title: scRNA-seq of zebrafish brain neurons expressing human alpha-synuclein - Fibrils fed (Fed-8)

city: Los Angeles

first: Bronstein

middle: M

last: Jeff

state: California

address: 710 Westwood Plaza

department: Department of Neurology, David Geffen School of Medicine

institute: University of California, Los Angeles

description:
Library name: Fed-8
Sample sequenced on two lanes using Illumina NextSeq 500 with dual indexing. Read 1 contains cell barcode and UMI; Read 2 contains cDNA sequence.

data_processing:
Demultiplexing was performed using Cell Ranger mkfastq (v7.0.1) on Illumina BCL files.
Read alignment was done using Cell Ranger count, aligning to a custom zebrafish reference (GRCz11) augmented with human α-synuclein (SNCA) sequence.
UMI quantification and gene-barcode matrix generation were performed by Cell Ranger using default settings.
Gene expression matrices were imported into R (v4.1.0) using the Seurat package (v4.0.3) for quality control, normalization, dimensionality reduction, and clustering.
Batch correction was performed using Seurat’s anchor-based integration. Differential expression and pathway analysis were performed using Wilcoxon Rank Sum test and Enrichr, respectively.
Assembly: Danio rerio GRCz11.101, customized to include human alpha-synuclein gene (SNCA)
Supplementary files format and content: Gene-barcode expression matrices
Supplementary files format and content: Seurat object files

organism: Danio rerio

extract_protocol:
Brains from 5-day post-fertilization zebrafish larvae were dissected in cold Ringer’s solution. Following washes in DPBS, tissue was dissociated using Accumax Cell Dissociation Solution at 37°C with periodic trituration using a fire-polished glass pipette. The resulting single-cell suspension was filtered through a 40 µm cell strainer and centrifuged. Viable cells were resuspended in 1x PBS + 0.04% BSA for library preparation.
Single-cell suspensions with >70% viability were processed using the 10X Genomics Chromium Single Cell 3’ v3 protocol to generate Gel Bead-in-Emulsion (GEM) libraries. Approximately 10,000 cells were targeted per sample. Reverse transcription and cDNA amplification were performed in GEMs, followed by library construction according to the manufacturer’s instructions. Libraries were sequenced on the Illumina NextSeq 500 platform with a target of 50,000 reads per cell.

value: Brain

value: Brain cells


title: scRNA-seq of zebrafish brain neurons expressing human alpha-synuclein - Fibrils fed (Fed-6)

status: Public on Jan 17 2026

type: SRA

country: USA

description:
Library name: Fed-6
Sample sequenced on two lanes using Illumina NextSeq 500 with dual indexing. Read 1 contains cell barcode and UMI; Read 2 contains cDNA sequence.

library_source: transcriptomic single cell

molecule: total RNA

source_name: Brain

tag: tissue

tag: cell type


title: P15-FUP2, F, LTR

type: genomic

city: Birtinya

first: Nathan

last: Wellington

state: QLD

address: 12 Innovation Pkwy,

department: Thompson Institute

country: Australia

institute: University of the Sunshine Coast

hyb_protocol: All DNA samples were bisulphite converted with the Zymo EZ-96 DNA Methylation kit.

scan_protocol: Samples were processed on an Illumina Human Methylation EPIC v2.0 Bead Chip utilising the Illumina Infinium HD Methylation assay protocol

data_processing:
Methylation package V1.9.0 in Illumina GenomeStudio V2011.1
Average Beta

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: PBMC

label_protocol: Standard Illumina protocol

extract_protocol: DNA was extracted using the DNeasy Blood and Tissue kit (Qiagen) RNA was extracted via the RNeasy mini kit (Qiagen) as per manufacturer’s instructions for cells

value: PBMC

tag: Sex

value: female

tag: age

tag: disease

value: Post Traumatic Stress Disorder

tag: treatment

value: Ketamine

tag: response

value: Long Term Responder

tag: timepoint

value: 4 Weeks Post Treatment (FUP2)


title: A. thaliana, S. indica-inoculated, 50 mM NaCl, biol rep 3

city: Pozuelo de Alarcón

first: Begoña

last: Benito-Casado

state: Madrid

address: Campus de Montegancedo, Autovía M-40 (km 38)

department: Centro de Biotecnolgía y Genómica de Plantas (UPM-INIA/CSIC)

country: Spain

institute: Universidad Politécnica de Madrid

description: Library name: Sample 12

library_source: transcriptomic

data_processing:
Novogene Co., LTD Genomics Service (Cambridge, UK)
Original image data files from the Illumina platform were transformed to sequenced reads by CASAVA base recognition.
Sequence reads were trimmed for the adaptor sequence/low-quality reads were deleted using a Novogene in-house script (quality parameter limit: 0.05)
Trimmed sequence reads were mapped against the TAIR10 Arabidopsis genome using hisat2 v2.0.5.
Assembly: TAIR10 Arabidopsis genome
Supplementary files format and content: tab-delimited text file includes raw read counts values for each Sample

organism: Arabidopsis thaliana

source_name: Roots

growth_protocol: Arabidopsis seeds were surface sterilized for 5 min in 5% (w/v) sodium hypochlorite from a commercial solution and finally rinsed five times with sterile water. After stratification for at least 48 h at 4ºC in darkness, the seeds were germinated in PNM-agar plates placed vertically for one week. The plants were grown under control conditions in a greenhouse with an 8-h light/16-h dark period at 22°C.

extract_protocol:
Fungal-inoculated plant root samples were obtained at seven days post inoculation (dpi) and growth in the presence or absence of 50 mM NaCl. The first 4-5 cm of roots starting from the seed were excised and immediately frozen in liquid nitrogen. Either non-inoculated or fungal-inoculated plant root samples were crushed to a fine powder in liquid nitrogen with mortars and pestles. Total RNA was extracted with TRIzol reagent (Invitrogen) and on-column DNase digestion was performed according to manufacturer's protocol. RNA was purified by passage through Nucleospin RNA Plant columns (Mackerey-Nagel). Triplicates of control or the different saline treatments were used for the construction and analysis of RNA-seq libraries. The quality of RNA samples was checked in an Agilent 2100 Bioanalyzer. Those RNA samples with an RNA Integrity number (RIN) >7.5 and rRNA 28S/18S ratio >1.5 were selected for further analysis.
Library construction and sequencing (150‑nt paired-end reads) on Illumina NovaSeqTM

treatment_protocol: For experiments carried out in Arabidopsis, fungal inoculation and transferring to saline conditions was carried out simultaneously. For that, two-week-old seedling were transferred to sterile square petri dishes containing PNM medium without supplemented glucose in the presence or absence of 50 mM NaCl and then directly were inoculated with 100 μl of a chlamydospore suspension (5 x 105 ml-1 in 0.002% (w/v) Tween20). Incubation was performed by placing the plates vertically in a Conviron phyto-chamber with a day/night cycle of 16/8 hours (light 21 intensity: 110 μmol m-2 s-1) at a temperature of 22/18°C. After one week, the plants were cut separately in the roots and shoots for further analysis, that is, for total root RNA extraction or cation content determination.

value: Roots

tag: genotype

value: S. indica-inoculated, 50 mM NaCl


title: P15-FUP1, F, LTR

value: 1 Week Post Treatment (FUP1)


title: 10-Yumm17_copEV_Nutlin_ChIP_H3R17me2

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: Library name: 10-Yumm17_copEV_Nutlin_ChIP_H3R17me2_S43

library_source: genomic

data_processing:
Sequencing reads were quality checked with FASTQC (v0.11.9)  and aligned to the GRCh37 (hg19) genome using STAR (v2.7.9a). Homer and macs2 were used for peak call and diffbind for diffrential bind. Deeptool used for bigwigfiles.
Assembly: mm10
Supplementary files format and content: CPM-normalized bigWig files were generated using Deeptools (v3.5.1). Score represents the normalized coverage of DNA fragment at a given coordinate.

organism: Mus musculus

growth_protocol: DMEM/F12 media, 10% FBS, 1%Penn/Strep, 1%NEAA

extract_protocol:
Non-histone samples were first crosslinked with EGS for 25 minutes. All cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, cells were sonicated with a Cavaris S220 Ultrasonicator.
Barcoded libraries were made using NEB Ultra II DNA Library Prep Kit for Illumina following manufacturer's instructions and quantified by Agilent 4200 Tapestation System.

treatment_protocol: Vehicle (DMSO), nutlin, doxycycline, or nutlin+doxycycline (24 hours)

tag: cell line

value: Mouse melanoma

value: Nutlin


title: scRNA-seq of zebrafish brain neurons expressing human alpha-synuclein - Fibrils fed (Fed-2)

description:
Library name: Fed-2
Sample sequenced on two lanes using Illumina NextSeq 500 with dual indexing. Read 1 contains cell barcode and UMI; Read 2 contains cDNA sequence.


title: 13-Yumm17_A2_5H_untreated_ChIP_citH3

description: Library name: 13-Yumm17_A2_5H_untreated_ChIP_citH3_S46

value: Vehicle


title: Experiment41

city: Beijing

first: xiaoqun

last: wang

state: Beijing

address: 15 Datun Road, Chaoyang District

department: Institute of Biophysics

country: China

institute: Chinese Academy of Sciences

data_processing:
Adapter and low-quality reads were discarded using Python script AfterQC (Chen et al., 2017). Paired-end reads were aligned to the mouse reference genome mm10 using STAR (v2.5.3a) with default parameters, except for the use of setting output type (–out-SAMtype) (Dobin et al., 2013). Reads were then counted with FeatureCounts (v1.5.3) (Liao et al., 2014). Cells with nGene > 3 000, percentage of mitochondrial genes < 10%, and percentage of ERCC < 5% were included. Genes with expression in at least one cell were included.
Assembly: mm10
Supplementary files format and content: tab-delimited text file include raw counts for each cell

source_name: substantia nigra

extract_protocol:
The RNA collected from neurons by patch-seq were converted to DNA using the Smart-seq2 protocol
RNA libaries were prepared with the HyperPlus kit following manufacturer's instruction

value: substantia nigra

value: dopaminergic neuron


title: scRNA-seq of zebrafish brain neurons expressing human alpha-synuclein - Fibrils fed (Control; Nonfed-5)

description:
Library name: Nonfed-5
Sample sequenced on two lanes using Illumina NextSeq 500 with dual indexing. Read 1 contains cell barcode and UMI; Read 2 contains cDNA sequence.


title: A. thaliana, S. indica-inoculated, 0 mM NaCl, biol rep 1

description: Library name: Sample 7

value: S. indica-inoculated, 0 mM NaCl


title: Experiment44


title: 14-Yumm17_A2_5H_untreated_ChIP_H3K27ac

description: Library name: 14-Yumm17_A2_5H_untreated_ChIP_H3K27ac_S47


title: P11-FUP2, F, NR, WB

source_name: Whole Blood

value: Whole Blood

value: Non responder


title: Experiment40


title: Experiment43


title: scRNA-seq of zebrafish brain neurons expressing human alpha-synuclein - Fibrils fed (Control; Nonfed-7)

description:
Library name: Nonfed-7
Sample sequenced on two lanes using Illumina NextSeq 500 with dual indexing. Read 1 contains cell barcode and UMI; Read 2 contains cDNA sequence.

value: Brain

value: Brain cells


title: Experiment39


title: A. thaliana, S. indica-inoculated, 0 mM NaCl, biol rep 2

description: Library name: Sample 8


title: A. thaliana, S. indica-inoculated, 0 mM NaCl, biol rep 3

description: Library name: Sample 9


title: control41


title: A. thaliana, S. indica-inoculated, 50 mM NaCl, biol rep 1

description: Library name: Sample 10


title: scRNA-seq of zebrafish brain neurons expressing human alpha-synuclein - Fibrils fed (Control; Nonfed-1)

description:
Library name: Nonfed-1
Sample sequenced on two lanes using Illumina NextSeq 500 with dual indexing. Read 1 contains cell barcode and UMI; Read 2 contains cDNA sequence.


title: P13-BAS, F, LTR

value: PBMC

value: female

value: Post Traumatic Stress Disorder

value: Baseline


title: P13-FUP1, F, LTR

value: Ketamine

value: Long Term Responder


title: scRNA-seq of zebrafish brain neurons expressing human Control C

description:
Library name: Control-Sibling-C
Sample sequenced on two lanes using Illumina NextSeq 500 with dual indexing. Read 1 contains cell barcode and UMI; Read 2 contains cDNA sequence.


title: P13-FUP2, F, LTR

value: 4 Weeks Post Treatment (FUP2)


title: control39


title: A. thaliana, non-inoculated, 50 mM NaCl, biol rep 2

description: Library name: Sample 5

value: Roots

value: mock-inoculated, 50 mM NaCl


title: A. thaliana, non-inoculated, 50 mM NaCl, biol rep 1

description: Library name: Sample 4


title: control40


title: control38


title: A. thaliana, S. indica-inoculated, 50 mM NaCl, biol rep 2

description: Library name: Sample 11

value: S. indica-inoculated, 50 mM NaCl


title: scRNA-seq of zebrafish brain neurons expressing human alpha-synuclein C

description:
Library name: a-syn-Sibling-C
Sample sequenced on two lanes using Illumina NextSeq 500 with dual indexing. Read 1 contains cell barcode and UMI; Read 2 contains cDNA sequence.


title: P11-FUP1, F, NR

source_name: Peripheral Blood Mononuclear Cells

value: Peripheral Blood Mononuclear Cells

value: 1 Week Post Treatment (FUP1)


title: A. thaliana, non-inoculated, 0mM NaCl, biol rep 3

description: Library name: Sample 3

value: mock-inoculated, 0 mM NaCl


title: scRNA-seq of zebrafish brain neurons expressing human Control B

description:
Library name: Control-Sibling-B
Sample sequenced on two lanes using Illumina NextSeq 500 with dual indexing. Read 1 contains cell barcode and UMI; Read 2 contains cDNA sequence.


title: A. thaliana, non-inoculated, 50 mM NaCl, biol rep 3

description: Library name: Sample 6


title: P11-FUP2, F, NR


title: scRNA-seq of zebrafish brain neurons expressing human Control A

description:
Library name: Control-Sibling-A
Sample sequenced on two lanes using Illumina NextSeq 500 with dual indexing. Read 1 contains cell barcode and UMI; Read 2 contains cDNA sequence.


title: Experiment37

value: substantia nigra

value: dopaminergic neuron


title: A. thaliana, non-inoculated, 0mM NaCl, biol rep 2

description: Library name: Sample 2


title: P11-BAS, F, NR, WB

value: Whole Blood

value: Non responder


title: P15-BAS, F, LTR

value: PBMC


title: NORMAL5.deadaptor

status: Public on Jan 16 2026

city: HEFEI

first: Dan

last: Cheng

state: Shushan

address: 中国安徽省合肥市蜀山区樊洼路安兴太阳湾小区

institute: The First Affiliated Hospital of Anhui University of Chinese Medicine

description: Library name: Sample10.deadaptor

data_processing:
Characteristic statistics list the fundamental qualities. Continuous variables were expressed as mean ± SEM. ANOVA was used to look into differences between three or more groups, while the Students' T-test was used to look into differences between two groups. Categorical variables were analyzed using the chi-squared test. The DESeq 2 approach was utilized to identify the differently expressed miRNA in the sequencing data, and the Benjamin-Hochberg method was employed to control the false discovery rate. Data processing and analysis were conducted using SPSS 19.0, with statistical significance levels set at P < 0.05, and P < 0.01.
Assembly: plasma exosomes
Supplementary files format and content: data file that contains data for all samples

source_name: plasma exosomes

extract_protocol:
Utilizing the miRNeasy serum/plasma kit, total RNA was isolated from the plasma.(Qiagen, catalog number 217184). Plasma (200 µL) was mixed with 5 volumes of QIAzol, vortexed and then incubated for 5 minutes at room temperature. After vortexing and incubating, the mixture was centrifuged at 12,000 rpm. After being poured into a fresh test tube, the supernatant was vortexed and combined with 1.5 times the volume of anhydrous ethanol. The sample was loaded on the chromatographic column and centrifuged at 13,000× g. After discarding the flow-through liquid, the chromatographic column was filled with the buffer RPE (500 µL) and centrifuged. Add anhydrous ethanol (80%) to the column and centrifuge. Once the flow-through liquid has been disposed of, centrifuge the column and empty it. After adding 14 µL of RNase-free water to the column's core, the RNA was centrifuged to extract it, and it was then kept cold—at -70°C.
By the guidelines provided by the manufacturer, the All-in-One miRNA qRT-PCR Detection Kit(QP015, GeneCopoeia, Rockville, MD, USA) was used to perform real-time PCR to quantify mature miRNAs. While the forward primers (Supplementary Table 1) were designed using the mature miRNA sequence, the reverse primers were provided by the kit manufacturer. Reverse transcription (RT) and PCR are the two phases in quantitative analysis. In a total amount of 10 μl, there was 0.5 μg of RNA, 5 μl of 2×TS miRNA Reaction Mix, and 0.5 μl of TransScript miRNA RT Enzyme Mix for every RT reaction. The gene amp PCR system 9700 (Applied Biosystems, USA) was used to perform the reaction for 60 minutes at 37°C. After that, it was thermally inactivated for 5 seconds at 85°C. The RT product was kept at -20°C after being diluted ten times in water devoid of nuclease.

value: plasma exosomes

tag: subject status

value: healthy volunteer


title: NORMAL3.deadaptor

address: 中国安徽省合肥市蜀山区樊洼路安兴太阳湾小区

description: Library name: Sample8.deadaptor


title: P11-FUP1, F, NR, WB

value: female

value: Post Traumatic Stress Disorder


title: NORMAL2.deadaptor

address: 中国安徽省合肥市蜀山区樊洼路安兴太阳湾小区

description: Library name: Sample7.deadaptor


title: Experiment38


title: CHF4.deadaptor

address: 中国安徽省合肥市蜀山区樊洼路安兴太阳湾小区

description: Library name: Sample4.deadaptor

value: patient with heart failure with reduced ejection fraction (HFrEF)


title: Rapamycin treated high fat diet rep6

city: La Jolla

first: Xue

last: Lei

state: CA

address: 10901 N Torrey Pines Rd

institute: SBP medical discovery institute

description: Library name: Rapa_rep6

data_processing:
Raw fastq files were aligned using STAR.
Aligned reads were filtered, sorted and indexed by SAMtools V1.1.0
Raw read counts were obtained by HTSeq V0.11.2
CuffLinks V2.2.160 was used to compute FPKM values
Assembly: mm10
Supplementary files format and content: FPKM matrix
Supplementary files format and content: raw count matrix

molecule: polyA RNA

source_name: liver

extract_protocol:
2-step perfusion, trizol RNA extraction
Genomics mRNA Library Prep Kit (Watchmaker Genomics) and Elevate Long UDI Adapters (Element Biosciences)

treatment_protocol: Three cohorts were examined: normal diet (ND) + vehicle, high fat diet (HFD, 60% calories from fat) + vehicle and high fat diet + rapamycin (42ppm). Mice were initiated on either ND + vehicle or ND + rapamycin at 4-months of age. Once mice reached 18-months of age, they were either maintained on ND + vehicle, or HFD + vehicle, HFD + rapamycin for 9-weeks. Mice were maintained until euthanized and heptocytes were isolated using 2-step perfusion protocol.

value: liver

value: hepatocyte

value: Rapamycin treated high fat diet

tag: batch


title: Experiment36


title: scRNA-seq of zebrafish brain neurons expressing human alpha-synuclein A

description:
Library name: a-syn-Sibling-A
Sample sequenced on two lanes using Illumina NextSeq 500 with dual indexing. Read 1 contains cell barcode and UMI; Read 2 contains cDNA sequence.

value: Brain

value: Brain cells


title: Rapamycin treated high fat diet rep5

description: Library name: Rapa_rep5


title: scRNA-seq of zebrafish brain neurons expressing human alpha-synuclein B

description:
Library name: a-syn-Sibling-B
Sample sequenced on two lanes using Illumina NextSeq 500 with dual indexing. Read 1 contains cell barcode and UMI; Read 2 contains cDNA sequence.


title: NORMAL1.deadaptor

address: 中国安徽省合肥市蜀山区樊洼路安兴太阳湾小区

description: Library name: Sample6.deadaptor


title: high fat diet rep6

description: Library name: HFD_rep6

value: high fat diet


title: Rapamycin treated high fat diet rep3

description: Library name: Rapa_rep3


title: high fat diet rep7

description: Library name: HFD_rep7


title: CHF3.deadaptor

address: 中国安徽省合肥市蜀山区樊洼路安兴太阳湾小区

description: Library name: Sample3.deadaptor


title: Rapamycin treated high fat diet rep7

description: Library name: Rapa_rep7


title: NORMAL4.deadaptor

address: 中国安徽省合肥市蜀山区樊洼路安兴太阳湾小区

description: Library name: Sample9.deadaptor


title: Rapamycin treated high fat diet rep4

description: Library name: Rapa_rep4


title: normal diet rep8

description: Library name: ND_rep8

value: normal diet


title: CHF1.deadaptor

address: 中国安徽省合肥市蜀山区樊洼路安兴太阳湾小区

description: Library name: Sample1.deadaptor


title: Rapamycin treated high fat diet rep2

description: Library name: Rapa_rep2


title: CHF5.deadaptor

address: 中国安徽省合肥市蜀山区樊洼路安兴太阳湾小区

description: Library name: Sample5.deadaptor


title: Rapamycin treated high fat diet rep8

description: Library name: Rapa_rep8


title: CHF2.deadaptor

address: 中国安徽省合肥市蜀山区樊洼路安兴太阳湾小区

description: Library name: Sample2.deadaptor


title: high fat diet rep5

description: Library name: HFD_rep5


title: normal diet rep7

description: Library name: ND_rep7


title: Rapamycin treated high fat diet rep1

description: Library name: Rapa_rep1


title: Rapamycin treated high fat diet rep9

description: Library name: Rapa_rep9


title: high fat diet rep3

description: Library name: HFD_rep3


title: high fat diet rep4

description: Library name: HFD_rep4


title: normal diet rep6

description: Library name: ND_rep6


title: normal diet rep4

description: Library name: ND_rep4


title: normal diet rep2

description: Library name: ND_rep2


title: A. thaliana, non-inoculated, 0mM NaCl, biol rep 1

description: Library name: Sample 1

value: Roots

value: mock-inoculated, 0 mM NaCl


title: normal diet rep5

description: Library name: ND_rep5


title: high fat diet rep2

description: Library name: HFD_rep2


title: WT VSMC specific overexpression, mouse 1, RNA

city: New York

first: Lauren

middle: E

last: Fries

state: NY

department: Medicine

institute: Columbia University

description:
Library name: sample8
tpm_values_genes_kallisto.txt
RA004

data_processing:
Analysis was completed using TOBIAS snakemake pipeline
Peaks were called for each sample using macs with shift set to 100, extension size set to 200, and broad peaks called
Peaks were annotated using UROPA and the condition .bam files were merged for subsequent analysis
The condition .bam files were corrected with ATACorrect and examined for binding affinity using FootprintScores
Using the PWM motifs that were specified, motif occurrences were determined and assigned scores related to the FootprintScores by BINDetect
Assembly: mm10
Supplementary files format and content: The footprints.bw files are the footprinting result bigwigs for each genotype.

source_name: Aorta

growth_protocol: VSMC isolation: The aorta was dissected from the ascending arch to the diaphragm and was predigested for 10 minutes at 37°C with 175U/ml Collagenase II and 1.25U/ml elastase in HBSS to allow for the removal of the adventitia. After removing the adventitia, the media layer was further digested in 400U/ml collagenase II, 2.5U/ml elastase, and 0.2mg/ml soybean trypsin inhibitor at 37°C for one hour in a rotating incubator. The cells were cultured in DMEM supplemented with 20% fetal bovine serum, 1% L-Glutamine, 1% sodium pyruvate, and 1% Penicillin Streptomycin. Cells between passages two and seven were used for experiments.

extract_protocol:
Cells were trypsinized and collected and 50,000 were counted then washed in PBS. Make resuspension buffer consisting of 10nm Tris-HCl, 10 mM NaCl, and 3 mM MgCl2 in H2O. Lysis buffer consisting of resuspension buffer with 0.1% NP-40, 0.1% Tween-20, and 0.01% Digitonin was added to the cells and the mixture incubated on ice for 3 minutes. Then was wash buffer consisting of resuspension buffer with 0.1% Tween-20 was added and the cells were centrifuged at 500 x g for 10 minutes at 4C. The supernantant was discarded and the pellet was kept. The transposition reaction mix, using Nextera DNA library prep kit, was made with 1X TD Buffer, 0.1% Tween 20, 0.01% Digitonin, and Tn5 Transposase. This was added to the pellet, resuspended, and then incubated at 37C for 30 minutes on a thermomixer at 1,000 rpm. The DNA was isolated using the Qiagen MinElute Reaction Cleanup Kit and the DNA was eltured in 10uL of Elution Buffer.  For RNA, after the cells were trypsinized and collected RNA was extracted using QIAGEN RNAeasy kit.
For PCR amplication, the purified transposed DNA was combined with Ad1_noMX primer, Ad2.*indexing primer, and NEBNext High-Fidelity 2X PCR Master Mix. The samples were amplified with the following program: 72C for 5 mins, 98 C the 30 seconds, then for five cycles to 98C for 10 seconds, 63 C for 30 seconds, and 72 C for 1 minute. Then, the PCR was continued after testing the appropriate number of cycles, for 98C for 30 seconds then 8 cycles of 98C for 10 seconds, 63C for 30 seconds, and 72C for 1 minute. The library was then purified using Zymo DNA clean and concentrator 5.

value: Aorta

value: primary vascular smooth muscle cell

value: VSMC-specific Adamts7 overexpression


title: WT VSMC specific overexpression, mouse 3, RNA

description:
Library name: sample10
tpm_values_genes_kallisto.txt
RA006


title: WT VSMCs, mouse 1, RNA

description:
Library name: sample5
tpm_values_genes_kallisto.txt
RA001

value: Wild type


title: normal diet rep1

description: Library name: ND_rep1


title: normal diet rep3

description: Library name: ND_rep3


title: WT VSMCs, mouse 2, RNA

description:
Library name: sample6
tpm_values_genes_kallisto.txt
RA002


title: high fat diet rep1

description: Library name: HFD_rep1


title: WT VSMCs, mouse 3, RNA

description:
Library name: sample7
tpm_values_genes_kallisto.txt
RA003


title: Inguinal WAT, Cebpa_ASKO 3

description:
Library name: RK006
Column name in tpm_values_genes_kallisto.txt: RK006

data_processing:
We use bases2fastq version 1.5.0.962525890 for converting BCL to fastq format, coupled with adaptor trimming. We perform a pseudoalignment to a kallisto index created from transcriptomes (Ensembl v96, Human:GRCh38.p12; Mouse:GRCm38.p6) using kallisto (0.44.0).
Assembly: GRCm38.p6
Supplementary files format and content: Transcripts per million from DESeq1 processing
Supplementary files format and content: Abundance files for each sample

source_name: Inguinal white adipose tissue

growth_protocol: Mice on a C57BL6/J background. 10-week-old female mice.

extract_protocol:
Both inguinal white adipose tissue depots were dissected out and extracted together and lymph nodes were removed from each mouse. RNA was extracted with the Qiagen Lipid Tissue Kit.
The Columbia University Medical Center Sequencing Core generated the libraries after submission of RNA samples. First, poly-A pull-down was used to enrich mRNAs from total RNA samples. Then, library construction was done using Illumina TruSeq chemistry. The final PCR step has been modified using the KAPA HiFi HotStart Ready Mix.

treatment_protocol: Mice were randomly fed.

value: Inguinal white adipose tissue

value: KO

value: 10 weeks old, ad libitum fed state


title: WT VSMC specific overexpression, mouse 2, RNA

description:
Library name: sample9
tpm_values_genes_kallisto.txt
RA005


title: Inguinal WAT, Cebpa_fl/fl 3

description:
Library name: RK005
Column name in tpm_values_genes_kallisto.txt: RK005

value: WT


title: WT VSMCs, mouse 2, ATAC

description:
Library name: sample2
column name in bindetect_results.txt : WT_mean_score WT_bound
WT_footprints.bw


title: Inguinal WAT, Cebpa_ASKO 2

description:
Library name: RK002
Column name in tpm_values_genes_kallisto.txt: RK002


title: Inguinal WAT, Cebpa_fl/fl 2

description:
Library name: RK004
Column name in tpm_values_genes_kallisto.txt: RK004


title: Inguinal WAT, Cebpa_ASKO 1

description:
Library name: RK001
Column name in tpm_values_genes_kallisto.txt: RK001


title: cKO_2

city: Zhengzhou

first: Peng

last: Wang

address: Science Avenue

institute: Zhengzhou University

description: Library name: Sample 4

data_processing:
Differential expressed genes were carried out byDEseq2 software. KEGG pathway enrichment was performed by KOBAS 3.0.28 (http://kobas.cbi.pku.edu.cn/). Protein and protein interaction networks were analyzed by String(https://string-db.org/) and visualized by Cytoscape.
Assembly: mm10
Supplementary files format and content: counts values for each Sample

source_name: Spleen

extract_protocol:
Bone marrow cells were isolated from 6-8 week-old male wild-type (WT) and TGM2KO mice and then bone marrow-derived macrophages (BMDMs) were obtained and cultured with the stimulation of M-CSF (25ng/ml) for 7 days.
The total RNA of the macrophage cells were extracted using TRIzol reagent (Thermo Fisher, 15596018) and sequencing was done by the Annoroad Gene Technology Co.,Ltd. (Beijing).

value: Spleen

value: Treg cells


title: Inguinal WAT, Cebpa_fl/fl 1

description:
Library name: RK003
Column name in tpm_values_genes_kallisto.txt: RK003


title: Adamts7 VSMC specific overexpression, mouse 2, ATAC

description:
Library name: sample4
column name in bindetect_results.txt : TG_mean_score TG_bound
TG_footprints.bw


title: cKO_1

description: Library name: Sample 3


title: Lung_Tumor_HDM_rep3

first: Shams

last: Al-Azzam

address: 9500 Gilman Dr

institute: University of California San Diego

description: Library name: M_39_1_T3

data_processing:
STAR is used to align reads to the mm39 reference genome
Adapters and low-quality bases were removed with Trim Galore (paired-end mode; Q20 trimming; minimum post-trim length 36 bp)
Gene-level read counts were generated with featureCounts (Subread) using the GTF gene_id attribute, exon-based summarization (default), paired-end fragment counting (-p), reverse-strand specificity (-s 2), and N threads (-T). The resulting matrix was post-processed by removing the header and retaining the Geneid and per-sample columns (sed '1d' | cut -f1,6-)
Assembly: mm39
Supplementary files format and content: tap-delimated raw counts of each sample

source_name: Lung

extract_protocol:
Macroscopic LLC tumors and normal adjacent lung tissues were manually dissected using a binocular microscope and a scalpel. The tissues were snap-frozen in liquid nitrogen and stored at -80 ºC until use. The samples were then sectioned into ~1 mg aliquots for nucleic acid extraction. Genomic DNA and total RNA were co-extracted using the AllPrep DNA/RNA Mini Kit (Qiagen, Cat. No. 80204). Tissue was homogenized with PowerTube beads (Cat. No. 13117-50) using the Omni Bead Ruptor 12 (Cat. No. 19-050A). DNA concentration was quantified using the Qubit™ 1X dsDNA HS Assay Kit (Cat. No. Q33231) on the Qubit 4 Fluorometer (Cat. No. Q33226). All DNA and RNA samples had a DNA Integrity Number (DIN) and RNA Integrity Number (RIN), respectively, greater than 6.
RNA-seq libraries were constructed by Novogene using a stranded dUTP workflow: total RNA was [poly(A)-selected or rRNA-depleted], fragmented, converted to cDNA, end-repaired, A-tailed, adaptor-ligated, PCR-amplified, and sequenced on Illumina (PE150)

value: Lung

tag: group

value: Tumor

value: HDM


title: Lung_Normal_HDM_rep3

description: Library name: M_37_3_H1

value: Normal


title: WT_2

description: Library name: Sample 2


title: WT_1

description: Library name: Sample 1


title: Adamts7 VSMC specific overexpression, mouse 1, ATAC

description:
Library name: sample3
column name in bindetect_results.txt : TG_mean_score TG_bound
TG_footprints.bw


title: WT VSMCs, mouse 1, ATAC

description:
Library name: sample1
column name in bindetect_results.txt : WT_mean_score WT_bound
WT_footprints.bw


title: Lung_Tumor_HDM_rep2

description: Library name: M_40_2_T2


title: Lung_Normal_HDM_rep2

description: Library name: M_39_3_H2


title: Lung_Tumor_VEH_rep1

description: Library name: M_37_2_T1

value: VEH


title: Lung_Normal_VEH_rep1

description: Library name: M_37_2_H1


title: Lung_Normal_HDM_rep1

description: Library name: M_39_1_H2


title: Lung_Tumor_VEH_rep2

description: Library name: M_38_2_T2


title: Lung_Tumor_HDM_rep1

description: Library name: M_39_3_T1


title: 17893-SYZ2

city: Fuzhou

first: Baogang

last: Zhang

state: Fujian Province

address: No. 15 Shangxiadian Road, Cangshan District

institute: Fujian Agriculture and Forestry University

description: Library name: RGSV P3

data_processing:
Raw FASTQ files were quality-checked with FastQC. Adapters and low-quality reads were trimmed using Trimmomatic. Clean reads were aligned to the rice nipponbare reference genome using Bowtie2 (v2.4.4) with --end-to-end --sensitive parameters. Duplicate reads were marked and removed using Picard MarkDuplicates.
Peaks were called using MACS2 with parameters --format BAM --qvalue 0.05 --nomodel --shift -100 --extsize 200 --call-summits, using the corresponding input library as control.
BigWig signal tracks were generated from sorted BAM files using deepTools bamCoverage with --normalizeUsing RPM --binSize 10 --smoothLength 30.
Differential peak analysis between SYZ2 and DZZ conditions was performed using DiffBind (or your tool) with DESeq2 normalization.
Assembly: Oryza sativa MSU Rice Genome Annotation Project Release 7 (MSU7)
Supplementary files format and content: BigWig (.bw) files contain normalized read coverage (RPM) for visualization in genome browsers. NarrowPeak files contain MACS2-called peaks with summit positions, fold enrichment, and q-values. XLS file contains differential peak analysis results including genomic coordinates, log2 fold change.

organism: Oryza sativa

source_name: leaf

growth_protocol: Rice plants were grown under long-day conditions (16 h light/8 h dark) at 28°C in soil until the desired developmental stage.

extract_protocol:
Genomic DNA was extracted from purified protein-DNA complexes using standard phenol-chloroform extraction followed by ethanol precipitation.
Sequencing libraries were prepared using the BGI (BGISEQ-500 platform) standard DNA library preparation protocol. Briefly, purified DNA was fragmented to an average size of ~300 bp by acoustic shearing (Covaris) fragmentation. Fragmented DNA was end-repaired, A-tailed, and ligated to indexed adapters. Adapter-ligated DNA was size-selected (300-500 bp range) and PCR-amplified (10-12 cycles) to generate the final double-stranded libraries for paired-end sequencing.

treatment_protocol: No additional treatment was applied. For DAP-Seq, purified recombinant RGSV P3 protein was used for in vitro binding.

value: leaf

tag: cultivar

value: Niponbare


title: Lung_Normal_VEH_rep3

description: Library name: M_38_2_H2


title: Palbociclib_2

city: Worcester

first: Marcus

last: Ruscetti

state: MA

address: 364 Plantation Street

department: MCCB

institute: UMass Chan Medical School

description: Library name: H2

data_processing:
Sequence reads were processed and analyzed with OneStopRNAseq
Sequence reads were trimmed for adapter sequence using fastp software
Trimmed sequence reads were mapped to mm10 using STAR software
Read count extraction and normalization were performed using featureCounts and DESeq2 software
Assembly: mm10
Supplementary files format and content: Excel file includes raw counts for each Sample
Supplementary files format and content: Excel file includes TPM values for each Sample

source_name: prostate

growth_protocol: Cells were cultured in a humidified incubator at 37°C with 5% CO2 and grown in DMEM supplemented with 10% FBS and 100 IU/ml penicillin/streptomycin (P/S).

extract_protocol:
Total RNA was extracted from tumor cells using the RNeasy Mini Kit (Qiagen).
Library preparation and sequencing on a NovaSeq 6000 were performed by Novogene. Approximately 30 million 150-bp paired-end reads were retrieved per replicate condition.

treatment_protocol: Cells were treated with DMSO, 25 nM trametinib, 1uM palboclib, 500 nM PF-06873600, 500 nM etoposide, 3.75 uM docetaxel, 500 nM alisertib, and/or 500nM Nutlin for 6 days. Drug containing media was replenished every 3 days.

value: prostate

value: Myc-CaP

value: prostate tumor

value: MYC overexpressing

value: Palbociclib


title: Palbociclib_3

description: Library name: H3


title: Nutlin-3_2

description: Library name: G2

value: Nutlin


title: 17893-DZZ

description: Library name: Input


title: Palbociclib_1

description: Library name: H1


title: Etoposide_3

description: Library name: F3

value: Etoposide


title: Etoposide_1

description: Library name: F1


title: Lung_Tumor_VEH_rep3

description: Library name: M_37_3_T2


title: Etoposide_2

description: Library name: F2


title: Nutlin-3_3

description: Library name: G3


title: T/P_3

description: Library name: E3

value: T/P


title: Docetaxel_1

description: Library name: D1

value: Docetaxel


title: T/P_1

description: Library name: E1


title: Lung_Normal_VEH_rep2

description: Library name: M_40_2_H2


title: Nutlin-3_1

description: Library name: G1


title: Alisertib_1

description: Library name: C1

value: Alisertib


title: Alisertib_2

description: Library name: C2


title: Docetaxel_3

description: Library name: D3


title: Docetaxel_2

description: Library name: D2


title: PF-06873600_3

description: Library name: B3


title: Alisertib_3

description: Library name: C3


title: PF-06873600_1

description: Library name: B1


title: T/P_2

description: Library name: E2


title: DMSO_2

description: Library name: A2

value: DMSO


title: E15.5 mouse embryonic pancreas, conditional KO of the mouse ortholog of LINC00673, biological replicate 3

city: Copenhagen

first: Luis

last: Arnes

address: Ole Maaløes Vej 5

country: Denmark

institute: Biotech Research & Innovation Centre

description: Library name: cKO6_rep3

data_processing:
Paired-end clean reads were mapped to the reference genome using HISAT2 software
Stringtie was used to assemble the set of transcript isoforms of each bam file obtained in the mapping step. gffcompare was used to compare Stringtie assemblies to reference annotation files to predict new gene structures.
Featurecounts was used to count the read numbers mapped of each gene, including known and novel genes
Assembly: mm39
Supplementary files format and content: tab separated text format

source_name: Pancreas

extract_protocol:
E15.5 embryonic pancreas was lysed with 350ul of RLT buffer supplemented with b-mercaptoethanol and extraction was performed using the Quiagen micro RNeasy columns and eluted in a volume of 14ul.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptorligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Pancreas

value: E15.5 embryos

value: cKO


title: PF-06873600_2

description: Library name: B2


title: E15.5 mouse embryonic pancreas, conditional KO of the mouse ortholog of LINC00673, biological replicate 2

description: Library name: cKO6_rep2


title: M3F_14v-1536 M3 Control

city: baltimore

first: yang

last: song

state: MD

address: 670 W. Baltimore St.

institute: university of maryland in baltimore

description: Library name: Control2

data_processing:
Generated cDNA libraries were sequenced on a NovaSeq 6000 sequencing system at the Institute for Genome Sciences in the University of Maryland, Baltimore.
Reads were demultiplexed, aligned to the GRCm38 mm10 assembly reference genome, and filtered; and cell barcodes and UMIs were quantified using the Cell Ranger 6.1 with default parameters (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome). 6.7 x 103 cells per sample were captured on the 10X Chromium chip.
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: proximal small intestine

extract_protocol:
The proximal third of the small intestine was harvested and gently irrigated in 5 ml of cold DPBS containing 1% BSA. The tissue was cut longitudinally and sliced into small fragments measuring 2 mm. These tissue fragments were incubated in 10 ml of ice-cold 20 mM RNase-free EDTA-DPBS for 60 min. During incubation, the tissue fragments were mixed every 15 min by pipetting through wide-bore tips. After the tissues fragments were incubated in EDTA-DPBS, the villus-rich supernatant was collected and filtered through a 30 µm MACS strainer. The filtrate was then centrifuged at 300 g for 5 min at 4°C in a swing bucket centrifuge, the supernatant was decanted, and the pellet washed twice in 10 ml DPBS containing 1% BSA. After the last wash, the pellet was set aside on ice. Concurrently, the tissue fragments were incubated in 5 ml TrypLE for 10 min at 37°C. After the TrypLE incubation, the tissue fragments were resuspended by pipetting through wide-bore tips; the crypt-rich supernatant was retrieved and filtered through a 30 µm MACS strainer. The sample was centrifuged at 300 g for 5 min at 4°C in a swinging bucket centrifuge, and the pellet washed twice in 10 ml DPBS containing 1% BSA. After the last wash, villus-rich and crypt-rich pellets were combined in 5 ml cold 0.04% BSA-PBS. Cell viability was immediately assessed using the Countess Automated Cell Counter; only samples with at least 80% viability and at least 1,000 cells/µl were used.
Single-cell libraries were generated using the Chromium Single cell 3’ GEM library from 10x Genomics

value: proximal small intestine


title: DMSO_1

description: Library name: A1


title: E15.5 mouse embryonic pancreas, conditional KO of the mouse ortholog of LINC00673, biological replicate 1

description: Library name: cKO6_rep1


title: 1_18v_1432 M1 Control

description: Library name: Control1


title: E15.5 mouse embryonic pancreas, wild type, biological replicate 1

description: Library name: WT_rep1

value: WT


title: E15.5 mouse embryonic pancreas, wild type, biological replicate 4

description: Library name: WT_rep4


title: DHEA for mice, Kidney

city: haidian district

first: yao

last: feng

address: No.38 xueyuan road

institute: Peking University

description:
Library name: DHEA_Kidney
10x Genomics

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 hg38 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Assembly: mm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Kidney

extract_protocol:
Tissues (ovary, uterus, thymus, brain, heart, intestine, kidney, liver and spleen) were freshly dissected and immediately transferred into RNA lysis buffer. Samples were mechanically homogenized using a tissue homogenizer. Total RNA was isolated using a kit-based extraction workflow according to the manufacturer’s instructions. RNA concentration was measured (e.g., spectrophotometry/fluorometry), and RNA quality was assessed prior to submission for library construction and high-throughput sequencing.
RNA libraries for RNA-seq were prepared using standard Illumina protocols.

treatment_protocol: Control group and DHEA-treated group were established. Mice in the DHEA group received DHEA treatment, while control mice received the corresponding control condition. After treatment, the indicated tissues were harvested for RNA extraction and bulk RNA-seq.

value: Kidney

value: DHEA


title: DHEA for mice, Liver

description:
Library name: DHEA_Liver
10x Genomics

source_name: Liver

value: Liver


title: DHEA for mice, Heart

description:
Library name: DHEA_Heart
10x Genomics

source_name: Heart

value: Heart


title: E15.5 mouse embryonic pancreas, wild type, biological replicate 3

description: Library name: WT_rep3


title: E15.5 mouse embryonic pancreas, wild type, biological replicate 2

description: Library name: WT_rep2


title: DHEA for mice, Lung

description:
Library name: DHEA_Lung
10x Genomics

value: Lung


title: DHEA for mice, Utery

description:
Library name: DHEA_Utery
10x Genomics

source_name: Utery

value: Utery


title: DHEA for mice, Spleen

description:
Library name: DHEA_Spleen
10x Genomics

value: Spleen


title: DHEA for mice, Intestine

description:
Library name: DHEA_Intestine
10x Genomics

source_name: Intestine

value: Intestine


title: DMSO_3

description: Library name: A3

value: prostate

value: Myc-CaP

value: prostate tumor

value: MYC overexpressing


title: DHEA for mice, Thymus

description:
Library name: DHEA_Thymus
10x Genomics

source_name: Thymus

value: Thymus


title: sasame oil for mice, Kidney

description:
Library name: CTRL_Kidney
10x Genomics

value: sasame oil


title: sasame oil for mice, Heart

description:
Library name: CTRL_Heart
10x Genomics


title: DHEA for mice, Ovary

description:
Library name: DHEA_Ovary
10x Genomics

source_name: Ovary

value: Ovary


title: sasame oil for mice, Spleen

description:
Library name: CTRL_Spleen
10x Genomics


title: sasame oil for mice, Lung

description:
Library name: CTRL_Lung
10x Genomics


title: DHEA for mice, Brain

description:
Library name: DHEA_Brain
10x Genomics

source_name: Brain

value: Brain


title: sasame oil for mice, Liver

description:
Library name: CTRL_Liver
10x Genomics

value: WT


title: sasame oil for mice, Utery

description:
Library name: CTRL_Utery
10x Genomics


title: sasame oil for mice, Intestine

description:
Library name: CTRL_Intestine
10x Genomics


title: sasame oil for mice, Brain

description:
Library name: CTRL_Brain
10x Genomics


title: CD8+ cells, C57BL/6J mice, Hmgb2fl/fl;Cd4-Cre-2, Day 5

city: SHANGHAI

first: WEIFENG

last: QU

address: No.180 Fenglin Road

institute: Zhongshan Hospital, Fudan university

description: Library name: ATAC-CKO-2

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.
Assembly: Mapping of pair-end reads. Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences. The clean reads were then aligned to reference genome sequences using the bwa program.
Supplementary files format and content: narrowPeak file including reads count for each sample

source_name: splenic CD8+ T cells

extract_protocol:
The Nextera DNA Library Preparation Kit (Illumina) was used to perform the transposition according to the manufacturer’s manual. 50 000 nuclei were pelleted and resuspended with transposase, for 30 minutes at 37 ℃. The transposed DNA fragments were purified immediately after with a MinElute PCR Purification Kit (Qiagen).
After Samples were PCR-amplified using 1X NEBNext High-Fidelity PCR Master Mix (New England Biolabs, MA). Subsequent libraries were purified with the MinElute PCR Purification Kit (Qiagen) and subjected to sequencing on Illumina Novaseq 6000 using PE150.

value: splenic CD8+ T cells


title: CD8+ cells, C57BL/6J mice, Control-1, Day 5

description: Library name: ATAC-NC-1

value: control


title: CD8+ cells, C57BL/6J mice, Hmgb2fl/fl;Cd4-Cre-1, Day 5

description: Library name: ATAC-CKO-1


title: Ppif_ALD3

city: Guangzhou

first: Zhaoyi

last: Che

state: Guangdong

address: 601 Huangpu Avenue West

institute: Jinan university

description: Library name: Sample9

data_processing:
1. Quality control: Raw data (raw reads) of fastq format were firstly processed through in-houseperl scripts. In this step, clean data (clean reads) were obtained by removing readscontaining adapter, reads containing ploy-N and low quality reads fromrawdata. At the same time, Q20, Q30 and GC content the clean data were calculated. All thedownstream analyses were based on the clean data with high quality.
2. Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded fromgenome website directly. Index of the reference genome was built using Hisat2 v2.0.5and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a databaseof splice junctions based on the gene model annotation file and thus a better mappingresult than other non-splice mapping tools.
3. Quantification of gene expression level: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to eachgene. And then FPKM of each gene was calculated based on the length of the geneand reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers theeffect of sequencing depth and gene length for the reads count at the same time, andiscurrently the most commonly used method for estimating gene expression levels.
4. Differential expression analysis:  Differential expression analysis of twoconditions/groups (two biological replicates per condition) was performed usingtheDESeq2 R package (1.16.1). DESeq2 provide statistical routines for determiningdifferential expression in digital gene expression data using a model based onthenegative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Geneswith an adjusted P-value <0.05 found by DESeq2 were assigned as differentiallyexpressed.
5. GO and KEGG enrichment analysis of differentially expressed genes: (1) Gene Ontology (GO) enrichment analysis of differentially expressed genes wasimplemented by the clusterProfiler R package, in which gene length bias wascorrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enrichedby differential expressed genes. (2) KEGG is a database resource for understanding high-level functions and utilitiesof the biological system, such as the cell, the organism and the ecosystem, frommolecular-level information, especially large-scale molecular datasets generatedbygenome sequencing and other high-through put experimental technologies(http://www.genome.jp/kegg/). We used clusterProfiler R package to test thestatistical enrichment of differential expression genes in KEGG pathways.
Assembly: mm10
Supplementary files format and content: standardized RNA values (FPKM) identified for each sample

source_name: liver

extract_protocol:
Total RNA extraction method:①RNA degradation and contamination was monitored on 1%agarose gels. ② RNA purity was checked using the NanoPhotometer®spectrophotometer (IMPLEN, CA, USA) . ③RNA integrity was assessed using the RNA Nano 6000 Assay Kit of theBioanalyzer 2100 system (Agilent Technologies, CA, USA).
1. Library preparation for Transcriptome sequencing: A total amount of 1 µg RNA per sample was used as input material for the RNAsample preparations. Sequencing libraries were generated using NEBNext®UltraTMRNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’srecommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attachedmagnetic beads. Fragmentation was carried out using divalent cations under elevatedtemperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strandcDNA was synthesized using random hexamer primer and M-MuLVReverseTranscriptase(RNase H - ). Second strand cDNA synthesis was subsequentlyperformed using DNA Polymerase I and RNase H. Remaining overhangs wereconverted into blunt ends via exonuclease/polymerase activities. After adenylationof 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure wereligated to prepare for hybridization. In order to select cDNAfragments of preferentially 250~300 bp in length, the library fragments were purified with AMPureXP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followedby5min at 95 °Cbefore PCR. Then PCR was performed with Phusion High -Fidelity DNApolymerase, Universal PCR primers and Index (X) Primer. At last, PCRproductswere purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. 2. Clustering and sequencing (GenechemExperimental Department): The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) accordingtothe manufacturer’s instructions. After cluster generation, the library preparations weresequenced on an Illumina Novaseq platform and 150 bp paired-end reads weregenerated.

value: liver

value: ethanol diet


title: ALD3

description: Library name: Sample6


title: Ppif_ALD1

description: Library name: Sample7


title: Ctrl2

description: Library name: Sample2

value: control diet


title: ALD1

description: Library name: Sample4


title: ALD2

description: Library name: Sample5


title: Ctrl3

description: Library name: Sample3


title: cortex,P2,WT

city: Shanghai

first: TongYe

last: Fu

address: 138 Yi Xue Yuan Road

institute: Fudan University

description: Library name: SAMPLES19

data_processing:
High quality sequences (clean reads) were obtained by removing low quality sequences and joints. The clean reads were then processed with cellranger-7.0.1 software to obtain quantitative information on gene expression.
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files

source_name: cortex

extract_protocol:
After deep anesthetizing the entire mouse, its brain/forelimb was immediately removed and immersed in ice-cold Hanks balanced salt solution (Gibco 14175-095). The dorsal cortex/humerus was dissected into small pieces and dissociated into single-cell suspensions using a papain cell dissociation kit (Miltenyi Biotec, catalog number 130-092-628) or collagenase type 2 according to the manufacturer's instructions. Single-cell RNA sequencing (scRNA-Seq) libraries were prepared using the Chromium droplet-based sequencing platform (10X Genomics), in accordance with the manufacturer’s guidelines (manual document part number: CG00052 Rev C). The cDNA libraries were purified, quantified using an Agilent 2100 Bioanalyzer, and sequenced on an Illumina HiSeq 6000.
The Chromium dropletbased sequencing platform (10X Genomics) was used to generate scRNA-Seq libraries, following the manufacturer’s instructions

value: cortex


title: cortex,P2,FGFR3

description: Library name: SAMPLES20


title: cortex,E18_5,WT

description: Library name: SAMPLES17


title: cortex,E18_5,FGFR3

description: Library name: SAMPLES18


title: bone,E18_5,FGFR3

description: Library name: SAMPLES12

source_name: forelimb

value: forelimb


title: cortex,E15_5,FGFR3

description: Library name: SAMPLES16


title: cortex,E15_5,WT

description: Library name: SAMPLES15


title: bone,E18_5,WT

description: Library name: SAMPLES11


title: sasame oil for mice, Thymus

description:
Library name: CTRL_Thymus
10x Genomics


title: cortex,E12_5,WT

description: Library name: SAMPLES13


title: sasame oil for mice, Ovary

description:
Library name: CTRL_Ovary
10x Genomics


title: bone,E17_5,WT

description: Library name: SAMPLES9


title: bone,E16_5,WT

description: Library name: SAMPLES7


title: bone,E16_5,FGFR3

description: Library name: SAMPLES8


title: CD8+ cells, C57BL/6J mice, Control-2, Day 5

description: Library name: ATAC-NC-2


title: bone,E15_5,WT

description: Library name: SAMPLES5


title: bone,E15_5,FGFR3

description: Library name: SAMPLES6


title: bone,E14_5,WT

description: Library name: SAMPLES3


title: bone,E13_5,FGFR3

description: Library name: SAMPLES2


title: bone,E14_5,FGFR3

description: Library name: SAMPLES4


title: Ppif_ALD2

description: Library name: Sample8


title: cortex,E12_5,FGFR3

description: Library name: SAMPLES14


title: mouse with DED treated by exosome eye drop 3

city: Taiyuan

first: yuxing

last: gong

state: Shanxi

address: yingze street

department: Ministry of Education, and the Department of Physiology

institute: Shanxi medical university

description:
Library name: EXO_3
EXO_3

data_processing:
Data processing step was finished with the help of Nevogene.
Assembly: mm9
Supplementary files format and content: Excel  files include counts values for each Sample

source_name: Cornea

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 .0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seg were prepared using NEBNext® UltraTM RNA Library Prep Kit following manufacturer's protocols.

value: Cornea

value: Cornea cells

value: DED treated by exo eye drop


title: mouse with DED treated by exosome i.v. 2

description:
Library name: EXOIV_2
EXOIV_2

value: DED treated by exo i.v.


title: mouse with DED treated by exosome i.v. 1

description:
Library name: EXOIV_1
EXOIV_1


title: Ctrl1

description: Library name: Sample1


title: control group3

description:
Library name: Control_3
Control_3

value: without treatment


title: model mouse with DED 3

description:
Library name: DED_3
DED_3

value: DED model


title: model mouse with DED 1

description:
Library name: DED_1
DED_1


title: model mouse with DED 2

description:
Library name: DED_2
DED_2


title: mouse with DED treated by exosome eye drop 2

description:
Library name: EXO_2
EXO_2


title: control group1

description:
Library name: Control_1
Control_1


title: Input  2iL rep2

city: Cambridge

first: David

last: Lando

address: Department Biochemistry , Sanger Bulding, Tennis Court Road

department: Biochemistry

country: United Kingdom

institute: University of Cambridge

description: Library name: 20

data_processing:
CutandRun paired-end reads were processed using a custom software script (https://github.com/tjs23). The script is a wrapper around hisat2 (https://daehwankimlab.github.io/hisat2) and bowtie2 (https://bowtie-bio.sourceforge.net/bowtie2/index.shtml), which can be used to assign reads to two different parental genomes. Mapping parameter settings similar to bowtie2 very-sensitive mode were used. Specifically, --score-min, L,-0.8,-0.8; -D, 20; -R, 3; -N, 1; -L, 20;  -i: S,1,0.5. In addition, Prior to mapping, adaptor sequences have been removed using TrimGalore with default setting (https://github.com/FelixKrueger/TrimGalore). Following the mapping with custom script, reads were filtered using samtools (samtools view -h -b -F 0x4 -f 0x2 -q 30) and duplicates were filtered using Picard. Peak calling was performed using MACS2 with –nomodel --shift -100 --extsize 200 -q 0.01.
Assembly: B6_v3_chr.fasta and CAST_v3_chr.fasta is a custom genome build of a mouse diploid ES cell line BC8, derived from C57BL/6 x M.m castaneus cross.
Supplementary files format and content: Summit peak files are tab-delimited .bed files containing chromosomal coordinates of all CutandRun peaks.
Library strategy: CUT&Run

growth_protocol: For routine cell culture, cell lines were maintained in N2B27 media supplemented with 2i and mouse leukemia inhibitory factor (mLIF). 50 % DMEM/F-12 medium (Gibco, 21041025) and 50 % Neurobasal™ Medium (Gibco, 12348017) was supplemented with 1 x N2 to a final concentration of 2.5 µg/ml insulin (provided in-house by the Cambridge Stem Cell Institute), 0.5x B-27™ Supplement (Gibco, 17504044), 1x minimum essential medium non-essential amino acids supplement (Sigma-Aldrich, M7145), 2 mM L-glutamine (Life tech, 25030024), and 0.1 mM 2-mercaptoethanol (Life tech, 21985023), 2i inhibitors (1 µM PD0325901, 3 µM CHIR99021) and 10 ng/ml mLIF (provided by the Biochemistry Department, University of Cambridge). Cells were routinely screened for mycoplasma contamination.

extract_protocol:
CutandRun was performed with 100K cells using the method described by Janssens and Henikoff 2019 protocols.io (https://www.protocols.io/view/cut-amp-run-targeted-in-situ-genome-wide-profiling-zcpf2vn).
PCR library amplification and barcoding was carried out using NEBNext® High-Fidelity 2X PCR Master Mix with NEBNext® index primers (NEB), following the manufactures instructions.

treatment_protocol: Naïve ES state cells were plated at a density of 10,000 cells/cm2 and grown in N2B27 with 2i and LIF for 48 hrs. Formative state cells were plated at the same density in N2B27 with 2i and no LIF. After 24 hrs the two inhibitors were removed and cells were grown in N2B27 only media for a further 24 hrs to obtain formative state cells or 48 hrs to obtain primed state cells.

value: Embryonic stem cell

value: naïve


title: Input  24h rep1

description: Library name: 21

value: formative


title: Input  24h rep2

description: Library name: 22

value: WT


title: Input  48h rep1

description: Library name: 23

value: primed


title: K27ac 48h rep2

description: Library name: 18


title: bone,E13_5,WT

description: Library name: SAMPLES1


title: Input  48h rep2

description: Library name: 24


title: K27ac 24h rep2

description: Library name: 16


title: K27ac 48h rep1

description: Library name: 17


title: K27ac 2iL rep2

description: Library name: 14


title: mouse with DED treated by exosome i.v. 3

description:
Library name: EXOIV_3
EXOIV_3


title: K27ac 2iL rep1

description: Library name: 13


title: control group2

description:
Library name: Control_2
Control_2


title: K27me3 48h rep1

description: Library name: 11


title: K27me3 48h rep2

description: Library name: 12


title: mouse with DED treated by exosome eye drop 1

description:
Library name: EXO_1
EXO_1


title: K4me3 48h rep2

description: Library name: 6


title: K4me3 24h rep1

description: Library name: 3


title: K27me3 24h rep2

description: Library name: 10


title: K4me3 2iL rep2

description: Library name: 2


title: K27me3 2iL rep2

description: Library name: 8


title: K4me3 24h rep2

description: Library name: 4


title: Input 2iL rep1

description: Library name: 19


title: Mouse_P1_oocyte_Rbpms2KO_3

city: Xuhui, Shanghai

first: Jie

last: Li

state: Shanghai

address: 320 Yueyang Road, Shanghai

institute: Center for Excellence in Brain Science and Intelligence Technology (Institute of Neuroscience), Chinese Academy of Sciences

description:
Library name: KO_3
Column name in FPKM_allsample.txt: KO3

data_processing:
Raw reads were firstly processed through cutadapt with the default parameters. In this step, clean reads were obtained by removing reads containing adapter and low-quality reads.Paired-end clean reads were aligned to the reference genome (GRCm38) using Hisat2.The abundance of genes was estimated from the aligned reads using HTSeq.FPKM (fragments per kilobase of transcript per million mapped reads) was used for further analysis.
When performing alignment with HISAT2, default parameters are used for non-strand-specific libraries. For strand-specific libraries, the library type needs to be specified (i.e., use --rna-strandness RF for the first type and --rna-strandness FR for the second type).
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited txt file includes FPKM for each sample

source_name: ovary P1

growth_protocol: To investigate the impact of Rbpms2 deficiency on transcriptional regulation, we conducted microarray analysis using total RNA extracted from Rbpms2-knockout P1 oocytes.

extract_protocol:
Five to ten putative primordial oocytes per group were collected by a mouth pipette into one tube for mRNA amplification which was performed following the manufacturer’s instructions (Vazyme, N712-03) with 18 amplification cycles. Library preparation followed the methods in (Chen et al., 2023).
Briefly, after test the concentration by Qubit Flex Fluorometer (Thermo Fisher Scientific) and fragment size by Agilent Bioanalyzer 2100, TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503) was used to prepare the library.

treatment_protocol: P1 ovaries of wild type or Rbpms2 knock out mice are digested with collagenase (2mg/ml) at 37°C for 5-10 minutes. Remove the collagenase and digest the ovaries with trypsin (0.25%) at 37°C for 5-10 minutes, and then pipette gently to dissociate into single cells. FBS is added to stop the reaction and cells are collected by centrifugation (500g, 5-10 min). Resuspend the cells in PBS.

value: ovary P1

value: Rbpms2 knock out


title: K4me3 2iL rep1

description: Library name: 1


title: K27ac 24h rep1

description: Library name: 15


title: K4me3 48h rep1

description: Library name: 5


title: Mouse_P1_oocyte_Rbpms2KO_1

description:
Library name: KO_1
Column name in FPKM_allsample.txt: KO1


title: Mouse_P1_oocyte_Ctrl_4

description:
Library name: WT_4
Column name in FPKM_allsample.txt: Ctrl4


title: Mouse_P1_oocyte_Ctrl_1

description:
Library name: WT_1
Column name in FPKM_allsample.txt: Ctrl1


title: Mouse_P1_oocyte_Ctrl_3

description:
Library name: WT_3
Column name in FPKM_allsample.txt: Ctrl3


title: Normoxia control - ZT20 - REP2

city: Irvine

first: Kousha

last: Changizi

address: 4038 Donald Bren Hall

department: Computer Science

institute: University of California, Irvine

description:
Library name: Sample 35
ZT_20_REP_2

data_processing:
Reads aligned to mm10 assembly and RefSeq genes using TopHat release 2.1.1
Gene expression results (FPKM) obtained using Cufflinks release 2.2.1
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Samples

growth_protocol: Male C57BL/6JRj mice (16 weeks old) were housed 5 per cage under a 12 h light : 12 h dark cycle (lights on = ZT0) at 22 ± 1 °C, 50–60 % humidity, with ad libitum access to LASQRodent Rod16 chow and water.

extract_protocol:
50–100 mg frozen liver was homogenised in 1 mL TRIzol Reagent (Invitrogen 15596026). RNA was isolated by chloroform extraction and isopropanol precipitation, washed in 75 % ethanol and resuspended in DEPC-treated water. Integrity was checked on Agilent TapeStation RNA ScreenTape.
1 µg total RNA → Illumina Stranded mRNA Prep, Ligation (poly-A selection). mRNA fragmented, first-strand cDNA synthesis with random primers, second-strand synthesis incorporating dUTP for strand specificity, A-tailing, adapter ligation, 10–11 PCR cycles, validation on TapeStation and Quantifluor. Libraries pooled equimolarly and sequenced 2 × 100 bp on NovaSeq 6000 (S4 XP).

treatment_protocol: Intermittent-hypoxia (IH) group: 60 hypoxia-reoxygenation cycles h-¹ (nadir 5 % FiO₂, peak 21 % FiO₂) delivered from ZT0–ZT8 daily for 4 weeks in a custom chamber; Control group: matched air–air cycles. After 4 weeks animals were sacrificed by decapitation and livers snap-frozen.

value: Liver

tag: strain

value: male

value: wild-type

value: normoxia control


title: Mouse_P1_oocyte_Rbpms2KO_2

description:
Library name: KO_2
Column name in FPKM_allsample.txt: KO2


title: Mouse_P1_oocyte_Rbpms2KO_4

description:
Library name: KO_4
Column name in FPKM_allsample.txt: KO4


title: Normoxia control - ZT16 - REP3

description:
Library name: Sample 33
ZT_16_REP_3


title: Normoxia control - ZT20 - REP3

description:
Library name: Sample 36
ZT_20_REP_3


title: Normoxia control - ZT8 - REP3

description:
Library name: Sample 27
ZT_8_REP_3


title: K27me3 2iL rep1

description: Library name: 7


title: Mouse_P1_oocyte_Ctrl_2

description:
Library name: WT_2
Column name in FPKM_allsample.txt: Ctrl2


title: Normoxia control - ZT8 - REP2

description:
Library name: Sample 26
ZT_8_REP_2


title: Normoxia control - ZT0 - REP3

description:
Library name: Sample 21
ZT_0_REP_3


title: Normoxia control - ZT4 - REP1

description:
Library name: Sample 22
ZT_4_REP_1


title: Normoxia control - ZT20 - REP1

description:
Library name: Sample 34
ZT_20_REP_1


title: Intermittent hypoxia - ZT16 - REP3

description:
Library name: Sample 15
ZT_16_REP_3

value: chronic intermittent hypoxia (4 wk)


title: Normoxia control - ZT8 - REP1

description:
Library name: Sample 25
ZT_8_REP_1


title: Intermittent hypoxia - ZT20 - REP3

description:
Library name: Sample 18
ZT_20_REP_3


title: Normoxia control - ZT12 - REP3

description:
Library name: Sample 30
ZT_12_REP_3


title: Normoxia control - ZT4 - REP3

description:
Library name: Sample 24
ZT_4_REP_3


title: Normoxia control - ZT12 - REP2

description:
Library name: Sample 29
ZT_12_REP_2


title: Intermittent hypoxia - ZT12 - REP3

description:
Library name: Sample 12
ZT_12_REP_3


title: Normoxia control - ZT16 - REP2

description:
Library name: Sample 32
ZT_16_REP_2


title: Intermittent hypoxia - ZT8 - REP3

description:
Library name: Sample 9
ZT_8_REP_3


title: K27me3 24h rep1

description: Library name: 9


title: Normoxia control - ZT12 - REP1

description:
Library name: Sample 28
ZT_12_REP_1


title: Normoxia control - ZT0 - REP2

description:
Library name: Sample 20
ZT_0_REP_2


title: Intermittent hypoxia - ZT16 - REP1

description:
Library name: Sample 13
ZT_16_REP_1


title: Normoxia control - ZT16 - REP1

description:
Library name: Sample 31
ZT_16_REP_1


title: Normoxia control - ZT4 - REP2

description:
Library name: Sample 23
ZT_4_REP_2


title: Intermittent hypoxia - ZT20 - REP1

description:
Library name: Sample 16
ZT_20_REP_1


title: Intermittent hypoxia - ZT12 - REP1

description:
Library name: Sample 10
ZT_12_REP_1


title: Intermittent hypoxia - ZT8 - REP2

description:
Library name: Sample 8
ZT_8_REP_2


title: Intermittent hypoxia - ZT12 - REP2

description:
Library name: Sample 11
ZT_12_REP_2


title: Normoxia control - ZT0 - REP1

description:
Library name: Sample 19
ZT_0_REP_1


title: Intermittent hypoxia - ZT4 - REP3

description:
Library name: Sample 6
ZT_4_REP_3


title: Intermittent hypoxia - ZT20 - REP2

description:
Library name: Sample 17
ZT_20_REP_2


title: Intermittent hypoxia - ZT4 - REP2

description:
Library name: Sample 5
ZT_4_REP_2


title: Intermittent hypoxia - ZT4 - REP1

description:
Library name: Sample 4
ZT_4_REP_1


title: Intermittent hypoxia - ZT0 - REP2

description:
Library name: Sample 2
ZT_0_REP_2


title: Intermittent hypoxia - ZT0 - REP3

description:
Library name: Sample 3
ZT_0_REP_3


title: E17pt5_ShhCre_Brd4_HET

city: Philadelphia

first: Sylvia

middle: N

last: Michki

address: 3615 Civic Center Blvd

department: Pulmonary & Sleep Medicine

institute: Children's Hospital of Philadelphia

description: Library name: 9483191535_Brd4_2_S6

data_processing:
Read alignment and cell calling using STAR-solo (velocyto output)
Ambient-RNA correction using scvi-tools scAR
h5ad file creation using anndata
Assembly: GRCm39
Supplementary files format and content: HDF5 format anndata objects (.h5ad) for combined experiment, containing cell barcodes, feature names, and counts matrices. The log1p(CPM) expression matrix is loaded in the `X` slot. The `layers` dictionary contains the log1p(CPM), spliced, unspliced, counts_raw, and counts_scAR keys, corresponding to the ln(1+CPM) expression, velocyto spliced/unspliced counts, the raw total (spliced + unspliced + ambiguous) counts, and the scAR ambient-RNA corrected total counts, respectively.

source_name: lung

extract_protocol:
Live, EPCAM+ cells sorted by FACS from mouse lungs at E17.5. 10X Chromium GEX v3 3’-biased scRNA-seq chemistry was used to extract mRNA from individual cells.
10X Genomics 3’-biased gene expression library construction (v3.1).

value: lung

value: epithelial

value: Shh-Cre/+, Brd4 fl/+


title: Intermittent hypoxia - ZT8 - REP1

description:
Library name: Sample 7
ZT_8_REP_1


title: 20269X4 DAC_Th1_3

city: Salt Lake City

first: Jeffrey

middle: Scott

last: Hale

state: Utah

address: 15 North Medical Drive

department: Pathology

institute: University of Utah

description: Library name: 20269X4

data_processing:
Sequencing data quality was assessed using FastQC v0.11.4. Adapters were trimmed from the sequencing reads using Trim Galore!v0.4.4.
Alignment to the mm10 reference genome was performed using Bismark v0.19.0. Deduplication was performed with deduplicate_bismark.
Library quality was considered sufficient if greater than 50% of reads uniquely aligned to the genome.
Bisulfite conversion efficiency was assessed by evaluating the percent of methylation observed in the CHH genome context and considered sufficient when this value was less than 3%.
Library genome coverage was considered sufficient if 80% of the genome had a depth of at least 10 reads. CpG positions in the reference genome were quantified using the Bismark Methylation Extractor v0.19.0.
This analysis pipeline was developed and executed in the Seven Bridges cloud platform, and included use of the Bismark Analysis public workflow.
Differentially methylated regions (DMR) were detected using Bsmooth, Bsmooth.tst and dmrFinder in the bsseq R package
Assembly: mm10
Supplementary files format and content: Tab-delimited bismark coverage files
Library strategy: EM-seq

source_name: Spleen

extract_protocol:
DNA was extracted from FAC Sorted T cell subsets using the Dneasy Blood and Tissue Kit (Qiagen)
DNA libraries were prepared uing the NEBNext Enzymatic Methyl-seq kit according to manufacturers protocols.

value: Spleen

value: Th1 Cell

value: Decitabine Treated


title: 20269X1 PBS_Tfh_3

description: Library name: 20269X1

value: Tfh Cell

value: PBS Treated


title: 19901X17 PBS_Tfh_2

description: Library name: 19901X17

value: WT


title: Intermittent hypoxia - ZT0 - REP1

description:
Library name: Sample 1
ZT_0_REP_1


title: E17pt5_ShhCre_Brd4_KO

description: Library name: 4575575880_Brd4_1_S5

value: Shh-Cre/+, Brd4 fl/fl


title: 19901X15 DAC_Tfh_2

description: Library name: 19901X15


title: 19901X7 KO_Tfh_3

description: Library name: 19901X7

value: Dnmt3a KO

value: untreated


title: 20269X2 PBS_Th1_3

description: Library name: 20269X2


title: 19901X3 KO_Tfh_2

description: Library name: 19901X3


title: 19901X4 KO_Th1_2

description: Library name: 19901X4


title: 19901X10 KO_Naive_3

description: Library name: 19901X10

value: Naive CD4+ T cell


title: 19901X16 DAC_Th1_2

description: Library name: 19901X16


title: 19901X8 KO_Th1_3

description: Library name: 19901X8


title: 19901X18 PBS_Th1_2

description: Library name: 19901X18


title: bone,E17_5,FGFR3

description: Library name: SAMPLES10

value: forelimb


title: 19901X9 KO_Naive_2

description: Library name: 19901X9


title: 19625X7 PBS_Th1_1

description: Library name: 19625X7


title: 19625X9 DAC_Th1_1

description: Library name: 19625X9


title: 19901X1 WT_Tfh_2

description: Library name: 19901X1


title: 19625X6 PBS_Tfh_1

description: Library name: 19625X6


title: 19901X2 WT_Th1_2

description: Library name: 19901X2


title: 19625X5 KO_Naive_1

description: Library name: 19625X5


title: 19625X4 KO_Th1_1

description: Library name: 19625X4


title: 20269X3 DAC_Tfh_3

description: Library name: 20269X3


title: 19625X3 WT_Th1_1

description: Library name: 19625X3


title: 19901X6 WT_Th1_3

description: Library name: 19901X6


title: 21075X11 KO_Tfh_3

description: Library name: 21075X11

data_processing:
The mouse GRCm38 genome and gene feature files were downloaded from Ensembl release 98. Reference database was created using STAR version 2.7.2c with splice junctions optimized for 150 base pair reads.
Optical duplicates were removed from the paired end FASTQ files using clumpify v38.34 and reads were trimmed of adapters using cutadapt 1.16.
The trimmed reads were aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes using featureCounts version 1.6.3. Differentially expressed genes were identified using DESeq2 version 1.30.1 with a 5% FDR.
Assembly: GRCm38
Supplementary files format and content: FeatureCount ouput files combined into a single tab-delimited matrix

extract_protocol:
Total RNA was Sorted Tfh, Th1, and Naïve SMARTA cells was extracted using the Zymo Direct-zol RNA miniprep kit.
Libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep with rRNA Depletion Kit (human,mouse,rat).


title: 21075X9 KO_Tfh_2

description: Library name: 21075X9


title: 19625X1 WT_Tfh_1

description: Library name: 19625X1


title: 21075X12 KO_Th1_3

description: Library name: 21075X12


title: 21075X10 KO_Th1_2

description: Library name: 21075X10


title: 21075X8 KO_Th1_1

description: Library name: 21075X8


title: 19625X8 DAC_Tfh_1

description: Library name: 19625X8


title: 21075X7 KO_Tfh_1

description: Library name: 21075X7


title: 19625X2 KO_Tfh_1

description: Library name: 19625X2


title: 21075X6 WT_Th1_3

description: Library name: 21075X6


title: Intermittent hypoxia - ZT16 - REP2

description:
Library name: Sample 14
ZT_16_REP_2

value: Liver

value: male

value: wild-type


title: 21075X5 WT_Th1_2

description: Library name: 21075X5


title: 21075X4 WT_Th1_1

description: Library name: 21075X4


title: 21075X2 WT_Tfh_2

description: Library name: 21075X2


title: NM injured losartan treated

city: Chicago

first: Han

last: Peng

state: IL

address: 303 E Chicago Ave, Ward 9-120

institute: Feinberg School of Medicine, Northwestern University

description: Library name: NM injured losartan treated

data_processing:
follow the protocol from 10X genomics
Assembly: GRCm38.91
Supplementary files format and content: matrix file

source_name: cornea/limbus

extract_protocol:
Whole eyes were harvested . The lens, retina, iris, and trabecular network were removed leaving the entire ocular anterior segment, from which most of the conjunctiva was carefully dissected and discarded. Dissect corneas with ice cold PBS and put corneas into one Eppendorf tube filled with 0.7mg/mL liberase TM (from Roche) in RPMI.  Place tube in 37 degree incubator with 5% CO2 for 1 hour. Then add 500ul 0.25%Trypsin for 15min. Use 40um filter into Eppendorf tube. Cell viability was checked and accepted with at least an 80% viability score. Such cells were processed for scRNA-seq using 10XGenomics pipeline in the Northwestern University NUseq Core.
follow the instructions from 10XGenomics

value: cornea/limbus

value: wt


title: NM injured saline treated

description: Library name: NM injured saline treated


title: 21075X1 WT_Tfh_1

description: Library name: 21075X1


title: intestine,ND1

city: Nanjing

first: Yue

last: Yang

address: 1 WenYuan Road

institute: Nanjing Normal University

description: Library name: N-1

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2.
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.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample.

source_name: intestine

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: intestine


title: intestine,Five Substances Powder with Poria4

description: Library name: H1-4


title: intestine,ND2

description: Library name: N-2


title: intestine,Five Substances Powder with Poria2

description: Library name: H1-2


title: intestine,ND3

description: Library name: N-3


title: intestine,HFD3

description: Library name: H-3


title: intestine,Five Substances Powder with Poria3

description: Library name: H1-3


title: intestine,HFD4

description: Library name: H-4


title: intestine,HFD2

description: Library name: H-2


title: WT CD8 T cells, LCMV cl13, rested

city: Lausanne

first: Tania

last: Wyss

address: Rue du Bugnon 25A

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

data_processing:
Demultiplexing and fastq generation were completed using bcl2fastq (v. 2.20.0.422).
Cells were called and read counts were summarized per gene per cell using the 10x cellranger pipeline (v6.0.2) against the Mus musculus genome (refdata-gex-mm10-2020-A, downloaded from the 10x Genomics website)
Assembly: mm10 (refdata-gex-mm10-2020-A, which corresponds to Ensembl release 98, and GENCODE M23)
Supplementary files format and content: For each library of single cells, we provide the 3 files generated by the Cell Ranger pipeline within the filtered_feature_bc_matrix folder (i.e the cells called by Cell Ranger): barcodes.tsv.gz (tab-separated file, contains the cell barcodes),  features.tsv.gz (tab-separated file, contains the genes included in the mm10 transcriptome) and matrix.mtx.gz (sparse matrix format, contains the raw counts per gene (in the rows), per cell (in the columns)). The prefix of the three files per library corresponds to the sample description.
Supplementary files format and content: We also provide the raw counts of the cells retained after QC filtering (csv file labeled with UMI_counts_retained_cells.csv, the first column contains gene symbols), and a csv file with meta data per cell (csv file labeled with metadata_retained_counts.csv, the first column contains the cell IDs matching the column names in UMI_counts_retained_cells.csv). The meta data file contains cluster ID and UMAP coordinate, generated using the Seurat package (v4.3.0). In the meta data, the condition column describes the LCMV strain and the genotype of the mouse from which the cells were extracted, as well as the rested/stimulated treatment (WT_Arm.no = LCMV Arm, rested; WT_Arm.stim = LCMV Arm, stimulated; WT_cl13.no = LCMV cl13, rested; WT_cl13.stim=LCMV cl13, stimulated, PD1KO_cl13.no = PD1-KO LCVM cl13, rested; PD1KO_cl13.stim = PD-KO LCMV cl13, stimulated).

source_name: splenocytes

extract_protocol:
Mouse P14 cells were flow sorted from the spleen of Vbeta5 hosts (CD45.1) transferred with WT or PD-1 KO Tcf7GFP P14 cells at d28 post LCMV infection. WT P14 cells were sorted from hosts infected with either Armstrong (Arm) or clone13 (cl13), while PD-1 KO Tcf7GFP P14 cells were exposed to cl13 only.  The sorted cells were restimulated in vitro with plate bound anti-CD3/28 antibodies for 4 h (stimulated) or were cultured without activation (rested) and then subjected to scRNAseq analysis. Rested and stimulated cells derived from the same donor mouse.
10x Genomics Dual Single Cell 3' v3 chemistry

value: splenocytes

value: P14 CD8 T cells

value: Tcf7GFP tg/+ TCRLCMV327 tg/+

value: LCMV clone 13  - Rested


title: intestine,HFD1

description: Library name: H-1


title: PD1 KO CD8 T cells, LCMV cl13, restimulated

value: PD1 -/-  Tcf7GFP tg/+ TCRLCMV327 tg/+

value: LCMV clone 13  - Restimulated in vitro with anti-CD3/28 antibodies for 4 h


title: WT CD8 T cells, LCMV cl13, restimulated


title: PD1 KO CD8 T cells, LCMV cl13, rested


title: 21075X3 WT_Tfh_3

description: Library name: 21075X3

value: Spleen

value: Tfh Cell

value: WT


title: tga_Pta 11528_24h_biol rep1

city: Madrid

first: Santiago

last: Michavila Puente-Villegas

address: c/Darwin 3

department: GMP

institute: CNB-CSIC

description: Library name: SMHH1_FKRN250015307-1A_E250062790

data_processing:
Raw paired-end reads were trimmed using default parameters with fastp tool
Sequences were mapped and quantified to the reference genome
Assembly: MpTak1_v6.1
Supplementary files format and content: Text format with one columns of gene_ID plus others with TPMs per sample

organism: Marchantia polymorpha

source_name: Thallus

growth_protocol: Marchantia polymorpha accession Takaragaike-1 (Tak-1; male),  Mptga mutant and SA-deficient Marchantia NahG plants (OE:PpNahG/MpTak-1) were used in this work. M. polymorpha plants were grown on half Gamborg's B5 medium containing 1% agar in vitro  (22 °C, 50–60 µmol m−2 s−1, 16 h light) for 3 weeks. After Pta 11528 infection, plants were transferred to vermiculite and to controlled environment chambers (average temperature of 22°C,  45%–65% relative humidity, 8 h light).

extract_protocol:
Total RNA from Marchantia was extracted with Rneasy Plant Mini Kit of QIAGEN and DNase on-column digestion (Qiagen) was performed to remove genomic DNA contamination
The RNA-seq library was prepared by Novogene, using standard Illumina protocols.

treatment_protocol: M. polymorpha plants were inoculated with Pseudomonas syringae pv. tabaci (Pta) 11528 by dipping into a bacterial suspension containing high levels of bacteria at 10^8 cfu/ml (OD600 = 0.2) with 0.04% Silwet L-77 for 5 minutes.

value: Thallus

value: tga


title: tga_Mock_24h_biol rep3

description: Library name: SMGG3_FKRN250015297-1A_E250062790


title: WT CD8 T cells, LCMV Arm, restimulated

value: LCMV Armstrong - Restimulated in vitro with anti-CD3/28 antibodies for 4 h


title: WT CD8 T cells, LCMV Arm, rested

value: LCMV Armstrong - Rested


title: tga_Mock_24h_biol rep1

description: Library name: SMGG1_FKRN250015295-1A_E250062790


title: tga_Mock_24h_biol rep2

description: Library name: SMGG2_FKRN250015296-1A_E250062790


title: NahG_Pta 11528_24h_biol rep2

description: Library name: SMDD2_FKRN250015302-1A_E250062790

value: NahG


title: NahG_Pta 11528_24h_biol rep1

description: Library name: SMDD1_FKRN250015301-1A_E250062790


title: NahG_Mock_24h_biol rep3

description: Library name: SMCC3_FKRN250015291-1A_E250062790


title: NahG_Mock_24h_biol rep1

description: Library name: SMCC1_FKRN250015289-1A_E250062790


title: Tak1_Pta 11528_24h_biol rep3

description: Library name: SMBB3_FKRN250015300-1A_E250062790


title: Tak1_Pta 11528_24h_biol rep2

description: Library name: SMBB2_FKRN250015299-1A_E250062790


title: 19901X5 WT_Tfh_3

description: Library name: 19901X5

value: untreated


title: Tak1_Pta 11528_72h_biol rep3

description: Library name: SMJJ3_FKRN250022386-1A_E250062790


title: Tak1_Mock_24h_biol rep2

description: Library name: SMAA2_FKRN250015287-1A_E250062790


title: NahG_Mock_24h_biol rep2

description: Library name: SMCC2_FKRN250015290-1A_E250062790


title: Tak1_Pta 11528_24h_biol rep1

description: Library name: SMBB1_FKRN250015298-1A_E250062790


title: Tak1_Mock_72h_biol rep3

description: Library name: SMII3_FKRN250015312-1A_E250062790


title: Tak1_Mock_24h_biol rep3

description: Library name: SMAA3_FKRN250015288-1A_E250062790


title: tga_Pta 11528_24h_biol rep3

description: Library name: SMHH3_FKRN250015309-1A_E250062790


title: Tak1_Mock_24h_biol rep1

description: Library name: SMAA1_FKRN250015286-1A_E250062790


title: NahG_Pta 11528_24h_biol rep3

description: Library name: SMDD3_FKRN250015303-1A_E250062790


title: Tak1_Pta 11528_72h_biol rep2

description: Library name: SMJJ2_FKRN250022385-1A_E250062790


title: tga_Pta 11528_24h_biol rep2

description: Library name: SMHH2_FKRN250015308-1A_E250062790


title: Persicaria chinensis

city: Beijing

first: Yueyue

last: Yan

address: No. 1 ShuaiFuyuan Road, Dongcheng District

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

description: Library name: Persicaria_chinensis

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKMvalues for each Sample

organism: Persicaria chinensis

source_name: leaf and stem

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, USA) from roots tissue of Scutellaria baicalensis Georgi according to protocol. Then, electrophoresis on a denaturing agarose gel and NanoDrop spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) were used for separating and measuring total RNA. Approximately 2 µg of total RNA with a concentration of 200 ng/µl from equal amount of RNA samples.
RNA libraries created with the QIAseq miRNA Library Kit (Qiagen, Valencia, CA, USA) from total RNA following manufacturer's protocols.

value: leaf and stem


title: Tak1_Pta 11528_72h_biol rep1

description: Library name: SMJJ1_FKRN250015313-1A_E250062790


title: Tak1_Mock_72h_biol rep1

description: Library name: SMII1_FKRN250015310-1A_E250062790


title: human chordoma_6_primary

type: RNA

city: Chongqing

first: Lei

last: Liu

address: 1 Youyi Road, Yuanjiagang, Yuzhong District

department: Department of Breast and Thyroid Surgery

institute: The First Affiliated Hospital of Chongqing Medical University, Chongqing, China

description: Human RNA expression value derived from Primeview Human Gene Expression (Affymetrix)

hyb_protocol: Array hybridization, washing, and staining were performed using the GeneChip® Hybridization, Wash and Stain Kit (Cat# 900720, Affymetrix, Santa Clara, CA, USA). Hybridization was carried out in a GeneChip® Hybridization Oven 645 (Cat# 00-0331-220V, Affymetrix), followed by washing and staining on a GeneChip® Fluidics Station 450 (Cat# 00-0079, Affymetrix), according to the manufacturer’s instructions.

scan_protocol: Microarray slides were scanned using a GeneChip® Scanner 3000 (Cat# 00-00212, Affymetrix, Santa Clara, CA, USA). Image acquisition and primary image processing were performed using GeneChip Command Console Software version 4.0 (Affymetrix) with default settings.

data_processing: Image data were acquired using GeneChip Command Console Software version 4.0 (Affymetrix) with default settings. Raw CEL files were imported into R software and normalized using the Robust Multi-array Average (RMA) algorithm implemented in the Bioconductor “affy” package. Differential gene expression analysis was performed using standard statistical methods, and statistical significance was defined as P < 0.05.

label: biotin

source_name: human chordoma

label_protocol: Approximately 2 μg of total RNA was used to generate biotin-labeled cRNA targets.

growth_protocol: Primary and recurrent chordoma tissue samples were obtained directly from patients at the time of surgical resection and were immediately processed for RNA extraction without in vitro culture.

extract_protocol: Total RNA was extracted from the above-mentioned tissues using TRIzol reagent (Invitrogen) according to the manufacturer’s protocol. RNA concentration and purity were measured using a NanoDrop ND-1000 spectrophotometer, and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: No treatments were applied to the biological materials prior to extract preparation.

value: primary chordoma


title: human chordoma_5_recurrence

value: recurrence chordoma


title: Tak1_Mock_72h_biol rep2

description: Library name: SMII2_FKRN250015311-1A_E250062790


title: human chordoma_4_recurrence


title: human chordoma_4_primary


title: human chordoma_2_primary


title: uninjured wt

description: Library name: uninjured wt

value: cornea/limbus

value: wt


title: human chordoma_2_recurrence


title: kidney biopsy_NH686

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

country: Canada

institute: University of Alberta

hyb_protocol: Amplified RNA (10ug) was hybridized for 16 hr at 45C on  GeneChip® PrimeView™ Human Gene Expression Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Gene Array Scanner 3000 7G (Affymetrix) and processed with GeneChip® Command Console® Software (AGCC)(Affymetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

source_name: kidney biopsy

label_protocol: Total RNA (0.5µg) was labeled using GeneChip 3` IVT Express Labeling kit. Quality of labeled aRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to GeneChip® PrimeView™ Human Gene Expression Array (Affymetrix, Santa Clara, CA).

extract_protocol: Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).

treatment_protocol: All human kidney biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.

tag: mmdx (abmr/mixed, no abmr/mixed)

value: No ABMR/Mixed

value: kidney biopsy


title: kidney biopsy_NH690


title: human chordoma_6_recurrence


title: kidney biopsy_NH677


title: human chordoma_1_primary


title: kidney biopsy_NH683


title: kidney biopsy_NH684


title: kidney biopsy_NH679


title: kidney biopsy_NH680


title: kidney biopsy_NH681

value: ABMR/Mixed


title: kidney biopsy_NH687


title: kidney biopsy_NH689


title: human chordoma_3_recurrence


title: kidney biopsy_NH688


title: kidney biopsy_NH672


title: kidney biopsy_NH676


title: kidney biopsy_NH674


title: kidney biopsy_NH675


title: kidney biopsy_NH682


title: kidney biopsy_NH678


title: human chordoma_1_recurrence


title: kidney biopsy_NH673


title: kidney biopsy_NH670


title: human chordoma_5_primary


title: kidney biopsy_NH667


title: kidney biopsy_NH668


title: kidney biopsy_NH664


title: kidney biopsy_NH669


title: kidney biopsy_NH666


title: kidney biopsy_NH665


title: kidney biopsy_NH685


title: kidney biopsy_NH663


title: kidney biopsy_NH662


title: kidney biopsy_NH657


title: kidney biopsy_NH661


title: intestine,Five Substances Powder with Poria1

description: Library name: H1-1

value: intestine


title: kidney biopsy_NH660


title: kidney biopsy_NH659


title: kidney biopsy_NH656


title: kidney biopsy_NH653


title: kidney biopsy_NH654


title: kidney biopsy_NH652


title: kidney biopsy_NH650


title: kidney biopsy_NH649


title: kidney biopsy_NH648


title: kidney biopsy_NH658


title: kidney biopsy_NH655


title: kidney biopsy_NH645


title: Day 14, low MOI control, MOI5, imatinib, MiniSeq_rep1

city: San Francisco

first: Stefan

last: Oberlin

address: 505 Parnassus Ave

department: Department of Microbiology and Immunology

institute: University of California, San Francisco

description:
Library name: D14_C3_MOI5_imatinib_MiniSeq_rep1
counts_sublib_screen.csv

data_processing:
Read preprocessing and counting of the sequencing data of the sub partitioned CRISPRi library used for the cell essentiality and drug tolerance screen was performed as follows. Forward reads are first trimmed with BBDuk (parameters: ktrim=l minlen=20 k=10 mink=6 hdist=1 tpe tbo skipr2) to remove the human U6 sequence trailing the spacer sequence (5’-TTGTGGAAAGGACGAAACACCG-3’). Forward and reverse reads are then hard clipped to 20 and 21 bases respectively. Forward reads are counted for perfect matches to the guide RNA library using R 4.5.0 with the packages ShortRead23  and dplyr. To validate sublibrary-specific cloning, guide RNA sequences were counted hierarchically, where reads are first counted only for the sublibrary the guide RNA is expected to originate from to avoid multiple counting of guide RNA represented in multiple of the sublibraries. Effect sizes at the gene level are estimated with MAGeCK (version 0.5.7)25  using non-target controls as control sgRNA. Within each condition day 0  samples are compared to untreated and treated samples at day 14.
Data processing of the dual guide RNA CRISPRi library used for the cell sorting screen of ICAM-1 levels was performed as follows. Forward reads are first trimmed with Cutadapt26  to remove the mouse U6 sequence trailing the spacer sequence (5’- ATCCCTTGGAGAACCACCTTGTTGG-3’). Forward, reverse and index 2 reads, representing guide RNA 1, guide RNA 2 and the associated barcode, are then hard clipped to 19, 19 and 10 bases respectively. Guide RNA 1 and guide RNA 2 to barcode combinations are individually counted for perfect matches to the guide RNA library and the 41 barcodes using R 4.5.0 with the packages ShortRead and dplyr. These individual counts are subsequently added yielding for each gene 41 individual barcode counts. These barcode counts are used to estimate gene-level score with MAGeCK again using non-target controls as control sgRNA.
Assembly: hg38
Supplementary files format and content: sgRNA quantification data per samples
Library strategy: CRISPR Screen

source_name: K-562 dCas9-Zim3

growth_protocol: K-562 cells are grown in advanced RPMI (Gibco), 10%FBS (Gibco), 1x Pen-Strep (Gibco) and grown at 37 °C, 5% CO2.

extract_protocol:
gDNA of live cells is extacted with the Quick-DNA 96 Kit (Zymo). gDNA of fixed cells is extacted by Phenol/Chloroform extraction. Cell pellets are resuspended and incubated overnight at 65 °C in 400µl of ChIP lysis buffer (1% SDS, 50 mM Tris, pH 8, 10 mM EDTA) with 16 µl 5 M NaCl. 8µl of RNAse A (10mg/ml - Thermo Fisher Scientific) is added the next day and incubated at 37 °C for 1 h followed by adding 8µl of Proteinase K (20mg/ml - Thermo Fisher Scientific) and a 1 h 55 °C incubation step. Genomic DNA was then isolated with phenol:chloroform:isoamyl alcohol, ethanol precipitated and washed with 70% ethanol. DNA was resuspended in water.
Genomic DNA is PCR amplified with NEBNext Ultra II Q5 polymerase with primers amplifying the sgRNA cassette.

treatment_protocol: Cells are treated for 14 days with Imatinib at IC50 (230 nM) or a corresponding DMSO control.

value: K-562 dCas9-Zim3


title: kidney biopsy_NH651


title: kidney biopsy_NH643


title: Day 14, low MOI control, MOI2p5, imatinib, MiniSeq_rep2

description:
Library name: D14_C3_MOI2p5_imatinib_MiniSeq_rep2
counts_sublib_screen.csv


title: kidney biopsy_NH642


title: Day 14, low MOI control, MOI30, imatinib, MiniSeq_rep2

description:
Library name: D14_C3_MOI30_imatinib_MiniSeq_rep2
counts_sublib_screen.csv


title: kidney biopsy_NH644


title: Day 0, low MOI control, MOI30, DMSO, MiniSeq_rep2

description:
Library name: D0_C3_MOI30_none_MiniSeq_rep2
counts_sublib_screen.csv


title: kidney biopsy_NH641