About file location

As the EGA is co-managed by the EMBL-EBI and CRG, files could be located in the UK and/or Spain, as indicated by their respective flags.

Alternatively, files could be located in one of the international Federated EGA nodes, as indicated next to the node's flag.
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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.

Request Access

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. To get the access to raw data, an agreement must be made first. Please fill in the form in https://github.com/zhangyybio/single-T-cell-data-access, and send me (cancerpku@pku.edu.cn) the document with signatures added. Particularly,in the page 4 of the agreement, table "Agreed for User Institution" should contain the signature of the person who can represent your institution, such as institution director

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