title: Patient HCL619 cell 145, aAP status: no

city: Copenhagen

first: Joachim

last: Weischenfeldt

address: Ole Maaløes Vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

description: Library name: 145

data_processing:
Reads were aligned to GRCh38 using STAR v2.7.0c, with the parameters outFilterScoreMinOverLread= 0.3, outFilterMatchNminOverLread= 0.3, outFilterMatchNmin=0 andoutFilterMismatchNmax=2 options.
Gene counts were computed using the R Genomic Alignments summerizeOverlaps function with the “IntersectionNotEmpty” option.
Assembly: GRCh38

molecule: nuclear RNA

source_name: glioblastoma tumor slice

extract_protocol:
At the end of patchclamp recordings, nuclei were extracted by gentle negative pressure, aspirated into the pipette, and expelled into the lysis buffer with RNase inhibitor (Takara)24. Samples were snap-frozen on dry ice and stored at –80 °C for transcriptomic processing.
Following nucleus collection, reverse transcription and cDNA amplification were performed using the SMART-seq v2 Ultra Low Input RNA Kit (Takara). The cDNA quality and yield were assessed via Bioanalyzer (Agilent Technologies). Libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina) and sequenced on Illumina NextSeq 500.

value: glioblastoma tumor slice

value: cultured slice

value: Tumor


title: left atrium_2151

status: Public on Apr 01 2026

type: RNA

city: Nantes

first: Marja

last: Steenman

address: 8 quai Moncousu

country: France

institute: L'institut du thorax

description: Left atrium tissue of a 54 year old male donor

hyb_protocol: Each Cy3-labeled sample was mixed with an equal amount of Cy5-labeled reference and hybridized to the microarrays

scan_protocol: Hybridized arrays were scanned by fluorescence confocal microscopy (Scan array 4000XL, GSI-Lumonics). Fluorescence signal measurements were obtained separately for each fluorochrome at 10 µm/pixel resolution. Hybridization signal intensities were measured using GenePix Pro 5.0 (Axon).

data_processing: A lowess normalization procedure was applied channel-by-channel. For each microarray, Cy3- and Cy5-signal intensities were separately normalized to a prototype defined as the median profile of all Cy3- or Cy5-signal intensities.

molecule: total RNA

organism: Homo sapiens

source_name: left atrium

label_protocol: Cy3- and Cy5 labeled cDNA was prepared using the CyScribe cDNA Post Labeling Kit (Amersham Pharmacia Biotech). Each sample was labeled individually with Cy3. A reference-pool was created from equal quantities of all samples and labeled with Cy5.

extract_protocol: Total RNA was extracted using Trizol following manufacturer's instructions and treated with Amplification-grade Dnase I (Invitrogen), followed by purification using the GenElute Mammalian Total RNA Isolation Kit (Sigma)

tag: Sex

value: male

tag: age

value: 54 years

tag: tissue

value: left atrium

source_name: pooled total RNA from all samples


title: left atrium_XXX

description: Left atrium tissue of an 18 year old male donor

value: 18 years


title: K562 cells, no doxycycline induction, IgG antibody, batch1

type: SRA

city: Portland

first: Julia

last: Maxson

state: Oregon

address: 3181 SW Sam Jackson Park Rd

country: USA

institute: Oregon Health and Science University

description: Library name: K562_noDOX_IgG_1

library_source: genomic

data_processing:
Paired-end reads were trimmed using Fastp with adapter detection and poly-G trimming.
Trimmed reads from K562 samples were aligned to the human genome (GRCh38/hg38) and trimmed reads from mouse Lin- samples were aligned to the mouse genome (GRCm38/mm10) using Bowtie2 with parameters “--local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700”.
Duplicates were marked using the Sambamba “markdup” subcommand.
Peaks were called with GoPeaks using IgG samples as negative controls.
K562 CUT&RUN samples were sequenced across multiple batches. Samples from Batch 3 use an in-batch IgG control (K562_noDOX_IgG_3) for peak calling. K562 CUT&RUN samples from Batch 2 use the IgG control (K562_noDOX_IgG_1) from Batch 1 for peak calling. The IgG from Batch 2 yielded insufficient read depth to reliably model background signal and was therefore not used. The Batch 1 IgG sample used for peak calling was prepared using the same cell line and protocols as the experimental samples, allowing for consistent background estimation and peak calling when in-batch controls were not usable.
Mouse lineage-negative CUT&RUN samples were sequenced across multiple batches. Batch 1 samples (KAT7 and KMT2A samples) used the Batch 1 IgG control (mouse_batch1_LUC_IgG) for peak calling, which had similarly high read depth as the experimental samples in that batch, making it suitable for background modeling. Batches 2-3 used the Batch 4 IgG control (mouse_batch4_LUC_IgG) for peak calling. Batch 2 (sequenced on NovaSeq 6000) did not originally include an IgG control, and Batch 3 included an IgG control that had insufficient read depth and could not be used to reliably model background signal. The Batch 4 IgG control had read depth similar to samples in Batches 2-3, allowing for consistent background estimation and peak calling when in-batch controls were not usable.
Spike-in DNA from E. coli K-12 MG1655 was provided in the Epicypher CUT&RUN kit and used according to the manufacturer's protocols. To determine normalization factors for signal visualization, reads were aligned to host and E. coli reference genomes, and uniquely aligned reads were retained. Spike-in percentages were calculated as the proportion of reads mapping to E. coli relative to reads mapping to the host genome. Normalization factors were then calculated based on the relative spike-in percentages, scaled to the sample with the lowest spike-in recovery within each antibody target, consistent with Epicypher guidelines. Spike-in normalization was applied to the histone mark samples (H3K14ac, H3K23ac), as these samples had consistent spike-in recovery across replicates within each condition. BigWig coverage tracks for these samples were generated using spike-in derived scale factors with deepTools bamCoverage (--binSize 10 --smoothLength 50 --scaleFactor <sample-specific value>). Other antibody targets were not spike-in normalized due to variable spike-in recovery across replicates. For these samples, counts-per-million (CPM) normalized bigWig tracks were generated using deepTools bamCoverage with parameters “--binSize 10 --smoothLength 50 --normalizeUsing CPM”.
Assembly: GRCh38 (hg38) for samples from K562 cells, GRCm38 (mm10) for samples from mouse lineage-negative bone marrow cells
Supplementary files format and content: BigWig files include either spike-in normalized (for histone marks) or CPM-normalized (for other antibody targets) read signal for each sample.
Library strategy: CUT&Run

molecule: genomic DNA

growth_protocol: K562 cells were grown in IMDM medium with 10% FBS, 2mM glutamine, 1x penicillin/streptomycin. Mouse lineage-negative (Lin-) bone marrow primary cells were grown in IMDM medium with 15% FBS, 2mM glutamine, 1x penicillin/streptomycin in the presence of SCF, IL6, and IL3.

extract_protocol:
Cells were harvested following the EpiCypher CUT&RUN kit protocol (EpiCypher CUTANA 14-1048).
CUT&RUN libraries were prepared using the New England Biolabs NEBNext Ultra II DNA Library Prep Kit for Illumina.

treatment_protocol: K562 cells were either induced with 250ng/mL of doxycycline or not induced with any doxycycline for 24 hours. For mouse lineage-negative (Lin-) CUT&RUN, lentivirus were generated by co-transfecting psPAX2 (Addgene: 12260), pMD2.G (Addgene: 12259), and pSMAL_Luciferase (control) or pSMAL_SETBP1D868N into LentiX cells (Takara) with Fugene 6 (Promega E2691), according to the manufacturer's instructions. Mouse lineage-negative bone marrow cells were lentivirally transduced with either a control (luciferase) or SETBP1D868N mutant and then GFP-sorted.

tag: cell line

tag: cell type

value: myeloid leukemia cell line

tag: treatment

value: No doxycycline induction

tag: cutrun antibody

value: IgG (EpiCypher, 13-0042k)

tag: genome assembly

value: GRCh38 (hg38)

tag: sequencing batch


title: Patient HCL934 cell 75, aAP status: no

description: Library name: 75

library_source: transcriptomic single cell


title: JHH352Org

city: Baltimore

first: Jacquelyn

last: Zimmerman

state: MD

address: 1650 Orleans St

institute: Johns Hopkins

description:
Library name: JHH352Org
Orgnanoid Patient 352, Monoculture

library_source: transcriptomic

data_processing:
Salmon v.1.9.0
Alignment was performed utilizing Salmon v1.9.0 on the Joint High-Performance Computing Exchange (JHPCE). “salmon_partial_sa_index__default.tgz” was used as the index for alignment for the HG38 genome, which was premade and available on refgenie (http://refgenomes.databio.org/v3/genomes/splash/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4). Salmon quantification, [salmon quant], was completed in mapping-based mode (--validateMappings) with automatic library detection. Salmon quantifications were the imported into R using tximport v1.20.0, with the use of the “tgMap.tsv” file also provided in the HG38 refgenie repository for accurate gene-level summarization.
We evaluated sample quality from the distribution of reads as visualized in a boxplot of log counts. We observed no samples with zero median expression, reflective of a low read count, so samples were not of low quality. We used principal component analysis (PCA) of the variance stabilization transform (vst) RNA-seq data to evaluate sample clustering. Projection of the discovered CoGAPS Pattern 7 onto the VST data was completed using ProjectR (V1.8.0). The bulk-seq normalized data and CoGAPs feature loadings were run through the projectR function of the package(14). The projection results were combined with the bulk-seq metadata and plotted using ggplot2 (V3.3.5) and paired t-test results added using ggpubr (V0.4.0)(14).
Analysis completed using DESeq2
Assembly: HG38
Supplementary files format and content: tab-separated values

source_name: pancreas

extract_protocol:
Cells that were coculture were sorted by FACS and immediately underwent RNA extraction (Qiagen RNeasy kit 74004) per manufacturers protocol. RNA was quantified at 260nm using NanoDrop1000 (Thermo Fisher Scientific) and 200ug of RNA was sent to Novogene Corporation Inc. RNA integrity (RIN) was measured at Novogene with Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA). All samples were required to demonstrate RIN > 6.8 and ranged from 7.2 to 10.0.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

value: pancreas

value: Patient-derived organoid

value: epithelium

value: monoculture


title: left atrium_3079

description: Left atrium tissue of a 21 year old male donor

value: 21 years


title: vHipp_38

city: New York

first: Jennifer

middle: C

last: Chan

state: New York

address: 1470 Madison Ave 9-201

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

description:
Library name: Sample 51
Illumina Stranded mRNA Prep

data_processing:
Alignment using Kallisto v.0.46.1
Reduce variation using RUV-seq v.1.32.0
Differential expression using DESeq2 v.1.38.3
Assembly: mm10
Supplementary files format and content: csv file with normalized counts containing all samples

molecule: polyA RNA

organism: Mus musculus

source_name: Brain

extract_protocol:
Homogenization of tissue in Trizol Reagent with subsequent clean-up using Rneasy Microcolumns.
TruSeq RNA Library Prep Kit v2 and Illumina Stranded mRNA Prep

value: Brain

tag: region

value: vHpc

tag: group

tag: virus

tag: ruvs k_value

tag: batch


title: JHH380CoCAF

description:
Library name: JHH380CoCAF
CAF Patient 380, Coculture

value: CAF

value: coculture


title: dHipp_39

description:
Library name: Sample 52
Illumina Stranded mRNA Prep

value: dHpc


title: left atrium_3141

description: Left atrium tissue of a 52 year old male donor

value: male

value: 52 years


title: left atrium_XVII

description: Left atrium tissue of a 52 year old female donor

value: female

value: left atrium


title: JHH380CAF

description:
Library name: JHH380CAF
CAF Patient 380, Monoculture


title: dHipp_38

description:
Library name: Sample 49
Illumina Stranded mRNA Prep


title: mPFC_38

description:
Library name: Sample 50
Illumina Stranded mRNA Prep

value: mPFC


title: Patient HCL560 cell 137, aAP status: no

description: Library name: 137

value: glioblastoma tumor slice

value: cultured slice

value: Tumor


title: left atrium_4049

description: Left atrium tissue of a 65 year old female donor

value: 65 years


title: Patient HCL560 cell 131, aAP status:  aAP

description: Library name: 131


title: left atrium_III

description: Left atrium tissue of a 48 year old male donor

value: 48 years


title: Patient HCL560 cell 135, aAP status:  aAP

description: Library name: 135


title: JHH362CAF

description:
Library name: JHH362CAF
CAF Patient 362, Monoculture

value: pancreas

value: Patient-derived organoid

value: monoculture


title: vHipp_37

description:
Library name: Sample 48
Illumina Stranded mRNA Prep

value: Brain

value: vHpc


title: Patient HCL560 cell 120, aAP status:  aAP

description: Library name: 120

value: Acute slice


title: JHH348CoCAF

description:
Library name: JHH348CoCAF
CAF Patient 348, Coculture

value: CAF

value: coculture


title: dHipp_37

description:
Library name: Sample 46
Illumina Stranded mRNA Prep

value: dHpc


title: Patient HCL560 cell 115, aAP status:  aAP

description: Library name: 115


title: left atrium_3126

description: Left atrium tissue of a 33 year old male donor

value: male

value: 33 years


title: left atrium_3091

description: Left atrium tissue of a 31 year old female donor

value: female

value: 31 years

value: left atrium


title: JHH348CAF

description:
Library name: JHH348CAF
CAF Patient 348, Monoculture


title: Patient HCL135 cell 62, aAP status:  aAP

description: Library name: 62

value: glioblastoma tumor slice

value: Tumor


title: left atrium_VIII

value: 52 years


title: vHipp_36

description:
Library name: Sample 45
Illumina Stranded mRNA Prep


title: mPFC_37

description:
Library name: Sample 47
Illumina Stranded mRNA Prep

value: mPFC


title: left atrium_4013

description: Left atrium tissue of a 23 year old male donor

value: 23 years


title: Patient HCL135 cell 60, aAP status:  aAP

description: Library name: 60


title: CMK cells, NC control, replicate 1

city: suzhou

first: yang

last: yang

address: zhongnan road

country: China

institute: soochow university

description: Library name: Sample 3

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and then mapped to hg38 whole genome and GENCODE v29 using STAR 2.7.10a with parameters --outFilterMismatchNoverReadLmax 0.04 --outFilterMultimapNmax 1
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using stringtie v2.1.7. Gene differential expression were calculated using DESeq2 v1.40.2.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include read counts and expression values of each gene for each sample and differential expression values between knockdown group and NC group.

source_name: CMK

extract_protocol:
Cells were harvested, and total RNA was extracted with TRIzol (Invitrogen) according to the manufacturer's protocol.  FastPure Cell/Tissue Total RNA Isolation Kit V2(( Vazyme , RC112-01)  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CMK

value: AML cell

value: Knockdown NC


title: Patient HCL135 cell 59, aAP status:  aAP

description: Library name: 59

value: Acute slice


title: left atrium_VI

description: Left atrium tissue of a 49 year old male donor

value: 49 years


title: dHipp_36

description:
Library name: Sample 43
Illumina Stranded mRNA Prep

value: Brain


title: left atrium_XXXI

description: Left atrium tissue of a 24 year old female donor

value: 24 years


title: left atrium_3165

description: Left atrium tissue of a 39 year old female donor

value: 39 years


title: CMK cells, NC control, replicate 2

description: Library name: Sample 4


title: CMK cells, knockdown USP1, replicate 2

description: Library name: Sample 2

value: Knockdown USP1


title: vHipp_32

description:
Library name: Sample 42
Illumina Stranded mRNA Prep

value: vHpc


title: mPFC_36

description:
Library name: Sample 44
Illumina Stranded mRNA Prep


title: Patient HCL629 cell 171, aAP status:  aAP

description: Library name: 171

value: cultured slice


title: mPFC_32

description:
Library name: Sample 41
Illumina Stranded mRNA Prep


title: left atrium_5048

description: Left atrium tissue of a 25 year old female donor

value: female

value: 25 years

value: left atrium


title: Patient HCL629 cell 164, aAP status:  aAP

description: Library name: 164

value: glioblastoma tumor slice

value: Tumor


title: dHipp_32

description:
Library name: Sample 40
Illumina Stranded mRNA Prep

value: dHpc


title: PC9,scNSR

city: Jerusalem

first: Xue

last: Sun

address: Hebrew University, Givat Ram campus

department: Biochemistry department

country: Israel

institute: The Hebrew University of Jerusalem

description:
Library name: scNSR_PC9
Raw reads from all lanes are merged.

data_processing:
The raw sequencing data were paired-end fastq files. In data QC, Read1 from all lanes was iterated through and filtered for reads possessing the correct barcode structure, and single-cell barcodes and UMIs were extracted. Barcodes that could be uniquely assigned to an accepted barcode with a Hamming distance of 2 nt or less were merged. UMI deduplication was performed by removing reads with duplicated UMIs under the same single-cell barcode. Unique UMI reads per barcode were counted and plotted in a histogram. Thresholds were determined based on the separation between the first and second peaks. This threshold was then applied in the filtering step, where a similar process was performed as in QC, but outputting reads with UMI counts greater than the threshold into barcode-specific fastq files. Single cell fastqs were then trimmed for Illumina adaptors, barcode spacers and repeated elements (20x A/T/G/C). Finally reads aligned to ribosomal RNA were removed. Raw data were then aligned in multiple rounds to exclusively map to total RNA. Reads were first mapped to the whole genome, then counted with different GTF files in each round. Only reads that failed to align proceeded to the next round. The alignment order was short RNA, long RNA exons, long RNA introns, and pseudogenes. Single cell matrix obtained from each round were combined in downstream analysis. Detailed processing method should be found in the manuscript.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

growth_protocol: PC9 cells were grown in DMEM supplemented with 10% fetal bovine serum, 50 μg/ml penicillin-streptomycin, 2 mM L-glutamine, and 1 mM sodium pyruvate. HCC827 cells were grown in RPMI 1640 (+Glu) supplemented with 10% fetal bovine serum, 50 μg/ml penicillin-streptomycin and 10mM HEPES. All cells were maintained in 5% CO2 in a humidified incubator at 37 °C.

extract_protocol:
Cells were detached from culture dish with treatment of 2mL trypsin for 10cm2 dish. After counting and checking viability, single cell suspension were prepared at concentration of 300,000 cells/mL in PBS containing 10% Optiprep.
The total RNA library was prepared in two steps. First, total RNA was captured in nanodroplets, and single-cell barcodes were assigned to reversely transcribed cDNA. Subsequently, the cDNA was pooled for in vitro amplification and integration of Illumina adapters. Briefly, using a microfluidics device, single cells were encapsulated in water-in-oil droplets containing a lysis buffer with reverse transcription (RT) enzymes and hydrogel beads carrying primers. These primers included single-cell barcodes and rDS/polyT sequences, as well as the Illumina adapter PE1 and a T7 promoter for in vitro transcription (IVT). Following reverse transcription, the cDNA from all droplets was pooled, unused primers were removed, and the cDNA was cleaned. The second strand was then synthesized prior to IVT amplification. The amplified RNA was slightly fragmented, and the Illumina adapter PE2 was integrated via a random RT step. Finally, the library was amplified by PCR, during which Illumina indexes were incorporated.

treatment_protocol: For drug treatment experiments, stock solutions of Osimertinib and Gefitinib were first diluted in DMSO and then in culture medium, maintaining a final DMSO concentration of 1% across all dilutions. Untreated cells were given 1% DMSO as a control. As start, 1 x 106 PC9 or HCC827 cells were seeded to a 10 cm2 plate. 24h after seeding, 1μM Osimertinib and Gefitinib were given to cells. Every 3 days, medium was changed with fresh drugs. After 9 days, remained cells were collected for sc-rDSeq. Control groups were treated with DMSO for 3 days. Cell survival relative to the control was about 1% for all groups.


title: left atrium_3143

description: Left atrium tissue of a 18 year old male donor

value: male

value: 18 years


title: Patient HCL629 cell 173, aAP status: no

description: Library name: 173


title: CMK cells, knockdown USP1, replicate 1

description: Library name: Sample 1

value: CMK

value: AML cell


title: left atrium_2158

description: Left atrium tissue of a 17 year old male donor

value: 17 years


title: PC9,bulk,polyT,RNA,longRT,rep2

description:
Library name: polyT_RNA_long_2
Raw reads from all lanes are merged. Data were aligned with STAR and quantified with cufflinks ("cufflinks_isoform") for SIRV+ERCC calibration


title: Patient HCL629 cell 153, aAP status: no

description: Library name: 153


title: vHipp_31

description:
Library name: Sample 39
Illumina Stranded mRNA Prep

value: Brain


title: left atrium_XXII

description: Left atrium tissue of a 61 year old male donor

value: 61 years


title: PC9,bulk,polyT,RNA,longRT,rep1

description:
Library name: polyT_RNA_long_1
Raw reads from all lanes are merged. Data were aligned with STAR and quantified with cufflinks ("cufflinks_isoform") for SIRV+ERCC calibration


title: JHH362CoCAF

description:
Library name: JHH362CoCAF
CAF Patient 362, Coculture

value: pancreas

value: Patient-derived organoid

value: CAF

value: coculture


title: Patient HCL619 cell 151, aAP status: no

description: Library name: 151

value: cultured slice


title: mPFC_31

description:
Library name: Sample 38
Illumina Stranded mRNA Prep

value: mPFC


title: dHipp_31

description:
Library name: Sample 37
Illumina Stranded mRNA Prep


title: Patient HCL629 cell 177, aAP status:  aAP

description: Library name: 177

value: Neuron


title: PC9,bulk,polyTN8,cell,rampRT,rep1

description:
Library name: polyTN8_cell_ramp_1
Raw reads from all lanes are merged. Data were aligned with STAR and quantified with cufflinks ("cufflinks_isoform") for SIRV+ERCC calibration


title: left atrium_VII

description: Left atrium tissue of a 57 year old female donor

value: female

value: 57 years

value: left atrium


title: vHipp_30

description:
Library name: Sample 36
Illumina Stranded mRNA Prep

value: vHpc

value: NP


title: Patient HCL629 cell 172, aAP status: no

description: Library name: 172

value: glioblastoma tumor slice


title: left atrium_XII

description: Left atrium tissue of a 50 year old male donor

value: male

value: 50 years


title: PC9,bulk,polyT,cell,rampRT,rep2

description:
Library name: polyT_cell_ramp_2
Raw reads from all lanes are merged. Data were aligned with STAR and quantified with cufflinks ("cufflinks_isoform") for SIRV+ERCC calibration


title: mPFC_30

description:
Library name: Sample 35
Illumina Stranded mRNA Prep

value: Brain


title: left atrium_2089

description: Left atrium tissue of a 36 year old female donor

value: 36 years


title: Patient HCL629 cell 168, aAP status: no

description: Library name: 168


title: Patient HCL629 cell 176, aAP status: no

description: Library name: 176


title: dHipp_30

description:
Library name: Sample 34
Illumina Stranded mRNA Prep

value: dHpc


title: PC9,bulk,polyT,cell,rampRT,rep1

description:
Library name: polyT_cell_ramp_1
Raw reads from all lanes are merged. Data were aligned with STAR and quantified with cufflinks ("cufflinks_isoform") for SIRV+ERCC calibration


title: PC9,bulk,polyT,cell,longRT,rep2

description:
Library name: polyT_cell_long_2
Raw reads from all lanes are merged. Data were aligned with STAR and quantified with cufflinks ("cufflinks_isoform") for SIRV+ERCC calibration


title: Patient HCL629 cell 152, aAP status: no

description: Library name: 152


title: PC9,bulk,polyTN8,cell,rampRT,rep2

description:
Library name: polyTN8_cell_ramp_2
Raw reads from all lanes are merged. Data were aligned with STAR and quantified with cufflinks ("cufflinks_isoform") for SIRV+ERCC calibration


title: vHipp_29

description:
Library name: Sample 33
Illumina Stranded mRNA Prep


title: left atrium_3112

description: Left atrium tissue of a 23 year old female donor

value: 23 years


title: PC9,bulk,polyT,cell,longRT,rep1

description:
Library name: polyT_cell_long_1
Raw reads from all lanes are merged. Data were aligned with STAR and quantified with cufflinks ("cufflinks_isoform") for SIRV+ERCC calibration


title: Patient HCL619 cell 148, aAP status:  aAP

description: Library name: 148


title: mPFC_29

description:
Library name: Sample 32
Illumina Stranded mRNA Prep


title: left atrium_3150

description: Left atrium tissue of a 30 year old male donor

value: 30 years


title: PC9,bulk,KAPA,RNA,rep2

description:
Library name: KAPA_PC9_RNA_2
Raw reads from all lanes are merged: Data were processed in three different ways: 1) STAR aligned and cufflinks quantified ("cufflinks_isoform") for SIRV+ERCC calibration 5) RSEM aligned for both gene counts (".lRNA.genes.results) and isoform counts (".lRNA.isoforms.results")


title: left atrium_5039

description: Left atrium tissue of a 17 year old male donor

value: 17 years


title: Patient HCL619 cell 147, aAP status:  aAP

description: Library name: 147

value: cultured slice


title: Patient HCL934 cell 81, aAP status: no

description: Library name: 81


title: PC9,bulk,KAPA,RNA,rep1

description:
Library name: KAPA_PC9_RNA_1
Raw reads from all lanes are merged: Data were processed in three different ways: 1) STAR aligned and cufflinks quantified ("cufflinks_isoform") for SIRV+ERCC calibration 4) RSEM aligned for both gene counts (".lRNA.genes.results) and isoform counts (".lRNA.isoforms.results")


title: vHipp_28

description:
Library name: Sample 30
Illumina Stranded mRNA Prep

value: PP


title: left atrium_2054

description: Left atrium tissue of a 39 year old male donor

value: 39 years


title: Patient HCL560 cell 138, aAP status: no

description: Library name: 138

value: Neuron


title: left atrium_2138

description: Left atrium tissue of a 25 year old female donor

value: female

value: 25 years


title: Patient HCL560 cell 136, aAP status:  aAP

description: Library name: 136


title: mPFC_28

description:
Library name: Sample 29
Illumina Stranded mRNA Prep

value: mPFC


title: dHipp_28

description:
Library name: Sample 28
Illumina Stranded mRNA Prep


title: Patient HCL560 cell 132, aAP status: no

description: Library name: 132


title: left atrium_I

description: Left atrium tissue of a 49 year old female donor

value: 49 years

value: left atrium


title: dHipp_29

description:
Library name: Sample 31
Illumina Stranded mRNA Prep

value: NP


title: PC9,bulk,KAPA,cell,rep2

description:
Library name: KAPA_PC9_cell_2
Raw reads from all lanes are merged: Data were processed in three different ways: 1) STAR aligned and cufflinks quantified ("cufflinks_isoform") for SIRV+ERCC calibration 3) RSEM aligned for both gene counts (".lRNA.genes.results) and isoform counts (".lRNA.isoforms.results")


title: PC9,bulk,KAPA,cell,rep1

description:
Library name: KAPA_PC9_cell_1
Raw reads from all lanes are merged: Data were processed in three different ways: 1) STAR aligned and cufflinks quantified ("cufflinks_isoform") for SIRV+ERCC calibration 2) RSEM aligned for both gene counts (".lRNA.genes.results) and isoform counts (".lRNA.isoforms.results")


title: PC9,bulk,rDSeq,RNA,rep2

description:
Library name: bulkrDSeq_PC9_RNA_2
Raw reads from all lanes are merged; Data were processed in three different ways: 1) STAR aligned and cufflinks quantified ("cufflinks_isoform") for SIRV+ERCC calibration 2) RSEM aligned for whole dataset which generated both gene counts (".lRNA.genes.results) and isoform counts (".lRNA.isoforms.results") 3) Fastq reads split into rDS or polyTN11 origin priori to RSEM alignment, only gene counts generated ("polyT.lRNA.genes.results" and "rDS.lRNA.genes.results")


title: left atrium_3064

description: Left atrium tissue of a 54 year old male donor

value: male

value: 54 years


title: vHipp_27

description:
Library name: Sample 27
Illumina Stranded mRNA Prep

value: Brain

value: vHpc


title: Patient HCL560 cell 130, aAP status:  aAP

description: Library name: 130

value: glioblastoma tumor slice


title: PC9,bulk,rDSeq,RNA,rep1

description:
Library name: bulkrDSeq_PC9_RNA_1
Raw reads from all lanes are merged; Data were processed in three different ways: 1) STAR aligned and cufflinks quantified ("cufflinks_isoform") for SIRV+ERCC calibration 2) RSEM aligned for whole dataset which generated both gene counts (".lRNA.genes.results) and isoform counts (".lRNA.isoforms.results") 3) Fastq reads split into rDS or polyTN10 origin priori to RSEM alignment, only gene counts generated ("polyT.lRNA.genes.results" and "rDS.lRNA.genes.results")


title: 3-day old B. rapa WT seedlings mock-treated (1 hour)_rep3_forward reads

city: Maynooth

first: Emmanuelle

last: Graciet

state: Kildare

address: Biology Department

department: Biology

country: Ireland

institute: Maynooth University

description: Library name: WT-Mock-3

data_processing:
Sequencing reads filtering with SOAPnuke
Genome mapping with HISAT2
Gene expression analysis with Bowtie2
Assembly: GCF_000309985.2
Supplementary files format and content: Prt6-2-3-Mock-VS-Prt6-2-3-flg22.DEseq2_Method.GeneDiffExp.txt
Supplementary files format and content: WT-Mock-VS-WT-flg22.DEseq2_Method.GeneDiffExp.txt

organism: Brassica rapa

source_name: Whole seedlings

growth_protocol: B. rapa seedlings were grown in continuous light conditions at 20°C in cups containing 0.5x MS agar supplemented with 0.5% (w/v) sucrose. After 3 days, 4 seedlings per genotype per treatment were transferred to a well of a 6-well plate containing 6 mL of 0.5x MS supplemented with 0.5% sucrose (liquid medium) and returned to the growth room for incubation overnight with mild shaking.

extract_protocol:
Whole seedlings were collected. The tissue was ground in liquid nitrogen and total RNA was extracted using Spectrum™ Plant Total RNA kit (Sigma-Aldrich).
Libraries were prepared by BGI Genomics (Hong Kong) following mRNA enrichment and purification

treatment_protocol: On day 4, seedlings were treated with 1 µM flg22 or an equivalent volume of water (mock treatment) for 1 hr. Seedlings were collected and frozen immediately in liquid nitrogen prior to RNA extraction with Spectrum Plant Total RNA Kit (Merck). Samples from three biological replicates were used.

value: Whole seedlings

tag: genotype

value: R-o-18 wild type

value: mock


title: Patient HCL560 cell 129, aAP status:  aAP

description: Library name: 129

value: cultured slice


title: PC9,bulk,rDSeq,cell,rep2

description:
Library name: bulkrDSeq_PC9_cell_2
Raw reads from all lanes are merged; Data were processed in three different ways: 1) STAR aligned and cufflinks quantified ("cufflinks_isoform") for SIRV+ERCC calibration 2) RSEM aligned for whole dataset which generated both gene counts (".lRNA.genes.results) and isoform counts (".lRNA.isoforms.results") 3) Fastq reads split into rDS or polyTN9 origin priori to RSEM alignment, only gene counts generated ("polyT.lRNA.genes.results" and "rDS.lRNA.genes.results")


title: left atrium_4015

description: Left atrium tissue of a 19 year old male donor

value: 19 years


title: left atrium_2017

description: Left atrium tissue of a 58 year old male donor

value: 58 years


title: 3-day old B. rapa WT seedlings mock-treated (1 hour)_rep2_forward reads

description: Library name: WT-Mock-2


title: mPFC_27

description:
Library name: Sample 26
Illumina Stranded mRNA Prep

value: PP


title: dHipp_27

description:
Library name: Sample 25
Illumina Stranded mRNA Prep

value: dHpc


title: Patient HCL560 cell 127, aAP status:  aAP

description: Library name: 127

value: Neuron


title: PC9,bulk,rDSeq,cell,rep1

description:
Library name: bulkrDSeq_PC9_cell_1
Raw reads from all lanes are merged; Data were processed in three different ways: 1) STAR aligned and cufflinks quantified ("cufflinks_isoform") for SIRV+ERCC calibration 2) RSEM aligned for whole dataset which generated both gene counts (".lRNA.genes.results) and isoform counts (".lRNA.isoforms.results") 3) Fastq reads split into rDS or polyTN8 origin priori to RSEM alignment, only gene counts generated ("polyT.lRNA.genes.results" and "rDS.lRNA.genes.results")


title: Patient HCL560 cell 126, aAP status:  aAP

description: Library name: 126


title: 3-day old B. rapa WT seedlings mock-treated (1 hour)_rep1_forward reads

description: Library name: WT-Mock-1


title: PC9,bulk,ratio,1,rep2

description:
Library name: bulk_ratio_1_2
Raw reads from all lanes are merged. Data were aligned with STAR and quantified with cufflinks ("cufflinks_isoform") for SIRV+ERCC calibration


title: 3-day old B. rapa WT seedlings flg22-treated (1 hour)_rep3_forward reads

description: Library name: WT-flg22-3


title: mPFC_24

description:
Library name: Sample 23
Illumina Stranded mRNA Prep

value: mPFC


title: dHipp_24

description:
Library name: Sample 22
Illumina Stranded mRNA Prep


title: 3-day old B. rapa WT seedlings flg22-treated (1 hour)_rep2_forward reads

description: Library name: WT-flg22-2


title: PC9,bulk,ratio,10,rep2

description:
Library name: bulk_ratio_10_2
Raw reads from all lanes are merged. Data were aligned with STAR and quantified with cufflinks ("cufflinks_isoform") for SIRV+ERCC calibration


title: Patient HCL738 cell 108, aAP status:  aAP

description: Library name: 108


title: vHipp_24

description:
Library name: Sample 24
Illumina Stranded mRNA Prep


title: left atrium_XVIII

description: Left atrium tissue of a 57 year old male donor

value: 57 years

value: left atrium


title: vHipp_23

description:
Library name: Sample 21
Illumina Stranded mRNA Prep

value: NP


title: PC9,bulk,ratio,10,rep1

description:
Library name: bulk_ratio_10_1
Raw reads from all lanes are merged. Data were aligned with STAR and quantified with cufflinks ("cufflinks_isoform") for SIRV+ERCC calibration


title: mPFC_23

description:
Library name: Sample 20
Illumina Stranded mRNA Prep


title: Patient HCL738 cell 109, aAP status: no

description: Library name: 109


title: 3-day old B. rapa WT seedlings flg22-treated (1 hour)_rep1_forward reads

description: Library name: WT-flg22-1


title: 3-day old B. rapa prt6.2/3 seedlings mock-treated (1 hour)_rep3_forward reads

description: Library name: PRT6-2-3-Mock-3

value: prt6.2 prt6.3 double mutant


title: PC9,bulk,ratio,1,rep1

description:
Library name: bulk_ratio_1_1
Raw reads from all lanes are merged. Data were aligned with STAR and quantified with cufflinks ("cufflinks_isoform") for SIRV+ERCC calibration


title: PC9,bulk,ratio,100,rep2

description:
Library name: bulk_ratio_100_2
Raw reads from all lanes are merged. Data were aligned with STAR and quantified with cufflinks ("cufflinks_isoform") for SIRV+ERCC calibration


title: Patient HCL738 cell 105, aAP status:  aAP

description: Library name: 105


title: dHipp_23

description:
Library name: Sample 19
Illumina Stranded mRNA Prep

value: Brain


title: Patient HCL738 cell 107, aAP status:  aAP

description: Library name: 107


title: PC9,bulk,ratio,1000,rep2

description:
Library name: bulk_ratio_1000_2
Raw reads from all lanes are merged. Data were aligned with STAR and quantified with cufflinks ("cufflinks_isoform") for SIRV+ERCC calibration


title: PC9,bulk,ratio,100,rep1

description:
Library name: bulk_ratio_100_1
Raw reads from all lanes are merged. Data were aligned with STAR and quantified with cufflinks ("cufflinks_isoform") for SIRV+ERCC calibration


title: Patient HCL738 cell 100, aAP status:  aAP

description: Library name: 100


title: 3-day old B. rapa prt6.2/3 seedlings mock-treated (1 hour)_rep2_forward reads

description: Library name: PRT6-2-3-Mock-2


title: vHipp_20

description:
Library name: Sample 18
Illumina Stranded mRNA Prep

value: vHpc


title: mPFC_20

description:
Library name: Sample 17
Illumina Stranded mRNA Prep


title: 3-day old B. rapa prt6.2/3 seedlings mock-treated (1 hour)_rep1_forward reads

description: Library name: PRT6-2-3-Mock-1


title: subgingival plaque, sample 25

city: Halle (Saale)

first: Danny

last: Misiak

address: Kurt-Mothes-Str. 3a

department: Molecular Cell Biology

country: Germany

institute: Martin Luther University Halle-Wittenberg

description: Library name: DS25

data_processing:
Pre-processing and quality filtering of raw tags were carried out using the QIIME2.
Raw reads were filtered using DADA2
Sequence error correction with DADA2, defining Amplicon Sequence Variants (ASV).
Taxonomic classification of ASVs was performed in QIIME2 using the classify-sklearn algorithm.
Species annotation in this study was based on the SILVA 138.1 reference database.
Assembly: Silva 138.1
Supplementary files format and content: Comma-separated text files including values for each sample or phylum abundance.
Library strategy: 16S rRNA-seq

source_name: subgingival plaque

extract_protocol:
Microbial DNA was extracted using AllPrep® Bact. DNA/RNA/Protein Kit  (Qiagen, Hilden, Germany) in line with the manufacturer's specifications.
Library preparation and indexing were conducted using the NEBNext® Ultra™ DNA Library Prep Kit (Illumina, San Diego, CA, USA).

value: subgingival plaque


title: 3-day old B. rapa prt6.2/3 seedlings flg22-treated (1 hour)_rep3_forward reads

description: Library name: PRT6-2-3-flg22-3

value: Whole seedlings


title: PC9,bulk,ratio,1000,rep1

description:
Library name: bulk_ratio_1000_1
Raw reads from all lanes are merged. Data were aligned with STAR and quantified with cufflinks ("cufflinks_isoform") for SIRV+ERCC calibration


title: dHipp_20

description:
Library name: Sample 16
Illumina Stranded mRNA Prep


title: 3-day old B. rapa prt6.2/3 seedlings flg22-treated (1 hour)_rep2_forward reads

description: Library name: PRT6-2-3-flg22-2


title: 3-day old B. rapa prt6.2/3 seedlings flg22-treated (1 hour)_rep1_forward reads

description: Library name: PRT6-2-3-flg22-1


title: Patient HCL738 cell 99, aAP status:  aAP

description: Library name: 99

value: glioblastoma tumor slice


title: Patient HCL738 cell 101, aAP status:  aAP

description: Library name: 101


title: Patient HCL738 cell 103, aAP status:  aAP

description: Library name: 103


title: mPFC_2

description:
Library name: Sample 14
Illumina Stranded mRNA Prep


title: Emu SPs, St 36 ventral, 4

city: Fukuoka

first: Seung June

last: Kwon

state: Fukuoka

address: 744 Motooka, Nishi-ku

department: Graduate School of Systems Life Sciences

country: Japan

institute: Kyushu University

description: Library name: Sample 24

data_processing:
Sequences were separated by sample barcodes with UMI-tools and aligned to reference genome using HISAT2.
featureCounts was used to generate raw count data assigned to genes.
DESeq2 was used to extract differentially expressed genes.
UMI-tools was used to demultiplex the raw fastq files (now should be treated as a single-end file).
Assembly: chicken: GRCg6a, GCA_000002315.5; emu: ZJU2.0, GCA_016128335.2
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Dromaius novaehollandiae

source_name: Sternal progenitors from LPM

extract_protocol:
After UV irradiation, total tissue lysate was collected and purified. 2nd strand DNA was synthesized using Rnase H, DNA pol I, and DNA ligase mix.
Only cDNAs from UV-irraidated region are filled-in to 5' end of T7 promotoer, being linearly amplified as RNAs via IVT reaction. RNA libraries were then reverse-transcribed and sequenced on Illumina NovaSeq 6000 (R1: UMI and barcode, R2: cDNA).

value: Sternal progenitors from LPM


title: Patient HCL738 cell 97, aAP status:  aAP

description: Library name: 97

value: cultured slice


title: subgingival plaque, sample 24

description: Library name: DS24


title: vHipp_2

description:
Library name: Sample 15
Illumina Stranded mRNA Prep


title: Patient HCL738 cell 96, aAP status:  aAP

description: Library name: 96


title: subgingival plaque, sample 23

description: Library name: DS23


title: Emu SPs, St 36 ventral, 3

description: Library name: Sample 23


title: dHipp_2

description:
Library name: Sample 13
Illumina Stranded mRNA Prep


title: subgingival plaque, sample 22

description: Library name: DS22


title: Patient HCL738 cell 95, aAP status:  aAP

description: Library name: 95


title: vHipp_17

description:
Library name: Sample 12
Illumina Stranded mRNA Prep


title: subgingival plaque, sample 21

description: Library name: DS21


title: subgingival plaque, sample 20

description: Library name: DS20


title: mPFC_17

description:
Library name: Sample 11
Illumina Stranded mRNA Prep


title: Patient HCL934 cell 82, aAP status: no

description: Library name: 82


title: Emu SPs, St 36 ventral, 1

description: Library name: Sample 21


title: Patient HCL934 cell 76, aAP status: no

description: Library name: 76


title: subgingival plaque, sample 19

description: Library name: DS19


title: dHipp_17

description:
Library name: Sample 10
Illumina Stranded mRNA Prep


title: Emu SPs, St 36 dorsal, 4

description: Library name: Sample 20


title: Patient HCL934 cell 83, aAP status: no

description: Library name: 83


title: Patient HCL934 cell 72, aAP status: no

description: Library name: 72


title: mPFC_16

description:
Library name: Sample 8
Illumina Stranded mRNA Prep


title: subgingival plaque, sample 18

description: Library name: DS18


title: vHipp_16

description:
Library name: Sample 9
Illumina Stranded mRNA Prep


title: subgingival plaque, sample 17

description: Library name: DS17


title: Emu SPs, St 36 dorsal, 2

description: Library name: Sample 18


title: Emu SPs, St 36 dorsal, 3

description: Library name: Sample 19


title: dHipp_16

description:
Library name: Sample 7
Illumina Stranded mRNA Prep


title: Emu SPs, St 36 ventral, 2

description: Library name: Sample 22


title: Patient HCL594 cell 143, aAP status:  aAP

description: Library name: 143

value: Acute slice


title: Patient HCL594 cell 142, aAP status: no

description: Library name: 142


title: subgingival plaque, sample 16

description: Library name: DS16


title: vHipp_10

description:
Library name: Sample 6
Illumina Stranded mRNA Prep


title: Emu SPs, St 36 dorsal, 1

description: Library name: Sample 17


title: mPFC_10

description:
Library name: Sample 5
Illumina Stranded mRNA Prep


title: subgingival plaque, sample 15

description: Library name: DS15


title: subgingival plaque, sample 14

description: Library name: DS14


title: Emu SPs, St 24, 3

description: Library name: Sample 15


title: dHipp_10

description:
Library name: Sample 4
Illumina Stranded mRNA Prep


title: Patient HCL560 cell 123, aAP status: no

description: Library name: 123


title: Patient HCL560 cell 124, aAP status: no

description: Library name: 124


title: Patient HCL594 cell 141, aAP status: no

description: Library name: 141


title: Emu SPs, St 24, 2

description: Library name: Sample 14


title: Patient HCL560 cell 122, aAP status: no

description: Library name: 122


title: subgingival plaque, sample 12

description: Library name: DS12


title: Emu SPs, St 24, 4

description: Library name: Sample 16


title: mPFC_1

description:
Library name: Sample 2
Illumina Stranded mRNA Prep


title: Emu SPs, St 24, 1

description: Library name: Sample 13


title: vHipp_1

description:
Library name: Sample 3
Illumina Stranded mRNA Prep


title: subgingival plaque, sample 11

description: Library name: DS11


title: Patient HCL560 cell 121, aAP status: no

description: Library name: 121


title: subgingival plaque, sample 13

description: Library name: DS13


title: dHipp_1

description:
Library name: Sample 1
Illumina Stranded mRNA Prep


title: High light 1 mM  nitrate replicate 2

city: Sevilla

first: Marcos

last: Ramos-González

address: Calle Américo Vespucio 49

country: Spain

institute: Universidad de Sevilla

description:
Library name: HL_1mMNO3_2
HL_1mMNO3_2

data_processing:
Quantification of gene expression from raw reads was performed using the computational pipeline MARACAS, selecting Chromochloris zofingiensis genome sequence assembly and annotation v5.6 as reference genome. Software selection used for quality control, read mapping, transcript assembly and gene expression quan-tification during the pipeline was FastQC, HISAT2 and StringTie, respectively. Quantile normalization was determined to be the most adequate for our data, based on the results of Bioconductor R package NormalyzerDE.
Assembly: Chromochloris zofingiensis v5.6 from Phytozome.
Supplementary files format and content: gene_expression.tsv: tabular tab-delimited format. It contains the normalized gene expression in FPKM for each of the 12 samples, one per column.

organism: Chromochloris zofingiensis

source_name: whole

growth_protocol: Arnon medium was modified to contain 4 mM K2HPO4 and different NaNO3 concentrations. Experiments were performed in glass photobioreactors with 2 L capacity (0.07 m diameter, 0.5 m height) containing 1.8 L cell suspension. Agitation was provided by continuous bubbling air (~30 L per L of culture per h). Temperature of the culture was maintained at 25 ºC by circulating water in reactor jacket. pH was maintained at 7.5 by pure CO2 injection on demand, using a pH-stat system. The cultures were illuminated by means of six white-light lamps (Osram ecopack-FQ24W/840HO) surrounding the photobioreactor. The irradiance impinging on the reactor surface was regulated by an automated system to simulate a solar neutral cycle (12h light/12h dark) increasing gradually from dark until a maximum irradiance (1000 mE m-2 s-1) on the reactor surface and decreasing again until dark. Six photobioreactors were inoculated simultaneously, with batch-grown cells and operated on batch regime for 3 days, to reach an appropriate cell density. Henceforth, the reactors were switched to operate in continuous mode feeding continuously with feed medium at 0.5 d-1 only during the period of illumination. Samples were collected 4 h after the beginning of the light period. Samples for analysis were collected for three consecutive days at 4 h after the start of the light cycle and analysed by triplicate.

extract_protocol:
RNA extraction was performed using mechanical disruption of the frozen cell pellets in a Mini Bead Beater (Biospec Products) mixed with 0.5 mm glass beads in the presence of an extraction buffer consisting of phenol:chloroform (1:1, v/v). Subse-quently, RNA was purified using ISOLATE II RNA Plant Kit (Bioline) following man-ufacturer’s instructions.
Sequencing libraries were generated according to Illumina TruSeq Stranded mRNA protocol and sequenced on an Illumina NextSeq 500 sequencer producing approxi-mately 17 million 150 nt long reads per sample.

treatment_protocol: Chromochloris zofingiensis was grown under two nitrate concentration in the feed medium (1 and 10 mM) and two maximum irradiance values on the reactor surface: 1000 µE m−2 s−1 for high light condition (HL) and 300 µE m−2 s−1 for low light condition (LL).

value: whole

value: WT

value: High light low nitrate


title: High light 1 mM  nitrate replicate 3

description:
Library name: HL_1mMNO3_3
HL_1mMNO3_3


title: subgingival plaque, sample 10

description: Library name: DS10


title: Patient HCL560 cell 119, aAP status: no

description: Library name: 119

value: Neuron


title: D21-bleomycin-rep3

city: Guangzhou

first: Shu

last: Meng

state: Guangdong

address: No.9, XingDaoHuanBei Road, Guangzhou International Bio-island, Haizhu District

department: Department of Basic Science Research

institute: Guangzhou National Laboratory

description: Library name: D21-bleomycin-rep3

data_processing:
Raw reads were first subjected to basic quality control including removal of poor quality reads and potential sequencing adapters. Then, clean reads were mapped to the mouse reference genome (GRCm38) using HISAT2 (v2.1.0). Raw reads count for each gene was quantified using HTSeq (v0.6.0). DESeq2 (v1.40.2) was used for differentially expressed gene analysis (p.adj < 0.05 and fold change > 1.5).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file with raw counts for each sample

source_name: whole lung

extract_protocol:
Lung tissues were collected at day 0, day 7, day 14, and day 21 following bleomycin treatment. Then, total RNA was extracted using RNeasy Plus Mini Kit (Cat# 74134, QIAGEN).
RNA-seq libraries were prepared according to the standard protocol of NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (Cat# E7530L, NEB, USA).

treatment_protocol: Mice were anesthetized with 1.25% Avertin (2,2,2-tribromoethanol) at a dose of 0.2 mL per 10 g of body weight. A 50 μL bleomycin solution (5 U/kg) was administered intratracheally. Lung tissues were collected at day 0, day 7, day 14, and day 21 following bleomycin treatment.

value: whole lung

tag: time point

tag: strain

value: belomycin


title: subgingival plaque, sample 9

description: Library name: DS9


title: High light 1 mM  nitrate replicate 1

description:
Library name: HL_1mMNO3_1
HL_1mMNO3_1


title: Patient HCL560 cell 118, aAP status:  aAP

description: Library name: 118


title: subgingival plaque, sample 8

description: Library name: DS8


title: High light 10 mM  nitrate replicate 3

description:
Library name: HL_10mMNO3_3
HL_10mMNO3_3

value: High light high nitrate


title: D21-bleomycin-rep2

description: Library name: D21-bleomycin-rep2


title: Patient HCL560 cell 117, aAP status:  aAP

description: Library name: 117


title: subgingival plaque, sample 7

description: Library name: DS7


title: Patient HCL560 cell 116, aAP status: no

description: Library name: 116


title: High light 10 mM  nitrate replicate 2

description:
Library name: HL_10mMNO3_2
HL_10mMNO3_2


title: High light 10 mM  nitrate replicate 1

description:
Library name: HL_10mMNO3_1
HL_10mMNO3_1


title: D14-bleomycin-rep4

description: Library name: D14-bleomycin-rep4


title: subgingival plaque, sample 6

description: Library name: DS6


title: Low light 1 mM  nitrate replicate 3

description:
Library name: LL_1mMNO3_3
LL_1mMNO3_3

value: Low light low nitrate


title: subgingival plaque, sample 5

description: Library name: DS5


title: Patient HCL560 cell 112, aAP status:  aAP

description: Library name: 112


title: D21-bleomycin-rep1

description: Library name: D21-bleomycin-rep1


title: Low light 1 mM  nitrate replicate 2

description:
Library name: LL_1mMNO3_2
LL_1mMNO3_2


title: subgingival plaque, sample 4

description: Library name: DS4


title: Patient HCL560 cell 110, aAP status: no

description: Library name: 110


title: Patient HCL560 cell 111, aAP status:  aAP

description: Library name: 111


title: subgingival plaque, sample 3

description: Library name: DS3


title: D14-bleomycin-rep3

description: Library name: D14-bleomycin-rep3


title: D14-bleomycin-rep2

description: Library name: D14-bleomycin-rep2


title: Low light 1 mM  nitrate replicate 1

description:
Library name: LL_1mMNO3_1
LL_1mMNO3_1


title: Patient HCL560 cell 113, aAP status:  aAP

description: Library name: 113


title: subgingival plaque, sample 2

description: Library name: DS2


title: Patient HCL738 cell 93, aAP status:  aAP

description: Library name: 93


title: Low light 10 mM  nitrate replicate 3

description:
Library name: LL_10mMNO3_3
LL_10mMNO3_3

value: Low light high nitrate


title: D14-bleomycin-rep1

description: Library name: D14-bleomycin-rep1


title: D7-bleomycin-rep3

description: Library name: D7-bleomycin-rep3


title: Low light 10 mM  nitrate replicate 2

description:
Library name: LL_10mMNO3_2
LL_10mMNO3_2


title: D7-bleomycin-rep4

description: Library name: D7-bleomycin-rep4


title: subgingival plaque, sample 1

description: Library name: DS1


title: D7-bleomycin-rep2

description: Library name: D7-bleomycin-rep2


title: Patient HCL738 cell 92, aAP status:  aAP

description: Library name: 92


title: Patient HCL738 cell 90, aAP status:  aAP

description: Library name: 90


title: carotid plaque, sample 25

description: Library name: DC25

source_name: carotid plaque

value: carotid plaque


title: D7-bleomycin-rep1

description: Library name: D7-bleomycin-rep1


title: Low light 10 mM  nitrate replicate 1

description:
Library name: LL_10mMNO3_1
LL_10mMNO3_1


title: carotid plaque, sample 24

description: Library name: DC24


title: Panorama_EXP-2-AD-R3_W7A2

city: Heidelberg

first: Julius

last: Michel

address: Im Neueunheimer Feld 280

department: Neuroimmunology and brain tumor immunology

description: Raw data files include tab-separated values files containing x-y-z location for each transcript (txt format) and staining images of DAPI and Thioflavin S stained section (tiff format).Processed data include transcript assignment tables (*_results_assigned.txt), containing individual RNA molecules with spatial coordinates and their assignment to segmented cells, cell-by-gene count matrices (*_segmentation_counts.txt), providing the number of detected transcripts per gene for each segmented cell, and cell metadata tables (*_segmentation_cell_stats.csv), containing per-cell information such as cell ID, spatial location (centroid), area, and quality control metrics.

hyb_protocol: Resolve Biosciences’ Molecular Cartography platform for labeling, hybridization, and imaging with 99-plex combinatorial single molecule fluorescence in-situ hybridization

data_processing: The detection of cell boundaries was performed with QuPath v0.3.2. Gene expression counts were computed per cell and extracted using Resolve Bioscience plugin in the ImageJ2 toolkit.

source_name: cerebral cortex

extract_protocol: Mouse brain or human brain was dissected and right or left hemisphere immersed in Tissue-Tek® (Sakura) on dry ice bath and stored at -80.  The frozen brains were sectioned into 7 μm coronal slices on a cryostat at -20°C.

value: cerebral cortex

tag: Sex

value: male

tag: braak stage

tag: apoe genotype

tag: caa stage according to thal


title: Patient HCL738 cell 87, aAP status:  aAP

description: Library name: 87

tag: tissue

tag: cell line

tag: cell type


title: Patient HCL738 cell 86, aAP status:  aAP

description: Library name: 86


title: Panorama_EXP-2-AD-R3_W7A1

scan_protocol: Resolve Biosciences’ Molecular Cartography platform for labeling, hybridization, and imaging with 99-plex combinatorial single molecule fluorescence in-situ hybridization

tag: age


title: carotid plaque, sample 22

description: Library name: DC22


title: carotid plaque, sample 21

description: Library name: DC21


title: Panorama_EXP-2-AD-R3_W7A3

label_protocol: Resolve Biosciences’ Molecular Cartography platform for labeling, hybridization, and imaging with 99-plex combinatorial single molecule fluorescence in-situ hybridization


title: D0-ctrl-rep2

description: Library name: D0-ctrl-rep2

tag: treatment


title: Patient HCL738 cell 85, aAP status:  aAP

description: Library name: 85


title: Panorama_EXP-2-AD-R3_W6A2


title: Patient HCL738 cell 84, aAP status: no

description: Library name: 84


title: D0-ctrl-rep1

description: Library name: D0-ctrl-rep1


title: carotid plaque, sample 20

description: Library name: DC20


title: Panorama_EXP-2-AD-R3_W6A1


title: carotid plaque, sample 19

description: Library name: DC19


title: Patient HCL738 cell 89, aAP status:  aAP

description: Library name: 89


title: D0-ctrl-rep4

description: Library name: D0-ctrl-rep4


title: KO

city: Cologne

first: Mauro

last: Corrado

address: Joseph-Stelzmann-Str. 26

institute: University of Cologne

description: Library name: SID208223

data_processing:
Samples were demultiplexed and aligned using Cell Ranger 8.0.1 (10X Genomics) to genome build GRCm38 to obtain a raw read count matrix of barcodes corresponding to cells and features corresponding to detected genes.
Assembly: GRCM38
Supplementary files format and content: Processed data are matrices with raw counts for features in sequenced cells. A list of cell barcodes and detected genes is also included for each sample.

source_name: Lamina propria

extract_protocol:
CD45+ single cells were sorted with BD Facs Aria Cell Sorter and prepared for single cell RNA sequencing using the 10X Genomics 3'scRNA v4 system
Libraries were sequenced on NovaSeq 6000 at 250M reads/sample. Samples were demultiplexed, quality checked, filtered and aligned genome build GRCm38 using pre-established pipelines implemented via cellranger v. 8.0.1

value: Lamina propria

value: PTPMT1 Deficient

value: CD45+ cells


title: carotid plaque, sample 23

description: Library name: DC23


title: Patient HCL934 cell 66, aAP status: no

description: Library name: 66

value: glioblastoma tumor slice


title: D0-ctrl-rep3

description: Library name: D0-ctrl-rep3


title: Panorama_EXP-2-AD-R3_W5A1


title: carotid plaque, sample 18

description: Library name: DC18


title: WT

description: Library name: SID208222

value: Wild Type


title: Panorama_EXP-2-AD-R3_W4A2


title: Patient HCL934 cell 64, aAP status: no

description: Library name: 64

value: Acute slice


title: E16_scRANseq_HTO

first: Minako

last: Ito

address: 3-1-1 Maidashi, Higashi-ku

description:
Library name: E16_scRANseq_HTO
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: tsv files and mtx files

extract_protocol:
Mice were anesthetized with intraperitoneal injection of sodium pentobarbital (100 mg/kg) and perfused transcardially with PBS, each organ was removed. For the preparation of brain cells, brain parenchyma was homogenized with a potter tissue grinder in RPMI containing FBS (2% v/v), 15 mM HEPES buffer and 0.54% glucose (Modified from Masuda et al. Nat Immunol. 202037). After straining and centrifugation, the pellet was suspended in 37% Percoll (Cytiva, 17-0891-01) diluted with RPMI and cells were isolated by centrifugation at 800 × g for 20 min at 4 °C with slow acceleration and deceleration. The pellet was collected, washed with RPMI supplemented with FBS (2% v/v), and stained for flow cytometry. CD45+CD90.2+ and/or CD45+NK1.1+ cells were sorted by FACSMelody (BD Biosciences).
Libraries were prepared according to the protocol of Chromuim Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) (10x Genomics, PN-1000263) using a Chromium controller (10x Genomics). Briefly, GEMs were first generated by Master Mix with barcoded Single Cell VDJ 5' Gel Beads, cells and distribution to Oil to Chromium Next GEM Chip K (10x Genomics, PN-1000286). Barcoded cDNA was then generated from the GEM. This cDNA was amplified by PCR reaction to generate, 5' Gene Expression library and Feature Barcode library (10x Genomics, PN-1000190, -1000256, -1000215, and -1000250). Sequencing was then performed by Novaseq 6000 (Illumina).

value: Brain

tag: time

value: Lymphocytes

value: Wild type or 15q dup


title: carotid plaque, sample 17

description: Library name: DC17


title: Patient HCL629 cell 170, aAP status: no

description: Library name: 170

value: cultured slice

value: Neuron


title: Panorama_EXP-2-AD-R3_W3A3


title: carotid plaque, sample 16

description: Library name: DC16


title: 6w_scRANseq_HTO

description:
Library name: 6w_scRANseq_HTO
10x Genomics

value: 6 weeks


title: Panorama_EXP-2-AD-R3_W3A2


title: E16_scRANseq_GEX

description:
Library name: E16_scRANseq_GEX
10x Genomics


title: Patient HCL629 cell 169, aAP status:  aAP

description: Library name: 169


title: Patient HCL629 cell 167, aAP status: no

description: Library name: 167


title: carotid plaque, sample 15

description: Library name: DC15


title: 6w_scRANseq_GEX

description:
Library name: 6w_scRANseq_GEX
10x Genomics


title: Panorama_EXP-2-AD-R3_W4A1


title: Patient HCL629 cell 165, aAP status: no

description: Library name: 165


title: Panorama_EXP-2-AD-R3_W3A1


title: carotid plaque, sample 14

description: Library name: DC14


title: Panorama_EXP-2-AD-R3_W2A2


title: Patient HCL629 cell 161, aAP status: no

description: Library name: 161


title: Patient HCL629 cell 160, aAP status:  aAP

description: Library name: 160


title: Panorama_EXP-2-AD-R3_W2A1


title: 4w_scRANseq_GEX

description:
Library name: 4w_scRANseq_GEX
10x Genomics

value: 4 weeks


title: Panorama_EXP-2-AD-R3_W1A1


title: carotid plaque, sample 11

description: Library name: DC11


title: 4w_scRANseq_HTO

description:
Library name: 4w_scRANseq_HTO
10x Genomics


title: carotid plaque, sample 13

description: Library name: DC13


title: Patient HCL629 cell 157, aAP status: no

description: Library name: 157


title: Panorama_EXP-2-AD-R3_W0A2


title: 2w3_scRANseq_HTO

description:
Library name: 2w3_scRANseq_HTO
10x Genomics

value: 2 weeks


title: 3w_scRANseq_GEX

description:
Library name: 3w_scRANseq_GEX
10x Genomics

value: 3 weeks


title: carotid plaque, sample 9

description: Library name: DC9

value: carotid plaque


title: Patient HCL629 cell 156, aAP status: no

description: Library name: 156


title: 3w_scRANseq_HTO

description:
Library name: 3w_scRANseq_HTO
10x Genomics


title: Panorama_EXP-2-AD-R3_W0A1

value: cerebral cortex

value: male


title: carotid plaque, sample 8

description: Library name: DC8


title: 2w3_scRANseq_GEX

description:
Library name: 2w3_scRANseq_GEX
10x Genomics


title: carotid plaque, sample 10

description: Library name: DC10


title: carotid plaque, sample 12

description: Library name: DC12


title: Patient HCL629 cell 154, aAP status:  aAP

description: Library name: 154


title: 2w2_scRANseq_HTO

description:
Library name: 2w2_scRANseq_HTO
10x Genomics


title: Patient HCL629 cell 158, aAP status: no

description: Library name: 158


title: Patient HCL619 cell 150, aAP status: no

description: Library name: 150


title: carotid plaque, sample 7

description: Library name: DC7


title: RfxCas13d expressing HEK293FT cells, pooled lncRNA library, before doxycycline induction, replicate 1

first: Wen-Wei

last: Liang

state: NY

address: 101 Avenue of the Americas

institute: New York Genome Center

description: Library name: HEK293FT_Day00_R1

data_processing:
Quality of the raw fastq files was assessed using MultiQC .We processed reads from pooled Cas13d screens following established pipelines. In brief, reads were de-multiplexed based on Illumina i7 barcodes and custom i5 barcodes. We trimmed reads to the expected gRNA length by identifying known anchor sequences relative to the guide sequence. We did this using Cutadapt (v.1.13) with the following parameters: -g CTGGTCGGGGTTTGAAAC -e 0.2 -O 5 --discard-untrimmed and -a TTTTTGAATTCGCTAGCT -e 0.1 -O 5 --minimum-length 15 --discard-untrimmed. We aligned processed reads to the designed crRNA reference using bowtie (v.1.1.2) allowing for up to three mismatches (parameters: -v 1 -m 3 –best -q). The raw gRNA counts were normalized using median-of-ratios (geometric mean), similar to DESeq2, and batch correction was applied using combat from the SVA R package (v.3.34.0). We removed nonreproducible technical outliers by pair-wise linear regression for each sample, collecting residuals, and taking the median value for each gRNA across biological replicates.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file include raw counts for each sample.

source_name: kidney

growth_protocol: HEK293FT and MDA-MB-231 cells were cultured in D10 medium:  Dulbecco’s Modified Eagle Medium with high glucose and stabilized L-glutamine (Cytiva SH30022.01) supplemented with 10% Serum Plus II (Sigma-Aldrich 14009C) and 5 µg/ml blasticidin. HAP1 and K562 cells were cultured in I10 medium: Iscove’s Modified Dulbecco’s Medium with L-glutamine (Cytiva SH30228.FS) supplemented with 10% Serum Plus II and 5 µg/ml blasticidin. THP-1 cells were cultured in R10 medium: HyClone RPMI 1640 Medium (Cytiva SH30255.FS) supplemented with 10% Serum Plus II and 5 µg/ml blasticidin. All cells were incubated at 37 °C with 5% carbon dioxide.

extract_protocol:
Genomic DNA was isolated from cell pellets via a modified salting out procedure. For that, 12 ml of NK Lysis Buffer (50 mM Tris, 50 mM EDTA, 1% SDS, pH 8) and 60 µl of 20 mg/ml Proteinase K (QIAGEN 19131) were added to 80 million cells and incubated at 55 °C overnight. The next day, 6 µl of 100 mg/ml RNase A (A.G. Scientific R-2000) was added to the lysed sample, which was then inverted 25 times and incubated at 37 °C for 30 min. Samples were cooled on ice before addition of 4 ml of pre-chilled 7.5M ammonium acetate (Sigma A1542) to precipitate proteins. After adding ammonium acetate, the samples were vortexed and centrifuged at 4,000 × g for 10 minutes. After the spin, 12 ml isopropanol was added to the collected supernatant, inverted 50 times and centrifuged at 4,000 × g for 10 minutes. The supernatant was discarded, 12 ml of freshly prepared 70% ethanol was added, the tube was inverted 10 times, and then centrifuged at 4,000 × g for 10 minutes. The supernatant was discarded, and remaining ethanol was removed. After air drying for 30 minutes, 500 µl of 0.2× TE buffer (Sigma 93283) was added, the tube was incubated at 65 °C for 1 hour and at room temperature overnight to fully resuspend the DNA. The next day, the gDNA samples were vortexed briefly. The gDNA concentration was measured using a Nanodrop (Thermo). We excluded one biological replicate (K562 day 0) due to low recovery after gDNA extraction.
We amplified gRNA cassettes and prepared them for sequencing using a two-step PCR. PCR1 was performed to amplify a region containing the crRNA cassette in the lentiviral genomic integrant using TaqB polymerase (Enzymatics P7250L). We performed 70 PCR1 reactions for each gDNA sample using 5 μg gDNA per 100 μl PCR1 reaction as follows: 94 °C for 3 min, 20× (94 °C for 10 s, 55 °C for 30 s, 68 °C for 45 s), 68 °C for 5 min. We then combined PCR1 products for the same sample together before PCR2, which was done to incorporate Illumina adaptors using Q5 High-Fidelity DNA Polymerase (NEB M0491). We performed 10 PCR2 reactions for each sample using 10 μl unpurified PCR1 product per 50 μl reaction as follows: 98 °C for 30 s, 6-10× (98 °C for 10 s, 63 °C for 30 s, 72 °C for 45 s), 72 °C for 5 min. The resulting amplicons from PCR2 (~270 bp) were pooled and then purified using double-sided SPRI beads clean up (Beckman B23317) or gel extracted using a QiaQuick Gel Extraction kit (Qiagen 28704). For double-sided SPRI clean up, the amplicon was first incubated with 0.6× SPRI to remove larger fragments (>350 bp bound to beads and removed), the supernatant was then transferred and further incubated with 0.8× SPRI beads (<200 bp in supernatant and removed).

treatment_protocol: Cas13d-expressing cells were transduced with the library lentivirus through separate infection replicates by spinfection at 1000 rpm for 1 hour at 37 °C, followed by overnight incubation. After 24 hours, new media with 1 μg/ml puromycin (Invivogen ant-pr-1) was added. Puromycin selection was completed within 48 hours for all cell lines, except for THP1. Because THP1 required an extended selection time, we maintained it in R10 but with 10% Tet-system approved serum (Gibco A4736201) substituted for Serum Plus II and with 1 μg/ml puromycin. THP1 cells took approximately two weeks for full selection. Following puromycin selection, RfxCas13d expression was induced by replenishing the growth medium containing 1 μg/ml puromycin, 5 μg/ml blasticidin and 1 μg/ml doxycycline. Cells were passaged every 2 to 4 days and split as needed, ensuring a guide representation of >1,000×. Samples with a guide abundance of 1,000-fold were harvested at 0, 7, and 14 days post-Cas13d induction.

value: kidney

value: embryonic kidney cells

value: lncRNAs knockdown

value: doxycycline induction


title: Patient HCL619 cell 149, aAP status:  aAP

description: Library name: 149

value: glioblastoma tumor slice


title: carotid plaque, sample 6

description: Library name: DC6


title: 247_SCAR

city: Valenzano-Bari

first: Sharon

middle: Natasha

last: Cox

department: Renal Lab

country: Italy

institute: Schena Foundation

hyb_protocol: 1 µg of labeled cDNA from each sample was hybridized on chip

scan_protocol: Agilent Feature Extraction v.10.7.3.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 072363_D_F_20150612) to obtain background-subtracted and spatially detrended Processed Signal intensities. Background correction was not applied (BG Method: No Background), while spatial detrending was enabled (Background Detrend: On (FeatNCRange, LoPass)) with Multiplicative Detrend: True and Additive Error: 4 (Green).

source_name: FFPE_Kidney_biopsy specimen

label_protocol: 1.7 µg of total amplified cDNA was converted into labeled cDNA coupled to Cy3 using Genomic DNA ULS labeling Kit (Agilent Technologies) following the Agilent Gene Expression FFPE Workflow

extract_protocol: Total RNA was extracted from formalin-fixed, paraffin-embedded (FFPE) renal tissue samples following deparaffinization and lysis. Briefly, eight freshly cut 5 µm sections were deparaffinized using a Qiagen deparaffinization solution at 56 °C for 3 minutes. The sections were then incubated in a lysis buffer containing proteinase K at 56 °C for 15 minutes to release RNA from crosslinked proteins, followed by a 15-minute incubation at 80 °C to reverse formalin-induced crosslinking. RNA was immediately extracted using the RNeasy FFPE Kit (Qiagen, GmbH, Hilden, Germany) and used for both microarray analysis and real-time PCR. Prior to microarray processing, RNA integrity was assessed using Agilent RNA nano chips on an Agilent 2100 Bioanalyzer, yielding RNA integrity numbers (RIN) between 2.1 and 2.9, with RNA fragments ranging from 100 to 200 nucleotides. Quantification was performed using a NanoDrop 1000 spectrophotometer.

tag: status

value: F

value: KIDNEY


title: 252_SCAR


title: carotid plaque, sample 5

description: Library name: DC5


title: human keratinocytes, plate 13

city: Nijmegen

first: Klaas

last: Mulder

address: Geert Grooteplein 26

department: Molecular Developmental Biology

country: Netherlands

institute: Radboud University

description: Library name: sample 11

library_source: other

data_processing:
Sequence data from the NextSeq500 (Illumina) was de-multiplexed using bcl2fastq software (Illumina). Then, all reads were processed using our dedicated IDseq R-package described in (PMID: 29921844). In short, the sequencing reads were split using a common “anchor sequence” identifying the position of the Unique Molecular Identifier (UMI) sequence, Barcode 1 (antibody specific) and Barcode 2 (well specific) sequence. After removing all duplicate reads, the number of UMI sequences were counted per barcode 1 and 2. Finally, barcode 1 (“antibody)” and barcode 2 (‘well’) sequences were matched to the corresponding antibody and well information.
Supplementary files format and content: tsv file with cell identifier, treatment, antibody/protein name, raw counts per antibody per cell, normalization factor, library size, tmm normalized antibody counts per antibody per cell.
Library strategy: scID-seq

molecule: other

source_name: foreskin

growth_protocol: Cells were cultured on a feeder layer of J2-3T3 cells in FAD medium (Ham’s F12 medium/Dulbecco’s modified Eagle medium (DMEM) (1:3) supplemented with 10% batch tested fetal calf serum (FCS) and a cocktail of 0.5 μg/ml of hydrocortisone, 5 μg/ml of insulin, 0.1 nM cholera enterotoxin, and 10 ng/ml of epidermal growth factor) supplemented with Rock inhibitor (Y-27632, 10 μM). J2-3T3 cells were cultured in DMEM containing 10% bovine serum and inactivated with MitomycinC (SCBT) upon seeding the epidermal stem cells. For experiments epidermal stem cells were transferred to Keratinocyte Serum Free Medium (KSFM) supplemented with 0.2 ng/ml Epidermal Growth Factor (EGF) and 30 μg/ml bovine pituitary extract from Life Technology until 70% confluency. All media were supplemented with 1% penicillin/streptomycin antibiotics.

extract_protocol:
Cells (> 3 x 106) were harvested with trypsin and cross-linked in suspension by incubating for 10 minutes with 4% paraformaldehyde (PFA) in PBS following a quenching step of 5 minutes with 125 mM Glycine in PBS. Removal of PFA and Glycine occurred through washing twice with a wash buffer (0.1x PierceTM Protein-Free Blocking Buffer from Thermo in PBS). Then, cells were blocked in 500μl blocking buffer (0.5x PierceTM Protein-Free Blocking Buffer, 200 μg/ml boiled salmon sperm DNA, 0.1% Triton-X 100, in PBS) at room temperature for 30-60 min. Pre-stainings were performed at room temperature for 1-2 hours and staining with the conjugate mix occurred overnight at 4°C in 500 μl blocking buffer. After each staining, cells were washed 3x in 5 ml wash buffer. Cells were sorted in single wells with the BD FACSAria SORP flow cytometer (BD biosciences) in 96 well PCR plates containing 1 μl release buffer (10 mM DTT in 15mM Tris, pH 8.8) and 7 µl Vapor-lock (Qiagen).
Library preparation was performed as described previously (PMID: 30466065). Briefly, 3 PCR steps were performed to amplify the antibody barcodes and to add barcodes specific for the well and the plate of each cell. The barcoding occurred with the same sequences used in (PMID: 30466065). For the first PCR step 15 cycles were run after adding to each well a 4 µl reaction mix containing the Herculase II Fusion DNA Polymerase (Agilent), dNTPs, 5x Herculase buffer and 0.1μM amplification primers. Directly after the first PCR step, 5 extra cycles were run after adding 1 µl mix containing Herculase buffer 0.2 μM forward amplification primer and 0.2 μM reverse well barcoding primer. Then all material was pooled per plate, Vapor-lock was removed and a clean-up was performed with the QIAquick PCR Purification Kit, followed by an exonuclease 1 treatment to degrade remaining primers and another purification. Another 5 cycles were run in PCR 3 with a 20 µl reaction containing the pooled and purified sample and 0.1 μM plate-barcoding primers. After repeating the clean-up procedure, the libraries were checked on agarose gel and with the Bioanalyzer (Agilent) to confirm the size of the DNA fragments (expected size around 185 bp) and sequenced on an Illumina NextSeq500 machine.

treatment_protocol: Cells were treated with p90RSK inhibitor BI-D1870 (10 μM, Sellekchem) or P70S6K inhibitor PF4708671 (10 μM, Sellekchem), followed by addition of 10ng/ml EGF for 30 minutes in the presence of the inhibitors.

value: foreskin

value: primary cell culture

value: keratinocytes

value: WT

value: vehicle, PF4708671 or BI-D1870


title: 2w2_scRANseq_GEX

description:
Library name: 2w2_scRANseq_GEX
10x Genomics

value: Brain

value: 2 weeks

value: Lymphocytes

value: Wild type or 15q dup


title: 2w1_scRANseq_GEX

description:
Library name: 2w1_scRANseq_GEX
10x Genomics


title: 241_SCAR

value: M


title: human keratinocytes, plate 12

description: Library name: sample 10


title: carotid plaque, sample 4

description: Library name: DC4

value: carotid plaque


title: carotid plaque, sample 3

description: Library name: DC3


title: 2w1_scRANseq_HTO

description:
Library name: 2w1_scRANseq_HTO
10x Genomics


title: 1w_scRANseq_HTO

description:
Library name: 1w_scRANseq_HTO
10x Genomics

value: 1 week


title: human keratinocytes, plate 10

description: Library name: sample 8


title: 129_NORM


title: Thymus_scRANseq_HTO

description:
Library name: Thymus_scRANseq_HTO
10x Genomics

source_name: Thymus

growth_protocol: WT and 15q dup mice at  3 weeks of age

extract_protocol:
Mice were anesthetized with intraperitoneal injection of sodium pentobarbital (100 mg/kg) and perfused transcardially with PBS, each organ was removed. For the preparation of brain cells, brain parenchyma was homogenized with a potter tissue grinder in RPMI containing FBS (2% v/v), 15 mM HEPES buffer and 0.54% glucose (Modified from Masuda et al. Nat Immunol. 202037). After straining and centrifugation, the pellet was suspended in 37% Percoll (Cytiva, 17-0891-01) diluted with RPMI and cells were isolated by centrifugation at 800 × g for 20 min at 4 °C with slow acceleration and deceleration. The pellet was collected, washed with RPMI supplemented with FBS (2% v/v), and stained for flow cytometry. For the preparation of dura cells, the dura mater was removed from the skull under a microscope and incubated with 1 mg/ml collagenase VIII (Sigma-Aldrich, C2139) and 0.4 mg/ml DNase I (Roche, 10104159001) at 37 °C for 20 minutes. Digested dura mater was disrupted by pipetting, filtrated through a 70 μm cell strainer and washed with 2% FBS/RPMI. For the preparation of intestinal cells, the feces in the colon and small intestine were washed out and cut into 1 cm pieces. Peyer's patches were cut from the small intestine under a microscope, grinded on a strainer, and cells were isolated by washing with 2% FBS/RPMI. Intestinal fragments were washed with PBS and incubated in 30 mM EDTA/PBS for 8 min at RT. After washing with PBS, they were further minced into small pieces and incubated with 1 mg/ml Collagenase D (Roche, 11088882001) and 0.1 mg/ml DNase I at 37 °C for 30 min. The tissue was digested by pipetting, and the supernatant was collected through a strainer. Then, 1 mg/ml Collagenase D was added and incubated at 37°C for 15 minutes, and the step of collecting the supernatant was repeated twice, and then all intestine was disrupted by pipetting and filtrated through a cell strainer. After centrifugation, cells were suspended in 36% Percoll diluted with RPMI, 72% Percoll diluted with PBS was injected into the bottom and centrifuged at 800 × g for 20 min at 25 ºC with slow acceleration and deceleration. A cell layer at the interface was collected and washed with RPMI supplemented with FBS (2% v/v) and stained for flow cytometry. For the preparation of lung cells, lungs were minced and incubated with 2 mg/ml CollagenaseD and 0.1 mg/ml DNase I at 37°C for 20 minutes. After the reaction, the supernatant was collected through a strainer, and the step of adding 2 mg/ml Collagenase D and 0.1 mg/ml DNase I to the precipitate again, reacting at 37°C for 20 minutes, and collecting the supernatant was repeated twice. After centrifugation, cells were suspended in 36% Percoll diluted with RPMI, 72% Percoll diluted with PBS was injected into the bottom and centrifuged at 800 × g for 20 min at 25°C with slow acceleration and deceleration. A cell layer at the interface was collected and washed with RPMI supplemented with FBS (2% v/v) and stained for flow cytometry. Spleen and thymus were filtrated through a 40 µm cell strainer. CD45+CD3ε+TCRγ/δ+TCR-Vγ6+ were sorted by FACSMelody (BD Biosciences).
Libraries were prepared according to the protocol of Chromuim Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) (10x Genomics, PN-1000263) using a Chromium controller (10x Genomics). Briefly, GEMs were first generated by Master Mix with barcoded Single Cell VDJ 5' Gel Beads, cells and distribution to Oil to Chromium Next GEM Chip K (10x Genomics, PN-1000286). Barcoded cDNA was then generated from the GEM. This cDNA was amplified by PCR reaction to generate, 5' Gene Expression library and Feature Barcode library (10x Genomics, PN-1000190, -1000256, -1000215, and -1000250). Sequencing was then performed by Novaseq 6000 (Illumina).

value: Thymus

value: 3 weeks

value: gammadelta T cells


title: carotid plaque, sample 2

description: Library name: DC2


title: 1w_scRANseq_GEX

description:
Library name: 1w_scRANseq_GEX
10x Genomics


title: human keratinocytes, plate 11

description: Library name: sample 9


title: 200_SCAR


title: human keratinocytes, plate 9

description: Library name: sample 7


title: Thymus_scRANseq_GEX

description:
Library name: Thymus_scRANseq_GEX
10x Genomics


title: carotid plaque, sample 1

description: Library name: DC1


title: human keratinocytes, plate 8

description: Library name: sample 6


title: WM115 FICZ RNA Rep 3

city: Beijing

first: Zexian

last: Zeng

address: No.5 Yiheyuan Road, Haidian District, Beijing

institute: Peking University

description:
Library name: WM115 FICZ RNA Rep 3
F3
WM115_count.csv
WM115_TPM.csv

data_processing:
STAR v2.6.1d, Salmon v0.13.1, tximport v1.22.0, DESeq2 v1.34.0
RNA-seq reads were aligned to hg38 genome v22 using STAR v2.6.1d.
Read alignments were quantified by Salmon v0.13.1 in its alignment-based mode.
Gene-level raw counts as well as transcript per million (TPM) from quantification files were prepared with tximport v1.22.0.
Normalization of raw counts and differential expression analysis were performed by DESeq2 v1.34.0 with default parameters.
Assembly: hg38
Supplementary files format and content: Comma-delimited csv files include TPM values for each sample.
Supplementary files format and content: Comma-delimited csv files include raw counts for each sample.

source_name: Skin

extract_protocol:
RNA was harvested using Trizol (Invitrogen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-Seq Library Prep Kit for Illumina following manufacturer's protocols.

value: Skin

value: 1 μM FICZ


title: Spleen_scRANseq_HTO

description:
Library name: Spleen_scRANseq_HTO
10x Genomics

source_name: Spleen

value: Spleen


title: WM115 FICZ RNA Rep 2

description:
Library name: WM115 FICZ RNA Rep 2
F2
WM115_count.csv
WM115_TPM.csv


title: 196_SCAR

value: KIDNEY


title: Spleen_scRANseq_GEX

description:
Library name: Spleen_scRANseq_GEX
10x Genomics


title: WM115 FICZ RNA Rep 1

description:
Library name: WM115 FICZ RNA Rep 1
F1
WM115_count.csv
WM115_TPM.csv


title: human keratinocytes, plate 6

description: Library name: sample 4

value: foreskin

value: primary cell culture

value: keratinocytes


title: 92_SCAR

value: F


title: 123_NORM


title: RfxCas13d expressing HEK293FT cells, pooled lncRNA library, 7 days after doxycycline induction, replicate 2

description: Library name: HEK293FT_Day07_R2

value: kidney

value: embryonic kidney cells

value: lncRNAs knockdown

value: doxycycline induction


title: WM115 DMSO RNA Rep 3

description:
Library name: WM115 DMSO RNA Rep 3
D3
WM115_count.csv
WM115_TPM.csv

value: WT

value: 0.1% DMSO


title: Lung_scRANseq_GEX

description:
Library name: Lung_scRANseq_GEX
10x Genomics

source_name: Lung

value: Lung

value: Wild type or 15q dup


title: human keratinocytes, plate 4

description: Library name: sample 3

value: vehicle, PF4708671 or BI-D1870


title: 265_NORM


title: human keratinocytes, plate 7

description: Library name: sample 5


title: human keratinocytes, plate 3

description: Library name: sample 2


title: Lung_scRANseq_HTO

description:
Library name: Lung_scRANseq_HTO
10x Genomics

value: 3 weeks

value: gammadelta T cells


title: Dura_scRANseq_HTO

description:
Library name: Dura_scRANseq_HTO
10x Genomics

source_name: Dura

value: Dura


title: human keratinocytes, plate 2

description: Library name: sample 1


title: 135_NORM

value: KIDNEY


title: 94_NORM

value: M


title: 93_NORM


title: Dura_scRANseq_GEX

description:
Library name: Dura_scRANseq_GEX
10x Genomics


title: 86_NORM


title: A375 ARNTKO RNA Rep 3

description:
Library name: A375 ARNTKO RNA Rep 3
sgARNT-3
A375_count.csv
A375_TPM.csv

value: Skin

value: ARNT KO


title: 77_NORM


title: WM115 DMSO RNA Rep 1

description:
Library name: WM115 DMSO RNA Rep 1
D1
WM115_count.csv
WM115_TPM.csv


title: A375 ARNTKO RNA Rep 2

description:
Library name: A375 ARNTKO RNA Rep 2
sgARNT-2
A375_count.csv
A375_TPM.csv


title: Colon_scRANseq_HTO

description:
Library name: Colon_scRANseq_HTO
10x Genomics

source_name: Colon

value: Colon


title: DMSO treated cells

city: London

first: Owen

last: Williams

address: 30 Guilford Street

country: United Kingdom

institute: UCL GOS ICH

description: Library name: NC4_S4_R1_001.fastq.gz

data_processing:
BCL output from the sequencer were converted to FASTQ, along with index demultiplexing using Illumina's BCL Convert v3.7.5.
All tools in the analysis were invoked through the Galaxy Project for NGS analysis, as follows:
5’ adapters were trimmed from the FASTQ files using the Cutadapt tool
sgRNA read counts were collected using the MAGeCK count tool
MAGeCKs test was used to perform sgRNA and gene ranking
Assembly: hg38
Supplementary files format and content: DMSOvIC90MBZ_Galaxy_MAGeCKs_test_Gene Summary.xlsx
Library strategy: CRISPR Screen

source_name: THP-1 cells, MLL-AF9 positive

growth_protocol: THP-1 cells (Acute Myeloid Leukemia cell line) (ATCC) were maintained in culture in RPMI 1640 medium containing 10% fetal bovine serum, 100 units/ml penicillin and 100 ug/ml streptomycin at 37°C with 5% CO2.

extract_protocol:
genomic DNA isolated using the QIAamp DNA Blood Maxi Kit (Qiagen, Manchester, UK).
The library was produced using forward and reverse barcode primers and the NEBNext High Fidelity PCR Master Mix (New England Biolabs, Hitchin, UK) according to previously published protocols (Joung et al 2017, Nature Protocols, 12(4):828-863. doi: 10.1038/nprot.2017.016) and pooled PCR products purified using the QIAquick PCR Purification Kit (Qiagen).

treatment_protocol: THP-1 cells transduced with the Brunello CRISPR library were exposed to DMSO or 1 micromolar mebendazole for 10 days.

value: THP-1 cells, MLL-AF9 positive

value: Acute Myeloid Leukemia

value: cell line

value: DMSO 10 days


title: Colon_scRANseq_GEX

description:
Library name: Colon_scRANseq_GEX
10x Genomics


title: Brain3_scRANseq_HTO

description:
Library name: Brain3_scRANseq_HTO
10x Genomics

source_name: Brain

value: Brain


title: A375 AHRKO RNA Rep 3

description:
Library name: A375 AHRKO RNA Rep 3
sgAHR-3
A375_count.csv
A375_TPM.csv

value: AHR KO


title: mebendazole treated cells

description: Library name: NC6_S6_R1_001.fastq.gz

value: 1uM mebendazole 10 days


title: Fibroblast cells, TGFβ, entinostat #2

city: Sugito-machi

first: Rii

last: Morimura

state: Saitama

address: 4-2-3 Takanodaiminami

institute: TOPPAN Holdings Inc.

description: Library name: sample8

data_processing:
Illumina adapter sequences were removed, and low-quality bases of raw reads were processed using Trimmomatic-0.38, with the phred33 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:30 MINLEN:40 option.
Assembly: Preprocessed reads were aligned onto the human genome (GRCh38/hg38) using HISAT2 (version 2.1.0) (28). After mapping, SAMtools (version 1.7) was used to convert the obtained SAM files to BAM files. Annotation and estimation of gene expression were performed using StringTie (version 1.3.5) and Gencode (version 31, Human Release 31 [GRCh38.p12]) as references. Gene count data were transformed from the obtained gene expression data using the prepDE.py program. Low-read-count genes were extracted using filterByExpr (default setting) in edge R (version 3.30.3, R version 4.0.2), and differentially expressed genes (DEGs) were identified using the edge R package after normalization and likelihood ratio testing.
Supplementary files format and content: csv file include TPM values for each samples

source_name: primary

extract_protocol:
A Maxwell® RSC simplyRNA Cells kit (Promega) and Maxwell RSC Instrument (Promega) were used to extract RNA from fibroblasts treated for 72 h
The extracted RNA was then subjected to paired-end sequencing (86 bp) using a NextSeq500 platform (Illumina).

value: primary

value: Fibroblast cells

value: TGFβ+entinostat from 24h


title: Fibroblast cells, TGFβ, entinostat #1

description: Library name: sample7


title: A375 AHRKO RNA Rep 2

description:
Library name: A375 AHRKO RNA Rep 2
sgAHR-2
A375_count.csv
A375_TPM.csv


title: Brain2_scRANseq_HTO

description:
Library name: Brain2_scRANseq_HTO
10x Genomics

value: 3 weeks

value: gammadelta T cells

value: Wild type or 15q dup


title: Fibroblast cells, TGFβ, TSA #2

description: Library name: sample6

value: TGFβ+TSA from 24h


title: Brain3_scRANseq_GEX

description:
Library name: Brain3_scRANseq_GEX
10x Genomics


title: A375 ARNTKO RNA Rep 1

description:
Library name: A375 ARNTKO RNA Rep 1
sgARNT-1
A375_count.csv
A375_TPM.csv

value: Skin


title: 76_NORM

value: M

value: KIDNEY


title: 291_SCAR


title: 68_NORM

value: F


title: 285_SCAR


title: 69_NORM


title: Brain2_scRANseq_GEX

description:
Library name: Brain2_scRANseq_GEX
10x Genomics


title: A375 Control RNA Rep 3

description:
Library name: A375 Control RNA Rep 3
sgNTC-3
A375_count.csv
A375_TPM.csv

value: Non-targeting control


title: dHipp_62

first: Jennifer

last: Chan

description:
Library name: Sample 88
Illumina Stranded mRNA Prep

data_processing:
Alignment using Kallisto v.0.46.1
Reduce variation using RUV-seq v.1.32.0
Differential expression using DESeq2 v.1.38.3
Assembly: mm10
Supplementary files format and content: csv file with normalized counts containing all samples

extract_protocol:
Homogenization of tissue in Trizol Reagent with subsequent clean-up using Rneasy Microcolumns.
TruSeq RNA Library Prep Kit v2 and Illumina Stranded mRNA Prep

tag: region

value: dHpc

tag: group

tag: virus


title: Brain_scRANseq_HTO

description:
Library name: Brain_scRANseq_HTO
10x Genomics

tag: genotype


title: 275_SCAR


title: A375 Control RNA Rep 2

description:
Library name: A375 Control RNA Rep 2
sgNTC-2
A375_count.csv
A375_TPM.csv


title: Brain_scRANseq_GEX

description:
Library name: Brain_scRANseq_GEX
10x Genomics


title: Fibroblast cells, TGFβ, #2

description: Library name: sample4

value: TGFβ from 24h


title: 73_NORM


title: A375 Control RNA Rep 1

description:
Library name: A375 Control RNA Rep 1
sgNTC-1
A375_count.csv
A375_TPM.csv


title: Fibroblast cells, Control, #2

description: Library name: sample2

value: DMSO from 24h


title: Fibroblast cells, TGFβ, #1

description: Library name: sample3


title: Blood_scRANseq_HTO

description:
Library name: Blood_scRANseq_HTO
10x Genomics

source_name: Blood

value: Blood


title: Fibroblast cells, TGFβ, TSA #1

description: Library name: sample5


title: SKMEL2 ARNTOE ChIP Rep 3

description: Library name: SKMEL2 ARNTOE ChIP Rep 3

data_processing:
Raw sequencing reads were assessed using FastQC to evaluate base quality, duplication levels, and adapter content.
Adapters and low-quality bases were removed using Trim Galore (v0.6.10) with paired-end mode and other default parameters.
Trimmed reads were aligned to the hg38 reference genome using Bowtie2 with --very-sensitive preset and maximum insert size of 2000 bp.
Properly paired reads with MAPQ >= 30, excluding secondary, supplementary, and duplicate alignments were retained, mitochondrial reads (chrM) were removed, and duplicate reads were removed using SAMtools (v1.17) pipeline.
Final BAM files were coordinate-sorted and indexed using SAMtools.
bigWig coverage tracks were generated using deepTools bamCoverage (v3.5.3) with 10 bp bin size and RPGC normalization (effective genome size: 2,862,010,428). chrX and chrM were excluded from normalization, and reads were extended to the estimated fragment size..
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
A total of 40 million cells for each group were fixed with 1% formaldehyde solution for 8 min. After quencing and cell lysis, chromatin was sonicated using a Qsonica Q800R (50% amplitude, 30 s on / 30 s off, for 20 cycles) to achieve a mean DNA fragment size of 300 bp.
Post-sonication, samples were centrifuged at 12,000×g for 5 min at 4°C, and the supernatant was collected and kept on ice. Samples were diluted 1:10 in dilution buffer  supplemented with 5 M NaCl to reach 150 mM NaCl, and incubated rotating with antibody and Protein A/G magnetic beads, to bind the anti-HA antibody and associated chromatin, for 3 h at 4°C. After washing seven times with high salt buffer and twice with TE buffer, samples were eluted from the beads for 15 min at 65°C in elution buffer. Eluates were treated with RNase A at 37°C for 30 min and reverse cross-linked overnight by heating at 65°C with Proteinase K. Samples were extracted with an equal volume of phenol:chloroform, vortexed, centrifuged at 12,000×g for 10 min. The aqueous phase (~400 μL) was transferred to a new tube and mixed with 1.6 μL GlycoBlue (250×), 40 μL 3 M sodium acetate (pH 5.2), and 800 μL ice-cold ethanol. DNA was precipitated at -20°C overnight. Samples were centrifuged at 12,000×g for 15 min at 4°C, washed twice with 75% ethanol, and resuspended in 20 μL nuclease-free water. The ChIP library for each sample was then prepared using VAHTS Universal Pro DNA Library Prep Kit for lllumina with VAHTS Multiplex Oligos Set 4 for Illumina and VAHTS DNA Clean Beads.

value: ARNT OE


title: Fibroblast cells, Control, #1

description: Library name: sample1

value: primary


title: Blood_scRANseq_GEX

description:
Library name: Blood_scRANseq_GEX
10x Genomics


title: SKMEL2 ARNTOE ChIP Rep 2

description: Library name: SKMEL2 ARNTOE ChIP Rep 2


title: 244_SCAR


title: Homo sapiens Telencephalon CS15 Rep2

first: Fursham

last: Hamid

address: 1 Newcomen St

institute: KCL

description:
Library name: AZI3602A6
Technical replicate

data_processing:
Short reads stored in FASTQ file formats were pre-processed and aligned to custom-built transcriptomes  using the CellRanger software (v3.0.2 or v3.1.0)
Assembly: GRCh38-3.0.0_GFP-tdT or mm10-3.0.0_GFP-tdT
Supplementary files format and content: The gene expression counts from predicted cells were stored in compressed H5 format (libname_filtered_feature_bc_matrix.h5).

source_name: Telencephalon

extract_protocol:
Single cell suspensions from each mouse and human sample were loaded into one and two lanes, respectively, of a Chromium Chip G (10X Genomics, PN-1000120) of 10X Chromium Controller (PN-120270
Sequencing libraries were prepared using  Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (PN-1000121) according to manufacturer’s protocol.

value: Telencephalon

tag: development stage

tag: replicate


title: wk3_KrasWT_Saline_B0241

first: Rohit

last: Chandwani

address: 413 East 69th St, BRB 1360G

department: Surgery

institute: Weill Cornell Medicine

data_processing:
The quality of the sequenced reads was assessed with FastQC v0.11.8 and QoRTs v1.3.6.
Sequencing reads were aligned with default parameters to the mouse reference genome (GRCm38.p6) using STAR v2.7.9a.
. Gene expression estimates were obtained with featureCounts v2.0.1 using composite gene models (union of the exons of all transcript isoforms per gene) from Gencode (version M25).
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include raw abundance values for each sample as obtained from featureCounts

source_name: Adult Pancreas

extract_protocol:
tdTomato+ acinar cells were FACS sorted into 1.5 mL Eppendorf tubes containing Trizol. Total RNA was purified using a standard phenol-chloroform extraction method.
Sequencing libraries were constructed using Illumina TruSeq Library Prep Kit (Non-Stranded and Poly-A selection) and sequenced on either Illumina HiSeq 2500 or NovaSeq 6000 (2x50 cycles paired-end run)

value: Adult Pancreas

value: KrasWT

value: Tamoxifen

value: Saline


title: HEK_105Q(IB+)_2

first: Walaa

middle: Ziad

last: Oweis

state: Israel

institute: Hebrew University of Jerusalem

description:
Library name: HEK_105Q(IB+)_2
counts_HEK_105Q.csv

data_processing:
Raw fastq files were checked for quality control using fastqc software.
Raw reads were trimmed to remove Illumina adapters using the Trimmomatic software version 0.39
Reads were aligned to the human RefSeq reference genome (GRCh38) using STAR aligner version 2.7.1a with the default parameters.
Raw counts for each gene were generated using - quantMode GeneCounts.
Assembly: GRCh38
Supplementary files format and content: Comma-separated values includes raw counts for each sample

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen)
mRNA libraries were prepared using KAPA Stranded mRNA-Seq kit.

value: HEK

value: IB+


title: Homo sapiens Telencephalon CS15 Rep1

description:
Library name: AZI3602A5
Technical replicate


title: SKMEL2 ARNTOE ChIP Rep 1

description: Library name: SKMEL2 ARNTOE ChIP Rep 1

value: Skin


title: wk3_KrasWT_Saline_4992


title: HEK_105Q(IB+)_1

description:
Library name: HEK_105Q(IB+)_1
counts_HEK_105Q.csv


title: HEK_105Q(IB-)_2

description:
Library name: HEK_105Q(IB-)_2
counts_HEK_105Q.csv

value: IB-


title: SKMEL2 AHROE ChIP Rep 3

description: Library name: SKMEL2 AHROE ChIP Rep 3

value: AHR OE


title: 67_SCAR

tag: Sex

value: M

value: KIDNEY


title: Homo sapiens Telencephalon CS13 Rep2

description:
Library name: AZI3602A4
Technical replicate


title: wk3_KrasWT_Saline_4953


title: Homo sapiens Telencephalon CS13 Rep1

description:
Library name: AZI3602A3
Technical replicate


title: 259_SCAR


title: HEK_105Q(IB-)_1

description:
Library name: HEK_105Q(IB-)_1
counts_HEK_105Q.csv


title: SKMEL2 AHROE ChIP Rep 2

description: Library name: SKMEL2 AHROE ChIP Rep 2


title: wk3_KrasWT_Saline_4952


title: Homo sapiens Telencephalon CS12 Rep2

description:
Library name: AZI357A10
Technical replicate


title: A375 AHRKO RNA Rep 1

description:
Library name: A375 AHRKO RNA Rep 1
sgAHR-1
A375_count.csv
A375_TPM.csv

value: AHR KO


title: SKMEL2 AHROE ChIP Rep 1

description: Library name: SKMEL2 AHROE ChIP Rep 1


title: wk3_KrasWT_Saline_4947


title: Homo sapiens Telencephalon CS12 Rep1

description:
Library name: AZI357A9
Technical replicate