title: Micro-C Replicate2_RSC

description: plasmid DNA

data_processing:
Analysis was performed using the MCC pipeline as described in Hua et al. (2021). Briefly, adapter sequences were removed using Trim Galore (Babraham Institute, v.0.3.1) and paired-end reads were reconstructed using FLASH (v.1.2.11) (Magoč & Salzberg, 2011). Reconstructed reads were then mapped to the ~3 Mbp plasmid library (chrV:5,599 to chrX:106,749) with the non-stringent aligner BLAT (Kent, 2002). Uninformative reads (e.g. plasmid backbone) were discarded, while the mapped reads in the FASTQ files were further mapped to the SacCer3 reference genome using Bowtie2 (Langmead & Salzberg, 2012). The aligned reads were then processed to identify the ligation junction and remove PCR duplicates using MCCanalyser.pl. The unique ligation junctions were identified if the fragment ends were less than 5 bp apart in the original read and separated by mapping with BLAT and Bowtie2.
The pairwise interaction list was further filtered for interactions that are inter-chromosomal, and interactions are less than 147 bp apart. The ligation junction was further shifted by 80 bp to map the nucleosome dyad. The read pair orientation was determined based on the direction of the read.
Assembly: SacCer3
Supplementary files format and content: Text file containing a list of the chimeric pairs, the base pair coordinates shifted from the ligation junction, strand information, direction of read (upstream or downstream of the ligation junction), read pair orientations, and distance between pairs

extract_protocol:
The chromatin was reverse cross-linked with the addition of 1 mg/mL Proteinase K (Life Technologies) and 0.5% SDS at 65ºC for ≥3 hours. For DNA extraction, the reaction was supplemented with glycogen and subjected to ethanol precipitation. The ligation products were assessed using Fragment Analyzer. A successful ligation is indicated by the increase in fragment sizes of > 320 bp. Unligated mono-nucleosomal fragments were further removed by purification with 0.9 volume of AMPure XP beads.
Approximately 150-200 ng of each library was sonicated to a mean fragment size of 200 bp using a Covaris S220 Ultrasonicator (peak incident power 175; duty factor 10%; cycles per burst 200; treatment time 250s). Bead cleanup with AMPure XP beads was then performed and the fragment size was assessed using Fragment Analyzer. Libraries were indexed using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) using 170-200 ng input. The manufacturer’s protocol was followed with the following deviations: To maximize library complexity and yield, the PCR was performed in duplicate per ligation reaction using Herculase II reagents (Agilent Technologies). The parallel library preparations and PCR reactions were subsequently pooled for each reaction. The quality of the indexed library and molar concentration were measured using Fragment Analyzer and Qubit.
in vitro Micro-C

treatment_protocol:
Remodeling reactions contained 1) 30 µL of SGD chromatin corresponding to about ~2.1 µg of DNA assembled into nucleosomes 2) transcription factors (TFs) Reb1 and Abf1 and 3) one of the chromatin remodeling enzymes, in assembly buffer (25.6 mM HEPES-NaOH pH 7.6, 3 mM MgCl2, 2.5 mM ATP, 1.25 mM TCEP, 10 mM creatine phosphate, 0.25 mM EGTA, 56 mM KOAc, 0.28 mM DTT, 13.4% glycerol, 10 µg/mL creatine kinase) for a total reaction volume of 100 µL. The GRFs, Reb1 and Abf1, were added at a final concentration of 50 nM each. The remodeling enzymes Chd1, ISW2, and INO80 were added to a final concentration of 24 nM and RSC was added to a final concentration of 12 nM.
SGD chromatin was was incubated with Disuccinimidyl glutarate (DSG) at final concentrations of 0.75 mM for 20 minutes at 30ºC after which it was added with formaldehyde (FA) at a final concentration of 0.05% and cross-linking was continued for another 10 minutes at 30ºC. The cross-linking reactions were quenched with Quenching Buffer (10 mM Tris-HCl pH 7.5, 2 mM lysine and 8 mM aspartate final concentration) for 15 minutes at 30ºC. Cross-linked chromatin was supplemented with 0.4 Ku/µL final concentration of MNase (New England Biolabs) in a total reaction volume of 200 µL containing digestion buffer (10 mM Tris-Cl pH 7.6, 1.7 mM CaCl2). The reaction was incubated at 30ºC for 5 minutes then stopped with STOP-Buffer (final concentration: 5 mM Tris-HCl pH 7.5, 10 mM EDTA, 200 mM NaCl and 1 mM EGTA). The cross-linked and MNase-digested chromatin was purified using an Amicon Ultra 50 kDa centrifugal filter to remove <100 bp fragments. The chromatin was loaded and filled to 1 mL with low salt buffer (20 mM HEPES-NaOH, 50 mM NaCl, 0.5 mM EDTA, 0.05% IGEPAL CA-630) and concentrated to 200 µL by centrifugation (2000 g, 2 minutes). It was again filled to 1 mL with low salt buffer and concentrated to 200 µL for two more times. In the last centrifugation step, the sample was concentrated to ~100 µL.

value: Abf1, Reb1, RSC


title: Micro-C Replicate2_Chd1

status: Public on Nov 23 2023

type: SRA

city: Göttingen

first: Elisa

last: Oberbeckmann

address: Justus-von-Liebig Weg 11

department: Molecular Biology

country: Germany

institute: University Medical Center Göttingen

description: plasmid DNA

library_source: genomic

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: whole cell

growth_protocol: For a high assembly degree, 46 µg of plasmid library DNA were mixed with 40 µg of recombinant S. cerevisiae histone octamers in 400 µL assembly buffer (10 mM HEPES-NaOH pH 7.6, 2 M NaCl, 0.5 mM EDTA pH 8, 0.05% IGEPAL CA-630, 0.2 µg/µL BSA). Samples were transferred to Slide-A-Lyzer dialysis cups which were placed in a 3 L beaker containing 300 mL high salt buffer (10 mM HEPES-NaOH pH 7.6, 2 M NaCl, 1 mM EDTA, 0.05% IGEPAL CA-630). Samples were gradually dialyzed against a total of 3 L low salt buffer (10 mM HEPES-NaOH pH 7.6, 50 mM NaCl, 0.5 mM EDTA, 0.05% IGEPAL CA-630) while stirring via a peristaltic pump over 12-14 hours at room temperature. After complete transfer of low salt buffer, samples were dialyzed against 1 L low salt buffer for 1 hour at room temperature with stirring. The chromatin was then centrifuged for 1 minute at 10,000 rpm at room temperature and the supernatant was transferred to a fresh protein low-binding tube. We refer to the in vitro reconstituted chromatin as “SGD chromatin”. DNA concentration of the SGD chromatin was measured using a spectrophotometer (Nanodrop) and it was stored in low salt buffer at 4ºC.

tag: source

value: in vitro-reconstituted chromatin

tag: atp-dependent remodeler_and_tfs_used

value: Abf1, Reb1, Chd1

tag: cross-linking condition

value: 0.75 mM DSG, 0.05% Formaldehyde

tag: restriction enzyme

tag: cell type

value: whole cell


title: Micro-C Replicate3_INO80_FA

description: plasmid DNA

value: Abf1, Reb1, INO80

value: 0.05% Formaldehyde


title: Micro-C Replicate3_INO80_DSG-FA

description: plasmid DNA


title: Micro-C Replicate2_ISW2

description: plasmid DNA

value: Abf1, Reb1, ISW2


title: KOLF_GATA4_2B2_HDR

city: Nedlands

first: Kathryn

middle: Olivia

last: Farley

state: WA

address: 15 Hospital Avenue

department: Precision Health

country: Australia

institute: Telethon Kids Institute

data_processing:
Illumina base space prepared the fastq files, after adaptor trimming
Reads analysed via Crispresso2:v2.0.30
Supplementary files format and content: .html files containing sequence reports for each sample and associated genotype
Library strategy: AmpSeq

organism: Homo sapiens

source_name: KOLF-2 cells

growth_protocol: KOLF-2 iPSCs were grown in TeSR-E8 medium (stemcell technologies).

extract_protocol:
Genomic DNA was extracted with PureLinkTM Genomic DNA Mini Kit, Life Technologies; Targeted 250bp amplicons were amplified by PCR from gDNA
Amplicon sequencing was performed by PCR addition of Truseq primers, and paired end 250bp amplicons, 45,000 reads

tag: cell line

value: KOLF-2 cells

value: induced pluripotent stem cells

tag: genotype

value: HDR

tag: clone id


title: KOLF_GATA4_4D1_WT

value: WT


title: KOLF_GATA4_1D1_HDR


title: KOLF_GATA4_3H1_HDR


title: FAPs_81

city: Nuthetal

first: Tim

middle: Julius

last: Schulz

address: Arthur-Scheunert-Allee 114-116

institute: German Institute of Human Nutrition

library_source: transcriptomic single cell

data_processing:
The trimming was done with Trimgalore, the alignment was performed with STAR and the gene counting was done with featureCounts.
Assembly: mm10
Supplementary files format and content: tab-seperated value files

molecule: polyA RNA

organism: Mus musculus

source_name: skeletal muscle

extract_protocol:
Muscle samples were isolated, minced and digested using Collagenase A for 45 min at 37 °C. Dispase II was added for 30 minutes to the muscle lysates. Muscles slurries were passed 10 times through a syringe and cell strainer and centrifugated. The pellet was re-suspended in Ammonium Chloride Potassium lysis buffer to eliminate red blood cells and centrifuged again. Cells were re-suspended in sorting buffer consisting of 100 µl Hank´s balanced salt solution (HBSS) containing 0.4% FBS. Fibro-adipogenic progenitors were isolated freshly using fluorescence-activated cell sorting (FACS) using the following surface marker profile: CD45-CD11b-CD31-SCA1+. For each single cell library, 4 independent chips using a commercial microfluidics platform (IFC, Fluidigm) were used with a capacity of capturing up to 96 individual cells per loaded chip. For each chip loading, cells were pooled from three mice (i.e. 4 pools per experimental group). Individual cell quality was checked as per manufacturers’ recommendation.
Successfully captured cells and corresponding cDNA samples of individuals cells were subsequently processed by Smart-Seq2 cDNA library preparation (Clontech) using the Nextera XT Indexing kit (Illumina). Quality control was performed using an Agilent Bioanalyzer DNA High Sensitivity Kit for electropherogram tracing.

tag: tissue

value: skeletal muscle

value: Fibro-adipogenic progenitors

tag: treatment

value: aged


title: FAPs_82


title: KOLF_GATA4_3G2_WT


title: KOLF_GATA4_3F2_WT


title: FAPs_80


title: B522, stationary, biol rep 2

city: Madrid

first: José

middle: Antonio

last: Escudero

state: Madrid

address: Av Puerta de Hierro s/n

department: Sanidad Animal

country: Spain

institute: Universidad Complutense de Madrid

description:
B522STB
ST_featureCounts.tsv
ST_DE_results_raw_chromosome.tsv

library_source: transcriptomic

data_processing:
Raw reads were trimmed using Trim Galore v0.6.6 with a quality threshold of 20 and removing adapters and reads shorter than 50 bp.
Trimmed paired reads were mapped to the V. cholerae N16961 reference genome (Accession number: chromosome 1 CP028827.1; chromosome 2 CP028828.1) using BWA-MEM v0.7.17.
featureCounts from the Rsubread v2.10.2 packaged was used to obtain read counts per annotated feature, including CDS, ncRNA, tmRNA, RNase P, tRNA, antisense RNA and SRP RNA.
Differential expression analysis was performed from raw counts using DESeq2 v1.36.067, by comparing the expression data of the deletion mutant (B522) against the WT strain (A001).
Assembly: chromosome 1 CP028827.1; chromosome 2 CP028828.1
Supplementary files format and content: XP_featureCounts.tsv includes raw counts of sequencing reads for the three biological replicates of V. cholerae A001 and V. cholerae B522 in exponential phase.
Supplementary files format and content: ST_featureCounts.tsv includes raw counts of sequencing reads for the three biological replicates of V. cholerae A001 and V. cholerae B522 in stationary phase.
Supplementary files format and content: XP_DE_results_raw_chromosome.tsv includes the list of differentially expressed genes in V. cholerae B522 in comparison to V. cholerae A001 in exponential phase.
Supplementary files format and content: ST_DE_results_raw_chromosome.tsv includes the list of differentially expressed genes in V. cholerae B522 in comparison to V. cholerae A001 in stationary phase.

molecule: total RNA

organism: Vibrio cholerae

source_name: prokaryote

growth_protocol: Vibrio cholerae was cultured in liquid Luria-Bertani (LB) medium at 37°C.

extract_protocol:
Total RNA was extracted from V. cholerae WT (A001) and V. cholerae ∆SI (B522) cultures grown in LB at 37˚C in both exponential (OD600 0,8) and stationary (OD600 2,8) growth phases using the RNeasy® Mini Kit (QIAGEN), following the manufacturer’s protocol.
Ribodepletion RNA library and sequencing was performed at the Oxford Genomics Centre using a NovaSeq6000 sequencing system (Illumina). Samples were depleted using NEB bacteria rRNA probes before conversion to cDNA. Second strand cDNA synthesis incorporated dUTP. The cDNA was end-repaired, A-tailed and adapter-ligated. Prior to amplification, samples underwent uridine digestion. The prepared libraries were size selected, multiplexed and QC’ed before paired end sequencing over one unit of a flow cell. Data were aligned to the reference and quality checked.

tag: strain

value: prokaryote

value: deltaSI

tag: growth phase

value: stationary (OD600 2.8)


title: B522, stationary, biol rep 3

description:
B522STC
ST_featureCounts.tsv
ST_DE_results_raw_chromosome.tsv


title: Astrocytes_ST2_WT_2

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

country: USA

institute: Dana Farber Cancer Institute

data_processing:
The sample is aligned to GRCm38 transcriptome and quantified using Kallisto, Cellranger and RSEM
Assembly: GRCm38
Supplementary files format and content: gzipped abundance.tsv output from Kallisto, Cellranger and RSEM

source_name: cells

growth_protocol: Cells in vitro were cultured in adherent culture or encapsulated in droplets ("droplets" contained in title)

extract_protocol:
In vivo: Each CNS was isolated per mouse. A cell suspension was generated by papain digestion, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, and washed in PBS. Cells were sorted by flow cytometry based on a negative selection strategy for astrocytes. In vitro: Cells from culture were lysed in RLT and processed by Qiagen RNeasy kit protocol.
Libraries were prepared by NEBNext Low Input kit.

treatment_protocol: In vivo: Induction of EAE in mice. EAE was induced by injecting 150 µg of MOG35-55 diluted in 100 µL of PBS emulsified in 100 µL of CFA per mouse. ICV injection: AREG or PBS was administered via ICV injection. In vitro: Cells were stimulated with AREG or Poly(I:C) or LPS or IL1b/TNFa.

value: Astrocyte

tag: age

value: 13 weeks


title: Astrocytes_ST2_WT_1


title: Micro-C Replicate1_RSC

description: plasmid DNA

value: in vitro-reconstituted chromatin

value: Abf1, Reb1, RSC

value: 0.75 mM DSG, 0.05% Formaldehyde


title: Micro-C Replicate2_TFs-only

description: plasmid DNA

value: Abf1, Reb1, no remodeler

value: whole cell


title: B522, stationary, biol rep 1

description:
B522STA
ST_featureCounts.tsv
ST_DE_results_raw_chromosome.tsv


title: Micro-C Replicate1_Chd1

description: plasmid DNA

value: Abf1, Reb1, Chd1


title: Micro-C Replicate2_INO80

description: plasmid DNA

value: Abf1, Reb1, INO80


title: Astrocytes_ST2_WT_3


title: B522, exponential, biol rep 3

description:
B522XPC
XP_featureCounts.tsv
XP_DE_results_raw_chromosome.tsv

value: exponential (OD600 0.8)


title: Micro-C Replicate1_ISW2

description: plasmid DNA

value: Abf1, Reb1, ISW2


title: Microglia_ST2_KO_2

value: Microglia


title: Microglia_ST2_KO_1


title: B522, exponential, biol rep 2

description:
B522XPB
XP_featureCounts.tsv
XP_DE_results_raw_chromosome.tsv


title: B522, exponential, biol rep 1

description:
B522XPA
XP_featureCounts.tsv
XP_DE_results_raw_chromosome.tsv


title: Micro-C Replicate1_INO80

description: plasmid DNA


title: A001, stationary, biol rep 2

description:
A001STB
ST_featureCounts.tsv
ST_DE_results_raw_chromosome.tsv

value: WT


title: Microglia_ST2_WT_2


title: FAPs_79

value: skeletal muscle

value: Fibro-adipogenic progenitors

value: aged


title: FAPs_76

value: young


title: A001, stationary, biol rep 3

description:
A001STC
ST_featureCounts.tsv
ST_DE_results_raw_chromosome.tsv

value: prokaryote

value: stationary (OD600 2.8)


title: Microglia_ST2_WT_3

value: 13 weeks


title: FAPs_77


title: FAPs_75


title: Microglia_ST2_KO_3


title: FAPs_74


title: A001, stationary, biol rep 1

description:
A001STA
ST_featureCounts.tsv
ST_DE_results_raw_chromosome.tsv


title: Micro-C Replicate1_TFs-only

description: plasmid DNA

value: in vitro-reconstituted chromatin


title: MNase-Seq Replicate3_INO80_DSG-FA

description: plasmid DNA

data_processing:
Sequencing data was mapped to the SacCer3 (R64) genome using Bowtie (Langmead et al. 2009).
After mapping, data was imported into R Studio using GenomicAlignments (Lawrence et al. 2013) and only fragments between 125-205 bp length were kept.
Nucleosome dyad length was reduced to 50 bp and smoothed by a 10 bp rolling window. Genome coverage was calculated.
Assembly: SacCer3/R64-1-1
Supplementary files format and content: bigwig containing sorted and smoothed nucleosome fragments

extract_protocol:
The chromatin was reverse cross-linked with the addition of 1 mg/mL Proteinase K (Life Technologies) and 0.5% SDS at 65ºC for ≥3 hours. For DNA extraction, the reaction was supplemented with glycogen and subjected to ethanol precipitation.
Approximately 15-20 ng of each library was indexed using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) using the manufacturer's protocol.

treatment_protocol:
Remodeling reactions contained 1) 30 µL of SGD chromatin corresponding to about ~2.1 µg of DNA assembled into nucleosomes 2) transcription factors (TFs) Reb1 and Abf1 and 3) one of the chromatin remodeling enzymes, in assembly buffer (25.6 mM HEPES-NaOH pH 7.6, 3 mM MgCl2, 2.5 mM ATP, 1.25 mM TCEP, 10 mM creatine phosphate, 0.25 mM EGTA, 56 mM KOAc, 0.28 mM DTT, 13.4% glycerol, 10 µg/mL creatine kinase) for a total reaction volume of 100 µL. The GRFs, Reb1 and Abf1, were added at a final concentration of 50 nM each. The remodeling enzymes Chd1, ISW2, and INO80 were added to a final concentration of 24 nM and RSC was added to a final concentration of 12 nM.
SGD chromatin was was incubated with Disuccinimidyl glutarate (DSG) at final concentrations of 0.75 mM for 20 minutes at 30ºC after which it was added with formaldehyde (FA) at a final concentration of 0.05% and cross-linking was continued for another 10 minutes at 30ºC. The cross-linking reactions were quenched with Quenching Buffer (50 mM Tris-HCl pH 7.5, 20 mM lysine and 80 mM aspartate final concentration) for 15 minutes at 30ºC. Cross-linked chromatin was supplemented with 0.4 Ku/µL final concentration of MNase (New England Biolabs) in a total reaction volume of 200 µL containing digestion buffer (10 mM Tris-Cl pH 7.6, 1.7 mM CaCl2). The reaction was incubated at 30ºC for 5 minutes then stopped with STOP-Buffer (final concentration: 5 mM Tris-HCl pH 7.5, 10 mM EDTA, 200 mM NaCl and 1 mM EGTA). The chromatin was then purified using an Amicon Ultra 50 kDa centrifugal filter to remove <100 bp fragments.

value: 0.75 mM DSG, 0.05% Formaldehyde


title: FAPs_73


title: Microglia_ST2_WT_1


title: MNase-Seq Replicate2_RSC

description: plasmid DNA

value: Abf1, Reb1, RSC


title: Microglia_KO_4


title: FAPs_72


title: MNase-Seq Replicate2_Chd1

description: plasmid DNA

value: whole cell


title: FAPs_78


title: A001, exponential, biol rep 2

description:
A001XPB
XP_featureCounts.tsv
XP_DE_results_raw_chromosome.tsv


title: Microglia_KO_3


title: A001, exponential, biol rep 3

description:
A001XPC
XP_featureCounts.tsv
XP_DE_results_raw_chromosome.tsv


title: MNase-Seq Replicate3_INO80_FA

description: plasmid DNA

value: 0.05% Formaldehyde


title: FAPs_71


title: MNase-Seq Replicate2_ISW2

description: plasmid DNA


title: Microglia_KO_1


title: A001, exponential, biol rep 1

description:
A001XPA
XP_featureCounts.tsv
XP_DE_results_raw_chromosome.tsv


title: FAPs_70


title: Microglia_KO_2


title: Microglia_WT_4


title: Microglia_WT_3


title: MNase-Seq Replicate1_Chd1

description: plasmid DNA

value: Abf1, Reb1, Chd1


title: MNase-Seq Replicate2_TFs-only

description: plasmid DNA

value: Abf1, Reb1, no remodeler


title: FAPs_69


title: FAPs_68


title: MNase-Seq Replicate1_RSC

description: plasmid DNA


title: FAPs_67


title: MNase-Seq Replicate1_ISW2

description: plasmid DNA

value: Abf1, Reb1, ISW2


title: 96-HPI-15-TR3_OZP1604_Inoculated

city: Bundoora

first: Yvonne

middle: Oby

last: Ogaji

state: VIC

address: 5 Ring Road

department: Department of Jobs, Precincts and Regions.

institute: AgriBio, Centre for AgriBioscience

data_processing:
Raw reads were processed using Fastp to remove adaptors and poly G’s and FASTQC was used to carry out quality control checks on the resulting trimmed and cleaned reads
Reads were aligned to the Pea genome reference published by  Kreplak et al (2019) and quality control checks on sample variability was carried out using differential expression for sequence count data (DESeq 2) method
Read counts generated to quantify the transcripts, quantification of transcripts was carried out with a total of 1000 bootstraps to minimise effects of technical variations using Salmon as described in Li et al (2021)
Count data was then converted to a readable form using the bioconductor package Wasabi (https://github.com/COMBINE-lab/wasabi). To identify differentially expressed genes, count data generated by Wasabi was analysed using the R package Sleuth. Sleuth was used to perform likelihood ratio tests and Wald tests to detect differences that were significant between treatments (q-value < 0.05), as well as fold change approximations between treatments for abundance of each transcript respectively
Low abundance reads were removed as described before conducting DEG analyses with DEG significance defined at q-value < 0.05 and ? 1.5 for absolute fold change. We interrogated the list of DEGs generated from the above analysis for the 21 genes confirmed to be AB resistant genes from Fondevilla et al (2014) to identify the presence or absence of those genes in our list.
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Lathyrus oleraceus

growth_protocol: Seeds were sown in pots prefilled with legume mix (Bio gro, Mount Gambier, South Australia, Australia) and grown in a controlled environment with light : dark ratio of 16:8 hr and day/night temperature of 24°/15° C until the plants were ready for inoculation

extract_protocol:
The total RNA from 100 mg of leaf sample was isolated using SpectrumTM Plant Total RNA kit (Sigma Aldrich, St. Louis, MO, USA) and Qiagen plant mini kit as per the manufacturer’s procedure. The quality of RNA samples was assessed by loading on to the 1% agarose gel and the concentration was checked by Nanodrop 2000 spectrophotometer (Thermal co., USA).
The total RNA extracted from each replicate was used to prepare transcriptome libraries using Agilent's Sure Select Strand Specific RNA Library Preparation Kit (Agilent Technologies) according to the manufacturer’s protocol

treatment_protocol:
The plants were transferred to a climate-controlled chamber one day prior to the inoculation. The climate-controlled chambers were maintained with light and dark periods of 12 hr each and a temperature of 15° C.
The plants were placed in the custom-made translucent tent fitted with pipes having holes through which misting was maintained using a humidifier. The plants were inoculated at 3-4 node stage with P. pinodes.

value: leave tissue

value: Inoculated with Peyronellaea pinodes

tag: time


title: 96-HPI-15-TR1_OZP1604_Inoculated


title: FAPs_65

value: skeletal muscle


title: 96-HPI-14-TR3_TWILIGHT_Inoculated

source_name: TWILIGHT

value: TWILIGHT


title: 96-HPI-15-TR2_OZP1604_Inoculated


title: Microglia_WT_1

value: Microglia


title: 100_ng_mL_LPS_EB_MG_drops_3

value: WT

value: fetal


title: MNase-Seq Replicate1_INO80

description: plasmid DNA

value: Abf1, Reb1, INO80


title: 96-HPI-14-TR1_TWILIGHT_Inoculated


title: 100_ng_mL_LPS_EB_MG_drops_2


title: MNase-Seq Replicate2_INO80

description: plasmid DNA


title: 96-HPI-11-TR3_WHARTON_Inoculated

source_name: WHARTON

value: WHARTON


title: Microglia_WT_2

value: 13 weeks


title: 96-HPI-11-TR2_WHARTON_Inoculated


title: FAPs_63

value: Fibro-adipogenic progenitors

value: young


title: FAPs_64

value: aged


title: 96-HPI-11-TR1_WHARTON_Inoculated


title: 96-HPI-14-TR2_TWILIGHT_Inoculated


title: Vehicle_MG_drops_3


title: FAPs_66


title: serum_mESC_500cells_TFAP2C_CR

city: Beijing

first: Lijia

address: Haidian District

department: School of Life Science

country: China

institute: Tsinghua University

data_processing:
library strategy: CUT&RUN
bulk RNA-seq reads were mapped to the mm9 reference genome using Tophat (version 2.0.11).The gene expression levels were calculated by Cufflinks (version 2.2.1). RefFlat database from UCSC genome browser was used with microRNA and repeats excluded.
CUT&RUN reads were aligned to the mm9 genome with the parameters: -t -q -N 1 -L 25 -X 2000 --no-mixed --no-discordant by Bowtie2 v2.3.5. Aligned reads were filtered with a minimum MAPQ of 20, and PCR duplicates were removed using Picard MarkDuplicates v1.119. Read coverages over mm9 genome were estimated by bamCoverage from deepTools v3.3.1 with parameters --binSize 100 --normalizeUsing RPKM.
Assembly: mm9
Supplementary files format and content: Bigwig for CUT&RUN, ATAC-seq tracks, gene expression table for RNA-seq data

source_name: serum mESC

growth_protocol: serum mES cells were cultured on 0.1% gelatin of porcine skin in DMEM (Gibco Cat. 11995-065) containing 15% FBS (Hyclone Cat. SH30396.03), leukemia inhibiting factor (LIF) (Millipore Cat. GSE1107), penicillin/streptomycin (Millipore Cat. TMS-AB2-C), GlutaMAX (Gibco Cat. 35050-061), nucleotides (Millipore Cat. ES-008-D), β-mercaptoethanol (Gibco Cat. 21985-023), and non-essential amino acids (Gibco Cat. 25-025-CIR).

extract_protocol:
Cells or embyos were lysed in wash buffer.
CUT&RUN was performed as previously reported (Skene et al., 2018; Skene and Henikoff, 2017) with modifications. Briefly, after removing the zona pellucida with Tyrode’s solution (Sigma-Aldrich, T1788) or 0.5% (m/v) Protease from Streptomyces griseus (Sigma-Aldrich, P8811), early embryos were incubated with Concanavalin-coated magnetic beads (Polyscience, 86057) for 10 min at room temperature on a thermomixer at 400 rpm. Samples were then incubated with primary antibody at a ratio of 1:100 at 4℃ for 3-5 hours on a thermomixer at 400 rpm. After washing for one time, beads were incubated with pA-MNase (to a final concentration of 400-700ng/mL) (a gift from Steven Henikoff lab) at 4℃ for 1 hours on a thermomixer at 400 rpm. After two times of washing, targeted digestion was performed by adding 2μL of 100mM CaCl2 for 30 mins on ice, followed by termination by adding an equal volume of 2  × stop buffer. Samples were then incubated at 37℃ for 20 mins for fragment releasing. The total samples or supernatants were digested with Proteinase K (NEB, P8107S) and purified using phenol:chloroform:isoamyl alcohol (25:24:1, v/v) followed by ethanol purification at -80℃ overnight. The next day, DNA was purified and subjected to Truseq library preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). Sequencing was done using the HiSeq X Ten system or  NovaSeq (Illumina) according to the manufacturer’s protocol.

value: wild type

tag: antibody

value: Tfap2c (Abclonal, A7739)


title: FAPs_62


title: FAPs_61


title: serum_mESC_2000cells_TFAP2C_CR


title: Vehicle_MG_drops_2


title: serum_mESC_1000cells_TFAP2C_CR


title: Vehicle_MG_drops_1


title: mTSC_500cells_TFAP2C_CR

source_name: mTSC

growth_protocol: Mouse TSCs) were cultured in RPMI 1640 medium (Invitrogen) containing 20% FBS, L-glutamine, 2-mercaptoethanol, 70% MEF-CM and 37.5 ng/ml FGF4 and 1.7 μg/ml heparin.

value: mix


title: FAPs_60


title: 10_ng_mL_AREG_Astro_drops_3

value: Astrocyte


title: FAPs_58


title: FAPs_59


title: 96-HPI-10-TR1_11HP302-12HO-1_Inoculated

value: leave tissue


title: 10_ng_mL_AREG_Astro_drops_2


title: 96-HPI-10-TR3_11HP302-12HO-1_Inoculated

value: Inoculated with Peyronellaea pinodes


title: 96-HPI-10-TR2_11HP302-12HO-1_Inoculated


title: 72-HPI-15-TR3_OZP1604_Inoculated


title: mTSC_50000cells_TFAP2C_CR

growth_protocol: Mouse TSCs) were cultured in RPMI 1640 medium (Invitrogen) containing 20% FBS, L-glutamine, 2-mercaptoethanol, 70% MEF-CM and 37.5 ng/ml FGF4 and 1.6 μg/ml heparin.


title: serum_Tfap2c_KO_mESC_2000cells_TFAP2C_CR

value: Tfap2c KO


title: 100_ng_mL_LPS_EB_MG_drops_1


title: FAPs_57

value: skeletal muscle


title: mTSC_2000cells_TFAP2C_CR

growth_protocol: Mouse TSCs) were cultured in RPMI 1640 medium (Invitrogen) containing 20% FBS, L-glutamine, 2-mercaptoethanol, 70% MEF-CM and 37.5 ng/ml FGF4 and 1.5 μg/ml heparin.


title: 72-HPI-15-TR2_OZP1604_Inoculated


title: FAPs_56


title: MNase-Seq Replicate1_TFs-only

description: plasmid DNA

value: in vitro-reconstituted chromatin

value: Abf1, Reb1, no remodeler

value: 0.75 mM DSG, 0.05% Formaldehyde

value: whole cell


title: 10_ng_mL_AREG_Astro_drops_1

value: WT

value: fetal


title: Vehicle_Astro_drops_3


title: E65_ExE_TFAP2C_CR_rep2

source_name: E6.5 ExE

growth_protocol: E5.5 -E7.5 embryo tissues were collected via previously described (Harrison et al. 1995). Briefly, female mice and male mice  were mated naturally, and the time when the vaginal plug was observed the next day was considered E0.5.

value: C57BL/6J x  PWK/PhJ


title: FAPs_55

value: Fibro-adipogenic progenitors

value: young


title: E65_ExE_TFAP2C_CR_rep1

value: wild type


title: 72-HPI-15-TR1_OZP1604_Inoculated


title: 72-HPI-14-TR3_TWILIGHT_Inoculated

value: TWILIGHT


title: E65_ExE_SOX2_CR_rep2

value: Sox2 (Abclonal, A11936)


title: Vehicle_Astro_drops_2

value: Astrocyte


title: FAPs_54

value: aged


title: Vehicle_Astro_drops_1


title: 72-HPI-14-TR2_TWILIGHT_Inoculated

value: leave tissue

value: Inoculated with Peyronellaea pinodes


title: FAPs_53

value: skeletal muscle


title: Cytoplus10_ng_mL_AREG_3


title: E65_ExE_SOX2_CR_rep1


title: FAPs_52


title: 72-HPI-14-TR1_TWILIGHT_Inoculated


title: 72-HPI-11-TR3_WHARTON_Inoculated

value: WHARTON


title: E35_ICM_TFAP2C_CR_rep1

source_name: E3.5 ICM

growth_protocol: For collection of wildtypes E3.5 ICM, 4–6-week-old C57BL/6J female mice were injected with pregnant mare serum gonadotropin followed by human chorionic gonadotropin (hCG; Ningbo Hormone Product Co., Cat # 110251283 Ltd., China 10 IU) 48 hours before being mated with PWK/PhJ mice. Fertilized 8 cell were flushed out from the oviduct with HEPES-buffered CZB medium at E2.5 (68-70h). In vitro cultured was carried out for one day with the 8-cell embryo in KSOM medium to get blastocyst.

value: Tfap2c (Abclonal, A7739)


title: Cytoplus10_ng_mL_AREG_1


title: Cytoplus10_ng_mL_AREG_2


title: FAPs_50


title: FAPs_51


title: E35_ICM_TFAP2C_CR_rep2


title: 10_ng_mL_AREG_3


title: 72-HPI-11-TR2_WHARTON_Inoculated


title: 8cell_TFAP2C_CR_rep2

source_name: 8-cell stage

growth_protocol: Embryos were collected from mice induced to superovulation by injections of 5 IU of pregnant mare's serum gonadotrophin (Ningbo Sansheng Pharmaceutical Co, Ltd) and 5 IU of human chorionic gonadotrophin (Ningbo Sansheng Pharmaceutical Co, Ltd) 44-48 hours_x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000__x0000_㽝㽛므羰_x0000__x0000__x0000__x0000__x0000_


title: 8cell_TFAP2C_CR_rep1


title: 72-HPI-11-TR1_WHARTON_Inoculated


title: FAPs_49


title: 10_ng_mL_AREG_2


title: 72-HPI-10-TR3_11HP302-12HO-1_Inoculated


title: FAPs_48


title: 4cell_TFAP2C_CR_rep2

source_name: 4-cell stage


title: 10_ng_mL_AREG_1


title: 72-HPI-10-TR2_11HP302-12HO-1_Inoculated


title: FAPs_47


title: 4cell_TFAP2C_CR_rep1


title: Cyto_3


title: 72-HPI-10-TR1_11HP302-12HO-1_Inoculated


title: FAPs_46


title: 2cell_TFAP2C_CR_rep2

source_name: late 2-cell stage

growth_protocol: Embryos were collected from mice induced to superovulation by injections of 5 IU of pregnant mare's serum gonadotrophin (Ningbo Sansheng Pharmaceutical Co, Ltd) and 5 IU of human chorionic gonadotrophin (Ningbo Sansheng Pharmaceutical Co, Ltd) 44-48 hours apart and mated to males.


title: Cyto_2


title: FAPs_45


title: Cyto_1


title: Vehicle_6


title: FAPs_44


title: 6-HPI-TR3-14_TWILIGHT_Inoculated


title: 6-HPI-TR3-11_WHARTON_Inoculated


title: FAPs_43


title: Vehicle_5


title: 2cell_TFAP2C_CR_rep1


title: 6-HPI-TR3-10_11HP302-12HO-1_Inoculated


title: FAPs_42


title: X2018 [Control]

type: genomic

city: Cusano Milanino

first: Luciano

last: Calzari

state: MI

address: Via Zucchi 18

country: Italy

institute: IRCCS Istituto Auxologico Italiano

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450K Beadchip using standard Illumina protocol

scan_protocol: Fluorescence intensities were captured by using the fluorescent scanner Illumina HiScan SQ (Illumina).

data_processing:
Quality control, pre-processing and generation of β-values matrix were performed by using the ChAMP package (Morris TJ et al., 2014) implemented R environment (version 3.6.2). Sites with a detection p-value above 0.01 (n=4761) and a bead count <3 in at least 5% of samples (n=250) were removed. Moreover, also non-CpG probes (n=3051), potentially SNP affected probes (n=57628) (Zhou Wet al., 2017) probes aligning to multiple locations (n=11) (Nordlund J et al., 2013) and of X and Y chromosomes (n=9718) were filtered out. As a final outcome of the filtering procedures, a total of 410093 CpG sites were retained.
ChAMP loading, Normalization (SWAN) and Batch Correction (ComBat)

label: Cy3, Cy5

source_name: Control

label_protocol: Standard Illumina protocol

extract_protocol: DNA was extracted from peripheral blood lymphocytes (Automated Extractor, Tecan Group Ltd. and Wizard Genomic DNA Purification Kit (Ref: A1125), Promega). Quality control and quantification of DNA was assessed by visualization of genomic DNA (gDNA) on 1% agarose gel electrophoresis and by using NanoPhotometer Pearl (Implen GmbH).

value: Whole Blood

tag: Sex

value: female

tag: disease state

value: Control


title: X2037 [Control]


title: X3030 [Control]


title: X2043 [Control]


title: 6-HPI-TR2-15_OZP1604_Inoculated


title: Vehicle_4

value: WT

value: fetal


title: sgAreg_Tomato_3

value: 13 weeks


title: FAPs_41

value: Fibro-adipogenic progenitors

value: young


title: FAPs_40


title: 6-HPI-TR2-14_TWILIGHT_Inoculated

value: TWILIGHT


title: sgAreg_Tomato_2


title: 6-HPI-TR3-15_OZP1604_Inoculated


title: 6-HPI-TR2-11_WHARTON_Inoculated


title: X3029 [Control]

value: male


title: FAPs_39


title: X2026 [Control]


title: sgAreg_Tomato_1

value: Astrocyte


title: 6-HPI-TR2-10_11HP302-12HO-1_Inoculated


title: FAPs_38

value: aged


title: X2022 [Control]


title: sgScrmbl_Tomato_3


title: 6-HPI-TR1-15_OZP1604_Inoculated

value: leave tissue


title: FAPs_37


title: X2021 [Control]


title: sgScrmbl_Tomato_2


title: 6-HPI-TR1-14_TWILIGHT_Inoculated

value: Inoculated with Peyronellaea pinodes


title: FAPs_36

value: skeletal muscle


title: X3019 [Control]


title: sgScrmbl_Tomato_1


title: FAPs_34


title: 6-HPI-TR1-10_11HP302-12HO-1_Inoculated


title: X3016 [Control]


title: 100_ng_AREG_ICV_3

value: 10 weeks


title: FAPs_35


title: 6-HPI-TR1-11_WHARTON_Inoculated

value: WHARTON


title: X2014 [Control]

value: Whole Blood


title: 6-HPI-CR3-15_OZP1604_Control


title: X2006 [Control]

value: female


title: 100_ng_AREG_ICV_2


title: 100_ng_AREG_ICV_1


title: FAPs_33


title: X2005 [Control]

value: Control


title: 6-HPI-CR3-14_TWILIGHT_Control


title: X2002 [Control]


title: FAPs_32


title: 1X_PBS_ICV_3

value: WT


title: 1X_PBS_ICV_2


title: 6-HPI-CR3-10_11HP302-12HO-1_Control


title: FAPs_30


title: X3052 [Control]


title: 1X_PBS_ICV_1


title: X3046 [Control]


title: FAPs_29


title: 6-HPI-CR2-15_OZP1604_Control


title: 6-HPI-CR2-14_TWILIGHT_Control


title: RNAseq_VP882 ∆vpdS 60 min replicate iii

city: Jena

first: Marcel

last: Sprenger

address: Winzerlaer Straße 2

department: Institute of Microbiology

institute: Friedrich Schiller University

data_processing:
cDNA reads were imported into CLC Genomics Workbench v 22.0.2 and analysed using mostly standard parameters.
3'adaptor- and quality trimming was performed using the trim reads command with the following settings: 3´ trim: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA; Trim quality scores limit 0.05, Trim ambiguous nucleotides 2
The trimmed reads were checked for quality and mapped to the V.cholerae reference genome: NCBI Acc.number: NC_002505, NC_002506, NC_009016.1 using the following settings: Mismatch cost =  2, Insertion cost = 3, Deletion cost = 3, Length fraction = 0.8, Similarity fraction = 0.8, Global alignment = Yes, Strand specific = both, Maximum number of hits for a read = 1, expression value: TPM
Assembly: NC_002505, NC_002506, NC_009016.1

growth_protocol: Vibrio cholerae C6706  Δtdh + JSP1269 wt and Δtdh + JSP1269 ∆vpdS were grown overnight in M9 minimal media, supplemented with 0.4% glucose. The following day bacteria were diluted 1:200 in fresh media. At OD 0.4, cells were back-diluted 1:10 in M9 with 0.4% glucose and 0.035% arabinose to induce VqmA phage and grow again to OD 0.2. Induction of phage VP882 was activated by addition of 25 µM DPO to V. cholerae. Samples were collected (pre, 30 min and 60 min)

extract_protocol:
RNA was isolated using Tri-reagent. Prepared RNA was digested for DNA contaminations (TurboDNase treatment) and cleaned up using standard nucleic acid precipitation procedures. Depletion of ribosomal RNA was performed by rRNA-capturing biotinylated oligos. Binding to magnetic streptavidin-beads removed rRNA. Depletion was verified by Bioanalyzer.  doi.org/10.1128/mBio.00010-20
The rRNA depleted RNAs samples were fragmented using magnesium fragmentation module (NEB). cDNA was synthesized by using the NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB) as specified by the manufacturer. cDNA libraries were column-based purified and cleaned left-sided using the Agencourt AMPure XP kit (Beckman Coulter Genomics). The quality and quantity of cDNA libraries was measured by Bioanalyzer and Qubit, respectively.

treatment_protocol: The bacteria were treated with 25 µM final concentration of 3,5-dimethylpyrazin-2-ol (DPO). 4 OD600 units of cells were harvested in tubes containing 1/5 vol. "stop-mix" (95% ethananol, 5% phenol).

value: 60 min

value: delta_tdh + JSP-1269 (VP882::kanR delta_vpdS)


title: FAPs_28

value: Fibro-adipogenic progenitors


title: FAPs_27


title: X3042 [Control]


title: RNAseq_VP882 ∆vpdS 60 min replicate ii


title: X3038 [Control]


title: 6-HPI-CR3-11_WHARTON_Control


title: FAPs_31


title: 6-HPI-CR2-11_WHARTON_Control


title: 6-HPI-CR2-10_11HP302-12HO-1_Control


title: RNAseq_VP882 ∆vpdS 30 min replicate iii

value: 30 min


title: FAPs_26


title: 6-HPI-CR1-15_OZP1604_Control


title: X2036 [Control]


title: 6-HPI-CR1-14_TWILIGHT_Control

value: TWILIGHT


title: FAPs_25

value: young


title: X2023 [Control]


title: FAPs_24


title: RNAseq_VP882 ∆vpdS 30 min replicate ii


title: 6-HPI-CR1-11_WHARTON_Control


title: FAPs_23


title: X2020 [Control]


title: FAPs_22


title: 6-HPI-CR1-10_11HP302-12HO-1_Control


title: 48-HPI-TR3-15_OZP1604_Inoculated


title: RNAseq_VP882 ∆vpdS pre replicate iii

value: pre


title: FAPs_21

value: aged


title: X3028 [Control]


title: X2011 [Control]


title: X2010 [Control]


title: RNAseq_VP882 ∆vpdS pre replicate i


title: RNAseq_VP882 ∆vpdS pre replicate ii


title: FAPs_19


title: RNAseq_VP882 ∆vpdS 60 min replicate i


title: FAPs_20


title: X2009 [Control]


title: RNAseq_VP882 wt 60 min replicate ii

value: delta_tdh + JSP-1269 (VP882::kanR)


title: 48-HPI-TR3-10_11HP302-12HO-1_Inoculated

value: leave tissue

value: Inoculated with Peyronellaea pinodes


title: 48-HPI-TR3-11_WHARTON_Inoculated


title: X2007 [Control]


title: FAPs_18

value: skeletal muscle


title: X2003 [Control]


title: 48-HPI-TR2-15_OZP1604_Inoculated


title: RNAseq_VP882 ∆vpdS 30 min replicate i


title: RNAseq_VP882 wt 60 min replicate iii


title: 48-HPI-TR3-14_TWILIGHT_Inoculated


title: RNAseq_VP882 wt 60 min replicate i


title: 48-HPI-TR2-14_TWILIGHT_Inoculated


title: X2013 [Control]


title: X2001 [Control]


title: RNAseq_VP882 wt 30 min replicate ii


title: ALS_CTR041 [Control]

description: Already submitted as: GSM4602910;GSM4609084

value: male


title: FAPs_15


title: 48-HPI-TR2-11_WHARTON_Inoculated

value: WHARTON


title: RNAseq_VP882 wt 30 min replicate i


title: 48-HPI-TR2-10_11HP302-12HO-1_Inoculated


title: RNAseq_VP882 wt 30 min replicate iii


title: FAPs_14


title: FAPs_17


title: ALS_A853 [Case]

source_name: Case

value: Whole Blood

value: female

value: sporadic ALS


title: FAPs_13


title: FAPs_12


title: RIPseq_hfq-3XFLAG plus DPO replicate iii

library_source: other

molecule: other

growth_protocol: Vibrio cholerae C6706  Δtdh + JSP1269 and ∆tdh hfq::3XFLAG + JSP-1269 were grown overnight in M9 minimal media, supplemented with 0.4% glucose. The following day bacteria were diluted 1:200 in fresh media. At OD 0.4, cells were back-diluted 1:10 in M9 with 0.4% glucose and 0.035% arabinose to induce VqmA phage and grow again to OD 0.2. Induction of phage VP882 was activated by addition of 25 µM DPO to V. cholerae. Samples were collected 60 min post induction.

extract_protocol:
Cells equivalent to 50 OD600 units were collected and cells were lysed using glass beads. RNA-Co-immunoprecipitation using anti-FLAG-antibody following protein G sepharose, Solution was washed and RNA fraction was isolated with phenol-chloroform-isoamylalcohol. RNA was treated with TurboDNase to remove DNA contaminations. doi.org/10.1073/pnas.1920753117
The rRNA depleted RNAs samples were fragmented using magnesium fragmentation module (NEB). cDNA was synthesized by using the NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB)  according to the manufacturer's instructions. cDNA libraries were column-based purified and cleaned left-sided using the Agencourt AMPure XP kit (Beckman Coulter Genomics). The quality and quantity of cDNA libraries was measured by Bioanalyzer and Qubit, respectively.

value: 60 min

value: hfq::3XFLAG delta_tdh + JSP-1269 (VP882::kanR)

value: CoIP


title: ALS_A828 [Case]


title: FAPs_11

value: Fibro-adipogenic progenitors


title: FAPs_16


title: ALS_A805 [Case]


title: 48-HPI-CR3-15_OZP1604_Control

value: Control


title: 48-HPI-TR1-11_WHARTON_Inoculated


title: 48-HPI-TR1-10_11HP302-12HO-1_Inoculated


title: RIPseq_hfq-3XFLAG plus DPO replicate ii


title: ALS_A796 [Case]


title: FAPs_9

value: young


title: RIPseq_hfq-3XFLAG plus DPO replicate i


title: 48-HPI-CR3-14_TWILIGHT_Control

value: TWILIGHT


title: FAPs_8


title: ALS_A789 [Case]


title: ALS_A865 [Case]


title: RNAseq_VP882 wt pre replicate iii

value: pre


title: 48-HPI-TR1-15_OZP1604_Inoculated


title: 48-HPI-TR1-14_TWILIGHT_Inoculated


title: ALS_CTR040 [Control]

description: Already submitted as: GSM4609091


title: FAPs_7

value: aged


title: FAPs_10


title: 48-HPI-CR3-11_WHARTON_Control

value: leave tissue


title: RNAseq_VP882 wt pre replicate i

value: delta_tdh + JSP-1269 (VP882::kanR)


title: RNAseq_VP882 wt pre replicate ii


title: ALS_CTR038 [Control]

description: Already submitted as: GSM4609090


title: ALS_A787 [Case]


title: FAPs_6

value: skeletal muscle


title: RIPseq_ctrl plus DPO replicate i


title: RIPseq_ctrl plus DPO replicate ii


title: 48-HPI-CR3-10_11HP302-12HO-1_Control


title: RIPseq_ctrl plus DPO replicate iii


title: 48-HPI-CR2-15_OZP1604_Control


title: FAPs_4


title: ALS_A729 [Case]

value: male


title: RIPseq_hfq-3XFLAG minus DPO replicate iii


title: ALS_A754 [Case]


title: 48-HPI-CR2-14_TWILIGHT_Control


title: 48-HPI-CR2-11_WHARTON_Control

value: WHARTON


title: FAPs_5


title: ALS_CTR037 [Control]

value: Whole Blood


title: RIPseq_hfq-3XFLAG minus DPO replicate i


title: FAPs_3


title: 48-HPI-CR2-10_11HP302-12HO-1_Control


title: FAPs_2


title: ALS_A723 [Case]


title: RIPseq_ctrl minus DPO replicate iii


title: 48-HPI-CR1-15_OZP1604_Control


title: RIPseq_ctrl minus DPO replicate ii


title: RIPseq_hfq-3XFLAG minus DPO replicate ii


title: ALS_A643 [Case]


title: FAPs_1


title: CD45+ DRG cells, HTO

city: Solna

first: Zerina

last: Kurtović

address: Kungshamra 47, lgh 1203

department: Physiology and Pharmacology

country: Sweden

institute: Karolinska Institutet

description: Hashtag-derived oligonucleotide

data_processing:
CellRanger to generate barcodes.tsv.gz, fgeatures.tsv.gz, matrix.mtx.gz by NGI at Scilifelab, Stockholm
Seurat was used for filtering and clustering and generation of object of male cells only which is included in the publication
Assembly: mm10-3.0.0
Supplementary files format and content: Lundetal.rds
Supplementary files format and content: *barcodes.tsv, *genes.tsv, *matrix.mtx

molecule: protein

source_name: dorsal root ganglia

extract_protocol:
Mice were perfused with ice- cold PBS and neural tissues dissected into cold PBS. On average 40 pooled cervical, thoracic and lumbar DRGs were used. The tissues were digested in 2mg/ml Collagenase I (Gibco 17100-017), 5mg/ml Dispase II (Sigma, D4693) and 0.5mg/ml DNAse I (Roche, 11284932001) at 37C for 30min (Brain) or 40min DRGs. Myelin was removed using 38% Percoll (Sigma, GE17-0891-02). Single cell suspensions of DRG cells from 3 male and 3 female BALB/cAnNRj mice were blocked with FcR blocking solution (Miltenyi Biotec l No.130-092-575) and stained with anti-CD45:PE (BioLegend 103105). Additionally, TotalSeq™ anti-mouse Hashtag antibodies were used to label individual samples The samples were strained  through a 35-micron filter. DAPI was added to the cell solution in order to exclude dead cells. CD45+DAPI− cells were sorted on a BD Influx sorter.
The sorted cells were pooled into a single lane on the 10x Genomics Chromium Single Cell 3 ′ v3 system. Library preparation and sequencing were performed at the SciLifeLab sequencing facility, Solna using an Illumina HiSeq  at 61,006 reads/cell.
scRNA seq with hashtags

value: dorsal root ganglia

value: WT

value: naive


title: 48-HPI-CR1-14_TWILIGHT_Control


title: ALS_A622 [Case]

value: female

value: sporadic ALS


title: RIPseq_ctrl minus DPO replicate i

value: 60 min

value: CoIP


title: 48-HPI-CR1-11_WHARTON_Control

value: Control


title: ALS_CTR036 [Control]

description: Already submitted as: GSM4602909;GSM4609083


title: 48-HPI-CR1-10_11HP302-12HO-1_Control


title: ALS_A550 [Case]


title: 24-HPI-CR3-14_TWILIGHT_Control

value: TWILIGHT


title: ALS_A491 [Case]


title: RILseq_hfq-3XFLAG plus DPO replicate i

data_processing:
Analysis with "ChimericFragments" DOI: 10.5281/zenodo.8376810
default parameters, exept: min_seed_length=15; autocomplete_utrs=false; bp_shift_weight=0.0; max_bp_fdr=0.4; max. fisher fdr:0.05; min_reads=5
Assembly: NC_002505, NC_002506, NC_009016.1
Library strategy: RIL-seq

growth_protocol: Vibrio cholerae C6706  Δtdh + JSP1269 and ∆tdh hfq::3XFLAG + JSP-1269 were grown overnight in M9 minimal media, supplemented with 0.4% glucose. The following day bacteria were diluted 1:200 in fresh media. At OD 0.4, cells were back-diluted 1:10 in M9 with 0.4% glucose and 0.035% arabinose to induce VqmA phage and grow again to OD 0.2. Induction of phage VP882 was activated by addition of 25 µM DPO to V. cholerae. Samples were collected 60 min.

extract_protocol:
first strand cDNA synthesis using SuperScript III and Primer AR2, RNA degradation, cDNA cleanup, ligation of second adaptor(3Tr3) to cDNA 3' ends, cDNA cleanup and PCR enrichment using P5_Enr primer and P7_BC1_Enr primer
RIL-seq (doi: 10.1038/nprot.2017.115)

treatment_protocol: RNA-protein crosslinking, cell lysis, CoIP using anti-FLAG-antibody, RNA ends trimmed using RNase A/T1, ligation of neighboring RNAs, Protein digestion using Proteinase K, RNA extraction, fragmentaton and DNase digestion, ribosomal RNA depletion and purification with AMPure XP beads

value: hfq::3XFLAG delta_tdh + JSP-1269 (VP882::kanR)

value: crosslinking + CoIP


title: RILseq_hfq-3XFLAG plus DPO replicate ii


title: S-Cn3

city: Paris

first: Hugo

last: Varet

address: 28 rue du Docteur Roux

country: France

institute: Institut Pasteur

data_processing:
Sequencing was performed on the Illumina HiSeq 2500 platform to generate paired-end 100 bp reads with strand specificity. Reads were processed to remove adapter sequences and low-quality sequences using cutadapt version 1.11. Only sequences with a minimum length of 25 nucleotides were considered for further analysis. Alignment to the reference genome was carried out using STAR version 2.7.0a with default parameters. Gene quantification was performed using featureCounts version 1.6.1 from the Subread package with the following parameters: parameters: -t gene -g gene_id -s 2.
Count data were analyzed using R version 3.5.3 and the Bioconductor package DESeq2 version 1.22.2. The normalization and dispersion estimation were performed with DESeq2 using the default parameters and statistical tests for differential expression were performed applying the independent filtering algorithm. A generalized linear model was set in order to test for the differential expression between uninfected, E-Cn-infected, S-Cn-infected and D-Cn-infected mice. For each pairwise comparison, raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure and genes with an adjusted p-value lower than 0.05 were considered differentially expressed.
Assembly: Mus musculus mm10 GRCm38 from Ensembl version 92
Supplementary files format and content: featureCounts output (one per sample) as well as results from the differential expression analysis performed with DESeq2

source_name: Bone marrow

growth_protocol: Macrophage differentiation was induced by incubating bone marrow cells in RPMI medium containing 20% fetal bovine serum (FBS), 30% L929-Cell Conditioned media (LCCM; enriched in CSF-1) and 1% penicillin/streptomycin (Pen/Strep) for 7 days. Cells were maintained at 5% CO2 and 37C.

extract_protocol:
After the interaction, the macrophage monolayer was washed, and total RNA was isolated using the RNAeasy kit (Qiagen) following the manufacturer's protocols. RNA quantification and integrity were assessed using the Agilent 2100 Bioanalyzer.
Polyadenylated RNA-enriched libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina) following the manufacturer's protocols.

treatment_protocol: Following the differentiation, BMDMs were plated overnight in RPMI containing 10% FBS, 5% LCCM and 1% Pen/Strep to achieve adherent resting macrophages. Subsequently, the monolayer of resting BMDMs was washed and then cultured in RPMI containing 10% FBS, 1% Pen/Strep and 10 ug/mL of the opsonizing antibody 18B7. BMDMs were either co-cultured with yeast cells at a Multiplicity of Infection (MOI) of 5 or kept without yeast cells. After 2 hours of co-culture, the BMDM monolayers were washed, refreshed with medium without 18B7, and further incubated for an additional 4 hours. This resulted in a total duration of 6 hours for the C. neoformans-macrophage interaction.

value: Bone marrow

tag: strain/background

value: Bone marrow-derived macrophages

value: Infected with stationary-phase yeast cells


title: S-Cn2


title: S-Cn1


title: 24-HPI-CR3-11_WHARTON_Control

value: leave tissue


title: E-Cn3

value: Infected with logarithm-phase yeast cells


title: ALS_CTR035 [Control]

description: Already submitted as: GSM4602908;GSM4609082

value: Whole Blood


title: RILseq_ctrl plus DPO replicate iii

value: delta_tdh + JSP-1269 (VP882::kanR)


title: RILseq_ctrl plus DPO replicate ii


title: 24-HPI-CR3-10_11HP302-12HO-1_Control


title: RILseq_hfq-3XFLAG plus DPO replicate iii


title: CD45+ DRG cells, GEX

description: polyA RNA

value: dorsal root ganglia

value: WT


title: E-Cn2


title: 24-HPI-CR2-14_TWILIGHT_Control


title: ALS_A517 [Case]

value: female


title: RILseq_ctrl plus DPO replicate i


title: 24-HPI-CR3-15_OZP1604_Control


title: E-Cn1


title: ALS_A417 [Case]

value: sporadic ALS


title: ALS_A460 [Case]

value: male


title: ALS_A449 [Case]


title: RILseq_hfq-3XFLAG minus DPO replicate iii

value: 60 min


title: 24-HPI-CR2-15_OZP1604_Control

value: Control


title: D-Cn3

value: Infected with dormant/VBNC yeast cells


title: ALS_CTR034 [Control]

description: Already submitted as: GSM4609089


title: 24-HPI-CR2-11_WHARTON_Control

value: WHARTON


title: RILseq_hfq-3XFLAG minus DPO replicate ii

value: hfq::3XFLAG delta_tdh + JSP-1269 (VP882::kanR)

value: crosslinking + CoIP


title: ALS_A407 [Case]


title: D-Cn1

value: Bone marrow

value: Bone marrow-derived macrophages


title: RILseq_ctrl minus DPO replicate iii


title: 24-HPI-CR2-10_11HP302-12HO-1_Control

value: leave tissue


title: D-Cn2


title: ALS_A406 [Case]


title: 24-HPI-CR1-15_OZP1604_Control


title: Uni3

value: Uninfected


title: Uni2


title: RILseq_ctrl minus DPO replicate ii


title: ALS_A405 [Case]

value: Whole Blood


title: Uni1


title: 24-HPI-CR1-11_WHARTON_Control


title: RILseq_ctrl minus DPO replicate i

value: delta_tdh + JSP-1269 (VP882::kanR)


title: ALS_CTR033 [Control]

description: Already submitted as: GSM4609088


title: 24-HPI-CR1-10_11HP302-12HO-1_Control


title: ALS_A394 [Case]


title: RILseq_hfq-3XFLAG minus DPO replicate i


title: 24-HPI-15-TR3_OZP1604_Inoculated

value: Inoculated with Peyronellaea pinodes


title: 30-ary memory T cells rep 2 (ATAC-seq)

city: Minneapolis

first: David

last: Masopust

state: MN

address: 2101 6th St SE

department: Microbiology and Immunology

institute: University of Minnesota

data_processing:
Reads were aligned to the mouse genome mm10 using BowTie2
SAMTools was used to generate sorted BAM files that contained mapped reads only
Genomic regions were visualized using Gviz
Assembly: mm10
Supplementary files format and content: The processed data in the manuscript are just visualized gene tracks based on aligned reads.

source_name: Spleen and lymph nodes

growth_protocol: CD45.1+ C57Bl/6 female mice were immunized with three heterologous prime boost immunizations (VSV-NJ VV-N, VSV-Ind) at >= 60 day intervals. H-2Kb/N52-59+ CD45.1+ tertiary memory CD8 T cells were sorted from spleen and lymph nodes and 1x10^5 cells were transferred to congenic CD45.2 recipients, which subsequently received three immunizations (VSV-Ind, VV-N, VSV-NJ) at 60+d intervals. Transfer & boost scheme was repeated until 45 immunizations were reached.

extract_protocol: Sorted cells were treated with Tn5 transposase following the procedure described in Buenrostro, J. D., Wu, B., Chang, H. Y. & Greenleaf, W. J. ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide. Curr Protoc Mol Biology 109, 21.29.1-21.29.9 (2015). Dual-indexed libraries from the transposed DNA was prepared using Nextera reagent kits.

treatment_protocol: N-specific memory T cells were isolated and FACS-sorted from the spleen and LNs using an H-2Kb/N52-59 tetramer

value: Spleen and lymph nodes

value: T cells

tag: cell type (sorted)

value: 30-ary memory T cells

value: B6 CD45.1 (B6.SJL-Ptprca Pepcb/BoyJ)

value: wild type

value: 30 immunizations


title: 56d

city: Kraków

first: Alicja

last: Wierzbicka

address: ul. Sarego 2

country: Poland

institute: National Research Institute of Animal Produstion

data_processing:
Quality control (fastQC)
Filtration of low quality reads (phred quality <20). Minimal length of reads set to 35. Removal of adaptors (Flexbar)
Mapping with default options (Tophat)
Counting reads to Ensembl GTF version 95 intervals (htseq-count) and differential expresion calculated with the use of Deseq2
Assembly: Sus Scrofa 11.1

organism: Sus scrofa

source_name: lung

extract_protocol:
Collected tissues were stored at -80°C. Genetic material was isolated using the RNeasy Micro Kit (QIAGEN, Hilden, Germany) in line with the recommendations. QuantSeq 3′mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, Vienna, Austria) with 100ng/ul total RNA was used to construct sequencing libraries.
Libraries were prepared for sequencing using standard Illumina protocols

value: lung

value: Male

value: standard dose of calcidiol


title: 63d

value: Female


title: 40d


title: 30-ary memory T cells rep 3 (ATAC-seq)


title: ALS_A359 [Case]

value: female

value: sporadic ALS


title: 24-HPI-15-TR2_OZP1604_Inoculated

value: leave tissue


title: ALS_CTR032 [Control]

value: male

value: Control


title: ALS_A627 [Case]

value: Whole Blood


title: Senary memory T cells rep 3 (ATAC-seq)

value: Senary memory T cells

value: 6 immunizations


title: 24-HPI-CR1-14_TWILIGHT_Control

value: TWILIGHT


title: ALS_A943 [Case]


title: 24-HPI-14-TR3_TWILIGHT_Inoculated

value: Inoculated with Peyronellaea pinodes


title: Senary memory T cells rep 2 (ATAC-seq)

value: Spleen and lymph nodes

value: T cells

value: B6 CD45.1 (B6.SJL-Ptprca Pepcb/BoyJ)


title: ALS_A941 [Case]


title: Senary memory T cells rep 1 (ATAC-seq)

value: wild type


title: 24-HPI-14-TR2_TWILIGHT_Inoculated


title: 24d

value: lung


title: Tertiary memory T cells rep 3 (ATAC-seq)

value: Tertiary memory T cells

value: 3 immunizations


title: ALS_CTR031 [Control]

description: Already submitted as: GSM4609087


title: 24-HPI-14-TR1_TWILIGHT_Inoculated


title: 16d

value: Female

value: standard dose of calcidiol


title: 23d

value: Male


title: ALS_A934 [Case]

value: female

value: sporadic ALS


title: 39d


title: 32d


title: 24-HPI-11-TR3_WHARTON_Inoculated

value: WHARTON

value: leave tissue


title: Tertiary memory T cells rep 2 (ATAC-seq)


title: 24-HPI-11-TR1_WHARTON_Inoculated


title: 30-ary memory T cells rep 1 (ATAC-seq)

value: 30-ary memory T cells

value: 30 immunizations


title: 24-HPI-11-TR2_WHARTON_Inoculated

value: Inoculated with Peyronellaea pinodes


title: 24-HPI-15-TR1_OZP1604_Inoculated


title: ALS_A932 [Case]

value: Whole Blood

value: male


title: Tertiary memory T cells rep 1 (ATAC-seq)

value: Spleen and lymph nodes

value: T cells

value: B6 CD45.1 (B6.SJL-Ptprca Pepcb/BoyJ)


title: 15d

value: lung


title: Naive T cells rep 3 (ATAC-seq)

value: Naive T cells

value: wild type

value: 0 immunizations


title: 31d

value: Male

value: standard dose of calcidiol


title: ALS_A908 [Case]

value: sporadic ALS


title: Naive T cells rep 2 (ATAC-seq)


title: 8d

value: Female


title: 24-HPI-10-TR3_11HP302-12HO-1_Inoculated

value: leave tissue


title: 7d


title: Naive T cells rep 1 (ATAC-seq)


title: ALS_CTR030 [Control]

description: Already submitted as: GSM4602911;GSM4609085

value: female

value: Control


title: ALS_A892 [Case]


title: 24-HPI-10-TR2_11HP302-12HO-1_Inoculated

value: Inoculated with Peyronellaea pinodes


title: 61c

value: increased dose of cholecalciferol+calcidiol


title: 24-HPI-10-TR1_11HP302-12HO-1_Inoculated


title: ALS_A820 [Case]

value: Whole Blood

value: male


title: Acute IR #2

city: Phoenix

first: Shwetal

last: Mehta

state: AZ

address: 350 W Thomas Rd

department: Ivy Brain Tumor Center

institute: Barrow Neurological Institute

data_processing:
Base calling was done using Bcl2fastq by Illumina
Alignment using Tophat2.1.1, default settings except for --library-type fr-firststrand; used hg19 gtf as reference
RPKM calculated using Cufflinks2.2.1, default setting except -u, --library-type fr-firststrand; used hg19 gtf as reference
Custom pipeline to convert the RPKM to attomoles using ERCC spike-in mix as reference
Average of replicates using custom pipeline
Calculation of relative RNA levels in quisinostat, radiation or quisinostat + radiation treated as compared to vehicle treated samples
Assembly: hg19; PR8 sequences downloaded from FluDB

source_name: GBM PDX tumor

growth_protocol: GB126TdT cells were grown in serum-free neural stem cell media supplemented with EGF and bFGF and puromycin. GB126TdT cells were injected intracranially to induce tumors

extract_protocol:
Total RNA was harvested using the Qiagen Rneasy kit
Library were constructed using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Human (Illumina) following the manufacturer's protocol.
RNA-seq (stranded)

treatment_protocol: For acute samples, mice were treated with vehicle, radiation (2 gy x 3; MWF), quisinostat (10mg/kg; MWF) or combination of IR + quisinostat for one week. For survival studies, similar treatments and treatment groupsw were included except quisinostat treatment was continued until animals were moribund.

value: GBM PDX tumor

value: GBM PDX-derived

tag: group

value: Acute

value: IR


title: ALS_A322 [Case]


title: ALS_CTR027 [Control]


title: 0-HPI-CR3-14_TWILIGHT_Control

value: TWILIGHT


title: ALS_A317 [Case]


title: ALS_A287 [Case]


title: 0-HPI-CR3-11_WHARTON_Control

value: WHARTON


title: Acute Combo #2

value: Combo


title: Survival IR #3

value: Survival


title: Survival Combo #3


title: Acute QST #2

value: QST


title: 29c

value: lung

value: Female


title: 6c

value: Male


title: 0-HPI-CR2-14_TWILIGHT_Control

value: leave tissue

value: Control


title: ALS_A172 [Case]

value: sporadic ALS


title: Acute QST #1


title: 0-HPI-CR3-15_OZP1604_Control


title: 21c

value: increased dose of cholecalciferol+calcidiol


title: ALS_CTR025 [Control]

value: Whole Blood

value: female


title: 0-HPI-CR2-11_WHARTON_Control


title: 53c


title: Acute Combo #3

value: GBM PDX tumor

value: GBM PDX-derived


title: 38c


title: 0-HPI-CR3-10_11HP302-12HO-1_Control


title: 44b

value: increased dose of cholecalciferol


title: ALS_CTR029 [Control]

description: Already submitted as: GSM4609086


title: Acute Vehicle #3

value: Acute

value: Vehicle


title: 14c


title: 0-HPI-CR2-15_OZP1604_Control


title: 30c


title: 0-HPI-CR2-10_11HP302-12HO-1_Control


title: Survival QST #2


title: ALS_CTR018 [Control]

value: male


title: 36b


title: ALS_B552 [Case]


title: ALS_B555 [Case]


title: 0-HPI-CR1-10_11HP302-12HO-1_Control


title: Survival QST #3

value: Survival


title: ALS_CTR023 [Control]


title: 0-HPI-CR1-14_TWILIGHT_Control

value: TWILIGHT


title: ALS_A747 [Case]


title: 20b

value: lung


title: ALS_CTR015 [Control]


title: 11b

value: Female


title: Survival Vehicle #2


title: Acute IR #1

value: IR


title: 42a

value: Male

value: standard dose of cholecalciferol


title: 27b


title: 19b


title: 0-HPI-15-TR2_OZP1604_Inoculated

value: leave tissue

value: Inoculated with Peyronellaea pinodes


title: ALS_A744 [Case]

value: Whole Blood

value: sporadic ALS


title: Acute Combo #1

value: GBM PDX tumor

value: Combo


title: ALS_A731 [Case]


title: 0-HPI-15-TR3_OZP1604_Inoculated


title: Acute QST #3

value: GBM PDX-derived

value: QST


title: 0-HPI-CR1-15_OZP1604_Control

value: Control


title: 12b

value: increased dose of cholecalciferol


title: 0-HPI-CR1-11_WHARTON_Control

value: WHARTON


title: 0-HPI-15-TR1_OZP1604_Inoculated


title: Survival Vehicle #1

value: Survival

value: Vehicle


title: Survival Vehicle #3


title: 41a

value: lung

value: Female


title: 0-HPI-14-TR3_TWILIGHT_Inoculated

value: TWILIGHT


title: ALS_CTR016 [Control]

value: male


title: Acute Vehicle #2

value: Acute


title: Acute IR #3

value: IR


title: ALS_A716 [Case]

value: Whole Blood


title: 0-HPI-14-TR1_TWILIGHT_Inoculated

value: leave tissue

value: Inoculated with Peyronellaea pinodes


title: 33a

value: standard dose of cholecalciferol


title: ALS_CTR021 [Control]


title: 0-HPI-14-TR2_TWILIGHT_Inoculated


title: Acute Vehicle #1

value: GBM PDX tumor

value: GBM PDX-derived


title: ALS_A677 [Case]

value: sporadic ALS


title: Survival IR #2


title: 26a

value: Male


title: 34a


title: Survival Combo #2

value: Combo


title: ALS_A676 [Case]

value: female


title: Survival IR #1

value: Survival


title: ALS_CTR014 [Control]

value: Control


title: 18a

value: lung


title: Survival Combo #1


title: 25a

value: Female


title: 17a


title: 0-HPI-11-TR2_WHARTON_Inoculated

value: WHARTON


title: 0-HPI-11-TR1_WHARTON_Inoculated


title: 0-HPI-11-TR3_WHARTON_Inoculated


title: 10a


title: 0-HPI-10-TR3_11HP302-12HO-1_Inoculated


title: ALS_A668 [Case]

value: male


title: Survival QST #1

value: QST


title: 0-HPI-10-TR2_11HP302-12HO-1_Inoculated


title: ALS_CTR013 [Control]

value: Whole Blood


title: 9a


title: 0-HPI-10-TR1_11HP302-12HO-1_Inoculated

value: leave tissue


title: L163_Sepsis_ADT

city: Clayton

first: Monash

middle: Bioinformatics

last: Platform

address: Wellington Road

institute: Monash Bioinformatics Platform

description:
PBMC, Mixed sample (Baby A11 Day 32 Enterobacter bloodstream infection; Baby B6 Day 38 NEC; Baby A5 Day 31 Proximal, ADT,HTO
ADT: TotalSeq™-B0139 anti-human TCR γ/δ, TotalSeq™-B0072 anti-human CD4, TotalSeq™-B0080 anti-human CD8a
HTO: TotalSeq™-B0252 anti-human Hashtag 2, TotalSeq™-B0254 anti-human Hashtag 4, TotalSeq™-B0256 anti-human Hashtag 6

data_processing:
Single cell data were processed individually by cellranger 5.0.1 using cellranger multi mode against the cellranger reference refdata-gex-GRCh38-2020-A. This mode was used to process gene expression data and antibody capture data for each sample simultaneously.
Data were then further processed in R (v4.0.2), using Seurat (v4.0.1), scater (v1.18.6) and harmony (v1.0 immunogenics lab) packages. Individual count matrices were loaded into Seurat and scater for processing. Demultiplexing was performed using Seurat's HTODemux function. The isOutlier function from scater was used to detect library size outliers, cells with low number of genes expressed and cells with a high percentage of mitochondrial reads. After the samples had been demultiplexed, further quality control and data normalisation was performed using the basic Seurat workflow
The six individual Seurat ojects were then merged to created one combined Seurat object before Harmony was used to performed integration with the RunHarmony function. This was to batch correct the sorted CD3+ samples (EL Pre and EL sepsis)
Cell annotation was performed using the SingleR package against the Monaco reference from the celldex package
Assembly: GRCh38
Supplementary files format and content: filtered_feature_bc_matrix.h5 - this contains the gene counts, HTO/ADT counts produced by the cellranger pipeline
Library strategy: CITE-seq

source_name: blood

extract_protocol:
PBMC were extracted from whole neonatal blood and frozen at -80C. Paired samples from the same baby were thawed on the day of the experiment and incubated with Totalseq antibodies or hashtag reagents prior to sorting of live PBMC (4/5 babies) or CD3+ T cells (1/5 babies).
Cells were loaded onto a 10x Chromium Chip A using reagents from the Chromium Single-Cell 3’ gene expression and antibody derived tag (ADT) libraries were prepared according to the manufacturer’s instructions. Samples were sequenced with the Illumina NextSeq 500 platform, or Hiseq 2500 High Output platform dependent on the experiment. For libraries names beginning 'EL_Pre' or 'EL_Sepsis'  sorted cells were loaded onto a 10x Genomics Chromium controller and 5’ gene expression and ADT libraries were prepared.

value: blood

value: PBMC

value: Mixed sample (Baby A11 Day 32 Enterobacter bloodstream infection; Baby B6 Day 38 NEC; Baby A5 Day 31 Proximal)


title: ALS_A655 [Case]


title: ALS_CTR020 [Control]


title: L163_Sepsis_GEX

description: PBMC, Mixed sample (Baby A11 Day 32 Enterobacter bloodstream infection; Baby B6 Day 38 NEC; Baby A5 Day 31 Proximal, GEX

data_processing:
Single cell data were processed individually by cellranger 5.0.1 using cellranger multi mode against the cellranger reference refdata-gex-GRCh38-2020-A. This mode was used to process gene expression data and antibody capture data for each sample simultaneously.
Data were then further processed in R (v4.0.2), using Seurat (v4.0.1), scater (v1.18.6) and harmony (v1.0 immunogenics lab) packages. Individual count matrices were loaded into Seurat and scater for processing. Demultiplexing was performed using Seurat's HTODemux function. The isOutlier function from scater was used to detect library size outliers, cells with low number of genes expressed and cells with a high percentage of mitochondrial reads. After the samples had been demultiplexed, further quality control and data normalisation was performed using the basic Seurat workflow
The six individual Seurat ojects were then merged to created one combined Seurat object before Harmony was used to performed integration with the RunHarmony function. This was to batch correct the sorted CD3+ samples (EL Pre and EL sepsis)
Cell annotation was performed using the SingleR package against the Monaco reference from the celldex package
Assembly: GRCh38
Supplementary files format and content: filtered_feature_bc_matrix.h5 - this contains the gene counts, HTO/ADT counts produced by the cellranger pipeline


title: ALS_A613 [Case]


title: 2a

value: standard dose of cholecalciferol


title: 1a


title: SHAM5 lnc

city: Jinan

first: Linchuan

state: Shandong

address: 16766# Jingshi Road

institute: Shandong University

data_processing:
cutadapt-1.9 (cutadapt.readthedocs.io/en/stable/)was used to remove the reads that contained adapter contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC v0.10.1 (www.bioinformatics.babraham.ac.uk/projects/fastqc/). We used hisat2-2.0.4 (ccb.jhu.edu/software/hisat2/)to map reads to the genome, Ensembl v96 (command line: hisat2 -1 R1.fastq.gz -2 R2.fastq.gz -S mapped.sam).
The mapped reads of each sample were assembled using stringtie-1.3.4(ccb.jhu.edu/software/stringtie/) with default parameters (command line: stringtie -p 2 -G genome.gtf -o output.gtf -l mapped.bam). Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using gffcompare (github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kb)]).
Transcripts that overlapped with known mRNAs and transcripts shorter than 200 bp were discarded. Then we utilized CPC0.9-r2 (cpc2.cbi.pku.edu.cn/) with default parameters(cpc2 -i novel.fa -o cpc2.out) and CNCI2.0 (wwww.bioinfo.org/software/cnci) with default parameters (CNCI.py -f novel.fa -o CNCI.result -p 1 -m ve -g novel.gtf -d genome.fa) to predict transcripts with coding potential. All transcripts with CPC score <-1 and CNCI score <0 were removed and remained transcripts were considered as lncRNAs.
Genome_build: Rnor_6.0.96
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Rattus norvegicus

source_name: Diabetic rats after sham operation

growth_protocol: Cohorts of rats used in the study received a 60 kcal% saturated high-fat diet (HFD) (60% of calories as fat) for four weeks and followed a single intraperitoneal injection with streptozotocin (35 mg/kg in sodium citrate buffer) after 16h of fasting to induce DM. Three days after the STZ administration, rats with fasting blood glucose consistently exceeded 16.7 mmol/L were considered as promising diabetic model.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 5 ug of total RNA was used to deplete ribosomal RNA according to the manuscript of the Epicentre Ribo-Zero Gold Kit (Illumina, San Diego, USA). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq 4000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Then the eligible animals were randomly divided into two body weight-matched groups (SG and SHAM) .

value: wistar

value: liver

value: Diabetic rats after sham operation

value: wild type


title: ALS_A595 [Case]

value: sporadic ALS


title: ALS_CTR017 [Control]

value: Control


title: Unbalanced Diet + large MFG 22 9 weeks

city: Rehovot

first: Jerome

last: Janssen

address: Herzl 229

country: Israel

institute: Hebrew University of Jerusalem

data_processing:
DADA2 pipeline (v1.24) for truncating, trimming, merging, removing chimeras
DECIPHER package (v2.24) and RDP_v18_July2020 training set was used for taxonomy assignment
FastTree (v. 2.1.11) was used to generate a phylogentic tree
DESeq2 (v1.36.0) was used for differential abbundance analysis
Assembly: RDP v18
Supplementary files format and content: txt file contains assigned taxonomy up to genus level
Supplementary files format and content: txt file includes raw counts generated by DADA2
Library strategy: Metagenomics (16S rRNA-seq)

organism: rat gut metagenome

source_name: Caecal stool

growth_protocol: 3 week old Sprague-Dawley rats were fed for 6 weeks with control or treatment diet

extract_protocol:
On the sacrifice day, caecum from all rats was collected and stored at -80°C. 0.25 gr of defrosted caecum content was extracted using the QIAamp PowerFecal kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. The DNA extraction was stored at -80°c until sent in dry ice to the University of Illinois in Chicago for 16S rRNA sequencing of the V4 region using 515F–806R primers.
Amplicons were generated using a two-stage PCR amplification protocol as described previously (Naqib et al. (2018)). The primers contained 5’ common sequence tags (known as common sequence 1 and 2, CS1 and CS2) as described previously (e.g. Moonsamy et al. 2013). First stage PCR amplifications were performed in 10 microliter reactions in 96-well plates, using MyTaq HS 2X mastermix (Bioline). PCR conditions were 95°C for 5 minutes, followed by 28 cycles of 95°C for 30”, 55°C for 45” and 72°C for 60”. Subsequently, a second PCR amplification was performed in 10 microliter reactions in 96-well plates. A mastermix for the entire plate was made using MyTaq HS 2X mastermix. Each well received a separate primer pair with a unique 10-base barcode, obtained from the Access Array Barcode Library for Illumina (Fluidigm, South San Francisco, CA; Item# 100-4876). These AccessArray primers contained the CS1 and CS2 linkers at the 3’ ends of the oligonucleotides. Cycling conditions were: 95°C for 5 minutes, followed by 8 cycles of 95°C for 30”, 60°C for 30” and 72°C for 30”. Libraries were then pooled in equal volume and the pool was purified using an AMPure XP cleanup protocol (0.6X, vol/vol; Agencourt, Beckmann-Coulter) to remove fragments smaller than 300 bp.

treatment_protocol: Control food according to the recommendation of the American Institute of Nutrition (AIN-93G). The UBD diet contained low protein (10% of kcal), low mineral and vitamin (50% of the recommended amount) and high fat (25% of kcal). Raw milk of a commercial herd containing 300 dairy cows, was separated by conventical milk separator (Beit El, Binyamina) to cream (large MFG) and skim (small MFG). Solid composition was determined by near infra redinfra-red spectroscopy (Lactoscan, FOSS). MFG size was determined in both fractions using light scattering (Mastersizer, Malvern, UK). The average diameter of large MFG was 3.4 µm and the small MFG was 2.4 µm. The concentration of fat was normalized with water to reach the level of 1.48 and 2.2 gr/100ml solution, and 1ml was administrated daily by oral gavage to experimental animals.

value: Caecal stool

value: female

value: 9 weeks

value: WT

value: Unbalanced Diet + large MFG


title: Unbalanced Diet + large MFG 14 9 weeks


title: L163_Pre_GEX

description: PBMC, Mixed sample (Baby A11 Day 18 Proximal; Baby B6 Day 30 Proximal; Baby A5 Day 26 NEC, GEX

value: Mixed sample (Baby A11 Day 18 Proximal; Baby B6 Day 30 Proximal; Baby A5 Day 26 NEC)


title: SHAM3 lnc


title: SHAM2 lnc


title: Unbalanced Diet + large MFG 24 9 weeks


title: BDNF+Dox, replicate 1

city: Sendai

first: Takaaki

last: Nakamura

address: 1-1 Seiryomachi, Aobaku

department: Department of Neuroscience and Organs

country: Japan

institute: Tohoku university

data_processing:
ChIP-seq reads were trimmed from 3' end, using cutadapt 1.1 and trimmomatic 0.32.
ChIP-seq reads were aligned to the GRCh38 genome using Bowtie 1. Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called using MACS v2.2.7.1 with the significannce cut-off p-value <= 0.01. Supplemented xls files were generated concomitantly with MACS2 callpeak.
Assembly: GRCh38 (Ensembl, release 92)
Supplementary files format and content: xls (except for input sample)

growth_protocol: DMEM, 10%FCS, 300 µg/ml Zeocin. Cells were cultured at 37 ℃ at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using Bioruptor Sonicator (Diagenode).
TruSeq ChIP Sample Prep kit

treatment_protocol: SH-SY5Ycells were neuronally differentiated over 10 days by culturing in 3%FCS DMEM supplemented wiith 10 µM RA for 6 days and DMEM without FCS supplemented with 50 ng/ml BDNF for following 4 days. α-synuclein was inducted for 3 days by 1 µg/ml doxycyline (Tet-on system). ChIP was conducted using H4R3me2s antibody.

tag: chip antibody

value: H4R3me2s (Epigentek)

value: RA+BDNF+Dox


title: BDNF+Dox, replicate 3


title: BDNF+Dox, replicate 2


title: SHAM4 lnc


title: Unbalanced Diet + large MFG 13 9 weeks


title: ALS_A563 [Case]

value: Whole Blood


title: SHAM1 lnc


title: ALS_CTR012 [Control]

value: male


title: BDNF, replicate 3

value: RA+BDNF


title: Unbalanced Diet + large MFG 11 9 weeks


title: ALS_A473 [Case]


title: L163_Pre_ADT

description:
PBMC, Mixed sample (Baby A11 Day 18 Proximal; Baby B6 Day 30 Proximal; Baby A5 Day 26 NEC, ADT,HTO
ADT: TotalSeq™-B0139 anti-human TCR γ/δ, TotalSeq™-B0072 anti-human CD4, TotalSeq™-B0080 anti-human CD8a
HTO: TotalSeq™-B0251 anti-human Hashtag 1, TotalSeq™-B0253 anti-human Hashtag 3, TotalSeq™-B0255 anti-human Hashtag 5

value: blood

tag: cell type

value: PBMC


title: SG5 lnc

source_name: Diabetic rats after sleeve gastrectomy

value: wistar

value: liver

value: diabetic rats after sleeve gastrectomy at 3 months


title: Unbalanced Diet + large MFG 23 9 weeks


title: Unbalanced Diet + small MFG 24 9 weeks

value: Unbalanced Diet + small MFG


title: BDNF, replicate 2

tag: cell line


title: Unbalanced Diet + small MFG 23 9 weeks

value: Caecal stool

tag: genotype


title: ALS_CTR024 [Control]

value: female

value: Control


title: SG4 lnc

value: wild type


title: Unbalanced Diet + large MFG 12 9 weeks

value: 9 weeks

value: WT

value: Unbalanced Diet + large MFG


title: SG3 lnc


title: Unbalanced Diet + small MFG 22 9 weeks


title: ALS_A376 [Case]

value: sporadic ALS


title: Naive, replicate 3

value: H4R3me2s (Epigentek)


title: ALS_CTR019 [Control]

value: Whole Blood

value: male


title: Unbalanced Diet + small MFG 21 9 weeks


title: SG2 lnc


title: Naive, replicate 1


title: Unbalanced Diet + small MFG 14 9 weeks


title: ALS_A326 [Case]


title: Naive, replicate 2


title: ALS_A320 [Case]


title: SHAM5

data_processing:
Cutadapt-1.9 (https://cutadapt.readthedocs.io/en/stable/) was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Tophat-2.0.10（http://ccb.jhu.edu/software/tophat/index.shtml） to map reads to the genome, Ensembl v96(command line: tophat2 –o outputFolder --transcriptomeindex=genome.fa --phred64-quals R1.fastq.gz R2.fastq.gz).
CIRCExlorer2 v2-2.2.6(http://yanglab.github.io/CIRCexplorer/) and CIRIv2.0.2(https://sourceforge.net/projects/ciri/) were used to identified circRNA.
circRNA was quantified and normalized according to SRPBM = number of circular reads/ (number of mapped reads (units in billion) * read length).
Genome_build: Rnor_6.0.96
Supplementary_files_format_and_content: tab-delimited text files include circRNA srpbm values for each Sample

extract_protocol:
Total RNA was isolated and purified using Trizol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Agilent 2100 with RIN number >7.0. Approximately 5 ug of total RNA was used to deplete ribosomal RNA according to the manuscript of the Ribo-Zero™ rRNA Removal Kit (Illumina, San Diego, USA). Then left RNAs were treated with Rnase R (Epicentre Inc, Madison, WI, USA) to remove linear RNAs and to enrich circRNAs. After removing ribosomal and linear RNAs, the enriched circRNAs were fragmented into small pieces using divalent cations under high temperature. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA,which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP.. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single-or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs,The ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300 bp (±50 bp). At last, we performed the paired-end sequencing on an Illumina Hiseq 4000 (LC Bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Diabetic rats after sham operation


title: Unbalanced Diet + small MFG 13 9 weeks


title: Input


title: Uninfected CD4 T cells, replicate 2 [U2]

city: Rockville

first: Peter

last: Sun

state: MD

address: 5625 Fishers lane

department: Division of Intramural Research

institute: National Institute of Allergy and Infectious Diseases

data_processing:
Data processed by Novogene sequencing service
Remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%).
Remove reads when low quality nucleotides (Base Quality less than 20) constitute more than 50 percent of the read. The Qscore (Quality value) of over 50% bases of these read is <= 5.
Mapping is done using STAR software by Novogene
Assembly: homo_sapiens_hg19
Supplementary files format and content: Reads, FPKM and pairwise comparisons

source_name: primary PBMC

growth_protocol: PBMC were isolated from healthy donor buffy coats and stimulated with anti-CD3 in RPMI supplemented with 10% FBS in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared by Novogene sequencing service.

treatment_protocol:
After two days stimulation, CD8 T cells depleted PBMC were infected with HIV-1 BAL or NL4-3 strains for 6 days in the presence of indicated treatments in RPMI suppplemented with 10% FBS.
All compounds were dissovled in DMSO and used as QVD-OPH 50uM, PD-0332991 1uM, BB-95 50uM.

value: primary PBMC

value: CD4 T cells

value: Uninfected

value: DMSO

value: Day 6


title: ALS_A415 [Case]


title: ALS_CTR022 [Control]


title: Unbalanced Diet + small MFG 11 9 weeks

value: Caecal stool

value: Unbalanced Diet + small MFG


title: BDNF, replicate 1

value: RA+BDNF


title: ALS_A318 [Case]

value: female


title: HIV-1 NL4-3 Vpu- infected CD4 T cells, replicate 2 [V2]

value: HIV-1 NL4-3 Vpu-


title: HIV-1 NL4-3 Nef- infected CD4 T cells, replicate 2 [D2]

value: HIV-1 NL4-3 Nef-


title: Unbalanced Diet 24 9 weeks

value: 9 weeks

value: WT

value: Unbalanced Diet


title: ALS_CTR028 [Control]

value: Whole Blood

value: Control


title: SHAM1

value: wistar

value: liver

value: Diabetic rats after sham operation

value: wild type


title: HIV-1 NL4-3 WT infected CD4 T cells, replicate 2 [W2]

value: primary PBMC

value: CD4 T cells

value: HIV-1 NL4-3 WT


title: Unbalanced Diet 23 9 weeks

value: Caecal stool


title: SG1 lnc

value: diabetic rats after sleeve gastrectomy at 3 months


title: ALS_A244 [Case]

value: male

value: sporadic ALS


title: Unbalanced Diet 22 9 weeks

value: female


title: HIV-1 BAL infected CD4 T cells, replicate 2 [BB2]

value: HIV-1 BAL

value: Day 6


title: Unbalanced Diet + small MFG 12 9 weeks

value: 9 weeks

value: WT

value: Unbalanced Diet + small MFG


title: SHAM4

value: wistar


title: Unbalanced Diet 21 9 weeks

value: Unbalanced Diet


title: Unbalanced Diet 14 9 weeks


title: SG3

value: liver


title: HIV-1 BAL infected CD4 T cells, replicate 2 [Q2]

value: 50uM QVD-OPH


title: SHAM3

value: Diabetic rats after sham operation

value: wild type


title: SHAM2


title: HIV-1 BAL infected CD4 T cells, replicate 2 [B2]

value: primary PBMC

value: CD4 T cells

value: DMSO


title: Unbalanced Diet 13 9 weeks

value: Caecal stool


title: ALS_CTR010 [Control]

value: Whole Blood

value: male

value: Control


title: SG2

value: diabetic rats after sleeve gastrectomy at 3 months


title: ALS_A145 [Case]

value: sporadic ALS


title: ALS_A138 [Case]


title: Uninfected CD4 T cells, replicate 1 [U1]

value: Uninfected

value: Day 6


title: ALS_A300_I [Case]


title: SG5

value: wistar


title: re_DM2

source_name: Diabetic rats with diabetic relapse after sleeve gastrectomy

value: diabetic relapse


title: ALS_A137 [Case]


title: Unbalanced Diet 12 9 weeks

value: female

value: 9 weeks

value: WT

value: Unbalanced Diet


title: Unbalanced Diet 11 9 weeks


title: SG4

value: liver

value: wild type


title: re_DM1


title: ALS_CTR011 [Control]


title: Control 24 9 weeks


title: HIV-1 NL4-3 Nef- infected CD4 T cells, replicate 1 [D1]

value: primary PBMC

value: CD4 T cells

value: HIV-1 NL4-3 Nef-


title: ALS_A070_I [Case]

value: Whole Blood

value: male


title: HIV-1 BAL infected CD4 T cells, replicate 2 [P2]

value: HIV-1 BAL


title: Control 23 9 weeks

value: Caecal stool

value: Control


title: K117E-3

first: Xian

last: Liu

address: 38 Life Science Park Street

institute: Beijing Institute of Life Omics

data_processing:
The raw data obtained from sequencing is filtered using SOAPnuke (v1.5.6) to remove 1) reads containing connectors (connector contamination); 2) Reads with an unknown base N content greater than 5%; 3) Low quality reads (reads with a base mass value below 15 accounting for more than 20% of the total base number of the reads are considered low quality reads), resulting in clean data. Subsequent use of Dr Tom Multi omics Data Mining System（ https://biosys.bgi.com ）Conduct data analysis, mapping, and mining.
Use HISAT2 (v2.1.0) software to compare clean data to the reference genome. Compare clean data to the reference gene set using Bowtie2 (v2.3.4.3) [3]. Use RSEM (v1.3.1) [4] software for gene expression quantification, and use pheatmap (v1.0.8) [5] to draw clustering heatmaps of gene expression levels in different samples. Use DESeq2 (v1.4.5) [6] (or DEGseq [7] or Poisson Dis [8]) for differential gene detection, with Q value ≤ 0.05 or FDR ≤ 0.001.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM and RPKM values for each Sample

source_name: pancreas

extract_protocol:
RNA was harvested using TRIzol Reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Optimal Dual-mode mRNA Library Prep Kit (BGI) following manufacturer's protocols.

value: pancreas

value: 9 weeks old


title: ALS_CTR009 [Control]


title: K117E-2


title: HIV-1 BAL infected CD4 T cells, replicate 1 [BB1]

value: Day 6


title: Control 22 9 weeks

value: female


title: SG1

value: wistar

value: diabetic rats after sleeve gastrectomy at 3 months


title: ALS_A022 [Case]

value: sporadic ALS


title: HIV-1 BAL infected CD4 T cells, replicate 1 [P1]


title: K117E-1


title: Control 21 9 weeks

value: 9 weeks

value: WT


title: ALS_CTR008 [Control]


title: WT-3


title: Control 14 9 weeks


title: HIV-1 BAL infected CD4 T cells, replicate 1 [Q1]

value: primary PBMC

value: 50uM QVD-OPH


title: WT-2


title: E65_Epi_TFAP2C_CR_rep2

data_processing:
library strategy: CUT&RUN
bulk RNA-seq reads were mapped to the mm9 reference genome using Tophat (version 2.0.11).The gene expression levels were calculated by Cufflinks (version 2.2.1). RefFlat database from UCSC genome browser was used with microRNA and repeats excluded.
CUT&RUN reads were aligned to the mm9 genome with the parameters: -t -q -N 1 -L 25 -X 2000 --no-mixed --no-discordant by Bowtie2 v2.3.5. Aligned reads were filtered with a minimum MAPQ of 20, and PCR duplicates were removed using Picard MarkDuplicates v1.119. Read coverages over mm9 genome were estimated by bamCoverage from deepTools v3.3.1 with parameters --binSize 100 --normalizeUsing RPKM.
Assembly: mm9
Supplementary files format and content: Bigwig for CUT&RUN, ATAC-seq tracks, gene expression table for RNA-seq data

source_name: E6.5 epiblast

extract_protocol:
Cells or embyos were lysed in wash buffer.
CUT&RUN was performed as previously reported (Skene et al., 2018; Skene and Henikoff, 2017) with modifications. Briefly, after removing the zona pellucida with Tyrode’s solution (Sigma-Aldrich, T1788) or 0.5% (m/v) Protease from Streptomyces griseus (Sigma-Aldrich, P8811), early embryos were incubated with Concanavalin-coated magnetic beads (Polyscience, 86057) for 10 min at room temperature on a thermomixer at 400 rpm. Samples were then incubated with primary antibody at a ratio of 1:100 at 4℃ for 3-5 hours on a thermomixer at 400 rpm. After washing for one time, beads were incubated with pA-MNase (to a final concentration of 400-700ng/mL) (a gift from Steven Henikoff lab) at 4℃ for 1 hours on a thermomixer at 400 rpm. After two times of washing, targeted digestion was performed by adding 2μL of 100mM CaCl2 for 30 mins on ice, followed by termination by adding an equal volume of 2  × stop buffer. Samples were then incubated at 37℃ for 20 mins for fragment releasing. The total samples or supernatants were digested with Proteinase K (NEB, P8107S) and purified using phenol:chloroform:isoamyl alcohol (25:24:1, v/v) followed by ethanol purification at -80℃ overnight. The next day, DNA was purified and subjected to Truseq library preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). Sequencing was done using the HiSeq X Ten system or  NovaSeq (Illumina) according to the manufacturer’s protocol.

value: wild type

value: C57BL/6J x  PWK/PhJ

value: Tfap2c (Abclonal, A7739)


title: Control 12 9 weeks


title: E65_Epi_TFAP2C_CR_rep1


title: Control 11 9 weeks


title: HIV-1 NL4-3 WT infected CD4 T cells, replicate 1 [W1]

value: CD4 T cells

value: HIV-1 NL4-3 WT


title: HIV-1 BAL infected CD4 T cells, replicate 1 [B1]

value: HIV-1 BAL

value: DMSO


title: Ethephon Treated Apex sampled at day 8, Rep 3 [TAP8.3]

status: Public on Nov 22 2023

city: Kunming

first: Yun

last: Zheng

state: Yunnan

address: 452 Fengyuan Road

institute: Yunnan Agricultural University

data_processing:
Reads whose first 25 nucleotides had sequencing scores less than 30 were discarded.
Reads with at least 18 nt after removing the 3'-adapters were kept.
The unique sequences of the remaining reads were obtained and aligned to the miRNA sequences using the BLAST algorithm with the options of ``-S 1 -m 8 -e 0.01".
The abundances of miRNAs were calculated.
Assembly: Acomosus_321_v3 from Phytozome
Supplementary files format and content: Text file to show the names of unique miRNAs and their sequences.
Supplementary files format and content: MS Excel file to show the abundances of unique miRNAs.

organism: Ananas comosus

source_name: Ethephon Treated Apex sampled at day 8

growth_protocol: A uniform plot with pineapple plants weighing 1.5 to 2 kg was selected in a commercial field (Cultivar 'MD1', PRI 73-50) at Dole Plantation, Wahiawa, Hawaii (21° 31’ 52.6 N; -158° 03’ 35.3 W) 6 weeks before commercial forcing.

extract_protocol:
Total RNA was extracted from the apex and leaf bases using the Qiagen RNeasy Plant Mini Kit (Qiagen, #74904) following the manufacturer's protocol. DNA was removed with the DNA-free DNA Removal Kit (Life Technologies, #AM1906M). Three biological replicates were sequenced for each sampling stage with three apices or leaf bases in each replication.
Total RNA (2 µg) was used for the preparation of the mRNA-Seq library using the TruSeq Stranded mRNA LT kit (Illumina, USA) according to the manufacturer’s protocol. The size of the RNA-Seq library was evaluated by electrophoresis (1 μl of sample + 1 μl of loading dye 6X, 1% Agarose, TBE 1X Buffer, 30 minutes, 60V) and 1 μl of sample was used for quantification with a Qubit Fluorometer (Invitrogen, USA) using the DNA HS assay kit.
The multiplexed pooled libraries were sequenced on Illumina HiSeq4000 with a 50 nt read length. Small RNA libraries were prepared from total RNA using the NEBNext Multiplex Small RNA Sample Kit for Illumina (E7300, NEB, Ipswich, MA) following the manufacturer’s protocol. The libraries were quantified by qPCR and sequenced in each lane with a read length of 50 nt.

treatment_protocol: The plot was divided into three replications with two treatments (control and treated) and ~50 plants in each treatment block. Water (10 ml) as control treatment or ethephon (50 mg ai in 10 ml) (Ethrel, Rhone-Poulenc, AG Company, North Carolina) as flower induction treatment was injected into the centre of the plant between 7:00 and 7:20 AM. At 8:30 to 8:45 am, three plants were harvested from each replication in the water control and ethephon-treated plants at each sampling time after treatment. Four grams of the "D" leaf base (most recently matured leaf) and the other leaves of the uprooted plants were trimmed in the field from the cut stem. The trimmed leaf bases and the trimmed stem were chilled and immediately returned to the laboratory on ice at 10 AM for further processing. The bases of the trimmed leaves were removed from the apex of the apex of the stem to expose the stem (Supplementary Figure SF1) and <1 g of the apex was taken from each stem and frozen in liquid nitrogen. This physical processing of the leaf bases and apex, especially the care needed to carefully remove the leaf bases from the shoot apex of the three control and treated plants of each of the three replications was completed by 2:00 PM and reported here 6 hours after ethephon or water control treatment. Subsequent leaf samples at the apex and ‘D’ were taken 1, 2, 3, 4, 5, 6 and 8 days after treatment between 8:00 and 8:30 AM and processed by noon in the laboratory. Leaf bases were included as a control to allow comparison with nonapex tissue, since leaf primordia remained on the excised apex. All samples were stored at -80 °C until ground into powder in liquid nitrogen for RNA extraction.

value: Ethephon Treated Apex sampled at day 8

value: ethephon (50 mg ai in 10 mL) (Ethrel, Rhone-Poulenc, AG Company, North Carolina) as the flower induction treatment


title: WT-1

value: pancreas

value: 9 weeks old


title: Ethephon Treated Apex sampled at day 8, Rep 2 [TAP8.2]


title: Ethephon Treated Apex sampled at day 6, Rep 2 [TAP7.2]

source_name: Ethephon Treated Apex sampled at day 6

value: Ethephon Treated Apex sampled at day 6


title: Ethephon Treated Apex sampled at day 6, Rep 3 [TAP7.3]


title: Ethephon Treated Apex sampled at day 6, Rep 1 [TAP7.1]


title: Ethephon Treated Apex sampled at day 5, Rep 3 [TAP6.3]

source_name: Ethephon Treated Apex sampled at day 5

value: Ethephon Treated Apex sampled at day 5


title: Ethephon Treated Apex sampled at day 5, Rep 2 [TAP6.2]


title: Ethephon Treated Apex sampled at day 5, Rep 1 [TAP6.1]


title: Ethephon Treated Apex sampled at day 4, Rep 1 [TAP5.1]

source_name: Ethephon Treated Apex sampled at day 4

value: Ethephon Treated Apex sampled at day 4


title: Ethephon Treated Apex sampled at day 3, Rep 3 [TAP4.3]

source_name: Ethephon Treated Apex sampled at day 3

value: Ethephon Treated Apex sampled at day 3


title: Ethephon Treated Apex sampled at day 4, Rep 2 [TAP5.2]


title: Ethephon Treated Apex sampled at day 3, Rep 2 [TAP4.2]


title: Ethephon Treated Apex sampled at day 2, Rep 2 [TAP3.2]

source_name: Ethephon Treated Apex sampled at day 2

value: Ethephon Treated Apex sampled at day 2


title: Ethephon Treated Apex sampled at day 2, Rep 1 [TAP3.1]


title: Ethephon Treated Apex sampled at day 2, Rep 3 [TAP3.3]


title: Ethephon Treated Apex sampled at day 3, Rep 1 [TAP4.1]


title: Ethephon Treated Apex sampled at day 1, Rep 3 [TAP2.3]

source_name: Ethephon Treated Apex sampled at  day 1

value: Ethephon Treated Apex sampled at  day 1


title: Ethephon Treated Apex sampled at day 1, Rep 2 [TAP2.2]


title: Ethephon Treated Apex sampled at day 8, Rep 1 [TAP8.1]


title: Ethephon Treated Apex sampled at 6 hours Rep 3 [TAP1.3]


title: Ethephon Treated Apex sampled at 6 hours Rep 1 [TAP1.1]


title: Non-Treated Apex sampled at day 8, Rep 3 [CAP8.3]

source_name: Non-Treated Apex sampled at day 8

value: Non-Treated Apex sampled at day 8

value: water (10 ml) as control


title: Ethephon Treated Apex sampled at 6 hours Rep 2 [TAP1.2]


title: Non-Treated Apex sampled at day 6, Rep 3 [CAP7.3]

source_name: Non-Treated Apex sampled at day 6

value: Non-Treated Apex sampled at day 6


title: Non-Treated Apex sampled at day 8, Rep 2 [CAP8.2]


title: Non-Treated Apex sampled at day 8, Rep 1 [CAP8.1]


title: Non-Treated Apex sampled at day 5, Rep 3 [CAP6.3]

source_name: Non-Treated Apex sampled at day 5

value: Non-Treated Apex sampled at day 5


title: Non-Treated Apex sampled at day 6, Rep 2 [CAP7.2]


title: Non-Treated Apex sampled at day 5, Rep 1 [CAP6.1]


title: Ethephon Treated Apex sampled at day 4, Rep 3 [TAP5.3]


title: HIV-1 NL4-3 Vpu- infected CD4 T cells, replicate 1 [V1]

value: primary PBMC

value: CD4 T cells

value: HIV-1 NL4-3 Vpu-

value: Day 6