title: Tumor_plus_NK, Cell_line_A, timepoint_2, EXP_9.5, rep_3

value: Day 10


title: Tumor_plus_NK, Cell_line_B, timepoint_1, EXP_9.5, rep_2

status: Public on Nov 26 2024

type: SRA

city: Vienna

first: CCRI

last: BiCU

address: Zimmermannpl. 10

department: Bioinformatics Core Unit

country: Austria

institute: St. Anna Children's Cancer Research Institute

library_source: genomic

data_processing:
Raw data was processed with nf-core/atacseq pipeline
Mapping reads to the reference genome with STAR alligner (v2.7.10a)
Duplicates identification with Picard (v2.27.4)
Peak calling with MACS2 (v2.2.7.1)
Assembly: GRCm38
Supplementary files format and content: broadPeak files, containting coordinates of called peaks and counts assigned to them
Supplementary files format and content: Consensus peaks with coordinates and counts assigned to them

molecule: genomic DNA

organism: Mus musculus

source_name: B

extract_protocol:
Cells were processed with the Illumina Tagmentation kit
Library preparation was conducted as in Buenrostro et al, 2015. PCR products were purified with Agencourt AMPure XP beads.

tag: cell line

value: B

tag: time

value: Day 4

tag: timepoint

tag: treatment


title: SCZ Line 12 Hairy Roots rep 3

city: Davis

first: Siobhan

last: Brady

state: CA

address: One Shields Avenue, GBSF Room 4409

department: Genome center

country: USA

institute: UC Davis

library_source: transcriptomic

data_processing:
Assembly: ITAG4.1 transcriptome (cDNA)
Column based data frame containing estimated raw pseudo-counts by Kallisto (v0.46.2)

molecule: total RNA

organism: Solanum lycopersicum

source_name: 3 cm roots tips from hairy root plates

growth_protocol: Hairy roots grown in MS+vitamins media with 3% sucrose

extract_protocol:
Total RNA was extracted using the Direct-zol RNA Miniprep kit (ZYMO).
RNAseq libraries were prepared using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD (Lexogen).
Barcoded libraries were then pooled together, and single 100-bp reads were sequenced on the HiSeq4000 SR100 instrument (Illumina) at the UC Davis DNA Technologies Core.

treatment_protocol: 3 cm from root tips was collected from all genotypes. 6-7 root tips from each genotype were pooled.

tag: tissue

value: 3 cm roots tips from hairy root plates

tag: cultivar

value: cv M82

tag: genotype

value: slscz mutant line 12


title: PNUTSdTAG_TTseq_dTAG_rep4

city: Oxford

first: Emilia

last: Dimitrova

address: South Parks Road

department: Biochemistry

country: United Kingdom

institute: University of Oxford

description: calibrated TT-seq

library_source: other

data_processing:
Reads that aligned to the mm10 and dm6 rDNA genomic sequences (GenBank: BK000964.3 and M21017.1) were first identified using Bowtie2 with ‘-very-fast’, ‘-no-mixed’ and ‘-no-discordant’ options) and discarded. Unmapped reads were then aligned to the concatenated mm10 and dm6 genomes using STAR. To improve mapping of intronic sequences, reads that failed to map using STAR were aligned using Bowtie2 with ‘-sensitive-local’, ‘-no-mixed’ and ‘-no-discordant’ options. Uniquely aligned reads from the last two steps were combined for further analysis and PCR duplicates were removed using Sambamba.
To internally calibrate TT-seq, we spiked-in a fixed number of Drosophila SG4 to each experimental sample. For data visualisation, mm10 reads were randomly subsampled using factors that reflected the total number of dm6 reads in each sample.
Read counts from biological triplicates were determined using custom scripts utilising SAMTools for a custom-built, non-redundant mm10 gene set. Briefly, mm10 refGene genes were filtered to remove very short genes with poor sequence mappability and highly similar transcripts which resulted in the final set of 20,633 genes. Raw mm10 reads prior to spike-in normalisation were used for read counts quantitation for differential expression analysis.
The final set of 20,633 genes were used for differential analysis using a custom R script adapting DESeq2 (Love et al., 2014) for spike-in calibrated TT-seq data. To incorporate spike-in calibration into this analysis, read counts for the spike-in genome at a control set of intervals were supplied to calculate DESeq2 size factors which were then used for DESeq2 normalisation of raw mm10 read counts. A set of unique dm6 refGene genes was used for spike-in normalisation of TT-seq. For a change to be called significant, we applied a threshold of p-adj < 0.05 and fold change > 1.5.
Assembly: mm10, dm6
Supplementary files format and content: Stranded bigWig files were generated using genomeCoverageBed from BEDTools representing genome coverage of merged spike-in normalised biological replicates.
Supplementary files format and content: DESeq2 results tables for differential gene expression analysis containing normalised read counts, raw and shrunk log2-fold changes (LFC), and statistical significance levels for a non-redundant set of mm10 refGene genes.
Library strategy: cTT-seq

molecule: other

organism:
Drosophila melanogaster
Mus musculus

source_name: E14 PNUTS-dTAG

growth_protocol: Mouse embryonic stem cells were grown in Dulbecco’s Modified Eagle Medium (Thermo Fisher Scientific) supplemented with  fetal bovine serum (FBS, 15% Biosera or 10% Sigma), 1x non-essential amino acids (Thermo Fisher Scientific), 2 mM L-glutamine (Thermo Fisher Scientific), 1x penicillin/streptomycin (Thermo Fisher Scientific), 0.5 mM beta-mercaptoethanol (Thermo Fisher Scientific), and 10 ng/ml leukaemia inhibitory factor (produced in-house). ESCs were grown on gelatinised plates at 37⁰C and 5% CO2.

extract_protocol:
cTT-seq was performed largely as described previously (Gregersen et al., 2020). In brief, 9 million ESCs and 3 million Drosophila SG4 cells were labelled with 500 µM 4-thiouridine (4sU, Glentham Life Sciences) for 15 min and harvested into TRIzol reagent. 4sU-labelled mouse and Drosophila cells were mixed and RNA was extracted and depleted from any gDNA carry-over using the Direct-zol RNA Miniprep Plus kit (R2072 Zymo Research) as per the manufacturer’s protocol. An equal quantity of RNA (80-100 µg) was taken into 100 µl nuclease free water and fragmented on ice with 20 µl 1 M NaOH for 20 min. Fragmentation was stopped with 80 μl 1 M Tris, pH 6.8 and the RNA was cleaned up with Micro Bio-Spin P-30 gel columns (Biorad). RNA was biotin-labelled with 50 μl 0.1 mg/ml MTSEA biotin-XX linker (Biotium) with 3 μl biotin buffer (833 mM Tris HCl, pH 7.4, 83.3 mM EDTA) for 30 min at RT. Biotin-labelled RNA was purified with a 1:1 ratio of phenol/chloroform/isoamyl alcohol (Thermo Fisher Scientific). Streptavidin pull-down was performed with the μMACS Streptavidin Kit (Miltenyi Biotec), washing the columns three times with 55 °C pull-down wash buffer (100 mM Tris HCl, pH 7.4, 10 mM EDTA, 1 M NaCl and 0.1% Tween 20) and 3x RT pull down wash buffer. Biotin-labelled RNA was eluted with 100 μl elution buffer (100 mM DTT in nuclease-free water) and cleaned up with the RNeasy MinElute Cleanup kit (QIAGEN), adjusting the amount of ethanol to capture RNA < 200 nucleotides in length.
RNA was quantified using the Qubit RNA HS assay kit and RNA libraries were prepared from 20 ng RNA with the Ultra II Directional RNA library prep kit, as per the manufacturer’s guidelines for rRNA depleted and FFPE RNA (NEB).

treatment_protocol: Cell lines expressing dTAG fusion proteins were treated with 100 nM dTAG13 to induce depletion of PNUTS. For rescue experiments, cells were treated with 1ug/ml DOX to induce the expression of PNUTS WT, PNUTS W401A or PNUTS TND-M and with 100 nM dTAG13 to deplete endogenous PNUTS protein.

value: E14 PNUTS-dTAG

tag: cell type

value: embryonic stem cell line

tag: tag

tag: rescue

tag: spike-in cell_line

tag: treatment time

tag: additional treatment

tag: additional treatment_time

tag: labelling

value: 500 µM 4-thiouridine

tag: labelling time

value: 15 min


title: E14-T3G-WT-UNT-rep1

description: calibrated TT-seq

source_name: E14 TETON-3G PNUTS-dTAG PNUTS-WT rescue

value: E14 TETON-3G PNUTS-dTAG PNUTS-WT rescue

value: dTAG

value: PNUTS-T7 WT

value: Untreated


title: PNUTSdTAG_TTseq_dTAG_rep2

description: calibrated TT-seq


title: Tumor_only, Cell_line_A, timepoint_1, EXP_9.5, rep_3

source_name: A

value: A


title: Tumor_only, Cell_line_A, timepoint_1, EXP_9.5, rep_1


title: Tumor_only, Cell_line_A, timepoint_1, EXP_9.5, rep_2


title: PNUTSdTAG_TTseq_dTAG_rep1

description: calibrated TT-seq


title: Tumor_only, Cell_line_D, timepoint_1, EXP_9.5, rep_3

source_name: D

value: D


title: E14-T3G-WT-dTAG-rep1

description: calibrated TT-seq


title: PNUTSdTAG_TTseq_UNT_rep4

description: calibrated TT-seq


title: PNUTSdTAG_TTseq_UNT_rep3

description: calibrated TT-seq


title: Tumor_only, Cell_line_C, timepoint_1, EXP_9.5, rep_3

source_name: C

value: C


title: SlEXO1 Line 7 Hairy Roots,rep 3

value: slexo1 mutant line 7


title: Tumor_only, Cell_line_B, timepoint_1, EXP_9.5, rep_1

value: B


title: PNUTSdTAG_TTseq_UNT_rep1

description: calibrated TT-seq


title: Tumor_plus_WT_NK, Cell_line_D, timepoint_2, rep_2

data_processing:
Reads were mapped to a genome assembly using STAR (v2.7.10a).
Reads counting was performed with the help of Salmon (v1.8.0) or GenomicAlignments (v1.36.0)
Assembly: GRCm38/GRCh38
Supplementary files format and content: quant.sf files contain counted reads
Supplementary files format and content: tsv files contain counted reads performed by GenomicAlignments package

extract_protocol:
Extraction was done with the AllPrep DNA/RNA Mini Kit (Qiagen) and samples were treated with DNase I (Thermo Fisher Scientific) or the Monarch Total RNA Miniprep Kit (New England Biolabs)
QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina (Lexogen)

value: Day 32

tag: time point

tag: genome assembly_used


title: Tumor_plus_WT_NK, Cell_line_A, timepoint_2, rep_3

tag: cell line

tag: time


title: Control rep 3

value: 3 cm roots tips from hairy root plates

value: Wild-type


title: Control rep 2

value: cv M82


title: Tumor_only, Cell_line_C, timepoint_1, EXP_9.5, rep_1

value: Day 4

tag: timepoint

tag: treatment


title: SCZ Line 12 Hairy Roots rep 2

tag: tissue

tag: cultivar

value: slscz mutant line 12


title: SCZ Line 12 Hairy Roots rep 4

tag: genotype


title: SCZ Line 5 Hairy Roots rep 4

value: slscz mutant line 5


title: SCZ Line 5 Hairy Roots rep 3


title: SlEXO1 Line 6 Hairy Roots,rep 4

value: slexo1 mutant line 6


title: SlEXO1 Line 6 Hairy Roots,rep 3


title: Tumor_plus_WT_NK, Cell_line_D, timepoint_2, rep_3


title: SCZ Line 5 Hairy Roots rep 2


title: Tumor_plus_Ifng_KO_NK, Cell_line_D, timepoint_2, rep_2


title: SlEXO1 Line 7 Hairy Roots,rep 1


title: Tumor_plus_WT_NK, Cell_line_D, timepoint_2, rep_1


title: SlEXO1 Line 7 Hairy Roots,rep 2


title: Tumor_plus_WT_NK, Cell_line_A, timepoint_2, rep_1


title: Tumor_plus_Ifng_KO_NK, Cell_line_D, timepoint_2, rep_1


title: Tumor_plus_Ifng_KO_NK, Cell_line_A, timepoint_2, rep_2


title: genomic DNA from mouse ID 35512

type: genomic

city: Bethesda

first: Frederic

last: Barr

state: MD

address: 10 Center Drive, Rm 3B55

institute: National Cancer Institute

description: Sample 28

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MouseMethylation285 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan system to produce Idat files

data_processing: Data were processed using Minfi with swan algorithm

label: Cy5 and Cy3

source_name: rhabdomuyosarcoma tumor

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from tumor samples using Qiagen Blood and Tissue according to standard instructions

tag: model

value: Pax7(CREERp/WT) Pax3(P3Fm/P3Fm) Trp53(F2-10/F2-10) Rb1(Flox/Flox)

value: rhabdomuyosarcoma tumor


title: Tumor_plus_WT_NK, Cell_line_A, timepoint_2, rep_2


title: Tumor_plus_Ifng_KO_NK, Cell_line_D, timepoint_2, rep_3


title: Tumor_plus_Ifng_KO_NK, Cell_line_A, timepoint_2, rep_3


title: genomic DNA from mouse ID 26568

description: Sample 30

value: Pax3(P3Fm/P3Fm) ROSA26(WT/WT) Trp53(F2-10/F2-10) Pax7(CreERp/WT)


title: genomic DNA from mouse ID 31430

description: Sample 29

value: Pax7(CREERp/WT) Pax3(P3Fm/P3Fm) Trp53(F2-10/F2-10) Rosa26(Lusap/WT)


title: SlEXO1 Line 6 Hairy Roots,rep 2


title: Tumor_plus_Ifng_KO_NK, Cell_line_A, timepoint_2, rep_1

value: A


title: genomic DNA from mouse ID 28285

description: Sample 26

value: Pax7(CREERp/WT) Pax3(P3Fm/P3Fm) Trp53(F2-10/F2-10) Rosa26(LUSAPm/WT)


title: genomic DNA from mouse ID 31431

description: Sample 25

value: Pax7(CREERp/WT) Pax3(P3Fm/P3Fm) Trp53(F2-10/F2-10) Rosa26(LUSAP/Any)


title: Tumor_only, Cell_line_D, timepoint_2, rep_2

value: D


title: Tumor_only, Cell_line_D, timepoint_2, rep_3


title: genomic DNA from mouse ID 33940

description: Sample 23


title: genomic DNA from mouse ID 34605

description: Sample 24

value: ROSA26(WT/WT) PTC1(F1-2m/WT) Trp53(F2-10/F2-10) Pax7(CreERp/WT)


title: genomic DNA from mouse ID 29138

description: Sample 31


title: Tumor_only, Cell_line_A, timepoint_2, rep_3

value: Day 32


title: Tumor_only, Cell_line_A, timepoint_2, rep_2


title: Tumor_only, Cell_line_D, timepoint_2, rep_1


title: genomic DNA from mouse ID 45065

description: Sample 22

value: Myf6(ICNm/WT) Pax3(P3Fm/P3Fm) Trp53(F2-10/F2-10) Rb1(Flox/Flox) Rosa26(LUSAP/WT)


title: genomic DNA from mouse ID 66788

description: Sample 21

value: Myf6(ICNm/WT) Pax3(P3Fm/P3Fm) Trp53(F2-10/F2-10) Rosa26(LUSAPp/Any) Hairless(SKH1/SKH1)


title: Tumor_only, Cell_line_A, timepoint_2, rep_1


title: Tumor_plus_WT_NK, Cell_line_D, timepoint_1, rep_1

value: Day 17


title: genomic DNA from mouse ID 38172

description: Sample 20

value: Myf6(ICNm/WT) Pax3(P3Fm/P3Fm) Trp53(F2-10/F2-10) Rb1(Flox/Flox) Rosa26(LUSAP/Any)


title: genomic DNA from mouse ID 38917

description: Sample 19

value: Myf6(ICNm/WT) Pax3(P3Fm/P3Fm) Trp53(F2-10/F2-10) Rb1(Flox/Flox)


title: Tumor_plus_WT_NK, Cell_line_D, timepoint_1, rep_3


title: genomic DNA from mouse ID 44927

description: Sample 18

value: Myf6(ICNm/WT) Pax3(P3Fm/P3Fm) Trp53(F2-10/F2-10) Hairless(SKH1/WT)


title: genomic DNA from mouse ID 26404

description: Sample 17


title: genomic DNA from mouse ID 29418

description: Sample 27

value: Pax7(CREERp/WT) Pax3(P3Fm/P3Fm) Trp53(F2-10/F2-10) Rosa26(LUSAPm/WT) ZRED-Tg(Bgeo/WT)


title: genomic DNA from mouse ID 35029

description: Sample 15


title: Tumor_plus_WT_NK, Cell_line_A, timepoint_1, rep_3


title: Tumor_plus_WT_NK, Cell_line_A, timepoint_1, rep_2


title: genomic DNA from mouse ID 21353

description: Sample 14


title: Tumor_plus_Ifng_KO_NK, Cell_line_D, timepoint_1, rep_3


title: Tumor_plus_WT_NK, Cell_line_D, timepoint_1, rep_2


title: genomic DNA from mouse ID 37125

description: Sample 13

value: Myf6(ICNm/WT) Trp53(F2-10/F2-10) Rosa26(LUSAP/Any) PTC1(WT/WT)


title: Tumor_plus_Ifng_KO_NK, Cell_line_D, timepoint_1, rep_1


title: Tumor_plus_Ifng_KO_NK, Cell_line_D, timepoint_1, rep_2


title: genomic DNA from mouse ID 32577

description: Sample 12

value: rhabdomuyosarcoma tumor


title: Tumor_plus_Ifng_KO_NK, Cell_line_A, timepoint_1, rep_3


title: Tumor_plus_Ifng_KO_NK, Cell_line_A, timepoint_1, rep_2


title: genomic DNA from mouse ID 20938

description: Sample 9


title: genomic DNA from mouse ID 23478

description: Sample 10

value: Myf5(ICNm/WT) PTC1(F1-2m/WT) Trp53(F2-10/F2-10) ROSA26(LUSAP)


title: Tumor_plus_Ifng_KO_NK, Cell_line_A, timepoint_1, rep_1


title: Tumor_only, Cell_line_D, timepoint_1, rep_2


title: Tumor_only, Cell_line_D, timepoint_1, rep_3


title: genomic DNA from mouse ID 24055

description: Sample 8


title: genomic DNA from mouse ID 24085

description: Sample 7


title: Tumor_only, Cell_line_D, timepoint_1, rep_1


title: genomic DNA from mouse ID 24988

description: Sample 6


title: genomic DNA from mouse ID 32945

description: Sample 16


title: Tumor_plus_WT_NK, Cell_line_A, timepoint_1, rep_1


title: genomic DNA from mouse ID 23969

description: Sample 5


title: Tumor_only, Cell_line_A, timepoint_1, rep_2


title: genomic DNA from mouse ID 24107

description: Sample 4


title: Tumor_only, Cell_line_A, timepoint_1, rep_1


title: genomic DNA from mouse ID 20745

description: Sample 3


title: Tumor_only, Cell_line_D, timepoint_0, rep_3

value: Day 0


title: genomic DNA from mouse ID 24014

description: Sample 11


title: genomic DNA from mouse ID 28402

description: Sample 1


title: Tumor_only, Cell_line_A, timepoint_1, rep_3

value: A


title: Tumor_only, Cell_line_D, timepoint_0, rep_1


title: SupT1 infected, RNASeq, 24hpi, rep2

city: Würzburg

first: Neva

last: Caliskan

address: Josef-Schneider-Str. 2/D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research (HIRI)

data_processing:
For PRICE analysis: (1) remove adapters cutadapt -a AGATCGGAAGAGCACACG -e 0.3 (2)  filter out short reads gedi -e FastqFilter -layout 2UI5U151 -min 18 (3) h.rRNA and mycoplasma removal  bowtie2 -un un --local -U (4) mapping reads STAR --runMode alignReads --alignIntronMax 1  --outSAMmode NoQS --outSAMtype BAM SortedByCoordinate --alignEndsType Extend5pOfRead1 --outSAMattributes nM MD NH (5) Convert BAM to CIT gedi -e BAM2CIT -umi (6) gedi -e CorrectCIT (7) deduplicate UMIs gedi -e DedupUMI (8) gedi -e MergeCIT (9) create report gedi -e Stats (10) P-site calling gedi -e Price
cutadapt 3.5, bowtie2 version 2.3.0, STAR version=2.7.10b, Gedi version 1.0.6, Price version 1.0.4
For differential gene expression analysis: (1) Count reads per genomic feature featureCounts -O (2) normalization and log2 fold change calculations by deltaTE/DTEG.R
featureCounts version 2.0.0, deltaTE (Chothani et al. 2019)
Assembly: GCF_000001405.36, AF324493
Supplementary files format and content: The PRICE codons BED files contain the genomic regions corresponding to predicted P-sites for each RiboSeq read. The "score" column equals to the read coverage at this position.
Supplementary files format and content: The countMatrix CSV files contain the read counts overlapping each genomic feature for every time point of infection for either cyclo RiboSeq or RNASeq.
Supplementary files format and content: The deltaTE text files contain the log2 fold changes (plus statistics) for each genomic feature, normalized by DESeq2 and calculated for each timepoint of infection against the 0h mock sample. This includes RiboSeq changes, RNASeq changes and  translation efficiency (TE) changes.
Supplementary files format and content: The DisomeSeq BED files contain the DisomeSeq reads that map to the HIV genome. The DisomeSeq text files contain the summed coverage per nucleotide for the HIV genome (column1: chromosome identifier; column2: genome position, column3: read coverage).
Supplementary files format and content: PRICE_report_harr_cyclo.tar contains quality control information for the RiboSeq PRICE pipeline, for both the cycloheximide and harringtonine treated samples. The index.html file allows interactive browsing through the different plots.
Supplementary files format and content: PRICE_report_disome.tar contains quality control information for the DisomeSeq PRICE pipeline. The index.html file allows interactive browsing through the different plots. Note that the p-site prediction is not valid for the DisomeSeq.
Supplementary files format and content: interactive_dTE_volcano_plots_DGE.tar contains interactive volcanoplots (translation efficiency) of the differential gene expression analysis with the deltaTE pipeline. Each infection timepoint was compared to the mock sample. Genes exceeding +/- 1 fold change and p_adj < 0.05 are colored based on consolidated gene ontology.
Supplementary files format and content: interactive_deltaTE_plots_DGE.tar contains interactive RiboSeq/RNASeq log2 fold change plots, of the differential gene expression analysis with the deltaTE pipeline. Each infection timepoint was compared to the mock sample. Only genes that are labelled as differentially expressed are plotted.

molecule: cytoplasmic RNA

organism:
Homo sapiens
Human immunodeficiency virus 1

growth_protocol: SupT1 cells (NIH HIV Reagent Program, Division of AIDS, NIAID, NIH: Sup-T1 Cells, ARP-100, contributed by Dr. Dharam Ablashi) were maintained in RPMI (Gibco) supplemented 10% FBS (Gibco), 1X L-Glutamine (Gibco), 100 μg/ml streptomycin and 100 U/ml penicillin. Cell lines were maintained at 37°C with 5% CO2.

extract_protocol:
Ribosome profiling samples were prepared as previously described (McGlincy and Ingolia., 2017) with modifications for suspension cell lines. Briefly, at each time point of infection, cells were treated with 100 μg/ml cycloheximide in DMSO at 37 °C for 5 min. For harringtonine treated samples, cells were treated with 2 μg/ml harringtonine in DMSO at 37 °C for 5 min, followed by cycloheximide treatment. Cells were immediately pelleted at 1000 RPM for 3 min at 4 °C, washed once with cold cycloheximide containing PBS and the cell pellet was snap-frozen in liquid nitrogen and stored at -80 °C, till further use. Cell pellet was thawed in the presence of ice-cold lysis buffer (20 mM Tris-Cl pH7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 μg/ml cycloheximide, 1% Triton-X, 25U/ml Turbo DNase ) and triturated 10 times through a 26G needle. The lysate was centrifuged at 17000g for 10 min at 4 °C and the supernatant was recovered. Cell lysates were subjected to RiboSeq and RNASeq.
RiboSeq libraries: RNase I footprinting of ribosomes, ribosome purification by ultracentrifugation through a sucrose cushion, RNA extraction, polyacrylamide gel size selection for footprint fragments, preadenylylated linker ligation, reverse transcription, first-strand cDNA circularization. RNASeq libraries from these samples were constructed using CORALL Total RNA-Seq Library Prep Kit (Lexogen), according to manufacturer’s instructions.

treatment_protocol: For ribosome, disome and polysome profiling experiments, SupT1 cells were either mock treated (with PBS) or infected with 50 µl of virus suspension per 40 million cells by spinoculation at 1500 g for 30 min at 37 °C, in presence of 8 µg/ml polybrene (Sigma). Cells were pelleted at 1000 RPM for 3 min at 37 °C, washed once with warm media, resuspended in 40 ml RPMI medium and incubated at 37 °C.

tag: cell type

value: T-cell

value: cycloheximide


title: genomic DNA from mouse ID 22520

description: Sample 2


title: Tumor_only, Cell_line_A, timepoint_0, rep_3


title: Tumor_only, Cell_line_A, timepoint_0, rep_2


title: SupT1 infected, RNASeq, 24hpi, rep1


title: Tumor_only, Cell_line_A, timepoint_0, rep_1


title: SupT1 infected, RNASeq, 16hpi, rep1


title: SupT1 infected, RNASeq, 8hpi, rep2


title: KO_Ly6a, clone 2, rep_2

value: Ly6a KO; clone 2


title: KO_Ly6a, clone 2, rep_3


title: Tumor_only, Cell_line_D, timepoint_0, rep_2

value: D


title: KO_Ly6a, clone 2, rep_1


title: KO_Ly6a, clone 1, rep_3

value: Ly6a KO; clone 1


title: DESynR AP-1 exp 2 lane 4 MULTI

city: Stanford

first: Andy

last: Chen

address: 240 Pasteur Dr.

institute: Stanford

description: MULTI-seq

data_processing:
scRNA-seq library FASTQs were pre-processed using Cell Ranger version 6.0.0 (10x Genomics) and aligned to the GRCh38-3.0.0 reference transcriptome.
MULTI-seq FASTQs were processed using deMULTIplex2 (Zhu, Conrad, and Gartner, Genome Biology, 2024)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: MULTI-seq

organism: Homo sapiens

source_name: T cells

growth_protocol: Primary human T cells were negatively selected from PBMCs isolated from leukoreduction chambers from healthy blood donors and activated by CD3/28 agonism in X-VIVO 15 supplemented with 5% FBS and 50 IU/mL recombinant human IL-2. 48 hours post-activation, T cells were electroporated with Cas9 ribonucleoprotein and a plasmid homology-directed repair template to enable integration of a multicistronic cassette encoding tNGFR, CD19-28z and variable natural and engineered AP-1 transcription factors within the continuous reading frame of the TRAC locus. Pre- and post-editing cells were maintained at 0.5-1e6/ml. Six days post editing and every two-three days thereafter, CAR T cells were challenged with CD19-expressing Nalm6 targets (six total stimulations).

extract_protocol:
Live-sorted CAR T cells (NGFR+) were tagged with MULTI-Seq barcodes (Sigma Aldrich), normalized and pooled, and processed using the Chromium Controller instrument (10x Genomics).
Libraries were prepared according to manufacturer's instructions (10x Genomics 5’ v2) with a separate MULTI-seq library preparation workflow performed following cDNA amplification, as described previously (McGinnis, Patterson, et al., Nature Methods, 2019).

treatment_protocol: All T cells in this sample were treated the same, the only difference between the T cells is which transcription factor they were edited to express.

value: T cells


title: SupT1 infected, RNASeq, 16hpi, rep2


title: SupT1 infected, RNASeq, 8hpi, rep1


title: WT_Ly6a, clone 2, rep_3

value: WT; clone 2


title: DESynR AP-1 exp 1 lane 3 MULTI

description: MULTI-seq


title: WT_Ly6a, clone 2, rep_1


title: DESynR AP-1 exp 1 lane 2 MULTI

description: MULTI-seq


title: WT_Ly6a, clone1, rep_1

value: WT; clone 1


title: DESynR AP-1 exp 1 lane 1 MULTI

description: MULTI-seq


title: KO_Ly6a, clone 1, rep_2


title: DESynR AP-1 exp 2 lane 1 MULTI

description: MULTI-seq


title: WT_Ly6a, clone 1, rep_3


title: Tumor_plus_PrfKO_NK, Cell_line_D, timepoint_2, EXP_9.8, rep_3

value: Day 14


title: WT_Ly6a, clone 1, rep_2


title: DESynR AP-1 exp 2 lane 3

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
scRNA-seq library FASTQs were pre-processed using Cell Ranger version 6.0.0 (10x Genomics) and aligned to the GRCh38-3.0.0 reference transcriptome.
MULTI-seq FASTQs were processed using deMULTIplex2 (Zhu, Conrad, and Gartner, Genome Biology, 2024)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA


title: KO_Ly6a, clone 1, rep_1


title: DESynR AP-1 exp 2 lane 2 MULTI

description: MULTI-seq


title: Tumor_plus_PrfKO_NK, Cell_line_D, timepoint_2, EXP_9.8, rep_2


title: WT_Ly6a, clone 2, rep_2


title: DESynR AP-1 exp 2 lane 1

description: 10x Genomics


title: DESynR AP-1 exp 2 lane 4

description: 10x Genomics


title: Tumor_plus_PrfKO_NK, Cell_line_D, timepoint_2, EXP_9.8, rep_1


title: DESynR AP-1 exp 2 lane 2

description: 10x Genomics


title: DESynR AP-1 exp 1 lane 4

description: 10x Genomics


title: Tumor_plus_PrfKO_NK, Cell_line_A, timepoint_2, EXP_9.8, rep_3


title: DESynR AP-1 exp 1 lane 3

description: 10x Genomics


title: Tumor_plus_PrfKO_NK, Cell_line_A, timepoint_2, EXP_9.8, rep_2


title: Tumor_plus_PrfKO_NK, Cell_line_A, timepoint_2, EXP_9.8, rep_1


title: Tumor_plus_WT_NK, Cell_line_D, timepoint_2, EXP_9.8, rep_3


title: Tumor_plus_WT_NK, Cell_line_D, timepoint_2, EXP_9.8, rep_1


title: Tumor_plus_WT_NK, Cell_line_D, timepoint_2, EXP_9.8, rep_2


title: MAFF_ATF3_BATF2-Week_2-2

data_processing:
Reads were trimmed for quality and adapter sequences using fastQC.
Trimmed reads were aligned to the hg38 reference genome using bowtie2.
Aligned reads were deduplicated using Picard.
Peakswere called using MACS2 from the paired endbed file (bedpe) using a false discovery thresh-old of 0.05 (-q 0.05).
Normalized bigwig files were created by normalizing the coverage track of the bedpe file by reads in peaks.
Assembly: hg38
Supplementary files format and content: Normalized bigwig files.

source_name: CD19-28z CAR T

extract_protocol:
Nuclei from live-sorted CAR T cells (NGFR+) were isolated by 10 minute-centrifugation at 750g and 4°C in diH2O supplemented with 10 mM Tris-HCl pH 7.4, 10 mM NaCL, 3 mM MgCl2, 0.1% Tween-20, 0.1% IGEPAL, 0.01% Digitonin and 1% BSA.
DNA was tagmented by Tn5 and then PCR-amplified with Nextera indexes for 12 cycles using NEB Next Ultra II Q5 polymerase. Libraries were double-size selected.

value: CD19-28z CAR T


title: MAFF_ATF3_BATF2-Week_2-1


title: Tumor_plus_WT_NK, Cell_line_A, timepoint_2, EXP_9.8, rep_1


title: JunB-Week_2-2


title: JunB-Week_2-1


title: FOSL1_BATF_MAFA-Week_2-239


title: DESynR AP-1 exp 1 lane 1

description: 10x Genomics


title: Tumor_only, Cell_line_D, timepoint_2, EXP_9.8, rep_3


title: FOSL1_BATF_MAFA-Week_2-2


title: FOSL1_BATF_MAFA-Week_2-237


title: Tumor_only, Cell_line_D, timepoint_2, EXP_9.8, rep_2


title: FOSL1_BATF_MAFA-Week_2-238


title: Tumor_only, Cell_line_D, timepoint_2, EXP_9.8, rep_1


title: cJUN_cFOS_BATF-Week_2-238


title: Tumor_only, Cell_line_A, timepoint_2, EXP_9.8, rep_3


title: DESynR AP-1 exp 1 lane 2

description: 10x Genomics


title: Tumor_only, Cell_line_A, timepoint_2, EXP_9.8, rep_2


title: cJUN_cFOS_BATF-Week_2-237


title: Tumor_only, Cell_line_D, timepoint_1, EXP_9.8, rep_3

value: Day 4


title: FOSL1_BATF_MAFA-Week_2-1


title: cJUN_cFOS_BATF-Week_2-239


title: Tumor_only, Cell_line_A, timepoint_2, EXP_9.8, rep_1


title: Tumor_plus_WT_NK, Cell_line_A, timepoint_2, EXP_9.8, rep_2


title: Tumor_plus_WT_NK, Cell_line_A, timepoint_2, EXP_9.8, rep_3


title: Tumor_only, Cell_line_A, timepoint_1, EXP_9.8, rep_3


title: CAR_GFP-Week_2-238


title: Tumor_only, Cell_line_A, timepoint_1, EXP_9.8, rep_2


title: CAR_GFP-Week_2-237


title: Tumor_only, Cell_line_A, timepoint_1, EXP_9.8, rep_1


title: Tumor_only, Cell_line_D, timepoint_0, EXP_9.8, rep_3


title: Tumor_only, Cell_line_D, timepoint_1, EXP_9.8, rep_1


title: BATF3_BATF2_MAFF-Week_2-239


title: BATF3_JDP2_BATF2-Week_2-2


title: CAR_GFP-Week_2-1


title: BATF3_JDP2_BATF2-Week_2-1


title: Tumor_only, Cell_line_D, timepoint_0, EXP_9.8, rep_1


title: Tumor_only, Cell_line_D, timepoint_0, EXP_9.8, rep_2


title: CAR_GFP-Week_2-239


title: BATF-Week_2-238


title: Tumor_only, Cell_line_D, timepoint_1, EXP_9.8, rep_2


title: BATF-Week_2-2


title: BATF3_BATF2_MAFF-Week_2-237


title: kidney, 20CBD, long-term,2

city: Kraków

first: Artur

last: Gurgul

address: Rędzina 1C

department: Center for Experimental and Innovative Medicine

country: Poland

institute: University of Agriculture in Krakow

data_processing:
Quality control, FastQC, v0.11.9
Filtering, Flexbar, 3.5.0
Alignment, STAR, 2.7.5c
Reads counting, Htseq-count, 1.99.2
Reads normalization, DESeq2 3.16
Assembly: GRCm39
Supplementary files format and content: Processed data files include raw read counts for all samples in tabular format, text files (.txt)

source_name: Kidney

extract_protocol:
Tissues were collected and immediately submerged in stayRNA™ (A&A Biotechnology) reagent. After 24 of cooling (4C), tissues were frozen at -80C until the time of RNA isolation. For RNA isolation, tissue scrapes (15-30 mg) were homogenized and used for RNA isolation with Trizol reagent (Thermo Fisher). Following isolation, RNA was controlled for quality with the TapeStation4150 system and quantified.
Libraries were prepared using CORALL mRNA-Seq V2 (Lexogen) following standard protocol.

treatment_protocol: The experiment was conducted on C57BL/6J laboratory mice strain (n=12), divided into subgroups receiving CBD at doses of 10, or 20 mg/kg of body weight, and a control group receiving placebo, administered for 28 days. CBD was administered once a day via intraperitoneal injection. RNA-Seq analysis of the kidney was conducted to identify alternations in mouse transcriptomes induced by CBD treatment in this organ.

value: Kidney

value: 20CBD, long-term


title: BATF-Week_2-239


title: Tumor_only, Cell_line_A, timepoint_0, EXP_9.8, rep_1


title: Tumor_only, Cell_line_A, timepoint_0, EXP_9.8, rep_2


title: kidney, 20CBD, long-term,4


title: Tumor_only, Cell_line_A, timepoint_0, EXP_9.8, rep_3


title: kidney, 10CBD, long-term,4

value: 10CBD, long-term


title: kidney, 20CBD, long-term,1


title: kidney, 10CBD, long-term,2


title: kidney, 10CBD, long-term,3


title: kidney, 10CBD, long-term,1


title: CAR_GFP-Week_2-2


title: BATF3_BATF2_MAFF-Week_2-238


title: kidney, Control, long-term,4

value: Control, long-term


title: LUADd56

city: Xi'an

first: Yanlu

last: Xiong

state: Shaanxi

address: 569 Xinsi Road, Baqiao District

department: Tangdu Hospital

country: China

institute: Air Force Medical University

description: Library name: Sample 56

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp.
We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Homo sapiens GRCh38. The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts.
StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: GRCh38
Supplementary files format and content: Comma-separated text file includes FPKM values for each Sample.

source_name: lung

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

value: lung

tag: disease

value: pN2 LUAD


title: LUADd55

description: Library name: Sample 55


title: LUADd54

description: Library name: Sample 54


title: BATF-Week_2-237


title: kidney, 20CBD, long-term,3


title: kidney, Control, long-term,3


title: LUADd53

description: Library name: Sample 53


title: LUADd51

description: Library name: Sample 51


title: kidney, Control, long-term,2


title: BATF-Week_2-1


title: LUADd49

description: Library name: Sample 49


title: LUADd50

description: Library name: Sample 50


title: osteal macrophage isolated from control mice3

city: Sapporo

first: Mohamad Alaa

last: Terkawi

state: Hokkaido

address: Kita-15, Nish-7, Kita-ku

department: Department of Orthopedic Surgery

country: Japan

institute: Hokkaido University

data_processing:
featureCounts v1.5.0-p3
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: Hisat2
Supplementary files format and content: excel file includes read counts for each samples

source_name: macrophage

growth_protocol: Osteal macrophages were isolated from ovariectomized and control mice 4 weeks after surgery. After isolation, they were submitted to exract RNA

extract_protocol:
Isolated osteal macrophages were lysed with TRIzol Reagent (Invitrogen, Thermo Fisher Scientific, CA) and RNA was extracted using NucleoSpin® RNA (TAKARA, Tokyo, Japan) according to the manufacturer's instructions.
Libraries were generated from 1 µg of RNA using a NEBNext Ultra II Directional RNA Library Prep Kit (MA, USA)

treatment_protocol: No treatment

value: macrophage

tag: condition

value: sham


title: Osteal macrophages OVX--Sham_scRNA

data_processing:
featureCounts v1.5.0-p3
The libraries were quantified using a KAPA Library Quantification Kit (KAPA Biosystems, Wilmington, MA) and sequenced via MGI DNBSEQ-G400 (MGI Tech, Shenzhen, China) (Table S11).
A total of 435,107,683 reads were obtained and, the raw data from each sample were demultiplexed, aligned to the mm10 reference genome, and UMI counts were quantified using the 10X Genomics Cell Ranger pipeline (v6.0.1, 10X Genomics), and the analyses, including clustering and trajectory, and defining DEGs and specific marker of each subset/cluster were performed by BBrowserX software (BioTuring Inc., San Diego, CA, USA: https://bioturing.com/bbrowserx).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: osteal

extract_protocol:
Isolated Omacs were washed once with ice-cold PBS containing 0.04% weight/volume BSA and counted using AO/PI staining by CellDropFL (DeNovix, Wilmington, DE). The cells were then subjected to cell hashing (TotalSeq™; BioLegend) and the resulting cells (1037 for OVX) and (1084 cells for sham) were loaded
Library was perfomed according to the manufacturers' instructions (Chromium Next GEM Single Cell 3’ Reagent Kits v3.1).

value: osteal

value: 4 weeks after surgery

value: multiplexed sample:control and ovariectomized mice

tag: hto

value: TotalSeqB_hashtag1:A0301 anti-mouse Hashtag 1 Antibody:Cells from OVX mice; TotalSeqB_hashtag2 = B0302 anti-mouse Hashtag 2 Antibody:Cells from Sham mice


title: LUADd57

description: Library name: Sample 57


title: LUADd52

description: Library name: Sample 52


title: LUADd58

description: Library name: Sample 58


title: DESynR AP-1 exp 1 lane 4 MULTI

description: MULTI-seq

value: T cells


title: LUADd48

description: Library name: Sample 48


title: osteal macrophage isolated from control mice2


title: Osteal macrophages OVX--Sham_scRNA_featurebarcode


title: LUADd47

description: Library name: Sample 47


title: LUADd46

description: Library name: Sample 46


title: osteal macrophage isolated from control mice1


title: LUADd45

description: Library name: Sample 45


title: osteal macrophage isolated from ovariectomized mice2

value: ovariectomized


title: osteal macrophage isolated from ovariectomized mice3


title: LUADd44

description: Library name: Sample 44


title: osteal macrophage isolated from ovariectomized mice1


title: LUADd43

description: Library name: Sample 43


title: Chondrocyte stimulated by IL-1β + SFRP5 recombinant 3

data_processing:
Data of 150 bp× 2 paired-end of 4-6G bases per sample (3 samples for each condition) was trimmed by fastp and mapped by alignment to the mouse mm10 reference genome using STAR. The reads were quantified using RSEM and the raw count data were subjected to Subio Platorm Plug-ins software (Tokyo, Japan)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: mouse chondrocyte

growth_protocol: Cartilages were harvested from mouse knee joint. After treatment of collagenase D solution overnight, chondrocytes were isolated and cultured in DMEM supplemented with 10% FBS and 25mg/l penicillin/streptomycin and 2mM L-glutamine.

extract_protocol:
Chondrocytes RNA was purified using TRIzol Reagent and RNA extraction kit (NucleoSpin®) according to the manufacturere's protocol
Libraries were generated from 1 µg of high-quality RNA using NEBNext Ultra II Directional RNA Library Prep Kit  .Data of 150 bp× 2 paired-end of 4-6G bases per sample (3 samples for each condition) was trimmed by fastp and mapped by alignment to the mouse mm10 reference genome using STAR. The reads were quantified using RSEM and the raw count data were subjected to Subio Platorm Plug-ins software .

treatment_protocol: Mice chondrocytes stimulated by IL-1β presence or absence of SFRP5 recombinant.

value: mouse chondrocyte

value: WT

value: IL-1Beta + SFRP5


title: LUADd41

description: Library name: Sample 41


title: Chondrocyte stimulated by IL-1β + SFRP5 recombinant 2


title: kidney, Control, long-term,1

value: Kidney


title: LUADd40

description: Library name: Sample 40


title: LUADd38

description: Library name: Sample 38


title: LUADd39

description: Library name: Sample 39


title: Chondrocyte stimulated by IL-1β alone 1


title: Control chondrocyte3

value: Control


title: Control chondrocyte1


title: LUADd34

description: Library name: Sample 34


title: LUADd33

description: Library name: Sample 33


title: LUADd31

description: Library name: Sample 31


title: LncRNA-NEAA1

city: Hangzhou

first: Yurong

last: Zhao

address: 886 Yuhangtang Road

institute: Zhejiang University

data_processing:
Sequence reads were trimmed for adaptor sequence using CLC genimic benchwork
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genimic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes FPKM values for each sample

source_name: Liver

extract_protocol:
Total RNA was harvested using Trizol (Takara)，and 1μg of RNA was used for the construction of sequencing libraries for lncRNA-seq.
RNA libraries for lncRNA-seq were prepared using NEB Next® Ultra™ RNA Library Prep Kit (New England Biolabs). following manufacturer's protocols.

value: Liver

value: Mouse primary hepatocytes

value: NEAA


title: LncRNA-NEAA2


title: LUADd32

description: Library name: Sample 32

value: lung

value: pN2 LUAD


title: Chondrocyte stimulated by IL-1β alone 3


title: LUADd36

description: Library name: Sample 36


title: LUADd37

description: Library name: Sample 37


title: Chondrocyte stimulated by IL-1β alone 2


title: Chondrocyte stimulated by IL-1β + SFRP5 recombinant 1


title: LUADd30

description: Library name: Sample 30


title: LUADd35

description: Library name: Sample 35


title: Control chondrocyte2


title: LncRNA-Ctrl2

value: control


title: LUADd42

description: Library name: Sample 42


title: LUADd27

description: Library name: Sample 27


title: LncRNA-Ctrl1


title: LUADd29

description: Library name: Sample 29


title: RIP-Pro-IP

extract_protocol:
The cultured cells were homogenized in polysome lysis buffer,and proteins from this supernatant were incubated with Magnetic Dynabeads pre-coated antibody. A portion of the supernatant was reserved as 'input'. The samples were washed and treated with DNase I and proteinase K to eliminate DNA and proteins. The immunoprecipitated RNA was harvested using Trizol (Takara). and 0.1μg of RNA was used for the construction of sequencing libraries for RIP-seq.
Immunoprecipitated RNA or Input was used for library construction with NEB Next® Ultra™ RNA Library Prep Kit (New England Biolabs) following manufacturer's protocols.

value: Proline


title: LUADd28

description: Library name: Sample 28


title: RIP-Pro-Input


title: RIP-Ctrl-IP

value: Ctrl


title: LUADd26

description: Library name: Sample 26


title: RIP-Ctrl-Input


title: DESynR AP-1 exp 2 lane 3 MULTI

description: MULTI-seq


title: LUADd23

description: Library name: Sample 23


title: M006D

city: Cambridge

first: Ramnik

last: Xavier

state: MA

address: 415 Main Street

institute: Broad Institute of MIT and Harvard

description: 10x Genomics

data_processing:
Single-cell RNA-seq data was processed using Cell Ranger (version 5.0.1) via the cumulus workflow
Assembly: mm10
Supplementary files format and content: mtx

source_name: Colon

extract_protocol:
Mouse colon tissue was dissected and straightened out onto a ruler. Four segments were cut for each colon to generate samples covering the proximal to distal axis of the colon (samples A, B, C, D). Segment A covering the proximal colon (C1) was generated by measuring 2 cm from the cecum. Segment D covering the distal colon (C3) was then generated by measuring 2 cm from the end of the colon. The remaining tissue was assigned as the middle colon (C2) and further segmented into two pieces B and C each accounting for ~1.5cm of tissue. To better discretize the regions C1, C2, and C3; 0.5cm of tissue was trimmed from the distal end of segment A, the proximal end of B, distal end of C, and proximal end of D. Each piece of tissue was then cut open longitudinally and content was washed away. Equal pieces of tissue were then generated from each segment utilizing a 3mm skin biopsy punch tool to generate 4 punches per segment which were then pooled to extract cells from in the subsequent steps.  Tissue was processed via an experiment specific, customized protocol involving a series of digestion steps where the first focussed on extracting high quality epithelial cells and the second on extracting and enriching for immune and stromal cells from the remaining tissue without the need for magnetic enrichment or cell sorting. First, tissue was subjected to mechanical disruption via stirring at 1,000rpm for 45 minutes using a small magnet and a magnetic stir plate in 5mL of RPMI 1640 media supplemented with 1% FBS and 2mM EDTA. Cells collected from this fraction constituted cells used to generate data on epithelial cells. Cells were washed with Advanced DMEM/F12 supplemented with 10% FBS. Cells were resuspended in 1 mL TripLE and incubated at 37 C for 10 minutes. After 10 minutes, cells were mixed by pipetting up and down 50 times to disrupt crypts and clumping to help create a single-cell suspension. Cells were washed in Advanced DMEM/F12 supplemented with 10% FBS and held on ice for mixing with the following fraction of cells. As the epithelial fraction was being processed as stated above, the flask containing the remaining tissue was subjected to a second epithelial strip to limit epithelial contamination in the final step. This was done in 5mL of RPMI 1640 media supplemented with 1% FBS and 5mM EDTA for 50 min at 1,600rpm. Media and cells from this fraction were decanted and discarded. Tissue was then digested via stirring at 1,600rpm for 60 minutes at 37 C in 5mL of RPMI 1640 media supplemented with 20% FBS and 0.5 mg/mL of Collagenase VIII (Sigma). Cells were then collected from this fraction to constitute the immune and stromal cells. These cells were then subjected to a 30% / 70% Percoll (Millipore Sigma) gradient to help deplete residual epithelial cells and enrich for immune and stromal cells by collecting the interphase post centrifugation. Cells from the epithelial fraction and immune/stromal fraction were then counted separately and mixed at approximately a 1:1 ratio to help capture more rare cell types in the immune/stromal fraction. 25,000 cells per sample were loaded per single channel following the 10x Chromium Single 3’ Gene Expression protocol (10x Genomics). Libraries were pooled and sequenced on a NovaSeq 6000 S4 300 cycles (Illumina).
Library was performed according to the manufacturer's instructions (single cell3' v3 protocol, 10x Genomics)

value: Colon

value: Epithelial/fibroblast/immune cells


title: M006C

description: 10x Genomics


title: LUADd20

description: Library name: Sample 20


title: M006B

description: 10x Genomics


title: LUADd19

description: Library name: Sample 19


title: LUADd17

description: Library name: Sample 17


title: M006A

description: 10x Genomics


title: M005C

description: 10x Genomics


title: LUADd25

description: Library name: Sample 25


title: M005B

description: 10x Genomics


title: LUADd24

description: Library name: Sample 24


title: M007C

description: 10x Genomics


title: LUADd22

description: Library name: Sample 22


title: M008C

description: 10x Genomics


title: M007B

description: 10x Genomics


title: M005A

description: 10x Genomics


title: LUADd14

description: Library name: Sample 14


title: M004D

description: 10x Genomics


title: LUADd13

description: Library name: Sample 13


title: LUADd21

description: Library name: Sample 21


title: M004C

description: 10x Genomics


title: LUADd18

description: Library name: Sample 18


title: LUADd11

description: Library name: Sample 11


title: M005D

description: 10x Genomics


title: LUADd16

description: Library name: Sample 16


title: LUADd15

description: Library name: Sample 15


title: LUADd10

description: Library name: Sample 10


title: M003B

description: 10x Genomics


title: M003A

description: 10x Genomics


title: LUADd12

description: Library name: Sample 12


title: LUADd6

description: Library name: Sample 6


title: M004B

description: 10x Genomics


title: M004A

description: 10x Genomics


title: M001D

description: 10x Genomics


title: PNUTSdTAG_NTD_UNT_rep3

description: Untreated control for total RNA Pol II (NTD) ChIP in PNUTS-dTAG mESCs

data_processing:
For cChIP-seq, paired-end reads were aligned to the concatenated mouse mm10 and spike-in genomes (mm10+hg19) using Bowtie2 with the ‘-no-mixed’ and ‘-no-discordant’ options. Reads that mapped more than once were discarded and PCR duplicates were removed using Sambamba.
Sequencing datasets were calibrated to the spike-in human genomes, as described previously (Fursova et al. 2019). For cChIP-seq, the number of mm10 reads were randomly downsampled to reflect the total number of hg19 reads in that sample. Furthermore, to adjust for any variation in cell mixing, each sample was adjusted using the percentage of dm6 reads relative to mm10 reads in the relevant input sample. After normalisation, read coverages for individual biological replicates were compared across regions of interest using the multiBamSummary and plotCorrelation functions from deepTools.
Assembly: mm10; hg19
Supplementary files format and content: Genome coverage tracks were generated using the pileup function from MACS2.
Supplementary files format and content: bigWig files showing the genome coverage for merged spike-in normalised biological replicates were generated using the pileup function from MACS2.

organism:
Homo sapiens
Mus musculus

growth_protocol: Mouse embryonic stem cells were grown in Dulbecco’s Modified Eagle Medium (Thermo Fisher Scientific) supplemented with  fetal bovine serum (FBS, 10% Sigma), 1x non-essential amino acids (Thermo Fisher Scientific), 2 mM L-glutamine (Thermo Fisher Scientific), 1x penicillin/streptomycin (Thermo Fisher Scientific), 0.5 mM beta-mercaptoethanol (Thermo Fisher Scientific), and 10 ng/ml leukaemia inhibitory factor (produced in-house). ESCs were grown on gelatinised plates at 37⁰C and 5% CO2.

extract_protocol:
5 x 10^7 ESCs were fixed with 1% formaldehyde (methanol-free, Thermo Fisher Scientific) for 10 min at 25⁰C. Fixation was quenched using glycine added to 125 mM. Cells were then pelleted at 1000xg for 5 min and washed with PBS. Cross-linked ESCs were mixed with 1 x 10^6 cross-linked HEK 293T(1% formaldehyde for 10 min). Chromatin was prepared by incubation in 1 ml FA-lysis buffer (50 mM HEPES pH 7.9, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.5% NP-40, 0.1% Na-deoxycholate, 0.1% SDS, 1x PIC, 10 mM NaF) on ice for 10 min. Chromatin was sonicated using a BioRuptor Pico sonicator (Diagenode) at 4⁰C for 23 cycles (30s on/off) to an average size of 0.5 kb. The sonicated material was pelleted at 20,000xg for 20 min, and the supernatant taken as sonicated chromatin. 300 μg chromatin was used per IP. Chromatin was diluted to 1 ml total volume per IP in FA-lysis buffer. An additional volume of diluted chromatin was taken to use as an input sample. Protein A agarose beads (Repligen) were blocked with 1 mg/ml BSA and 1 mg/ml yeast tRNA in 1x TE buffer at 4⁰C for 1 hr. Chromatin was pre-cleared with agarose beads (40 μl slurry beads per ChIP) at 4⁰C for 1 - 2 hr. The input sample was taken from the pre-cleared chromatin, and the remainder was immunoprecipitated overnight at 4⁰C with the respective antibody. Antibody-bound chromatin was precipitated for 3 hr at 4⁰C using 40 μl slurry of blocked Protein A agarose beads. Washes were carried out for 5 min each at 4⁰C, using ice-cold FA-lysis buffer, FA-lysis buffer with 500 mM NaCl, 1x DOC buffer (10 mM Tris HCl, pH 8, 250 mM LiCl, 1 mM EDTA , 0.5% NP-40, 0.5% Na-deoxycholate), and 2 washes with TE buffer. DNA was eluted in elution buffer (1% SDS and 0.1 M NaHCO3). Cross-links were reversed for ChIPs and inputs at 65⁰C overnight with 200 mM NaCl and 2 μl RNase A (Sigma). Samples were then incubated with 20 μg Proteinase K for 1 hr at 45⁰C. DNA for ChIPs and inputs was purified using a ChIP DNA Clean & Concentrator kit (Zymo Research). Purified DNA was analysed using ChIP-qPCR.
cChIP-seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina or NEBNext UltraExpress DNA Library Prep Kit for Illumina, following manufacturer’s guidelines. Samples were indexed using NEBNext Multiplex Oligos. The average size and concentration of all libraries were analysed using the 2100 Bioanalyzer High Sensitivity DNA Kit (Agilent) followed by quantification using Qubit HS DNA assay. Libraries were sequenced as 40 bp paired-end reads in at least biological triplicate on Illumina NextSeq 500 platform.

treatment_protocol: PNUTS-dTAG E14 mESCs were treated with 100 nM dTAG-13 (Tocris Bioscience) 2 hours to induce protein depletion.

value: E14 PNUTS-dTAG

value: Mouse embryonic stem cells

tag: spike-in cell_line

value: untreated

tag: treatment time

tag: antibody

value: anti-RBP1 NTD (Cell Signaling (D8L4Y))

tag: replicate


title: LUADd9

description: Library name: Sample 9


title: PNUTSdTAG_NTD_UNT_rep1


title: M002A

description: 10x Genomics

value: WT


title: LUADd8

description: Library name: Sample 8


title: PNUTSdTAG_NTD_UNT_rep2


title: M003C

description: 10x Genomics


title: LUADd5

description: Library name: Sample 5


title: M002D

description: 10x Genomics


title: LUADd4

description: Library name: Sample 4


title: LUADd1

description: Library name: Sample 1


title: M003D

description: 10x Genomics


title: PNUTSdTAG_NTD_dTAG_rep1

description: Total RNA Pol II (NTD) ChIP in PNUTS-dTAG mESCs treated with dTAG-13 to deplete PNUTS-dTAG

value: 100 nM dTAG13


title: E14-T3G-WT-Rescue-T7-rep2

description: PNUTS ChIP using T7 antibody in PNUTS WT rescue line

source_name: E14 TetON-3G PNUTS-dTAG WT rescue

treatment_protocol: PNUTS-dTAG E14 mESCs were treated with 100 nM dTAG-13 (Tocris Bioscience) 2 hours to induce protein depletion. For rescue experiments in the E14 TetON-3G PNUTS-dTAG ESC line, DOX induction of the rescue protein (WT, W401A or TND-M) was started 2 hours prior dTAG treatment.

value: E14 TetON-3G PNUTS-dTAG WT rescue

tag: additional treatment

value: 4h DOX

value: anti-T7 (D9E1X, Cell Signaling)


title: LUADd2

description: Library name: Sample 2


title: PNUTSdTAG_NTD_dTAG_rep2

tag: cell line


title: M001C

description: 10x Genomics


title: E14-T3G-WT-Rescue-T7-rep1


title: LUADd7

description: Library name: Sample 7


title: M001A

description: 10x Genomics


title: E14-T3G-WT-Rescue-NTD-rep2

description: Total RNA Pol II (NTD) ChIP in PNUTS WT rescue line


title: M002B

description: 10x Genomics


title: LUADd3

description: Library name: Sample 3


title: E14-T3G-WT-Rescue-NTD-rep1


title: SPF Colon DSS D30 1

description: Fresh frozen spatial transcriptome sequencing

data_processing:
Raw sequencing BCL files were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to mm10 genome to generate gene expression counts using Space Ranger's default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

extract_protocol:
Fresh frozen intestinal tissue from  WT SPF, GF, and FMT mice and DSS treated WT mice was swiss rolled and OCT embedded, and 10um frozen sections were cut with cryostat.
Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visium Spatial Gene Expression Slides & Reagent kit following the manufacturer's instruction.

value: intestinal tissue

value: SPF DSS


title: E14-T3G-W401A-Rescue-T7-rep1

description: PNUTS ChIP using T7 antibody in PNUTS W401A rescue line

source_name: E14 TetON-3G PNUTS-dTAG W401A rescue

value: E14 TetON-3G PNUTS-dTAG W401A rescue


title: E14-T3G-W401A-Rescue-NTD-rep1

description: Total RNA Pol II (NTD) ChIP in PNUTS W401A rescue line


title: FMT Colon 2

value: GF


title: E14-T3G-W401A-Rescue-T7-rep2


title: PNUTSdTAG_NTD_dTAG_rep3

source_name: E14 PNUTS-dTAG


title: M001B

description: 10x Genomics


title: GF Colon 1


title: E14-T3G-W401A-Rescue-NTD-rep2


title: PNUTSdTAG-SPT6-UNT-rep3

description: Untreated control for SPT6 ChIP in PNUTS-dTAG mESCs

value: anti-SPT6 (Cell Signaling (D6J9H))


title: SPF Colon DSS D73 1


title: 574

city: Moscow

first: Vasiliy

last: Akimov

email: VAkimov@cspfmba.ru, vasoakim@gmail.com

address: Pogodinskaya Street, 10, bld. 1

country: Russia

institute: Centre for Strategic Planning of FMBA of Russia

description:
Library name: 574
10x Genomics 3' v3

library_source: genomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger ATAC 1.2.0 pipeline (10x Genomics, Inc.)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PBMC

extract_protocol:
The research materials were samples of nuclei isolated from PBMC cell suspensions. Nuclei were isolated using the following method: cells were pelleted and resuspended in 100 μl of lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% Nonidet P40 Substitute, 0.01% Digitonin, 1% BSA, nuclease-free water), incubated for 5 min and added 1 ml of wash buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1% BSA, nuclease-free water) , the nuclei were precipitated for 5 min at 500 rcf at a temperature of 4°C, then resuspended in the prepared Diluted Nuclei Buffer. Nuclear quality control was carried out using a Countess II FL counter and cell viability analyzer and an EVOS M7000 microscope.
For sample preparation of libraries, nuclei were used that met the requirements of the protocol. The sample of nuclei under study was added to the prepared Transposition Mix, 10 μl per sample. The volume of the sample was calculated based on the concentration of nuclei using the formula (10000*1.53)/n = x, where n is the concentration of nuclei in the sample, x is the required volume of the sample. The mixture was incubated for 60 min at 37°C. Next, 60 μl of the prepared Master Mix was added to the samples, mixed using an automatic dispenser 10 times and applied to the chip to generate an emulsion. Afterwards, gel particles and oil were applied to the chip. The loaded chip was processed at The Chromium Controller station. The resulting emulsion was amplified. After amplification, the emulsion was purified: 125 μl of Recovery Agent was added to each sample, the tubes with the mixture were carefully inverted 10 times, then briefly centrifuged and 130 μl of the lower pink phase was collected; This was followed by cleaning with magnetic Dynabeads MyOne SILANE and then cleaning with Beckman Coulter SPRIselect Reagent magnetic particles. After purifications, indexing PCR was performed. For it, we used Single Index Kit N Set A for one-way indexing. To 40 μl of sample, 57.5 μl of the prepared Sample Index PCR Mix and 2.5 μl of index were added. The number of cycles in the indexing PCR was set to 9. After indexing, the samples were subjected to double purification on magnetic particles and the quality of the resulting libraries was controlled using a Tape Station 4200 with a High Sensitivity D1000 kit, an Agilent Bioanalyzer 2100 with a High Sensitivity DNA chip kit, and a Qubit 4 fluorimeter. Ready-made libraries sequenced to a coverage of >250 million reads per sample.

value: PBMC

tag: Sex

value: female

tag: age

tag: disease state

value: Severe/Critical


title: 564

description:
Library name: 564
10x Genomics 3' v3

tag: tissue

value: male


title: 68

description:
Library name: 68
10x Genomics 3' v3

value: Mild/Moderate


title: 562

description:
Library name: 562
10x Genomics 3' v3


title: E14-T3G-TND-M-Rescue-T7-rep2

description: PNUTS ChIP using T7 antibody in PNUTS TND-M rescue line

source_name: E14 TetON-3G PNUTS-dTAG TND-M rescue

value: E14 TetON-3G PNUTS-dTAG TND-M rescue

value: Mouse embryonic stem cells

tag: treatment


title: 563

description:
Library name: 563
10x Genomics 3' v3


title: PNUTSdTAG-SPT6-UNT-rep1

value: E14 PNUTS-dTAG

value: untreated


title: E14-T3G-TND-M-Rescue-T7-rep1

value: 100 nM dTAG13


title: GF Jejunum 2 1

source_name: Jejunum

value: Jejunum

tag: genotype

value: WT


title: E14-T3G-TND-M-Rescue-NTD-rep2

description: Total RNA Pol II (NTD) ChIP in PNUTS TND-M rescue line

value: 4h DOX

value: anti-RBP1 NTD (Cell Signaling (D8L4Y))


title: PNUTSdTAG_SPT5_UNT_rep3

description: Untreated control for SPT5 ChIP in PNUTS-dTAG mESCs

value: anti-SPT5 (Proteintech (165111AP))


title: PNUTSdTAG_SPT5_UNT_rep1


title: E14-T3G-TND-M-Rescue-NTD-rep1


title: 417

description:
Library name: 417
10x Genomics 3' v3


title: 67

description:
Library name: 67
10x Genomics 3' v3


title: GF Ileum 3

source_name: Ileum

value: Ileum

value: intestinal tissue

value: GF


title: 419

description:
Library name: 419
10x Genomics 3' v3

value: PBMC

value: female


title: 418

description:
Library name: 418
10x Genomics 3' v3


title: PNUTSdTAG-SPT6-dTAG-rep3

description: SPT6 ChIP in PNUTS-dTAG mESCs treated with dTAG-13 to deplete PNUTS-dTAG

value: anti-SPT6 (Cell Signaling (D6J9H))


title: GF Jejunum 1 2


title: PNUTSdTAG_SPT5_dTAG_rep3

description: SPT5 ChIP in PNUTS-dTAG mESCs treated with dTAG-13 to deplete PNUTS-dTAG


title: GF Duodenum 1

source_name: Duodenum

value: Duodenum


title: PNUTSdTAG-SPT6-dTAG-rep2


title: PNUTSdTAG_SPT5_dTAG_rep2


title: 414

description:
Library name: 414
10x Genomics 3' v3

value: male

value: Mild/Moderate


title: PNUTSdTAG_S5P_UNT_rep2

description: Untreated control for Ser5P RNA Pol II ChIP in PNUTS-dTAG mESCs

value: E14 PNUTS-dTAG

value: Mouse embryonic stem cells

value: anti-RNAPII S5P (Cell Signaling (D9N5I))


title: FMT Duodenum 2

value: FMT


title: PNUTSdTAG-SPT6-dTAG-rep1

value: 100 nM dTAG13


title: PNUTSdTAG_SPT5_UNT_rep2

value: untreated


title: 416

description:
Library name: 416
10x Genomics 3' v3


title: PNUTSdTAG-SPT6-UNT-rep2


title: GF Ileum 1

value: WT


title: PNUTSdTAG_SPT5_dTAG_rep1

value: anti-SPT5 (Proteintech (165111AP))


title: 415

description:
Library name: 415
10x Genomics 3' v3


title: PNUTSdTAG_S5P_UNT_rep3


title: FMT Ileum 2

value: Ileum


title: PNUTSdTAG_S5P_dTAG_rep2

description: Ser5P RNA Pol II ChIP in PNUTS-dTAG mESCs treated with dTAG-13 to deplete PNUTS-dTAG


title: 245

description:
Library name: 245
10x Genomics 3' v3

value: Reconvalescence


title: PNUTSdTAG_S5P_UNT_rep1


title: PNUTSdTAG_S2P_UNT_rep3

description: Untreated control for Ser2P RNA Pol II ChIP in PNUTS-dTAG mESCs

value: anti-RNAPII S2P (Cell Signaling (E1Z3G))


title: 215

description:
Library name: 215
10x Genomics 3' v3

value: PBMC

value: Healthy


title: 218

description:
Library name: 218
10x Genomics 3' v3

value: female


title: PNUTSdTAG_S2P_UNT_rep2


title: PNUTSdTAG_S5P_dTAG_rep3


title: GF Jejunum 1 1

value: Jejunum

value: intestinal tissue

value: GF


title: 212

description:
Library name: 212
10x Genomics 3' v3


title: 413

description:
Library name: 413
10x Genomics 3' v3

value: Mild/Moderate


title: FMT Jejunum 1 2


title: PNUTSdTAG_S2P_UNT_rep1

value: E14 PNUTS-dTAG

value: Mouse embryonic stem cells


title: PNUTSdTAG_S5P_dTAG_rep1

value: anti-RNAPII S5P (Cell Signaling (D9N5I))


title: FMT Duodenum 1

value: Duodenum

value: FMT


title: PNUTSdTAG_S2P_dTAG_rep3

description: Ser2P RNA Pol II ChIP in PNUTS-dTAG mESCs treated with dTAG-13 to deplete PNUTS-dTAG

value: 100 nM dTAG13


title: PNUTSdTAG_S2P_dTAG_rep2


title: PNUTSdTAG_S2P_dTAG_rep1


title: 210

description:
Library name: 210
10x Genomics 3' v3

value: male


title: FMT Ileum 1

value: Ileum

value: WT


title: PNUTSdTAG_PNUTS-T7_UNT_rep2

description: PNUTS ChIP using T7 antibody in untreated PNUTS-dTAG mESCs

value: HEK293T T7-Rbp5

value: untreated

value: anti-T7 (D9E1X, Cell Signaling)


title: PNUTSdTAG_PNUTS-T7_dTAG_rep3

description: PNUTS ChIP using T7 antibody in PNUTS-dTAG mESCs treated with dTAG-13 to deplete PNUTS-dTAG

value: HEK293T T7-Rbp3


title: PNUTSdTAG_PNUTS-T7_UNT_rep3

value: HEK293T T7-Rbp6


title: FMT Jejunum 1 1

value: Jejunum

value: intestinal tissue


title: 208

description:
Library name: 208
10x Genomics 3' v3

value: PBMC

value: Reconvalescence


title: FMT Jejunum 2 2


title: PNUTSdTAG_PNUTS-T7_dTAG_rep2

value: E14 PNUTS-dTAG

value: Mouse embryonic stem cells

value: HEK293T T7-Rbp2


title: PNUTSdTAG_PNUTS-T7_dTAG_rep1

value: HEK293T T7-Rbp1


title: 207

description:
Library name: 207
10x Genomics 3' v3

value: Healthy


title: PNUTSdTAG_PNUTS-T7_UNT_rep1

value: HEK293T T7-Rbp4


title: SPF Colon Dark 1

value: Colon

value: SPF dark


title: 170

description:
Library name: 170
10x Genomics 3' v3

value: female


title: PNUTSdTAG_PAF1_UNT_rep3

description: Untreated control for PAF1 ChIP in PNUTS-dTAG mESCs

value: untreated

value: anti-PAF1 (Bethyl (A300-172A))


title: 172

description:
Library name: 172
10x Genomics 3' v3

value: male


title: PNUTSdTAG_PAF1_dTAG_rep2

description: PAF1 ChIP in PNUTS-dTAG mESCs treated with dTAG-13 to deplete PNUTS-dTAG

value: 100 nM dTAG13


title: PNUTSdTAG_PAF1_UNT_rep1


title: FMT Colon 1

description: Fresh frozen spatial transcriptome sequencing

value: WT

value: FMT


title: PNUTSdTAG_PAF1_dTAG_rep3


title: 166

description:
Library name: 166
10x Genomics 3' v3

value: PBMC


title: 167

description:
Library name: 167
10x Genomics 3' v3

value: Reconvalescence


title: PNUTSdTAG_PAF1_UNT_rep2

value: E14 PNUTS-dTAG


title: PNUTSdTAG_PAF1_dTAG_rep1

value: Mouse embryonic stem cells


title: GF Colon 3

value: intestinal tissue

value: GF


title: FMT Jejunum 2 1

value: Jejunum


title: GF Colon Dark 1

value: GF dark


title: PNUTSdTAG_NELF_UNT_rep4

description: Untreated control for NELF-B ChIP in PNUTS-dTAG mESCs

value: anti-NELF-B/COBRA1 (Cell Signaling (D6K9A))


title: PNUTSdTAG_NELF_dTAG_rep4

description: NELF-B ChIP in PNUTS-dTAG mESCs treated with dTAG-13 to deplete PNUTS-dTAG


title: 165

description:
Library name: 165
10x Genomics 3' v3

value: Healthy


title: PNUTSdTAG_NELF_UNT_rep3


title: 151

description:
Library name: 151
10x Genomics 3' v3

value: Mild/Moderate


title: SPF Colon 3

value: Colon

value: SPF


title: PNUTSdTAG_NELF_dTAG_rep3


title: SPF Colon 2


title: PNUTSdTAG_NELF_UNT_rep2

value: untreated


title: 148

description:
Library name: 148
10x Genomics 3' v3

value: male


title: SPF Colon 1

value: WT


title: PNUTSdTAG_NELF_dTAG_rep2

value: 100 nM dTAG13


title: 147

description:
Library name: 147
10x Genomics 3' v3

value: PBMC


title: PNUTSdTAG_NELF_dTAG_rep1


title: PNUTSdTAG_LEO1_UNT_rep3

description: Untreated control for LEO1 ChIP in PNUTS-dTAG mESCs

value: anti-LEO1 (Bethyl (A300-175A))


title: GF Ileum 2

value: Ileum


title: 144

description:
Library name: 144
10x Genomics 3' v3


title: PNUTSdTAG_LEO1_UNT_rep2

value: E14 PNUTS-dTAG

value: Mouse embryonic stem cells


title: PNUTSdTAG_LEO1_UNT_rep1


title: PNUTSdTAG_LEO1_dTAG_rep3

description: LEO1 ChIP in PNUTS-dTAG mESCs treated with dTAG-13 to deplete PNUTS-dTAG


title: GF Colon 2

value: intestinal tissue

value: GF


title: 134

description:
Library name: 134
10x Genomics 3' v3


title: SPF Ileum 3


title: 115

description:
Library name: 115
10x Genomics 3' v3

value: female


title: PNUTSdTAG_LEO1_dTAG_rep1


title: SPF Ileum 2


title: PNUTSdTAG_LEO1_dTAG_rep2


title: PNUTSdTAG_CDK9_UNT_rep4

description: Untreated control for CDK9 ChIP in PNUTS-dTAG mESCs

value: anti-CDK9 (Abcam (ab239364))


title: PNUTSdTAG_NELF_UNT_rep1

value: anti-NELF-B/COBRA1 (Cell Signaling (D6K9A))


title: SPF Ileum 1


title: 114

description:
Library name: 114
10x Genomics 3' v3

value: Healthy


title: PNUTSdTAG_CDK9_UNT_rep1


title: PNUTSdTAG_CDK9_dTAG_rep3

description: CDK9 ChIP in PNUTS-dTAG mESCs treated with dTAG-13 to deplete PNUTS-dTAG


title: PNUTSdTAG_CDK9_dTAG_rep4


title: GF Jejunum 2 3

value: Jejunum


title: 111

description:
Library name: 111
10x Genomics 3' v3


title: SPF Jejunum 2 3

value: SPF


title: PNUTSdTAG_CDK9_dTAG_rep2


title: GF Jejunum 2 2


title: PNUTSdTAG_CDK9_dTAG_rep1


title: PNUTSdTAG_CDK9_UNT_rep2

value: untreated


title: 113

description:
Library name: 113
10x Genomics 3' v3

value: male


title: 109

description:
Library name: 109
10x Genomics 3' v3


title: SPF Jejunum 2 2

value: WT


title: PNUTSdTAG-BRD4-UNT-rep3

description: Untreated control for BRD4 ChIP in PNUTS-dTAG mESCs

value: anti-BRD4 (Cell Signaling (E2A7X))


title: 110

description:
Library name: 110
10x Genomics 3' v3

value: PBMC


title: PNUTSdTAG-BRD4-UNT-rep1


title: 108

description:
Library name: 108
10x Genomics 3' v3

value: Reconvalescence


title: SPF Jejunum 2 1


title: PNUTSdTAG-BRD4-dTAG-rep3

description: BRD4 ChIP in PNUTS-dTAG mESCs treated with dTAG-13 to deplete PNUTS-dTAG

value: 100 nM dTAG13


title: PNUTSdTAG-BRD4-dTAG-rep1

value: E14 PNUTS-dTAG


title: HFDPC, EC-CM_2

city: Kobe

first: Ken-ichi

last: Mizutani

state: Hyogo

address: 1-1-3 Minatojima, Chuo-ku

institute: Kobe Gakuin University

description: Library name: Sample 4

data_processing:
DRAGEN with the human reference genome.
Assembly: GENCODE/GRCh38 [hg38]
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

source_name: Dermal papilla cells

extract_protocol:
We used the Direct-Zol RNA miniprep kit (Zymo Research) and the Agilent 2200 TapeStation to extract total RNA and determine its quality, respectively. 100ng of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were prepared using the SMART-Seq v4 Ultra Low Input Kit for Sequencing (TaKaRa).

value: Dermal papilla cells

value: conditioned medium (CM) treatment


title: SPF Jejunum 1 3

value: intestinal tissue


title: PNUTSdTAG_CDK9_UNT_rep3

value: Mouse embryonic stem cells


title: HFDPC, EC-CM_1

description: Library name: Sample 3


title: PNUTSdTAG-BRD4-dTAG-rep2


title: PNUTSdTAG-INT11-UNT-rep3

description: Untreated control for INTS11 ChIP in PNUTS-dTAG mESCs

value: anti-INTS11 (Bethyl (A301-274A))


title: PNUTSdTAG-INT11-dTAG-rep3

description: INTS11 ChIP in PNUTS-dTAG mESCs treated with dTAG-13 to deplete PNUTS-dTAG


title: GF Jejunum 1 3

value: GF


title: SPF Jejunum 1 2


title: HFDPC, control_2

description: Library name: Sample 2

value: control


title: PNUTSdTAG-TFIIS-dTAG-rep3

description: TFIIS ChIP in PNUTS-dTAG mESCs treated with dTAG-13 to deplete PNUTS-dTAG

value: anti-TFIIS (TCEA1) (Abcam (ab185947))


title: PNUTSdTAG-INT11-UNT-rep2


title: PNUTSdTAG-INT11-dTAG-rep1


title: PNUTSdTAG-TFIIS-UNT-rep3

description: Untreated control for TFIIS ChIP in PNUTS-dTAG mESCs


title: SPF Jejunum 1 1

value: Jejunum

value: SPF


title: PNUTSdTAG-INT11-UNT-rep1

value: untreated


title: PNUTSdTAG-TFIIS-dTAG-rep2


title: ZCF4

description: Library name: Sample 69

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp.
We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Homo sapiens GRCh38. The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts
StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

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

value: lung

tag: group

value: ZCF


title: ZCF5

description: Library name: Sample 70


title: PNUTSdTAG-BRD4-UNT-rep2

tag: cell type

value: anti-BRD4 (Cell Signaling (E2A7X))


title: PNUTSdTAG-TFIIS-dTAG-rep1


title: PNUTSdTAG-TFIIS-UNT-rep1


title: SPF Duodenum 3

value: Duodenum

value: WT


title: ZCF2

description: Library name: Sample 67


title: SPF Duodenum 2


title: GF Duodenum 2


title: ZCF1

description: Library name: Sample 66


title: ZCF3

description: Library name: Sample 68


title: SPF Duodenum 1


title: PNUTSdTAG-TFIIS-UNT-rep2

value: E14 PNUTS-dTAG


title: YWA20

description: Library name: Sample 65

value: YWA


title: 5523-TH-7

city: Nashville

first: Lance

last: Riley

state: TN

address: 9445 MRB4, 2213 Garland Ave

department: Biomedical Engineering

institute: Vanderbilt University

data_processing:
Sequenced reads were mapped and gene counts were quantified using Illumina DRAGEN RNA pipeline v. 3.6.3
Gene count data was compiled using tximport
Differential gene expression was determined using DESeq2 using Cook's outliers to filter out low expression and alpha = 0.01 to for significance.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw counts for every gene and every sample.
Supplementary_files_format_and_content: Matrix table with DEseq2 counts for every gene and every sample.

growth_protocol: CDH11+/+ and CDH11-/- mice were injured via uninephrectomy with angiotensin II (Unx/AngII) infusion. One kidney was removed from each mouse, then had osmotic pumps implanted to secrete AngII at a rate of 800 ng/kg/min, and mice were sacrificed 4 weeks after the surgery.

extract_protocol:
Trizol reagent and kidney tissue were added to Lysing Matrix D tubes (MPBio), then mechanically homogenized. RNA was extracted with a Zymo Direct-Zol Miniprep kit using the standard protocol.
Libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kits according to standard protocols.

treatment_protocol: Kidneys were dissected from adult male mice and flash frozen. Tissue was untreated prior to RNA extraction.

value: Kidney

tag: timepoint

value: 4 weeks post-injury

tag: strain background

value: Mixed:129S1/Sv x C57BL/6


title: 5523-TH-8


title: 5523-TH-6


title: WT_3

city: 上海

first: 润华

last: 杜

address: 上海市浦东新区

institute: 上海药物所

data_processing:
RNA-seq reads were mapped to reference genome of Illumina iGenomes UCSC hg38 using TopHat version 2.1.0.
Mapped reads were summarized for each gene using featureCounts version 1.5.0.
Differential expression analysis was implemented using edgeR version 3.16.5.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using edgeR version 3.16.5.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include RPKM values for each Sample

source_name: brain

extract_protocol:
the total RNA of these two groups with 3 biological replicates was extracted by RNeasy Plus Kits and used for construction of the library.
The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification using QIAseq Stranded RNA Library Kit by Novogene company

value: brain

value: human glioblastoma

value: shSUCLG1 rSUCLG1 WT


title: PNUTSdTAG-INT11-dTAG-rep2

value: Mouse embryonic stem cells

value: 100 nM dTAG13

value: anti-INTS11 (Bethyl (A301-274A))


title: YWA19

description: Library name: Sample 64


title: HFDPC, control_1

description: Library name: Sample 1

value: Dermal papilla cells

value: control


title: GF Duodenum 3

value: intestinal tissue

value: GF


title: YWA18

description: Library name: Sample 63

value: lung


title: WT_1


title: 5523-TH-5


title: YWA17

description: Library name: Sample 62


title: K192R_5

value: shSUCLG1 rSUCLG1 K192R


title: 5523-TH-4


title: K192R_4


title: YWA16

description: Library name: Sample 61


title: 5523-TH-3


title: MM_6

city: London

first: Richard

middle: James

last: Mitter

state: LONDON

address: 1 Midland Road

department: Bioinformatics & Biostatistics

institute: The Francis Crick Institute

data_processing:
Reads were trimmed to remove Illumina adapter sequences using cutadapt v1.18 before separate alignment to the Homo sapiens GRCh38 (target) and S. cerevisiae sacCer3 (spike-in) genomes using the STAR v2.5.2a RNA-seq aligner (Dobin et al, 2013) with the “-quantMode GeneCounts” option to quantify gene level abundance against Ensembl release 86 transcript annotations.
The yeast gene-level counts were used to calculate per-sample scale-factors necessary for the downstream normalisation of the human data.  Counts were imported into R and passed to the estimateSizeFactors function of the Bioconductor package DESeq2 (Love at al, 2014).
Human genome normalised coverage was calculated for each sample in a strand-specific manner using BEDTools v2.27.1 genomecov function, providing the reciprocal of the yeast derived scale factor via the “-scale” option, (Quinlan et al, 2010). The resulting coverage matrix was then converted to bigwig format at single-bp resolution.
Assembly: GRCh38
Supplementary files format and content: Per-sample, strand-specific, spike-in normalised coverage bigwig files.

source_name: HEK293 FlpIn TREx

growth_protocol: Standard culture conditions for HEK293 FlpIn Trex as recommended by manufacturer

extract_protocol: TTchem-seq (Gregersen et al., 2020)

treatment_protocol: Cells were either left untreated or treated with 15j/m3 UVC and allowed to grow for the indicated time.

value: HEK293 FlpIn TREx

value: CSB KO

value: 2h UV 15J


title: YWA13

description: Library name: Sample 58

source_name: lung

value: YWA


title: MM_8

value: STK19 KO B3

value: 5h UV 15J


title: MM_53

value: 36h UV 15J


title: MM_9


title: YWA12

description: Library name: Sample 57


title: MM_50

value: 20h UV 15J


title: MM_7

value: Parental


title: MM_54


title: YWA14

description: Library name: Sample 59


title: MM_52


title: YWA11

description: Library name: Sample 56


title: 5628-TH-6

growth_protocol: CDH11+/+ and CDH11-/- mice were injured using an aristolochic acid nephropathy (AAN) model. Mice were injected with 3 mg/kg aristolochic acid every day for 5 days and then sacrificed 2 weeks after the final injection.

value: Kidney

value: 2 weeks post-injury

value: Mixed:129S1/Sv x C57BL/6


title: WT_2

value: brain

value: human glioblastoma

value: shSUCLG1 rSUCLG1 WT


title: MM_5


title: 5628-TH-5


title: 5628-TH-7


title: YWA10

description: Library name: Sample 55

value: lung


title: K192R_6

value: shSUCLG1 rSUCLG1 K192R


title: MM_48

value: HEK293 FlpIn TREx

value: 12h UV 15J


title: MM_49


title: YWA15

description: Library name: Sample 60


title: YWA9

description: Library name: Sample 54


title: MM_47


title: MM_46


title: 5523-TH-2

value: 4 weeks post-injury


title: 5628-TH-8


title: 5628-TH-3


title: MM_51

value: CSB KO


title: YWA8

description: Library name: Sample 53

value: YWA


title: 5628-TH-2


title: MM_45

value: 5h UV 15J


title: 5628-TH-1


title: YWA7

description: Library name: Sample 52


title: MM_42

value: 2h UV 15J


title: MM_43


title: MM_44

value: STK19 KO B3


title: 5628-TH-4


title: MM_41


title: YWA5

description: Library name: Sample 50


title: MM_39

value: untreated


title: YWA6

description: Library name: Sample 51


title: MM_38


title: MM_40

value: Parental


title: MM_4


title: MM_36

value: 36h UV 15J


title: P10KOM_6_514

city: Worcester

first: Gregory

last: Pazour

address: 373 Plantation St.

department: Program in Molecular Medicine

institute: UMass Chan School of Medicine

data_processing:
The sequences were demultiplexed and underwent bar code and adapter sequence removal using the SOAPnuke software (Chen et al 2018). The steps for demultiplexing, bar code removal and adapter removal were carried out by BGI.
Omiras (Müller et al 2013) pipeline:
Mirdeep2 package (Friedländer MR et al 2012) for mapping processed reads, quanitfying reads, and predicting secondary structure
Deseq for differential miRNA expression
Assembly: mm10
Supplementary files format and content: "p06_omiras.xlsx" and "p10_omiras.xlsx" contain normalized and raw read counts for all samples for all identified small RNAs and differential expression analysis. Normalization by DESeq median of ratios.
Supplementary files format and content: Individual sample files "Title.xlsx" contain raw counts, normalized by # of mapping loci, molecule type, most prominent tag sequence, raw count and number of loci.

source_name: whole kidney

growth_protocol: C5/BL6 background. Experimental "KO" were CAGG-CreER; Pkd2null/flox. Control "WT" were CAGG-CreER; Pkd2+/flox and Cre-negative; Pkd2null/flox.

extract_protocol:
Total RNA was prepared using the Qiagen RNeasy minikits, with on-column DNA digestion. Samples were submitted to BGI for library preparation.
RNA sequencing libraries were prepared by BGI according to manufacturer's protocols.
Eukaryotic small RNA RNA sequencing

treatment_protocol:
All animals underwent intraperitoneal injection of tamoxifen in canola oil on postndatal day 2.
Mice were sacrificed and bilateral kidneys collected for RNA extraction at the designated time points.

value: whole kidney

tag: postnatal age

value: Day 10

value: Pkd2 KO

value: M


title: MM_37


title: YWA3

description: Library name: Sample 48

value: lung


title: MM_35


title: YWA2

description: Library name: Sample 47


title: MM_33

value: 20h UV 15J


title: P10KOM_8_513


title: P10KOM_1_506


title: MM_32

value: HEK293 FlpIn TREx


title: YWA4

description: Library name: Sample 49


title: YWA1

description: Library name: Sample 46


title: P10KOM_2_535


title: MM_31


title: WJR17

description: Library name: Sample 45

value: WJR


title: MM_3


title: P10KOF_9_511

value: F


title: MM_30

value: CSB KO

value: 12h UV 15J


title: P10KOF_10_536


title: MM_29


title: MM_28


title: WJR16

description: Library name: Sample 44


title: P10KOM_3_515


title: MM_27

value: 5h UV 15J


title: MM_26


title: WJR15

description: Library name: Sample 43


title: P10KOF_7_534


title: P10KOF_5_521


title: MM_34


title: MM_25


title: WJR14

description: Library name: Sample 42


title: MM_24

value: 2h UV 15J


title: MM_23

value: STK19 KO B3


title: P10KOF_4_512


title: P06KOM_14_504

value: Day 6


title: MM_22

value: Parental


title: MM_21

value: untreated


title: WJR13

description: Library name: Sample 41


title: WJR12

description: Library name: Sample 40


title: MM_20


title: MM_2


title: P06KOM_13_540

value: whole kidney


title: MM_19


title: WJR10

description: Library name: Sample 38


title: P06KOM_12_505


title: P06KOM_10_517


title: MM_17

value: 36h UV 15J


title: MM_16


title: WJR9

description: Library name: Sample 37


title: P06KOM_8_522

value: Pkd2 KO


title: MM_15


title: WJR8

description: Library name: Sample 36


title: MM_14


title: MM_13


title: MM_12


title: P06KOM_4_523

value: M


title: WJR7

description: Library name: Sample 35

value: lung


title: MM_11


title: P06KOM_1_527


title: MM_18


title: MM_10


title: MM_1


title: WJR6

description: Library name: Sample 34


title: WJR11

description: Library name: Sample 39


title: WJR4

description: Library name: Sample 32


title: P06KOF_9_530


title: Tumor_only, Cell_line_C, timepoint_2, EXP_9.7, rep_1

city: Vienna

first: CCRI

last: BiCU

address: Zimmermannpl. 10

institute: St. Anna Children's Cancer Research Institute

data_processing:
Reads were mapped to a genome assembly using STAR (v2.7.10a).
Reads counting was performed with the help of Salmon (v1.8.0) or GenomicAlignments (v1.36.0)
Assembly: GRCm38/GRCh38
Supplementary files format and content: quant.sf files contain counted reads
Supplementary files format and content: tsv files contain counted reads performed by GenomicAlignments package

source_name: C

extract_protocol:
Extraction was done with the AllPrep DNA/RNA Mini Kit (Qiagen) and samples were treated with DNase I (Thermo Fisher Scientific) or the Monarch Total RNA Miniprep Kit (New England Biolabs)
QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina (Lexogen)

value: C

tag: time

value: Day 16

tag: time point

tag: genome assembly_used


title: Tumor_only, Cell_line_B, timepoint_2, EXP_9.7, rep_1

source_name: B

value: B


title: P06KOF_11_525

value: F


title: Tumor_only, Cell_line_D, timepoint_2, EXP_9.7, rep_1

source_name: D

value: D


title: WJR5

description: Library name: Sample 33

value: WJR


title: Tumor_only, Cell_line_A, timepoint_2, EXP_9.7, rep_1

source_name: A

value: A


title: WJR3

description: Library name: Sample 31


title: Tumor_plus_NK, Cell_line_D, timepoint_2, EXP_9.7, rep_3


title: P06KOF_3_501


title: Tumor_plus_NK, Cell_line_B, timepoint_2, EXP_9.7, rep_3


title: Tumor_plus_NK, Cell_line_D, timepoint_2, EXP_9.7, rep_2


title: Tumor_plus_NK, Cell_line_D, timepoint_2, EXP_9.7, rep_1


title: Tumor_plus_NK, Cell_line_C, timepoint_2, EXP_9.7, rep_3


title: P06KOF_5_502


title: Tumor_plus_NK, Cell_line_C, timepoint_2, EXP_9.7, rep_2


title: WJR1

description: Library name: Sample 29


title: P06KOF_7_546


title: Tumor_plus_NK, Cell_line_A, timepoint_2, EXP_9.7, rep_3


title: P10WTM_8_507

value: Day 10

value: WT


title: Tumor_plus_NK, Cell_line_A, timepoint_2, EXP_9.7, rep_2


title: JRX23

description: Library name: Sample 28

value: JRX


title: P10WTM_7_508


title: WJR2

description: Library name: Sample 30


title: Tumor_plus_NK, Cell_line_B, timepoint_2, EXP_9.7, rep_2


title: JRX20

description: Library name: Sample 25


title: Tumor_plus_NK, Cell_line_D, timepoint_1, EXP_9.7, rep_3

value: Day 6


title: JRX22

description: Library name: Sample 27


title: JRX19

description: Library name: Sample 24


title: Tumor_plus_NK, Cell_line_C, timepoint_2, EXP_9.7, rep_1


title: Tumor_plus_NK, Cell_line_B, timepoint_2, EXP_9.7, rep_1


title: Tumor_plus_NK, Cell_line_A, timepoint_2, EXP_9.7, rep_1


title: P10WTM_4_520


title: P06KOF_6_503


title: Tumor_plus_NK, Cell_line_D, timepoint_1, EXP_9.7, rep_2


title: P10WTF_9_509


title: Tumor_plus_NK, Cell_line_C, timepoint_1, EXP_9.7, rep_2


title: JRX18

description: Library name: Sample 23


title: Tumor_plus_NK, Cell_line_C, timepoint_1, EXP_9.7, rep_3


title: P06KOF_2_547


title: JRX21

description: Library name: Sample 26


title: P10WTF_5_519


title: Tumor_plus_NK, Cell_line_B, timepoint_1, EXP_9.7, rep_2


title: P10WTF_6_542


title: Tumor_plus_NK, Cell_line_B, timepoint_1, EXP_9.7, rep_3


title: JRX16

description: Library name: Sample 21


title: JRX17

description: Library name: Sample 22


title: JRX15

description: Library name: Sample 20


title: P10WTF_2_538


title: Tumor_plus_NK, Cell_line_B, timepoint_1, EXP_9.7, rep_1


title: JRX14

description: Library name: Sample 19


title: Tumor_plus_NK, Cell_line_D, timepoint_1, EXP_9.7, rep_1


title: Tumor_plus_NK, Cell_line_A, timepoint_1, EXP_9.7, rep_1


title: Tumor_plus_NK, Cell_line_A, timepoint_1, EXP_9.7, rep_3


title: P10WTF_1_510


title: JRX13

description: Library name: Sample 18


title: P10WTF_3_541


title: Tumor_only, Cell_line_D, timepoint_1, EXP_9.7, rep_3


title: JRX12

description: Library name: Sample 17


title: Tumor_only, Cell_line_D, timepoint_1, EXP_9.7, rep_1


title: Tumor_only, Cell_line_B, timepoint_1, EXP_9.7, rep_3


title: Tumor_only, Cell_line_C, timepoint_1, EXP_9.7, rep_3


title: Tumor_only, Cell_line_C, timepoint_1, EXP_9.7, rep_2


title: P06WTM_11_506


title: P06WTM_14_531


title: Tumor_plus_NK, Cell_line_C, timepoint_1, EXP_9.7, rep_1


title: Tumor_only, Cell_line_B, timepoint_1, EXP_9.7, rep_2


title: JRX10

description: Library name: Sample 15


title: Tumor_plus_NK, Cell_line_A, timepoint_1, EXP_9.7, rep_2


title: P06WTM_13_526


title: Tumor_only, Cell_line_B, timepoint_1, EXP_9.7, rep_1


title: JRX11

description: Library name: Sample 16


title: Tumor_only, Cell_line_D, timepoint_1, EXP_9.7, rep_2


title: Tumor_only, Cell_line_A, timepoint_1, EXP_9.7, rep_2


title: Tumor_only, Cell_line_A, timepoint_1, EXP_9.7, rep_1


title: P06WTM_10_524


title: Tumor_only, Cell_line_A, timepoint_1, EXP_9.7, rep_3


title: JRX9

description: Library name: Sample 14


title: Tumor_only, Cell_line_C, timepoint_1, EXP_9.7, rep_1


title: P06WTM_5_528


title: P06WTM_9_518


title: Tumor_only, Cell_line_B, timepoint_2, EXP_9.6, rep_1

value: Day 14


title: Tumor_only, Cell_line_C, timepoint_2, EXP_9.6, rep_1


title: JRX7

description: Library name: Sample 12


title: Tumor_only, Cell_line_A, timepoint_2, EXP_9.6, rep_1


title: P06WTM_1_532

value: whole kidney


title: Tumor_plus_NK, Cell_line_D, timepoint_2, EXP_9.6, rep_2


title: JRX8

description: Library name: Sample 13


title: Tumor_plus_NK, Cell_line_D, timepoint_2, EXP_9.6, rep_1


title: Tumor_plus_NK, Cell_line_C, timepoint_2, EXP_9.6, rep_3


title: JRX6

description: Library name: Sample 11


title: P06WTF_12_529


title: Tumor_plus_NK, Cell_line_C, timepoint_2, EXP_9.6, rep_2


title: JRX5

description: Library name: Sample 10


title: P06WTF_8_507


title: Tumor_plus_NK, Cell_line_C, timepoint_2, EXP_9.6, rep_1


title: JRX4

description: Library name: Sample 9


title: Tumor_plus_NK, Cell_line_B, timepoint_2, EXP_9.6, rep_3


title: P06WTF_7_516


title: Tumor_plus_NK, Cell_line_B, timepoint_2, EXP_9.6, rep_2


title: Tumor_plus_NK, Cell_line_A, timepoint_2, EXP_9.6, rep_3


title: JRX3

description: Library name: Sample 8


title: Tumor_only, Cell_line_D, timepoint_2, EXP_9.6, rep_1


title: Tumor_plus_NK, Cell_line_B, timepoint_2, EXP_9.6, rep_1


title: Tumor_plus_NK, Cell_line_A, timepoint_2, EXP_9.6, rep_2


title: JRX2

description: Library name: Sample 7


title: Tumor_plus_NK, Cell_line_D, timepoint_1, EXP_9.6, rep_3

value: Day 4


title: Tumor_plus_NK, Cell_line_A, timepoint_2, EXP_9.6, rep_1


title: JRX1

description: Library name: Sample 6


title: P06WTF_4_533


title: FLA5

description: Library name: Sample 5

value: FLA


title: Tumor_plus_NK, Cell_line_D, timepoint_1, EXP_9.6, rep_2


title: P06WTF_2_539


title: P06WTF_3_545


title: FLA4

description: Library name: Sample 4


title: Tumor_plus_NK, Cell_line_D, timepoint_1, EXP_9.6, rep_1


title: P10KOM_10_556

description:
p10_kallisto_count_data_genes_expression_expected_count.csv
deseq2_p10WTKO_alldetected.csv

data_processing:
DolphinNext RNA-seq Pipeline
Read quality was assessed using FastQC (v0.11.8)
Transcript abundance was estimated based on pseudoalignments using Kallisto (v0.46.0)
Differential gene expression analysis was performed in DEBrowser (v1.19.0) using DESeq2. Low count filtering by counts per million (cpm) >2 in 19/20 samples (Day 10) or >2 in 27/28 samples (Day 6)
Assembly: mm10
Supplementary files format and content: comma-separated text files include raw transcript abundances from kallisto pseudoalignment for each sample
Supplementary files format and content: comma-separated text files include gene expression normalized counts using median of ratios and differential expression analysis performed using DESeq2

source_name: KO

extract_protocol:
RNA was harvested using Rneasy mini kit with on-column DNA digestion (Qiagen). RNA samples were submitted to BGI for library preparation.
RNA sequencing libraries were prepared by BGI according to manufacturer's protocols.

value: CAGG-CreER; Pkd2null/flox

tag: strain

value: M


title: FLA3

description: Library name: Sample 3

value: lung


title: P06WTF_6_548


title: Tumor_plus_NK, Cell_line_B, timepoint_1, EXP_9.6, rep_2


title: Tumor_plus_NK, Cell_line_B, timepoint_1, EXP_9.6, rep_3


title: P10KOM_8_554


title: FLA2

description: Library name: Sample 2


title: Tumor_plus_NK, Cell_line_B, timepoint_1, EXP_9.6, rep_1


title: Tumor_plus_NK, Cell_line_A, timepoint_1, EXP_9.6, rep_3


title: P10KOM_9_555


title: FLA1

description: Library name: Sample 1


title: SlyD-mut-3

city: Shenyang

first: Shuwen

last: Zheng

state: --- Select One ---

address: No.155 NanjingBei Street, Heping District

institute: the First Hospital of China Medical University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp (version 0.23.4) (parameter arsg: -l 39 --dont_eval_duplication  --qualified_quality_phred 20 --unqualified_percent_limit 8 --adapter_sequence  --adapter_sequence_r2  --fix_mgi_id)
Trimmed reads were mapped to GRCh38 using STAR software (version 2.5.3a) (parameters- --outSAMtype BAM SortedByCoordinate)
Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter -T 10 -d 30 -D 1000 -C -s 1 -t {exon} -g {geneid} --primary -O -a {gff_annotation_file}）
Assembly: GRCh38
Supplementary files format and content: Excel file includes RPKM values for each Sample

source_name: AGS

growth_protocol: All H. pylori strains were cultured under microaerobic conditions at 37°C on brain-heart infusion plates supplemented with 10% defibrillated sheep blood.

extract_protocol:
RNA was harvested using TRIzol Reagent (Invitrogen, cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following manufacturer's protocols.

treatment_protocol: The AGS cells were treated with H. pylori 26695 and ΔSlyD for 24h at a multiplicity of infection (MOI) = 100, respectively.

value: AGS

value: gastric cancer cell

value: SlyD mutant

value: treated with SlyD inactivated H. pylori mutant strain


title: P10KOM_6_577


title: P10KOM_7_546


title: Tumor_plus_NK, Cell_line_A, timepoint_1, EXP_9.6, rep_2


title: Tumor_plus_NK, Cell_line_A, timepoint_1, EXP_9.6, rep_1


title: Tumor_only, Cell_line_D, timepoint_1, EXP_9.6, rep_2

value: D


title: Tumor_only, Cell_line_D, timepoint_1, EXP_9.6, rep_3


title: Tumor_plus_NK, Cell_line_C, timepoint_1, EXP_9.6, rep_3

value: C


title: SlyD-mut-2


title: P10KOF_5_562

value: Day 10

value: F


title: P10KOF_4_553


title: Tumor_only, Cell_line_C, timepoint_1, EXP_9.6, rep_3


title: Tumor_only, Cell_line_D, timepoint_1, EXP_9.6, rep_1


title: Tumor_plus_NK, Cell_line_C, timepoint_1, EXP_9.6, rep_2


title: SlyD-mut-1


title: Tumor_plus_NK, Cell_line_C, timepoint_1, EXP_9.6, rep_1


title: Tumor_only, Cell_line_C, timepoint_1, EXP_9.6, rep_2