title: tumor 1Q

description: surgically resected


title: CP9 strain, biofilm, 8 hr, rep 2

status: Public on Dec 31 2025

type: SRA

city: Merced

first: Clarissa

last: Nobile

state: California

address: 5200 N Lake road

department: Molecular and Cell Biology

country: USA

institute: University of California MERCED

description: Library name: CP9_2_biofilm_8hr

library_source: transcriptomic

data_processing:
The paired-end reads were assessed for quality using FastQC (v0.11.9).
The reference genome was indexed using the subread-buildindex function in subread (v2.0.6). We then mapped the paired-end reads to the reference genome using the subread-align function in subread (v2.0.6), including multi-mapped reads, mapping to the best 10 genomic loci (parameters: –multiMapping, -B 10)
Transcript abundance for each gene was computed using the featureCounts function in subread (v2.0.6), counting only read-pairs where both ends map to the same chromosome (parameters: -B, -C, –countReadPairs). The transcript abundance table was generated by consolidating all serial isolates, biological replicates, time point (90 minutes, 8 hours and 24 hours) and growth condition (biofilm and planktonic growth condition) using a custom Python script (v3.8.18) and were used for subsequent differential expression analyses.
Differential expression analysis was performed using DESeq2 (v1.44.0).
Assembly: ASM18276v2
Supplementary files format and content: tab-delimited txt file contains transcript abundance counts for all samples.

molecule: total RNA

organism: Candida parapsilosis

source_name: biofilm

growth_protocol: Biofilms were harvested by gently pipetting up and down along the bottoms of the 12-well plates and combining the biofilm slurry of the same strain from each well of one 12-well plate into a 50 mL conical tube. Planktonic cultures of a given biological replicate were combined in a 50 mL conical tube.

extract_protocol:
The conical tubes were centrifuged at 4,000 x g for 5 minutes and the supernatant was aspirated. Pellets were snap-frozen and stored at -80°C until RNA extraction. Total RNA was extracted using the Ribopure RNA Purification Kit for Yeast (AM1926). mRNA was separated from total RNA using the NEBNext Poly(A) mRNA Isolation Module (E7490L).
500 ng of purified mRNA were made into cDNA libraries using the NEBNext Ultra II RNA Library Prep Kit for Illumina (E7775L).

tag: cell type

value: biofilm

tag: genotype

tag: time

value: 8 hr


title: tumor 15M

type: RNA

city: Tokyo

first: Manabu

last: Takamatsu

address: 3-8-31 Ariake Koto-ku

department: Pathology

country: Japan

institute: Cancer Institute

description: surgically resected

hyb_protocol: Hybridization was performed using the NanoString nCounter protocol, incubated at 65°C for 18 hours.

scan_protocol: Post-hybridization processing was performed, and data were collected using the analyzer SPRINT.

data_processing: Raw RCC files were analyzed using NanoString nSolver v4.0. Background correction and normalization were performed using positive controls and housekeeping genes.

molecule: polyA RNA

organism: Homo sapiens

source_name: primary pancreatic cancer

label_protocol: Not applicable

extract_protocol: Total RNA was extracted from fresh frozen tissue using the RNeasy Kit (Qiagen) per manufacturer’s instructions. RNA integrity was confirmed by Bioanalyzer (Agilent).

tag: clusterid

value: M


title: 3C-seq of S. muelleri plate with 25 ug/ml Rifampicin for 30 min

city: Vienna

first: Silvia

last: Bulgheresi

address: Djerassiplatz 1

department: Functional and Evolutionary Ecology

country: Austria

institute: University of Vienna

library_source: genomic

data_processing:
Raw contact maps were built as described previously (Lioy and Cournac 2018). Briefly, each read was assigned to a restriction fragment. Non- informative events such as self-circularized restriction fragments, or uncut co- linear restriction fragments were discarded. The chromosome of each bacterium was divided into 5 kb bins and the frequencies of contacts between genomic loci for each bin were assigned. Contact frequencies were visualized as heatmaps. Raw contact maps used for comparative analyses were built using 1 million valid reads. Raw contact maps were normalized using Iterative correction and eigenvector decomposition (ICE; Imakaev, et all 2012 https://pubmed.ncbi.nlm.nih.gov/22941365/). To facilitate visualization, normalized contact matrices are visualized as log matrices. A Gaussian filter of H=0.5 is used when plotting the matrices. To quantify the frequency of interactions in the secondary diagonals (Supplementary Figure 4), we applied to our data a method based on the filtering of significant 3C contacts and developed as described (Wang et al, science, 2015).
Assembly: CP083930.1
Supplementary files format and content: raw and ICE-normalized matrices
Library strategy: 3C-Seq

molecule: genomic DNA

organism: Simonsiella muelleri

source_name: bacterial cell culture

extract_protocol:
3C libraries were prepared as previously described (Lioy et al., 2021b, 2018; Marbouty et al., 2015b). Cells were plated from glycerol stock onto agar plates and grown at 37C for 24 hours and 48 hours, after which they were scraped off and transferred to BSTSY/FBS containing 6% f.c formaldehyde, fully resuspended, and fixed at room temperature at 120 rpm, followed by 30 min more at 4C. Glycine (250 mM f.c.) was added, and the cells incubated 30 min at 4C at 120 rpm. After fixation, cells were collected by centrifugation for 10 min at 3,500 g at 4C, resuspended in fresh medium, collected again by centrifugation, and resuspended in 1 ml fresh medium before final collection by centrifugation. Cell pellets were stored at -70C. For digestion, cell pellets were thawed on ice for 10 min, resuspended in 500 l Tris 10 mM EDTA 0.5 mM (TE) (pH 8), and lysed using 4 l Ready-lyse lysozyme (Epicentre) for 20 min at 37C, 300 rpm. SDS (0.5% f.c.) was added and incubated for 10 min at room temperature. 500 l lysed cells were then transferred to a tube containing 4.5 ml digestion buffer (1% Triton X-100, 1x Cutsmart buffer (New England Biolabs)), and 100 l cells (non-digested control) were transferred to a tube containing 0.9 ml of digestion buffer. 100U of HpaII (New England Biolabs) were added to the 5 ml digestion mix. Both tubes were incubated for 3 h at 37C. After digestion, 1 ml of digestion mix was put on ice (digested control) together with the non-digested control. The remaining digestion mix was split into 4 parts, centrifuged for 20 min at 20,000 g, and pellets were carefully resuspended in 1 ml water each, and pooled into 7 ml ligation buffer (1X ligation buffer 3 (New England Biolabs; without ATP), 1mM ATP, 1 mg/ml BSA, 500 U of T4 DNA ligase 5 U/l (ThermoFisher)). Ligation was carried out at 16C for 4 h, followed by incubation together with the two control tubes overnight at 65C with proteinase K (0.25 mg/ml f.c.) and EDTA (6 mM f.c.). The next day, DNA of the ligated sample was precipitated with 1/10 volume of 3 M sodium acetate (pH 5.2) and 2 volumes of isopropanol, and after one hour at -80C, DNA was pelleted by centrifugation for 30 min at 10,000 g at 4C, and resuspended in 500 l 1X TE buffer. DNA in all tubes (ligation and two controls) were extracted once with 400 l phenol-chloroform pH 8.0 (vortexed for 1 min and centrifuged for 5 min 16,000 g at 4C), precipitated (see above; 30 min at -80C, followed by centrifugation for 20 min at 16,000 x g at 4C), washed with 400 l 80% cold ethanol, and diluted in 30 l 1X TE buffer supplemented with RNase A (1 mg/ml f.c.; ThermoFisher). Tubes containing ligated DNA were pooled. A 1% agarose gel was run with aliquots of the ligated and two control DNA to check for efficiency of digest and ligation. Ligated DNA was adjusted with water for 130 l with approx. 5 g, and sheared using a Covaris S220 (Duty cycle 5, Intensity 5, cycles/burst 200, time 60 s for 4 cycles), and the DNA purified using the QIAquick PCR purification kit (40 l elution buffer; Quiagen), and DNA end-repaired with 1X T4 DNA ligase buffer (New England Biolabs), 0.4 mM dNTP mix, 15 U T4 polynucleotide kinase (New England Biolabs), 5U Klenow DNA polymerase (Roche), and incubated for 30 min at RT. DNA was purified using MinElute columns (Qiagen). A-tailing was done with 1X NEBuffer 2 (New England Biolabs), 0.2 mM dATP, and 15 U Klenow exo (New England Biolabs), for 30 min at 37C before inactivation for 20 min at 65C, and DNA again purified using MinElute columns (Qiagen). Sequencing adapters were ligated with 0.5 mM custom-made adapters, 2.106 U T4 DNA ligase, and 1X T4 DNA ligase buffer, for 2 hours at RT, followed by inactivation for 20 min at 65C. DNA fragments were purified in a size from 400 to 900 bp using a PippinPrep apparatus (SAGE Science). Each library was amplified in 12 cycles with 1X Phusion Buffer (ThermoFisher) , 0.2 dNTPs, 0.2 M Illumina primers PE1.0 (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGA) and PE2.0 (CAAGCAGAAGACGGCATACGAGAT), 3 l of 3C library, and 1U of Taq Phusion polymerase (ThermoFisher; 98 C 30 s, 12 cycles of 65C 30 s, and 72C 30 s, and 72C for 7 min). The PCR reaction was purified using MinElute PCR purification kit (Qiagen), and libraries sequenced on an Illumina NextSeq500 with 75 bp paired-end reads. Reads have been trimmed of adapter sequences and deduplicated (see paper for details).
Ligated DNA (5 µg) was adjusted with water to 130 µl, and sheared using a Covaris S220 (Duty cycle 5, Intensity 5, cycles/burst 200, time 60 s for 4 cycles), and the DNA purified using the QIAquick PCR purification kit (40 µl elution buffer; Qiagen), and DNA end-repaired with 1X T4 DNA ligase buffer (New England Biolabs), 0.4 mM dNTP mix, 15 U T4 polynucleotide kinase (New England Biolabs), 5 U Klenow DNA polymerase (Roche), and incubated for 30 min at RT. DNA was purified using MinElute columns (Qiagen). A-tailing was done with 1X NEBuffer 2 (New England Biolabs), 0.2 mM dATP, and 15 U Klenow exo (New England Biolabs), for 30 min at 37°C before inactivation for 20 min at 65°C, and DNA again purified using MinElute columns (Qiagen). Sequencing adapters were ligated with 0.5 mM custom-made adapters, 2.106 U T4 DNA ligase, and 1X T4 DNA ligase buffer, for 2 hours at RT, followed by inactivation for 20 min at 65°C. DNA fragments were purified in a size from 400 to 900 bp using a PippinPrep apparatus (SAGE Science). Each library was amplified in 12 cycles with 1X Phusion Buffer (ThermoFisher) , 0.2 mM dNTPs, 0.2 µM Illumina primers PE1.0 (5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGA-3’) and PE2.0 (5’-CAAGCAGAAGACGGCATACGAGAT-3’), 3 µl of 3C library, and 1U of Taq Phusion polymerase (ThermoFisher; 98 °C 30 s, 12 cycles of 65°C 30 s, and 72°C 30 s, and 72°C for 7 min). The PCR reaction was purified using MinElute PCR purification kit (Qiagen), and libraries sequenced on an Illumina NextSeq500 with 75 bp paired-end reads.

tag: strain

value: bacterial cell culture

tag: group


title: T2D_MDM_2h +Mtb biol rep 1

city: San Antonio

first: Larry

last: Schlesinger

state: TX

address: 8715 W Military Dr

institute: Texas Biomedical Research Institute

description:
Library name: LS_19_T2D_MDM_2h +Mtb
LS_19_T2D_MDM_2h +Mtb

data_processing:
CLC Genomics Workbench v 20.0
Low-quality sequences and adapters were trimmed.
Trimmed reads were mapped to the human hg38 reference genome.
The reads were assigned to the transcripts using the EM algorithm.
The TMM normalization  in EdgeR and multi-factorial statistics based on a negative binomial Generalized Linear Model (GLM) were carried out for differential expression analysis.
Assembly: hg38
Supplementary files format and content: RawCounts.xlsx
Supplementary files format and content: This file contains the raw counts of all the samples

source_name: Blood

extract_protocol:
Cells were retrieved from plates using 5mM EDTA (Sigma) and incubating the cells on ice for 30mins. Cells were stored in RNALater (Invitrogen) at -80C. Prior to shipment the cells were spun down and RNALater replaced with Trizol. RNA was isolated using Quick-RNA Microprep Kit (R1050; Zymo Research) as per the manufacturer’s instructions. Isolated RNA was quantified using the Qubit RNA High Sensitivity Assay Kit (Q32852) and Qubit 4 Fluorometer (both from ThermoFisher Scientific).
RNA sequencing libraries were prepared from 25-500ng of Total RNA using the NEB Next directional RNA library preparation Kit with poly (A) enrichment module (Ipswich, MA).
stranded RNA-seq

tag: tissue

value: Blood

value: Monocyte-derived Macrophage

tag: donor number

tag: diabetes status

value: Type 2 diabetes (T2D)

tag: treatment

value: Mtb infected

value: 2h post infection


title: Young_1_ProxCol

city: Jena

first: Jing

last: Lu

state: Thuringia

address: Beutenbergstraße 11

country: Germany

institute: Leibniz Institute on Aging – Fritz Lipmann Institute (FLI)

description: Single cell RNA sequencing

library_source: transcriptomic single cell

data_processing:
The fastq files are mapped against mm10.e87 genome following by counting the UMI and removing duplicates for single cells using 'cellranger count' (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/count ) with default parameters.
Assembly: mm10.e87
Supplementary files format and content: epithelialF_single_F3.rds, the processed data is an rds file denoting the seurat object of quantitative matrix

organism: Mus musculus

source_name: proximal colon

growth_protocol: 3 Young (about 12week) and 6 old (about 108week) female wild-type C57BL6/J mice were group housed and maintained in a specific pathogen-free animal facility

extract_protocol:
Crypts from different sections of intestine were isolated as described previously(Asad A Ahmad et al., 2014). After centrifugation, the crypts were re-suspended in 3ml of Single-Cell Isolation Solution (TrypLE supplemented with: 1mg/ml DNaseI, 5mM MgCl2, 80μM Y27) and incubated at 37°C for 20min, vortexing for 5 seconds after first 10min. Reaction was quenched by addition of 27ml ice-cold PBS and cells were centrifuged at 1000g for 5minutes at 4°C. Cell pellet was re-suspended in FACS staining medium (FSM - PBS supplemented with 2% Fetal Bovine Serum, 80μM Y27, 3mM EDTA) and treated with CD326 (EpCAM) (G8.8), PE-Cyanine7 coupled rat monoclonal antibody and a TotalSeq Hashtag antibody for 30min on ice in the dark. The cells were then centrifuged at 450g for 5min at 4°C and re-suspended in 500μl fresh FSM. An input of 10000 EpCAM positive FACS sorted single cells per compartment was added to each 10X Chromium Controller channel.
The 10X Single Cell 3’ v2 or v3.1 reagent kit (10X Genomics) was used for cell partitioning, cDNA amplification and library construction.

value: proximal colon

tag: cell line

value: Young (about 12week)

tag: Sex

value: female

value: Aging


title: tumor 9M

description: surgically resected


title: 3C-seq of S. muelleri overnight culture

value: overnight culture


title: 3C-seq of S. muelleri in exponential phase

value: in exponential phase


title: tumor 14N

description: surgically resected

value: N


title: Young_1_DistCol

description: Single cell RNA sequencing

source_name: distal colon

value: distal colon


title: tumor 13O

description: surgically resected

value: O


title: Young_1_Cecum

description: Single cell RNA sequencing

source_name: cecum

value: cecum


title: T2D_MDM_2h -Mtb biol rep 4

description:
Library name: LS_78_T2D_MDM_2h -Mtb
LS_78_T2D_MDM_2h -Mtb

value: Uninfected

value: 2h post culture


title: T2D_MDM_2h -Mtb biol rep 3

description:
Library name: LS_54_T2D_MDM_2h -Mtb
LS_54_T2D_MDM_2h -Mtb

value: Blood


title: 3C-seq of S. muelleri 48 h on plate, replicate1

value: bacterial cell culture

value: 48 h on plate


title: tumor 12O

description: surgically resected


title: Young_1_DistSI

description: Single cell RNA sequencing

source_name: distal small intestine

value: distal small intestine


title: T2D_MDM_2h +Mtb biol rep 3

description:
Library name: LS_53_T2D_MDM_2h +Mtb
LS_53_T2D_MDM_2h +Mtb

value: Monocyte-derived Macrophage

value: Type 2 diabetes (T2D)

value: Mtb infected

value: 2h post infection


title: T2D_MDM_2h -Mtb biol rep 2

description:
Library name: LS_32_T2D_MDM_2h -Mtb
LS_32_T2D_MDM_2h -Mtb


title: Young_2_ProxSI

description: Single cell RNA sequencing

source_name: proximal small intestine

value: proximal small intestine

value: Young (about 12week)

value: female

value: Aging


title: Young_1_IntSI

description: Single cell RNA sequencing

source_name: intermediate small intestine

value: intermediate small intestine


title: tumor 12N

description: surgically resected

value: N


title: tumor 11M

description: surgically resected

value: M


title: Liver, 15 degrees, no pesticides, PKD, replicate 6

city: Lausanne

first: Rébecca

last: Beauvais

address: EPFL-ENAC-IIE-GE, Station 2

country: Switzerland

institute: Swiss Centre for applied ecotoxicology

description: Library name: PKD_6

data_processing:
The reads were aligned to the reference transcriptome GCF_901001165.1_fSalTru1.1 (over 42’000 transcripts) and counted using the program kallisto (Bray et al., 2016).
We excluded one replicate due to a considerable difference in number of reads sequenced (18 million reads) compared to the other samples (27 to 37 million reads per sample). Before differential gene expression (DGE) analysis, we additionally filtered out outlier samples (based on clustering and principal component analyzes) and genes (very low, <20 raw counts in at least one sample and very high counts, >20’000 raw counts in at least one sample). The remaining data set contained 28 samples and 26’375 transcripts for the brain, and 27 samples and 14’413 transcripts for the liver.
The DGE analysis was performed with edgeR after Trimmed Mean of M-values normalization on the open source, web-based platform Galaxy version 20.09.rc1 (usegalaxy.org) (Jalili et al. 2021)
Assembly: GCF_901001165.1_fSalTru1.1
Supplementary files format and content: tab-delimited text files include raw counts for each experiment

organism: Salmo trutta

source_name: liver

growth_protocol: Juvenile brown trout (Salmo trutta) were obtained from the fish farm Biasca e dintorni (Loderio, Switzerland) and transported by car from the fish farm to the Centre for Fish and Wildlife Health (FIWI, University of Bern, Switzerland) in continuously oxygenated water on April 30th, 2019. Trout were quarantined for three months in three 130 L glass tanks supplied with > 100 L/h tap water at an average water temperature of 13 ± 0.47 °C and a 12 h light / 12 h dark photoperiod. No systemic infection was found, and fish were tested negative for T. bryosalmonae. After the quarantine, fish were distributed into 20 experimental 35 L glass flow-through tanks and acclimated for one month to experimental conditions.

extract_protocol:
Total RNA was isolated from whole brain and a piece of liver tissue using Qiagen’s RNeasy Plus Mini Kit (Hilden, Germany) following the manufacturer’s instructions. RNA concentration and purity were measured by spectrophotometry (Nanodrop ND-1000, Thermo Fisher Scientific, Waltham, MA, USA) and integrity was verified using the RNA 6000 Nano Chip on the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Ratios of 260/280 and 260/230 were above 2.0 and 2.1, respectively. Median RIN (RNA integrity number) values were 9.1 (brain) and 9.6 (liver). Samples were diluted with RNase-free water to 100 ng/mL (brain) and 125 ng/mL (liver), then treated with DNAse I (amplification grade, Invitrogen, Carlsbad, CA, USA).
RNA libraries were prepared from the DNAse I treated total RNA extracted from liver samples. One μg of total RNA was used for library preparation (TruSeq™ RNA Sample Prep Kit v2; Illumina, San Diego, USA) following the manufacturer’s instructions.

treatment_protocol: Fish were exposed for 14 days to one (at 12°C) or two (at 15°C) sublethal concentrations of a pesticide mixture (fluopyram, epoxiconazole, diuron, chlorpyrifos, λ-cyhalothrin).  Immediately following the 14-day pesticide exposure, fish were exposed 4 days to the causative agent of proliferative kidney disease (PKD), the parasite T. bryosalmonae.

value: liver tissue

value: 4 days exposure after temperature traitment

value: no pesticides

tag: batch

value: 15 degrees

value: liver


title: Young_1_ProxSI

description: Single cell RNA sequencing


title: T2D_MDM_2h -Mtb biol rep 1

description:
Library name: LS_20_T2D_MDM_2h -Mtb
LS_20_T2D_MDM_2h -Mtb

value: Blood

value: Uninfected

value: 2h post culture


title: Liver, 15 degrees, no pesticides, PKD, replicate 5

description: Library name: PKD_5


title: T2D_MDM_2h -Mtb biol rep 5

description:
Library name: LS_90_T2D_MDM_2h -Mtb
LS_90_T2D_MDM_2h -Mtb

value: Monocyte-derived Macrophage

value: Type 2 diabetes (T2D)


title: T2D_HAM_72h +Mtb biol rep 7

description:
Library name: LS_107_T2D_HAM_72h +Mtb
LS_107_T2D_HAM_72h +Mtb

source_name: Bronchoalveolar lavage fluid

value: Bronchoalveolar lavage fluid

value: Alveolar macrophage

value: Mtb infected

value: 72h post infection


title: Input DNA from WT Treg.

city: Lille

first: Artemii

last: Nikitin

address: 1,  Rue du Professeur Calmette

country: France

institute: Inserm

data_processing:
Reads were mapped to the mouse genome (mm10) using Bowtie 2
Mapped reads were filtered to remove duplicates
Regions with significant changes in H3K27me3 ChIP-seq signals induced by RORA deficiency were identified using PePr (Zhang Y, Lin YH, Johnson TD, Rozek LS, Sartor MA. PePr: A peak-calling prioritization pipeline to identify consistent or differential peaks from replicated ChIP-Seq data. Bioinformatics. 2014.)
Assembly: mm10
Supplementary files format and content: Bed files reporting H3K27ac UP, DOWN in RORA KO vs WT Treg, regions identified using PePr

source_name: FOXP3-CRE adult female mice

growth_protocol: Mice were housed in a temperature-controlled room (22–24°C) with a 12h dark-light cycle. Animal studies were performed in compliance with European Community specifications regarding the use of laboratory animals and approved by the Nord-Pas de Calais Ethical Committee for animal use.

extract_protocol:
ChIP was performed as follows. Cells were washed and incubated in 1% formaldehyde in PBS for cross-linking of chromatin. Nuclei were isolated using hypotonic buffer and lysed in SDS-buffer. Chromatin was sonicated using Diagenode Bioruptor and incubated with 2ug anti-H3K27me3 (Millipore) overnight. Immune complexes were incubated with A/G magnaetic beads (Thermo) for 6 hours. Beads were washed with LiCl (Sigma) containing buffer and TE. Cross-linking was reversed in SDS and NaHCO3 containing buffer at 65°C overnight. DNA was isolated using Qiagen MinElute PCR-purification kit.
Libraries were prepared with Truseq kit (illumina) and sequenced using single-end NextSeq technology (illumina).

treatment_protocol: Mouse primary splenic Treg were prepared by FACS based on CD4 and FOXP3 expression. Cells were treated with IL-2, IL-4, IFNg antibodies and activation beads for 6 days in RPMI with 10% FCS, L-glutamine, NEAA, Sodium Pyruvate. ChIP-seq was performed using an H3K27me3 antibody (H3K27me3 Millipore ref 07449).

value: WT

tag: antibody


title: tumor 10O

description: surgically resected

value: O


title: Liver, 15 degrees, no pesticides, PKD, replicate 4

description: Library name: PKD_4


title: H3K27me3 ChIP-seq KO Treg 3

description: H3K27me3 ChIP-seq KO Treg 3

source_name: RORA-FLOX-FOXP3-CRE adult female mice

value: KO

value: H3K27me3 from Millipore ref 07449


title: Liver, 15 degrees, no pesticides, no PKD, replicate 6

description: Library name: Control_6

value: liver tissue

value: 4 days exposure after temperature traitment


title: T2D_HAM_72h +Mtb biol rep 4

description:
Library name: LS_75_T2D_HAM_72h +Mtb
LS_75_T2D_HAM_72h +Mtb


title: Liver, 15 degrees, no pesticides, no PKD, replicate 5

description: Library name: Control_5

value: no pesticides

value: 15 degrees


title: H3K27me3 ChIP-seq KO Treg 1

description: H3K27me3 ChIP-seq KO Treg 1


title: T2D_HAM_72h +Mtb biol rep 2

description:
Library name: LS_41_T2D_HAM_72h +Mtb
LS_41_T2D_HAM_72h +Mtb


title: 3C-seq of S. muelleri 24 h on plate, replicate1

value: bacterial cell culture

value: 24 h on plate


title: Liver, 15 degrees, no pesticides, no PKD, replicate 4

description: Library name: Control_4

value: liver


title: Synaptoneurosome Mimic Rep 4

city: Independencia

first: Wladimir

middle: Antonio

last: Corrales

address: Olivos 1007

department: Biochemistry and Molecular Biology

country: Chile

institute: Universidad de Chile

hyb_protocol: Five point five micrograms (5.5 μg) of amplified biotin-cDNAs were fragmented and hybridized to each array for 16 hours at 45°C in a rotating hybridization oven. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification per the GeneChip Hybridization, Wash and Stain Kit and user manual following protocol FS450-0001.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000 and data was obtained using Transcriptome Analysis Console (TAC) Software.

data_processing: To analyze the microarray datasets, Transcriptome Analysis Console (Affymetrix, USA) version 4.0.3 was used. A log2 scaled expression value was obtained for each probe after background correction and normalization between samples with RMA+DABG algorithm. In order to evaluate the quality of the microarray data and to identify any unusual data in the array slides, several plots (Box plots, density plots, MA plots) were generated for both raw and normalized data. The statistical significance p-value of the log2 ratio for each probe was determined by a modification of the standard t-test by using an empirical Bayesian approach.

label: biotin

organism: Rattus norvegicus

source_name: synaptoneurosome, ventral hippocampus, male, mimic miR-17-5p

label_protocol: One hundred nanograms (100 ng) of total RNA were amplified and labeled as directed using the Affymetrix WT Plus Reagent Kit (WT Plus Kit).

extract_protocol: To purify RNA from the whole extract, 262 μL of chloroform was added to the total homogenate fraction in Qiazol. The mixture was shaken and incubated for 3 min at room temperature and centrifuged at 12,000 g for 15 min at 4°C. Then, the aqueous phase of the mixture was collected, and 1.5 volumes of 100% ethanol were added. The RNA was purified using the RNeasy Mini Kit (Qiagen, Germany). Briefly, the aqueous phase was added to a RNeasy Mini spin column and centrifuged at 12,000 g for 15 s at room temperature. Then, the column was washed consecutively with RWT buffer and RPE buffer. Finally, the total RNA was eluted with 30 μL of nuclease-free water.  To obtain RNA from synaptoneurosomes, 100 μL of chloroform was added to the synaptoneurosomes-enriched fraction in Qiazol. The mixture was shaken vigorously, incubated for 3 min at room temperature, and centrifuged at 12,000 g for 15 min at 4°C. The aqueous phase was collected and 10 μg of glycogen was added. Then, 100% isopropanol was added in a 1:1 volume and allowed to precipitate for 1 hour on ice, the mixture was centrifuged at maximum speed for 10 min at 4°C, and the supernatant was discarded. The RNA was washed 3 times with 1 mL of ice-cold 75% ethanol and the tubes were air-dried until no supernatant remained. Finally, the RNA was resuspended with 20 μL of nuclease-free water.

treatment_protocol: Gain-of-function experiments in vivo were performed to determine the role of miR-17-5p in the vHPC. After 24 hours of basal sucrose preference measurements, rats were anesthetized with 1.5% v/v isoflurane and mounted on a David Kopf stereotaxic as we described before (29). A total of 200 pmol of the miR-17-5p mimic (Qiagen, Germany) dissolved in 1.5 µl of sterile nuclease-free water was injected bilaterally into the vHPC (AP: Bregma – 0.55 cm, LL: ± 0.5 cm, DV: 0.65 cm, 0.2 µl/min). The needle was kept for 10 min to allow mimic diffusion and then removed slowly (1 µm/min) to avoid liquid back pressure. As a control, a commercially available scrambled sequence (Qiagen, Germany) was injected. After removing the administration syringe, the holes in the skull were sealed with bone wax, and the skin was sutured. Finally, Naxpet (Ketoprofen 3 mg/kg/day, s.c.) was administered 15 min before ending the surgery and for the next 3 days. The animals were maintained in their home cages for 3 to 5 days and then regrouped in 3 or 4 rats per cage according to their experimental condition.

tag: gender

value: male

tag: age

value: two months old


title: T2D_HAM_72h +Mtb biol rep 1

description:
Library name: LS_17_T2D_HAM_72h +Mtb
LS_17_T2D_HAM_72h +Mtb

value: Bronchoalveolar lavage fluid

value: Type 2 diabetes (T2D)


title: Liver, 15 degrees, no pesticides, PKD, replicate 3

description: Library name: PKD_3


title: T2D_HAM_72h -Mtb biol rep 6

description:
Library name: LS_108_T2D_HAM_72h -Mtb
LS_108_T2D_HAM_72h -Mtb

value: Alveolar macrophage

value: Uninfected

value: 72h post culture


title: Synaptoneurosome Mimic Rep 3


title: H3K27me3 ChIP-seq KO Treg 2

description: H3K27me3 ChIP-seq KO Treg 2


title: H3K27me3 ChIP-seq WT Treg 3

description: H3K27me3 ChIP-seq WT Treg 3

value: WT


title: H3K27me3 ChIP-seq WT Treg 2

description: H3K27me3 ChIP-seq WT Treg 2


title: Synaptoneurosome Mimic Rep 5


title: Synaptoneurosome Mimic Rep 2


title: T2D_HAM_72h +Mtb biol rep 6

description:
Library name: LS_99_T2D_HAM_72h +Mtb
LS_99_T2D_HAM_72h +Mtb

value: Mtb infected

value: 72h post infection


title: T2D_HAM_72h -Mtb biol rep 2

description:
Library name: LS_42_T2D_HAM_72h -Mtb
LS_42_T2D_HAM_72h -Mtb


title: H3K27me3 ChIP-seq WT Treg 1

description: H3K27me3 ChIP-seq WT Treg 1

value: H3K27me3 from Millipore ref 07449


title: Input DNA from WT Treg

data_processing:
Reads were mapped to the mouse genome (mm10) using Bowtie 2
Mapped reads were filtered to remove duplicates
Regions with significant changes in H3K27ac ChIP-seq signals induced by RORA deficiency were identified using PePr (Zhang Y, Lin YH, Johnson TD, Rozek LS, Sartor MA. PePr: A peak-calling prioritization pipeline to identify consistent or differential peaks from replicated ChIP-Seq data. Bioinformatics. 2014.)
Assembly: mm10
Supplementary files format and content: Bed files reporting H3K27ac UP, DOWN in RORA KO vs WT Treg, regions identified using PePr

extract_protocol:
ChIP was performed as follows. Cells were washed and incubated in 1% formaldehyde in PBS for cross-linking of chromatin. Nuclei were isolated using hypotonic buffer and lysed in SDS-buffer. Chromatin was sonicated using Diagenode Bioruptor and incubated with 2ug anti-H3K27ac (ActiveMotif), anti-H3K27me3 (Millipore) overnight. Immune complexes were incubated with A/G magnaetic beads (Thermo) for 6 hours. Beads were washed with LiCl (Sigma) containing buffer and TE. Cross-linking was reversed in SDS and NaHCO3 containing buffer at 65°C overnight. DNA was isolated using Qiagen MinElute PCR-purification kit.
Libraries were prepared with Truseq kit (illumina) and sequenced using single-end NextSeq technology (illumina).

treatment_protocol: Mouse primary splenic Treg were prepared by FACS based on CD4 and FOXP3 expression. Cells were treated with IL-2, IL-4, IFNg antibodies and activation beads for 6 days in RPMI with 10% FCS, L-glutamine, NEAA, Sodium Pyruvate. ChIP-seq was performed using an H3K27ac antibody (Active Motif ref 39685).


title: Synaptoneurosome Mimic Rep 1


title: Liver, 15 degrees, no pesticides, no PKD, replicate 2

description: Library name: Control_2

value: liver tissue

value: 4 days exposure after temperature traitment


title: Synaptoneurosome Control Rep 5

source_name: synaptoneurosome, ventral hippocampus, male, control


title: Synaptoneurosome Control Rep 4


title: Liver, 15 degrees, no pesticides, PKD, replicate 2

description: Library name: PKD_2

value: no pesticides

value: 15 degrees


title: T2D_HAM_72h -Mtb biol rep 5

description:
Library name: LS_100_T2D_HAM_72h -Mtb
LS_100_T2D_HAM_72h -Mtb


title: Input DNA from KO Treg

value: KO


title: Liver, 15 degrees, no pesticides, PKD, replicate 1

description: Library name: PKD_1

value: liver


title: T2D_HAM_72h -Mtb biol rep 1

description:
Library name: LS_18_T2D_HAM_72h -Mtb
LS_18_T2D_HAM_72h -Mtb


title: T2D_HAM_24h +Mtb biol rep 6

description:
Library name: LS_97_T2D_HAM_24h +Mtb
LS_97_T2D_HAM_24h +Mtb

value: 24h post infection


title: Synaptoneurosome Control Rep 3

value: male

value: two months old


title: Liver, 15 degrees, no pesticides, no PKD, replicate 1

description: Library name: Control_1


title: Liver, 15 degrees, no pesticides, no PKD, replicate 3

description: Library name: Control_3


title: T2D_HAM_24h +Mtb biol rep 5

description:
Library name: LS_85_T2D_HAM_24h +Mtb
LS_85_T2D_HAM_24h +Mtb

value: Bronchoalveolar lavage fluid

value: Type 2 diabetes (T2D)


title: Synaptoneurosome Control Rep 1


title: T2D_HAM_24h +Mtb biol rep 4

description:
Library name: LS_73_T2D_HAM_24h +Mtb
LS_73_T2D_HAM_24h +Mtb

value: Alveolar macrophage


title: H3K27ac ChIP-seq KO Treg 2

description: H3K27ac ChIP-seq KO Treg 2

value: H3K27ac from Active Motif ref 39685


title: T2D_HAM_24h +Mtb biol rep 3

description:
Library name: LS_59_T2D_HAM_24h +Mtb
LS_59_T2D_HAM_24h +Mtb


title: H3K27ac ChIP-seq KO Treg 3

description: H3K27ac ChIP-seq KO Treg 3


title: Synaptoneurosome Control Rep 2


title: H3K27ac ChIP-seq WT Treg 3

description: H3K27ac ChIP-seq WT Treg 3

value: WT


title: Liver, 15 degrees, no pesticides, replicate 5

description: Library name: L15_0_5

value: 14 days exposure


title: H3K27ac ChIP-seq KO Treg 1

description: H3K27ac ChIP-seq KO Treg 1


title: Liver, 15 degrees, no pesticides, replicate 4

description: Library name: L15_0_4


title: T2D_HAM_24h +Mtb biol rep 2

description:
Library name: LS_51_T2D_HAM_24h +Mtb
LS_51_T2D_HAM_24h +Mtb

value: Mtb infected


title: H3K27ac ChIP-seq WT Treg 2

description: H3K27ac ChIP-seq WT Treg 2


title: Liver, 15 degrees, pesticides concentration 1, replicate 6

description: Library name: L15_1_6

value: pesticides concentration 1


title: Liver, 15 degrees, no pesticides, replicate 3

description: Library name: L15_0_3

value: liver tissue


title: T2D_HAM_24h +Mtb biol rep 1

description:
Library name: LS_39_T2D_HAM_24h +Mtb
LS_39_T2D_HAM_24h +Mtb


title: H3K27ac ChIP-seq WT Treg 1

description: H3K27ac ChIP-seq WT Treg 1


title: mRNA_CH16

city: Berlin

first: Frederik

middle: Richard

last: Heinrich

state: Berlin

address: Chariteplatz 1

department: Bioinformatics

description: Th1 cells after 1 week

data_processing:
Sequence reads were mapped to mouse GRCm38/mm10 genome with TopHat2 in very-sensitive settings for Bowtie2 and EnsEMBL annotation release 67.
Gene expression was quantified by feature featureCounts.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files including raw counts for genes.

source_name: spleen

extract_protocol:
isolation protocol: Succesive CD4+ and C62L+ T cell isolation using positive selection with MACS Beads from wildtype mouse splenocytes. Cells were either harvested directly, or activated for 48 hrs with anti-CD3 and anti-CD28 under Th1, Th2 or Th17 polarizing conditions and the cultured for 1 week or repeatedly restimulated with anti-CD3 and anti-CD28 and cultured for 4 weeks. After each week the viable cells were collected by Ficoll grandient centrifugation.
FACS sort: none, viable cells were obtained by Ficoll gradient centrifugation
RNA isolation protocol: RNA of cells was extracted using RNeasy Plus Micro Kit (Qiagen) and RNA quality was assessed by an Agilent 2100 Bioanalyzer.
Illumina® Stranded Total RNA Prep, Ligation with Ribo-Zero Plus

value: C57BL/6J background

value: 1 week

tag: sorting strategy

value: viable cells


title: Homogenate Mimic Rep 4

source_name: homogenate, ventral hippocampus, male, mimic miR-17-5p


title: Liver, 15 degrees, pesticides concentration 5, replicate 6

description: Library name: L15_5_6

value: pesticides concentration 5

value: 15 degrees


title: Liver, 15 degrees, no pesticides, replicate 6

description: Library name: L15_0_6

value: no pesticides

value: liver


title: T2D_HAM_24h -Mtb biol rep 6

description:
Library name: LS_98_T2D_HAM_24h -Mtb
LS_98_T2D_HAM_24h -Mtb

tag: cell type

value: Uninfected

value: 24h post culture


title: Liver, 15 degrees, pesticides concentration 5, replicate 5

description: Library name: L15_5_5


title: Liver, 15 degrees, pesticides concentration 1, replicate 5

description: Library name: L15_1_5


title: mRNA_CH15

description: Naive Th cells

value: Naive Th cells

value: 0 weeks


title: T2D_HAM_24h -Mtb biol rep 2

description:
Library name: LS_52_T2D_HAM_24h -Mtb
LS_52_T2D_HAM_24h -Mtb

value: Bronchoalveolar lavage fluid

value: Alveolar macrophage

value: Type 2 diabetes (T2D)


title: T2D_HAM_24h -Mtb biol rep 4

description:
Library name: LS_74_T2D_HAM_24h -Mtb
LS_74_T2D_HAM_24h -Mtb


title: Liver, 15 degrees, pesticides concentration 1, replicate 4

description: Library name: L15_1_4

value: 14 days exposure


title: T2D_HAM_24h -Mtb biol rep 5

description:
Library name: LS_86_T2D_HAM_24h -Mtb
LS_86_T2D_HAM_24h -Mtb


title: Homogenate Control Rep 5

source_name: homogenate, ventral hippocampus, male, control

value: male

value: two months old


title: T2D_HAM_24h -Mtb biol rep 3

description:
Library name: LS_60_T2D_HAM_24h -Mtb
LS_60_T2D_HAM_24h -Mtb


title: mRNA_CH14

description: Th17 cells after 4 weeks

value: C57BL/6J background

value: 4 weeks


title: mRNA_CH11

description: Th2 cells after 1 week

value: 1 week

value: viable cells


title: mRNA_CH13

description: Th17 cells after 1 week


title: Homogenate Mimic Rep 2


title: Homogenate Mimic Rep 1


title: C deletion RNase E replicate 2

city: Worcester

first: Scarlet

last: Shell

state: MA

address: 100 Institute Rd

department: Biology and Biotechnology

institute: Worcester Polytechnic Institute

description: Library name: D825 2

data_processing:
Reads were aligned to the NC_008596 reference genome using the Burrows-Wheeler Aligner
FeatureCount was used to align reads to genomic features
Assembly: NC_008596
Supplementary files format and content: Read count table generated by FeatureCount

organism: Mycolicibacterium smegmatis

source_name: Mycolicibacterium smegmatis mc2155 derivative

growth_protocol: Log phase growth in 7H9 supplemented with glycerol, BSA, dextrose, NaCl, catalase

extract_protocol:
RNA was extracted as described in (Vargas-Blanco DA, Zhou Y, Zamalloa LG, Antonelli T, Shell SS 2019. mRNA Degradation Rates Are Coupled to Metabolic Status in Mycobacterium smegmatis. mBio 10:10.1128/mbio.00957-19.)
rRNA was depleted as described in (Culviner, P.H., Guegler, C.K. and Laub, M.T. (2020) A simple, cost-effective, and robust method for rRNA depletion in RNA-sequencing studies. MBio, 11, 10.1128/mbio. 00010-00020.). Libraries were constructed as described in Culviner, Peter H. et al. Cell, Volume 188, Issue 23, 6620 - 6635.e14.

tag: genotype

value: C deletion RNase E

value: exponential phase


title: T2D_HAM_2h +Mtb biol rep 7

description:
Library name: LS_103_T2D_HAM_2h +Mtb
LS_103_T2D_HAM_2h +Mtb

value: Mtb infected

tag: time

value: 2h post infection


title: Homogenate Control Rep 3


title: Liver, 15 degrees, pesticides concentration 5, replicate 4

description: Library name: L15_5_4

value: liver tissue

value: pesticides concentration 5

value: 15 degrees

value: liver


title: Homogenate Control Rep 4


title: Homogenate Mimic Rep 5


title: Homogenate Mimic Rep 3


title: Homogenate Control Rep 1


title: mRNA_CH12

description: Th2 cells after 4 weeks


title: mRNA_CH9

description: Th2 cells after 1 week


title: Homogenate Control Rep 2


title: C deletion RNase E replicate 3

description: Library name: D825 3

value: Mycolicibacterium smegmatis mc2155 derivative


title: T2D_HAM_24h -Mtb biol rep 1

description:
Library name: LS_40_T2D_HAM_24h -Mtb
LS_40_T2D_HAM_24h -Mtb

value: Bronchoalveolar lavage fluid

value: Alveolar macrophage

value: Type 2 diabetes (T2D)

value: Uninfected

value: 24h post culture


title: Liver, 15 degrees, pesticides concentration 1, replicate 3

description: Library name: L15_1_3

value: 14 days exposure

value: pesticides concentration 1


title: mRNA_CH10

description: Th2 cells after 4 weeks

value: C57BL/6J background

value: 4 weeks

value: viable cells


title: C deletion RNase E replicate 1

description: Library name: D825 1

value: C deletion RNase E

value: exponential phase


title: mRNA_CH8

description: Th1 cells after 4 weeks


title: T2D_HAM_2h +Mtb biol rep 4

description:
Library name: LS_71_T2D_HAM_2h +Mtb
LS_71_T2D_HAM_2h +Mtb

value: Mtb infected

value: 2h post infection


title: T2D_HAM_2h +Mtb biol rep 6

description:
Library name: LS_95_T2D_HAM_2h +Mtb
LS_95_T2D_HAM_2h +Mtb


title: nongyao, replicate 1, scRNAseq

city: Beijing

first: Xiasang

last: Chen

address: 2 Yuanmingyuan West Road. Institute of Apicultural Research, Chinese Academy of Agricultural Sciences

country: China

institute: State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest).
Assembly: Amel_HAv3.1
Supplementary files format and content: Tab-separated values files and matrix files

organism: Apis mellifera

source_name: Mushroom bodies

extract_protocol:
Whole dissociation was placed in the ice-cold phosphate-buffered solution plate, removed the coating membrane and the optic lope, antennal lobe, then the mushroom bodies were fetched into the tube, washed double times using cold PBS solution, added the tissue into the 300 μL activated enzyme blended solution and brain dissociation kit enzyme mix overall, incubated in the automated dissociator by the 37℃, 200 rpm, 30 min, every 10 minutes used a wide-bore pipette tip to mix the cells gently and thoroughly, Used a 40 μm cell strainer to remove any remaining cell debris and large clumps, Centrifuged cells at 300 rcf for 10 min, 4℃. Removed supernatant without disrupting the cell pellet. Using a wide-bore pipette tip, add 1 ml 1× PBS with 0.04% BSA to the tube. Gently mixed 5 times and inverted tubes to re-suspend the cell pellet. Centrifuged the cells at 300 rcf for 10 min. Removed supernatant without disrupting the cell pellet, used DMEM + 10% FBS to re-suspend, and fitted the volume to obtain the target cell concentration.
Library was performed according to the manufacter's instructions (single cell 3' v3 protocol, 10x Genomics).Briefly,Mushroom body cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an llumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriated sized fragments were selectes with SPRIselect reagent for subsequent library construction. During the library construction. During the library construction llumina R2 Primer sequences, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Mushroom bodies

value: newly emerged workers

value: mainly Kenyon cells

value: wild type

value: thiacloprid


title: Liver, 15 degrees, pesticides concentration 1, replicate 1

description: Library name: L15_1_1

value: liver tissue

value: 15 degrees

value: liver


title: Liver, 15 degrees, pesticides concentration 1, replicate 2

description: Library name: L15_1_2

value: 14 days exposure


title: N and C deletion RNase E replicate 3

description: Library name: BD330 3

value: Mycolicibacterium smegmatis mc2155 derivative

value: N and C deletion RNase E


title: T2D_HAM_2h +Mtb biol rep 5

description:
Library name: LS_83_T2D_HAM_2h +Mtb
LS_83_T2D_HAM_2h +Mtb

value: Bronchoalveolar lavage fluid

value: Alveolar macrophage

value: Type 2 diabetes (T2D)


title: Liver, 15 degrees, pesticides concentration 5, replicate 1

description: Library name: L15_5_1

value: pesticides concentration 5


title: N deletion RNase E replicate 2

description: Library name: D330 2

value: N deletion RNase E

value: exponential phase


title: Liver, 15 degrees, pesticides concentration 5, replicate 3

description: Library name: L15_5_3


title: mRNA_CH7

description: Naive Th cells

value: C57BL/6J background

value: Naive Th cells

value: 0 weeks

value: viable cells


title: mRNA_CH4

description: Th17 cells after 1 week

value: 1 week


title: N deletion RNase E replicate 1

description: Library name: D330 1


title: Liver, 15 degrees, pesticides concentration 5, replicate 2

description: Library name: L15_5_2

value: liver tissue


title: Liver, 15 degrees, no pesticides, replicate 2

description: Library name: L15_0_2

value: no pesticides

value: 15 degrees


title: T2D_HAM_2h +Mtb biol rep 3

description:
Library name: LS_49_T2D_HAM_2h +Mtb
LS_49_T2D_HAM_2h +Mtb

value: Mtb infected

value: 2h post infection


title: T2D_HAM_2h +Mtb biol rep 1

description:
Library name: LS_13_T2D_HAM_2h +Mtb
LS_13_T2D_HAM_2h +Mtb


title: mRNA_CH3

description: Th1 cells after 4 weeks

value: 4 weeks


title: mRNA_CH5

description: Th17 cells after 4 weeks


title: Full Length RNase E replicate 3

description: Library name: Full_rne 3

source_name: Mycolicibacterium smegmatis mc2155

value: Mycolicibacterium smegmatis mc2155

value: Full Length RNase E


title: T2D_HAM_2h -Mtb biol rep 7

description:
Library name: LS_96_T2D_HAM_2h -Mtb
LS_96_T2D_HAM_2h -Mtb

value: Bronchoalveolar lavage fluid

value: Alveolar macrophage

value: Type 2 diabetes (T2D)

value: Uninfected

value: 2h post culture


title: mRNA_CH1

description: Naive Th cells

value: C57BL/6J background

value: Naive Th cells


title: Full Length RNase E replicate 2

description: Library name: Full_rne 2

value: exponential phase


title: N deletion RNase E replicate 3

description: Library name: D330 3

value: Mycolicibacterium smegmatis mc2155 derivative

value: N deletion RNase E


title: Liver, 15 degrees, no pesticides, replicate 1

description: Library name: L15_0_1

value: liver tissue

value: 14 days exposure

value: no pesticides

value: liver


title: T2D_HAM_2h -Mtb biol rep 8

description:
Library name: LS_104_T2D_HAM_2h -Mtb
LS_104_T2D_HAM_2h -Mtb


title: Liver, 12 degrees, pesticides concentration 5, replicate 6

description: Library name: L12_5_6

value: pesticides concentration 5

value: 12 degrees


title: T2D_HAM_2h -Mtb biol rep 6

description:
Library name: LS_84_T2D_HAM_2h -Mtb
LS_84_T2D_HAM_2h -Mtb


title: setB_Ikzf1_circIkzf1

description: Th0 cells

data_processing:
The Cell Ranger Single Cell Software Suite 3.0.2 was used in default parameter settings to perform sample demultiplexing, barcode processing, and single cell 5’ gene counting for transcriptome wirh refdata-cellranger-mm10-1.2.0 as reference and expected-cells number of 3000 for each sample.
Assembly: mm10
Supplementary files format and content: h5: aggregated gene count matrix in hdf5 format.

extract_protocol:
C4+ T cells were isolated from mouse spleens using MACS beads for positive selection. Cells were activated using anti-CD3 and anti-CD28 for 40 hrs, then transduced with combined concentrated ecotropic retrovirus supernatants for circIkzf1 (30), control1(28), Ikzf1 (38) and control2 (8) using spin infection. Cells were then cultured until day 5, when they were FACS sorted for the expression of the two transduction markers hCD4 and GFP. Sorted cells were subjected to single cell capturing according to the 10x Genomics 5' GEX protocol.
The purified cDNA was amplified using 14 cycles of PCR and then used for 5’ gene expression (GEX). Through fragmentation, adapter ligation and index PCR the final libraries were obtained. The quality of single cell 5’ GEX was assessed by Qubit quantification and fragment analysis (HS DNA Kit, Agilent).The sequencing was performed on a NextSeq500 device (Illumina) with the recommended sequencing conditions for 5’ GEX libraries (read1: 26nt, read2: 98nt, index1: 8nt, index2:0).

value: spleen

value: female

value: T helper cells

value: wildtype C57BL/6J

value: activated, retrovirus transduced, expanded and FACS sorted


title: Full Length RNase E replicate 1

description: Library name: Full_rne 1

value: Mycolicibacterium smegmatis mc2155

value: Full Length RNase E


title: T2D_HAM_2h -Mtb biol rep 5

description:
Library name: LS_72_T2D_HAM_2h -Mtb
LS_72_T2D_HAM_2h -Mtb

value: Bronchoalveolar lavage fluid

value: Alveolar macrophage

value: Type 2 diabetes (T2D)

value: Uninfected

value: 2h post culture


title: setB_Ikzf1_control1

description: Th0 cells


title: TNF-α-biol rep 3

city: shenzhen

first: weihao

last: zhang

address: futian

department: Department of Orthopedics, The Eighth Affiliated Hospital

institute: Sun Yat-sen university

description: Library name: SAMPLES6

data_processing:
V1-Dr. TOM I
raw data were filtered with SOAPnuke (v1.5.2) by removing adaptors and low-quality reads
Clean reads were mapped to hg38 genome using HISAT2 (v2.0.4) and then aligned to the hg38 reference using Bowtie (v2.2.5)
Assembly: hg38
Supplementary files format and content: xlsx file includes read counts for each examples

source_name: Mesenchymal stem cells

extract_protocol:
Total RNA was extracted in MSCs using TRIzol reagent (Invitrogen).
Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China).

value: Mesenchymal stem cells


title: Liver, 12 degrees, pesticides concentration 5, replicate 4

description: Library name: L12_5_4

value: liver tissue

value: 14 days exposure


title: N and C deletion RNase E replicate 1

description: Library name: BD330 1

value: Mycolicibacterium smegmatis mc2155 derivative

value: N and C deletion RNase E

value: exponential phase


title: T2D_HAM_2h -Mtb biol rep 3

description:
Library name: LS_50_T2D_HAM_2h -Mtb
LS_50_T2D_HAM_2h -Mtb


title: Liver, 12 degrees, no pesticides, replicate 5

description: Library name: L12_0_5

value: no pesticides

value: 12 degrees

value: liver


title: T2D_HAM_2h +Mtb biol rep 2

description:
Library name: LS_21_T2D_HAM_2h +Mtb
LS_21_T2D_HAM_2h +Mtb

value: Mtb infected

value: 2h post infection


title: setB_control2_control1

description: Th0 cells

value: spleen

value: female

value: T helper cells

value: wildtype C57BL/6J

value: activated, retrovirus transduced, expanded and FACS sorted


title: N and C deletion RNase E replicate 2

description: Library name: BD330 2


title: Liver, 12 degrees, no pesticides, replicate 6

description: Library name: L12_0_6


title: T2D_HAM_2h -Mtb biol rep 4

description:
Library name: LS_58_T2D_HAM_2h -Mtb
LS_58_T2D_HAM_2h -Mtb

value: Bronchoalveolar lavage fluid

value: Alveolar macrophage

value: Type 2 diabetes (T2D)

value: Uninfected

value: 2h post culture


title: TNF-α-biol rep 1

description: Library name: SAMPLES4

value: Mesenchymal stem cells


title: T2D_HAM_2h -Mtb biol rep 2

description:
Library name: LS_22_T2D_HAM_2h -Mtb
LS_22_T2D_HAM_2h -Mtb


title: mRNA_CH2

description: Th1 cells after 1 week

value: C57BL/6J background

value: 1 week

value: viable cells


title: Liver, 12 degrees, pesticides concentration 5, replicate 3

description: Library name: L12_5_3

value: liver tissue

value: 14 days exposure

value: pesticides concentration 5

value: 12 degrees

value: liver


title: setA_Ikzf1_circIkzf1

description: Th0 cells

value: spleen

value: female

value: T helper cells

value: wildtype


title: setB_control2_circIkzf1

description: Th0 cells

value: wildtype C57BL/6J

value: activated, retrovirus transduced, expanded and FACS sorted


title: Liver, 12 degrees, pesticides concentration 5, replicate 2

description: Library name: L12_5_2


title: T2D_HAM_2h -Mtb biol rep 1

description:
Library name: LS_14_T2D_HAM_2h -Mtb
LS_14_T2D_HAM_2h -Mtb

value: Bronchoalveolar lavage fluid

value: Alveolar macrophage

value: Type 2 diabetes (T2D)

value: Uninfected


title: NC-biol rep 3

description: Library name: SAMPLES3

value: Mesenchymal stem cells


title: Liver, 12 degrees, pesticides concentration 5, replicate 5

description: Library name: L12_5_5


title: Liver, 12 degrees, pesticides concentration 5, replicate 1

description: Library name: L12_5_1


title: NC-biol rep 2

description: Library name: SAMPLES2


title: setA_Ikzf1_control1

description: Th0 cells


title: MDA-SA146-Tumor

city: Dallas

first: Lei

last: Guo

address: 5323 Harry Hines Blvd

department: Department of Population and Data Sciences

institute: University of Texas Southwestern Medical Center

data_processing:
Adaptors were trimmed using Trim Galore (v0.6.4). The trimmed reads were then aligned to the human genome (GRCH38) using STAR (2.7.3a). The subsequent mapped reads were quantified by featureCounts of the Subread (v1.6.3) package.
Assembly: GRCH38
Supplementary files format and content: Tab-delimited text file

source_name: Patient sample

extract_protocol: following the protocol from Corces MR et al, Nat Methods. 2017 Oct;14(10):959-962.

value: Bone

value: Osteosarcoma


title: setA_control2_circIkzf1

description: Th0 cells


title: Liver, 12 degrees, no pesticides, replicate 4

description: Library name: L12_0_4

value: liver tissue

value: 14 days exposure

value: no pesticides


title: R1088-7-MDA-SA175-T


title: setA_control2_control1

description: Th0 cells


title: TNF-α-biol rep 2

description: Library name: SAMPLES5


title: Liver, 12 degrees, no pesticides, replicate 3

description: Library name: L12_0_3

value: 12 degrees

value: liver


title: SAT, sample_SAT60, snRNAseq

city: Aarhus

first: Joanna

middle: Maria

last: Kalucka

address: Høegh-Guldbergs Gade, 10

department: Biomedicine

country: Denmark

institute: Aarhus University

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger software v6.1.2, Include_introns = T
Assembly: human GRCh38 reference genome
Supplementary files format and content: barcodes tab-separated values files (contains the unique barcodes for each cell)
Supplementary files format and content: features tab-separated values files (contains the list of genes)
Supplementary files format and content: matrix.mtx file (contains the count matrix for all genes per cells)

molecule: nuclear RNA

source_name: Subcutaneous Adipose tissue

extract_protocol:
Nuclei were isolated from human subcutaneous adipose tissue samples according to a previously published protocol with slight modification (Herold, J. & Kalucka, J. in Angiogenesis 235-250 (Springer, 2022)). Approximately 1g of frozen human subcutaneous adipose tissue was finely minced in a petri dish on dry ice and transferred to a 15mL douncer containing 6.5mL Tween salt-Tris (TST) buffer [ST buffer (146mM NaCl, 10mM Tris-HCl (PH 7.5), 1mM CaCl2, 21mM MgCl2, 1mM DTT, and 0.2U/mL RNAse inhibitor containing 0.01% BSA and 0.03% Tween 20 in nuclease-free water] on ice. Samples were homogenized using the douncer, applying 7 strokes with the loose pestle and 5 strokes with the tight pestle. Another 3mL of TST buffer was added and the homogenate was left to rest on ice for 10 minutes, during which occasional strokes were applied to ensure complete homogenization. The homogenate was then filtered through a 40mm cell strainer and thoroughly washed with 9mL of ST buffer, then centrifuged at 500g for 10 minutes at 4 ºC. The nuclear pellet was washed once with 3mL ST buffer and then twice with 3mL FANS buffer (1% BSA, 1mM DTT, and 0.2U/mL RNAse inhibitor in RNAse free DPBS) and was centrifuged at 500g for 10 minutes at 4 ºC after each wash. Finally, the nuclear pellet was resuspended in 750mL FANS buffer and filtered through a 40mm cell strainer prior to nuclear sorting. All solutions were sterile filtered prior to use.
Isolated nuclei were stained with Hoechst and subjected to fluorescence-activated nuclear sorting (FANS) on a 3 laser FACSAria III high speed cell sorter into FANS buffer containing 2% BSA. A small proportion of the sorted Hoechst-positive events were stained with propidium iodide (PI) and counted on a Luna-FL automated fluorescence cell counter and nuclei were submitted for snRNA-seq using the 10x Genomics system. Immediately following FANS, nuclei were loaded onto the 10x Genomics Chromium controller. Libraries were prepared according to the manufacturer’s instructions using the 10x Genomics Single-Cell 3’ v3.1 (Chromium Next GEM Single Cell 3’ Kit v3.1, 16 rxns, Chromium Next GEM Chip G Single Cell Kit, 48 rxns, and Dual Index Kit TT Set A, 96 rxns. Libraries were sequenced on a DNBSEQ-G400 platform.

value: Subcutaneous Adipose tissue

value: male

tag: condition

value: lean

tag: bmi


title: MDA_SA118


title: nlsGFP, control for HEY1 2, replicate 2, CUT&RUN

city: San Francisco

first: Jeremy

last: Reiter

address: 555 Mission Bay Boulevard South

institute: UCSF

data_processing:
FASTQs were trimmed using trimmomatic with a second trimming step to remove any remaining read-through adaptors (CUT&RUNtools)
Reads were aligned with bowtie2 (Langmead B. 22388286) using parameters --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700.
Samples were filtered for reads under 120bp and duplicates were marked, but not removed, with picard MarkDuplicates.
MACS2 was used to call peaks on merged replicates using parameters --keep-dup all -q 0.0001. A merged NLS-GFP control containing all four NLS-GFP replicates was utilized as a control in the MACS2 callpeaks command.
Assembly: mm10
Supplementary files format and content: Bigwigs for individual replicates
Supplementary files format and content: MACS2 narrow peak files for merged MYCL-GFP and HEY1-GFP replicates.
Library strategy: CUT&RUN

source_name: trachea

growth_protocol: Mouse tracheal epithelial cells (mTECs) were purified and cultured as previously described (You and Brody, 2013).

extract_protocol:
CUT&RUN was performed as described (Meers et al., 2019; Peter J. Skene and Henikoff, 2017), with protocol and buffers detailed in Protocol 2: High Ca2+/low salt (https://www.protocols.io/view/cut-amp-run-targeted-in-situ-genome-wide-profiling-14egnr4ql5dy/v3). Briefly, MYCL-GFP, HEY1-GFP or NLS-GFP transduced mTECs were dissociated in 0.05% trypsin-EDTA in cell dissociation buffer for 15 min at 37°C. Cells were collected in in mTEC Basic medium with 2% Nu-Serum, washed twice in 5 mL of CUT&RUN Wash Buffer, and resuspended in CUT&RUN Wash Buffer. One million cells of each sample were aliquoted in 1.5 mL Eppendorf tubes and brought up to a volume of 1 mL with CUT&RUN Wash Buffer. Cells were incubated with 10 uL activated concavalin A beads (Bangs Laboratories, Cat #BP531) at room temperature for 10 min with gentle rocking. Cells were incubated overnight with anti-GFP (Abcam, Cat #ab290) diluted 1:100 in 0.05% digitonin in CUT&RUN Wash Buffer.  Following two washes in CUT&RUN Wash Buffer, samples were incubated for 1 hour at room temperature in 1:100 rabbit anti-guinea pig IgG in 0.05% digitonin in CUT&RUN Wash Buffer. Samples were incubated with Protein A/G-MNase fusion protein (Addgene, Cat #123461) at 700 ng/mL for 1 hour at 4°C. Following two washes in 0.05% digitonin in CUT&RUN Wash Buffer and one wash in CUT&RUN Low-Salt Rinse Buffer, samples were digested for 10 min at 0°C in cold CUT&RUN Incubation Buffer. Chromatin fragments were released by incubation at 37°C for 30 min and then collected by phenol-chloroform extraction.
Library preparation was performed with the NEB Next Ultra II DNA Library Prep Kit for Illumina (NEB, Cat #E7645S) using 25 uL of CUT&RUN DNA as input, as detailed by Liu N. (https://www.protocols.io/view/library-prep-for-cut-amp-run-with-nebnext-ultra-ii-kxygxm7pkl8j/v2)

treatment_protocol: mTECs were plated in 6.5 mm transwells and transduced with 1-15 ul of lentivirus in mTEC Plus medium supplemented with 50 nM retinoic acid and 10 uM ROCK inhibitor, as modified from a previously transduction protocol (Horani et al., 2013). Basal media was changed 24 hours after transduction and apical media was changed 48 hours after transduction. Media in both chambers was changed at 72 hours post transduction and mTECs were differentiated

value: trachea

tag: cut&run antibody

value: GFP (Abcam, ab290)

value: NLS-GFP lentivrial transduction


title: SAT, sample_SAT58, snRNAseq

description: 10X Genomics

tag: tissue


title: MDA_SA100


title: Liver, 12 degrees, no pesticides, replicate 2

description: Library name: L12_0_2


title: Brain, 15 degrees, no pesticides, replicate 5

description: Library name: B15_0_5

source_name: brain

value: brain tissue

value: 15 degrees

value: brain


title: NC-biol rep 1

description: Library name: SAMPLES1

value: Mesenchymal stem cells


title: SAT, sample_SAT51, snRNAseq

description: 10X Genomics

value: female

value: obese


title: Brain, 15 degrees, no pesticides, replicate 6

description: Library name: B15_0_6


title: MDA_SA99

value: Bone

value: Osteosarcoma


title: nlsGFP, control for MYCL 1, GFP antibody, replicate 1, CUT&RUN


title: SAT, sample_SAT34, snRNAseq

description: 10X Genomics


title: SAT, sample_SAT18, snRNAseq

description: 10X Genomics


title: SAT, sample_SAT39, snRNAseq

description: 10X Genomics


title: MDA_SA117


title: nlsGFP, control for HEY1 1, replicate 1 , CUT&RUN


title: nlsGFP, control for MYCL 2, GFP antibody, replicate 2, CUT&RUN


title: Liver, 12 degrees, no pesticides, replicate 1

description: Library name: L12_0_1

source_name: liver

value: liver tissue

value: 14 days exposure

value: no pesticides


title: SAT, sample_SAT4, snRNAseq

description: 10X Genomics

value: Subcutaneous Adipose tissue


title: Brain, 15 degrees, no pesticides, replicate 4

description: Library name: B15_0_4


title: Cap1703-6-ID19

source_name: Bone

growth_protocol: The cell lines were maintained in high-glucose Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin. All cells were incubated in a humidified atmosphere at 37°C with 5% CO2.

value: Osteosarcoma cell line


title: HEY1-GFP, replicate 1, CUT&RUN

value: HEY1-GFP lentivrial transduction


title: Cap1709-6-HTID040


title: Hos_TE85


title: MYCL-GFP, GFP antibody, replicate 2, CUT&RUN

value: trachea

value: MYCL-GFP lentivrial transduction


title: HEY1-GFP, replicate 2, CUT&RUN

value: GFP (Abcam, ab290)


title: SAT, sample_SAT1, snRNAseq

description: 10X Genomics

value: male


title: MG63


title: Brain, 15 degrees, pesticides concentration 1, replicate 6

description: Library name: B15_1_6

value: brain tissue

value: pesticides concentration 1

value: 15 degrees


title: Brain, 15 degrees, no pesticides, replicate 3

description: Library name: B15_0_3

value: brain


title: MYCL-GFP, GFP antibody, replicate 1, CUT&RUN


title: B16-F3-LPC-rep3

city: Melbourne

first: Pacman

last: Szeto

state: VIC

address: 89 Commercial Road

department: Medicine

country: Australia

institute: Monash University

data_processing:
FASTQ files were processed using Laxy (https://zenodo.org/record/3767372) which encompasses the RNAsik pipeline (https://joss.theoj.org/papers/10.21105/joss.00583). Briefly, GRCm38 reference genome was used for STAR alignment (PubmedID: 23104886)
Genome_build: GRCm38
Supplementary_files_format_and_content: Raw gene count matrix

source_name: melanoma

growth_protocol: The B16 mouse melanoma cell line was obtained from ATCC and maintained in culture in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin.

extract_protocol:
Total cell RNA was extracted from FACS-purified LPC or HPC populations using the PureLink RNA Mini kit (ThermoFisher), according to the manufacturer’s instructions, including an on-column DNase treatment.
RNA was quantitated using Qubit RNA HS (Thermo Fisher Scientific) and 100 ng total RNA input was used for library preparation according to standard protocols (QuantSeq 3’ mRNA-Seq FWD, Lexogen). Indexed libraries were pooled and sequenced on a NextSeq 500 sequencer (Illumina).

value: mouse melanoma cell line

value: Low-pigmented


title: Brain, 15 degrees, pesticides concentration 1, replicate 5

description: Library name: B15_1_5


title: SAT, sample_SAT54, snRNAseq

description: 10X Genomics

value: female

value: lean


title: Brain, 15 degrees, pesticides concentration 5, replicate 6

description: Library name: B15_5_6

value: 14 days exposure

value: pesticides concentration 5


title: CCH_OS_O

value: Bone


title: B16-F3-LPC-rep2


title: SAT, sample_13S, snRNAseq

description: 10X Genomics

value: Subcutaneous Adipose tissue


title: SJSA_GFP

value: Osteosarcoma cell line


title: B16-F3-HPC-rep3

value: High-pigmented


title: Brain, 15 degrees, pesticides concentration 5, replicate 5

description: Library name: B15_5_5


title: SAT, sample_SAT22, snRNAseq

description: 10X Genomics

value: obese diabetic


title: SAT, sample_10S, snRNAseq

description: 10X Genomics


title: SAT, sample_17S, snRNAseq

description: 10X Genomics


title: B16-F3-HPC-rep2


title: B16-F3-LPC-rep1


title: Brain, 15 degrees, pesticides concentration 5, replicate 4

description: Library name: B15_5_4


title: A4574


title: Brain, 15 degrees, pesticides concentration 1, replicate 4

description: Library name: B15_1_4


title: CCHD

value: CCHD


title: SAT, sample_9S, snRNAseq

description: 10X Genomics

value: obese


title: Brain, 15 degrees, pesticides concentration 1, replicate 3

description: Library name: B15_1_3

value: brain tissue


title: Brain, 15 degrees, pesticides concentration 1, replicate 2

description: Library name: B15_1_2

value: pesticides concentration 1


title: NU-LN21

city: Izumo

first: Kunihiro

last: Ichinose

address: 89-1 Enya-cho

department: Department of Rheumatology

institute: Shimane University Faculty of Medicine

data_processing:
MGI DNBseq-G400 FAST was used to perform the amplicons deep sequencing following the standard operation protocol. The sequence format was 150bp pair read for all samples.
All sequencing reads were trimmed low-quality bases and adapters with Trimmomatic (v.0.38) .
Raw counts for each gene were estimated in each sample using RSEM version 1.3.0 and Bowtie 2. Calculation of the log fold-change (log FC) and p-value were performed using edgeR.
Assembly: hg38
Supplementary files format and content: tab-delimited text file. normalized CPM count matrix with GeneSymbol index.

source_name: kidney biopsy

extract_protocol:
Total RNA was obtained from kidney cortex bulk and extracted using RNeasy Plus Kits, in accordance with the manufacturer’s instructions. The RNA quality was evaluated by an Agilent technologies 2200Tapestation.
The total RNA sample was treated using a MGI Easy rRNA Depletion Kit to deplete rRNA, and cDNA libraries were prepared and sequenced at MGI DNBSEQ-G400 FAST system.

value: kidney biopsy

tag: activity of ln

tag: Stage

value: Class V


title: Hth83-CAP3

first: xinyu

last: mang

address: Dongdan Three

institute: Peking Union Medical College,

description:
Hth83_exp_count.txt
Hth83_exp_TPM.txt

data_processing:
The hisat2 Genomic Analysis Software v2.2.1 was used to align the reads to the genome, generate raw counts corresponding to each known gene
calculate the Transcript per million(TPM) values.
Assembly: grch38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: Cal27, A375, and Hth83 cells were cultured in Dulbecco’s modified eagle medium (DMEM, Corning, USA) supplemented with 10% fetal bovine serum (FBS, Gibco, USA) and penicillin-streptomycin (Gibco, USA), and maintained in an incubator with 5% CO2 at 37°C.Fadu cells were cultured in MEM containing 10% FBS.

extract_protocol:
The total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: The Cal27, A375,Fadu and Hth83  cells were seeded in 6-well plates overnight and then treated with Piezo-CAP (0 and 60 s) for 24 h.

value: Head and neck cancer cells

value: WT

tag: treatment

value: treated with Piezo-CAP for 24 hours at durations of  60 s


title: NU-LN20

value: Class IV


title: Sample_R21071403-ZW-24

city: shanghai

first: yuanxin

last: yang

address: 100 Haike Road, Zhangjiang Hi-tech Park, Pudong, Shanghai

institute: the Interdisciplinary Research Center of Biology and Chemistry

data_processing:
For RNA-Seq comparison, Sequencing reads were mapped to mouse with Hisat2 by default parameter. The read counts for each genes were calculated by featurecounts. The count files were used as input to DESeq2 for differential expression analysis.
Genome_build: GRCm38
Supplementary_files_format_and_content: DESeq was used for calling differential expression.tab-delimited text files include normalized read counts,foldChange,pvalue

source_name: skin

extract_protocol: RNA libraries were prepared according to instructions of Vazyme VAHTS mRNA-seq V3 Library Prep Kit for Illumina(NR611-01)

tag: strain

value: skin

value: 12 weeks

value: Zmpste24-/-; RIPK1D138N/D138N


title: LM7

value: Bone

tag: cell line


title: Brain, 15 degrees, pesticides concentration 1, replicate 1

description: Library name: B15_1_1

value: 14 days exposure

tag: batch

value: 15 degrees

value: brain


title: Saos2

value: Osteosarcoma cell line


title: Hth83-CAP2

description:
Hth83_exp_count.txt
Hth83_exp_TPM.txt


title: NU-LN19

value: Class II


title: Sample_R21071403-ZW-23


title: Brain, 15 degrees, pesticides concentration 5, replicate 3

description: Library name: B15_5_3

value: brain tissue

value: pesticides concentration 5


title: Hth83-CAP1

description:
Hth83_exp_count.txt
Hth83_exp_TPM.txt


title: NU-LN18

value: kidney biopsy

value: Class III


title: Sample_R21071403-ZW-22


title: Hth83-Control3

description:
Hth83_exp_count.txt
Hth83_exp_TPM.txt

value: Head and neck cancer cells

value: No treatment


title: Brain, 15 degrees, pesticides concentration 5, replicate 1

description: Library name: B15_5_1


title: Sample_R21071403-ZW-21


title: Hth83-Control2

description:
Hth83_exp_count.txt
Hth83_exp_TPM.txt

value: WT


title: Sample_R21071403-ZW-20


title: NU-LN16


title: Brain, 15 degrees, pesticides concentration 5, replicate 2

description: Library name: B15_5_2


title: B16-F3-HPC-rep1

value: mouse melanoma cell line

value: High-pigmented


title: Hth83-Control1

description:
Hth83_exp_count.txt
Hth83_exp_TPM.txt


title: NU-LN17

value: Class IV


title: NU-LN15

value: Class V


title: Fadu-CAP3

description:
Fadu_exp_count.txt
Fadu_exp_TPM.txt

source_name: Fadu

value: Fadu

value: treated with Piezo-CAP for 24 hours at durations of  60 s


title: Brain, 15 degrees, no pesticides, replicate 2

description: Library name: B15_0_2

value: 14 days exposure

value: no pesticides

value: 15 degrees


title: NU-LN14


title: Sample_R21071403-ZW-18

source_name: intestine

value: intestine

value: 12 weeks

value: Zmpste24-/-; RIPK1D138N/D138N


title: Sample_R21071403-ZW-19

value: skin


title: Brain, 15 degrees, no pesticides, replicate 1

description: Library name: B15_0_1

value: brain tissue

value: brain


title: Brain, 12 degrees, pesticides concentration 5, replicate 6

description: Library name: B12_5_6

value: pesticides concentration 5

value: 12 degrees


title: Fadu-CAP2

description:
Fadu_exp_count.txt
Fadu_exp_TPM.txt

value: Head and neck cancer cells

value: WT


title: Sample_R21071403-ZW-17


title: NU-LN13

value: kidney biopsy


title: Brain, 12 degrees, pesticides concentration 5, replicate 5

description: Library name: B12_5_5


title: Fadu-CAP1

description:
Fadu_exp_count.txt
Fadu_exp_TPM.txt


title: Sample_R21071403-ZW-16


title: NU-LN12

value: Class IV


title: Brain, 12 degrees, pesticides concentration 5, replicate 4

description: Library name: B12_5_4


title: Fadu-Control3

description:
Fadu_exp_count.txt
Fadu_exp_TPM.txt

value: Fadu

value: No treatment


title: Brain, 12 degrees, no pesticides, replicate 6

description: Library name: B12_0_6

value: 14 days exposure


title: NU-LN11


title: Brain, 12 degrees, no pesticides, replicate 5

description: Library name: B12_0_5

value: no pesticides


title: Sample_R21071403-ZW-14


title: Fadu-Control1

description:
Fadu_exp_count.txt
Fadu_exp_TPM.txt


title: NU-LN10


title: Fadu-Control2

description:
Fadu_exp_count.txt
Fadu_exp_TPM.txt


title: Brain, 12 degrees, pesticides concentration 5, replicate 3

description: Library name: B12_5_3


title: NU-LN9

value: Class V


title: Brain, 12 degrees, pesticides concentration 5, replicate 2

description: Library name: B12_5_2


title: A375-CAP3

description:
A375_exp_count.txt
A375_exp_TPM.txt

value: treated with Piezo-CAP for 24 hours at durations of  60 s


title: Brain, 12 degrees, pesticides concentration 5, replicate 1

description: Library name: B12_5_1


title: Sample_R21071403-ZW-11

value: intestine

value: 12 weeks


title: Sample_R21071403-ZW-12


title: A375-CAP1

description:
A375_exp_count.txt
A375_exp_TPM.txt


title: NU-LN7

value: Class II


title: A375-CAP2

description:
A375_exp_count.txt
A375_exp_TPM.txt


title: NU-LN6


title: Sample_R21071403-ZW-10


title: A375-Control3

description:
A375_exp_count.txt
A375_exp_TPM.txt


title: Sample_R21071403-ZW-9

value: liver

value: Zmpste24-/-; RIPK1D138N/D138N


title: Sample_R21071403-ZW-15


title: NU-LN5

value: Class III


title: Brain, 12 degrees, no pesticides, replicate 3

description: Library name: B12_0_3

value: brain tissue

value: 12 degrees

value: brain


title: Sample_R21071403-ZW-8


title: A375-Control2

description:
A375_exp_count.txt
A375_exp_TPM.txt

value: Head and neck cancer cells

value: WT


title: NU-LN4

value: kidney biopsy

value: Class IV


title: Sample_R21071403-ZW-13


title: Brain, 12 degrees, no pesticides, replicate 2

description: Library name: B12_0_2

value: 14 days exposure


title: A375-Control1

description:
A375_exp_count.txt
A375_exp_TPM.txt

value: No treatment


title: NU-LN8

value: mixed


title: Brain, 12 degrees, no pesticides, replicate 1

description: Library name: B12_0_1

value: no pesticides


title: Cal27-CAP3

description:
Cal27_exp_count.txt
Cal27_exp_TPM.txt

value: treated with Piezo-CAP for 24 hours at durations of  60 s


title: NU-LN2


title: Sample_R21071403-ZW-6

value: 12 weeks


title: NU-LN3


title: RH_3

city: shenyang

first: Gao

middle: jun

last: ying

address: 120 Dongling Road

department: College of Animal Science and Veterinary Medicine

institute: Shenyang Agricultural University

description:
Library name: Sample6
RH_1

data_processing:
The DESeq2 R package (v. 1.20.0) was used for differential expression analysis of ΔTgNF7 and WT strains.
Assembly: Toxoplasma gondii type I strain GT1
Supplementary files format and content: gene_count

organism: Toxoplasma gondii

source_name: tachyzoite

growth_protocol: All Toxoplasma gondii used in this study were maintained in Vero cells cultured at 37 ℃ in 5% CO2 in complete Dulbecco’s Modified Eagle Medium supplemented with 8% heat-inactivated fetal bovine serum, 100 unit/mL penicillin, and 100 μg/mL streptomycin

extract_protocol:
RNA was harvested using Trizol reagent, and 1 ug of total RNA was used for the construction of sequencing libraries RNA libraries were prepared for sequencing using standard Illumina protocols
Alignment to the ToxoDB GT1 reference genome was performed using HISAT2 (v. 2.0.5).

value: tachyzoite

value: toxoplasma gondii RH

value: wild type

value: no


title: Sample_R21071403-ZW-5

value: liver


title: NU-LN1

value: Class V


title: Cal27-CAP2

description:
Cal27_exp_count.txt
Cal27_exp_TPM.txt


title: Brain, 12 degrees, no pesticides, replicate 4

description: Library name: B12_0_4

data_processing:
The reads were aligned to the reference transcriptome GCF_901001165.1_fSalTru1.1 (over 42’000 transcripts) and counted using the program kallisto (Bray et al., 2016).
We excluded one replicate due to a considerable difference in number of reads sequenced (18 million reads) compared to the other samples (27 to 37 million reads per sample). Before differential gene expression (DGE) analysis, we additionally filtered out outlier samples (based on clustering and principal component analyzes) and genes (very low, <20 raw counts in at least one sample and very high counts, >20’000 raw counts in at least one sample). The remaining data set contained 28 samples and 26’375 transcripts for the brain, and 27 samples and 14’413 transcripts for the liver.
The DGE analysis was performed with edgeR after Trimmed Mean of M-values normalization on the open source, web-based platform Galaxy version 20.09.rc1 (usegalaxy.org) (Jalili et al. 2021)
Assembly: GCF_901001165.1_fSalTru1.1
Supplementary files format and content: tab-delimited text files include raw counts for each experiment

extract_protocol:
Total RNA was isolated from whole brain and a piece of liver tissue using Qiagen’s RNeasy Plus Mini Kit (Hilden, Germany) following the manufacturer’s instructions. RNA concentration and purity were measured by spectrophotometry (Nanodrop ND-1000, Thermo Fisher Scientific, Waltham, MA, USA) and integrity was verified using the RNA 6000 Nano Chip on the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Ratios of 260/280 and 260/230 were above 2.0 and 2.1, respectively. Median RIN (RNA integrity number) values were 9.1 (brain) and 9.6 (liver). Samples were diluted with RNase-free water to 100 ng/mL (brain) and 125 ng/mL (liver), then treated with DNAse I (amplification grade, Invitrogen, Carlsbad, CA, USA).
RNA libraries were prepared from the DNAse I treated total RNA extracted from liver samples. One μg of total RNA was used for library preparation (TruSeq™ RNA Sample Prep Kit v2; Illumina, San Diego, USA) following the manufacturer’s instructions.

value: brain tissue

value: 12 degrees

value: brain


title: Sample_R21071403-ZW-4


title: RH_2

description:
Library name: Sample5
RH_1


title: Cal27-CAP1

description:
Cal27_exp_count.txt
Cal27_exp_TPM.txt

value: Head and neck cancer cells

value: WT


title: RH_1

description:
Library name: Sample4
RH_1


title: KO_3

description:
Library name: Sample3
KO_1

value: TgNF7 knockout


title: ChIP_Seq_CEBPB_ChIP_rep1

city: Hong Kong

first: Jian

last: Yan

state: Hong Kong Special Administrative Region

address: 83 Tat Chee Avenue, Kowloon

department: Department of Biomedical Sciences

institute: City University of Hong Kong

data_processing:
The raw ChIP-Seq data were quality-controlled using FastQC (v0.11.7) with default parameters.
ChIP-seq reads were aligned to human genome (hg19) using bowtie2 (v2.3.4) with default parameters and only the uniquely mapped reads were kept for the subsequent analyses.
Sam files were converted to bam files by using samtools (v1.9) with default parameters.
Binding peaks for each repeat were identified by using MACS2 software (v2.1.2) with default parameters.
Common peaks of two experiment repeats were identified by IDR software (v2.0.3) with default parameters.
Peaks were annotated by using bedtools (v2.25.0).
All peaks and reads distribution were visualized by using IGV software (v2.4.14).
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak files were generated by MACS2 (v2.1.2) which include the detail informations for all binding peaks;
Supplementary_files_format_and_content: the tab-delimited text file include common peaks results of two experiment repeats which generated by IDR software (v2.0.3).

source_name: NCM460 cell

growth_protocol: the NCM460 cells were cultured in DMEM (Dulbecco's Modified Eagle Medium; C11995500BT, Gibco) supplemented with 10% inactivated FBS (10270, Gibco) and antibiotics (penicillin and streptomycin, 10378016, Gibco) at 37 °C with 5% CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody (ab32358, Abcam).
Sequencing libraries were made following the protocol of NEB Next ChIP-Seq DNA Sample Prep Kit with minor modifications. To perform end repair of DNA fragments, 12 μL mixture (5µL NEB T4 DNA ligase buffer with 10mM ATP, 2µL dNTPs mix 10mM each, 2µL T4 DNA polymerase 3u/µL, 1µL Klenow DNA polymerase 5u/µL, 2µL T4 PNK 10u/µL) was added to 38 μL of IP DNA and input DNA (20 ng in 38 μL) and incubated for 30 min at 20 °C. The DNA was then purified using VAHTS® DNA Clean Beads (N411-01, Vazyme) and eluted in 41 μL H2O, following the manufacturer’s instructions. To prepare the DNA fragments for ligation to adapters by adding an “A” base to the 3' end, 9 μL mix (5µL NEB Buffer 2, 1µL dATP 100mM, 3µL Klenow 3'-5' exo minus 5u/µL) was added to 41 μL DNA from previous step and incubated for 30 min at 37 °C. After “A” base addition, the DNA was then purified using VAHTS® DNA Clean Beads (N411-01, Vazyme) and eluted in 42 μL H2O. To ligate adapters to DNA fragments, 8 µL reaction mixture (1µL adapter mix (1uM) (1000005282, MGI), 5µL NEB T4 DNA ligase buffer, 2µL NEB T4 DNA ligase) was added to 42 μL DNA from the previous step and incubated at 16 °C overnight. Size selection (200–500 bp) was achieved using a 1.5% agarose gel and NEB Monarch DNA Gel Extraction Kit (T1020S), and the DNA was eluted in 20 μL H2O. Finally, the libraries were amplified by 18 PCR cycles using Phusion High-Fidelity DNA Polymerases (M0530L, NEB) with the DNA from size selection and purified as size selection. The libraries were sequenced with an MGIseq2000 instrument (BGI, Shenzhen) using a paired-end scheme (PE100).

tag: chip antibody

value: CEBPB


title: ChIP_Seq_CEBPB_ChIP_rep2


title: Sample_R21071403-ZW-2


title: ChIP_Seq_input_rep2

value: input


title: KO_2

description:
Library name: Sample2
KO_1


title: Cal27-Control3

description:
Cal27_exp_count.txt
Cal27_exp_TPM.txt

value: No treatment


title: Sample_R21071403-ZW-1


title: Cal27-Control2

description:
Cal27_exp_count.txt
Cal27_exp_TPM.txt


title: Sample_R21071403-ZW-7

value: Zmpste24-/-; RIPK1D138N/D138N


title: ChIP_Seq_input_rep1


title: KO_1

description:
Library name: Sample1
KO_1


title: Liver, 3.33 µg EE2/g, rep10

status: Public on Dec 30 2025

city: Ste-Anne-de-Bellevue

first: Yeon-Seon

last: Jeon

state: Quebec

address: 21111 Lakeshore

department: Natural Resource Sciences

country: Canada

institute: McGill University

description:
ELS JQ FvsM_count table_lociID.txt
ELS JQ FvsM_count table_EntrezID.txt
T17

data_processing:
Processed using the Kallisto Module on EcoOmicsAnalyst.ca and manually formatted for ExpressAnalyst.ca
Assembly: Cortunix japonica 2.1 genome (GCA_001577835.2)
Supplementary files format and content: Count table in a tab-delimited text file format with loci IDs or Entrez IDs in rows and samples in columns

organism: Coturnix japonica

source_name: Left-lobe liver

growth_protocol: Incubation at 37°C and 60% humidity

extract_protocol:
Liver tissue was homogenized in buffer RLT using a TissueLyser II (Qiagen, Toronto, ON, CA), and RNA was extracted using the RNeasy® Mini QIAcube Kit (Qiagen) following the manufacturer’s protocol. An extra DNase I digestion step was included to eliminate genomic DNA contamination.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Aircell injection of 10 µl dosing solution prior to incubation

value: Left-lobe liver

tag: developmental stage

value: embryonic day 9

tag: Sex

value: Female

value: 3.33 µg EE2/g egg weight


title: Liver, 3.33 µg EE2/g, rep9

description:
ELS JQ FvsM_count table_lociID.txt
ELS JQ FvsM_count table_EntrezID.txt
T22


title: Cal27-Control1

description:
Cal27_exp_count.txt
Cal27_exp_TPM.txt


title: Liver, 3.33 µg EE2/g, rep8

description:
ELS JQ FvsM_count table_lociID.txt
ELS JQ FvsM_count table_EntrezID.txt
T18


title: Liver, 3.33 µg EE2/g, rep7

description:
ELS JQ FvsM_count table_lociID.txt
ELS JQ FvsM_count table_EntrezID.txt
T16


title: Liver, 3.33 µg EE2/g, rep4

description:
ELS JQ FvsM_count table_lociID.txt
ELS JQ FvsM_count table_EntrezID.txt
T07

value: Male


title: Liver, 3.33 µg EE2/g, rep5

description:
ELS JQ FvsM_count table_lociID.txt
ELS JQ FvsM_count table_EntrezID.txt
T08


title: Liver, 3.33 µg EE2/g, rep3

description:
ELS JQ FvsM_count table_lociID.txt
ELS JQ FvsM_count table_EntrezID.txt
T06


title: Liver, 3.33 µg EE2/g, rep6

description:
ELS JQ FvsM_count table_lociID.txt
ELS JQ FvsM_count table_EntrezID.txt
T13


title: Liver, solvent, rep10

description:
ELS JQ FvsM_count table_lociID.txt
ELS JQ FvsM_count table_EntrezID.txt
S23

value: DMSO (solvent)


title: Liver, 3.33 µg EE2/g, rep1

description:
ELS JQ FvsM_count table_lociID.txt
ELS JQ FvsM_count table_EntrezID.txt
T01


title: Liver, solvent, rep9

description:
ELS JQ FvsM_count table_lociID.txt
ELS JQ FvsM_count table_EntrezID.txt
S07


title: Sample_R21071403-ZW-3

value: liver

tag: age

value: 12 weeks


title: Liver, solvent, rep8

description:
ELS JQ FvsM_count table_lociID.txt
ELS JQ FvsM_count table_EntrezID.txt
S22


title: Liver, solvent, rep4

description:
ELS JQ FvsM_count table_lociID.txt
ELS JQ FvsM_count table_EntrezID.txt
S13


title: Liver, solvent, rep2

description:
ELS JQ FvsM_count table_lociID.txt
ELS JQ FvsM_count table_EntrezID.txt
S10


title: Liver, solvent, rep3

description:
ELS JQ FvsM_count table_lociID.txt
ELS JQ FvsM_count table_EntrezID.txt
S11


title: Liver, solvent, rep1

description:
ELS JQ FvsM_count table_lociID.txt
ELS JQ FvsM_count table_EntrezID.txt
S04


title: Rbfox2 cKO fiSC 1

first: Tom

last: Cheung

state: Please Select...

address: Clear Water Bay

country: Hong Kong

institute: HKUST

data_processing:
HISAT2 v2.1.0 was used to map the reads to the reference genome GRCm38, with parameter "--dta" to enable longer anchor length.
The alignment was then assembled by StringTie v1.3.6 with paramter "-e -B" to measure the gene abundance against the gene annotation of GENCODE vM22 .
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

source_name: skeletal muscle

extract_protocol:
RNA was extracted using NucleoSpin RNA XS kit (Macherey-Nagel). 10ng RNA of each sample was used for library construction
cDNA was generated following the SMART-Seq protocol. libraries were generated using the MGIEasy Library Prep Kit (MGI).

value: skeletal muscle

tag: cell type

value: muscle stem cell

value: Rbfox2 knockout

value: freshly isolated


title: BMSC cells, FBS_fed, rep2

city: Houston

first: Junfeng

last: Zhang

address: 2130 W. Holcombe Blvd

department: Department of Cancer Biology

institute: The University of Texas MD Anderson Cancer Center

description: Library name: FBS_fed_BMSC_rep2

data_processing:
Libraries were sequenced on an BGISEQ-500 platform. STAR 2.4.2a was used to align the RNA-seq reads to the reference human genome (hg38) and to count the number of reads mapping to each gene in the Ensembl GRCh38.p14 gene model. Differential expression analysis was performed using the DESeq2 665 package (v.1.10.0). Gene Ontology (GO) analysis was performed using the clusterProfiler R package (v3.0.0), GO terms with corrected p values < 0.05 were deemed significantly enriched. Gene set enrichment analysis was performed using GSEA (v.3.0) incorporating gene sets from MSigDB (v.5.0). Normalized enrichment scores (NES) and FDR/q values were used to explore enriched pathways in each phenotype. Data visualization and generating plots were performed in the R environment (v4.3.1) (https://www.r-project.org/).
Assembly: hg38
Supplementary files format and content: csv files includes raw counts for each sample

source_name: BMSC

growth_protocol: Cells were cultured in Low-Glucose Dulbecco's Modified Eagle's Medium (DMEM/F-12, basal medium; Gibco, USA) supplemented with 10% fetal bovine serum (Gibco) , NBIF or ABIF,  and 1% penicillin/streptomycin (Thermo Fisher Scientific). The cultures were maintained at 37°C with 5% CO2, with medium changes every other day until approximately 90% confluence was reached. Passages 1-3 of the BMSCs were used for in vitro experiments. All cell lines used in this study were confirmed Mycoplasma-negative using the Universal Mycoplasma Detection Kit (ATCC).

extract_protocol:
RNA was isolated from cells expanded under the indicated conditions using the FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme).
RNA sequencing on BMSC cells with indicate treatment was performed in the BGI Genomics.

value: BMSC

value: primary human bone marrow stromal cells


title: RNA-seq of zea mays: T48h Root 1-NR

city: Cold Spring Harbor

first: Sunita

last: Kumari

state: New York

address: One Bungtown Road

institute: Cold Spring Harbor Lab

description:
Library name: zma_T2d_root_r1
T48h Root 1-NR

data_processing:
Adapter trimming and quality filtering were performed using Trimmomatic. Filtered reads were aligned to the Zea mays B73 v5 reference genome using STAR. Transcript assembly and quantification were performed using StringTie. Gene-level count matrices were generated for downstream differential expression. Differential expression analysis was conducted using DESeq2.
Raw reads were trimmed and filtered using Trimmomatic. Clean reads were aligned to the Sorghum bicolor BTx623 v3.1.1 reference genome using STAR. Transcript assembly and abundance estimation were performed using StringTie. Gene-level counts were exported for statistical analysis. Differential expression was performed using DESeq2.
Assembly: reference genome (https://ftp.ebi.ac.uk/ensemblgenomes/pub/release-62/plants/gff3/zea_mays/)
Supplementary files format and content: Expression_TPM_Leaves-maize.csv
Supplementary files format and content: Expression_TPM_Roots-maize.csv

organism: Zea mays

source_name: root

growth_protocol: Maize seeds (Zea mays inbred line B73) were germinated on moist rag dolls and maintained under controlled growth chamber conditions. At 7 days after germination (DAG), seedlings were transferred to hydroponic tanks containing full-strength Hoagland nutrient solution. Plants were grown for 12 days under nitrate-sufficient conditions before treatment. Growth conditions were maintained at ~28°C with a 16-hour light / 8-hour dark photoperiod.

extract_protocol:
Root and leaf tissues were immediately frozen in liquid nitrogen at harvest. Total RNA was extracted using a standard plant RNA isolation protocol based on phenol-chloroform or silica-column purification. RNA quality was assessed using an Agilent Bioanalyzer, and samples with high RNA integrity (RIN > 7) were used for library preparation. Each biological replicate consisted of pooled tissue from five plants.
RNA-seq libraries were constructed using the NEBNext RNA-seq Library Prep Kit following the manufacturer’s guidelines. mRNA was enriched using poly(A) selection, fragmented, and converted to cDNA. Libraries were indexed, PCR-amplified, and quality-checked before sequencing. Sequencing was performed on the Illumina NextSeq 2000 platform.

treatment_protocol: At the 5th leaf stage (15 DAG), plants were transferred to a nitrate-limiting hydroponic solution in which Ca(NO₃)₂ and Mg(NO₃)₂ were replaced with CaCl₂ and MgSO₄. Root and leaf tissues were collected at the following time points under nitrate limitation: 0 min, 30 min, 3 hours, and 24 hours. After 24 hours of nitrate deprivation, nitrate was reintroduced to the nutrient solution. Recovery tissues were harvested at: 24h + 30 min and 24h + 48 h.

tag: genotype

value: nitrogen recovery

value: root

tag: replicate


title: RNA-seq of zea mays: T48h Root 3-NR

description:
Library name: zma_T2d_root_r3
T48h Root 3-NR

tag: time


title: Control fiSC 1

value: Control


title: ScRNA-seq of adjacent normal tissue

city: nanjing

first: Qingsong

address: xianlin

institute: Nanjing University of Chinese medicine

description:
Library name: Sample 2
DNBelab C

data_processing:
After sequencing using the DNBseq-T7 platform, the sequencing images were transformed into raw reads through the basecalling pipeline within BGI. Subsequently, strict quality control was carried out on the original sequencing data to remove low-quality reads and linker sequence contamination.
Assembly: homo sapiens
Supplementary files format and content: matrix files

source_name: normal

extract_protocol:
The cDNA library was prepared using the BGI MGIEasy RNA Library Preparation Kit (940-001820-00), including terminal repair, linker ligation, PCR amplification, fragment screening and purification.
DNA fragments are first subjected to Rolling Circle Amplification (RCA) to form DNA Nanoballs (DNBs). Subsequently, DNBs were loaded onto the chip and Paired-End sequencing was performed using the Combinatorial Probe-Anchor Synthesis (cPAS) technique.

value: normal


title: Liver, solvent, rep6

description:
ELS JQ FvsM_count table_lociID.txt
ELS JQ FvsM_count table_EntrezID.txt
S16

value: Left-lobe liver

value: embryonic day 9


title: BMSC cells, NBIF_fed, rep1

description: Library name: NBIF_fed_BMSC_rep1


title: BMSC cells, NBIF_fed, rep2

description: Library name: NBIF_fed_BMSC_rep2


title: BMSC cells, FBS_fed, rep1

description: Library name: FBS_fed_BMSC_rep1


title: Liver, solvent, rep5

description:
ELS JQ FvsM_count table_lociID.txt
ELS JQ FvsM_count table_EntrezID.txt
S14

value: Female


title: BMSC cells, NBIF_fed, rep3

description: Library name: NBIF_fed_BMSC_rep3


title: Control fiSC 2


title: Liver, solvent, rep7

description:
ELS JQ FvsM_count table_lociID.txt
ELS JQ FvsM_count table_EntrezID.txt
S20

value: Male


title: RNA-seq of zea mays: T24.5h Root 3-NR

description:
Library name: zma_T1d30min_root_r3
T24.5h Root 3-NR


title: RNA-seq of zea mays: T48h Root 2-NR

description:
Library name: zma_T2d_root_r2
T48h Root 2-NR


title: Rbfox2 cKO fiSC 2


title: BMSC cells, FBS_fed, rep3

description: Library name: FBS_fed_BMSC_rep3


title: Liver, 3.33 µg EE2/g, rep2

description:
ELS JQ FvsM_count table_lociID.txt
ELS JQ FvsM_count table_EntrezID.txt
T03

value: 3.33 µg EE2/g egg weight


title: ScRNA-seq of breast carcinosarcoma

description:
Library name: Sample 1
DNBelab C

source_name: tumor

value: tumor


title: RNA-seq of zea mays: T24.5h Root 1-NR

description:
Library name: zma_T1d30min_root_r1
T24.5h Root 1-NR


title: RNA-seq of zea mays: T24h Root 3-ND

description:
Library name: zma_T1d_root_r3
T24h Root 3-ND

value: nitrogen deprivation


title: RNA-seq of zea mays: T24.5h Root 2-NR

description:
Library name: zma_T1d30min_root_r2
T24.5h Root 2-NR


title: RNA-seq of zea mays: T24h Root 2-ND

description:
Library name: zma_T1d_root_r2
T24h Root 2-ND


title: RNA-seq of zea mays: T24h Root 1-ND

description:
Library name: zma_T1d_root_r1
T24h Root 1-ND


title: RNA-seq of zea mays: T3h Root 1-ND

description:
Library name: zma_T3h_root_r1
T3h Root 1-ND


title: RNA-seq of zea mays: T3h Root 2-ND

description:
Library name: zma_T3h_root_r2
T3h Root 2-ND


title: RNA-seq of zea mays: T3h Root 3-ND

description:
Library name: zma_T3h_root_r3
T3h Root 3-ND


title: RNA-seq of zea mays: T0.5h Root 1-ND

description:
Library name: zma_T30min_root_r1
T0.5h Root 1-ND


title: RNA-seq of zea mays: T0.5h Root 3-ND

description:
Library name: zma_T30min_root_r3
T0.5h Root 3-ND


title: RNA-seq of zea mays: T0h Root 1-NN

description:
Library name: zma_T0_root_r1
T0h Root 1-NN

value: normal nitrogen


title: RNA-seq of zea mays: T48h Leaves 3-NR

description:
Library name: zma_T2d_leaves_r3
T48h Leaves 3-NR

source_name: leaves

value: leaves


title: RNA-seq of zea mays: T0.5h Root 2-ND

description:
Library name: zma_T30min_root_r2
T0.5h Root 2-ND


title: RNA-seq of zea mays: T0h Root 3-NN

description:
Library name: zma_T0_root_r3
T0h Root 3-NN


title: RNA-seq of zea mays: T24.5h Leaves 2-NR

description:
Library name: zma_T1d30min_leaves_r2
T24.5h Leaves 2-NR


title: RNA-seq of zea mays: T24.5h Leaves 1-NR

description:
Library name: zma_T1d30min_leaves_r1
T24.5h Leaves 1-NR

value: nitrogen recovery (NR)


title: RNA-seq of zea mays: T0h Root 2-NN

description:
Library name: zma_T0_root_r2
T0h Root 2-NN


title: RNA-seq of zea mays: T48h Leaves 1-NR

description:
Library name: zma_T2d_leaves_r1
T48h Leaves 1-NR


title: RNA-seq of zea mays: T24h Leaves 2-ND

description:
Library name: zma_T1d_leaves_r2
T24h Leaves 2-ND


title: RNA-seq of zea mays: T24.5h Leaves 3-NR

description:
Library name: zma_T1d30min_leaves_r3
T24.5h Leaves 3-NR


title: RNA-seq of zea mays: T24h Leaves 1-ND

description:
Library name: zma_T1d_leaves_r1
T24h Leaves 1-ND


title: RNA-seq of zea mays: T3h Leaves 3-ND

description:
Library name: zma_T3h_leaves_r3
T3h Leaves 3-ND


title: RNA-seq of zea mays: T3h Leaves 1-ND

description:
Library name: zma_T3h_leaves_r1
T3h Leaves 1-ND


title: RNA-seq of zea mays: T0.5h Leaves 3-ND

description:
Library name: zma_T30min_leaves_r3
T0.5h Leaves 3-ND


title: O2

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

description: Gene expression data from normal distal colon mucosa within aged adults

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16 hr at 45℃ on Clariom D Array(human, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Genechips were scanned by GeneChip® Scanner 3000.

data_processing: The data were analyzed with Expression Console™, Version 1.3.1.

source_name: old adult aged 72 years

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-8 ug total RNA

growth_protocol: Normal clinical colon mucosa tissue samples from different colorectal cancer patients were collected immediately after surgical resection prior to any other therapeutic intervention

extract_protocol: Total RNA was extracted from tissues using Trizol reagent (Life Technologies, Carlsbad, CA, USA) and purified with a RNeasy mini kit (Qiagen, Valencia, CA, USA).

treatment_protocol: All tissue samples were stored at -80 °C.

tag: gender

value: female

value: distal colon mucosa


title: O5

source_name: old adult aged 81 years

value: male


title: Y1

description: Gene expression data from normal distal colon mucosa within young adults

source_name: young adult aged 27 years


title: RNA-seq of zea mays: T3h Leaves 2-ND

description:
Library name: zma_T3h_leaves_r2
T3h Leaves 2-ND


title: RNA-seq of zea mays: T0.5h Leaves 2-ND

description:
Library name: zma_T30min_leaves_r2
T0.5h Leaves 2-ND


title: RNA-seq of zea mays: T0.5h Leaves 1-ND

description:
Library name: zma_T30min_leaves_r1
T0.5h Leaves 1-ND

value: nitrogen deprivation (ND)