作者闷旧，Evil Genius
生活不易，且行且珍惜钧唐，指不定哪天就找不見這個(gè)人了忙灼，這個(gè)舉報(bào)速度，看來被人搞是注定的钝侠。
不知道大家怎么看WBG和BLG的半決賽该园。
今天我們更新方法，單細(xì)胞空間數(shù)據(jù)分析譜系追蹤帅韧。
知識(shí)積累
腫瘤的進(jìn)展是由癌細(xì)胞與其周圍微環(huán)境之間的動(dòng)態(tài)相互作用驅(qū)動(dòng)的里初。研究腫瘤的時(shí)空演化可以提供重要的見解，了解癌細(xì)胞內(nèi)部的變化和微環(huán)境的外部變化如何協(xié)同驅(qū)動(dòng)腫瘤進(jìn)展的不同階段忽舟。在這個(gè)過程中双妨，當(dāng)癌細(xì)胞積累遺傳和表觀遺傳改變時(shí)淮阐，微環(huán)境通過諸如空間限制、信號(hào)分子斥难、養(yǎng)分和氧氣有效性枝嘶、免疫滲透等因素施加選擇壓力。反過來哑诊，腫瘤生長重塑了周圍的微環(huán)境群扶，例如，通過重組細(xì)胞外基質(zhì)和改變浸潤間質(zhì)細(xì)胞的組成和狀態(tài)镀裤。
核心分析點(diǎn)：腫瘤的進(jìn)化動(dòng)力學(xué)及其在原生空間背景下的微環(huán)境組成竞阐。
整合腫瘤系統(tǒng)發(fā)育分析，研究腫瘤內(nèi)癌細(xì)胞的譜系關(guān)系暑劝，結(jié)合空間信息骆莹，為理解腫瘤微環(huán)境與進(jìn)展之間的相互作用提供了一個(gè)全面的框架。
空間組學(xué)方法進(jìn)一步闡明了基因組改變的空間分布如何導(dǎo)致克隆生長担猛、具有不同驅(qū)動(dòng)突變的亞克隆的分散幕垦、與免疫系統(tǒng)的相互作用以及轉(zhuǎn)移。
高分辨率空間轉(zhuǎn)錄組學(xué) + 譜系追蹤功能
計(jì)算工具使空間分解的癌細(xì)胞系統(tǒng)發(fā)育推理成為可能
空轉(zhuǎn)分辨率在腫瘤微環(huán)境的原生環(huán)境中建立癌癥細(xì)胞的譜系傅联，能夠探索同一腫瘤中越來越相關(guān)的亞克隆的空間定位先改。
空間轉(zhuǎn)錄組學(xué)揭示肺腺癌的生態(tài)系統(tǒng)
腫瘤亞克隆快速擴(kuò)張有助于形成缺氧區(qū)，降低癌細(xì)胞可塑性
亞克隆擴(kuò)增伴隨著免疫抑制和纖維化的微環(huán)境重塑
空間分辨的譜系揭示了原發(fā)腫瘤中引發(fā)轉(zhuǎn)移誘導(dǎo)位點(diǎn)的進(jìn)化
轉(zhuǎn)移性定植伴有膠原沉積和纖維化增加
為了實(shí)現(xiàn)這個(gè)分析蒸走，需要很多的準(zhǔn)備工作
convert: Convert the FASTQs into an unmapped BAM, while parsing any barcode and/or UMI sequences into BAM tags.
filter_bam: Filter reads with low-quality barcode and/or UMI sequences from the unmapped bam.
error_correct_cellbcs_to_whitelist**: For sequencing chemistries that have a predefined (cell) barcode whitelist, this steps perform correction of sequencing errors using this whitelist.
collapse: Collapse reads into UMIs by constructing one or more consensus sequences for each UMI using the set of reads with that UMI.
resolve: Resolve a single sequence for each UMI by choosing the most likely sequencing read to represent each UMI in a cell.
align: Align sequences to the reference target site using the Smith-Waterman local alignment algorithm.
call_alleles: Call alleles with respect to the reference target site and the alignment of a sequence, thereby reporting the set of mutations that a target site sequence contains.
error_correct_intbcs_to_whitelist: For experimental designs for which each target site vector molecule has a unique barcode (“intBC”), and the set of intBCs present in the sequenced sample are known beforehand, this step performs sequencing error correction of these intBCs to the provided whitelist.
error_correct_umis: Error-correct UMIs whose mutation data is identical and whose UMI barcode sequences are similar enough.
filter_molecule_table: Filter UMIs that have conflicting allele information, too few reads, or do not meet other quality control criteria.
call_lineages: Split up cells into clonal populations, based on their shared set of integration barcodes (intBCs).
