title: ChIP-seq-A-SPT5-SPT5AID-VCPiAuxin

description: ChIP-seq SPT5

value: SPT5 (BD Biosciences # 611107)

value: genomic DNA


title: ChIP-seq-A-SPT5-SPT5AID-Auxin

status: Public on Aug 31 2021

type: SRA

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

country: USA

institute: Northwestern University Feinberg School of Medicine

description: ChIP-seq SPT5

library_source: genomic

data_processing:
For ChIP-seq, single-end raw reads trimmed by Trimmomatic 0.33 (Bolger et al., 2014) were aligned to a concatenated genome comprised of human hg38 and mouse mm10 assemblies, using bowtie 2.2.6 (Langmead and Salzberg, 2012) with --sensitive option. The aligned reads with MAPQ ≥ 30 were extended to 150 bp and read counts were normalized to total reads aligned to spike-in genome. Metaplots of ChIP-seq signals were generated using deepTools 3.1.1 (Ramírez et al., 2016).
For PRO-seq, low-quality bases and adapters from 3’ ends of reads were removed using cutadapt 1.14 (Martin, 2011) requiring a read length of 16–36 bp. Reads derived from ribosomal RNA were filtered out by mapping reads on human and fly ribosomal DNA. The remaining reads were aligned using bowtie 2.2.6 with --very-sensitive option (Langmead and Salzberg, 2012), to a concatenated genome comprised of human hg38 and fly dm6 assemblies. The 5’ ends of aligned reads with MAPQ ≥ 30 were taken by bedtools genomecov 2.25 (Quinlan and Hall, 2010) with -strand and -5 options, and strands of the 5’ ends of reads were then swapped. Read counts were normalized to total reads aligned to the spike-in genome.  Heatmaps and metaplots of PRO-seq signal were generated by deepTools 3.1.1 (Ramírez et al., 2016).
For TT-seq, single-end raw reads trimmed by Trimmomatic 0.33 (Bolger et al., 2014) were aligned to human genome hg38 assemblies, using bowtie 2.2.6 (Langmead and Salzberg, 2012) with --sensitive option. Heatmaps of ChIP-seq signals were generated using deepTools 3.1.1 (Ramírez et al., 2016).
Genome_build: hg38, mm10, dm6
Supplementary_files_format_and_content: bigWig files with normalized read counts were provided for all samples.

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Human DLD-1 cells that constitutively express OsTIR1 were cultured at 37°C in DMEM (Sigma #D6429) supplemented with 10% FBS (Sigma #F2442), 1% Pen-Strep (Gibco #15140-122) in CO2 incubators. Yeast cells were grown in YPAD medium

extract_protocol:
For ChIP-seq in human DLD1 cells, 20-50 million cells were crosslinked with 1% paraformaldehyde (Electron Microscopy Sciences) in PBS for 10 min at r.t. Spike-in mouse embryonic fibroblast fixed cells were added to samples as described previously (Orlando et al., 2014). Chromatin was sonicated with the Covaris E220 for 4 min with 10% duty cycle, 140 peak intensity power, 200 cycles per burst. Immunoprecipitations were carried out with antibodies and Dynabeads Protein G (Invitrogen). For ChIP-seq in yeast cells, cells were fixed with 2.2% formaldehyde for 15 min.    PRO-seq sample preparation was performed according to the previously described qPRO-seq protocol (Judd et al., 2020). ~5 million DLD-1 nuclei  mixed with spike-in Drosophila S2 nuclei were used for nuclear run-on assay.     For pulse-chase nascdnt RNA labeling with TT-seq, cells were treated with 250 nM NVP-2 for 1 h, followed by nascent RNA labeling with 500 µM 4-thiouridin (Sigma # T4509) for 15 min.
For ChIP-seq, DNA libraries were prepared by the HTP Library Preparation Kit for Illimina (KAPA). For PRO-seq, adapter sequences previously described (Mahat et al., 2016) were used. PRO-seq libraries were prepared according to the previously described qPRO-seq protocol (Judd et al., 2020). TT-seq library was prepared as described previously (Schwalb et al., 2016; Rosencrance wt al., 2020).

treatment_protocol: To induce degradation of AID-tagged proteins, 500 µM auxin was added to culture. To induce anchor-away depletion, exponentially growing yeast cultures were treated with 1.0 ug/mL Rapamycin.

tag: cell line

tag: cell type

value: Colorectal adenocarcinoma

tag: genotype

value: SPT5-AID OsTIR1

tag: treatment

value: Auxin

tag: antibody

tag: molecule subtype


title: ChIP-seq-A-input-SPT5AID-Vehicle

description: ChIP-seq input

value: Vehicle

value: none (input)


title: Daxx +/+ GMP 3wpi 1

city: Bonn

first: Paolo

last: Salomoni

address: Sigmund-Freud-Str. 27

country: Germany

institute: DZNE e.V.

description:
210215_GMP_3wpi_NormalizedCounts_Gene.txt
GMP_AllGenotypes.cntTable

library_source: transcriptomic

data_processing:
Illumina Casava 1.8.4 for base calling and demultiplexing
Sequencing reads were adapter trimmed using Cutadapt 1.13 and aligned against mm10 (GENCODE release M14) using STAR aligner 2.5.3 with standard settings. For repeat element analysis STAR aligner was run with the following options: --outFilterMultimapNmax 100 --winAnchorMultimapNmax 100.
Reads mapping to rRNA, the mitochondrial genome and non-uniquely were removed. For repeat element expression analysis only reads mapping to the mitochondrial genome were removed.
Differentially expressed genes and repeat elements were obtained by running DESeq2 1.16.1.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file with DESeq2 normalized counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: Hematopoietic Progenitor Cell

extract_protocol:
Primary hematopoietic stem/progenitor cells were isolated form bone marrow and populations sorted by flow cytometry. Total RNA was extracted using Trizol reagent.
Illumina sequencing libraries were created with the Ovation SoLo RNA-seq kit from NuGEN Technologies according to the manufacturer's instructions.

tag: strain

tag: tissue

value: Bone marrow

tag: mouse line

value: Daxx +/+ Cre +/-

tag: time after end of induction

value: 3 wpi


title: Pu.1 F/F KLS 1

description:
210215_KLS_Pu1FFvsWT_3wpi_NormalizedCounts_Gene.txt
Pu1singleKO_wt1.cntTable

source_name: Hematopoietic Stem/Progenitor Cell

value: Pu.1 F/F Cre +/-


title: ChIP-seq-A-NELFA-SPT5AID-VCPiAuxin

description: ChIP-seq NELFA

value: VCPiAuxin

value: NELF-A (Proteintech # 10456-1-AP)


title: ChIP-seq-A-SPT5-SPT5AID-Vehicle

description: ChIP-seq SPT5


title: ChIP-seq-A-NELFA-SPT5AID-Auxin

description: ChIP-seq NELFA


title: Daxx F/F Pu.1 F/F KLS 3wpi 1 Lo54

description:
210215_KLS_3wpi_NormalizedCounts_Gene.txt
KLS_DaxxFFPu1FFvsDaxxWt.cntTable

value: Daxx F/F Pu.1 F/F Cre +/-


title: ChIP-seq-A-Pol2-SPT5AID-VCPiAuxin

description: ChIP-seq Pol II

value: RPB1 NTD (Cell signaling # 14958S)


title: Mon-385-Endo

city: Guildford

first: Fernando

middle: O

last: Martinez Estrada

state: Surrey

address: Stag Hill

department: Faculty of Health & Medical Sciences

country: United Kingdom

institute: University of Surrey

data_processing:
Reads were aligned with HISAT2 to GRCh38.p3, sorted and duplicates marked using Sambamba and primary alignment reads counted at the exon and summarized at gene level using Feature Counts.
Differential expression analysis was performed on TPM (Transcripts per million) values.
Genome_build: GRCh38.p3
Supplementary_files_format_and_content: RNAseq Data Processed data.txt represents TPM (Transcripts per million) values.

source_name: Human blood

growth_protocol: Monocytes and macrophages for RNAseq analysis were isolated by Ficoll gradient followed by the Negative isolation Kit II from Miltenyi according to manufacturer instructions.

extract_protocol:
Total RNA was extracted using the Trizol and the Quiazol kit according to manufacturer’s instructions.
After verifying that the integrity of total RNA was above a RIN score of 8 on a Tape Station 2200 (Agilent), 200ng of total RNA was used as input for poly-A selection and Illumina library construction using the NEBNext Ultra Directional Library Kit (NEB) according to the manufacturer’s instructions.
Samples were sequenced on an Illumina NextSeq 500 platform with 42bp paired-end reads.

tag: disease state

value: Endometriosis

value: Blood

value: Total monocytes


title: Daxx +/+ KLS 3wpi 2 Lo53

description:
210215_KLS_3wpi_NormalizedCounts_Gene.txt
KLS_DaxxFFvsDaxxWt.cntTable


title: Daxx +/+ KLS 3wpi 3


title: Mon-384-Endo


title: Mon-382-Endo


title: ChIP-seq-A-Pol2-SPT5AID-Auxin

description: ChIP-seq Pol II

value: genomic DNA


title: Daxx +/+ KLS 3wpi 1 Lo52


title: ChIP-seq-A-Pol2-SPT5AID-Vehicle

description: ChIP-seq Pol II

value: Colorectal adenocarcinoma


title: Mon-381-Endo


title: cRel_EBV_PDBu-1

city: MONTREAL

first: David

last: Langlais

state: QC

address: 740 Ave Dr Penfield, rm 4203, McGill Genome Centre

department: Human Genetics

country: Canada

institute: McGill University

data_processing:
The resulting sequence reads were assessed for quality with FastQC v0.11.8 (Babraham Bioinformatics); sequencing adapters and low-quality nucleotides were trimmed with Trimmomatic v.0.36.
Experimental and input control sequence reads were mapped to the human hg38 reference genome assembly with Bowtie 1.1.2.
Genomic binding sites of c-Rel were identified using peak detection algorithm MACS (version 1.4.2, default parameters), with comparisons for read enrichment against control input DNA from the same cells, and using a p-value threshold <10-5.
Peak heights were retrieved with the Homer v4.11 annotatePeaks tool77 and further filtered for a fold-enrichment >3 [ChIP vs Input], with peak heights >3 reads per million retained.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: bigWig and bed files

source_name: EBV cells

growth_protocol: Naïve B cells and naïve CD4+ T cells were freshly isolated from three healthy donors PBMCs using Miltenyi Biotec columns and EBV cells were cultured in RPMI supplemented with 10% AB human serum.

extract_protocol:
ChIP was performed as previously described [Langlais et al., JEM, 2016] with minor modifications. Briefly, cells were fixed by incubation with 1% formaldehyde in the culture medium for 10 minutes at room temperature. Crosslinking was stopped by adding 0.125 M glycine, cells were washed with cold PBS and nuclei were extracted. Nuclei were resuspended in sonication buffer and the chromatin was sheared during four 30 s sonication cycles separated by intervals of 30 s, with a Bioruptor Pico (Diagenode); the sonicated fragments were 100-500 bp in size. Bead immunocomplexes were prepared by overnight incubation of 20 μl of Dynabeads Protein G and 20 μl of Dynabeads Protein A (Life Technologies) with 5 μg of anti-c-Rel antibody (D5G1A) or with a rabbit normal IgG control (2729S), both from Cell Signaling Technologies. Immunoprecipitation was performed by overnight incubation of the antibody-bead matrices with sheared chromatin from the equivalent of 2.5x10^6 cells, followed by successive medium-stringency washes. Samples were de-crosslinked by overnight incubation at 65̊°C in 1% SDS buffer, followed by RNase A and proteinase K enzymatic treatments and were then subjected to DNA purification with the QIAquick PCR Purification kit (Qiagen).
ChIP-seq libraries were prepared with the KAPA Hyperprep ChIP Library Preparation kit (Roche) and sequenced on one lane of an SP flow cell on an Illumina NovaSeq 6000 sequencer in a 50 bp paired-end read configuration. Input DNA for each cell type was sequenced as a negative control.

treatment_protocol: Cells were plated in 12-well plates in RPMI with 10% AB human serum and stimulated as follows for 2 h: B cells (NS, CD40L and F(ab’)2 goat anti-human IgM [Jackson ImmunoResearch; 20 ug/ml], or PMA [40 ng/ml]); naïve CD4+ T cells (NS or PMA); EBV-B cells (NS or PDBu [10-7 M]).

value: EBV cells

tag: chip antibody

value: c-Rel antibody (D5G1A; Cell Signaling Technologies)


title: Mon-392-Endo


title: Mon-391-Control

value: Pain Only


title: Daxx +/+ LTHSC 2

description:
210215_LTHSC_3dpi_Rosa_NormalizedCounts_Genes.txt
210215_LTHSC_3dpi_Rosa_NormalizedCounts_TE.txt

source_name: Long-term hematopoietic stem cells

value: RosaCreER

value: 3 dpi


title: Mon-369-Endo


title: Daxx F/F LTHSC 2

value: Bone marrow

value: Daxx F/F Cre +/-


title: Daxx F/F KLS 3wpi 1 Lo22

value: 3 wpi


title: Daxx F/F KLS 3wpi 2 Lo23


title: cRel_EBV_PDBu-2


title: cRel_EBV_NS

value: NS


title: Input_EBV


title: Mon-390-Control


title: Daxx +/+ LTHSC 1

value: Daxx +/+ Cre +/-


title: cRel_Bcells_PMA

source_name: Freshly isolated naive B cells from a pool of three healthy donors PBMCs

tag: diagnosis

value: Healthy

value: Naive B cells

value: PMA


title: Mon-379-Control

value: Blood


title: Mon-374-Control

value: Total monocytes


title: Daxx F/F LTHSC 1


title: Input_Bcells


title: cRel_Bcells_NS


title: Daxx F/F LTHSC 3


title: Daxx F/F KLS 3wpi 3 Lo24


title: Mon-389-Control


title: Mon-373-Control


title: Daxx +/F LTHSC 2

value: Daxx +/F Cre +/-


title: Daxx +/F LTHSC 1


title: cRel_CD4T_PMA

source_name: Freshly isolated naive CD4 T cells from a pool of three healthy donors PBMCs

value: Naive CD4 T cells


title: cRel_CD4T_NS


title: cRel_Bcells_CD40L-IgM


title: Daxx F/F Pu.1 F/F KLS 3wpi 2

description:
tagmented genomic DNA
KLS_ATACseq_DaxxFFPu1FFvsDaxxWtWt_diffsite.txt
KLS_DKO.idr.conservative_peak.narrowPeak

data_processing:
Illumina Casava 1.8.4 for base calling and demultiplexing
Sequencing reads were adapter trimmed using Cutadapt 1.13 and aligned against mm10 (GENCODE release M14) using STAR aligner 2.5.3 with the following options: --alignIntronMax 1 --alignMatesGapMax 1800.
Reads mapping to the the mitochondrial genome and non-uniquely were removed. In addition, read duplicates were removed and start position of reads was offset by +4 bp if mapping to the positive strand and -5 bp if mapping to the negative strand.
For peak calling the ENCODE ATAC-seq analysis pipeline 0.3.4 was used.
Peak files were sorted by coordinate and overlapping peaks were merged with bedtools merge.
Identification of differentially accessible sites using diffreps with 600 bp window size.
Genome_build: mm10
Supplementary_files_format_and_content: Bed/NarrowPeak file with merged ATAC-seq peak positions and/or tab-delimited files with differentially accessible regions identified with diffreps

extract_protocol:
Primary hematopoietic stem/progenitor cells were isolated form bone marrow and populations sorted by flow cytometry.
ATAC-seq libraries were created as described in Buenrostro et al. 2015. Briefly, cells were lysed and treated with Tn5 Transposase from the Nextera Library Prep kit from Illumina for 30 min at 37°C. DNA was purified with Qiagen MinElute PCR purification kit and libraries were generated by PCR amplification using Nextera Index Primers from Illumina.

value: Daxx F/F Pu.1 F/F Cre +/-


title: Daxx F/F Pu.1 F/F KLS 3wpi 1


title: Daxx +/+ KLS 3wpi 1

description:
tagmented genomic DNA
KLS_Wildtype.idr.conservative_peak.narrowPeak


title: D129-D123T123

city: Paris

first: Elodie

last: Segura

address: 156 rue de Vaugirard

department: INSERM U1151

country: France

institute: INSERM

data_processing:
Quality of RNA-seq data was assessed using FastQC.
Trimming was performed using Atropos.
Reads were aligned to the transcriptome using STAR
Genome_build: hg38
Supplementary_files_format_and_content: Count matrix (raw counts) was obtained using DESeq2.

source_name: human monocyte

growth_protocol: Human CD14+ monocytes were cultured with M-CSF and IL-4 with or without TNF-a for 3h or 6h.

extract_protocol:
Cells were lyzed and mRNA extracted using Qiagen RNEasy Mini kit including on-column DNAse digestion.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Stranded mRNA Library Prep Kit (Illumina). 500 ng of RNA was used for each sample.
Sequencing was performed in 4 sequencing unit of NovaSeq 6000 (Illumina) (100-nt-length reads, paired end) with an average depth of 40 millions of clusters per sample.

tag: donor


title: D129-D123T120


title: D129-D123T122


title: Input_CD4T


title: D129-D123T119


title: D129-D123T121


title: D129-D123T124


title: Daxx F/F LT.HSC 3dpi 3

description:
tagmented genomic DNA
LTHSC_ATACseq_3dpi_DaxxFFvsDaxxWtWt_diffsite.txt
DaxxFF.idr.conservative_peak.narrowPeak

source_name: Hematopoietic Stem Cell


title: Daxx F/F KLS 3wpi 3

description:
tagmented genomic DNA
KLS_ATACseq_DaxxFF_diffsite.txt
KLS_DaxxFF.idr.conservative_peak.narrowPeak


title: D129-D123T116


title: Daxx +/+ LT.HSC 3dpi 2

description:
tagmented genomic DNA
DaxxWtWt.idr.conservative_peak.narrowPeak


title: Daxx F/F KLS 3wpi 1


title: Daxx F/F LT.HSC 3dpi 2


title: D129-D123T118


title: Sample 11: Input_shScr_KCl_2

city: Mississauga

first: iva

last: zovkic

state: ON

address: 3359 Mississauga road North

institute: University of Toronto Mississauga

description: Input

data_processing:
Reads were aligned using Bowtie 2.
The data were analyzed using relative enrichment measurements at genomic landmarks, including established H2A.Z peaks in the mouse hippocampus
Read counts were normalized using deepTools
Genome_build: UCSC mm10

source_name: primary cells

growth_protocol: primary neurons were made from E16 embryos. Gentle dissociation with Trypsin was followed by manual dissociation and neurons were plated on Poly L lysine coated plates

extract_protocol:
ChIP was conducted on Mnase digested chromatin with antibodies against H2A.Z (millipore cat#Abe1363)
Library prep was conducted by Genome Quebec using NEBNext Ultra II library prep kit
Adapters: IlluminaTruSeq LT

treatment_protocol: neurons were either left untreated or treated with 55mM KCl before fixing and collection

value: mouse hippocampal neurons

tag: developmental stage

value: 9 DIV

tag: condition

value: 30'after KCl


title: D129-D123T115


title: Sample 10: Input_shScr_KCl_1

description: Input


title: Daxx +/+ LT.HSC 3dpi 1


title: Daxx F/F LT.HSC 3dpi 1


title: Sample 12: Input_shScr_KCl_3

description: Input


title: Sample 9: Input_shScr_veh_3

description: Input

value: Vehicle/untreated


title: Daxx +/+ KLS 3wpi 2

value: Bone marrow


title: Daxx F/F KLS 3wpi 2

value: Daxx F/F Cre +/-


title: Sample 6: Input_shAnp_KCl_3

description: Input


title: ANGII and QDG2

city: Fuzhou

first: Jun

last: Peng

state: Fujian

address: 1 Qiuyang Road, Minhou Shangjie

department: Academy of Integrative Medicine

country: China

institute: Fujian University of Traditional Chinese Medicine

data_processing:
Data were filtered using the following specifications fastq software，The filtering standards from raw data to clean reads are:：  Check the sample for contamination and, if there is pollution, remove it  If the reads contains a joint sequence, the joint sequence is cut off first  a base having an average base mass of less than 15 on both ends of the readth window is cut with four base lengths as a sliding window;  Remove the number of threads with a high N content. If the N content in a read is more than 5%, the whole read is removed, and the read pair with high low-quality base content is removed. If the low-quality base in one read (the mass value is not higher than the base of 20) exceeds 30%, the whole pair of the reads is removed;  if the truncated read length is less than 50 bp, the entire read is removed  Remove unmatched reads  Q30，Q20 explanation：  Q30 indicates that the sequencing error rate of the base is 0.1%.  Q20 indicates that the sequencing error rate of the base is 1%.
Using String Tie for readcount and FPKM calculation.
Differential expression analyses were performed using the limma package.
Genome_build: GRCm38.92
Supplementary_files_format_and_content: tab_delimited text files include FPKM values for each Sample

source_name: heart tissue

extract_protocol:
The hearts were dissected and cardiac tissues were stored in liquid nitrogen and stored in low temperature.Total RNA was extracted with Trizol (Tiangen, Beijing, China). RNA integrity was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and RNA concentration was measured by Qubit RNA Assay Kit in a Qubit Fluorometer (Invitrogen, CA, USA).
A total amount of 1 μg RNA per sample was used. In brief, the NEBNext rRNA Depletion Kit was used to remove rRNA from the total RNA. The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, Beijing, China) was used to construct the libraries for sequencing following the manufacturer’s instructions.

value: heart

tag: Sex

value: male

value: AngII and QDG Treatment


title: ANGII and QDG3


title: AngII5

value: AngII


title: Sample 4: Input_shAnp_KCl_1

description: Input


title: Sample 3: Input_shAnp_veh_3

description: Input


title: D129-D123T106


title: AngII4


title: ANGII and QDG5


title: D129-D123T114


title: ANGII and QDG4


title: Sample 8: Input_shScr_veh_2

description: Input


title: D129-D123T112


title: D129-D123T111


title: Sample 2: Input_shAnp_veh_2

description: Input


title: Sample 5: Input_shAnp_KCl_2

description: Input


title: D129-D123T117


title: AngII2


title: D129-D123T105


title: D129-D123T109


title: ANGII and QDG1


title: AngII1


title: D129-D123T107


title: D129-D123T110


title: Sample 7: Input_shScr_veh_1

description: Input


title: Sample 12: H2A-Z_shScr_KCl_3

description: H2A.Z ChIP


title: D129-D123T108


title: D129-D123T102


title: Control5

value: Control


title: Sample 9: H2A-Z_shScr_veh_3

description: H2A.Z ChIP


title: Sample 10: H2A-Z_shScr_KCl_1

description: H2A.Z ChIP


title: Sample 8: H2A-Z_shScr_veh_2

description: H2A.Z ChIP


title: CF, transduced with HIV-GFP [CFB-25-19_HIV-GFP]

city: Iowa City

first: Alejandro

middle: A.

last: Pezzulo

state: Iowa

address: 6316 Pappajohn Biomedical Discovery Building

department: Department of Internal Medicine

institute: Universty of Iowa

data_processing:
Raw fastq files were aligned to a hybrid genome consisting of human genome assembly GRCh38.p13 and lentivirus genome sequence. Filtering, barcode counting, and UMI counting were performed with 10x CellRanger software version 3.0.2 with the argument --expect-cells=5000.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: HDF5 format file containing counts for each gene (row) and cell barcode (column)

molecule: polyA RNA

source_name: CF_transduced with HIV-GFP

extract_protocol:
Cultured cells were rinsed in PBS -/- and lifted in TrypLE for 45 min at 37C. Cells were centrifuged for 5 min at 200xrcf, supernatent was removed, and cells were resuspended in Phenol red-free DMEM:F12 with 0.04% non-acetylated BSA and counted.
10x Genomics Chromium Single Cell 3’ Reagent Kits v3 system

tag: subject id

tag: subject status

value: cystic fibrosis (CF)

value: lung

value: primary basal cells

value: HIV-GFP


title: Control1


title: Sample 7: H2A-Z_shScr_veh_1

description: H2A.Z ChIP

tag: cell type


title: AngII3

tag: treatment


title: CF, transduced with HIV-CFTR [CFB-25-19_HIV-CFTR]

source_name: CF_transduced with HIV-CFTR

value: HIV-CFTR


title: Sample 1: Input_shAnp_veh_1

description: Input


title: Sample 5: H2A-Z_shAnp_KCl_2

description: H2A.Z ChIP


title: D129-D123T103


title: CF, transduced with HIV-GFP [CFB-16-19_HIV-GFP]


title: D129-D123T104


title: Sample 3: H2A-Z_sh_Anp_veh_3

description: H2A.Z ChIP


title: Control4


title: D129-D123T101


title: Sample 11: H2A-Z_shScr_KCl_2

description: H2A.Z ChIP


title: CF, untreated [CFB-25-19_untreated]

value: untreated


title: Control3


title: Sample 1: H2A-Z_shAnp_veh_1

description: H2A.Z ChIP

value: mouse hippocampal neurons


title: Premutation 11

city: Alicante

first: Luis

middle: M

last: Valor

state: Alicante

address: Av. Pintor Baeza, 12

country: Spain

institute: ISABIAL

description:
960_plasma
Small RNA

data_processing:
Base calling using Illumina CASAVA software
After adapter removal using “Cutadapt” , reads were aligned to the human genome (hg38 build) using “Bowtie2”.
The following Bioconductor-based software packages were used for conversion of BAM files (“RSamtools”) and gene annotation (“GenomicFeatures” and “GenomicAlignments”) using the Ensembl annotation package “Db.Hsapiens.v86” after filtering the “miRNA” gene biotype.
Genome_build: Human GRCh38
Supplementary_files_format_and_content: tab-delimited text file with Ensembl ID and read counts for all the samples

source_name: Plasma

extract_protocol:
Two hundred µl of plasma was used to isolate circulating small RNA using the miRNeasy Serum/Plasma Kit (Qiagen) following manufacturer’s instructions.
TruSeq Small RNA Library Preparation Kit, Illumina

tag: genotype

value: FMR1 premutation carrier

value: Female

tag: age


title: Sample 6: H2A-Z_shAnp_KCl_3

description: H2A.Z ChIP

value: 9 DIV

value: 30'after KCl


title: P0-Bcl11ab3 (Bcl11a/b-DCKO Cortex P0)

city: shanghai

first: heng

last: du

address: 131 Dong'an Road

department: Institutes of Brain Science

institute: Fudan University

description: Emx1-Cre; Bcl11aFlox/Flox; Bcl11bFlox/Flox cortical tissues

data_processing:
After base recognition and error filtering, the original sequencing fragments which can be used for analysis were obtained and stored in FASTQ format. Then the clean reads were obtained through filtering by Seqtk.
Genome mapping of preprocessed reads was performed using Hisat2 (version:2.0.4) to generate a BAM file.
The obtained count data were transformed into FPKM as the normalized gene expression value by counting fragments from each gene using Stringtie (version:1.3.0) and normalizing with TMM (trimmed mean of M values).
EdgeR was used to analyze the differential genes between samples. Then the differentiated genes was screened by q-value defined as the corrected P-value not more than 0.05 and fold-change calculated according to the value of FPKM was not less than 2.
Genome_build: mm10

source_name: Bcl11a/b-DCKO Cortex

extract_protocol:
Total RNA was extracted using mir VanaTM miRNA Isolation kit (Cat#AM1561, Ambion)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
The cDNA libraries were sequenced using Illumina high throughput sequencer.

treatment_protocol: E13.5, E15.5 and P0 control and mutant cortices were carefully dissected under a clean environment, flash frozen on dry ice.

tag: strain

value: Cortex

value: Post natal day 0


title: Premutation 9

description:
824_plasma
Small RNA


title: CF, transduced with HIV-CFTR [CFB-16-19_HIV-CFTR]

tag: tissue


title: Sample 4: H2A-Z_shAnp_KCl_1

description: H2A.Z ChIP


title: Sample 2: H2A-Z_shAnp_veh_2

description: H2A.Z ChIP

value: Vehicle/untreated


title: non-CF, transduced with HIV-CFTR [B-23-19_HIV-CFTR]

source_name: non-CF_transduced with HIV-CFTR

value: non-cystic fibrosis (non-CF)


title: Control2

value: heart

value: male


title: P0-Bcl11ab2 (Bcl11a/b-DCKO Cortex P0)


title: Premutation 8

description:
799_plasma
Small RNA


title: PD+LIF_Stiff_t2.2_1

city: Cambridge

first: Celine

last: Labouesse

address: Puddicombe Way

department: Cambridge Stem Cell Institute

institute: University of Cambridge

description:
counts_PD_LIF_CHIRONremoval
SLX-13568 Sample Bb3

data_processing:
Read trimming: Reads trimmed using trim galore with default arguments.
Read aligning: Reads aligned using Tophat v 2.1.0 with options --no-coverage-search --read-mismatch 1 --max-multihits 1 and -G using ensembl release 86 gtf file
Read mapping: Featurecount v1.5.0. using annotations from Ensembl release 86.
Count normalisation and Differential Expression Analysis: DESeq2
Genome_build: mm10

source_name: Embryonic stem cell culture

growth_protocol: E14 mouse embryonic stem cells were cultured on fibronectin-coated StemBond hydrogels of varying stiffness for 12hrs in 2i+LIF. Afterwards, PD03  or CHIRON was removed leaving cells in either CHIRON+LIF or PD03+LIF for 2hrs and 12hrs. RNA lysates were collected at those timepoints and in 2i+LIF for control.

extract_protocol:
RNA lysates were collected from cell cultures using RLT buffer. RNA was subsequently extracted from the lysates using RNEasy Kit (QIAGEN) including a genomic DNA digestion step.
Ribozero and Nextflex kits were used to prepare libraries.

treatment_protocol: Cells cultured on different substrates. Medium was changed from 2i+LIF to CHIRON+LIF or PD03+LIF at t=0hrs. Concentrations prior to removing inhibitors are 1µM PD03 and 3µM CHIRON.

tag: strain/genotype

value: 129m wt

value: E14 mouse embryonic stem cells

value: Stiff, t = 2hr, PD+LIF


title: P0-Bcl11ab1 (Bcl11a/b-DCKO Cortex P0)


title: Patient #6t-scRNA

city: Shanghai

first: Jia

last: Wang

state: Shanghai China

address: Huashan Rd. 1940, build 3.  Shanghai,

institute: SJTU CHINA

data_processing:
CellRanger was used to base-calling, alignment, filtering and generation of normalized abundance measurements.
Read 1: contains the 16bp 10x barcode and the 10bp UMI (bases 17-26).Index contains the sample barcode. Read 2 contains the cDNA information
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include normalized median scaling values for each cell

source_name: ccRCC tumor tissue

extract_protocol:
Tumor tissues were ressected by biopsy surgery and transported in DMEM/F12 medium on ice to the laboratory within an hour.
For scRNA-seq, the tissues were dissociated into single cells suspensions using digestion buffer (DMEM/F12 Medium+ 2 mg/ml of collagenase IV + 100 IU/ml DNase I), and single cell GEMs were generated by 10X genomics Chromium Controller. cDNA library was constructed following the manufacture’s protocol.

value: clear cell renal cell carcinoma (ccRCC) patient

tag: tumor stage

tag: tissue type

value: tumor tissue


title: R18037291LR01-Bcl11a-3 (Bcl11a-CKO Cortex P0)

description: Emx1-Cre; Bcl11aFlox/Flox cortical tissues

source_name: Bcl11a-CKO Cortex

value: Emx1-Cre; Bcl11aFlox/Flox


title: Premutation 10

description:
835_plasma
Small RNA


title: CF, untreated [CFB-16-19_untreated]

value: cystic fibrosis (CF)

value: lung

value: primary basal cells

value: untreated


title: PD+LIF_Stiff_t12.2_1

description:
counts_PD_LIF_CHIRONremoval
SLX-13568 Sample Cb3

value: Stiff, t = 12hr, PD+LIF


title: R18037290LR01-Bcl11a-2 (Bcl11a-CKO Cortex P0)

value: Cortex


title: non-CF, transduced with HIV-GFP [B-23-19_HIV-GFP]

source_name: non-CF_transduced with HIV-GFP

value: HIV-GFP


title: Premutation 7

description:
798_plasma
Small RNA

value: FMR1 premutation carrier

value: Male


title: non-CF, untreated [B-23-19_untreated]

value: non-cystic fibrosis (non-CF)


title: Patient #5n-scRNA

source_name: ccRCC para-tumor tissue

value: Female

value: para-tumor tissue


title: R18037289LR01-Bcl11a-1 (Bcl11a-CKO Cortex P0)

value: Post natal day 0


title: Patient #5t-scRNA


title: Premutation 6

description:
631_plasma
Small RNA


title: P0Cor3 (Control Cortex P0)

description: wildtype cortical tissues

source_name: Control Cortex

value: wildtype


title: PD+LIF_Stiff_t0.2_1

description:
counts_PD_LIF_CHIRONremoval
SLX-13568 Sample Ab3

value: 129m wt

value: E14 mouse embryonic stem cells

value: Stiff, t = 0hr, 2i+LIF, (CONTROL)


title: PD+LIF_Stiff_t12.1_1

description:
counts_PD_LIF_CHIRONremoval
SLX-13568 Sample Cb2


title: Patient #7t-scRNA

value: clear cell renal cell carcinoma (ccRCC) patient


title: Premutation 5

description:
566_plasma
Small RNA


title: Patient #4n-scRNA


title: PD+LIF_Stiff_t2.1_1

description:
counts_PD_LIF_CHIRONremoval
SLX-13568 Sample Bb2

value: Stiff, t = 2hr, PD+LIF


title: Premutation 4

description:
185_plasma
Small RNA


title: P0Cor2 (Control Cortex P0)

description: wildtype cortical tissues


title: PD+LIF_Stiff_t0.1_1

description:
counts_PD_LIF_CHIRONremoval
SLX-13568 Sample Ab1


title: P0Cor1 (Control Cortex P0)

description: wildtype cortical tissues


title: Patient #4t-scRNA

value: ccRCC T2 accompanied pRCCT3

value: tumor tissue


title: Premutation 3

description:
184_plasma
Small RNA


title: PD+LIF_Soft_t2.2_1

description:
counts_PD_LIF_CHIRONremoval
SLX-13568 Sample Ba3

value: Soft, t = 2hr, PD+LIF


title: PD+LIF_Soft_t12.2_1

description:
counts_PD_LIF_CHIRONremoval
SLX-13568 Sample Ca2

value: Soft, t = 12hr, PD+LIF


title: PD+LIF_Soft_t2.1_1

description:
counts_PD_LIF_CHIRONremoval
SLX-13568 Sample Ba1


title: E15-5-3jin (Bcl11a/b-DCKO Cortex E15.5)

value: Cortex

value: Embryonic day 15.5


title: E15-5-6jin (Bcl11a/b-DCKO Cortex E15.5)


title: E15-5-1jin (Bcl11a/b-DCKO Cortex E15.5)


title: Premutation 1

description:
006_plasma
Small RNA

value: FMR1 premutation carrier

value: Male


title: Patient #3n-scRNA


title: Control 6

description:
C6_plasma
Small RNA

value: control


title: Patient #3t-scRNA


title: PD+LIF_Soft_t12.1_1

description:
counts_PD_LIF_CHIRONremoval
SLX-13568 Sample Ca1


title: Premutation 2

description:
183_plasma
Small RNA

value: Female


title: PD+LIF_Soft_t0.2_1

description:
counts_PD_LIF_CHIRONremoval
SLX-13568 Sample Aa2

value: Soft, t = 0hr, 2i+LIF, (CONTROL)


title: E15-5-5jin-zuo-L (Bcl11a-CKO Cortex E15.5)

value: Emx1-Cre; Bcl11aFlox/Flox


title: Patient #2n-scRNA

value: para-tumor tissue


title: E15-5-5jin-you-R (Bcl11a-CKO Cortex E15.5)


title: Patient #1n-scRNA


title: Patient #2t-scRNA


title: PD+LIF_Soft_t0.1_1

description:
counts_PD_LIF_CHIRONremoval
SLX-13568 Sample Aa1

value: 129m wt

value: E14 mouse embryonic stem cells


title: Patient #1t-scRNA

value: clear cell renal cell carcinoma (ccRCC) patient


title: Control 5

description:
C5_plasma
Small RNA


title: E15-5-4jin-you-R (Bcl11a-CKO Cortex E15.5)


title: Control 4

description:
C4_plasma
Small RNA


title: CH+LIF_Stiff_t2.2_1

description:
counts_CH_LIF_PD03removal
SLX-12942 Sample 12

value: Stiff, t = 2hr, CH+LIF


title: Control 2

description:
C2_plasma
Small RNA


title: CH+LIF_Stiff_t2.1_1

description:
counts_CH_LIF_PD03removal
SLX-12942 Sample 11


title: E15-5-7jin-you-R (Control Cortex E15.5)

description: wildtype cortical tissues

value: wildtype


title: Control 3

description:
C3_plasma
Small RNA


title: CH+LIF_Stiff_t12.2_1

description:
counts_CH_LIF_PD03removal
SLX-12942 Sample 10

value: Stiff, t = 12hr, CH+LIF


title: E15-5-2jin-you-R (Control Cortex E15.5)

description: wildtype cortical tissues


title: CH+LIF_Stiff_t0.2_1

description:
counts_CH_LIF_PD03removal
SLX-12942 Sample 8

value: Stiff, t = 0hr, 2i+LIF, (CONTROL)


title: E13-5-4jin-1-8 (Bcl11a/b-DCKO Cortex E13.5)

description: Emx1-Cre; Bcl11aFlox/Flox; Bcl11bFlox/Flox cortical tissues

value: Embryonic day 13.5


title: CH+LIF_Stiff_t0.1_1

description:
counts_CH_LIF_PD03removal
SLX-12942 Sample 7


title: E13-5-3jin-1-8 (Bcl11a/b-DCKO Cortex E13.5)

value: Cortex


title: E13-5-C-1-2 (Bcl11a/b-DCKO Cortex E13.5)


title: CH+LIF_Soft_t2.2_1

description:
counts_CH_LIF_PD03removal
SLX-12942 Sample 6

value: Soft, t = 2hr, CH+LIF


title: CH+LIF_Soft_t2.1_1

description:
counts_CH_LIF_PD03removal
SLX-12942 Sample 5


title: HGD-1 biol rep 6

city: Singapore

first: Guillaume

last: Thibault

address: 60 Nanyang Dr

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

data_processing:
The clustering was done using the Illumina® HiSeq 3000/4000 (Paired-End) Cluster kit on the cbot 2 system. This was then followed by sequencing performed using the Illumina HISEQ 4000 Sequencers with the Illumina® HiSeq 3000/4000 SBS (300 cycle) Kit. The bcl files were converted into fastq files using the bcl2fastq2.
The fastq reads were filtered to remove all the reads that did not pass filtering, leaving only useable Passed Filtered (PF) reads. The primary analysis result was then generated as the Demultiplexed_Stats file and reviewed, and the PF fastq files were then passed on for further analysis.
Alignment was conducted by mapping to GCF_000002985.6 whole genome and annotated with WBcel235 using Rsubread (v2.6.4) in Rstudio
Feature Counts were obtained using featureCount() function in Rsubread (v2.4.3)
Differentially expressed genes were calculated using DESeq2 (1.30.1) with lowly-expressed (<10 counts) genes filtered out
Genome_build: GCF_000002985.6
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Caenorhabditis elegans

source_name: N2 (C. elegans var Bristol)

growth_protocol: All strains were grown at 20°C using standard C. elegans methods as previously described{Brenner, 1974 #120;Stiernagle, 2006 #121}. Nematode growth media (NGM) agar plates were seeded with Escherichia coli strain OP50 (UV-killed bacteria) for normal growth. NGM agar plates were supplemented with 2% glucose (high glucose diet, HGD) when indicated. C. elegans strains wild type N2 and bacteria strains OP50 awere gifted from the Caenorhabditis Genetics Centre. A single pool of ~ 6,000 synchronised worms was grown on ND to day 1 of adulthood (D1). From the same single pool, a subset of ~2,000 worms was fed HGD-1. The second subset of ~2,000 worms grown on ND was fed HGD-5 at day 5 of adulthood (D5). Worms fed ND, HGD-1, and HGD-5 were harvested at D8. All samples were collected in six biological replicates.

extract_protocol:
Pelleted worms were lysed by beat beating in TRIzol reagent (Thermo Fisher, Waltham, MA). Total RNA was isolated using Nucleospin RNA (Macherey Nagel) following the manufacturer’s protocol. Contaminant genomic DNA was removed from samples with TURBO DNase (Thermo Fisher) following the manufacturer’s protocol. mRNA quality was assessed by NanoDrop 1000 v3.8 (Thermo Scientific), and 100 ng/µl of the samples with RNA integrity number above 8.0 were proceeded with library preparation.
The total RNA quality and RIN value was confirmed with a Tapestation from Agilent and Agilent RNA ScreenTape. Library preparation was done using a commercially available kit, Illumina’s TruSeq® Stranded mRNA Library Prep, following the manufacturer’s protocol. The different libraries were then pooled together and QC using Agilent high sensitivity DNA kit and KAPA quantification.

treatment_protocol: See growth protocol for high glucose diet treatment details.

value: day 8 of adulthood (D8)

tag: growth condition


title: HGD-5 biol rep 6


title: E13-5-6jin-1-8 (Bcl11a-CKO Cortex E13.5)

description: Emx1-Cre; Bcl11aFlox/Flox cortical tissues


title: CH+LIF_Soft_t12.2_1

description:
counts_CH_LIF_PD03removal
SLX-12942 Sample 4

value: Soft, t = 12hr, CH+LIF


title: E13-5-5jin-1-8 (Bcl11a-CKO Cortex E13.5)


title: E13-5-B-1-2 (Bcl11a-CKO Cortex E13.5)


title: KS19

city: Memphis

first: Sherif

last: Abdelhamed

state: TN

address: 262 Danny Thomas Place

department: Pathology

institute: St Jude Children's Research Hospital

description: Plasma EV RNA

data_processing:
Raw data was de-multiplexed and FASTQ files for each sample was generated using the bcl2fastq software (Illumina inc.). FASTQ data were checked using the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
low count filtering: ≥10CPM in ≥2 samples
normalization: trimmed mean of M-values method (R package edgeR)
transformation of expression values: log-CPM with associated sample wise quality weight and observational precision weights using voom method (R package edgeR)
Genome_build: GRCh37
Supplementary_files_format_and_content: csv; differential expression results and normalized CPM in each sample

source_name: Texas Children's Cancer Center

growth_protocol: Plasma samples were collected under Texas Children's Cancer Center's IRB-approved protocol, Evs were isolated by serial high-speed centrifugation.

extract_protocol:
Total RNA was extracted using miRNeasy kit (Qiagen, MD).
RNA was converted into microRNA NGS libraries using NEBNEXT library generation kit (New England Biolabs).
miRNA-sequencing was performed using Illumina NextSeq500 (Illumina, CA).

value: Plasma

tag: disease

value: AML Patient


title: E15-5-7jin-zuo-L (Control Cortex E15.5)

description: wildtype cortical tissues

value: Embryonic day 15.5


title: E13-5-2jin-1-8 (Control Cortex E13.5)

description: wildtype cortical tissues


title: CH+LIF_Soft_t12.1_1

description:
counts_CH_LIF_PD03removal
SLX-12942 Sample 3


title: HGD-1 biol rep 5


title: CH+LIF_Soft_t0.2_1

description:
counts_CH_LIF_PD03removal
SLX-12942 Sample 2

value: Soft, t = 0hr, 2i+LIF, (CONTROL)


title: HGD-5 biol rep 5


title: ND biol rep 6

value: ND


title: KS18

description: Plasma EV RNA


title: ND biol rep 5


title: E13-5-1jin-1-8 (Control Cortex E13.5)

description: wildtype cortical tissues


title: CH+LIF_Soft_t0.1_1

description:
counts_CH_LIF_PD03removal
SLX-12942 Sample 1

value: 129m wt


title: HGD-5 biol rep 4


title: HGD-1 biol rep 4


title: CH+LIF_Stiff_t12.1_1

description:
counts_CH_LIF_PD03removal
SLX-12942 Sample 9

value: E14 mouse embryonic stem cells


title: Control 1

description:
C1_plasma
Small RNA

value: control

value: Female


title: E13-5-A-1-2 (Control Cortex E13.5)

description: wildtype cortical tissues

value: wildtype


title: KS16

description: Plasma EV RNA


title: ND biol rep 4


title: SOF_48_Ser_2

data_processing:
Read alignment/trimming: STAR 2.5.2a
Read mapping: Htseq-count: Annotations from Ensembl 87
Count normalisation & Differential analysis: FPKM and DESeq
Genome_build: mm10
Supplementary_files_format_and_content: text file, count data

growth_protocol: Embyronic stem cells were culture on different substrates for 24hrs or 48hrs in different medium conditions.

extract_protocol:
RNA lysates were collected from cell cultures using RLT buffer. RNA was subsequently extracted from the lysates using RNEasy Kit (QIAGEN) including a genomic DNA digestion step.
Libraries were prepared from RNA samples using NuGen kit

value: Embryonic stem cells

value: Soft 48hrs, serum


title: HGD-5 biol rep 3


title: KS13

description: Plasma EV RNA


title: SOF_48_Ser_1


title: SOF_48_Ser_plus_LIF_3

value: Soft 48hrs, serum+LIF


title: HGD-1 biol rep 3


title: ND biol rep 3


title: SOF_48_Ser_plus_LIF_2


title: KS12

description: Plasma EV RNA


title: SOF_48_Ser_plus_LIF_plus_PD03_3

value: Soft 48hrs, serum+LIF+PD03


title: K18

description: Plasma EV RNA


title: SOF_48_Ser_plus_LIF_1


title: K17

description: Plasma EV RNA


title: HGD-5 biol rep 2


title: 12mo_5mpi_AD_6 [X5610.5mpi.pos]

city: St Lucia

first: Jay

last: Rasmussen

state: QLD

address: Building 79

department: Queensland Brain Institute

country: Australia

institute: University of Queensland

description: processed data file: 12mo_counts.txt

data_processing:
Reads aligned to GRCm38 with STAR
Duplicates marked with picard
Reads counted and DEG performed with edgeR
Genome_build: GRCm38
Supplementary_files_format_and_content: tables with TMM-normalised CPMs for each sample

extract_protocol:
Qiagen RNeasy Mini Kit
Mature messenger RNA was isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) followed by fragmentation and priming with NEBNext First Strand Synthesis Reaction buffer and NEBNext Random Primers. First and second strand synthesis were completed using ProtoScript II Reverse Transcriptase and Second Strand Synthesis Enzyme Mix (NEB), respectively. Double-stranded cDNA was purified with AxyPrep Mag PCR Clean-up (Axygen) and End Prep Enzyme Mix was used to repair ends and A-tail followed by addition of adaptors with T-A ligation (NEB). AxyPrep Mag PCR Clean-up was used for selection of ~360bp fragments and these were amplified with 11 cycles of PCR using P5 and P7 primers. Libraries were purified with AxyPrep Mag PCR Clean-up and quantified using and Agilent 2100 Bioanalyzer and Qubit 2.0 Fluorometer (Invitrogen).

treatment_protocol: mice were injected with either control or Alzheimer's disease brain extracts

value: 12 months old (12mo)

tag: incubation

value: 5 month post injection (5mpi)

value: Alzheimer's disease injection (AD)

value: mouse hippocampus


title: KS11

description: Plasma EV RNA

value: Plasma

value: AML Patient


title: 12mo_5mpi_AD_7 [X5615.5mpi.pos]

description: processed data file: 12mo_counts.txt


title: 12mo_5mpi_AD_4 [X5607.5mpi.pos]

description: processed data file: 12mo_counts.txt


title: 12mo_5mpi_AD_5 [X5608.5mpi.pos]

description: processed data file: 12mo_counts.txt


title: KS17

description: Plasma EV RNA


title: HGD-1 biol rep 2

value: day 8 of adulthood (D8)


title: 12mo_5mpi_AD_3 [X5604.5mpi.pos]

description: processed data file: 12mo_counts.txt


title: KS14

description: Plasma EV RNA


title: K14

description: Plasma EV RNA


title: HGD-5 biol rep 1

value: UV-killed OP50 with 2% glucose from day 5 adulthood (High glucose diet, HGD-5)


title: 12mo_5mpi_AD_2 [X5597.5mpi.pos]

description: processed data file: 12mo_counts.txt


title: ND biol rep 2

value: ND


title: K12

description: Plasma EV RNA


title: SOF_48_Ser_3

value: 129m wt


title: 12mo_5mpi_AD_1 [X5591.5mpi.pos]

description: processed data file: 12mo_counts.txt


title: SOF_48_Ser_plus_PD03_6

value: Soft 48hrs, serum+PD03


title: SOF_48_Ser_plus_LIF_plus_PD03_2


title: KS10

description: Plasma EV RNA

value: Healthy Donor


title: HGD-1 biol rep 1

value: UV-killed OP50 with 2% glucose from day 1 adulthood (High glucose diet, HGD-1)


title: KS9

description: Plasma EV RNA


title: 12mo_5mpi_Ctrl_7 [X5617.5mpi.neg]

description: processed data file: 12mo_counts.txt

value: Control injected (Ctrl)


title: dpy-7syn1-rpb-6_L4_rep2

city: London

first: Dimitris

last: Katsanos

address: Sir Alexander Fleming building, Imperial College Road

department: Life Sciences

institute: Imperial College London

description: amplicons of GATC-6mA-methylated genomic DNA fragments

data_processing:
Library strategy: DamID-seq
Sequencing data were fully processed using the automated pipeline defined by the perl script damidseq_pipeline v1.4.5 (Marshall and Brand, 2015) (available at https://github.com/owenjm/damidseq_pipeline). The pipeline  was used calling Bowtie 2 v2.3.4 (Langmead and Salzberg, 2012) for alignment to C. elegans bowtie indices from genome assembly WBcel235 (available from illumina® iGenomes page), Samtools v1.9 (Li et al., 2009) for alignment manipulations and generation of BAM files. Using a GATC fragment file with the coordinates of all GATC fragments across the C. elegans genome in gff format, built from a WBcel235 FASTA file (available at https://www.ensembl.org/Caenorhabditis_elegans/Info/Index) using the gatc.track.marker.pl script (available at https://github.com/owenjm/damidseq_pipeline). The pipeline calculated genome-wide log2(dam:rpb-6/dam:NLS-GFP) signal enrichment scores per GATC fragment of the genome as gff files from pairs of BAM files from replicates of dam:rpb-6 and dam:NLS-GFP samples from the same cell-type and  developmental stage.
Using damidseq_pipeline v1.4.5 all pairwise calculations of log2(dam:rpb-6/dam:NLS-GFP) scores between pairs of dam:rpb-6 and dam:NLS-GFP samples replicates from the same cell-type and developmental stage were performed producing 4 independet gff signal files for each cell-type at each developmental stage.
The 4 gff signal files were averaged arithmetically per GATC fragment of the genome to genarate the single averaged signal gff file for each cell-type at each developmental stage.
Genes with statistically significant RPB-6 occupancy (FDR<0.05) were identified by the Rscript polii.gene.call (Marshall and Brand, 2015) (available at https://github.com/owenjm/polii.gene.call) using the WBcel235.36 annotation.
Gene lists were updated to the WBCel235.99 annotation post-processing.
Genome_build: WBCel235
Supplementary_files_format_and_content: *gatc.gff: log2(dam:rpb-6/dam:NLS-GF) signal per GATC fragment
Supplementary_files_format_and_content: *allreps_pairwise_averageoflogs.gff: averaged log2(dam:rpb-6/dam:NLS-GFP) signal across replicates per GATC fragment
Supplementary_files_format_and_content: *protein-coding_genes.txt: expressed genes list
Supplementary_files_format_and_content: GFF interval files representing coordinates of GATC fragments of the genome with a log2(dam:rpb-6/dam:NLS-GFP) score each
Supplementary_files_format_and_content: Lists of expressed genes based on RPB-6 occupancy as TXT documents including the Wormbase_ID, sequence_ID and name of genes, an averaged across the gene body occupancy value, the numbers of GATC fragments making up the gene and the FDR value.

source_name: hypodermis

growth_protocol: For each replicate of each strain used for TaDa nine 55 mm NGM plates seeded with dam-/dcm- bacterial lawns and fully populated by gravid adults were used for large-scale egg preparation with isolated embryos seeded in new dam-/dcm- plates that were incubated at 20 °C. Half of the resulting synchronised populations were collected in a 15 ml centrifuge tube after 24 hours at the L2 stage and the other half after 48 hours at the L4 stage. All collected populations pellets (~100 μl) underwent extensive washing with 10 ml M9 at least 5 times.

extract_protocol:
gDNA for each sample was extracted by lysing animal pellets with Cell Lysis Solution (QIAGEN) containing Proteinase K. RNA was removed by treating with RNase A  and DNA was isolated after treatment with Protein precipitation solution (QIAGEN) by percipitating in isopropanol and washing with 70% ethanol. gDNA was redissolved in water. For isolation and amplification of the GATC methylated gDNA fragments the protocol followed was an adapted version of the one presented in (Marshall et al., 2016)
Amplicon sonication and library preparation was outsourced to GENEWIZ which used illumina protocols for sequencing on the Illumina HiSeq 4000 platform

tag: cell-type

value: hypodermis - dpy7syn1 expression domain

tag: developmental stage

tag: biological replicate

value: Replicate 2


title: SOF_48_Ser_plus_PD03_4

value: Embryonic stem cells

tag: condition


title: dpy-7syn1-NLS-GFP_L4_rep2


title: 12mo_5mpi_Ctrl_6 [X5612.5mpi.neg]

description: processed data file: 12mo_counts.txt

value: 12 months old (12mo)


title: SOF_48_Ser_plus_PD03_3


title: SOF_48_Ser_plus_LIF_plus_PD03_1

value: Soft 48hrs, serum+LIF+PD03


title: srf-3i1-rpb-6_L4_rep2

source_name: seam cells

value: seam cells - srf-3i1 expression domain


title: KS8

description: Plasma EV RNA


title: SOF_48_Ser_plus_PD03_2


title: 12mo_5mpi_Ctrl_3 [X5592.5mpi.neg]

description: processed data file: 12mo_counts.txt

value: 5 month post injection (5mpi)

value: mouse hippocampus


title: 12mo_5mpi_Ctrl_4 [X5598.5mpi.neg]

description: processed data file: 12mo_counts.txt


title: srf-3i1-NLS-GFP_L4_rep2


title: STF_48_Ser_plus_PD03_3

value: Stiff, 48hrs, serum+PD03


title: dpy-7syn1-rpb-6_L4_rep1

value: Replicate 1


title: 12mo_5mpi_Ctrl_2 [X5580.5mpi.neg]

description: processed data file: 12mo_counts.txt


title: SOF_48_Ser_plus_PD03_1


title: KS6

description: Plasma EV RNA

value: Plasma


title: STF_48_Ser_plus_PD03_2


title: KS4

description: Plasma EV RNA


title: 12mo_5mpi_Ctrl_1 [X5575.5mpi.neg]

description: processed data file: 12mo_counts.txt


title: KS5

description: Plasma EV RNA


title: ND biol rep 1

value: day 8 of adulthood (D8)

value: UV-killed OP50 (normal diet, ND)


title: dpy-7syn1-NLS-GFP_L4_rep1


title: SOF_48_Ser_plus_PD03_5

value: 129m wt

value: Soft 48hrs, serum+PD03


title: 12mo_3mpi_AD_6 [X5613.3mpi.pos]

description: processed data file: 12mo_counts.txt

value: 3 month post injection (3mpi)

value: Alzheimer's disease injection (AD)


title: STF_48_Ser_plus_PD03_1


title: 12mo_5mpi_Ctrl_5 [X5609.5mpi.neg]

description: processed data file: 12mo_counts.txt

value: Control injected (Ctrl)


title: KS7

description: Plasma EV RNA

value: Healthy Donor


title: dpy-7syn1-rpb-6_L2_rep2

value: hypodermis - dpy7syn1 expression domain

value: Replicate 2


title: KS2

description: Plasma EV RNA


title: srf-3i1-NLS-GFP_L4_rep1


title: KS1

description: Plasma EV RNA


title: 12mo_3mpi_AD_5 [X5602.3mpi.pos]

description: processed data file: 12mo_counts.txt

value: 12 months old (12mo)


title: dpy-7syn1-NLS-GFP_L2_rep2


title: STF_48_Ser_plus_LIF_plus_PD03_3

value: Embryonic stem cells

value: Stiff, 48hrs, serum+LIF+PD03


title: 12mo_3mpi_AD_3 [X5593.3mpi.pos]

description: processed data file: 12mo_counts.txt

value: mouse hippocampus


title: C4-2_SAL_rep3

city: Kiel

first: Seyed Mohammd Mahdi

last: Rasa

state: Schleswig-Holstein

address: Michaelisstrasse 5

department: Institut for Immunology

institute: Universitätsklinikum Schleswig-Holstein

description: transcriptional profiling (RNA sequencing)

data_processing:
The first 4 nucleotide was removed from the sequenced reads using fastx_trimmer (FASTX Toolkit 0.0.13). The low quality nucleotides from the end of each read was removed using fastq_quality_trimmer(FASTX Toolkit 0.0.13) with -Q 33 -t 20 -l 25 parameters. Only the first sequenced read form the pair end (R1) was used for the downstream analysis.
The fastq files were mapped to the hg19 genome using tophat (v2.1.0) with the following parameters --bowtie1 --no-coverage-search -a 5.
The number of reads covered by each gene was calculated using htseq-count (0.11.2) with -s no -a 0 -t exon -m intersection-nonempty parameters and hg19 gencode.v19 annotation.
Genome_build: hg19
Supplementary_files_format_and_content: Htseq-count text file

source_name: C4-2 human PCa cell line

growth_protocol: cells were cultured in 5% FBS DMEM

extract_protocol:
Total RNA was isolated using peqGOLD TriFast (Peqlab, Erlangen, Germany) according to the manufacturer’s protocol.
Sequencing library was prepared using SMARTer® Stranded Total RNA Sample Prep Kit - HI Mammalian (TAKARA)

treatment_protocol: cells were treated in DMEM for 72h with DMSO or 1nM R1881

tag: cell line

value: PCa cell line

value: Treated with 1nM R1881


title: STF_48_Ser_plus_LIF_plus_PD03_2

tag: cell type


title: 12mo_3mpi_AD_2 [X5579.3mpi.pos]

description: processed data file: 12mo_counts.txt

tag: treatment


title: STF_48_Ser_1

value: Stiff, 48hrs, serum


title: KS3

description: Plasma EV RNA

value: Plasma


title: STF_48_Ser_plus_LIF_plus_PD03_1


title: srf-3i1-rpb-6_L4_rep1

value: seam cells - srf-3i1 expression domain

value: Replicate 1


title: K1

description: Plasma EV RNA


title: 12mo_3mpi_Ctrl_6 [X5614.3mpi.neg]

description: processed data file: 12mo_counts.txt


title: 12mo_3mpi_AD_1 [X5573.3mpi.pos]

description: processed data file: 12mo_counts.txt


title: dpy-7syn1-rpb-6_L2_rep1


title: C4-2_SAL_rep1


title: STF_48_Ser_3

value: 129m wt


title: 12mo_3mpi_Ctrl_5 [X5603.3mpi.neg]

description: processed data file: 12mo_counts.txt

value: 3 month post injection (3mpi)


title: STF_48_Ser_2


title: srf-3i1-NLS-GFP_L2_rep2


title: 12mo_3mpi_AD_4 [X5600.3mpi.pos]

description: processed data file: 12mo_counts.txt

value: Alzheimer's disease injection (AD)


title: K7

description: Plasma EV RNA


title: STF_48_Ser_plus_LIF_3

value: Stiff, 48hrs, serum+LIF


title: dpy-7syn1-NLS-GFP_L2_rep1


title: 12mo_3mpi_Ctrl_4 [X5601.3mpi.neg]

description: processed data file: 12mo_counts.txt

value: Control injected (Ctrl)


title: STF_48_Ser_plus_LIF_2


title: C4-2_DMSO_rep2

value: DMSO (Control)


title: C4-2_DMSO_rep3


title: srf-3i1-rpb-6_L2_rep1


title: C4-2_SAL_rep2


title: srf-3i1-NLS-GFP_L2_rep1


title: CTL_48_Ser_plus_LIF_3

value: Tissue culture plastic, 48hrs, serum+LIF


title: 12mo_3mpi_Ctrl_3 [X5599.3mpi.neg]

description: processed data file: 12mo_counts.txt

value: 12 months old (12mo)


title: 12mo_3mpi_Ctrl_2 [X5594.3mpi.neg]

description: processed data file: 12mo_counts.txt


title: srf-3i1-rpb-6_L2_rep2

value: Replicate 2


title: STF_48_Ser_plus_LIF_1

value: Embryonic stem cells


title: Cold BMKO rep3

city: Duarte

first: Ke

last: Ma

state: CA

address: 1500 E. Duarte Rd

department: Diabetes Complications & Metabolism

institute: City of Hope-BRI

data_processing:
RNA-seq sequencing reads were aligned with STAR software to mouse reference genome mm10
Unique read counts were quantified using HTSeq-count, with GENCODE gene annotations.
Read counts for genes were normalized to FPKM or RPKM and log-transformed into using DESeq2, limma and edgeR packages.
Genome_build: mm10
Supplementary_files_format_and_content: Raw gene read counts and log2 fpkm for every gene and every sample in four different groups

source_name: subcutaneous white adipose tissue

extract_protocol:
Total RNA was extracted using Trizol followed by DNase digestion and Qiagen RNeasy column purification.
Sequencing libraries were prepared with Kapa RNA mRNA HyperPrep kit according to the manufacturer's protocol, and sequenced on Illumina HiSeq 2500 with SR V4 Kit with the single read mode of 51cycle of read1 and 7 cycles of index read.

treatment_protocol: Cold acclimation will be tested by subjecting them to cold at 10oC for two weeks.

value: inguinal subcutaneous adipose tissue

tag: genotype

value: BMKO

value: cold group


title: 12mo_3mpi_Ctrl_1 [X5581.3mpi.neg]

description: processed data file: 12mo_counts.txt

tag: age

value: mouse hippocampus


title: C4-2_DMSO_rep1

value: PCa cell line


title: Cold BMKO rep2

tag: strain


title: CTL_48_Ser_plus_LIF_1


title: CTL_48_Ser_plus_LIF_2


title: 12mo_1mpi_AD_6 [X5618.1mpi.pos]

description: processed data file: 12mo_counts.txt

value: 1 month post injection (1mpi)

tag: tissue


title: Cold BMKO rep1


title: The WT strain_rep1

city: Yangzhou

first: Chengkun

last: Zheng

address: East wenhui road No.48

institute: Yangzhou University

description: The transcriptome of the WT strain

data_processing:
The clean reads were mapped to the S. suis SC84 genome (GenBank accession no.: NC_012924.1) using Bowtie2.
Gene expression levels were evaluated using featureCounts and differentially expressed genes (DEGs) were identified using DESeq2.
Those genes with a fold change greater than 2 and an adjusted P value less than 0.05 were defined as DEGs.
Genome_build: Streptococcus suis SC84, complete genome (NC_012924.1).
Supplementary_files_format_and_content: read counts for each gene.
Supplementary_files_format_and_content: TPM values for each gene.

organism: Streptococcus suis

source_name: the WT strain of S. suis

growth_protocol: Overnight cultures of the WT and ΔadcR strains were diluted 1:100 in fresh TSBS and grown to mid-exponential phase.

extract_protocol:
RNA was extracted using an Eastep Super Total RNA Isolation Kit (Promega, Shanghai, China), according to the manufacturer’s instructions. RNA integrity and concentration were analyzed by gel electrophoresis and spectrophotometric analysis using a Nanodrop 200, respectively.
The ribosomal RNA was removed using a rRNA Removal Kit. Then, the mRNA was fragmented into short fragments (200-300 bp) and used as template for cDNA synthesis. The cDNA was added with sequencing adapters and enriched by PCR amplification.

treatment_protocol: Bacterial cells were harvested by centrifugation; the cells were immediately used for RNA extraction.

tag: medium

value: TSBS

value: wildtype

tag: phase

value: mid-exponential phase


title: The WT strain_rep3

description: The transcriptome of the WT strain


title: The WT strain_rep2

description: The transcriptome of the WT strain


title: ΔadcR strain_rep3

description: The transcriptome of the ΔadcR mutant

source_name: the ΔadcR strain of S. suis

value: deltaadcR


title: SOF_24_Ser_plus_LIF_3

tag: strain/genotype

value: 129m wt

value: Soft substrate, 24hrs, serum+LIF


title: ΔadcR strain_rep2

description: The transcriptome of the ΔadcR mutant


title: 12mo_1mpi_AD_5 [X5595.1mpi.pos]

description: processed data file: 12mo_counts.txt

value: Alzheimer's disease injection (AD)


title: SOF_24_Ser_plus_LIF_2


title: 12mo_1mpi_AD_4 [X5589.1mpi.pos]

description: processed data file: 12mo_counts.txt


title: ΔadcR strain_rep1

description: The transcriptome of the ΔadcR mutant


title: Cold BMCtr rep3

value: BMCtr


title: Cold BMCtr rep2


title: Cold BMCtr rep1


title: SOF_24_Ser_plus_LIF_1


title: 12mo_1mpi_AD_3 [X5584.1mpi.pos]

description: processed data file: 12mo_counts.txt

value: 12 months old (12mo)


title: Apex replicate 3

city: Louisville

first: Jae Yeon

last: Hwang

state: Kentucky

address: 505 S. Hancock Street

department: Division of Medical Oncology & Hematology

institute: University of Louisville

data_processing:
RNA-Seq reads were aligned to the galGal5 genome assembly using STAR version 2.5.4b with the following configurations --runThreadN 16 --outSAMtype BAM SortedByCoordinate --outFilterMismatchNmax 3 --alignEndsType EndToEnd
FPKM values for all samples were obtained by running Cuffdiff version 2.2.1 with default setting.
Genome_build: galGal5
Supplementary_files_format_and_content: Text file which contains FPKM values of all samples

organism: Gallus gallus

source_name: Chicken cochlea

growth_protocol: Post-hatch day 1 chickens were taken to extract mRNA from cochlear duct.

extract_protocol:
Chickens were euthanized by carbon dioxide inhalation followed by decapitation. The head was hemi-sectioned and the cochlea duct was isolated in cold DEPC-treated PBS. The basilar papilla was dissected from the cochlear duct and divided into three pieces: base, middle, and apex. Each piece was collected in a separate tubes containing Trizol reagent and quickly frozen to minimize RNA degradation. Total RNA from 12 chickens (24 cochleas) were used for 3 biological replicates for each region. RNA was isolated using Trizol reagent according to the manufacturere's instructions.
1μg of total RNA from each sample was reverse transcribed into cDNA and amplified using Illumina TruSeq RNA Sample Prep Kit v2. For library preparation, mRNA was enriched by oligo-dT to minimize DNA contamination. The PCR products for the cDNA library were purified and selected using the AMPure XP bead (Beckman Coulter). The DNA was quantified using Tapestation2100 – D1000 Screen Tape. The cDNA libraries were multiplexed and sequenced on the Illumina Hi-Seq 4000 platform, and 101-bp paired-end reads were generated.

treatment_protocol: No treatment among different samples

value: Apex region of cochlea

value: untreated

value: Post-hatch day 1


title: STF_24_Ser_plus_LIF_3

value: Embryonic stem cells

value: Stiff substrate, 24hrs, serum+LIF


title: Apex replicate 2


title: STF_24_Ser_plus_LIF_2


title: Ambient BMKO rep2

value: inguinal subcutaneous adipose tissue

value: BMKO

value: ambient group


title: Apex replicate 1


title: Ambient BMKO rep3


title: 12mo_1mpi_AD_2 [X5574.1mpi.pos]

description: processed data file: 12mo_counts.txt

value: 1 month post injection (1mpi)

value: mouse hippocampus


title: 12mo_1mpi_AD_1 [X5570.1mpi.pos]

description: processed data file: 12mo_counts.txt


title: Mid replicate 3

value: Middle region of cochlea


title: 12mo_1mpi_Ctrl_4 [X5616.1mpi.neg]

description: processed data file: 12mo_counts.txt

value: Control injected (Ctrl)


title: Mid replicate 2


title: 12mo_1mpi_Ctrl_3 [X5596.1mpi.neg]

description: processed data file: 12mo_counts.txt


title: Ambient BMKO rep1


title: SLX_16495 Sample 17

data_processing:
Read trimming: Trim Galore v 0.4.4_dev: Trimming of reads to remove Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) and remove low-quality reads & too short reads
Read alignment: GSNAP version 2015-09-29 : Alignment of genome to genome build mm10, using a mismatch parameter of m=10. Other parameters were default values. 61% of reads were mapped to the genome
Read mapping: HTSeq: Genes were annotated using Ensembl release 81 and read counts were quantified using HTSeq
Quality control: R: Used ERCC spike-in counts to check for homogeneous sequencing depth. Removed sample 7 with 2x more ERCC read counts than in other samples for the same amount of endogenous read counts.
Count normalisation and Differential Expression Analysis: DESeq2: Differential expression analysis was computed using DESeq2 on protein coding genes, using the DESeq2 normalisation, from pairwise comparisons of samples with either same AHA concentration or same stiffness
Genome_build: mm10
Supplementary_files_format_and_content: counts1.txt: raw counts matrix, tab separated txt format: Each column corresponds to a sample, row corresponds to genes. Unfiltered matrix.

growth_protocol: E14 mouse embryonic stem cells were cultured on fibronectin-coated StemBond hydrogels of varying stiffness and adhesiveness for 24hrs in serum+LIF medium (3 samples per condition)

extract_protocol:
RNA lysates were collected from cell cultures using RLT buffer. RNA was subsequently extracted from the lysates using RNEasy Kit (QIAGEN) including a genomic DNA digestion step.
Libraries were prepared using Clonetech pico mammalian v2 kit (Takara)

treatment_protocol: Cells cultured on different substrates for 24hr before RNA collection

value: 129m wt

value: E14 mouse embryonic stem cells

value: "Stiff80":Stiff hydrogel, High adhesiveness


title: SLX_16495 Sample 18


title: SLX_16495 Sample 16


title: 12mo_1mpi_Ctrl_2 [X5590.1mpi.neg]

description: processed data file: 12mo_counts.txt


title: STF_24_Ser_plus_LIF_1


title: Ambient BMCtr rep2

value: BMCtr


title: Mid replicate 1


title: Ambient BMCtr rep1


title: 12mo_1mpi_Ctrl_5 [X5572.1mpi.neg]

description: processed data file: 12mo_counts.txt

value: 12 months old (12mo)


title: Base replicate 3

value: Base region of cochlea


title: SLX_16495 Sample 15

value: "Stiff48":Stiff hydrogel, Mid adhesiveness


title: Base replicate 2

value: untreated

value: Post-hatch day 1


title: SLX_16495 Sample 14


title: 3mo_5mpi_AD_3 [X6107.5mpi.plus]

description: processed data file: 3mo_counts.txt

value: 3 months old (3mo)

value: 5 month post injection (5mpi)

value: Alzheimer's disease injection (AD)


title: Base replicate 1


title: 3mo_5mpi_AD_2 [X6102.5mpi.plus]

description: processed data file: 3mo_counts.txt


title: SLX_16495 Sample 13


title: 3mo_5mpi_AD_1 [X6101.5mpi.plus]

description: processed data file: 3mo_counts.txt


title: SLX_16495 Sample 12

value: "Stiff16":Stiff hydrogel, Low adhesiveness


title: Sftpc-GFP #2

city: Los Angeles

first: Fremont

last: Gao

state: California

address: 2011 Zonal Ave, HMR 903

institute: USC

description: Sample 21260

data_processing:
The unaligned raw reads were processed on PartekFlow platform.
Reads alignment and gene annotation & quantification were based on mouse genome (mm10) and transcriptome (GENECODE genes-release 7); Tophat2 and Upper Quartile were algorithms used for mapping and normalization.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file with normalized reads for each sample

source_name: Lung

extract_protocol:
Lungs were dissected from mouse pups at PN14; cells were separated using gentleMACS dissociator; GFP+ cells were collected by FACs; RNA was extracted using Qiagen RNeasy micro kit; total RNA was sent to the sequencing facility at Caltech for sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Lung

value: post natal day 14

value: Sftpc-GFP


title: Ambient BMCtr rep3

value: inguinal subcutaneous adipose tissue

value: ambient group


title: Sftpc-GFP #3

description: Sample 21261


title: SLX_16495 Sample 11

value: 129m wt

value: E14 mouse embryonic stem cells


title: 3mo_5mpi_Ctrl_5 [X6108.5mpi.minus]

description: processed data file: 3mo_counts.txt

value: Control injected (Ctrl)

value: mouse hippocampus


title: SLX_16495 Sample 10


title: 12mo_1mpi_Ctrl_1 [X5585.1mpi.neg]

description: processed data file: 12mo_counts.txt

value: 12 months old (12mo)

value: 1 month post injection (1mpi)


title: Ctrl-2

first: Hong

last: Zhang

address: 600 Yishan Road, Xuhui  District

institute: Shanghai Diabetes Institute

data_processing:
Quality of the RNA-seq data was estimated using RSeQC software (version 2.6.4), and the script geneBody_coverage.py was used to calculate the coverage of the reads over the gene body.
Only the paired reads without adaptor sequences, with an average Phred quality score ≥ 15, and read length ≥ 36 were retained for paired-end sequencing data.
The cleaned reads were aligned to the index file of the mm10 genome using HISAT2 (version 2.0.5).
The aligned Sequence Alignment/Map (SAM) files were converted to Binary Alignment Map (BAM) files and sorted by read name using SAMtools (version 1.4).
Read counts for each gene were generated using HTSeq-count; the read counts were normalized and the differentially expressed genes were determined using the edgeR package in R.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with RPKM values for every gene and every sample

source_name: gastrocnemius muscle

growth_protocol: Mice were housed at 21 ℃ ± 1 ℃, with a humidity of 55% ± 10%, and under a 12-h light/dark cycle. Mice were fed either a normal chow diet or a high-fat diet (60% kcal from fat, 20% kcal from carbohydrate and 20% kcal from protein; D12492, Research Diets) at the age of 8 weeks, after administration of AAV. The mice had ad libitum access to food and water during the course of the experiment.

extract_protocol:
Gastrocnemius muscles were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. TruSeq RNA LT Sample Prep Kit v2 (Illumina) was used  for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 50 μL of 1011 vector genomes (vg) of AAV9-FGF6 and AAV9-Ctrl were injected into either side of the gastrocnemius muscle.

value: gastrocnemius muscle


title: Ctrl-3


title: FGF6-3


title: SLX_16495 Sample 9

source_name: Embryonic stem cell culture

value: "Soft80":Soft hydrogel, High adhesiveness


title: 3mo_5mpi_Ctrl_3 [X6084.5mpi.minus]

description: processed data file: 3mo_counts.txt

value: 3 months old (3mo)


title: 3mo_5mpi_Ctrl_2 [X6083.5mpi.minus]

description: processed data file: 3mo_counts.txt

value: 5 month post injection (5mpi)


title: SLX_16495 Sample 8


title: Ctrl-1


title: Sftpc-GFP #1

description: Sample 21258


title: 3mo_5mpi_Ctrl_1 [X6078.5mpi.minus]

description: processed data file: 3mo_counts.txt


title: SLX_16495 Sample 6

value: "Soft48":Soft hydrogel, Mid adhesiveness


title: SLX_16495 Sample 7


title: FGF6-1


title: SLX_16495 Sample 5


title: 3mo_3mpi_AD_5 [X6105.3mpi.plus]

description: processed data file: 3mo_counts.txt

value: 3 month post injection (3mpi)

value: Alzheimer's disease injection (AD)


title: 10X_GC_HET_R3

city: New York City

first: Christopher

middle: Russell

last: Chin

state: NY

address: 413 E 69th Street, Belfer Building, BB-1462

institute: Weill Cornell

data_processing:
Cell Ranger
Further processing was done in R 4.0.2 with Seurat 4.0.0 and slingshot 1.6.1
Genome_build: mm10
Supplementary_files_format_and_content: gzipped matrix mtx files and tsv barcode and feature files

source_name: GC B Cells

extract_protocol: 10x Chromium - single cell gene expression

value: GC B Cells

value: Cgamma1-Cre Smc3 +/-


title: 3mo_5mpi_Ctrl_4 [X6092.5mpi.minus]

description: processed data file: 3mo_counts.txt


title: 3mo_3mpi_AD_4 [X6099.3mpi.plus]

description: processed data file: 3mo_counts.txt


title: FGF6-2


title: 10X_GC_HET_R2


title: 3mo_3mpi_AD_3 [X6095.3mpi.plus]

description: processed data file: 3mo_counts.txt


title: SLX_16495 Sample 4


title: 10X_GC_HET_R1


title: SLX_16495 Sample 3

value: "Soft16":Soft hydrogel, Low adhesiveness


title: 3mo_3mpi_AD_2 [X6082.3mpi.plus]

description: processed data file: 3mo_counts.txt


title: SLX_16495 Sample 2


title: 3mo_3mpi_AD_1 [X6076.3mpi.plus]

description: processed data file: 3mo_counts.txt


title: 10X_GC_WT_R2

value: Cgamma1-Cre WT Control


title: 10X_GC_WT_R3


title: 10X_GC_WT_R1


title: Sertoli cells, TZEA30_3

city: Qingdao

first: JunLin

last: Song

address: Changcheng Road

institute: JunLin Song

data_processing:
Illumina Casava1.7 software used for basecalling.
Index of the reference genome was built using Hisat2 v2.0.4 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.4
HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Supplementary_files_format_and_content: Excel file includes gene expression count for each Sample

organism: Equus asinus

source_name: Sertoli cells

extract_protocol:
Cultured setoli cells were dissected and stored in liquid nitrogen individually.Total RNA from each tank was isolated by TRIzol reagent (Invitrogen, UK).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 30 μM ZEA treated

value: Sertoli cells

tag: growth protocol

value: primary cultured


title: 3mo_3mpi_Ctrl_4 [X6100.3mpi.minus]

description: processed data file: 3mo_counts.txt

value: Control injected (Ctrl)

value: mouse hippocampus


title: Limb bud cells (Bmp2) Rep2

city: Suita

first: Yoshifumi

last: Takahata

state: Osaka

department: Dentistry

country: Japan

institute: Osaka University

data_processing:
Illumina Casava1.8.2 software was used for base calling
Mapped to mm10 whole genome using bowtie2 v 2.3.5
The fragmentsper kilobase of exon per million mapped fragments (FPKMs) werecalculated using Cufflinks version 2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample ...

source_name: Limb bud

extract_protocol:
Limb bud cells infected with Venus, Runx2, or Bmp2 adenovirus. After 4 days incubation, total RNA was extracted using Nucleospin RNA Plus Kit (Takara)
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina)

value: wild type

value: embryonic day 12.5

value: limb bud


title: 3mo_3mpi_Ctrl_5 [X6106.3mpi.minus]

description: processed data file: 3mo_counts.txt

value: 3 months old (3mo)


title: genomic DNA from unstable plaque 4

type: genomic

city: Beijing

first: Hang

last: Yang

state: Beijing

address: No.1 West Beichen Road,Chaoyang District

institute: CAS

description:
unstable atherosclerotic plaque
unstable4

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 and Methylation850 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Array data were evaluated and preprocessed using the minfi R package (version 1.32.0). The 450K and EPIC data were merged with the combineArrays function, the batch effect was corrected with sva R package (version3.34.0)

label: Cy5 and Cy3

source_name: unstable atherosclerotic plaque 4

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from frozen tissue specimens using the QIAamp DNA Mini Kit (Qiagen) following the manufacturer’s instructions.

tag: gender

value: male

tag: sample type

value: unstable atherosclerotic plaque

tag: disease state

value: unstable lesion


title: genomic DNA from unstable plaque 2

description:
unstable atherosclerotic plaque
unstable2

source_name: unstable atherosclerotic plaque 2


title: 3mo_3mpi_Ctrl_3 [X6097.3mpi.minus]

description: processed data file: 3mo_counts.txt

tag: incubation

value: 3 month post injection (3mpi)


title: genomic DNA from unstable plaque 6

description:
unstable atherosclerotic plaque
unstable6

source_name: unstable atherosclerotic plaque 6


title: genomic DNA from unstable plaque 3

description:
unstable atherosclerotic plaque
unstable3

source_name: unstable atherosclerotic plaque 3


title: genomic DNA from stable plaque 8

description:
stable atherosclerotic plaque
stable8

source_name: stable atherosclerotic plaque 8

value: stable atherosclerotic plaque

value: stable lesion


title: Limb bud cells (Bmp2) Rep1


title: genomic DNA from unstable plaque 5

description:
unstable atherosclerotic plaque
unstable5

source_name: unstable atherosclerotic plaque 5


title: 3mo_3mpi_Ctrl_2 [X6081.3mpi.minus]

description: processed data file: 3mo_counts.txt


title: Sertoli cells, TZEA30_1


title: Sertoli cells, TZEA10_3

value: 10 μM ZEA treated


title: Limb bud cells (Runx2) Rep2


title: 3mo_3mpi_Ctrl_1 [X6074.3mpi.minus]

description: processed data file: 3mo_counts.txt


title: genomic DNA from stable plaque 6

description:
stable atherosclerotic plaque
stable6

source_name: stable atherosclerotic plaque 6


title: genomic DNA from stable plaque 4

description:
stable atherosclerotic plaque
stable4

source_name: stable atherosclerotic plaque 4


title: Sertoli cells, TZEA10_2


title: 3mo_1mpi_AD_6 [X6093.1mpi.plus]

description: processed data file: 3mo_counts.txt

value: 1 month post injection (1mpi)

value: Alzheimer's disease injection (AD)


title: SLX_16495 Sample 1

value: 129m wt

value: E14 mouse embryonic stem cells

value: "Soft16":Soft hydrogel, Low adhesiveness


title: Limb bud cells (Venus) Rep2

value: Venus


title: Sertoli cells, TZEA30_2

value: 30 μM ZEA treated

value: Sertoli cells

value: primary cultured


title: Limb bud cells (Venus) Rep1

value: wild type

value: embryonic day 12.5

value: limb bud


title: Sertoli cells, TDON30_3

value: 30 μM DON treated


title: mDRG_H3 (Proinflammatory cytokines stimulated mDRGs pre-treated with a lentivirus expressing LCA, replicate 3)

city: Dublin

first: Jiafu

address: Collins Avenue,, Glasnevin

country: Ireland

institute: Dublin City University

data_processing:
DNBSEQ Platform used for basecalling.
Sequencing data is called raw reads or raw data, and quality control (QC) is then performed on the raw reads to determine whether the sequencing data is suitable for subsequent analysis. After quality control, the filtered clean reads were aligned to the reference sequence. After the alignment, the statistics of the mapping rate and the distribution of reads on the reference sequence are used to determine whether the alignment result passes the second QC of alignment. If it passes, we perform quantitative gene analysis and other analysis based on gene expression (principal component, correlation, differential gene screening, etc.), and perform GO function significance enrichment analysis on differentially expressed genes among the screened samples, Pathway saliency enrichment analysis, clustering, protein interaction networks, and transcription factors, and more in-depth mining analysis.
This project uses the filtering software SOAPnuke developed by BGI independently for filtering. The specific steps are as follows:  1) Remove the reads containing the adaptor (adaptor pollution);   2) Remove reads whose N content is greater than 5%;   3) Remove low-quality reads (we define reads with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads). Software Information  SOAPnuke:Version v1.5.2. Parameters -l 15 -q 0.2 -n 0.05.
Hierarchical Indexing for Spliced Alignment of Transcripts (HISTAT) is software for mapping RNA-seq reads. Compared with other software, HISAT has the advantages of high speed, high sensitivity and accuracy, and low memory consumption. HISAT's index based on Burrows-Wheeler transform and Ferragina-Manzini (FM) uses two types of indexes: whole genome indexes and partial genome indexes. See the HISAT alignment diagram for the details and statistics of genome mapping results. First, HISAT will use the global FM index to anchor the position of partial sequences in each read on the genome; then, use the partial genome indexes of these alignment positions to align the remaining sequences of each read to extend the alignment area. Software information: Software Information, HISAT2; Version：v2.0.4. Parameters：--phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000.
Genome_build: Mus_musculus NICB genome
Supplementary_files_format_and_content: mDRGsFPKMDEG.xlsx: Excel file includes FPKM values for each Sample.

source_name: mouse dorsal root ganglion neurons

growth_protocol: Dorsal root ganglia were dissociated by dispase II and collagenase I. Dissociated mDRGs were seeded in 24-well plates precoated with polyL-lysine and laminin (typically ~10,000 cells/well) and cultured in medium [DMEM containing 5% (v/v) foetal bovine serum, 2% B27 , 100 IU/ml penicillin, 100 μg/ml streptomycin and NGF (50 ng/ml)].

extract_protocol:
Extraction of total RNA from the treated mDRGs was performed using TRIzol reagent. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purify mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. Afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on DNBseq platform (BGI-Shenzhen, China).

treatment_protocol: mDRGs pretreated with lentivirus expressing either GFP or LCA for 5 days were incubated with 100 ng/ml LPS stimulated J774A.1 supernatant containing various cytokines for 4 h at 37°C.

tag: developmental stage

value: postnatal day 2-3

value: sensory ganglia

tag: culture

value: primary culture

value: lentivirus expressing LCA


title: Sertoli cells, TDON30_2


title: 3mo_1mpi_AD_5 [X6089.1mpi.plus]

description: processed data file: 3mo_counts.txt

value: 3 months old (3mo)

value: 1 month post injection (1mpi)

value: mouse hippocampus


title: 3mo_1mpi_AD_3 [X6085.1mpi.plus]

description: processed data file: 3mo_counts.txt

value: Alzheimer's disease injection (AD)


title: genomic DNA from stable plaque 7

description:
stable atherosclerotic plaque
stable7

source_name: stable atherosclerotic plaque 7

value: male

value: stable atherosclerotic plaque

value: stable lesion


title: mDRG_H2 (Proinflammatory cytokines stimulated mDRGs pre-treated with a lentivirus expressing LCA, replicate 2)


title: Limb bud cells (Runx2) Rep1

tag: condition


title: Sertoli cells, TDON30_1

tag: cell type

value: Sertoli cells


title: genomic DNA from stable plaque 5

description:
stable atherosclerotic plaque
stable5

source_name: stable atherosclerotic plaque 5


title: Sertoli cells, TZEA10_1

tag: treatment

value: 10 μM ZEA treated

value: primary cultured


title: 3mo_1mpi_AD_4 [X6086.1mpi.plus]

description: processed data file: 3mo_counts.txt


title: 3mo_1mpi_AD_2 [X6079.1mpi.plus]

description: processed data file: 3mo_counts.txt


title: Sertoli cells, TDON10_3

value: 10 μM DON treated


title: mDRG_H1 (Proinflammatory cytokines stimulated mDRGs pre-treated with a lentivirus expressing LCA, replicate 1)


title: 3mo_1mpi_AD_1 [X6075.1mpi.plus]

description: processed data file: 3mo_counts.txt


title: Sertoli cells, TDON10_2


title: 3mo_1mpi_Ctrl_5 [X6094.1mpi.minus]

description: processed data file: 3mo_counts.txt

value: Control injected (Ctrl)


title: genomic DNA from stable plaque 3

description:
stable atherosclerotic plaque
stable3

source_name: stable atherosclerotic plaque 3


title: 3mo_1mpi_Ctrl_4 [X6087.1mpi.minus]

description: processed data file: 3mo_counts.txt


title: Sertoli cells, TDON10_1


title: Sertoli cells, TCON3

value: 0 μM DON or ZEA treated


title: mDRG_G3 (Proinflammatory cytokines stimulated mDRGs pre-treated with a lentivirus expressing GFP, replicate 3)

value: postnatal day 2-3

value: lentivirus expressing GFP


title: G. sulfurreducens - Fumarate

city: Fuzhou

first: Zhenhua

last: Shi

address: No.15 Shangxiadian Road

institute: Fujian Agriculture and Forestry University

data_processing:
Library strategy: DNA-seq
Sequencing reads were processed and mapped to the reference sequences (RefSeq AE017180.2) using the software program BLASR.
BLASR generates a Mapping QV representing the confidence that the read maps are unique to the selected genomic interval.
Base modification and motif detection was performed using the modification and motif detection protocol in the software program SMRTPipe v.1.3.3.
Positions with coverage of > 25× and kinetic scores of QV > 30 were considered modified as previous study has suggested.
The QV is the −10 * log (P value), where the P value was determined from a t test between the sample and the in silico model (http://pacb.com/applications/base_modification/index.html).
Genome_build: RefSeq AE017180.2
Supplementary_files_format_and_content: tab-delimited text files include positon, Modif Type, coverage, IPDRatio, identification Qv, context, PositionType, Gene, Strand, and Product

organism: Geobacter sulfurreducens

source_name: G. sulfurreducens cells

growth_protocol: G. sulfurreducens PCA (ATCC 51573) was routinely cultured anaerobically at 30 °C in mineral-based medium containing 20 mM sodium acetate (Sinopharm Chemical Reagent Co., Ltd., CAS: 127-09-3) as electron donors and any of the following as electron acceptors: 50 mM Fe (III) citrate (Sigma, CAS: 3522-50-7), 40 mM fumarate (Sigma, CAS: 110-17-8), or 50 mM HFO.All media were adjusted to pH 6.8 and flushed with oxygen-free N2/CO2 (80/20, v/v) prior to sealing with butyl rubber stoppers and autoclaving.

extract_protocol:
For DNA extraction samples, Fe (III) citrate and fumarate cultures were harvested directly by centrifugation (10,000 rpm, 1 min). Conversely, HFO cultures were first dissolved with oxalate. DNA was isolated with the TIANamp Bacteria DNA Kit (TIANGEN, Cat. No. DP302-02).
Libraries of replicates of G. sulfurreducens were prepared for SMRT sequencing using a previously described library construction. These libraries were sequenced to a mean genome coverage depth of > 175×on the PacBioRS (Pacific Biosciences; Menlo Park, CA, USA) using standard protocols. Average read lengths were > 10 kbp and read quality was > 0.7 in all libraries (Supplementary Figure S1 B and C). Sequencing reads were processed and mapped to the reference sequences (RefSeq AE017180.2) using the software program BLASR. BLASR generates a Mapping QV representing the confidence that the read maps are unique to the selected genomic interval. Base modification and motif detection was performed using the modification and motif detection protocol in the software program SMRTPipe v.1.3.3. Positions with coverage of > 25× and kinetic scores of QV > 30 were considered modified as previous study has suggested.11 The QV is the −10 * log (P value), where the P value was determined from a t test between the sample and the in silico model (http://pacb.com/applications/base_modification/index.html). Positions with coverage of ≤ 25 × and QV ≤ 30 were excluded from analysis.

value: PCA

value: fumarate

tag: growth phase

value: mid-exponential phase


title: G. sulfurreducens - HFO

treatment_protocol: electron acceptors: 50 mM Fe (III) citrate (Sigma, CAS: 3522-50-7), 40 mM fumarate (Sigma, CAS: 110-17-8), or 50 mM HFO

value: hydrous ferric oxide (HFO)


title: genomic DNA from control 4

description:
normal artery
control4

source_name: internal mammary artery 4

value: normal artery

value: normal


title: 3mo_1mpi_Ctrl_3 [X6080.1mpi.minus]

description: processed data file: 3mo_counts.txt

tag: age

value: 3 months old (3mo)

value: 1 month post injection (1mpi)

value: mouse hippocampus


title: mDRG_G2 (Proinflammatory cytokines stimulated mDRGs pre-treated with a lentivirus expressing GFP, replicate 2)

tag: strain

value: sensory ganglia

value: primary culture


title: 3mo_1mpi_Ctrl_2 [X6077.1mpi.minus]

description: processed data file: 3mo_counts.txt

tag: tissue


title: mDRG_G1 (Proinflammatory cytokines stimulated mDRGs pre-treated with a lentivirus expressing GFP, replicate 1)


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2A6_A, resequencing

status: Public on Aug 30 2021

city: Bethesda

first: Augusto

last: Dulanto Chiang

state: Maryland

address: 9000 Rockville Pike

institute: NIAID

data_processing:
Adapters were trimmed using Trimmomatic
Reads were mapped to reference using BWA v0.7.17 using default parameters
Samtools v1.11 and Picard CollectRnaSeqMetrics (Picard tools v2.25.0) were used to obtain QC metrics.
Bam alignments from 10 resequenced libraries were merged using samtools. All Bam files and the PAO1 reference GFF file (Available from https://pseudomonas.com/downloads/pseudomonas/pgd_r_20_2/Pseudomonas_aeruginosa_PAO1_107/Pseudomonas_aeruginosa_PAO1_107.gff.gz , accessed 01/18/2021) were used to generate read counts for each sample with HTseq v0.11.4, using the htseq-count -s reverse -m union flags
Genome_build: GCA_000006765.1
Supplementary_files_format_and_content: htseq-count tabular format (.tsv)

organism: Pseudomonas aeruginosa

source_name: Liquid culture (LB broth)

growth_protocol: Each isolate was streaked onto TSA with 5% Sheep Blood agar plates from glycerol stocks frozen at -80°C and incubated at 37°C for 20 hours. A quarter-loop of colonies was transferred and resuspended in fresh LB, in triplicate. Three biological replicates per isolate were included for the RNA-seq experiment. From these, 10mL liquid subcultures with a starting OD600 of 0.01 were grown in a vented 50mL tube at 37°C with shaking at 220 RPM for 12 hrs. At the mid-log growth phase (5 and 5.5 hours for the hypermutator and wild-type cells, respectively) 1.5mL of culture was mixed with 3mL of RNA-Protect Reagent (Qiagen, Germantown, MD, USA). Cell harvest was conducted as per the manufacturer’s instructions.

extract_protocol:
Total RNA was extracted with MagMAX Viral/Pathogen kit, modified to include a DNAse incubation step. One microgram of RNA underwent rRNA depletion with the NEBNext rRNA depletion kit for bacteria.
RNA-Seq libraries were prepared with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® and NEBNext Multiplex Oligos for Illumina on an epMotion 5075 instrument.

treatment_protocol: Bacterial cultures were serially passaged on increasing concentrations of Ceftazidime-avibactam prior to whole-genome sequencing and RNA-seq.

tag: genotype

value: mutSTn

value: Ceftazidime/avibactam


title: hypg15_4_Microarray

type: RNA

city: Zurich

first: Cora

middle: S.

last: Thiel

address: Winterthurerstrasse 190

department: Institute of Anatomy

country: Switzerland

institute: University of Zurich

hyb_protocol: DNA targets were hybridized for 17h at 45°C on GeneChip Human Transcriptome Arrays 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the standard GeneChip Expression Wash, Stain and Scan protocol (Affymetrix GeneChip Wash, Stain and Scan Kit, 900720).

scan_protocol: Subsequently, the GeneChips were scanned using the Affymetrix 3000 7G scanner.

data_processing: RMA normalization with Bioconductor package Oligo, filtering out non-main probes with Bioconductor package affycoretools, differential expression analysis with Bioconductor package limma.

label: biotin

source_name: Jurkat cells (ATCC Clone E6-1, TIB152™)

label_protocol: The fragmented and biotinylated DNA targets were prepared according to the standard Affymetrix WT PLUS Reagent Kit protocol (Affymetrix GeneChip® WT PLUS Reagent Kit, 902280) from 100 ng total RNA starting material and 5.5 µg cDNA intermediate product.

growth_protocol: Grown in RPMI + 10% FCS + Penicillin/Streptomycin, split every second day, feeding every day

extract_protocol: Cells were fixed by quickly releasing them into TRIzol. Cells were sheared with a needle and syringe. After chloroform extraction, 0.6ml RLT buffer was added to the aqueous supernatent. RNA was extracted with Quiagen Rneasy mini kit.

treatment_protocol: Jurkat cells were exposed to 15 minutes of hypergravity or to normal gravity

tag: gravity

value: 9g, 15 min


title: hypg15_2_Microarray


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2X0_A, resequencing

description: 11232020_PA_RNA_2X0_A_ADC_NX13_S39_S39_RS

value: No antibiotic


title: hypg15_3_Microarray


title: Sertoli cells, TCON1

source_name: Sertoli cells

value: 0 μM DON or ZEA treated

value: Sertoli cells

value: primary cultured


title: Ctrl_4_Microarray


title: hypg15_1_Microarray


title: G. sulfurreducens - Fe(III) citrate

value: PCA

value: Fe(III) citrate


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2A2_C, resequencing

description: 11182020_PA_RNA_2A2_C_ADC_NX13_S43_S43_RS


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2A2_B, resequencing

description: 11182020_PA_RNA_2A2_B_ADC_NX13_S42_S42_RS


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 1X0_C, resequencing

value: wild-type


title: 3mo_1mpi_Ctrl_1 [X6073.1mpi.minus]

description: processed data file: 3mo_counts.txt

data_processing:
Reads aligned to GRCm38 with STAR
Duplicates marked with picard
Reads counted and DEG performed with edgeR
Genome_build: GRCm38
Supplementary_files_format_and_content: tables with TMM-normalised CPMs for each sample

extract_protocol:
Qiagen RNeasy Mini Kit
Mature messenger RNA was isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) followed by fragmentation and priming with NEBNext First Strand Synthesis Reaction buffer and NEBNext Random Primers. First and second strand synthesis were completed using ProtoScript II Reverse Transcriptase and Second Strand Synthesis Enzyme Mix (NEB), respectively. Double-stranded cDNA was purified with AxyPrep Mag PCR Clean-up (Axygen) and End Prep Enzyme Mix was used to repair ends and A-tail followed by addition of adaptors with T-A ligation (NEB). AxyPrep Mag PCR Clean-up was used for selection of ~360bp fragments and these were amplified with 11 cycles of PCR using P5 and P7 primers. Libraries were purified with AxyPrep Mag PCR Clean-up and quantified using and Agilent 2100 Bioanalyzer and Qubit 2.0 Fluorometer (Invitrogen).

value: Control injected (Ctrl)


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 1A15_A, resequencing

description: 11182020_PA_RNA_1A15_A_ADC_NX13_S52_S52_RS


title: Ctrl_1_Microarray


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2X0_A


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 1D16_B, resequencing

description: 11182020_PA_RNA_1D16_B_ADC_NX13_S71_S71_RS


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2X0_C


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 1X0_A, resequencing


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2X0_B


title: Sertoli cells, TCON2


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 1B6_A, resequencing

description: 11182020_PA_RNA_1B6_A_ADC_NX13_S10_S10_RS


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 1B6_B, resequencing

description: 11182020_PA_RNA_1B6_B_ADC_NX13_S14_S14_RS


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2D7_C


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2D6_C


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2D7_A


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2X0_A_2


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2D7_B


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2D6_A


title: Ctrl_2_Microarray


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2D4_B


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2D2_C


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2D3_A


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2D3_B


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2D3_C


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2D1_C


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2D1_A


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2B6_C_2


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2B6_C


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2B4_C


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2B6_A


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2B6_B


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2B4_A


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2B3_C


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2B2_C


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2A7_A


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2B3_B


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2B2_B


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2A5_C


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2A6_C


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2A6_A


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2A5_B


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2A4_A


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2A4_C


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2A4_B


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2A5_A


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2D2_A


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2B3_A


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2A2_B


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2A3_A


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2A2_A


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2A2_C


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2A1_C


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2A1_B


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2A1_A


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 1X0_C


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 1X0_B


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 1X0_A_2


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2A6_B


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 1X0_A


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 1D16_C


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 1C14_C


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 1C14_B


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 1D16_A


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 1C14_A_2


title: RNA-seq of P. aeruginosa CZA-adapted isolates, sample: 2A3_B