title: GSM4505175: Thymus 9 CD123+; Homo sapiens; RNA-Seq
library_construction_protocol: Single cells were captured into barcoded hydrogels using the 10X (Thymuses 1, 2, 3, and 7) or Indrops (Thymuses 4, 5) microfluidics platforms. For thymus 6, single cells were index sorted into a 96 well plate (two 96 well plates, 1 cell/ well) containing RNA extraction buffer (BD Precise WTA Single Cell Kit (BD Genomics, PN 634100, 96 well plates). Cell type information based on FACS for thymus 6 is provided as a csv file. Cell barcodes used for sequencing are provided as csv files for plate 1 (S1) and plate 2 (S2). RNA was extracted from FACS sorted CD34+CD7+CD1a-CD19-CD4-CD8-CD123+ cells for thymuses 8 (367 cells)  and 9 (600 cells) using the Arcturus picopure kit  and then used for making bulk RNA-Seq libraries. Single cell RNA-Seq libraries were prepared using the 10x Genomics Chromium Single Cell v2 kit (thymus 1), the 10x Genomics Chromium Single Cell v3.2 kit (thymuses 2,3,and 7), the Indrops protocol (Zilionis et al, Nature Protocols, 2017) (thymuses  4,5), or the BD Precise WTA Single Cell Kit (BD Genomics, PN 634100, thymus 6) . The indrops v3 and v2 protocols were used for Thymus 4 and thymus 5 respectively.Bulk RNA-Seq libraries (thymuses 8 and 9) were prepaered by extracting RNA using the Arcturus picopure RNA extraction kit followed by  libraray preparation using the The Smart-Seq V4 ultralow input RNA-Seq kit (Clontech) . Illumina Hiseq (Thymuses 1,3,7,8,and 9; 150 base pair paired end) or Nextseq500 (thymuses 2,4-6). The Nextseq high output (150 cycles,  thymus 2),  mid output kit (150 cycles,  thymus 6) , or high output  (75 cycles, thymuses 4 and 5) kits were used. For thymus 2, the cycles were distributed as read 1 (96 bases) and read 2 (28 bases). For thymus 4, cycles were distributed as read 1 (61 cycles, biological read), read 2 (8 cycles, first half of the gel barcode), read 3  (8 cycles, library index ), and  read 4 (14 cycles, the second half of the gel barcode, the UMI and a fraction of the polyA tail) (indrops v3). For thymus 5 cycles were distributed as read 1 (37 cycles, biological read), read 2 (51 cycles, metadata read),  and index read (6 cycles, library index) (indrops v2). For thymus 6 the cycles were distributed as read 1 (50 cycles) and read 2 (100 cycles).
attributes.tag: GEO Accession
attributes.value: GSM4505175