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Sample GSM4471648 Query DataSets for GSM4471648
Status Public on Jul 23, 2020
Title HCT-116_SP1-HyPBase_scCC
Sample type SRA
Source name HCT-116
Organism Homo sapiens
Characteristics cell line: HCT-116
tissue: colorectal cancer
Treatment protocol HCT-116 cells were transfected using Neon electroporation with the aforementioned settings. Each replicate for electroporation was comprised of 2e6 cells. For single cell calling cards analysis of SP1 binding in HCT-116 cells, we transfected four replicates each with 5 µg PB-SRT-Puro and 5 µg SP1-HyPBase. These libraries were not mixed. We used the demultiplexed data from the cell line mixing experiment with HyPBase as controls. Cells were cultured independently and mixed immediately prior to generating single cell emulsions. All cells were allowed to recover for 24 hours before undergoing puromycin selection. A negative control replicate, transfected only with PB-SRT-Puro, was treated identically in parallel. Replicates were harvested once the negative control cells had died.
Growth protocol Cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% of either penicillin-streptomycin or antibiotic-antimycotic. Cells were grown at 37ºC with 5% carbon dioxide (CO2). Media was replenished every 2 days.
Extracted molecule polyA RNA
Extraction protocol Single cell RNA-seq libraries were prepared using 10x Genomics’ Chromium Single Cell 3’ Library and Gel Bead Kit. Each replicate was targeted for recovery of 6,000 cells. Library preparation followed a modified version of the manufacturer’s protocol. We prepared the Single Cell Master Mix without RT Primer, replacing it with an equivalent volume of Low TE Buffer. Gel-in-emulsion (GEM) generation and GEM-RT incubation proceeded as instructed. At the end of Post GEM-RT cleanup, we added 36.5 µl Elution Solution I and transferred 36 µl of the eluted sample to a new tube (instead of 35.5 µl and 35 µl, respectively). The eluate was split into two 18 µl aliquots and kept at –20ºC until ready for further processing. One fraction was kept for single cell calling cards library preparation, while the other half was further processed into a single cell RNA-seq library.
To amplify self-reporting transcripts from single cell RNA-seq libraries, we took 9 µl of RT product (the other half was kept in reserve) and added it to 25 µl Kapa HiFi HotStart ReadyMix and 15 µl ddH2O. We then prepared a PCR primer cocktail comprising 5 µl of 100 µM Bio_Illumina_Seq1_scCC_10X_3xPT primer, 5 µl of 100 µM Bio_Long_PB_LTR_3xPT, and 10 µl of 10 mM Tris-HCl, 0.1 mM EDTA buffer. One µl of this cocktail was added to the PCR mixture and placed in a thermocycler. Thermocycling settings were as follows: 98ºC for 3 minutes; 20-22 cycles of 98ºC for 20 seconds–67ºC for 30 seconds–72ºC for 5 minutes; 72ºC for 10 minutes; 4ºC forever. PCR purification was performed with 30 µl AMPure XP beads (0.6x ratio) as described previously. The resulting library was quantitated on an Agilent TapeStation 4200 System using the High Sensitivity D5000 ScreenTape. Single cell calling card library preparation was performed using the Nextera Mate Pair Sample Prep Kit with modifications to the manufacturer’s protocol. The library was circularized by bringing 300 fmol (approximately 200 ng) of DNA up to a final volume of 268 µl with ddH2O, then adding 30 µl Circularization Buffer 10x and 2 µl Circularization Ligase (final concentration: 1 nM). This reaction was incubated overnight (12-16 hours) at 30ºC. After removal of linear DNA (following manufacturer’s instructions), we sheared the library on a Covaris E220 Focused-ultrasonicator with the following settings–peak power intensity: 200; duty factor: 20%; cycles per burst: 200; time: 40 seconds; temperature: 6ºC. The library preparation was performed per manufacturer’s instructions until adapter ligation. We designed custom adapters (Table S5) so that the standard Illumina sequencing primers would not interfere with our library. Adapters were prepared by combining 4.5 µl of 100 µM scCC_P5_adapter, 4.5 µl of 100 µM scCC_P7_adapter, and 1 µl of NEBuffer 2, then heating in a thermocycler at 95ºC for 5 minutes, then holding at 70ºC for 15 minutes, then ramping down at 1% until it reached 25ºC, holding at that temperature for 5 minutes, before keeping at 4ºC forever. One microliter of this custom adapter mix was used in place of the manufacturer’s recommended DNA Adapter Index. The ligation product was cleaned per manufacturer’s instructions. For the final PCR, the master mix was created by combining 20 µl Enhanced PCR Mix with 28 µl of ddH2O and 1 µl each of 25 µM scCC_P5_primer and 25 µM scCC_P7_primer. This was then added to the streptavidin bead-bound DNA and amplified under the following conditions: 98ºC for 30 seconds; 15 cycles of: 98ºC for 10 seconds–60ºC for 30 seconds–72ºC for 2 minutes; 72ºC for 5 minutes; 4ºC forever. All of the PCR supernatant was transferred to a new tube and purified with 35 µl (0.7x) AMPure XP beads following manufacturer’s instructions. The final library was eluted in 25 µl Elution Buffer and quantitated on an Agilent TapeStation 4200 System using the High Sensitivity D1000 ScreenTape.
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina NextSeq 500
Description Single cell calling cards library
SRRs represent biological replicates.
Data processing Read 1 sequenced the cell barcode and unique molecular index of each self-reporting transcript. Read 2 began with GGTTAA (end of the piggyBac terminal repeat and insertion site motif) before continuing into the genome. Reads containing this exact hexamer were trimmed using cutadapt with the following settings: -g "^GGTTAA" --minimum-length 1 --discard-untrimmed -e 0 --no-indels. Reads passing this filter were then trimmed of any trailing P7 adapter sequence, again using cutadapt and with the following settings: -a "AGAGACTGGCAAGTACACGTCGCACTCACCATGANNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG" --minimum-length 1. Reads passing these filters were aligned using 10x Genomics’ cellranger with the following settings: --expect-cells=6000 --nosecondary --chemistry=SC3Pv2 --localcores=16 --localmem=30. This workflow also managed barcode validation and collapsing of UMIs. Aligned reads were validated by verifying that they mapped adjacent to TTAA tetramers. Reads were then converted to calling card format (.ccf.txt). Finally, to minimize the presence of intermolecular artifacts, we required that each insertion must have been tagged by at least two different UMIs. We used the set of validated cell barcodes from each scRNA-seq library to demultiplex library-specific barcoded insertions from the scCC data. This approach requires no shared cell barcodes between individual scCC (and scRNA-seq) libraries. As a result, we excluded insertions from non-unique cell barcodes, which represented a very small number of total cells lost (< 1% per multiplexed library).
Genome_build: hg38
Supplementary_files_format_and_content: BAM files contain aligned and annotated calling card reads. Barcode files contain validated single cell barcodes. ccf.txt files contain processed calling card data. Peaks file provides details on regions significantly enriched for calling card insertions. describes calling card-specific BAM tags.
Submission date Apr 10, 2020
Last update date Jul 23, 2020
Contact name Robi D Mitra
Organization name Washington University in St. Louis
Department Genetics
Street address 4515 McKinley Ave
City St. Louis
State/province Missouri
ZIP/Postal code 63143
Country USA
Platform ID GPL18573
Series (1)
GSE148448 Self-reporting transposons enable simultaneous readout of gene expression and transcription factor binding in single cells
BioSample SAMN14573313
SRA SRX8094413

Supplementary file Size Download File type/resource
GSM4471648_HCT-116_SP1-HyPBase_scCC.bam 374.8 Mb (ftp)(http) BAM
GSM4471648_HCT-116_SP1-HyPBase_scCC.ccf.txt.gz 975.9 Kb (ftp)(http) TXT
GSM4471648_HCT-116_SP1-HyPBase_scCC_barcodes.txt.gz 110.4 Kb (ftp)(http) TXT
GSM4471648_HCT-116_SP1-HyPBase_scCC_peaks.tsv.gz 147.5 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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