title: Endoderm Ngn3GFP HM 24ss b2 018, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_018


title: MB2-24h-W+FR (H) RIR110

status: Public on Jan 15 2025

type: SRA

city: Valencia

first: jaume

middle: f

last: martinez-garcia

state: Valencia

address: CPI, Edifici 8E, Campus UPV, Carrer Enginyer Fausto Elio s/n

department: Development and Hormonal Action in Plants

country: Spain

institute: IBMCP, CSIC

description: MB2-24h-W+FR (H)

library_source: transcriptomic

data_processing:
RNA-seq reads were mapped against Arabidopsis thaliana (TAIR10) reference genome with STAR/2.5.3a (ENCODE parameters)
Genes were quantified with RSEM/1.3.0 with default parameters
The gene annotation file was Arabidopsis_thaliana.TAIR10.36
Assembly: TAIR10
Supplementary files format and content: Raw counts (tsv)

molecule: total RNA

organism: Arabidopsis thaliana

source_name: floral bud

growth_protocol: Plants were grown on soil under long day (LD, 16 h light + 8 h dark) photoperiods in which white light (W) was generated by horizontal fluorescent tubes that provided  a PAR of ~100 µmol m-2 s-1, R:FR of ~3.0) until they flower

extract_protocol: Total RNA was extracted from the floral buds of a minimum of 4 inflorescences with the Maxwell 16 LEV simplyRNA Tissue Kit (Promega).

treatment_protocol: W treatment refer to long day (LD, 16 h light + 8 h dark) photoperiods provided by horizontal fluorescent tubes (W of a PAR of ~100 µmol m-2 s-1, R:FR of ~3.0). Simulated shade or W+FR treatments refer to LD photoperiods in with W was supplemented with far red light (FR) (W+FR, PAR of ~100 µmol m-2 s-1, R:FR of ~0.05-0.06) provided by LEDs.

tag: tissue

value: floral bud

tag: genotype

value: MB2 (pAP1:AP1-GR in ap1 cal background)

tag: treatment

value: 24h white + far red light


title: pos_P30007_1027_cs1

city: Stockholm

first: Anastasios

middle: Erik

last: Damdimopoulos

state: Huddinge

address: Hälsovägen 7c

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

data_processing:
Bcl files were converted and demultiplexed to fastq using the bcl2fastq (v2.20.0.422) program
STAR (2.7.10a) was used to index the human genome (Homo sapiens, GRCh38) obtained from Ensembl and then map the fastq files.
featureCounts (v2.0.6) was used to count mapped reads in annotated exons using gene annotations from Ensembl (Homo_sapiens.GRCh38.101.gtf).
Assembly: Homo sapiens, GRCh38
Supplementary files format and content: Tab delimited text file that contains Ensembl gene IDs and the gene raw counts, one column for each sample.

molecule: polyA RNA

organism: Homo sapiens

source_name: vaginal biopsy

extract_protocol:
Qiagen RNeasy mini kit.
Illumina stranded mRNA ligation protocol.

value: vaginal biopsy


title: Endoderm Ngn3GFP HM 24ss b2 017, scRNA-seq

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

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_017

library_source: transcriptomic single cell

data_processing:
For the Smart-seq3xpress scRNA-seq data, initial quality control was executed with FastQC version 0.11.9 under default settings. Index, primer, and adaptor sequences were then trimmed from paired-end reads using Trimmomatic version 0.39 with default parameters. Alignment of trimmed reads to the Mus musculus Genome assembly GRCm38 (mm10) was accomplished using HISAT version 2.1.0.
Assembly: mm10
Supplementary files format and content: Smart-seq3xpress output files: Tab-separated rexpression values matrix files

organism: Mus musculus

source_name: Endoderm

extract_protocol:
Endodermal and gut tissues from 9SS to 27SS, were enzymatically dissociated using 0.25% trypsin (Gibco, 25200-056) for roughly 4 minutes at 37°C. The reaction was halted by the addition of 0.4 volumes of fetal bovine serum (FBS). The resultant cell suspension was centrifuged at 1000 rpm for 5 minutes at 4°C, followed by supernatant removal. To prepare single-cell suspensions from endodermal and gut samples, cells were incubated with anti-EpCAM-APC antibody (Invitrogen, 17-5791-82, dilution 1:100) in FACS buffer (comprising HBSS buffer with 1% FBS) for 20 minutes at 4°C in darkness. Following incubation, cells were washed with FACS buffer and subjected to analysis and sorting using BD FACSAriaTM Fusion flow cytometers. Dead cells were excluded from the analysis through staining with 1 µg/mL DAPI (Macklin, D807022).
The Smart-seq3xpress libraries were prepared following Smart3-seq3xpress's protocols.

value: Endoderm

tag: strain

tag: time


title: pos_P30007_1025_cs4


title: pos_P30007_1021_cs3


title: pos_P30007_1023_cs5


title: pos_P30007_1019_cs2


title: MB2-24h-W (G) RIR107

description: MB2-24h-W (G)

value: 24h white light


title: pos_P30007_1018_cs3


title: Endoderm Ngn3GFP HM 24ss b2 015, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_015


title: pos_P30007_1012_cs4


title: MB2-24h-W (G) RIR106

description: MB2-24h-W (G)


title: Endoderm Ngn3GFP HM 24ss b2 014, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_014


title: pos_P31315_1031_cs2


title: pos_P30007_1011_cs5


title: pos_P31315_1044_cs4


title: MB2-24h-W (G) RIR105

description: MB2-24h-W (G)


title: Endoderm Ngn3GFP HM 24ss b2 013, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_013


title: MB2-0h-W (F) RIR86

description: MB2-0h-W (F)

value: 0h white light


title: pos_P31315_1019_cs5


title: Endoderm Ngn3GFP HM 24ss b2 012, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_012


title: pos_P31315_1010_cs2


title: pos_P31315_1009_cs4


title: MB2-24h-W+FR (H) RIR109

description: MB2-24h-W+FR (H)


title: MB2-0h-W (F) RIR85

description: MB2-0h-W (F)


title: Endoderm Ngn3GFP HM 24ss b2 011, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_011


title: pos_P31315_1005_cs3


title: Endoderm Ngn3GFP HM 24ss b2 010, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_010


title: Endoderm Ngn3GFP HM 24ss b2 016, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_016


title: pos_P31315_1001_cs2


title: WT-24h-W+FR (E) RIR83

description: WT-24h-W+FR (E)

value: WT


title: Endoderm Ngn3GFP HM 24ss b2 009, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_009


title: Endoderm Ngn3GFP HM 24ss b2 008, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_008


title: pos_P31315_1023_cs2


title: MB2-0h-W (F) RIR87

description: MB2-0h-W (F)


title: Endoderm Ngn3GFP HM 24ss b2 007, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_007


title: WT-24h-W+FR (E) RIR81

description: WT-24h-W+FR (E)


title: pos_P31315_1011_cs4


title: Endoderm Ngn3GFP HM 24ss b2 006, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_006


title: WT-24h-W (D) RIR79

description: WT-24h-W (D)


title: Endoderm Ngn3GFP HM 24ss b2 005, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_005


title: WT-24h-W (D) RIR78

description: WT-24h-W (D)


title: WT-24h-W (D) RIR77

description: WT-24h-W (D)


title: Endoderm Ngn3GFP HM 24ss b2 004, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_004


title: WT-24h-W+FR (E) RIR82

description: WT-24h-W+FR (E)


title: WT-3h-W+FR (C) RIR75

description: WT-3h-W+FR (C)

value: 3h white + far red light


title: Endoderm Ngn3GFP HM 24ss b2 003, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_003


title: WT-3h-W+FR (C) RIR73

description: WT-3h-W+FR (C)


title: Endoderm Ngn3GFP HM 24ss b2 002, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_002


title: Endoderm Ngn3GFP HM 24ss b2 001, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_001


title: WT-1h-W+FR (B) RIR67

description: WT-1h-W+FR (B)

value: 1h white + far red light


title: Endoderm Ngn3GFP HM 21ss b2 054, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_054


title: WT-3h-W+FR (C) RIR74

description: WT-3h-W+FR (C)


title: WT-1h-W+FR (B) RIR66

description: WT-1h-W+FR (B)


title: RPE_donor4_3_deep_group143

city: La Jolla

first: Ying

last: Yuan

address: Palmilla Dr.

department: MATS

country: USA

institute: UCSD

library_source: genomic

data_processing:
Reads from FASTQ files were mapped using YAP (Yet Another Pipeline) software (cemba-data v1.6.9), as previously described (PMID:38092918). First, FASTQ files were demultiplexed for each cell barcode. Next, reads were assessed for quality, then two-pass mapping was performed with bismark (v0.20, with bowtie2 v2.3). BAM file processing and QC was performed using samtools (v1.9) and Picard (v3.0.0). Chromatin contacts were called and methylome profiles were generated using Allcools (v1.0.23). All reads were mapped to the hg38 genome assembly. We filtered for high quality cells based on DNA methylation by requiring mapping rate for both reads R1 and R2 > 0.5; total final reads > 100,000; overall mCCC level < 0.03; overall mCH level < 0.2; and overall mCG level > 0.5. Single-cell DNA methylome profiles were stored in the 'all cytosine' (ALLC) format, a tab-separated table compressed and indexed by bgzip/tabix. We used the generate-dataset command in the ALLCools package to generate a methylome cell-by-feature tensor dataset (MCDS) in Zarr format.
Assembly: hg38
Supplementary files format and content: YAP output files: 3C.contact.tsv.gz
Supplementary files format and content: YAP output files: mC.allc.tsv.gz, mC.allc.tsv.gz.tbi
Library strategy: snm3c-seq

molecule: genomic DNA

source_name: RPE

extract_protocol:
The eye globes were collected from three unrelated human donors (aged 21, 27 and 43 years) with the collaboration of San Diego Eye Bank. The sample processing time starting from eye enucleation to dissection was restricted within 2 hours to identify the macula, a visible yellowish/whiteish indent that is slightly lateral to the optic disk inside the globe. Prior dissection, the eye globe with proper label was collected in a sterile moist chamber. At first the cornea was removed by cutting 2-3 mm around the limbus using a surgical blade. Pull off the iris and lens. This will leave you with the eye cup, which contains the posterior pole. After removing enough vitreous and aqueous fluid the temporal region can be located by two main blood vessels that curl around the macula. Using a sterile 3mm skin biopsy punch, the macula was collected. Sections were made for the other regions, temporal, nasal, superior and inferior. For all these regions, the retina and RPE tissue were separated and stored immediately in Liquid Nitrogen. Retina tissues were pulverized using a dounce tissue chamber and two pestles ("Loose" and "Tight") on ice for each sample. Pulverized retina tissues were resuspended in 1ml of chilled NIM-DP-L buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM Tris-HCl pH 7.5, 1 mM DTT, 1x protease inhibitor (Pierce), 1U μl-1 recombinant RNase inhibitor (Promega, PAN2515) and 0.1% Triton X-100). Tissue was dounce homogenized with a loose pestle (5-10 strokes) followed by a tight pestle (15-25 strokes) or until the solution was uniform. Nuclei were filtered using a 30 μm CellTrics filter (Sysmex, 04-0042-2316) into a LoBind tube (Eppendorf, 22431021). Nuclei were pelleted (at 1000 rcf, for 10 min at 4°C; Eppendorf, 5920R) then resuspended in 1mL PBS with 2% formaldehyde for crosslinking for 10 minutes at room temperature on a rotator. 2.5M glycine was added to achieve 0.22M glycine and incubated for 5 minutes at room temperature on a rotator. Nuclei were pelleted 1000 rcf, for 10 min at 4°Cpelleted (at 1000 rcf, for 10 min at 4°C; Eppendorf, 5920R) then resuspended in 1mL of cold PBS. Nuclei were then pelleted at 2,500 x g for 5 min at 4°C. All supernatant was removed and pellets were snap frozen in liquid nitrogen and stored at -80°C.
In situ 3C treatment was performed during the nucleus preparation, enabling the capture of the chromatin conformation modality as described previously (PMID: 31501549). These steps were performed using the Arima-3C BETA Kit (Arima Genomics). The nuclei were isolated and sorted into 384-well plates using previous described methods (PMID: 34616061). Briefly, nuclei were stained with DRAQ7 (ThermoFisher Scientific, D15106) and then processed for fluorescence-activated nucleus sorting (FANS) using the Sony SH800 cell sorter with single-cell (1 drop single) mode. The snm3C-seq samples were prepared according to a previously described library preparation protocol (PMID: 31501549,34616061). This protocol has been automated using the Beckman Biomek i7 instrument to facilitate large-scale applications. The snm3C-seq libraries were shallow sequenced on the Illumina NovaSeq 2000 to 2-10M reads to check quality. Successful libraries were deeply sequenced on the NovaSeq X Plus instrument, using one lane of 25B flow cell per 4 384-well plates and using 150 bp paired-end mode.

value: RPE

tag: age

tag: Sex

value: Male


title: Endoderm Ngn3GFP HM 21ss b2 053, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_053


title: RPE_donor4_2_deep_group139


title: RPE_donor4_3_deep_group144


title: RPE_donor4_1_deep_group136


title: RPE_donor4_2_deep_group138


title: WT-1h-W+FR (B) RIR65

description: WT-1h-W+FR (B)


title: WT-0h-W (A) RIR59

description: WT-0h-W (A)


title: Endoderm Ngn3GFP HM 21ss b2 052, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_052


title: RPE_donor4_2_deep_group140


title: RPE_donor4_1_deep_group134


title: RPE_donor4_3_deep_group142


title: RPE_donor4_1_deep_group135


title: RPE_donor4_3_deep_group141


title: RPE_donor4_2_deep_group137


title: RPE_donor4_1_deep_group133


title: RPE_donor3_3_deep_group131


title: RPE_donor3_3_deep_group132


title: Endoderm Ngn3GFP HM 21ss b2 051, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_051


title: RPE_donor3_2_deep_group127


title: RPE_donor3_2_deep_group128


title: WT-0h-W (A) RIR58

description: WT-0h-W (A)


title: RPE_donor3_3_deep_group129


title: Endoderm Ngn3GFP HM 21ss b2 049, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_049


title: Endoderm Ngn3GFP HM 21ss b2 050, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_050


title: WT-0h-W (A) RIR57

description: WT-0h-W (A)


title: RPE_donor3_1_deep_group124


title: MIA-PaCa-TKOv3-P8-ARC-500

city: Buffalo

first: Jianxin

last: Wang

state: NY

address: 665 Elm Street

department: Molecular and Cellular Biology

institute: Roswell Park Comprehensive Cancer Center

description: Library name: RS-04142268

data_processing:
Row fastq files are processed through the mageck(v.5.9) pipeline using the Toronto KnockOut (TKO) CRISPR Library - Version 3.
Supplementary files format and content: Tab delimited text file with guide RNAs in rows and samples in columns.
Library strategy: CRISPR

source_name: Mia-PaCa

growth_protocol: HCC1806 and  MiaPaCa-2 cell lines were  grown in RPMI and DMEM media respectively supplemented with 10% FBS. The cellswere maintained in 37°C with 5% CO2 and tested to be mycoplasma-free.

extract_protocol:
Genomic DNA exptration was carried out using the Wizard Genomic DNA purification kit (Promega, A1120)  according to the manufacturer's protocol
A two step PCR was performed to enrich guide RNA regions in the genome and to amplify the guide RNAs with Illumina TruSeq adapters with i5 and i7 indices.

treatment_protocol: The positive and negative selections of the guide sequences in HCC1806 and MiaPaCa-2 cells were carried out using 0.1% DMSO, INX-315 (500 nM). Palbocicli was used at 500 nM and 250 nM for HCC1806 and MiaPaCa-2 cell lines respectively.

tag: cell line

value: Mia-PaCa


title: Endoderm Ngn3GFP HM 21ss b2 047, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_047


title: MIA-PaCa-TKOv3-P8-Palbo-250

description: Library name: RS-04142269

value: Palbo P8, 250mM


title: RPE_donor3_1_deep_group122


title: RPE_donor3_2_deep_group125


title: RPE_donor3_2_deep_group126


title: MIA-PaCa-TKOv3-P1-control

description: Library name: RS-04142265

value: Control, P1


title: Endoderm Ngn3GFP HM 21ss b2 045, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_045


title: Endoderm Ngn3GFP HM 21ss b2 048, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_048


title: RPE_donor3_1_deep_group123


title: MIA-PaCa-TKOv3-P8-control

description: Library name: RS-04142266

value: Control, P8


title: RPE_donor2_3_deep_group120


title: RPE_donor3_3_deep_group130


title: HCC1806-TKO-ARC-500-P8    2

description: Library name: RS-03896496


title: Endoderm Ngn3GFP HM 21ss b2 046, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_046


title: Endoderm Ngn3GFP HM 21ss b2 043, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_043


title: Endoderm Ngn3GFP HM 21ss b2 044, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_044


title: RPE_donor2_3_deep_group118


title: RPE_donor2_3_deep_group119


title: HCC1806-TKO-DMSO-P8  1

description: Library name: RS-03896492


title: Endoderm Ngn3GFP HM 21ss b2 041, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_041


title: RPE_donor2_2_deep_group116


title: HCC1806-TKO-ARC-500-P8   1

description: Library name: RS-03896495


title: HCC1806-TKO-P0

description: Library name: RS-03896491

value: Control, P0


title: RPE_donor3_1_deep_group121


title: HCC1806-TKO-DMSO-P8   2

description: Library name: RS-03896493


title: Endoderm Ngn3GFP HM 21ss b2 040, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_040


title: RPE_donor2_2_deep_group114


title: RPE_donor2_3_deep_group117


title: RPE_donor2_1_deep_group111


title: RPE_donor1_3_deep_group108


title: Endoderm Ngn3GFP HM 21ss b2 039, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_039


title: Endoderm Ngn3GFP HM 21ss b2 042, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_042


title: RPE_donor2_2_deep_group113


title: RPE_donor2_1_deep_group110


title: RPE_donor2_2_deep_group115


title: Endoderm Ngn3GFP HM 21ss b2 038, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_038


title: RPE_donor2_1_deep_group112


title: HCC-TKO-T0

description: Library name: RS-03750342


title: RPE_donor1_3_deep_group106


title: RPE_donor1_2_deep_group104


title: RPE_donor1_3_deep_group105


title: RPE_donor2_1_deep_group109


title: HCC-palbo-TKO-P8

description: Library name: RS-03750344


title: RPE_donor1_3_deep_group107


title: RPE_donor1_2_deep_group103


title: HCC-DMSO-TKO-P8

description: Library name: RS-03750343


title: Endoderm Ngn3GFP HM 21ss b2 034, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_034


title: RPE_donor1_2_deep_group102


title: Retina_donor4_3_deep_group96

source_name: Retina

value: Retina


title: Endoderm Ngn3GFP HM 21ss b2 037, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_037


title: Endoderm Ngn3GFP HM 21ss b2 036, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_036


title: Endoderm Ngn3GFP HM 21ss b2 035, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_035


title: 206993480060_R01C01

type: genomic

city: Chicago

first: Drew

last: Duckett

state: IL

address: 541 N Fairbanks Ct, 8th Floor

department: Pathology

institute: Northwestern Medicine

description: SAMPLE 52

hyb_protocol: MethylationEPIC beadarrays were performed according to the Infinium HD Methylation Assay Protocol, as previously described with minor changes. Eight µl of restored FFPE bs-DNA was used for each sample and 28 µl of hybridization volume was used when loading the microarray.

scan_protocol: Samples were scanned using Illumina's iScan according to manufacturer's recommendations for infinuim arrays

data_processing: Bioconductor (Version 3.17) package minifi (Version 1.43) using function 'preprocessIllumina'  Average beta

label: biotin/DNP

source_name: Brain Metastasis

label_protocol: Bisulfite conversion: Samples ranging from 50 ng to 500 ng of FFPE DNA was pipetted into strip tubes and processed using the EZ-96 DNA Methylation kit (Zymo Research Corp., CA, USA) following the manufacturer's recommendations for Infinium assays.

extract_protocol: Samples included in the study were all formalin-fixed for 8 hours followed by paraffin-embedding (FFPE) and stored at room temperature. All samples were extracted using either Covaris (FFPE DNA Kit, Covaris, Inc., MA, USA) or Purigen Biosystems (FFPE DNA Kit, Purigen Biosystems, CA, USA) following the manufacturer’s instructions.

tag: tissue preparation

value: FFPE

tag: tumor type

value: Prostate adenocarcinoma


title: Endoderm Ngn3GFP HM 21ss b2 033, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_033


title: Endoderm Ngn3GFP HM 21ss b2 032, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_032


title: 206993480040_R05C01

description: SAMPLE 50

value: poorly differentiated carcinoma (unknown origin)


title: RPE_Donor1_1_deep_group100


title: Endoderm Ngn3GFP HM 21ss b2 031, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_031

value: Endoderm


title: Retina_donor4_2_deep_group92


title: 206993480060_R02C01

description: SAMPLE 53

value: lung adenocarcinoma


title: Retina_donor4_3_deep_group93


title: Endoderm Ngn3GFP HM 21ss b2 030, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_030


title: RPE_donor1_2_deep_group101


title: Retina_donor4_2_deep_group90


title: RPE_Donor1_1_deep_group99


title: 206772660112_R05C01

description: SAMPLE 49


title: 206993480040_R06C01

description: SAMPLE 51

value: esophageal adenocarcinoma


title: Retina_donor4_3_deep_group94

value: WT


title: RPE_Donor1_1_deep_group98


title: 206772660112_R04C01

description: SAMPLE 48


title: Retina_donor4_2_deep_group91


title: Retina_donor4_3_deep_group95


title: RPE_Donor1_1_deep_group97


title: Retina_donor4_1_deep_group88


title: Retina_donor4_1_deep_group87


title: Retina_donor4_1_deep_group85


title: 206522580083_R08C01

description: SAMPLE 46

value: pleomorphic dermal sarcoma


title: Retina_donor4_2_deep_group89


title: Endoderm Ngn3GFP HM 21ss b2 027, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_027


title: Retina_donor3_3_deep_group84


title: Retina_donor3_3_deep_group82


title: Endoderm Ngn3GFP HM 21ss b2 029, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_029


title: Retina_donor4_1_deep_group86


title: Endoderm Ngn3GFP HM 21ss b2 028, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_028


title: Endoderm Ngn3GFP HM 21ss b2 026, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_026


title: 206648960114_R02C01

description: SAMPLE 45


title: L-iKras 20 weeks ON 1, week OFF

city: Ann Arbor

first: Stefanie

last: Galban

state: MI

address: 109 Zina Pitcher Place

department: Radiology

institute: University of Michigan

description: 1 male L-iKras mouse and 1 female L-iKras mouse had induction of KrasG12D expression by adding doxycycline (Sigma-Aldrich, catalog number D9891) to drinking water at a concentration of 0.5 mg/ml for 20 weeks and mutant Trp53 expression by one-time intranasal instillation of adenovirus-Cre recombinase with 3x107 PFU/50 µL/mouse at study start. After 20 weeks, doxycycline was removed. Lung were harvested 1 week after doxycycline removal.

data_processing:
Raw data were processed and aligned by the University of Michigan Advanced Genomics Core. Cell Ranger count version 6.0.0 (10× Genomics, Pleasanton, CA) was used with default settings, with an initial expected cell count of 10,000.
Assembly: mm10-2020-A
Supplementary files format and content: Raw and filtered Cell Ranger outputs

source_name: Lung

extract_protocol:
Lung tissues were mechanically minced and enzymatically digested with collagenase P (1 mg/mL in Roswell Park Memorial Institute (RPMI) 1640) at 37°C for 30 minutes. Cell suspensions were filtered through 500 μm, 100 μm, and 40 μm mesh cell strainers. Dead cells were removed using the MACS Dead Cell Removal Kit (Miltenyi Biotec, catalog number 130-090-101). Single-cell complementary DNA libraries were prepared and sequenced at the University of Michigan Advanced Genomics Core using the 10× Genomics Platform
Samples were run using 50-cycle, paired-end reads on the HiSeq 4000 (Illumina, San Diego, CA) to a depth of 100,000 reads.

value: Lung

tag: number of_mice_pooled

tag: cell ranger_version

tag: genome


title: 206522580120_R01C01

description: SAMPLE 47

value: rencal cell carcinoma, TFE-3+


title: 206915410081_R04C01

description: SAMPLE 44

value: poorly differentiated carcinoma c/w lung primary


title: Endoderm Ngn3GFP HM 21ss b2 023, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_023


title: Endoderm Ngn3GFP HM 21ss b2 025, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_025


title: Retina_donor3_3_deep_group81

value: Male


title: 206915410081_R01C01

description: SAMPLE 43

value: breast adenocarcinoma


title: Retina_donor3_3_deep_group83


title: Retina_donor3_2_deep_group78


title: Endoderm_27ss_B1_scRNA-seq

description: 10x Genomics

data_processing:
For the 10x-v3 scRNA-seq data, raw data processing was conducted with Cell Ranger 6.0.0 using default settings, and alignment was performed against the mm10 reference genome (v1.2.0).
Assembly: mm10
Supplementary files format and content: Tab-seprated values files and matirx files

extract_protocol:
Endodermal and gut tissues from 9SS to 27SS, were enzymatically dissociated using 0.25% trypsin (Gibco, 25200-056) for roughly 4 minutes at 37°C. The reaction was halted by the addition of 0.4 volumes of fetal bovine serum (FBS). The resultant cell suspension was centrifuged at 1000 rpm for 5 minutes at 4°C, followed by supernatant removal. To prepare single-cell suspensions from endodermal and gut samples, cells were incubated with anti-EpCAM-APC antibody (Invitrogen, 17-5791-82, dilution 1:100) in FACS buffer (comprising HBSS buffer with 1% FBS) for 20 minutes at 4°C in darkness. Following incubation, cells were washed with FACS buffer and subjected to analysis and sorting using BD FACSAriaTM Fusion flow cytometers. Dead cells were excluded from the analysis through staining with 1 µg/mL DAPI (Macklin, D807022).
For 10x Genomics scRNA-seq, libraries were constructed using the Single Cell 3′ Reagent Kit v3.0 instructions from 10x Genomics, following manufacturer's protocols.

tag: batch

value: batch  1


title: Endoderm Ngn3GFP HM 21ss b2 022, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_022


title: Endoderm Ngn3GFP HM 21ss b2 021, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_021


title: Retina_donor3_2_deep_group80


title: Endoderm_24ss_B2_scRNA-seq

description: 10x Genomics

value: batch  2


title: 206522580146_R07C01

description: SAMPLE 39

value: renal clear cell carcinoma


title: RetinaDonor2_deep_group72

value: Retina


title: L-iKras 21 weeks ON

description: 1 male L-iKras mouse and 1 female L-iKras mouse had induction of KrasG12D expression by adding doxycycline (Sigma-Aldrich, catalog number D9891) to drinking water at a concentration of 0.5 mg/ml for 21 weeks and mutant Trp53 expression by one-time intranasal instillation of adenovirus-Cre recombinase with 3x107 PFU/50 µL/mouse at study start. Lungs were harvested 21 weeks after induction of KrasG12D and mutant Trp53.


title: 206648960034_R07C01

description: SAMPLE 37

value: FFPE


title: Retina_donor3_2_deep_group79


title: 206772660112_R01C01

description: SAMPLE 42


title: Endoderm Ngn3GFP HM 21ss b2 024, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_024


title: Retina_donor3_1_deep_group75


title: 206648960169_R07C01

description: SAMPLE 41


title: Retina_donor3_2_deep_group77


title: Endoderm_24ss_B1_scRNA-seq

description: 10x Genomics


title: Retina_donor3_1_deep_group76


title: 206522580146_R05C01

description: SAMPLE 38


title: RetinaDonor2_deep_group71


title: Endoderm_27ss_B2_scRNA-seq

description: 10x Genomics


title: 206522580045_R08C01

description: SAMPLE 36

value: high-grade neoplasm (likely prostate origin)


title: Endoderm_21ss_B2_scRNA-seq

description: 10x Genomics


title: Endoderm_21ss_B1_scRNA-seq

description: 10x Genomics


title: RetinaDonor2_deep_group70


title: RetinaDonor2_deep_group69


title: Endoderm Ngn3GFP HM 21ss b2 019, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_019


title: Retina_donor3_1_deep_group74


title: 206648960169_R06C01

description: SAMPLE 40


title: Endoderm Ngn3GFP HM 21ss b2 018, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_018


title: Endoderm_18ss_B2_scRNA-seq

description: 10x Genomics


title: Endoderm Ngn3GFP HM 21ss b2 015, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_015


title: 206522570158_R06C01

description: SAMPLE 35

value: renal carcinoma (favor papillary renal cell carcinoma)


title: Retina_Donor2_3_deep_group64


title: Endoderm Ngn3GFP HM 21ss b2 017, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_017

value: Endoderm


title: Endoderm Ngn3GFP HM 21ss b2 016, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_016


title: Endoderm_18ss_B1_scRNA-seq

description: 10x Genomics


title: RetinaDonor2_deep_group66


title: RetinaDonor2_deep_group67


title: Endoderm_15ss_B2_scRNA-seq

description: 10x Genomics


title: RetinaDonor2_deep_group68


title: Endoderm Ngn3GFP HM 21ss b2 014, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_014


title: Endoderm Ngn3GFP HM 21ss b2 020, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_020


title: 206467000124_R07C01

description: SAMPLE 32

value: adenocarcinoma (ddx:upper GI or pancreatobiliary)


title: Endoderm_15ss_B1_scRNA-seq

description: 10x Genomics


title: Retina_donor3_1_deep_group73


title: Endoderm Ngn3GFP HM 21ss b2 013, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_013


title: Endoderm Ngn3GFP HM 21ss b2 012, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_012


title: Endoderm_12ss_B2_scRNA-seq

description: 10x Genomics


title: Endoderm Ngn3GFP HM 21ss b2 011, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_011


title: 206522570158_R04C01

description: SAMPLE 33

value: colorecatal carcinoma


title: Retina_Donor2_3_deep_group63

value: WT


title: RetinaDonor1_deep_group60


title: 206522570158_R05C01

description: SAMPLE 34


title: Endoderm_12ss_B1_scRNA-seq

description: 10x Genomics


title: Endoderm Ngn3GFP HM 21ss b2 010, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_010


title: 206915410052_R07C01

description: SAMPLE 31

value: Prostate adenocarcinoma


title: RNA, islets, Clec KO RFD biol rep4

first: Emily

last: Walker

address: 1000 Wall Street

data_processing:
Alignment options followed ENCODE standards for RNA-seq. FastQC was used in an additional post-alignment step to ensure that only high-quality data were used for expression quantitation and differential expression. Reads were preprocessed by BBDuk which removes adapters, trims reads for quality from the 3′ end, and discards reads that are too short after trimming. Preprocessed reads were aligned by STAR aligner and quantification was done using featureCounts. FastQC reports, alignment statistics and rRNA/globin depletion rate QC information is automatically summarized by the MultiQC tool.Data were pre-filtered to remove genes with 0 counts in all samples. Differential gene expression analysis was performed using DESeq2, using a negative binomial generalized linear model (thresholds: linear fold change >1.5 or <-1.5, Benjamini-Hochberg FDR (Padj) <0.05). Plots were generated using variations of DESeq2 plotting functions and other packages with Genialis (Boston, MA, USA).
Assembly: Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR (v2.6.1b) and assigned count estimates to genes with RSEM (v1.3.1).
Supplementary files format and content: Tab-delimited text files include raw counts

source_name: islets

growth_protocol: Islets were cultured overnight after isolation prior to RNA isolation. Liver was flash frozen prior to RNA isolation.

extract_protocol:
For both islets and liver: Total RNA was isolated from cultured islets or frozen liver samples and DNase treated using commercially available kits (Omega Biotek and Ambion, respectively).
Libraries were constructed and subsequently subjected to 151 bp paired-end cycles on the NovaSeq-6000 platform (Illumina). FastQC (v0.11.8) was used to ensure the quality of data.
RNA-sequencing was performed by the Advanced Genomics Core at University of Michigan Medical School.

value: islets

value: Clec KO

tag: diet

value: RFD


title: Retina_Donor2_3_deep_group62

value: Male


title: Endoderm Ngn3GFP HM 21ss b2 008, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_008


title: RNA, islets, Clec KO RFD biol rep3


title: RNA, islets, Clec KO RFD biol rep2


title: Endoderm_09ss_B1_scRNA-seq

description: 10x Genomics


title: Endoderm Ngn3GFP HM 21ss b2 007, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_007


title: 206430120064_R07C01

description: SAMPLE 26

value: high-grade serous adenocarcinoma of the ovary


title: RNA, islets, Clec KO RFD biol rep1


title: Endoderm Ngn3GFP HM 21ss b2 006, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_006


title: 206430120064_R03C01

description: SAMPLE 29

value: lung mucinous adenocarcinoma


title: 206116790060_R01C01

description: SAMPLE 27

value: poorly differentiated carcinoma (ddx:gastrointestinal, pacreatobiliary or gastrointestinal-type gynecological carcinoma)


title: RNA, islets, Clec KO HFD biol rep5

value: HFD


title: 206430120064_R05C01

description: SAMPLE 24

value: Endometrioid endometrial adenocarcinoma


title: Endoderm Ngn3GFP HM 21ss b2 004, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_004


title: RNA, islets, Clec KO HFD biol rep4


title: RetinaDonor2_deep_group65

value: Retina


title: 206430120064_R06C01

description: SAMPLE 25

value: FFPE

value: ?breast adenocarcinoma


title: Endoderm Ngn3GFP HM 21ss b2 005, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_005

value: Endoderm


title: RNA, islets, Clec KO HFD biol rep3


title: 207255330123_R06C01

description: SAMPLE 20

source_name: Thyroid Tumor

value: Medullary Thyroid


title: RetinaDonor1_deep_group59


title: 206430120093_R01C01

description: SAMPLE 30

value: esophageal adenocarcinoma


title: Endoderm Ngn3GFP HM 21ss b2 003, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_003


title: 206430120064_R04C01

description: SAMPLE 28

value: colorecatal carcinoma


title: 207255330123_R04C01

description: SAMPLE 19


title: Retina_Donor2_3_deep_group61

value: WT


title: RetinaDonor1_deep_group57


title: RNA, islets, Clec KO HFD biol rep2

value: islets


title: Endoderm Ngn3GFP HM 21ss b2 002, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_002


title: RetinaDonor1_deep_group58


title: 206113360057_R05C01

description: SAMPLE 23

value: breast adenocarcinoma


title: RNA, islets, Clec KO HFD biol rep1

value: Clec KO


title: Endoderm Ngn3GFP HM 21ss b2 001, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_001


title: RetinaDonor1_deep_group53

value: Male


title: Endoderm Ngn3GFP HM 21ss b2 009, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_21ss_b2_009


title: RetinaDonor1_deep_group56


title: RetinaDonor1_deep_group55


title: Endoderm Ngn3GFP HM 18ss b2 017, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_18ss_b2_017


title: 207255330061_R03C01

description: SAMPLE 7


title: RetinaDonor1_deep_group54


title: Retina_Donor1_3_deep_group52


title: RNA, islets, Clec control RFD biol rep3

value: Clec control

value: RFD


title: 207255330123_R05C01

description: SAMPLE 8


title: 207255330123_R07C01

description: SAMPLE 9


title: RNA, islets, Clec control RFD biol rep2


title: Endoderm Ngn3GFP HM 18ss b2 015, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_18ss_b2_015


title: RNA, islets, Clec control RFD biol rep1


title: 206116800045_R04C01

description: SAMPLE 6

source_name: Kidney Tumor

value: renal clear cell carcinoma


title: Endoderm Ngn3GFP HM 18ss b2 014, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_18ss_b2_014


title: RNA, islets, Clec control HFD biol rep6

value: HFD


title: Endoderm Ngn3GFP HM 18ss b2 013, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_18ss_b2_013


title: Macula_donor4_3_deep_group48

source_name: Macula

value: Macula


title: RNA, islets, Clec control RFD biol rep4


title: RNA, islets, Clec control HFD biol rep5


title: E233S,Input

city: Qingdao

first: Qihong

last: Huang

state: Shandong

address: 72 Binhaidadao, Aoshanwei, Jimo

institute: Shandong University

data_processing:
Base calling were performed with Illumina CASAVA pipeline.
Reads were trimmed with Skewer （Jiang H,2014）to remove adapter or low quality bases. Any read with more than 10% N , with more than 50% low quality base(Q<5)  or less than 18nt after trimming was filtered out.
Bowtie2 (Langmead, B.,2012) was used to perform alignments of reads to a reference genome with the default parameters. Reads that MAPQ score less than 13 and duplicated reads were removed before peaking calling.
MASC 2 (Zhang Y,2008) was employed to call peak with a threshold of q 0.05. The gene that have functional components overlapping with the peaks or nearest the peak were considered as peak-related genes
Assembly: REY15A
Supplementary files format and content: bigwig, peakAnno.xlsx (except for Input sample)

organism: Saccharolobus islandicus

source_name: microbial cells

growth_protocol: S. islandicus strains were grown in MTSUV medium (Basic mineral medium+Typtone+Sucrose+Uracil+Vatamin) at 75 oC.

extract_protocol:
Formaldehyde was added to an exponentially growing culture at the final concentration of 1 % and the culture was incubated on a shaking platform for 15 min at room temperature for cross-linking. The whole cells were harvested by centrifugation at 5,000 g for 10 min and washed with PBS buffer. The pellet was resuspended in 3 mL TBSTT buffer (20 mM Tris, 150 mM NaCl, 0.1 % Tween-20, 0.1 % Triton X-100, pH 7.5) and sonicated on ice by JY92- Ⅱ Ultrasonicator (Scientz biotechnology, Ningbo, China) to obtained the DNA fragment with a size around 200-1000 bp. Immunoprecipitation was performed by incubating 5 µL anti-PerR antibody-coated protein A beads (Cytiva, USA) in TBSTT buffer.
ChIP-seq libraries were constructed using NEBNext DNA library prep kit per manufacturer’s instructions. 50ng of DNA was ligated to adaptor with NEBNext DNA library prep kit, after end repair and adenylation. Size selection and gel purification, followed by PCR with primers specific to the sequencing platform. Library concentration was quantified by Qubit® 2.0 Flurometer (Life Technologies, CA, USA) and quantitative PCR, and the insert size was assayed on Agilent Bioanalyzer 2100 system.

tag: cell type

value: microbial cells

value: wild type

tag: antibody

value: input


title: Endoderm Ngn3GFP HM 18ss b2 012, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_18ss_b2_012

tag: tissue

value: Endoderm


title: 206915410081_R02C01

description: SAMPLE 2

source_name: Breast Tumor

value: FFPE


title: Endoderm Ngn3GFP HM 18ss b2 011, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_18ss_b2_011

tag: genotype


title: RNA, islets, Clec control HFD biol rep3


title: E233S,SisPerR,ChIP

value: anti-SisPerR


title: Endoderm Ngn3GFP HM 18ss b2 010, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_18ss_b2_010


title: Macula_donor4_3_deep_group47


title: Retina_Donor1_3_deep_group51

value: Retina


title: Retina_Donor1_3_deep_group50

value: WT


title: macrophages, R3_20h_CyjiS

city: Würzburg

first: Alexander

last: Westermann

address: Josef-Schneider Straße 2

country: Germany

institute: HIRI

description:
Raw_count_table_mouse.csv
Raw_count_table_Salmonella.csv

data_processing:
Base-calling with Illumina NextSeq RTA v3.10.30
FASTQ conversion with BCL Convert v4.0.3 (Illumina)
FASTQ quality and adapter trimming using Cutadapt (Martin, 2011) v2.5 (parameters: --nextseq-trim=20 -m 1 -a ACTGTCTCTTATACACATCT)
Read tagging based on mouse and Salmonella genomes via FastQ Screen (Wingett, 2018) v0.15.2 (parameters: --aligner bowtie2 --tag --subset 0)
Read assignment to either mouse or Salmonella via FastQ Screen (parameters: --filter '03' --subset 0 for mouse and  --filter '30' --subset 0 for Salmonella)
Alignment of Salmonella assigned reads to Salmonella reference genome using segemehl v0.2.0 with READemption (Förstner et al., 2014) v0.4.5 (parameters: align -l 12 -a 95 -R)
Calculation of Salmonella read counts via READemption (parameters: gene_quanti -o 10 --features "3UTR,5UTR,CDS,rRNA,sRNA,transcript,tRNA" -a)
Alignment of mouse assigned reads to mouse genome using STAR (Dobin et al., 2013) v2.7.2b with default parameters based on exons from RefSeq annotation version 109
Calculation of mouse read counts on exon level summarized for each gene (RefSeq annotation version 109 for GRCm39) using featureCounts v1.6.4 from Subread package (Liao et al., 2014) (parameters: -s 2 -t exon -M -O --fraction)
Assembly: RefSeq GRCm39 (mouse), GCF_000210855.2 (Salmonella)
Supplementary files format and content: Character (TAB) separated value file containing raw read counts

organism:
Mus musculus
Salmonella enterica

source_name: RAW264.7 (ATCC TIB-71)

growth_protocol: Raw macrophages were cultured in RPMI (Gibco) supplemented with 10% FCS, 2 mM L-glutamine, 1 mM sodium pyruvate in a 5% CO2, humidified atmosphere at 37°C.

extract_protocol:
Trizol
Total RNA quality was checked using a 2100 Bioanalyzer with the RNA 6000 Nano kit (Agilent Technologies). The RIN for all samples was ≥5.0. DNA libraries suitable for sequencing were prepared from 500 ng of total RNA using the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero™ Plus (Illumina) according to manufacturer’s instructions. After 14 cycles of PCR amplification, the size distribution of the barcoded DNA libraries was estimated ~330 bp by electrophoresis on Agilent DNA 1000 Bioanalyzer microfluidic chips.
Dual RNA-seq

treatment_protocol: Infection was carried out following the protocol of (Schulte et al., 2011) with the indicated Salmonella Typhimurium (SL1344) strain in 6-well format. At the indicated time point post-infection, cells were harvested and sorted for invaded (GFP+) and non-infected (GFP-) host cells using a FACSAria III device (BD).

value: RAW264.7 (ATCC TIB-71)

value: macrophages

tag: infection condition

value: yjiS complemented Salmonella

tag: timepoint post_infection

tag: biological replicate


title: 206467000160_R03C01

description: SAMPLE 1

value: breast adenocarcinoma


title: RNA, islets, Clec control HFD biol rep2

value: islets

value: Clec control


title: 206772660112_R03C01

description: SAMPLE 3

source_name: Gynecological Tumor

value: Endometrioid endometrial adenocarcinoma


title: Retina_Donor1_3_deep_group49

tag: age

value: Male


title: RNA, islets, Clec control HFD biol rep4

value: HFD


title: Endoderm Ngn3GFP HM 18ss b2 009, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_18ss_b2_009

tag: strain

tag: time


title: 206772660112_R02C01

description: SAMPLE 5

tag: tissue preparation

value: renal clear cell carcinoma


title: macrophages, R3_20h_DyjiS

tag: cell line

value: yjiS deleted Salmonella


title: Endoderm Ngn3GFP HM 18ss b2 008, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_18ss_b2_008


title: RNA, islets, Clec control HFD biol rep1


title: macrophages, R3_20h_WT

value: WT Salmonella


title: 206522580146_R06C01

description: SAMPLE 4

tag: tumor type


title: stem; input; replicate 2

first: CHUAN

last: HE

state: Illinois

address: 929 East 57th Street, GCIS E313

institute: University of Chicago

data_processing:
The code for sequencing processing and mutation calling has been packaged, and all the analysis can be achieved by running one line of code. The source code is publicly available on GitHub (https://github.com/y9c/pseudoU-BIDseq).
Assembly: TAIR-10
Supplementary files format and content: TSV
Library strategy: BID-seq

source_name: stem

extract_protocol:
Total RNA isolation: total RNA was isolated according to TRIzol reagent manufacturer’s protocol, followed by isopropanol precipitation. PolyA+ RNA isolation: Dynabeads™ mRNA Purification Kit (Invitrogen™) was used for polyA+ RNA enrichment, from the purified total RNA.
With 10 ng synthetic RNA oligos carrying 0%, 20%, 40%, 60%, 80%, or 100% pseudouridine, 5′-phosphorylation were conducted with T4 polynucleotide kinase (PNK) (catalog no. EK0032, Thermo Fisher Scientific). To perform 3′-adapter ligation, 10 µl 5′-phosphorylated RNA fragments were incubated with 1.0 µl 20 µM RNA 3′ SR Adapter (5′App-NNNNN AGATCGGAAGAGCACACGTCT-3SpC3, with ATCACG as the inline barcode) at 70 °C for 2 mins and placed immediately on ice. Then, 2.5 µl 10× T4 RNA Ligase Reaction Buffer (catalog no. M0373L, NEB), 7.5 µl PEG8000 (50%), 1 µl SUPERase•In RNase Inhibitor and 2 µl T4 RNA Ligase 2 truncated KQ (catalog no. M0373L, NEB) were added to the RNA–adapter mixture48,49. The reaction was incubated at 25 °C for 2 h followed by 16 °C for 10 h. The reaction was further diluted to 47 µl with nuclease-free water, and the excessive adapters were removed with 2 µl 5′-deadenylase (catalog no. M0331S, NEB) at 30 °C for 30 min followed by adding 1 µl RecJf (catalog no. M0264L, NEB) for ssDNA digestion at 37 °C for 30 min. The 3′-end-ligated RNA was extracted by RNA Clean and Concentrator (Zymo Research) and eluted with 9.3 µl RNase-free water.  The purified RNA was incubated with 1.2 µl 10 µM 5′ SR Adapter (5′-GUUCAGAGUUCUACAGUCCGACGAUC-3′) at 70 °C for 2 mins and placed immediately on ice. Then 2.5 µl 10× T4 RNA ligase reaction buffer, 1.0 µl 25 mM ATP, 10 µl PEG8000 (50%) and 1 µl T4 RNA Ligase 1 (high concentration, catalog no. M0437M, NEB) were added to the RNA–adapter mixture. The reaction was mixed well and incubated at 25 °C for 8 h, followed by RNA Clean and Concentrator (Zymo Research) purification, eluting with 10 µl RNase-free water.  A 1.5 µl aliquot of the purified RNA was saved for ‘Input’ library construction, 8.5 µl was subjected to BID-seq optimized bisulfite treatment, as the ‘Treated’ sample. The 8.5 µl RNA was mixed with 45 µl freshly prepared BID-seq BS reagent (2.4 M Na2SO3 and 0.36 M NaHSO3, prepared by dissolving 270 mg Na2SO3 and 34 mg NaHSO3 in 900 µl RNase-free water) and incubated at 70 °C for 3 h. Then, 75 µl RNase-free H2O, 270 µl RNA binding buffer (RNA Clean and Concentrator), and 400 µl ethanol were added to the reaction mixture, which was mixed well and loaded on a RNA Clean and Concentrator-5 column. After spinning and washing once with 200 µl RNA wash buffer (RNA Clean and Concentrator), 200 µl RNA Desulphonation Buffer (catalog no. R5001-3-40, Zymo Research) was added to the column and incubated at room temperature for 1 h. This was followed by spinning and washing twice with 700 µl RNA wash buffer (RNA Clean and Concentrator), followed by eluting RNA with 10.5 µl RNase-free water. Then the ‘Input’ was diluted to 10.5 µl with RNase-free water. Both ‘Input’ and ‘Treated’ samples were mixed with 1.0 µl 2.0 µM SR RT primer (5′-AGACGTGTGCTCTTCCGATCT -3′) at 65 °C for 2 min and moved immediately onto ice. To this was added 4 µl 5× SSIV Buffer, 2 µl 10 mM dNTP Solution Mix (NEB), 1 µl 100 mM dithiothreitol, 0.5 µl RNaseOUT Recombinant Ribonuclease Inhibitor (catalog no. 10777019, Thermo Scientific) and 1 µl SuperScript IV Reverse Transcriptase (SSIV, catalog no. 18090050, Thermo Scientific). The reaction was mixed well and incubated at 50 °C for 1 h, followed by adding 1 µl RNase H (catalog no. M0297L, NEB) and incubating at 37 °C for 20 min. The reaction mixture was heated at 70 °C for 5 min and then cDNA was purified using DNA Clean and Concentrator (Zymo Research). The eluted cDNAs (20 µl) were stored at –80 °C; 4 µl was used for each 15-cycle PCR amplification reaction, which was performed with the SR Primer for Illumina (NEB) and indexed primers (from NEBNext Multiplex Oligos for Illumina). All libraries were purified on a 3.5% low melting point agarose gel and sequenced on Illumina Nova-seq 6000 with single-end 100 bp read length.

value: stem

tag: ecotype


title: Macula_donor4_3_deep_group45

value: Macula

tag: Sex


title: Macula_donor4_2_deep_group44


title: Endoderm Ngn3GFP HM 18ss b2 016, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_18ss_b2_016

value: Endoderm


title: Endoderm Ngn3GFP HM 18ss b2 007, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_18ss_b2_007


title: Macula_donor4_3_deep_group46


title: Macula_donor4_2_deep_group42


title: stem; input; replicate 1


title: macrophages, R3_1h_CyjiS

value: 1 h


title: Macula_donor4_2_deep_group43

value: WT


title: Endoderm Ngn3GFP HM 18ss b2 006, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_18ss_b2_006


title: Macula_donor4_2_deep_group41


title: macrophages, R3_1h_DyjiS

value: RAW264.7 (ATCC TIB-71)


title: stem; treated; replicate 2


title: Endoderm Ngn3GFP HM 18ss b2 005, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_18ss_b2_005


title: stem; treated; replicate 1


title: macrophages, R3_1h_WT

value: macrophages


title: Endoderm Ngn3GFP HM 18ss b2 004, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_18ss_b2_004


title: macrophages, R2_20h_CyjiS

value: yjiS complemented Salmonella


title: silique; input; replicate 2

source_name: silique

value: silique


title: macrophages, R2_20h_DyjiS


title: Endoderm Ngn3GFP HM 18ss b2 003, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_18ss_b2_003


title: Endoderm Ngn3GFP HM 18ss b2 002, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_18ss_b2_002


title: silique; input; replicate 1


title: Macula_donor3_3_deep_group36


title: macrophages, R2_20h_WT


title: Endoderm Ngn3GFP HM 18ss b2 001, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_18ss_b2_001


title: silique; treated; replicate 2


title: Macula_donor4_1_deep_group39


title: silique; treated; replicate 1


title: Endoderm Ngn3GFP HM 15ss b2 016, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_15ss_b2_016


title: macrophages, R2_1h_DyjiS


title: Macula_donor3_3_deep_group35


title: shoot; input; replicate 2

source_name: shoot

value: shoot


title: Macula_donor4_1_deep_group37


title: Endoderm Ngn3GFP HM 15ss b2 015, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_15ss_b2_015

source_name: Endoderm


title: Macula_donor4_1_deep_group38


title: macrophages, R2_1h_WT


title: shoot; input; replicate 1


title: Macula_donor3_3_deep_group34


title: macrophages, R1_20h_CyjiS


title: macrophages, R2_1h_CyjiS


title: Endoderm Ngn3GFP HM 15ss b2 013, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_15ss_b2_013


title: Macula_donor3_3_deep_group33


title: Endoderm Ngn3GFP HM 15ss b2 012, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_15ss_b2_012


title: macrophages, R1_20h_WT


title: shoot; treated; replicate 1


title: seedling; input; replicate 2

source_name: seedling

value: seedling


title: Macula_donor3_2_deep_group32


title: Endoderm Ngn3GFP HM 15ss b2 011, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_15ss_b2_011


title: Macula_donor4_1_deep_group40


title: seedling; input; replicate 1


title: macrophages, R1_1h_CyjiS


title: Endoderm Ngn3GFP HM 15ss b2 010, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_15ss_b2_010


title: Endoderm Ngn3GFP HM 15ss b2 014, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_15ss_b2_014


title: Macula_donor3_2_deep_group31


title: macrophages, R1_1h_DyjiS


title: shoot; treated; replicate 2


title: Macula_donor3_2_deep_group30


title: seedling; treated; replicate 2


title: macrophages, R1_20h_DyjiS


title: macrophages, R1_1h_WT


title: Macula_donor3_2_deep_group29


title: Endoderm Ngn3GFP HM 15ss b2 008, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_15ss_b2_008


title: seedling; treated; replicate 1


title: SiS_INP_rep2

city: Trieste

first: Silvano

last: Piazza

address: localita' Padriciano 99

country: Italy

institute: ICGEB

description:
U2-OS control siSFPQ; DNA is immunoprecipated with antibody against Normal rabbit IgG, Santa Cruz sc-2027/Normal rabbit IgG Santa Cruz sc-2027
SiS_INP_vs_SiC_INP_annotatedpeaks.txt.gz
SiC_INP_vs_SiS_INP_annotatedpeaks.txt.gz

data_processing:
DNA-seq quality control performed with FastQC
ChIP-seq analysis was performed with the ChiP-AP pipeline, performing quality control (FastQC), read trimming and filtering (Bbduk and Trimmomatic), genome mapping (BWA-MEM), peak calling (Genrich, HOMER, MACS2, SICER2), peak merging and annotation (HOMER).
Using R/Bioconductor environment, peaks that were called by three out of four peak calling methods were considered as present.  Peaks were considered differentially expressed when having p-value < 0.05 for at least three methods. In particular, for HOMER, MACS2, and SICER2, the Fold Change must be greater than 1 or for Genrich the enrichment score must be positive (up-regulated peaks
Assembly: human genome version GRCh38
Supplementary files format and content: tab delimited text file with the annotated peaks for the different comparisons. For each peak calling software (Genrich, HOMER, MACS2, SICER2) the enrichment values and the statistical significances are reported

source_name: Bone

growth_protocol: U-2 OS cells (osteosarcoma, ATCC HTB-96) were cultured in low glucose Dulbecco’s modified Eagle’s (DMEM) medium (Euroclone) with 10% foetal bovine serum (Corning), 1% L- glutamine (Gibco), 1% penicillin/streptomycin (Gibco)

extract_protocol:
DNA was extracted as described in G. Della Chiara et al., ‘Epigenomic landscape of human colorectal cancer unveils an aberrant core of pan-cancer enhancers orchestrated by YAP/TAZ’, Nat Commun, vol. 12, no. 1, p. 2340, Apr. 2021, doi: 10.1038/s41467-021-22544-y.
Libraries were constructed with the Truseq ChIPseq library prep, 150 base pair reads (pair ends).

treatment_protocol: Specific siRNA for SFPQ were transfected using RNAi-MAX Lipofectamine (Invitrogen) at 30 nM final concetration, according to the manufacturer’s suggestions.

value: Bone

value: Osteosarcoma Cell Line

value: Polyploid

tag: treatment

value: control siSFPQ

tag: chip antibody


title: Endoderm Ngn3GFP HM 15ss b2 007, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_15ss_b2_007


title: seed; input; replicate 2

source_name: seed

value: seed


title: Endoderm Ngn3GFP HM 15ss b2 006, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_15ss_b2_006


title: Macula_donor2_3_deep_group24

value: Male


title: SiS_INP_rep1

tag: cell type

value: Normal rabbit IgG, Santa Cruz sc-2027/Normal rabbit IgG Santa Cruz sc-2027


title: Macula_donor3_1_deep_group27

value: Macula


title: Endoderm Ngn3GFP HM 15ss b2 009, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_15ss_b2_009

value: Endoderm


title: seed; treated; replicate 2


title: SiS_H3-3_rep2

description:
U2-OS control siSFPQ; DNA is immunoprecipated with antibody against H3.3, MILLIPORE 09-838 1.5 μg
SiS_H3-3_vs_SiS_INP_annotatedpeaks.txt.gz
SiS_H3-3_vs_SiC_H3-3_annotatedpeaks.txt.gz


title: Macula_donor3_1_deep_group28


title: Macula_donor3_1_deep_group26


title: Endoderm Ngn3GFP HM 15ss b2 005, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_15ss_b2_005


title: SiS_H3-3_rep1


title: Macula_donor3_1_deep_group25


title: seed; input; replicate 1


title: Endoderm Ngn3GFP HM 15ss b2 004, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_15ss_b2_004


title: Endoderm Ngn3GFP HM 15ss b2 003, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_15ss_b2_003


title: rosettaLeaf; input; replicate 2

source_name: rosetta

value: rosetta


title: Macula_donor2_2_deep_group20

value: WT


title: SiS_DAXX_rep1

description:
U2-OS control siSFPQ; DNA is immunoprecipated with antibody against DAXX, BETHYL A301-353A 2.5 μg
SiS_DAXX_vs_SiS_INP_annotatedpeaks.txt.gz
SiS_DAXX_vs_SiC_DAXX_annotatedpeaks.txt.gz

value: DAXX, BETHYL A301-353A 2.5 μg


title: rosettaLeaf; input; replicate 1


title: Endoderm Ngn3GFP HM 15ss b2 002, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_15ss_b2_002


title: SiC_SFPQ_rep2

description:
U2-OS control siRNA; DNA is immunoprecipated with antibody against SFPQ/PSF, Bethyl A301-321A 2.5 μg
SiC_SFPQ_vs_SiC_INP_annotatedpeaks.txt.gz
SiC_SFPQ_vs_SiS_INP_annotatedpeaks.txt.gz

value: control siRNA

value: SFPQ/PSF, Bethyl A301-321A 2.5 μg


title: Macula_donor2_3_deep_group22


title: rosettaLeaf; treated; replicate 2


title: Endoderm Ngn3GFP HM 15ss b2 001, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_15ss_b2_001


title: rosettaLeaf; treated; replicate 1


title: Endoderm Ngn3Cre 27ss b2 069, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_069

value: Ngn3-Cre; Ai6


title: seed; treated; replicate 1


title: SiC_SFPQ_rep1


title: Macula_donor2_3_deep_group23


title: SiS_DAXX_rep2


title: Macula_donor2_3_deep_group21


title: SiC_INP_rep2

description:
U2-OS control siRNA; DNA is immunoprecipated with antibody against Normal rabbit IgG, Santa Cruz sc-2027/Normal rabbit IgG Santa Cruz sc-2027
SiC_INP_vs_SiS_INP_annotatedpeaks.txt.gz
SiS_INP_vs_SiC_INP_annotatedpeaks.txt.gz


title: Endoderm Ngn3Cre 27ss b2 068, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_068


title: root; input; replicate 1

source_name: root

value: root


title: Endoderm Ngn3Cre 27ss b2 067, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_067


title: Endoderm Ngn3Cre 27ss b2 066, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_066


title: Macula_donor2_2_deep_group18


title: SiC_H3-3_rep2

description:
U2-OS control siRNA; DNA is immunoprecipated with antibody against H3.3, MILLIPORE 09-838 1.5 μg
SiC_H3-3_vs_SiC_INP_annotatedpeaks.txt.gz
SiS_H3-3_vs_SiC_H3-3_annotatedpeaks.txt.gz


title: SiC_H3-3_rep1


title: root; treated; replicate 2


title: Endoderm Ngn3Cre 27ss b2 065, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_065


title: Macula_donor2_2_deep_group17


title: SiC_INP_rep1


title: SiC_DAXX_rep2

description:
U2-OS control siRNA; DNA is immunoprecipated with antibody against DAXX, BETHYL A301-353A 2.5 μg
SiC_DAXX_vs_SiC_INP_annotatedpeaks.txt.gz
SiS_DAXX_vs_SiC_DAXX_annotatedpeaks.txt.gz


title: root; input; replicate 2


title: Endoderm Ngn3Cre 27ss b2 064, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_064


title: flower; input; replicate 2

source_name: flower

value: flower


title: SiC_DAXX_rep1

value: Bone


title: root; treated; replicate 1


title: flower; input; replicate 1


title: Macula_donor2_1_deep_group16


title: Endoderm Ngn3Cre 27ss b2 063, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_063


title: Macula_donor2_2_deep_group19


title: flower; treated; replicate 2


title: Macula_donor2_1_deep_group15


title: Endoderm Ngn3Cre 27ss b2 062, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_062


title: Macula_donor2_1_deep_group14


title: rs9331896 dye-swap Risk vs NonRisk

type: other

city: Philadelphia

first: Yijing

last: Su

state: PA

address: Levy 326

department: Department of Oral Medicine

institute: University of Pennsylvania

hyb_protocol: SNPs are probed to the TF arrays in pairs as a competition assay, with one allele labeled with Cy3 and the other labeled with Cy5. For each pair, the arrays are performed in duplicate, with the allele colors swapped. For example, on one array the Cy3 risk and Cy5 non-risk are probed, while the Cy5 risk and Cy3 non-risk are probed to another array. Prior to the competition assay, TF arrays are blocked with Blocking Buffer (25 mM HEPES at pH7.5, containing 50 mM Potassium Glutamate, 8 mM Magnesium Acetate, 3 mM DTT, 10% glycerol, 0.1% Triton X-100, and 3% BSA) for 3 hours at 4C. After blocking, Cy5 and Cy3 alleles are mixed in 1X Hybridization buffer (10 mM Tris-Cl at pH8.0, containing 50 mM Potassium Chloride, 1 mM Magnesium Chloride, 1 mM DTT, 5% glycerol, 10 mM Zinc Chloride, and 3 mg/mL BSA) to a final concentration of 40 nM of each allele. Blocking buffer is removed from the arrays, and then the mixed hybridization reaction is added and incubated overnight at 4C. After overnight incubation, arrays are washed once with 3mL ice cold TBST for 5 minutes, briefly rinsed with water, and then dried via centrifugation.

scan_protocol: Arrays are scanned in both the Cy5 (635nm) and Cy3 (532nm) channels separately at 1000 PMT using the GenePix 4000B scanner (Molecular Devices). GenePix Pro 7 software determines the foreground and local background intensities for each detected fluorescent spot at every location on the corresponding alignment grid (GAL file). For each image, a .TIFF file and a .GPR file are generated and saved for analysis.

data_processing: For each spot on the alignment grid, the background and foreground intensities were determined by the GenePix Pro 7 software. Using these values, ratiometric binding analysis was performed as follows for each spot on the TF arrays using RStudio: R* = Log2(sqrt((Cy3 NonRisk*Cy5 NonRisk)/(Cy3 Risk*Cy5 Risk))).Ratiometric binding values that are highly positive or highly negative indicate strong preferential binding for the non-risk or risk allele of the given SNP, respectively. Values above +/- 1 were considered significant differential binding events for the purposes of this study. Raw GPR Files and processed data obtained in this study are provided.

molecule: other

organism: synthetic construct

label_protocol: Each of the selected SNPs for this study were synthesized (Integrated DNA Technologies) with 15bp flanking contextual sequences on either side, and an additional common modified T7 priming sequence (5’- ACCCTATAGTGAGTGCTATTA – 3’) at the 3’ end. Cy3, Cy5, and biotin primers complementary to the T7 priming site were also synthesized (Integrated DNA Technologies). Fluorescent/biotin primers were incubated at a 1:1 molar ratio in 1X NEB II Buffer (NEB). Mixtures were boiled at 95C for 10 minutes, then cooled slowly to room temperature to allow for annealing to occur. Once the mixture was fully cooled, 3U of Klenow Large Fragment 3’-5’ exo- (NEB M0210) and dNTPs (final concentration 1.5 mM) were added to each reaction. Reactions were incubated at 37C for 20 minutes to generate double stranded probes.

extract_protocol: not provided

value: Synthetic oligo (IDT)

tag: raw file 1 labels

value: Replicate 1:NonRisk = cy3; Risk = cy5; Scan = cy3

tag: raw file 2 labels

value: Replicate 1:NonRisk = cy3; Risk = cy5; Scan = cy5

tag: molecule subtype

value: synthetic DNA

value: Replicate 2:NonRisk = cy5; Risk = cy3; Scan = cy3

value: Replicate 2:NonRisk = cy5; Risk = cy3; Scan = cy5


title: Endoderm Ngn3Cre 27ss b2 061, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_061

tag: tissue

tag: genotype


title: rs9304861 dye-swap Risk vs NonRisk


title: flower; treated; replicate 1


title: Endoderm Ngn3Cre 27ss b2 060, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_060


title: caulineLeaf; input; replicate 2

source_name: cauline

value: cauline


title: Macula_donor2_1_deep_group13

value: Macula

value: Male


title: RPE, donor 3, multiome ATAC

data_processing:
CellRanger
Assembly: hg38
Supplementary files format and content: CellRanger output files: RNA.barcodes.tsv.gz, RNA.features.tsv.gz, RNA.matrix.mtx.gz
Supplementary files format and content: CellRanger output files: atac_fragments.tsv.gz, atac_fragments.tsv.gz.tbi
Library strategy: 10x multiome

source_name: RPE

extract_protocol: The eye globes were collected from three unrelated human donors (aged 21, 27 and 43 years) with the collaboration of San Diego Eye Bank. The sample processing time starting from eye enucleation to dissection was restricted within 2 hours to identify the macula, a visible yellowish/whiteish indent that is slightly lateral to the optic disk inside the globe. Prior dissection, the eye globe with proper label was collected in a sterile moist chamber. At first the cornea was removed by cutting 2-3 mm around the limbus using a surgical blade. Pull off the iris and lens. This will leave you with the eye cup, which contains the posterior pole. After removing enough vitreous and aqueous fluid the temporal region can be located by two main blood vessels that curl around the macula. Using a sterile 3mm skin biopsy punch, the macula was collected. Sections were made for the other regions, temporal, nasal, superior and inferior. For all these regions, the retina and RPE tissue were separated and stored immediately in Liquid Nitrogen. Retina tissues were pulverized using a dounce tissue chamber and two pestles (“Loose” and “Tight”) on ice for each sample. Pulverized retina tissues were resuspended in 1ml of chilled NIM-DP-L buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM Tris-HCl pH 7.5, 1 mM DTT, 1x protease inhibitor (Pierce), 1U μl-1 recombinant RNase inhibitor (Promega, PAN2515) and 0.1% Triton X-100). Tissue was dounce homogenized with a loose pestle (5-10 strokes) followed by a tight pestle (15-25 strokes) or until the solution was uniform. Nuclei were filtered using a 30 μm CellTrics filter (Sysmex, 04-0042-2316) into a LoBind tube (Eppendorf, 22431021). Nuclei were centrifuged 1000 rcf, for 10 min at 4°C then the pellet was resuspended in 1ml NIM-DP buffer (0.25 M sucrose, 25 mM KCl, 5mM MgCl2, 10 mM Tris-HCl pH 7.5, 1mM DTT, 1x protease inhibitor, 1U μl-1 recombinant RNase inhibitor) and pelleted (1000 rcf, 10 min at 4°C). Pelleted nuclei were resuspended in 400 μl 2 μM 7-AAD (Invitrogen, A1310) in sort buffer (1mM EDTA, 1U μl-1 recombinant RNase inhibitor, 1x protease inhibitor, 1% fatty acid-free BSA in PBS). A total of 150,000 nuclei was sorted (Sony, SH800S) into a LoBind tube containing a collection buffer (5U μl-1 recombinant RNase inhibitor, 1x protease inhibitor, 5% fatty acid-free BSA in PBS). Then, 5x permeabilization buffer (50 mM Tris-HCl pH 7.4, 50 mM NaCl, 15 mM MgCl2, 0.05% Tween-20, 0.05% IGEPAL, 0.005% Digitonin, 5% fatty acid-free BSA in PBS, 5mM DTT, 1U μl-1 recombinant RNase inhibitor, 5x protease inhibitor) was added for a final concentration of 1x. Nuclei were incubated in ice for 1 min, then centrifuged (500 rcf, 5 min at 4°C). The supernatant was discarded and 650 μl of wash buffer (10 mM Tris-HCl pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1% fatty acid-free BSA in PBS, 1mM DTT, 1U μl-1 recombinant RNase inhibitor, 1x protease inhibitor) was added without disturbing the pellet followed by centrifuging(500 rcf, 5 min at 4°C). The supernatant was removed, and the pellet was resuspended in 7μl of 1x nucleus buffer (nucleus buffer (10x Genomics), 1mM DTT, 1U μl-1 recombinant RNase inhibitor). Nuclei (1μl) were diluted in 1x nucleus buffer, stained with Trypan Blue (Invitrogen, T10282) and counted, In total, 16000-20000 nuclei were used for the tagmentation reaction and controller loading and libraries were generated according to the manufacturer’s recommended protocol (https://www.10xgenomics.com/support/single-cell-multiome-atac-plus-gene-expression).

value: RPE

value: Healthy unaffcted


title: Macula_donor1_3_deep_group12

source_name: Macula

value: WT


title: rs9271192 dye-swap Risk vs NonRisk


title: caulineLeaf; input; replicate 1


title: Retina, donor 3, multiome ATAC

source_name: retina

value: retina


title: Macula_donor1_3_deep_group10


title: caulineLeaf; treated; replicate 2


title: rs857551 dye-swap Risk vs NonRisk


title: Endoderm Ngn3Cre 27ss b2 058, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_058

value: Endoderm

value: Ngn3-Cre; Ai6


title: Macula, donor 3, multiome ATAC

source_name: macula

value: macula


title: Macula_donor1_3_deep_group9


title: rs7920721 dye-swap Risk vs NonRisk


title: caulineLeaf; treated; replicate 1


title: rs769449 dye-swap Risk vs NonRisk


title: RPE, donor 2, multiome ATAC


title: rs75635567 dye-swap Risk vs NonRisk


title: Macula_donor1_2_deep_group8


title: Macula_donor1_3_deep_group11


title: Endoderm Ngn3Cre 27ss b2 059, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_059


title: Macula_donor1_2_deep_group7


title: Retina, donor 2, multiome ATAC


title: Macula_Donor1_1_deep_group4


title: RPE, donor 1, multiome ATAC


title: Retina, donor 1, multiome ATAC


title: Endoderm Ngn3Cre 27ss b2 056, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_056


title: Macula_donor1_2_deep_group6


title: Endoderm Ngn3Cre 27ss b2 055, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_055


title: Endoderm Ngn3Cre 27ss b2 053, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_053


title: Mild-drought_fixed_rep2

city: Ghent

first: Bert

last: De Rybel

address: Technologiepark 71

department: Center for Plant Systems Biology

country: Belgium

institute: VIB

description: BD Rhapsody

data_processing:
Read alignment + counting; BD Rhapsody sequence analysis pipeline; v2.0
Assembly: Arabidopsis thaliana TAIR10
Supplementary files format and content: zip file containing raw and filtered count matrix (output BD Rhapsody analysis pipeline)
Supplementary files format and content: Merged Seurat file in .rds format

source_name: 14DAS third true leaf

growth_protocol: Arabidopsis (A. thaliana) was grown under a long-day regime (16-h light and 8-h dark, intensity 110–120 μmol m−2s−1) at 21°C on the weighing, imaging and watering automated machine (WIWAM) platform (http://www.wiwam.be). The seeds were sown in 85 ± 1 g of Saniflor compost (Van Isreal N.V., Geraardsbergen, Belgium) with an average absolute water content of 70%.Five seedlings were grown per pot in order to obtain 80 seedlings per sample (per replicate, per condition).

extract_protocol:
The cell wall digestion protocol was adapted fromRyu et al. (2019). Briefly, the third leaf of 80 plants per sample was harvested, chopped in 1 mL enzyme solution (0.4 M mannitol, 10 mM CaCl2, 20 mM MES, 20 mM KCl, 2% (wt/vol, 5.7 pH) cellulase, and 0.5% (wt/vol) macero enzyme). Chopped samples were transferred to a 70-μm cell strainer (model Corning, Merck) placed within a 6-well plate, in a total volume of 5  mL of the enzyme solution. In the fixed samples, 50uM of Actinomycin D (Sigma A9415) was added to the cell wall digestion solution. Samples were incubated, constantly shaking for 75 min at room temperature. After a 7-min centrifugation at 200g, the pellet was resuspended in 1 mL washing solution (0.4 M mannitol, 10 mM CaCl2, 20 mM MES, and 20 mM KCl). Cells were sorted on the LeviCell magnetic sorter. Subsequently, cells were collected in wash buffer (0.4 M mannitol, 10 mM CaCl2, 20 mM MES, and 20 mM KCl) and counted.
Cellular suspensions were loaded into a BD Rhapsody HT Cartridge (BD) according to the manufacturer’s instructions.

treatment_protocol: Plants were watered daily until 8 days after stratification (DAS) with a well‐watered (WW) regime of soil relative water content 69% (2.2 gwater/gsoil). At 9 DAS, half of the pots (randomized) were not watered until harvest (14 DAS, MD), while the other half kept the WW regime.

value: 14DAS third true leaf

tag: condition

value: Mild drought

tag: fixation

value: Actinomycin D


title: Well-watered_fixed_rep2

description: BD Rhapsody

value: Well-watered


title: Macula, donor 2, multiome ATAC

tag: age


title: rs7431992 dye-swap Risk vs NonRisk

value: Synthetic oligo (IDT)

value: Replicate 1:NonRisk = cy3; Risk = cy5; Scan = cy3

value: Replicate 1:NonRisk = cy3; Risk = cy5; Scan = cy5

value: synthetic DNA


title: Endoderm Ngn3Cre 27ss b2 054, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_054

tag: strain

tag: time


title: rs73239797 dye-swap Risk vs NonRisk

value: Replicate 2:NonRisk = cy5; Risk = cy3; Scan = cy3

value: Replicate 2:NonRisk = cy5; Risk = cy3; Scan = cy5


title: Mild-drought_rep2

description: BD Rhapsody

value: mock


title: rs7039300 dye-swap Risk vs NonRisk


title: Endoderm Ngn3Cre 27ss b2 057, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_057


title: Endoderm Ngn3Cre 27ss b2 052, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_052


title: Mild-drought_fixed_rep1

description: BD Rhapsody


title: rs679515 dye-swap Risk vs NonRisk


title: Macula_donor1_2_deep_group5

value: Macula

value: Male


title: Macula_Donor1_1_deep_group3

value: WT


title: Macula, donor 1, multiome ATAC

value: Healthy unaffcted


title: Well-watered_rep2

description: BD Rhapsody


title: Well-watered_fixed_rep1

description: BD Rhapsody


title: Macula_Donor1_1_deep_group2


title: Endoderm Ngn3Cre 27ss b2 051, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_051

value: Endoderm

value: Ngn3-Cre; Ai6


title: RPE, donor 3, multiome RNA

molecule: nuclear RNA

value: RPE


title: Macula_Donor1_1_deep_group1


title: Mild-drought_rep1

description: BD Rhapsody

value: 14DAS third true leaf

value: Mild drought


title: Endoderm Ngn3Cre 27ss b2 050, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_050


title: Endoderm Ngn3Cre 27ss b2 049, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_049


title: rs6738181 dye-swap Risk vs NonRisk


title: Endoderm Ngn3Cre 27ss b2 048, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_048


title: RPE, donor 2, multiome RNA


title: Endoderm Ngn3Cre 27ss b2 047, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_047


title: rs6665019 dye-swap Risk vs NonRisk


title: Macula, donor 3, multiome RNA

value: macula


title: Endoderm Ngn3Cre 27ss b2 046, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_046


title: root; treated; replicate 4

first: Chang

last: Ye

description: root; treated; replicate 4

data_processing:
The code for sequencing processing and mutation calling has been packaged, and all the analysis can be achieved by running one line of code. The source code is publicly available on GitHub (https://github.com/y9c/pseudoU-BIDseq).
Assembly: TAIR-10
Supplementary files format and content: TSV
Library strategy: BID-Seq

value: root


title: Retina, donor 3, multiome RNA

value: retina


title: root; treated; replicate 5

description: root; treated; replicate 5


title: RPE, donor 1, multiome RNA


title: rs519113 dye-swap Risk vs NonRisk

value: Synthetic oligo (IDT)

value: Replicate 1:NonRisk = cy3; Risk = cy5; Scan = cy3

value: Replicate 1:NonRisk = cy3; Risk = cy5; Scan = cy5


title: rs4420638 dye-swap Risk vs NonRisk

value: synthetic DNA

value: Replicate 2:NonRisk = cy5; Risk = cy3; Scan = cy3

value: Replicate 2:NonRisk = cy5; Risk = cy3; Scan = cy5


title: root; treated; replicate 3

description: root; treated; replicate 3


title: Retina, donor 2, multiome RNA


title: rs4676049 dye-swap Risk vs NonRisk


title: rs429358 dye-swap Risk vs NonRisk


title: Retina, donor 1, multiome RNA


title: root; treated; replicate 6

description: root; treated; replicate 6


title: root; treated; replicate 2

description: root; treated; replicate 2


title: Endoderm Ngn3Cre 27ss b2 044, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_044


title: Well-watered_rep1

description: BD Rhapsody

value: Well-watered

value: mock


title: Macula, donor 2, multiome RNA

value: Healthy unaffcted


title: root; treated; replicate 1

description: root; treated; replicate 1


title: Macula, donor 1, multiome RNA


title: rs35862341 dye-swap Risk vs NonRisk


title: rs56131196 dye-swap Risk vs NonRisk


title: Endoderm Ngn3Cre 27ss b2 042, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_042

value: Endoderm


title: MSC 355 3D

city: Berlin

first: Mark

last: Rosowski

address: Gusav-Meyer-Allee 25

institute: TU Berlin

data_processing:
RAW data were demultiplexed and processed on the Galaxy Project Platorm, using the FASTQ Groomer tool to convert the output data into Sanger sequencing data. Fragments were then mapped against the human genome (hg38) to detect splice junctons between exons by HISAT2. Mapped reads were processed by the FeatureCount tool. The Galaxy Community. [The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update,; Nucleic Acids Research, Volume 52, Issue W1, 5 July 2024, Pages W83–W94, https://doi.org/10.1093/nar/gkae410; https://usegalaxy.org/]
Assembly: hg38
Supplementary files format and content: tab-delimited text file include raw counts and GeneID for each sample

source_name: bone marrow

growth_protocol: Mesenchymal stromal cells were isolated from femoral heads and propagated in standard culture conditions (DMEM; 10%FCS; 1% Penicillin–Streptomycin).

extract_protocol:
whole RNA was isolated by the Nucleo Spin RNA Kit (Macherey & Nagel)
for samples from Donor 125 and 135: The indexed cDNA library was generated using the TruSeq Stranded mRNA LT Sample Prep Kit 24 (Illumina), according to the TruSeq Stranded mRNA Sample PreparaCon Protocol LS (Illumina). The inital quantity of total RNA was 800 ng for bone marrow stromal cells for samples from donor 351 and 355: Total RNA samples were quantified using a Qubit Fluorometer, and RNA integrity was checked on a TapeStation (Agilent). Double-indexed stranded mRNA-Seq libraries were prepared using the ILMN Stranded mRNA Library Prep Kit (Illumina, #20040534), starting from 500 ng of input material according to the manufacturer’s instructions.
for samples from donor 125 and 135: Libraries were quality checked by qPCR and equimolarly pooled based concentration measurements (nanodrop). The sequencing was performed on the Illumina MiSeq System. for sampls from donor 351 and 355: Libraries were equimolarly pooled based on Qubit concentration measurements and TapeStation size distributions. The loading concentration of the pool was determined using a qPCR assay (Roche, #7960573001). Libraries were then sequenced on the Illumina NovaSeq X Plus platform using PE100 sequencing mode, with a target of 50 million reads per library.

treatment_protocol: For 3D culture, ceramic scaffolds were seeded with mesenchymal stromal cells and cultured for seven days in standard culture conditions. As a control, the same biological donors were kept in a 2D monolayer culture (DMEM; 10%FCS; 1% Penicillin–Streptomycin).

value: bone marrow

tag: cell line

value: primary cells

value: mesencymal stromal cells

value: wild type


title: Endoderm Ngn3Cre 27ss b2 043, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_043

value: Ngn3-Cre; Ai6


title: shoot; treated; replicate 5

description: shoot; treated; replicate 5

value: shoot


title: rs2279590 dye-swap Risk vs NonRisk


title: Endoderm Ngn3Cre 27ss b2 041, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_041


title: MSC 351 3D


title: Endoderm Ngn3Cre 27ss b2 040, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_040


title: rs2075650 dye-swap Risk vs NonRisk


title: Endoderm Ngn3Cre 27ss b2 045, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_045


title: MSC 355 ML

value: monolayer


title: rs186588455 dye-swap Risk vs NonRisk

value: Synthetic oligo (IDT)


title: shoot; treated; replicate 2

description: shoot; treated; replicate 2


title: rs17767225 dye-swap Risk vs NonRisk

value: Replicate 1:NonRisk = cy3; Risk = cy5; Scan = cy3


title: rs17366218 dye-swap Risk vs NonRisk

value: Replicate 1:NonRisk = cy3; Risk = cy5; Scan = cy5


title: Endoderm Ngn3Cre 27ss b2 039, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_039


title: MSC 351 ML


title: Endoderm Ngn3Cre 27ss b2 038, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_038


title: shoot; treated; replicate 1

description: shoot; treated; replicate 1


title: rs145049847 dye-swap Risk vs NonRisk

value: synthetic DNA


title: Endoderm Ngn3Cre 27ss b2 037, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_037


title: seed; treated; replicate 5

description: seed; treated; replicate 5

value: seed


title: rs143638193 dye-swap Risk vs NonRisk

value: Replicate 2:NonRisk = cy5; Risk = cy3; Scan = cy3

value: Replicate 2:NonRisk = cy5; Risk = cy3; Scan = cy5


title: shoot; treated; replicate 4

description: shoot; treated; replicate 4


title: 4T1 KDHmgcr B rep 3

type: RNA

city: Salamanca

first: L. Francisco

last: Lorenzo-Martín

state: Castilla y León

address: Campus Miguel de Unamuno

institute: University of Salamanca (USAL) – Centro de Investigación del Cáncer (CIC)

description: Gene expression data from 4T1 cells.

hyb_protocol: Clariom S arrays (Affymetrix) under standard conditions.

scan_protocol: Standard Affymetrix protocol.

data_processing: Upon microarray hybridization, the raw data was normalized with RMA using R (v.3.6.3).

label: biotin

source_name: 4T1 cells transduced with lentiviral shRNAs to Hmgcr transcripts, clone B, biological replicate 3

label_protocol: Total RNA was quantified using 6000 Nano Chips (Agilent Technologies, Santa Clara, CA) and used (2.3 mg/sample) to generate labeled cRNA probes according to the manufacturer's instructions (Affymetrix).

growth_protocol: 4T1 cells were cultured in RPMI medium supplemented with 10% fetal bovine serum, penicillin (10 µg/ml), and streptomycin (100 µg/ml) at 37ºC with 5% CO2.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer´s instructions.

treatment_protocol: The shRNA-mediated knock-down was carried out with prepackaged Mission TRC lentiviral particles (Sigma-Aldrich, MO, USA) according to the manufacturer´s instructions. To generate Hmgcr overexpressing 4T1 cells, cells were infected with lentiviral particles encoding Hmgcr (pLVX-Hmgcr) in the presence of polybrene and, subsequently, selected with hygromycin.

value: Breast cancer

value: Hmgcr knock-down B


title: Endoderm Ngn3Cre 27ss b2 036, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_036

data_processing:
For the Smart-seq3xpress scRNA-seq data, initial quality control was executed with FastQC version 0.11.9 under default settings. Index, primer, and adaptor sequences were then trimmed from paired-end reads using Trimmomatic version 0.39 with default parameters. Alignment of trimmed reads to the Mus musculus Genome assembly GRCm38 (mm10) was accomplished using HISAT version 2.1.0.
Assembly: mm10
Supplementary files format and content: Smart-seq3xpress output files: Tab-separated rexpression values matrix files

value: Endoderm


title: seed; treated; replicate 4

description: seed; treated; replicate 4


title: shoot; treated; replicate 3

description: shoot; treated; replicate 3


title: Endoderm Ngn3Cre 27ss b2 035, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_035


title: Endoderm Ngn3Cre 27ss b2 034, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_034


title: seed; treated; replicate 2

description: seed; treated; replicate 2


title: rs116530595 dye-swap Risk vs NonRisk


title: rs143083071 dye-swap Risk vs NonRisk


title: seed; treated; replicate 3

description: seed; treated; replicate 3


title: 4T1 KDHmgcr B rep 2

description: Gene expression data from 4T1 cells.

source_name: 4T1 cells transduced with lentiviral shRNAs to Hmgcr transcripts, clone B, biological replicate 2


title: rs11168036 dye-swap Risk vs NonRisk


title: 4T1 KDHmgcr B rep 1

description: Gene expression data from 4T1 cells.

source_name: 4T1 cells transduced with lentiviral shRNAs to Hmgcr transcripts, clone B, biological replicate 1


title: seed; treated; replicate 1

description: seed; treated; replicate 1


title: 4T1 KDHmgcr A rep 3

description: Gene expression data from 4T1 cells.

source_name: 4T1 cells transduced with lentiviral shRNAs to Hmgcr transcripts, clone A, biological replicate 3

value: Hmgcr knock-down A


title: Endoderm Ngn3Cre 27ss b2 033, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_033

source_name: Endoderm


title: rosettaLeaf; treated; replicate 7

description: rosettaLeaf; treated; replicate 7

value: rosetta


title: rs10792832 dye-swap Risk vs NonRisk


title: 4T1 KDHmgcr A rep 1

description: Gene expression data from 4T1 cells.

source_name: 4T1 cells transduced with lentiviral shRNAs to Hmgcr transcripts, clone A, biological replicate 1


title: rosettaLeaf; treated; replicate 6

description: rosettaLeaf; treated; replicate 6


title: 4T1 KDHmgcr A rep 2

description: Gene expression data from 4T1 cells.

source_name: 4T1 cells transduced with lentiviral shRNAs to Hmgcr transcripts, clone A, biological replicate 2


title: Endoderm Ngn3Cre 27ss b2 032, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_032


title: rs10273775 dye-swap Risk vs NonRisk


title: Multiplexed_PBMCs(HC_S_NS)

city: Daejeon

first: Taylor

last: Roh

address: 266, Munhwa-ro

department: Microbiology

country: South Korea

institute: Chungnam National University

description: Library name: Sample 1

data_processing:
Single cell RNA sequencing data analysis The raw sequencing data (FASTQ) was processed using the BD Rhapsody WTA Analysis Pipeline v2.0 (BD Biosciences) and aligned against the human reference data (GRCh38).
Assembly: Human reference data (GRCh38)
Supplementary files format and content: Barcodes, features, and matrix file for each samples.

source_name: Peripheral Blood Mononuclear Cell

extract_protocol:
Cell stocks were thawed in 37℃ 10% FBS/DMEM. Samples were washed twice with cold Ca2+ and Mg2+ free 0.04 % BSA/PBS at 300g for 5min at 4°C. Samples were gently resuspended in cold Ca2+ and Mg2+ free 0.04% BSA/PBS, and then counted using a LUNA-FX7™ Automated Fluorescence Cell Counter (Logos Biosystems) with AO/PI staining.
Multiplexing individual samples for scRNA-seq
To multiplex samples, each sample was tagged with antibody-polyadenylated DNA barcode for human cells (BD Biosciences, cat no. 633781). Briefly, cells were stained with multiplexing antibody for 20 min at room temperature, and then washed 3 times by using stain buffer (BD Biosciences, cat no. 554656). After final washing, samples were gently resuspended in cold sample buffer (BD Biosciences, cat no. 664887), counted with a LUNA-FX7™ Automated Fluorescence Cell Counter (logos biosystems), and then pooled.
Single cell capture and cDNA synthesis
Single cell capture was performed using BD Rhapsody Express instrument according to the manufacturer’s instruction (BD Bioscience). Briefly, pooled cells from each sample in cold sample buffer were loaded into the BD Rhapsody cartridge (BD Biosciences, cat no. 664887). After cells separation, cell barcode-magnetic beads were loaded into the cartridge. Cells were lysed and the mRNA capture bead were retrieved. cDNA synthesis and Exonuclease I treatment were performed on the mRNA capture beads using BD Rhapsody cDNA kit (BD Biosciences, cat no. 633773).
The purified WTA and Sample tag libraries were quantified using qPCR according to the qPCR Quantification Protocol Guide (KAPA), and qualified using the Agilent Technologies 4200 TapeStation (Agilent technologies). The libraries were sequenced using NovaSeq platform (Illumina).

tag: disease state

value: Healthy + Sepsis

value: Peripheral Blood Mononuclear Cell

value: wildtype

value: untreated


title: Endoderm Ngn3Cre 27ss b2 031, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_031

extract_protocol:
Endodermal and gut tissues from 9SS to 27SS, were enzymatically dissociated using 0.25% trypsin (Gibco, 25200-056) for roughly 4 minutes at 37°C. The reaction was halted by the addition of 0.4 volumes of fetal bovine serum (FBS). The resultant cell suspension was centrifuged at 1000 rpm for 5 minutes at 4°C, followed by supernatant removal. To prepare single-cell suspensions from endodermal and gut samples, cells were incubated with anti-EpCAM-APC antibody (Invitrogen, 17-5791-82, dilution 1:100) in FACS buffer (comprising HBSS buffer with 1% FBS) for 20 minutes at 4°C in darkness. Following incubation, cells were washed with FACS buffer and subjected to analysis and sorting using BD FACSAriaTM Fusion flow cytometers. Dead cells were excluded from the analysis through staining with 1 µg/mL DAPI (Macklin, D807022).
The Smart-seq3xpress libraries were prepared following Smart3-seq3xpress's protocols.

value: Ngn3-Cre; Ai6


title: 4T1 pLKO rep 3

description: Gene expression data from 4T1 cells.

source_name: 4T1 cells transduced with the empty pLKO lentiviral vector, biological replicate 3

value: Control


title: rosettaLeaf; treated; replicate 5

description: rosettaLeaf; treated; replicate 5

source_name: rosetta


title: Endoderm Ngn3Cre 27ss b2 030, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_030


title: Multiplexed_PBMCs(UT_Fu-Hp)

description: Library name: Sample 1

data_processing:
Single cell RNA sequencing data analysis The raw sequencing data (FASTQ) was processed using the BD Rhapsody WTA Analysis Pipeline v2.0 (BD Biosciences) and aligned against the human reference data (GRCh38).
Assembly: Human reference data (GRCh38)
Supplementary files format and content: Barcodes, features, and matrix file for each sample.

extract_protocol:
Single cells preparation
Cell stocks were thawed in 37℃ 10% FBS/DMEM. Samples were washed twice with cold Ca2+ and Mg2+ free 0.04 % BSA/PBS at 300g for 5min at 4°C. Samples were gently resuspended in cold Ca2+ and Mg2+ free 0.04% BSA/PBS, and then counted using a LUNA-FX7™ Automated Fluorescence Cell Counter (Logos Biosystems) with AO/PI staining.
Multiplexing individual samples for scRNA-seq
To multiplex samples, each sample was tagged with antibody-polyadenylated DNA barcode for human cells (BD Biosciences, cat no. 633781). Briefly, cells were stained with multiplexing antibody for 20 min at room temperature, and then washed 3 times by using stain buffer (BD Biosciences, cat no. 554656). After final washing, samples were gently resuspended in cold sample buffer (BD Biosciences, cat no. 664887), counted with a LUNA-FX7™ Automated Fluorescence Cell Counter (logos biosystems), and then pooled.
Single cell capture and cDNA synthesis
Single cell capture was performed using BD Rhapsody Express instrument according to the manufacturer’s instruction (BD Bioscience). Briefly, pooled cells from each sample in cold sample buffer were loaded into the BD Rhapsody cartridge (BD Biosciences, cat no. 664887). After cells separation, cell barcode-magnetic beads were loaded into the cartridge. Cells were lysed and the mRNA capture bead were retrieved. cDNA synthesis and Exonuclease I treatment were performed on the mRNA capture beads using BD Rhapsody cDNA kit (BD Biosciences, cat no. 633773).
The purified WTA and Sample tag libraries were quantified using qPCR according to the qPCR Quantification Protocol Guide (KAPA), and qualified using the Agilent Technologies 4200 TapeStation (Agilent technologies). The libraries were sequenced using NovaSeq platform (Illumina).

value: Healthy

value: untreated + Fucosylated haptoglobin


title: HFF cells, H3K14ac, HSV1, 14hpi, rep2

city: Freiburg

first: Florian

last: Full

address: Hermann-Herder-Str. 11

institute: institute of Virology, University Medical Center Freiburg

description: Library name: H3K14ac_HSV1_14hpi_rep2

data_processing:
Sequence reads were mapping to hg38 by STAR or bowtie2
Assembly: hg38
Supplementary files format and content: counts files were generated by featurecounts or TEcounts and bigwig files were generated by deeptools
Library strategy: CUT&RUN

source_name: cell line

extract_protocol:
Cells were resuspended in Trizol (Invitrogen) and RNA extracted from Trizol.
RNA-sequencing libraries were constructed using commercial kits (New England Biolabs) total RNA-seq with rRNA depletion as indicated; CUT&RUN was performed according to the CUT&RUN: Targeted in situ genome-wide profiling with high efficiency for low cell numbers V.3 protocol.

value: cell line

value: HFF

value: HFF cells

value: WT


title: rosettaLeaf; treated; replicate 4

description: rosettaLeaf; treated; replicate 4


title: Endoderm Ngn3Cre 27ss b2 029, scRNA-seq

first: Cheng-ran

last: Xu

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_029


title: HFF cells, H3K14ac, HSV1, 14hpi, rep1

description: Library name: H3K14ac_HSV1_14hpi_rep1


title: rosettaLeaf; treated; replicate 3

description: rosettaLeaf; treated; replicate 3


title: Endoderm Ngn3Cre 27ss b2 028, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_028


title: 4T1 pLKO rep 2

description: Gene expression data from 4T1 cells.

source_name: 4T1 cells transduced with the empty pLKO lentiviral vector, biological replicate 2

value: Breast cancer


title: rosettaLeaf; treated; replicate 2

description: rosettaLeaf; treated; replicate 2


title: rosettaLeaf; treated; replicate 1

description: rosettaLeaf; treated; replicate 1


title: HFF cells, H3K14ac, HSV1, 6hpi, rep1

description: Library name: H3K14ac_HSV1_6hpi_rep1


title: HFF cells, H3K14ac, Mock, rep2

description: Library name: H3K14ac_Mock_rep2

value: Mock


title: 4T1 Hmgcr rep 2

description: Gene expression data from 4T1 cells.

source_name: 4T1 cells transduced with lentiviral vectors expressing Hmgcr, biological replicate 2

value: Hmgcr overexpression


title: 4T1 Hmgcr rep 3

description: Gene expression data from 4T1 cells.

source_name: 4T1 cells transduced with lentiviral vectors expressing Hmgcr, biological replicate 3


title: 4T1 Hmgcr rep 1

description: Gene expression data from 4T1 cells.

source_name: 4T1 cells transduced with lentiviral vectors expressing Hmgcr, biological replicate 1


title: 4T1 pLVX rep 3

description: Gene expression data from 4T1 cells.

source_name: 4T1 cells transduced with the empty pLVX lentiviral vector, biological replicate 3


title: stem; treated; replicate 7

description: stem; treated; replicate 7

source_name: stem

value: stem


title: Endoderm Ngn3Cre 27ss b2 025, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_025

value: Endoderm


title: stem; treated; replicate 6

description: stem; treated; replicate 6


title: Endoderm Ngn3Cre 27ss b2 024, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_024


title: Endoderm Ngn3Cre 27ss b2 026, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_026


title: HFF cells, H3K9me3, HSV1, 14hpi, rep2

description: Library name: H3K9me3_HSV1_14hpi_rep2


title: 4T1 pLVX rep 2

description: Gene expression data from 4T1 cells.

source_name: 4T1 cells transduced with the empty pLVX lentiviral vector, biological replicate 2


title: 4T1 pLVX rep 1

description: Gene expression data from 4T1 cells.

source_name: 4T1 cells transduced with the empty pLVX lentiviral vector, biological replicate 1


title: HFF cells, H3K9me3, HSV1, 14hpi, rep1

description: Library name: H3K9me3_HSV1_14hpi_rep1


title: stem; treated; replicate 5

description: stem; treated; replicate 5


title: macrophages, R3_20h_Mock

source_name: RAW264.7 (ATCC TIB-71)

value: RAW264.7 (ATCC TIB-71)

value: macrophages

tag: infection condition

value: mock

tag: timepoint post_infection

tag: biological replicate


title: Endoderm Ngn3Cre 27ss b2 023, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_023


title: 4T1 pLKO rep 1

description: Gene expression data from 4T1 cells.

source_name: 4T1 cells transduced with the empty pLKO lentiviral vector, biological replicate 1

tag: treatment


title: stem; treated; replicate 4

description: stem; treated; replicate 4


title: macrophages, R3_1h_Mock

tag: cell type

value: 1 h


title: Endoderm Ngn3Cre 27ss b2 027, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_027

source_name: Endoderm

value: Ngn3-Cre; Ai6


title: stem; treated; replicate 3

description: stem; treated; replicate 3


title: HFF cells, H3K14ac, HSV1, 6hpi, rep2

description: Library name: H3K14ac_HSV1_6hpi_rep2


title: HFF cells, H3K9me3, HSV1, 6hpi, rep2

description: Library name: H3K9me3_HSV1_6hpi_rep2


title: macrophages, R2_20h_Mock


title: HFF cells, H3K14ac, Mock, rep1

description: Library name: H3K14ac_Mock_rep1


title: Endoderm Ngn3Cre 27ss b2 020, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_020


title: HFF cells, H3K9me3, HSV1, 6hpi, rep1

description: Library name: H3K9me3_HSV1_6hpi_rep1


title: stem; treated; replicate 2

description: stem; treated; replicate 2


title: macrophages, R2_1h_Mock


title: macrophages, R1_20h_Mock


title: HFF cells, H3K9me3, Mock, rep1

description: Library name: H3K9me3_Mock_rep1


title: Endoderm Ngn3Cre 27ss b2 019, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_019


title: Endoderm Ngn3Cre 27ss b2 022, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_022


title: HFF cells, SETDB1, HSV1, 14hpi, rep2

description: Library name: SETDB1_HSV1_14hpi_rep2


title: caulineLeaf; treated; replicate 5

description: caulineLeaf; treated; replicate 5

source_name: cauline

value: cauline


title: Endoderm Ngn3Cre 27ss b2 015, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_015


title: HFF cells, SETDB1, HSV1, 14hpi, rep1

description: Library name: SETDB1_HSV1_14hpi_rep1