=4). Corset software (4.6 version) was used for hierarchical clustering (parameter -m 10)
Seven databases have been applied for gene functional annotation: Nr, Nt, Pfam, KOG/COG, Swiss-Prot, KEGG and GO.
CDS prediction using blast and EST-scan
De novo transcriptome filtered by Corset (4.6 version) used as a reference for mapping reads back to transcriptome and quantify the expression level using RSEM.
DESeq2 (1.26.0 version) used for gene expression difference analysis
Assembly: FASTA assembled sequences
Supplementary files format and content: Microsoft excell file containing raw readcounts of all unigenes in each sample

organism: Lactuca sativa

source_name: Leaf

growth_protocol: The experiment was conducted in a transparent box (40 x 20 x 10 cm), containing pumice as an inert substrate wetted with 1 L of Hoagland solution. Lettuce seedlings (Lactuca sativa L.) were provided by a local nursery and 10 seedlings at the “four true leaves” stage were transplanted in each box in a completely random design, performing five biological replicates for treatments. The seedlings were grown for 6 days in a growth chamber at 25 ± 2°C, with a 16-h photoperiod and they were irrigated every day with 100 mL distilled water.

extract_protocol:
Leaf tissue was collected both in treated (C. vulgaris and S. quadricauda) and untreated plants after 4 days from the treatment and immediately frozen in liquid nitrogen and stored at -80°C until further use. RNA isolation was carried out by using the Spectrum Plant Total RNA Extraction kit (Sigma-Aldrich, St. Louis, MO, USA) according to the manufacturer’s instructions.
All samples passed through three steps before library construction: Nanodrop for preliminary quantitation, agarose gel electrophoresis to tests RNA degradation and potential contamination, Agilent 2100 to checks RNA integrity and quantitation. After the QC procedures, mRNA from is enriched from total RNA using oligo(dT) beads. The mRNA is then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) is added, with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation and AMPure XP beads is used to purify the cDNA. The final cDNA library is ready after a round of purification, terminal repair, Atailing, ligation of sequencing adapters, size selection and PCR enrichment. Libraries are fed into Illumina machines according standard Illumina protocol.

treatment_protocol: After a period of acclimatization (6 days), the treatment was performed by irrigating the inert substrate with Hoagland solution (500 mL) containing either Chlorella vulgaris (LsCv sample) or Scenedesmus quadricauda (LsSq sample) extracts at the concentration of 1 mg of organic carbon per liter (Corg L-1), whereas the untreated plants (LsCK) received only 500 mL of Hoagland solution.

value: Leaf

value: 500 mL of Hoagland solution + Chlorella vulgaris extraxt


title: control replicate 2

type: SRA

library_source: transcriptomic

molecule: total RNA

tag: tissue

tag: treatment

value: 500 mL of Hoagland solution


title: Chlorella vulgaris treated replicate 2


title: control replicate 1


title: Scenedesmus quadricauda treated replicate 2

value: 500 mL of Hoagland solution + Scenedesmus quadricauda extraxt


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S44_CGATGT

city: Philadelphia

first: Hao

last: Wu

state: PA

address: 415 Curie Boulevard

department: Genetics

country: USA

institute: University of Pennsylvania

library_source: genomic

data_processing:
The pre-processing (read alignment, quality filtering and read deduplication) was performed for snhmC/Joint-snhmC-seq datasets of individual single cells as previously described with minor modifications6. Briefly, demultiplexing of inline barcodes was first performed allowing up to 1-nt mismatch. The data quality was examined with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Raw sequencing reads were trimmed for adaptor sequences and inline barcodes using Cutadapt with the following parameters in paired-end mode: -f fastq -q 20 -u 16 -U 16 -m 30 -a AGATCGGAAGAGCACACGTCTGAAC -A AGATCGGAAGAGCGTCGTGTAGGGA. The trimmed R1 and R2 reads were mapped independently against the reference genome (mm10) using Bismark (v0.18.2) with following parameters: --bowtie2 -D 15 -R 2 -L 20 -N 0 –score_min L,0,-0.2 (--pbat option was turned on for mapping R1 reads). Uniquely mapped reads were filtered for minimal mapping quality (MAPQ>=10) using samtools9. PCR duplicates were removed using the Picard MarkDuplicates (http://broadinstitute.github.io/picard/). To eliminate reads from strands not deaminated by A3A, reads with three or more consecutive non-converted cytosines in the CH context were removed using filter_non_conversion in Bismark. Low quality snhmC/Joint-snhmC-seq datasets were removed using the following set of criteria. First, Mapping rate of raw sequencing reads is set to be at least 20%; Second, we set a minimum on the number of pass filter reads (uniquely mapped, deduplicated, MAPQ>=10, <=3 consecutive 5mCH sites) to be 100,000 per cell; Third, the 5mCG deamination rate in spike-in lambda phage control is higher than 90%. Base calling of unmethylated and methylated cytosines was performed by bismark_methylation_extractor in Bismark in each individual nucleus. 5hmC signals were calculated as % of C/(C+T) at each cytosine base.
Assembly: mm10
Supplementary files format and content: Tab-delimited bismark methylation calling files include genomic coordinates (columan 1-3: chromosome, start, and end), 5hmC signal (column 4: % of 5hmC levels normalized to total reads), 5hmC read (column 5), and unmodified read (column 6) for all detected CpG (._CpG.mm10.bismark.cov)  or CpH (._CpH.mm10.bismark.cov) sites across the mouse genome in individually sequenced cell.
Library strategy: bisulfite-assisted ACE-seq

molecule: genomic DNA

organism: Mus musculus

source_name: Cortex

growth_protocol: All experiments were conducted in accordance with the guidelines of the Institutional Animal Care and Use Committee (IACUC) at the University of Pennsylvania. Mice were group-housed in cages of three to five in a 12-hr light/dark cycle with food and water provided ad libitum. All mice used for experiments were naïve to behavioral assays and other procedures. For all bulk-nucleus and single-nucleus experiments, 6-10 weeks old, wild-type, male mice in a pure C57BL/6J background were used. For prospectively isolating inhibitory (Inh) and excitatory (Ex) neuronal subtypes to benchmark snhmC-seq and joint-snhmC-seq, 9-week-old transgenic mice (Mecp2Tavi/y, NexCre/+, Rosa26BirA/BirA) from a C57BL/6J background were used as previously described (Johnson et al. 2017; PMID: 28920956).

extract_protocol:
Nuclei isolation from mouse cortical tissues was performed as described with minor modifications (Hu* & Fabyanic* et al., 2017; PMID: 29220646). Briefly, mouse brains were rapidly resected on ice. Cortices were flash-frozen in liquid nitrogen and stored at -80°C before nuclear isolation. Nuclei were isolated and purified as previously described with some modifications3. Briefly, 14mL sucrose cushion (1.8M sucrose (Sigma-Aldrich, RNase and DNase free, ultra-pure grade), 10mM Tris-HCl pH 8.0, 3mM MgAc2 (Sigma-Aldrich), and protease inhibitor cocktail (Roche)) was added to the bottom of centrifuge tubes (Beckman Coulter). Using a glass homogenizer (Wheaton), a frozen mouse cortical sample was dounce homogenized (19 times with loose pestle followed by 4 times with tight pestle) in 12mL homogenization buffer (0.32M sucrose, 5mM CaCl2 (Sigma-Aldrich), 3mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton X-100 (Sigma-Aldrich), 0.1mM EDTA (Invitrogen), protease inhibitor cocktail (Roche)). Homogenates (~12ml) were carefully layered onto the sucrose cushion in the centrifuge tubes, and 10mL homogenization buffer was added atop of the homogenates. The tubes were then balanced and centrifuged in a Beckman Coulter L7-65 Ultracentrifuge at 82,705 g at 4°C for 2hr using a Beckman Coulter SW28 swing bucket rotor (Beckman Coulter). The supernatant was carefully removed via aspiration. 1ml chilled DPBS was added to resuspend the nuclear pellet, and nuclei were subsequently transferred to a 1.5-mL tube. Nuclei were pelleted at 500 g for 10 min at 4C, and then resuspended in 0.01% BSA (Sigma-Aldrich) in DPBS. After resuspension, nuclei were filtered through a 40-μm cell strainer (Fisher Scientific), visually inspected for morphology and quality assurance, and counted using a Fuchs-Rosenthal counting chamber before FANS.
All steps of library preparation were performed in a horizontal laminar flow hood (AirCleanⓇ600 PCR Workstation) to minimize environmental DNA contamination. To profile both 5hmC and true 5mC in the same single cell through physical splitting, bisulfite conversion of single nuclei was first carried out using the EZ-96 DNA Methylation-Direct™ Kit (Zymo, Deep Well Format, D5023). Briefly, 96-well plates containing FANS-isolated single nuclei were heated at 50°C for 20min and stored in -80°C for later use. 32.5μL CT Conversion Reagent was added to each well, followed by sealing the plate and shaking to mix. Plates were treated with the following program using a thermocycler: two cycles of [98°C for 8min, 64°C for 1h45min], and 4°C forever. Purification was performed using Zymo-Spin™ I-96 Binding Plates preloaded with 250μL M-binding buffer according to kit instructions with following modifications. For the Joint-snhmC-seq, 20µl of nuclease-free water was used as the elution buffer. The 9µl eluent retained for the snmC-seq2/split (bisulfite-only) workflow will proceed directly to random priming. To the other 9μl eluent retained for snhmC-seq2/split workflow, 7µl nuclease-free water was added to the eluant, for a total reaction volume of 16µl. The 16µl of bisulfite-treated DNA were denatured at 95°C for 1min and snap cooled by transfer to an isopropanol dry ice bath and then to the −80°C pre-incubated PCR tube rack. To snap-cooled samples, 8µl of deamination enzyme mix (2.4µl of 10x reaction buffer (50mM Bis-Tris (pH 6.0) with 0.1% Triton X-100), 0.48µl BSA, 0.48µl of commercial A3A (at a final concentration of ~500 nM, NEB, E7125L) or in-house A3A (~1000 nM), and 4.64µL nuclease-free water) was added into each well. The deamination reactions were incubated for 30 minutes at 37°C, tapped to mix, and spun down before undergoing an additional incubation for 2.5h at 37°C. Post-incubation, these reactions were purified with 2x commercial SPRI beads (Beckman Coulter B23318), and eluted in 9µl of Low EDTA TE buffer (IDT). For the Joint-snhmC-seq, P5L random primers were added to split single nuclei samples as described for snhmC-seq. Briefly, 1µl of matched, individual 250µM random primers was added to each reaction (9µl) to allow for subsequent multiplexing (up to 24-plex) and pairing of snmC-seq2/split to snhmC-seq2/split reactions of the same single cell. Plates were then heated at 95°C using a thermocycler for 3min to denature and were immediately chilled on ice for 2min. Next, 10µl of enzyme mix (2µl o f10x Isothermal Amplification Buffer II, 0.8µl of Bst 3.0 DNA Polymerase (8,000 U/ml), 1.2µl 100 mM MgSO4 (these three reagents all from NEB M0374L), 2.8µl of 10mM dNTP (NEB N0447L), and 3.2µl water) was added to each well (a 20µl reaction) and reactions were mixed by shaking. Reactions were then incubated at 60°C for 1h. Following this, 2μL Exonuclease 1 (20U/μl, Enzymatics X8010L) and 1μL Shrimp Alkaline Phosphatase (rSAP) (1U/μl, NEB M0371L) was added to each reaction followed by vortexing and incubation in a thermocycler at 37°C for 30min followed by 4°C forever. To multiplex subsequent adaptor ligation reactions, 18.4μl (0.8x) homebrew SPRI beads were added to each reaction and 8 sample/bead mixtures were pooled (up to 24 samples if all inline barcodes were used). The sample/bead mixtures were incubated at room temperature for 5min before being placed on a 96-well magnetic separator (DynaMag™-96 Side Magnet, ThermoFisher 12331D). Supernatant was removed from each well, followed by three rounds of washing with 180μl 80% ethanol. Beads were air dried at room temperature and 10μl Low EDTA TE buffer (IDT) was added to each well to fully resuspend the beads. Eluted samples were then transferred to either new PCR strips (for bulk sample) or 96-well plates (for single nuclei). The reactions were denatured in a thermocycler at 95°C for 3min and subsequently chilled on ice for 2min. 10.5μl Adaptase master mix (2μl Buffer G1, 2μl Reagent G2, 1.25μl Reagent G3, 0.5μl Enzyme G4, 0.5μl Enzyme G5, and 4.25μl Low EDTA TE buffer from xGenTM Methyl-Seq Lib Prep kit, IDT, 10009860) was added to each reaction, followed by vortexing. Reactions were incubated in a thermocycler at 37°C for 30min then 4°C forever. Finally, to amplify the pooled library and add dual indexing barcodes, 30μl PCR mix (25μl KAPA HiFi HotStart ReadyMix, Roche/KAPA Biosystems KK2602, 1μl of 30μM P5 (D501-508) indexing primer, and 5μl of 10μM P7 (D701-712) indexing primer) were added to each well, followed by mixing with vortexing. Reactions were transferred to a thermocycler programmed with the following stages: 95°C for 2min, 98°C for 30sec, 15 cycles of [98°C for 15sec, 64°C for 30sec, 72°C for 2min] (for pooled single nucleus reactions), 72°C for 5min, and 4°C forever. For bulk samples, we perform qPCR and subtract two cycles from the inflection point for each sample to determine optimal cycle number for amplification. PCR products were cleaned with two rounds of 0.8x SPRI beads, concentration was determined via QbitⓇ dsDNA High Sensitivity Assay Kit (Invitrogen Q32851), and library size was determined via Bioanalyzer (Agilent High Sensitivity DNA Kit, 5067-4626). Reactions were sequenced on Illumina NovaSeq 6000 (300-cycle v1.5 kit) sequencers.

value: Cortex

tag: developmental stage

value: Postnatal 6-10 weeks

tag: Sex

value: Male

tag: genotype

value: wild-type


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S44_GCCAAT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S43_TGACCA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S44_ATCACG


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S44_CTTGTA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S45_ATCACG


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S44_ACTTGA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S44_TAGCTT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S43_GCCAAT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S44_CAGATC


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S43_CGATGT


title: Scenedesmus quadricauda treated replicate 1


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S42_TGACCA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S43_TAGCTT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S43_CAGATC


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S43_ATCACG


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S42_GCCAAT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S43_CTTGTA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S42_TAGCTT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S42_CTTGTA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S42_CGATGT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S44_TGACCA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S42_ACTTGA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S42_ATCACG


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S42_CAGATC


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S43_ACTTGA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S41_TGACCA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S41_GCCAAT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S41_CGATGT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S41_CTTGTA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S41_TAGCTT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S41_CAGATC


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S41_ACTTGA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S41_ATCACG


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S40_TAGCTT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S40_TGACCA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S38_TGACCA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S40_GCCAAT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S40_ACTTGA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S40_CTTGTA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S39_CGATGT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S40_CAGATC


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S39_CTTGTA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S38_TAGCTT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S40_ATCACG


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S39_ATCACG


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S39_TAGCTT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S40_CGATGT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S38_CTTGTA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S39_ACTTGA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S39_CAGATC


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S39_TGACCA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S38_CGATGT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S38_GCCAAT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S39_GCCAAT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S38_ATCACG


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S38_CAGATC


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S38_ACTTGA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S37_TAGCTT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S37_GCCAAT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S37_CTTGTA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S37_CGATGT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S37_ATCACG


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S24_TGACCA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S24_CGATGT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S37_ACTTGA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S24_CTTGTA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S24_TAGCTT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S24_GCCAAT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S23_TAGCTT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S23_CGATGT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S23_CTTGTA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S24_ATCACG


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S24_CAGATC


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S24_ACTTGA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S23_GCCAAT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S23_CAGATC


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S37_TGACCA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S22_TGACCA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S22_GCCAAT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S22_TAGCTT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S22_CTTGTA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S22_CGATGT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq08.03.2021_S37_CAGATC


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S23_TGACCA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S21_TGACCA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S22_ACTTGA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S22_ATCACG


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S21_GCCAAT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S21_TAGCTT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S23_ACTTGA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S23_ATCACG


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S21_CGATGT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S21_CAGATC


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S21_ACTTGA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S20_GCCAAT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S20_CGATGT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S20_CTTGTA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S22_CAGATC


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S20_ATCACG


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S19_TAGCTT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S20_ACTTGA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S19_CAGATC


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S19_ATCACG


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S19_CGATGT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S18_TGACCA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S19_GCCAAT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S19_ACTTGA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S18_TAGCTT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S19_CTTGTA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S18_ATCACG


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S21_ATCACG


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S20_TAGCTT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S18_GCCAAT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S21_CTTGTA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S18_CGATGT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S20_CAGATC


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S17_CTTGTA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S17_CAGATC


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S17_ATCACG


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S17_CGATGT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S17_TGACCA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S18_ACTTGA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S16_TGACCA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S17_GCCAAT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S17_ACTTGA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S16_GCCAAT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S16_CTTGTA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S16_TAGCTT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S18_CTTGTA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S16_ATCACG


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S16_CAGATC


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S17_TAGCTT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S15_TGACCA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S16_ACTTGA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S16_CGATGT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S15_GCCAAT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S15_TAGCTT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S15_CTTGTA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S18_CAGATC


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S15_ATCACG


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S15_CAGATC


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S14_TGACCA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S15_ACTTGA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S15_CGATGT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S14_TAGCTT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S14_GCCAAT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S14_CTTGTA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S14_CGATGT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S14_ATCACG


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S14_CAGATC


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S14_ACTTGA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S13_TAGCTT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S13_TGACCA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S13_CGATGT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S13_GCCAAT


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S13_CTTGTA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S13_ATCACG


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S13_CAGATC


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S13_ACTTGA


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S46_CAGATC


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S46_TGACCA


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S46_ACTTGA


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S47_ACTTGA


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S47_GCCAAT


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S47_TGACCA


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S46_CGATGT


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S48_TGACCA


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S48_TAGCTT


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S45_TAGCTT


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S46_ATCACG


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S48_ATCACG


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S48_CGATGT


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S47_TAGCTT


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S46_GCCAAT


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S47_CAGATC


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S48_CTTGTA


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S47_CTTGTA


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S45_TGACCA


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S45_CTTGTA


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S47_ATCACG


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S48_ACTTGA


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S47_CGATGT


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S48_GCCAAT


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S45_CGATGT


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S45_GCCAAT


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S46_TAGCTT


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S46_CTTGTA


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S48_CAGATC


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S45_ATCACG


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S45_CAGATC


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S44_CAGATC


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S44_CTTGTA


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S44_TAGCTT


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S44_CGATGT


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S44_GCCAAT


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S44_ACTTGA


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S45_ACTTGA


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S43_GCCAAT


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S43_CAGATC


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S43_ATCACG


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S43_CTTGTA


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S44_TGACCA


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S42_ATCACG


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S43_TGACCA


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S43_TAGCTT


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S42_CTTGTA


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S43_CGATGT


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S43_ACTTGA


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S42_CAGATC


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S42_CGATGT


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S42_ACTTGA


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S42_TAGCTT


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S42_GCCAAT


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S44_ATCACG


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S42_TGACCA


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S41_TGACCA


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S41_CTTGTA


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S41_ATCACG


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S41_ACTTGA


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S41_CGATGT


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S40_TGACCA


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S40_TAGCTT


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S41_TAGCTT


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S40_ATCACG


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S40_GCCAAT


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S40_ACTTGA


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S39_TGACCA


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S40_CGATGT


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S40_CAGATC


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S39_CTTGTA


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S39_ACTTGA


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S39_ATCACG


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S39_GCCAAT


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S39_CAGATC


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S39_TAGCTT


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S39_CGATGT


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S38_TGACCA


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S38_GCCAAT


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S40_CTTGTA


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S38_CTTGTA


title: snhmCseq2.split_Cortex.WT_NeuN_pos_novaseq06.25.2021_S20_TGACCA


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S38_CAGATC


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S41_GCCAAT


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S38_TAGCTT


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S37_CTTGTA


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S38_ATCACG


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S37_CAGATC


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S37_TAGCTT


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S37_ATCACG


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S37_GCCAAT


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S37_CGATGT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S24_TGACCA

value: NEX/Neurod6-Cre reporter


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S37_ACTTGA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S24_TAGCTT


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S38_CGATGT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S23_TGACCA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S24_CAGATC


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S24_CGATGT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S24_ACTTGA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S24_ATCACG


title: snhmCseq2.split_Cortex.WT_NeuN_neg_novaseq06.25.2021_S38_ACTTGA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S23_GCCAAT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S23_TAGCTT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S22_TGACCA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S23_ATCACG


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S23_CGATGT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S23_CTTGTA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S23_CAGATC


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S22_CTTGTA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S22_TAGCTT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S22_CAGATC


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S22_ATCACG


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S23_ACTTGA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S22_ACTTGA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S22_GCCAAT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S21_TAGCTT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S22_CGATGT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S24_CTTGTA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S24_GCCAAT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S21_CTTGTA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S21_GCCAAT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S21_CAGATC


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S21_ATCACG


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S20_TGACCA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S21_ACTTGA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S20_TAGCTT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S20_GCCAAT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S20_CGATGT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S20_CTTGTA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S20_ATCACG


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S20_CAGATC


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S21_TGACCA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S20_ACTTGA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S19_TAGCTT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S19_TGACCA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S19_GCCAAT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S19_CAGATC


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S18_CGATGT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S18_CTTGTA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S18_TGACCA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S18_CAGATC


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S21_CGATGT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S19_CTTGTA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S18_ATCACG


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S19_ATCACG


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S19_CGATGT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S18_GCCAAT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S19_ACTTGA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S18_TAGCTT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S17_TGACCA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S17_CGATGT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S17_TAGCTT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S17_ACTTGA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S17_ATCACG


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S17_GCCAAT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S16_TGACCA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S16_TAGCTT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S16_GCCAAT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S16_CTTGTA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S16_CAGATC


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S16_CGATGT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S16_ATCACG


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S18_ACTTGA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S15_TGACCA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S16_ACTTGA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S15_TAGCTT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S15_CGATGT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S15_CTTGTA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S15_GCCAAT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S15_ATCACG


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S14_GCCAAT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S14_CTTGTA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S14_TGACCA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S14_TAGCTT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S15_ACTTGA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S14_CAGATC


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S15_CAGATC


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S14_CGATGT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S14_ATCACG


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S14_ACTTGA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S13_TGACCA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S13_CTTGTA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S13_CGATGT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S13_GCCAAT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S13_CAGATC


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S13_TAGCTT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S13_ATCACG


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq08.03.2021_S13_ACTTGA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S48_TAGCTT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S48_TGACCA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S48_CTTGTA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S48_GCCAAT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S48_CAGATC


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S48_CGATGT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S47_TGACCA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S48_ACTTGA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S47_GCCAAT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S47_TAGCTT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S47_CGATGT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S46_ATCACG


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S46_TAGCTT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S46_CTTGTA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S46_TGACCA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S47_ACTTGA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S46_GCCAAT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S47_ATCACG


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S45_TGACCA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S46_CGATGT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S47_CAGATC


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S46_ACTTGA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S45_TAGCTT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S47_CTTGTA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S45_GCCAAT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S45_CTTGTA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S45_CGATGT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S48_ATCACG


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S44_TAGCTT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S45_ATCACG


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S45_ACTTGA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S44_TGACCA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S44_CTTGTA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S46_CAGATC


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S44_CAGATC


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S44_ACTTGA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S44_CGATGT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S44_ATCACG


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S45_CAGATC


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S43_TAGCTT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S43_GCCAAT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S43_TGACCA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S43_ATCACG


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S43_ACTTGA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S42_TAGCTT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S43_CAGATC


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S43_CTTGTA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S41_TAGCTT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S42_TGACCA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S42_ATCACG


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S41_GCCAAT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S43_CGATGT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S42_CTTGTA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S41_ATCACG


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S41_CAGATC


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S41_ACTTGA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S41_CGATGT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S40_TGACCA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S40_GCCAAT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S40_CTTGTA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S40_CGATGT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S41_CTTGTA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S42_CGATGT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S42_GCCAAT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S42_CAGATC


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S42_ACTTGA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S41_TGACCA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S40_CAGATC


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S40_ACTTGA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S40_ATCACG


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S39_TGACCA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S39_CGATGT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S39_CAGATC


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S39_TAGCTT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S38_TGACCA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S39_GCCAAT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S39_ATCACG


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S39_CTTGTA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S39_ACTTGA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S38_CGATGT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S38_GCCAAT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S38_CAGATC


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S37_TGACCA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S38_TAGCTT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S40_TAGCTT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S38_ACTTGA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S37_TAGCTT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S37_GCCAAT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S37_CTTGTA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S37_ATCACG


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S24_TGACCA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S37_ACTTGA


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S24_TAGCTT


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S24_GCCAAT


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S24_CTTGTA


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S24_CAGATC


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S24_ACTTGA


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S24_CGATGT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S38_ATCACG


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S23_TAGCTT


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S22_TGACCA


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S23_ACTTGA


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S23_CTTGTA


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S23_CAGATC


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S22_GCCAAT


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S23_CGATGT


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S22_CTTGTA


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S22_CAGATC


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S22_CGATGT


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S22_TAGCTT


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S23_GCCAAT


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S37_CGATGT


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S22_ATCACG


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S22_ACTTGA


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S21_TGACCA


title: snhmCseq2.split_Cortex.NEXcre_Inh_novaseq06.25.2021_S37_CAGATC


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S21_TAGCTT


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S21_CTTGTA


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S23_TGACCA


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S21_GCCAAT


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S21_CGATGT


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S21_CAGATC


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S20_TGACCA


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S21_ATCACG


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S24_ATCACG


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S23_ATCACG


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S21_ACTTGA


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S20_GCCAAT


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S20_CGATGT


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S20_CTTGTA


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S20_ATCACG


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S20_CAGATC


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S19_TGACCA


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S20_ACTTGA


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S19_GCCAAT


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S19_ACTTGA


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S19_TAGCTT


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S19_CTTGTA


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S19_CGATGT


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S18_TGACCA


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S18_TAGCTT


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S19_ATCACG


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S19_CAGATC


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S18_GCCAAT


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S18_CAGATC


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S20_TAGCTT


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S18_ACTTGA


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S18_CGATGT


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S18_CTTGTA


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S17_CTTGTA


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S17_TAGCTT


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S17_CGATGT


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S17_GCCAAT


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S17_ATCACG


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S17_CAGATC


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S17_ACTTGA


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S17_TGACCA


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S16_TAGCTT


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S16_CTTGTA


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S16_ATCACG


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S16_CAGATC


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S16_TGACCA


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S16_CGATGT


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S16_GCCAAT


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S18_ATCACG


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S15_TGACCA


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S16_ACTTGA


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S15_TAGCTT


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S15_CTTGTA


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S15_GCCAAT


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S15_ATCACG


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S15_CAGATC


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S15_ACTTGA


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S14_CTTGTA


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S14_TAGCTT


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S14_CGATGT


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S14_GCCAAT


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S14_TGACCA


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S14_CAGATC


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S14_ACTTGA


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S13_TGACCA


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S13_CTTGTA


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S13_GCCAAT


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S13_CGATGT


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S13_CAGATC


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S15_CGATGT


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S13_ACTTGA


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S13_ATCACG


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S14_ATCACG


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S9_CTTGTA

extract_protocol:
Nuclei isolation from mouse cortical tissues was performed as described with minor modifications (Hu* & Fabyanic* et al., 2017; PMID: 29220646). Briefly, mouse brains were rapidly resected on ice. Cortices were flash-frozen in liquid nitrogen and stored at -80°C before nuclear isolation. Nuclei were isolated and purified as previously described with some modifications3. Briefly, 14mL sucrose cushion (1.8M sucrose (Sigma-Aldrich, RNase and DNase free, ultra-pure grade), 10mM Tris-HCl pH 8.0, 3mM MgAc2 (Sigma-Aldrich), and protease inhibitor cocktail (Roche)) was added to the bottom of centrifuge tubes (Beckman Coulter). Using a glass homogenizer (Wheaton), a frozen mouse cortical sample was dounce homogenized (19 times with loose pestle followed by 4 times with tight pestle) in 12mL homogenization buffer (0.32M sucrose, 5mM CaCl2 (Sigma-Aldrich), 3mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton X-100 (Sigma-Aldrich), 0.1mM EDTA (Invitrogen), protease inhibitor cocktail (Roche)). Homogenates (~12ml) were carefully layered onto the sucrose cushion in the centrifuge tubes, and 10mL homogenization buffer was added atop of the homogenates. The tubes were then balanced and centrifuged in a Beckman Coulter L7-65 Ultracentrifuge at 82,705 g at 4°C for 2hr using a Beckman Coulter SW28 swing bucket rotor (Beckman Coulter). The supernatant was carefully removed via aspiration. 1ml chilled DPBS was added to resuspend the nuclear pellet, and nuclei were subsequently transferred to a 1.5-mL tube. Nuclei were pelleted at 500 g for 10 min at 4C, and then resuspended in 0.01% BSA (Sigma-Aldrich) in DPBS. After resuspension, nuclei were filtered through a 40-μm cell strainer (Fisher Scientific), visually inspected for morphology and quality assurance, and counted using a Fuchs-Rosenthal counting chamber before FANS.
All steps of library preparation were performed in a horizontal laminar flow hood (AirCleanⓇ600 PCR Workstation) to minimize environmental DNA contamination. Bisulfite conversion of bulk nuclei was carried out using the EZ DNA Methylation-Direct™ Kit (Zymo, D5020). Bisulfite conversion of single nucleus was carried out using the EZ-96 DNA Methylation-Direct™ Kit (Zymo, Deep Well Format, D5023). PCR tubes containing FANS-isolated nuclei (100-10,000 nuclei), or 96-well plates containing FANS-isolated single nuclei, were heated at 50°C for 20min. 130μL (for bulk) or 32.5μL (for single nuclei) CT Conversion Reagent was added to each well, followed by pipetting up and down to mix. Plates were treated with the following program using a thermocycler: 98°C for 8min, 64°C for 3.5h, and 4°C forever. Zymo-Spin™ columns or Zymo-Spin™ I-96 Binding Plates were preloaded with either 600μl (bulk) or 250μl (single nuclei) M-binding buffer, respectively. Both bulk and single-cell samples were further purified according to their respective kit instructions, except Low EDTA TE Buffer (IDT) was used as the elution buffer. To perform A3A deamination, 3 µl of denaturing buffer (1.5µl 200mM MES buffer (pH 6.0) with 0.1% Tween-20 and 1.5µl DMSO) was first added to the 9μl eluent retained or each sample. The samples were denatured at 95°C for 1min and snap cooled by transfer to a PCR tube rack pre-incubated at −80°C (for bulk samples) or transfer to an isopropanol dry ice bath and then to the −80°C pre-incubated PCR tube rack (for 96-well plates containing single nuclei). Before thawing, 3 µl of enzymatic reaction mix (1.5µl 200 mM buffer (pH 6.0) with 0.1% Tween-20 and 1.5µl 5μM in-house A3A) was added to each reaction (for a final concentration of 500nM/µl A3A in 15 µl). The deamination reactions were incubated at 37°C for 2h, purified with 1.6x homebrew SPRI beads, eluted in 9µL Low EDTA TE buffer (IDT). To perform random priming and add inline barcodes, 1µL of individual 250µM random primer (with 8-plex inline barcodes: P5L_AD002_H, P5L_AD006_H, P5L_AD008_H, P5L_AD010_H, P5L_AD001_H, P5L_AD004_H, P5L_AD007_H, or P5L_AD012_H) was added to each reaction to allow for subsequent multiplexing reactions during downstream library preparation. Reactions or plates were heated at 95°C using a thermocycler for 3 min to denature and were immediately chilled on ice for 2 min. 10µl enzyme mix (2µl Blue Buffer (Enzymatics B0110), 1µl 10mM dNTP (NEB N0447L), 1µl Klenow (3′→ 5′ exo-) (50U/µl, Enzymatics P7010-HC-L), and 6µl water) was added to each well (a 20µl reaction) and reactions were mixed by vortexing. Plates or reactions were treated with the following program using a thermocycler: 4°C for 5min, ramp up to 25°C at 0.1°C/sec, 25°C for 5min, ramp up to 37°C at 0.1°C/sec, 37°C for 60min, 4°C forever. Next, 2μl Exonuclease 1 (20U/μl, Enzymatics X8010L) and 1μl Shrimp Alkaline Phosphatase (rSAP) (1U/μl, NEB M0371L) was added to each reaction followed by vortexing and incubation in a thermocycler at 37°C for 30min followed by 4°C forever. To multiplex subsequent adaptor ligation reactions, 18.4μl (0.8x) homebrew SPRI beads were added to each reaction and 8 sample/bead mixtures were pooled (up to 24 samples if all inline barcodes were used). The sample/bead mixtures were incubated at room temperature for 5min before being placed on a 96-well magnetic separator (DynaMag™-96 Side Magnet, ThermoFisher 12331D). Supernatant was removed from each well, followed by three rounds of washing with 180μl 80% ethanol. Beads were air dried at room temperature and 10μl Low EDTA TE buffer (IDT) was added to each well to fully resuspend the beads. Eluted samples were then transferred to either new PCR strips (for bulk sample) or 96-well plates (for single nuclei). The reactions were denatured in a thermocycler at 95°C for 3min and subsequently chilled on ice for 2min. 10.5μl Adaptase master mix (2μl Buffer G1, 2μl Reagent G2, 1.25μl Reagent G3, 0.5μl Enzyme G4, 0.5μl Enzyme G5, and 4.25μl Low EDTA TE buffer from xGenTM Methyl-Seq Lib Prep kit, IDT, 10009860) was added to each reaction, followed by vortexing. Reactions were incubated in a thermocycler at 37°C for 30min then 4°C forever. Finally, to amplify the pooled library and add dual indexing barcodes, 30μl PCR mix (25μl KAPA HiFi HotStart ReadyMix, Roche/KAPA Biosystems KK2602, 1μl of 30μM P5 indexing primer, and 5μl of 10μM P7 indexing primer; P5 (D501-508) and P7 (D701-712) indexing primers are listed in Supplementary Sequence 3) were added to each well, followed by mixing with vortexing. Reactions were transferred to a thermocycler programmed with the following stages: 95°C for 2min, 98°C for 30sec, 15 cycles of [98°C for 15sec, 64°C for 30sec, 72°C for 2min] (for pooled single nucleus reactions), 72°C for 5min, and 4°C forever. For bulk samples, we perform qPCR and subtract two cycles from the inflection point for each sample to determine optimal cycle number for amplification. PCR products were cleaned with two rounds of 0.8x SPRI beads, concentration was determined via QbitⓇ dsDNA High Sensitivity Assay Kit (Invitrogen Q32851), and library size was determined via Bioanalyzer (Agilent High Sensitivity DNA Kit, 5067-4626). Reactions were sequenced on Illumina NextSeq 500 (300-cycle High Output v2 Kit) or NovaSeq 6000 (300-cycle v1 kit) sequencers.

value: 6-10 weeks


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S8_TGACCA


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S8_ACTTGA


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S8_CTTGTA


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S9_TAGCTT


title: snhmCseq2.split_Cortex.NEXcre_Ex_novaseq06.25.2021_S13_TAGCTT


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S9_CAGATC


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S9_ACTTGA


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S9_TGACCA


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S7_CTTGTA


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S7_GCCAAT


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S7_CAGATC


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S7_ACTTGA


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S6_TGACCA


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S8_CGATGT


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S7_CGATGT


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S6_GCCAAT


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S9_CGATGT


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S7_ATCACG


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S6_TAGCTT


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S8_CAGATC


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S8_GCCAAT


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S6_CGATGT


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S6_CTTGTA


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S6_CAGATC


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S6_ATCACG


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S5_TGACCA


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S5_GCCAAT


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S5_CTTGTA


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S5_CGATGT


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S5_CAGATC


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S4_GCCAAT


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S3_TGACCA


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S4_CTTGTA


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S3_GCCAAT


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S6_ACTTGA


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S3_ATCACG


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S3_CTTGTA


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S3_CGATGT


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S1_TGACCA


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S2_CGATGT


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S2_CTTGTA


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S2_GCCAAT


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S2_ATCACG


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S1_CTTGTA


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S1_CGATGT


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S1_CAGATC


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S12_TAGCTT


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S12_GCCAAT


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S4_CGATGT


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S5_ATCACG


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S12_CTTGTA


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S4_ACTTGA


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S12_CGATGT


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S11_TGACCA


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S11_TAGCTT


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S11_GCCAAT


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S11_CTTGTA


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S11_CGATGT


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S12_ATCACG


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S11_CAGATC


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S1_ACTTGA


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S10_CGATGT


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S10_TAGCTT


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S10_CTTGTA


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S10_CAGATC


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S9_TGACCA


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S9_CTTGTA


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S9_GCCAAT


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S9_CAGATC


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S9_CGATGT


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S9_TAGCTT


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S9_ACTTGA


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S8_TAGCTT


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S8_CGATGT


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S12_ACTTGA


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S12_CAGATC


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S8_CAGATC


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S8_GCCAAT


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S8_ATCACG


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S8_ACTTGA


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S11_ACTTGA


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S7_CGATGT


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S7_ACTTGA


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S7_TAGCTT


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S7_CTTGTA


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S6_CGATGT


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S7_CAGATC


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S6_GCCAAT


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S6_TAGCTT


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S5_GCCAAT


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S5_CTTGTA


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S5_CGATGT


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S5_ACTTGA


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S4_CTTGTA


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S5_TAGCTT


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S6_CAGATC


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S5_CAGATC


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S3_ACTTGA


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S4_CGATGT


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S4_CAGATC


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S4_GCCAAT


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S1_CTTGTA


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S4_ATCACG


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S4_TGACCA


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S12_TAGCTT


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S3_CTTGTA


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S4_ACTTGA


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S12_CTTGTA


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S12_TGACCA


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S12_CGATGT


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S12_ATCACG


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S11_TAGCTT


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S11_CTTGTA


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S11_TGACCA


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S12_ACTTGA


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S11_GCCAAT


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S11_CGATGT


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S10_TAGCTT


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S11_ATCACG


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S10_TGACCA


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S11_CAGATC


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S10_GCCAAT


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S10_CAGATC


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S10_ACTTGA


title: snhmCseq_Brain3_Ex_novaseq10.21.2020_S10_ATCACG


title: snhmCseq_Brain2_NeuN_pos_novaseq11.21.2019_S8_CGATGT


title: snhmCseq_Brain2_NeuN_pos_novaseq11.21.2019_S7_GCCAAT


title: snhmCseq_Brain2_NeuN_pos_novaseq11.21.2019_S7_CGATGT


title: snhmCseq_Brain2_NeuN_pos_novaseq11.21.2019_S7_CTTGTA


title: snhmCseq_Brain2_NeuN_pos_novaseq11.21.2019_S6_CGATGT


title: snhmCseq_Brain2_NeuN_pos_novaseq11.21.2019_S6_GCCAAT


title: snhmCseq_Brain2_NeuN_pos_novaseq11.21.2019_S5_CTTGTA


title: snhmCseq_Brain2_NeuN_pos_novaseq11.21.2019_S6_ACTTGA


title: snhmCseq_Brain2_NeuN_pos_novaseq11.21.2019_S5_GCCAAT


title: snhmCseq_Brain2_NeuN_pos_novaseq11.21.2019_S5_CGATGT


title: snhmCseq_Brain2_NeuN_pos_novaseq11.21.2019_S4_ACTTGA


title: snhmCseq_Brain2_NeuN_pos_novaseq11.21.2019_S3_GCCAAT


title: snhmCseq_Brain2_NeuN_pos_novaseq11.21.2019_S5_ATCACG


title: snhmCseq_Brain2_NeuN_pos_novaseq11.21.2019_S5_ACTTGA


title: snhmCseq_Brain2_NeuN_pos_novaseq11.21.2019_S2_CGATGT


title: snhmCseq_Brain2_NeuN_pos_novaseq11.21.2019_S4_CGATGT


title: snhmCseq_Brain2_NeuN_pos_novaseq11.21.2019_S4_CTTGTA


title: snhmCseq_Brain2_NeuN_pos_novaseq11.21.2019_S12_ACTTGA


title: snhmCseq_Brain2_NeuN_pos_novaseq11.21.2019_S11_CGATGT


title: snhmCseq_Brain2_NeuN_pos_novaseq11.21.2019_S1_GCCAAT


title: snhmCseq_Brain2_NeuN_pos_novaseq11.21.2019_S1_CGATGT


title: snhmCseq_Brain2_NeuN_pos_novaseq11.21.2019_S11_GCCAAT


title: snhmCseq_Brain2_NeuN_pos_novaseq11.21.2019_S11_ACTTGA


title: snhmCseq_Brain2_NeuN_pos_novaseq11.21.2019_S9_GCCAAT


title: snhmCseq_Brain2_NeuN_pos_novaseq11.21.2019_S10_ACTTGA


title: snhmCseq_Brain2_NeuN_neg_novaseq11.21.2019_S9_GCCAAT


title: snhmCseq_Brain2_NeuN_neg_novaseq11.21.2019_S8_CTTGTA


title: snhmCseq_Brain2_NeuN_neg_novaseq11.21.2019_S8_GCCAAT


title: snhmCseq_Brain2_NeuN_neg_novaseq11.21.2019_S9_ATCACG


title: snhmCseq_Brain2_NeuN_neg_novaseq11.21.2019_S7_TAGCTT


title: snhmCseq_Brain2_NeuN_neg_novaseq11.21.2019_S9_CAGATC


title: snhmCseq_Brain2_NeuN_neg_novaseq11.21.2019_S8_CGATGT


title: snhmCseq_Brain2_NeuN_neg_novaseq11.21.2019_S7_CGATGT


title: snhmCseq_Brain2_NeuN_neg_novaseq11.21.2019_S7_GCCAAT


title: snhmCseq_Brain2_NeuN_neg_novaseq11.21.2019_S7_CTTGTA


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S7_TGACCA


title: snhmCseq_Brain2_NeuN_pos_novaseq11.21.2019_S3_ACTTGA


title: snhmCseq_Brain3_Inh_novaseq10.21.2020_S7_TAGCTT


title: snhmCseq_Brain2_NeuN_neg_novaseq11.21.2019_S7_CAGATC


title: snhmCseq_Brain2_NeuN_neg_novaseq11.21.2019_S6_TGACCA


title: snhmCseq_Brain2_NeuN_neg_novaseq11.21.2019_S6_CGATGT


title: snhmCseq_Brain2_NeuN_neg_novaseq11.21.2019_S6_GCCAAT


title: snhmCseq_Brain2_NeuN_neg_novaseq11.21.2019_S5_TGACCA


title: snhmCseq_Brain2_NeuN_neg_novaseq11.21.2019_S5_GCCAAT


title: snhmCseq_Brain2_NeuN_neg_novaseq11.21.2019_S6_ACTTGA


title: snhmCseq_Brain2_NeuN_neg_novaseq11.21.2019_S5_CGATGT


title: snhmCseq_Brain2_NeuN_neg_novaseq11.21.2019_S5_CAGATC


title: snhmCseq_Brain2_NeuN_neg_novaseq11.21.2019_S3_TGACCA


title: snhmCseq_Brain2_NeuN_neg_novaseq11.21.2019_S4_GCCAAT


title: snhmCseq_Brain2_NeuN_neg_novaseq11.21.2019_S4_CGATGT


title: snhmCseq_Brain2_NeuN_neg_novaseq11.21.2019_S4_CAGATC


title: snhmCseq_Brain2_NeuN_neg_novaseq11.21.2019_S9_CTTGTA


title: snhmCseq_Brain2_NeuN_neg_novaseq11.21.2019_S2_CGATGT


title: snhmCseq_Brain2_NeuN_neg_novaseq11.21.2019_S3_CGATGT


title: snhmCseq_Brain2_NeuN_neg_novaseq11.21.2019_S2_CAGATC


title: snhmCseq_Brain2_NeuN_neg_novaseq11.21.2019_S1_GCCAAT


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S9_TAGCTT


title: snhmCseq_Brain2_NeuN_neg_novaseq11.21.2019_S11_TGACCA


title: snhmCseq_Brain2_NeuN_neg_novaseq11.21.2019_S1_ACTTGA


title: snhmCseq_Brain2_NeuN_neg_novaseq11.21.2019_S1_TGACCA


title: snhmCseq_Brain2_NeuN_neg_novaseq11.21.2019_S10_GCCAAT


title: snhmCseq_Brain2_NeuN_neg_novaseq11.21.2019_S2_ACTTGA


title: snhmCseq_Brain2_NeuN_neg_novaseq11.21.2019_S11_GCCAAT


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S9_ATCACG


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S9_ACTTGA


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S8_TGACCA


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S8_CTTGTA


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S8_GCCAAT


title: snhmCseq_Brain2_NeuN_neg_novaseq11.21.2019_S4_ACTTGA


title: snhmCseq_Brain2_NeuN_neg_novaseq11.21.2019_S2_GCCAAT


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S8_ATCACG


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S8_CGATGT


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S7_GCCAAT


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S5_TGACCA


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S8_ACTTGA


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S5_GCCAAT


title: snhmCseq_Brain2_NeuN_neg_novaseq11.21.2019_S1_CGATGT


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S7_ACTTGA


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S7_CGATGT


title: snhmCseq_Brain2_NeuN_neg_novaseq11.21.2019_S10_TGACCA


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S5_CGATGT


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S4_CAGATC


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S5_ACTTGA


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S4_GCCAAT


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S3_CGATGT


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S3_ACTTGA


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S3_TGACCA


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S2_CGATGT


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S7_CAGATC


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S2_TGACCA


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S2_TAGCTT


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S2_ATCACG


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S2_CTTGTA


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S2_GCCAAT


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S1_GCCAAT


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S2_CAGATC


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S1_TGACCA


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S1_CTTGTA


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S1_CAGATC


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S12_CTTGTA


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S1_CGATGT


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S11_TGACCA


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S12_GCCAAT


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S5_ATCACG


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S12_ACTTGA


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S11_ACTTGA


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S10_TGACCA


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S10_GCCAAT


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S10_ACTTGA


title: snhmCseq_Brain1_NeuN_neg_novaseq11.21.2019_S9_ACTTGA


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S12_ATCACG


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S12_CGATGT


title: snhmCseq_Brain1_NeuN_neg_novaseq11.21.2019_S4_CTTGTA


title: snhmCseq_Brain1_NeuN_neg_novaseq11.21.2019_S8_CGATGT


title: snhmCseq_Brain1_NeuN_neg_novaseq11.21.2019_S7_CTTGTA


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S11_CAGATC


title: snhmCseq_Brain1_NeuN_neg_novaseq11.21.2019_S5_CGATGT


title: snhmCseq_Brain1_NeuN_neg_novaseq11.21.2019_S6_TGACCA


title: snhmCseq_Brain1_NeuN_pos_novaseq11.21.2019_S11_ATCACG


title: snhmCseq_Brain1_NeuN_neg_novaseq11.21.2019_S5_GCCAAT


title: snhmCseq_Brain1_NeuN_neg_novaseq11.21.2019_S8_CTTGTA


title: snhmCseq_Brain1_NeuN_neg_novaseq11.21.2019_S4_CGATGT


title: snhmCseq_Brain1_NeuN_neg_novaseq11.21.2019_S5_ACTTGA


title: snhmCseq_Brain1_NeuN_neg_novaseq11.21.2019_S3_GCCAAT


title: snhmCseq_Brain1_NeuN_neg_novaseq11.21.2019_S11_CTTGTA


title: snhmCseq_Brain1_NeuN_neg_novaseq11.21.2019_S3_CGATGT


title: snhmCseq_Brain1_NeuN_neg_novaseq11.21.2019_S1_TGACCA


title: snhmCseq_Brain1_NeuN_neg_novaseq11.21.2019_S2_CAGATC


title: snhmCseq_Brain1_NeuN_neg_novaseq11.21.2019_S3_ACTTGA


title: snhmCseq_Brain1_NeuN_neg_novaseq11.21.2019_S9_CGATGT


title: snhmCseq_Brain1_NeuN_neg_novaseq11.21.2019_S7_CAGATC


title: snhmCseq_Brain1_NeuN_neg_novaseq11.21.2019_S10_CGATGT


title: snhmCseq_Brain1_NeuN_neg_novaseq11.21.2019_S6_CTTGTA


title: Old_ABT_replicate_2

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

description: Lung cells pooled from two ABT treated old mice  - replicate_2

library_source: transcriptomic single cell

data_processing:
Pre-processing of sequencing results and generation of count matrices was performed using the Cell Ranger version 6.1.1 (10x Genomics) with prebuilt annotation platform mm10-2020-A.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

molecule: polyA RNA

source_name: lung

extract_protocol:
Samples pooled from 2 mice per group included 25 mg of lung tissue from each mouse, making a total 50 mg used for the subsequent tissue dissociation. Each pool of 50 mg of lung tissue was placed into a Miltenyi C tube filled with 2 ml of a mixture of RPMI media, 0.2 mg/ml Liberase TL, and 0.1 mg/ml Elastase. The following program was then run in the Gentlemacs Octodissociator (Miltenyi) at a constant temperature of 37C: 20 min, 50 rpm; 30 sec, 2000 rpm (clockwise); 30 sec, 2000 rpm (counterclockwise). Samples were afterwards passed through a MACS SmartStrainer (70 µm), centrifuged, and the remaining pellets were resuspended in RPMI + 20% FBS. Following collection and dissosiation of the mouse lungs, cells were first incubated for 5 min with 5 µl of TruStain FcX™ PLUS (anti-mouse CD16/32) blocking reagent followed by a 15-min incubation with 5 μl of anti-mouse Ter119-Pacific Blue and 5 μl of anti-mouse CD45-PE/Cyanine7 for 15 min at 25°C. Cells were washed with 1 ml of DMEM supplemented with 15% FBS and then resuspended in 500 μl of DMEM supplemented with 15% FBS, 2 μg/ml of propidium iodide, and 50 mM EDTA. Lastly, 25,000 cells were sorted using FACS Aria FUSION (BD Bioscience).
Single-cell libraries were constructed using the Chromium Next GEM Single Cell 3' Kit v3.1 with Chromium Next GEM Chip G Single Cell Kit in a Chromium Controller (10x Genomics) according to manufacturer’s protocol.

tag: age

value: 24 mo

value: male

value: lung

tag: cell type

value: Lung cells

value: ABT


title: Old_VPF_replicate_2

description: Lung cells pooled from two VPF treated old mice  - replicate_2

value: VPF


title: Old_DMSO_replicate_2

description: Lung cells pooled from two DMSO treated old mice  - replicate_2

value: DMSO


title: Young_DMSO_replicate_2

description: Lung cells pooled from two DMSO treated young mice  - replicate_2

value: 3 mo


title: snhmCseq_Brain1_NeuN_neg_novaseq11.21.2019_S11_CGATGT


title: Old_DMSO_replicate_1

description: Lung cells pooled from two DMSO treated old mice  - replicate_1


title: Young_DMSO_replicate_1

description: Lung cells pooled from two DMSO treated young mice  - replicate_1


title: Old_ABT_replicate_1

description: Lung cells pooled from two ABT treated old mice  - replicate_1


title: snhmCseq_Brain1_NeuN_neg_novaseq11.21.2019_S2_CGATGT


title: eWAT,Tumour Bearing-21

city: Wuhan

first: Yong

last: Hu

state: State...

address: Wuhan

country: China

institute: Wuhan university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm9
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: adipose

extract_protocol:
20 mg of adipose tissue RNA was harvested using 1mLTrizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
5 weeks (in total of 10 times) exosomes injection via tail vein injection
MDA-MB-231 cells establish orthotopic tumours

value: adipose

value: Wild Type

value: Tumour

tag: time

value: week 12


title: Mouse_C57BL/6_BMT_HOMER_1

city: Boston

first: I-Hsiu

last: Lee

state: Massachusetts

address: 185 Cambridge Street

department: Center for Systems Biology

institute: Mass General Hospital/Harvard University

data_processing:
10X Genomics Cell Ranger (version 7.0.1) was used to demultiplex raw base call files from the Illumina sequencer to produce fastq files.
Cell Ranger was used to align the reads, filter out background-associated-barcodes, count barcodes and UMIs, and generate gene-barcode matrices.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: FACS-purfied left atrial non-cardiomyocytes

extract_protocol:
Viable (DAPI-), metabolically active (Calcein+), nucleated (VDR+), single cells were FACS-purified from digested left atrial tissues, and subsequently loaded on a 10X Genomics Chromium Single Cell G chip as outlined by the 10X Genomics Chromium Single Cell 3’ Reagent Kits v3.1 (Dual Index) user guide.
Libraries were prepared as outlined by the 10X Genomics Chromium Single Cell 3’ Reagent Kits v3.1 (Dual Index) user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration (as recommended by 10X Genomics). Constructed libraries were validated and quantified with the Agilent High Sensitivity DNA chip and by real-time qPCR, and subsequently sequenced on an Illumina NovaSeq 6000 system.

tag: disease status

value: HOMER

value: left atrial tissue

value: non-cardiomyocytes

value: control


title: Mouse_Spp1-/-_BMT_HOMER_1


title: Mouse_Spp1-/-_BMT_HOMER_2


title: Old_VPF_replicate_1

description: Lung cells pooled from two VPF treated old mice  - replicate_1


title: Mouse_C57BL/6_BMT_HOMER_2


title: eWAT,Tumour Bearing-22


title: snhmCseq_Brain1_NeuN_neg_novaseq11.21.2019_S12_GCCAAT

value: Cortex

value: 6-10 weeks

value: Male

value: wild-type


title: eWAT,untreated-10

value: WT


title: eWAT,MDA-MB-231 EV-37

value: EV treatment


title: eWAT,untreated-7


title: eWAT,untreated-4


title: eWAT,Tumour Bearing-17


title: eWAT,MDA-MB-231 EV-36


title: eWAT,MDA-MB-231 EV-41


title: KO Atg16L1 sample

city: Zwijnaarde

first: VIB

last: Single Cell Core

address: Technologiepark-Zwijnaarde 71

department: VIB Single cell core

country: Belgium

institute: VIB

data_processing:
BCL files were demultiplexed using Cell Ranger mkfastq generating FastQ files
FastQ files were processed using the Cell Ranger 4.0.0 count pipeline generating count matrices
Assembly: GRCm38.99
Supplementary files format and content: h5 files containing the count matrix (output from Cell Ranger)

source_name: Skin

growth_protocol: Mice were housed in individually-ventilated cages at the VIB Center for Inflammation Research, in a specific pathogen-free animal facility. All experiments on mice were conducted according to institutional, national and European animal regulations. Animal protocols were approved by the ethics committee of Ghent University.

extract_protocol:
Single cell suspensions were obtained as previously described in Hoste, E., et al., Epithelial HMGB1 Delays Skin Wound Healing and Drives Tumor Initiation by Priming Neutrophils for NET Formation. Cell Rep, 2019. 29(9): p. 2689-2701 e4. Live cells were sorted on FACS and resuspended in PBS with 0.04% BSA at a final concentration of 1000 cells/ml.
Cellular suspensions were loaded on a GemCode Single-Cell Instrument (10x Genomics, Pleasanton) to generate single-cell Gel Bead-in-Emulsion (GEMs). Single-cell RNA-Seq libraries were prepared using GemCode Single-Cell V2 3’Gel Bead and Library kit (10x Genomics) according to the manufacturer’s instructions.

value: Skin

value: Atg16L1 KO

value: untreated


title: WT Atg16L1 sample


title: F2R103 M-WT-SPG

city: Shanghai

first: Wen

last: Xiao

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology

institute: Shanghai Institutes for Biological Sciences, CAS

description: M-WT-SPG

data_processing:
The preprocessing steps of smRNA-seq are as follows: intercept the first 50bp of reads and filter out low-quality sequences (-q 20, -p 90); After quality-filtering, sequencing reads were clipped from the 3′ adapter allowing for a minimum match of 10 nt from the 5′ end. Reads unable to match the adapter sequence or with lengths shorter than 17 bp were discarded, and the remaining reads were mapped to genome by bowtie (hamster: BCM_Maur_2.0, mouse: mm10), bowtie version 1.2.1.1, parameters -k=100 -v=0). If the reads mapped more than 100 loci to the genome, 100 of all mapped loci are randomly output. The reads were aligned sequentially to known miRNA, tRNA, rRNA, snoRNA, and snRNA sequences by Bowtie without any mismatch allowed (bowtie parameter is -k=100 -v=0 -norc), and reads that aligned to pre-miRNA were identified as miRNAs. The remaining reads of the specified length were extracted and used to identify piRNAs according to the previously described method (Jung et al. 2014) with slight modifications. The length of candidate piRNAs in male samples is 25~32nt, and the length of candidate piRNAs in female samples is 17~32nt. The clustering parameters were determined as MinReads = 5 and Eps = 2500 bp by running a series of k-dist analyses of our data with different Eps and MinReads. All of the candidate clusters that satisfied these parameters were considered piRNA clusters, and the remaining sequences located in these clusters were defined as piRNAs without any further filtering. Reads in each library were normalized by sequencing depth or reads count of miRNA or reads count of exogenous spike-in.
The preprocessing steps of RNA-seq are as follows: The raw paired-end fastq reads were removed adapter and quality-filtered by TrimGalore-0.5.0 with the parameters --paired --quality 20 --phred33 --stringency 1 --length 35. The remaining reads were mapped to the genome or identified TE by STAR v2.9, respectively. Uniquely mapped reads and multiple mapped reads with fewer than 10,000 genome copies were used for downstream analysis. The specific alignment parameters are as follows: --winAnchorMultimapNmax 10000 --outFilterMultimapNmax 10000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --twopassMode Basic --outSAMprimaryFlag AllBestScore. Calculate the reads count of known genes or TEs by featureCounts v1.6.4 with the parameters -p -B -C -M -Q 20, The expression of known genes or TEs was normalized to the ERCC or mapped reads. Genes or TEs with normalized count>2 in 40% or more of samples were used for differential analysis. Differentially expressed genes or TEs were identified by applying combined thresholds on the basis of fold change (≥2 or ≤0.5) and Welch two-sample t-test (P ≤ 0.05).
Assembly: hamster: BCM_Maur_2.0, mouse: mm10
Supplementary files format and content: testis_processed_file.xlsx and oocyte_processed_file.xlsx:tab-delimited text files include normalized values by ERCC and gene length for each Sample;
Supplementary files format and content: spermatogenesis_processed_file.xlsx:tab-delimited text files include normalized values by total reads and gene length for each Sample

source_name: testes

extract_protocol:
Samples were incubated at 72°C for 3 min to release and unfold the small RNAs or RNA.
small RNA libraries construction: Briefly, Samples were incubated at 72°C for 3 min to release and unfold the small RNAs. After 3’ adapter ligation, 5U of lambda exonuclease and 25U of 5’ deadenylases, which performed better than the combination of RecJf and 5’ deadenylases, were used to remove the excess 3’ adaptor. Then, a 5’ adapter was ligated and small RNAs were reverse transcribed. Pre-amplification was performed and then 1 μl of amplified product was used as a template for final amplification. The amplified libraries were separated on a 6% polyacrylamide gel and 130-160 bp DNA fragments were sliced to recover the library of small RNAs.  mRNA library construction:In brief, Samples were incubated at 72°C for 3 min to release the RNAs. For every single oocyte or embryo, 0.125 μL 1/100,000 dilution of the ERCC RNA Spike-In Mix (Invitrogen, Cat# 4456740) was used. Following reverse transcription and PCR pre-amplification, cDNA libraries were purified by Agencourt Ampure XP beads (0.8:1 ratio) (Beckman Coulter, Cat#A63881) and 2 ng of purified cDNA was used for a tagmentation reaction with Tn5 transposase. Amplified libraries were purified by Agencourt Ampure XP beads (1:1 ratio).

value: testes

value: male

tag: Stage

value: adult spermatogonia

value: wild type

value: FACS


title: IL-6-KO_PRA_rep3

city: Aurora

first: Mary

last: Weiser-Evans

state: CO

address: 12700 East 19th Avenue, C281

department: Renal Diseases & Hypertension

institute: University of Colorado Anschutz Medical Campus

data_processing:
Paired-end RNA-Seq reads were obtained using Illumina analysis Pipeline.
Fastq files were preprocessed with Flexbar 3.5.0 to trim 9 bases at the left side of reads and remove adapter sequences.
The fastq files were were aligned to the Mus musculus GRCm39 reference genome (Ensembl, release 104) using HISAT2 version 2.2.1 with the following options: -p 7 --dta --rna-strandness FR
Samtools 1.13 were used to sort the aligned reads and HTSeq 0.11.3 were used to produce raw counts uniquely mapping to genes for each samples.
Assembly: GRCm39 (Ensembl release 104)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Liver

extract_protocol:
RNA was isolated from hepatic tissue using QIAshredders and RNeasy Plus mini kit (Qiagen). RNA quality and quantity were analyzed using TapeStation Systems (Agilent)
PolyA selected total RNA library preparation and sequencing (Paired end 150 cycle 2x150, using NovaSEQ 6000) were conducted at The Genomics Shared Resource at the University of Colorado Cancer Center.

treatment_protocol: Mice were treated with intraperitoneal (IP) injection of two doses of 4 mg of furosemide or vehicle 3 hours apart. 6 hours after the first dose, liver tissues were harvested.

tag: strain

value: liver

value: furosemide-induced pre-renal azotemia


title: IL-6-KO_Veh_rep1

value: vehicle


title: IL-6-KO_PRA_rep1


title: IL-6-KO_Veh_rep2


title: IL-6-KO_Veh_rep3


title: IL-6-KO_Veh_rep4


title: WT_PRA_rep4


title: IL-6-KO_PRA_rep2


title: WT_PRA_rep2


title: WT_PRA_rep3


title: WT_PRA_rep1


title: WT_Veh_rep4


title: WT_Veh_rep3


title: WT_Veh_rep1


title: Normal_rep4

value: non-injected; normal control


title: Normal_rep2


title: Normal_rep3


title: Normal_rep1


title: Murine RPE, KO, right eye, 12 months, ET 858

first: Kevin

last: Zhang

address: 3400 Civic Center Blvd

description: KO 858 OD

data_processing:
Sequencing was done on an Illumina NovaSeq 6000 on an S1 flowcell. 101 bases of the cDNA insert were sequenced with 8 bp dual indexes. The first index was used to demultiplex the raw data into FASTQ files.
Real-Time Analysis v3.4.4 and HiSeq Control software 1.5.6.1074 were used
Raw data was mapped to the mouse transcriptome defined in Gencode M24 (www.gencodegenes.org) using Salmon (https://salmon.readthedocs.io/en/latest/).
Assembly: Gencode M24 which is built onGRCm38.p6
Supplementary files format and content: Excel file includes raw counts, normalized counts, and variance stabilized counts for each sample

source_name: Retinal pigment epithelium

growth_protocol: AlbCre+, Hepcf/f and AlbCre-, Hepcf/f (control) mice were generated and housed in standard conditions at 26°C with water and fed ad libitum with a diet 1738 containing approximately 300 ppm of iron. Mice were maintained in cyclic light conditions with a 12 h:12 h light-dark cycle.

extract_protocol:
RNA was isolated using the RNeasy Kit (Qiagen).
RNA libraries were constructed with the following parameters: RNA RIN values: 7-9 RIN (median 8.15); RNA concentration: 2.1-6.2 ng/uL (median 3.8 ng/uL); library molarities: 4-12 nM; library insert size: 220-240 bp; library prep kit: NEB Ultra Stranded mRNA; RNA used: 20 ng total RNA put into prep

treatment_protocol: No treatment was given as the experiment examined differences between genotype

value: Retinal pigment epithelium

value: AlbCre+, Hepcf/f

value: 12 months


title: Murine RPE, KO, right eye, 12 months, ET 856

description: KO 856 OD


title: Murine RPE, control, right eye, 12 months, ET 857

description: Ctl 857 OD

value: AlbCre-, Hepcf/f


title: Murine RPE, KO, right eye, 12 months, ET 810

description: KO 810 OD


title: Murine RPE, control, left eye, 12 months, ET 855

description: Ctl 855 OS


title: Murine RPE, control, right eye, 12 months, ET 855

description: Ctl 855 OD


title: Young, 7 days post-injury (rep2)

city: Boulder

first: Jesse

middle: Vigoda

last: Kurland

state: Colorado

address: 1925 Colorado Avenue

department: MCDB

institute: University of Colorado Boulder

data_processing:
FastQC (v0.11.8) was used for initial quality control of Fastq files
transcript reads were mapped with the CellRanger Software Suite (10x Genomics, v3.0.1) using a  mm10 reference package
Assembly: mm10 pre-mRNA (Millay, 2020)
Supplementary files format and content: paired-end fastq files from the Illumina NovaSeq 6000
Supplementary files format and content: raw_bc_matrix files from cellranger aggregate

source_name: tibialis anterior muscle

growth_protocol: Mice were bred and housed according to National Institutes of Health (NIH) guidelines for the ethical treatment of animals in a pathogen-free facility at the University of Colorado at Boulder. University of Colorado Institutional Animal Care and Use Committee (IACUC) approved animal protocols and procedures.

extract_protocol:
TA muscles were dissected and placed into 400U/mL collagenase at 37°C for 1h with shaking and then placed into Ham’s F-12C supplemented with 15% horse serum to inactivate the collagenase. Cells were passed through three strainers of 100µm, 70µm, and 40µm (BD Falcon) and flow through was centrifuged at 1500×g for 5 min and the cell pellets were re-suspended in Ham’s F-12C. To remove dead cells and debris, cells were passed over the Miltenyi, dead cell removal kit columns (Cat# 130-090-101). To remove red blood cells (RBC), cells were incubated with antiTer119 micro magnetic beads and passed over a Miltenyi column (Cat#130-049-901). For the adult and aged uninjured TAs, 6 TA muscles (from 3 mice) were pooled together. For the injured TA muscles 2 TA muscles from 2 different mice were pooled together. Cells were then counted using a BioRad TC20 automated cell counter and processed with the 10X genomics single cell sequencing kit.
To capture, label, and generate transcriptome libraries of individual cells we used the 10X genomics Chromium Single Cell 3’ Library and Gel Bead Kit v2 (Cat #PN-120237) following the manufactures protocols.
single-cell RNA-seq, paired end, Illumina Nextseq500

treatment_protocol: Mice were anesthetized with isoflurane followed by injection with 50μl of 1.2% BaCl2 in normal saline into the TA and EDL muscles.

value: tibialis anterior muscle

tag: cell line

value: 4-8 months old

value: Wild type

value: 7 days post-injury


title: Aged, 4 days post-injury (rep3)

value: 24-28 months old

value: 4 days post-injury


title: Aged, 4 days post-injury (rep2)

value: male


title: Young, 4 days post-injury (rep2)


title: WT_Veh_rep2

value: WT


title: Aged, 7 days post-injury (rep2)


title: 7F_M_2921

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: GP


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