title: 4 weeks after transplantation kidney of GalT-/-;hCD39;hCD55 pig

status: Public on Dec 31 2023

type: SRA

city: Jeongeup-si

first: Hanna

last: Suh

address: 30, Baekhak 1-gil, Jeongeup-si, Jeollabuk-do, Republic of Korea

country: South Korea

institute: Korea institute of toxicology

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to Sus Scrofa (NCBI) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: Sscrofa11.1
Supplementary files format and content: tab-delimited text files include read count values for each Sample

molecule: total RNA

organism: Sus scrofa

source_name: Kidney

extract_protocol:
2 μg total RNA was extracted from pig normal kidney (untransplanted) and transplanted kidney using the Phenol/Chloroform extraction method.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

tag: tissue

value: Kidney

tag: genotype

tag: treatment

value: Transplantation


title: 6 weeks after transplantation kideny of GalT-/-;hCD39;hCD46;hCD55;TBM pig


title: Untransplanted kidney of GalT-/-;hCD39;hCD55 pig

value: Untransplanted


title: Untransplanted GalT-/-;hCD39;hCD46;hCD55;TBM pig


title: mycelia, wt_RPF

city: Kunming

first: Yunkun

last: Dang

state: Yunnan

address: South Section, East Outer Ring Road, Chenggong District

department: School of Life Sciences

country: China

institute: Yunnan university

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim_galore(Parameter: default. Version: 0.6.6)
Trimmed sequence reads were mapped to the rRNA sequences and tRNA sequences were removed with bowtie. Then the rRNA depleted reads were mapped to the N. crassa reference sequences (coding sequences with upstream 100 bp and downstream 100 bp) using  bowtie with m mode (m =1) to ensure that retained reads have exactly one target in the  reference sequences. (Version:1.3.0)
To visualize the RPF distribution, we only selected RPF reads with 28-32nt long to generate the histogram graphs with SAMtools(1.6).Only reads mapped to plus  strand were calculated in order to eliminate the possible disturbance from antisense RNA.
The ribosomal A sites where codon selection occurs were considered as nucleotide positions 16-18 and the 5' most nucleotide of each sequenced reads as position 1 .The trimmed alignment files were processed with bedtools(v2.30.0) to generate bedgraph files containing the footprints of codons at ribosomal A site, meanwhile the inframe proportion of specific lenth of reads must more than 75%, so the reads could be used for bedgaph file.
To determine the frame distribution for each gene, the footprints of codons at ribosomal A site were categorized as inframe, minus frame and plus frame
Assembly: NC12
Supplementary files format and content: tab-delimited bedgraph file includes  footprints of codons at ribosomal A site
Supplementary files format and content: tab-delimited tab file includes frame distribution for each gene

organism: Neurospora crassa

source_name: mycelia

growth_protocol: Fresh conidia were germinated in 200 mL growth medium (Vogel's minimal medium + 2% glucose) at room temperate with orbital shaking (200 rpm) under constant light for 12 hr.

extract_protocol:
The extraction for mRNA RPFs were based on the ARTseq yeast ribosome profiling kit (Illumina), according to the accompanying protocol.
The library constructions for mRNA RPFs were based on the ARTseq yeast ribosome profiling kit (Illumina), according to the accompanying protocol.

value: mycelia

value: WT


title: Shoot 0.2 mM Nitrogen (severe limitation), Replicate 2

city: Invergowrie / Dundee

first: Raul

last: Huertas

state: Perth and Kinross

address: Errol Road

department: Environmental and Biochemical Sciences

country: United Kingdom

institute: The James Hutton Institute

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence and mapped using to reference genome (v4.1) using HISAT2 2.0.5 and Stringtie 1.2.4 using default parameters.
Read count extraction and normalization were performed using Cuffdiff software.
Assembly: Panicum virgatum v4.1
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Panicum virgatum

source_name: Shoot

growth_protocol: Germinated seedling were growth in cones (6.9 cm in diameter X 25.4 cm in depth) filled with 40% all-purpose sand, 40% Q-ROK silica sand and 20% fine (2-4 mm particle size) perlite.

extract_protocol:
Total RNA was extracted using a cetyltrimethylammonium bromide (CTAB) and LiCl method (Chang, Puryear, & Cairney, 1993). RNA was treated with DNase I to remove genomic DNA.
RNA libraries were prepared using Illumina TruSeq RNA library preparation kit following manufacturer's protocols

treatment_protocol: Plants were watered daily to field capacity during a 4-week growth period with a modified nutrient solutions

value: Shoot

value: WT cv. Alamo

value: N limitation (severe)


title: Shoot 0.2 mM Nitrogen (severe limitation), Replicate 3


title: RNA_dcl1-7_rep1

city: Shanghai

first: Xiang

last: Yu

state: Shanghai

address: 800 DongChuan

institute: Shanghai Jiao Tong University

description: Illumina Hi-Seq2000 50 nt strand-specific

data_processing:
3' adapter sequences were trimmed using cutadapt (version 1.4.2 with parameters -e 0.06 -O 6 -m 14)
Trimmed reads were aligned to the cDNA seqeunce of Arabidopsis genome (TAIR10) using STAR  (version 2.4.0 with parameters “--outFilterMultimapNmax 10 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.10”)
Reads mapped to cDNA sequence of each gene were counted and then normalized to RPKM (Reads Per Kilobase per Million mapped reads) using custom script
Genome_build: TAIR10
Supplementary_files_format_and_content: The .txt files report RPKMs.

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: immature inflorescence

growth_protocol: Arabidopsis plants were grown under 16hr light 8hr dark days, and buds were harvested at approximately 4 weeks of age.

extract_protocol:
Bud tissue was ground with a mortar and pestle. RNA was extracted with Qiazol (Qiagen; Valencia, CA) and then further purified with the Qiagen miRNeasy RNA isolation kit following the included protocol (Qiagen; Valencia, CA).
TruSeq small RNA sequencing kit [illumina, Valencia, CA]), as previously described (Willmann et al. 2014; Li et al. 2012).

treatment_protocol: Plants were not otherwise treated

tag: genotype/variation

value: immature inflorescence

tag: replicate


title: RNA_dcl1-7_rep2


title: GMUCT_dcl1-7

data_processing:
library strategy: GMUCT-seq
3' adapter sequences were trimmed using cutadapt (version 1.4.2 with parameters -e 0.06 -O 6 -m 14)
Trimmed reads were aligned to the cDNA seqeunce of Arabidopsis genome (TAIR10) using STAR  (version 2.4.0 with parameters “--outFilterMultimapNmax 10 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.10”)
Reads mapped to cDNA sequence of each gene were counted and then normalized to RPKM (Reads Per Kilobase per Million mapped reads) using custom script
Genome_build: TAIR10
Supplementary_files_format_and_content: The .txt files report RPKMs.

tag: method

value: GMUCT


title: Shoot 0.6 mM Nitrogen (moderate limitation), Replicate 3

value: N limitation (moderate)


title: Shoot 0.6 mM Nitrogen (moderate limitation), Replicate 1


title: Shoot 2.0 mM Nitrogen (mild limitation), Replicate 3

value: N limitation (mild)


title: Shoot 0.6 mM Nitrogen (moderate limitation), Replicate 2


title: Shoot 2.0 mM Nitrogen (mild limitation), Replicate 2


title: Shoot 2.0 mM Nitrogen (mild limitation), Replicate 1


title: Root 0.6 mM Nitrogen (moderate limitation), Replicate 3

source_name: Root

value: Root


title: Root 0.6 mM Nitrogen (moderate limitation), Replicate 2


title: Root 0.2 mM Nitrogen (severe limitation), Replicate 3


title: Root 0.2 mM Nitrogen (severe limitation), Replicate 2


title: Root 2.0 mM Nitrogen (mild limitation), Replicate 3


title: Root 0.2 mM Nitrogen (severe limitation), Replicate 1


title: Root 2.0 mM Nitrogen (mild limitation), Replicate 2


title: Root 0.6 mM Nitrogen (moderate limitation), Replicate 1


title: Shoot 0.2 mM Nitrogen (severe limitation), Replicate 1


title: hbs1_GMUCT_rep3

city: Philadelphia

first: Rong

last: Guo

state: PA

address: 433 S University Ave

department: Department of Biology

country: USA

institute: University of Pennsylvania

data_processing:
For all the sequencing data, adaptors were trimmed using Cutadapt with default parameters (Martin, 2011). The trimmed reads were mapped to the mature mRNA sequences (primary isoforms according to available annotations) using STAR tool with the parameters “--outFilterMultimapNmax 1 --outFilterMismatchNmax 1 --outFilterMismatchNoverLmax 0.10” (Dobin et al., 2013). For GMUCT data, the SAM files were further converted to BED files containing only the 5’ most nucleotide of each read, denoting the 5’ P intermediates. The 5’ P read ends overlapping with the 100 nt regions flanking stop codons were calculated using BEDTools (Quinlan and Hall, 2010). All reads were normalized to reads per million (RPM). For mRNA-seq and polysome-seq data, reads mapped to CDSs of mature mRNA sequences were counted by HT-Seq counts (Anders et al., 2015). The significantly down-regulated mRNAs were identified using DESeq2 (Love et al., 2014). The mRNAs with log2 fold changes smaller than -0.58 and adjusted p-values lower than 0.05 were considered significantly down-regulated.
Assembly: TAIR10
Supplementary files format and content: TSI and CRI Value; TXT file
Library strategy: GMUCT

source_name: 12-day-old seedlings

growth_protocol: Plants were grown on 1/2X Murashige and Skoog plates with 1% agar at 22°C under ~150 umol/m2/s-1 white light under a long-day photoperiod.

extract_protocol:
Total RNA for both GMUCT and mRNA-Seq was extracted using QIAzol reagent according to the manufacturer’s instructions.
Total RNA was first subjected to two rounds of polyA+ selection as described previously (Willmann et al., 2014). The polyA+ mRNA was then separated into two portions for GMUCT libraries and mRNA-seq libraries. The GMUCT libraries were constructed as described previously (Willmann et al., 2014). Briefly, the polyA+ RNA was directly ligated with a 5’ RNA adapter to capture the 5’ monophosphate-bearing degradation intermediates. The products were then subjected to another round of polyA+ selection in order to remove the unligated 5’ adapter sequences. Next, the 5’ adapter ligated mRNA fragments were reverse transcribed with random hexamers with a 3’ Illumina sequencing adapter on its 5’ end. After that, the library indexes were added while the libraries are amplified by limited rounds of PCR. Finally, the products were purified using 6% TBE polyacrylamide gels in order to remove any adapter-adapter clones. The mRNA-seq libraries were constructed as previously described (Li et al., 2012). Briefly, the polyA+ mRNA was first fragmented, purified by 15% TBE-Urea polyacrylamide gel, then subjected to 5’ phosphorylation before adaptors were ligated. These products were gel purified again to remove the adaptor-adaptor clones and then PCR amplified. The PCR product was further purified using a 6% TBE polyacrylamide gel.

value: 12-day-old seedlings


title: hbs1_GMUCT_rep2


title: hbs1_GMUCT_rep1


title: WT_GMUCT_rep3


title: Root 2.0 mM Nitrogen (mild limitation), Replicate 1


title: pel1_GMUCT_rep1


title: hbs1_mRNA-Seq_rep1

data_processing:
For all the sequencing data, adaptors were trimmed using Cutadapt with default parameters (Martin, 2011). The trimmed reads were mapped to the mature mRNA sequences (primary isoforms according to available annotations) using STAR tool with the parameters “--outFilterMultimapNmax 1 --outFilterMismatchNmax 1 --outFilterMismatchNoverLmax 0.10” (Dobin et al., 2013). For GMUCT data, the SAM files were further converted to BED files containing only the 5’ most nucleotide of each read, denoting the 5’ P intermediates. The 5’ P read ends overlapping with the 100 nt regions flanking stop codons were calculated using BEDTools (Quinlan and Hall, 2010). All reads were normalized to reads per million (RPM). For mRNA-seq and polysome-seq data, reads mapped to CDSs of mature mRNA sequences were counted by HT-Seq counts (Anders et al., 2015). The significantly down-regulated mRNAs were identified using DESeq2 (Love et al., 2014). The mRNAs with log2 fold changes smaller than -0.58 and adjusted p-values lower than 0.05 were considered significantly down-regulated.
Assembly: TAIR10
Supplementary files format and content: Count from HT-Seq; TXT file


title: WT_mRNA-Seq_rep1


title: hbs1_mRNA-Seq_rep2


title: WT_GMUCT_rep1


title: WT_mRNA-Seq_rep2


title: fer4_RALF1_3

city: Changsha

first: Fan

last: Xu

state: Hunan

address: N.O. 52 Tianma street

institute: Hunan University

description: Replicate 3 of fer-4 treated with RALF1_roots

library_source: transcriptomic single cell

data_processing:
The Cell Ranger software pipeline (version 3.1.0) provided by 10× Genomics was utilized to demultiplex cellular barcodes, map reads to the Arabidopsis genome BSgenome object (‘‘BSgenome. Athaliana. TAIR. TAIR9’’) with TAIR10 gene annotation file using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts for each cell. We processed the unique molecular identifier (UMI) count matrix using the R package Seurat version 3.1.1. To remove low-quality cells and likely multiple captures, which is a major concern in microdroplet-based experiments, we removed any cell whose UMI/gene number fell within mean ± two of standard deviations, assuming a Gaussian distribution of UMI/gene numbers for each cell. Following visual inspection of the distribution of mitochondrial genes expressed in each cell, we further discarded low-quality cells where >10 % of the counts belonged to mitochondrial genes. After applying these quality control criteria, approximately 13,000 single cells were retained for downstream analyses. Library size normalization was performed with the NormalizeData function in Seurat to obtain normalized counts. Specifically, the global-scaling normalization method “LogNormalize” normalized the gene expression measurements for each cell by the total expression levels, multiplied by a scaling factor (10,000 by default), and the results were Log transformed.
Assembly: TAIR10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: Arabidopsis thaliana root

extract_protocol:
Seeds for the Arabidopsis accession Columbia-0 (Col-0) and the fer-4 mutant were surface sterilized with 15% (v/v) NaClO, sown on agar plates containing solidified half-strength MS medium (pH 5.8, 0.8% [w/v] sucrose, 1% phytoagar), and grown vertically at 22°C in long-day conditions (16 h light/8 h dark). The roots of 7-day-old seedlings were treated with liquid half-strength MS medium (pH 5.8, 0.8% [w/v] sucrose) containing 2 μM synthesized RALF1 peptide for 2 h. To expose the roots to treatment and to avoid light, a piece of filter paper (1.5 cm × 8 cm) was soaked in liquid medium containing RALF1 and placed on top of the roots. Approximately 3,000 treated roots were excised approximately 1.5 cm from their tip, broadly sliced with a scalpel, and then passed through a 70-μm cell strainer above one in a 35-mm well of a six-well plate containing 8% [w/v] mannitol. After rinsing out the debris of solidified medium, the root fragments were treated with 10 mL protoplasting solution optimized for scRNA-seq from a protocol based on (57). Immediately before use, the enzyme solution was prepared (1.25% [w/v] cellulase [ONOZUKA R-10, Yakult] 0.1% [w/v] pectolyase [P-3026, Sigma-Aldrich], 8% [w/v] mannitol, 20 mM MES [pH 5.7], 20 mM KCl, 10 mM CaCl2, 0.1% [w/v] bovine serum albumin). The enzyme solution was activated by heating at 55°C for 10 min. The plate was shaken at 90 rpm for 1 h at 25°C, and then the cell solution was centrifuged at 300 g for 10 min 25°C and the pellet was resuspended in 500 μL washing solution (8% [w/v] Mannitol, 20 mM MES [pH 5.7], 20 mM KCl, 10 mM CaCl2, 0.1% [w/v] bovine serum albumin). The cell suspension was centrifuged again at 100g for 6 min at 25°C, the entire procedure was repeated twice. All resuspended protoplasts were filtered through a 40-μm cell strainer. The supernatant was discarded and the cells collected by the cell strainer were resuspended with 100 μL of 8% (w/v) mannitol. Eighteen μL of resuspended protoplasts was mixed with 2 μL of 0.4% (w/v) trypan blue. The stained protoplasts were observed under a microscope, and four photographs were taken for each sample. The living and stained protoplasts and debris were counted and calculate the protoplast density, cell activity, and debris rate. The cell number was adjusted to ~1,000 cell/μL as recommended by the Chromium 10× Genomics manual. The protoplast suspension was loaded into a Chromium microfluidic chip with 30 v2 chemistry and barcoded with a 103 Chromium Controller (10× Genomics).
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: Whole root

value: treated with RALF1 roots


title: fer4_Mock_3

description: Replicate 3 of fer-4 Mock_roots

value: Mock


title: fer4_Mock_1

description: Replicate 1 of fer-4 Mock_roots


title: col_RALF1_3

description: Replicate 3 of Col-0 treated with RALF1_roots


title: col_RALF1_2

description: Replicate 2 of Col-0 treated with RALF1_roots


title: At, GNLox, SUC_3

city: Freising

first: Jan

last: Sala

address: Emil-Ramann-Str. 8

department: Plant Systems Biology

country: Germany

institute: Technical University of Munich

data_processing:
CLC Genomics Workbench.
Sequence reads were trimmed using CLC Genomics Workbench - Quality limit: 0.05.
Trimmed sequence reads were mapped to the TAIR10 release of Arabidopsis thaliana Col-0 genome using CLC Genomics Workbench - Mismath cost: 2, Insertion cost: 3, Deletion cost: 3, Length fraction: 0.5, Similarity fraction: 0.8.
Read count extraction and normalization were performed using CLC Genomics Workbench.
Assembly: TAIR10 release of Arabidopsis thaliana Col-0.
Supplementary files format and content: Tab-delimited text files, including TPM.

source_name: 3 days-old seedling

growth_protocol: Col-0, gnc gnl and GNLox seedlings were grown at 21ºC in dark on half-strength Murashige and Skoog medium for three days. All genotypes are in Arabidopsis thaliana ecotype Columbia (Col-0).

extract_protocol: Total RNA was extracted using a NucleoSpin RNA kit (Macherey-Nagel).

treatment_protocol: Half-strength Murashige and Skoog medium was supplemented, when decsribed, with 1% sucrose.

value: 3 days-old seedling

value: GNLox

value: 1/2 MS supplemented with 1% sucrose


title: pel1_GMUCT_rep3


title: pel1_GMUCT_rep2


title: At, GNLox, SUC_2


title: col_Mock_1

description: Replicate 1 of Col-0 Mock_roots


title: col_Mock_2

description: Replicate 2 of Col-0 Mock_roots


title: WT_GMUCT_rep2


title: At, GNLox, MS_2


title: fer4_RALF1_2

description: Replicate 2 of fer-4 treated with RALF1_roots


title: At, GNLox, SUC_1


title: fer4_RALF1_1

description: Replicate 1 of fer-4 treated with RALF1_roots


title: pel1_mRNA-Seq_rep1


title: pel1_mRNA-Seq_rep2


title: At, gnc gnl, SUC_3

value: gnc gnl


title: At, gnc gnl, MS_2


title: fer4_Mock_2

description: Replicate 2 of fer-4 Mock_roots


title: At, Col-0, SUC_3


title: At, GNLox, MS_1


title: At, gnc gnl, MS_1


title: col_RALF1_1

description: Replicate 1 of Col-0 treated with RALF1_roots


title: At, Col-0, SUC_1


title: At, Col-0, MS_3


title: col_Mock_3

description: Replicate 3 of Col-0 Mock_roots


title: At, Col-0, MS_2


title: At, GNLox, MS_3


title: At, Col-0, MS_1


title: At, gnc gnl, SUC_1


title: At, gnc gnl, SUC_2


title: At, gnc gnl, MS_3


title: At, Col-0, SUC_2


title: KYDS_5

city: Zhengzhou

first: Ming-Liang

last: Zhang

state: Henan Province

address: No. 19, Renmin Road

institute: The First Affiliated Hospital of Henan U

description:
Paired-end was used for sequencing, and only R1 files were used for analysis
M_yang5

data_processing:
CLC Genomics Workbench v 11.0
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmednce reads were mapped to Grcm38/mm10 using CLC genomic benchwork(parameters-mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Rattus norvegicus

source_name: Liver

extract_protocol:
Total RNA was extracted from liver tissues using Trizol reagent (Invitrogen, USA) according to the manufacturer’s protocol, and genomic DNA was removed using DNase I (TaKara). RNA quality was assessed with a Bioanalyzer 2100 (Agilent) and measured with a NanoDrop 2000 spectrophotometer. Only a high-quality RNA sample (OD260/280 = 1.8 ~ 2.2, OD260/230 ≥ 2.0, RNA integrity number (RIN) ≥ 6.5, 28 S:18 S ≥ 1.0, > 1 µg) was used to construct the sequencing library.
RNA-seq transcriptome libraries were prepared using a TruSeqTMRNA sample preparation kit from Illumina (San Diego, CA) and sequenced with the Illumina HiSeq xten/NovaSeq 6000 sequencer under standard protocols. All samples had a Q30 (bases of Q ≥ 30 /all bases of sequencing) of > 91%.

treatment_protocol: The rats were randomly divided into four separate groups (N=5), which were administered with 0.5% sodium carboxymethylcellulose (CMC-Na) (CON group); BGZ_L powder, 0.9 g/kg (BGZ_L group, BGZ_L); hydrocortisone, 25 mg/kg (KYDS group); BGZ_L powder (0.9 g/kg) and hydrocortisone (25 mg/kg) (KYDS+BGZ_L group).

value: Liver

tag: gender

value: Male

tag: disease state

value: kidney‑yang deficiency syndrome

value: hydrocortisone


title: KYDS+BGZ_L_5

description:
Paired-end was used for sequencing, and only R1 files were used for analysis
MBL_yan5


title: KYDS+BGZ_L_3

description:
Paired-end was used for sequencing, and only R1 files were used for analysis
MBL_yan3


title: KYDS+BGZ_L_1

description:
Paired-end was used for sequencing, and only R1 files were used for analysis
MBL_yan1


title: KYDS+BGZ_L_2

description:
Paired-end was used for sequencing, and only R1 files were used for analysis
MBL_yan2


title: KYDS_4

description:
Paired-end was used for sequencing, and only R1 files were used for analysis
M_yang4


title: KYDS_1

description:
Paired-end was used for sequencing, and only R1 files were used for analysis
M_yang1


title: KYDS_2

description:
Paired-end was used for sequencing, and only R1 files were used for analysis
M_yang2


title: BGZ_L_5

description:
Paired-end was used for sequencing, and only R1 files were used for analysis
BL_5

value: healthy


title: KYDS+BGZ_L_4

description:
Paired-end was used for sequencing, and only R1 files were used for analysis
MBL_yan4


title: BGZ_L_4

description:
Paired-end was used for sequencing, and only R1 files were used for analysis
BL_4


title: BGZ_L_3

description:
Paired-end was used for sequencing, and only R1 files were used for analysis
BL_3


title: Thymus_wk3_control littermate_rep_6

type: RNA

city: Frederick

first: Heekyong

middle: R

last: Bae

state: MD

address: Building 560, Room 31-23, NCI at Frederick

institute: National Cancer Institute

description: Gene expression in thymus from ARE-Del control littermate at 3 weeks of age

hyb_protocol: Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in Agilent fragmentation buffer and Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom Agilent array called Agilent-026855, with 39488 unique reporters, each represented in replicate (about 4 times). In total there are 180880 reporters (including controls) so the target distribution contains 180880 points, each of which is the average across all arrays. After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 and 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 1x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Mus musculus

source_name: Thymus, wk3, control littermate, rep_6

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer.

extract_protocol: RNA was extracted from the spleen, thymus, kidney, and blood collected from homozygous and heterozygous ARE-Del mice at 3, 6, and 12 weeks of age, and comparisons were made with control littermates.

value: female

value: thymus

tag: age

value: wt


title: Thymus_wk3_control littermate_rep_1

source_name: Thymus, wk3, control littermate, rep_1


title: Thymus_wk3_control littermate_rep_4

source_name: Thymus, wk3, control littermate, rep_4


title: KYDS_3

description:
Paired-end was used for sequencing, and only R1 files were used for analysis
M_yang3


title: Thymus_wk3_control littermate_rep_8

source_name: Thymus, wk3, control littermate, rep_8


title: Thymus_wk3_control littermate_rep_2

source_name: Thymus, wk3, control littermate, rep_2


title: Thymus_wk6_control littermate_rep_5

description: Gene expression in thymus from ARE-Del control littermate at 6 weeks of age

source_name: Thymus, wk6, control littermate, rep_5


title: Thymus_wk3_control littermate_rep_3

source_name: Thymus, wk3, control littermate, rep_3


title: Thymus_wk6_control littermate_rep_3

source_name: Thymus, wk6, control littermate, rep_3


title: CON_5

description:
Paired-end was used for sequencing, and only R1 files were used for analysis
CON_5

value: 0.5% CMC-Na


title: BGZ_L_1

description:
Paired-end was used for sequencing, and only R1 files were used for analysis
BL_1


title: Thymus_wk3_control littermate_rep_5

source_name: Thymus, wk3, control littermate, rep_5


title: CON_4

description:
Paired-end was used for sequencing, and only R1 files were used for analysis
CON_4


title: Thymus_wk6_control littermate_rep_7

source_name: Thymus, wk6, control littermate, rep_7


title: Thymus_wk6_control littermate_rep_1

source_name: Thymus, wk6, control littermate, rep_1


title: CON_3

description:
Paired-end was used for sequencing, and only R1 files were used for analysis
CON_3


title: BGZ_L_2

description:
Paired-end was used for sequencing, and only R1 files were used for analysis
BL_2


title: Thymus_wk6_control littermate_rep_2

source_name: Thymus, wk6, control littermate, rep_2


title: Thymus_wk3_control littermate_rep_7

source_name: Thymus, wk3, control littermate, rep_7


title: CON_2

description:
Paired-end was used for sequencing, and only R1 files were used for analysis
CON_2


title: Thymus_wk12_control littermate_rep_4

description: Gene expression in thymus from ARE-Del control littermate at 12 weeks of age

source_name: Thymus, wk12, control littermate, rep_4


title: Thymus_wk6_control littermate_rep_6

source_name: Thymus, wk6, control littermate, rep_6


title: Thymus_wk6_control littermate_rep_4

source_name: Thymus, wk6, control littermate, rep_4


title: CON_1

description:
Paired-end was used for sequencing, and only R1 files were used for analysis
CON_1

source_name: Liver


title: Thymus_wk12_control littermate_rep_3

source_name: Thymus, wk12, control littermate, rep_3


title: Thymus_wk12_control littermate_rep_2

source_name: Thymus, wk12, control littermate, rep_2


title: Thymus_wk3_homozygote_rep_7

description: Gene expression in thymus from ARE-Del homozygote at 3 weeks of age

source_name: Thymus, wk3, homozygote, rep_7

value: ko


title: Thymus_wk3_homozygote_rep_6

source_name: Thymus, wk3, homozygote, rep_6


title: Fmr1 Knock-out,rep3

city: Athens

first: Dimitris

last: Valakos

address: Soranou Ephessiou 4

department: Center of Basic Research

country: Greece

institute: Biomedical Reasearch Foundation Academy of Athens

data_processing:
For RNAseq samples, Quality Control (QC) was performed at the FASTQ raw data file for each sample using the FASTQC software. FASTQ files were aligned to rn6 rat genome using HISAT2 . Counts were defined using HTSeq htseq-count command with the “intersection non-empty” option. The count files were used as input for DESeq2.
Assembly: rn6
Supplementary files format and content: Regarding RNAseq analysis, the file Raw_Counts.xlsx contains all the counts per gene for all the samples. The WildType_vs_Knock-out.xlsx file contains the results from  DESeq2 analysis

source_name: Hippocampus

extract_protocol:
Trizol RNA extraction according to manufacturer’s instructions (Thermo Fischer Scientific)
Libraries were constructed using the NEBNext Ultra II RNA Library Prep Kit for Illumina (E7775) according to the manufacturer’s guidelines

value: Hippocampus


title: Fmr1 Knock-out,rep2


title: Fmr1 Knock-out,rep1


title: WildType,rep2

value: WT


title: WildType,rep1


title: Thymus_wk12_control littermate_rep_1

source_name: Thymus, wk12, control littermate, rep_1


title: Thymus_wk3_homozygote_rep_5

source_name: Thymus, wk3, homozygote, rep_5


title: Thymus_wk3_homozygote_rep_3

source_name: Thymus, wk3, homozygote, rep_3


title: WildType,rep3


title: Thymus_wk3_homozygote_rep_2

source_name: Thymus, wk3, homozygote, rep_2


title: Model3

city: beijing

first: yan

last: zhang

state: Beijing

address: 16 Dongzhimen Inner South Street, Dongcheng District, Beijing

institute: China Academy of Chinese Medical Sciences

data_processing:
Fastp software was utilized to process raw reads into clean sequences.
The clean data were mapped to compare with the GCF_015227675.2_mRatBN7.2 using HISAT2.
The FPKM of each gene was calculated using Cufflinks and the sequence counts for each gene were obtained by HTSeqcount.
Differential expression analysis was performed using the DESeq (2012) R package. P value < 0.05 and fold-change (FC)> 2 or FC < 0.5 were set as the thresholds for differential expressed genes
Assembly: GCF_015227675.2_mRatBN7.2
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Supplementary files format and content: tab-delimited text files include conut values for each Sample

source_name: SDRat ,Duodenum

extract_protocol:
Total RNA was extracted from the duodenum by Trizol (qiagen, China) reagent according to the instructions.
The transcriptome library was constructed using the VAHTS Universal V5 RNA-seq Library Prep kit (Vazyme, China) following the manufacturer’s protocol.

value: SDRat ,Duodenum


title: Thymus_wk3_homozygote_rep_1

source_name: Thymus, wk3, homozygote, rep_1


title: Model1


title: Model4


title: Model2


title: JWXS4


title: Thymus_wk6_homozygote_rep_4

description: Gene expression in thymus from ARE-Del homozygote at 6 weeks of age

source_name: Thymus, wk6, homozygote, rep_4


title: Thymus_wk3_homozygote_rep_4

source_name: Thymus, wk3, homozygote, rep_4


title: JWXS3


title: JWXS2


title: Thymus_wk6_homozygote_rep_3

source_name: Thymus, wk6, homozygote, rep_3


title: Thymus_wk6_homozygote_rep_1

source_name: Thymus, wk6, homozygote, rep_1


title: Thymus_wk6_homozygote_rep_2

source_name: Thymus, wk6, homozygote, rep_2


title: JWXS1


title: Thymus_wk12_homozygote_rep_5

description: Gene expression in thymus from ARE-Del homozygote at 12 weeks of age

source_name: Thymus, wk12, homozygote, rep_5


title: Control4


title: Thymus_wk12_homozygote_rep_4

source_name: Thymus, wk12, homozygote, rep_4


title: Control3


title: Thymus_wk12_homozygote_rep_3

source_name: Thymus, wk12, homozygote, rep_3


title: Control2


title: Control1


title: PGC3 Desertliving Cistanche herb treatment

city: zheng zhou

first: shuo

last: tian

address: Jinshui East Road

institute: Henan University of Chinese Medicine

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter.
HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Ensembl_101
The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters
StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]).
Assembly: Ensembl_101
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Femur

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA), the RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA).
The poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94C 5-7min.

value: Femur


title: PGC2 Desertliving Cistanche herb treatment


title: Thymus_wk3_heterozygote_rep_6

description: Gene expression in thymus from ARE-Del heterozygote at 3 weeks of age

source_name: Thymus, wk3, heterozygote, rep_6

value: het


title: Thymus_wk12_homozygote_rep_2

source_name: Thymus, wk12, homozygote, rep_2


title: Thymus_wk3_heterozygote_rep_7

source_name: Thymus, wk3, heterozygote, rep_7


title: Thymus_wk3_heterozygote_rep_5

source_name: Thymus, wk3, heterozygote, rep_5


title: PGC1 Desertliving Cistanche herb treatment


title: Thymus_wk3_heterozygote_rep_4

source_name: Thymus, wk3, heterozygote, rep_4


title: MC2 Ovariectomized rats


title: MC3 Ovariectomized rats


title: BC3 SD rat


title: BC2 SD rat


title: Thymus_wk3_heterozygote_rep_3

source_name: Thymus, wk3, heterozygote, rep_3


title: MC1 Ovariectomized rats


title: BC1 SD rat


title: Thymus_wk3_heterozygote_rep_1

source_name: Thymus, wk3, heterozygote, rep_1


title: Thymus_wk12_homozygote_rep_1

source_name: Thymus, wk12, homozygote, rep_1


title: Thymus_wk6_heterozygote_rep_6

description: Gene expression in thymus from ARE-Del heterozygote at 6 weeks of age

source_name: Thymus, wk6, heterozygote, rep_6


title: Gene editing RAG1 exon 2 [HD-D-g13-RAG1]

city: Segrate

first: Ivan

last: Merelli

state: Milano

address: via F.lli Cervi 93

department: Istituto di Tecnologie Biomediche

country: Italy

institute: Consiglio Nazionale delle Ricerche

library_source: genomic

data_processing:
Elaborated using the CRISPresso pipeline
Assembly: GENCODE version hg38 primary assembly v35
Supplementary files format and content: tab-delimited text files include read counts values for each Sample
Library strategy: Deep-Sequencing

molecule: genomic DNA

organism: Homo sapiens

source_name: Hematopoietic stem and progenitor cells

growth_protocol: Hematopoietic stem/progenitor cells were stimulated for three days before gene editing  in serum-free StemSpan™ SFEM (StemCell Technology) medium supplemented with specific early-acting cytokines

extract_protocol:
QiAmp DNA micro kit (QIAGEN)
Amplicon libraries were generated by two rounds of PCR by using specific barcoded and adaptor primers

treatment_protocol: Gene editing was perfomed by electroporationa of gRNA#13 RNP using P3 Primary Cell 4D-Nucleofector X Kit and Nucleofector device (program EO-100). Cells were collected 96h after the editing, and untreated cells were used as negative control.

tag: cell type

value: Hematopoietic stem and progenitor cells

value: Wild Type

value: Cas9 and g13 RNA


title: Gene editing RAG1 exon 2 [HD-D-RAG1]

value: untreated


title: Gene editing RAG1 exon 2 [HD-D-g13-7]


title: Gene editing RAG1 exon 2 [HD-D-g13-8]


title: Thymus_wk3_heterozygote_rep_2

source_name: Thymus, wk3, heterozygote, rep_2


title: Thymus_wk6_heterozygote_rep_5

source_name: Thymus, wk6, heterozygote, rep_5


title: Gene editing RAG1 exon 2 [HD-D-g13-6]


title: Thymus_wk6_heterozygote_rep_2

source_name: Thymus, wk6, heterozygote, rep_2


title: Thymus_wk6_heterozygote_rep_7

source_name: Thymus, wk6, heterozygote, rep_7


title: Thymus_wk6_heterozygote_rep_3

source_name: Thymus, wk6, heterozygote, rep_3


title: Thymus_wk6_heterozygote_rep_1

source_name: Thymus, wk6, heterozygote, rep_1


title: Thymus_wk6_heterozygote_rep_4

source_name: Thymus, wk6, heterozygote, rep_4


title: Thymus_wk12_heterozygote_rep_4

description: Gene expression in thymus from ARE-Del heterozygote at 12 weeks of age

source_name: Thymus, wk12, heterozygote, rep_4


title: Thymus_wk12_heterozygote_rep_3

source_name: Thymus, wk12, heterozygote, rep_3


title: Gene editing RAG1 exon 2 [HD-D-g13-4]


title: Thymus_wk12_heterozygote_rep_2

source_name: Thymus, wk12, heterozygote, rep_2


title: Gene editing RAG1 exon 2 [HD-D-g13-3]


title: Gene editing RAG1 exon 2 [HD-D-g13-2]


title: Gene editing RAG1 exon 2 [HD-D-g13-17]


title: Thymus_wk12_heterozygote_rep_1

source_name: Thymus, wk12, heterozygote, rep_1


title: Gene editing RAG1 exon 2 [HD-D-g13-16]


title: Spleen_wk12_control littermate_rep_6

description: Gene expression in spleen from ARE-Del control littermate at 12 weeks of age

source_name: Spleen, wk12, control littermate, rep_6

value: spleen


title: Spleen_wk12_control littermate_rep_5

source_name: Spleen, wk12, control littermate, rep_5


title: Spleen_wk12_control littermate_rep_4

source_name: Spleen, wk12, control littermate, rep_4


title: Spleen_wk12_control littermate_rep_3

source_name: Spleen, wk12, control littermate, rep_3


title: Gene editing RAG1 exon 2 [HD-D-g13-5]


title: Gene editing RAG1 exon 2 [HD-D-g13-15]


title: Spleen_wk3_control littermate_rep_8

description: Gene expression in spleen from ARE-Del control littermate at 3 weeks of age

source_name: Spleen, wk3, control littermate, rep_8


title: Spleen_wk12_control littermate_rep_2

source_name: Spleen, wk12, control littermate, rep_2


title: Spleen_wk12_control littermate_rep_1

source_name: Spleen, wk12, control littermate, rep_1


title: Gene editing RAG1 exon 2 [HD-D-g13-14]

source_name: Hematopoietic stem and progenitor cells


title: Gene editing RAG1 exon 2 [HD-D-g13-13]


title: Gene editing RAG1 exon 2 [HD-D-g13-10]


title: Gene editing RAG1 exon 2 [HD-D-8]


title: Gene editing RAG1 exon 2 [HD-D-7]


title: Gene editing RAG1 exon 2 [HD-D-g13-11]


title: Gene editing RAG1 exon 2 [HD-D-6]


title: Spleen_wk3_control littermate_rep_6

source_name: Spleen, wk3, control littermate, rep_6


title: Spleen_wk3_control littermate_rep_5

source_name: Spleen, wk3, control littermate, rep_5


title: Gene editing RAG1 exon 2 [HD-D-5]


title: Gene editing RAG1 exon 2 [HD-D-4]


title: Spleen_wk3_control littermate_rep_4

source_name: Spleen, wk3, control littermate, rep_4


title: Spleen_wk6_control littermate_rep_7

description: Gene expression in spleen from ARE-Del control littermate at 6 weeks of age

source_name: Spleen, wk6, control littermate, rep_7


title: Spleen_wk3_control littermate_rep_1

source_name: Spleen, wk3, control littermate, rep_1


title: Spleen_wk3_control littermate_rep_2

source_name: Spleen, wk3, control littermate, rep_2


title: Spleen_wk3_control littermate_rep_3

source_name: Spleen, wk3, control littermate, rep_3


title: Spleen_wk6_control littermate_rep_6

source_name: Spleen, wk6, control littermate, rep_6


title: Spleen_wk6_control littermate_rep_5

source_name: Spleen, wk6, control littermate, rep_5


title: Gene editing RAG1 exon 2 [HD-D-3]


title: Gene editing RAG1 exon 2 [HD-D-2]


title: Spleen_wk6_control littermate_rep_3

source_name: Spleen, wk6, control littermate, rep_3


title: Gene editing RAG1 exon 2 [HD-D-17]


title: Gene editing RAG1 exon 2 [HD-D-16]


title: Gene editing RAG1 exon 2 [HD-D-g13-12]


title: Gene editing RAG1 exon 2 [HD-D-15]


title: Gene editing RAG1 exon 2 [HD-D-14]


title: Gene editing RAG1 exon 2 [HD-D-13]


title: Gene editing RAG1 exon 2 [HD-D-12]


title: Gene editing RAG1 exon 2 [HD-D-11]


title: Spleen_wk6_control littermate_rep_2

source_name: Spleen, wk6, control littermate, rep_2


title: Gene editing RAG1 exon 2 [HD-D-10]


title: Gene editing RAG1 exon 2 [HD-B-RAG1]


title: Spleen_wk3_homozygote_rep_7

description: Gene expression in spleen from ARE-Del homozygote at 3 weeks of age

source_name: Spleen, wk3, homozygote, rep_7


title: Gene editing RAG1 exon 2 [HD-B-g13-RAG1]


title: Spleen_wk6_control littermate_rep_1

source_name: Spleen, wk6, control littermate, rep_1


title: Gene editing RAG1 exon 2 [HD-B-g13-9]


title: Gene editing RAG1 exon 2 [HD-B-g13-8]


title: Spleen_wk12_homozygote_rep_3

description: Gene expression in spleen from ARE-Del homozygote at 12 weeks of age

source_name: Spleen, wk12, homozygote, rep_3


title: Spleen_wk6_control littermate_rep_4

source_name: Spleen, wk6, control littermate, rep_4


title: Spleen_wk12_homozygote_rep_2

source_name: Spleen, wk12, homozygote, rep_2


title: Spleen_wk3_homozygote_rep_5

source_name: Spleen, wk3, homozygote, rep_5


title: Spleen_wk3_homozygote_rep_6

source_name: Spleen, wk3, homozygote, rep_6


title: Gene editing RAG1 exon 2 [HD-B-g13-7]

source_name: Hematopoietic stem and progenitor cells


title: Gene editing RAG1 exon 2 [HD-B-g13-6]


title: Gene editing RAG1 exon 2 [HD-B-g13-5]


title: Gene editing RAG1 exon 2 [HD-B-g13-4]


title: Spleen_wk12_homozygote_rep_1

source_name: Spleen, wk12, homozygote, rep_1


title: Spleen_wk6_homozygote_rep_2

description: Gene expression in spleen from ARE-Del homozygote at 6 weeks of age

source_name: Spleen, wk6, homozygote, rep_2


title: Spleen_wk6_homozygote_rep_1

source_name: Spleen, wk6, homozygote, rep_1


title: Spleen_wk3_homozygote_rep_4

source_name: Spleen, wk3, homozygote, rep_4


title: Spleen_wk12_heterozygote_rep_3

description: Gene expression in spleen from ARE-Del heterozygote at 12 weeks of age

source_name: Spleen, wk12, heterozygote, rep_3


title: Spleen_wk3_homozygote_rep_3

source_name: Spleen, wk3, homozygote, rep_3


title: Spleen_wk3_homozygote_rep_2

source_name: Spleen, wk3, homozygote, rep_2


title: Spleen_wk3_homozygote_rep_1

source_name: Spleen, wk3, homozygote, rep_1


title: Spleen_wk6_homozygote_rep_3

source_name: Spleen, wk6, homozygote, rep_3


title: Gene editing RAG1 exon 2 [HD-B-g13-3]


title: Spleen_wk12_heterozygote_rep_2

source_name: Spleen, wk12, heterozygote, rep_2


title: Gene editing RAG1 exon 2 [HD-B-g13-2]


title: Gene editing RAG1 exon 2 [HD-B-g13-17]


title: Gene editing RAG1 exon 2 [HD-B-g13-16]


title: Gene editing RAG1 exon 2 [HD-B-g13-15]


title: Spleen_wk12_heterozygote_rep_1

source_name: Spleen, wk12, heterozygote, rep_1


title: Gene editing RAG1 exon 2 [HD-B-g13-14]


title: Gene editing RAG1 exon 2 [HD-B-g13-13]


title: Spleen_wk3_heterozygote_rep_7

description: Gene expression in spleen from ARE-Del heterozygote at 3 weeks of age

source_name: Spleen, wk3, heterozygote, rep_7


title: Gene editing RAG1 exon 2 [HD-B-g13-11]


title: Gene editing RAG1 exon 2 [HD-B-g13-12]


title: Spleen_wk3_heterozygote_rep_6

source_name: Spleen, wk3, heterozygote, rep_6


title: Spleen_wk3_heterozygote_rep_4

source_name: Spleen, wk3, heterozygote, rep_4


title: Spleen_wk3_heterozygote_rep_3

source_name: Spleen, wk3, heterozygote, rep_3


title: Spleen_wk3_heterozygote_rep_5

source_name: Spleen, wk3, heterozygote, rep_5


title: Spleen_wk3_heterozygote_rep_2

source_name: Spleen, wk3, heterozygote, rep_2


title: Spleen_wk3_heterozygote_rep_1

source_name: Spleen, wk3, heterozygote, rep_1


title: Gene editing RAG1 exon 2 [HD-B-g13-10]

source_name: Hematopoietic stem and progenitor cells


title: Spleen_wk6_heterozygote_rep_7

description: Gene expression in spleen from ARE-Del heterozygote at 6 weeks of age

source_name: Spleen, wk6, heterozygote, rep_7


title: Gene editing RAG1 exon 2 [HD-B-7]


title: Gene editing RAG1 exon 2 [HD-B-8]


title: Gene editing RAG1 exon 2 [HD-B-6]


title: Gene editing RAG1 exon 2 [HD-B-9]


title: Spleen_wk6_heterozygote_rep_6

source_name: Spleen, wk6, heterozygote, rep_6


title: Gene editing RAG1 exon 2 [HD-B-5]


title: Spleen_wk6_heterozygote_rep_5

source_name: Spleen, wk6, heterozygote, rep_5


title: Gene editing RAG1 exon 2 [HD-B-4]


title: Gene editing RAG1 exon 2 [HD-B-2]


title: Gene editing RAG1 exon 2 [HD-B-3]


title: Spleen_wk6_heterozygote_rep_3

source_name: Spleen, wk6, heterozygote, rep_3


title: Kidney_wk3_control littermate_rep_8

description: Gene expression in kidney from ARE-Del control littermate at 3 weeks of age

source_name: Kidney, wk3, control littermate, rep_8

value: kidney


title: Spleen_wk6_heterozygote_rep_4

source_name: Spleen, wk6, heterozygote, rep_4


title: Gene editing RAG1 exon 2 [HD-B-16]


title: Gene editing RAG1 exon 2 [HD-B-17]


title: Spleen_wk6_heterozygote_rep_2

source_name: Spleen, wk6, heterozygote, rep_2


title: Spleen_wk6_heterozygote_rep_1

source_name: Spleen, wk6, heterozygote, rep_1


title: Gene editing RAG1 exon 2 [HD-B-15]


title: Kidney_wk3_control littermate_rep_6

source_name: Kidney, wk3, control littermate, rep_6


title: Gene editing RAG1 exon 2 [HD-B-14]


title: Kidney_wk3_control littermate_rep_5

source_name: Kidney, wk3, control littermate, rep_5


title: Gene editing RAG1 exon 2 [HD-B-13]


title: Kidney_wk3_control littermate_rep_7

source_name: Kidney, wk3, control littermate, rep_7


title: Kidney_wk3_control littermate_rep_3

source_name: Kidney, wk3, control littermate, rep_3


title: Gene editing RAG1 exon 2 [HD-B-11]


title: Gene editing RAG1 exon 2 [HD-B-10]


title: Kidney_wk3_control littermate_rep_4

source_name: Kidney, wk3, control littermate, rep_4


title: Gene editing RAG1 exon 2 [HD-A-RAG1]


title: Gene editing RAG1 exon 2 [HD-A-g13-RAG1]


title: Gene editing RAG1 exon 2 [HD-A-g13-9]


title: Gene editing RAG1 exon 2 [HD-A-g13-8]


title: Gene editing RAG1 exon 2 [HD-A-g13-7]


title: Gene editing RAG1 exon 2 [HD-B-12]


title: Kidney_wk3_control littermate_rep_2

source_name: Kidney, wk3, control littermate, rep_2


title: Gene editing RAG1 exon 2 [HD-A-g13-6]


title: Kidney_wk3_control littermate_rep_1

source_name: Kidney, wk3, control littermate, rep_1


title: Gene editing RAG1 exon 2 [HD-A-g13-5]


title: Gene editing RAG1 exon 2 [HD-A-g13-4]


title: Kidney_wk6_control littermate_rep_3

description: Gene expression in kidney from ARE-Del control littermate at 6 weeks of age

source_name: Kidney, wk6, control littermate, rep_3


title: Kidney_wk6_control littermate_rep_7

source_name: Kidney, wk6, control littermate, rep_7


title: Gene editing RAG1 exon 2 [HD-A-g13-3]

source_name: Hematopoietic stem and progenitor cells


title: Kidney_wk6_control littermate_rep_4

source_name: Kidney, wk6, control littermate, rep_4


title: Kidney_wk6_control littermate_rep_5

source_name: Kidney, wk6, control littermate, rep_5


title: Kidney_wk6_control littermate_rep_1

source_name: Kidney, wk6, control littermate, rep_1


title: Gene editing RAG1 exon 2 [HD-A-g13-2]


title: Gene editing RAG1 exon 2 [HD-A-g13-16]


title: Kidney_wk6_control littermate_rep_2

source_name: Kidney, wk6, control littermate, rep_2


title: Kidney_wk6_control littermate_rep_6

source_name: Kidney, wk6, control littermate, rep_6


title: Kidney_wk12_control littermate_rep_6

description: Gene expression in kidney from ARE-Del control littermate at 12 weeks of age

source_name: Kidney, wk12, control littermate, rep_6


title: Kidney_wk12_control littermate_rep_5

source_name: Kidney, wk12, control littermate, rep_5


title: Kidney_wk12_control littermate_rep_3

source_name: Kidney, wk12, control littermate, rep_3


title: Gene editing RAG1 exon 2 [HD-A-g13-15]


title: Kidney_wk12_control littermate_rep_2

source_name: Kidney, wk12, control littermate, rep_2


title: Kidney_wk12_control littermate_rep_4

source_name: Kidney, wk12, control littermate, rep_4


title: Kidney_wk12_control littermate_rep_1

source_name: Kidney, wk12, control littermate, rep_1


title: Kidney_wk3_homozygote_rep_6

description: Gene expression in kidney from ARE-Del homozygote at 3 weeks of age

source_name: Kidney, wk3, homozygote, rep_6


title: Kidney_wk3_homozygote_rep_7

source_name: Kidney, wk3, homozygote, rep_7


title: Gene editing RAG1 exon 2 [HD-A-g13-14]


title: Gene editing RAG1 exon 2 [HD-A-g13-13]


title: Kidney_wk3_homozygote_rep_5

source_name: Kidney, wk3, homozygote, rep_5


title: Gene editing RAG1 exon 2 [HD-A-g13-10]


title: Gene editing RAG1 exon 2 [HD-A-9]


title: Gene editing RAG1 exon 2 [HD-A-8]


title: Kidney_wk3_homozygote_rep_3

source_name: Kidney, wk3, homozygote, rep_3


title: Kidney_wk3_homozygote_rep_4

source_name: Kidney, wk3, homozygote, rep_4


title: Kidney_wk6_homozygote_rep_3

description: Gene expression in kidney from ARE-Del homozygote at 6 weeks of age

source_name: Kidney, wk6, homozygote, rep_3


title: Gene editing RAG1 exon 2 [HD-A-7]

source_name: Hematopoietic stem and progenitor cells


title: Kidney_wk3_homozygote_rep_2

source_name: Kidney, wk3, homozygote, rep_2


title: Gene editing RAG1 exon 2 [HD-A-6]


title: Kidney_wk6_homozygote_rep_4

source_name: Kidney, wk6, homozygote, rep_4


title: Kidney_wk3_homozygote_rep_1

source_name: Kidney, wk3, homozygote, rep_1


title: Gene editing RAG1 exon 2 [HD-A-3]


title: Kidney_wk6_homozygote_rep_2

source_name: Kidney, wk6, homozygote, rep_2


title: Gene editing RAG1 exon 2 [HD-A-17]


title: Gene editing RAG1 exon 2 [HD-A-g13-11]


title: Gene editing RAG1 exon 2 [HD-A-g13-12]


title: Gene editing RAG1 exon 2 [HD-A-16]


title: Kidney_wk12_homozygote_rep_6

description: Gene expression in kidney from ARE-Del homozygote at 12 weeks of age

source_name: Kidney, wk12, homozygote, rep_6


title: Kidney_wk6_homozygote_rep_1

source_name: Kidney, wk6, homozygote, rep_1


title: Kidney_wk12_homozygote_rep_2

source_name: Kidney, wk12, homozygote, rep_2


title: Kidney_wk12_homozygote_rep_3

source_name: Kidney, wk12, homozygote, rep_3


title: Gene editing RAG1 exon 2 [HD-A-5]


title: Kidney_wk12_homozygote_rep_5

source_name: Kidney, wk12, homozygote, rep_5


title: Kidney_wk12_homozygote_rep_1

source_name: Kidney, wk12, homozygote, rep_1


title: Kidney_wk12_homozygote_rep_4

source_name: Kidney, wk12, homozygote, rep_4


title: Kidney_wk3_heterozygote_rep_7

description: Gene expression in kidney from ARE-Del heterozygote at 3 weeks of age

source_name: Kidney, wk3, heterozygote, rep_7


title: Gene editing RAG1 exon 2 [HD-A-14]


title: Gene editing RAG1 exon 2 [HD-A-4]


title: Gene editing RAG1 exon 2 [HD-A-2]


title: Gene editing RAG1 exon 2 [HD-A-13]


title: Gene editing RAG1 exon 2 [HD-A-12]


title: Gene editing RAG1 exon 2 [HD-A-10]


title: Gene editing RAG1 exon 2 [HD-A-11]


title: Kidney_wk3_heterozygote_rep_5

source_name: Kidney, wk3, heterozygote, rep_5


title: Kidney_wk3_heterozygote_rep_4

source_name: Kidney, wk3, heterozygote, rep_4


title: SGC7901_miR-192oe

city: Shiyan

first: Qin

last: Shanshan

address: Renmin Road 30, Maojian District

institute: Institute of Basic Medical Sciences, School of Basic Medical Sciences, Hubei University of Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. 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 the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2 with default parameters.
HTSeq v0.11.2 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_29/gencode.v29.annotation.gtf.gz.
Assembly: GRCh38
Supplementary files format and content: Fileinclude FPKM valueforeachsample

growth_protocol: The human gastric cancer cell lines were purchased from the Shanghai Cell Bank of Chinese Academy of Sciences (Shanghai, China). The two gastric cancer cell lines were cultured in DMEM medium containing 10% fetal bovine serum (FBS), 100 U/mL penicillin, 100 U/mL streptomycin and 0.03% glutamine at 37 oC in 5% CO2.

extract_protocol:
After 48 hours, remove the medium and directly add 800μL Trizol into the 6-well plate to harvest samples. Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: The human cell lines  were grown as usual in 6-well plates. After 48 hours of transfection with miRNA mimics, the cells were digested for next studies.

tag: cell line

value: gastric cancer cell


title: SGC7901_si-NC

value: NC


title: BGC823_miR-192oe


title: Gene editing RAG1 exon 2 [HD-A-15]


title: Kidney_wk3_heterozygote_rep_2

source_name: Kidney, wk3, heterozygote, rep_2

value: female


title: BGC823_si-NC


title: Kidney_wk3_heterozygote_rep_6

source_name: Kidney, wk3, heterozygote, rep_6


title: Kidney_wk6_heterozygote_rep_6

description: Gene expression in kidney from ARE-Del heterozygote at 6 weeks of age

source_name: Kidney, wk6, heterozygote, rep_6


title: GW24, pos3

city: BeiJing

first: hao

last: dong

address: Datun Rd

institute: ibp

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software(https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: hg19
Supplementary files format and content: Tab-separated values files and matrix files

source_name: spinal cord

extract_protocol:
Freshly collected tissue processed as 10x protocal
Library was performed according to the single cell 3’ v2,v3 protocol, and Visium protocal of 10x Genomics.

value: spinal cord

tag: time point


title: Kidney_wk3_heterozygote_rep_3

source_name: Kidney, wk3, heterozygote, rep_3


title: GW25, pos2

description: 10x Genomics


title: GW24, pos2

description: 10x Genomics


title: Kidney_wk6_heterozygote_rep_4

source_name: Kidney, wk6, heterozygote, rep_4


title: GW25, pos3

description: 10x Genomics


title: Kidney_wk6_heterozygote_rep_3

source_name: Kidney, wk6, heterozygote, rep_3


title: Kidney_wk3_heterozygote_rep_1

source_name: Kidney, wk3, heterozygote, rep_1


title: Kidney_wk12_heterozygote_rep_6

description: Gene expression in kidney from ARE-Del heterozygote at 12 weeks of age

source_name: Kidney, wk12, heterozygote, rep_6


title: GW20, pos3

description: 10x Genomics


title: Kidney_wk6_heterozygote_rep_7

source_name: Kidney, wk6, heterozygote, rep_7


title: GW20, pos1

description: 10x Genomics


title: Kidney_wk12_heterozygote_rep_5

source_name: Kidney, wk12, heterozygote, rep_5


title: Kidney_wk12_heterozygote_rep_3

source_name: Kidney, wk12, heterozygote, rep_3


title: Kidney_wk6_heterozygote_rep_2

source_name: Kidney, wk6, heterozygote, rep_2


title: GW25, pos1

description: 10x Genomics


title: Kidney_wk6_heterozygote_rep_5

source_name: Kidney, wk6, heterozygote, rep_5


title: Kidney_wk12_heterozygote_rep_1

source_name: Kidney, wk12, heterozygote, rep_1


title: Kidney_wk12_heterozygote_rep_2

source_name: Kidney, wk12, heterozygote, rep_2


title: Kidney_wk6_heterozygote_rep_1

source_name: Kidney, wk6, heterozygote, rep_1


title: GW24, pos1

description: 10x Genomics


title: GW16, pos3

description: 10x Genomics


title: Whole blood_wk3_control littermate_rep_7

description: Gene expression in whole blood from ARE-Del control littermate at 3 weeks of age

source_name: Whole blood, wk3, control littermate, rep_7

value: whole blood

value: wt


title: GW18, pos1

description: 10x Genomics


title: GW18, pos2

description: 10x Genomics


title: GW20, pos2

description: 10x Genomics


title: GW11, pos3

description: 10x Genomics


title: Kidney_wk12_heterozygote_rep_4

source_name: Kidney, wk12, heterozygote, rep_4


title: Whole blood_wk3_control littermate_rep_8

source_name: Whole blood, wk3, control littermate, rep_8


title: Whole blood_wk3_control littermate_rep_6

source_name: Whole blood, wk3, control littermate, rep_6


title: GW18, pos3

description: 10x Genomics

source_name: spinal cord


title: Whole blood_wk3_control littermate_rep_3

source_name: Whole blood, wk3, control littermate, rep_3


title: GW11, pos2

description: 10x Genomics


title: Whole blood_wk3_control littermate_rep_5

source_name: Whole blood, wk3, control littermate, rep_5


title: GW11, pos1

description: 10x Genomics


title: Whole blood_wk3_control littermate_rep_2

source_name: Whole blood, wk3, control littermate, rep_2


title: GW16, pos2

description: 10x Genomics


title: GW16, pos1

description: 10x Genomics


title: GW10, pos2

description: 10x Genomics


title: GW10, pos1

description: 10x Genomics


title: Whole blood_wk3_control littermate_rep_4

source_name: Whole blood, wk3, control littermate, rep_4


title: Whole blood_wk6_control littermate_rep_6

description: Gene expression in whole blood from ARE-Del control littermate at 6 weeks of age

source_name: Whole blood, wk6, control littermate, rep_6


title: GW9, pos1

description: 10x Genomics


title: GW9, pos3

description: 10x Genomics


title: GW9, pos2

description: 10x Genomics


title: Whole blood_wk6_control littermate_rep_4

source_name: Whole blood, wk6, control littermate, rep_4


title: GW8, pos2

description: 10x Genomics


title: GW8, pos3

description: 10x Genomics


title: GW8, pos1

description: 10x Genomics


title: GW10, pos3

description: 10x Genomics


title: GW7, pos3

description: 10x Genomics


title: GW7, pos2

description: 10x Genomics


title: Whole blood_wk6_control littermate_rep_2

source_name: Whole blood, wk6, control littermate, rep_2


title: GW7, pos1

description: 10x Genomics


title: Whole blood_wk6_control littermate_rep_1

source_name: Whole blood, wk6, control littermate, rep_1


title: Gene editing RAG1 exon 2 [HD-A-g13-17]

source_name: Hematopoietic stem and progenitor cells


title: Whole blood_wk12_control littermate_rep_6

description: Gene expression in whole blood from ARE-Del control littermate at 12 weeks of age

source_name: Whole blood, wk12, control littermate, rep_6


title: Whole blood_wk6_control littermate_rep_3

source_name: Whole blood, wk6, control littermate, rep_3


title: Whole blood_wk3_control littermate_rep_1

source_name: Whole blood, wk3, control littermate, rep_1


title: Whole blood_wk12_control littermate_rep_3

source_name: Whole blood, wk12, control littermate, rep_3


title: Whole blood_wk12_control littermate_rep_4

source_name: Whole blood, wk12, control littermate, rep_4


title: BI2-CMs

first: Bin

last: Li

address: Jinzun Road

institute: Shanghai jiaotong University

data_processing:
Libraries with different indices were multiplexed and loaded on an Illumina HiSeq instrument according to manufacturer’s instructions (Illumina, San Diego, CA, USA). Sequencing was carried out using a 2x150bp paired-end (PE) configuration; image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument.
Pass filter data of fastq format were processed by Cutadapt (V1.9.1) to be high quality clean data.
Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website; Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence; Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: HiPSC-derived cardiomyocytes

extract_protocol:
Total mRNAs were isolated from nTL- and sTL- hiPSC-derived cardiomyocytes using TRIZOL (Invitrogen) according to the directions. The poly(A) mRNA isolation was performed using Poly(A) mRNA Magnetic Isolation Module or rRNA removal Kit.
CDNA libraries were prepared for sequencing using standard Illumina protocols.

value: HiPSC-derived cardiomyocytes

value: BIBR-treated


title: Whole blood_wk6_control littermate_rep_5

source_name: Whole blood, wk6, control littermate, rep_5


title: Whole blood_wk12_control littermate_rep_5

source_name: Whole blood, wk12, control littermate, rep_5


title: Whole blood_wk12_control littermate_rep_1

source_name: Whole blood, wk12, control littermate, rep_1


title: Whole blood_wk12_control littermate_rep_2

source_name: Whole blood, wk12, control littermate, rep_2


title: BI1-CMs


title: UC3-CMs

value: control


title: BI3-CMs


title: UC2-CMs


title: UC1-CMs


title: H9, P8i-3, 48h

first: Yiyang

last: Sun

address: 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health

data_processing:
Sequence reads were mapped to hg38 using Hisat2.
Transcript assembly and quantification with StringTie.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include counts for each Sample

growth_protocol: H9 human embryonic stem cells were maintained in mTeSR in humidified atmosphere with 5% CO2 at 37⁰C

extract_protocol:
RNA was harvested using TRIzol reagent (Invitrogen). 3 ug of total RNA was used for the construction of sequencing libraries.
The sequencing libraries were generated using a NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB, Ispawich, USA) according to the manufacturer’s instructions.

value: human embryonic stem cell

value: PRPF8 knockdown

value: mTeSR culture


title: H9, NT, 48h

value: WT


title: Whole blood_wk3_homozygote_rep_6

description: Gene expression in whole blood from ARE-Del homozygote at 3 weeks of age

source_name: Whole blood, wk3, homozygote, rep_6

value: ko


title: H9, P8i-3, 24h


title: Whole blood_wk3_homozygote_rep_2

source_name: Whole blood, wk3, homozygote, rep_2


title: Whole blood_wk3_homozygote_rep_4

source_name: Whole blood, wk3, homozygote, rep_4


title: H9, NT, 24h


title: Healthy 5

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

data_processing:
Base calling was performed with the Illumina CASAVA 1.9 pipeline
10X Genomics Cell Ranger Software Suite (v6.1.1) used for alignment and expression quantification
Seurat package (v4.0) used to perform integrated analyses of single cells
Assembly: hg38
Supplementary files format and content: HDF5 files for raw, filtered and molecule info per sample

source_name: Ileum

extract_protocol:
De-identified surgical specimens from inflamed terminal ileal mucosa were obtained from CD patients diagnosed by established clinical, radiologic, and histopathologic criteria. Tissues were immediately placed in ice-cold RPMI and processed within 1 h of resection. For comparison, biopsy specimens were obtained from age- and sex-matched healthy controls. To control for variations in immune cell populations residing in the intestinal micro-organization, tissue resections were subjected to sampling using biopsy forceps along the mucosa of the resection specimens, collecting approximately 20 biopsies from each. Biopsies were stored in HypoThermosol® FRS (BioLife Solutions) on ice and later transferred to CryoStor® CS10 (StemCell) in 1.5 ml cryogenic vials. Samples were frozen at -80°C overnight and stored in liquid nitrogen until single-cell suspensions were prepared. Healthy controls consisted of patients evaluated for gastrointestinal symptoms (i.e., abdominal pain, diarrhea, rectal bleeding) who were found to have normal endoscopic evaluations.
Whole live cells were washed twice in 1x PBS + 0.04% BSA and immediately submitted to the Core for single cell partitioning. Cells were counted and measured for viability using the Vi-Cell XR Cell Viability Analyzer (Beckman-Coulter, Brea, CA). The barcoded Gel Beads were thawed from -80°C and the cDNA master mix was prepared according to the manufacture’s instruction for Chromium Next GEM Single Cell 3’ Library and Gel Bead Kit (10x Genomics, Pleasanton, CA).  Based on the desired number of cells to be captured for each sample, a volume of live cells was mixed with the cDNA master mix. A per sample concentration of 500,000 cells per milliliter or better was required for the standard targeted cell recovery of approximately 5,000 cells.  The stock concentration requirements would not change for higher cell recovery numbers. The cell suspension and master mix, thawed Gel Beads and partitioning oil were added to a Chromium Single Cell G chip. The filled chip was loaded into the Chromium Controller, where each sample was processed and the individual cells within the sample were partitioned into uniquely labeled GEMs (Gel Beads-In-Emulsion). The GEMs were collected from the chip and taken to the bench for reverse transcription, GEM dissolution, and cDNA clean-up. The resulting cDNA contained a pool of uniquely barcoded molecules. A portion of the cleaned and measured, pooled cDNA continued to library construction, where standard Illumina sequencing primers and a 10X Genomics unique i7 sample index were added to each cDNA pool. All cDNA pools and resulting libraries were measured using Qubit High Sensitivity assays (Thermo Fisher Scientific, Waltham, MA) and Agilent Bioanalyzer High Sensitivity chips (Agilent, Santa Clara, CA). Libraries were sequenced at between 40,000 and 50,000 fragment reads per cell following Illumina’s standard protocol using the Illumina cBot and HiSeq 3000/4000 PE Cluster Kit (Illumina, San Diego, CA).  The flow cells were sequenced as 100 X 2 paired end reads on an Illumina HiSeq 4000 HD using HiSeq 3000/4000 sequencing kit and HCS v3.4.0.38 collection software.

tag: condition

value: Healthy control

value: Male


title: Healthy 3

value: Female


title: Healthy 2


title: Healthy 4


title: Healthy 6


title: CD 5

value: Crohn's disease


title: Whole blood_wk3_homozygote_rep_1

source_name: Whole blood, wk3, homozygote, rep_1


title: CD 4


title: CD 3


title: Whole blood_wk3_homozygote_rep_5

source_name: Whole blood, wk3, homozygote, rep_5


title: CD 2


title: Whole blood_wk3_homozygote_rep_7

source_name: Whole blood, wk3, homozygote, rep_7


title: Whole blood_wk6_homozygote_rep_1

description: Gene expression in whole blood from ARE-Del homozygote at 6 weeks of age

source_name: Whole blood, wk6, homozygote, rep_1


title: Healthy 1


title: Whole blood_wk12_homozygote_rep_5

description: Gene expression in whole blood from ARE-Del homozygote at 12 weeks of age

source_name: Whole blood, wk12, homozygote, rep_5


title: Whole blood_wk6_homozygote_rep_2

source_name: Whole blood, wk6, homozygote, rep_2


title: Whole blood_wk12_homozygote_rep_3

source_name: Whole blood, wk12, homozygote, rep_3


title: Whole blood_wk12_homozygote_rep_2

source_name: Whole blood, wk12, homozygote, rep_2


title: Whole blood_wk3_homozygote_rep_3

source_name: Whole blood, wk3, homozygote, rep_3


title: Whole blood_wk3_heterozygote_rep_6

description: Gene expression in whole blood from ARE-Del heterozygote at 3 weeks of age

source_name: Whole blood, wk3, heterozygote, rep_6

value: het


title: 121v3

city: Wien

first: Andreas

middle: B

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

data_processing:
fastQ quality assessment
cutadapt adater trimming
bowtie1 genome alignment
miRDeep2 miRNA quantification
edgeR differential expression
Assembly: GRCh38.p12 (GCA_000001405.28)
Supplementary files format and content: CSV with miRNA quantifications (raw and rpm)

source_name: serum

extract_protocol:
RNA extraction was performed in 200 microL of serum samples with miRNeasy Mini Kits (Qiagen)
RealSeq-Biofluids Plasma/Serum miRNA Library kit for Illumina sequencing

value: serum

value: osteoporosis

value: Denosumab

tag: group

value: Postmenopausal

tag: timepoint

tag: patient


title: 121v6


title: CD 1


title: 121v1


title: Whole blood_wk6_homozygote_rep_3

source_name: Whole blood, wk6, homozygote, rep_3

value: female

value: whole blood


title: Whole blood_wk3_heterozygote_rep_5

source_name: Whole blood, wk3, heterozygote, rep_5


title: Whole blood_wk6_homozygote_rep_4

source_name: Whole blood, wk6, homozygote, rep_4


title: 118v6


title: Whole blood_wk12_homozygote_rep_4

source_name: Whole blood, wk12, homozygote, rep_4


title: Whole blood_wk3_heterozygote_rep_2

source_name: Whole blood, wk3, heterozygote, rep_2


title: Whole blood_wk12_homozygote_rep_1

source_name: Whole blood, wk12, homozygote, rep_1


title: Whole blood_wk3_heterozygote_rep_7

source_name: Whole blood, wk3, heterozygote, rep_7


title: Whole blood_wk3_heterozygote_rep_3

source_name: Whole blood, wk3, heterozygote, rep_3


title: Whole blood_wk6_heterozygote_rep_6

description: Gene expression in whole blood from ARE-Del heterozygote at 6 weeks of age

source_name: Whole blood, wk6, heterozygote, rep_6


title: Whole blood_wk3_heterozygote_rep_4

source_name: Whole blood, wk3, heterozygote, rep_4


title: Whole blood_wk6_heterozygote_rep_7

source_name: Whole blood, wk6, heterozygote, rep_7


title: Whole blood_wk3_heterozygote_rep_1

source_name: Whole blood, wk3, heterozygote, rep_1


title: Whole blood_wk6_heterozygote_rep_5

source_name: Whole blood, wk6, heterozygote, rep_5


title: 117v6


title: 118v1


title: 117v1


title: Whole blood_wk6_heterozygote_rep_3

source_name: Whole blood, wk6, heterozygote, rep_3


title: 117v3


title: 114v3


title: 114v6


title: 114v1


title: 113v6


title: 118v3


title: 113v3


title: Ruminococcus gnavus cells, agarooligosaccharide added, biol rep 3

city: Toyoake

first: Tadashi

last: Fujii

state: Aichi

address: 1-98 Dengakugakubo Kutsukake-cho

department: School of Medicine, Gastroenterology and Hepatology

country: Japan

institute: FUJITA HEALTH UNIVERSITY

data_processing:
After reading and writing the alignment data in the SAM and BAM formats with the SAMtools, the data were sorted and indexed.
The read counts per gene were obtained using the featureCounts (ver. 2.0.3).
The relative expression level of each gene was normalized by the RPKM (Reads per Kilobase Million) and Transcripts Per Million methods.
After normalization using the DEGES normalization method implemented in TCC (ver. 1.34.0), we performed a differential gene expression analysis using edgeR (ver. 3.36.1).
Assembly: Bowtie2 (ver. 2.5.0) was used to read the alignment and mapping of the CP043051.1 reference genomes.
Supplementary files format and content: Exeel files include RPKM and TPM  values for each Sample

organism: Mediterraneibacter gnavus

growth_protocol: R. gnavus was inoculated into 3 mL of RF-medium containing 0.1% glucose with or without 0.1% AOS, and cultured at 37°C using AnaeroPack system. Samples containing AOS were incubated for 72 hours with 100 µL of inoculum (final OD660 = 0.04), and samples without AOS were incubated for 48 hours with 10 µL of inoculum (final OD660 = 0.21).

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.
After removing rRNA in samples by riboPool (siTOOLs Biotech, Planegg, Germany), the NGS library was prepared by MGIEasy RNA Directional Library Prep Set (MGI Tech, Shenzhen, China) according to the manufacturer’s protocol.

treatment_protocol: After incubation, the cells were ice-cooled for 10 minutes, centrifuged at 6,000 rpm for 5 minutes at 4°C, and 0.6 mL of RNA later® (Thermo Fisher Scientific) was added to the precipitate.

value: with agarooligosaccharide


title: Ruminococcus gnavus cells, Control, biol rep 3

value: without agarooligosaccharide


title: 113v1


title: 107v6


title: Ruminococcus gnavus cells, agarooligosaccharide added, biol rep 1


title: 107v3


title: 107v1


title: Whole blood_wk6_heterozygote_rep_2

source_name: Whole blood, wk6, heterozygote, rep_2


title: Whole blood_wk12_heterozygote_rep_3

description: Gene expression in whole blood from ARE-Del heterozygote at 12 weeks of age

source_name: Whole blood, wk12, heterozygote, rep_3


title: Whole blood_wk6_heterozygote_rep_1

source_name: Whole blood, wk6, heterozygote, rep_1


title: Whole blood_wk12_heterozygote_rep_4

source_name: Whole blood, wk12, heterozygote, rep_4


title: Ruminococcus gnavus cells, Control, biol rep 2


title: Whole blood_wk12_heterozygote_rep_5

source_name: Whole blood, wk12, heterozygote, rep_5


title: Whole blood_wk12_heterozygote_rep_1

source_name: Whole blood, wk12, heterozygote, rep_1


title: 105v6

source_name: serum


title: Whole blood_wk6_heterozygote_rep_4

source_name: Whole blood, wk6, heterozygote, rep_4


title: Whole blood_wk12_heterozygote_rep_6

source_name: Whole blood, wk12, heterozygote, rep_6


title: Whole blood_wk12_heterozygote_rep_2

source_name: Whole blood, wk12, heterozygote, rep_2


title: 105v1


title: 102v3


title: 102v1


title: 102v6


title: Ruminococcus gnavus cells, agarooligosaccharide added, biol rep 2


title: 105v3


title: Single cells from tumor core sample of donor 20180110

city: Beijing

first: Yao

last: He

state: Haidian District

address: Room 307A, Intergrated Science Building 2, Peking University,, No.5 Yiheyuan Road

institute: BIOPIC

data_processing:
Smart-seq2 sequencing data were aligned with STAR, using genome reference hg38 and annotation downloaded from NCI GDC (Genomic Data Commons) (https://api.gdc.cancer.gov/data/254f697d-310d-4d7d-a27b-27fbf767a834)
Gene-specific read counts were calculated using featureCounts with parameters ‘-M -O–fraction -Q 30’. Quality of cells were then assessed based on three metrics step by step: (1) The number of total counts per cell (library size); (2) The number of detected genes per cell; (3) The proportion of mitochondrial gene counts. Low-quality cells were filtered if the library size or the number of detected genes was below the median of all cells minus 3× the median absolute deviation. We also removed all cells with the proportion of mitochondrial gene counts higher than 10%.
The size factor for each cell was computed using a pooling strategy implemented in the R function computeSumFactors in scran package. Normalized counts/expression were then computed by dividing the counts for each cell by the size factor for that cells. A log2 transformation was applied to normalized counts. A total of  9017 cells were retained for downstream analysis.
Genome_build: hg38
Supplementary_files_format_and_content: The CSV file and the R object file containg raw counts matrix, normalized expression and cell annotations

source_name: Tumor core

extract_protocol: Based on FACS analysis, single CD45+/- cells (anti-human CD45, HI30, eBiocience) of the samples of patients were sorted into wells of 96-well plates (Axygen) for plated-based scRNA-seq, prepared with lysis buffer which contained 1 mL 10 mM dNTP mix (Fermentas), 1 mL 10 mM Oligo dT primer, 1.9 mL 1% Triton X-100 (Sigma) plus 0.1 mL 40 U/ml RNase Inhibitor (Takara). The sealed plates were stored frozen at 80oC.Reverse transcription and transcriptome amplifications were performed following Smart-seq2 protocol. The amplified cDNA products were purified with 1x Agencourt XP DNA beads (Beckman). Following the first round of beads purification, the cDNA of each single cell was quantified with qPCR of GAPDH, and fragment analysis (using fragment analyzer AATI). The DNA products with high quality were further cleaned with 0.5x Agencourt XP DNA beads (Beckman) to eliminate short fragments (less than 500bp). The concentration of each sample was then quantified with Qubit HsDNA kits (Invitrogen). The libraries were constructed with the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme Biotech). Constructed libraries were analyzed by an Illumina Hiseq 4000 with 150bp paired-end reads

tag: individual

value: tumor


title: Single cells from tumor edge sample of donor 20180110

source_name: Tumor edge

tag: tissue


title: Single cells from adjacent liver sample of donor 20180110

source_name: Adjacent liver

value: adjacent liver


title: Fervidibacter sacchari, xanthan gum, biol 1

city: Las Vegas

first: Nancy

last: Nou

state: NV

address: 4505 S Maryland Parkway

institute: University of Nevada, Las Vegas

data_processing:
Illumina library was constructed and sequenced 2x151 using the Illumina NovaSeq S4 platform
BBDuk v.38.94 was used to remove contaminants, trim reads that contained adapter sequence and homopolymers of G's of size 5 or more at the ends of the reads, right quality trim reads where quality drops below 6, remove reads containing 1 or more 'N' bases, remove reads with average quality score across the read less than 10, having minimum length <= 49bp or 33% of the full read length
Reads mapped with BBMap to human, cat, dog, and mouse references at 93% identity were separated into a chaff file
Reads aligned to masked common microbial contaminants were separated into a chaff file
Assembly: GCA_030520105.1
Supplementary files format and content: Excel file includes raw counts for features of interest

organism: Fervidibacter sacchari

source_name: bacterial cells

growth_protocol: Fervidibacter sacchari cells were grown in Fervidibacter medium, with xyloglucan replaced by the described treatment, at 80 °C until mid-exponential phase.

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Mini Kit using the enzymatic lysis procedure and on-column DNase treatment. 100 ng of total RNA was used to deplete rRNA using the QiaSeq FastSelect 5S/16S/23S Kit.
Using TruSeq stranded mRNA kit (Illumina), the 300 - 400 bp heat-fragmented RNA was reverse transcribed to create the first strand of cDNA with random hexamers and SuperScript II Reverse Transcriptase (Thermo Fisher Scientific) followed by second strand synthesis. The double stranded cDNA fragments were treated with A-tailing, ligation with JGI's unique dual indexed adapters (IDT) and enriched using 10 cycles of PCR. The prepared libraries were quantified using KAPA Biosystems' next-generation sequencing library qPCR kit and run on a Roche LightCycler 480 real-time PCR instrument.

treatment_protocol: Cell cultures were cooled in a dry ice/ethanol bath and immediately centrifuged. Cell pellets were stored at -80 °C until extraction.

value: bacterial cells

value: xanthan gum carbon source


title: Fervidibacter sacchari, starch, biol 2

value: starch carbon source


title: Fervidibacter sacchari, xyloglucan, biol 3

value: xyloglucan carbon source


title: Fervidibacter sacchari, xanthan gum, biol 3


title: Fervidibacter sacchari, xanthan gum, biol 2


title: Fervidibacter sacchari, xyloglucan, biol 2


title: Fervidibacter sacchari, xyloglucan, biol 1


title: Fervidibacter sacchari, starch, biol 3


title: Ruminococcus gnavus cells, Control, biol rep 1

value: WT


title: Single cells from tumor edge sample of donor 20180108


title: Single cells from tumor sample of donor 20171229

source_name: Tumor


title: Fervidibacter sacchari, starch, biol 1


title: Single cells from adjacent liver sample of donor 20171229


title: Fervidibacter sacchari, locust bean gum, biol 2

value: locust bean gum carbon source


title: Fervidibacter sacchari, locust bean gum, biol 3


title: Fervidibacter sacchari, locust bean gum, biol 1


title: Single cells from tumor sample of donor 20171220


title: Fervidibacter sacchari, gellan gum, biol 3

value: gellan gum carbon source


title: Single cells from adjacent liver sample of donor 20171220


title: Fervidibacter sacchari, gellan gum, biol 2


title: Single cells from tumor sample of donor 20171215


title: Single cells from adjacent liver sample of donor 20171215


title: Fervidibacter sacchari, gellan gum, biol 1


title: Fervidibacter sacchari, corn stover, biol 2

value: corn stover carbon source


title: Single cells from tumor sample of donor 20171109


title: Single cells from tumor core sample of donor 20180108


title: Fervidibacter sacchari, chondroitin sulfate, biol 3

value: chondroitin sulfate carbon source


title: Single cells from adjacent liver sample of donor 20171109


title: Fervidibacter sacchari, corn stover, biol 1


title: Single cells from tumor sample of donor 20170412


title: Single cells from blood sample of donor 20171109

source_name: Blood

value: blood


title: Fervidibacter sacchari, chondroitin sulfate, biol 2


title: Single cells from blood sample of donor 20170322


title: Single cells from tumor sample of donor 20170327


title: Single cells from blood sample of donor 20170327


title: Single cells from tumor sample of donor 20170227


title: Single cells from adjacent liver sample of donor 20170412


title: Fervidibacter sacchari, beta-glucan, biol 1

value: beta-glucan carbon source


title: Fervidibacter sacchari, beta-glucan, biol 2


title: Fervidibacter sacchari, chondroitin sulfate, biol 1


title: 1RA_COPD_2_S49

city: Berwick

first: Habtamu

middle: Biyazen

last: Derseh

state: VIC

address: 100 Clyde Rd

country: Australia

institute: Federation University

data_processing:
Sequenced reads were downloaded and checked for quality using FastQC (v0.11.9).
The reads were then trimmed and NexteraPE adaptors removed using trimmomatic (v0.39) to a length of minimum length of 36 nucleotides. Following trimming, the reads were mapped to the sheep genome (GCF_016772045.1_ARS-UI_Ramb_v2.0) using the aligner STAR (v2.7.10b). The resulting BAM files were then concatenated using FeatureCounts (Subread v1.6.3) and imported into R studio (v4.2.1).
Meta and count data were pre-processed using R packages SummarizedExperiment (v1.28.0) and tidybulk (v 1.10.0). Lowly abundant reads were removed and scaled to the sample by the largest library size. Multidimensional scaling (MDS) was used to check for outlying samples and batch effects.
EdgeR (v3.40.2) was used to detect differentially expressed genes, with a threshold of logFC >1 and logFC <-1, and FDR of 0.05.
Differentially expressed genes were visualised using ggplot2 (v3.4.0). Gene enrichment tests were performed using GO terms using the package ClusterProfiler (v4.6.0) with a sheep annotation file built using AnnotationHub (v 3.6.0)
Assembly: Oar_rambouillet_v1.0(GCA_002742125.1)
Supplementary files format and content: tab.delimited .xlsx file includes raw counts for each samples

organism: Ovis aries

source_name: tissue

extract_protocol:
total RNA was extracted using RNeasy Micro Kit (Qiagen) according to the kit instruction
Novel RNA-Seq pipeline (Version 01/09/2021). Briefly index is added during initial pA priming and pooled samples amplified using template switching oligo. P5 is added by tagmentation by Nextera transposase and PCR

value: tissue

value: Saline


title: Fervidibacter sacchari, beta-glucan, biol 3


title: Single cells from tumor sample of donor 20170322


title: Single cells from adjacent liver sample of donor 20170327


title: Single cells from tumor sample of donor 20170222


title: 2RA_COPD_1_S2


title: Single cells from blood sample of donor 20170412


title: 7RA_COPD_3_S43

value: Control


title: Single cells from adjacent liver sample of donor 20170322


title: 2RA_COPD_2_S17


title: 1RA_COPD_1_S46


title: 1RA_COPD_3_S52


title: 7RA_COPD_2_S28


title: Single cells from adjacent liver sample of donor 20170222


title: Single cells from blood sample of donor 20170222


title: 2RA_COPD_3_S32


title: Single cells from blood sample of donor 20170227


title: hSpt16-deltaA51R-4HPI- rep 3

city: Dallas

first: Dustin

middle: C

last: Hancks

state: Texas

address: 6000 Harry Hines Blvd

department: Immunology

institute: UT Southwestern Medical Center

data_processing:
fastq files were aligned to version 38 of human reference genome GRCh38 using STAR aligner v.2.5.2b  post removal of possible adpater seuqences and poor quiality nucelotides using Trimmomatic v.0.36
BAM files from alignments were summarized and unique gene hit counts calculated using featureCounts algorithms
Differential expression analysis by comparison of gene expression between the groups of samples was performed using DESeq2  and Wald test to generate p-values and log2 fold changes (p-values <0.05 and absolute log2 foldchange >1)
Differential expressed genes further filtered with abosulte log2fold change of >0.58 (≥ 1.5 fold) and an adjusted p-value of ≤ 0.01
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Matrix table(xlsx file) with raw gene counts for every gene and every sample

source_name: A549 cells expressing hSpt16 shRNA

extract_protocol:
Total RNA was extracted from frozen cell pellet samples using Qiagen RNeasy Plus Universal mini kit followed by Manufacturer’s instructions (Qiagen, Hilden, Germany).
RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA).      rRNA depletion was performed using Ribozero rRNA Removal Kit (Illumina, San Diego, CA, USA).  RNA sequencing library preparation used NEBNext Ultra RNA Library Prep Kit for Illumina by following the manufacturer’s recommendations (NEB, Ipswich, MA, USA). Briefly, enriched RNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized.  cDNA fragments were end repaired and adenylated at 3’ends, and universal adapter was ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated using the Agilent Tapestation 4200 (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (Applied Biosystems, Carlsbad, CA, USA).     The sequencing libraries were clustered on two lanes of a flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions.  The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.

value: lung adenocarcinoma


title: 7RA_COPD_1_S13


title: 16RA_COPD_3_S40


title: 16RA_COPD_2_S25


title: hSpt16-deltaA51R-4HPI- rep 2


title: 15RA_COPD_2_S23


title: pLKO1-deltaA51R-4HPI- rep 1

source_name: A549 cells expressing control shRNA


title: 15RA_COPD_3_S38


title: 15RA_COPD_1_S8


title: hSpt16-deltaA51R-4HPI- rep 1


title: 16RA_COPD_1_S10


title: 11RA_COPD_2_S20


title: hSpt16-deltaA51RFA51R-4HPI- rep 3


title: 11RA_COPD_1_S5


title: pLKO1-deltaA51R-4HPI- rep 3


title: hSpt16-deltaA51RFA51R-4HPI- rep 2


title: pLKO1-deltaA51R-4HPI- rep 2


title: 11RA_COPD_3_S35


title: 8RA_COPD_3_S33


title: pLKO1-deltaA51RFA51R-4HPI- rep 3


title: 8RA_COPD_1_S3


title: 14RA_COPD_3_S36


title: hSpt16-Mock-4HPI- rep 3

value: Mock-infected


title: COPD_9RA4_3_S45


title: pLKO1-deltaA51RFA51R-4HPI- rep 1


title: 14RA_COPD_2_S21


title: pLKO1-Mock-4HPI- rep 3


title: hSpt16-deltaA51RFA51R-4HPI- rep 1


title: pLKO1-deltaA51RFA51R-4HPI- rep 2


title: hSpt16-Mock-4HPI- rep 2


title: 14RA_COPD_1_S6


title: hSpt16-Mock-4HPI- rep 1


title: COPD_9RA4_2_S30


title: pLKO1-Mock-4HPI- rep 2


title: COPD_9RA4_1_S15


title: 8RA_COPD_2_S18


title: pLKO1-Mock-4HPI- rep 1


title: Quiescent_UC_20

city: Kaunas

first: Rūta

last: Inčiūraitė

address: Mickeviciaus st. 9

country: Lithuania

institute: Lithuanian University of Health Sciences

data_processing:
Processing of the raw reads: nf-core/smrnaseq v1.0.0 analysis pipeline with default parameters and "illumina" protocol to process .fastq files (Nextflow version v20.01.0)
Trimming of adapter sequences: Trim Galore (v0.6.3) to remove 3’ adapter (5’ - TGGAATTCTCGGGTGCCAAGG - 3’) sequences from the reads
Collapsing and alignment of the reads: seqcluster to collapse reads with identical sequences and Bowtie1 v1.2.2 to align collapsed reads against mature and hairpin miRNA sequences in miRbase database v22.1
MiRNA annotation: mirTOP v0.4.23 to annotate miRNA
Genome_build: Ensembl build GRCh37
Supplementary_files_format_and_content: Tab-separated values (.tsv) file includes miRNA and iso-miRNA counts for all samples

source_name: Colon tissue

extract_protocol:
Standard protocol of miRNeasy Mini Kit (Qiagen)
TruSeq Small RNA Sample Preparation Kit (Illumina)

value: Male

tag: height (cm)

tag: weigth (kg)

tag: stool frequency (mayo subscore)

tag: rectal bleeding (mayo subscore)

tag: endoscopic mayo subscore

tag: global assessment score (mayo subscore)

tag: mayo score


title: COPD_2LC4B_3_S54

tag: treatment

value: Porcine elastase + Lipopolysaccharide


title: Quiescent_UC_19

tag: gender

value: Female

tag: age

value: #N/A


title: COPD_2LC4B_1_S48


title: Quiescent_UC_18


title: 8LC3_COPD_3_S53


title: Quiescent_UC_16


title: 8LC3_COPD_2_S50


title: COPD_2LC4B_2_S51


title: Quiescent_UC_17


title: 1LC_COPD_2_S16


title: 8LC3_COPD_1_S47


title: 18LC_COPD_1_S12


title: 1LC_COPD_3_S31


title: Quiescent_UC_11


title: Quiescent_UC_15


title: 1LC_COPD_1_S1


title: Quiescent_UC_12


title: Quiescent_UC_14


title: Quiescent_UC_9


title: Quiescent_UC_10


title: Quiescent_UC_13


title: 18LC_COPD_2_S27


title: Quiescent_UC_8


title: Quiescent_UC_7


title: 16LC_COPD_1_S11


title: 16LC_COPD_2_S26


title: 18LC_COPD_3_S42


title: Quiescent_UC_6


title: 15LC_COPD_2_S24


title: 16LC_COPD_3_S41


title: 15LC_COPD_3_S39


title: Quiescent_UC_5


title: Quiescent_UC_3


title: 14LC_COPD_2_S22


title: Quiescent_UC_4


title: 14LC_COPD_3_S37


title: Quiescent_UC_2


title: Active_UC_22


title: Active_UC_21


title: 14LC_COPD_1_S7


title: Active_UC_20


title: 11LC3_COPD_2_S29


title: Quiescent_UC_1


title: 10LC_COPD_3_S34


title: 10LC_COPD_2_S19


title: 11LC3_COPD_1_S14


title: 10LC_COPD_1_S4


title: Active_UC_18


title: Spleen_wk3_control littermate_rep_7

first: Heekyong

last: Bae

address: Building 560, Room 31-23, NCI at Frederick

institute: National Cancer Institute

description: Gene expression in spleen from ARE-Del control littermate at 3 weeks of age

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Spleen, wk3, control littermate, rep_7

extract_protocol: RNA was extracted from the spleen, thymus, kidney, and blood collected from homozygous and heterozygous ARE-Del mice at 3, 6, and 12 weeks of age, and comparisons were made with control littermates.

value: female

value: spleen

tag: genotype

value: wt


title: 15LC_COPD_1_S9


title: Active_UC_17


title: Active_UC_16


title: Basal condition rep2

city: Johannesburg

first: Wai Yin

last: Chan

state: Gauteng

address: 1 Modderfontein Road, Sandringham,

country: South Africa

institute: National Institute for Communicable Disease

description: Control (Laboratory condition using PDA media) 2

data_processing:
Raw reads were quality controlled and filtered (Q>5 and length > 50 bp) using FastQC (v0.11.8) and trim Galore (v0.6.2; https://github.com/FelixKrueger/TrimGalore), respectively.
Transcript quantification was performed by quasi-mapping the clean reads onto the genome of B. bassiana strain ARSEF 2860 as the reference, using Salmon 1.5.2
Differentially expressed genes (DEGs) were identified using DESeq2 (version 1.18.1)
In conjuction with Salmon read abundance quantification tool
Supplementary files format and content: tab-delimited text files include Transcripts per million (TPM)  values for each Sample

organism: Beauveria bassiana

source_name: B. bassiana SAN01

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
Library was constructed using Nextera DNA Flex Library Prep Kit

treatment_protocol: Beauveria bassiana was grown banana corm extract, on wheat bran and potato dextrose broth to depict the different trophic/environmental conditions.

tag: cell type

value: B. bassiana SAN01


title: Basal condition rep1

description: Control (Laboratory condition using PDA media) 1

growth_protocol: Beauveria bassiana was grown banana corm extract, on wheat bran and potato dextrose broth


title: 11LC3_COPD_3_S44


title: Fermentation condition rep1

description: Fermentation/ Saprophytic 1 (Wheat bran)


title: Active_UC_23


title: Active_UC_19


title: 110_36h_2

city: Yunnan Kunming

first: xie

middle: mei

last: hua

address: 121 street

institute: Yunnan university

data_processing:
The data from high-throughput sequencing were analyzed using the OmicShare tools, a free online platform for data analysis (www.majorbio.com).
Genome_build: https://www.ncbi.nlm.nih.gov/assembly/GCF_000225545.1
Supplementary_files_format_and_content: Expression analysis table include TPM values for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Orbilia oligospora

source_name: Arthrobotrys oligospora and nematode

growth_protocol: The WT and ΔAoswi6 mutant strains were cultured in PD shaking at 28 °C, 180 rpm for 5 days.

extract_protocol: The mycelium was divided and induced with about 600 nematodes for 0, 12, 24, and 36 h, respectively.

treatment_protocol: Mycelium was collected and washed three times with 0.1 Mphosphate buffer saline (PBS) (pH 6.8-7.2).

value: Fungal hyphae

tag: time point


title: 110_24h_2


title: 110_36h_1


title: 110_24h_3


title: 110_24h_1


title: 110_12h_3


title: Endophytic condition rep1

description: Endophytic condition 1 Banana corm extract (Freeze dried)


title: Active_UC_12


title: 110_12h_1


title: Active_UC_11


title: 110_0h_3


title: Active_UC_10


title: 110_0h_1


title: 110_0h_2


title: Active_UC_15


title: Fermentation condition rep2

description: Fermentation/ Saprophytic 1 (Oatmeal)


title: 110_36h_3


title: AO_36h_3


title: Active_UC_14


title: Endophytic condition rep2

description: Endophytic condition 2 Banana corm extract (Crude liquid extract)


title: AO_36h_2


title: AO_36h_1


title: Active_UC_13


title: 110_12h_2


title: AO_24h_3


title: Active_UC_7


title: AO_24h_1


title: AO_24h_2


title: AO_12h_3


title: Active_UC_9


title: AO_0h_3


title: AO_0h_2


title: Active_UC_4


title: AO_0h_1


title: Active_UC_8


title: AE-IPF_4

city: Shenyang,

first: Jia

middle: Ran

last: Wang

state: Liaoning

address: No. 79 Chongshan East Road, Huanggu District,

institute: Liaoning University of Traditional Chinese Medicine

description: lncRNAs,circRNAs, miRNAs,mRNAs

hyb_protocol: Data were extracted with Feature Extraction software 12.0.3.1 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm. The microarray experiments were performed by following the protocol of Agilent technologies at LC Sciences Corporation（Hangzhou，China）.RNA samples of each group were then used to generate biotinylated cRNA targets for the LC Human ceRNA array V1.0（4*180K, Design ID:085202）.

scan_protocol: The biotinylated cRNA targets were then hybridized with the slides. After hybridization, slides were scanned on the Agilent Microarray Scanner G5761A (Agilent technologies, Santa Clara, CA, US).

data_processing:
Data were extracted with Feature Extraction software 12.0.3.1 (Agilent technologies, Santa Clara, CA, US).
Raw data were normalized by Quantile algorithm. The microarray experiments were performed by following the protocol of Agilent technologies at LC Sciences Corporation (Hangzhou, China)

source_name: whole blood

label_protocol: Total RNA was checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

extract_protocol: Total RNA was isolated using RNA Isolation Kit #58000(Norgen, Canada) according to the manufacturer’s instructions, and purified by using a RNeasy Mini Kit (Qiagen, Germany) .

tag: disease state

value: Acute exacerbation of idiopathic pulmonary fibrosis (AE-IPF)

value: whole blood


title: B.bovis tick 3

city: Pullman

first: Massaro

middle: Wilson

last: Ueti

state: Washington

address: 3003 ADBF Washington State Univ, 3003 ADBF, Grimes Way

institute: USDA ARS Animal Disease Research Unit

description:
L4P15
RNAseqHemocytes_all_with raw reads count 09182023.xlsx

data_processing:
HiSeq control software HCS 2.2.58 RTA 1.18.64
TopHat v2.0.12 alignment
HTC v 0.6.1 counts
edgeR 3.12.1. DE analysis
Supplementary files format and content: Excel with  RefSeq_ID/ baseMean mapped counts /fold change/ log2FoldChange / lfcSE / stat / pvalue / padj

organism: Rhipicephalus microplus

source_name: hemolymph

extract_protocol:
TriZol extraction
Illumina TruSeq mRNA, poly A selected

value: hemolymph

value: hemocyte

tag: infection

value: Babesia infected


title: B.bovis tick 2

description:
L4P14
RNAseqHemocytes_all_with raw reads count 09182023.xlsx


title: B.bovis tick 1

description:
L4P13
RNAseqHemocytes_all_with raw reads count 09182023.xlsx


title: Active_UC_5


title: AO_12h_2

state: Yunnan


title: uninfected tick 3

description:
L4P9
RNAseqHemocytes_all_with raw reads count 09182023.xlsx

value: uninfected


title: AE-IPF_3

description: lncRNAs,circRNAs, miRNAs,mRNAs


title: AE-IPF_2

description: lncRNAs,circRNAs, miRNAs,mRNAs

value: male


title: AE-IPF_5

description: lncRNAs,circRNAs, miRNAs,mRNAs


title: Active_UC_1


title: AE-IPF_1

description: lncRNAs,circRNAs, miRNAs,mRNAs


title: uninfected tick 2

description:
L4P8
RNAseqHemocytes_all_with raw reads count 09182023.xlsx