title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590786]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590784]

status: Public on Aug 08 2025

type: SRA

city: Heidelberg

first: Leo

middle: Carl

last: Förster

state: Deutschland

address: Im Neuenheimer Feld 581

country: Germany

institute: DKFZ

library_source: transcriptomic single cell

data_processing:
Read1 sequences were processed to extract and trim UMIs, storing them in the FASTQ identifier field. Processed paired-end reads were trimmed using trim-galore v0.5.0 and mapped to the mm10 genome reference with Ensembl96 gene annotations using STAR v2.5.3a setting "--bamRemoveDuplicatesType UniqueIdentical --outFilterMismatchNmax 9999 --outFilterScoreMinOverLread 0.2 --outFilterMatchNminOverLread 0.2 --alignSJoverhangMin 3 --alignSplicedMateMapLminOverLmate 0.2 --twopassMode Basic". UMI-containing readpairs were quantified with a custom script based on HTSeq to identify exonic and intronic UMIs and deduplicate them, reporting a merged UMI-counts matrix.  Cell transcriptomes were subset to 1:1 human-mouse orthologs reported in Ensembl102 to be consistent with our downstream human analyses. We excluded cells with fewer than 2000 UMIs or under 500 detected genes.
Assembly: mm10
Supplementary files format and content: counts: comma separated matrix of deduplicated UMI counts per cell (columns) per gene (rows). Metadata: comma separated matrix relating metdata (columns) per cell (rows)

molecule: polyA RNA

organism: Mus musculus

source_name: Brain, SVZ

extract_protocol:
RNA molecules were captured using an oligo dT(30) primer. mRNA was reverse-transcribed using a template switching oligonucleotide contianing an 8 bp unique molecular identifier to obtain cDNA which was subsequently amplified and purified using AMPureXP beads.
Purified cDNA was then used for Illumina Nextera XP library preparation according to Hagemann-Jensen et al. 2020 with modifications reported in Cerrizuela and Kaya et al. 2022.

tag: tissue

value: Brain, SVZ

tag: genotype


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590780]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590790]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590826]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590776]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590782]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590778]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590774]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590770]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590772]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590762]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590766]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590760]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590756]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590754]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590768]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590758]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590752]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590750]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590748]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590764]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590742]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590740]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590746]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590744]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590734]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590738]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590732]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590730]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590720]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590724]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590722]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590716]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590726]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590718]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590714]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590706]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590712]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590710]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590704]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590702]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590698]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590700]


title: SVZ NSC lineage cell, OB rep2 [OB2_591447]

source_name: Brain, olfactory bulb

value: Brain, olfactory bulb


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590736]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590696]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590690]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590692]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590688]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590682]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590680]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590686]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590728]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590674]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590672]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590676]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590678]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590666]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590670]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590662]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590668]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590664]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590658]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590656]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590654]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590650]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590648]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590646]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590644]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590694]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590642]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590640]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590634]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590636]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590632]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590638]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590618]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590628]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590626]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590616]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590806]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590630]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590620]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590624]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590614]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590608]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590606]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590652]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590610]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590602]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590600]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590598]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590660]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590604]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590594]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590590]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590588]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590586]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590596]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590622]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590584]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590582]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590574]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590576]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590578]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590568]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590572]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590560]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590562]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590556]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590558]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590570]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590554]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590550]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590580]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590564]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590592]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590566]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589961]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589957]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589949]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589959]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589951]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589953]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589947]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589945]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589943]


title: SVZ NSC lineage cell, SVZ rep2 [SVZ2_590552]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589941]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589939]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589937]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589935]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589933]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589963]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589965]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589929]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589927]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589923]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589925]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589955]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589917]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589913]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589919]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589911]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589921]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589915]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589901]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589909]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589907]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589899]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589897]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589893]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589905]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589889]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589887]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589885]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589883]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589891]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589873]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589877]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589875]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589869]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589871]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589867]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589861]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589903]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589859]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589855]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589863]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589853]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589865]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589895]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589857]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589849]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589847]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589845]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589841]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589843]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589881]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589835]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589837]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589833]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589839]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589829]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589879]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589827]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589821]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589825]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589815]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589817]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589823]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589813]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589819]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589801]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589851]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589797]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589795]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589811]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589809]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589791]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589831]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589785]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589805]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589783]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589789]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589777]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589779]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589781]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589771]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589773]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589767]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589787]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589769]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589765]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589761]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589763]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589751]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589807]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589799]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589757]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589755]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589739]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589745]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589759]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589747]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589793]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589737]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589735]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589731]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589733]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589727]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589729]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589721]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589719]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589725]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589713]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589715]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589741]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589711]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589707]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589749]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589709]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589743]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589705]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589703]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589701]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589699]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589689]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589687]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589691]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589685]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589683]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589723]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589681]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589677]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589675]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589679]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589671]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589673]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589669]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589661]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589663]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589717]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589665]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589695]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589657]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589653]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589651]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589693]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589649]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589647]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589659]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589643]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589641]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589645]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589667]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589639]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589633]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589623]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589631]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589629]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589627]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589621]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589625]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589619]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589611]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589615]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589617]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589607]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589655]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589603]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589609]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589597]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589605]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589601]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589599]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589595]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589593]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589591]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589635]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589637]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589589]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589587]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589583]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589579]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589581]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589577]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589575]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589573]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589571]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589569]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589567]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589613]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589565]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589555]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589559]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589557]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589561]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589551]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589539]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589543]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589537]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589549]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589533]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589535]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589541]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589529]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589527]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589547]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589531]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589523]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589521]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589525]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589553]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589519]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589517]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589511]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589507]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589509]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589515]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589513]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589505]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589503]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589493]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589497]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589495]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589491]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589487]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589489]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589481]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589485]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589469]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589483]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589563]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589479]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589477]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589465]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589473]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589467]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589459]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589461]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589501]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589457]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589475]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589455]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589447]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589453]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589441]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589445]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589443]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589451]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589449]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589435]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589439]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589433]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589429]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589425]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589423]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589463]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589421]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589417]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589419]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589427]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589431]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589415]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589411]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589413]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589409]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589407]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589437]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589405]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589401]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589399]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589395]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589397]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589391]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589387]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589393]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589385]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589375]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589371]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589383]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589373]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589367]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589369]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589377]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589363]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589359]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589357]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589361]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589365]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589403]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589355]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589349]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589347]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589353]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589389]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589351]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589379]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589345]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589331]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589343]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589545]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589319]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589337]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589335]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589303]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589311]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589307]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589341]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589333]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589301]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589329]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589327]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589325]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589295]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589321]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589283]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589287]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589315]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589281]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589317]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589279]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589309]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589305]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589297]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589323]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589299]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589293]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589339]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589291]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589289]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589259]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589313]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589271]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589285]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589265]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589253]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589255]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589277]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589245]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589275]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589273]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589269]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589249]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589241]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589237]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589261]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589251]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589263]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589257]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589243]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589239]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589219]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589225]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589227]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589247]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589233]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589229]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589231]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589209]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589213]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589215]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589217]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589235]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589223]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589205]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589203]


title: SVZ NSC lineage cell, OB rep1 [OB1_588925]


title: SVZ NSC lineage cell, OB rep1 [OB1_588923]


title: SVZ NSC lineage cell, OB rep1 [OB1_588917]


title: SVZ NSC lineage cell, OB rep1 [OB1_588915]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589207]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589199]


title: SVZ NSC lineage cell, OB rep1 [OB1_588911]


title: SVZ NSC lineage cell, OB rep1 [OB1_588927]


title: SVZ NSC lineage cell, OB rep1 [OB1_588929]


title: SVZ NSC lineage cell, OB rep1 [OB1_588919]


title: SVZ NSC lineage cell, OB rep1 [OB1_588905]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589201]


title: SVZ NSC lineage cell, SVZ rep1 [SVZ1_589211]


title: SVZ NSC lineage cell, OB rep1 [OB1_588903]


title: SVZ NSC lineage cell, OB rep1 [OB1_588907]


title: SVZ NSC lineage cell, OB rep1 [OB1_588899]


title: SVZ NSC lineage cell, OB rep1 [OB1_588897]


title: SVZ NSC lineage cell, OB rep1 [OB1_588921]


title: SVZ NSC lineage cell, OB rep1 [OB1_588891]


title: SVZ NSC lineage cell, OB rep1 [OB1_588893]


title: SVZ NSC lineage cell, OB rep1 [OB1_588901]


title: SVZ NSC lineage cell, OB rep1 [OB1_588887]


title: SVZ NSC lineage cell, OB rep1 [OB1_588895]


title: SVZ NSC lineage cell, OB rep1 [OB1_588879]


title: SVZ NSC lineage cell, OB rep1 [OB1_588881]


title: SVZ NSC lineage cell, OB rep1 [OB1_588885]


title: SVZ NSC lineage cell, OB rep1 [OB1_588875]


title: SVZ NSC lineage cell, OB rep1 [OB1_588873]


title: SVZ NSC lineage cell, OB rep1 [OB1_588913]


title: SVZ NSC lineage cell, OB rep1 [OB1_588909]


title: SVZ NSC lineage cell, OB rep1 [OB1_588869]


title: SVZ NSC lineage cell, OB rep1 [OB1_588863]


title: SVZ NSC lineage cell, OB rep1 [OB1_588865]


title: SVZ NSC lineage cell, OB rep1 [OB1_588867]


title: SVZ NSC lineage cell, OB rep1 [OB1_588857]


title: SVZ NSC lineage cell, OB rep1 [OB1_588859]


title: SVZ NSC lineage cell, OB rep1 [OB1_588855]


title: SVZ NSC lineage cell, OB rep1 [OB1_588861]


title: SVZ NSC lineage cell, OB rep1 [OB1_588849]


title: SVZ NSC lineage cell, OB rep1 [OB1_588847]


title: SVZ NSC lineage cell, OB rep1 [OB1_588839]


title: SVZ NSC lineage cell, OB rep1 [OB1_588843]


title: SVZ NSC lineage cell, OB rep1 [OB1_588851]


title: SVZ NSC lineage cell, OB rep1 [OB1_588877]


title: SVZ NSC lineage cell, OB rep1 [OB1_588883]


title: SVZ NSC lineage cell, OB rep1 [OB1_588853]


title: SVZ NSC lineage cell, OB rep1 [OB1_588833]


title: SVZ NSC lineage cell, OB rep1 [OB1_588837]


title: SVZ NSC lineage cell, OB rep1 [OB1_588831]


title: SVZ NSC lineage cell, OB rep1 [OB1_588871]


title: SVZ NSC lineage cell, OB rep1 [OB1_588825]


title: SVZ NSC lineage cell, OB rep1 [OB1_588823]


title: SVZ NSC lineage cell, OB rep1 [OB1_588821]


title: SVZ NSC lineage cell, OB rep1 [OB1_588829]


title: SVZ NSC lineage cell, OB rep1 [OB1_588817]


title: SVZ NSC lineage cell, OB rep1 [OB1_588819]


title: SVZ NSC lineage cell, OB rep1 [OB1_588815]


title: SVZ NSC lineage cell, OB rep1 [OB1_588811]


title: SVZ NSC lineage cell, OB rep1 [OB1_588809]


title: SVZ NSC lineage cell, OB rep1 [OB1_588889]


title: SVZ NSC lineage cell, OB rep1 [OB1_588803]


title: SVZ NSC lineage cell, OB rep1 [OB1_588813]


title: SVZ NSC lineage cell, OB rep1 [OB1_588805]


title: SVZ NSC lineage cell, OB rep1 [OB1_588807]


title: SVZ NSC lineage cell, OB rep1 [OB1_588841]


title: SVZ NSC lineage cell, OB rep1 [OB1_588789]


title: SVZ NSC lineage cell, OB rep1 [OB1_588795]


title: SVZ NSC lineage cell, OB rep1 [OB1_588793]


title: SVZ NSC lineage cell, OB rep1 [OB1_588801]


title: SVZ NSC lineage cell, OB rep1 [OB1_588787]


title: SVZ NSC lineage cell, OB rep1 [OB1_588827]


title: SVZ NSC lineage cell, OB rep1 [OB1_588785]


title: SVZ NSC lineage cell, OB rep1 [OB1_588781]


title: SVZ NSC lineage cell, OB rep1 [OB1_588835]


title: SVZ NSC lineage cell, OB rep1 [OB1_588797]


title: SVZ NSC lineage cell, OB rep1 [OB1_588791]


title: SVZ NSC lineage cell, OB rep1 [OB1_588777]


title: SVZ NSC lineage cell, OB rep1 [OB1_588773]


title: SVZ NSC lineage cell, OB rep1 [OB1_588775]


title: SVZ NSC lineage cell, OB rep1 [OB1_588771]


title: SVZ NSC lineage cell, OB rep1 [OB1_588769]


title: SVZ NSC lineage cell, OB rep1 [OB1_588845]


title: SVZ NSC lineage cell, OB rep1 [OB1_588759]


title: SVZ NSC lineage cell, OB rep1 [OB1_588757]


title: SVZ NSC lineage cell, OB rep1 [OB1_588755]


title: SVZ NSC lineage cell, OB rep1 [OB1_588753]


title: SVZ NSC lineage cell, OB rep1 [OB1_588765]


title: SVZ NSC lineage cell, OB rep1 [OB1_588751]


title: SVZ NSC lineage cell, OB rep1 [OB1_588749]


title: SVZ NSC lineage cell, OB rep1 [OB1_588747]


title: SVZ NSC lineage cell, OB rep1 [OB1_588745]


title: SVZ NSC lineage cell, OB rep1 [OB1_588783]


title: SVZ NSC lineage cell, OB rep1 [OB1_588735]


title: SVZ NSC lineage cell, OB rep1 [OB1_588741]


title: SVZ NSC lineage cell, OB rep1 [OB1_588733]


title: SVZ NSC lineage cell, OB rep1 [OB1_588743]


title: SVZ NSC lineage cell, OB rep1 [OB1_588737]


title: SVZ NSC lineage cell, OB rep1 [OB1_588779]


title: SVZ NSC lineage cell, OB rep1 [OB1_588727]


title: SVZ NSC lineage cell, OB rep1 [OB1_588729]


title: SVZ NSC lineage cell, OB rep1 [OB1_588725]


title: SVZ NSC lineage cell, OB rep1 [OB1_588731]


title: SVZ NSC lineage cell, OB rep1 [OB1_588715]


title: SVZ NSC lineage cell, OB rep1 [OB1_588719]


title: SVZ NSC lineage cell, OB rep1 [OB1_588713]


title: SVZ NSC lineage cell, OB rep1 [OB1_588763]


title: SVZ NSC lineage cell, OB rep1 [OB1_588721]


title: SVZ NSC lineage cell, OB rep1 [OB1_588767]


title: SVZ NSC lineage cell, OB rep1 [OB1_588709]


title: SVZ NSC lineage cell, OB rep1 [OB1_588707]


title: SVZ NSC lineage cell, OB rep1 [OB1_588699]


title: SVZ NSC lineage cell, OB rep1 [OB1_588703]


title: SVZ NSC lineage cell, OB rep1 [OB1_588705]


title: SVZ NSC lineage cell, OB rep1 [OB1_588697]


title: SVZ NSC lineage cell, OB rep1 [OB1_588693]


title: SVZ NSC lineage cell, OB rep1 [OB1_588691]


title: SVZ NSC lineage cell, OB rep1 [OB1_588739]


title: SVZ NSC lineage cell, OB rep1 [OB1_588689]


title: SVZ NSC lineage cell, OB rep1 [OB1_588717]


title: SVZ NSC lineage cell, OB rep1 [OB1_588685]


title: SVZ NSC lineage cell, OB rep1 [OB1_588683]


title: SVZ NSC lineage cell, OB rep1 [OB1_588677]


title: SVZ NSC lineage cell, OB rep1 [OB1_588681]


title: SVZ NSC lineage cell, OB rep1 [OB1_588711]


title: SVZ NSC lineage cell, OB rep1 [OB1_588673]


title: Legionella pneumophila strain Ofk308, target, rep_3

city: Yamaguchi City

first: Istiana

middle: Nur

last: Vidayanti

state: Yamaguchi Prefecture

address: 1677-1 Yoshida

country: Japan

institute: Yamaguchi University

description:
Library name: Ofk_rep_3 (GE)
Normalized read_All samples (GE).csv

library_source: transcriptomic

data_processing:
Libraries were sequenced on an Illumina NovaSeq 6000.
The raw reads were mapped onto the Genomic Contig Format (GCF)_001753085.1 L. pneumophila sequence.
Comparative expression analysis was performed using the RNA-Seq analysis tool of CLC Genomics Workbench.
Assembly: GCF_001753085.1
Supplementary files format and content: csv file include RPKM value for each sample
Supplementary files format and content: csv file include normalized gene expression value, fold change, and p value

molecule: total RNA

organism: Legionella pneumophila

source_name: bacteria

extract_protocol:
total RNA was prepared using the Maxwell RSC Simply RNA Tissue Kit (Promega). Following rRNA removal with the NEBNext rRNA Depletion Kit (New England BioLabs)
the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England BioLabs) was used with 20 ng of total RNA for library construction.

treatment_protocol: Phil-1 and Ofk308 strains were cultured at 37°C to the exponential phase in AYE, then diluted and cultured again at 30°C for 24 h

tag: cell type

value: bacteria

value: strain Ofk308

tag: treatment

value: Culture at 37 and trasfer into 30 ℃

tag: batch

value: 48 hours


title: SVZ NSC lineage cell, OB rep1 [OB1_588675]


title: SVZ NSC lineage cell, OB rep1 [OB1_588669]


title: Legionella pneumophila strain Ofk308, target, rep_2

description:
Library name: Ofk_rep_2 (GE)
Normalized read_All samples (GE).csv


title: SVZ NSC lineage cell, OB rep1 [OB1_588671]


title: Legionella pneumophila strain Ofk308, target, rep_1

description:
Library name: Ofk_rep_1 (GE)
Normalized read_All samples (GE).csv


title: SVZ NSC lineage cell, OB rep1 [OB1_588667]


title: Mnase-seq, pc293T, Replicate 3

city: Jupiter

first: Cameron

middle: James

last: Douglas

state: FL

address: 120 Scripps Way

department: Chemistry

country: USA

description: Library name: pc293T 3

library_source: genomic

data_processing:
Raw FASTQ reads were analyzed with the nf-core/cutandrun pipeline (v3.2.2) using Nextflow (v25.04.4) under a Singularity profile. Adapter trimming and base-quality filtering were performed with Trim Galore (v0.6.6) wrapping Cutadapt (v2.10), with read quality assessed pre- and post-trimming using FastQC (v0.12.1). Trimmed reads were aligned to the human reference genome (GRCh38, Ensembl release 111) using Bowtie2 (v2.4.4), with duplicate marking via Picard MarkDuplicates (v3.1.0). Spike-in normalization was applied using Drosophila melanogaster (BDGP6.54, Ensembl release 114) alignments for scaling. Mitochondrial reads (chromosome prefix "MT") were removed post-alignment using SAMtools (v1.17). Peak calling was conducted with MACS2 (v2.2.7.1) at a q-value threshold of 0.01, incorporating IgG controls scaled by a factor of 0.5 and blacklist filtering using the hg38 blacklist (hg38-blacklist.v2.bed.gz, sourced from https://github.com/Boyle-Lab/Blacklist). Consensus peaks were generated via BEDTools (v2.31.0) merging. Quality control metrics included fragment length distributions, library complexity estimation with Preseq (v3.1.1), and multi-sample correlations/heatmaps via deepTools (v3.5.1). All intermediate alignment files were retained, and full pipeline parameters are detailed in the configuration file (params.yaml, available upon request)
Assembly: GRCh38.p14
Supplementary files format and content: Normalized coverage tracks in bigWig format representing mononucleosome signal intensity across the genome.Nucleosome position calls generated by DANPOS2 (v 2.2.2) dpos algorithm reported in aligned.smooth.positions.xls files
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Cells were cultured in DMEM supplemented with 10% FBS, 1% Pencicilin and Streptomycin. pc293T cells were grown with the addition of  400ug//mL Zeocin, and 100ug/mL Hygromycin.

extract_protocol: Libraries were prepped by The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology Genomics Core.

treatment_protocol: Mononucleosome associated DNA was isolated by MNase digestion following the manufacturer’s protocol for the EZ Nucleosomal DNA Prep Kit (Zymo Research # D5220). Digested DNA was separated by electrophoresis on a 2% agarose gel. Mononucleosome DNA bands were excised and purified using Monarch DNA Gel Extraction Kit (New England Biolabs # T1020). Purified DNA was submitted to the The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology Genomics Core for library prep and sequencing. Sequencing was conducted on a NextSeq 2000 at >40m reads per sample. Three bioreplicates were run using 1x106 cells per replicate of either WT HEK293T or pc293T cells.

tag: cell line

value: Kidney


title: GSHFe2_17863902_532

type: RNA

city: Santiago

first: Victor

last: Aliaga

address: Camino La Pirámide 5750

country: Chile

institute: Universidad Mayor

description: This sample correspond to  Enterococcus faecalis OG1RF copΔ  iron treatment (0.5 mM FeCl3-NTA), second of two technical microarray hybridization replicates.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com. Special support performe by ROCHE-Chile, Santiago, Chile. See www.roche.cl

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: All data was processes automatically using DNASTAR software Array star 5.0. See www.dnastar.com.

organism: Enterococcus faecalis OG1RF

source_name: Enterococcus faecalis  OG1RF ghsΔ 0.5 mM FeCl3-NTA

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com. Special support performe by ROCHE-Chile, Santiago, Chile. See www.roche.cl

growth_protocol: Enterococcus faecalis OG1RF wild-type and gshΔ were grown to mid-log phase (O.D600nm 1.0), aerobically estandar condition at 37°C in N medium (Peptone 1 % (Difco), yeast extract 0.5 % (Difco), Na2HPO4 1 % (Merck) and glucose 1 % (Oxoid), Odermatt A, Solioz M. J Biol Chem 1995, 270(9).  In treatment cultures, gshΔ strain was gowth at the same condition by adding copper (0.5 mM of FeCl3-NTA) to the control medium.

extract_protocol: The total RNA was extracted using a Qiagen RNeasy mini kit (Qiagen). Residual contaminating genomic DNA was removed with RQ1 RNase-free DNase (Promega) treatment according to the manufacturer’s protocol. The integrity of the RNA was assessed by gel electrophoresis.

treatment_protocol: Iron treated cells were exposed for 3 hours prior to harvesting (at mid-log phase, OD600nm 1.0); the untreated cells were collected simultaneously.

value: mutant strain (gshΔEF3089)

tag: phenotype

value: GSH sensitive


title: GSH2_14287802_532

description: This sample correspond to  Enterococcus faecalis OG1RF gshΔ  second of two technical microarray hybridization replicates.

source_name: Enterococcus faecalis  OG1RF gshΔ


title: GSHFe1_17863802_532

description: This sample correspond to  Enterococcus faecalis OG1RF copΔ  iron treatment (0.5 mM FeCl3-NTA), first of two technical microarray hybridization replicates.


title: GSH1_14287202_532

description: This sample correspond to  Enterococcus faecalis OG1RF gshcopΔ  first of two technical microarray hybridization replicates.


title: SVZ NSC lineage cell, OB rep1 [OB1_588663]


title: WT1_14282302_532

description: This sample correspond to wild-type Enterococcus faecalis OG1RF strain, first of two technical microarray hybridization replicates.

source_name: Enterococcus faecalis  OG1RF wild-type

value: Wild-type

value: normal


title: WT2_14282402_532

description: This sample correspond to wild-type Enterococcus faecalis OG1RF strain, second of two technical microarray hybridization replicates.


title: Mnase-seq, pc293T, Replicate 1

institute: The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology

description: Library name: pc293T 1


title: Mnase-seq, WT HEK293T, Replicate 3

description: Library name: WT HEK293T 3


title: Mnase-seq, pc293T, Replicate 2

description: Library name: pc293T 2


title: SVZ NSC lineage cell, OB rep1 [OB1_588661]


title: SVZ NSC lineage cell, OB rep1 [OB1_588659]


title: SVZ NSC lineage cell, OB rep1 [OB1_588657]


title: Mnase-seq, WT HEK293T, Replicate 2

description: Library name: WT HEK293T 2


title: SVZ NSC lineage cell, OB rep1 [OB1_588655]


title: pc293T, IgG Control, Replicate 3

description: Library name: IgG 3

data_processing:
Raw FASTQ reads were analyzed with the nf-core/cutandrun pipeline (v3.2.2) using Nextflow (v25.04.4) under a Singularity profile. Adapter trimming and base-quality filtering were performed with Trim Galore (v0.6.6) wrapping Cutadapt (v2.10), with read quality assessed pre- and post-trimming using FastQC (v0.12.1). Trimmed reads were aligned to the human reference genome (GRCh38, Ensembl release 111) using Bowtie2 (v2.4.4), with duplicate marking via Picard MarkDuplicates (v3.1.0). Spike-in normalization was applied using Drosophila melanogaster (BDGP6.54, Ensembl release 114) alignments for scaling. Mitochondrial reads (chromosome prefix "MT") were removed post-alignment using SAMtools (v1.17). Peak calling was conducted with MACS2 (v2.2.7.1) at a q-value threshold of 0.01, incorporating IgG controls scaled by a factor of 0.5 and blacklist filtering using the hg38 blacklist (hg38-blacklist.v2.bed.gz, sourced from https://github.com/Boyle-Lab/Blacklist). Consensus peaks were generated via BEDTools (v2.31.0) merging. Quality control metrics included fragment length distributions, library complexity estimation with Preseq (v3.1.1), and multi-sample correlations/heatmaps via deepTools (v3.5.1). All intermediate alignment files were retained, and full pipeline parameters are detailed in the configuration file (params.yaml, available upon request)
Assembly: GRCh38.p14
Supplementary files format and content: Normalized coverage tracks in bigWig format representing CUT&Tag signal intensity across the genome. Genomic regions of significant enrichment (peaks) identified by MACS2 peak caller from CUT&RUN data, reported in BED format with genomic coordinates.
Library strategy: CUT&Tag

growth_protocol: Cells were cultured in DMEM supplemented with 10% FBS, 1% Pencicilin and Streptomycin, 400ug//mL Zeocin, and 100ug/mL Hygromycin.

extract_protocol:
CUT&Tag was performed using the CUT&Tag-IT® Assay Kit (Active Motif # 53160). The manufacturer protocol was followed with the application of the following antibodies:  DYKDDDDK Tag (EpiCypher #13-2031), H3.3 (EpiCypher # 13-0061), and Rabbit IgG (Cell Signaling #2729S). Each target was run in triplicate with 2x105 pcHEK293T cells per sample. 20ul of CUT&Tag-IT Spike-In Control, Anti Rabbit nuclei were added as normalization control (Active Motif #53168)
Libraries were prepped as described in manufacturer protocol for CUT&Tag-IT® Assay Kit (Active Motif # 53160).


title: pc293T, IgG Control, Replicate 2

description: Library name: IgG 2


title: SVZ NSC lineage cell, OB rep1 [OB1_588701]


title: SVZ NSC lineage cell, OB rep1 [OB1_588649]


title: SVZ NSC lineage cell, OB rep1 [OB1_588651]


title: SVZ NSC lineage cell, OB rep1 [OB1_588653]


title: pc293T, IgG Control, Replicate 1

description: Library name: IgG 1


title: SVZ NSC lineage cell, OB rep1 [OB1_588643]


title: Mnase-seq, WT HEK293T, Replicate 1

description: Library name: WT HEK293T 1


title: pc293T, Histone H3.3, Replicate 2

description: Library name: H3.3 2


title: SVZ NSC lineage cell, OB rep1 [OB1_588641]


title: pc293T, Histone H3.3, Replicate 1

description: Library name: H3.3 1


title: SVZ NSC lineage cell, OB rep1 [OB1_588635]


title: SVZ NSC lineage cell, OB rep1 [OB1_588639]


title: pc293T, FLAG, Replicate 2

description: Library name: FLAG 2


title: pc293T, FLAG, Replicate 3

description: Library name: FLAG 3


title: SVZ NSC lineage cell, OB rep1 [OB1_588637]


title: pc293T, FLAG, Replicate 1

description: Library name: FLAG 1


title: SVZ NSC lineage cell, OB rep1 [OB1_588631]


title: SVZ NSC lineage cell, OB rep1 [OB1_588629]


title: pc293T, Histone H3.3, Replicate 3

description: Library name: H3.3 3


title: pc293T, FLAG, Replicate 1

description: Library name: FLAG 1

data_processing:
CUT&RUN samples were processed using the nf-core/cutandrun pipeline (v3.2.2, https://nf-co.re/cutandrun/3.2.2/ ) with Singularity containerization. Sequencing reads were aligned to the human reference genome GRCh38.p14. The pipeline was modified to exclude quality trimming and duplicate removal steps, remove mitochondrial reads, and perform peak calling using MACS2. Coverage tracks were normalized using counts per million (CPM). Data visualization was performed using the Integrative Genomics Viewer (IGV), and heatmaps were generated with deepTools.
Assembly: GRCh38.p14
Supplementary files format and content: Normalized coverage tracks in bigWig format representing CUT&Tag signal intensity across the genome. Genomic regions of significant enrichment (peaks) identified by MACS2 peak caller from CUT&RUN data, reported in BED format with genomic coordinates.
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag was performed using the CUT&Tag-IT® Assay Kit (Active Motif # 53160). The manufacturer protocol was followed with the application of the following antibodies: Histone H3K27me3 (Active Motif #39157), H3K27ac (Active Motif #39134), DYKDDDDK Tag (EpiCypher #13-2031), and Rabbit IgG (Cell Signaling #2729S). Each target was run in triplicate with 2x105 pcHEK293T cells per sample.
Libraries were prepped as described in manufacturer protocol for CUT&Tag-IT® Assay Kit (Active Motif # 53160).


title: pc293T, FLAG, Replicate 3

description: Library name: FLAG 3


title: pc293T, H3K27me3, Replicate 3

description: Library name: H3k27me3 3


title: SVZ NSC lineage cell, OB rep1 [OB1_588625]


title: SVZ NSC lineage cell, OB rep1 [OB1_588633]


title: pc293T, H3K27me3, Replicate 2

description: Library name: H3k27me3 2


title: pc293T, FLAG, Replicate 2

description: Library name: FLAG 2


title: SVZ NSC lineage cell, OB rep1 [OB1_588623]


title: pc293T, H3K27me3, Replicate 1

description: Library name: H3k27me3 1


title: SVZ NSC lineage cell, OB rep1 [OB1_588621]


title: pc293T, H3K27ac, Replicate 3

description: Library name: H3K27ac 3


title: pc293T, H3K27ac, Replicate 1

description: Library name: H3K27ac 1


title: SVZ NSC lineage cell, OB rep1 [OB1_588615]


title: pc293T, H3K27ac, Replicate 2

description: Library name: H3K27ac 2


title: pc293T, IgG Control, Replicate 2

description: Library name: IgG 2


title: LV tissue, C57BL/6J mouse, HFpEF diet, Biological Replicate 2

city: Stanford

first: Mark

middle: Emile

last: Pepin

state: CA

address: 870 Quarry road

department: Cardiovascular Medicine

institute: Stanford University

description:
Library name: Sample 11
10x Genomics
J_Cardiomyocyte_HFpEF.vs.Ctrl_DEGs.xlsx
J_EC_HFpEF.vs.Ctrl_DEGs.xlsx
J_Fibroblast_HFpEF.vs.Ctrl_DEGs.xlsx
J_Lymphoid_HFpEF.vs.Ctrl_DEGs.xlsx
J_Mast_Cell_HFpEF.vs.Ctrl_DEGs.xlsx
J_Mural_Cell_HFpEF.vs.Ctrl_DEGs.xlsx
J_Myeloid_HFpEF.vs.Ctrl_DEGs.xlsx
J_Neural_Cell_HFpEF.vs.Ctrl_DEGs.xlsx
SampleID: 20

data_processing:
Reads were aligned to the mm10 mouse genome using Cell Ranger v6.1.0.
A detailed description of our bioinformatic workflow is provided as a GitHub repository (https://github.com/mepepin/HFpEF_snRNASeq) and interactive Web interface (https://markpepin.shinyapps.io/HFpEF_Transcriptomics/), with quality metrics summarized as Table S1. Raw Cellranger output data were filtered to remove ambient RNA using Cellbender in full running mode. The output files, which constitute feature-barcode matrices and cluster assignments, were then imported into the R (4.4.1) environment using the Seurat package (5.0.1) for downstream preprocessing, annotation, and differential expression. To improve data quality, we excluded cells containing <200 detected genes; those containing >10% mitochondrial gene content were also excluded from downstream analysis. DoubletFinder (v2.0.4) was subsequently used to detect and remove doublets from our integrated dataset.
Normalization and scaling were performed using the LogNormalize method with a scaling factor of 10 000. Highly variable genes were identified using the vst method, and the 10 000 genes with the highest variance were retained for subsequent analysis. Unsupervised clustering via Uniform Manifold Approximation and Projection (UMAP) was performed on the scaled and variable gene expression data, and the top 30 principal components were used to define Louvain clustering with the FindClusters function (resolution=0.2). To identify the resolution needed to discriminate among clusters, we used an iterative approach with a range of arbitrary resolutions (0.2, 0.4, 0.6, 0.8, and 1.0); we found resolution 0.2 adequately separated clusters. Cellular origins of each sequenced nucleus were individually estimated using singleR (2.6.0), which computes a Pearson correlation between our single-cell transcriptome and that of known cells; we used the myocardial cell atlas developed by Litviňuková et al24 as our curated reference dataset.
Assembly: mm10 (GCF_000001635.27)
Supplementary files format and content: cell-type specific analysis reported as summary statistics in an .xlsx file containing differential expression data for HFpEF vs. Standard diet within each genotype

molecule: nuclear RNA

source_name: Left Ventricle

extract_protocol:
Left ventricle tissue samples were homogenized using a TissueLyzer II (Qiagen) in homogenization buffer (250 mmol/L sucrose, 25 mmol/L KCl, 5 mmol/L MgCl2, 10 mmol/L Tris-HCl, 1 mmol/L dithiothreitol, and 1× protease inhibitor). The lysate was filtered through a 40-µm strainer (Greiner) and centrifuged at 1200g for 5 minutes at 4 °C. The supernatant, containing cytoplasmic total RNA, was collected and stored at −80 °C. The remaining nuclei pellet was resuspended in storage buffer (1× PBS, 4% BSA, 0.2 U/µL Protector RNase Inhibitor). Nuclei were stained with NucBlue Live ReadyProbes Reagent (Thermo Fisher Scientific), and Hoechst-positive nuclei were purified by fluorescence-activated cell sorting (Aria, BD Biosciences). Fluorescence-activated cell sorting–sorted nuclei were processed on the Chromium iX (10× Genomics) with a targeted recovery of 10 000 nuclei per run, following the manufacturer’s protocol.
The 3′ gene expression libraries were prepared using the Chromium Single-Cell Reagent Kits v3.1 (10× Genomics). Libraries were sequenced on a NovaSeq 6000 (Illumina) at a depth of 30 000 to 40 000 read pairs per nucleus.

treatment_protocol: The initial pilot experiment consisted of twenty 12-week-old male mice from the C57BL/6N and C57BL/6J backgrounds that were purchased from 2 vendors (N=5 per diet-genotype)—Janvier and Charles River laboratory—and housed at the Klinisch Experimenteller Bereich mouse facility of Heidelberg University. All cohorts were group-housed (≤4 mice/cage) on a 12:12-hour light-dark cycle from 06:00 to 18:00 at 25±1 °C and constant humidity with either ad libitum access to control laboratory diet (CON, no. 2916; Teklad) and water (CON) or HFD (58.0 kcal% fat, D12492) with water containing L-NAME (0.5 g/L, pH=7.4; Sigma-Aldrich) stored in light-sensitive bottles (HFD+L-NAME), as previously described.

value: Left Ventricle

value: HFpEF


title: LV tissue, C57BL/6J mouse, HFpEF diet, Biological Replicate 3

description:
Library name: Sample 12
10x Genomics
J_Cardiomyocyte_HFpEF.vs.Ctrl_DEGs.xlsx
J_EC_HFpEF.vs.Ctrl_DEGs.xlsx
J_Fibroblast_HFpEF.vs.Ctrl_DEGs.xlsx
J_Lymphoid_HFpEF.vs.Ctrl_DEGs.xlsx
J_Mast_Cell_HFpEF.vs.Ctrl_DEGs.xlsx
J_Mural_Cell_HFpEF.vs.Ctrl_DEGs.xlsx
J_Myeloid_HFpEF.vs.Ctrl_DEGs.xlsx
J_Neural_Cell_HFpEF.vs.Ctrl_DEGs.xlsx
SampleID: 21


title: LV tissue, C57BL/6J mouse, HFpEF diet, Biological Replicate 1

description:
Library name: Sample 10
10x Genomics
J_Cardiomyocyte_HFpEF.vs.Ctrl_DEGs.xlsx
J_EC_HFpEF.vs.Ctrl_DEGs.xlsx
J_Fibroblast_HFpEF.vs.Ctrl_DEGs.xlsx
J_Lymphoid_HFpEF.vs.Ctrl_DEGs.xlsx
J_Mast_Cell_HFpEF.vs.Ctrl_DEGs.xlsx
J_Mural_Cell_HFpEF.vs.Ctrl_DEGs.xlsx
J_Myeloid_HFpEF.vs.Ctrl_DEGs.xlsx
J_Neural_Cell_HFpEF.vs.Ctrl_DEGs.xlsx
SampleID: 19


title: LV tissue, C57BL/6N mouse, HFpEF diet, Biological Replicate 3

description:
Library name: Sample 9
10x Genomics
N_Cardiomyocyte_HFpEF.vs.Ctrl_DEGs.xlsx
N_EC_HFpEF.vs.Ctrl_DEGs.xlsx
N_Fibroblast_HFpEF.vs.Ctrl_DEGs.xlsx
N_Lymphoid_HFpEF.vs.Ctrl_DEGs.xlsx
N_Mast_Cell_HFpEF.vs.Ctrl_DEGs.xlsx
N_Mural_Cell_HFpEF.vs.Ctrl_DEGs.xlsx
N_Myeloid_HFpEF.vs.Ctrl_DEGs.xlsx
N_Neural_Cell_HFpEF.vs.Ctrl_DEGs.xlsx
SampleID: 9


title: pc293T, IgG Control, Replicate 1

description: Library name: IgG 1


title: LV tissue, C57BL/6N mouse, HFpEF diet, Biological Replicate 2

description:
Library name: Sample 8
10x Genomics
N_Cardiomyocyte_HFpEF.vs.Ctrl_DEGs.xlsx
N_EC_HFpEF.vs.Ctrl_DEGs.xlsx
N_Fibroblast_HFpEF.vs.Ctrl_DEGs.xlsx
N_Lymphoid_HFpEF.vs.Ctrl_DEGs.xlsx
N_Mast_Cell_HFpEF.vs.Ctrl_DEGs.xlsx
N_Mural_Cell_HFpEF.vs.Ctrl_DEGs.xlsx
N_Myeloid_HFpEF.vs.Ctrl_DEGs.xlsx
N_Neural_Cell_HFpEF.vs.Ctrl_DEGs.xlsx
SampleID: 8


title: SVZ NSC lineage cell, OB rep1 [OB1_588627]


title: LV tissue, C57BL/6N mouse, HFpEF diet, Biological Replicate 1

description:
Library name: Sample 7
10x Genomics
N_Cardiomyocyte_HFpEF.vs.Ctrl_DEGs.xlsx
N_EC_HFpEF.vs.Ctrl_DEGs.xlsx
N_Fibroblast_HFpEF.vs.Ctrl_DEGs.xlsx
N_Lymphoid_HFpEF.vs.Ctrl_DEGs.xlsx
N_Mast_Cell_HFpEF.vs.Ctrl_DEGs.xlsx
N_Mural_Cell_HFpEF.vs.Ctrl_DEGs.xlsx
N_Myeloid_HFpEF.vs.Ctrl_DEGs.xlsx
N_Neural_Cell_HFpEF.vs.Ctrl_DEGs.xlsx
SampleID: 7


title: SVZ NSC lineage cell, OB rep1 [OB1_588613]


title: U2OS cells siDICER +4OHT

city: Oxford

first: Monika

last: Gullerova

address: S Parks Rd

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

description:
Library name: siDICER_Damage_m5C
Direct sequencing of chromatin bound RNA in damage induced DICER KD U2OS cells

data_processing:
Nanopore signals generated by MinION as pod5 files were basecalled using Dorado basecaller (version 1.1.0-linux-x64). High Accuracy (HAC) models for canonical bases as well modified bases such as pseudo-uridine, inosine, m6A, m5c were used in the basecalling step. The default parameters for read quality filteration were kept as it is
The basecalled reads were aligned to hg38 genome assemble using Dorado aligner in 'splice' preset mode
Modified bases were identified using modkit pileup (https://github.com/nanoporetech/modkit) with a modification threshold of 0.7 which output a bedMethyl table showing the percentage of modification at each position in the genome
BedMethyl tables were used for all downstream analysis like differential modification analysis.
Differential m⁵C modification between conditions was assessed using modkit dmr pair.
Assembly: hg38
Supplementary files format and content: BedGraph files showing proportion of RNA modification (m5C) around the two representative double strand break sites

source_name: Bone

growth_protocol: Cells were maintained in high-glucose Dulbecco's modified Eagle’s medium (DMEM) medium (Life Technologies, 31966047) with 10% (v/v) fetal bovine serum (Merck, F9665-500ml), 2 mM L-glutamine (Life Technologies, 25030024) and 100 units/ml penicillin–streptomycin solution (Life Technologies, 15140122) at 37°C with 5% CO2 supplement.

extract_protocol:
RNA was extracted by Trizol/chloroform RNA extraction, and further cleaning (to get rid of DNA contamination) with Monarch® Total RNA Miniprep Kit (NEB, T2010S) by following manufacturer's protocol.
Sequencing library preparation for RNA004 MinION flow-cell was carried out using the Direct RNA Sequencing Kit (SQK-RNA004) from Oxford Nanopore Technologies (ONT)

treatment_protocol: The wild-type U2OS or AsiSI-ER U2OS cells with proper RNAi reaching 50%-70% confluency in 15cm dish (~4-8 million cells) before starting of work. Following DSB induction, cells were washed and harvested by gently scrapping into 5mL PBS and pelleted by centrifuge (400g, 5min, 4°C). The cell pellets were lysed with 4 mL HLB+N buffer [10mM Tris-HCl (pH 7.5), 10 mM NaCl, 2.5 mM MgCl2, 0.5% NP-40], and underlaid with 1 mL HLB+NS buffer [10 mM Tris-HCl (pH 7.5), 10 mM NaCl, 2.5 mM MgCl2, 0.5% NP-40, 10% sucrose] before spin at 400g for 5min (4°C) to collect the nuclear pellets. Cytoplasmic fragment was collected for western blot to confirm the successful breakage of cells. Next, nuclear pellets were lysed and resuspended in 125 µL NUN1 buffer [20 mM Tris-HCl (pH 7.9), 75 mM NaCl, 0.5 mM EDTA, 50% glycerol], and chromatin was extracted by incubating in 1.2 mL NUN2 buffer [20 mM HEPES-KOH (pH 7.6), 300 mM NaCl, 0.2 mM EDTA, 7.5 mM MgCl2, 1% NP-40, 1M urea] on ice for 15min with interval vortex in every 3-4 min. The chromatin samples were then collected by full speed spin at 4°C for 15min. To digest DNA and chromatin-associated proteins, 2µL/sample Proteinase K(20ug/uL)(NEB,P8107S) and 1µL/sample Turbo DNase in 1X Turbo DNase Buffer (100µL/sample)(Thermo fisher, AM2238) was added to digest chromatin pellets at 37°C with 1000rpm shake until pellets were dissolved.

value: Bone

value: osteosarcoma

value: siDICER +4OHT

value: single


title: LV tissue, C57BL/6J mouse, Control diet, Biological Replicate 3

description:
Library name: Sample 6
10x Genomics
J_Cardiomyocyte_HFpEF.vs.Ctrl_DEGs.xlsx
J_EC_HFpEF.vs.Ctrl_DEGs.xlsx
J_Fibroblast_HFpEF.vs.Ctrl_DEGs.xlsx
J_Lymphoid_HFpEF.vs.Ctrl_DEGs.xlsx
J_Mast_Cell_HFpEF.vs.Ctrl_DEGs.xlsx
J_Mural_Cell_HFpEF.vs.Ctrl_DEGs.xlsx
J_Myeloid_HFpEF.vs.Ctrl_DEGs.xlsx
J_Neural_Cell_HFpEF.vs.Ctrl_DEGs.xlsx
SampleID: 15

value: Standard Diet


title: U2OS cells siNSUN2 +4OHT

description:
Library name: siNSUN2_Damage_m5C
Direct sequencing of chromatin bound RNA in damage induced NSUN2 KD U2OS cells

value: siNSUN2 +4OHT


title: SVZ NSC lineage cell, OB rep1 [OB1_588609]

value: Brain, olfactory bulb


title: LV tissue, C57BL/6J mouse, Control diet, Biological Replicate 2

description:
Library name: Sample 5
10x Genomics
J_Cardiomyocyte_HFpEF.vs.Ctrl_DEGs.xlsx
J_EC_HFpEF.vs.Ctrl_DEGs.xlsx
J_Fibroblast_HFpEF.vs.Ctrl_DEGs.xlsx
J_Lymphoid_HFpEF.vs.Ctrl_DEGs.xlsx
J_Mast_Cell_HFpEF.vs.Ctrl_DEGs.xlsx
J_Mural_Cell_HFpEF.vs.Ctrl_DEGs.xlsx
J_Myeloid_HFpEF.vs.Ctrl_DEGs.xlsx
J_Neural_Cell_HFpEF.vs.Ctrl_DEGs.xlsx
SampleID: 14


title: SVZ NSC lineage cell, OB rep1 [OB1_588607]


title: LV tissue, C57BL/6N mouse, Control diet, Biological Replicate 3

description:
Library name: Sample 3
10x Genomics
N_Cardiomyocyte_HFpEF.vs.Ctrl_DEGs.xlsx
N_EC_HFpEF.vs.Ctrl_DEGs.xlsx
N_Fibroblast_HFpEF.vs.Ctrl_DEGs.xlsx
N_Lymphoid_HFpEF.vs.Ctrl_DEGs.xlsx
N_Mast_Cell_HFpEF.vs.Ctrl_DEGs.xlsx
N_Mural_Cell_HFpEF.vs.Ctrl_DEGs.xlsx
N_Myeloid_HFpEF.vs.Ctrl_DEGs.xlsx
N_Neural_Cell_HFpEF.vs.Ctrl_DEGs.xlsx
SampleID: 3


title: U2OS cells siCtrl +4OHT

description:
Library name: Damage_m5C
Direct sequencing of chromatin bound RNA in damage induced U2OS cells

value: siCtrl +4OHT


title: SVZ NSC lineage cell, OB rep1 [OB1_588617]


title: LV tissue, C57BL/6N mouse, Control diet, Biological Replicate 2

description:
Library name: Sample 2
10x Genomics
N_Cardiomyocyte_HFpEF.vs.Ctrl_DEGs.xlsx
N_EC_HFpEF.vs.Ctrl_DEGs.xlsx
N_Fibroblast_HFpEF.vs.Ctrl_DEGs.xlsx
N_Lymphoid_HFpEF.vs.Ctrl_DEGs.xlsx
N_Mast_Cell_HFpEF.vs.Ctrl_DEGs.xlsx
N_Mural_Cell_HFpEF.vs.Ctrl_DEGs.xlsx
N_Myeloid_HFpEF.vs.Ctrl_DEGs.xlsx
N_Neural_Cell_HFpEF.vs.Ctrl_DEGs.xlsx
SampleID: 2


title: LV tissue, C57BL/6J mouse, Control diet, Biological Replicate 1

description:
Library name: Sample 4
10x Genomics
J_Cardiomyocyte_HFpEF.vs.Ctrl_DEGs.xlsx
J_EC_HFpEF.vs.Ctrl_DEGs.xlsx
J_Fibroblast_HFpEF.vs.Ctrl_DEGs.xlsx
J_Lymphoid_HFpEF.vs.Ctrl_DEGs.xlsx
J_Mast_Cell_HFpEF.vs.Ctrl_DEGs.xlsx
J_Mural_Cell_HFpEF.vs.Ctrl_DEGs.xlsx
J_Myeloid_HFpEF.vs.Ctrl_DEGs.xlsx
J_Neural_Cell_HFpEF.vs.Ctrl_DEGs.xlsx
SampleID: 13


title: SVZ NSC lineage cell, OB rep1 [OB1_588605]


title: SVZ NSC lineage cell, OB rep1 [OB1_588603]


title: U2OS cells

description:
Library name: U2OS_m5C
Direct sequencing of chromatin bound RNA in U2OS cells

value: WT


title: LV tissue, C57BL/6N mouse, Control diet, Biological Replicate 1

description:
Library name: Sample 1
10x Genomics
N_Cardiomyocyte_HFpEF.vs.Ctrl_DEGs.xlsx
N_EC_HFpEF.vs.Ctrl_DEGs.xlsx
N_Fibroblast_HFpEF.vs.Ctrl_DEGs.xlsx
N_Lymphoid_HFpEF.vs.Ctrl_DEGs.xlsx
N_Mast_Cell_HFpEF.vs.Ctrl_DEGs.xlsx
N_Mural_Cell_HFpEF.vs.Ctrl_DEGs.xlsx
N_Myeloid_HFpEF.vs.Ctrl_DEGs.xlsx
N_Neural_Cell_HFpEF.vs.Ctrl_DEGs.xlsx
SampleID: 1


title: Germ cells, Nrf1KO/KO, rep3

city: Mainz

first: Joan

last: Barau

address: 4 Ackermannweg

institute: Institute of Molecular Biology IMB - Mainz

description:
imb_barau_2024_11_15_Nrf1_KO_rep3
Nrf1_KOvsWT.txt
DKOvsNrf1_KO.txt
D3C_KOvsNrf1_KO.txt
D3C_NRF1_mutants.tpm.csv

data_processing:
Reads were aligned on the Mus musculus genome assembly GRCm38 (GENCODE release M25) using STAR (version 2.7.3a, parameters: --outMultimapperOrder Random  --outSAMattributes NH HI AS nM MD  –outSJfilterReads All --outSAMunmapped Within --outFilterMismatchNoverReadLmax 0.04 --outFilterMismatchNmax 999 --winAnchorMultimapNmax 100 --outFilterMultimapNmax 100).
The TEtranscripts program (version 2.2.3, parameters: --mode multi --sortByPos --stranded reverse) was used to annotate reads to both genes and transposable elements.
Differentially expressed analysis was determined using DESeq2 (release: 1.44.0) with corrected pvalue (Benjamini and Hochberg, FDR) < 0.01.
TElocal (version 1.1.1, parameters: --mode multi --sortByPos --stranded reverse) was used to quantify transposable element expression at the locus level, and the counts were normalized to TPM (Transcripts Per Million) values.
Assembly: mm10
Supplementary files format and content: TXT files include raw counts for genes and transposable elements across each sample and the differential expression analysis for each pair-wise comparison.
Supplementary files format and content: CSV file includes TPM (Transcripts Per Million) values for transposable elements at the locus level across each sample.

source_name: testes

extract_protocol:
Dissected whole testis of mutants and littermate controls were collected and frozen  in Trizol until triplicates of each genotype were collected. Testes were homogenized in Trizol using an IKA T10 basic homogenizer and RNA extraction was performed using the DirectZol RNA MicroPrep kit (Zymo, R2061).
NGS library prep was performed with Illumina's Stranded mRNA Prep Ligation Kit following Stranded mRNA Prep Ligation ReferenceGuide (April 2021) (Document 1000000124518 v02). Libraries were prepared with a starting amount of 29 ng and amplified in 12 PCR cycles. Two post PCR purification steps were performed to exclude residual primer and adapter dimers. Libraries were profiled in a High Sensitivity DNA on a 2100 Bioanalyzer (Agilent technologies) and quantified using the Qubit 1x dsDNA HS Assay Kit, in a Qubit 4.0 Fluorometer (Invitrogen by Thermo Fisher Scientific). All samples were pooled in equimolar ratio and sequenced on a NextSeq2000 P4 FC (200 cycles), PE for 2x 108 cycles plus 2x 10 cycles for the dual index read and 1 dark cycle upfront both R1 and R2.

value: testes

value: Germ cells and somatic cells

value: Germ cells type spermatogonia and somatic cells


title: SVZ NSC lineage cell, OB rep1 [OB1_588619]


title: SVZ NSC lineage cell, OB rep1 [OB1_588611]


title: Rspo2-AAV 5

city: Memphis

first: Bhupesh

last: Singla

state: TN

address: 881 Madison Ave

institute: UNIVERSITY OF TENNESSEE HEALTH SCI CTR

description: Library name: Rspo2-AAV 5

data_processing:
Samples were sequenced using the Illumina platform (NovaSeq PE150, 20-30 million reads). Obtained reads were aligned using Hisat2 v2.0.5. with C57BL/6J mouse genome (GRCm38, mm10) and revealed more than 90% mapping. After the quantitation of gene expression (featureCounts v1.5.0-p3), differential gene expression was analyzed and normalized with the DESeq2 R package (1.20.0)
Assembly: Obtained reads were aligned using Hisat2 v2.0.5. with C57BL/6J mouse genome (GRCm38, mm10)
Supplementary files format and content: SRA Accessions provided
Supplementary files format and content: csv files include FPKM values for each sample

source_name: Liver

extract_protocol:
Total RNA from Gfp-AAV- or Rspo2-AAV-injected mice liver samples was isolated using TRIzol reagent according to the manufacturer's instructions. The quality of RNA was determined using the Agilent 2100 Bioanalyzer System. The samples with RNA Integrity Numbers of more than 8 were used for bulk RNA-sequencing.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library

value: Liver

value: Apoe knockout


title: Rspo2-AAV 7

description: Library name: Rspo2-AAV 7


title: Rspo2-AAV 6

description: Library name: Rspo2-AAV 6


title: Germ cells, Dnmt3CKO/KO, Nrf1KO/KO rep3

description:
imb_barau_2024_11_14_DKO_rep5
DKOvsD3C_KO.txt
DKOvsNrf1_KO.txt
DKOvsWT.txt
D3C_NRF1_mutants.tpm.csv

value: Dnmt3CKO/KO Nrf1KO/KO


title: Germ cells, Dnmt3CKO/KO, rep3

description:
imb_barau_2024_11_13_D3C_KO_rep4
D3C_KOvsNrf1_KO.txt
D3C_KOvsWT.txt
DKOvsD3C_KO.txt
D3C_NRF1_mutants.tpm.csv


title: Rspo2-AAV 4

description: Library name: Rspo2-AAV 4


title: SVZ NSC lineage cell, OB rep1 [OB1_588601]


title: Rspo2-AAV 2

description: Library name: Rspo2-AAV 2


title: Rspo2-AAV 1

description: Library name: Rspo2-AAV 1


title: SVZ NSC lineage cell, OB rep1 [OB1_588599]


title: SVZ NSC lineage cell, OB rep1 [OB1_588597]


title: Control 6

description: Library name: Control Gfp-AAV 6

value: Control-AAV


title: SVZ NSC lineage cell, OB rep1 [OB1_588595]


title: Control 5

description: Library name: Control Gfp-AAV 5


title: Germ cells, Nrf1KO/KO, rep1

description:
imb_barau_2024_11_10_Nrf1_cKO_rep1
Nrf1_KOvsWT.txt
DKOvsNrf1_KO.txt
D3C_KOvsNrf1_KO.txt
D3C_NRF1_mutants.tpm.csv


title: Control 4

description: Library name: Control Gfp-AAV 4


title: Control 3

description: Library name: Control Gfp-AAV 3


title: Control 2

description: Library name: Control Gfp-AAV 2


title: SVZ NSC lineage cell, OB rep1 [OB1_588593]


title: Germ cells, WT, rep2

description:
imb_barau_2024_11_06_WT_rep2
D3C_KOvsWT.txt
DKOvsWT.txt
Nrf1_KOvsWT.txt
D3C_NRF1_mutants.tpm.csv

value: wild type


title: SVZ NSC lineage cell, OB rep1 [OB1_588591]


title: Germ cells, Nrf1KO/KO, rep2

description:
imb_barau_2024_11_05_Nrf1_KO_rep2
Nrf1_KOvsWT.txt
DKOvsNrf1_KO.txt
D3C_KOvsNrf1_KO.txt
D3C_NRF1_mutants.tpm.csv


title: SVZ NSC lineage cell, OB rep1 [OB1_588589]


title: Germ cells, Dnmt3CKO/KO, Nrf1KO/KO rep2

description:
imb_barau_2024_11_04_DKO_rep2_B
DKOvsD3C_KO.txt
DKOvsNrf1_KO.txt
DKOvsWT.txt
D3C_NRF1_mutants.tpm.csv


title: SVZ NSC lineage cell, OB rep1 [OB1_588583]


title: snRNAseq-mouse placenta-IVF-46

city: San Francisco

first: Reza

last: Oqani

address: 513 Parnassus Ave.

institute: UCSF

description: Library name: IVF3_S3_L004_I2_001.fastq

data_processing:
FASTQ files were mapped to mm10 (GRCm38) using StarSolo (2.7.10b) and the 10Xv3 cell barcode whitelist. Cell barcode matching and filtering used 1MM and Emptydrops_CR default settings, respectively.  Downstream data processing and analyses were performed using Python (3.11) and ScanPy (1.9.4).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Placenta

extract_protocol:
cDNA libraries were prepared using the 10X Genomics Chromium Next GEM Single Cell 3' Reagent Kit v3.1 (dual index)
The prepared cDNA libraries were sequenced on an Illumina NovaSeq 6000 platform using an S4 flow cell. Sequencing was performed to generate paired-end reads, with a target read depth of approximately 500M reads per GEX, sufficient for high-quality transcriptome coverage.

value: Placenta

value: Trophoblast

value: in vitro fertilization (IVF)


title: snRNAseq-mouse placenta-IVF-47

description: Library name: IVF3_S3_L004_R1_001.fastq


title: snRNAseq-mouse placenta-IVF-48

description: Library name: IVF3_S3_L004_R2_001.fastq


title: Germ cells, Dnmt3CKO/KO, rep2

description:
imb_barau_2024_11_03_D3C_KO_rep2
D3C_KOvsNrf1_KO.txt
D3C_KOvsWT.txt
DKOvsD3C_KO.txt
D3C_NRF1_mutants.tpm.csv


title: snRNAseq-mouse placenta-IVF-43

description: Library name: IVF3_S3_L003_R1_001.fastq


title: snRNAseq-mouse placenta-IVF-44

description: Library name: IVF3_S3_L003_R2_001.fastq


title: SVZ NSC lineage cell, OB rep1 [OB1_588577]


title: SVZ NSC lineage cell, OB rep1 [OB1_588579]


title: snRNAseq-mouse placenta-IVF-42

description: Library name: IVF3_S3_L003_I2_001.fastq


title: SVZ NSC lineage cell, OB rep1 [OB1_588575]


title: Germ cells, Dnmt3CKO/KO, Nrf1KO/KO rep1

description:
imb_barau_2024_11_02_DKO_rep1
DKOvsD3C_KO.txt
DKOvsNrf1_KO.txt
DKOvsWT.txt
D3C_NRF1_mutants.tpm.csv


title: snRNAseq-mouse placenta-IVF-40

description: Library name: IVF3_S3_L002_R2_001.fastq


title: snRNAseq-mouse placenta-IVF-38

description: Library name: IVF3_S3_L002_I2_001.fastq


title: Germ cells, WT, rep1

description:
imb_barau_2024_11_08_WT_rep1
D3C_KOvsWT.txt
DKOvsWT.txt
Nrf1_KOvsWT.txt
D3C_NRF1_mutants.tpm.csv


title: Germ cells, Dnmt3CKO/KO, rep1

description:
imb_barau_2024_11_01_D3C_KO_rep1
D3C_KOvsNrf1_KO.txt
D3C_KOvsWT.txt
DKOvsD3C_KO.txt
D3C_NRF1_mutants.tpm.csv


title: SVZ NSC lineage cell, OB rep1 [OB1_588573]


title: Control 1

description: Library name: Control Gfp-AAV 1


title: snRNAseq-mouse placenta-IVF-36

description: Library name: IVF3_S3_L001_R2_001.fastq


title: SVZ NSC lineage cell, OB rep1 [OB1_588571]


title: snRNAseq-mouse placenta-IVF-33

description: Library name: IVF3_S3_L001_I1_001.fastq


title: snRNAseq-mouse placenta-IVF-45

description: Library name: IVF3_S3_L004_I1_001.fastq


title: Spc cells, WT, rep2

description:
imb_barau_2023_05_14_Spc_WT_rep2
Spc_KOvsWT.txt
Spc.tpm.csv

data_processing:
Sequence reads were trimmed for adapter sequence using cutadapt (version 4.0, parameters: --adapter Illumina=CTGTCTCTTATA --overlap=5 --minimum-length 30 --nextseq-trim=20 --error-rate 0.1 -A CTGTCTCTTATA)
Trimmed reads were aligned on the Mus musculus genome assembly GRCm38 (GENCODE release M25) using STAR (version 2.7.3a, parameters: --outMultimapperOrder Random  --outSAMattributes NH HI AS nM MD  –outSJfilterReads All --outSAMunmapped Within --outFilterMismatchNoverReadLmax 0.04 --outFilterMismatchNmax 999 --winAnchorMultimapNmax 100 --outFilterMultimapNmax 100).
The TEtranscripts program (version 2.2.3, parameters: --mode multi --sortByPos --stranded reverse) was used to annotate reads to both genes and transposable elements.
Differentially expressed analysis was determined using DESeq2 (release: 1.44.0) with corrected pvalue (Benjamini and Hochberg, FDR) < 0.01.
TElocal (version 1.1.1, parameters: --mode multi --sortByPos --stranded reverse) was used to quantify transposable element expression at the locus level, and the counts were normalized to TPM (Transcripts Per Million) values.
Assembly: mm10
Supplementary files format and content: TXT files include raw counts for genes and transposable elements across each sample and the differential expression analysis for each pair-wise comparison.
Supplementary files format and content: CSV files include TPM (Transcripts Per Million) values for transposable elements at the locus level across each sample.

extract_protocol:
Sorted germ cells of littermates were collected and frozen in Trizol until triplicates of each genotype were collected. RNA extraction was performed using the DirectZol RNA MicroPrep kit (Zymo, R2061).
NGS library prep was performed with Illumina's Stranded mRNA Prep Ligation Kit following Stranded mRNA Prep Ligation ReferenceGuide (April 2021) (Document 1000000124518 v02). Libraries were prepared with a starting amount of 10 ng and amplified in 13 PCR cycles. Two post PCR purification steps were performed to exclude residual primer and adapter dimers. Libraries were profiled in a DNA High Sensitivity chip on a 2100 Bioanalyzer (Agilent technologies) and quantified using the Qubit 1x dsDNA HS Assay Kit, in a Qubit 4.0 Fluorometer (Invitrogen by Thermo Fisher Scientific).  All samples were pooled together in equimolar ratio aiming for at least 50M reads per sample and sequenced on a NextSeq 2000 P3 (200 cycles) FC, PE for 2x108 cycles plus 2x10 cycles for the index reads and 1 dark cycle upfront R1 and R2.

value: germ cells

value: Spermatocytes


title: snRNAseq-mouse placenta-IVF-32

description: Library name: IVF2_S2_L004_R2_001.fastq


title: SVZ NSC lineage cell, OB rep1 [OB1_588569]


title: snRNAseq-mouse placenta-IVF-39

description: Library name: IVF3_S3_L002_R1_001.fastq


title: SVZ NSC lineage cell, OB rep1 [OB1_588565]


title: snRNAseq-mouse placenta-IVF-35

description: Library name: IVF3_S3_L001_R1_001.fastq


title: Spc cells, Dnmt3CKO/KO, rep4

description:
imb_barau_2023_05_12_Spc_KO_rep4
Spc_KOvsWT.txt
Spc.tpm.csv


title: Spc cells, WT, rep3

description:
imb_barau_2023_05_15_Spc_WT_rep3
Spc_KOvsWT.txt
Spc.tpm.csv


title: SVZ NSC lineage cell, OB rep1 [OB1_588563]


title: snRNAseq-mouse placenta-IVF-30

description: Library name: IVF2_S2_L004_I2_001.fastq


title: snRNAseq-mouse placenta-IVF-29

description: Library name: IVF2_S2_L004_I1_001.fastq


title: Spc cells, WT, rep4

description:
imb_barau_2023_05_16_Spc_WT_rep4
Spc_KOvsWT.txt
Spc.tpm.csv


title: Spc cells, Dnmt3CKO/KO, rep3

description:
imb_barau_2023_05_11_Spc_KO_rep3
Spc_KOvsWT.txt
Spc.tpm.csv


title: snRNAseq-mouse placenta-IVF-27

description: Library name: IVF2_S2_L003_R1_001.fastq


title: SVZ NSC lineage cell, OB rep1 [OB1_588561]


title: snRNAseq-mouse placenta-IVF-25

description: Library name: IVF2_S2_L003_I1_001.fastq


title: snRNAseq-mouse placenta-IVF-28

description: Library name: IVF2_S2_L003_R2_001.fastq


title: snRNAseq-mouse placenta-IVF-26

description: Library name: IVF2_S2_L003_I2_001.fastq


title: Spc cells, Dnmt3CKO/KO, rep2

description:
imb_barau_2023_05_10_Spc_KO_rep2
Spc_KOvsWT.txt
Spc.tpm.csv


title: Spc cells, WT, rep1

description:
imb_barau_2023_05_13_Spc_WT_rep1
Spc_KOvsWT.txt
Spc.tpm.csv


title: snRNAseq-mouse placenta-IVF-24

description: Library name: IVF2_S2_L002_R2_001.fastq


title: Spc cells, Dnmt3CKO/KO, rep1

description:
imb_barau_2023_05_09_Spc_KO_rep1
Spc_KOvsWT.txt
Spc.tpm.csv


title: snRNAseq-mouse placenta-IVF-34

description: Library name: IVF3_S3_L001_I2_001.fastq


title: snRNAseq-mouse placenta-IVF-23

description: Library name: IVF2_S2_L002_R1_001.fastq


title: snRNAseq-mouse placenta-IVF-31

description: Library name: IVF2_S2_L004_R1_001.fastq


title: SVZ NSC lineage cell, OB rep1 [OB1_588555]


title: snRNAseq-mouse placenta-IVF-21

description: Library name: IVF2_S2_L002_I1_001.fastq


title: snRNAseq-mouse placenta-IVF-22

description: Library name: IVF2_S2_L002_I2_001.fastq


title: Spg cells, WT, rep3

description:
imb_barau_2023_05_08_Spg_WT_rep4
Spg_KOvsWT.txt
Spg.tpm.csv

value: Spermatogonia


title: Spg cells, WT, rep2

description:
imb_barau_2023_05_06_Spg_WT_rep2
Spg_KOvsWT.txt
Spg.tpm.csv


title: snRNAseq-mouse placenta-IVF-41

description: Library name: IVF3_S3_L003_I1_001.fastq


title: snRNAseq-mouse placenta-IVF-19

description: Library name: IVF2_S2_L001_R1_001.fastq


title: snRNAseq-mouse placenta-IVF-20

description: Library name: IVF2_S2_L001_R2_001.fastq


title: SVZ NSC lineage cell, OB rep1 [OB1_588549]

value: Brain, olfactory bulb


title: snRNAseq-mouse placenta-IVF-16

description: Library name: IVF1_S1_L004_R2_001.fastq


title: snRNAseq-mouse placenta-IVF-15

description: Library name: IVF1_S1_L004_R1_001.fastq


title: snRNAseq-mouse placenta-IVF-17

description: Library name: IVF2_S2_L001_I1_001.fastq


title: Spg cells, WT, rep1

description:
imb_barau_2023_05_05_Spg_WT_rep1
Spg_KOvsWT.txt
Spg.tpm.csv


title: Spg cells, Dnmt3CKO/KO, rep2

description:
imb_barau_2023_05_02_Spg_KO_rep2
Spg_KOvsWT.txt
Spg.tpm.csv


title: snRNAseq-mouse placenta-IVF-18

description: Library name: IVF2_S2_L001_I2_001.fastq


title: SVZ NSC lineage cell, OB rep1 [OB1_588559]


title: snRNAseq-mouse placenta-IVF-14

description: Library name: IVF1_S1_L004_I2_001.fastq


title: Spg cells, Dnmt3CKO/KO, rep3

description:
imb_barau_2023_05_04_Spg_KO_rep4
Spg_KOvsWT.txt
Spg.tpm.csv


title: SVZ NSC lineage cell, OB rep1 [OB1_588553]


title: snRNAseq-mouse placenta-IVF-13

description: Library name: IVF1_S1_L004_I1_001.fastq


title: snRNAseq-mouse placenta-IVF-12

description: Library name: IVF1_S1_L003_R2_001.fastq


title: SVZ NSC lineage cell, OB rep1 [OB1_588541]


title: SVZ NSC lineage cell, OB rep1 [OB1_588537]


title: SVZ NSC lineage cell, OB rep1 [OB1_588547]


title: snRNAseq-mouse placenta-IVF-10

description: Library name: IVF1_S1_L003_I2_001.fastq


title: snRNAseq-mouse placenta-IVF-37

description: Library name: IVF3_S3_L002_I1_001.fastq


title: ProSpg cells, control, NRF1, rep2

data_processing:
Paired-end reads were quality-trimmed using Trim Galore (v.0.6.10) with a minimum read length of 10 bp, and quality reports were generated using FastQC.
Reads were aligned to the mm10 reference genome using Bowtie2 (v.2.5.3) in local alignment mode  allowing a minimum fragment length of 10 bp and a maximum of 1000 bp, while excluding mixed and discordant alignments.
BAM files were first indexed using Samtools (v.1.10). Then, BigWig files were generated from the BAM files using bamCoverage (v. 2.27.1) , with normalization set to RPGC.
For Peak calling, BAM files of replicates were merged using Samtools (v.1.10).
Peak calling was performed using MACS2 (v.2.1.2) on aligned BAM files, with no control BAM files specified. The analysis was conducted using broad peak calling mode, with genome size set to 'mm' (for mouse) and otherwise default settings.
Assembly: mm10
Supplementary files format and content: bigWig, broadPeak
Library strategy: CUT&Tag

extract_protocol:
Chromatin profiling was performed using the CUT&Tag protocol as described by Kaya-Okur et al. (2020). Briefly, cells were immobilized on concanavalin A-coated beads and incubated with a primary antibody specific to the histone modification of interest. Following binding with a secondary antibody, protein A-Tn5 transposase was added 1:400 to introduce sequencing adapters at target sites.
DNA was extracted using Zymo DNA Clean & Concentrator (Cat. No.: D4014) and ibraries were amplified by PCR using 15 amplification cycles.


title: snRNAseq-mouse placenta-IVF-8

description: Library name: IVF1_S1_L002_R2_001.fastq


title: snRNAseq-mouse placenta-IVF-9

description: Library name: IVF1_S1_L003_I1_001.fastq


title: snRNAseq-mouse placenta-IVF-7

description: Library name: IVF1_S1_L002_R1_001.fastq


title: Spg cells, Dnmt3CKO/KO, rep1

description:
imb_barau_2023_05_01_Spg_KO_rep1
Spg_KOvsWT.txt
Spg.tpm.csv


title: ProSpg cells, control, NRF1, rep1


title: snRNAseq-mouse placenta-IVF-6

description: Library name: IVF1_S1_L002_I2_001.fastq


title: Spg cells, control, CREB1, rep2


title: SVZ NSC lineage cell, OB rep1 [OB1_588535]


title: snRNAseq-mouse placenta-IVF-5

description: Library name: IVF1_S1_L002_I1_001.fastq


title: SVZ NSC lineage cell, OB rep1 [OB1_588557]


title: SVZ NSC lineage cell, OB rep1 [OB1_588531]


title: snRNAseq-mouse placenta-IVF-3

description: Library name: IVF1_S1_L001_R1_001.fastq


title: Spg cells, control, NRF1, rep2

description:
Spg_WT_NRF1_rep2
imb_barau_2024_01_CnT_Spg_WT_NRF1.broadPeak


title: Spg cells, Dnmt3CKO/KO, CREB1, rep2


title: snRNAseq-mouse placenta-IVF-11

description: Library name: IVF1_S1_L003_R1_001.fastq


title: snRNAseq-mouse placenta-IVF-1

description: Library name: IVF1_S1_L001_I1_001.fastq


title: SVZ NSC lineage cell, OB rep1 [OB1_588529]


title: snRNAseq-mouse placenta-FB-47

description: Library name: FB3_S6_L004_R1_001.fastq

value: in vivo fertilization (FB)


title: snRNAseq-mouse placenta-FB-48

description: Library name: FB3_S6_L004_R2_001.fastq


title: SVZ NSC lineage cell, OB rep1 [OB1_588525]


title: snRNAseq-mouse placenta-FB-46

description: Library name: FB3_S6_L004_I2_001.fastq


title: snRNAseq-mouse placenta-FB-45

description: Library name: FB3_S6_L004_I1_001.fastq


title: Spg cells, control, CREB1, rep1


title: SVZ NSC lineage cell, OB rep1 [OB1_588519]


title: snRNAseq-mouse placenta-IVF-2

description: Library name: IVF1_S1_L001_I2_001.fastq


title: snRNAseq-mouse placenta-FB-44

description: Library name: FB3_S6_L003_R2_001.fastq


title: SVZ NSC lineage cell, OB rep1 [OB1_588533]


title: snRNAseq-mouse placenta-FB-42

description: Library name: FB3_S6_L003_I2_001.fastq


title: SVZ NSC lineage cell, OB rep1 [OB1_588517]


title: Spg cells, control, NRF1, rep1

description:
Spg_WT_NRF1_rep1
imb_barau_2024_01_CnT_Spg_WT_NRF1.broadPeak


title: snRNAseq-mouse placenta-FB-43

description: Library name: FB3_S6_L003_R1_001.fastq


title: snRNAseq-mouse placenta-IVF-4

description: Library name: IVF1_S1_L001_R2_001.fastq


title: snRNAseq-mouse placenta-FB-40

description: Library name: FB3_S6_L002_R2_001.fastq


title: snRNAseq-mouse placenta-FB-41

description: Library name: FB3_S6_L003_I1_001.fastq


title: SVZ NSC lineage cell, OB rep1 [OB1_588515]


title: Spg cells, Dnmt3CKO/KO, CREB1, rep1


title: SVZ NSC lineage cell, OB rep1 [OB1_588527]


title: Spg cells, Dnmt3CKO/KO, NRF1, rep1

description:
Spg_KO_NRF1_rep1
imb_barau_2024_01_CnT_Spg_KO_NRF1.broadPeak


title: SVZ NSC lineage cell, OB rep1 [OB1_588513]


title: snRNAseq-mouse placenta-FB-38

description: Library name: FB3_S6_L002_I2_001.fastq


title: snRNAseq-mouse placenta-FB-39

description: Library name: FB3_S6_L002_R1_001.fastq


title: snRNAseq-mouse placenta-FB-37

description: Library name: FB3_S6_L002_I1_001.fastq


title: Spg cells, Dnmt3CKO/KO, NRF1, rep2

description:
Spg_KO_NRF1_rep2
imb_barau_2024_01_CnT_Spg_KO_NRF1.broadPeak


title: SVZ NSC lineage cell, OB rep1 [OB1_588511]


title: Spc cells, Dnmt3CKO/KO, NRF1, rep2

description:
Spc_KO_NRF1_rep2
imb_barau_2024_01_CnT_Spc_KO_NRF1.broadPeak


title: snRNAseq-mouse placenta-FB-36

description: Library name: FB3_S6_L001_R2_001.fastq


title: SVZ NSC lineage cell, OB rep1 [OB1_588507]


title: snRNAseq-mouse placenta-FB-34

description: Library name: FB3_S6_L001_I2_001.fastq


title: snRNAseq-mouse placenta-FB-33

description: Library name: FB3_S6_L001_I1_001.fastq


title: snRNAseq-mouse placenta-FB-31

description: Library name: FB2_S5_L004_R1_001.fastq


title: SVZ NSC lineage cell, OB rep1 [OB1_588505]


title: Spc cells, Dnmt3CKO/KO, NRF1, rep1

description:
Spc_KO_NRF1_rep1
imb_barau_2024_01_CnT_Spc_KO_NRF1.broadPeak


title: snRNAseq-mouse placenta-FB-32

description: Library name: FB2_S5_L004_R2_001.fastq


title: snRNAseq-mouse placenta-FB-30

description: Library name: FB2_S5_L004_I2_001.fastq


title: snRNAseq-mouse placenta-FB-29

description: Library name: FB2_S5_L004_I1_001.fastq


title: snRNAseq-mouse placenta-FB-28

description: Library name: FB2_S5_L003_R2_001.fastq


title: Spg Cells, H3K27ac, Dnmt3CKO/KO, rep2

data_processing:
Paired-end reads were quality-trimmed using Trim Galore (v.0.6.10) with a minimum read length of 10 bp, and quality reports were generated using FastQC.
Reads were aligned to the mm10 reference genome using Bowtie2 (v.2.5.3) in local alignment mode  allowing a minimum fragment length of 10 bp and a maximum of 1000 bp, while excluding mixed and discordant alignments.
BAM files were first indexed using Samtools (v.1.10). Then, BigWig files were generated from the BAM files using bamCoverage (v. 2.27.1) , with normalization set to RPGC.
Peak calling was performed using MACS2 (v.2.1.2) on aligned BAM files, specifying the corresponding IgG file as control BAM. The analysis was conducted using broad peak calling mode, with genome size set to 'mm' (for mouse) and otherwise default settings.
Assembly: mm10
Supplementary files format and content: bigWig, broadPeak
Library strategy: CUT&Tag


title: snRNAseq-mouse placenta-FB-26

description: Library name: FB2_S5_L003_I2_001.fastq


title: Spg Cells, H3K27ac, Control, rep2


title: SVZ NSC lineage cell, OB rep1 [OB1_588503]


title: snRNAseq-mouse placenta-FB-27

description: Library name: FB2_S5_L003_R1_001.fastq


title: Spc cells, Control, NRF1, rep2

description:
Spc_WT_NRF1_rep2
imb_barau_2024_01_CnT_Spc_WT_NRF1.broadPeak


title: SVZ NSC lineage cell, OB rep1 [OB1_588509]


title: snRNAseq-mouse placenta-FB-23

description: Library name: FB2_S5_L002_R1_001.fastq


title: Spg Cells, H3K27ac, Dnmt3CKO/KO, rep1


title: Spg Cells, H3K27ac, Control, rep1


title: SVZ NSC lineage cell, OB rep1 [OB1_588497]


title: snRNAseq-mouse placenta-FB-20

description: Library name: FB2_S5_L001_R2_001.fastq


title: snRNAseq-mouse placenta-FB-22

description: Library name: FB2_S5_L002_I2_001.fastq


title: snRNAseq-mouse placenta-FB-25

description: Library name: FB2_S5_L003_I1_001.fastq


title: SVZ NSC lineage cell, OB rep1 [OB1_588501]


title: snRNAseq-mouse placenta-FB-35

description: Library name: FB3_S6_L001_R1_001.fastq


title: snRNAseq-mouse placenta-FB-19

description: Library name: FB2_S5_L001_R1_001.fastq


title: SVZ NSC lineage cell, OB rep1 [OB1_588495]


title: Spc cells, Control, NRF1, rep1

description:
Spc_WT_NRF1_rep1
imb_barau_2024_01_CnT_Spc_WT_NRF1.broadPeak


title: snRNAseq-mouse placenta-FB-18

description: Library name: FB2_S5_L001_I2_001.fastq


title: Spc Cells, H3K27ac, Control, rep1


title: SVZ NSC lineage cell, OB rep1 [OB1_588489]


title: SVZ NSC lineage cell, OB rep1 [OB1_588487]


title: Spc Cells, H3K27ac, Dnmt3CKO/KO, rep2


title: snRNAseq-mouse placenta-FB-16

description: Library name: FB1_S4_L004_R2_001.fastq


title: SVZ NSC lineage cell, OB rep1 [OB1_588481]


title: snRNAseq-mouse placenta-FB-13

description: Library name: FB1_S4_L004_I1_001.fastq


title: snRNAseq-mouse placenta-FB-24

description: Library name: FB2_S5_L002_R2_001.fastq


title: snRNAseq-mouse placenta-FB-17

description: Library name: FB2_S5_L001_I1_001.fastq


title: ProSpg Cells, H3K27ac, rep2

value: Prospermatogonia


title: ProSpg Cells, H3K27ac, rep1

value: testes


title: snRNAseq-mouse placenta-FB-21

description: Library name: FB2_S5_L002_I1_001.fastq


title: SVZ NSC lineage cell, OB rep1 [OB1_588477]


title: snRNAseq-mouse placenta-FB-11

description: Library name: FB1_S4_L003_R1_001.fastq


title: snRNAseq-mouse placenta-FB-12

description: Library name: FB1_S4_L003_R2_001.fastq


title: SVZ NSC lineage cell, OB rep1 [OB1_588493]


title: SVZ NSC lineage cell, OB rep1 [OB1_588475]


title: Spc Cells, H3K27ac, Control, rep2


title: snRNAseq-mouse placenta-FB-9

description: Library name: FB1_S4_L003_I1_001.fastq


title: SVZ NSC lineage cell, OB rep1 [OB1_588467]


title: snRNAseq-mouse placenta-FB-10

description: Library name: FB1_S4_L003_I2_001.fastq


title: Spc Cells, H3K9me3, Dnmt3CKO/KO, rep2


title: SVZ NSC lineage cell, OB rep1 [OB1_588465]


title: snRNAseq-mouse placenta-FB-7

description: Library name: FB1_S4_L002_R1_001.fastq


title: snRNAseq-mouse placenta-FB-8

description: Library name: FB1_S4_L002_R2_001.fastq


title: Spc Cells, H3K27me3, Dnmt3CKO/KO, rep2


title: Spc Cells, H3K9me2, Dnmt3CKO/KO, rep2


title: snRNAseq-mouse placenta-FB-15

description: Library name: FB1_S4_L004_R1_001.fastq


title: SVZ NSC lineage cell, OB rep1 [OB1_588461]


title: snRNAseq-mouse placenta-FB-14

description: Library name: FB1_S4_L004_I2_001.fastq


title: Spc Cells, H3K27ac, Dnmt3CKO/KO, rep1


title: snRNAseq-mouse placenta-FB-4

description: Library name: FB1_S4_L001_R2_001.fastq


title: snRNAseq-mouse placenta-FB-5

description: Library name: FB1_S4_L002_I1_001.fastq


title: snRNAseq-mouse placenta-FB-2

description: Library name: FB1_S4_L001_I2_001.fastq


title: snRNAseq-mouse placenta-FB-6

description: Library name: FB1_S4_L002_I2_001.fastq


title: Spc Cells, H3K27me3, Control, rep2


title: snRNAseq-mouse placenta-FB-1

description: Library name: FB1_S4_L001_I1_001.fastq


title: SVZ NSC lineage cell, OB rep1 [OB1_588459]


title: SVZ NSC lineage cell, OB rep1 [OB1_588457]


title: ATAC_Rec_B36934_Vehicle_rep2

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

description: Library name: ATAC_Rec_B36934_Vehicle_rep2

data_processing:
Raw sequencing reads were trimmed and filtered for quality (Q>15) and adapter content using version 0.4.5 of TrimGalore and running version 1.15 of cutadapt and version 0.11.5 of FastQC.
Version 2.3.4.1 of bowtie2 was employed to align reads to mouse assembly mm9 and alignments were deduplicated using MarkDuplicates in Picard Tools v2.16.0.
Enriched regions were discovered using MACS2 with a p-value setting of 0.001 and then filtered for blacklisted regions.
The BEDTools suite was used to create normalized bigwig files scaled to a sequencing depth of 10 million uniquely mapped fragments.
Assembly: mm9
Supplementary files format and content: normalized bigwigs

source_name: thyroid

growth_protocol: Cells were grown in F12 Coons', 5% FBS, 1% PSG

extract_protocol:
For ATAC-seq, cells were lysed and incubated with transposition reaction mix containing PBS, 1% Digitonin, Tween-20, and Transposase (llumina). Samples were incubated for 30 minutes at 37C in a thermomixer at 1000rpm. Prior to amplification, samples were concentrated with the DNA Clean and Concentrator Kit-5 (Zymo).
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with either DMSO, 20ng/ml murine interferon gamma, 10nM trametinib or the combination of interferon gamma and trametinib for 96 hours.

value: thyroid

value: anaplastic thyroid cancer cell line Braf-CAV600E/p53

value: recurrent tumor

value: DMSO


title: Spc Cells, H3K9me3, Control, rep2


title: SVZ NSC lineage cell, OB rep1 [OB1_588455]


title: Spc Cells, H3K4me3, Dnmt3CKO/KO, rep2


title: Spc Cells, H3K9me2, Control, rep2


title: ATAC_Rec_B36934_Tram_rep2

description: Library name: ATAC_Rec_B36934_Tram_rep2

value: trametinib (10nM)


title: ATAC_Rec_B36934_Vehicle_rep1

description: Library name: ATAC_Rec_B36934_Vehicle_rep1


title: ATAC_Rec_B36934_Tram_rep1

description: Library name: ATAC_Rec_B36934_Tram_rep1


title: ATAC_Rec_B36934_IFNGandTram_rep2

description: Library name: ATAC_Rec_B36934_IFNGandTram_rep2

value: IFNγ (20ng/ml) and trametinib (10nM)


title: ATAC_Rec_B36934_IFNG_rep2

description: Library name: ATAC_Rec_B36934_IFNG_rep2

value: IFNγ (20ng/ml)


title: SVZ NSC lineage cell, OB rep1 [OB1_588451]


title: ATAC_Rec_B36934_IFNGandTram_rep1

description: Library name: ATAC_Rec_B36934_IFNGandTram_rep1


title: ATAC_Rec_B36934_IFNG_rep1

description: Library name: ATAC_Rec_B36934_IFNG_rep1


title: SVZ NSC lineage cell, OB rep1 [OB1_588453]


title: Spc Cells, H3K4me3, Control, rep2

value: wild type


title: Spc Cells, H3K27me3,Dnmt3CKO/KO, rep1


title: snRNAseq-mouse placenta-FB-3

description: Library name: FB1_S4_L001_R1_001.fastq

value: Placenta

value: Trophoblast


title: ATAC_Prim_B92_Vehicle_rep1

description: Library name: ATAC_Prim_B92_Vehicle_rep1

value: primary tumor


title: Spc Cells, H3K9me3,Dnmt3CKO/KO, rep1

value: germ cells

value: Spermatocytes


title: SVZ NSC lineage cell, OB rep1 [OB1_588447]

value: Brain, olfactory bulb


title: SVZ NSC lineage cell, OB rep1 [OB1_588445]


title: Spc Cells, H3K9me2, Dnmt3CKO/KO, rep1


title: ATAC_Prim_B92_Tram_rep1

description: Library name: ATAC_Prim_B92_Tram_rep1


title: ATAC_Prim_B92_IFNGandTram_rep1

description: Library name: ATAC_Prim_B92_IFNGandTram_rep1


title: ATAC_Prim_B92_IFNGandTram_rep2

description: Library name: ATAC_Prim_B92_IFNGandTram_rep2


title: SVZ NSC lineage cell, OB rep1 [OB1_588439]


title: Spc Cells, H3K27me3, Control, rep1


title: ATAC_Prim_B92_IFNG_rep2

description: Library name: ATAC_Prim_B92_IFNG_rep2


title: RNA_Rec_B36934_Vehicle_rep3

description: Library name: RNA_Rec_B36934_Vehicle_rep3

data_processing:
Raw sequencing reads were trimmed and filtered for quality (Q>15) and adapter content using version 0.4.5 of TrimGalore and running version 1.15 of cutadapt and version 0.11.5 of FastQC.
Reads were aligned to mouse assembly mm9 with STAR v2.4 using default parameters
Assembly: mm9
Supplementary files format and content: Raw counts table

extract_protocol:
For RNA-seq, RNA was extracted from cells utlizing TRIzol protocol according to the manufacturers instructions (Thermo Fisher Scientific).
Libraries were prepared for sequencing using standard Illumina protocols


title: Spc Cells, H3K9me3, Control, rep1


title: RNA_Rec_B36934_Vehicle_rep2

description: Library name: RNA_Rec_B36934_Vehicle_rep2


title: SVZ NSC lineage cell, OB rep1 [OB1_588435]


title: SVZ NSC lineage cell, OB rep1 [OB1_588437]


title: Spc Cells, H3K9me2, Control, rep1


title: RNA_Rec_B36934_Tram_rep2

description: Library name: RNA_Rec_B36934_Tram_rep2


title: ATAC_Prim_B92_Tram_rep2

description: Library name: ATAC_Prim_B92_Tram_rep2


title: Spc Cells, H3K4me3, Control, rep1


title: RNA_Rec_B36934_Vehicle_rep1

description: Library name: RNA_Rec_B36934_Vehicle_rep1


title: RNA_Rec_B36934_Tram_rep1

description: Library name: RNA_Rec_B36934_Tram_rep1


title: SVZ NSC lineage cell, OB rep1 [OB1_588443]


title: SVZ NSC lineage cell, OB rep1 [OB1_588431]


title: RNA_Rec_B36934_IFNGandTram_rep1

description: Library name: RNA_Rec_B36934_IFNGandTram_rep1


title: RNA_Rec_B36934_IFNGandTram_rep2

description: Library name: RNA_Rec_B36934_IFNGandTram_rep2


title: SVZ NSC lineage cell, OB rep1 [OB1_588429]


title: Spc Cells, H3K4me3, Dnmt3CKO/KO, rep1


title: RNA_Rec_B36934_IFNG_rep3

description: Library name: RNA_Rec_B36934_IFNG_rep3


title: ProSpg Cells, H3K9me3,  rep2


title: RNA_Rec_B36934_IFNGandTram_rep3

description: Library name: RNA_Rec_B36934_IFNGandTram_rep3


title: RNA_Rec_B36934_IFNG_rep1

description: Library name: RNA_Rec_B36934_IFNG_rep1


title: SVZ NSC lineage cell, OB rep1 [OB1_588421]


title: SVZ NSC lineage cell, OB rep1 [OB1_588423]


title: ProSpg Cells, H3K9me2,  rep2


title: RNA_Rec_B36934_IFNG_rep2

description: Library name: RNA_Rec_B36934_IFNG_rep2


title: RNA_Prim_B92_Vehicle_rep2

description: Library name: RNA_Prim_B92_Vehicle_rep2


title: ProSpg Cells, H3K4me3,  rep2


title: RNA_Prim_B92_Vehicle_rep1

description: Library name: RNA_Prim_B92_Vehicle_rep1


title: SVZ NSC lineage cell, OB rep1 [OB1_588419]


title: RNA_Prim_B92_Vehicle_rep3

description: Library name: RNA_Prim_B92_Vehicle_rep3


title: ATAC_Prim_B92_Vehicle_rep2

description: Library name: ATAC_Prim_B92_Vehicle_rep2


title: ProSpg Cells, H3K27me3,  rep1


title: RNA_Prim_B92_Tram_rep1

description: Library name: RNA_Prim_B92_Tram_rep1


title: SVZ NSC lineage cell, OB rep1 [OB1_588415]


title: RNA_Rec_B36934_Tram_rep3

description: Library name: RNA_Rec_B36934_Tram_rep3


title: RNA_Prim_B92_Tram_rep3

description: Library name: RNA_Prim_B92_Tram_rep3


title: SVZ NSC lineage cell, OB rep1 [OB1_588411]


title: SVZ NSC lineage cell, OB rep1 [OB1_588417]


title: ProSpg Cells, H3K9me2,  rep1


title: RNA_Prim_B92_IFNGandTram_rep3

description: Library name: RNA_Prim_B92_IFNGandTram_rep3


title: ProSpg Cells, H3K9me3,  rep1


title: ProSpg Cells, H3K4me3,  rep1


title: ProSpg Cells, H3K27me3,  rep2


title: RNA_Prim_B92_IFNGandTram_rep1

description: Library name: RNA_Prim_B92_IFNGandTram_rep1


title: SVZ NSC lineage cell, OB rep1 [OB1_588433]


title: RNA_Prim_B92_IFNGandTram_rep2

description: Library name: RNA_Prim_B92_IFNGandTram_rep2


title: RNA_Prim_B92_IFNG_rep3

description: Library name: RNA_Prim_B92_IFNG_rep3


title: SVZ NSC lineage cell, OB rep1 [OB1_588409]


title: SVZ NSC lineage cell, OB rep1 [OB1_588407]


title: Spg Cells, IgG, Dnmt3CKO/KO, rep2

value: Spermatogonia