title: brainstem, low workload, ZT21, rep1

description:
BRS_L_ZT21_X21
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: mp42_CD4_nDP_2

status: Public on Feb 14 2024

type: SRA

city: Moscow

first: Ekaterina

last: Serebrovskaya

address: Ostrovityanova st., 1

country: Russia

institute: Russian National Research Medical University

library_source: transcriptomic

data_processing:
Sequencing reads were processed with MiXCR software (MiLaboratories) in order to extract TCRβ CDR3 clonotypes. MiXCR aligns reads to human V, D and J TCR gene segments.
VDJtools software was used for processing of MiXCR output TCR repertoire data, calculation of TCR repertoire diversity, and pre-processing of TCR repertoires (i.e., pooling of joined TCR repertoires and down-sampling of TCR repertoires)
Supplementary_files_format_and_content: Tab delimeted text files include the TCR clonotype tables in VDJtools output format

molecule: total RNA

organism: Homo sapiens

source_name: CD39 PD-1 not-double-positive (not-DP) CD4+ melanoma TILs

growth_protocol: TILs were expanded from the separate tumor fragments in different cultivation conditions. For patient mp26 conditions were - IL2(300IU/ml); IL2(200 IU/ml)+IL21(25ng/ml); Nivolumab(20 μg/mL)+IL2+IL21; Nivolumab+IL2+IL21+IFNγ(100 μg/ml). For patients mp34 and mp41 conditions were: IL2(300IU/ml); IL2(200 IU/ml; IL2(200 IU/ml)+IL21(25ng/ml); Nivolumab(20 μg/mL)+IL2+IL21).

extract_protocol:
RNA from fresh-frozen tumor fragments was isolated using TRIzol reagent(Invitrogen). RNA from RLT-lysed cells was extracted using the RNeasy mini kit (Qiagen) according to the manufacturer's protocol. RNA concentration was measured with the Qubit RNA HS Assay Kit (Thermo Fisher Scientific, US). No more than 500 ng of total RNA was used for cDNA synthesis.
cDNA libraries were generated using the Human RNA TCR Multiplex kit (MiLaboratories), according to the manufacturer's protocol.
other: targeted RNA-seq (TCR amplicon seq)

treatment_protocol: CD39+PD-1+ (double-positive, DP) and non-DP CD4+ and CD8+ T cells from TILs freshly isolated from lymph node metastases from 8 melanoma patients.

tag: subset

value: CD4+ CD39 PD-1 not-DP

tag: patient

value: melanoma patient 42

tag: tcr chain

value: TCR beta


title: mp24_CD8_DP_1

source_name: CD39+ PD-1+ CD8+ melanoma TILs

value: melanoma patient 24


title: mp42_CD4_DP_2

source_name: CD39+ PD-1+ CD4+ melanoma TILs


title: brainstem, low workload, ZT17, rep2

city: La Jolla

first: Laura

last: van Rosmalen

state: California

address: 10010 N Torrey Pines Rd

department: RBIO-P

country: USA

institute: Salk Institute for Biological Studies

description:
BRS_L_ZT17_X25
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

data_processing:
Sequencing quality was assessed using FastQC, version 0.11.9
Cutadapt v4.1 was used to trim adapter sequences
Sequence reads were aligned to the Mus musculus (house mouse) genome GRCm38 (mm10) and counted per gene using STAR aligner v2.7.10a
Gene counts were filtered for low counts and normalized per tissue using DESeq2 v1.34.0
TES_L_ZT21_X27 was removed from the analysis because it was an extreme outlier
Assembly: mm10
Supplementary files format and content: csv file includes raw counts for each sample
Supplementary files format and content: csv file includes normalized counts for each sample

organism: Mus musculus

source_name: brainstem

extract_protocol:
Total RNA was extracted from neural and peripheral tissues using TRIzol reagent according to the manufacturer’s instructions. 300ng of total RNA was used for the construction of sequencing libraries
Libraries were prepared using Illumina’s TruSeq Stranded mRNA (PolyA+) kit according to the manufacturer’s instructions

tag: tissue

value: brainstem

tag: strain

value: CBA/CaJ

tag: Sex

value: male

tag: treatment

value: low workload

tag: zeitgeber time


title: CFP_Fucci G1 ISCs batch 1

city: Canterbury

first: Jerome

last: Korzelius

state: Kent

address: Ingram Building, University of Kent

country: United Kingdom

institute: University of Kent

data_processing:
Reads mapped to Drosophila genome using HISAT2 in the Galaxy user suite
Mapped reads were counted using the HTSeq count package in the Galaxy user suite
Differential expression analysis was done using DeSeq2 in the Galaxy user suite
Assembly: BDGP6

organism: Drosophila melanogaster

source_name: Intestine

growth_protocol: 3-5 day old adult female Drosophila were shifted from 25C to 29C for 2 days to induce expression of FlyFucci.

extract_protocol:
Total RNA was isolated using the Arcturus PicoPure kit. From this, we amplified mRNA using the Riboamp HS kit (ThermoFisher)
Libraries were generated using the TruSeq Stranded mRNA Library Prep Kit (Illumina) without the mRNA enrichment steps
50 bp single-end RNA-Seq

treatment_protocol: Guts were dissociated using Elastase as described previously. CFP and CFP+YFP cells were sorted using the FACSAria II system

value: Intestine

tag: cell type

value: ISC

tag: genotype

value: w; esg-Gal4, P{UAS-CFP.E2f.1-230}4 P{UAS-Venus.CycB.1-266}7;P{His2AV-mRFP1}/tub-Gal80ts, Su(H)-Gal80

value: 5-7 day old female adults shifted to 29C for 2 days to induce expression


title: T24ISOb_S35

city: New York

first: Hong

last: Sun

state: NY

address: 341 East 25 Street

department: Medicine

institute: NYU School of Medicine

data_processing:
Raw sequence data (Fastq) were loaded into Biomedical Genomics Workbench Version 3.5.3 (Qiagen) for data analysis.
The raw Fastq files were trimmed to remove any remaining adaptors and ambiguous nucleotides.
The trimmed sequence files were aligned to human genome (Hg38) allowing two mismatches.
Reads mapped to the exons of a gene were summed at the gene level. Gene expression levels were quantified as total read per million (TPM).
Differential gene expression was analyzed using Advance RNA-seq plug-in tool (Qiagen) by comparing each treated group versus corresponding control group. TMM (trimmed mean of M values) normalization was performed to adjust library sizes before differential expression analysis.
Assembly: Hg38
Supplementary files format and content: tab-delimited text files includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files includes RPKM values for each Sample

growth_protocol: T24 bladder cancer cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum and antibiotics in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
RNA was harvested using the TRI-zol reagent (Life Technologies, Gaithersburg, MD)
RNA-Seq libraries were prepared using Illumina TruSeq RNA-sample preparation kit according to the manufacture’s instruction

treatment_protocol: Cells were treated with or without 20 μM ISO

tag: cell line

value: Urinary bladder epithelial

value: 20 μM Isorhapontigenin for 24 h


title: mp42_CD4_nDP_1


title: brainstem, low workload, ZT17, rep1

description:
BRS_L_ZT17_X19
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: T24ISOa_S34


title: brainstem, low workload, ZT13, rep1

description:
BRS_L_ZT13_X11
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: brainstem, low workload, ZT13, rep2

description:
BRS_L_ZT13_X5
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: T24b_S33

value: Untreated


title: mp41_CD4_nDP_2

value: melanoma patient 41


title: SPC-A-1 cells, sh_NCAPD3_3

city: Fuzhou

first: Xiangqi

last: Chen

address: NO.29 of Xinquan Road, Gulou District

country: China

institute: Fujian Medical University Union Hospital

data_processing:
Trimmomatic (version 0.36)
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed. clean data were mapped to the reference genome of human using STRA software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated. Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1). A p-value cutoff of 0.05 and fold-change cutoff of 2 were used to judge the statistical significance of gene expression differences.
Gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis for differentially expressed genes were both implemented by KOBAS software (version: 2.1.1) with a pvalue cutoff of 0.05 to judge statistically significant enrichment.
Alternative splicing events were detected by using rMATS (version 3.2.5) with a FDR value cutoff of 0.05 and an absolute value of Δψ of 0.05.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
RNA was extracted using TRIzol Reagent (Invitrogen).2 μg total RNAs were used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KCTM Stranded mRNA Library Prep Kit following manufacture's protocols.

value: Human lung adenocarcinoma cellS

value: NCAPD3 Knockdown


title: mp41_CD4_nDP_1

value: CD4+ CD39 PD-1 not-DP


title: SPC-A-1 cells, sh_NCAPD3_2


title: brainstem, low workload, ZT09, rep2

description:
BRS_L_ZT09_X29
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: mp41_CD4_DP_1

value: TCR beta


title: brainstem, low workload, ZT05, rep2

description:
BRS_L_ZT05_X26
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: mp41_CD4_DP_2


title: mp44_CD4_DP_1

value: melanoma patient 44


title: brainstem, low workload, ZT05, rep1

description:
BRS_L_ZT05_X12
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: brainstem


title: SPC-A-1 cells, sh_NC_3

value: WT


title: mp39_CD4_nDP_1

value: melanoma patient 39


title: SPC-A-1 cells, sh_NCAPD3_1


title: mp42_CD4_DP_1

value: melanoma patient 42


title: SPC-A-1 cells, sh_NC_1


title: mp39_CD4_DP_2


title: brainstem, low workload, ZT01, rep1

description:
BRS_L_ZT01_X10
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: CBA/CaJ

value: male

value: low workload


title: brown adipose tissue, high workload, ZT21, rep2

description:
BAT_H_ZT21_X28
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

source_name: brown adipose tissue

value: brown adipose tissue

value: high workload


title: T56-Treg

city: Dijon

first: Romain

last: Boidot

address: 1, rue Pr Marion

country: France

institute: CGFL

data_processing:
Raw FASTQ files were trimmed for residual adapter sequences and quality filtered through Trimmomatic software.
Reads were pseudo-aligned against hg19 genome through Kallisto software.
Differential expression analysis was performed using DEseq-2 R script and SARTools package in R environment (Galaxyeast, Galaxy instance).
Genome_build: hg19

source_name: Treg

growth_protocol: Frozen PBMC samples were thawed at 37°C in culture medium (RPMI 1640 medium, 10% FBS, 1% PSA) and dead and dying cells were removal with magnetic depletion (Dead Cell Removal Kit). PBMC were stained with Fixable Viability Stain 780 and sorted by FACS according to the following phenotype: FVS780- CD3+ CD4+ CD25hi CD127-. Cells were directly recovered into 50 μL of lysis buffer (RLT Buffer, Qiagen) and stored at -80°C.

extract_protocol:
Total RNA was extracted from cell pellet using the Maxwell RSC RNA FFPE kit (Promega) according to the manufacturer’s protocol without the step at 80°C.
500 ng of total RNA were ribodepleted and used for library construction. Libraries were prepared thanks to NEBNext Ultra II Directional RNA Prep kit for Illumina according to manufacturer's instructions.

treatment_protocol: unstimulated cells

tag: disease state

value: healthy donor sample

value: Treg


title: GEM-Bx-6584_S25

first: Yajas

last: Shah

address: 1300 York Ave

institute: Weill Cornell Medicine

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore
Trimmed sequence reads were mapped to GRCh38 using best practices associated with STAR
Read count extraction was performed by htseq-count and relative abundance was estimated using Cufflinks
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: kidney

extract_protocol:
RNA was harvested using miRNeasy mini kit (Qiagen)
RNA libraries for RNA-seq were prepared using TruSeq Library Prep Kit (Illumina) following manufacturer's protocols.

value: kidney

value: kidney allograft

value: TCMR


title: T24a_S32

value: Urinary bladder epithelial

value: Untreated


title: brown adipose tissue, high workload, ZT21, rep1

description:
BAT_H_ZT21_X18
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: GEM-Bx-6549_S23


title: mp39_CD4_DP_1

value: TCR beta


title: T54-Treg


title: brainstem, low workload, ZT01, rep2

description:
BRS_L_ZT01_X20
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: brainstem


title: brown adipose tissue, high workload, ZT17, rep2

description:
BAT_H_ZT17_X24
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: GEM-Bx-6264_S22


title: brainstem, low workload, ZT09, rep1

description:
BRS_L_ZT09_X23
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: brown adipose tissue, high workload, ZT17, rep1

description:
BAT_H_ZT17_X16
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: T52-Treg


title: mp39_CD4_nDP_2

value: CD4+ CD39 PD-1 not-DP


title: GEM-Bx-6174_A1_S20


title: T01-Treg


title: AH37-Treg

value: wAIHA patient sample


title: brown adipose tissue, high workload, ZT13, rep2

description:
BAT_H_ZT13_X8
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: brown adipose tissue, high workload, ZT13, rep1

description:
BAT_H_ZT13_X2
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: brown adipose tissue, high workload, ZT09, rep2

description:
BAT_H_ZT09_X9
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: AH23-Treg


title: brown adipose tissue, high workload, ZT09, rep1

description:
BAT_H_ZT09_X15
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: GEM-Bx-334_S2


title: GEM-Bx-2314_S10


title: AH11-Treg


title: GEM-Bx-2934_S13


title: brown adipose tissue, high workload, ZT05, rep2

description:
BAT_H_ZT05_X3
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: SPC-A-1 cells, sh_NC_2

value: Human lung adenocarcinoma cellS

value: WT


title: GEM-Bx-220_S1

value: aABMR


title: AH10-Treg


title: brown adipose tissue, high workload, ZT05, rep1

description:
BAT_H_ZT05_X13
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: CBA/CaJ

value: male


title: brown adipose tissue, high workload, ZT01, rep2

description:
BAT_H_ZT01_X7
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: brown adipose tissue

value: high workload


title: mTEC, ATAC, Tspan8neg, MHCIIhigh, bio repl 2

city: Marburg

first: Kristin

last: Rattay

address: Karl-von-Frisch-Strasse 2

country: Germany

institute: University of Marburg

library_source: genomic

data_processing:
Raw reads were assessed for quality using FastQC.
ATAC reads were aligned to the mm10 genome using Bowtie2.
Mitochondrial reads, multimapping reads, low-quality reads and non-unique alignments were removed using SAMtools.
Peak-calling was performed using MACS2. Consensus peaks were generated by merging called MACS2 peaks using bedtools merge.
peak regions were annotated using HOMER to identify the nearest genes and genomic features.
Counts of reads mapped to consensus peaks were generated using featureCounts with default settings.
Assembly: mm10
Supplementary files format and content: count matrix
Supplementary files format and content: bw

molecule: genomic DNA

source_name: thymus

extract_protocol:
Genomic DNA was extracted from FACS-isolated mTECs, being Tspan8pos or Tspan8neg and MHCIIlow or MHCIIhigh according to the published method in J. D. Buenrostro, et al., Nat Methods 10, 1213-1218 (2013).
Library preparation was performed according to the published method in J. D. Buenrostro, et al., Nat Methods 10, 1213-1218 (2013).

value: thymus

value: mTEC

value: wt


title: 9_ACTTGA

value: kidney

value: kidney allograft

value: TCMR


title: mTEC, ATAC, Tspan8pos, MHCIIhigh, bio repl 2


title: brown adipose tissue, high workload, ZT01, rep1

description:
BAT_H_ZT01_X1
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: mTEC, ATAC, Tspan8pos, MHCIIlow, bio repl 2


title: 8A_S9

value: No Rejection


title: AH31-Treg

value: Treg


title: brown adipose tissue, low workload, ZT21, rep2

description:
BAT_L_ZT21_X27
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: low workload


title: mTEC, ATAC, Tspan8neg, MHCIIlow, bio repl 2


title: 7_ATCACG


title: brown adipose tissue, low workload, ZT21, rep1

description:
BAT_L_ZT21_X21
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: GEM-Bx-2491_S11


title: brown adipose tissue, low workload, ZT17, rep2

description:
BAT_L_ZT17_X25
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: brown adipose tissue, low workload, ZT17, rep1

description:
BAT_L_ZT17_X19
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: 52_GGCTAC


title: 7A_S22


title: mTEC, ATAC, Tspan8pos, MHCIIlow, bio repl 1


title: brown adipose tissue, low workload, ZT13, rep2

description:
BAT_L_ZT13_X5
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: mTEC, ATAC, Tspan8neg, MHCIIlow, bio repl 1


title: 51_TAGCTT


title: brown adipose tissue, low workload, ZT13, rep1

description:
BAT_L_ZT13_X11
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: 4A_S27


title: brown adipose tissue, low workload, ZT09, rep2

description:
BAT_L_ZT09_X29
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: 9A_S18


title: 50_GATCAG


title: brown adipose tissue, low workload, ZT09, rep1

description:
BAT_L_ZT09_X23
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: mTEC, Tspan8pos, MHCIIlow, bio repl 1

data_processing:
ERCC spike-ins were used for estimation of technical noise levels and for calling of significantly highly variable genes.
Raw reads were assessed for quality using FastQC.
Reads were aligned to the mouse reference transcriptome (Gencode vM10) using Salmon (v1.8.0).
Data normalization and differential gene expression analysis was performed using DESeq2 (v1.30.0) in R.
Assembly: mm10
Supplementary files format and content: raw count matrix table

extract_protocol:
Total RNA was extracted from FACS-isolated mTECs, being Tspan8pos or Tspan8neg and MHCIIlow or MHCIIhigh.
Library preparation was performed using TruSeq stranded mRNA kit (Illumina) following the manufacturers` protocol.

value: medullary thymic epithelial cells (mTEC)

tag: cell subtype

value: MHCII low


title: 49_ACTTGA


title: 8_TTAGGC


title: mTEC, ATAC, Tspan8pos, MHCIIhigh, bio repl 1


title: mp39_CD8_nDP_2

source_name: CD39 PD-1 not-double-positive (not-DP) CD8+ melanoma TILs

value: CD8+ CD39 PD-1 not-DP

value: melanoma patient 39

value: TCR beta


title: mp39_CD8_nDP_1


title: 48_TTAGGC


title: mTEC, Tspan8pos, MHCIIhigh, bio repl 1

value: MHCII high


title: brown adipose tissue, low workload, ZT05, rep1

description:
BAT_L_ZT05_X12
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: brown adipose tissue

value: CBA/CaJ

value: male


title: brown adipose tissue, low workload, ZT05, rep2

description:
BAT_L_ZT05_X26
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: mp39_CD8_DP_2


title: mTEC, Tspan8neg, MHCIIlow, bio repl 2

value: thymus


title: mTEC, ATAC, Tspan8neg, MHCIIhigh, bio repl 1

value: mTEC

value: wt


title: brown adipose tissue, low workload, ZT01, rep2

description:
BAT_L_ZT01_X20
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: brown adipose tissue, low workload, ZT01, rep1

description:
BAT_L_ZT01_X10
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: 46A_S35

value: kidney

value: kidney allograft

value: caABMR


title: mTEC, Tspan8neg, MHCIIlow, bio repl 1


title: mTEC, Tspan8pos, MHCIIlow, bio repl 2


title: 45A_S25


title: mp36_CD4_nDP_2

value: CD4+ CD39 PD-1 not-DP

value: melanoma patient 36


title: mTEC, Tspan8neg, MHCIIhigh, bio repl 2

value: medullary thymic epithelial cells (mTEC)


title: mp39_CD8_DP_1


title: arcuate nucleus, high workload, ZT21, rep2

description:
ARC_H_ZT21_X28
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

source_name: arcuate nucleus

value: arcuate nucleus

value: high workload


title: 44A_S2


title: mp36_CD4_nDP_1


title: mTEC, Tspan8pos, MHCIIhigh, bio repl 2


title: arcuate nucleus, high workload, ZT21, rep1

description:
ARC_H_ZT21_X18
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: 43A_S12


title: mp36_CD4_DP_2


title: arcuate nucleus, high workload, ZT17, rep2

description:
ARC_H_ZT17_X24
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: mTEC, Tspan8neg, MHCIIhigh, bio repl 1


title: 42A_S13

value: TCMR


title: mp36_CD4_DP_1

value: TCR beta


title: N1E115_4%O2_HIF1A_replicate2

city: Rochester

first: Tamas

last: Ordog

state: MN

address: 200 1st St SW

institute: Mayo Clinic

data_processing:
Data were analyzed by the HiChIP pipeline developed by the Mayo Clinic Bioinformatics Core (PMCID: PMC4152589)
ChIP-seq reads were aligned to the mm10 genome assembly using BWA
Paired-end reads were aligned by BWA against the mm10 genome build. Duplicate reads were filtered out with Picard. Peak calling was performed with MACS2.
Genome_build: mm10
Supplementary_files_format_and_content: Peak file is in bed format with column headers chr, peak_start, peak_end, peakname, pileup, peakCall, fold-change, -10logpvalue, -10logqvalue, peak_summit_position

source_name: NOS1+ N1E115 mouse neuroblastoma cells

growth_protocol: NOS1+ N1E115 mouse neuroblastoma cells were cultured at high (20%) and low (4%) oxygen levels in the presence of 5% CO2 at ambient barometric pressure for 3 days.

extract_protocol:
Chromatin immunoprecipitation was performed on fixed and fragmented DNA isolated from N1E115 cells using anti-HIF1A and ARNT antibodies.
ThruPLEX DNA-seq Kit (Takara Bio USA)

value: brain

value: neuroblastoma


title: 47A_S44


title: mp24_CD4_nDP_2

value: melanoma patient 24


title: 41_CGATGT


title: N1E115_4%O2_input5

treatment_protocol: NOS1+ N1E115 mouse neuroblastoma cells were cultured at high (20%) and low (4%) oxygen levels in the presence of 5% CO2 at ambient barometric pressure for 3 days.


title: arcuate nucleus, high workload, ZT13, rep2

description:
ARC_H_ZT13_X2
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: CBA/CaJ

value: male


title: 40A_S43


title: mp24_CD4_nDP_1


title: 3A_S17

value: No Rejection


title: N1E115_4%O2_HIF1A_replicate1


title: N1E115_4%O2_ARNT_replicate1


title: mp24_CD4_DP


title: arcuate nucleus, high workload, ZT13, rep1

description:
ARC_H_ZT13_X8
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: N1E115_4%O2_input4


title: arcuate nucleus, high workload, ZT09, rep2

description:
ARC_H_ZT09_X9
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: 39_TAGCTT


title: Hatchling 3

type: RNA

city: Hayes

first: Alexandrea

middle: (Lexi)

last: Duscher

state: VA

address: 1730 Sawgrass Pointe Dr

institute: University of Florida

hyb_protocol: Performed by NanoString Technologies

scan_protocol: Perfomed by NanonString Technologies. Used the nCounter Analysis System and nCounter SPRINT Profiler.

data_processing: Data were filtered and normalized using nSolver analysis software (v4.0; NanoString Technologies). Background subtraction was performed using the geometric mean of the negative controls and data was normalized using the geometric mean of positive controls and housekeeping genes (actB3 and pyc1). Voom transformation from the limma package (v3.8) in R was applied to the normalized counts. This transformation used the empirical Bayes method by pooling estimates of sample variance to assess the expression level variance within samples and transform data into log2-counts per million (CPM). This method has been shown to be more useful for smaller sample size studies, such as with NanoString assays (Ritchie et al., 2015; Van Laar, Lincoln, & Van Laar, 2018). The voom transformed data were passed to a linear model in the limma package to remove the mean-variance relationship and assess statistically significant differentially expressed genes (Ritchie et al., 2015).

label: biotin

organism: Euprymna scolopes

source_name: Light organ tissue

label_protocol: Performed by NanoString Technologies. Optimal fluorescently tagged probes of 100 bp length were designed and synthesized at NanoString Technologies, Inc. in Seattle, WA for the selected genes to ensure no off-target binding. Probes were designed to hit whole genes and not specific isoforms. There were a total of 33 target genes and two housekeeping genes designed and successfully assayed by NanoString gene expression technology. During hybridization, the specific Reporter Tags and universal Capture Tag hybridize to a pair of target-specific oligonucleotide probes, which in turn hybridize directly to the single-stranded RNA or DNA target (FIGURE 1.2). Probe A hybridizes to a specific Reporter Tag and the 5’ region of the target nucleic acid sequence. Probe B hybridizes to the universal Capture Tag and the 3’ region of the target nucleic acid sequence. Each complete structure—containing the target RNA or DNA, two oligonucleotide probes, and the Reporter and Capture Tags—is referred to as a Tag Complex

growth_protocol: Mature E. scolopes squid were maintained in aquaria within an environmental growth chamber at 23°C on a 12 h light/dark cycle. Clutches of eggs were removed from the adult tanks and incubated separately in individual aquaria for their full developmental cycle (~ 21 days). After hatching, the juvenile squid were maintained in filtered-sterilized seawater (FSW) as either aposymbiotic (i.e., no symbiosis-competent V. fischeri) or rendered symbiotic. For symbiotic treatments, animals were inoculated with 1 × 105 cells of V. fischeri ES114 per ml of FSW. The concentration of V. fischeri was determined spectrophotometrically (A600nm) as an OD of 1 corresponds to 4 × 108 cells per ml of culture, as previously determined by plate counts (Boettcher & Ruby, 1990). In all treatments, the onset of symbiosis was monitored by luminescence levels using an ATP photometer (GloMax 20/20 Luminometer, Promega, Corps., Madison, WI).

extract_protocol: Total RNA was extracted in triplicate from dissected light organs using RNeasy and Qiashredder kits according to the manufacturer’s protocol (Qiagen, Germantown, MD). A minimum of three light organs was used for each replicate RNA extraction. RNA was pooled from a minimum of three separate extractions derived from three different technical replicates of HARV exposure to increase overall genetic variability and to ensure that gene expression results were not based on variability between egg clutches.   RNA quantity was assessed using Qubit 2.0 (Thermo Fisher Scientific, Waltham, MA) and RNA quality was assessed with a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). All samples were normalized to 20 ng per µl of RNA and 100 ng of RNA was run for each sample on the NanoString nCounter MAX system (NanoString Technologies, Seattle, WA).

treatment_protocol: To simulate the LSMMG conditions, a rotary culture system was used with 16 replicate 50-mL volume high-aspect ratio vessels (HARVs; Synthecon, Houston, TX) and rotated at a constant 13 rpm (Figure 1d). The HARVs were either rotated around a horizontal axis to simulate LSMMG or a vertical axis to serve as a normal gravity (1 x g) control as previously described (Duscher et al., 2018; Schwarz et al., 1992). For all time points, gravity controls were conducted in HARVs where the axis of rotation was perpendicular to the test system to ensure that the phenotypes detected were not simply the results of being in the HARV system. Both LSMMG treatments and gravity controls were run simultaneously within a environmental growth chamber on a 12 h light/dark cycle and maintained at a constant 23°C. Juvenile squid were kept aposymbiotic or symbiotic as described above. The animals were added to the HARVs through an opening on the surface of the HARVs and then sealed with zero headspace. A semipermeable membrane provided aeration for the host and symbiont. Previous studies have shown no change in oxygen levels during animal and bacteria co-incubations (Vroom et al., 2022). A total of four replicate animals were incubated in each HARV vessel for 2, 6, 8, 10, 12, 16, 18, or 24 h and then animals were removed and immediately flash frozen in liquid nitrogen and stored at -80°C. Additionally, a subset of animals were collected within 5 min (i.e., 0 h) of hatching and frozen in liquid nitrogen for comparison purposes.

tag: developmental stage

value: juvenile

value: Light organ tissue

value: Hatchling


title: arcuate nucleus, high workload, ZT09, rep1

description:
ARC_H_ZT09_X15
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: N1E115_4%O2_ARNT_replicate2


title: 39A_S34

value: kidney

value: kidney allograft

value: caABMR


title: arcuate nucleus, high workload, ZT05, rep2

description:
ARC_H_ZT05_X3
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: 38_GATCAG


title: Hatchling 2


title: Hatchling 1


title: N1E115_20%O2_ARNT_replicate2


title: N1E115_20%O2_HIF1A_replicate2


title: arcuate nucleus, high workload, ZT05, rep1

description:
ARC_H_ZT05_X13
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: 37_ACTTGA


title: arcuate nucleus, high workload, ZT17, rep1

description:
ARC_H_ZT17_X16
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: N1E115_20%O2_input5


title: arcuate nucleus, high workload, ZT01, rep2

description:
ARC_H_ZT01_X7
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: 36_TTAGGC


title: Microgravity 24h apo 2

value: Microgravity 24h apo


title: N1E115_20%O2_ARNT_replicate1


title: Microgravity 24h apo 1


title: 36A_S39


title: Microgravity 24h apo 3


title: arcuate nucleus, high workload, ZT01, rep1

description:
ARC_H_ZT01_X1
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: arcuate nucleus


title: N1E115_20%O2_HIF1A_replicate1


title: arcuate nucleus, low workload, ZT21, rep2

description:
ARC_L_ZT21_X27
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: low workload


title: Gravity 24h sym 3

value: Gravity 24h sym


title: 35_ATCACG


title: N1E115_20%O2_input4


title: Gravity 24h sym 2


title: arcuate nucleus, low workload, ZT21, rep1

description:
ARC_L_ZT21_X21
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: 34_CTTGTA


title: arcuate nucleus, low workload, ZT17, rep2

description:
ARC_L_ZT17_X25
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: Gravity 24h sym 1


title: mTEC, ChIP anti-Fezf2

data_processing:
Data quality was evaluated using FASTQC, filtered and trimmed with Atropos, and mapped to the mm10 mouse genome build using BWA.
After removing multi-mapping reads and duplicates, peaks were called MACS2  with default parameters.
Peak quality was evaluated with ChIPQC. Coverage and the reproducibility of peaks across replicates was evaluated with DeepTools.
ChIPseeker   was used to annotate peaks to the closest transcriptional start site and perform functional enrichment analysis.
Assembly: mm10
Supplementary files format and content: bedGraph

extract_protocol:
Nuclei from FACS-isolated mTECs were sonnicated using a Covari M220. Chromatin immunoprecipitation and Tagmentation was performed using the ChIPmentation method.
Library preparation was performed using Kapa HiFi HotStart Ready Mix (Roche) and Nextera custom primers.

value: thymus

value: mTEC

value: wt

value: ChIP anti-Fezf2


title: 33_CAGATC


title: 33A_S19


title: arcuate nucleus, low workload, ZT13, rep2

description:
ARC_L_ZT13_X5
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: CBA/CaJ


title: mTEC, ChIP anti-Elf3

value: ChIP anti-Elf3


title: 31_ACAGTG

value: aABMR


title: Gravity 24h apo 2

value: juvenile

value: Gravity 24h apo


title: mTEC, ChIP anti-Ehf

value: ChIP anti-Ehf


title: arcuate nucleus, low workload, ZT13, rep1

description:
ARC_L_ZT13_X11
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: male


title: Gravity 24h apo 1

value: Light organ tissue


title: 31A_S4

value: kidney

value: kidney allograft

value: No Rejection


title: mTEC, input control Klf4

value: input control Klf4


title: arcuate nucleus, low workload, ZT09, rep2

description:
ARC_L_ZT09_X29
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: arcuate nucleus

value: low workload


title: Microgravity 18h sym 3

value: Microgravity 18h sym


title: 30_TGACCA


title: Microgravity 18h sym 2


title: 2A_S10


title: mTEC, ChIP anti-Klf4

value: thymus

value: mTEC

value: wt

value: ChIP anti-Klf4


title: mTEC, input control Ehf

value: input control Ehf


title: arcuate nucleus, low workload, ZT09, rep1

description:
ARC_L_ZT09_X23
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: CBA/CaJ


title: Microgravity 18h sym 1

value: juvenile


title: mTEC, input control Elf3

value: input control Elf3


title: arcuate nucleus, low workload, ZT05, rep1

description:
ARC_L_ZT05_X12
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: male


title: arcuate nucleus, low workload, ZT17, rep1

description:
ARC_L_ZT17_X19
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: Microgravity 18h apo 3

value: Light organ tissue

value: Microgravity 18h apo


title: 28_GGCTAC

value: kidney

value: kidney allograft

value: aABMR


title: Gravity 24h apo 3

value: Gravity 24h apo


title: iMLL-AF9 BM LSCs, IOX5, rep4

city: Edinburgh

first: Yuka

last: Kabayama

address: 5 Little France Drive

institute: University of Edinburgh

data_processing:
Adapters were trimmed with Cutadapt (version 1.18) using options: -a AGATCGGAAGAGC -m 50
Processed reads were mapped to GRCm38 genome_tran (release 84) with HISAT2 (version 2.2.1)
Mapped reads per gene were counted with htseq-count (HTSeq version 2.0.1)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read count for each sample

source_name: Bone marrow

extract_protocol:
RNA was harvested using RNeasy Plus Universal Mini Kit (Qiagen). 500 ng of total RNA was used for the construction of sequencing libraries.
Libraries for RNA-seq were prepared using NEBNext® UltraTM II Directional RNA Library Prep Kit for Illumina (NEB) with Poly(A) mRNA Magnetic Isolation Module following manufacturer's protocols.

value: Bone marrow

value: Leukaemic stem cells

value: WT


title: arcuate nucleus, low workload, ZT01, rep1

description:
ARC_L_ZT01_X20
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: arcuate nucleus

value: low workload


title: Microgravity 18h apo 2


title: iMLL-AF9 BM LSCs, IOX5, rep3


title: C_L_Q_3 (QJHTD 3, Q3)

city: Chengdu

first: Jing

last: Yang

state: Sichuan

address: No.33, Mashi Street, Wenjiang District

institute: Chengdu Fifth People's Hospital

description: COPD treated with QJHTD.

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp software.
Trimmed sequence reads were mapped to GRCh38.p6 mouse genome.
Read count extraction and normalization were performed using RSEM software.
Assembly: GRCh38.p6
Supplementary files format and content: gene.tpm.matrix.annot.xls: Excel file includes RPKM values for each Sample.

source_name: Lung

extract_protocol:
RNA was harvested using RNeasy mini plus kit (VZ6). 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: BALB/c

value: Lung

tag: diagnosis

value: COPD

value: Qing-Jin-Hua-Tan decoction

tag: group

value: QJHTD


title: 25_ACTTGA


title: 1A_S21

value: No Rejection


title: Microgravity 18h apo 1

value: juvenile

value: Light organ tissue


title: iMLL-AF9 BM LSCs, IOX5, rep2


title: Gravity 18h sym 3

value: Gravity 18h sym


title: 18A_S16

value: kidney

value: kidney allograft

value: TCMR


title: C_L_Q_2 (QJHTD 2, Q2)

description: COPD treated with QJHTD.


title: iMLL-AF9 BM LSCs, IOX5, rep1

value: Bone marrow


title: mTEC, input control Fezf2

value: thymus

value: mTEC

value: wt

value: input control Fezf2


title: C_L_Q_1 (QJHTD 1, Q1)

description: COPD treated with QJHTD.

value: BALB/c

value: WT


title: 17A_S40


title: arcuate nucleus, low workload, ZT05, rep2

description:
ARC_L_ZT05_X26
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: arcuate nucleus

value: CBA/CaJ

value: male

value: low workload


title: 29A_S32

value: aABMR


title: Gravity 18h sym 2

value: juvenile

value: Light organ tissue


title: iMLL-AF9 BM LSCs, DMSO, rep4

value: Leukaemic stem cells

value: DMSO


title: Gravity 18h sym 1

value: Gravity 18h sym


title: C_L_2 (Model 2, M2)

value: Lung

value: COPD

value: Model


title: C_L_3 (Model 3, M3)


title: iMLL-AF9 BM LSCs, DMSO, rep3

value: Bone marrow


title: Gravity 18h apo 3

value: Gravity 18h apo


title: 14A_S8

value: kidney

value: kidney allograft

value: TCMR


title: iMLL-AF9 BM LSCs, DMSO, rep2

value: WT


title: C_L_1 (Model 1, M1)

value: BALB/c


title: 13A_S24


title: Gravity 18h apo 2


title: Ctrl_3 (Control 3, C3)

value: Normal

value: Control


title: iMLL-AF9 BM LSCs, DMSO, rep1


title: Gravity 18h apo 1

value: juvenile


title: 12_GATCAG


title: MPC3.shRNF185.3_rep6

first: Ze'ev

middle: A.

last: Ronai

state: CA

address: 10901 North Torrey Pines Road

department: Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center

institute: Sanford Burnham Prebys Medical Discovery Institute

description:
Batch3
Counts_ComBat-Seq.txt.gz
CountsPerMillion_ComBat-Seq.txt.gz

data_processing:
Illumina Truseq adapters and polyA/polyT sequences were trimmed from raw reads using Cutadapt version 2.3.
Trimmed reads were aligned to mouse genome version mm10 and Ensembl gene annotations version 84 using STAR version 2.7.0d_0221 adopting alignment parameters from ENCODE long RNA-seq pipeline (https://github.com/ENCODE-DCC/long-rna-seq-pipeline).
RSEM version 1.3.1 was used to obtain gene level estimated counts and transcripts per million (TPM).
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include batch corrected counts and counts per million (CPM).

extract_protocol:
RNA from samples were purified using a GenElute total RNA purification kit (Sigma-Aldrich).
PolyA RNA was isolated using NEBNext® Poly(A) mRNA Magnetic Isolation Module, and bar-coded libraries were constructed using the NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® (NEB, Ipswich MA). Libraries were pooled and sequenced from a single-end (1X75) on an Illumina NextSeq 500 system using the High output V2 kit (Illumina Inc., San Diego, CA).

value: RNF185 KD


title: 12A_S23

value: No Rejection


title: MPC3.shRNF185.3_rep5


title: Ctrl_1 (Control 1, C1)


title: Microgravity 16h sym 3

value: Light organ tissue

value: Microgravity 16h sym


title: Ctrl_2 (Control 2, C2)

value: Lung


title: Microgravity 16h sym 2


title: MPC3.shRNF185.3_rep4

description:
Batch2
Counts_ComBat-Seq.txt.gz
CountsPerMillion_ComBat-Seq.txt.gz


title: 10A_S28


title: 11A_S38


title: 16A_S30


title: no uveitis dataset mRNA

city: SAN FRANCISCO

first: Mianmian

last: Yin

address: 513 Parnassus Avenue

department: Department of Microbiology and Immunology

institute: University of California, San Francisco

library_source: transcriptomic single cell

data_processing:
Fastq files from 10x gene expression and TCR library were processed with Cell Ranger, using default parameters.
Assembly: mouse vdj_GRCm38_alts_ensembl or mm10
Supplementary files format and content: For each sample, gene expression (mRNA) file contains a named filtered_feature_bc_matrix.rar file, TCR expression file(TCR) contains a filtered_contig_annotations.csv file

source_name: Lymph nodes

extract_protocol:
P2+ cells were sorted from lymph nodes of AireGW/+ Lyn-/-mice, and then send to genomic core of UCSF to generate the library by using the kits.
libraries were prepared using the 10x Genomics Chromium Single Cell 5′ Reagent (GEX + VDJ) Kit version 1.1 according to manufacturer’s protocol
10x Genomics Chromium Single Cell 5′

value: Lymph nodes

value: CD4 single positive T cells

value: AireGW/+ Lyn-/-

value: without uveitis


title: Microgravity 16h sym 1


title: Microgravity 16h apo 3

value: Microgravity 16h apo


title: uveitis dataset2 mRNA

value: uveitis


title: no uveitis dataset TCR


title: MPC3.shRNF185.3_rep2

description:
Batch1
Counts_ComBat-Seq.txt.gz
CountsPerMillion_ComBat-Seq.txt.gz


title: MPC3.shRNF185.3_rep3


title: Microgravity 16h apo 2


title: uveitis dataset2 TCR


title: Microgravity 16h apo 1


title: MPC3.shRNF185.3_rep1


title: uveitis dataset1 mRNA


title: MPC3.shRNF185.1_rep6


title: Gravity 16h sym 3

value: Gravity 16h sym


title: MPC3.shRNF185.1_rep5


title: Gravity 16h sym 1


title: testicular tissue, HO-1-WT-3 (lncRNA+circRNA)

city: Hangzhou

first: Ning

last: He

state: Zhejiang

address: No. 79 Qingchun Road

department: Department of Urology

institute: The First Affiliated Hospital, Zhejiang University School of Medicine

description:
all.circ_expression.txt (for circRNA)
all.ncRNA_expression.txt (for lncRNA)

data_processing:
For circRNA:
a.Raw reads were treated with Trimmomatic tools(V0.36) to remove adapters. Following reads quality con- trol: Scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below 15, drop reads which are less than 35% of initiation read length. Then reads quality was inspected using the FastQC software then output statistical result.
b. Two algorithms, CIRI2 and CIRCexplorer2 were used to detect circRNAs. Reads were mapped to rat reference genome rn6 by BWA-MEM or Tophat, respectively. CIRI2 de- tects the paired chiastic clipping (PCC) signals from the mapping information of reads by local alignment with BWA-MEM and combines with systematic filtering steps to remove potential false positives.CIRCexplorer2 uses TopHat and TopHat-Fusion alignment output to detect circRNAs.
c.If a circRNA can be detected by both methods, it will be consided as an identified cirRNA. Back-spliced junction reads identified in CIRI2 were combined and scaled to RPM (Reads Per Million mapped reads, bwa- mem mapping) to quantify every circRNAs.
For lncRNA:
a.The clean reads were obtained after removal of reads containing adapter, ploy-N and at low quality from raw data. HISAT2 was used to align the clean reads to the rat reference genome rn6 with default parame- ters. HTSeq was subsequently employed to convert aligned short reads into read counts for each gene model.
b.Differential expression was assessed by DEseq using read counts as input. The Benjamini–Hochberg multiple test correction method was enabled. Differentially expressed genes were chosen according to the criteria of fold change > 2 and adjusted p-value < 0.05. All the differentially expressed genes were used for heat map analysis and KEGG ontology enrichment analyses.
Assembly: rn6
Supplementary files format and content: all.ncRNA_expression.txt (counts)
Supplementary files format and content: all.circ_expression.txt (RPMs and counts)

organism: Rattus norvegicus

source_name: testicle

growth_protocol: Zebrafish embryos were collected and maintained in E3 medium in a 28.5 °C incubator

extract_protocol:
Total RNA was isolated from cells/tissues using the Trizol (invitrogen) according to the manufacturer’s protocol. RNA purity was assessed by ND-1000 Nanodrop required A260/280≥1.8, A260/A230≥2.0. RNA integrity (RIN) was evaluated by Agilent 2200 TapeStation (Agilent Technologies, USA) requiring RIN≥7.0.
Briefly, rRNAs were removed from Total RNA using Epicentre Ribo-Zero rRNA Removal Kit (illumina, USA) , then RNA was treated with RNase R (Epicentre, USA) and fragmented to approximately 200bp. Subsequently, the purified RNA fragments were subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycle according to instructions of NEBNext® UltraTM RNA Library Prep Kit for Illumina (NEB, USA). The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit®2.0(Life Technologies, USA) and then sequenced on HiSeq 3000 with 2 X 150 bp mode.

value: testicle

value: WT

value: Male

value: Sprague Dawley

value: testis cell

value: the testicle suffered from reperfusion 3 days after ischemia 2 hours


title: MPC3.shRNF185.1_rep4

value: RNF185 KD


title: Gravity 16h apo 3

value: juvenile

value: Light organ tissue

value: Gravity 16h apo


title: MPC3.shRNF185.1_rep3


title: MPC3.shRNF185.1_rep2


title: LIN28B HIGH, NB24

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

country: Italy

institute: università di padova

description: Gene expression data from SH-SY5Y cell line after lentiviral infection with LIN28B plasmid and 7 days of doxycycline induction, fourth replicate

hyb_protocol: 5.5ug of sscDNA were fragmentated and 5.2 ug were hybridized for 16 hr at 45°C on GeneChip Human Clariom S Array (GPL23159 Platform). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scan GCS3000.

data_processing: The data were normalized using RMA in TAC Software v4.0.2.15

source_name: doxycycline-inducible SH-SY5YLIN28B at 7 days

label_protocol: Biotinylated cRNA were prepared according to the standardThermoFisher protocol starting  from 100ng of Total RNA using the ThermoFisher WTA Kit

growth_protocol: The CTRL and iLIN28B cells were cultured in RPMI 1640 medium (Gibco) supplemented with 1% Glutamine (Gibco), 1% Penicillin/Streptomycin (Gibco), and 10% FBS (Gibco). The cell lines were kept at 37 °C, 5% CO2, and 95% humidity.

extract_protocol: RNA extraction was performed using Zymo Direct-zol (Zymo Research) columns according to the manifacturer’s recommendations, and the concentration of RNA was measured using Qubit (Invitrogen, Thermo Fisher)

treatment_protocol: Cells were exposed to 1 μM doxycycline for 0 hours (basal), 48 hours (medium) or 7 days (high).

tag: sample group

value: LIN28B HIGH


title: testicular tissue, HO-1-WT-2 (lncRNA+circRNA)


title: Gravity 16h apo 1


title: ctrl HIGH, NB20

description: Gene expression data from SH-SY5Y cell line after lentiviral infection with control plasmid and 7 days of doxycycline induction, fourth replicate

source_name: SH-SY5YCTR at 7 days

value: ctrl HIGH


title: LIN28B HIGH, NB23

description: Gene expression data from SH-SY5Y cell line after lentiviral infection with LIN28B plasmid and 7 days of doxycycline induction, third replicate


title: LIN28B HIGH, NB21

description: Gene expression data from SH-SY5Y cell line after lentiviral infection with LIN28B plasmid and 7 days of doxycycline induction, first replicate


title: ctrl HIGH, NB19

description: Gene expression data from SH-SY5Y cell line after lentiviral infection with control plasmid and 7 days of doxycycline induction, third replicate


title: testicular tissue, HO-1-1-3 (lncRNA+circRNA)

value: HO-1 knockout


title: testicular tissue, HO-1-WT-1 (lncRNA+circRNA)


title: Gravity 16h apo 2


title: testicular tissue, HO-1-1-2 (lncRNA+circRNA)


title: MPC3.shRNF185.1_rep1


title: MPC3.plko_rep6

value: Control


title: Microgravity 12h sym 3

value: Microgravity 12h sym


title: uveitis dataset1 TCR

value: Lymph nodes

value: CD4 single positive T cells

value: AireGW/+ Lyn-/-

value: uveitis


title: Microgravity 12h sym 2


title: MPC3.plko_rep5


title: MPC3.plko_rep4


title: F64_Ctrl_4

city: Bethesda

first: Jason

last: Brenchley

state: MD

address: 4 Center Drive

institute: NIAID

data_processing:
RNA-seq samples were sequenced as 101bp paired-end libraries on a Novaseq S4. All samples had over 70 million reads.
Reads were trimmed using Cutadapt (v1.18) and aligned to the Mmul_10/RheMac10 reference genome and Gencode (Ensembl release 108) using STAR (v2.7.6a) in 2-pass basic mode. Expression levels were quantified with RSEM (v1.3.3) before being converted into FPKM values.
Assembly: RheMac10
Supplementary files format and content: RSEM_genes_expected_counts.tsv
Supplementary files format and content: RSEM.genes.FPKM.all_samples.txt

molecule: polyA RNA

organism: Macaca mulatta

source_name: liver

extract_protocol:
RNA was extracted from pelleted cells resuspended in Buffer RLT Plus (Qiagen) with 1% BME. RNA was extracted using RNeasy Micro kit (Qiagen).
SMART-Seq® v4 Ultra® Low Input RNA was used for mRNA library preparation.

treatment_protocol: Autologous transplantation with barcoded lentivirally-transduced CD34+ HSPCs was performed

value: liver

value: Macrophage


title: Microgravity 12h sym 1


title: LIN28B MEDIUM, NB15

description: Gene expression data from SH-SY5Y cell line after lentiviral infection with LIN28B plasmid and 48 hours of doxycycline induction, third replicate

source_name: doxycycline-inducible SH-SY5YLIN28B at 48 hours

value: LIN28B MEDIUM


title: ctrl HIGH, NB18

description: Gene expression data from SH-SY5Y cell line after lentiviral infection with control plasmid and 7 days of doxycycline induction, second replicate


title: testicular tissue, HO-1-1-1 (lncRNA+circRNA)

value: testicle

value: Male

value: Sprague Dawley

value: testis cell

value: the testicle suffered from reperfusion 3 days after ischemia 2 hours


title: LIN28B HIGH, NB22

description: Gene expression data from SH-SY5Y cell line after lentiviral infection with LIN28B plasmid and 7 days of doxycycline induction, second replicate

value: LIN28B HIGH


title: MPC3.plko_rep3


title: DBv1_Ctrl_3


title: Gravity 16h sym 2

value: juvenile

value: Light organ tissue

value: Gravity 16h sym


title: LIN28B MEDIUM, NB16

description: Gene expression data from SH-SY5Y cell line after lentiviral infection with LIN28B plasmid and 48 hours of doxycycline induction, fourth replicate


title: Microgravity 12h apo 3

value: Microgravity 12h apo


title: LIN28B MEDIUM, NB13

description: Gene expression data from SH-SY5Y cell line after lentiviral infection with LIN28B plasmid and 48 hours of doxycycline induction, first replicate


title: MPC3.plko_rep2

value: Control


title: Microgravity 12h apo 2


title: ZJ31_GFPpos_2

value: Stem cell transplant


title: MPC3.plko_rep1


title: ZJ31_GFPneg_1


title: LIN28B MEDIUM, NB14

description: Gene expression data from SH-SY5Y cell line after lentiviral infection with LIN28B plasmid and 48 hours of doxycycline induction, second replicate


title: Microgravity 12h apo 1


title: Lung, LPS, 10 weeks, biol rep 3

city: Rehovot

first: Valery

last: Krizhanovsky

state: Israel

address: 234 Herzl St.

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

data_processing:
Raw data were processed with the User-friendly Transcriptome Analysis Pipeline (UTAP)
Only reads with unique mapping to the 3’ of RefSeq annotated genes (mm10, NCBI Mus musculus Annotation Release 109) were analyzed.
For differential gene expression analysis, we used DESeq2, following standard workflow, to analyze RNA-seq count data derived from lung epithelial cells, comparing LPS to PBS.
Genes with < 30 UMIs across samples were pre-filtered. Differentially expressed genes (DEGs) were selected to have |fold-change| > 1.25 and Benjamini-Hochberg adjusted P<0.05.
Assembly: mm10
Supplementary files format and content: tab-delimited excel file include DESeq2 outcomes for each file

source_name: lung

extract_protocol:
10000 cells of lung epithelium (EpCam+ CD31- CD45-) were sorted into 50 μL of lysis/binding buffer (Life Technologies). mRNA was captured with 15 μl of Dynabeads oligo(dT) (Life Technologies) and eluted according to the manufacturer protocol.
cDNA libraries were prepared from pooled samples  (10000 cells per sample) according to a bulk variation of MARSseq

treatment_protocol: For chronic LPS exposure, mice were exposed to an aerosolized PBS alone or PBS containing Escherichia coli LPS (0.5 mg/ml; Sigma, #L2630) for 30 min, 3 times a week for 10 weeks.

value: lung

value: epithelial

value: LPS


title: Ctrl_F64_28

data_processing:
ATAC-seq samples were sequenced as 151bp paired-end libraries on a Novaseq S4. All samples had over ?? million reads.
Samples were trimmed for adapters using Cutadapt v 1.18 before alignment. The trimmed reads were aligned to the RheMac10 reference using Bowtie2 v2.3.4.1 with flag -k 10.
Assembly: RheMac10
Supplementary files format and content: The peaks were called using Genrich v0.6 with the following flags -j -y -r -v -d 150 -m 5 -e chrM,chrY.
Supplementary files format and content: Genrich-produced bedgraphs were normalized by library size (reads per million sequenced reads, RPM) for visualization.

extract_protocol:
Up to 10,000 sorted cells from each population were pelleted and resuspended in 2x Tagmentation Buffer (Illumina), 0.02% Digitonin, and 0.1% Tween-20, with Tagment DNA TDE1 Enzyme (Illumina) and incubating at 37°C for one hour.  The mix was then incubated with proteinase K for 30 minutes at 40°C.
High molecular weight DNA was removed with a 0.7x selection ratio of Agencourt AMPureXP beads (Beckman Coulter) and low molecular weight DNA was isolated from the remainder with a 1.2x selection ratio. Library amplification was performed with KAPA HiFi HotStart ReadyMix (KAPA) and i5 and i7 indexing primers (Nextera DNA CD Indexes) for 11-15 total cycles depending on the sample concentration reached after 5 cycles (KAPA Library Quantification kit). Library DNA was purified with a 1x selection ratio of AMPureXP beads. The final library was verified by High Sensitivity DNA Bioanalyzer (Agilent).

value: liver

value: Macrophage


title: ctrl HIGH, NB17

description: Gene expression data from SH-SY5Y cell line after lentiviral infection with control plasmid and 7 days of doxycycline induction, first replicate

value: ctrl HIGH


title: ctrl MEDIUM, NB10

description: Gene expression data from SH-SY5Y cell line after lentiviral infection with control plasmid and 48 hours of doxycycline induction, second replicate

source_name: SH-SY5YCTR at 48 hours

value: ctrl MEDIUM


title: ctrl MEDIUM, NB11

description: Gene expression data from SH-SY5Y cell line after lentiviral infection with control plasmid and 48 hours of doxycycline induction, third replicate


title: Gravity 12h sym 3

value: Gravity 12h sym


title: Gravity 12h sym 2


title: Lung, LPS, 10 weeks, biol rep 1


title: Lung, LPS, 10 weeks, biol rep 2


title: Gravity 12h sym 1


title: Lung, PBS, 10 weeks, biol rep 5

value: PBS


title: Ctrl_DBv1_27


title: GFPneg_ZJ31_24


title: ctrl MEDIUM, NB12

description: Gene expression data from SH-SY5Y cell line after lentiviral infection with control plasmid and 48 hours of doxycycline induction, fourth replicate


title: Gravity 12h apo 2

value: Gravity 12h apo


title: GFPneg_ZG41_21


title: Lung, PBS, 10 weeks, biol rep 4


title: Lung, PBS, 10 weeks, biol rep 3


title: Gravity 12h apo 1


title: Lung, PBS, 10 weeks, biol rep 2


title: LIN28B BASAL, NB08

description: Gene expression data from SH-SY5Y cell line after lentiviral infection with LIN28B plasmid and 0 hours of doxycycline induction, fourth replicate

source_name: doxycycline-inducible SH-SY5YLIN28B at 0 hours

value: LIN28B BASAL


title: GFPpos_ZJ31_25


title: LIN28B BASAL, NB07

description: Gene expression data from SH-SY5Y cell line after lentiviral infection with LIN28B plasmid and 0 hours of doxycycline induction, third replicate


title: LIN28B BASAL, NB06

description: Gene expression data from SH-SY5Y cell line after lentiviral infection with LIN28B plasmid and 0 hours of doxycycline induction, second replicate


title: LIN28B BASAL, NB05

description: Gene expression data from SH-SY5Y cell line after lentiviral infection with LIN28B plasmid and 0 hours of doxycycline induction, first replicate


title: Lung, PBS, 10 weeks, biol rep 1


title: Microgravity 10h sym 2

value: juvenile

value: Microgravity 10h sym


title: Ctrl_4016_26


title: Lung, LPS, p16 pos, 10 weeks, biol rep 4

extract_protocol:
5000 cells of alveolar macrophages were sorted into 50 μL of lysis/binding buffer (Life Technologies). mRNA was captured with 15 μl of Dynabeads oligo(dT) (Life Technologies) and eluted according to the manufacturer protocol.
cDNA libraries were prepared from pooled samples  (5000 cells per sample) according to a bulk variation of MARSseq

value: alveolar macrophages


title: GFPpos_RQ7387_20


title: Microgravity 10h sym 1

value: Light organ tissue


title: Lung, LPS, p16 neg, 10 weeks, biol rep 4


title: GFPneg_RQ7387_19


title: Pod, susceptible replicate 2

city: Bandung

first: Popi

last: Septiani

state: West Java

address: Jl. Ganesha no. 10

department: School of Life Sciences and Technology

country: Indonesia

institute: Institut Teknologi Bandung

library_source: other

data_processing:
Sequencing reads were checked for quality using FastQC v0.11.9.
All samples (4 libraries) with adapter contamination were trimmed using Trimmomatic v0.39. Subsequently, small RNAs within the length range of 18 to 28 base pairs were chosen as the target miRNA length.
Read mapping on the reference genome and Read quantification on the four samples was performe using featurecount from Rsubread v2.10.5
Assembly: GCA_000403535.1
Supplementary files format and content: tab-delimited text file include raw count for each samples

molecule: other

organism: Theobroma cacao

source_name: Cacao pod skin

growth_protocol: The samples were collected from the Indonesian coffee and cacao research institute (PUSLITKOKA) plantation in Jember, East Java, Indonesia, with a mature age of 5 months, cacao plants grown at an altitude of 75 meters above sea level, with conditions of humidity 77.81%, average temperature 27.55 ⁰C, light intensity 64.11%, and wind speed 0.29 m/s.

extract_protocol:
Total small RNA was extracted using miRPremier miRNA Isolation Kit by Sigma-Aldrich Germany, following manufacturer's protocols, then was used for miRNA libraries contruction
miRNA libraries for miRNA-seq were prepared using TruSeq Small RNA Library Preparation Kit following manufacturer's protocols

treatment_protocol: Samples of resistant and susceptible cacao varieties infected with BPD were collected directly from the plantation of PUSLIKTKOKA for 2 replicates, the sample pods were thinly sliced and then stored in liquid nitrogen to prevent damage until the extraction of nucleid acid material.

value: Cacao pod skin

tag: variety

value: susceptible

value: WT

value: Black pod disease infected


title: ctrl BASAL, NB03

description: Gene expression data from SH-SY5Y cell line after lentiviral infection with control plasmid and 0 hours of doxycycline induction, third replicate

source_name: SH-SY5YCTR at 0 hours

value: ctrl BASAL


title: GFPpos_ZG41_22

value: liver

value: Stem cell transplant


title: Pod, resistance, replicate 2

value: resistance

value: Control


title: Microgravity 10h apo 2

value: Microgravity 10h apo


title: Lung, PBS, p16 pos, 10 weeks, biol rep 4

value: lung

value: PBS


title: Pod, susceptible replicate 1


title: Lung, PBS, p16 neg, 10 weeks, biol rep 4


title: Microgravity 10h apo 1


title: ctrl BASAL, NB02

description: Gene expression data from SH-SY5Y cell line after lentiviral infection with control plasmid and 0 hours of doxycycline induction, second replicate


title: Microgravity 10h sym 3


title: ctrl MEDIUM, NB09

description: Gene expression data from SH-SY5Y cell line after lentiviral infection with control plasmid and 48 hours of doxycycline induction, first replicate

value: ctrl MEDIUM


title: Lung, LPS, p16 pos, 10 weeks, biol rep 3

value: LPS


title: Microgravity 10h apo 3

value: juvenile


title: ctrl BASAL, NB04

description: Gene expression data from SH-SY5Y cell line after lentiviral infection with control plasmid and 0 hours of doxycycline induction, fourth replicate


title: Gravity 10h sym 3

value: Gravity 10h sym


title: Pod, resistance, replicate 1


title: Lung, LPS, p16 neg, 10 weeks, biol rep 3

value: alveolar macrophages


title: Gravity 10h sym 2

value: Light organ tissue


title: Lung, PBS, p16 pos, 10 weeks, biol rep 3


title: Gravity 10h sym 1


title: MC_R2

city: Belvaux

first: Sylvain

last: Legay

address: 41, rue du Brill

department: ERIN department

country: Luxembourg

institute: Luxembourg Institute of Science and Technology

data_processing:
Generated FASTQ files were imported in CLC Genomics Workbench v.11.0.1. Sequences were filtered using the following criteria: sequence quality score < 0.01, no ambiguity in the sequence and sequence minimum length of 35 bases. The sequences were trimmed to remove Illumina TruSeq adaptors, poly-A and poly-G sequences, and hard trimmed 8 bases at the 5' end and 3 bases at the 3' end.
De novo assembly was performed using CLC genomics Workbench (version 11.0.1) and Trinity. De novo assembly with CLC genomics Workbench was performed in two steps. First, word size was optimised. Assemblies with word sizes ranging from 21 to 61 by 5 increments, an auto bubble size of 50 and a minimum contig length of 300 bp were performed. Word size of 51 gave the best results. Secondly, bubble size was optimised by keeping word size fixed to 51, minimum contig length of 300 and varying bubble size from 50 to 1000 (Supplementary table). An optimal de novo assembly was obtained with a bubble size of 500.
De novo assembly was performed twice with Trinity (Grabherr et al., 2011; Haas et al., 2013), using the version integrated into Blast2GO PRO (v. 5.2.5) with the following parameters: paired-end reads, strand-specific forward, pairs distance of 100 and 200 bases. The three assemblies were merged, and cd-hit-est (Li & Godzik, 2006; Fu et al., 2012), v. 4.7; with parameters -c 1 -n 11) was performed to remove redundant contigs. After that, TransDecoder (v. 5.5.0, https://github.com/TransDecoder/TransDecoder) was performed on the non-redundant merged transcripts to extract putative coding sequences (cds) and peptide sequences. Another step of cd-hit-est (with parameters -c 0.95 -n 10) was performed on the cds to obtain a list of non-redundant peptides, using a 95% sequence identity cut-off. The transcripts corresponding to the non-redundant peptides were then extracted. The thus selected transcripts were blasted against the annotated S. purpurea transcriptome (US Department of Energy Joint Genome Institute), obtained from Phytozome v12.1 (Goodstein et al., 2012), https://phytozome.jgi.doe.gov/). Top hit sequences were filtered at 10-5. Finally, filtered reads were mapped against the de novo assembled transcriptome using CLC genomics with the following criteria: mismatch cost of 2, insertion and deletion costs of 3, and length and similar fraction of at least 0.8.
To identify DEGs, count tables generated by CLC genomics were analysed using edgeR (v. 3.28.1 (Robinson et al., 2009)) after filtering out low-expressed transcripts (count per million < 0.5). Two statistical models were used depending on the aim of the analysis. To detect DEGs, the following model was used: Direct effect= Condition of interest-CT, where Condition of interest is either CC, MT or MC. Genes were considered differentially expressed when the absolute value of their adjusted fold-change was greater than 2, and their FDR-adjusted p-value was lower than 0.01.
Assembly: S.viminalis_root_transcriptome V1.0.cds.fa
Supplementary files format and content: S.viminalis_root_transcriptome V1.0.annotation.txt
Supplementary files format and content: Processed data.txt

organism: Salix viminalis

source_name: Roots

growth_protocol: Cuttings of 10 cm of one individual S. viminalis were rooted in containers filled with a mix of 25 kg of potting soil and 17.5 kg sand under a controlled environment (23/20°C, 60% relative humidity, 16/8h photoperiod). After three weeks, plantlets were transferred to individual pots and half of them were exposed to a mixture of heavy metals (1.5 ppm Cd, 175 ppm Cu, 30 ppm Ni, 500 ppm Zn). After 40 days, half of the plants were randomly chosen and cold-acclimated (7/5°C, 60% relative humidity, 16/8h photoperiod) while the remaining was kept under control conditions. A total of four temperature-polymetallic contamination combinations were obtained, namely Control soil Temperate (CT), Control soil Cold acclimated (CC), Metals-polluted soil Temperate (MT) and Metals-polluted soil Cold acclimated (MC). Three biological replicates per stress combination were analysed. During the four weeks of cold treatment, chlorophyll fluorescence was measured at several time points, and the Fv/Fm ratio calculated. After four weeks, plants were uprooted, and the roots were rinsed. About one gram of roots was used to determine root frost tolerance and the remaining was snap-frozen in liquid nitrogen and stored at -80°C until subsequent use.

extract_protocol:
Root samples (250 mg) were ground into a fine powder using mortar and pestle in liquid nitrogen. Total RNA was extracted following a modified CTAB buffer extraction protocol (Legay et al., 2015) and cleaned using the RNeasy plant mini kit (Qiagen, Leusden, The Netherlands) according to the manufacturer's instructions, using an extra DNAse I treatment to remove genomic DNA. RNA purity and quantity were assessed by measuring the absorbance at 230, 260 and 280 nm using a Nanodrop ND1000 spectrophotometer (Thermo Scientific, Villebon-Sur-Yvette, France). Total RNA integrity was assessed using the RNA Nano 6000 assay (Agilent Technologies, Diegem, Belgium) and a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). All RNAs had RIN above 7.
Libraries were prepared using SMARTer Stranded RNA-Seq kit (Takara Bio Inc., Mountain View, CA, USA) following the manufacturer's instructions. Briefly, mRNA was isolated from 5 µg of total RNA using Magnosphere UltraPure mRNA Purification Kit (Takara Bio Inc.). The quality of the purified mRNA was assessed using RNA 6000 Pico assay (Agilent Technologies) and a 2100 Bioanalyzer. After purification, mRNA was sheared into fragments of approximately 300 bp, reverse-transcribed into cDNA using random primers, and ligated to Illumina Indexing Primer Set (Takara Bio Inc.), corresponding to Illumina TruSeq indexes 1 to 12. An enrichment step was carried out using 13 cycles of PCR. The samples' average fragment size was determined using a High Sensitivity DNA assay (Agilent Technologies) and a 2100 Bioanalyzer. The pooled libraries were sequenced on an Illumina NextSeq500 (Illumina NextSeq 500/550 High Output Kit v2.5 (300 cycles)) to generate 150 base-pairs pair-end reads.

value: Roots

value: Heavy metal soil/Cold Temperature 4°C


title: Lung, PBS, p16 neg, 10 weeks, biol rep 3


title: Gravity 10h apo 3

value: Gravity 10h apo


title: MC_R1


title: Lung, LPS, p16 pos, 10 weeks, biol rep 2


title: ctrl BASAL, NB01

description: Gene expression data from SH-SY5Y cell line after lentiviral infection with control plasmid and 0 hours of doxycycline induction, first replicate

value: ctrl BASAL


title: MT_R3

value: Heavy metal soil/Control Temperature 22°C


title: Lung, LPS, p16 neg, 10 weeks, biol rep 2


title: Gravity 10h apo 1


title: MT_R2


title: Lung, PBS, p16 pos, 10 weeks, biol rep 2


title: Microgravity 8h sym 3

value: Microgravity 8h sym


title: Lung, PBS, p16 neg, 10 weeks, biol rep 2


title: MT_R1


title: Microgravity 8h sym 2


title: Lung, LPS, p16 pos, 10 weeks, biol rep 1


title: CC_R3

value: Control soil/Cold Temperature 4°C


title: CC_R2


title: Microgravity 8h apo 3

value: Microgravity 8h apo


title: MC_R3


title: CC_R1


title: Microgravity 8h apo 2


title: Lung, PBS, p16 neg, 10 weeks, biol rep 1


title: Microgravity 8h apo 1


title: CT_R2

value: Control soil/Control Temperature 22°C


title: Gravity 10h apo 2


title: Gravity 8h sym 3

value: Gravity 8h sym


title: K, replicate 1, scRNAseq

city: Beijing

first: Gongxin

last: Peng

address: NO.5 Dongdan Santiao

institute: Peking Union Medical College

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Pancreas

extract_protocol:
Min6 cellswere assigned to 6-well plates at a confluency of 30–70%. A GFP/Puro double-labeled lentiviral expression vector for all K+ channels and a control vector were constructed by OBiO Technology; Min6 cells were then infected with lentivirus (5.0 × 107 pfu) for 72 hours. After transduction, the cells were seeded for seven days under 5 µg/mL puromycin selection. Then, the Cas9 protein was transfected into the cells using Neon transfection system. Control and potassium sample was annalysed by single cell RNA sequencing.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs 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 Ilumina 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 apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Pancreas

value: CRISPR–Cas9-mediated knockout of all 83 K+ channels


title: Microgravity 8h sym 1


title: C, replicate 1, scRNAseq

description: 10x Genomics

value: control vector


title: Gravity 8h sym 2

value: juvenile


title: KO_IVNEG2

city: Scottsdale

first: Henrique

last: Borges da Silva

state: Arizona

address: 13400 E Shea Blvd, 3-364 (Office)

department: Immunology

institute: Mayo Clinic Arizona

data_processing:
DNBSEQ-G50
Sequence reads were trimmed for adaptor sequence/low-quality sequence by the BGI Americas bioinformatics team.
Trimmed sequence reads were mapped to GrCM38/mm10 using HISAT. Clean reads were aligned to the reference genes using Bowtie2.
Read count extraction and normalization were performed by the BGI Americas bioinformatics team.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text files include TPM, FPKM, Read Counts values for each Sample; it also shows log2 fold differences, P-values and Q-Values (FDR) between the indicated groups.

source_name: Lung parenchymal CD4 T cells, P2RX7-KO, 7d post Flu-2W

extract_protocol:
RNA was extracted using the QIAgen RNeasy kit following manufacturer instructions.
RNA samples were submitted to BGI Americas, where libraries were constructed and sequence was done using the DNBSEQ-G50 platform.

treatment_protocol: 2W-tetramer+ CD4+ T cells were sorted from pooled spleens, lung vascular (intravenous CD45+) or lung parenchyma (intravenous CD45-) (n=5 mice per group per replicate) of WT or T cell-specific P2RX7-KO mice (CD4-Cre and CD4-Cre P2RX7fl/fl, respectively) at day 7 post-Flu-2W infection.

value: Lung

value: CD4 T cell

value: 7d post-Flu-2W infection


title: Lung, LPS, p16 neg, 10 weeks, biol rep 1

value: lung

value: alveolar macrophages

value: LPS


title: Gravity 8h apo 3

source_name: Light organ tissue

value: Light organ tissue

value: Gravity 8h apo


title: Gravity 8h sym 1


title: BG3 cells, CapH2 Rep1, RNA-seq

city: Philadelphia

first: Eric

last: Joyce

state: PA

address: 415 Curie Blvd, CRB 570

institute: Perelman School of Medicine, University of Pennsylvania

data_processing:
RNA-seq reads were adapter-trimmed using fastp and aligned to the repeat-masked BG3 assembly with the consensus TE seequences appended.
Alignment was performed using hisat2
Raw read counts for genes and Tes were generated using htseq-count
Assembly: dm6
Supplementary files format and content: BG3_CapH2_DE.csv contains the differentially expressed genes
Supplementary files format and content: BG3_CapH2_NC.csv contains the normalized read counts

growth_protocol: BG3 cells were cultured in M3 media supplemented with 10% FBS and 10ug/mL insulin. Cultures were split 1:4 twice per week.

extract_protocol:
phenol-chloroform extraction
RNA libraries were prepared using Illumina Tru-Seq mRNA stranded kit.

treatment_protocol: 4x106 cells were incubated with 20ug of dsRNA in 1mL of serum-free medium for 30 mins in each well of a six-well plate. After incubation, 3mL of complete medium was added to the cells. Cells were cultured for four days.

value: CapH2 Knockdown


title: WT_IVNEG2

source_name: Lung parenchymal CD4 T cells, WT, 7d post Flu-2W


title: BG3 cells, Brown Rep2, RNA-seq

value: WT


title: Gravity 8h apo 2

extract_protocol: Total RNA was extracted in triplicate from dissected light organs using RNeasy and Qiashredder kits according to the manufacturer’s protocol (Qiagen, Germantown, MD). A minimum of three light organs was used for each replicate RNA extraction. RNA was pooled from a minimum of three separate extractions derived from three different technical replicates of HARV exposure to increase overall genetic variability and to ensure that gene expression results were not based on variability between egg clutches.   RNA quantity was assessed using Qubit 2.0 (Thermo Fisher Scientific, Waltham, MA) and RNA quality was assessed with a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). All samples were normalized to 20 ng per µl of RNA and 100 ng of RNA was run for each sample on the NanoString nCounter MAX system (NanoString Technologies, Seattle, WA).


title: WT_IVNEG1


title: BG3 cells, CapH2 Rep2, RNA-seq


title: KO_IVPOS2

source_name: Lung vascular-associated CD4 T cells, P2RX7-KO, 7d post Flu-2W


title: Lung, PBS, p16 pos, 10 weeks, biol rep 1

value: PBS


title: Gravity 8h apo 1


title: KO_IVPOS1


title: BG3_SLMBKD_rep2_HiC

description:
slmb_merged_dm6.hic
slmb_merged_custombuild.hic

data_processing:
Hi-C reads were processed using HiC-Pro (v.2.11.1) (Servant et al. 2015) to obtain putative interactions with the default parameters, except for LIGATION_SITE = GATCGATC,GANTGATC,GANTANTC,GATCANTC and GENOME_FRAGMENT generated by digest_genome.py using "-r ^GATC G^ANTC" parameters.
HiC-Pro output was converted to .hic files using the hicpro2juicebox.sh utility
Assembly: dm6 and BG3_custom_build (PRJNA1008196)
Supplementary files format and content: .dm6.hic files are aligned to the dm6 genome build
Supplementary files format and content: custombuild.hic files are aligned to the custom_BG3_build (PRJNA1008196)

extract_protocol:
Arima-HiC+ Kit
Kapra Hyper Prep Kit

treatment_protocol: 4x10^6 cells were incubated with 20ug of dsRNA in 1mL of serum-free medium for 30 mins in each well of a six-well plate. After incubation, 3mL of complete medium was added to the cells. Cells were cultured for four days.

value: SLMB Knockdown


title: BG3_SLMBKD_rep1_HiC


title: CT_R1

value: Roots

value: Control soil/Control Temperature 22°C


title: Microgravity 6h sym 2

data_processing: Data were filtered and normalized using nSolver analysis software (v4.0; NanoString Technologies). Background subtraction was performed using the geometric mean of the negative controls and data was normalized using the geometric mean of positive controls and housekeeping genes (actB3 and pyc1). Voom transformation from the limma package (v3.8) in R was applied to the normalized counts. This transformation used the empirical Bayes method by pooling estimates of sample variance to assess the expression level variance within samples and transform data into log2-counts per million (CPM). This method has been shown to be more useful for smaller sample size studies, such as with NanoString assays (Ritchie et al., 2015; Van Laar, Lincoln, & Van Laar, 2018). The voom transformed data were passed to a linear model in the limma package to remove the mean-variance relationship and assess statistically significant differentially expressed genes (Ritchie et al., 2015).

value: Microgravity 6h sym


title: BG3_CapH2KD_rep2_HiC

description:
CapH2_merged_dm6.hic
CapH2_merged_custombuild.hic

value: Cap-H2 Knockdown


title: WT_IVPOS1

source_name: Lung vascular-associated CD4 T cells, WT, 7d post Flu-2W


title: CT_R3


title: KO_IVNEG1


title: BG3_CapH2KD_rep1_HiC


title: Microgravity 6h apo 3

value: juvenile

value: Microgravity 6h apo


title: BG3 cells, Brown Rep1, RNA-seq


title: SPLKO2

source_name: Spleen CD4 T cells, P2RX7-KO, 7d post Flu-2W

value: Spleen

value: CD4 T cell


title: BG3_BrownKD_rep2_HiC

description:
brown_merged_dm6.hic
brown_merged_custombuild.hic

value: Brown Knockdown


title: WT_IVPOS2

value: Lung

value: 7d post-Flu-2W infection


title: Microgravity 6h sym 3

value: Light organ tissue


title: Microgravity 6h apo 2


title: SPLKO1


title: SPLWT2

source_name: Spleen CD4 T cells, WT, 7d post Flu-2W


title: BG3_BrownKD_rep1_HiC


title: SPLWT1


title: Gravity 6h sym 3

value: Gravity 6h sym


title: Microgravity 6h apo 1


title: P:C_0.70_Rep1

city: Cambridge

first: Soumen

last: Khan

address: Babraham Hall

department: Epigenetics

institute: Babraham Institute

data_processing:
Reads were trimmed using Trim Galore and aligned to the Drosophila genome (BDGP6) using Hisat2 with deafult settings
Aligned reads were converted to BAM format using Samtools. Unmapped, discordant and secondary alignments were filtered (samtools view -F 0x256 -F 0x4 -F 0x8 )
Raw reads analysed using Seqmonk and raw counts calculated
Differentially expressed genes list identified using the DESeq2
Assembly: BDGP6
Supplementary files format and content: Tab delimited file containing raw counts for all samples

source_name: whole drosophila

growth_protocol: The flies for the experiment originated from a large, outbred Baseline Population (BP), maintained at 25°C with a 14-day generation cycle, fed a baseline diet of corn, sugar, and yeast with a protein-to-carbohydrate ratio 0.4. The population's growth involved collecting approximately 300 eggs every generation in seven bottles, transferring the emerging adults to a cage, and initiating the next generation from eggs laid on a fresh media plate.

extract_protocol:
On the 13th day after egg collection, Female flies were collected and snap frozen in Trizol. RNA was isolated using Trizol based extraction. RNA quality and quantity was checked on Bioanalyzer (Agilent Bioystems) as well as TapeStation (Agilent Biosystems)
100ng of Total RNA was taken for mRNA isolation, fragmentation and priming. The fragmented and primed mRNA was further subjected to first strand synthesis followed by second strand synthesis. The double stranded cDNA was purified using NEBNext Sample Purification Beads. The purified cDNA was end-repaired, adenylated and ligated to Illumina multiplex barcode adapters as per NEBNext Ultra II RNA Library Prep Kit for Illumina protocol.

treatment_protocol: Five isocaloric treatment diets with distinct P:C ratios: 0.2, 0.25, 0.4, 0.55, and 0.7. These ratios were adjusted by modifying the amounts of sugar and yeast in the food, while maintaining consistent caloric values (see Table S1 for exact recipes). The P:C 0.4 diet matches the baseline, P:C 0.2 represents the maximum carbohydrate and minimum protein, and P:C 0.7 is the converse.

value: whole drosophila

value: female

tag: dietary condition

tag: time point

value: on the 13th day post egg collection


title: Gravity 6h sym 2

tag: tissue


title: Ifnar_LPS_LPS1.5h

city: Los Angeles

first: Carolina

last: Chavez

address: 10833 LeConte Ave

institute: UCLA

data_processing:
Samples were sequenced on DNBSEQ-G400 (100bp).
Raw data was filtered for adapter sequences or low-quality sequences using SOAPnuke. Reads were aligned to the mm10 genome using STAR.
Aligned reads were filtered based on mapping score (MAPQ ≥ 30) using Samtools.
Transcript read counts were computed using the featureCounts function in the Subread package.
Assembly: mm10
Supplementary files format and content: Raw count tables are provided (unnormalized).

growth_protocol: BMDMs were generated by isolating bone marrow from the femurs and tibias of age and sex-matched mice. Bone marrow cells were incubated in L929-conditioned media (RPMI + 30% L929 media, 10% FBS, 100 IU/ml penicillin, 100 ug/ml streptomycin, 2 mM L-glutamine, 55 µM 2-mercaptoethanol) at 37C in 15cm plates. On Day 4, cells were detached using a cell lifter and replated into experimental culture plates.

extract_protocol:
Cells were lysed with TRIzol reagent (Life Technologies), and total RNA was purified using DIRECTzol RNA miniprep kit (Zymo Research).
RNA samples were submitted to BGI Genomics for selection of polyadenylated RNA and paired-end library preparation.

treatment_protocol: Cells were stimulated on Day 7 with PBS, IFNγ (100ng/mL), or LPS (100 ng/mL) for 8 hours, the stimulus was removed, and after 66 hours the cells were re-challenged with LPS (0.1ng/mL) for 0, 1.5, or 3 hours.

value: Ifnar-/-

value: bone marrow-derived macrophage

value: LPS 100ng/mL + LPS 0.1 ng/mL


title: Gravity 6h sym 1


title: Gravity 6h apo 3

value: Gravity 6h apo


title: P:C_0.55_Rep3


title: Microgravity 6h sym 1

value: Microgravity 6h sym


title: Ifnar_LPS_LPS0h


title: P:C_0.55_Rep2


title: Gravity 6h apo 2

value: juvenile


title: Ifnar_PBS_LPS3h

value: PBS + LPS 0.1ng/mL


title: P:C_0.55_Rep1


title: Gravity 6h apo 1


title: P:C_0.40_Rep3


title: Ifnar_PBS_LPS0h


title: Microgravity 2h sym 3

value: Microgravity 2h sym


title: P:C_0.70_Rep3


title: Microgravity 2h sym 2


title: Irf1_IFNg_LPS3h

value: IFNgamma 100 ng/mL + LPS 0.1 ng/mL


title: P:C_0.70_Rep2


title: P:C_0.40_Rep2


title: Irf1_IFNg_LPS1.5h


title: P:C_0.40_Rep1


title: Ifnar_LPS_LPS3h


title: P:C_0.25_Rep3


title: Irf1_IFNg_LPS0h


title: Microgravity 2h sym 1


title: P:C_0.25_Rep2


title: Irf1_LPS_LPS3h


title: Microgravity 2h apo 2

value: Microgravity 2h apo


title: Microgravity 2h apo 1


title: P:C_0.25_Rep1


title: Irf1_LPS_LPS1.5h


title: IgG Rep2 Human endometrial stromal cells, Cut & Run

city: Houston

first: Hari

middle: Krishna

last: Yalamanchili

state: Texas

address: 1250 Moursund St

department: Pediatrics

institute: Children’s Nutrition Research Center

data_processing:
*library strategy: Cut & Run
Raw fastq files were processed to remove adapters from sequenced reads using Trimmomatic v 0.39 (2:15:4:4: true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:25) with the Truseq3.PE.fa adapter library, and then trimmed again using the kseq script
Quality of trimmed reads was assessed using FastQC v0.11.9. Reads were aligned to both the hg38 (GENCODE GRCh38.p14 primary assembly release 43) and spike-in Ecoli K12 genomes (GCF_000005845.2_ASM584v2), using bowtie2 version 2.4.2 (--dovetail --phred33)
BAM files of aligned reads were converted to BED files, and then bedgraphs, using BEDTools v2.30.0
Blacklisted regions, from the hg38 blacklist downloaded from CUT & RUN Tools, were removed from the BED files. Each sample was normalized to its internal Ecoli spike-in using the spike_in_calibration.sh
Spike-in normalized bedgraphs were converted to bigwigs using the UCSC bedGraphToBigWig utility. Integrated Genome Viewer (IGV) v2.11.1 was used to examine spike-in normalized bigwig tracks at individual loci
GREB1 peaks were identified using MACS2 with a p-adjusted (qValue) cutoff of 0.05. PR peaks were identified in a previous study, also using MACS2 with a p-adjusted (qValue) cutoff of. 0.01. Overlapping peaks were identified using BEDTools, with the overlap defined as 1 bp. Peak-associated genes were identified as peaks within 5 kb of the TSS of a gene. BigWigs of individual replicates were merged using wiggletools and UCSC utilities wigToBigWig. Merged bigwigs were used to generate a heatmap of CUT& RUN peaks with deeptools v 3.5.4
Assembly: hg38 (GENCODE GRCh38.p14 primary assembly release 43)
Supplementary files format and content: bigwigs

source_name: Primary endometrial stromal cells

growth_protocol: DMEM/F-12 media containing 10% FBS, 100 units/ml penicillin and 0.1 mg/ml streptomycin

extract_protocol:
Overexpressed cells were collected by trypsin digestion and frozen viably in the freezing medium (90% FBS with 10% DMSO) until experiment day. A total of 10 x 106 cells were incubated with IgG, and GREB1 antibody and processed further following the CUT&RUN Assays (Epicypher) manual
Sequencing libraries were prepared using NEBNext Ultra II DNA Library Prep Kit (New England BioLabs, Cat #E7645). Paired end 150 bp sequencing was performed on a NEXTSeq550 (Illumina) platform and each sample was targeted for 10-15 million reads

treatment_protocol: Human endometrial stromal cells were overexpressed with GREB1 plasmid construct (Genecopoeia, catalogue number: EX-Y4970-M91) and then treated with MPA for 4 hr

value: Primary endometrial stromal cells

value: stromal cells

value: MPA TREATMENT


title: Ifnar_PBS_LPS1.5h


title: Irf1_LPS_LPS0h


title: Gravity 2h sym 3

first: Alexandrea

last: Duscher

address: 1730 Sawgrass Pointe Dr

institute: University of Florida

value: Light organ tissue

value: Gravity 2h sym


title: IgG Rep1 Human endometrial stromal cells, Cut & Run


title: Gravity 2h sym 2


title: Irf1_PBS_LPS3h


title: Irf1_PBS_LPS1.5h


title: GREB1 Rep2 Human endometrial stromal cells, Cut & Run


title: Gravity 2h sym 1


title: GREB1 Rep1 Human endometrial stromal cells, Cut & Run


title: Gravity 2h apo 2

value: Gravity 2h apo


title: Irf1_PBS_LPS0h


title: Gravity 2h apo 3


title: MARV_40h_3

city: Frankfurt am Main

first: Benjamin

middle: Florian

last: Koch

address: Theodor-Stern-Kai 7

department: Nephrology

institute: Goethe University Hospital

data_processing:
Basecalls performed using CASAVA version 1.4 and
Illumina BCL files were converted to FASTQ by bcl-convert.
Next FASTQ reads were aligned to a human reference genome (GRCh38.p12 cDNA) index by kallisto (version 0.46.1).
Afterwards Omics Playground (version 2.8.5., Akhmedov et al. NAR Genomics and Bioinformatics 2020;2:lqz019) was employed for differential expression analysis  (adjusted p-value (q-value) <0.05).
Assembly: hg38
Supplementary files format and content: tab-separated (tsv) value files containing kallisto TPM -and gene counts for each sample
Supplementary files format and content: as well as the Omics Playground output file from differential expression analysis (xslx).

source_name: Primary proximal tubular cells

extract_protocol:
Total RNA was extracted 20 and 40 hours post infection by Qiagen RNeasy Maxi Kit (Qiagen, Germany), including on-column removal of DNA by digestion with rDNase for 15 min at room temperature, and 1000 ng (each showing a RIN score from >9) were used for library preparation.
After depletion of ribosomal RNA (NEBNext rRNA Depletion Kit, #E6310, New England Biolabs, Germany) directional libraries were prepared with a NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® sequencing (#E7420S, New England Biolabs, Germany).

treatment_protocol: PTC grown in 6-well plates were either left uninfected or were infected with MARV(musoke-80) at a MOI = 1

value: Primary proximal tubular cells

value: infected 40h


title: WT_IFNg_LPS1.5h

value: WT

value: bone marrow-derived macrophage


title: Microgravity 2h apo 3

city: Hayes


title: MARV_40h_1


title: Gravity 2h apo 1


title: WT_IFNg_LPS3h


title: AK-10_3

city: Busan

first: Jungwook

last: Park

address: Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 609-735, Korea

department: Microbiology

country: South Korea

institute: Pusan National University

description: Korean fir seedlings treated with Aureobasidium pullulans AK10 to induce stress tolerance

data_processing:
Raw fastq.gz reads were refined using the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Raw fastq.gz reads were refined by eliminating sequences with suboptimal quality scores. A bespoke Python script ensured the alignment of the forward and reverse reads.
Curated reads were mapped to the reference genome using the Burrows-Wheeler Aligner (BWA), employing the maximal exact match approach.
Using SAMtools, we converted the mapping outcome from SAM to BAM format and sorted it according to genomic coordinates.
The Subread package and featureCounts tool tallied the reads for each coding sequence.
Gene transcript levels were assessed using the RPKM metric.
Assembly: Pseudotsuga menziesii GCA_001517045.1
Supplementary files format and content: txt: tab-delimited text files include RPKM values for each sample

organism: Abies koreana

source_name: seedlings

growth_protocol: Three-year-old A. koreana seedlings were obtained, and maintained in a greenhouse at 25 ± 5°C with daily watering. Drought stress was simulated by withholding water. The AK10 treatment was performed by culturing in yeast extract peptone dextrose (YPD) broth for 24 h at 25°C under constant agitation.

extract_protocol:
After surface sterilization with 70% ethanol and rinsing, 1 g of leaf tissue was ground in liquid nitrogen and homogenized in 15 mL of extraction buffer (100 mM Tris-HCl, 2% CTAB, 30 mM ethylenediaminetetraacetic acid, 2 M NaCl, 0.05% spermidine, 2% polyvinylpolypyrrolidinone, 2% 2-mercaptoethanol, and 1.5 mg/mL proteinase K). After incubation at 42°C for 90 min and chloroform-isoamyl alcohol extraction, RNAs were precipitated with 10 M LiCl, washed with ethanol, and resuspended in diethylpyrocarbonate-treated water.
Using the TruSeq RNA Sample Preparation Kit (Illumina, CA, USA), 1 µg of total RNAs was processed to produce cDNA libraries. These libraries were sequenced on a HiSeq 2000 platform (Illumina) by Macrogen (Seoul, Korea), generating 101-bp paired-end reads.

treatment_protocol: After adjusting the optical density of the AK-10 culture to 0.8, Tween-20 was added to a final concentration of 250 µg/mL. This mixture was foliar-sprayed onto seedlings three times: 7 d before, 4 d before, and 4 d after the initiation of drought stress. A control treatment was YPD broth with 250 µg/mL Tween-20.

tag: stress

value: drought stress

value: Aureobasidium pullulans AK10

tag: age

value: three-years-old

value: wild type

value: seedlings


title: WT_LPS_LPS1.5h

tag: treatment

value: LPS 100ng/mL + LPS 0.1 ng/mL


title: WT_LPS_LPS3h


title: MARV_20h_2

value: infected 20h


title: AK-10_1


title: AK-10_2


title: MARV_20h_1


title: WT_LPS_LPS0h


title: stress_3

description: Korean fir seedlings under the drought stress state

value: YPD broth with 250 microg/mL Tween-20


title: mock_3

value: untreated


title: WT_PBS_LPS3h

value: PBS + LPS 0.1ng/mL


title: stress_2


title: Gravity 12h apo 3

value: juvenile

value: Light organ tissue

value: Gravity 12h apo


title: WT_PBS_LPS1.5h


title: stress_1


title: mock_1

value: Primary proximal tubular cells


title: WT_PBS_LPS0h


title: WT_IFNg_LPS0h

value: IFNgamma 100 ng/mL + LPS 0.1 ng/mL


title: MARV_40h_2

value: infected 40h


title: MARV_20h_3


title: Tape_stripped_skin_replicate_IL22KO_2

status: Public on Feb 13 2024

city: Boston

first: Manuel

last: Leyva-Castillo

state: MA

address: 300 Longwood Ave

institute: Boston Children's Hospital

data_processing:
Run metrics, read alignment and detection of on-target transcripts was done using Torrent Suite Software 5.12.1 according to standard analysis procedures
CHP files were generated using Ion AmpliSeq RNA plug-in
N/A
N/A
N/A
Assembly: mm9
Supplementary files format and content: CHP format. Processed data files (.chp) contain normalized counts (read per million) .
Supplementary files format and content: N/A

source_name: skin

extract_protocol:
Total RNA extraction was performed using RNeasy Mini Kit (Qiagen) and RNA was retrotranscribed using SuperScript VILO cDNA Synthesis Kit (ThermoFisher Scientific)
cDNA libraries were prepare using Ion AmpliSeqTM Transcriptome Mouse Gene Expression Panel, Chef-Ready Kit in the the Ion Chef System

treatment_protocol: Skin samples were stored in RNAlater and store at -80 C until RNA extraction

value: skin

value: IL22 deficient

value: Tape stripped


title: Tape_stripped_skin_replicate_IL22KO_3


title: Tape_stripped_skin_replicate_Mcpt8+/+_3


title: Tape_stripped_skin_replicate_IL22KO_4


title: Tape_stripped_skin_replicate_Mcpt8+/+_1


title: Tape_stripped_skin_replicate_Mcpt8DTR/+_1


title: Tape_stripped_skin_replicate_Mcpt8DTR/+_2


title: Tape_stripped_skin_replicate_Mcpt8DTR/+_3


title: Tape_stripped_skin_replicate_Mcpt8+/+_2


title: Tape_stripped_skin_replicate_IL17KO_3

value: IL17 deficient


title: Tape_stripped_skin_replicate_IL17KO_2


title: Tape_stripped_skin_replicate_IL17KO_1


title: Tape_stripped_skin_replicate_IL17KO_4


title: Tape_stripped_skin_replicate_WT_3

value: WT Balb/c


title: Hxk2, IgG control, rep3

city: Merced

first: Clarissa

last: Nobile

address: 5200 N Lake road

department: Molecular and Cell Biology

institute: University of California MERCED

data_processing:
CUT&RUN analysis workflow (doi:10.3791/63655)
FastQ quality check with FastQC version 0.11.9
Adapter trimming with cutadapt version 3.5
Alignment to Candida albicans genome assembly 21 using Bowtie2 version 2.4.4
Remove PCR duplicated reads using MarkDuplicates function of Picard version 2.26.6
Filter reads less than 20 bp and greater than 120 bp in length using SamTools version 1.14
Subsample reads from GFP or IgG samples based on E. coli read count in each paired sample using SamTools version 1.14
Peaks were called using Macs2 version 2.2.7.1
Assembly: ASM18296v3
Supplementary files format and content: narrowPeak files  generated using from Macs2 version 2.2.7.1 during peak calling step
Library strategy: CUT&RUN

organism: Candida albicans

source_name: planktonic

growth_protocol: Precultured GFP-tagged Hxk1 and GFP-tagged Hxk2 strains in SC (synthetic complete) + glycerol (3%) overnight at 30°C. After 16 hours, transfered the cells to fresh SC glycerol with an OD of 0.3. Added 2% glucose to cells when cells were OD = 1.0. Collected cells after 20 minutes.

extract_protocol:
Nuclei isolation using zymolyase. TF-DNA complex were isolated with antibody.
Libraries were prepared using the NEBNextUltra II DNA Library Prepkit. Briefly, DNA was end-repaired and adapter ligated. After a DNA clean-up without size-selection, PCR enrichment of adapter-ligated samples was performed. After a second round of DNA clean-up, libraries are size selected by Polyacrylamide Gel Electrophoresis and cleaned up for sequencing.

value: planktonic

tag: strain

tag: cut&run antibody

value: Rabbit IgG negative control antibody (Epicypher:cat# 13-0042)


title: Hxk2, IgG control, rep2

tag: cell type


title: mock_2


title: Hxk2, IgG control, rep1