title: Cal-27_NC_mRNA_3

city: Kunming

first: Weizhou

last: Wang

state: Yunnan

address: Chunrong West Road

institute: Kunming Medical University

description:
G3
fpkm_NC3

data_processing:
We sequence 6 samples used BGISEQ platform.
The raw data was filtered with SOAPnuke by 1) Removing reads containing adapters (adapter contamination); 2) Removing reads whose unknown base ('N' base) ratio is more than 10%; and 3) Removing reads whose low-quality base ratio (Base quality less than or equal to 15) is more than 50%, afterwards clean reads were obtained and stored in FASTQ format.
The clean data were mapped to the assembled unique gene by Bowtie2 (v2.2.5). The expression level of genes was calculated by RSEM (v1.2.8).
Annotating assembled Unigene with seven major functional databases (KEGG, GO, NR, NT, SwissProt, Pfam, and KOG), and predicting the transcription factors.
Assembly: mm10
Supplementary files format and content: gene_expression.txt: Tab-delimited text file includes FPKM values, TPM values, and counts for each Sample.

growth_protocol: Cal-27 cells were cultured in high glucose DMEM supplemented with 10% fetal bovine serum (Gibco, USA).

extract_protocol:
Total RNA was extracted using Trizol reagent (Thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511), high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat.1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA libraries were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: The hOMF-Exo or CAFs-Exo were co-cultured with Cal-27 for 48h, and a control group was set up. There were three replicate samples in each group. Total RNA was extracted from each sample in the NC group, hOMF-exo group, and CAF-exo group.

value: tongue squamous carcinoma cells

value: WT

value: Normal Control


title: 928

status: Public on May 16 2023

type: SRA

city: Chicago

first: Zhou

last: Zhang

state: IL

address: 680 North Lake Shore Drive, Suite 1400

department: Preventive Medicine

country: USA

institute: Northwestern University

library_source: genomic

data_processing:
library strategy: 5hmC-Seal-seq
Bcl2fastq v2.17 software used to change the bcl files to fastq files.
Sequenced reads were trimmed for adaptor sequence using software trimmomatic v0.36, and masked for low-complexity or low-quality sequence, then mapped to hg19  genome using bowtie v2.26
Duplicate reads were marked using picard v1.141. The reads were counted for overlap with gene bodies (annotated by the GENCODE Project) using featureCounts v1.5.0-p3.
Assembly: hg19
Supplementary files format and content: A CSV file include edgR normalized 5hmC levels for all sample.

molecule: genomic DNA

organism: Homo sapiens

source_name: plasma

extract_protocol:
Circulating cfDNA was isolated using the QIAamp Circulating Nucleic Acid Kit (Qiagen) from 0.5 mL of frozen serum per study subject. Genomic DNA (gDNA) was isolated from ~5 mg of frozen DLPFC using the Monarch Genomic DNA Purification Kit (New England Biolabs).
To obtain sequencing-amenable ~200 bp fragments of gDNA from brain samples, we performed enzymatic fragmentation using the KAPA HyperPlus Kit (Roche). After ligation of unique dual index barcoded sequencing adapters, DNA fragments proceeded through the 5hmC-Seal protocol to construct sequencing libraries.

tag: subject id

tag: tissue

value: plasma


title: 926


title: AT AA LN Tvm 5

city: Daejeon

first: Su-Hyung

last: Park

address: 291, Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Advanced Institute of Science and Technology

description: AT AA LN Tvm 5

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: LN

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: LN

tag: cell type

value: Lymphocytes


title: 927


title: Cal-27_NC_mRNA_2

country: China

description:
G2
fpkm_NC2

tag: cell line

tag: genotype

tag: treatment


title: Sham2

city: Chiyoda-ku, Tokyo

first: Yoshinori

last: Hayashi

address: 1-8-13, Kandasurugadai

department: Physiology

country: Japan

institute: Nihon University

data_processing:
De-multiplexing and conversion to FASTQ format were performed using the bcl2fastqsoftware (v2.19).
The sequence reads were mapped to the Rat reference genome (rn6) using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b)
featureCounts (v1.5.0-p3) was used to count the read numbers mapped to each gene.
Differential expression analysis of two groups were performed using the DESeq2 R package (v1.20.0).
Assembly: rn6
Supplementary files format and content: A excel file includes FPKM values for all samples and comparing results.

organism: Rattus norvegicus

source_name: inferior alveolar nerve

extract_protocol:
RNA was harvested TRIsure reagent(NipponGenetics) and precipitated by a precipitationcarrier(Takara).
RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer's protocols.

value: inferior alveolar nerve


title: AT AA LN Tvm 6

description: AT AA LN Tvm 6


title: Sham1


title: AT AA LN Tn 2

description: AT AA LN Tn 2


title: 933


title: Sham3


title: Cal-27_HOMF_EXO_mRNA_3

description:
F3
fpkm_HOMF_EXO3

value: Cells were co-cultured with hMOF exosomes


title: 923


title: 922


title: Cal-27_HOMF_EXO_mRNA_2

description:
F2
fpkm_HOMF_EXO2


title: AT AA LN Tn 1

description: AT AA LN Tn 1


title: IANX3

value: transfection


title: IANX2


title: AT AA skin CD44shi 3

description: AT AA skin CD44shi 3

source_name: Skin

value: Skin


title: Cal-27_HOMF_EXO_mRNA_1

description:
F1
fpkm_HOMF_EXO1


title: 921


title: Cal-27_CAFs_EXO_mRNA_3

description:
E3
fpkm_CAFs_EXO3

value: Cells were co-cultured with CAFs exosomes


title: AT AA skin CD44shi 2

description: AT AA skin CD44shi 2


title: Cal-27_CAFs_EXO_mRNA_2

description:
E2
fpkm_CAFs_EXO2


title: 920


title: AT AA skin CD44shi 1

description: AT AA skin CD44shi 1


title: IANX1


title: 919


title: 924


title: Cal-27_CAFs_EXO_mRNA_1

description:
E1
fpkm_CAFs_EXO1


title: Cal-27_NC_mRNA_1

description:
G1
fpkm_NC1


title: 918


title: AT AA LN CD44shi 3

description: AT AA LN CD44shi 3


title: AT AA LN CD44shi 2

description: AT AA LN CD44shi 2


title: 917


title: T347c-n3_RNA

city: Dublin

first: Leonie

last: Young

state: Dublin

address: 31A York Street

department: Surgery

country: Ireland

institute: RCSI

description: 2x100 paired-end sequence reads

data_processing:
Quality control to remove adapter sequences and low-quality reads was performed using FASTQC (v0.11.9) and MultiQC (v1.7) was used to summarize the reports.
Salmon (v0.14.1) workflow was used for quantification of RNA-seq data with the human reference genome NCBI build 38 (GRCH38).
DESeq2 package was used to calculate differential gene expression between cell lines pairs (LY2-MCF7, T347-MCF7).
Genome_build: Human reference genome NCBI build 38, GRCh38
Supplementary_files_format_and_content: DESeq normalized counts (counts(dds, normalized=T)

source_name: human breast cancer cell line T347

growth_protocol: The T347 cell line was derived from a patient with a breast cancer brain metastatic tumour (ER+, PR−, HER2+). The tumour was previously expanded in NOD-SCID mice and the harvested tumour cells were cultured in human breast epithelial cell (HBEC) media (10770245, Hyclone DMEM/F12 1:1) supplemented with 10 mM HEPES (H3537, Sigma-Aldrich), 5% FBS, 1 mg/ml insulin (I9278, Sigma), 0.5 µg/ml hydrocortisone H0888, Sigma-Aldrich). Cells were incubated in a humidified incubator at 5% CO2 at 37°C.

extract_protocol:
Total RNA isolation was carried out using the RNeasy mini kit (74104, Qiagen) according to the manufacturer's instructions.
Library prep was performed by BGI (Hong Kong) from 200 ng of total RNA.

value: breast cancer brain metastatic tumour derived

tag: replicate number

value: Replicate 3


title: T347c-n2_RNA

description: 2x100 paired-end sequence reads

value: Replicate 2


title: AT AA LN CD44shi 1

description: AT AA LN CD44shi 1


title: 916


title: Htt+/+ Cortex Input control for HTT Knockdown No Treatment Group

city: Baltimore

first: Amol

middle: Carl

last: Shetty

state: Maryland

address: 670 W. Baltimore Street, Floor 3

department: Institute for Genome Sciences

institute: University of Maryland Baltimore

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software.
Sequencing reads were aligned to the mouse genome (mm9) using HISAT2.
Peak-calling was then performed with MACS2.2
Genome_build: mm9
Supplementary_files_format_and_content: peak text files

source_name: cortex

growth_protocol: Four-month-old male HttQ111/+  and age-matched Htt+/+ mice underwent unilateral intracerebroventricular injection of 500ug pan-huntingtin antisense oligonucleotide (Ionis #444652) or received no treatment, Fresh-frozen cortical tissue ipsilateral to the injection was collected for ChIP at four weeks post injection.

extract_protocol:
IPs were performed using Abcam Anti-huntingtin antibody EPR5526 (#ab109115).
NEB NextUltra DNA Library Preparation kit following the manufacturer’s recommendations (Illumina, San Diego, CA, USA).

treatment_protocol: For each ChIP preparation, chromatin DNA was prepared using ipsilateral cortical tissue from three mice.  Tissue was transferred to a glass dounce on ice and homogenized in cold PBS with protease inhibitors.

value: brain

tag: chip antibody

value: Input

tag: agent


title: Htt+/+ Cortex Input control for HTT Knockdown HTT-ASO Treatment Group

value: HTT-ASO


title: Htt+/+ Cortex HTT ChIP for HTT Knockdown No Treatment Group

value: anti-HTT EPR5526


title: AT AA LN Tvm 4

description: AT AA LN Tvm 4


title: HttQ111/+ Cortex Input control for HTT Knockdown No Treatment Group


title: Htt+/+ Cortex HTT ChIP for HTT Knockdown HTT-ASO Treatment Group


title: T347c-n1_RNA

description: 2x100 paired-end sequence reads

value: Replicate 1


title: 915


title: 914


title: HttQ111/+ Cortex HTT ChIP for HTT Knockdown No Treatment Group


title: AT AA LN Tvm 3

description: AT AA LN Tvm 3


title: LY2-n3_RNA

description: 2x100 paired-end sequence reads

source_name: human breast cancer cell line LY2

growth_protocol: LY2 endocrine-resistant breast cancer cells, a gift from Robert Clarke (Georgetown, USA), were cultured in phenol red free MEM (51200_046, Gibco Sigma-Aldrich) supplemented with 10% charcoal dextran stripped (CDS), 2 mM l-glutamine and 10-8M 4-hydroxytamoxifen (4-OHT) (H7904, Sigma-Aldrich). Cells were incubated in a humidified incubator at 5% CO2 at 37°C.

value: endocrine-resistant breast cancer


title: AT AA LN Tvm 2

description: AT AA LN Tvm 2


title: HttQ111/+ Cortex Input control for HTT Knockdown HTT-ASO Treatment Group


title: 913

value: plasma


title: LY2-n2_RNA

description: 2x100 paired-end sequence reads


title: 912


title: LY2-n1_RNA

description: 2x100 paired-end sequence reads


title: Naïve LN Tvm 4

description: Naïve LN Tvm 4

value: LN


title: HttQ111/+ Cortex HTT ChIP for HTT Knockdown HTT-ASO Treatment Group


title: MCF7-n3_RNA

description: 2x100 paired-end sequence reads

source_name: human breast cancer cell line MCF7

growth_protocol: Breast cancer MCF7 endocrine sensitive cells were purchased from (ATCC, UK), cultured in MEM (M2279, Sigma-Aldrich) supplemented with 10% FCS (F7524, Sigma-Aldrich). Cells were incubated in a humidified incubator at 5% CO2 at 37°C.

value: endocrine-sensitive breast cancer


title: 911


title: 910


title: MCF7-n2_RNA

description: 2x100 paired-end sequence reads


title: Naïve LN Tvm 3

description: Naïve LN Tvm 3

value: Lymphocytes


title: Naïve LN Tvm 2

description: Naïve LN Tvm 2


title: 909


title: Naïve LN Tvm 1

description: Naïve LN Tvm 1


title: T347c-n3_MeRIP

description:
2x100 paired-end sequence reads
T347c_MeRIP_peaks.narrowPeak

data_processing:
Library strategy: MeRIP-seq
Quality control checks were performed using FASTQC (v0.11.9) and MultiQC (v1.7). MCF7_rep3 fastq files were removed from further analysis after MCF7_rep3_2.fq.gz was reported as truncated.
MeRIP-seq reads were mapped GRCH38 human reference genome using Bowtie2. The SAM files from Bowtie were then sorted by coordinate and, using Picard Tools, they were converted to BAM file format.
Coverage files (bigWig) of the mapped reads were obtained running the genomecov tool from BEDTools software suite followed by the bedGraphToBigWig tool from the ucscGenomeBrowser/kent repository on GitHub.
For each individual cell line pooled narrowPeak files were obtained using the MACS2-callpeak tool from SevenBridges platform (https://www.sevenbridges.com/), with the default q-value (FDR) cutoff of 0.05.
Differential m6A methylation sites between cell lines (LY2-MCF7, T347-MCF7, MCF7-LY2) were predicted using the MeTDiff package (PEAK_CUTOFF_FDR = 0.05, DIFF_PEAK_CUTOFF_FDR = 0.05) with the IP/control (MeRIP/RNA) pairs as input.
Genome_build: Human reference genome NCBI build 38, GRCh38
Supplementary_files_format_and_content: Genome-wide read depth information in bigWig format.
Supplementary_files_format_and_content: Peaks of signal enrichment information based on pooled, normalized data.
Supplementary_files_format_and_content: Differential m6A methylation sites in Excel format.

extract_protocol:
Total RNA isolation was carried out using the RNeasy MIDI kit (74144, Qiagen) according to the manufacturer's instructions.
M6A IP library prep was performed by BGI (Hong Kong) using 200-350 μg of RNA and the Magna MeRIP™ m6A Kit (17-10499, Merck Millipore).


title: 908


title: Naïve LN Tn 3

description: Naïve LN Tn 3


title: T347c-n2_MeRIP


title: 907


title: Naïve LN Tn 2

description: Naïve LN Tn 2


title: AT AA LN Tvm 1

description: AT AA LN Tvm 1


title: T347c-n1_MeRIP


title: 906


title: LY2-n3_MeRIP

description:
2x100 paired-end sequence reads
LY2_MeRIP_peaks.narrowPeak


title: 905


title: Naïve LN Tn 1

description: Naïve LN Tn 1


title: K279a_mutant_smlt2053_Biol_Replicate_1

city: Bellaterra

first: Isidre

last: Gibert

state: Barcelona

address: Carrer de la Vinya, s/n

department: Institut de Biotecnologia i de Biomedicina (IBB)

country: Spain

institute: Universitat Autònoma de Barcelona (UAB)

data_processing:
Sequence mapping was perfomed with STAR/2.5.3a
Quantification with RSEM/1.3.0
The differential gene expression analysis was performed using the DESeq2 R package using an adjusted p-value < 0.05 (FDR of 5%) as a cut-off for statistical significance
To remove unwanted variation, the SVA method (Leek et al., 2012) was used
Assembly: Stenotrophomonas maltophilia K279a NC_010943.1 (2017)
Supplementary files format and content: norm_counts; fold change and p-values for each compared condition

organism: Stenotrophomonas maltophilia K279a

source_name: Bacterial culture

growth_protocol: All bacterial cultures were done in LB at 37C in a shaking incubator at 200 rpm.

extract_protocol:
RNA was harvested using RNeasy Mini Kit (Qiagen).
TruSeqTM Stranded Total RNA kit protocol (Illumina Inc.) was used to construct the stranded total RNA-Seq libraries

value: Bacterial culture

tag: strain background

value: smlt2053 defective


title: Spontaneous AA LN Tvm 3

description: Spontaneous AA LN Tvm 3


title: 904


title: LY2-n2_MeRIP


title: K279a_WT_Biol_Replicate_2

value: wild type


title: MCF7-n1_RNA

description: 2x100 paired-end sequence reads


title: Spontaneous AA LN Tvm 2

description: Spontaneous AA LN Tvm 2


title: K279a_WT_Biol_Replicate_3


title: LY2-n1_MeRIP


title: 903


title: Mesenchymal stem cell, TWIST1-overexpression rep2

type: RNA

city: Osaka-Sayama

first: Toshiyuki

last: Takehara

state: Osaka

address: 377-2, Ohno-Higashi

department: Faculty of Medicine

institute: Kindai Universty Hospital

description: gene expression data from TWIST1 expression MSC

hyb_protocol: Following fragmentation, 5 ug of fragmented and labeled ss-cDNA were hybridized for 16 hr at 45℃ on GeneChip Clariom S array, mouse. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Gene chip Scanner 7G, affymetrix.

data_processing: The raw data of the array were collected as CEL files and analysed using the Transcriptome Analysis Console (TAC 4.1) software. The gene expression was analysed with the Gene Level SST-RMA summarization method.

label: biotin

source_name: Mesenchymal stem cell

label_protocol: Biotinylated ss-cDNA were prepared according to the standard Affymetrix protocol from 1 ng total RNA(Gene Chip WT Pico kit, Affymetrix)

growth_protocol: Cells were cultured in α-MEM supplemented with 200 mM L-glutamine, 10% fetal bovine serum under 5%CO2 and 5%O2 at 37℃.

extract_protocol: Trizol extraction of total RNA and DNase treatment were performed according to the manufacturer's instructions

treatment_protocol: GFP or Twist1-overexpression cells were infected with the SeVdp vectors at a MOI of 5 and incubated overnight at 37°C. The viral medium was replaced, and 10 μg/mL puromycin was added to purify the MSCs stably expressing the SeVdp-TWIST1 or GFP


title: MCF7-n2_MeRIP

description:
2x100 paired-end sequence reads
MCF7_MeRIP_peaks.narrowPeak


title: Spontaneous AA LN Tvm 1

description: Spontaneous AA LN Tvm 1


title: K279a_WT_Biol_Replicate_1


title: Mesenchymal stem cell, GFP-overexpression rep1

description: gene expression data from GFP expression MSC

value: GFP


title: Mesenchymal stem cell, GFP-overexpression rep2


title: K279a_mutant_smlt2053_Biol_Replicate_3


title: 902


title: Mesenchymal stem cell, TWIST1-overexpression rep1


title: Spontaneous AA LN CD44shi 2

description: Spontaneous AA LN CD44shi 2


title: MCF7-n1_MeRIP


title: K279a_mutant_smlt2053_Biol_Replicate_2


title: 901


title: Spontaneous AA LN CD44shi 1

description: Spontaneous AA LN CD44shi 1


title: 780

source_name: brain


title: 779


title: mHSC, scRNAseq

city: Guangzhou

first: chen

last: minqi

state: Guangdong

address: No.74, 2nd Zhongshan Road

institute: Sun Yat-sen University

description:
HSCs purified from challenged wild-type C57BL/6J mice with Listeria monocytogenes (LM) at 6 weeks after LM infection.
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: CellRanger matrix files.

source_name: bone marrow

extract_protocol:
In brief, intact bone marrows from mice at the age of 6-8 weeks were flushed from mouse femora and tibiae. Bone marrow cells by pipetting with 1 mL syringe, and then underwent red blood cell lysis using 0.16 M ammonium chloride solution.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

tag: strain

value: bone marrow

value: challenged with Listeria monocytogenes (LM)

tag: time

value: 6 weeks after challenge

tag: age

value: 6-8 weeks old


title: 778

value: brain


title: Immortalized MEFs WT3

city: hangzhou

first: RUIZHU

last: ZHANG

state: 浙江省

address: Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China 310058

institute: 浙江大学生命科学研究院

description: immortalized MEFs

data_processing:
Raw reads were trimmed to 50 bp and mapped to the mouse   genome (mm9) using Tophat v2.1.1 with default parameters. Only uniquely mapped   reads were subsequently assembled into transcripts guided by the reference   annotation (UCSC gene models) using Cufflinks v2.2.1. The RNA abundance of each   gene was quantified with FPKM (fragments per kilobase of exon per million mapped   fragments). Genes with FPKM < 1 in all samples were excluded, and for the remaining   genes, all FPKM values smaller than 1 were set to 1 in subsequent analyses.   Differential expressed genes were identified using the criteria |FC| > 2. GO enrichment   was performed using “metascape” web server.
Assembly: mm10
Supplementary files format and content: All of the processed data files format are "txt", which are descrebe the gene's expression level in different samples.

source_name: MEFs

extract_protocol:
Total RNA was isolated from immortalized MEFs or 3 pairs (WT and G2A littermates)   of E12.5 fetal livers using the Trizol method.
Next-generation sequencing was done by   BGI (Shenzhen, China). Raw reads were trimmed to 50 bp and mapped to the mouse   genome (mm9) using Tophat v2.1.1 with default parameters.

value: MEFs

value: mouse embryonic fibroblasts

value: WT

value: No treatment


title: Immortalized MEFs WT2

description: immortalized MEFs

growth_protocol: Total RNA was isolated from immortalized MEFs or 3 pairs (WT and G2A littermates)   of E12.5 fetal livers using the Trizol method.


title: Immortalized MEFs G2A3

description: immortalized MEFs


title: Sorted blood myeloid cells from aged mice 24h poststroke

city: Milan

first: Giulia

middle: Maria

last: Scotti

state: Milan

address: Viale Rita Levi Montalcini, 1

department: National Facility for Data Handling and Analysis

country: Italy

institute: Fondazione Human Technopole

data_processing:
FASTQ files were demultiplexed from the raw base call (BCL) files with the 'mkfastq' command in Cell Ranger (v2.1.1) with default setting.
The feature-barcode matrices were generated using 10X Genomic Cellranger analysis pipelines  (CellRanger v2.1.1).
Genome_build: mm10 (refdata-cellranger-mm10-1.2.0)
Supplementary_files_format_and_content: tab-delimited text file includes mRNA molecule raw count values for all the samples

source_name: Myeloid cells from blood

extract_protocol:
Cells were FACS-stained and thereafter sorted for CD11b+ Ly6G– and CD11b+ Ly6G+ cells
Chromium Single Cell 3′ Library & Gel Bead Kit v2 kit (10xGenomics).

value: Myeloid cells from blood

value: 18-24 months old

value: 24h after transient proximal Middle Cerebral Artery Occlusion (MCAo)


title: 777


title: Sorted blood myeloid cells from young mice 24h poststroke

value: 2-4 months old


title: Immortalized MEFs G2A2

description: immortalized MEFs


title: CD62L lo blood neutrophils- MCAo [16_AS4B_P6]

description:
16_AS4B_P6
Aged MCAo 4

data_processing:
Low quality reads and Illumina adapters were trimmed using Trimmomatic (version 0.36)
Retained reads were mapped to the reference mouse genome, GRCm38, using STAR (version 2.5.3a)
Uniquely mapped reads were assigned to the corresponding genes using the featureCounts function in the Rsubread R package. Only reads mapped to exons were considered in the counting procedure. Genomic features were annotated according to Gencode basic annotations, version M16
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: CD62L lo blood neutrophils- MCAo

extract_protocol:
Cells were FACS-stained and thereafter sorted. The total RNA was extracted with ReliaPrep RNA Cell Miniprep System (Promega, Z6011)
cDNA libraries were prepared using the SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Bio Inc., Otsu, Shiga, Japan) performing 17 cycles of amplification

value: 18 months old

value: CD62L low neutrophils from blood


title: 776


title: Immortalized MEFs G2A1

description: immortalized MEFs


title: 2401029

city: Toronto

first: Vikas

last: Patil

state: Ontario

address: 610 University Ave.

country: Canada

institute: Princess Margaret Cancer Center

description:
Synthetic oligonucleotide pool corresponding to all panel gene targets used for normalization, 500-300ng input sample
Nanostring nCounter® PanCancer IO 360™ Panel

data_processing: RNA was extracted from FFPE tissue and gene expression profiling using nCounter® PanCancer IO 360™ Panel performed by Nanostring. Nanostring raw data was normalized to housekeeping genes in nCounter Software (Default settings). Data is log2 transformed.

label: NanoString

source_name: Glioblastoma

extract_protocol: Total RNA extracted from FFPE tissue

tag: sample type

value: recurrent glioma


title: 2401016


title: 2401005


title: 2401030


title: 774


title: CD62L lo blood neutrophils- MCAo [15_AS3_P6]

description:
15_AS3_P6
Aged MCAo 3


title: 2401017


title: CD62L lo blood neutrophils- MCAo [14_AS2B_P6]

description:
14_AS2B_P6
Aged MCAo 2


title: 2401015


title: MOUSE E12.5 LIVER G2A02

description: E12.5 mouse liver

source_name: Liver

value: Liver


title: 2401004


title: nHSC, scRNAseq

description:
HSCs from wild-type C57BL/6J naïve mice.
10x Genomics

value: wild type

value: bone marrow


title: Immortalized MEFs WT1

description: immortalized MEFs


title: 775


title: 2401013


title: CD62L lo blood neutrophils- MCAo [13_AS1_P6]

description:
13_AS1_P6
Aged MCAo 1


title: MOUSE E12.5 LIVER G2A01

description: E12.5 mouse liver


title: CD62L lo blood neutrophils- MCAo [12_YS4_P6]

description:
12_YS4_P6
Young MCAo 4

value: 3 months old


title: MOUSE E12.5 LIVER WT03

description: E12.5 mouse liver


title: 773


title: 770


title: 2401012


title: 772


title: 769


title: 2401014


title: MOUSE E12.5 LIVER WT02

description: E12.5 mouse liver


title: 2401028


title: 768


title: 767


title: CD62L lo blood neutrophils- MCAo [11_YS3B_P6]

description:
11_YS3B_P6
Young MCAo 3


title: MOUSE E12.5 LIVER WT01

description: E12.5 mouse liver


title: CD62L lo blood neutrophils- MCAo [10_YS2_P6]

description:
10_YS2_P6
Young MCAo 2


title: K279a_AHLs_Biol_Replicate_3

description:
GIBERT_01_new_annot_wo_outlier_DMSO_vs_AHL_results.xlsx
GIBERT_01_new_annot_wo_outlier_DMSO_vs_AHL_norm_counts.txt

data_processing:
Sequence mapping was perfomed with STAR/2.5.3a
Quantification with RSEM/1.3.0
The differential gene expression analysis was performed using the DESeq2 R package using an adjusted p-value < 0.05 (FDR of 5%) as a cut-off for statistical significance, with the Benjamini-Hochberg correction for multiple testing
Assembly: Stenotrophomonas maltophilia K279a NC_010943.1 (2017)
Supplementary files format and content: excel files include Fold change and p-values for each compared condition

treatment_protocol: Quorum sensing conditions were created either by growing cells to stationary phase or by adding the autoinducers DSF or AHL.

value: Bacterial culture

value: growth with added AHLs


title: 2401045


title: CD62L lo blood neutrophils- basal  [8_AN42_P6]

description:
8_AN42_P6
Aged basal 4

source_name: CD62L lo blood neutrophils- basal

value: untreated


title: 2401042


title: CD62L lo blood neutrophils- basal  [7_AN4_P6]

description:
7_AN4_P6
Aged basal 3


title: K279a_AHLs_Biol_Replicate_2


title: 766

value: brain


title: CD62L lo blood neutrophils- MCAo [9_YS1_P6]

description:
9_YS1_P6
Young MCAo 1


title: MOUSE E12.5 LIVER G2A03

description: E12.5 mouse liver


title: K279a_AHLs_Biol_Replicate_1


title: 765


title: 2401006


title: 2401040


title: K279a_DSF_Biol_Replicate_2

description:
GIBERT_01_new_annot_wo_outlier_DMSO_vs_DSF_results.xlsx
GIBERT_01_new_annot_wo_outlier_DMSO_vs_DSF_norm_counts.txt

value: growth with added DSF


title: CD62L lo blood neutrophils- basal  [6_AN2_P6]

description:
6_AN2_P6
Aged basal 2


title: 2401038


title: K279a_DSF_Biol_Replicate_1


title: CD62L lo blood neutrophils- basal  [5_AN1_P6]

description:
5_AN1_P6
Aged basal 1


title: 2401036


title: 763


title: CD62L lo blood neutrophils- basal  [4_YN4_P6]

description:
4_YN4_P6
Young basal 4


title: 762


title: 2401037


title: CD62L lo blood neutrophils- basal  [3_YN3_P6]

description:
3_YN3_P6
Young basal 3


title: K279a_DMSO_Biol_Replicate_3

description:
GIBERT_01_new_annot_wo_outlier_DMSO_vs_AHL_results.xlsx
GIBERT_01_new_annot_wo_outlier_DMSO_vs_DSF_results.xlsx
GIBERT_01_new_annot_wo_outlier_DMSO_vs_AHL_norm_counts.txt
GIBERT_01_new_annot_wo_outlier_DMSO_vs_DSF_norm_counts.txt

value: growth with added DMSO


title: 761


title: K279a_DMSO_Biol_Replicate_2


title: 2401009


title: CD62L lo blood neutrophils- basal  [2_YN2_P6]

description:
2_YN2_P6
Young basal 2


title: 760


title: 2401039


title: K279a_DMSO_Biol_Replicate_1


title: CD62L lo blood neutrophils- basal  [1_YN1_P6]

description:
1_YN1_P6
Young basal 1


title: Pooled input control DNA experiment in striatum of B6.Htt+/+ mouse rep 3

data_processing:
Primary data analysis, including base calling and quality scoringis, performed by real-time analysis using a new implementation of RTA called RTA 2.0
ChIP-seq reads were aligned to the mm10 genome assembly using BWA with default settings
Peaks were called using either the MACS or SICER algorithms. MACS default cutoff is pvalue 1e-7 for narrow peaks and 1e-1 for broad peaks, and SICER default cutoff is FDR 1e-10 with gap parameter of 600 bp.
Genome_build: mm10
Supplementary_files_format_and_content: peak text files

source_name: striatum

growth_protocol: Fresh frozen striatal tissue from five male four-month-old HttQ111/+  and age-matched Htt+/+ mice were pooled per replicate

extract_protocol:
Complexes were captured using protein A agarose beads (Invitrogen)
Illumina sequencing libraries were prepared from ChIP and Input DNA by end-polishing, dA-addition, and adaptor ligation. Libraries were quantified and sequenced on Illumina’s NextSeq 500 (75nt single end reads).

treatment_protocol: DNA was sonicated to an average fragment length of 300-500bp, and 25ug chromatin was incubated with antibody targeting EZH2, H3K27me3, H3K4me3, or H3K27ac (Active Motif catalog numbers 39901, 39155, 399159, and 39133, respectively)

value: Input


title: K279a_LOG_Biol_Replicate_3

description:
GIBERT_01_new_annot_wo_outlier_STAT_vs_LOG_results.xlsx
GIBERT_01_new_annot_wo_outlier_STAT_vs_LOG_norm_counts.txt

tag: growth phase

value: Log growth phase


title: 758


title: 759


title: 2401021


title: H3K4me3 ChIPSeq experiment in striatum of B6.Htt+/+ mouse rep 3


title: 757


title: K279a_STAT_Biol_Replicate_3

value: stationary growth phase


title: 764


title: K279a_LOG_Biol_Replicate_1


title: 2401026


title: H3K4me3 ChIPSeq experiment in striatum of B6.Htt+/+ mouse rep 2


title: 756


title: 2401007


title: H3K4me3 ChIPSeq experiment in striatum of B6.Htt+/+ mouse rep 1


title: K279a_STAT_Biol_Replicate_2


title: 755


title: K279a_STAT_Biol_Replicate_1


title: H3K4me3 ChIPSeq experiment in striatum of B6.HttQ111/+ mouse rep 3


title: H3K4me3 ChIPSeq experiment in striatum of B6.HttQ111/+ mouse rep 2


title: 2401018


title: K279a_LOG_Biol_Replicate_2


title: 2401001


title: H3K4me3 ChIPSeq experiment in striatum of B6.HttQ111/+ mouse rep 1


title: 2401020


title: 2401046.2


title: 752


title: 751


title: H3K27me3 ChIPSeq experiment in striatum of B6.Htt+/+ mouse rep 3


title: 750


title: DV3_24h_C

city: Bielefeld

first: Christian

last: Ruckert-Reed

address: Sequenz 1

department: Medical School OWL

country: Germany

institute: Bielefeld University

data_processing:
Basecalls were performed using RTA v 2.11.3.0
Sequenced reads were mapped to the whole genome of GCA_022760195.1 using bowtie2 v2.4.1 with parameters -X 600
Raw read counts per gene were calculated using featureCounts v2.0.0 with parameters -O -M -t gene -g ID -s 1
Read cound normalization and data analysis were performed using DESeq2
Assembly: GCA_022760195.1
Supplementary files format and content: tab-delimited matrix table with raw read counts for every gene and every sample
Supplementary files format and content: tab-delimited matrix table with read counts normalized with DESeq2 for every gene and every sample

organism: Streptomyces rimosus subsp. rimosus

growth_protocol: OTC production in complex medium was conducted in two steps, including pre-culturing, followed by main cultures for production. First, strains were propagated on MS agar at 30°C for 7 days, upon which the sporulating mycelium was amended with 5 mL sterile deionized water. Afterwards, spores were collected using a glass cell spreader and centrifugation of the obtained suspension (5,500 × g, 4°C, 6 min). The obtained pellet was resuspended in 4 mL 20% ice-cold glycerol. The content of viable spores in the suspension was determined using serial dilutions that were prepared in triplicate on tryptone soy broth agar (30 g L-1, Sigma Aldrich).  The spore suspension was used to inoculate a pre-culture in vegetative medium (50 mL in 500 mL non-baffled shake flasks) to an initial concentration of 1 × 10^7 spores mL-1. The vegetative pre-culture medium (pH 7.0) contained per litre: 30.0 g of corn starch (Sigma Aldrich, Steinheim, Germany), 5.0 g of NaCl, 4.0 g of CaCO3, 4.0 g of corn steep liquor (Sigma Aldrich), 4.0 g of (NH4)2SO4, 3.0 g of soy flour (Schoenenberger Hensel), and 150 of mg KH2PO4. The pre-culture was incubated for 24 h on a rotary shaker at 30°C, 230 rpm, and 80% humidity (Multitron, Infors AG, Bottmingen, Switzerland). Afterwards, 5 mL pre-culture broth was used to inoculate the main culture in production medium, which was then incubated under the same conditions. The OTC production medium (pH 7.0) contained per litre: 75.0 g of corn starch (Sigma Aldrich), 10.0 g of soy flour (Schoenenberger Hensel), 7.0 g of CaCO3, 7.0 g of (NH4)2SO4, 2.5 g of corn steep liquor (Sigma Aldrich), 2.0 g of NaCl, 75.0 mg of amylase (Sigma Aldrich), 75 mg KH2PO4, and 5 mg of CoCl2. Experiments were conducted in triplicate.

extract_protocol:
Total RNA was isolated using the Quick-RNA Miniprep Plus kit (Zymo Research, Freiburg, Germany). After DNase treatment, the obtained RNA was purified (RNA Clean & Concentrator-5 kit, Zymo Research) and quantified (DropSense 16, Trinean NV, Gent, Belgium).
To construct whole transcriptome cDNA libraries, 2.5 μg of total RNA each was depleted of rRNA (Ribo-Zero rRNA Removal Kit (Bacteria), Illumina, San Diego, CA, USA). Successful rRNA removal was validated (Agilent RNA Pico 6000 kit, Agilent 2100 Bioanalyzer, Agilent Technologies). The obtained mRNA was converted into a cDNA library according to the TruSeq Stranded mRNA Sample Preparation guide (Illumina). Appropriate cDNA quality and quantity was validated (Agilent High Sensitivity DNA kit, Agilent 2100 Bioanalyzer, Agilent Technologies). Sequencing was performed on an Illumina NextSeq 500 instrument using 75 bases read length (Illumina).

value: null mutant


title: DV3_24h_B


title: 2401033.2


title: 2401019


title: HP_24h_C

value: hyperproducer


title: 749


title: 754


title: 2401032.2


title: H3K27me3 ChIPSeq experiment in striatum of B6.HttQ111/+ mouse rep 3


title: 753


title: 2401003


title: 2401027.2


title: 748


title: 2401024.2


title: H3K27me3 ChIPSeq experiment in striatum of B6.HttQ111/+ mouse rep 2


title: DV3_24h_A


title: 747


title: 2401023.2


title: H3K27me3 ChIPSeq experiment in striatum of B6.Htt+/+ mouse rep 2


title: H3K27me3 ChIPSeq experiment in striatum of B6.HttQ111/+ mouse rep 1


title: H3K27me3 ChIPSeq experiment in striatum of B6.Htt+/+ mouse rep 1


title: 746


title: R7_24h_B

value: wildtype


title: R7_24h_C


title: R7_24h_A


title: H3K27ac ChIPSeq experiment in striatum of B6.Htt+/+ mouse rep 3


title: 745


title: HP_24h_B


title: HP_24h_A


title: 2401011.2

value: recurrent glioma


title: H3K27ac ChIPSeq experiment in striatum of B6.Htt+/+ mouse rep 2


title: 2401008.2


title: 744


title: H3K27ac ChIPSeq experiment in striatum of B6.Htt+/+ mouse rep 1


title: 743


title: Primary chondrocyte from Myl3-KO mice

first: he

last: cao

state: 广东

address: The Third Affiliated Hospital of Southern Medical University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Rib cartilage

growth_protocol: The purified primary chondrocytes were resuspended, then maintained as a monolayer in DMEM/F12 with 10% FBS, 100 U/mL penicillin and 100 mg/mL streptomycin sulfate at 37°C under 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol and 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 for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: None.

value: Rib cartilage

value: Primary chondrocyte

value: Myl3 knockout


title: S1

city: Roslin

first: rose

middle: ruiz

last: daniels

address: The University Of Edinburgh

country: United Kingdom

institute: The University of Edinburgh

description: snRNA-seq 10x

data_processing:
As the closest related shark species with a published reference genome, the genome of the whale shark (Rhincodon typus; NCBI accession: ASM164234v2) was used for alignment and feature counting. Sequences for five nurse shark genes of specific interest but absent from the whale shark genome annotation, were appended to the genome annotation GTF file (AICDA, Cd79a, Il-21, and two Tnfsf13b paralogs)
StarSolo v2.7.7a was used to align reads with the following changes to default settings: --soloUMIdedup 1MM_Directional, --soloCellFilter TopCells 25000, --outFilterMatchNminOverLread 0.15, --outFilterScoreMinOverLread 0.15, --outMultimapperOrder Random, --soloFeatures GeneFull. Reads mapping to introns were retained to account for the large quantity of unspliced transcripts present in snRNA-seq data and the top 25,000 nuclei by UMI count were retained to ensure retention of the transcriptionally quiet erythrocytes
To account for sequence dissimilarity between whale shark and nurse shark, the alignment filtering thresholds –outFilterMatchNminOverLread and –outFilterScoreMinOverLread, corresponding to minimum alignment length and alignment score were optimized to return the highest UMI per nuclei and genes per nucleus. A score of 0.15 was found to be optimal for these parameters (Supplementary Table 2).  Quality control was performed on each sample separately. Genes expressed in fewer than five nuclei were excluded. Nuclei with fewer than 500 genes or 800 UMIs were excluded.
Assembly: whale shark (Rhincodon typus; NCBI accession: ASM164234v2)
Supplementary files format and content: Tab-separated values files and matrix files

organism: Ginglymostoma cirratum

source_name: Spleen

extract_protocol:
Animals were immunized subcutaneously in the ventral side of the pectoral fin with 300 µg R-phycoerythrin (PE) emulsified in Freund’s complete adjuvant, spleens flash frozen immediately
for libraries s1 and s2 we followed the nuclei extraction protocol of Taylor & Ruiz Daniels 2022
dx.doi.org/10.17504/protocols.io.261genwm7g47/v2
Nuclei were processed through the 10X Chromium™ Single Cell Platform using the Chromium™ Single Cell 3` Library and Gel Bead Kit v3.1 and Chromium™ Single Cell A Chip Kit (both 10X Genomics) as per the manufacturer’s protocol with the aim of recovery of 7000 nuclei.

value: Spleen

tag: tissue preparation

value: frozen tissue

tag: cell compartment

value: nucleus

tag: protocol

value: single nucleus

value: immunized subcutaneously


title: H3K27ac ChIPSeq experiment in striatum of B6.HttQ111/+ mouse rep 3

value: brain


title: 741

data_processing:
library strategy: 5hmC-Seal-seq
Bcl2fastq v2.17 software used to change the bcl files to fastq files.
Sequenced reads were trimmed for adaptor sequence using software trimmomatic v0.36, and masked for low-complexity or low-quality sequence, then mapped to hg19  genome using bowtie v2.26
Duplicate reads were marked using picard v1.141. The reads were counted for overlap with gene bodies (annotated by the GENCODE Project) using featureCounts v1.5.0-p3.
Assembly: hg19
Supplementary files format and content: A CSV file include edgR normalized 5hmC levels for all sample.

extract_protocol:
Circulating cfDNA was isolated using the QIAamp Circulating Nucleic Acid Kit (Qiagen) from 0.5 mL of frozen serum per study subject. Genomic DNA (gDNA) was isolated from ~5 mg of frozen DLPFC using the Monarch Genomic DNA Purification Kit (New England Biolabs).
To obtain sequencing-amenable ~200 bp fragments of gDNA from brain samples, we performed enzymatic fragmentation using the KAPA HyperPlus Kit (Roche). After ligation of unique dual index barcoded sequencing adapters, DNA fragments proceeded through the 5hmC-Seal protocol to construct sequencing libraries.

tag: subject id

tag: tissue


title: 2401047.2


title: H3K27ac ChIPSeq experiment in striatum of B6.HttQ111/+ mouse rep 2

tag: cell type


title: Primary chondrocyte from control mice

institute: The Third Affiliated Hospital of Southern Medical University

tag: genotype

value: WT


title: 2401033.1


title: H3K27ac ChIPSeq experiment in striatum of B6.HttQ111/+ mouse rep 1


title: 2401046.1


title: 2401002.2


title: 2401027.1


title: EZH2 ChIPSeq experiment in striatum of B6.Htt+/+ mouse rep 3


title: S2

description: snRNA-seq 10x

tag: treatment


title: 738


title: 739


title: EZH2 ChIPSeq experiment in striatum of B6.HttQ111/+ mouse rep 3


title: EZH2 ChIPSeq experiment in striatum of B6.Htt+/+ mouse rep 1


title: 2401032.1


title: 737


title: 740


title: EZH2 ChIPSeq experiment in striatum of B6.HttQ111/+ mouse rep 2


title: 736


title: 2401024.1


title: 2401023.1


title: 735


title: 742


title: EZH2 ChIPSeq experiment in striatum of B6.HttQ111/+ mouse rep 1


title: blood of young mice at steady-state

data_processing:
FASTQ files were demultiplexed from the raw base call (BCL) files using 10x Genomics 'cellranger demux' (CellRanger v3.0.2).
The whitelist of cell barcodes was identified with the 'umi_tools whitelist' command, then reads of the whitelisted cells were extracted with the 'umi_tools extract' command
Extracted reads were aligned with STAR aligner (v2.5.3a) to the primary assembly of murine genome GRCm38
Mapped reads were assigned to gene_name attributes from GENCODE basic annotation (v. M22) using Subread featureCounts (v1.6.4).
Per gene counts were summarized for each cell using the 'umi_tools count' command
Assembly: mm10 (Gencode basic annotations v. M22)
Supplementary files format and content: tab-delimited text file includes mRNA molecule count values for all the samples

source_name: blood

extract_protocol:
FACS sorting used to enrich cell fractions from the blood or the bone marrow, see also above at cell type;
Chromium Single Cell 3′ Reagent Kit v3.1 (10xGenomics)

value: blood

value: from peripheral blood sorted CD11b+ Ly6G- and CD11b+ Ly6G+ cells

value: wild-type

value: no treatment


title: Bone marrow (BM) of aged mice 24h poststroke

description: BMSA

value: bone marrow

value: Gr1+ and c-kit+-enriched cell fractions from BM

value: middle cerebral artery occlusion 24h before


title: blood of aged mice at steady-state


title: Bone Marrow of young mice at steady state

description: Y


title: Bone marrow of aged mice at steady-state

description: AB


title: Wildtype Mouse 6

city: Madison

first: Dale

last: Bjorling

state: WI

address: 2015 Linden Drive

department: Surgical Sciences

institute: University of Wisconsin School of Veterinary Medicine

data_processing:
data were trimmed, quality checked, and mapped to the mouse genome
Analysis of differentially expressed genes was performed using the DESeq2 R package (1.20.0)
DESeq2 identifies differential expression using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with
Resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value less than, or equal to, 0.05 as determined by DESeq2 were considered differentially expressed (Ito, Nomura et al. 2021).
Assembly: GRC38/mm10
Supplementary files format and content: single text file with count and fpkm values for all samples

source_name: bladder

extract_protocol:
Bladders were collected and stored in RNA later (Qiagen, Valencia, CA). Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA) and treated with DNAse I (Ambion, Austin, TX) to remove genomic DNA.
Preparation of sequencing libraries and Illumina sequencing were carried out at Novogene (Sacramento, CA). Briefly, sequencing libraries were built using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, MA, USA)

treatment_protocol: Results of RNAseq performed on bladders of male age-matched wild-type (C5/bl6) and Mir29a-/- mice

value: bladder


title: EZH2 ChIPSeq experiment in striatum of B6.Htt+/+ mouse rep 2


title: 732


title: 2401011.1

value: recurrent glioma


title: 2401008.1


title: 731


title: 2401047.1


title: Wildtype Mouse 5


title: Neoadjuvant-P07_C

city: Tianjin

first: Xiubao

last: Ren

address: West Huan-Hu Rd, Ti Yuan Bei, Hexi District

institute: Tianjin Medical University Cancer Institute & Hospital,

description: 10x Genomics

data_processing:
For 10X data, Cell Ranger 3.1.0 was used to quantify gene expression level.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: cancer tumor tissues

extract_protocol:
Surgically resected fresh tumor tissue from six patients treated with two cycles of NAPC and one patient treated with two cycles of NAC was cut into pieces of approximately 1-3 mm³ (Clinicopathological information, cell counts and response to neoadjuvant therapy for single cell sequencing patients are shown in supplementary Table 1). Then, the pieces were transferred to the gentle MACS C Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany), with 5 mL of digestive enzyme included in Tumor Dissociation Kit (Miltenyi Biotec, Bergisch Gladbach, Germany). Then the tissues were made into single-cell suspension using the gentleMACS Dissociator (Miltenyi Biotec, Bergisch Gladbach, Germany) for 60 min on a rotor at 37℃ according to the manufacturer’s instructions. After removing of red blood cells using erythrocyte lysis solution (Miltenyi Biotec, Bergisch Gladbach, Germany), the cells were filtered using a 40 µm strainer (BD Falcon, New York, USA). CD45+ cells were sorted by using the Human CD45 Microbeads Isolation Kit (Miltenyi Biotec, Bergisch Gladbach, Germany).
Cell suspensions (700-1200 living cells/μL determined by trypan blue staining) were loaded on a 10x Genomics ChromiumTM Single Cell Controller Instrument (10x Genomics, Pleasanton, CA, USA) to generate single-cell gel beads in emulsions (GEMs) by using Chromium Single Cell 5' Library & Gel Bead Kit v1.0 (10x Genomics, Cat# 1000006) and Single Cell A Chip Kit (10x Genomics, Cat# 1000152). Captured cells were lysed and the released RNA was barcoded through reverse transcription in individual GEM. Barcoded cDNAs were pooled and cleanup by using DynaBeads MyOne Silane Beads (Thermo Fisher, Cat# 37002D), and then amplified and cleanup for further next generation library construction.

value: cancer tumor tissues

value: CD45+ immune cells

tag: pathology

value: AD


title: bone marrow of young mice 24h poststroke

description: BMSY


title: Wildtype Mouse 4


title: Neoadjuvant-P06_C

description: 10x Genomics

value: SCC


title: 730


title: Neoadjuvant-P05_C

description: 10x Genomics


title: mes-ot3-24h

city: Suzhou

first: Zhengkui

address: No. 199, Renai Road, Suzhou Industrial Park

department: Institutes of Biology and Medical Science

institute: Soochow University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Mapped to the mouse reference genome GRCm39 (mm39) using STAR (version 2.7) (Dobin et al., 2013) with default settings
Genes reads were counted using  HTSeq2 (Anders et al., 2015) (version 0.11.1)
Count data were analyzed in RStudio (v2022.07.1) with DESeq2 (version1.36.0) (Love et al., 2014)
Assembly: mm39
Supplementary files format and content: raw counts matrix

source_name: Female Kras G12D/+; Trp53 R172H/+; Pdx-1 Cre mouse pancreatic ductal adenocarcinoma genetic model

growth_protocol: Cells were cultured in DMEM supplemented with 9% fetal bovine serum (Sigma) plus 100 U/ml penicillin and 0.1 mg/ml streptomycin (Gibco).

extract_protocol:
Cells were then lysed by adding 600 µl of buffer RLT  and their total RNA extracted using NucleoSpin RNA kit, according to the manufacturer’s instructions.
After mRNA enrichment by Oliogo dT selection and the following library preparation, RNA-seq was performed in the DNBseq platform (Beijing Genomics Institute, BGI, Hongkong)

treatment_protocol: 2 × 10E6 KPC3-OVA cells (Epithelial or Mesenchymal type) were coculture with 1 × 10E6 OT-I T cells for 0, 6 or 24 hours.

value: mouse pancreatic tumor KPC3 cells

tag: type

value: Mes

value: OT-I CD8+ T cells

tag: cell line

value: KPC3-OVA ::Tet-On ALK5 CA


title: Wildtype Mouse 3


title: 729

first: Zhou

address: 680 North Lake Shore Drive, Suite 1400

institute: Northwestern University

value: brain


title: 2401002.1


title: mes-ot2-24h


title: Wildtype Mouse 2


title: Neoadjuvant-P04_C

description: 10x Genomics


title: 728


title: mes-ot1-24h


title: Wildtype Mouse 1


title: mes-ot3-6h

value: 6 h


title: Knockout Mouse 6


title: Neoadjuvant-P03_C

description: 10x Genomics


title: 725


title: mes-ot2-6h


title: Neoadjuvant-P01_C

description: 10x Genomics

value: Chemo


title: Knockout Mouse 5


title: Neoadjuvant-P02_C

description: 10x Genomics


title: 724


title: mes-ot1-6h


title: Knockout Mouse 4


title: 723


title: Bovine assembled blastoids day 4

city: Dallas

first: Carlos

last: Pinzon

state: Texas

address: 5323 Harry Hines Boulevard,  NA5.124

department: Molecular Biology

institute: UT Southwestern Medical Center

description: 10x Genomics

data_processing:
For 10X Genomics single-cell data, we used the Cell Ranger pipeline (v.3.1.0) with default parameters to generate the expression count matrix. The bovine reference genome and gene annotation file were downloaded from Ensembl database (UMD3.1) and generated by Cell Ranger mkfastq with default parameters. Seurat35 (3.1.4) was used to single-cell quality control. To reduce multiplets and dead cells, we screened cells with expressed gene numbers between 200 and 6000, unique molecular identifiers (UMIs) between 5000 and 30,000, and mitochondrial RNA genes counts below 15 percent.
Assembly: UMD3.1
Supplementary files format and content: Tab-separated values files and matrix files

organism: Bos taurus

source_name: Blastoid

extract_protocol: Bovine blastoids were single cell dissociated and strained cells were prepared as stated adobe. Cells were washed in PBS containing 0.04% BSA and centrifuged at 90° x500g for 5 min. Cell were resuspended in PBS containing 0.04% BSA at a single cell suspension of 1,000 cells/µL. Cells were loaded into a 10x Genomics Chromium Chip following manufacturer instruction (10x Genomics, Pleasanton, CA, Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1) and sequenced by Illumina NextSeq 500/550 sequencing systems (Illumina).

value: Blastoid

value: Bovine EPSCs and TSCs


title: Knockout Mouse 3


title: 722

city: Chicago

last: Zhang


title: mes-ctrl-02

value: 0 h


title: Knockout Mouse 2


title: LN hematopoietic cells cryopreserved in Cryostor for 18 mo (patient #3; histology with atypical lymphocytic infiltrate)

city: Philadelphia

first: Joshua

middle: Daniel

last: Brandstadter

state: Pennsylvania

address: BRB II/III, Room 446, 421 Curie Blvd

institute: University of Pennsylvania

description:
10x Genomics
Lymph node hematopoietic cells cryopreserved in Cryostor for 18 months (patient #3; histology with atypical lymphocytic infiltrate)

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: LN

extract_protocol:
Fresh or thawed cryopreserved samples were incubated in 37°C water bath with 3mL enzymatic digestion solution. Enzymatic digestion of fresh or thawed, cryopreserved tissue was performed otherwise similarly to prior descriptions (31, 32). An enzymatic medium was prepared by adding 2 mg/mL dispase II (Gibco), 0.6 mg/ml collagenase P (Sigma Aldrich), and 0.3 mg/mL DNase I (Sigma Aldrich) to pre-warmed RPMI with 2% FBS and 20mM HEPES. Every 10 minutes, samples were agitated by pipetting using a 1000µl micropipette. Every 15 minutes, the digestion medium with cells in suspension was aspirated, transferred through 70µm filter to 20mL ice-cold FACS buffer (PBS containing 2% FBS, 20mM HEPES, and 2mM EDTA) before being spun at 1500rpm for 5 minutes and resuspended in fresh FACS buffer. Fresh digestion medium was immediately added to the residual tissue for a total of three serial, 15-minute digestions.  Flow cytometric cell sorting was performed with the FACSDIVA software on a BD FACSAria (Franklin Lakes, NJ) set to 20 psi with a 100µm nozzle. The sorting protocol was as previously described, although we did not require any bead-based enrichment prior to sorting and could compensate successfully with antibody-stained UltraComp eBeads Compensation Beads (Invitrogen, Waltham, MA) (31). We sorted ≥ 30,000 CD45- EpCAM- live singlet cells into 1.5mL DNA LoBind tubes (Eppendorf, Hamburg, Germany) containing 40µl FBS. Purity was routinely > 95%. Tubes were spin-concentrated with only a part of the supernatant removed by gentle aspiration to leave ~50µl volume in the tube. The concentrated cells were then fully resuspended in the remaining volume and counted with a hemacytometer using a Trypan Blue viability dye. Flow cytometric analysis was performed using FlowJo v.10.6.1 (Ashland, OR).
Library preparation was performed according to the manufacter’s instructions (single cell 3’ v3.2 protocol, 10x Genomics).

value: LN

value: 14 years


title: mes-ctrl-01


title: LN hematopoietic cells processed fresh (patient #3; histology with atypical lymphocytic infiltrate)

description:
10x Genomics
Lymph node hematopoietic cells processed fresh (patient #3; histology with atypical lymphocytic infiltrate)


title: Knockout Mouse 1

value: bladder


title: 721

source_name: brain


title: LN stromal cells cryopreserved in Cryostor for 18 mo (patient #3; histology with atypical lymphocytic infiltrate)

description:
10x Genomics
Lymph node stromal cells cryopreserved in Cryostor for 18 months (patient #3; histology with atypical lymphocytic infiltrate)


title: 727


title: 719


title: epi-ot3-24h

value: Epi


title: Pink1-/-, 24month [PKKO24M2]

city: Seongnam-si

first: Min Heui

last: Ha

address: Pangyo-ro 335

institute: CHA univeristy

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Tophat
FPKM calculation using Cufflink
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: whole kidney

growth_protocol: PINK1 knockout male C57BL/6 mice were maintained under a standard environment with a regular light/dark cycle and free access to water and a chow diet.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.

value: whole kidney

tag: strain background

value: 24 month


title: epi-ot2-24h


title: Pink1-/-, 24month [PKKO24M1]


title: LN stromal cells cryopreserved in Cryostor for 2 days (patient #2; reactive histology)

description:
10x Genomics
Lymph node stromal cells cryopreserved in Cryostor for 2 days (patient #2; reactive histology)

value: 50 years


title: 718


title: epi-ot1-24h

value: mouse pancreatic tumor KPC3 cells


title: 717


title: mes-ctrl-03

value: Mes


title: Pink1-/-, 4month [PKKO4M2]

value: 4 month


title: LN stromal cells processed fresh (patient #2; reactive histology)

description:
10x Genomics
Lymph node stromal cells processed fresh (patient #2; reactive histology)


title: epi-ot3-6h

value: OT-I CD8+ T cells

value: KPC3-OVA ::Tet-On ALK5 CA


title: LN stromal cells cryopreserved in Cryostor for 2 days (patient #1; hyaline vascular Castleman Disease histology)

description:
10x Genomics
Lymph node stromal cells cryopreserved in Cryostor for 2 days (patient #1; hyaline vascular Castleman Disease histology)

value: 58 years


title: 716

value: brain


title: Pink1-/-, 4month [PKKO4M1]


title: 715


title: Pink1+/+, 24month [WT_24M_2]


title: LN stromal cells processed fresh (patient #1; hyaline vascular Castleman Disease histology)

description:
10x Genomics
Lymph node stromal cells processed fresh (patient #1; hyaline vascular Castleman Disease histology)


title: epi-ot1-6h

value: 6 h


title: 714


title: Reactive LN stromal cells processed fresh_3

description: 10x Genomics

molecule: polyA RNA

value: 63 years


title: epi-ctrl-03

value: 0 h


title: LN stromal cells processed fresh (patient #3; histology with atypical lymphocytic infiltrate)

description:
10x Genomics
Lymph node stromal cells processed fresh (patient #3; histology with atypical lymphocytic infiltrate)

value: LN


title: 713


title: epi-ctrl-02


title: 712


title: Reactive LN stromal cells processed fresh_2

description: 10x Genomics

value: 42 years


title: Pink1+/+, 24 month [WT_24M_1]


title: Pink1+/+, 4month [WT_4M_2]


title: Reactive LN stromal cells processed fresh_1

description: 10x Genomics

value: 18 years


title: Pink1+/+, 4month [WT_4M_1]


title: 711


title: epi-ctrl-01

value: Epi


title: Tonsil stromal cells cryopreserved AFTER enzymatic digestion in Cryostor for 2 days (patient #4)

description: 10x Genomics

source_name: Tonsil

value: Tonsil

value: 6 years


title: epi-ot2-6h


title: HOMF_EXO_miRNA_2

city: Kunming

first: Weizhou

last: Wang

address: Chunrong West Road

institute: Kunming Medical University

description:
D2
exp_hOMF2

data_processing:
In this project, we sequence 6 samples used DNBSEQ platform, averagely generating about 10.58G Gb bases per sample.
The sequencing data was filtered with SOAPnuke by Removing reads containing sequencing adapter.
Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%.
Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
Assembly: mm10
Supplementary files format and content: gene_expression.txt: Tab-delimited text file includes FPKM values and counts for each Sample.

source_name: hOMF

growth_protocol: hOMF (CellResearchCorp, Singapore) were cultured in high glucose DMEM supplemented with 10% fetal bovine serum (Gibco, USA). The hOMF was treated with 30 ng/ml of PDGF-BB (Peprotech, UK) for 72 h and will be induced into CAFs.

extract_protocol:
1. Take the sample (40 mL cell culture). If the sample was stored at -80°C, thaw the sample at 37°C or room temperature; 2. Cell culture: The 40 mL cell culture is filtered via a 0.22 μm sterile syringe filter; 3. An ultra-filter device (Ultra-15 10K) is taken. 5 mL 1×PBS (pH7.4) is used as a balance solution to balance the ultra-filter column. Centrifuge at 4000×g and 4℃ for 8 mins and remove the supernatant; 4. The sample is transferred into an ultra-filter tube. Centrifuge at 4000×g and 4°C for 15 mins to concentrate the sample to 1~1.2 mL; 5. Pipette repetitively the concentrated solution in the ultra-filter tube to mix the concentrated solution thoroughly and avoid air bubbles formation. The concentrated solution is then taken and transferred into a new centrifuge tube; 6. Cell culture: Add 0.5 times total volume of Total Exosome Isolation (from cell culture media); 7. Incubate at 4°C for 2 hours; 8. Centrifuge at 10,000×g and 4°C for 20 mins and remove the supernatant while the pellets are exosomes (Exosomes from cell culture cannot see by naked eyes); 9. Centrifuge at 10,000×g and 4°C for 1 min to remove the supernatant; 10. Add 140 μL of (cell culture) 1×PBS into the pellet, incubate at 37°C for 3 mins with shaking; 11. Resuspend exosome pellet thoroughly using a vortex mixer.
1. Sample QC: Select the corresponding testing methods for quality inspection according to the requirements of samples and products; 2. Fragments Selection: Special samples are not Fragments Selection electrophoresed: Take a certain amount of RNA sample, purified 18-30nt small RNA with PAGE gel; 3. Adapter Ligation: The purified RNA is combined with 3’ Adapter, and incubated. Then combine 5’ Adapter, and incubate; 4. RT-PCR: Prepare the Reverse Transcription Reaction Mixture, into the thermocycler and run the program. Prepare the PCR Reaction Mixture, into the thermocycler and run the program; 5. Purify PCR products: Then the PCR products are purified with PAGE gel, dissolve the recycled products in EB solution; 6. Library QC: The corresponding library quality control protocol will be selected depending upon product requirements; 7. Circularization: Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested; 8. Sequencing: Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

treatment_protocol: CAFs and hOMF were washed 3 times with PBS and incubated with Exo-ClearTM Complete Cell Growth Medium (SBI, USA) for 48 h.

value: hOMF

value: Fibroblasts

tag: source

value: Exosomes

value: Normal Control


title: TPMPik3r1_RNAseq_2

city: Xi’an, China

first: lei

last: zhao

state: Shaanxi

address: Youyixi Road 21

department: School of Ecology and Environment

institute: Northwestern Polytechnical University

data_processing:
Sequenced reads were mapped to mm10 reference using STAR
Counts were normalized by deseq2
Assembly: mm10
Supplementary files format and content: csv file with gene counts,  csv file with gene deseq2 normalized

source_name: EC tumor organoids

growth_protocol: The EC tumor organoids were cultured from various EC mouse models.

extract_protocol:
RNA was extracted with Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Organoids of TPK, TPM, TPMPik3ca and TPMPik3r1 EC mouse models.

tag: strain

value: nude mice

value: EC tumor organoids

tag: ec mouse model


title: TPMPik3r1_RNAseq_1


title: 710


title: TPMPik3ca_RNAseq_2


title: HOMF_EXO_miRNA_3

description:
D3
exp_hOMF3


title: HOMF_EXO_miRNA_1

description:
D1
exp_hOMF1


title: 708


title: 709


title: TPMPik3ca_RNAseq_1


title: CAFs_EXO_miRNA_3

description:
C3
exp_CAFs3

value: Cells were co-cultured with 30ng/ml PDGF-BB for 72h


title: Tonsil stromal cells cryopreserved in Cryostor for 2 days (patient #4)

description: 10x Genomics

tag: age


title: 707

value: brain


title: TPM_model_RNAseq_2

value: TPM


title: 706


title: CAFs_EXO_miRNA_2

description:
C2
exp_CAFs2


title: Tonsil stromal cells processed fresh (patient #4)

description: 10x Genomics


title: Tonsil stromal cells cryopreserved in Cryostor for 2 days (patient #2)

description: 10x Genomics

value: 21 years


title: TPM_model_RNAseq_1


title: CAFs_EXO_miRNA_1

description:
C1
exp_CAFs1


title: Tonsil stromal cells processed fresh (patient #2)

description: 10x Genomics


title: 705


title: Tonsil stromal cells cryopreserved in Cryostor for 2 months (patient #1)

description: 10x Genomics

value: 17 years


title: TPK_model_RNAseq_2

value: TPK


title: 704


title: HOMF_EXO_mRNA_3

description:
B3
fpkm_p1_hOMF3

data_processing:
In this project, we sequence 6 samples used DNBSEQ platform, averagely generating about 10.58G Gb bases per sample.
The sequencing data was filtered with SOAPnuke by Removing reads containing sequencing adapter.
Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%.
Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
Assembly: mm10
Supplementary files format and content: gene_expression.txt: Tab-delimited text file includes FPKM values, TPM values, and counts for each Sample.

extract_protocol:
1. Take the sample (40 mL cell culture). If the sample was stored at -80°C, thaw the sample at 37°C or room temperature; 2. Cell culture: The 40 mL cell culture is filtered via a 0.22 μm sterile syringe filter; 3. An ultra-filter device (Ultra-15 10K) is taken. 5 mL 1×PBS (pH7.4) is used as a balance solution to balance the ultra-filter column. Centrifuge at 4000×g and 4℃ for 8 mins and remove the supernatant; 4. The sample is transferred into an ultra-filter tube. Centrifuge at 4000×g and 4°C for 15 mins to concentrate the sample to 1~1.2 mL; 5. Pipette repetitively the concentrated solution in the ultra-filter tube to mix the concentrated solution thoroughly and avoid air bubbles formation. The concentrated solution is then taken and transferred into a new centrifuge tube; 6. Cell culture: Add 0.5 times total volume of Total Exosome Isolation (from cell culture media); 7. Incubate at 4°C for 2 hours; 8. Centrifuge at 10,000×g and 4°C for 20 mins and remove the supernatant while the pellets are exosomes (Exosomes from cell culture cannot see by naked eyes); 9. Centrifuge at 10,000×g and 4°C for 1 min to remove the supernatant; 10. Add 140 μL of (cell culture) 1×PBS into the pellet, incubate at 37°C for 3 mins with shaking; 11. Resuspend exosome pellet thoroughly using a vortex mixer.
RNA libraries for RNA-seq were prepared using RNA-Seq Library Prep Kit following manufacturer's protocols.


title: HOMF_EXO_mRNA_2

description:
B2
fpkm_p1_hOMF2


title: 703


title: TPK_model_RNAseq_1


title: Tonsil stromal cells cryopreserved in 10% DMSO/90% FBS for 2 days (patient #2)

description: 10x Genomics


title: Tonsil stromal cells processed fresh (patient #1)

description: 10x Genomics


title: HOMF_EXO_mRNA_1

description:
B1
fpkm_p1_hOMF1


title: 702


title: CAFs_EXO_mRNA_3

description:
A3
fpkm_p1_CAFs3


title: AA_Skin

city: Daejeon

first: Su-Hyung

last: Park

address: 291, Daehak-ro, Yuseong-gu

institute: Korea Advanced Institute of Science and Technology

description: polyA RNA + protein

library_source: other

data_processing:
The purified libraries were quantified using qPCR according to the qPCR Quantification Protocol Guide(KAPA) and qualified using the Agilent Technologies 4200 TapeStation(Agilent technologies).
AndthenthelibrariesweresequencedusingHiSeq platform(Illumina)accordingtothereadlengthintheuserguide. Data processing was done by Macrogen (South Korea).
Assembly: mm10, GRCm38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

molecule: other

source_name: Skin

extract_protocol:
CD45+ cells from the lymph nodes and skin of both naive and AA mice were purified by flow cytometry. Purified cells were then stained with Antibody Derived Tag directed against CD4, CD8a, Ly6C, CD11b, Ly6G, CD44, CD19, CD11c, CD62L, F4.80, IA.IE, NK1.1, TCRab, CD3, CD69, CD103, CXCR3, KLRG1, CD14, CD207, CD169, CX3CR1, XCR1, CD49a. After CITE-tagged cells were counted and checked for viability useing a hematocytometer, approximately 8,000 cells were injected for each sample.
Library was prepared using Chromium Single Cell 3ʹ Gel Bead and Library Kit v2 (10x Genomics). Cellular mRNA and antibody-derived oligos were reverse-transcribed and indexed with a shared cellular barcode. Indexed cDNAs were then pooled and amplified by PCR according to the Chromium Single Cell 3’ v2 protocol (10x Genomics) and with specific primers amplifying the antibody-derived tags.

tag: condition

value: alopecia areata

value: Skin

value: Lymphocytes

tag: library type

value: mRNA + ADT


title: Naïve_LN

description: polyA RNA + protein

value: Naïve

value: LN


title: AA_LN

description: polyA RNA + protein


title: head kidney tissue of Odontobutis potamophila after infection with Aeromonas veronii

city: Urumqi

first: Zhang

middle: Qing

last: hua

state: Xinjiang

address: Liudao Bay Street

institute: The Second Affiliated Hospital of Xinjiang Medical University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
We used the Seurat R package (v4.1.3) to perform unsupervised clustering of the single cells using the reads count matrix as input. First, the read counts for each cell were divided by the total counts for that cell and multiplied by the scale factor (10,000), and then natural-log transformed. We performed principal component analysis (PCA) on the normalized expression matrix using highly variable genes identified by ‘‘SCTransform’’ function
Marker genes for each cluster were identified with the Wilcoxon rank-sum test with default parameters via the FindAllMarkers function in Seurat. Differential expression analysis was carried out using ‘‘FindMarkers’’ function, implemented in the Seurat package, with log-scaled fold change >=0.25 and P value <= 0.05 (Wilcoxon Rank Sum test).
Assembly: full-length transcriptome of Odontobutis potamophila
Supplementary files format and content: Tab-separated values files and matrix files

organism: Odontobutis potamophilus

source_name: head kidney tissue

extract_protocol:
Fresh tumor immersed in a complete medium containing 90% Dulbecco’s modified eagle medium (DMEM; Cat# 11054001, GIBCO) and 10% fetal bovine serum (FBS; Cat# 16140071, GIBCO), and transported to the lab in a refrigerated container. Suitable small tissue blocks (no necrotic foci / no hemorrhagic foci /less fibrous connective tissue) were cut into pieces (diameter 1-3 mm). The pieces were transferred to the gentle MACS C Tubes (Cat# 130-096-334, Miltenyi Biotec), with 5 mL of digestive enzyme included in Tumor Dissociation Kit (Cat# 130-095-929, MiltenyiBiotec). Then the tissues were made into single-cell suspension using the gentleMACS Dissociator (Cat# 130-093-235, MiltenyiBiotec) following these steps: milled; incubated at 37C for 30 min on a shaker; milled; incubated at 37C for 30 min; milled; filtered through a 70 mm filter, plus 2% FBS. Finally, the single-cell suspension was centrifugated at 400 g for 7 mins, resuspended in CELLSAVING (Cat# C40050, NCM biotech), cryopreserved in Cryotubes (Cat# 430488, Corning) and then stored at -80℃.
This process is based on the microfluidic platform Chromium ™ Single cell 3'Solution. The primers were composed of full-length Illumina TruSeq Read 1 sequencing primer, 16bp 10X Barcode sequence (used to distinguish cells), 12 bp unique molecular identifier (UMI) (to distinguish different transcripts of unified cells and remove PCR Duplications), and 30 bp poly dT reverse transcription primer. The prepared cell suspension, 10X barcode gel magnetic beads and oil drops were added to different channels (8 channels in total) of Chromium Chip B respectively, and GEM was formed through the microfluidic "double cross" cross system. In order to obtain a single cell reaction system, the concentration of cell suspension was controlled at 700-1200 cells/ul, so 90-99% of GEM produced did not conThis process is based on the microfluidic platform Chromium ™ Single cell 3'Solution. The primers were composed of full-length Illumina TruSeq Read 1 sequencing primer, 16bp 10X Barcode sequence (used to distinguish cells), 12 bp unique molecular identifier (UMI) (to distinguish different transcripts of unified cells and remove PCR Duplications), and 30 bp poly dT reverse transcription primer. The prepared cell suspension, 10X barcode gel magnetic beads and oil drops were added to different channels (8 channels in total) of Chromium Chip B respectively, and GEM was formed through the microfluidic "double cross" cross system. In order to obtain a single cell reaction system, the concentration of cell suspension was controlled at 700-1200 cells/ul, so 90-99% of GEM produced did not contain cells, and most of the remaining GEM contained one cell

value: head kidney tissue

tag: group

value: infection with Aeromonas veronii


title: 701


title: CAFs_EXO_mRNA_1

description:
A1
fpkm_p1_CAFs1

value: hOMF

value: Fibroblasts

value: Exosomes


title: head kidney tissue of Odontobutis potamophila

description: 10x Genomics

value: control


title: Naïve_Skin

description: polyA RNA + protein


title: Tonsil stromal cells cryopreserved in Cryostor for 2 days (patient #1)

description: 10x Genomics

value: Tonsil


title: inhibitor-24h-Root-3

status: Public on May 15 2023

city: Richland

first: Hugh

middle: D

last: Mitchell

state: Washington

address: 902 Battelle Blvd, P.O. Box 999, MSIN J4-18

department: Computational Biology

institute: Pacific Northwest National Laboratory

data_processing:
Quality control was performed using FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Read alignment to the genome was performed using the STAR software (https://github.com/alexdobin/STAR)
Read mapping/gene counting was performed using featureCounts (https://subread.sourceforge.net/).
Assembly: P. trichocarpa v3.1.1) available at Phytozome (https://phytozome.jgi.doe.gov)
Supplementary files format and content: For counts.txt files, columns are gene ID, chromosome, gene start(s), gene stop(s), strand orientation(s), gene length, gene counts

organism: Populus tremula x Populus alba

source_name: root

growth_protocol: Populus tremula × Populus alba, clone INRA 717-1B4 one-year-old woody stem cuttings with 6-8 dormant buds were provided by Dr. Stephen DiFazio (West Virginia State University) and stored at -80℃ until use. One week before the start of planting, the woody cuttings were transferred to 4℃. Followed by that, the woody cuttings were planted in Pro-mix BX soil (Promix, PA, USA), and kept in a walk-in growth chamber with a temperature of 24 °C /18 °C (day/night), a light intensity of 400µM/sec and a photoperiod of 16h/18h (day/night). The poplar cuttings were fertilized once per week using 100 ppm of Jack’s professional fertilizer (Jr Peters Inc, PA, USA). After approximately one month, they were transplanted to bigger soil pots (4"x4"x9.5") to facilitate root growth and grown for an additional one month. Once shoots were formed on the main woody stems, leafy cuttings with 4-5 inches in size, were excised from the apical shoot tips and the internodes below apical tips. Each cutting had just one leaf left on them to reduce transpiration. The stem base of all cuttings was treated with commercially available rooting powder (Rhizopon AA#2, Hortus USA Corp., NY, USA) and planted in the Pro-mix BX soil in 4” square pots to enable the rooting process. The cuttings were grown under similar growth conditions as described above. After 21 days, the leafy cuttings were checked for newly formed roots and then transplanted onto 4"x4"x9.5" pots containing Pro-mix BX soil and fertilized. The cuttings were allowed to grow for an additional two weeks and the newly developed leaves in the 4-5 weeks old cuttings were used for auxin foliar spraying experiments.

extract_protocol:
The 11-day hormone-treated and control plant tissues were harvested between 10:00 am to 11:00 am (4-5 hours post-dawn). Stem and root samples were frozen in liquid nitrogen and ground into a fine powder using mortar and pestle. Total RNA was extracted from 100mgs of tissue powder using GeneJet Plant RNA purification mini kit (Thermo scientific, USA), and the concentration of RNA was measured using a nanodrop (Thermo scientific, USA). One microgram RNA was shipped to Genewiz (NJ, USA) on dry ice and used for polyA selection, and cDNA library was generated and sequenced using Illumina HiSeq 2x150 bp sequencing.
Library construction was performed by GENEWIZ corporation, using polyA selection.

treatment_protocol: For Auxin enhancers (AEs), 3 µM NAA (α143 Naphthalene Acetic Acid) and 4.5 µM IBA (Indole-3-Butyric Acid) were mixed and sprayed as an enhancer cocktail while for auxin inhibitors (AI), 100 µM NPA (Naphthylphthalamic Acid) was used. AE and AI were prepared in 1N KOH (control solution) as per manufacturer recommendation (Phytotechnology Laboratories Inc, KA, USA). Since there were no earlier reports of foliar spraying of these auxin modulators in poplar, we optimized the spraying concentration based on (i) our previous experiences in foliar spraying in other plant species like Petunia hybrida (Ahkami et al. 2013) which served as our base concentration, and (ii) published literatures on woody plants where NPA (auxin inhibitor) were directly sprayed at the root initiation site which served as our upper limit concentration 151 (Valladares et al. 2020). We were mindful of the fact that very high concentrations of these synthetic auxin modulators can result in chemical stresses on source leaves with potential reduction in plant biomass development, as reported in other studies (Nassef and El-aref 2018; Di Benedetto et al. 2015; 154 Rastogi et al. 2013). Based on these factors, in our pilot experiment, we optimized AE and AI concentrations that resulted in changes in root phenotype but not altered source leaf growth in terms of the number of leaves, leaf greenness, and dry weight. The control plants were sprayed with 1N KOH solution which grew normally and established leaf growth regularly at the end of the spraying experiment. Therefore, 1N KOH caused no negative phenotypic effects on leaves. The leaves of a minimum 6-8 rooted cuttings were sprayed between 10:00 AM and 11:00 AM, with AE and AI agents for a period of 11 days. We adopted 11 days as a treatment timeline for this study based on a pilot experiment, in which we determined that this duration resulted in a measurable difference in root phenotypes between AE and AI, without any detrimental effects on foliar tissues. For the foliar spraying, we used 8, 6, and 8 rooted cuttings for control, AE, and AI treatments, respectively. Each treated plant was sprayed with 5 mL of AE or AI reagents for the first 4 days, followed by 6.2 mL for the consecutive 2 days, and 7.4 mL until plant harvest. After 11 days of foliar spraying, plants were carefully uplifted, soil was removed by gentle washing in water, and stem and root tissues were harvested and flash-frozen in liquid nitrogen. The various tissue samples were kept at -80 °C until being processed for omics analyses. A separate batch of hormone-sprayed plants was harvested and dried at 60℃ for two days and used to measure dry biomass weights. All sample collections for downstream molecular works were performed between 10:00-11:00 AM (4-5 hours post dawn).

value: root

value: Auxin inhibitor (100 uM naphthylphthalamic acid)

tag: read depth

value: acceptable


title: inhibitor-24h-Root-1

value: low counts, not recommended for routine use


title: inhibitor-11d-Root-4


title: inhibitor-24h-Root-2


title: inhibitor-11d-Root-5


title: enhancer-24h-Root-2

value: Auxin enhancer (3 uM alpha-naphthalene acetic acid and 4.5 uM indole-3-butyric acid)


title: inhibitor-11d-Root-3


title: inhibitor-11d-Root-2


title: inhibitor-11d-Root-1


title: enhancer-24h-Root-1


title: enhancer-24h-Root


title: CAFs_EXO_mRNA_2

state: Yunnan

description:
A2
fpkm_p1_CAFs2

value: Cells were co-cultured with 30ng/ml PDGF-BB for 72h


title: enhancer-11d-Root-6


title: enhancer-11d-Root-5


title: enhancer-11d-Root-4


title: enhancer-11d-Root-3


title: enhancer-11d-Root-2


title: Rhesus34403

city: San Antonio

first: Brian

middle: P.

last: Hermann

state: TX

address: 1 UTSA Circle

department: Department of Biology

institute: University of Texas at San Antonio

data_processing:
Illumina base-calling and demultiplexing with BCL-2-Fastq.
Trimmed FASTQ files were generated using the Cell Ranger v3.1.0 (10x Genomics) mkfastq command using default parameters. Alignment of trimmed reads, filtering, and UMI counting were performed using CellRanger v3.1.0 count function using mouse GRCm38 (mm10), human GRCh38 (hg38), Papio anubis (olive baboon) Panubis1.0 (Ensemble GCA_008728515.1) and rhesus macaque Mmul_10 (Ensemble GCA_003339765.3) references.
Gene expression matrices for each dataset were imported into Seurat (v3.2.3) and merged by species to produce aggregated gene-barcode matrices which were subsequently filtered, normalized and used for cell clustering.
Assembly: Papio anubis (olive baboon) Panubis1.0 (Ensemble GCA_008728515.1) and rhesus macaque Mmul_10 (Ensemble GCA_003339765.3)
Supplementary files format and content: A single gene-barcode matrix file (MTX). Each sparse matrix is stored in Market Exchange Format (MEX), which contains TSV files with features (genes) and barcode sequences corresponding to row and column indices, respectively.

organism: Macaca mulatta

source_name: Testis

extract_protocol:
Donor cells were recovered from olive baboon and rhesus macaque testes using  two-step enzymatic digestion approach.  Briefly, testicular parenchyma were digested with 1mg/ml Collagenase Type IV (Worthington Biochemicals) for 2-3 minutes at 37°C, washed with Hank’s Buffered Salt Solution (HBSS) to remove interstitial cells, digested with 0.25% trypsin/EDTA containing 1.4mg/ml DNase I (Sigma) for 7-9 minutes at 37°C, and quenched with 10% FBS. Testis cell suspensions were filtered through a nylon mesh to generate a single-cell suspension.  Single-cell transcriptomes were generated using the 10x Genomics Chromium Cell Gene Expression kit (v2 chemistry) per manufacturer recommendations (Zheng et al., 2017) at the UTSA Genomics Core as previously described (Hermann et al., 2018). For each replicate, we targeted collection of 5,000 single-cell gelbead emulsions (GEMs) containing single cells and generated libraries as per manufacturer recommendations (Zheng et al., 2017). Libraries were sequenced at the Genome Sequencing Facility (GSF) at Greehey Children’s Cancer Research Institute at UT Health San Antonio (UTHSA) on a HiSeq2500 (Illumina) instrument.
10x Genomics Single-cell 3' libraries were prepared according to manufacturer recommendations (Single Cell 3' v3 chemistry for 37979, Single Cell 3' v2 chemistry for all others).

treatment_protocol: Animal were untreated and testes obtained at necropsy for another purpose

value: Testis

value: Testicular cells

value: 10x Genomics 3' single-cell Gene Expression


title: C-Inh-24h-Root-3

value: control (1 N KOH)


title: E9.5_mouse_whole_embryo_20200613

city: Beijing

first: Zeyuan

last: Liu

address: 15 Datun Road, Chaoyang District, Beijing, 100101, China

institute: Institute of Biophysics,Chinese Academy of Sciences

data_processing:
Illumina Casava1.8 software used for basecalling
Reads were aligned to hg19 human genome by Cellranger(v2.0.1 and v3.0.2)
Filtered count matrix was merged by Scanpy Package(v1.4.2)
Genome_build: hg19, mm10
Supplementary_files_format_and_content: Filtered count matrix was formatted by mtx, and barcode and gene information was with tsv format

source_name: mouse embryo

extract_protocol:
Human embryo samples were collected in ice-cold artificial cerebrospinal fluid (ACSF), single cell was selected by FACS
Chromium™ Single Cell 3’ Reagent Kits v2

value: embryo

tag: region

value: whole embryo


title: E10.5_mouse_whole_embryo_20200613

tag: tissue


title: C-Inh-24h-Root-1


title: C-Inh-11d-Root-4


title: enhancer-11d-Root-1


title: C-Inh-24h-Root-2


title: C-Inh-11d-Root-3


title: C-Inh-11d-Root-2


title: 25mM ALA treatment, harvest at 2h Replicate 4

city: São Paulo

first: Janice

last: Onuki

state: SP

address: Av. Vital Brasil, 1500 - Butantã

country: Brazil

institute: Butantan Institute

description: Biological replicate 4 of 4. treated with 25 mM ALA and harvested after 2 h.

hyb_protocol: RNA Spike-In Kit, two-color, was used as a positive hybridization control.

scan_protocol: Scanned on an Microarray Agilent SureScan scanner using AgilentG3_GX_2color protocol. Images were quantified Agilent Feture Extraction Software (version A.10.7.1.1).

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.

source_name: HepG2 cell line (code 0103)

label_protocol: Double-stranded cDNA was generated from 100 ng total RNA using the Low Input Quick Amp Labeling Kit, two-color with Cyanine 3-CTP or Cyanine 5-CTP.

growth_protocol: The HepG2 cell line (code 0103), from Rio de Janeiro Cell Bank (BR), was cultivated in DMEM-low glucose with 100 IU/mL penicillin and 0.1 mg/mL streptomycin (Thermo Fisher, USA), supplemented with 10% fetal bovine serum (FBS) (Cultilab, BR), and maintained at 37° C in 5% CO2 atmosphere.

extract_protocol: Total RNA was extracted using the RNAspin Mini RNA isolation kit (GE Healthcare, USA)

treatment_protocol: After reaching 80% confluence, the cells were treated or not with ALA 2.5 mM or 25 mM for 2 h or 24 h (identified as: Control, ‘2.5mM-2h’, ‘2.5mM-24h’, ‘25mM-2h’, ‘25mM-24h’)

tag: time

value: 2 h

value: ALA 25 mM

source_name: Control

value: ALA 0 mM


title: C-Inh-11d-Root-1


title: 25mM ALA treatment, harvest at 2h Replicate 2

description: Biological replicate 2 of 4. treated with 25 mM ALA and harvested after 2 h.


title: 2.5mM ALA treatment, harvest at 2h Replicate 4

description: Biological replicate 4 of 4. treated with 2.5 mM ALA and harvested after 2 h.

value: ALA 2.5 mM


title: 2.5mM ALA treatment, harvest at 2h Replicate 3

description: Biological replicate 3 of 4. treated with 2.5 mM ALA and harvested after 2 h.


title: 25mM ALA treatment, harvest at 2h Replicate 1

description: Biological replicate 1 of 4. treated with 25 mM ALA and harvested after 2 h.


title: 2.5mM ALA treatment, harvest at 2h Replicate 2

description: Biological replicate 2 of 4. treated with 2.5 mM ALA and harvested after 2 h.


title: C-enh-24h-Root-3


title: 25mM ALA treatment, harvest at 2h Replicate 3

description: Biological replicate 3 of 4. treated with 25 mM ALA and harvested after 2 h.


title: 2.5mM ALA treatment, harvest at 2h Replicate 1

description: Biological replicate 1 of 4. treated with 2.5 mM ALA and harvested after 2 h.


title: Wild-type(N2)_D6_B, RNA-seq

city: Martinsried/Planegg

first: Martin

last: Mueller

address: Am Klopferspitz 18

institute: MPI of Biochemistry

description:
Counts_NC40_aged_mRNA.txt
N2B

data_processing:
Sequencing reads were demultiplexed and trimmed using a custom awk script. Barcodes used for Ribo-seq - replicate A: ATCGT; replicate B: AGCTA
The UMI were extracted using UMI-tools using the option ‘--extract-method=regex --bc-pattern="^(?P<umi_1>.{2}).+(?P<umi_2>.{6})$"’, which serves to remove duplicated reads arising from library amplification. The clipped reads were then mapped against ncRNA/rRNA indices using Bowtie2 (v2.4.2) with the parameters ‘-N 1 -L 15’. Unaligned reads were mapped against the genome using STAR (v2.7.10a) with parameters ‘--outFilterMismatchNmax 2 --quantMode TranscriptomeSAM GeneCounts --outSAMattributes MD NH --outFilterMultimapNmax 1’. The P-site offset and metagene plots were computed using the R package “riboWaltz” (Lauria, 2018). Transcript enrichment was calculated with the R package “DESeq2” (Love, 2014) or “DEBrowser” (Kucukural, 2019).
Assembly: hg38 and WBcel235(ce11)
Supplementary files format and content: tab-delimited text file with raw counts

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: The Bristol strain N2 was used as wild-type. Strains used in this study are listed in the Key Resource Table. Worms were grown on nematode growth medium (NGM) seeded with OP50 bacteria and maintained at 20°C unless otherwise indicated. For liquid culture, worm eggs were collected by bleaching and synchronized populations of L1 larvae were obtained by overnight growth in M9 medium. The L1 larvae were grown in S Basal in presence of OP50 bacteria.

extract_protocol:
C. elegans  Synchronized nematodes were transferred to 1 l S-Basal and grown in liquid culturentil D1 of adulthood or until D6, when indicated. FUdR (200 µM) was added when the culture had reached the L4/young adult stage. After thorough washing in M9, the nematodes were frozen in lysis buffer (25 mM Hepes-KOH pH 7.4, 100 mM KoAC, 10 mM MglCl2, 0.5 mM DTT, 2x EDTA free protease inhibitor, 0.1 U/μL SUPERase*In, 100 μg/mL cycloheximide) by dropwise transfer into liquid nitrogen. The nematodes were lysed with a Retsch Cryomill MM400 at 30 Hz for 3 times 90 s with cooling between cycles. The lysate was cleared for 10 min at 20,000 x g and 4oC. Ribosome protected fragments (RPFs) were recovered, and libraries were prepared as previously described {McGlincy, 2017 #78}.  HEK293T cells  HEK293T cells were seeded into 15 cm plates 24 h prior to treatment. The cells were treated with 10 nM CC-885 and 20 μg/ml G418 for 4 h. Ribosome protected fragments (RPFs) were recovered, and libraries were prepared as previously described {McGlincy, 2017 #78}.
C. elegans  The procedure for immunoprecipitation (IP) of GCN-1 bound ribosomes was adapted from {Matsuo, 2021 #75}. Nematodes were synchronized by bleaching. L1 larvae were transferred to 1 L S-Basal. The animals were harvested at D1 of adulthood. Bacteria were removed by repeated washes in M9. In the last washing step, M9 was replaced by lysis buffer (25 mM Hepes-KOH pH 7.4, 100 mM KoAC, 10 mM MglCl2, 0.5 mM DTT, 2x EDTA free protease inhibitor, 0.1 U/μL SUPERase*In, 100 μg/mL cycloheximide). After a quick spin, the worms were flash frozen in liquid nitrogen. The frozen worms were lysed with a Retsch cryomill MM400 at 30 Hz as above. The lysate was thawed on ice and clarified by centrifugation at 4,000 x g for 10 min at 4oC. Protein concentration was determined by Bradford assay. The supernatant fraction (80 mg of total protein) was partially digested with 3 units per 1 mg RNA RNase I (Epicenter) at 4oC for 1 h. Ribosomes were pelleted through a sucrose cushion (1 M, 20 U/mL SUPERase*In (Invitrogen)) at 55.000 rpm in a SW 55 Ti rotor (Beckman Coulter) for 2 h at 4oC and resuspended in lysis buffer supplemented with 10% glycerol. The IP was performed at 4oC for 1 h using M2 anti-FLAG magnetic agarose beads (Invitrogen). The beads were washed 10 times with lysis buffer and bound material was digested with 12.5 units of RNase I (Epicenter) at 23oC for 45 min (strong RNase I treatment). Ribosome protected mRNA fragments were eluted by adding TRIzol reagent (Invitrogen). Libraries were prepared as previously described (McGlincy, 2017 #78) and sequenced on an Illumina NextSeq 500 system.  HEK293T cells  Cells (treated with CC-885 or untreated) were harvested, washed with PBS and lysed by trituration through a 26 G needle for 10 times in lysis buffer (20 mM Tris, pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 µg/ml cycloheximide, 1 % Triton-X 100). The lysate was cleared at 4,000 x g for 10 min and an equivalent of 5 mg RNA input was digested with 15 units of RNAse I. The digested lysate was then layered over a sucrose cushion (1 M, 20 U/mL SUPERase*In (Invitrogen)) and centrifuged at 55.000 rpm in a SW 55 Ti rotor (Beckman Coulter) for 2 h at 4oC. The pelleted ribosomes were resuspended in lysis buffer supplemented with 10 % glycerol and incubated with GCN1 antibody (A301-843A, Thermo Fisher) coupled to protein G Dynabeads (10003D, Invitrogen) (5 µg antibody per 50 µl of protein G beads) for 2 h at 4oC. The beads were washed 10 times and digested with 4 units RNAse I for 45 min at 23oC. RPFs were isolated by TRIzol and libraries were prepared as previously described (McGlincy, 2017).

treatment_protocol: HEK293T cells were cultured in DMEM (Thermo Scientific, 11995073) supplemented with 10% FBS (Gibco, 10270106) at 5% CO2 and 37°C. Subsequently, cells were treated with 10 nM CC-885 and 20ug/ul G418 for 4 hours.

value: whole organism

tag: ip antibody

tag: genotype


title: 25mM ALA treatment, harvest at 24h Replicate 2

description: Biological replicate 2 of 4. treated with 25 mM ALA and harvested after 24 h.

tag: treatment


title: C-enh-24h-Root-2

value: root


title: 25mM ALA treatment, harvest at 24h Replicate 4

description: Biological replicate 4 of 4. treated with 25 mM ALA and harvested after 24 h.


title: 25mM ALA treatment, harvest at 24h Replicate 3

description: Biological replicate 3 of 4. treated with 25 mM ALA and harvested after 24 h.


title: Wild-type(N2)_D6_A, RNA-seq

description:
Counts_NC40_aged_mRNA.txt
N2A


title: 25mM ALA treatment, harvest at 24h Replicate 1

description: Biological replicate 1 of 4. treated with 2.5 mM ALA and harvested after 24 h.


title: GCN-1(nc40)_D6_B, RNA-seq

description:
Counts_NC40_aged_mRNA.txt
GCN1B


title: C-enh-24h-Root-1


title: 2.5mM ALA treatment, harvest at 24h Replicate 3

description: Biological replicate 3 of 4. treated with 2.5 mM ALA and harvested after 24 h.