title: OAP2_rep 3

city: xi'an

first: Wei

last: Gaofei

state: Shaanxi

address: beilin

institute: Northwestern Polytechnical University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: 4T1 Cells

extract_protocol:
Total RNA was extracted usingTrizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. 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 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. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: 4T1 Cells

value: adherent cell line


title: invitroNK_Donor9792_ML_GEX

status: Public on Jun 28 2024

type: SRA

city: Saint Louis

first: Todd

last: Fehniger

state: Missouri

address: 660 South Euclid Avenue, Campus Box 8007

department: Medicine

country: USA

institute: Washington University School of Medicine

description:
9792_ML_HTO_GEXbarcodes.tsv.gz
9792_ML_HTO_GEXfeatures.tsv.gz
9792_ML_HTO_GEXmatrix.mtx.gz

library_source: transcriptomic

data_processing:
CellRanger 6.1.2 was used to align the fastq files to the genome, including determing antibody derived tag and hashtag counts. CellRanger was run separately for ADT and HTO reads.
Assembly: GRCh38; mm10 for human/mouse experiments
Supplementary files format and content: filtered_feature_bc_matrix from cellranger outs. CellRanger was run separately for ADT and HTO libraries
Supplementary files format and content: The feature reference csv files for hashtag demultiplexing and ADT assignments.
Library strategy: CITE-seq

molecule: polyA RNA

organism:
Homo sapiens
Mus musculus

source_name: human natural killer cells

growth_protocol: NK cells were isolated from LRS chambers from normal human donors, and cultured in vitro in 1 ng/mL IL-15 or activated with IL-12/15/18 overnight and then cultured in low-dose IL-15.

extract_protocol:
Single-cell suspensions of samples were processed according to manufacturer's instructions for 10x Genomics 5' droplet-based scRNA-seq, including staining of CITE-seq and hashtagging antibodies for pooling and demultiplexing for 30 minutes.
cDNA was prepared after 10x Genomics GEM generation and barcoding, followed by the GEM-RT reaction and bead cleanup steps. Purified cDNA was amplified before being cleaned up using SPRIselect beads. The supernatant was then collected for the Cell Surface Protein Library. Samples were then run on a Bioanalyzer to determine the cDNA concentration for the GEX library preparation. GEX (Gene Expression) and TotalSeqC Feature libraries were prepared as recommended by 10x Genomics for Feature Barcode technology for Cell Surface Protein(v1/v2 Chemistry) user guides with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer's protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the IlluminaNovaSeq6000instrument.

tag: donor

tag: cell type

value: human natural killer cells

tag: library type

value: GEX


title: OAP2_rep 2

country: China

molecule: total RNA

organism: Mus musculus

tag: cell line

tag: genotype

value: WT

tag: treatment


title: Cotton-like structure, biological rep2

type: RNA

city: Kyoto

first: Megumi

last: Ikeda

address: 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, JAPAN

department: Department of Clinical Application

country: Japan

institute: Center for iPS Cell Research and Application, Kyoto University

hyb_protocol: Hybridization was performed using Applied Biosystems, GeneChip® Hybridization Oven 640.

scan_protocol: GeneChips were scanned using Applied Biosystems, GeneChip® Scanner 3000 7G System.

data_processing: The data were analyzed with Applied Byosystems GeneChip® Expression Console Software ver 1.3.0. (RMA)

label: biotin

organism: Homo sapiens

source_name: An organoid with cotton-like structure generated from human iPS cells in cortical differentiation culture (day35).

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (GeneChip® 3' IVT Pico Reagent Kit, P/N 703308 Rev. 1).

growth_protocol: Human iPS cells are cultured following cortical organoid differentiation protocol described in Kitahara et al., 2020 for 35 days.

extract_protocol: Extraction of total RNA was performed using RNeasy micro kit (QIAGEN) following manufacturer's protocol.

treatment_protocol: Each morphological structures in organoids were dissected under the stereo microscope.

value: organoid generated from human iPS cells

tag: morphology

value: Cotton-like structure


title: invitroNK_Donor9792_ML_ADT_HTO

description:
Bulk ML NK cells, either unstimulated (Hashtag-1), IL-12/15 for 2 hours (Hashtag-2), K562 for 2 hours (Hashtag-3), IL-12/15 for 4 hours (Hashtag-4), or K562 for 4 hours (Hashtag-5). Use Hashtag_five.csv.
9792_ML_HTO_GEXbarcodes.tsv.gz
9792_ML_HTO_GEXfeatures.tsv.gz
9792_ML_HTO_GEXmatrix.mtx.gz

library_source: other

molecule: protein


title: OAP2_rep 1


title: P25801_120

city: Rochester

first: Xiaojia

last: Tang

state: MN

address: 200 1st ST SW

institute: Mayo Clinic

data_processing:
Library preparation, sequencing and data processing was done at SciLifeLab, Stockholm (Sweden) and was carried out under ISO/IEC 17025 accreditation. All samples had  a >=Q30 (aggregated percentage of bases that have quality score more the Q30) above 90%.
Mayo Analysis Pipeline for RNA sequencing (MAP-RSeq, version 3.1.1) was used to process raw RNA-Seq fastq data for read alignment, quality control, and gene expression quantification. Specifically, the RNA-Seq  reads were aligned to the human genome build GRCh38 (hg38) by the STAR aligner (version 2.5.2b). Gene expression quantification was performed using the Subread package (version1.5.1) for raw and RPKM counts
Assembly: Human (Homo sapiens, GRCh38)
Supplementary files format and content: Tab-separated values (TSV) containing merged gene count for all samples

source_name: breast

growth_protocol: The human breast cancer cell lines MDA-MB 231 were obtained from ATCC (Manassas, VA, USA). SUM149-PT breast cancer cells were obtained from Dr. Couch’s laboratory (Mayo Clinic). All cell lines were maintained in DMEM medium containing 5 mM glutamine, 1% penicillin/streptomycin and 10% FBS at 37 C in 5% CO2 atmosphere. PDX-derived TNBC cells (M14, M25 and M40) were established from metastatic PDX models in Dr. Sarkaria’s laboratory (Mayo Clinic Cancer Center).

extract_protocol:
Frozen cell pellets stored in RNAlater (Applied Biosystems) were allowed to thaw on ice, diluted 1:2 with cold PBS (Gibco) and centrifugated for 10 min at 200 xg for MDA-MB-231 and 300xg for SUM149-PT cells. The supernatatant was discarded and the cell pellet was resuspended in cold PBS and centrifugated at 200xg. RNA was extracted using the RNeasy mini kit (Qiagen) following the manufacturer’s instruction (including DNAse digestion). The RNA amount was determined with Qbit and RIN score of selected samples were assessed using Agilent BioAnalyzer (Agilent Technologies).
RNA samples were then processed for further quality control and library preparation at SciLifeLab (Stockholm, Sweden). All samples passed SciLifeLab’s reception quality control and were processed by the Illumina TruSeq Stranded mRNA (polyA) protocol. Samples were sequenced on NovaSeq6000 (NovaSeq Control Software 1.7.5/RTA v3.4.4) with a 151nt(Read1)-19nt(Index1)-10nt(Index2)-151nt(Read2) setup using 'NovaSeqXp' workflow in 'S4' mode flowcell. The Bcl to FastQ conversion was performed using bcl2fastq_v2.20.0.422 from the CASAVA software suite. The quality scale used was Sanger / phred33 / Illumina 1.8+.
RNA-seq , bulk (llumina TruSeq Stranded mRNA (polyA))

treatment_protocol: Scrambled (control) and GFP-tagged NOTCH3 and PD-L1 shRNA, lenti-vectors were purchased by OriGene Technologies (Rockville, MD, USA) and used according to the manufacturer’s instructions. Antibody treatment was carroued out as described in the mansucript

tag: tissue

value: breast

value: epithelial

value: control

tag: mreads

tag: average fragment_size


title: P25801_110


title: APAP_rep 3

value: APAP


title: P25801_109


title: invitroNK_Donor9792_control_GEX

description:
9792_LD_HTO_GEXbarcodes.tsv.gz
9792_LD_HTO_GEXfeatures.tsv.gz
9792_LD_HTO_GEXmatrix.mtx.gz


title: Balloon-like structure, biological-rep3

source_name: An organoid with balloon-like structure generated from human iPS cells in cortical differentiation culture (day35).

value: Balloon-like structure


title: APAP_rep 2


title: invitroNK_Donor9792_control_ADT_HTO

description:
Control NK cells, either unstimulated (Hashtag-1), IL-12/15 for 2 hours (Hashtag-2), K562 for 2 hours (Hashtag-3), IL-12/15 for 4 hours (Hashtag-4), or K562 for 4 hours (Hashtag-5). Use Hashtag_five.csv.
9792_LD_HTO_GEXbarcodes.tsv.gz
9792_LD_HTO_GEXfeatures.tsv.gz
9792_LD_HTO_GEXmatrix.mtx.gz


title: Balloon-like structure, biological-rep1


title: APAP_rep 1


title: invitroNK_Donor9792_overnight_control_GEX

description:
9792_overnight_LD_HTO_GEXbarcodes.tsv.gz
9792_overnight_LD_HTO_GEXfeatures.tsv.gz
9792_overnight_LD_HTO_GEXmatrix.mtx.gz


title: Oxa_rep 3

value: Oxa


title: D7invitroNK_Donor3228_GEX

description:
3228_HTO_GEXbarcodes.tsv.gz
3228_HTO_GEXfeatures.tsv.gz
3228_HTO_GEXmatrix.mtx.gz


title: invitroNK_Donor9792_overnight_control_ADT_HTO

description:
Hashtag-2 is rested in 1 ng/mL IL-15 overnight. Hashtag-3 is rested in IL-12/15/18 overnight. Uses 9792_overnight_LD_HTO_featureref.csv for hashtags.
9792_overnight_LD_HTO_GEXbarcodes.tsv.gz
9792_overnight_LD_HTO_GEXfeatures.tsv.gz
9792_overnight_LD_HTO_GEXmatrix.mtx.gz


title: P25801_107


title: P25801_111


title: Cotton-like structure, biological rep1


title: Balloon-like structure, biological-rep2


title: P25801_118


title: Potato-like structure, biological rep2

source_name: An organoid with potato-like structures generated from human iPS cells in cortical differentiation culture (day35).

value: Potato-like structure


title: Potato-like structure, biological rep3


title: D7invitroNK_Donor3228_ADT_HTO

description:
Hashtag-1 is ctrl NK cells in 1 ng/mL IL-15 for 1 week, Hashtag-2 is bulk ML NK cells. Uses 730_hashtag_featureref.csv file.
3228_HTO_GEXbarcodes.tsv.gz
3228_HTO_GEXfeatures.tsv.gz
3228_HTO_GEXmatrix.mtx.gz


title: Potato-like structure, biological rep1


title: P25801_116


title: P25801_117


title: PBS_rep 3

value: DMSO


title: P25801_115


title: A. castellanii_C.jejuni_3

city: LONDON

first: Fauzy

last: Nasher

state: Please select

address: London School Of Hygiene & Tropical Medicine, Keppel Street

country: United Kingdom

institute: London School of Htgiene and Tropical Medicine

data_processing:
The paired-end reads were trimmed and filtered using Conda; Kallisto was used to map the reads against the reference sequence, Genome assembly Acastellanii.strNEFF v1 GCA_000313135.1. Kallisto was also used to convert annotations from GFF to GTF format. Statistical analysis was performed in R using the combined data generated from the bioinformatics as well as metadata associated with the study (multifactorial design). Adjusted p-value significance cut-off of <0.05, and log fold change cut-off of >2, was used for multiple comparison.
Assembly: Genome assembly Acastellanii.strNEFF v1 GCA_000313135.1.
Supplementary files format and content: abundance.tsv. Files contain "target_id" "length" "eff_length" "est_counts" "tpm"

organism: Acanthamoeba castellanii

source_name: Eukaryotic

extract_protocol:
RNA was extracted using Triazole (Sigma Aldrich, England, UK) following manufacturer’s protocol.
Total RNA was sent out to Genewiz (Azenta) for processing using illumina kits following manufactures protocol.
This was conducted according to illumina protocol by Genewiz (Azenta).

treatment_protocol: RNA-Seq was used to identify differentially expressed genes between A. castellanii infected with C. jejuni strain 11168H and uninfected control (which was incubated in the absence of bacteria) after a total of 4 h. Experiments were performed as described above; briefly, A. castellanii 106 were infected with C. jejuni 11168H (M.O.I of 200) for 3 h and washed three times to remove extracellular bacteria. Gentamycin was added to a final concentration of 100 μg/mL; this culture was incubated for a further 1 h before washing three times

value: Eukaryotic

value: Infected


title: P25801_108


title: Oxa_rep 1

value: 4T1 Cells


title: A. castellanii_C.jejuni_2


title: PBS_rep 2

value: adherent cell line


title: Rosette structures, biological rep3

source_name: An organoid with rossettes structures generated from human iPS cells in cortical differentiation culture (day35).

value: Rosette structures


title: P25801_114


title: gut, CG6295 RNAi-1, rep3

city: Shanghai

first: ying

last: sun

address: 2005 Songhu road

institute: Fudan University

data_processing:
Raw data reads quality was checked by Fastp. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count. Differential gene expression analysis was performed using DESeq2.
Assembly: Drosophila melanogaster reference genome sequence (UCSC dm6 assembly) or rat genome (UCSC rn6 assembly)
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

organism: Drosophila melanogaster

source_name: gut

growth_protocol: Eclosed flies were raised on standard cornmeal fly food at 29 °C with 60% relative humidity in a 12 hours light/dark cycle; Rat small intestinal epithelial cell line (IEC-6) were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% antibiotics (penicillin-streptomycin) at 37 °C in a 5% CO2 incubator.

extract_protocol:
Total RNA was extracted from fly guts or IEC-6 cells with Trizol reagent (15596018CN, Invitrogen, Massachusetts, USA), and treated with DNase I (EN401, Vazyme, Nanjing, China) to eliminate genomic DNA. 1 μg of total RNA was used for the construction of sequencing libraries.
The RNA-seq libraries were then generated using VAHTS Universal V6 RNA-seq Library Prep Kit (NR604, Vazyme, Nanjing, China).

value: gut

value: CG6295 knockdown


title: D7invitroNK_Donor730_ADT_HTO

description:
Hashtag-1 is ctrl NK cells in 1 ng/mL IL-15 for 1 week, Hashtag-2 is bulk ML NK cells. This sample did not include IgG2b during CITE-seq staining. Uses 730_hashtag_featureref.csv file.
730_HTO_GEXbarcodes.tsv.gz
730_HTO_GEXfeatures.tsv.gz
730_HTO_GEXmatrix.mtx.gz

value: human natural killer cells


title: Oxa_rep 2

value: WT


title: Rosette structures, biological rep2

value: organoid generated from human iPS cells


title: A. castellanii_C.jejuni_1


title: P25801_113

value: breast

value: epithelial


title: A. castellanii_3

value: Uninfected


title: Rosette structures, biological rep1


title: D7invitroNK_Donor730_GEX

description:
730_HTO_GEXbarcodes.tsv.gz
730_HTO_GEXfeatures.tsv.gz
730_HTO_GEXmatrix.mtx.gz

value: GEX


title: P25801_106


title: gut, CG6295 RNAi-1, rep1


title: 4-OI treated RAW264.7 cells, 8h [4-OI-input]

city: Beijing

first: Zhaoli

last: Luo

address: You An Men Wai, Feng Tai District

institute: Capital Medical University

library_source: genomic

data_processing:
Basecalls were performed using fastp v0.23.2 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, discarding reads left with < 20 bp. The minimum allowable reads length is 36nt.
ChIP-seq clean reads were aligned to the UCSC mm10 genome by using Short Oligonucleotide Analysis Package (SOAP) v2.21 aligner. No more than 2 mismatches were allowed in the alignment.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 100-300bp, including adaptor sequence to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
CallPeaks were used MACS v1.4.2 with the significance cut-off p-value <0.005. Different peaks were used MAnorm software with the significance cut-off| M_value_rescaled | > 1 and -log10 (p-value)> 5.
Assembly: mm10
Supplementary files format and content: bw

molecule: genomic DNA

source_name: RAW264.7 cells

growth_protocol: RAW264.7 cells were cultured in the DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
RAW264.7 cells were fixed by 1% formalin (Sigma-Aldrich) for 10 minutes.  After RAW264.7 cells were washed and lysed, chromatin was sonicated using aultrasonicator (VCX150, Sonics).
ChIP DNA and related input samples were tested with spectrophotometer and Qubit fluorometer to inspect the quality. Qualified samples were end-repaired to create blunt-ended, 5’-phsphorylated fragments, and then single dA was added to 3’ end of each fragment. Adaptors for high-throughput sequencing were ligated to the dA-tailed fragments, and the library was then amplified by PCR. The libraries with 100-500 bp insert fragments were then inspected with Qubit fluorometer, Agilent bioanalyzer and StepOnePlus Real-Time PCR. Qualified libraries were sequenced by Illumina NovaSeq 6000 instrument of illumine HiSeq platform.

treatment_protocol: RAW264.7 cells were treated 120μM 4-OI (MedChemExpress) or Vehicle for 8h.

value: RAW264.7 cells

value: Mouse mononuclear macrophage leukemia cells

tag: chip antibody


title: 4-OI treated RAW264.7 cells, 8h [4-OI-Nrf2]


title: Vehicle treated RAW264.7 cells, 8h [Vehicle-Nrf2]

value: IgG (Applygen, #C1755)


title: gut, control, rep3


title: P25801_104


title: P25801_105


title: A. castellanii_1

value: Eukaryotic


title: gut, control, rep2


title: Vehicle treated RAW264.7 cells, 8h [Vehicle-input]


title: gut, H2

city: Changchun

first: Yutao

last: Li

address: Jingyue Street

institute: Northeast Normal University

data_processing:
Raw sequencing data format was shown as “.fastq” and the joint sequence (adapter) was removed from the original tags using CUTADAPT 1.9. Low quality and repetitive sequences were filtered to obtain clean data. De novo splicing in TRINITY tool (Version 2.4.0) was selected to assemble the clean reads and then the software was used to perform the transcript clustering based on shared sequences contents. The longest transcript in each cluster was regarded as one Unigene. All obtained Unigenes were annotated based on known databases. Quantitative assessment for fragments per kilobase of transcript per million mapped reads (FPKM) of each Unigene was executed with the SALMON package.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample
Supplementary files format and content: gene RNA-seq result

organism: Acipenser schrenckii

extract_protocol:
Commercial RNA sample extraction kit (DP419, TIANGEN, China) was selected to extract the total RNA in gut tissues. 100 mg fresh intestine tissue was ground by high-speed homogenizer (DHFSTPRP-32D, LAWSON, China) with 1 mL lysis buffer RZ to obtain homogenate and then trichloromethane was added. After staying at room temperature for 7 min, the mixture was centrifuged at 12500 rpm to obtain the aqueous phase that was mixed with absolute ethyl alcohol. RD solution was used to remove residual protein impurity in RNA samples and the purified total RNA was stored at RNase-free tubes after repeated centrifugation.
When RNA integrity number > 7.0 and A260/280 > 1.8, messenger RNA (mRNA) with poly A was caught using oligo(dT) dynabeads (25-61005, THERMO FISHER, USA) and then broken into fragment with the specific kit (E6150S, NEBNEST, USA). Double-strands complementary DNA was synthesized based on the reverse transcriptase and E. coli DNA polymerase I that was provided by LIANCHUAN BIO TECHNOLOGIES Co., LTD (Hangzhou, China). Paired-ends of the complementary DNA were added with a “A” base, which could combine with the adapter sequence. After the second strand was digested, the sequencing library (150 bp) was established by amplifying the target sequences.

value: Acipenser schrenkii

value: fed with Limnodrilus for 30 d


title: Growth plate cartilage, Idh1 mutant rep3

city: Madison

first: jianhong

last: ou

state: WI

address: 330 N Orchard Street

institute: Morgridge institute for research

data_processing:
RNA-seq reads were trimmed by Trim Galore (v 0.6.4) and mapped with STAR [ref]  (v 2.6.1d, with parameters --twopassMode Basic --runDirPerm All_RWX and supplying the Ensembl GRCm38 annotation) to mouse genome (GRCm38).
The mapped reads were counted using featureCounts [ref]  (v 1.6.4).
Bioconductor package DESeq2 [ref]  (v 1.28.1) was employed to analyze differential expressions (DE) with genotype information.
Assembly: GRCm38
Supplementary files format and content: text, raw counts

source_name: E18.5 Growth plate cartilage

growth_protocol: Animals were bred in accordance to Duke University IACUC protocols and aged to 2 months.

extract_protocol: Animals were euthanized according to IACUC protocol and hind limbs were isolated. Surrounding tissues were dissected off growth plates (GP) from distal femur and proximal tibia were washed with PBS and snap frozen.

value: Col2a1-Cre; Idh1 LSL/+

tag: age

value: distal femur and proximal tibia

value: Growth plate chondrocytes


title: PBS_rep 1

value: 4T1 Cells

value: adherent cell line

value: DMSO


title: P25801_103

value: control


title: gut, H3

value: gut


title: P25801_102

value: breast

value: epithelial


title: gut, control, rep1

value: WT


title: gut, H1


title: control, replicate2, Hi-C

city: Moscow

first: Anna

last: Kononkova

address: Nobel st., Building 1

department: Skoltech Center of Life Sciences

country: Russia

institute: Skolkovo Institute of Science and Technology

data_processing:
Fastq files were trimmed with Trim Galore (--stringency 3) and then processed with Distiller-nf. For read mapping dm3/R5 Drosophila genome version was used. Filter  mapq_30 (mapq1>=30 and mapq2>=30) was applied.
Assembly: dm3/R5
Supplementary files format and content: Processed data files have mcool format. The files contain Hi-C matrices of intra- and interchromosomal contacts at multiple resolutions.

growth_protocol: Drosophila melanogaster S2 cell line (from IMG collection) was grown at 25°C in Schneider’s Drosophila Medium (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (FBS, Gibco), 50 units/ml penicillin, and 50 µg/ml streptomycin.

extract_protocol:
5–10 million cells were fixed in 1× phosphate-buffered solution (PBS) with 2% formaldehyde for 10 min with occasional mixing. The reaction was stopped by the addition of 2 M glycine to give a final concentration of 125 mM. Cells were centrifuged (1,000 x g, 10 min., 4 °C), resuspended in 50 μl of 1× PBS, snap-frozen in liquid nitrogen, and stored at -80 °C. Defrozen cells were lysed in 1.5 ml isotonic buffer (50 mM Tris-HCl pH 8.0, 150 mM NaCl, 0.5% (v/v) NP-40 substitute (Fluka), 1% (v/v) Triton-X100 (Sigma), 1× Halt™ Protease Inhibitor Cocktail (Thermo Scientific) on ice for 15 min. Cells were centrifuged at 2,500 x g for 5 min, resuspended in 100 μl of 1× DpnII buffer (NEB), and pelleted again. The pellet was resuspended in 200 μl of 0.3% SDS in 1.1× DpnII buffer and incubated at 37 °C for 1 hour. Then, 330 μl of 1.1× DpnII buffer and 53 μl of 20% Triton X-100 (Sigma) were added, and the suspension was incubated at 37 °C for 1 hour. Next, 600 U of DpnII enzyme (NEB) were added, and the chromatin was digested overnight (14–16 hours) at 37 °C with shaking (1,400 rpm). On the following day, 200 U of DpnII enzyme were added, and the cells were incubated for an additional 2 hours. DpnII was then inactivated by incubation at 65 °C for 20 min. After DpnII inactivation, the nuclei were harvested for 10 min at 5,000 x g, washed with 100 μl of 1× NEBuffer 2, and resuspended in 50 μl of 1× NEBuffer 2. Cohesive DNA ends were biotinylated by the addition of 7.6 μl of the biotin fill-in mixture prepared in 1× NEBuffer 2 (0.025 mM dATP (Thermo Scientific), 0.025 mM dGTP (Thermo Scientific), 0.025 mM dTTP (Thermo Scientific), 0.025 mM biotin-14-dCTP (Invitrogen), and 0.8 U/μl Klenow enzyme (NEB)). The samples were incubated at 37 °C for 75 min with shaking (1,400 rpm). Nuclei were centrifuged at 3,000 x g for 5 min, resuspended in 100 μl of 1× T4 DNA ligase buffer (Fermentas), and pelleted again. The pellet was resuspended in 400 μl of 1× T4 DNA ligase buffer, and 75 U of T4 DNA ligase (Fermentas) were added. Chromatin fragments were ligated at 20 °C for 6 hours. The cross-links were reversed by overnight incubation at 65 °C in the presence of proteinase K (100 μg/ml). After cross-link reversal, the DNA was purified by single phenol-chloroform extraction followed by ethanol precipitation with 20 μg/ml glycogen (Thermo Scientific) as the co-precipitator. After precipitation, the pellets were dissolved in 100 μl 10 mM Tris-HCl pH 8.0. To remove residual RNA, samples were treated with 50 μg of RNase A (Thermo Scientific) for 45 min at 37 °C. To remove residual salts and DTT, the DNA was additionally purified using Agencourt AMPure XP beads (Beckman Coulter). Biotinylated nucleotides from the non-ligated DNA ends were removed by incubating the Hi-C libraries (2 μg) in the presence of 6 U of T4 DNA polymerase (NEB) in NEBuffer 2 supplied with 0.025 mM dATP and 0.025 mM dGTP at 20 °C for 4 hours. Next, the DNA was purified using Agencourt AMPure XP beads.
The DNA was dissolved in 500 μl of sonication buffer (50 mM Tris-HCl (pH 8.0), 10 mM EDTA, 0.1% SDS) and sheared to a size of approximately 100–1,000 bp using a VirSonic 100 (VerTis). The samples were concentrated (and simultaneously purified) using AMICON Ultra Centrifugal Filter Units to a total volume of approximately 50 μl. The DNA ends were repaired by adding 62.5 μl MQ water, 14 μl of 10× T4 DNA ligase reaction buffer (Fermentas), 3.5 μl of 10 mM dNTP mix (Fermentas), 5 μl of 3 U/μl T4 DNA polymerase (NEB), 5 μl of 10 U/μl T4 polynucleotide kinase (NEB), 1 μl of 5 U/μl Klenow DNA polymerase (NEB), and then incubating at 20 °C for 30 min. The DNA was purified with Agencourt AMPure XP beads and eluted with 50 μl of 10 mM Tris-HCl (pH 8.0). To perform an A-tailing reaction, the DNA samples were supplemented with 6 μl 10× NEBuffer 2, 1.2 μl of 10 mM dATP, 1 μl of MQ water, and 3.6 μl of 5 U/μl Klenow (exo-) (NEB). The reactions were carried out for 30 min at 37 °C in a PCR machine, and the enzyme was then heat-inactivated by incubation at 65 °C for 20 min. The DNA was purified using Agencourt AMPure XP beads and eluted with 100 μl of 10 mM Tris-HCl (pH 8.0). Biotin pulldown of the ligation junctions was performed as described previously, with minor modifications. Briefly, 4 μl of MyOne Dynabeads Streptavidin C1 (Invitrogen) beads were used to capture the biotinylated DNA, and the volumes of all buffers were decreased by 4-fold. The washed beads with captured ligation junctions were resuspended in 50 μl of adapter ligation mixture comprising 41.5 μl MQ water, 5 μl 10× T4 DNA ligase reaction buffer (Fermentas), 2.5 μl of Illumina TruSeq adapters, and 1 μl of 5 U/μl T4 DNA ligase (Fermentas). Adapter ligation was performed at 22 °C for 2.5 hours, and the beads were sequentially washed twice with 100 μl of TWB (5 mM Tris-HCl (pH 8.0), 0.5 mM EDTA, 1 M NaCl, 0.05% Tween-20), once with 100 μl of 1× binding buffer (10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 2 M NaCl), once with 100 μl of CWB (10 mM Tris-HCl (pH 8.0) and 50 mM NaCl), and then resuspended in 20 μl of MQ water. Test PCR reactions containing 4 μl of the streptavidin-bound Hi-C library were performed to determine the optimal number of PCR cycles required to generate sufficient PCR products for sequencing. The PCR reactions were performed using KAPA High Fidelity DNA Polymerase (KAPA) and Illumina PE1.0 and PE2.0 PCR primers (10 pmol each). The temperature profile was 5 min at 98 °C, followed by 6, 9, 12, 15, and 18 cycles of 20 s at 98 °C, 15 s at 65 °C, and 20 s at 72 °C. The PCR reactions were separated on a 2% agarose gel containing ethidium bromide, and the number of PCR cycles necessary to obtain a sufficient amount of DNA was determined based on the visual inspection of gels (typically 12–15 cycles). Four preparative PCR reactions were performed for each sample. The PCR mixtures were combined, and the products were separated on a 1.8% agarose gel. 200–600 bp DNA fragments were excised from the gel and purified with a QIAGEN Gel Extraction Kit. Two biological replicates were performed.

treatment_protocol: For RNAi treatment of S2 cells, dsRNAs against LacZ (control), Lam, or Elys were prepared as was described previously (Shevelyov et al. 2009) using primers indicated in Supplementary Table S9. Cells were treated with dsRNAs during four days, or during three days with an additional treatment for two days using previously described protocol (Clemens et al. 2000).

value: embryonic, cultured

value: normal

value: siRNA  against LacZ


title: Growth plate cartilage, Idh1 mutant rep2


title: gut, CG6295 RNAi-1, rep2

value: CG6295 knockdown


title: control, replicate1, Hi-C


title: P25801_101


title: Growth plate cartilage, Idh1 mutant rep1


title: A. castellanii_2

value: Eukaryotic

value: Uninfected


title: Growth plate cartilage, control rep3

value: Idh1 LSL/+


title: gut, Q2

value: Acipenser schrenkii

value: fed with commerial feed for 30 d


title: gut, Q3

value: fed with commerial feed for 30d


title: Elys-KD, replicate2, Hi-C

value: siRNA against Elys


title: HBVAF_VZV_rep3

city: Burlington

first: Seth

last: Frietze

state: VT

address: 149 Beaumont Avenue

department: Biomedical and Health Sciences

institute: University of Vermont

data_processing:
Raw RNA-seq reads were assessed for quality, adaptor content, and duplication rates using FastQC version 0.11.9 (PMID: 24381581).
Alignment of RNA-seq reads to human genome version hg38/GRCh38 was performed by STAR version 2.7.1a (PMID: 23104886).
For gene quantification, raw counts were obtained using STAR mapping-based mode using the GRCh38 GENCODE (v36) reference annotation file.
Gene level counts were used for differential gene expression analysis using DESeq2 version 1.36.0 (PMID: 25516281).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw count values for each sample

source_name: HBVAFs

extract_protocol:
Rneasy Mini Kit from Qiagen according to manufacterer's guidelines
RNA libraries for RNA-seq were prepared using Universal Plus mRNA-Seq following manufacturer's protocols.

treatment_protocol: Cells were treated at supernatant total media 1:5 ratio (~10e6 number of exosomes) and harvested 36 hours later for RNA.

value: HBVAFs

value: vzv exosome treated


title: Elys-KD, replicate1, Hi-C

treatment_protocol: For RNAi treatment of S2 cells, dsRNAs against LacZ (control), or Elys were prepared as was described previously (Shevelyov et al. 2009).  Cells were treated with dsRNAs during four days, or during three days with an additional treatment for two days using previously described protocol (Clemens et al. 2000).

value: dsRNA against Elys


title: gut, Q1

value: gut


title: Hemin treated WT BMDMs, 12h, rep3

description: sample 12-WT-Hemin-3

data_processing:
DNBSEQ-T7 platform used for sequence
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence
using HISAT2 and StringTie to mapping reads to mouse genome and to reconstruct transcripts
using bowtie2 and RSEM to mapping reads to gene and to calculate gene expression
Functional enrichment analyses including Gene Ontology (GO) and KEGG were performed to identify which DEGs were signifcantly enriched in GO terms or metabolic pathways
Assembly: NCBI RefSeq GRCm39 (mm39)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: mouse bone marrow

growth_protocol: BMDMs from WT and Irg1KO  mice were cultured in the α-MEM supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomycin, and 20 ng/µL murine macrophage colony stimulating factor (M-CSF) for 7 days in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was extracted from BMDMs by TRIzol reagent (life technologies) according to the manufacturer’s protocol and used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard MGI protocols

treatment_protocol: BMDMs from WT mice were treated 120μM 4-OI (MedChemExpress) for 15h. BMDMs from WT mice were treated 15μM Hemin (Frontier Scientific) or Vehicle for 12h. BMDMs from Irg1KO mice were treated Vehicle for 12h.

value: mouse bone marrow

value: BMDMs

value: macrophages

value: Hemin, 12h


title: Growth plate cartilage, control rep1

data_processing:
RNA-seq reads were trimmed by Trim Galore (v 0.6.4) and mapped with STAR (v 2.6.1d, with parameters --twopassMode Basic --runDirPerm All_RWX and supplying the Ensembl GRCm38 annotation) to mouse genome (GRCm38).
The mapped reads were counted using featureCounts  (v 1.6.4).
Bioconductor package DESeq2  (v 1.28.1) was employed to analyze differential expressions (DE) with genotype information.
Assembly: GRCm38
Supplementary files format and content: text, raw counts

value: distal femur and proximal tibia

value: Growth plate chondrocytes


title: HBVAF_VZV_rep1


title: VCaP, ERG

city: Bloomington

first: Stephanie

last: Metcalf

state: IN

address: 1001 E Third St

institute: Indiana University Bloomington

data_processing:
Alignment of reads was performed using Bowtie2 for the reference genome hg19
Blacklist region was removed via bedtools
Duplicates were removed via Picard-2.14.0
MACS2 was used to call peaks with a p-value of 0.001
Assembly: hg19
Supplementary files format and content: xlsx, broad peak

source_name: Prostate

growth_protocol: Cells were grown in DMEM supplemented with 10% FBS and 1% Penicillin-Streptomycin

extract_protocol:
Cells were fixed with 1% v/v formaldehyde for 15 minutes and quenched with 2M Glycine for 5 minutes. Cells were then lysed and sonicated using a Diagenode Biorupter Pico.
ChIP-Seq libraries were generated by pooling at least three ChIPs per condition and sonicating to approximately 150bps. 10ng of IP was used as starting material and fragment end repair was done using Klenow DNA polymerase, T4 DNA ploymerase, and T4 DNA Ligase followed by QIAQuick PCR Purification. TruSeq adaptors were ligated via T4 DNA Ligase after which libraries were amplified through 18 cycles and products were size selected on a 2% agarose gel and AMPure XP bead cleanup.

value: Prostate

value: VCaP

value: epithelial cell

value: shRNA ERG

tag: antibody

value: DO-1, sc-126, Santa Cruz Biotechnology


title: HBVAF_MOCK_rep3

value: mock exosome treated


title: VCaP, Control

value: shRNA Luciferase


title: HBVAF_MOCK_rep2

value: HBVAFs


title: Hemin treated WT BMDMs, 12h, rep2

description: sample 11-WT-Hemin-2

value: WT


title: ARN, Input3

city: clermont ferrand

first: yoan

last: renaud

address: place henri dunand

country: France

institute: igred

description:
Input3
RPKM_all.txt

data_processing:
Quality score trimming and filtering were performed with cutadapt.
reads were aligned to the annotated Dm6 genome (Ensembl release 70) using Hisat2 (v2.1.0)
Per gene read counts were calculated from the Hisat2 output using htseq-count (v0.11.2)
Differential gene expression was analyzed using the R package DESeq2 (v1.22.2)
Assembly: BDGP dm6
Supplementary files format and content: tab-delimited text file includes FBgn number, gene symbols and RPKM values for each sample.

source_name: 0h After Pupae Formation imaginal whole leg disc cells

extract_protocol:
Zymo Quick-RNA microprep
NEBNext Ultra RNA library prep kit for illumina
oligodT

treatment_protocol: cell dissociation : collagenase + papain

value: control cells (whole leg disc cells)

tag: time

value: 0h After Pupae Formation


title: Hemin treated WT BMDMs, 12h, rep1

description: sample 10-WT-Hemin-1

value: mouse bone marrow


title: ARN, Input2

description:
Input2
RPKM_all.txt


title: HBVAF_MOCK_rep1


title: 68N8_Rep1

city: New York City

first: Christopher

middle: Russell

last: Chin

state: NY

address: 413 E 69th Street, Belfer Building, BB-1462

institute: Weill Cornell

description: normoxia 8 weeks

data_processing:
Reads were trimmed for Nextera and Illumina adapter sequences using trimgalore with default parameters. Trimmed reads were mapped to hg19 (GRCh37) reference using STAR (v2.7.1a), and the reads mapped to the genes annotated in the ENSEMBL GRCh37.p13 GTF (release 75) were quantified using HTSeq-count (v0.11.2). Differentially expressed genes across hypoxia-normoxia conditions were identified after controlling for cell line and batch effects (FDR≤0.05), using DESeq2 (v1.26.0).
Assembly: hg19
Supplementary files format and content: tab-delimited text files with raw counts

growth_protocol: CTC lines derived from patients with luminal breast tumors were cultured in ultra-low attachment plates (Corning) with RPMI 1640 supplemented with 20 ng/ml EGF, 20 ng/ml bFGF, 1X B27 and 1X antibiotic/antimycotic. CTCs were maintained in a Nuaire NU-5831 incubator at 4% O2 and 5% CO2, and media was changed every 3 or 4 days in regular cell culture hood in ambient oxygen. For normoxia vs hypoxia experiments, equal number of cells were plated and kept in normoxia or hypoxia (4% O2) conditions for 8 weeks.

extract_protocol:
Cells were collected into tubes containing PBS, centrifuged and lysed with Quick RNA lysis buffer to proceed with RNA extraction with  Quick-RNA MicroPrep (Zymo) according to the manufacturer’s instructions. RNA integrity was measured using Bioanalyzer (Agilent).
Sequencing libraries were prepared with KAPA stranded RNA-Seq Kit with RiboErase (Kapa Biosystems) according to manufacturer’s instructions, and single-end 75 bp sequencing was performed at the USC Molecular Genomics Core, using a NextSeq high output 75 cycle kit (Illumina).

value: patient derived CTC line

value: Normoxia


title: HBVAF_VZV_rep2

value: vzv exosome treated


title: 68N8_Rep2

description: normoxia 8 weeks


title: 68H_Rep2

description: hypoxia 8 weeks

value: Hypoxia


title: Veh treated Irg1KO  BMDMs, 12h, rep3

description: sample 9-Irg1KO-Veh-3

value: BMDMs

value: macrophages

value: Vehicle, 12h


title: ARN, GFP3

description:
GFP3
RPKM_all.txt

source_name: 0h After Pupae Formation imaginal leg disc myoblasts

value: GFP-positive myoblasts


title: Veh treated Irg1KO  BMDMs, 12h, rep2

description: sample 8-Irg1KO-Veh-2


title: Veh treated Irg1KO  BMDMs, 12h, rep1

description: sample 7-Irg1KO-Veh-1


title: ARN, GFP2

description:
GFP2
RPKM_all.txt


title: Growth plate cartilage, control rep2

value: Idh1 LSL/+

value: distal femur and proximal tibia

value: Growth plate chondrocytes


title: ARN, Input1

description:
Input1
RPKM_all.txt


title: 68H_Rep1

description: hypoxia 8 weeks


title: actβ mutant biological replicate 4

city: Minneapolis

first: Michael

middle: B

last: O'Connor

address: 321 Church St SE

department: Genetics Cell Biology and Development

institute: University of Minnesota

description: Act80-4E 4

data_processing:
2 x 150bp fastq.gz paired-end reads for samples (n=30.3 Million average reads per sample) were trimmed using Trimmomatic (v 0.33) enabled with the “-q” option; 3bp sliding-window trimming from 3’ end requiring minimum Q30.  Quality control on raw sequence data for each sample was performed with fastq.gzC. Read mapping was performed via Hisat2 (v2.1.0) using the Drosophila genome (Drosophila melanogaster (BDGP6.28) as a reference. Gene quantification was done via Feature Counts for raw read counts.
Assembly: Drosophila melanogaster (BDGP6.28)
Supplementary files format and content: excel spread sheet for each biological replicate including raw counts

source_name: whole animal

extract_protocol:
Eight early L3 larvae were homogenized in 500 ml Trizol.  100 ml of cholorform was added and samples were shaken and then incubated at room temperature for 2 minutes.  Samples were then spun at 11k for 15’ at RT and the aqueous phase was removed.  Equal volumes of absolute ethanol was added and applied to a Zymo RNAmicroprep column.  RNA was purified per manufactures protocol.  RNA concentrations were quantified using a nanodrop. 3 ug RNA was submitted for library prep.
TruSeq RNA preparation kit v2

value: whole animal

tag: developmental stage

value: early L3 larvae


title: Veh treated WT BMDMs, 12h, rep3

description: sample 6-WT-Veh-3

value: WT


title: ARN, GFP1

description:
GFP1
RPKM_all.txt


title: actβ mutant biological replicate 5

description: Act80-4E 5


title: actβ mutant biological replicate 3

description: Act80-4E 3


title: RNA bound with hPAC

city: Chengdu

first: pengliang

last: chi

state: Sichuan province

address: No.17 People's South Road

institute: Sichuan University

data_processing:
The quality of sequence data was checked by FastQC software (v0.11.8) .
(1) For data from xPAC sample, 5’adaptor and 3’-adaptor trimmed reads were aligned to the reference genome of Spodoptera frugiperda (fall armyworm) using STAR (v2.7.1a) with default parameters and the NCBI annotation version 1.0 was used (https://www.ncbi.nlm.nih.gov/assembly/GCF_011064685.1/). The 1.24 million reads including unique and multiple mapped reads were retained. The gene expression was quantified using the HTSeq (v0.11.2) with parameters of “-s yes” and “--nonunique all”. Genes with raw counts of less than 10 reads were filtered out. Gene biotypes and tRNA types were from the gene transfer format (GTF) file.
(2) For data from the hPAC sample, 5’-adaptor and 3’-adaptor trimmed reads were aligned to the reference genome of hg38 using BWA (0.7.17-r1198-dirt) with default parameters, and the NCBI annotation version 14 was used (https://www.ncbi.nlm.nih.gov/genome/?term=GRCh38.p14). A total of 1.7 million reads including unique and multiple mapped reads were retained. The gene expression was quantified using the HTSeq (v0.11.2) with parameters of “-s yes” and “--nonunique all”. Gene biotypes and tRNA types were from the GTF file.
The gene expression was quantified using the HTSeq (v0.11.2) with parameters of “-s yes” and “--nonunique all”.
Genes with raw counts of less than 10 reads were filtered out.
Assembly: (1) Spodoptera frugiperda version 1.0; (2) Homo sapiens reference genome GRCh38.p14.
Supplementary files format and content: The tab-delimited text files include gene biotypes, gene raw counts and RPKM values for each sample
Library strategy: Hydro-tRNAseq

molecule: other

source_name: WT

growth_protocol: (1) Sf9 cells were maintain in SIM SF Expression Medium (Sino Biological Inc.) with 120 rpm at 27°C in a shaker. (2) HEK293F cells were maintained in SMM 293T-II medium (Sino Biological Inc.) at 37 °C, 5% CO2, and 130 rpm shaking.

extract_protocol:
(1) The xPAC was expressed in Sf9 and the cells were centrifuged at 800 × g for 15 min and suspended in lysis buffer (25 mM Tris, 150 mM NaCl, pH 8.0) with protease inhibitors (1 mM phenylmethylsulfonyl fluoride, 0.8 µM aprotinin, 2 µM pepstatin A and 5 µg/mL leupeptin). The collected cells were flash-frozen in liquid nitrogen and stored at −80 °C before purification. The thawed cells were solubilized by adding 2% (w/v) n-Dodecyl β-D-maltoside (DDM, Anatrace) and stirring at 4 °C for 2 h. The resulting cell lysate was centrifuged at 27,000 × g at 4 °C for 30 min. The supernatant was incubated with Strep-tactin resin (GE Healthcare) at 4 °C for 1 h. The resin was washed with lysis buffer supplemented with either 0.06% (w/v) digitonin (Biosynth). Proteins were eluted with elution buffer (25 mM Tris, 150 mM NaCl, 5 mM desthiobiotin, pH 8.0) containing with 0.06 % digitonin. The protein samples were further purified by size-exclusion chromatography (SEC, Superose 6 increase 10/300 GL, GE Healthcare) in lysis buffer containing 0.06% digitonin. The purified xPAC proteins were used to extract RNA by using a phenol-chloroform extraction followed by ethanol precipitation. (2) The hPAC was expressed in HEK293F cells. The purification procedure was similar to that described for xPAC, with the following modification. The wash buffer contained 25 mM Tris pH 8.0, 150 mM NaCl, and 0.05% DDM. The protein was eluted with elution buffer containing 25 mM Tris, pH 8.0, 150 mM NaCl, 0.05% DDM, and 5 mM desthiobiotin. The RNAs enriched in the hPAC samples were extracted using the phenol-chloroform method followed by ethanol precipitation.
The purified RNA was demethylated by rtStarTM tRF&tiRNA Pretreatment Kit (Arraystar, AS-FS-005) and partially hydrolyzed according to Hydro-tRNAseq mothod. The library was prepared by using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® kit (New England Biolabs, E7300L/E7850L)

treatment_protocol: (1) For expression xPAC, recombinnant baculovirus were generated following the standard protocol of Bac-to-Bac Expression Systems (Invitrogen), Sf9 cell (cell density: 1.5-2.0 ×10^6 cells/ml) were infected with P2 virus,  and incubated at 27 °C for 60 hours. (2) For expression hPAC, expression plasmids were transfected into HEK293F cells (cell density: 1.5-2.0 ×10^6 cells/ml)  using PEI (25 kDa, Polysciences Inc.). The transfected cells were incubated at 37 °C for 60 hours.

value: human embryonal kidney (HEK) cells

value: transient expression of wild type human acid-sensitive outwardly rectifying channel ASOR

value: Day 3


title: Veh treated WT BMDMs, 12h, rep2

description: sample 5-WT-Veh-2

value: mouse bone marrow


title: actβ mutant biological replicate 2

description: Act80-4E 2


title: actβ mutant biological replicate 1

description: Act80-4E 1


title: pre-metastatic liver, pancreatic cancer, patient #84

city: New York

first: Linda

last: Bojmar

address: 413 E 69th St, Belfer Research Bldg

department: Department of Pediatrics

institute: Weill Cornell Medicine

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcoding, gene counting and aggregation was made using the Cell Ranger software v 2.1.1
Assembly: hg19
Supplementary files format and content: h5, barcodes.tsv, genes.tsv, matrix.mtx

source_name: liver

extract_protocol:
Single cell isolation was performed on a subset of patients with adequate liver tissue as follows: a portion of the specimen was minced with scissors to 1mm pieces and digested in HBSS with 1mg/mL Collagenase IV (Worthington) and 1U/mL DNAse I (Roche) for 20 min at 37˚C with constant agitation. After washing and straining through a 70μm mesh, the non-parenchymal cells (NPCs) were separated by density gradient centrifugation with 40% Optiprep solution as previously described. Specifically, the cell suspension was combined with the Optiprep, underlayed in GBSS buffer, and spun at 900xg for 20 min. The NPCs were concentrated at the interface, were collected and subjected to red blood cell lysis using ACK lysis buffer (Gibco). Isolated NPCs were validated to be >90% CD45+ cells by flow cytometry on BD FACS Canto with the FACSDiva software (BD Biosciences). Analysis was performed using FlowJo v.10 (FlowJo LLC). The isolated hepatic NPC (>90% CD45+) were cryopreserved in 10% DMSO/90% FBS mix until the time of analysis. Upon retrieval, live cells were sorted by exclusion on ethidium homodimer-1 and gating on calcein violet, validated by trypan blue staining, and submitted to downstream processing for scRNAseq if viability was >80%.
Library construction was performed according to the manufacturer's instructions (single cell 3' v2 protocol, 10x Genomics)

value: liver

value: Hepatic non-parenhymal cells (predominantly CD45+)

tag: disease state

value: pre-metastatic liver, pancreatic cancer


title: w1118 (WT control) biological replicate 6

description: w1118 6


title: Veh treated WT BMDMs, 12h, rep1

description: sample 4-WT-Veh-1

value: BMDMs


title: control liver, low-grade intraductal papillary mucinous neoplasm (IPMN), patient #86

description: 10x Genomics


title: Hi-C of Bos taurus DNA Zoo Sample6834, DIY sirloin jerky in a food dehydrator, 3.5h, rep2

city: Houston

first: Olga

last: Dudchenko

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Hi-C-guided genome assembly (3D-DNA, JBAT)
Reference-guided 3D genome assembly (Anonamos, 3D-DNA, JBAT)
Construction of the chromosome-length Hi-C contact map (BWA, Juicer, 3D-DNA)
liftover (KentUtils, 3D-DNA)
Gene annotation (TOGA)
Compartment annotation (CRUSH)
Loop calling and aggregate analysis (HiCCUPS, Juicer Tools, SIP, SIP META)
Aggregate chromosome analysis (3D-DNA)
Modeling of 3D structures of woolly mammoth chromosomes (OpenMiChroM)
DNA degradation simulations (NuChroM, custom script)
Assembly: The following existing genome builds were used in parts of the study: Loxafr3.0 (GCA_000001905.1), ASM1433276v1 (GCA_014332765.1), EquCab2.0 (GCF_000002305.2), ASM303372v1 (GCA_003033725.1), bosTau9 (GCF_002263795.3), ASM651725v1 (GCF_006517255.1), ASM3043605v1 (GCF_030436055.1), ASM331443v2 (GCF_003314435.2), hg38, hg19.
Supplementary files format and content: fasta.gz: chromosome-length nucleotide sequences generated usign Hi-C-guided genome assembly
Supplementary files format and content: hic: contact maps generated by aligning Hi-C data to reference sequences. In addition to "standard" hic maps build against chromosome-length references included are "assembly" maps generated by 3D-DNA for before and after genome assembly and an aggregate chromosome analysis (ACA) map.
Supplementary files format and content: bedpe: chromatin loops
Supplementary files format and content: bedgraph: A/B compartment annotations
Supplementary files format and content: sw: HDF5-based file for storing 3D structure ensembles
Supplementary files format and content: assembly: text file describing the relationship between the draft assembly and the chromosome-length upgrade
Supplementary files format and content: bed: gene annotations

organism: Bos taurus

source_name: sirloin

extract_protocol:
The protocol is described in detail in Sandoval-Velasco, Dudchenko, Rodríguez, Pérez Estrada et al., 2024. Briefly, PaleoHi-C is a a modified in situ Hi-C protocol, tailored towards working with highly degraded samples. The principal modifications were: (i) immediate preservation in the field using ethanol to reduce microbial activity; and (ii) sequestration of chromatin bodies on beads; (iii) removal of shearing and size selection given the lack of high molecular weight DNA; and (iv) library amplification using a paleo-compatible workflow
Library contruction protocol is described in detail in Sandoval-Velasco, Dudchenko, Rodríguez, Pérez Estrada et al., 2024.

value: sirloin


title: Hi-C of Bos taurus DNA Zoo Sample6834, DIY sirloin jerky in a food dehydrator, 2.5h, rep2


title: 4-OI treated WT BMDMs, 15h, rep3

description: sample 3-WT-4-OI-3

value: macrophages


title: w1118 (WT control) biological replicate 5

description: w1118 5


title: w1118 (WT control) biological replicate 4

description: w1118 4


title: Hi-C of Bos taurus DNA Zoo Sample6834, DIY sirloin jerky in a food dehydrator, 3.5h, rep1


title: pre-metastatic liver, pancreatic cancer, patient #80

description: 10x Genomics


title: control liver, low-grade pancreatic neuroendocrine neoplasm (PaNET), patient #82

description: 10x Genomics


title: 4-OI treated WT BMDMs, 15h, rep2

description: sample 2-WT-4-OI-2


title: Hi-C of Bos taurus DNA Zoo Sample6834, DIY sirloin jerky in a food dehydrator, 4.5h


title: w1118 (WT control) biological replicate 3

description: w1118 3


title: Hi-C of Bos taurus DNA Zoo Sample6834, DIY sirloin jerky in a food dehydrator, 2.5h, rep1


title: 4-OI treated WT BMDMs, 15h, rep1

description: sample 1-WT-4-OI-1


title: Cronobacter_turicencer_BHI_2

city: Zürich

first: Marc

last: Stevens

address: Winterthurerstrasse 272

department: Vetsuisse

country: Switzerland

institute: University of Zurich

data_processing:
Sequencing data were assessed for quality using fastqc 0.11.9 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The RNAseq reads  were mapped against the C. turicensis z3032 genome (accesion numbers NC_013282.2-NC_013285.1) using botwie2. Samtools was used to convert and sort the output and featureCounts summarized the aligned reads. Data normalization and determination of significance of differential expression was performed in R (R-project.org) using the GLM method in the EdgeR package as described previously [CIT].
Assembly: z3032 genome (NC_013282.2-NC_013285.1)
Supplementary files format and content: .csv file with edgeR normalised read counts

organism: Cronobacter turicensis

source_name: stationary phase cell culture

extract_protocol:
Cronobacter turicensis  z3032 cultures grown in LB to stationary phase (18 – 24 h).Cell were harvested and RNA extractions were performed using the miRNeasy Mini kit (Qiagen) according to the manufacturer’s protocols. An additional DNase treatment was performed with a TURBO DNA-free kit (Ambion) according to the manufacturer’s protocols. The concentration of the extracted RNA was measured using a NanoDrop Spectrophotometer.
125 bp paired-end RNA Sequencing on a HiSeq2500 (Illumina) were performed at the Functional Genomic Center at University Zurich (FGCZ), Zurich, Switzerland, accoring to the Illumina protocl

value: stationary phase cell culture

value: LB


title: w1118 (WT control) biological replicate 2

description: w1118 2


title: pre-metastatic liver, pancreatic cancer, patient #89

description: 10x Genomics


title: Hi-C of Bos taurus DNA Zoo Sample6834, DIY sirloin jerky in a food dehydrator, 1.5h, rep1


title: w1118 (WT control) biological replicate 1

description: w1118 1


title: Cronobacter_turicencer_BHI_1


title: pre-metastatic liver, pancreatic cancer, patient #71

description: 10x Genomics


title: Hi-C of Bos taurus DNA Zoo Sample6834, DIY sirloin jerky in a food dehydrator, control


title: Mouse control sgRNA 3 [A8]

status: Public on Jun 27 2024

city: Monrovia

first: Lili

last: Wang

state: CALIFORNIA

address: 1218 South Fifth Ave.

department: Systems biology

institute: City of Hope

description:
A8
Mouse splenic B

data_processing:
In house developed pipelines
Assembly: mm10
Supplementary files format and content: Tab-limited text with raw counts for each sample

source_name: Spleen

extract_protocol:
Total RNA was extracted from splenic B cells isolated from murine CLL and RT donor cells. ~200-300 ng was used to prepare the RNAseq libraries
Total RNA libraries were prepared using Ultra Lowinput library NugGen Kit following manufacturer instructions

value: Spleen

value: Control


title: Hi-C of Bos taurus DNA Zoo Sample6834, DIY sirloin jerky in a food dehydrator, 1.5h, rep2


title: Mouse control sgRNA 2 [A7]

description:
A7
Mouse splenic B


title: Mouse control sgRNA 4 [A9]

description:
A9
Mouse splenic B


title: Mouse control  with no sgRNA  [A5]

description:
A5
Mouse splenic B

value: Control with no sgRNA


title: Mouse CLL2 [A4]

description:
A4
Mouse splenic B

value: Chronic lymphocytic leukemia

value: MGA KO


title: Mouse CLL1 [A3]

description:
A3
Mouse splenic B


title: pre-metastatic liver, pancreatic cancer, patient #75

description: 10x Genomics


title: Mouse RT NSG2 [A2]

description:
A2
Mouse splenic B

value: Richters transformation


title: Mouse RT NSG1 [A1]

description:
A1
Mouse splenic B


title: control liver, ampullary adenoma, patient #83

description: 10x Genomics

value: control liver, ampullary adenoma


title: circRNA AC2

first: Yongzhi

state: Shanghai

address: Huashan Road 1954

institute: Shanghai Jiao Tong University

data_processing:
Data quality control was performed on raw RNA-sequencing results. For the mRNA and lncRNA sequencing data, we utilized the FastQC software (version 0.11.9) for initial quality checks and Cutadapt (version 4.2) software for adapter trimming. Following quality control, the sequencing reads were mapped to the mouse reference genome (Mus musculus GRCm38) using the HISAT2 software (version 2.2.1). Quantitative analysis of the RNA-Seq data was conducted using the StringTie software (version 2.1.5). The original expression profile was compared to the mouse annotation file to distinguish mRNA from lncRNA for further analysis.
For the miRNA sequencing data, quality control was performed and sequencing adapters were removed using Cutadapt software (version 4.2). After rigorous sequence filtering, target sequences within the 18 to 35 nucleotide (nt) range were selected. The distribution of these target sequences primarily fell within the 20 to 24 nt range, aligning with the typical length of microRNAs. Subsequently, the target sequences were mapped to the mouse reference genome (mm38) using Bowtie2 software (version 2.5.1). The aligned sequences were extracted and further mapped to the mouse reference microRNAs in miRbase using the Bowtie2 software (version 2.5.1). The CIRI2 software was employed for quantification and differential expression analysis of circle RNA.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: Male C57BL/6 mice (n=45, six weeks old) were randomly assigned to three groups: the CCl4-induced liver cancer group (liver cancer group), the PTH and CCl4-treated group (treatment group), and the control group (normal control group), with 15 mice per group. The mice in the normal control group received intragastric administration of double distilled water daily and intraperitoneal injections of olive oil twice a week. The liver cancer group was treated with intragastric administration of double distilled water daily and intraperitoneal injection of CCl4 twice a week. PTH was administrated intragastrically once a day for the treatment group, and CCl4 was injected intraperitoneally twice a week. In the 22nd week, we selected six mice from each group for RNA sequencing.

extract_protocol:
We extracted RNA from the mice liver tissues following the TRIzol reagent protocol provided by the manufacturer(Sigma).
After the removal of ribosomal RNA, two sequencing libraries were generated: NEBNext RNA Library Prep Kit (from NEB, USA) was used for lncRNA, circRNA, and mRNA sequencing, while the small RNA libraries were constructed using VAHTS Small RNA Library Prep Kit for Illumina (Vazyme #NR801) following the manufacturer's recommendations, respectively. Following the manufacturer's instructions, subsequent sequencing was performed on the Illumina HiSeq 4000 platform for paired-end 150 bp sequencing of lncRNAs, circRNAs and mRNAs, and on the Illumina NovaSeq platform for paired-end 50 bp sequencing of miRNAs.

treatment_protocol: We construct two groups liver cancer mice model using CCl4, one group treated with PZH and the other not.

value: water week 22


title: circRNA AC3


title: Brain, Mut3

city: Rancagua

first: Nicolas

last: Santander

address: Libertador Bernardo O'Higgins 611

country: Chile

institute: Universidad de O´Higgins

data_processing:
Align to mm10 with Rsubread
Quantification with FeatureCounts
Normalization and diffierential expression with DESeq2
Assembly: mm10
Supplementary files format and content: tab delimited file with raw counts for each sample
Supplementary files format and content: tab delimited file with results of differential expression analysis

source_name: Brain

extract_protocol:
Rneasy Plus micro kit Qiagen
NEBNext Ultra II RNA Library Prep Kit
Unstranded

value: Brain

value: Flvcr1a fl/fl; NestinCre+


title: Brain, Het2

value: Flvcr1a fl/+; NestinCre+


title: Brain, Mut1


title: Brain, Mut2


title: Brain, Het3


title: Brain, Het1


title: T47D_Pool2_Full_21day_Rep2

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

country: Austria

institute: Medical University Vienna

data_processing:
Hard trimming was performed using Trim-Galore v0.4.0 (--hardtrim5 20)
Reads were mapped to the sgRNA library using Bowtie v2.2.9 (PMID: 22388286). Reads with MAPQ lower than 30 were excluded from further analyses.
sgRNA counts were derived from the aligned reads using functions in the GenomicAlignments R package.
Assembly: Custom (design.fa.gz)
Supplementary files format and content: txt (tab-delimited, raw count for each sgRNA)

growth_protocol: Red Media condition (full growth media +oestrogen): T47D-dcas9-KRAB were maintained in DMEM (Gibco #11885-084) supplemented with 10% FBS (Seradigm #1500-500, Lot:077B15), 10mM HEPES, 1mM Sodium-Pyruvate, 1% P/S. For White Media (oestrogen-deprived media): T47D-dCas9-KRAB and LTED-dCas9-KRAB were maintained in Phenol-free DMEM (Gibco #11880-028) supplemented with 10% Fetal Bovine Serum, charcoal-stripped, USDA-approved regions (Gibco #12676029), 2mM L-Glutamine, 10mM HEPES, 1mM Sodium-Pyruvate, 1% P/S.

extract_protocol:
Cells were harvested and sgDNA isolated using the QIAamp DNA maxi kit (QIAGEN).
Amplicons containing the sgRNA sequences were amplified using NEBNext High-Fidelity (NEB).

treatment_protocol: T47D-dCas9-KRAB cells were infected with lentiviral particles at low MOI (≈0.3) in two independent replicates. We transduced ≈1'000 cells per plasmid present in the library to guarantee a good representation of all sgRNAs in the population of cells under screening. The cells were selected using 2μg/ml puromycin (Invitrogen) starting at 24 hours post-transduction and maintained in culture in CellStacks (Corning) in the described conditions and for the indicated time points.

tag: sgrna pool

tag: medium

tag: days post_transfection

tag: replicate


title: T47D_lib.Pool1.rep2

tag: cell line


title: T47D_lib.Pool2.rep2


title: T47D_Pool2_Full_21day_Rep1

value: Red Media condition (full growth media +oestrogen)


title: T47D_Pool2_Full_14day_Rep2


title: Mouse control sgRNA 1 [A6]

description:
A6
Mouse splenic B

tag: cell type

tag: genotype


title: T47D_Pool2_Full_14day_Rep1


title: T47D_Pool2_Depleted_7day_Rep2

value: White Media (oestrogen-deprived media)


title: T47D_Pool2_Depleted_7day_Rep1


title: T47D_Pool2_Depleted_60day_Rep1


title: T47D_Pool2_Depleted_21day_Rep1


title: T47D_Pool2_Depleted_14day_Rep2


title: T47D_Pool2_Depleted_21day_Rep2


title: circRNA AC4

city: Shanghai

value: liver

tag: treatment


title: T47D_Pool2_Depleted_14day_Rep1


title: T47D_Pool1_Full_14day_Rep2


title: T47D_Pool1_Full_21day_Rep1


title: T47D_Pool1_Full_14day_Rep1


title: T47D_Pool1_Depleted_7day_Rep1


title: T47D_Pool1_Depleted_60day_Rep1


title: T47D_Pool1_Depleted_21day_Rep1


title: T47D_Pool1_Depleted_21day_Rep2


title: T47D_Pool1_Depleted_60day_Rep2


title: T47D_Pool1_Depleted_7day_Rep2


title: T47D_Pool1_Depleted_14day_Rep2


title: hpEIN2[24_3]_20

city: Acton

first: Ian

middle: K

last: Greaves

state: act

address: clunies ross street

country: Australia

institute: csiro

data_processing:
Reads were trimmed using cut adapt -a TGGAATTCTCGGGTGCCAAGG --minimum-length=23
Reads were further timmed using cut adapt -u 4 -u -4
Trimmed reads were mapped to the Arabidopsis genome, EIN2 cDNA , hpEIN2 sequence including 35s promoter and sense strand of the different   asymmetric bulge stems
Reads were mapped using Bowtie 1.3.1 with options -v 0 -a --best --strata -l 18
awk commands were used to only retain reads which mapped to ein2 cDNA,  hpRNA or  stem sense strand sequences with only unique reads retained for downstream analysis
Assembly: TAIR10_chr_all.fas
Supplementary files format and content: raw files are in .fastq.gz format
Supplementary files format and content: processed files are unique reads mapped to the EIN2 sequence in a .bed format.  Rows are 1 = mapping to EIN2 or asymmetric bulge sense strands; 2 = Start; 3= End; 4 = read name; 5 = quality; 6 = strand; 7 = sRNA size

organism: Arabidopsis thaliana

growth_protocol: hpEIN2 T2 seedlings were grown on kaanmycin sterilized wild-type and T2 transgenic seeds were grown on ½  MS media (without organics) supplemented with 5mg/L 1-aminocyclopropane-1-carboxylic acid (ACC) and kanamycin (excluding WT lines). The plates were sealed tightly with parafilm and exposed under light for 10 h at 22° to promote germination, and then incubated in dark for 4 days.

extract_protocol:
RNA was extracted using trizol
NEXTFLEX Small RNA v3 library preperation with bead size selection
libraries sequenced on a Novaseq, 100 cycle

tag: tissue

value: whole seedling

tag: ecotype

value: Col

value: 4 day in dark


title: T47D_Pool1_Depleted_14day_Rep1


title: T47D_Pool2_Depleted_60day_Rep2


title: hpEIN2[24_2]_5


title: hpEIN2[24_3]_6


title: hpEIN2[24_3]_3


title: hpEIN2[24_1]_12


title: ChIP-Seq SAMD1 PaTu8988t FBXO11 KO (Exp 3)

city: Marburg

first: Robert

last: Liefke

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute of Molecular Biology and Tumor Research (IMT)

country: Germany

institute: Philipps University of Marburg

data_processing:
ChIP-Seq data were aligned to human Genome hg38 using bowtie allowing one mismatch.
Bigwig files were obtained using deepTools/bamCoverage normalized via RPKM.
Assembly: hg38
Supplementary files format and content: bigwig

growth_protocol: Patu8988t cells were cultured in DMEM, high glucose, GlutaMAX™ Supplement (Thermo Fisher Scientific; 61965026) supplemented with 5% fetal bovine serum (Thermo Fisher Scientific; 10270106).

extract_protocol:
ChIP experiments were performed in accordance to the One Day ChIP kit protocol (Diagenode).
For ChIP-Seq library five nanograms of precipitated DNA were used for indexed sequencing library preparation using the Microplex library preparation kit v2 (Diagenode).

treatment_protocol: SAMD1 and FBXO11 KO PaTu8988t cells were obtained using CRISPR/Cas9 mediated genome editing.

value: PDAC cell line

value: FBXO11 KO

value: SAMD1 (self-made)


title: hpEIN2[24_2]_13


title: hpEIN2[24_1]_7


title: hpEIN2[23]_14


title: hpEIN2[24_1]_6


title: ChIP-Seq SAMD1 PaTu8988t Control (Exp 2)

value: WT


title: hpEIN2[23]_7


title: ChIP-Seq SAMD1 PaTu8988t SAMD1 KO (Exp 1)

value: SAMD1 KO


title: T47D_Pool1_Full_21day_Rep2


title: hpEIN2[23]_5


title: ChIP-Seq SAMD1 PaTu8988t Control (Exp 3)


title: ChIP-Seq SAMD1 PaTu8988t Control (Exp 1)


title: hpEIN2[22]_10


title: RNA-Seq PaTu8988t SAMD1 KO repl3

data_processing:
RNA-Seq data were aligned to human transcriptome GenCode.v36 using RNA Star. Counts per gene were determined using FeatureCounts. Differentially expressed genes and normalized reads were determined using DeSeq2.
Assembly: hg38
Supplementary files format and content: tabular

extract_protocol:
Total RNA was extracted by using the RNeasy Mini system (Qiagen) including an on-column DNaseI digestion.
RNA-Seq libraries were prepared using the TruSeq Stranded mRNA Library Prep kit (Illumina).

treatment_protocol: SAMD1 KO PaTu8988t cells were obtained using CRISPR/Cas9 mediated genome editing.


title: hpEIN2[22]_4


title: hpEIN2[WT]_9


title: RNA-Seq PaTu8988t Control repl3

value: Control


title: RNA-Seq PaTu8988t SAMD1 KO repl1


title: hpEIN2[WT]_7


title: RNA-Seq PaTu8988t Control repl2


title: hpEIN2[WT]_5


title: hpEIN2[24_2]_7


title: RNA-Seq PaTu8988t Control repl1


title: Col_rep2

source_name: control


title: ChIP-Seq SAMD1 PaTu8988t FBXO11 KO (Exp 2)


title: EOSRC, tumor, sample 37

city: Hyderabad

first: Murali

middle: Dharan

last: Bashyam

address: Inner ring road, Uppal

country: India

institute: Centre for DNA Fingerprinting and Diagnostics

data_processing:
Quality assessment of raw RNA-Seq data was done using FastQC and subsequent filtering was done using Trimmomatic. Reads were aligned to GRCh38 reference human genome assembly from Ensemble using STAR. Transcript normalization and quantification was performed using RSEM and featureCounts.
Assembly: GRCh38
Supplementary files format and content: tab delimited text with normalized counts for each sample

source_name: rectal adenocarcinoma

growth_protocol: 37 EOSRC samples as part of the well annotated microsatellite stable CRC tissue repository

extract_protocol:
Total RNA from tissue samples was isolated using the TriZol reagent (Life Technologies, Grand Island, NY, USA) and RNeasy Kit (Qiagen, Valencia, CA, USA) following the manufacturer’s protocol.
Transcriptome sequencing was outsourced to Medgenome Labs Ltd, Bangalore, India. The libraries were prepared using Illumina TruSeq2 kit, following rRNA depletion and sequenced on HiSeq 2000 platform to generate 2x100 bp paired-end sequence reads.

value: rectal adenocarcinoma

tag: Sex

value: M

tag: tissue subtype

value: early-onset sporadic rectal cancer (EOSRC)


title: EOSRC, tumor, sample 35


title: Col_rep1


title: EOSRC, tumor, sample 36


title: EOSRC, tumor, sample 33

value: F


title: EOSRC, tumor, sample 32


title: hpEIN2[22]_8


title: EOSRC, tumor, sample 31


title: EOSRC, tumor, sample 30


title: EOSRC, tumor, sample 29


title: EOSRC, tumor, sample 27


title: RNA-Seq PaTu8988t SAMD1 KO repl2


title: EOSRC, tumor, sample 28


title: EOSRC, tumor, sample 26


title: EOSRC, tumor, sample 34


title: EOSRC, tumor, sample 24


title: EOSRC, tumor, sample 25


title: EOSRC, tumor, sample 23


title: EOSRC, tumor, sample 22


title: EOSRC, tumor, sample 21


title: VL RNA FLY at baseline before Bedrest rep6

city: Irvine

first: Fadia

last: Haddad

state: CA

address: 101 Academy Way, Suite 150

department: Pediatrics/Exercise Medicine Division

institute: University of California Irvine

description: Gene Expression at Baseline before Bed Rest

hyb_protocol: 1.2 ug of Cy3-labeled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x GEx hybridization bufferHI-RPM was added to the fragmentation mixture and hybridized to and hybridized to Agilent Human Gene Expression (8x60 k) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C with GE Wash buffer 2 (Agilent). Triton X-102 was added at 0.005% to all wash buffers before use.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan resolution 3um).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters. Text files were imported in GeneSpring software version 14.9.1, data was processed and quantile normalized. Additional data filtration was perfomed to exclude non detected and nonuniform /outlier features before further analysis

source_name: Vastus Lateralis muscle RNA Control at baseline before Bedrest+flywheel exercise

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200ng RNA using the One-Color Low RNA Input Quick Amp labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Adult male subjects (25-45y/o) were randomized to one of three groups: 1) control; no exercise, bed rest only (CON; n = 7), 2) bed rest + exercise using traditional exercise equipment (EX;  n = 7), and 3) bed rest + exercise using a flywheel device (FLY; n = 8).

extract_protocol: Total RNA was extracted from muscle using the Trizol reagent following the manufacturer's recommendations (Life technologies). Total RNA was cleaned using Qiagen RNeasy then quantified using a Nanovue GE-spectrophotometer and quality was assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Muslce biopsies were collected from vastus lateralis muscle from participants at Baseline before bedrest, then ~70 days after bedrest with or without exercise intervention.

value: Vastus Lateralis Skeletal Muscle

tag: gender

value: male

tag: age (y)


title: VL RNA FLY at baseline before Bedrest rep7


title: EOSRC, tumor, sample 20


title: VL RNA FLY at baseline before Bedrest rep8


title: VL RNA after 70d Bedrest+Flywheel Exercise rep7

description: Gene Expression after 70d Bed Rest with Flywheel Exercise protocol

source_name: Vastus Lateralis muscle RNA Control post 70d Bedrest+flywheel exercise


title: VL RNA after 70d Bedrest+Flywheel Exercise rep6


title: EOSRC, tumor, sample 18


title: VL RNA after 70d Bedrest+Flywheel Exercise rep8


title: EOSRC, tumor, sample 17


title: VL RNA after 70d Bedrest+Flywheel Exercise rep5


title: VL RNA after 70d Bedrest+Flywheel Exercise rep2


title: VL RNA after 70d Bedrest+Flywheel Exercise rep3


title: VL RNA FLY at baseline before Bedrest rep5


title: EOSRC, tumor, sample 15


title: EOSRC, tumor, sample 16


title: VL RNA FLY at baseline before Bedrest rep2


title: VL RNA FLY at baseline before Bedrest rep4


title: EOSRC, tumor, sample 14


title: VL RNA FLY at baseline before Bedrest rep1


title: VL RNA FLY at baseline before Bedrest rep3


title: EOSRC, tumor, sample 13


title: EOSRC, tumor, sample 19


title: EOSRC, tumor, sample 12


title: VL RNA after 70d Bedrest+Flywheel Exercise rep4


title: EOSRC, tumor, sample 11


title: VL RNA after 70d Bedrest+Flywheel Exercise rep1


title: VL RNA after 70d Bedrest+traditional exercise rep6

description: Gene Expression after 70d Bed Rest with standard Exercise protocol

source_name: Vastus Lateralis muscle RNA Control post 70d Bedrest+traditional exercise


title: VL RNA EX at baseline before Bedrest rep6

source_name: Vastus Lateralis muscle RNA Control at baseline before Bedrest+traditional exercise


title: EOSRC, tumor, sample 10


title: VL RNA after 70d Bedrest+traditional exercise rep7


title: VL RNA EX at baseline before Bedrest rep5


title: EOSRC, tumor, sample 8


title: EOSRC, tumor, sample 7


title: EOSRC, tumor, sample 6


title: VL RNA EX at baseline before Bedrest rep4


title: VL RNA EX at baseline before Bedrest rep3


title: VL RNA EX at baseline before Bedrest rep7


title: EOSRC, tumor, sample 5


title: EOSRC, tumor, sample 3


title: VL RNA after 70d Bedrest+traditional exercise rep4


title: EOSRC, tumor, sample 2


title: EOSRC, tumor, sample 1


title: VL RNA Control after 70d Bedrest rep7

description: Gene Expression after 70d Bed Rest with no exercise intervention

source_name: Vastus Lateralis muscle RNA Control post 70d Bedrest


title: VL RNA after 70d Bedrest+traditional exercise rep1


title: VL RNA after 70d Bedrest+traditional exercise rep3


title: VL RNA after 70d Bedrest+traditional exercise rep5


title: VL RNA after 70d Bedrest+traditional exercise rep2


title: VL RNA EX at baseline before Bedrest rep1


title: EOSRC, tumor, sample 9


title: VL RNA Control at baseline before Bedrest rep5

source_name: Vastus Lateralis muscle RNA Control baseline before Bedrest


title: I, replicate 3

city: Beijing

first: Xin

last: Zhang

state: Beijing

address: 38 Xueyuan Road

department: Institute of Systems Biomedicine

institute: Peking University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp (v0.20.1, https://github.com/OpenGene/fastp) with default parameters.
Trimmed sequence reads were mapped to GRCm38 using hisat2 (v2.2.1, http://daehwankimlab.github.io/hisat2/) with default parameters.
Read count extraction was performed using featureCounts (v2.0.1, https://subread.sourceforge.net/featureCounts.html) with default parameters.
The FPKM value of read count was calculated using the R program for normalization.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: RAW264.7 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was isolated with Trizol reagent (Vazyme).
Total RNA was then purified using poly-T oligo-attached magnetic beads. RNA-seq libraries were constructed using NEBNext® UltraTM RNA 24 Library Prep Kit for Illumina® (NEB, USA) and sequenced on an Illumina platform.

treatment_protocol: DMEM containing 10% inactivated FBS and 100 ng/ml LPS with 50 ng/ml mIFNγ were used for M1 polarization. During polarization, potassium iodide was added at the concentration of 20mM for I group.

value: Macrophage cells

value: LPS + mIFNgamma + I-


title: VL RNA Control at baseline before Bedrest rep6


title: VL RNA EX at baseline before Bedrest rep2


title: VL RNA Control after 70d Bedrest rep6


title: VL RNA Control at baseline before Bedrest rep7


title: I, replicate 2


title: EOSRC, tumor, sample 4


title: M1,replicate 3

value: LPS + mIFNgamma


title: M1,replicate 2


title: VL RNA Control at baseline before Bedrest rep4


title: M1,replicate 1


title: VL RNA Control after 70d Bedrest rep4


title: VL RNA Control after 70d Bedrest rep5


title: VL RNA Control after 70d Bedrest rep3


title: Mock,replicate 3

value: Mock


title: VL RNA Control at baseline before Bedrest rep3


title: MCF7.Pool2_Full_7day_Rep2

data_processing:
Hard trimming was performed using Trim-Galore v0.4.0 (--hardtrim5 20)
Reads were mapped to the sgRNA library using Bowtie v2.2.9 (PMID: 22388286). Reads with MAPQ lower than 30 were excluded from further analyses.
sgRNA counts were derived from the aligned reads using functions in the GenomicAlignments R package.
Genome_build: Custom (design.fa.gz)
Supplementary_files_format_and_content: txt (tab-delimited, raw count for each sgRNA)

growth_protocol: RM condition (full growth media +oestrogen): MCF7-dcas9-KRAB were maintained in DMEM (Gibco #11885-084) supplemented with 10% FBS (Seradigm #1500-500, Lot:077B15), 10mM HEPES, 1mM Sodium-Pyruvate, 1% P/S. For WM (oestrogen-deprived media): MCF7-dCas9-KRAB and LTED-dCas9-KRAB were maintained in Phenol-free DMEM (Gibco #11880-028) supplemented with 10% Fetal Bovine Serum, charcoal-stripped, USDA-approved regions (Gibco #12676029), 2mM L-Glutamine, 10mM HEPES, 1mM Sodium-Pyruvate, 1% P/S.

treatment_protocol: MCF7-dCas9-KRAB and LTED-dCas9-KRAB cells were infected with lentiviral particles at low MOI (≈0.3) in two independent replicates. We transduced ≈1'000 cells per plasmid present in the library to guarantee a good representation of all sgRNAs in the population of cells under screening. The cells were selected using 2μg/ml puromycin (Invitrogen) starting at 24 hours post-transduction and maintained in culture in CellStacks (Corning) in the described conditions and for the indicated time points.

tag: sgrnas pool

value: Red Media

tag: days post transfection


title: Mock,replicate 2


title: MCF7.Pool2_Full_7day_Rep1


title: Mock,replicate 1


title: VL RNA Control after 70d Bedrest rep2


title: MCF7.Pool2_Full_21day_Rep2


title: PKD2 mutant kidney_organoid

city: Jinan

first: liqiang

last: guo

state: Shandong

address: No. 107, Wenhua West Road

department: Shandong University

institute: Qilu Hospital

data_processing:
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 reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
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. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: HISAT2 v2.0.5
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PKD2 mutant kidney

extract_protocol:
RNA libaries were prepared for sequencing using standard Illumina protocols
RNA libraries for scRNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: PKD2 mutant kidney

value: Primary cells

value: Kidney cells

value: Organoid

value: organoid culture


title: PKD1 mutant kidney_organoid

source_name: PKD1 mutant kidney

value: PKD1 mutant kidney


title: MCF7.Pool2_Full_21day_Rep1


title: I, replicate 1

value: WT


title: HC, PMN, rep3

city: Helsinki

first: Tomas

last: Strandin

address: Haartmaninkatu 3

department: Virology

country: Finland

institute: University of Helsinki

data_processing:
Illumina Bcl2fastq2 Conversion Software (version v2.20.0.422) was used to convert BCL files to FASTQ file format and demultiplex samples.   Sample specific read files were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic (v.0.39). Trimmed reads were aligned to mouse genome using STAR aligner (v.2.7.6a) in two-pass mode. Reference genome and gene annotations were based on GENCODE release v44 (GRCh38.p14). Counts per gene were then collected using featureCounts from Subread package (v2.0.1).   ------------------------------------------------ References: Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer for Illumina Sequence Data. Bioinformatics, btu170. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25. PMID: 23104886; PMCID: PMC3530905. Liao Y, Smyth GK and Shi W (2014). featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics, 30(7):923-30.   In addition we used FastQC (version 0.11.9) and MultiQC (v1.9) to check the quality of the data
Conversion and Demultiplexing: Illumina Bcl2fastq2 Conversion Software (version v2.20.0.422) was used to convert BCL files to FASTQ file format and demultiplex samples.
Quality Control and Trimming: Sample-specific read files were trimmed for adaptor sequences and masked for low-complexity or low-quality sequences using Trimmomatic (v0.39) .
Quality Assessment: FastQC (version 0.11.9) and MultiQC (v1.9) were used to check the quality of the data.
Read Alignment: Trimmed reads were aligned to the mouse genome using STAR aligner (v2.7.6a) in two-pass mode .
Quantification: Counts per gene were collected using featureCounts from the Subread package (v2.0.1) .
Assembly: The reference genome and gene annotations were based on GENCODE release v44 (GRCh38.p14).
Supplementary files format and content: Gene expression table (.txt): A table with gene expression levels for each sample. The table includes gene identifiers and normalized read counts for each gene across all samples.
Supplementary files format and content: MultiQC Report (html): A comprehensive report generated by MultiQC that summarizes the quality control metrics for both raw and aligned sequence data. This includes per-base sequence quality, GC content, sequence duplication levels, overrepresented sequences, and alignment statistics.
Supplementary files format and content: FeatureCounts: generated by the featurecounts tool.Text files (format). Contains raw read counts for each gene in each sample, summary of read assignment results including counts of successfully assigned reads and unassigned reads, and log file with details of the featureCounts run, parameters used, and summary of the process.

source_name: Peripheral blood neutrophils (PMN)

extract_protocol:
RNA was extracted from the samples using the Trizol method followed by RNA isolation using the RNeasy micro kit.
RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (# E7760) combined with NEBNext Poly(A) mRNA Isolation Module (NEB #E7490)
Library preps were started with 25 ng input and 14x cycles were used in the indexing PCR. Library pool was sequenced as 1.3 pM with 1% PhiX in NextSeq 500 high output 1x75bp flowcell.

value: Peripheral blood neutrophils (PMN)

value: Polymorphonuclear neutrophils (PMNs)

value: Healthy control


title: HC, PMN, rep2


title: VL RNA Control at baseline before Bedrest rep1

value: Vastus Lateralis Skeletal Muscle


title: HC, PMN, rep4


title: MCF7.Pool2_Full_14day_Rep2


title: MCF7.Pool2_Depleted_7day_Rep2

value: White Media


title: HC, PMN, rep1


title: MCF7.Pool2_Full_14day_Rep1


title: MCF7.Pool2_Depleted_7day_Rep1


title: PUUV, PMN, rep4

value: PUUV-infected


title: PUUV, PMN, rep3


title: PUUV, PMN, rep2


title: MCF7.Pool2_Depleted_60day_Rep2


title: VL RNA Control after 70d Bedrest rep1

value: male


title: MCF7.Pool2_Depleted_60day_Rep1


title: PUUV, PMN, rep1

source_name: Peripheral blood neutrophils (LDG)

value: Peripheral blood neutrophils (LDG)

value: Low-density granulocytes (LDGs)


title: MCF7.Pool2_Depleted_14day_Rep2


title: MCF7.Pool1_Full_7day_Rep1

value: Red Media


title: PUUV, LDG, rep8


title: PUUV, LDG, rep7


title: PUUV, LDG, rep5


title: PUUV, LDG, rep6


title: MCF7.Pool2_Depleted_21day_Rep2


title: MCF7.Pool1_Full_7day_Rep2


title: PUUV, LDG, rep3


title: PUUV, LDG, rep4


title: PUUV, LDG, rep2


title: MCF7.Pool1_Full_14day_Rep2


title: SaOs2cells, Negative control GapmeRs, replicate 3

city: Berlin

first: January

last: Weiner

address: Charitéplatz 1

department: CUBI

institute: Berlin Institute of Health, Charité Medical University of Berlin

data_processing:
QC of the sequencing was performed with the help of fastqc, dupradar,
Reads were mapped to human genome, GRCh37p7 using the STAR aligner
For quantification, the GENCODE model GRCh38 v.25 was used
Differential gene expression was performed with DESeq2 package, v. 1.30.1
Gene set enrichment analysis was done with the tmod R package, version 0.50.1
Assembly: GRCh38 p7
Supplementary files format and content: Tab separated value file containing gene IDs and raw counts

source_name: bone

growth_protocol: SaOS-2 cells were cultured in complete growth medium Alpha MEM Eagle (PAN-Biotech GmbH) supplemented with 10% fetal bovine serum and 50 mg/mL gentamicin.

extract_protocol:
Total RNA was extracted from SaOS-2 cells using the RNeasy Mini Kit (Qiagen).
500 ng total RNA of transfected cell cultures were used for library generation with the TrueSeq stranded total RNA kit (Illumina). Libraries were sequenced with 16 million reads (75 bp single end) on a NextSeq 500 using the NextSeq 500/550 High Output Kit v2.5 (75 Cycles).

treatment_protocol: SaOS-2 cells were seeded at a density of 100 cells per 6-well with Lipofectamine 2000 one day prior to GapmeRs (single-stranded antisense oligos) transfection. 3 cell cultures of SaOS-2 cells were transfected with LNA GapmeRs targeting the main transcript of CEBPB or negative control GapmeRs and harvested after 48 hours.

value: bone

value: primary osteogenic sarcoma

value: Negative control GapmeRs


title: PUUV, LDG, rep1


title: MCF7.Pool1_Full_21day_Rep1


title: MCF7.Pool1_Full_21day_Rep2


title: MCF7.Pool1_Full_14day_Rep1


title: MCF7.Pool1_Depleted_7day_Rep2


title: MCF7.Pool1_Depleted_7day_Rep1


title: SaOs2cells, GapmeRs targetting CEBPB, replicate 3

value: GapmeRs targetting CEBPB


title: MCF7.Pool1_Depleted_60day_Rep2


title: SaOs2cells, Negative control GapmeRs, replicate 2


title: SaOs2cells, Negative control GapmeRs, replicate 1


title: MCF7.Pool2_Depleted_21day_Rep1


title: MCF7.Pool2_Depleted_14day_Rep1


title: MCF7.Pool1_Depleted_60day_Rep1


title: SaOs2cells, GapmeRs targetting CEBPB, replicate 1


title: MCF7.Pool1_Depleted_14day_Rep2


title: MCF7.Pool1_Depleted_14day_Rep1


title: P4, ST-seq

description: 10x Visium

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Space Ranger software v1.3.0 (https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger)
R package Seurat (4.0.3) was used for downstream analysis such as normalization, integration, dimensionality reduction and clustering (https://satijalab.org/seurat/).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files, matrix files and HE figure

source_name: thyroid

growth_protocol: Our study was approved by the Ethics Committee of Peking University Third Hospital (LM2023126). Six patients, including 4 diagnosed with PTC in combination with Hashimoto thyroiditis and 2 diagnosed with Hashimoto thyroiditis were recruited in our study. All the patients signed the informed written consent for each subject and agreed to donate the specimens. For samples of adequate size, small fragments of each sample were snap frozen in optical cutting tissue (OCT) compound (Fisher Healthcare) and/or fixed in 10% formalin (Sigma-Aldrich).

extract_protocol:
The ST protocol was optimized for PTC and HT tissues according to manufacturer’s instructions (10x Genomics, CG000239 Rev E). The optimal incubation time for permeabilization was determined to be 22 min. Once optimal conditions were established, the cryosections (10 μm thick) per patient were cut onto the ST slides and processed immediately. Fixation, H&E staining, and imaging protocols were as describe by the manufacturer (10x Genomics, CG000239 Rev E). Sectioned slides were incubated at 37 ℃ for 1 min, fixed in 3.7% - 3.8% formaldehyde (Sigma-Aldrich) in PBS for 10 min, and then washed in 1x PBS (Medicago). For staining, sections were incubated in Mayer’s hematoxylin (Dako, Agilent) for 4 min, bluing buffer (Dako) for 30 sec, followed by eosin (Sigma-Aldrich) diluted 1:5 in Tris-base (0.45 M Tris, 0.5 M acetic acid, pH 6.0) for 30 sec. The slides were washed in water free of RNase and DNase after each of the staining steps. After air-drying, the slides were mounted with 85% glycerol (Merck Millipore) and coverslips. Bright-field images were taken at 20 × magnification using a Metafer Slide Scanning platform (MetaSystems). Raw images were stitched with VSlide software (MetaSystems). The coverslips and glycerol were removed after imaging by immersing slides in water free of RNase and DNase.
Library was performed according to the manufacter’s instructions (10x Genomics, CG000239 Rev E). After Reverse transcription, wells were washed with 0.1×SSC and incubated at 56 ℃ with interval shaking for 1.5 h with a tissue removal mix of Proteinase K (QIAGEN) and PKD buffer (QIAGEN, pH7.5) at a 1:1 ratio. The spatially barcoded cDNA was enzymatically released as previously described. Supernatants containing released cDNA were collected and transferred to 96-well plates for ST library preparation with an automated MBS 8000 system. Second-strand cDNA synthesis was followed by in vitro transcription, adaptor ligation, and a second RT. Sequencing handles and indexes were added in an indexing PCR, and the finished libraries were purified and quantified according to the manufacturer’s instructions (Visium spatial gene expression reagent kits, No. CG000239 Rev E). The libraries were sequenced on an Illumina NextSeq platform.

value: thyroid


title: LTED.Pool2_7day_Rep2


title: P2, ST-seq

description: 10x Visium


title: MCF7.Pool1_Depleted_21day_Rep2


title: P1, ST-seq

description: 10x Visium


title: LTED.Pool2_7day_Rep1


title: LALB-CN-RNAseq-Rep2

city: Rome

first: Stefano

last: Di Giovenale

address: Via Elio Chianesi,  53

country: Italy

institute: IRCCS National Cancer Institute Regina Elena

data_processing:
RNAseq samples were aligned to hg19 through STAR and quantified with RSEM. Both the alignment and quantification were performed through the nf-core/rnaseq v3.0 from NEXTFLOW v21.05.0-edg with parameters: --aligner star_rsem.
Assembly: hg19

source_name: Bone Marrow

extract_protocol:
Total RNA was extracted from patient samples using Qiazol (Qiagen, IT), purified from DNA contamination through a DNase I (Qiagen, IT) digestion step and further enriched by Qiagen RNeasy columns for gene expression profiling (Qiagen, IT)
RNA libraries were generated using the same amount of RNA for each sample according to the Illumina TruSeq Stranded Total RNA kit with an initial ribosomal depletion step using Ribo Zero Gold (Illumina, CA). The libraries were quantified by qPCR and sequenced in paired-end mode (2×75 bp) with NextSeq 500 (Illumina, CA).

value: Bone Marrow

tag: disease state

value: Pediatric B-cell acute lymphoblastic leukemia

value: Primary B-cell CD138+

value: LAL-B


title: LALB-K27Ac

data_processing:
Reads of each experiment were quality controlled with FASTQC v0.11.9 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) combined with MultiQC v.1.9 and aligned to the reference genome hg19 using bowtie2 v.2.3.5.1 setting    local mode with default parameters. The generated sequence alignments were stored into SAM format files and converted into BAM format, sorted, and indexed with SAMtools v.1.2. The duplicated reads were removed by utilizing MarkDuplicated tool available in GATK4 suite v.4.1.8.1. Peaks were called using the function callpeak of MACS2 v.2.2.6 tool (parameters: --format AUTO --broad -B -q 0.1 -g hs), and those matching backlisted regions of hg19 were removed. Peaks stored in bedGraph format files were sorted and converted in bigWig format with bedGraphToBigWig v.4.
Assembly: hg19

extract_protocol:
Chromatin immunoprecipitation (ChIP) assays were performed as previously described (Bruno T, Cancer Cell, 2002) by using anti-acetyl-Histone H3 (Lys27) antibody (Millipore). Equal amounts of precleared chromatin were added to antibody-bound Dynabeads (Thermo Fisher Scientific). About 6 ng of the immunoprecipitated chromatin was used to prepare the libraries for sequencing by following the manufacturer’s instructions (Swift Bioscences, Cat. No. 21024).
ChIP: The final libraries were controlled on an Agilent 2100 Bioanalyzer (Agilent Technologies) and sequenced in paired-end mode (2×75 bp) with NextSeq 500 (Illumina, CA).


title: LALB-HIC-Pro-Cap

description: LALB-HIC-Pro-Cap

data_processing:
Promoter Capture Hi-C: paired-end FASTQ files were aligned against the hg19 genome. The KR-normalized contact matrices and the loop annotation were performed with Juicer v 1.9.9. Loops were called at 5kb, 10kb, and 25kb resolution.
Assembly: hg19

extract_protocol:
Promoter-Capture HiC : Cells were crosslinked with 1% formaldheyde, digested with a restriction enzyme cocktail, end-labeled with Biotin-14-dATP and then followed by ligation. The ligated chromatin was reverse cross-linked and sonicated using Bioruptor ultrasonicator to produce 300-500 bp fragments. Fragmented DNA was then size-selected to have a size distribution between 200-600 bp, and finally subjected to biotin enrichment
Promoter-Caputre HiC : DNA libraries were prepared using Accel-NGS 2S Plus DNA Library Kit (Swift Bioscences, Cat. No. 21024), and the resulting libraries were amplified using the KAPA library amplification kit. Subsequently libraries were hybridized to specific SureSelect XT Human capture libraries (Agilent Technologies) and sequenced in paired-end mode (2×75 bp) with NextSeq 500 (Illumina, CA).


title: LTED.Pool2_14day_Rep2


title: LALB-CN-RNAseq-Rep3


title: LTED.Pool2_21day_Rep2


title: LTED.Pool2_14day_Rep1


title: LTED.Pool2_21day_Rep1


title: Onset_11_RNAseq

value: B-cell CD138+

tag: tumor stage

value: Primary


title: SaOs2cells, GapmeRs targetting CEBPB, replicate 2

value: WT


title: LALB-CN-RNAseq-Rep1


title: LTED.Pool1_7day_Rep1

tag: medium

value: White Media


title: Onset_16_RNAseq


title: LTED.Pool1_7day_Rep2