title: Hyperoxia

city: ChengDu

first: Yanrong

last: Long

address: No. 17, Section 3, Renmin South Road, Wuhou District

department: State Key Laboratory of Biotherapy

institute: Sichuan University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: mm10
Supplementary files format and content: barcodes.tsv, features.tsv, matrix.mtx files.

source_name: Lung

growth_protocol: Mice reared in normoxia or hyperoxia.

extract_protocol:
Lungs were perfused with PBS, minced with scissors and digested in an enzymatic mixture (dispase II: 200 μg/ml, collagenase I: 200 μg/ml, DNase I: 40 μg/ml) for 35 min at 37°C. Following enzymatic digestion, the samples were filtered, and red blood cells were lysed. Then, single cells were resuspended in MACS buffer (DPBS + 0.1% BSA + 2 mM EDTA). Ensure cell viability exceeded 80% as determined by AO/PI reagent staining. The following sequencing steps were performed by 10X Genomics. Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software (version 2.20). Cell Ranger pipelin (version 6.1.1) was used for sample demultiplexing, barcode processing and single-cell 3' gene counting, and scRNA-seq data were aligned to the reference genome. Seurat (Version 4.0) was used for dimensional reduction, clustering and analysis of scRNA-seq data. Each group contained eight mice mixed into one sample for scRNA-seq.
Library was performed according to the manufacturer’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Illumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriately sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: Mice were either maintained in room air (21% O2) or in hyperoxia (80% O2) from P0 to P14.

value: Lung

tag: strain

tag: age

value: 2 weeks

value: Hyperoxia


title: hESCs_0_circRMST_b5_rep5 [20200617_24_N286_12]

status: Public on Nov 07 2022

type: SRA

city: Aarhus N

first: Morten

middle: T

last: Veno

state: DK

address: Aabogade 15

country: Denmark

institute: Omiics ApS

library_source: transcriptomic

data_processing:
Raw reads were filtered and trimmed using trim_galore (version 0.6.5dev, using parameters: -a AAAAAAAAAAAA --clip_R1 12).  The filtered QuantSeq 3’ mRNA-Seq reads were mapped to the human reference genome (hg19) using STAR (version 2.7.3a) with default setting. Read mapping results per gene were then quantified using the tool featureCounts with gene annotation from Gencode (version 28). All samples used for downstream analysis in the corresponding manuscript "A circular RNA expressed from the FAT3 locus regulates neural development " are indicated in the column "Samples used for downstream analysis".
Assembly: hg19
Supplementary files format and content: FeatureCounts output file with mRNA expression as raw reads for each sample. Tab delimited text file

molecule: polyA RNA

organism: Homo sapiens

source_name: H9 hESCs

growth_protocol: H9 hESCs were transferred to 4-well plates in N2B27 medium (1:1 mix of neurobasal medium and DMEM/F12 medium, 1% insulin/transferrin/selenium, 1x N2 supplement, 1x retinol-free B27 supplement, 0.3% glucose, and 1% p/s (all components are from Gibco, Thermo Fisher Scientific)) for 11 days of differentiation. For rostral NPC differentiation, SB431542 (SB, 10 μM; Tocris, Bristol, UK) and LDN193189 (LDN, 0.1uM; STEMCELL Technologies, BC, Canada) was added to the media for four days. The cells were further cultured with SB, LDN, and FGF2 (20 ng/ml; STEMCELL Technologies) until day seven. Between day 7 and 11, the cell media was only supplemented with FGF2 (20 ng/ml). For caudal NPC differentiation, SB431542 (10 μM) and CHIR99021 (CHIR; 3 μM; STEMCELL Technologies) was added to the media from days zero to four. The cells were further cultured from days 4 to 11 in the absence of SB and CHIR, but with FGF2 (20 ng/ml).

extract_protocol:
Total RNA was extracted with TRIzol Reagent (Invitrogen) following the manufacturer’s guidelines.
RNA quality was controlled using the RNA 6000 Nano Kit (Agilent Technologies, CA, USA) on a Bioanalyzer 2100 (Agilent Technologies), and RNA quantity determined using the Qubit RNA HS Assay Kit (Thermo Fisher Scientific) on a Qubit 4 Fluorometer (Thermo Fisher Scientific). The TURBO DNA-free Kit (Thermo Fisher Scientific) was used for DNA removal and followed by an additional RNA precipitation step.  For library generation, the QuantSeq 3’mRNA-Seq Library Kit (Lexogen, Vienna, Austria) was utilized according to the manufacturer’s instructions.

tag: cell line

value: H9 hESCs

tag: batch

tag: genotype

value: circRMST KD

tag: treatment/time point

value: undifferentiated; Day 0

tag: samples used_for_downstream_analysis

value: yes


title: FSK_miRNA_1

city: Jupiter

first: Sathyanarayanan

middle: V

last: Puthanveettil

state: Florida

address: 130 Scripps Way

department: Neuroscience

country: USA

institute: Scripps Florida

data_processing:
All samples were processed and sequenced on a NextSeq 500. The quality of the reads overall was quite high with no decrease in quality over the course of sequencing.
After quality control, the reads were mapped to the mouse transcriptome using Salmon using paired end settings (Salmon reference was made using Ensembl: ftp://ftp.ensembl.org/pub/release-99/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.abinitio.fa.gz)
Differential analysis was performed using DEseq
Genome_build: ftp://ftp.ensembl.org/pub/release-99/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.abinitio.fa.gz
Supplementary_files_format_and_content: Excel file contaiining gene counts and differentially expressed genes

molecule: total RNA

organism: Mus musculus

source_name: Primary Hippocampal neurons

growth_protocol: Hippocampi were cultured from P0 mice for generating RNA at DIV 16.

extract_protocol:
RNA was extracted using traditional Trizol/chloroform extraction method
RNA libraries were prepared for sequencing using Illumina TruSeq Stranded Total RNA Sample Prep

tag: tissue

value: DIV 16 neurons

tag: developmental stage

value: P0 pups

tag: agent

value: FSK


title: DHPG_miRNA_6

value: DHPG


title: ChIP_Seq_Pol_III_Untreated_anti_SSRP1_rep2

city: Beijing

first: Xiong

last: Ji

address: Haidian District, Beijing Summer Palace Road No. 5

department: School of Life Sciences

country: China

institute: Peking University

description: ChIP_Seq_Pol_III_Untreated_anti_SSRP1_merged.bw

library_source: genomic

data_processing:
Adapters were trimmed with cutadapt (v2.10) in paired-end mode with the following parameters: -q 15,15 –minimum-length 18 -a CCCCCCCCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT. Trimmed reads were first aligned to the mouse reference genome (mm10) using Bowtie2 (v2.3.5.1) with default options
SAMtools (v 0.1.19) and sambamba (v0.7.0) were used to filter unmapped reads, multiple mapped reads, and potential PCR duplicates.
Only uniquely aligned reads were retained before calling peaks with MACS2 (v2.2.5) (Zhang et al., 2008). High-confidence peaks shared across two biological replicates with irreproducible discovery rate (IDR) < 0.05 were selected for each condition.
For visualization, bam files of individual replicates for each condition were combined and then converted to bigwig files, binned (10 bp), and normalized to 1x depth of reads per genome coverage (RPGC) using the bamCoverage from the deepTools suite (v3.4.3) with parameters “–normalizeUsingRPGC –bs 10” (Ramirez et al., 2014).
Downstream analyses such as TSS plots, metagene plots, and heatmaps were also performed using deepTools with a bin size of 50 bp.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files

molecule: genomic DNA

source_name: mouse embryonic stem cells (V6.5)

growth_protocol: For ChIP-Seq, WT, Pol I, Pol II Pol III and RPAC1 degron mouse embryonic stem cells were cultured in DMEM-KO (Thermo Fisher, Cat#10829018) supplemented with 15% FBS (Gibco, Cat#10099141C), 1× penicillin/ streptomycin (Gibco, Cat#15140122), 1 × L-glutamine (Gibco, Cat#25030081), 1 × non-essential amino acids (Gibco, Cat#11140050), 143 uM 2-mercaptoethanol (Thermo Fisher, Cat#M3148) with MEF and maintained at 37℃ cell incubator with 5% CO2. After two passages of MEF feeders, cells were harvested for experiment.

extract_protocol:
Cross-linked cells were subjected to chromatin fraction isolation as reported (Ji et al., 2015), and the chromatin was pretreated with 40U MNase (NEB, M0247), followed by sonication as previously described (Jiang et al., 2020). 1μg antibodies and 30μl Protein G beads (Thermo Fisher, 10004D) were used for each replicate..
ChIP DNA were subjected to TELP library construction (Peng et al., 2015). 200bp-400bp DNA libraries were gel-selected, purified, and delivered to Novogene company for sequencing.

treatment_protocol: Cells were treated with 1 μg/ml Doxycycline for 12 hr to induce OsTIR1 expression, then treated with or without 500 μM IAA for 1 hr to induce targeted proteins degradation. Cells were crosslinked with 1% formaldehyde for 10 min at room temperature.

tag: treatment

value: Pol III_degron mESCs untreated

tag: antibody


title: HMEC-FL2 - uncoated 2

city: Helsinki

first: Pekka

last: Katajisto

state: helsinki

address: Viikinkaari 5

country: Finland

institute: University of Helsinki

data_processing:
Base-calling and demultiplexing was performed using CASAVA software with default settings generating Fastq files
Bcl files were converted and demultiplexed to fastq using the bcl2fastq v1.8.4 program
STAR v2.5.2b (Dobin et al., 2013) was used to index the human reference genome (hg38) and align the resulting fastq files
Mapped reads were then counted in annotated exons using featureCounts v1.5.1 (Liao et al., 2014)
The entrez gene annotations and reference genome were obtained from UCSC. The count table from featureCounts was imported into R/Bioconductor and differential gene expression was performed using the EdgeR (Robinson et al., 2009) package and its general linear models pipeline
Genome_build: hg38
Supplementary_files_format_and_content: count text file

source_name: Human mammary epithelial cell line

growth_protocol: HMECs were grown on laminin-111, -421 or -521 coated (50 ug/ml) 6-well plates  in mammary epithelial basal medium (MEGM; Lonza) for 48 hours. Cells were lysed directly on plates with RNAeasy Kit lysis buffer.

extract_protocol:
RNeasy Kit (Qiagen) was used for RNA extraction following the manufacturer’s instructions. RNA was stored at -80 until further processing.
To construct libraries suitable for Illumina sequencing the Illumina TruSeq Stranded mRNA Sample preparation protocol which includes cDNA synthesis, ligation of adapters and amplification of indexed libraries was used
Illumina HiSeq 2000 for a 50-cycle v3 sequencing run generating 50 bp single-end reads

value: Cultured on uncoated plate


title: hESCs_0_circRMST_b4_rep4 [20200617_20_N286_42]


title: DHPG_miRNA_5


title: ChIP_Seq_Pol_III_IAA_anti_TBP_rep1

value: Pol III_degron mESCs IAA 1hr


title: DHPG_miRNA_3


title: Tg1

city: Rennes

first: Simon

last: Leonard

address: 2 avenue du Prof Léon Bernard

country: France

institute: Université Rennes

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10 and hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Spleen

extract_protocol: protocol chromium Next GEM Single cell 3' reagent kits V3.1 (CG000204 Rev D )

treatment_protocol: single immunization of mice with i.p. injection of sheep red blood cells , 10 days before sacrifice

value: Spleen

tag: cell type

value: whole tissue cells

value: Tg 3'RR-BCL2


title: ChIP_Seq_Pol_III_Untreated_anti_TBP_rep1

description: ChIP_Seq_Pol_III_Untreated_anti_TBP_merged.bw


title: KI1

value: KI Igk-BCL2


title: hESCs_0_circRMST_b2_rep2 [20200617_8_N286_4]


title: ChIP_Seq_Pol_III_Untreated_anti_TBP_rep2


title: WT1

value: sorted B cells

value: Wt


title: DHPG_miRNA_4


title: Ctl2_PMA [primary CD4+ T cells]

city: Doha

first: Nico

last: Marr

address: Education City

country: Qatar

institute: Hamad Bin Khalifa University

data_processing:
The RSeQC package (Wang et al., Bioinformatics. 2012 Aug 15;28(16):2184-5. doi: 10.1093/bioinformatics/bts356) (http://rseqc.sourceforge.net) was used for quality evaluation of the raw high throughput sequence data.
Raw RNA -seq reads were aligned with UCSC human genome assembly version hg38 using STAR (Dobin et al., Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635) (https://github.com/alexdobin/STAR/releases).
HTseq-count (Anders et al., Bioinformatics. 2015 Jan 15;31(2):166-9. doi: 10.1093/bioinformatics/btu638) (https://htseq.readthedocs.io/en/master) was used to count the reads mapping to each gene feature.
Genome_build: hg38
Supplementary_files_format_and_content: Log2 normalized read count

source_name: primary CD4+ T cells

growth_protocol: Frozen PBMCs were thawed and negatively-sorted naive CD4+ T cells were rested overnight in X-VIVO 20 medium prior to stimulation.

extract_protocol:
Total RNA was extracted with the RNeasy Plus Micro Kit (QIAGEN), according to the manufacturer’s instructions.
cDNA was prepared with the SMART-Seq RNA kit (Takara Bio) for low-input RNA and DNA library preparation. We used the Nextera XT DNA Library Preparation Kit (Illumina) and the Nextera XT Index Kit v2 set A (Illumina), respectively, for idexing with low DNA input requirements.

treatment_protocol: The naïve CD4+ T cells were stimulated for two hours with beads coated with the indicated combination of anti-CD2, anti-CD3 and anti-CD28 mAbs (Miltenyi Biotec), or were left untreated.

tag: disease

value: healthy Control

value: PMA

tag: time point


title: hESCs_0_circRMST_b1_rep1 [20200617_12_N286_8]

value: H9 hESCs

value: circRMST KD

value: undifferentiated; Day 0


title: ChIP_Seq_RPAC1_IAA_anti_Pol_II_rep2

description: ChIP_Seq_RPAC1_IAA_anti_Pol_II_merged.bw

value: RPAC1_degron mESCs IAA 1hr


title: ChIP_Seq_RPAC1_Untreated_anti_Pol_II_rep2

description: ChIP_Seq_RPAC1_Untreated_anti_Pol_II_merged.bw

value: RPAC1_degron mESCs untreated


title: hESCs_0_circFAT3_b5_rep5 [20200617_22_N286_10]

value: circFAT3 KD

value: yes


title: Plastic day 7_4

city: Ulm

first: Manfred

last: Frick

address: Albert-Einstein Allee 11

country: Cote d'Ivoire

institute: University of Ulm

data_processing:
Sequenced read quality was checked with FastQC v0.11.2
RNA-Seq reads from all samples were aligned to the genome using the STAR Aligner v2.5.2a11
Duplication rates of the RNA-Seq samples were computed with bamUtil v1.0.11 to mark duplicate reads and the dupRadar v1.4 Bioconductor R package for assessment
The gene expression profiles were quantified using Cufflinks software version 2.2.1 to get the Reads Per Kilobase of transcript per Million mapped reads (RPKM) as well as read counts from the feature counts software package
VST values were determiend with DESeq2 (Love et al., 2014 doi: 10.1186/s13059-014-0550-8)
Assembly: ensembl84
Supplementary files format and content: tab-delimited text files contain RPKM and VST (variance stabilizing transformation) data for each sample

organism: Rattus norvegicus

source_name: Lung fibroblasts

growth_protocol: Primary lung fibroblasts were isolated using CD90 positive bead sorting (Miltenyi Microbeads). Cells were seeded on 38 µg/ml rat tail collagen I solution (Advanced BioMatrix Inc., San Diego, US) coated plastic or 3-5 kPa PDMS (Sylgard 527, Dow Corning) in MucilAir™ medium (Epithelix, Genève, Switzerland). Seeding density of the primary fibroblasts was between  5 x 10^5 cells / cm2 and XY cells / cm2.

extract_protocol:
RNA was harvested using my-Budget RNA Mini Kit (Bio-Budget Technologies GmbH, Krefeld, Germany). The Sequencing library preparation has been done using 200 ng of total RNA input with the TrueSeq RNA Sample Prep Kit v2-Set B (RS-122–2002, Illumina Inc, San Diego, CA) producing a 275 bp fragment including adapters in average size.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Primary lung fibroblasts

value: Sprague-Dawley

value: Lung

value: fibroblasts

tag: culture method

value: Plastic

tag: time (day)


title: Plastic day 14_4

tag: strain


title: PDMS day 14_4

value: PDMS


title: PDMS day 4_4


title: Plastic day 4_4


title: hESCs_0_circFAT3_b9_rep7 [20200617_60_N286_60]

value: no


title: hESCs_0_circFAT3_b6_rep6 [20200617_2_N286_33]


title: DHPG_miRNA_2

value: DIV 16 neurons

value: P0 pups

value: DHPG


title: PDMS day 7_4


title: Room Air

description: 10x Genomics

tag: age

value: 2 weeks

tag: condition

value: Normoxia


title: hESCs_0_circFAT3_b2_rep2 [20200617_6_N286_2]

tag: cell line

value: H9 hESCs

tag: batch

value: undifferentiated; Day 0


title: DMSO_miRNA_4

value: DMSO


title: hESCs_0_circFAT3_b4_rep4 [20200617_18_N286_40]

tag: genotype

value: circFAT3 KD

tag: treatment/time point


title: DMSO_miRNA_1

tag: tissue


title: PDMS day 14_3


title: hESCs_0_circFAT3_b1_rep1 [20200617_10_N286_6]

tag: samples used_for_downstream_analysis

value: yes


title: DHPG_miRNA_1

tag: developmental stage

tag: agent


title: ChIP_Seq_RPAC1_Untreated_anti_Pol_II_rep1

tag: treatment

value: RPAC1_degron mESCs untreated

tag: antibody


title: hESCs_0_circFAT3_b3_rep3 [20200617_14_N286_37]


title: PDMS day 2_4

tag: cell type

value: Primary lung fibroblasts

value: Sprague-Dawley


title: ChIP_Seq_Pol_III_Untreated_anti_Pol_II_rep2

description: ChIP_Seq_Pol_III_Untreated_anti_Pol_II_merged.bw

value: Pol III_degron mESCs untreated


title: DMSO_miRNA_2


title: ChIP_Seq_RPAC1_Input

value: RPAC1_degron mESCs input


title: PDMS day 7_3

value: Lung

value: fibroblasts

value: PDMS


title: ChIP_Seq_Pol_III_Untreated_anti_Pol_II_rep1


title: ChIP_Seq_Pol_III_IAA_anti_Pol_II_rep1

description: ChIP_Seq_Pol_III_IAA_anti_Pol_II_merged.bw

value: Pol III_degron mESCs IAA 1hr


title: ChIP_Seq_RPAC1_IAA_anti_Pol_II_rep1

value: RPAC1_degron mESCs IAA 1hr


title: DMSO_miRNA_3

value: DIV 16 neurons

value: P0 pups


title: hESCs_0_ciRS7_b5_rep5 [20200617_23_N286_11]

value: H9 hESCs

value: ciRS-7 KD


title: ChIP_Seq_Pol_III_IAA_anti_Pol_I_rep1

description: ChIP_Seq_Pol_III_IAA_anti_Pol_I_merged.bw

value: RPA1(Santa Cruz, Cat#sc-48385, lot#L1317)


title: ChIP_Seq_Pol_III_IAA_anti_Pol_II_rep2


title: hESCs_0_ciRS7_b9_rep7 [20200617_61_N286_61]

value: undifferentiated; Day 0

value: no


title: ko-jsh2 RNA3-2 RNA

city: Shanghai

first: Ni

last: Li

state: Shanghai

address: 320 Yueyang Road, Shanghai, 200025 P.R. China

institute: Institute of Health Sciences, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences

data_processing:
The mRNA was enriched by oligodT according to instructions of NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB,USA). And then fragmented to approximately 200bp. Subsequently, the RNA fragmentswere subjected to first strand and second strand cDNA synthesis following by adaptor ligaion and enrichment with a low-cycleaccording to instructions ofNEBNext® Ultra™ RNA Library Prep Kit for Illumina.
The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit(Thermo Fisher  Scientific, USA). The libraries were sequenced by Illumina (Illumina, USA) with paired-end 150bp at Ribobio Co. Ltd (Ribobio, China).
HISAT2 was used to align the clean reads to the mouse reference genome mm10 with default parameters.
HTSeq was subsequently employed to convert aligned short reads into read counts for each gene
Differential expression was assessed by DESeq2 using read counts as input.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count and TPM values for each sample

source_name: epithelium deriverd from subcutaneous tumors

growth_protocol: Myc-CaP expressing sgARID1A or control vector subcutaneously inoculated into 6-week-old male FVB mice. 16 days later, JSH-23 in DMSO were diluted in corn oil for in vivo administration through gavage daily for 2 weeks. Epithelial cells (EpCAM+; CD45− )  in xenografts  were sorted for RNA-Seq.

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: JSH-23 in DMSO were diluted in corn oil for in vivo administration through gavage daily. Corn oil was used as a control.

value: Myc-CaP Arid1a KO

value: FVB


title: ctrl-jsh2 RNA3-2 RNA

value: Myc-CaP EV


title: Plastic day 4_3

value: Primary lung fibroblasts

value: Sprague-Dawley

value: Plastic


title: ctrl-jsh2 RNA3-1 RNA


title: PDMS day 2_3

value: Lung

value: fibroblasts


title: Plastic day 14_3


title: hESCs_0_ciRS7_b6_rep6 [20200617_3_N286_34]

value: yes


title: ko-jsh2 RNA3-1 RNA


title: hESCs_0_ciRS7_b1_rep1 [20200617_11_N286_7]


title: ChIP_Seq_Pol_III_Untreated_anti_Pol_I_rep1

description: ChIP_Seq_Pol_III_Untreated_anti_Pol_I_merged.bw

value: Pol III_degron mESCs untreated


title: ko-2 RNA

value: vehicle


title: Plastic day 7_3


title: ChIP_Seq_Pol_III_Untreated_Input

value: Pol III_degron mESCs input


title: PDMS day 14_2

value: PDMS


title: ko-1 RNA


title: ChIP_Seq_Pol_III_IAA_anti_Pol_I_rep2

value: Pol III_degron mESCs IAA 1hr


title: hESCs_0_ciRS7_b4_rep4 [20200617_19_N286_41]

value: H9 hESCs

value: ciRS-7 KD


title: PDMS day 4_3


title: ChIP_Seq_Pol_II_IAA_anti_Pol_III_rep2

description: ChIP_Seq_Pol_II_IAA_anti_Pol_III_merged.bw

value: Pol II_degron mESCs IAA 1hr


title: ChIP_Seq_Pol_III_Untreated_anti_Pol_I_rep2

value: RPA1(Santa Cruz, Cat#sc-48385, lot#L1317)


title: hESCs_0_CTRL_b6_rep6 [20200617_1_N286_32]

value: CTRL

value: undifferentiated; Day 0


title: PDMS day 7_2

value: Primary lung fibroblasts


title: hESCs_0_ciRS7_b2_rep2 [20200617_7_N286_3]


title: ChIP_Seq_Pol_II_IAA_anti_Pol_III_rep1


title: WT-H3K4me3

data_processing:
Paired-end fastq files were trimmed and uniquely aligned to the GRCm38/mm10 mouse genome assembly using BWA.
After alignment, reads mapped to the same genomic positions were filtered by PICARD-MarkDuplicates (Galaxy Version 2.18.2.2)
The nonredundant reads were used for peak calling. MACS2-callpeak (Galaxy Version 2.1.1.20160309.6) was used for performing peak calling with the threshold, p value ≤ 0.005.
Bam coverage was used to transform the BAM alignment files to their representative BigWig files.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: Myc-CaP cell line

growth_protocol: Myc-CaP cells were cultured in DMEM media supplemented with 10% FBS at 37°C under 5% CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Purified DNA was prepared for sequencing as per the manufacturer’s instructions (Illumina). Libraries were quantified and sequenced on the Illumina HiSeq 2500 Sequencer (125-nucleotide read length).

value: Myc-CaP

value: Myc-CaP EV

value: no treatment

tag: chip antibody

value: H3K4me3 (Cell Signaling Technology; 9751S)


title: ctrl-1 RNA

value: FVB


title: ctrl-2 RNA


title: WT-H3K4me

value: H3K4me (Cell Signaling Technology; 56795S)


title: hESCs_0_CTRL_b9_rep7 [20200617_59_N286_59]

value: no


title: Plastic day 14_2

value: Sprague-Dawley

value: Lung

value: fibroblasts

tag: culture method

value: Plastic


title: ChIP_Seq_Pol_II_Untreated_anti_Pol_III_rep2

description: ChIP_Seq_Pol_II_Untreated_anti_Pol_III_merged.bw

value: Pol II_degron mESCs untreated


title: Plastic day 4_2

tag: time (day)


title: hESCs_0_ciRS7_b3_rep3 [20200617_15_N286_38]

value: H9 hESCs

value: ciRS-7 KD

value: yes


title: input-2

value: none (input)


title: ChIP_Seq_Pol_II_Untreated_anti_Pol_III_rep1


title: input


title: hESCs_0_CTRL_b3_rep3 [20200617_13_N286_36]

value: CTRL

value: undifferentiated; Day 0


title: hESCs_0_CTRL_b5_rep5 [20200617_21_N286_9]


title: PDMS day 4_2

value: Primary lung fibroblasts

tag: strain

value: PDMS


title: KO-Brg1

value: Myc-CaP

value: Myc-CaP Arid1a KO

value: no treatment

value: BRG1 (Abcam, catalog ab110641)


title: hESCs_0_CTRL_b4_rep4 [20200617_17_N286_39]


title: ChIP_Seq_Pol_II_IAA_anti_Pol_I_rep2

description: ChIP_Seq_Pol_II_IAA_anti_Pol_I_merged.bw

value: Pol II_degron mESCs IAA 1hr

value: RPA1(Santa Cruz, Cat#sc-48385, lot#L1317)


title: PDMS day 2_2

value: Sprague-Dawley

value: Lung

value: fibroblasts


title: hESCs_0_CTRL_b2_rep2 [20200617_5_N286_1]

value: H9 hESCs


title: ChIP_Seq_Pol_II_IAA_anti_Pol_I_rep1


title: hESC_0_CTRL_b1_rep1 [20200617_9_N286_5]


title: WT-Brg1

value: Myc-CaP EV


title: cNPCs_11_circRMST_b5_rep3 [20200617_50_N286_26]

value: circRMST KD

value: cNPCs; Day 11

value: yes


title: Plastic day 7_1

value: Plastic


title: Plastic day 14_1

value: Primary lung fibroblasts


title: WT-H3K27ac

value: H3K27ac (Cell Signaling Technology; 92964S)


title: cNPCs_11_circRMST_b9_rep4 [20200617_54_N286_58]

value: no


title: KO_ATAC

data_processing:
ATAC-seq libraries were sequenced on the Illumina HiSeq 2500 (125-nucleotide read length, paired end).
FastQC initially processed raw sequence reads for quality control, and then adapter sequences and poor quality reads were removed.
Quality filtered reads were then mapped to reference genome using BWA and only uniquely mapped reads were kept,
Filtered bam files were used for peak calling by MACS2 and an initial threshold q-value of 0.01 as cutoff.
Bam coverage was used to transform the BAM alignment files to their representative BigWig files.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

extract_protocol:
Cells were collected and lysed to obtain purified nucleus; The Tn5 enzyme transposable reaction was carried out and the open regions of chromatin were fragmented; the fragmented DNA was purified; the purified DNA was amplified. The amplified DNA was sized to remove non-target fragments.
ATAC libraries were prepared for sequencing using TruePrepTM DNA Library Prep Kit V2 for Illumina kit.Purified fragmented DNA were amplified by PCR reaction,and the libraries were first purified by MinElute PCR purification column(Qiagen)and then further size-selected by VAHTS DNA Clean Beads to obtain libraries with a size distribution between 100 and 1500 bp.

value: Myc-CaP Arid1a KO


title: PDMS day 7_1

value: PDMS


title: ChIP_Seq_Pol_I_IAA_anti_Pol_III_rep2

description: ChIP_Seq_Pol_I_IAA_anti_Pol_III_merged.bw

value: Pol I_degron mESCs IAA 1hr


title: ChIP_Seq_Pol_I_IAA_anti_Pol_III_rep1


title: WT_ATAC

value: no treatment


title: PDMS day 14_1


title: ChIP_Seq_Pol_II_Untreated_anti_Pol_I_rep1

description: ChIP_Seq_Pol_II_Untreated_anti_Pol_I_merged.bw

value: Pol II_degron mESCs untreated

value: RPA1(Santa Cruz, Cat#sc-48385, lot#L1317)


title: PDMS day 2_1

value: Sprague-Dawley

value: Lung


title: cNPCs_11_circRMST_b4_rep2 [20200617_46_N286_54]

value: H9 hESCs


title: PDMS day 4_1

value: fibroblasts


title: ChIP_Seq_Pol_I_Untreated_anti_Pol_III_rep2

description: ChIP_Seq_Pol_I_Untreated_anti_Pol_III_merged.bw

value: Pol I_degron mESCs untreated


title: Plastic day 4_1


title: cNPCs_11_circRMST_b1_rep1 [20200617_42_N286_50]

value: circRMST KD

value: cNPCs; Day 11


title: KO-H3K27ac

value: Myc-CaP


title: ChIP_Seq_Pol_I_Untreated_anti_Pol_III_rep1


title: cNPCs_11_circFAT3_b5_rep3 [20200617_48_N286_24]

value: circFAT3 KD

value: yes


title: KO-2

data_processing:
The mRNA was enriched by oligodT according to instructions of NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB,USA). And then fragmented to approximately 200bp. Subsequently, the RNA fragmentswere subjected to first strand and second strand cDNA synthesis following by adaptor ligaion and enrichment with a low-cycleaccording to instructions ofNEBNext® Ultra™ RNA Library Prep Kit for Illumina.
The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit(Thermo Fisher  Scientific, USA). The libraries were sequenced by Illumina (Illumina, USA) with paired-end 150bp at Ribobio Co. Ltd (Ribobio, China).
HISAT2 was used to align the clean reads to the mouse reference genome mm10 with default parameters.
HTSeq was subsequently employed to convert aligned short reads into read counts for each gene
Differential expression was assessed by DESeq2 using read counts as input.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM or TPM values for each sample

treatment_protocol: Epithelial cells were isolated from 3-month-old PtenPC−/− and PtenPC−/−; Arid1aPC−/− mice through isolating EpCAM+; CD45− cells.

value: Myc-CaP cell line

value: FVB

tag: age


title: cNPCs_11_circFAT3_b9_rep4 [20200617_52_N286_56]

value: no


title: ChIP_Seq_Pol_II_Untreated_Input

value: Pol II_degron mESCs input


title: cNPCs_11_circFAT3_b1_rep1 [20200617_40_N286_48]


title: WT-1

value: Myc-CaP EV


title: P. aeruginosa, RNA protect, replicate 3

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

institute: Center Algatech, Institute of Microbiology of the Czech Academy of Science

data_processing:
Sequencing was performed on the NovaSeq 6000 instrument (Illumina). The demultiplexed raw fastq-files were quality-controlled using the FASTQ-mcf suite (https://github.com/ExpressionAnalysis/ea-utils). Low quality bases (Phred-score < 30) and Illumina adaptors were clipped. Reads were mapped to the reference genome using bowtie2 (Langmead et al., 2012) with default parameters for single end reads. Ambiguously mapping reads were randomly distributed between all regions to which they could be assigned. The resulting sam-files were converted to indexed binary format and pile-up format using samtools (Li et al., 2009). The program featureCounts (Liao et al., 2014) was used to count the reads mapping to genes.
Assembly: NC_008463.1
Supplementary files format and content: tab-delimited text file contains reads per gene

organism: Pseudomonas aeruginosa PA14

source_name: P. aeruginosa in LB medium in replication-coupled growth phase

growth_protocol: 50 mL of LB medium was inoculated with an overnight culture to an OD600 of 0.2. The culture was grown for 5 h in a shaker at 37°C and 180 rpm.

extract_protocol:
For RNA protect: 1 mL of culture was mixed with the same volume RNAprotect™ Bacteria Reagent incubated for 10 min and centrifuged. The pellets were flash-frozen and stored at -70°C. RNA extraction was carried out with the RNeasy Plus Kit in combination with QIAshredder™ columns. Treatment with DNase I was performed in solution. For FACS: Key to successful RNA recovery is the gentle formaldehyde fixation at 4˚C. Aliquots of fixed samples were adjusted to approx. 1.8*107 cells/mL in 30 ml volume each and stained with SYBR Green. Sorting of 5.4*108 cells based on the FITC-signal directly into RNAprotect was performed with the BD FACSAria Fusion. The sorted cells were collected on a filter from which RNA was extracted using a combination of Lysozyme and Proteinase K digestion with bead beating, and purified with NucleoZOL. Ribosomal RNA depletion was performed with the NEBNext Bacteria kit.
The libraries were prepared with the Illumina TruSeq kit

tag: fraction

value: RNA protect fixed

tag: replicate


title: cNPCs_11_ciRS7_b9_rep4 [20200617_53_N286_57]

tag: cell line

tag: batch

value: ciRS-7 KD


title: ChIP_Seq_Pol_II_Untreated_anti_Pol_I_rep2

value: Pol II_degron mESCs untreated

value: RPA1(Santa Cruz, Cat#sc-48385, lot#L1317)


title: ChIP_Seq_Pol_I_IAA_anti_Pol_II_rep1

description: ChIP_Seq_Pol_I_IAA_anti_Pol_II_merged.bw

value: Pol I_degron mESCs IAA 1hr


title: KO-1

tag: genotype

value: Myc-CaP Arid1a KO


title: KO-A

source_name: prostate epithelium

tag: tissue

value: prostate epithelium

value: PtenPC-/-; Arid1aPC-/-


title: ChIP_Seq_Pol_I_Untreated_anti_Pol_II_rep1

description: ChIP_Seq_Pol_I_Untreated_anti_Pol_II_merged.bw

value: Pol I_degron mESCs untreated


title: WT-2


title: cNPCs_11_circFAT3_b4_rep2 [20200617_44_N286_52]

value: H9 hESCs

tag: treatment/time point

value: cNPCs; Day 11

tag: samples used_for_downstream_analysis


title: ChIP_Seq_Pol_I_Untreated_Input

value: Pol I_degron mESCs input


title: P. aeruginosa, formaldehyde, replicate 1

value: formaldehyde fixed


title: Ctrl-B

value: PtenPC-/-


title: P. aeruginosa, RNA protect, replicate 1


title: P. aeruginosa, RNA protect, replicate 2


title: ChIP_Seq_Pol_I_IAA_anti_Pol_II_rep2


title: KO-C


title: cNPCs_11_CTRL_b5_rep3 [20200617_47_N286_23]

value: CTRL

value: yes


title: P. aeruginosa, cells with 2 chromosomes, replicate 2

value: FACS sorted, 2 chromosomes


title: ChAR-Seq_Pol_III_IAA_rep1

description:
TELP libraries
ChAR-Seq_Pol_III_IAA_plus.bw
ChAR-Seq_Pol_III_IAA_minus.bw

data_processing:
Library strategy: ChAR-Seq
ChAR-seq raw data were processed using a custom pipeline that builds on published workflows with minor modifications. Briefly, ribosomal reads were first removed by mapping to one copy of the mouse rDNA sequence. After adapter trimming and quality control with cutadapt and RseQC separately, clean reads were then aligned to a concatenated genome comprised of mouse mm10 and fly dm6 assemblies using bowtie2 with options (-very-sensitive-local) as described in the ChIP-seq section.
Only reads that were properly paired and uniquely aligned were retained for subsequent processing. Reads that mapped to the mouse (or human) genome were normalized to total reads originating from Drosophila spike-in cells, and the normalization factor was calculated as previously described (Jiang et al., 2020).
Plus- and minus-strand were assigned to uniquely mapped reads using SAMtools, and the final BAM files were converted to bigwig, separated by strand, and normalized to spike-in controls using bamCoverage from deeptools. Finally, bigWig score tracks for visualization prepared for different biological replicates but for the same treatment were merged to an averaged signal using the mean operator from the WiggleTools (v1.2) package (Zerbino, Johnson, et al. 2014).
Then raw read counts were calculated per gene, in a strand-specific manner, based on annotations described in the Gene list definition section below, using featureCounts (Liao et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files

growth_protocol: For ChAR-Seq, Pol III degron mouse embryonic stem cells were cultured in DMEM-KO (Thermo Fisher, Cat#10829018) supplemented with 15% FBS (Gibco, Cat#10099141C), 1× penicillin/ streptomycin (Gibco, Cat#15140122), 1 × L-glutamine (Gibco, Cat#25030081), 1 × non-essential amino acids (Gibco, Cat#11140050), 143 uM 2-mercaptoethanol (Thermo Fisher, Cat#M3148) with MEF and maintained at 37℃ cell incubator with 5% CO2. After two passages of MEF feeders, cells were harvested for experiment. The Schneider 2(S2) cells were cultured in complete Schneider’s Drosophila Medium (Invitrogen, Cat#21720024) supplemented with 10% FBS (CellMax, Cat#SA311.02) at room temperature.

extract_protocol:
Pol III degron cells were collected and mixed with 10% S2 cells. The chromatin-associated RNA were collected as reported (Dev M. Bhatt et al., 2012) and extracted with Trizol reagents as manufacture instruction.
Chromatin-associated RNA were delivered to Novogene Company. The concentration, purity, and integrity of RNA were examined and followed by ribosomal RNA depletion and strand-specific library construction.

treatment_protocol: Cells were treated with 1 μg/ml Doxycycline for 12 hr to induce OsTIR1 expression, then treated with or without 500 μM IAA for 1 hr to induce Pol III degradation.

value: Pol III degron 1h mESCs


title: P. aeruginosa, formaldehyde, replicate 3


title: P. aeruginosa, cells with 2 chromosomes, replicate 1


title: ChAR-Seq_Pol_III_Untreated_rep2

description:
TELP libraries
ChAR-Seq_Pol_III_Untreated_plus.bw
ChAR-Seq_Pol_III_Untreated_minus.bw

value: Pol III untreated mESCs


title: ChIP_Seq_Pol_I_Untreated_anti_Pol_II_rep2


title: cNPCs_11_CTRL_b4_rep2 [20200617_43_N286_51]


title: P. aeruginosa, replicating cells, replicate 3

value: FACS sorted, replicating


title: cNPCs_11_ciRS7_b5_rep3 [20200617_49_N286_25]

value: ciRS-7 KD


title: KO-B


title: P. aeruginosa, formaldehyde, replicate 2


title: cNPCs_11_ciRS7_b4_rep2 [20200617_45_N286_53]


title: Plate7_scRNAseq_HS

city: Erlangen

first: Harald

last: Schuhwerk

address: Glückstrasse 6

country: Germany

description:
SortSeq
FAU-MS-s007

data_processing:
Data pre-processing and quality control was performed by the Single Cell Discoveries (https://www.scdiscoveries.com/technology/sort-seq/ _and Muraro et al. 2016). Briefly, paired-end reads were aligned to the ensemble transcriptome using BWA (Li and Durbin, 2010). Read 1 was used for assigning reads to correct cells and libraries, while read 2 was mapped to gene models. The corresponding transcript count table was generated using a custom-written script (https://github.com/anna-alemany/transcriptomics/tree/master/mapandgo).
Post transcript count generation, further quality control and filtering (UMIs, total genes and percentage of mitochondrial reads), normalization, feature detection, dimensionality reduction, clustering and differential expression analysis between clusters or groups was performed using the packages Scran version 1.18.5 (Lun et al., 2016) and Scater version 1.18.5 (McCarthy et al., 2017).
Assembly: Hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Breast cancer (mammary gland)

extract_protocol:
Routinely cultured MDA-MB-231 cells were collected by trypsinization, resuspended in PBS and randomly spotted as single cells into 384-well 'capture plates'  purchased from Single Cell Discoveries (SCD, Utrecht, NL) containing barcoded primers and mineral oil using a MoFlo Astrios EQ 1 fluorescence activated cell sorter (Beckman Coulter). The plates were then briefly centrifuged at high speed and stored at -80°C until shipping on dry ice and further processing at Single Cell Discoveries (SCD).
Library preparation according to the CEL-Seq2 protocol was performed by SCD. Briefly, after heat-lysis of the cells at 65° C, sequential barcoding, amplification and in vitro transcription was performed to generate a final cDNA library containing TruSeq small RNA primers (Illumina) for sequencing. Pleaase also see https://www.scdiscoveries.com/support/materials-methods/

value: Breast cancer (mammary gland)


title: Ctrl-A


title: scRNAseq_fat3_90d_22

data_processing:
Raw basecall images from the Illumina Nextseq500 machine were demultiplexed using Illumina’s bcl2fastq command line tool. Read-1 of the paired-end fastq files contained the cellular barcode (12 nucleotides) and the Unique Molecular Identifier (UMI, 8 nucleotides), which standard practice when sequencing a droplet-based single-cell library. Read-2 consisted of 64 nucleotides.  Raw fastq files were processed with the help of Drop-seq_tools-2.3.0 (https://github.com/broadinstitute/Drop-seq) and picard-tools-2.21.6 (https://broadinstitute.github.io/picard/). The whole data processing was written in snakemake (https://snakemake.readthedocs.io/) and it follows the standard Drop-seq pipeline steps. First R1 and R2 files were merged into a single .bam file. Then, each read was tagged with its own cell-barcode (CB) and UMI. Each read was polyA- and adapter trimmed. Reads were then mapped with STAR (2.7.1a) in single-end mode, and each read was tagged with a gene. After barcode repair (substitution-errors and synthesis-errors) a Digital Expression Matrix was created (DGE) for each sample to be used for further downstream data analysis.
Assembly: not provided
Supplementary files format and content: Expression matrix, rows are cells, columns are genes. Cell barcodes are in first row, first column contains gene names

source_name: H9 hESC

extract_protocol: After methanol fixation, cells were pelleted at 3000xg for 5 min and rehydrated in 1 ml PBS with 0.01% BSA and 1:100 Superasein. The cells were then resuspended in 300 μl rehydration buffer, containing PBS-BSA 0.1% plus 1 U/μl RNase Inhibitor (RiboLock; Thermo Fisher). Cells were filtered through a 40 μm cell strainer, counted using an automated cell counter (Countess; Thermo Fisher), and diluted to approximately 350 cells/μl in 250 μl rehydration buffer. Barcoded beads (ChemGenes, Macosko- 2011- 10 (V+)) with chilled lysis buffer (6% Ficoll PM-400, 0.2% Sarkosyl, 20 mM EDTA, 200 mM Tris pH 7.5, 50 mM DTT in nuclease-free water) and cells were used for encapsulation into lipid droplets using the Nadia instrument (Dolomite Bio, Hertfordshire, UK) based on manufacturer’s guidelines. The conceptual principle is based on the DropSeq scRNA-seq approach. Library preparation including recovery of beads, reverse transcription, exonuclease treatment, and second strand synthesis procedures were followed as described previously (Emanuel W, Kirstin M, Vedran F, Asija D, Theresa GL, Roberto A, et al. Transcriptomic profiling of SARS-CoV-2 infected human cell lines identifies HSP90 as target for COVID-19 therapy. iScience. 2021;24(3):102151.). After incubation with second strand synthesis mix for 60 min at 37°C, beads were washed twice with 1 ml TE/0.01% Tween, once with 1 ml TE, and twice with water. cDNA amplification was achieved by dividing beads into 24 PCR reactions with SMART PCR mix in a total reaction volume of 50 μl using 4+9 cycle settings. After pooling 25 μl of each PCR reaction, the PCR products were cleaned-up using AMPure XP beads (Beckman Coulter). cDNA library quality and quantity were checked on a Bioanalyzer High Sensitivity Chip (Agilent) and the Qubit dsDNA HS Assay system (ThermoFisher). For each sample, 1000 pg of the cDNA library was used for Tagmenation using Nextera XT v2 DNA sample preparation (Illumina) including custom primers for amplification purposes. After PCR purification, quality and quantity assessment, paired-end sequencing was performed on a NextSeq500 (Illumina) and the NextSeq 500/550 High Output v2 Kit (75 cycles) (Read1CustSeqB custom primer for read 1 = 21 bp; read 2 = 63 bp).

value: H9 hESC

tag: time (days)

value: circFAT3 KD


title: Spinal 2

city: Chengdu

first: Donghang

last: Zhang

state: Sichuan

address: No.37, guoxue lane, wuhou district, chengdu city, sichuan province

institute: West China Hospital of Sichuan University

data_processing:
Basecalls performed using  bcl2fastq tools
Raw single-cell RNA-seq data were processed using 10X Genomics Cell Ranger (v5.0.1), including demultiplexing the FASTQ reads, aligning them to the human reference genome (GRCh38, v3.0.0, from 10X Genomics), and counting the unique molecular identifier (UMI) (by using ‘cellranger count’ function).
Genome_build: GRCh38
Supplementary_files_format_and_content: UMI_count_matrix

source_name: Spinal cord

extract_protocol:
Nuclei were isolated using a Nucleus Isolation Kit (catalogue no. 52009-10, SHBIO, China) according to the manufacturer’s instructions. Nuclei suspension was loaded onto a Chromium single cell controller (10x Genomics) to generate single-nucleus gel beads in the emulsion (GEM) using single cell 3' Library and Gel Bead Kit V3.1 (10x Genomics, 1000075) and Chromium Single Cell B Chip Kit (10x Genomics, 1000074) according to the manufacturer’s protocols.
The 10x snRNA-seq library was established using Single Cell 3’ Library and Gel Bead Kit V3.1, according to the manufacturer’s instructions.

value: spinal cord

value: 46 years old


title: P. aeruginosa, cells with 1 chromosome, replicate 3

value: FACS sorted, 1 chromosome


title: cNPCs_11_ciRS7_b1_rep1 [20200617_41_N286_49]

value: H9 hESCs

value: cNPCs; Day 11


title: ATAC-Seq_Pol_III_Untreated_rep2

description:
TELP libraries
ATAC-Seq_Pol_III_Untreated_merged.bw

data_processing:
ATAC-seq data were processed as published. Briefly, sequenced reads were first adapter trimmed and quality verified with cutadapt and FastQC (v0.11.7). Clean reads were then aligned to the mm10 mouse genome using Bowtie2.
Uniquely aligned reads were subsequently processed into sorted, indexed BAM files using SAMtools. PCR duplicates and mitochondrial reads were discarded before further analysis.
The remaining reads were corrected to account for the 9 bp insert introduced by the Tn5 transposase by offsetting the 5' ends by either +4 (for plus strand) or -5 (for minus strand) as described previously.
Nucleosome positioning and the corresponding signal tracks were calculated from replicate-merged ATAC-seq data using the nucleoATAC algorithm (v0.3.4) with default parameters (Schep et al., 2015).
ATAC-seq signal tracks (bigwig format) were obtained for visualization on merged bam files with the command "bamCoverage --binSize 10 --normalizeUsing RPGC".
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files

growth_protocol: For ATAC-seq, Pol I, Pol II and Pol III degron mouse embryonic stem cells were cultured in DMEM-KO (Thermo Fisher, Cat#10829018) supplemented with 15% FBS (Gibco, Cat#10099141C), 1× penicillin/ streptomycin (Gibco, Cat#15140122), 1 × L-glutamine (Gibco, Cat#25030081), 1 × non-essential amino acids (Gibco, Cat#11140050), 1 × nucleoside (Millipore, Cat#ES-008-D), 3 μM CHIR99021 (Selleck, Cat#S1263), 0.5 μM PD0325901 (Selleck, Cat#S1036), 143 uM 2-mercaptoethanol (Thermo Fisher, Cat#M3148) and maintained at 37℃ cell incubator with 5% CO2.

extract_protocol:
ATAC-Seq were conducted as "Corces, M. R., Trevino, A. E., Hamilton, E. G., Greenside, P. G., Sinnott-Armstrong, N. A., Vesuna, S., ... & Chang, H. Y. (2017). An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nature methods, 14(10), 959-962." described.
ATAC-Seq libraries were conducted with Nextera™ DNA Sample Prep Kit (Illumina, Cat # FC-121-1030).

treatment_protocol: Cells were treated with 1 μg/ml Doxycycline for 12 hr to induce OsTIR1 expression, then treated with or without 500 μM IAA for 1 hr to induce Pol I, Pol II and Pol III degradation.

tag: treatment


title: ChAR-Seq_Pol_III_IAA_rep2


title: P. aeruginosa, cells with 1 chromosome, replicate 2


title: cNPCs_11_CTRL_b9_rep4 [20200617_51_N286_55]

data_processing:
Raw reads were filtered and trimmed using trim_galore (version 0.6.5dev, using parameters: -a AAAAAAAAAAAA --clip_R1 12).  The filtered QuantSeq 3’ mRNA-Seq reads were mapped to the human reference genome (hg19) using STAR (version 2.7.3a) with default setting. Read mapping results per gene were then quantified using the tool featureCounts with gene annotation from Gencode (version 28). All samples used for downstream analysis in the corresponding manuscript "A circular RNA expressed from the FAT3 locus regulates neural development " are indicated in the column "Samples used for downstream analysis".
Assembly: hg19
Supplementary files format and content: FeatureCounts output file with mRNA expression as raw reads for each sample. Tab delimited text file

value: no


title: MPNST-2-084

city: CINCINNATI

first: Lai Man

middle: (Natalie)

last: Wu

state: OH

address: 3333 Burnet Avenue, MLC7013,Lu lab, T6.525

institute: CCHMC

data_processing:
For 10X Genomics data, CellRanger was used for base-calling, alignment, filtering and generation of normalized abundance measurements.
Read 1: contains the 16bp 10x barcode and the 10bp UMI (bases 17-26).Index contains the sample barcode. Read 2 contains the cDNA information
Genome_build: hg19
Supplementary_files_format_and_content: CellRanger output files

source_name: Peripheral nerve tumor

extract_protocol: For human patient samples, tumor tissues were resected by surgery, cut into pieces of up to 2 mm and cryopreserved in 10% DMSO in liq N2. Tissues requested were shipped and  transported to Lu lab in dry ice from Johns Hopkins NF repository. For scRNA-seq, the tissues were dissociated into single cells suspensions using digestion buffer (DMEM Medium+ 2 mg/ml of collagenase IV), and single cells were processed through the 10X Chromium 3' Single Cell Platform using the Chromium Single Cell 3’ Library, Gel Bead and Chip Kits (10X Genomics, Pleasanton, CA), following the manufacturer’s protocol. Briefly, up to 16,000 cells were loaded to each channel of a chip to be partitioned into Gel Beads in Emulsion (GEMs) in the Chromium instrument, followed by cell lysis and barcoded reverse transcription of RNA in the droplets. Breaking of the emulsion was followed by amplification, fragmentation and addition of adapter and sample index. The libraries were pooled and sequenced on NovaSeq 6000 (Illumina).

value: MPNST


title: MPNST-2-016


title: ATAC-Seq_Pol_I_IAA_rep2

description:
TELP libraries
ATAC-Seq_Pol_I_IAA_merged.bw

value: Pol I degron 1h mESCs


title: scRNAseq_circFAT3_30d_2


title: ChAR-Seq_Pol_III_Untreated_rep1


title: P. aeruginosa, cells with 2 chromosomes, replicate 3


title: scRNAseq_circFAT3_30d_1


title: Plate8_scRNAseq_HS

description:
SortSeq
FAU-MS-s008

value: MDA-MB-231 (plus unspecified cells for a different study)


title: ATAC-Seq_Pol_III_IAA_rep2

description:
TELP libraries
ATAC-Seq_Pol_III_IAA_merged.bw


title: P. aeruginosa, replicating cells, replicate 2


title: Ctrl-C

value: prostate epithelium

value: PtenPC-/-


title: Spinal 1

value: 38 years old


title: ATAC-Seq_Pol_III_IAA_rep1

value: Pol III degron 1h mESCs


title: ATAC-Seq_Pol_III_Untreated_rep1

value: Pol III untreated mESCs


title: scRNAseq_fat3_90d_12


title: scRNAseq_circFAT3_90d_2


title: cNPCs_11_CTRL_b1_rep1 [20200617_39_N286_47]

extract_protocol:
Total RNA was extracted with TRIzol Reagent (Invitrogen) following the manufacturer’s guidelines.
RNA quality was controlled using the RNA 6000 Nano Kit (Agilent Technologies, CA, USA) on a Bioanalyzer 2100 (Agilent Technologies), and RNA quantity determined using the Qubit RNA HS Assay Kit (Thermo Fisher Scientific) on a Qubit 4 Fluorometer (Thermo Fisher Scientific). The TURBO DNA-free Kit (Thermo Fisher Scientific) was used for DNA removal and followed by an additional RNA precipitation step.  For library generation, the QuantSeq 3’mRNA-Seq Library Kit (Lexogen, Vienna, Austria) was utilized according to the manufacturer’s instructions.

value: CTRL

value: yes


title: P. aeruginosa, cells with 1 chromosome, replicate 1


title: P. aeruginosa, replicating cells, replicate 1

value: FACS sorted, replicating


title: ATAC-Seq_Pol_I_Untreated_rep1

description:
TELP libraries
ATAC-Seq_Pol_I_Untreated_merged.bw

value: Pol I untreated mESCs


title: MPNST-2-015


title: ATAC-Seq_Pol_I_IAA_rep1


title: MPNST-2-023


title: ATAC-Seq_Pol_I_Untreated_rep2


title: P. aeruginosa, FA fixed and FACS unsorted, replicate 2

value: FACS unsorted


title: pNF-2-026

value: plexiform neurofibroma


title: shCreb5_Condition_AB_4

city: Boston

first: Zhu

last: Zhuo

state: MA

address: 401 Park Dr

department: Department of Biostatistics

institute: Harvard TH Chan School of Public Health

data_processing:
The RNA-Seq data were processed using the bcbio-nextgen pipeline.
Raw counts were obtained using Salmon.
Genome_build: Bovine genome UMD3.1 (release 94)
Supplementary_files_format_and_content: CSV, raw counts for each gene

organism: Bos taurus

source_name: Bovine superficial zone articular chondrocytes

growth_protocol: Newly isolated bovine superficial zone articular chondrocytes were cultured (in DMEM/F12 plus 10% FBS) for two days before infection.

extract_protocol:
RNA was extracted using Trizol agents (Life Technologies)
KAPA mRNA HyperPrep Kits (Roche)

treatment_protocol: Ultracentrifuge-concentrated shScramble or shCreb5 lentivirus was added into DMEM/F12 medium (with 10% FBS) containing 7.5 μg/ml DEAE-Dextran (to increase infection efficiency). Twenty-four hours after infection, medium was replaced with new DMEM/F12 medium (with 10% FBS) containing 0.8 μg/ml puromycin for selection. After puromycin selection for 5 days, shScramble or shCreb5 infected superficial zone articular chondrocytes were replated onto low attachment tissue culture plates (Corning #3471 or #3473) in DMEM/F12 medium (with 10% FBS) for forty-eight hours in either the presence of TGF-α (100 ng/ml) alone (condition A) or in the presence of both TGF-α (100 ng/ml) and TGF-β2 (20 ng/ml) (condition AB).

value: Articular cartilage

value: Chondrocytes

tag: shRNA treatment

value: Creb5 3#shRNA

tag: tgf treatment

value: TGFalpha and TGFβ2


title: scRNAseq_ctrl_90d_22

value: H9 hESC


title: P. aeruginosa, FA fixed and FACS unsorted, replicate 1


title: pNF-2-090


title: shScramble_Condition_AB_4

tag: cell type

value: Scramble shRNA


title: pNF-2-017


title: shCreb5_Condition_A_4

value: TGFalpha


title: pNF-2-019


title: scRNAseq_circFAT3_90d_1

value: circFAT3 KD


title: scRNAseq_ctrl_30d_2


title: P. aeruginosa, FA fixed and FACS unsorted, replicate 3


title: Ocln-KO whole rep1

first: Winnie

last: Shum

address: 393 Hua Xia Middle Rd. Pudong District

institute: ShanghaiTech University

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Genome_build: GRCm38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: Ocln-KO whole epididymis

extract_protocol:
prefrontal cortex were rharvested , flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: All animals were housed in a standard specific pathogen-free animal house, kept on a 12-hour light/dark cycle, and received sterilised food and autoclaved water ad libitum.

value: Ocln-/-

value: adult

value: whole epididymis


title: Ocln-KO whole rep2


title: shScramble_Condition_A_4


title: pNF-2-084


title: scRNAseq_ctrl_90d_12

value: CTRL


title: Ocln-KO whole rep3


title: pNF-2-013


title: scRNAseq_ctrl_90d_1


title: scRNAseq_ctrl_30d_1


title: WT whole rep3

source_name: WT whole epididymis

value: wild type


title: shCreb5_Condition_AB_3


title: shScramble_Condition_AB_3


title: pNF-2-003


title: pNF-2-006


title: shScramble_Condition_A_3


title: pNF-2-004


title: WT whole rep2


title: intestine,CORT,Bio rep 3

first: Guanhao

last: Wang

address: Siping Road

institute: Tongji University

data_processing:
A cDNA library constructed by technology from the pooled RNA from < MWTL1,MWTL2,MWTL3,MCORTL1,MCORTL2,MCORTL3,WTMI1,WTMI2,WTMI3,CORTMI1,CORTMI2,CORTMI3> samples of homo sapiens was sequenced run with Illumina Novaseq TM 6000 sequence platform.
The raw paire-end reads were trimmed and quality controlled by SeqPrep and Sickle with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software.
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
The expression level of each transcript was calculated according to the transcripts per million reads (TPM) method. Transcript abundances were quantified using RSEM software tool.
Assembly: Mus_musculus GRCm39
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: intestine

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent (Plant RNA Purification Reagent for plant tissue) according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara).
RNA-seq transcriptome library was prepared with 1μg of total RNA using TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA).

value: intestine

value: CORT


title: shCreb5_Condition_A_3


title: WT whole rep1


title: shCreb5_Condition_AB_2


title: scRNAseq_ctrl_90d_2


title: pNF-2-021


title: Input control RAD21* 13h

city: Guangzhou

first: Alexander

middle: V.

last: Strunnikov

state: Guangdong

address: 190 Kai Yuan Avenue

institute: GIBH

data_processing:
The NGS’ paired reads were initially cleaned from low quality reads and adapters using fastp (Chen, 2018).
For genome-wide analysis, tags were aligned using Bowtie (Langmead, 2009) to the human genome hg38.
Peak calling with MACS2.2 (Zhang, 2008; Liu, 2014) was limited to chromosome-assigned elements, with input ChIP-seq reads used as a reference.
Assembly: Human genome GRCh38.p12 (hg38), NCBI Assembly ID: 5800238.
Supplementary files format and content: Processed data files are bigWig files.

growth_protocol: The DLD-1 (ATCC® CCL-221™) cell line was cultured in IMDM (Hyclone) with 10% FBS.

extract_protocol:
For ChIP-On-ChEPseq, designed to extract pure fixed chromatin under stringent chaotropic conditions (PMID: 25101823, PMID: 36179046), 10 to 20 million cells were resuspended in 1 ml of nuclei lysis buffer (25 mM Tris-HCl, 85 mM KCl, 0.1% Triton-X100, pH 7.4, Roche PIC), centrifuged at 2300 g, resuspended again in the same buffer containing 200 µg/ml RNase A, and the samples were incubated in thermomixer at 37˚C for 15 min at 1000 rpm. After that, samples were spun at 2300 g for 5 min at 4˚C, pellets were resuspended in 500 µl of nuclei disrupting buffer (4% SDS, 50 mM Tris-HCl, 10 mM EDTA, pH 7.4), and mixed with 1.5 ml of urea buffer (8 M urea, 10 mM Tris-HCl, 1 mM EDTA, pH 7.4). After gentle mixing leading to the clarification of the solution, it was centrifuged at 16,100 g for 30 min at 23°C. After decanting of the supernatant, resulting pure chromatin was washed twice with sonication buffer (20 mM Tris-HCl, 150 mM NaCl, 1% Triton-X100, 0.1% Na deoxycholate, 0.1% SDS, 1 mM EDTA, 1 mM PMSF) , and samples were reconstituted with sonication buffer to 1 ml volume. Chromatin fragmentation was done in 2-ml tubes in Covaris S220 with the following settings: 100W peak incident power, 10% duty factor, 10W average incident power, 30/30s duration/delay, 200 cycles/burst, 30 repeats.
TruSeq Nano DNA library kit (Illumina).

treatment_protocol: To synchronize DLD-1 cells, 2x10^6 to 3x10^6 cells were plated into a 10 cm culture dish at 20-30% confluence and incubated overnight. Then, thymidine, 2 mM final concentration, was added, and the culture was incubated for 18 h. After washing cells with 10 ml of pre-warmed 1x PBS, pre-warmed fresh medium was added, followed by a 12 h incubation, then 2 mM thymidine was added the second time, followed by 24 h incubation. G1/S cells were then released into pre-warmed fresh media after washing with 1xPBS. Samples were collected for immunoblotting and FACS at 0 h to 13 h time points.

value: adenocarcinoma, colon epithelium

tag: time point

tag: antibody


title: RAD21* site2 ChIP 13h

value: mAbs against IEEPSR C-terminus


title: intestine,CORT,Bio rep 2


title: intestine,CORT,Bio rep 1


title: RAD21* site2 ChIP 12h


title: shScramble_Condition_AB_2

value: Articular cartilage


title: intestine,veh,Bio rep 3

value: vehicle


title: 20G00953_Metastase_TN

city: Montpellier

first: Jacques

last: Colinge

address: 208, avenue des Apothicaires

institute: Inserm

description:
single cell RNAseq 10x
Patient 5 metastasis

data_processing:
Image analysis using Novaseq Control Software
Basecalling performed using Real-Time Analysis software from Illumina
Demultiplexing using cellranger mkfastq (production of fastq files)
Control check performed mixing the sequences with the ones of the spike PhiX
Control quality using FastQC (11.8)
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell (barcode)

source_name: triple negative (CAF)

extract_protocol:
Fresh tumors had been submitted to mechanical and enzymatic digestion. The cell supsensions obtained were stained for EPCAM, CD45 and CD31. The libraries of the fractions sequenced were prepared using  Single Cell 3' Reagent kits V3 from 10x genomics
RNA libraries were prepared for sequencing using  Single Cell 3' Reagent kits V3 from 10x genomics

tag: cell markers

value: Cancer Associated Fibroblasts

tag: subject id

value: Patient 5


title: intestine,veh,Bio rep 2


title: 20G00953_Metastase_EPCAM_CD45

description:
single cell RNAseq 10x
Patient 5 metastasis
Prior to sequencing, the two populations were pooled in comparable amounts.

source_name: cancer and immune cells

value: Malignant and immune cells


title: liver,CORT,Bio rep 3

source_name: liver

value: liver


title: shCreb5_Condition_AB_1

value: Chondrocytes

value: Creb5 3#shRNA

value: TGFalpha and TGFβ2


title: Input control RAD21* 12h


title: NF_2-004

data_processing:
For 10X genomics datasets, we used Cellranger v5.0.1 to align reads to the mm10 or hg19 human reference sequence.
Genome_build: mm10 for mouse; hg19 for human

extract_protocol:
Nerve tumors were dissociated into single cells suspensions using digestion buffer (DMEM Medium+ 2 mg/ml of collagenase IV). Cells were washed in 1x PBS and red blood cells were lysed using RBC lysis buffer (Roche) for 10 minutes at room temperature. Cells were filtered using a 40um strainer followed by lysis in Nuclei EZ buffer for 3-5 min. 1 ml nuclei wash buffer was pipetted into lysed nuclei, which were then centrifuged for 5 min at 500 x g. Nuclei were resuspended at appropriate concentration for scATACseq in Nuclei Buffer supplied by 10X Genomics.
single-cell libraries were generated using the GemCode Single-cell instruments and the Single Cell ATAC Library & Gel Bead Kit and ChIP Kit from 10x Genomics, according to the manufacturer’s instructions. The samples were incubated at 37°C for 1 h with 10 μl of transposition mix (per reaction, 7 μl ATAC Buffer, and 3 μl ATAC Enzyme (10x Genomics)). Following the generation of nanoliter-scale Gel bead-in-EMulsions (GEMs), GEMs were reverse transcribed in a C1000 Touch Thermal Cycler (Bio-Rad) programmed at 72°C for 5 min, 98°C for 30 s, 12 cycles of 98°C for 10 s, 59°C for 30 s, and 72°C for 1 min, and held at 15°C. After reverse transcription, single-cell droplets were broken and the single-strand cDNA was isolated, cleaned up and amplified. Amplified cDNA and final libraries were assessed on an Agilent BioAnalyzer using a High Sensitivity DNA Kit (Agilent Technologies) at the Gene Expression Core at CCHMC. The libraries were pooled and sequenced on NovaSeq 6000 (Illumina) at a depth of approximately 400M reads per sample at the DNA Sequencing Core at CCHMC.

value: plexiform neurofibroma


title: RAD21* site2 ChIP 10h


title: shScramble_Condition_A_2

value: Scramble shRNA

value: TGFalpha


title: Tp Iron limitation N3

city: Seattle

first: Shiri

last: Graff van Creveld

state: WA

address: 616 NE Northlake Place

department: Oceanography

institute: University of Washingtom

data_processing:
Sequence reads were trimmed using Trimmomatic 0.39,25 run in paired-end mode with cut adaptor and other Illumina-specific sequences (ILLUMINACLIP) set to TruSeq3-PE.fa:2:30:10:1:true, Leading and Trailing thresholds of 25, a sliding window trimming approach (SLIDINGWINDOW) of 4:15, an average quality level (AVGQUAL) of 20, and a minimum length (MINLEN) of 60.
Reads were mapped to the genome of T. pseudonana or T. oceanica using Hisat2-2.1.0. De-novo transcriptome assemblies were generated from RNA sequences extracted from isolate cultures of Amphora, Chaetoceros, and Cylindrotheca. Each species' quality-controlled RNA sequencing data was assembled using Trinity v2.12.0 using default settings and with sequences provided as un-merged paired end reads. The pre-assembly RNA sequencing reads were then mapped back to their respective assemblies as a quality control step, and at least 85% of the reads from all cultures successfully mapped onto the resulting assemblies. The assembly resulted in 53,401 contigs for Amphora, 37,507 contigs for Chaetoceros, and 73,553 contigs for Cylindrotheca
We calculated the number of T. pseudonana or T. oceanica reads that aligned to the gene models from resulting SAM alignment files with aligned sequences used in subsequent analyses.
Assembly: Thaps3 FilteredModels2 or ThaOc_1.0
Supplementary files format and content: csv files include TPM values for each sample,

organism: Thalassiosira pseudonana

source_name: algal cell

growth_protocol: 16:8 hours light:dark cycles and a light intensity of about 100 μmol photons·m-2·sec-1. Specific growth conditions for each species marked under 'growth conditions' as: temprature (C), salts, nutrients, and day of harvest after initiating the experiment, in replete or no iron media. Hydrogen peroxide was added to replete cultures about 2 hours before harvest for RNA-Seq.

extract_protocol:
Total RNA was extracted from 0.2 µm membrane filters with the Zymo Direct-zol RNA MiniPrep Plus kit.
Poly-A-selection, library preparation and sequencing were performed at the Northwest Genomics Center (University of Washington) with standard Illumina NextSeq protocols

value: algal cell

tag: strain

value: CCMP 1335

value: iron limitation

tag: growth conditions

value: 20C, EASW, f/2, 3days


title: shScramble_Condition_AB_1


title: Input control RAD21* 11h

tag: cell line

value: adenocarcinoma, colon epithelium


title: intestine,veh,Bio rep 1

value: intestine


title: liver,CORT,Bio rep 2

value: CORT


title: shCreb5_Condition_A_2

value: Articular cartilage


title: RAD21* site2 ChIP 11h

value: mAbs against IEEPSR C-terminus


title: Input control RAD21* 10h


title: Tp Iron limitation N2


title: MPNST_2-084

value: MPNST


title: shCreb5_Condition_A_1


title: RAD21* site2 ChIP 9h


title: shScramble_Condition_A_1


title: Input control RAD21* 9h


title: liver,veh,Bio rep 3

value: liver

value: vehicle


title: Tp Hydrogren peroxide N3

value: Hydrogen peroxide treated


title: liver,veh,Bio rep 2


title: Col0_JA_JA_rep4_RNA-seq

city: Sheffield

first: Jurriaan

last: Ton

state: South Yorkshire

address: Western Bank

department: Animal and Plant Sciences

country: United Kingdom

institute: University of Sheffield

data_processing:
Reads were trimmed using Trimmomatic (v0.38) with the parameters: ‘SE’, ‘HEADCROP:15’
Reads were aligned to the TAIR10 genome assembly using STAR (v2.6.1b) with the default parameters.
Reads were counted using HTSeq (v0.9.1) with the parameter: ‘--stranded=no’
Genome_build: TAIR10
Supplementary_files_format_and_content: csv files contain raw read count and normalised CPM (counts per million) values for all genes in the Ensembl Plants TAIR10.40 genome annotation.

organism: Arabidopsis thaliana

source_name: Leaf tissue from five-week-old plants

growth_protocol: Seeds were stored at 4 °C, in the dark and suspended in deionised H2O (dH2O) for 4 days to break dormancy, after which they were sown onto soil consisting of Scott’s Levington M3 compost (Everris) and sand in a 3:1 ratio and cultivated under the following conditions: 8.5:15.5 hr day:night, 21 °C, 45-70% relative humidity (RH) and 100-150 μE m−2 s−1.

extract_protocol:
8 leaves, 4 from each of 2 plants, were pooled, flash frozen and ground to a powder. Total RNA was extracted as previously described (Furci et al., 2019) DOI: https://doi.org/10.7554/eLife.40655
Selection of poly(A)+ RNA fraction, cDNA library preparation and 50 bp single-ended sequencing was performed by BGI genomics.

treatment_protocol:
Plants were spray treated at two weeks old (seedlings) with a 1 mM JA solution and at five weeks old (>9 true leaves) with a 0.1 mM JA solution.  All solutions were supplemented with 0.02% of the surfactant silwet L-77.
Plants were spray treated at two weeks old (seedlings) with water (control) or 1 mM JA and then again at five weeks old (>9 rosette leaves) with water (control) or 0.1 mM JA. The water control treatments were supplemented with the same percentage ethanol as in the corresponding JA solutions. To ensure an even distribution over all upper leaf surfaces, solutions were supplemented with 0.02% of the surfactant silwet L-77.

tag: ecotype

value: Rosette leaves

tag: plant age

value: 5 weeks old

value: JA treatment at 2 weeks old (seedling) and JA treatment at 5 weeks old (>9 rosette leaves).

tag: harvest timepoint

value: 4 hours after the second treatment.


title: Tp Hydrogren peroxide N2

value: algal cell


title: liver,veh,Bio rep 1

tag: tissue


title: Tp Hydrogren peroxide N1

value: CCMP 1335


title: Input control RAD21* 8h


title: Tp Control N3

value: Control


title: liver,CORT,Bio rep 1


title: RAD21* site2 0h


title: Input control RAD21* 0h


title: SRSF10_ LACEseq_rep2

first: Qingyuan

last: Sun

state: Beijing

address: Beichen West Rd., Chaoyang

department: State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
The first 4 nt at 5' end of read1 and read2 were extracted as UMI and then the adaptor sequences, poly(A) tails at the 3’ end and low-quality reads were removed using fastp63 with parameters “--detect_adapter_for_pe -m -e 20 -l 18 -y -Y 10 -c --overlap_len_require 10 --overlap_diff_percent_limit 10 -U --umi_loc per_read --umi_len 4--poly_x_min_len 5”. Clean reads were then first mapped to mouse pre-rRNA using Bowtie2 software (v.2.1.0)64, and the remaining unmapped reads were aligned to mouse mm9 genome using HISAT265. PureCLIP66 was used to identify peaks with default parameters. For motif analysis, LACE-seq peaks were firstly extended 20 nt to the 5’ upstream, and the overrepresented hexamers were identified using the resultant peaks with Homer67. The enrichment of mRNA in each sample was calculated using cufflinks 2.2.1 and expressed as fragments per kilobase of exon per million reads mapped (FPKM).
Assembly: mm9
Supplementary files format and content: The txt files for FPKM contain gene names and the FPKM value for samples. The bw files for each samples.

source_name: P6 testes

growth_protocol: All mice were maintained under specific-pathogen-free (SPF) conditions in compliance with the guidelines of the Animal Care and Use Committee of the Institute of Zoology at the Chinese Academy of Sciences (CAS).

extract_protocol:
The samples were firdtly irradiated twice with UV-Clight on ice at 400mJ. 10 µl of protein A/G magnetic beads (per sample, Thermo Scientific, 26162) were washed twice with BSA/PBS solution (0.1% BSA in 1 × PBS) and incubated with 200 µl blocking buffer (1 × PBS, 0.2 mg/ml glycogen, 0.2 mg/ml BSA) at room temperature (RT) for 1 h. The blocked beads were then washed once with 0.1 M Na-phosphate buffer (93.2 mM Na2HPO4, 6.8 mM NaH2PO4, 0.05% tween 20, pH 8.0) and then resuspended in 40 µl of 0.1 M Na-phosphate buffer containing 5 µg SRSF10 antibody (Cat No.) or IgG (Cat No.), incubating at RT for 1 h. The antibody-coupled beads were washed twice with wash buffer (1 × PBS, 0.1% SDS, 0.5% NP-40, 0.5% sodium deoxycholate) and resuspended in 10 µl of wash buffer per sample. The cross-linked samples were lysed on ice with 50 µl of wash buffer for 10 min. After removal of genomic DNA with 4 µl of RQ1 DNase (Promega, M6101) in the presence of 1µl of RNase inhibitor (Thermo Scientific, EO0381), 10 µl of antibody-coupled beads were added to the lysate and incubated for 1 h at 4 °C. Bead-bound antibody-RNA complexes were then washed twice with wash buffer, once with high-salt wash buffer (5 × PBS, 0.1% SDS, 0.5% NP-40, 0.5% sodium deoxycholate), and once with PNK buffer (50 mM Tris-HCl, pH 7.4, 10 mM MgCl2, 0.5% NP-40). The immunoprecipitated RNAs were then fragmented with 1×10-5 U of micrococcal nuclease (MNase, New England BioLabs, M0247S) in 1 × MN reaction buffer (50 mM Tris-HCl, pH 8.0, 5 mM CaCl2) for 3 min at 37 °C. After another round of extensive washing (twice with 1 × PNK + EGTA buffer (50 mM Tris-HCl, pH 7.4, 20 mM EGTA, 0.5% NP-40), twice with wash buffer, and twice with PNK buffer), the RNA 3’ ends were dephosphorylated on beads with FastAP alkaline phosphatase (Thermo Scientific, EF0651) for 15 min in FastAP buffer. After washing beads twice with 1 × PNK + EGTA buffer, twice with 1 × PNK buffer, and twice with BSA solution (0.2 mg/ml BSA in DEPC water), the 3’ linker was ligated with T4 RNA ligase 2 (New England BioLabs, M0242) for 2.5 h at RT. After washing beads three times with 1 × PNK buffer, the RNA was reverse transcribed with Superscript II reverse transcriptase (Thermo Scientific,18064014) according to the manufacturer’s instruction. Then excess T7-RT primer was digested with Exonuclease I (New England BioLabs, M0293), first-strand cDNA was released from Protein A/G beads by treatment with RNase H (Thermo Scientific, EN0202) and captured by streptavidin C1 beads (Thermo Scientific, 650002). After washing beads twice with 1 × B & W buffer (5 mM Tris-HCl, pH 7.5, 0.5 mM EDTA, 1 M NaCl), once with BSA solution, the cDNA 3’ linker was ligated with T4 RNA ligase 1 (New England BioLabs, M0437) overnight at RT.
The cDNA was pre-amplified using KAPA HiFi HotStart ReadyMix (KAPA Biosystems, KK2601), and PCR products were purified with Ampure XP beads (Beckman Coulter, A63881). Then in vitro transcription was performed, the DNA template was removed with TURBO DNase (Thermo Scientific, AM2238) and the RNA was purified with Agencourt RNA Clean beads (Beckman Coulter, A63987). After reverse transcription and indexed PCR, the PCR products were size-selected on a 2% agarose gel, and regions corresponding to 250–500 bp were purified using Gel Extraction Kit (Qiagen, 28604). The LACE-seq library was paired-end sequenced using Illumina NovaSeq 6000 at Novogene.

treatment_protocol: Isolated spermatogonia (THY1+ cells) for LACE-seq were enriched from P6 control and Srsf10cKO testes using MACS method anti-THY1 antibody.

value: Testes

tag: genotype

value: WT

value: isolated THY1+ cells


title: Tp Control N2

value: 20C, EASW, f/2, 3days


title: Tp Control N1


title: RNA_RB2

city: Pretoria

first: John

last: Osei Sekyere

state: Gauteng

address: 05 Bopheloweg Off Dr. Savage Road

department: Department of Medical Microbiology

country: South Africa

institute: University of Pretoria

data_processing: All analysis was conducted within SMRTLINK v10.1

organism: Acinetobacter baumannii

source_name: Fluid Aspirate

growth_protocol: isolates on the swabs were grown in an enrichment broth overnight prior to plating on a blood plate

extract_protocol:
Zymo DNA extraction kits were used to extract DNA for PCR confirmation of the resistance genes
HMW gDNA was isolated using NEB Mornach HMW DNA isolation kit (https://international.neb.com/protocols/2020/10/27/protocol-for-high-molecular-weight-dna-hmw-dna-extraction-from-bacteria). HMW gDNA was quantified using Qubit HS dsDNA Assay and qualified on Tapestation using genomics screentape. HMW gDNA was shared to ~10kb fragments using covaries g-Tubes and QC’d using the above method. SMRTbell libraries were performed using PacBio’s Microbial Multiplexing workflow (see attached)     The resulting libraries were size selected using BluePippin Size selection using U1 marker (10-18kb). QC was performed using the above method. Libraries were then prepared for sequencing following the online SMRTlink guided protocol (Binding kit 2.0 and Control 1.0, Sequel II Sequencing plate 2.0 and SMRT cell 8M.)
size selection was done by Blue-Pippin and sequenced with PacBio for DNA WGS

treatment_protocol: The plates were impregnated with colistin and/ or carbapenems to inhibit all but carbapenem and/or colistin-resistant isolates

value: bacterial cells


title: IgG_LACEseq


title: Col0_JA_JA_rep2_RNA-seq


title: Col0_JA_W_rep4_RNA-seq

treatment_protocol:
Plants were spray treated at two weeks old (seedlings) with a 1 mM JA solution and at five weeks old (>9 true leaves) with a water control solution. The water control solution was supplemented with the same percentage of ethanol as in the corresponding JA treatment solution. All solutions were supplemented with 0.02% of the surfactant silwet L-77.
Plants were spray treated at two weeks old (seedlings) with water (control) or 1 mM JA and then again at five weeks old (>9 rosette leaves) with water (control) or 0.1 mM JA. The water control treatments were supplemented with the same percentage ethanol as in the corresponding JA solutions. To ensure an even distribution over all upper leaf surfaces, solutions were supplemented with 0.02% of the surfactant silwet L-77.

value: JA treatment at 2 weeks old (seedling) and Water treatment at 5 weeks old (>9 rosette leaves).


title: Col0_JA_JA_rep1_RNA-seq


title: SRSF10_ LACEseq_rep1


title: OTI Snx9 KO pool B

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

data_processing:
Primary data analysis was performed with the Illumina RTA version 3.4.4 and Base-calling Version bcl2fastq-2.20.0.422.
Read quality was assessed with the FastQC tool (version 0.11.5)
Raw FASTQ files were processed using STARsolo (STAR version 2.7.9a) for sample demultiplexing, barcode processing, alignement of reads to the mouse genome (mm10) and UMI counting on gene models from Ensembl 102. The options "outFilterType=BySJout", "outFilterMultimapNmax=10", "outSAMmultNmax=1", "outFilterScoreMin=30", "soloCBmatchWLtype=1MM_multi_Nbase_pseudocounts", "soloUMIlen=12", "soloUMIfiltering=MultiGeneUMI_CR", "soloUMIdedup=1MM_CR", "soloCellFilter=None" were used.
For each sample, empty droplets were detected and removed using the emptyDrops() function from the Bioconductor DropletUtils package (version 1.14.0; using 5000 iterations, the option test.ambient = TRUE, a lower threshold of 100 UMIs and an FDR threshold of 0.1%).
Assembly: mm10
Supplementary files format and content: cells_integrated_clustered_annotated.rds: An R .rds file including a Seurat object including the final dataset used in the paper (7017 cells x 21214 genes), with normalized intensities, clustering, annotation and reduced dimensions information
Supplementary files format and content: mm10_ensdb_102_sce.rds: An R .rds file including a SingleCellExperiment class object. All droplets detected as not empty were included (11843 droplets x 55487 genes), see "data processing step" above. Read counts matrix is accessible via "counts(sce)". Information about cells is accessible via colData(sce). Information about genes is accessible via rowData(sce).

source_name: Mouse CD8+ OTI T cells

growth_protocol: For the generation of murine antigen-specific Snx9 KO T cells, we harvested spleen and axial, cervical and inguinal lymph nodes from “OTI” mice (C57BL/6-Tg(TcraTcrb)1100Mjb/J, RRID:IMSR_JAX:003831), in which all CD8+ T cells recognize ovalbumin (OVA257-264, H-2Kb). Spleens and lymph nodes were strained over a 70 mm strainer and washed with PBS, incubated in red blood cell lysis buffer for 1min and wash with PBS again. Cells were then resuspended at 1.5 Mio/ml in murine T cell medium (supplemented RPMI medium as above for human T cells, but with 10% heat inactivated FCS instead of human AB+ serum). Cells were then stimulated by addition of 100 ng/ml SIINFEKL (Invivogen, OVA257-264) and 100 U/ml recombinant human IL2 (cross-reactive with murine IL-2 receptor; Proleukin, Clinigen Healthcare) and incubated at 37°C. After two days of stimulation, 900 pmol Alt-R-crRNA (sgSNX9_9 and sgSNX9_IDT_AF; IDT) and 900 pmol Alt-R-tracrRNA (IDT) were annealed by heating to 95°C for 5min, then cooled to 25°C at -0.1°C per minute. 1.5 ml of these aligned crRNA-tracrRNA complexes was then incubated with 15 ml of 40 mM Cas9-NLS protein (Berkeley, QB3) for 30min at room temperature in the dark and used immediately (referred to as Cas9-RNP). 2 days after stimulation, 10mio of the splenocytes and lymphocyte mixture was collected per condition, spun at 90g for 10min and then resuspended in 100ul P4 nucleofection buffer, the Cas9-RNPs and electroporated with the CM137 program. Immediately 900ul medium was added and rested for 20min at 37°C. Then cells were transferred to wells at 1.5 Mio/ml with 100 U/ml IL-2. Cells were expanded to reach 1.5 Mio/ml with fresh 100 U/ml IL-2 daily for 4 days.

extract_protocol:
Sorted single cells were then loaded onto a 10x Genomics Chromium NEXT GEM chip G.
Libraires were prepared following the 10x Genomics protocol for 3′ gene expression profiling (CG000315, Rev C) and cDNA or library quality was assessed using a 4200 TapeStation System (Agilent). A total of four individual libraries were prepared and sequenced using an Illumina NovaSeq 6000 instrument aiming to obtain 50,000 reads per cell.

treatment_protocol: CD57BL/6 mice were injected subcutaneously with 1 Mio MC38-OVA and 1.5 Mio OTI T cells were transferred intravenously 12 days post tumor injection. After 12 days, the tumors (7 per condition) were removed separated from fibrous, necrotic and lymphoid tissue and cut into pieces of 1mm3. These pieces were then digested in the digestion mix as described above and dissociated using a gentle MACS dissociator (Miltenyi, using a C-tube, program m_impTumor_02). The mixture was then incubated for 15min on a rotating shaker (200 rpm) at 37°C. Then the mixture was again dissociated using the m_impTumor_03 program on the gentle MACS dissociator. Cells were then strained through a 100 mm MACS SmartStrainer (Miltenyi) and washed using PBS with 2% FCS. Cells were stained for CD45 (30-F11 clone in V450, BD 560501) and CD19 (1D3 clone in FITC, BD 553785) and analyzed for lymph node contamination. Samples with more than 5% CD19+ cells among CD45+ live cells were excluded due to lymph node contamination (3 samples: 2 intergenic and 1 Snx9 KO). The remaining samples were pooled into 2 pools (2-3 mice) per condition. These pools were sorted for DAPI- CD3e+ F4/80- Ly6G- CD19- CD8a+ CD45.1+ CD45.2- single cells using an AriaIII sorter (intergenic A: 6787 cells, intergenic B: 1975 cells; Snx9 KO A: 6163 cells, Snx9 KO B: 2295).

value: Snx9 KO

tag: timepoint

value: 13 days post transfer


title: Col0_JA_JA_rep3_RNA-seq

tag: treatment


title: Col0_JA_W_rep3_RNA-seq


title: Col0_JA_W_rep2_RNA-seq


title: 19G02977_Big_Ep_Cam

description:
single cell RNAseq 10x
Patient 4 metastasis A

source_name: cancer cells

value: Malignant cells

value: Patient 4


title: B16, aPD-1, TBK1 sgRNA-2, Replicate 4

city: Cambridge

first: Seth

middle: Allen

last: Anderson

address: 75 Ames Street

department: Cancer Program

institute: Broad Institute of MIT and Harvard

data_processing:
Cellranger v3.0.1 mkfastq command to convert bcl files to fastq files and to demultiplex fastq files
Cellranger v3.0.1 count command to generate raw and filtered count matrices
Assembly: Assembly: mm10
Supplementary files format and content: Tab-seperated values (.tsv.), matrix files (.mtx), hierarchical data file (.h5), and fastq (.fastq)

source_name: melanoma subcutaneous tumor

growth_protocol: For tumor challenges, 2E6 B16 tumor cells were resuspended in Hanks balanced salt solution (Gibco), mixed 1:1 by volume with Matrigel (Corning) and subcutaneously injected into the right flank on day 0. Each tumor injected contained only a single sgRNA targeting TBK1 or control sgRNA.

extract_protocol:
On day 13, tumors were dissected from the surrounding fascia, mechanically minced, and dissociated with the mouse Tumor Dissociation Kit (Miltenyi Biotec) as per manufacturer’s instructions. After filtering through a 70-μm filter, live cells were isolated using a gradient with Lympholyte-M separation media (Fisher Scientific) as per manufacturer’s instructions. tumor-infiltrating immune cells were enriched by CD45+ MACS positive selection (Miltenyi Biotec).
Four representative samples each of Tbk1-null (sgRNA-2) or control (sgRNA-1) samples were selected, counted, and loaded onto the Chromium Controller (10X Genomics). Subsequent generation of 3' sequencing libraries was performed as per manufacturer’s instructions (10X Genomics). Characterization of the sequencing library was performed with TapeStation (Agilent) and Qubit (ThermoFisher) instruments.

treatment_protocol: Mice were vaccinated on days 1 and 4 with 1E6 previously irradiated GM-CSF-secreting B16 (GVAX) cells and treated with 200 μg of rat monoclonal anti-PD1 antibodies (BioXCell, clone: 29F.1A12) via intraperitoneal injection on days 6, 9 and 12. Animals were randomized before treatment. No blinding was performed.

tag: group

value: TBK1 sgRNA

value: melanoma subcutaneous tumor

value: CD45+ immune cells


title: Col0_W_JA_rep3_RNA-seq

treatment_protocol:
Plants were spray treated at two weeks old (seedlings) with a water control solution and at five weeks old (>9 true leaves) with a 0.1 mM JA solution. The water control solution was supplemented with the same percentage of ethanol as in the JA seedling treatment solution. All solutions were supplemented with 0.02% of the surfactant silwet L-77.
Plants were spray treated at two weeks old (seedlings) with water (control) or 1 mM JA and then again at five weeks old (>9 rosette leaves) with water (control) or 0.1 mM JA. The water control treatments were supplemented with the same percentage ethanol as in the corresponding JA solutions. To ensure an even distribution over all upper leaf surfaces, solutions were supplemented with 0.02% of the surfactant silwet L-77.

value: Rosette leaves

value: 5 weeks old

value: Water treatment at 2 weeks old (seedling) and JA treatment at 5 weeks old (>9 rosette leaves).

value: 4 hours after the second treatment.


title: Young_adipose_4

city: North Chicago

first: Ameya

middle: S

last: Kulkarni

state: Illinois

address: 1 N Waukegan Road

department: Genomics Research Center

institute: AbbVie

data_processing:
The raw sequence reads, obtained as fastq files were subjected to quality control using OpenGene’s fastp (v0.19.4) preprocessor.
The processed reads were aligned to the mm10 mouse reference genome prebuilt with gene annotations within 10X’s cellranger 3.0.2. software. The alignment was performed using the STAR aligner employed within cellranger 3.0.2.
Gene expression was quantified using each cell-barcode combination’s unique molecular identifiers (UMIs) using the default cellranger 3.0.2. pipeline.
The quantified counts for the raw, unfiltered cell barcodes were stored as a gene x cell matrix and exported for further downstream analyses.
Genome_build: mm10
Supplementary_files_format_and_content: *_raw_feature_bc_matrix.tar: Tar archive includes raw feature x barcode matrix output from cellranger processing pipeline; barcodes, features and count matrix files.
Supplementary_files_format_and_content: *_filtered_feature_bc_matrix.tar: Tar archive includes filtered feature x barcode matrix output from cellranger processing pipeline; barcodes, features and count matrix files.

source_name: Adipose SVF

extract_protocol: We applied single-cell RNA-Seq on mouse muscle and adipose tissues using 10X Single Cell 3’ v2 kit using ~3000 cells per lane on the 10X Chromium microfluidics device (10X Genomics, Pleasanton, CA). The libraries were sequenced at a target depth of 50 million reads/sample on Illumina NovaSeq 6000.

value: Adipose SVF

tag: condition

value: Young

tag: Sex

value: Male


title: 19G00635_Tnbis

description:
single cell RNAseq 10x
Patient 3 metastasis

tag: cell type

value: Cancer Associated Fibroblasts

value: Patient 3


title: Col0_W_JA_rep2_RNA-seq


title: 19G02977_Small_TN

description:
single cell RNAseq 10x
Patient 4 metastasis B


title: 19G00635_TN1


title: RAD21* site2 ChIP 8h

value: adenocarcinoma, colon epithelium

tag: time point

tag: antibody

value: mAbs against IEEPSR C-terminus


title: Young_adipose_3


title: OTI Snx9 KO pool A

value: Snx9 KO

value: 13 days post transfer


title: Col0_JA_W_rep1_RNA-seq

value: JA treatment at 2 weeks old (seedling) and Water treatment at 5 weeks old (>9 rosette leaves).


title: 19G02977_Small_Ep_Cam

tag: cell markers

value: Malignant cells

tag: subject id

value: Patient 4


title: Wild Type NPCs [E16.5_WT]

city: New Orleans

first: Hongbing

last: Liu

address: 1430 Tulane Ave

institute: Tulane University

data_processing:
10x Cellranger V.2.1.0 was used to generate Fastq files, perform alignment,filtering,barcode counting,UMI counting and aggregation.
Seurat V.4.1.1  for scRNA QC and Monocle 3.0 for pseudotime analysis
Assembly: mm10
Supplementary files format and content: H5 file filtered-gene-barcode-matrix can be deconvoluted to tsv and mtx files

source_name: Embryonic Kidneys

extract_protocol:
Libraries were prepared from individual cells  (for the respective genotypes) using the droplet-based method as was outlined by10X Genomics. Indexed libraries were sequenced on a NextSeq500 (Illumina) sequencer to obtain 75 bp paired-end reads using the v2 chemistry.
v2.chemistry 10X Genomics

value: Embryonic Kidneys

tag: strain background

value: Six2+ NPCs

value: Wild Type


title: 19G02977_Big_TN


title: Col0_W_W_rep4_RNA-seq

treatment_protocol:
Plants were spray treated at two weeks old (seedlings) and then again at five weeks old (> 9 rosette leaves) with water control solutions supplemented with the same percentage of ethanol as in the corresponding JA treatment solutions. All solutions were supplemented with 0.02% of the surfactant silwet L-77.
Plants were spray treated at two weeks old (seedlings) with water (control) or 1 mM JA and then again at five weeks old (>9 rosette leaves) with water (control) or 0.1 mM JA. The water control treatments were supplemented with the same percentage ethanol as in the corresponding JA solutions. To ensure an even distribution over all upper leaf surfaces, solutions were supplemented with 0.02% of the surfactant silwet L-77.

value: Rosette leaves

value: 5 weeks old

value: Water treatment at 2 weeks old (seedling) and water treatment at 5 weeks old (>9 rosette leaves).


title: Col0_W_JA_rep4_RNA-seq

value: Water treatment at 2 weeks old (seedling) and JA treatment at 5 weeks old (>9 rosette leaves).

value: 4 hours after the second treatment.


title: OTI intergenic pool B

value: intergenic


title: Young_muscle_3

source_name: Gastrocnemius muscle

value: Gastrocnemius muscle

value: Young

tag: strain

value: Male


title: B16, aPD-1, TBK1 sgRNA-2, Replicate 3

value: TBK1 sgRNA

value: melanoma subcutaneous tumor

tag: cell line

value: CD45+ immune cells


title: Col0_W_JA_rep1_RNA-seq

tag: ecotype

tag: plant age


title: B16, aPD-1, TBK1 sgRNA-2, Replicate 2

tag: tissue


title: Young_muscle_4


title: Tp Iron limitation N1

value: algal cell

value: CCMP 1335

value: iron limitation

tag: growth conditions

value: 20C, EASW, f/2, 3days


title: B16, aPD-1, Control sgRNA-1, Replicate 4

value: control

tag: genotype


title: Hdac1 and Hdac2 condition null NPCs [E16.5_Hdac1&2_null]

value: Embryonic Kidneys

value: Hdac1&2 null NPCs

value: Mutant


title: 19G00635_Ep_Cam_plus

value: Malignant cells

value: Patient 3


title: SC_196081_T_neg

description:
single cell RNAseq 10x
Patient 1 metastasis

value: Cancer Associated Fibroblasts

value: Patient 1


title: B16, aPD-1, Control sgRNA-1, Replicate 3

tag: treatment


title: 19G00619_Tnmoins

description:
single cell RNAseq 10x
Patient 2 metastasis

value: Patient 2


title: Sense1 Total RNA

city: Jupiter

first: Sathyanarayanan

last: Puthanveettil

address: 130 Scripps Way

institute: Scripps Florida

data_processing:
All samples were processed and sequenced on a NextSeq 500. The quality of the reads overall was quite high with no decrease in quality over the course of sequencing.
After quality control, the reads were mapped to the mouse transcriptome using Salmon using paired end settings (Salmon reference was made using Ensembl: ftp://ftp.ensembl.org/pub/release-99/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.abinitio.fa.gz)
Differential analysis was performed using DEseq
Genome_build: N/A
Supplementary_files_format_and_content: Excel file contaiining gene counts and differentially expressed genes

source_name: Primary Hippocampal neurons

growth_protocol: Hippocampi were cultured from P0 mice for generating RNA at DIV 16.

extract_protocol:
RNA was extracted using DirectZol RNA kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: DIV 16 neurons from P0 pups


title: Young_adipose_2

value: Adipose SVF

value: Young

value: Male


title: B16, aPD-1, TBK1 sgRNA-2, Replicate 1

tag: group

value: TBK1 sgRNA

value: melanoma subcutaneous tumor

value: CD45+ immune cells


title: Col0_W_W_rep3_RNA-seq

value: Rosette leaves

value: 5 weeks old

value: Water treatment at 2 weeks old (seedling) and water treatment at 5 weeks old (>9 rosette leaves).

tag: harvest timepoint

value: 4 hours after the second treatment.


title: Ca_72hr_3

first: Christoph

last: Grundner

address: 1900 9th Ave

department: Center for Global Infectious Disease Research

institute: Seattle Children's Research Institute

data_processing:
Read alignment was performed using the Bowtie 2 custom processing pipeline (https://github.com/robertdouglasmorrison/DuffyNGS, https://github.com/robertdouglasmorrison/DuffyTools), as previously described (PMID: 25784701)
The pipeline consists of 2 stages: 1) a pre-alignment filtering step to remove unwanted transcripts such as rRNA, and 2) a genomic alignment step using Bowtie2 with the command line option 'very-sensitive.'
BAM files from step 2 are combined into read depth wiggle tracks that record both uniquely mapped and multiply mapped reads from each of the forward and reverse strangs of the genome. Multiply mapped reads are prorated over all highest-quality aligned locations. Transcript abundance is quantified by summing total reads landing inside annotated gene boundaries, expressed by RPKM.
Assembly: MT_H37Rv_V3
Supplementary files format and content: Transcript abundance is quantified by summing total reads landing inside annotated gene boundaries, expressed by RPKM.

organism: Mycobacterium tuberculosis

growth_protocol: Mycobacteria tuberculosis strain H37Rv (ATCC 27294) was grown to an OD600 of ~1 in Middlebrook 7H9 medium (Difco) with 0.2 % glycerol, 10% OADC supplement and 0.05% Tween80 medium. Cells were washed twice with Chelex treated Sauton's medium (CTSM) and subculture in CTSM starting at an OD600 of 0.05 and was grown to an OD600 of ~1. The culture was again subcultured in CTSM starting at an OD600 of 0.05 and incubated at 37°C to an OD600 of 0.2.

extract_protocol:
RNA was isolated using published protocols (Rustad TR, Harrell MI, Liao R, Sherman DR (2008) The Enduring Hypoxic Response of Mycobacterium tuberculosis. PLoS ONE 3(1): e1502). In summary, cell pellets were resuspended in Trizol and lysed by bead beating for 30sec at 6m/s for three cycles with intermittent cooling on ice. Cell debris were pelleted at 20,000g for 1min, and the supernatant was transferred to a heavy phase lock gel tube containing 300 µl chloroform. The tubes were inverted for 2min and centrifuged at 20,000g for 5min. RNA in the aqueous phase was precipitated using 300 μl isopropanol and 300 μl high salt solution (0.8M Na citrate, 1.2M NaCl). RNA was purified using QIAGEN RNeasy kit and ribosomal RNA was depleted using the Ribo-Zero rRNA removal magnetic kit (Illumina) according to manufacturer's instructions.
The cDNA library was generated using the NEBNext Ultra II RNA Library Prep Kit and each replicate was barcoded in the DNA library using the NEBNext Multiplex Oligos for Illumina. Libraries were quantified using the KAPA qPCR quantification kit, pooled, and sequenced at the University of Washington Northwest Genomics Center with the Illumina NextSeq 500 High Output v2 Kit.

treatment_protocol: The cultures were supplemented with or without 1mM CaCl2 in triplicate. Bacteria were harvested at the indicated timepoints.

tag: time

value: Day 3


title: Young_adipose_1

tag: condition

tag: Sex


title: Metformin-treated_adipose_4

value: Treated


title: B16, aPD-1, Control sgRNA-1, Replicate 2

value: control

tag: cell type


title: Young_muscle_2

value: Gastrocnemius muscle


title: 19G00619_Ep_Cam_plus

tag: cell markers

value: Malignant cells


title: Col0_W_W_rep1_RNA-seq


title: B16, aPD-1, Control sgRNA-1, Replicate 1


title: Ca_72hr_2


title: Antisense3 Total RNA


title: Antisense2 Total RNA


title: Metformin-treated_adipose_3


title: Antisense1 Total RNA


title: Metformin-treated_adipose_2


title: Sense3 Total RNA


title: Col0_W_W_rep2_RNA-seq


title: SC_196081_Ep_Cam_plus

tag: subject id

value: Patient 1


title: ros1-4_rep3_Bisulfite-seq

data_processing:
Reads were trimmed using Trimmomatic (v0.38) with the parameters: ‘SLIDINGWINDOW:4:25’, ‘HEADCROP:6’, MINLEN:36’.
Trimmed reads were aligned to the TAIR10 genome assembly using Bismark (v0.22.3) and Bowtie2 (v2.3.4.3) with default parameters.
Read deduplication was performed using the 'deduplicate_bismark' tool from the Bismark suite (v0.22.3) with the setting: "--paired".
Methylated and unmethylated read counts per cytosine (C) position were generated using the Bismark (v0.22.3) tool ‘bismark_methylation_extractor’ with the parameters: ‘--paired-end’, ‘--no_overlap’, ‘--ignore_3prime_r2 90’, ‘--comprehensive’, ‘--bedGraph’, ‘--CX’, ‘--cytosine_report’.
Assembly: TAIR10
Supplementary files format and content: Genome-wide cytosine reports output by the 'bismark_methylation_extractor' tool. The column headers in the text files are as follows: <chromosome> <position> <strand> <count methylated> <count unmethylated> <C-context> <trinucleotide context>.

source_name: Aerial tissue from two- to three-week-old plants.

growth_protocol: Seeds were stored at 4 °C, in the dark and suspended in deionised H2O (dH2O) for 4 days to break dormancy, after which they were sown onto soil consisting of Levington Advance Pot & Bedding M3 compost (ICL) and sand in a 3:1 ratio and cultivated under the following conditions: 16:8 hr day:night, 22 °C, 60% relative humidity (RH) and 150 μmol m−2 s−1.

extract_protocol:
28-35 seedlings were pooled for each replicate, flash frozen and ground to a powder. Genomic DNA was extracted using the GenElute Plant Genomic DNA Miniprep Kit (Sigma-Aldrich).
Bisulfite treatment, library preparation and 150 bp paired-end sequencing was performed by BGI genomics.

treatment_protocol: Plants were grown under stress free conditions.

value: Aerial tissue

value: 2-3 weeks old