Single-cell atlas of the developing brain to investigate the cellular origins of pediatric brain tumors

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Dataset ID	Description	Technology	Samples
EGAD00001005128	We profiled two human fetal brainstem specimens at 17 and 19 post-conception weeks by single-cell RNA-seq using 10X Chromium Single Cell 3'. The BAM files are provided.	Illumina HiSeq 4000	2
EGAD00001005129	We profiled 11 patient tumor samples by single-cell and single-nuclei RNA-seq using 10X Chromium 3'. These include samples from the following entities: WNT-subtype medulloblastoma (N=3), embryonal tumors with multilayered rosettes (N=3), and atypical teratoid-rhabdoid tumors (N=5). The BAM files are provided.	Illumina HiSeq 4000 unspecified	11
EGAD00001005130	We profiled 43 normal human adult brain and 11 normal human fetal brain specimens by bulk RNA-seq. The raw fastqs are provided.	unspecified	54
EGAD00001005131	We profiled 186 patient tumor samples by bulk RNA-seq. These includes 38 embryonal brain tumors, 101 high-grade gliomas, 24 low-grade gliomas, 10 medulloblastoma and 13 matched normals. The raw fastqs are provided.	Illumina HiSeq 2000 Illumina HiSeq 2500 Illumina HiSeq 4000 unspecified	186

Publications	Citations
Stalled developmental programs at the root of pediatric brain tumors. Jessa S, Blanchet-Cohen A, Krug B, Vladoiu M, Coutelier M, Faury D, Poreau B, De Jay N, Hébert S, Monlong J, Farmer WT, Donovan LK, Hu Y, McConechy MK, Cavalli FMG, Mikael LG, Ellezam B, Richer M, Allaire A, Weil AG, Atkinson J, Farmer JP, Dudley RWR, Larouche V, Crevier L, Albrecht S, Filbin MG, Sartelet H, Lutz PE, Nagy C, Turecki G, Costantino S, Dirks PB, Murai KK, Bourque G, Ragoussis J, Garzia L, Taylor MD, Jabado N, Kleinman CL. Nat Genet 51: 2019 1702-1713	200
Epigenomic programming in early fetal brain development. Li L, Maire CL, Bilenky M, Carles A, Heravi-Moussavi A, Hong C, Tam A, Kamoh B, Cho S, Cheung D, Li I, Wong T, Nagarajan RP, Mungall AJ, Moore R, Wang T, Kleinman CL, Jabado N, Jones SJ, Marra MA, Ligon KL, Costello JF, Hirst M. Epigenomics 12: 2020 1053-1070	9
Histone H3.3G34-Mutant Interneuron Progenitors Co-opt PDGFRA for Gliomagenesis. Chen CCL, Deshmukh S, Jessa S, Hadjadj D, Lisi V, Andrade AF, Faury D, Jawhar W, Dali R, Suzuki H, Pathania M, A D, Dubois F, Woodward E, Hébert S, Coutelier M, Karamchandani J, Albrecht S, Brandner S, De Jay N, Gayden T, Bajic A, Harutyunyan AS, Marchione DM, Mikael LG, Juretic N, Zeinieh M, Russo C, Maestro N, Bassenden AV, Hauser P, Virga J, Bognar L, Klekner A, Zapotocky M, Vicha A, Krskova L, Vanova K, Zamecnik J, Sumerauer D, Ekert PG, Ziegler DS, Ellezam B, Filbin MG, Blanchette M, Hansford JR, Khuong-Quang DA, Berghuis AM, Weil AG, Garcia BA, Garzia L, Mack SC, Beroukhim R, Ligon KL, Taylor MD, Bandopadhayay P, Kramm C, Pfister SM, Korshunov A, Sturm D, Jones DTW, Salomoni P, Kleinman CL, Jabado N. Cell 183: 2020 1617-1633.e22	121
Failure of human rhombic lip differentiation underlies medulloblastoma formation. Hendrikse LD, Haldipur P, Saulnier O, Millman J, Sjoboen AH, Erickson AW, Ong W, Gordon V, Coudière-Morrison L, Mercier AL, Shokouhian M, Suárez RA, Ly M, Borlase S, Scott DS, Vladoiu MC, Farooq H, Sirbu O, Nakashima T, Nambu S, Funakoshi Y, Bahcheli A, Diaz-Mejia JJ, Golser J, Bach K, Phuong-Bao T, Skowron P, Wang EY, Kumar SA, Balin P, Visvanathan A, Lee JJY, Ayoub R, Chen X, Chen X, Mungall KL, Luu B, Bérubé P, Wang YC, Pfister SM, Kim SK, Delattre O, Bourdeaut F, Doz F, Masliah-Planchon J, Grajkowska WA, Loukides J, Dirks P, Fèvre-Montange M, Jouvet A, French PJ, Kros JM, Zitterbart K, Bailey SD, Eberhart CG, Rao AAN, Giannini C, Olson JM, Garami M, Hauser P, Phillips JJ, Ra YS, de Torres C, Mora J, Li KKW, Ng HK, Poon WS, Pollack IF, López-Aguilar E, Gillespie GY, Van Meter TE, Shofuda T, Vibhakar R, Thompson RC, Cooper MK, Rubin JB, Kumabe T, Jung S, Lach B, Iolascon A, Ferrucci V, de Antonellis P, Zollo M, Cinalli G, Robinson S, Stearns DS, Van Meir EG, Porrati P, Finocchiaro G, Massimino M, Carlotti CG, Faria CC, Roussel MF, Boop F, Chan JA, Aldinger KA, Razavi F, Silvestri E, McLendon RE, Thompson EM, Ansari M, Garre ML, Chico F, Eguía P, Pérezpeña M, Morrissy AS, Cavalli FMG, Wu X, Daniels C, Rich JN, Jones SJM, Moore RA, Marra MA, Huang X, Reimand J, Sorensen PH, Wechsler-Reya RJ, Weiss WA, Pugh TJ, Garzia L, Kleinman CL, Stein LD, Jabado N, Malkin D, Ayrault O, Golden JA, Ellison DW, Doble B, Ramaswamy V, Werbowetski-Ogilvie TE, Suzuki H, Millen KJ, Taylor MD. Nature 609: 2022 1021-1028	96
Glioblastoma heterogeneity at single cell resolution. Eisenbarth D, Wang YA. Oncogene 42: 2023 2155-2165	97
Heterogeneity and tumoral origin of medulloblastoma in the single-cell era. Sheng H, Li H, Zeng H, Zhang B, Lu Y, Liu X, Xu Z, Zhang J, Zhang L. Oncogene 43: 2024 839-850	14
A group 3 medulloblastoma stem cell program is maintained by OTX2-mediated alternative splicing. Saulnier O, Zagozewski J, Liang L, Hendrikse LD, Layug P, Gordon V, Aldinger KA, Haldipur P, Borlase S, Coudière-Morrison L, Cai T, Martell E, Gonzales NM, Palidwor G, Porter CJ, Richard S, Sharif T, Millen KJ, Doble BW, Taylor MD, Werbowetski-Ogilvie TE. Nat Cell Biol 26: 2024 1233-1246	5
ETMR stem-like state and chemo-resistance are supported by perivascular cells at single-cell resolution. de Faria FW, Riedel NC, Münter D, Interlandi M, Göbel C, Altendorf L, Richter M, Melcher V, Thomas C, Roy R, Schoof M, Bedzhov I, Moreno N, Graf M, Hotfilder M, Holdhof D, Hartmann W, Bruns AK, Brentrup A, Liesche-Starnecker F, Maerkl B, Sandmann S, Varghese J, Dugas M, Pinto PH, Balbach ST, Lu IN, Rossig C, Soehnlein O, Canak A, Ebinger M, Schuhmann M, Schittenhelm J, Frühwald MF, Schüller U, Albert TK, Walter C, Bruder JM, Kerl K. Nat Commun 16: 2025 5394	1