title: input-FSK

status: Public on Oct 27 2021

city: La Jolla

first: Sam

last: Van de Velde

state: CA

address: 10010 North Torrey Pines Road

department: PBL

institute: Salk Institute

data_processing:
Reads were aligned to the mm10 mouse genome assembly using STAR
Aligned reads were further processed using Homer: sam files were converted to Homer tag directories and subsequently binding peaks were identified.
Multiwig hubs were made using Homer
Genome_build: mm10
Supplementary_files_format_and_content: peak file

source_name: 3T3L1 adipocytes

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were constructed using the NEBNext ChIP-Seq Library Kit (E6240) according to the manufacturer's instructions

treatment_protocol: Cells were treated for 1 hour

value: adipocyte

tag: chip antibody

value: no IP

value: 10 uM forskolin 1 hour


title: spinal cord with TSCI rep1

type: SRA

city: Jinan

first: Bin

last: Ning

address: Jiefang Road #105

country: China

institute: Shandong University

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed.
We aligned reads of samples to the reference genome using Hisat2 package.
The mapped reads of each sample were assembled using StringTie, all transcriptomes were merged to reconstruct a comprehensive transcriptome.
Unmapped reads were still mapped to genome using tophat-fusion. CIRCExplorer2 and CIRI were used to  identified circRNAs.
Genome_build: Mus_musculus Ensembl release-90
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: spinal cord

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s procedure. The total RNA quantity and purity were analysis of Aglient 2100 Bioanalyzer and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Approximately 5 ug of total RNA was used to deplete ribosomal RNA according to the manuscript of the Ribo-Zero™ Magnetic Gold Kit (Illumina, San Diego, USA).Then the left RNA was fragmented into pieces using divalent cations under elevated temperature. The cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, USA).

treatment_protocol: Briefly, 48 adult male C57BL/6 mice were randomly divided into the SCI (n=8)×3 and sham (n=8)×3 groups. Mice in the SCI group underwent  T8–10 vertebral laminectomy to expose the spinal cord after anesthesia was induced with 3% pentobarbital. Then, moderate SCI was induced using a modified Allen’s weight-drop apparatus, subsequently, the muscles and skin were sutured layer by layer. Mice in the sham group underwent the same laminectomy but without SCI.

tag: strain

tag: tissue

value: spinal cord

tag: age

value: post natal 8 weeks

tag: treatment

value: traumatic spinal cord injury


title: JM_FSU_RNA1307-52_all_RNAseq

status: Public on Oct 19 2021

city: Jena

first: JenAge

last: Project

address: Beutenbergstr. 11

country: Germany

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

data_processing:
Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step.
Reads were mapped using STAR (2.4.1d).
Reads per gene were counted using featureCounts (1.4.6-p4).
Counts were normalized to RPKM values as described in Mortazavi et al. (2008).
Genome_build: genome: WBcel235, and respective gene annotation (WBcel235.84)
Supplementary_files_format_and_content: The Excel files include raw counts (sample_counts.xls) and RPKM values (sample_rpkms.xls) of all genes for each sample.

organism: Caenorhabditis elegans

extract_protocol:
Extraction was done as described in Baumgart et al. 2012. (PMID:22487494)
Library preparation was done using Illumina's TruSeq Stranded mRNA Library Preparation Kit following the manufacturer's instruction.

value: whole worms

value: 15 days

tag: Sex

value: hermaphrodite

tag: perturbation


title: JM_FSU_RNA1307-51_all_RNAseq

source_name: N2_10 days_prp-19


title: JM_FSU_RNA1307-50_all_RNAseq

source_name: N2_10 days_skp-1


title: JM_FSU_RNA1307-48_all_RNAseq


title: JM_FSU_RNA1307-49_all_RNAseq


title: JM_FSU_RNA1307-53_all_RNAseq


title: SUDLH5_EV_MYC_ChipSeq

status: Public on Oct 11 2021

city: Kiel

first: Elmar

last: Wolf

state: Schleswig-Holstein

address: Rudolf-Höber-Str. 1

department: Biochemical Institute

institute: Christian-Albrechts-University Kiel

library_source: genomic

data_processing:
Fastq files were mapped to the human genome (hg19) using Bowtie v2.27. and normalized to the sample with the spike in control where applicable.
bedgrpah files as defined by UCSC (https://genome.ucsc.edu/goldenpath/help/bedgraph.html).
Genome_build: hg19

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Human DLBCL (SU-DHL-5) cells were grown in RPMI supplemented with 20% FCS and 2% glutamine; for spike-in: murine T-Lymphoma(MYC-Tet-OFF) cells were cultured in RPMI supplemented with 10% FCS, 1% penicillin/streptomycin, 1% MEM non-essential amino acids, 1% glutamine, 50 mM beta-mercaptoethanol

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 5 min. 6% murine T-lymphoma cells were added during cell lysis as exogenous spkie-in for normalization. After cell lysis, nuclei were re-suspended in RIPA buffer (10 mM Tris/HCl pH 7.5, 150 mM NaCl, 1% NP40, 1% deoxycholic acid (DOC), 0.1% SDS, 1 mM EDTA) and DNA was fragmented to a size <300 bp using a Branson sonifier or using the Covaris Focused Ultrasonicator M220 for 100 min per ml lysate. Chromatin was immunoprecipitated with 15 µg of corresponding antibody for 6 to 8 hours. Chromatin was eluted with 1% SDS and crosslinking was reverted overnight. For purification, chloroform/phenol extraction was used.
NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina® or NEBNext® Ultra II DNA Library Prep with Sample Purification Beads (New England Biolabs). Purified DNA was end-repaired, A-tailed, ligated to Illumina adaptors, size-selected (200 bp) and purified with Qiagen gel extraction kit or Sample Purification Beads. DNA fragments were amplified by 17 cycles of PCR and library size was tested with the Fragment Analyzer (Advanced Analytical). The amount of library DNA was quantified using a picogreen assay.

treatment_protocol: no treatment

value: empty vector

tag: sirna

tag: antibody

value: MYC (abcam, ab32072)


title: iSC_2TF.r3

status: Public on Oct 15 2021

city: Ramat Gan

first: Nitzan

last: Gonen

address: Bar-Ilan University

department: Life Sciences

country: Israel

institute: Bar-Ilan University

description: Bulk RNA-Seq

data_processing:
Cutadapt v1.9.1 (Martin, 2011) was used to trim adapter sequences from reads with the following options: -a AGATCGGAAGAGC –A AGATCGGAAGAGC -e 0.1 –q 10.
Gene-level abundance estimates were calculated with RSEM v1.3.0 (Li and Dewey, 2011), using STAR v2.5.2a (Dobin et al., 2013) to align reads against the GRCm38 genome assembly with Ensembl release 86 transcript annotations.
The pipeline used to create the abundance estimates is feely available here: https://github.com/crickbabs/BABS-RNASeq/tree/c3c13518a009fba9aa8afa228fab8cb779815ca5
Genome_build: GRCm38
Supplementary_files_format_and_content: *.genes.results.txt: RSEM gene-level abundance estimates including expected_count, TPM and FPKM. Gene ids are represented by Ensembl v86 identifiers.

source_name: Induced embryonic Sertoli-like cells (induced by overexpression of Nr5A1 and Dmrt1)

growth_protocol:
ESCs were routinely cultured on 0.1% Gelatin coated dishes with 2i/LIF media. For differentiation, ESCs cultured on 2i/LIF were seeded for 1 passage on dishes coated with Gel-MEF: 0.1% gelatin coating for 15 minutes followed by coating with MEF media for at least 2 hours [DMEM, 10% FCS, P/S, L-Glu]. ESCs were seeded in KSR media [Ad-DMEM/F12, 20% knock out serum replacement, P/S, L-Glu, Beta-mercaptoethanol and 1000 U/ml of LIF].
For epiblast-like cell (EpiLC) differentiation, 2.5x10^5 cells were seeded on Gel-MEF coated 6-well dish wells. EpiLC differentiation was performed as previously described (Hayashi et al., 2011). Briefly, EpiLCs were induced by culturing ESC in N2B27 minus Vitamin A medium containing 20 ng/ml activin A, 12 ng/ml bFGF and 1% knockout serum replacement for 2.5 days (~60 hours).
Early mesoderm differentiation was induced by growing the cells as previously described (Bernardo et al., 2011) in a chemically defined medium (CDM) containing PVA and supplemented with 20 ng/ml bFGF, 10 μM LY294002 and 10 ng/ml BMP4, named FLyB for 36 hours.

extract_protocol:
Total RNA was extracted using Trizol according to the manufacturer’s instructions. RNA quantity and quality were quantified using Nano-drop, Qbit and Tape station.
Libraries were prepared using the TruSeq Library Prep kit V2 (Illumina) according to the manufacturer’s instructions. Libraries were sequenced on the Illumina HiSeq 4000 following the manufacturer's protocols (Paired end, 75 bp).

treatment_protocol:
IM1: bFGF (5ng/ml) + BMP (20ng/ml).
IM2: bFGF (5ng/ml) + BMP (20ng/ml) + RA (100nM) + Activin A (10ng/ml).
IM3: bFGF (5ng/ml) + BMP (20ng/ml) + RA (100nM).
IM4: bFGF (5ng/ml) + BMP (20ng/ml) + RA (100nM) + CHIR 0.3 μM.
IM5: bFGF (5ng/ml) + BMP (20ng/ml) + RA (100nM) + Activin A (10ng/ml) + CHIR (0.3 μM).

tag: cell type

value: ES-derived induced embryonic Sertoli-like cells

value: F1:C57BL/6 x CBA

tag: genotype

value: Tesco-CFP; R26-rtTA XY cells, clone 7


title: ATAC_T185_5_r1

status: Public on Sep 07 2021

city: Planegg-Martinsried

first: Gunnar

last: Schotta

address: Grosshaderner Strasse 9

department: Biomedical Center

institute: LMU Munich

data_processing:
Reads were mapped to the mouse genome (mm10) using bowtie (Langmead et al., 2009)
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated from Homer tag directories using makeBigWig.pl

source_name: ES cells

growth_protocol: Feeder-independent ES cells were cultured on 10cm gelatin-coated plates with ES cell medium containing Serum and LIF

extract_protocol:
The OmniATAC transposition reaction was performed with 50 000 cells as previously described (Corces, Trevino et al. 2017) using the Tagment DNA TDE1 Enzyme (Illumina, 20034197). DNA was purified using the PCR clean-up MinElute kit (Qiagen, 28006).
The transposed DNA was subsequently amplified in 50µl reactions with custom primers as previously described (Buenrostro et al., 2013). Libraries were purified and size selected for fragments less than 600bp using the Agencourt AMPure XP beads (Beckman Coulter, A63882).

tag: cell line

value: Morc3_dN rescue

value: mouse embryonic stem cells (ESCs)


title: JM_FSU_RNA1307-46_all_RNAseq


title: Visium-A

status: Public on Sep 21 2021

city: New York

first: Miranda

last: Hunter

state: NY

address: 418 E 68th St

country: USA

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Illumina RTA v2 software was used for basecalling and quality determination.
The Visium raw FASTQ data was processed using 10X Genomics proprietary SpaceRanger (v1.0.0) pipeline.
The single-cell RNA-seq raw FASTQ data was processed using the 10X Genomics proprietary CellRanger (v3.1.0) pipeline
Genome_build: GRCz10.88
Supplementary_files_format_and_content: For 10x Genomics spatial transcriptomic data: output of SpaceRanger pipeline, including gene expression and spatial contents. For 10x Genomics single-cell RNA-Seq: output of CellRanger pipeline, including gene expression, features and barcodes.
Supplementary_files_format_and_content: *_image.tif: Tissue section used for Spatial Transcriptomics experiment.

organism: Danio rerio

source_name: Zebrafish melanomas (BRAF-V600E)

extract_protocol:
For spatial transcriptomics using the Visium platform from 10X genomics: Adult tumor-bearing fish were euthanized on ice and washed in 1X PBS. After dissection of the head and tail, the remaining tissue was equilibrated in cold OCT for 2 minutes, before transfer to a tissue mold filled with fresh OCT for snap-freezing in liquid nitrogen-chilled isopentane. Tissue blocks were stored at -80°C. For cryosectioning, both the tissue block and the ST slide were equilibrated inside the cryostat for 15-30 minutes at 16°C before sectioning. Transverse sections through the entire fish were cut at a thickness of 10 µm and immediately placed on the ST slide (Visium Spatial Gene Expression Slides, 10X Genomics). ST slides containing sections were stored at -80°C for a maximum of one week before use. For single-cell RNA-seq using the 10X genomics 3’ GEX (v3) platform: Adult tumor-bearing fish were dissected to obtain only the tumor and surrounding tissues (i.e head and tail were removed). Tissue was minced with a fresh scalpel and incubated in 0.16 mg/mL liberase (Sigma-Aldrich #5401020001) in 0.9X PBS for 15 minutes at RT. Tissue was then further dissociated by repeated pipetting with a wide-bore P1000, followed by incubation for an additional 15 minutes at RT. After adding 500 uL FBS to stop the dissociation reaction, samples were filtered through a 70 µm filter and centrifuged at 500g for 5 minutes at RT. The resulting pellet was resuspended in DMEM supplemented with 2% FBS, and cells were sorted at room temperature to remove debris and doublets, using a BD FACSAria III cell sorter (BD Biosciences). Equal numbers of GFP+ (tumor) and GFP- (macroenvironment) cells were collected.
For spatial transcriptomics using the Visium platform from 10X genomics: Samples were processed according to the Visium Spatial Gene Expression User Guide (10X Genomics) and all reagents were from the Visium Spatial Gene Expression Kit (10X Genomics). Briefly, sections were fixed in chilled methanol for 30 min at -20°C, stained with hematoxylin and eosin, and mounted in 85% glycerol for imaging. Imaging was performed on a Leica SCN400 F whole-slide scanner at 40X magnification. After imaging, sections were permeabilized at 37°C for 45 minutes. After permeabilization, the on-slide reverse transcription (RT) reaction was performed at 53°C for 2 hours. Permeabilization time and RT reaction length were determined using the Visium Spatial Tissue Optimization Kit (10X Genomics). Second strand synthesis was subsequently performed on-slide for 15 minutes at 65°C. All on-slide reactions were performed in a thermocycler with a metal slide adaptor plate. Following second strand synthesis, samples were transferred to tubes for cDNA amplification and cleanup. Library quality was assayed using a Bioanalyzer High Sensitivity chip (Agilent). For single-cell RNA-seq using the 10X genomics 3’ GEX (v3) platform: Equal numbers of sorted GFP+ (tumor) and GFP- (macroenvironment) cells were centrifuged at 300g for 5 minutes at RT, and resuspended in DMEM + 10% FBS. Droplet-based scRNA-seq was performed using the Chromium Single Cell 3’ Library & Gel Bead Kit v3 (10X Genomics) and Chromium Single Cell 3’ Chip G (10X Genomics). Approximately 10,000 cells from two fish were split encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions.

tag: sample type

value: Tissue cryosections


title: T6_3340_125_CTL_HW_M_G1_21034

status: Public on Sep 08 2021

city: Duarte

first: Denis

last: OMeally

state: California

address: 1500 E Duarte Rd

department: Arthur Riggs Diabetes & Metabolism Research Institute

institute: City of Hope

description:
microRNA
MicroRNAseq library prep.
training_mature_normalized_CPM.tsv
training_mature_mirTOPcounts.tsv

data_processing:
Cutadapt preprocesssing was performed to remove the first three bases and adapter sequences with the parameters "cutadapt -a TCTGGAATTCTCGGGTGCCAAGGAACTCC -m 16 -u 3"; fastqs in this submission from validation cohort timepoint 5 have already been trimmed.
Cutadapt trimmed reads were processed with the nf-core smRNASeq pipeline version 1.0 using the GRCm38 genome reference (with the parameter --genome GRCm38) and adapters for the Illumina small RNA protocol (by setting --protocol Illumina). Briefly, trimmed reads were mapped using bowtie to miRBase mature miRNAs (using the parameters -k 50 --best --strata), and the number of reads mapping to each was counted using samtools stats and miRTOP. Each library was also subjected to extensive quality control, including estimation of library complexity, contamination, sequence quality, read length and depth, among other metrics detailed in the pipeline repository. Mapped reads were merged into a matrix of counts per gene for each sample at each timepoint and normalized to counts per million (CPM) reads mapped, as implemented in edgeR. Surrogate variable analysis was used to check for confounding experimental effects and none were apparent.
Genome_build: GRCm38
Supplementary_files_format_and_content: *.tsv: Expression matrices of miRNAs in rows and samples in columns.

source_name: PBMC

growth_protocol: The expression of the leukemogenic fusion gene Cbfb-MYH11 (CM) in conditional CM knock-in mice (Cbfb56M/+/Mx1-Cre) leads to development of AML with a median survival of approximately 4 months after induction of CM. This model recapitulates the human inv(16) AML, one of the common subsets of AML characterized by the rearrangement of chromosome 16 at bands p13 and q22, which at the molecular level creates the chimeric fusion gene CBFB-MYH11. To induce CM expression, 6-8 weeks old CM knock-in mice were injected intraperitoneally with polyinosinic–polycytidylic acid [poly (I:C)] (InvivoGen, tlrl-picw-250) at 14 mg/kg/dose every other day for a total of 7 doses. Age-matched littermates lacking the transgene were similarly treated and used as control. All mice were maintained in an Association for Assessment and Accreditation of Laboratory Animal Care–accredited animal facility and all experimental procedures were performed in accordance with federal and state government guidelines and established institutional guidelines and protocols approved by the Institutional Animal Care and Use Committee at City of Hope.

extract_protocol:
Total RNA was isolated from PBMC using AllPrep DNA/RNA Kit (Qiagen).
Testing cohort samples were allocated to randomized batches for library preparation, such that samples from each timepoint were distributed evenly over all sequencing runs. Validation cohort samples were processed in batches as collected. All libraries were prepared using the Illumina TruSeq Small RNA protocol with minor modification following the manufacturer’s instructions. Briefly, for each sample, 280 ng of total RNA was ligated to the sRNA 3′ adaptor (5’-TCTGGAATTCTCGGGTGCCAAGGAACTCC-3’) with T4 RNA Ligase 2, truncated (New England BioLabs) for 1 h at 22°C, and subsequently ligated to a 5′ adaptor: 5’-GUUCAGAGUUCUACAGUCCGACGAUCNNN-3’) with T4 RNA ligase 1 (New England BioLabs) for 1 h at 20°C. The constructed small RNA library was first reverse-transcribed using GX1 (5′- GGAGTTCCTTGGCACCCGAGA) as the RT primer then subjected to PCR amplification for 13 cycles, using the primers GX1 (5′-CAAGCAGAAGACGGCATACGAGAT[NNNNNN]GTGACTGGAGTTCCTTGGCACCCGAGAATTCCA-3’) and GX2 (5′- AATGATACGGCGACCACCGAGATCTACAC[NNNNNNNN]CGACAGGTTCAGAGTTCTACAGTCCGA-3’), followed by 6% TBE PAGE gel purification with size selection (for targeted small RNAs of 17–35 nt). Individual libraries were prepared using a unique index primer (NNNNNNNN in the GX1 and GX2 primer) in order to allow for pooling of multiple samples prior to sequencing.

value: PBMC

tag: timepoint

value: CTL

value: HW

value: Male


title: JM_FSU_RNA1307-54_all_RNAseq


title: HSPCs, mRNA-derived cDNA

status: Public on Aug 13 2021

city: illkirch

first: giovanni

last: cova

address: 1 Rue Laurent Fries

country: France

institute: igbmc

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
polyA RNA

Flow cytometry purified HSPC (Lin-Sca1+ckit+ cells) from 2 WT and 2 Helios deficient mice were stained for the cell surface proteins CD41, CD48, CD150 and Flt3 with oligonucleotide-tagged antibodies to perform CITE-sequencing. HSPC from each mouse were labelled with a unique oligonucleotide-tagged antibody anti-CD45 and anti-MHCI (HASH-sequencing) to identify them. Equal amount of HSPC (2500 cells) from each mouse were pooled and loaded to perform scRNA sequencing.

data_processing:
Library strategy: CITE-seq
Pre-processing of sequencing results to generate count matrices (gene expression, ADT and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline where ADT and HTO sequences were concatenated and treated as Custom library with default settings (v3.0.2) and aligned to the mm10 genome build and Ensembl 93 annotations.
Further processing was done with Seurat v3.0.0 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Genome_build: mm10
Supplementary_files_format_and_content:
barcodes.tsv
features.tsv
matrix.mtx
barhash.csv (Contains barcodes linked to the hashtag of interest.  Hashtag 1 and 2 are the two Helios KO samples: KO1 and KO2. Hashtag 3 and 4 are the two WT samples: WT1 and WT2. Negative and Doublet are barcodes that need to be excluded.)
filteredinbarcodes.csv (Contains the good barcodes, and it is used to exclude Doublet and Negative.)

molecule: polyA RNA

source_name: Bone Marrow

extract_protocol:
Lin-Sca1+ckit+ (LSK) cells from two WT and two Helios deficient mice were purified by flow cytometry. Purified cells were then stained with Antibody Derived Tag directed against CD41, CD48, CD150 and Flt3 and barcoded with a unique Oligonucleotide Hash Tag. After Hash- and Cite-tagged cells were counted and checked for viability using a hematocytometer, 10e4 cells (2500 LSK cells for each mouse) were loaded into a Chromium Controller (10X Genomics).
Library was prepared using Chromium Single Cell 3ʹ v2 protocol (10x Genomics). Cellular mRNA and antibody-derived oligos were reverse-transcribed and indexed with a shared cellular barcode. Indexed cDNAs were then pooled and amplified by PCR according to the Chromium Single Cell 3’ v2 protocol (10x Genomics) and with specific primers amplifying the antibody-derived tags. SPRI bead size selection was performed in order to separate both the mRNA-derived cDNA (>300bp) and the antibody-derived tagged cDNAs (180bp). For the mRNA derived cDNA library preparation, we further proceeded according to the manufacturer’s instructions for Single Cell 3’ v2 protocol (10x Genomics). For antibody-derived tagged library, we used the KAPA HiFI HotStart Library Amplification Kit (Roche) with the following primers and amplification program:
-CITE-seq library: amplification was performed at 95°C for 3’ followed by ten cycles at 95°C f¬¬or 20’’; 60°C for 30’’; 72°C for 20’’ and final elongation 72°C for 5’ with 5’-CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA-3’ Small RNA RPI1 primer as i7 primer (Illumina).
-HASH-seq library: amplification was performed at 95°C for 3’ followed by ten cycles 95°C for 20’’; 64°C for 30’’; 72°C for 20’’ and final elongation 72°C for 5’ with 5’-CAAGCAGAAGACGGCATACGAGATCGAGTAATGTGACTGGAGTTCAGACGTGTGC-3’ TruSeq D701_s primer as i7 primer (Illumina).
The following 5’- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTC-3’ SI-PCR primer as i5 primer (Illumina) was used for both CITE- and HASH- seq library amplification.
Following the final bead purification, all three libraries were pooled as 80% mRNA library, 10% ADT library and 10% HTO library before sequencing.

value: Bone Marrow

value: Hematopoietic Stem and Progenitor Cells (HSPCs)

value: mixed sample (WT and Helios-deficient)

tag: library type

value: mRNA

tag: antibodies/tags


title: HSPCs, HTO-derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)

Flow cytometry purified HSPC (Lin-Sca1+ckit+ cells) from 2 WT and 2 Helios deficient mice were stained for the cell surface proteins CD41, CD48, CD150 and Flt3 with oligonucleotide-tagged antibodies to perform CITE-sequencing. HSPC from each mouse were labelled with a unique oligonucleotide-tagged antibody anti-CD45 and anti-MHCI (HASH-sequencing) to identify them. Equal amount of HSPC (2500 cells) from each mouse were pooled and loaded to perform scRNA sequencing.

molecule: protein

value: Cell Hashing

value: Anti CD45 + Anti MHC classI:KO--/TotalSeq-A0301; KO--/TotalSeq-A0302; WT--/TotalSeq-A0303; WT--/TotalSeq-A0304


title: HSPCs, ADT-derived cDNA

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)

Flow cytometry purified HSPC (Lin-Sca1+ckit+ cells) from 2 WT and 2 Helios deficient mice were stained for the cell surface proteins CD41, CD48, CD150 and Flt3 with oligonucleotide-tagged antibodies to perform CITE-sequencing. HSPC from each mouse were labelled with a unique oligonucleotide-tagged antibody anti-CD45 and anti-MHCI (HASH-sequencing) to identify them. Equal amount of HSPC (2500 cells) from each mouse were pooled and loaded to perform scRNA sequencing.

value: Antibody derived tag

value: Anti-CD135/TotalSeq-A0098; Anti-CD150/TotalSeq-A0203; Anti CD48/TotalSeq-A0429; Anti CD41/TotalSeq-A0443


title: H3K4ME3_36_WT_CnR

city: Cambridge

first: Carla

last: Concepcion

state: MA

address: 500 Main Street, 76-431

department: Koch Institute

institute: MIT

description: H3K4ME3 CUT&RUN

data_processing:
Illumina pipeline version 1.3+ used for basecalling and sequence read generation
Reads were mapped to the mouse transcriptome (UCSC annotation, genome build mm9) using bowtie2 v2.2.6; BAMs were processed to remove duplicates using Picard MarkDuplicates v2.17.0; Alignments were sorted by read name using samtools v1.5 and converted to BED format using bedtools bamtobed and subsequently to bedgraph using bedtools genomecov (BEDTools v2.29.2). Peaks were called using SEACR v1.2 (Meers MP, Tenenbaum D, Henikoff S., 2019)    by selecting the top 0.5% of regions by area under the curve (AUC).
Genome_build: mm9
Supplementary_files_format_and_content: Tar gzipped archive of BED files with peak calls per Cut&Run sample

source_name: Murine KP Lung Adenocarcinoma tumor-derived cell line, 36

growth_protocol: Cell lines were cultured in DMEM supplemented with 10% fetal bovine serum and 1X penicillin-streptomycin.

extract_protocol:
DNA was extracted using PCI and chloroform.
Libraries were constructed using NEB UltraII.
Cut&Run (paired end 25mer reads)

treatment_protocol: Cells were subjected to a published CUT&RUN protocol (Skene, Henikoff and Henikoff, Nature Protocols 2018).

value: KrasG12D/+; Trp53-/-; Smarca4+/+


title: JM_FSU_RNA1307-47_all_RNAseq

value: whole worms

value: 15 days

value: hermaphrodite


title: Antibiotics-3_16S

status: Public on Aug 06 2021

city: Guangzhou

first: Xiaoyun

last: Wang

state: Guangdong

address: 190 Kaiyuan Avenue, Huangpu

department: Infection and Immunity

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

description:
16S rDNA
The midguts were dissected from 3-day-old sixth instar larvae

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house Perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data. At the same time, Q20, Q30, GC-content, and sequence duplication levels of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
For RNA-seq data, the adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the S. frugiperda genome sequence (NCBI: ZJU_Sfru_1.0). Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Hisat2 (version 2.0.4) tools soft were used to map with reference genome by the parameters “--dta -p 6 --max intronlen 5000000”.
For RNA-seq clean data, the mapped reads were assembled with the StringTie software (version 1.3.4d) with the parameters “--merge -F 0.1 -T 0.1”.
For RNA-seq clean data, after detecting transcriptome library was eligible, The library preparations were sequenced on an Illumina platform nova-seq6000. The FPKM（Fragments Per Kilobase of transcript per Million fragments mapped）value representing the expression level of transcripts was calculated.
For RNA-seq clean data, differential expression analysis of the control and antibiotics-treated groups was performed using the DESeq2 (version 1.6.3) with the parameter "default:test="Wald",fitType="parametric". DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value < 0.01 found by DESeq2 were assigned as differentially expressed.
For 16S-seq data, the gut microbiota was sequenced on the Illumina nova-seq6000 platform with the paired-end method. The raw reads were filtered by using the software Trimmomatic (version 0.33).The primer sequences were identified and removed by using the CutAdapt (version 1.9.1) software.
For 16S-seq data, high-quality reads were spliced by using the software FLASH (version 1.2.7), and clean reads were obtained.
For 16S-seq clean data, chimerism was removed by using the software Uchime (version 4.2), and the effective reads were obtained.
Genome_build: Spodoptera frugiperda genome sequence (NCBI: ZJU_Sfru_1.0).
Supplementary_files_format_and_content: Tab-delimited text file (.txt) includes raw read counts for the RNA-seq data and OTU counts for the 16S-seq data of all samples. In addition, the sequences for the counted genes of the RNA-seq data are provided by a  FASTA file (.fa).

organism:
Spodoptera frugiperda
insect gut metagenome

source_name: Midgut

growth_protocol: The larvae were fed on the artificial diet including soybean powder, wheat germ, and yeast as described previously (Jia et al., 2009) for three generations at 27±1°C, 70±5% relative humidity, and the photoperiod light: dark =16 h: 8 h.

extract_protocol:
The genomic bacterial DNA was extracted by using the classical Phenol/Chloroform/Proteinase K method (Bargues et al., 2007). Total RNA from the midguts of S. frugiperda in the control and antibiotics-treated group was extracted by using the TRIzol reagent according to the manufacturer’s protocol (Invitrogen, California, USA).
RNA concentration and purity were measured using NanoDrop 2000 (Thermo Fisher Scientific, Wilmington, DE). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA). mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First-strand cDNA was synthesized using a random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with the AMPure XP system (Beckman Coulter, Beverly, USA). The library preparations were sequenced on an Illumina platform nova-seq6000 and paired-end reads were generated.
RNA-seq and 16S rDNA-seq

treatment_protocol: The newly hatched larvae were fed on the artificial diet with four antibiotics mixtures consisted of 500 µg/mL each of penicillin, gentamicin, rifampicin, and streptomycin, and the control larvae were fed on the artificial diet without antibiotics.

value: 3-day-old sixth instar larvae

tag: culture environment

value: Feed on artificial diet

value: with antibiotics

tag: replicate


title: Antibiotics-2_16S

tag: strain


title: Embryonic Stem Cell dervived Hypothalamus-like Neurons (RNA-Seq) Replicate 1

status: Public on Oct 01 2021

city: Philadelphia

first: Matthew

middle: C

last: Pahl

state: PA

address: 3615 Civic Center Blvd

institute: Children's Hospital of Philadelphia

description:
total RNA - rRNA depleted
HypothalamusESC_rnaseq_tpm_perReplicate.csv
HPvsHN.DE_rnaseq_edgeR.txt
ESCvsHN.DE_rnaseq_edgeR.txt

data_processing:
Bases were called using Illumina bcl2fastq2 conversion v2.29
Paired-end sequences were aligned to reference genome using STAR (v2.6.0c)
Read counts were calculated using HTSeq-count (v0.6.1). with parameter settings -f bam -r pos -s reverse -t exon -m intersect. Reads were mapped to a curated annotation consisting of GencodeV19 with lincRNA and sno/miRNA annotation from the UCSC Tabler Browser.
Genes located on mitochondiral genomes or annotated as rRNA were excluded from analysis
Differential analysis was performed using edgeR (v3.16.5). Raw reads per genes features were converted to CPM (read Counts Per Million mapped reads). The gene features with median value of less than 0.7 CPM (10 ~ 18 reads per gene feature) across all samples were filtered from differential analysis. The trimmed mean of M-values (TMM) method were used to calculate normalization scaling factors. The differentially expressed genes between ESCs, HPs, and HNs were identified with thresholds of FDR < 0.05 and absolute log2FC > 1.
TPM values were calculated for all genes
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: WiCell

growth_protocol: Human ESC H9 (W09; WiCell) were seeded on Matrigel plates (16 million cells/148 cm2) in DMEM KO medium supplemented with 15% KnockOut Serum Replacement, 0.1mM MEM Non-Essential Amino Acids, 2mM GlutaMAX, 0.06 mM 2-Mercaptoethanol) with FGF-Basic (20 ng/ml media), and 10 mM Rock inhibitor.

extract_protocol:
RNA was isolated from each sample using TRIzol Reagent. RNA was then purified using the Direct-zol RNA Miniprep Kit and depleted of contaminating genomic DNA using DNAse I. Purified RNA was then checked for quality on the Bioanalyzer 2100 using the Nano RNA Chip and samples with a RIN number above 7 were used for RNA-seq library synthesis.
RNA samples were depleted of rRNA using the QIAseq FastSelect RNA Removal Kit then processed into libraries using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina according to manufacturer’s instructions. Quality and quantity of the libraries was measured using the Bioanalyzer 2100 DNA chip and Qubit Fluorometer. Libraries were pooled and sequenced on the NovaSeq 6000 platform using paired-end 51bp reads at the Center for Spatial and Functional Genomics at CHOP.

treatment_protocol: ESC were untreated. Upon confluency, cells were cultured in ESC medium without FGF-Basic and Y-27632, but supplemented with Shh (100 ng/ml), Purmorphamine (2 μM), 10 μM SB431542, and 2.5 μM LDN193289. From days 5 to 8, ESC medium was gradually replaced with neuroprogenitor medium (DMEM/F-12 supplemented with 0.1 mM MEM Non-Essential Amino Acids, N-2 Supplement, 0.2 μM ascorbic acid, 0.16% glucose). At day 9, cells were switched into neuronal differentiation medium (DMEM/F-12 supplemented with 0.1 mM MEM Non-Essential Amino Acids, N-2 Supplement, B-27 Supplement minus Vitamin A, 0.2 μM ascorbic acid, 0.16% glucose containing 10 μM DAPT). On day 12, cells were collected with TrypLE Express Enzyme at 37°C for 7 min and washed twice including filtration through pre-wetted 40 μm Corning Sterile Cell Strainer. The hypothalamic progenitor cell pellet was then resuspended with neuronal differentiation medium containing 10 μM Y-27632 for plating on 148 cm2 dishes coated with Poly-L-Ornithine solution (0.01%) and laminin (4 μg/ml) at a seeding density of 16 million cells/148 cm2. After 4 hours (once the cells had completely attached to the plate), the medium was changed to neuronal differentiation medium supplemented with 10 μM DAPT. On day 15, the neuronal differentiation medium was supplemented with 20 ng/ml BDNF (Peprotech Cat # 450-02) until collection on day 27.

tag: esc line

value: Hypothalamic Neuron

tag: age (differentiation protocol)

tag: sample origin

value: human ESC H9


title: Antibiotics-1_16S

tag: treatment


title: Visium-B

value: Tissue cryosections


title: Control-3_16S

value: without antibiotics


title: Antibiotics-3_RNA

description:
PolyA RNA
The midguts were dissected from 3-day-old sixth instar larvae

organism: Spodoptera frugiperda


title: Antibiotics-2_RNA


title: Control-2_16S


title: Control-3_RNA


title: Control-1_16S


title: Antibiotics-1_RNA


title: Control-2_RNA


title: APAP3

status: Public on Aug 01 2021

city: HangZhou

first: jingyang

last: qian

address: No. 886, Yuhangtang Road

institute: Zhejiang University

data_processing:
The raw sequencing data from 10X Genomics were aligned and quantified using the CellRanger (10X Genomics) suite (version 3.0.2). The mouse genome mm10 was used as the reference genome and the CellRanger count module was used to map reads.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: barcodes.tsv, features.tsv, matrix.mtx files. Matrix table with raw gene counts for every gene and every cell.

source_name: Liver, APAP

extract_protocol:
Liver NPCs were isolated from mice according to a two-step collagenase method. In detail, murine livers were perfused in situ via the inferior vana cava with calcium-free Hank’s Balanced Salt Solution (HBSS, Gibco, Cat#14170112) containing 0.2 mg/mL EDTA (Sigma, Cat#E6758), followed by 0.4 mg/mL pronase (Sigma, Cat#P5147-1G) and 0.2% collagenase type II (Worthington, Cat#LS004176) at a perfusion rate of 8 mL/minute. Then livers were surgically removed and cut into small pieces. Tissues were transferred in HBSS containing 0.2% collagenase type II, 0.4 mg/mL pronase and 0.1 mg/mL DNase I (Roche, Cat#10104159001), and then incubated for digestion at 37℃ in a water bath for 20 minutes. DMEM (Mediatech, Cat#10-013-CV) containing 10% serum (FBS, Gibco, Cat#10099-141C) was added at the end of the incubation. Sequentially, hepatocytes removal was achieved by centrifugation for 3 minutes at 50 g. Then cell suspension was filtered using a 40 μm nylon cell strainer (Falcon, Cat#352340). Erythrocytes were lysed by treatment with 3-5 mL ACK lysing buffer (Gibco, Cat#A1049201) for 5 minutes after which PBS (Beyotime Biotec, Cat#C0221A) was added to terminate the lysis. The resulting suspension was subjected to Dead Cell Removal Kit (Miltenyi Biotec, Cat#130090101) to remove dead cells according to the manufacturer’s recommendations. The obtained cell pellet was washed twice and suspended in PBS. Cell viability was assessed by Trypan Blue (Gibco, Cat#15250-061).
Liver NPCs single cell suspensions were loaded onto the 10x Genomics Chromium chip (10x Genomics; Pleasanton, CA, USA) to generate droplets. Then the obtained Gel Beads-in-emulsion (GEMs) were transferred into a PCR tube strip, followed by reverse transcription using ProFlex PCR System (Thermo Fisher, MA, USA). The resulting cDNA was purified and amplified for 12 cycles before cleanup with SPRIselect beads (Beckman, Cat#B23318). Based on the cDNA concentration determined by Qubit (Thermo Fisher, MA, USA), libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v3 (10x Genomics; Pleasanton, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: Model of alcoholic liver disease was constructed by two weeks of chronic ethanol feeding plus a single binge ethanol feeding. Model of non-alcoholic steatohepatitis was built by a long-term feeding of methionine/choline deficient diet (MCD) containing 45 kcal% fat. Model of liver ischemia-reperfusion injury was established by the surgery that 70% warm hepatic ischemia for 45 min and reperfusion for 24 h. Model of drug-induced liver injury was constructed by once intraperitoneal injection of 300 mg/kg acetaminophen for 24 h. Model of cholestatic liver injury was established by bile duct ligation for 10 days. Subsequently, unbiased scRNA-seq analysis and validation experiments were performed.

tag: disease model

value: Drug-induced liver injury

value: Liver non-parenchymal cells (NPCs)


title: CS27_CpxR-IHMA87_01740_IHMA87_rep2

status: Public on Jul 27 2021

city: Zurich

first: Julian

last: Trouillon

address: Otto-Stern-Weg 3

department: Institute of Molecular Systems Biology

country: Switzerland

institute: ETH Zurich

description: adaptor-ligated sheared genomic DNA

data_processing:
Library strategy: DAP-seq
Read trimming using Trimmomatic
Alignment using Bowtie2
Peak calling using MACS2
closest features called with BEDtools
Genome_build: PAO1, PA14, IHMA87
Supplementary_files_format_and_content: excel table, list of RRs binding to the promoter region of each gene

organism: Pseudomonas aeruginosa

source_name: purified genomic DNA from liquid cultures

extract_protocol:
After cell-fre protein expression, soluble His-tagged proteins were bound to cobalt magnetic beads and incubated with adaptor-ligated sheared genomic DNA. After washes and isolation of bead-protein-DNA complexes, the bound DNA regions were eluted by heating and then used for library preparation.
DNA libraries were prepared for sequencing using standard Illumina protocols


title: Visium-C


title: APAP2


title: SK-MEL-28 treated with salubrinal polysome fraction rep 1

status: Public on Jul 15 2021

city: Leuven

first: Eleonora

last: Leucci

address: Herestraat 49, bus 818 room 06.423

department: Oncology

country: Belgium

institute: KU Leuven

data_processing:
Library strategy: Ribo-seq
Quality control of raw reads was performed with FastQC v0.11.5.
Adapters were filtered with eautils v1.2.2.18.
Splice- aware alignment was performed with STAR against the human hg19 human genome assembly. The number of allowed mismatches was 2. Reads that mapped to more than one site to the reference genome were discarded. The minimal score of align- ment quality to be included in count analysis was 10. Resulting SAM and BAM alignment files were handled with Samtools v0.1.19.24.
Quantification of reads per gene was performed with HT-Seq count v0.5.3p3.
Count-based differential expres- sion analysis was done with R-based (The R Foundation for Statistical Computing, Vienna, Austria) Bioconductor package DESeq.
Genome_build: human hg19 human genome assembly
Supplementary_files_format_and_content: Count files from HT-Seq count v0.5.3p3 containing quantification of genes per sample.

source_name: SK-MEL-28 melanoma cell line

growth_protocol: Sk-MEL-28 were grown in RPMI 1640 (Gibco, Invitrogen) supplemented with 10% FBS (Gibco, Invitrogen).

extract_protocol:
Cells were treated with 100 µg mL-1 of Cycloheximide (CHX, Sigma-Aldrich) for 12 min at 37 °C and resuspended in lysis buffer.  Lysates were then loaded on a sucrose gradient (the linear sucrose gradient 5-20%). Samples were then centrifugated in an SW41Ti rotor (Beckman Coulter) at 37.000 rpm for 170 min at 4 °C. The fractions were obtained with a BioLogic LP System (Bio-Rad). 14 fractions were collected from each sample, with each fraction having a final volume of 600 µL. From the initial 14 fractions, 4 final samples were obtained (by pulling together some of them): 40S, 60S, 80S and polysomes.
Libraries were prepared with TruSeq Stranded Total RNA kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: Cells were on treatment with salubrin for 72h before polysome preparation

tag: fraction

value: Polysome

value: Salubrinal


title: SK-MEL-28 treated with salubrinal 60S fraction rep 1


title: Control-1_RNA


title: ca_NM_3d_rep2 [H06423]

status: Public on Jul 05 2021

first: Daniela

last: Esser

address: Arnold-Heller-Str. 3

department: Institute of Clinical Chemistry

institute: University Hospital Schleswig-Holstein

description:
H06423
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt

data_processing:
Library strategy: 16S rRNA sequencing
16S rRNA: After assembling the reads using SeqPrep, subsequent identification of chimera with ChimeraSlayer and manual verification, chimera were removed from the data set. The sequences were further analyzes using QIIME 1.9.0.
RNA-Seq: After quality filtering (fastq_illumina_filter, prinseq-lite, cutadapt), sequencing reads were mapped against the Drosophila melanogaster reference BDGP6 using TopHat v2.1.0 with sensitive option. The read counts per transcript were calculated with the Python script HTSeq v0.6.1p1 using the mode ‘intersection-strict’.
Genome_build: Drosophila melanogaster BDGP6
Supplementary_files_format_and_content: *_counts.tsv: Tab-delimited text files include read counts per gene for each sample.
Supplementary_files_format_and_content: otu_table_mc50_w_tax_wochimera_ctrl_50filtered.txt: Tab-delimited text file includes read counts per OTU for each sample.

organism: insect gut metagenome

source_name: midguts of 5 Drosophila melanogaster individuals

growth_protocol: We used homozygous flies containing esg-Gal4, UAS-GFP, tubulin-Gal80ts on the 2nd chromosome, and UAS-Luciferase on the 3rd chromosome and crossed them to homozygous UAS-RAFgof flies to obtain the F1 generation with a temperature inducible tumor phenotype. As a control we crossed EGT;Luc2 to w1118 wildtype flies. All fly lines were raised on a cornmeal based standard medium at 20 °C. The F1 generation was shifted to 29 °C 5-7 days post eclosion to induce the expression of UAS-dependent genes.

extract_protocol:
DNA for 16S rRNA sequencing was extracted with the DNeasy Blood & Tissue Kit (Qiagen, #69504) following the manufacturer´s protocol for Pretreatment for Gram-Positive Bacteria, followed by the protocol for Purification of Total DNA from Animal Tissues. For RNA isolation 15 midguts per treatment were dissected in S2 medium, immediately transferred to a 2 ml screw cap tube containing 1 ml RNA Magic (Bio-Budget, #56-1000-100) and homogenized for 2 min at 3.25 m/sec using a bead mill homogenizer with 3 zirconium beads per tube. The homogenate was incubated for 5 min at RT and stored at -20 °C until further processing. Samples were thawed on ice for subsequent RNA isolation. 200 μl chloroform were added into each tube. Tubes were inverted (not vortexed) several times to provide homogenous mixing and incubated for 5 min at RT prior to 15 min centrifugation at 12.000 xg and 4 °C. The upper aqueous phase was transferred into a new tube (about 500 μl) and 500 μl 99% EtOH were added. The samples were centrifuged for 45 min at 17.000 xg and 4 °C after vigorously inverting the tubes for 30 sec. The supernatant was carefully removed and the RNA containing pellet was washed by adding 200 μl 99% EtOH and centrifuging for 5 min at 12.000 xg and 4 °C. The supernatant was completely removed and the pellet was air-dried for 3 min. The pellet was subsequently resuspended in 13 ml RNase-free ddH2O.
The bacterial variable regions 1 and 2 of 16S rRNA genes were amplified as described by Rausch et al. (2016). RNA-Seq libraries were created with the TruSeq Stranded mRNA Library Kit (Illumina, San Diego, USA).

treatment_protocol: We used a standard corn meal based medium for all stock flies and crossings. All assays were conducted on low-melt fly food containing 1.5% agar, 2% bacto yeast extract and 7% corn syrup (NM). The medium was boiled and supplemented with 0.1% propionic acid and 0.3% nipagin to prevent microbial growth. For dietary restriction (DR) the amount of bacto yeast was reduced to 0.1%. The recurrent diet consisted of an alternating regimen of four days DR followed by feeding on NM for three days.

tag: tissue

value: Midguts

tag: disease state

value: Cancer

tag: diet

value: NM

tag: feeding time

value: 3 days


title: SK-MEL-28 treated with salubrinal 80S fraction rep 1

tag: cell line


title: Treatment_Cu_1

status: Public on Jun 28 2021

city: Nan Jing

first: Qian

last: Gao

address: No 1, Weigang

institute: Nanjing Agricultural University

data_processing:
All RNA-seq reads passed filter were trimmed to remove low-quality bases and adaptor sequences. Reads then were aligned to the susScr11 reference genome using tophat2 (v2.0.13).
Reads aligned to genes are counted by cufflinks (v2.2.1). The FPKMs are normalized using cuffnorm. Differentially expressed genes are calculated using cuffdiff.
Genome_build: susScr11 (Sscrofa11.1)
Supplementary_files_format_and_content: raw_expression.csv: Comma-separated matrix table with FPKMs for every gene and every sample.

organism: Sus scrofa

source_name: porcine oocyte

extract_protocol:
The cell was lysed and the RNA was amplificated according to Smart-seq2 procedures.
The mRNA library was constructed using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, Ipswich, MA) according to the instruction manual, which includes sequential RNA fragmentation, reverse transcription using random primers, second strand cDNA synthesis, end repair, dA-tailing, adapter ligation, U excision, and PCR enrichment.

tag: Sex

value: Female

tag: cell type

value: Oocytes

tag: Stage

value: Metaphase II

value: Copper


title: Developing mouse embryo sections D08G02_S332

status: Public on Jul 01 2021

city: Seattle

first: Sanjay

middle: R

last: Srivatsan

state: WA

address: 3720 15TH Ave NE Genome Sciences S Foefe Bldg

department: Genome Sciences

institute: University of Washington

description:
Developing mouse embryo sections
sci-Space Slides 1-6
single Cell RNA sequencing library containing hash molecules denoting where a nucleus originated from and the transcriptome measured for each cell

data_processing:
Basecalls performed using bcl2fastq version 2.20
Poly-dT adapters were trimmed using Trimmomatic and aligned to mm10 using STAR. Mapped reads were then deduplicated and assigned to a gene (GENCODE vM15 - mouse). UMIs were enumerated for each cell/gene combination and finally a count matrix was made.
Count matrix was loaded into Monocle3 for further analysis
Genome_build: mm10
Supplementary_files_format_and_content: Count Matrix (matrix marker file- .mtx), Cell Metadata (tab separated values- .tsv), Gene Metadata (tab separated values- .tsv)

source_name: E14 saggital sections 8-10um thick

extract_protocol:
Nuclei were extracted with a permeabilization buffer, sonicated and fixed. cDNA molecules within nuclei are extracted after tagmentation through the use of denaturants.
3' end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis, tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it, a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.

tag: genotype

value: E14 Mouse Embryo

tag: sample type

value: Sagigital section


title: MC3T3-E1 Cell Line_treated_rep3

status: Public on Jul 14 2021

city: Los Angeles

first: Xiuju

last: Wu

address: 650 Charles Young Dr East, CHS A2-237

institute: University of California, Los Angeles

data_processing:
The reads were mapped to the mouse genome (GRCm38) with respect to GENCODE (vM13) annotation using STAR, version 2.5.3a.
Gene counts were generated along the mapping by only using uniquely mapped reads.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file with raw gene counts for every sample

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen).
Libraries were constructed according to manufacturer's instructions using KAPA DNA HyperPrep Kit (Kapa Biosystems).

treatment_protocol: MC3T3-E1 cells were treated with 10μM SB216763 for 14 days.


title: Apc_tumor_2

city: Nashville

first: Ken

last: Lau

state: TN

address: 2215 Garland Ave. MRBIV10475

department: Cell and Developmental Biology

institute: Vanderbilt University

data_processing:
After sequencing, reads were filtered, sorted by their barcode of origin and aligned to the reference transcriptome using inDrops pipeline (https://github.com/indrops/indrops). Mapped reads were quantified into UMI-filtered counts per gene, and barcodes that correspond to cells were retrieved based on previously established methods
Barcodes with number of unique UMIs greater than a threshold (Klein et al., 2015) were selected, resulting in the processed data table.
Technical read: read2 - UMI/cell barcode - the oligo barcodes are inDrop Version 2 which is positioned exactly as in (Klein et al. 2015)
Biological read: read1 - 3' end
Genome_build: Mouse: GRCm38.85
Supplementary_files_format_and_content: Delimited tables, with cells and genes, as columns and rows

source_name: tumor Lrig1;Apc

growth_protocol: in vivo mouse model

extract_protocol:
Mouse epithelial cell suspensions were obtained by standard dissociation (refer to manuscript). Viable cells were enriched with MACS. Cells were encapsulated using the inDrop platform (1CellBio), and RNA was extracted according to the protocol of Klein et al., 2015.
CEL-Seq linear amplification of RNA/cDNA followed by index primer-based amplification
RNA-Seq was performed on NextSeq500 with a 2 x 75 paired-end kit using custom read lengths

treatment_protocol: standard AOM/DSS regimen or injection with tamoxifen (refer to manuscript)

value: tumor Lrig1;Apc


title: SW1353_RRBS_rep1_G30_batch3

status: Public on Jun 24 2021

city: Shanghai

first: Jianing

address: Dongchuan Road

institute: Shanghai JiaoTong University

data_processing:
RRBS reads were trimmed using Trim Galore ,reads containing adapter were discarded. then used Bismark to align trimed reads to hg38 genome, next Bismark comes with a supplementarybismark_methylation_extractor script which operates on Bismark result files and extracts the methylation call for every single C analyzed
p value under a certain methylation level was calculated base on binomial distribution ,and selected the CpG sites with a p-value larger than 0.1 as highly-methylated sites
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include chromsome position and methylation level for each highly-methylated CpG site

source_name: Fibroblast Cells

growth_protocol: The cells were cultured with DMEM/F-12 medium (Biological Industries, Israel) containing 20% fetal bovine serum (Gibco BRL/Invitrogen, Carlsbad, CA, USA), 100μg/ml streptomycin, and 100IU/ml penicillin, and incubated with 37℃ and 5% CO2.

extract_protocol:
Genomic DNA from Jurkat and SW1353 was extracted by using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany) following the manufacturer’s protocol.
Two microgram of genomic DNA was used to construct the RRBS library by NEBNext Ultra II library kit and EZ DNA Methylation-Gold™ Kit  (Zymo Research) following the manufacturer’s protocol. The quality of libraries was assessed with Agilent 2100 Bioanalyzer (Agilent, United States).

treatment_protocol: Serum starvation for 24h before collecting the sample

tag: tissue type

value: Fibroblast Cells

value: Normal culture

tag: cell cycle

value: Interphase


title: SW1353_RRBS_rep1_G30_batch2


title: SW1353_RRBS_rep1_G30_batch1


title: SW1353_RRBS_rep1_G20_batch2


title: SW1353_RRBS_rep1_G20_batch1


title: Jurkat_RRBS_rep1_G30_batch1

source_name: lymphocyte cells

growth_protocol: The cells were cultured with RPMI1640 medium (Biological Industries, Israel) containing 20% fetal bovine serum (Gibco BRL/Invitrogen, Carlsbad, CA, USA), 100μg/ml streptomycin, and 100IU/ml penicillin, and incubated with 37℃ and 5% CO2.

value: Jurkat

value: lymphocyte cells


title: Jurkat_RRBS_rep1_G30_batch2


title: Jurkat_RRBS_rep1_G20_batch3


title: RNA0288_APC73_Plate_4_39

status: Public on Jun 10 2021

city: Singapore

first: Florent

last: Ginhoux

address: 8A Biomedical Grove, Immunos Building, Level 3

country: Singapore

institute: Singapore Immunology Network (SIgN), A*STAR

description: Human Skin RNA-seq

data_processing:
Raw reads were aligned to the human reference genome GRCh38 from GENCODE using RSEM program version 1.3.0 with default parameters. Gene expression values in transcripts per million (TPM) were calculated using the same RSEM program and the human GENCODE annotation version 25.
Genome_build: GRCh38.p7
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each Sample

source_name: Human Skin

extract_protocol:
We index-sorted cutaneous DC and monocyte-macrophages using flow cytometry based on expression of characteristic patterns of surface markers/proteins into 96 well plates containing Lysis buffer.
Single-cell cDNA libraries were prepared using the Smart-seq v2 protocol with the following modifications: (i) 1 mg/mL BSA Lysis buffer (Ambion Thermo Fisher Scientific, Waltham, MA, USA); and (ii) 200 pg cDNA with 1/5 reaction of Illumina Nextera XT kit. The length distribution of the cDNA libraries was monitored using a DNA High Sensitivity Reagent Kit on the Perkin Elmer Labchip. All samples were subjected to an indexed paired-end sequencing run of 2x151 cycles on an Illumina HiSeq 4000 system for about 1 million reads per sample.

value: Skin

tag: donor

tag: condition

value: AD


title: ARPE-19_RRBS_rep1_G30_batch2

status: Public on Jun 08 2021

data_processing:
RRBS reads were trimmed using Trim Galore, reads containing adapter were discarded. Then used Bismark to align trimmed reads to hg38 genome, next Bismark comes with a supplementarybismark_methylation_extractor script which operates on Bismark result files and extracts the methylation call for every single C analyzed.
p-value under a certain methylation level was calculated based on binomial distribution, and selected the CpG sites with a p-value smaller than 0.01 as highly-methylated sites.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: highly_methyalted_CpG.txt: Tab-delimited text file includes chromosome position and methylation level for each highly-methylated CpG site.

source_name: ARPE-19 cell line

extract_protocol:
Genomic DNA from ARPE-19 was extracted by using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany) following the manufacturer’s protocol.
Two microgram of genomic DNA was used to construct the RRBS library by NEBNext Ultra II library kit and EZ DNA Methylation-Gold™ Kit (Zymo Research) following the manufacturer’s protocol. The quality of libraries was assessed with Agilent 2100 Bioanalyzer (Agilent, United States).

treatment_protocol: Serum starvation for 24h before collecting the sample.

value: Epithelial Cells

tag: treatment


title: Jurkat_RRBS_rep1_G20_batch1


title: ARPE-19_RRBS_rep1 G20_batch1


title: SK-MEL-28 treated with salubrinal 40S fraction rep 1

value: Salubrinal


title: ARPE-19_RRBS_rep1 _G30_batch1


title: ARPE-19_RRBS_rep1_G20_batch2


title: PRISM_PDB_280Case

status: Public on Jun 03 2021

type: genomic

city: Doha

first: Omar

middle: M E

last: Albagha

address: Luqta Street, Education City

department: Health and Life Sciences

country: Qatar

institute: Hamad Bin Khalifa University

description: DNA CpG sites

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing:
The R package RnBeads version 1.10.8 was used for quality control. Samples with low methylated or unmethylated median intensity (<11.0) were excluded (n=35) along with samples with sex mismatch between reported and predicted sex (n=0). Probes with the following criteria were excluded: detection P value >0.05, cross reactive probes, containing a SNP within 3 bp of nucleotide extension site, or those located on sex chromosomes. Additionally, 723 sites were further excluded from the dataset for previously established association with smoking. A total of 56,356 probes were excluded from the initial 485,512 leaving 429,156 CpGs for analysis.
The Enmix method from RnBeads was used for background correction whilst
SWAN from RnBeads was used for between and within array normalization
The M-values, derived using the formulae log2((methylated signal+1)/(unmethylated signal+1)), were used

label: Cy3, Cy5

source_name: white blood cells

label_protocol: standard Illumina protocol

extract_protocol: Genomic DNA was extracted from peripheral blood using standard protocols. Bisulfite conversion was performed on 500µg of DNA using Zymo EZ-96 DNA methylation Kit (Zymo Research, USA). DNA methylation profiling was performed using the Illumina Infinium HumanMethylation 450K array (Illumina, USA) by following the manufacturer’s protocol

tag: mmed

tag: umed

tag: phenotype

value: Case

tag: array

tag: slide

value: white blood cells


title: PRISM_PDB_353Case

description: DNA CpG sites

tag: tissue


title: PRISM_PDB_409Case

description: DNA CpG sites


title: PRISM_PDB_289Case

description: DNA CpG sites


title: PRISM_PDB_295Case

description: DNA CpG sites


title: PRISM_PDB_1Case

description: DNA CpG sites


title: PRISM_PDB_290Case

description: DNA CpG sites


title: PRISM_PDB_344Case

description: DNA CpG sites


title: PRISM_PDB_225Case

description: DNA CpG sites


title: PRISM_PDB_22Case

description: DNA CpG sites


title: Jurkat_RRBS_rep1_G20_batch2

tag: cell line


title: PRISM_PDB_346Case

description: DNA CpG sites


title: PRISM_PDB_44Case

description: DNA CpG sites


title: PRISM_PDB_149Case

description: DNA CpG sites


title: KA sample 3

city: Cologne

first: Jennifer

last: Maßen

address: Joseph-Stelzmann-Straße 9B

institute: MPI Biology of Ageing

data_processing:
sequencing reads were mapped to yeast genome (R64)
Gene counts were obtained from featureCounts of the Rsubread package (R/Bioconductor).
Gene set enrichment analysis was performed using R package fgsea
Genome_build: sacCer3
Supplementary_files_format_and_content: sample (columns) and genes (rows) -wise read count table

organism: Saccharomyces cerevisiae

source_name: liquid culture

growth_protocol: Yeast was grown in YPD to mid-log phase

extract_protocol:
RNA was isolated using the hot phenol protocol
RNA-seq libraries were prepared for sequencing using standard Illumina protocols

tag: growth phase

value: mid-log phase


title: PRISM_PDB_356Case

description: DNA CpG sites


title: PRISM_PDB_92Case

description: DNA CpG sites


title: PRISM_PDB_101Case

description: DNA CpG sites


title: PRISM_PDB_326Case

description: DNA CpG sites


title: PRISM_PDB_448Case

description: DNA CpG sites


title: PRISM_PDB_221Case

description: DNA CpG sites


title: PRISM_PDB_246Case

description: DNA CpG sites


title: PRISM_PDB_457Case

description: DNA CpG sites


title: PRISM_PDB_320Case

description: DNA CpG sites


title: PRISM_PDB_436Case

description: DNA CpG sites


title: PRISM_PDB_184Case

description: DNA CpG sites


title: PRISM_PDB_58Case

description: DNA CpG sites


title: PRISM_PDB_446Case

description: DNA CpG sites


title: PRISM_PDB_224Case

description: DNA CpG sites


title: PRISM_PDB_52Case

description: DNA CpG sites


title: PRISM_PDB_173Case

description: DNA CpG sites


title: PRISM_PDB_18Case

description: DNA CpG sites


title: PRISM_PDB_465Case

description: DNA CpG sites


title: PRISM_PDB_412Case

description: DNA CpG sites


title: PRISM_PDB_310Case

description: DNA CpG sites


title: PRISM_PDB_293Case

description: DNA CpG sites


title: PRISM_PDB_450Case

description: DNA CpG sites


title: PRISM_PDB_347Case

description: DNA CpG sites


title: PRISM_PDB_145Case

description: DNA CpG sites


title: PRISM_PDB_152Case

description: DNA CpG sites


title: PRISM_PDB_445Case

description: DNA CpG sites


title: Nil (PEP-3 – CD45.1) [M_P_18_S48]

status: Public on Aug 17 2021

city: Manchester

first: Amir

middle: Saam

last: Youshani

address: Oxford Road

department: Faculty of Biology, Medicine and Health

country: United Kingdom

institute: University of Manchester

description:
M_P_18_S48
experiment#2
RNA - cDNA
processed data file: normalised_gene_counts.csv

data_processing:
Unmapped paired-end sequences from an Illumina HiSeq4000 sequencer were tested by FastQC.
Sequenced reads were mapped to mm9/NCBI37 whole genome and quantified using STAR v2.5.0a with parameters --alignSJDBoverhangMin 999 --outFilterMultimapNmax 10 --quantMode TranscriptomeSAM
Mapped reads were quantified using RSEM v1.3.0 with parameters --paired-end
Gene abundance estimates from RSEM output were corrected for library size as well as batch and nine surrogate variables inferred using R package sva v3.22.0 in a linear model. Low counts (less than 10 counts per million) were removed.
Genome_build: mm9/NCBI37
Supplementary_files_format_and_content: normalised_gene_counts.csv: File with comma-separated values for each experiment include normalised counts for all samples.

source_name: Microglia

growth_protocol: GL-261 cells were cultured in RPMI media with 10% FCS and 5mM L-glutamine. Cells were grown to confluency. After 3-days culturing, cells were trypsinised and suspended in fresh GL-261 media at an aliquot of 50,000 cells for intracranial implantation.

extract_protocol:
Single cell suspensions were obtained from four populations following mouse brain dissociation, antibody staining and flow-cell sorting. RNA and cDNA conversion was completed using the Clontech SMART-Seq v4 Ultra Low Input RNA kit for Sequencing, according to manufacturer's guidelines.
Library was constructed by the Genomic Core Facility at the University of Manchester.

treatment_protocol: No treatment given.

tag: recipient strain

tag: source tissue

value: brain

tag: cell type

value: Normal Microglia


title: PRISM_PDB_237Case

description: DNA CpG sites


title: PRISM_PDB_183Case

description: DNA CpG sites


title: PRISM_PDB_474Case

description: DNA CpG sites


title: PRISM_PDB_337Case

description: DNA CpG sites


title: PRISM_PDB_200Case

description: DNA CpG sites


title: PRISM_PDB_297Case

description: DNA CpG sites


title: PRISM_PDB_105Case

description: DNA CpG sites


title: PRISM_PDB_381Case

description: DNA CpG sites


title: PRISM_PDB_79Case

description: DNA CpG sites


title: PRISM_PDB_206Case

description: DNA CpG sites


title: PRISM_PDB_296Case

description: DNA CpG sites


title: PRISM_PDB_190Case

description: DNA CpG sites


title: PRISM_PDB_13Case

description: DNA CpG sites


title: PRISM_PDB_333Case

description: DNA CpG sites


title: PRISM_PDB_220Case

description: DNA CpG sites


title: PRISM_PDB_171Case

description: DNA CpG sites


title: PRISM_PDB_157Case

description: DNA CpG sites


title: PRISM_PDB_242Case

description: DNA CpG sites


title: PRISM_PDB_186Case

description: DNA CpG sites


title: PRISM_PDB_7Case

description: DNA CpG sites


title: PRISM_PDB_236Case

description: DNA CpG sites


title: PRISM_PDB_170Case

description: DNA CpG sites


title: Ovarian_2

status: Public on Nov 12 2021

city: San Francisco

first: Hugo

last: Gonzalez

address: 513 Parnassus Avenue

department: Anatomy

institute: University of California San Francisco

data_processing:
After sequencing attemping 50,000 counts per cell captured by the 10X chip, Cell Ranger count pipeline (Version 3.0.2 from 10X Genomics) was used to map the FASTQ files to the human genome GRCh38, which generates a gene vs cell expression matrix (See Matrix.mtx.gz and Metrics_Summary.csv files).
The LogNormalized_Data was generated for each sample using the Seurat NormalizeData function. Briefly, counts for each cell are divided by the total counts for that cell and multiplied by the scale.factor 10000. This is then natural-log transformed using log1p
Genome_build: GRCh38
Supplementary_files_format_and_content: raw counts matrix
Supplementary_files_format_and_content: Features for downstream processing
Supplementary_files_format_and_content: Single Cell barcodes for downstream processing
Supplementary_files_format_and_content: Cell Ranger Quality Metrics per each sample
Supplementary_files_format_and_content: Normalized Expression per each sample
Supplementary_files_format_and_content: Annotations of the Cell types described in the study.

source_name: Human Brain Metastasis

extract_protocol: Single-cell libraries were generated via the Chromium Controller and the Single Cell Reagent Kit 3’ v2 (10x Genomics, Pleasanton, CA) according to the manufacturer’s instructions

tag: type of tumor

value: Metastatic Tumor, Brain Tumor

value: Ovarian Cancer Brain Metastasis


title: PRISM_PDB_230Case

description: DNA CpG sites


title: PRISM_PDB_308Case

description: DNA CpG sites


title: PRISM_PDB_437Case

description: DNA CpG sites


title: PRISM_PDB_429Case

description: DNA CpG sites


title: PRISM_PDB_438Case

description: DNA CpG sites


title: PRISM_PDB_304Case

description: DNA CpG sites


title: PRISM_PDB_229Case

description: DNA CpG sites


title: PRISM_PDB_257Case

description: DNA CpG sites


title: PRISM_PDB_253Case

description: DNA CpG sites


title: PRISM_PDB_27Case

description: DNA CpG sites


title: PRISM_PDB_201Case

description: DNA CpG sites


title: PRISM_PDB_132Case

description: DNA CpG sites


title: PRISM_PDB_430Case

description: DNA CpG sites


title: PRISM_PDB_342Case

description: DNA CpG sites


title: PRISM_PDB_73Case

description: DNA CpG sites


title: PRISM_PDB_78Case

description: DNA CpG sites


title: PRISM_PDB_452Case

description: DNA CpG sites


title: PRISM_PDB_380Case

description: DNA CpG sites


title: PRISM_PDB_311Case

description: DNA CpG sites


title: PRISM_PDB_216Case

description: DNA CpG sites


title: PRISM_PDB_386Case

description: DNA CpG sites


title: PRISM_PDB_158Case

description: DNA CpG sites


title: PRISM_PDB_69Case

description: DNA CpG sites


title: PRISM_PDB_214Case

description: DNA CpG sites


title: PRISM_PDB_12Case

description: DNA CpG sites


title: PRISM_PDB_138Case

description: DNA CpG sites


title: PRISM_PDB_160Case

description: DNA CpG sites


title: PRISM_PDB_5Case

description: DNA CpG sites


title: PRISM_PDB_6Case

description: DNA CpG sites


title: PRISM_PDB_261Case

description: DNA CpG sites


title: PRISM_PDB_88Case

description: DNA CpG sites


title: PRISM_PDB_102Case

description: DNA CpG sites


title: PRISM_PDB_193Case

description: DNA CpG sites


title: PRISM_PDB_301Case

description: DNA CpG sites


title: PRISM_PDB_199Case

description: DNA CpG sites


title: PRISM_PDB_309Case

description: DNA CpG sites


title: PRISM_PDB_32Case

description: DNA CpG sites


title: PRISM_PDB_317Case

description: DNA CpG sites


title: PRISM_PDB_168Case

description: DNA CpG sites


title: PRISM_PDB_393Case

description: DNA CpG sites


title: PRISM_PDB_249Case

description: DNA CpG sites


title: PRISM_PDB_243Case

description: DNA CpG sites


title: PRISM_PDB_266Case

description: DNA CpG sites


title: PRISM_PDB_194Case

description: DNA CpG sites


title: PRISM_PDB_440Case

description: DNA CpG sites


title: PRISM_PDB_391Case

description: DNA CpG sites


title: PRISM_PDB_136Case

description: DNA CpG sites


title: PRISM_PDB_467Case

description: DNA CpG sites


title: PRISM_PDB_271Case

description: DNA CpG sites


title: PRISM_PDB_451Case

description: DNA CpG sites


title: PRISM_PDB_187Case

description: DNA CpG sites


title: PRISM_PDB_475Case

description: DNA CpG sites


title: PRISM_PDB_425Case

description: DNA CpG sites


title: PRISM_PDB_81Case

description: DNA CpG sites


title: PRISM_PDB_74Case

description: DNA CpG sites


title: PRISM_PDB_50Case

description: DNA CpG sites


title: PRISM_PDB_417Case

description: DNA CpG sites


title: PRISM_PDB_55Case

description: DNA CpG sites


title: PRISM_PDB_247Case

description: DNA CpG sites


title: PRISM_PDB_453Case

description: DNA CpG sites


title: PRISM_PDB_368Case

description: DNA CpG sites


title: PRISM_PDB_202Case

description: DNA CpG sites


title: PRISM_PDB_376Case

description: DNA CpG sites


title: PRISM_PDB_421Case

description: DNA CpG sites


title: PRISM_PDB_63Case

description: DNA CpG sites


title: PRISM_PDB_83Case

description: DNA CpG sites


title: PRISM_PDB_46Case

description: DNA CpG sites


title: PRISM_PDB_125Case

description: DNA CpG sites


title: PRISM_PDB_287Case

description: DNA CpG sites


title: PRISM_PDB_240Case

description: DNA CpG sites


title: PRISM_PDB_360Case

description: DNA CpG sites


title: PRISM_PDB_172Case

description: DNA CpG sites


title: PRISM_PDB_109Case

description: DNA CpG sites


title: PRISM_PDB_351Case

description: DNA CpG sites


title: PRISM_PDB_260Case

description: DNA CpG sites


title: PRISM_PDB_378Case

description: DNA CpG sites


title: PRISM_PDB_488Case

description: DNA CpG sites


title: PRISM_PDB_65Case

description: DNA CpG sites


title: PRISM_PDB_203Case

description: DNA CpG sites


title: PRISM_PDB_226Case

description: DNA CpG sites


title: PRISM_PDB_39Case

description: DNA CpG sites


title: PRISM_PDB_31Case

description: DNA CpG sites


title: PRISM_PDB_402Case

description: DNA CpG sites


title: PRISM_PDB_318Case

description: DNA CpG sites


title: PRISM_PDB_279Case

description: DNA CpG sites


title: PRISM_PDB_70Case

description: DNA CpG sites


title: PRISM_PDB_416Case

description: DNA CpG sites


title: PRISM_PDB_431Case

description: DNA CpG sites


title: PRISM_PDB_227Case

description: DNA CpG sites


title: PRISM_PDB_292Case

description: DNA CpG sites


title: PRISM_PDB_324Case

description: DNA CpG sites


title: PRISM_PDB_265Case

description: DNA CpG sites


title: PRISM_PDB_274Case

description: DNA CpG sites


title: PRISM_PDB_2Case

description: DNA CpG sites


title: PRISM_PDB_11Case

description: DNA CpG sites


title: PRISM_PDB_56Case

description: DNA CpG sites


title: PRISM_PDB_361Case

description: DNA CpG sites


title: PRISM_PDB_96Case

description: DNA CpG sites


title: PRISM_PDB_245Case

description: DNA CpG sites


title: PRISM_PDB_140Case

description: DNA CpG sites


title: PRISM_PDB_371Case

description: DNA CpG sites


title: PRISM_PDB_117Case

description: DNA CpG sites


title: PRISM_PDB_131Case

description: DNA CpG sites


title: PRISM_PDB_286Case

description: DNA CpG sites


title: PRISM_PDB_130Case

description: DNA CpG sites


title: PRISM_PDB_422Case

description: DNA CpG sites


title: PRISM_PDB_47Case

description: DNA CpG sites


title: PRISM_PDB_489Case

description: DNA CpG sites


title: PRISM_PDB_62Case

description: DNA CpG sites


title: PRISM_PDB_90Case

description: DNA CpG sites


title: PRISM_PDB_34Case

description: DNA CpG sites


title: PRISM_PDB_210Case

description: DNA CpG sites


title: PRISM_PDB_30Case

description: DNA CpG sites


title: PRISM_PDB_379Case

description: DNA CpG sites


title: PRISM_PDB_267Case

description: DNA CpG sites


title: PRISM_PDB_72Case

description: DNA CpG sites


title: PRISM_PDB_189Case

description: DNA CpG sites


title: PRISM_PDB_169Case

description: DNA CpG sites


title: PRISM_PDB_188Case

description: DNA CpG sites


title: PRISM_PDB_282Case

description: DNA CpG sites


title: PRISM_PDB_114Case

description: DNA CpG sites


title: PRISM_PDB_175Case

description: DNA CpG sites


title: PRISM_PDB_367Case

description: DNA CpG sites


title: PRISM_PDB_252Case

description: DNA CpG sites


title: PRISM_PDB_471Case

description: DNA CpG sites


title: PRISM_PDB_111Case

description: DNA CpG sites


title: PRISM_PDB_51Case

description: DNA CpG sites


title: PRISM_PDB_38Case

description: DNA CpG sites


title: PRISM_PDB_364Case

description: DNA CpG sites


title: PRISM_PDB_180Case

description: DNA CpG sites


title: PRISM_PDB_148Case

description: DNA CpG sites


title: PRISM_PDB_479Case

description: DNA CpG sites


title: PRISM_PDB_119Case

description: DNA CpG sites


title: PRISM_PDB_258Case

description: DNA CpG sites


title: PRISM_PDB_162Case

description: DNA CpG sites


title: PRISM_PDB_288Case

description: DNA CpG sites


title: PRISM_PDB_294Case

description: DNA CpG sites


title: PRISM_PDB_241Case

description: DNA CpG sites


title: PRISM_PDB_339Case

description: DNA CpG sites


title: PRISM_PDB_401Case

description: DNA CpG sites


title: PRISM_PDB_396Case

description: DNA CpG sites


title: PRISM_PDB_477Case

description: DNA CpG sites


title: PRISM_PDB_24Case

description: DNA CpG sites


title: PRISM_PDB_382Case

description: DNA CpG sites


title: PRISM_PDB_331Case

description: DNA CpG sites


title: PRISM_PDB_61Case

description: DNA CpG sites


title: PRISM_PDB_338Case

description: DNA CpG sites


title: PRISM_PDB_385Case

description: DNA CpG sites


title: PRISM_PDB_57Case

description: DNA CpG sites


title: PRISM_PDB_390Case

description: DNA CpG sites


title: PRISM_PDB_3Case

description: DNA CpG sites


title: PRISM_PDB_234Case

description: DNA CpG sites


title: PRISM_PDB_127Case

description: DNA CpG sites


title: PRISM_PDB_383Case

description: DNA CpG sites


title: PRISM_PDB_370Case

description: DNA CpG sites


title: PRISM_PDB_135Case

description: DNA CpG sites


title: PRISM_PDB_454Case

description: DNA CpG sites


title: PRISM_PDB_48Case

description: DNA CpG sites


title: PRISM_PDB_196Case

description: DNA CpG sites


title: PRISM_PDB_411Case

description: DNA CpG sites


title: PRISM_PDB_359Case

description: DNA CpG sites


title: PRISM_PDB_112Case

description: DNA CpG sites


title: PRISM_PDB_272Case

description: DNA CpG sites


title: PRISM_PDB_21Case

description: DNA CpG sites


title: GFP-2

status: Public on May 31 2021

city: Birmingham

first: Rita

middle: M

last: Cowell

state: AL

address: 2000 9th Avenue South

department: Neuroscience

institute: Southern Research

data_processing:
Basecalling was performed using DRAGEN Host Software Version 01.011.222.02.04.04.36875
Raw reads were aligned using STAR version 2.6.0c using parameters --outReadsUnmapped Fastx; --outSAMtype BAM SortedByCoordinate; --outSAMattributes All
Transcript abundaces were calculated using HTSeq-Count version 0.10.0 using paramters -r pos; -t exon; -I gene_id; -a 10; -s no; -f bam
Normalization and differential expression was performed using DESeq2 version 1.20.0 using default parameters
Genome_build: Gencode GRCh38 p7 Release 25
Supplementary_files_format_and_content: tab-delimited Excel file containing raw counts for each Ensembl ID for each sample

source_name: SH-SY5Y_GFP Ad Transfection

growth_protocol: DMEM Media FBS 10% P/S 1% grown in 10 cm plates until 80% confluent before treatment

extract_protocol:
Total RNA isolated with Trizol/Chloroform/Isopropanol/Ethanol then quantified with nanodrop
Poly A Method
Addition of directional library preparation module to retain strand information in RNA library preparation

treatment_protocol: Cells were transfected with 2 ul of either GFP or PGC-1a Adenovirus for 48 hours and then RNA was isolated

value: GFP Ad Transfection

value: neuronal progenitor


title: NJA02201.I12

status: Public on May 30 2021

city: Stockholm

first: Martin

last: Enge

address: CCK, Z4

department: Dep of Oncology-Pathology

country: Sweden

institute: Karolinska Institute

data_processing:
Sequencing reads were trimmed, adapter sequences removed
Reads aligned to the mm10 reference assembly using STAR with default parameters
Duplicate reads were removed using picard
Transcript counts were obtained using HTSeq35 and mm10 UCSC exon/transcript annotations
Single cell profiles with the following features were deemed to be of poor quality and removed: 1) cells with less than a specified total number of valid counts in exonic regions (1.8x104 and 4x104 for the mouse gut and sorted multiplets dataset, respectively), 2) cells with low actin TPM, and 3) cells with high fractions of ERCC reads. To determine a cut-off for actin TPM, we used the normal distribution with empirical mean and standard deviation from log2 transformed actin TPM, which is normally distributed in successful experiments. The cut-off was set to the 0.01 quantile (eg. the lower 0.01 % of the bell curve). A similar strategy was used for fractions of ERCC reads, samples with a log2 transformed fraction of ERCC reads above the 0.99 % quantile were rejected.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: htseq-format of raw counts

source_name: spleen

growth_protocol: Small intestine and colon were removed from C57BL/J wild-type mice and kept on ice in phosphate buffered saline (PBS). Lumina of colon and small intestine were washed three times with PBS and adipose tissue connected to the exterior of the small intestine or colon was removed. Colon and small intestine were opened longitudinally, and any remaining mucous on covering the epithelial layer was gently rubbed off. Tissues were washed once in PBS before being cut into 0.5 - 1 mm long fragments. Colon fragments were immersed in 10mM EDTA-PBS and incubated for 105 minutes on ice, with shaking every 15 minutes. Small intestinal fragments were similarly immersed in 10mM EDTA-PBS on ice and shaken. After 15 minutes, small intestinal fragments were allowed to settle at the bottom and the supernatant was discarded and replaced with new 10mM EDTA-PBS and shaken vigorously. This procedure was repeated 1-2 times, with supernatant fractions investigated through light microscopy before discarding, in order to enrich for crypts. Small intestinal fragments were then incubated on ice for 45-60 minutes for a total of 105 minutes. Following EDTA-PBS treatment fractions were triturated 10-15 times. Colon fractions were strained through a 100 um filter while small intestinal fractions were strained through a 70 um filter. Fractions were centrifuged at 300g for 5 minutes and dissociated using TrypLE Express (Invitrogen) at 37°C for 15-20 minutes. Enzymatic dissociation was supervised using light microscopy during regular intervals to obtain an appropriate amount of single cells and multiplets. Dead cells were removed using Dead Cell Removal Kit (Miltenyi Biotec) according to the manufacturer's protocol before staining for FACS sorting was performed.

extract_protocol:
For mouse intestine, cells were stained with FITC anti-CD326 and 7AAD (Sony Biotechnology) in order to monitor number of epithelial cells and select live cells. Additionally, paneth cells were enriched using Brilliant Violent anti-CD24. For spleen, cells were sorted with only 7AAD to remove dead cells, not other antibodies. Single cells were distinguished from multiplets using FSC-H and FSC-W gating and the gating scheme was visually confirmed via phase contrast microscopy (Fig. 1a). Cells were sorted into 384- or 96-well plates containing hypotonic lysis buffer using a SH800S FACS sorter (Sony). Plates were sealed immediately after sorting with microseal F foil (Biorad) and centrifuged at 4000g at 4°C for 5 min before being frozen on dry ice and stored at -80°C.
Single-cell and multiplet RNA-Seq libraries were generated as described. Briefly, single-cells collected in 384-well plates were lysed, followed by reverse transcription with template-switch using an LNA-modified template switch oligo to generate cDNA. After 21 cycles of pre-amplification, DNA was purified and analysed on an automated Fragment Analyzer (Advanced Analytical). Each cell’s cDNA fragment profile was individually inspected and only wells with successful amplification products (concentration higher than 0.06 ng/ul) and with no detectable RNA degradation were selected for final library preparation. Tagmentation assays and barcoded sequencing libraries were prepared using Nextera XT kit (Illumina) according to the manufacturer's instructions. Barcoded libraries were pooled and subjected to 75 bp paired-end sequencing on the Illumina NextSeq 500 instrument.

tag: strain

value: spleen

tag: facs cellnumber

value: Singlet

tag: age (days)


title: PGC-2

source_name: SH-SY5Y_PGC-1a Ad Transfection

value: PGC-1a Ad Transfection


title: PGC-1


title: GFP-1


title: PGC-3


title: PRISM_PDB_424Case

description: DNA CpG sites


title: Vero E6 population 2 screen 1 (CoV-2 Resistant cell)

status: Public on May 28 2021

city: Cambridge

first: John

middle: G

last: Doench

address: 75 Ames St.

department: Genetic Perturbation Platform

institute: Broad Institute

data_processing:
Raw read counts were retrieved (from corresponding authors for publicly available data; from sequencing data using PoolQ version 3.2.9-3.2.11 for new data generated for Rebendenne et al, 2021)
Read counts were log-normalized, then averaged across conditions if applicable
Log-fold changes were calculated relative to pDNA
Fit a natural cubic spline between the control and infected conditions and calculated residuals from this spline (anchors package)
Z-scored residuals at the guide-level (anchors package)
Averaged across guides and conditions to get gene-level average z-score (anchors package)
Applied filter based on number of guides per gene then ranked genes where a rank of 1 was assigned to the top resistance hit
Genome_build: Vero-E6 samples: NCBI Chlorocebus_sabeus_1.1 primary assembly; all other samples: NCBI GRCh38 primary assembly
Supplementary_files_format_and_content: Spreadsheets with data from each individual screen structured such as that sheet 1: gene symbols with gene-level average z-scores and ranks for each screen, sheet 2: raw read counts, sheet 3: guide-gene annotation mapping
Supplementary_files_format_and_content: One summarized spreadsheet (Supplementary_Data_2_all_primary_KO.xlsx) with gene-level avrage z-scores and ranks for all screens being compared in meta-analysis

organism: Chlorocebus sabaeus

source_name: VeroE6 cell line

growth_protocol: Dulbecco's modified Eagle medium (DMEM) supplemented with 10% foetal bovine serum and penicillin/streptomycin, 37°C, 5%CO2

extract_protocol:
NucleoSpin Blood XL kit as per the manufacturer's instructions
For PCR amplification, gDNA was divided into 100 μL reactions such that each well had at most 10 μg of gDNA. Plasmid DNA (pDNA) was also included at a maximum of 100 pg per well. Per 96 well plate, a master mix consisted of 150 μL DNA Polymerase (Titanium Taq; Takara), 1 mL of 10x buffer, 800 μL of dNTPs (Takara), 50 μL of P5 stagger primer mix (stock at 100 μM concentration), 500 μL of DMSO, and water to bring the final volume to 4 mL. Each well consisted of 50 μL gDNA plus water, 40 μL PCR master mix, and 10 μL of a uniquely barcoded P7 primer (stock at 5 μM concentration). PCR cycling conditions were as follows: an initial 1 min at 95 °C; followed by 30 s at 94 °C, 30 s at 52.5 °C, 30 s at 72 °C, for 28 cycles; and a final 10 min extension at 72 °C. PCR primers were synthesized at Integrated DNA Technologies (IDT). PCR products were purified with Agencourt AMPure XP SPRI beads according to manufacturer’s instructions (Beckman Coulter, A63880). Prior to sequencing the sample was quantitated by qPCR and diluted to 2nM. 5 µL of the  sample was then further diluted and denatured with 5 µL 0.1N NaOH and 490 µL HT1 buffer (Illumina). Samples were sequenced on a HiSeq2500 HighOutput (Illumina) with a 5% spike-in of PhiX.

treatment_protocol: Infection with SARS-CoV-2 (BetaCoV/France/IDF0372/2020 isolate), MOI 0.005

value: VeroE6 cell line

tag: oerturbation type

value: CRISPR knock-out

tag: crispr library

value: Simian library

tag: infected with sars-cov-2?

value: YES


title: Vero E6 CRISPR population 2: CRISPR transduction efficiency 50%

value: NO


title: Vero E6 population 1 screen 2 (CoV-2 Resistant, infection 2, started independently of 1A and 1B with lower cell density


title: Vero E6 population 1 screen 1B (CoV-2 Resistant cells, round 2 - performed on 1A surviving cells)


title: PRISM_PDB_357Case

description: DNA CpG sites

tag: mmed

tag: umed

value: Case


title: Vero E6 population 1 screen 1A (CoV-2 Resistant cells, infection 1, round 1


title: Vero E6 CRISPR population 1: CRISPR transduction efficiency 7%


title: Calu-3 Calabrese B resistant population screen #2

source_name: Calu-3 cell line

value: Calu-3 cell line

value: CRISPR activation

value: Calabrese B library


title: PRISM_PDB_178Case

description: DNA CpG sites

tag: phenotype

tag: array

value: white blood cells


title: PRISM_PDB_17Case

description: DNA CpG sites

tag: slide

tag: tissue


title: PRISM_PDB_414Case

description: DNA CpG sites


title: Calu-3 Calabrese A initial population screen #2

tag: cell line

value: Calabrese A library


title: Calu3 Gattinara screen 4.2 resistant population

value: Gattinara library


title: Calu-3 Calabrese A resistant population


title: Calu3 Gattinara screen 4 initial population


title: Calu3 Gattinara screen 1 resistant population


title: Calu-3 Calabrese B initial population screen #2


title: PRISM_PDB_349Case

description: DNA CpG sites


title: Calu-3 Calabrese A resistant population screen #2


title: GP9A

status: Public on May 25 2021

city: Toronto

first: Jason

last: Moffat

state: ON

address: 686 Bay Street, Room 13.9705

department: Molecular Genetics

country: Canada

institute: University of Toronto

description: Patient-derived cell line

data_processing:
FASTQ files were aligned to Gencode v25 gene annotations and hg38 genome build using the STAR short-read aligner (v2.6.1a)
Gene expression estimates (FPKM) were computed using cufflinks (v.2.2.1) using the Gencode v25 gene annotations and default parameters.
Gene expression files (genes.fpkm_tracking) generated by cufflinks were merged with gene annotations in R
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text; FPKM values from cufflinks

source_name: Pancreatic ductal adenocarcinoma cell line

growth_protocol: Cells were cultured in appropriate media supplemented with FBS and 1% Penicillin/Streptomycin for 48 hours.  Specific FBS concentrations and other media components noted under "growth media".

extract_protocol:
Trizol protocol
1000 ng RNA per sample was processed using the NuGEN Encore Complete strand-specific RNA Library Prep Kits.  Sequencing was performed on an Illumina HiSeq 2000 sequencer.

treatment_protocol: No treatment was performed

tag: library prep kit

value: EncoreMR

tag: growth media


title: GFP-3

tag: treatment

value: GFP Ad Transfection

tag: cell type

value: neuronal progenitor


title: Calu-3 Calabrese A initial population


title: B_418_Seronegative

status: Public on May 01 2021

city: Bethesda

first: Hye Kyung

last: Lee

state: MD

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

data_processing:
RNA-seq data were trimmed using trimmomatic (Bolger et al., Bioinformatics, 2014) and subsequently aligned to the reference genome hg19 applying STAR RNA-seq aligner (Dobin et al., Bioinformatics, 2013). HTSeq(Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
HTSeq(Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
Genome_build: hg19
Supplementary_files_format_and_content: HTSeq counts from RNA-seq samples

source_name: PBMCs

growth_protocol: Blood samples were collected from the healthy subjects, Seronegative subjects and COVID-19 patients.

extract_protocol:
The buffy coat was extracted by centrifuge after blood sample collection and RBC was removed using RBC lysis buffer in the buffy coat. Total RNA was isolated with TRIzol reagent.
Libraries for sequencing were prepared with TruSeq Stranded mRNA Kit following standard Illumina protocols.

tag: age

tag: gender

value: Male

tag: diseas state

value: highly exposed, Seronegative

tag: severity

value: Seronegative, highly exposed

tag: location

value: PBMC


title: B_352_Seronegative

value: Female


title: Calu3 Gattinara screen 3 resistant population

tag: oerturbation type

value: CRISPR knock-out

tag: crispr library

tag: infected with sars-cov-2?

value: YES


title: Calu3 Gattinara screen 2 resistant population


title: Calu3 Gattinara screen 3 initial population

value: NO


title: Calu3 Gattinara screen 1/2 initial population

value: Calu-3 cell line


title: Lenti_OSM_2_Day7_E09

status: Public on Apr 23 2021

city: Rehovot

first: Rony

last: Chanoch

state: Israel

address: Weizmann Institute of Science, 234 Herzl Street

institute: Weizmann Instititue

data_processing:
Paired-end reads from mouse model were mapped to the UCSC mm10 mouse transcriptome using Bowtie. Expression values were calculated by RSEM in paired-end mode using parameters, from which TPM values for each gene were extracted. Reads from 10x were aligned using CellRanger
We examined as quality control the number of genes detected in each cell. We observed a bimodal distribution and conservatively excluded sequenced cells with fewer than 3,000 detected genes.
For the remaining cells, we calculated Eavg(i) = log2(mean(TPMi,1...n)+1) for each gene, and excluded genes with Eavg < 4
Genome_build: mm10, hg19
Supplementary_files_format_and_content: Comma-separated value containing TPM values (transcript-per-million reads).

source_name: Glioblastoma single cell

extract_protocol:
For mice samples, collected brains were mechanically and enzymatically dissociated using a papain-based brain tumor dissociation kit (Miltenyi Biotec) supplemented with 0.1% typeI collagenase (Thermo Fisher Scientific) / PBS. The dissociated cells were first stained with calcein Blue AM (Thermo Fisher Scientific) and Zombie NIR (BioLegend) for 25 min at 4 ℃, and with anti-mouse CD16/32 (BD Biosciences) for 5min. After washing cells with ice-cold 1% BSA / PBS, the cells were then stained with a combination of following antibodies; PerCP anti-mouse CD45 (clone 30-F11, BD Biosciences), phycoerythrin (PE) anti-mPdgfra (clone APA5, BioLegend), Allophycocyanin (APC) anti-mPodoplanin (clone 8.1.1, BioLegend), and APC anti-CD11b (clone M1/70, BioLegend), for 30 min at 4 ℃. Sorting was performed with Becton Dickinson Influx cytometer (Becton Dickinson). Side scatter (SSC) width versus forward scatter (FSC) area, and Trigger Pulse Width versus FSC criteria were used to discriminate doublets and gate only singleton cells. Viable single cells were identified as calcein blue AM positive and Zombine NIR negative. We sorted viable CD45 negative/ GFP positive or CD45 positive/ CD11b positive single-cells into 96-well plates containing 5uL of TCL buffer (QIAGEN) with 1% beta-mercaptoethanol. Plates were frozen immediately after sorting and stored at -80 ℃ prior to whole transcriptome amplification, library preparation and sequencing.
Libraries from isolated single cells from mouse model were generated based on the Smart-seq2 protocol (Picelli 2014) with the following modifications. RNA from single cells was first purified with Agencourt RNAClean XP beads (Beckman Coulter) before oligo-dT primed reverse transcription with Maxima reverse transcriptase and locked TSO oligonucleotide, which was followed by 20 cycle PCR amplification using KAPA HiFi HotStart ReadyMix (KAPA Biosystems) with subsequent Agencourt AMPure XP bead purification as described. Libraries were tagmented using the Nextera XT Library Prep kit (Illumina) with custom barcode adapters (sequences available upon request). Libraries from 768 cells with unique barcodes were combined and sequenced with paired-end, 38-base reads, using a NextSeq 500 sequencer (Illumina). Comma-seperated file containing TPM values (transcript-per-million reads) for 6608 genes across 679 cells. For the cell lines, scRNA-seq libraries were generated using the 10X Genomics Chromium Single Cell 3’ Kit v2 and the 10x Chromium Controller (10x Genomics) according to the 10X Single Cell 3’ v2 protocol. The cell lines were processed as a pool that consisted of 6 total cell lines, 4 of which were used in this study (MGG23, MGG75, MGH143, MGG18). Two of the used cell lines, MGG23 and MGH143 were profiled again in a different pool. Briefly, we generated a single cell suspension of the pool in 0.04% PBS-BSA (95% viability) and loaded approximately 10,500 single cells to the Chromium Controller with a targeted recovery of 6,000 cells. Single cells, reagents and single gel beads containing barcoded oligonucleotides were encapsulated into nanoliter-sized droplets and subjected to reverse transcription. Droplets were broken and the barcoded cDNAs were purified with DynaBeads and amplified by 12 cycles of PCR (98°C for 45 s; [98°C for 20 s, 67°C for 30 s, 72°C for 1 min] x 12; 72°C for 1 min). The amplified cDNA was fragmented, end-repaired, ligated with index adaptors, and size-selected with clean-ups between each step using the SPRIselect Reagent Kit (Beckman Coulter). Quality control of the resulting barcoded libraries was performed with the Agilent TapeStation and by PCR with primers specific to the P5 and P7 sequence (NEBNext Library Quant Kit for Illumina, New England Biolabs).
single cell RNA-seq

tag: strain


title: Caco2 screen 2.1 initial population

source_name: Caco-2 cell line

value: Caco-2 cell line

value: Brunello library


title: Caco2 screen 2.1 resistant population


title: Caco2 screen 1 resistant population


title: PRISM_PDB_415Case

description: DNA CpG sites

tag: mmed

tag: umed

tag: phenotype

value: Case

tag: array

value: white blood cells