title: [PRO-Seq] K562 cells, LP recombination, WT_eNMU, rep2

description: Library name: Sample 16

data_processing:
For all NGS sequencing data, the quality of FASTQ files was first accessed using FastQC, and the Illumina sequencing adaptors were trimmed using fastp.
To enable accurate alignment of sequencing reads to the eNMU locus in the recombinant cell lines, we built a custom genome for each recombinant TF motif mutant using the reform command line tool. Each custom genome incorporated the exact mutant sequence flanked by Bxb1 recombination sites. For PRO-seq data analysis, rRNA read removal, alignment, and deduplication (with UMI-tools) were performed using the published bash script at https://github.com/JAJ256/PROseq_alignment.sh.
Unnormalized 3'-end bigwigs files for PRO-seq were first generated from bam alignment files by PINTS using the option “pints_visualizer -e R1_5 --reverse-complement”. To calculate scaling factors for PRO-seq data, a collapsed list of all GENCODE v46 transcripts was first generated using the reduceByGene() function in the BRGenomics R package. The unnormalized bigwig files were loaded into Rstudio, and a DESeq2 object was generated for the combined list of all PRO-seq samples using the getDESeqDataSet() function in BRGenomics, using the collapsed transcript list to specify genomic regions of interest. Scaling factors calculated by DESeq2 were applied to each bigwig file using the applyNFsGRanges() function in BRGenomics before data export. Unnormalized 5'-end bigwigs files for PRO-seq were generated from bam alignment files by PINTS using the option “pints_visualizer -e R2_5” and normalized using the same scaling factors calculated from the 3'-end bigwigs files. Normalized bigwig files of two biological replicates were merged using kentUtils of the UCSC Genome Browser for visualization.
PROseq bigwig files are all at single basepair resolution, with 3'-end read position files labled as "PRO_3p_XXX" and 5'-end read position files labled as "PRO_5p_XXX".
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: PRO-Seq

extract_protocol:
All buffer compositions and reaction conditions followed the published protocol of Mahat and Kwak et al. (2016) unless otherwise specified. Briefly, 5 million K562 cells were mixed with 250,000 Drosophila S2 cells (5% spike-in), pelleted at 1000 r.c.f. for 5 min at 4°C, washed once with ice-cold PBS, resuspended with ice-cold permeabilization buffer at a density of 1 million cells/mL, and incubated on ice for 5 min. Cells were washed twice with the same volume of ice-cold permeabilization buffer, and resuspended in 100 μL storage buffer before immediate nuclear run-on or flash-freezing in liquid nitrogen for long-term storage at –80°C. Prior to the run-on reaction, 40 μL Dynabeads MyOne Streptavidin C1 beads (Thermo Fisher) per sample were pre-washed sequentially with Hydrolysis Buffer (0.1N NaOH + 50 mM NaCl), High Salt Wash Buffer, and Binding Buffer. Pre-washed beads were resuspended in 60 μL Binding Buffer per sample. The nuclear run-on reaction was performed at 37°C for 5 min with a final concentration of 20 µM each of Biotin-11-CTP, Biotin-11-UTP, ATP, and GTP. Following RNA extraction by Trizol LS (Invitrogen) and RNA fragmentation by base hydrolysis, 30 μL pre-washed C1 beads and 30 μL Binding Buffer were added to the ~60 μL RNA sample, and bead binding was performed at room temperature for 20 min on a rotational device. Beads were then washed twice using 500 μL High Salt Wash Buffer and once using 500 μL Low Salt Wash Buffer, with tube swap after each wash. Biotinylated RNA was eluted from beads by Trizol extraction, and 3' RNA adaptor ligation was performed in a total volume of 20 μL with 5 µM final adaptor concentration and 2 μL T4 RNA Ligase I, High Concentration (NEB). The reaction was incubated at 20°C for 4 h and held at 4°C overnight. On the next day, 50 μL Binding buffer and 30 μL pre-washed C1 beads were added to the reaction, and another round of bead binding and bead washing was performed as described above. Subsequent 5' enzymatic modifications of RNA were performed on beads with a reaction volume of 20 μL assuming 1 μL bead volume: 5' decapping reaction involved 1 μL RppH (NEB) and 1-h incubation at 37°C; 5' hydroxyl repair involved 1 μL T4 PNK (NEB) and 1-h incubation at 37°C. Beads were then washed once with 300 μL Binding Buffer, and 5' RNA adaptor ligation was performed on beads in a total volume of 20 μL with 5 µM final adaptor concentration and 2 μL T4 RNA Ligase I, High Concentration (NEB), incubated at room temperature for 1 h on a rotational device. Beads were washed twice using 500 μL High Salt Wash Buffer and once using 500 μL Low Salt Wash Buffer, with tube swap after each wash. RNA was eluted from beads by Trizol extraction and resuspended in 13 μL RT resuspension mix (8 μL DEPC H2O, 4 μL of 10 μM Illumina RP1 primer, 1 μL of 10 mM dNTPs). RNA was denatured at 65°C for 5 min and snap cooled on ice, and 7 μL RT master mix was added to the sample (4 μL of 5× RT Buffer, 1 μL of 100 mM DTT, 1 μL Invitrogen SUPERase·In RNase Inhibitor, 1 μL Thermo Scientific Maxima H Minus Reverse Transcriptase). RT reaction program was: 50°C for 30 min, 65°C for 15 min, 85°C for 5 min, hold at 4°C. The resulting cDNA was diluted with an equal volume of DEPC H2O.
A test amplification was performed on 1:4 serial dilutions of 2 μL cDNA sample and run on 6% native PAGE TBE gel to determine the optimal PCR cycle number (N). Final amplification was performed in 100 μL volume (32.5 μL DEPC H2O, 20 μL of 5× Phusion HF Buffer, 20 μL of 5 M betaine, 2.5 μL of 10 µM Illumina RP1 primer, 2.5 μL of 10 µM Illumina indexing RPI-n primer, 2.5 μL of 10 mM dNTPs, 1 μL homemade Phusion polymerase, 19 μL cDNA sample). PCR program was: initial denaturation 95°C for 2 min; 5 cycles of 95°C for 30 s, 56°C for 30 s, 72°C for 30 s; N cycles of 95°C for 30 s, 65°C for 30 s, 72°C for 30 s; final extension 72°C for 5 min. PCR products were sequentially purified using the MinElute PCR purification kit (Qiagen) and homebrew SPRI beads (1.5× bead ratio) to remove all unused primers. DNA concentration was measured by the Qubit dsDNA High Sensitivity assay (Thermo Fisher). The libraries were pooled for sequencing on the Element Biosciences AVITI (2 × 80 bp paired-end sequencing) or Illumina NovaSeq 6000/X Plus platform (2 × 150 bp paired-end sequencing). Note that the 3' and 5' RNA adaptors contain a 6-nt unique molecular identifier (UMI) to enable accurate identification of PCR duplicates in downstream bioinformatic analysis. The complete sequences of the adaptors can be found in Judd et al., 2020.


title: K562 cells, LP recombination, e1_mGATA1, rep1 (Input)

status: Public on Jun 15 2025

type: SRA

city: Ithaca

first: Zhou

last: Zhou

state: New York

address: 526 Campus Rd, 417 Biotechnology Building

department: Molecular Biology and Genetics

country: USA

institute: Cornell University

description: Library name: Sample 9

library_source: genomic

data_processing:
For all NGS sequencing data, the quality of FASTQ files was first accessed using FastQC, and the Illumina sequencing adaptors were trimmed using fastp.
To enable accurate alignment of sequencing reads to the eNMU locus in the recombinant cell lines, we built a custom genome for each recombinant TF motif mutant using the reform command line tool. Each custom genome incorporated the exact mutant sequence flanked by Bxb1 recombination sites. Alignment was performed using the bowtie2 aligner: for ChIP-seq, “-end-to-end --very-sensitive” mode was used; Picard MarkDuplicates was then used for deduplication.
To better normalize genomics datasets across different clonal lines, we applied a “reads-under-peaks” approach to calculate scaling factors for each sample. ChIP-seq peaks were called for each biological replicate and for pooled replicates using MACS2 with the input samples as control and the parameters “--broad --broad-cutoff 0.05 --keep-dup all”. Consensus peak sets from each group of replicates was generated using a published bash script (Additional file 5 of Reske et al., 2020), which identifies pooled peaks that show >50% reciprocal overlap with each biological replicate. These consensus peak sets were then merged to create a union peak set.
To generate the read count matrix for ChIP-seq datasets, read pairs overlapping union peaks were quantified using featureCounts. DESeq2 was then used to calculate scaling factors for normalization. bamCoverage was used to generate normalized bigwig files at a bin size of 50 bp for ChIP-seq.
Merged bigwig files from two biological replicates were generated using kentUtils of the UCSC Genome Browser.
Assembly: hg38
Supplementary files format and content: bigwig

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: All the K562 lines were cultured in RPMI 1640 media supplemented with GlutaMAX (Gibco) and 10% heat-inactivated FBS (Avantor) at 37°C with 5% CO2 in a humidified sterile incubator. Cell density was maintained between 0.1 ~ 1 × 10⁶ cells/mL, and mycoplasma testing was performed routinely.

extract_protocol:
Cells were first crosslinked with 2 mM disuccinimidyl glutarate (Santa Cruz) at room temperature for 30 min, washed 3 times with PBS and then crosslinked with 1% formaldehyde at room temperature for 5 min before quenching with 200 mM glycine at room temperature for 5 min. Two additional PBS washes were performed, and cell pellets were lysed with Farnham Lysis Buffer (5 mM PIPES, pH 8, 85 mM KCl, 0.5% NP40, 10 mM glycine, 1× Thermo Scientific Pierce Protease Inhibitor) on ice for 20 min. After centrifugation and supernatant removal, the nuclear pellet was resuspended in RIPA Lysis Buffer (10 mM Tris-HCl, pH 8, 150 mM NaCl, 1 mM EDTA, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, 1× Thermo Scientific Pierce Protease Inhibitor) and incubated on ice for 10 min. Sonication was carried out using a Diagenode Bioruptor device at High Setting, 30 sec on/30 sec off for three rounds of 10-min cycle to shear chromatin to a size of 100~300 bp. The lysate was then clarified by centrifugation at 20,000 r.c.f., 4°C for 15 min, of which 2% was kept as ChIP input. Each IP used 4 million cells/4 µg antibody/40 µL Dynabeads Protein G (Thermo Scientific). Beads were washed three times with 5 mg/mL BSA in PBS and incubated with corresponding antibodies at 4°C for 6 h to overnight with rotation. Another three BSA/PBS washes were performed to remove unbound antibodies, and the clarified chromatin lysate was added to the beads and incubated overnight at 4°C with rotation. Beads were then washed with the following buffers, each for three times: Low Salt Wash Buffer (20 mM Tri-HCl, pH 8, 2 mM EDTA, 150 mM NaCl, 1% Triton X-100, 0.1% SDS), High Salt Wash Buffer (20 mM Tri-HCl, pH 8, 2 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.1% SDS), and LiCl Wash Buffer (10 mM Tri-HCl, pH 8, 1 mM EDTA, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate). After one final wash with TE Buffer (10 mM Tris-Cl, pH 8, 1 mM EDTA), chromatin was eluted from beads by two rounds of incubation with ChIP elution buffer (1% SDS, 0.1 M sodium bicarbonate). Each incubation involved 15 min shaking at 1200 rpm at 65°C, followed by 15 min rotation at room temperature. The eluates and input samples were treated with RNase A at 37°C for 30 min, de-crosslinked at 65°C overnight with 900 rpm shaking, followed by Proteinase K treatment at 45°C for 2 h with shaking. DNA was purified using MinElute PCR Purification Kit (Qiagen).
For p300 ChIP, sequencing libraries were prepared using a Tn5 tagmentation-based protocol. Briefly, 20 μL tagmentation reactions were set up with 0.35 ng of ChIP DNA or 1 ng of input DNA, 1× TAPS-DMF Buffer (10 mM TAPS-NaOH, pH 8.5, 5 mM MgCl2, 10% DMF), and 1 μL of 1:15 diluted homemade Tn5 transposase (a kind gift from Dr. Roman Spektor). The reaction was incubated at 55°C for 10 min, and 2 μL of 1% SDS was added immediately, followed by another 55°C incubation for 7 min to strip off Tn5 from DNA. Post-tagmentation PCR was carried out in 100 μL volume with 10 μL of the tagmentation reaction, 1× Phusion HF Buffer, 200 μM dNTPs, 400 nM of each Illumina Nextera index primer, and 1 μL of homemade Phusion polymerase. The PCR program was: initial extension 72°C for 3 min; initial denaturation 98°C 30s; 13 cycles of 98°C for 10 s, 63°C for 30 s, 72°C for 3 min; and final extension 72°C for 5 min. PCR products were purified first using the MinElute PCR purification kit (Qiagen), followed by an additional cleanup with homemade SPRI beads (1.5× bead ratio) to ensure complete removal of unused primers. DNA concentration was measured by the Qubit dsDNA High Sensitivity assay (Thermo Fisher). The libraries were pooled for sequencing on the Element Biosciences AVITI platform (2 × 80 bp paired-end sequencing).

tag: cell line

tag: cell type

value: erythroleukemia

tag: genotype

value: LP recombination, e1_mGATA1


title: PBL053 with plasmacytic differentiation

type: RNA

city: Badalona

first: Miriam

last: Verdú-Bou

state: Barcelona

address: Ctra de Can Ruti, Camí de les Escoles, s/n

country: Spain

institute: Josep Carreras Leukaemia Research Institute

description: miRNA expression data from FFPE samples of PBL.

hyb_protocol: RNA was processed to add a Polu(A) tail and labeled with biotin. Then, was hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using ThermoFisher fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The array image was acquired using ThermoFihser GeneChip® Operating Software. CHP data was generated with Gene Expression Console. The algorithm used was RMA
affymetrix-algorithm-name = rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish
affymetrix-algorithm-version = 1.0

label: Biotin

molecule: total RNA

source_name: Homo sapiens PBL

label_protocol: As per manufacturer (ThermoFisher), with Biotin

extract_protocol: Total RNA extracction from formalin-fixed paraffin-embedded samples using RecoverAll Total Nucleic Acid Isolation according to the manufacturer's instructions.

tag: sample

value: FFPE

tag: group

value: Plasmablastic lymphoma (PBL)

tag: tissue


title: PBL054 with plasmacytic differentiation


title: ITS O2-Z4

city: Murdoch

first: Viet

last: Dang

address: 90 South Street

country: Australia

institute: Murdoch University

description: Library name: ITS O2-Z4

data_processing:
Amplicon sequence variant (ASV) tables were constructed based on the DADA2 pipeline with default parameters. Read adapters were removed from raw read sequences using cutadapt, and read quality was inspected using FastQC. Chimeric sequences were removed from merged reads, and taxonomy was then assigned using the DADA2 "assignTaxonomy " function.
Assembly: metagenome
Supplementary files format and content: table files include ASV count and taxa
Supplementary files format and content: fasta files contain ASV sequences

organism: soil metagenome

source_name: 0-10cm soil

extract_protocol:
DNeasy PowerSoil Kit (Qiagen Laboratories, Inc.)
Sequencing was carried out using Amplicon sequencing on Illumina MiSeq 2 × 250-bp PE platform

value: 0-10cm soil


title: LIB5455514_SAM24414654_S3_L002

city: South San Francisco

first: Marc

last: Hafner

state: CA

address: Building 45-1, 1 DNA Way

department: Oncology Bioinformatics

institute: Genentech

description:
SAM24414654_LIB5455514
NextSeq1

library_source: transcriptomic single cell

data_processing:
CMO data was processed using CellRanger and scRNA-Seq was processed using STARsolo with standard parameters.
Cumulus workflow with default settings was used for demultiplexing
Assembly: GRCh38 (GENCODE v32/Ensembl 98)

source_name: Colon

growth_protocol: The cells were seeded to 6-well plates. All samples were treated with compound combinations starting at different days and harvested together. Upon sample collection, cells were trypsinized from the plate and hashed by using the cholesterol modified oligo (CMO) following the MULTI-seq protocol

extract_protocol:
Cells from each sample were washed and re-suspended in 180µl of PBS+1%BSA and transferred to a round-bottom 96-well plate. Then 20µl of each anchor-barcode mix was added to the suspension for a final concentration of 2µM. After the incubation for 15 minutes at room temperature, 20µl of co-anchor was added to each sample (final concentration of 2µM) and incubate for another 15 minutes at RT. Cells were then washed by 500µl of cold PBS+1% BSA twice before pooling together.
The library construction was done following the manufacturer’s manual with a few modifications to accommodate the MULTI-seq protocol: (1) during the cDNA amplification 1µl of the following primer (10µM) was added to the master mix, 5’-CTTGGCACCCGAGAATTCC-3’; (2) the supernatant from the 0.6X SPRI beads cleanup for cDNA was kept and further cleaned up by using 2.0X SPRI beads; (3) the CMO libraries were made by performing 8 cycles of the indexing PCR using the supernatant. The transcriptome and CMO libraries were then sequenced by using either the Illumina NovaSeq or NextSeq machines

tag: library name

value: Colon

value: CRC line

tag: sample name


title: K562 cells, LP recombination, e2_mSTAT5, rep2 (ChIP)

description: Library name: Sample 8

value: LP recombination, e2_mSTAT5

tag: chip antibody


title: PBL055


title: PBL051


title: ITS O2-Z5

description: Library name: ITS O2-Z5


title: LIB5455514_SAM24414654_S3_L001

description:
SAM24414654_LIB5455514
NextSeq1


title: PBL058


title: PBL045


title: ITS O2-Z7

description: Library name: ITS O2-Z7


title: K562 cells, LP recombination, e1_mRUNX1, rep2 (ChIP)

description: Library name: Sample 6

value: LP recombination, e1_mRUNX1


title: LIB5455513_SAM24414654_S2_L002

description:
SAM24414654_LIB5455513
NextSeq1


title: ITS O2-Z8

description: Library name: ITS O2-Z8


title: K562 cells, LP recombination, e2_mSTAT5, rep1 (ChIP)

description:
Library name: Sample 7
"merge" bw files are merged from rep1 and rep2 bw


title: ITS O1-G7

description: Library name: ITS O1-G7


title: ITS O2-Z9

description: Library name: ITS O2-Z9


title: PBL043 with plasmacytic differentiation


title: K562 cells, LP recombination, e1_mGATA1, rep2 (ChIP)

description: Library name: Sample 4


title: LIB5455512_SAM24414654_S1_L002

description:
SAM24414654_LIB5455512
NextSeq1


title: LIB5455513_SAM24414654_S2_L001

description:
SAM24414654_LIB5455513
NextSeq1


title: K562 cells, LP recombination, e1_mGATA1, rep1 (ChIP)

description:
Library name: Sample 3
"merge" bw files are merged from rep1 and rep2 bw


title: PBL049


title: LIB5455517_SAM24414655_S6_L002

description:
SAM24414655_LIB5455517
NextSeq1


title: ITS O1-G9

description: Library name: ITS O1-G9


title: K562 cells, LP recombination, WT_eNMU, rep2 (ChIP)

description: Library name: Sample 2

value: LP recombination, WT_eNMU


title: ITS O1-G8

description: Library name: ITS O1-G8


title: LIB5455512_SAM24414654_S1_L001

description:
SAM24414654_LIB5455512
NextSeq1


title: LIB5455517_SAM24414655_S6_L001

description:
SAM24414655_LIB5455517
NextSeq1


title: PBL041


title: PBL039


title: PBL042 with plasmacytic differentiation


title: ITS O1-L1

description: Library name: ITS O1-L1


title: PBL037


title: LIB5455516_SAM24414655_S5_L002

description:
SAM24414655_LIB5455516
NextSeq1


title: K562 cells, LP recombination, WT_eNMU, rep1 (ChIP)

description:
Library name: Sample 1
"merge" bw files are merged from rep1 and rep2 bw


title: K562 cells, LP recombination, e1_mRARA, rep2

description: Library name: Sample 24

data_processing:
For all NGS sequencing data, the quality of FASTQ files was first accessed using FastQC, and the Illumina sequencing adaptors were trimmed using fastp. Note that one of the ATAC-seq samples was sequenced at 2 × 150 bp instead of 2 × 80 bp. To ensure consistency across samples, the raw FASTQ files for this sample were trimmed to 80 bp prior to any analysis.
To enable accurate alignment of sequencing reads to the eNMU locus in the recombinant cell lines, we built a custom genome for each recombinant TF motif mutant using the reform command line tool. Each custom genome incorporated the exact mutant sequence flanked by Bxb1 recombination sites. Alignment was performed using the bowtie2 aligner: for ATAC-seq, “-end-to-end --very-sensitive” mode was used, with a subsequent step to remove mitochondrial reads using samtools view; Picard MarkDuplicates was then used for deduplication.
To better normalize ATAC-seq datasets across different clonal lines, we applied a “reads-under-peaks” approach to calculate scaling factors for each sample. ATAC-seq peaks were called for each sample using HMMRATAC in the MACS3 software with “-u 90 -l 30 -c 10” parameters. To create a unified peak set for count normalization, we first identified reciprocal >50% overlaps between peaks from biological replicates using bedtools intersect "-f 0.50 -r". Consensus peak sets from each group of replicates were then merged to create a union peak set.
To generate the read count matrix for ATAC-seq datasets, read pairs overlapping union peaks were quantified using featureCounts. DESeq2 was then used to calculate scaling factors for normalization. bamCoverage was used to generate normalized bigwig files at a bin size of 1 bp.
Merged bigwig files from two biological replicates were generated using kentUtils of the UCSC Genome Browser.
Assembly: hg38
Supplementary files format and content: bigwig

extract_protocol:
ATAC-seq was performed on 50,000 K562 cells with all buffer compositions and reaction conditions following the published Omni-ATAC protocol (Corces et al., 2017) unless otherwise specified. Briefly, cells were pelleted, washed once with ice-cold PBS, resuspended in ice-cold Lysis Buffer, and incubated on ice for 3 min. Upon addition of Wash Buffer and gentle inversion, nuclei were pelleted, and supernatant (cytoplasm) was discarded. Nuclei were then resuspended gently in 50 μL transposition reaction mix containing 1 μL homemade Tn5 transposase and incubated at 37°C for 30 min with 1000 rpm shaking. DNA was purified using the MinElute PCR purification kit (Qiagen) and eluted in 21 μL volume.
The entire purified product (~20 μL) was mixed with 2.5 μL of each Nextera index primer (25 μM) and 25 μL NEBNext High-Fidelity 2X PCR Master Mix and subjected to a first round of PCR: initial extension 72°C for 5 min; initial denaturation 98°C 30s; 5 cycles of 98°C for 10 s, 63°C for 30 s, 72°C for 1 min. To determine additional cycles needed to avoid over-amplification, a qPCR analysis was performed using 5 μL of the first-round PCR reaction (Buenrostro et al., 2015). For all ATAC-seq libraries, 3~4 additional cycles of amplification were performed on the remaining 45 μL PCR reaction, followed by sequential cleanup using the MinElute PCR purification kit (Qiagen) and homebrew SPRI beads (1.5× bead ratio). DNA concentration was measured by the Qubit dsDNA High Sensitivity assay (Thermo Fisher). The libraries were pooled for sequencing on the Element Biosciences AVITI (2 × 80 bp paired-end sequencing) or Illumina NovaSeq X Plus platform (2 × 150 bp paired-end sequencing).

value: LP recombination, e1_mRARA


title: LIB5455516_SAM24414655_S5_L001

description:
SAM24414655_LIB5455516
NextSeq1


title: PBL036


title: K562 cells, LP recombination, e1_mRARA, rep1

description:
Library name: Sample 23
"merge" bw files are merged from rep1 and rep2 bw


title: LIB5455515_SAM24414655_S4_L002

description:
SAM24414655_LIB5455515
NextSeq1


title: K562 cells, LP recombination, LTRen_mKLF, rep2

description: Library name: Sample 22

value: LP recombination, LTRen_mKLF


title: LIB5455515_SAM24414655_S4_L001

description:
SAM24414655_LIB5455515
NextSeq1


title: 16T-TRa1, replicate 2, scRNA-Seq

city: Bethesda

first: Yuelin

middle: Jack

last: Zhu

state: MD

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

institute: NCI

description: 10X Genomics

data_processing:
10X Genomics cellranger-6.0.0 was used for demultipliexing, alignment, filtering, generating feature-barcode matrices, etc.
genome build: GRCh38
Supplementary files format and content: tab-delimited file and matrix files

source_name: xenograft tumor

growth_protocol: 16T parental cells and 16T-TRa1 cells were innoculated into nude mice. After 49 days, the xenograft tumors were dissected.

extract_protocol:
After the tumors were dissected from the nude mice, single tumor cells were prepared and subjected to single cell RNA-sequencing.
Library was prepared according to manufacturer's instructions (singel cell 5' v2 protocol, 10X genomic).

treatment_protocol: No treatment

value: xenograft tumor

value: ATC 16T-TRa1

value: xenograft tumor cells


title: K562 cells, LP recombination, LTRen_mKLF, rep1

description:
Library name: Sample 21
"merge" bw files are merged from rep1 and rep2 bw


title: K562 cells, LP recombination, LTRpr_mKLF, rep1

description:
Library name: Sample 19
"merge" bw files are merged from rep1 and rep2 bw

value: LP recombination, LTRpr_mKLF


title: K562 cells, LP recombination, LTRpr_mKLF, rep2

description: Library name: Sample 20


title: 11T parental, replicate 2, scRNA-Seq

description: 10X Genomics

value: ATC 11T


title: 16T-TRa1, replicate 1, scRNA-Seq

description: 10X Genomics


title: PBL027_second relapse


title: 11T parental, replicate 1, scRNA-Seq

description: 10X Genomics


title: Basal Ganglia_THC:CBD-SIV_6MPI, 40872 (Sup)

city: San Antonio

first: Mahesh

last: Mohan

state: Texas

address: 8715 West Military Road

department: Host Pathogen Interaction Program

institute: Southwest National Primate Research Center

description:
TCART1
raw data file: 40872.txt

hyb_protocol: 2.5 ug of Cy3 and Cy5 labeled RNAs were mixed. 22.5 uL 2X hybridization buffer (Agilent) was added to the mixture to a final volume of 45uL. The mixture was heated at 100C for 5 min and immediately chilled to 0C. 45 uL was used to hybridize onto the microarray at 55C for 20 hrs. The slides were washed at room in 6XSSC/0.005% Triton X-102 for 10 min and 0.1X SSC/0.005% Triton X-102 for 5 min.

scan_protocol: The microarray slides were scanned on an Agilent microarray scanner (model G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images. Raw intensities of IP (immunoprecipitated, Cy5-labelled) and Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities. Multiple probes for the same small RNA (miRNA/tsRNA/pre-miRNA) were averaged and consoliated into one RNA level. “m6A abundance” was analyzed based on the Cy5-labelled IP (modified RNA) normalized intensities. Differentially m6A-methylated RNAs between two comparison groups were identified by fold change (FC) and statistical significance (p-value) thresholds. Hierarchical Clustering heatmap was plotted to display m6A-modification patterns among samples by R software.

organism: Macaca mulatta

source_name: Brain (Basal Ganglia)

label_protocol: 1~5 ug total RNA per sample was immunoprecipitated with 4 ug anti-m6A antibody. The modified RNAs were eluted from the immunoprecipitated magnetic beads as the “IP”. The unmodified RNAs were recovered from the supernatant as “Sup”. The “IP” and “Sup” RNAs were separately dephosphorylated with T4 polynucleotide kinase (T4 PNK) to remove possible phosphate (P) or cyclic phosphate (cP) groups from the 3' end of the RNAs to form 3’-OH end. To disrupt RNA structure, the RNA was heated to 100C for 3 min in the presence of DMSO. The labeling ligation was carried out in 1X ligase buffer with BSA with 50 mM pCp-Cy5 (for “IP”) or pCp-Cy3 (for “Sup”) respectively, using 15 units of T4 RNA ligase in a 28 uL reaction at 16C overnight.

extract_protocol: RNA was prepared using the miRneasy mini kit (catalog # 217004) (Qiagen, Germantown, MD, USA) following the manufacturer's recommendations.

value: Basal Ganglia

tag: fraction

value: m6A supernatant RNA (Sup, m6A unmodified)


title: K562 cells, LP recombination, e1_mRUNX1, rep2

description: Library name: Sample 14

value: erythroleukemia


title: K562 cells, LP recombination, e2_mSTAT5, rep1

description:
Library name: Sample 15
"merge" bw files are merged from rep1 and rep2 bw


title: PBL030

value: FFPE

value: Plasmablastic lymphoma (PBL)


title: PBL026


title: Basal Ganglia_VEH-SIV_6MPI, 40876 (Sup)

description:
VSART3
raw data file: 40876.txt


title: CutRun_ESC_WT_GFP_Unt_r2

city: Adelaide

first: Luke

middle: Thomas

last: Isbel

state: South Australia

address: 4 North Terrace, AHMS, Lvl 9

institute: SAiGENCI

description:
Library name: Sample 6
Cut and Run for GFP

data_processing:
Illumina RTA 2.4.11 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing. Cut and Run reads were trimmed using cutadapt version 1.18, (Martin, M. EMBnet.journal 17, 10 (2011)) with parameters -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -m 10 --overlap=1 and then mapped to mm10 using QuasR (Gaidatzis et al, Bioinformatics 2015) with default parameters.
Assembly: mm10
Supplementary files format and content: wig files were generated using the qExportWig function from the QuasR package with scaling=1e6. The scores in the wig file represent the number of fragment midpoints per 100bp window and per million reads in the library.
Library strategy: CUT&Run

organism: Mus musculus

source_name: embryonic cells

growth_protocol: Mouse ES cells were cultured as previously described (Mohn, F. et al. Mol. Cell, 2008). Briefly, cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM, Invitrogen), supplemented with 15 % Fetal Calf Serum (Invitrogen), L-Glutamine (Gibco) and nonessential amino acids (Gibco), betamercaptoethanol (Sigma) and leukemia inhibitory factor (LIF; produced in-house). All experiments were performed with cells grown for several passages on plates coated with 0.2% gelatin (Sigma).

extract_protocol:
DNA was purified by using the MinElute PCR Purification Kit (Qiagen)
Immunoprecipitated DNA was subjected to library preparation (NEBNext Ultra II DNA Library Prep Kit, Illumina) with Cut and Run-specific PCR cycling parameters. In the library preparation protocol, samples were amplified using a total of 14 PCR cycles.

treatment_protocol: Cells (0.5x10^6) were seeded into 6-well plates the day before the experiment. Doxorubicin (1uM) compound were added to specific samples to activate p53. Cut and Run waw performed with the EpiCypher CUTANA pAG-MNase (15-1016) reagent and according to manufactures protocol. Briefly, 0.5x10^6 cells were resuspended in 0.1ml of Wash buffer (20mM HEPES, pH 7.5, 150mM NaCl, 0.5mM Spermidine, 1xRochecOmplete-TM Mini EDTA-free Protease Inhibitor in water). Cells were centrifuged at 600g for 3 min at room temp, then resuspended in Wash buffer for a second time and re-centrifuged. Pellets were suspended wash buffer with 10ul activated magnetic ConA beads (10ul beads) and incubated at room temp for 10 minutes. Beads/cells were magnet-imobalized and supernatant removed, then resuspended in Antibody buffer (0.001% digitonin, 2mM EDTA in Wash buffer) with 0.5 ul antibody at 4DegC and incubated overnight on nutator. Beads/cells were magnet-imobalized and supernatant removed, washed twice with 200ul Digitonin buffer (0.001% digitonin, in Wash buffer), resuspended in 50ul Digitonin buffer + 2.5ul pAG-MNase and incubated at room temp for 10 minutes. Beads/cells were magnet-imobalized and supernatant removed, washed twice with 200ul Digitonin buffer (0.001% digitonin, in Wash buffer), resuspended in 50ul Digitonin buffer + 1ul 100mM CaCl2 and incubated at 4DegC for 2 hours on nutator. Reactions were stopped with Stopping buffer (340 mM NaCl, 20 mM EDTA 4 mM EGTA, 50 µg/mL RNase, A 50 µg/mL Glycogen in water) and beads/cells were magnet-imobalized and supernatant taken for DNA extraction using the MinElute PCR Purification Kit (Qiagen). The eluted DNA was subjected to NEBNext® UltraTM II Library Prep Kit for Illumina® per manufacturer's instructions with the following modifications. After adaptor ligation DNA was cleaned up with 1.1x AMPure beads to retain >150bp fragments, Cut and Run-specific PCR cycling conditions: a. 45 sec @ 98ºC → activation of hot-start Q5 polymerase. b. 15 sec @ 98ºC → DNA melting. c. 10 sec @ 60ºC → hybrid primer annealing & short extension (<700 bp). d. Repeat “step b-c” for a total of 14x. e. 1 min @ 72ºC. DNA was cleaned up with 1.1x AMPure beads.

value: embryonic cells

value: 129S6/SvEvTac stem cells

value: embryonic stem cells

value: CagGFP consituitive expressing

tag: treatment

value: basal p53

tag: batch

tag: antibody


title: Basal Ganglia_THC:CBD-SIV_6MPI, 40874 (Sup)

description:
TCART2
raw data file: 40874.txt


title: CutRun_ESC_WT_GFP_Unt_r1

description:
Library name: Sample 5
Cut and Run for GFP


title: K562 cells, LP recombination, e1_mRUNX1, rep1

description:
Library name: Sample 13
"merge" bw files are merged from rep1 and rep2 bw

value: LP recombination, e1_mRUNX1


title: PBL027


title: K562 cells, LP recombination, e2_mSTAT5, rep2

description: Library name: Sample 16

value: LP recombination, e2_mSTAT5


title: PBL035 with plasmacytic differentiation


title: Basal Ganglia_THC:CBD-SIV_6MPI, 40878 (Sup)

description:
TCART3
raw data file: 40878.txt


title: Basal Ganglia_VEH-SIV_6MPI, 40875 (Sup)

description:
VSART2
raw data file: 40875.txt


title: Basal Ganglia_VEH-SIV_6MPI, 40879 (Sup)

description:
VSART4
raw data file: 40879.txt


title: PBL025


title: PBL026_second relapse


title: Basal Ganglia_Uninfected, IR97 (Sup)

description:
Control 4
raw data file: IR97.txt


title: Basal Ganglia_VEH-SIV_6MPI, 40873 (Sup)

description:
VSART1
raw data file: 40873.txt


title: PBL11

value: Control

value: reactive lymph nodes


title: K562 cells, LP recombination, e1_mGATA1, rep2

description: Library name: Sample 12

value: LP recombination, e1_mGATA1


title: CutRun_ESC_dp53_p53_Act_r1

description:
Library name: Sample 3
Cut and Run for p53

value: degron-tagged p53

value: activated p53

value: Invitrogen, v5 R96025


title: Basal Ganglia_Uninfected, HH69 (Sup)

description:
Control 2
raw data file: HH69.txt

value: Basal Ganglia

value: m6A supernatant RNA (Sup, m6A unmodified)


title: Basal Ganglia_Uninfected, HH75 (Sup)

description:
Control 3
raw data file: HH75.txt


title: Control HIV-pos 6

description:
miRNA expression data from FFPE samples of reactive lymph nodes.
018/13

source_name: Homo sapiens control HIV-pos

value: FFPE


title: CutRun_ESC_dp53_p53_Act_r2

description:
Library name: Sample 4
Cut and Run for p53


title: K562 cells, LP recombination, e1_mGATA1, rep1

description:
Library name: Sample 11
"merge" bw files are merged from rep1 and rep2 bw

value: erythroleukemia


title: Control HIV-pos 7

description:
miRNA expression data from FFPE samples of reactive lymph nodes.
019/13


title: K562 cells, LP recombination, WT_eNMU, rep2

description: Library name: Sample 10

value: LP recombination, WT_eNMU


title: Control HIV-neg 7

description:
miRNA expression data from FFPE samples of reactive lymph nodes.
015/13

source_name: Homo sapiens control HIV-neg


title: CutRun_ESC_dp53_p53_Unt_r1

description:
Library name: Sample 1
Cut and Run for p53

value: embryonic cells

value: 129S6/SvEvTac stem cells


title: HBEC3KT, Pam2+ODN, 4h, Rep3

city: Houston

first: Scott

middle: E

last: Evans

state: TX

address: 6565 MD Anderson Blvd, Unit 1059

department: Pulmonary Medicine

institute: University of Texas MD Anderson Cancer Center

description:
Library name: 12_ID-80-PAM2-ODN_cJun_3
Column name in processed file: PO-3_cJun_GRCh38/ Tag Count in given bp (37266837.0 Total, normalization factor = 0.27, effective total = 10000000)

data_processing:
The single-end sequencing reads generated by Illumina sequencing are mapped to the genome hg38 using the BWA algorithm (“bwa aln/samse”) with default settings. Alignment information for each read is stored in the BAM format.
Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. In addition, duplicate reads (“PCR duplicates”) are removed.
Determination of fragment density of aligned reads ("tags") were calculated per sample, and combined per treatment with HOMER's makeTagDirectory function using default settings.
Regions of enriched tags ("peaks") were calculated per treatment against a pooled input, and combined per TF with HOMER's findPeaks and mergePeaks function using default settings. These combined peaks were used to define a TFBS consensus of DNA-binding regions per TF. The TFBS consensus was annotated, and tag numbers were calculated and normalized for all samples with HOMER's annotatePeak function using default settings.
Assembly: hg38
Supplementary files format and content: A TXT file containing TFBS tag counts, normalized using each directory by the total number of tags such that each directory contains 10 million tags.

source_name: Lung; Bronchus

growth_protocol: Cell cultures were maintained in filter sterilized growth medium (GM) of keratinocyte serum-free media supplemented with human recombinant epidermal growth factor and bovine pituitary extract and 1 percent volume/volume (% v/v) of antibiotic-antimycotic (100X).

extract_protocol:
Cell were harvested after a 5–10-minute incubation with 1 mL of 0.25 % trypsin-EDTA, further neutralized with 4 mL of 2 % v/v fetal bovine serum in filter sterilized phosphate-buffered saline (PBS). Detached cells were centrifuged at 250 g for 5 minutes at room temperature (25 ºC) and the resulting cell pellet was reconstituted in 10 mL of GM. Cell counting was performed. A frozen pellet of 10,000,000 cells per sample was prepared and sent according to Active Motif for their end-to-end ChIP-seq service according to manufacturer's instructions.
Chromatin preparation, sonication, sample quality/integrity assessment, ChIP and library generation, QC of NGS library, and sequencing using Illumina platform were performed using proprietary standard protocols and analysis by Active Motif.

treatment_protocol: Cells were exposed to 10 mL (for 100mm dishes) of fresh GM with either 1% v/v PBS, 4 µM Pam2 only, 1 µM ODN only, or both 4 µM Pam2 and 1 µM ODN (Pam2+ODN) and followed up for the indicated timepoints per experiment

value: Lung; Bronchus

value: Epithelial cell

tag: time


title: K562 cells, LP recombination, WT_eNMU, rep1

description:
Library name: Sample 9
"merge" bw files are merged from rep1 and rep2 bw


title: ChIPseq_ESC_Unt_IgG_r2

description:
Library name: Sample 6
ChIPseq for IgG

data_processing:
Illumina RTA 1.18.64 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing for single-read experiments. Illumina RTA 2.4.11 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing for paired-read experiments. ChIP-seq samples were aligned to the mm10/hg19 assembly of the mouse genome using QuasR (Gaidatzis et al, Bioinformatics 2015), which internally uses Bowtie (Langmead, Genome Biology 2009). Bowtie was run with QuasR default parameters, allowing only for uniquely mapping reads.
Assembly: mm10
Supplementary files format and content: wig files were generated using the qExportWig function from the QuasR package with default parameters except scaling=1e6 and setting shift to 80. The scores in the wig file therefore represent the number of shifted alignments per 100bp window and per million reads in the library.

growth_protocol: Mouse ES cells were cultured as previously described (Mohn, F. et al. Mol. Cell, 2008). Briefly, cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM, Invitrogen), supplemented with 15 % Fetal Calf Serum (Invitrogen), L-Glutamine (Gibco) and nonessential amino acids (Gibco), betamercaptoethanol (Sigma) and leukemia inhibitory factor (LIF; produced in-house). All experiments were performed with cells grown for several passages on plates coated with 0.2% gelatin (Sigma). The human primary cell line (HMEC) were cultured in Mammary Epithelial Cell Growth Medium (Gibco MEGM) supplemented with growth factors (Gibco MEGM-SingleQuots CC-4136) BPE, hydrocortisone, hEGF, insulin and gentamicin/amphotericin-B (37°C, 7% CO2).

extract_protocol:
DNA was purified by Phenol:Chloroform extraction.
Immunoprecipitated DNA was subjected to library preparation (NEBNext Ultra II DNA Library Prep Kit, Illumina). In the library preparation protocol, samples were amplified using 12 PCR cycles.

treatment_protocol: Cells (1.5x10^7) were seeded into 15 cm plates the day before the experiment. Doxorubicin (1uM)  compound were added to specific samples to activate p53. Chromatin Immunoprecipitation (ChIP) was carried out as previously described (Lienert, F. et al. Nat. Genet., 2011) with following modifications: (1) chromatin was sonicated for 22 cycles of 20 sec. on and 40 sec. off using a Diagenode Bioruptor Pico, (2) 75ug of chromatin was used per IP, (3) protein A magnetic Dynabeads (Thermo Fisher Scientific) were used.

value: embryonic stem cells

value: wild type

value: basal p53

value: Sigma Aldrich, IgG M7023


title: K562 cells, e2 deletion, rep2

description: Library name: Sample 8

value: delta e2


title: K562 cells, e2 deletion, rep1

description:
Library name: Sample 7
"merge" bw files are merged from rep1 and rep2 bw


title: ChIPseq_ESC_Unt_IgG_r1

description:
Library name: Sample 5
ChIPseq for IgG


title: Basal Ganglia_THC:CBD-SIV_6MPI, 40878 (IP)

description:
TCART3
raw data file: 40878.txt

value: m6A immunoprecipitated RNA (IP, m6A modified)


title: CutRun_ESC_dp53_p53_Unt_r2

description:
Library name: Sample 2
Cut and Run for p53

value: degron-tagged p53


title: K562 cells, e1 deletion, rep2

description: Library name: Sample 6

value: delta e1


title: ChIPseq_ESC_Unt_Usp7_r2

description:
Library name: Sample 4
ChIPseq for Usp7

value: Thermo Fisher Scientific, USP7 A300-033A


title: Basal Ganglia_Uninfected, HF34 (Sup)

description:
Control 1
raw data file: HF34.txt

value: Basal Ganglia

value: m6A supernatant RNA (Sup, m6A unmodified)


title: K562 cells, e1 deletion, rep1

description:
Library name: Sample 5
"merge" bw files are merged from rep1 and rep2 bw

value: erythroleukemia


title: Basal Ganglia_THC:CBD-SIV_6MPI, 40874 (IP)

description:
TCART2
raw data file: 40874.txt


title: Control HIV-pos 3

description:
miRNA expression data from FFPE samples of reactive lymph nodes.
011/13

value: FFPE

value: Control

value: reactive lymph nodes


title: ChIPseq_ESC_Unt_Usp7_r1

description:
Library name: Sample 3
ChIPseq for Usp7

value: embryonic cells

value: 129S6/SvEvTac stem cells


title: K562 cells, eNMU deletion, rep2

description: Library name: Sample 4

value: delta eNMU


title: ChIPseq_ESC_Act_Usp7_r2

description:
Library name: Sample 2
ChIPseq for Usp7

value: embryonic stem cells

value: wild type

value: activated p53


title: ChIPseq_ESC_Act_Usp7_r1

description:
Library name: Sample 1
ChIPseq for Usp7


title: Control HIV-pos 4

description:
miRNA expression data from FFPE samples of reactive lymph nodes.
012/13


title: Basal Ganglia_VEH-SIV_6MPI, 40879 (IP)

description:
VSART4
raw data file: 40879.txt


title: K562 cells, eNMU deletion, rep1

description:
Library name: Sample 3
"merge" bw files are merged from rep1 and rep2 bw


title: Control HIV-pos 5

description:
miRNA expression data from FFPE samples of reactive lymph nodes.
013/13


title: K562 cells, LP recombination, e1_mRUNX1, rep1 (ChIP)

value: LP recombination, e1_mRUNX1


title: P21_Treatment_Sun1-GFP_bulkRNAseq_rep2

city: Piscataway

first: Tulsi

last: Patel

state: New Jersey

address: 683 Hoes Lane West

department: Neuroscience and Cell Biology

institute: Rutgers University

description: bulk RNAseq

library_source: transcriptomic

data_processing:
RSEM alignment for bulk RNAseq data
CellRanger for 10x genomics data
Assembly: mm10
Supplementary files format and content: genes, counts, fpkm, tpm for bulk data.
Supplementary files format and content: Input needed for Seurat for 10x genomics data

source_name: Spinal Cord

extract_protocol:
protocol for nuclei purification + FACs in Patel et al., 2022 Nature Neuroscience
SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian for bulk RNAseq, 10x Genomics kit for multiome

treatment_protocol: AAV-ChatEn-Isl1 + AAV-ChatEn-Lhx3 were injected ICV at P1

value: Spinal Cord

value: AAV-Isl1 + AAV-Lhx3


title: Control HIV-pos 2

description:
miRNA expression data from FFPE samples of reactive lymph nodes.
010/13


title: Basal Ganglia_THC:CBD-SIV_6MPI, 40872 (IP)

description:
TCART1
raw data file: 40872.txt

value: m6A immunoprecipitated RNA (IP, m6A modified)


title: Basal Ganglia_VEH-SIV_6MPI, 40876 (IP)

description:
VSART3
raw data file: 40876.txt


title: P21_Treatment_Sun1-GFP_bulkRNAseq_rep1

description: bulk RNAseq


title: Control HIV-neg 6

description:
miRNA expression data from FFPE samples of reactive lymph nodes.
009/13


title: Control HIV-neg 3

description:
miRNA expression data from FFPE samples of reactive lymph nodes.
003/13


title: K562 cells, wildtype, rep1

description:
Library name: Sample 1
"merge" bw files are merged from rep1 and rep2 bw

value: wildtype


title: Basal Ganglia_Uninfected, IR97 (IP)

description:
Control 4
raw data file: IR97.txt

value: Basal Ganglia


title: Control HIV-pos 1

description:
miRNA expression data from FFPE samples of reactive lymph nodes.
006/13


title: Basal Ganglia_VEH-SIV_6MPI, 40875 (IP)

description:
VSART2
raw data file: 40875.txt


title: Basal Ganglia_VEH-SIV_6MPI, 40873 (IP)

description:
VSART1
raw data file: 40873.txt


title: Wt_1

status: Public on Jun 14 2025

city: Hong Kong

first: KIM

last: Jin Young

address: Tat Chee Avenue, Kowloon, Hong Kong

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

data_processing:
RNA-seq raw reads were mapped to the UCSC mouse reference genome (mm10) and calculation of gene counts using STAR (version 2.7.2b) with default parameters.
The multi-mapped reads were filtered out and only the uniquely mapped reads were retained.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: Primary neuronal cultures

growth_protocol: The cortices of embryonic day 17.5 were dissected, and then incubated in 0.025% trypsin-EDTA at 37°C for 15 min. After neutralization in NM10 medium, tissues were mechanically triturated into dissociated cells in the neuronal culture media containing Neurobasal (Gibco) supplemented with B27 (Gibco), 10 mM GlutaMax (Gibco) and 1% Penicillin-Streptomycin (Sigma). Dissociated cells were plated on poly-D-lysine coated tissue culture dishes. After 3-day culture, primary cultures were treated with 5 μM of cytosine β-D-arabinofuranoside for 18 h to eliminate proliferating cells. Primary neurons were cultured for 6 more days at 37°C with 5% CO2 to fully differentiate.

extract_protocol:
Total RNAs were extracted from primary neuronal cultures using the RNA extraction kit (MiniBEST Universal RNA extraction kit; TaKaRa).
Libraries were prepared according to the library construction procedures of BGISEQ-500 and then sequenced on the BGIseq500 (Illumina) platforms (Beijing Genomics Institute, China)

treatment_protocol: 10 days in vitro (DIV 10) neuronal cultures were exposed to either 2μM Aβ42, 20μM Aβ42, or 1x PBS (vehicle-treated control) for 24 hours to induce the early and late Aβ toxicity, respectively. For glutamate excitotoxicity, DIV 10 neuronal cultures were exposed to either 100μM glutamate or 0.1M HCl (vehicle-treated control) for 24 hours.

value: Primary neuronal cultures

tag: neuron subtype

value: Wild type neuron

value: Batch 3


title: BKO_2

value: Bmal1 deleted neuron


title: BKO_1


title: PBL040

description: miRNA expression data from FFPE samples of PBL.

value: FFPE

value: Plasmablastic lymphoma (PBL)


title: Control_Excitotoxicity_2

value: vehicle-treated control for the excitotoxicity

value: Batch 1


title: Control_Excitotoxicity_1


title: Basal Ganglia_Uninfected, HH69 (IP)

description:
Control 2
raw data file: HH69.txt


title: Control HIV-neg 5

description:
miRNA expression data from FFPE samples of reactive lymph nodes.
008/13

value: Control

value: reactive lymph nodes


title: Control HIV-neg 2

description:
miRNA expression data from FFPE samples of reactive lymph nodes.
002/13


title: Basal Ganglia_Uninfected, HF34 (IP)

description:
Control 1
raw data file: HF34.txt


title: Control HIV-neg 1

description:
miRNA expression data from FFPE samples of reactive lymph nodes.
001/13


title: Excitotoxicity_r2

value: glutamate excitotoxicity


title: K562 cells, wildtype, rep2

description: Library name: Sample 2

value: erythroleukemia


title: Control_Aβ toxicity_2

value: vehicle-treated control for the A{Beta} toxicity

value: Batch 2


title: Excitotoxicity_r1


title: Control_Aβ toxicity_1


title: Wt_2


title: Control HIV-neg 4

description:
miRNA expression data from FFPE samples of reactive lymph nodes.
004/13


title: Late Aβ toxicity_r2

value: late A{Beta} toxicity


title: Eary Aβ toxicity_r2

value: early A{Beta} toxicity


title: Late Aβ toxicity_r1


title: Basal Ganglia_Uninfected, HH75 (IP)

description:
Control 3
raw data file: HH75.txt

value: Basal Ganglia

value: m6A immunoprecipitated RNA (IP, m6A modified)


title: B3

city: Changchun

first: Boyin

last: Jia

state: Jilin

address: 2888 Xincheng Street

department: College of Animal Science and Technology

country: China

institute: Jilin Agricultural University

description:
Library name: Sample 6
4T1 cells were collected from Au/MoS2/Bi2S3+NIR group for 48 h

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq 6000 platform and paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-houseperl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The left files (read1 files) from all libraries/samples were pooled into one big left.fq file, and right files (read2 files) into one big right.fq file. Transcriptome assembly was accomplished based on the left.fq and right.fq using Trinity (Grabherr et al, 2011) with min_kmer_cov set to 2 by default and all other parameters set default.
Assembly: reference sequence used for mice
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: breast

growth_protocol: 4T1 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidifed atmosphere with 5% CO2 at 37℃

extract_protocol:
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. 4T1 cells transcriptomics were analyzed by Illumina NovaSeq 6000 for high-throughput deep sequencing. The mRNA libraries were constructed and sequenced. In brief, mRNA was purified with poly-T oligo beads and fragmented. First-strand cDNA was synthesized by random hexamer primers, and followed by second-strand synthesis. cDNA products were end-repaired and A-tailed before size selection and adapter ligation. The AMPure XP system was preferentially selected cDNA fragments between 150 and 200 bp in length. Individual sequence libraries were amplified by PCR. Libraries were pooled, and 150 basepair paired-end reads were sequenced.
the mRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 4T1 cells (5 × 105) were seeded in a confocal dishes and incubated for 24 h, and then Au/MoS2/Bi2S3 (125 µg·mL-1) were added to the dishes and then incubated in an incubator overnight. The next day, the cells were exposed to NIR irradiation for 8 min, and the cells were washed with PBS after another 24 h of incubation.

value: breast

value: cancer cell

value: WT


title: B2

description:
Library name: Sample 5
4T1 cells were collected from Au/MoS2/Bi2S3+NIR group for 48 h


title: A3

description:
Library name: Sample 3
4T1 cells were collected from Control group for 48 h


title: A2

description:
Library name: Sample 2
4T1 cells were collected from Control group for 48 h


title: MEF_PUS10KO_tdR-5-GlyGCC_n4

city: Lund

first: Phuong

last: Cao Thi Ngoc

address: BMC, B1222b, Klinikgatan 26

country: Sweden

institute: Lund University

description: Library name: Sample 6

data_processing:
The raw reads were trimmed from the 3’ adaptor sequence (AGATCGGAAGAG) by cutadapt and mapped to the mouse genome using STAR. Reads were allowed to map to 1 locus (unique mapping) or 100 loci (multiple mapping). Read quantification was performed using TEtranscript and TElocus (https://github.com/mhammell-laboratory/TElocal). Bioconductor package DESeq2 was used to analyze differential gene expression.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw count for each Sample

source_name: Mouse embryonic fibroblasts

extract_protocol:
For the RNA sequencing upon transfection with the tdRs, PUS10 KO MEFs were plated in gelatin-coated 10cm plates at a density of 1 × 106 cells and transfected with 20 nM of tdR-5-GlyGCC or tdR-SCR. 24h post transfection, cells were harvested and lysed in TRIzol. RNA was isolated using the Quick-RNA Miniprep Kit (Zymo Research).
Sequencing libraries were generated using 500 ng of total RNA with the TruSeq Stranded Total RNA Library Prep Kit (Illumina) according to the manufacturers’ instructions. Libraries were sequenced on an Illumina NovaSeq 6000 with paired end 150 cycles.

value: Mouse embryonic fibroblasts

value: PUS10 KO


title: MEF_PUS10KO_tdR-5-GlyGCC_n3

description: Library name: Sample 5


title: MEF_PUS10KO_tdR-5-GlyGCC_n1

description: Library name: Sample 4


title: MEF_PUS10KO_tdR_SCR_n2

description: Library name: Sample 2


title: MEF_PUS10KO_tdR_SCR_n1

description: Library name: Sample 1


title: MEF_PUS10KOpoly_n3

description: Library name: Sample 18

library_source: other

data_processing:
The raw reads were trimmed from the 3’ adaptor sequence (AGATCGGAAGAG) by cutadapt and mapped to the mouse genome using STAR. Differential expression at transcription and translation levels and translation efficiency analyses were performed using the Bioconductor package DESeq2.
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw count for each Sample

molecule: other

growth_protocol: MEFs hTERT WT or PUS10 KO were cultured in 10cm dishes to have them at approximately 70-80% confluency on the day of the experiment.

extract_protocol:
Cells were incubated for 10 min at 37oC in media supplemented with 10 mg/mL cycloheximide (CHX) (Sigma-Aldrich). After washing with ice-cold PBS containing 10 mg/mL CHX cells were lysed in 450 ml polysome lysis buffer (PLB) with 10 mM Tris-HCl pH 8.0, 150 mM NaCl, 1.5 mM MgCl2, 0.25% NP-40, 0.1% Triton X-100, 320 U/mL SUPERase-In RNase Inhibitor (Thermo Fisher Scientific), 150 mg/mL CHX (Sigma-Aldrich) and 20 mM DTT. Lysates were incubated on ice for 40 min, mixed every 10 min and cleared at 15,000 rpm for 10 min at 4oC. Equal amounts of lysates were layered onto a linear 10%–60% sucrose (Thermo Fisher Scientific) (w/v) gradients in 25 mM Tris-HCl pH 7.4, 25 mM NaCl, 5 mM MgCl2, 0.1 mg/mL heparin and 2 mM DTT in nuclease-free water. Samples were centrifuged using a SW41Ti rotor (Beckman) for 2.5 hr at 37,000 rpm at 4oC and fractioned using a BioComp Gradient Station (BioComp). To each 650 μL fraction, 800 μL of TRIzol was added and samples were immediately snap-frozen on dry ice. For individual sucrose gradient fractions, RNA isolation was carried out using Direct-Zol RNA Miniprep (Zymo Research) with the in-column DNAse treatment according to manufacturer’s protocol. For normalization, 5 ng of an in vitro-transcribed luciferase RNA (5 ng) was added to each sample before RNA isolation.
Sequencing libraries were generated using 500 ng of total or polysomal RNA with the TruSeq Stranded Total RNA Library Prep Kit (Illumina) according to the manufacturers’ instructions. Libraries were sequenced on an Illumina NovaSeq 6000 with paired end 150 cycles.


title: MEF_PUS10KOpoly_n2

description: Library name: Sample 17


title: MEF_WTpoly_n3

description: Library name: Sample 15


title: MEF_PUS10KOpoly_n1

description: Library name: Sample 16


title: MEF_WTpoly_n2

description: Library name: Sample 14


title: MEF_WTpoly_n1

description: Library name: Sample 13


title: MEF_PUS10KOmono_n3

description: Library name: Sample 12


title: MEF_PUS10KOmono_n2

description: Library name: Sample 11


title: MEF_PUS10KOmono_n1

description: Library name: Sample 10


title: MEF_WTmono_n2

description: Library name: Sample 8


title: MEF_WTmono_n3

description: Library name: Sample 9


title: Eary Aβ toxicity_r1

value: Primary neuronal cultures


title: MEF_PUS10KOinp_n2

description: Library name: Sample 5


title: MEF_PUS10KOinp_n3

description: Library name: Sample 6


title: MEF_PUS10KOinp_n1

description: Library name: Sample 4


title: MEF_WTmono_n1

description: Library name: Sample 7


title: B1

description:
Library name: Sample 4
4T1 cells were collected from Au/MoS2/Bi2S3+NIR group for 48 h


title: MEF_WTinp_n3

description: Library name: Sample 3


title: A1

description:
Library name: Sample 1
4T1 cells were collected from Control group for 48 h


title: MEF_WTinp_n2

description: Library name: Sample 2


title: HSC control RNA-seq #2

data_processing:
Reads were trimmed 3'adapter (AGATCGGAAGAG) using cutadapt. The trimmed reads were aligned to the mm10 annotation ofmouse genomeusing STAR v2.7.8a with the parameter outFilterMultimapNmax set to 1
Bioconductorpackage DESeq2 was used to analyzedifferential gene expression.
Gene expression levels, log2of normalized counts by DESeq2, were used to input into GSEA v4.3.2 for gene set enrichment analysis.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw count for each Sample
Supplementary files format and content: tab-delimited text file includes normalized abundance by DESeq2 for each Sample

molecule: polyA RNA

source_name: Murine hematopoietic stem cells

extract_protocol:
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 10ng of total RNA with a Bioanalyzer RIN score greater than 8.0.
ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

value: Murine hematopoietic stem cells


title: MEF_WTinp_n1

description: Library name: Sample 1


title: MEF_PUS10KO_tdR_SCR_n3

description: Library name: Sample 3


title: HSC PUS10KO RNA-seq #1

value: KO


title: HSC control RNA-seq #1


title: mononuclear cells, quadriceps, day 1 post BaCl2-induced acute muscle injury

city: New York

first: Gregory

last: Smith

address: 1 Gustave L Levy Pl

institute: Icahn School of Medicine at Mount Sinai Hospital

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: quadriceps

extract_protocol:
Cryo-preserved cells were used directely for library construction for scRNA-seq. Cells were thawed, washed, and resuspended at 1,000 cells/ul for processing 10x scRNAseq v3.1 protocol.
10X Genomics Single Cell 3' Reagent Kits V3.1, following the User Guidelines. Briefly, GEM RNAseq was performed as described (10x Genomics, Pleasanton, CA), following the Single Cell 3’ Reagents Kits V3 User Guides. Cells were filtered, counted on a Nexcelome instrument, and the final concentration was set at 1,000 cells/μl for cells. The amount of cells or nuclei loaded on the chip was determined based on the 10X Genomics protocol. The 10X chip (Chromium Single Cell 3’ v3 chip kit B PN-2000060) was loaded to target 5,000 cells final. Reverse-transcription was performed in the emulsion and cDNA was amplified before library construction following the Chromium protocols v3. Each library was tagged with a different index for multiplexing (Chromium i7 Multiplex kit PN-12062). Quality control and quantification of the amplified cDNA were assessed on a Bioanalyzer (High-Sensitivity DNA Bioanalyzer kit). Sequencing was carried out at the New York Genome Center on Illumina Novaseq using  98+26 paired-end reads.

value: quadriceps

value: muscle mononuclear cells

value: multiple cell types

value: one day after BaCl2-induced acute injury


title: siN16.sample_3

city: St Louis

first: Sabine

last: Dietmann

state: MO

address: 4565 McKinley Avenue

institute: Washington University School of Medicine

data_processing:
Raw reads were trimmed using TrimGalore in paired-end mode excluding reads with low quality (-q 30) and < 25 nt length.
Quality-trimmed reads were aligned to the mouse GRCm38/mm10 genome with Hisat2 (version 2.2.1).
Counts were extracted using featureCounts using the options -M -O -p -C -B -s 2 for paired-end mode and strand-specific libraries.
Assembly: Mouse GRCm38/mm10
Supplementary files format and content: Processed data files contain counts per ENSEMBL (101) protein coding and lncRNA genes obtained by featureCounts

source_name: ascites from Abelson murine leukemia virus-induced tumor

growth_protocol: Raw264.7 cells were maintained in D-MEM High Glucose supplemented with 10 % heat-inactivated fetal bovine serum (FBS) and antibiotics (100 units/ml penicillin and 100 μg/ml of streptomycin)

extract_protocol:
Total RNA was extracted with Direct-zol RNA Miniprep Kit (ZYMO RESEARCH). 1ug RNA was subjected to library construction for RNA-seq.
mRNA was enriched by Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA, USA) and library was constructed with NEBNext® Ultra™II Directional RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA, USA) following manifacture protocol

treatment_protocol: Raw264.7 cells were transfected with siRNA for Nop16(20 nM) using Lipofectamine RNAi Max for 3 days.

value: macrophage

value: Nop16 KD

value: no


title: siN16.sample_2

value: ascites from Abelson murine leukemia virus-induced tumor


title: mononuclear cells, quadriceps, day 3 post BaCl2-induced acute muscle injury

value: three day after BaCl2-induced acute injury


title: siCont.sample_3


title: P60_alpha_86

city: Beijing

first: Cheng-ran

last: Xu

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

department: School of Basic Medical Sciences

institute: Peking University

description:
pancreatic P60 α cell, scRNAseq
Smart-seq3xpress

data_processing:
For smart-seq3xpress scRNA-seq, the index, primer and adaptor sequences in the paired-end reads were trimmed with Trimmomatic (v0.39). The trimmed reads were aligned to the Mus musculus reference genome (GRCm38/mm10) using Hisat242 (V2.1.0) with the default parameters. The reads were assigned to genes using featureCounts (v2.0.1) with default parameters.
Assembly: mm10
Supplementary files format and content: Smart-seq3xpress output files: Tab-separated rexpression values matrix files

source_name: pancreas

extract_protocol:
For the isolation of adult mouse islets, firstly, euthanize mice and expose abdominal organs. Next, clamp the duodenum at the upper and lower position where the common bile duct enters the duodenum. Then, inject pre-cold 1 mg/ml collagenase P into the common bile duct to inflate whole pancreas. Digest pancreas in 37℃ water bath for 6-8 min with gently shaking, and then manually pick out islets using microscope. These islets were digested into single-cell suspension with 0.25% trypsin for 5 min at 37℃. For the digestion of embryonic mouse pancreas, firstly, E14.5-18.5 pancreas were dissected and digested with 1 mg/ml collagenase P for 3-5 min which varies depending on pancreas size. Then, dissociated pancreas were treated with 0.25% trypsin for 5 min at 37℃. Cell suspension obtained after digestion can be directly sorted using the endogenous fluorescent protein carried by the cells and BD FACSAria Fusion flow cytometer.
For smart-seq3xpress, single cells were collected according to two strategies: one was to sort single cells into 384-well plates containing lysis buffer, and the other was to pick single cells manually from FACS-purified bulk cells by using a mouth pipette.

value: pancreas

value: islet cell

tag: strain

value: GcgGFP

tag: Sex

value: Male

tag: age


title: siCont.sample_1

tag: cell line

tag: cell type

value: WT


title: P60_alpha_82

tag: genotype


title: siCont.sample_2


title: P60_alpha_83


title: P60_alpha_84


title: P60_alpha_81


title: P60_alpha_80


title: P60_alpha_75


title: P60_alpha_74


title: P60_alpha_78


title: HSC PUS10KO RNA-seq #2


title: P60_alpha_73


title: P60_alpha_70


title: siN16.sample_1


title: P60_PP_114

description:
pancreatic P60 PP cell, scRNAseq
Smart-seq3xpress

value: PpymNeptune


title: P60_PP_113


title: P60_PP_116


title: P60_alpha_72


title: P60_PP_112


title: P60_PP_111


title: P60_alpha_69


title: P60_PP_115


title: P60_alpha_85


title: P60_PP_110


title: P60_PP_109


title: P60_PP_108


title: P60_alpha_71


title: P60_PP_104


title: P60_PP_107


title: P60_PP_106


title: P60_alpha_76


title: P60_alpha_77


title: P60_PP_102


title: P60_PP_105


title: P60_PP_101


title: P60_PP_100


title: P60_PP_98


title: P60_PP_99


title: P60_PP_96


title: P60_PP_95


title: P60_PP_97


title: P60_PP_94


title: P60_PP_93


title: P60_PP_91


title: P60_PP_86


title: P60_PP_89


title: P60_PP_88


title: P60_PP_87


title: P60_PP_92


title: P60_PP_90


title: P60_PP_85


title: P60_PP_83


title: P60_PP_81


title: P60_PP_80


title: P60_PP_84


title: P60_PP_82


title: P60_PP_103


title: P60_PP_79


title: P60_alpha_79


title: P60_PP_78


title: P60_PP_77


title: P60_PP_76


title: P60_PP_75


title: P60_PP_73


title: P60_PP_72


title: P60_PP_70


title: P60_PP_71


title: P60_PP_69


title: P60_PP_67


title: P60_PP_66


title: P60_PP_65


title: P60_PP_63


title: P60_PP_62


title: P1_PP_76

description:
pancreatic P1 PP cell, scRNAseq
Smart-seq3xpress


title: P60_PP_64


title: P1_PP_77


title: P1_PP_75


title: P1_PP_79


title: P1_PP_78


title: P1_PP_73


title: P1_PP_72


title: P1_PP_70


title: P1_PP_74


title: P1_PP_69


title: P1_PP_67


title: P1_PP_65


title: P60_PP_74


title: P1_PP_64


title: P1_PP_63


title: P1_PP_68


title: P1_PP_61


title: P1_PP_62


title: P1_PP_60


title: P1_PP_58


title: P60_PP_68


title: P1_PP_57


title: P1_PP_56


title: P1_PP_55


title: P1_PP_54


title: P1_PP_52


title: P1_PP_53


title: P1_PP_50


title: P1_PP_71


title: P1_PP_51


title: P1_PP_49


title: P1_PP_48


title: P1_PP_47


title: P1_alpha_97

description:
pancreatic P1 α cell, scRNAseq
Smart-seq3xpress


title: P1_PP_46


title: P1_alpha_96


title: P1_PP_44


title: P1_PP_45


title: P1_alpha_98


title: P1_alpha_95


title: P1_PP_66


title: P1_alpha_94


title: P1_PP_59


title: P1_alpha_92


title: P1_alpha_90


title: P1_alpha_93


title: P1_alpha_89


title: P1_alpha_91


title: P1_alpha_88


title: P1_alpha_86


title: P1_alpha_85


title: P1_alpha_84


title: P1_alpha_82


title: P1_alpha_81


title: P1_alpha_79


title: P1_alpha_78


title: P1_alpha_77


title: P1_alpha_74


title: P1_alpha_76


title: P1_alpha_71


title: P1_alpha_69


title: P1_alpha_72


title: P1_alpha_67


title: P1_alpha_66


title: P1_alpha_68


title: P1_alpha_70


title: P1_alpha_73


title: E13.5TAM_E14.5_87

description:
pancreatic Ins1-RFP+Gcg-GFP+ cell, scRNAseq
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E13.5, with analysis conducted on E14.5 embryos

value: Gcg-Cre;Ins-DreER;Rosa-LSL-RSR-EGFP


title: P1_alpha_65


title: E13.5TAM_E14.5_86


title: P1_alpha_63


title: P1_alpha_64


title: P1_alpha_87


title: E13.5TAM_E14.5_85


title: P1_alpha_62


title: P1_alpha_83


title: E13.5TAM_E14.5_84


title: E13.5TAM_E14.5_88


title: E13.5TAM_E14.5_83


title: E13.5TAM_E14.5_82


title: P1_alpha_80


title: E13.5TAM_E14.5_81


title: P1_alpha_75


title: E13.5TAM_E14.5_80


title: E13.5TAM_E14.5_78


title: E14.0TAM_E14.5_76

description:
pancreatic Ins1-RFP+Gcg-GFP+ cell, scRNAseq
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E14.0, with analysis conducted on E14.5 embryos


title: E14.0TAM_E14.5_75


title: E14.0TAM_E14.5_77


title: E14.0TAM_E14.5_74


title: E14.0TAM_E14.5_73


title: E14.0TAM_E14.5_72


title: E13.5TAM_E16.5_74

description:
pancreatic Ins1-RFP+Gcg-GFP+ cell, scRNAseq
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E13.5, with analysis conducted on E16.5 embryos


title: E13.5TAM_E16.5_75


title: E13.5TAM_E16.5_71


title: E13.5TAM_E16.5_72


title: E13.5TAM_E16.5_70


title: E13.5TAM_E16.5_69


title: E13.5TAM_E16.5_68


title: E13.5TAM_E16.5_65


title: E14.0TAM_E14.5_71

description:
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E14.0, with analysis conducted on E14.5 embryos

source_name: pancreatic Ins1-RFP+Gcg-GFP+ cell, scRNAseq


title: E14.0TAM_E14.5_70


title: E14.0TAM_E14.5_68


title: E14.0TAM_E14.5_69


title: E14.0TAM_E14.5_66


title: E14.0TAM_E14.5_67


title: E13.5TAM_E16.5_64


title: E13.5TAM_E16.5_67


title: E13.5TAM_E16.5_66


title: E14.0TAM_E14.5_65


title: E13.5TAM_E14.5_79


title: E14.0TAM_E14.5_63


title: E14.0TAM_E14.5_61


title: E14.0TAM_E14.5_60


title: E14.0TAM_E14.5_62


title: E14.0TAM_E14.5_59


title: E14.0TAM_E14.5_58


title: E13.5TAM_E16.5_73


title: E14.0TAM_E14.5_56


title: E14.0TAM_E14.5_57


title: E14.0TAM_E14.5_55


title: E14.0TAM_E14.5_54


title: E14.0TAM_E14.5_52


title: E14.0TAM_E14.5_49


title: E14.0TAM_E14.5_50


title: E14.0TAM_E14.5_48


title: E13.5TAM_E16.5_62

description:
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E13.5, with analysis conducted on E16.5 embryos


title: E13.5TAM_E16.5_58


title: E14.0TAM_E14.5_64


title: E14.0TAM_E14.5_53


title: E13.5TAM_E16.5_57


title: E13.5TAM_E16.5_55


title: E13.5TAM_E16.5_60


title: E13.5TAM_E16.5_63


title: E13.5TAM_E16.5_61


title: E14.0TAM_E14.5_47


title: E13.5TAM_E16.5_54


title: E13.5TAM_E16.5_53


title: E13.5TAM_E16.5_52


title: E13.5TAM_E16.5_51


title: E13.5TAM_E16.5_49


title: E13.5TAM_E16.5_48


title: E13.5TAM_E16.5_59


title: E13.5TAM_E16.5_50


title: E13.5TAM_E16.5_47


title: E13.5TAM_E16.5_44


title: E13.5TAM_E16.5_46


title: E13.5TAM_E16.5_45


title: E14.0TAM_E14.5_51


title: E13.5TAM_E16.5_42


title: E13.5TAM_E16.5_43


title: E13.5TAM_E16.5_41


title: E13.5TAM_E16.5_40


title: E13.5TAM_E16.5_56


title: E13.5TAM_E16.5_38


title: E13.5TAM_E16.5_37


title: E13.5TAM_E16.5_35


title: E13.5TAM_E16.5_36


title: P1_P1_GcgPpy_Bihormonal_279

source_name: pancreatic P1 GcgPpy bihormonal cell, scRNAseq

value: GcgGFP;PpymNeptune


title: P1_P1_GcgPpy_Bihormonal_284


title: P1_P1_GcgPpy_Bihormonal_280


title: P1_P1_GcgPpy_Bihormonal_283


title: P1_P1_GcgPpy_Bihormonal_278


title: E13.5TAM_E16.5_34


title: P1_P1_GcgPpy_Bihormonal_277


title: P1_P1_GcgPpy_Bihormonal_281


title: P1_P1_GcgPpy_Bihormonal_282


title: P1_P1_GcgPpy_Bihormonal_275


title: P1_P1_GcgPpy_Bihormonal_272


title: P1_P1_GcgPpy_Bihormonal_273


title: P1_P1_GcgPpy_Bihormonal_276


title: P1_P1_GcgPpy_Bihormonal_274


title: P1_P1_GcgPpy_Bihormonal_269


title: P1_P1_GcgPpy_Bihormonal_270


title: P1_P1_GcgPpy_Bihormonal_268


title: P1_P1_GcgPpy_Bihormonal_266


title: P1_P1_GcgPpy_Bihormonal_263


title: P1_P1_GcgPpy_Bihormonal_262


title: P1_P1_GcgPpy_Bihormonal_264


title: E13.5TAM_E16.5_39


title: P1_P1_GcgPpy_Bihormonal_265


title: P1_P1_GcgPpy_Bihormonal_259


title: P1_P1_GcgPpy_Bihormonal_257


title: P1_P1_GcgPpy_Bihormonal_258


title: P1_P1_GcgPpy_Bihormonal_253


title: P1_P1_GcgPpy_Bihormonal_246


title: P1_P1_GcgPpy_Bihormonal_255


title: P1_P1_GcgPpy_Bihormonal_245


title: P1_P1_GcgPpy_Bihormonal_244


title: P1_P1_GcgPpy_Bihormonal_261


title: P1_P1_GcgPpy_Bihormonal_243


title: P1_P1_GcgPpy_Bihormonal_241


title: P1_P1_GcgPpy_Bihormonal_260


title: P1_P1_GcgPpy_Bihormonal_271


title: P1_P1_GcgPpy_Bihormonal_256


title: P1_P1_GcgPpy_Bihormonal_252


title: P1_P1_GcgPpy_Bihormonal_254


title: P1_P1_GcgPpy_Bihormonal_250


title: P1_P1_GcgPpy_Bihormonal_251


title: P1_P1_GcgPpy_Bihormonal_248


title: P1_P1_GcgPpy_Bihormonal_247


title: P1_P1_GcgPpy_Bihormonal_234


title: P1_P1_GcgPpy_Bihormonal_233


title: P1_P1_GcgPpy_Bihormonal_242


title: P1_P1_GcgPpy_Bihormonal_267


title: P1_P1_GcgPpy_Bihormonal_232


title: P1_P1_GcgPpy_Bihormonal_230


title: P1_P1_GcgPpy_Bihormonal_231


title: P1_P1_GcgPpy_Bihormonal_240


title: P1_P1_GcgPpy_Bihormonal_227


title: P1_P1_GcgPpy_Bihormonal_238


title: P1_P1_GcgPpy_Bihormonal_237


title: P1_P1_GcgPpy_Bihormonal_249


title: P1_P1_GcgPpy_Bihormonal_239


title: P1_P1_GcgPpy_Bihormonal_225


title: P1_P1_GcgPpy_Bihormonal_235


title: P1_P1_GcgPpy_Bihormonal_226


title: P1_P1_GcgPpy_Bihormonal_222


title: P1_P1_GcgPpy_Bihormonal_229


title: P1_P1_GcgPpy_Bihormonal_221


title: P1_P1_GcgPpy_Bihormonal_218


title: P1_P1_GcgPpy_Bihormonal_219


title: P1_P1_GcgPpy_Bihormonal_217


title: P1_P1_GcgPpy_Bihormonal_220


title: P1_P1_GcgPpy_Bihormonal_216


title: P1_P1_GcgPpy_Bihormonal_236


title: P1_P1_GcgPpy_Bihormonal_215


title: P1_P1_GcgPpy_Bihormonal_214


title: P1_P1_GcgPpy_Bihormonal_213


title: P1_P1_GcgPpy_Bihormonal_211


title: P1_P1_GcgPpy_Bihormonal_228


title: P1_P1_GcgPpy_Bihormonal_212


title: P1_P1_GcgPpy_Bihormonal_210


title: P1_P1_GcgPpy_Bihormonal_208


title: P1_P1_GcgPpy_Bihormonal_224


title: P1_P1_GcgPpy_Bihormonal_207


title: P1_P1_GcgPpy_Bihormonal_206


title: P1_P1_GcgPpy_Bihormonal_204


title: P1_P1_GcgPpy_Bihormonal_201


title: P1_P1_GcgPpy_Bihormonal_223


title: P1_P1_GcgPpy_Bihormonal_200


title: P1_P1_GcgPpy_Bihormonal_199


title: P1_P1_GcgPpy_Bihormonal_203


title: P1_P1_GcgPpy_Bihormonal_197


title: P1_P1_GcgPpy_Bihormonal_202


title: P1_P1_GcgPpy_Bihormonal_195


title: P1_P1_GcgPpy_Bihormonal_193


title: P1_P1_GcgPpy_Bihormonal_194


title: P1_P1_GcgPpy_Bihormonal_192


title: P1_P1_GcgPpy_Bihormonal_191


title: P1_P1_GcgPpy_Bihormonal_190


title: P1_P1_GcgPpy_Bihormonal_198


title: P1_P1_GcgPpy_Bihormonal_188


title: P1_P1_GcgPpy_Bihormonal_189


title: P1_P1_GcgPpy_Bihormonal_187


title: P1_P1_GcgPpy_Bihormonal_209


title: P1_P1_GcgPpy_Bihormonal_186


title: P1_P1_GcgPpy_Bihormonal_184


title: P1_P1_GcgPpy_Bihormonal_205


title: P1_P1_GcgPpy_Bihormonal_183


title: P1_P1_GcgPpy_Bihormonal_181


title: P1_P1_GcgPpy_Bihormonal_182


title: P1_P1_GcgPpy_Bihormonal_180


title: P1_P1_GcgPpy_Bihormonal_179


title: P1_P1_GcgPpy_Bihormonal_177


title: P1_P1_GcgPpy_Bihormonal_178


title: P1_P1_GcgPpy_Bihormonal_175


title: P1_P1_GcgPpy_Bihormonal_176


title: P1_P1_GcgPpy_Bihormonal_174


title: P1_P1_GcgPpy_Bihormonal_173


title: P1_P1_GcgPpy_Bihormonal_196


title: P1_P1_GcgPpy_Bihormonal_172


title: P1_P1_GcgPpy_Bihormonal_171


title: P1_P1_GcgPpy_Bihormonal_169


title: P1_P1_GcgPpy_Bihormonal_170


title: P1_P1_GcgPpy_Bihormonal_168


title: P1_P1_GcgPpy_Bihormonal_163


title: P1_P1_GcgPpy_Bihormonal_166


title: P1_P1_GcgPpy_Bihormonal_165


title: P1_P1_GcgPpy_Bihormonal_185


title: P1_P1_GcgPpy_Bihormonal_159


title: P1_P1_GcgPpy_Bihormonal_162


title: P1_P1_GcgPpy_Bihormonal_160


title: P1_P1_GcgPpy_Bihormonal_161


title: P1_P1_GcgPpy_Bihormonal_158


title: P1_P1_GcgPpy_Bihormonal_157


title: P1_P1_GcgPpy_Bihormonal_156


title: P1_P1_GcgPpy_Bihormonal_153


title: P1_P1_GcgPpy_Bihormonal_154


title: P1_P1_GcgPpy_Bihormonal_152


title: P1_P1_GcgPpy_Bihormonal_151


title: P1_P1_GcgPpy_Bihormonal_155


title: P1_P1_GcgPpy_Bihormonal_149


title: P1_P1_GcgPpy_Bihormonal_148


title: P1_P1_GcgPpy_Bihormonal_146


title: P1_P1_GcgPpy_Bihormonal_145


title: P1_P1_GcgPpy_Bihormonal_144


title: P1_P1_GcgPpy_Bihormonal_147


title: P1_P1_GcgPpy_Bihormonal_143


title: P1_P1_GcgPpy_Bihormonal_167


title: P1_P1_GcgPpy_Bihormonal_142


title: P1_P1_GcgPpy_Bihormonal_164


title: P1_P1_GcgPpy_Bihormonal_141


title: P1_P1_GcgPpy_Bihormonal_139


title: P1_P1_GcgPpy_Bihormonal_140


title: P1_P1_GcgPpy_Bihormonal_138


title: P1_P1_GcgPpy_Bihormonal_135


title: P1_P1_GcgPpy_Bihormonal_136


title: P1_P1_GcgPpy_Bihormonal_133


title: P1_P1_GcgPpy_Bihormonal_134


title: P1_P1_GcgPpy_Bihormonal_131


title: P1_P1_GcgPpy_Bihormonal_129


title: P1_P1_GcgPpy_Bihormonal_150


title: P1_P1_GcgPpy_Bihormonal_126


title: P1_P1_GcgPpy_Bihormonal_127


title: P1_P1_GcgPpy_Bihormonal_123


title: P1_P1_GcgPpy_Bihormonal_122


title: P1_P1_GcgPpy_Bihormonal_120


title: P1_P1_GcgPpy_Bihormonal_124


title: P1_P1_GcgPpy_Bihormonal_121


title: P1_P1_GcgPpy_Bihormonal_119


title: P1_P1_GcgPpy_Bihormonal_137


title: P1_P1_GcgPpy_Bihormonal_125


title: P1_P1_GcgPpy_Bihormonal_132


title: P1_P1_GcgPpy_Bihormonal_118


title: P1_P1_GcgPpy_Bihormonal_128


title: P1_P1_GcgPpy_Bihormonal_117


title: P1_P1_GcgPpy_Bihormonal_115


title: P1_P1_GcgPpy_Bihormonal_114


title: P1_P1_GcgPpy_Bihormonal_113


title: P1_P1_GcgPpy_Bihormonal_112


title: P1_P1_GcgPpy_Bihormonal_130


title: P1_P1_GcgPpy_Bihormonal_111


title: P1_P1_GcgPpy_Bihormonal_110


title: P1_P1_GcgPpy_Bihormonal_108


title: P1_P1_GcgPpy_Bihormonal_109


title: P1_P1_GcgPpy_Bihormonal_107


title: P1_P1_GcgPpy_Bihormonal_103


title: P1_P1_GcgPpy_Bihormonal_105


title: P1_P1_GcgPpy_Bihormonal_104


title: P1_P1_GcgPpy_Bihormonal_102


title: P1_P1_GcgPpy_Bihormonal_95


title: P1_P1_GcgPpy_Bihormonal_98


title: P1_P1_GcgPpy_Bihormonal_97


title: P1_P1_GcgPpy_Bihormonal_96


title: P1_P1_GcgPpy_Bihormonal_94


title: P1_P1_GcgPpy_Bihormonal_99


title: P1_P1_GcgPpy_Bihormonal_93


title: P1_P1_GcgPpy_Bihormonal_100


title: P1_P1_GcgPpy_Bihormonal_116


title: P1_P1_GcgPpy_Bihormonal_90


title: P1_P1_GcgPpy_Bihormonal_88


title: P1_P1_GcgPpy_Bihormonal_92


title: P1_P1_GcgPpy_Bihormonal_89


title: WT leaf, three-years-old, rep3

city: Nanjing

first: Yiping

last: Zou

address: 159 Longpan Road

institute: Nanjing Forestry University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: Subsequent analyses were performed using the high quality. The clean reads, which were filtered from the raw reads, were mapped to a I. latifolia reference genome (https://download.cncb.ac.cn/gwh/Plants/Ilex_latifolia_Lachesis_assembly_changed_GWHBIST00000000/GWHBIST00000000.genome.fasta.gz) using HISAT v2.0.4 software with default parameters.
Supplementary files format and content: Compare files for all samples to the reference genome. The files formats are  .bam. and .bam.bai.

organism: Ilex

source_name: leaf

growth_protocol: he study sampled the green leaf cultivar I. x ‘Nellies R. Stevens’ (WT) and its natural bud mutant cultivar with yellow leaves, ‘Whoa Nellies’ (YT). The plants were three-years-old and grown under the identical environmental conditions at Nanjing Qingzhuguo Landscape Horticulture Ltd. Co., in Nanjing, China (32°13′N, 118°49′E).

extract_protocol:
After collection, the leaves were frozen immediately in liquid nitrogen after collection and stored at −80℃ for subsequent experiments. Total RNA was isolated from green leaves of WT and golden leaves of YT using the NEBNext® Ultra™ Plant RNA Extraction Kit (TaKaRa, Dalian, China). Three biological replicates were analyzed for each RNA sample.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq 6000 platform and 150bp paired-end.

treatment_protocol: In November 2022, leaves were collected with three biological replicates.

value: leaf

tag: line

value: Ilex x Nellie R. Stevens

value: wild type (WT)


title: P1_P1_GcgPpy_Bihormonal_87

tag: tissue


title: WT leaf, three-years-old, rep2

value: grown under the identical environmental conditions


title: YT leaf, three-years-old, rep3

value: Ilex x Whoa Nellie

value: yellow leaf mutant (YT)


title: P1_P1_GcgPpy_Bihormonal_85


title: P1_P1_GcgPpy_Bihormonal_106


title: P1_P1_GcgPpy_Bihormonal_86


title: P1_P1_GcgPpy_Bihormonal_83


title: P1_P1_GcgPpy_Bihormonal_84


title: YT leaf, three-years-old, rep2


title: P1_P1_GcgPpy_Bihormonal_82


title: P1_P1_GcgPpy_Bihormonal_101


title: P1_P1_GcgPpy_Bihormonal_81


title: YT leaf, three-years-old, rep1


title: P1_P1_GcgPpy_Bihormonal_91


title: H9_P3_82_DTX

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

data_processing:
Illumina CASAVA version 1.8 were used to do the basecalling.
Reads were trimmed to remove the adapter sequences and low quality bases. For single cell RNA-seq, the cleaned reads were aligned to the human hg19 reference using Tophat (v2.0.12) with default settings and the --no-novel-juncs argument (Trapnell et al., 2009).
PCR duplicates were removed using samtools (v1.3.1)(Li et al., 2009), gene counts were computed using HTseq (v0.6.1) (Anders et al., 2015)
Assembly: hg19
Supplementary files format and content: scRNAseq.counts.csv  file gives the read counts described above for each sample (columns) and gene (rows).

source_name: cell line

growth_protocol: CTC cultures were grown in suspension in ultra-low attachment plates (Corning) in tumor sphere medium - RPMI-1640, EGF (20 ng/ml), bFGF (20 ng/ml), 1X B27, 1X antibiotic/antimycotic (Life Technologies) under hypoxic (4% O2) conditions. CTC lines were routinely checked for mycoplasma, using a mycoplasma detection kit (MycoAlert, Lonza).

extract_protocol:
Prior to extraction, live cells (determined by live/dead dye) were flow sorted into 96 wells with lysis buffer using the Smart-Seq2 protocol (Illumina).
96-well plates containing cell lysates were thawed on ice, spun down at 1500 rpm for 30s, and mixed with Agencourt RNAClean XP SPRI beads (Beckman Coulter) for RNA purification. Purified RNA was resuspended in 4μl of Mix-1, denatured at 72°C for 3 min and transferred to ice for 1 min before 7μl of Mix-2 was added. Reverse transcription was carried out at 50°C for 90 min, followed by 5 minincubation at 85°C. 14μl of Mix-3 was added in each well and the whole-transcriptome amplification step was performed at 98°C for 3 min, followed by 21 cycles at (98°C for 15 s, 67°C for 20 s and 72°C for 6 min), and final extension at 72°C for 5min. cDNAwas then purified with Agencourt AMPureXP SPRI beads (Beckman Coulter), to remove all primer dimer residues. cDNA concentration measurements were performed using the Qubit dsDNA high sensitivity assay kit on the Synergy H1 Hybrid Microplate Reader (BioTek). Libraries were generated using the Nextera XT Library Prep kit (Illumina) with custom indexing adapters64in a 384-well PCR plate, followed by a cleanup step to remove residual primer dimers. Combined libraries from different cells were then sequenced on a NextSeq 500 sequencer (Illumina), using paired-end 38-base reads.

treatment_protocol: Cutures were treated with Docetaxel 10nM for 4 days.

value: cell line

value: derived from CTCs

value: Docetaxel

tag: persistor

value: proficient


title: H8_P3_82_DTX


title: P1_P1_GcgPpy_Bihormonal_80

value: pancreas

value: islet cell


title: H7_P3_82_DTX


title: H4_P3_82_DTX


title: P1_P1_GcgPpy_Bihormonal_77

value: Male


title: H5_P3_82_DTX


title: P1_P1_GcgPpy_Bihormonal_79


title: P1_P1_GcgPpy_Bihormonal_76


title: H2_P3_82_DTX


title: H11_P3_82_DTX


title: P1_P1_GcgPpy_Bihormonal_75


title: P1_P1_GcgPpy_Bihormonal_74


title: H10_P3_82_DTX


title: WT leaf, three-years-old, rep1


title: P1_P1_GcgPpy_Bihormonal_73


title: H3_P3_82_DTX


title: G7_P3_82_DTX


title: P1_P1_GcgPpy_Bihormonal_71


title: P1_P1_GcgPpy_Bihormonal_70


title: G4_P3_82_DTX


title: P1_P1_GcgPpy_Bihormonal_69


title: G1_P3_82_DTX


title: P1_P1_GcgPpy_Bihormonal_68


title: P1_P1_GcgPpy_Bihormonal_78


title: G12_P3_82_DTX


title: G11_P3_82_DTX


title: P1_P1_GcgPpy_Bihormonal_65


title: P1_P1_GcgPpy_Bihormonal_67


title: P1_P1_GcgPpy_Bihormonal_66


title: F9_P3_82_DTX


title: F8_P3_82_DTX


title: F7_P3_82_DTX


title: P1_P1_GcgPpy_Bihormonal_64


title: F5_P3_82_DTX


title: P1_P1_GcgPpy_Bihormonal_61


title: F6_P3_82_DTX


title: P1_P1_GcgPpy_Bihormonal_62


title: P1_P1_GcgPpy_Bihormonal_63


title: P1_P1_GcgPpy_Bihormonal_72


title: P1_P1_GcgPpy_Bihormonal_60


title: F3_P3_82_DTX


title: F4_P3_82_DTX


title: F2_P3_82_DTX


title: P1_P1_GcgPpy_Bihormonal_58


title: P1_P1_GcgPpy_Bihormonal_59


title: F1_P3_82_DTX


title: G3_P3_82_DTX


title: F11_P3_82_DTX


title: G2_P3_82_DTX


title: P60_GcgPpy_Bihormonal_170

source_name: pancreatic P60 GcgPpy bihormonal cell, scRNAseq


title: F10_P3_82_DTX


title: P1_P1_GcgPpy_Bihormonal_57


title: P60_GcgPpy_Bihormonal_169


title: E9_P3_82_DTX


title: P60_GcgPpy_Bihormonal_168


title: P60_GcgPpy_Bihormonal_167


title: E7_P3_82_DTX


title: P60_GcgPpy_Bihormonal_166


title: E4_P3_82_DTX


title: E6_P3_82_DTX


title: P60_GcgPpy_Bihormonal_164


title: E3_P3_82_DTX


title: P60_GcgPpy_Bihormonal_163


title: E2_P3_82_DTX


title: P60_GcgPpy_Bihormonal_162


title: E12_P3_82_DTX


title: P60_GcgPpy_Bihormonal_161


title: E10_P3_82_DTX


title: P60_GcgPpy_Bihormonal_160


title: P60_GcgPpy_Bihormonal_159


title: D9_P3_82_NT

value: Control


title: P60_GcgPpy_Bihormonal_158


title: D8_P3_82_NT


title: P60_GcgPpy_Bihormonal_157


title: D7_P3_82_NT


title: P60_GcgPpy_Bihormonal_156


title: D6_P3_82_NT


title: D5_P3_82_NT


title: P60_GcgPpy_Bihormonal_155


title: P60_GcgPpy_Bihormonal_154


title: D4_P3_82_NT


title: E5_P3_82_DTX


title: P60_GcgPpy_Bihormonal_165


title: P60_GcgPpy_Bihormonal_152


title: P60_GcgPpy_Bihormonal_153


title: D2_P3_82_NT


title: P60_GcgPpy_Bihormonal_151


title: E1_P3_82_DTX


title: D1_P3_82_NT


title: D12_P3_82_NT


title: P60_GcgPpy_Bihormonal_150


title: D11_P3_82_NT


title: P60_GcgPpy_Bihormonal_149


title: D10_P3_82_NT


title: C9_P3_82_NT


title: P60_GcgPpy_Bihormonal_146


title: C8_P3_82_NT


title: P60_GcgPpy_Bihormonal_145


title: C7_P3_82_NT


title: P60_GcgPpy_Bihormonal_147


title: C6_P3_82_NT


title: P60_GcgPpy_Bihormonal_144


title: P60_GcgPpy_Bihormonal_143


title: P60_GcgPpy_Bihormonal_142


title: C5_P3_82_NT


title: P60_GcgPpy_Bihormonal_141


title: C4_P3_82_NT


title: C3_P3_82_NT


title: D3_P3_82_NT


title: P60_GcgPpy_Bihormonal_140


title: P60_GcgPpy_Bihormonal_139


title: C12_P3_82_NT


title: P60_GcgPpy_Bihormonal_138


title: C2_P3_82_NT


title: P60_GcgPpy_Bihormonal_148


title: C1_P3_82_NT


title: C11_P3_82_NT


title: P60_GcgPpy_Bihormonal_134


title: B9_P3_82_NT


title: P60_GcgPpy_Bihormonal_136


title: P60_GcgPpy_Bihormonal_133


title: B6_P3_82_NT


title: B7_P3_82_NT


title: P60_GcgPpy_Bihormonal_130


title: C10_P3_82_NT


title: P60_GcgPpy_Bihormonal_131


title: P60_GcgPpy_Bihormonal_135


title: B5_P3_82_NT


title: B3_P3_82_NT


title: P60_GcgPpy_Bihormonal_129


title: P60_GcgPpy_Bihormonal_128


title: P60_GcgPpy_Bihormonal_132


title: B2_P3_82_NT


title: P60_GcgPpy_Bihormonal_127


title: B1_P3_82_NT


title: P60_GcgPpy_Bihormonal_126


title: B12_P3_82_NT


title: P60_GcgPpy_Bihormonal_137


title: P60_GcgPpy_Bihormonal_125


title: B11_P3_82_NT


title: B10_P3_82_NT


title: P60_GcgPpy_Bihormonal_124


title: P60_GcgPpy_Bihormonal_123


title: B8_P3_82_NT


title: P60_GcgPpy_Bihormonal_122


title: A9_P3_82_NT


title: A8_P3_82_NT


title: P60_GcgPpy_Bihormonal_121


title: P60_GcgPpy_Bihormonal_120


title: B4_P3_82_NT


title: A7_P3_82_NT


title: P60_GcgPpy_Bihormonal_119


title: A5_P3_82_NT


title: A4_P3_82_NT


title: P60_GcgPpy_Bihormonal_118


title: A2_P3_82_NT


title: A1_P3_82_NT


title: A12_P3_82_NT


title: A3_P3_82_NT


title: P1_PP_6

source_name: pancreatic P1 α cell, scRNAseq

extract_protocol:
For the isolation of adult mouse islets, firstly, euthanize mice and expose abdominal organs. Next, clamp the duodenum at the upper and lower position where the common bile duct enters the duodenum. Then, inject pre-cold 1 mg/ml collagenase P into the common bile duct to inflate whole pancreas. Digest pancreas in 37℃ water bath for 6-8 min with gently shaking, and then manually pick out islets using microscope. These islets were digested into single-cell suspension with 0.25% trypsin for 5 min at 37℃. For the digestion of embryonic mouse pancreas, firstly, E14.5-18.5 pancreas were dissected and digested with 1 mg/ml collagenase P for 3-5 min which varies depending on pancreas size. Then, dissociated pancreas were treated with 0.25% trypsin for 5 min at 37℃. Cell suspension obtained after digestion can be directly sorted using the endogenous fluorescent protein carried by the cells and BD FACSAria Fusion flow cytometer.
For smart-seq3xpress, single cells were collected according to two strategies: one was to sort single cells into 384-well plates containing lysis buffer, and the other was to pick single cells manually from FACS-purified bulk cells by using a mouth pipette.
smart-seq3xpress scRNA-seq

value: PpymNeptune


title: A10_P3_82_NT


title: A11_P3_82_NT


title: P1_PP_7


title: P1_PP_9


title: P1_PP_8


title: P1_PP_43


title: P1_PP_5


title: P1_PP_42


title: P1_PP_41


title: NS134-BRX394-Docetaxel-7

value: deficient


title: P1_PP_40


title: A6_P3_82_NT


title: NS134-BRX394-Docetaxel-5


title: P1_PP_39


title: P60_GcgPpy_Bihormonal_117

value: GcgGFP;PpymNeptune


title: P1_PP_38


title: NS134-BRX394-Docetaxel-4


title: NS134-BRX394-Docetaxel-3


title: P1_PP_37


title: NS134-BRX394-Docetaxel-2


title: P1_PP_36


title: NS134-BRX394-Docetaxel-26


title: P1_PP_35


title: P1_PP_34


title: NS134-BRX394-Docetaxel-25


title: NS134-BRX394-Docetaxel-24


title: NS134-BRX394-Docetaxel-9


title: P1_PP_33


title: NS134-BRX394-Docetaxel-23


title: P1_PP_31


title: P1_PP_30


title: P1_PP_32


title: NS134-BRX394-Docetaxel-6


title: NS134-BRX394-Docetaxel-21


title: P1_PP_3


title: NS134-BRX394-Docetaxel-20


title: NS134-BRX394-Docetaxel-8


title: NS134-BRX394-Docetaxel-19


title: P1_PP_4


title: NS134-BRX394-Docetaxel-1


title: NS134-BRX394-Docetaxel-18


title: P1_PP_27


title: P1_PP_29


title: NS134-BRX394-Docetaxel-17


title: P1_PP_26


title: NS134-BRX394-Docetaxel-16


title: P1_PP_25


title: NS134-BRX394-Docetaxel-15


title: NS134-BRX394-Docetaxel-14


title: P1_PP_23


title: NS134-BRX394-Docetaxel-13


title: NS134-BRX394-Docetaxel-22


title: P1_PP_21


title: NS134-BRX394-Docetaxel-12


title: NS134-BRX394-Docetaxel-11


title: P1_PP_20


title: P1_PP_2


title: NS134-BRX394-Docetaxel-10


title: P1_PP_19


title: P1_PP_18


title: NS134-BRX394-Control-7


title: P1_PP_28


title: NS134-BRX394-Control-8


title: NS134-BRX394-Control-9


title: P1_PP_17


title: NS134-BRX394-Control-6


title: P1_PP_16


title: NS134-BRX394-Control-5


title: NS134-BRX394-Control-4


title: P1_PP_14


title: P1_PP_13


title: NS134-BRX394-Control-3


title: NS134-BRX394-Control-2


title: P1_PP_24


title: P1_PP_22


title: P1_PP_12


title: NS134-BRX394-Control-18


title: P1_PP_10


title: NS134-BRX394-Control-17


title: P1_PP_11


title: P1_PP_1


title: P1_GcgPpy_Bihormonal_9


title: P1_GcgPpy_Bihormonal_8


title: NS134-BRX394-Control-15


title: NS134-BRX394-Control-14


title: NS134-BRX394-Control-12


title: P1_GcgPpy_Bihormonal_6


title: P1_GcgPpy_Bihormonal_7


title: NS134-BRX394-Control-13


title: NS134-BRX394-Control-11


title: P1_GcgPpy_Bihormonal_55


title: P1_PP_15


title: P1_GcgPpy_Bihormonal_56


title: NS134-BRX394-Control-10


title: P1_GcgPpy_Bihormonal_54


title: H9_P1_29_DTX


title: P1_GcgPpy_Bihormonal_53


title: NS134-BRX394-Control-1


title: P1_GcgPpy_Bihormonal_52


title: P1_GcgPpy_Bihormonal_51


title: H6_P1_29_DTX


title: H7_P1_29_DTX


title: H8_P1_29_DTX


title: H5_P1_29_DTX


title: P1_GcgPpy_Bihormonal_50


title: P1_GcgPpy_Bihormonal_5


title: H4_P1_29_DTX


title: NS134-BRX394-Control-16


title: P1_GcgPpy_Bihormonal_49


title: H3_P1_29_DTX


title: P1_GcgPpy_Bihormonal_48


title: P1_GcgPpy_Bihormonal_46


title: H1_P1_29_DTX


title: H12_P1_29_DTX


title: H10_P1_29_DTX


title: P1_GcgPpy_Bihormonal_45


title: H2_P1_29_DTX


title: P1_GcgPpy_Bihormonal_44


title: P1_GcgPpy_Bihormonal_42


title: P1_GcgPpy_Bihormonal_47