title: Cardiac Microvascular Endothelial Cells 2

city: Jerusalem

first: Avner

last: Ehrlich

address: Silberman 3-512, Edmond J. Safra Campus (Givat Ram)

department: Bioengineering

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
RNA-seq reads for adult and fetal human cardiac tissues were downloaded from GSEA series GSE156707 along with accompanying metadata. AC16 data was downloaded from GSEA series GSE201076 along with accompanying metadata. RNA-seq reads for atrial muscle, ventricle muscle, SA node, and AV node were downloaded from GSEA series GSE203372 with accompanying metadata. Endocardium data was downloaded from GSE195911, epicardium was downloaded from GSE165450, and cardiac fibroblasts were downloaded from GSE167368. The reads were mapped to the UCSC human transcriptome (genome build hg19) using Bowtie2 . Expression levels of all genes were quantified using RSEM, yielding an expression matrix of inferred gene counts . Differential expression analysis was performed using R package DESeq2 using the default parameter . Reported are p-values from a negative binomial Wald-test.    In the endothelial marker analysis, The reads were mapped to the UCSC rat transcriptome (genome build rn6) using Bowtie2 . Expression levels of all genes were quantified using RSEM, yielding an expression matrix of inferred gene counts . Differential expression analysis was performed using R package DESeq2 using the default parameter . Isolated primary rat endothelial cells were downloaded from GSE133717.
Hierarchical clustering, heat maps, correlation plots, and similarity matrices were created in Morpheus. Gene ontology enrichment analyses and clustering were performed using DAVID Informatics Resources 6.7  and PANTHER Classification System . Metabolic network maps were created using McGill’s Network Analyst Tool using the KEGG database .
Assembly: genome build hg19; genome build rn6
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Rattus norvegicus

source_name: Cardiac Microvascular Endothelial Cells

growth_protocol: Human induced pluripotent stem cell lines: UN-1 (healthy Middle Eastern male, 35 years old), ACS-1021 (healthy Caucasian male, 72 years old), and ACS-1028 (healthy African American female, 31 years old) were cultured on growth factor reduced Matrigel (BD Biosciences, San Jose, CA) in mTeSR-1 media (StemCell Technologies, Canada) with daily medium changes. Cells were obtained from the Technion (Prof. Lior Gepstein) and ATCC (Maryland, USA) respectively, authenticated at the source, and tested for mycoplasma contamination using PCR. Cells were serially passaged using 0.5X TrypLE Enzyme (Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 0.5mM EDTA (Invitrogen, Thermo Fisher Scientific).  HEK 293T cells (ATCC, USA) were seeded in 10 cm cell culture plates at a density of 4x106 cells/plate. The cells were maintained in 293T medium composed of DMEM high glucose (4.5 g/l; Merck, USA) supplemented with 10% FBS (BI, Israel), 1x NEAA (BI, Israel), and 2 mM L-alanine-L-glutamine (BI, Israel).  Rat primary cardiac microvascular endothelial cells (CECs; Vec Technologies, USA) were cultured on gelatin-coated flasks using Endothelial Cell Growth Medium-2MV (Lonza, Switzerland) according to the manufacturer’s directions.  All cells were cultured under standard conditions in a humidified incubator at 37°C under 5% CO2. All cultured cells were tested routinely for mycoplasma contamination using PCR.

extract_protocol:
RNA was extracted in three separate experimental repeats from ACS-1021 hiPSC-derived cardiomyocyte (2D) and ACS-1021 cardiac organoid cultures using RNeasy Micro kit (Qiagen, USA) according to the manufacturer’s direction.
Library preparation and RNA sequencing were performed by the Hebrew University Center for Genomic Technologies. Briefly, library construction was conducted using Illumina TruSeq RNA Library Prep V2 Kit (Illumina, USA) and sequenced on Illumina NextSeq500 with single-end, 86 bp reads using the High Output V2 Kit.

treatment_protocol: Cardiac differentiation of human hiPSCs  The hiPSCs were seeded on Matrigel in mTeSR-1 medium and allowed to reach 80-90% confluence. Cardiac differentiation was conducted as previously described 90. Briefly, a basal medium named CDM3 was used (RPMI-1640, 500μg/mL recombinant human serum albumin, 213 μg/mL L-ascorbic acid 2-phosphate, and 1% penicillin/streptomycin). At day zero of differentiation, the medium was replaced with CDM3 supplemented with 6μmol/L CHIR99021 (Stemgent) for two days. On day two of the differentiation, the culture medium was switched to CDM3 medium supplemented with 2μM Wnt-C59 (Selleckchem), for an additional two days. From day four onward, cells were cultured with RPMI supplemented with B27 without Insulin; Gibco, USA). Generation of GFP-CECs Plasmid encoding GFP reporter upstream of a minimal CMV promoter was purchased from System Biosciences and validated in-house. Plasmids were acquired as bacterial LB-agar stabs and used per the manufacturer’s instructions. Briefly, each stab was first seeded into agar LB (Bacto Agar; BD, USA) in 10 cm plates. Then, single colonies were inoculated into flasks containing LB (BD Difco LB Broth, Lennox; BD, USA) and 100 µg/ml penicillin (BI, Israel). Transfection-grade plasmid DNA was isolated from each flask using the ZymoPURE II Plasmid Maxiprep Kit (Zymo Research, USA) according to the manufacturer’s instructions. HEK 293T cells were transfected with a GFP-expressing plasmid and the packaging plasmids using the TransIT-LT1 transfection reagent (Mirus Bio, USA) according to the provider’s instructions. Briefly, 6.65 µg GFP lentivector plasmid, 3.3µg pVSV-G, and 5µg psPAX2 were mixed in Opti-MEM reduced serum medium (Gibco, USA), with 45µl of TransIT-LT1, kept at room temperature to complex and then added to each plate. Following 18h of incubation, the transfection medium was replaced with 293T medium and virus-rich supernatant was harvested after 48h and 96h. The supernatant was clarified by centrifugation (500 x g, 5 min) and filtred (0.45 µm, Millex-HV, MerckMillipore). Packaging plasmids were a kind gift from the Nissim Benvenisti Lab, HUJI, Jerusalem, Israel.  Organoid Culture 4.5×106 hiPS-derived cardiomyocytes and 2.3×106 microvascular cardiac endothelial cells were counted and mixed in 100 µl of growth factor reduced Matrigel (BD Biosciences, San Jose, CA). A volume of 1.1 μl of the cell mixture was injected into each microwell and left to gel at 37C for 30 minutes. Cardiac organoid medium was composed of  RPMI-1640 supplemented with B27 minus insulin and 5 ng/ml Vascular Endothelial Growth Factor (VEGF-A, Peprotech). Cardiac organoid medium was added following gelation and changed every 48 hours. The cell mixture aggregates by day 4, start beating on day 10, and creates a smooth cardiac organoid with a synchronized beating by day 25 of seeding (Fig. 1A-B). The average organoid diameter was approximately 500 µm.

value: Cardiac Microvascular Endothelial Cells

value: RCEC


title: KPC_allograft_screen_Dox_R4

status: Public on Jun 01 2024

type: SRA

city: Kiel

first: Elmar

last: Wolf

state: Schleswig-Holstein

address: Rudolf-Höber-Str. 1

department: Biochemical Institute

country: Germany

institute: Christian-Albrechts-University Kiel

description: PCR amplified gDNA

library_source: genomic

data_processing:
Fastq files were generated on Illumina’s BaseSpace platform and overall sequencing quality was analyzed with the FastQC script.
Bowtie1 (version 1.2.2) alignment (option -v 0) to the shRNA oligonucleotide reference
Counting of alignment per shRNA (bash script)
Differential enrichment (DESeq2)
Assembly: NA, fastq files were aligned to a custom reference containing the shRNA oligonucleotide sequences
Supplementary files format and content: .csv file containing raw read counts per shRNA sequence

molecule: genomic DNA

organism: Mus musculus

source_name: tumor

growth_protocol: KPC cells were grown in DMEM supplemented with 10 % FCS and 1% Penicillin/Streptomycin. 100,000 KPC cells were orthotopically transplanted into the pancreata of C57BL/6J mice in 50 µl PBS/Matrigel (1:1)

extract_protocol:
Cells/Tumors were lysed in lysis buffer (10 mM TRIS/HCl, pH 8, 100 mM NaCl, 10 mM EDTA, 0.5 % SDS, 400 µg/ml proteinase K) at 56 °C overnight. gDNA was isolated by phenol/chloroform/isoamylalcohol extraction and isopropanol precipitation.
PCR amplification of mirE sequences from gDNA followed by PCR amplification with barcoded index primers.
OTHER: PCR amplification of mirE sequences from gDNA followed by PCR amplification with barcoded index primers.

treatment_protocol: Cells were treated with 1 µg/ml doxycycline. Control cells were treated with ethanol. Mice were treated with doxycycline by feeding them with chow containing 625 mg/kg doxycycline (ssniff) ad libitum. Control mice received control chow.

tag: tissue

value: tumor

tag: cell line

value: KPC

tag: cell type

value: pancreatic ductal adenocarcinoma

tag: genotype

value: Kras G12D/+; Tp53 R172H/+; Ptf1a-Cre

tag: treatment

value: Doxycycline chow


title: Control-2

city: Farmington

first: Anthony

last: Vella

state: Connecticut

address: 263 Farmington Ave

department: Immunology

country: USA

institute: UConn Health

library_source: transcriptomic

data_processing:
Base-calling was done using Offline Base Caller (Illumina) v. 1.9.4
alignment was done using STAR v 2.7.1a under default specfications
BAM files were generated and indexed using Samtools v 1.9 under default specifications
Peak-calling was done using Stringtie v 2.1.0 under parameter -B to first generate a usable list of ballgown files to prep for DESeq2 analysis. A separate python script (prepDE.py) was then used to convert the ballgown list (sample_list.txt) to gene and transcript counts as well as FPKM values for each sample as a list of gtf files (using python2.7 - python 3.7.4 does not work).
Analysis of counts was performed using R v 4.0.5, Rstudio v 1.2.1, DESeq2 v 1.30.1 using the filtering parameters of FDR<.05
Splicing analysis was done using rMATS v. 4.1.1
Assembly: hg38
Supplementary files format and content: tab delimited file of counts on a per gene basis (generated from Stringtie)
Supplementary files format and content: tab delimited file of counts on a transcript basis (generated from Stringtie)
Supplementary files format and content: tab delimited file of FPKM values on a transcript basis (generated from Stringtie)

molecule: total RNA

organism: Homo sapiens

source_name: Health Donor PBMCs

extract_protocol:
QIAGEN miRNEasy Micro Kit
SMARTerUltra-lowPOLYA-V4

value: Health Donor PBMCs

value: CD8+ T cell


title: WAC15_HET_F

city: Davis

first: Karol

last: Cichewicz

state: CA

address: 1544 Newton Ct

department: Center for Neuroscience

institute: UC Davis

data_processing:
Alignment with STAR (version 2.5.4b)
Gene counts were generated using featureCounts
Assembly: GRCm38/mm10
Supplementary files format and content: CSV gene counts

molecule: polyA RNA

source_name: Forebrain

extract_protocol:
Total RNA was extracted using Ambion RNAqueous Total RNA Isolation Kit (cat# AM1912)
Illumina poly-A-enriched mRNA libraries

value: Forebrain

value: HET

tag: time


title: WAC14_WT_M

value: WT


title: Naïve-1


title: Fish3 zAcaa2-sg1

city: New York

first: Ting-Hsiang

last: Huang

state: New York

institute: Memorial Sloan Ketteting Cancer Center

description:
Fish3
zAcaa2-sg1

data_processing:
The results of the amplicon were aligned and percent of indels at the target site was quantified using R version 4.0.5 and CrispRVariants 1.18.0 as previously described (Linsay et. al. 2016).
Assembly: GRCz10
Library strategy: CRISPR-Seq

organism: Danio rerio

source_name: melanoma

growth_protocol: Tumors generated by TEAZ were dissected out from randomly picked fish.

extract_protocol:
Mince the tumor tissue into small sizes with a razor and transfer the pieces immediately to a 15 ml conical tube containing tissue digestion buffer. After tissue dissociation, suspension cells were filtered through a 70 mm strainer to remove tissue debris followed by counterstaining with Hoechst 33342. After FACS, tdTomato and Hoechst double positive melanomas were lysed for phenol-chloroform based whole genome extraction. To validate gene editing using CRISPR-seq, primer pairs were set to flank 200-280 bp of the sequence that should encompass mutation sites within 100 bp from the beginning or end of it.
The sequence was amplified from 50-100 ng of genomic DNA using Phusion High-Fidelity DNA Polymerase master mix PCR protocol.

value: melanoma

tag: knockout


title: rat 4W Test3

city: shanghai

first: Hai

last: Tang

state: shanghai

address: zhengmin road

country: China

institute: Shanghai Pulmonary Hospital affiliated to Tongji University

data_processing:
cutadapt (v1.9.3)
Raw data quality control was performed first using the Q30 value.
Use cutadapt software (v1.9.3) to remove adapters, remove low-quality reads, and obtain high-quality clean reads.
The clean reads were aligned to the rat reference genome (rn6) using hisat2 software. Then, under the guidance of the Ensembl gtf gene annotation file, the cuffdiff software was used to obtain the gene-level mRNA FPKM value as the mRNA expression profile.
Supplementary files format and content: mRNA FPKM (Fragments per kilobase of exon per million  fragments mapped)
Supplementary files format and content: mRNA Expression Profiling

source_name: Subcutaneous tissue/muscle

growth_protocol: SPF grade animal room

extract_protocol:
Total RNA was extracted from tissue with TRIzol reagent (TaKaRa), which was used to remove the rRNAs by Ribo-Zero rRNA Removal Kits (Illumina) following the manufacturer’s instructions.
RNA libraries were constructed by using rRNA-depleted RNA with the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s instructions.Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc.).

treatment_protocol: The control group was implanted with GelMA, and the test group was implanted with MFN+GelMA

value: Subcutaneous tissue/muscle

value: MFN+GelMA


title: KPC_allograft_screen_Dox_R2

description: PCR amplified gDNA


title: KPC_allograft_screen_Dox_R3

description: PCR amplified gDNA


title: WAC13_HET_M


title: KPC_allograft_screen_Dox_R1

description: PCR amplified gDNA


title: Tra2bPE-1


title: rat 4W Test2


title: WAC12_HET_M


title: Control-1


title: Cardiac Microvascular Endothelial Cells 1


title: Control-3


title: rat 2W Test3


title: rat 4W Test1


title: KPC_allograft_screen_Ctrl_R4

description: PCR amplified gDNA

value: Control (standard chow)


title: rat 2W Test2


title: WAC10_WT_M


title: KPC_allograft_screen_Ctrl_R3

description: PCR amplified gDNA


title: rat 2W Test1


title: C4-2 cells, H3K27ac 2D-14

city: Lexington

first: Yanquan

last: Zhang

state: KY

address: 760 Press Ave, Rm 352/HKRB

department: Toxicology and Cancer Biology

institute: U of Kentucky

data_processing:
Paired-end sequencing reads were trimmed using Trimmomatic(v0.39)to remove adapters and low quality bases. Trimmed reads were mapped to the human reference genome assembly GRCh37 (hg19) using Bowtie2(v2.3.5.1), allowing fragments up to 2kb to be aligned.
The alignment result was further filtered by SAMtoolsto remove reads unmapped, not primary alignment, reads failing platform, reads mapped to mitochondria, reads mapped to ENCODE blacklisted genomic regions and multi-mapped reads.
PCR duplicates were removed using Picard(v2.26.8). Peaks were called by MACS2(v2.2.7.1). The coverage track bigwig files were generated with bin size 10 and were normalized by reads per genome coverage using deeptools(v3.5.1).
Assembly: GRCh37
Supplementary files format and content: 1) bigwig file 2) broad peak file

growth_protocol: C4-2 cells were maintained in RPMI supplemented with 10% FBS and 1% penicillin and streptomycin

extract_protocol:
For BRD4 and H3K27Ac CUT&RUN, 0.5x10^6 C4-2 cells bound to Concanavalin A-coated beads were incubated with indicated primary antibodies and secondary antibody.  pA-MNase was used to digest chromatin/DNA bound by the antibodies-protein complex in CUT&RUN, followed by Proteinase K digestion and PCI extraction.
CUT&RUN libraries were prepared from 15-20ng DNA using NEBNext® Ultra™ II DNA Library Prep Kit (NEB, E7645S), according to the manufacturer’s instructions. Postamplification libraries were size selected at 160-320bp (CUT&RUN) in length using Agencourt AMPure XP beads from Beckman Coulter and were quantified using the Library Quantification Kit from Illiumina (Kapa Biosystems, KK4603). All CUT&RUN Libraries were pooled to a final concentration of 10nM and sequenced single-end using the Illumina HiSeq 4000.

value: Human prostate cancer cells

value: 200 ng/mL nocodazole

tag: chip antibody


title: C4-2 cells, BRD4 2D-12


title: C4-2 cells, H3K27ac 2D-13


title: WAC9_HET_F


title: WAC11_WT_M


title: WAC8_WT_F


title: KPC_allograft_screen_Ctrl_R1

description: PCR amplified gDNA


title: rat 4W Control3

value: GelMA


title: C4-2 cells, BRD4 2D-11


title: KPC_allograft_screen_Ctrl_R2

description: PCR amplified gDNA

value: tumor


title: C4-2 cells, H3K27ac 2A-10


title: WAC7_WT_M


title: rat 4W Control2


title: KPC_culture_screen_Dox_R3

description: PCR amplified gDNA

value: KPC

value: Doxycycline


title: KPC_allograft_screen_Ctrl_R5

description: PCR amplified gDNA

value: pancreatic ductal adenocarcinoma

value: Kras G12D/+; Tp53 R172H/+; Ptf1a-Cre


title: WAC6_HET_F


title: rat 4W Control1


title: C4-2 cells, H3K27ac 2A-9


title: rat 2W Control3


title: C4-2 cells, BRD4 2A-8


title: WAC5_HET_M


title: KPC_culture_screen_Dox_R1

description: PCR amplified gDNA


title: KPC_culture_screen_Ctrl_R3

description: PCR amplified gDNA

value: Control (Ethanol)


title: WAC4_WT_F


title: C4-2 cells, H3K27ac WT-6

value: BRD4 WT


title: rat 2W Control1


title: WAC3_WT_F

value: Forebrain


title: C4-2 cells, BRD4 2A-7


title: C4-2 cells, H3K27ac WT-5


title: WAC2_WT_M


title: KPC_culture_screen_Ctrl_R1

description: PCR amplified gDNA


title: KPC_culture_screen_Dox_R2

description: PCR amplified gDNA


title: GH3, T3

city: Changchun

first: wenzhi

last: ren

state: Jilin

address: Linyuan street

department: Department of Laboratory Animals

institute: College of Animal Sciences, Jilin University

data_processing:
The data collected from the samples were first compared to the reference genome using the mapping information from HISAT2.
RSeQC was used for the redundant sequence analysis and the insertion fragment distribution analysis based on the matching results.
Qualimap was used to check the homogeneity distribution and to analyze the genomic structure distribution based on the matching results
The distribution of sequences on the chromosomes was determined using BEDTools, as well as by statistical analysis of gene coverage
BCFtools was used to identify possible SNP loci based on mapping results, and SnpEff was used to determine the effect of SNP loci on genes.
Supplementary files format and content: GENE-FPKM-TPM.txt, gene_counts.txt

source_name: Rat pituitary tumor cell

growth_protocol: GH3 cells were cultured in F10 medium containing 15% horse serum (HS), 2.5% fetal bovine serum (FBS) and 1% penicillin and streptomycin (Gibco)

extract_protocol:
RNA was harvested using  FastQuant RT Kit. 1.3 ug of total RNA was used for the construction of sequencing libraries.
To generate total RNA samples for subsequent library construction, we performed cell fragmentation, nucleic acid extraction and purification, and quality control on the samples from GH3 cells. The RNA concentration was measured using a Qubit 2.0 instrument (Invitrogen, Q32866), and RNA integrity and genomic contamination were analyzed on agarose gels. After the samples met the quality requirements for library sequencing, the Illumina Xten platform was used for sequencing

treatment_protocol: GH3 cells were treated with 100nM TRH

value: Rat pituitary tumor cell

value: TRH


title: GH3, T2

value: WT


title: rat 2W Control2

value: Subcutaneous tissue/muscle


title: C4-2 cells, BRD4 WT-4


title: ChIPseq_RUVBL1_KPC_AID_Ruvbl1_Ctrl

data_processing:
Base calling was performed using bcl2fastq (version 3.7.4)
Alignment against mouse (mm10) and human (hg19, spike-in) genome with Bowtie2 (version 2.3.4.1)
Normalization according to spike-in
Conversion to bedgraphs with bedtools genomecov (version 2.26.0)
Peak calling with MACS2 (version 2.2.7.1) and p-value cutoffs 0.01 (MYC) and 0.001 (RUVBL1)
Assembly: mm10/hg19
Supplementary files format and content: bedGraph files as defined by UCSC (https://genome.ucsc.edu/goldenpath/help/bedgraph.html).
Supplementary files format and content: narrowPeak files contain MYC and RUVBL1 peak locations

growth_protocol: KPC-AID-Ruvbl1 cells were grown in DMEM suplemented with 10 % FCS and 1% Penicillin/Streptomycin.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. Formaldehyde was quenching with glycine, cells were lysed and chromatin was sonicated.
NEBNext Ultra II DNA Library Prep Kit for Illumina, libraries were amplified for 13 cycles and concentration and size distribution were evaluated using an Agilent Fragment Analyzer.

treatment_protocol: KPC-AID-Ruvbl1 cells were treated with 1 uM 5-Ph-IAA for 15 h.

value: Kras G12D/+; Tp53 R172H/+; Ptf1a-Cre, AID-Ruvbl1

value: Control


title: ChIPseq_RUVBL1_KPC_AID_Ruvbl1_Auxin

value: 1 uM 5-Ph-IAA 15 h


title: GH3, T1


title: NTG_3

city: Wuhan

first: Ziying

last: Zhou

state: Hubei

address: Jiefang Road 238

institute: Renmin Hospital of Wuhan University

data_processing:
Raw sequencing reads containing more than 2-N bases were first discarded. Subsequently, the raw reads were trimmed of adaptors and low-quality bases using a FASTX-Toolkit (v.0.0.13;http://hannonlab.cshl.edu/fastxtoolkit/).
In addition, short reads of less than 16 nt were dropped to retain clean reads, which were subsequently aligned to the GRch38 genome by HISAT2 . Uniquely mapped reads were ultimately used to calculate read number and paired-end fragments per kilobase of exon per million fragments mapped (FPKM) for each gene.
The software DEseq2, which is specifically used to analyze the differential expression of genes, was applied to screen the RNA-seq data for DEGs. The results were analyzed based on the fold change (FC≥2 or ≤0.5) and false discovery rate (FDR<0.05) to determine whether a gene was differentially expressed.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include reads counts for each Sample

source_name: Left ventricular

extract_protocol:
Firstly, total RNA was isolated from cardiac tissue by TRIzol Reagent and RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). Then RNA-seq library were preparated, after PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system, clustering and sequencing on an Illumina Novaseq platform.
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 First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). 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: Left ventricular

value: Aortic banding


title: WAC1_WT_M


title: C4-2 cells, IgG-2

value: Human prostate cancer cells

value: 200 ng/mL nocodazole

value: IgG


title: GH3, NC3

value: NC


title: C4-2 cells, IgG-1


title: ChIPseq_MYC_KPC_AID_Ruvbl1_Ctrl

value: KPC

value: pancreatic ductal adenocarcinoma


title: GH3, NC2


title: ChIPseq_MYC_KPC_AID_Ruvbl1_Auxin


title: NTG_1


title: Hct116 cells, CRISPRi RNF146, rep3

city: Santa Barbara

first: Chris

last: Richardson

address: UCSB

department: Molecular, Cellular, and Developmental Biology

institute: UCSB

data_processing:
Sequence reads were trimmed for adaptor sequence and quality using trim_galore 0.6.6 (cutadapt 4.1)
Trimmed reads were aligned to the GRCh38 assembly and gencode human release 40 gene annotation using STAR (2.7.11a). Gene-level counts were exported directly from STAR using the --quantMode GeneCounts option.
Raw counts from each sample were merged in R and imported to Deseq2 for expression analysis.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file includes counts per gene for each sample.

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle Media (10565018, DMEM, Gibco) supplemented with 10% fetal bovine serum (FBS, S11150H, R&D Systems), 1% penicillin/streptomycin (15140122, Gibco), and 2 mM L-Glutamine, and kept at 37°C and 5% CO2 in a humidified incubator

extract_protocol:
Qiagen RNeasy
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. Final steps included end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: Cells were cultured to ~80% confluency and harvested

value: Colorectal Carcinoma

value: RNF146 knockdown


title: KPC_culture_screen_Ctrl_R2

description: PCR amplified gDNA

value: Kras G12D/+; Tp53 R172H/+; Ptf1a-Cre

value: Control (Ethanol)


title: GH3, NC1

value: Rat pituitary tumor cell

value: WT


title: Hct116 cells, CRISPRi RNF146, rep2


title: HINT2_TG_2


title: ChIPseq_Input_KPC_AID_Ruvbl1_merged

value: Kras G12D/+; Tp53 R172H/+; Ptf1a-Cre, AID-Ruvbl1

value: Input


title: N2_FC [N2_24]

city: CAMBRIDGE

first: Rahia

last: Mashoodh

state: Cambridgeshire

address: Downing Street, Zoology, University of Cambridge

department: Zoology

country: United Kingdom

institute: University of Cambridge

description: processed data file: gene_count_matrix.csv

data_processing:
RNAseq samples were processed as described in Pertea et al. 2016 Nature Methods using the HiSat/StringTie pipeline
Bisulfite sequencing samples were quality checked (FastQC), adaptor and quality trimmed (FastQC), mapped with Bismark and were quantified following deduplication.
Genome_build: GCF_001412225.1
Supplementary_files_format_and_content: gene level counts are presented in a counts matrix for all samples
Supplementary_files_format_and_content: bismark coverage files are provided for each sample

organism: Nicrophorus vespilloides

source_name: N2_FC_larvae heads

extract_protocol: NOT PROVIED; REQUESTED

tag: group

value: larvae heads


title: Hct116 cells, CRISPRi RNF146, rep1


title: C4-2 cells, BRD4 WT-3

value: BRD4 WT


title: N2_FC [N2_21]


title: N2_FC [N2_18]


title: HINT2_TG_1

value: Left ventricular

value: Aortic banding


title: Hct116 cells, CRISPRi PEX19, rep2

value: PEX19 knockdown


title: Hct116 cells, CRISPRi PEX19, rep3


title: NTG_2


title: Cre- 5d Bleo treatment

city: New Haven

first: Elizabeth

middle: Ann

last: Caves

address: 260 Whitney Ave

department: Molecular, Cellular and Developmental Biology

institute: Yale University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoding, gene counting and aggregation were made using the Cell Ranger v2.1.1
Assembly: mm10
Supplementary files format and content: Cell-Ranger filtered_feature h5 files

source_name: skin

extract_protocol:
Mouse skin was manually dissociated with scissors and then enzymatically with Liberase TL dissociated in a 37C shaking water minutes for 30minutes. The enzymatic reaction was halted. Cells were filtered through a 40um mesh.
Library was performed by the manufacturers instructions

treatment_protocol: AdiCreER; mT/mG; Atgl fl/fl male mice between 6-8 weeks are shaved and receive 1 dose of topical tamoxifen (5mg/ml in 100% ethanol) on the back skin 2 days prior to injections. Mice were then injected subcutaneously for 5 days with either 100ul of 300ug/ml PBS or Bleomycin Sulfate. Back skin was collected and dissociated and submitted for scRNA-sequencing.

value: skin

tag: strain

value: AdiCreER; mTmG; Atgl fl/fl

tag: age

value: 6-8 weeks

value: Cre-, Atgl fl/fl

value: Bleomycin


title: Cre+ 5d Bleo treatment

description: 10x Genomics

value: Cre+, Atgl fl/fl


title: N2_FC [N2_17]


title: Hct116 cells, CRISPRi PEX1, rep3

value: Colorectal Carcinoma

value: PEX1 knockdown


title: GBM15_DMSO_DF2

type: RNA

city: Rostock

first: Dirk

last: Koczan

address: Schillingallee 70

department: Institute for Immunology

institute: University of Rostock

description:
Gene expression data of glioblastoma cells treated with DMSO
M_GBM15_DMSO_DF2

hyb_protocol: Hybridization was performed for 16 hours at 45 degrees celsius using the GeneChip Hybridization Oven 645 (Affymetrix, St. Clara, USA).

scan_protocol: Scanning was done using the GeneChip Scanner 3000/7G (Affymetrix, St. Clara, USA) with 0.7 micron resolution.

data_processing:
The gene expression datasets were filtered with an adjusted p-value < 0.01 and a FC ± > 2 to identify differentially expressed genes (DEGs)
probe group file: Clariom_S_Human.r1.pgf and meta-probeset file: Clariom_S_Human.r1.na36.hg38.a1.transcript.csv were used.
Transcriptome Analysis Console 4.0.3.14.

label: biotin

source_name: primary cell culture

label_protocol: 100 ng total RNA was labeled using WT-labeling protocol (Affymetrix/Thermofisher).

growth_protocol: Tumor pieces were homogenized using a cell strainer (100 μm) and seeded in 6-well plates containing DMEM/Hams F12 130 medium, supplemented with 20% FCS, 6 mM L-glutamine, and 1% penicillin/streptomycin and incubated at 37°C in a humidified atmosphere of 5% CO2. Continually growing cell cultures were serially passaged and regularly stored at low passages.

extract_protocol: Spheroids were grown in AggreWell™400 plates, treated as described, harvested and pelleted by centrifugation. The total RNA was isolated using Rneasy Kit (Qiagen), including column-based DNase I digestion

treatment_protocol: Tumor cell cultures were treated witht the substances (GSK126, Abemaciclib, combination or DMSO as control) for 2 x 72 hours, with a complete medium change after 72 hours.

value: patient derived glioblastoma cells (GBM15)

value: DMSO


title: Cre- 5d PBS treatment

description: 10x Genomics

value: PBS


title: HINT2_TG_3


title: GBM15_DMSO_DF3

description:
Gene expression data of glioblastoma cells treated with DMSO
M_GBM15_DMSO_DF3


title: Epcam+ cells

first: Xiangyi

last: Ke

address: 650 West 168th Street

institute: Columbia University

data_processing:
Cellranger v2.1.1 was used for demultiplexing, alignment and mapping using Mus musculus reference genome v10 (mm10)
Assembly: mm10
Supplementary files format and content: tab seperated values files and matrix files

source_name: E14.5 Lung

extract_protocol:
To obtain a single cell suspension for scRNAseq, two C57/B6 females were euthanized and E14.5 embryos were collected. Lungs were dissected out and kept in ice-cold HBSS until the start of dissociation. Lungs were pooled and minced manually with a blade into pieces of ~1mm in diameter in 4ml dissociation buffer (0.8ml HBSS (1X), 2ml Dispase II, Stemcell Technologies #7913, 2.5 U/ml, 400μl Collagenase A, Roche #10103578001, 800ul DNase 1, 200ug/ml, Sigma, Cat# DN25) Dissociation followed in an insitu hybridization oven at 37°C for 1 hour on a rotator with gentle P1000 pipette trituration every 20 minutes. Then, ice-cold FACS buffer (2% FBS,2mM EDTA, 5μM Y27632, 1M HEPES in HBSS) was added, the suspension was filtered through a 70μm filter, spun down at 5 minutes at 400g, and incubated 5 minutes in red blood cell lysis buffer (sigma). The buffer was diluted with FACS buffer, spun down 5 minutes at 400g and resuspended in 1ml FACS buffer. The suspension was then passed through a 40μm filter, cells were counted and incubated 40 minutes with Epcam-APC antibody (1:150) and Icam1-PE antibody(1:150) on ice in the dark. After staining, the suspension was three times washed in FACS buffer and spun down 5 minutes at 400g. Finally, DAPI was added at a final concentration of 1μM in FACS buffer.
Single Cell 3’ libraries were prepared using the Chromium Single Cell 3’ v3 Protocol according to the manufacturer’s manual (10× Genomics). The pooled, 3’- end libraries were sequenced using Illumina NovaSeq6000

value: Lung

value: Epcam+ cells


title: N2_NC [N2_10]

source_name: N2_NC_larvae heads

value: larvae heads


title: GBM15_DMSO_DF1

description:
Gene expression data of glioblastoma cells treated with DMSO
M_GBM15_DMSO_DF1


title: N2_NC [N2_08]


title: GBM15_Kombi_DF3

description:
Gene expression data of glioblastoma cells treated with GSK126 and abemaciclib
M_GBM15_Kombi_DF3

value: GSK126 and abemaciclib


title: Hct116 cells, CRISPRi PEX1, rep2


title: Epcam+ Icam+ cells, replicate2

value: Epcam+ Icam+ cells


title: Hct116 cells, CRISPRi PEX1, rep1


title: GBM15_Kombi_DF2

description:
Gene expression data of glioblastoma cells treated with GSK126 and abemaciclib
M_GBM15_Kombi_DF2


title: Hct116 cells, CRISPRi PEX19, rep1

value: PEX19 knockdown


title: Hct116 cells, CRISPRi NTC, rep2

value: Mock knockdown


title: Ischemia_Brain TCR

city: Fukuoka

first: Minako

last: Ito

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

country: Japan

institute: Kyushu University

description:
10x Genomics
Ischemia_Brain_barcodes.tsv.gz
Ischemia_Brain_features.tsv.gz
Ischemia_Brain_matrix.mtx.gz

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Excel file includes raw counts for each Sample
Supplementary files format and content: Excel text file includes FPKM values for each Sample

source_name: Brain

extract_protocol:
Twenty-three days after induction of EAE or stroke, mice were anesthetized by inhalation with isoflurane, and after PBS perfusion, the brain parenchyma was removed and homogenized in 2% FBS/RPMI solution containing glucose and HEPES. After straining and centrifugation at 400 x g for 5 minutes, the pellet was resuspended in 37% Percoll (Cytiva), cells were isolated by centrifugation with slow acceleration/deceleration 800 x g for 20 minutes and resuspended with filtered 0.5% BSA/PBS. Totalseq-Hashtag antibody (BioLegend) was incubated with each sample, and CD45.2+ cells were sorted by FACSMelody (BD Biosciences).
Libraries were prepared according to the protocol of the Chromuim Next GEM Single Cell 5' Reagent Kits v2 (Dual Index, 10x Genomics, Pleasanton, CA, USA) using a Chromium controller (10x Genomics). Briefly, GEMs were prepared by loading barcoded Single Cell VDJ 5' Gel Beads, master mix containing cells and RT enzymes, and Oil onto Chromium Next GEM Chip K. Barcoded cDNA was then generated from the GEM. This cDNA was amplified by PCR reaction to generate V(D)J, 5' Gene Expression and Feature Barcode libraries.

treatment_protocol: Foxp3-hCD2-KI mice were induced EAE or middle cerebral artery occlusion models.

value: Brain

tag: Sex

value: male

value: Treg

value: Ischemia model D23


title: N2_FC [N2_16]


title: Ischemia_Brain GEX


title: Epcam+ Icam+ cells, replicate1


title: GBM15_Kombi_DF1

description:
Gene expression data of glioblastoma cells treated with GSK126 and abemaciclib
M_GBM15_Kombi_DF1


title: GBM15_GSK_DF3

description:
Gene expression data of glioblastoma cells treated with GSK126
M_GBM15_GSK_DF3


title: N2_NC [N2_03]


title: N2_NC [N2_06]


title: N2_NC [N2_07]


title: Hct116 cells, CRISPRi NTC, rep1


title: GBM15_GSK_DF2

description:
Gene expression data of glioblastoma cells treated with GSK126
M_GBM15_GSK_DF2


title: Hct116 cells, CRISPRi IDE, rep3

value: IDE knockdown


title: Ischemia_Brain Tag


title: N2_NC [N2_01]


title: EAE_SC TCR

description:
10x Genomics
EAE_SC_barcodes.tsv.gz
EAE_SC_features.tsv.gz
EAE_SC_matrix.mtx.gz

source_name: Spinal cord

value: Spinal cord

value: female

value: EAE model D23


title: Hct116 cells, CRISPRi IDE, rep2

value: Colorectal Carcinoma


title: N1_NC [N1_40]

source_name: N1_NC_larvae heads


title: RIP cauda-3

city: Lanzhou

first: shaoke

last: guo

state: Gansu

address: West Lake Street

department: Lanzhou institute of husbandry and pharmaceutical sciences

data_processing:
Trimmomatic software was used to trim the raw reads of the generated FASTQ format sequence
BLASTN software was used to compared with the nucleotide library
SortMeRNA software was used to remove ribosomal RNA
HISAT2 software was used to compare clean reads to the yak reference
Guitar R package and deepTools software were used for quality inspection of genome comparison result data
Assembly: LU_Bosgru_v3.0
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample …

organism: Bos grunniens

source_name: epididymis

growth_protocol: In this study, all animal-related procedures conformed to the China Council on Animal Care and the Ministry of Agriculture of the People’s Republic of China guidelines. All yak-handling procedures were approved by The Animal Care and Use Committee of the Lanzhou Institute of Husbandry and Pharmaceutical Sciences Chinese Academy of Agricultural Sciences (Permit No: LIHPS-2022-0144).

extract_protocol:
The total RNA was isolated and purified using the TRIzol reagent . The amount and purity of the RNA samples were quantified using the NanoDrop ND-1000.
The qualified RNA samples were constructed into a cDNA library, and oligo-dT magnetic beads were used to specifically capture mRNA with polyadenylate by two rounds of purification. A magnesium ion interruption kit was used for fragmentation of captured mRNA at 86°C for 7 min. The fragmented mRNA was pre-mixed with the immunomagnetic beads Dynabeads Antibody Coupling Kit  and m6A Antibody  in immunoprecipitation (IP) buffer (50 mM Tris-HCl, 750 mM NaCl, and 0.5% Igepal CA-630) before conducting IP. The IP product was passed through reverse transcriptase . Then E. coli DNA polymerase I was combined with RNase H and mixed with dUTP solution for two-strand synthesis and RNA degradation. AMPure XP beads were used to select the fragment size, and a 300 ± 50 bp library was obtained. Finally, two-terminal sequencing was performed on the Illumina NovaSeq 6000 platform with sequencing mode PE150

treatment_protocol: Select 6 healthy adult (4-year-old) male yaks from Gannan Tibetan Autonomous Prefecture. After local examination of the tests, they were casted by vegetables to obtain epididymis tissue. Rinse the collected epididymal tissue with physiological saline, and then separate the head, body, and tail of the epididymis according to anatomical structure. Some tissues were fixed with 4% neutral paraformaldehyde, while the remaining tissues were frozen in liquid nitrogen.

value: epididymis

tag: developmental stage

value: after  sexual maturity


title: Hct116 cells, CRISPRi IDE, rep1


title: Hct116 cells, CRISPRi NTC, rep3


title: EAE_SC GEX


title: N1_NC [N1_37]


title: GBM15_Abemaciclib_DF3

description:
Gene expression data of glioblastoma cells treated with abemaciclib
M_GBM15_Abemaciclib_DF3

value: patient derived glioblastoma cells (GBM15)

value: abemaciclib


title: GBM15_Abemaciclib_DF1

description:
Gene expression data of glioblastoma cells treated with abemaciclib
M_GBM15_Abemaciclib_DF1


title: EAE_Brain TCR

description:
10x Genomics
EAE_Brain_barcodes.tsv.gz
EAE_Brain_features.tsv.gz
EAE_Brain_matrix.mtx.gz


title: N1_NC [N1_35]

value: larvae heads


title: GBM15_Abemaciclib_DF2

description:
Gene expression data of glioblastoma cells treated with abemaciclib
M_GBM15_Abemaciclib_DF2


title: EAE_SC Tag


title: Hct116 cells, parental, rep3

value: WT


title: N1_NC [N1_32]


title: Hct116 cells, parental, rep2


title: RIP corpus-3

institute: Chinese Academy of Agricultural Sciences


title: EAE_Brain GEX


title: Hct116 cells, parental, rep1


title: RIP corpus-2


title: EAE_Brain Tag


title: N1_NC [N1_30]


title: Hct116 CRISPRi, 7days +zeocin, rep2

description:
Amplicon-sequencing
B2-Z-T7

library_source: other

data_processing:
Guide-RNA regions within the amplicon were aligned against an index of human v2 CRISPRi guide sequences using bowtie2 (2.5.1).
Guide count tables were extracted using the samtools (1.1.8) idxstats command.
Assembly: custom genome included as CRISPRi_v2_human_librarytable.pexscreen.txt
Supplementary files format and content: GoldStandard_MageckCountsTable_GEO.txt
Supplementary files format and content: CRISPRi_v2_human_librarytable.pexscreen.txt
Library strategy: Amplicon-sequencing

molecule: other

growth_protocol: Cells were cultured for 35 days in 5-Chamber CellStack vessels, splitting cells every 48-72hrs and harvesting 2.40 x 10^8 cells every 7 days per condition. Minimum culture size was 60 x 10^7 cells per replicate to ensure >500x library coverage. Cells were cultured in Dulbecco’s Modified Eagle Media supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin, and 2 mM L-Glutamine, and zeocin was maintained at a final concentration of 25ng/uL where indicated. Cells were kept at 37°C and 5% CO2 in a humidified incubator.

extract_protocol:
Genomic DNA was purified using Macherey-Nagel NucleoSpin Blood XL Maxi Kit, digested with SbfI, and gel purified. See PMID: 24992097 for details.
Genomic DNA was amplified using custom primers containing Illumina Adaptor sequences.

treatment_protocol: Cells were cultured for the indicated amount of time with or without zeocin.

value: Hct116 CRISPRi cells harboring genome-wide library

value: Zeocin (25 ng/µL) treated 7 days


title: RIP corpus-1


title: RIP cauda-1


title: Hct116 CRISPRi, 28days +zeocin, rep2

description:
Amplicon-sequencing
B2-Z-T28

value: Zeocin (25 ng/µL) treated 28 days


title: RIP cauda-2


title: RIP caput-3


title: Hct116 CRISPRi, 21days +zeocin, rep2

description:
Amplicon-sequencing
B2-Z-T21

value: Zeocin (25 ng/µL) treated 21 days


title: liver,KO,3months,mouse9

city: EVRY

first: Corre

last: Guillaume

address: 1 rue de l'internationale

country: France

institute: GENETHON

data_processing:
paired-end reads were aligned to the reference transcriptome using SALMON 1.9.0 using default settings and  -l A and --validateMappings arguments
Read count extraction was performed using R 4.3.0 and the tximport package (v1.28.0)
Differential gene expression was performed using R and the package DESeq2 (v1.40.1) on genes with more than 100 reads across samples and using arguments lfcThreshold = 0, pAdjustMethod = "fdr", independentFiltering = T
Assembly: GRCm39 ensembl cDNA release 110
Supplementary files format and content: tab-delimited file containing counts per gene (row) and sample (columns) from tximport function
Supplementary files format and content: tab-delimited file containing effective length per gene (row) and sample (columns) from tximport function
Supplementary files format and content: tab-delimited file containing abundance per gene (row) and sample (columns) from tximport function
Supplementary files format and content: tab-delimited file containing the differential gene expression analysis for each biological sample between edited VS un-edited samples

source_name: liver

extract_protocol:
RNA extraction was performed by Azenta
RNA with PolyA selection  with ERCC spike-in

value: liver

tag: animal

value: KO


title: RIP caput-2


title: N1_FC [N1_27]

source_name: N1_FC_larvae heads


title: N1_NC [N1_33]


title: liver,KO,3months,mouse8


title: N1_FC [N1_25]


title: Hct116 CRISPRi, 28days no drug, rep2

description:
Amplicon-sequencing
B2-Un-T28

value: Mock treated 28 days


title: N1_FC [N1_26]


title: N1_FC [N1_23]


title: N1_FC [N1_22]


title: liver,WT,3months,mouse2


title: input cauda-3


title: liver,KO,3months,mouse5


title: input cauda-1


title: liver,KO,3months,mouse12

value: treated


title: N1_FC [N1_29]


title: input cauda-2


title: F2_NC [F2_47]

source_name: F2_NC_larvae heads


title: RIP caput-1


title: Hct116 CRISPRi, 7days +zeocin, rep1

description:
Amplicon-sequencing
B1-Z-T7


title: Hct116 CRISPRi, 28days +zeocin, rep1

description:
Amplicon-sequencing
B1-Z-T28


title: liver,KO,3months,mouse10


title: liver,KO,3months,mouse11


title: input corpus-3


title: Hct116 CRISPRi, 21days +zeocin, rep1

description:
Amplicon-sequencing
B1-Z-T21


title: liver,WT,3months,mouse1


title: input corpus-2


title: F2_NC [F2_45]


title: Hct116 CRISPRi, 7days no drug, rep2

description:
Amplicon-sequencing
B2-Un-T7

value: Mock treated 7 days


title: input corpus-1


title: F2_NC [F2_43]


title: F2_NC [F2_41]


title: liver,KO,8months,mouse9


title: Hct116 CRISPRi, 28days no drug, rep1

description:
Amplicon-sequencing
B1-Un-T28


title: input caput-3


title: Hct116 CRISPRi, 21days no drug, rep2

description:
Amplicon-sequencing
B2-Un-T21

value: Mock treated 21 days


title: Hct116 CRISPRi, 7days no drug, rep1

description:
Amplicon-sequencing
B1-Un-T7

value: Colorectal Carcinoma


title: input caput-2

value: epididymis


title: liver,KO,8months,mouse5


title: F2_NC [F2_36]


title: liver,KO,8months,mouse6


title: Hct116 CRISPRi, 21days no drug, rep1

description:
Amplicon-sequencing
B1-Un-T21


title: GBM15_GSK_DF1

description:
Gene expression data of glioblastoma cells treated with GSK126
M_GBM15_GSK_DF1


title: liver,WT,3months,mouse3


title: F2_FC [F2_32]

source_name: F2_FC_larvae heads


title: Hct116 CRISPRi, 35days +zeocin, rep2

description:
Amplicon-sequencing
B2-Z-T35

value: Zeocin (25 ng/µL) treated 35 days


title: F2_FC [F2_34]


title: Adipose 7 day graft 5 [Sample_15]

city: Daegu

first: Taehee

last: Jo

address: 1035 Dalgubeol daero

department: Department of Plastic and Reconstructive Surgery

country: South Korea

institute: Keimyung University Dongsan Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
The adapter sequences and the ends of the reads less than Phred quality score 20 were trimmed and simultaneously the reads shorter than 50 bp were removed by using cutadapt v.2.8. Filtered reads were mapped to the reference genome related to the species using the aligner STAR v.2.7.1a following ENCODE standard options with “-quantMode TranscriptomeSAM” option for estimation of transcriptome expression level. Gene expression estimation was performed by RSEM v.1.3.1
Read count and FPKM(Fragment per Kilobase of transcript per Million mapped reads) were calculated.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Mus

source_name: Adipose tissue

extract_protocol:
The tissues were then homogenized with appropriate volume of Trizol reagent (Invitrogen, USA) in independent bead containing safe lock tubes. After Trizol/chloroform extraction, the aqueous phase was mixed with 100% EtOH, and then loaded onto RNeasy column (Qiagen, USA). The RNA extraction process was continued according to the manufacturer’s protocol.
The libraries were prepared for 151bp paired-end sequencing using TruSeq stranded mRNA Sample Preparation Kit (Illumina, USA)

value: Adipose tissue

value: 7 weeks

value: wild type


title: input caput-1

value: after  sexual maturity


title: Adipose 7 day graft 4 [Sample_14]


title: Adipose 7 day graft 3 [Sample_13]


title: liver,WT,8months,mouse2

value: WT


title: Hct116 CRISPRi, 35days no drug, rep1

description:
Amplicon-sequencing
B1-Un-T35

value: Hct116 CRISPRi cells harboring genome-wide library

value: Mock treated 35 days


title: liver,WT,8months,mouse3


title: Adipose 7 day graft 2 [Sample_12]


title: liver,KO,8months,mouse12


title: liver,KO,8months,mouse11


title: Hct116 CRISPRi, 14days +zeocin, rep1

description:
Amplicon-sequencing
B1-Z-T14

value: Zeocin (25 ng/µL) treated 14 days


title: Hct116 CRISPRi, 14days +zeocin, rep2

description:
Amplicon-sequencing
B2-Z-T14


title: Hct116 CRISPRi, 35days +zeocin, rep1

description:
Amplicon-sequencing
B1-Z-T35


title: F2_NC [F2_38]

value: larvae heads


title: liver,KO,8months,mouse4

value: liver

value: KO


title: Hct116 CRISPRi, 14days no drug, rep2

description:
Amplicon-sequencing
B2-Un-T14

value: Mock treated 14 days


title: F2_FC [F2_27]


title: F2_FC [F2_26]


title: Adipose 3 day graft 5 [Sample_10]


title: liver,WT,8months,mouse1


title: Hct116 CRISPRi, 14days no drug, rep1

description:
Amplicon-sequencing
B1-Un-T14


title: D32-SC-2

data_processing:
Bcl2fastq (v2.17.1.14) was used to processed the original image data for base calling and preliminary quality analysis. The Illumina built-in software determines whether to keep or discard each of the sequencing fragments (namely reads) based on the quality of the first 25 bases.
The raw data (Pass Filter Data) obtained from this step is stored in FASTQ format, which contains the base sequence (the second line of a FASTQ record) and the corresponding sequencing quality information (the fourth line of a FASTQ record).The raw data (Pass Filter Data) obtained from this step is stored in FASTQ format, which contains the base sequence (the second line of a FASTQ record) and the corresponding sequencing quality information (the fourth line of a FASTQ record).
Quality assessment of the sequencing data was evaluated using FastQC (v0.10.1).
A small number of target sequences might be reads into adapter sequences, and bases toward the 3'-end might have low quality due to the lengthy sequencing cycles. To eliminate the negative effect of these technical issues low-quality reads and contaminations were filtered out before data analysis. In addition, adapter sequences were removed at this step. Cutadapt (version 1.9.1)
Short-read alignment was performed using Hisat2 (v2.0.1) (Nat Methods. 2015 Apr; Kim D, et al.) with default parameters.
Assembly: mm10
Supplementary files format and content: Excel file includes raw counts for each Sample
Supplementary files format and content: Excel text file includes FPKM values for each Sample

extract_protocol:
RNA was harvested using Rneasy micro plus lit (Qiagen).
RNA libraries for RNA seq were prepared using NEBNext PolyA stranded Ultra II Directional RNA Library Prep

value: Spinal cord

value: female

value: EAE model


title: Adipose 3 day graft 4 [Sample_9]


title: D32-SC-1


title: Hct116 CRISPRi, 35days no drug, rep2

description:
Amplicon-sequencing
B2-Un-T35

value: Colorectal Carcinoma


title: D32-Cerebrum-2

source_name: Cerebrum

value: Cerebrum


title: F1_FC [F1_17]

source_name: F1_FC_larvae heads


title: F2_FC [F2_28]


title: F1_FC [F1_18]


title: F2_FC [F2_31]


title: Hct116 CRISPRi, time zero, rep2

description:
Amplicon-sequencing
B2-T0

value: Untreated


title: Adipose 3 day graft 1 [Sample_6]

value: Adipose tissue

value: 7 weeks


title: Hct116 CRISPRi, time zero, rep1

description:
Amplicon-sequencing
B1-T0


title: D32-Cerebrum-1


title: Adipose 3 day graft 2 [Sample_7]

value: wild type


title: F1_FC [F1_16]


title: D32-Cerebellum-2

source_name: Cerebellum

value: Cerebellum

value: WT


title: TFK1, combination, biol rep 3 [NR3]

first: Ningyu

last: Wang

address: JIEFANG ROAD1277#

department: Cancer Center, Union Hospital

institute: Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China

data_processing:
Clustering and sequencing( Illumina NovaSeq 6000)
Quality control
Reads mapping to the reference genome
Quantification of gene expression level
Differential expression analysis
Enrichment analysis of differentially expressed genes
Assembly: hg38
Supplementary files format and content: tab-delimited text fles include RPKM values for each Sample

source_name: Cholangiocarcinoma

growth_protocol: TFK1 cells were maintained in RPMI 1640 supplemenied with 10% fetalboyne serm EBS) and anibioics in humidifed atmosphere with 5% CO2 at 37℃

extract_protocol:
Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seg Library Prep Kit following manufacturer's protocols

treatment_protocol: We used a cholangiocarcinoma cell line TFK1, and set up a blank control group, a radiotherapy group (6Gy), a chemotherapy group  (nab-paclitaxel 1.62ng/ml), and a combination treatment group (nab-paclitaxel 1.62ng/ml+RT 6Gy). After 24 hours of treatment, total RNA was extracted for transcriptome sequencing in different treatment groups.

value: Cholangiocarcinoma

value: cancer cell line


title: TFK1, combination, biol rep 1 [NR1]


title: Adipose Control 4 [Sample_4]


title: D18-SC-2


title: D32-Cerebellum-1


title: TFK1, nab_paclitaxel, biol rep 3 [N3]


title: D18-SC-1


title: F1_FC [F1_15]

value: larvae heads


title: F1_NC [F1_09A]

source_name: F1_NC_larvae heads


title: F1_NC [F1_06]


title: Adipose Control 5 [Sample_5]


title: TFK1, combination, biol rep 2 [NR2]


title: Adipose Control 2 [Sample_2]


title: F1_FC [F1_20]


title: Adipose 3 day graft 3 [Sample_8]


title: F1_NC [F1_04]


title: TFK1, nab_paclitaxel, biol rep 2 [N2]


title: D18-Cerebrum-2


title: F1_NC [F1_03]


title: F1_FC [F1_14]


title: TFK1, RT_6Gy, biol rep 2 [R2]


title: Adipose 7 day graft 1 [Sample_11]


title: TFK1, RT_6Gy, biol rep 1 [R1]


title: Adipose Control 3 [Sample_3]


title: TFK1, nab_paclitaxel, biol rep 1 [N1]


title: Adipose Control 1 [Sample_1]


title: SP-10

source_name: Spleen

value: Spleen

value: male

value: Treg


title: D18-Cerebrum-1


title: TFK1, RT_6Gy, biol rep 3 [R3]


title: D18-Cerebellum-2


title: EAE-SC-8

value: Spinal cord

value: EAE model D28


title: NCNC [NCNC_02]

source_name: NCNC_larvae heads

value: NCNC


title: EAE-SC-7

value: female


title: NCFC [NCFC_03]

source_name: NCFC_larvae heads

value: NCFC


title: Animal_G28_W8_D0

city: Palo Alto

first: Dmitri

middle: A

last: Kazmin

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

institute: Stanford University

data_processing:
Reads were aligned using STAR 2.7.10a
Assembly: Mmul-10
Supplementary files format and content: Reads per transcript, tab-delimited text

organism: Macaca mulatta

source_name: PBMC

extract_protocol:
The blood Paxgene tubes were stored until all samples were collected. The whole blood samples were then subjected to RNA extraction using the Thermo Fisher “MagMAX™ for Stabilized Blood Tubes RNA Isolation Kit, compatible with PAXgene Blood RNA Tubes.”
Sample QC was performed with Agilent 2100 bioanalyzer to identify samples with RIN > 7. Qualified RNA from each sample was processed with non-stranded mRNAseq library prep (with globin mRNA removal). In brief, mRNA molecules were purified from total RNA using oligo(dT)-attached magnetic beads. Globin mRNA was depleted using globin mRNA probes. mRNA molecules were fragmented into small pieces using a fragmentation reagent, and the first-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. They were then end-repaired, followed by A-tailing and adapter ligation reactions. The library was subsequently PCR enriched and purified by the Ampure XP bead size selection method. All libraries are quantified by Agilent Technologies 2100 bioanalyzer. The double-stranded PCR products were heat-denatured and circularized by the splint oligo sequence. The single-strand circle DNA (ssCir DNA) was formatted as the final library. The library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular. The DNBs were loaded into the patterned nanoarray and paired-end 150-base reads were generated by sequencing using the sequencer G400.

value: PBMC

tag: week

tag: day

tag: regimen


title: Animal_G28_W12_D0

tag: tissue


title: Animal_G28_W4_D0


title: Animal_G28_W8_D1


title: NCNC [NCNC_04]


title: Animal_G28_W9_D0


title: Animal_G28_W0_D1


title: EAE-Br-6

source_name: Brain

value: Brain


title: NCNC [NCNC_03]


title: TFK1, control biol, rep 3 [C3]

tag: cell line

value: control


title: TFK1, control biol, rep 2 [C2]

tag: cell type


title: SP-9

tag: genotype


title: NCNC [NCNC_01]


title: TFK1, control, biol rep 1 [C1]

tag: treatment


title: SMR90, DLBCL, Naive, Female

city: Chapel Hill

first: Yuri

last: Fedoriw

state: NC

address: 160 Medical Drive

institute: University of North Carolina

data_processing:
STAR 2.7.6a was used for read alignment
Salmon 1.4.0 was used for transcript quantification
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: FFPE tumor

extract_protocol:
Omega FFPE RNA extraction kit
KAPA Hyper Prep RNA with Riboerase kit
Eukaryotic strand-specific mRNA sequencing, sequenced on Illumina NovaSeq 6000 S4, paired-end 150 bp

value: FFPE tumor

value: Female

value: Naive

tag: disease state

value: DLBCL


title: NCFC [NCFC_01]


title: Animal_DCGM_W27_D0

value: DCGM


title: Animal_G28_W1_D0


title: F1_NC [F1_01]

value: larvae heads


title: SMR92, DLBCL, HIVneg, Male

value: Male

value: HIVneg


title: NCFC [NCFC_02]


title: D18-Cerebellum-1

value: Cerebellum

tag: time

value: WT

value: EAE model


title: SMR91, DLBCL, Exp, Male

value: Exp


title: SMR89, DLBCL, Exp, Female


title: Ischemia-3

value: male

value: Treg

value: MCAO model D28


title: Animal_G28_Baseline_D0

value: PBMC

value: Baseline


title: SMR9, DLBCL, Exp, Female

value: FFPE tumor


title: Ischemia-4

value: Brain


title: EAE-Br-5

value: female

value: EAE model D28


title: Animal_DCGM_W24_D0

value: DCGM


title: SMR88, DLBCL, Exp, Male

value: DLBCL


title: FCNC [FCNC_04]

source_name: FCNC_larvae heads

value: FCNC

value: larvae heads


title: APP-1

value: App NL-G-F/Foxp3-hCD2-KI

value: 1 year old


title: SMR86, DLBCL, Exp, Male

value: Male


title: FCNC [FCNC_01]


title: colon10 [LC_50]

city: Jinan

first: Yanqing

last: Li

state: Shandong province

address: No. 44 Wenhua West Road，Lixia district,

department: Gastroenterology

institute: Shandong University

data_processing:
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100). And After removed the low quality bases and undetermined bases ,we used HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) to map reads to the genome ,(command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam). The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam). Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64). After the final transcriptome was generated, StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by R package edgeR(https://bioconductor.org/packages/release/bioc/html/edgeR.html) or DESeq2(http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html),and then analysis GO enrichment and KEGG enrichment to the differentially expressed mRNAs.
Assembly: mm10
Supplementary files format and content: genes_fpkm_expression.xlsx
Supplementary files format and content: gene_count_matrix.xlsx

source_name: colon

extract_protocol:
Total RNA was isolated and purified usingTRIzol reagent (Invitrogen, Carlsbad, CA, USA)following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp.At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: colon

value: WT

value: drinking water with 3%dss for 7days along with 5um 4-HDHA diluted in PBS intravenous injection(200ul/20g/per day)


title: Animal_DCGM_W1_D0


title: SMR87, DLBCL, Exp, Male

value: Exp


title: FCNC [FCNC_03]


title: colon9 [LC_49]

value: drinking water with 3%dss for 7days along with 5um 4-HDHA intravenous injection(200ul/20g/per day)


title: Animal_DCGM_W23_D1

value: PBMC


title: Animal_DCGM_W23_D0


title: SMR85, FL/DLBCL, HIVneg, Male

value: FFPE tumor

value: HIVneg

value: FL/DLBCL


title: Animal_DCGM_W4_D0


title: APP-2

value: Brain

value: male

value: Treg


title: Animal_DCGM_W0_D1

value: DCGM


title: SMR84, DLBCL, HIVneg, Male

value: DLBCL


title: FCFC [FCFC_01]

source_name: FCFC_larvae heads

value: FCFC

value: larvae heads


title: FCNC [FCNC_02]

value: FCNC


title: colon7 [LC_47]

value: colon


title: FCFC [FCFC_03]


title: Animal_DCDD_W27_D0

value: DCDD


title: Animal_DCGM_Baseline_D0

value: Baseline


title: SMR81, DLBCL, Naive, Female

value: Female

value: Naive


title: colon8 [LC_48]

value: WT

value: drinking water with 3%dss for 7days along with 5um 4-HDHA intravenous injection(200ul/20g/per day)


title: colon5 [LC_45]

value: drinking water with 3%dss for 7days along with PBS intravenous injection(200ul/20g/per day)


title: SMR8, EBV+ DLBCL, Naive, Female

value: FFPE tumor

value: EBV+ DLBCL


title: SMR82, DLBCL, Exp, Male

value: Male

value: Exp


title: Animal_DCDD_W23_D1

value: PBMC


title: Animal_DCDD_W24_D0


title: SMR79, DLBCL, Naive, Female

value: DLBCL


title: FCFC [FCFC_02]

value: FCFC


title: Animal_DCDD_W23_D0


title: colon3 [LC_43]


title: colon4 [LC_44]


title: Animal_DCDD_W4_D0


title: SMR78, DLBCL, Naive, Female


title: SMR77, DLBCL, HIVneg, Male

value: HIVneg


title: colon6 [LC_46]


title: IL-17A-stimulated entheseal tissue_1

city: Sendai

first: Shin

last: Ebihara

address: 2-1 Seiryo, Aoba, Sendai, Miyagi 980-8575

department: 1)	Department of Pathology

institute: Tohoku University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K v2 ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor

source_name: Entheseal tissue, histoculture, IL-17A-stimulation

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: Total RNA was isolated from the entheseal tissue culture samples using the RNeasy Plus Universal Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. RNA samples were quantified using an ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and the quality was checked using an Agilent 2200 Tape Station.

value: Enthesis


title: SMR76, DLBCL, Exp, Male


title: Animal_DCDD_W1_D0


title: colon1 [LC_41]

value: colon


title: Animal_DCDD_W0_D1

value: DCDD


title: OPC, P720, Male, 6_8

city: Baltimore

first: Dwight

last: Bergles

state: MD

address: 725 North Wolfe St., WBSB 1001

department: Neuroscience

institute: Johns Hopkins University

description:
10x Genomics
P720M-68

data_processing:
kallisto-bustools
Monocle 3
Supplementary files format and content: The raw data has been preprocessed to generate a cell x gene matrix using kallisto-bustools
Supplementary files format and content: The preprocessed cell x gene matrices have been combined into a single cell_data_set (cds) and processed using the Monocle 3 pipeline to generate the final annotated cds

source_name: Cortex

extract_protocol:
After making single-cell suspensions of dissected cortices from P30, P180, P360, and P720 Matn4mEGFP/+ mice, GFP+ OPCs were FACS isolated and collected in an EDTA-free buffer.
10x Chromium Next GEM Single Cell 3' v3 & v3.1

value: Cortex

value: M

tag: # of_cells_in_the_final_dataset


title: colon2 [LC_42]


title: IL-17A-stimulated entheseal tissue_3


title: SC-Naïve-Poised-Formative/Primed-113h

city: Beijing

first: Xuehui

last: Lv

address: No.5 Yiheyuan Road, Haidian district, Beijing, 100871, China

institute: Peking University

description: 10x Genomics

data_processing:
We used cell ranger count pipeline 3.0.2 against the hg38 genome to generate count matrix for each sample. All the sample batches were merged together by cell ranger aggr pipeline. We removed the cells as the following criteria: 1) expressed genes in each cell less than 2,000; 2) the percentage of mitochondrion gene expression in each cell more than 5%. Then, Seurat R package was used for downstream analyses, including normalization, clustering, and dimension reduction. Seurat R package was used for downstream analyses, including normalization, clustering, and dimension reduction.
Assembly: hg38
Supplementary files format and content: barcodes/features/matrix/mtx.gz files of each time points were provided

extract_protocol:
Samples were dissociated into single cells and resuspended in 0.04% w/v BSA.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics).

value: hESC


title: Animal_DCDD_Baseline_D0

value: Baseline

tag: group


title: OPC, P720, Male, 10

description:
10x Genomics
P720M-10


title: IL-17A-stimulated entheseal tissue_2

tag: strain


title: Non-stimulated entheseal tissue_3

source_name: Entheseal tissue, histoculture, non-stimulation


title: Non-stimulated entheseal tissue_1


title: SMR69, DLBCL, HIVneg, Female

value: Female


title: SC-Naïve-Poised-Formative/Primed-41h

description: 10x Genomics

value: WT


title: Animal_DCAP_W27_D0

value: DCAP


title: SMR67, DLBCL, Exp, Male

value: FFPE tumor


title: SMR71, EBV+ DLBCL, Exp, Female

value: EBV+ DLBCL


title: SC-Naïve-Poised-Formative/Primed-77h

description: 10x Genomics


title: OPC, P720, Female, 9

description:
10x Genomics
P720F-9

tag: age

value: F


title: OPC, P720, Female, 3_16

description:
10x Genomics
P720F-316

tag: Sex


title: Animal_DCAP_W24_D0

value: PBMC


title: SMR66, DLBCL, Exp, Male

value: Male

value: Exp

value: DLBCL


title: Non-stimulated entheseal tissue_2

value: Enthesis


title: SC-Naïve-Poised-Formative/Primed-0h

description: 10x Genomics


title: Animal_DCAP_W23_D1


title: OPC, P720, Female, 2

description:
10x Genomics
P720F-2


title: SMR65, DLBCL, Exp, Female


title: Animal_DCAP_W23_D0


title: OPC, P360, Male, 8

description:
10x Genomics
P360M-8


title: HeLa Cells, pcDNA3-circSMARCA5, untreated, rep2 [S_Unt02]

city: San Sebastián

first: David

last: Otaegui

state: Guipuzcoa

address: Paseo Dr begiristain s/n

department: Neurosciences

country: Spain

institute: Biodonostia Research institute

data_processing:
For circRNA detection, reads were mapped to the human genome (hg19) using STAR or BWA. Subsequently, circRNA prediction was performed by CIRCexplorer2 and CIRI2. Only circRNAs supported with at least two reads by both algorithms were considered as bona fide circRNAs and used in subsequent analyses. Their expression level was quantified based on back-spliced junctions-spanning reads according to CIRI2 quantification.
Kallisto version 0.44.0 (http://pachterlab.github.io/ kallisto/) algorithm was used for transcript pseudoalignment, identification and quantification
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes DESeq2 normalized circRNA counts
Supplementary files format and content: tab-delimited text file includes Kallisto normalized linear RNA counts

source_name: HeLa

extract_protocol:
miRNeasy mini kit
rRNA was depleted from the total RNA sample using the Ribo-Zero rRNA removal kit, followed by purification and fragmentation steps. To construct the sequencing libraries, a strand-specific cDNA synthesis was performed, the 3’ ends were adenylated and adaptors were ligated

treatment_protocol: cells were washed with DPBS 1X, trypsinized, resuspended in DMEM and pelleted (1500rpm x 5 min). Then, the cell pellet was resuspended in QiaZol (Qiagen)

value: HeLa

value: epithelial cells

value: untreated


title: SMR63, EBV+ DLBCL, HIVneg, Female

value: HIVneg


title: OPC, P360, Male, 13

description:
10x Genomics
P360M-13

value: Cortex

value: M


title: SC-Naïve-Poised-Formative/Primed-36h

description: 10x Genomics

value: hESC


title: SMR61, DLBCL, Exp, Female

value: Female


title: Animal_DCAP_W4_D0

value: DCAP


title: HeLa Cells, pcDNA3-circSMARCA5, poly(I:C) treated, rep2 [S_Tre02]

value: poly (I:C)


title: OPC, P360, Male, 1

description:
10x Genomics
P360M-1


title: Animal_DCAP_W0_D1


title: Animal_DCAP_W1_D0


title: OPC, P360, Female, 5

description:
10x Genomics
P360F-5


title: HeLa Cells, pcDNA3-circSMARCA5, poly(I:C) treated, rep1 [S_Tre01]


title: HeLa Cells, pcDNA3-circRELL1, untreated, rep2 [R_Unt02]


title: OPC, P360, Female, 2

description:
10x Genomics
P360F-2


title: Animal_DCAP_Baseline_D0

value: Baseline


title: SMR56, EBV+ DLBCL, Exp, Female

value: FFPE tumor

value: EBV+ DLBCL


title: HeLa Cells, pcDNA3-circRELL1, poly(I:C) treated, rep2 [R_Tre02]


title: OPC, P180, Male, 1

description:
10x Genomics
P180M-1


title: HeLa Cells, pcDNA3-circRELL1, untreated, rep1 [R_Unt01]


title: Animal_DC9D_W12_D0

value: PBMC


title: HeLa Cells, pcDNA3-circSMARCA5, untreated, rep1 [S_Unt01]


title: HeLa Cells, pcDNA3-circRELL1, poly(I:C) treated, rep1 [R_Tre01]


title: Animal_DC9D_W9_D0


title: SMR55, DLBCL, HIVneg, Female


title: OPC, P180, Female, 4

description:
10x Genomics
P180F-4

value: F


title: OPC, P180, Female, 3

description:
10x Genomics
P180F-3


title: SMR54, DLBCL, Exp, Male

value: Male

value: Exp

value: DLBCL


title: Animal_DC9D_W8_D1


title: HeLa Cells, pcDNA3-empty, untreated, rep2 [P_Unt02]

value: HeLa

value: epithelial cells


title: SMR60, DLBCL, Exp, Male


title: Animal_DC9D_W8_D0


title: OPC, P180, Female, 2

description:
10x Genomics
P180F-2


title: HeLa Cells, pcDNA3-empty, untreated, rep1 [P_Unt01]

value: untreated


title: SMR52, DLBCL, HIVneg, Female

value: HIVneg


title: HeLa Cells, pcDNA3-empty, poly(I:C) treated, rep2 [P_Tre02]


title: SMR51, DLBCL, Naive, Male

value: Naive


title: SMR59, DLBCL, Exp, Male


title: OPC, P30, Male, 4

description:
10x Genomics
P30M-4

value: Cortex

value: M


title: SMR6, DLBCL, Naive, Male


title: HeLa Cells, pcDNA3-empty, poly(I:C) treated, rep1 [P_Tre01]


title: Animal_DC9D_W1_D0


title: OPC, P30, Male, 17

description:
10x Genomics
P30M-17


title: OPC, P30, Male, 10

description:
10x Genomics
P30M-10


title: SMR50, DLBCL, Naive, Female

value: Female


title: Animal_DC9D_W0_D1


title: Animal_DC9D_Baseline_D0


title: SMR48, DLBCL, Exp, Male


title: HeLa Cells, pcDNA3-circCAMSAP1, untreated, rep2 [C_Unt02]


title: HeLa Cells, pcDNA3-circCAMSAP1, untreated, rep1 [C_Unt01]


title: SMR46, DLBCL, Exp, Male


title: OPC, P30, Female, 2

description:
10x Genomics
P30F-2


title: Animal_DC8V_W27_D0


title: SMR45, DLBCL, Exp, Male


title: HeLa Cells, pcDNA3-circCAMSAP1, poly(I:C) treated, rep2 [C_Tre02]

value: poly (I:C)


title: Animal_DC8V_W24_D0


title: OPC, P30, Female, 13

description:
10x Genomics
P30F-13


title: SMR43, DLBCL, HIVneg, Male


title: Animal_DC9D_W4_D0


title: HeLa Cells, pcDNA3-circCAMSAP1, poly(I:C) treated, rep1 [C_Tre01]


title: Animal_DC8V_W23_D1


title: SMR41, DLBCL, Exp, Female


title: Lin- cells_scRNA-seq

city: Chongqing

first: CHENGFANG

last: ZHOU

address: No. 30, Gaotanyan Street.

department: Department of Hematology, Southwest Hospital

institute: Army Medical University

data_processing:
Differential expression of each cluster was calculated using the ‘bimod’ test as implemented in Seurat FindMarkers function.Genes with a log2 average expression difference 0.585 and P < 0.05 were identified as marker genes. Cell clusters were annotated using canonical markers of known cell types.
Seurat-Bimod statistical test was used to find differentially expressed genes between each group of cells and other groups of cells (FDR <= 0.05 and |log2 Fold Change| >= 1.5)
Assembly: mm10

source_name: bone marrow

extract_protocol:
Lin- cells were enriched from C57/B6 mice according to the EasySep™ Mouse Hematopoietic Progenitor Cell Isolation Kit.
Library was performed according to che manufacter's instrucions  (Single Cell 3′ library and Gel Bead Kit v.3 protocol,10 Genomics ). Briefly, Lin- cells Cells were loaded onto the 10X Chromium Single Cell Platform (10X Genomics) at a concentration of 1,000 cells per μl as described in the manufacturer’s protocol. Generation of gel beads in emulsion (GEMs), barcoding, GEM-RT clean-up, complementary DNA amplification and library construction were all performed as per the manufacturer’s protocol. Qubit was used for library quantification before pooling.The final library pool was sequenced on the Illumina Nova6000 instrument using 150-base-pair paired-end reads

value: 8 weeks old

value: wild type

value: bone marrow

value: LSK


title: Animal_DC8V_W23_D0

value: PBMC


title: SMR40, DLBCL, HIVneg, Male

value: FFPE tumor

value: Male


title: Animal_DC8V_W4_D0


title: SMR4, FL/DLBCL, HIVneg, Female

value: FL/DLBCL


title: cko3

data_processing:
Nynrinfl/flTie2-Cre vs Nynrinfl/fl mice
FPKM of differential genes
Assembly: mm10
Supplementary files format and content: Raw_counts_expression.txt

source_name: Bone marrow

growth_protocol: HSCs isolated from BM of mice

extract_protocol:
About 3000 HSCs of BMs from Nynrinfl/flTie2-Cre or Nynrinfl/fl mice were sorted by FACS,and extraction and Purification of total RNA using Trizol. 5 ng cDNA was used for the construction of sequencing libraries.
The construct of the whole cDNA library for low number HSCs from from Nynrin cko mice was performed as previously described (Chen et al., 2017, PMID: 28207000).

treatment_protocol: Nynrinfl/flTie2-Cre and Nynrinfl/fl mice

value: Bone marrow

value: HSCs

value: Nynrin CKO


title: SMR39, DLBCL, HIVneg, Female

value: HIVneg

value: DLBCL


title: OPC, P30, Male, 1

description:
10x Genomics
P30M-1

value: Cortex


title: Animal_DC8V_W1_D0


title: cko4


title: SMR38, DLBCL, HIVneg, Female


title: cko1


title: SMR37, DLBCL, Exp, Female

value: Exp


title: N4


title: Animal_A8X014_W12_D0


title: SMR36, DLBCL, Naive, Female

value: Female

value: Naive


title: Animal_DC8V_Baseline_D0

value: Baseline


title: Animal_A8X014_W9_D0


title: N2

value: wild type

value: 8 weeks old


title: Animal_A8X014_W8_D1


title: N3


title: SMR34, DLBCL, HIVneg, Female


title: Animal_A8X014_W8_D0


title: SMR33, DLBCL, Naive, Female


title: SMR35, DLBCL, Exp, Male


title: Animal_A8X014_W4_D0


title: Lin_2_input_for_Nynrin

data_processing:
Using Cutadapt to remove splice sequences from Raw data,the Trimmomatic program to remove low-quality sequences
Using  FastQC program for quality control analysis of Clean data, Bowtie2 program for comparing  Clean data t tothe reference genome
Calculating  the capture efficiency, ChIP coverage and average sequencing depth
Using MACS2 for Peak-calling analysis on the genome,  IDR program for peak screening with high confidence between samples
Using the ChIPseeker package for comments on Peaks, MEME program for Motif analysis, MAnorm program for Peaks
Assembly: mm10

source_name: Lineage-negative cells

growth_protocol: PBS+1%FBS, cells were incubated on ice

extract_protocol:
Lineage-negative cells of BM from  3×Flag-Nynrin-Tg mice were fixed with 1% formaldehyde for 10min.Then cells were demobilized and lysed.
ChIP-seq libraries were prepared using TruePrepTM DNA Library Prep Kit V2  from  Vazyme. 10ng of DNA was used as starting material for input and IP samples.Libraries were amplified using 16 cycles on thermocycler.Post amplification libraries were size selected at  100-500bp in length using Agencourt AMPure XP beads from Beckman Coulter.Libraries were validated using Agilent High Sensitivity DNA kit

value: 3xFlag-Nynrin-Tg mice

value: Lineage-negative cells

tag: chip antibody

value: input


title: SMR32, DLBCL, HIVneg, Female

value: FFPE tumor


title: Lin_2_Chip_Seq_for_Nynrin

value: Flag


title: SMR31, DLBCL, Naive, Male

value: Male


title: cko2

value: Bone marrow

value: HSCs


title: Lin_1_input_for_Nynrin


title: Animal_A8X014_W1_D0

value: PBMC

tag: animal


title: SMR30, DLBCL, Naive, Female

value: DLBCL


title: Animal_A8X014_W0_D1

tag: week


title: Animal_DC8V_W0_D1

tag: day


title: Lin_1_Chip_Seq_for_Nynrin


title: SMR3, DLBCL, Exp, Male


title: KO_NPC_WGBS_Rep2

city: Shanghai

first: Yan

last: Jiang

address: 131 Dongan rd

department: Institutes of Brain Science

institute: Fudan University

data_processing:
WGBS reads were filtered and trimmed with “fastp” (version 0.23.4, -q 20 -u 50 -n 5).
Quality control was conducted by FastQC (version 0.11.9).
High quality clean reads were aligned to mouse genome mm10 and lambda phage genome with Bowtie2 (version 2.2.3) in default settings.
Aligned reads were deduplicated with “deduplicate_bismark” function of Bismark (version 0.22.1).
Methylation measurement was extracted with “bismark_methylation_extractor” function of Bismark (--no_overlap --ignore_r2 2 --comprehensive), and the bisulfite conversion rate was calculated according to the methylation level of spiked-in lambda DNA.
Assembly: mm10
Supplementary files format and content: COV: Coverage text files, tab delimited

source_name: Neural progenitor cells

growth_protocol: Ganglionic eminences of fetal brains were harvested, dissociated with Accutase solution (Sigma A6964), and cultured in ultra-low attachment plates (Corning 3471) with advanced DMEM/F-12 (Gibco 12634-010) supplemented with N-2 (Gibco 17502048), B-27 (Gibco 12587010), GlutaMAX (Gibco 35050061), P/S (Sigma V900929), heparin (5 ug/ml), EGF (20 ng/ml) and FGF (20 ng/ml). Fresh medium was added every 3 days, and neurospheres were dissociated with Accutase and passed every 5 days.

extract_protocol:
2 million cultured cells were harvested, washed in PBS and lysed with NP40 lysis buffer (0.32 M sucrose, 5 mM CaCl2, 3 mM Mg(Ace)2, 0.1 mM EDTA, 10 mM Tris pH8, 0.1% NP40). Nuclei were collected with centrifugation, incubated with 5 μl of 10 mg/ml RNase A (Sigma R6513) in 500 μl PK lysis buffer (1 M Tris pH8, 50 mM EDTA, 2% SDS, 2 M NaCl) at 37 ℃ for 15 minutes, and then with 10 μl of 20 mg/ml proteinase K (Sigma P2308) at 52 ℃ overnight with rotation. The samples were then added with phenol/chloroform (1:1) (Solarbio P1021), mixed with vortex, and centrifugated with 15000 g at RT for 10 minutes. The supernatant was taken and precipitated with isopropanol. The precipitated genomic DNA (gDNA) was washed in 70% ethanol, air dried and dissolved in buffer EB (Qiagen 19086).
The gDNA was spiked in with 1% of unmethylated lambda DNA (Promega D1521) for efficiency validation of bisulfite conversion. 500 ng of gDNA was taken and sonicated to ~250 bp with Covaris M220 ultrasonicator. The DNA fragments were end-repaired and A-tailed with NEBNext Ultra II End Repair/dA-Tailing Module (NEB E7546), and then ligated with NEBNext Multiplex Oligos for Illumina (Methylated Adaptor, Index Primers Set 1, NEB E7535). After size-selected to 300~400 bp with Ampure XP beads (Beckman A63881), DNA was bisulfite converted with EZ DNA methylation kit (Zymo Research D5001), PCR amplified with KAPA HiFi HotStart Uracil+ ReadyMix (Kapa Biosystems KK2801), and the library was finally size-selected to 300~500 bp with Ampure XP beads. After analysis with Agilent Tapestation 4200, the library was sent for deep sequencing on Illumina NovaSeq 6000 (paired-end, 150bp).

value: Neural progenitor cells from ganglionic eminence

value: Embryonic day 15.5

tag: fetus id


title: KO_NPC_WGBS_Rep1


title: Animal_A8X014_Baseline_D0

tag: tissue

tag: regimen


title: Animal_A7N155_W9_D0


title: SMR28, FL/DLBCL, Exp, Male

value: Exp

value: FL/DLBCL


title: WT_NPC_WGBS_Rep2

tag: cell type

value: Wildtype


title: N1

tag: genotype

value: wild type


title: SMR27, DLBCL, Exp, Female

value: Female

tag: treatment


title: WT_NPC_WGBS_Rep1


title: KO_NPC_CTCF_Rep3

data_processing:
Quality control of ChIP-seq reads was conducted with FastQC (version 0.11.9).
Reads were trimmed with Trim Galore (version 0.6.7, --quality 20 --phred33 --stringency 1 --length 20 --fastqc --paired).
Reads were aligned to mm10 with Bowtie2 (version 2.4.1) in default settings.
Reads were binarized, sorted, deduplicated and indexed with SAMtools (version 1.6).
Narrow peaks were called with MACS2 (version 2.2.7.1) in default settings.
Assembly: mm10
Supplementary files format and content: NARROWPEAK: Narrow peak text files, tab delimited

extract_protocol:
Three million NPCs were harvested, washed in PBS and lysed with NP40 lysis buffer (0.32 M sucrose, 5 mM CaCl2, 3 mM Mg(Ace)2, 0.1 mM EDTA, 10 mM Tris pH8, 0.1% NP40). For native ChIP (nChIP, for H3K9me3), nuclei were collected through centrifugation, resuspended in douncing buffer (10 mM Tris pH8, 4 mM MgCl2, 1 mM CaCl2) and chromatin was fragmentized with micrococcal nuclease (Sigma N3755). Hypotonic solution (0.2 mM EDTA, cOmplete inhibitor (Roche 11697498001), 0.1% NP40) was added for nuclei lysis and chromatin release. For fixed ChIP (xChIP, for CTCF), nuclei were collected through centrifugation, fixed in 1% formaldehyde (Sigma 252549) at room temperature for 5 minutes with rotation, and quenched in 0.125 M glycine at RT for 10 minutes with rotation. After collected with centrifugation, the fixed nuclei were resuspended in FSB solution (5 mM EDTA, 20 mM Tris pH8, 500 mM NaCl) supplemented with 0.1% SDS and cOmplete inhibitor, and sonicated with Covaris E220 ultrasonicator system to 300~500 bp. For both nChIP and xChIP, protein-DNA complexes were isolated with antibody.
ChIP DNA was blunted with End-it DNA Repair Kit (Epicentre ER0720), A-tailed with Klenow Exo-minus (Epicentre KL06041K), ligated with adapter (Vazyme N802-01) using Fast-Link kit (Epicentre LK11025) and amplified with VAHTS HiFi Universal Amplification Mix for Illumina (Vazyme N618-02). The library was size-selected with SPRIselect beads (Beckman B23318) and sent for sequencing on Illumina NovaSeq 6000 (paired-end, 150 bp).


title: Animal_A7N155_W8_D0


title: SMR26, DLBCL, HIVneg, Male

value: HIVneg

tag: disease state


title: Animal_A7N155_W4_D0


title: SMR24, DLBCL, HIVneg, Male


title: Animal_A7N155_W1_D0


title: SMR25, DLBCL, HIVneg, Male


title: KO_NPC_CTCF_Rep1


title: Animal_A7N155_Baseline_D0

value: Baseline


title: Animal_A7N155_W12_D0


title: SMR23, DLBCL, Naive, Male

value: Naive


title: Animal_A7N155_W0_D1


title: Animal_A7N137_W12_D0


title: SMR22, DLBCL, Naive, Female

value: FFPE tumor


title: WT_NPC_CTCF_Rep2


title: WT_NPC_CTCF_Rep3


title: SMR29, DLBCL, Naive, Male


title: Animal_A7N155_W8_D1


title: SMR20, EBV+ DLBCL, HIVneg, Male

value: EBV+ DLBCL


title: WT_NPC_CTCF_Rep1


title: KO_NPC_H3K9me3_Rep3


title: SMR2, DLBCL, Exp, Female


title: Animal_A7N137_W8_D1


title: KO_NPC_H3K9me3_Rep2


title: Animal_A7N137_W8_D0


title: Animal_A7N137_W9_D0


title: SMR18, DLBCL, HIVneg, Male

value: Male


title: KO_NPC_H3K9me3_Rep1


title: Animal_A7N137_W4_D0


title: KO_NPC_CTCF_Rep2


title: WT_NPC_H3K9me3_Rep3


title: Animal_A7N137_W1_D0


title: SMR15, DLBCL, Exp, Male


title: WT_NPC_H3K9me3_Rep2


title: SMR13, DLBCL, HIVneg, Male


title: SMR14, EBV+ DLBCL, Exp, Male


title: Animal_A7N137_W0_D1


title: Animal_A7N137_Baseline_D0


title: KO_NPC_Hi-C_Rep3

data_processing:
Quality control was conducted by FastQC (version 0.11.9), and reads were trimmed with Trim Galore (version 0.6.7, --quality 20 --phred33 --stringency 1 --length 20 --fastqc --paired).
Restriction sites of MboI on mm10 were generated with “hiccup_digester” function of HiCUP (version 0.8.0).
High quality clean reads were aligned to mm10 with Bowtie2 program (version 2.4.1) in HiCUP (max di-tag length: 700, min di-tag length: 50).
“ValidPairs” were generated with the “mapped_2hic_fragments.py” script of HiC-Pro (version 2.11.4) in default settings.
“.hic” files were generated with “hicpro2juicebox.sh” utility of HiC-Pro and JuicerTools (version 1.22.01).
Assembly: mm10
Supplementary files format and content: HIC: binary contact matrix for visualization in Juicebox

extract_protocol:
3 million cells were lysed in NP40 lysis buffer (0.32 M sucrose, 5 mM CaCl2, 3 mM Mg(Ace)2, 0.1 mM EDTA, 10 mM Tris pH8, 0.1% NP40) , fixed in 1% formaldehyde (Sigma 252549) at RT for 5 minutes and quenched with 125 mM glycine at RT for 10 minutes. Nuclei were incubated in 0.5% SDS at 62 ℃ for 10 minutes, and quenched with 1.25% Triton X-100 (Sigma 93443) at 37 ℃ for 15 minutes. Chromatin was digested with 100 U of MboI restriction enzyme (NEB R0147) in 1X NEBuffer2 (NEB B7002S) at 37 ℃ overnight with rotation. Enzyme digestion was inactivated with incubation at 65 ℃ for 20 minutes, and nuclei were collected with centrifugation. Restriction fragment overhangs were filled and DNA ends were marked with biotin using End-it DNA Repair Kit (Epicentre ER0720) supplemented with 0.256 mM biotin-14-dATP (Life Technologies 19524-016), 0.4 mM dCTP, 0.4 mM dGTP and 0.4 mM dTTP (NEB N0446S). For proximity ligation, DNA fragments were ligated with 2000 U of T4 DNA ligase (NEB M0202) in 1200 μl of ligation master mix (T4 DNA ligase buffer (NEB B0202), 0.83% Triton X-100, 0.1 mg/ml bovine serum albumin (NEB B9200S)) at RT for 4 hours with slow rotation. After ligase inactivation at 65 ℃ for 5 minutes, nuclei were collected with centrifugation, and the chromatin was reverse-crosslinked in PK lysis buffer (1 M Tris pH8, 50 mM EDTA, 2% SDS, 2 M NaCl) at 65 ℃ for 4 hours, followed by RNase A (Sigma R6513) and proteinase K (Sigma P2308) digestion. DNA was further purified by phenol/chloroform (1:1) and ethanol precipitation, dissolved in buffer EB (Qiagen 19086) and sonicated to ~ 300 base pairs by Covaris E220 ultrasonicator system. For biotin pull-down, 100 μl per sample of 10 mg/ml Dynabeads MyOne Streptavidin T1 beads (Life technologies 65602) was washed with 400 μl per sample of 1 X TWB (5 mM Tris-HCl pH7.5, 0.5 mM EDTA, 1 M NaCl, 0.05% Tween-20), resuspended in 100 μl per sample of 2X binding buffer (10 mM Tris-HCl pH7.5, 1 mM EDTA, 2 M NaCl) and incubated with samples at RT for 15 minutes with rotation. The beads were separated on magnetic stand, washed three times with 1 X TWB (pre-warmed to 55 ℃) and once in 100 μl buffer EB (Qiagen 19086).
The beads were collected for DNA end repair with End-it DNA Repair Kit, A-tailing with Klenow Exo-minus (Epicentre KL06041K), adapter (Vazyme N802-01) ligation with Fast-Link kit (Epicentre LK11025) and PCR amplification with VAHTS HiFi Universal Amplification Mix for Illumina (Vazyme N618-02). Supernatant was taken as the library, which was further size-selected with SPRIselect beads (Beckman B23318) and sent for deep sequencing on Illumina NovaSeq 6000 (paired-end, 150 bp).

tag: restriction enzyme

value: MboI


title: SMR16, DLBCL, HIVneg, Male


title: Animal_A7N104_W12_D0


title: SMR10, DLBCL, Exp, Male


title: SMR19, DLBCL, Naive, Female


title: SMR11, DLBCL, HIVneg, Male


title: KO_NPC_Hi-C_Rep1


title: Animal_A7N104_W9_D0


title: wild type adult hermaphrodite on xrn-2 RNAi, screen group rep n/a

city: Bethesda

first: Katherine

last: McJunkin

address: 50 South Drive, Building 50 Room 3148

institute: National Institutes of Health

data_processing:
Deep sequencing data were analyzed using the miTRATA web interface (https://wasabi.ddpsc.org/~apps/ta/) after preprocessing the data using miTRATA’s accompanying Python3-based preprocess.seq pipeline, installed on the NIH High Performance Computing Cluster in a dedicated miniconda environment. The matureC. elegansmiRNAs from miRBase Release 22.1 were used for miTRATA mapping. A custom C++ script reformatted the miTRATA output by consolidating read numbers for all reads meeting the following criteria into a tabular format: a tail:head ratio >0.12 and a tail length≤3nt. These reformatted tailing data were further analyzed in RStudio. (One non-unique miRNA pair was of sufficient abundance to be included in tailing analysis—mir-44/45-3p;mir-45-3pwas therefore culled from tabular data to avoid plotting this data twice). To calculate reads per million, reads were normalized by the number of genome-mapping reads in the library (Supplementary Table S3). The number of genome-mapping reads was determined using Bowtie to align to the C. elegans genome (WS215) with the arguments -v 3 -f -B 1 -a –best –strata. Alignments were then filtered based on the length of the reads and the number of mismatches as follows: for sequence lengths 16–17, 18–19, 20–24or >24: zero, one, twoor three mismatches were allowed, respectively. Reads passing this threshold were considered ‘genome-mapping reads’. A custom bash/R pipeline was used to calculate trimming relative to canonical miRNA length from the miTRATA output files.
Assembly: WBcel_235
Assembly: WS215
Supplementary files format and content: xlsx file containing sample metadata, normalized reads and percent tailing for microRNAs above minimum abundance threshhold

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: N2 (wild type) and SX1137 (pash-1(mj100) I) worms were maintained at 15°C. For RNA samples, L1s were synchronized by alkaline hypochlorite lysis of gravid adults followed by hatching in M9 with 1 mM cholesterol at 15°C for 48–72 h. L1s were plated on NGM seeded with either OP50 or RNAi bacteria and maintained at 15°C until early day one of gravid adulthood (until just a few embryos were laid on the plate, ∼76 h after plating). (This time point was chosen because it achieved the best synchrony of SX1137, which tends to develop slightly asynchronously, even at permissive temperature). This time point was harvested for N2 samples, SX1137 samples in the RNAi screen, and served as 0h in time courses involving SX1137. Additional SX1137 plates were shifted to 25°C, and samples were collected at the indicated time points after upshift for time courses on OP50 or RNAi. pup-1(tm1021), pup-2(tm4344) and pup-1/-2(om129) mutations were maintained over a balancer chromosome at 15–20°C; RNA was isolated from homozygous F2 (M-Z-) 1-day adult hermaphrodites raised at 22°C.

extract_protocol:
Total RNA was isolated by Trizol extraction. Spike-ins were added at a final concentration of 0.1pg/μl (OP50 samples) or 1pg/μl (RNAi samples) in 100ng/μl total RNA.
Library preparation was performed using the NEBNext Small RNA Library Prep Set for Illumina with modifications. Size selection was performed only after reverse transcription, using 8% urea gels to purify ~65-75nt RT products. Prior to loading on the gel, each RT reaction was treated with 5000units of RNAse H (New England Biolabs) for 30 minutes at 37C.

treatment_protocol: RNAi plates were supplemented with 1μg/ml IPTG and 1μg/ml Carbenicillin (and poured no more than two weeks prior to use and stored at 4°C). The RNAi bacteria (HT115 expressing an RNAi vector) were prepared from single clones derived from the Ahringer library (Source Bioscience), the Vidal library (Source Bioscience), or custom RNAi vectors (Supplementary Table S1). All previously-reported RNAi phenotypes were observed. Furthermore, a robust RNAi response in each sample was confirmed by the presence of abundant siRNAs mapping to the targeted locus.

tag: sample

tag: time point

tag: RNAi

tag: replicate

tag: sample group

value: screen

tag: dev stage

value: adult

value: hermaphrodite

value: whole animal


title: wild type adult hermaphrodite on usip-1 RNAi, screen group rep n/a

description: Library preparation was performed using the NEBNext Small RNA Library Prep Set for Illumina with modifications. Size selection was performed only after reverse transcription, using 8% urea gels to purify ~65-75nt RT products. Prior to loading on the gel, each RT reaction was treated with 5000units of RNAse H (New England Biolabs) for 30 minutes at 37C.

tag: strain

tag: Sex


title: Animal_A7N104_W8_D0

value: PBMC

tag: animal

tag: week

tag: day

tag: group


title: wild type adult hermaphrodite on xrn-1 RNAi, screen group rep n/a

tag: tissue


title: sample13 permanent atrial fibrillation

city: Kobe

first: Takuo

last: Emoto

state: Hyogo

address: 7-5-1 Kusunoki-cho, Chuo-ku

department: Division of Cardiovascular Medicine, Department of Internal Medicine

institute: Kobe University Graduate School of Medicine

description: 10x Genomics

data_processing: Cell Ranger Single Cell Software (v 6.1.2) by 10X Genomics against the GRCh38 human reference genome with default parameter

source_name: cell, permanent atrial fibrilattion

extract_protocol: cell：Each sample was washed, chopped into small pieces, and digested in enzymatic digestion buffer with 450 U/ml collagenase I (Sigma, C0130), 125 U/ml collagenase XI (Sigma, C7657), 60 U/ml DNase I (Roche, 04536282001) and 60 U/ml hyaluronidase (Sigma, H3506) at 37 °C for 30 minutes while shaking.1 The digested samples were filtered through 40-μm cell strainers (BD, 352340), washed, and centrifuged at 300g for 10 minutes.　nuclei：LA samples were cut into small pieces and frozen into liquid nitrogen within 8 hours after sample collection. Nuclei isolation was performed according to Chromium Nuclei Isolation Kit with RNase Inhibitor (PN-1000494). Frozen tissue samples are homogenized with a pestle in Lysis Buffer and passed through a column. Next, debris is removed via centrifugation in Debris Removal Buffer. The isolated nuclei are then washed and resuspended and loaded directly into compatible 10x Genomics protocol for making libraries.

value: heart

tag: cell type

value: immune cell


title: WT_NPC_Hi-C_Rep2

value: Neural progenitor cells from ganglionic eminence

tag: genotype

value: Wildtype

tag: age

value: Embryonic day 15.5

tag: fetus id


title: wild type adult hermaphrodite on tsn-1 RNAi, screen group rep n/a

tag: sample

value: wild type


title: SMR1, DLBCL, Exp, Male

tag: treatment

value: Exp

tag: disease state

value: DLBCL


title: WT_NPC_H3K9me3_Rep1

tag: chip antibody


title: Animal_A7N104_W4_D0

tag: regimen


title: Animal_A7N104_W1_D0


title: wild type adult hermaphrodite on T15H9.6 RNAi, screen group rep n/a

tag: time point

tag: RNAi

tag: replicate

tag: sample group

tag: dev stage


title: Animal_A7N104_W0_D1

tag: animal

tag: week

tag: day


title: KO_NPC_Hi-C_Rep2

tag: cell type

tag: strain

tag: restriction enzyme