title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E12_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D9_MemorySeq384_2

status: Public on Feb 02 2022

type: SRA

city: Cambridge

first: Xiaojie

last: Qiu

state: MA

address: 455 Main St, Cambridge, MA

country: USA

institute: Whitehead Institute

description:
HL60_memory_seq.h5ad
NovaSeq 5000

library_source: transcriptomic

data_processing:
Library strategy: SLAM-seq
For the HL60 10x dataset, we followed the standard pipeline of kb-python to quantify the total, spliced and unspliced RNA. For the HL60 metabolic labeling based scRNA-seq experiment with clone tracing, we used the NASC-seq pipeline (https://github.com/sandberg-lab/NASC-seq) developed in to quantify the new and total RNA read counts.
For the scNT-seq experiment of the human hematopoiesis, we developed dynast (https://github.com/aristoteleo/dynast-release), an inclusive and efficient command-line toolkit for preprocessing data from metabolic labeling–based scRNA-seq experiments and quantifying the following four types of mRNA species: unspliced, spliced, labeled (or new), and total RNAs (details will be reported elsewhere). Samples from days 4 and 7 were each subjected to standard dynast runs, using human genome hg38 as the alignment reference. The resultant objects were first filtered to keep only high quality cells and then merged to obtain in total about 2,000 high-quality cells. This merged object was then used for all downstream analyses.
Genome_build: hg38
Supplementary_files_format_and_content: file format is h5ad/csv. For h5ad files, they include the spliced, unspliced, labeled and total RNA counts for each gene in each cell from our scSLAM-seq and scNT-seq experiment. Only spliced and unspliced RNA counts for each gene in each cell are available for the 10x dataset. For the edge_df.csv file, it is the clone linkage information between different cells, processed from the static barcodes.

molecule: total RNA

organism: Homo sapiens

extract_protocol: To facilitate lineage tracing in scSLAM-seq libraries, cellular barcodes (GBCs) were introduced using a lentiviral transduction strategy (Adamson et al., 2016). Given that the success of this experiment critically depended on the uniqueness of barcode sequence to each cell at the start of the experiment, i.e. low barcode collision rate, and the capture of clone cells (clones with the same barcodes) across different days, we used an experimental scheme in which the starting population of the HL60 cells were infected at a low (2%) multiplicity of infection (MOI). This scheme has two benefits: first, we obtained a small number of barcoded single cells (~2000 in 1 ml of media in each well of a 24-well plate) so that we could capture clone cells via plate-based SLAM-seq (scRNA-seq augmented by metabolic labeling) characterized of low throughput; second, co-culturing the small number of infected cells with a large population of uninfected cells enabled us to differentiate infected cells more conveniently, as a small number of cells are difficult to grow and differentiate. Single cells carrying barcodes and expressing the blue fluorescent protein (BFP) reporter were sorted (Sony SH800) at five timepoints, days 0, 1, 2, 3, and 5, during differentiation in the presence of ATRA. cDNA from single cells was prepared in a 96-well format as previously described (Tabula Muris Consortium, 2020) following alkylation and RNA cleanup (Erhard et al., 2019; Hendriks et al., 2019). Sequencing libraries were either reformatted into a 384-well format and prepared using TTP Mosquito automated liquid handlers, or in a 96- well format using a multichannel pipette. GBC sequencing libraries were prepared by dual PCR amplification to enrich for GBC cDNA and to add Illumina adapters and dual indexes complimentary to that cell's transcriptome sequencing library indexes. GBC sequencing libraries were spiked into transcriptome libraries at 1:10 and sequenced on the NextSeq or MiSeq platform (Illumina). Transcriptome libraries were sequenced separately using a NovaSeq5000 S2 300-cycle kit.

tag: cell line

tag: treatment

value: neutrophil lineage differentiation in the presence of  ATRA

tag: gender

value: female

tag: age

tag: ethnicity


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D9_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E13_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKK096

city: Verona

first: Alessandra

last: Dal Molin

address: Via Roveggia 43B

country: Italy

institute: Personal Genomics

description: rawcounts.txt

data_processing:
BCL to FASTQ file conversion has been performed using bcl2fastq v2.20
Trimming of miRNA sequencing adapter was performed with cutadapt version 1.18
Trimmed reads were aligned on the miRbase human hairpin database release 22.1 using SHRiMP version 2.2.3 with the following configurations: mode “mirna”, parameter “-Q”, “--strata” option.
The BEDTools suite version 2.27.0  was used to select overlapping mappings on miRNA hairpins with mature miRNAs. PCR duplicates filtering and UMI counts summarization was performed using a custom script.
Genome_build: miRbase human hairpin database release 22.1
Supplementary_files_format_and_content: txt file contains raw UMI counts

source_name: serum

extract_protocol:
Serum miRNAs were extracted using the miRNeasy Serum/Plasma Advanced kit (Qiagen) according to the manufacturer's instructions
Libraries were prepared using QIAseq miRNA Library kit (Qiagen) following the manufacturer’s instructions

tag: collection site

value: GOE

tag: phenotypic group

value: CTR


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D8_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKK100

description: rawcounts.txt


title: si-NC3_input

city: Shenyang

first: JiaPeng

last: Huang

address: No. 155 in Nanjing North Street

department: Department of Thyroid Surgery

country: China

institute: The First Hospital of China Medical University

data_processing:
Library strategy: MeRIP-Seq
Basecalls performed using CASAVA version 1.8.
MeRIP-seq reads were mapped to human genome by BWA-MEM software by default parameters except -T = 19
mRNAs were detected and annotated with CIRI software.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Methylated_RNA_sites.mRNA.xlsx: Excel format

source_name: K1 PTC cells

extract_protocol:
RNA extraction protocol.
Library construction protocol.

tag: cell type

value: Papillary thyroid cancer cell line

tag: sirna

tag: antibody


title: DKK106

description: rawcounts.txt


title: si-NC2_input


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E12_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D8_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKK095

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E10_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: si-FTO1_input

value: si-FTO


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E11_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKK102

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E11_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D6_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E10_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: D10 WT No Dox rep 1

city: Berkeley

first: Michael

last: Ly

address: 565 Li Ka Shing Center

institute: UC Berkeley

data_processing:
Sequencing data was converted into fastq format using the Illumina bcl2fastq software on the sequencing center's local linux server
Sequenced reads were trimmed using TrimGalore v0.4.4 at default settings except --stringency 3 and mapped onto the concatenated genome using STAR v2.7.1a.
For differential gene expression analysis, CuffDiff (CuffLinks v2.2.1) was used to compare two conditions (e.g. untreated versus dox-induced), using all three biological replicates from each condition. The default settings for CuffDiff were mostly used except -library-type fr-firststrand, -library-norm-method classic-fpkm, and -p 20. All genes with FPKM value of 0 were removed, and for genes with multiple transcript isoforms, only the most highly expressed transcript isoform was used for downstream analysis.
Prior to calculating fold-change, the FPKM value for each transcript was normalized to the sum of ERCC spike-in FPKM values from each condition to control for differences in library size.
Genome_build: hg19 concatenated with vaccinia virus (Western Reserve strain; NC_006998.1) genome and ERCC RNA spike-in sequence
Supplementary_files_format_and_content: All files contain FPKM and fold-change values, and some contain exon information for host genes.
Supplementary_files_format_and_content: D10_WT_InducibleCells.xlsx: abundance measurements of host transcripts, exon information, and their fold-change values upon D10 WT induction
Supplementary_files_format_and_content: D10_MUT_InducibleCells.xlsx: abundance measurements of host transcripts and their fold-change values upon D10 E144Q/E145Q induction
Supplementary_files_format_and_content: D9_D10_ActivityViralGenes.xlsx: abundance measurements of viral transcripts and their fold-change values reflecting D9 or D10 activity
Supplementary_files_format_and_content: MockvsWT_3hr.xlsx: abundance measurements of host transcripts and their fold-change values with WT VACV infection at 3 hpi relative to mock
Supplementary_files_format_and_content: MockvsWT_6hr.xlsx: abundance measurements of host transcripts and their fold-change values with WT VACV infection at 6 hpi relative to mock
Supplementary_files_format_and_content: MockvsWT_18hr.xlsx: abundance measurements of host transcripts and their fold-change values with WT VACV infection at 18 hpi relative to mock
Supplementary_files_format_and_content: MockvsdeltaD9_18hr.xlsx: abundance measurements of host transcripts and their fold-change values with deltaD9 VACV infection at 18 hpi relative to mock
Supplementary_files_format_and_content: MockvsD9muD10mu_18hr.xlsx: abundance measurements of host transcripts and their fold-change values with D9muD10mu VACV infection at 18 hpi relative to mock
Supplementary_files_format_and_content: deltaD9vsD9muD10mu_18hr.xlsx: abundance measurements of host transcripts, exon information, and their fold-change values with D9muD10mu VACV infection relative to deltaD9 VACV infection at 18 hpi. Reflects D10 activity on host transcripts during infection.
Supplementary_files_format_and_content: deltaD9vsD9muD10mu_18hr_viralvshost.xlsx: abundance measurements of host and viral transcripts, and their fold-change values with D9muD10mu VACV infection relative to deltaD9 VACV infection at 18 hpi. Reflects D10 activity on host vs viral transcripts.

source_name: Tissue culture

extract_protocol:
Total RNA was extracted from samples using TRIzol and treated with TURBO DNase. Afterwards, the RNA was isolated using RNA Clean & Concentrator - 5 kit, and 2μL of ERCC RNA spike-ins (1:100 diluted) was added to each sample.
RNA-Seq libraries were prepared using services provided by QB3 UC Berkeley. Illumina Ribo-Zero rRNA Removal Kits were used to deplete the RNA. Subsequent   library preparation steps of fragmentation, adapter ligation and cDNA synthesis were  done on the depleted RNA using the KAPA RNA HyperPrep kit (KK8540).   Truncated universal stub adapters were used for ligation, and indexed primers were  used during PCR amplification to complete the adapters and to enrich the libraries for  adapter-ligated fragments. Samples were checked for quality on an Agilent  Fragment Analyzer. Samples were then transferred to the Vincent J. Coates Genomics  Sequencing Laboratory (GSL), another QB3-Berkeley Core Research Facility at UC Berkeley,  where Illumina sequencing library molarity was measured with quantitative PCR with the Kapa  Biosystems Illumina Quant qPCR Kits on a BioRad CFX Connect thermal cycler. Libraries were then  pooled evenly by molarity and sequenced.

value: HEK293T cells

tag: genotype

value: Integrated doxycycline-inducible D10 WT gene using lentivirus

value: Untreated


title: si-FTO2_IP


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D8_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E10_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D6_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKK103

description: rawcounts.txt


title: DKK105

description: rawcounts.txt


title: si-FTO1_IP


title: DKK093

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E13_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D7_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: si-FTO3_IP


title: si-NC3_IP


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D5_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D7_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKK084

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D4_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: si-NC1_input


title: DKK089

description: rawcounts.txt


title: DKK087

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D7_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D4_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: si-NC2_IP


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D3_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D9_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D6_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D3_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKK081

description: rawcounts.txt


title: LC2.R.2: LC_2_Ad_RXDX_105_2

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

data_processing:
Illumina adapters were removed, along with the first 12 base pairs using BBDuk and reads <50bp after trimming were discarded
Reads were aligned and quantified using STAR (2.6.0a) to the Ensembl human transcriptome (hg38.p12, release 95)
Lowly abundant genes were removed as those <1 mean raw count or <1 mean count per million (CPM) across the dataset
Differential gene expression was calculated using the voom function in limma
Genome_build: GRCh38
Supplementary_files_format_and_content: Text file containing STAR gene count values

molecule: polyA RNA

growth_protocol: CUTO22 and CUTO32 cells were grown in RPMI with 10% fetal bovine serum. LC-2/Ad cells were grown in 50% RPMI + 50% HAMS F12 with 10% fetal bovine serum.

extract_protocol:
Qiagen Rneasy Mini Kit
NuGen Technologies Universal Plus mRNA Libray Kit
150bp single end reads, Illumina HiSeq 4000

treatment_protocol: Cells were treated with 100nM RXDX-105 for 24 hours or vehicle control (DMSO). Three biologic replicates were performed.


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D5_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D24_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D24_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D23_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D5_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D4_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKK075

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D2_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKK073

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D21_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D2_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D3_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D20_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: si-NC1_IP


title: DKK090

description: rawcounts.txt


title: DKK082

description: rawcounts.txt


title: DKK077

description: rawcounts.txt


title: DKK083

description: rawcounts.txt


title: C32.R.2: CUTO32_RXDX_105_2


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D2_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D1_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: LC2.R.3: LC_2_Ad_RXDX_105_3


title: LC2.R.1: LC_2_Ad_RXDX_105_1


title: DKK062

description: rawcounts.txt


title: DKK079

description: rawcounts.txt


title: LC2.D.2: LC_2_Ad_DMSO_2

value: DMSO


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D1_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKK074

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D21_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: LC2.D.1: LC_2_Ad_DMSO_1


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D23_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D22_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKK066

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D22_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D20_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D23_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: C32.D.2: CUTO32_DMSO_2


title: C32.R.3: CUTO32_RXDX_105_3


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D19_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKK049

description: rawcounts.txt


title: LC2.D.3: LC_2_Ad_DMSO_3


title: DKK067

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D19_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKK056

description: rawcounts.txt


title: C22.R.2: CUTO22_RXDX_105_2


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D1_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D21_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D19_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: C32.D.1: CUTO32_DMSO_1


title: C32.D.3: CUTO32_DMSO_3


title: C32.R.1: CUTO32_RXDX_105_1


title: C22.R.3: CUTO22_RXDX_105_3


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D17_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D17_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: C22.R.1: CUTO22_RXDX_105_1


title: DKK036

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D18_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKK037

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D20_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKK033

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D15_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: C22.D.3: CUTO22_DMSO_3


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D18_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKK044

description: rawcounts.txt


title: DKK046

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D15_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D18_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D16_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKK029

description: rawcounts.txt


title: C22.D.1: CUTO22_DMSO_1


title: C22.D.2: CUTO22_DMSO_2


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D16_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D17_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: H9C2 cells, HG-2

city: Wenzhou

first: guang

last: liang

state: Wenzhou

address: Wenzhou medical university of  higher education park  chashan town

department: School of Pharmaceutical Sciences

institute: Wenzhou Medical University

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter.
Then sequence quality was also verified using fastp. We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Homo sapiens GRCh38
The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare
StringTie was used to perform expression level for mRNAs by calculating FPKM
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: H9C2 cells

growth_protocol: Embryonic rat heart-derived H9C2 cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM; Gibco/BRL life 138 Technologies, Eggenstein, Germany) containing 1 g/L glucose.

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: H9C2 cells were transfected with FGFR1 siRNA. Cells were then exposed to 33 mM glucose (HG) for 8 hours.

value: Embryonic rat heart-derived cells

value: treated with HG (33 mM) for 8 hours

value: control


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D16_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D14_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKK030

description: rawcounts.txt


title: H9C2 cells, siFGFR1+HG-1

value: transfected with FGFR1 siRNA, then treated with HG (33 mM) for 8 hours

value: FGFR1 knockdown


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D13_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D15_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKK026

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D12_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKK025

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D14_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D13_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D14_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D13_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: H9C2 cells, siFGFR1+HG-2


title: H9C2 cells, Ctrl-1

value: untreated


title: DKK024

description: rawcounts.txt


title: DKK023

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D12_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D11_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D11_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D12_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C9_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: ICA CTRL

city: Farmington

first: Duomeng

last: Yang

address: 263 Farmington Avenue

institute: Uconn health

description: normal saline treatment  cardiac cells purified by Percoll

data_processing:
Libraries were sequenced on Illumina NovaSeq using paired-end 150bp (according to 10X Chromium Single Cell 3' protocol)
Sequences were aligned to Rnor6 using cellranger v2.2.0 pipeline
Gene expression data was processed with Seurat v2.3.4
Initial data filtering (minimum cells to express an included gene = 10, minium genes to be expressed in an included cell = 200)
Log-normalization of expression data
Cell annotations in metadata derived from shared nearest neighbor clustering
Genome_build: Rnor6
Supplementary_files_format_and_content: zipped, matrix market exchange format for raw transcript count matrices; csv files of single-cell metadata information

source_name: Rat heart

growth_protocol: The neonatal Sprague-Dawley rats (1-3 days) were deeply anesthetized with CO2 and the hearts were excised and washed in cold PBS to remove the blood. Heart tissues were minced into approximately 1mm3 masses and digested using 0.125% trypsin. (1) Cells were prepared using a modified Percoll gradient procedure described previously to enrich ICA cells.

extract_protocol:
Single-cell RNA-sequencing libraries were prepared using a Chromium Single Cell 3' Reagent Kit (10X Genomics, v2 kit) following the directions of the manufacturer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cells were treated with saline(control group) and lps (1ug/ml, 055:B strain) for 2h,After treatment, cells were digested by 0.125% trypsin with EDTA and collected in complete DMEM. The cell viability was up to more than 90% determined by a cell count system.

value: Intrinsic cardiac adrenergic (ICA) cells

value: 1-3 days

tag: Sex

value: pooled male and female

value: saline


title: DKK022

description: rawcounts.txt

value: GOE

value: CTR


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C9_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000

value: neutrophil lineage differentiation in the presence of  ATRA

value: female


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C8_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C9_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D10_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKK020

description: rawcounts.txt


title: ICA LPS

description: LPS treatment cardiac cells purified by Percoll

value: LPS 1 ug/ml


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C8_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKK019

description: rawcounts.txt


title: Rat OR fed with standard food - replica 3 [Rat-OR-Std-Heart-C866]

city: Brussels

first: Frederick

last: Libert

address: 808 route de Lennik

department: IRIBHM

country: Belgium

institute: ULB

data_processing:
Sequenced reads were trimmed for adaptor sequence (Trimmomatic)
Paired-end reads were mapped against the Rattus norvegicus reference genome Rnor_6.0 using the STAR software to generate read alignments.
The annotation file Rattus_norvegicus.Rnor_6.0.104.gtf was obtained from the ftp.Ensembl.org server
Following transcript assembly, gene level counts were obtained using HTSeq
Genome_build: Rattus_norvegicus Rnor_6.0
Supplementary_files_format_and_content: Excel xlsx file includes counts per 20 millions of aligned reads values for each sample.

source_name: Rat OR fed with standard food_heart

growth_protocol: Diet-induced obesity-prone (OP) rats fed with high fat food for a period of 12 months and obesity-resistant (OR) rats fed with standard food for a period of 12 months

extract_protocol:
Total RNA was extracted from three myocardial tissue from 12-month OP and OR rats, using TRIzol reagent followed by a chloroform/ethanol extraction and a final purification using QIAGEN RNeasy® Mini kit. Libraries were obtained using the TruSeq mRNA sample preparation kit (Illumina)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: Sprague Dawley

tag: strain

value: Obesity-resistant (OR)

tag: diet

value: Standard

tag: period

value: 12 months

tag: tissue

value: Heart


title: DKK027

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D10_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000

tag: cell line


title: DKK018

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C7_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000

tag: treatment


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D10_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000

tag: gender


title: H9C2 cells, HG-1

value: Embryonic rat heart-derived cells

value: treated with HG (33 mM) for 8 hours

value: control


title: DKK017

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C8_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000

tag: age


title: Rat OP fed with HF food - replica 3 [Rat-OP-HF-Heart-C763]

source_name: Rat OP fed with HF food_heart

value: Diet-induced obesity-prone (OP)

value: High fat diet


title: H9C2 cells, Ctrl-2

value: untreated


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C6_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000

tag: ethnicity


title: DKK021

description: rawcounts.txt

tag: collection site


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C7_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKK013

description: rawcounts.txt

tag: phenotypic group


title: Rat OR fed with standard food - replica 2 [Rat-OR-Std-Heart-C815]


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C5_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C5_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C6_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Rat OP fed with HF food - replica 1 [Rat-OP-HF-Heart-C641]


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C6_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C5_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKK011

description: rawcounts.txt


title: DKK014

description: rawcounts.txt


title: DKK010

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C4_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C4_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C4_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C3_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C7_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Rat OP fed with HF food - replica 2 [Rat-OP-HF-Heart-C732]


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C3_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKK009

description: rawcounts.txt


title: U87WT 5 vs U87Mut 5 cells, IGF1 50nM+ OSI906 0.5uM for 24hs

type: RNA

city: Ciudad Autónoma de Buenos Aires

first: Patricia

last: Pennisi

address: Gallo 1330

department: División de Endocrinología

country: Argentina

institute: Centro de Investigaciones Endocrinológicas “Dr. César Bergadá” (CEDIE) CONICET- FEI

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent Hi-RPM Hybridization Buffer) were added, and samples were applied to microarrays enclosed in Agilent SureHyb hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2600D scanner. Images were quantified using Agilent Feature Extraction Software (version 12.0.3.1).

data_processing: R limma package was used for normexp background correction, loess normalization within arrays and aquantile normalization between arrays

source_name: U87WT 5 (U87 glioblastoma cells- transfected GFP-IGF1R)

label_protocol: 100 µg of total RNA were labeled with Cy5 (U87WT 5) or Cy3 (U87Mut 5) and primed with 0.8µl of T7 Mix primer at 65°C for 10 min. Next samples were reversed transcribed at 40°C for 2 h with Affinity Script RNase Block Mix (Agilent), and 10 mM dNTP Mix

growth_protocol: U87 cells were grown in Minimum Essential Medium Eagle (MEM) supplemented with 10% FBS and maintained at 37 °C in a humidified 5% CO2 environment.

extract_protocol: Cell RNA was obtained using Direct-Zol RNA Kit (Zymo Research, Irvine, CA, USA) following manufacturer’s protocol

treatment_protocol: U87WT 5 ans U87Mut 5 cells were seeded on six-well plates and  allowed to grow up to 80% confluence in complete medium. After this, cells were cultured for 24 h with or without 50 nM IGF1 and preincubated with OSI906 (0.5uM) for 24 h. Finally cells were washed and harvested by trypsinization.

tag: transfected vector

tag: igf1r localization

value: Nuclear

tag: medium

source_name: U87Mut 5 (U87 glioblastoma cells- transfected GFP-IGF1R1025x-1100x-1120x)

value: Non-Nuclear


title: DKK012

description: rawcounts.txt

value: GOE

value: CTR


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C2_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000

value: neutrophil lineage differentiation in the presence of  ATRA

value: female


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C3_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sorbitol Rep B time 0

city: Boston

first: Zarmik

last: Moqtaderi

address: 240 Longwood Avenue C2-355

department: BCMP

institute: Harvard Medical School

description:
3' READS library
MATa, his3∆0, leu2∆0, met15∆0, ura3∆0, rpo21::RPO21–FRB, rpl13::RPL13–FK512
reanalysis of GSM4568407

data_processing:
Prep for mapping (removal of adapters, counting and removal of initial Ts, discarding reads with ambiguous base calls), python
Mapping to yeast genome build Sac cer3 (first 17 non-A bases; accepting perfect matches and unique reads only), bowtie
Discard mapped reads with fewer initial Ts than there are As in the adjacent genome, python
Tally reads by UTR position if they map to the first 400nt after an ORF end, python
Normalization to the S. pombe spike-in control
Genome_build: S. cerevisiae Sac cer 3, S. pombe EF2
Supplementary_files_format_and_content: Tab-delimited text files with isoform reads by position

organism: Saccharomyces cerevisiae

source_name: Yeast cells

growth_protocol: Cells were cultured to OD600 0.3 to 0.4 in the specified growth medium before being treated with 1µg/ml final rapamycin for the indicated time in minutes

extract_protocol:
Hot acid phenol RNA extraction followed by Qiagen RNeasy purification
3' READS (Jin, Y. et al., 2015 Curr Protoc Mol Biol 110, 4.23.21-24.23.17)

tag: genotype

value: MATa, his3<delta>0, leu2<delta>0, met15<delta>0, ura3<delta>0, rpo21::RPO21-FRB, rpl13::RPL13-FK512

tag: spike-in

value: 2x10^6 S. pombe cells

tag: growth medium

value: YPD + 1M Sorbitol

tag: culture phase

value: log phase

tag: time point

value: 0 min


title: DKK008

description: rawcounts.txt


title: U87WT 5 vs U87Mut 5 cells, Serum free media for 24hs

value: Serum free media 24h


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D11_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Rat OR fed with standard food - replica 1 [Rat-OR-Std-Heart-C784]

tag: strain background

value: Sprague Dawley

tag: strain

value: Obesity-resistant (OR)

tag: diet

value: Standard

tag: period

value: 12 months

value: Heart


title: DKK007

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C24_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000

tag: cell line

tag: treatment

tag: gender


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C2_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000

tag: age

tag: ethnicity


title: Sorbitol Rep A time 0

description:
3' READS library
MATa, his3∆0, leu2∆0, met15∆0, ura3∆0, rpo21::RPO21–FRB, rpl13::RPL13–FK512
reanalysis of GSM4568406

treatment_protocol: 1µg/ml final rapamycin for the indicated time in minutes


title: Minimal Rep B time 0

description:
3' READS library
MATa, his3∆0, leu2∆0, met15∆0, ura3∆0, rpo21::RPO21–FRB, rpl13::RPL13–FK512
reanalysis of GSM4568405

value: Minimal medium


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C24_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C2_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKK006

description: rawcounts.txt

tag: collection site

tag: phenotypic group


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C21_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: 13771

description: rawcounts.txt

value: UNIBO


title: DKK003

description: rawcounts.txt

value: GOE


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C22_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C23_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKK004

description: rawcounts.txt

value: CTR


title: YPD Rep B time 0

description:
3' READS library
MATa, his3∆0, leu2∆0, met15∆0, ura3∆0, rpo21::RPO21–FRB, rpl13::RPL13–FK512
reanalysis of GSM4568399

value: YPD


title: YPGal Rep A time 0

description:
3' READS library
MATa, his3∆0, leu2∆0, met15∆0, ura3∆0, rpo21::RPO21–FRB, rpl13::RPL13–FK512
reanalysis of GSM4568402

value: YP + 2% Galactose


title: 13801

description: rawcounts.txt


title: 13751

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C20_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000

value: neutrophil lineage differentiation in the presence of  ATRA

value: female


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C23_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sorbitol Rep B time 90

description:
3' READS library
MATa, his3∆0, leu2∆0, met15∆0, ura3∆0, rpo21::RPO21–FRB, rpl13::RPL13–FK512

data_processing:
Prep for mapping (removal of adapters, counting and removal of initial Ts, discarding reads with ambiguous base calls), python.
Mapping to yeast genome build SacCer3 (first 17 non-A bases; accepting perfect matches and unique reads only), bowtie.
Discard mapped reads with fewer initial Ts than there are As in the adjacent genome, python.
Tally reads by UTR position if they map to the first 400nt after an ORF end, python.
Normalization to the S. pombe spike-in control.
Genome_build: S. cerevisiae sacCer3, S. pombe EF2
Supplementary_files_format_and_content: *.txt: Tab-delimited text files with isoform reads by position.

growth_protocol: Cells were cultured to OD600 0.3 to 0.4 in the specified growth medium before being treated with 1µg/ml final rapamycin for the indicated time in minutes.

extract_protocol:
Hot acid phenol RNA extraction followed by Qiagen RNeasy purification.
3' READS (Jin, Y. et al., 2015 Curr Protoc Mol Biol 110, 4.23.21-24.23.17).

value: MATa, his3<delta>0, leu2<delta>0, met15<delta>0, ura3<delta>0, rpo21::RPO21-FRB, rpl13::RPL13-FK512

value: 2x10^6 S. pombe cells

value: YPD + 1M Sorbitol

value: rapamycin

value: 90 min


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C22_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: U87WT 5 vs U87Mut 5 cells, IGF1 50nM for 24hs

tag: transfected vector

tag: igf1r localization

value: Nuclear

tag: medium

value: IGF1 50nM 24h

value: Non-Nuclear


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C19_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sorbitol Rep B time 60

treatment_protocol: 1µg/ml final rapamycin for the indicated time in minutes.

tag: genotype

tag: spike-in

tag: growth medium

value: log phase

value: 60 min


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C19_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C23_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sorbitol Rep B time 40

tag: culture phase

tag: time point

value: 40 min


title: Sorbitol Rep B time 20

tag: strain

value: 20 min


title: YPGal Rep B time 0

description:
3' READS library
MATa, his3∆0, leu2∆0, met15∆0, ura3∆0, rpo21::RPO21–FRB, rpl13::RPL13–FK512
reanalysis of GSM4568403

value: 0 min


title: Minimal Rep A time 0

description:
3' READS library
MATa, his3∆0, leu2∆0, met15∆0, ura3∆0, rpo21::RPO21–FRB, rpl13::RPL13–FK512
reanalysis of GSM4568404

value: Minimal medium


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C17_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C21_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: 13321

description: rawcounts.txt

value: UNIBO

value: CTR


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C21_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000

value: neutrophil lineage differentiation in the presence of  ATRA

value: female


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C1_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sorbitol Rep A time 120

value: MATa, his3<delta>0, leu2<delta>0, met15<delta>0, ura3<delta>0, rpo21::RPO21-FRB, rpl13::RPL13-FK512

value: 2x10^6 S. pombe cells

value: 120 min


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C20_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: YPD Rep A time 0

description:
3' READS library
MATa, his3∆0, leu2∆0, met15∆0, ura3∆0, rpo21::RPO21–FRB, rpl13::RPL13–FK512
reanalysis of GSM4568398

value: YPD


title: 13521

description: rawcounts.txt


title: 13581

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C18_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C18_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sorbitol Rep B time 120

value: YPD + 1M Sorbitol

value: rapamycin


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C20_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C17_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C17_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sorbitol Rep A time 90

value: 90 min


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C18_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C16_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C1_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: 13551

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C1_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sorbitol Rep A time 60

value: log phase


title: 13671

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C19_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: 13241

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C15_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: 13301FUP001

description: rawcounts.txt


title: Sorbitol Rep A time 40


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C15_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C16_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C15_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C14_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: 13151

description: rawcounts.txt


title: 13131

description: rawcounts.txt


title: Minimal Rep B time 120


title: Minimal Rep B time 90


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C16_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C14_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: 13101

description: rawcounts.txt


title: 13079

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C13_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C12_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C13_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C14_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: 13221

description: rawcounts.txt


title: Minimal Rep B time 60

value: 60 min


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C12_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Minimal Rep B time 40

value: 40 min


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C11_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: 13069

description: rawcounts.txt


title: Minimal Rep A time 120


title: 13011

description: rawcounts.txt


title: 13119

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C13_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C10_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: 13019

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C11_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C10_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C12_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sorbitol Rep A time 20

value: 20 min


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C10_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: 11730

description: rawcounts.txt

value: CENT


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B9_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Minimal Rep A time 90

value: Minimal medium


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C11_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B8_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B9_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: 11670

description: rawcounts.txt

value: UNIBO


title: Minimal Rep A time 60


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B8_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: 11710

description: rawcounts.txt


title: Minimal Rep B time 20


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B7_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B7_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B8_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: 11620

description: rawcounts.txt


title: YPGal Rep B time 80

value: YP + 2% Galactose

value: 80 min


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B6_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000

value: neutrophil lineage differentiation in the presence of  ATRA

value: female


title: YPGal Rep B time 120

value: MATa, his3<delta>0, leu2<delta>0, met15<delta>0, ura3<delta>0, rpo21::RPO21-FRB, rpl13::RPL13-FK512

value: 2x10^6 S. pombe cells


title: YPGal Rep B time 100

value: 100 min


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B5_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B6_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B9_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B7_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: 11600

description: rawcounts.txt


title: 11650

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B5_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: 11640

description: rawcounts.txt


title: YPGal Rep B time 60


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B5_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: 11550

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B3_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Minimal Rep A time 40


title: 11610

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B4_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Minimal Rep A time 20


title: YPGal Rep B time 40


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B6_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: YPGal Rep A time 120

value: 120 min


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B4_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: YPGal Rep B time 20

value: rapamycin


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B2_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B4_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: 11340

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B3_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: YPGal Rep A time 60


title: 11300FUP001

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B24_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: 11310

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B2_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B2_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B3_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: YPGal Rep A time 100


title: YPGal Rep A time 80


title: YPD Rep B time 120

value: YPD


title: 11250

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B23_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B21_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: 11210

description: rawcounts.txt


title: YPGal Rep A time 40

value: log phase


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B24_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: 11230

description: rawcounts.txt


title: 11160

description: rawcounts.txt


title: YPGal Rep A time 20


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B22_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B20_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B23_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: 11130

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B23_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: 11330

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B20_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: 11220

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B20_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: 11120

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B21_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: YPD Rep B time 60

value: 60 min


title: 11180

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B19_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B1_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B1_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B21_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: YPD Rep B time 40

value: 40 min


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B19_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: YPD Rep B time 90

value: 90 min


title: YPD Rep A time 120


title: YPD Rep A time 90


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B19_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B1_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: YPD Rep A time 60


title: 11100

description: rawcounts.txt

value: CENT


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B18_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B18_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B18_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: YPD Rep B time 20

value: 20 min


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B22_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B17_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B16_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B17_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B16_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: YPD Rep A time 40


title: 11010

description: rawcounts.txt

value: UNIBO


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B16_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: 11090

description: rawcounts.txt


title: 11080

description: rawcounts.txt


title: YPD Rep A time 20


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B15_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: rep3_HEY_shCIP2A_556

city: Turku

first: Teemu

middle: Daniel

last: Laajala

address: Turun yliopisto

country: Finland

institute: University of Turku

data_processing:
Base sequencing was performed according to standard Illumina guideline practices generating FASTA files.
Sequenced single-strand reads from FASTA were aligned to the human reference genome hg19 using TopHat (v2.0.13) with Bowtie (v2.2.3.0) with standard parameters.
Raw read counts were subsequently processed with limma-package (v3.46.0) with voom-transformation, normalization, and log-transformation prior to calling differentially expressed genes.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM gene expression in Excel .xlsx format

source_name: HEY CIP2A-silenced sample

growth_protocol: Ovarian cancer cell lines were cultured in the appropriate cell culture media supplemented with 10 % heat-inactivated fetal calf serum, 2 mM L-glutamine, penicillin (50 U/ml) and streptomycin (50 µg/ml). For HEY, OVCAR-8 (CVCL_1629) and OVCAR-3 (CVCL_0465) cell lines the recommended media was RPMI-1640, and for CAOV-3 (CVCL_0201) and SKOV-3 (CVCL_0532) DMEM was used. The cells were routinely tested for negative mycoplasma contamination. Primary OvCa cells from mice tumors were cultured as described in Connolly et al., 2003.

extract_protocol:
Nucleospin RNA Mini Kit (Macherey-Nagel 740955.50) was used to isolate total RNA of OvCa cells. Concentration and purity of RNA was confirmed with NanodropTM spectrophotometer. RNA-sequences were extracted using Illumina TruSeq Stranded mRNA sample preparation at Finnish Functional Genomics Centre (Turku, Finland).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HEY cells were transduced with polybrene (8 µg/ml). After infection, the cells were selected for puromycin resistance, and if the number of GFP-positive cells was low, the cells were GFP sorted with FACS for further experiments.

value: dysfunctional

value: HEY

tag: shRNA

tag: tissue source

value: ovary


title: rep1_HEY_shCIP2A_556

tag: cell line


title: 11030

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B15_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000

tag: treatment

value: neutrophil lineage differentiation in the presence of  ATRA

tag: gender

value: female


title: 11050

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B17_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000

tag: age

tag: ethnicity


title: rep2_HEY_shCIP2A_556


title: S09_301

city: Groningen

first: Emma

last: Gerrits

email: e.gerrits@rug.nl, e.gerrits@umcg.nl

state: Groningen

address: Antonius Deusinglaan 1

department: BSCS

country: Netherlands

institute: UMCG

description: countmtx.csv

data_processing:
[data processing step 10x Genomics samples]  Cellranger version 3.0.0
[data processing step Bulk alignment]  Hisat v0.1.5
[data processing step Bulk sorting reads]  samtools v1.2
[data processing step Bulk counting reads]  HTSeq v0.6.1
Genome_build: Bulk GRCh37, human SC GRCh38, mouse SC GRCm38
Supplementary_files_format_and_content: Countfiles with raw counts per sample (bulk) or droplet barcode (single-cell)

source_name: brain

extract_protocol:
[Macrophage isolation human]  Mechanical tissue dissociation followed by percoll gradient centrifugation. FACS sorting for CD45posCD11Bpos cells.
[Macrophage isolation mouse]  Enzymatic isolation at 4C using protease from Bacillus lichenformis and L-cysteine. FACS sorted on tdTomato Red cells.
Qiagen Rneasy lipid mini kit
3’ Quantseq FWD kit from Lexogen for bulk RNAseq. 3’ single cell RNAseq v2 from 10x Genomics for single cell.

treatment_protocol: [diet protocol mice]  Mice were fed 0.2% cuprizone in their diet ad libitum. Control animals received similarly prepared chow but without cuprizone

tag: group

value: NAWM

tag: cell type

value: total brain tissue

tag: postmortem delay

tag: rin

tag: cell isolation

tag: rna isolation

value: Qiagen Rneasy mini lipid kit

tag: sequencing method

value: 3’ Quantseq FWD


title: S09_014

description: countmtx.csv

value: F


title: rep3_HEY_NS_shRNA_520

source_name: HEY scrambled control

value: functional

value: scrambled


title: S07_254

description: countmtx.csv


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B14_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B15_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: S07_051

description: countmtx.csv

value: M


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B13_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B12_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: S06_253

description: countmtx.csv


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B12_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B13_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B14_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: rep2_HEY_NS_shRNA_520


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B11_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: rep3_HEY

source_name: HEY non-scrambled control

value: control


title: S06_208_NAWM

description: countmtx.csv


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B14_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B11_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B10_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B13_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: rep1_HEY_NS_shRNA_520


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B10_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B11_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: large artery atherosclerotic stroke 6

city: Qingdao

first: Qi

last: Xiao

state: China

address: No. 59 Haier Road, Qingdao, Shandong Province, China.

institute: The Affiliated Hospital of Qingdao University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.
After cluster generation, the libraries were sequenced on an Illumina Hiseq 2500 platform and 150 bp pairedend reads were generated.
HisAT2 was used for comparative analysis of the reference genome of filtered clean reads.
The circRNA was identified using find_circ (Sebastian Memczak et al., 2013).
Genome_build: Ensenmbal
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample.

source_name: plasma exosome

extract_protocol:
Plasma  were collected, extracted exosomes, and RNA was obtained using miRNeasy Serum/Plasma Advanced kit. RNA quantification and qualification. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA), and RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 2.0 Flurometer (Life Technologies, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols. The sequencing libraries were generated by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

tag: disease

value: LAA stroke


title: healthy control 6

value: healthy control


title: SD042_13

description: countmtx.csv

value: Control


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B10_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: rep1_HEY


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A8_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: S06_178

description: countmtx.csv


title: rep2_HEY


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B12_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A8_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A9_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: SB10

city: Faridabad

first: Jaskaran

last: Kaur

state: Haryana

address: NCR Biotech Science cluster Gurugram-Faridabad Expressway

department: Infection and immunology

country: India

institute: THSTI

data_processing:
Paired-end sequencing was performed on Illumina HiSeq 2500 system.
FastQC, Version 0.11.9 was used for quality check followed by adapter removal through Trim galore, Version 0.6.5
Mapping was done using Bowtie and Tophat 2.1.1 and expression of the assembled transcriptomes was estimated using Cufflinks 2.2.1
The FPKM (Fragments Per Kilobases per Million fragments) was used.
DAVID, METASCAPE was used for pathway enrichment analysis
Genome_build: GRCh38

source_name: K562 cells

growth_protocol: K562 cells were maintained in T75 flasks in IMDM with 10% FBS.

extract_protocol:
K562 cells were harvested at different time points and the pellet in Trizol was used for RNA extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols (NEB, USA)

treatment_protocol: Mock-or dengue virus infected K562 cells were treated with PMA to induce differentiation for 3 or 6 Days.

tag: disease condition

value: Dengue-infected differentiated


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A9_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A7_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: SD054_13

description: countmtx.csv


title: SD055_12

description: countmtx.csv


title: SB8

value: Mock-infected differentiated


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A8_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: SD036_12

description: countmtx.csv


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A6_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A6_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: SB7


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A4_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: SD034_15

description: countmtx.csv


title: SD034_08

description: countmtx.csv


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A5_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: SB9


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A7_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: SB11


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A4_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: SD032_09

description: countmtx.csv


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A4_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: SD031_14

description: countmtx.csv


title: SB5


title: SD033_11

description: countmtx.csv


title: SB6


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A6_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A5_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A3_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: SB4


title: SD030_09

description: countmtx.csv


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A2_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A3_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: SD030_12

description: countmtx.csv


title: SD027_11

description: countmtx.csv


title: SD023_09

description: countmtx.csv


title: SB1

value: Mock-infected Undifferentiated


title: SD024_10

description: countmtx.csv


title: SD019_15

description: countmtx.csv


title: Mother_3 - BulkRNA

city: New York

first: Stefan

last: Feske

state: NY

address: 550 First Avenue

institute: New York University School of Medicine

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software
The fastq files were trimmed for adaptor sequences using trimmomatic version 0.36 in paried end mode with parameters - minimal read length option set to 35 base pairs, trailing set to 5 and sliding window set to 4:15.
After trimming, the data was aligned to the human genome (hg38) using STAR.
The featureCounts program was used to generate raw counts for each gene.
Genome_build: (hg38)
Supplementary_files_format_and_content: The raw counts are stored in .csv format.

source_name: CD4+ T Cells

growth_protocol: CD4+ T cells were isolated from peripheral blood mononuclear cells (PBMC)

extract_protocol:
Total RNA was extracted using the RNeasy Micro Kit (Qiagen, 74004) and RNA quality was analyzed using a Bioanalyzer 2100 (Agilent) using PICO chips. RNA-Seq libraries were prepared using the TruSeq RNA sample prep v2 kit (Illumina TruSeq Stranded mRNA, RS-122-2001) and 100 ng total RNA following the manufacturer’s instructions.
The amplified libraries were purified using AMPure beads (Beckman Coulter, A63881), quantified by Qubit 2.0 fluorometer (Life Technologies), and visualized using an Agilent Tapestation 2200.
The libraries were pooled equimolarly, loaded on the HiSeq 2500 DNA Sequencer (Illumina) and run as single 50 nucleotide reads.

treatment_protocol: CD4+ T cells were left untreated or stimulated with 5 μg/ml plate-bound anti-CD3 (clone OKT3, 14-0037-82) and 10 μg/ml soluble anti-CD28 (clone CD28.2, 14-0289-82, both eBioscience) antibodies for 6 h in RPMI1640 medium supplemented with 10% FBS, 1% L-glutamine, and 1% penicillin-streptomycin.

value: no stimulation

tag: disease state

value: Healthy donor


title: SB2


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A22_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000

value: neutrophil lineage differentiation in the presence of  ATRA

value: female


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A23_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A24_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Mother_2 - BulkRNA

value: anti-CD3 / anti-CD28 (6 hours)


title: SD019_10

description: countmtx.csv

value: total brain tissue

value: Qiagen Rneasy mini lipid kit

value: 3’ Quantseq FWD


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A21_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A21_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A20_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A23_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: SD018_11

description: countmtx.csv

value: F


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A20_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A24_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A2_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A1_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A1_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: SD016_11

description: countmtx.csv

value: M


title: Mother_4 - BulkRNA


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A2_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Father_3 - BulkRNA


title: SD016_10

description: countmtx.csv


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A20_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Father_2 - BulkRNA


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A19_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Father_4 - BulkRNA


title: SD015_12

description: countmtx.csv


title: Patient_1 - BulkRNA


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A22_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A16_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A16_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A19_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A16_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: SD013_09

description: countmtx.csv


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A18_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A18_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A15_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A17_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A18_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Patient_4 - BulkRNA


title: SD011_15

description: countmtx.csv


title: SD014_10

description: countmtx.csv


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A14_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A17_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A15_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A13_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Patient_3 - BulkRNA


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A14_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: HD_4 - BulkRNA


title: S12_122

description: countmtx.csv

value: Lesion


title: Patient_2 - BulkRNA


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A11_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A14_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: SD007_14

description: countmtx.csv


title: SD005_14

description: countmtx.csv


title: Brother_1 - BulkRNA


title: HD_3 - BulkRNA


title: S99_248

description: countmtx.csv

value: NAWM


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A13_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: HD_1 - BulkRNA


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A11_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Brother_3 - BulkRNA


title: S99_154

description: countmtx.csv


title: Brother_4 - BulkRNA


title: Human embryonal palatal mesenchyme cells_rep3

city: Bonn

first: Karharina

last: Ruff

address: Venusberg-Campus 1

country: Germany

institute: Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital

data_processing:
The Quality of the fastq files was checked using FastQC (v0.11.7).
Adapter sequences were trimmed using bbduk (BBMap v37.44).
The alignment of the reads to theGRCh37/hg19 reference genome was performed using STAR Aligner (v2.5.2b)
The gene expression with Ensembl Human GRCh37.p13 annotation as reference, was quantified using featureCounts (v1.5.1).
The quality of our data was checked using MultiQC (v1.2).
Genome_build: Human GRCh37.p13 - hg19
Supplementary_files_format_and_content: 3'RNA-seq read counts per gene

source_name: Human embryonal palatal mesenchyme cells (HEPM cells)

growth_protocol: Cells were cultivated in in DMEM-Dulbecco's Modified Eagle Medium (high Glucose), 10% heat inactivated fetal bovine serum (FBS) and Penicillin/Streptomycin, at a concentration of 1X at 37 °C and 5% CO2. The medium was changed every two days and the cells were split after five days with  0.25% Trypsin/EDTA.

extract_protocol:
The RNaeasy® kit (QIAGEN, Germany) was used according the manufacturer's protocol.
The QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen, Austria) was used according to the manufacturer's protocol. The samples were sequenced with 1x50 bp on an Illumina HiSeq2500 yielding ~20 mio reads per sample.
3'mRNA-seq

treatment_protocol: The cells were untreated

value: untreated


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A12_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000

data_processing:
Library strategy: SLAM-seq
For the HL60 10x dataset, we followed the standard pipeline of kb-python to quantify the total, spliced and unspliced RNA. For the HL60 metabolic labeling based scRNA-seq experiment with clone tracing, we used the NASC-seq pipeline (https://github.com/sandberg-lab/NASC-seq) developed in to quantify the new and total RNA read counts.
For the scNT-seq experiment of the human hematopoiesis, we developed dynast (https://github.com/aristoteleo/dynast-release), an inclusive and efficient command-line toolkit for preprocessing data from metabolic labeling–based scRNA-seq experiments and quantifying the following four types of mRNA species: unspliced, spliced, labeled (or new), and total RNAs (details will be reported elsewhere). Samples from days 4 and 7 were each subjected to standard dynast runs, using human genome hg38 as the alignment reference. The resultant objects were first filtered to keep only high quality cells and then merged to obtain in total about 2,000 high-quality cells. This merged object was then used for all downstream analyses.
Genome_build: hg38
Supplementary_files_format_and_content: file format is h5ad/csv. For h5ad files, they include the spliced, unspliced, labeled and total RNA counts for each gene in each cell from our scSLAM-seq and scNT-seq experiment. Only spliced and unspliced RNA counts for each gene in each cell are available for the 10x dataset. For the edge_df.csv file, it is the clone linkage information between different cells, processed from the static barcodes.

extract_protocol: To facilitate lineage tracing in scSLAM-seq libraries, cellular barcodes (GBCs) were introduced using a lentiviral transduction strategy (Adamson et al., 2016). Given that the success of this experiment critically depended on the uniqueness of barcode sequence to each cell at the start of the experiment, i.e. low barcode collision rate, and the capture of clone cells (clones with the same barcodes) across different days, we used an experimental scheme in which the starting population of the HL60 cells were infected at a low (2%) multiplicity of infection (MOI). This scheme has two benefits: first, we obtained a small number of barcoded single cells (~2000 in 1 ml of media in each well of a 24-well plate) so that we could capture clone cells via plate-based SLAM-seq (scRNA-seq augmented by metabolic labeling) characterized of low throughput; second, co-culturing the small number of infected cells with a large population of uninfected cells enabled us to differentiate infected cells more conveniently, as a small number of cells are difficult to grow and differentiate. Single cells carrying barcodes and expressing the blue fluorescent protein (BFP) reporter were sorted (Sony SH800) at five timepoints, days 0, 1, 2, 3, and 5, during differentiation in the presence of ATRA. cDNA from single cells was prepared in a 96-well format as previously described (Tabula Muris Consortium, 2020) following alkylation and RNA cleanup (Erhard et al., 2019; Hendriks et al., 2019). Sequencing libraries were either reformatted into a 384-well format and prepared using TTP Mosquito automated liquid handlers, or in a 96- well format using a multichannel pipette. GBC sequencing libraries were prepared by dual PCR amplification to enrich for GBC cDNA and to add Illumina adapters and dual indexes complimentary to that cell's transcriptome sequencing library indexes. GBC sequencing libraries were spiked into transcriptome libraries at 1:10 and sequenced on the NextSeq or MiSeq platform (Illumina). Transcriptome libraries were sequenced separately using a NovaSeq5000 S2 300-cycle kit.


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A12_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A10_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: scNT-seq of HSPC day 4 timepoint

data_processing:
For the HL60 10x dataset, we followed the standard pipeline of kb-python to quantify the total, spliced and unspliced RNA. For the HL60 metabolic labeling based scRNA-seq experiment with clone tracing, we used the NASC-seq pipeline (https://github.com/sandberg-lab/NASC-seq) developed in to quantify the new and total RNA read counts.
For the scNT-seq experiment of the human hematopoiesis, we developed dynast (https://github.com/aristoteleo/dynast-release), an inclusive and efficient command-line toolkit for preprocessing data from metabolic labeling–based scRNA-seq experiments and quantifying the following four types of mRNA species: unspliced, spliced, labeled (or new), and total RNAs (details will be reported elsewhere). Samples from days 4 and 7 were each subjected to standard dynast runs, using human genome hg38 as the alignment reference. The resultant objects were first filtered to keep only high quality cells and then merged to obtain in total about 2,000 high-quality cells. This merged object was then used for all downstream analyses.
Genome_build: hg38
Supplementary_files_format_and_content: file format is h5ad/csv. For h5ad files, they include the spliced, unspliced, labeled and total RNA counts for each gene in each cell from our scSLAM-seq and scNT-seq experiment. Only spliced and unspliced RNA counts for each gene in each cell are available for the 10x dataset. For the edge_df.csv file, it is the clone linkage information between different cells, processed from the static barcodes.

source_name: Human hematopoietic stem and progenitor cells

extract_protocol: For the human hematopoiesis dataset, we cultured primary human CD34+ hematopoietic stem and progenitor cells obtained from the Fred Hutchinson Cancer Research Center. Cells were thawed and cultured in StemSpan SFEM II human hematopoietic stem cell expansion media (StemCell Technologies, Cat#02690) supplemented with StemSpan CC100 (StemCell Technologies, Cat#02690) and 50 ng/ml TPO (PeproTech, Cat#300-18-100UG). Cells were allowed to differentiate over the course of 1 week.

value: day 4, during differentiation in the presence of maintenance medium

value: Caucasian


title: Human embryonal palatal mesenchyme cells_rep1

value: Human embryonal palatal mesenchyme cells (HEPM cells)


title: HD_2 - BulkRNA


title: Brother_2 - BulkRNA


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A10_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: scNT-seq of HSPC day 7 timepoint

value: Human hematopoietic stem and progenitor cells

value: day 7, during differentiation in the presence of maintenance medium


title: S96_264

description: countmtx.csv