title: TC5, SOS1i+MEKi, tumor2

city: Ridgefield

first: Abhishek

last: Kashyap

state: CT

address: 900 Ridgebury Rd

institute: Boehringer Ingelheim

description:
10x Genomics
scGEX_170

data_processing:
Fastq files were used as an input to CellRanger (version 7.0.0) to generate count matrices, with mm10 as the mouse genome reference and default parameters. Downstream analysis was done using Scanpy (version 1.9.3, 191 python version 3.8.2).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tumor

extract_protocol:
Tumors were harvested and processed on the gentleMACS Octo Dissociator. Digestion cocktail contained 800ug/ml Dispase II,100ug/ml DNase I and 400ug/ml Collagenase P. Cell viability was assessed with Zombie Yellow Fixable viability dye.
Single-cell sequencing library preparation was performed using the 10x Genomics Chromium Controller and Chromium Next GEM Single Cell 3’ Kit v3.1 Chemistry Library, Gel Bead, and Chip Kits (10x Genomics) according to the manufacturer’s protocols & instructions. A total of 10,000 cells were targeted per library and processed in parallel. Any samples with a proportion >10% of cDNA 150bp-400bp, were subjected to an additional 0.6xSpri cleanup before proceeding with the remainder of library preparation. Libraries produced were checked for quality control using the Agilent Tapestation, quantified using the KAPA library Quantification Kit, diluted as appropriate, then sequenced using a NovaSeq6000 with paired-end sequencing and dual indexing as appropriate for the library preparation. Dual Index libraries were sequenced using cycling conditions 28, 10, 10, and 90 for Read 1, i7 index, i5 index and Read 2 respectively.

treatment_protocol: Clinical grade SOS1i (BI 1701963) and MEKi (BI 3011441) compounds were formulated in Gelucire Solvent (1% Tween-80(v/v) + 15% Gelucire 44/14(v/v) + 84% DI H2O(v/v)) and dosed at final concentration of 50mg/kg and 0.3mg/kg respectively through oral gavage b.i.d.

value: Tumor

value: Female

tag: strain

value: WT


title: DKO cells, siFOXA2, repeat 3

status: Public on Apr 22 2024

type: SRA

city: Boston

first: Zifeng

last: Wang

state: Massachusetts

address: 100 Morrissey Blvd, ISC/4610

department: CPCT

country: USA

institute: UMASS Boston

library_source: transcriptomic

data_processing:
The sequence quality of raw reads was checked by FastQC (version 0.11.9).
Raw reads were aligned to the human reference genome (hg19) /GRCm38 using STAR (version 2.7.2) followed by counting with featureCounts (v2.0.1) from GRCh37 Ensembl reference.
Gene level read counts was produced by setting the parameter 'quantMode' as 'GeneCounts' in STAR
Assembly: GRCh37/GRCm38
Supplementary files format and content: tab-deliminated text files include raw gene counts

molecule: total RNA

organism: Mus musculus

source_name: DKO (Pten-/-/Rb-/-) murine PCa cells

growth_protocol: PC3,LNCaP cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C. NCI-H660 cells were cultured in RPMI-1640 base medium supplemented with 5% FBS, 10nM β-estradiol, 10nM hydrocortisone, and 1% Insulin-Transferrin-Selenium. DKO cells were cultured in DMEM base medium supplemented with 10% FBS

extract_protocol:
RNA was extracted with Rneasy Mini Kit (QIAGEN) following manufacturer’s protocol
RNA libraries for RNA-seq were prepared using TruSeq Strnd Total,RNA LT (Illumina)  mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: PC3,NCI-H660 cells were treated with vehicle versus  ORY-1001, or C12 for 4hrs

tag: cell line

value: DKO (Pten-/-/Rb-/-) murine PCa cells

tag: cell type

value: Prostate cancer cell line

tag: treatment

value: FOXA2 knockdown


title: S. pombe, Set1_del, rep1

city: 南京

first: 冯

last: 刚

address: 江苏省南京市仙林街道南京师范大学

country: China

institute: 南京师范大学

description:
WT-vs-set1_del.all.annot.txt
WT-vs-set1_del.filter.annot.txt

data_processing:
First, the descending raw reads was quality-controlled using the fastp
clean reads were aligned to the ribosome database of this species using the short reads alignment tool bowtie2[2], the reads on the upper ribosomes were removed without mismatch allowed, and the retained unmapped reads was used for subsequent transcriptome analysis.
Using the HISAT2 software, a reference genome-based alignment analysis was performed.
Based on the alignment results of the HISAT2, we reconstructed the transcripts using the Stringtie and calculated the expression levels of all the genes in each sample using the RSEM
Input data for gene differential expression analysis are the reads count data obtained from gene expression level analysis and were analyzed using DESeq2[6] software
Using the STRING protein interaction database (http://string-db.org).
Assembly: Ensembl_release45
Supplementary files format and content: Each txt file corresponds to the information of one sample, with a total of two tables, namely all gene expression and significant gene expression.

organism: Schizosaccharomyces pombe

source_name: Schizosaccharomyces strains

extract_protocol:
Total RNA was extracted using Trizol reagent kit.The RNA libraries of RNA-Seq were enriched for mRNA using Oligo (dT), reverse transcribed to cDNA, after PCR amplification, and then sequenced.
The RNA libraries of RNA-Seq were enriched for mRNA using Oligo (dT), following manufacturer's protocols.

tag: genotype

value: Set1 knockdown


title: GES1, TCF7, CST, rep 1

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

library_source: genomic

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
ChIP-seq reads were aligned to hg38 reference human genome, using bowtie2(v2.3.3.1)
Duplication reads were removed from aligned file by using picard-tools-2.18.21.
Alignments were filtered for ENCODE blacklisted regions (ENCODE Project Consortium, 2012, doi: 10.1038/nature11247).
The mapped sequence reads were extended to 100 bp and converted to the continuous signal data in bedGraph format using HOMER makeUCSCfile command. BedGraph files were converted to bigwig files using UCSC BedGraphToBigWig program.
Assembly: hg38
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: For GES1 and SNU719, RPMI1640, 10% fetal bovine serum, 1×penicillin/streptomycin. Cells were cultured at 37C at 5% CO2; For YCC10, EMEM, 10% fetal bovine serum, 1×penicillin/streptomycin. Cells were cultured at 37C at 5% CO2

extract_protocol:
ChIP: Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using Picorupter (Diagenode); ATAC and CUT&TAG: Cell nuclei were transposed by Tn5 Transpose
ChIP-seq libraries were prepared using KAPA Hyper Prep Kit (KAPA Biosystems) following the manufacturer’s protocol; ATAC-seq libraries were amplified from the transposed DNA fragments. CUT&Tag libraries were amplified by KAPA HiFi HotStart Ready Mix.

value: Human gastric epithelial cell

tag: chip antibody


title: S. pombe, H2BP102L, rep3

address: 江苏省南京市仙林街道南京师范大学

description:
WT-vs-H2BP102L.all.annot.txt
WT-vs-H2BP102L.filter.annot.txt


title: TC5, SOS1i+MEKi, tumor1

description:
10x Genomics
scGEX_169

library_source: transcriptomic single cell

tag: tissue

tag: Sex


title: HaCaT shIQGAP3 cells without stimulation, biol. rep 1

city: Moscow

first: Alena

middle: D

last: Zolotarenko

address: Gubkina street 3

country: Russia

institute: Vavilov Institute of General Genetics Russian Academy of Sciences

data_processing: none provided

source_name: keratinocytes

extract_protocol: none provided

value: keratinocytes

value: HaCaT

value: Human immortalized keratinocytes

value: no treatment


title: YCC10, ATAC, rep 2

value: Human gastric cancer


title: DKO cells, siFOXA2, repeat 2


title: TC5, Vehicle, tumor3

description:
10x Genomics
scGEX_168

value: Vehicle


title: YCC10, ATAC, rep 1


title: S. pombe, H2BP102L, rep2

address: 江苏省南京市仙林街道南京师范大学


title: DKO cells, siFOXA2, repeat 1


title: DKO cells, vehicle,ChIP-FOXA2

data_processing:
The sequence quality of raw reads was checked by FastQC (version 0.11.9).
Raw reads were mapped to the hg19 human genome using bwa (version 0.7.17-r1188) with aln and samse or sampe sub-commands.
Samtools (version 1.9) was used to convert sam files to bam format.
MACS2 (version 2.1.4) was used to call peak on the bam files.
bedGraph files generated from MACS2 were converted into bigwig files with UCSC tools (version 357).
Assembly: mm10
Supplementary files format and content: bigWig, bed

growth_protocol: DKO cells were cultured in DMEM base with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Cells were crosslinked with 1% formaldehyde and then sonicated. DNA were immunoprecipitatted with antibody and protein A/G beads. After reverse crosslinking, DNA were purifed with Qiagen PCR purification kit.
Libraries were constructed using the SMARTer ThruPLEX DNA-Seq Prep Kit (Takara Bio USA).

treatment_protocol: DKO cells were treated with vehicle versus  ORY-1001,for 4hrs


title: S. pombe, H2BP102L, rep1

address: 江苏省南京市仙林街道南京师范大学


title: TC5, Vehicle, tumor2

description:
10x Genomics
scGEX_167


title: Collection group (pear pollen), mouthparts [YH3]

city: Jinzhong

first: Lina

last: Guo

state: Shanxi

address: No.1, Mingxian South Road, Taigu District

institute: Shanxi Agricultural University

data_processing:
cBot Cluster Generation System
Sequence reads were trimmed for adaptor sequence/low-quality sequence using BMKCloud(www.biocloud.net) (parameter- Quality limit: 0.05)
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Hisat2 tools soft were used to map with reference genome.
Gene function was annotated based on the following databases:Nr (NCBI non-redundant protein sequences)；Nt (NCBI non-redundant nucleotide sequences)；Pfam (Protein family)；KOG/COG (Clusters of Orthologous Groups of proteins)；Swiss-Prot (A manually annotated and reviewed protein sequence database)；KO (KEGG Ortholog database)；GO (Gene Ontology).
Assembly: Apis_mellifera
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Apis mellifera

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: mouthparts

value: Collection group (Olea europaea pollen)


title: TC5, SOS1i+MEKi, tumor4

description:
10x Genomics
scGEX_172


title: SNU719, ATAC, rep 2


title: DKO cells, siNC, repeat 2

value: Negative control knockdown


title: TC5, SOS1i+MEKi, tumor3

description:
10x Genomics
scGEX_171

value: Tumor


title: SNU719, TCF7, CST, rep 2


title: Collection group (pear pollen), mouthparts [YH2]


title: S. pombe, H2BG52D, rep3

address: 江苏省南京市仙林街道南京师范大学

description:
WT-vs-H2BG52D.all.annot.txt
WT-vs-H2BG52D.filter.annot.txt


title: S. pombe, H2BG52D, rep2

address: 江苏省南京市仙林街道南京师范大学


title: TC4, SOS1i+MEKi, tumor4

description:
10x Genomics
scGEX_165

value: Female


title: YCC10, H3K27ac, Active Motif, rep 2

value: H3K27ac (Active Motif, #91193)


title: TC4, SOS1i+MEKi, tumor3

description:
10x Genomics
scGEX_164

value: WT


title: S. pombe, H2BG52D, rep1

address: 江苏省南京市仙林街道南京师范大学


title: S. pombe, H2BE112K, rep3

address: 江苏省南京市仙林街道南京师范大学

description:
WT-vs-H2BE112K.all.annot.txt
WT-vs-H2BE112K.filter.annot.txt


title: TC4, SOS1i+MEKi, tumor2

description:
10x Genomics
scGEX_163


title: YCC10, H3K27ac, Active Motif, rep 1


title: GES1, ATAC, rep 1


title: Collection group (pear pollen), mouthparts [YH1]


title: Collection group (pear pollen), mouthparts [LH3]

value: Collection group (pear pollen)


title: Collection group (pear pollen), mouthparts [LH2]


title: S. pombe, H2BE112K, rep1

address: 江苏省南京市仙林街道南京师范大学


title: Collection group (pear pollen), mouthparts [LH1]


title: S. pombe, H2BE112K, rep2

address: 江苏省南京市仙林街道南京师范大学


title: TC4, SOS1i+MEKi, tumor1

description:
10x Genomics
scGEX_162


title: TC4, Vehicle, tumor3

description:
10x Genomics
scGEX_161


title: SNU719, H3K27ac, Active Motif, rep 2


title: TC5, Vehicle, tumor1

description:
10x Genomics
scGEX_166


title: SNU719, H3K27ac, Active Motif, rep 1


title: YCC10, H3K4me1, CST, rep 2


title: YCC10, H3K4me1, CST, rep 1


title: S. pombe, H2BE75Q, rep2

address: 江苏省南京市仙林街道南京师范大学

description:
WT-vs-H2BE75Q.all.annot.txt
WT-vs-H2BE75Q.filter.annot.txt


title: TC4, Vehicle, tumor1

description:
10x Genomics
scGEX_159


title: TC4, Vehicle, tumor2

description:
10x Genomics
scGEX_160


title: S. pombe, H2BE75Q, rep3

address: 江苏省南京市仙林街道南京师范大学


title: SNU719, H3K4me1, CST, rep 2


title: Control group (no pollen), mouthparts [CH2]

source_name: Control group (no pollen), mouthparts

value: Control group (no pollen)


title: TC3, SOS1i+MEKi, tumor4

description:
10x Genomics
scGEX_158


title: Collection group (Olea europaea pollen), tentacles [YC3]

value: tentacles


title: Control group (no pollen), mouthparts [CH1]


title: S. pombe, H2BE34K, rep3

address: 江苏省南京市仙林街道南京师范大学

description:
WT-vs-H2BE34K.all.annot.txt
WT-vs-H2BE34K.filter.annot.txt


title: YCC10, HiChIP

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
HiChIP reads were aligned to hg38 reference human genome, using bowtie2(v2.3.3.1)
Valid interactions were conducted from the mapped sequence reads by HiC-Pro (v2.11.4)
Assembly: hg38
Supplementary files format and content: HiC
Library strategy: HiChIP

growth_protocol: For GES1 and SNU719, RPMI1640, 10% fetal bovine serum, 1×penicillin/streptomycin. Cells were cultureed at 37C at 5% CO2; For YCC10, EMEM, 10% fetal bovine serum, 1×penicillin/streptomycin. Cells were cultureed at 37C at 5% CO2

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using Covaris E220
HiChIP libraries were prepared using Nextera XT DNA Library Preparation Kit (#FC-131-1096) following the manufacturer’s protocol.

tag: antibody


title: Collection group (Olea europaea pollen), tentacles [YC2]


title: SNU719, H3K4me1, CST, rep 1


title: TC3, SOS1i+MEKi, tumor3

description:
10x Genomics
scGEX_157


title: TC3, SOS1i+MEKi, tumor2

description:
10x Genomics
scGEX_156


title: S. pombe, H2BE34K, rep2

address: 江苏省南京市仙林街道南京师范大学


title: SNU719, HiChIP


title: Collection group (Olea europaea pollen), tentacles [YC1]


title: Control group (no pollen), mouthparts [CH3]


title: TC3, Vehicle, tumor3

description:
10x Genomics
scGEX_154


title: S. pombe, H2BE34K, rep1

address: 江苏省南京市仙林街道南京师范大学


title: Collection group (pear pollen), tentacles [LC3]


title: S. pombe, H2BD67N, rep3

address: 江苏省南京市仙林街道南京师范大学

description:
WT-vs-H2BD67N.all.annot.txt
WT-vs-H2BD67N.filter.annot.txt


title: shZDHHC20_3

city: Changsha

first: Huaiyuan

last: Liang

address: 183 Renmin Middle Road

institute: Institute of Urological Cancer, Central South University

data_processing:
Total RNA qualification
mRNA enrichment
Double-strand cDNA synthesis
End repair, ploy-A & adaptor addition
Fragment selection and PCR
Library qualty assessement
illumina sequencing
Assembly: hg19
Supplementary files format and content: tab-delimited text files include read count values for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: pancreas

growth_protocol: PANC-1 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and incubated at 37 °C in 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent (#15596026, Invitrogen, USA). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: pancreas

value: PANC-1 cells

value: pancreatic cancer cells

value: the treat group of knockdown of ZDHHC20 by shRNA

value: transfection infection


title: Collection group (pear pollen), tentacles [LC2]


title: GES1, HiChIP

value: Human gastric epithelial cell


title: TC3, SOS1i+MEKi, tumor1

description:
10x Genomics
scGEX_155


title: TC3, Vehicle, tumor2

description:
10x Genomics
scGEX_153

value: Vehicle


title: S. pombe, H2BD67N, rep2

address: 江苏省南京市仙林街道南京师范大学


title: shZDHHC20_2


title: TC3, Vehicle, tumor1

description:
10x Genomics
scGEX_152


title: Collection group (pear pollen), tentacles [LC1]


title: S. pombe, H2BD67N, rep1

address: 江苏省南京市仙林街道南京师范大学


title: shZDHHC20_1


title: Control group (no pollen), tentacles [CC2]

source_name: Control group (no pollen), tentacles


title: S. pombe, H2BE75Q, rep1

address: 江苏省南京市仙林街道南京师范大学


title: shControl_2

value: the control group of knockdown of ZDHHC20 by shRNA


title: S. pombe, WT, rep2

address: 江苏省南京市仙林街道南京师范大学


title: Control group (no pollen), tentacles [CC1]


title: Control group (no pollen), tentacles [CC3]


title: shControl_3


title: S. pombe, WT, rep1

address: 江苏省南京市仙林街道南京师范大学


title: 4T1 Cryo Lane3 MULTI

city: Palo Alto

first: Christopher

last: McGinnis

state: CA

address: Biomedical Innovations Building 4600, 240 Pasteur Drive

department: Pathology

institute: Stanford University

description: MULTI-seq

data_processing:
scRNA-seq library FASTQs were pre-processed using Cell Ranger version 6.0.0 (10x Genomics) and aligned to the mm-10-3.0.0 reference transcriptome.
MULTI-seq FASTQs were processed using deMULTIplex2 (Zhu, Conrad, and Gartner, Genome Biology, 2024)
Assembly: mm10
Supplementary files format and content: Cellranger output files: mRNA barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: deMULTIplex2 output files: MULTI-seq count table csv

source_name: Lung

extract_protocol:
Lungs from PyMT or 4T1 tumor-bearing mice were surgically removed and dissociated using a custom dissociation media containing dispase, dnase I, and collagenase P. Single-cell suspensions were washed with PBS prior to barcoding with MULTI-seq lipid-modified oligonucleotides. Barcoded samples were pooled into BSA-containing PBS and stained with a live-dead stain and CD45, CD31, and Ter119 antibodies prior to FACS isolation of CD45+ CD31- Ter119- lung immune cells.
Libraries were prepared according to manufacturers instructions (10x Genomics V3.1) with a separate MULTI-seq library prep workflow performed following cDNA amplification, as described previously (McGinnis, Patterson, et al., Nature Methods, 2019)
scRNA-seq with MULTI-seq

value: Lung

value: Balb/c

value: 2, 4, 6, 8, 10, 12, 14, and 21 days post-transplant with 8, 14, and 21-day post-sham surgery and no-surgery controls


title: 4T1 Cryo Lane2 MULTI

description: MULTI-seq


title: 4T1 Cryo Lane4 MULTI

description: MULTI-seq


title: 4T1 Cryo Lane1 MULTI

description: MULTI-seq


title: shControl_1


title: Brain, Atx2_delta_PAM2, rep2

city: Mandi

first: Baskar

last: Bakthavachalu

state: Himachal Pradesh

address: Kamand

department: School of Biosciences and Bioengineering

country: India

institute: Indian Institute of Technology

description: TRIBE experimental samples

data_processing:
Sequencing Data obtained was processed similar to McMahon et al, 2016
Briefly the transcriptome data was mapped to dm6 genome using Tophat2
Uniquely mapped SAM file was converted to a matrix file.
A threshold of 20 reads and 15 percent editing was employed to identify editing events. Code for RNA editing analysis is available at (https://github.com/rosbashlab/TRIBE)
Genome_build: dm6
Supplementary_files_format_and_content: tab delimited text file reports RNA editing events

organism: Drosophila melanogaster

source_name: Brain

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: Brain

value: Ataxin-2 PAM2 Domain Deletion TRIBE


title: SNU719, 4C-seq, CRISPRi, sgCtrl, rep1

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
4C-seq reads were aligned to hg38 reference human genome quantified using w4Cseq.
Assembly: hg38
Supplementary files format and content: bedgraph
Library strategy: 4C-seq

growth_protocol: For SNU719, RPMI1640, 10% fetal bovine serum, 1×penicillin/streptomycin. Cells were cultured at 37C at 5% CO2; For YCC10, EMEM, 10% fetal bovine serum, 1×penicillin/streptomycin. Cells were cultured at 37C at 5% CO2

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10 min, quenched with 0.2 M of glycine, lysed with lysis buffer, and digested with primary restriction enzyme, DpnII. The digested DNA fragments were then subjected to ligation by using T4 DNA ligase (Roche). After digested with the second restriction enzyme, Csp6I, and circularization by T4 DNA ligase, the 4C template was amplified by a PCR reaction and purified with AMPure XP beads.
Extracted 4C templates were amplified with primers, which consist sequence of the bait MYB promoter region. After 1st PCR, amplified DNA was extracted using Ampure XP beads, and 2nd PCR using primers consist NGS adaptor sequence and index was performed. After 2nd PCR, the amplified 4C-seq library was extracted using QIAGEN PCR purification kit following the manufacturer's protocol.

value: Human gastric cancer


title: SNU719, 4C-seq, siTCF7, rep 1


title: PyMT Fresh Lane6 MULTI

description: MULTI-seq

value: FVB

value: PyMT and WT

value: 6, 10, and 13 weeks


title: SNU719, 4C-seq, CRISPRi, sgMYB, enhancer, rep1


title: PyMT Fresh Lane5 MULTI

description: MULTI-seq


title: HD17-V2D2, PBMC

city: Chicago

first: Kai

last: Huang

state: IL

address: 909 S. Wolcott Ave COMRB Room 3060

department: Medicine

institute: University of Illinois at Chicago

data_processing:
Sequence reads were trimmed for adaptor/low quality sequences using fastp with default settings.
Reads were mapped to hg38 and quantified using salmon v1.6.0 with default settings.
Reads were imported into a count matrix using the R package tximeta
Assembly: hg38
Supplementary files format and content: raw unormalized count matrix with all samples is supplied in csv format.

source_name: peripheral blood

extract_protocol:
PBMCs were extracted from heparinized blood using Ficoll-Paque PLUS (Cytiva) density gradient centrifugation. Extracted cells were preserved in -80 in RNAlater (Invitrogen). RNA was harvested using the PureLink RNA Mini kit (Invitrogen).
RNA libraries were prepared using 50ng of RNA with the NEBNext Ultra II Directional RNA Library Prep kit and NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) following manufacturer directions.

value: peripheral blood

value: PBMC

tag: time

tag: disease

value: hemodialysis

tag: batch

tag: sars cov2_hx

value: Yes

tag: age

tag: gender

value: Female

tag: diabetes


title: Brain, Atx2_delta_PAM2, rep1

description: TRIBE experimental samples


title: S. pombe, WT, rep3

address: 江苏省南京市仙林街道南京师范大学

value: WT


title: PyMT Fresh Lane4 MULTI

description: MULTI-seq


title: HD17-V2D0, PBMC


title: HD17-V1D7, PBMC


title: HD17-V2D7, PBMC


title: C10

city: Valencia

first: Patricia

last: Sebastian-Leon

state: Valencia

address: EDIFICIO BIOPOLO - LA FE, Avenida Fernando Abril Martorell, 106 - Torre A, Planta 1ª

department: Genomics and Systems Reproductive Medicine

country: Spain

institute: IVI-RMA Foundation

data_processing:
Raw data were trimmed using fastp (v0.21), evaluated using FastQC v0.11.5 tool for read quality process. STAR was employed for mapping quality data, using as reference human genome GRCh38 and obtaining raw counts.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample.

extract_protocol:
All endometrial biopsies were collected by endometrial aspiration using an intrauterine cannula (Cornier pipelle) and preserved in RNA Later (Invitrogen, ref. AM7021) until cryopreservation at -80ºC. Total RNA was extracted from the thawed endometrial biopsies using the miRNeasy Mini Kit (Qiagen, ref. 1038703), according to the instructions of the RNeasy FFPE Handbook protocol. The amount of total RNA isolated from the 24 tissues was quantifed with NanoDropTM One spectrophotometer (ThermoFisher) while RNA integrity was assessed using the Fragment Analyzer System (Agilent).
Sequencing libraries were constructed using the TruSeq stranded mRNA protocol (Illumina) following the manufacturer’s instructions.

value: Endometrium

value: benign gynecological disorders not related to endometrium

tag: menstrual phase

value: Early secretory


title: PyMT Fresh Lane3 MULTI

description: MULTI-seq

value: Lung

tag: strain


title: C9

value: Late secretory


title: HD17-V1D2, PBMC


title: PyMT Fresh Lane2 MULTI

description: MULTI-seq


title: SNU719, 4C-seq, siCtrl, rep 1

tag: cell line

value: siCtrl


title: M2584_KO_TAC

city: Los Angeles

first: Yao Wei

last: Lu

address: 2011 Zonal Ave

department: Department of Medicine

institute: University of Southern California

data_processing:
FASTQ files were extracted and sequencing adapters and low-quality reads were removed by Cutadapt (v.2.3)
Quality of the processed FASTQ files were checked by FastQC (Babraham Bioinformatics), then aligned to the mouse genome (Esembl GRCm38 genome obtained from GENCODE) using HISAT2 (v.2.1.0)
EdgeR (v.3.26.1) was used to identify differentially expressed genes.
Assembly: Esembl GRCm38.102
Supplementary files format and content: CSV, raw counts of sequencing reads on the gene level

source_name: Heart

growth_protocol: All animal experiments were approved by Ethnics Committee of Clinical Research and Experimental Animals of the First Affiliated Hospital of Sun Yat-sen University and the Institutional Animal Care and Use Committee at Boston Children’s Hospital.

extract_protocol:
Total RNA from the apex of heart was isolated using TRIzol (Invitrogen) from tissues using standard protocol.
Poly A-selected libraries were generated with the TruSeq RNA Library Preparation Kit (Illumina)
RNA-sequencing was processed by GENEWIZ using Illumina platform (paired-ended, 150bp read-length)

treatment_protocol: Mice with a body weight of 25-30g were anesthetized with isoflurane (3%–4% isoflurane for induction, 1%–2% isoflurane for maintenance). The chest was shaved and disinfected with alcohol. The chest was opened by left second intercostal thoracotomy. A 26-gauge needle was put on the ascending aorta. The needle and the ascending aorta were tightly ligated together using a 7-0 nylon suture at the transverse aorta, and the 26-gauge needle was removed immediately after ligation. In the sham operation, all procedures were the same except that no ligation was performed. Dissected intercostal space and chest skin were closed using a 6-0 silk suture. Mice genotypes were blinded to the surgeon. Samples were collected 4 weeks post surgery.

value: Heart

value: CARDINAL-KO

value: TAC


title: Mouse small intestine immune cells WT/Bmal1/Apc/Dko scRNA-seq 20220504

city: Irvine

first: Shannon

middle: M

last: Pfeiffer

address: 847 Health Sciences Rd, Room 3131

department: Biological Chemistry

institute: University of California, Irvine

description: 10x Genomics

data_processing:
Multiplexed, single cell gene expression libraries were sequenced on the Illumina HiSeq. Alignment of 3’ end counting libraries from scRNAseq analyses was completed utilizing 10× Genomics cellranger-6.1.2. Each library was aligned to an indexed mm10 genome using Cell Ranger Count.
Assembly: mm10
Supplementary files format and content: Zipped tabed-separated values barcodes, features, and matrix files.

source_name: small intestine

extract_protocol:
FACS-isolated CD45+ cells from the small intestine of WT, Bmal1-/-, Apc+/- and Apc+/-;Bmal1-/- mice (n=3 mice/genotype) were washed once in PBS with 0.04% BSA, and a total of 0.2-2x106  cells per genotype were used for cell multiplexing barcoding using the CellPlex Kit (10X Genomics), according to manufacturer’s instructions. Briefly, cells were pelleted after washing by centrifugating at 300 rcf, for 5 minutes at room temperature, and resuspended in 100 µl Cell Multiplexing Oligos (one oligo/barcode per genotype). Oligos were allowed to bind cell membranes by incubating at room temperature for 5 min, and unbound multiplexing oligos were washed 3 times with 2 ml ice-cold ml PBS + 1% BSA. After washing, cells were resuspended in chilled PBS + 1% BSA to a concentration of approximately 1,000 cell/μL, and loaded onto the 10X Genomics Chromium Controller for droplet-enabled scRNAseq according to the manufacturer’s instructions.
Library generation was performed following the Chromium NextGEM Single Cell v3.1 Cell Multiplexing Reagents Kits User Guide: CG000388Rev B. A total of 3 libraries were generated, each of them consisting of a pool of equal cell numbers from CD45+ cells from the small intestine of each genotype.

value: small intestine

tag: cell type

value: CD45+ immune cells

value: wild type, Bmal1-/-, Apc+/-, Apc+/-;Bmal1-/-


title: Mouse small intestine immune cells WT/Bmal1/Apc/Dko scRNA-seq 20220328

description: 10x Genomics


title: C8

value: Proliferative


title: Mouse small intestine immune cells WT/Bmal1/Apc/Dko scRNA-seq 20220505

description: 10x Genomics


title: PyMT Fresh Lane1 MULTI

description: MULTI-seq

value: FVB

value: PyMT and WT

tag: treatment

value: 6, 10, and 13 weeks


title: M3468_KO_TAC

tag: genotype


title: HD12-V2D7, PBMC

value: peripheral blood

value: PBMC

value: hemodialysis

value: No

value: Male

value: Yes


title: PyMT Cryo Lane 9 MULTI

description: MULTI-seq

value: Lung

value: 6-14 weeks


title: M3436_KO_TAC

value: Heart

value: CARDINAL-KO


title: C7

value: Endometrium

value: benign gynecological disorders not related to endometrium


title: HD12-V2D2, PBMC


title: C5


title: PyMT Cryo Lane 7 MULTI

description: MULTI-seq


title: M2589_Control_TAC

value: WT

value: TAC


title: C14

value: Proliferative


title: HD12-V1D7, PBMC


title: PyMT Cryo Lane 8 MULTI

description: MULTI-seq

value: FVB

value: PyMT and WT


title: M2588_Control_TAC


title: HD12-V2D0, PBMC

value: peripheral blood


title: PyMT Cryo Lane 6 MULTI

description: MULTI-seq


title: HD17-V1D0, PBMC

value: PBMC

value: Female


title: M2587_Control_TAC


title: HD12-V1D2, PBMC

value: hemodialysis

value: No


title: HD12-V1D0, PBMC

value: Male

value: Yes


title: C11

value: Early secretory


title: PyMT Cryo Lane 4 MULTI

description: MULTI-seq

value: Lung

value: 6-14 weeks


title: C12

value: Endometrium


title: HD11-V2D7, PBMC


title: M3473_Control_TAC

value: Heart


title: COV14

value: Amenhorrea


title: PyMT Cryo Lane 3 MULTI

description: MULTI-seq


title: HD11-V2D2, PBMC


title: M3433_KO_TAC

value: CARDINAL-KO

value: TAC


title: M3336_KO_Sham

value: Sham


title: HD11-V2D0, PBMC


title: PyMT Cryo Lane 1 MULTI

description: MULTI-seq

value: FVB

value: PyMT and WT


title: PyMT Cryo Lane 2 MULTI

description: MULTI-seq


title: COV15


title: C3

value: benign gynecological disorders not related to endometrium

value: Proliferative


title: HD11-V1D7, PBMC

value: peripheral blood

value: PBMC

value: hemodialysis

value: Female


title: COV7


title: COV11

value: Late secretory


title: M3335_KO_Sham


title: PyMT Cryo Lane 5 MULTI

description: MULTI-seq

value: Lung


title: HD11-V1D2, PBMC

value: No


title: M3332_KO_Sham


title: COV6

value: Endometrium


title: 4T1 Cryo Lane4

description: 10x Genomics

molecule: polyA RNA

value: Balb/c

value: WT

value: 2, 4, 6, 8, 10, 12, 14, and 21 days post-transplant with 8, 14, and 21-day post-sham surgery and no-surgery controls


title: HD11-V1D0, PBMC


title: M3324_Control_Sham

value: Heart


title: COV13


title: 4T1 Cryo Lane3

description: 10x Genomics


title: M3216_Control_Sham

value: Sham


title: M3432_KO_Sham

value: CARDINAL-KO


title: HD9-V2D7, PBMC

value: Yes


title: 4T1 Cryo Lane2

description: 10x Genomics


title: M3206_Control_Sham


title: 4T1 Cryo Lane1

description: 10x Genomics


title: HD9-V2D2, PBMC


title: PyMT Fresh Lane6

description: 10x Genomics

value: FVB

value: PyMT and WT

value: 6, 10, and 13 weeks


title: M3635_Control_Sham


title: Group-14-184-PanO2

city: Baltimore

first: Elana

middle: Judith

last: Fertig

state: MD

address: 670 W. Baltimore Street, 3rd floor

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

data_processing:
The adapter and low quality sequences were trimmed by Trimmomatic-0.36 software.
The reads from the clean data after trimming were mapped to reference genes (ENSEMBL GRCm38.84) by Bowtie-0.12.9 software
The gene expression was calculated by MMSEQ_1.0.2 software.
Genome_build: ESEMBL GRCm38.84
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and sample

source_name: Subcutaneous Pan02 tumors

growth_protocol: Mice were euthanized at end of treatment or when tumors reached 1-2 cm3 for mT3-2D tumors or 3 cm3 for other tumors or when mice showed signs of pain or distress, via CO2 inhalation. Volume was calculated using (length × width 2)/2.

extract_protocol:
Subcutaneous Pan02 tumors were collected in RNAlater after 1, 7 or 14 days of BXCL701 or PBS treatment. RNA was extracted from each sample using RNeasy mini kit (QAIGEN, Cat. 74106).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were injected into the right flank of C57BL/6J or Balb/c wild-type mice. Mice were given either 20 ug BXCL701 daily by oral gavage or 200ug of anti-PD1 (clone: RMP1-14, BioXcell) twice per week by intraperitoneal (i.p.) injection or both.

tag: group

tag: animal id

tag: dose level (mg/kg)

value: 20 ug/ mouse

tag: dosing frequency & duration

value: QD*14 Days

tag: harvest time (day/h)

value: Day14 / 16hr


title: PyMT Fresh Lane5

description: 10x Genomics

tag: tissue


title: Group-14-144-PanO2


title: HD9-V1D2, PBMC

value: peripheral blood

value: PBMC

tag: time

tag: disease

value: hemodialysis

tag: batch

value: Female


title: COV8

value: Endometrium

tag: age

value: Late secretory


title: Group-14-065-PanO2


title: PyMT Fresh Lane4

description: 10x Genomics

value: Lung


title: HD9-V1D0, PBMC

tag: sars cov2_hx

tag: gender

tag: diabetes

value: No


title: HD9-V2D0, PBMC


title: Group-13-177-PanO2

value: Day14 / 8hr


title: PyMT Fresh Lane2

description: 10x Genomics

tag: strain


title: COV1

tag: menstrual phase

value: Proliferative


title: PyMT Fresh Lane3

description: 10x Genomics

tag: treatment


title: PyMT Fresh Lane1

description: 10x Genomics

tag: genotype


title: Group-13-121-PanO2

tag: group


title: PyMT Cryo Lane 9

description: 10x Genomics

value: 6-14 weeks


title: HD8-V2D7, PBMC

tag: cell type

value: Male


title: Group-13-095-PanO2

tag: animal id

tag: dose level (mg/kg)


title: HD8-V2D2, PBMC


title: HD8-V2D0, PBMC


title: COV3

value: Early secretory


title: PyMT Cryo Lane 8

description: 10x Genomics

value: FVB

value: PyMT and WT


title: Group-12-140-PanO2

value: 20 ug/ mouse

tag: dosing frequency & duration

value: QD*14 Days

tag: harvest time (day/h)

value: Day14 / 1hr


title: Group-12-164-PanO2


title: PyMT Cryo Lane 7

description: 10x Genomics

tag: tissue


title: HD8-V1D2, PBMC

value: peripheral blood

value: PBMC

tag: time

tag: disease


title: HD9-V1D7, PBMC

value: hemodialysis

tag: batch

value: Yes

tag: age

value: Female


title: PyMT Cryo Lane 6

description: 10x Genomics

value: Lung


title: Group-12-127-PanO2


title: HD8-V1D0, PBMC

tag: sars cov2_hx

value: No

tag: gender


title: PyMT Cryo Lane 5

description: 10x Genomics

tag: strain


title: HD7-V2D7, PBMC

tag: diabetes


title: Group-11-150-PanO2

tag: treatment

value: Day14 / 0hr


title: Group-11-098-PanO2


title: PyMT Cryo Lane 4

description: 10x Genomics

tag: genotype


title: HD7-V2D2, PBMC


title: PyMT Cryo Lane 3

description: 10x Genomics


title: HD7-V2D0, PBMC


title: HD7-V1D7, PBMC


title: PyMT Cryo Lane 2

description: 10x Genomics


title: Group-10-161-PanO2

tag: group

value: Vehicle


title: Group-11-056-PanO2


title: Group-10-073-PanO2


title: HD8-V1D7, PBMC

tag: cell type


title: Group-09-181-PanO2

tag: animal id

value: QD*7 Days

value: Day7 / 16hr


title: HD7-V1D0, PBMC


title: METTL3-Flox-4 mouse, I/R 6h

city: Wu Han

first: jun

last: gong

state: Hu Bei

address: 1095 Jiefang Ave

institute: Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text fles include FPKM values for each Sample

source_name: liver

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 μg of total RNA was used for the construction of sequencing libraries.
RNA libaries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Hepatocyte-specific METTL3 knockdown (METTL3-HKD) mice and METTL3-Flox mice were subjected to 1 h of ischemia and subsequent reperfusion for 6 h.

value: liver


title: Group-09-143-PanO2

tag: dose level (mg/kg)


title: METTL3-Flox-2 mouse, I/R 6h

value: 1 h of ischemia and subsequent reperfusion for 6 h


title: METTL3-Flox-3 mouse, I/R 6h


title: HD6-V2D7, PBMC


title: HD6-V2D0, PBMC


title: HD6-V1D7, PBMC


title: Group-09-103-PanO2

tag: dosing frequency & duration


title: METTL3-HKD-4 mouse, I/R 6h

value: Hepatocyte-specific METTL3 knockdown


title: Group-08-162-PanO2

value: 20 ug/ mouse

tag: harvest time (day/h)

value: Day7 / 8hr


title: METTL3-HKD-3 mouse, I/R 6h

tag: tissue


title: Group-10-119-PanO2

value: QD*14 Days


title: METTL3-HKD-2 mouse, I/R 6h


title: HD7-V1D2, PBMC

value: peripheral blood

tag: time


title: PyMT Cryo Lane 1

description: 10x Genomics

value: FVB

value: PyMT and WT

value: 6-14 weeks


title: HD5-V2D7, PBMC

value: PBMC

tag: disease

value: hemodialysis

value: Yes

value: Male


title: HD6-V1D0, PBMC

tag: batch

value: Female


title: Group-08-141-PanO2

value: QD*7 Days


title: KO_3

city: Saint-Hyacinthe

first: Nour

last: Abou Nader

state: Québec

address: 3200 rue sicotte

department: Biomédecine vétérinaire

country: Canada

institute: Université de Montréal

data_processing:
Gene expression was obtained using the RNA-seq quantitation pipeline in SeqMonk NGS visualization and analysis tool (v1.48.1, Babraham Institute)
Gene expression was normalized into reads per kilobase of transcripts per million mapped reads (RPKM) values and log2 tranformed using SeqMonk
DeSeq2 version 1.22.2  was then used to detect differential expression. Thresholds used for P-value and fold change were 0.05 and ±1.5 or ±2
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Testes

extract_protocol:
Whole testes conserved at -80 were defrozen and total RNA was extracted using the RNeasy Mini kit (Qiagen), according to the manufacturer’s instructions.
BAM files were generated from the IRIC sequencing platform using STAR

value: Testes

tag: Sex


title: Group-07-153-PanO2

value: Day7 / 1hr


title: HD5-V2D2, PBMC

tag: sars cov2_hx

tag: age


title: KO_2


title: FO B cells stimulated with CpG plus IFNa (CpG + IFNa), rep3

city: Fukuoka

first: Ryota

last: Higuchi

address: Maidashi, 3-1-1

institute: Kyushu university

data_processing:
Read1(barcode read) was extracted by using UMI-tools (ver. 1.1.2) with the following command “umi_tools extract -I read1.fastq --read2-in=read2.fastq --bc-pattern=NNNNNNNNNNCCCCCCCCC --read2-stdout”.
Adaptor sequence and low-quality sequence were removed and read length below 20bp were discarded by using Trim Galore (ver. 0.6.7), and reads were mapped to the GRCm38 reference using HISAT2 (ver. 2.2.1).
Read counts for each genes was obtained by featureCounts(ver. 2.0.1) and UMI duplication is removed by UMI-tools with following command “umi_tools count --method=unique --per-gene --per-cell --gene-tag=XT”. Tlr9 reference was then extended by 3 kbp to add UTR reads to the counts.
Assembly: GRCm38
Supplementary files format and content: compressed tab separated files(.tsv.gz, .txt.gz)

extract_protocol:
RNA was extracted from cells using miRNeasy Micro Kit (Qiagen).
BRB-seq(Alpern D et al.) was performed for library preparation with some following modifications. Barcoded dT primer(5’-GCCGGTAATACGACTCACTATAGGGAGTTCTACAGTCCGACGATCNNNNNNNNNNCCCCCCCCCTTTTTTTTTTTTTTTTTTTTTTTTV -3’ ; (10)N=UMI, (9)C=cell barcode) was used for reverse transcription. Second Strand Synthesis Module (NEB, #E6111) was used for double-stranded cDNA synthesis. In-house MEDS-B Tn5 transposase (Picelli S et al., Sato et al.) was used for tagmentation and libraries were amplified by 10 cycles of PCR using Phusion High-Fidelity DNA Polymerase(Thermo Scientific, #M0530) with following primers(5’ -AATGATACGGCGACCACCGAGATCTACACindexGTTCAGAGTTCTACAGTCCGA-3',5’-CAAGCAGAAGACGGCATACGAGATindex GTCTCGTGGGCTCGGAGATGT-3').

value: B cells

value: Stimulated with CpG plus IFNa for 12 hours


title: Group-07-142-PanO2

value: 20 ug/ mouse


title: METTL3-HKD-1 mouse, I/R 6h

value: liver

value: Hepatocyte-specific METTL3 knockdown

value: 1 h of ischemia and subsequent reperfusion for 6 h


title: HD5-V2D0, PBMC

value: peripheral blood

tag: gender


title: KO_1


title: Group-06-183-PanO2

value: Day7 / 0hr


title: FO B cells stimulated with CpG plus IFNa (CpG + IFNa), rep1


title: Group-07-129-PanO2


title: CONT_3


title: FO B cells stimulated with CpG plus IFNa (CpG + IFNa), rep2


title: METTL3-Flox-1 mouse, I/R 6h


title: HD5-V1D7, PBMC

tag: diabetes


title: HD6-V1D2, PBMC

tag: treatment


title: Group-08-163-PanO2

value: Day7 / 8hr


title: HD5-V1D2, PBMC

value: PBMC


title: CONT_2

tag: genotype


title: FO B cells stimulated with CpG (CpG), rep3

value: Stimulated with CpG for 12 hours


title: FO B cells stimulated with CpG (CpG), rep2


title: Group-06-139-PanO2

tag: group


title: Group-06-125-PanO2


title: HD5-V1D0, PBMC

tag: cell type

value: hemodialysis

value: Yes


title: CONT_1

value: Male


title: C9orf72,mut,female,S35863_2

city: Munich

first: Paul

last: Lingor

address: Ismaninger Str. 22

department: Department of Neurology – Lingor Lab

country: Germany

institute: Rechts der Isar Hospital of the Technical University Munich

data_processing:
NextFlow Core smRNASeq pipeline, version 1.0
Reads trimmed and aligned against miRBase using Bowtie1, both for mature miRNA and hairpins.
miRNAs with at least ten counts in 50% of the samples of any condition and sex were kept and the rest were filtered out.
Data was log2 transformed and quantile normaliued
Assembly: miRBase (version 22.1)
Supplementary files format and content: Quantile normalized count matrix for hairpin sRNAs

source_name: Mouse prefrontal cortex

extract_protocol:
Total RNA was isolated from human and animal prefrontal cortex samples using Trizol Reagent (Sigma Aldrich, Taufkirchen, Germany). All RNA-related experiments were performed under an RNA-workstation fume hood. Briefly, 500 μl of TRI Reagent was added to each sample and tissues were homogenized using plastic homogenizer, followed by addition of 50μl of 1-Bromo-3-Chlor-Propane (Sigma Aldrich, Taufkirchen, Germany). The reaction tubes were mixed by inversion for 10 - 15 seconds and incubated at room temperature for 3 minutes. The lysates were centrifuged at 12.000 x g for 15 minutes / 4°C, leading to phase separation. The RNA-containing aqueous phase was collected and transferred to a fresh Nuclease-free tube. RNA precipitation was performed by adding 250 μl of 2-propanol (AppliChem, Darmstadt, Germany) and 2 μl GlycoBlue Co-precipitant (15 mg/ml) (ThermoFisher, Waltham, MA, USA), followed by mixing and overnight incubation at -20°C. The day after, samples were centrifuged at 12.000 x g for 30 minutes / 4°C, the supernatant was discarded and the RNA pellets were washed three times with 75% ice-cold ethanol (AppliChem, Darmstadt, Germany). The pellets were air-dried for a few minutes under the fume hood. Pellets were reconstituted with 15-20 μl of Nuclease-free water (Sigma Aldrich, Taufkirchen, Germany) followed by 2 minutes of incubation at 55°C in a thermoshaker in order to completely dissolve the RNA. After the RNA isolation, a DNAse treatment was performed in order to remove any DNA contamination from the samples. For that, 5μl of 10X DNAse I Incubation buffer (LifeTechnologies, Carlsbad, CA, United States), 5μl DNase I (2U/μL) and 0.5μl - RNase OUT (40U/μl) were added to each sample. Samples volume was filled up to 50 μl by the addition of Nuclease-free water, followed by incubation at 37°C for 20 minutes. Finally, the RNA samples were cleaned and concentrated with the RNAClean & Concentrator-5 KIT (Zymo Research, Irvine, CA, USA), following the manufacturer’s instructions. Directly after RNA / DNA isolation, nucleic acid concentration and purity were measured in the NanoDrop One spectrophotometer (ThermoFisher, Waltham, MA, USA). RNA integrity was assessed with the Agilent 6000 NanoKit in the 2100 Bioanalyzer (Agilent).
small RNA sequencing experiments were performed in the Functional Genomics Center in Zurich. Total RNA libraries were prepared using the SMARTer® Stranded Total RNA-Seq Kit v2 -Pico Input Mammalian (A Takara Bio Company, California, USA)(Short Read Sequencing). Total RNA samples (0.25–10 ng) were reverse-transcribed using random priming into double-stranded cDNA in the presence of a template switch oligo (TSO). This results in a cDNA fragment that contains sequences derived from the random priming oligo and TSO. PCR amplification using primers binding to these sequences adds full-length Illumina adapters, including the index for multiplexing. Ribosomal cDNA is cleaved by ZapR in the presence of the mammalian-specific R-Probes. Remaining fragments are enriched with a second round of PCR amplification using primers designed to match Illumina adapters. The product was a smear with an average fragment size of approximately 360 bp. These libraries were normalized to 5nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20. The quality and quantity of the isolated RNA and the enriched libraries were validated using the Tapestation (Agilent, Waldbronn, Germany).

value: Mouse prefrontal cortex

tag: strain

tag: condition

value: mut

value: female


title: HD4-V2D2, PBMC

value: No


title: Group-05-179-PanO2

tag: animal id

value: Vehicle

tag: dose level (mg/kg)

tag: dosing frequency & duration

value: QD*7 Days


title: FO B cells stimulated with IFNa (IFNa), rep3

tag: tissue

value: B cells

value: Stimulated with IFNa for 12 hours


title: HD4-V2D7, PBMC

tag: time

tag: disease


title: FO B cells stimulated with CpG (CpG), rep1


title: Group-05-174-PanO2

tag: harvest time (day/h)


title: C9orf72,mut,female,S35863_1

tag: Sex


title: HD4-V2D0, PBMC

tag: batch

tag: sars cov2_hx

tag: age


title: C9orf72,mut,male,S35850_5

value: male


title: FO B cells stimulated with IFNa (IFNa), rep2

tag: treatment


title: Group-05-169-PanO2


title: HD4-V1D7, PBMC

value: peripheral blood

tag: gender

tag: diabetes


title: C9orf72,mut,female,S35828_4


title: Group-04-175-PanO2

tag: group

value: 20 ug/ mouse

value: Single dose

value: Day1 / 16hr


title: HD4-V1D2, PBMC

tag: cell type

value: PBMC


title: C9orf72,mut,male,S35828_2

tag: strain

tag: condition


title: Unstimulated FO B cells (Unstimulated), rep3

value: Unstimulated


title: FO B cells stimulated with IFNa (IFNa), rep1


title: Group-04-128-PanO2

tag: animal id

tag: dose level (mg/kg)


title: C9orf72,mut,male,S35828_1

tag: tissue


title: HD2-V2D7, PBMC

tag: time

value: hemodialysis

value: Yes


title: Group-04-105-PanO2

tag: dosing frequency & duration


title: HD4-V1D0, PBMC

tag: disease

value: Male


title: Unstimulated FO B cells (Unstimulated), rep2


title: Group-03-180-PanO2

tag: harvest time (day/h)

value: Day1 / 8hr


title: Unstimulated FO B cells (Unstimulated), rep1


title: C9orf72,mut,male,S35483_1

value: Mouse prefrontal cortex

value: mut

tag: Sex


title: HD2-V2D0, PBMC

tag: batch

tag: sars cov2_hx

value: No


title: Group-03-173-PanO2

tag: treatment


title: C9orf72,mut,female,S34176_2

value: female


title: Liver_Doxorubicin_5

city: china

first: Yao

last: Tao

state: zhejiang

address: zhejiang province

institute: First Affiliated Hospital, Zhejiang University

data_processing:
Reads with phred quality scores less than 20 and less than 35 bp after trimming were removed from further analysis using trimgalore version 0.4.1. Quatilty-filtered reads were then aligned to the mouse reference genome GRCm38 (mm10) using the HISAT (v 2.0.1) aligner using default settings and marked duplicates using Sembamba version 0.6.6. Aligned reads were quantified using ‘featurecount’ (v1.4.6) per gene ID against mouse Gencode version 20. Generation of normalized counts and analysis of differential gene expression was done using the R package EdgeR.
Assembly: mm10
Supplementary files format and content: text files of normalized counts for every sample and every gene.

source_name: Liver

growth_protocol: 8-week-old C57BL/6J male mice were randomized into indicated groups before the treatments, respectively.

extract_protocol:
Total RNA was isolated from freshly frozen liver tissues from the mice treated with indicated chemotherapy agents by TRIzol reagent (#T9424, Invitrogen).
RNA library for RNA-seq was prepared as following: mRNA was purified from total RNA using polyT and then fragmented into 300~350 bp fragments. The first strand cDNA was reverse-transcribed using fragmented RNA and dNTPs (dATP, dTTP, dCTP and dGTP) and second strand cDNA synthesis was subsequently performed. Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, sequencing adaptors were ligated to the cDNA and the library fragments were purified. The template was enriched by PCR, and the PCR product was purified to obtain the final library. After library construction, the concentration of library was measured by the Qubit fluorometer. The accurate concentration of cDNA library was again examined using qPCR. The size distribution of library was detected by agarose gel electrophoresis.

treatment_protocol: The chemotherapy agents were delivered via intraperitoneal (i.p.) administration and dosed once: doxorubicin (2 mg/mL in sterile water; 10 mg/kg body weight)

value: Liver;

value: Doxorubicin for 1 day


title: Group-03-159-PanO2


title: Liver_Doxorubicin_3

value: Liver


title: Group-02-185-PanO2

value: Day1 / 1hr


title: C9orf72,ctrl,male,S35863_3

value: ctrl

value: male


title: Liver_Doxorubicin_4

treatment_protocol: The chemotherapy agents were delivered via intraperitoneal (i.p.) administration and dosed once: doxorubicin (2 mg/mL in sterile water; 10 mg/kg body weight).


title: Liver_Doxorubicin_2


title: C9orf72,ctrl,male,S35850_6


title: Liver_Doxorubicin_1


title: Group-02-176-PanO2

value: 20 ug/ mouse

value: Single dose


title: C9orf72,ctrl,male,S35850_4


title: Group-02-182-PanO2


title: Liver_Cisplatin_5

treatment_protocol: The chemotherapy agents were delivered via intraperitoneal (i.p.) administration and dosed once: cisplatin (1 mg/mL in 0.9% saline; 10 mg/kg body weight).

value: Cisplatin for 1day


title: HD10-V2D7, PBMC

value: peripheral blood

value: PBMC

value: hemodialysis

tag: age

tag: gender


title: Group-01-167-PanO2

tag: group

value: Vehicle

value: Day1 / 0hr


title: C9orf72,mut,male,S35483_2

value: Mouse prefrontal cortex

value: mut


title: HD2-V1D0, PBMC

tag: cell type

value: Yes

value: Male

tag: diabetes

value: No


title: HD2-V2D2, PBMC


title: HD10-V2D2, PBMC


title: C9orf72,ctrl,female,S35850_3

tag: strain

tag: condition

value: female


title: Group-01-123-PanO2

tag: animal id

tag: dose level (mg/kg)


title: HD10-V2D0, PBMC

tag: tissue

tag: time


title: C9orf72,ctrl,female,S35850_2


title: C9orf72,mut,male,S34175_3


title: Liver_Cisplatin_3

treatment_protocol: The chemotherapy agents were delivered via intraperitoneal (i.p.) administration and dosed once:  cisplatin (1 mg/mL in 0.9% saline; 10 mg/kg body weight).

value: Liver;


title: HD2-V1D7, PBMC

tag: disease


title: Liver_Cisplatin_2

value: Cisplatin for 1 day


title: HD10-V1D7, PBMC


title: C9orf72,ctrl,male,S35828_3

value: ctrl

value: male


title: HD2-V1D2, PBMC


title: HD10-V1D2, PBMC


title: C9orf72,ctrl,female,S35483_6


title: Liver_Cisplatin_1


title: nrpe1_RIP_rep2

city: Guangzhou

first: Chen

last: Chen

state: Guangdong

address: 723 Xinke Rd.

institute: South China Botanical Garden, Chinese Academy of Science

data_processing:
adapters were removed from raw sequencing reads with cutadapt (version 3.4, -m 10)
ChIP-seq reads were mapped to the Arabidopsis genome (TAIR10) by Bowtie2 with default settings
PCR duplicates were removed by using samtools (for pair-end reads) or running the MACS2-filterdup program (for single-end reads)
To identify read-enriched regions (peaks), the MACS2 program was employed to perform peak calling with the following settings (-g 135000000, -nomodel, and -p 0.01).
Highly confident peaks were generated by running idr (2.0.3) (--idr-threshold 0.01) with biological replicates
bigWig files were generated using bamCoverage with RPGC normalization
Assembly: TAIR10
Supplementary files format and content: Bigwig files.

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Seeds were stratified in the dark at 4°C for 3 days before being sown on agar plates containing 2.22 g/L Murashige and Skoog basal medium with vitamins mix (Cat. M519, PhytoTech LABS), 1.5% sucrose (pH 5.75), and 0.8% agar. Plant growth was in long-day photoperiod (16h light/8h dark cycles) at 22°C

extract_protocol:
plants were crosslinked with 1% formaldehyde for 20 min under vacuum at room temperature and quenched with 0.125 M glycine under vacuum for an additional 5 min. Approximately 500 milligrams of tissues were used for each ChIP assay. The chromatin was sonicated using a Covaris M220 sonicator (peak power: 75; duty factor: 20; cycles/burst: 200) for 210 s at 6°C. The lysates were centrifuged at 18,000 g for 10 min at 4°C to remove debris. 10 µL of supernatant was used as the input sample, whereas the remaining supernatant was kept for the downstream procedure. 10 µL of Dynabeads Protein A (Cat. 10002D, ThermoFisher SCIENTIFIC) were added to each sample to prewash for 1 h at 4°C with gentle rotating. ChIP was carried out using antibodies as follows: anti-GFP (Cat. ab290, Abcam) and anti-Pol II CTD repeat YSPTSPS (Cat. ab817, Abcam). 40 µL of Dynabeads Protein A were mixed with 4 µL of antibodies and incubated for approximately 6 h on a rotator at 4°C to form antibody-bead complexes. Finally, ChIP-DNA were recovered by Phenol/chloroform extraction. Approximately 400 milligrams of seedlings were used per sample. Additionally, equal amounts of spike-in nuclei extracted from Saccharomyces cerevisiae were added to each sample before MNase treatment, which worked as the internal control among samples. For smRNA sequencing, total RNA was extracted from 10-day-old seedlings using TRIzol (Invitrogen, 15596-018). RNA samples were separated on a PAGE gel, and the 18- to 30-nt fraction of the gel was cut for small RNA purification. Library preparation and sequencing were performed using Illumina reagents according to the manufacturer’s instructions. For the bisulfite sequencing, the DNA was extracted from 10-day old seedlingds and directly sent to the NovoGene for whole-genome bisulfite sequencing (WGBS). For RNA immunoprecipitation followed sequencing (RIP-seq),
ChIP libraries were prepared by using the NEBNext® Ultra™ DNA Library Prep Kit (E7370S) following the manufacturer’s instructions, and subsequently used for Illumina

treatment_protocol: 10-day old seedlings

tag: cell line

value: seedlings

tag: antibody

value: anti-GFP


title: Liver_saline_5

treatment_protocol: Normal saline is administered intraperitoneally (IP) and administered once: the same dose as chemotherapy.

value: Liver

value: Saline for 1day


title: NRPE1GFP_RIP_rep2


title: Liver_Cisplatin_4

value: Cisplatin for 1day


title: C9orf72,ctrl,female,S34176_3

tag: Sex


title: Liver_saline_4


title: HD1-V2D0, PBMC

value: peripheral blood

value: PBMC

value: hemodialysis

tag: batch

tag: sars cov2_hx


title: RNA_WT_rep3


title: Liver_saline_3

tag: treatment

value: Saline for 1 day


title: RNA_WT_rep2


title: Group-01-050-PanO2

value: Vehicle

tag: dosing frequency & duration

value: Single dose

tag: harvest time (day/h)

value: Day1 / 0hr


title: HD1-V1D7, PBMC

tag: cell type

value: No

tag: age

tag: gender

value: Male


title: SOD1,mut,male,S1503

value: Mouse prefrontal cortex

tag: strain

tag: condition

value: mut


title: SOD1,mut,male,S1502

value: male


title: RNA_WT_rep1

value: seedlings


title: Liver_saline_1

value: Liver;


title: HD1-V1D2, PBMC

tag: diabetes


title: Liver_saline_2

tag: tissue


title: HD1-V1D0, PBMC

tag: time


title: SOD1,mut,male,S1458


title: spt6lNRPE1GFP_RIP_rep2

value: anti-GFP


title: HD10-V1D0, PBMC

tag: disease

value: Yes


title: HC9-V2D7, PBMC

value: healthy control


title: RNA_spt6l_rep2

tag: cell line


title: C9orf72,mut,female,S35863_2

data_processing:
NextFlow Core RNASeq pipeline, version 3.0
Salmon was used for pseudo alignment and quantitation
Filtering: keeping genes with at least ten counts in 50% of the samples of any condition and sex
DESeq2 for further normalization and VST transformation
Assembly: GRCm39 with annotations from GENCODE vM26
Supplementary files format and content: VST transformed count data

extract_protocol:
Total RNA was isolated from human and animal prefrontal cortex samples using Trizol Reagent (Sigma Aldrich, Taufkirchen, Germany). All RNA-related experiments were performed under an RNA-workstation fume hood. Briefly, 500 μl of TRI Reagent was added to each sample and tissues were homogenized using plastic homogenizer, followed by addition of 50μl of 1-Bromo-3-Chlor-Propane (Sigma Aldrich, Taufkirchen, Germany). The reaction tubes were mixed by inversion for 10 - 15 seconds and incubated at room temperature for 3 minutes. The lysates were centrifuged at 12.000 x g for 15 minutes / 4°C, leading to phase separation. The RNA-containing aqueous phase was collected and transferred to a fresh Nuclease-free tube. RNA precipitation was performed by adding 250 μl of 2-propanol (AppliChem, Darmstadt, Germany) and 2 μl GlycoBlue Co-precipitant (15 mg/ml) (ThermoFisher, Waltham, MA, USA), followed by mixing and overnight incubation at -20°C. The day after, samples were centrifuged at 12.000 x g for 30 minutes / 4°C, the supernatant was discarded and the RNA pellets were washed three times with 75% ice-cold ethanol (AppliChem, Darmstadt, Germany). The pellets were air-dried for a few minutes under the fume hood. Pellets were reconstituted with 15-20 μl of Nuclease-free water (Sigma Aldrich, Taufkirchen, Germany) followed by 2 minutes of incubation at 55°C in a thermoshaker in order to completely dissolve the RNA. After the RNA isolation, a DNAse treatment was performed in order to remove any DNA contamination from the samples. For that, 5μl of 10X DNAse I Incubation buffer (LifeTechnologies, Carlsbad, CA, United States), 5μl DNase I (2U/μL) and 0.5μl - RNase OUT (40U/μl) were added to each sample. Samples volume was filled up to 50 μl by the addition of Nuclease-free water, followed by incubation at 37°C for 20 minutes. Finally, the RNA samples were cleaned and concentrated with the RNAClean & Concentrator-5 KIT (Zymo Research, Irvine, CA, USA), following the manufacturer’s instructions. Directly after RNA / DNA isolation, nucleic acid concentration and purity were measured in the NanoDrop One spectrophotometer (ThermoFisher, Waltham, MA, USA). RNA integrity was assessed with the Agilent 6000 NanoKit in the 2100 Bioanalyzer (Agilent).
mRNA sequencing experiments were performed in the Functional Genomics Center in Zurich. For the mRNA sequencing, total RNA libraries were prepared using the TruSeq Stranded mRNA (Illumina, Inc, California, USA)(Short Read Sequencing). Briefly, total RNA samples (100-1000 ng) were poly-A enriched and then reverse-transcribed into double-stranded cDNA. The cDNA samples were fragmented, end-repaired and adenylated before ligation of TruSeq adapters containing unique dual indices (UDI) for multiplexing. Fragments containing TruSeq adapters on both ends were selectively enriched with PCR. This produces a smear with an average fragment size of approximately 260 bp. The libraries were normalized to 10nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20. The quality and quantity of the isolated RNA and the enriched libraries were validated using a Fragment Analyzer (Agilent, Santa Clara, California, USA).

value: female


title: SOD1,mut,male,S1183


title: HD1-V2D7, PBMC

value: peripheral blood

value: PBMC


title: C9orf72,ctrl,female,S35483_5

value: ctrl


title: C9orf72,ctrl,female,S34176_1


title: C9orf72,mut,female,S35863_1


title: RNA_spt6l_rep1

tag: antibody


title: C9orf72,mut,male,S35850_5

tag: Sex


title: SOD1,mut,female,S8921


title: smRNA-seq WT rep3

tag: chip antibody


title: HC9-V2D1, PBMC

tag: batch

tag: sars cov2_hx


title: SOD1,mut,female,S8919


title: HC9-V2D0, PBMC

tag: treatment


title: C9orf72,mut,female,S35828_4


title: smRNA-seq WT rep2


title: HC9-V1D7, PBMC


title: RNA_spt6l_rep3


title: SOD1,mut,female,S8917


title: C9orf72,mut,male,S35828_2


title: smRNA-seq WT rep1


title: HC9-V1D1, PBMC


title: C9orf72,mut,male,S35828_1


title: SOD1,mut,female,S8899


title: SOD1,mut,female,S8935


title: smRNA-seq spt6l rep3


title: C9orf72,mut,male,S35483_2


title: HC62-V2D7, PBMC

value: Female


title: smRNA-seq spt6l rep2


title: SOD1,ctrl,male,S1434


title: C9orf72,mut,male,S35483_1


title: smRNA-seq spt6l rep1


title: SOD1,ctrl,male,S2604


title: SPT6LdeltaWG Input


title: C9orf72,mut,female,S34176_2


title: HC62-V2D1, PBMC


title: SOD1,ctrl,male,S2608


title: SPT6LdeltaWG/GW IP rep2


title: HC62-V2D0, PBMC


title: C9orf72,mut,male,S34175_3


title: C9orf72,ctrl,male,S35863_3


title: SPT6LdeltaWG/GW IP rep1


title: HC62-V1D1, PBMC


title: HC9-V1D0, PBMC


title: SOD1,ctrl,male,S2605


title: C9orf72,ctrl,male,S35850_6


title: HC62-V1D0, PBMC


title: SOD1,ctrl,male,S2611


title: SOD1,ctrl,male,S2610


title: RIP-seq nrpe1

value: anti-GFP (Abcam, ab290)


title: C9orf72,ctrl,male,S35850_4


title: HC61-V2D7, PBMC


title: SOD1,ctrl,female,S8926


title: RIP-seq NRPE1-GFP spt6l


title: RIP-seq NRPE1-GFP


title: SOD1,ctrl,female,S8909


title: HC61-V2D1, PBMC


title: C9orf72,ctrl,female,S35850_2


title: HC61-V2D0, PBMC


title: SPT6L-GFP spt5l IP rep2


title: SPT6L-GFP spt5l IP rep1


title: SOD1,ctrl,female,S8908


title: SOD1,ctrl,female,S8905


title: C9orf72,ctrl,male,S35828_3


title: HC62-V1D7, PBMC


title: C9orf72,ctrl,female,S35483_6


title: HC61-V1D7, PBMC


title: SPT6L-GFP nrpe1 IP rep2


title: HC61-V1D1, PBMC


title: SOD1,ctrl,female,S8950


title: C9orf72,ctrl,female,S35483_5


title: TDP43,mut,male,S1845


title: SPT6L-GFP nrpe1 IP rep1


title: C9orf72,ctrl,female,S34176_3


title: HC61-V1D0, PBMC


title: C9orf72,ctrl,female,S35850_3


title: NRPE1-GFP spt6l IP rep2


title: TDP43,mut,female,S1843


title: NRPE1-GFP spt6l IP rep1


title: HC52-V2D7, PBMC


title: HC52-V2D0, PBMC


title: SOD1,mut,male,S1503


title: C9orf72,ctrl,female,S34176_1


title: TDP43,mut,female,S1840


title: HC52-V1D7, PBMC


title: spt6l input


title: TDP43,mut,female,S1835


title: NRPE1-GFP IP rep2


title: HC52-V1D1, PBMC


title: SOD1,mut,male,S1502


title: TDP43,mut,male,S1827


title: SOD1,mut,male,S1458


title: TDP43,mut,female,S1821


title: NRPE1-GFP IP rep1


title: SOD1,mut,male,S1183


title: HC49-V2D7, PBMC


title: nrpe1 input


title: TDP43,mut,male,S1816


title: SOD1,mut,female,S8921


title: NRPE1-GFP input


title: TDP43,mut,male,S1815


title: BS-seq WT rep2


title: SOD1,mut,female,S8919


title: HC49-V2D0, PBMC


title: TDP43,mut,male,S1814


title: HC49-V1D7, PBMC


title: BS-seq spt6l rep2


title: SOD1,mut,female,S8899


title: TDP43,mut,female,S1812


title: TDP43,ctrl,female,S0850


title: BS-seq spt6l rep1


title: BS-seq WT rep1


title: HC49-V1D0, PBMC


title: HC52-V1D0, PBMC


title: TDP43,ctrl,female,S0849


title: SOD1,ctrl,male,S1434


title: SOD1,mut,female,S8935


title: BS-seq spt6ldeltaWG/GW


title: HC48-V2D7, PBMC


title: SOD1,ctrl,male,S2604


title: TDP43,ctrl,female,S0848


title: TDP43,ctrl,female,S0847


title: HC48-V2D1, PBMC


title: HC49-V2D1, PBMC


title: SOD1,ctrl,male,S2608


title: SOD1,mut,female,S8917


title: BS-seq nrpe1 spt6l rep1


title: TDP43,ctrl,female,S0846


title: HC48-V2D0, PBMC


title: BS-seq nrpe1 rep2


title: HC48-V1D7, PBMC


title: HC49-V1D1, PBMC


title: SOD1,ctrl,male,S2605


title: TDP43,ctrl,male,S0845


title: TDP43,ctrl,male,S0844


title: SOD1,ctrl,male,S2611


title: HC48-V1D1, PBMC


title: HC48-V1D0, PBMC


title: SOD1,ctrl,female,S8926


title: TDP43,ctrl,male,S0843


title: Haloferax mediterranei R4, denitrifying, rep2

city: San Vicente del Raspeig

first: Jose

middle: María

last: Miralles-Robledillo

state: Alicante

address: Carretera San Vicente S/N

institute: Universidad de Alicante

data_processing:
Data quality of the sequencing data was carried out using FastQC v0.11.8
Sequence reads were trimmed for adaptors using Trimmomatic v0.39
Trimmed sequence reads were aligned to the reference genome using Bowtie2 v2.3.5.1 and SAM files were converted to BAM files and indexed using SAMtools
Quality of the alignment was checked by qualimap v.2.2.2 and, the count table was built with featureCounts v1.6.4
Differential expression analysis was performed using DESeq2 v1.24.0
Assembly: GCF_005406325.1
Supplementary files format and content: tab-delimited text files of the DESeq2 output

organism: Haloferax mediterranei

growth_protocol: Hfx. mediterranei strain R4 was grown in defined media supplemented with nitrate: 27.75 mM (0.5% w/v), glucose, 1 mM Pi (K2HPO4/KH2PO4), 15 mM NH4Cl, 10 mM KNO3, 0.03 mM FeCl3, 2.67 M NaCl, 0.16 M MgSO4·7H2O, 0.133 M MgCl2·6H2O, 53.33 mM KCl, 1.6 mM NaHCO3, 4.53 mM NaBr, 6.6 mM CaCl2 and buffered with 50 mM MOPS ((3-(N-morpholino) propanesulfonic acid). Cultures were established using two distinct methods: aerobiosis and denitrifying conditions, both at a pH of 7.3 (adjusted with NaOH) and a temperature of 42°C. The aerobic cultures were cultivated with agitation at 170 rpm and in a high air chamber occupying 90% of the flask volume. These cultures were allowed to reach an optical density at 600 nm (OD600 nm) of 0.2 before transitioning to denitrifying conditions. To create the denitrifying environment, the cultures were transferred to sealed bottles without an air chamber for 36 hours, preventing any gas exchange. All experimental cultures were carried out in triplicate.

extract_protocol:
RNA was harvested using QIAGEN RNeasy Kit and tretaed with DNAse. Subsequently, rRNA from samples was depleted using riboPOOL specific probes for Hfx. volcanii (siTOOLS Biotech)
Libraries were prepared using NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina according to the manufacturer's protocol

tag: genotype

value: WT

tag: growth condition

value: denitrifying


title: HC47-V2D7, PBMC

tag: cell type

value: No

tag: age


title: TDP43,ctrl,male,S0842

value: Mouse prefrontal cortex

tag: strain


title: BS-seq nrpe1 spt6l rep2


title: SOD1,ctrl,male,S2610

tag: condition


title: SOD1,ctrl,female,S8909


title: HC47-V2D1, PBMC

tag: gender

tag: diabetes


title: TDP43,ctrl,male,S0841

tag: tissue


title: BS-seq nrpe1 rep1


title: Haloferax mediterranei R4, denitrifying, rep1


title: SOD1,ctrl,female,S8908


title: Haloferax mediterranei R4, oxic, rep3

value: oxic


title: HC47-V1D7, PBMC

tag: time

tag: disease


title: SOD1,ctrl,female,S8905


title: FUS,ctrl,male,S586

value: male


title: FUS,ctrl,male,S781


title: Haloferax mediterranei R4, oxic, rep2


title: SOD1,ctrl,female,S8950


title: Haloferax mediterranei R4, oxic, rep1


title: FUS,ctrl,male,S780


title: HC47-V1D0, PBMC


title: Haloferax mediterranei R4, denitrifying, rep3


title: TDP43,mut,male,S1845

value: mut


title: FUS,ctrl,male,S776


title: HC44-V2D7, PBMC


title: mpglr-9 systemic 3

city: Madrid

first: Enrique

last: Rojo

state: Madrid

address: Darwin 3

department: Plant Molecular Genetics

institute: CSIC

data_processing:
reads were mapped to Genome build MpTak1v5.1 with HISAT2 and read counts per gene were measured using HTseq-count
Assembly: MpTak1v5.1
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

organism: Marchantia polymorpha

source_name: Thallus

growth_protocol: Plants were grown for 28 days on soil before the experiment.

extract_protocol:
Total RNA was extracted with Favorgen Total RNA Purification Mini Kit and treated with DNAse.
RNA sample was used for library preparation using NEB Next® Ultra RNA Library Prep Kit for Illumina®. Indices were included to multiplex multiple samples.
Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis.The library was ready after end repair, A-tailing, adapter ligation, and size selection. After amplification and purification, insert size of the library was validated on an Agilent 2100 and quantified using quantitative PCR (Q-PCR). Libraries were then sequenced on Illumina NovaSeq 6000 S4 flowcell with PE150 according to results from library quality control and expected data volume.

value: Thallus

value: systemic undamaged tissues of wounded plants


title: TDP43,mut,female,S1843


title: mpglr-9 systemic 2


title: HC44-V2D1, PBMC


title: HC44-V2D0, PBMC


title: mpglr-9 systemic 1


title: FUS,ctrl,female,S875


title: FUS,ctrl,female,S876


title: TDP43,mut,female,S1835


title: HC44-V1D7, PBMC


title: HC47-V1D1, PBMC


title: FUS,ctrl,female,S571


title: mpglr-9 wounded 2

value: damaged tissues of wounded plants


title: FUS,ctrl,female,S850


title: mpglr-9 wounded 3


title: TDP43,mut,male,S1827


title: HC44-V1D1, PBMC

value: healthy control


title: FUS,ctrl,female,S565

value: female


title: mpglr-9 wounded 1


title: TDP43,mut,female,S1821


title: HC44-V1D0, PBMC

value: peripheral blood


title: mpglr-9 control 3

value: Intact plants


title: TDP43,mut,male,S1816


title: HC43-V2D7, PBMC

value: PBMC


title: FUS,ctrl,male,S572

value: ctrl


title: TDP43,mut,male,S1815


title: HC43-V2D1, PBMC

value: Female


title: FUS,mut,male,S881


title: TDP43,mut,female,S1840


title: TDP43,mut,male,S1814


title: HC43-V2D0, PBMC


title: HC43-V1D7, PBMC


title: FUS,mut,male,S567


title: TDP43,ctrl,female,S0850


title: wild type systemic 3

value: WT


title: TDP43,mut,female,S1812


title: HC43-V1D1, PBMC


title: wild type systemic 2


title: TDP43,ctrl,female,S0849


title: FUS,mut,female,S782


title: wild type systemic 1


title: FUS,mut,male,S784


title: wild type wounded 3


title: FUS,mut,female,S785


title: mpglr-9 control 2


title: HC42-V2D1, PBMC

value: Yes


title: TDP43,ctrl,female,S0847


title: wild type wounded 2


title: TDP43,ctrl,female,S0846


title: HC42-V2D7, PBMC

value: No


title: mpglr-9 control 1


title: FUS,mut,male,S578

value: Mouse prefrontal cortex


title: HC42-V2D0, PBMC


title: FUS,mut,female,S581


title: TDP43,ctrl,male,S0845


title: FUS,mut,female,S575


title: wild type wounded 1


title: HC42-V1D7, PBMC


title: wild type control 3


title: HC43-V1D0, PBMC


title: TDP43,ctrl,male,S0844


title: wild type control 2


title: FUS,mut,female,S574


title: HC42-V1D1, PBMC


title: TDP43,ctrl,female,S0848


title: ATAC SNU484

first: Michael

middle: A

last: Beer

address: 733 N. Broadway

department: Biomedical Engineering and Genetic Medicine

institute: Johns Hopkins University

data_processing:
Sequenced reads were mapped to the human genome assembly (hg38) using Bowtie2. Mitochondrial and viral reads were removed.
Peaks were called on each sample using MACS2 callpeak function.
Assembly: hg38
Supplementary files format and content: bigwig, bed

extract_protocol:
ATAC-seq was performed as described in Corces MR et al Nat Methods 2017. Cells were lysed in ATAC-resuspension buffer containing 0.5% NP40, 0.5 % Tween-20 and 0.01% Digitonin. Nuclei were then resuspended in 50 μl transposition mixture containing 25 μl of 2x TD buffer, 16.5 μl of PBS, 5 μl nuclease free water, 0.5 μl of 1% digitonin, 0.5 μl of 10% Tween-20 and 2.5 μl of transposase (Illumina Tagment DNA enzyme 1, #20034198) and incubated at 37°C for 30 minutes with agitation. DNA was extracted using the NEB Monarch® PCR & DNA cleanup kit (#T1030L) and used for PCR using the Illumina/Nextera primers. Library clean-up was performed using Ampure XP beads.
ATAC-seq: Libraries were sequenced on a NextSeq platform (Illumina).

tag: cell line

value: Gastric cancer cell line


title: TDP43,ctrl,male,S0843

tag: Sex

value: male


title: HC42-V1D0, PBMC


title: wild type control 1


title: HC41-V2D7, PBMC


title: ATAC YCC21


title: ATAC YCC10


title: ATAC SNU719


title: TDP43,ctrl,male,S0841


title: FUS,ctrl,male,S586


title: HC41-V2D1, PBMC


title: FUS,ctrl,male,S780


title: ATAC SNU1967


title: HC41-V2D0, PBMC


title: HC41-V1D7, PBMC


title: NoStress_Saline 4

city: Cardiff

first: Hannah

last: Scott

address: Hadyn Ellis Building, Maindy Road

department: UK Dementia Research Institute

country: United Kingdom

institute: Cardiff University

description:
NS_v_SM.csv
NS_v_SS.csv

data_processing:
For each sample, the data from both lanes were pooled before running the analysis pipeline. Alignment of the sequencing reads was performed via TopHat using the rat reference genome Rnor_6.0 (GenBank Assembly ID GCA_000001895.4). HTSeq was used to generate read counts from the resulting BAM files.
Differential expression analysis was performed using DESeq.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: CSV files containing the DESeq output, including mean counts per experimental condition, fold changes and p values, for every detected Ensembl ID and gene name. Processed data files are provided for every possible pair-wise comparison between the 3 experimental groups.

organism: Rattus norvegicus

source_name: Frontal cortex

growth_protocol: Female Sprague-Dawley rats (initial body weight: 240–250g; Charles River, Margate, Kent, UK) were maintained on ad libitum standard rat chow and filtered tap water under a 12:12-h light-dark cycle (lights on at 07:00h). Rats were group housed (4-6/cage) in individually ventilated cages until gestational day (GD) 16 and individually thereafter. All animal procedures were conducted in accordance with the UK Animals (Scientific Procedures) Act 1986 and the European Directive (2010/63/EU) and with institutional approval from the Roslin Institute Animal Welfare and Ethical Review Body at the University of Edinburgh.

extract_protocol:
RNA was extracted from 50 mg of foetal frontal cortex using the RNeasy Mini kit (Qiagen) and subjected on-column incubation with RNase-free DNase according to manufacturer’s protocol (Qiagen). RNA quality and integrity was measured on the 2100 Bioanalyzer (Agilent Technologies).
Libraries were prepared using the TruSeq Stranded mRNA Linrary Preparation Kit from Illumina.

treatment_protocol: On GD16, pregnant rats were weighed and 4% (w/w) lidocaine cream was applied topically to the tail prior to administration of either 0.9% sterile saline (vehicle; 0.34 ml/kg) or 125 µM nanoparticle-bound mitoquinone (MitoQ-NP; 0.34 ml/kg) i.v. into the tail vein. Approximately 1 h later, half of the vehicle and MitoQ-NP-treated rats were exposed to 10 min social stress, while the remainder served as non-stressed controls and remained undisturbed in their home cage.

tag: foetal age

tag: maternal exposure

value: No Stress

tag: maternal injection

value: Saline


title: ATAC SNU16


title: NoStress_Saline 2

description:
NS_v_SM.csv
NS_v_SS.csv


title: FUS,ctrl,male,S776


title: Stress_Saline 4

description:
SM_v_SS.csv
NS_v_SS.csv

value: Stress


title: NoStress_Saline 3

description:
NS_v_SM.csv
NS_v_SS.csv


title: Stress_Saline 3

description:
SM_v_SS.csv
NS_v_SS.csv


title: ATAC NCC59


title: HC41-V1D1, PBMC

tag: treatment

tag: batch

tag: sars cov2_hx


title: FUS,ctrl,female,S876


title: NoStress_Saline 1

description:
NS_v_SM.csv
NS_v_SS.csv


title: HC41-V1D0, PBMC

tag: cell type


title: TDP43,ctrl,male,S0842


title: ATAC NCC24


title: Stress_MitoQ 4

description:
NS_v_SM.csv
SM_v_SS.csv

value: MitoQ-NP


title: HC37-V2D7, PBMC

value: healthy control

tag: age


title: FUS,ctrl,female,S850

tag: strain

value: female


title: ATAC NCC20


title: FUS,ctrl,female,S875

tag: condition


title: FUS,ctrl,female,S571


title: ATAC NCC19


title: Stress_MitoQ 3

description:
NS_v_SM.csv
SM_v_SS.csv


title: HC37-V2D0, PBMC

value: peripheral blood

tag: gender


title: HC37-V2D1, PBMC

tag: diabetes


title: Stress_MitoQ 2

description:
NS_v_SM.csv
SM_v_SS.csv


title: HC37-V1D7, PBMC

tag: tissue


title: FUS,ctrl,male,S572


title: HC37-V1D1, PBMC

tag: time


title: Stress_MitoQ 1

description:
NS_v_SM.csv
SM_v_SS.csv


title: ATAC IM95


title: ATAC GSU

source_name: GSU

value: GSU


title: Stress_Saline 1

description:
SM_v_SS.csv
NS_v_SS.csv


title: FUS,mut,male,S881

value: mut


title: HC37-V1D0, PBMC

value: PBMC

tag: disease


title: HC31-V2D7, PBMC

value: Female


title: Ctrl_TAC_4

data_processing:
Quality of the cleaned FASTQ files were checked by FastQC (Babraham Bioinformatics), then aligned to the mouse genome (Esembl GRCm38 genome obtained from GENCODE) using HISAT2 (v.2.1.0)
EdgeR (v.3.26.1) was used to identify differentially expressed genes.
Assembly: Esembl GRCm38.97
Supplementary files format and content: CSV, raw counts of sequencing reads on the gene level

extract_protocol:
Total RNA from the apex of heart was isolated using TRIzol (Invitrogen) from tissues using standard protocol.
Poly A-selected libraries were generated with BGI using their in-house DNB-Seq platform
RNA-sequencing was processed by BGI using their in-house DNBSeq platform (single-ended, 50bp read-length)

value: Heart

tag: genotype

value: TAC


title: Stress_Saline 2

description:
SM_v_SS.csv
NS_v_SS.csv


title: ATAC OCUM1

tag: cell line


title: ATAC AGS

source_name: AGS

value: AGS


title: HC31-V2D1, PBMC

data_processing:
Sequence reads were trimmed for adaptor/low quality sequences using fastp with default settings.
Reads were mapped to hg38 and quantified using salmon v1.6.0 with default settings.
Reads were imported into a count matrix using the R package tximeta
Assembly: hg38
Supplementary files format and content: raw unormalized count matrix with all samples is supplied in csv format.

extract_protocol:
PBMCs were extracted from heparinized blood using Ficoll-Paque PLUS (Cytiva) density gradient centrifugation. Extracted cells were preserved in -80 in RNAlater (Invitrogen). RNA was harvested using the PureLink RNA Mini kit (Invitrogen).
RNA libraries were prepared using 50ng of RNA with the NEBNext Ultra II Directional RNA Library Prep kit and NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) following manufacturer directions.

value: No


title: ATAC YCC6

value: Gastric cancer cell line


title: FUS,mut,male,S567

value: Mouse prefrontal cortex

tag: Sex

value: male


title: HC31-V2D0, PBMC


title: FUS,mut,male,S858


title: ATAC KATOIII

source_name: KATOIII

value: KATOIII


title: Ctrl_TAC_3


title: Ctrl_TAC_1


title: FUS,mut,male,S784


title: HC31-V1D7, PBMC


title: ATAC YCC2


title: ATAC CLS145


title: FUS,ctrl,female,S565

value: ctrl


title: FUS,mut,female,S782


title: Ctrl_Sham_4

value: Sham


title: HC31-V1D1, PBMC

value: healthy control


title: Ctrl_TAC_7


title: Ctrl_Sham_3


title: FUS,mut,male,S578


title: Ctrl_Sham_2


title: HC31-V1D0, PBMC


title: ATAC NUGC3


title: FUS,mut,female,S581

value: female


title: FUS,mut,female,S575


title: HC3-V2D1, PBMC

value: peripheral blood


title: FUS,mut,female,S574


title: ATAC MKN1


title: HC3-V2D0, PBMC


title: 39_TAC_6


title: ATAC SH.10.TC


title: PVN_Input

city: Houston

first: Haichao

last: Wei

state: TX

address: 1825 Pressler St., SRB 637.C

institute: UTHealth

data_processing:
ChIP-Seq of BMAL1 in the PVN was performed on the Illumina platform. All reads were mapped to the mm10 reference genome using Bowtie2, and only unique mapped reads were used for subsequent analysis.
ChIP-seq peaks were called using MACS2 at default thresholds.
The called peaks with q_value (FDR) < 0.05 and fold-enrichment > 2 were annotated with gene names.These filtered peaks lying within 5 kb upstream of the TSS of a gene or within its gene body were retained for peak annotation.
Assembly: mm10
Supplementary files format and content: S24.peakData.bed.gz (bed, narrowPeak)
Supplementary files format and content: S25.peakData.bed.gz (bed, narrowPeak)

source_name: hypothalmic/PVN cells

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was digested using MNase treatment on the heatblock at 37C for 20 minutes. The samples were immunopercipitated overnight with BMAL1 antibody. DNA was eluted  according to the Cell signaling kit protocol.
The purified and fragmented DNA samples were submitted to Cancer Genomics Center at The University of Texas Health Science Center at Houston (CPRIT RP180734). The 100bp-300bp DNA fragments were selected by Kapa Pure Beads (#7983280001, Roche Holding AG), which were used for library preparation. The libraries were prepared following the protocol of KAPA Hyper Prep Kit (KK8502, Roche Holding AG). Briefly, the fragmented DNAs were repaired both ends, and an adenine (A) was added to the repaired ends. This end-repair and A-tailing procedure was performed at 20 0C for 30 minutes followed by 65 0C for 30 minutes. Then, the adapters with unique indexes, which can identify each sample during sequencing, were ligated to both ends of each fragmented DNA. After ligation, the DNA fragments with adapters were cleaned up by magnet beads. The proper sizes of DNA fragments were selected. The selected DNA fragments were quantified by quantitative polymerase chain reaction (qPCR) and amplified by Bio-Rad C1000 Touch Thermal Cycler (Bio-Rad Laboratories). The final library was qualified by Agilent Bioanalyzer 2100 (Agilent Technologies) and quantified by qPCR. The libraries were pooled and subjected to a paired-end 75-cycle sequencing on an Illumina NextSeq 550 System using High Output Kit v2.5 (#20024907, Illumina, Inc.).

value: hypothalmic/PVN cells

tag: chip antibody


title: HC3-V1D7, PBMC


title: ATAC LMSU

source_name: LMSU

value: LMSU


title: PVN_2


title: ATAC HS746T


title: HC3-V1D1, PBMC

value: PBMC


title: PVN_1


title: FUS,mut,female,S785

value: mut


title: ATAC NCC_STC_K140


title: 39_TAC_1

value: Heart


title: HC3-V1D0, PBMC

value: Female


title: 39_Sham_4


title: HC27-V2D7, PBMC

value: Male


title: HC3-V2D7, PBMC

value: No


title: PC3 cells, vehicle,ChIP-FOXA2

city: Boston

first: Zifeng

last: Wang

address: 100 Morrissey Blvd, ISC/4610

institute: UMASS Boston

data_processing:
The sequence quality of raw reads was checked by FastQC (version 0.11.9).
Raw reads were mapped to the hg19 human genome using bwa (version 0.7.17-r1188) with aln and samse or sampe sub-commands.
Samtools (version 1.9) was used to convert sam files to bam format.
MACS2 (version 2.1.4) was used to call peak on the bam files.
bedGraph files generated from MACS2 were converted into bigwig files with UCSC tools (version 357).
Assembly: hg19
Supplementary files format and content: bigWig, bed

growth_protocol: PC3,LNCaP cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Cells were crosslinked with 1% formaldehyde and then sonicated. DNA were immunoprecipitatted with antibody and protein A/G beads. After reverse crosslinking, DNA were purifed with Qiagen PCR purification kit.
Libraries were constructed using the SMARTer ThruPLEX DNA-Seq Prep Kit (Takara Bio USA) or Qiagen Qiaseq UltraLow Input Library Kit

value: Prostate cancer cell line


title: Day7,naïve,replicate4 [RNA-Seq]

city: Cincinnati

last: Jankowski

state: OH

address: 3333 Burnet Ave

department: Anesthesia

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Sequence reads were trimmed using Trim Galore! v0.4.2 and cutadapt v1.9.1.
The trimmed reads were aligned to the reference mouse genome version mm9 using STAR v2.6.1e.
Aligned reads were stripped of duplicate reads with the program sambamba v0.6.8.
Read counting was done with the program featureCounts v1.6.2 from the Rsubread package (7).
Raw counts were normalized as  transcripts per million (TPM).
Assembly: mm9
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Peritoneal isolated

extract_protocol:
RNA was harvested with Qiagen microRNA kit stopping after total RNA extraction, 2ng were used for library prep.
RNA was cleaned up with the Nucleospin XS kit, and library prepped with the SMARTer Stranded PicoV2 kit from Takara

value: Peritoneal isolated

value: Macrophage

value: LysM;TdTomato

value: naive


title: ATAC GES1

value: Gastric cancer cell line


title: PC3 cells,vehicle, ChIP-FOXA2


title: 39_Sham_3

value: Sham


title: Ctrl_Sham_1


title: 39_TAC_5

value: TAC


title: HC27-V2D1, PBMC

city: Chicago

first: Kai

last: Huang

address: 909 S. Wolcott Ave COMRB Room 3060

institute: University of Illinois at Chicago

source_name: peripheral blood

value: peripheral blood

value: healthy control


title: YCC10, MYB, KD, siMYB, rep 1

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

institute: Chiba University

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
Read were aligned with HISAT v2.1.0.
Fragments per kilobase of exon model per million mapped fragments (FPKM) were calculated using Cufflinks v2.2.1. Command line options for cufflinks were '--max-bundle-flags 4000000' for RNA-seq
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

extract_protocol:
RNA was harvested using Direct-zol RNA mini-prep (ZYMO Research), 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Sample Prep Kit (Illumina)  following manufacture's protocols.

value: Human gastric cancer

value: MYB knockdown


title: HC27-V2D0, PBMC

value: PBMC


title: SNU719, MYB, KD, siMYB, rep 1


title: 39_Sham_2

city: Los Angeles

first: Yao Wei

last: Lu

address: 2011 Zonal Ave

institute: University of Southern California

source_name: Heart

value: Heart


title: Day7,naïve,replicate2 [RNA-Seq]


title: 39_TAC_4


title: Day7,naïve,replicate1 [RNA-Seq]


title: HC27-V1D7, PBMC


title: 39_Sham_1


title: YCC10, MYB, KD, siCtrl, rep 1

value: WT


title: Day35,naïve,replicate4 [RNA-Seq]


title: HC27-V1D1, PBMC

value: Male


title: Day7,naïve,replicate3 [RNA-Seq]


title: Day35,naïve,replicate3 [RNA-Seq]


title: SNU719, MYB, KD, siCtrl, rep 1


title: HC27-V1D0, PBMC

value: No


title: SNU719, ATAC, rep 1

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
ChIP-seq reads were aligned to hg38 reference human genome, using bowtie2(v2.3.3.1)
Duplication reads were removed from aligned file by using picard-tools-2.18.21.
Alignments were filtered for ENCODE blacklisted regions (ENCODE Project Consortium, 2012, doi: 10.1038/nature11247).
The mapped sequence reads were extended to 100 bp and converted to the continuous signal data in bedGraph format using HOMER makeUCSCfile command. BedGraph files were converted to bigwig files using UCSC BedGraphToBigWig program.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
ChIP: Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using Picorupter (Diagenode); ATAC and CUT&TAG: Cell nuclei were transposed by Tn5 Transpose
ChIP-seq libraries were prepared using KAPA Hyper Prep Kit (KAPA Biosystems) following the manufacturer’s protocol; ATAC-seq libraries were amplified from the transposed DNA fragments. CUT&Tag libraries were amplified by KAPA HiFi HotStart Ready Mix.


title: Day35,naïve,replicate2 [RNA-Seq]


title: Day35,naïve,replicate1 [RNA-Seq]


title: HC26-V2D7, PBMC


title: senescent_fastGRO-seq_shMETTL14_knockdown_ replicate 2

first: Yuan

last: Qi

address: 1400 Pressler St

department: Bioinformatics & Computational Biology

institute: University of Texas M.D. Anderson Cancer Center

data_processing:
library strategy: fastGRO-seq
Reads were aligned to the hg19 human genome by STAR and bam files were normalized based on the drosophila spike-in RNA among each group.
bigwig files were generated with deeptools 3.3.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: nuclear RNA

source_name: IMR90 cells

growth_protocol: IMR90 primary human diploid lung embryonic fibroblasts were cultured in DMEM medium supplemented with 10% fetal bovine serum (FBS), l-glutamine, sodium pyruvate, non-essential amino acids, sodium bicarbonate and 1% penicillin-streptomycin under low oxygen tension (2%).

extract_protocol:
Nascent RNA was extracted from nuclei and purified through RNA Clean and Purification kit.
Purified RNA was used to constructed RNA sequencing libraries using the NEBNext Ultra II Directional RNA Library Prep kit.

treatment_protocol: Senescence was induced in primary human lung fibroblasts (IMR90) cells through the inducible expression of a fusion protein (estrogen receptor and H-RASG12V, ER: RAS). fastGro-seq was performed to monitor nascent gene transcription in control and senescent IMR90 cell lines with vector, METTL3, or METTL14 knockdown.

value: IMR90 cells

value: human fibroblast

value: senescent


title: HC26-V2D1, PBMC


title: Boscalid, uninfected biol rep 3

city: Winnipeg

first: Mark

last: Belmonte

state: MB

address: 50 Sifton Road

institute: University of Manitoba

description:
BoscU3
B.napus_RawCounts.txt

data_processing:
Read quality was determined using FastQC
Reads were aligned using HISAT2 and raw counts were generated using featureCounts
DESeq2 was used to conduct differencial gene expression analysis
Assembly: B.napus genome v5.0 - GenBank assembly accession: GCA_000751015.1 (Chalhoub et al. 2014)
Assembly: S. sclerotiorum genome - RefSeq assembly accession: GCF_000146945.2 (Amselem et al., 2011)
Supplementary files format and content: B.napus_RawCounts.txt - tab delimited txt file including raw counts for each sample aligned to B. napus
Supplementary files format and content: S.sclerotiorum_RawCounts.txt - tab delimited txt file including raw counts for each sample aligned to S. sclerotiorum

organism: Brassica napus

source_name: Leaf

growth_protocol: Canola (B. napus) cultivar Westar was grown to the 30% flowering stage in Sungrow mix #4 supplemented with Osmocote fertilizer (1.5-2g/pot) in pots sized 8.5cm x 8.5cm x 9cm. Plants were grown in greenhouse, long day conditions.

extract_protocol:
RNA was extracted using the Qiagen RNEasy Plant Mini Kit with the addition of Qiagen's on-column DNAse treatment. 1µg of RNA was sent to Genome Québec for library construction.
Genome Québec constructed cDNA libraries according to their mRNA stranded library preparation protocol. Paired-end 100bp reads were sequenced (Illumina NovaSeq 6000)

treatment_protocol: Plants were treated with 4.5mL of foliar spray treatment per plant. Treatments consisted of distilled water, 40mM boric acid (as a boron source), and 10 ppm boscalid. Treatment remained on the plants for 24 hours prior to incoulation. As inoculant, 4.0mL of S. sclerotiorum ascospore suspension was sprayed onto plants (1x10^6 spores/mL in potato dextrose broth). Plants then went into a humidty chamber to maintain 90-100% humidity for four day sto allow for infection to progress. At this point, leaves were collected and flash frozen in liquid N  as samples for RNA extraction.

value: Leaf

value: Cultivar - Westar

value: Boscalid, uninfected


title: HC26-V2D0, PBMC


title: senescent_fastGRO-seq_shMETTL3_knockdown_ replicate 1


title: Boscalid, uninfected biol rep 2

description:
BoscU2
B.napus_RawCounts.txt


title: systemic versus non wounded repl. 2

type: RNA

description: Biological replicate 2 of 2. Systemic undamaged and intact tissues

hyb_protocol: 825 ng of Cy3 and Cy5 probes were mixed and hybridized for 17 hours at 65ºC in GEx Hybridization Buffer HI-RPM in a hybridization oven. Arrays were washed according to the manufacturer’s instructions and dried by centrifugation.

scan_protocol: Images were scanned at 2um resolution in an Agilent DNA Microarrays Scanner (G2565BA, Agilent Technologies) and  were with Feature Extraction 9.0 software (Agilent Technologies).

data_processing: Raw intensities were background-substracted by NORMEXP method with a offset of 50. Signals (in log2 scale) were then normalized by LOWESS algorithm (intra-arrays normalization) followed by adjustment of their quantiles (inter-arrays normalization).

source_name: tissues from intact plants

label_protocol: 200 ng of total RNA was reverse transcribed used T7 promotor primer and the cDNA was converted to aRNA using T7 RNA polymerase, wich simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two color Microarray-Based GeneExpression Analysis Protocol )

growth_protocol: For wound assays, plants of Marchantia polymorpha Tak-1 were grown in soil for 4 weeks.

extract_protocol: Total RNA was extracted with Favorgen Total RNA Purification Mini Kit and treated with DNAse. Each RNA sample from an independent biological replicate was extracted from a pool of 10 plants

treatment_protocol: Wounding was performed by thoroughly crushing one lobe of tallus. Thallus samples from intact plants (NW, non-wounded) and from locally damaged lobes (W, wounded) and systemic non-wounded lobes from damaged plants (SD, systemic tissues of damaged plants) were collected 4 hours after wounding and immediately frozen in liquid nitrogen before further analysis.

tag: accession

value: 4 weeks

source_name: systemic undamaged tissues from wounded plants


title: senescent_fastGRO-seq_shMETTL3_knockdown_ replicate 2

tag: treatment


title: Day35,Day7-incised,replicate3 [RNA-Seq]

value: Peritoneal isolated

value: Macrophage

value: LysM;TdTomato

value: incised


title: Day35,Day7-incised,replicate4 [RNA-Seq]


title: senescent_fastGRO-seq_shcontrol_knockdown_ replicate 2

value: shcontrol


title: HC26-V1D1, PBMC

value: peripheral blood

value: PBMC

value: healthy control

tag: batch


title: Day35,Day7-incised,replicate1 [RNA-Seq]


title: HC26-V1D7, PBMC

tag: sars cov2_hx

value: Male


title: Day35,Day7-incised,replicate2 [RNA-Seq]

tag: cell type


title: senescent_fastGRO-seq_shcontrol_knockdown_ replicate 1


title: Boron, uninfected biol rep 3

description:
BoronU3
B.napus_RawCounts.txt

value: Boron, uninfected


title: systemic versus non wounded repl. 1

description: Biological replicate 1 of 2. Systemic undamaged and intact tissues

tag: age


title: Boron, uninfected biol rep 2

description:
BoronU2
B.napus_RawCounts.txt


title: Day7,naïve,replicate3

data_processing:
Datasets were processed and analyzed using an in-house automated pipeline ; the following steps describe briefly the characteristics of the NextGenAligner pipeline.
Basic quality control for raw sequencing reads was performed using FASTQC (version 0.11.2) (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
The quality controlled reads were aligned to the reference human genome (hg19; chromosomes 1-22, X, Y, M) using bowtie2 (version 2.3.4.1)(Langmead and Salzberg, 2012).
Adapter sequences were removed using Trim Galore (version 0.4.2) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), a wrapper script that runs cutadapt (version 1.9.1) to remove the detected adapter sequence from the reads.
Aligned reads were then sorted using samtools (version 1.8)(Li et al., 2009) and duplicate reads were removed using picard (version 1.89) (https://broadinstitute.github.io/picard/).
Peaks were called using MACS2 (version 2.1.0) (https://github.com/taoliu/MACS)(Zhang et al., 2008).
ENCODE blacklist regions (Amemiya et al., 2019) were removed
Assembly: mm9
Supplementary files format and content: Peaks called by MACS2 in narrowPeak format, peak text files in standard MACS2 output format for narrow peak mode (columns : chromosome,start,end,name,score,strand,signalValue,pValue,qValue,peak)
Supplementary files format and content: Normalized bigwig files are generated using a scaling factor proportional to the total number of reads in the BAM file

extract_protocol:
Transposase Tn5 with adapter sequences was used to cut accessible DNA (Buenrostro et al. 2015).
Accessible DNA with adaptor sequences were isolated, then libraries were prepared from 17-50,000 cells using the OMNI protocol (Corces et al. 2017).

value: naive

value: Day 7


title: HC21-V2D7, PBMC

value: Yes

value: No


title: wounded versus non wounded repl. 1

description: Biological replicate 1 of 2. Locally damaged and intact tissues

source_name: locally wounded tissues


title: control_fastGRO-seq_replicate 2

value: IMR90 cells

value: human fibroblast

value: WT

value: control


title: control_fastGRO-seq_replicate 1


title: Day7,naïve,replicate2

value: Peritoneal isolated

value: Macrophage


title: Boron, uninfected biol rep 1

description:
BoronU1
B.napus_RawCounts.txt

value: Leaf

value: Cultivar - Westar


title: HC21-V2D1, PBMC

value: peripheral blood