title: AO_12h_1


title: MSS Left Colon Cancer [Control]

status: Public on Dec 31 2023

type: RNA

city: Braamfontein

first: Michelle

middle: Lynn

last: McCabe

state: Gauteng

address: National Health Laboratory Services, Corner Hospital and De Korte street

department: Human Genetics

country: South Africa

institute: NHLS

description:
Control
Qiagen miHS-102Z miScript miRNA PCR Array Human Cancer Pathway Finder

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: https://dataanalysis.qiagen.com/mirna/arrayanalysis.php
For the normalization it uses the average of six housekeeping genes: SNORD61, SNORD68, SNORD72, SNORD95, SNORD6196A, RNU6-6P.
Target gene signals normalized to housekeeping genes; 2^(-Avg.(Delta(Ct)), where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Matrix normalized worksheet reports normalized signal (against housekeeping genes).
Fold Change worksheet reports test/control (i.e., MSI-L LCC/MSS LCC) ratios.

label: SYBR Green

molecule: total RNA

organism: Homo sapiens

source_name: FFPE tumour tissue

label_protocol: PCR assays were performed using the miHS-102Z miScript miRNA PCR Array Human Cancer Pathway Finder (QIAGEN) following the Manufacturer’s instructions. Reverse transcription was performed from 250 ng total RNA using the miScript II RT kit for cDNA synthesis  (QIAGEN)). Quantitative real-time PCR were performed (Applied Biosystems® 7500 ) with initial activation step at 95oC for 15 seconds and 40 cycles at 94 oC for 15 seconds , 55 oC for 30 seconds and 70oC for 30 seconds.

extract_protocol: Total RNA was extracted with the Rneasy FFPE Kit followed by DNase I treatment.

tag: disease state

value: Colon Cancer

tag: tissue

value: Tumour FFPE tissue

tag: Stage

value: Stage II-III


title: uninfected tick 1

type: SRA

city: Pullman

first: Massaro

middle: Wilson

last: Ueti

state: Washington

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

country: USA

institute: USDA ARS Animal Disease Research Unit

description:
L4P7
RNAseqHemocytes_all_with raw reads count 09182023.xlsx

library_source: transcriptomic

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

tag: cell type

value: hemocyte

tag: infection

value: uninfected


title: Active_UC_3

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)

tag: gender

value: Female

tag: age

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: B.bigemina tick 3

description:
L4P6
RNAseqHemocytes_all_with raw reads count 09182023.xlsx

value: Babesia infected


title: MSS Right colon cancer [Test]

description:
Test
Qiagen miHS-102Z miScript miRNA PCR Array Human Cancer Pathway Finder


title: B.bigemina tick 2

description:
L4P5
RNAseqHemocytes_all_with raw reads count 09182023.xlsx


title: MSI-L Left colon cancer [Test]


title: Active_UC_6

value: Male


title: B.bigemina tick 1

description:
L4P4
RNAseqHemocytes_all_with raw reads count 09182023.xlsx


title: AP2EXP_TGCATGCA_AP2_Domain1_rep2

type: protein

city: State College

first: Manuel

last: Llinás

state: Pennsylvania

address: W122 Millennium Science Complex, Pollock Road

department: Biochemistry and Molecular Biology

institute: Pennsylvania State University

description:
Plasmodium falciparum protein expressed in BL21-CodonPlus(DE3)-RIL E. coli
Testing the binding of the only APETALA2 (AP2) domain of AP2-EXP protein to the TGCATGCA motif surrounded by P. falciparum genomic context, replicate 2

hyb_protocol: Each purified GST-tagged DNA-binding domain protein stock was validated for DNA-binding specificity using 4x44k universal protein-binding microarrays (Agilent Technologies) as detailed in the previously published protocol (Berger et al. 2009) before testing on the Plasmodium falciparum-specific genomic-context protein-binding microarray (gcPBM) design. Amounts of recombinant protein necessary for robust DNA binding was empirically determined during these universal PBM experiments (average amount added around 25μg; identified by A280 signal on NanoDrop 2000 Spectrophotometer [Thermo Scientific]). The single-stranded gcPBM DNA microarray was double-stranded by solid-state primer extension as detailed in the published protocol (Berger et al. 2009). The 24bp primer sequence (5`-GTCTTGATTCGCTTGACGCTGCTG-3`) was used to double-strand all gcPBM slides for this study. The major components of the protein-binding mixture are as follows: 1% milk, 0.2mg/mL BSA, 0.5% salmon testes DNA, and 0.03% TritonX-100 in 1xPBS. The protein-binding microarray method includes 5 major steps with 1xPBS with 0.01-0.5% Tween20 washes in between each step: (1) Blocking the microarray with 2% milk in 1xPBS for one hour in the dark, (2) Applying the protein-binding mixtures to the microarray for one hour, (3) Probing protein-DNA interactions with an anti-GST, rabbit IgG, Alexa488-conjugated antibody (1:40 dilution in 2% milk blocking solution; Invitrogen, A11131) for one hour, (4) Scanning the microarray for Alexa488 signal (GenePix Pro version 7.2 software), and (5) Identifying enriched DNA sequence using a gapped 8-mer DNA motif-searching perl script modified from original script to normalize only based on local neighboring probes instead of Cy3 signal introduced from double-stranding the microarray.

scan_protocol: Immediately after completing the gcPBM experiment, each microarray chamber was scanned using the GenePix 4400A Microarray Scanner (Molecular Devices) at a resolution of 2.5μm, with the 488nm wavelength laser, along with the GenePix Pro7 software to generate image files (.tif).

data_processing:
The image files were aligned with the GenePix Array List (.gal) file to associate raw signal intensity to the P. falciparum genome-derived DNA sequences, which generates a GenePix Results (.gpr) file. The .gpr files were then further processed and normalized using the previously published Masliner script and downstream analysis made by the Bulyk lab and modified by the Gordân lab31,33,78,79.
Final values used for this study are a single data point representing the highest natural log median binding intensity value between either the 5` or 3` orientation replicates for each DNA sequence.

label: Anti-GST, Alexa488 conjugate antibody (Invitrogen A11131)

molecule: protein

organism: Plasmodium falciparum

source_name: Binding of the only APETALA2 (AP2) domain of AP2-EXP protein with N-terminal GST tag, technical replicate 2

label_protocol: Each protein was expressed with an N-terminal GST tag from cloning the DNA-binding domain sequenc into the pGEX-4-T1 vector (GE Life Sciences).

growth_protocol: Each AP2 domain or homeodomain was previously cloned into the pGEX-4-T1 vector (GE Life Sciences) and transformed into BL21-CodonPlus(DE3)-RIL E. coli (Stratagene) for protein production (De Silva et al. 2008 & Campbell et al. 2010). From an overnight starter culture, cells were grown in Luria broth (LB) with 100μg/mL ampicillin (AMP) and 50μg/mL chloramphenicol (CAM) at 37C (constantly shaking at 210 rpm) until OD600=0.5 then transferred to room temperature. Once culture equilibrated to room temperature, the cells were induced overnight (~16 hours) using 0.2mM Isopropyl β-d-1-thiogalactopyranoside (IPTG), while constantly shaking at 210 rpm.

extract_protocol: The cells were subsequently sonicated on ice (Branson Digital Sonifier) in Complete GST Buffer (25mM Tris-HCl [pH 8.0], 30mM NaCl) at 45% amplitude (0.5 seconds on and 0.5 seconds off during 30-second intervals) with a 1cm-diameter tip until sufficient cell lysis (3-7 rounds). Then recombinant proteins were each purified using GST-affinity purification beads (Thermo Scientific Pierce Glutathione Superflow Agarose beads), eluted in fresh elution buffer (50mM Tris-HCl [pH 8.0], 0.075w/v% L-glutathione reduced, 2x protease inhibitors), and stored as single-use aliquots in 25% glycerol stocks at -80C. Verification of a successful GST-tagged protein purification was demonstrated by running protein samples on 4-15% stacking SDS-PAGE gel and stained with Coomassie Blue. Integrity of GST tag was subsequently checked via Western blotting of the purified recombinant protein using anti-GST antibodies (Invitrogen 71-7500) [1:1,500 dilution].

tag: strain

value: Sequence from P. falciparum 3D7 strain

tag: product

value: Recombinant DNA-binding domain from GST-affinity purification


title: Symptomatic_control_32


title: Symptomatic_control_31


title: S-IPF_2

city: Shenyang,

first: Jia

middle: Ran

last: Wang

state: Liaoning

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

country: China

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) .

value: stable IPF (S-IPF)

value: whole blood

value: female


title: AP2EXP_TGCATGCA_AP2_Domain1_rep1

description:
Plasmodium falciparum protein expressed in BL21-CodonPlus(DE3)-RIL E. coli
Testing the binding of the only APETALA2 (AP2) domain of AP2-EXP protein to the TGCATGCA motif surrounded by P. falciparum genomic context, replicate 1

source_name: Binding of the only APETALA2 (AP2) domain of AP2-EXP protein with N-terminal GST tag, technical replicate 1


title: MSI-L Riight colon cancer [Test]


title: S-IPF_1

description: lncRNAs,circRNAs, miRNAs,mRNAs


title: S-IPF_5

description: lncRNAs,circRNAs, miRNAs,mRNAs

value: male


title: S-IPF_3

description: lncRNAs,circRNAs, miRNAs,mRNAs


title: Symptomatic_control_30


title: HDP1_GTGCAC_HD_Domain1

description:
Plasmodium falciparum protein expressed in BL21-CodonPlus(DE3)-RIL E. coli
Testing the binding of the only homeodomain (HD) of HDP1 protein to the GTGCAC motif surrounded by P. falciparum genomic context

source_name: Binding of the only homeodomain (HD) of HDP1 protein with N-terminal GST tag


title: AP2G_GTAC_AP2_Domain1_rep2

description:
Plasmodium falciparum protein expressed in BL21-CodonPlus(DE3)-RIL E. coli
Testing the binding of the only APETALA2 (AP2) domain of AP2-G protein to the GTAC motif surrounded by P. falciparum genomic context, replicate 2

source_name: Binding of the only APETALA2 (AP2) domain of AP2-G protein with N-terminal GST tag, technical replicate 2


title: LasPlant_rep3

city: Beijing

first: Xuncheng

address: 5 Yiheyuan Road

institute: Peiking University

description: polyA RNA isolated

data_processing:
RNA-seq reads were then mapped to the Las1 genome using hisat2 with default parameters (99). Differential expression was assessed using the R/Bioconductor package limma (v.3.0.8) (100). Genes with an FDR < 0.05 and a fold change >1.5, as determined by limma, were identified as differentially expressed.
Genome_build: Las1 in L. theobromae
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

molecule: polyA RNA

organism: Lasiodiplodia theobromae

source_name: fungal mycelia

growth_protocol: The L. theobromae strain Las1 was selected for inoculation tests on detached Vitis vinifera cv. ‘Summer Black’ branches. Briefly, wounds of green grapevine shoots were inoculated with mycelium plugs (5 mm in diameter) cut with a cork borer and then maintained under an alternating dark/light cycle inside a growth chamber with constant humidity and a temperature of 25 °C. All the inoculated grapevine tissues were collected at 24 h post-inoculation, and fungal mycelia collected from PDA at 24 h post-culturing at 25 °C were used for subsequent RNA-seq analyses.

extract_protocol:
Total RNA was extracted and processed following Novogene Company methodologies for preparing Illumina RNA-seq libraries.
First- and second-strand cDNAs were generated using SuperScript II reverse transcriptase (Invitrogen) and random hexamer primers. Double-stranded cDNAs were fragmented by nebulization and used for RNA-seq library construction following the  Novogene Company methods.

value: L.theobromae in plant

value: mycelia


title: AP2G_GTAC_AP2_Domain1_rep1

description:
Plasmodium falciparum protein expressed in BL21-CodonPlus(DE3)-RIL E. coli
Testing the binding of the only APETALA2 (AP2) domain of AP2-G protein to the GTAC motif surrounded by P. falciparum genomic context, replicate 1

source_name: Binding of the only APETALA2 (AP2) domain of AP2-G protein with N-terminal GST tag, technical replicate 1


title: Symptomatic_control_29


title: AP2HC_CACACA_AP2_Domain1

description:
Plasmodium falciparum protein expressed in BL21-CodonPlus(DE3)-RIL E. coli
Testing the binding of the only APETALA2 (AP2) domain of AP2-HC protein to the CACACA motif surrounded by P. falciparum genomic context

source_name: Binding of the only APETALA2 (AP2) domain of AP2-HC protein with N-terminal GST tag


title: SIP2_GTGCAC_AP2_Domain1

description:
Plasmodium falciparum protein expressed in BL21-CodonPlus(DE3)-RIL E. coli
Testing the binding of the first APETALA2 (AP2) domain of SIP2 protein to the GTGCAC motif surrounded by P. falciparum genomic context

source_name: Binding of the first APETALA2 (AP2) domain of SIP2 protein with N-terminal GST tag


title: LasPlant_rep2

description: polyA RNA isolated


title: AP2I_GTGCAC_AP2_Domain3_rep2

description:
Plasmodium falciparum protein expressed in BL21-CodonPlus(DE3)-RIL E. coli
Testing the binding of the third APETALA2 (AP2) domain of AP2-I protein to the GTGCAC motif surrounded by P. falciparum genomic context, replicate 2

source_name: Binding of the third APETALA2 (AP2) domain of AP2-I protein with N-terminal GST tag, technical replicate 2


title: LasPlant_rep1

description: polyA RNA isolated


title: Symptomatic_control_27


title: Symptomatic_control_28


title: AP2LT_CACACA_AP2_Domain1_rep2

description:
Plasmodium falciparum protein expressed in BL21-CodonPlus(DE3)-RIL E. coli
Testing the binding of the only APETALA2 (AP2) domain of AP2-LT protein to the CACACA motif surrounded by P. falciparum genomic context, replicate 2

source_name: Binding of the only APETALA2 (AP2) domain of AP2-LT protein with N-terminal GST tag, technical replicate 2


title: Las_rep3

description: polyA RNA isolated

value: L.theobromae in PDA


title: S-IPF_4

description: lncRNAs,circRNAs, miRNAs,mRNAs


title: AP2I_GTGCAC_AP2_Domain3_rep1

description:
Plasmodium falciparum protein expressed in BL21-CodonPlus(DE3)-RIL E. coli
Testing the binding of the third APETALA2 (AP2) domain of AP2-I protein to the GTGCAC motif surrounded by P. falciparum genomic context, replicate 1

source_name: Binding of the third APETALA2 (AP2) domain of AP2-I protein with N-terminal GST tag, technical replicate 1


title: Symptomatic_control_26


title: AP2LT_CACACA_AP2_Domain1_rep1

description:
Plasmodium falciparum protein expressed in BL21-CodonPlus(DE3)-RIL E. coli
Testing the binding of the only APETALA2 (AP2) domain of AP2-LT protein to the CACACA motif surrounded by P. falciparum genomic context, replicate 1

source_name: Binding of the only APETALA2 (AP2) domain of AP2-LT protein with N-terminal GST tag, technical replicate 1


title: PF3D70420300_CACACA_AP2_Domain1

description:
Plasmodium falciparum protein expressed in BL21-CodonPlus(DE3)-RIL E. coli
Testing the binding of the first APETALA2 (AP2) domain of PF3D7_0420300 protein to the CACACA motif surrounded by P. falciparum genomic context

source_name: Binding of the first APETALA2 (AP2) domain of PF3D7_0420300 protein with N-terminal GST tag


title: Las_rep2

description: polyA RNA isolated


title: E. coli W grown in a minimal M9 medium supplemented with L-cysteine replicate 2

city: San Diego

first: Bernhard

middle: O.

last: Palsson

state: California

address: 9500 Gilman Dr

department: Bioengineering

institute: University of California, San Diego

data_processing:
Raw-sequencing reads were aligned to the reference genome of the MG1655 strain (accession number: NC_000913.3) using Bowtie. Transcripts per million (TPM) calculation and differentially expressed genes were obtained by DESeq2 (v1.22.1).
Assembly: NC_000913.3
Supplementary files format and content: csv and log tpm

organism: Escherichia coli W

source_name: ATCC 9637

growth_protocol: E. coli W was grown in the presence and the absence of Cys. Pre-cultures were prepared in the LB medium. Overnight cultured cells were washed twice with the M9 medium and inoculated at an OD600 of 0.05 in the same medium. RNA sequencing data were generated under aerobic exponential growth conditions in M9 medium and supplemented with 5 mM Cys. The cells were collected at an OD600 of 0.6.

extract_protocol:
Cells were treated using the Qiagen RNA-protect bacterial reagent (Hilden, Germany) according to the instruction from the manufacturer. Pelleted cells were stored at -80oC, and after cell resuspension and partial lysis, they were ruptured with a beat beater. Subsequently, the total RNA was extracted using a Qiagen RNA purification kit. After total RNA extraction, ribosomal RNA was removed and the quality was assessed using an Aglient Bioanalyser using an RNA 6000 kit.
Paired-end RNA sequencing libraries were prepared by using a KAPA RNA HyperPrep kit from Kapa Biosystems (Wilmington, MA, USA)

tag: genotype

value: W wildtype

tag: carbon sources

value: Glucose

tag: supplements


title: Symptomatic_control_25

value: #N/A


title: E. coli W grown in a minimal M9 medium supplemented with L-cysteine replicate 1


title: Las_rep1

description: polyA RNA isolated

tag: tissue


title: E. coli W grown in a minimal M9 medium replicate 2


title: Symptomatic_control_24


title: E. coli W grown in a minimal M9 medium replicate 1


title: sldml2_season1_2

city: Shenzhen

first: yujing

last: lin

address: No. 1088 Xueyuan Avenue, Nanshan District, Shenzhen City, Guangdong Province

institute: Southern University of Science and Technology

library_source: genomic

data_processing:
To remove low-quality sequence and adapters via Trimmomatic (Bolger, Lohse, & Usadel, 2014) was used
The paired-end reads were mapped to the SL4.0 genome of Solanum lycopersicum by BSMAP with -r parameter to remove PCR duplications
To extract methylation ratio with methyratio.py script from BASMAP
DMRs and DMCs were identified using the R packages, methylKit (Akalin et al., 2012)
Genome_build: SL4.0
Supplementary_files_format_and_content: Bigwig files that represent the number of reads that contain methylated sites

molecule: genomic DNA

organism: Solanum lycopersicum

source_name: Fruits

growth_protocol: Wild type tomato (Solanum lycopersicum) Ailsa Craig (AC), NAC-NOR CRISPR mutant (slnor), and SlDML2 CRIPSR mutant (sldml2) plants (AC background) were grown in a condition-controlled greenhouse (16 h:8 h, 25 ℃:20 ℃, light:dark cycle).

extract_protocol:
WGBS was performed according to a previous published protocol (Zhang et al., 2016).
DNA samples were sent to LC-Bio Technologies (Hangzhou) CO., LTD. (Hangzhou, China) for library construction and sequencing or sent to the Genomics Core Facilities of the Shanghai Center for Plant Stress Biology, SIBS, CAS (Shanghai, China) for library construction and Illumina sequencing.

value: fruit

tag: cultivar

value: Ailsa Craig (AC)

tag: season

tag: replicate


title: Symptomatic_control_23

source_name: Colon tissue

tag: gender

value: Female

tag: age


title: sldml2_season1_1


title: SEDM_Nrf2KO2

city: University Pk

first: Robert

last: Paulson

state: PA

address: 115 Henning Building, Penn State University

department: Veterinary and Biomedical Sciences

institute: Penn State University

data_processing:
After raw sequencing reads were filtered, clean reads were aligned to the GRCm38 mouse reference genome with HISAT2 (v2.2.0).
The output was processed by SAMtools (v1.4) to generate sorted BAM files.
Gene expression (fragments per kilobase of exon model per million reads mapped, FPKM) was quantified by StringTie (v2.1.4).
The output was processed by DESeq2 (v1.30.1) to perform differential gene expression analysis.
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Mus musculus

source_name: Stress erythroid progenitor cells

growth_protocol: Bone marrow cells were obtained by flushing femur and tibia (cut both ends) with cold phosphate buffered saline (PBS). The marrow cells were thoroughly mixed and filtered through a 70 µm cell strainer. After red blood cell (RBC) lysis, the cells were filtered again and washed twice by PBS. To allow the expansion of SEPs, bone marrow cells were cultured in stress erythropoiesis expansion media (SEEM) at a starting concentration of 6 x 105 cells/ml for 5 days. For differentiation cultures, non-adherent cells harvested from SEEM cultures were resuspended in stress erythropoiesis differentiation media (SEDM) at 3 x 105 cells/ml, and they were seeded back to the original culture flask/dish to culture for another 3 days. SEEM was prepared by supplementing IMDM (Thermo Fisher Scientific) with 10% (v/v) FBS (R&D Systems), 0.0007% (v/v) 2-mercaptoethanol (Thermo Fisher Scientific), 0.01 g/ml BSA (Fisher Scientific), 10 µg/ml ciprofloxacin (Fisher Scientific), 2 mM L-glutamine (Thermo Fisher Scientific), 10 µg/ml insulin (Sigma-Aldrich), 200 µg/ml holo-transferrin (Alfa Aesar), 50 ng/ml murine SCF (GoldBio), 15 ng/ml human BMP4 (Thermo Fisher Scientific), 25 ng/ml murine SHH (GoldBio) and 30 ng/ml murine GDF15 (Biomatik). SEDM was prepared by additionally supplementing SEEM with 3 U/ml human Epo. SEEM were cultured in ambient air (20% O2), while SEDM were cultured in a hypoxia chamber (2% O2) to maximize differentiation potential. All cultures were incubated in 5% CO2 at 37 °C.

extract_protocol:
Total RNA was extracted from progenitor cells with TRIzol reagent (Thermo Fisher Scientific) and the quality of extracted RNA (concentration, total mass, RNA integrity and 28S/18S ratio) was validated on the Agilent 2100 Bioanalyzer.
The mRNA molecules were enriched from total RNA by VAHTS mRNA Capture Beads, followed by fragmentation to generate an insert size of 150 bp. After cDNA synthesis, double-stranded cDNA fragments were subjected to end repair and A-tailing. The adenylated cDNA products were ligated to adaptors and then amplified by PCR reaction. Purified PCR products were denatured and circularized to obtain the final library (single-stranded circle DNA). RNA sequencing was performed on a BGISEQ-500 sequencer with 50 bp single-end read length.

treatment_protocol: For expansion cultures, unfractionated WT bone marrow cells were cultured in Stress Erythropoiesis Expansion Medium (SEEM) for 3 days, followed by the addition of either vehicle (DMSO) or 10 μM 1400w for another 2 days. For differentiation cultures, WT and Nrf2-/- bone marrow cells were cultured in SEEM for 5 days, followed by switching to Stress Erythropoiesis Differentiation Medium (SEDM) medium for another 3 days. When cultured in SEDM, WT cells were treated with either vehicle or 1400w, and Nrf2-/- cells were treated with equal volume of vehicle. Samples were prepared in biological triplicates.

tag: developmental stage

value: Differentiation stage

tag: treatment

value: Vehicle (DMSO)


title: SEDM_Nrf2KO3


title: SEDM_WT_1400w2

value: Wild-type


title: slnor_season1_2

value: slnor


title: SEDM_WT_1400w3


title: SEDM_WT_1400w1


title: slnor_season1_1


title: SEDM_Nrf2KO1


title: Symptomatic_control_21

value: Male

tag: height (cm)

tag: weigth (kg)


title: WT_season1_2

value: WT


title: Symptomatic_control_20

tag: endoscopic mayo subscore


title: Symptomatic_control_22


title: WT_season1_1


title: Symptomatic_control_19


title: Symptomatic_control_18


title: SEEM_WT_1400w3

value: Expansion stage


title: SEDM_WT_CTL1


title: SEDM_WT_CTL3


title: SEEM_WT_1400w2


title: SEEM_WT_1400w1


title: SEEM_WT_CTL3


title: SEEM_WT_CTL2


title: Symptomatic_control_17


title: B2x27_p3r3

city: Berkeley

first: Dirk

last: Hockemeyer

state: CA

address: 400 Li Ka Shing Center

department: Department of Molecular & Cell Biology

institute: University of California, Berkeley

library_source: other

data_processing:
Raw sequencing files were demultiplexed on Illumina BaseSpace.
Sequencing reads were trimed to 150bp.
Reads were aligned to reference amplicon sequences and quantifiled with CRISPResso2.
Assembly: BRCA2 exon 2 reference sequence,  ttccagcgcttctgagttttacctcagtcacataataaggaatgcatccctgtgtaagtgcattttggtcttctgttttgcagacttatttaccaagcattggaggaatatcgtaggtaaaaatgcctattggatccaaagagaggccaacattttttgaaatttttaagacacgctgcaacaaagcaggtattgacaaattttatataactttataaattacaccgagaaagtgttttctaaaaaatgcttgctaaaaacccagtacgtcaca; BRCA2 exon 27 reference sequence, tgtaaaggggagaaagagattgatgaccaaaagaactgcaaaaagagaagagccttggatttcttgagtagactgcctttacctccacctgttagtcccatttgtacatttgtttctccggctgcacagaaggcatttcagccaccaaggagttgtggcaccaaatacgaaacacccataaagaaaaaagaactgaattctcctcagatgactccatttaaaaaattcaatgaaatttctcttttggaaagtaattcaatagctgacgaagaacttgc
Supplementary files format and content: plain text, aligned allele sequences and quantification
Library strategy: Amplicon sequencing

molecule: other

growth_protocol: Human pluripotent cells were cultured on 4.1x105/cm2 irradiated mouse embryonic fibroblasts (MEF) in hPSC medium (Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12 (DMEM/F12), 20% KnockOut Serum Replacement (KOSR), 1x Non-Essential Amino Acids (NEAA), 1mM Glutamine, 1x penicillin/streptomycin, 0.1mM ß-mercaptoethanol and 4 ng/ml heat-stable basic FGF). The culture medium was changed daily, and cells were passaged with 1mg/ml collagenase IV every 5-7 days. The day before and after passage, the medium was supplemented with 10µM Y27632 (CD0141, Chemdea) to increase cell survival.

extract_protocol:
Phenol-chloroform extraction for genomic DNA
Using primers containing NGS barcode attachment sites (GCTCTTCCGATCT), the mutagenized regio was amplified with GXL DNA polymerase. Amplicons were then purified using an automated SPRI beads purification protocol at the UC Berkeley DNA Sequencing Facility, i5/i7 barcoded and pooled.

treatment_protocol: Drug sensitivity screening was started on day 21 with at least 0.3 million cells were used in each replicate, and cells were collected on day 28.

tag: cell line

tag: cell type

value: Embryonic stem cells (ESCs)

value: BRCA2 loHAPs

tag: time

value: Day 21


title: B2x27_p3r2

tag: genotype


title: SEEM_WT_CTL1

tag: strain


title: Symptomatic_control_15


title: Hi-C_pig_spleen_r1

city: Yangzhou

first: yu

middle: zhuo

last: li

state: 江苏省

address: No. 88, daxuenanlu Road

department: veterinary

institute: Yangzhou University

data_processing:
The clean Hi-C reads were iteratively mapped to the pig genome by the HiC-Pro v3.1.0 (Servant et al., 2015). We pooled the valid pairs of the two replicates together for further analysis.
The TAD structure (insulation/boundaries) was defined with Arrowhead by juicer tools v1.6 (Durand et al., 2016b).
Loops of Hi-C data were analyzed by HiCCUPS (Rao et al., 2014) with minor modifications. The resolution parameter was set as “-r 5000,10000,25000 --ignore_sparsity”.
Assembly: Sscrofa11
Supplementary files format and content: hic file for the interaction matrix
Supplementary files format and content: BED file for the identified TADs
Supplementary files format and content: BED file for the identified loops

organism: Sus scrofa

source_name: spleen

extract_protocol: Hi-C experiments were performed following previous study (Lieberman-Aiden et al., 2009) with slight modifications. In brief, following cross-linking with 1% formaldehyde and nuclei extraction, the chromatin was digested with Dpn Ⅱ and labeled with biotinylated residue after the 5' overhangs were filled. Blunt-end ligation of crosslinked DNA fragments was performed to obtain circular molecules, and then the DNA product was purified and sonicated into DNA fragments. Hi-C library was constructed by capturing the labeled target DNA fragments with biotin labeling precipitation technique followed by size selection. Finally, the obtained Hi-C library was sequenced by BGI company as 150 bp paired-end reads on DNBSEQ platform.

value: spleen


title: Symptomatic_control_16


title: SEDM_WT_CTL2


title: B2x27_p3r1


title: Hi-C_pig_spleen_r2


title: Symptomatic_control_14


title: Symptomatic_control_13


title: Symptomatic_control_12


title: Symptomatic_control_11


title: B2x27_p2r2

value: Day 14


title: B2x27_p2r1


title: B2x27_p1r3

value: Day 7


title: B2x27_p1r2


title: Symptomatic_control_10


title: B2x27_p1r1


title: B2x27_p2r3


title: Symptomatic_control_9


title: B2x27_Or3

value: Olaparib


title: B2x27_Or2


title: Symptomatic_control_8


title: Symptomatic_control_7


title: B2x27_Or1


title: Symptomatic_control_6


title: B2x27_Nr3

value: Niraparib


title: HNC098_TestingSet

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: Gene-level signal were derived from CEL files using sst-RMA algorithm implemente in Affymetrix Expression Console software

label: biotin

source_name: HNSCC

label_protocol: RNA from each sample was labeled according to the manufacturers recommendations (Affymetrix).

extract_protocol: RNA was extracted with miRNeasy FFPE kit (Qiagen) in accordance with the manufacture's protocol.

tag: diagnosis

value: HNSCC

tag: lts vs sts

value: LTS


title: HNC096_TestingSet


title: HNC092_TestingSet

value: STS


title: HNC091_TestingSet


title: HNC093_TestingSet


title: Symptomatic_control_5

value: Female


title: HNC090_TestingSet


title: HNC099_TestingSet


title: HNC094_TestingSet


title: HNC100_TestingSet


title: Symptomatic_control_4


title: HNC088_TestingSet


title: B2x27_Nr2


title: B2x27_Nr1


title: HNC084_TestingSet


title: HNC095_TestingSet


title: HNC089_TestingSet


title: HNC083_TestingSet


title: Symptomatic_control_3


title: HNC082_TestingSet


title: HNC097_TestingSet


title: HNC086_TestingSet


title: HNC087_TestingSet


title: HNC085_TestingSet


title: HNC081_TestingSet


title: Symptomatic_control_2


title: HNC080_TrainingSet

tag: tissue

value: FFPE tissue specimen

tag: Stage

value: III

value: nivolumab


title: B2x27_Mr2

value: Mock


title: Symptomatic_control_1


title: B2x27_Mr3


title: CD66a+_colon_cells Quiescent_UC_15

data_processing:
Processing of the raw reads: nf-core/smrnaseq v1.0.0 analysis pipeline with default parameters and "nextflex" 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 and additional 4 nucleotides from both 5’ and 3’ ends of 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

extract_protocol:
Standard protocol of Single Cell RNA Purification Kit (Norgen)
Standard protocol of NEXTFLEX Small RNA-seq Kit v3 (Bioo Scientific)

tag: smoking

value: Ex-smoker

tag: localization

value: Pancolitis

tag: extraintestinal manifestations

value: No

tag: surgical treatment

tag: stool frequency

value: Normal

tag: bleeding

value: Not observed

tag: sulfalazine use

tag: oral mesalazine use

tag: rectal mesalazine use

tag: azathioprine use

value: Yes

tag: other biologic medicines use

tag: glucocorticoids use


title: HNC079_TrainingSet

value: IV

tag: treatment


title: B2x27_IRr3

tag: cell line

tag: cell type

value: Embryonic stem cells (ESCs)

tag: genotype

value: BRCA2 loHAPs

value: Irradiation


title: HNC078_TrainingSet

tag: tissue

tag: diagnosis

value: HNSCC

tag: Stage

value: II


title: CD44+_colon_cells Quiescent_UC_15

tag: gender

value: Female

tag: age

tag: smoking

tag: localization

tag: endoscopic mayo subscore

tag: extraintestinal manifestations


title: HNC077_TrainingSet

value: FFPE tissue specimen


title: HNC076_TrainingSet

value: III


title: B2x27_IRr2


title: CD66a+_colon_cells Quiescent_UC_14

value: Male

value: Current

tag: surgical treatment

tag: stool frequency

tag: bleeding

tag: sulfalazine use

tag: oral mesalazine use

tag: rectal mesalazine use


title: B2x27_Mr1

tag: cell line

tag: cell type

tag: treatment

value: Mock


title: B2x27_IRr1

tag: genotype


title: CD44+_colon_cells Quiescent_UC_14

value: Pancolitis

tag: azathioprine use

tag: other biologic medicines use

tag: glucocorticoids use


title: HNC072_TrainingSet

tag: tissue

tag: diagnosis

tag: Stage

value: nivolumab


title: HNC073_TrainingSet


title: TK4_10µM Karanjin treated

city: Guwahati

first: Anil

middle: Mukund

last: Limaye

state: Assam

address: IIT Guwahati

department: Department of Biosciences and Bioengineering

country: India

institute: Indian Institute of Technology Guwahati

data_processing:
FastQC Version 0.11.5
Trimmomatic Version 0.36
FastQC Version 0.11.5
STAR Aligner Version 2.7.6a
Assembly: Ensemble Homo sapiens GRCh38 genome
featureCounts v2.0.0

source_name: T47D cells

growth_protocol: T47D cells were grown in a humidified chamber maintained at 37 °C and 5% CO2. The cells were cultured in RPMI-1640 Medium, supplemented with 10% heat-inactivated fetal bovine serum, 100 units/mL penicillin, and 100 μg/mL streptomycin (M1 medium).

extract_protocol:
Total RNA was isolated using RNA extraction reagent prepared in-house as per Chomczynski and Sacchi, with modifications
mRNA enrichment was performed using KAPA mRNA capture kit. Libraries were prepared according to instructions accompanying the KAPA RNA Hyper prep kit (Roche, Switzerland). mRNA was fragmented and reverse transcribed using oligo-dT primers to synthesize cDNA. The double-stranded cDNAs were end-repaired, polyadenylated, and ligated with adapter sequences. Sequencing was performed using Nextseq2K Platform in 150 paired-end reads length format.

treatment_protocol: T47D cells were seeded at a density of 0.2 million cells/ well using M1 medium in 6-well plates. After 48 hours of seeding, the cells were given phenol red-free RPMi-1640 supplemented with 10% heat-inactivated charcoal-stripped fetal bovine serum, 100 units/mL penicillin, and 100 μg/mL streptomycin (M2 medium) for 24 h. Then the cells were treated with M2 medium containing 10 μM Karanjin or 0.1% DMSO (vehicle control) for 24 h.

value: Treated with 10 µM Karanjin for 24 hours

value: Breast cancer cell line

value: Wild type


title: CD66a+_colon_cells Quiescent_UC_13

tag: gender

tag: age

tag: smoking

value: Never

tag: localization

tag: endoscopic mayo subscore

tag: extraintestinal manifestations

value: No

value: Normal

value: Not observed

value: Yes


title: HNC071_TrainingSet

value: HNSCC

value: IV


title: HNC070_TrainingSet

value: FFPE tissue specimen


title: HNC074_TrainingSet

value: III


title: TK2_10µM Karanjin treated


title: CD44+_colon_cells Quiescent_UC_13

value: Male

tag: surgical treatment

tag: stool frequency

tag: bleeding

tag: sulfalazine use

tag: oral mesalazine use

tag: rectal mesalazine use


title: CD66a+_colon_cells Quiescent_UC_12

value: Female

value: Proctitis

tag: azathioprine use

tag: other biologic medicines use


title: CD44+_colon_cells Quiescent_UC_12

tag: glucocorticoids use


title: TK1_10µM Karanjin treated

tag: treatment

tag: cell line

tag: genotype


title: HNC075_TrainingSet

tag: tissue

tag: diagnosis

tag: Stage


title: TD4_DMSO treated_Vehicle control

value: Treated with 0.1% DMSO for 24 hours


title: HNC065_TrainingSet

value: nivolumab


title: TK3_10µM Karanjin treated

value: Treated with 10 µM Karanjin for 24 hours


title: HNC064_TrainingSet


title: HNC069_TrainingSet


title: HNC068_TrainingSet


title: HNC067_TrainingSet


title: HNC060_TrainingSet


title: HNC061_TrainingSet


title: HNC066_TrainingSet


title: CD66a+_colon_cells Quiescent_UC_11

tag: gender

tag: age

tag: smoking

tag: localization

value: Pancolitis

tag: endoscopic mayo subscore

value: Rarely observed


title: TD3_DMSO treated_Vehicle control

value: Breast cancer cell line

value: Wild type


title: HNC062_TrainingSet


title: HNC063_TrainingSet

value: I


title: CD66a+_colon_cells Quiescent_UC_10

value: Never

value: Proctosigmoiditis

tag: extraintestinal manifestations

value: No

tag: surgical treatment

tag: stool frequency

value: 1-2 times higher

tag: bleeding

value: Not observed

tag: sulfalazine use


title: HNC059_TrainingSet

value: FFPE tissue specimen

value: HNSCC

value: IV


title: CD44+_colon_cells Quiescent_UC_11

value: Female

value: Normal

tag: oral mesalazine use

value: Yes

tag: rectal mesalazine use

tag: azathioprine use

tag: other biologic medicines use

tag: glucocorticoids use


title: TD2_DMSO treated_Vehicle control

tag: treatment

value: Treated with 0.1% DMSO for 24 hours

tag: cell line

tag: genotype


title: HNC058_TrainingSet

tag: tissue

tag: diagnosis

tag: Stage

value: III

value: nivolumab


title: TD1_DMSO treated_Vehicle control

value: Breast cancer cell line


title: CD44+_colon_cells Quiescent_UC_10

tag: gender

tag: age

tag: smoking

tag: localization

tag: endoscopic mayo subscore


title: HNC056_TrainingSet


title: HNC057_TrainingSet


title: CD66a+_colon_cells Quiescent_UC_9

value: Pancolitis

tag: extraintestinal manifestations

tag: surgical treatment

tag: stool frequency

tag: bleeding

tag: sulfalazine use


title: HNC054_TrainingSet


title: HNC055_TrainingSet


title: CD44+_colon_cells Quiescent_UC_9

tag: oral mesalazine use

tag: rectal mesalazine use

tag: azathioprine use

tag: other biologic medicines use

tag: glucocorticoids use


title: RH4_DMSO_24h_HiC

city: Bethesda

first: Javed

last: Khan

state: MD

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

data_processing:
RNA-seq was mapped using STAR with hg19 as reference.
RNA-seq read abundance for each gene counted (TPM) using RSEM
RNA-seq raw reads normalized using DESeq2
ChIP-seq was mapped using BWA with hg19 as reference.
ChIP-seq peaks were called using MACS2. https://github.com/CBIIT/ChIP_seq.
ATAC-seq was mapped using BWA with hg19 as reference.
ATAC-seq peaks were called using MACS2. https://github.com/CBIIT/ChIP_seq.
scRNA-seq demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2
Hi-C was mapped to hg19 using omni-c_qc.sh from Dovetail Github (https://github.com/dovetail-genomics)
Hi-C Technical repliaces were merged using Pairtools' merge.
Assembly: hg19/GRCh37
Supplementary files format and content: ChIP-seq peak files are tab delimited bed text files for each sample.
Supplementary files format and content: RNA-seq processed files are quantification matrices of TPM (transcripts per million) at the gene level.
Supplementary files format and content: ATAC-seq peak files are tab delimited bed text files for each sample.
Supplementary files format and content: scRNA-seq files are Tab delimited values files and matrix files
Supplementary files format and content: Hi-C files are merged processed .hic files

source_name: muscle

growth_protocol: Cells were maintained in DMEM with 10% FBS and Penn/Strep at 37 °C incubation.

extract_protocol:
Bulk RNA is extracted using QIAGEN Rneasy Plus Mini Kit. ChIP samples were fixed with 1% formaldehyde for 15 mins, sonicated, immunoprecipitated using antibody and Dynabeads, washed, eluted, and reverse crosslinked.  ATAC samples were tagmented, PCR amplified, and purified. scRNA-seq samples were processed using the 10x Genomics Chromium Next GEM single cell 3' kit.  Hi-C samples were processed using the Dovetail Micro-C kit.
Illumina TruSeq Stranded mRNA and Total RNA library prep, Illumina TruSeq ChIP Library Prep, scRNA-seq using Chromium Next GEM single Cell 3' Reagent kits v3.1, ATAC library from tagmentation and PCR amplification, Hi-C library contructed using Dovetail Micro-C kit

treatment_protocol: Cells were treated with either DMSO or compound of interest for the specified amount of time.

tag: tissue

value: muscle

tag: cell line

tag: cell type

value: Rhabdomyosarcoma

tag: genotype

value: wt

tag: time

value: 24 hr

tag: treatment

value: DMSO


title: HNC053_TrainingSet

tag: diagnosis

tag: Stage


title: HNC051_TrainingSet


title: HNC052_TrainingSet

value: II


title: RH4_PFI90_16h_Tsc

value: 16 hr


title: CD66a+_colon_cells Quiescent_UC_8

tag: gender

tag: age

tag: smoking

value: Never

tag: localization

tag: endoscopic mayo subscore

tag: extraintestinal manifestations

value: No

tag: surgical treatment

value: Not observed


title: RH4_DMSO_16h_Tsc


title: CD44+_colon_cells Quiescent_UC_8

value: Female

tag: stool frequency

value: Normal

tag: bleeding

tag: sulfalazine use

tag: oral mesalazine use

tag: rectal mesalazine use

tag: azathioprine use

tag: other biologic medicines use


title: CD66a+_colon_cells Quiescent_UC_7

value: Yes

tag: glucocorticoids use


title: CD44+_colon_cells Quiescent_UC_7


title: CD66a+_colon_cells Quiescent_UC_6

value: Male

value: Ex-smoker

value: Proctosigmoiditis


title: HNC049_TrainingSet

tag: tissue

value: FFPE tissue specimen

tag: diagnosis

value: HNSCC

value: IV

tag: treatment

value: nivolumab


title: HNC047_TrainingSet

tag: Stage


title: HNC048_TrainingSet


title: HNC046_TrainingSet

value: III


title: IAV_T4_18h_3

city: Braunschweig

first: Andreas

last: Jeron

state: Nierdersachsen

address: Inhoffenstraße 7

department: Viral Immunology

country: Germany

institute: Helmholtz Center for Infection Research

description: Pooled AECII from 3 - 5 mice per condition

hyb_protocol: Hybridization was performed according to Affymetrix Clariom S microarray recommendations

scan_protocol: Scanning was performed according to Affymetrix Clariom S microarray recommendations

data_processing: Microarray data were processed with Transcriptome Analysis Console (Thermo Fisher Scientific) using the SST-RMA algorithm.

source_name: alveolar type 2 epithelial cells

label_protocol: Labeling was performed according to Affymetrix Clariom S microarray recommendations

growth_protocol: Female C57BL/6JOlaHsd mice of age 10 - 14 weeks maintained under specific-pathogen-free conditions

extract_protocol: Lung single cells suspensions were obtained by enzymatic (dis-pase/DNase digestion) and mechanical dissociation of whole lungs. Pooled cells from n = 3 - 5 mice/cohort were stained with PE- or APC-conjugated antibodies (from either BD or BioLegend) against murine F4/80 (clone: BM8), CD93 (clone: AA4-1), CD11c (clone: N418), CD19 (clone: 6D5), CD31 (clone: 390), CD11b (M1/70), CD16/32 (clone: 2.4G2) and CD45 (clone: 30-F11). AECII were sort-purified by negative selection (PE-, APC-, autofluorescence-high, side-scatter-high) using FACS Aria II and Fusion instruments (BD) and maximum purity masks (4-way purity mode). RNA was isolated using the RNeasy Plus Mini Kit (Qiagen) and DNase digestion.

treatment_protocol: If indicated, mice were intranasally infected with 7.9 TCID50 IAV (H1N1, PR/8/34, mouse-adapted) in 25µL of PBS following ketamine/xylazine anesthesia. 14 day post IAV infection secondary S.pn. infection was performed. For S.pn.infections the serotype 4 strain TIGR4 (ATCC BAA-334), 19F strain (BHN100) [46] and 7F strain (BHN54) were used. Single colonies of S.pn. were resuspended in fresh Todd-Hewitt yeast medium and bacterial suspension was grown to mid-logarithmic phase (OD600nm ~ 0.4). Bacteria were spun down, washed once and diluted in PBS to obtain the final inoculum for infection. CFU were retrospectively determined by plating. For bacterial infections, mice were anesthetized by i.p. injection of ketamine/xylazine and 40 µL of the pneumococcal inoculum were administered by oropharyngeal aspiration. If indicated, control mice were treated with matching volumes of PBS via the same application method.

tag: first treatment

value: IAV day 14

tag: second treatment

tag: s.pn. serotype

tag: hours after second tratment


title: IAV_T4_18h_1


title: HNC045_TrainingSet


title: IAV_T4_18h_2


title: CD44+_colon_cells Quiescent_UC_6

tag: gender

tag: age

tag: smoking

tag: localization

tag: endoscopic mayo subscore

tag: extraintestinal manifestations

tag: surgical treatment


title: HNC038_TrainingSet


title: HNC042_TrainingSet


title: HNC040_TrainingSet


title: HNC034_TrainingSet


title: CD66a+_colon_cells Quiescent_UC_5

value: Pancolitis

tag: stool frequency

value: 1-2 times higher

tag: bleeding

tag: sulfalazine use

tag: oral mesalazine use

tag: rectal mesalazine use

tag: azathioprine use

tag: other biologic medicines use


title: HNC044_TrainingSet

tag: tissue

tag: diagnosis

tag: Stage

tag: treatment


title: HNC036_TrainingSet


title: HNC037_TrainingSet

value: I


title: IAV_7F_18h_2

tag: first treatment

tag: second treatment

tag: s.pn. serotype

tag: hours after second tratment


title: HNC039_TrainingSet


title: IAV_7F_18h_3


title: HNC041_TrainingSet


title: HNC043_TrainingSet


title: HNC035_TrainingSet


title: HNC033_TrainingSet


title: IAV_7F_18h_1


title: CD44+_colon_cells Quiescent_UC_5

tag: gender

tag: age

tag: smoking

value: Never

tag: localization

tag: endoscopic mayo subscore

tag: extraintestinal manifestations

value: No

tag: glucocorticoids use


title: CD66a+_colon_cells Quiescent_UC_4

tag: surgical treatment

tag: stool frequency

tag: bleeding

value: Not observed

tag: sulfalazine use

tag: oral mesalazine use

tag: rectal mesalazine use

tag: azathioprine use


title: HNC031_TrainingSet

tag: tissue

tag: diagnosis

tag: Stage

tag: treatment


title: HNC032_TrainingSet


title: HNC030_TrainingSet


title: CD44+_colon_cells Quiescent_UC_4

tag: gender

tag: age

value: Normal

tag: other biologic medicines use


title: CD44+_colon_cells Quiescent_UC_3

value: Female

tag: smoking

tag: localization

tag: endoscopic mayo subscore

value: Yes


title: CD66a+_colon_cells Quiescent_UC_3

tag: extraintestinal manifestations

tag: surgical treatment

tag: glucocorticoids use


title: CD66a+_colon_cells Quiescent_UC_2

value: Male

value: Ex-smoker

value: Left-sided colitis

tag: stool frequency

tag: bleeding

tag: sulfalazine use


title: IAV_19F_18h_3

tag: first treatment

tag: second treatment

tag: s.pn. serotype

tag: hours after second tratment


title: IAV_19F_18h_2


title: IAV_T4_4h_3


title: CD66a+_colon_cells Quiescent_UC_1

tag: oral mesalazine use

tag: rectal mesalazine use

tag: azathioprine use


title: HNC027_TrainingSet

tag: tissue

value: FFPE tissue specimen

tag: diagnosis

value: HNSCC

tag: Stage

tag: treatment


title: HNC029_TrainingSet

value: nivolumab


title: HNC026_TrainingSet

value: III


title: HNC025_TrainingSet

value: IV


title: IAV_19F_18h_1

value: IAV day 14


title: IAV_T4_4h_1


title: HNC021_TrainingSet


title: IAV_T4_4h_2


title: CD44+_colon_cells Quiescent_UC_2

tag: gender

tag: age

tag: smoking

tag: localization

tag: endoscopic mayo subscore

tag: extraintestinal manifestations

tag: other biologic medicines use


title: IAV_7F_4h_2

tag: first treatment

tag: second treatment


title: IAV_7F_4h_3

tag: s.pn. serotype

tag: hours after second tratment


title: HNC050_TrainingSet


title: HNC019_TrainingSet


title: HNC024_TrainingSet


title: HNC020_TrainingSet


title: HNC022_TrainingSet

value: II


title: HNC017_TrainingSet


title: HNC028_TrainingSet


title: CD44+_colon_cells Quiescent_UC_1

tag: surgical treatment

tag: stool frequency

tag: bleeding

tag: sulfalazine use

tag: oral mesalazine use

tag: rectal mesalazine use

tag: glucocorticoids use


title: HNC023_TrainingSet

tag: tissue

tag: diagnosis

tag: Stage

tag: treatment


title: HNC018_TrainingSet


title: HNC013_TrainingSet


title: HNC016_TrainingSet

value: I


title: CD66a+_colon_cells Active_UC_15

tag: gender

tag: age

tag: smoking

value: Never

tag: localization

value: Pancolitis

tag: endoscopic mayo subscore

tag: extraintestinal manifestations

value: 1-2 times higher

tag: azathioprine use


title: HNC012_TrainingSet


title: HNC015_TrainingSet


title: CD44+_colon_cells Active_UC_16

value: Current

value: No

tag: surgical treatment

tag: stool frequency

value: Rarely observed

tag: other biologic medicines use


title: IAV_7F_4h_1

tag: first treatment

tag: second treatment

tag: s.pn. serotype

tag: hours after second tratment


title: HNC014_TrainingSet

tag: tissue

tag: diagnosis


title: CD44+_colon_cells Active_UC_15

value: Female

tag: bleeding

value: Not observed

tag: sulfalazine use

tag: oral mesalazine use

tag: rectal mesalazine use

value: Yes

tag: glucocorticoids use


title: CD66a+_colon_cells Active_UC_14

tag: gender

value: Male

tag: age

tag: smoking

tag: localization

tag: endoscopic mayo subscore


title: CD66a+_colon_cells Active_UC_16

tag: extraintestinal manifestations

tag: surgical treatment

tag: stool frequency

tag: azathioprine use

tag: other biologic medicines use


title: CD44+_colon_cells Active_UC_14


title: IAV_19F_4h_2

tag: first treatment

tag: second treatment

tag: s.pn. serotype

tag: hours after second tratment


title: posterior intestine - PBS i.p. - 3 days after infection

city: Shanghai

first: dahai

last: Yang

address: No.130, Meilong Road, Xuhui District

institute: East China University of Science and Technology

library_source: transcriptomic single cell

data_processing:
Raw data was processed with the cellranger pipeline
Seurat was used to analyse h5 file from cellranger output, and clustering the cells, running umap and finding biomarkers were finished by seurat
Feature score of each cells was performed with seurat
Assembly: Turbot ensembl v98
Supplementary files format and content: h5 table with raw gene counts for every gene and every sample

organism: Scophthalmus maximus

source_name: posterior intestine

growth_protocol: Turbot was cultured in a circulation system with 17 °C seawater. Edwardsiella piscicida EIB202 was cultivated in tryptic yeast medium (TYB) at 30°C

extract_protocol:
Using percoll discontinuous density gradient centrifugation to enrich posterior intestinal cells, and Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (CG000204 Rev B) was used to extract mRNA
RNA-libraries were prepared according to to Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (CG000204 Rev B)

treatment_protocol: Turbots were intraperitoneally injected (i.p.) with a volume of 100 μl (working concentration 1 mg/ml) of β-glucan or the same volume of PBS as control group.Turbots were immersed in a 40 L system with 2×107 CFU/ml E. piscicida for 10 minutes

tag: treatment

value: PBS i.p. - infected with E. piscicida

tag: tissue

value: posterior intestine

tag: sampling time

value: 3 days after infection


title: posterior intestine - β-glucan i.p. - 3 days after infection

value: β-glucan i.p. - infected with E. piscicida


title: HNC010_TrainingSet

value: FFPE tissue specimen

tag: diagnosis

value: HNSCC

tag: Stage

value: III

value: nivolumab


title: IAV_19F_4h_3

value: IAV day 14


title: IAV_19F_4h_1


title: HNC009_TrainingSet


title: Antler-comb chicken 11

type: genomic

city: Guangzhou

first: Wei

last: Luo

state: Guangdong

address: Wushan Road

department: The College of Animal Science

institute: South China Agricultural University

description:
Geno-wide genotyping
H09-4-11

hyb_protocol: Prepare hybridization buffers and perform array hybridization at 49℃ in GeneTitan .After 23.5 hours hybridization, arrays were washed in GeneTitanaccording to Affymetrix Axiom™ Assay User Manual.

scan_protocol: GeneTitan™ Multi-Channel (MC) system was used to scan.

data_processing:
Arrays were scanned by GeneTitan and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings. Raw data passed quality control were further analyzed by Affymetrix® Axiom Analysis Suite (Affymetrix, Santa Clara, CA, US).
36 chickens were genome-wide genotyped in 559,898 position using Affymatrix 600K Axiom® Genome-Wide Chicken Genotyping Array, along with its signal strength given.

organism: Gallus gallus

source_name: 120-d chicken, blood

label_protocol: Sample DNA was digested by restriction enzymes NspI, adaptors were ligated to the fragment DNA to perform a PCR amplification. Amplified DNA was labeled and further fragmented using Affymetrix Axiom array kit and reagent kit bundle, (Cat#901835, Affymetrix, Santa Clara, CA,US)followed the manufacturer’s instruction Affymetrix Axiom™ Assay User Manual (Cat#703038 Rev. 3, Affymetrix, Santa Clara, CA, US) to obtain biotin labeled DNA.

extract_protocol: Sample DNA was extracted using DNeasy Blood &Tissue Kit (Cat#69506, QIAGEN, GmBH, Germany), following the manufacturer’s instructions. We use Nano Drop (Cat#ND-2000, Thermo Fisher, Waltham, MA, US) and run a 1% agarose gel electrophoresis to check the quantity and quality of purified DNA.

tag: phenotype

value: Antler-comb

tag: Sex


title: HNC011_TrainingSet


title: IAV_PBS_4h_3

value: PBS


title: Antler-comb chicken 10

description:
Geno-wide genotyping
H08-4-10


title: CD44+_colon_cells Active_UC_13

tag: gender

tag: age

tag: smoking

value: Current

tag: localization

value: Pancolitis

tag: endoscopic mayo subscore

value: No

value: 1-2 times higher

tag: bleeding

tag: sulfalazine use

tag: oral mesalazine use

tag: rectal mesalazine use

tag: glucocorticoids use


title: Antler-comb chicken 9

description:
Geno-wide genotyping
H07-4-9

value: Female


title: IAV_PBS_4h_1

tag: first treatment

tag: second treatment

tag: s.pn. serotype

tag: hours after second tratment


title: PBS_T4_18h_3


title: Antler-comb chicken 8

description:
Geno-wide genotyping
H06-4-8


title: HNC005_TrainingSet

tag: tissue

tag: diagnosis

tag: Stage

tag: treatment


title: HNC006_TrainingSet

value: II


title: HNC004_TrainingSet


title: HNC002_TrainingSet

value: IV


title: HNC007_TrainingSet


title: HNC001_TrainingSet

value: I


title: Antler-comb chicken 12

description:
Geno-wide genotyping
H10-4-12

tag: phenotype

tag: Sex


title: CD66a+_colon_cells Active_UC_13

tag: gender

value: Male

tag: age

tag: smoking

tag: localization

tag: extraintestinal manifestations

tag: surgical treatment

tag: stool frequency

value: Rarely observed

value: Yes

tag: azathioprine use

tag: other biologic medicines use


title: HNC003_TrainingSet

value: FFPE tissue specimen

value: HNSCC


title: Antler-comb chicken 7

description:
Geno-wide genotyping
H05-4-7


title: PBS_T4_18h_2

tag: first treatment

tag: second treatment

tag: s.pn. serotype


title: Antler-comb chicken 5

description:
Geno-wide genotyping
H03-4-5


title: CD44+_colon_cells Active_UC_12

value: Never

tag: endoscopic mayo subscore

tag: bleeding

tag: sulfalazine use

tag: oral mesalazine use

tag: rectal mesalazine use

tag: glucocorticoids use


title: CD66a+_colon_cells Active_UC_11

tag: gender

tag: age

value: 5 times higher

value: Clearly visible


title: CD66a+_colon_cells Active_UC_12

tag: smoking

tag: localization


title: Antler-comb chicken 6

description:
Geno-wide genotyping
H04-4-6

tag: phenotype

value: Antler-comb

tag: Sex


title: Antler-comb chicken 3

description:
Geno-wide genotyping
H01-4-3


title: CD44+_colon_cells Active_UC_11

tag: extraintestinal manifestations

tag: surgical treatment

tag: stool frequency

tag: azathioprine use


title: Antler-comb chicken 2

description:
Geno-wide genotyping
G12-4-2


title: Wildtype-comb chicken 24

description:
Geno-wide genotyping
G10-3-24

value: Wildtype-comb


title: PBS_7F_18h_3

tag: first treatment

value: PBS

tag: second treatment

tag: s.pn. serotype

tag: hours after second tratment


title: IAV_PBS_4h_2

value: IAV day 14


title: Wildtype-comb chicken 22

description:
Geno-wide genotyping
G08-3-22


title: PBS_7F_18h_1


title: Antler-comb chicken 4

description:
Geno-wide genotyping
H02-4-4


title: PBS_T4_18h_1


title: Wildtype-comb chicken 21

description:
Geno-wide genotyping
G07-3-21


title: Antler-comb chicken 1

description:
Geno-wide genotyping
G11-4-1


title: CD44+_colon_cells Active_UC_9

value: Ex-smoker

value: Pancolitis

tag: endoscopic mayo subscore

value: No

value: Normal

tag: bleeding

value: Not observed

tag: sulfalazine use

tag: oral mesalazine use

tag: other biologic medicines use


title: Wildtype-comb chicken 20

description:
Geno-wide genotyping
G06-3-20

value: Female


title: CD66a+_colon_cells Active_UC_10

tag: gender

tag: age

tag: smoking

value: 1-2 times higher

tag: rectal mesalazine use

tag: glucocorticoids use


title: PBS_7F_18h_2


title: CD44+_colon_cells Active_UC_8

value: Male

value: Current

tag: localization

value: Proctosigmoiditis

tag: extraintestinal manifestations

tag: surgical treatment

value: 3-4 times higher

value: Rarely observed

value: Yes


title: CD66a+_colon_cells Active_UC_8

tag: stool frequency

tag: azathioprine use


title: PBS_19F_18h_3

tag: first treatment

tag: second treatment

tag: s.pn. serotype


title: Wildtype-comb chicken 15

description:
Geno-wide genotyping
G01-3-15

tag: phenotype

tag: Sex


title: Wildtype-comb chicken 14

description:
Geno-wide genotyping
F12-3-14


title: Wildtype-comb chicken 17

description:
Geno-wide genotyping
G03-3-17


title: PBS_19F_18h_2

tag: hours after second tratment


title: PBS_19F_18h_1


title: Wildtype-comb chicken 13

description:
Geno-wide genotyping
F11-3-13


title: CD44+_colon_cells Active_UC_10

value: Never

tag: endoscopic mayo subscore

tag: bleeding

tag: sulfalazine use

tag: oral mesalazine use

tag: other biologic medicines use


title: Wildtype-comb chicken 23

description:
Geno-wide genotyping
G09-3-23

value: Wildtype-comb


title: CD66a+_colon_cells Active_UC_7

tag: gender

tag: age

tag: smoking

tag: rectal mesalazine use

tag: glucocorticoids use


title: CD66a+_colon_cells Active_UC_9

tag: localization

tag: extraintestinal manifestations

tag: surgical treatment

tag: stool frequency

tag: azathioprine use


title: Wildtype-comb chicken 12

description:
Geno-wide genotyping
F10-3-12

tag: phenotype

tag: Sex


title: Wildtype-comb chicken 19

description:
Geno-wide genotyping
G05-3-19


title: PBS_T4_4h_3

tag: first treatment

value: PBS

tag: second treatment

tag: s.pn. serotype

tag: hours after second tratment


title: Wildtype-comb chicken 11

description:
Geno-wide genotyping
F09-3-11


title: Wildtype-comb chicken 18

description:
Geno-wide genotyping
G04-3-18


title: CD44+_colon_cells Active_UC_7

tag: endoscopic mayo subscore

tag: bleeding

tag: sulfalazine use

tag: oral mesalazine use

tag: other biologic medicines use


title: Wildtype-comb chicken 10

description:
Geno-wide genotyping
F08-3-10


title: Wildtype-comb chicken 9

description:
Geno-wide genotyping
F07-3-9


title: Wildtype-comb chicken 8

description:
Geno-wide genotyping
F06-3-8


title: Wildtype-comb chicken 16

description:
Geno-wide genotyping
G02-3-16


title: PBS_T4_4h_2


title: Wildtype-comb chicken 5

description:
Geno-wide genotyping
F03-3-5


title: Wildtype-comb chicken 6

description:
Geno-wide genotyping
F04-3-6


title: Wildtype-comb chicken 7

description:
Geno-wide genotyping
F05-3-7


title: Wildtype-comb chicken 4

description:
Geno-wide genotyping
F02-3-4


title: CD44+_colon_cells Active_UC_6

tag: gender

tag: age

tag: smoking

value: Proctitis

tag: rectal mesalazine use

tag: glucocorticoids use


title: CD66a+_colon_cells Active_UC_5

value: Ex-smoker

tag: localization

tag: extraintestinal manifestations

tag: surgical treatment

tag: stool frequency

tag: azathioprine use


title: CD66a+_colon_cells Active_UC_6


title: Wildtype-comb chicken 3

description:
Geno-wide genotyping
F01-3-3

tag: phenotype

tag: Sex


title: Wildtype-comb chicken 2

description:
Geno-wide genotyping
E12-3-2


title: CD44+_colon_cells Active_UC_5

value: Pancolitis

tag: endoscopic mayo subscore


title: PBS_7F_4h_3

tag: first treatment

tag: second treatment

tag: s.pn. serotype

tag: hours after second tratment


title: CD66a+_colon_cells Active_UC_4

tag: gender

value: No

value: 5 times higher

tag: bleeding

tag: sulfalazine use

tag: oral mesalazine use

tag: other biologic medicines use


title: CD80low MZ B cells from male C57BL/6 mice

city: Suwon

first: Sujin

last: Lee

address: Seoburo 2066

department: Immunology

country: South Korea

institute: Sungkyunkwan Univ

description: Total RNA was processed for preparing mRNA sequencing library using MGIEasy RNA Directional Library Prep Kit (MGI) at LAS (Life is Art of Science) Laboratory (Gimpo-si, Korea).

data_processing:
Preparocessing to have chean data for trustworthy analyses (FastQC version 0.11.5, Skewer version 0.2.2)
Read mapping on the reference genome sequence (STAR version 2.6)
Expression quantification, followed by differentially expressed gene analysis (Cuffquant, Cuffnorm and Cuffdiff of Cufflinks package version 2.2.1)
Assembly: mm10
Supplementary files format and content: Excel file include FPKM values for each sample

source_name: Spleen

extract_protocol:
Total RNA was isolated from tissue using Maxwell (Promega) based method.
One μl of total RNA was precessed for preparing mRNA sequencing library using MGIEasy RNA Directional Livrary Prep Kit (MGI) according to manufacturer's instruction.

tag: tissue

value: Spleen

tag: cell line

value: primary cell

tag: cell type

value: B cell

tag: genotype

value: wild type

tag: treatment

value: No treatement


title: CD80high MZ B cells from male C57BL/6 mice


title: PBS_7F_4h_1


title: CD44+_colon_cells Active_UC_4

value: Male

tag: age

tag: smoking

tag: localization

tag: extraintestinal manifestations

tag: surgical treatment

tag: stool frequency

value: Not observed

tag: rectal mesalazine use

tag: azathioprine use

tag: glucocorticoids use


title: PBS_7F_4h_2

tag: first treatment

tag: second treatment

tag: s.pn. serotype

tag: hours after second tratment


title: PBS_19F_4h_3


title: KMM cell, Day4, rep3

city: Pittsburgh

first: Luping

last: Chen

address: 5117 Centre Avenue

institute: University of Pittsburgh

data_processing:
QIAGEN CLC Workbench 22.0
Sequence reads were trimmed for adaptor sequence by using cutadapt package.
Trimmed sequence reads were mapped to mRatBN7.2 using CLC Workbench (mismatch cost: 2, insertion cost:3, deletion cost:3, length fraction: 0.8, sililarity fraction: 0.8).
Read count extraction and normalization were performed using CLC Workbench.
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Rattus norvegicus

source_name: KMM

growth_protocol: MM cells were cultured in DMEM with 10% fetal bovine serum and 1% Penicillin-Streptomycin solution. KMM cells were cultured in the same medium with 250 µg/mL hygromycin.

extract_protocol:
Total RNA was extracted from cells using TRI reagent, and mRNA was isolated using Oligo(dT) beads.
library was prepared following the Illumina TruSeq Stranded mRNA Library Prep Kit.

treatment_protocol: Both MM and KMM cells treated with 0.1 µM dexamethasone for 0, 2 and 4 days.

tag: cell line

value: KMM

value: dexamethasone


title: PBS_19F_4h_2


title: PBS_19F_4h_1


title: KMM cell, Day4, rep2


title: CD44+_colon_cells Active_UC_3

city: Kaunas

first: Rūta

address: Mickeviciaus st. 9

institute: Lithuanian University of Health Sciences

tag: gender

tag: endoscopic mayo subscore

value: Yes

value: 3-4 times higher

tag: bleeding

value: Rarely observed

tag: sulfalazine use

tag: oral mesalazine use

tag: other biologic medicines use


title: CD66a+_colon_cells Active_UC_3

tag: age

tag: smoking

tag: localization

value: Proctitis

tag: extraintestinal manifestations


title: KMM cell, Day2, rep3

tag: treatment


title: KMM cell, Day4, rep1


title: KMM cell, Day2, rep1


title: KMM cell, Day2, rep2


title: KMM cell, Day0, rep3

value: NT


title: CD66a+_colon_cells Active_UC_2

value: Never

value: Pancolitis

tag: surgical treatment

tag: stool frequency

value: 1-2 times higher

tag: rectal mesalazine use

tag: azathioprine use

tag: glucocorticoids use


title: KMM cell, Day0, rep2

tag: cell line


title: CD44+_colon_cells Active_UC_2

tag: gender

value: No


title: KMM cell, Day0, rep1


title: CD66a+_colon_cells Active_UC_1

value: Proctosigmoiditis

tag: endoscopic mayo subscore


title: PBS_PBS_1

tag: first treatment

value: PBS

tag: second treatment

tag: s.pn. serotype

tag: hours after second tratment


title: CD44+_colon_cells Active_UC_1

tag: age

tag: bleeding

tag: sulfalazine use

tag: oral mesalazine use

tag: other biologic medicines use


title: MM cell, Day2, rep3

source_name: MM

value: MM

tag: treatment


title: MM cell, Day4, rep1


title: PBS_PBS_3


title: MM cell, Day2, rep2


title: g318 KO

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

country: Spain

institute: Hospital del Mar Research Institute

description: Gene expression data from mouse adipose tissue-derived and in vitro differentiated adipocytes (Olfm2 knockout)

hyb_protocol: Sample was hybridized to Affymetrix Clariom S Mouse array using an Affymetrix GeneChip Hybridization Oven 645

scan_protocol: GeneChip was scanned using the Affymetrix Expression Wash, Stain and Scan User Manual (P/N 702731 Rev. 3)  (Affymetrix Inc., Santa Clara, CA, USA) using Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed using the RMA algorithm and then LIMMA was applied to calculate significant differential expression between samples

label: Biotin

label_protocol: 100ng of total RNA from each sample was processed and labelled according to manual GeneChip WT PLUS Reagent kit (P/N 703174 Rev. 2, Affymetrix Inc., Santa Clara, CA, USA)

extract_protocol: Total RNA was extracted following Qiagen protocol

tag: genotype

value: Olfm2 knockout

tag: tissue

value: adipose tissue, g


title: MM cell, Day2, rep1


title: CD44+_colon_cells Symptomatic_control_17

last: Inčiūraitė

value: Female

tag: smoking


title: MM cell, Day0, rep2


title: g309 WT

description: Gene expression data from mouse adipose tissue-derived and in vitro differentiated adipocytes (Wild-type)

value: Wild-type


title: g308 WT

source_name: mouse adipose tissue-derived and in vitro differentiated adipocytes


title: MM cell, Day0, rep1


title: CD66a+_colon_cells Symptomatic_control_16


title: g320 KO


title: PBS_PBS_2


title: MM cell, Day4, rep2

value: dexamethasone


title: g307 WT


title: CD44+_colon_cells Symptomatic_control_16


title: Wildtype-comb chicken 1

description:
Geno-wide genotyping
E11-3-1

tag: phenotype

value: Wildtype-comb

tag: Sex


title: g317 KO


title: g300 KO


title: MM cell, Day0, rep3

tag: cell line


title: CD66a+_colon_cells Symptomatic_control_15

tag: gender

value: Male

value: Current

tag: endoscopic mayo subscore


title: MM cell, Day4, rep3


title: CD44+_colon_cells Symptomatic_control_15


title: PBS_T4_4h_1

tag: first treatment

tag: second treatment


title: CD66a+_colon_cells Symptomatic_control_17


title: CD66a+_colon_cells Symptomatic_control_14


title: db-m-7

first: Yan

last: Huang

address: No.22 ,Zhongguancun South Avenue, Haidian District

institute: Peking University School and Hospital of Stomatology

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

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

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, circRNAs and mRNAs that at The Agilent Feature

source_name: parotid gland

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

extract_protocol: Frozen parotid glands from db/m and db/db mice were cryo pulverized using biopulverizer (Biospec) and homogenized with TRIzol (Invitrogen Life Technologies) by Mini-Bead-Beater-16 (Biospec). RNA was collected from each sample based on the manufacturer’s protocols.

treatment_protocol: The fresh parotid glands of mice are preserved at -80 degrees Celsius.

tag: disease state

value: control

value: db-m

value: parotid gland

value: male


title: db-m-8


title: RWA_SG

city: Stellenbosch

first: Anna-Maria

last: Oberholster

state: Western Cape

address: JC Smuts Building, Van der Bijl Street

department: Genetics

institute: University of Stellenbosch

data_processing:
Quality check with FastQC
Trimming, using Trimmomatic v0.39, ILLUMINACLIP:./adapters/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:5:30 HEADCROP:20 MINLEN:40
De novo assembly, Trinity v2.8.6
Transcript quanitification, Trinity v2.8.6 making use of RSEM
Assembly: De novo
Supplementary files format and content: tab delimited text file with 7 columns; 1:gene_id, 2:transcript_id, 3:length, 4:effective_length, 5:expected_count, 6:TPM, 7:FPKM

organism: Diuraphis noxia

source_name: Salivary Glands

growth_protocol: Aphids were reared on several Susceptible (Tugela, SST387)  and Resistant cultivars (Tugela Dn1, Gamtoos R)

extract_protocol:
Qiagen RNeasy kit
TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E protocol

tag: biotype

value: SA1 and SAM2.0

tag: sample size

value: 200 glands

tag: developmental stage

value: Adult


title: db-m-2

city: Beijing


title: CD66a+_colon_cells Symptomatic_control_13

tag: age

value: Never


title: db-m-5


title: db-db-5

value: model of spontaneous type 2 DM

value: db-db


title: g287 WT

value: adipose tissue, g


title: CD44+_colon_cells Symptomatic_control_13


title: db-db-8


title: db-db-1


title: CD66a+_colon_cells Symptomatic_control_12

value: Ex-smoker


title: g286 WT

value: Wild-type


title: g306 KO

value: Olfm2 knockout


title: sc320KO

value: adipose tissue, sc


title: CD66a+_colon_cells Symptomatic_control_11

value: Male


title: db-db-2


title: H3K4me3 cKit control ChIP rep 2

city: Kanazawa

first: Kenta

last: Nitahara

state: Ishikawa

address: 13-1, Takaramachi

department: Department of Histology and Cellular Biology

country: Japan

institute: Kanazawa Univeristy

data_processing:
Trimming of adapter sequences was performed with Trimmomatic (version 0.39).
RNA-seq: The total amount of each transcript was calculated with the use of a series of programs including HISAT2 (version 2.1.0) and edgeR (version 3.16) with a quantile-adjusted conditional maximum likelihood method to estimate common and tagwise dispersions. An exact test for single comparison was used to assess differential expression. RNA-seq reads were mapped against the mouse (mm10) genome.
ChIP-seq: The pair-end reads were mapped to mm10 genome with bowtie2 (version 2.4.5), and duplicated reads were removed with samtools (version 1.14). Markedly enriched regions of the genome were identified with the MACS2 peak caller (version 2.2.7.1, with the option “-p 1e-5 --gsize mm --nomodel --extsize 160”). Peak annotation was identified with the ChIPseeker (1.34.1), and heatmap and density profiles were created using deepTools (3.5.1) including the functions of "bamCompare" (with the option "--operation subtract --scaleFactorsMethod SES"), "computeMatrix" (with the option "--maxThreshold 1000 --missingDataAsZero --skipZeros"), and "plotHeatmap".
Assembly: mm10
Supplementary files format and content: BedGraph files were generated using MACS2.
Supplementary files format and content: Text files include featurecounts and edgeR results.

source_name: Testis

extract_protocol:
RNA was extracted from the enriched spermatogonia with the use of a PureLink RNA Mini Kit and the preparation of a cDNA library was conducted by Rhelixa Co., Ltd using NEBNext® Poly(A) mRNA Magnetic Isolation Module (Cat No. E7490) and NEBNext® Ultra™II Directional RNA Library Prep Kit (Cat No. E7760). ChIP was subjected with antibodies to CHD8 or H3K4me3. The extracted DNA was size-selected with AMPure XP and E-gel electrophoresis system. A DNA library was prepared with a ThruPLEX DNA-Seq kit (TAKARA).
RNA-seq and ChIP-seq libraries were prepared for sequencing using standard protocols.

value: Testis

tag: cell type

value: c-Kit+ Spermatogonia

tag: strain

value: 10 dpp

tag: antibody

value: H3K4me3 (Abcam, #ab8580)


title: H3K4me3 cKit CKO input rep 1

tag: tissue

tag: genotype

value: male


title: H3K4me3 cKit control ChIP rep 1


title: H3K4me3 cKit control input rep 2


title: H3K4me3 cKit CKO ChIP rep 2


title: H3K4me3 cKit CKO input rep 2


title: H3K4me3 cKit CKO ChIP rep 1


title: sc317KO


title: CHD8 cKit CKO ChIP rep 2

description: CHD8 (in-house made [Katayama Y, et al. CHD8 haploinsufficiency results in autistic-like phenotypes in mice. Nature 537, 675-679 (2016)])

value: CHD8 (in-house made)


title: H3K4me3 cKit control input rep 1


title: sc309WT


title: CD44+_colon_cells Symptomatic_control_11

tag: smoking

value: Current


title: CHD8 cKit CKO ChIP rep 1

tag: Sex


title: CHD8 cKit CKO input rep 1


title: CHD8 cKit control ChIP rep 2


title: sc318KO


title: sc308WT


title: sc307WT


title: CD44+_colon_cells Symptomatic_control_10

value: Female


title: HNC008_TrainingSet

value: FFPE tissue specimen

tag: diagnosis

value: HNSCC

tag: Stage

value: III

tag: treatment

value: nivolumab


title: CHD8 cKit control ChIP rep 1


title: CD66a+_colon_cells Symptomatic_control_9

tag: gender

value: Never

tag: endoscopic mayo subscore


title: CHD8 cKit control input rep 1


title: CHD8 Thy1 CKO ChIP rep 1

value: Thy1+ Spermatogonia


title: CHD8 cKit control input rep 2


title: CD44+_colon_cells Symptomatic_control_9


title: CHD8 cKit CKO input rep 2


title: NC_4

city: Hershey

first: Yuka

last: Imamura Kawasawa

address: 500 University Dr.

department: College of Medicine, Pharmacology

data_processing:
De-multiplexed and adapter-trimmed sequencing reads were generated using Illumina bcl2fastq (released version 2.18.0.12) allowing no mismatches in the index read. R2 reads were generated as UMI sequences that were later used to extract PCR duplicates. R1 and R3 reads were used as paired sequencing reads. To assess the read quality, FastQC was run, and low quality reads were removed using sickle with default setting. BBDuk version 36_49  was used to trim/filter low quality sequences using “qtrim=lr trimq=10 maq=10” option. Next, alignment of the filtered reads to the human reference genome GRCh38 was done using HISAT2 version 2.1.0 applying --no-mixed and --no-discordant options. UMI specific workflow that was developed and distributed by Tecan Genomics was used to extract reads that are free from PCR artifacts i.e., deduplication. The resulting deduplicated reads were summarized to each gene using HTseq-count version 0.11.2 by supplementing Ensembl gene annotation GRCh38.78 and ERCC spike-in genes.
Genome_build: GRCh38
Genome_build: mm9
Supplementary_files_format_and_content: Raw read counts are provided in TS_LC_WC_NC.txt and MouseAB_Rawcount.txt files, respectively.
paired-end (R1 and R3, R2 is UMI)

organism: blank sample

source_name: Water

growth_protocol:
Coverslips Fisher Scientific, 12-545-80 were coated with Poly-L-Lysine PLL by incubation in PLL solution 0.01% for 30 minutes at 37°C. TOV-21G ATCC, CRL-11730 cells were grown for 48 hours on cover slips in the Complete Growth Medium [a 1:1 mixture of MCDB 105 1.5 g/L sodium bicarbonate and MCDB 199 2.2 g/L sodium bicarbonate added with fetal bovine serum at a final concentration of 15%] for RNA collection.
Mice were deeply anesthetized with isoflurane Halocarbon. A block of brain containing motor cortex MCx was removed and coronal slices 300 μm thick were cut on a vibrating microtome Leica in ice-cold physiological solution ACSF. The solution contained the following in mM: 130 NaCl, 3 KCl, 1.25 KH2PO4, 20 NaHCO3, 10 glucose, 1.3 MgSO4, 2.5 CaCl2 pH 7.35-7.4, in 95% O2-5% CO2. All solutions were made with nuclease-free, de-ionized, not DEPC-treated water Ambion AM 9938. Slices were incubated for 1 hour at 30°C, then kept at room temperature. For electrophysiological extraction of RNA, slices were held in a chamber on a motorized stage microscope Olympus BX61WI, Gibraltar Burleigh and superfused with ACSF. The location of motor cortex MCx was identified by 1.5-2.0 mm rostral to the start of the hippocampus.

extract_protocol:
For RNA extraction, cultures and slices were held separately in a chamber on a motorized stage on a motorized microscope Olympus BX61WI, Gibraltar Burleigh Thorlabs. Cultures were superfused 2-4 ml/min in a bath solution of in mM: 145 N-methylglucamine NMG, 2 CaCl2, 1 MgCl2, 10 HEPES, 60 glucose pH 7.3, osmolality 300, in 95% O2-5% CO2 . All procedures were performed with a Multiclamp 700B patch-clamp amplifier Molecular Devices, LLC and using borosilicate glass pipettes with filament, OD 1.5 mm, ID 1.10 mm, Sutter and the input resistance was in the range of 3-9 MΩ. RNA was extracted with a 1440A Digidata AD board Molecular Devices, LLC under pClamp v10. Electrodes pipettes were filled with in mM: 100 KCl, 35 N-methylglucamine NMG, 10 EGTA, 1 CaCl2, 4 MgCl2, and 10 HEPES pH 7.3, 290 mOsm for the RNA extraction from the TOV-21G cells. Electrodes were filled with in mM: 130 K-gluconate, 10 KCl, 10 HEPES, 10 EGTA, 2 MgCl2, 2 Na-ATP, 0.2 Na-GTP, and 5 glutathione pH 7.3, 280-290 mOsm for the RNA extraction from the Thy1-YFP L5 neurons. For the RNA extraction from the Thy1-GCaMP6f L2/3 neurons, electrodes were filled with in mM: 110 K-gluconate, 4 KCl, 4 NaCl, 0.2 CaCl2, 10 HEPES, 1.1 EGTA, 2 Mg-ATP, 1 MgCl2, and 5 glutathione pH 7.2-7.3, 300 mOsm. Membrane voltages were corrected for an estimated liquid junction potential of about 10 mV. Perforation was performed using -escin antibiotics 50 M from a stock solution 25 mM respective for each cellular population. All solutions were made with nuclease-free, de-ionized, not DEPC-treated water Ambion AM 9938. Lucifer yellow 50 mM was added to the electrode intracellular working solution for all cellular populations. The intercellular working solution including the antibiotics and dye was prepared fresh daily and used at room temperature and were backfilled into the electrodes for the patch-clamp experiments. Holding potentials for TOV-21G cells and cortical neurons were -80 mV and -70 mV, respectively. Electrodes were made by a PP-830 Narishige puller and positive pressure was applied as the pipettes were advanced to the cell of interest. The leak current Ilk was then used for the holding current in the current-clamp protocol and it was noted before and after the current was injected in all cellular populations. Seven current injection steps of 5 pA each was applied for a duration of 500 ms per step for the RNA extraction. Following RNA extraction, electrodes were slowly retracted while leaving the cell intact in its native environment, and the pipette solution was collected for sequencing. Each sample tube was prefilled with 2 µL of IGEPAL working mixture per tube, and positive pressure was applied to eject the internal contents of the electrode into a sample tube. The IGEPAL working mixture contained 65 µL nuclease-free de-ionized water Ambion, AM9938, 25 µL RNaseOUT™ Recombinant Ribonuclease Inhibitor ThermoFisher, 10 µL IGEPAL CA-630 Alfa Aesar, J61055 and was stored in 4°C for up two weeks. RNA was collected in 0.5 mL tubes Protein LoBind Tube 0.5 mL, Eppendorf, 022431064. After RNA extraction, samples were transferred on dry ice and stored at -80°C. After each RNA extraction, the electrode holder and silver-chloride recording electrode were cleaned with 70% ethanol. Cytosolic extraction for all cellular populations was performed by first doing whole-cell patch-clamp, then applying negative pressure light suction to harvest cellular content into IGEPAL working mixture.
The cDNA libraries were prepared using Ovation SoLo RNA-Seq System Tecan Genomics.  UMIs are used to eliminate possible PCR duplicates in sequencing datasets and facilitate unbiased gene expression profiling. For some experiments, ERCC RNA Spike-In Mix Thermo Fisher Scientific was included in the library preparation. The processed libraries were assessed for its size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent Technologies. The libraries were pooled and loaded onto a TruSeq SBS v3 flow cells on an Illumina HiSeq 2500 Illumina or an S1 flow cell on an Illumina NovaSeq 6000 Illumina , and run for 2X50 cycles according to the manufacturer's instructions. De-multiplexed and adapter-trimmed sequencing reads were generated using Illumina bcl2fastq version 2.18.0.12 allowing no mismatches in the index read.

treatment_protocol: For some experiments, TOV-21G cells were cultured in the Complete Growth Medium added with a IκB kinase IKK inhibitor, IKK-16 IKK Inhibitor VII Sigma-Aldrich at 1 µM for 72 hours before RNA collection.

tag: collection

value: Water


title: CHD8 Thy1 CKO input rep 1


title: sc300KO

value: Olfm2 knockout

value: adipose tissue, sc


title: sc306KO


title: CHD8 Thy1 CKO input rep 2

value: Testis


title: CD66a+_colon_cells Symptomatic_control_8

value: Male

value: Ex-smoker


title: NC_3


title: CHD8 Thy1 CKO ChIP rep 2

value: 10 dpp


title: CHD8 Thy1 control ChIP rep 2

value: male


title: NC_2


title: CHD8 Thy1 control ChIP rep 1

value: CHD8 (in-house made)


title: sc287WT

value: Wild-type


title: CD44+_colon_cells Symptomatic_control_8


title: CD66a+_colon_cells Symptomatic_control_10

value: Female


title: CHD8 Thy1 control input rep 2


title: CHD8 unsorted WT ChIP rep 3

value: Testicular cells

value: WT

value: 12 dpp


title: NC_1


title: CHD8 unsorted WT ChIP rep 2


title: CHD8 Thy1 control input rep 1


title: BMDCs treated with circRNA for 24 h replicate 3

city: Richmond

first: Guizhi

last: Zhu

state: VA

address: 410 N 12th St

institute: Virginia Commonwealth University

data_processing:
merging reads with bbmerge [bbmerge.sh in1=${FASTA_R1} in2=${FASTA_R2} out=${merged_reads} outu1=${unmerged1} outu2=${unmerged2}]
alignment with bowtie2 [bowtie2 -x ${REF_CIRCRNA_INDEX} ${merged_reads} -p 16 --no-unal --sensitive-local --rg-id ${filename} --rg SM:${filename} --rg LB:${filename} --rg PU:${filename} --rg PL:"ILLUMINA" 2> circRNA_vaccine/${filename}_bt2_2xseq.circ.log | $samtools sort -@ 16 -O bam > ${OUT_FILE}]
variant call step 1: [lofreq viterbi -f ${REF_CIRCRNA} ${OUT_FILE} | $samtools sort - > ${f_bam_viterbi}]
variant call step 2: [lofreq indelqual -f ${REF_CIRCRNA} --dindel ${f_bam_viterbi} | $samtools sort - > ${f_bam_indelqual}]
variant call step 3: [lofreq alnqual -b ${f_bam_indelqual} ${REF_CIRCRNA} | $samtools sort - > ${f_out_bam}]
variant call step 4: [lofreq call-parallel --pp-threads 48 -f ${REF_CIRCRNA} -o ${f_out_vcf} --no-default-filter --bonf 1 --sig 1 --call-indels ${f_out_bam}]
Assembly: circRNA sequence
Supplementary files format and content: VCFs - detected SNPs and INDELs in each sample
Supplementary files format and content: xlsx - summary of detected SNPs (authenticity rates)

extract_protocol:
circRNA were recovered from the corresponding transfected cells, total RNA was isolated using Allprep DNA/RNA/miRNA Universal Kit (QIAGEN). Synthetic circRNA without cell transfection was used as a control.
circRNA libraries were constructed using 2 μg total RNA (RIN > 7), ribosomal RNA was depleted using Ribo-Zero as well as an enzymatic depletion method (Illumina), and was purified with AMPure XP Beads (Beckman Coulter). Linear RNA was then digested by RNase R (Biosearch Technologies). The resulting circRNA was purified with AMPure XP Beads. circRNA was then cation fragmented at 95 oC for 2 min. Next, reverse transcription and library construction were performed using Illumina® Stranded Total RNA Prep, followed by ligation with Ribo-Zero Plus Sample Preparation Guide (Illumina). Final libraries were size analysis by Agilent HS DNA chips (Agilent) and quantified by Qubit dsDNA HS Assay (Invitrogen). Following quality control, the resulting barcoded libraries were pooled in equal molarities and were paired-end (2 x 150 bp) sequenced on a NextSeq 2000 instrument (Illumina).

tag: cell line

value: mouse bone marrow dendritic cells

value: bone marrow cells

value: No treatment


title: CHD8 unsorted WT input rep 3


title: CHD8 unsorted WT ChIP rep 1


title: CD44+_colon_cells Symptomatic_control_7

value: Never


title: CD66a+_colon_cells Symptomatic_control_7


title: CHD8 unsorted WT input rep 2


title: CD66a+_colon_cells Symptomatic_control_6


title: BMDCs treated with circRNA for 24 h replicate 2


title: CD44+_colon_cells Symptomatic_control_6


title: CHD8 unsorted WT input rep 1


title: cKit CHD8 CKO rep 3

description: mRNA

value: c-Kit+ Spermatogonia


title: cKit CHD8 CKO rep 2

description: mRNA


title: BMDCs treated with circRNA for 24 h replicate 1


title: CD66a+_colon_cells Symptomatic_control_5


title: sc286WT

value: adipose tissue, sc


title: CD66a+_colon_cells Symptomatic_control_4


title: synthetic circRNA replicate 3


title: synthetic circRNA replicate 2


title: cKit CHD8 CKO rep 1

description: mRNA

value: Testis


title: synthetic circRNA replicate 1


title: CD44+_colon_cells Symptomatic_control_5

value: Male


title: cKit control rep 2

description: mRNA


title: cKit control rep 1

description: mRNA


title: cKit control rep 3

description: mRNA


title: Thy1 CHD8 CKO rep 3

description: mRNA

value: Thy1+ Spermatogonia


title: CD44+_colon_cells Symptomatic_control_4


title: Thy1 CHD8 CKO rep 2

description: mRNA

value: 10 dpp


title: tumor treated with circRNA + anti-PD-1 replicate 3

data_processing:
Raw reads QC with fastqc [fastqc ${FASTA} -t ${NTHRDS} --outdir=${OUTDIR} --extract --quiet]
Trimming adapters with BBMap tools [BBMap/bbmap/bbduk.sh in1=${FASTA_R1} in2=${FASTA_R2} out1=${OUT1} out2=${OUT2} ref=${ref} stats=${fbname}_stats.txt threads=${NTHRDS} ktrim=r k=23 mink=11 hdist=1 tbo]
Alignment with STAR-2.7.9a [${SPLICE_AWARE_ALIGNER_} --runThreadN ${NTHRDS} --genomeDir ${INDEX_DIR} --readFilesIn ${FASTA_R1} ${FASTA_R2} --readFilesCommand gunzip -c --outFileNamePrefix ${OUT_FileNamePrefix} --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts]
Library strandness inferred with RSeQC tool [RSeQC/bin/infer_experiment.py --input-file=$INPUT_FILE --refgene=$REFGENE_BED]
Counting with featureCounts from subread-2.0.3-Linux-x86_64 [featureCounts -p --countReadPairs -B -T 16 -s 2 -t exon -g gene_name -a ${GTF_} -o ${FILE_OUT} ${FILES_}]
Assembly: mm39vM30
Supplementary files format and content: TXT file: full featureCounts results
Supplementary files format and content: CSV file: filtered read counts table [keeping genes with row sum >= 10]

source_name: tumor tissue

extract_protocol:
Total RNA was isolated following the instructions for the AllPrep DNA/RNA Mini Kit (QIAGEN) with in-column DNase 1 digestion to ensure DNA-free RNA. The integrity of extracted RNA was analyzed using the Agilent RNA 6000 Pico Kit (Agilent).
An aliquot of 1 μg of total RNA (RIN > 8) was used to prepare mRNA-seq libraries following the instruction of Illumina stranded mRNA-seq preparation Guide (Illumina). In short, mRNA was captured by oligo (dT) magnetic beads from total RNA, cation fragmented, and reverse transcribed into complementary DNA (cDNA). cDNA was end repaired, ligated with RNA index anchor and PCR amplified to produce indexed libraries with IDT for illumined UD indexes. Following quality control, the resulting barcoded libraries were pooled in equal molarities and were paired-end (2 x 150 bp) sequenced on NextSeq 2000 instrument (Illumina).

value: tumor tissue

value: tumor cells

value: circRNA + anti-PD-1


title: Thy1 CHD8 CKO rep 1

description: mRNA

value: male


title: CD66a+_colon_cells Symptomatic_control_3

value: Female


title: Thy1 control rep 3

description: mRNA


title: Thy1 control rep 2

description: mRNA


title: tumor treated with circRNA + anti-PD-1 replicate 1

value: WT


title: CD44+_colon_cells Symptomatic_control_3


title: tumor treated with circRNA + anti-PD-1 replicate 2


title: CD66a+_colon_cells Symptomatic_control_2

value: Current


title: Thy1 control rep 1

description: mRNA


title: tumor treated with circRNA replicate 3

value: circRNA


title: CD44+_colon_cells Symptomatic_control_2


title: tumor treated with circRNA replicate 2


title: CD66a+_colon_cells Symptomatic_control_1


title: tumor treated with circRNA replicate 1


title: MLE-12 cells, NP-2 (RNA-seq)

city: hefei

first: Se

middle: Ruo

last: Li

state: anhui

address: furong road 678

department: Respiratory and Critical Care Medicine

institute: The Second Affiliated Hospital of Anhui Medical University

data_processing:
Reads were aligned to the mouse Ensemble genome GRCm38 using Hisat2 aligner (v2.1.0) under parameters: “--rna-strandness RF”. The reads mapped the genome were calculated using featureCounts (v1.6.3). Differential gene expression analysis was performed using the DESeq2 R-package.GO and KEGG analysis were performed using clusterProfiler R package (v3.6.0).
Assembly: mm10
Supplementary files format and content: All.count_mRNAseq.txt (tab-delimited text files include count values for each Sample)

source_name: lung

extract_protocol:
Total RNA was extracted from each tissue sample using the Trizol method.
VAHTS Stranded mRNA-seq Library Prep Kit for Illumina V2 (Vazyme Biotech, NR612-02) was used for library preparation according to the instructions.

value: lung


title: MLE-12 cells, NP-3 (RNA-seq)


title: MLE-12 cells, NP-2 (Ribo-seq)

data_processing:
Adapter sequences were removed from raw sequencing data using cutadapt software. Meanwhile, reads with length between 25 and 35 bp were kept for downstream analysis. Then reads were aligned to rRNA and tRNA sequences so as to remove rRNA and tRNA reads using bowtie software, remaining reads were used to align to reference genome and transcriptome(Ensembl Version 91)  using hisat2 and bowtie software separately. The trinucleotide periodicity of ribosomes and codon usage frequency were estimated using revised riboWaltz package. ORF identification was performed using Price software. Read counts were calculated using featureCounts software. Raw counts were further normalized as RPKM values using fpkm function in DESeq2 package. Translational efficiencies were determined as the ratio of (normalized abundance determined by ribosome profiling)/(normalized abundance determined by RNA-seq). GO and KEGG analysis were performed using clusterProfiler package in R software.
Assembly: mm10
Supplementary files format and content: All.count.txt (tab-delimited text files include count values for each Sample)
Library strategy: Ribo-seq

extract_protocol:
Ribosome profiling was performed using Epi™ Ribosome Profiling Kit (Epibiotek, R1814). Subsquently, RPFs (ribosome-protected RNA fragments) was extracted using RNA clean&ConcentratorTM-5 kit (ZYMO, R1016).
EpiTM RiboRNA Depletion Kit (Mouse) (Epibiotek, R1805) was used for rRNA depletion. Sequencing libraries were constructed using QIAseq miRNA Library kit (QIAGEN, 1103679).

treatment_protocol: A total of 10^7 cells were prepared for cell lysis. Then, the cell medium was discarded, and the cells were washed twice with ice-cold PBS containing 100 μg/mL cycloheximide (Adooq, 66-81-9)


title: MLE-12 cells, Ctrl1 (RNA-seq)

value: control


title: CD44+_colon_cells Symptomatic_control_1

data_processing:
Processing of the raw reads: nf-core/smrnaseq v1.0.0 analysis pipeline with default parameters and "nextflex" 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 and additional 4 nucleotides from both 5’ and 3’ ends of 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

extract_protocol:
Standard protocol of Single Cell RNA Purification Kit (Norgen)
Standard protocol of NEXTFLEX Small RNA-seq Kit v3 (Bioo Scientific)

value: Never


title: MLE-12 cells, NP-3 (Ribo-seq)


title: MLE-12 cells, Ctrl2 (RNA-seq)


title: MLE-12 cells, Ctrl2 (Ribo-seq)


title: MLE-12 cells, Ctrl1 (Ribo-seq)


title: tumor treated with PBS replicate 2

value: PBS


title: tumor treated with PBS replicate 3