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cfMethyl-seq data (cfSort study) from serial plasma samples of NSCLC patients

The cfMethyl-Seq libraries of the serial plasma cfDNA samples from the four NSCLC patients were constructed following the standard protocol. 10 ng of cfDNA in the volume of 25 µl was used as input material. 5’-end dephosphorylation was done with 3 µl 10xCutSmart buffer and 2 µl quick CIP from NEB (Ipswich, MA) at 37 oC for 30 min then heat-inactivated at 80 oC for 5 min. The 3’-end blocking was done with 0.5 µl 10xCutSmart buffer, 3 µl 2.5 mM CoCl2, 1 µl terminal transferase (all from NEB), and 0.5 µl 1 mM ddGTP at 37 oC for 2 h followed by 75 oC for 20 min. The mixture was then purified with 2x AmpureXP beads (Beckman Coulter, Indianapolis, IN) and eluted in 21.5 µl RT-PCR grade water (Thermo-Fisher, Waltham, MA). Restriction digestion was done with 2.5 µl 10xCutSmart buffer and 1 µl MspI (NEB) for 18 h at 37  oC and 20 min at 65 oC . 0.5 µl 10xCutSmart buffer, 0.3 µl dACGTP mixture (100 mM dATP, 10 mM dCTP, 10 mM dGTP), 1 µl Klenow (exo-, 5U/µl, NEB) and 2.6 µl RT-PCR water, 0.6 µl 50 mM DTT (ThermoFisher) was added to the mixture for end repair and A-overhang addition with the program 30  oC for 20 min, 37 oC for 1 h and 75 oC for 20 min. Adapter ligation was then performed with 1 µl 10xThermoFisher HC T4 ligase buffer, 0.4 µl 100 mM ATP (ThermoFisher), 0.2 µl 50 mM DTT, 1 µl ThermoFisher HC T4 DNA ligase (30 Weiss Unit/µl), 5 ng home-made duplex UMI adapter with all the cytosines methylated (protocol adopted from Kennedy et al.) at 16 oC for 20 h and 65 oC for 20 min. Bisulfite conversion of the adapter-ligated product was carried out with QIAGEN EpiTect plus DNA bisulfite kit following their protocol for two rounds of conversion. The converted product was purified with Qiagen MinElute spin column and eluted with 20 µl RT-PCR water. PCR amplification was done using the NEBNext Multiplex Oligos for Illumina (2.5 µl of universal and index primer each) and 25 µl KAPA HiFi HotStart Uracil+ ReadyMix (Roche) with the following cycling conditions: 98  oC for 45 s, 15 cycles of 98  oC for 15 s, 60  oC for 30 s and 72  oC for 30 s, followed by a final extension at 72  oC for 5 min. The PCR product was purified with 1x AmpureXP beads and eluted with 30 µl EB buffer. DNA concentration was measured by Qubit 1xdsDNA HS assay. 5% TBE-UREA PAGE and bioanalyzer assay was performed as quality control on each library before sequencing.

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The data usage policy (cfSort study) for the RRBS and cfMethyl-Seq data

https://labs.dgsom.ucla.edu/zhou/files/view/docs/DAA_DAC_for_cfSort_study_EGAS00001007213.docx

Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.

Study ID Study Title Study Type
EGAS00001007213 Other

This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.

ID File Type Size Located in
EGAF00008074277 fastq.gz 4.7 GB
EGAF00008074278 fastq.gz 5.1 GB
EGAF00008074279 fastq.gz 4.6 GB
EGAF00008074280 fastq.gz 4.4 GB
EGAF00008074281 fastq.gz 4.9 GB
EGAF00008074282 fastq.gz 4.6 GB
EGAF00008074283 fastq.gz 6.0 GB
EGAF00008074284 fastq.gz 6.7 GB
EGAF00008074285 fastq.gz 6.7 GB
EGAF00008074286 fastq.gz 6.4 GB
EGAF00008074287 fastq.gz 7.8 GB
EGAF00008074288 fastq.gz 7.4 GB
EGAF00008074289 fastq.gz 5.7 GB
EGAF00008074290 fastq.gz 6.4 GB
EGAF00008074291 fastq.gz 6.6 GB
EGAF00008074292 fastq.gz 6.3 GB
EGAF00008074293 fastq.gz 8.2 GB
EGAF00008074294 fastq.gz 8.0 GB
EGAF00008074295 fastq.gz 7.2 GB
EGAF00008074296 fastq.gz 7.9 GB
EGAF00008074297 fastq.gz 6.8 GB
EGAF00008074298 fastq.gz 6.5 GB
EGAF00008074299 fastq.gz 7.0 GB
EGAF00008074300 fastq.gz 6.5 GB
24 Files (152.5 GB)