title: intermittent fasted, ctrl [HFD-IF]

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

description: 10X genomics

data_processing:
Demultiplexing, barcode processing, gene counting using the Cell Ranger software v5.0.0
Cellbender, to distinguish cell-containing droplets
DoubletFinder, to exclude potential droplets
Seurat pipeline for batch-correction, clustering and signature gene identification
Cellchat, for Ligand-receptor interactions
Assembly: GRCm38.p6 GENCODE Release M23
Supplementary files format and content: Tab-separated values files and matrix files

source_name: eWAT

extract_protocol:
eWAT depots were immediately flash frozen in liquid nitrogen after harvesting. Frozen tissues were thawn, carefully minced in lysis Buffer (10 mM Tris-Hcl, 146 mM NaCl, 21 mM MgCl2, 1 mM CaCl2, 0.1 % CHAPs pH=7.4) and grinded by using a tight douncer (Thermo Fisher Scientific, Waltham, MA, United States) on ice. Homogenized tissue was filtered through a 40 µm sieve (Corning, Massachusetts, United States), centrifuged at 500 x g for 5 min at 4 °C to pellet the nuclei and resuspended in buffer supplemented with 1 % BSA and 0.2 U/µl RNAnase inhibitor.
10X-based libraries were generated following manufacture’s protocol (10X Genomics, Pleasanton, CA, United States). Briefly, 1000 nuclei/ µl suspension was loaded to 10X chromium with a V3 kit. Sequencing was performed using a S1 Novaseq Flowcell (Illumina, Eindhoven, Netherlands).

value: eWAT

value: p53 floxed

value: Ctrl

value: intermittent fasted


title: Yeast, synHPRT1 integrated on chrXI, H3K4me3 ChIP, rep 1

status: Public on Jan 16 2024

type: SRA

city: New York

first: Brendan

middle: R.

last: Camellato

state: New York

address: 435 E 30th St

department: Institute for Systems Genetics

country: USA

institute: NYU Langone Health

library_source: genomic

data_processing:
Demultiplexing and fastq generation was performed using Illumina bcl2fastq v2.20
bowtie2 (v2.2.9) was used to align reads to custom references in which the synthetic HPRT1 and HPRT1R sequences were present on separate chromosomes or inserted at their specific integration sites in the SacCer_April2011/sacCer3 genome (produced using the reform tool, https://gencore.bio.nyu.edu/reform/).
Samtools (v1.9) was used to sort and index bam files.
Coverage tracks were produced in bigWig format using bamCoerage (deepTools v3.5.0) with options: -bs 1 --normalizeUsing RPGC --effectiveGenomeSize 12100000.
Signal enrichment peaks were called using macs2 (v2.1.0) callpeak with options: --nomodel -f BAMPE -g 1.2e7 --keep-dup all
Assembly: SacCer_April2011/sacCer3 + HPRT1/HPRT1R, SacCer_April2011/sacCer3 reformed with HPRT1/HPRT1R custom genomes
Supplementary files format and content: bigWig - coverage depth tracks for visualiztion
Supplementary files format and content: narrowPeak - called peaks of ChIP-seq signal enrichment (for H3K4me3 ChIP only)

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: BY4741 with synHPRT1 integrated on chrXI

growth_protocol: Yeast were cultured overnight at 30C in SC-Leu for YAC strains and YPD for integrated strains. In the morning, cultures were diluted to OD 0.1 and cultured for another 6 hours to reach  mid-log phase at an OD of ~0.6.

extract_protocol:
Cells were pelleted at 3,000 rcf for 5 minutes, washed twice with water, and resuspended in spheroplasting buffer (1.4 M Sorbitol, 40 mM HEPES-KOH pH 7.5, 0.5 mM MgCl2, 0.5 mM 2-mercaptoethanol). Spheroplasting was performed by adding 0.125 U/μL Zymolyase (Zymo Research E1004) and incubating at 37oC for 45 minutes on a rotator. Nuclei were prepared as previously described (Orsi, G.A., et al., Curr Protoc Mol Biol, 2015). Resuspended nuclei were split into aliquots of ~108 nuclei each and snap frozen in liquid nitrogen.
~10^8 frozen nuclei were thawed and processed for CUT&RUN using the CUTANA™ ChIC/CUT&RUN kit (EpiCy-pher 14-1048) according to the manufacturer’s protocol. Antibodies were  used at 0.5 μg: rabbit IgG negative control (EpiCypher 13-0042), H3K4me3 (EpiCypher 13-0041). Sequencing libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (New England Biolabs E7645L) according to the manufacturer's protocol.

tag: strain

tag: cell type

value: Yeast

tag: genotype


title: iRBD9

city: Shanghai

first: Wei

last: Liu

state: Shanghai

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology

country: China

institute: Chinese Academy of Sciences

library_source: transcriptomic

data_processing:
We used cutadapt to clip adaptor and filter low quality reads. Reads failing to match the adaptor or reads with lengths shorter than 17 nt were discarded. Redundant sequences were collapsed as useful reads for further analysis. Then, we aligned the reads to reference sequences by bowtie. To assess the expression levels of the miRNAs, the 3’ ends of miRNA with ≤ 3 nt deletions or additional sequences derived from pri-miRNAs were counted as miRNAs. The miRNA expression level was normalized by size factor from DEseq2.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include log2-transformed normalized read counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Extracellular vesicle

extract_protocol:
Frozen plasma samples were thawed in thermostat water bath for 2 min at 37 °C and then centrifuged at 2,500 × g for 15 min at 4 °C to remove precipitated proteins and lipids. ~0.5-1 ml plasma was used as the starting material for each EVs isolation by exoRNeasy Midi kit (Qiagen; Cat#77144) according to the manufacturer’s instructions. For EV-RNA extraction, 1 ml Trizol reagent (Invitrogen; Cat#15596026) was added to the column and centrifuged at 3,000 × g for 1 min. Total EV-RNA was isolated by Trizol reagent according to manufacturer’s recommendations.
A total amount of 0.5-1 ng RNA per sample was used as input material for the RNA sample preparations. The cDNA libraries establishment of small RNAs included adaptor ligation, adapter depletion, first-strand cDNA synthesis, Cas9/sgRNA in vitro cleavage treatment, PCR amplification and gel purification.

treatment_protocol: For each blood collection, 2 ml venous blood was collected into 10 ml BD K2EDTA Vacutainer tubes to prevent coagulation. The anticoagulant-treated blood samples were immediately inverted several times and transferred to 2 ml conical tubes (Eppendorf; Cat# 0030120094). To obtain plasma, blood samples were centrifuged at 1,300 × g for 10 min at room temperature (RT). The upper layer containing plasma was transferred to new tubes and centrifuged twice at 2,500 × g for 15 min at RT to obtain platelet poor plasma (PPP). Each plasma supernatant was carefully transferred to 1 ml fresh tubes and then stored at -80 °C until further use.

tag: tissue

value: Blood plasma

tag: disease state

value: iRBD


title: Liver, Chow Vehicle 24 w, Rep 2 [16184]

city: Hørsholm

first: Henrik

last: Hansen

address: Hørsholm Kongevej 11

department: Histology & NGS

country: Denmark

institute: Gubra

data_processing:
Reads were aligned to the GRCm38 Ensembl Mus musculus genome and counted using STAR v.2.7.0f with default settings.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text file contaning raw counts from each sample

molecule: polyA RNA

organism: Mus musculus

source_name: Liver

extract_protocol:
Liver tissue (Chow mice, GAN DIO-NASH mice, and chow-reversal mice) were collected and snap-frozen in liquid nitrogen. RNA was isolated using the NucleoSpin® kit (MACHEREY-NAGEL).
RNA sequence libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, USA) and sequenced on the NextSeq 500 (Illumina) with NextSeq 500/550 High Output Kit V2 (75 CYS, Illumina, San Diego, USA).

value: Liver

tag: treatment

value: Chow Vehicle 24 w


title: Liver, Vehicle 8 w, Rep 2 [16185]

value: Vehicle 8 w


title: Yeast, synHPRT1 YAC, H3K4me3, rep 2

source_name: BY4741 with synHPRT1R YAC


title: Yeast, synHPRT1 YAC, IgG ChIP, rep 2


title: intermittent fasted, p53 KO [HFD-IF-KO]

description: 10X genomics

library_source: transcriptomic single cell

value: Adipoq-CreERT2 x p53-floxed

value: KO


title: Liver, Chow-reversal 24 w, Rep 1 [16183]

value: Chow-reversal 24 w


title: iRBD8


title: iRBD7


title: hTNFtg197 + Il23mc Fap+ synovial cells HTO library

city: Erlangen

first: Hashem

last: Mohammadian

address: Ulmenweg 18

department: Department of Medicine 3 - Rheumatology and Immunology

country: Germany

institute: University of Erlangen-Nürnberg

description:
5 individual animals (HTO#1/2/3/4/5 hTNFtg197 + Il23mc)
FapPos_hTNFtg_Il23mc_barcodes.tsv.gz
FapPos_hTNFtg_Il23mc_features.tsv.gz
FapPos_hTNFtg_Il23mc_matrix.mtx.gz

library_source: other

data_processing:
The barcoded processing, gene counting and HTO processing were made using the Cell Ranger software v6.0.6
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: protein

source_name: protein

extract_protocol:
Cells were sorted and purified cells were stained for 30 min on ice in PBS containing 1 % (w/v) BSA with hashtag antibodies (TotalSeq-B0301/B0302/B0303/B0304/B0305 anti-mouse Hashtag 1/2/3/4/5, respectively, Biolegend). Cells were washed, counted and concentrated to 1,000 cells / µl prior to pooling.
Up to 25,000 cells (hyper-loading) pooled from 4 animals were loaded into a single well of a Chromium chip G (10x Genomics). 3’ gene expression libraries were generated using Chromium Next GEM Single Cell 3' Kit 3.1 with 3' Feature Barcode Kit and dual indexing (10x Genomics protocol CG000316 Rev C or D). Libraries were sequenced as PE150 by Illumina sequencing to 65-80% saturation by the external provider Novogene.

value: protein

tag: library type

value: HTO

tag: antibodies/tags

value: mouse_1:ACCCACCAGTAAGAC, mouse_2:GGTCGAGAGCATTCA, mouse_3:CTTGCCGCATGTCAT, mouse_4:AAAGCATTCTTCACG, mouse_5:CTTTGTCTTTGTGAG


title: ad libitum fed, ctrl [HFD-AL]

description: 10X genomics


title: Yeast, synHPRT1 YAC, IgG ChIP, rep 1

source_name: BY4741 with synHPRT1 YAC


title: iRBD6


title: Yeast, synHPRT1 YAC, H3K4me3 ChIP, rep 1


title: Liver, Chow-reversal 16 w, Rep 1 [16180]

value: Chow-reversal 16 w


title: iRBD5


title: Liver, Vehicle 16 w, Rep 1 [16178]

value: Vehicle 16 w


title: hTNFtg197 + Il23mc + IL-17i and wilde type gene expression library

description:
4 individual animals (HTO#1/2/3 hTNFtg197 + Il23mc + anti-mIL-17a, HTO#4 HC)
hTNFtg_Il23mc_IL-17i_barcodes.tsv.gz
hTNFtg_Il23mc_IL-17i_features.tsv.gz
hTNFtg_Il23mc_IL-17i_matrix.mtx.gz

source_name: synovial ankle/wrist joints

value: synovial cells

value: synovial ankle/wrist joints

value: hTNFtg197+ and WT

value: Il23mc + IL-17i (wild type sample is untreated)

value: mRNA

tag: age

value: 8-10 weeks old


title: Liver, Chow-reversal 8 w, Rep 1 [16177]

value: Liver

value: Chow-reversal 8 w


title: hTNFtg197 + Il23mc + TNFi and wilde type healthy HTO library

description:
4 individual animals (HTO#1/2/3 hTNFtg197 + Il23mc + anti-hTNF, HTO#4 HC)
hTNFtg_Il23mc_TNFi_barcodes.tsv.gz
hTNFtg_Il23mc_TNFi_features.tsv.gz
hTNFtg_Il23mc_TNFi_matrix.mtx.gz

value: Mouse 1 hTNFtg197+:ACCCACCAGTAAGAC, Mouse 2 hTNFtg197+:GGTCGAGAGCATTCA, Mouse 3 hTNFtg197+:CTTGCCGCATGTCAT, Mouse 4 wt control:AAAGCATTCTTCACG


title: hTNFtg197 + Il23mc + IL-17i and wilde type HTO library


title: Yeast, synHPRT1R integrated on chrXI, rep 2, CAGE

data_processing:
Demultiplexing and fastq generation was performed using Illumina bcl2fastq v2.20
5’ reads only were aligned using bowtie2 (v2.2.9) to custom references in which the synthetic HPRT1 and HPRT1R sequences were present on separate chromosomes or inserted at their specific integration sites in the SacCer_April2011/sacCer3 genome (produced using the reform tool, https://gencore.bio.nyu.edu/reform/).
Samtools (v1.9) was used to sort and index bam files.
Coverage tracks were produced in bigWig format using bamCoerage (deepTools v3.5.0) with options: -bs 1 --normalizeUsing RPGC --effectiveGenomeSize 12100000 --filterRNAstrand forward/reverse --scaleFactor (-)1 --extendReads 100
Signal enrichment peaks were called using macs2 (v2.1.0) callpeak with options: --nomodel -f BAM -g 1.2e7 --keep-dup all
Assembly: SacCer_April2011/sacCer3 + HPRT1/HPRT1R, SacCer_April2011/sacCer3 reformed with HPRT1/HPRT1R custom genomes
Supplementary files format and content: bigWig - coverage depth tracks for visualiztion
Supplementary files format and content: narrowPeak - called peaks of CAGE-seq signal enrichment

source_name: BY4741 with synHPRT1R integrated on chrXI

extract_protocol:
Yeast were pelleted at 3,000 rcf for 5 minutes, washed once with water, pelleted again at 3,000 rcf for 5 minutes, and cell pellets were frozen at -80oC. Frozen pellets were resuspended in 200 μL lysis buffer (50 mM Tris-HCl pH 8, 100 mM NaCl) and lysed by disruption with an equal volume of acid washed glass beads, vortexing 10 x 15 seconds. 300 μL lysis buffer was added and samples were mixed by inversion followed by a short centrifugation to collect all liquid in the tube. 450 μL of supernatant was mixed with an equal volume of phenol:chloroform:isoamyl alcohol, vortexed for 1 minute, and centrifuged at max speed for 5 minutes. 350 μL of the aqueous layer was then mixed with an equal volume of phenol:chloroform:isoamyl alcohol, vortexed for 1 minute, and centrifuged at max speed for 5 minutes. RNA was precipitated from 300 μL of the aqueous phase by adding 30 μL of 3 M NaOAc and 800 μL of cold 99.5% ethanol, briefly vortexing, and centrifuging at max speed for 10 minutes. The pellet was rinsed with 70% ethanol and dried at room temperature before dissolving in 100 μL of RNase-free DNase set (Qiagen 79254) and incubating at room temperature for 10 minutes to remove DNA. RNA was purified using the RNeasy Plus Mini kit (Qiagen 74136) and eluted in 30 μL RNase-free water.
CAGE libraries were prepared as previously described (Murata, M., et al., Methods Mol Biol, 2014), starting with 5 μg RNA, with the following modifications. SuperScript™ IV Reverse Transcriptase (Invitrogen 18090010) was used for the reverse transcription step. AMPure XP beads (Beckman Coulter A63881) were used for all bead cleanup steps. We also used custom-made linker and primer oligos so that linkers are universal to all samples and primers contain sample-specific barcodes. Libraries were amplified using universal forward and reverse primers with 20 cycles of PCR

value: Yeast


title: iRBD3

value: Blood plasma

value: iRBD


title: iRBD4


title: Yeast, synHPRT1R integrated on chrXI, rep 1, CAGE


title: hTNFtg197 + Il23mc + TNFi and wilde type gene expression library

value: Il23mc + TNFi (wild type sample is untreated)


title: Yeast, synHPRT1R YAC, rep 2, CAGE


title: iRBD2


title: Liver, Chow Vehicle 24 w, Rep 1 [16174]

value: Chow Vehicle 24 w


title: hTNFtg197 + Il23mc and wilde type healthy HTO library

description:
4 individual animals (HTO#1/2/3 hTNFtg197 + Il23mc, HTO#4 HC)
hTNFtg_Il23mc_barcodes.tsv.gz
hTNFtg_Il23mc_features.tsv.gz
hTNFtg_Il23mc_matrix.mtx.gz

value: protein

value: HTO


title: hTNFtg197 + Il23mc Fap+ synovial cells gene expression library


title: PD53

value: PD


title: hTNFtg197 + Il23mc and wilde type healthy gene expression library

value: synovial cells

value: Il23mc (hTNFtg197+) and untreated (WT)


title: Yeast, synHPRT1R YAC, rep 1, CAGE


title: Male genitalia, SpDAM-, Msx2Rtta-, Dox+, Tam+, biorep4

city: St. Louis

first: Meade

last: Haller

state: MO

address: 660 S Euclid Ave

institute: Washington University School of Medicine

data_processing:
Reads were aligned to the mm10 mouse reference genome sequence using the Burrows-Wheeler Aligner (BWA) using the mem algorithm.
Per base read counts were obtained using Samtools mpileup algorithm.
BedGraph files were created using a custom script using mpileup files as input.
BedGraph files were averaged between biological replicates and averages were compared between sample conditions using a custom script. Analysis was performed pairwise between each experimental sample and its pooled littermate controls.
Nearest mouse genes were identified using a custom script and a reference file of human-mouse ortholog gene locations within the mm10 mouse reference sequence.
HOMER (http://homer.ucsd.edu/homer/ngs/)70 was used to call and annotate SpDam peaks.
Assembly: mm10
Supplementary files format and content: txt

source_name: external genitalia

growth_protocol: plug was considered E0.5

extract_protocol:
Freshly collected, never-frozen tissue followed by gentle enzymatic (non-mechanical) digestion is imperative to minimize background signal due to DNA breakage prior to DpnI methyl-specific blunt-end digestion. Freshly collected genital tubercles were subjected to digestion in 500uL PK lysis solution (100mM TrisCl pH 8.5, 5mM EDTA, 2% SDS, 20mM NaCl, with 0.5uL proteinase K per specimen, incubated at 52-55C overnight with shaking) followed by phenol-chloroform DNA extraction using Gel Lock Gel Heavy according to manufacturer’s protocol.
Following precipitation, resuspension, and treatment with RNaseA, 2.5ug gDNA per specimen was subjected to DpnI digestion (NEB cat. #R0176S) at 37C overnight in a total volume of 10uL and 20U DpnI enzyme per reaction, with heat inactivation at 80C for 20 minutes. In the same tube, samples were immediately subjected to bluntend ligation of double stranded adaptors (pre-annealed oligos 5’-CTAATACGACTCACTATAGGGCAGCGTGGTCGCGGCCGAGGA-3’ and 5’-TCCTCGGCCG-3’ using T4 ligase (NEB cat. #M0202S) overnight at 16C with inactivation at 65C for 10 minutes. Immediately following adapter ligation, 3uL of DNA was subjected to adapter-specific PCR amplification using GoTaq-G2 polymerase (One 50uL RXN = 3uL adapter-ligated gDNA, 10uL 5x GoTaq buffer, 2uL 25x dNTPs, 1.25uL 50uM primer 5’phospho-GGTCGCGGCCGAGGATC-3’, 33.5uL water, and 0.25uL GoTaq enzyme) under the cycling conditions pre-PCR 72C 10min  pre-PCR 94C 1min  pre-PCR 55C 5min  pre-PCR 72C 15min  6 cycles of 94C 1min followed by 55C 1min followed by 72C 10min,  25 cycles of 94C 1min followed by 55C 1min followed by 72C 2min  4C hold. The use of GoTaq-G2 negates the need for A-tailing prior to sequencing preparation due to the presence of single 3’-A overhangs in >80% of PCR products. At least 8 PCR reactions per specimen were pooled for PCR cleanup (Qiagen cat. #28104) to maximize library yield, with one additional reaction being used to run to agarose gel for quality control alongside untreated negative controls. Each DNA specimen was then prepared for sequencing by T4-ligation of pre-annealed Illumina index adapters (3uL at 50uM per 50uL RXN) in a reaction containing 5ug DNA according to manufacturer’s protocol (NEB cat. #M0202S) overnight at 16C with inactivation at 65C for 10 minutes. Samples then underwent a second PCR cleanup, followed by size-exclusion by gel purification to avoid adapter dimers (Qiagen cat. #28704), followed by a third PCR cleanup to minimize buffer carryover. Samples then underwent an enrichment PCR prior to sequencing, again performing 8 or more reactions per sample to increase yield and pooling during purification. Phusion enrichment PCR (NEB cat. #M0530S) was performed using 250ng DNA per reaction and Y-adapter specific primers 5’- AATGATACGGCGACCACCGAGATCTACAC-3’ and 5’-CAAGCAGAAGACGGCATACGAGAT-3’ with cycling conditions 98C 30sec  20 cycles of 98C 40sec followed by 60C 30 sec followed by 72C 45sec  72C 5min  4C hold. This was followed by PCR cleanup, size-exclusion by gel extraction, and a final PCR-cleanup to minimize buffer carryover from gel extraction. Indexed samples were pooled at equimolar ratios for Illumina sequencing.
OTHER: In vivo SpDAM seq

treatment_protocol: Doxycycline hyclate (Sigma cat. # D9891-10G) was prepared in water at a concentration of 25mg/mL and given to the females at concentration of 100mg/kg by daily gavage from E13.5 to E16.5. Similarly, tamoxifen (Sigma cat. #T5648-1G) was prepared in corn oil at a concentration of 25mg/mL and given to the females at a concentration of 200mg/kg by daily gavage from E14.5 to E16.5. Embryos were harvested at E17.5 and genital tubercles were carefully dissected for downstream preparation.

value: external genitalia

tag: developmental stage

tag: Sex

value: Male

value: SpDAM-; Msx2Rtta-

value: Dox+; Tam+


title: iRBD1


title: Liver, Vehicle 24 w, Rep 1 [16181]

value: Liver

value: Vehicle 24 w


title: Male genitalia, SpDAM-, Msx2Rtta-, Dox+, Tam+, biorep5


title: Synovial Fibs, R5 healthy/STA mice HTO library

description:
R5_STA_r2_Fibroblasts_barcodes.tsv.gz
R5_STA_r2_Fibroblasts_features.tsv.gz
R5_STA_r2_Fibroblasts_matrix.mtx.gz

extract_protocol:
Cells were sorted and purified cells were stained for 30 min on ice in PBS containing 1 % (w/v) BSA with hashtag antibodies (TotalSeq-B0301/B0302/B0303/B0304B0305 anti- mouse Hashtag 1/2/3/4/5, respectively, Biolegend). Cells were washed, counted and concentrated to 1,000 cells / µl prior to pooling.
Up to 25,000 cells (hyper-loading) pooled from 4 animals were loaded into a single well of a Chromium chip G (10x Genomics). 3’ gene expression libraries were generated using Chromium Next GEM Single Cell 3' Kit 3.1 with 3' Feature Barcode Kit and dual indexing (10x Genomics protocol CG000316 Rev D). Libraries were sequenced as PE150 by Illumina sequencing to 65-80% saturation by the external provider Novogene.


title: Male genitalia, SpDAM-, Msx2Rtta-, Dox+, Tam+, biorep3


title: PD51


title: Yeast, synHPRT1 YAC, rep 2, CAGE


title: Male genitalia, SpDAM-, Msx2Rtta-, Dox+, Tam+, biorep2


title: Synovial Fibs, R5 healthy/STA mice gene expression library

value: synovial ankle/wrist joints

value: R5 x R26tdTomato

value: Il5 wt/Cre; R26 tdTom/tdTom

value: unstreaed/STA

value: mRNA

value: 8-10 weeks old


title: PD50

value: Blood plasma


title: Yeast, synHPRT1 YAC, rep 1, CAGE

value: Yeast


title: Male genitalia, SpDAM-, Msx2Rtta-, Dox+, Tam+, biorep1


title: Liver, Vehicle 8 w, Rep 1 [16175]

value: Vehicle 8 w


title: Yeast, synHPRT1 integrated on chrXI, rep 2, CAGE


title: Synovial ILCs, R5 healthy/STA mice HTO library

description:
R5_STA_r2_ILCs_barcodes.tsv.gz
R5_STA_r2_ILCs_features.tsv.gz
R5_STA_r2_ILCs_matrix.mtx.gz

value: protein

value: HTO


title: Synovial ILCs, R5 healthy/STA mice gene expression library

value: synovial cells

value: untreated/STA


title: Male genitalia, SpDAM+, Msx2Rtta+, Dox+, Tam+, biorep7

value: external genitalia

value: Male

value: SpDAM+; Msx2Rtta+


title: PD52

value: PD


title: PD49


title: Yeast, synHPRT1R YAC, rep 2

data_processing:
Demultiplexing and fastq generation was performed using Illumina bcl2fastq v2.20
bowtie2 (v2.2.9) was used to align reads to custom references in which the synthetic HPRT1 and HPRT1R sequences were present on separate chromosomes or inserted at their specific integration sites in the SacCer_April2011/sacCer3 genome (produced using the reform tool, https://gencore.bio.nyu.edu/reform/).
Samtools (v1.9) was used to sort and index bam files.
Coverage tracks were produced in bigWig format using bamCoerage (deepTools v3.5.0) with options: -bs 1 --normalizeUsing RPGC --effectiveGenomeSize 12100000.
Signal enrichment peaks were called using macs2 (v2.1.0) callpeak with options: --nomodel -f BAMPE -g 1.2e7 --keep-dup all
Assembly: SacCer_April2011/sacCer3 + HPRT1/HPRT1R, SacCer_April2011/sacCer3 reformed with HPRT1/HPRT1R custom genomes
Supplementary files format and content: bigWig - coverage depth tracks for visualiztion
Supplementary files format and content: narrowPeak - called peaks of ATAC-seq signal enrichment

extract_protocol:
~5x106 cells were taken from each culture, pelleted at 3,000 rcf for 5 minutes, washed twice with 500 μL spheroplasting buffer (1.4 M Sorbitol, 40 mM HEPES-KOH pH 7.5, 0.5 mM MgCl2), resuspended in 100 μL spheroplasting buffer with 0.2 U/μL zymolyase (Zymo Research E1004), then incubated for 30 minutes at 30°C on a rotator. Spheroplasts were washed twice with 500 μL spheroplasting buffer then resuspended in 50 μL 1x TD buffer with TDE (Illumina 20034197).
Tagmentation was performed for 30 minutes at 37oC on a rotator and DNA was purified using the DNA Clean and Concentrator 5 kit (Zymo Research D4004). PCR was performed as previously described (Buenrostro, J.D., et al., Curr Protoc Mol Biol, 2015) using barcoded primers for 11 total cycles.


title: Yeast, synHPRT1R integrated on chrXI, rep 1


title: Male genitalia, SpDAM+, Msx2Rtta+, Dox+, Tam+, biorep6

value: Dox+; Tam+


title: Male genitalia, SpDAM+, Msx2Rtta+, Dox+, Tam+, biorep5


title: Yeast, synHPRT1R integrated on chrXI, rep 2


title: Yeast, synHPRT1R YAC, rep 1


title: Yeast, synHPRT1 integrated on chrXI, rep 1, CAGE


title: Synovial ILCs, R5 STA + IL23  mice HTO library

description:
R5_STA_r1_ILCs_STA_Il23mc_barcodes.tsv.gz
R5_STA_r1_ILCs_STA_Il23mc_features.tsv.gz
R5_STA_r1_ILCs_STA_Il23mc_matrix.mtx.gz

value: mouse_1= "mouse 1 ILCs":ACCCACCAGTAAGAC,mouse_2= "mouse 2 ILCs":GGTCGAGAGCATTCA,mouse_3= "mouse 3 ILCs":CTTGCCGCATGTCAT


title: Yeast, synHPRT1 integrated on chrXI, rep 2


title: PD45


title: Synovial Fibroblasts, R5 healthy/STA/STA+Il23 mice HTO library

description:
R5_STA_r1_Fibroblasts_barcodes.tsv.gz
R5_STA_r1_Fibroblasts_features.tsv.gz
R5_STA_r1_Fibroblasts_matrix.mtx.gz

value: condition_1= "healthy":ACCCACCAGTAAGAC,condition_2= "STA":GGTCGAGAGCATTCA,condition_3= "STA + Il23":CTTGCCGCATGTCAT


title: PD46


title: Synovial ILCs, R5 STA + IL23 mice gene expression library

value: synovial ankle/wrist joints

value: R5 x R26tdTomato

value: Il5 wt/Cre; R26 tdTom/tdTom

value: STA + Il23mc


title: Yeast, synHPRT1 integrated on chrXI, rep 1

value: Yeast


title: Yeast, synHPRT1 YAC, rep 2


title: PD48

value: Blood plasma


title: Synovial ILCs, R5 STA mice HTO library

description:
R5_STA_r1_ILCs_STA_barcodes.tsv.gz
R5_STA_r1_ILCs_STA_features.tsv.gz
R5_STA_r1_ILCs_STA_matrix.mtx.gz

value: protein


title: Male genitalia, SpDAM+, Msx2Rtta+, Dox+, Tam+, biorep4


title: Male genitalia, SpDAM+, Msx2Rtta+, Dox+, Tam+, biorep3


title: Synovial ILCs, R5 STA mice gene expression library

value: STA

value: mRNA

value: 8-10 weeks old


title: Male genitalia, SpDAM+, Msx2Rtta+, Dox+, Tam+, biorep2

value: external genitalia


title: Yeast, synHPRT1 YAC, rep 1


title: PD43


title: PD47


title: ST, RNAseq, rep2

city: Austin

first: Mijeong

last: Kim

address: 2506 Speedway, NMS 4.246

institute: The University of Texas at Austin

description: Time_course_differentiation_EVT_count.xlsx

data_processing:
Paired-end or single reads were aligned to human transcript (hg38) using Salmon mapper (v1.4.0)
Expression levels of each gene were calculated using R library tximport as transcripts per million (TPM), and the count of each gene was quantified and normalized by R package DEseq2.
Assembly: hg38
Supplementary files format and content: Count information in excel files

source_name: Placenta

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (74136) following the manufacturer’s instructions.
mRNA was enriched from total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490). RNA-seq libraries were generated with 300 ng of total RNA using NEBNext Ultra II RNA Library Prep with (E7775) and NEBNext Multiplex Oligos for Illumina (E7600S) following the manufacturer’s protocol.

value: Placenta

tag: cell line

value: Human trophoblast stem cells


title: PD42

value: PD


title: Synovial Fibroblasts, R5 healthy/STA/STA+Il23 mice gene expression library

value: synovial cells

value: untreated/STA/STA + IL23mc


title: Male genitalia, SpDAM+, Msx2Rtta+, Dox+, Tam+, biorep1

value: Male

value: SpDAM+; Msx2Rtta+

value: Dox+; Tam+


title: Synovial ILCs, R5 healthy mice gene expression library

description:
R5_STA_r1_ILCs_HC_barcodes.tsv.gz
R5_STA_r1_ILCs_HC_features.tsv.gz
R5_STA_r1_ILCs_HC_matrix.mtx.gz

value: synovial ankle/wrist joints

value: R5 x R26tdTomato

value: Il5 wt/Cre; R26 tdTom/tdTom

value: untreated


title: PD40

value: Blood plasma


title: ST, RNAseq, rep1


title: EVT_D8, RNAseq, rep2


title: PD41


title: Il23mc induced arthritis, synovial and skin cells Balb/c background HTO

first: Simon

last: Rauber

department: Medicine 3

source_name: hind paw/ankle joint, skin from hind pwas

extract_protocol:
Cell suspension obtanied by tissue enzymatic digestion was stained with a cocktail of flow cytomety antibodies. Cell sorting was performed accordingly and the resulted cells population were incubated for 30 min on ice in PBS containing 1 % (w/v) BSA with hashtag antibodies (TotalSeq-B0301/B0302/B0303/B0304/B0305 anti-mouse Hashtag 1/2/3/4/5, respectively, Biolegend and anti-APC custom Hashtaq). Cells were washed, counted and concentrated to 1,000 cells / µl prior to pooling.
Up to 25,000 cells (hyper-loading) were loaded into a single well of a Chromium chip G (10x Genomics). 3’ gene expression libraries were generated using Chromium Next GEM Single Cell 3' Kit 3.1 with 3' Feature Barcode Kit and dual indexing (10x Genomics protocol CG000316 Rev C). Libraries were sequenced as PE150 by Illumina sequencing to 65-80% saturation by the external provider Novogene.

value: synovial and skin cells

value: Kaede +

value: HTO

value: #1 ACCCACCAGTAAGAC:skin CD45- KAEDEgreen, #2 GGTCGAGAGCATTCA:skin CD45+ KAEDEred, #3 CTTGCCGCATGTCAT:joint CD45- KAEDEgreen, #4 AAAGCATTCTTCACG:joint CD45+ KAEDEred, #5 CTTTGTCTTTGTGAG:joint CD45+ KAEDEgreen, #6 custom TTAACCGTCTCCCTT:skin CD45+ KAEDEgreen


title: PD44


title: EVT_D8, RNAseq, rep1

value: Placenta


title: Epithelial cells AT2-depleted and dividing epithelial cells, SRC mice, injured lung, day2

city: Heidelberg

first: Cihan

last: Erkut

address: Im Neuenheimer Feld 581

department: Applied Functional Genomics

institute: German Cancer Research Center

description: SRC Epithelial AT2-depleted day2

data_processing:
Raw sequencing data was processed with 10x Genomics Cell Ranger v3.1.0
Supplementary files format and content: Tab-separated value files and matrix files

source_name: lung

extract_protocol:
PBS-perfused lungs were inflated with 2 ml of digestion cocktail containing 50 U/ml dispase (Corning), 250 U/ml collagenase type I (Worthington), 5 U/ml elastase (Worthington), and 60 U/ml DNAse I (Roche). Trachea was clipped distally and lungs were dissected in a petri dish on ice to remove extrapulmonary airways (trachea and main bronchi). Lung lobes were placed in a C tube (Miltenyi) containing 3 ml of digestion cocktail, and the m_lung_01 program was run on gentleMACS (Miltenyi). C tubes were placed in a rotating incubation oven at 37ºC for 30 minutes. The m_lung_02 program was run again, and the tubes were placed on ice for the next steps. The lung cells were passed through a 70 µm cell strainer (Corning) and centrifuged at 400 g for 5 minutes. The pellet was resuspended in a red blood lysis buffer solution (0.15 M NH4Cl, 10 mM KHCO3, 0.1 mM EDTA), incubated for 2 minutes on ice, and washed with EasySep buffer (STEMCELL Technologies) at 400 g for 5 minutes. To isolate mesenchymal cells, a milder digestion cocktail was used containing only 375 U/ml collagenase and 60 U/ml DNase I.
Libraries were prepared using Chromium Next GEM Single Cell 3’ v2 (samples 1 to11) or Chromium Next GEM Single Cell 3’ v3.1 (samples 12 to16) and following the manufacturer’s protocol (10x Genomics)

value: lung

value: epithelial

value: Scgb1a1-CreER x Rosa26R-DTA x CycB1-GFP

value: 2 x 4mg tamoxifen


title: PD39

value: PD


title: Il23mc induced arthritis, synovial and skin cells Balb/c background GEX

value: hind paw/ankle joint, skin from hind pwas

value: mRNA

value: 8-10 weeks old


title: Il23mc induced arthritis, synovial and skin cells B6 background HTO


title: Epithelial cells AT2-depleted, SRC mice, uninjured lung, day0

description: SRC Epithelial AT2-depleted day0


title: EVT_D5, RNAseq, rep1

value: Human trophoblast stem cells


title: Epithelial cells AT2-depleted and dividing epithelial cells, SRC mice, injured lung, day4

description: SRC Epithelial AT2-depleted day4


title: EVT_D5, RNAseq, rep2


title: PD38


title: PD37


title: Synovial ILCs, R5 healthy mice HTO library

value: protein

value: mouse_1= "mouse 1 ILCs":ACCCACCAGTAAGAC,mouse_2= "mouse 2 ILCs":GGTCGAGAGCATTCA,mouse_3= "mouse 3 ILCs":CTTGCCGCATGTCAT


title: EVT_D4, RNAseq, rep1


title: Il23mc induced arthritis, synovial and skin cells B6 background GEX


title: Dividing mesenchymal cells, SRC mice, injured lung, day2

description: SRC Mesenc GFP+ day2

value: mesenchymal

value: 4mg tamoxifen


title: Epithelial cells AT2-depleted and dividing epithelial cells, SRC mice, injured lung, day3

description: SRC Epithelial AT2-depleted day3


title: EVT_D4, RNAseq, rep2


title: Epithelial cells AT2- and ciliated-depleted and dividing epithelial cells, SfSRC mice, injured lung, day3

description: SfSRC Epithelial AT2- and ciliated-depleted day3

value: Sftpc-CreER x Scgb1a1-CreER x Rosa26R-DTA x CycB1-GFP


title: Epithelial cells AT2- and ciliated-depleted and dividing epithelial cells, SfSRC mice, injured lung, day2

description: SfSRC Epithelial AT2- and ciliated-depleted day2


title: Mesenchymal cells, SRC mice, injured lung, day3

description: SRC Mesenc total day3


title: Mesenchymal cells, SRC mice, uninjured lung, day0

description: SRC Mesenc total day0


title: Mesenchymal cells, SRC mice, injured lung, day2

description: SRC Mesenc total day2


title: PD36

value: Blood plasma


title: EVT_D3, RNAseq, rep2


title: Epithelial cells AT2- and ciliated-depleted and dividing epithelial cells, SfSRC mice, uninjured lung, day0

description: SfSRC Epithelial AT2- and ciliated-depleted day0


title: EVT_D3, RNAseq, rep1


title: PD33


title: PD32


title: PD34


title: Dividing epithelial and mesenchymal cells, SRC mice, injured lung, day3

description: SRC GFP+ day3

value: epithelial and mesenchymal


title: EVT_D2, RNAseq, rep2

value: Placenta


title: Epithelial cells AT2- and ciliated-depleted and dividing epithelial cells, SRC mice, injured lung, day2

description: SRC Epithelial AT2- and ciliated- depleted day2

value: lung


title: Epithelial cells AT2- and ciliated-depleted and dividing epithelial cells, SRC mice, uninjured lung, day0

description: SRC Epithelial AT2- and ciliated- depleted day0

value: epithelial


title: Dividing epithelial and mesenchymal cells, SRC mice, injured lung, day2

description: SRC GFP+ day2

value: Scgb1a1-CreER x Rosa26R-DTA x CycB1-GFP


title: EVT_D2, RNAseq, rep1


title: Dividing mesenchymal cells, SRC mice, injured lung, day3

description: SRC Mesenc GFP+ day3


title: PD30


title: MG132 neurites rep3

city: Montreal

first: Celia

last: Alecki

state: QC

address: McIntyre Medical Sciences Building 3655 promenade Sir-William-Osler

country: Canada

institute: McGill University

data_processing:
Adaptors and sequence with a quality below 20 were removed using trimmomatic (galaxy version 0.38.0)
Reads were aligned on mm10 genome using RNA star (galaxy version 2.7.8a+galaxy0)
Number of reads per transcript was determined using FeatureCounts (galaxy version 2.0.1+galaxy2)
Differential gene expression was determined using DESeq2 (galaxy version 2.11.40.7+galaxy1)
Assembly: mm10
Supplementary files format and content: Featurecounts files, reads aligned on mm10 genome

source_name: Hippocampal neurons

extract_protocol:
RNA were isolated from neurites and soma as described in Arora et al., Bio-protocol, 2021
polyA selection and library preparation using kit KAPA Hyperprep RNA (Roche)

treatment_protocol: 10 uM MG132 for 7H

value: Hippocampal neurons

tag: culture

value: DIV17/18 primary neurons

value: neurites


title: PD31

value: PD


title: PD28


title: EVT_D1, RNAseq, rep1


title: Ctrl neurites rep3

value: Ctrl


title: PD29


title: MG132 soma rep3

value: soma


title: EVT_D1, RNAseq, rep2

value: Human trophoblast stem cells


title: Lung, COVID plasma and 1,25(OH)D3, 5

city: Athens

first: Spyros

last: Foutadakis

address: Soranou

country: Greece

institute: Biomedical Research Foundation Academy of Athens

description:
COVID_VITD_5
Normalised sequencing counts.xlsx

data_processing:
The quality of sequencing reads was assessed using the Fastqc algorithm (Galaxy Version 0.72+galaxy1).
Fastq files were aligned to the mouse genome version mm9 with the use of HISAT2 (Galaxy Version 2.1.0+galaxy7) using the Reverse Strand parameter.
Sequencing reads falling into genes were counted with HT-seq count algorithm (Galaxy Version 0.9.1) using the Union mode and Reverse Stranded options.
Coverage files in bigwig format were constructed using the bamcoverage option (Galaxy Version 3.3.2.0.0) from deeptools using RPKM normalization.
Assembly: mm9
Supplementary files format and content: Excel file containinng DESeq2 normalised counts for each sample
Supplementary files format and content: Excel file containinng DESeq2 results
Supplementary files format and content: bigwig files for each sample

source_name: mouse lung samples

extract_protocol:
RNA was isolated from mice lung segments stored in RNAlater (Qiagen, Hilden, Germany), following the RNeasy mini kit protocol (QIAGEN) according to the manufacturer's recommendations.
RNA-seq libraries were prepared with the NebNext Ultra II directional RNA library prep kit for Illumina following manufactrurer's protocols

treatment_protocol: Mice treated with intravenous injection of plasma from patients with COVID-19 ARDS  with or without 1,25(OH)D3 supplementation

value: mouse lung samples

value: WT

value: Mice were treated with intravenous injection of 100 μl plasma from patients with COVID-19 ARDS for 3 consecutive days plus 0.25μg human 1,25(OH)D3 for 3 consecutive days


title: TSC, RNAseq, rep1


title: Lung, COVID plasma and 1,25(OH)D3, 3

description:
COVID_VITD_3
Normalised sequencing counts.xlsx


title: TSC, RNAseq, rep2


title: PD27


title: MG132 neurites rep2


title: Lung, COVID plasma and 1,25(OH)D3, 4

description:
COVID_VITD_4
Normalised sequencing counts.xlsx


title: PD26


title: Lung, COVID plasma and 1,25(OH)D3, 1

description:
COVID_VITD_1
Normalised sequencing counts.xlsx


title: PD35


title: MG132 soma rep2


title: Lung, COVID plasma and 1,25(OH)D3, 2

description:
COVID_VITD_2
Normalised sequencing counts.xlsx


title: PD25


title: Lung, COVID plasma, 6

description:
COVID_6
Normalised sequencing counts.xlsx

value: Mice were treated with intravenous injection of 100 μl of plasma from patients with COVID-19 ARDS for 3 consecutive days


title: B3-Input

city: Suzhou

first: Jin

last: Tao

state: Jiangsu

address: 199 Ren-Ai Road

department: Physiology and Neurobiology

institute: Soochow University

data_processing:
adaptor and low-quality bases of raw reads were trimmed using cutadapt software (v1.9.3)
sequence reads were aligned to the rat genome version RN5 with HISAT2 software (v2.0.4)
MACS software was used to identify methylated genes in each sample
Differentially methylated genes were identified using diffReps software
MeRIP enriched regions (peaks) were visualized using Integrative Genomics Viewer (IGV)
Assembly: Rnor_5.0
Supplementary files format and content: "Methylated_RNA_sites.mRNA.xlsx" includes all methylated sites on all genes in each sample

organism: Rattus norvegicus

source_name: rat trigeminal ganglion, ALKBH5-up

extract_protocol:
samples were collected and total RNA was extracted and then randomly fragmented into fragments of approximately 200 nt. After 10% of fragmented mRNA was saved as input, remained mRNA was immunoprecipitated with anti-m6A antibodies and eluted.
The libraries were prepared using the GenSeq® Low Input Whole RNA Library Prep Kit  followed by sequencing on the NovaSeq sequencer

treatment_protocol: For the vector-1, vector-2 and vector-3 groups, the rats were intra-TG injected with NC-up. For the lv-ALKBH5-1, lv-ALKBH5-2 and lv-ALKBH5-3 groups, the rats were intra-TG injected with ALKBH5-up.

value: trigeminal ganglion

value: Sprague-Dawley

value: male

tag: rip antibody

value: none (input)

value: ALKBH5-up  injection


title: Ctrl soma rep3


title: Lung, COVID plasma, 5

description:
COVID_5
Normalised sequencing counts.xlsx


title: Ctrl neurites rep2


title: PD24

value: Blood plasma


title: PD23


title: B2-Input


title: MG132 neurites rep1

value: Hippocampal neurons


title: Ctrl soma rep2

value: DIV17/18 primary neurons


title: Lung, COVID plasma, 3

description:
COVID_3
Normalised sequencing counts.xlsx


title: B1-Input


title: MG132 soma rep1


title: Lung, COVID plasma, 2

description:
COVID_2
Normalised sequencing counts.xlsx


title: 19_5_7

city: Stillwater,

first: Khursheed

last: Iqbal

state: OK

address: 310 N Monroe St,

institute: Oklahoma state university

description: 10x genomics sequencing

data_processing:
The Cell Ranger Single-Cell Software Suite (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) was used to perform sample demultiplexing, barcode processing, and single-cell 3' gene counting. The reads were aligned to the rn6 reference genome. BAM files produced by the 10x Genomics/Cell Ranger pipeline
Assembly: rn6
Supplementary files format and content: Genes.tsv, Barcodes.tsv, Matrix.mtx

source_name: rat 19.5 uterine-placental interface

extract_protocol: Single cells were captured into droplets using 10x chromium device followed by preparation of single-cell cDNA libraries with the 10x protocol.

value: rat 19.5 uterine-placental interface


title: Lung, COVID plasma, 4

description:
COVID_4
Normalised sequencing counts.xlsx


title: PD20

value: PD


title: Lung, COVID plasma, 1

description:
COVID_1
Normalised sequencing counts.xlsx


title: PD21


title: FOXP3_GFP_Tom_WPRE_Sample4

city: Albuquerque

first: Laura

middle: Gonzalez

last: Gonzalez Bosc

state: NM

department: Cell Biology and Physiology

institute: University of New Mexico Health Sciences Center

description: 10x Genomics

data_processing:
Illumina NovaSEQ 6000 at University of Colorado Anschutz Medical Campus Genomics Shared Resource Cancer Center, demultiplexed with bcl2fastq v2.20.0.422 with “--barcode-mismatches” set to 1
Aligned and counted with CellRanger v3.1.1
Assembly: mm10
Supplementary files format and content: CellRanger (v3.2.2) output files

source_name: spleen

extract_protocol: Cell concentrations and viability were determined using the Cell Countess II FL (ThermoFisher) prior to calculating cell counts and loading the suspension into the Next GEM Chip G and Chromium Controller (10x Genomics) per the manufacturer’s protocol for GEM formation. The 10x Chromium Next GEM 3’ protocol was used to create 3’ libraries; briefly, cells were lysed and barcoded within each GEM prior to first strand cDNA synthesis, also within each GEM. After GEM’s are broken, cells are pooled prior to library completion as described in the manufacture’s protocol. Library quality was assess after cDNA synthesis and after completion on the BioAnalyzer using a DNA High Sensitivity Chip (Agilent). Prior to sequencing, Agilent Tape Station 4200 and Invitrogen Qubit 4.0 reagents were used determine final library concentrations prior to dilution, normalization and pooling at 4nM. qPCR was used to determine cluster efficiency.

treatment_protocol: Mice were fed a diet from Envigo (TD.140229 TAM Diet 2020, 500, B) containing 500 mg tamoxifen/kg diet for 2 wk. The dose was 80 mg/kg body weight per day. After at least 3 days receiving regular diet, mice were exposed to 380 mmHg (inspired PO2= 70 mmHg) for 5 days (chronic hypoxia) or left under normoxia (~630 mmHg in Albuquerque, NM, inspired PO2= 122 mmHg).

value: spleen

value: splenocytes

value: tamoxifen - normoxia - replicate 2


title: B2-IP


title: Ctrl neurites rep1

value: neurites

value: Ctrl


title: Ctrl soma rep1

value: soma


title: B1-IP


title: A3-Input

source_name: rat trigeminal ganglion, NC-up

value: NC-up injection


title: PD19

source_name: Extracellular vesicle


title: COR-5449-D2

city: Ithaca

first: Jennifer

middle: K

last: Grenier

state: NY

address: 526 Campus Rd

department: Biomedical Sciences

institute: Cornell University

data_processing:
cellranger mkfastq was used to generate fastq files by the sequencing facility
Because some samples were sequenced on different (or multiple) Illumina sequencers with different read lengths, all reads were trimmed for analysis and for upload to GEO (R1=28bp, R2=55bp). Samples are annotated with the number of different sequencer models used (NextSeq, HiSeq, and NovaSeq) and final fastq files are annotated by the instrument that generated the majority of reads.
cellranger count (v6) was used to generate raw count tables (h5 files), with the following parameters: --expect-cells=5000 --r1-length=28 --r2-length=55 --nosecondary
Assembly: 10x Genomics reference: refdata-gex-GRCh38-2020-A
Supplementary files format and content: h5

source_name: PBMCs

extract_protocol:
Whole blood was collected in EDTA tubes before and 24h after a cardiopulmonary exercise test (CPET) for each subject in the study. PBMCs were isolated with SepMate tubes  and cryopreserved with 1-10 x10^6 cells per vial. Frozen PBMCs were recovered following the 10x Genomics Demonstrated Protocol: Fresh Frozen Human Peripheral Blood Mononuclear Cells for Single Cell RNA Sequencing (CG00039) and resuspended in 1x PBS containing 0.04% BSA. For a target of 5,000 cells per final library, 8,000 cells were loaded onto the 10x Chromium chip.
Libraries were constructed using the Chromium Single Cell 3ʹ v3 kit (10x Genomics)

value: PBMCs

tag: collection day

value: control

value: F

tag: age bin

tag: chromium batch

value: batch 13

tag: number of sequencer models used


title: A2-Input

value: trigeminal ganglion

tag: strain

value: Sprague-Dawley

value: male

value: none (input)


title: COR-5449-D1

tag: cell type


title: FOXP3_GFP_Tom_WPRE_Sample2

description: 10x Genomics

tag: tissue

tag: genotype

value: tamoxifen - chronic hypoxia 5 days - replicate 2


title: A1-IP

tag: treatment


title: Mice cerebral Cortex, High dose dose IL-1B KO mice 6

city: Noda City

first: Gaku

last: Ichihara

address: 2641 Yamazaki

country: Japan

institute: Tokyo University of Science

data_processing:
Adapter trimming of sequencing data was performed by using cutadapt 3.4, and trimmed reads were mapped to reference RNA (build GRCm38 release-101) by using bowtie2-2.4.2 by the following parameters: -p 8 -N 1 -L 16 –very-sensitive-local –seed 656565 –nofw.
Then, read counts of each gene in each samples were counted by using awk, sort, and uniq -c commands.Resulted gene-expression count data was summarized by same Gene Symbol and all of the expression table was full-outer joined by Gene Symbol by using dplyr-1.0.7 package.
Supplementary files format and content: one txt file contain the count reads of all samples

source_name: Cerebral Cortex

extract_protocol:
RNA was extracted using PROMEGA ReliaPrep™ RNA Tissue Miniprep System, 5 ug of the total RNA was used to construct the RNA Liberary
RNA libraries for RNA-seq were prepared using KAPA Library Quantification Kit (KAPA Biosystems)

value: Cerebral Cortex

value: IL-1B KO mice

value: 25 mg/ kg Acylamide


title: BMDMs, LA 3

city: Rochester

first: Aditya

last: Bhagwate

state: MN

address: 200 1st Street SW

institute: Mayo Clinic

data_processing:
The bioinformatics analysis of the ATAC sequencing data was performed using the HiChIP pipeline
Paired-end sequencing reads were mapped to the mouse genome (mm10/GRCm38) using Burrows-Wheeler Aligner (BWA, v0.5.9)
Post-mapping, read pairs mapping to multiple locations in the genome  were filtered out using in-house scripts and only those read pairs which mapped uniquely to the genome were retained for downstream analysis. Reads arising from PCR amplifications were discarded as duplicate reads using Picard MarkDuplicates.
For identifying accessible and enriched chromatin regions (“peaks”)  against a genome-wide random background, the software package “Model-Based Analysis of ChIP-Seq” (MACS2, v2.0.10)59 was used
Assembly: mm10/GRCm38
Supplementary files format and content: BED (contains peak calls from MACS2)

source_name: BMDMs

extract_protocol:
To get BMDMs, bone marrow cells isolated from C57/BL6 mice were cultured  in RPMI 1640 differentiation medium containing 10% fetal bovine serum, 1 mM sodium pyruvate, antibiotics, and 30% L929 supernatant for 7 days. BMDMs were harvested and replated in 20% L929 medium one day before treatments. All cells were cultured in humidified atmosphere with 5% CO2 at 37 °C
ATAC-seq library preparation were performed by Mayo Clinic Epigenomic Development Laboratory and Recharge Center

treatment_protocol: BMDMs were incubated with 100 ng/ml LPS, with or without L-(+)-lactic acid (LA) at 10 mM, for 3 hours. Cells were harvested and 50,000 cells/sample were delivered for sequncing

value: BMDMs

value: LA


title: Mice cerebral Cortex, High dose dose IL-1B KO mice 4


title: B3-IP

value: ALKBH5-up  injection


title: COR-1141-D2

tag: disease state


title: A3-IP


title: A2-IP


title: PD13

extract_protocol:
Frozen plasma samples were thawed in thermostat water bath for 2 min at 37 °C and then centrifuged at 2,500 × g for 15 min at 4 °C to remove precipitated proteins and lipids. ~0.5-1 ml plasma was used as the starting material for each EVs isolation by exoRNeasy Midi kit (Qiagen; Cat#77144) according to the manufacturer’s instructions. For EV-RNA extraction, 1 ml Trizol reagent (Invitrogen; Cat#15596026) was added to the column and centrifuged at 3,000 × g for 1 min. Total EV-RNA was isolated by Trizol reagent according to manufacturer’s recommendations.
A total amount of 0.5-1 ng RNA per sample was used as input material for the RNA sample preparations. The cDNA libraries establishment of small RNAs included adaptor ligation, adapter depletion, first-strand cDNA synthesis, Cas9/sgRNA in vitro cleavage treatment, PCR amplification and gel purification.

value: Blood plasma

value: PD


title: PD22


title: A1-Input

value: NC-up injection


title: COR-1141-D1

value: PBMCs

value: control


title: BMDMs, LA 2

growth_protocol: To get BMDMs, bone marrow cells isolated from C57/BL6 mice were cultured  in RPMI 1640 differentiation medium containing 10% fetal bovine serum, 1 mM sodium pyruvate, antibiotics, and 30% L929 supernatant for 7 days. BMDMs were harvested and replated in 20% L929 medium one day before treatments. All cells were cultured in humidified atmosphere with 5% CO2 at 37 °C


title: PD15


title: COR-3309-D2

value: case

value: F

value: batch 8


title: FOXP3_GFP_Tom_WPRE_Sample1

description: 10x Genomics

value: spleen

value: splenocytes

value: tamoxifen -chronic hypoxia 5 days - replicate 1


title: PD17


title: PD12


title: Mice cerebral Cortex, High dose dose IL-1B KO mice 5

value: Cerebral Cortex


title: COR-4271-D1

value: M

value: batch 10


title: PD16


title: Mice cerebral Cortex, High dose dose IL-1B KO mice 3

value: IL-1B KO mice

value: 25 mg/ kg Acylamide


title: PD14


title: Mice cerebral Cortex, High dose dose IL-1B KO mice 2


title: FOXP3_GFP_Tom_WPRE_Sample3

description: 10x Genomics

value: tamoxifen -normoxia - replicate 1


title: PD18

value: Blood plasma


title: COR-4271-D2


title: BMDMs, LA 1

value: BMDMs

value: LA


title: PD11

value: PD


title: COR-8852-D2

value: PBMCs

value: control

value: batch 12


title: COR-3309-D1

value: case

value: F

value: batch 8


title: PD10


title: COR-4994-D2


title: BMDMs, LPS +LA 2

value: LPS+LA


title: COR-4994-D1


title: COR-8852-D1


title: PD9


title: PD8


title: Mice cerebral Cortex, Low dose IL-1B KO mice 6

value: Cerebral Cortex

value: 12.5 mg/ kg Acylamide


title: BMDMs, LPS +LA 3


title: Mice cerebral Cortex, Low dose IL-1B KO mice 2


title: Mice cerebral Cortex, High dose dose IL-1B KO mice 1


title: PD7


title: Mice cerebral Cortex, Low dose IL-1B KO mice 4


title: Mice cerebral Cortex, Low dose IL-1B KO mice 5


title: BMDMs, LPS +LA 1


title: PD5


title: Mice cerebral Cortex, Low dose IL-1B KO mice 3


title: Mice cerebral Cortex, Low dose IL-1B KO mice 1


title: COR-9348-D2


title: COR-9348-D1


title: PD6


title: BMDMs, LPS 1

value: LPS


title: COR-6308-D2

value: batch 9


title: PD4


title: Mice cerebral Cortex, Control IL-1B KO mice 6

value: IL-1B KO mice

value: 0 mg/ kg Acylamide


title: BMDMs, Control 3


title: PD3

value: Blood plasma


title: COR-6308-D1


title: BMDMs, LPS 3

value: BMDMs


title: BMDMs, LPS 2


title: BMDMs, Control 2


title: Mice cerebral Cortex, Control IL-1B KO mice 5


title: Mice cerebral Cortex, Control IL-1B KO mice 3


title: PD2


title: PD1


title: COR-5429-D1

value: batch 10


title: COR-4616-D2

value: batch 7


title: C60

value: Healthy


title: Mice cerebral Cortex, Control IL-1B KO mice 2


title: COR-4616-D1

value: PBMCs


title: BMDMs, Control 1


title: C59


title: Mice cerebral Cortex, Control IL-1B KO mice 1


title: COR-1002-D2

value: control


title: 20µM-N-80/C-25_2

city: Charlottesville

first: Anwaruddin

last: Mohammad

state: VA

address: Pinn Hall

department: Bioinformatics Core

institute: University of Virginia

data_processing:
Bulk RNAseq analysis: On average we received 30 million paired ends for each of the replicates. RNAseq libraries were checked for their quality using the fastqc program http://www.bioinformatics.babraham.ac.uk/projects/fastqc/. The results from fastqc were aggregated using multiqc software1. Reads were mapped with the “splice aware” aligner ‘STAR’,2 to the transcriptome and genome of mm10 genome build. The HTseq3 software will be used to count aligned reads that map onto each gene. The count table was imported to R to perform differential gene expression analysis using the DESeq2 package4. Low expressed genes (genes expressed only in a few replicates and had low counts) was excluded from the analysis before identifying differentially expressed genes. Data normalization, dispersion estimates, and model fitting (negative binomial) was carried out with the DESeq function. The log-transformed, normalized gene expression of 500 most variable genes will be used to perform an unsupervised principal component analysis. The differentially expressed genes was ranked based on the log2fold change and FDR corrected p-values. The ranked file was used to perform pathway analysis using GSEA software5.  The enriched pathways were selected based on enrichment scores as well as normalized enrichment scores. The Enrichment Analysis for Gene Ontology was performed by topGO. The heatmaps were generated using pheatmap function in R.
Assembly: Pseudomonas_aeruginosa_PA14_662
Supplementary files format and content: Tab-separated values files and matrix files

organism: Pseudomonas aeruginosa PA14

source_name: Bacteria

growth_protocol: A 1:100 dilution of an overnight culture of PA14 was grown in LB growth medium to reach the mid-log phase (OD600 = 0.5) after 3.5 to 4.0 hours. 0.5 ml of the cells (2.5x10^8 cells) were gently pelleted (12000xg, 30 sec) to avoid excessive force on cells and resuspended in 0.5 ml of 1 mM Na2HPO4, 0.18 mM KH2PO4, 0.27 mM KCl, 13.7 mM NaCl, pH 7.2.

extract_protocol:
RNA isolation from the cells was carried out using the RNeasy mini kit (74104, Qiagen). To begin, 700 ul of RLT buffer (from the kit) supplemented with 1% β-mercaptoethanol was added to the cells and vortexed for 30 sec. The mixture was then centrifuged at 8000xg for 2 min, and 700 ul of the resulting supernatant was carefully recovered and mixed thoroughly with 500 ul of ethanol by pipetting. Subsequently, 700 ul of the mixture was transferred to a mini kit column and centrifuged at 8000xg for 30 sec. The flowthrough was discarded, and 350 ul of RW1 buffer (from the kit) was added to the column prior to spinning at 8000xg for 30 sec. The flowthrough was once again removed, and 80 ul of Dnase I solution, which contained 10 ul of Rnase-free Dnase Set and 70 ul of buffer RDD (79254, Qiagen), was added to the column. The column was then incubated for 15 min at room temperature. Following this, 350 ul of RW1 buffer was added to the column prior to spinning at 8000xg for 30 sec. The column was then transferred to a new collection tube, and 500 ul of RPE buffer (supplemented with ethanol) was added to the column prior to spinning at 8000xg for 30 sec. The flowthrough was removed, and 500 ul of RPE buffer was added to the column prior to spinning at 8000xg for 2 min. The flowthrough was once again removed, and the column was dried by spinning at 8000xg for 1 min. Finally, the column was transferred to a new collection tube, and RNA was eluted with 30 ul and then 20 ul of DEPC-treated water each time for 1 min of spinning at 8000xg. The resulting RNA samples were stored at -80oC. The quality of the RNA samples was examined prior to sequencing by using gel electrophoresis, which revealed two sharp peaks with very low background . An RNA Integrity Number equivalent (RINe) of 8.4-9.2 and a concentration of approximately 40-60 ng/ul were obtained. Three independent RNA samples were sequenced for each experimental condition.
Library construction and sequencing were executed at the Genome Analysis and Technology Core of the University of Virginia. Specifically, mRNA enrichment was conducted using the NEBNext® rRNA Depletion Kit (Bacteria) (E7850L, New England BioLabs). Transcriptome sequencing was then performed with 150-bp pair-end reads produced. The range of raw reads for each sample varied from 8-10 million, thus ensuring an optimal depth of sequencing.

treatment_protocol: The cells were then incubated without treatment or with 5 or 20 uM N-104 (or 20 uM N-80/C-25) for 45 min at 35oC. Cells were pelleted again (12000xg, 5 min), and supernatants were gently removed while leaving ~25 ul of it to prevent cell loss. The cells were then resuspended in 0.5 ml of TE buffer (12-090-015, Invitrogen), followed by adding 1 ml of RNA-protect Bacteria Reagent (76506, Qiagen) and vortexing for 5 sec prior to incubation for 5 min at room temperature. Cells were pelleted (5000xg, 10 min), and the supernatant was removed completely.

value: Bacteria

value: PA14 cells treated with 20 µM lacritin N-80/C-25


title: 20µM-N-80/C-25_3


title: 20µM-N-104_3

value: PA14 cells treated with 20 µM lacritin N-104


title: COR-1002-D1

value: F

value: batch 8


title: 20µM-N-80/C-25_1


title: C58

data_processing:
We used cutadapt to clip adaptor and filter low quality reads. Reads failing to match the adaptor or reads with lengths shorter than 17 nt were discarded. Redundant sequences were collapsed as useful reads for further analysis. Then, we aligned the reads to reference sequences by bowtie. To assess the expression levels of the miRNAs, the 3’ ends of miRNA with ≤ 3 nt deletions or additional sequences derived from pri-miRNAs were counted as miRNAs. The miRNA expression level was normalized by size factor from DEseq2.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include log2-transformed normalized read counts for each sample


title: 20µM-N-104_2


title: Mice cerebral Cortex, High dose wild type mice 5

value: Cerebral Cortex

value: Wild Type Mice

value: 25 mg/ kg Acylamide


title: C57


title: Mice cerebral Cortex, High dose wild type mice 4


title: C56


title: 20µM-N-104_1


title: Mice cerebral Cortex, Control IL-1B KO mice 4

value: IL-1B KO mice


title: COR-5429-D2

value: case


title: COR-3985-D1

value: batch 13


title: C55

value: Blood plasma


title: 5µM-N-104_3

value: PA14 cells treated with 5 µM lacritin N-104


title: 5µM-N-104_2


title: Mice cerebral Cortex, High dose wild type mice 2


title: COR-5136-D1

value: batch 5


title: C54

value: Healthy


title: Mice cerebral Cortex, High dose wild type mice 6


title: COR-5136-D2

value: PBMCs


title: C52


title: Mice cerebral Cortex, High dose wild type mice 1


title: Mice cerebral Cortex, Low dose wild type mice 6

value: 12.5 mg/ kg Acylamide


title: COR-5554-D2

value: control

value: batch 10


title: Untr_3

value: Bacteria

value: Untreated PA14 cells


title: 5µM-N-104_1


title: C51


title: COR-3985-D2

value: F


title: Mice cerebral Cortex, Low dose wild type mice 5

value: Cerebral Cortex


title: COR-5878-D2

value: batch 12


title: C50


title: C49


title: Untr_1


title: Mice cerebral Cortex, Low dose wild type mice 4

value: Wild Type Mice


title: COR-5878-D1


title: Mice cerebral Cortex, High dose wild type mice 3

value: 25 mg/ kg Acylamide


title: Mice cerebral Cortex, Low dose wild type mice 3


title: SFTSV 6dpi rep3

first: Yang

last: Li

address: 2005 Songhu Road

institute: Fudan University

description: tick infection with SFTSV by blood-feeding on A6 for 2days and incubation for 4days

data_processing:
Clean reads were obtained from the raw reads by removing the adaptor sequences, reads with > 5% ambiguous bases (noted as N) and low-quality reads containing more than 20 percent of bases with qualities of < 20
De novo assembly of transcriptome was accomplished based on clean reads from all libraries using Trinity with default parameters
Gene function was annotated based on the following databases: nr (NCBI non-redundant protein sequences), nt (NCBI non-redundant nucleotide sequences), pfam (Protein family), KOG/COG (Clusters of Orthologous Groups of proteins), Swiss-Prot (A manually annotated and reviewed protein sequence database), KO (KEGG Ortholog database), GO (Gene Ontology).
Differential expression analysis of any two groups was performed using the DESeq R package and the differentially expressed genes between samples were identified by |log2fold change|> 1 and p-value< 0.05
Gene Ontology (GO) analysis was applied to analyze the primary functions of the differentially expressed genes. Fisher’s exact test was applied to identify the significant GO categories.
Supplementary_files_format_and_content: tab-delimited text files include reads counts, FPKM values and gene annotation information for each Sample

organism: Haemaphysalis longicornis

source_name: tick whole body

extract_protocol:
Total RNA was extracted from ticks using TRIzol reagent.
Enrichment of poly (A)-RNA preparation for RNA Sequencing was performed using NEBNext Poly (A) mRNA Magnetic Isolation Module (NEB) kit. The cDNA libraries were constructed for each pooled RNA sample using the NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina according to the manufacturer’s instructions. The products were purified and enriched by PCR to create the final cDNA libraries and quantified by Agilent2200. The tagged cDNA libraries were pooled in equal ratio and used for 150 bp paired-end sequencing in a single lane of the Illumina HiSeqXTen.

tag: infection

value: SFTSV

tag: infection way

value: blood-feeding

tag: mice strains


title: Mice cerebral Cortex, Low dose wild type mice 2


title: C48

first: Wei

last: Liu

value: Blood plasma


title: SFTSV 6dpi rep2


title: C53


title: C47


title: Untr_2


title: COR-3315-D1

tag: Sex

value: M

value: batch 6


title: COR-5554-D1


title: Mice cerebral Cortex, Low dose wild type mice 1


title: C46

value: Healthy


title: COR-3427-D2

value: PBMCs

value: case

value: batch 3


title: Mice cerebral Cortex, Control wild type mice 6

value: 0 mg/ kg Acylamide


title: Control 6dpi rep2

description: tick blood-feeding on A6 for 2days and incubation for 4days

value: control


title: Mice cerebral Cortex, Control wild type mice 5


title: C45


title: COR-3427-D1


title: Control 6dpi rep3


title: COR-4181-D2

value: batch 11


title: Control 6dpi rep1


title: COR-4181-D1


title: Control 2dpi rep3

description: tick blood-feeding on A6 for 2days


title: C43


title: Mice cerebral Cortex, Control wild type mice 4


title: COR-3315-D2


title: Mice cerebral Cortex, Control wild type mice 3


title: Control 2dpi rep2

description: tick blood-feeding on A6 for 2days


title: C44


title: Mice cerebral Cortex, Control wild type mice 2


title: SFTSV 6dpi rep1


title: C41


title: Mice cerebral Cortex, Control wild type mice 1


title: COR-5623-D2

value: F


title: Control 2dpi rep1

description: tick blood-feeding on A6 for 2days


title: C40


title: K-NAA, CT23_rep2

city: Setagaya-ku

first: Shingo

last: Hiroki

state: Tokyo

address: 2-1-6 Kamikitazawa

institute: Tokyo Metropolitan Instituite of Medical Sciences

data_processing:
TPM for each transcript was quantified using Salmon.
TPM was concatanated by gene.
The circadian periodicity and related parameters were calculated using BioCycle.
Assembly: ce10
Supplementary files format and content: Excel file with TPM values and BioCycle statistics for each gene at each timepoint.

organism: Caenorhabditis elegans

source_name: whole body

growth_protocol: JDW259 strain were cultivated on NGM plates seeded with NA22 E.coli.

extract_protocol:
RNA was extracted using TRIzol(ThermoFisher) and RNeasy mini kit(Qiagen)
The library was constructed by BGI(China).

treatment_protocol: Animals were transfered to NGM plates with/without 0.4 mM K-NAA 12h prior to sampling.

value: whole body

tag: developmental stage

value: adult

value: JDW259:wrdSi55[eft-3p:TIR1:F2A:mTagBFP2:tbb-2 3'UTR, I:-5.32] ; nhr-23(kry61(nhr-23::AID*::TEV::3xFLAG))

value: K-NAA

tag: time


title: COR-5623-D1

value: batch 12


title: C42

institute: Chinese Academy of Sciences


title: D2_rfx1

first: Haizhu

last: Zhang

address: No. 131 Dong'an Road, Xuhui District

department: Institutes of Biomedical Sciences

description: ChIP-seq targeting RFX1 was applied to C2C12 cells in day2 of differentiation stage.

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 or mm10 whole genome using bowtie2 v2.2.6 with parameters with the parameters -X2000 and -m1.
Peak calling with macs2 v 2.2.1
Motif finding with homer(findMotifsGenome.pl)
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak files were generated using macs2

growth_protocol: Mouse C2C12 cells were cultured in DMEM supplemented with 10% FBS, 2 mM L-glutamine, 100 U/mL penicillin and 100 g of streptomycin (1% Pen/Strep) at 37 °C and 5% CO2. For myogenic differentiation, cells were shifted to DMEM containing 2% horse serum (differentiation medium) when they reached 90% confluence.

extract_protocol:
Cells were fixed with 1% formaldehyde and lysed with lysis buffer (50 mM HEPES/KOH (pH 7.5), 500 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 1 mM EDTA, 0.1% SDS and protease inhibitors). The cell lysates were sonicated with a Bioruptor Plus sonicator (Diagenode) at a high level for 50 min, with 30 seconds-on and 30 seconds-off cycles.
DNA libraries were prepared for sequencing using Accel-NGS® 2S DNA Library Kits.

treatment_protocol: ChIP-seq targeting RFX1 was applied to C2C12 cells in proliferation stage and   day 2 in differentiation stage.

tag: antibody

value: chip antibody:rfx1

tag: Stage

value: differentiation day2 stage


title: COR-7101-D2

tag: collection day

tag: age bin

value: batch 1


title: C39

address: 320 Yueyang Road

value: Blood plasma


title: P_rfx1

description: ChIP-seq targeting RFX1 was applied to C2C12 cells in proliferation stage.

value: proliferation stage


title: C38

value: Healthy


title: COR-1203-D2

value: PBMCs

value: case

value: M

tag: chromium batch

value: batch 9

tag: number of sequencer models used


title: D2_2

description: The ATAC-seq was applied to discover the dynamic change of the chromatin accessibility in muscle myoblast differentiation. There were 5 differential stages.   P   represents proliferation stage, and   D2   represents day 2 in differentiation (D2 stage).

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 or mm10 whole genome using bowtie2 v2.2.6 with parameters with the parameters -X2000 and -m1.
Remove mitochondrial DNA with removeChrom.py
Peak calling with macs2 v 2.2.1
Motif finding with homer(findMotifsGenome.pl)
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: narrowPeak files were generated using macs2

source_name: C2C12 cell

growth_protocol: Cell lines 293T were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and Pen-Strep (100 U / ml penicillin, 100 mg / ml streptomycin) at 37℃, 5% CO2.

extract_protocol:
Cells were harvested and wash once with cold 1x PBS buffer, and then resuspended in 1 mL cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 1mM PMSF). This cell lysis reaction was incubated on ice for 10 min.
DNA libraries were prepared for sequencing using TruePrepTM DNA Library Prep Kit V2 for Illumina（）.

treatment_protocol: 1.ATAC-seq was applied to 293T, HeLa, HepG2 and MCF7 cell line. 2.ATAC-seq was applied to mouse liver rhythm model.3. ChIP-seq was applied to different cells with different treatment.

value: Rfx1 and myod

tag: cell type


title: C37

tag: tissue


title: K-NAA, CT21_rep2

tag: strain

tag: genotype


title: COR-4856-D2

tag: disease state

value: F

value: batch 11


title: C36


title: P_1

description: The ATAC-seq was applied to discover the dynamic change of the chromatin accessibility in muscle myoblast differentiation. There were 5 differential stages.   P   represents proliferation stage, and   D2   represents day 2 in differentiation (D2 stage).      The ATAC-seq was applied to discover the dynamic change of the chromatin accessibility in muscle myoblast differentiation. There were 5 differential stages.   P   represents proliferation stage, and   D2   represents day 2 in differentiation (D2 stage).


title: COR-1203-D1


title: ZT7

description: The ctATAC-seq was applied to the mouse liver circadian model. ZT4 presents the time at 4 o  clock and the ZT7 represents 7 o  clock.

source_name: Mouse Liver

value: liver


title: C35


title: COR-4856-D1


title: K-NAA, CT21_rep1

value: whole body

value: adult

value: JDW259:wrdSi55[eft-3p:TIR1:F2A:mTagBFP2:tbb-2 3'UTR, I:-5.32] ; nhr-23(kry61(nhr-23::AID*::TEV::3xFLAG))

tag: treatment


title: K-NAA, CT19_rep2

value: K-NAA


title: ZT4


title: Td_c

description: We designed and expressed a novel Tn5-dCas9 fusion protein to perform ATAC-seq.   Td   represents Tn5-dCas9.   sg   means ATAC-seq with targeted sgRNA.   c   represented ATAC-seq with control sgRNA.


title: K-NAA, CT17_rep1


title: COR-7101-D1


title: K-NAA, CT17_rep2


title: Td_sg


title: COR-6685-D2

value: control

value: batch 7


title: C33

value: Blood plasma


title: K-NAA, CT23_rep1


title: C34


title: COR-6685-D1


title: C32


title: COR-8066-D2

value: batch 10


title: COR-8066-D1


title: C31

value: Healthy


title: K-NAA, CT15_rep1


title: ΔChp1 yeast RP, total translatome, rep2

first: Ilgin

last: Kotan

address: Im Neuenheimer Feld 329

institute: Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH)

description: dChp1 RP

data_processing:
3’ Adapters were trimmed using Cutadapt v 3.2 with the following command: cutadapt --cores=8 --nextseq-trim=20 -m23 --discard-untrimmed -O6 -a ATCG-TAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -o '/'outfile.fastq.gz' '/infile.fastq.gz' 1> '/'Cutadapt_report.txt. Unique molecular identifiers (UMI) were removed using a custom Julia script (Script 1). julia -p 8 '.jl' '<input_path>/'infile.fastq.gz' '<input_path>/outfile.fastq.gz' --umi3 5 --umi5 2.
To remove rRNA, the reads were aligned to S. cerevisiae rRNA sequences with bowtie2 v 2.4.2 and only the reads that do not align were kept: bowtie2 -p8 -t -x '<ref_file_path>' -q infile.fastq.gz' --un '<outfile_path>/outfile.fastq' -S /dev/null 2> '<outfile_path>/Bowtie2_report.txt'.
The remaining rRNA depleted reads were aligned to the S. cerevisiae S288C Genome (Assembly: GCA_000146045.2) with STAR v 2.7.7a. The TEF2 entry in the fasta file was removed to allow both TEF1 and TEF2 reads to align to the TEF1 sequence. The STAR index with the modified fasta file was generated using the following command: STAR --runMode genomeGenerate --runThreadN 8 --genomeDir <input_path> --genomeFastaFiles infile.dna.toplevel.fa --genomeSAindexNbases 10 --sjdbGTFfile <out-file_path>/outfile.gtf. As TEF1 and TEF2 differ from each other by two mutations at position 762 (T->C), and position 834 (T->C), the threshold for the allowed maximum number of mismatches per pair was set to 2. The alignment was performed with the following command: STAR --runThreadN 7 --genomeDir '<ref_file_path>' --readFilesIn '<infile_path>/infile.fastq' --outSAMmultNmax 1 --outFilterType BySJout --outFilterMismatchNmax 2 --alignIntronMin 5 --outFileNamePrefix '<outfile_path>' --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All XS --quantMode GeneCounts --twopassMode Basic --limitBAMsortRAM 1185598524.
Reads from PCR duplicates were collapsed to a single read and positions of ribosomal a, p, and e-sites on footprints were assigned with a custom Julia script (Script 2): julia -p 8 script.jl -g /annotation_file.gff3 -o //infile.bam" -u -c 1.
The data was analyzed using a custom R package RiboSeqTools (accessible from: https://github.com/ilia-kats/RiboSeqTools). The analysis was performed exclusively using p-site assigned reads for all datasets.
Assembly: SGD R64-1-1GCA_000146045.2
Supplementary files format and content: Processed data are stored in HDF5 files. Each HDF5 file contains one data set per gene. Each data set consists of a 2-row matrix, with the first row containing the 1-based position within the CDS, and the second row the number of detected P-site reads at this position. Additional information is stored in the data set attributes, including: gene and protein names, length of the coding sequence, chromosome and strand location of the gene. In this study the p-site assignments stored in such HDF5 files were further analyzed using RiboSeqTools
Library strategy: Ribosome Profiling

growth_protocol: Yeast cultures were grown for roughly 6 hours at 30 °C until they have reached early log phase in YPD media (in 1 L for SeRP and in 200 mL for total translatomes)

extract_protocol:
RNA from ribosomes precipitated via sucrose cushion, or from ribosomes that co-IP with GFP-binder coupled beads were extracted using the hot acid phenol method as described in Galmozzi and Merker et al. 2019, for total translatome and IP samples respectively.
Libraries were constructed as decribed in Galmozi and Merker et al. 2019

treatment_protocol: Cells were harvested by rapid filtration and frozen in liquid nitrogen. The frozen cell pellets were lysed by cryo-milling. Lysates were thawed,and treated with10U/A260 RNase I for 30 min at 4 °C.

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 chp1{delta}::kanMX

tag: fraction

value: total translatome


title: C30


title: WT yeast RP, total translatome, rep2

description: WT RP

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0


title: COR-2674-D2

value: PBMCs

value: batch 9


title: K-NAA, CT13_rep2


title: COR-2674-D1

value: F


title: K-NAA, CT19_rep1


title: WT yeast RP, total translatome, rep1

description: WT RP


title: COR-7414-D1


title: WT untagged yeast SeRP, total translatome, rep2

description: Mock SeRP total


title: K-NAA, CT11_rep1


title: K-NAA, CT11_rep2


title: C29


title: C28


title: C26


title: COR-7414-D2


title: C27


title: K-NAA, CT15_rep2


title: WT untagged yeast SeRP, total translatome, rep1

description: Mock SeRP total


title: K-NAA, CT9_rep2


title: K-NAA, CT9_rep1


title: C25


title: WT untagged yeast SeRP, GFP IP, rep2

description: Mock SeRP IP

value: IP


title: WT untagged yeast SeRP, GFP IP, rep1

description: Mock SeRP IP


title: COR-9818-D1

value: case

value: M

value: batch 11


title: K-NAA, CT7_rep2

value: whole body

value: adult

value: JDW259:wrdSi55[eft-3p:TIR1:F2A:mTagBFP2:tbb-2 3'UTR, I:-5.32] ; nhr-23(kry61(nhr-23::AID*::TEV::3xFLAG))


title: Chp1-GFP ΔNAC yeast SeRP, total translatome, rep2

description: dNAC Chp1 SeRP total

value: MATa his3{delta}1 leu2{delta}0 ura3{delta}0 CHP1-sfGFP-kanMX egd1{delta}::hphNT1 btt1{delta}::hisMX6 egd2{delta}::natNT2


title: K-NAA, CT7_rep1

value: K-NAA


title: COR-9818-D2


title: C23

value: Blood plasma


title: ΔChp1 yeast RP, total translatome, rep1

description: dChp1 RP


title: Chp1-GFP ΔNAC yeast SeRP, total translatome, rep1

description: dNAC Chp1 SeRP total


title: COR-2465-D2

value: control

value: batch 6


title: C22

value: Healthy


title: COR-6176-D2


title: K-NAA, CT13_rep1


title: Chp1-GFP ΔNAC yeast SeRP, GFP IP, rep2

description: dNAC Chp1 SeRP IP


title: COR-6176-D1


title: K-NAA, CT5_rep2


title: COR-2465-D1


title: Chp1-GFP ΔNAC yeast SeRP, GFP IP, rep1

description: dNAC Chp1 SeRP IP


title: COR-7256-D2

value: batch 4


title: K-NAA, CT3_rep2


title: C20


title: Chp1-GFP yeast SeRP, total translatome, rep2

description: Chp1 SeRP total

value: MATa his3{delta}1 leu2{delta}0 ura3{delta}0 CHP1-sfGFP::kanMX

value: total translatome


title: C24


title: COR-7256-D1

value: PBMCs

value: F


title: C18


title: K-NAA, CT3_rep1


title: COR-9198-D1

value: case


title: K-NAA, CT1_rep2


title: C19


title: Chp1-GFP yeast SeRP, GFP IP, rep2

description: Chp1 SeRP IP

value: IP


title: C17


title: COR-9198-D2


title: COR-6302-D2

value: batch 2


title: K-NAA, CT1_rep1

value: whole body


title: Chp1-GFP yeast SeRP, GFP IP, rep1

description: Chp1 SeRP IP


title: C16


title: COR-6302-D1


title: C2C12-D3 ATAC-seq

source_name: C2C12 cells

growth_protocol: Human cell lines HeLa, HepG2 and MCF-7 were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and Pen-Strep (100 U / ml penicillin, 100 mg / ml streptomycin) at 37℃, 5% CO2. Mouse C2C12 were cultured in DMEM supplemented with 10% FBS, 2 mM -glutamine, 100 U/ml penicillin and 100 g of streptomycin (1% Pen/Strep) at 37℃, 5% CO2. For myogenic differentiation, cells were shifted to DMEM containing 2% horse serum (differentiation medium).

extract_protocol:
Cells were harvested and wash once with cold 1x PBS buffer, and then resuspended in 1 mL cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 1mM PMSF). This cell lysis reaction was incubated on ice for 10 min.
DNA libraries were prepared for sequencing using TruePrepTM DNA Library Prep Kit V2 for Illumina.

treatment_protocol:
1.Final concentration of 20 ng/mL TNF-α was added into the cell culture medium and HeLa cells were incubated in 37 °C for 15 min, 30 min and 60 min. Cells were harvested in cold 1x PBS buffer and counted.
2.When the density of MCF7 cells was up to 70%, DMEM was changed to Phenol Red-free DMEM with 2.5% FBS for 24 h and then Phenol Red-free DMEM only for 24 h. Final concentration of 100 nM 17β-estradiol(E2) and 2 uM 4-hydroxytamoxifen(4-HT) were added into the cell culture medium, cells were incubated in 37 °C for 2 h. Cells were harvested in cold 1x PBS buffer and counted.

tag: cell line


title: Mock, CT23_rep1

value: adult

value: mock


title: C15


title: C2C12-D2 ATAC-seq


title: K-NAA, CT5_rep1

value: JDW259:wrdSi55[eft-3p:TIR1:F2A:mTagBFP2:tbb-2 3'UTR, I:-5.32] ; nhr-23(kry61(nhr-23::AID*::TEV::3xFLAG))


title: Mock, CT21_rep2


title: C2C12-D1 ATAC-seq


title: COR-8468-D1

tag: Sex


title: Mock, CT21_rep1

tag: developmental stage


title: C14


title: C13


title: COR-8468-D2


title: C2C12-BD ATAC-seq


title: COR-5218-D1

value: M


title: Mock, CT19_rep2

tag: time


title: C11

value: Blood plasma


title: C2C12-P ATAC-seq


title: COR-5218-D2


title: COR-1481-D1

value: control

value: batch 3


title: C10

value: Healthy


title: Mock, CT17_rep2


title: COR-1481-D2


title: C9


title: Mock, CT23_rep2


title: DN3 KO2

city: Planegg-Martinsried

first: Taku

last: Kureha

address: Grosshaderner Str. 9

department: Institute for Immunology

institute: Ludwig-Maximilians-Universität

data_processing:
Raw reads processed with kallisto (version 0.46, default paramters) for calculation of read counts and TPM per gene
Assembly: GRCm38, Ensembl annotation version 101
Supplementary files format and content: Tab delimited file with estimated_counts and tpm values

source_name: Arpp21 KO_thymocytes

extract_protocol:
Total RNA was isolated with the NucleoSpin RNA kit (Macherey-Nagel).
Library preparation was performed using SmartSeq V4 with Nextera. The libraries were sequenced with a length of 150 bp, paired-end on an Illumina HiSeq1500 sequencer.

treatment_protocol: The populations of DN2 and DN3 developmental stages are sorted by flow cytometry.

value: thymocytes

value: Arpp21 KO


title: Mock, CT17_rep1


title: C8

city: Shanghai


title: COR-5723-D2

value: batch 6


title: Mock, CT15_rep2


title: DN3 KO1


title: DN3 WT3

value: Wildtype


title: C7


title: Mock, CT15_rep1


title: COR-5723-D1

value: PBMCs


title: C12


title: COR-9546-D2

value: F

value: batch 1


title: DN3 KO3


title: Mock, CT19_rep1


title: Mock, CT13_rep2


title: C6


title: DN3 WT2


title: Mock, CT13_rep1


title: DN3 WT1


title: COR-9546-D1


title: DN2 KO2


title: COR-8843-D1

value: batch 5


title: C5


title: Mock, CT11_rep2

value: whole body


title: C4


title: DN2 KO1


title: COR-8843-D2


title: C3


title: Mock, CT11_rep1

value: adult


title: COR-8763-D1

value: case

value: batch 4


title: Mock, CT9_rep2

value: JDW259:wrdSi55[eft-3p:TIR1:F2A:mTagBFP2:tbb-2 3'UTR, I:-5.32] ; nhr-23(kry61(nhr-23::AID*::TEV::3xFLAG))

value: mock


title: DN2 WT3


title: C2

value: Blood plasma


title: COR-8763-D2


title: DN2 WT2


title: Mock, CT9_rep1


title: COR-8330-D2

value: batch 3


title: C1

value: Healthy


title: Mock, CT7_rep2


title: Arpp21 KO-iCLIP

data_processing:
Reads were de-multiplexed based on the experimental barcode and adapter sequences were removed from the read ends (Flexbar v3.5.0). UMIs were trimmed and added to the read names. Individual samples were mapped to the respective genome (assembly version GRCm38.p6 for all mouse samples) and its annotation (GENCODE release M25 for all mouse samples) using STAR (v2.7.6a). Reads were de-duplicated if they had identical UMIs.
Normalized bigwig files were using bedtools (2.29) genomecov and ucsc-wigtobigwig
Peaks in WT samples with KO serving as backgorund contrl were called using Homer (4.11)
Assembly: mm10
Supplementary files format and content: Bigwig files were generated using bed GraphToBigWig.

source_name: ARpp21 KO_thymocytes

extract_protocol: Cells were washed once with PBS and cross-linked twice with 200 mJ/cm2 UV light (254 nm) in a Stratalinker. After cross-linking, cells were lysed and partial RNA digestion was perfomed by using optimized RNase I dilution (Ambion) together with Turbo DNase (Ambion). After centrifugation, cell lysates were loaded onto a Proteus Clarification Mini Spin Column (Generon) and spun. Protein lysates were incubated with the antibody-coupled beads. After stringent washing, RNA 3’ ends were dephosphorylated with T4 PNK and subsequentlys the 3’ adaptor was ligated. The samples were radioactively end-labled and were subjected to NuPAGE gel electrophoresis and tranferred onto Nitrocellulose Membrane. The RNA was isolated from the membrane by treatment with proteinase K. After phonol/chloroform extraction and precipitation, the RNA was reversed transcribed and cDNA was purified with Dynabeads MyOne Silane (Invitrogen). The 5’ adaptor was ligated. First-strand cDNA was synthesized with 6 cycles and size-selected using ProNex Size-Selective Purification System (Promega). Libraries were PCR amplified for 8–13 cycles and sequencing was performed on a Illumina HiSeq1500 sequencer.

value: thymocytes

value: ARpp21 KO

tag: iclip antibody

value: rabbit anti-Arpp21 antibody (Proteintech, Cat. 11829-1-AP)


title: COR-8330-D1


title: Mock, CT7_rep1


title: DN2 WT1

value: Wildtype


title: G700

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 or mm10 whole genome using bowtie2 v2.2.6 with parameters with the parameters -X2000 and -m1.
Remove mitochondrial DNA with removeChrom.py
Peak calling with macs2 v 2.2.1
Motif finding with homer(findMotifsGenome.pl)
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak files were generated using macs2

source_name: 293T cells

growth_protocol: Human cell lines 293T were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and Pen-Strep (100 U / ml penicillin, 100 mg / ml streptomycin) at 37℃, 5% CO2.

extract_protocol:
Cells were harvested and wash once with cold 1x PBS buffer, and then resuspended in 1 mL lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 1mM PMSF). This cell lysis reaction was incubated at room temperature for 10 min.
DNA libraries were prepared for sequencing using TruePrepTM DNA Library Prep Kit V2 for Illumina.

treatment_protocol: Q Sepharose was added to 1.5 mL EP tubes, and washed gently with 20 mM NaCl for 3 times, for every time, the Q Sepharose was centrifuged for 2 min at 300 × g at room temperature. Cells were crosslinked, permeabilized and incubated with transposons. After tagmentation with transposons, the mixture was incubated with Q Sepharose for 10 min and shortly centrifuged for 30 s at 300× g. The supernatant was collected into a new tube as FT (flow-through). The Q Sepharose was then washed with 20 mM, 100 mM, 200 mM, 300 mM, 500 mM, 700 mM, and 1000 mM NaCl successively. The supernatant was collected into new tubes. For ATAC-seq, a reverse-crosslinked solution (with final concentration of 50 mM Tris–HCl, 1 mM EDTA, 1% SDS, 0.2 M NaCl, 5 ng/ml proteinase K) was added to each group. The mixture was incubated at 65 °C at 1,000 r.p.m. with shaking in a heat block overnight, then purified with Qiagen Mini-purification kit and eluted in 17 μL Quiagen EB elution buffer. Sequencing libraries were prepared using TruePrep Index Kit V2 for Illumina (Vazyme TD202) and purified using VAHTS DNA Clean Beads (Vazyme N411).


title: COR-1126-D1

value: PBMCs

value: control


title: G500


title: COR-1126-D2

value: F


title: G300


title: Mock, CT5_rep1


title: COR-6215-D1

value: batch 5


title: G200


title: Arpp21-iCLIP2

value: WT


title: Arpp21-iCLIP1


title: COR-6215-D2


title: Mock, CT3_rep1

value: whole body

value: adult


title: G100


title: COR-7349-D2

value: case

value: batch 2


title: Arpp21-iCLIP SM-Input2

value: none (input)


title: G1000


title: Arpp21-iCLIP SM-Input1


title: Mock, CT1_rep2

value: JDW259:wrdSi55[eft-3p:TIR1:F2A:mTagBFP2:tbb-2 3'UTR, I:-5.32] ; nhr-23(kry61(nhr-23::AID*::TEV::3xFLAG))

value: mock


title: G20


title: Mock, CT1_rep1


title: Mock, CT5_rep2


title: COR-7349-D1


title: Arpp21-iCLIP4


title: Arpp21-iCLIP3


title: FT


title: Mock, CT3_rep2


title: md-RAD_A. selago adult 1

status: Public on Jan 15 2024

first: Christopher

last: Peterson

state: TX

address: 2415 Speedway #C0930

department: Integrative Biology

institute: University of Texas

description:
lane1-A1-A_S1_L001_1.trim_bismark_bt2_pe.deduplicated.bismark.cov.gz
Both whole genome bisulfite-seq and md-RAD data were in the generation of the processed data files.

data_processing:
WGBS reads trimmed with Trim Galore 0.6.7
Trimmed adult WGBS reads aligned to Amil v2.1 with Bismark v 0.24.2 with with mapping parameters -N 1 --score_min L,0,-0.8
md-RAD reads trimmed and aligned with Bowtie2 v. 2.5.0
Adult WGBS and md-RAD alignments variant called with ANGSD 0.940
Fixed SNP differences between adults were determine from variant calls, then used to create N-masked reference genomes for each pair of parents, with SNPsplit’s genome preparation script
Offspring WGBS files aligned to parent-specific masked genomes, using Bismark v 0.24.2.
Offspring alignments separated by parental alleles using SNPsplit v 0.6
Methylation calls extracted from adult WGBS alignments and offspring allele-specific alignments using Bismark’s methylation extraction script.
Assembly: Acroproa millepora, v2.1
Supplementary files format and content: Gzipped tab separated coverage file, created by Bismark’s methylation extraction script; Columns are: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>
Supplementary files format and content: Offspring have separate coverage files for each allele-specific alignment
Library strategy: md-RAD

organism: Acropora selago

source_name: Coral Fragment

growth_protocol: Specimens of A. millepora and A. selago were collected and placed into raceways 7 days before spawning. Sperm and egg were collected from each colony on the night of spawning and separated to be fertilized in controlled crosses. Larvae were kept at 27 °C for 5 days until larval development completed. After development, we fixed larvae from each successful cross in 100% Ethanol and stored at -80 °C.

extract_protocol:
DNA was extracted from adult corals and from individual and pooled larvae (approximately 10 larvae per pool).  Samples were lysed through bead beating and 2-hour incubation with CTAB buffer at 65 °C. Subsequently, an organic DNA extraction is performed using phenol:chloroform:isoamyl alcohol (25:24:1). DNA was then cleaned using the Zymo Clean & Concentrate kit.
Whole genome bisulfite (WGBS) preparation was only completed on adult coral samples and pooled larvae using the Zymo-Seq WGBS Library Kit.

value: Coral Fragment

tag: protocol

value: md-RAD

value: Parent


title: ICB, rep 3

city: Boston

first: Dan

last: Duda

state: MA

address: 55 Fruit St

department: Radiation Oncology

institute: Massachusetts General Hospital

data_processing:
The quality control of RNA-Seq raw data was performed by FastQC.
After quality control, the low-quality bases and adaptors contamination was removed by Cutadapt.
The quality of clean yield data was examined again by FastQC software.
Next, the clean data were aligned to mouse reference genome mm10 by Hisat2 with a maximum of 2 mismatches per read.
After data mapping, samtools and HTSeq-count were used to count the number of reads aligned to the gene features.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample

source_name: tumor (Intrahepatic cholangiocarcinoma)

extract_protocol:
Total RNA was extracted from the 425-ICC tumor tissues using Qiagen kits.
RNA libraries for RNA-seq were prepared using Qiagen Stranded RNA Library Kits following manufacturer's protocols.

value: tumor (Intrahepatic cholangiocarcinoma)

value: ICB


title: ICB, rep 1


title: md-RAD_A. selago adult 2

description:
lane1-A2-B_S2_L001_1.trim_bismark_bt2_pe.deduplicated.bismark.cov.gz
Both whole genome bisulfite-seq and md-RAD data were in the generation of the processed data files.


title: A. selago adult 2

data_processing:
WGBS reads trimmed with Trim Galore 0.6.7
Trimmed adult WGBS reads aligned to Amil v2.1 with Bismark v 0.24.2 with with mapping parameters -N 1 --score_min L,0,-0.8
md-RAD reads trimmed and aligned with Bowtie2 v. 2.5.0
Adult WGBS and md-RAD alignments variant called with ANGSD 0.940
Fixed SNP differences between adults were determine from variant calls, then used to create N-masked reference genomes for each pair of parents, with SNPsplit’s genome preparation script
Offspring WGBS files aligned to parent-specific masked genomes, using Bismark v 0.24.2.
Offspring alignments separated by parental alleles using SNPsplit v 0.6
Methylation calls extracted from adult WGBS alignments and offspring allele-specific alignments using Bismark’s methylation extraction script.
Assembly: Acroproa millepora, v2.1
Supplementary files format and content: Gzipped tab separated coverage file, created by Bismark’s methylation extraction script; Columns are: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>
Supplementary files format and content: Offspring have separate coverage files for each allele-specific alignment

value: whole genome bisulfite-seq


title: A. selago adult 1


title: A. selago offspring s1xs2

source_name: Larval Pool

value: Larval Pool

value: Offspring


title: A. selago offspring s2xs1


title: ICB, rep 2


title: GC, rep 3

value: GC


title: GC, rep 1


title: GC, rep 2


title: Combination, rep 2

value: Combination


title: Combination, rep 1


title: Control, rep 2

value: Control


title: Control, rep 1


title: Control, rep 3


title: Neonatal Mice Cardiac Fibroblasts, OE_TEAD1_input DNA_1

first: shuai

last: song

address: No. 1609 Xietu Road, Xuhui District, Shanghai

department: Department of Cardiology

institute: Zhongshan  Hospital, Fudan University

data_processing:
Translated with www.DeepL.com/Translator (free version)
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC mm39 genome using Bowtie version 1.1.2.
Only uniquely mapping reads with at most two mismatches were retained. To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments. Call Peak was performed using the MACS2 software with a screening threshold of qvalue < 0.05. The parameters used were macs2 callpeak --nomodel -f BAMPE --keep-dup 1 -q 0.05 -B -SPMR.
Assembly: mm39
Supplementary files format and content: Tab-delimited text files

source_name: Neonatal Mice Cardiac Fibroblasts

extract_protocol:
Samples were fixed with 1% formaldehyde (sigma,47608). Nuclear chromatin was extracted, sonicated and fragmented to 100-400bp, 5% was removed as INPUT and the remainder was used for immunoprecipitation.
Primary antibodies were incubated with beads, together with fragmented chromatin, at 4°C for 6 h. Antibody-bead-protein-DNA complexes were washed sequentially with high-salt and low-salt buffers, and then the IP product was eluted. the IP product and the input were de-crosslinked with RNase A (NEB, T3018L) and Proteinase K (NEB, P8107S). The uncrosslinked input DNA and IP DNA were purified with a kit (QIAquick PCR Purification Kit, 28106). The purified Input DNA and IP DNA were constructed using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S).

value: Neonatal Mice Cardiac Fibroblasts


title: Neonatal Mice Cardiac Fibroblasts, OE_NC_input DNA_1

value: OE-NC


title: Neonatal Mice Cardiac Fibroblasts, OE-TEAD1_1


title: Neonatal Mice Cardiac Fibroblasts, OE-NC_1


title: Esophageal squamous cell carcinoma tissue 1

type: RNA

city: Guangzhou

first: kai

last: lei

address: 107 Yan Jiang West Road

department: Department of Thoracic Surgery

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

description: Biological replicate 1 of 3.Tumor tissue of esophageal squamous cell carcinoma

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 × 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 using the Agilent Scanner 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 using the R software limma package. Differentially expressed circRNAs with statistical significance between two groups were identified through Volcano Plot filtering. Differentially expressed circRNAs between two samples were identified through Fold Change filtering. Hierarchical Clustering was performed to show the distinguishable circRNAs expression pattern among samples.
Quantile normalization of raw data and subsequent data processing were performed using the R software limma package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 3 out of 6 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses.

label_protocol: The enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super 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.

growth_protocol: During operation, tumor tissues and adjacent normal esophageal epithelial tissues of 3 patients with esophageal squamous cell carcinoma were taken

extract_protocol: Total RNA from each sample was quantified using the NanoDrop ND-1000. The sample preparation and microarray hybridization were performed based on the Arraystar’s standard protocols. Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs.

treatment_protocol: Fresh oesophageal squamous carcinoma tumour tissue and normal oesophageal epithelial tissue for subsequent microarray analysis

value: ESCC


title: Esophageal squamous cell carcinoma tissue 2

description: Biological replicate 2 of 3.Tumor tissue of esophageal squamous cell carcinoma


title: Normal esophageal epithelial tissue 1

description: Biological replicate 1 of 3.Normal epithelial tissue of the esophagus

source_name: Normal esophageal epithelial tissue

value: adjacent normal epithelial tissue


title: Esophageal squamous cell carcinoma tissue 3

description: Biological replicate 3 of 3.Tumor tissue of esophageal squamous cell carcinoma


title: Normal esophageal epithelial tissue 2

description: Biological replicate 2 of 3.Normal epithelial tissue of the esophagus


title: Normal esophageal epithelial tissue 3

description: Biological replicate 3 of 3.Normal epithelial tissue of the esophagus