title: Product

first: Duc

middle: Trung

last: Nguyen

address: Clear Water Bay

department: Life Science

institute: The Hong Kong University of Science and Technology

data_processing:
The sequencing samples were processed as described previously (Nguyen et al., 2022). Initially, we utilized cutadapt to excise the adapters from both ends of the raw reads (-a TGGAATTCTC GGGTGCCAAGG -A GATCGTCGGACTGTAGAACTCTGAAC -m 10). Subsequently, fastq-join was employed to concatenate the paired-end reads (Aronesty, 2013). We then eliminated low-quality reads using fastq_quality_filter (-q 20 -p 90) and removed duplicate reads, which contain identical 4 nt or 6 nt randomized barcodes at both ends, using fastx_collapser (default parameters) (FASTX-Toolkit, version 0.0.13). Following this, the original substrate and cleaved product samples were processed separately. For the original substrate reads, the randomized barcodes at both ends (4 nt at the 5' end and 6 nt at the 3' end) were first trimmed using cutadapt (cutadapt -u 6 -u -4) (Martin, 2011). Each trimmed read contained a full-length shRNA sequence (FL), a 6-bp constant sequence (5'-GCTTGC...5'-GCAAGC), and a 32-nt barcode (32N). The constant sequence was utilized to demarcate FL and 32N (cutadapt -g GCTTGC...GCAAGC -m 32 -M 32 --discard-untrimmed) (Martin, 2011). To determine which variant each 32N in the FL-32N pair belonged to, we aligned FL reads to a 46,336-variant reference using BWA (Li and Durbin, 2010) and selected perfectly aligned sequences. The FL-32N pair was then converted into a variant-32N pair. Among all variant-32N pairs, any pairs sharing the same 32N sequence but differing in variants were discarded to create a “variant-32N dictionary.” The raw count of a variant was the total of read counts of the variant in this dictionary. Only variants with more than 30 raw counts were selected for further analysis. For the cleaved product reads, the 4-nt randomized barcodes at both ends were trimmed using cutadapt (cutadapt -u 4 -u -4). Each trimmed read contained a cleaved product (CP), the 6-bp constant sequence, and 32N. These reads were also split into CP and 32N to generate CP-32N pairs. We aligned 32N in CP-32N pairs with the “variant-32N dictionary” obtained earlier to assign each CP to its respective variant. The pairwise2 library (local alignment mode) was used to map each CP to its assigned variant and determine cleavage sites of a CP. The cleavage site of a CP was designated as (x, y), where x and y are the numbers of nucleotides from the cleavage sites to the variant ends on the 5p and 3p strands, respectively. If a bulge exists within the window, it is excluded from counting. Each shRNA variant without 32N was 72 nt long. The cleavage site (x, y) was classified into 1-nt, 2-nt, and 3-nt overhangs as follows: 1-nt overhang at x if 19 ≤ x ≤ 23 and y = 71 – x; 2-nt overhang at x if 19 ≤ x ≤ 23 and y = 72 – x; and 3-nt overhang at x if 19 ≤ x ≤ 23 and y = 73 – x.
Assembly: shRNA construct sequences
Supplementary files format and content: reference_sequences.txt: Tab-delimited text file contains the reference sequences of all variants
Supplementary files format and content: control_count.txt: Tab-delimited text file contains the barcode and read counts of control samples
Supplementary files format and content: product_count.txt: Tab-delimited text file contains the raw counts of cleaved products for each variant
Library strategy: cleavage assay

organism: synthetic construct

source_name: Product

extract_protocol:
Illumina adapter sequences were incorporated to the libraries using PCR.
Firstly, we ligated 4N-RA3 adapter to the RNA - the original substrates (OS), double cleavage (DC) using T4 RNA Ligase 2, truncated KQ enzyme (NEB, M0373L). The ligated RNA products were purified from unligated RNA and free adapter by gel extraction. From this step, we used different cloning schemes for the original substrates (OS), double cleavage (DC) library preparation. For the original substrates (OS), we use cirRTP primer and Superscript IV Reverse Transcriptase (Invitrogen) for reverse transcription reactions to obtain the linear cDNA and the remaining RNA is degraded by 100mM NaOH. After gel purification, the cDNA was circularized by CircLigase ssDNA Ligase. The circular cDNA was separated from linear cDNA by using 18% urea-PAGE gel. After gel extraction, we obtained the OS library by PCR using RP1 and RPIx primers. For the double cleavage (DC), the ligated DC fragments were ligated to 4N-RA5 using T4 RNA Ligase 1 (NEB). We used Superscript IV Reverse Transcriptase and the R-RA3 primer to do RT reaction with these ligated RNA products. The resultant cDNAs were amplified using the RP1 and RPIx primers. The DNA quality was confirmed by Qubit™ dsDNA HS Assay Kit and Fragment Analyzer system. The DNA library were sequenced by the Illumina NovaSeq 6000 machinery using 150 bp paired-end method.

value: RNA after processing by DCL1


title: H11_P1_29_DTX

status: Public on Jun 14 2025

type: SRA

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

country: USA

institute: Massachusetts General Hospital

library_source: transcriptomic single cell

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).

molecule: polyA RNA

organism: Homo sapiens

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.

tag: tissue

value: cell line

tag: cell line

tag: cell type

value: derived from CTCs

tag: treatment

value: Docetaxel

tag: persistor

value: deficient


title: P1_GcgPpy_Bihormonal_40

city: Beijing

first: Cheng-ran

last: Xu

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

department: School of Basic Medical Sciences

country: China

institute: Peking University

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

molecule: total RNA

organism: Mus musculus

source_name: pancreatic P1 GcgPpy bihormonal 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: pancreas

value: islet cell

tag: strain

tag: genotype

value: GcgGFP;PpymNeptune

tag: Sex

value: Male

tag: age


title: P1_GcgPpy_Bihormonal_41


title: Control

city: Hong Kong

country: Hong Kong

library_source: other

molecule: other

source_name: Control

value: RNA before processing by DCL1


title: P1_GcgPpy_Bihormonal_39


title: G8_P1_29_DTX


title: 18-112-GTS-unstim

city: NEW YORK

first: Hyomin

last: Seo

state: NY

address: 1 Gustave L. Levy Pl

department: Neurosciences

institute: Icahn school of medicine at Mount Sinai

library_source: transcriptomic

data_processing:
The libraries were sequenced as 150 bp on fragments with an average read depth of 28 million (ranging from 0.06-128M) read pairs on the Illumina HiSeq 2500.
RNA-seq data was processed using the RAPiD pipeline. RAPiD aligns samples to the hg38 genome build using STAR using the GENCODE v30 transcriptome reference and calculates quality control metrics using Picard.
Picard. RNA-seq quality control was performed applying four filters to remove samples
Estimated transcript abundance was obtained using RSEM and transcripts were summed to the gene level with tximport.
Genes with more than 1 read count per million (CPM) in 50% of the samples were kept for downstream analysis. Gene level read counts were normalized as transcripts per million mapped reads (TPM) to adjust for sequencing library size differences.
Assembly: Hg 38 build
Supplementary files format and content: Txt file includes raw counts for each Sample
Supplementary files format and content: Txt file includes raw TPM for each Sample
Supplementary files format and content: Txt file includes Metadata associated with each Sample

source_name: Brain

growth_protocol: Post-mortem brain samples were obtained from the Netherlands Brain Bank (NBB). The permission to collect human brain material was obtained from the Ethical Committee of the VU University Medical Center, Amsterdam, The Netherlands. Informed consent for autopsy, the use of brain tissue and accompanied clinical information for research purposes was obtained per donor ante-mortem. Neuropathological assessments have been performed by the NBB.

extract_protocol:
Brain tissue was stored in Hibernate media (Gibco) at 4 °C upon processing within 24 hours after autopsy.
Microglial RNA was isolated using the TRIzol method and cDNA libraries were generated by Genewiz (Azenta) using the Ultra-low input system which uses Poly-A selection. SMART-Seq v4 Ultra Low Input RNA Kit was used for library construction using 100 ng of RNA

treatment_protocol: 100 ng/mL lipopolysaccharide (LPS) from Escherichia coli 0111:B4 (Merck, Germany), or with 50 ng/ml interferon gamma INF-γ (Peprotech, London, UK), Resiquimod (R848), 50 ng/ml tumor necrosis factor alpha (Sigma-Aldrich, The Netherlands), 40 ng/ml IL-4 (Peprotech, London, UK), 1000 nM dexamethasone (Sigma-Aldrich, The Netherlands), or 1 mM ATP (Sigma-Aldrich, The Netherlands) for 6 h.

value: Brain

value: Microglia

value: unstim


title: P1_GcgPpy_Bihormonal_43


title: G7_P1_29_DTX


title: P1_GcgPpy_Bihormonal_4


title: 18-112-GTS-LPS

value: LPS


title: P1_GcgPpy_Bihormonal_37


title: P1_GcgPpy_Bihormonal_38


title: 18-112-GFM-unstim


title: P1_GcgPpy_Bihormonal_36


title: G9_P1_29_DTX


title: P1_GcgPpy_Bihormonal_35


title: 18-112-GFM-LPS


title: P1_GcgPpy_Bihormonal_34


title: P1_GcgPpy_Bihormonal_33


title: G4_P1_29_DTX


title: 18-112-GFM-IFNgamma

value: IFNgamma


title: G3_P1_29_DTX


title: P1_GcgPpy_Bihormonal_31


title: P1_GcgPpy_Bihormonal_30


title: 18-112-GFM-DEX

value: DEX


title: P1_GcgPpy_Bihormonal_3


title: G6_P1_29_DTX


title: G2_P1_29_DTX


title: P1_GcgPpy_Bihormonal_28


title: P1_GcgPpy_Bihormonal_29


title: G1_P1_29_DTX


title: 18-112-GFM-ATP

value: ATP


title: P1_GcgPpy_Bihormonal_25


title: G5_P1_29_DTX


title: P1_GcgPpy_Bihormonal_24


title: 18-105-THA-LPS


title: P1_GcgPpy_Bihormonal_27


title: P1_GcgPpy_Bihormonal_23


title: 18-105-GFM-unstim


title: P1_GcgPpy_Bihormonal_26


title: G11_P1_29_DTX


title: G10_P1_29_DTX


title: P1_GcgPpy_Bihormonal_32


title: 18-105-GFM-LPS


title: P1_GcgPpy_Bihormonal_21


title: P1_GcgPpy_Bihormonal_22


title: P1_GcgPpy_Bihormonal_20


title: F9_P1_29_DTX


title: P1_GcgPpy_Bihormonal_2


title: 18-105-GFM-DEX


title: F8_P1_29_DTX


title: P1_GcgPpy_Bihormonal_19


title: G12_P1_29_DTX


title: 18-105-THA-unstim


title: P1_GcgPpy_Bihormonal_17


title: F6_P1_29_DTX


title: 18-079-SVZ-R848


title: F7_P1_29_DTX


title: P1_GcgPpy_Bihormonal_16


title: 18-079-SVZ-LPS


title: P1_GcgPpy_Bihormonal_14


title: P1_GcgPpy_Bihormonal_13


title: P1_GcgPpy_Bihormonal_15


title: P1_GcgPpy_Bihormonal_12


title: 18-079-SVZ-IFNgamma


title: F4_P1_29_DTX


title: P1_GcgPpy_Bihormonal_10


title: 18-079-GFM-unstim


title: 18-074-SVZ-unstim


title: P1_GcgPpy_Bihormonal_1


title: P1_alpha_8

source_name: pancreatic P1 α cell, scRNAseq

value: GcgGFP


title: 18-074-SVZ-R848


title: F2_P1_29_DTX

value: cell line


title: P1_alpha_7


title: F1_P1_29_DTX

value: derived from CTCs


title: 18-074-SVZ-LPS


title: P1_alpha_61


title: P1_GcgPpy_Bihormonal_18


title: F12_P1_29_DTX

value: Docetaxel


title: P1_alpha_60


title: P1_alpha_6


title: F5_P1_29_DTX

value: deficient


title: F11_P1_29_DTX


title: P1_GcgPpy_Bihormonal_11

value: pancreas


title: P1_alpha_57

value: islet cell


title: 18-074-GTS-LPS


title: 18-074-GTS-unstim


title: P1_alpha_58


title: P1_alpha_59


title: E9_P1_29_DTX


title: P1_alpha_55


title: P1_alpha_56


title: 18-074-SVZ-IFNgamma


title: F10_P1_29_DTX


title: E8_P1_29_DTX


title: 18-064-THA-unstim


title: P1_alpha_53


title: P1_alpha_54


title: P1_alpha_9


title: P1_alpha_52


title: 18-064-THA-LPS


title: P1_alpha_51


title: E7_P1_29_DTX


title: P1_alpha_50


title: 18-064-GTS-LPS


title: E6_P1_29_DTX


title: P1_alpha_49


title: E5_P1_29_DTX


title: 18-064-GFM-LPS


title: E4_P1_29_DTX


title: P1_alpha_46


title: P1_alpha_45


title: 18-064-GFM-IL4


title: P1_alpha_48


title: P1_alpha_47


title: 18-064-GFM-DEX


title: P1_alpha_43


title: P1_alpha_44


title: E3_P1_29_DTX


title: P1_alpha_42


title: E2_P1_29_DTX


title: 18-039-SVZ-R848


title: P1_alpha_41


title: E1_P1_29_DTX


title: P1_alpha_4


title: P1_alpha_40


title: P1_alpha_38


title: 18-021-THA-unstim


title: 18-064-GTS-unstim


title: P1_alpha_39


title: P1_alpha_5


title: E11_P1_29_DTX


title: P1_alpha_37


title: P1_alpha_36


title: E10_P1_29_DTX


title: P1_alpha_35


title: P1_alpha_34


title: 18-021-GFM-unstim


title: P1_alpha_32


title: P1_alpha_33


title: D9_P1_29_NT

value: Control


title: 18-0198-GFM-LPS


title: D8_P1_29_NT


title: P1_alpha_31

value: Male


title: 18-018-THA-unstim


title: 18-039-SVZ-IFNgamma


title: P1_alpha_29


title: P1_alpha_3


title: 18-018-SVZ-unstim


title: D6_P1_29_NT


title: P1_alpha_30


title: E12_P1_29_DTX


title: 18-018-SVZ-LPS


title: P1_alpha_25


title: 18-021-GTS-LPS


title: P1_alpha_24


title: P1_alpha_28


title: D5_P1_29_NT


title: P1_alpha_27


title: D7_P1_29_NT


title: 18-018-SVZ-IFNgamma


title: P1_alpha_26


title: D4_P1_29_NT


title: P1_alpha_23


title: D3_P1_29_NT


title: P1_alpha_21


title: 18-018-GFM-IFNgamma


title: D2_P1_29_NT


title: P1_alpha_20


title: D1_P1_29_NT


title: 18-018-GFM-DEX


title: P1_alpha_2


title: P1_alpha_19


title: 18-018-GFM-ATP


title: D12_P1_29_NT


title: P1_alpha_18


title: D11_P1_29_NT


title: P1_alpha_17


title: 18-010-THA-unstim


title: 18-010-THA-LPS


title: P1_alpha_15


title: P1_alpha_12


title: P1_alpha_11


title: 18-010-THA-IFNgamma


title: 18-018-GFM-unstim


title: P1_alpha_14


title: C9_P1_29_NT


title: D10_P1_29_NT


title: P1_alpha_13


title: C8_P1_29_NT


title: P1_alpha_1


title: 18-010-SVZ-unstim


title: P1_alpha_22


title: E14.5_InsGcg_Doublet_9

description:
Smart-seq3xpress
Artificial doublets, crafted by combining an α cell with a β cell

source_name: pancreatic E14.5 InsGcg Doublet, scRNAseq


title: 18-010-SVZ-R848


title: P1_alpha_10


title: C7_P1_29_NT


title: E14.5_InsGcg_Doublet_88


title: 18-010-SVZ-LPS


title: E14.5_InsGcg_Doublet_87


title: C6_P1_29_NT


title: P1_alpha_16


title: 18-010-SVZ-IFNgamma


title: E14.5_InsGcg_Doublet_89


title: E14.5_InsGcg_Doublet_86


title: C4_P1_29_NT


title: E14.5_InsGcg_Doublet_85


title: E14.5_InsGcg_Doublet_84


title: C3_P1_29_NT


title: E14.5_InsGcg_Doublet_83


title: E14.5_InsGcg_Doublet_82


title: E14.5_InsGcg_Doublet_81


title: 18-010-GTS-IFNgamma


title: E14.5_InsGcg_Doublet_80


title: C1_P1_29_NT


title: E14.5_InsGcg_Doublet_8


title: 18-010-GFM-unstim


title: E14.5_InsGcg_Doublet_79


title: C12_P1_29_NT


title: E14.5_InsGcg_Doublet_78


title: 18-010-GFM-LPS


title: C11_P1_29_NT


title: E14.5_InsGcg_Doublet_76


title: 17-148-SVZ-unstim


title: E14.5_InsGcg_Doublet_75


title: C10_P1_29_NT


title: E14.5_InsGcg_Doublet_74


title: 18-010-GTS-unstim


title: 17-148-GTS-LPS


title: E14.5_InsGcg_Doublet_72


title: E14.5_InsGcg_Doublet_73


title: E14.5_InsGcg_Doublet_71


title: 17-148-SVZ-LPS


title: C2_P1_29_NT


title: E14.5_InsGcg_Doublet_70


title: 18-010-GTS-LPS


title: B6_P1_29_NT


title: E14.5_InsGcg_Doublet_7


title: E14.5_InsGcg_Doublet_69


title: 17-136-SVZ-LPS


title: E14.5_InsGcg_Doublet_68


title: B5_P1_29_NT


title: E14.5_InsGcg_Doublet_67


title: E14.5_InsGcg_Doublet_77


title: E14.5_InsGcg_Doublet_66


title: 17-136-GFM-unstim


title: B4_P1_29_NT


title: B9_P1_29_NT


title: E14.5_InsGcg_Doublet_65


title: E14.5_InsGcg_Doublet_63


title: 17-136-GFM-LPS


title: E14.5_InsGcg_Doublet_62


title: B2_P1_29_NT


title: B7_P1_29_NT


title: B3_P1_29_NT


title: E14.5_InsGcg_Doublet_61


title: E14.5_InsGcg_Doublet_60


title: 17-124-THA-unstim


title: E14.5_InsGcg_Doublet_59


title: 17-136-SVZ-unstim


title: E14.5_InsGcg_Doublet_6


title: B1_P1_29_NT


title: E14.5_InsGcg_Doublet_58


title: B12_P1_29_NT


title: 17-124-THA-LPS


title: B10_P1_29_NT


title: 17-124-THA-IFNgamma


title: E14.5_InsGcg_Doublet_55


title: B11_P1_29_NT


title: E14.5_InsGcg_Doublet_57


title: E14.5_InsGcg_Doublet_54


title: 17-124-SVZ-unstim


title: 17-136-GFM-R848


title: E14.5_InsGcg_Doublet_56


title: E14.5_InsGcg_Doublet_53


title: E14.5_InsGcg_Doublet_64


title: E14.5_InsGcg_Doublet_52


title: A9_P1_29_NT


title: 17-124-SVZ-R848


title: 17-136-GFM-IFNgamma


title: 17-124-SVZ-LPS


title: E14.5_InsGcg_Doublet_5


title: E14.5_InsGcg_Doublet_50


title: E14.5_InsGcg_Doublet_49


title: 17-124-SVZ-IFNgamma


title: E14.5_InsGcg_Doublet_48


title: A6_P1_29_NT


title: E14.5_InsGcg_Doublet_47


title: 17-124-GFM-unstim


title: A5_P1_29_NT


title: E14.5_InsGcg_Doublet_46


title: E14.5_InsGcg_Doublet_45


title: E14.5_InsGcg_Doublet_44


title: E14.5_InsGcg_Doublet_43


title: 17-124-GFM-LPS


title: A4_P1_29_NT


title: 17-102-THA-unstim


title: E14.5_InsGcg_Doublet_40


title: E14.5_InsGcg_Doublet_42


title: A2_P1_29_NT


title: A3_P1_29_NT


title: 17-102-THA-LPS


title: E14.5_InsGcg_Doublet_41


title: A8_P1_29_NT


title: A1_P1_29_NT


title: E14.5_InsGcg_Doublet_51


title: E14.5_InsGcg_Doublet_4


title: A7_P1_29_NT


title: E14.5_InsGcg_Doublet_38


title: E14.5_InsGcg_Doublet_39


title: 17-102-SVZ-unstim


title: 17-102-SVZ-R848


title: E14.5_InsGcg_Doublet_36


title: A11_P1_29_NT


title: E14.5_InsGcg_Doublet_37


title: E14.5_InsGcg_Doublet_35


title: A10_P1_29_NT


title: 17-102-SVZ-LPS


title: E14.5_InsGcg_Doublet_34


title: 17-102-SVZ-IFNgamma


title: E14.5_InsGcg_Doublet_33


title: NS134-BRX142-Docetaxel-9

value: proficient


title: E14.5_InsGcg_Doublet_32


title: NS134-BRX142-Docetaxel-8


title: E14.5_InsGcg_Doublet_31


title: 17-102-GTS-unstim

value: Brain


title: NS134-BRX142-Docetaxel-7


title: 17-102-GTS-LPS

value: Microglia


title: E14.5_InsGcg_Doublet_28


title: 17-102-GFM-unstim

value: unstim


title: E14.5_InsGcg_Doublet_3


title: E14.5_InsGcg_Doublet_30


title: E14.5_InsGcg_Doublet_27


title: NS134-BRX142-Docetaxel-5


title: E14.5_InsGcg_Doublet_29


title: 17-102-GFM-LPS

value: LPS


title: NS134-BRX142-Docetaxel-6


title: E14.5_InsGcg_Doublet_24


title: E14.5_InsGcg_Doublet_25


title: E14.5_InsGcg_Doublet_26


title: 17-099-THA-LPS


title: E14.5_InsGcg_Doublet_23


title: E14.5_InsGcg_Doublet_22


title: NS134-BRX142-Docetaxel-3


title: E14.5_InsGcg_Doublet_21


title: 17-099-THA-IFNgamma

value: IFNgamma


title: NS134-BRX142-Docetaxel-2


title: E14.5_InsGcg_Doublet_20


title: E14.5_InsGcg_Doublet_2


title: E14.5_InsGcg_Doublet_19


title: 17-099-SVZ-R848


title: E14.5_InsGcg_Doublet_18


title: E14.5_InsGcg_Doublet_17


title: NS134-BRX142-Docetaxel-18


title: E14.5_InsGcg_Doublet_16


title: 17-099-THA-unstim


title: 17-099-SVZ-LPS


title: NS134-BRX142-Docetaxel-16


title: E14.5_InsGcg_Doublet_14


title: NS134-BRX142-Docetaxel-17


title: E14.5_InsGcg_Doublet_15


title: 17-099-GTS-unstim


title: NS134-BRX142-Docetaxel-4


title: 17-099-GTS-LPS


title: E14.5_InsGcg_Doublet_13


title: E14.5_InsGcg_Doublet_12


title: NS134-BRX142-Docetaxel-15


title: E14.5_InsGcg_Doublet_1


title: E14.5_InsGcg_Doublet_10


title: 17-099-GTS-IFNgamma


title: E14.5_InsGcg_Doublet_11


title: NS134-BRX142-Docetaxel-14


title: E14.5_InsGcg_Bihormonal_9

source_name: pancreatic E14.5 InsGcg bihormonal cell, scRNAseq


title: NS134-BRX142-Docetaxel-1


title: NS134-BRX142-Docetaxel-13


title: E14.5_InsGcg_Bihormonal_7


title: 17-099-SVZ-unstim


title: 17-099-GFM-unstim


title: E14.5_InsGcg_Bihormonal_8


title: 17-099-GFM-R848


title: NS134-BRX142-Docetaxel-12


title: E14.5_InsGcg_Bihormonal_5


title: E14.5_InsGcg_Bihormonal_4


title: NS134-BRX142-Docetaxel-11


title: E14.5_InsGcg_Bihormonal_38


title: 17-099-GFM-IFNgamma


title: NS134-BRX142-Docetaxel-10


title: 17-097-SVZ-unstim


title: 17-099-GFM-LPS


title: E14.5_InsGcg_Bihormonal_37


title: NS134-BRX142-Control-9


title: 17-097-SVZ-R848


title: NS134-BRX142-Control-8


title: E14.5_InsGcg_Bihormonal_36


title: E14.5_InsGcg_Bihormonal_32


title: E14.5_InsGcg_Bihormonal_29


title: 17-097-SVZ-LPS


title: NS134-BRX142-Control-7


title: E14.5_InsGcg_Bihormonal_31


title: 17-097-GTS-unstim


title: E14.5_InsGcg_Bihormonal_33


title: 17-097-SVZ-IFNgamma


title: E14.5_InsGcg_Bihormonal_6


title: NS134-BRX142-Control-6


title: E14.5_InsGcg_Bihormonal_30


title: E14.5_InsGcg_Bihormonal_3


title: E14.5_InsGcg_Bihormonal_28


title: 17-097-GTS-LPS


title: NS134-BRX142-Control-4


title: 17-097-GFM-unstim


title: E14.5_InsGcg_Bihormonal_26


title: E14.5_InsGcg_Bihormonal_27


title: E14.5_InsGcg_Bihormonal_24


title: NS134-BRX142-Control-3


title: E14.5_InsGcg_Bihormonal_34


title: E14.5_InsGcg_Bihormonal_25


title: 17-097-GFM-R848


title: NS134-BRX142-Control-2


title: E14.5_InsGcg_Bihormonal_39


title: E14.5_InsGcg_Bihormonal_35


title: E14.5_InsGcg_Bihormonal_22


title: E14.5_InsGcg_Bihormonal_23


title: 17-097-GFM-LPS


title: NS134-BRX142-Control-5


title: E14.5_InsGcg_Bihormonal_20


title: E14.5_InsGcg_Bihormonal_16


title: E14.5_InsGcg_Bihormonal_19


title: 17-094-THA-unstim


title: 17-097-GFM-IFNgamma


title: E14.5_InsGcg_Bihormonal_18


title: NS134-BRX142-Control-17


title: E14.5_InsGcg_Bihormonal_17


title: E14.5_InsGcg_Bihormonal_21


title: E14.5_InsGcg_Bihormonal_2


title: E14.5_InsGcg_Bihormonal_15


title: 17-094-THA-IFNgamma


title: E14.5_InsGcg_Bihormonal_14


title: 17-094-THA-LPS


title: NS134-BRX142-Control-1


title: E14.5_InsGcg_Bihormonal_13


title: NS134-BRX142-Control-16


title: NS134-BRX142-Control-15


title: E14.5_InsGcg_Bihormonal_12


title: 17-094-SVZ-R848


title: NS134-BRX142-Control-14


title: 17-094-SVZ-unstim


title: NS134-BRX142-Control-13


title: E14.5_InsGcg_Bihormonal_10


title: E14.5_InsGcg_Bihormonal_1


title: E14.5_beta_99

source_name: pancreatic E14.5 β cell, scRNAseq


title: NS134-BRX142-Control-12


title: 17-094-SVZ-LPS


title: NS134-BRX142-Control-18


title: E14.5_beta_98


title: 17-094-GTS-unstim


title: NS134-BRX142-Control-11


title: 17-094-SVZ-IFNgamma


title: E14.5_beta_94


title: E14.5_beta_95


title: E14.5_InsGcg_Bihormonal_11


title: NS141-BRx330.10d_DTXL_IC50.repII

data_processing:
Trimmomatic was used to crop reads to length 50 and to remove the TruSeq3-PE-2 Illumina adapters
The paired-end reads were then aligned using tophat2 and bowtie1 with the no-novel-juncs argument set with human genome version hg19 and transcriptome defined by the hg19 genes.gtf table from http://genome.ucsc.edu
Reads that did not align or aligned to multiple locations were discarded.
The number of reads aligning to each gene was then determined using htseq-count.
Samples that had less than 105 reads were discarded.
Assembly: hg19
Supplementary files format and content: The docetaxelRNAseq.counts.csv  file gives the read counts described above for each sample (columns) and gene (rows).

extract_protocol:
Prior to extraction, live cells were separated from dead cells using Ficoll-Paque Plus (Cytiva) enrichment by centrifuging at 400×g for 5 minutes at room temperature and removing the top layer and washing it with PBS. RNA was isolated from live cells using the Quick-RNA Microprep Kit (Zymo).
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 min incubation at 85°C.  cDNA was 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 adapters in 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: Docetaxel, solubilized in DMSO, was applied to cells at a 10nM concentration for 16 hours. RNA was extracted at 4 and 10 days past exposure to docetaxel and from non-treated (NT) cells.

tag: replicate


title: 17-094-GTS-LPS


title: E14.5_beta_93


title: E14.5_beta_96


title: 17-094-GFM-unstim


title: E14.5_beta_90


title: NS141-BRx330.4d_DTXL_IC50.repII


title: NS141-BRx330.10d_DTXL_IC50.repI


title: 17-094-GFM-R848


title: E14.5_beta_9


title: E14.5_beta_92


title: 17-094-GFM-LPS


title: E14.5_beta_91


title: E14.5_beta_88


title: NS141-BRx330.4d_DTXL_IC50.repI


title: E14.5_beta_87


title: NS141-BRx330.NT.repII

value: NT


title: E14.5_beta_86


title: 17-094-GFM-IFNgamma


title: E14.5_beta_85


title: NS134-BRX142-Control-10


title: E14.5_beta_97


title: 17-090-SVZ-IFNgamma


title: E14.5_beta_83


title: NS141-BRx330.NT.repI


title: E14.5_beta_84


title: E14.5_beta_81


title: E14.5_beta_89


title: NS141-BRx292.10d_DTXL_IC50.repII


title: 17-078-SVZ-LPS


title: 17-078-SVZ-unstim


title: NS141-BRx292.10d_DTXL_IC50.repI


title: E14.5_beta_8


title: E14.5_beta_78


title: E14.5_beta_80


title: 17-078-GFM-unstim


title: E14.5_beta_77


title: E14.5_beta_79


title: 17-078-GFM-R848


title: E14.5_beta_76


title: NS141-BRx292.4d_DTXL_IC50.repI


title: NS141-BRx292.NT.repII


title: E14.5_beta_75


title: E14.5_beta_74


title: 17-078-GFM-LPS


title: 17-078-GFM-IFNgamma


title: NS141-BRx292.NT.repI


title: E14.5_beta_82


title: E14.5_beta_73


title: 17-074-THA-unstim


title: E14.5_beta_72


title: NS141-BRx189.10d_DTXL_IC50.repIII


title: 17-074-THA-LPS


title: NS141-BRx292.4d_DTXL_IC50.repII


title: E14.5_beta_7


title: E14.5_beta_71


title: NS141-BRx189.10d_DTXL_IC50.repII


title: E14.5_beta_70


title: E14.5_beta_69


title: NS141-BRx189.10d_DTXL_IC50.repI


title: E14.5_beta_67


title: E14.5_beta_68


title: 17-074-GFM-LPS


title: E14.5_beta_64


title: NS141-BRx189.4d_DTXL_IC50.repIII


title: 17-043-THA-unstim


title: E14.5_beta_66


title: E14.5_beta_65


title: NS141-BRx189.4d_DTXL_IC50.repII


title: E14.5_beta_63


title: E14.5_beta_62


title: NS141-BRx189.4d_DTXL_IC50.repI


title: E14.5_beta_61


title: 17-043-SVZ-unstim


title: E14.5_beta_60


title: NS141-BRx189.NT.repIII


title: E14.5_beta_6


title: 17-043-SVZ-LPS


title: 17-074-GFM-unstim


title: E14.5_beta_59


title: E14.5_beta_58


title: E14.5_beta_57


title: 17-043-GTS-unstim


title: 17-043-GFM-unstim


title: E14.5_beta_54


title: BRx142_10d.DTXL.IC50_rep2


title: 17-043-GFM-R848


title: BRx142_10d.DTXL.IC50_rep1


title: E14.5_beta_53


title: 17-043-GFM-LPS


title: E14.5_beta_52


title: BRx142_4d.DTXL.IC50_rep2


title: 17-043-THA-LPS


title: 17-043-GFM-IFNgamma


title: E14.5_beta_5


title: E14.5_beta_49


title: E14.5_beta_56


title: 17-032-THA-unstim


title: E14.5_beta_48


title: E14.5_beta_55


title: NS141-BRx189.NT.repII


title: BRx142_NT_rep2


title: E14.5_beta_47


title: 17-032-THA-LPS


title: E14.5_beta_46


title: NS141-BRx189.NT.repI


title: E14.5_beta_51


title: BRx142_NT_rep1


title: E14.5_beta_45


title: 17-032-THA-IFNgamma


title: E14.5_beta_44


title: BRx82_4d.DTXL.IC50_rep1


title: E14.5_beta_50


title: E14.5_beta_43


title: BRx82_NT_rep2


title: 17-032-SVZ-R848


title: E14.5_beta_4


title: BRx142_4d.DTXL.IC50_rep1


title: E14.5_beta_39


title: 17-032-SVZ-LPS


title: BRx82_10d.DTXL.IC50_rep2


title: E14.5_beta_38


title: 17-032-SVZ-IFNgamma


title: BRx82_10d.DTXL.IC50_rep1


title: E14.5_beta_37


title: E14.5_beta_36


title: BRx82_4d.DTXL.IC50_rep2


title: E14.5_beta_35


title: 17-032-GTS-unstim


title: E14.5_beta_34


title: BRx68_10d.DTXL.IC50_rep2


title: E14.5_beta_33


title: E14.5_beta_32


title: E14.5_beta_31


title: 17-032-GTS-LPS


title: BRx68_10d.DTXL.IC50_rep1


title: 17-032-SVZ-unstim


title: E14.5_beta_41


title: E14.5_beta_42


title: E14.5_beta_40


title: E14.5_beta_30


title: BRx82_NT_rep1


title: E14.5_beta_3


title: 17-029-SVZ-unstim


title: E14.5_beta_29


title: 17-029-SVZ-R848


title: E14.5_beta_28


title: E14.5_beta_27


title: 17-029-SVZ-LPS


title: E14.5_beta_26


title: E14.5_beta_25


title: BRx68_NT_rep2


title: 17-032-GTS-IFNgamma


title: BRx68_NT_rep1


title: E14.5_beta_24


title: E14.5_beta_23


title: 17-029-SVZ-IFNgamma


title: 17-029-GTS-LPS


title: BRx50_10d.DTXL.IC50_rep2


title: E14.5_beta_21


title: E14.5_beta_20


title: BRx50_10d.DTXL.IC50_rep1


title: E14.5_beta_22


title: E14.5_beta_2


title: 17-021-SVZ-unstim


title: 17-029-GFM-unstim


title: E14.5_beta_19


title: BRx50_4d.DTXL.IC50_rep2


title: 17-017-THA-LPS


title: BRx68_4d.DTXL.IC50_rep2


title: BRx50_4d.DTXL.IC50_rep1


title: E14.5_beta_17


title: BRx68_4d.DTXL.IC50_rep1


title: 17-017-SVZ-unstim


title: E14.5_beta_18


title: E14.5_beta_16


title: BRx50_NT_rep2


title: E14.5_beta_14


title: 17-017-SVZ-R848


title: E14.5_beta_15


title: E14.5_beta_13


title: BRx50_NT_rep1


title: E14.5_beta_113


title: Brx211_05_19

data_processing:
Trimmomatic was used to crop reads to length 50 and to remove the TruSeq3-PE-2 Illumina adapters
The paired-end reads were then aligned using tophat2 and bowtie1 with the no-novel-juncs argument set with human genome version hg19 and transcriptome defined by the hg19 genes.gtf table from http://genome.ucsc.edu
Reads that did not align or aligned to multiple locations were discarded.
The number of reads aligning to each gene was then determined using htseq-count.
Samples that had less than 105 reads were discarded.
Assembly: hg19
Supplementary files format and content: The CTClinesRNAseq.counts.csv  file gives the read counts described above for each sample (columns) and gene (rows).

treatment_protocol: RNA-Seq was performed on breast cancer circulating tumor cells derived cultures at basal growth untreated conditions.


title: E14.5_beta_12


title: 17-017-SVZ-LPS


title: 17-017-SVZ-IFNgamma


title: E14.5_beta_112


title: E14.5_beta_114


title: E14.5_beta_110


title: NS72-BRX292


title: Brx168


title: E14.5_beta_11


title: E14.5_beta_111


title: 17-017-GTS-LPS


title: 17-017-GTS-unstim


title: E14.5_beta_108


title: NS72-BRX250-16-5-17


title: 17-017-GFM-unstim


title: NS72-BRX142-4-1


title: E14.5_beta_107


title: E14.5_beta_109


title: E14.5_beta_106


title: 17-017-GFM-R848


title: BRX189_S24


title: E14.5_beta_105


title: E14.5_beta_104


title: 17-017-GFM-IFNgamma


title: E14.5_beta_103


title: BRX401_S23


title: E14.5_beta_102


title: BRX394-DRAW-1_S22


title: 17-013-SVZ-unstim


title: E14.5_beta_1


title: E14.5_beta_100


title: E14.5_beta_10


title: E14.5_beta_101


title: 17-013-SVZ-LPS


title: E14.5_alpha_8

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

source_name: pancreatic E14.5 α cell, scRNAseq


title: E14.5_alpha_71


title: 17-013-SVZ-IFNgamma


title: E14.5_alpha_70


title: E14.5_alpha_9


title: BRX319_S20


title: 17-013-GFM-unstim


title: E14.5_alpha_7


title: 17-013-GFM-LPS


title: BRx-29-p


title: E14.5_alpha_68


title: BRx-82_pool_071715


title: 17-005-SVZ-unstim


title: E14.5_alpha_67


title: E14.5_alpha_66


title: BRx-68


title: E14.5_alpha_65


title: 17-005-SVZ-R848


title: E14.5_alpha_64


title: BRX390_S21


title: E14.5_alpha_63


title: 17-005-SVZ-LPS


title: BRx-61--5-8


title: BRx-50


title: E14.5_alpha_61


title: E14.5_alpha_62


title: BRX330-12-13-16_S11


title: 17-005-SVZ-IFNgamma


title: 17-013-SVZ-R848


title: E14.5_alpha_69


title: E14.5_alpha_60


title: BRx-42--3-10


title: E14.5_alpha_6


title: E14.5_alpha_59


title: 17-005-GFM-R848


title: 17-005-GTS-IFNgamma


title: E14.5_alpha_57


title: 17-005-GFM-IFNgamma


title: E14.5_alpha_58


title: E14.5_alpha_56


title: E14.5_alpha_55


title: 17-003-THA-unstim


title: E14.5_alpha_52


title: 17-003-THA-LPS


title: serum, miRNA, PF5473

city: Tokyo

first: Yifan

last: ZHANG

address: Otemachi Bldg. 1-6-1 Otemachi, Chiyoda-ku

country: Japan

institute: Preferred Networks, Inc.

description: miRNA

data_processing:
trim Illumina adapter using "cut_adapt"
identify QIAseq miRNA NGS 3-prime Adapter and UMI by "umi_tools"
filter out reads without proper adapters or UMI length
align reads to grch37 using "bowtie -v0"
quantization of features using "featureCounts"
Assembly: GRCh37
Supplementary files format and content: csv file for TPM values of all samples

source_name: serum

extract_protocol:
Small RNAs were automatically extracted from 300 μL of serum using the Maxwell RSC miRNA Plasma and Serum Kit (Promega) with the Equipment Maxprep Liquid Handler (Promega) and Maxwell RSC (Promega). The purifications were performed according to the manufacturer’s instruction manual.
cDNA libraries were synthesized from 5 μL of RNA eluate with 22 cycles of PCR using the QIAseq miRNA Library Kit (QIAGEN) with the Biomek i5 Automated Liquid Handling Workstation (Beckman Coulter). The concentration of each amplification product was measured with a QuantiFluor ONE ds DNA System (Promega). cDNA libraries were merged in one tube at a final concentration of 1.0–1.5 pmol/L. Small RNA sequence data were obtained using NextSeq 550Dx with the NextSeq 500/550 High Output Kit v2.5, 75 cycles (Illumina) and the NextSeq Phix Control Kit (Illumina). An automated program was set up for each instrument according to the manufacturer’s instruction manual, and all the samples were processed using the same program.

value: serum


title: serum, miRNA, PF5471

description: miRNA


title: E14.5_alpha_51

value: GcgGFP


title: E14.5_alpha_50


title: E14.5_alpha_5


title: 17-003-THA-IFNgamma


title: serum, miRNA, PF5470

description: miRNA


title: E14.5_alpha_49


title: 17-003-SVZ-unstim


title: 17-003-SVZ-R848


title: serum, miRNA, PF5469

description: miRNA


title: serum, miRNA, PF5474

description: miRNA


title: E14.5_alpha_47


title: E14.5_alpha_48


title: serum, miRNA, PF5468

description: miRNA


title: BRx-07

value: cell line


title: E14.5_alpha_45


title: serum, miRNA, PF5467

description: miRNA


title: E14.5_alpha_43


title: E14.5_alpha_46


title: E14.5_alpha_44


title: 17-003-SVZ-IFNgamma


title: 17-003-SVZ-LPS


title: E14.5_alpha_53


title: E14.5_alpha_42


title: serum, miRNA, PF5472

description: miRNA


title: serum, miRNA, PF5466

description: miRNA


title: E14.5_alpha_54


title: 17-003-GTS-unstim


title: E14.5_alpha_40


title: E14.5_alpha_4


title: 17-003-GTS-IFNgamma


title: serum, miRNA, PF5424

description: miRNA


title: E14.5_alpha_39


title: serum, miRNA, PF5422

description: miRNA


title: E14.5_alpha_36


title: 16-137-SVZ-unstim


title: 16-137-SVZ-R848


title: E14.5_alpha_38


title: E14.5_alpha_37


title: 16-137-SVZ-LPS


title: serum, miRNA, PF5421

description: miRNA


title: E14.5_alpha_35


title: E14.5_alpha_33


title: serum, miRNA, PF5419

description: miRNA


title: E14.5_alpha_34


title: 16-118-SVZ-unstim


title: E14.5_alpha_32


title: E14.5_alpha_30


title: serum, miRNA, PF5423

description: miRNA


title: serum, miRNA, PF5418

description: miRNA


title: 16-118-SVZ-R848


title: E14.5_alpha_3


title: serum, miRNA, PF5417

description: miRNA


title: E14.5_alpha_41


title: 16-118-SVZ-LPS


title: E14.5_alpha_29


title: serum, miRNA, PF5416

description: miRNA


title: E14.5_alpha_28


title: 16-118-SVZ-IFNgamma


title: serum, miRNA, PF5415

description: miRNA


title: E14.5_alpha_25


title: 16-118-GTS-unstim


title: E14.5_alpha_23


title: E14.5_alpha_31


title: E14.5_alpha_22


title: serum, miRNA, PF5414

description: miRNA


title: E14.5_alpha_20


title: serum, miRNA, PF5413

description: miRNA


title: E14.5_alpha_21


title: E14.5_alpha_24


title: E14.5_alpha_2


title: 16-118-GFM-unstim


title: E14.5_alpha_19


title: E14.5_alpha_27


title: E14.5_alpha_26


title: 16-118-GTS-IFNgamma


title: E14.5_alpha_18


title: E14.5_alpha_17


title: 16-118-GFM-R848


title: serum, miRNA, PF5407

description: miRNA


title: E14.5_alpha_16


title: serum, miRNA, PF5410

description: miRNA


title: 16-118-GFM-LPS


title: serum, miRNA, PF5408

description: miRNA


title: 16-118-GTS-LPS


title: serum, miRNA, PF5406

description: miRNA


title: E14.5_alpha_14


title: E14.5_alpha_13


title: E14.5_alpha_12


title: 16-117-THA-unstim


title: E14.5_alpha_11


title: E14.5_alpha_10


title: serum, miRNA, PF5401

description: miRNA


title: 16-117-THA-LPS


title: E14.0TAM_E14.5_9

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

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


title: E14.5_alpha_1


title: serum, miRNA, PF5400

description: miRNA


title: serum, miRNA, PF5399

description: miRNA


title: E14.0TAM_E14.5_5


title: 16-117-SVZ-LPS


title: E14.0TAM_E14.5_8


title: E14.0TAM_E14.5_7


title: E14.0TAM_E14.5_46


title: 16-117-THA-IFNgamma


title: E14.0TAM_E14.5_6


title: 16-117-SVZ-R848


title: serum, miRNA, PF5397

description: miRNA


title: E14.0TAM_E14.5_45


title: 16-117-SVZ-IFNgamma


title: serum, miRNA, PF5398

description: miRNA


title: serum, miRNA, PF5396

description: miRNA


title: E14.0TAM_E14.5_43


title: E14.5_alpha_15


title: 16-118-GFM-IFNgamma


title: serum, miRNA, PF5403

description: miRNA


title: E14.0TAM_E14.5_44


title: 16-117-GTS-unstim


title: E14.0TAM_E14.5_42


title: serum, miRNA, PF5391

description: miRNA


title: 16-117-GFM-unstim


title: E14.0TAM_E14.5_41


title: E14.0TAM_E14.5_40


title: serum, miRNA, PF5390

description: miRNA


title: E14.0TAM_E14.5_39


title: serum, miRNA, PF5387

description: miRNA


title: E14.0TAM_E14.5_4


title: 16-117-GFM-R848


title: serum, miRNA, PF5386

description: miRNA


title: E14.0TAM_E14.5_36


title: E14.0TAM_E14.5_37


title: serum, miRNA, PF5385

description: miRNA


title: 16-117-GFM-LPS


title: E14.0TAM_E14.5_35


title: E14.0TAM_E14.5_38


title: E14.0TAM_E14.5_34


title: 16-117-GFM-IFNgamma


title: 16-112-THA-unstim


title: E14.0TAM_E14.5_32


title: E14.0TAM_E14.5_33


title: 16-117-GFM-DEX

value: DEX


title: 16-112-THA-LPS


title: serum, miRNA, PF5384

description: miRNA


title: serum, miRNA, PF5376

description: miRNA


title: serum, miRNA, PF5379

description: miRNA


title: E14.0TAM_E14.5_30


title: E14.0TAM_E14.5_27


title: 16-112-SVZ-LPS


title: 16-112-SVZ-unstim


title: 16-112-GTS-unstim


title: serum, miRNA, PF5369

description: miRNA


title: E14.0TAM_E14.5_28


title: E14.0TAM_E14.5_26


title: E14.0TAM_E14.5_31


title: serum, miRNA, PF5370

description: miRNA


title: serum, miRNA, PF5368

description: miRNA


title: E14.0TAM_E14.5_24


title: E14.0TAM_E14.5_23


title: E14.0TAM_E14.5_3


title: 16-112-GTS-LPS


title: 16-112-GTS-IFNgamma


title: E14.0TAM_E14.5_21


title: E14.0TAM_E14.5_20


title: E14.0TAM_E14.5_2


title: 16-112-GFM-unstim


title: E14.0TAM_E14.5_29


title: E14.0TAM_E14.5_19


title: serum, miRNA, PF5363

description: miRNA


title: 16-112-GFM-LPS


title: serum, miRNA, PF5359

description: miRNA


title: E14.0TAM_E14.5_18


title: E14.0TAM_E14.5_17


title: serum, miRNA, PF5357

description: miRNA


title: E14.0TAM_E14.5_25


title: E14.0TAM_E14.5_15


title: E14.0TAM_E14.5_16


title: 16-112-GFM-IFNgamma


title: serum, miRNA, PF5356

description: miRNA


title: serum, miRNA, PF5366

description: miRNA


title: E14.0TAM_E14.5_22


title: 16-110-THA-unstim


title: E14.0TAM_E14.5_13


title: E14.0TAM_E14.5_12


title: serum, miRNA, PF5352

description: miRNA


title: 16-110-THA-LPS


title: E14.0TAM_E14.5_10


title: 16-110-SVZ-unstim


title: E14.0TAM_E14.5_1


title: serum, miRNA, PF5350

description: miRNA


title: 16-110-SVZ-R848


title: serum, miRNA, PF5345

description: miRNA


title: E13.5TAM_E16.5_5

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


title: E13.5TAM_E16.5_6


title: 16-110-SVZ-IFNgamma


title: E13.5TAM_E16.5_7


title: serum, miRNA, PF5344

description: miRNA


title: 16-110-GTS-unstim


title: E13.5TAM_E16.5_4


title: E14.0TAM_E14.5_14


title: E13.5TAM_E16.5_9


title: E13.5TAM_E16.5_33


title: 16-110-GTS-LPS


title: E13.5TAM_E16.5_32


title: serum, miRNA, PF5341

description: miRNA


title: serum, miRNA, PF5342

description: miRNA


title: E13.5TAM_E16.5_31


title: 16-110-GTS-IFNgamma


title: serum, miRNA, PF5340

description: miRNA


title: 16-110-GFM-unstim


title: serum, miRNA, PF5347

description: miRNA


title: E14.0TAM_E14.5_11


title: E13.5TAM_E16.5_8


title: serum, miRNA, PF5337

description: miRNA


title: 16-110-GFM-R848


title: E13.5TAM_E16.5_29


title: E13.5TAM_E16.5_27


title: 16-110-GFM-LPS


title: E13.5TAM_E16.5_25


title: E13.5TAM_E16.5_26


title: E13.5TAM_E16.5_24


title: serum, miRNA, PF5328

description: miRNA


title: 16-110-GFM-IFNgamma


title: serum, miRNA, PF5326

description: miRNA


title: 16-082-SVZ-unstim


title: E13.5TAM_E16.5_22


title: E13.5TAM_E16.5_30


title: E13.5TAM_E16.5_23


title: E13.5TAM_E16.5_21


title: E13.5TAM_E16.5_20


title: serum, miRNA, PF5322

description: miRNA


title: E13.5TAM_E16.5_3


title: 16-082-SVZ-R848


title: E13.5TAM_E16.5_2


title: serum, miRNA, PF5319

description: miRNA


title: E13.5TAM_E16.5_19


title: 16-082-SVZ-LPS


title: E13.5TAM_E16.5_18


title: E13.5TAM_E16.5_17


title: E13.5TAM_E16.5_28


title: serum, miRNA, PF5333

description: miRNA


title: serum, miRNA, PF5312

description: miRNA


title: serum, miRNA, PF5311

description: miRNA


title: 16-082-SVZ-ATP

value: ATP


title: 16-082-SVZ-IFNgamma


title: E13.5TAM_E16.5_15

value: pancreas


title: E13.5TAM_E16.5_14

value: islet cell


title: 16-080-SVZ-unstim


title: serum, miRNA, PF5306

description: miRNA


title: E13.5TAM_E16.5_11


title: E13.5TAM_E16.5_13


title: E13.5TAM_E16.5_12


title: serum, miRNA, PF5305

description: miRNA


title: E13.5TAM_E16.5_1


title: 16-080-SVZ-R848


title: 16-080-SVZ-LPS


title: serum, miRNA, PF5302

description: miRNA


title: E13.5TAM_E14.5_9

description:
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E13.5, with analysis conducted on E14.5 embryos


title: serum, miRNA, PF5304

description: miRNA


title: E13.5TAM_E16.5_10


title: E13.5TAM_E16.5_16


title: 16-080-SVZ-IFNgamma


title: serum, miRNA, PF5300

description: miRNA


title: serum, miRNA, PF5299

description: miRNA


title: E13.5TAM_E14.5_75


title: E13.5TAM_E14.5_77


title: E13.5TAM_E14.5_8


title: E13.5TAM_E14.5_76


title: 16-062-THA-unstim


title: 16-062-THA-LPS


title: E13.5TAM_E14.5_73


title: E13.5TAM_E14.5_74


title: serum, miRNA, PF5297

description: miRNA


title: E13.5TAM_E14.5_72


title: 16-062-THA-IFNgamma


title: E13.5TAM_E14.5_71


title: serum, miRNA, PF5291

description: miRNA


title: E13.5TAM_E14.5_70


title: E13.5TAM_E14.5_69


title: serum, miRNA, PF5288

description: miRNA


title: E13.5TAM_E14.5_7


title: 16-062-SVZ-R848


title: serum, miRNA, PF5287

description: miRNA


title: E13.5TAM_E14.5_68


title: E13.5TAM_E14.5_66


title: 16-062-SVZ-LPS


title: serum, miRNA, PF5286

description: miRNA


title: E13.5TAM_E14.5_65


title: 16-062-SVZ-IFNgamma


title: serum, miRNA, PF5284

description: miRNA


title: E13.5TAM_E14.5_63


title: serum, miRNA, PF5283

description: miRNA


title: E13.5TAM_E14.5_61


title: E13.5TAM_E14.5_62


title: 16-062-GTS-unstim


title: E13.5TAM_E14.5_60


title: E13.5TAM_E14.5_6


title: 16-062-GTS-IFNgamma


title: serum, miRNA, PF5281

description: miRNA


title: 16-062-SVZ-unstim


title: E13.5TAM_E14.5_59


title: serum, miRNA, PF5277

description: miRNA


title: E13.5TAM_E14.5_58


title: E13.5TAM_E14.5_57


title: 16-062-GFM-unstim


title: E13.5TAM_E14.5_67


title: E13.5TAM_E14.5_55


title: serum, miRNA, PF5273

description: miRNA


title: 16-062-GFM-R848


title: serum, miRNA, PF5272

description: miRNA


title: E13.5TAM_E14.5_56


title: E13.5TAM_E14.5_64


title: serum, miRNA, PF5271

description: miRNA


title: E13.5TAM_E14.5_52


title: E13.5TAM_E14.5_51


title: 16-062-GFM-IFNgamma


title: 16-062-GTS-LPS


title: E13.5TAM_E14.5_54


title: serum, miRNA, PF5270

description: miRNA


title: 16-049-THA-unstim


title: E13.5TAM_E14.5_5


title: E13.5TAM_E14.5_48


title: 16-049-THA-LPS


title: serum, miRNA, PF5269

description: miRNA


title: E13.5TAM_E14.5_49


title: serum, miRNA, PF5268

description: miRNA


title: serum, miRNA, PF5267

description: miRNA


title: E13.5TAM_E14.5_46


title: E13.5TAM_E14.5_50


title: E13.5TAM_E14.5_47


title: E13.5TAM_E14.5_45


title: serum, miRNA, PF5264

description: miRNA


title: E13.5TAM_E14.5_44


title: 16-062-GFM-LPS


title: E13.5TAM_E14.5_53


title: 16-049-SVZ-LPS


title: E13.5TAM_E14.5_43


title: 16-049-SVZ-IFNgamma


title: serum, miRNA, PF5260

description: miRNA


title: E13.5TAM_E14.5_41


title: E13.5TAM_E14.5_40


title: serum, miRNA, PF5257

description: miRNA


title: E13.5TAM_E14.5_4


title: 16-049-GTS-unstim


title: E13.5TAM_E14.5_39


title: serum, miRNA, PF5256

description: miRNA


title: E13.5TAM_E14.5_38


title: 16-049-GTS-LPS


title: 16-049-SVZ-unstim


title: serum, miRNA, PF5245

description: miRNA


title: E13.5TAM_E14.5_37


title: E13.5TAM_E14.5_35


title: E13.5TAM_E14.5_36


title: E13.5TAM_E14.5_34


title: 16-049-SVZ-R848


title: 16-049-GTS-IFNgamma


title: 16-049-GFM-unstim


title: serum, miRNA, PF5240

description: miRNA


title: E13.5TAM_E14.5_33


title: E13.5TAM_E14.5_31


title: serum, miRNA, PF5232

description: miRNA


title: 16-049-GFM-LPS


title: E13.5TAM_E14.5_42


title: E13.5TAM_E14.5_30


title: E13.5TAM_E14.5_32


title: E13.5TAM_E14.5_3


title: 16-049-GFM-R848


title: serum, miRNA, PF5230

description: miRNA


title: E13.5TAM_E14.5_29


title: serum, miRNA, PF5229

description: miRNA


title: E13.5TAM_E14.5_28


title: 16-049-GFM-IFNgamma


title: E13.5TAM_E14.5_27


title: 16-028-THA-LPS


title: E13.5TAM_E14.5_24


title: E13.5TAM_E14.5_23


title: 16-028-THA-unstim


title: serum, miRNA, PF5236

description: miRNA


title: 16-028-GTS-unstim


title: E13.5TAM_E14.5_26


title: 16-028-GTS-LPS


title: serum, miRNA, PF5228

description: miRNA


title: E13.5TAM_E14.5_22


title: E13.5TAM_E14.5_2


title: 16-028-GFM-unstim


title: serum, miRNA, PF5223

description: miRNA


title: E13.5TAM_E14.5_25


title: E13.5TAM_E14.5_21


title: serum, miRNA, PF5219

description: miRNA


title: E13.5TAM_E14.5_17


title: serum, miRNA, PF5216

description: miRNA


title: E13.5TAM_E14.5_16


title: serum, miRNA, PF5215

description: miRNA


title: E13.5TAM_E14.5_18


title: 16-028-GFM-LPS


title: serum, miRNA, PF5214

description: miRNA


title: serum, miRNA, PF5224

description: miRNA


title: 16-027-THA-LPS


title: E13.5TAM_E14.5_14


title: 16-027-THA-unstim


title: E13.5TAM_E14.5_13


title: serum, miRNA, PF5210

description: miRNA


title: 16-027-GFM-unstim


title: serum, miRNA, PF5209

description: miRNA


title: E13.5TAM_E14.5_20


title: E13.5TAM_E14.5_15


title: E13.5TAM_E14.5_19


title: E13.5TAM_E14.5_10


title: 16-003-THA-unstim


title: E13.5TAM_E14.5_11


title: E13.5TAM_E14.5_1


title: 16-003-THA-LPS


title: P60_PP_7

source_name: pancreatic P60 PP cell, scRNAseq

value: PpymNeptune


title: E13.5TAM_E14.5_12

value: Male


title: serum, miRNA, PF5207

description: miRNA


title: 16-003-THA-IFNgamma


title: serum, miRNA, PF5201

description: miRNA


title: P60_PP_9


title: serum, miRNA, PF5203

description: miRNA


title: P60_PP_8


title: 16-003-SVZ-R848


title: serum, miRNA, PF5197

description: miRNA


title: P60_PP_61


title: 16-003-SVZ-unstim


title: P60_PP_60


title: P60_PP_57


title: P60_PP_56


title: P60_PP_59


title: 16-003-SVZ-IFNgamma


title: serum, miRNA, PF5189

description: miRNA


title: P60_PP_58


title: 16-003-GFS-unstim


title: 16-003-SVZ-LPS


title: serum, miRNA, PF5188

description: miRNA


title: P60_PP_53


title: P60_PP_55


title: P60_PP_54


title: 16-003-GFS-LPS


title: 16-003-GFS-IFNgamma


title: P60_PP_52


title: P60_PP_50


title: P60_PP_6


title: serum, miRNA, PF5187

description: miRNA


title: P60_PP_51


title: P60_PP_49


title: serum, miRNA, PF5199

description: miRNA


title: P60_PP_5


title: P60_PP_48


title: serum, miRNA, PF5185

description: miRNA


title: 16-003-GFM-unstim


title: serum, miRNA, PF5196

description: miRNA


title: P60_PP_47


title: P60_PP_46


title: serum, miRNA, PF5184

description: miRNA


title: serum, miRNA, PF5179

description: miRNA


title: P60_PP_44


title: serum, miRNA, PF5176

description: miRNA


title: 16-003-GFM-LPS


title: P60_PP_45


title: 16-003-GFM-R848


title: P60_PP_42


title: 16-003-GFM-IFNgamma


title: serum, miRNA, PF5175

description: miRNA


title: P60_PP_41


title: P60_PP_43


title: P60_PP_38


title: P60_PP_4


title: 15-055-GTS-unstim


title: 15-089-GTS-LPS


title: 15-055-GFM-unstim


title: serum, miRNA, PF5174

description: miRNA


title: P60_PP_39


title: P60_PP_36


title: serum, miRNA, PF5172

description: miRNA


title: P60_PP_37


title: 15-055-GFM-IL4


title: P60_PP_34


title: serum, miRNA, PF5168

description: miRNA


title: P60_PP_35


title: P60_PP_33


title: P60_PP_32


title: 15-032-GTS-LPS


title: P60_PP_30


title: P60_PP_40


title: serum, miRNA, PF5163

description: miRNA


title: serum, miRNA, PF5159

description: miRNA


title: 15-032-GTS-unstim


title: 15-024-THA-unstim


title: 15-041-GFM-LPS


title: P60_PP_27


title: serum, miRNA, PF5165

description: miRNA


title: serum, miRNA, PF5162

description: miRNA


title: serum, miRNA, PF5160

description: miRNA


title: P60_PP_29


title: P60_PP_26


title: P60_PP_23


title: P60_PP_25


title: P60_PP_24


title: serum, miRNA, PF5158

description: miRNA


title: 15-024-GFM-LPS


title: P60_PP_31


title: P60_PP_3


title: 15-024-GFM-IL4


title: P60_PP_21


title: P60_PP_28


title: serum, miRNA, PF5157

description: miRNA


title: serum, miRNA, PF5153

description: miRNA


title: 15-024-GFM-DEX


title: 15-024-GFM-unstim


title: P60_PP_2


title: serum, miRNA, PF5152

description: miRNA


title: P60_PP_19


title: 15-024-GFM-ATP


title: P60_PP_17


title: 15-021-THA-LPS


title: P60_PP_18


title: serum, miRNA, PF5150

description: miRNA


title: P60_PP_16


title: serum, miRNA, PF5151

description: miRNA


title: P60_PP_15


title: serum, miRNA, PF5147

description: miRNA


title: 15-018-GFM-LPS


title: 15-018-GFM-IL4


title: P60_PP_10


title: P60_PP_11


title: serum, miRNA, PF5148

description: miRNA


title: P60_PP_20


title: P60_PP_12


title: P60_PP_14


title: serum, miRNA, PF5143

description: miRNA


title: P60_PP_22


title: P60_PP_1


title: P60_GcgPpy_Doublet_9

description:
Smart-seq3xpress
Artificial doublets, crafted by combining an α cell with a PP cell

source_name: pancreatic P60 GcgPpy Doublet, scRNAseq

value: GcgGFP/PpymNeptune


title: 14-078-GFM-unstim

value: Brain


title: serum, miRNA, PF5144

description: miRNA


title: 15-018-GFM-DEX

value: Microglia


title: 15-018-GFM-unstim

value: unstim


title: P60_GcgPpy_Doublet_5


title: 14-075-GTS-unstim


title: P60_GcgPpy_Doublet_6


title: P60_GcgPpy_Doublet_43


title: P60_PP_13


title: serum, miRNA, PF5140

description: miRNA


title: serum, miRNA, PF5141

description: miRNA


title: serum, miRNA, PF5149

description: miRNA


title: P60_GcgPpy_Doublet_8


title: P60_GcgPpy_Doublet_7


title: 14-075-GTS-LPS

value: LPS


title: 14-075-GTS-IFNgamma

value: IFNgamma


title: P60_GcgPpy_Doublet_41


title: P60_GcgPpy_Doublet_39


title: P60_GcgPpy_Doublet_40


title: serum, miRNA, PF5133

description: miRNA


title: P60_GcgPpy_Doublet_44


title: 14-075-GFM-unstim


title: 14-078-GFM-IL4


title: serum, miRNA, PF5131

description: miRNA


title: serum, miRNA, PF5130

description: miRNA


title: 14-075-GFM-LPS


title: P60_GcgPpy_Doublet_36


title: P60_GcgPpy_Doublet_4


title: 14-074-GFM-unstim


title: serum, miRNA, PF5128

description: miRNA


title: P60_GcgPpy_Doublet_34


title: P60_GcgPpy_Doublet_35


title: serum, miRNA, PF5135

description: miRNA


title: P60_GcgPpy_Doublet_38


title: serum, miRNA, PF5126

description: miRNA


title: 14-075-GFM-IFNgamma


title: P60_GcgPpy_Doublet_32


title: P60_GcgPpy_Doublet_31


title: P60_GcgPpy_Doublet_37


title: P60_GcgPpy_Doublet_33


title: P60_GcgPpy_Doublet_30


title: 14-074-CC-unstim


title: serum, miRNA, PF5124

description: miRNA


title: P60_GcgPpy_Doublet_3


title: 14-074-CC-LPS


title: P60_GcgPpy_Doublet_29


title: P60_GcgPpy_Doublet_28


title: P60_GcgPpy_Doublet_27


title: serum, miRNA, PF5121

description: miRNA


title: serum, miRNA, PF5123

description: miRNA


title: 14-069-SVZ-unstim


title: P60_GcgPpy_Doublet_25


title: 14-069-GTS-unstim


title: serum, miRNA, PF5116

description: miRNA


title: P60_GcgPpy_Doublet_23


title: 14-069-SVZ-LPS


title: serum, miRNA, PF5115

description: miRNA


title: P60_GcgPpy_Doublet_26


title: P60_GcgPpy_Doublet_20


title: 14-069-GFM-unstim


title: P60_GcgPpy_Doublet_24


title: P60_GcgPpy_Doublet_22


title: serum, miRNA, PF5120

description: miRNA


title: 14-069-GTS-IFNgamma


title: serum, miRNA, PF5114

description: miRNA


title: P60_GcgPpy_Doublet_2


title: 14-069-GFM-LPS


title: P60_GcgPpy_Doublet_21


title: serum, miRNA, PF5112

description: miRNA


title: P60_GcgPpy_Doublet_18


title: P60_GcgPpy_Doublet_19


title: P60_GcgPpy_Doublet_17


title: P60_GcgPpy_Doublet_16


title: serum, miRNA, PF5111

description: miRNA


title: P60_GcgPpy_Doublet_15


title: 14-069-GFM-IFNgamma


title: serum, miRNA, PF5110

description: miRNA


title: P60_GcgPpy_Doublet_13


title: 14-069-GFM-DEX


title: 14-069-GFM-IL4


title: P60_GcgPpy_Doublet_14


title: P60_GcgPpy_Doublet_11


title: serum, miRNA, PF5108

description: miRNA


title: P60_GcgPpy_Doublet_12


title: 14-063-CC-LPS


title: P60_GcgPpy_Doublet_42


title: serum, miRNA, PF5109

description: miRNA


title: 14-063-CC-unstim


title: P60_GcgPpy_Doublet_10


title: P60_GcgPpy_Bihormonal_98

source_name: pancreatic P60 GcgPpy bihormonal cell, scRNAseq

value: GcgGFP;PpymNeptune


title: P60_GcgPpy_Bihormonal_99


title: serum, miRNA, PF5105

description: miRNA

value: serum


title: P60_GcgPpy_Bihormonal_96


title: 14-063-CC-IFNgamma


title: serum, miRNA, PF5107

description: miRNA


title: 14-055-GTS-LPS


title: serum, miRNA, PF5104

description: miRNA


title: P60_GcgPpy_Bihormonal_95


title: 14-055-GFM-LPS


title: P60_GcgPpy_Bihormonal_93


title: P60_GcgPpy_Bihormonal_92


title: P60_GcgPpy_Doublet_1


title: serum, miRNA, PF5102

description: miRNA


title: P60_GcgPpy_Bihormonal_90


title: 14-055-GFM-IFNgamma


title: P60_GcgPpy_Bihormonal_89


title: P60_GcgPpy_Bihormonal_91


title: P60_GcgPpy_Bihormonal_9


title: 14-055-GFM-IL4


title: serum, miRNA, PF5101

description: miRNA


title: 14-055-CC-unstim


title: serum, miRNA, PF5099

description: miRNA


title: 14-055-GFM-DEX


title: P60_GcgPpy_Bihormonal_88


title: P60_GcgPpy_Bihormonal_87


title: P60_GcgPpy_Bihormonal_86


title: P60_GcgPpy_Bihormonal_84


title: 14-055-CC-LPS


title: 14-055-CC-IFNgamma


title: P60_GcgPpy_Bihormonal_85


title: serum, miRNA, PF5095

description: miRNA


title: P60_GcgPpy_Bihormonal_83


title: P60_GcgPpy_Bihormonal_94


title: serum, miRNA, PF5090

description: miRNA


title: P60_GcgPpy_Bihormonal_81


title: P60_GcgPpy_Bihormonal_82


title: serum, miRNA, PF5103

description: miRNA


title: 14-053-CC-unstim


title: P60_GcgPpy_Bihormonal_97


title: serum, miRNA, PF5089

description: miRNA


title: P60_GcgPpy_Bihormonal_80


title: P60_GcgPpy_Bihormonal_8


title: serum, miRNA, PF5084

description: miRNA


title: P60_GcgPpy_Bihormonal_78


title: serum, miRNA, PF5098

description: miRNA


title: P60_GcgPpy_Bihormonal_79


title: P60_GcgPpy_Bihormonal_77


title: serum, miRNA, PF5082

description: miRNA


title: 14-051-GFM-R848


title: P60_GcgPpy_Bihormonal_76


title: serum, miRNA, PF5079

description: miRNA


title: P60_GcgPpy_Bihormonal_74


title: 14-051-GFM-LPS


title: P60_GcgPpy_Bihormonal_73


title: serum, miRNA, PF5078

description: miRNA


title: P60_GcgPpy_Bihormonal_71


title: 14-048-CC-unstim


title: serum, miRNA, PF5077

description: miRNA


title: P60_GcgPpy_Bihormonal_72


title: P60_GcgPpy_Bihormonal_70


title: 14-048-CC-LPS


title: P60_GcgPpy_Bihormonal_7


title: serum, miRNA, PF5076

description: miRNA


title: P60_GcgPpy_Bihormonal_69


title: 14-053-CC-LPS


title: 14-048-CC-IFNgamma


title: serum, miRNA, PF5075

description: miRNA


title: P60_GcgPpy_Bihormonal_67


title: P60_GcgPpy_Bihormonal_68


title: 14-053-CC-IFNgamma


title: 14-046-GTS-LPS


title: P60_GcgPpy_Bihormonal_75


title: P60_GcgPpy_Bihormonal_65


title: P60_GcgPpy_Bihormonal_66


title: serum, miRNA, PF5072

description: miRNA


title: P60_GcgPpy_Bihormonal_64


title: 14-046-GFM-IFNgamma


title: P60_GcgPpy_Bihormonal_62


title: serum, miRNA, PF5068

description: miRNA


title: serum, miRNA, PF5067

description: miRNA


title: P60_GcgPpy_Bihormonal_59


title: P60_GcgPpy_Bihormonal_6


title: serum, miRNA, PF5066

description: miRNA


title: 14-046-CC-unstim


title: P60_GcgPpy_Bihormonal_60


title: P60_GcgPpy_Bihormonal_57


title: P60_GcgPpy_Bihormonal_58


title: serum, miRNA, PF5065

description: miRNA


title: P60_GcgPpy_Bihormonal_56


title: P60_GcgPpy_Bihormonal_55


title: 14-046-CC-IFNgamma


title: serum, miRNA, PF5061

description: miRNA


title: serum, miRNA, PF5074

description: miRNA


title: 14-029-GTS-unstim


title: P60_GcgPpy_Bihormonal_54


title: 14-029-GTS-LPS


title: P60_GcgPpy_Bihormonal_53


title: serum, miRNA, PF5058

description: miRNA


title: P60_GcgPpy_Bihormonal_52


title: P60_GcgPpy_Bihormonal_63


title: P60_GcgPpy_Bihormonal_61


title: serum, miRNA, PF5056

description: miRNA


title: P60_GcgPpy_Bihormonal_50


title: 14-046-CC-LPS


title: 14-029-CC-LPS


title: P60_GcgPpy_Bihormonal_5


title: serum, miRNA, PF5055

description: miRNA


title: P60_GcgPpy_Bihormonal_49


title: 14-015-GTS-unstim


title: serum, miRNA, PF5054

description: miRNA


title: P60_GcgPpy_Bihormonal_48


title: P60_GcgPpy_Bihormonal_47


title: P60_GcgPpy_Bihormonal_46


title: 14-015-GTS-LPS


title: P60_GcgPpy_Bihormonal_45


title: serum, miRNA, PF5053

description: miRNA


title: serum, miRNA, PF5052

description: miRNA


title: P60_GcgPpy_Bihormonal_43


title: P60_GcgPpy_Bihormonal_42


title: 14-015-GFM-unstim


title: 14-046-GFM-R848


title: serum, miRNA, PF5051

description: miRNA


title: P60_GcgPpy_Bihormonal_44


title: P60_GcgPpy_Bihormonal_51


title: 14-015-CC-unstim


title: serum, miRNA, PF5049

description: miRNA


title: P60_GcgPpy_Bihormonal_40


title: P60_GcgPpy_Bihormonal_4


title: 14-029-CC-unstim


title: P60_GcgPpy_Bihormonal_41


title: 14-015-CC-LPS


title: P60_GcgPpy_Bihormonal_39


title: serum, miRNA, PF5048

description: miRNA


title: P60_GcgPpy_Bihormonal_38


title: serum, miRNA, PF5044

description: miRNA


title: P60_GcgPpy_Bihormonal_37


title: P60_GcgPpy_Bihormonal_36


title: 14-010-CC-LPS


title: P60_GcgPpy_Bihormonal_35


title: serum, miRNA, PF5036

description: miRNA


title: P60_GcgPpy_Bihormonal_34


title: 14-005-GTS-unstim


title: 14-015-GFM-LPS


title: serum, miRNA, PF5035

description: miRNA


title: P60_GcgPpy_Bihormonal_32


title: P60_GcgPpy_Bihormonal_33


title: 14-005-GFM-unstim


title: P60_GcgPpy_Bihormonal_31


title: serum, miRNA, PF5031

description: miRNA


title: P60_GcgPpy_Bihormonal_3


title: 14-005-GFM-R848


title: 14-005-GFM-LPS


title: P60_GcgPpy_Bihormonal_28


title: P60_GcgPpy_Bihormonal_30


title: P60_GcgPpy_Bihormonal_29


title: P60_GcgPpy_Bihormonal_27


title: 14-005-GFM-IFNgamma


title: P60_GcgPpy_Bihormonal_25


title: serum, miRNA, PF5029

description: miRNA


title: 14-005-CC-unstim


title: P60_GcgPpy_Bihormonal_24


title: serum, miRNA, PF5030

description: miRNA


title: 14-010-CC-unstim


title: serum, miRNA, PF5028

description: miRNA


title: P60_GcgPpy_Bihormonal_23


title: P60_GcgPpy_Bihormonal_26


title: P60_GcgPpy_Bihormonal_22


title: serum, miRNA, PF5026

description: miRNA


title: 14-002-CC-unstim


title: P60_GcgPpy_Bihormonal_21


title: serum, miRNA, PF5025

description: miRNA


title: P60_GcgPpy_Bihormonal_20


title: serum, miRNA, PF5022

description: miRNA


title: 14-002-CC-LPS


title: P60_GcgPpy_Bihormonal_19


title: serum, miRNA, PF5021

description: miRNA


title: P60_GcgPpy_Bihormonal_18


title: 13-095-GFM-unstim


title: serum, miRNA, PF5018

description: miRNA


title: P60_GcgPpy_Bihormonal_17


title: 13-087-CC-unstim


title: 14-005-CC-LPS


title: P60_GcgPpy_Bihormonal_16


title: 13-087-CC-LPS


title: P60_GcgPpy_Bihormonal_15


title: P60_GcgPpy_Bihormonal_13


title: serum, miRNA, PF5016

description: miRNA


title: serum, miRNA, PF5017

description: miRNA


title: serum, miRNA, PF5015

description: miRNA


title: P60_GcgPpy_Bihormonal_14


title: 13-077-CC-unstim


title: 13-087-CC-IFNgamma


title: P60_GcgPpy_Bihormonal_116


title: P60_GcgPpy_Bihormonal_114


title: P60_GcgPpy_Bihormonal_113


title: 13-077-CC-LPS


title: P60_GcgPpy_Bihormonal_2


title: serum, miRNA, PF5008

description: miRNA


title: P60_GcgPpy_Bihormonal_111


title: 13-077-CC-IFNgamma


title: P60_GcgPpy_Bihormonal_110


title: serum, miRNA, PF5007

description: miRNA


title: P60_GcgPpy_Bihormonal_109


title: 13-074-CC-LPS


title: P60_GcgPpy_Bihormonal_11


title: P60_GcgPpy_Bihormonal_108


title: 13-074-CC-IFNgamma


title: serum, miRNA, PF5006

description: miRNA


title: P60_GcgPpy_Bihormonal_12


title: P60_GcgPpy_Bihormonal_115


title: P60_GcgPpy_Bihormonal_107


title: P60_GcgPpy_Bihormonal_106


title: P60_GcgPpy_Bihormonal_103


title: serum, miRNA, PF5005

description: miRNA


title: 13-056-GTS-unstim


title: serum, miRNA, PF5001

description: miRNA


title: serum, miRNA, PF5003

description: miRNA


title: P60_GcgPpy_Bihormonal_102


title: 13-056-GFM-LPS


title: serum, miRNA, PF5010

description: miRNA


title: P60_GcgPpy_Bihormonal_100


title: P60_GcgPpy_Bihormonal_112


title: P60_GcgPpy_Bihormonal_10


title: 13-056-GFM-IFNgamma


title: P60_GcgPpy_Bihormonal_1


title: 13-054-CC-unstim


title: 13-054-CC-LPS


title: WT_Zymd_2

city: Jinan

first: Xiaochen

last: Cheng

state: Shandong

address: 44 Wenhua Xi Rd.

institute: Shandong University

description: Library name: WT_Zymd_2

data_processing:
Sequence reads were trimmed for adapters and low-quality bases using fastp (v0.23.2) with default parameters.
Assembly: GRCm39
Supplementary files format and content: txt file contains gene-level read counts for each sample

source_name: BMDM, TBK1fl/fl, Zymd, 2 h

growth_protocol: Mice were housed under specific-pathogen-free conditions with free access to food and water. Bone marrow cells were flushed from femurs and tibias of 6–8 week old mice and cultured in RPMI-1640 medium supplemented with 10% FBS and 20 ng/ml M-CSF for 7 days to generate BMDMs.

extract_protocol:
Total RNA was was conducted by BGI (Beijing Genomics Institute) folling the manufacturer’s protocol. RNA quality was assessed using a Bioanalyzer.
The cDNA library was prepared using the Illumina TruSeq Stranded mRNA Sample Preparation Kit (Illumina) following the manufacturer’s protocol

treatment_protocol: BMDMs were treated with heat-killed Candida albicans hyphae (HKCA-H), yeast form (HKCA-Y), Zymosan depleted particles (Zymd), or PBS as control for 2 h.

value: Bone marrow-derived macrophages

value: Macrophage

value: Zymd


title: P60_GcgPpy_Bihormonal_105


title: P60_alpha_7

source_name: pancreatic P60 α cell, scRNAseq

value: GcgGFP


title: P60_alpha_8


title: P60_alpha_68


title: P60_GcgPpy_Bihormonal_104


title: P60_alpha_9


title: WT_HKCA-Y_3

description: Library name: WT_HKCA-Y_3

source_name: BMDM, TBK1fl/fl, HKCA-Y, 2 h

value: HKCA-Y


title: 13-054-CC-IFNgamma


title: 13-056-GFM-unstim


title: WT_HKCA-Y_2

description: Library name: WT_HKCA-Y_2


title: P60_alpha_65

value: pancreas


title: P60_alpha_67

value: islet cell


title: 13-051-NA-unstim


title: 13-051-NA-LPS


title: P60_GcgPpy_Bihormonal_101


title: WT_HKCA-Y_1

description: Library name: WT_HKCA-Y_1


title: P60_alpha_63


title: WT_Zymd_3

description: Library name: WT_Zymd_3


title: P60_alpha_64


title: WT_HKCA-H_3

description: Library name: WT_HKCA-H_3

source_name: BMDM, TBK1fl/fl, HKCA-H, 2 h

value: HKCA-H


title: P60_alpha_62

value: Male


title: P60_alpha_61


title: WT_HKCA-H_2

description: Library name: WT_HKCA-H_2


title: P60_alpha_60


title: pancreatic islet, P60,SstBFP, biol rep3, 10x Genomics scRNAseq

description: 10x Genomics

data_processing:
For 10x Genomics scRNA-seq, the demultiplexing, barcoded processing, gene counting and aggregation were made using the Cellranger toolkit (v3.1.0; https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) with default settings
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

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 10x Genomics, the procedure was performed according to the user guide of Chromium Single Cell 3’ Reagent Kits v3 from 10× Genomics.
10x Genomics scRNA-seq

value: SstBFP


title: WT_Zymd_1

description: Library name: WT_Zymd_1


title: P60_alpha_6


title: WT_HKCA-H_1

description: Library name: WT_HKCA-H_1


title: P60_alpha_59


title: P60_alpha_58


title: P60_alpha_57


title: pancreatic islet, P60,SstBFP, biol rep2, 10x Genomics scRNAseq

description: 10x Genomics


title: WT_CTRL_3

description: Library name: WT_CTRL_3

source_name: BMDM, TBK1fl/fl, PBS, 2 h

value: PBS


title: P60_alpha_66


title: pancreatic islet, P60,SstBFP, biol rep1, 10x Genomics scRNAseq

description: 10x Genomics


title: P60_alpha_55


title: P60_alpha_56


title: P60_alpha_53


title: WT_CTRL_2

description: Library name: WT_CTRL_2


title: KO_Zymd_3

description: Library name: KO_Zymd_3

source_name: BMDM, TBK1fl/fl Lyz2-Cre, Zymd, 2 h

value: TBK1fl/fl Lyz2-Cre


title: P60_alpha_52


title: pancreatic islet, P60,Ins1RFP, 10x Genomics scRNAseq

description: 10x Genomics


title: pancreatic islet, P60,PpymNeptune, biol rep2, 10x Genomics scRNAseq

description: 10x Genomics

value: PpymNeptune


title: P60_alpha_54


title: KO_Zymd_1

description: Library name: KO_Zymd_1


title: KO_Zymd_2

description: Library name: KO_Zymd_2


title: P60_alpha_51


title: pancreatic islet, P60,PpymNeptune, biol rep1, 10x Genomics scRNAseq

description: 10x Genomics


title: P60_alpha_5


title: 13-051-NA-IFNgamma

source_name: Brain

value: Brain

value: Microglia


title: pancreatic islet, P60,Ins1BFP, biol rep2, 10x Genomics scRNAseq

description: 10x Genomics


title: KO_HKCA-Y_3

description: Library name: KO_HKCA-Y_3

source_name: BMDM, TBK1fl/fl Lyz2-Cre, HKCA-Y, 2 h


title: P60_alpha_49


title: P60_alpha_48


title: P60_alpha_47


title: P60_alpha_45


title: KO_HKCA-Y_2

description: Library name: KO_HKCA-Y_2


title: P60_alpha_44


title: KO_HKCA-Y_1

description: Library name: KO_HKCA-Y_1


title: pancreatic islet, P60,GcgGFP, biol rep2, 10x Genomics scRNAseq

description: 10x Genomics


title: pancreatic islet, P60,Ins1BFP, biol rep1, 10x Genomics scRNAseq

description: 10x Genomics


title: P60_alpha_50


title: P60_alpha_42


title: P60_alpha_41


title: KO_HKCA-H_2

description: Library name: KO_HKCA-H_2

source_name: BMDM, TBK1fl/fl Lyz2-Cre, HKCA-H, 2 h


title: pancreatic islet, P60,GcgGFP, biol rep1, 10x Genomics scRNAseq

description: 10x Genomics


title: P60_alpha_46


title: P60_alpha_40


title: P60_alpha_43


title: KO_HKCA-H_1

description: Library name: KO_HKCA-H_1


title: KO_CTRL_3

description: Library name: KO_CTRL_3

source_name: BMDM, TBK1fl/fl Lyz2-Cre, PBS, 2 h


title: P60_alpha_38


title: KO_HKCA-H_3

description: Library name: KO_HKCA-H_3


title: P60_alpha_36


title: P60_alpha_39


title: P60_alpha_37


title: DSP-1001660020631-H-F01, NPC-25_011_PanCK+, NanoString GeoMx DSP

city: HK

first: Lai Shun Dittman

last: CHUNG

state: HK

address: 21 Sassoon Road, Pokfulam

department: Department of Clinical Oncology

institute: the University of Hong Kong

description:
Library name: DSP-1001660020631-H-F01
Whole transcriptom atlas (WTA) by NanoString GeoMx Digial Spatial Profilier

data_processing:
After quality control, batch effect removal, and Q3 normalisation using the top 25% of expressers to normalize across region of interest (ROI). The counts of the oligonucleotide tags were finally used to calculate the abundance of the corresponding mRNAs.
Assembly: hg38 & EBV genome (NC_007605)
Supplementary files format and content: .dcc and .pkc
Library strategy: Spatial Transcriptomics

source_name: primary nasopharyngeal carcinoma

extract_protocol:
Clinical NPC FFPE samples were sectioned into 5-µm slide
tissue sections were fluorescently stained with DNA dye (SYTO 13) and the primary antibodies targeting CD20 (NanoString Technologies, clone ID: IGEL/773), CD45 (NanoString Technologies, clone ID: D9M8I), PanCK (NanoString Technologies, clone ID: AE-1/AE-3), as well as the secondary antibody (Thermofisher Goat Anti-rabbit, A-11012). RNA probes coupled with photocleavable oligonucleotide barcodes were used to bind specifically to target mRNAs  during the incubation process on the DSP platform on the basis of in situ hybridisation. Then, each segment was exposed to UV radiation, detaching the barcodes from the probes/antibodies. The cleaved barcodes in units of segments were then collected into multiwell plates for next-generation sequencing on an Illumina sequencer.

value: primary nasopharyngeal carcinoma

value: MET


title: DSP-1001660020631-H-F05, NPC-27_013_PanCK+, NanoString GeoMx DSP

description:
Library name: DSP-1001660020631-H-F05
Whole transcriptom atlas (WTA) by NanoString GeoMx Digial Spatial Profilier

value: nonMET


title: KO_CTRL_2

description: Library name: KO_CTRL_2

value: Bone marrow-derived macrophages

value: Macrophage


title: P60_alpha_35

value: GcgGFP


title: DSP-1001660020631-H-F03, NPC-26_012_PanCK+, NanoString GeoMx DSP

description:
Library name: DSP-1001660020631-H-F03
Whole transcriptom atlas (WTA) by NanoString GeoMx Digial Spatial Profilier


title: P60_alpha_4


title: DSP-1001660020631-H-E11, NPC-24_010_PanCK+, NanoString GeoMx DSP

description:
Library name: DSP-1001660020631-H-E11
Whole transcriptom atlas (WTA) by NanoString GeoMx Digial Spatial Profilier


title: DSP-1001660020631-H-E09, NPC-23_009_PanCK+, NanoString GeoMx DSP

description:
Library name: DSP-1001660020631-H-E09
Whole transcriptom atlas (WTA) by NanoString GeoMx Digial Spatial Profilier


title: P60_alpha_32


title: MEF_PUS10KO_H3K4me3

city: Lund

first: Phuong

last: Cao Thi Ngoc

address: BMC, B1222b, Klinikgatan 26

country: Sweden

institute: Lund University

description: Library name: Sample 4

library_source: genomic

data_processing:
All paired-end reads were aligned to the mouse genome sequence using hisat2 program with parameters --no-mixed --no-discordant --no-spliced-alignment, and peaks for H3K4me3 were called using MACS2 from bam files. Signal profiles of H3K4me3 were plotted by deepTools.
Assembly: mm10
Supplementary files format and content: bigwig files
Library strategy: CUT&Run

molecule: genomic DNA

source_name: Mouse embryonic fibroblasts

extract_protocol:
5 × 105 WT and Pus10KO cells were washed twice (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 1× Roche cOmplete protease inhibitors) and attached to 10 μL (per cell line per antibody) ConA-coated magnetic beads (Bangs Laboratories) that had been pre-activated in binding buffer (20 mM HEPES pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). Cells were then resuspended in 50 μL buffer (20 mM HEPES pH 7.5, 0.15 M NaCl, 0.5 mM Spermidine, 1× Roche complete protease inhibitors, 0.05% w/v digitonin, 2 mM EDTA) containing 1:50 dilution of the primary antibody (goat anti-rabbit IgG (Abcam, CAT#ab97047), rabbit anti-H3K4me3 (Active motif CAT#39159) and incubated at 4 °C overnight. Beads were washed thoroughly with digitonin buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1× Roche cOmplete protease inhibitors, 0.05% digitonin). After the last wash, pA-MNase (a generous gift from Steve Henikoff) was added in digitonin buffer and incubated with the cells at 4 °C for 1 hr. Bead-bound cells were washed twice, resuspended in 100 μL digitonin buffer, and chilled to 0–2 °C. Genome cleavage was stimulated by addition of 2 mM CaCl2 at 0 °C for 30 min. The reaction was quenched in 100 mL 2 stop buffer (0.35 M NaCl, 20 mM EDTA, 4mM EGTA, 0.05% digitonin, 50 ng/mL glycogen, 50 ng/mL RNase A and vortexing. After 10 min incubation at 37 °C to release cleaved fragments, cells and beads were pelleted by centrifugation (16,000 × g, 5 min, 4 °C) and the supernatant purified by a PCR clean-up kit (Macherey-Nagel).
Illumina sequencing libraries were prepared using the Hyperprep kit (KAPA) with unique dual indexed adapters (KAPA), pooled and sequenced on a Nextseq500 instrument (Illumina).

value: Mouse embryonic fibroblasts

value: PUS10 KO


title: P60_alpha_34

value: pancreas

value: islet cell


title: P60_alpha_33

value: Male


title: DSP-1001660020631-H-E07, NPC-22_008_PanCK+, NanoString GeoMx DSP

description:
Library name: DSP-1001660020631-H-E07
Whole transcriptom atlas (WTA) by NanoString GeoMx Digial Spatial Profilier


title: P60_alpha_31


title: DSP-1001660020631-H-E05, NPC-21_007_PanCK+, NanoString GeoMx DSP

description:
Library name: DSP-1001660020631-H-E05
Whole transcriptom atlas (WTA) by NanoString GeoMx Digial Spatial Profilier


title: MEF_H3K4me3

description: Library name: Sample 2

value: WT


title: P60_alpha_30


title: P60_alpha_3


title: DSP-1001660020631-H-E02, NP-3_005_PanCK+, NanoString GeoMx DSP

description:
Library name: DSP-1001660020631-H-E02
Whole transcriptom atlas (WTA) by NanoString GeoMx Digial Spatial Profilier

value: Normal


title: P60_alpha_29


title: P60_alpha_27


title: DSP-1001660020631-H-E01, NPC-17_004_PanCK+, NanoString GeoMx DSP

description:
Library name: DSP-1001660020631-H-E01
Whole transcriptom atlas (WTA) by NanoString GeoMx Digial Spatial Profilier


title: P60_alpha_28


title: P60_alpha_26


title: P60_alpha_24


title: P60_alpha_25


title: Organoid_ATF3-/-KRAS_repl 2

city: London

first: Christopher

middle: L

last: Pin

state: Ontario

address: 1151 Richmond St

country: Canada

institute: University of Western Ontario

description: Batch org2

data_processing:
Quality check was performed using Fastqc
Reads were aligned to mouse genome mm10 and sorted by coordinate using STAR 2.7.9a
Gene counts were generated using the featureCounts function of the Subread aligner v2.0.3
Subsequent differential expression analysis was performed using the DESeq2 v1.38.3
Assembly: mm10
Supplementary files format and content: tab delimited format (txt) includes raw counts for each sample.

source_name: Pancreas

extract_protocol:
RNA was isolated from pancreatic tissue and isolated acinar cells 22 days after initial TX gavage using Trizol (ThermoFisher Scientific, 15596018) and the PureLink RNA mini kit (ThermoFisher Scientific, 12183018A). RNA from organoids was isolated using RNeasy Mini Kit (Qiagen, cat #74104).
Illumina NextSeq High Output 150 cycle sequencing kit was used for library making following rRNA reduction.

value: Pancreas

value: Organoid culture


title: MEF_IgG

description: Library name: Sample 1


title: DSP-1001660020631-H-D02, NP-2_023_PanCK+, NanoString GeoMx DSP

description:
Library name: DSP-1001660020631-H-D02
Whole transcriptom atlas (WTA) by NanoString GeoMx Digial Spatial Profilier


title: P60_alpha_22


title: P60_alpha_23


title: DSP-1001660020631-H-D01, NP-1_022_PanCK+, NanoString GeoMx DSP

description:
Library name: DSP-1001660020631-H-D01
Whole transcriptom atlas (WTA) by NanoString GeoMx Digial Spatial Profilier


title: Organoid_ATF3-/-KRAS_repl 1

description: Batch org2


title: P60_alpha_21


title: MEF_PUS10KO_IgG

description: Library name: Sample 3


title: Organoid_KRAS_repl 2

description: Batch org2


title: P60_alpha_2


title: P60_alpha_19


title: P60_alpha_20


title: DSP-1001660020631-H-C10, NPC-15_019_PanCK+, NanoString GeoMx DSP

description:
Library name: DSP-1001660020631-H-C10
Whole transcriptom atlas (WTA) by NanoString GeoMx Digial Spatial Profilier


title: DSP-1001660020631-H-C12, NP-1_021_PanCK+, NanoString GeoMx DSP

description:
Library name: DSP-1001660020631-H-C12
Whole transcriptom atlas (WTA) by NanoString GeoMx Digial Spatial Profilier


title: P60_alpha_18


title: P60_alpha_16


title: P60_alpha_17


title: Organoid_ATF3-/-KRAS_repl 3

description: Batch org1


title: DSP-1001660020631-H-D11, NPC-16_003_PanCK+, NanoString GeoMx DSP

description:
Library name: DSP-1001660020631-H-D11
Whole transcriptom atlas (WTA) by NanoString GeoMx Digial Spatial Profilier


title: Organoid_KRAS_repl 1

description: Batch org1


title: Tissue_ATF3-/-KRAS_repl 3

value: Tamoxifen oral gavage


title: P60_alpha_15


title: DSP-1001660020631-H-C03, NPC-13_014_PanCK+, NanoString GeoMx DSP

description:
Library name: DSP-1001660020631-H-C03
Whole transcriptom atlas (WTA) by NanoString GeoMx Digial Spatial Profilier


title: DSP-1001660020631-H-C02, NPC-12_013_PanCK+, NanoString GeoMx DSP

description:
Library name: DSP-1001660020631-H-C02
Whole transcriptom atlas (WTA) by NanoString GeoMx Digial Spatial Profilier


title: P60_alpha_12


title: Tissue_ATF3-/-KRAS_repl 1


title: Tissue_ATF3-/-KRAS_repl 2


title: P60_alpha_14


title: P60_alpha_13


title: P60_alpha_10


title: DSP-1001660020631-H-B12, NPC-11_012_PanCK+, NanoString GeoMx DSP

description:
Library name: DSP-1001660020631-H-B12
Whole transcriptom atlas (WTA) by NanoString GeoMx Digial Spatial Profilier


title: P60_alpha_11


title: Organoid_KRAS_repl 3

description: Batch org1


title: Acinar_WT_repl 3

description: Batch acini2


title: P60_alpha_1


title: ΔcueR strain_rep3

city: Yangzhou

first: Chengkun

last: Zheng

address: No.48 East Wenhui Road

institute: Yangzhou university

description:
Library name: CueR3
cueR3_FPKM

data_processing:
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.
Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3. (Langmead, B. and S. L. Salzberg, 2012).
HTSeq v0.6.1 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 (Trapnell, Cole, et al., 2010).
Assembly: Vibrio parahaemolyticus RIMD2210633, complete genome (NC_004603.1; NC_004605.1)
Supplementary files format and content: gene expression (read counts and fpkm for each strain).

organism: Vibrio parahaemolyticus

growth_protocol: The Vibrio parahaemolyticus RIMD 2210633 and ΔcueR strains were cultured in LB at 37℃ until the early-exponential phase (OD600 of 0.6–0.8).

extract_protocol:
RNA was extracted using an Eastep Super Total RNA Isolation Kit (Promega, Shanghai, China), according to the manufacturer’s instructions. RNA integrity and concentration were evaluated by gel electrophoresis and spectrophotometric analysis, respectively.
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: The strains were treated with 1 mM Cu for 15 min.

value: cueR knockout


title: DSP-1001660020631-H-B10, NPC-10_011_PanCK+, NanoString GeoMx DSP

description:
Library name: DSP-1001660020631-H-B10
Whole transcriptom atlas (WTA) by NanoString GeoMx Digial Spatial Profilier

value: primary nasopharyngeal carcinoma


title: ΔcueR strain_rep1

description:
Library name: CueR1
cueR1_FPKM


title: ΔcueR strain_rep2

description:
Library name: CueR2
cueR2_FPKM


title: DSP-1001660020631-H-B08, NPC-9_010_PanCK+, NanoString GeoMx DSP

description:
Library name: DSP-1001660020631-H-B08
Whole transcriptom atlas (WTA) by NanoString GeoMx Digial Spatial Profilier

value: MET


title: Acinar_WT_repl 1

description: Batch acini1


title: DSP-1001660020631-H-C06, NPC-14_016_PanCK+, NanoString GeoMx DSP

description:
Library name: DSP-1001660020631-H-C06
Whole transcriptom atlas (WTA) by NanoString GeoMx Digial Spatial Profilier


title: 10x Visium Spatial Transcriptomics, FFPE slides, patient1

description:
Library name: Spatial_Transcriptomics_FFPE_NPCpatient1
10x Visium spatial transcriptome sequencing

data_processing:
The spatial transcriptome library was sequenced on a NovaSeq 6000 (Illumina) and mapped to the human genome (hg38) using Spatial Ranger (v 1.3.1, 10× Genomics). The processed gene-voxel matrices  were further analyzed in Seurat (v 4.0). The spatial sequencing data were normalized using the SCTransform function followed by PCA reduction. Since each spatial spot contained multiple cells with varied lineages, we deconvoluted the spatial data using the SCTransformed NPC scRNA-seq data as a reference and estimated the underlying cellular composition in each voxel via the FindTransferAnchors function (normalization method = “SCT”) and the TransferData function (anchorset = anchors identified by the FindTransferAnchors function), implemented in Seurat (v 4.0).
Assembly: hg38 & EBV genome (NC_007605)
Supplementary files format and content: barcode.tsv.gz, matrix.mtx.gz, features.tsv.gz
Supplementary files format and content: aligned_fiducials.jpg, detected_tissue_image.jpg, scalefactors_json.json, tissue_hires_image.png, tissue_lowres_image.png, tissue_positions_list.csv
Library strategy: Spatial Transcriptomics

source_name: Tissue

growth_protocol: FFPE slides

extract_protocol:
tissue optimization experiments were conducted using the Visium spatial tissue optimization slide & reagents kit (10× Genomics) to determine the RNA quality (RIN > 7.0) and optimal permeabilization time. 6-minute tissue permeabilization yielded the highest fluorescence signal in both frozen sections. The frozen tissues were placed onto Visium spatial gene expression slide (10× Genomics), fixed, and permeabilized to release RNA, which bonded to adjacent capture probes.
RNA reverse transcription, cDNA synthesis, denaturation and amplification, quality control as well as spatial gene library construction were performed using Visium spatial gene expression reagents kit (10× Genomics).

treatment_protocol: primary and treatment-naïve NPC patient

value: NPC biopsy

value: No treatment


title: DSP-1001660020631-H-B06, NPC-8_009_PanCK+, NanoString GeoMx DSP

description:
Library name: DSP-1001660020631-H-B06
Whole transcriptom atlas (WTA) by NanoString GeoMx Digial Spatial Profilier


title: The wild type strain_rep3

description:
Library name: WT3
WT3_FPKM


title: L1EID2100342-Ctrl3.R1.raw.fastq.gz

city: Tianjin

first: Zhiqiang

last: Liu

address: 22 Qixiangtai Rd

department: Pathophysiology

institute: Tianjin Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: Homo sapiens hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: blood

growth_protocol: LP-1 were cultured in RPMI-1640 medium with 15% FBS.

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Using short-hairpin RNA (shRNA) depleted RNF5 expression in LP-1 cells

value: blood

value: tumor cell

value: Ctrl


title: The wild type strain_rep2

description:
Library name: WT2
WT2_FPKM


title: Acinar_ATF3-/-KRAS_repl 2

description: Batch acini2


title: DSP-1001660020631-H-B04, NPC-7_008_PanCK+, NanoString GeoMx DSP

description:
Library name: DSP-1001660020631-H-B04
Whole transcriptom atlas (WTA) by NanoString GeoMx Digial Spatial Profilier


title: DSP-1001660020631-H-B02, NPC-6_007_PanCK+, NanoString GeoMx DSP

description:
Library name: DSP-1001660020631-H-B02
Whole transcriptom atlas (WTA) by NanoString GeoMx Digial Spatial Profilier


title: L1EID2100341-Ctrl2.R1.raw.fastq.gz


title: The wild type strain_rep1

description:
Library name: WT1
WT1_FPKM


title: Acinar_ATF3-/-KRAS_repl 1

description: Batch acini1


title: L1EID2100340-Ctrl1.R1.raw.fastq.gz


title: DSP-1001660020631-H-A12, NPC-5_006_PanCK+, NanoString GeoMx DSP

description:
Library name: DSP-1001660020631-H-A12
Whole transcriptom atlas (WTA) by NanoString GeoMx Digial Spatial Profilier


title: DSP-1001660020631-H-A09, NPC-4_004_PanCK+, NanoString GeoMx DSP

description:
Library name: DSP-1001660020631-H-A09
Whole transcriptom atlas (WTA) by NanoString GeoMx Digial Spatial Profilier

value: nonMET


title: Acinar_KRAS_repl 2

description: Batch acini2


title: TWGBS batch_C_ddm1_2_G6,rep2

city: WIEN

first: Pierre

last: Bourguet

address: Dr. Bohr Gasse 3

country: Austria

institute: GMI

description: Library name: TWGBS_batch_C_ddm1_2_G6_rep2

data_processing:
Libraries for cdca7α/β and ddm1 mutants (Fig. 2, 3) were randomly subsampled to 30 million reads to improve depth homogeneity, since there were up to 2-fold more reads in some samples. The data were analyzed with the nfcore methylseq pipeline v2.3.0 (https://nf-co.re/methylseq) (Ewels et al., 2020) with Nextflow (v22.10.7). Cytosine positions covered by fewer than 3 reads (--meth_cutoff 3) were excluded. Tagmentation creates gaps in the double-stranded DNA which are later filled by unmethylated cytosines during gap repair. These nucleotides were excluded from the analysis by trimming reads with the "clip" and "ignore" options, using M-bias plots to ensure the removal of unmethylated fragment ends. The parameters were as follow: --meth_cutoff 4 --comprehensive --cytosine_report --clip_r1 14 --three_prime_clip_r1 4 --three_prime_clip_r2 2 --ignore_3prime_r2 17. Note that the unmethylated cytosines are incorporated at the 5' end of read 2, while the options mentioned above suggest we ignored the 3' end of read 2 instead, but methylseq v2.3.0 had an issue which made it clip the wrong end of read 2 (see https://github.com/nf-core/methylseq/issues/299). Using M-bias plots, we noticed a 5' bias on read 1 that resembled the Tn5 sequence bias (Wolpe et al. 2023), and removed it by clipping 14 nucleotides at the 5' end of read 1. We also excluded additional small methylation biases at the 3' end of read 1 and read 2.
Assembly: TAIR10
Supplementary files format and content: methylation ratios provided for CG, CHG and CHH as bigwig files

organism: Arabidopsis thaliana

source_name: 31-day-old rosette leaves

growth_protocol: grown in soil in long days at 21°C in a climatic chamber

extract_protocol:
Genomic DNA was extracted from rosette leaves with the DNeasy Plant Pro kit (Qiagen, reference 69206), following the manufacturer’s instructions.
Illumina libraries of sodium bisulfite-converted DNA were prepared with a tagmentation-based approach (Wang et al. 2013) with modifications (Montgomery and Berger, 2023, bioRxiv). Briefly, we tagmented 50 ng of DNA with Tn5 (Molecular Biology Services, IMP, Vienna, Austria). Tagmented DNA was purified with the Zymo DNA Clean and Concentrator kit (Zymo Research) instead of SPRI beads. After oligonucleotide replacement, gap repair, and purification, we used the entirety of the eluted DNA for bisulfite conversion, which was performed with the EZ DNA Methylation-Gold Kit from Zymo (reference D5006). The rest of the protocol was performed as indicated by Wang et al (2013). Directional libraries were amplified with Nextera-compatible unique dual indices and sequenced on a NovaSeq 6000 instrument using an S4 flow cell to generate paired-end 150 bp reads with around 25 million reads per sample.

value: 31-day-old rosette leaves

tag: batch

value: C


title: TWGBS batch_C_ddm1_2_G3,rep2

description: Library name: TWGBS_batch_C_ddm1_2_G3_rep2


title: Acinar_WT_repl 2

description: Batch acini2


title: Acinar_KRAS_repl 3

description: Batch acini2


title: TWGBS batch_C_ddm1_2_G6,rep1

description: Library name: TWGBS_batch_C_ddm1_2_G6_rep1


title: DSP-1001660020631-H-A07, NPC-3_003_PanCK+, NanoString GeoMx DSP

description:
Library name: DSP-1001660020631-H-A07
Whole transcriptom atlas (WTA) by NanoString GeoMx Digial Spatial Profilier


title: Acinar_KRAS_repl 1

description: Batch acini1


title: TWGBS batch_C_ddm1_2_G3,rep1

description: Library name: TWGBS_batch_C_ddm1_2_G3_rep1


title: L1EID2100337-KD1.R1.raw.fastq.gz

value: RNF5 KD


title: DSP-1001660020631-H-A05, NPC-2_002_PanCK+, NanoString GeoMx DSP

description:
Library name: DSP-1001660020631-H-A05
Whole transcriptom atlas (WTA) by NanoString GeoMx Digial Spatial Profilier


title: MEF PUS10KO small RNA-seq #3

data_processing:
The raw sequence data were trimmed the 3’ adaptor sequence (TGGAATTCTCGGGTGCCAAGG) by cutadapt v2.9 with parameter -m set to 23. The sequence reads were aligned to an rRNA reference using Bowtie v.1.2.2.
The unaligned reads were collected and the rRNA alignments were discarded to reduce rRNA contamination.
For tRNA analysis, Bowtie was used to map the reads to tRNA sequences from GtRNAdb2. The data was quantified using samtools idxstats and read counts generated for each tRNA isoacceptor were combined.
For tRNA fragments (tRFs) analysis, the reads were annotated using MINTmap software (Loher et al., 2017). Each fragment sequence was grouped according to tRNA isoacceptor, origin (5′, 3′ or internal) and length (fragment or half) according to MINTmap annotation. DESeq2 was used to determine differentially expressed tRFs in WT and PUS10-KO cells.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw count for tRFs

extract_protocol:
Total DNA-free RNA was isolated using Quick-RNA Miniprep Kit (Zymo Research). Following, RNA quality assessment by Bioanalyzer RNA 6000 Nano assay (Agilent).
Libraries were prepared using NEXTFLEX®Small RNA-Seq Kit v4 (Perkin-Elmer) according to manufacturer’s instructions. Library quality was verified by Bioanalyzer High Sensitivity DNA Analysis (Agilent). Sequencing was carried out on the Illumina NextSeq 500 System in a single-read approach.

value: Mouse embryonic fibroblasts

value: PUS10 KO


title: MEF PUS10KO small RNA-seq #4


title: DSP-1001660020631-H-A03, NPC-1_001_PanCK+, NanoString GeoMx DSP

description:
Library name: DSP-1001660020631-H-A03
Whole transcriptom atlas (WTA) by NanoString GeoMx Digial Spatial Profilier


title: 231-Input

first: Yongjia

last: Zeng

address: 10 You’anmen Outer West 1st Street

department: Biochemistry and Molecular Biology

institute: Capital Medical University

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads used the fastp software, version 0.19.11, parameter setting length_ required=50; n_ base_ limit=6; poly_ x_ min_ len=10. (1) Reads with a quality value less than 15 that exceeded 40% of the number of reads for that base were removed; (2) More than 6 reads with the base n were truncated; (3) Removal of reads with adapter (adaptor); (4) Reads shorter than 50 BP after trimming were discarded
ChIP-seq reads were aligned to the reference genome using BWA (burrows Wheeler aligner) software, version 0.7.12-r1039,.
To create ChIP-seq coverage plots, Frags were predicted using macs2 software (version 2.1.0)_ sizes.
Peaks were called uing MACS v2.1.0 with the significance cut-off p-value =0.001
Assembly: hg38
Supplementary files format and content: bigWig

source_name: Breast cancer

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: Breast cancer

value: epithelial cell


title: 231-UNC5D-ChIP

value: Antibody:UNC5D( PA5-116191)


title: TWGBS batch_C_Col_0,rep2

description: Library name: TWGBS_batch_C_Col_0_rep2