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Sample GSM2935201 Query DataSets for GSM2935201
Status Public on May 17, 2018
Title Run1751
Sample type SRA
Source name Fetal kidney
Organism Homo sapiens
Characteristics fetal age: 105 days
tissue: kidney
Extracted molecule total RNA
Extraction protocol All tissues were shipped overnight in Belzer’s solution at 4 degrees Celsius and were processed immediately upon arrival to the laboratory, as follows. One kidney was dissected in ice-cold PBS and finely minced in a petri dish on ice using razor blades. About 20 mg of tissue were added to 1 ml of cold active protease solution (PBS, 10 mg of Bacillus Licheniformis protease [Sigma, #P5380], 5 mM CaCl2, 20 U DNAse I [Roche, #4716728001]). The tissue was incubated in a 2 ml reaction tube for 15-20 min on a slow moving shaker (nutator) in a coldroom at 4°C with repeated trituration steps for 20 seconds every 5 minutes. Single cell dissociation was confirmed with a microscope. The dissociation was stopped with 1 ml ice cold PBS supplemented with 10% fetal bovine serum (FBS). Afterwards the cells were immediately pelleted at 300x g for 5 min at 4°C. Subsequently, the supernatant was discarded and cells were suspended in 2 ml PBS/10%FBS and pelleted again at 300x g for 5 min at 4°C. Then cells were suspended in PBS/0.01%BSA and pelleted again (300x g for 5 min at 4°C), suspended in 1 ml PBS/0.01%BSA, and passed through a 30 µM filter mesh (Miltenyi MACS smart strainer). Viability was then investigated with the Trypan-blue exclusion test and cell concentration was determined with a hemocytometer and adjusted to 200,000 cells/ml for Drop-seq.
Uniformly dispersed 1 nl-sized droplets were generated using self-built polydimethylsiloxane (PDMS) microfluidic co-flow devices on the basis of the AutoCAD design provided by the McCarroll group. The devices were treated with a water repellant solution (Aquapel) to create a hydrophobic channel surface. Drop-Seq runs followed closely the procedure published by Macosko et al. (Online Dropseq protocol v. 3.1 Barcoded beads (ChemGenes Corp., Wilmington, MA), suspended in lysis buffer, were co-flown with a single cell suspension and a droplet generation mineral oil (QX200, Bio-Rad Laboratories). Resulting droplets were collected in a 50 ml tube and immediately disrupted after adding 30 ml high-salt saline-sodium citrate buffer (6xSSC) and 1 ml perfluorooctanol. Subsequently, captured mRNA’s were reverse transcribed for 2 hours using 2,000 U of the Maxima H Minus Reverse Transcriptase (ThermoFisher) followed by an exonuclease treatment for 45 minutes to remove unextended primers. After two washing steps with 6xSSC buffer about 70,000 remaining beads (60% of input beads) were aliquoted (5,000 beads per 50 µl reaction) and PCR-amplified (5 cycles at 65˚C and 12 cycles at 67˚C annealing temperature). Aliquots of each PCR reaction were pooled and double-purified using 0.5x volume of Agencourt AMPure XP beads (# A63881, Beckman Coulter) and finally eluted in 10 µl EB buffer. Quality and quantity of the amplified cDNAs were analyzed on a BioAnalyzer High Sensitivity DNA Chip (Agilent Technologies, Santa Clara, CA). About 600 pg cDNA was fragmented and amplified (17 cycles) to generate a next-generation sequencing library by using the Nextera XT DNA sample preparation kit (Illumina).
The libraries were purified, quantified (Agilent High sensitivity DNA chip), and then sequenced (paired end 26x115 bases) on the Illumina HiSeq2500 platform. Custom primer (5’-GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC-3’) was used for the first sequence read to identify all different cell barcodes und unique molecular identifier (UMI) sequences.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Description R1 contains the cell barcode, R2 contains mRNA read
Data processing The quality of the fastq files from the sequencer were first checked using FastQC (v0.11.4).
Sequence aligned using Star
Next, using the tools embedded in Picard tools (picard-tools-1.115) and the DropSeq analysis pipeline developed by the McCarroll lab (, the fastq files were processed and the data matrix table containing the gene expression of the barcoded cells was generated. Individual cells were labeled with barcodes, and transcripts within each cell were tagged with distinct UMIs (Unique Molecular Identifiers) in order to determine absolute transcript abundance.
Genome_build: GRCh38
Supplementary_files_format_and_content: Data matrix table is in text format
Submission date Jan 15, 2018
Last update date May 17, 2018
Contact name Rajasree Menon
Phone 7346159720
Organization name University of Michigan
Department Department of Computational Medicine and Bioinformatics
Street address 4544E, MSRB2, Catherine Street, University of Michigan
City Ann Arbor
State/province Michigan
ZIP/Postal code 48109
Country USA
Platform ID GPL11154
Series (1)
GSE109205 Single-cell analysis of progenitor cell dynamics and lineage specification of the human fetal kidney
BioSample SAMN08366477
SRA SRX3584963

Supplementary file Size Download File type/resource
GSM2935201_FetalKidney_Run1751_105days.txt.gz 2.8 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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