title: Stage E7.0 embryo 1 section 10 region A

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_10A


title: Stage E7.5 with L/R sections embryo 2 section 7 region EP

status: Public on Aug 15 2023

type: SRA

city: Boston

first: Jiehui

last: Chen

state: MA

address: 320 Longwood Ave

country: USA

institute: Boston Children’s Hospital

description:
E7.5_LR_2.txt
E7.5_LR_2_7EP

library_source: transcriptomic

data_processing:
Raw reads were mapped to mm10 version of the mouse genome using the Tophat2 v2.0.4 program.
We calculated fragment per kilobase per million (FPKM) as expression level using Cufflinks v2.0.2 with default parameters.
Genes with the FPKM value > 1.0 in at least one sample across all samples were retained for further analysis.
The expression levels were transformed to logarithmic space by using log2(FPKM+1).
Batch effects were corrected using ComBat function in R.
Genome_build: mm10
Supplementary_files_format_and_content: Textfile includes FPKM values for each embryo

molecule: total RNA

organism: Mus musculus

source_name: Mouse embryonic cells

growth_protocol: Embryos from pre-gastrulation to late-gastrulation mouse were embedded with OCT and subjected to cryosection.

extract_protocol:
According to Geo-seq (Chen et al., 2017), RNA from LCM samples were extracted by 5M GuSCN (Invitrogen, # 20012-043), then RNA was precipitated by ethanol with the help of RNA carrier.
Libraries were constructed using illumina Nextera XT DNA sample preparation kit.

treatment_protocol: Sample from each location was laser-microdissected and collected for single-cell based RNA sequencing. For the single cells isolated from known positions, embryos were dissected from the decidua in 10% FBS-DMEM medium, and cells were isolated from a specific position of the embryo by mouth pipetting guided by microscopy, then subject to Smart-seq2.

tag: developmental stage

tag: strain

tag: tissue

value: embryo


title: Shield, omf201, whole embryo, replicate 5

city: Oklahoma

first: Christopher

middle: Lee

last: Sansam

state: OK

address: 825 NE 13th Street

department: Cell Cycle and Cancer Biology Program

institute: Oklahoma Medical Research Foundation

description:
Shield_omf201_WE_5
Counts.csv
Smoothed.csv
ZScores.csv
Log2Ratios.csv
Quotients.csv

library_source: genomic

data_processing:
Raw reads were trimmed with fastp.
Trimmed reads were aligned to the zebrafish genome with BWA-MEM.
Duplicate reads were marked with Picard MarkDuplicates.
Properly-paired and non-duplicated reads with MapQ scores of at least 20 were filtered with Bamtools.
Alignments were read into GenomicRanges for downstream analysis in R.
Reads were removed if they were within a set of 100 bp windows with anomalously high read counts (exceeding 1.5 times the interquartile range in at least 4 out of 65 whole genome sequencing runs from this study and previously published work). Genomic windows for calculating RT were defined as regions with a minimum of 400 reads in every sample. An S/G1 quotient was calculated for each window, and quotients were smoothed and Log2 transformed
Assembly: GRCz11
Supplementary files format and content: Counts.csv has read counts in replication timing windows for all samples.
Supplementary files format and content: Quotients.csv has S/G1 Quotients calculated from read counts in replication timing windows for all samples.
Supplementary files format and content: Smoothed.csv  has smoothed quotients.
Supplementary files format and content: Log2Ratios.csv has Log2 transformations of all smoothed S/G1 Quotients
Supplementary files format and content: ZScores.csv has Z Scores of all smoothed S/G1 Quotients
Library strategy: DNA-seq

molecule: genomic DNA

organism: Danio rerio

source_name: whole organism

growth_protocol: Adult breeding fish were housed in an aquatic animal facility in tanks of ∼30 fish per tank and maintained at 26.5°C with 10-hour light and 14-hour dark cycles.

extract_protocol:
Genomic DNA was prepared from whole embryo pellets or sorted nuclei using the Quick-DNA Miniprep Plus Kit (D4069; Zymo Research). mRNA was prepared from whole embryos using the RNeasy Mini Kit (74104; Qiagen).
For whole-genome sequencing, 50ng - 2μg of gDNA was sheared to approximately 300 bp fragments using a sonicator (Covaris). The gDNA libraries were prepared using the KAPA Hyper Prep Kit (Roche) with SeqCap (Roche) or Illumina TruSeq (Illumina) adapters. Genomic DNA libraries were sequenced in 150bp paired-end read fragments on an Illumina HiSeq 2500 or NovaSeq 6000.

treatment_protocol: Zebrafish were spawned, and cohorts of embryos were collected within 10 minutes of fertilization. Embryos were incubated at 28.5°C. Before collection, clutches were visually inspected to ensure that all embryos were developing synchronously. Unfertilized or morphologically abnormal embryos were removed before collection. Pools of >100 whole embryos at preMBT, dome, or shield stage were treated as S-phase samples, since a high percentage cells at these stages are in S phase. Nuclei from bud or 24 hpf embryos were sorted based on DNA content to isolate G1 and S-phase fractions. Whole embryo pools to be used for gDNA were rapidly frozen and stored at −80°C for later processing. For DNA content FACS-sorting of cells, bud stage or 24 hpf embryos were dechorionated with Pronase, deyolked, and then triturated to a single cell suspension in Phosphate Buffered Saline. Nuclei were prepared from the cells were incubated in DNA staining solution (PBS; 1% Bovine Serum Albumin; 50 ug/ml Propidium iodide P4170-25mg Sigma-Aldrich; 100 ug/ml RNAse A 12091039 Invitrogen) on ice for at least one hour before sorting. The nuclei were then filtered through a 40μm mesh before analysis on a BD LSRII (shield and bud), BD Biosciences FACSAria IIIu (28hpf) or BD Biosciences FACSCalibur.

value: whole organism

tag: time

value: 6 hpf

tag: genotype

value: rif1 omf201/omf201

tag: cell cycle_phase

value: Asynchronous


title: Stage E7.0 embryo 1 section 9 region M

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_9M


title: Shield, omf201, whole embryo, replicate 4

description:
Shield_omf201_WE_4
Counts.csv
Smoothed.csv
ZScores.csv
Log2Ratios.csv
Quotients.csv


title: Stage E7.5 with L/R sections embryo 2 section 7 region A

description:
E7.5_LR_2.txt
E7.5_LR_2_7A


title: Shield, WT, whole embryo, replicate 3

description:
Shield_WT_WE_3
Counts.csv
Smoothed.csv
ZScores.csv
Log2Ratios.csv
Quotients.csv

value: WT


title: Stage E7.0 embryo 1 section 9 region EP

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_9EP


title: Stage E7.5 with L/R sections embryo 2 section 6 region R2

description:
E7.5_LR_2.txt
E7.5_LR_2_6R2


title: Shield, omf201, whole embryo, replicate 2

description:
Shield_omf201_WE_2
Counts.csv
Smoothed.csv
ZScores.csv
Log2Ratios.csv
Quotients.csv


title: Shield, omf201, whole embryo, replicate 1

description:
Shield_omf201_WE_1
Counts.csv
Smoothed.csv
ZScores.csv
Log2Ratios.csv
Quotients.csv


title: Stage E7.5 with L/R sections embryo 2 section 6 region R1

description:
E7.5_LR_2.txt
E7.5_LR_2_6R1


title: Stage E7.0 embryo 1 section 9 region EA

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_9EA


title: preMBT, WT, whole embryo, replicate 1

description:
preMBT_WT_WE_1
Counts.csv
Smoothed.csv
ZScores.csv
Log2Ratios.csv
Quotients.csv


title: Stage E7.0 embryo 1 section 8 region M

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_8M


title: Stage E7.0 embryo 1 section 8 region EP

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_8EP


title: Stage E7.5 with L/R sections embryo 2 section 7 region EA

description:
E7.5_LR_2.txt
E7.5_LR_2_7EA


title: Stage E7.0 embryo 1 section 8 region EA

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_8EA


title: preMBT, omf201, whole embryo, replicate 3

description:
preMBT_omf201_WE_3
Counts.csv
Smoothed.csv
ZScores.csv
Log2Ratios.csv
Quotients.csv


title: Stage E7.5 with L/R sections embryo 2 section 6 region MPR

description:
E7.5_LR_2.txt
E7.5_LR_2_6MPR


title: Stable MGUS patient_303

type: RNA

city: Little Rock

first: Fumou

last: Sun

state: Arkansas

address: 4301 W. Markham, Slot 508

department: Internal Medicine

institute: University of Arkansas for Medical Sciences

description:
S303
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).

hyb_protocol: Double-stranded complementary DNA (cDNA) and biotinylated complementary RNA (cRNA) were hybridized to GeneChip microarrays (Affymetrix, Santa Clara, CA), which were washed and scanned according to procedures developed by the manufacturer.

scan_protocol: The arrays were scanned using Hewlett Packard confocal laser scanner and visualized using Affymetrix 3.3 software (Affymetrix).

data_processing: The data were processed using Microarray Suite version 5.0 (MAS 5.0) with Affymetrix default analysis settings and global scaling as the normalization method. The trimmed mean target intensity of each array was standardized to a value of 100 as a reference point.

label: Biotin

organism: Homo sapiens

source_name: Bone marrow Stable MGUS patient

label_protocol: Double-stranded cDNA is synthesized from 6 ug total RNA. An in vitro transcription (IVT) reaction is then done to produce biotin-labeled cRNA from the cDNA. The cRNA is fragmented before hybridization. The protocol according to the manufacturer's instructions Expression Analysis Technical Manual, 2001, Affymetrix.

growth_protocol: Plasma cells were enriched by anti-CD138 immunomagnetic bead selection of mononuclear cell fractions from bone marrow aspirates in a central laboratory. All samples analyzed by microarray contained more than 85% plasma cells as determined by 2-color flow cytometry (CD38+ and CD45–/dim) performed after selection.

extract_protocol:
Fresh plasma cells were used directly for RNA extraction.
Total RNA was isolated with RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.

tag: cell type

value: Bone marrow plasma cells

tag: disease state

value: Stable MGUS


title: Stable MGUS patient_304

description:
S304
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_302

description:
S302
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Shield, omf201, whole embryo, replicate 3

description:
Shield_omf201_WE_3
Counts.csv
Smoothed.csv
ZScores.csv
Log2Ratios.csv
Quotients.csv


title: Stable MGUS patient_300

description:
S300
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_301

description:
S301
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_299

description:
S299
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_297

description:
S297
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.0 embryo 1 section 7 region EP

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_7EP


title: Stable MGUS patient_305

description:
S305
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 with L/R sections embryo 2 section 6 region MAR

description:
E7.5_LR_2.txt
E7.5_LR_2_6MAR


title: Stable MGUS patient_298

description:
S298
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: preMBT, omf201, whole embryo, replicate 1

description:
preMBT_omf201_WE_1
Counts.csv
Smoothed.csv
ZScores.csv
Log2Ratios.csv
Quotients.csv


title: Stable MGUS patient_296

description:
S296
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 with L/R sections embryo 2 section 6 region P

description:
E7.5_LR_2.txt
E7.5_LR_2_6P


title: Stage E7.5 with L/R sections embryo 2 section 6 region MAL

description:
E7.5_LR_2.txt
E7.5_LR_2_6MAL


title: Stage E7.0 embryo 1 section 7 region EA

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_7EA


title: Stage E7.5 with L/R sections embryo 2 section 6 region L2

description:
E7.5_LR_2.txt
E7.5_LR_2_6L2


title: Stage E7.5 with L/R sections embryo 2 section 6 region L1

description:
E7.5_LR_2.txt
E7.5_LR_2_6L1


title: Stage E7.0 embryo 1 section 6 region M

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_6M


title: Stage E7.0 embryo 1 section 6 region EP

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_6EP


title: Stage E7.0 embryo 1 section 7 region M

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_7M


title: Stage E7.5 with L/R sections embryo 2 section 6 region MPL

description:
E7.5_LR_2.txt
E7.5_LR_2_6MPL


title: 20C_CCNT1_1stim

city: Seattle

first: Terry

last: Hafer

email: tjhafe@gmail.com, thafer@fredhutch.org

state: Washington

address: 1100 Fairview Ave N

department: Human Biology

institute: Fred Hutchinson Cancer Center

description:
primary_bulk_counts.tsv
20C_CCNT1_1stim_S20

data_processing:
Image analysis and basecalling was performed using Illumina's Real Time Analysis v3.4.4 software, followed by demultiplexing of indexed reads and generation of FASTQ files with Illumina's bcl2fastq-2.20 software.
Sequenced reads were aligned to a  custom reference (described below) or iGenome's UCSC hg38 using STAR2 aligner v2.7.7a in the two-pass mode.
STAR2's internal quantification method was used to generate gene-level raw counts. A custom GTF file was used for the cell line data which was based on UCSC hg38 annotations, shifted appropriately downstream of the insertion on chr 9. Gencode v38 annotations were used for the primary cell data.
Assembly: cell lines custom genome based on GRCh38/hg38 with HIV integrated into chr9 as in J-Lat MN989412 reference
Assembly: primary cells hg38
Supplementary files format and content: tab-delimited file containing raw gene counts per sample

molecule: polyA RNA

source_name: T Lymphocyte

growth_protocol: J-Lat cells were cultured in RPMI 1640 media (ThermoFisher, 11875093) supplemented with Pen/Strep, 10% Fetal Bovine Serum (FBS), and 10 mM HEPES (ThermoFisher, 15630080). Cells were maintained at 37ºC with 5% CO2. Primary CD4+ T cell media used was RPMI 1640 + 1x Anti-Anti (Gibco, 15240096), 1x GlutaMAX (ThermoFisher Scientific; 35050061), 10 mM HEPES, and 10% FBS. CD4+ T cells were isolated from PBMCs using the EasySep Human CD4+ T cell Isolation Kit (Stemcell Technologies, 17952) and subsequently activated using the T Cell Activation/Expansion Kit (Miltenyi Biotec, 130-091-441). From this point forward, CD4+ T cells were cultured in RPMI + IL-2 (final concentration 100 U/mL, Roche, 10799068001), IL-7 (final conc. 2 ng/mL, Peprotech, 200-07) and IL-15 (final conc. 2 ng/mL, Peprotech, 200-15).

extract_protocol:
In both J-Lat and primary CD4+ T cell RNA isolation experiments, 0.1-2E6 cells were isolated and resuspended in 350 uL of RLT Plus (Qiagen, 1053393) + 1% 2-mercaptoethanol (Millipore Sigma, M3148). Cells were frozen in buffer RLT plus until ready to continue with isolation. Thawed RLT lysates were then run over a QIAshredder column (Qiagen, 79654) and subsequently over a gDNA eliminator column. Qiagen RNeasy Plus Mini Kit was then used in order to obtain purified total RNA. RNA was submitted for TapeStation RNA assay or HighSense RNA assay (Fred Hutch Core Facilities) and RINe scores were all found to be greater than or equal to 9.6.
For J-Lat cells, library was prepared using Illumina TruSeq stranded mRNA standard protocol. For primary CD4+ T cells, library was prepared using Takara/Clontech SMARTv4 + Ilumina Nextera XT protocol.

treatment_protocol: For J-Lat Cells: For RNA isolated from J-Lat 10.6 cells, cells first were passaged and split equally three times prior to isolation. J-Lat 10.6 either wild-type for CCNT1 or knocked out for CCNT1 were each treated with TNFα (Peprotech, 300-01A) at 10 ng/mL or unstimulated in triplicate. RNA was harvested after 24 hours of LRA treatment. For Primary CD4+ T cells: CD4+ T cells were activated using the T Cell Activation/Expansion Kit (Miltenyi Biotec, 130-091-441) for two days, at which point the activation beads were magnetically removed. Three days later, cells were electroporated following the protocol above, and treated with CD3/CD28 antibody co-stimulation after cells were allowed to recover for two additional days. CD3 antibody (Tonbo, 40-0038-U500) was used at a concentration of 10 ug/mL and CD28 antibody (Tonbo, 40-0289-U500) at a concentration of 5 ug/mL. After 24 hours of CD3/CD28 antibody co-stimulation, RNA was harvested and genomic DNA was simultaneously collected to assess knockout by genomic analysis.

value: T Lymphocyte

tag: treatment

value: Cyclin T1 KO + CD3/CD28 antibody co-stimulation


title: preMBT, omf201, whole embryo, replicate 2

description:
preMBT_omf201_WE_2
Counts.csv
Smoothed.csv
ZScores.csv
Log2Ratios.csv
Quotients.csv


title: 19C_AAVS1_1stim

description:
primary_bulk_counts.tsv
19C_AAVS1_1stim_S19

value: Control KO + CD3/CD28 antibody co-stimulation


title: 18B_CCNT1_2stim

description:
primary_bulk_counts.tsv
18B_CCNT1_2stim_S18


title: Stage E7.5 with L/R sections embryo 2 section 6 region EP

description:
E7.5_LR_2.txt
E7.5_LR_2_6EP


title: Stable MGUS patient_295

description:
S295
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: 17B_AAVS1_2stim

description:
primary_bulk_counts.tsv
17B_AAVS1_2stim_S17


title: Stage E7.0 embryo 1 section 5 region M

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_5M


title: Stage E7.5 with L/R sections embryo 2 section 6 region A

description:
E7.5_LR_2.txt
E7.5_LR_2_6A


title: 15A_AAVS1_2stim

description:
primary_bulk_counts.tsv
15A_AAVS1_2stim_S15


title: Stage E7.0 embryo 1 section 5 region EP

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_5EP


title: 16A_CCNT1_2stim

description:
primary_bulk_counts.tsv
16A_CCNT1_2stim_S16


title: Stable MGUS patient_294

description:
S294
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_292

description:
S292
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_293

description:
S293
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_291

description:
S291
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 with L/R sections embryo 2 section 5 region R2

description:
E7.5_LR_2.txt
E7.5_LR_2_5R2


title: Stage E7.5 with L/R sections embryo 2 section 5 region R1

description:
E7.5_LR_2.txt
E7.5_LR_2_5R1


title: Stage E7.0 embryo 1 section 5 region EA

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_5EA


title: 14C_CCNT1_1

description:
primary_bulk_counts.tsv
14C_CCNT1_1_S14

value: Cyclin T1 KO


title: Stage E7.0 embryo 1 section 4 region EP

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_4EP


title: Stable MGUS patient_289

description:
S289
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.0 embryo 1 section 4 region M

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_4M


title: Stage E7.0 embryo 1 section 6 region EA

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_6EA


title: Stable MGUS patient_290

description:
S290
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 with L/R sections embryo 2 section 5 region P

description:
E7.5_LR_2.txt
E7.5_LR_2_5P


title: 11B_AAVS1_2

description:
primary_bulk_counts.tsv
11B_AAVS1_2_S11

value: Control KO


title: 12B_CCNT1_2

description:
primary_bulk_counts.tsv
12B_CCNT1_2_S12


title: 13C_AAVS1_1

description:
primary_bulk_counts.tsv
13C_AAVS1_1_S13


title: Stage E7.5 with L/R sections embryo 2 section 5 region MPR

description:
E7.5_LR_2.txt
E7.5_LR_2_5MPR


title: Stage E7.5 with L/R sections embryo 2 section 6 region EA

description:
E7.5_LR_2.txt
E7.5_LR_2_6EA


title: Stage E7.0 embryo 1 section 4 region EA

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_4EA


title: Stage E7.5 with L/R sections embryo 2 section 5 region MPL

description:
E7.5_LR_2.txt
E7.5_LR_2_5MPL


title: Stage E7.0 embryo 1 section 3 region M

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_3M


title: Stage E7.0 embryo 1 section 3 region EP

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_3EP


title: 10A_CCNT1_2

description:
primary_bulk_counts.tsv
10A_CCNT1_2_S10


title: 9A_AAVS1_2

description:
primary_bulk_counts.tsv
9A_AAVS1_2_S9


title: Stable MGUS patient_287

description:
S287
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 with L/R sections embryo 2 section 5 region MAL

description:
E7.5_LR_2.txt
E7.5_LR_2_5MAL


title: Stage E7.0 embryo 1 section 3 region EA

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_3EA


title: Stable MGUS patient_286

description:
S286
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: 8B_CCNT1_1stim

description:
primary_bulk_counts.tsv
8B_CCNT1_1stim_S8


title: Stable MGUS patient_288

description:
S288
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.0 embryo 1 section 2 region M

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_2M


title: Stage E7.5 with L/R sections embryo 2 section 5 region L2

description:
E7.5_LR_2.txt
E7.5_LR_2_5L2


title: Stable MGUS patient_285

description:
S285
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_284

description:
S284
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: 7B_AAVS1_1stim

description:
primary_bulk_counts.tsv
7B_AAVS1_1stim_S7


title: 6A_CCNT1_1stim

description:
primary_bulk_counts.tsv
6A_CCNT1_1stim_S6


title: Stage E7.5 with L/R sections embryo 2 section 5 region EP

description:
E7.5_LR_2.txt
E7.5_LR_2_5EP


title: 4B_CCNT1_1

description:
primary_bulk_counts.tsv
4B_CCNT1_1_S4


title: 5A_AAVS1_1stim

description:
primary_bulk_counts.tsv
5A_AAVS1_1stim_S5


title: Stage E7.0 embryo 1 section 2 region EP

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_2EP


title: Stage E7.0 embryo 1 section 1 region EAP

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_1EAP


title: Stage E7.5 with L/R sections embryo 2 section 5 region MAR

description:
E7.5_LR_2.txt
E7.5_LR_2_5MAR


title: Stable MGUS patient_283

description:
S283
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 with L/R sections embryo 2 section 5 region EA

description:
E7.5_LR_2.txt
E7.5_LR_2_5EA


title: Stage E7.5 with L/R sections embryo 2 section 5 region A

description:
E7.5_LR_2.txt
E7.5_LR_2_5A


title: Stage E7.0 embryo 1 section 11 region M

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_11M


title: Stage E7.5 with L/R sections embryo 2 section 4 region R2

description:
E7.5_LR_2.txt
E7.5_LR_2_4R2


title: Stage E7.0 embryo 1 section 11 region EP

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_11EP


title: Stable MGUS patient_282

description:
S282
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_281

description:
S281
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_280

description:
S280
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_279

description:
S279
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_278

description:
S278
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.0 embryo 1 section 2 region EA

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_2EA


title: Stage E7.5 with L/R sections embryo 2 section 4 region R1

description:
E7.5_LR_2.txt
E7.5_LR_2_4R1


title: 1A_AAVS1_1

description:
primary_bulk_counts.tsv
1A_AAVS1_1_S1

value: Control Knockout (KO)


title: Stage E7.0 embryo 1 section 11 region EA

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_11EA


title: Stage E7.5 with L/R sections embryo 2 section 5 region L1

description:
E7.5_LR_2.txt
E7.5_LR_2_5L1


title: 2A_CCNT1_1

description:
primary_bulk_counts.tsv
2A_CCNT1_1_S2


title: Stable MGUS patient_277

description:
S277
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Jlat106 KO3C TNFa Rep3

description:
JLat_bulk_counts.tsv
18_Jlat106_KO3C_TNFa_3_S18

source_name: Jurkat (J-Lat 10.6)

tag: agent

value: TNFa

tag: cell line

value: Jurkat (J-Lat 10.6)


title: Stage E7.5 with L/R sections embryo 2 section 4 region P

description:
E7.5_LR_2.txt
E7.5_LR_2_4P


title: Stage E7.5 with L/R sections embryo 2 section 4 region MPL

description:
E7.5_LR_2.txt
E7.5_LR_2_4MPL


title: Stage E7.0 embryo 1 section 10 region EP

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_10EP


title: Jlat106 KO3C TNFa Rep1

description:
JLat_bulk_counts.tsv
16_Jlat106_KO3C_TNFa_1_S16


title: Stage E7.0 embryo 1 section 10 region M

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_10M


title: Stage E7.5 with L/R sections embryo 2 section 4 region MPR

description:
E7.5_LR_2.txt
E7.5_LR_2_4MPR


title: Stable MGUS patient_276

description:
S276
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.0 embryo 1 section 10 region EA

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_10EA


title: 3B_AAVS1_1

description:
primary_bulk_counts.tsv
3B_AAVS1_1_S3


title: Jlat106 KO3C TNFa Rep2

description:
JLat_bulk_counts.tsv
17_Jlat106_KO3C_TNFa_2_S17


title: Stage E7.5 with L/R sections embryo 2 section 4 region MAR

description:
E7.5_LR_2.txt
E7.5_LR_2_4MAR


title: Stable MGUS patient_275

description:
S275
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.0 embryo 3 section 9 region R

description:
E7.0_3.txt
E7.0_3_9R


title: Stable MGUS patient_273

description:
S273
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 with L/R sections embryo 2 section 4 region MAL

description:
E7.5_LR_2.txt
E7.5_LR_2_4MAL


title: Stable MGUS patient_274

description:
S274
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Jlat106 KO3B TNFa Rep2

description:
JLat_bulk_counts.tsv
14_Jlat106_KO3B_TNFa_2_S14


title: Stage E7.0 embryo 3 section 9 region P

description:
E7.0_3.txt
E7.0_3_9P


title: Stable MGUS patient_272

description:
S272
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 with L/R sections embryo 2 section 4 region L2

description:
E7.5_LR_2.txt
E7.5_LR_2_4L2


title: Jlat106 KO3B TNFa Rep3

description:
JLat_bulk_counts.tsv
15_Jlat106_KO3B_TNFa_3_S15


title: Stage E7.0 embryo 3 section 9 region M

description:
E7.0_3.txt
E7.0_3_9M


title: Jlat106 KO3B TNFa Rep1

description:
JLat_bulk_counts.tsv
13_Jlat106_KO3B_TNFa_1_S13


title: Stage E7.5 with L/R sections embryo 2 section 4 region L1

description:
E7.5_LR_2.txt
E7.5_LR_2_4L1


title: Stage E7.0 embryo 3 section 9 region L

description:
E7.0_3.txt
E7.0_3_9L


title: Jlat106 TNFa Rep3

description:
JLat_bulk_counts.tsv
12_Jlat106_TNFa_3_S12

value: wildtype


title: Stable MGUS patient_271

description:
S271
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 with L/R sections embryo 2 section 4 region EP

description:
E7.5_LR_2.txt
E7.5_LR_2_4EP

value: embryo


title: Jlat106 TNFa Rep2

description:
JLat_bulk_counts.tsv
11_Jlat106_TNFa_2_S11


title: Stage E7.0 embryo 3 section 9 region EP

description:
E7.0_3.txt
E7.0_3_9EP


title: Stage E7.5 with L/R sections embryo 2 section 4 region EA

description:
E7.5_LR_2.txt
E7.5_LR_2_4EA


title: Jlat106 TNFa Rep1

description:
JLat_bulk_counts.tsv
10_Jlat106_TNFa_1_S10


title: Stage E7.0 embryo 3 section 9 region EA

description:
E7.0_3.txt
E7.0_3_9EA


title: Stable MGUS patient_270

description:
S270
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.0 embryo 3 section 9 region A

description:
E7.0_3.txt
E7.0_3_9A


title: Jlat106 KO3C Rep3

description:
JLat_bulk_counts.tsv
9_Jlat106_KO3C_3_S9


title: Stage E7.5 with L/R sections embryo 2 section 4 region A

description:
E7.5_LR_2.txt
E7.5_LR_2_4A


title: Stage E7.5 with L/R sections embryo 2 section 3 region R2

description:
E7.5_LR_2.txt
E7.5_LR_2_3R2


title: Stable MGUS patient_269

description:
S269
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_268

description:
S268
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_267

description:
S267
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Jlat106 KO3C Rep2

description:
JLat_bulk_counts.tsv
8_Jlat106_KO3C_2_S8


title: Stage E7.0 embryo 3 section 8 region M

description:
E7.0_3.txt
E7.0_3_8M


title: Stage E7.5 with L/R sections embryo 2 section 3 region R1

description:
E7.5_LR_2.txt
E7.5_LR_2_3R1


title: Stage E7.5 with L/R sections embryo 2 section 3 region P

description:
E7.5_LR_2.txt
E7.5_LR_2_3P


title: Jlat106 KO3B Rep3

description:
JLat_bulk_counts.tsv
6_Jlat106_KO3B_3_S6


title: Stable MGUS patient_266

description:
S266
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_265

description:
S265
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 with L/R sections embryo 2 section 3 region MPR

description:
E7.5_LR_2.txt
E7.5_LR_2_3MPR


title: Stage E7.0 embryo 3 section 8 region EA

description:
E7.0_3.txt
E7.0_3_8EA


title: Stage E7.0 embryo 3 section 8 region EP

description:
E7.0_3.txt
E7.0_3_8EP


title: Stage E7.0 embryo 3 section 7 region P

description:
E7.0_3.txt
E7.0_3_7P


title: Jlat106 KO3B Rep1

description:
JLat_bulk_counts.tsv
4_Jlat106_KO3B_1_S4


title: Stage E7.0 embryo 3 section 7 region M

description:
E7.0_3.txt
E7.0_3_7M


title: Jlat106 Rep3

description:
JLat_bulk_counts.tsv
3_Jlat106_3_S3


title: Stage E7.5 with L/R sections embryo 2 section 3 region MAR

description:
E7.5_LR_2.txt
E7.5_LR_2_3MAR


title: Stage E7.0 embryo 3 section 7 region EP

description:
E7.0_3.txt
E7.0_3_7EP


title: Stage E7.0 embryo 3 section 8 region P

description:
E7.0_3.txt
E7.0_3_8P


title: Stable MGUS patient_263

description:
S263
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Jlat106 Rep2

description:
JLat_bulk_counts.tsv
2_Jlat106_2_S2


title: Stable MGUS patient_264

description:
S264
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_262

description:
S262
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 with L/R sections embryo 2 section 3 region MAL

description:
E7.5_LR_2.txt
E7.5_LR_2_3MAL


title: Stage E7.5 with L/R sections embryo 2 section 3 region L2

description:
E7.5_LR_2.txt
E7.5_LR_2_3L2


title: Jlat106 KO3C Rep1

description:
JLat_bulk_counts.tsv
7_Jlat106_KO3C_1_S7


title: Stage E7.0 embryo 3 section 7 region EA

description:
E7.0_3.txt
E7.0_3_7EA


title: Jlat106 Rep1

description:
JLat_bulk_counts.tsv
1_Jlat106_1_S1


title: Stable MGUS patient_259

description:
S259
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_261

description:
S261
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_258

description:
S258
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_260

description:
S260
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 with L/R sections embryo 2 section 3 region EP

description:
E7.5_LR_2.txt
E7.5_LR_2_3EP


title: Stage E7.0 embryo 3 section 6 region P

description:
E7.0_3.txt
E7.0_3_6P


title: Stage E7.5 with L/R sections embryo 2 section 3 region A

description:
E7.5_LR_2.txt
E7.5_LR_2_3A


title: Jlat106 KO3B Rep2

description:
JLat_bulk_counts.tsv
5_Jlat106_KO3B_2_S5


title: Stage E7.5 with L/R sections embryo 2 section 3 region EA

description:
E7.5_LR_2.txt
E7.5_LR_2_3EA


title: Stage E7.5 with L/R sections embryo 2 section 2 region R

description:
E7.5_LR_2.txt
E7.5_LR_2_2R


title: Stage E7.0 embryo 3 section 6 region EP

description:
E7.0_3.txt
E7.0_3_6EP


title: Stage E7.0 embryo 3 section 6 region R

description:
E7.0_3.txt
E7.0_3_6R


title: Stable MGUS patient_257

description:
S257
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.0 embryo 3 section 6 region L

description:
E7.0_3.txt
E7.0_3_6L


title: Stage E7.0 embryo 3 section 6 region M

description:
E7.0_3.txt
E7.0_3_6M


title: Stage E7.5 with L/R sections embryo 2 section 3 region L1

description:
E7.5_LR_2.txt
E7.5_LR_2_3L1


title: Stage E7.5 with L/R sections embryo 2 section 3 region MPL

description:
E7.5_LR_2.txt
E7.5_LR_2_3MPL


title: C3N-00495-T1_CPT0078510004_snRNA_ccRCC

city: St Louis

first: Alla

last: Karpova

state: MO

address: 700 Rosedale avenue Campus Box 1000

institute: Washington University St Louis

description: 10xV3.1 snRNA-seq

data_processing:
To process sequenced sc/snRNA-seq samples, Cell Ranger (v6.0.2) from 10X Genomics (with Count functionality) was used for aligning reads to the prebuilt GRCh38 genome reference version 2020-A (refdata-gex-GRCh38-2020-A) with the addition of pre-mRNA references. The Cellranger report from each sample was then carefully evaluated and we included samples with no critical errors or warnings. Examples of errors for which samples were excluded: “ERROR: Low Fraction Reads Confidently Mapped To Transcriptome”, or “ERROR: GEX Reads mapping to transcriptome is low.” Additionally, samples were excluded for less than 700 median genes per cell (except in certain cases where a high number of cells was detected).
To process sequenced snATAC-seq and snMutiome-seq data, we used the CellRanger-atac count (v2.0, 10X Genomics) and CellRanger-arc count (v2.0, 10X Genomics) pipelines, respectively. These pipelines filter and map snATAC-seq reads and identify transposase cut sites and the CellRanger-arc pipeline also performs filtering and alignment of snRNA-seq reads. The GRCh38 human reference was used for the read mapping. The CellRanger report from each sample was carefully evaluated and we excluded samples with few errors, except the “Number of cells is too high” error, while keeping samples with no errors or with just warnings. Examples of errors for which we removed samples are: “ATAC High-quality fragments in cells is low”, “ATAC TSS enrichment is low”, and “ATAC Fragments in peaks is low”.
Assembly: hg38
Supplementary files format and content: All files are standard Cellranger output files https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/overview or Cellranger-atac output files https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/output/overview

molecule: nuclear RNA

source_name: Kidney

extract_protocol:
15-25 mg of pulverized tissue was placed in a 5mL Eppendorf tube on ice. Using a wide-bore pipette tip (Rainin), a lysis buffer prepared from the Nuclei Isolation protocol (10X Genomics) and SuperRNase inhibitor (Invitrogen) was added to the tube. The tissue solution was gently pipetted until the lysis liquid turned a slightly cloudy color. (The number of pipetting iterations depended on the specific tissue.) The tissue homogenate was then filtered through a 40-micron strainer (pluriSelect) and washed with a BSA wash buffer (2% BSA + 1x PBS + RNase inhibitor). The filtrate was collected, centrifuged at 500 x g for 6 minutes at 4°C, and resuspended with a BSA wash buffer. 100 uL of cell lysis solution was set aside for unstained reference, while the rest was stained with DRAQ5 or 7AAD for RNA or ATAC sequencing, respectively. Namely, snRNA-seq nuclei were stained with 1 uL of DRAQ5 per 300 uL of the sample, and snATAC-seq nuclei were stained with 1 uL of 7AAD per 500 uL of the sample. Sorting gates were based on size, granularity, and dye staining signal. Nuclei and barcoded beads were isolated in oil droplets via the 10x Genomics Chromium instrument. Single nuclei suspensions were counted and adjusted to a range of 500 to 1800 nuclei/µL using a hemocytometer. Reverse transcription was subsequently performed to incorporate cell and transcript-specific barcodes.
All snRNA-seq samples were run using the Chromium Next GEM Single Cell 3’ Library and Gel Bead Kit v3.1 (10x Genomics). For snATAC-seq, Chromium Next GEM Single Cell ATAC Library and Gel Bead Kit v1.1 prep (10x Genomics) were used for all samples. Barcoded libraries were then pooled and sequenced on the Illumina NovaSeq 6000 system with specific flow cell types (snRNA-seq: S4; snATAC-seq: S1).

value: Kidney


title: C3N-00242-N_CPT0014470002_snRNA_ccRCC_NAT

description: 10xV3.1 snRNA-seq


title: C3L-00908-T1_CPT0086350004_snRNA_ccRCC

description: 10xV3.1 snRNA-seq


title: Stage E7.5 with L/R sections embryo 2 section 2 region P

description:
E7.5_LR_2.txt
E7.5_LR_2_2P


title: C3L-00079-N_CPT0001270002_snRNA_ccRCC_NAT

description: 10xV3.1 snRNA-seq


title: C3L-01313-T1_CPT0086820004_snRNA_ccRCC

description: 10xV3.1 snRNA-seq


title: C3L-01287-T1_CPT0079410004_snRNA_ccRCC

description: 10xV3.1 snRNA-seq


title: Stage E7.5 with L/R sections embryo 2 section 2 region MPR

description:
E7.5_LR_2.txt
E7.5_LR_2_2MPR


title: C3N-01213-T1_CPT0075720013_snRNA_ccRCC

description: 10xV3.1 snRNA-seq


title: Stable MGUS patient_255

description:
S255
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_254

description:
S254
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_252

description:
S252
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.0 embryo 3 section 6 region A

description:
E7.0_3.txt
E7.0_3_6A


title: Stable MGUS patient_256

description:
S256
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: C3N-01200-N_CPT0075170013_snRNA_ccRCC_NAT

description: 10xV3.1 snRNA-seq


title: Stage E7.0 embryo 3 section 5 region P

description:
E7.0_3.txt
E7.0_3_5P


title: Stable MGUS patient_251

description:
S251
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.0 embryo 3 section 6 region EA

description:
E7.0_3.txt
E7.0_3_6EA


title: C3N-01200-T1_CPT0075130004_snRNA_ccRCC

description: 10xV3.1 snRNA-seq


title: Stage E7.5 with L/R sections embryo 2 section 2 region MAL

description:
E7.5_LR_2.txt
E7.5_LR_2_2MAL


title: Stage E7.0 embryo 3 section 5 region EP

description:
E7.0_3.txt
E7.0_3_5EP


title: Stage E7.0 embryo 3 section 5 region M

description:
E7.0_3.txt
E7.0_3_5M


title: C3L-01302-T1_CPT0063630004_snRNA_ccRCC

description: 10xV3.1 snRNA-seq


title: Stage E7.5 with L/R sections embryo 2 section 2 region L

description:
E7.5_LR_2.txt
E7.5_LR_2_2L


title: C3N-00733-T1_CPT0025880013_snRNA_ccRCC

description: 10xV3.1 snRNA-seq


title: Stage E7.0 embryo 3 section 4 region P

description:
E7.0_3.txt
E7.0_3_4P


title: Stable MGUS patient_253

description:
S253
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_249

description:
S249
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: C3L-00610-T1_CPT0025110004_snRNA_ccRCC

description: 10xV3.1 snRNA-seq


title: Stable MGUS patient_247

description:
S247
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.0 embryo 3 section 4 region M

description:
E7.0_3.txt
E7.0_3_4M


title: Stage E7.5 with L/R sections embryo 2 section 2 region EA

description:
E7.5_LR_2.txt
E7.5_LR_2_2EA


title: Stable MGUS patient_250

description:
S250
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 with L/R sections embryo 2 section 1 region P

description:
E7.5_LR_2.txt
E7.5_LR_2_1P


title: Stable MGUS patient_248

description:
S248
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.0 embryo 3 section 4 region EP

description:
E7.0_3.txt
E7.0_3_4EP


title: Stable MGUS patient_246

description:
S246
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 with L/R sections embryo 2 section 2 region MPL

description:
E7.5_LR_2.txt
E7.5_LR_2_2MPL


title: Stage E7.5 with L/R sections embryo 2 section 2 region MAR

description:
E7.5_LR_2.txt
E7.5_LR_2_2MAR


title: C3L-00917-T1_CPT0023690004_snRNA_ccRCC

description: 10xV3.1 snRNA-seq


title: C3L-00583-T1_CPT0019130004_snRNA_ccRCC

description: 10xV3.1 snRNA-seq


title: Stable MGUS patient_245

description:
S245
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: C3L-00790-T1_CPT0065690004_snRNA_ccRCC

description: 10xV3.1 snRNA-seq


title: Stage E7.5 with L/R sections embryo 2 section 1 region EAP

description:
E7.5_LR_2.txt
E7.5_LR_2_1EAP


title: Stage E7.5 with L/R sections embryo 2 section 2 region EP

description:
E7.5_LR_2.txt
E7.5_LR_2_2EP


title: Stage E7.0 embryo 3 section 5 region EA

description:
E7.0_3.txt
E7.0_3_5EA


title: Stage E7.0 embryo 3 section 4 region EA

description:
E7.0_3.txt
E7.0_3_4EA


title: Stable MGUS patient_244

description:
S244
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: C3N-00242-T1_CPT0014450005_snRNA_ccRCC

description: 10xV3.1 snRNA-seq


title: C3N-00437-T1_CPT0012550012_snRNA_ccRCC

description: 10xV3.1 snRNA-seq


title: Stage E7.5 with L/R sections embryo 1 section 9 region R2

description:
E7.5_LR_1.txt
E7.5_LR_1_9R2


title: Stage E7.5 with L/R sections embryo 2 section 1 region A

description:
E7.5_LR_2.txt
E7.5_LR_2_1A


title: Stage E7.0 embryo 3 section 3 region R

description:
E7.0_3.txt
E7.0_3_3R


title: Stage E7.0 embryo 3 section 3 region P

description:
E7.0_3.txt
E7.0_3_3P


title: Stage E7.5 with L/R sections embryo 1 section 9 region R1

description:
E7.5_LR_1.txt
E7.5_LR_1_9R1


title: Stage E7.0 embryo 3 section 3 region M

description:
E7.0_3.txt
E7.0_3_3M


title: C3N-00317-T1_CPT0012280004_snRNA_ccRCC

description: 10xV3.1 snRNA-seq


title: Stage E7.5 with L/R sections embryo 1 section 9 region P

description:
E7.5_LR_1.txt
E7.5_LR_1_9P


title: Stage E7.0 embryo 3 section 3 region L

description:
E7.0_3.txt
E7.0_3_3L


title: Stage E7.0 embryo 3 section 3 region EP

description:
E7.0_3.txt
E7.0_3_3EP


title: C3L-00448-T1_CPT0010160004_snRNA_ccRCC

description: 10xV3.1 snRNA-seq


title: Stage E7.5 with L/R sections embryo 1 section 9 region MPR

description:
E7.5_LR_1.txt
E7.5_LR_1_9MPR


title: C3L-00416-T2_CPT0010100001_snRNA_ccRCC

description: 10xV3.1 snRNA-seq


title: Stable MGUS patient_243

description:
S243
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_242

description:
S242
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_240

description:
S240
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 with L/R sections embryo 1 section 9 region MPL

description:
E7.5_LR_1.txt
E7.5_LR_1_9MPL


title: C3L-00004-T1_CPT0001540013_snRNA_ccRCC

description: 10xV3.1 snRNA-seq


title: C3L-00026-T1_CPT0001500003_snRNA_ccRCC

description: 10xV3.1 snRNA-seq


title: Stage E7.0 embryo 3 section 3 region EA

description:
E7.0_3.txt
E7.0_3_3EA


title: Stage E7.5 with L/R sections embryo 1 section 9 region MAR

description:
E7.5_LR_1.txt
E7.5_LR_1_9MAR


title: Stage E7.0 embryo 3 section 3 region A

description:
E7.0_3.txt
E7.0_3_3A


title: Stage E7.5 with L/R sections embryo 1 section 9 region MAL

description:
E7.5_LR_1.txt
E7.5_LR_1_9MAL


title: Stage E7.5 with L/R sections embryo 1 section 9 region L2

description:
E7.5_LR_1.txt
E7.5_LR_1_9L2


title: C3L-00079-T1_CPT0001260013_snRNA_ccRCC

description: 10xV3.1 snRNA-seq


title: Stage E7.0 embryo 3 section 2 region P

description:
E7.0_3.txt
E7.0_3_2P


title: C3L-00010-T1_CPT0001220012_snRNA_ccRCC

description: 10xV3.1 snRNA-seq


title: Stable MGUS patient_241

description:
S241
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.0 embryo 3 section 2 region M

description:
E7.0_3.txt
E7.0_3_2M


title: Stable MGUS patient_239

description:
S239
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_238

description:
S238
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_237

description:
S237
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.0 embryo 3 section 2 region EP

description:
E7.0_3.txt
E7.0_3_2EP


title: Stable MGUS patient_236

description:
S236
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: C3L-00096-T1_CPT0001180011_snRNA_ccRCC

description: 10xV3.1 snRNA-seq


title: Stable MGUS patient_235

description:
S235
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: C3L-00088-T2_CPT0000880001_snRNA_ccRCC

description: 10xV3.1 snRNA-seq


title: Stage E7.5 with L/R sections embryo 1 section 9 region L1

description:
E7.5_LR_1.txt
E7.5_LR_1_9L1


title: Stage E7.0 embryo 3 section 2 region EA

description:
E7.0_3.txt
E7.0_3_2EA


title: Stable MGUS patient_234

description:
S234
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_233

description:
S233
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.0 embryo 3 section 1 region P

description:
E7.0_3.txt
E7.0_3_1P


title: C3N-00242-N_CPT0014470002_snATAC_ccRCC_NAT

description: 10xv1.1 snATAC-seq


title: C3L-00088-T1_CPT0000870003_snRNA_ccRCC

description: 10xV3.1 snRNA-seq


title: Stage E7.0 embryo 3 section 1 region EAP

description:
E7.0_3.txt
E7.0_3_1EAP


title: Stage E7.5 with L/R sections embryo 1 section 8 region R2

description:
E7.5_LR_1.txt
E7.5_LR_1_8R2


title: Stage E7.5 with L/R sections embryo 1 section 9 region A

description:
E7.5_LR_1.txt
E7.5_LR_1_9A


title: C3L-00079-N_CPT0001270002_snATAC_ccRCC_NAT

description: 10xv1.1 snATAC-seq


title: Stage E7.5 with L/R sections embryo 1 section 9 region EA

description:
E7.5_LR_1.txt
E7.5_LR_1_9EA


title: C3L-01313-T1_CPT0086820004_snATAC_ccRCC

description: 10xv1.1 snATAC-seq


title: Stable MGUS patient_231

description:
S231
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_232

description:
S232
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.0 embryo 3 section 11 region M

description:
E7.0_3.txt
E7.0_3_11M


title: Stage E7.5 with L/R sections embryo 1 section 9 region EP

description:
E7.5_LR_1.txt
E7.5_LR_1_9EP


title: Stable MGUS patient_230

description:
S230
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.0 embryo 3 section 11 region P

description:
E7.0_3.txt
E7.0_3_11P


title: C3L-00908-T1_CPT0086350004_snATAC_ccRCC

description: 10xv1.1 snATAC-seq


title: Stage E7.0 embryo 3 section 11 region EP

description:
E7.0_3.txt
E7.0_3_11EP


title: Stage E7.5 with L/R sections embryo 1 section 8 region P

description:
E7.5_LR_1.txt
E7.5_LR_1_8P


title: Stage E7.0 embryo 3 section 11 region EA

description:
E7.0_3.txt
E7.0_3_11EA


title: Stable MGUS patient_228

description:
S228
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 with L/R sections embryo 1 section 8 region MPL

description:
E7.5_LR_1.txt
E7.5_LR_1_8MPL


title: C3L-01287-T1_CPT0079410004_snATAC_ccRCC

description: 10xv1.1 snATAC-seq


title: C3N-00495-T1_CPT0078510004_snATAC_ccRCC

description: 10xv1.1 snATAC-seq


title: Stage E7.5 with L/R sections embryo 1 section 8 region MAR

description:
E7.5_LR_1.txt
E7.5_LR_1_8MAR


title: Stable MGUS patient_229

description:
S229
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 with L/R sections embryo 1 section 8 region R1

description:
E7.5_LR_1.txt
E7.5_LR_1_8R1


title: Stable MGUS patient_226

description:
S226
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_225

description:
S225
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 with L/R sections embryo 1 section 8 region MAL

description:
E7.5_LR_1.txt
E7.5_LR_1_8MAL


title: C3N-01200-N_CPT0075170013_snATAC_ccRCC_NAT

description: 10xv1.1 snATAC-seq


title: Stage E7.0 embryo 3 section 10 region EP

description:
E7.0_3.txt
E7.0_3_10EP


title: Stage E7.0 embryo 3 section 10 region EA

description:
E7.0_3.txt
E7.0_3_10EA


title: Stage E7.5 with L/R sections embryo 1 section 8 region MPR

description:
E7.5_LR_1.txt
E7.5_LR_1_8MPR


title: C3N-01200-T1_CPT0075130004_snATAC_ccRCC

description: 10xv1.1 snATAC-seq


title: Stage E7.5 with L/R sections embryo 1 section 8 region L1

description:
E7.5_LR_1.txt
E7.5_LR_1_8L1


title: Stage E7.0 embryo 2 section 9 region R

description:
E7.0_2.txt
E7.0_2_9R


title: C3L-00790-T1_CPT0065690004_snATAC_ccRCC

description: 10xv1.1 snATAC-seq


title: Stable MGUS patient_227

description:
S227
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: C3L-01302-T1_CPT0063630004_snATAC_ccRCC

description: 10xv1.1 snATAC-seq


title: Stage E7.0 embryo 3 section 10 region P

description:
E7.0_3.txt
E7.0_3_10P


title: Stable MGUS patient_224

description:
S224
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.0 embryo 2 section 9 region P

description:
E7.0_2.txt
E7.0_2_9P


title: Stage E7.5 with L/R sections embryo 1 section 8 region EA

description:
E7.5_LR_1.txt
E7.5_LR_1_8EA


title: Stage E7.0 embryo 2 section 9 region M

description:
E7.0_2.txt
E7.0_2_9M


title: Stable MGUS patient_223

description:
S223
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: C3N-01213-T1_CPT0075720013_snATAC_ccRCC

description: 10xv1.1 snATAC-seq


title: C3N-00733-T1_CPT0025880013_snATAC_ccRCC

description: 10xv1.1 snATAC-seq


title: Stage E7.0 embryo 3 section 10 region M

description:
E7.0_3.txt
E7.0_3_10M


title: Stage E7.5 with L/R sections embryo 1 section 8 region L2

description:
E7.5_LR_1.txt
E7.5_LR_1_8L2


title: C3L-00610-T1_CPT0025110004_snATAC_ccRCC

description: 10xv1.1 snATAC-seq


title: Stage E7.5 with L/R sections embryo 1 section 8 region A

description:
E7.5_LR_1.txt
E7.5_LR_1_8A


title: Stable MGUS patient_222

description:
S222
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_221

description:
S221
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_220

description:
S220
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 with L/R sections embryo 1 section 7 region R2

description:
E7.5_LR_1.txt
E7.5_LR_1_7R2


title: C3L-00917-T1_CPT0023690004_snATAC_ccRCC

description: 10xv1.1 snATAC-seq


title: Stable MGUS patient_219

description:
S219
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.0 embryo 2 section 9 region EP

description:
E7.0_2.txt
E7.0_2_9EP


title: C3L-00583-T1_CPT0019130004_snATAC_ccRCC

description: 10xv1.1 snATAC-seq


title: Stage E7.5 with L/R sections embryo 1 section 8 region EP

description:
E7.5_LR_1.txt
E7.5_LR_1_8EP


title: Stage E7.0 embryo 2 section 9 region EA

description:
E7.0_2.txt
E7.0_2_9EA


title: Stage E7.0 embryo 2 section 9 region A

description:
E7.0_2.txt
E7.0_2_9A


title: Stage E7.5 with L/R sections embryo 1 section 7 region MPR

description:
E7.5_LR_1.txt
E7.5_LR_1_7MPR


title: Stable MGUS patient_218

description:
S218
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_217

description:
S217
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: C3N-00242-T1_CPT0014450005_snATAC_ccRCC

description: 10xv1.1 snATAC-seq


title: Stage E7.5 with L/R sections embryo 1 section 7 region MPL

description:
E7.5_LR_1.txt
E7.5_LR_1_7MPL


title: C3N-00437-T1_CPT0012550012_snATAC_ccRCC

description: 10xv1.1 snATAC-seq


title: Stage E7.0 embryo 2 section 8 region P

description:
E7.0_2.txt
E7.0_2_8P


title: Stage E7.5 with L/R sections embryo 1 section 7 region MAR

description:
E7.5_LR_1.txt
E7.5_LR_1_7MAR


title: Stage E7.0 embryo 2 section 9 region L

description:
E7.0_2.txt
E7.0_2_9L


title: Stable MGUS patient_216

description:
S216
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.0 embryo 2 section 8 region M

description:
E7.0_2.txt
E7.0_2_8M


title: C3N-00317-T1_CPT0012280004_snATAC_ccRCC

description: 10xv1.1 snATAC-seq


title: Stage E7.5 with L/R sections embryo 1 section 7 region MAL

description:
E7.5_LR_1.txt
E7.5_LR_1_7MAL


title: Stage E7.5 with L/R sections embryo 1 section 7 region P

description:
E7.5_LR_1.txt
E7.5_LR_1_7P


title: Stage E7.5 with L/R sections embryo 1 section 7 region L2

description:
E7.5_LR_1.txt
E7.5_LR_1_7L2


title: Stage E7.0 embryo 2 section 8 region EA

description:
E7.0_2.txt
E7.0_2_8EA


title: Stage E7.0 embryo 2 section 8 region EP

description:
E7.0_2.txt
E7.0_2_8EP


title: C3L-00416-T2_CPT0010100001_snATAC_ccRCC

description: 10xv1.1 snATAC-seq


title: Stage E7.0 embryo 2 section 7 region P

description:
E7.0_2.txt
E7.0_2_7P


title: C3L-00026-T1_CPT0001500003_snATAC_ccRCC

description: 10xv1.1 snATAC-seq


title: Stage E7.5 with L/R sections embryo 1 section 7 region L1

description:
E7.5_LR_1.txt
E7.5_LR_1_7L1


title: Stage E7.0 embryo 2 section 7 region M

description:
E7.0_2.txt
E7.0_2_7M


title: C3L-00004-T1_CPT0001540013_snATAC_ccRCC

description: 10xv1.1 snATAC-seq


title: Stable MGUS patient_215

description:
S215
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_213

description:
S213
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_212

description:
S212
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 with L/R sections embryo 1 section 7 region EP

description:
E7.5_LR_1.txt
E7.5_LR_1_7EP


title: C3L-00079-T1_CPT0001260013_snATAC_ccRCC

description: 10xv1.1 snATAC-seq


title: Stage E7.5 with L/R sections embryo 1 section 7 region EA

description:
E7.5_LR_1.txt
E7.5_LR_1_7EA


title: Stage E7.0 embryo 2 section 7 region EA

description:
E7.0_2.txt
E7.0_2_7EA


title: C3L-00448-T1_CPT0010160004_snATAC_ccRCC

description: 10xv1.1 snATAC-seq


title: Stage E7.5 with L/R sections embryo 1 section 7 region A

description:
E7.5_LR_1.txt
E7.5_LR_1_7A


title: C3L-00010-T1_CPT0001220012_snATAC_ccRCC

description: 10xv1.1 snATAC-seq


title: Stage E7.5 with L/R sections embryo 1 section 6 region R2

description:
E7.5_LR_1.txt
E7.5_LR_1_6R2


title: C3L-00096-T1_CPT0001180011_snATAC_ccRCC

description: 10xv1.1 snATAC-seq


title: Stage E7.5 with L/R sections embryo 1 section 6 region R1

description:
E7.5_LR_1.txt
E7.5_LR_1_6R1


title: Stage E7.0 embryo 2 section 6 region P

description:
E7.0_2.txt
E7.0_2_6P


title: C3L-00088-N_CPT0000890002_snATAC_ccRCC_NAT

description: 10xv1.1 snATAC-seq


title: Stable MGUS patient_210

description:
S210
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_214

description:
S214
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_211

description:
S211
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_209

description:
S209
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.0 embryo 2 section 7 region EP

description:
E7.0_2.txt
E7.0_2_7EP


title: Stable MGUS patient_207

description:
S207
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_208

description:
S208
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 with L/R sections embryo 1 section 6 region P

description:
E7.5_LR_1.txt
E7.5_LR_1_6P


title: C3L-00088-T2_CPT0000880001_snATAC_ccRCC

description: 10xv1.1 snATAC-seq


title: Stable MGUS patient_206

description:
S206
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 with L/R sections embryo 1 section 6 region MPR

description:
E7.5_LR_1.txt
E7.5_LR_1_6MPR


title: C3L-00088-T1_CPT0000870003_snATAC_ccRCC

description: 10xv1.1 snATAC-seq


title: Stage E7.0 embryo 2 section 6 region EP

description:
E7.0_2.txt
E7.0_2_6EP


title: Stable MGUS patient_205

description:
S205
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.0 embryo 2 section 6 region R

description:
E7.0_2.txt
E7.0_2_6R


title: Stage E7.0 embryo 2 section 6 region EA

description:
E7.0_2.txt
E7.0_2_6EA


title: Stage E7.5 with L/R sections embryo 1 section 6 region MPL

description:
E7.5_LR_1.txt
E7.5_LR_1_6MPL


title: C3N-03186_CPT0206880004_snATAC_GBM

description: 10xv1.1 snATAC-seq

source_name: Brain

value: Brain


title: C3N-02784_CPT0206000015_snATAC_GBM

description: 10xv1.1 snATAC-seq


title: Stage E7.5 with L/R sections embryo 1 section 6 region MAR

description:
E7.5_LR_1.txt
E7.5_LR_1_6MAR


title: Stage E7.0 embryo 2 section 6 region A

description:
E7.0_2.txt
E7.0_2_6A


title: Stage E7.0 embryo 2 section 5 region P

description:
E7.0_2.txt
E7.0_2_5P


title: Stage E7.5 with L/R sections embryo 1 section 6 region MAL

description:
E7.5_LR_1.txt
E7.5_LR_1_6MAL


title: C3N-02783_CPT0205890014_snATAC_GBM

description: 10xv1.1 snATAC-seq


title: Stage E7.0 embryo 2 section 6 region M

description:
E7.0_2.txt
E7.0_2_6M


title: Stage E7.5 with L/R sections embryo 1 section 6 region L2

description:
E7.5_LR_1.txt
E7.5_LR_1_6L2


title: Stable MGUS patient_203

description:
S203
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_202

description:
S202
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.0 embryo 2 section 5 region M

description:
E7.0_2.txt
E7.0_2_5M


title: C3N-02769_CPT0205570014_snATAC_GBM

description: 10xv1.1 snATAC-seq


title: Stable MGUS patient_200

description:
S200
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_204

description:
S204
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 with L/R sections embryo 1 section 6 region L1

description:
E7.5_LR_1.txt
E7.5_LR_1_6L1


title: Stable MGUS patient_201

description:
S201
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: C3N-02188_CPT0168830014_snATAC_GBM

description: 10xv1.1 snATAC-seq


title: Stage E7.0 embryo 2 section 5 region EP

description:
E7.0_2.txt
E7.0_2_5EP


title: Stage E7.5 with L/R sections embryo 1 section 6 region EP

description:
E7.5_LR_1.txt
E7.5_LR_1_6EP


title: C3N-02186_CPT0168720014_snATAC_GBM

description: 10xv1.1 snATAC-seq


title: Stable MGUS patient_199

description:
S199
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 with L/R sections embryo 1 section 6 region EA

description:
E7.5_LR_1.txt
E7.5_LR_1_6EA


title: Stage E7.0 embryo 2 section 5 region EA

description:
E7.0_2.txt
E7.0_2_5EA


title: Stage E7.5 with L/R sections embryo 1 section 6 region A

description:
E7.5_LR_1.txt
E7.5_LR_1_6A


title: Stage E7.0 embryo 2 section 4 region P

description:
E7.0_2.txt
E7.0_2_4P


title: C3N-02181_CPT0168380014_snATAC_GBM

description: 10xv1.1 snATAC-seq


title: C3N-01818_CPT0168270014_snATAC_GBM

description: 10xv1.1 snATAC-seq


title: Stage E7.0 embryo 2 section 4 region M

description:
E7.0_2.txt
E7.0_2_4M


title: Stable MGUS patient_197

description:
S197
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 with L/R sections embryo 1 section 5 region R2

description:
E7.5_LR_1.txt
E7.5_LR_1_5R2


title: Stage E7.0 embryo 2 section 4 region EP

description:
E7.0_2.txt
E7.0_2_4EP


title: Stable MGUS patient_198

description:
S198
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: C3N-01816_CPT0168080014_snATAC_GBM

description: 10xv1.1 snATAC-seq


title: Stage E7.0 embryo 2 section 4 region EA

description:
E7.0_2.txt
E7.0_2_4EA


title: Stage E7.5 with L/R sections embryo 1 section 5 region P

description:
E7.5_LR_1.txt
E7.5_LR_1_5P


title: Stable MGUS patient_195

description:
S195
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_194

description:
S194
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.0 embryo 2 section 3 region R

description:
E7.0_2.txt
E7.0_2_3R


title: C3N-01814_CPT0167860015_snATAC_GBM

description: 10xv1.1 snATAC-seq


title: Stage E7.5 with L/R sections embryo 1 section 5 region MPR

description:
E7.5_LR_1.txt
E7.5_LR_1_5MPR


title: C3N-01798_CPT0167750015_snATAC_GBM

description: 10xv1.1 snATAC-seq


title: Stage E7.0 embryo 2 section 3 region P

description:
E7.0_2.txt
E7.0_2_3P


title: Stage E7.5 with L/R sections embryo 1 section 5 region MPL

description:
E7.5_LR_1.txt
E7.5_LR_1_5MPL


title: C3N-01518_CPT0167640014_snATAC_GBM

description: 10xv1.1 snATAC-seq


title: Stage E7.5 with L/R sections embryo 1 section 5 region MAR

description:
E7.5_LR_1.txt
E7.5_LR_1_5MAR


title: Stage E7.5 with L/R sections embryo 1 section 5 region MAL

description:
E7.5_LR_1.txt
E7.5_LR_1_5MAL


title: C3N-01334_CPT0125220004_snATAC_GBM

description: 10xv1.1 snATAC-seq


title: Stage E7.5 with L/R sections embryo 1 section 5 region L2

description:
E7.5_LR_1.txt
E7.5_LR_1_5L2


title: C3N-00663_CPT0087730014_snATAC_GBM

description: 10xv1.1 snATAC-seq


title: Stage E7.0 embryo 2 section 3 region M

description:
E7.0_2.txt
E7.0_2_3M


title: Stable MGUS patient_192

description:
S192
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: C3N-00662_CPT0087680014_snATAC_GBM

description: 10xv1.1 snATAC-seq


title: Stable MGUS patient_193

description:
S193
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_191

description:
S191
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.0 embryo 2 section 3 region EP

description:
E7.0_2.txt
E7.0_2_3EP


title: Stage E7.5 with L/R sections embryo 1 section 5 region L1

description:
E7.5_LR_1.txt
E7.5_LR_1_5L1


title: Stage E7.0 embryo 2 section 3 region EA

description:
E7.0_2.txt
E7.0_2_3EA


title: Stable MGUS patient_188

description:
S188
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_196

description:
S196
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: C3L-03968_CPT0228220004_snATAC_GBM

description: 10xv1.1 snATAC-seq


title: Stage E7.5 with L/R sections embryo 1 section 5 region EP

description:
E7.5_LR_1.txt
E7.5_LR_1_5EP


title: Stage E7.0 embryo 2 section 3 region A

description:
E7.0_2.txt
E7.0_2_3A


title: Stage E7.0 embryo 2 section 3 region L

description:
E7.0_2.txt
E7.0_2_3L


title: Stage E7.0 embryo 2 section 2 region P

description:
E7.0_2.txt
E7.0_2_2P


title: Stage E7.5 with L/R sections embryo 1 section 5 region EA

description:
E7.5_LR_1.txt
E7.5_LR_1_5EA


title: Stable MGUS patient_189

description:
S189
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: C3L-03405_CPT0224600013_snATAC_GBM

description: 10xv1.1 snATAC-seq


title: C3L-02705_CPT0189650015_snATAC_GBM

description: 10xv1.1 snATAC-seq


title: Stable MGUS patient_190

description:
S190
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 with L/R sections embryo 1 section 5 region A

description:
E7.5_LR_1.txt
E7.5_LR_1_5A


title: C3N-03186_CPT0206880004_snRNA_GBM

description: 10xV3.1 snRNA-seq


title: Stage E7.5 with L/R sections embryo 1 section 4 region R2

description:
E7.5_LR_1.txt
E7.5_LR_1_4R2


title: Stage E7.0 embryo 2 section 2 region M

description:
E7.0_2.txt
E7.0_2_2M


title: Stage E7.0 embryo 2 section 2 region EP

description:
E7.0_2.txt
E7.0_2_2EP


title: Stage E7.0 embryo 2 section 2 region EA

description:
E7.0_2.txt
E7.0_2_2EA


title: C3N-02783_CPT0205890014_snRNA_GBM

description: 10xV3.1 snRNA-seq


title: Stage E7.5 with L/R sections embryo 1 section 4 region R1

description:
E7.5_LR_1.txt
E7.5_LR_1_4R1


title: C3N-02784_CPT0206000015_snRNA_GBM

description: 10xV3.1 snRNA-seq


title: Stable MGUS patient_186

description:
S186
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 with L/R sections embryo 1 section 4 region P

description:
E7.5_LR_1.txt
E7.5_LR_1_4P


title: Stable MGUS patient_185

description:
S185
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_183

description:
S183
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.0 embryo 2 section 1 region P

description:
E7.0_2.txt
E7.0_2_1P


title: C3N-02769_CPT0205570014_snRNA_GBM

description: 10xV3.1 snRNA-seq


title: Stable MGUS patient_187

description:
S187
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_184

description:
S184
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_182

description:
S182
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 with L/R sections embryo 1 section 4 region MPR

description:
E7.5_LR_1.txt
E7.5_LR_1_4MPR


title: C3N-02188_CPT0168830014_snRNA_GBM

description: 10xV3.1 snRNA-seq


title: Stage E7.5 with L/R sections embryo 1 section 4 region MPL

description:
E7.5_LR_1.txt
E7.5_LR_1_4MPL


title: Stage E7.0 embryo 2 section 11 region P

description:
E7.0_2.txt
E7.0_2_11P


title: Stage E7.5 with L/R sections embryo 1 section 4 region MAR

description:
E7.5_LR_1.txt
E7.5_LR_1_4MAR


title: Stage E7.0 embryo 2 section 11 region M

description:
E7.0_2.txt
E7.0_2_11M


title: C3N-01816_CPT0168080014_snRNA_GBM

description: 10xV3.1 snRNA-seq


title: C3N-01814_CPT0167860015_snRNA_GBM

description: 10xV3.1 snRNA-seq


title: C3N-02181_CPT0168380014_snRNA_GBM

description: 10xV3.1 snRNA-seq


title: Stage E7.5 with L/R sections embryo 1 section 4 region MAL

description:
E7.5_LR_1.txt
E7.5_LR_1_4MAL


title: Stage E7.0 embryo 2 section 11 region EP

description:
E7.0_2.txt
E7.0_2_11EP


title: Stage E7.0 embryo 2 section 11 region EA

description:
E7.0_2.txt
E7.0_2_11EA


title: Stage E7.5 with L/R sections embryo 1 section 4 region L2

description:
E7.5_LR_1.txt
E7.5_LR_1_4L2


title: Stable MGUS patient_181

description:
S181
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_180

description:
S180
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.0 embryo 2 section 1 region EAP

description:
E7.0_2.txt
E7.0_2_1EAP


title: Stable MGUS patient_178

description:
S178
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 with L/R sections embryo 1 section 4 region L1

description:
E7.5_LR_1.txt
E7.5_LR_1_4L1


title: Stage E7.0 embryo 2 section 10 region P

description:
E7.0_2.txt
E7.0_2_10P


title: Stable MGUS patient_179

description:
S179
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 with L/R sections embryo 1 section 4 region EP

description:
E7.5_LR_1.txt
E7.5_LR_1_4EP


title: Stable MGUS patient_177

description:
S177
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.0 embryo 2 section 10 region M

description:
E7.0_2.txt
E7.0_2_10M


title: Stable MGUS patient_176

description:
S176
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 with L/R sections embryo 1 section 4 region EA

description:
E7.5_LR_1.txt
E7.5_LR_1_4EA


title: Stage E7.0 embryo 2 section 10 region EP

description:
E7.0_2.txt
E7.0_2_10EP


title: C3N-00662_CPT0087680014_snRNA_GBM

description: 10xV3.1 snRNA-seq


title: C3L-03968_CPT0228220004_snRNA_GBM

description: 10xV3.1 snRNA-seq


title: Stable MGUS patient_175

description:
S175
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.0 embryo 2 section 10 region EA

description:
E7.0_2.txt
E7.0_2_10EA


title: Stage E7.5 with L/R sections embryo 1 section 4 region A

description:
E7.5_LR_1.txt
E7.5_LR_1_4A


title: Stage E7.5 with L/R sections embryo 1 section 3 region R2

description:
E7.5_LR_1.txt
E7.5_LR_1_3R2


title: C3N-01798_CPT0167750015_snRNA_GBM

description: 10xV3.1 snRNA-seq


title: Stage E6.5 embryo 2 section 8 region P

description:
E6.5_2.txt
E6.5_2_8P


title: C3L-02705_CPT0189650015_snRNA_GBM

description: 10xV3.1 snRNA-seq


title: C3N-01334_CPT0125220004_snRNA_GBM

description: 10xV3.1 snRNA-seq


title: Stage E6.5 embryo 2 section 8 region EP

description:
E6.5_2.txt
E6.5_2_8EP


title: C3N-02186_CPT0168720014_snRNA_GBM

description: 10xV3.1 snRNA-seq


title: Stage E7.5 with L/R sections embryo 1 section 3 region P

description:
E7.5_LR_1.txt
E7.5_LR_1_3P


title: Stable MGUS patient_173

description:
S173
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E6.5 embryo 2 section 8 region EA

description:
E6.5_2.txt
E6.5_2_8EA


title: C3N-01518_CPT0167640014_snRNA_GBM

description: 10xV3.1 snRNA-seq


title: Stage E6.5 embryo 2 section 8 region A

description:
E6.5_2.txt
E6.5_2_8A


title: C3L-03405_CPT0224600013_snRNA_GBM

description: 10xV3.1 snRNA-seq


title: Stable MGUS patient_172

description:
S172
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 with L/R sections embryo 1 section 3 region MPR

description:
E7.5_LR_1.txt
E7.5_LR_1_3MPR


title: Stage E7.5 with L/R sections embryo 1 section 3 region MPL

description:
E7.5_LR_1.txt
E7.5_LR_1_3MPL


title: Stable MGUS patient_170

description:
S170
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_174

description:
S174
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 with L/R sections embryo 1 section 3 region MAR

description:
E7.5_LR_1.txt
E7.5_LR_1_3MAR


title: Stage E6.5 embryo 2 section 7 region P

description:
E6.5_2.txt
E6.5_2_7P


title: C3N-00663_CPT0087730015_snRNA_GBM

description: 10x Multiome snRNA-seq


title: Stable MGUS patient_171

description:
S171
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 with L/R sections embryo 1 section 3 region R1

description:
E7.5_LR_1.txt
E7.5_LR_1_3R1


title: Stable MGUS patient_169

description:
S169
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_167

description:
S167
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 with L/R sections embryo 1 section 3 region MAL

description:
E7.5_LR_1.txt
E7.5_LR_1_3MAL


title: Stage E7.5 with L/R sections embryo 1 section 3 region L2

description:
E7.5_LR_1.txt
E7.5_LR_1_3L2


title: Stage E6.5 embryo 2 section 7 region EA

description:
E6.5_2.txt
E6.5_2_7EA


title: C3N-01818_CPT0168270014_snRNA_GBM

description: 10xV3.1 snRNA-seq


title: Stable MGUS patient_168

description:
S168
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E6.5 embryo 2 section 7 region A

description:
E6.5_2.txt
E6.5_2_7A


title: Condition 12-6wk replicate 2

city: Helsinki

first: Biswajyoti

last: Sahu

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

data_processing:
The sample quality of the RNA-seq datasets were evaluated by the tool FastQC. Sequence reads were aligned to the human reference genome (UCSC GRCh38/hg38) using STAR aligner (v2.7.5c) with default parameters. Samtools (v1.9) was used to sort the bam files.
Gene counts were quantified using HTSeq-count (v0.11.2).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

source_name: Human foreskin fibroblasts

growth_protocol: HFFs (ATCC, #CRL-2429) were cultured in fibroblast medium (DMEM supplemented with 10% FBS, 2 mM L-Glutamine, 1 mM Sodium pyruvate and 1% penicillin-streptomycin).

extract_protocol:
Total RNA was isolated using RNeasy Plus Mini Kit (Qiagen, #74134) following manufacturer’s instruction.
Libraries were prepared from 500ng of total RNA for each sample using KAPA mRNA HyperPrep Kit for Illumina (Roche, #KR1352) following manufacturer’s instruction.

treatment_protocol: Early-passage HFFs were transduced with constructs for TF expression and kept in defined reprogramming medium to induce cell fate convertion (See Methods). The reprogramming cells were collected at different time points for gene expression analysis. Mock HFFs were used as control.

value: Human foreskin fibroblasts

value: Transduced with 4-TF cocktail

tag: time point


title: Stage E7.5 with L/R sections embryo 1 section 3 region L1

description:
E7.5_LR_1.txt
E7.5_LR_1_3L1


title: Condition 12-6wk replicate 1


title: Stage E6.5 embryo 2 section 6 region P

description:
E6.5_2.txt
E6.5_2_6P


title: Condition 12-4wk replicate 3