title: ros1_Gen1_Line1


title: h2az_Gen3_Line1

status: Public on Nov 13 2023

type: SRA

city: Klosterneuburg

first: Daniel

last: Zilberman

address: Am Campus 1

country: Austria

institute: Institute of Science and Technology Austria

library_source: genomic

data_processing:
Assembly: Araport 11
GFF files containing C/T counts for cytosines in the CG context

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: leaf tissue

extract_protocol:
Genomic DNA (gDNA) was extracted from 1-month-old Arabidopsis thaliana rosette leaves with the DNeasy plant mini kit (Qiagen, cat. no. 69104) per the manufacturer’s instructions.
Libraries were produced with the Ultra II DNA Library prep kit according to manufacturer’s instructions (New England Biolabs, cat. no. E7645L). Bisulfite conversion of DNA was carried out according to manufacturer’s protocol (Zymo, EZ DNA Methylation Lightning Kit, cat. no. D5046). DNA was converted twice to ensure complete bisulfite conversion of unmethylated cytosine.

tag: tissue

value: leaf tissue

tag: generation

tag: genotype

tag: lineage


title: ros1_Gen2_Line1_sib


title: ros1_Gen0_rep2


title: cmt2cmt3_Gen3_Line2_sib


title: cmt2cmt3_Gen3_Line1_sib


title: ros1_Gen0_rep1


title: ros1_Gen3_Line2_sib


title: cmt2cmt3_Gen3_Line1


title: cmt2cmt3_Gen2_Line2_sib


title: cmt2cmt3_Gen2_Line2


title: cmt2cmt3_Gen3_Line2


title: cmt2cmt3_Gen0_rep2


title: cmt2cmt3_Gen1_Line2


title: cmt2cmt3_Gen1_Line1


title: cmt2cmt3_Gen2_Line1


title: ros1_Gen2_Line2


title: cmt2cmt3_Gen0_rep1


title: ddcc_Gen5_LineC1

value: ddcc


title: ddcc_Gen5_LineC1_sib


title: ddcc_Gen4_LineC1


title: ros1_Gen1_Line2


title: ddcc_Gen4_LineC1_sib


title: ddcc_Gen3_LineC2_sib QW21L_8


title: ddcc_Gen3_LineC2_sib QW19Q_6


title: ddcc_Gen3_LineC2


title: ddcc_Gen3_LineC1


title: ddcc_Gen3_LineB2


title: ddcc_Gen3_LineB2_sib


title: ddcc_Gen3_LineB1_sib


title: ddcc_Gen3_LineA2


title: ddcc_Gen3_LineB1


title: ddcc_Gen3_LineA2_sib


title: cmt2cmt3_Gen2_Line1_sib


title: ddcc_Gen3_LineA1


title: ddcc_Gen2_LineC2


title: ddcc_Gen2_LineC1_sib


title: ddcc_Gen2_LineB1


title: ddcc_Gen2_LineB2_sib


title: ddcc_Gen2_LineB2


title: ddcc_Gen2_LineC2_sib


title: ddcc_Gen2_LineC1


title: ddcc_Gen2_LineA1


title: ddcc_Gen2_LineA2


title: ddcc_Gen1_LineC2


title: ddcc_Gen2_LineA1_sib


title: ddcc_Gen2_LineA2_sib


title: ddcc_Gen2_LineB1_sib


title: ddcc_Gen1_LineB1


title: ddcc_Gen1_LineA2


title: ddcc_Gen0_LineB_rep2

value: B


title: ddcc_Gen0_LineC_rep2

value: C


title: ddcc_Gen0_LineA_rep2

value: A


title: ddcc_Gen1_LineA1


title: ddcc_Gen0_LineB_rep1


title: ddcc_Gen0_LineA_rep1


title: drm1drm2_Gen5_Line1


title: drm1drm2_Gen5_Line2


title: ddcc_Gen1_LineC1


title: drm1drm2_Gen5_Line1_sib


title: ddcc_Gen1_LineB2


title: drm1drm2_Gen4_Line1_sib


title: drm1drm2_Gen3_Line2


title: drm1drm2_Gen4_Line2


title: drm1drm2_Gen4_Line1


title: drm1drm2_Gen4_Line2_sib


title: drm1drm2_Gen3_Line2_sib


title: drm1drm2_Gen2_Line2_sib


title: ddcc_Gen0_LineC_rep1


title: drm1drm2_Gen5_Line2_sib


title: drm1drm2_Gen2_Line2


title: drm1drm2_Gen2_Line1


title: drm1drm2_Gen3_Line1_sib


title: drm1drm2_Gen3_Line1


title: drm1drm2_Gen0_rep1


title: drm1drm2_Gen2_Line1_sib


title: drm1drm2_Gen1_Line2


title: cmt2_Gen5_Line2_sib


title: cmt2_Gen5_Line1


title: cmt2_Gen4_Line2


title: drm1drm2_Gen1_Line1


title: cmt2_Gen4_Line2_sib


title: cmt2_Gen4_Line1_sib


title: cmt2_Gen3_Line2_sib


title: cmt2_Gen3_Line1


title: drm1drm2_Gen0_rep2


title: cmt2_Gen4_Line1


title: cmt2_Gen3_Line2


title: cmt2_Gen2_Line2_sib


title: cmt2_Gen2_Line1


title: WT_Gen5_Line1

value: WT


title: cmt2_Gen1_Line2


title: cmt2_Gen3_Line1_sib


title: WT_Gen5_Line2_sib


title: cmt2_Gen0_rep2


title: WT_Gen5_Line1_sib


title: cmt2_Gen2_Line1_sib


title: WT_Gen4_Line2


title: cmt2_Gen1_Line1


title: WT_Gen5_Line2


title: WT_Gen4_Line1_sib


title: cmt2_Gen2_Line2


title: cmt2_Gen0_rep1


title: cmt2_Gen5_Line2


title: WT_Gen3_Line2_sib


title: cmt2_Gen5_Line1_sib


title: WT_Gen3_Line1


title: WT_Gen3_Line1_sib


title: WT_Gen2_Line2_sib


title: WT_Gen4_Line2_sib


title: WT_Gen4_Line1


title: WT_Gen2_Line1


title: WT_Gen2_Line1_sib


title: WT_Gen1_Line2


title: WT_Gen1_Line1


title: cmt3_Gen5_Line2_sib


title: cmt3_Gen3_Line1_sib


title: cmt3_Gen4_Line2_sib


title: cmt3_Gen4_Line2


title: cmt3_Gen4_Line1_sib


title: cmt3_Gen5_Line1


title: WT_Gen3_Line2


title: cmt3_Gen2_Line2


title: cmt3_Gen3_Line2_sib


title: cmt3_Gen3_Line2


title: cmt3_Gen5_Line1_sib


title: cmt3_Gen2_Line1


title: cmt3_Gen5_Line2


title: cmt3_Gen4_Line1


title: cmt3_Gen2_Line2_sib


title: cmt3_Gen2_Line1_sib


title: cmt3_Gen3_Line1


title: PDGF-BB treatment

type: RNA

city: Baltimore

first: jiekang

last: wang

state: MD

address: 365 homeland Southway unit 3A

country: USA

institute: Johns Hopkins University

description: test

data_processing: The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: https://geneglobe.qiagen.com/us/analyze  For the normalization it uses the ACTB.

label: SYBR Green

molecule: total RNA

organism: Mus musculus

source_name: test

extract_protocol: Total RNA was extracted with Rneasy plus Mini Kit

value: cerebral microvascular

tag: treatment

value: 20ng rmPDGF-BB


title: cmt3_Gen1_Line2


title: cmt3_Gen1_Line1


title: control

description: control

source_name: control

value: control


title: COR: Oocytes, cor, rep1

city: Ceske Budejovice

first: Lenka

last: Gahurova

address: Branisovska 1760

department: Department of molecular biology and genetics

country: Czech Republic

institute: University of South Bohemia

library_source: transcriptomic

data_processing:
read trimming (Trim Galore! v0.6.1)
read mapping (Hisat2 v2.1.0)
data quantification (Seqmonk)
Assembly: HetGla2/HetGla_female_1.0; Cavpor3.0; degu sequences XM_023711114.1, XM_004630806.2 and XM_023716073.1
Supplementary files format and content: txt file with raw read counts of individual genes

organism: Spalacopus cyanus

source_name: oocytes

growth_protocol: Oocytes were isolated from freshly sacrificed females by manual disruption of the ovary in M2 media and washed in PBS.

extract_protocol:
Picopure RNA extraction kit (Arcturus)
Ribosomal RNA was depleted with NEBNext rRNA Depletion Kit v2 (Human/Mouse/Rat) with sample purification beads (NEB, E7405) according to the manufacturer’s instructions, including DNase treatment by TURBO DNase (Thermo Fisher Scientific, AM2238) followed by library preparation using NEBNext Ultra II Directional RNA Library Prep with sample purification beads (NEB, E7765S) according to the manufacturer’s instructions.

tag: cell type

value: oocytes


title: WT_Gen2_Line2


title: Adjacent Normal Tissue of Primary Human Gastric Cancer Tissue6_rep1

city: Wuhan

first: Rongzhang

last: Dou

state: Hubei

address: No.169 Donghu Road

department: Department of Gastrointestinal Surgery

country: China

institute: Zhongnan Hospital, Wuhan University

description:
6N
Gene expression in adjacent normal stomach tissue from patient6

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 5 out of 10 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.

organism: Homo sapiens

source_name: Adjacent normal stomach tissue from patient6_rep1

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

value: Adjacent normal stomach tissue

tag: patient

tag: gender

value: Female

tag: age

tag: tnm stage

tag: pathological type

value: adenocarcinoma

tag: grade


title: Donor 6 - 2D

city: Groningen

first: Janette

middle: K

last: Burgess

state: Groningen

address: Hanzeplein 1

country: Netherlands

institute: Umcg

data_processing:
Clustering and DNA sequencing using the NovaSeq6000 was performed according to manufacturer's protocols. NovaSeq control software NCS v1.7 was used.
Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA3.4.4 and Bcl2fastq v2.2
For each sample the single-end FASTQ sequence reads were aligned to the hg38 reference genome using STAR (version 2.7.3a) with an overhang of 100 bases
After mapping, duplicate strands were removed using the UMI strands. The resulting mapped FASTQ files were checked using several quality control procedures, including first multiqc (version 1.7) to assess the mapping quality.
Lastly, the gene counts were calculated using HTseq (version 7.3)
Supplementary files format and content: tab-delimeted text file includes raw counts for each sample

source_name: Lung

growth_protocol: Primairy human lung fibroblasts were maintained in low glucose DMEM supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin in a humidified incubator at 5% CO2 and 37 °C

extract_protocol:
RNA was extracted from the fibroblasts using 2-Mercaptoethanol and RA1 lysis buffer and purified using the NucleoSpin RNA Kit according to the manufacturer's protocol. RNA quantity and quality were checked using the TapeStation system and RNA integrity number and RNA concentration were calculated using TapeStation Analysis Software 3.2.
The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used to process the samples.

treatment_protocol: No treatments were given to the cells during the culture

value: Lung

tag: cell line

value: Primairy cells

value: Fibroblast

value: 2D culture


title: Donor 6 - 3D

value: 3D culture


title: MiaPaca2 cells, GTA+5-Aza, replicate3

city: palo alto

first: Jiangbin

last: ye

state: California

address: 269 Campus Drive CCSR-South 1245

institute: Stanford university

data_processing:
Sequence data were trimmed and filtered with trim galore.
High quality and clean data were aligned to the human reference genome GRCh38 using hisat2 (version: 2.2.1).
HTseq (version:  v2.0.1) was used to calculate the read counts.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file included read counts for each sample

source_name: MiaPaca2 cells treated with 2mM GTA + 1µM 5-Aza for 24 hours

growth_protocol: All the cells were maintained in DMEM/F12 medium supplemented with 10% FBS, 2.5mM glutamine and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was isolated from cells using TRIzol Reagent (Invitrogen) protocol
RNA library was constructed by Novogene. The protocol is following the manufacturer's protocol

treatment_protocol: Plate the cells into 60cm plates and allow the cells attach to the plates. Treat the cells with DMSO, CPT, GTA+5-Aza, CPT+GTA+5-Aza for 24 hours

value: Pancreas

value: PDAC

value: GTA (2mM)+5-Aza (1µM)


title: MiaPaca2 cells, Control, replicate1

source_name: MiaPaca2 cells treated with DMSO for 24 hours

value: DMSO


title: MiaPaca2 cells, CPT+GTA+5-Aza, replicate2

source_name: MiaPaca2 cells treated with 1µM CPT + 2mM GTA + 1µM 5-Aza for 24 hours

value: WT

value: CPT (1µM)+GTA (2mM)+5-Aza (1µM)


title: MiaPaca2 cells, CPT, replicate3

source_name: MiaPaca2 cells treated with 1µM CPT for 24 hours

value: CPT (1µM)


title: MiaPaca2 cells, GTA+5-Aza, replicate1


title: MiaPaca2 cells, CPT+GTA+5-Aza, replicate1


title: MiaPaca2 cells, Control, replicate3


title: MiaPaca2 cells, CPT+GTA+5-Aza, replicate3


title: MiaPaca2 cells, GTA+5-Aza, replicate2


title: Donor 5 - 3D


title: MiaPaca2 cells, CPT, replicate1


title: Donor 7 - 3D


title: MiaPaca2 cells, CPT, replicate2


title: Donor 7 - 2D


title: Donor 5 - 2D


title: Primary Human Gastric Cancer Tissue6_rep1

description:
6CA
Gene expression in primary gastric cancer tissues from patient6

source_name: Primary gastric cancer tissues from patient6_rep1

value: Primary gastric cancer tissue


title: MiaPaca2 cells, Control, replicate2


title: Primary Human Gastric Cancer Tissue5_rep1

description:
5CA
Gene expression in primary gastric cancer tissues from patient5

source_name: Primary gastric cancer tissues from patient5_rep1

value: Male


title: Donor 4 - 3D


title: Primary Human Gastric Cancer Tissue3_rep1

description:
3CA
Gene expression in primary gastric cancer tissues from patient3

source_name: Primary gastric cancer tissues from patient3_rep1


title: Adjacent Normal Tissue of Primary Human Gastric Cancer Tissue3_rep1

description:
3N
Gene expression in adjacent normal stomach tissue from patient3

source_name: Adjacent normal stomach tissue from patient3_rep1

value: Adjacent normal stomach tissue


title: Adjacent Normal Tissue of Primary Human Gastric Cancer Tissue1_rep1

description:
1N
Gene expression in adjacent normal stomach tissue from patient1

source_name: Adjacent normal stomach tissue from patient1_rep1


title: Donor 3 - 3D


title: Donor 4 - 2D


title: Adjacent Normal Tissue of Primary Human Gastric Cancer Tissue4_rep1

description:
4N
Gene expression in adjacent normal stomach tissue from patient4

source_name: Adjacent normal stomach tissue from patient4_rep1


title: Primary Human Gastric Cancer Tissue4_rep1

description:
4CA
Gene expression in primary gastric cancer tissues from patient4

source_name: Primary gastric cancer tissues from patient4_rep1


title: Donor 2 - 2D


title: Adjacent Normal Tissue of Primary Human Gastric Cancer Tissue5_rep1

description:
5N
Gene expression in adjacent normal stomach tissue from patient5

source_name: Adjacent normal stomach tissue from patient5_rep1


title: Donor 1 - 2D


title: Donor 1 - 3D


title: Donor 2 - 3D


title: Donor 3 - 2D


title: Primary Human Gastric Cancer Tissue2_rep1

description:
2CA
Gene expression in primary gastric cancer tissues from patient2

source_name: Primary gastric cancer tissues from patient2_rep1


title: Primary Human Gastric Cancer Tissue1_rep1

description:
1CA
Gene expression in primary gastric cancer tissues from patient1

source_name: Primary gastric cancer tissues from patient1_rep1


title: Adjacent Normal Tissue of Primary Human Gastric Cancer Tissue2_rep1

description:
2N
Gene expression in adjacent normal stomach tissue from patient2

source_name: Adjacent normal stomach tissue from patient2_rep1


title: H9_D30_rep1

city: Beijing

first: Xi-Yin

last: Zhang

address: College Road

department: Neuroscience Research Institute

institute: Peking University

description: Day 30

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software. The mapped reads of each sample were assembled by StringTie in a reference-based approach.
Assembly: hg38 & mm38
Supplementary files format and content: Read counts in .csv files

molecule: polyA RNA

source_name: cortical organoids

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions. Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8-2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions (Illumina, San Diego, CA). The RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation from Illumina (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina). Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by Qubit 4.0, paired-end RNA-seq sequencing library was sequenced with the NovaSeq 6000 sequencer (2 × 150 bp read length).

value: cortical organoids

value: human ESCs

value: CDYL+/+


title: KO_D30_rep2

description: Day 30

value: CDYL-/-


title: H9_D30_rep2

description: Day 30


title: input_H

data_processing:
Raw data (raw reads) of fastq format were firstly processed using fastp (version 0.19.11, Chen et al., 2018)  software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of  the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using BWA (v 0.7.12) and clean reads were aligned to the reference genome using BWA mem (v 0.7.12).
For a specific ChIP-seq binding site, individual reads mapping to the plus or minus strand and present significant enrich. For single-end sequencing, the fragment size was estimated with MACS2 (Zhang et al., 2008) predicted method with default parameters. MACS2 scan all the genome with a specific window size and calculate the reads enrichment level. A particular number of windows were used as samples to build enrichment model and to predict fragment size. The following peak calling analysis was based on this predicted fragment size.
After mapping reads to the reference genome, we used the MACS2 (version 2.1.0) peak calling software to identify regions of IP enrichment over background. A q-value threshold of 0.05 was used for all data sets. After peak calling, the distribution of chromosome distribution, peak width, fold enrichment, significant level and peak summit number per peak were all displayed.
Assembly: hg38 & mm38
Supplementary files format and content: bigwig .bw files

extract_protocol:
ChIP DNA degradation and contamination was monitored on agarose gels. DNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). DNA concentration was measured using Qubit® DNA Assay Kit in Qubit® 3.0 Flurometer (Life Technologies, CA, USA).
The purified DNA was used for ChIP-seq library preparation. The library was constructed by Novogene Corporation (Beijing, China). Subsequently, pair-end sequencing of sample was performed on Illumina platform (Illumina, CA, USA). Library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: chip antibody


title: KO_D30_rep1

description: Day 30


title: AP_100

value: CDYL (Proteintech, 17763-1-AP)


title: AP_500


title: KO_D30_rep3

description: Day 30


title: KO_D80_rep3

description: Day 80


title: ab_100

value: CDYL (Abcam, ab5188)


title: H9_D30_rep3

description: Day 30


title: KO_D80_rep2

description: Day 80


title: KO_D80_rep1

description: Day 80


title: H9_D80_rep2

description: Day 80


title: H9_D80_rep1

description: Day 80


title: HSMM_6days_RNAseq_rep2

city: Boston

first: Richard

middle: Stefan

last: Isaac

state: MA

address: 77 Avenue Louis Pasteur, NRB 356

department: Genetics

institute: Harvard Medical School

description:
paired-end 100 nt reads
6d_0d_DESeq2.txt

data_processing:
Reads trimmed with cutadapt v1.14
Aligned using STAR's default parameters to the reference hg38 genome
Rsubread featureCounts used to count uniquely-mapping reads across coding sequences
Differential expression analyses performed using DESeq2 with GAPDH/HPRT1/RPS12 in the controlGenes parameter of the estimateSizeFactors function
Assembly: hg38
Supplementary files format and content: .txt file of DESeq2 output including log2 fold-change

source_name: Human skeletal muscle myoblasts

growth_protocol: HSMM cells were maintained in Human Skeletal Muscle Cell Basal Media with growth supplement (Cell Application, INC)

extract_protocol:
Total RNA was extracted by lysing cells in RIPA, incubating on ice, and mixing with Trizol LS
Using the SMARTer Stranded Total RNA HI Mammalian Kit (Takara 634873)

treatment_protocol: HSMM differentiation was induced by switching cells at 80% confluency to DMEM containing glucose and pyruvate supplemented with 2% Heat Inactived Horse Serum (Thermo Fisher Scientific) and 0.4 µg/mL dexamethasone

value: Human skeletal muscle myoblasts

value: 2% Horse Serum 0.4 µg/mL dexamethasone 6 days


title: H9_D80_rep3

description: Day 80


title: HSMM_3days_RNAseq_rep2

description:
paired-end 100 nt reads
3d_0d_DESeq2.txt

value: 2% Horse Serum 0.4 µg/mL dexamethasone 3 days


title: HSMM_0days_RNAseq_rep1

description: paired-end 100 nt reads


title: HSMM_6days_RNAseq_rep1


title: HSMM_0days_RNAseq_rep2

description: paired-end 100 nt reads


title: HSMM_3days_RNAseq_rep1


title: CD8OSD11_Ef

city: Toulouse

first: Leila

last: Khajavi

address: TOULOUSE

country: France

institute: INSERM

description: raw counts

data_processing:
STAR; version 2.6.0c
RSEM; version 1.3.0
Assembly: Homo sapiens primary genome sequence, Gencode: GRCh38, v27
Supplementary files format and content: Tab-delimited text file containing raw counts for each sample

source_name: Blood

extract_protocol:
Cryopreserved PBMCs were thawed and washed in RPMI medium supplemented with 1% L-glutamine (100x), 1% sodium pyruvate (100mM), 1% non essential amino acids (100x), 1% penicillin-streptomycine (10,000 U/ml), 1% HEPES (1M) and 5% filtered and inactivated human AB-serum. Cells were then resuspended in PBS at 10 million/mL. Cell sorting was performed using a BD FACSAria Fusion with an antibody panel against CD3 (BD Horizon), CD4 (BD BioSciences), CD8α (BD Pharmingen), CCR7 (BD Horizon) and CD45RA (BD BioSciences) as well as eBioscience Fixable Viability Dye AF488. The T-cell subset sorting scheme used CCR7 and CD45RA cell surface markers to identify the four T-cell subsets. Post sorting, the cell number and viability were analyzed with the FlowJo software.
Library preparation (SMART-seq v4, Takara Bio) and RNA-sequencing (Illumina NovaSeq) were performed by the Genomics Facility Basel in Switzerland.

value: Blood

value: CD8 T-cell


title: CD8OSD08_EM

description: raw counts


title: CD8OSD11_CM

description: raw counts


title: CD8OSD10_Ef

description: raw counts


title: CD8OSD10_EM

description: raw counts


title: CD8OSD08_CM

description: raw counts


title: CD8OSD11_EM

description: raw counts


title: CD8OSD11_Nv

description: raw counts


title: CD8OSD08_Ef

description: raw counts


title: CD8OSD07_Ef

description: raw counts


title: CD8OSD09_EM

description: raw counts


title: CD8OSD10_CM

description: raw counts


title: CD8OSD08_Nv

description: raw counts


title: CD8OSD07_CM

description: raw counts


title: CD8OSD10_Nv

description: raw counts


title: CD8OSD07_EM

description: raw counts


title: CD8OSD09_Nv

description: raw counts


title: CD8OSD06_Nv

description: raw counts


title: CD8OSD09_Ef

description: raw counts


title: CD8OSD07_Nv

description: raw counts


title: CD8OSD06_Ef

description: raw counts


title: CD8OSD06_CM

description: raw counts


title: CD8OSD05_Nv

description: raw counts


title: CD8OSD05_Ef

description: raw counts


title: CD8OSD05_CM

description: raw counts


title: CD8OSD04_Nv

description: raw counts


title: CD8OSD04_EM

description: raw counts


title: CD8OSD03_Nv

description: raw counts


title: CD8OSD01_Nv

description: raw counts


title: CD8OSD06_EM

description: raw counts


title: CD8OSD02_Ef

description: raw counts


title: CD8OSD01_EM

description: raw counts


title: CD8OSD05_EM

description: raw counts


title: CD8OSD03_CM

description: raw counts


title: CD8OSD02_Nv

description: raw counts


title: CD8OSD03_Ef

description: raw counts


title: CD8OSD03_EM

description: raw counts


title: CD8NAR11_EM

description: raw counts


title: CD8NAR11_Nv

description: raw counts


title: CD8NAR10_Ef

description: raw counts


title: CD8NAR09_Nv

description: raw counts


title: CD8OSD04_Ef

description: raw counts


title: CD8NAR10_CM

description: raw counts


title: CD8NAR10_EM

description: raw counts


title: CD8NAR10_Nv

description: raw counts


title: CD8OSD01_CM

description: raw counts


title: CD8NAR09_EM

description: raw counts


title: CD8NAR11_Ef

description: raw counts


title: CD8OSD09_CM

description: raw counts


title: CD8NAR09_Ef

description: raw counts


title: CD8OSD02_EM

description: raw counts


title: CD8OSD04_CM

description: raw counts


title: CD8OSD02_CM

description: raw counts


title: CD8NAR08_Nv

description: raw counts


title: CD8OSD01_Ef

description: raw counts


title: CD8NAR09_CM

description: raw counts


title: CD8NAR08_CM

description: raw counts


title: CD8NAR07_Ef

description: raw counts


title: CD8NAR07_EM

description: raw counts


title: CD8NAR07_CM

description: raw counts


title: CD8NAR05_EM

description: raw counts


title: CD8NAR06_EM

description: raw counts


title: CD8NAR05_Nv

description: raw counts


title: CD8NAR05_CM

description: raw counts


title: CD8NAR04_EM

description: raw counts


title: CD8NAR06_CM

description: raw counts


title: CD8NAR03_EM

description: raw counts


title: CD8NAR04_Ef

description: raw counts


title: CD8NAR02_EM

description: raw counts


title: CD8NAR02_CM

description: raw counts


title: CD8NAR04_Nv

description: raw counts


title: CD8NAR05_Ef

description: raw counts


title: CD8NAR02_Ef

description: raw counts


title: CD8NAR08_Ef

description: raw counts


title: CD8NAR02_Nv

description: raw counts


title: CD8NAR03_Ef

description: raw counts


title: CD8NAR01_Nv

description: raw counts


title: CD8NAR03_Nv

description: raw counts


title: CD8NAR01_Ef

description: raw counts


title: CD8NAR08_EM

description: raw counts


title: CD8NAR01_EM

description: raw counts


title: CD8NAR06_Ef

description: raw counts


title: CD8NAR01_CM

description: raw counts


title: CD8NAR07_Nv

description: raw counts


title: CD8HD11_EM

description: raw counts


title: CD8HD11_Nv

description: raw counts


title: CD8NAR06_Nv

description: raw counts


title: CD8HD10_Ef

description: raw counts


title: CD8HD09_Nv

description: raw counts


title: CD8HD11_CM

description: raw counts


title: CD8HD10_Nv

description: raw counts


title: CD8HD10_CM

description: raw counts


title: CD8HD09_CM

description: raw counts


title: CD8HD09_Ef

description: raw counts


title: CD8HD08_EM

description: raw counts


title: CD8HD07_EM

description: raw counts


title: CD8HD08_Ef

description: raw counts


title: CD8HD07_Nv

description: raw counts


title: CD8HD07_Ef

description: raw counts


title: CD8HD06_CM

description: raw counts


title: CD8HD05_Nv

description: raw counts


title: CD8HD06_EM

description: raw counts


title: CD8HD06_Ef

description: raw counts


title: CD8HD07_CM

description: raw counts


title: CD8HD06_Nv

description: raw counts


title: CD8HD04_Nv

description: raw counts


title: CD8HD05_CM

description: raw counts


title: CD8HD11_Ef

description: raw counts


title: CD8HD05_EM

description: raw counts


title: CD8HD09_EM

description: raw counts


title: CD8HD05_Ef

description: raw counts


title: CD8HD04_Ef

description: raw counts


title: CD8HD03_Ef

description: raw counts


title: CD8HD03_Nv

description: raw counts


title: CD8HD10_EM

description: raw counts


title: CD8HD04_EM

description: raw counts


title: CD8HD02_Nv

description: raw counts


title: CD8HD02_EM

description: raw counts


title: CD8HD08_Nv

description: raw counts


title: CD8HD02_Ef

description: raw counts


title: CD8HD03_EM

description: raw counts


title: CD8HD08_CM

description: raw counts


title: CD8HD03_CM

description: raw counts


title: CD8HD02_CM

description: raw counts


title: CD8HD01_Nv

description: raw counts


title: CD4OSD11_EM

description: raw counts

value: CD4 T-cell


title: CD4OSD11_Nv

description: raw counts


title: CD4OSD10_Nv

description: raw counts


title: CD4OSD11_Ef

description: raw counts


title: CD8HD01_Ef

description: raw counts


title: CD4OSD11_CM

description: raw counts


title: CD4OSD10_Ef

description: raw counts


title: CD4OSD10_EM

description: raw counts


title: CD4OSD10_CM

description: raw counts


title: CD4OSD09_EM

description: raw counts


title: CD4OSD09_Nv

description: raw counts


title: dormouse #IBA7 sampled in interbout arousal

city: Ulm

first: Annika

last: Herwig

address: Albert-Einstein-Allee 11

department: Institute of Neurobiology

country: Germany

institute: Ulm University

data_processing:
FastQC 0.11.9
trim-galore 0.6.6
Trinity 2.8.5
Assembly: GRCm39, Mus musculus
blastx 2.5.0+
extract_hits_from_fasta.rb
hits_to_genemap.rb
bowtie 1.3.0
rsem 1.3.1
Supplementary files format and content: .genes.results, non-normalized gene expression

organism: Eliomys quercinus

source_name: hypothalamus

growth_protocol: outdoor breeding colony at the Research Institute of Wildlife Ecology (University of Veterinary Medicine, Vienna, Austria; latitude 48°15`N, longitude 16°22`E)

extract_protocol:
The hypothalamus was dissected and homogenized in about 3 mL TriFast by using a micropestle. Total RNA was isolated using peqGOLD TrifastTM (Peqlab, Erlangen, Germany) and purified by using the Crystal RNA MiniKit (Biolabproducts, Bebensee, Germany) including an on-column digestion with RNase-free DNase (Quiagen, Hilden, Germany).
mRNA-Seq was conducted in 2017 on an Illumina NextSeq 500 (paired end, 4 lanes)

treatment_protocol: constant darkness without food and water at 5 °C

value: hypothalamus

tag: development stage

value: adult, hibernating

tag: housing

value: constant darkness without food and water at 5 C

tag: Sex

value: f

tag: date of_sacrifice

tag: terminal tb_[c]

tag: terminal body_mass_[g]

tag: rna-extraction

tag: months of_storage


title: dormouse #IBA6 sampled in interbout arousal

tag: tissue

value: m


title: dormouse #LT07 sampled in late torpor


title: dormouse #LT05 sampled in late torpor


title: CD4OSD09_CM

description: raw counts

tag: cell type


title: dormouse #IBA3 sampled in interbout arousal


title: dormouse #IBA2 sampled in interbout arousal


title: CD8NAR11_CM

description: raw counts


title: dormouse #LT02 sampled in late torpor


title: CD4OSD08_Nv

description: raw counts


title: CD4OSD08_EM

description: raw counts


title: CD4OSD08_Ef

description: raw counts


title: CD8HD01_EM

description: raw counts


title: dormouse #LT01 sampled in late torpor


title: dormouse #ET05 sampled in early torpor


title: CD8HD01_CM

description: raw counts


title: CD4OSD08_CM

description: raw counts


title: dormouse #ET03 sampled in early torpor


title: CD4OSD07_EM

description: raw counts


title: CD4OSD07_Nv

description: raw counts


title: RNAseq_H.volcanii_delta2753_p2_R2

city: Freiburg

first: Rick

last: Gelhausen

state: Baden Württemberg

address: Georges-Köhler-Allee 106

department: Department of Computer Science

institute: Albert-Ludwigs-University Freiburg

description: Total RNA extracted from delta HV0_2753 mutant strain, DNaseI digested, rRNA depleted, fragmented and subjected to cDNA library preparation

data_processing:
Base calling with Illumina NextSeq RTA v2.11.3
FASTQ conversion with bcl2fastq v2.20.0.422
FASTQ quality and adapter trimming using Cutadapt (Martin, 2011) version 2.1 (cutadapt parameters: -q 20 --trim-n -m 10 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) (HRIBO 1.6.0)
Mapping with segemehl 0.3.4 (HRIBO 1.6.0)
rRNA filtering was done using samtools 1.9 (HRIBO 1.6.0)
Coverage files were created using HRIBO 1.6.0
bigwig files were generated with full read coverage and normalized to the size of the minimal sample size among all samples.
Assembly: GCF_000025685.1
Supplementary files format and content: bigwig format files containing normalized read coverage for each sample

organism: Haloferax volcanii DS2

source_name: Haloferax volcanii DS2 H26

growth_protocol: H. volcanii cells were grown to exponential phase

extract_protocol:
Total RNA was extracted using  phenol-chloroform-isoamyl alcohol (25:24:1, Roth).
Total RNA was first rRNA-depleted, fragmented then subjected to cDNA library preparation. First, an oligonucleotide adapter was ligated to the 3' end of the RNA molecules. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase and the 3’ adapter as primer. The first strand cDNA was purified and the 5' Illumina TruSeq sequencing adapter was ligated to the 3' end of the antisense cDNA. The resulting cDNA was PCR-amplified to about 10-20 ng/μl using a high fidelity DNA polymerase. The cDNA was purified  using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and was analyzed by capillary electrophoresis.
Adapter ligation protocol for RNA-seq performed at Vertis Biotechnology

treatment_protocol: No treatment applied during growth.

tag: genotype

value: delta HV0_2753 mutant strain


title: dormouse #ET02 sampled in early torpor


title: dormouse #ET01 sampled in early torpor


title: CD4OSD07_CM

description: raw counts


title: CD4OSD07_Ef

description: raw counts


title: RNAseq_H.volcanii_delta2753_p2_R1


title: CD4OSD06_Nv

description: raw counts


title: CD4OSD06_CM

description: raw counts


title: RNAseq_H.volcanii_H26WT_p2_R2

description: Total RNA extracted from WT strain, DNaseI digested, rRNA depleted, fragmented and subjected to cDNA library preparation (WT for delta  HV0_2753 mutant strain)

value: WT


title: RNAseq_H.volcanii_H26WT_p2_R1


title: CD4OSD09_Ef

description: raw counts


title: CD4OSD06_EM

description: raw counts


title: CD4OSD05_EM

description: raw counts


title: RNAseq_H.volcanii_d0758_p1_R2

description: Total RNA extracted from delta HV0_0758 mutant strain, DNaseI digested, rRNA depleted, fragmented and subjected to cDNA library preparation

value: delta HV0_0758 mutant strain


title: RNAseq_H.volcanii_d0758_p1_R1


title: CD4OSD05_Nv

description: raw counts


title: CD4OSD05_Ef

description: raw counts


title: RNAseq_H.volcanii_H26WT_p1_R2

description: Total RNA extracted from WT strain, DNaseI digested, rRNA depleted, fragmented and subjected to cDNA library preparation (WT for delta  HV0_0758 mutant strain)


title: RNAseq_H.volcanii_H26WT_p1_R1


title: wt_total_an_2

city: Lebanon

first: Christine

last: Alewine

state: NH

address: One Medical Center Drive, Williamson 651,

institute: Dartmouth Cancer Center

data_processing:
The Illumina reads in FASTQ format were first trimmed by Cutadapt 58 to remove the adaptor sequences and low quality reads.
After quality control with FASTQC 0.11.9, the trimmed reads were processed with the RNA-Seq pipeline READemption version 2.0.3.
Reads longer than 12 nucleotides were aligned to the Escherichia coli str. K-12 substr. MG1655 reference sequence (NC_000913.3) from the NCBI. In addition to the known genes and small RNAs in the annotation published previously, we manually curated 87 tRNA genes and operon precursors by comparing the sequences and the annotations in EcoCyc (https://ecocyc.org), further discussed in supplemental materials and methods.
Nucleotide-wise coverage files in wiggle format and gene-wise normalized read counts were generated for visualization and comparison. Differential gene expression analysis was performed with DESeq2 using fold-change of 2.0 or higher and the adjusted p-value below 0.1 as the threshold.
Assembly: Ecoli K-12 MG1655 NC_000913.3
Supplementary files format and content: YhbS-HqbA.RawCount.RPKM.xlsx which contains 3 sheets of the raw count and RPKM, corresponding to the S4, S5 and S7 tables of the manuscropt aerobic, anaerobic and tRNA only data.
Supplementary files format and content: E.coli_K12_MG1655_NC000913.3_tRNA_annotation.xlsx is the E.coli K12 MG1655 tRNA annotation manually curated by Dr. Susan Gottesman.

growth_protocol: The strains were cultured in LB supplemented with 5 mM NaNO3 at 37 °C with agitation. When the OD600 reached 0.3, each culture was split into two aliquots and pelleted by centrifuging at 4500 rpm for 10 min at room temperature.

extract_protocol:
When the OD600 reached 0.9 to 1.0, 20 OD600 of cells were collected and lysed by vortexing with 212-300 mm glass beads (Sigma) in a total volume of 2 ml lysis buffer (20 mM Tris-HCl/pH 8.0, 150 mM KCl, 1 mM MgCl2 and 1 mM DTT). The isolation of total RNA and Hfq-IP RNA was performed as previously described 38 with following modifications. 1.9 ml of cell lysate were mixed with 200 ml of Hfq antibody and 240 mg of protein A-Sepharose CL-4B (GE Healthcare). Hfq-IP RNA was isolated from protein A-Sepharose beads by extraction with phenol : chloroform : isoamyl alcohol (25:24:1), followed by ethanol precipitation. Total RNA was isolated from 100 ml of cell lysate by Trizol (ThermoFisher Sciientific) extraction followed by chloroform extraction and isopropanol precipitation. RNA were dissolved in 15 ml of DEPC water.
cDNA libraries were constructed based on a protocol adapted to capture the bacterial sRNAs 57. 400 ng RNA samples were used as input and the index primers were listed in Table S3. 7 cycles of PCR were performed at the last step to enrich each library.

treatment_protocol: The pellet of one aliquot was resuspended in the same volume of medium and grew continuously under aerobic condition. The other aliquot was moved to an anaerobic chamber and resuspended in the same volume of deoxygenated LB with NaNO3 (5 mM) and grew anaerobically.

tag: strain

tag: growth condition

value: anaerobically

tag: treatment

value: Total RNA


title: CD4OSD05_CM

description: raw counts


title: progression_CRLM8_2

city: RTP

middle: David

last: Fannin

state: NC

address: 111 Tw Alexander Dr, MD D204

department: NIEHS/NIH

institute: Mr.

description: Immortalized human leiomyoma cells, female, benign tumor, age unknown.

hyb_protocol: Reporter and Capture probes were added according to the manufacturer’s directions (nanostring.com) to 50 ng of total RNA in a final volume of 15ul followed by hybridization for at least 14 hours at 65oC

scan_protocol: After sample processing according to manufacturer’s instructions on the nCounter Prep Station Model 5S, sample cartridges were scanned on an nCounter Digital Analyzer Model 5S, using 555 Fields of Vision (FOV) and the .rlf file 'NS_Cancerprog_C4972'.

data_processing: Data were adjusted utilizing the manufacturer's positive and negative control probes, as well as internal housekeeping genes. This nSolver adjusted data were then imported into Partek(v7.0), log2 transformed and quantile normalized.

source_name: human leiomyoma

growth_protocol: A human uterine leiomyoma cell line immortalized via retroviral transfection of telemorase (ht-UtLM) was generated by our laboratory. Human fibroblast and vulvar leiomyosarcoma (SKS-LMS-1) cell lines were cultured in DMEM medium supplemented with 10% FBS. All cultures were kept in a standard tissue culture incubator at 37°C with 5% CO2.

extract_protocol: Total RNA was isolated by extracting with Trizol ™ Reagent (ThermoFisher Cat# 15596026) and subsequently purifying with an Rneasy Mini Kit (Qiagen Cat#74104).

treatment_protocol: For 8-week Cd-exposure experiment, the ht-UtLM cultures were maintained continuously in ht-UtLM culture medium supplemented with 10 μM CdCl2 for 8 weeks. The culture medium was replaced with fresh medium with 10 μM CdCl2 every 3 days. Passage-matched control ht-UtLM cultures were run concurrently with Cd exposed cells. All cultures were kept in a standard tissue culture incubator at 37°C with 5% CO2.

value: cadmium-treated

value: female


title: progression_LM8_2

value: control

value: human uterine leiomyoma cell line immortalized via retroviral transfection of telemorase (ht-UtLM)


title: progression_CRLM8_3


title: progression_LM8_1


title: wt_total_an_1

organism: Escherichia coli str. K-12 substr. MG1655


title: progression_CRLM8_1


title: CD4OSD04_EM

description: raw counts

value: Blood


title: wt_ip_an_2

value: Hfq co-IP RNA


title: wt_total_ae_1

value: aerobically


title: CD4OSD04_Nv

description: raw counts

value: CD4 T-cell


title: wt_ip_an_1


title: Lung, SARS-CoV-2-infected IL-33 KO C57BL/6 mice, Day4, replicate 4, RNAseq

city: Galveston

first: Lynn

last: Soong

state: TX

address: 301 University Blvd

department: Microbiology and Immunology

institute: University of Texas Medical Branch

description:
2×150bp paired-endsequencing (PE150)
D4_KO_4

data_processing:
Data was analyzed by ROSALIND® (https://rosalind.bio/), with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA). Reads were trimmed using cutadapt1. Quality scores were assessed using FastQC2. Reads were aligned to the Mus musculus genome build mm10 using STAR3. Individual sample reads were quantified using HTseq4 and normalized via Relative Log Expression (RLE) using DESeq2 R library5. Read Distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step using RSeQC6. DEseq2 was also used to calculate fold changes and p-values and perform optional covariate correction. Clustering of genes for the final heatmap of differentially expressed genes was done using the PAM (Partitioning Around Medoids) method using the fpc R library7. Hypergeometric distribution was used to analyze the enrichment of pathways, gene ontology, domain structure, and other ontologies. The topGO R library8, was used to determine local similarities and dependencies between GO terms in order to perform Elim pruning correction. Several database sources were referenced for enrichment analysis, including Interpro9, NCBI10, MSigDB11,12, REACTOME13, WikiPathways14. Enrichment was calculated relative to a set of background genes relevant for the experiment.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include DESeq2-normalized counts

source_name: Lung

extract_protocol:
Male WT C57BL/6j mice (stock #000664, age 8-10 wks) and IL-33 knockout (KO) mice (B6 background) were anesthetized via isoflurane, followed by the intranasal infection with mouse adapted SARS-CoV-2 CMA3p20 (5×10^5 PFU). Mock mice were administrated with identical volumes of cell culture medium. Lungs were perfused with cold PBS and harvested at days 2 and 4 post-infection. Lung RNA was isolated by Qiagen RNeasy Kits. Total RNA (≥ 1ug) was sent to LC Sciences (Houston, TX) for Poly(A) RNA-Seq Sequencing Service.
The total RNA quantity and purity were analyzed by the Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). High-quality RNA samples with RIN number > 7.0 were used to construct sequencing library. mRNA was purified from total RNA using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat. e6150, USA, under 94℃ 5-7min). Then, the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were then used to synthesize U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat. m0209, USA), RNase H (NEB, cat. m0297, USA) and dUTP Solution (Thermo Fisher, cat. R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat. m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec, and then final extension at 72℃ for 5 min. The average insert sizes for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150 bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC Sciences, Houston, TX, US) following the vendor's recommended protocol.

value: Lung

value: IL-33 KO C57BL/6j

tag: age

value: 8-10 weeks

tag: time

value: Day 4


title: wt_ip_ae_2


title: Lung, SARS-CoV-2-infected IL-33 KO C57BL/6 mice, Day4, replicate 5, RNAseq

description:
2×150bp paired-endsequencing (PE150)
D4_KO_5


title: Lung, SARS-CoV-2-infected IL-33 KO C57BL/6 mice, Day4, replicate 2, RNAseq

description:
2×150bp paired-endsequencing (PE150)
D4_KO_2


title: Lung, SARS-CoV-2-infected IL-33 KO C57BL/6 mice, Day4, replicate 3, RNAseq

description:
2×150bp paired-endsequencing (PE150)
D4_KO_3


title: wt_ip_ae_1


title: dely_total_an_2

source_name: hqbA (XL678)

value: hqbA (XL678)


title: CD4OSD04_Ef

description: raw counts


title: progression_LM8_3


title: CD4OSD04_CM

description: raw counts


title: dely_total_an_1


title: CD4OSD03_Nv

description: raw counts


title: dely_total_ae_2


title: dely_ip_an_2


title: wt_total_ae_2


title: Lung, SARS-CoV-2-infected WT C57BL/6 mice, Day4, replicate 4, RNAseq

description:
2×150bp paired-endsequencing (PE150)
D4_WT_4


title: CD4OSD03_EM

description: raw counts


title: Lung, SARS-CoV-2-infected WT C57BL/6 mice, Day4, replicate 3, RNAseq

description:
2×150bp paired-endsequencing (PE150)
D4_WT_3


title: dely_ip_an_1


title: CD4OSD03_Ef

description: raw counts


title: Lung, SARS-CoV-2-infected WT C57BL/6 mice, Day4, replicate 2, RNAseq

description:
2×150bp paired-endsequencing (PE150)
D4_WT_2


title: d98_total_an_1

source_name: hqbAD98AE102A (XL675)

value: hqbAD98AE102A (XL675)


title: CD4OSD03_CM

description: raw counts


title: d98_total_ae_2


title: dely_ip_ae_1


title: d98_total_an_2


title: Lung, SARS-CoV-2-infected WT C57BL/6 mice, Day4, replicate 1, RNAseq

description:
2×150bp paired-endsequencing (PE150)
D4_WT_1


title: Lung, SARS-CoV-2-infected IL-33 KO C57BL/6 mice, Day4, replicate 1, RNAseq

description:
2×150bp paired-endsequencing (PE150)
D4_KO_1


title: d98_total_ae_1


title: Lung, mock-infected C57BL/6 mice, Day4, replicate 3, RNAseq

description:
2×150bp paired-endsequencing (PE150)
D4_Mock_3

value: culture medium


title: d98_ip_an_2

value: anaerobically


title: CD4OSD02_EM

description: raw counts


title: CD4OSD02_Nv

description: raw counts


title: Lung, mock-infected C57BL/6 mice, Day4, replicate 2, RNAseq

description:
2×150bp paired-endsequencing (PE150)
D4_Mock_2


title: d98_ip_ae_2


title: d98_ip_an_1


title: d98_ip_ae_1


title: dely_total_ae_1

value: Total RNA


title: CD4OSD02_Ef

description: raw counts


title: Lung, mock-infected C57BL/6 mice, Day4, replicate 1, RNAseq

description:
2×150bp paired-endsequencing (PE150)
D4_Mock_1


title: CD4OSD02_CM

description: raw counts


title: Lung, SARS-CoV-2-infected IL-33 KO C57BL/6 mice, Day2, replicate 4, RNAseq

description:
2×150bp paired-endsequencing (PE150)
D2_KO_4

value: Day 2


title: dely_ip_ae_2


title: hip1_+N_rep3

city: Newcastle upon Tyne

first: Simon

last: Whitehall

address: Framlington Place

department: Biosciences Institute

country: United Kingdom

institute: Newcastle University

data_processing:
Aligned using STAR default settings
stranded bigwig files generated using STAR
Genome_build:  ASM294v2
Supplementary_files_format_and_content: All processed files are stranded bigwig files

organism: Schizosaccharomyces pombe

source_name: fission yeast

growth_protocol: ML phase S. pombe cells were washed and resuspended in EMM - Nitrogen for 24 hours. Quiescent samples were then collected (half of the sample). The rest were re-fed with YE5S (nitrogen containing rich media) for 90 minutes, then were collected too.

extract_protocol:
Total RNA was extracted using acidic phenol chloroform.
Stranded RNAseq libraries were made using the NEBNext® Ultra RNA Library Prep Kit for Illumina® kit

value: re-fed with nitrogen for 60 minutes


title: hip1_+N_rep2


title: CD4OSD01_Nv

description: raw counts


title: hip1_+N_rep1


title: Lung, SARS-CoV-2-infected IL-33 KO C57BL/6 mice, Day2, replicate 3, RNAseq

description:
2×150bp paired-endsequencing (PE150)
D2_KO_3


title: CD4OSD01_Ef

description: raw counts


title: HSMM_6days_mito_rep3

data_processing:
Generate CCS reads (ccs) with HiFi kinetics
Predict m6A positions using HiFi kinetics (fibertools predict-m6a)
Align reads using pbmm2
Extract fiberseq data and generate bed file (fibertools ft extract)
Footprints identified using an HMM (custom scripts available at hhtps://github.com/churchmanlab)
Assembly: Hg38 (aligned to custom modifications of chrM, available at https://github.com/churchmanlab)
Supplementary files format and content: bed formatted mapped molecule locations with ZMW ID in column 4 and methylation locations in column 12
Supplementary files format and content: tsv formatted per-read footprint information with read ID in column 1. Each additional column represents a position in the genome. A positive value indicates a footprint/protection and a negative value indicates accessible DNA. The number indicates the size of the region covering that genomic position
Supplementary files format and content: pq formatted read info file to go along with tsv file. Contains information on individual footprinted reads including ZMW ID, read ID corresponding to TSV, and methylation count.

growth_protocol:
HeLa S3 cells were maintained in DMEM + 10% Fetal Bovine Serum (FBS) in humidified atmosphere with 5% CO2 at 37C
U2-OS cells were maintained in McCoy's 5A Media + 10% Fetal Bovine Serum (FBS) in humidifed atmosphere with 5% CO2 at 37C
HSMM cells were maintained in Human Skeletal Muscle Cell Basal Media with growth supplement (Cell Applications, INC)

extract_protocol:
Phenol:chloroform:isoamyl alcohol extraction followed by ethanol precipitation. Extracted DNA was treated with RNase A and XmaI. DNA from HeLa cells was linearized with BamHI, and DNA from HSMM with EagI. This was followed by a Phenol:Chloroform:Isoamyl Alcohol extraction, a chloroform:isoamyl alcohol extraction, and a second ethanol precipitation.
PacBio SMRTbell libraries were prepared from linearized DNA (102-182-700)

treatment_protocol:
HSMM differentiation was induced by switching cells at 80% confluency to DMEM containing glucose and pyruvate supplemented with 2% Heat Inactivated Horse Serume (Thermo Fisher Scientific) and 0.4 µg/mL dexamethasone
Mitochondria were isolated by cellular fractionation, permeabilized in Permeabilization Buffer (20 mM Tris, pH 7.4; 70 mM Potassium Acetate; 250 mM Sucrose; 0.25% Tween-20; 0.25% NP-40/Igepal-630). Mitochondria were treated with MTase as above in Reaction Buffer (20 mM Tris, pH 7.4; 70 mM Potassium Acetate; 250 mM Sucrose) and DNA was extracted and subjected to PacBio library construction

tag: cell line

value: Human skeletal muscle myoblasts

tag: cell treatment

value: 2% Horse Serum, 0.4 ug/mL Dexamethasone, 6 days

tag: mtase conditions

value: 500 U Hia5 for 10 min at 37C


title: HSMM_3days_mito_rep3

value: 2% Horse Serum, 0.4 ug/mL Dexamethasone, 3 days


title: Lung, SARS-CoV-2-infected IL-33 KO C57BL/6 mice, Day2, replicate 1, RNAseq

description:
2×150bp paired-endsequencing (PE150)
D2_KO_1


title: Lung, SARS-CoV-2-infected IL-33 KO C57BL/6 mice, Day2, replicate 2, RNAseq

description:
2×150bp paired-endsequencing (PE150)
D2_KO_2


title: wildtype_+N_rep2

value: wildtype

value: nitrogen starved for 24 hours


title: wildtyped_+N_rep1


title: CD4OSD01_CM

description: raw counts

value: Blood

value: CD4 T-cell


title: HSMM_0days_mito_rep3


title: CD4NAR11_Nv

description: raw counts


title: hip1_Q_rep2


title: Lung, SARS-CoV-2-infected WT C57BL/6 mice, Day2, replicate 3, RNAseq

description:
2×150bp paired-endsequencing (PE150)
D2_WT_3

value: Lung

value: 8-10 weeks


title: HeLa_mito_DMSO_control_rep4

source_name: HeLa S3

value: HeLa S3

value: Vehicle control (DMSO) 24 hours


title: HeLa_mito_2CMA_rep4

value: 100 uM 2'-C-methyladenosine 24 hours


title: Lung, SARS-CoV-2-infected WT C57BL/6 mice, Day2, replicate 1, RNAseq

description:
2×150bp paired-endsequencing (PE150)
D2_WT_1


title: Lung, SARS-CoV-2-infected WT C57BL/6 mice, Day2, replicate 2, RNAseq

description:
2×150bp paired-endsequencing (PE150)
D2_WT_2


title: HeLa_mito_2CMA_rep3


title: hip1_Q_rep1


title: CD4NAR11_Ef

description: raw counts


title: CD4NAR11_EM

description: raw counts


title: wildtype_+N_rep3


title: wildtype_Q_rep3


title: CD4OSD01_EM

description: raw counts


title: CD4NAR11_CM

description: raw counts


title: Lung, mock-infected C57BL/6 mice, Day2, replicate 3, RNAseq

description:
2×150bp paired-endsequencing (PE150)
D2_Mock_3

value: culture medium


title: wildtype_Q_rep2


title: HeLa_mito_DMSO_control_rep3


title: HeLa_mito_100uM_AMA_rep2

value: 100 uM Antimycin A 24 hours


title: hip1_Q_rep3


title: wildtype_Q_rep1


title: CD4NAR10_Nv

description: raw counts


title: Lung, mock-infected C57BL/6 mice, Day2, replicate 1, RNAseq

description:
2×150bp paired-endsequencing (PE150)
D2_Mock_1

value: Day 2


title: HeLa_mito_100nM_AMA_rep2

value: 100 nM Antimycin A 24 hours


title: HeLa_mito_EtOH_rep2

value: Vehicle control (EtOH) 24 hours


title: CD4NAR10_Ef

description: raw counts


title: CD4NAR10_EM

description: raw counts


title: Control_C9

city: Portland

first: Brett

last: Davis

state: Oregon

address: 3181 SW Sam Jackson Park Rd

institute: Oregon Health and Science University

data_processing:
Check data quality with FastQC(v0.11.8)
Trim with TrimGalore (v0.6.1) with the RRBS parameter
Trimmed reads were aligned to the human reference (GRCh38) with Bismark v0.20.0 (15) using default parameters
Methylation rates and counts were extracted with bismark_methylation_extractor
CpGs were filtered to remove CpGs with less than 5X coverage and greater than the 99.9th percentile highest coverage
Coverage files were filtered to contain only canonical chromosomes, and read into MethylKit for differential analysis
Assembly: GRCh38
Supplementary files format and content: coverage files from bismark containing canonical chromosomes

source_name: saliva

extract_protocol:
Oragene OC-175 ORAcollect for pediatric samples and Oragene DNA Purification kit (Genotek, OGR-500) for adult samples
Reduced Representation Bisulfite Sequencing libraries were generated as described in Gu et al. 2011. Bruefly, between 100-200 ng of genomic DNA was digested for 2 hours with MspI restriction enzyme (New England Biolabs) which cuts the DNA at every occurrence of the CCGG sequence, resulting in fragments starting with a CpG site. Libraries were prepared with the NEBNext Ultra II Modules (New England Biolabs) and the NEBNext Methylated Adaptor (New England Biolabs). The ligated DNA was size-selected using Ampure XP magnetic beads (Beckman Coulter) to produce a final library size of approximately 200 bp. Bisulfite conversion was performed with the EZ DNA Methylation-Gold Kit for single use (D5005, Zymo Research), followed by PCR amplification with the NEBNext Q5U polymerase and NEBNext Multiplex Oligos for Illumina (New England Biolabs) to barcode each library.

value: saliva

value: buccal epithelial cells

tag: condition

value: Control

tag: donor source

value: Child

tag: family id

tag: Sex

value: M


title: CD4NAR10_CM

description: raw counts

value: Blood


title: HeLa_mito_100uM_AMA_rep1

value: 500 U Hia5 for 10 min at 37C


title: Control_C7

value: F


title: HeLa_mito_100nM_AMA_rep1


title: Control_C6


title: CD4NAR09_Nv

description: raw counts

value: CD4 T-cell


title: HeLa_mito_EtOH_rep1

value: HeLa S3


title: DSS_DCA2

city: Tianjin

first: Chen

last: Wang

state: Tianjin

address: 154 Anshan Road,Heping District,Tianjin,China

institute: Tianjin Medical University General Hospital

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mmu10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: colonic tissue

growth_protocol: All mice were housed in the animal center under a specific pathogen-free (SPF) facility, with a strict 12 h light/ dark cycle (8:00 a.m. to 8:00 p.m.), humidity at 50 ±15%, a temperature of 22±1 °C, and access to food and water.

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

treatment_protocol: Mice were administered 2% DSS for 7 days followed by DCA enema.

value: colonic tissue

value: intestinal epithelial cells

value: WT

value: DSS and DCA


title: DSS_DCA1


title: DSS4

value: DSS


title: Lung, mock-infected C57BL/6 mice, Day2, replicate 2, RNAseq

description:
2×150bp paired-endsequencing (PE150)
D2_Mock_2

value: Lung

value: 8-10 weeks

value: culture medium

value: Day 2


title: CD4NAR09_EM

description: raw counts


title: Control_C5

value: saliva

value: buccal epithelial cells

value: Control


title: CD4NAR09_Ef

description: raw counts

value: Blood


title: DSS2


title: HeLa_TetOn_TFAM_doxycycline_rep3

value: TetOn TFAM-HA

value: 100 ng/mL doxycycline 48 hours

value: 500 U Hia5 for 10 min at 37C


title: Control_C4

value: Child

value: M


title: DSS1

value: colonic tissue

value: intestinal epithelial cells


title: CD4NAR09_CM

description: raw counts

value: CD4 T-cell


title: HeLa_TetOn_TFAM_DMSO_rep3

value: HeLa S3

value: Vehicle control (DMSO) 48 hours


title: DSS_DCA4

value: WT

value: DSS and DCA


title: microinject siRNA-Eif4a3, Day5, rep3

city: Nanjing

first: Jianhua

last: Chen

state: Jiangsu

address: 101 Longmian Road

institute: Nanjing Medical University State Key Laboratory of Reproductive Medicine

data_processing:
Sequence quality control was performed by FastQC (version 0.11.9) and fastp (version 0.20.1).
Subsequently, RNA-Seq reads were mapped to genome GRCm38/mm10 using STAR (version 2.7.6a).
The bam files resulting from STAR were quantified by featureCounts (version 2.0.1) and the quantification file was further analyzed in software R (version 4.1.1).
DESeq2 R package (version 1.34.0) was used to load count matrices and identify differentially expressed genes (DEGs) with padj<0.05 and |log2FoldChange|>2.
Multivariate Analysis of Transcript Splicing for replicates (rMATS version 4.1.0) software was performed to detect differential alternative splicing events of two consecutive adjacent stages from RNA-Seq data with parameters: rmats.py --b1 stage1_path.txt --b2 stage2_path.txt --gtf gtf –od out –nthread 1 –readLength 90 -t paired –tmp_tmp.
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: embryo

extract_protocol: The embryos were then placed in SMART lysate and sent to LC-Bio Technologies (Hangzhou) Co., Ltd for Smart-seq2 sequencing, which was conducted using the Illumina NovaseqTM 6000 150PE platform.

value: embryo

value: Eif4a3 knock down


title: CD4NAR08_Nv

description: raw counts


title: Control_C8

value: saliva

value: buccal epithelial cells


title: U2OS_mito_rep1


title: microinject siRNA-Eif4a3, Day5, rep2


title: CD4NAR08_EM

description: raw counts

value: Blood


title: U2OS_mito_rep2


title: Control_C2

value: Control

value: F


title: Control_C1


title: CD4NAR08_Ef

description: raw counts


title: HeLa_mito_500U_Hia5_120min

value: 500 U Hia5 for 120 min at 37C SAM spike-in at 60 minutes


title: microinject siRNA-Eif4a3, Day5, rep1


title: microinject siRNA-NC, Day5, rep3

value: NC


title: HeLa_mito_500U_Hia5_60min_rep2

value: 500 U Hia5 for 60 min at 37C


title: CD4NAR08_CM

description: raw counts


title: CD4NAR07_Nv

description: raw counts


title: Control_M9

value: Mother


title: microinject siRNA-NC, Day5, rep2


title: Control_M10


title: Control_M8


title: HeLa_mito_500U_Hia5_rep6

value: 500 U Hia5 for 10 min at 37C


title: Control_C3

value: Child

value: M


title: HeLa_mito_500U_Hia5_rep5

value: HeLa S3


title: Input_M

source_name: cortex

value: cortex

tag: chip antibody


title: microinject siRNA-NC, Day5, rep1


title: Control_M7


title: CD4NAR07_EM

description: raw counts

value: CD4 T-cell


title: HeLa_mito_500U_Hia5_rep4


title: CD4NAR07_Ef

description: raw counts


title: pro6

value: CDYL (Proteintech, 17763-1-AP)


title: Control_M6


title: CD4NAR07_CM

description: raw counts


title: invitro_mtDNA_30uM_TFAM_rep2

source_name: in vitro mtDNA

growth_protocol:
HeLa S3 cells were maintained in DMEM + 10% Fetal Bovine Serum (FBS) in humidified atmosphere with 5% CO2 at 37C
HSMM cells were maintained in Human Skeletal Muscle Cell Basal Media with growth supplement (Cell Applications, INC)

value: in vitro mtDNA

value: 200 U Hia5 for 10 min at 37C


title: pro2


title: CD4NAR06_Nv

description: raw counts


title: invitro_mtDNA_20uM_TFAM_rep2


title: Control_M4

value: saliva

value: buccal epithelial cells


title: CD4NAR06_EM

description: raw counts

value: Blood


title: pro1


title: Control_M3

value: Control

value: F


title: KO_rep3

value: CDYL-/-


title: KO_rep2


title: invitro_mtDNA_5uM_TFAM_rep2


title: invitro_mtDNA_10uM_TFAM_rep2


title: Control_M2


title: Control_M1


title: KO_rep1


title: CD4NAR06_CM

description: raw counts


title: invitro_mtDNA_30uM_TFAM_rep1


title: Early_PE_C10

value: Early Preelampsia


title: WT_rep3

value: CDYL+/+


title: Early_PE_C9


title: Control_M5

value: Mother


title: WT_rep2


title: CD4NAR05_Ef

description: raw counts


title: invitro_mtDNA_10uM_TFAM_rep1


title: Early_PE_C8

value: Child


title: invitro_mtDNA_5uM_TFAM_rep1


title: Early_PE_C6

value: M


title: CD4NAR06_Ef

description: raw counts


title: invitro_mtDNA_0uM_TFAM_rep1


title: CD4NAR05_Nv

description: raw counts


title: RNAD-Ellen_Schill-R_Newberry_2nd_Sample_080322_S1

city: Saint Louis

first: Ellen

middle: Merrick

last: Schill

state: MO

address: 660 S. Euclid Ave, Campus Box 8124

institute: Washington University

library_source: transcriptomic single cell

data_processing:
Data was analyzed using Partek Flow.  Clusters identified as inconsistent with macrophages were excluded and cells were reclustered. Differentially expressed genes were defined by Gene Set Analysis (GSA) with false discovery rate of less than or equal to 0.05, and fold change of greater than 2 or less than -2. Trajectory and pseudotime analysis were performed with Monocle 3
Assembly: mmu10
Supplementary files format and content: Data was analyzed in Partek Flow. Tags were trimmed, Aligned genes, quantified to the annotation model, genes counted, normalized to CPM, filtered noise.  Processed files generated from this node.

source_name: colon

extract_protocol:
Appropriate cells were identified as Live, CD45+ CD11clo/- CX3CR1+ and collected in supplemented RPMI 1640 media. RNA Barcoding, library preparation, and sequencing was performed using the 10X Chromium Controller and 10X Genomics 3’ v3.1 platform through the McDonnell Genome Institute at the Genome Technology Access Center at Washington University in Saint Louis School of Medicine. Briefly, 3v3.1 cDNA was prepared after the GEM generation and barcoding, followed by the GEM-RT reaction and bead cleanup steps. Purified cDNA was amplified for 11-13cycles before being cleaned up using SPRIselect beads. Samples were then run on a Bioanalyzer to determine the cDNA concentration
GEX libraries were prepared as recommended by the 10X Genomics Chromium Single Cell3’ Reagent Kits User Guide (v3.1 Chemistry Dual Index) with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10x Genomics platform, the Chromium Next GEM Single Cell3’Kit v3.1, 16 rxns (PN-1000268),Chromium Next GEM ChipGSingle Cell Kit, 48 rxns (PN-1000120), andDual Index Kit TT Set A, 96 rxns(PN-1000215) were used. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer’s protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument

value: colon

value: macrophage

value: CX3CR1-GFP heterozygous

value: Vancomycin


title: CD4NAR05_EM

description: raw counts

value: CD4 T-cell


title: invitro_mtDNA_0uM_TFAM_rep2

value: in vitro mtDNA

value: 200 U Hia5 for 10 min at 37C


title: CD4NAR04_Nv

description: raw counts


title: Early_PE_C5

value: saliva

value: buccal epithelial cells


title: HSMM_6days_mito_rep2

value: Human skeletal muscle myoblasts

value: 2% Horse Serum, 0.4 ug/mL  Dexamethasone, 6 days

value: 500 U Hia5 for 10 min at 37C


title: RNAD-Ellen_Schill-R_Newberry_S1

value: Control


title: invitro_mtDNA_20uM_TFAM_rep1


title: HODEs_3

first: JingJie

last: Duan

address: No22.Qixiangtai Rd.,Heping Dist,Tianjin P.R. China

institute: tianjin medical university

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mus musculus,Ensembl_v101
Supplementary files format and content: excle files include FPKM values for each Sample

source_name: liver

extract_protocol:
Total RNA was extracted usingTrizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: liver


title: Early_PE_C4

value: Early Preelampsia

value: F


title: CD4NAR04_CM

description: raw counts

value: Blood


title: HSMM_3days_mito_rep2

source_name: Human skeletal muscle myoblasts

value: 2% Horse Serum, 0.4 ug/mL  Dexamethasone, 3 days


title: Early_PE_C3

value: Child


title: HODEs_2


title: CD4NAR04_Ef

description: raw counts

source_name: Blood


title: WT_rep1

value: cortex

value: CDYL+/+


title: CD4NAR04_EM

description: raw counts

value: CD4 T-cell


title: HSMM_0days_mito_rep2


title: Early_PE_C2

value: M


title: CD4NAR03_Nv

description: raw counts


title: HSMM_6days_mito_rep1


title: ctrl_3

value: vechicle


title: HODEs_1


title: CD4NAR05_CM

description: raw counts


title: HSMM_3days_mito_rep1


title: Early_PE_M10

value: saliva

value: Mother


title: ctrl_2


title: HSMM_0days_mito_rep1

value: Human skeletal muscle myoblasts


title: ctrl_1


title: Early_PE_M9

value: buccal epithelial cells


title: CD4NAR03_CM

description: raw counts


title: Early_PE_M8


title: CD4NAR02_Nv

description: raw counts


title: NLRP3(STZ) rep3

city: Cincinnati

first: Soona

last: Shin

state: Cincinnati

address: 3333 Burnet Ave, OH

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Sequence reads were trimmed using Trim Galore! v0.4.2 and cutadapt v1.9.1.
The trimmed reads were aligned to the reference mouse genome version mm10 using STAR v2.6.1e.
Aligned reads were stripped of duplicate reads with the program sambamba v0.6.8.
Read counting was done with the program featureCounts v1.6.2 from the Rsubread package.
Raw counts were normalized as transcripts per million (TPM).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: placenta

extract_protocol:
Placenta were homogenised. CD45+ cells were sorted by flow cytometry and collected for RNA isolation.
The cDNA synthesis and amplification were done as recommended by Clontech. cDNA libraries were prepared using Nextera XT DNA Sample preparation reagents. Fragmented and tagged libraries were quantified using an agilent bio-analyzer, pooled and sequenced on a HiSeq 6000 platform (Illumina) using the pair-end 75-bp sequencing strategy.

tag: developmental stage

value: E17 embryo

tag: disease state

value: diabetic  pregnancy

value: placenta

value: CD45+ cells

value: NLRP3-deficient CD45+ cells isolated from placenta derived from diabetic  pregnancy


title: HeLa_TetOn_TFAM_DMSO_rep2

value: HeLa S3

value: TetOn TFAM-HA

value: Vehicle control (DMSO)  48 hours

value: 500 U Hia5 for 10 min at 37C


title: NLRP3(STZ) rep1

tag: tissue

tag: cell type


title: NLRP3(STZ) rep2

tag: strain

tag: genotype


title: CD4NAR02_EM

description: raw counts

value: Blood


title: HeLa_mito_doxycyline_rep2

value: 100 ng/mL doxycycline  48 hours


title: Early_PE_M4

value: Early Preelampsia

value: F


title: Early_PE_C1

value: saliva

value: Child


title: HeLa_TetOn_TFAM_doxycycline_rep1


title: CD4NAR02_Ef

description: raw counts

value: CD4 T-cell


title: CD4NAR03_EM

description: raw counts


title: CD4NAR02_CM

description: raw counts


title: HeLa_TetOn_TFAM_DMSO_rep1


title: WT(STZ) rep3

value: WT

tag: treatment

value: WT CD45+ cells isolated from placenta derived from diabetic  pregnancy


title: WT(STZ) rep2

value: E17 embryo

value: diabetic  pregnancy


title: Early_PE_M1

value: buccal epithelial cells

value: Mother


title: HeLa_mito_doxycyline_rep1

value: HeLa S3


title: Early_PE_M2


title: CD4NAR03_Ef

description: raw counts


title: HeLa_TetOn_TFAM_doxycycline_rep2

value: TetOn TFAM-HA


title: CD4NAR01_Nv

description: raw counts


title: HeLa_mito_2CMA_rep2

value: 100 uM 2'-C-methyladenosine  24 hours


title: Late_PE_C8

value: Late Preeclampsia


title: Late_PE_C9


title: Ctrl rep3

value: placenta

value: CD45+ cells

value: WT CD45+ cells isolated from placenta derived from normal pregnancy


title: Early_PE_M6

value: Early Preelampsia

value: F


title: HeLa_mito_DMSO_control_rep2

value: Vehicle control (DMSO)  24 hours

value: 500 U Hia5 for 10 min at 37C


title: CD4NAR01_EM

description: raw counts

value: Blood

value: CD4 T-cell


title: CD4NAR01_Ef

description: raw counts


title: Ctrl rep2

value: E17 embryo

value: WT


title: HeLa_mito_2CMA_rep1


title: Ctrl rep1

value: diabetic  pregnancy


title: Late_PE_C5

value: saliva

value: buccal epithelial cells

value: Child


title: HeLa_mito_DMSO_control_rep1

value: HeLa S3


title: CD4HD11_Nv

description: raw counts


title: Late_PE_C4

value: Late Preeclampsia

value: M


title: CD4NAR01_CM

description: raw counts


title: HeLa_mito_500U_Hia5_60min

value: 1000 U Hia5 for 60 min at 37C


title: WT(STZ) rep1

value: placenta

value: CD45+ cells

value: WT CD45+ cells isolated from placenta derived from diabetic  pregnancy


title: CD4HD11_Ef

description: raw counts


title: RRBS_WT(AKITA) rep1

data_processing:
reads werealigned to mm10 reference genome byBismark(v0.18.2)
CpG methylation calls were extracted from the alignment using the Bismark methylation extractor
Assembly: mm10
Supplementary files format and content: Bismark coverage file : Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count non-methylated>

source_name: WT LSK cells isolated from the BM of adult offspring born to diabetic pregnancy

extract_protocol:
LSK cells were isolated by FACS, and DNA was extracted using the QIAamp DNA Mini Kit (Qiagen) as per the manufacturer’s instructions. Genomic DNA was bisulfite-converted with the EZ DNA Methylation Kit (Zymo Research, Irvine, USA).
Libraries were sequenced on the Illumina Novaseq6000 with 100 bp paired end reads

value: adult offspring

value: Bone Marrow

value: LSK cells

value: diabebtic  pregnancy


title: Late_PE_C3

value: F


title: HeLa_mito_500U_Hia5_45min

value: 500 U Hia5 for 45 min at 37C


title: Late_PE_C2


title: HeLa_mito_500U_Hia5_30min

value: 500 U Hia5 for 30 min at 37C


title: CD4HD11_CM

description: raw counts

value: Blood

value: CD4 T-cell


title: Late_PE_C1

value: saliva

value: buccal epithelial cells

value: Child


title: RRBS_Control rep2

source_name: WT LSK cells isolated from the BM of adult offspring born to normal pregnancy

value: normal pregnancy


title: Late_PE_M7

value: Late Preeclampsia

value: Mother


title: RRBS_Control rep1


title: Late_PE_C7

value: M


title: HeLa_mito_500U_Hia5_rep3

value: HeLa S3

value: 500 U Hia5 for 10 min at 37C


title: HeLa_mito_1000U_Hia5

value: 1000 U Hia5 for 10 min at 37C


title: Late_PE_M6


title: CD4HD10_EM

description: raw counts


title: ATAC_WT(AKITA) rep4

data_processing:
Sequence reads were trimmed using Trim Galore! v0.4.2 and cutadapt v1.9.1.
The trimmed reads were aligned to the reference mouse genome version mm10 using Bowtie2 v2.3.4.1 with parameters "--very-sensitive-local -X 2000".
Aligned reads were stripped of duplicate reads with the program sambamba v0.6.8.
Aligned reads were stripped of duplicate reads using sambamba v0.6.8. Peaks were called with MACS v2.1.4 using the parameters “-g mm -p 0.01 --shift -75  --extsize 150 --nomodel -B --SPMR --keep-dup all --call-summits”.
Raw counts were normalized as transcripts per million (TPM).
Assembly: mm10
Supplementary files format and content: peak text files in standard MACS2 output format  (columns : chromosome,start,end,name,score,strand,signalValue,pValue,qValue,peak)

extract_protocol:
Isolated nuclei were prepared from 50,000 sorted LSK cells puriifed by flow cytometry.  the transposase reaction was performed for 60 min at 37°C.  mix.
The transposed DNA was purified using a Qiagen MinElute kit and amplified using 1XNEBnext PCR master. The libraries were purified with SPRI beads double size selection (0.4/1.2X) and then sequenced on the Illumina NovaSeq X Plus with PE150, aiming >120M read pairs per sample.

value: adult offspring

value: Bone Marrow

value: LSK cells

value: diabetic  pregnancy


title: CD4HD11_EM

description: raw counts


title: ATAC_WT(AKITA) rep3


title: HeLa_mito_750U_Hia5

value: 750 U Hia5 for 10 min at 37C


title: CD4HD10_Ef

description: raw counts

value: Blood


title: CD4HD10_CM

description: raw counts

value: CD4 T-cell


title: RRBS_WT(AKITA) rep2

value: diabebtic  pregnancy


title: HeLa_mito_500U_Hia5_rep2


title: Late_PE_M4

value: saliva

value: buccal epithelial cells

value: F


title: ATAC_WT(AKITA) rep2


title: Late_PE_M2

value: Late Preeclampsia


title: ATAC_WT(AKITA) rep1


title: CD4HD09_Nv

description: raw counts


title: HeLa_mito_200U_Hia5

value: 200 U Hia5 for 10 min at 37C


title: ATAC_Control rep3

value: normal pregnancy


title: CD4HD09_EM

description: raw counts


title: U373 final 2

city: Istanbul

first: Hamzah

last: Syed

address: Rumelifeneri Yolu

department: School of Medicine

country: Turkey

institute: Koç University

description:
Final collection
U373_Domain_Level.count_normalized
U373_Domain_Level.gene_summary
U373_Domain_Level.sgrna_summary
U373_Gene_Level.count_normalized
U373_Gene_Level.gene_summary
U373_Gene_Level.sgrna_summary

data_processing:
library strategy: amplicon sequencing; CRISPR screen
Initial sequencing was carried out with Illumina Hiseq2500 at Vincent J. Coates Genomic Sequencing Laboratory of University of Berkeley.
NGS results were analyzed by Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) (version 0.5.8). RRA algorithm and median normalization was used for count files and sgrna/gene summaries for both domain and gene levels.
RNA-seq: Adapter sequence trimming with trimGalore
RNA-seq: Transcriptome alignment with STAR
RNA-seq: Quantification using Salmon
RNA-seq: tximport for gene-level quantification
RNA-seq: DESeq2 for normalisation
Assembly: GENCODE GRCh38
Supplementary files format and content: EpiDoKOL screen data files are in txt format containing MAGeCK outputs for both domain and gene level as normalized counts, gene summary and sgRNA summary.
Supplementary files format and content: Raw gene-level counts matrix in .xlsx format
Supplementary files format and content: VST normalised counts matrix in .xlsx format

growth_protocol: U373 and T98G cells were cultured with DMEM supplemented with 10% Fetal Bovine Serum (FBS) and 1% Penicillin/Streptomycin(P/S).

extract_protocol:
Total RNA was isolated using MN Nucleospin RNA isolation kit according to the manufacturer's instructions. Genomic DNA was isolated from cell pellets using MN Nucleospin Tissue kit according to the manufacturer's instructions.
Library was prepared from the isolated genomic DNA with Illumina compatible primers using nested PCR. Initial PCR was carried out using 250x coverage input gDNA. Initial PCR products were used for second PCR with reverse index primers and forward stagger primers. Final amplicons were loaded on agarose gel, and isolated using MN Nucleospin Gel and PCR Cleanup kit according to the manufacturer's instructions.

treatment_protocol: For RNA sequencing, U373 cells were transducted with NT2 or ASH2L gRNA containing lentiviruses. Following transduction, cells were selected with Puromycin and cultured until 14 days after transduction. At Day14, pellets are collected. For CRISPR screens, both cell lines were transduced with EpiDoKOL virus and initial pellet was collected after transduction. Following puromycin selection, cells were separated into two sets and final pellets were collected Day 30. Initial pellets were single, final pellets were dublicates per cell line.

value: Glioblastoma cell line

value: EpiDoKOL transduction


title: HeLa_mito_500U_Hia5_rep1

value: HeLa S3

value: 500 U Hia5 for 10 min at 37C


title: CD4HD10_Nv

description: raw counts

data_processing:
STAR; version 2.6.0c
RSEM; version 1.3.0
Assembly: Homo sapiens primary genome sequence, Gencode: GRCh38, v27
Supplementary files format and content: Tab-delimited text file containing raw counts for each sample

extract_protocol:
Cryopreserved PBMCs were thawed and washed in RPMI medium supplemented with 1% L-glutamine (100x), 1% sodium pyruvate (100mM), 1% non essential amino acids (100x), 1% penicillin-streptomycine (10,000 U/ml), 1% HEPES (1M) and 5% filtered and inactivated human AB-serum. Cells were then resuspended in PBS at 10 million/mL. Cell sorting was performed using a BD FACSAria Fusion with an antibody panel against CD3 (BD Horizon), CD4 (BD BioSciences), CD8α (BD Pharmingen), CCR7 (BD Horizon) and CD45RA (BD BioSciences) as well as eBioscience Fixable Viability Dye AF488. The T-cell subset sorting scheme used CCR7 and CD45RA cell surface markers to identify the four T-cell subsets. Post sorting, the cell number and viability were analyzed with the FlowJo software.
Library preparation (SMART-seq v4, Takara Bio) and RNA-sequencing (Illumina NovaSeq) were performed by the Genomics Facility Basel in Switzerland.


title: ATAC_Control rep2

value: adult offspring

value: Bone Marrow


title: HeLa_mito_0U_Hia5

value: 0 U Hia5 for 10 min at 37C


title: U373 final 1


title: ATAC_Control rep1

value: LSK cells


title: T98G final 2

description:
Final collection
T98_Domain_Level.count_normalized
T98_Domain_Level.gene_summary
T98_Domain_Level.sgrna_summary
T98_Gene_Level.count_normalized
T98_Gene_Level.gene_summary
T98_Gene_Level.sgrna_summary


title: MM13_WT_Mock_Rep2

city: Ann Arbor

first: Teresa

last: O'Meara

state: MI

address: 1150 W. Medical Center Dr

institute: University of Michigan

data_processing:
Galaxy suite - FastQC, CutAdapt, KallistoQuant, DEseq2
Assembly: GRCm38B
Supplementary files format and content: tabular counts (Kallisto format)

source_name: J2 iBMDM

extract_protocol:
trizol, DNAse treatment with TurboDNAse, phenol chloroform
poly A enrichment

value: J2 iBMDM

value: macrophage

value: mock


title: 44-RED-e

city: Marseille

first: Karel

last: Naiman

address: BD Lei Roure

institute: CRCM

data_processing:
The reads were mapped using bowtie2
Polymerase usage was determined by the tools published and described in detail in Daigaku et al., 2015 and Keszthelyi et al. 2015.
Assembly: Schizosaccharomyces pombe reference sequence (http://www.pombase.org/downloads/genome-datasets) with inserted replication fork barrier RTS1, 10xrDNA barrier
Supplementary files format and content: CSV files contain read counts corresponding to incorporated rNTPs sorted into 300bp bins on each chromosome. They are in two files for forward and reverse strands separately.

source_name: cdc20-M630F Nat:ADH1:rtf1 rnh201-RED:Kan Rura-ChrII RTS1::phleo ura4-D18 ade6-704 leu1-32

growth_protocol: Cells were grown at 30C in YE media to log phase. For ‘wt’ datasets two strains were used, both strains containing  rnh201-RED mutant deficient in rNTP recognition together with either polymerase δ (cdc6-L591G) or polymerase ε (cdc20-M630F) mutations. These strains incorporate more rNTPs on the strands synthetized by the mutant polymerase. These sites can be mapped by Pu-seq.

extract_protocol:
DNA was prepared using the QIAGEN 100/G Genomic-tip. The isolated DNA was then subjected to RnaseH2 treatment that digested the DNA at the positions of rNTP incorporation and the double strands were separeated by heating. The resulting ssDNA fragments were size selected on agarose gel (fragments between 300-500bp were isolated).
Polymerase usage sequence (Pu-seq) technique was performed as previously described (Daigaku et al., 2015 and Keszthelyi et al. 2015) with minor modifications: size selection was performed using Blue Pippin (Sage Science). We used rnh201-RED instead of rnh201::kan (see results).


title: 44-KK1582-rpn10-e

source_name: rpn10Δ cdc20-M630F NAT:ADH1:rtf1 rnh201-RED:KAN Rura-ChrII RTS1::phleo ura4-D18 ade6-704 leu1-32

value: rpn10{delta} cdc20-M630F NAT:ADH1:rtf1 rnh201-RED:KAN Rura-ChrII RTS1::phleo ura4-D18 ade6-704 leu1-32


title: CD4HD08_EM

description: raw counts

value: Blood

value: CD4 T-cell


title: CD4HD08_Nv

description: raw counts


title: MM1_WT_Mock_Rep1


title: 43-RED-e

source_name: cdc20-M630F rtf1::Nat rnh201-RED:Kan Rura-ChrII RTS1::phleo ura4-D18 ade6-704 leu1-32


title: CD4HD08_Ef

description: raw counts


title: MM27_WT_Candida_Rep3

value: Candida


title: MM25_WT_CANDIDA_Rep4


title: 41-RED-e

value: cdc20-M630F rtf1::Nat rnh201-RED:Kan Rura-ChrII RTS1::phleo ura4-D18 ade6-704 leu1-32


title: i6_U_ASH_3

description:
raw_TPM_counts.xlsx
VST_normalised_counts.xlsx

data_processing:
Initial sequencing was carried out with Illumina Hiseq2500 at Vincent J. Coates Genomic Sequencing Laboratory of University of Berkeley.
NGS results were analyzed by Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) (version 0.5.8). RRA algorithm and median normalization was used for count files and sgrna/gene summaries for both domain and gene levels.
RNA-seq: Adapter sequence trimming with trimGalore
RNA-seq: Transcriptome alignment with STAR
RNA-seq: Quantification using Salmon
RNA-seq: tximport for gene-level quantification
RNA-seq: DESeq2 for normalisation
Assembly: GENCODE GRCh38
Supplementary files format and content: EpiDoKOL screen data files are in txt format containing MAGeCK outputs for both domain and gene level as normalized counts, gene summary and sgRNA summary.
Supplementary files format and content: Raw gene-level counts matrix in .xlsx format
Supplementary files format and content: VST normalised counts matrix in .xlsx format

value: ASH2L Knockout

value: transduced with guide RNA


title: T98G final 1

value: Glioblastoma cell line

value: EpiDoKOL transduction


title: T98G initial 1

description:
Initial collection
T98_Domain_Level.count_normalized
T98_Domain_Level.gene_summary
T98_Domain_Level.sgrna_summary
T98_Gene_Level.count_normalized
T98_Gene_Level.gene_summary
T98_Gene_Level.sgrna_summary


title: CD4HD08_CM

description: raw counts


title: i5_U_ASH_2


title: 43-KK1581-rpn10-d

source_name: rpn10Δ cdc6-L591G NAT:ADH1:rtf1 rnh201-RED:KAN Rura-ChrII RTS1::phleo ura4-D18 ade6-704 leu1-32

value: rpn10{delta} cdc6-L591G NAT:ADH1:rtf1 rnh201-RED:KAN Rura-ChrII RTS1::phleo ura4-D18 ade6-704 leu1-32


title: 41-KK1523-nup132-e

source_name: nup132Δ cdc20-M630F NAT:ADH1:rtf1 rnh201-RED:KAN Rura-ChrII RTS1::phleo ura4-D18 ade6-704 leu1-32

value: nup132{delta} cdc20-M630F NAT:ADH1:rtf1 rnh201-RED:KAN Rura-ChrII RTS1::phleo ura4-D18 ade6-704 leu1-32


title: CD4HD07_Nv

description: raw counts


title: i4_U_ASH_1


title: 40-RED-d

source_name: cdc6-L591G Nat:ADH1:rtf1 rnh201-RED:Kan Rura-ChrII RTS1::phleo ura4-D18 ade6-704 leu1-32


title: MM3_WT_Candida_Rep1


title: CD4HD07_EM

description: raw counts


title: i3_U_NT2_3

value: Control


title: MM15_WT_Candida_Rep2


title: CD4HD09_CM

description: raw counts


title: U373 initial 1

description:
Initial collection
U373_Domain_Level.count_normalized
U373_Domain_Level.gene_summary
U373_Domain_Level.sgrna_summary
U373_Gene_Level.count_normalized
U373_Gene_Level.gene_summary
U373_Gene_Level.sgrna_summary


title: MM14_KO_Mock_Rep2

value: c57bl6 ire1 null


title: CD4HD09_Ef

description: raw counts


title: i2_U_NT2_2


title: CD4HD07_Ef

description: raw counts


title: MM2_KO_Mock_Rep1


title: CD4HD07_CM

description: raw counts


title: i1_U_NT2_1


title: MM28_KO_Candida_Rep3


title: 38-RED-d

source_name: cdc6-L591G rtf1::Nat rnh201-RED:Kan Rura-ChrII RTS1::phleo ura4-D18 ade6-704 leu1-32


title: CD4HD06_Nv

description: raw counts


title: CD4HD06_EM

description: raw counts


title: 28-KK1524-e


title: 37-RED-d

value: cdc6-L591G rtf1::Nat rnh201-RED:Kan Rura-ChrII RTS1::phleo ura4-D18 ade6-704 leu1-32


title: MM26_KO_CANDIDA_Rep4

value: J2 iBMDM


title: CD4HD06_Ef

description: raw counts


title: MM16_KO_Candida_Rep2

value: macrophage


title: AD_control_s157_Cmpd-60-157

city: Amsterdam

first: Man

middle: Iman

last: Hu

address: Meibergdreef 9

department: Laboratory Genetic Metabolic Diseases

institute: Amsterdam UMC Location University of Amsterdam

data_processing:
Reads were subjected to quality control FastQC trimmed using Trimmomatic v0.32 and aligned using HISAT2 v2.1.0. Counts were obtained using HTSeq (v0.11.0, default parameters) using the corresponding GTF taking into account the directions of the reads.
Supplementary files format and content: table delimited row counts

source_name: AD-control mouse treated with cmpd-60

growth_protocol: Natural aged, approx. 20 months old, male BL6 mice were acquired from Taconic and single housed under a 12:12-hour light-dark cycle in a room set to 23°C (+/- 0.2°C).

extract_protocol:
Mouse tissues were homogenized with a 5 mm steel bead using a TissueLyser II (QIAGEN) for 5 min at frequency of 30 times/second. RNA was extracted according to the instructions of the RNaesy Mini Kit (QIAGEN). Contaminating genomic DNA was removed using RNase-Free DNase (QIAGEN). RNA was quantified with a NanoDrop 2000 spectrophotometer (Thermo Scientific; Breda, The Netherlands) and stored at -80°C until use.
RNA libraries were prepared and sequenced with the Illumina platform by Genome Scan (Leiden, The Netherlands). The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used to process the sample(s).
The sample preparation was performed according to the protocol "NEBNext Ultra II Directional RNA Library Prep Kit for Illumina" (NEB #E7760S/L). Briefly, mRNA was isolated from total RNA using the oligo-dT magnetic beads. After fragmentation of the mRNA, cDNA synthesis was performed. This was used for ligation with the sequencing adapters and PCR amplification of the resulting product. The quality and yield after sample preparation was measured with the Fragment Analyzer.

treatment_protocol: All animals were fed a regular chow diet. Mice received daily i.p. injections with either Cmpd60 (n=6) or vehicle (n=7) for 14 days total.

value: brain

value: male

tag: strain background


title: AD_control_s158_Cmpd-60-158


title: CD4HD05_Nv

last: Khajavi

address: TOULOUSE

institute: INSERM

description: raw counts

value: Blood


title: CD4HD06_CM

description: raw counts

value: CD4 T-cell


title: MM4_KO_Candida_Rep1

value: Candida


title: AD_control_s155_vehicle-155

source_name: AD-control mouse treated with vehicle

value: vehicle


title: 27-KK1520-e

source_name: nup132Δ cdc20-M630F rtf1::NAT rnh201-RED:KAN Rura-ChrII RTS1::phleo ura4-D18 ade6-704 leu1-32

value: nup132{delta} cdc20-M630F rtf1::NAT rnh201-RED:KAN Rura-ChrII RTS1::phleo ura4-D18 ade6-704 leu1-32


title: AD_control_s156_Cmpd-60-156


title: AD_control_s154_vehicle-154


title: 26-KK1518-d

source_name: nup132Δ cdc6-L591G NAT:ADH1:rtf1 rnh201-RED:KAN Rura-ChrII RTS1::phleo ura4-D18 ade6-704 leu1-32

value: nup132{delta} cdc6-L591G NAT:ADH1:rtf1 rnh201-RED:KAN Rura-ChrII RTS1::phleo ura4-D18 ade6-704 leu1-32