title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 108

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_108
sci-RNA-seq3
L1_rice_combined.RData


title: RBEC_OGDR_3

status: Public on Jul 01 2025

type: SRA

city: Szeged

first: Maria

last: Deli

address: Temesvari krt. 62.

department: Institute of Biophysics

country: Hungary

institute: HUN-REN Biological Research Centre

description: Library name: CTR3

library_source: transcriptomic

data_processing:
Unprocessed sequencing reads were adapter-trimmed and quality-trimmed using Cutadapt (3.4). FastQC (0.11.9) was used to assess the quality of sequencing reads.
Cleaned reads were mapped to the reference genome using STAR (2.7.10a), allowing for spliced alignments.
Quantification of mapped reads to each gene was performed STAR (2.7.10a]) and RSEM (1.3.3).
Raw counts were TPM-normalized by dividing each count with the sum of all counts for each sample multiplied by one million
Differential expression analysis was performed using DESeq2 (version 1.38)
Assembly: Rnor_6.0
Supplementary files format and content: Excel file including all raw counts for each sample
Supplementary files format and content: Excel file including all TPM normalized counts for each sample

molecule: total RNA

organism: Rattus norvegicus

source_name: primary brain endothelial cell

extract_protocol:
Total RNA was extracted by column based extraction kit (Zymo)
RNA-Seq libraries (NEBNext Ultra II Directional) were prepared according to the manual of the manufacturers. Summarized, enriched poly-Adenylated mRNA is fragmented, followed by cDNA synthesis using random hexamers. The cDNA fragments undergo end repair, A-tailing followed by ligation of Illumina P5 and P7 adapters. After PCR amplification using a minimum number of cycles, purification by SPRI beads, the quality of the libraries was controlled for size-distribution and quantity. Sequencing was performed on an Illumina NEXTSEQ 500 instrument with 1x75 bps.

tag: cell type

value: primary brain endothelial cell


title: Control,Day90-4

city: chengdu

first: lixin

last: gong

address: No. 4, North Fourth Section, Second Ring Road

country: China

institute: The Second Affiliated Hospital of Chengdu Medical College Nuclear Industry 416 Hospital

data_processing:
After obtaining the clean reads, we use Bowtie2 to align the clean reads to the reference genome sequence.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text file includes raw count for each Sample
Supplementary files format and content: tab-delimited text file includes raw RPKM values foe each Sample

organism: Mus musculus

source_name: Lung

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manual instructions. For tissue samples, grind about 60mg with liquid nitrogen into powder and transfer the powder samples into the 2ml tube contains 1.5ml Trizol reagent. The mix was centrifuge at 12000×g for 5min at 4°C. The supernatant was transferred to a new 2.0ml tube which was added 0.3ml of Chloroform/isoamyl alcohol (24:1) per 1.5ml of Trizol reagent. After the mix was centrifuged at 12000×g for 10min at 4°C, the aqueous phase was transferred to a new 1.5mL tube which was add equal volume of supernatant of isopropyl alcohol. The mix was centrifuged at 12000×g for 20min at 4°C and then removed the supernatant. After washed with 1ml 75% ethanol, the RNA pellet was air-dried in the biosafety cabinet and then dissolved by add 25µL~100µL of DEPC-treated water. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Library was prepared with 1 μg total RNA for each sample. Total RNA was purified by electrophoretic separation on a 15% urea denaturing polyacrylamide gel electrophoresis (PAGE) gel and small RNA regions corresponding to the 18–30 nt bands in the marker lane (14-30 ssRNA Ladder Marker, TAKARA) were excised and recovered. Then the 18–30 nt small RNAs were ligated to a 5′-adaptor and a 3′-adaptor. The adapter-ligated small RNAs were subsequently transcribed into cDNA by SuperScript II Reverse Transcriptase (Invitrogen, USA) and then several rounds of PCR amplification with PCR Primer Cocktail and PCR Mix were performed to enrich the cDNA fragments. The PCR products were selected by agarose gel electrophoresis with target fragments 100~120 bp, and then purified by QIAquick Gel Extraction Kit (QIAGEN, Valencia, CA). The library was quality and quantitated in two methods: check the distribution of the fragments size using the Agilent 2100 bioanalyzer, and quantify the library using real-time quantitative PCR (QPCR) (TaqMan Probe). The final ligation PCR products were sequenced using the BGISEQ-500 platform (BGI-Shenzhen, China).

tag: tissue

value: Lung

tag: time point

tag: agent

value: Control


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 103

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_103
sci-RNA-seq3
L1_rice_combined.RData

data_processing:
Demultiplexing, barcoded processing, and gene counting were preformed using the Cell Ranger software. Data filtering was performed with Seurat
Assembly: Os-Nipponbare-Reference-IRGSP-1.0  and Sorghum bicolor v3.0.1
Supplementary files format and content: Seurat object
Library strategy: sci-RNA-seq3

molecule: nuclear RNA

organism: Sorghum bicolor

source_name: seedling

growth_protocol: 5 day old seedlings grown on soil were exposed to light and harvested at different time points during de-etiolation.

extract_protocol:
Frozen tissue from each time point was crushed using a bead bashing approach, and nuclei released from homogenate by resuspending in Nuclei Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2). The resulting suspension was passed through a 30-um filter. To enrich the filtered solution for nuclei, an Optiprep (Sigma) gradient was used. Enriched nuclei were then stained with Hoechst, before being FACS purified.
Library construction was performed according to the manufacturer's specification (Chromium Next GEM Single Cell 3' HT Kit v3.0, 10x Genomics)

value: seedling

tag: age


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 106

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_106
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 102

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_102
sci-RNA-seq3
L1_rice_combined.RData


title: CRISPR_T2

city: Shanghai

first: Xianghuo

last: He

address: No 270, Dong An Road

institute: Fudan University

library_source: genomic

data_processing:
For ChIP-seq assays, raw FASTQ ﬁles were trimmed for adaptor sequence and low-quality bases, then mapped to hg38 whole genome using Bowtie with standard alignment parameters. For RNA-seq assays, the paired-end reads were aligned to hg38 using STAR. After calculating raw gene expression levels (raw read counts) with FeatureCounts, normalized profiling data were obtained with DESeq2 for differential expression analysis.
For CRISPR screening, the raw FASTQ ﬁles were demultiplexed using Geneious 7.0 (Biomatters Inc.) and processed such that they contained only the unique sgRNA sequence. The designed barcode sequences from the library were assembled into a mapping reference sequence to align the processed reads to the library. The reads were then aligned to the reference sequence using the "Map to Reference" function in Geneious 7.0. After alignment, the number of uniquely aligned reads for each library sequence was calculated. The number of reads of each unique sgRNA for a certain sample was normalized as follows: normalized read counts per unique barcode = reads per barcode/total reads for all barcodes in the sample × 10^6 + 1. The sgRNA score was generated and ranked according to the depletion or enrichment of the normalized sgRNA counts (Sequence_results_T_vs_C.xlsx).
For ChIP-seq assays, bam files were converted to BigWig files using deepTools.
For ChIP-seq assays, peaks were identified using the MACS2 peak caller with the following parameters: -t treatment -c input –f BAMPE –keep-dup all –g hs –q 0.01
Assembly: For RNA-seq and ChIP-seq assays, hg38. For CRISPR screening, the reads were aligned to the reference sequence of the library.
Supplementary files format and content: peak files were generated using MACS2.

molecule: genomic DNA

organism: Homo sapiens

source_name: liver

growth_protocol: HUH7 was cultured in DMEM (Invitrogen, CA, USA) supplemented with 10% fetal bovine serum (FBS) (Gibco, CA, USA) and antibiotics in an incubator at 37°C with 5% CO2.

extract_protocol:
ChIP-seq was performed as described previously (Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT.  ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions.  Methods.2009;48:240-8)；
Total RNA extracted using TRIzol was used for library preparation with an Illumina mRNA sequencing (mRNAseq) sample preparation kit.  Quality control of the RNA sequencing libraries was performed using a Bioanalyzer 2100 (Agilent, CA, USA) prior to paired-end sequencing on the HiSeq 6000 platform (Illumina, CA, USA);  ChIP-seq was performed according to the manufacturer’s protocol (NEB, Shanghai, China). For CRISPR screening, Genomic DNA of day 0 cell samples and xenograft tumor samples were extracted with the Qiagen Blood & Cell Culture Midi Kit (Qiagen, Hilden, Germany). SgRNA cassettes were amplified from genomic DNA samples as the ﬁrst PCR, the amplicons resulting from the second PCR were extracted with beads (Beckman Coulter, USA), quantiﬁed, mixed, and sequenced using a NextSeq 500 instrument (Illumina, USA).

treatment_protocol: siRNAs targeting DDX41 and negative control siRNAs (NC) were procured from RiboBio (Guangzhou, China).  Cells were transfected with the specified targeted or control siRNA  using Lipofectamine RNAiMAX reagent (Invitrogen, CA, USA).  After 48 hours of transfection, the cells were collected for further experiments.HUH7 cells with stable overexpression of Flag-DDX41, Flag-RNASEH1-Mu (for R-ChIP assay), Flag-NR2C1, Flag-NR2C2 were collected for further experiments. For CRISPR screening, customized library containing 4992 sgRNAs specifically targeting 832 transcription factor (TF) and chromatin regulator (CR) genes (6 sgRNAs per gene), with 500 negative control sgRNAs and 12 positive control sgRNAs for 2 validated oncogenes. HUH7 cells were transduced with the pooled sgRNA lentiviral library at a low MOI value of 0.3. After 7 days of puromycin (Invitrogen, USA) selection (5 μg/ml), the surviving cells were considered to be the day 0 sample, and 3×10^7 of these cells were stored for further processing. The remaining cells were counted, and 1×10^7 cells per mouse were subcutaneously injected into NOD/Scidil2Rγ-/- (NSG) mice for xenograft tumor formation. Genomic DNA of day 0 cell samples (C1-C5) and xenograft tumor samples (T1-T5) were extracted and amplified for sequencing.

value: liver

tag: cell line

value: HCC cells

tag: genotype

tag: treatment

value: HUH7 cell stable transfected with Cas9-GFP-Luc and sgRNA library lentivirus


title: Control,Day90-3


title: Control,Day90-1


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 100

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_100
sci-RNA-seq3
L1_rice_combined.RData


title: CRISPR_T1


title: CRISPR_C5


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 101

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_101
sci-RNA-seq3
L1_rice_combined.RData


title: RBEC_normoxia_6

description: Library name: N6


title: CRISPR_C4


title: RBEC_OGDR_1

description: Library name: CTR1


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 099

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_099
sci-RNA-seq3
L1_rice_combined.RData


title: Control,Day14-4


title: Control,Day180-3


title: CRISPR_C3


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 098

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_098
sci-RNA-seq3
L1_rice_combined.RData


title: Control,Day14-3


title: CRISPR_C2


title: RBEC_normoxia_5

description: Library name: N5


title: RBEC_normoxia_4

description: Library name: N4


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 097

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_097
sci-RNA-seq3
L1_rice_combined.RData


title: CRISPR_C1


title: Control,Day14-2


title: Control,Day90-2


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 096

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_096
sci-RNA-seq3
L1_rice_combined.RData


title: RBEC_OGDR_2

description: Library name: CTR2


title: RBEC_normoxia_3

description: Library name: N3


title: RBEC_normoxia_2

description: Library name: N2


title: Ser3_cladeI_PT_time20_replicate3

city: ORLANDO

first: Taj

last: Azarian

state: FL

address: 6700 Lake Nona Blvd

institute: University of Central Florida

data_processing:
Quality of RNA sequencing data was assessed using FastQC 0.11.9, and reads with low quality or high N content were filtered out using fastp with default setting
Assembly: Filtered reads were then mapped to the S. pneumoniae serotype 3 SPN-OXC141 reference genome (NCBI GenBank: FQ312027.1) using Bowtie2 v2.4.5, and the number of reads mapped to each gene were counted using featureCounts
Supplementary files format and content: tab-delimited text including raw count for each strain

organism: Streptococcus pneumoniae

source_name: cultures

extract_protocol:
Cultures were then centrifuged at 5000g for 10 mins. The pellet was resuspended in Buffer RLT and transferred to a MP biomedicals Lysing matrix B tube. Bacterial cells were disrupted in the TissueLyser (Qiagen) for 5 mins at 30Hz and supernatant was used as lysate input into the Qiagen RNeasy mini kit.
Purified RNA was measured using Qubit and stored at -80℃. cDNA libraries were made using Illumina stranded RNA library preparation kits with RiboZero Plus rRNA depletion.
Libraries were sequenced on NextSeq 550 to a target depth of 12M paired end reads (2x50bp) per sample.

value: cultures

tag: strain

value: Strain that belong to clade I of Clonal Complex 180

value: Serotype 3


title: Ramos cell line, control, grown in atmospheric oxygen, replicate 1

city: Prague

first: Pavel

last: Klener

address: U Nemocnice 5

country: Czech Republic

institute: Institute of Pathological Physiology First Faculty of Medicine, Charles University

data_processing:
Read pairs were mapped to the hg19 reference genome with TopHat2
Сounts were obtained using HTSeq
Differential expression was assessed using a EdgeR, limma and fastgsea R packages
Assembly: GRCh37.p13
Supplementary files format and content: Processed files are provided in the gene counts format

source_name: Ramos

growth_protocol: Cells were grown in IMDM supplemented with 15% Fetal Bovine Serum and pen/strep. Controls were grown in 5% CO2 and atmospheric oxygen.

extract_protocol:
The RNA was isolated using RNeasy® Mini Kit (QIAGEN)
The libraries were prepared using Agilent SureSelect mRNA Strand Specific kit

treatment_protocol: Hypoxia-adapted cells were grown in the same medium as controls, under 1% O2 and 5% CO2.

value: Ramos

value: Burkitt lymphoma

tag: phenotype

value: control

value: atmospheric oxygen


title: RBEC_normoxia_1

description: Library name: N1


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 095

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_095
sci-RNA-seq3
L1_rice_combined.RData


title: Ramos cell line, adapted to hypoxia, grown in 1% oxygen, replicate 2

value: adapted to hypoxia

value: 1% oxygen


title: Ramos cell line, control, grown in atmospheric oxygen, replicate 2


title: Ser3_cladeI_PT_time20_replicate1


title: SLS3_S16

city: Paris

first: Chloé

last: Talarmin-Gas

state: Ile de France

address: 2, rue ambroise Paré

department: Biochemistry

country: France

institute: APHP

description:
Library name: SAMPLE 18
SLS3_S16.resultsRSEM.genes.results

data_processing:
Fastq files were aligned using STAR algorithm (version 2.7.6a), on the Ensembl release 104, Caenorhabditis elegans WBcel23581.
Reads were counted with RSEM (v1.3.1) and statistical analyses were performed with R Core Team83 (2015, version 3.6.3), platform: x86_64-pc-linux-gnu (64-bit) and DESeq284 (DESeq2_1.26.0) to determine the proportion of differentially expressed genes (DEGs) between two conditions.
The standard DESeq2 normalization method (DESeq2’s median of ratios with the DESeq function) was used, with a pre-filter of reads and genes (reads uniquely mapped on the genome, or up to 10 different loci with a count adjustment, and genes with at least 10 reads in at least 3 different samples85).
The Wald test with the contrast function and Benjamini-Hochberg FDR control procedure was used to identify DEGs (adjusted p-value < 0.05). The R scripts and parameters used in this study are freely available on GitHub (https://github.com/BSGenomique/genomic-rnaseq-pipeline/releases/tag/v1.0420).
The standard DESeq2 normalization method (DESeq2’s median of ratios with the DESeq function) was used.
Assembly: Ensembl release 104, Caenorhabditis elegans Wbcel 235
Supplementary files format and content: tab-delimited text file includes raw counts (RSEMresults) and names for all the samples

organism: Caenorhabditis elegans

source_name: Wild-type strain

growth_protocol: All strains were cultured at 20°C on nematode growth medium (NGM) agar plates seeded with E.coli OP50 in lysogeny broth (LB) (referred to as NGM agar/OP50). Unless specifically stated, prior to each experiment, worms were synchronized with a bleaching solution [0,5N NaOH and 3% solution of sodium hypochlorite in M9 buffer77 (22 mM KH2PO4, 42 mM Na2HPO4, 86 mM NaCl, 1 mM MgSO4) and the larval stage was visually assessed under a S9E binocular stereo microscope (Leica, Wetzlar, Germany). To prepare NGM/chemical agar plates, a selected chemical (POE, SLS, FA, BR or MIT) was added to cooling NGM agar at a temperature of < 60°C after autoclaving and prior to pouring at a concentration of 0.01% w/v. NGM/FA plates were also prepared with concentrations of 0.001% w/v and 0.02% w/v. Worms were then transferred onto fresh NGM control (C) or chemical agar plates for 24h, after which they were directly prepared for RNA extraction.

extract_protocol:
Total RNA was extracted from approximately 300 L4 stage worms using TRIzol® (Thermo Fisher Scientific, Waltham, MA) according to the manufacturer’s protocol. RNA quantification and purity assessment were performed using a NanoDrop™ 2000 (Thermo Fisher Scientific) and the RNA quality assessment using a 2100 Bioanalyzer (Agilent Technologies).
library(biomaRt) library(tximport) library(readr) library(DESeq2) library(reshape) library(ggplot2) library(RColorBrewer) library(pheatmap) library(ggrepel) library(factoextra)

value: Wild-type strain

tag: developmental stage

value: L4 stage

value: N2 Bristol

value: WT

value: Sodium lauryl sulfate


title: Ramos cell line, adapted to hypoxia, grown in 1% oxygen, replicate 1


title: Control,Day14-1

value: Lung

value: Control


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 093

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_093
sci-RNA-seq3
L1_rice_combined.RData

value: seedling


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 092

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_092
sci-RNA-seq3
L1_rice_combined.RData


title: SLS2_S10

description:
Library name: SAMPLE 17
SLS2_S10.resultsRSEM.genes.results

treatment_protocol: To prepare NGM/chemical agar plates, a selected chemical (POE, SLS, FA, BR or MIT) was added to cooling NGM agar at a temperature of < 60°C after autoclaving and prior to pouring at a concentration of 0.01% w/v. NGM/FA plates were also prepared with concentrations of 0.001% w/v and 0.02% w/v. Worms were then transferred onto fresh NGM control (C) or chemical agar plates for 24h, after which they were directly prepared for RNA extraction.


title: Ser3_cladeI_PT_time15_replicate3

value: cultures


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 094

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_094
sci-RNA-seq3
L1_rice_combined.RData


title: HBL2 cell line, control, grown in atmospheric oxygen, replicate 2

value: Human mantle cell lymphoma


title: SLS1_S4

description:
Library name: SAMPLE 16
SLS1_S4.resultsRSEM.genes.results


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 091

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_091
sci-RNA-seq3
L1_rice_combined.RData


title: Ser3_cladeI_PT_time15_replicate2

value: Strain that belong to clade I of Clonal Complex 180

value: Serotype 3


title: Ser3_cladeI_PT_time20_replicate2


title: POE3_S14

description:
Library name: SAMPLE 15
POE3_S14.resultsRSEM.genes.results

value: Phenoxyethanol


title: HBL2 cell line, control, grown in atmospheric oxygen, replicate 1

value: control


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 090

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_090
sci-RNA-seq3
L1_rice_combined.RData


title: Ser3_cladeI_PT_time15_replicate1


title: HBL2 cell line, adapted to hypoxia, grown in 1% oxygen, replicate 2


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 089

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_089
sci-RNA-seq3
L1_rice_combined.RData


title: POE2_S8

description:
Library name: SAMPLE 14
POE2_S8.resultsRSEM.genes.results


title: HBL2 cell line, adapted to hypoxia, grown in 1% oxygen, replicate 1


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 088

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_088
sci-RNA-seq3
L1_rice_combined.RData


title: POE1_S2

description:
Library name: SAMPLE 13
POE1_S2.resultsRSEM.genes.results


title: Ser3_cladeI_PT_time10_replicate2


title: MIT3_S18

description:
Library name: SAMPLE 12
MIT3_S18.resultsRSEM.genes.results

value: Methylisothiazolinone


title: Ser3_cladeI_PT_time10_replicate1


title: MIT2_S12

description:
Library name: SAMPLE 11
MIT2_S12.resultsRSEM.genes.results


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 087

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_087
sci-RNA-seq3
L1_rice_combined.RData


title: MIT1_S6

description:
Library name: SAMPLE 10
MIT1_S6.resultsRSEM.genes.results


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 085

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_085
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 086

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_086
sci-RNA-seq3
L1_rice_combined.RData


title: FA3_S17

description:
Library name: SAMPLE 9
FA3_S17.resultsRSEM.genes.results

value: Formaldehyde


title: Ser3_cladeI_PT_time0_replicate2


title: Ser3_cladeI_PT_time0_replicate1


title: FA2_S11

description:
Library name: SAMPLE 8
FA2_S11.resultsRSEM.genes.results


title: Ser3_cladeII_ND_time20_replicate3

value: Strain that belong to clade II of Clonal Complex 180


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 083

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_083
sci-RNA-seq3
L1_rice_combined.RData


title: Ser3_cladeI_PT_time10_replicate3


title: MM.1S treated with 5 nM  LBH589, biological rep3

type: RNA

city: Chengdu

first: Qiang

last: Qiu

state: Sichuan

address: No. 17, the Third Part of Renmin South Road

institute: SKLB

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using GeneBASE software. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.
HTA-2_0.r1.pgf
HTA-2_0.r1.Psrs.mps

label: biotin

source_name: multiple myeloma cell line

label_protocol: Samples were enzymatically fragmented and biotinylated using the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix)

growth_protocol: Cells were clutured with RPMI1640 with 10% FBS

extract_protocol: After 24 h of HL13 and LBH589 treatment, cells were collected and used to isolate total RNA

treatment_protocol: HL13 and LBH589 were dissolved in DMSO

value: multiple myeloma cell line


title: FA1_S5

description:
Library name: SAMPLE 7
FA1_S5.resultsRSEM.genes.results

value: Wild-type strain

value: L4 stage


title: C3_S13

description:
Library name: SAMPLE 6
C3_S13.resultsRSEM.genes.results

value: N2 Bristol

value: WT


title: MM.1S treated with 5 nM LBH589, biological rep1


title: Ser3_cladeII_ND_time20_replicate1


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 081

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_081
sci-RNA-seq3
L1_rice_combined.RData


title: C2_S7

description:
Library name: SAMPLE 5
C2_S7.resultsRSEM.genes.results


title: MM.1S treated with 5 nM HL13, biological rep3


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 080

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_080
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 084

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_084
sci-RNA-seq3
L1_rice_combined.RData


title: Control,Day180-2

value: Lung


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 079

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_079
sci-RNA-seq3
L1_rice_combined.RData


title: Ser3_cladeII_ND_time15_replicate2


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 082

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_082
sci-RNA-seq3
L1_rice_combined.RData


title: Ser3_cladeI_PT_time0_replicate3


title: MM.1S treated with 5 nM HL13, biological rep1


title: MM.1S treated with 5 nM HL13, biological rep2


title: MM.1S treated with 5 nM  LBH589, biological rep2


title: MM.1S treated with DMSO, biological rep3


title: Ser3_cladeII_ND_time20_replicate2


title: BR3_S15

description:
Library name: SAMPLE 3
BR3_S15.resultsRSEM.genes.results

value: Bronopol


title: Ser3_cladeII_ND_time15_replicate1


title: MM.1S treated with DMSO, biological rep2


title: Female_Ads_Ctnnb1KO, rep 6

city: Ann Arbor

first: Ormond

middle: A.

last: MacDougald

state: MI

address: 2800 Plymouth Rd

department: Molecular & Integrative Physiology

institute: University of Michigan

description:
Library name: Sample 33
Column name in DESeq2_raw_counts.csv and DESeq2_rlogNormalized_counts.csv: 33-KO6AF

data_processing:
FastQC (v.0.12.1) was used to check the quality of the raw read data. Alignment was conducted using STAR (version 2.7.11a), using UCSC mm39 as the reference genome sequence. A second quality control was performed post-alignment using FastQC to ensure that only high-quality data were used for gene expression quantitation and differential expression analyses. Differential expression analysis was conducted using DESeq2.
Assembly: UCSC mm39
Supplementary files format and content: DESeq2_raw_counts.csv contains raw counts for each sample
Supplementary files format and content: DESeq2_rlogNormalized_counts.csv contains rlogNormalized counts for each sample

extract_protocol:
Epididymal WAT (eWAT) and posterior subcutaneous WAT (psWAT) depots were excised from Ctnnb1fl/fl and Ctnnb1AdKO mice as described [51]. eWAT and psWAT depots were minced with scissors and then digested for 20 and 30 min, respectively, at 37°C in 500 U/ml collagenase type I (Worthington Biochemical) in Krebs-Ringer-HEPES (KRH; pH 7.4) buffer containing 1 g/l glucose and 500 nM adenosine with shaking (100 rpm). Cell suspensions were filtered through 300 μm cell strainers and then centrifuged at 80 x g for 8 min. Buoyant adipocytes were separated from the pelleted SVCs. Fractions were washed three times with KRH buffer. Total RNA was isolated and purified from adipocytes or SVCs using RNA STAT-60 (AMSBIO) according to the manufacturer’s instructions.
After DNAse treatment, samples were subjected to quality control, library preparation, and strand-specific mRNA sequencing (Beijing Genomics Institute, China).

value: Adipocytes

tag: gender

value: Female


title: Ser3_cladeII_ND_time15_replicate3

value: cultures


title: BR2_S9

description:
Library name: SAMPLE 2
BR2_S9.resultsRSEM.genes.results


title: Ser3_cladeII_ND_time10_replicate3


title: MM.1S treated with DMSO, biological rep1


title: BR1_S3

description:
Library name: SAMPLE 1
BR1_S3.resultsRSEM.genes.results


title: Female_Ads_Ctnnb1KO, rep 5

description:
Library name: Sample 32
Column name in DESeq2_raw_counts.csv and DESeq2_rlogNormalized_counts.csv: 32-KO5AF

source_name: Epididymal WAT (eWAT) and posterior subcutaneous WAT (psWAT) depots


title: H929 D1 Untreated

city: Boston

first: Mehmet

middle: Kemal

last: Samur

state: MA

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

hyb_protocol: The targets are then hybridized onto GeneChip® Human Transcriptome Array 2.0 . They are hybridized at 45C for 16-18 hours. The arrays were washed and stained on Fluidics Stations 450 using the Affymetrix Hybe/Wash/Stain.

scan_protocol: The arrays were scanned on GeneChip Scanner 3000 7G

data_processing: R oligo, pd.hta.2.0 and limma packages were used

source_name: H929 cell line

label_protocol: The Affymetrix GeneChip WT Plus Reagent Kit is used to convert 100ng of total RNA into biotinylated sense-strand DNA targets.

extract_protocol: total RNA was extracted from MM cell lines by using Rneasy kit from Qiagen

value: Untreated


title: Female_Ads_Ctnnb1KO, rep 3

description:
Library name: Sample 30
Column name in DESeq2_raw_counts.csv and DESeq2_rlogNormalized_counts.csv: 30-KO3AF

value: Epididymal WAT (eWAT) and posterior subcutaneous WAT (psWAT) depots


title: Ser3_cladeII_ND_time10_replicate2

value: Serotype 3


title: LNCaP extracted RNA, 5NIA

first: Chase

middle: Andrew

last: Weidmann

address: 1150 W. Medical Center Drive

department: Biological Chemistry

data_processing:
fastqs were processed, aligned, and had mutations counted by shapemapper2 software
SHAPE reactivities were used to inform RNA secondary structure modeling in the RNAStructure software, generating minimum-free energy structure and pairing probabilities.
Assembly: DRAIC fasta files used for alignment are included as processed data files.
Supplementary files format and content: .fa files are fasta files containg the DRAIC sequences used in analysis
Supplementary files format and content: .map file is tab-separated value outputs of shapemapper2, which include mutation rates and calculated normalized SHAPE reactivities
Supplementary files format and content: .ct file is the output of the RNAStructure wrapper program SuperFold, including the minimum free energy structure model of DRAIC RNA
Supplementary files format and content: .dp files are pairing probabilities for DRAIC (output of RNAStructure partition)
Library strategy: SHAPE-MaP

source_name: LNCaP

growth_protocol: LNCaP cells were cultured in RPMI 1640 medium supplemented with 10% FBS, 1% penicillin/streptomycin, 1 mmol/L sodium pyruvate, and 10 mmol/L HEPES buffer

extract_protocol:
RNA was extracted from LNCaP cells, cDNA was generated by MaP RT primed with a DRAIC RNA-specific primer
Cells were lysed with proteinase K, and RNA was extracted with PCA and buffer exchanged into folding buffer over a column.
cDNA was generated by MaP RT with Superscript II including a DRAIC-specific primer. Final sequencing libraries were generated by PCR using DRAIC-specific primers, with indexing barcodes added in a second round of PCR.

treatment_protocol: extracted RNAs were folded for 20 minutes at 37C in folding buffer, followed by treatment of 25 mM 5NIA SHAPE reagent or DMSO control for 10 minutes at 37C.

value: LNCaP

value: 37C folding 20 min, 25mM 5NIA 37C 10min


title: C1_S1

description:
Library name: SAMPLE 4
C1_S1.resultsRSEM.genes.results

value: Control


title: Ser3_cladeII_ND_time10_replicate1

value: Strain that belong to clade II of Clonal Complex 180


title: LNCaP extracted RNA, DMSO

value: 37C folding 20 min, DMSO 37C 10min


title: Female_Ads_Ctnnb1KO, rep 2

description:
Library name: Sample 29
Column name in DESeq2_raw_counts.csv and DESeq2_rlogNormalized_counts.csv: 29-KO2AF


title: UPN662_T3_SNPa

type: genomic

city: Perugia

first: Cristina

last: Mecucci

address: Piazzale Menghini n.9

department: Department of Medicine, Hematology and Bone Marrow Transplantation Unit

country: Italy

institute: University of Perugia

hyb_protocol: DNA was restriction digested, ligated, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G

data_processing:
Protocol was supported by Affymetrix GeneChip Command Console (AGCC) software. Analysis was performed through Affymetrix Chromosome Analysis 4.3 (ChAS) software with filters set at 400 Kb for Copy Number Alterations (CNAs) and 10 Mb for copy neutral Loss Of Heterozygosity (cnLOH). Our data refer to NetAffx Build 20211122 (hg19) database
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: Biotin

source_name: Unsorted Bone Marrow Cells

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA were extracted from bone marrow cells of patients using All Prep DNA/RNA Mini Kit (Qiagen). DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, Bioanalyzer and/or Tapestation visualization (Agilent 2100 Bioanalyzer) and agarose gel electrophoresis

tag: cytogenetics

tag: mutations

value: SRSF2 p.(Pro95_Arg102del),  IDH2 p.(Arg140Gln)


title: Female_Ads_Ctnnb1KO, rep 1

description:
Library name: Sample 28
Column name in DESeq2_raw_counts.csv and DESeq2_rlogNormalized_counts.csv: 28-KO1AF


title: Ser3_cladeII_ND_time0_replicate3


title: Female_Ads_Ctnnb1KO, rep 4

description:
Library name: Sample 31
Column name in DESeq2_raw_counts.csv and DESeq2_rlogNormalized_counts.csv: 31-KO4AF


title: UPN662_T1_SNPa

value: SRSF2 p.(Pro95_Arg102del)


title: H929 D1 Treated_2

source_name: H929 cell line with depleted lnc-17-92

value: ASO1 Treated


title: Ser3_cladeII_ND_time0_replicate1


title: UPN661_T3_SNPa

value: SRSF2 p.(Pro95_Arg102del),  IDH2 p.(Arg140Gln), ASXL1 p.(Arg1068*), KRAS p.(Ala18Asp), RUNX1 p.(Arg166Gln)


title: Ser3_cladeII_ND_time0_replicate2


title: H929 D1 Treated


title: 1_AMO1 D1 Untreated

source_name: AMO1 cell line


title: Female_Ads_Ctnnb1flfl, rep 4

description:
Library name: Sample 25
Column name in DESeq2_raw_counts.csv and DESeq2_rlogNormalized_counts.csv: 25-WT4AF


title: D39_time20_replicate3

value: Streptococcus pneumoniae str. D39

value: Serotype 2


title: UPN660_T3_SNPa

value: SRSF2 p.(Pro95_Arg102del),  IDH2 p.(Arg140Gln), RUNX1 p.(Ala187Pro)


title: Female_Ads_Ctnnb1flfl, rep 5

description:
Library name: Sample 26
Column name in DESeq2_raw_counts.csv and DESeq2_rlogNormalized_counts.csv: 26-WT5AF

value: Adipocytes

value: Female


title: WT_Vehicle_r1

city: Sydney

first: Justin

middle: J-L

last: Wong

address: Charles Perkins Centre Lvl4 West, The University of Sydney, Camperdown, NSW, Australia

department: School of Medical Sciences, Faculty of Medicine and Health,

country: Australia

institute: University of Sydney

description: Library name: R_3420

data_processing:
Low-quality reads and adaptors were remives using TRIMMOMATIC v0.39
Clean reads were mapped to mm10 using STAR v2.7.8a
Gene quantification was performed using featureCounts v2.0.2
Assembly: mm10
Supplementary files format and content: Comma-separated value file provides counts for each gene for each sample

source_name: Whole aortic tree

extract_protocol:
Total RNA was extracted using the TRIZOL reagent according to manufacturer's instructions
Poly-A enriched mRNA library was prepared using the TruSeq Stranded Library Preparation Kit per manufacturers instructions.

value: Whole aortic tree

value: WT

value: Vehicle


title: WT_Vehicle_r2

description: Library name: R_3423


title: D39_time20_replicate2

value: cultures


title: UPN660_T2_SNPa


title: Female_Ads_Ctnnb1flfl, rep 3

description:
Library name: Sample 24
Column name in DESeq2_raw_counts.csv and DESeq2_rlogNormalized_counts.csv: 24-WT3AF

value: Epididymal WAT (eWAT) and posterior subcutaneous WAT (psWAT) depots


title: D39_time20_replicate1


title: WT_Treatment_r2

description: Library name: R_6829

value: VitD


title: Female_Ads_Ctnnb1flfl, rep 2

description:
Library name: Sample 23
Column name in DESeq2_raw_counts.csv and DESeq2_rlogNormalized_counts.csv: 23-WT2AF


title: D39_time15_replicate3


title: Female_Ads_Ctnnb1flfl, rep 6

description:
Library name: Sample 27
Column name in DESeq2_raw_counts.csv and DESeq2_rlogNormalized_counts.csv: 27-WT6AF


title: 4_AMO1 D1 Treated

source_name: AMO1 cell line with depleted lnc-17-92


title: 2_AMO1 D1 Untreated

value: Untreated


title: WT_Treatment_r1

description: Library name: R_6828


title: UPN660_T1_SNPa


title: 3_AMO1 D1 Treated


title: Female_Ads_Ctnnb1flfl, rep 1

description:
Library name: Sample 22
Column name in DESeq2_raw_counts.csv and DESeq2_rlogNormalized_counts.csv: 22-WT1AF


title: D39_time15_replicate2


title: KO_Vehicle_r2

description: Library name: R_3419

value: VSMC-specific Tet2 Knockout


title: H929 D1 Untreated_2


title: UPN661_T1_SNPa

value: SRSF2 p.(Pro95_Arg102del),  IDH2 p.(Arg140Gln), ASXL1 p.(Arg1068*)


title: Male_SVC_Ctnnb1KO, rep 4

description:
Library name: Sample 21
Column name in DESeq2_raw_counts.csv and DESeq2_rlogNormalized_counts.csv: 21-KO4SM

value: SVC

value: Male


title: D39_time15_replicate1


title: KO_Treatment_r2

description: Library name: R_3421


title: PCC3

city: Nanjing

first: Xiao

last: Wang

state: Jiangsu

address: No. 1 Weigang Road

institute: Nanjing Agricultural University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis.
Short reads alignment tool Bowtie2  (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads will be removed. The remaining reads were further used in assembly and analysis of transcriptome.
The rRNA removed reads of each sample were then mapped to reference genome by TopHat2  (version 2.1.1), respectively.
Gene abundances were quantified by software RSEM(version 1.2.19). There were two steps for RSEM to quantify gene abundances. Firstly, a set of reference transcript sequences were generated and preprocessed according to known transcripts and new transcripts (in FASTA format) and gene annotation files (in GTF format). Secondly, RNA-seq reads were realigned to the reference transcripts by Bowtie alignment program and the resulting alignments were used to estimate gene abundances.
Genome_build: Ensembl release 34 TGACv1 (GCA_900067645)

organism: Triticum aestivum

source_name: wheat plants

growth_protocol: Plants were grown in growth chamber, with a day/night temperature of approximate 20°C/16°C, and with a 16 h/8 h light/dark cycle, 500 μmol m−2 s−1 light intensity

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.
RNA libraries were prepared for sequencing using standard illumina protocols

treatment_protocol: At three-leaf stage, the plants were with or without drought priming by 5% PEG (φ= -0.37 Mpa) for 6 h or kept in the normal culture solution, followed by recovery for 6 days. Both the primed and non-primed plant were drought stressed with 15% PEG (φ= -0.78 Mpa) for 24 h or kept under control conditions.

value: root tips

value: seedling


title: PCC1


title: KO_Vehicle_r1

description: Library name: R_3418


title: PCB2


title: D39_time10_replicate3

value: Streptococcus pneumoniae str. D39

value: Serotype 2


title: D39_time10_replicate2


title: KO_Treatment_r1

description: Library name: R_6831


title: Male_SVC_Ctnnb1KO, rep 2

description:
Library name: Sample 19
Column name in DESeq2_raw_counts.csv and DESeq2_rlogNormalized_counts.csv: 19-KO5SM


title: PCC2


title: Male_SVC_Ctnnb1KO, rep 3

description:
Library name: Sample 20
Column name in DESeq2_raw_counts.csv and DESeq2_rlogNormalized_counts.csv: 20-KO3SM


title: Male_SVC_Ctnnb1flfl, rep 3

description:
Library name: Sample 15
Column name in DESeq2_raw_counts.csv and DESeq2_rlogNormalized_counts.csv: 15-WT5SM


title: D39_time10_replicate1


title: CD45+ cells, MIKO, rep2

city: Ulsan

first: Hyowon

last: Ki

address: 50, UNIST-gil, Eonyang-eup

country: South Korea

institute: UNIST

description: Library name: MIKO2

library_source: transcriptomic single cell

data_processing:
Processing of gene expression matrices generated by the Cell Ranger toolkit and all subsequent analyses, including graphs and statistics, were performed using RStudio and Seurat.
Assembly: Mouse mm10
Supplementary files format and content: Tab seperated values files and matrix values

source_name: Heart

extract_protocol:
Immune cells were isolated from infarcted hearts of sham- or LAD-operated Pcsk9+/+ and LAD-operated Pcsk9-/- mice and washed with MACS buffer. CD45+ immune cells were selectively isolated using CD45 magnetic microbeads, MACS columns, and a separator.
Libraries were constructed from collected single-cell suspensions, which were then subjected to 3' single-cell RNA sequencing, using Single Cell A Chip Kit, Single Cell 3' Library and Gel Bead Kit V2 and i7 Multiplex Kit (all from 10x Genomics) with a cell recovery target of 10000, following the manufacturer’s instructions.

value: Heart

value: CD45+ cells


title: PCB3


title: Male_SVC_Ctnnb1KO, rep 1

description:
Library name: Sample 17
Column name in DESeq2_raw_counts.csv and DESeq2_rlogNormalized_counts.csv: 17-KO6SM


title: PCB1


title: CD45+ cells, MIKO, rep1

description: Library name: MIKO1


title: Male_SVC_Ctnnb1flfl, rep 2

description:
Library name: Sample 14
Column name in DESeq2_raw_counts.csv and DESeq2_rlogNormalized_counts.csv: 14-WT4SM


title: D39_time0_replicate2


title: PCA3


title: Male_SVC_Ctnnb1flfl, rep 1

description:
Library name: Sample 12
Column name in DESeq2_raw_counts.csv and DESeq2_rlogNormalized_counts.csv: 12-WT2SM


title: D39_time0_replicate1


title: CD45+ cells, MI, rep1

description: Library name: MI1


title: CD45+ cells, MI, rep2

description: Library name: MI2


title: PCA2


title: Male_Ads_Ctnnb1KO, rep 5

description:
Library name: Sample 11
Column name in DESeq2_raw_counts.csv and DESeq2_rlogNormalized_counts.csv: 11-KO6AM

value: Adipocytes


title: D39_time0_replicate3


title: M1002.8

first: yunjie

last: shi

address: No 800，Xiangyin Road

institute: Naval Medical University

data_processing:
Using FLASH v1.2.7 software, the reads of each sample are spliced by overlap, and the spliced sequence is the raw Tags.Using Trimmomatic v0.33 software, the Raw Tags obtained by splicing were filtered to obtain high-quality Tags data (Clean Tags)
Using UCLUST in QIIME(version 1.8.0) software to cluster Tags at the similarity level in ninety-seven percent, OTU was obtained, and the OTU was taxonomically annotated based on Silva (bacteria) and UNITE (fungi) taxonomic databases.
Comparing the representative sequence of the OTUs with a microbial reference database to obtain species classification information corresponding to each OTU, and counting the composition of each sample community at each level,
The Alpha diversity index of samples was evaluated using the Mothur (version v.1.30) software. In general, the index of diversity was compared among samples, and the number of sequences contained in samples was standardized for analysis.
The PICRUSt software was used to deduce the functional gene composition in samples by comparing the species composition information obtained from 16S sequencing data, so as to analyze the functional differences between different samples or subgroups.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Library strategy: 16S rRNA-seq

organism: feces metagenome

source_name: fecal samples of mice

extract_protocol:
Extraction of total genomic DNA through the DNA Extraction Kit (Tiangen Biotechnology Company, Beijing, China) was conducted following the instructions of the kit.
DNA libraries for 16s-rDNA sequencing were prepared using SMARTER DNA-Seq Library Prep Kit following manufacturer's protocols.

value: fecal samples of mice


title: CD45+ cells, Sham

description: Library name: Sham


title: PCA1


title: M1002.7


title: CDC3


title: M1002.6


title: Male_Ads_Ctnnb1KO, rep 4

description:
Library name: Sample 10
Column name in DESeq2_raw_counts.csv and DESeq2_rlogNormalized_counts.csv: 10-KO4AM


title: CDC2


title: Olfactory bulb, Day 6, rep 3

city: Tokyo

first: Julia

last: Matsuo-Dapaah

address: 4-6-1 Shirokanedai, Minato-ku

department: Institute of Medical Science

country: Japan

institute: University of Tokyo

description: Library name: Day6_No.15

data_processing:
TopHat2, BowTie2, SAMtools
Assembly: mapped to the mouse reference genome sequence GRCm38 (mm10)
Supplementary files format and content: Counts were normalized using DESeq2 via SARTools

source_name: Olfactory bulb

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen) and the total RNA integrity was confirmed using the RNA 6000 Nano kit on Agilent 2100 Bioanalyzer, ensuring all samples had an RIN ≥8.
cDNA library was constructed using TruSeq stranded mRNA library prep kit (Illumina).

treatment_protocol: Female wildtype C57BL/6 mice were intraperitoneally infected with Plasmodium berghei ANKA parasites at 1x106 infected erythrocytes. On day 3 or day 6 after infection, and without infection for naïve, olfactory bulb of the mice were collected into TRIzol after transcardiac perfusion with D-PBS.

value: Olfactory bulb

value: wild type

tag: disease state

value: Day6 post-PbA infection


title: Olfactory bulb, Day 6, rep 4

description: Library name: Day6_No.16


title: M1002.5


title: Olfactory bulb, Day 6, rep 2

description: Library name: Day6_No.12


title: Olfactory bulb, Day 6, rep 1

description: Library name: Day6_No.11


title: Male_Ads_Ctnnb1KO, rep 2

description:
Library name: Sample 8
Column name in DESeq2_raw_counts.csv and DESeq2_rlogNormalized_counts.csv: 8-KO2AM

value: Epididymal WAT (eWAT) and posterior subcutaneous WAT (psWAT) depots


title: CDB3


title: Male_Ads_Ctnnb1KO, rep 1

description:
Library name: Sample 7
Column name in DESeq2_raw_counts.csv and DESeq2_rlogNormalized_counts.csv: 7-KO1AM


title: M1002.3


title: Male_Ads_Ctnnb1flfl, rep 6

description:
Library name: Sample 6
Column name in DESeq2_raw_counts.csv and DESeq2_rlogNormalized_counts.csv: 6-WT6AM


title: Male_Ads_Ctnnb1flfl, rep 5

description:
Library name: Sample 5
Column name in DESeq2_raw_counts.csv and DESeq2_rlogNormalized_counts.csv: 5-WT5AM


title: M1002.2


title: Olfactory bulb, Day 3, rep 2

description: Library name: Day3_No.3

value: Day3 post-PbA infection


title: Male_Ads_Ctnnb1flfl, rep 4

description:
Library name: Sample 4
Column name in DESeq2_raw_counts.csv and DESeq2_rlogNormalized_counts.csv: 4-WT4AM


title: CDB2


title: M1002.1


title: Male_Ads_Ctnnb1KO, rep 3

description:
Library name: Sample 9
Column name in DESeq2_raw_counts.csv and DESeq2_rlogNormalized_counts.csv: 9-KO3AM


title: CDB1


title: CDA3


title: CDC1


title: M1002.4


title: CDA2


title: Olfactory bulb, Naïve, rep 4

description: Library name: Naïve_No.4

value: No PbA infection


title: Olfactory bulb, Day 3, rep 1

description: Library name: Day3_No.1


title: Olfactory bulb, Naïve, rep 3

description: Library name: Naïve_No.3


title: Male_Ads_Ctnnb1flfl, rep 2

description:
Library name: Sample 2
Column name in DESeq2_raw_counts.csv and DESeq2_rlogNormalized_counts.csv: 2-WT2AM


title: CDA1


title: DSS. 7

value: DSS


title: DSS. 6


title: Male_Ads_Ctnnb1flfl, rep 1

description:
Library name: Sample 1
Column name in DESeq2_raw_counts.csv and DESeq2_rlogNormalized_counts.csv: 1-WT1AM


title: DSS. 8


title: Olfactory bulb, Naïve, rep 2

description: Library name: Naïve_No.2


title: PDC3


title: 976, brain, contra, peri, CsA

city: Bron

first: Emmanuelle

last: Canet Soulas

address: bât. B13, Groupement Hospitalier Est, 59 Boulevard Pinel

institute: Universite Claude Bernard Lyon 1

description:
Library name: 976_7
SR75

data_processing:
demultiplexing, and fastq generation were carried out using Bcl2fastq v2.17.1.14 and Cutadapt v1.9.1
For trimming the threshold quality score was set to 30, minimum length of 50 bases after trimming, the maximum rate of undetermined bases (“N”s) was set to 30% and adapters were trimmed with 3 bases overlap and a maximum error rate of 10%.
Alignment and quantification were performed using Salmon v1.6.0
Assembly: Macaca fascicularis (Ensembl Release 106)
Supplementary files format and content: raw_count : tabular separated text format. NumReads from Salmon count or all sample
Supplementary files format and content: corrected_normalized_count.txt : tabular separated text format. Normalized count with DESeq2, corrected with ComBat_seq for breeding

organism: Macaca fascicularis

source_name: brain

extract_protocol:
NextFlex Rapid Directional mRNA-Seq v2.0 (Bioo-Scientific, PerkinElmer)
Illumina flow cell High Output v2.5

value: brain

tag: individu

tag: side

value: contra

tag: zone

tag: breeding

value: CsA

tag: batch


title: Olfactory bulb, Day 3, rep 3

description: Library name: Day3_No.4

tag: tissue


title: Olfactory bulb, Naïve, rep 1

description: Library name: Naïve_No.11


title: 976, brain, contra, infarct, CsA

description:
Library name: 976_5
SR75

value: infractus


title: PDC2

value: root tips

value: seedling


title: DSS. 5

tag: cell type


title: DSS. 4


title: PDC1


title: Hezuo pig3, liver, Day 15, -15℃±2℃

city: Lanzhou

first: Jihong

last: Yan

state: Gansu

address: Yintan Road Subdistrict, Yingmen Village, No. 1

institute: Gansu Agricultural University

description: Library name: HT3

data_processing:
Filter out the low-quality reads (reads with Q≤20 and the number of bases exceeding 1 or containing N) to obtain high-quality reads
Filter out the reads without 3' adapters, and extract the sequences before the 3' adapters for subsequent analysis
Filter out the reads containing 5' adapters
Filter out the reads without insert fragments and those with insert fragment lengths less than 18 nt
Filter out the reads containing poly A (more than 70% of the bases in a read are A),  For animal samples, filter out the small RNA tags with read frequencies lower than 2.
Assembly: Sus scrofa Ensembl_release95
Supplementary files format and content: Gene expression matrices are provided as xls files, It includes the calculated TPM value.

organism: Sus scrofa

source_name: liver

growth_protocol: The rearing of pigs is controlled by temperature according to different treatment methods (normal temperature 23 ± 2℃, cold stress -15 ± 2℃), maintaining ventilation, dryness, hygiene and cleanliness, and providing balanced nutrition feed.

extract_protocol:
Extract total RNA from liver tissues of all pigs in the control group and the cold treatment group for 15 days using TRIzol (Life Technologies, Carlsbad, CA, USA)
Firstly, total RNA is extracted. Then, RNA molecules within the range of 18-30 nt are enriched and selected by polyacrylamide gel electrophoresis (PAGE). 3’ and 5’ adapters are ligated to the selected RNA molecules respectively. Subsequently, reverse transcription and PCR amplification are performed on the ligated products. Finally, the bands of approximately 140 bp are recovered and purified by PAGE gel, dissolved in EB solution, and the small RNA library construction and sequencing are completed.

value: liver

value: cold stress,-15±2℃


title: Male_Ads_Ctnnb1flfl, rep 3

description:
Library name: Sample 3
Column name in DESeq2_raw_counts.csv and DESeq2_rlogNormalized_counts.csv: 3-WT3AM

value: Adipocytes

value: Male


title: 976, brain, ispi, peri, CsA

description:
Library name: 976_3
SR75

value: ipsi


title: DSS. 3

value: fecal samples of mice


title: Hezuo pig2, liver, Day 15, -15℃±2℃

description: Library name: HT2

treatment_protocol: normal temperature 23 ± 2℃, cold stress -15 ± 2℃


title: PDB3


title: 976, brain, ispi, infarct, CsA

description:
Library name: 976_1
SR75


title: DSS. 2


title: PDB2


title: 892, brain, contra, peri, placebo

description:
Library name: 892_7
SR75

value: placebo


title: Hezuo pig1, liver, Day 15, -15℃±2℃

description: Library name: HT1


title: PDB1


title: Hezuo pig3, liver, Day 15, 23℃±2℃

description: Library name: HC3

value: Room temperature, 23±2℃


title: PDA3


title: DSS. 1


title: 892, brain, contra, infarct, placebo

description:
Library name: 892_5
SR75


title: RNA-seq of mus musculus:adult male liver tdTomato-negative ECs, sample 2, homeostasis

first: Zhicong

last: Liu

state: Shanghai

address: Chinese Academy of Sciences

institute: Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences

description: Library name: liver_tdT_negative_2

data_processing:
RNA quality control — Assessed by NanoDrop and Agilent 2100 bioanalyzer.
cDNA synthesis and amplification — Full-length cDNA generated from poly(A)+ RNA using reverse transcription and PCR.
Fragmentation and size selection — Fragment buffer and AMPure XP used to create suitable insert sizes.
Library QC — Library integrity and size assessed using Agilent 2100 bioanalyzer and RT–qPCR.
Library amplification and sequencing — Circularized ssDNA amplified into DNA nanoballs using phi29, then sequenced on MGISEQ-2000RS (paired-end, 100 bp).
Assembly: mm10
Supplementary files format and content: Gene expression count matrix in tab-delimited text format, listing gene identifiers and raw or normalized read counts for each sample.

extract_protocol:
Total RNA was extracted using the RNeasy Micro Kit (QIAGEN) following the manufacturer’s protocol. Briefly, cells were lysed in Buffer RL, mixed with 70% ethanol, and passed through RNeasy MinElute columns. RNA was purified with sequential washes (Buffer RW1, DNase I, Buffer RPE, and 80% ethanol), followed by elution in RNase-free water. RNA integrity and concentration were measured using NanoDrop and Agilent 2100 bioanalyzer.
Poly(A)+ RNA was reverse-transcribed using oligo(dT) primers, followed by PCR amplification to synthesize full-length cDNA. The cDNA was fragmented, size-selected using AMPure XP-Medium Kit (Thermo Fisher Scientific), and quantified using the Agilent 2100 bioanalyzer. Circular single-stranded DNA libraries were generated, quality-controlled by bioanalyzer and RT–qPCR, and DNA nanoballs were produced via phi29 amplification. Libraries were sequenced using paired-end 100-bp reads on the MGISEQ-2000RS platform (BGI-Shenzhen).

value: endothelial cells

value: Ki67-CrexER; Cdh5-DreER; R26-RL-tdT

value: homeostasis,collect at adult


title: Hezuo pig1, liver, Day 15, 23℃±2℃

description: Library name: HC1


title: 892, brain, ispi, peri, placebo

description:
Library name: 892_3
SR75

value: brain


title: PDA2


title: RNA-seq of mus musculus:adult male liver tdTomato-negative ECs, sample 3, homeostasis

description: Library name: liver_tdT_negative_3


title: 892, brain, ispi, infarct, placebo

description:
Library name: 892_1
SR75


title: Bama pig3, liver, Day 15, -15℃±2℃

description: Library name: BT3


title: 658, brain, contra, iperi, CsA

description:
Library name: 658_7
SR75

value: contra


title: RNA-seq of mus musculus:adult male liver tdTomato-positive ECs, sample 3, homeostasis

description: Library name: liver_tdT_positive_3


title: RNA-seq of mus musculus:adult male liver tdTomato-negative ECs, sample 1, homeostasis

description: Library name: liver_tdT_negative_1


title: PDA1


title: CKC3


title: Bama pig2, liver, Day 15, -15℃±2℃

description: Library name: BT2


title: 658, brain, contra, infarct, CsA

description:
Library name: 658_5
SR75

value: CsA


title: RNA-seq of mus musculus:adult male liver tdTomato-positive ECs, sample 2, homeostasis

description: Library name: liver_tdT_positive_2


title: Bama pig1, liver, Day 15, -15℃±2℃

description: Library name: BT1


title: CKC2


title: RNA-seq of mus musculus:adult male liver tdTomato-positive ECs, sample 1, homeostasis

description: Library name: liver_tdT_positive_1


title: Bama pig3, liver, Day 15, 23℃±2℃

description: Library name: BC3


title: Hezuo pig2, liver, Day 15, 23℃±2℃

description: Library name: HC2


title: CKC1


title: 658, brain, ispi, infarct, CsA

description:
Library name: 658_1
SR75

value: infractus


title: Bama pig2, liver, Day 15, 23℃±2℃

description: Library name: BC2


title: CKB3

value: root tips


title: RNA-seq of mus musculus:adult male heart OR, sample 2, homeostasis

description: Library name: heart_OR_2

source_name: heart

value: heart

value: WT


title: 653, brain, contra, peri, placebo

description:
Library name: 653_7
SR75


title: CKB2

value: seedling


title: Tim-3 KO Effector T cells, replicate 3

city: Pittsburgh

first: Lawrence

middle: P.

last: Kane

state: PA

address: 5051 Centre Ave.

department: Immunology

institute: University of Pittsburgh

description: Library name: KO-3

data_processing:
Read alignment (Partek)
Assembly: GRCm39
Supplementary files format and content: Excel file with individual sample read counts

source_name: Spleen

extract_protocol:
SmartSeq cDNA
Nextera XT libraries

treatment_protocol: Cells were isolated on day 8 from mice infected with LCMV Armstrong

value: Spleen

value: P14 CD8 T cells

value: Day 8 post-LCMV armstrong infection

tag: sample group

value: Tim-3 KO Effector T cells


title: 653, brain, contra, infarct, placebo

description:
Library name: 653_5
SR75

value: placebo


title: CKB1


title: 653, brain, ispi, peri, placebo

description:
Library name: 653_3
SR75

value: ipsi


title: RNA-seq of mus musculus:adult male heart VS, sample 3, homeostasis

description: Library name: heart_VS_3

value: endothelial cells

tag: genotype


title: RNA-seq of mus musculus:adult male heart OR, sample 1, homeostasis

description: Library name: heart_OR_1

tag: treatment


title: RNA-seq of mus musculus:adult male heart VS, sample 2, homeostasis

description: Library name: heart_VS_2


title: CKA3


title: 658, brain, ispi, peri, CsA

description:
Library name: 658_3
SR75


title: Tim-3 KO Effector T cells, replicate 1

description: Library name: KO-1


title: RNA-seq of mus musculus:adult male heart VS, sample 1, homeostasis

description: Library name: heart_VS_1


title: 639, brain, contra, peri, CsA

description:
Library name: 639_7
SR75


title: Tim-3 T2 Effector T cells, replicate 3

description: Library name: T2-3

value: Tim-3 T2 Effector T cells


title: 639, brain, contra, infarct, CsA

description:
Library name: 639_5
SR75


title: CKA2


title: RNA-seq of mus musculus:adult male heart LV, sample 3, homeostasis

description: Library name: heart_LV_3

value: homeostasis,collect at adult


title: CKA1


title: RNA-seq of mus musculus:adult male heart OR, sample 3, homeostasis

description: Library name: heart_OR_3


title: Tim-3 T2 Effector T cells, replicate 2

description: Library name: T2-2


title: RNA-seq of mus musculus:adult male heart LV, sample 2, homeostasis

description: Library name: heart_LV_2


title: Tim-3 T2 Effector T cells, replicate 1

description: Library name: T2-1


title: Bama pig1, liver, Day 15, 23℃±2℃

description: Library name: BC1

value: liver

value: Room temperature, 23±2℃


title: FAP+ CAFs-3

city: nanjing

first: Qinglin

state: jiangsu

address: Jiangsu Cancer Hospital

institute: Jiangsu Cancer Hospital

description: Library name: sample12

data_processing:
Fastp was used to remove adapter sequences and low-quality bases (Q<20).
Assembly: hg38
Supplementary files format and content: CSV format contained.rawcounts.

source_name: lung adenocarcinoma

extract_protocol:
Total RNA was extracted from CAFs using the RNeasy Mini Plus Kit (Qiagen) according to the manufacturer's instructions. 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for bulk RNA-seq were prepared using the NEBNext Ultra II RNA Library Prep Kit following manufacturer's protocols.

value: lung adenocarcinoma

tag: cell line

value: primary cell

value: cancer associated fibroblasts

value: isolating FAP+CAFs from FAP- CAFs


title: Tim-3 KO Effector T cells, replicate 2

description: Library name: KO-2

value: WT


title: RNA-seq of mus musculus:adult male heart LV, sample 1, homeostasis

description: Library name: heart_LV_1

value: heart


title: FAP+ CAFs-2

description: Library name: sample11


title: WT P14 Effector T cells, replicate 3

description: Library name: WT-3

value: Spleen

value: WT P14 Effector T cells


title: 639, brain, ispi, infarct CsA

description:
Library name: 639_1
SR75

value: brain

value: infractus

value: CsA


title: 638, brain, contra, peri, placebo

description:
Library name: 638_7
SR75

value: contra

value: placebo


title: FAP+ CAFs-1

description: Library name: sample10


title: 653, brain, ispi, infarct, placebo

description:
Library name: 653_1
SR75

value: ipsi


title: RNA-seq of mus musculus:adult male heart Apex, sample 3, homeostasis

description: Library name: heart_Apex_3

value: endothelial cells

value: homeostasis,collect at adult


title: 638, brain, contra, infarct, placebo

description:
Library name: 638_5
SR75


title: RNA-seq of mus musculus:adult male heart Apex, sample 2, homeostasis

description: Library name: heart_Apex_2


title: WT P14 Effector T cells, replicate 2

description: Library name: WT-2

value: P14 CD8 T cells

value: Day 8 post-LCMV armstrong infection


title: FAP- CAFs-2

description: Library name: sample8

value: lung adenocarcinoma

value: primary cell


title: 638, brain, ispi, peri, placebo

description:
Library name: 638_3
SR75


title: RNA-seq of mus musculus:adult male heart Apex, sample 1, homeostasis

description: Library name: heart_Apex_1


title: 639, brain, ispi, peri, CsA

description:
Library name: 639_3
SR75


title: WT P14 Effector T cells, replicate 1

description: Library name: WT-1


title: FAP- CAFs-1

description: Library name: sample7

value: cancer associated fibroblasts

value: isolating FAP+CAFs from FAP- CAFs


title: Brain Cortical Endothelial cells-beta-catenin GOF-3

city: Houston

first: Peeyush Kumar

last: Thankamani Pandit

state: TEXAS

address: 6431 Fannin St,

department: Neurosurgery

institute: University of Texas Health Science Center Houston

description: Library name: Sample 12

data_processing:
mRNA-seq reads were quality checked using FastQC [www.bioinformatics.babraham.ac.uk/projects/fastqc/] after removing adaptors with cutadapt. .
Raw reads were mapped with STAR read aligner and default parameters against build mm10 of the mouse reference genome and the latest annotation of mouse genome from the mouse GENCODE repository
We used featureCounts to count reads on each gene for gene expression quantification.
Differentially expressed genes were detected and ranked using DESeq2
Assembly: mm10
Supplementary files format and content: tab limited file contain normalised counts for each samples

source_name: Brain

extract_protocol:
The FACS sorted cells were suspended in solution as suggested by SMART-Seq v4 PLUS Kit User Manual (Takara Bio, Japan). The sorted cells were frozen on dry ice as soon as the sorting was done at The University of Texas Health Science Center in Houston (CPRIT RP180734).
Libraries were prepared with SMART-Seq V4 PLUS Kit (R400752, Takara Bio, Japan) following the manufacturer’s instructions. Agilent High Sensitive DNA Kit (#5067-4626) by Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, USA) was used to check the quality of the final libraries and the library concentrations were determined by qPCR using Collibri Library Quantification kit (#A38524500, Thermo Fisher Scientific, Texas, USA). The libraries were pooled evenly and went for the paired-end 150-cycle sequencing on an Illumina NovaSeq X plus System (Illumina, Inc., USA).

treatment_protocol: Mice endothelial cells were subjected to specific deletion of Hdac2 and Ezh2, or beta-catenin constitutive activation, using  Hdac2lox/lox:Cdh5CreERT2, Ezh2lox/lox:Cdh5CreERT2 or Ctnnb1lox/lox:Cdh5CreERT2 mice.  Mice were  treated with five doses of Tamoxifen (75mg/Kg body weight). After 2 months brains were harvested and brain endothelial cells were isolated using FACS sorting.

value: Brain

value: Endothelial cells

value: beta-catenin GOF


title: Macrophage specific Rictor KO tumor

city: Vienna

first: Mario

last: Mikula

address: Währingerstrasse 10

country: Austria

institute: Medical University of vienna

description:
Library name: 94652
10x Genomics

data_processing:
library strategy: 5' scRNA-seq
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger v2.0.2 pipeline
Assembly: Assembly: GRCh38
Supplementary files format and content: Tab-seperateted value files and matrix files

source_name: skin tumor

growth_protocol: C57/BL6 Rictor fl LysMcre littermates (Rictor WT: Rictor fl/fl +/+ and Rictor KO: Rictor fl/fl cre/+) were injected with B16-F10 cells intradermally into the right and left flank. Tumor growth was observed until the biggest tumor exceeded 1000 mm3.

extract_protocol:
Tumor tissues of Rictor WT and KO mice was cut into pieces about 2 mm3 and digested with MACS tumor dissociation kit for 30 min. Suspended cells were filtered with 70-μm Cell-Strainer (Catalog No. 352350, BD, Franklin Lakes, NJ) in RPMI-1640 medium (Catalog No. 0045092EF, Invitrogen, Carlsbad, CA) and then centrifuged at 400 g for 5 min. To lyse red blood cells, pelleted cells were suspended in red blood cell lysis buffer (Catalog No. R1010, Solarbio, Beijing, China) and incubated on ice for 2 min. Finally, cell pellets were tested for viability and resuspended in ice cold methanol for 10xgenomics profiling.
Library was performed according to the manufacturer’s instructions (single cell 5` v1.1 protocol, 10x Genomics). Single cells were processed through the 10x Genomics Chromium Platform according to manufacturer’s instructions (10x Genomics). Briefly, cells were encapsulated into Gel Beads in Emulsion (GEMs) droplets using the Chromium instrument. After encapsulation and cell lysis, cDNA expression libraries were generated following the manufacturers protocol, including barcoded reverse transcription, cDNA amplification, enzymatic fragmentation, adapter ligation and sample indexing steps.

treatment_protocol: Isogenic tumor grafting

value: skin tumor

value: melanoma

value: WT

value: invivo growth


title: Macrophape specific Rictor WT tumor

description:
Library name: 94651
10x Genomics


title: si-NC-3

description: Library name: sample6

value: si-NC transfection


title: 635, brain, contra, peri, CsA

description:
Library name: 635_7
SR75

value: brain

value: contra

value: CsA


title: Brain Cortical Endothelial cells-beta-catenin GOF-2

description: Library name: Sample 11


title: si-NC-2

description: Library name: sample5


title: 635, brain, contra, infarct, CsA

description:
Library name: 635_5
SR75

value: infractus


title: Tim-3 pos CD8+ Cd44hiCd62Llo cells, LCMV Arm d8, replicate 5

description: Library name: M6_TIM_3pos

data_processing:
Read alignment (Partek)
Assembly: GRCm39
Supplementary files format and content: Excel file with individual sample read counts
Library strategy: TCR-seq

molecule: polyA RNA

extract_protocol:
Illumina Stranded mRNA (PolyA+)
Takara Smarter Seq low input

value: Spleen

value: CD8 T cells

value: Day 8 post-LCMV armstrong infection


title: Tim-3 pos CD8+ Cd44hiCd62Llo cells, LCMV Arm d8, replicate 4

description: Library name: M4_TIM_3pos


title: FAP- CAFs-3

description: Library name: sample9

value: lung adenocarcinoma

value: primary cell

value: cancer associated fibroblasts


title: Brain Cortical Endothelial cells-beta-catenin GOF-1

description: Library name: Sample 10

value: Brain

value: Endothelial cells


title: Brain Cortical Endothelial cells-Ezh2 ECKO-3

description: Library name: Sample 9

value: Ezh2 ECKO


title: si-NC-1

description: Library name: sample4


title: Tim-3 pos CD8+ Cd44hiCd62Llo cells, LCMV Arm d8, replicate 3

description: Library name: M3_TIM_3pos


title: siLINC01711-3

description: Library name: sample3

value: si-LINC01711 transfection


title: Tim-3 pos CD8+ Cd44hiCd62Llo cells, LCMV Arm d8, replicate 2

description: Library name: M2_TIM_3pos

value: WT


title: 635, brain, ispi, infarct, CsA

description:
Library name: 635_1
SR75

value: ipsi


title: Brain Cortical Endothelial cells-Ezh2 ECKO-2

description: Library name: Sample 8


title: 376, brain, contra, peri, placebo

description:
Library name: 376_7
SR75

value: placebo


title: 638, brain, ispi, infarct, placebo

description:
Library name: 638_1
SR75

value: brain


title: Tim-3 pos CD8+ Cd44hiCd62Llo cells, LCMV Arm d8, replicate 1

description: Library name: M1_TIM_3pos


title: siLINC01711-1

description: Library name: sample1


title: Tim-3 neg CD8+ Cd44hiCd62Llo cells, LCMV Arm d8, replicate 5

description: Library name: M6_TIM_3neg


title: 376, brain, contra, infarct, placebo

description:
Library name: 376_5
SR75

value: contra


title: Brain Cortical Endothelial cells-Hdac2 ECKO-3

description: Library name: Sample 6

value: Hdac2 ECKO


title: Stearic_acid_42_S17

city: Seattle

first: Richard

middle: M

last: Jones Jr

state: WA

address: 750 Republican St

department: Microbiology

institute: University of Washington

data_processing:
DuffyTools R package used for processing
Assembly: ASM19595v2
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Mycobacterium tuberculosis

source_name: broth cultures

extract_protocol:
Trizol reagent used with bead beating in Lysing Matrix B tube followed by separation using Heavy Phase Lock tube and chloroform. Further purification using Qiagen RNeasy column was performed, including on-column DNase digest.
NEB Ultra II library prep kit was used

value: broth cultures


title: 635, brain, ispi, peri, CsA

description:
Library name: 635_3
SR75

value: CsA


title: 376, brain, ispi, peri, placebo

description:
Library name: 376_3
SR75


title: 376, brain, ispi, infarct, placebo

description:
Library name: 376_1
SR75

value: infractus


title: Tim-3 neg CD8+ Cd44hiCd62Llo cells, LCMV Arm d8, replicate 3

description: Library name: M3_TIM_3neg

value: Spleen

value: CD8 T cells

value: Day 8 post-LCMV armstrong infection


title: Brain Cortical Endothelial cells-Hdac2 ECKO-1

description: Library name: Sample 4


title: Tim-3 neg CD8+ Cd44hiCd62Llo cells, LCMV Arm d8, replicate 4

description: Library name: M4_TIM_3neg


title: Stearic_acid_14_S30


title: 1PH, brain, contra, peri, placebo

description:
Library name: 1PH11_7
SR75


title: Brain Cortical Endothelial cells-WT-3

description: Library name: Sample 3


title: siLINC01711-2

description: Library name: sample2

value: lung adenocarcinoma

value: primary cell

value: cancer associated fibroblasts


title: Stearic_acid_0_S29


title: Tim-3 neg CD8+ Cd44hiCd62Llo cells, LCMV Arm d8, replicate 2

description: Library name: M2_TIM_3neg


title: Tim-3 neg CD8+ Cd44hiCd62Llo cells, LCMV Arm d8, replicate 1

description: Library name: M1_TIM_3neg


title: RUL_Cav_R2_18mm_X_12mm_8_S21


title: Brain Cortical Endothelial cells-WT-2

description: Library name: Sample 2

value: Brain

value: Endothelial cells


title: 1PH, brain, ispi, peri, placebo

description:
Library name: 1PH11_3
SR75


title: Brain Cortical Endothelial cells-Ezh2 ECKO-1

description: Library name: Sample 7

value: Ezh2 ECKO


title: Brain Cortical Endothelial cells-WT-1

description: Library name: Sample 1

value: WT


title: RPM_CGRP_Primary_Tumors_AI731_AI732_CMO

city: Durham

first: Trudy

last: Oliver

email: tgo@duke.edu, trudy.oliver@duke.edu

state: NC

address: Duke University, Box 3813, LSRC Room C138B, 308 Research Drive

department: Pharmacology & Cancer Biology

institute: Duke University

description:
Library name: RPM_CGRP_Primary_Tumors_AI731_AI732_CMO
10X Genomic 3' CellPlex (CMO)

data_processing:
Demulitplexed with 10x cellranger mkfastq to create fastq files with sample index (I1, I2) and read files (R1, R2).
Reads were aligned to the custom mouse genome (mm10) plus Venus and firefly Luciferase (fLuc) sequences to aid in detecting recombination, and GFP.CDS and CellTag.UTR sequences (as described in Kong et al., Nature Protocols, 2020) for CellTagged samples using cellranger mkref. For primary tumors, reads were aligned to a distinct custom genome (mm10) plus EGFP, Cas9, Venus, and firefly Luciferase (fLuc) sequences  to aid in detecting recombination for various mouse models using cellranger mkref. Custom sequences includes as supplementary fasta files.
Count barcodes and UMIs were then generated using cellranger count or cellranger multi for CellPlexed/multiplexed samples.
For CellTag analysis, filtered bam files were generated according to the CellTagR workflow (https://github.com/morris-lab/CellTagR).
Downstream visualization and further analysis of scRNA seq data was performed in R with Seurat and/or Python with Scanpy.
Assembly: Custom mm10-2020-A plus EGFP, Cas9, Venus, fLuc sequences (for primary tumors) and Venus, fLuc, GFP.CDS, and CellTag.UTR sequences (for CellTagged organoids and allografts).
Supplementary files format and content: Filtered feature-barcode matrices from cellranger count or cellranger multi.

source_name: Primary lung tumor

extract_protocol:
Organoids were subject to dissociation by TrypLE for 30 minutes into a single cell suspension. Allograft and primary tumors were subject to enzymatic/mechanical digestion into a single cell suspension. Select samples were multiplexed with 10x Genomics CellPlex technology. 10x Genomics gel beads and reverse transcription reagents were added to cell suspensions and loaded to a chromium single cell controller to form gel-bead-in emulsions (GEMs). From GEMs, cDNA was generated from barcoded mRNA and subsequent A tailing, end repair, adaptor ligation, and sample indexing was performed according to manufacturer. Libraries were assessed on Agilent D5000 ScreenTape on an Agilent Tech 2200 tapestation system and quantified by Kapa Biosystems Library Quantification Kit for Illumina Platforms. Libraries were sequenced on the Novaseq 6000, Novaseq X Plus, or NextSeq 1000 with paired end seq targeting > ~30k reads/cell for gene expression (GEX) libraries or ~5k reads/cell for CellPlexing/Cell multiplexing oligo (CMO) libraries.
10X Genomics Single-Cell 3' RNA Dual Index v3 and 10X Genomics 3’ Feature Barcode Kit for CellPlexed samples

value: Primary lung tumor

tag: cellplex oligo

tag: celltag experiment

value: tumor

value: Rb1 fl/fl; Trp53 fl/fl;H11b-LSL-MycT58A-Ires-Luc (RPM); RPM-Cas9-Ires-GFP (RPMC9)

value: CGRP-Cre


title: RPM_CGRP_Primary_Tumors_AI731_AI732_GEX

description:
Library name: RPM_CGRP_Primary_Tumors_AI731_AI732_GEX
10X Genomic 3' GEX


title: Brain Cortical Endothelial cells-Hdac2 ECKO-2

description: Library name: Sample 5

value: Hdac2 ECKO


title: RUL_Cav_R1_30mm_X_22mm_26_S27

value: broth cultures


title: 1PH, brain, ispi, infarct, placebo

description:
Library name: 1PH11_1
SR75

value: brain

value: ipsi

value: infractus

value: placebo


description: Library name: M4_TIM_3pos_S8

value: Spleen

value: CD8 T cells

value: Day 8 post-LCMV armstrong infection


title: 1NN, brain contra, peri, CsA

description:
Library name: 1NN11_7
SR75

value: contra

value: CsA


title: Tim-3 pos CD8+ Cd44hiCd62Llo cells, LCMV Arm d8, replicate 5

description: Library name: M6_TIM_3pos_S10


title: RUL_Cav_R2_18mm_X_12mm_27_S28


title: Stearic_acid_28_S16


title: 1NN, brain, contra, infarct, CsA

description:
Library name: 1NN11_5
SR75


title: RPM_K5_Primary_Tumor_AI652_rep2-3_CMO

description:
Library name: RPM_K5_Primary_Tumor_AI652_rep2-3_CMO
10X Genomic 3' CellPlex (CMO)

value: AI652_central (CMO312), AI652_tracheal (CMO311)

value: Rb1 fl/fl; Trp53 fl/fl;H11b-LSL-MycT58A-Ires-Luc (RPM)


description: Library name: M3_TIM_3pos_S6

value: WT


title: RLL_Cav_R3_28_S15


description: Library name: M2_TIM_3pos_S4


title: 1PH, brain, contra, infarct, placebo

description:
Library name: 1PH11_5
SR75


title: 1NN, brain, ispi, peri, CsA

description:
Library name: 1NN11_3
SR75


title: RPM_K5_Primary_Tumor_AI652_rep2,3_GEX

description:
Library name: RPM_K5_Primary_Tumor_AI652_rep2-3_GEX
10X Genomic 3' GEX

value: Primary lung tumor

value: tumor


title: RLL_Cav_Cluster_R4_13mm_23_S26


title: 1NN, brain, ispi, infarct, CsA

description:
Library name: 1NN11_1
SR75


title: RPM_K5_Primary_Tumor_AI651_rep1_GEX

description:
Library name: RPM_K5_Primary_Tumor_AI651_rep1_GEX
10X Genomic 3' GEX


description: Library name: M1_TIM_3pos_S2


description: Library name: M6_TIM_3neg_S9


description:
Library name: RPM_Basal_Allograft_CellTagged_PostCre_Allo4_GEX
10X Genomic 3' GEX

source_name: Basal-organoid-derived allograft tumor

value: Basal-organoid-derived allograft tumor

value: Experiment_B (RPM CellTagged post-Cre)

value: CellTag post-CMV-Cre


title: R006_9_S7

value: broth cultures


title: 1NH, brain, contra, infarct, placebo

description:
Library name: 1NH11_5
SR75

value: brain


title: R006_7_S6


description:
Library name: RPM_Basal_Allograft_CellTagged_PostCre_Allo3_GEX
10X Genomic 3' GEX


description: Library name: M3_TIM_3neg_S5


title: R006_19_S11


description: Library name: M2_TIM_3neg_S3


title: R006_17_S10


title: RPR2_Basal_Allograft_GEX

description:
Library name: RPR2_Basal_Allograft_GEX
10X Genomic 3' GEX

value: Rb1 fl/fl; Trp53 fl/fl; Rbl1/p130 fl/fl (RPR2)

value: CellTag pre-CMV-Cre


title: 1NH, brain, ispi, peri, placebo

description:
Library name: 1NH11_3
SR75

value: ipsi

value: placebo


title: RLL_Cav_R3_18mm_X_15mm_16_S23


description: Library name: M1_TIM_3neg_S1

value: Spleen

value: CD8 T cells

value: Day 8 post-LCMV armstrong infection


title: 1NH, bain, ipsi, infarct, placebo

description:
Library name: 1NH11_1
SR75

value: infractus


description:
Library name: RPMA_Basal_Allograft_CellTagged_PreCre_rep1_GEX
10X Genomic 3' GEX

value: Experiment_C (RPMA CellTag pre-Cre)

value: Rb1 fl/fl; Trp53 fl/fl;H11b-LSL-MycT58A-Ires-Luc; Ascl1 fl/fl (RPMA)


description:
Library name: RPM_Basal_Organoids_CMV_CellTagged_PostCre_GEX
10X Genomic 3' GEX

source_name: Tracheal-basal organoid

value: Tracheal-basal organoid

value: organoid

value: Rb1 fl/fl; Trp53 fl/fl;H11b-LSL-MycT58A-Ires-Luc (RPM)


title: R006_11_S8


title: Mouse brain endothelial cells, ipsilateral hemisphere, PF-429242 treated MCAO

city: Toronto

first: Philippe

last: Monnier

state: ON

address: 60 Leonard Ave., 7KD-407

country: Canada

institute: University Health Network

description:
Library name: Sample 5
10x Genomics

data_processing:
The 10x Genomics scRNA-seq data was processed using Cell Ranger v6.1.2 with the Mouse reference, mm10 (GENCODE vM23/ Ensembl 98).
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: brain endothelium

extract_protocol:
For FACS sorting, cell suspensions were obtained upon digesting brain tissue in 2 mg/ml Dispase II (D4693, Sigma-Aldrich), 2 mg/mL Collagenase IV (#1710401, Thermo Fisher Scientific, Zurich, Switzerland) and 2 mM CaCl2 PBS (40 min at 37°C). The suspension was filtered through 100/70/40 μm cell strainers (#431751, Corning, New York, USA) and cells were then centrifuged 300 g for 7 min, and resuspended in 9 ml PBS, followed by another round of centrifugation. Cell pellets were resuspended in 3 mL of ACK hemolytic buffer. To stop the reaction, 30 mL of ice-cold PBS was added and centrifuged at 300 g for 7 min. Pellets were resuspended in PBS + 1% BSA. For FACS sorting, cells were stained with anti-CD31 and anti-CD45 (see Table 3). Following washes with PBS + 1% BSA the suspension was passed through a 35 μm cell strainer of a FACS sorting tube (#352235, Corning). Cells were sorted by a FACS Aria III (648282D2, BD Bioscience) sorter using the four-way purity sorting mode.  Live events were acquired and analyzed using Flowjo 10.0.6 software (Tree Star Inc.).  FACS-sorted endothelial cells were resuspended at a 1,000 cells/μL.
scRNA-seq libraries were obtained following the 10x Genomics recommended protocol using the reagents included in the Chromium Single Cell v3.3 Reagent Kit. Libraries were sequenced on a NextSeq 500 (Illumina, Inc., San Diego, CA, USA) at the Princess Marget Genomics Center (University Health Network, Toronto, ON, Canada), aiming at 50k reads per cell.

treatment_protocol: Injection of PF-429242 or vehicle

value: brain endothelium

value: endothelial cells

value: wild-type

tag: age

value: 8-12 weeks

tag: Sex

value: male

tag: strain


title: 1LT, brain, contra, peri, placebo

description:
Library name: 1LT11_7
SR75

value: brain

value: contra


title: Mouse brain endothelial cells, contralateral hemisphere, PF-429242 treated MCAO

description:
Library name: Sample 4
10x Genomics


title: C10_6

city: Jinan

first: Liu

last: Zhaochao

address: Wenhua West Road

institute: Shandong University

description:
Library name: CC6
C10_6

data_processing:
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data). The steps are: 1) Trim Smart-seq2 public primer sequence from the Reads (If the length of trimmed Reads is lower than 30bp, reads should be discarded. If it is PE sequence, both of the reads must be removed ); 2) Remove the contaminated reads for adapters (The contaminated reads for adapters was defined that the Read Bases contained more than 5bp of adapter sequences. If either one of the PE Reads was polluted, we will remove both ends of the reads); 3) Remove the low quality reads (The low quality reads was defined that the number of Reads Bases whose phred Quality value was less than or equal to 19 accounted for more than 15% . If either one of the PE Reads defined as low quality, we will remove both ends of the reads); 4) Remove the reads whose N base more than 5% for total bases (If either one of the PE Reads had high Ns bases, we will remove both ends of the reads).
Assembly: mm10
Supplementary files format and content: xls file include count and FPKM value for each sample

source_name: nasal mucosa

extract_protocol:
Chronic rhinosinusitis (CRS) mice model To establish CRS mice model, mice in CRS group were treated intranasally with 20μg Papain (Sigma-Aldrich, P5306-25MG, USA) which was dissolved in 20μL phosphate buffer saline (PBS) on days 0-2 and 7-11. Drug treatment The treatment dosage of C10 (MCE, HY-19357, CHN) drug solution for intranasal administration in CRS mice were 10 mg/mL, with bilateral administration (10 μl/side, bilateral intranasal instillation). Starting from the initial administration of papain, treatment was continued for 10 consecutive days, with once-daily application. The concentration 10 ng/mL of IL-13 (MCE, HY-P72795, CHN) was used to stimulate Beas-2b and HNECs for 48 hours.
A total amount of 1-3μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina ® （NR604-01/02）following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Then we added fragmentation buffer to break the mRNA into short fragments. First strand cDNA was synthesized using random hexamer primer and RNase H. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. And then, the double stranded cDNA was purified by AMPure P beads or QiaQuick PCR kit. The purified double stranded cDNA was repaired at the end, added a tail and connected to the sequencing connector, then the fragment size was selected, and finally the final cDNA library was obtained by PCR enrichment.

value: nasal mucosa


title: 1LT, brain, contra, infarct, placebo

description:
Library name: 1LT11_5
SR75

value: placebo


title: R002_9_S3

value: broth cultures


title: 1LT, brain, ispi, peri, placebo

description:
Library name: 1LT11_3
SR75

value: ipsi


title: 1NH, brain, contra, peri, placebo

description:
Library name: 1NH11_7
SR75


description: Library name: M4_TIM_3neg_S7

value: Spleen

value: CD8 T cells

value: WT

value: Day 8 post-LCMV armstrong infection


title: C10_5

description:
Library name: CC5
C10_5


title: Mouse brain endothelial cells, ipsilateral hemisphere, vehicle treated MCAO

description:
Library name: Sample 3
10x Genomics

value: vehicle


title: R002_7_S2


title: 1LT, brain, ispi, infarct, placebo

description:
Library name: 1LT11_1
SR75

value: infractus


title: R006_13_S9


title: 1DY, brain, contra, peri, CsA

description:
Library name: 1DY11_7
SR75

value: CsA


title: R002_3_S1


title: C10_3

description:
Library name: CC3
C10_3


title: Mouse brain endothelial cells, ipsilateral hemisphere, vehicle treated sham

description:
Library name: Sample 1
10x Genomics

value: brain endothelium

value: endothelial cells


title: C10_2

description:
Library name: CC2
C10_2


title: R002_14_S5


title: Cav3.1 KO female mice with chronic stress 3

city: Kumamoto

first: Yasushi

last: Yabuki

state: Kumamoto

address: 2-2-1, Honjo, Chuo-ku

department: Genomic neurology

institute: Kumamoto University

description: Library name: KOf with stress 3

data_processing:
Fastq files were processed for quality check and adapter trimming with Trimgalore! (0.6.6; https://github.com/FelixKrueger/TrimGalore). Trimmed reads were used for mapping the mouse genome (mm10) using STAR (2.7.9a). RSEM (1.3.1) was used to obtain read counts. The gene expression in each sample was further processed using DESeq2 (version 1.36.0) and expressed as normalized counts in a regularized logarithm (rlog). GO analysis was performed via over representation analysis in clusterProfiler v4.2.2.
Assembly: Mus Musculus
Supplementary files format and content: Fastq files; GeneMat_Count data

source_name: brain tissue

growth_protocol: The generation of Cav3.1 KO mice with a C57BL/6J genetic background is described in a previous study (Anesthesiology. 2007;106(6):1177-1185. ). Cav3.1 KO mice (RBRC01465) were obtained from the RIKEN BioResource Research Center (RIKEN BRC, Japan). WT male and female C57BL/6J mice were purchased from Clea Japan, Inc. (Tokyo, Japan).  All experiments used adult male and female mice (aged 8–12 weeks). The animals were housed under conditions with a constant temperature at 23°C ± 2°C and humidity at 55% ± 5% in a 12-h light and dark cycle (light: 7:30 am–7:30 pm). The animals had unlimited access to food and water.

extract_protocol:
Total RNA was extracted from mPFC in WT and Cav3.1 KO with or without chronic stress  using an RNeasy Kit.
DNA libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit

treatment_protocol: Chronic stress; The forced swim test (FST) and tail suspension test (TST) were performed. In the FST, the mice were placed individually in glass cylinders (height: 20 cm; diameter: 15 cm) filled with water with a temperature of 25℃. The total duration of animal immobility within the 5-min test period was scored. In the TST, acoustically and visually isolated mice were suspended 50 cm above the floor using an adhesive tape placed approximately 1 cm from the tip of the tail. The immobility time was recorded for 5 min. The mice were considered immobile only when they hung passively and remained completely motionless. The mouse was subjected to either behavioral test once a day for 5 days. Some opto-probe-implanted mice could not swim well and could drown during FST. Hence, the mice for the optogenetic experiments were only subjected to the TST. The mouse behaviors were recorded using a video camera, and their immobility time was measured by the recorded movies.

value: medial prefrontal cortex (mPFC)

value: Chronic stress


title: 1DY, brain, ispi, peri, CsA

description:
Library name: 1DY11_3
SR75

value: brain


title: C10_1

description:
Library name: CC1
C10_1


title: Cav3.1 KO female mice with chronic stress 2

description: Library name: KOf with stress 2


title: 1DY, brain, ipsi, infarct, CsA

description:
Library name: 1DY11_1
SR75


title: R002_12_S4


title: CRS_6

description:
Library name: CRS6
CRS_6


title: Cav3.1 KO female mice with chronic stress 1

description: Library name: KOf with stress 1


title: LUL_Cav_L1_15_S14


title: LUL_Cav_L1_15mm_12_S22


title: HI-hip-3

city: Fuzhou

first: Jianjie

last: Wei

state: Please Select

address: No. 134, East Street, Gulou District

institute: Fujian Province Hospital

data_processing:
Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis (http://www.genome.jp/kegg/) were used to explore the biological processes and pathways involved in the differential expression of  mRNA in the two groups of samples.
Using these relevant records, plots were made using the Cytoscape v2.8.3 tool.
plots were made using the Cytoscape v2.8.3 tool.
Assembly: Rnor6

source_name: hippocampus

extract_protocol:
Total RNA was extracted by TRIzol method, and the concentration of RNA was ensured to be in the range of A260/A280 ratio of 1.8~2.1
1 - 2 μg total RNA was taken from each sample to construct sequencing library. The mRNA is purified, fragmented, and PCR amplified according to the assay. Prepare the mixed library according to the experimental design, ensure that the final concentration of the mixed library is 2 nM, and the volume is greater than or equal to 10 µL. The prepared library is stored at -80℃. Prepare the sample of the library for sequencing on

value: hippocampus

value: Hypoxic ischemic brain damage (HIBD)


title: LLL_Cav_L2_20mm_21_S25


title: C10_4

description:
Library name: CC4
C10_4

value: nasal mucosa


title: Cav3.1 KO female mice without chronic stress 3

description: Library name: KOf3


title: CRS_4

description:
Library name: CRS4
CRS_4


title: Mouse brain endothelial cells, contralateral hemisphere, vehicle treated MCAO

description:
Library name: Sample 2
10x Genomics

value: wild-type

value: 8-12 weeks

value: male


title: LLL_Cav_L2_20mm_18_S24

value: broth cultures


title: HI-hip-1


title: CRS_3

description:
Library name: CRS3
CRS_3


title: CRS_5

description:
Library name: CRS5
CRS_5


title: Cav3.1 KO female mice without chronic stress 1

description: Library name: KOf1


title: HI-hip-2


title: Cav3.1 KO female mice without chronic stress 2

description: Library name: KOf2


title: CON-hip-3

value: Sham


title: WT female  mice with chronic stress 3

description: Library name: WTf with stress 3


title: KA_2_S12


title: CRS_2

description:
Library name: CRS2
CRS_2


title: WT female mice with chronic stress 2

description: Library name: WTf with stress 2


title: 1DY, brain, contra, infarct, CsA

description:
Library name: 1DY11_5
SR75

value: contra


title: iMTB_42_S20


title: KA_3_S13


title: CON_6

description:
Library name: C6
CON_6


title: WT female mice with chronic stress 1

description: Library name: WTf with stress 1


title: CON-hip-1


title: HI-colon-3

source_name: colon

value: colon


title: CON_5

description:
Library name: C5
CON_5


title: iMTB_28_S19


title: iMTB_0_S31


title: WT female mice without chronic stress 3

description: Library name: WTf3


title: CON_4

description:
Library name: C4
CON_4


title: HN878_R2_1Probe


title: HN878_R1_1Probe


title: WT female mice without chronic stress 1

description: Library name: WTf1


title: CON_3

description:
Library name: C3
CON_3


title: HI-colon-1


title: WT female mice without chronic stress 2

description: Library name: WTf2


title: HI-colon-2


title: CON-colon-3


title: CON-hip-2


title: B16_PulledDown_S11


title: CON_2

description:
Library name: C2
CON_2


title: CRS_1

description:
Library name: CRS1
CRS_1


title: CON-colon-2


title: CON_1

description:
Library name: C1
CON_1


title: Luminal cells

city: Beijing

first: Pan

last: Jingyu

address: Haiding Street

department: School of basic medicine sciences

institute: Tsinghua university

description: Library name: Sample1

data_processing:
Cutadapt--HISAT2--HTSEQ--DESeq2/EdgeR
Assembly: mm39, hg38
Supplementary files format and content: raw counts

source_name: Mammary gland

extract_protocol:
RNA was extracted by RNAiso reagent. 0.1-1ug total RNA was used for constructing RNA-seq library
RNA-seq library was constructed by NEB kit according to the manufacturer's protocol

value: Mammary gland

value: Primary cell

value: Normal cell

value: WT

value: No


title: Cav3.1 KO mice with chronic stress 3

description: Library name: KO with stress 3

data_processing:
Fastq files were processed for quality check and adapter trimming with Trimgalore! (0.6.6; https://github.com/FelixKrueger/TrimGalore). Trimmed reads were used for mapping the mouse genome (mm10) using STAR (2.7.9a). RSEM (1.3.1) was used to obtain read counts. The gene expression in each sample was further processed using DESeq2 (version 1.36.0) and expressed as normalized counts in a regularized logarithm (rlog). GO analysis was performed via over representation analysis in clusterProfiler v4.2.2.
Assembly: Mus Musculus
Supplementary files format and content: GeneMat_Count data

source_name: medial prefrontal cortex (mPFC)

value: medial prefrontal cortex (mPFC)

value: brain tissue

value: Chronic stress


title: CON-colon-1


title: B15_PulledDown_S10


title: FFA180_03

city: Memphis

last: Lee

state: TN

address: 262 Danny Thomas Place

department: Department of Chemical Biology and Therapeutics

institute: St. Jude Children's Research Hospital

data_processing:
Illumina Casava1.8 software used for basecalling.
The resulting reads were saved in FASTQ format and data was processed through the High-Performance Computing Facility at St. Jude.
Adapter content and quality trimming was performed using Cutadapt. The quality of the raw and trimmed reads was assessed using FastQC and MultiQC.
The resulting processed reads were aligned to the reference Mycobacterium abscessus ATCC19977 (Genome accession: NC_010397) using STAR2.7.1a and aligned reads were counted using featureCounts.
Differential gene expression analysis was analyzed using DESeq2 in the R statistical computing environment.
Assembly: Mycobacterium abscessus ATCC19977 (Genome accession: NC_010397)
Supplementary files format and content: Binary Alignment Map (.bam) files include aligned reads to M. abscessus ATCC19977 reference genome (Genome accession: NC_010397).
Supplementary files format and content: tab-delimitated text (.txt) files include raw counts for each Sample

organism: Mycobacteroides abscessus ATCC 19977

source_name: Planktonic

growth_protocol: M. abscessus ATCC19977 was cultured in cation-adjusted mueller hinton broth shaking at 225 rpm at 37 °C.

extract_protocol:
After treatment, 5 mL of Bacterial RNAprotect (Qiagen) was added for 5 minutes at room temperature. The culture was then centrifuged at 3214 xg for 10 minutes at 4 °C and the supernatant discarded. An RNAeasy Plus Mini Kit (Qiagen; Cat. No. 74134) was used to extract the RNA following the manufacturer’s instructions utilizing mechanical lysis for Gram-positive bacteria.
Libraries were prepared from ribosomal RNA-depleted total RNA using Illumina Stranded Total RNA Prep, ligation with Ribo-Zero Plus mRNA Library Prep Kit according to the manufacturer’s instructions (Illumina, PN 20037135). Libraries were analyzed for insert size distribution using the 2100 BioAnalyzer High Sensitivity kit (Agilent). Libraries were quantified using the Quant-iT PicoGreen ds DNA assay (ThermoFisher). Paired-end 100 cycle sequencing was performed on a NovaSeq X Plus (Illumina).

treatment_protocol: Five mL of mid-log cultures (OD600 0.4-0.6) were treated with 1/2 MIC of chloramphenicol (256 mg/L) for 30 minutes, 25µM of florfenicol for 30 minutes and 3 hours, 25µM of florfenicol amine for 30 minutes and 3 hours, or equilalent vehicle control (DMSO) for 30 minutes or 3 hours shaking at 225 rpm at 37 °C.

value: Planktonic

value: Florfenicol amine-0.025mM-3 hours


title: B13_PulledDown_S9