title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J9_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Liver - 11d - ind_4

status: Public on Feb 02 2022

type: SRA

city: Ankara

first: Mehmet

last: Somel

address: Dumlupınar Bulvarı No:1

department: Biology

country: Turkey

institute: Middle East Technical University

library_source: transcriptomic

data_processing:
Raw sequencing reads were filtered with Trimmomatic to remove adaptor content with parameters: PE ILLUMINACLIP: TruSeq3-PE-2.fa:2:30:1:0:8:true, SLIDINGWINDOW:4:15, MINLEN:25
Remaining high quality reads were aligned to reference genome GRCm38 using STAR-2.5.3 with parameters:  --sjdbOverhang 99 --outSAMattrIHstart 0 --outSAMstrandfield intronMotif --sjdbGTFfile GRCm38.gtf
Uniquely aligned reads were retrieved using: samtools -q 255
Expression levels were calculated as FPKM using cufflinks, yielding 51608 genes in total. Only the protein-coding genes were included in the analysis (using biotype feature of biomaRt) and the genes which are not detected (zero FPKM) in 25% or more of the samples (15/63) were excluded from the analysis, resulting in 15063 protein-coding genes in total.
FPKM values were 1+log2 transformed and quantile normalized using all the samples together.
Genome_build: GRCm38
Supplementary_files_format_and_content: comma separated files contain ENSEMBL gene ids and normalized expression levels for each sample

molecule: total RNA

organism: Mus musculus

source_name: Liver

extract_protocol:
RNA sequencing was performed as previously described (Liu et al. 2016)  with slight modifications. Total RNA was extracted using Trizol reagent (Invitrogen).
For sequencing library construction, all samples were randomized first and prepared with TruSeq RNA Sample Preparation Kit (Illumina) according to the manufacturer’s instruction. Libraries were sequenced on the Illumina Hi-seq 4000 system in three lanes within one flow-cell, using the 150-bp paired-end module

tag: strain

tag: tissue

value: Liver

tag: age

tag: individual

tag: gender

value: male


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J2_MemorySeq384_3

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

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.

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

value: female

tag: ethnicity


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J24_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU1039iMNC

city: La Jolla

first: Erika

last: Lin

state: CA

address: 9500 Gilman Dr,

department: Pediatrics

institute: University of California, San DIego

data_processing:
Sequencing output was processed using Ceto (NGS analysis system put together in a collaboration between the Bartom computational Lab, the Shilatifard lab, and other scientists at Northwestern University)
Aligned data was normalized and transformed using EdgeR.
Differentially expressed genes were assessed using DeSeq2.
Output files were visualized in the Morpheus browser. Hierarchical clustering of samples was performed and K-means clustering of genes were generated using 1000 iterations  was performed within the browser
WGCNA analysis was performed using the CEMiTool.
Filtered counts tables were normalized using VST.
Gene list output from K-means clustering the WGCNA was then used as input for GOrilla to search for significant gene ontology (GO) terms for biological processes, function, and components
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Umbilical cord blood

extract_protocol:
Umbilical venous cord blood collected at birth into a cord blood bag or EDTA tube. We stored cord blood  specimens at 4ºC and performed monocyte isolation within 36 hours of delivery.
RNA libraries were prepared for sequencing using standard Illumina protocols (NextSeq 500/550 High Output v2  kit)

tag: cell population

value: iMNC

value: Umbilical cord

tag: gestational age


title: Liver - 61d - ind_7


title: NU1043cMNC

value: cMNC


title: Liver - 5d - ind_3


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J23_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J2_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU1043iMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J6_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Liver - 2d - ind_1


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J24_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU1058cMNC


title: Liver - 2d - ind_2


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J3_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J23_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Lung - 904d - ind_16

source_name: Lung

value: Lung


title: NU1039cMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J3_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J4_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU1036iMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J22_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J4_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Lung - 904d - ind_15


title: NU1036cMNC


title: Lung - 654d - ind_14


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J21_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J21_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU1034cMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J19_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J1_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J20_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J1_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Lung - 649d - ind_13


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J18_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J18_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Lung - 232d - ind_11


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J20_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU1024iMNC


title: Lung - 303d - ind_12


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J19_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU1034iMNC


title: NU1023iMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J22_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J17_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU1024cMNC


title: Lung - 144d - ind_10


title: Lung - 93d - ind_9


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J16_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J16_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU1023cMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J15_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Lung - 93d - ind_8


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J14_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J17_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Lung - 32d - ind_6


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J13_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Lung - 61d - ind_7


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J15_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Lung - 20d - ind_5


title: NU999iMNC


title: Lung - 11d - ind_4


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J13_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J14_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J11_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J12_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU997iMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J11_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J12_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU996iMNC


title: NU997cMNC


title: Lung - 5d - ind_3


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J10_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Lung - 2d - ind_1


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J10_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I9_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I9_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU995cMNC


title: Lung - 2d - ind_2


title: NU995iMNC


title: Cerebral Cortex - 904d - ind_15

source_name: Cerebral Cortex

value: Cerebral Cortex


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I8_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU949iMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I7_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I5_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Cerebral Cortex - 303d - ind_12


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I5_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU999cMNC


title: NU949cMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I5_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Cerebral Cortex - 232d - ind_11


title: NU872ncMNC

value: ncMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I8_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Cerebral Cortex - 654d - ind_14


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I6_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU872iMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I6_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I9_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU996cMNC


title: Cerebral Cortex - 144d - ind_10


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I4_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I7_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I4_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I3_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I7_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU869iMNC


title: NU872cMNC


title: Cerebral Cortex - 649d - ind_13


title: Cerebral Cortex - 93d - ind_8


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I3_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I2_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU869ncMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I24_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU869cMNC


title: NU867iMNC


title: Cerebral Cortex - 93d - ind_9


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I3_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I2_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I24_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU867ncMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I23_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I22_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Cerebral Cortex - 61d - ind_7


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I23_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Cerebral Cortex - 20d - ind_5


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I20_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I21_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Cerebral Cortex - 2d - ind_2


title: NU828ncMNC


title: NU828iMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I22_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Cerebral Cortex - 11d - ind_4


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I21_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Cerebral Cortex - 2d - ind_1


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I20_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU822iMNC


title: NU867cMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I1_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I19_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I19_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Striatum WT Female (CAG17_3_Str)

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

data_processing:
The generated reads were mapped to the mouse genome GRCm38 with aligner STAR with default parameter settings
Raw counts were obtained with HTSeq using refSeq gene model (mm10) as reference.  Only uniquely mapped reads were used for the subsequent analyses.
Genome_build: Genome version Mouse GRCm38
Supplementary_files_format_and_content: Counts  for each sample

source_name: Striatum WT 6 mon Female

extract_protocol:
Qiagen RNeasy kit with QIAshredder columns
TruSeq Stranded RNA (100 ng)

treatment_protocol: Mice were perfused with PBS in DEPC-treated H2O. Cortex, Striatum and cerebellum were dissected out and fresh frozen in dry ice immediately.

tag: strain background

value: FvB

tag: genotype

value: WT

value: 6 mon

tag: Sex

value: Female

value: Striatum


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I19_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Cerebral Cortex - 32d - ind_6


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I18_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Striatum BAC-CAG Female (CAG19_1_Str)

source_name: Striatum BAC-CAG 6 mon Female

value: Tg


title: NU822cMNC


title: NU822ncMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I17_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Striatum BAC-CAG Female (CAG17_1_Str)


title: NU797cMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I1_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I21_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Striatum WT Female (CAG17_2_Str)


title: NU797iMNC


title: Striatum BAC-CAG Female (CAG15_1_Str)


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I16_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Cerebral Cortex - 5d - ind_3


title: NU793iMNC


title: NU797ncMNC


title: Striatum BAC-CAG Male (CAG16_2_Str)

source_name: Striatum BAC-CAG 6 mon Male

value: Male


title: NU828cMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I23_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I1_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I17_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU793ncMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I16_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I17_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I14_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I18_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Striatum BAC-CAG Male (CAG3_3_Str)


title: NU765ncMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I12_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU765iMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I15_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Striatum WT Male (CAG2_2_Str)

source_name: Striatum WT 6 mon Male


title: NU761iMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I11_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Striatum WT Male (CAG14_2_Str)


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I10_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU761ncMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I10_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Striatum BAC-CAG Female (CAG1_5_Str)


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I15_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I13_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Striatum BAC-CAG Male (CAG3_2_Str)


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I15_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Striatum BAC-CAG Male (CAG14_1_Str)


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I14_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I13_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H8_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU793cMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I13_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU765cMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I11_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I11_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU752ncMNC


title: Striatum WT Male (CAG3_1_Str)


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H7_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Striatum WT Female (CAG1_2_Str)


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H9_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H6_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU745ncMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H9_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H5_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Cortex BAC-CAG Male (CAG16_2_Ctx)

source_name: Cortex BAC-CAG 6 mon Male

value: Cortex


title: NU752cMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, I12_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU745iMNC


title: Striatum WT Male (CAG2_1_Str)


title: Striatum WT Female (CAG1_1_Str)


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H6_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU761cMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H7_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Cortex BAC-CAG Female (CAG15_1_Ctx)

source_name: Cortex BAC-CAG 6 mon Female


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H7_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H9_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H8_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU752iMNC


title: Cortex BAC-CAG Female (CAG19_1_Ctx)


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H5_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H8_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Cortex WT Female (CAG17_3_Ctx)

source_name: Cortex WT 6 mon Female


title: NU744cMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H6_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Cortex BAC-CAG Female (CAG17_1_Ctx)


title: Cortex BAC-CAG Male (CAG14_1_Ctx)


title: Cortex WT Female (CAG17_2_Ctx)


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H3_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU744iMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H2_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H2_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H24_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H4_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H4_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H4_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H3_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU708iMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H5_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Cortex BAC-CAG Male (CAG3_3_Ctx)


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H3_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU745cMNC


title: NU744ncMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H2_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Cortex WT Male (CAG14_2_Ctx)

source_name: Cortex WT 6 mon Male


title: NU722iMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H23_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H22_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H22_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU722ncMNC


title: NU708ncMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H24_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Cortex WT Male (CAG2_1_Ctx)


title: Cortex WT Female (CAG1_2_Ctx)


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H21_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Cortex WT Male (CAG2_2_Ctx)


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H23_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H20_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Cortex WT Male (CAG3_1_Ctx)


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H23_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU708cMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H1_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU694iMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H22_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H21_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Cortex BAC-CAG Female (CAG1_5_Ctx)


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H20_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU699iMNC


title: Cortex BAC-CAG Male (CAG3_2_Ctx)


title: NU722cMNC


title: NU699ncMNC


title: Striatum WT Male (CAG_34_5_str)

source_name: Striatum WT 2 mon Male

value: 2 mon


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H19_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000

value: neutrophil lineage differentiation in the presence of  ATRA


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H21_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000

value: female


title: NU694cMNC


title: NU699cMNC


title: Striatum WT Male (CAG_40_3_str)


title: Striatum BAC-CAG Male (CAG_34_3_str)

source_name: Striatum BAC-CAG 2 mon Male


title: NU674iMNC

value: iMNC


title: NU674ncMNC

value: Umbilical cord


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H1_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H17_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Striatum BAC-CAG Male (CAG_34_2_str)


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H1_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Cortex WT Female (CAG1_1_Ctx)


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H20_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Striatum WT Female (CAG_37_0_str)

source_name: Striatum WT 2 mon Female


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H19_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H17_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H18_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU694ncMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H18_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H16_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU664iMNC


title: Striatum BAC-CAG Female (CAG_33_5_str)

source_name: Striatum BAC-CAG 2 mon Female


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H18_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H15_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Striatum WT Male (CAG_40_2_str)


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H15_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H17_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU637ncMNC


title: Striatum WT Female (CAG_33_4_str)


title: NU674cMNC

value: cMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H13_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU664cMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H19_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU637cMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H13_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H16_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H12_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU636iMNC


title: Striatum WT Female (CAG_33_3_str)


title: Striatum BAC-CAG Female (CAG_33_2_str)


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H12_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU664ncMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H14_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H14_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Striatum BAC-CAG Male (CAG_34_1_str)


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H16_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H12_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU637iMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H14_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Cortex WT Male (CAG_40_2_ctx)

source_name: Cortex WT 2 mon Male


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H15_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H13_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H11_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Cortex WT Female (CAG_37_0_ctx)

source_name: Cortex WT 2 mon Female


title: Cortex WT Male (CAG_35_1_ctx)


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H11_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Cortex BAC-CAG Male (CAG_34_3_ctx)

source_name: Cortex BAC-CAG 2 mon Male


title: Cortex BAC-CAG Male (CAG_34_2_ctx)


title: Striatum BAC-CAG Female (CAG_33_1_str)


title: Cortex BAC-CAG Male (CAG_34_1_ctx)


title: NU636ncMNC

source_name: Umbilical cord blood


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G9_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G8_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU604iMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H10_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H10_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G7_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU602ncMNC


title: Cortex WT Female (CAG_33_4_ctx)


title: Cortex WT Male (CAG_34_5_ctx)


title: NU636cMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G8_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G9_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Cortex WT Female (CAG_33_3_ctx)


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G6_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU604cMNC


title: NU604ncMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H11_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU601ncMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G5_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Cortex BAC-CAG Female (CAG_33_1_ctx)

source_name: Cortex BAC-CAG 2 mon Female


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G5_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU597iMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G8_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G9_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G4_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Cortex BAC-CAG Female (CAG_33_2_ctx)


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G4_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Striatum WT Male (CAG_G_2_Str)

source_name: Striatum WT 12 mon Male

value: 12 mon


title: Cortex BAC-CAG Female (CAG_33_5_ctx)


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G5_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G3_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU602cMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G6_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G7_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G2_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU601cMNC


title: Striatum WT Male (CAG_F_7_Str)


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G4_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU595ncMNC


title: NU601iMNC


title: NU597ncMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G6_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, H10_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G7_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G22_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Striatum BAC-CAG Female (CAG_c_1_Str)

source_name: Striatum BAC-CAG 12 mon Female


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G2_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G22_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU586ncMNC


title: NU597cMNC


title: NU602iMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G2_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU586cMNC


title: Striatum WT Male (CAG_F_8_Str)


title: Striatum WT Male (CAG_G_1_Str)


title: Striatum BAC-CAG Male (CAG_G_3_Str)

source_name: Striatum BAC-CAG 12 mon Male


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G3_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G24_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G20_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G23_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU583ncMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G24_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU583cMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G1_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Striatum WT Female (CAG_a_6_Str)

source_name: Striatum WT 12 mon Female


title: Striatum BAC-CAG Male (CAG_F_6_Str)


title: NU586iMNC


title: NU595cMNC


title: NU595iMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G23_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G19_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G3_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Striatum BAC-CAG Female (CAG_c_2_Str)


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G19_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU581cMNC


title: Striatum BAC-CAG Female (CAG_b_2_Str)


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G23_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU579iMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G20_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU579ncMNC


title: Striatum WT Female (CAG_b_5_Str)


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G18_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G17_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU583iMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G17_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G20_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G17_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU579cMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G16_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G21_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G21_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Striatum WT Female (CAG_b_4_Str)


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G16_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G1_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G1_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G15_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G21_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Striatum BAC-CAG Female (CAG_b_3_Str)


title: Cortex WT Male (CAG_F_7_Ctx)

source_name: Cortex WT 12 mon Male


title: Striatum WT Female (CAG_a_5_Str_1)


title: Cortex BAC-CAG Male (CAG_F_6_Ctx)

source_name: Cortex BAC-CAG 12 mon Male


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G14_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU581iMNC


title: NU570ncMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G19_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU570iMNC


title: Striatum BAC-CAG Male (CAG_A_5_Str)


title: Striatum BAC-CAG Male (CAG_A_4_Str)


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G18_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Cortex BAC-CAG Male (CAG_G_3_Ctx)


title: NU570cMNC


title: Cortex BAC-CAG Female (CAG_c_1_Ctx)

source_name: Cortex BAC-CAG 12 mon Female


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G12_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G11_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G18_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Cortex WT Male (CAG_G_1_Ctx)


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G11_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Cortex WT Male (CAG_G_2_Ctx)


title: Cortex BAC-CAG Female (CAG_b_3_Ctx)


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G14_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G12_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G10_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G14_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G16_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Cortex WT Male (CAG_F_8_Ctx)


title: NU571iMNC


title: NU571cMNC


title: p-PDH A1_ChIP-Seq

city: Chuncheon

first: Jubayer

middle: Abu

last: Hossain

state: Gangwon-do

address: Chuncheon, Gangwon-do, 24252

department: Medical science

country: South Korea

institute: Hallym University College Of Medicine

library_source: genomic

data_processing:
Illumina Casava1.8 software used for basecalling.
The reads were trimmed and aligned using Bowtie2 (Langmead and Salzberg, 2012).
We used MACS (Model-based Analysis of ChIP-Seq) to identify peaks from the alignment file.
Genome_build: hg19

molecule: genomic DNA

source_name: Human Hepatocellular Carcinoma HepG2 Cells

growth_protocol: HepG2 cells were cultured in DMEM media, supplemented with 10% FBS and 1% penicillin/Streptomycin antibiotics. In 100 mm (diameter) dishes, the cells were seeded (1×107 – 3×107 cells per dish) and then incubated for two days for complete growth.

extract_protocol:
Lysates were clarified by sonication and Chromatin-DNA complexes were immunopricipited with selctive antibodies
The construction of library was performed using NEBNext®UltraTM DNA Library Prep Kit for Illumina (New England Biolabs, UK) according to the manufacturer’s instructions.

treatment_protocol: After complete groth of HepG2 cells then media was exchanged for DMEM without serum for 12 h and the cells were then treated with 100 nM insulin for 48 h

tag: cell type

tag: passages

tag: company

value: korean Cell Bank (KCB)

tag: chip antibody

value: p-PDH A1 (cat:92696, Abcam)


title: NU571ncMNC

value: ncMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G15_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F9_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G13_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G15_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F9_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G13_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU569iMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F8_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Cortex WT Female (CAG_b_4_Ctx)

source_name: Cortex WT 12 mon Female

value: FvB

value: WT


title: Cortex WT Female (CAG_b_5_Ctx)

value: Female


title: DKP162

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: dnPD


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G11_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000

tag: age


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G12_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Cortex BAC-CAG Female (CAG_b_2_Ctx)

value: Tg

tag: tissue


title: IgG_ChIP-Seq

value: IgG ( cat:2729S, Cell Signaling technology)


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F7_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000

tag: gender


title: NU569cMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F9_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000

tag: cell line


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G13_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000

tag: treatment


title: Cortex BAC-CAG Female (CAG_c_2_Ctx)

value: Cortex


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F7_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000

value: neutrophil lineage differentiation in the presence of  ATRA

tag: ethnicity


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G10_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000

value: female


title: RIP Eif4a2 KO + Eif4a2flag rep2

city: Vienna

first: Martin

last: Leeb

address: Dr.-Bohr-Gasse 9/3

department: Max Perutz Labs

country: Austria

institute: University of Vienna

description: 87628_GCGCTG_CD4K4ANXX_7_20190621B_20190621

data_processing:
Reads were trimmed using bbduk (Version 38.57). Reads were mapped to the mm10 mouse reference genome with STAR (Version 2.5.3a). Afterwards indexing was performed using samtool (Version 1.5) and reads in transcripts were counted with HTSeq-count (Version 0.11.2).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

source_name: RIP Eif4a2 KO + Eif4a2flag_ESCs

growth_protocol: ESCs were cultured in ES-DMEM/2i, which consists of DMEM high-glucose (Sigma-Aldrich, D5671) supplemented with 15% FBS (Gibco, 10270-106), 2mM L-Glutamine (Sigma-Aldrich, G7513), 0.1mM NEAA (Sigma-Aldrich, M7145), 1mM Sodium Pyruvate (Sigma-Aldrich, S8636), 10 µg/ml penicillin-streptomycin (Sigma-Aldrich, P4333) 55µM β-mercaptoethanol (Fisher-Scientific, 21985-023), 2i (1.5μM CHIR99021 and 0.5μM PD0325901) and 10 ng/ml LIF (batch tested, in-house)

extract_protocol:
RIP was performed using the MAGNA-RIP kit (Millipore 17-700). 5µg of anti-FLAG M2 antibody (Sigma-Aldrich, F1804) were incubated with the lysates for 3 hours at 4°C to immunoprecipitate either the empty vector or Eif4a2flag
Libraries were prepared using the QuantSeq 3′mRNA-Seq Library Prep Kit for Illumina FWD (Lexogen, R3142)

value: Eif4a2 KO + Eif4a2flag

value: embryonic stem cells (ESCs)

tag: culture condition

tag: sample type

value: RIP Eif4a3


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F6_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Cortex WT Female (CAG_a_6_Ctx)

tag: strain background

value: 12 mon


title: NU569ncMNC

tag: cell population

value: Umbilical cord

tag: gestational age


title: DKP156

description: rawcounts.txt


title: PKM2_ChIP-Seq

tag: cell type

value: korean Cell Bank (KCB)

value: PKM2 (cat:4053,Cell Signaling technology)


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G10_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: RIP Eif4a2 KO + EV rep2

description: 87624_GGCCAA_CD4K4ANXX_7_20190621B_20190621

source_name: RIP Eif4a2 KO + EV_ESCs

tag: genotype

value: Eif4a2 KO

value: RIP EV


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F5_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKP152

description: rawcounts.txt


title: RIP Eif4a2 KO + EV rep1

description: 87623_TGGATT_CD4K4ANXX_7_20190621B_20190621


title: Cortex BAC-CAG Male (CAG_A_5_Ctx)

value: FvB

tag: Sex

value: Male


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F4_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Cortex WT Female (CAG_a_5_Ctx_1)

value: WT

value: Female


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F8_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F8_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Cortex BAC-CAG Male (CAG_A_4_Ctx)

value: Tg


title: Input Eif4a2 KO + Eif4a2flag rep1

description: 87621_AAGTGG_CD4K4ANXX_7_20190621B_20190621

source_name: Input Eif4a2 KO + Eif4a2flag_ESCs

value: input


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F3_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000

value: neutrophil lineage differentiation in the presence of  ATRA


title: DKP148

description: rawcounts.txt

value: GOE

value: dnPD


title: RIP Eif4a2 KO + Eif4a2flag rep1

description: 87627_CCTGCT_CD4K4ANXX_7_20190621B_20190621

value: Eif4a2 KO + Eif4a2flag

value: embryonic stem cells (ESCs)

value: RIP Eif4a2


title: DKP146

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F7_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000

value: female


title: Input Eif4a2 KO + EV rep1

description: 89537_GAACCT_CD4K4ANXX_7_20190621B_20190621

source_name: Input Eif4a2 KO + EV_ESCs


title: DKP157

description: rawcounts.txt


title: DKP161

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F2_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKP145

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F4_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F4_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F2_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F24_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F24_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Smg6 KO 6h U rep1

data_processing:
library strategy: Quant-seq
SLAM-DUNK (Version 0.2.4)
Genome_build: mm10
Supplementary_files_format_and_content: Matrix with CPM and read counts for T conversions for each transcripts

source_name: Smg6 KO 6h U_ESCs

growth_protocol: ESCs were cultured in N2B27/2i, which consists of a 1:1 mix of DMEM/F12 (Gibco, 21331020) and Neurobasal medium (Gibco, 21103049) supplemented with 0.5x N2 (homemade), 1x B-27 Serum-Free Supplement (Gibco, 17504-044), 2mM L-Glutamine (Sigma-Aldrich, G7513), 0.1mM NEAA (Sigma-Aldrich, M7145), 10 µg/ml penicillin-streptomycin (Sigma-Aldrich, P4333) 55µM β-mercaptoethanol (Fisher-Scientific, 21985-023) and 2i (3μM CHIR99021 and 1μM PD0325901)

extract_protocol:
RNA was extracted with Trizol. RNA was resuspended in 1mM DTT. 5µg of RNA were treated with 10mM iodoacetamide (Sigma-Aldrich, I1149) followed by ethanol precipitation
Libraries were prepared using the QuantSeq 3′mRNA-Seq Library Prep Kit for Illumina FWD (Lexogen, R3142)

treatment_protocol: ESCs were pulsed with 4SU for 12 hours (4SU samples) then they were subjected to a Uridine chase for either 3 hours (3h U samples) or 6 hours (6 h U samples)

value: Smg6 KO

value: 12 hours 4SU treatment and 6 hours Uridine chase


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F23_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Input Eif4a2 KO + Eif4a2flag rep2

description: 87622_CTCATA_CD4K4ANXX_7_20190621B_20190621


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F3_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F5_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKP150

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F6_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F6_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F5_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F22_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKP151

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F21_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKP134

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F23_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F21_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F20_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKP159

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F23_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F20_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Input Eif4a2 KO + EV rep2

description: 87618_GCAGCC_CD4K4ANXX_7_20190621B_20190621

value: Eif4a2 KO


title: DKP138

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F3_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F2_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKP132

description: rawcounts.txt


title: DKP137

description: rawcounts.txt


title: DKP131

description: rawcounts.txt


title: DKP144

description: rawcounts.txt


title: Smg6 KO 6h U rep2


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F22_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F19_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKP141

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F18_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKP129

description: rawcounts.txt


title: DKP133

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F1_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F18_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKP124

description: rawcounts.txt


title: Smg5 KO 6h U rep1

source_name: Smg5 KO 6h U_ESCs

value: Smg5 KO


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F17_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: WT 3h U rep2

source_name: WT 3h U_ESCs

value: wild-type

value: 12 hours 4SU treatment and 3 hours Uridine chase


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F1_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKP123

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F21_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: WT 6h U rep2

source_name: WT 6h U_ESCs


title: WT 6h U rep1


title: Smg6 KO 4SU rep2

source_name: Smg6 KO 4SU_ESCs

value: 12 hours 4SU treatment


title: DKP128

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F15_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Smg5 KO 3h U rep2

source_name: Smg5 KO 3h U_ESCs


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F20_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Smg6 KO 3h U rep2

source_name: Smg6 KO 3h U_ESCs


title: Smg5 KO 3h U rep1


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F14_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F14_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Smg5 KO 6h U rep2


title: DKP118

description: rawcounts.txt


title: WT 4SU rep2

source_name: WT 4SU_ESCs


title: Smg6 KO 3h U rep1


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F16_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: WT 3h U rep1


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F1_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F18_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F17_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F14_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F16_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F19_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKP114

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F13_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F15_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F15_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F13_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Smg6 KO t0 rep2

source_name: Smg6 KO t0_ESCs

value: untreated


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F17_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKP112

description: rawcounts.txt


title: Smg5 KO 4SU rep1

source_name: Smg5 KO 4SU_ESCs


title: DKP119

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F11_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Smg5 KO 4SU rep2


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F16_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKP122

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F12_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F10_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F12_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKP113

description: rawcounts.txt


title: Smg5 KO t0 rep1

source_name: Smg5 KO t0_ESCs


title: DKP117

description: rawcounts.txt


title: Smg6 KO 4SU rep1


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F11_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E9_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E9_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: WT 4SU rep1


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E8_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E9_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F13_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: 49-3, Input

city: Chengdu

first: Qin

last: Guo

address: Baoguang Road, Xindu district, Chengdu, Sichuan

department: Department of Gastroenterology

country: China

institute: chengdu medical college

data_processing:
Reads were harvested from Illumina HiSeq sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
Clean reads of input libraries were aligned to reference genome (UCSC HG19) by Hisat2 software (v2.0.4).
After that, The MACS (v1.4.2) software compares the clean reads with the human genome to identify the methylation sites (peaks) on RNAs.
Differentially m6A methylated sites were identified by diffReps (v1.55.3).
These peaks identified by both software with overlapping mRNA exons were identified by home-made scripts.
Genome_build: UCSC HG19
Supplementary_files_format_and_content: Bed files were generated using
Supplementary_files_format_and_content: peak text files

source_name: CRC adjacent normal tissue

extract_protocol:
RNA was extracted using TRIzol Reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's instructions. The NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Ipswich, MA, USA) was used to remove ribosomal RNA from the total RNA. The concentration and purity of RNA were detected using a NanoDrop ND-1000 spectrophotometer (Thermo, Waltham, MA, USA), and the integrity of RNA was evaluated using denaturing gel electrophoresis.
Briefly, m6A RNA immunoprecipitation was performed with the GenSeqTM m6A-MeRIP Kit (GenSeq Inc., China) by following the manufacturer’s instructions. Both the input samples without immunoprecipitation and the m6A IP samples were used for RNA-seq library generation with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA). The library quality was evaluated with BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina Hiseq instrument with 150bp paired-end reads.
Methyl-seq

tag: individual

value: patient 49

tag: disease state

value: colorectal cancer (CRC)

value: CRC adjacent normal tissue

value: 73 years old

tag: Stage


title: Smg6 KO t0 rep1


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E7_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000

value: neutrophil lineage differentiation in the presence of  ATRA

tag: age


title: 48-3, Input

value: patient 48

tag: tissue

value: 59 years old


title: DKP109

description: rawcounts.txt

source_name: serum

tag: collection site

value: GOE

tag: phenotypic group

value: dnPD


title: DKP093

description: rawcounts.txt


title: DKP108

description: rawcounts.txt


title: 48-2, Input

source_name: CRC

value: CRC


title: WT t0 rep2

source_name: WT t0_ESCs

value: embryonic stem cells (ESCs)

tag: treatment


title: DKP111

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F12_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000

tag: cell line

tag: gender

value: female

tag: ethnicity


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F10_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F10_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKP103

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F11_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Smg5 KO t0 rep2

value: Smg5 KO

tag: culture condition


title: DKP092

description: rawcounts.txt


title: DKP110

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E6_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E6_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E7_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: 25-3, Input

value: patient 25

value: 80 years old


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E6_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: WT t0 rep1

value: wild-type


title: DKP082

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E8_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: 49-2, Input


title: DKP099

description: rawcounts.txt


title: DKP105

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E5_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E8_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: 24-3, Input

value: patient 24

value: 56 years old


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F19_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKP079

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E5_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E4_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E5_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKP077

description: rawcounts.txt


title: DKP081

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E7_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E3_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: 25-2, Input

value: colorectal cancer (CRC)


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E4_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E4_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKP072

description: rawcounts.txt


title: 24-2, Input


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E24_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: 49-3, ChIP

value: patient 49

value: CRC adjacent normal tissue


title: 23-2, Input

value: patient 23

value: 70 years old


title: DKP075

description: rawcounts.txt


title: 49-2, ChIP

value: 73 years old


title: 23-3, Input


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E24_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000

value: neutrophil lineage differentiation in the presence of  ATRA


title: 48-3, ChIP

value: patient 48

value: 59 years old


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E23_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E2_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E3_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKP070

description: rawcounts.txt

value: GOE

value: dnPD


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E2_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000

value: female


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E2_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E23_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKP062

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E3_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKP063

description: rawcounts.txt


title: 48-2, ChIP

value: CRC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E22_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E21_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E22_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKP054

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E21_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: 25-2, ChIP

value: patient 25

value: 80 years old


title: DKP059

description: rawcounts.txt


title: 25-3, ChIP


title: DKP051

description: rawcounts.txt


title: 24-3, ChIP

value: patient 24


title: 24-2, ChIP

value: 56 years old


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E21_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E1_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E20_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E23_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E20_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: 23-3, ChIP

value: colorectal cancer (CRC)


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E1_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E19_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E19_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E1_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: 23-2, ChIP


title: DKP049

description: rawcounts.txt


title: DKP044

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E18_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKP060

description: rawcounts.txt


title: D10 E144Q/E145Q No Dox rep 3

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

value: Integrated doxycycline-inducible D10 E144Q/E145Q gene using lentivirus

value: Untreated


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E17_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E17_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: D10 E144Q/E145Q Plus Dox rep 3

value: Treated with 1 μg/mL doxycycline for 8 hours


title: DKP039

description: rawcounts.txt


title: DKP047

description: rawcounts.txt


title: DKP046

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E17_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E16_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E20_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E16_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKP038

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E18_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: D10 WT No Dox rep 3

value: Integrated doxycycline-inducible D10 WT gene using lentivirus


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E16_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000

value: neutrophil lineage differentiation in the presence of  ATRA


title: D10 WT Plus Dox rep 3


title: D10 E144Q/E145Q No Dox rep 2


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E15_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E19_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: D10 WT Plus Dox rep 2


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E15_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKP031

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E18_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKK113

description: rawcounts.txt

value: CTR


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E14_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKP019

description: rawcounts.txt


title: DKP003

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E15_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: D10 WT No Dox rep 2


title: DKK112

description: rawcounts.txt


title: DKK110

description: rawcounts.txt


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E14_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: DKK107

description: rawcounts.txt


title: D10 E144Q/E145Q No Dox rep 1


title: D10 E144Q/E145Q Plus Dox rep 2


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E12_MemorySeq028

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: D10 WT Plus Dox rep 1


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E14_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E11_MemorySeq010

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: si-FTO3_input

city: Shenyang

first: JiaPeng

last: Huang

address: No. 155 in Nanjing North Street

department: Department of Thyroid Surgery

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.

value: Papillary thyroid cancer cell line

tag: sirna

value: si-FTO

tag: antibody


title: si-FTO2_input

tag: cell type


title: D10 E144Q/E145Q Plus Dox rep 1

tag: genotype


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E13_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000