title: gRNA IL2validation popIL2 rep2

city: Stanford

first: Howard

middle: Y

last: Chang

address: CCSR 2130, 269 Campus Drive

department: Center for Personal Dynamic Regulomes

institute: Stanford University

data_processing:
Demultiplexed gRNA enrichment fastq files were inputted into a custom python3 script to count gRNA reads, perform in silico pairing of dual gRNAs from paired end reads, and generate a raw read counts per gRNA matrix. Count matrices were loaded in R and analyzed.
gRNA pairs were filtered using the sum of raw read counts across all sorted populations: sum > 200 (primary screens) or sum > 300 reads (validation screen). Reads were later normalized per sample by dividing by the total reads per sample and scaling by 1e6, and log2 transformed with a pseudocount of 1. Fold change was calculated between each population versus the cytokine-negative population (NEG).
Assembly: NA
Supplementary files format and content: counts.csv files represent raw gRNA counts for each gRNA pair and sorted population for a given gRNA pool after filtering out gRNA pairs with low raw read counts summed across populations
Library strategy: gRNA enrichment

source_name: Jurkat

extract_protocol:
Cells were sorted by FACS for live cells and for the cell populations expressing the constructs of interest. Genomic DNA (gDNA) was extracted from sorted cells for different cytokine populations using Quick-DNA Miniprep kit (Zymo) or a custom precipitation-based gDNA extraction protocol.
gRNA enrichment libraries were prepared from gDNA using a 3-step custom PCR protocol using gRNA-specific nested primers.

treatment_protocol: Lentiviral infection of perturbation and non-targeting control gRNAs, doxycycline

value: Jurkat

value: T cell

value: expresses dCas9 and gRNA

tag: sorted population


title: HS578T, siPOU4F1-1 rep2

status: Public on Mar 14 2024

type: SRA

city: Guangzhou

first: jiahui

last: zhang

state: Guangdong

address: 107 Yanjiang West Road

country: China

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

library_source: transcriptomic

data_processing:
Sequencing raw reads were preprocessed by filtering out ribosomal RNA reads, sequencing adapters, short-fragment reads and other low-quality reads.
Hisat2 (v.2.0.4) was used to map the cleaned reads to the human GRCh37 reference genome with two mismatches.
After genome mapping, StringTie (v.1.3.0) was run with a reference annotation to generate fragments per kilobase of transcript per million mapped reads (FPKM) for known gene models
Assembly: GRCh37
Supplementary files format and content: Tab-delimited text file includes FPKM values for each sample

molecule: total RNA

organism: Homo sapiens

growth_protocol: HS578T and BT549 were maintained in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was extracted from cell lines by using Trizol reagent
RNA libraries were prepared using KAPA Stranded RNA-Seq Library Prep Kit according to the manufacturer's protocol.

treatment_protocol: Cells were transfected with POU4F1 siRNA or control siRNA.

tag: cell line

tag: cell type

value: Basal-like breast cancer cell line

tag: treatment

value: POU4F1 knockdown


title: 11_SCF_Tet2

city: Cambridge

first: Fabiana

last: Duarte

state: Massachusetts

address: 7 Divinity Avenue

department: HSCRB

country: USA

institute: Harvard University

library_source: genomic

data_processing:
Raw sequencing reads were trimmed using custom python scripts to remove adapter sequences.
The reads were aligned to mm10 genome using Bowtie2 (Langmead et al. 2012) with maximum fragment length set to 2 kb, and all other default settings (bowtie2 -X2000 --rg-id).
Mitochondrial, discordant and low quality reads were removed using SAMtools (Li et al. 2009) (samtools view -b -q 30 -f 0x2).
Duplicate sequences were removed using the picard toolkit (http:// broadinstitute.github.io/picard/).
Assembly: mm10
Supplementary files format and content: Counts file is a tab-delimited file of reads in peaks across samples in sparse matrix format. Row names for peaks can be pulled from .bed peak file (that is also provided with the scATAC-seq data).

molecule: genomic DNA

organism: Mus musculus

source_name: Mouse bone marrow

growth_protocol: Immortalization of murine BM cells with HoxB8-ER was done as previously described with the following modifications. Filtered BM cells were layered over Ficoll-Plaque-Plus (GE Healthcare Biosciences), and centrifuged at 400 x g for 25 min at RT without break to enrich for mononuclear cells. Cells were incubated in a 6-well tissue culture plate for 48 hours at 37C with 5% CO2 prior to the retroviral transduction in RPMI (RPMI-1640, Corning) with 10% 2 mM L-glutamine, and 100U penicillin/streptomycin (all from Thermo Fisher), supplemented with 20 ng/ml stem cell factor (SCF), 10 ng/ml interleukin-3 (IL-3), and 10 ng/ml interleukin-6 (IL-6). Non-adherent cells were harvested and 500,000 cells were plated onto a 12-well tissue culture plate (Corning) coated with 10 mg/ml human fibronectin (Sigma). 1 ml of ecotropic retrovirus encoding MSCVneo-HA-ER-Hoxb8 was applied in the presence of 8 mg/ml polybrene and spinoculation was performed at 1000 x g for 60 min at RT. After transduction cells were maintained in RPMI supplemented with 0.5 uM beta-estradiol (Sigma, E2758) and conditioned media containing approximately 100 ng/ml SCF for the generation of neutrophil-biased cells or GM-CSF 10 ng/ml (Peprotech) for the generation of macrophage progenitors. Antibiotic selection was performed by adding G418 at 1 mg/ml final concentration until untransduced control cells were not viable (usually ~7 days). After selection, cells were FACS sorted into 96 well plates with culture media for the generation of single cell clones. For generation of Tet2 KO lines, each clone was transduced with integrase-defective lentiviral vector encoding for Cre recombinase or GFP as control at a Multiplicity of Infection (MOI) of 200.

extract_protocol:
Cells were washed twice with 1x PBS, counted, and resuspended to a concentration of 0.5 x 10^6 cells/mL.
2 μL of cells in 1x PBS (1,000 cells) were mixed with 2 μL of barcoded Tn5, 5 μL 2x Illumina Tagment DNA Buffer (TD), 0.1 μL 10% NP40 (final concentration 0.1%) and 0.9 μL H2O in a 96 well plate. Each well contained a different sample and Tn5 barcode. Cells were mixed and agitated on a ThermoMixer (Eppendorf) for 30 min at 37C. All the wells were pooled together on ice to prevent cross-contamination between Tn5 barcodes. Tagmented DNA was purified using a MinElute PCR Purification Kit (Qiagen), then minimally amplified for sequencing as previously described. Final libraries were purified using the MinElute PCR Purification Kit (Qiagen), and sequenced on a NextSeq 550 (150 cycles), using the following parameters: Read 1 92 cycles, i7 index read 8 cycles, and Read 2 66 cycles, 50% of PhiX Sequencing Control. A custom sequencing primer is required for Read 1 (16005986, Bio-Rad).

tag: tissue

value: Mouse bone marrow

tag: clone

value: SCF

tag: genotype

value: Tet2 KO


title: gRNA IL2validation popIL2 rep3

state: CA


title: 11_SCF_Control

value: Control


title: BT549, siPOU4F1-2 rep1


title: 10_SCF_Control


title: HS578T, siPOU4F1-1 rep1


title: MDA 231 cells, Lactate 2

city: Farmington

first: Yasir

last: Suhail

state: Connecticut

address: 263 Farmington Avenue

department: BME

institute: UCHC

data_processing:
Transcripts per million were calculated using hisat2 -> featureCounts
Assembly: GRCh38
Supplementary files format and content: TPM values

source_name: in-vitro

extract_protocol:
Stardard RNA extraction
Standard NoveSeq RNA library construction

value: in-vitro

value: MDA 231

value: epithelial cell

value: Lactate


title: HS578T, siCtrl, rep2

value: WT


title: gRNA IL2validation popIL2 rep1


title: MDA 231 cells, Lactate 3


title: HS578T, siCtrl, rep1


title: MDA 231 cells, Lactate 1


title: BT549, siPOU4F1-2 rep2

source_name: cell line

value: cell line


title: 22Rv1_ATAC_DMSO_EtOH_rep2

city: Kuopio

first: Ville

last: Paakinaho

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

data_processing:
Basecalls performed using CASAVA, and FASTX-toolkit was used to trim low quality reads.
The reads were aligned to human reference genome version hg38 by using Bowtie2 software version 2.3.4.1. with end-to-end sensitive mode allowing no mismatches.
Peaks were called using HOMER program version 4.10. using findPeaks with style factor, FDR<0.01, >25 tags, >4-fold over control sample and local background. Transposase treated naked DNA sample was used as the control sample (GSE214757).
Assembly: hg38
Supplementary files format and content: bedGraph (HOMER makeUCSCfile command) from alignment file.

growth_protocol: 22Rv1 cells were grown in RPMI-1640 medium supplemented with 10% fetal bovine serum, 1 U/µl penicillin, 1 µg/ml streptomycin and 2 mM L-glutamine. VCaP cells were grown in DMEM medium supplemented with 10% fetal bovine serum, 1 U/µl penicillin and 1 µg/ml streptomycin. All cells were kept at 37 °C in a humidified 95% air/ 5% CO2 incubator.

extract_protocol:
For ATAC-seq, 100 000 isolated nuclei were treated with 2.5 µl Tn5 Transposase loaded with sequencing adapters.
ATAC-seq libraries were prepared with loaded Diagenode Tagmentase (#C01070012) according to instructions.

treatment_protocol: 22Rv1 and VCaP cells were grown in the presence or absence of 10 µM enzalutamide (ENZ) for at least 21 days (ENZ3w) before the start of treatments. 22Rv1 and VCaP cells were treated with vehicle (DMSO) or 1 µM A485 for 24 h and with vehicle (EtOH) or 100 nM of Dexamethasone (Dex) for the last 1 h before the start of nuclei extraction.

value: CWR22 xenograft derived human prostate carcinoma epithelial cell line

tag: enz treatment

tag: inhibitor treatment

tag: hormone treatment


title: 9_SCF_Tet2


title: 13_SCF_Control


title: MDA 231 cells, Oscillatory Hypoxia 2

value: Oscillatory Hypoxia


title: gRNA IL2validation popNEG rep2

value: Jurkat


title: MDA 231 cells, Hypoxia 2

value: Hypoxia


title: 9_SCF_Control


title: gRNA IL2validation popNEG rep1

value: T cell

value: expresses dCas9 and gRNA


title: MDA 231 cells, Oscillatory Hypoxia 1


title: gRNA IL2validation popUN rep2


title: MDA 231 cells, Hypoxia 3


title: 8_SCF_Tet2


title: gRNA IL2validation popNEG rep3


title: MDA 231 cells, Hypoxia 1


title: MDA 231 cells, Control 3


title: gRNA IFNG popIFNG rep3


title: MDA 231 cells, Control 2


title: gRNA IFNG popIFNG rep2


title: 5_SCF_Tet2


title: 5_SCF_Control


title: MDA 231 cells, Oscillatory Hypoxia 3


title: 7_SCF_Control


title: gRNA IFNG popDP rep3


title: MDA 231 cells, Control 1


title: gRNA IFNG popIFNG rep1


title: gRNA IL2validation popUN rep1


title: 10_SCF_Tet2


title: gRNA IFNG popDP rep2


title: 7_SCF_Tet2


title: 4_SCF_Control


title: 4_SCF_Tet2


title: gRNA IL2validation popUN rep3


title: gRNA IFNG popDP rep1


title: Xu142fl_1_rep3

city: Science Avenue

first: YingQiang

last: Long

address: Science Avenue

institute: School of Agricultural Sciences, Zhengzhou University

data_processing:
The mRNA with polyA tail was enriched by Oligo (dT) magnetic beads.
Fragmentation buffer was added to randomly break the mRNA into short fragments.
The cDNA was synthesized by reverse transcription using short fragments as templates, and then the cDNA ends were repaired, A-tailed, and connected with UMI tags and sequencing connectors
Finally, the library was obtained by PCR amplification
Assembly: https://www.cottongen.org/species/Gossypium_hirsutum/CRI-TM1
Supplementary files format and content: tab-delimited text files include readcount values for each Sample …

organism: Gossypium hirsutum

source_name: ovule

extract_protocol:
1 μg of total RNA was used to generate the sequencing libraries, which were sequenced using the Illumina platform by Beijing novogene Co., Ltd. (www.novogene.com, Beijing, China).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: ovule

tag: dpa

value: Unhandled


title: 8_SCF_Control

value: Mouse bone marrow

value: SCF


title: gRNA IFNG popIL2 rep2


title: gRNA IFNG popIL2 rep3


title: 3_SCF_Control

value: Control


title: Xu142fl_1_rep1


title: gRNA IFNG popIL2 rep1


title: Xu142fl_0_rep3


title: 2_SCF_Tet2

value: Tet2 KO


title: 2_SCF_Control


title: Xu142fl_0_rep2


title: 1_SCF_Control


title: gRNA IFNG popNEG rep2


title: Xu142fl_0_rep1


title: 1_SCF_Tet2


title: gRNA IFNG popUN rep3


title: Xu142fl_n1_rep3


title: gRNA IFNG popNEG rep3


title: Xu142fl_n1_rep2


title: Lin_neg_CD11b_Tet2_Sox4OE_Rep1

library_source: genomic single cell

data_processing:
Per-read bead barcodes were parsed and trimmed using UMI-TOOLs (https://github.com/CGATOxford/UMI-tools). Constitutive elements of the bead barcodes were assigned to the closest known sequence allowing for up to 1 mismatch per 6-mer or 7-mer (mean >99% parsing efficiency across experiments).
Paired-end reads were aligned to mm10 using BWA (http://bio-bwa.sourceforge.net/).
We used bead-based ATAC-seq processing (BAP) (https://github.com/caleblareau/bap), to identify systematic biases (i.e. reads aligning to an inordinately large number of barcodes), barcode-aware deduplicate reads, and perform merging of multiple bead barcode instances associated with the same cell. Barcode merging is necessary due to the nature of the BioRad SureCell scATAC-seq procedure used in this study, which enables multiple beads per droplet. BAP uses as input an alignment (.bam) file for a given experiment with a bead barcode identifier indicated by a SAM tag.
Genome-wide chromatin accessibility peaks were called using MACS v2 (MACS2) on the merged aligned scATAC-seq reads per condition, generating a list of peak summit calls per condition. To generate a non-overlapping set of peaks, we first extended summits of each condition to 800-bp windows (±400 bp). We combined these 800-bp peaks, ranked them by their summit significance value and retained specific non-overlapping peaks on the basis of this ordering. We further added to the peak list all non-overlapping peaks from the ImmGen ATAC-seq atlas, after also extending the ImmGen peaks to 800-bp windows (https://sharehost.hms.harvard.edu/immgen/ImmGenATAC18_AllOCRsInfo.csv). This resulted in a filtered list of disjoint peaks (n=297,361), which were finally resized to 301 bp (i.e. ±150 bp from each peak summit) and used for all downstream analyses.
A matrix of reads in peaks counts for single cells was obtained by counting the number of uniquely aligned fragments (with coordinates offset +4/-5 bp for the +/- strand to adjust for Tn5 integration) overlapping the determined peak window genomic ranges, grouped by cell barcode ID, done using custom R code.
Assembly: mm10
Supplementary files format and content: Peak file (BED) contains chromosome, start and end coordinates for determined chromatin accessibility peak window ranges. cellMeta file contains single cell barcode information for the final set of filtered scATAC-seq cells used in the analysis. Fragments.tsv.gz files contain all Tn5-corrected coordinates for aligned fragments generated using BAP, which can be used to overlap with peaks to get counts of Tn5 insertions falling within peaks for each cell barcode. Raw_counts.mtx file contains the peaks x cells count matrix and is indexed by gene (row), cell (column), and count.

growth_protocol: Tet2 fl/fl mice (#017573, The Jackson Laboratory) were crossed to Mx1-Cre mice (#003556, The Jackson Laboratory). Mx1-Cre negative littermates were utilized as controls. 4 doses of 12.5 ug/g pI:pC (Amersham) were administered intraperitoneally to induce Cre activity.

extract_protocol:
Cell sorting was performed on FACS Aria II (BD Biosciences). Single stained and Fluorescence Minus One stained cells were used as controls. Samples were incubated with the antibody cocktail in PBS 2% FBS for 30 minutes at 4 degrees before sorting. 7-AAD Viability Staining Solution (BioLegend) was included in the sample preparation for flow cytometry to exclude dead cells. For a detailed description of tagmentation protocols and buffer formulations refer to the SureCell ATAC-Seq Library Prep Kit User Guide (17004620, Bio-Rad). Sorted cells and tagmentation related buffers were chilled on ice. Lysis was performed simultaneously with tagmentation. Washed and pelleted cells were resuspended in Whole Cell Tagmentation Mix containing 0.1% Tween-20, 0.01% Digitonin, 1x PBS supplemented with 0.1% BSA, ATAC Tagmentation Buffer and ATAC Tagmentation Enzyme (ATAC Tagmentation Buffer and Enzyme are both included in the SureCell ATAC-Seq Library Prep Kit (17004620, Bio-Rad)). Cells were mixed and agitated on a ThermoMixer for 30 min at 37°C. Tagmented cells were kept on ice prior to encapsulation.
Tagmented cells were loaded onto a ddSEQ Single-Cell Isolator. Single-cell ATAC-seq libraries were prepared using the SureCell ATAC-Seq Library Prep Kit (17004620, Bio-Rad) and SureCell ddSEQ Index Kit (12009360, Bio-Rad). Bead barcoding and sample indexing were performed in a C1000 Touch™ Thermal cycler with a 96-Deep Well Reaction Module: 37°C for 30 min, 85°C for 10 min, 72°C for 5 min, 98°C for 30 sec, 8 cycles of 98°C for 10 sec, 55°C for 30 sec, and 72°C for 60 sec, and a single 72°C extension for 5 min to finish. Emulsions were broken and products cleaned up using Ampure XP beads. Barcoded amplicons were further amplified using a C1000 Touch™ Thermal cycler with a 96-Deep Well Reaction Module: 98°C for 30 sec, 6-9 cycles (cycle number depending on the cell input, Section 4 Table 3 of the User Guide) of 98°C for 10 sec, 55°C for 30 sec, and 72°C for 60 sec, and a single 72°C extension for 5 min to finish. PCR products were purified using Ampure XP beads and quantified on an Agilent Bioanalyzer using the High-Sensitivity DNA kit. Libraries were loaded at 1.5 pM on a NextSeq 550 using the NextSeq High Output Kit and sequencing was performed using the following read protocol: Read 1 118 cycles, i7 index read 8 cycles, and Read 2 40 cycles. A custom sequencing primer is required for Read 1 (16005986, Bio-Rad; included in the kit).

tag: replicate

tag: overexpression

value: Sox4 OE


title: Lin_neg_CD11b_Tet2_Rep4


title: Xu142fl_n1_rep1


title: gRNA IFNG popNEG rep1


title: gRNA IL2primary popIFNG rep3


title: 3_SCF_Tet2


title: gRNA IFNG popUN rep1


title: Xu142_1_rep3


title: Xu142fl_1_rep2


title: Lin_neg_CD11b_Tet2_Rep3


title: Xu142_1_rep2


title: Xu142_1_rep1


title: GMP_Tet2_Sox4OE_Rep1


title: GMP_Tet2_Sox4OE_Rep2


title: gRNA IL2primary popIFNG rep1


title: gRNA IL2primary popIFNG rep2


title: GMP_Tet2_Rep4


title: Xu142_0_rep3


title: gRNA IL2primary popDP rep2


title: GMP_Tet2_Rep3


title: Lin_neg_CD11b_Tet2_Sox4OE_Rep2


title: Xu142_0_rep2


title: gRNA IFNG popUN rep2


title: gRNA IL2primary popIL2 rep3


title: Retina, IgG_P17_OIR_rep2

city: Boston

first: Emil

last: Kriukov

address: 20 Staniford St

institute: Schepens Eye Research Institute

data_processing:
Data processing and analysis were performed using an automated chromatin Immunoprecipitation sequencing analysis pipeline, ChIP-AP (https://github.com/JSuryatenggara/ChIP-AP) with default settings.
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

source_name: Retina

extract_protocol:
Freshly isolated retinas from three mice were minced and pooled as a group sample. The pooled retina was incubated in NE1 buffer (20 mM HEPES pH7.8, 10 mM KCl, 0.5 mM spermidine, 0.1% Triton X-100, 20% glycerol, Roche proteinase inhibitor) for 10 min on ice, then homogenized by Dounce homogenizer. The suspension was centrifuged at 100 x g for 30 sec at 4°C. The supernatant containing nuclei was transferred to a fresh tube. The nuclei number was counted by a hemacytometer.
A half million nuclei were conjugated to activated concanavalin A-coated magnetic beads (Bangs Laboratories, BP531). The beads were separated by a magnet stand and resuspended in Wash buffer (20 mM HEPES pH7.5, 150 mM NaCl, 2.0 mM EDTA, 0.5 mM spermidine, 0.01% digitonin, Roche proteinase inhibitor) with primary antibody (1:50 dilution). After incubation at 4°C overnight on a rotator, the beads were separated, resuspended in Wash buffer with secondary antibody, guinea pig anti-rabbit antibody (1:100 dilution), and incubated for 30 min at RT on a rotator. The beads were washed with Wash buffer once and resuspended in 300-Wash buffer (20 mM HEPES pH 7.5 300 mM NaCl, 0.5 mM spermidine, 0.01% digitonin, Roche proteinase inhibitor) with pAG-Tn5 (EpiCypher, 15-1017). After incubation for 1 hour at RT, the beads were washed with 300-Wash buffer while the beads were on a magnet stand. For tagmentation of DNA, the beads were resuspended in Tagmentation buffer (300-Wash buffer with 10 mM MgCl2) and incubated for 1 hour at 37°C. The tagmentation was eliminated by adding 0.5 M EDTA, 10% SDS, and 20 µg/µl proteinase K (final concentration 16 mM EDTA, 0.1% SDS, 0.16 µg/µl proteinase K) with incubation for 10 min at 70°C. The tagmented DNA was extracted by phenol-chloroform extraction, precipitated by ethanol precipitation, and dissolved in 21 µl TE buffer (1 mM Tris pH8.0, 0.1 mM EDTA). To prepare CUT&Tag libraries, 2 µl of 10 µM i5 primer, 2 µl of 10 µM barcoded i7 primer, and 25 µl of NEBNext HiFi 2x Master mix (NEB, M0541L)) were added. PCR was performed 12 cycles. Following the manufacturer's instructions, the libraries were purified using AMPure XP bead (Beckman Coulter, A63880).

tag: age

value: Retina

tag: cut&tag antibody

value: guinea pig anti-rabbit (Antibodies-Online, ABIN101961)

value: Oxygen-induced retinopathy


title: gRNA IL2primary popIL2 rep2


title: Xu142_n1_rep1


title: Xu142_n1_rep3


title: Xu142_n1_rep2


title: Retina, IgG_P17_Norm_rep2

value: Normoxia


title: gRNA IL2primary popIL2 rep1


title: Primary mouse neuron-derived sEVs long-read rep3 [NE3]

city: La Jolla

first: Jerold

last: Chun

address: 1090 N. Torrey Pines Rd

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
*library strategy: PacBio bulk Iso-Seq
ccs was used to generate high-quality reads
lima was used to demultiplex and remove primers
isoseq3 was used to generate non-concatemeric, full-length reads
minimap2 was used to map reads to the genome in a splice-aware manner
cDNA_Cupcake was used to collapse reads into non-redundant isoforms
Isoforms were annotated and filtered using a modified version of SQANTI3
SQANTI3-annotated isoforms aggregated using isoSeQL
Assembly: GRCm39
Supplementary files format and content: primaryCellExo_commonJxn_allinfo_countMat.txt: text file describing all the isoforms detected in the samples by gene annotation, isoform structural category, and read count information for each sample
Supplementary files format and content: expNum_map.txt: the samples are referred to using exp_ids in the primaryCellExo_commonJxn_allinfo_countMat.txt, this file assigns each sample to its exp_id

molecule: polyA RNA

source_name: Brain

extract_protocol:
RNA was extracted from sEVs using the Qiagen RNeasy Micro kit according to the manufacturer’s instructions, including an on-column DNase treatment. RNA was also extracted from sEV-source cells using the Qiagen RNeasy Mini kit according to manufacturer’s instructions including on-column DNase treatment.
cDNA libraries from sEV RNA and cell RNA were generated using the NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® underwent 10 cycles of reamplification using the same kit. Samples were cleaned up with 1.2X ProNex beads (VWR NG2001). 20ng of cDNA from each human sample or 100ng of each murine sample was used as input for the preparation of SMRTbell® libraries according to the “PacBio® Barcoded Overhang Adapters for Multiplexing Amplicons” protocol using the SMRTbell express template prep kit 2.0. Human samples were pooled according to their group: AD bulk, AD sEVs, ND bulk, or ND sEVs. Sequencing primer v4 kit and Sequel II Binding Kit 2.1 were used for human samples. Each human sample group was sequenced on 1 SMRTCell on the PacBio Sequel II with a movie time of 10 hours. Murine samples were combined by sample type: the first pool consisted of astrocyte, microglia, and neurons cells and the second pool consisted of astrocyte, microglia, or neuron sEVs. Sequencing primer 3.1 kit and Sequel II Binding Kit 3.1 were used for murine samples. Each pool was sequenced on 2 SMRTCells on the PacBio Sequel II with a movie time of 24 hours.

value: Brain

value: Primary cell culture

value: Neuron


title: Primary mouse neuron-derived sEVs long-read rep2 [NE2]


title: gRNA IL2primary popNEG rep3

value: Jurkat


title: Retina, IgG_P14_OIR_rep1


title: Retina, IgG_P14_OIR_rep2


title: gRNA IL2primary popDP rep3

value: T cell


title: Primary mouse neuron-derived sEVs long-read rep1 [NE1]


title: Retina, IgG_P14_Norm_rep2


title: gRNA IL2primary popNEG rep1

value: expresses dCas9 and gRNA


title: Primary mouse microglia-derived sEVs long-read rep2 [ME2]

value: Microglia


title: Retina, IgG_P14_Norm_rep1


title: Xu142_0_rep1

value: ovule

value: Unhandled


title: gRNA IL2primary popUN rep2


title: Retina, H3K4me3_P17_OIR_rep2

value: Histone H3K4me3 antibody (pAb) (Active Motif, 39159)


title: Retina, IgG_P17_OIR_rep1


title: gRNA IL2primary popUN rep1


title: Primary mouse microglia-derived sEVs long-read rep1 [ME1]


title: Retina, IgG_P17_Norm_rep1


title: YoungOT1_Tum_Tterm_replicate5_ATACseq

first: Alex Chang-Yu

last: Chen

state: MA

address: 149 13th Street, 7th floor, Room 7103

department: Krantz Family Center for Cancer Research

institute: Massachusetts General Hospital

description:
YoungOT1_Tum_Tterm_5
NormCountsATAC_Intrinsic.txt

data_processing:
Raw fastq files were downloaded from Illumina BaseSpace and merged across lanes
Quality trimming and primer removal in raw fastq files were done with Trimmomatric (v.0.36) using the following parameters: LEADING:15 TRAILING:15 SLIDINGWINDOW:4:15 MINLEN:30 CROP:35.
Trimmed reads were aligned to mm10 with Bowtie2 (v.2.2.9) using a maximum insert size of 1,000.
Aligned bams were sorted, duplicates marked (Picard v.2.8.0) , and reads mapping to the blacklist region removed.
Peak-calling using MACS (v.2.1.1) was performed on merged bam files (Samtools v. 1.3.1) from biological replicates using a q-value threshold of 0.001. Consensus peaks from all biological conditions were merged to create a single peak universe. Cut sites were extracted from each biological replicate and the number of cuts in each peak region was quantified to generate a raw counts matrix.
Normalization and differential expression were performed using DESeq2 (v 1.28.1)
Assembly: mm10
Supplementary files format and content: tab-delimited text file including DESeq2 normalized counts

source_name: B16-OVA Tumor

extract_protocol:
DNA was purified using a QIAgen MinElute Reaction Cleanup kit
Post-PCR bead cleanup was done using Agencourt AMPure XP bead cleanup (Beckman Coulter/Agencourt), and library quality was verified using Tapestation analysis.

value: CD8+ T cells

tag: cell subset

value: Tterm

tag: cell state

value: terminally exhausted

value: B16-OVA Tumor

tag: strain

value: 10-12 weeks old

tag: sequencing batch

value: Batch 4 & 5

value: Wild type


title: Retina, H3K4me3_P17_Norm_rep2

value: Retina

value: Normoxia


title: Primary mouse astrocyte-derived sEVs long-read rep3 [AE3]

value: Brain

tag: cell line

value: Primary cell culture

tag: cell type

value: Astrocyte


title: Primary mouse astrocyte-derived sEVs long-read rep2 [AE2]

tag: tissue


title: Retina, H3K4me3_P17_OIR_rep1

tag: treatment

value: Oxygen-induced retinopathy


title: YoungOT1_Tum_Tterm_replicate3_ATACseq

description:
YoungOT1_Tum_Tterm_3
NormCountsATAC_Intrinsic.txt

tag: genotype


title: YoungOT1_Tum_Tterm_replicate4_ATACseq

description:
YoungOT1_Tum_Tterm_4
NormCountsATAC_Intrinsic.txt


title: iNPC derived organoid, Replicate 2 d21, GEX Library

city: Los Angeles

first: Kari

middle: Ann

last: Koppitch

address: 1425 San Pablo Street, BCC 312

department: Stem Cell

institute: USC

description:
GEX_iNPC2
10X Chromium multiome ATAC + gene expression kit

data_processing:
Sequencing reads were aligned to the human genome (GRCh38) with the Cell Ranger ARC software (version 2.0.2) using STAR aligner on the University of Southern California High Performance Cluster.
Assembly: arc-GRCh38-2020-A-2.0.0
Supplementary files format and content: atac_fragaments_tsv.gz, Tab-separated file containing fragment information
Supplementary files format and content: atac_fragaments_tsv.gz.tbi, Index of the tab-separated file
Supplementary files format and content: H5 file containing the filtered gene by cell gene expression and peak by cell matrices
Library strategy: snRNA-seq + snATAC-seq

source_name: Kidney organoids

growth_protocol: Kidney organoids were cultured with Stage III medium (Advanced RPMI 1640 medium with 1X B27 and 200nM A83-01), 37C, 5% CO2

extract_protocol:
Orgnaoids were miccrodissected and digested in CAP digestion solution (10mg/ml Cold Active Protease+ 2.5 mg/ml Collagenase type 4 + 0.125U/ul Dnase1) at 12°C for 30 mins. Cells were then spun down at 350G for 5 mins and resuspended in cold autoMACS Running Buffer. Cell viablity was accessed (99% Live) and cells spun down again. 10X genomics Demonstarated Proocol CG000365 (REV C) was then used to isolate nuclei with 5 min lysis time. The single nuclei suspension was than transposed and run through a microfuidic chip (Chip J) for barcoding.
10X Chromium Single Cell Multiome + Gene Expression protocol (CG000338 Rev E)

value: Kidney organoids

value: Kidney cells


title: iNPC derived organoid, Replicate 2 d21, ATAC Library

description:
ATAC_iNPC2
10X Chromium multiome ATAC + gene expression kit

value: Kidney organoids were cultured with Stage III medium


title: gRNA IL2primary popNEG rep2

value: Jurkat

value: T cell

value: expresses dCas9 and gRNA

tag: sorted population


title: YoungOT1_Tum_Tterm_replicate2_ATACseq

description:
YoungOT1_Tum_Tterm_2
NormCountsATAC_Intrinsic.txt

value: CD8+ T cells

value: Tterm

value: terminally exhausted


title: Retina, H3K4me3_P17_Norm_rep1

value: Histone H3K4me3 antibody (pAb) (Active Motif, 39159)


title: Primary mouse astrocyte-derived sEVs long-read rep1 [AE1]


title: Primary mouse microglia-derived sEVs long-read rep3 [ME3]

value: Microglia


title: Retina, H3K4me3_P14_OIR_rep2

value: Retina


title: Primary mouse neurons long-read rep3 [NC3]

value: Neuron


title: iNPC derived organoid, Replicate 1 d21, GEX Library

description:
GEX_iNPC1
10X Chromium multiome ATAC + gene expression kit


title: Retina, H3K4me3_P14_OIR_rep1


title: Primary mouse neurons long-read rep2 [NC2]

value: Brain


title: YoungOT1_Tum_Tterm_replicate1_ATACseq

description:
YoungOT1_Tum_Tterm_1
NormCountsATAC_Intrinsic.txt

value: B16-OVA Tumor

value: 10-12 weeks old

value: Batch 4 & 5

value: Wild type


title: Retina, H3K4me3_P14_Norm_rep1

value: Normoxia


title: YoungOT1_Tum_Tprog_replicate2_ATACseq

description:
YoungOT1_Tum_Tprog_2
NormCountsATAC_Intrinsic.txt

value: Tprog

value: progenitor exhausted


title: AGS_NC-2

city: Shiyan

first: Qin

last: Shanshan

address: Renmin Road 30, Maojian District

institute: Institute of Basic Medical Sciences, School of Basic Medical Sciences, Hubei University of Medicine

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 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2 with default parameters.
HTSeq v0.13.5 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_29/gencode.v29.annotation.gtf.gz.
Assembly: GRCh38
Supplementary files format and content: FileincludeCount and FPKM valuesforeachsample

source_name: AGS

growth_protocol: The human GC cell line AGS was purchased from the Shanghai Cell Bank of Chinese Academy of Sciences (Shanghai, China). The AGS cell line were cultured in DMEM medium containing 10% fetal bovine serum (FBS), 100 U/mL penicillin, 100 U/mL streptomycin and 0.03% glutamine at 37 oC in 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: The AGS cells were seeded into 6-well plates and grown overnight. The next day, when the cell plating density reached 70%, AGS cells were treated with human recombinant FGF2 protein (20 ng/mL). After 24 hours, cells were harvested for RNA sequencing.

value: AGS

value: gastric cancer cell line

value: NC


title: iNPC derived organoid, Replicate 1 d21, ATAC Library

description:
ATAC_iNPC1
10X Chromium multiome ATAC + gene expression kit

value: Kidney organoids

value: Kidney cells

value: Kidney organoids were cultured with Stage III medium


title: Primary mouse neurons long-read rep1 [NC1]

value: Primary cell culture


title: YoungOT1_Tum_Tprog_replicate1_ATACseq

description:
YoungOT1_Tum_Tprog_1
NormCountsATAC_Intrinsic.txt

value: CD8+ T cells


title: Retina, H3K4me3_P14_Norm_rep2

value: Retina

value: Histone H3K4me3 antibody (pAb) (Active Motif, 39159)


title: Retina, H3K27me3_P17_OIR_rep2

value: Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb (CST, 9733S)

value: Oxygen-induced retinopathy


title: Retina, H3K27me3_P17_OIR_rep1


title: Primary mouse microglia long-read rep2 [MC2]

value: Brain

value: Microglia


title: AGS_FGF2-2


title: AgedOT1_Tum_Tterm_replicate5_ATACseq

description:
AgedOT1_Tum_Tterm_5
NormCountsATAC_Intrinsic.txt

value: Tterm

value: terminally exhausted

value: B16-OVA Tumor

value: 64-68 weeks old

value: Batch 4 & 5

value: Wild type


title: AGS_NC-1

value: AGS

value: gastric cancer cell line

value: NC


title: AgedOT1_Tum_Tterm_replicate4_ATACseq

description:
AgedOT1_Tum_Tterm_4
NormCountsATAC_Intrinsic.txt


title: Primary mouse microglia long-read rep3 [MC3]

value: Primary cell culture


title: Primary mouse microglia long-read rep1 [MC1]


title: Retina, H3K27me3_P17_Norm_rep2

value: Normoxia


title: Primary mouse astrocytes long-read rep3 [AC3]

value: Astrocyte


title: AgedOT1_Tum_Tterm_replicate3_ATACseq

description:
AgedOT1_Tum_Tterm_3
NormCountsATAC_Intrinsic.txt

value: CD8+ T cells


title: Retina, H3K27me3_P17_Norm_rep1

value: Retina

value: Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb (CST, 9733S)


title: AGS_FGF2-1


title: CLL B cells, VIVIT treated, 4h, sample 4

city: Milano

first: Michela

last: Riba

address: via Olgettina 60

department: COSR, Center for Omics Sciences

country: Italy

institute: IRCCS, Ospdale San Raffaele

description:
VIVIT4
all.counts_MuzioM_1827_v1.txt

data_processing:
COSR Center (Center for Omics Science, Ospedale San Raffaele custom pipeline
Quality checks have been done on raw data using FastQC and MultiQC
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic
Trimmed sequence reads were mapped to Hg38 using STAR
Read count extraction has been made using Rsubread library, featureCounts function
Assembly: Hg38
Supplementary files format and content: text file contains raw counts data for all the samples

source_name: primary B cells

growth_protocol: 3*10^6 cells/ml of RPMI+10%FBS

extract_protocol:
Total RNA was extracted using RNeasy plus mini kit  (Qiagen). RNA quantification was carried out using Qubit Fluorimetric Quantification (Life Technologies) and 100ng of RNA were used to prepare the library.
RNA libraries for RNA-seq were prepared using Lexogen Stranded Quantseq following manufacturer's protocols.

value: primary B cells

value: CLL (Chronic Lymphocytic Leukemia) primary cells

value: treated with 10µM VIVIT

tag: time


title: CLL B cells, VIVIT treated, 4h, sample 3

description:
VIVIT3
all.counts_MuzioM_1827_v1.txt


title: Primary mouse astrocytes long-read rep2 [AC2]

value: Brain


title: Retina, H3K27me3_P14_OIR_rep2

value: Oxygen-induced retinopathy


title: Primary mouse astrocytes long-read rep1 [AC1]


title: Retina, H3K27me3_P14_OIR_rep1


title: AgedOT1_Tum_Tterm_replicate1_ATACseq

description:
AgedOT1_Tum_Tterm_1
NormCountsATAC_Intrinsic.txt

value: Tterm

value: terminally exhausted

value: B16-OVA Tumor

value: 64-68 weeks old


title: CLL B cells, VIVIT treated, 4h, sample 2

description:
VIVIT2
all.counts_MuzioM_1827_v1.txt


title: Young_Spl_Naive_replicate2_ATACseq

description:
Young_Spl_Naive_2
NormCountsATAC_Intrinsic.txt

source_name: Spleen

value: Naive

value: naïve

value: Spleen

value: 10-12 weeks old

value: Batch 3

value: Wild type


title: D-Gel, Day7-3

city: changchun

first: Junfeng

last: Ding

state: Jilin

address: No. 5625 Renmin Rd.

institute: Changchun Institute of Applied Chemistry, Chinese Academy of Sciences

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq   format were firstly processed through fastp software.
Clean data (clean reads)   were obtained by removing reads containing adapter, reads containing N base and low   quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data   were calculated. All the downstream analyses were based on the clean data with high   quality.
Index of the reference genome was built using Hisat2 (v2.0.5)  and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5).
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
We used clusterProfiler  R package (3.8.1) to test the statistical enrichment of differential expression genes in  KEGG pathways.
Assembly: mm10
Supplementary files format and content: excel file includes raw counts and FPKM values for each sample

source_name: hydrogel tissue

extract_protocol:
mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads.
In order   to select cDNA fragments of preferentially 370~420 bp in length, the library fragments   were purified with AMPure XP system (Beckman Coulter, Beverly, USA).

value: hydrogel tissue

value: WT


title: Retina, H3K27me3_P14_Norm_rep2

value: Retina

value: Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb (CST, 9733S)

value: Normoxia


title: D-Gel, Day7-2


title: Young_Spl_Naive_replicate1_ATACseq

description:
Young_Spl_Naive_1
NormCountsATAC_Intrinsic.txt

value: CD8+ T cells


title: AgedOT1_Tum_Tterm_replicate2_ATACseq

description:
AgedOT1_Tum_Tterm_2
NormCountsATAC_Intrinsic.txt

value: Batch 4 & 5


title: D-Gel, Day7-1


title: CLL B cells, DMF treated, 4h, sample 5

description:
DMF5
all.counts_MuzioM_1827_v1.txt

value: primary B cells

value: CLL (Chronic Lymphocytic Leukemia) primary cells

value: treated with 100µM DMF


title: Retina, H3K27ac_P17_OIR_rep2

value: Histone H3K27ac antibody (pAb) (Active Motif, 39133)

value: Oxygen-induced retinopathy


title: CLL B cells, DMF treated, 4h, sample 4

description:
DMF4
all.counts_MuzioM_1827_v1.txt


title: gRNA IL2primary popDP rep1

value: Jurkat

value: T cell

value: expresses dCas9 and gRNA


title: CLL B cells, DMF treated, 4h, sample 3

description:
DMF3
all.counts_MuzioM_1827_v1.txt


title: L-Gel, Day7-3


title: Retina, H3K27ac_P17_OIR_rep1


title: Aged_Spl_Naive_replicate1_ATACseq

description:
Aged_Spl_Naive_1
NormCountsATAC_Intrinsic.txt

value: Naive

value: naïve

value: Spleen

value: 64-68 weeks old

value: Batch 3


title: L-Gel, Day7-2

value: hydrogel tissue

value: WT


title: Retina, H3K27me3_P14_Norm_rep1

value: Retina

value: Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb (CST, 9733S)

value: Normoxia


title: CLL B cells, DMF treated, 4h, sample 2

description:
DMF2
all.counts_MuzioM_1827_v1.txt

value: primary B cells

value: CLL (Chronic Lymphocytic Leukemia) primary cells


title: Retina, H3K27ac_P17_Norm_rep2

value: Histone H3K27ac antibody (pAb) (Active Motif, 39133)


title: L-Gel, Day7-1


title: CLL B cells, DMF treated, 4h, sample 1

description:
DMF1
all.counts_MuzioM_1827_v1.txt

value: treated with 100µM DMF


title: mLN iNKT cells, aGC, male, KO FT, rep 2

city: Toronto

first: Thierry

middle: Robert

last: Mallevaey

state: ON

address: 1 King's College Circle

department: Immunology

country: Canada

institute: University of Toronto

data_processing:
FASTQ files were merged across 4 lanes into 1 file per sample using a custom bash script.
Index file was built using Kallisto and reads were aligned to NCBI GRCm38/mm10 mouse genome
Merged FASTQ files were aligned to index file by Kallisto and transcript abundance were imported into tximport. Transcript counts were collapsed into gene counts.
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text file containing raw counts of all samples

source_name: Mesenteric lymph nodes

growth_protocol: iNKT cells were sorted from the mLNs of WT FT and KO FT mice at 24 h after oral gavage

extract_protocol:
Total RNA was extracted using the Single Cell RNA Purification Kit according to manufacturer's instructions.
RNA libraries for RNA-seq were prepared through NexteraXT DNA Library Preparation (Illumina FC-131-1096) using the Nextera XT Index Kit V1 or V2 Set A (FC-131-1002 or 2001) according to the manufacturer's instructions.

treatment_protocol: Mice were oral gavaged with 2μg aGC (in 200μL PBS) or same volume of vehicle (in 200μL PBS)

value: Mesenteric lymph nodes

value: iNKT cells

value: KO FT

value: aGC


title: mLN iNKT cells, aGC, male, KO FT, rep 1


title: mLN iNKT cells, aGC, male, KO FT, rep 3


title: Retina, H3K27ac_P14_OIR_rep2

value: Oxygen-induced retinopathy


title: CLL B cells,  VIVIT treated, 4h, sample 1

description:
VIVIT1
all.counts_MuzioM_1827_v1.txt

value: treated with 10µM VIVIT


title: CLL B cells, untreated, 4h, sample 5

description:
control5
all.counts_MuzioM_1827_v1.txt

value: not treated


title: mLN iNKT cells, aGC, female, KO FT, rep 3


title: Aged_Spl_Naive_replicate2_ATACseq

description:
Aged_Spl_Naive_2
NormCountsATAC_Intrinsic.txt

value: CD8+ T cells

value: Naive

value: naïve

value: Spleen

value: 64-68 weeks old

value: Batch 3

value: Wild type


title: mLN iNKT cells, aGC, female, KO FT, rep 2


title: CLL B cells, untreated, 4h, sample 4

description:
control4
all.counts_MuzioM_1827_v1.txt

value: primary B cells

value: CLL (Chronic Lymphocytic Leukemia) primary cells


title: Intrinsic_agedOT1CD8T_youngTME_scRNAseq

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Gzipped files include 10x format single cell gene expression matrices, including barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz.
Supplementary files format and content: tab-delimited text file including log normalized counts for each cell generated using Seurat in R

extract_protocol:
Live tumor-infiltrating CD8+ T cells (or OT-1 CD8+ T cells) and/or intratumoral CD45+ cells were sorted from tumors on day 15 after tumor inoculation by BD FACSSymphony S6 Sorter (BD).  Sorted cells were pooled into groups (five biological replicates per group) with independent mice being labeled with TotalSeq-B Hashtags (Biolegend). Cells were counted and loaded onto the Chromium Controller (10X Genomics) for a target recovery of 10,000 single cells per run.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics).

value: OT-1 CD8+ T cells

value: B16-OVA Tumor

value: 10-12 weeks old


title: Extrinsic_OT1CD8T_youngTME_scRNAseq

description: 10x Genomics


title: CLL B cells, untreated, 4h, sample 3

description:
control3
all.counts_MuzioM_1827_v1.txt


title: Extrinsic_OT1CD8T_agedTME_scRNAseq

description: 10x Genomics


title: Retina, H3K27ac_P14_Norm_rep2

value: Retina

value: Histone H3K27ac antibody (pAb) (Active Motif, 39133)

value: Normoxia


title: Retina, H3K27ac_P14_Norm_rep1


title: Retina, Fos_P17_OIR_rep2

value: c-Fos (9F6) Rabbit mAb (CST, 2250S)

value: Oxygen-induced retinopathy


title: mLN iNKT cells, PBS, male, KO FT, rep 2

value: Mesenteric lymph nodes

value: iNKT cells

value: KO FT

value: PBS


title: Retina, H3K27ac_P17_Norm_rep1


title: CLL B cells, untreated, 4h, sample 2

description:
control2
all.counts_MuzioM_1827_v1.txt

value: not treated


title: Endogenous_OT1CD8T_young_aged_beforeTransfer_scRNAseq

description: 10x Genomics

value: Spleen


title: CLL B cells, untreated, 4h, sample 1

description:
control1
all.counts_MuzioM_1827_v1.txt


title: Endogenous_CD8T_youngTME_scRNAseq

description: 10x Genomics

value: Endogenous CD8+ T cells


title: Intrinsic_youngOT1CD8T_youngTME_scRNAseq

description: 10x Genomics


title: Retina, Fos_P17_Norm_rep1


title: Retina, Fos_P17_OIR_rep1


title: Pool2, snRNA-seq

city: NEW YORK

first: RUI

last: FU

state: NY

address: 101 6th Ave

department: Computational Biology

institute: New York Genome Center

description: 10x Genomics

data_processing:
10x Genomics Cell Ranger (6.0.0) was used to perform alignment, cell calling, and gene quantification on the RNA library
For the hashing (HTO) library, the antibody sequence list was pre-processed using the “kite” pipeline (https://github.com/pachterlab/kite) to allow pseudo-alignment to both the exact sequences and those with one base difference. A reference index was created using Kallisto (v0.46.0), and then Kallisto and bustools (v0.39.3) were used to obtain a cell x tag UMI count matrix
Assembly: mm10
Supplementary files format and content: Comma/tab separated value files and matrix files

molecule: nuclear RNA

source_name: brain

growth_protocol: C57BL/6J mice were housed in groups (two to five mice per cage) and maintained on a 12 h light/dark cycle with access to food and water ad libitum.

extract_protocol:
Tissue was dissected using a tissue puncher and flash frozen in dry ice. Samples were homogenized, and the nuclei were purified using an iodixanol cushion.
We performed library preparations using the 10X Chromium platform and sequenced them on the Illumina NovaSeq.

treatment_protocol: Entire litters were randomized at postnatal day 1 (P1) and pups within each litter were divided into maternal separated and control groups.

value: brain

value: Neuron, Astrocytes, Oligodendrocytes, etc

value: control and maternal separation, pooled


title: Retina, H3K27ac_P14_OIR_rep1


title: mLN iNKT cells, PBS, female, KO FT, rep 3


title: Endogenous_CD8T_agedTME_scRNAseq

description: 10x Genomics

value: B16-OVA Tumor

value: 64-68 weeks old


title: Retina, Fos_P17_Norm_rep2

value: Retina


title: Pool1, snRNA-seq

description: 10x Genomics


title: Retina, Fos_P14_OIR_rep2


title: mLN iNKT cells, PBS, female, KO FT, rep 1


title: Lin_neg_CD11b_Tet2_Rep2

data_processing:
Base call files were demultiplexed, for each flow cell directory, into FASTQ files using Cellranger v3.1.0 (https://github.com/10XGenomics/cellranger) mkfastq with default parameters. FASTQ files were then processed using Cellranger count with default parameters.
Gene-mapped counts were loaded into R as a Seurat object and used for downstream analysis. Genes with at least one UMI across cells were retained, and cells with a number of unique feature counts > 200 and total UMIs > 5000 and mitochondrial read percentage of < 5 % were initially retained. Normalization and scaling of RNA gene expression levels was then performed.
Assembly: mm10
Supplementary files format and content: Decomposed counts matrix. Counts data is indexed by gene (row), cell (column), and count where the geneNames file and cellMeta file provide annotations for rows and columns.

extract_protocol:
Cell sorting was performed on FACS Aria II (BD Biosciences). Single stained and Fluorescence Minus One stained cells were used as controls. Samples were incubated with the antibody cocktail in PBS 2% FBS for 30 minutes at 4 degrees before sorting. 7-AAD Viability Staining Solution (BioLegend) was included in the sample preparation for flow cytometry to exclude dead cells.
scRNA-seq was performed on a Chromium Single-Cell Controller (10X Genomics) using the Chromium Single Cell Reagent Kit v2, Chromium Next GEM Chip A and Chromium i7 Multiplex Kit according to the manufacturer’s instructions. Briefly, single cells were partitioned in Gel Beads in Emulsion (GEMs) and lysed, followed by RNA barcoding, reverse transcription and PCR amplification (according to the available cDNA quantity). scRNA-seq libraries were prepared according to the manufacturer’s instructions, checked and quantified on Tapestation 4200 (Agilent) and Qubit 4 fluorometer (Invitrogen).
Chromium Single Cell Reagent Kit v2, Chromium Next GEM Chip A and Chromium i7 Multiplex Kit

value: Mouse bone marrow

value: Tet2 KO


title: mLN iNKT cells, PBS, female, KO FT, rep 2


title: mLN iNKT cells, aGC, female, KO FT, rep 1

value: aGC


title: Lin_neg_CD11b_Control_Rep2

value: Control


title: Retina, Fos_P14_Norm_rep2

value: c-Fos (9F6) Rabbit mAb (CST, 2250S)

value: Normoxia


title: mLN iNKT cells, aGC, male, WT FT, rep 3

value: Mesenteric lymph nodes

value: iNKT cells

value: WT FT


title: mLN iNKT cells, aGC, male, WT FT, rep 2


title: mLN iNKT cells, PBS, male, KO FT, rep 3

value: KO FT

value: PBS


title: Retina, Fos_P14_Norm_rep1


title: GMP_Tet2_Rep2


title: mLN iNKT cells, PBS, male, KO FT, rep 1


title: mLN iNKT cells, aGC, male, WT FT, rep 1


title: Primary mouse neuron-derived sEVs rep3

data_processing:
Salmon (v1.8.0) quant function was used to map and quantify the reads.
Downstream analysis was performed in DESeq2 after importing the salmon quantification files using tximport (v1.22.0)
Assembly: GRCm39
Supplementary files format and content: comma-separated file of normalized counts from DESeq2

extract_protocol:
RNA was extracted from sEVs using Qiagen RNeasy Micro kit according to the manufacturer’s instructions, including an on-column DNase treatment. RNA was also extracted from ½ of the sEV-source cells using Qiagen RNeasy Mini kit according to manufacturer’s instructions including on-column DNase treatment.
cDNA from sEV RNA and cell RNA was prepared using NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (E6421), which utilizes poly-DT primed cDNA synthesis to enrich for poly-adenylated transcripts. Libraries were amplified with 15 cycles of PCR. Barcoded sequencing libraries were prepared using Illumina’s Nextera-XT DNA Library Preparation Kit (FC-131-1096) and IDT for Illumina Nextera DNA unique dual indexes (20027215).

value: Brain

value: Primary cell culture

value: neuron-derived sEVs


title: GMP_Control_Rep2


title: Lin_neg_CD11b_Tet2_Rep2


title: gRNA CRISPRi double perturbation rep3

description:
gRNA_Sp_D3
gRNA_barcodes.tsv.gz
gRNA_features.tsv.gz
gRNA_matrix.mtx.gz
D3_protospacer_calls_per_cell.csv

data_processing:
Demultiplexed scRNA- and sc gRNA-seq fastq files were inputted into the Cell Ranger Count pipeline (10x Genomics, version 5.0.0) to generate barcoded count matrices of RNA and gRNA data. gRNA expression was quantified using cellranger count (10x Genomics, version 5.0.0) by specifying gRNA sequences and corresponding genes in features.csv as a pipeline input file. For each sample, count matrices were loaded in R and analyzed in Seurat (version 2.3.4).
For sc gRNA-seq: gRNA labels for each cell were assigned based on cellranger feature calls. Only cells with 1 or 2 cellranger-detected gRNAs were retained for single gRNA and double gRNA captures, respectively. gRNA groups with < 250 cells with target gene detected or with low cell numbers (n < 20) were removed. Data was normalized and scaled using NormalizeData(... normalization.method = "RC", scale.factor = 100); RC means relative counts.
For scRNA-seq: cells were filtered: number of genes > 200, number of genes < 5500-8300, transcriptome UMIs < 27000-75000, percent mitochondrial reads < 10%, with exact parameters differing for each capture. Data was normalized and scaled using NormalizeData(... normalization.method = "LogNormalize", scale.factor = 10000).
Assembly: hg38
Supplementary files format and content: tsv and mtx files represent raw gene and gRNA counts for each barcode/cell in the file scRNA-seq and sc gRNA-seq dataset.
Supplementary files format and content: protospacer_calls_per_cell.csv files represent Cellranger count pipeline gRNA calls for each barcode/cell in the scRNA-seq and sc gRNA-seq dataset.
Supplementary files format and content: K562_cell_metadata.csv file represents meta data labels for cells post filtering
Supplementary files format and content: features.csv file represents the Cellranger count pipeline input file for gRNA calling
Library strategy: sc-gRNA-seq

extract_protocol:
Cells were sorted by FACS for live cells and for the cell populations expressing the constructs of interest.
Joint scRNA- and gRNA-seq libraries were prepared using the 10x Genomics Single Cell 5' Reagent Kit with Feature Barcode Technology. RNA libraries were constructed according to manufacturer's recommendations. For gRNA libraries, custom oligos complementary to the gRNAs were spiked into the reverse transcription reaction and gRNA library construction was performed using a custom PCR protocol following cDNA amplification.

value: lymphoblast cells from CML

value: expresses dCas9 and gRNA


title: Lin_neg_CD11b_Control_Rep2


title: mLN iNKT cells, aGC, female, WT FT, rep 2


title: GMP_Tet2_Rep2

value: GMP


title: gRNA CRISPRa double perturbation rep3

description:
gRNA_Sa_D3
gRNA_barcodes.tsv.gz
gRNA_features.tsv.gz
gRNA_matrix.mtx.gz
D3_protospacer_calls_per_cell.csv


title: Primary mouse neurons rep3

value: Neuron


title: Retina, Fos_P14_OIR_rep1

value: Retina

value: Oxygen-induced retinopathy


title: mLN iNKT cells, aGC, female, WT FT, rep 1

value: aGC


title: GMP_Control_Rep2

value: Control


title: gRNA CRISPRi double perturbation rep2

description:
gRNA_Sp_D2
gRNA_barcodes.tsv.gz
gRNA_features.tsv.gz
gRNA_matrix.mtx.gz
D2_protospacer_calls_per_cell.csv


title: Primary mouse neurons rep2


title: Primary mouse neuron-derived sEVs rep2


title: mLN iNKT cells, PBS, male, WT FT, rep 2


title: gRNA CRISPRa double perturbation rep2

description:
gRNA_Sa_D2
gRNA_barcodes.tsv.gz
gRNA_features.tsv.gz
gRNA_matrix.mtx.gz
D2_protospacer_calls_per_cell.csv


title: Primary mouse neuron-derived sEVs rep1


title: Lin_neg_CD11b_Tet2_Rep1

value: Tet2 KO


title: gRNA CRISPRi double perturbation rep1

description:
gRNA_Sp_D1
gRNA_barcodes.tsv.gz
gRNA_features.tsv.gz
gRNA_matrix.mtx.gz
D1_protospacer_calls_per_cell.csv


title: Lin_neg_CD11b_Control_Rep1


title: mLN iNKT cells, PBS, male, WT FT, rep 3

value: Mesenteric lymph nodes


title: gRNA CRISPRa double perturbations rep1

description:
gRNA_Sa_D1
gRNA_barcodes.tsv.gz
gRNA_features.tsv.gz
gRNA_matrix.mtx.gz
D1_protospacer_calls_per_cell.csv


title: Primary mouse neurons rep1


title: gRNA CRISPRi single perturbation S3

description:
gRNA_Sp_S3SaSp
gRNA_barcodes.tsv.gz
gRNA_features.tsv.gz
gRNA_matrix.mtx.gz
S3SaSp_protospacer_calls_per_cell.csv


title: GMP_Tet2_Rep1


title: mLN iNKT cells, aGC, female, WT FT, rep 3

value: iNKT cells


title: Primary mouse microglia-derived sEVs rep3

value: microglia-derived sEVs


title: mLN iNKT cells, PBS, male, WT FT, rep 1

value: WT FT


title: GMP_Control_Rep1


title: mLN iNKT cells, PBS, female, WT FT, rep 3

value: PBS


title: gRNA CRISPRa single perturbation S3

description:
gRNA_Sa_S3SaSp
gRNA_barcodes.tsv.gz
gRNA_features.tsv.gz
gRNA_matrix.mtx.gz
S3SaSp_protospacer_calls_per_cell.csv


title: mLN iNKT cells, PBS, female, WT FT, rep 2


title: Primary mouse microglia rep3

value: Brain

value: Microglia


title: Polyadenylated standards replicate 2

first: Heidi

last: Cook-Andersen

address: 2880 Torrey Pines Scenic Drive, Rm 4811

department: Department of Reproductive Medicine

institute: University of California, San Diego

data_processing:
Raw fast5 files were basecalled with Guppy (version 6.0.6) following parameters: --config dna_r9.4.1_450bps_hac.cfg --fast5_out --trim_strategy none --records_per_fastq 0 --device cuda:all:100% --recursive. and full length reads with all adapter sequences (from the CRTA, PCR primers, and sequencing adapter) were filtered by Pychopper (version 2.5.0) following parameters: -k PCS110. Only full-length reads with a minimum basecalling Q-value score of 9 and all adapter sequences were retained for further analysis. Reads were mapped to the GRCm38 mouse transcriptome with minimap (version 2.17) using the following parameters: -a -x map-ont. Reads per transcript were quantified with Salmon (version 0.14.1) using the following parameters: salmon quant -l A --noErrorModel. Read counts were normalized with ERCC standards by dividing read counts for each gene by the mean read count amongst ERCCs. Differential expression analysis was performed with DESeq2 (version 1.34.0).
Assembly: GRCm38
Supplementary files format and content: CountData.tsv file is a tab-delimited text file that contains normalized read counts exported from DESeq2 for each sample. Tail_lengths.tsv files contain measured poly(A) tail lengths for all genes or polyadenylated standards.

organism: synthetic construct

source_name: synthetic

growth_protocol: Mouse oocytes were isolated from C57B6J female mice. For GV oocytes, 4-week old females were stimulated by intraperitoneal injection of 5 IU pregnant mare serum gonadotropin (PMSG; Lee BioSolutions, 493-10), ovaries were harvested 48 hours after PMSG injection, and denuded oocytes collected after brief digestion with trypsin (Fisher Scientific, 25200056), collagenase (Sigma-Aldrich, C9407), and DNAse in M2 media (Sigma-Aldrich, M7167). For MII oocytes, mice were injected with 5 IU HCG (Sigma-Aldrich, C1063) 48 hours after PMSG induction and ovulated MII oocytes collected from the ampulla 15 hours post-HCG and cumulus cells by brief hyaluronidase (Sigma-Aldrich, H4272) digestion per standard protocol. Mouse embryos were isolated from B6D2F1/J female mice mated with C57B6J males of known fertility at the time of hCG injection. 1-cell, early 2-cell, and late 2-cell embryos were collected at 27-28, 30-32, and 46-48 hrs post-HCG.

extract_protocol:
For each stage and replicate, total RNA was isolated from ~400 oocytes or embryos with Trizol reagent (Fisher Scientific, 15-596-018), followed by ethanol precipitation and RNA Clean & Concentrator-5 kit (Zymo Research, R1014) as per manufacturer’s protocol. RNA was eluted in 7 ul nuclease-free water and used immediately for Nanopore PCR-cDNA sequencing library prep. cDNA standards with the following sequences were obtained from IDT:  pA_cDNA_standard_10: CTTGCCTGTCGCTCTATCTTCTTTTTTTTTTACCAACGGCGACGAATAGTAGTTTACTTCCTCCCTGCGGGCCCCTCCTGAAGTGCCACCTATACGGCTTGTTGAAGCCGATTAGTACAATAGATTTATTCAACCCCAAAGGTCTACACTCCCGGCTTACTCTTAGCTGATATGTCGCGCAATATCAGCACCAACAGAAA  pA_cDNA_standard_40: CTTGCCTGTCGCTCTATCTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCGGCAAAGAGACAATTATAGCGGCTAGGAACGCAACTAGTTATAACGAACGGCCTCGAATAGTAGAAAATATCCCTCCTCCGGGCACCTCCTGAAATGCCACATATTCGGGTTATTGGCAATATCAGCACCAACAGAAA  pA_cDNA_standard_50: CTTGCCTGTCGCTCTATCTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAGAGAGCCAGCAACAATTGCAAATGTCAGATCAAAGTAATATTAGCAAACAATAAGTCCCTAACTAGTTGTGACCTTTTGTAAAGTGAATTTCATTATATATGCTGTGCAATATCAGCACCAACAGAAA   pA_cDNA_standard_70 :  CTTGCCTGTCGCTCTATCTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGCAACGGGGAGCCGAGATTATTGAGTGATCACCAGTAGCTGTACTATTATATAAGCTATTAAAGATTGATCAAAGTAAACATACCGCGCAATATCAGCACCAACAGAAA  pA_cDNA_standard_100: CTTGCCTGTCGCTCTATCTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCCCAAGCGAAAACGGGTGCGTGGACTAGCGAGGAGCAAACGAAAATTCTTGGCCTGCGCAATATCAGCACCAACAGAAA  pA_cDNA_standard_130: CTTGCCTGTCGCTCTATCTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAGGAGGCAATTCTATAAGAATGCATACGCAATATCAGCACCAACAGAAA   pA_cDNA_standard_150: CTTGCCTGTCGCTCTATCTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCGAGCACGCAATATCAGCACCAACAGAAA
Approximately 400 oocytes or embryos per biological replicate per stage were used per sequencing run. An identical amount of ERCC spike-in standards51 per cell was added to samples at the beginning of RNA extraction. Nanopore PCR-cDNA sequencing (PCS) was performed with an early access cDNA-PCR Sequencing Kit (PCS-110) as per manufacturer’s protocol (Fig. S1A). This kit is most similar to the currently available cDNA-PCR Sequencing Kit (PCS-111). Briefly, ligation of Nanopore’s proprietary cDNA-RT adapter (CRTA) to the 3’ end of polyadenylated mRNAs enriched for transcripts with a minimum polyA tail length of 10 nt. Following enzymatic digestion of the adapter, RT with strand switching was performed, followed by selection of full-length transcripts by PCR amplification for 18 cycles. Sequencing adapters are then attached, followed by loading of the library onto a R9.4.1 flow cell (FLO-MIN106D) and sequenced in a Minion sequencing device with Minknow software (version 22.05.5). Libraries comprised of polyadenylated cDNA standards were prepared by PCR amplification using the following barcoded PCR primers from the Nanopore PCR-cDNA Barcoding Kit (SQK-PCB109), followed by attachment of sequencing adapters from the PCS-110 kit and sequencing on the Minion as per the PCS-110 protocol: pA_cDNA_standard_10: BC01, pA_cDNA_standard_40: BC02, pA_cDNA_standard_50: BC03, pA_cDNA_standard_70: BC04, pA_cDNA_standard_100: BC05, pA_cDNA_standard_130: BC06, and pA_cDNA_standard_150: BC07.

value: synthetic


title: gRNA CRISPRi single perturbation S2

description:
gRNA_Sp_S2Sp
gRNA_barcodes.tsv.gz
gRNA_features.tsv.gz
gRNA_matrix.mtx.gz
S2Sp_protospacer_calls_per_cell.csv

value: lymphoblast cells from CML


title: Primary mouse microglia-derived sEVs rep2

value: Primary cell culture


title: mLN iNKT cells, PBS, female, WT FT, rep 1


title: gRNA CRISPRa single perturbation S1

description:
gRNA_Sa_S1Sa
gRNA_barcodes.tsv.gz
gRNA_features.tsv.gz
gRNA_matrix.mtx.gz
S1Sa_protospacer_calls_per_cell.csv

value: expresses dCas9 and gRNA


title: Polyadenylated standards replicate 1


title: SZ6  kidneys

city: Beijing

first: Jiawei

last: Song

state: China

address: 1 Xiannongtan Street

department: Institute of Materia Medica

institute: Peking Union Medical College

description:
SZ6
SZ-A treated CKD rats

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome using hisat2 v2.0.5.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell, Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: https://ftp.ensembl.org/pub/release-108/fasta/rattus_norvegicus/dna/Rattus_norvegicus.mRatBN7.2.dna.toplevel.fa.gz , https://ftp.ensembl.org/pub/release-108/gtf/rattus_norvegicus/Rattus_norvegicus.mRatBN7.2.108.gtf.gz
Supplementary files format and content: Tab-delimited text file includes FPKM values for each Sample.

organism: Rattus norvegicus

source_name: kidneys

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: kidneys

value: adenine 100mg/kg*day + SZ-A 300 mg/kg*day


title: scRNA double perturbation rep3

first: Howard

last: Chang

address: CCSR 2130, 269 Campus Drive

institute: Stanford University

description:
scRNA_D3
RNA_barcodes.tsv.gz
RNA_features.tsv.gz
RNA_matrix.mtx.gz

data_processing:
Demultiplexed scRNA- and sc gRNA-seq fastq files were inputted into the Cell Ranger Count pipeline (10x Genomics, version 5.0.0) to generate barcoded count matrices of RNA and gRNA data. gRNA expression was quantified using cellranger count (10x Genomics, version 5.0.0) by specifying gRNA sequences and corresponding genes in features.csv as a pipeline input file. For each sample, count matrices were loaded in R and analyzed in Seurat (version 2.3.4).
For sc gRNA-seq: gRNA labels for each cell were assigned based on cellranger feature calls. Only cells with 1 or 2 cellranger-detected gRNAs were retained for single gRNA and double gRNA captures, respectively. gRNA groups with < 250 cells with target gene detected or with low cell numbers (n < 20) were removed. Data was normalized and scaled using NormalizeData(... normalization.method = "RC", scale.factor = 100); RC means relative counts.
For scRNA-seq: cells were filtered: number of genes > 200, number of genes < 5500-8300, transcriptome UMIs < 27000-75000, percent mitochondrial reads < 10%, with exact parameters differing for each capture. Data was normalized and scaled using NormalizeData(... normalization.method = "LogNormalize", scale.factor = 10000).
Assembly: hg38
Supplementary files format and content: tsv and mtx files represent raw gene and gRNA counts for each barcode/cell in the file scRNA-seq and sc gRNA-seq dataset.
Supplementary files format and content: protospacer_calls_per_cell.csv files represent Cellranger count pipeline gRNA calls for each barcode/cell in the scRNA-seq and sc gRNA-seq dataset.
Supplementary files format and content: K562_cell_metadata.csv file represents meta data labels for cells post filtering
Supplementary files format and content: features.csv file represents the Cellranger count pipeline input file for gRNA calling


title: Primary mouse microglia-derived sEVs rep1


title: Primary mouse microglia rep2


title: Primary mouse microglia rep1


title: scRNA double perturbation rep1

description:
scRNA_D1
RNA_barcodes.tsv.gz
RNA_features.tsv.gz
RNA_matrix.mtx.gz


title: SZ3  kidneys

description:
SZ3
SZ-A treated CKD rats


title: Primary mouse astrocyte-derived sEVs rep3

value: astrocyte-derived sEVs


title: scRNA double perturbation rep2

description:
scRNA_D2
RNA_barcodes.tsv.gz
RNA_features.tsv.gz
RNA_matrix.mtx.gz


title: SZ4  kidneys

description:
SZ4
SZ-A treated CKD rats


title: SZ2  kidneys

description:
SZ2
SZ-A treated CKD rats


title: scRNA CRISPRi single perturbation S2

description:
scRNA_S2Sp
RNA_barcodes.tsv.gz
RNA_features.tsv.gz
RNA_matrix.mtx.gz


title: DU145_shNC_1

city: Zhuhai

first: Feng

last: Shu

state: State...

address: No.52, Meihua East Road, Xiangzhou District, Zhuhai

institute: Sun Yat-sen University

data_processing:
Sequnce reads were trimmed for adaptor sequence/low-quality sequence using the software Trimmomatic. Trimmed sequence reads were mapped to reference genomics using the software hisat2. Gene FPKM value was quantified using cufflinks.
Assembly: hg38
Supplementary files format and content: FPKM value was included for each sample.

extract_protocol:
RNA was harvested using mirVana™ miRNA ISOlation Kit，Ambion-156. 4 ug of total RNA was used for mRNA purification, fragment and the construction of squencing libraries.
RNA libraries were prepared according to the protocols from the oebiotech company (Shanghai).

value: cell line

value: prostate cancer


title: DU145_shNFIB_1


title: DU145_shNFIB_2


title: DU145_shNC_2


title: Primary mouse astrocytes rep3

value: Astrocyte


title: hTau_30_male_body

city: Houston

first: Hongjie

last: Li

state: TX

address: One Baylor Plaza

department: Huffington Center on Aging

institute: Baylor College of Medicine

description:
10x Genomics
adata_adfca_body_v1.0.h5ad.gz

data_processing:
Raw snRNA-seq data, in the form of FASTQ files, underwent alignment to the Drosophila melanogaster reference genome (FlyBase release 6.31) using the Cell Ranger software (v6.1.2), employing a pre-mRNA gene transfer format (GTF) file generated by the FCA algorithm (Li et al., 2022). Subsequent steps involved the removal of ambient RNA contamination via CellBender (Fleming et al., 2023) and the identification and exclusion of potential doublet cells using scDblFinder (Germain et al., 2022). Quality control criteria necessitated the elimination of cells exhibiting fewer than 200 genes or 500 UMIs. Genes detected in fewer than three nuclei were removed from our analysis. Furthermore, cells with gene or UMI counts exceeding five median absolute deviations from the median were also excluded from analysis. Additionally, cells harboring over 5% of mitochondrial transcripts were eliminated.  The majority of the snRNA-seq data analysis was conducted using the Scanpy package (v1.8.2) (Wolf et al., 2018).
Assembly: FlyBase release 6.31
Supplementary files format and content: H5ad files containing all cell-type annotations were generated using Scanpy. Matrix files were generated using Cell Ranger count.

organism: Drosophila melanogaster

source_name: body

extract_protocol:
Single-nucleus  suspensions  were  prepared  following  the  protocol  we described previously (McLaughlin et al., 2022). Next, we used the BD AriaIII FACS sorter for collecting nuclei. Nuclei were stained by Hoechst-33342 on ice (1:1000; >5min). Hoechst+ nuclei were collected during sorting. Since polyploidy is common for many tissue types in Drosophila, we observed different populations of nuclei according to DNA content (Hoechst signal). In order to include all cell populations with different nuclear sizes, we included  all  nuclear  populations  from  the  FACS  in  samples  for  single-nucleus  RNA sequencing. Individual nuclei were collected into one 1.5ml RNAase free Eppendorf tube with 200µl 1x PBS with 0.5% BSA as the receiving buffer (RNase inhibitor added). For each 10x Genomics run, 200k nuclei were collected. Nuclei were spun down for 10 min at 950g at 4 ̊C, and then resuspended using 80µl or desired amount of 1x PBS with 0.5% BSA (RNase inhibitor added). 2µl of nucleus suspension was used for counting the nuclei with hemocytometers to calculate the concentration. We loaded 50-60K nuclei to the 10x controller to target >20k nuclei for each channel.
We performed snRNA-seq using the 10x Genomics platform with the Chromium Next GEM Single Cell 3' HT(high-throughput) Reagent Kits v3.1 (Dual Index) with following settings. All PCR reactions were performed using the BioRad C1000 Touch Thermal cycler with 96-Deep Well Reaction Module. The recommended cycle numbers from 10x protocol were used for cDNA amplification and sample index PCR. As per 10x protocol, 1:10 dilutions of amplified cDNA and final libraries were evaluated on a bioanalyzer. The final library was sent to Novogene Corporation Inc. for Illumina NovaSeq PE150 S4 lane sequencing with the dual index configuration Read 1 28 cycles, Index 1 (i7) 10 cycles, Index 2 (i5) 10 cycles and Read 2 90 cycles. A PhiX control library was spiked in at 0.2 to 1% concentration. The sequencing depth is about 30-40K reads per nucleus.
snRNA-seq

value: body

tag: Sex

value: male

value: hTau


title: SZ5  kidneys

description:
SZ5
SZ-A treated CKD rats


title: scRNA CRISPRa single perturbation S1

city: Stanford

description:
scRNA_S1Sa
RNA_barcodes.tsv.gz
RNA_features.tsv.gz
RNA_matrix.mtx.gz


title: hTau_30_male_head

description:
10x Genomics
adata_adfca_head_v1.0.h5ad.gz

source_name: head

value: head


title: hTau_20_male_body


title: Primary mouse astrocytes rep2


title: CKD6  kidneys

description:
CKD6
CKD model

value: adenine 100mg/kg*day


title: scRNA CRISPRa or CRISPRi single perturbation S3

description:
scRNA_S3SaSp
RNA_barcodes.tsv.gz
RNA_features.tsv.gz
RNA_matrix.mtx.gz


title: SZ1  kidneys

description:
SZ1
SZ-A treated CKD rats


title: Primary mouse astrocyte-derived sEVs rep1

value: Brain


title: hTau_20_male_head


title: Primary mouse astrocyte-derived sEVs rep2


title: CKD5  kidneys

description:
CKD5
CKD model


title: hTau_30_female_body

value: female


title: Primary mouse astrocytes rep1


title: hTau_20_female_body


title: CKD4  kidneys

description:
CKD4
CKD model


title: CKD3  kidneys

description:
CKD3
CKD model


title: CKD2  kidneys

description:
CKD2
CKD model


title: Wildtype mouse, age P14, hyperoxia, replicate 2

city: San Francisco

first: Vincent

last: Auyeung

department: Medicine

institute: University of California, San Francisco

description: 10x Genomics

data_processing:
Demultiplexing, barcode processing, gene counting and aggregation were made using the 10x Genomics Cloud Analysis with Cell Ranger software (https://www.10xgenomics.com/products/cloud-analysis)
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix

source_name: lung

extract_protocol:
Mouse lungs were harvested after perfusion through the right ventricle with PBS. After mincing with razor blades, tissues were suspended in protease solution [0.25 % Collagenase A, 1 U/ml Dispase II, 2000 U/ml Dnase I in DMEM containing 10 mM HEPES and 2% FBS. The suspension was incubated at 37°C for 25 min with trituration by glass Pasteur pipette every 8 minutes. The digestion was then quenched for 5 minutes in ice-cold PBS containing 5% FBS and 2 mM EDTA, and cells were passed through a 100 μm cell strainer. Cells were pelleted and resuspended in RBC lysis buffer for 5 minutes. RBC lysis was quenched with 5% FBS/PBS and cells were passed through a 70 μm cell strainer, washed, and resuspended in 5% FBS/PBS containing antibodies for FACS purification. Approximately 100k CD45+ cells, 100k CD31+ cells, and 1x10e6 CD45-/CD31- cells were sorted for each sample and collected in 10% FBS/PBS.
Sorted cells were then counted and labeled with oligonucleotide tags for multiplexing using 10x Genomics 3’ CellPlex Kit Set A. All 8 biologic samples for P7 timepoint were pooled and 60,000 cells / lane were loaded onto 2 lanes of a Chromium Next GEM Chip (10x Genomics). The same workflow was used for P14 samples with all 8 P14 biologic samples pooled together and loaded onto 2 lanes as well. Each lane therefore represents a technical replicate for each biologic sample. Chromium Single Cell 3’ v3.1 (10x Genomics) reagents were used for library preparation according to the manufacturer’s protocol. The libraries were sequenced on an Illumina NovaSeq 6000 S4 flow cell.

treatment_protocol: Wildtype (Tgfbr2 flox/flox) or KO (Nkx2.1-cre;Tgfbr2 flox/flox) littermate mice were maintained in either normoxia (RA) or hyperoxia (75% O2) from birth (P0) until P10, after which they were recovered in normoxia until harvest. Nursing dams were rotated every 48 hours for maternal health and to maintain adequate nutrition for neonatal mice. Pups were euthanized to harvest both lungs on either P7 or 14.

value: lung

value: Tgfbr2 flox/flox (WT)

value: Hyperoxia (O2)

tag: biological replicate


title: CKD1  kidneys

description:
CKD1
CKD model


title: hTau_20_female_head


title: Tgfbr2 knockout mouse, age P14, hyperoxia, replicate 2

description: 10x Genomics

value: Nkx2.1-cre;Tgfbr2 flox/flox (KO)


title: AB42_20_male_body


title: Tgfbr2 knockout mouse, age P14, hyperoxia, replicate 1

description: 10x Genomics


title: NC6  kidneys

description:
NC6
CTRL

value: kidneys


title: Tgfbr2 knockout mouse, age P14, normoxia, replicate 2

description: 10x Genomics

value: Normoxia (RA)


title: NC5  kidneys

description:
NC5
CTRL


title: AB42_10_male_body


title: AB42_20_male_head


title: Tgfbr2 knockout mouse, age P14, normoxia, replicate 1

description: 10x Genomics


title: NC4  kidneys

description:
NC4
CTRL


title: AB42_10_male_head


title: NC3  kidneys

description:
NC3
CTRL


title: hTau_30_female_head


title: Wildtype mouse, age P14, hyperoxia, replicate 1

description: 10x Genomics


title: AB42_20_female_body


title: Wildtype mouse, age P14, normoxia, replicate 1

description: 10x Genomics


title: NC2  kidneys

description:
NC2
CTRL


title: Tgfbr2 knockout mouse, age P7, hyperoxia, replicate 2

description: 10x Genomics


title: AB42_20_female_head


title: MF_2

city: Berlin

first: Dipthi

last: Bachamanda Somesh

address: Robert-Rössle Str. 10

country: Germany

institute: Berlin heals

data_processing:
HiSeq Control Software 2.2.58, Base-calling: RTA 1.18.64.0.
High-quality sequence reads, and the known gene models were aligned to the reference genome using STAR (Spliced Transcripts Alignment to a Reference).
Reads were aligned to the rn6 genome. Counts per gene were calculated as the sum of all mapped reads within a gene region. Raw counts of protein-coding genes were normalized and variance stabilizing transformed using DESeq2 (1.28.1) in R (A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/; 4.0.2).
Assembly: rn6
Supplementary files format and content: gene_count_matrix.csv, normalized_data.txt, raw_counts.txt, vst_data.txt

source_name: Cardiac cell

growth_protocol: CFs were plated into gelatin-coated vessels and cultured in high glucose Dulbecco's modified eagle medium (DMEM) supplemented with 10 % fetal bovine serum (FBS) and 1 % penicillin/streptomycin (P/S, standard medium) at 37 °C and 5 % CO2 in a humified incubator.

extract_protocol:
Total RNA was isolated using the Qiagen RNeasy Mini Kit. Genomic DNA was removed with DNAse I.
For RNA sequencing data analysis, raw sequencing data were processed using fastp software to remove poor quality bases and generate clean data for downstream analysis by performing adapter trimming, quality filtering, and per-read quality pruning. High-quality sequence reads, and the known gene models were aligned to the reference genome using STAR (Spliced Transcripts Alignment to a Reference). 150 bp paired reads were generated from each sequencing library on the NovaSeq sequencing platform.

treatment_protocol: CFs were differentiated to Myofibroblasts (MFs) by continuous passaging with low serum medium. The differentiated myofibroblasts were subjected to 1 and 2μA direct current for 72 h, and maintained in standard medium, composed of high glucose DMEM supplemented with 10 % FBS and 1 % P/S. After microcurrent treatment  RNA isolation and RNA sequencing was performed.

value: myofibroblast cells

value: cardiac fibroblasts differentiated to Myofibroblasts


title: Tgfbr2 knockout mouse, age P7, hyperoxia, replicate 1

description: 10x Genomics


title: Wildtype mouse, age P14, normoxia, replicate 2

description: 10x Genomics


title: MF_1


title: Wildtype mouse, age P7, hyperoxia, replicate 2

description: 10x Genomics


title: AB42_10_female_body


title: Wildtype mouse, age P7, hyperoxia, replicate 1

description: 10x Genomics


title: NC1 kidneys

description:
NC1
CTRL


title: control_30_male_body

value: control


title: control_20_male_body


title: CF_2

value: neonatal cardiac fibroblasts


title: Tgfbr2 knockout mouse, age P7, normoxia, replicate 2

description: 10x Genomics


title: CF_1


title: Tgfbr2 knockout mouse, age P7, normoxia, replicate 1

description: 10x Genomics


title: AB42_10_female_head


title: MF +2μA_2

value: treatment of myofibroblast cells with 2μA microcurrent


title: MF +2μA_1


title: control_30_male_head

value: male


title: control_10_male_body

value: body


title: Wildtype mouse, age P7, normoxia, replicate 2

description: 10x Genomics


title: MF +1μA_2

value: treatment of myofibroblast cells with 1μA microcurrent


title: Wildtype mouse, age P7, normoxia, replicate 1

description: 10x Genomics


title: Uterus from AMS_P3

city: Suzhou

first: zhixing

last: jin

address: 889 Pinghai Road

institute: Soochow University Affiliated No 1 People\'s Hospital: First Affiliated Hospital of Soochow University

data_processing:
High quality reads were mapped to the mouse reference genome using HISAT2 (https://ccb.jhu.edu/software/hisat2/index.shtml). Gene expression levels were estimated as fragments per kilobase of transcript per million mapped reads. FPKM  of each gene was calculated and the read counts of each gene were obtained by HTSeq-count . PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples. Differential expression analysis was performed using the DESeq2 . Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include FPKM values and Counts for all Sample

source_name: Uterus

extract_protocol:
Total RNA was extracted using the TRIzol reagent  (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and RNA samples with RIN >7.0 were subjected to further processing.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: Uterus

value: tamoxifen+primidone

value: 13 week


title: control_10_male_head

value: head


title: control_20_male_head


title: MF +1μA_1


title: Uterus from AMS_P2

value: female


title: control_20_female_body


title: Uterus from AMS_P1


title: control_10_female_body


title: Uterus from AMS3

value: tamoxifen+vesicle


title: control_30_female_head


title: Uterus from AMS2


title: control_20_female_head


title: Uterus from AMS1


title: control_30_female_body


title: control_10_female_head


title: Uterus from Control 3

value: vesicle


title: L2 oocyte replicate 2

description: processed data file header: L2_r1

data_processing:
Raw fast5 files were basecalled with Guppy (version 6.0.6) following parameters: --config dna_r9.4.1_450bps_hac.cfg --fast5_out --trim_strategy none --records_per_fastq 0 --device cuda:all:100% --recursive. and full length reads with all adapter sequences (from the CRTA, PCR primers, and sequencing adapter) were filtered by Pychopper (version 2.5.0) following parameters: -k PCS110. Only full-length reads with a minimum basecalling Q-value score of 9 and all adapter sequences were retained for further analysis. Reads were mapped to the GRCm38 mouse transcriptome with minimap (version 2.17) using the following parameters: -a -x map-ont. Reads per transcript were quantified with Salmon (version 0.14.1) using the following parameters: salmon quant -l A --noErrorModel. Read counts were normalized with ERCC standards by dividing read counts for each gene by the mean read count amongst ERCCs. Differential expression analysis was performed with DESeq2 (version 1.34.0).
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text file includes normalized read counts exported from DESeq2 for each sample.

source_name: L2 oocyte

extract_protocol:
For each stage and replicate, total RNA was isolated from ~400 oocytes or embryos with Trizol reagent (Fisher Scientific, 15-596-018), followed by ethanol precipitation and RNA Clean & Concentrator-5 kit (Zymo Research, R1014) as per manufacturer’s protocol. RNA was eluted in 7 ul nuclease-free water and used immediately for Nanopore PCR-cDNA sequencing library prep.
Approximately 400 oocytes or embryos per biological replicate per stage were used per sequencing run. An identical amount of ERCC spike-in standards51 per cell was added to samples at the beginning of RNA extraction. Nanopore PCR-cDNA sequencing (PCS) was performed with an early access cDNA-PCR Sequencing Kit (PCS-110) as per manufacturer’s protocol (Fig. S1A). This kit is most similar to the currently available cDNA-PCR Sequencing Kit (PCS-111). Briefly, ligation of Nanopore’s proprietary cDNA-RT adapter (CRTA) to the 3’ end of polyadenylated mRNAs enriched for transcripts with a minimum polyA tail length of 10 nt. Following enzymatic digestion of the adapter, RT with strand switching was performed, followed by selection of full-length transcripts by PCR amplification for 18 cycles. Sequencing adapters are then attached, followed by loading of the library onto a R9.4.1 flow cell (FLO-MIN106D) and sequenced in a Minion sequencing device with Minknow software (version 22.05.5). Libraries comprised of polyadenylated cDNA standards were prepared by PCR amplification using the following barcoded PCR primers from the Nanopore PCR-cDNA Barcoding Kit (SQK-PCB109), followed by attachment of sequencing adapters from the PCS-110 kit and sequencing on the Minion as per the PCS-110 protocol: pA_cDNA_standard_10: BC01, pA_cDNA_standard_40: BC02, pA_cDNA_standard_50: BC03, pA_cDNA_standard_70: BC04, pA_cDNA_standard_100: BC05, pA_cDNA_standard_130: BC06, and pA_cDNA_standard_150: BC07.

value: L2 oocyte


title: Uterus from Control 2


title: L2 oocyte replicate 1

description: processed data file header: L2_r1


title: E2 oocyte replicate 2

description: processed data file header: E2_r1

source_name: E2 oocyte

value: E2 oocyte


title: Uterus from Control 1


title: Tumor DNA from adamantinomatous craniopharyngioma Tumor 013

type: genomic

city: Ribeirão Preto

first: Junier

middle: Marrero

last: Gutiérrez

state: São Paulo

address: Av Bandeirantes, 3900

department: Pediatric

country: Brazil

institute: Ribeirão Preto Medical School-University of São Paulo

hyb_protocol: Standard Illumina protocol

scan_protocol: Raw methylation data were obtained using the Illumina iScan system (RRID:SCR_016388) according to Illumina protocol.

data_processing: Minfi software program in R computing language (RRID:SCR_012830)

label: Cy5 and Cy3

source_name: Adamantinomatous craniopharyngioma

label_protocol: Standard Illumina protocol

extract_protocol: DNA from microdissected, fresh frozen tumor samples was extracted using the QIAamp DNA Mini Kit (QIAGEN, Hilden, Germany) according to the manufacturer's instruction. DNA quantification was performed by fluorometry using the Qubit dsDNA BR Assay (Thermo Fisher Scientific, Waltham, MA), and the integrity was assessed by electrophoresis using the Tape Station 4200 System (Agilent, Santa Clara, CA). DNA integrity number (DIN) ≥ 6 was considered adequate.

tag: sexo

value: Male

tag: age at diagnosis(years)

value: not available

tag: hypothalamic invasion

value: type 2

tag: tumor ctnnb1 mutation

value: Yes


title: Tumor DNA from adamantinomatous craniopharyngioma Tumor 002

value: type 1


title: Tumor DNA from adamantinomatous craniopharyngioma Tumor 006


title: NF1-MET;sgP53 cells, Capmatinib, rep 2

city: Grand Rapids

first: Matthew

last: Steensma

state: MI

address: 333 Bostwick Ave NE

institute: Van Andel Institute

data_processing:
Base calling was done by Illumina RTA3 and output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0.
Sequencing adapters were trimmed using Trimgalore v0.4.2 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Bases with a quality score less than 20 were also removed from the ends of reads.
Trimmed data were quality controlled with FastQC v0.11.7 and then mapped with STAR v2.5.2b to the mm10 genome using the default settings.
Raw gene counts (minimum of 30M counts per sample and a mean of 34.92) were generated by STAR.
Assembly: mm10
Supplementary files format and content: txt; raw gene counts with ensemble ID and gene symbol

growth_protocol: NF1-MET and NF1-MET;sgP53 cells were cultured at  37 °C in a humidified atmosphere in 5% CO2 in low pH DMEM supplemented with 10% FBS and 1% Penicillin Streptomycin

extract_protocol:
RNA was isolated using RNeasy Mini Kit and RNase-Free DNase set (Qiagen) following the manufactures protocol.
RNA libraries for RNA-seq were prepared from 500 ng of total RNA using the KAPA mRNA Hyperprep kit (v4.17)

treatment_protocol: Cells were plated in a 6-well plate, grown in 10% FBS overnight, and then treated in duplicate with 100 nM capmatinib or DMSO for 24 hours.

value: MPNST

value: Trp53 KO

value: Capmatinib

value: biol rep 2


title: Tumor DNA from adamantinomatous craniopharyngioma Tumor 030

value: Female


title: Tumor DNA from adamantinomatous craniopharyngioma Tumor 031


title: Tumor DNA from adamantinomatous craniopharyngioma Tumor 003

value: type 0


title: E2 oocyte replicate 1

description: processed data file header: E2_r1


title: NF1-MET;sgP53 cells, Capmatinib, rep 1

value: biol rep 1


title: Tumor DNA from adamantinomatous craniopharyngioma Tumor 033


title: ZY oocyte replicate 2

description: processed data file header: ZY_r1

source_name: ZY oocyte

value: ZY oocyte


title: Tumor DNA from adamantinomatous craniopharyngioma Tumor 007


title: NF1-MET;sgP53 cells, Vehicle, rep 2

value: DMSO


title: Tumor DNA from adamantinomatous craniopharyngioma Tumor 025


title: Tumor DNA from adamantinomatous craniopharyngioma Tumor 022


title: Tumor DNA from adamantinomatous craniopharyngioma Tumor 021


title: ZY oocyte replicate 1

description: processed data file header: ZY_r1


title: Tumor DNA from adamantinomatous craniopharyngioma Tumor 020


title: Tumor DNA from adamantinomatous craniopharyngioma Tumor 029


title: MII oocyte replicate 2

description: processed data file header: MII_r1

source_name: MII oocyte

value: MII oocyte


title: NF1-MET;sgP53 cells, Vehicle, rep 1


title: NF1-MET cells, Capmatinib, rep 2

value: WT


title: Tumor DNA from adamantinomatous craniopharyngioma Tumor 005


title: HFD_KO_2

city: Tainan

first: Siao Muk

last: Cheng

address: No. 367, Sheng-Li Rd., North District

country: Taiwan

institute: National Institutes of Cancer Research

data_processing:
CLC genomic workbench 20.0.4 (CLC Bio)
Sequence reads were trimmed for adaptor sequence/low quality sequence using CLC genomic workbench
Trimmed sequence reads were mapped to Grcm39/mm10 using CLC genomic workbench
Read cound extraction and normalization were performed using CLC genomic workbench
Assembly: mm10
Supplementary files format and content: text file includes raw counts for each sample
Supplementary files format and content: text file includes RPKM/TPM/CPM for each sample

source_name: liver

growth_protocol: mice were housed (4–5 per cage) in a temperature- (temperature: 25 ± 2 °C; humidity: around 60-80%) and light-control environment under a 12:12 h light-dark cycle (lights on at 6:00 AM)

extract_protocol:
TRIzol reagent (Invitrogen)
cDNA libraries were prepared based on the MGIEasy RNA Directional Library Prep Kit Guide (MGI Tech, Cat. 1000006385).

treatment_protocol: High fat diet feeding

value: liver

value: liver cells

value: ADAR2 KO

value: high fat diet for 12 week


title: Tumor DNA from adamantinomatous craniopharyngioma Tumor 014

value: No


title: NF1-MET cells, Capmatinib, rep 1


title: HFD_KO_1


title: GV oocyte replicate 2

city: La Jolla

description: processed data file header: GV_r1

source_name: GV oocyte

value: GV oocyte


title: HFD_WT_2


title: Tumor DNA from adamantinomatous craniopharyngioma Tumor 008

value: Male

value: not available

value: Yes


title: NF1-MET cells, Vehicle, rep 2

value: MPNST

value: biol rep 2


title: Tumor DNA from adamantinomatous craniopharyngioma Tumor 017

value: Female

value: type 2


title: Tumor DNA from adamantinomatous craniopharyngioma Tumor 026


title: Tumor DNA from adamantinomatous craniopharyngioma Tumor 011


title: GV oocyte replicate 1

description: processed data file header: GV_r1


title: NF1-MET cells, Vehicle, rep 1

value: biol rep 1


title: Tumor DNA from adamantinomatous craniopharyngioma Tumor 004


title: Tumor DNA from adamantinomatous craniopharyngioma Tumor 009

value: type 0


title: Tumor DNA from adamantinomatous craniopharyngioma Tumor 018


title: Tumor DNA from adamantinomatous craniopharyngioma Tumor 010


title: RNA_JK05_4hrauxin_L3_rep1 [HW16]

status: Public on Mar 13 2024

city: New York

first: Jun

last: Kim

address: 100 Washington Square East 1009 Silver Center

department: Biology

institute: NYU

description: DEseq2FC_4hrauxin_smc3depl_over_CA1200.tab

data_processing:
Single-end read RNA-seq data was mapped to WS220 C. elegans genome using HISAT2 version 2.2.1 (Kim et al., 2019) with the parameter --rna-strandness R. The SAM output from HISAT2 and WS220 gtf file were used to calculate counts per gene using HTSeq version 0.13.5 (Anders et al., 2015). The raw counts were normalized FPKM using cufflinks version 2.2.1 (Roberts et al., 2011), and then FPKM was converted to TPM. For comparing between conditions, the raw counts were used for the R package DESeq2 version 1.30.0 (Love et al., 2014).
Assembly: WS220
Supplementary files format and content: tab file contains Deseq normalized counts data for each replicates and log2fc for treatment vs control

organism: Caenorhabditis elegans

source_name: whole worms

growth_protocol: Mixed developmental stage embryos were obtained by bleaching gravid adults. To isolate synchronized L2/L3 worms, gravid adults were bleached and embryos were hatched overnight in M9 buffer. The resulting starved L1s were grown for 24 hours at 22°C. L3 worms were kept on plates with or without auxin prior to collection.

extract_protocol:
L3 larvae were collected and stored in Trizol (Invitrogen) at -70C. Total RNA were extracted through freeze-crack method. RNA was cleaned up using Qiagen RNeasy MinElute Cleanup kit. mRNAs were purified using Sera-Mag Oligo (dT) beads (Thermo Scientific), then fragmented using Ambion (AM8740), and cleaned using Qiagen RNAeasy minElute kit. RNA was reverse transcribed using Superscript III system (Invitrogen, 18080-051). Residual dNTP was removed using ethanol precipitation. The second strand was synthesized using DNA polymerase I (Invitrogen). dsDNA was purified using Qiagen DNA minElute kit.
30 ng of input DNA were ligated to Illumina TruSeq adapters and amplified by PCR. Library DNA between 250 and 600 bp was gel purified.

treatment_protocol: collected worms were treated with auxin using NGM media containing 1 mM auxin. The worms were left on NGM plate to crawl around for an hour.

value: whole worms

tag: development stage

value: 4hr auxin

tag: chip antibody


title: Tumor DNA from adamantinomatous craniopharyngioma Tumor 012


title: RNA_JK06_4hrauxin_L3_rep2 [HW19]

description: DEseq2FC_4hrauxin_wapldepl_over_CA1200.tab

tag: strain


title: RNA_CA1200_4hrauxin_L3_rep2 [HW15]

description:
DEseq2FC_4hrauxin_smc3depl_over_CA1200.tab
DEseq2FC_4hrauxin_wapldepl_over_CA1200.tab


title: RNA_JK06_4hrauxin_L3_rep1 [HW18]


title: RNA_CA1200_4hrauxin_L3_rep1 [HW14]


title: Tumor DNA from adamantinomatous craniopharyngioma Tumor 035


title: MII oocyte replicate 1

description: processed data file header: MII_r1

value: MII oocyte


title: input_JK06_1hrauxin_L3_rep4 [HW45]

description:
DEseq2FC_4hrauxin_wapldepl_over_CA1200.tab
PQN85_JK06_1hrauxin_inputsubt_avg.bw
PQN85_JK06_1hrauxin_avg_chip_peaks.bed
PQN85_JK06_1hrauxin_avg_chip_summits.bed

data_processing:
Bowtie2 version 2.4.2 was used to align 75 bp single-end reads to WS220 with default parameters. Bam sorting and indexing was performed using samtools version 1.11. BamCompare tool in Deeptools version 3.5.0 was used to normalize for the sequencing depth using CPM and create ChIP-Input coverage with a bin size of 10 bp and 200 bp read extension. Only reads with a minimum mapping quality of 20 were used, and mitochondrial DNA, PCR duplicates, and blacklisted regions were removed. The average coverage data was generated by averaging ChIP-Input enrichment scores per 10 bp bins across the genome.  ChIP-seq peaks are identified using MACS2 version 2.1.1 (https://github.com/macs3-project/MACS). Peaks are called using both the individual replicates and combined bam files with minimum false discovery rate of 0.05. The peaks shown below average ChIP-seq tracks are peaks called using the combined bam files, whereas the peaks shown below individual replicates are peaks called using the corresponding replicate.
Assembly: WS220
Supplementary files format and content: bw file contains signal track, input subtracted enrichment at each binned genomic loci
Supplementary files format and content:bed file contains binarized chip enrichment across the genome

extract_protocol:
ChIP-seq: L2/L3s and adult worms were dounce-homogenized in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl) and sonicated in 0.1% sarkosyl to obtain chromatin fragments between 200 and 800 bp. 2 mg of protein extract and 3 to 10 ug of antibody was used per ChIP.
ChIP-seq: half of the ChIP DNA and 30 ng of input DNA were ligated to Illumina TruSeq adapters and amplified by PCR. Library DNA between 250 and 600 bp was gel purified.

value: input


title: input_JK06_1hrauxin_L3_rep3 [HW44]


title: SMC3_JK06_1hrauxin_L3_rep4 [HW49]

description:
SMC3_JK06_1hrauxin_inputsubt_rep4.bw
SMC3_JK06_1hrauxin_inputsubt_rep4.bw
SMC3_JK06_1hrauxin_rep4_chip_peaks.bed

value: SMC3 (SDIX,Q4469)


title: RNA_JK05_4hrauxin_L3_rep2 [HW17]