title: AD brain, 9-month-old male biol rep #4


title: P24-N-II

status: Public on Jul 08 2024

type: SRA

city: Beijing

first: Zemin

last: Zhang

state: Beijing

address: Yiheyuan Road

department: BIOPIC

country: China

institute: Peking University

library_source: transcriptomic

data_processing:
For 10X data, Cell Ranger 3.1.0 was used to quantify gene expression level and identify TCR sequences.
Assembly: GRCh38 for RNA expression
Supplementary files format and content: text files for expression matrices, cell metadata

molecule: polyA RNA

organism: Homo sapiens

source_name: Adjacent normal tissue

extract_protocol:
For tissue samples, collected tumor or adjacent normal biopsies was stored in the tissue storage solution immediately after resection and transferred on ice. Samples were washed twice and cut into approximately 1-2 mm3 pieces before being collected in the RPMI-1640 medium (Gibco) with 10% fetal bovine serum (FBS, Gibco), and projected to enzymatical digestion with gentleMACS Tumor Dissociation Kit (Miltenyi Biotec) for 60 min on a rotor at 37°C according to the manufacturer’s protocol. The dissociated cells then passed through a 100-mm SmartStrainer in the RPMI-1640 medium (Invitrogen) with 10% FBS and centrifuged at 400 g for 5 min. After the removal of the supernatant, the pelleted cells were suspended in 1 mL of red blood cell lysis buffer (TIANDZ) and incubated on ice for 1 min for red blood cell lysis and quickly terminate the reaction with RPMI-1640 medium (Invitrogen, with 10% FBS). After being centrifuged at 400 g for another 5 min, the cell pellets would be re-suspended in sorting buffer (PBS supplemented with 1% FBS).  Blood samples were collected in EDTA anticoagulant tubes and kept on ice for transferring. After restoring to room temperature and mixing thoroughly, peripheral blood mononuclear cells (PBMCs) were isolated using HISTOPAQUE-1077 (Sigma-Aldrich) solution. Briefly, peripheral blood was carefully layered onto equal volume HISTOPAQUE-1077 without breaking the plasma-HISTOPAQUE-1077 interface. After centrifugation at 400 g for 30 min, the lymphocyte layer was carefully transferred to a new tube and washed twice with 1x phosphate-buffered saline (PBS, Invitrogen). After red blood cells lysis following the aforementioned procedure, the collected lymphocytes were then re-suspended in sorting buffer (PBS supplemented with 1% FBS).
To obtain high-quality cell pools before subsequent library construction, single cell suspensions collected from blood or tissue samples were stained with antibodies against 7AAD (Thermo Fisher), CD235a (BioLegend) for FACS sorting (BD Aria III instrument). By gating 7AAD- CD235a- cells, living cells were enriched, and residuary red blood cells were excluded.  Gated cells were sorted into 1.5 mL LoBind tubes (Eppendorf) and counted manually under the microscope. The concentration of single cell suspensions was adjusted to 500-1200 cells/l. 10,000~18,000 cells were loaded for the 10x Chromium Single cell 5’ and VDJ library construction (10x Genomics), with subsequent steps performed following the standard manufacturer’s protocols. Purified libraries were analyzed by an Illumina NovaSeq with 150-bp paired-end reads.
10x Chromium Single cell 5’ + VDJ Library

tag: tissue

value: Adjacent normal tissue

tag: treatment stage

value: Post

tag: patientid

tag: cancer type

value: CRC


title: GrowshA1_5

city: Cambridge

first: Ioana

last: Olan

state: Cambridgeshire

address: Robinson Way

department: Cancer Research UK Cambridge Institute

country: United Kingdom

institute: University of Cambridge

data_processing:
Libraries were aligned using STAR (Dobin et al. 2013) against the hg19 genome and transcriptome (GENCODE19) reference.
Reads were counted over genes using the GENCODE19 annotation and the featureCounts functionality from the subread package (Liao et al. 2014).
Supplementary files format and content: TXT: Tab-separated raw read counts (per sample).

growth_protocol: IMR90 and H1299 cells were cultured in DMEM (Gibco #12481-023) with 10% fetal calf serum (FCS) at 37°C in 5% (IMR90) or atmospheric (H1299) O2 and 5% CO2.

extract_protocol:
RNA was purified using the QIAGEN RNeasy plus kit according to the manufacturer’s instructions. The quality was checked using the Agilent High Sensitivity RNA Bioanalyser or ScreenTape System.
Libraries were prepared from six biological replicates of each condition using TruSeq stranded mRNA or Illumina Stranded mRNA Prep Kit (Illumina), according to the manufacturer’s instructions, and sequenced using using the HiSeq-4000 or the Novaseq-6000 platforms (Illumina).

treatment_protocol: For RIS samples,IMR90 ER:HRAS(G12V) cells were treated for 6 days with 100nM 4OHT.

tag: cell line

tag: cell type

value: lung fibroblast

tag: genotype

value: pLNCX2 ER:HRAS G12V

tag: treatment

value: pMSCV miR shHMGA1

tag: shcebpb


title: GrowshA1_2


title: AD brain, 6-month-old female biol rep #3

city: Lebanon

first: Arti

last: Gaur

state: NH

address: 1 Medical Center Dr

department: Neurology

country: USA

institute: Dartmouth-Hitchcock Medical Center

data_processing:
Raw data were pre-processed by removing adapter sequences using Cutadapt (v3.4)
Raw data were aligned to the mm10 reference genome using HISAT2 (v2.1.0)
Read counts were quantified using the Featurecounts function (v2.0.1) from the subreads package to generate a gene expression matrix for downstream processing
Pseudogenes and genes without canonical names were filtered from the matrix
ComBat-seq (Zhang, 2020) was applied to adjust for sequencing batch effects
Assembly: mm10
Supplementary files format and content: comma-separated values file includes raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: Bulk brain

extract_protocol:
Brain tissue was dissected from animals following perfusion with PBS and heparin. Samples were flash-frozen in liquid nitrogen and stored at -80°C. Samples were later placed in a deep-well 96-well plate with stainless steel RNase-free homogenization beads and QIAzol lysis buffer. Plates were inserted into the SPEX SamplePrep 1600 MiniG tissue homogenizer and run at maximum speed for 5 minutes. Following homogenization, the tissue solution was added to QIAzol lysis buffer and stored at -80°C. Lysed tissue solution was subsequently added to the QIAGEN miRNeasy Micro Kit for purification of total RNA.
RNA libraries for RNA-seq were prepared using the Kapa RNA HyperPrep kit (Roche) following the manufacturer’s instructions.

value: Bulk brain

tag: Sex

value: Female

tag: age (months)

tag: sequencing batch_#


title: JUN Cut&Tag, WT mESCs (EpiLC-0h), Rep1

first: Xuehui

last: Lv

address: No.5 Yiheyuan Road, Haidian district, Beijing, 100871, China

library_source: genomic

data_processing:
For the bioinformatics analysis, the adapters were cut by Trimmomatic. The data were aligned to mouse genome sequence (mm10) using Bowtie2 with options: –local–very-sensitive-local–no-unal–nomixed–no-discordant–phred33 -I 10 -X 700 . Samtools was used to remove duplication from bam files. The bigWig files were generated by bamCoverage using CPM as normalization method to show IGV examples . The differential peaks between samples were called using Macs2 with default parameters. ComputerMatrix was used to calculate the peak signals around poised-specific genes from bigWig file normalized by CPM, and the results were visualized by plotHeatmap. The read counts in each peak were extracted using bedtools .
Assembly: mm10
Supplementary files format and content: The bigWig files normalized by CPM of each sample were provided to visualize in IGV or UCSC genome browser.
Library strategy: Cut&Tag

molecule: genomic DNA

growth_protocol: The mESCs stated as EpiLC 0h/2iLif were cultured in 2i/Lif medium, while those stated as EB D0/SL were cultured in Serum/Lif medium.ADFNK differentiation medium and N2B27 basal medium were used for EB differentiation and EpiLC differentiation, respectively.

extract_protocol:
Briefly, cells were harvested, counted, and centrifuged for 3 min at 1,000 rpm at room temperature. About 10,000 cells were washed using washing buffer followed by incubation with Concanavalin A beads at room temperature for 10 min. Next, 1 μl primary antibody was incubated with cells on a rotating platform at 4°C overnight. Secondary antibody incubation followed by pA/G-Tn5 incubation were performed on a rotating platform at room temperature each for 1 h. Between each of the above steps, the beads were washed using corresponding buffer. To activate the activity of Tn5, the beads were incubated in Tagmentation buffer at 37°C for 1 h followed by stop tagmentation using EDTA and extract DNA using DNA clean beads.
Cut&Tag libraries preparation using Hyperactive universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903)

value: mESCs

value: WT


title: P24-B-II

source_name: Peripheral blood

value: Peripheral blood


title: AD brain, 24-month-old female biol rep #2


title: JUN Cut&Tag, Flii-/- mESCs (EpiLC-0h), Rep1

value: FLII knockout


title: P24-T-I

source_name: Tumor

value: Tumor

value: Pre


title: GrowshA1_4


title: AD brain, 24-month-old female biol rep #3


title: H3K27ac Cut&Tag, Flii-/- mESCs (EpiLC-1h), Rep2


title: RIS_8

value: 4OHT (6 days)

value: pMSCV miR v


title: Control brain, 21-month-old male biol rep #1

value: Male


title: RIS_7


title: P24-T-II


title: H3K27ac Cut&Tag, Flii-/- mESCs (EpiLC-0h), Rep2


title: P24-N-I

value: Adjacent normal tissue


title: P23-T-IV

value: Post


title: AD brain, 12-month-old female biol rep #3


title: P24-B-I

value: CRC


title: RIS_6

value: lung fibroblast


title: AD brain, 9-month-old male biol rep #5


title: RIS_5

value: pLNCX2 ER:HRAS G12V


title: H3K27ac Cut&Tag, WT mESCs (EpiLC-1h), Rep2


title: AD brain, 6-month-old female biol rep #2


title: P23-N-IV


title: GrowshA1_1

value: pMSCV miR shHMGA1


title: H3K27ac Cut&Tag, Flii-/- mESCs (EpiLC-6h), Rep2


title: H3K27ac Cut&Tag, WT mESCs (EpiLC-0h), Rep2


title: RIS_4


title: AD brain, 24-month-old female biol rep #1

value: Bulk brain


title: P23-B-IV


title: H3K27ac Cut&Tag, Flii-/- mESCs (EpiLC-6h), Rep1


title: AD brain, 9-month-old male biol rep #3


title: RIS_3


title: AD brain, 6-month-old female biol rep #1

value: Female


title: H3K27ac Cut&Tag, Flii-/- mESCs (EpiLC-1h), Rep1

value: mESCs


title: RIS_2


title: H3K27ac Cut&Tag, Flii-/- mESCs (EpiLC-0h), Rep1


title: P23-B-III

value: On


title: AD brain, 9-month-old male biol rep #2


title: RIS_1


title: P23-T-III


title: AD brain, 9-month-old male biol rep #1


title: P23-T-II


title: Grow_7


title: Grow_8


title: AD brain, 21-month-old female biol rep #5


title: H3K27ac Cut&Tag, WT mESCs (EpiLC-1h), Rep1

value: WT


title: P23-N-II


title: H3K27ac Cut&Tag, WT mESCs (EpiLC-0h), Rep1


title: P23-B-II

value: Peripheral blood


title: Grow_6


title: AD brain, 21-month-old female biol rep #4


title: P23-N-III


title: RNAPII Cut&Tag, Flii-/- mESCs (EpiLC-6h), Rep2

value: FLII knockout


title: AD brain, 21-month-old female biol rep #3


title: Grow_5


title: P23-T-I

value: Tumor

value: Pre


title: RNAPII Cut&Tag, Flii-/- mESCs (EpiLC-1h), Rep2


title: Grow_4

value: pMSCV miR v


title: H3K27ac Cut&Tag, WT mESCs (EpiLC-6h), Rep1


title: GrowshA1_3


title: H3K27ac Cut&Tag, WT mESCs (EpiLC-6h), Rep2


title: P23-B-I


title: P23-N-I


title: Grow_2


title: Grow_3


title: RNAPII Cut&Tag, WT mESCs (EpiLC-6h), Rep2


title: P22-T-III


title: AD brain, 21-month-old female biol rep #1


title: P22-N-III


title: Grow_1


title: AD brian, 18-month-old male biol rep #2

value: Male


title: RNAPII Cut&Tag, Flii-/- mESCs (EpiLC-0h), Rep2


title: Day10_mKate2_Pos_rep3

city: Boston

first: Qianxia

state: MA

address: 3 Blackfan Circle, RM 3117.16

institute: Boston Children's Hospital

data_processing:
Demultiplexed sequencing reads were trimmed using Cutadapt (v2.5) to remove vector-derived sequences, yielding only 20 bp sequences corresponding to sgRNAs.
The statistical analysis of sgRNA enrichment was performed using MAGeCK-VISPR (v0.5.6) with the "MAGeCK-RRA" experimental configuration and visualized using the MAGeCKFlute R package (v2.0.0).
Assembly: Human Brunello CRISPR knockout pooled sgRNA library
Supplementary files format and content: tab-delimited txt file includes CRISPR screening scores
Library strategy: Targeted genomic sequencing

growth_protocol: 4D6 cells were maintained in RPMI supplemented with 10% FBS, 1% L-glutamine

extract_protocol:
Genomic DNA was extracted using the DNeasy Blood and Tissue Kit (QIAGEN, #69504) and cleaned using the OneStep PCR Inhibitor Removal Kit (Zymo Research, #D6030).
Sequencing libraries were generated by PCR amplification as previously described (Doench JG et al, 2016), pooled at an equal molar concentration, purified using the MinElute Reaction Cleanup Kit (Qiagen, #28204) to enrich for the 350-360bp amplicons

treatment_protocol: The engineered 4D6 cells were transduced with lentiviral Human Brunello CRISPR knockout pooled sgRNA library [a gift from David Root and John Doench (Addgene #73178-LV)7] at a MOI of 0.4, aiming for 500-fold representation of each sgRNA. Library transduced cells were selected under 1 mg/ml puromycin for 2 days and further expanded for another 7 or 10 days. Cells were treated with 1 µg/ml Dox 24 hrs prior to sorting to induce EGFP-P2A-Gal4DBD-AireCTT expression, and then top-5% and bottom-5% of the population were sorted based on mKate2/EGFP ratios on the SH800S Cell Sorter (Sony Biotechnology).

value: thymic epithelial cells

value: Lentiviral library transduction, puromycin selection, Dox treatment, sorting

tag: time

tag: phenotype

value: mKate2 positive


title: RNAPII Cut&Tag, WT mESCs (EpiLC-1h), Rep2


title: P22-LN-III

source_name: LN

value: LN

value: Post

value: CRC


title: RNAPII Cut&Tag, WT mESCs (EpiLC-0h), Rep2


title: Control brian, 18-month-old male biol rep #3

value: Bulk brain


title: Day10_mKate2_Pos_rep2


title: RNAPII Cut&Tag, Flii-/- mESCs (EpiLC-6h), Rep1


title: AD brain, 18-month-old male biol rep #1


title: Control brian, 18-month-old male biol rep #2


title: P22-B-III


title: Day10_mKate2_Pos_rep1


title: AD brain, 21-month-old female biol rep #2

value: Female


title: RNAPII Cut&Tag, Flii-/- mESCs (EpiLC-1h), Rep1

value: mESCs


title: P22-T-II

value: On


title: Control brain, 18-month-old male biol rep #1


title: Day10_mKate2_Neg_rep3

value: mKate2 negative


title: P22-B-II

value: Peripheral blood


title: RNAPII Cut&Tag, Flii-/- mESCs (EpiLC-0h), Rep1

value: FLII knockout


title: Control brain, 18-month-old female biol rep #2


title: Day10_mKate2_Neg_rep1


title: RNAPII Cut&Tag, WT mESCs (EpiLC-6h), Rep1

value: WT


title: RNAPII Cut&Tag, WT mESCs (EpiLC-1h), Rep1


title: Day7_mKate2_Pos_rep3


title: RNAPII Cut&Tag, WT mESCs (EpiLC-0h), Rep1


title: AD brain, 12-month-old female biol rep #1


title: P21-T-III

value: Tumor


title: P22-B-I

value: Pre


title: Day7_mKate2_Pos_rep2


title: AD brain, 12-month-old female biol rep #2


title: Control brain, 18-month-old female biol rep #3


title: Day7_mKate2_Pos_rep1


title: Control brain, 15-month-old male biol rep #3

value: Male


title: Day7_mKate2_Neg_rep3

value: thymic epithelial cells


title: P21-N-III

value: Adjacent normal tissue


title: Day10_mKate2_Neg_rep2

value: Lentiviral library transduction, puromycin selection, Dox treatment, sorting


title: P22-N-I


title: Control brain, 15-month-old male biol rep #2


title: P21-B-II


title: Control brian, 15-month-old male biol rep #1


title: Day7_mKate2_Neg_rep2


title: Control brain, 15-month-old female biol rep #3


title: P21-T-I


title: Day7_mKate2_Neg_rep1


title: P22-T-I


title: P21-N-I


title: Control brain, 15-month-old female biol rep #2


title: P21-B-III


title: P21-B-I


title: RNA pulldown-Seq, 0.01 μM DMDA-PatA, 30 min

city: Wako

first: Shintaro

last: Iwasaki

address: 2-1 Hirosawa

department: Cluster for Pioneering Research

country: Japan

institute: RIKEN

data_processing:
Basecalling with Illumina Casava 1.8 software, 3' adapter trimming with FastX-toolkit, non-coding RNA alignment with STAR, alignment to transcripts with STAR, Read quantitation using custom scripts
Assembly: hg38, custom mitochondrial transcript reference
Supplementary files format and content: text files contain three columns: 1. transcript name; 2. CDS length ;3. read counts. txt files including mito in the file name are for transcripts encoded in the mitochondrial genome.
Library strategy: RNA pulldown-Seq

source_name: HEK293 Flp-In T-Rex

growth_protocol: cells were maintained in DMEM + GlutaMAX supplemented with 10% FBS

extract_protocol:
eIF4A1 bound RNAs collection with streptavidin beads, RNA extraction
preadenylated linker ligation, rRNA depletion, reverse transcription, cDNA circularization, PCR amplification

treatment_protocol: 0.01 μM DMDA-PatA, 30 min

value: HEK293 Flp-In T-Rex

value: SBP-tagged eIF4A1 integrant

value: 0.01 microM DMDA-PatA, 30 min


title: Control brain, 15-month-old female biol rep #1

value: Bulk brain


title: RNA pulldown-Seq, 0.1 μM DMDA-PatA, 30 min

treatment_protocol: 0.1 μM DMDA-PatA, 30 min

value: 0.1 microM DMDA-PatA, 30 min


title: P20-T-III

value: Post

value: CRC


title: RNA pulldown-Seq, 0.1 % DMSO, 30 min, rep1

treatment_protocol: 0.1 % DMSO, 30 min

value: 0.1 percent DMSO, 30 min


title: RNA pulldown-Seq, 0.1 % DMSO, 30 min, rep2


title: Control brain, 6-month-old male biol rep #1


title: JUN Cut&Tag, WT mESCs (EpiLC-1h), Rep1

value: mESCs


title: P20-B-III

value: Peripheral blood


title: Control brain, 6-month-old male biol rep #3


title: Control brain, 6-month-old male biol rep #2


title: P20-T-II

value: On


title: ribosome profiling, 1 μM Hipp, 15 min

data_processing:
Basecalling with Illumina Casava 1.8 software, 3' adapter trimming with FastX-toolkit, non-coding RNA alignment with bowtie2, alignment to transcripts with bowtie2, Read quantitation using custom scripts
Assembly: hg38, custom mitochondrial transcript reference
Supplementary files format and content: text files contain three columns: 1. transcript name; 2. CDS length ;3. read counts. txt files including mito in the file name are for transcripts encoded in the mitochondrial genome.
Library strategy: Ribosome profiling

extract_protocol:
Rnase I footprinting, ribosome pelleting, RNA extraction
preadenylated linker ligation, rRNA depletion, reverse transcription, cDNA circularization, PCR amplification

treatment_protocol: 1 μM Hipp, 15 min

value: WT

value: 1 microM Hipp, 15 min


title: ribosome profiling, 0.1 μM Hipp, 15 min

treatment_protocol: 0.1 μM Hipp, 15 min

value: 0.1 microM Hipp, 15 min


title: Control brain, 6-month-old female biol rep #3

value: Female


title: Control brain, 6-month-old female biol rep #1


title: P20-N-II

value: Adjacent normal tissue


title: ribosome profiling, 0.1 % DMSO, 15 min, rep1

treatment_protocol: 0.1 % DMSO, 15 min

value: 0.1 percent DMSO, 15 min


title: ribosome profiling, 0.1 % DMSO, 15 min, rep2

value: HEK293 Flp-In T-Rex


title: P20-B-II


title: AD brain, 18-month-old female biol rep #3


title: P20-T-I

value: Tumor

value: Pre


title: ribosome profiling, 1 μM San, 30 min

treatment_protocol: 1 μM San, 30 min

value: 1 microM San, 30 min


title: Control brain, 18-month-old female biol rep #1

value: Bulk brain


title: AD brain, 18-month-old female biol rep #2


title: P20-N-III

value: Post


title: P20-N-I

value: CRC


title: AD brain, 18-month-old female biol rep #1


title: ribosome profiling, 0.1 μM DMDA-PatA, 30 min

value: 0.1 microM DMDA-PatA, 30 min


title: ribosome profiling, 0.01 μM DMDA-PatA, 30 min

value: 0.01 microM DMDA-PatA, 30 min


title: AD brain, 15-month-old male biol rep #3

value: Male


title: Control brain, 6-month-old female biol rep #2


title: AD brain, 15-month-old male biol rep #2


title: ribosome profiling, 0.1 % DMSO, 30 min, rep2

value: 0.1 percent DMSO, 30 min


title: ribosome profiling, 0.1 % DMSO, 30 min, rep1

tag: 1 = genotype

value: WT


title: P19-T-II

value: On


title: P19-N-III


title: ribosome profiling, 20 μM SAN, 30 min

treatment_protocol: 20 μM San, 30 min

value: 20 microM San, 30 min


title: P19-B-III

value: Peripheral blood


title: P19-N-II

value: Adjacent normal tissue


title: AD brain, 15-month-old male biol rep #1


title: AD brain, 15-month-old female biol rep #3

value: Female


title: AD brain, 15-month-old female biol rep #2


title: P19-T-I


title: AD brain, 15-month-old female biol rep #1


title: P19-N-I


title: Control brain, 12-month-old male biol rep #1


title: P19-B-I


title: Control brain, 12-month-old male biol rep #2


title: Control brain, 12-month-old male biol rep #3


title: P20-B-I


title: P18-T-III


title: Control brain, 12-month-old female biol rep #3


title: POX00418-3

city: Nanning

first: shen

last: xin

address: Daxue Road

institute: College of Life Science and Technology, Guangxi University

data_processing:
The original file sequenced by the MGI high-throughput sequencer is an image file. After base calling and Bcl2Fastq conversion, the original sequenced reads in FASTQ (fq for short) format can be obtained, which is called raw data or raw reads.
The original sequencing data will contain linker information, low-quality bases, and undetected bases (represented by N). These information will cause great interference to subsequent information analysis. These interference information will be removed by fine filtering methods. The final data is valid data, we call it Clean data or Clean read.
Use SOAPnuke software (v2.1.0) to filter Raw reads to get Clean reads. The main parameters are: –lowQual=20, –nRate=0.005, –qualRate=0.5, other parameters are default. The steps of data processing are as follows: 1) Filter out the paired reads containing the linker sequence.2) Remove paired reads with a ratio of N (N means that the base information cannot be determined) greater than 0.5%.3) Remove low-quality paired reads (reads with Qphred<=20 bases accounting for more than 50% of the entire read length).
Image recognition, decontamination, and adapter removal of sequencing results. Statistical results include the number of sequencing reads, data yield, Q20 content, Q30 content, GC content, etc
Assembly: HISAT2
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Penicillium oxalicum

source_name: Mycelium

growth_protocol: Penicillium oxalicum strains were cultured on PDA at 28°C for 4 days, and the spores were washed with 0.2% Tween-80 to obtain fresh spore fluid.

extract_protocol:
RNA was extracted with Trizol,  the purity of RNA (OD260/280) was detected by Nanodrop2000. The integrity of RNA were accurately detected by Agilent 2100,the detection indicators include: RIN value, 28S/18S, whether the map baseline is raised, 5S peak, and electrophoresis to detect whether the RNA sample is diffuse or has a genome DNA contamination.
After the sample is qualified, the library is constructed. The main process is as follows: 1) mRNA enrichment for total RNA by mRNA enrichment method: Enrich mRNA with polyA tail using magnetic beads with Oligo dT. 2) Fragment the RNA obtained by interrupting the buffer, perform reverse transcription with random N6 primers, and synthesize the double-stranded cDNA to form double-stranded DNA. 3) Fill in the end of the synthesized double-stranded DNA and phosphorylate the 5' end, form a sticky end with a protruding "A" at the 3' end, and then connect a bubbling linker with a protruding "T" at the 3' end. 4) The ligation product is amplified by PCR with specific primers. 5) The PCR product is thermally denatured into single-stranded DNA, and then a single-stranded circular DNA library is obtained by circularizing the single-stranded DNA with a bridge primer.

treatment_protocol: Fresh spore fluid was inoculated into the glucose medium for 24 hours and then transferred to the enzyme-producing medium containing raw starch as the only carbon source for 24 hours.

value: Mycelium

value: POX00418 was deleted in {delta}PoxKu70

value: Culture in enzyme production medium with Avicel after transfer 24h


title: P19-T-III

value: Tumor


title: POX00418-2


title: P18-N-III


title: POX00418-1


title: P18-B-III


title: POXKu70_3


title: P19-B-II


title: P18-T-II


title: Control brain, 9-month-old male biol rep #3

value: Bulk brain


title: day9_WT_rep3_5FU - ATAC

city: Saint Louis

first: Changxu

last: Fan

state: Missouri

address: 4515 McKinley Avenue, Room 5213

department: Genetics

institute: Washington University in St. Louis

data_processing:
Data were processed using the "count" function of cellranger-arc (v2.0)
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz: gene-by-cell expression matrices and peak-by-cell chromatin accessibility matrices
Supplementary files format and content: fragments.tsv.gz: ATAC fragments
Library strategy: single cell multiome (ATAC)

source_name: Bone Marrow

extract_protocol:
LK and LSK cells were FACS-sorted from the bone marrow and combined at a ratio of 1:1
Nuclei were isolated following the 10x protocol CG000365 • Rev B. Isolated nuclei were further processed using the 10x “Single Cell Multiome ATAC + Gene Expression” platform (CG000338 Rev B).

treatment_protocol: Mice were injected i.p. with one dose of 5-FU (Sigma, Cat#: F6627) in PBS (150 mg/kg or 250 mg/kg body weight). Cells were sorted from BM 9 or 11 days post 5-FU treatment

value: Bone Marrow

value: Hematopoietic stem and progenitor cells (HSPCs)

value: 5-FU (day9 post treatment)


title: POXKu70_2


title: day9_WT_rep3_5FU - GEX

data_processing:
Data were processed using the "count" function of cellranger-arc (v2.0)
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz: gene-by-cell expression matrices and peak-by-cell chromatin accessibility matrices
Supplementary files format and content: fragments.tsv.gz: ATAC fragments
Library strategy: single cell multiome (GEX)


title: Control brain, 9-month-old male biol rep #2


title: P18-N-II

value: CRC


title: P18-B-II


title: Control brain, 9-month-old male biol rep #1

value: Male


title: Control brain, 9-month-old female biol rep #1


title: P18-T-I

value: Pre


title: POXKu70_1

value: WT


title: POX08340_3

first: Di

last: Tian

address: DaXue east road

institute: College of Life Science and Technology,GuangXi university

value: POX08340 was deleted in deltaPoxKu70


title: POX08340_2


title: Control brain, 12-month-old female biol rep #2


title: day11_WT_5FU - GEX

value: 5-FU (day11 post treatment)


title: day9_WT_rep2_5FU - GEX


title: day11_WT_5FU - ATAC


title: POX08340_1


title: Control brain, 12-month-old female biol rep #1


title: P18-N-I


title: P18-B-I

value: Peripheral blood


title: POX01907_3

value: POX01907 was deleted in deltaPoxKu70


title: PJI WT mice 2

city: White/Caucasian

first: Tammy

last: Kielian

state: NE

address: 985900 Nebraska Medical Center

institute: UNMC

data_processing:
Raw FASTQ files were important into Partek Flow 11.0.23.1204 for data processing and analysis.
Reads were checked for quality and trimmed to meet a minimum quality score (20) before alignment to the Mus musculus genome (mm10) via STAR alligner.
Resulting gene counts were again subjected to quality check and features with low read counts (<10) were removed.
Resulting gene counts were normalized by counts per million plus 1E-4 before differential analysis.
Assembly: mm10
Supplementary files format and content: normalized counts in .txt file

source_name: Tissue

extract_protocol:
CD45+Ly6G+ Granulocytes were isolated from WT and TNF KO C57BL/6 mice 7 days following craniotomy or prosthetic joint infection. Granulocytes from 3 mice were pooled into each sample, lysed, and RNA isolated via Quick-RNA Microprep Kit with target of 500 ng total RNA.
RNA libraries were prepared using 50 ng of input RNA and the Nugen Universal mRNA Library Prep Kit according to manufacturer instructions. Sequencing was performed on a NextSeq500 (Illumina) with 150 mid-output cycles (75 paired-end reads) at a sequencing depth of ~10 million paired reads per sample.

value: Tissue

tag: strain

value: Granulocyte (CD45+Ly6G+)


title: day9_KO_rep3_5FU - GEX

value: Baf155 cKO (Vav-cre)


title: PJI WT mice 3


title: PJI WT mice 1


title: P17-T-II

value: Post


title: POX01907_2

value: Mycelium

value: Culture in enzyme production medium with Avicel after transfer 24h


title: PJI TNF KO mice 3

value: TNF KO


title: P17-N-II

value: Adjacent normal tissue


title: POX01907_1


title: P17-B-II


title: PJI TNF KO mice 2


title: PoxKu70_WT 3


title: day9_KO_rep2_5FU - GEX

value: Bone Marrow

value: Hematopoietic stem and progenitor cells (HSPCs)

value: 5-FU (day9 post treatment)


title: day9_KO_rep3_5FU - ATAC


title: day9_KO_rep2_5FU - ATAC


title: day9_WT_rep2_5FU - ATAC


title: P17-T-I

value: Tumor

value: Pre

value: CRC


title: PJI TNF KO mice 1


title: day11_KO_5FU - GEX

value: 5-FU (day11 post treatment)


title: P17-N-I


title: PoxKu70_WT 2

value: WT


title: day11_KO_5FU - ATAC


title: PoxKu70_WT 1


title: Craniotomy WT mice 3

source_name: Galea

value: Galea


title: Craniotomy WT mice 2


title: P17-B-I

value: Peripheral blood


title: P16-T-II


title: Craniotomy WT mice 1

value: Granulocyte (CD45+Ly6G+)


title: Craniotomy TNF KO mice 3


title: circRMST KD_3 (104494-001-006)

city: Utrecht

first: Ronald

middle: Jeroen

last: Pasterkamp

state: Utrecht

address: Universiteitsweg 100

department: Translational Neuroscience

country: Netherlands

institute: University Medical Center Utrecht

data_processing:
Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA3.4.4 and Bcl2fastq v2.20.
Per sample ~18 Gb, 60 million paired-end reads were obtained.  Differential expression was analysed by DESeq2.
Raw data is in fastq.gz format and contains one or more read files per sample. Raw files with prefixes HC7 and H7T are data acquired from different flowcells on the sequencer.
Adapter sequences were trimmed withfastp v0.20.1. and reads were mapped toMus_musculus.GRCm38usingSTAR-2.5.4b with default settings.
Feature counting wasdetermined with HYSeq v0.11.0. Fornormalisation (without differential expression)Cufflinks v2.2.1 was used.
DESeq2 was applied for differential expression, using genes with more than 10 aligned reads (sum of all samples) for the analysis.
Sequencing files are as read 1(R1 suffix), UMI read (R2 suffix) and read 2 (R3 suffix).
Assembly: GRCm38/mm10
Supplementary files format and content: COUNT files contain read counts of different samples, TSV files contain FPKM counts.
Supplementary files format and content: TXT files contain list of differentially expressed genes.

source_name: ventral midbrain

extract_protocol:
At 3 DIV, 2-3 wells per condition were harvested in Quiazol and stored at -80°C until processing. RNA was extracted using miRNeasy mini kit (Qiagen).
The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used to process the sample(s). The sample preparation was performed according to the protocol "NEBNext Ultra II Directional RNA Library Prep Kit for Illumina" (NEB #E7760S/L).
Briefly, rRNA was depleted from total RNA using the rRNA depletion kit (NEB#E6310). After fragmentation of the rRNA reduced RNA, a cDNA synthesis was performed. This was used for ligation with the sequencing adapters and PCR amplicification of the resulting product. The quality and yield after sample preparation was measured with the Fragment Analyzer. Clustering and DNA sequencing using the NovaSeq6000 was performed according to manufacturer's protocols. A concentration of 1.1 nM of DNA was used. Three independent cultures were used for sequencing. Library preparation and Illumina NovaSeq6000 sequencing (Paired-End, 150 bp.) was performed at Genome Scan (Leiden).

treatment_protocol: Primary vMB cultures were prepared from E14 WT embryos as described in the manuscript. 150 000 cells were plated per well. On the day of plating, cells were infected with lentivirus expressing pll3.7-Scr2 (control) or pll3.7-shRmstI (circRmst KD) (MOI5).

value: ventral midbrain

value: primary cells

value: Dopamine neurons

value: circRMST KD


title: Colon, BEC, Sv-4

city: Chicago

first: Daria

last: Esterhazy

state: IL

address: 924 E 57th Street

department: Pathology

institute: University of Chicago

data_processing:
Kallisto
Initial filtering removed genes with expression under 2 cpm
Assembly: GRCm39
Supplementary files format and content: csv file includes raw count for each sample
Supplementary files format and content: csv file includes counts per million for each sample

source_name: Colon

extract_protocol:
RNA was harvested from 250 sorted blood and lymphatic endothelial cells using RNA cleanup XP beads
RNA was eluted for 1 min in RT-cDNA synthesis mix 1 (0.5 µl P1-T31 (20µM), 0.3 ml RNasinplus (Promega), 1.5µl 10µM dNTP, 3.5 µl 10µM Tris pH 7.5-0.5% IGEPAL CA-630 (Sigma) and 1.7 µl RNase free ddH2O) and pipetted up and down to mix. The eluted sample was then incubated for 3 min at 72ºC, followed by 1 min on ice, then 7.5 µl of mix 2 was added (3µl 5X RT Buffer, 0.375 µl 100 mM DTT, 0.375 µl RNasin plus, 0.5 µl P1-RNA-TSO (40 µM), 0.75 µl Maxima RT Minus H (Thermo Scientific), 1.8 µl 5M Betaine (Sigma), 0.9 µl 50 mM MgCl2 and 0.175 µl RNase free ddH2O and mixed well. Samples were placed in a thermocycler and subjected to the following protocol: 42ºC for 90 s, (50ºC for 2 min, 42ºC for 2 min) x10 cycles, 70ºC for 15 min. The cDNA was then amplified using 13.5 µl cDNA, 20 µl KAPA HiFi 2x Mix, 1.5µl P1-PCR, and 5 µl H2O. Samples were subjected to the following protocol: 98ºC for 3 min, (98ºC for 15 s, 67ºC for 20 s, 72ºC for 6 min) x12 cycles, 72ºC for 5 min. cDNA was cleaned up using RNA Clean XP beads and eluted in water. 0.25ng cDNA was used as input and tagemented using Nextera XT index kit per manufacturers instructions with 0.5X the indicated volume.

treatment_protocol: 8 week old C57BL/6J mice were infected with S. venezeluensis sub cutaneously. 8 days after infection, the mice, along with non-infected controls, were harvested.

value: Colon

value: Blood Endothelial Cell

value: S. venezeluensis, day 8


title: Colon, BEC, Sv-3


title: P16-N-II

value: Adjacent normal tissue

value: Post


title: Colon, BEC, Sv-2


title: P16-LN-II

value: LN


title: Craniotomy TNF KO mice 2

value: TNF KO


title: circRMST KD_1 (104494-001-004)


title: Scramble Control_3 (104494-001-003)

value: Control KD


title: P16-B-II

value: CRC


title: Colon,BEC, NI-4

value: Non-infected


title: Scramble Control_2 (104494-001-002)

value: WT


title: D7_repeat4

city: Melbourne VIC 3004, AU

first: Cameron

middle: Gerard

last: Williams

state: VIC

address: 792 Elizabeth Street

department: Department of Microbiology and Immunology

country: Australia

institute: University of Melbourne

data_processing:
Data was aligned using the STAR pipeline.
Assembly: GRCm39
Assembly: PlasmoDB Plasmodium chabaudi chabaudi AS build 43
Supplementary files format and content: Tab-separated matrix files and barcode coordinates files
Library strategy: Spatial Transcriptomics

source_name: Spleen

extract_protocol:
Spleen samples were embedded in OCT compound and flash-frozen immediately after dissection. Fresh frozen tissue was cut into 5μm-thick sections and placed on a 3mm diameter circular array of 10μm diameter mRNA capture beads. Beads were coated in mRNA capture probes consisted of location-specific barcode, a probe-specific UMI, and an mRNA-capturing polyT sequence. Tissue was permeabilised, and mRNAs were captured and ligated to probes.
Sequencing libraries were prepared using the Slide-seqV2 protocol (Stickels et al. 2020 - PMID: 33288904).

value: Spleen

value: All splenic cells

value: P chabaudi infected

tag: age

value: 6-12 weeks


title: P16-T-I

tag: tissue

value: Tumor

value: Pre


title: Colon,BEC, NI-3

value: Colon


title: D7_repeat3


title: P16-N-I

tag: treatment stage


title: Scramble Control_1 (104494-001-001)

value: ventral midbrain

value: primary cells

value: Dopamine neurons


title: Colon,BEC, NI-2

value: Blood Endothelial Cell


title: D7_repeat2


title: Cartridge2

city: Miaoli

first: Pei-Ju

last: Tsai

state: Taiwan

address: 35, Keyan Road, Zhunan Town

department: Immunology research center

country: Taiwan

institute: NHRI

data_processing:
The FASTQ files were processed by using BD RhapsodyTM WTA pipeline v1.9 on Seven Bridge Genomics.
Quality filtered R1 reads were analysed to identify the cell label and unique molecular identifier (UMI) sequence.
Filtered R2 reads were used STAR to map the transcriptome.
Genome_build: GRCm38
Supplementary_files_format_and_content: Metrix file with cells and gene counts was exported as csv format.
Supplementary_files_format_and_content: Raw counts
Supplementary_files_format_and_content: Assigned Sample Taq for cells
Supplementary_files_format_and_content: AbSeq reference

source_name: B cells

growth_protocol: Non-B cells were depleted by biotin-conjugated antibody cocktail composed of anti-NK1.1, Thy1.2, Gr1, DX5, CD11b, CD11c, Ter119 and enriched by IMagTM Streptavidin Particles Plus beads (BD). Splenic B cells of purities between 94-98% were used in following experiment.

extract_protocol:
B cells were labeled  with BD™ Abseq antibody-oligo-conjugates B220, CD19, IgD, CD21, CD23, CD5, CD40, CD80, CD86, CD95, CD138, MHCII. The labeled cells were transferred into nano-well cartridges loaded with Cell Capture Beads. The BD Rhapsody™ WTA Reagent Kit 4 pack (Cat#633802) were use for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using BD Rhapsody™ protocols

treatment_protocol: B cells (2 x 106) were treated upon conditions of resting, 1μM CpG, and 1μM CpG plus 5 μM SB203580 for 2h

value: spleen

value: mixed sample (non-demultiplexed)


title: Cartridge1

description: Cartridge1_S1_L002_R2_001.fastq.gz was corrupted and could not be loaded at SRA. Cartridge1_S1_L002_R1_001.fastq.gz is available as a single-end fastq file in SRR15068941.


title: P16-B-I

value: Peripheral blood

tag: patientid


title: Ileum, BEC, Sv-4

source_name: Ileum

value: Ileum

value: S. venezeluensis, day 8


title: Colon,BEC, NI-1

value: Non-infected


title: D7_repeat1

value: Spleen


title: circRMST KD_2 (104494-001-005)

value: WT

value: circRMST KD


title: P15-T-II

value: Post

tag: cancer type

value: CRC


title: D0_repeat4

value: All splenic cells

value: saline control

value: 6-12 weeks


title: P15-N-II

value: Adjacent normal tissue


title: Colon, BEC, Sv-1

value: Colon


title: Ileum, BEC, Sv-3

value: Blood Endothelial Cell


title: Craniotomy TNF KO mice 1

value: Galea

value: Granulocyte (CD45+Ly6G+)

value: TNF KO


title: Lung TCRδ+ cells, GEX

city: Burlington

first: Jonathan

middle: E

last: Boyson

state: Vermont

address: 89 Beaumont Ave.

department: Surgery

institute: University of Vermont

description:
Prepared using 10X Genomics 5' Reagent Kits v1.1 and 26x91 paired-end sequencing
poly A RNA library

data_processing:
The gene expression and CSP libraries' raw sequence reads were processed using Cell Ranger software (v4.0.0) and mapped to the GRCm38 (mm10) mouse reference genome using the "cellranger count" argument. RNA and CSP reads were processed together in two steps, specifying only ADT or HTO oligonucleotide sequences each time. This resulted in two different kinds of outputs - "RNA_HTO" and “RNA_ADT”, where the RNA counts are thesame in both. Seurat was used for downstream quality control and analysis, and three assays were created while creating theSeurat object - RNA, ADT, and HTO. The Seurat function "HTODemux()" was used on the HTO assay to demultiplex single cells back to their sample of origin. For the analysis of V(D)J library sequences, Cell Ranger v6.1.2 was used to map the TCR V(D)J reads to a custom-made reference containing sequences from the IMGT database using the "cellranger vdj" argument. Finally, each barcoded cell's paired V(D)J information was exported as an Excel file ("custom_processed_VDJ_TRGV_TRDV_paired.xlsx") and integrated with RNA, ADT, and HTO data as metadata of theSeurat object.
Assembly: mm10
Supplementary files format and content: cellranger count outputs (RNA+HTO): RNA_HTO_barcodes.tsv.gz, RNA_HTO_features.tsv.gz, RNA_HTO_matrix.mtx.gz, RNA_HTO_filtered_feature_bc_matrix.h5
Supplementary files format and content: cellranger count outputs (RNA+ADT): RNA_ADT_barcodes.tsv.gz, RNA_ADT_features.tsv.gz, RNA_ADT_matrix.mtx.gz, RNA_ADT_filtered_feature_bc_matrix.h5
Supplementary files format and content: cellranger vdj output: VDJ_all_contig_annotations.csv
Supplementary files format and content: barcode matched paired VDJ output: custom_processed_VDJ_TRGV_TRDV_paired.xlsx

source_name: Adult (week 13-14) lung

extract_protocol:
Freshly collected thymus tissues are processed by passing them through nylon mesh to obtain single-cell suspensions. Lung tissue is finely minced and digested using a buffer containing collagenase and DNase, followed by trituration and filtration to obtain single-cell suspensions, with subsequent RBC lysis. Thymocytes are stained with anti-TCRδ-PE antibody and enriched using the anti-PE MicroBeads kit (Miltenyi Biotec), except the E17 thymi cells. Live/dead staining is performed, and cells are then stained with antibodies targeting surface markers and oligo-tagged antibodies (HTOs and ADTs). Finally, TCRδ+ cells were sorted from a CD11b-CD11c-CD19-TCRb- population of CD45.2+ live lymphocytes.
The 10X Genomics Chromium Next GEM Single Cell 5' V(D)J with feature barcoding kit (version 1.1) is utilized for preparing three libraries – CSP, RNA and VDJ, with modifications to the V(D)J enrichment procedure. Live γδ T cells from B6 and B6.SAP-/- mice are pooled and captured (between 5000 – 7000 cells) using a 10x Chromium controller. Following cDNA preparation, gene expression (RNA) and cell surface protein (CSP) libraries are created according to the manufacturer's instructions. Custom mouse γ and δ chain-specific primers are used to obtain TCR gamma and delta chain sequences. These primers are utilized in two rounds of PCR amplification, with specific cycling conditions for each chain. Following PCR product purification, the γ-chain and δ-chain amplicons undergo a second round of enrichment separately. Subsequently, the second round PCR products are quantified, combined in equal quantity, and the final TCR VDJ library is prepared. Finally, all three libraries (RNA, CSP, and VDJ are sequenced using paired-end sequencing on an Illumina HiSeq 1500 sequencer.
cCITEseq

value: Adult (week 13-14) lung

value: Lung TCR-delta+ cells

tag: library type

value: RNA


title: D0_repeat3

value: Spleen

tag: cell type


title: Lung TCRδ+ cells, HTO+ADT

description:
Prepared using 10X Genomics 5' Reagent Kits v1.1 with feature barcoding and 26x91 paired-end sequencing
Cell Surface Protein (Library) with both Hashtag-derived oligonucleotide (HTO) and Antibody-derived oligonucleotide (ADT) information

tag: genotype

value: CSP (HTO+ADT)

tag: adt

value: TotalSeq-C0212 anti-mouse CD24, TotalSeq-C0211 anti-mouse Vg4, TotalSeq-C0930 anti-mouse SLAMF6, TotalSeq-C0203 anti-mouse SLAMF1, TotalSeq-C0077 anti-mouse CD73

tag: hto

value: TotalSeq-C0303 anti-mouse hashtag 3 (Pooled B6, n=3), TotalSeq-C0304 anti-mouse hashtag 4 (Pooled SAPKO, n=3)


title: Ileum, BEC, Sv-2

value: Ileum

tag: treatment

value: S. venezeluensis, day 8


title: P15-T-I

value: Tumor

value: Pre

value: CRC


title: D0_repeat2

value: All splenic cells

value: saline control

value: 6-12 weeks


title: P15-B-II

value: Peripheral blood

value: Post


title: D0_repeat1


title: Ileum, BEC, Sv-1

value: Blood Endothelial Cell


title: WT3_KSL_ATAC

data_processing:
ATAC data were first processed using the AIAP (v1.1) pipeline. As a part of the pipeline: locations of Tn5 insertion events were inferred from properly paired, non-PCR duplicate reads with MAPQ >= 10; each Tn5 insertion event was extended from insertion site up and down 75 bp to generate a 150 bp “pseudo read”; pseudo reads were piled up to generate an ATAC signal profile.
ATAC signal profiles were normalized against both sequencing depth and the percentage of reads in promoter regions, similar to the normalization in ArchR (Granja et al, Nature Genetics. 2021).
Assembly: mm10
Supplementary files format and content: bw: normalized signal profiles

extract_protocol:
GMP (CD34+CD16/32+ LK) and LSK cells were FACS-sorted from the bone marrow
DNA was extracted according to a previously published protocol (Wu, J. et al. Requisite Chromatin Remodeling for Myeloid and Erythroid Lineage Differentiation from Erythromyeloid Progenitors. Cell Reports 33, 108395 (2020).)

value: Bone Marrow

value: Hematopoietic stem and progenitor cells (HSPCs, KSL)

value: WT

value: No treatment


title: P15-B-I

data_processing:
For 10X data, Cell Ranger 3.1.0 was used to quantify gene expression level and identify TCR sequences.
Assembly: GRCh38 for RNA expression
Supplementary files format and content: text files for expression matrices, cell metadata


title: D9 thymus TCRδ+ cells, HTO+ADT

source_name: Neonatal Day 9 (D9) Thymi

value: Neonatal Day 9 (D9) Thymi

value: D9 thymus TCR-delta+ cells

value: CSP (HTO+ADT)

value: TotalSeq-C0212 anti-mouse CD24, TotalSeq-C0211 anti-mouse Vg4, TotalSeq-C0930 anti-mouse SLAMF6, TotalSeq-C0203 anti-mouse SLAMF1, TotalSeq-C0077 anti-mouse CD73

value: TotalSeq-C0301 anti-mouse hashtag 1 (B6-1), TotalSeq-C0302 anti-mouse hashtag 2 (B6-2), TotalSeq-C0303 anti-mouse hashtag 3 (B6-3), TotalSeq-C0304 anti-mouse hashtag 4 (SAPKO-1), TotalSeq-C0305 anti-mouse hashtag 5 (SAPKO-2), TotalSeq-C0306 anti-mouse hashtag 6 (SAPKO-3), TotalSeq-C0308 anti-mouse hashtag 8 (ADT-control)


title: Ileum, BEC, NI-4

value: Ileum

value: Non-infected


title: D9 thymus TCRδ+ cells, GEX

value: RNA


title: Ileum, BEC, NI-3


title: WT3_GMP_ATAC

value: granulocyte-monocyte progenitor (GMP) cells


title: P14-T-III

value: Tumor

value: CRC


title: Ileum, BEC, NI-1


title: P14-N-III

source_name: Adjacent normal tissue

value: Adjacent normal tissue

value: Post


title: E17 thymus TCRδ+ cells, GEX

source_name: Embryonic Day 17 (E17) Thymi

value: Embryonic Day 17 (E17) Thymi

value: E17 thymus TCR-delta+ cells


title: Ileum, BEC, NI-2

value: Blood Endothelial Cell


title: WT2_GMP_ATAC

value: Bone Marrow

value: WT

value: No treatment


title: Jejunum, BEC, Sv-4

source_name: Jejunum

value: Jejunum

value: S. venezeluensis, day 8


title: P14-B-III

source_name: Peripheral blood

value: Peripheral blood


title: P14-T-II

source_name: Tumor

value: On


title: DGCR8 FLII double knockouts mESC, Rep2

description:
DF-dKO_Rep2
Knockout_cellline.txt

data_processing:
For PolyA(+) RNA-seq,Adapteor was removed by trimmomatic-0.39, HISAT2 software was used to align sequencing reads to reference mRNA.,mouse Cdna database(UCSC, NCBI37)  was used for alignment. Reads per Million was calculated for the normalization
Assembly: mm10,hg38
Supplementary files format and content: the txt file provide the CPM of each gene in every sample

growth_protocol: The mESCs stated as EpiLC 0h/2iLif were cultured in 2i/Lif medium, while  those stated as EB D0/SL were cultured in Serum/Lif medium.The human naïve hESCs (WIBR3) were cultured on MEF feeder layer in 5i/L/A medium.ADFNK differentiation medium and N2B27 basal medium were used for EB differentiation and EpiLC differentiation, respectively.

extract_protocol:
TRIzol reagent (Invitrogen) was used to isolate total RNA according to the manufacturer’s instructions.
The RNA was reverse transcribed with superscript IV, followed by 3’ DNA adaptor ligation using T4 RNA ligase (NEB). Libraries were amplified with Q5 2× Master Mix. Finally, the DNA above 175 bp in libraries was isolated by gel-purification.

tag: cell line

value: mESCs

value: DGCR8 FLII double knockouts


title: WT1_KSL_ATAC

value: Hematopoietic stem and progenitor cells (HSPCs, KSL)


title: W6 thymus TCRδ+ cells, HTO+ADT

source_name: Adult week 6 (W6) Thymi

value: Adult week 6 (W6) Thymi

value: W6 thymus TCR-delta+ cells

value: CSP (HTO+ADT)

value: TotalSeq-C0212 anti-mouse CD24, TotalSeq-C0211 anti-mouse Vg4, TotalSeq-C0930 anti-mouse SLAMF6, TotalSeq-C0203 anti-mouse SLAMF1, TotalSeq-C0077 anti-mouse CD73

value: TotalSeq-C0301 anti-mouse hashtag 1 (B6-1), TotalSeq-C0302 anti-mouse hashtag 2 (B6-2), TotalSeq-C0303 anti-mouse hashtag 3 (B6-3), TotalSeq-C0304 anti-mouse hashtag 4 (SAPKO-1), TotalSeq-C0305 anti-mouse hashtag 5 (SAPKO-2), TotalSeq-C0306 anti-mouse hashtag 6 (SAPKO-3), TotalSeq-C0308 anti-mouse hashtag 8 (ADT-control)


title: Jejunum, BEC, Sv-3


title: DGCR8 FLII double knockouts mESC, Rep1

description:
DF-dKO_Rep1
Knockout_cellline.txt


title: P14-N-II

extract_protocol:
For tissue samples, collected tumor or adjacent normal biopsies was stored in the tissue storage solution immediately after resection and transferred on ice. Samples were washed twice and cut into approximately 1-2 mm3 pieces before being collected in the RPMI-1640 medium (Gibco) with 10% fetal bovine serum (FBS, Gibco), and projected to enzymatical digestion with gentleMACS Tumor Dissociation Kit (Miltenyi Biotec) for 60 min on a rotor at 37°C according to the manufacturer’s protocol. The dissociated cells then passed through a 100-mm SmartStrainer in the RPMI-1640 medium (Invitrogen) with 10% FBS and centrifuged at 400 g for 5 min. After the removal of the supernatant, the pelleted cells were suspended in 1 mL of red blood cell lysis buffer (TIANDZ) and incubated on ice for 1 min for red blood cell lysis and quickly terminate the reaction with RPMI-1640 medium (Invitrogen, with 10% FBS). After being centrifuged at 400 g for another 5 min, the cell pellets would be re-suspended in sorting buffer (PBS supplemented with 1% FBS).  Blood samples were collected in EDTA anticoagulant tubes and kept on ice for transferring. After restoring to room temperature and mixing thoroughly, peripheral blood mononuclear cells (PBMCs) were isolated using HISTOPAQUE-1077 (Sigma-Aldrich) solution. Briefly, peripheral blood was carefully layered onto equal volume HISTOPAQUE-1077 without breaking the plasma-HISTOPAQUE-1077 interface. After centrifugation at 400 g for 30 min, the lymphocyte layer was carefully transferred to a new tube and washed twice with 1x phosphate-buffered saline (PBS, Invitrogen). After red blood cells lysis following the aforementioned procedure, the collected lymphocytes were then re-suspended in sorting buffer (PBS supplemented with 1% FBS).
To obtain high-quality cell pools before subsequent library construction, single cell suspensions collected from blood or tissue samples were stained with antibodies against 7AAD (Thermo Fisher), CD235a (BioLegend) for FACS sorting (BD Aria III instrument). By gating 7AAD- CD235a- cells, living cells were enriched, and residuary red blood cells were excluded.  Gated cells were sorted into 1.5 mL LoBind tubes (Eppendorf) and counted manually under the microscope. The concentration of single cell suspensions was adjusted to 500-1200 cells/l. 10,000~18,000 cells were loaded for the 10x Chromium Single cell 5’ and VDJ library construction (10x Genomics), with subsequent steps performed following the standard manufacturer’s protocols. Purified libraries were analyzed by an Illumina NovaSeq with 150-bp paired-end reads.
10x Chromium Single cell 5’ + VDJ Library

value: Adjacent normal tissue

value: CRC


title: WT1_GMP_ATAC

value: Bone Marrow

value: granulocyte-monocyte progenitor (GMP) cells


title: W6 thymus TCRδ+ cells, GEX

value: RNA


title: DGCR8-/- mESC, Rep3

description:
Dgcr8-/- Rep3
Knockout_cellline.txt

value: DGCR8 knockout


title: P15-N-I

value: Pre


title: Jejunum, BEC, Sv-2

value: Jejunum

value: Blood Endothelial Cell

value: S. venezeluensis, day 8


title: KO3_KSL_ATAC

value: Baf155 cKO (Vav-cre)

value: No treatment


title: P14-B-II

value: Peripheral blood

value: On


title: E17 thymus TCRδ+ cells, HTO+ADT

value: Embryonic Day 17 (E17) Thymi

value: E17 thymus TCR-delta+ cells

value: CSP (HTO+ADT)

value: TotalSeq-C0212 anti-mouse CD24, TotalSeq-C0073 anti-mouse CD44, TotalSeq-C1063, anti-mouse CD45RB, TotalSeq-C0209 anti-mouse Vg1, TotalSeq-C0211 anti-mouse Vg4, TotalSeq-C0930 anti-mouse SLAMF6, TotalSeq-C0203 anti-mouse SLAMF1, TotalSeq-C0077 anti-mouse CD73

value: TotalSeq-C0301 anti-mouse hashtag 1 (B6-1), TotalSeq-C0302 anti-mouse hashtag 2 (B6-2), TotalSeq-C0303 anti-mouse hashtag 3 (B6-3), TotalSeq-C0304 anti-mouse hashtag 4 (B6-4), TotalSeq-C0305 anti-mouse hashtag 5 (SAPKO-1), TotalSeq-C0306 anti-mouse hashtag 6 (SAPKO-2), TotalSeq-C0307 anti-mouse hashtag 7 (SAPKO-3), TotalSeq-C0308 anti-mouse hashtag 8 (SAPKO-4)


title: Flii-/- mESC, Rep3

description:
Flii-/- Rep3
Knockout_cellline.txt

value: mESCs

value: FLII knockout


title: WT2_KSL_ATAC

value: Bone Marrow

value: Hematopoietic stem and progenitor cells (HSPCs, KSL)

value: WT


title: P14-T-I

value: Tumor

value: Pre

value: CRC


title: Jejunum, BEC, Sv-1

value: Jejunum

value: Blood Endothelial Cell

value: S. venezeluensis, day 8


title: KO3_GMP_ATAC

value: granulocyte-monocyte progenitor (GMP) cells

value: Baf155 cKO (Vav-cre)

value: No treatment


title: KO2_KSL_ATAC


title: P14-N-I

value: Adjacent normal tissue


title: Flii-/- mESC, Rep1

description:
Flii-/- Rep1
EB_D0_Flii-/- Rep1 (alternative name)
Knockout_cellline.txt
EB_FLIIKO.txt


title: KO2_GMP_ATAC


title: Jejunum, BEC, NI-3

value: Non-infected


title: P14-B-I

value: Peripheral blood


title: WT mESC, Rep3

description:
WT_Rep3
Knockout_cellline.txt

value: mESCs


title: Jejunum, BEC, NI-2


title: KO1_KSL_ATAC


title: P12-T-II

value: Post


title: P12-B-II


title: KO1_GMP_ATAC

value: Bone Marrow


title: Duodenum, BEC, Sv-4

source_name: Duodenum

value: Duodenum


title: P12-T-I


title: Atg7 Cre+ (biol rep 3)

city: St. Louis

first: Jennifer

last: Philips

state: MO

address: 660 South Euclid Avenue

data_processing:
Raw fastq files were processed using TPP software (), which extracts counts of transposon interstions at individual TA sites in the H37Rv genome from TnSeq experiments (https://transit.readthedocs.io/en/latest/tpp.html)
Resulting wig output files are suitable for further analysis using TRANSIT software ((https://transit.readthedocs.io/en/latest/index.html)
Assembly: H37Rv ASM19595v2.38
Supplementary files format and content: wig file outputs from TPP software that mapped TA sites to the H37Rv genome and reduced to unique template counts for subsequent use in TRANSIT software
Library strategy: TnSeq

organism: Mycobacterium tuberculosis

source_name: Mycobacterium tuberculosis H37Rv

growth_protocol: H37Rv Himar transposon mutant library was grown in 7H9 medium containing 0.05% Tween 80 (Sigma), OADC, and kanamycin (25 µg/ml) prior to BMDM infection

extract_protocol:
After three weeks of growth, colonies were harvested by scraping, and genomic DNA was extracted as described in Long JE, DeJesus M, Ward D, Baker RE, Ioerger T, Sassetti CM (2015). Identifying essential genes in Mycobacterium tuberculosis by global phenotypic profiling, Methods Mol Biol: 1279:79-95.
Libraries were prepared for Illumina sequencing using custom primers as described in Long JE, DeJesus M, Ward D, Baker RE, Ioerger T, Sassetti CM (2015). Identifying essential genes in Mycobacterium tuberculosis by global phenotypic profiling. Methods Mol Biol 1279:79-95.

treatment_protocol:
Single cell suspension were made of the bacterial mutants, which were then used to infect murine BMDMs of four different genotypes (Atg5 cKO, Atg7 cKO, and their littermate Cre- controls). BMDMs were treated with 200 units/mL of IFN-γ (R&D Systems) 24 h before infection. There were three biological replicates per condition.
After 5 days of infection, macrophages were lysed with 0.01 triton X-100 in PBS, lysates were plated on 7H11 agar plates, and all CFU were collected 15–21 d later for isolation of genomic DNA from surviving bacilli.

value: Mycobacterium tuberculosis H37Rv

value: H37Rv Himar Transposon library

value: passed through murine IFN-g treated Atg7fl/fl LysM-Cre+ BMDMs


title: P0 Pitx3-GFP+ 3

city: Aarhus N

first: Morten

middle: T

last: Veno

state: DK

address: Aabogade 15

country: Denmark

institute: Omiics ApS

description: Long-read circRNA-seq

data_processing:
Basecalling and demultiplexing was done using Guppy (version 5.0.11+2b6dbff)
Fastq files were analyzed using https://github.com/omiics-dk/long_read_circRNA. This tool was specifically designed to analyze circRNA ONT data generated using the method used in this study. This tool does quality filtering, genome mapping, circRNA detetction, quantification and annotation.
Assembly: mm10
Supplementary files format and content: Tab delimited txt file. Contains the genomic coordininates of detected circRNAs. Also has tabs showing host gene, matching annotation from circBase, circAtlas and CIRCpedia. Columns with the total number of reads spanning back splice junctions (bsj) and the bsj spanning read numbers for the individual samples.

source_name: primary

extract_protocol:
RNA was harvested using Rneasy micro kit (Qiagen). 10 to 50 ng of total RNA was used for the construction of sequencing libraries.
Nanopore libraries were constructed using the circPanel-LRS method described in a previous paper (PMID: 34571139). Briefly, CircPanel-LRS uses circRNA-specific primers (CSP) for cDNA synthesis and an adjacent outward pointing primer for second strand cDNA synthesis. CSP primers are modified at the 5′ end to be compatible with ONT-cPRM-adaptor primers for library amplification and nanopore long-read sequencing.

value: primary

value: dopamine neurons

value: purification by FACS


title: Atg7 Cre+ (biol rep 1)


title: P0 Pitx3-GFP+ 2

description: Long-read circRNA-seq


title: Duodenum, BEC, Sv-3

value: Blood Endothelial Cell

value: S. venezeluensis, day 8


title: Jejunum, BEC, NI-4

value: Jejunum


title: P12-B-I

first: Zemin

address: Yiheyuan Road

value: Pre

value: CRC


title: Flii-/- mESC, Rep2

description:
Flii-/- Rep2
Knockout_cellline.txt

value: FLII knockout


title: Duodenum, BEC, Sv-2


title: Atg7 Cre- (biol rep 3)

value: passed through murine IFN-g treated Atg7fl/fl Cre- BMDMs


title: P0 Pitx3-GFP+ 1

description: Long-read circRNA-seq


title: Atg7 Cre- (biol rep 2)


title: E14 Pitx3-GFP+ 3

description: Long-read circRNA-seq


title: P11-T-II

value: Tumor


title: P11-N-II

value: Adjacent normal tissue

value: Post


title: Duodenum, BEC, NI-4

value: Duodenum

value: Non-infected


title: Atg7 Cre- (biol rep 1)

value: Mycobacterium tuberculosis H37Rv

value: H37Rv Himar Transposon library


title: Jejunum, BEC, NI-1


title: E14 Pitx3-GFP+ 2

description: Long-read circRNA-seq

value: primary


title: Atg7 Cre+ (biol rep 2)

value: passed through murine IFN-g treated Atg7fl/fl LysM-Cre+ BMDMs


title: Atg5 Cre+ (biol rep 3)

value: passed through murine IFN-g treated Atg5fl/fl LysM-Cre+ BMDMs


title: P11-T-I


title: Duodenum, BEC, NI-2

value: Blood Endothelial Cell


title: Duodenum, BEC, NI-3


title: E14 Pitx3-GFP+ 1

description: Long-read circRNA-seq

value: dopamine neurons

value: purification by FACS


title: Atg5 Cre+ (biol rep 2)


title: Duodenum, BEC, NI-1


title: P11-N-I

value: Pre


title: 100 varieties, mix

city: shanghai

first: yijing

last: zhang

address: 2005 Songhu Road

department: Biochemistry

institute: Fudan University

data_processing:
Trimmomatic version 0.39 and Sickle version 1.33 were used to trim adaptors and eliminate bases with low quality scores (<20) and/or short read lengths (<20 bp).
The Burrows–Wheeler Aligner version 1.2.3 was used to align the remaining clean reads to the International Wheat Genome Sequencing Consortium reference genome (v1.0).
Use bcftools mpileup version 1.8 to generate the initial vcf file, then use bcftools call to perform variant detection on vcf, and output variant site information.
Bcftools filter retains site information with QUAL greater than 20 and DP value greater than 10.
VCFtools version 0.1.16 was used to calculate the pi value.
Assembly: International Wheat Genome Sequencing Consortium (IWGSC) reference sequence (version 1.0)
Supplementary files format and content: txt, pi-value of whole genome computed from DHS data.

organism: Triticum aestivum

source_name: leaf

extract_protocol:
1cm-long-leaves of the plants were harvested, mixed together and fixed with 1% formaldehyde in HEPES buffer (50 mM HEPES, 1 mM EDTA, pH 8.0, 0.1 M NaCl, and 1 mM PMSF). The fixed leaves were ground to a fine powder in liquid nitrogen. Wheat nuclei were extracted with H1B buffer (20 mM Tris-HCl, pH 8.0, 50 mM EDTA, 5 mM spermidine, 0.15 mM spermine, 40% glycerol, and 0.1% mercaptoethanol). The extracted nuclei were purified with H1B buffer supplemented with 0.5% Triton X-100. The purified nuclei were washed once with RSB buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, and 3 mM MgCl2). The pelleted nuclei were resuspended with 2 ml RSB buffer and then divided equally into five 1.5-ml Eppendorf tubes. The aliquoted nuclei were digested with DNase I (0, 0.01, 0.03, 0.05, and 0.08 units). The resulting digested nuclei were extracted using 1 volume of phenol, phenol:chloroform, and chloroform, after which the DNA from each digestion was resuspended in 2 volumes of cold ethanol and then pelleted.
A DNase-sequencing library was prepared from 0.03 U DNase I-digested nuclei. Approximately 2 µg DNA was separated by 1.5% agarose gel electrophoresis, and DNA fragments (50-300 bp) were cut and purified to prepare the DNase-sequencing library with the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB).

value: leaf

tag: develomental stage


title: P11-B-I

last: Zhang

value: Peripheral blood

value: CRC


title: P12-N-I


title: P09-T-II

value: Tumor


title: Atg5 Cre+ (biol rep 1)


title: Atg5 Cre- (biol rep 3)

value: passed through murine IFN-g treated Atg5fl/fl Cre- BMDMs


title: Colon, LEC, Sv-3

value: Colon

value: Lymphatic Endothelial Cell

value: S. venezeluensis, day 8


title: Colon, LEC, Sv-4


title: Atg5 Cre- (biol rep 2)

value: Mycobacterium tuberculosis H37Rv


title: Duodenum, BEC, Sv-1

value: Duodenum


title: P09-N-II

value: Adjacent normal tissue

value: Post


title: Atg5 Cre- (biol rep 1)

value: H37Rv Himar Transposon library


title: P09-B-II


title: Colon, LEC, Sv-1


title: P09-T-I


title: Lung TCRδ+ cells, VDJ

description:
Prepared using 10X Genomics 5' Reagent Kits v1.1 with custom γδ VDJ enrichment and 150x150 paired-end sequencing
VDJ library from custom primer enriched γδ TCR transcripts

value: Adult (week 13-14) lung

value: Lung TCR-delta+ cells

value: VDJ


title: P09-N-I

value: Pre


title: Colon, LEC, NI-4

value: Non-infected


title: W6 thymus TCRδ+ cells, VDJ

description:
Prepared using 10X Genomics 5' Reagent Kits v1.1 with custom γδ VDJ enrichment and 26x91 paired-end sequencing
VDJ library from custom primer enriched γδ TCR transcripts

value: Adult week 6 (W6) Thymi

value: W6 thymus TCR-delta+ cells


title: Colon, LEC, NI-3


title: P09-B-I

value: Peripheral blood

value: CRC


title: D9 thymus TCRδ+ cells, VDJ

value: Neonatal Day 9 (D9) Thymi

value: D9 thymus TCR-delta+ cells


title: E17 thymus TCRδ+ cells, VDJ

value: Embryonic Day 17 (E17) Thymi

value: E17 thymus TCR-delta+ cells


title: Colon, LEC, NI-2

value: Colon

value: Lymphatic Endothelial Cell


title: P08-T-IV

value: Tumor

value: Post


title: P08-N-IV

value: Adjacent normal tissue


title: Colon, LEC, Sv-2

value: S. venezeluensis, day 8


title: Colon, LEC, NI-1


title: Ileum, LEC, Sv-4

value: Ileum


title: Bottom_2

first: Chao

last: Chen

address: Datun

department: CAS Key Laboratory of Infection and Immunity

institute: Institute of Biophysics, Chinese Academy of Sciences

data_processing:
1) Merge the double-ended data with FLASH (v1.2.11) to obtain the double-ended reads, and add the unmerged R1 reads to the double-ended reads file to obtain the total clean data;
2) Cut the frame sequence at the left and right ends of the sgRNA using cutadapt (v4.1) to obtain a clean sgRNA fastq sequence with a length of 20 nt and perform quality control using FastQC (v0.11.9);
3) Align the obtained clean sgRNA fastq sequence to the human membrane transporter CRISPRi library sequence with bowtie (v1.3.1), and then convert the sam file into a bam file with samtools to sort and create an index. Bowtie comparison parameters -v 0 -k 1 --best -S;
4) calculate the number of expression counts of sequences in each sgRNA library using the multicov command of bedtools (v2.30.0). Parameters: -f 1.00 -r;
5) Analysis of differentially significant genes between two groups with MAGeCK (v0.5.9.5).
Supplementary files format and content: Excel, top_Bottom_final

growth_protocol: 293T cells were obtained from ATCC and cultured in DMEM medium supplemented with 10% fetal bovine serum (FBS, Gibco) and 100 µg ml−1 penicillin-streptomycin.

extract_protocol: Cells were washed in PBS and stored at -80°C for isolation of genomic DNA (gDNA), which was performed with the Blood & Cell Culture DNA Maxi Kit (Qiagen). PCR were performed for identification of sgRNA inserts.

value: human embryonic kidney cell line

value: the lowest 25% of cBioITA’s intensity


title: Ileum, LEC, Sv-3


title: P08-B-IV

institute: Peking University


title: Top_2

value: the highest 25% of cBioITA’s intensity


title: P08-N-III

value: On


title: P08-T-III


title: Top_1


title: Ileum, LEC, Sv-2


title: Ileum, LEC, Sv-1


title: Dicer-/- mESC, Rep3

first: Xuehui

address: No.5 Yiheyuan Road, Haidian district, Beijing, 100871, China

value: mESCs

value: Dicer knockout mESC


title: Ileum, LEC, NI-4

value: Non-infected


title: Bottom_1


title: P08-T-II

value: CRC


title: Dicer-/- mESC, Rep2

description:
Dicer-/-_Rep2
Knockout_cellline.txt


title: Ileum, LEC, NI-3


title: Dicer-/- mESC, Rep1

description:
Dicer-/-_Rep1
Knockout_cellline.txt


title: P08-B-II

value: Peripheral blood


title: DGCR8-/- mESC, Rep2

description:
Dgcr8-/- Rep2
Knockout_cellline.txt

value: DGCR8 knockout


title: Ileum, LEC, NI-1


title: P08-B-III


title: Ileum, LEC, NI-2


title: DGCR8-/- mESC, Rep1

description:
Dgcr8-/- Rep1
Knockout_cellline.txt


title: P08-T-I

value: Pre


title: P08-TN-I

source_name: TN

value: TN


title: Jejunum, LEC, Sv-4

value: Jejunum

value: Lymphatic Endothelial Cell


title: WT mESC, Rep2

description:
WT_Rep2
Knockout_cellline.txt

value: WT


title: P08-N-II

value: Adjacent normal tissue


title: Jejunum, LEC, Sv-3

value: S. venezeluensis, day 8


title: Blood at day1, after noise rep2

type: RNA

city: Seoul

first: Sohyeon

last: Park

state: Seoul

address: 71, Daehak-ro

department: Interdisciplinary Program in Neuroscience

country: South Korea

institute: Seoul National University College of Natural Sciences

description: microRNA list from CN after noise at day1

hyb_protocol: The labeled RNA was fractionated and hybridized for 16 hr at 48C on Affymetrix 450 Fluidics Station (Affymetrix, Santa Clara, California, United States).

scan_protocol: GeneChops were scanned with an Affymetrix GCS 3000 scanner (Affymetrix, Santa Clara, California, United States).

data_processing:
The data were analyzed with 'rma' function in R library 'oligo' (version 1.58.0)
normalized Affy microarray intensity

label: biotin

organism: Rattus norvegicus

source_name: Peripheral Blood, after noise, day1

label_protocol: RNA samples were labeled with the FlashTag Biotin RNA Labeling Kit (Genisphere, Hatfield, PA, USA).

growth_protocol: SD rats were maintained under a 12-hour light-dark cycle, with free access to food and water.

extract_protocol: Whole brain tissue was separated from the craninal bone and each CN, SOC, IC, AC and peripheral blood were harvested and total RNA was extracted in Trizol solution.

treatment_protocol: SD rats were exposed to white noise(2-20kHz) at 115 dB SPL for 2 hours in a sound-attenuating booth under anesthesia.

value: Sprague-Dawley

value: Peripheral Blood

value: 5 weeks

tag: gender

value: male

value: after noise, day1


title: Blood at day3, control rep1

description: microRNA list from CN control at day3

source_name: Peripheral Blood, control, day3

value: control, day3


title: P08-N-I

city: Beijing


title: WT mESC, Rep1

last: Lv

description:
WT_Rep1
Knockout_cellline.txt

value: mESCs


title: Jejunum, LEC, Sv-2


title: CP2_IgG_rep2

city: Taipei

first: Yi-Shuian

last: Huang

address: 128 Sec. 2, Academia Rd. Nankang

institute: Institute of Biomedical Sciences, Academia Sinica

description:
total RNA
RNAs precipitated by CPEB3 IgG
SurePrint G3 Mouse GE 8x60K Microarray

hyb_protocol: 0.6 μg Cy3-labled cRNA was fragmented to ~50-100 nt by incubation with fragmentation buffer at 60°C for 30 minutes, which were used for array (Agilent SurePrint G3 Mouse GE 8x60K Microarray) hybridization at 65°C for 17 h.

scan_protocol: Microarrays are scanned with an Agilent microarray scanner at 535 nm for Cy3.

data_processing: The images were analyzed and quantified by using Feature extraction 10.5.1.1 software (Agilent).

source_name: CP2 IgG RIP, replicate 2

label_protocol: RNA (0.2 μg per sample) was amplified by a Low Input Quick-Amp Labeling kit (Agilent) and labeled with Cy3 (CyDye, Agilent).

growth_protocol: 8-week-old male C57BL/6 mice from LASCO, Taiwan

extract_protocol: RNA was extracted using phenol:chloroform:isoamyl alcohol pH4.5.

treatment_protocol: corticohippocampal lysate incubated with either control or CPEB2 IgG-bound beads for 3 hours

value: corticohippocampal tissue

value: 8 weeks


title: P08-B-I

value: Peripheral blood

value: CRC


title: Jejunum, LEC, Sv-1


title: P05-T-II

value: Tumor

value: Post


title: Blood at day1, control rep3

description: microRNA list from CN control at day1

source_name: Peripheral Blood, control, day1

value: control, day1


title: Blood at day1, control rep4

description: microRNA list from CN control at day1


title: Mammary epithelial tumor-derived cells from wild-type NIC mice with conditional Cpt1a alleles_2B [WT_8905B_biol rep 2]

city: Montreal

first: Sherif

middle: Samer

last: Attalla

state: Quebec

address: 1160 Ave. Pine W

department: Goodman Cancer Institute

country: Canada

institute: McGill

description: Processed data file column S

data_processing:
Adaptor sequences and low quality score bases (Phred score < 30) were trimmed using Trimmomatic (Bolger et al., 2014)
Reads were aligned to the GRCm38 mouse reference genome assembly using STAR (Dobin et al., 2012)
Read counts were obtained using HTSeq (Anders et al., 2015) with parameters -m intersection-nonempty -stranded=no
Raw counts were normalized using edgeR’s TMM algorithm (Robinson et al., 2010) and were then transformed to log2-counts per million (logCPM) using the voom function implemented in the limma R package (Ritchie et al., 2015)
To assess differences in gene expression levels between the different conditions, we fitted a linear model using limma’slmfit function(method="robust" parameter was applied for end-stage tumor dataset)
Nominal p-values were corrected for multiple testing using the Benjamini-Hochberg method
Assembly: Distinct patterns of gene expression changes were identified using unsupervised hierarchical clustering method (R function hclust with Euclidean distance and complete linkage metrics)
Supplementary files format and content: GrCM38/mm10
Supplementary files format and content: A tab-delimited text files includes RPKM values for all samples.

source_name: Mammary epithelium

growth_protocol: Mammary tumors at 8 weeks post-palpation were excised from female MMTV-NIC and MMTV-NIC/Cpt1a flx flx mice, dissociated and plated in Complete Media, consisting of DMEM (Wisent, 319-005-CL) supplemented with 2% FBS (Wisent, 080-150), 5ng/ml EGF (Winsent, 511-110-UM) 1 μg/ml Hydrocortisone (Sigma, H4001), 5 μg/ml Insulin (Wisent, 511-016-UG), 35 μg/ml Bovine Pituitary Extract (BPE – Hammond CellTech, 1078-NZ) and 50 ug/ml Penicillin/Streptomycin (Wisent, 450-200-EL). Cells were maintained in a humidified, 5% CO2, 37 degrees C incubator in Complete Media. Cells were authenticated by PCR-based genotyping (oligonucleotide details in Supplementary Table S1) and by immunoblotting to detect Cpt1a expression. All cell lines were tested biweekly for mycoplasma using the MycoAlert Kit (Lonza, LT07-118). All cells used in this study were negative for mycoplasma contamination.

extract_protocol:
Qiagen RNEasy Mini kit was used according to the manufacturer's instructions
RNA libraries for RNA-seq were prepared using the NEBNext Ultra II Library Prep Kit following manufacturer's protocols.

treatment_protocol: No treatments were applied to the biological material prior to extraction.

value: Mammary epithelium

value: Primary mammary epithelial cells

value: NIC/wild-type


title: Blood at day3, control rep2

description: microRNA list from CN control at day3

value: Sprague-Dawley


title: Blood at day3, control rep4

description: microRNA list from CN control at day3

value: Peripheral Blood


title: Blood at day1, control rep1

description: microRNA list from CN control at day1

value: 5 weeks


title: Blood at day3, control rep3

description: microRNA list from CN control at day3

value: male


title: Jejunum, LEC, NI-4

value: Jejunum

value: Lymphatic Endothelial Cell

value: Non-infected


title: Mammary epithelial tumor-derived cells from wild-type NIC mice with conditional Cpt1a alleles_2A [WT_8905A_biol rep 1]

description: Processed data file column R


title: Blood at day1, after noise rep4

value: after noise, day1


title: Blood at day3, after noise rep4

description: microRNA list from CN after noise at day3

source_name: Peripheral Blood, after noise, day3

value: after noise, day3


title: Blood at day1, control rep2

description: microRNA list from CN control at day1


title: Blood at day3, after noise rep3


title: Blood at day1, after noise rep3


title: Blood at day1, after noise rep1


title: Jejunum, LEC, NI-3


title: control_IgG_rep2

description:
total RNA
RNAs precipitated by control IgG
SurePrint G3 Mouse GE 8x60K Microarray

source_name: control IgG RIP, replicate 2

value: corticohippocampal tissue

value: 8 weeks


title: P05-B-II

value: Peripheral blood

value: CRC


title: P05-N-II

source_name: Adjacent normal tissue

value: Adjacent normal tissue

value: Post


title: Mammary epithelial tumor-derived cells from wild-type NIC mice with conditional Cpt1a alleles_1B [WT_5257B_biol rep 2]

description: Processed data file column Q

value: Mammary epithelium

value: Primary mammary epithelial cells


title: Mammary epithelial tumor-derived cells from wild-type NIC mice with conditional Cpt1a alleles_1A [WT_5257A_biol rep 1]

description: Processed data file column P

value: NIC/wild-type


title: Blood at day3, after noise rep1

value: Sprague-Dawley

value: Peripheral Blood


title: Blood at day3, after noise rep2

value: 5 weeks

value: male


title: Mammary epithelial tumor-derived cells from NIC mice without conditional Cpt1a alleles_4B [KO_4258B_biol rep 2]

description: Processed data file column O

value: NIC/conditional Cpt1a KO


title: AC at day1, control rep3

description: microRNA list from AC control at day1

source_name: Auditory Cortex, control, day1

value: Auditory Cortex

value: control, day1


title: AC at day1, control rep2

description: microRNA list from AC control at day1


title: CP2_IgG_rep1

source_name: CP2 IgG RIP, replicate 1


title: control_IgG_rep1

source_name: control IgG RIP, replicate 1


title: P05-T-I

source_name: Tumor

value: Tumor

value: Pre


title: Jejunum, LEC, NI-1

source_name: Jejunum

value: Jejunum

value: Lymphatic Endothelial Cell

value: Non-infected


title: Mammary epithelial tumor-derived cells from NIC mice without conditional Cpt1a alleles_4A [KO_4258A_biol rep 1]

description: Processed data file column N


title: Duodenum, LEC, Sv-4

source_name: Duodenum

value: Duodenum

value: S. venezeluensis, day 8


title: Mammary epithelial tumor-derived cells from NIC mice without conditional Cpt1a alleles_3B [KO_2768B_biol rep 2]

description: Processed data file column M

value: Mammary epithelium


title: P04-N-III

value: Adjacent normal tissue

value: Post

value: CRC


title: Duodenum, LEC, Sv-3


title: Mammary epithelial tumor-derived cells from NIC mice without conditional Cpt1a alleles_2B [KO_1925B_biol rep 2]

description: Processed data file column K

value: Primary mammary epithelial cells


title: P04-T-III


title: P04-B-III

source_name: Peripheral blood

value: Peripheral blood


title: Jejunum, LEC, NI-2


title: Mammary epithelial tumor-derived cells from NIC mice without conditional Cpt1a alleles_2A [KO_1925A_biol rep 1]

description: Processed data file column J


title: AC at day1, control rep1

description: microRNA list from AC control at day1

value: Sprague-Dawley

value: 5 weeks

value: male


title: P04-T-II

value: On


title: Duodenum, LEC, Sv-1


title: Mammary epithelial tumor-derived cells from NIC mice without conditional Cpt1a alleles_1B [KO_1922B_biol rep 2]

description: Processed data file column I

value: NIC/conditional Cpt1a KO


title: P04-N-II


title: Mammary epithelial tumor-derived cells from NIC mice without conditional Cpt1a alleles_1A [KO_1922A_biol rep 1]

description: Processed data file column H


title: P05-B-I

value: Pre


title: Duodenum, LEC, NI-3


title: P04-B-II


title: Duodenum, LEC, Sv-2


title: AC at day3, control rep2

description: microRNA list from AC control at day3

source_name: Auditory Cortex, control, day3

value: Auditory Cortex

value: control, day3


title: AVIL+ tuft cells from human ileum 2

first: Amir

last: Giladi

address: Uppsalalaan 8

institute: Hubrecht Institute

description:
HUB-LH-s003
metadata.txt

library_source: transcriptomic single cell

data_processing:
STAR (version 2.7.8a)
Reads were demultiplexed and collapsed into UMI tables using umi_tools (version 1.1.1) allowing up to one hamming distance of the cell barcode. Cells with less than 500 UMI, or with more than 40% mitochondrial genes were excluded from analysis.
Single cell RNA-seq libraries of organoid derived material, and KIT+ enriched cells from fetal and adult intestines were sequenced on an Illumina NextSeq platform, at a median sequencing depth of 49,861 reads per cell. Reads were mapped to a human genome (hg38) integrated with the Clover transcript using STAR (version 2.7.8a), reads with multiple mapping positions were excluded. Reads were associated with genes if they were mapped to an exon. Reads were demultiplexed and collapsed into UMI tables using umi_tools (version 1.1.1) allowing up to one hamming distance of the cell barcode. Cells with less than 500 UMI, or with more than 40% mitochondrial genes were excluded from analysis.
Assembly: hg38
Supplementary files format and content: Genes x cells tab delimited table
Supplementary files format and content: A metadata file containing relevant information (experiment condition, etc.) for each sequenced cell

source_name: Ileum

growth_protocol: Human intestinal organoids were split once a week by mechanic dissociation. In this study, basic culture medium includes advanced Dulbecco’s modified Eagle’s medium/F12 (Gibco) supplemented with 100 U/ml penicillin/streptomycin (Gibco), 10 mM HEPES (Gibco), 1× Glutamax (Gibco), 1× B-27 Supplement (Life Technologies), 1.25 mM N-acetylcysteine (Sigma-Aldrich) and 1% (v/v) recombinant Noggin (U-Protein Express).

extract_protocol:
Single cell samples were lysed, barcoded and processed according to the CEL-Seq2 technique. Cells were sorted into 384 well plates, containing UMI barcode primers, frozen and incubated at 65°C for 5min to ensure lysis. First and second strand synthesis (Invitrogen) was performed and all wells of a single plate were pooled. Afterinvitrotranscription (Ambion), the amplified RNA was reverse transcribed and amplified for 10-12 cycles with Illumina Truseq primers.
Organoids were dissociated into single cells using TrypLE (TrypLE Express, Life Technologies) with 10 μM Rho kinase inhibitor (Abmole) in 37°C and mechanical disruption by pipetting every 5 minutes.
Single cell sequencing was performed according to the Sort-seq method (Muraro, M. J. et al. A Single-Cell Transcriptome Atlas of the Human Pancreas, Cell Syst 3, 385-394 e383, doi:10.1016/j.cels.2016.09.002) 2016

treatment_protocol: Organoids were expanded in human expansion medium as described before. For differentiation toward tuft cells, organoids were washed 30 minutes in DMEM+++ at day 4 and the medium is replaced for tuft cell differentiation medium (diff): 0.5 nM Wnt surrogate (U-Protein Express), 20% (v/v) R-spondin1 (condition medium), 50 ng/ml recombinant human EGF (Peprotech), 10 μM Notch inhibitor DAPT (Sigma-Aldrich) in basic culture medium. For tuft cell differentiation with IL-4 and IL-13, EGF was withdrawn, 5 ng/ml human IL-4 (Peprotech) and 5 ng/ml human IL-13 (Peprotech) were supplemented to tuft cell differentiation medium (diff).

value: Ileum

value: KIT+ tuft cells and KIT- epithelial cells

tag: patient age

value: adult


title: Duodenum, LEC, NI-2

value: Duodenum

value: Lymphatic Endothelial Cell

value: Non-infected


title: P04-T-I

value: Tumor

value: CRC


title: Duodenum, LEC, NI-1


title: AVIL+ tuft cells from human ileum 1

description:
HUB-LH-s002
metadata.txt


title: HCC1395-COMBO-C

city: Boston

first: Amy

last: Schade

address: 77 Avenue Louis Pasteur

department: Medicine

institute: Brigham and Women's Hospital

data_processing:
Raw reads were processed through fastp. Reads were aligned using Hisat2 v2.0.5. Data were then further processed using DESeq2.
Assembly: hg38
Supplementary files format and content: DESeq2 normalized counts are uploaded and processed using DESeq2 with count files as input.

source_name: cell line

growth_protocol: HCC38, HCC1395, and HCC1937 cells were treated EZH2i (5 uM tazemetostat), AKTi (5 uM ipatasertib) or EZH2i+AKTi.  On day -5, MDA-MB-468 cells were seeded at 40% confluency and treated with 5uM tazemetostat or DMSO. On day -3, cells were passaged again at 40% confluency and maintained in DMSO or tazemetostat. On day -1, cells were seeded into 6cm plates at 250,000 cells per plate and maintained in DMSO or tazemetostat. On day 0, cells were treated in media containing 2% FBS with AKTi (ipatasertib) and/or EZH2i (tazemetostat). Cells were collected at 24 hours, cells were isolated and then prepared for ATACseq.

extract_protocol:
RNA was extracted using Qiagen Rneasy Plus Kit.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads.  After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.  After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

treatment_protocol: Tazemetostat (EZH2i) was treated at 5 uM. Ipatasertib (AKTi) was dosed at 5 uM.

value: cell line

value: breast cancer


title: AC at day3, control rep3

description: microRNA list from AC control at day3

value: Sprague-Dawley

value: 5 weeks


title: P04-N-I

value: Adjacent normal tissue


title: P04-B-I

value: Peripheral blood


title: AC at day1, after noise rep3

description: microRNA list from AC after noise at day1

source_name: Auditory Cortex, after noise, day1

value: male

value: after noise, day1


title: Duodenum, LEC, NI-4


title: HCC1395-COMBO-B


title: Ileum, SV-4, 8 dpi

extract_protocol:
Samples were defrosted on ice and mucosal scrapes were transferred into 2mL Bead Mill Tubes pre-filled with ceramic beads and 1mL cold TRIzolTM Reagent (Thermo Fisher). Samples were lysed with a bead beater then transferred to a new Tube and processed according to manufacturer’s instructions. Briefly, the samples were incubated at RT then spun down at 4ºC and the supernatant was transferred to a new tube with chloroform to extract the RNA and spin down again. The RNA was precipitated by adding equal volumes of 70% EtOH and continuing the RNA purification process with the PicoPure RNA Isolation Kit (Thermo Fisher).
RNA samples were normalized to 200 ng/µl with ddH2O. 1000 ng of RNA was then used as the starting material for cDNA synthesis and tagmentation using the NEBNext Poly A kit per the manufacturer’s instructions.

treatment_protocol: 8 week old C57BL/6J mice were infected with S. venezeluensis sub cutaneously. 5 and 8 days after infection, the mice, along with non-infected controls, were harvested.

value: Intestinal mucosa

value: S. venezeluensis, day 8


title: AC at day1, after noise rep2

value: Auditory Cortex


title: Ileum, SV-3, 8 dpi

value: Ileum


title: AC at day3, control rep1

description: microRNA list from AC control at day3

value: control, day3


title: P03-T-III

value: Post


title: HCC1395-COMBO-A


title: Ileum, SV-2, 8 dpi


title: AC at day3, after noise rep1

description: microRNA list from AC after noise at day3

source_name: Auditory Cortex, after noise, day3

value: after noise, day3


title: AC at day3, after noise rep3


title: AC at day1, after noise rep1


title: P03-N-III


title: IC at day1, control rep3

description: microRNA list from IC control at day1

source_name: Inferior Colliculus, control, day1

value: Inferior Colliculus

value: control, day1


title: AC at day3, after noise rep2


title: P03-B-III

value: CRC


title: Ileum, SV-1, 8 dpi


title: HCC1395-EZH2-C

value: cell line

value: breast cancer


title: HCC1395-EZH2-B


title: IC at day1, control rep2

description: microRNA list from IC control at day1

value: Sprague-Dawley

value: 5 weeks


title: IC at day1, control rep1

description: microRNA list from IC control at day1


title: P03-T-II

value: Tumor

value: On


title: IC at day3, control rep3

description: microRNA list from IC control at day3

source_name: Inferior Colliculus, control, day3

value: male


title: Jejunum, SV-3, 8 dpi

value: Intestinal mucosa

value: Jejunum


title: HCC1395-EZH2-A


title: P03-T-I

value: Pre


title: HCC1395-AKT-C

value: AKTi


title: Jejunum, SV-2, 8 dpi

value: S. venezeluensis, day 8


title: Jejunum, SV-1, 8 dpi


title: HCC1395-AKT-B


title: IC at day3, control rep2

description: microRNA list from IC control at day3

value: control, day3


title: IC at day3, control rep1

description: microRNA list from IC control at day3


title: P03-B-I

value: Peripheral blood


title: HCC1395-AKT-A


title: HCC1395-DMSO-C

value: DMSO


title: Duodenum, SV-4, 8 dpi

value: Duodenum


title: Jejunum, SV-4, 8 dpi


title: P02-T-II

value: Post

value: CRC


title: HCC1395-DMSO-B

value: cell line

value: breast cancer


title: IC at day1, after noise rep3

description: microRNA list from IC after noise at day1

source_name: Inferior Colliculus, after noise, day1

value: Sprague-Dawley

value: Inferior Colliculus

value: 5 weeks

value: after noise, day1


title: Duodenum, SV-2, 8 dpi

value: Intestinal mucosa


title: Duodenum, SV-3, 8 dpi


title: P02-B-II


title: Duodenum, SV-1, 8 dpi


title: IC at day1, after noise rep2

value: male


title: HCC1395-DMSO-A


title: P03-N-I

value: Adjacent normal tissue

value: Pre


title: P02-T-I

value: Tumor


title: IC at day1, after noise rep1


title: IC at day3, after noise rep3

description: microRNA list from IC after noise at day3

source_name: Inferior Colliculus, after noise, day3

value: after noise, day3


title: HCC1937-COMBO-C


title: Ileum, SV-4, 5 dpi

value: Ileum

value: S. venezeluensis, day 5


title: HCC1937-COMBO-B


title: P02-N-I

source_name: Adjacent normal tissue


title: IC at day3, after noise rep1


title: P02-B-I

value: Peripheral blood


title: Ileum, SV-2, 5 dpi


title: SOC at day1, control rep3

description: microRNA list from SOC control at day1

source_name: Superior Olivary Complex, control, day1

value: Superior Olivary Complex

value: control, day1


title: P02-N-II

value: Post

value: CRC


title: P01-T-IV


title: HCC1937-COMBO-A

value: cell line

value: breast cancer


title: P01-N-IV


title: Ileum, SV-1, 5 dpi


title: HCC1937-DMSO-C

value: DMSO


title: HCC1937-DMSO-B


title: Jejunum, SV-4, 5 dpi

value: Jejunum


title: P01-B-IV


title: Jejunum, SV-3, 5 dpi

value: Intestinal mucosa


title: HCC1937-DMSO-A


title: P01-T-III

value: On


title: HCC38-COMBO-C


title: Jejunum, SV-2, 5 dpi


title: P01-N-III

value: Adjacent normal tissue


title: HCC38-COMBO-B


title: Ileum, SV-3, 5 dpi


title: SOC at day1, control rep1

description: microRNA list from SOC control at day1

value: Sprague-Dawley

value: 5 weeks

value: male


title: Jejunum, SV-1, 5 dpi


title: HCC38-COMBO-A


title: SOC at day3, control rep3

description: microRNA list from SOC control at day3

source_name: Superior Olivary Complex, control, day3

value: control, day3


title: IC at day3, after noise rep2

value: Inferior Colliculus

value: after noise, day3


title: P01-B-III

value: Peripheral blood


title: SOC at day3, control rep1

description: microRNA list from SOC control at day3

value: Superior Olivary Complex


title: SOC at day3, control rep2

description: microRNA list from SOC control at day3


title: SOC at day1, control rep2

description: microRNA list from SOC control at day1

value: control, day1


title: HCC38-DMSO-C


title: SOC at day1, after noise rep3

description: microRNA list from SOC after noise at day1

source_name: Superior Olivary Complex, after noise, day1

value: after noise, day1


title: P01-T2-II

source_name: Tumor

value: Tumor

value: CRC


title: P01-T1-II


title: Duodenum, SV-3, 5 dpi

value: Duodenum

value: S. venezeluensis, day 5


title: Duodenum, SV-2, 5 dpi

value: Intestinal mucosa


title: HCC38-DMSO-B

value: cell line

value: breast cancer

value: DMSO


title: SOC at day1, after noise rep1

value: Sprague-Dawley

value: 5 weeks


title: Duodenum, SV-1, 5 dpi


title: HCC38-DMSO-A


title: P01-B-II

value: On


title: P01-T-I

value: Pre


title: SOC at day3, after noise rep3

description: microRNA list from SOC after noise at day3

source_name: Superior Olivary Complex, after noise, day3

value: male

value: after noise, day3


title: Ileum, NI-4

value: Ileum

value: Non-infected


title: P01-N-I

value: Adjacent normal tissue


title: Duodenum, SV-4, 5 dpi

source_name: Duodenum


title: Ileum, NI-3


title: MDA-MB-468-DOC24-C

growth_protocol: MDA-MB-468 cells were treated with either docetaxel or EZH2i+AKTi. For cells treated with docetaxel, cells were seeded into 10cm plates after 24 hr they were dosed with 10 nM docetaxel. RNA was collected at 8 and 24 hours of docetaxel treatment. For cells treated with EZH2i+AKTi, On day -5, MDA-MB-468 cells were seeded at 40% confluency and treated with 5uM tazemetostat or DMSO. On day -3, cells were passaged again at 40% confluency and maintained in DMSO or tazemetostat. On day -1, cells were seeded into 6cm plates at 250,000 cells per plate and maintained in DMSO or tazemetostat. On day 0, cells were treated in media containing 2% FBS with AKTi (ipatasertib) and/or EZH2i (tazemetostat). Cells were collected at 24 hours, RNA was isolated and then sequenced using NGS.

treatment_protocol: Tazemetostat (EZH2i) was treated at 5 uM. Ipatasertib (AKTi) was dosed at 5 uM. Docetaxel was dosed at 10 nM.

value: WT

value: docetaxel (10 nM)


title: MDA-MB-468-DOC24-A


title: MDA-MB-468-DOC24-B


title: Ileum, NI-2


title: MDA-MB-468-DOC8-C


title: sensitive5

city: Guang Zhou

first: Yiwen

last: Lu

state: China

address: 107 Yanjiang West Road Guangzhou 510120, P.R.China

institute: Sun Yat-Sen University 2nd Affiliated Hospital: Sun Yat-Sen Memorial Hospital

data_processing:
Sequencing was carried out using the Illumina novaseq-6000 instrument
Read quality was checked for each sample using FastQC v0.11.2(http:// www.bioinformatics.babraham.ac.uk/projects/fastqc/).
StringTie software was used to calculate the FPKM value for each sample, and the values were log2 transformed.
Alignment was initially to the transcriptome (hg38)
Mapping of RNA-Seq reads were performed using STAR aligner.
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: breast cacer

extract_protocol:
For RNA extraction, total RNA from each biopsies obtained as described above were isolated using the standard TRIzol protocol (Invitrogen, Carlsbad, CA, USA). RNA quality was examined by gel electrophoresis and with a Nanodrop spectrophotometer (Thermo, Waltham, MA, USA). Strand-specific libraries were constructed using the TruSeq RNA sample preparation kit (Illumina, San Diego, CA, USA), and sequencing was carried out based on the Illumina novaseq-6000 instrument. The raw data was handled by Perl and data quality was checked by FastQC v0.11.2
TruSeq RNA sample preparation kit (Illumina, San Diego, CA, USA)

value: breast cacer

value: therapeutic sensitive


title: Ileum, NI-1

data_processing:
Kallisto
Initial filtering removed genes with expression under 2 cpm
Assembly: GRCm39
Supplementary files format and content: csv file includes raw count for each sample
Supplementary files format and content: csv file includes counts per million for each sample

value: Intestinal mucosa


title: MDA-MB-468-DOC8-B

value: cell line


title: SOC at day3, after noise rep2

value: Superior Olivary Complex


title: CN at day1, control rep2

description: microRNA list from CN control at day1

source_name: Cochler Nucleus, control, day1

value: Cochlear Nucleus

value: control, day1


title: SOC at day1, after noise rep2

value: Sprague-Dawley

value: 5 weeks

value: after noise, day1


title: CN at day1, control rep3

description: microRNA list from CN control at day1

value: male


title: SOC at day3, after noise rep1

value: after noise, day3


title: CN at day3, control rep3

description: microRNA list from CN control at day3

source_name: Cochler Nucleus, control, day3

value: control, day3


title: CN at day1, control rep1

description: microRNA list from CN control at day1


title: CN at day3, control rep2

description: microRNA list from CN control at day3


title: MDA-MB-468-DOC8-A

source_name: cell line

value: breast cancer


title: Jejunum, NI-3

source_name: Jejunum

value: Jejunum

value: Non-infected


title: MDA-MB-468-COMBO-C

description: COMBO-C

value: WT

value: tazemetostat (5 uM) + ipatasertib (5 uM)


title: MDA-MB-468-COMBO-B

description: COMBO-B


title: Jejunum, NI-2


title: sensitive1

value: breast cacer

value: therapeutic sensitive


title: MDA-MB-468-COMBO-A

description: COMBO-A

value: cell line


title: P01-B-I

source_name: Peripheral blood

value: Peripheral blood

value: Pre

value: CRC


title: Jejunum, NI-1

value: Intestinal mucosa


title: sensitive2


title: resistant4

value: therapeutic resistant


title: sensitive3


title: Duodenum, NI-4

value: Duodenum


title: MDA-MB-468-DMSO-C

description: DMSO-C

value: DMSO


title: Duodenum, NI-2


title: sensitive4


title: MDA-MB-468-DMSO-B

description: DMSO-B


title: Duodenum, NI-3


title: Jejunum, NI-4


title: MDA-MB-468-DMSO-A

description: DMSO-A


title: resistant1


title: CN at day3, control rep1

description: microRNA list from CN control at day3

value: Sprague-Dawley

value: Cochlear Nucleus

value: 5 weeks

value: male


title: CN at day1, after noise rep3

source_name: Cochler Nucleus, after noise, day1

value: after noise, day1


title: CN at day1, after noise rep2


title: CN at day3, after noise rep3

source_name: Cochler Nucleus, after noise, day3

value: after noise, day3


title: CN at day1, after noise rep1


title: CN at day3, after noise rep2


title: Duodenum, NI-1

value: Non-infected


title: shCerS4 Caprin-1

status: Public on Jul 07 2024

city: Charleston

first: Wyatt

last: Wofford

state: SC

address: 86 Jonathan Lucas St

institute: MUSC

data_processing:
Partek
Sequence reads were aligned using STAR - 2.7.8a tool in Partek.
Sequence reads were quantified to Ensembl Transcripts annotation model with strict paired-end compatibility and a minimum 100% read overlap with feature using Partek.
Read count extraction and and normalization were performed using Partek.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw count for each sample

growth_protocol: 4T1 cells were maintained in DMEM plus 10% FBS, 1x antibiotics,  plasmocin prophylactic, and 4ug/mL puromycin in a humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Qiazol (Qiagen). 500ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNAseq were constructed using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocol.

value: cancer cell

value: stably expressing CerS4 shRNA


title: shSCR Caprin-1

value: stably expressing SCR


title: shSCR IgG