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Direct Comparative Analysis of 10X Genomics Chromium and Smart-seq2

Single cell RNA sequencing (scRNA-seq) is widely used for profiling transcriptomes of individual cells. The droplet-based 10X Genomics Chromium (10X) approach and the plate-based Smart-seq2 full-length method are two frequently-used scRNA-seq platforms, yet there are only a few thorough and systematic comparisons of their advantages and limitations. Here, by directly comparing the scRNA-seq data by the two platforms from the same samples of CD45- cells, we systematically evaluated their features using a wide spectrum of analysis. Smart-seq2 detected more genes in a cell, especially low abundance transcripts as well as alternatively spliced transcripts, but captured higher proportion of mitochondrial genes. The composite of Smart-seq2 data also resembled bulk RNA-seq data better. For 10X-based data, we observed higher noise for mRNA in the low expression level. Despite the poly(A) enrichment, approximately 10-30% of all detected transcripts by both platforms were from non-coding genes, with lncRNA accounting for a higher proportion in 10X. 10X-based data displayed more severe dropout problem, especially for genes with lower expression levels. However, 10X-data can better detect rare cell types given its ability to cover a large number of cells. In addition, each platform detected different sets of differentially expressed genes between cell clusters, indicating the complementary nature of these technologies. Our comprehensive benchmark analysis offers the basis for selecting the optimal scRNA-seq strategy based on the objectives of each study.

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Data access policy of sequencing data from BIOPIC, Peking University.The DATA ACCESS AGREEMENT is provided at https://github.com/zhangyybio/single-T-cell-data-access. Applicants can request access to the data by directly downloading it or by sending an email to cancerpku@pku.edu.cn. The process that is used to approve an application includes verifying the institution, participants and research purposes of the application, and the authorization by EGA. In general this process will take about two weeks. In principal, any academic research institutions complying with the laws and bioethic regulation policies of China will be approved.

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
EGAS00001003973 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
EGAF00002831277 fq.gz 169.3 MB
EGAF00002831278 fq.gz 205.2 MB
EGAF00002831279 fq.gz 216.6 MB
EGAF00002831280 fq.gz 264.4 MB
EGAF00002831281 fq.gz 303.7 MB
EGAF00002831282 fq.gz 343.6 MB
EGAF00002831283 fq.gz 235.7 MB
EGAF00002831284 fq.gz 281.7 MB
EGAF00002831285 fq.gz 321.9 MB
EGAF00002831286 fq.gz 385.8 MB
EGAF00002831287 fq.gz 334.3 MB
EGAF00002831288 fq.gz 403.8 MB
EGAF00002831289 fq.gz 213.7 MB
EGAF00002831290 fq.gz 257.9 MB
EGAF00002831291 fq.gz 253.4 MB
EGAF00002831292 fq.gz 304.5 MB
EGAF00002831293 fq.gz 226.9 MB
EGAF00002831294 fq.gz 270.6 MB
EGAF00002831295 fq.gz 237.4 MB
EGAF00002831296 fq.gz 277.8 MB
EGAF00002831297 fq.gz 272.7 MB
EGAF00002831298 fq.gz 340.3 MB
EGAF00002831299 fq.gz 225.4 MB
EGAF00002831300 fq.gz 265.2 MB
EGAF00002831301 fq.gz 195.7 MB
EGAF00002831302 fq.gz 231.8 MB
EGAF00002831303 fq.gz 214.5 MB
EGAF00002831304 fq.gz 254.1 MB
EGAF00002831305 fq.gz 239.5 MB
EGAF00002831306 fq.gz 282.8 MB
EGAF00002831307 fq.gz 230.3 MB
EGAF00002831308 fq.gz 272.3 MB
EGAF00002831309 fq.gz 224.3 MB
EGAF00002831310 fq.gz 273.0 MB
EGAF00002831311 fq.gz 212.1 MB
EGAF00002831312 fq.gz 256.5 MB
EGAF00002831313 fq.gz 230.5 MB
EGAF00002831314 fq.gz 280.7 MB
EGAF00002831315 fq.gz 256.6 MB
EGAF00002831316 fq.gz 314.0 MB
EGAF00002831317 fq.gz 244.4 MB
EGAF00002831318 fq.gz 297.9 MB
EGAF00002831319 fq.gz 218.7 MB
EGAF00002831320 fq.gz 267.1 MB
EGAF00002831321 fq.gz 206.0 MB
EGAF00002831322 fq.gz 251.0 MB
EGAF00002831323 fq.gz 196.3 MB
EGAF00002831324 fq.gz 222.4 MB
EGAF00002831325 fq.gz 221.7 MB
EGAF00002831326 fq.gz 268.6 MB
EGAF00002831327 fq.gz 251.6 MB
EGAF00002831328 fq.gz 308.1 MB
EGAF00002831329 fq.gz 272.6 MB
EGAF00002831330 fq.gz 327.7 MB
EGAF00002831331 fq.gz 286.7 MB
EGAF00002831332 fq.gz 342.7 MB
EGAF00002831333 fq.gz 208.8 MB
EGAF00002831334 fq.gz 253.5 MB
EGAF00002831335 fq.gz 269.5 MB
EGAF00002831336 fq.gz 327.3 MB
EGAF00002831337 fq.gz 239.0 MB
EGAF00002831338 fq.gz 289.7 MB
EGAF00002831339 fq.gz 215.6 MB
EGAF00002831340 fq.gz 258.9 MB
EGAF00002831341 fq.gz 286.1 MB
EGAF00002831342 fq.gz 343.0 MB
EGAF00002831343 fq.gz 231.7 MB
EGAF00002831344 fq.gz 279.3 MB
EGAF00002831345 fq.gz 265.0 MB
EGAF00002831346 fq.gz 305.1 MB
EGAF00002831347 fq.gz 255.0 MB
EGAF00002831348 fq.gz 295.6 MB
EGAF00002831349 fq.gz 175.4 MB
EGAF00002831350 fq.gz 206.2 MB
EGAF00002831351 fq.gz 266.4 MB
EGAF00002831352 fq.gz 319.2 MB
EGAF00002831353 fq.gz 230.9 MB
EGAF00002831354 fq.gz 272.8 MB
EGAF00002831355 fq.gz 245.8 MB
EGAF00002831356 fq.gz 289.3 MB
EGAF00002831357 fq.gz 307.2 MB
EGAF00002831358 fq.gz 368.1 MB
EGAF00002831359 fq.gz 239.5 MB
EGAF00002831360 fq.gz 288.5 MB
EGAF00002831361 fq.gz 255.2 MB
EGAF00002831362 fq.gz 308.5 MB
EGAF00002831363 fq.gz 237.0 MB
EGAF00002831364 fq.gz 285.5 MB
EGAF00002831365 fq.gz 241.5 MB
EGAF00002831366 fq.gz 294.1 MB
EGAF00002831367 fq.gz 264.4 MB
EGAF00002831368 fq.gz 317.4 MB
EGAF00002831369 fq.gz 256.9 MB
EGAF00002831370 fq.gz 310.1 MB
EGAF00002831371 fq.gz 217.3 MB
EGAF00002831372 fq.gz 262.3 MB
EGAF00002831373 fq.gz 281.4 MB
EGAF00002831374 fq.gz 335.5 MB
EGAF00002831375 fq.gz 233.0 MB
EGAF00002831376 fq.gz 278.9 MB
EGAF00002831377 fq.gz 284.1 MB
EGAF00002831378 fq.gz 335.5 MB
EGAF00002831379 fq.gz 236.9 MB
EGAF00002831380 fq.gz 269.6 MB
EGAF00002831381 fq.gz 303.9 MB
EGAF00002831382 fq.gz 364.0 MB
EGAF00002831383 fq.gz 318.7 MB
EGAF00002831384 fq.gz 378.8 MB
EGAF00002831385 fq.gz 308.6 MB
EGAF00002831386 fq.gz 375.3 MB
EGAF00002831387 fq.gz 279.5 MB
EGAF00002831388 fq.gz 340.6 MB
EGAF00002831389 fq.gz 292.2 MB
EGAF00002831390 fq.gz 357.7 MB
EGAF00002831391 fq.gz 221.3 MB
EGAF00002831392 fq.gz 264.8 MB
EGAF00002831393 fq.gz 289.6 MB
EGAF00002831394 fq.gz 347.5 MB
EGAF00002831395 fq.gz 230.4 MB
EGAF00002831396 fq.gz 288.9 MB
EGAF00002831397 fq.gz 271.2 MB
EGAF00002831398 fq.gz 333.9 MB
EGAF00002831399 fq.gz 228.9 MB
EGAF00002831400 fq.gz 277.9 MB
EGAF00002831401 fq.gz 193.4 MB
EGAF00002831402 fq.gz 234.2 MB
EGAF00002831403 fq.gz 248.9 MB
EGAF00002831404 fq.gz 299.7 MB
EGAF00002831405 fq.gz 234.4 MB
EGAF00002831406 fq.gz 275.2 MB
EGAF00002831407 fq.gz 413.6 MB
EGAF00002831408 fq.gz 479.0 MB
EGAF00002831409 fq.gz 229.2 MB
EGAF00002831410 fq.gz 269.7 MB
EGAF00002831411 fq.gz 261.5 MB
EGAF00002831412 fq.gz 318.4 MB
EGAF00002831413 fq.gz 271.5 MB
EGAF00002831414 fq.gz 322.3 MB
EGAF00002831415 fq.gz 239.5 MB
EGAF00002831416 fq.gz 289.8 MB
EGAF00002831417 fq.gz 282.6 MB
EGAF00002831418 fq.gz 346.8 MB
EGAF00002831419 fq.gz 270.4 MB
EGAF00002831420 fq.gz 326.4 MB
EGAF00002831421 fq.gz 290.6 MB
EGAF00002831422 fq.gz 341.5 MB
EGAF00002831423 fq.gz 268.2 MB
EGAF00002831424 fq.gz 326.0 MB
EGAF00002831425 fq.gz 230.0 MB
EGAF00002831426 fq.gz 283.6 MB
EGAF00002831427 fq.gz 247.1 MB
EGAF00002831428 fq.gz 320.5 MB
EGAF00002831429 fq.gz 315.0 MB
EGAF00002831430 fq.gz 386.0 MB
EGAF00002831431 fastq.gz 8.3 GB
EGAF00002831432 fastq.gz 9.9 GB
156 Files (60.9 GB)