title: ECCITE-seq, replicate 2

city: Cambridge

first: Alisdair

last: Russell

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing and gene counting were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Guide barcodes in cells were detected using cite-seq-count v. 1.4.2
Final cell guide assignments using bespoke R script (supplied with publication)
Assembly: grch38 ensembl release 99
Supplementary files format and content: Tab-separated values files and matrix files from cellranger
Supplementary files format and content: Filtered counts matrix

source_name: Breast

extract_protocol:
MCF7 cells, transduced with a CROP-seq library targeting ER cofactors and selected for 6 days, were harvested by trypsinisation and libraries prepared using the 10x Chromium single cell 5' library and gel bead kit.
Library prep was performed as per manufacturers instructions (chromium single cell 5' kit, 10x Genomics). Briefly, single-cell RNA-seq libraries were prepared iusing the following: Chromium Single Cell 5′ Library & Gel Bead Kit, PN-1000006; Chromium Single Cell A Chip Kit, PN-120236; Chromium i7 Multiplex Kit, PN-120262; and the Single-Cell V(D)J Reagent Kit (10X Genomics). To amplify gRNAs, 12 pmol RT primer (gd_RT_v4) was spiked into the library prep as described by Mimitou et al (2019) Nature Methods16:409-412

value: Breast

value: ER positive breast cancer

value: Mixed

value: CRISPR KO of 13 genes


title: Input_H4k20me3_NOAA

status: Public on Dec 31 2024

type: SRA

city: Los Angeles

first: Siavash

middle: K

last: Kurdistani

state: CA

address: 615 Charles E Young Dr South

department: Biological Chemistry

country: USA

institute: UCLA

library_source: genomic

data_processing:
Reads were mapped to the Human (hg19) genome using Bowtie software. Only reads that aligned to a unique position in the genome with no more than two sequence mismatches were retained for further analysis. Duplicate reads that mapped to the same exact location in the genome were counted only once to reduce clonal amplification effects. To estimate ChIP enrichment, IP and corresponding input files were randomly sub-sampled to equalize the number of reads. The genome was tiled with 50 bp windows. Each read was extended by 150 bases (so we refer to tags as the extend read counts within a bin). With custom Python script, the total counts of the input and ChIP samples were normalized to each other and determined enrichment P-value using Poisson distribution.
Genome_build: hg19
Supplementary_files_format_and_content: bed

molecule: genomic DNA

organism: Homo sapiens

source_name: Cell line

growth_protocol: HeLa cells were maintained in DMEM (Cellgro #10-013-CV) supplemented with 10% fetal bovine serum (FBS) (Thermo Fisher HyClone #SV30014.03).

extract_protocol:
Cells were crosslinked with 1% formaldehyde. Cell lysates were cleared from sonicated nuclei and protein-DNA complexes were isolated with indicated antibodies.
DNA obtained from ChIP experiments was quantified using Qubit assays (Invitrogen #Q32854). 2 ng DNA from each ChIP and corresponding input samples were used to prepare libraries using the NuGEN Ovation Ultralow Library System (NuGEN Technologies #0331) or the KAPA LTP kit (KAPA Biosystems #8230) and sequenced with Illumina Hi-seq platforms to obtain 50 bp-long reads.

treatment_protocol: Media containing complete amino acids (AA) were made from DMEM powder (US Biological #D9802) and supplemented with an additional 3.5 g/L D-glucose (for a total of 4.5 g/L), 1 mM sodium pyruvate (Gibco #11360070), 3.7 g/L sodium bicarbonate, and 0.0159 g/L sodium phenol red (US Biological #P4040). Media without AA were made from DMEM without amino acids powder (US Biological #D9800-013) and supplemented with an additional 3.5 g/L D-glucose, 1 mM sodium pyruvate (Gibco #11360070), and 3.7 g/L sodium bicarbonate. pH of media was adjusted to 7.2 by the addition of HCl before being filter sterilized and supplemented with 10% dialyzed FBS (Gibco #26400-044).

tag: antibody

tag: cell line

value: HeLa

tag: treatment

value: without AA


title: MB7434 strain (DHB4 + pAL-FevREco105-CYTO-FLAG) treated at 30°C, replicate 3

city: Ipswich

first: Augusto

middle: Emanuel

last: Garcia

state: MA

address: 240 County Rd

department: Research

institute: New England Biolabs

library_source: transcriptomic

data_processing:
To remove reads mapping to rRNA, the reads were first aligned to a custom .fasta file containing the DNA sequences coding for rRNA in the complete genome reference of Escherichia coli K-12 strain DHB4 (GenBank accession CP014270.1) using Bowtie2 version 2.3.4.1 set for paired-end reads through Galaxy.
The remaining reads (unaligned reads from previous step) were aligned to Escherichia coli str. K-12 substr. MG1655 complete genome reference (NCBI Reference Sequence accession NC_000913.3) using Bowtie2 (version 2.3.4.1) set for paired-end reads, with >80% of the reads aligning concordantly exactly 1 time through Galaxy.
Aligned reads were summarized using featureCounts from the subread package (version 1.6.4) through Galaxy, using the “Unstranded” setting, to obtain a table of counts for each of the annotation features labelled as “gene” in the NC_000913.3.gff3 file downloaded directly from NCBI. Genes labelled with locus_tag were converted to gene names through the curated annotations in Ecocyc database using Ecocyc SmartTables tools.
The obtained tables of counts were imported into RStudio and analyzed using DESeq2 (version 1.28.1) Counts from replicates were compared using PCA plots. Based on the dissimilarities among replicates observed in these plots, one of the 30°C replicates was dropped for each of the MB7409, MB7410 and MB7434 strains.
For Differential Expression of Genes in DESeq2, the conditions compared were the following:  At 30°C  MB7410 vs MB7409  MB7434 vs MB7409  MB7180 vs MB7050  MB7433 vs MB7050  At 42°C  MB7410 vs MB7409  MB7434 vs MB7409  MB7180 vs MB7050  MB7433 vs MB7050
Genome_build: NC_000913.3
Supplementary_files_format_and_content: The log2FoldChange and p-adj values for each gene for each comparison, obtained by differential expression analysis from DESeq2, were merged into a single matrix.

molecule: total RNA

organism: Escherichia coli K-12

growth_protocol: Cells were grown overnight in 5ml LB media + 10µg cloramphenicol and diluted 1/100 into 15ml of the same media in a 25ml flask. These cultures were grown for 4 hours until they reached exponential phase before applying treatment (changing temperature)

extract_protocol:
1.5ml of each culture was harvested by centrifugation and total RNA was extracted using RNAeasy Mini Kit (Qiagen cat#74104) including the DNAse treatment step with RNase-Free DNase Set (Qiagen cat#79254) following the vendor guidelines. An extra DNase treatment step was added after extraction using DNase I (RNase-free, New England Biolabs cat#M0303S) and RNA was purified using Monarch® RNA Cleanup Kit (New England Biolabs cat#T2040L) eluting in 10µl. Concentration was measured using QubitTM dsDNA BR Assay Kits (Invitrogen cat#Q32850) on a Qubit 2.0 Fluorometer, and the RNA Integrity Number (RIN) was corroborated to be >9 using RNA 6000 Nano Kit (Agilent cat#5067-1511) on an Agilent 2100 Bioanalyzer System.
For samples MB7409, MB7410 and MB7434 treated at 30°C: library preparation, sequencing and analysis was performed by CD genomics. Firstly, the ribosomal RNA depletion was performed using NEBNext® rRNA Depletion Kit (Bacteria, New England Biolabs cat#E7860S). The rRNA-depleted RNA was purified by 2x RNAClean XP beads (Beckman Coulter) and eluted in 45ul of nuclease-free water. The purified RNA was then mixed with 4ul of NEBNext First Strand Synthesis Reaction Buffer and 1ul of random primers. The reaction was incubated at 94C for 12 mins for fragmentation. Subsequently, to perform first strand cDNA synthesis, 8ul of NEBNext Strand Specificity Reagent and 2ul of NEBNext First Strand Synthesis Enzyme Mix was added to the reaction and the reaction was incubated at 25C 10 mins, 42C 30 mins, 70C 15 mins. Second strand reaction was then performed by adding 8ul of NEBNext Second Strand Synthesis Reaction Buffer with dUTP Mix (10X), 4ul of NEBNext Second Strand Synthesis Enzyme Mix, and 48ul of nuclease-free water. The reaction was incubated at 16C 1hr. The cDNA was purified by 1.8x SPRIselect Beads (Beckman Coulter) and eluted in 50ul of nuclease-free water. The reaction was incubated at 16C 1hr. The cDNA was purified by 1.8x SPRIselect Beads (Beckman Coulter) and eluted in 50ul of nuclease-free water. Subsequently, end prep reaction was performed by adding 7ul of NEBNext Ultra II End Prep Reaction Buffer and 3ul of NEBNext Ultra II End Prep Enzyme Mix into 50 ul purified cDNA. Endprep reaction was incubated at 20C 30 mins and 65C 20 mins. Adaptor ligation reaction was then performed by adding 1ul of NEBNext Ligation Enhancer, 30ul of NEBNext Ultra II Ligation Master Mix, and 2.5ul of NEBNext Adaptor, diluted to 0.5uM in Adaptor Dilution Buffer. The mix was incubated at 20C 15 mins. 3ul of USER Enzymer (New England Biolabs) was then added to the ligation product and the reaction was incubated at 37C 15 mins. The ligated product was purified by SPRIselect Beads (Beckman Coulter) and eluted in 15ul of nuclease-free water. PCR was carried out by adding 25ul of NEBNext Ultra II Q5 Master Mix, 5ul of i5 Primer, and 5ul of i7 Primer into 15ul of purified ligated product. PCR was performed at 98C 30 seconds, 15 cycles of 98C 10 seconds and 65C 75 seconds, and a final extension at 65C 5 mins.  The final library was then purified by SPRIselect Beads and loaded into Illumina NovaSeq6000 paired end 150 bp mode for sequencing. For the rest of the samples: Ribosomal RNA was removed from the total RNA with NEBNext® rRNA Depletion Kit (Bacteria, New England Biolabs cat#E7860S). Libraries were prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs cat#E7760L) using oligos for indexing from NEBNext® Multiplex Oligos for Illumina® (96 Unique Dual Index Primer Pairs, New England Biolabs cat#E6440S). Final library quality and concentration was estimated using High Sensitivity DNA Kit (Agilent cat#5067-4626) on an Agilent 2100 Bioanalyzer System and all the libraries were pooled at 4nM in 20uL and sequenced on the Illumina Nextseq 500 Mid Output 2x75+8i+8i  following the manufacturer's protocols.

treatment_protocol: After reaching exponential phase (first 4 hours of growth), cells were grown in the conditions specified for each sample (either 0.5h or 1h at at either 30°C or 42°C).

tag: strain

tag: genotype

value: Wild-type

tag: plasmid

tag: growth time and  temperature

value: 4h at 30°C

tag: treatment time and temperature

value: 0.5h at 30°C


title: Control Female 01

city: Bristol

first: Benjamin

middle: Thomas

last: Gillard

address: Dorothy Hodgkin Building

department: Bristol Medical School

country: United Kingdom

institute: University of Bristol

data_processing:
BBDuk, read trimming
FastQC, read quality control
Rsubread, Alignment to Jac genome (GCA_00028075.1)
FeatureCounts Read summarisation
DESeq2 Differential Expression Analysis
Assembly: GCA_00028075.1
Supplementary files format and content: Featurecounts raw counts file
Supplementary files format and content: DESeq2 results from dehydration vs control comparison
Supplementary files format and content: DESeq2 results from rehydration vs control comparison

molecule: polyA RNA

organism: Jaculus jaculus

source_name: Supraoptic nucleus (hypothalamus)

growth_protocol: All animals were kept single housed at 25°C constant temperature, 12-hour light cycle, with free access to dry food pellets throughout.

extract_protocol: Fresh frozen brains were sliced on the coronal plane at 100microns on a cryostat. Twelve bilateral punches of the SON were taken using a 1mm sample core within the cryostat chamber kept at -20C and kept on dry ice. A pestle and mortar with liquid nitrogen was used to break up the sample. Powdered tissue was lysed using no more than 100ml/mg of Trizol. Chloroform phase separation was used to isolate RNA then cleaned up using Zymo Direct-Zol RNA miniprep kit as per manufacturer's instructions. All storage was at -80C.

treatment_protocol: Animals were randomly assigned to three experimental groups: Control (access to water ad libitum), Dehydrated (water restriction 11 days), and Rehydration (water restriction 7 days followed by access to water ad libitum 3 days).

tag: tissue

value: Supraoptic nucleus (hypothalamus)

tag: Sex

value: Female

value: Control


title: HeLa_AA_chromRNAseq

description: total RNA

data_processing:
Reads were mapped to the Human genome (hg19) and to spike-in reference sequences using default parameters of TopHat. SAMMate software was used to determine the transcript RPKM (reads per kilobase of exon per million of reads) for mRNA-seq libraries. The sums of RPKM values from the spike-in controls were used to normalize across samples and to adjust transcripts RPKM.
Genome_build: hg19
Supplementary_files_format_and_content: Excel workbook with normalized RPKM values for all samples except the chromRNAseq samples. For chromRNAseq samples, we used mapped counts around the gene regions to illustrate newly synthesized transcripts.   Therefore, processed data for those two libraries are mapped read coverage in wig format (available on the sample records).

extract_protocol:
Total RNA was extracted using the Trizol reagents (Ambion #15596026) and treated with TURBO DNase (Ambion #AM2239).
1 μg of total RNA was used to prepare sequencing library using the Illumina TruSeq RNA sample preparation kit. A mixture of external RNA spike-in controls (Ambion #4456740) was added to total RNA prior to library preparation. Libraries were sequenced with Illumina Hi-seq platforms to obtain 50 bp-long reads. No spike-in control was added to biological replicate 2, and 100 bp-long reads were obtained from those two libraries.  For chromatin RNA-seq, chromatin subcellular fractionation was isolated. Total RNA-seq libraries were prepared and sequenced with Illumina Hi-seq platforms to obtain 50 bp-long reads.

value: AA

tag: sirna mediated knockdown and plasmid


title: ECCITE-seq, replicate 2 (guideLib)

description: 10x Genomics

library_source: transcriptomic single cell

tag: cell type


title: Rehydrated Male 01

value: Male

value: Rehydrated


title: Dehydrated Male 09

value: Dehydrated


title: ECCITE-seq, replicate 1 (guideLib)

description: 10x Genomics


title: A-eMSCs EGR1-KD-2

city: Nanjing

first: Tao

last: Gui

state: Jiangsu

address: NO.100 Shizi Street, Hongshan Road

country: China

institute: Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine

data_processing:
Illumina NovaSeq6000 sequencer was used and the sequencing mode was PE150.
Quality control standard: the data volume is about 6G/ sample, and the proportion of each base mass greater than 20 (Q20 ratio) is not less than 90%.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include FPKM and count values for each Sample

source_name: Eutopic endometrium from patients with adenomyosis

growth_protocol: A-eMSCs were maintained in DMEM/F12 supplemented with 10% fetal bovine serum and 100 µg/ml streptomycin and 100 IU/ml penicillin at 37˚C in a 5% CO2 incubator.

extract_protocol:
Total RNA was extracted using MagBeads Total RNA Extraction Kit (Cat#T02-096) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries for RNA-seq were prepared using KAPA RNA HyperPrep Kit following manufacturer's protocols. The concentration was detected and quatified by Qubit® 2.0 Fluorometerand Labchip.

treatment_protocol: Adipogenic differentiation was induced by treatment of 2-day post confluent cells (designated day 0, D0) with 10ug/ml insulin (Sigma),

value: Endometrial mesenchymal stem cells (eMSCs)

value: Adenomyotic eutopic endometrial mesenchymal stem cells (A-eMSCs)

value: WT

value: Lentivirus-mediated EGR1 knockdown


title: Input_H4k20me3_AA


title: Ovarian immature teratoma, patient 2

type: RNA

city: Shanghai

first: Kezhe

last: Tan

address: Luding Road 355, Shanghai, China

institute: Shanghai Children's Hospital

description: Gene expression after 12hr  in 8Gy-irradiated human blood

hyb_protocol: Hybridzation was performed as follows: 1. Load a clean gasket slide into the Agilent SureHyb chamber base with the label facing up and aligned with the rectangular section of the chamber base. Ensure that the gasket slide is flush with the chamber base and is not ajar; 2. Slowly dispense all of the volume of the hybridization sample onto the gasket well in the center; 3. Slowly place an array “active side” down onto the SureHyb gasket slide, so that the “Agilent”-labeled barcode is facing down and the numeric barcode is facing up. Verify that the sandwich-pair is properly aligned; 4. Place the SureHyb chamber cover onto the sandwiched slides and slide the clamp assembly onto both pieces; 5. Firmly hand-tighten the clamp onto the chamber;6. Vertically rotate the assembled chamber to wet the gasket and assess the mobility of the bubbles. If necessary, tap the assembly on a hard surface to move stationary bubbles; 7. Place assembled slide chamber in rotisserie in a hybridization oven set to 55°C. Set your hybridization rotator to rotate at 20rpm; 8. Hybridize at 55°C for 20 hours.

scan_protocol: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Next, Genespring software (version 14.8, Agilent Technologies) was employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm. The probes that at least 100.0 percent of samples in any 1 condition out of 2 conditions have flags in Detected were chosen for further data analysis.

data_processing: Differentially expressed miRNAs were then identified through fold change as well as P value calculated using t-test. The threshold set for up- and down-regulated genes was a fold change >= 2.0 and a P value <= 0.05. Target genes of differentially expressed miRNAs were the intersection predicted with  2 databases (miRDB, miRWalk). GO analysis and KEGG analysis were applied to determine the roles of these target genes. Hierarchical Clustering was performed to show the distinguishable miRNAs expression pattern among samples.

source_name: Ovarian immature teratoma, patient 2

label_protocol: The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols. Briefly, total RNA were dephosphorylated, denaturated and then labeled with Cyanine-3-CTP. After purification the labeled RNAs were hybridized onto the microarray. After washing, the arrays were scanned with the Agilent Scanner G2505C (Agilent Technologies).

growth_protocol: Not applicable

extract_protocol: Total RNA was extracted from ten 10-µm-thick sections of FFPE samples using an RecoverAll FFPE Kit (Thermo Fisher Scientific, USA, #AM1975). The RNA concentration and quality were measured using an Agilent 2100 bioanalyzer (Agilent, USA, #G2939BA) according to the manufacturer’s instruction. Quality control was set as follows: 1) mass>130ng; 2) concentration>17ng/μL; 3) A260/280 value between 1.8 and 2.1.

treatment_protocol: The enrolled patients underwent tumor resection and the samples were collected, including 18 cases using the formalin-fixed, paraffin-embedded (FFPE) approach, of which 2 cases of ovarian cyst, 3 cases of mature teratoma, 6 cases of immature teratoma, 3 cases of yolk sac tumor, 3 cases of juvenile granulosa cell tumor, and 1 case of dysgerminoma; 2 cases were fresh frozen tissue samples preserved in -81℃ environment, including one mature teratoma and one yolk sac tumor.

value: tissue

tag: gender

value: female

tag: age (year)


title: Ovarian cyst, patient 2

description: Gene expression after 6hr in 0.5Gy-irradiated human blood

source_name: Ovarian cyst, patient 2


title: Ovarian dysgerminoma, patient 1

description: Gene expression after 6hr in 2Gy-irradiated human blood

source_name: Ovarian dysgerminoma, patient 1


title: MB7434 strain (DHB4 + pAL-FevREco105-CYTO-FLAG) treated at 30°C, replicate 1


title: Ovarian cyst, patient 1

description: Gene expression after 6hr in 0Gy-irradiated human blood

source_name: Ovarian cyst, patient 1


title: Rehydrated Male 06


title: MB7410 strain (DHB4 + pAL-FevRCit-CYTO-FLAG) treated at 30°C, replicate 3

value: pAL-FevRCit-CYTO-FLAG


title: HR+ breast cancer, luminal A, Post-treatment, Resistant, S14

city: Hangzhou

first: Chao

last: Ni

state: Zhejiang

address: 88 Jiefang Road,Shangcheng District

department: Second Affiliated Hospital

institute: The Second Affiliated Hospital, Zhejiang University School of Medicine

description:
10X Genomics platform
barcodes.tsv.gz (a_S12)
features.tsv.gz
matrix.mtx.gz
XP0203_S12

data_processing:
The Cell Ranger software pipeline (version 3.1.0) provided by 10X Genomics was used to demultiplexe cellular barcodes, map reads to the GRCh38 human reference genome merged cells and genes with low quality as well as doublets were excluded.
The raw gene expression matrix generated from each sample were merged using Seurat (v4.1.0)
Assembly: GRCh38 for RNA expression
Supplementary files format and content: Cell Ranger output files: barcodes.tsv (cell barcode files), features.tsv (gene files), matrix.mtx (gene-barcode counts)

extract_protocol:
Tumor biopsy and resection samples were first stored in RNAlater RNA stabilization reagent (QIAGEN) after collection and kept on ice to avoid RNA degradation. Samples were then collected in the RPMI-1640 medium (Gibco) with 10% FBS (Gibco), and enzymatically digested with gentle MACS Tumor Dissociation Kit (Miltenyi Biotec) for 60 min on a rotor at 37 °C according to the manufacturer’s protocol. The dissociated cells were next passed through a 40-µm cell-strainer (BD) in the RPMI-1640 medium (Invitrogen) with 10% FBS until uniform cell suspensions were obtained. Subsequently, the suspended cells were passed through cell strainers and centrifuged at 400 g for 10 min. Red blood cells were removed via the same procedure described above. After washing twice with 1x PBS (Invitrogen), the cell pellets were re-suspended in sorting buffer (PBS supplemented with 1% FBS).
ScRNA-seq libraries were constructed using Chromium Next GEM Single Cell 3’ Library Construction Kit v3.1 (10x GENOMICS) according to the manufacturer’s protocol.

value: breast

tag: disease state

value: HR+ breast cancer, luminal A

tag: treatment state

value: Post-treatment

tag: response

value: Resistant


title: H4k20me3_ChIPseq_AA

tag: antibody

value: Anti-H4K20me3 antibody, Abcam, ab9053

value: HeLa


title: Ovarian granulosa cell tumor, patient 1

description: Gene expression after 6hr in 5Gy-irradiated human blood

source_name: Ovarian granulosa cell tumor, patient 1


title: HR+ breast cancer, luminal A, Post-treatment, Resistant, S12

description:
10X Genomics platform
barcodes.tsv.gz (a_S11)
features.tsv.gz
matrix.mtx.gz
0106jxh_S11


title: Input_H3k36me3_NOAA

tag: cell line

value: without AA


title: MB7410 strain (DHB4 + pAL-FevRCit-CYTO-FLAG) treated at 30°C, replicate 2

value: Wild-type

value: 4h at 30°C

value: 0.5h at 30°C


title: HR+ breast cancer, luminal B, Post-treatment, Resistant, S11

description:
10X Genomics platform
barcodes.tsv.gz (a_S15)
features.tsv.gz
matrix.mtx.gz
1106ZD_S15

value: HR+ breast cancer, luminal B


title: H4k20me3_ChIPseq_NOAA

tag: treatment


title: ECCITE-seq, replicate 1

description: 10x Genomics

value: Breast

value: ER positive breast cancer

value: Mixed

value: CRISPR KO of 13 genes


title: H3k36me3_ChIPseq_NOAA

value: Anti-H3K36me3 antibody, Abcam, ab9050


title: MB7410 strain (DHB4 + pAL-FevRCit-CYTO-FLAG) treated at 30°C, replicate 1

tag: strain

value: pAL-FevRCit-CYTO-FLAG


title: MB7434 strain (DHB4 + pAL-FevREco105-CYTO-FLAG) treated at 30°C, replicate 2

tag: genotype


title: Sample21

city: New York

first: Varshini

last: Vasudevaraja

state: New York

address: 240 East 38th street

institute: NYU Langone Health

description: RNA from tumor

hyb_protocol: Each 350-ng sample of RNA from tumour samples was hybridized with the PanCancer Pathway CodeSet (NanoString Technologies) at 65∘C overnight. Further purification and binding of the hybridized probes to the optical cartridge were performed on the nCounterPrep Station, and finally the cartridge was scanned on thenCounter Digital Analyzer. Further purification and binding of the hybridized probes to the optical cartridge were performed on the nCounterPrep Station, and finally the cartridge was scanned on thenCounter Digital Analyzer.

scan_protocol: Th stained sections were scanned at a 20X magnification (pixel size 0.45 μm) on a Nanozoomer (Model C9600-12, NDP.scan v3.1.9) whole slide scanner (Hamamatsu) and the image files uploaded on an image data management system.

data_processing: Data was analyzed by ROSALIND® (https://rosalind.bio/), with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA). Read Distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step. Normalization, fold changes and p-values were calculated using criteria provided by Nanostring. ROSALIND® follows the nCounter® Advanced Analysis protocol of dividing counts within a lane by the geometric mean of the normalizer probes from the same lane. Housekeeping probes to be used for normalization are selected based on the geNorm algorithm as implemented in the NormqPCR R library1. Abundance of various cell populations is calculated on ROSALIND using the Nanostring Cell Type Profiling Module. ROSALIND performs a filtering of Cell Type Profiling results to include results that have scores with a p-Value greater than or equal to 0.05. Fold changes and pValues are calculated using the fast method as described in the nCounter® Advanced Analysis 2.0 User Manual. P-value adjustment is performed using the Benjamini-Hochberg method of estimating false discovery rates (FDR). Clustering of genes for the final heatmap of differentially expressed genes was done using the PAM (Partitioning Around Medoids) method using the fpc R library2 that takes into consideration the direction and type of all signals on a pathway, the position, role and type of every gene, etc. Hypergeometric distribution was used to analyze the enrichment of pathways, gene ontology, domain structure, and other ontologies. The topGO R library3, was used to determine local similarities and dependencies between GO terms in order to perform Elim pruning correction. Several database sources were referenced for enrichment analysis, including Interpro4, NCBI5, MSigDB6,7, REACTOME8, WikiPathways9. Enrichment was calculated relative to a set of background genes relevant for the experiment.Background sub-traction was carried out by subtracting the mean valueof the eight negative controls from the raw counts ofall endogenous genes.

label: Biotin

label_protocol: Labeling was carried with customized probes taregting  770-gene expression panel combining markers for 24 different immune cell types and 30 common cancer antigens,including key checkpoint blockade genes, on the nanos-tring Ncounter system (NanoString Technologies, Seat-tle, WA, USA).

extract_protocol: For each specimen, ten 10-μm-thick formalin-fixedparaffin-embedded (FFPE) sections were cut froma single representative block. Tumour enrichmentin was performed in order to reach an optimal tumour content by macrodissection with a scalpel, based onthe areas premarked by the reviewing pathologist. The goal of tumour enrichment was to reach 70% tumourpurity. RNAlibraries were generated essentially as follows. RNAwas obtained with PicoPure RNA Extraction Kits(Thermo Fisher, Life Technologies, Waltham, MA,USA), and this was followed by abead purification step with the Sphere Quality Controlkit (Thermo Fisher, Life Technologies).  RNA was quantified with the Qubit 2.0 Fluorometer (LifeTechnologies). Quality metrics for extracted RNA included both quan-titative and qualitative parameters. RNA quantifica-tion was performed with the Qubit 2.0 Fluorometer(Life Technologies). Qualitative RNA integrity was per-formed with the Agilent 2100 Bioanalyzer System (Agi-lent software, Santa Clara, CA, USA) and correspondingRNA kits. Electropherograms showing fragment distri-bution were reviewed; only cases with an RNA integritynumber of>3 were selected.

tag: survival status

value: alive


title: HR+ breast cancer, luminal B, Post-treatment, Sensitive, S10

description:
10X Genomics platform
barcodes.tsv.gz (a_S8)
features.tsv.gz
matrix.mtx.gz
1216ZJY_S8

value: breast

value: Sensitive


title: Input_H3k36me3_AA

value: AA


title: MB7409 strain (DHB4 + pAL-0) treated at 30°C, replicate 3

description:
MB7410-30-FevRcit.xlsx
MB7434-30-FevReco105.xlsx

tag: plasmid

tag: growth time and  temperature


title: Sample20

description: RNA from tumor


title: Sample19

description: RNA from tumor


title: HR+ breast cancer, luminal B, Post-treatment, Sensitive, S9

description:
10X Genomics platform
barcodes.tsv.gz (a_S16)
features.tsv.gz
matrix.mtx.gz
1023ZD_S16

tag: tissue

value: Post-treatment


title: Input_Myc_NOAA

value: HeLa


title: MB7409 strain (DHB4 + pAL-0) treated at 30°C, replicate 2

tag: treatment time and temperature


title: MB7409 strain (DHB4 + pAL-0) treated at 30°C, replicate 1


title: HR+ breast cancer, luminal A, Pre-treatment, Resistant, S8

description:
10X Genomics platform
barcodes.tsv.gz (b_S25)
features.tsv.gz
matrix.mtx.gz
0826_lin_S25

value: HR+ breast cancer, luminal A

value: Pre-treatment

value: Resistant


title: HR+ breast cancer, luminal A, Pre-treatment, Resistant, S7

description:
10X Genomics platform
barcodes.tsv.gz (b_S24)
features.tsv.gz
matrix.mtx.gz
0826_wen_S24


title: Sample22

description: RNA from tumor


title: H3k36me3_ChIPseq_AA


title: Sample18

description: RNA from tumor


title: BY-2_stac_3

city: Praha 6

first: Karel

last: Muller

address: Rozvojová 263

department: Lab. of hormonal regulations in plants

country: Czech Republic

institute: Institute of Experimenal Botany of the Czech Academy of Sciences

description: GATC Biotech

data_processing:
reads were quality filterred by rcorrector and trimmomatic
transcript quantification and normalization done by Salmon v1.3.0 with parameters--seqBias, --gcBias, --PosBias, --numBootstraps 30
Assembly: Nicotiana tabacum v1 Edwards 2017
Supplementary files format and content: sf files generated by Salmon software, include TPM values

organism: Nicotiana tabacum

source_name: suspension cell culture

growth_protocol: Auxin autonomous tobacco cell line BY-2H (Nicotiana tabacum L. cv. Bright Yellow 2) was maintained in liquid Murashige and Skoog (MS). VBI-0 culture (Nicotiana tabacum cv. 'Virginia Bright Italia') were grown in modified Heller medium supplemented with 2,4-D and NAA. Auxin-autonomous VBI-2 cells were grown in modified Heller's medium without the supplemented auxins. All lines were cultivated in the dark, at 27°C, under continuous shaking (150 rpm; orbital diameter 30 mm) and sub-cultured every 14 days.

extract_protocol:
protocol from Plant Total RNA Mini Kit, QIAGEN
performed by sequencing service company (GATC Biotech or Novogene)

treatment_protocol: no treatments

tag: cultivar

value: Bright Yellow 2

tag: biological replicates

value: suspension cell culture

tag: life cycle_stage

value: stationary

tag: growth conditions

value: auxin supplemented


title: Sample17

description: RNA from tumor


title: Myc_ChIPseq_NOAA

value: without AA


title: HR+ breast cancer, luminal A, Pre-treatment, Resistant, S6

description:
10X Genomics platform
barcodes.tsv.gz (b_S2)
features.tsv.gz
matrix.mtx.gz
0804_ZD_S2

tag: disease state


title: Sample16

description: RNA from tumor


title: BY-2_stac_2

description: GATC Biotech

tag: cell type


title: Input_Myc_AA


title: Sample15

description: RNA from tumor


title: Sample14

description: RNA from tumor


title: Myc_ChIPseq_AA


title: Input_Pol-II_NOAA


title: HR+ breast cancer, luminal B, Pre-treatment, Sensitive, S3

description:
10X Genomics platform
barcodes.tsv.gz (b_S27)
features.tsv.gz
matrix.mtx.gz
0623_HZH_S27

value: HR+ breast cancer, luminal B

tag: treatment state

tag: response


title: VBI-2_exp_3

description: GATC Biotech

value: Virginia Bright Italia

value: exponential

value: auxin free


title: HR+ breast cancer, luminal A, Pre-treatment, Resistant, S5

description:
10X Genomics platform
barcodes.tsv.gz (b_S5)
features.tsv.gz
matrix.mtx.gz
0716_SRM_S5

value: breast


title: BY-2_stac_1

description: GATC Biotech


title: Ser2P-Pol-II_ChIPseq_NOAA

tag: antibody

value: Anti-Ser2P Pol II antibody, Abcam, ab5095

tag: cell line


title: Total-Pol-II_ChIPseq_NOAA

value: Anti-Pol II antibody, Covance, MMS-126R; clone 8WG16

tag: treatment


title: Sample13

description: RNA from tumor

value: alive


title: HR+ breast cancer, luminal B, Pre-treatment, Sensitive, S1

description:
10X Genomics platform
barcodes.tsv.gz (b_S22)
features.tsv.gz
matrix.mtx.gz
CNS-002

value: Sensitive


title: HR+ breast cancer, luminal B, Pre-treatment, Resistant, S4

description:
10X Genomics platform
barcodes.tsv.gz (b_S10)
features.tsv.gz
matrix.mtx.gz
0702_ZD_S10


title: Input_Pol-II_AA

value: HeLa

value: AA


title: VBI-2_stac_3

description: GATC Biotech


title: VBI-2_stac_2

description: GATC Biotech


title: Sample12

description: RNA from tumor

source_name: DPAC


title: VBI-2_exp_2

description: GATC Biotech


title: Ser2P-Pol-II_ChIPseq_AA


title: VBI-2_exp_1

description: GATC Biotech


title: Sample11

description: RNA from tumor


title: VBI-2_stac_1

description: GATC Biotech


title: EOC-4

city: Shenyang

first: Qian

last: Li

address: Liaoning

institute: Cancer Hospital of China Medical University/ Lianning Cancer Hospital&Institute

data_processing:
Filtering of Clean Reads: to get high quality   clean reads, reads were further filtered by fastp(version 0.18.0). The parameters were as follows:  1) removing reads containing adapters;  2) removing reads containing more than 10% of unknown nucleotides (N);  3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Alignment with Ribosome RNA (rRNA): Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
Alignment with Reference Genome: An index of the reference genome was built, and paired-end clean reads were mapped to the   reference genome using HISAT2. 2.4 with “-rna-strandness RF” and other parameters set as a default.
Quantification of Gene Abundance: The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of  transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using StringTie software.
Assembly: Ensembl_release98
Supplementary files format and content: Excel: Gene expression abundance(FPKM) of each sample

source_name: ovarian cancer tissue

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA).RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT)   beads, while prokaryotic mRNA was enriched by removing rRNA by Ribo-ZeroTM Magnetic   Kit (Epicentre, Madison, WI, USA). Then the enriched mRNA was fragmented into short   fragments using fragmentation buffer and reverse transcripted into cDNA with random   primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and   buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen,   Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing   adapters. The ligation products were size selected by agarose gel electrophoresis, PCR   amplified, and sequenced using Illumina NovaSeq6000.

treatment_protocol: Take each tissue of soybean grain size, rinse the tissue with pre-cooled PBS for 3 times, and then quickly put it into liquid nitrogen for preservation

value: ovarian cancer tissue

value: Primary surgery, no chemotherapy


title: Total-Pol-II_ChIPseq_AA


title: OV-4

source_name: cancer-free ovarian tissue

value: cancer-free ovarian tissue

value: surgery


title: Sample10

description: RNA from tumor


title: Sample9

description: RNA from tumor

value: dead


title: Sample8

description: RNA from tumor


title: OV-3


title: Sample6

description: RNA from tumor


title: Input_H4k20me1_NOAA

value: without AA


title: VBI-0_stac_3

description: GATC Biotech

value: suspension cell culture

value: stationary

value: auxin supplemented


title: EOC-3


title: VBI-0_exp_3

description: GATC Biotech

value: Virginia Bright Italia

value: exponential


title: H4k20me1_ChIPseq_NOAA

value: Anti-H4K20me1 antibody, Abcam, ab9051


title: HR+ breast cancer, luminal B, Pre-treatment, Sensitive, S2

description:
10X Genomics platform
barcodes.tsv.gz (b_S44)
features.tsv.gz
matrix.mtx.gz
CNS-004

value: breast

value: HR+ breast cancer, luminal B

value: Pre-treatment


title: OV-2


title: Input_H4k20me1_AA

value: HeLa


title: H4k20me1_ChIPseq_AA

value: AA


title: Sample4

description: RNA from tumor

value: alive


title: EOC-2

value: ovarian cancer tissue

value: Primary surgery, no chemotherapy


title: OV-1

value: cancer-free ovarian tissue

value: surgery


title: VBI-0_stac_2

description: GATC Biotech


title: Sample5

description: RNA from tumor


title: VBI-0_stac_1

description: GATC Biotech


title: 52101_Far__08

city: Tampa

first: Chia-Ho

last: Cheng

address: 12902 USF Magnolia Drive

institute: Moffitt Cancer Center

description: cancer cells >500 microns from B cell cluster

hyb_protocol: Hybridization of biotinylated reporter probes was carried out according to the manufacturer's protocol

scan_protocol: Scanning was perfomred on the nCounter Digital Analyzer at 550 FOV

data_processing: The raw data was normalized using NanoStringNorm R package.Endogenous probes were normalized to the positive control probe counts using “geo.mean” method and to the housekeeping gene counts using the ‘housekeeping.geo.mean’ method.

label: biotin

source_name: Surgically removed Ovarian Cancer tumor tissue

extract_protocol: OCT sections of HGSOC tissues, known to contain Tertiary Lymphoid Structures, were stained with anti-human CD19, followed by laser captured microdisscetion of cancer cells in proximity or far from the B cell conglomerates. Total RNA was extracted using RNeasy Plus micro kit and Genomic DNA was removed by on column DNase treatment

value: high-grade serous ovarian carcinoma (HGSOC)


title: Sample1

description: RNA from tumor


title: VBI-0_exp_1

description: GATC Biotech

value: suspension cell culture


title: S15R03-NRDE2 KD

first: Hong

address: 320 YueYang Road

department: Shanghai Institute of Biochemistry and Cell Biology

institute: Shanghai Institutes for Biological Sciences

description: rRNA depletion

data_processing:
RNA-seq reads were cleaned and mapped to the human genome (hg19 version) TopHat2.0. 13-16 million reads were mapped to genome after quality filtering and collapsing of identical reads. For genome annotation, data were downloaded from the UCSC genome browser website, eRNA containing datasets (FANTOM database, http://fantom.gsc.riken.jp/5/datafiles/latest/extra/Enhancers/), PROMPTS (Ntini, E. et al, 2013) and lnc/lincRNA (Derrien, T. et al, 2012; Cabili, M.N. et al, 2011) were downloaded as referrence.
To compare the gene expression, firstly, we carried out spike-in control normalization. The number of reads mapped to spike-in control was used to normalize the variation of different samples. Secondly, corrected reads per million (RPM) of each transcript was calculated, the fold changes were computed based on the correct RPM
Basecalls performed using TopHat2.0,fastx_toolkit-0.0.13.2 (Q33)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: uterine cervix

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle’s medium supplying l0% fetal bovine serum (FBS) and penicillin/streptomycin (100IU/ml and 100ug/ml, respectively) under 5% CO2 in humid conditions at 37 0C.

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen). To compare the RNA level in each sample in unbiased fashion, equal amount of ERCC RNA spike-in control mix (ambion) was added to 4 mg of total RNA according to the manufacture’s instruction. rRNA was depleted and stranded cDNA libraries were generated with TruSeq Stranded Total RNA Sample Prep Kit (Illumina) according to the manufacturer’s instructions
Libraries were generated with TruSeq Stranded Total RNA Sample Prep Kit (Illumina) according to the manufacturer’s instructions. Index for Flag-eif4A3 overexpression: CGATCG; for Flag-NRDE2 overexpression: TGACCA; for cntrl KD:ACAGTG; for NRDE2 KD: GCCAAT

treatment_protocol: NPKO-1 cells were infected with lentivius to knock down NRDE2 by shRNA targeting NRDE2, shRNA targeting luciferase was used as negative control.

value: shRNA targeting NRDE2


title: S15R032-Cntrl KD

description: rRNA depletion

value: shRNA targeting luciferase


title: EOC-1


title: 22607_Far_04

label_protocol: Hybridization of biotinylated reporter probes was carried out according to the manufacturer's protocol

value: cancer cells >500 microns from B cell cluster


title: HCT-116_Treated_3 (miRNA-seq)

city: Chicago

first: Gail

middle: B

last: Mahady

state: IL

address: 833 S Wood St

department: Pharmacy Practice

institute: University of Illinois

data_processing:
Raw reads were trimmed to remove adapters sequence using cutadapt (Martin, 2011). Reads with no adapter were discarded. Remaining trimmed reads were reads were aligned to mature known human microRNA database obtained from miRbase using BWA ALN (Li and Durbin, 2010). miRNA expression levels where quantified by counting the number of reads mapped to each miRNA sequence, and normalized to counts-per-million units for direct comparison between samples.
Differential expression statistics were computed using edgeR (McCarthy, Chen, & Smyth, 2012; Robinson, McCarthy, & Smyth, 2010) on raw expression counts with the exactTest function. P-values were adjusted for multiple testing using the false discovery rate (FDR) correction of Benjamini and Hochberg (Benjamini & Hochberg, 1995). k-means clustering was performed using R.
Assembly: hg38 (human mature miRNA)
Supplementary files format and content: Table of raw counts per gene – tabular text file

source_name: ATCC

growth_protocol: HCT-116 cells were cultured in McCoy’s 5a Medium (Gibco, Life Technology, Grand Island, NY, USA) supplemented with 10% FBS and 1% Penicillin/Streptomycin and incubated at 37°C in a humidified atmosphere of 5% CO2 and 95% air. At 80% confluence, cells were harvested by adding 0.25% trypsin/EDTA and counted by means of Trypan blue and hemocytometer. The cells were then re-suspended at appropriate concentration and plated in 96 or 6 well plates for cellular assays. Cell were treated with ATRA+D2+D3 at the IC50 concentration (1mM), then harvested and RNA isolated using Trizol

extract_protocol: RNA isolated using Trizol

value: ATRA+D2+D3 Treatment


title: S15R031-NRDE2 KD

description: rRNA depletion

data_processing:
RNA-seq reads were cleaned and mapped to the human genome (hg19 version) TopHat2.0. 13-16 million reads were mapped to genome after quality filtering and collapsing of identical reads. For genome annotation, data were downloaded from the UCSC genome browser website, eRNA containing datasets (FANTOM database, http://fantom.gsc.riken.jp/5/datafiles/latest/extra/Enhancers/), PROMPTS (Ntini, E. et al, 2013) and lnc/lincRNA (Derrien, T. et al, 2012; Cabili, M.N. et al, 2011) were downloaded as referrence.
To compare the gene expression, firstly, we carried out spike-in control normalization. The number of reads mapped to spike-in control was used to normalize the variation of different samples. Secondly, corrected reads per million (RPM) of each transcript was calculated, the fold changes were computed based on the correct RPM
Basecalls performed using TopHat2.0,fastx_toolkit-0.0.13.2 (Q33)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample

treatment_protocol: HeLa cells were infected with lentivius to express Flag-eif4a3, Flag-NRDE2 respectively, or knock down NRDE2 by shRNA targeting NRDE2, shRNA targeting luciferase was used as negative control.

value: HeLa J


title: S15R030-Cntrl KD

description: rRNA depletion


title: HCT-116_Treated_1 (miRNA-seq)


title: 81908_Far__02

description: cancer cells >500 microns rom B cell cluster


title: HCT-116_Treated_2 (miRNA-seq)


title: mAID-RNaseh2a Pole1-M630F, replicate 1

city: Okazaki

first: Tomomi

last: Tsubouchi

state: Aichi

address: Nishigonaka 38, Myodaiji

country: Japan

institute: National Institute for Basic Biology

description:
Library name: mAID-RNaseh2a OsTIR Pole11-M630F set1
The ribonucleotide incorporation into genomic DNA in mAID-RNaseh2a Pole1-M630F, replicate 1

data_processing:
Those reads which aligned to multiple genomic locations with the same mismatch scores (AS and XS scores as outputted by Bowtie2) were excluded by a custom Perl script: sam-dup-align-exclude-v2.pl (available at the GitHub site: https://github.com/yasukasu/sam-dup-align-exclude). The position of the 5′ end of each R1 read (which corresponds to the 5′ end of ssDNA hydrolysed by alkali treatment, rNTP corporated position) was determined, and the number of reads in 1-kb bins across the genome were counted separately for the Watson and Crick strands using a custom Perl script: pe-sam-to-bincount.pl (available at the GitHub site: https://github.com/yasukasu/pe-sam-to-bincount).
This generated the four data sets for the analysis of one polymerase usage. In case of Polε: at the chromosome coordinate x, Nwε(x), is the count for mAID-RNaseh2a Pole1-M630F on the Watson strand; Ncε(x) is the count for mAID-RNaseh2a Pole1-M630F on the Crick strand; Nw+(x) is the count for mAID-RNaseh2a Pol+ on the Watson strand; Nc+(x) is the count for mAID-RNaseh2a Pol+ on the Crick strand.
These datasets were normalised using the total number of reads: e.g. N’wε(x) = Nwε(x)/∑ Nwε on the Watson strand (where N’ indicates normalisation). These normalised data were used to calculate relative polymerase usage: e.g. Ew(x) = N’wε(x)/N’w+(x) for usage of Polε on the Watson strand; Ec(x) = N’cε(x)/N’c+(x) for usage of Polε on the Crick strand. When these data were plotted or used for further analysis (below) they were smoothed using moving average of 2m+1, where m is an arbitrary number the value of which is given in the relevant context. Thus the data point for each bin is an average of 2m+1 bins: the point of origin and the m bins either side(when the file name cotain MA30, m=30).
The difference between each neighbouring bin of polymerase usage was calculated as ΔEw(x), ΔEc(x), with Ew(x), Ec(x), which were smoothed using the value m = 30. These differential data were further smoothed by application of a moving average with value m = 15. At each location where all two polymerase profiles exhibit consistent patterns for initiating bidirectional replication forks (ΔEw(x)>0 ∩ ΔEc(x)<0) or patterns consistent with the merging of two forks (ΔEw(x)<0 ∩ ΔEc(x)>0) an initiation index was defined as: Ini(x)= ΔEw (x)-ΔEc (x). This data was subjected to Z-score normalisation (mean = 0, standard deviation = 1) and Z(0) were subtracted to maintain the original + or – information, which represent increased levels of replication initiation and termination in the cell population respectively.
Genomic regions with continuous positive ini-indexes are defined as initiation zones (IZs). When two such regions are found next to each other with less than 10kb apart, the two regions are considered as a single IZ.
Assembly: GRCm39
Supplementary files format and content: bigWig format files for polymerase usage, initiation index bed format files for initiation-zone and  bedgraph format files for initiation-peak

organism: Mus musculus

growth_protocol: For the AID system, cells were treated with doxycycline to induce OsTIR1 and auxinole to prevent background degradation for 24 hrs and this medium was replaced with medium containg doxycycline and IAA. The cells were incubated for further 12 hrs.

extract_protocol:
gDNA was prepared using the QIAGEN Blood & Cell Culture DNA Kits (20/G)
Up to 25 μg of genomic DNA was treated in 0.3 M NaOH at 55 °C for 2 hrs, then loaded onto a 1.5% agarose gel and run for 2 hrs at 135 V. The gel was stained with acridine orange (final concentration 5 μg/ml) for 2 hrs at room temperature with gentle shaking followed by overnight destaining in water. Fragments of 300–2000 bp were excised from the gel and isolated with NucleoSpin Gel and PCR Clean-up kit (Macherey-Nagel #740609.250). Library preparation was performed as previously described in Daigaku et al Nat Struct Mol Biol 2015 (doi:10.1038/nsmb.2962).

tag: genotype


description:
Library name: mAID-RNaseh2a OsTIR set2
The ribonucleotide incorporation into genomic DNA in mAID-RNaseh2a (the parent cell line of Pole1-M630F cells), rep 2


title: mAID-RNaseh2a Pole1-M630F, replicate 2

description:
Library name: mAID-RNaseh2a OsTIR Pole11-M630F set2
The ribonucleotide incorporation into genomic DNA in mAID-RNaseh2a Pole1-M630F, replicate 2


title: 120406_Far__06


title: 52101_Proximal_07

description: cancer cells <500 microns rom B cell cluster


title: VBI-0_exp_2

description: GATC Biotech

value: Virginia Bright Italia

value: exponential

value: auxin supplemented


title: HCT-116_Control_3 (miRNA-seq)

value: Control


description:
Library name: mAID-RNaseh2a OsTIR set1
The ribonucleotide incorporation into genomic DNA in mAID-RNaseh2a (the parent cell line of Pole1-M630F cells), rep 1


title: HCT-116_Control_2 (miRNA-seq)


title: spinal cord, morphine, III

first: Chun-Yi

last: Jiang

institute: Nanjing Medical University

data_processing:
bcl2fastq2 (v2.19.0)
Sequence reads were trimmed for adaptor sequence/low-quality sequence  using Trimmomatic (quality score limit :15).
Trimmed sequence reads were compared to genome using STAR  (Spliced Transcripts Alignment to a Reference) .
Reads count extraction and normalization were performed using RSEM.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes fpkm values for each sample

source_name: spinal cord

growth_protocol: Mice were housed five to six per cage under pathogen-free conditions with soft bedding under controlled temperature (22°C ± 2°C) and photoperiods (12:12-hour light–dark cycle).

extract_protocol:
Total RNA from spinal cord L4-L5 of mice extracted with PureLink/Trizol according to the manufacturer’s instructions.
Sequencing libraries were generated using KAPA Stranded RNA-Seq Kit (KAPA, USA) following manufacturer’s recommendations.

treatment_protocol: Mice were intrathecally injected with saline or morphine  (10 ug/10uL) for 7 days.

value: spinal cord

value: WT

value: intrathecal injection with morphine


title: 22607_Proximal_03

description: cancer cells <500 microns from B cell cluster


title: 120406_Proximal_05

value: cancer cells <500 microns from B cell cluster


title: HCT-116_Control_1 (miRNA-seq)


title: AN_STAGE4_R3

city: East Lansing

first: Frances

last: Trail

state: MI

address: 612 Wilson Road, Room 342

department: Plant Biology

institute: Michigan State University

data_processing:
Base calling was done by Illumina Real Time Analysis (RTA) v2.7.7 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0. The low-quality reads were removed using the read filtering tool, Trimmomatic, Version 0.39. The 3’ ends of NovaSeq6000 single-end 100 bp reads were trimmed to 50 bp reads (keeping the first 50 bp) using Trimmomatic Version 0.39.
The trimmed reads were mapped to the indexed reference sequences using HISAT 2.2.1.
The HISAT alignments in SAM format were then sorted and converted to BAM format using SAM tools.
Count files were then generated using HTSeq Version 0.11.1.
The DESeq2 package Version 1.30.1 in R was used to normalize the read counts and to perform differential expression analysis.
Assembly: The reference sequence used for the alignment are A. fumigatus AF293 (GCA_000002655.1), A. nidulans A4 (GCA_000149205.2), and F. oxysporum NRRL 32931 (GCA_000271745.2)
Supplementary files format and content: Tab-demilited text file includes raw counts for each sample

organism: Aspergillus nidulans

source_name: Germinated conidia

growth_protocol: For total RNA extraction of each germination stage on standard medium (Bird agar medium), a 200 µL aliquot of the conidial suspension (1 x 106 conidia/mL) of each species was inoculated onto a sterile cellophane sheet overlaid on Bird medium in a Petri dish (60 x 15 mm). Petri dishes containing inoculated sheets were then incubated at RT till the conidia reached respective germination stages.

extract_protocol:
Total RNA  from cellophane membranes was isolated using Trizol reagent. RNA was treated with RNase-Free DNase (Qiagen), purified further using RNA Clean and ConcentratorTM - 5 (ZymoResearch)
Libraries were prepared using the Illumina Stranded mRNA Prep - Ligation kit with IDT for Illumina RNA UD Indexes.

value: Germinated conidia

tag: Stage

value: Bird medium


title: spinal cord, morphine, I


title: 81908_Proximal_01

description: cancer cells <500  microns from B cell cluster

value: high-grade serous ovarian carcinoma (HGSOC)


title: RHT6153: B4_cLVX+

city: Singapore

first: Farah

last: Tasnim

state: Singaore

address: 31 Biopolis Way, #05-01, Nanos Building

country: Singapore

institute: Institute of Bioengineering and Bioimaging

data_processing:
Base calling was done using Illumina bcl2fastq software
Reads were prepared using the nf-core/rnaseq workflow 1.4.2. Reads were trimmed for adaptor sequence using Trim Galore v0.6.4, then aligned to human genome build GRCh38 using STAR_2.6.1d
Aligned reads are summarized into count matrices using featureCounts (v1.6.4) with the gene annotation file (GTF) from GENCODE (v37).
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: iPSC-derived hepatocytes

growth_protocol: iPSC IMR90 cells were differentiated to hepatocytes and Kuffer cells. Please see paper for more details on differeniation and coculture conditions.

extract_protocol:
iHeps cultured in mono-culture and co-culture were separated by magnetic activated cell sorting: iKC bind to CD163 beads, leaving iHep in the flowthrough. Cells were snap frozen in liquid nitrogen before storage in -80C until RNA extraction by TRIzol.
Illumina Stranded mRNA multiplexing was done with unique 96 dual indices, and all samples sequenced on the same lane of NovaSeq 6000 S4 flowcell.

treatment_protocol: Cells were incubated in media +/- LPS and drug or vehicle for 48h before lysis.

tag: cell types in culture

value: iHep + iKC co-culture

tag: lps stimulation

value: 100ng/ml lipopolysaccharide

tag: drug treatment

value: Levofloxacin (25 uM)


title: AN_STAGE4_R2

tag: tissue


title: RHT6152: B4_cLVX-

value: Untreated


title: S15R029-NRDE2 overexpression

description: rRNA depletion

value: expressing Flag-NRDE2


title: AN_STAGE4_R1


title: spinal cord, control, III

value: intrathecal injection with saline


title: RHT6151: B4_cTVX+

value: Trovafloxacin (25 uM)


title: Plus_COMP3_biological rep3

city: Pyeongchang-gun

first: Minsoo

last: Kang

state: Gangwon-do

address: 1447, Pyeongchang-daero, Daehwa-myeon

department: graduate school of international agricultural technology

country: South Korea

institute: Seoul National University, Republic of Korea

description:
GPR39 overexpressed HEK293 cells after TC-G-1008 stimulation
Plus_COMP3_3

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: GPR39 Overexpressed HEK293 Cell

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: HEK293cell line (ATCC, Manassas, VA) was maintained in DMEM (Gibco) with 10% Fetal Bovine Serum (FBS) (Gibco) under 5% CO2 condition at 37°C

extract_protocol: After washing and lysing the cells with Buffer RLT, the complete RNA was extracted using the RNeasy Mini Kit (QIAGEN, Basel, Switzerland) as instructed by the manufacturer, including the on-column DNA digestion stage (RNase-Free DNase Set; QIAGEN).

treatment_protocol: HEK293 cell line (ATCC, Manassas, VA) was treated in DMEM with 10% FBS (Gibco) with Cumate 0.03mg/mL or not and TC-G-1008 (1uM) or not

value: GPR39 Overexpressed


title: AN_STAGE3_R3


title: spinal cord, control, I


title: S15R028-eif4A3 overexpression

description: rRNA depletion

value: HeLa J

value: expressing Flag-eif4A3


title: AN_STAGE3_R2


title: RHT6149: B4_cVeh+

value: Vehicle (0.2% DMSO)


title: Plus_COMP3_biological rep1

description:
GPR39 overexpressed HEK293 cells after TC-G-1008 stimulation
Plus_COMP3_1


title: RHT6150: B4_cTVX-


title: Plus_COMP3_biological rep2

description:
GPR39 overexpressed HEK293 cells after TC-G-1008 stimulation
Plus_COMP3_2


title: spinal cord, morphine, II

value: spinal cord

value: WT


title: AN_STAGE3_R1


title: Plus_cumate_biological rep2

description:
GPR39 overexpressed HEK293 cells
Plus_cumate_2

value: Cumate 0.03mg/mL


title: RHT6148: B4_cVeh-


title: RHT6147: B4_mLVX+

value: iHep mono-culture


title: AN_STAGE2_R3

value: Germinated conidia

value: Bird medium


title: Plus_cumate_biological rep1

description:
GPR39 overexpressed HEK293 cells
Plus_cumate_1


title: S-5,uIRI45min,5d,scRNA-seq

city: Beijing

first: Weijian

last: YAO

state: Beijing

address: No. 8 Xishiku Street, Xicheng District

department: Renal division

institute: Peking university first hospital

description: 10× genomics

data_processing:
Raw sequencing data were analyzed following the standard Chromium’s Cell Ranger pipeline to align the raw sequence reads according to the reference genome (mm10-2.1.0) using STAR. The count matrices from different batches were merged, integrated and processed with the Seurat pipeline
Assembly: mm10-2.1.0
Supplementary files format and content: Tab-separated values files and and matrix files

source_name: Spleen

extract_protocol:
Flow cytometry sorting (FACS)of monocyte or macrophages from kidneys, spleen, and Blood at different time points after uIRI 45 minutes.F4/80+ cells and Cd11b+ cells were sorted separately from kidney samples and mixed at the ratio of 1:1. Cd11b+ cells and Ly6c+ cells were sorted separately from blood samples and collected at a ratio of 1:1. Cd11b+ cells were sorted from spleen samples.
FACS-sorted cells were resuspended to a final cell concentration of 700~1200 cells/μl with more than 85% viability as determined by CountessTM II (Thermo Fisher Scientific). 8,000 to 12,000 cells were captured in droplets (10x Genomics Chromium Single Cell V2,V3,3ʹ Reagent Kits). After the reverse transcription step, fifty nanograms of amplified cDNA was fragmented and end-repaired, and sequenced on an Illumina platform using 150 paired-end reads at a coverage of 40,000 mean reads per cell.

value: Spleen

value: MPC

value: Cd11b+,Ly6c+ cells

tag: gender

value: Male

tag: age

value: Non


title: RHT6146: B4_mLVX-

value: Untreated

value: Levofloxacin (25 uM)


title: Minus_cumate_biological rep3

description:
Mock control HEK293 cells
Minus_cumate_3

source_name: naïve HEK293 Cell

value: naïve


title: spinal cord, control, II

value: intrathecal injection with saline


title: Plus_cumate_biological rep3

description:
GPR39 overexpressed HEK293 cells
Plus_cumate_3

value: GPR39 Overexpressed


title: KM-10,uIRI45min,10d,scRNA-seq

description: 10× genomics

source_name: Kidney

value: Kidney


title: Minus_cumate_biological rep2

description:
Mock control HEK293 cells
Minus_cumate_2


title: RHT6145: B4_mTVX+

value: 100ng/ml lipopolysaccharide

value: Trovafloxacin (25 uM)


title: AN_STAGE2_R1

value: WT


title: Minus_cumate_biological rep1

description:
Mock control HEK293 cells
Minus_cumate_1


title: RHT6144: B4_mTVX-

value: iHep mono-culture


title: KM-7,uIRI45min,7d,scRNA-seq

description: 10× genomics


title: S-17,uIRI45min,17d,scRNA-seq

description: 10× genomics


title: AN_STAGE1_R3

source_name: Conidia

value: Conidia


title: S-10,uIRI45min,10d,scRNA-seq

description: 10× genomics


title: AN_STAGE1_R2

value: Bird medium


title: RHT6143: B4_mVeh+

value: Vehicle (0.2% DMSO)


title: AN_STAGE1_R1


title: B-17,uIRI45min,17d,scRNA-seq

description: 10× genomics

source_name: Blood

value: Blood

value: MPC


title: RHT6142: B4_mVeh-


title: AN_STAGE2_R2

value: Germinated conidia


title: liver_MYCREG3A_tumor_18months_Mice4

city: VILLEJUIF

first: Nicolas

middle: Benoni

last: Moniaux

address: 12 Avenue Paul Vaillant Couturier

country: France

institute: INSERM

description: Gene expression data from tumor liver of MYC and REG3A double transgenic mice aged of 18 months

hyb_protocol: Following fragmentation and end-labelling, 3.0 μg of cDNAs were hybridized for 16 hours at 45oC on GeneChip® Mouse Gene 2.0 ST arrays. The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix).

scan_protocol: GeneChips were scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm.

data_processing:
Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 4.1.2.
CEL files were further processed with Affymetrix Expression Console software version 1.4.1 to calculate probe set signal intensities using Robust Multi-array Average (RMA) algorithms with default settings.

source_name: tumor liver of MYC/REG3A double transgenic mice aged of 18 months

label_protocol: Biotinylated single strand cDNA targets prepared using 200 ng of total RNA, using the Ambion WT Expression Kit (Cat # 4411974) and the Affymetrix GeneChip® WT Terminal Labeling Kit (Cat # 900671) according to Affymetrix recommendations.

growth_protocol: A genetically engineered mouse model of liver cancer was initiated by breeding REG3A-TG to WHC-MYC-TG (expressing C-MYC oncogene in the liver under the control of the woodchuck hepatitis virus (Etiemble et al oncogene 1994)) mice. The resulting heterozygous animals were mated to generate syngeneic MYC-TG and MYC/REG3A-TG founder mice in the C57BL/6J background.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: At age of 18 months, mice were sacrificed, liver collected and dissected to separate pairwise non-tumor and tumor samples. Each sample was snap frozen in liquid nitrogen before being keep at -80°C until further process.

value: tumor liver


title: liver_MYCREG3A_tumor_18months_Mice3


title: liver_MYCREG3A_tumor_18months_Mice2


title: RHT6141: B3_cLVX+

value: iHep + iKC co-culture


title: N.furzeri brain/Control - Rep8

city: Jena

first: Domenico

last: Di Fraia

address: Beutenbergstraße 11

country: Germany

institute: Leibniz-Institut für Alternsforschung - Fritz-Lipmann-Institut e.V. (FLI)

data_processing:
All libraries were sequenced on a NovaSeq6000 SP 300 cycles v1.5; paired end 151 bp (one pair for each of the projects). Total RNA libraries were pooled and sequenced in three lanes. Small RNA libraries were pooled and sequenced in one lane. Sequence information was extracted in FastQ format using Illumina’s bcl2FastQ v2.20.0.422, against the Nothobranchius furzeri reference genome (Nfu_20150522, annotation nfurzeri_genebuild_v1.150922). Alignment to the reference genome was performed using STAR (Dobin et al. 2012) with the following parameters: --outSAMmultNmax 1 --outFilterMultimapNmax 1 -- outFilterMismatchNoverLmax 0.04 --sjdbOverhang 99 --alignIntronMax 1000000 -- outSJfilterReads Unique. Deduplication step was performed using the umi_tool v1.1.1 (Smith, Heger, and Sudbery 2017), using the following parameters: extract --bcpattern= NNNNNNNNNNN`, `dedup --chimeric-pairs discard --unpaired-reads discard -- paired.
Assembly: Nfu_20150522, annotation nfurzeri_genebuild_v1.150922
Supplementary files format and content: tab-delimited files include TPM values for each sample

organism: Nothobranchius furzeri

source_name: Brain

extract_protocol:
Individual brains from the fish were collected and snap-frozen in liquid nitrogen. The protein amount was estimated based on fresh tissue weight (assuming 5% of protein w/w) and ice-cold 1x PBS with protease/ phosphatase inhibitors (Roche,11836170001, 4906837001) was added accordingly to a final concentration of 2 μg/μL. Samples were then vortexed (5 times) before sonication (Bioruptor Plus) for 10 cycles (60 sec ON/30 sec OFF) at the high setting, at 4 °C. The samples were then centrifuged at 3000 xg for 5 min at 4 °C, and the supernatant was transferred to 2 mL Eppendorf tubes. 1.5 mL of ice-cold Qiazol (Qiagen, 79306) reagent was added to 150 μL of homogenate, vortexed five times, and snap-frozen in liquid nitrogen. On the day of the experiment, samples were thawed on ice, vortexed five times, and incubated at room temperature for 5 min before the addition of 300 μL of chloroform. Samples were mixed vigorously, incubated for 3 min at room temperature, and centrifuged at 12000 xg for 20 min at 4 °C. The upper aqueous phase (600 μL) was carefully transferred into a fresh tube and the remaining volume (phenol/chloroform phase) was kept on ice for DNA isolation. The aqueous phase was mixed with 1.1 volume of isopropyl alcohol, 0.16 volumes of sodium acetate (2 M; pH 4.0), and 1 μL of GlycoBlue (Invitrogen, AM9515) to precipitate RNA. After 10 min incubation at room temperature, samples were centrifuged at 12000 xg for 30 min at 4 °C. The supernatant was completely removed, and RNA pellets were washed by adding 80% (v/v) ethanol and centrifuging at 7500 xg for 5 min at 4 °C. The washing steps were performed twice. The resulting pellets were air-dried for no more than 5 min and dissolved in 10 μL nuclease-free water. To ensure full dissolution of RNA in water, samples were then incubated at 65 °C for 5 min, before storage at -80 °C.
Sequencing of RNA samples was done using Illumina’s next-generation sequencing methodology (Bentley et al. 2008). In detail, quality check and quantification of total RNA was done using the Agilent Bioanalyzer 2100 in combination with the RNA 6000 pico kit (Agilent Technologies, 5067-1513). Total RNA library preparation was done by introducing 500 ng total RNA into Illumina’s NEBNext Ultra II directional mRNA (UMI) kit (NEB, E7760S), following the manufacturer’s instructions. The quality and quantity of all libraries were checked using Agilent’s Bioanalyzer 2100 and DNA 7500 kit (Agilent Technologies, 5067-1506).

treatment_protocol: Adult animals (12–14 wph) were subjected to pharmacological intervention via intraperitoneal injections (IP) during a 4-weeks period of treatment. On each of the sixth day (t = 0, t = 6 d, t = 12d, t = 18d, t = 24d), fish were anesthetized with 200 mg/l buffered MS-222 (PharmaQ) and gently manipulated to deliver IP of either different drugs at 500 μM or vehicle (1% DMSO in physiological salt solution) at a dosage of 10 μl/g body weight. Animals from the same hatch were randomly allocated to the experimental groups. Both male and female fish were included in each experimental group. Individual brains from the fish were collected on the last day of treatment and snap-frozen in liquid nitrogen.

value: Brain

value: DMSO


title: liver_MYCREG3A_tumor_18months_Mice1


title: N.furzeri brain/Control - Rep7


title: TonEBP haploinsufficiency 3

city: JINJU

first: GU SEOB

last: ROH

address: 15, 816 Beon-gil, Jinju-daero

institute: Gyeongsang National University

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

source_name: Hippocampus

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

value: Hippocampus

tag: strain

value: TonEBP+/-


title: B-10,uIRI45min,10d,scRNA-seq

description: 10× genomics

value: Cd11b+,Ly6c+ cells

value: Male

value: Non


title: KM-5,uIRI45min,5d,scRNA-seq

description: 10× genomics

value: Kidney


title: RHT6140: B3_cLVX-

value: Untreated

value: Levofloxacin (25 uM)


title: B-5,uIRI45min,5d,scRNA-seq

description: 10× genomics


title: N.furzeri brain/Control - Rep6


title: RHT6139: B3_cTVX+

value: 100ng/ml lipopolysaccharide

value: Trovafloxacin (25 uM)


title: TonEBP haploinsufficiency 2


title: N.furzeri brain/Control - Rep5


title: liver_MYCREG3A_non-tumor_18months_Mice4

description: Gene expression data from non-tumor liver of MYC and REG3A double transgenic mice aged of 18 months

source_name: non-tumor liver of MYC/REG3A double transgenic mice aged of 18 months

value: non tumor liver


title: TonEBP haploinsufficiency 1


title: N.furzeri brain/Control - Rep4


title: RHT6137: B3_cVeh+

value: Vehicle (0.2% DMSO)


title: WT3

value: wild type


title: N.furzeri brain/Control - Rep2


title: RHT6135: B3_mLVX+

value: iHep mono-culture


title: N.furzeri brain/Control - Rep3


title: RHT6136: B3_cVeh-

value: iHep + iKC co-culture


title: WT2


title: liver_MYCREG3A_non-tumor_18months_Mice1


title: liver_MYC_tumor_18months_Mice4

description: Gene expression data from tumor liver of MYC transgenic mice aged of 18 months

value: tumor liver


title: RHT6138: B3_cTVX-


title: WT1


title: RHT6134: B3_mLVX-


title: RHT6132: B3_mTVX-


title: N.furzeri brain/Control - Rep1

value: Brain

value: DMSO


title: N.furzeri brain/Proteasome Inhibition - Rep7

value: Bortezomib


title: liver_MYC_tumor_18months_Mice3

source_name: tumor liver of MYC transgenic mice aged of 18 months


title: N.furzeri brain/Proteasome Inhibition - Rep8


title: liver_MYCREG3A_non-tumor_18months_Mice3


title: liver_MYCREG3A_non-tumor_18months_Mice2


title: liver_MYC_tumor_18months_Mice2


title: RHT6131: B3_mVeh+


title: N.furzeri brain/Proteasome Inhibition - Rep6


title: liver_MYC_tumor_18months_Mice1


title: NK-P_rep1

city: Hefei

first: Zhou

last: Yonggang

state: Anhui

address: 443 HuangShan Road

department: School of Life Science and Medical Center

institute: University of Science and Technology of China

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-qualty sequence, then mapped to mm9 whole genome.
Cufflinks are used for assemble transcripts and remap and quanilty gene-exprssion level, which is estimate by FPKM value.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Uterine NK cells_P

extract_protocol:
Total RNA was extracted and purified using miRNeasy Mini Kit (Qiagen, Cat# 217004) and RNase-Free Dnase Set.
RNA libranes were prepared for sequencing using standard Illumina protocols.

treatment_protocol: CD3-CD45+NK1.1+ NK cells from uterine tissues of mice have been sorted by FACS Aria.

tag: strain background

value: mating with male B6 mice

tag: Sex

value: female

tag: gestational day (gd)

value: at gd11.5

tag: genotype/variation

value: uterine

value: CD3-CD45+NK1.1+ NK cells


title: NK-NP_rep2

source_name: Uterine NK cells_NP

value: Pbx1f/f; Ncr1Cre

tag: cell type


title: NK-P_rep2


title: RHT6130: B3_mVeh-

value: Untreated


title: NK-NP_rep1


title: N.furzeri brain/Proteasome Inhibition - Rep5


title: CSR_SAPPKHL-3

first: Shan

last: Zha

state: NY

address: 1130 Saint Nicholas Ave.

institute: Columbia University

description:
Class Switch Recombination junctions
Pool_PKSHL_240610_IgH_putback added.xlsx

data_processing:
Basecalls performed using Illumina RTA version 1.18.54
Miseq reads was first de-multiplexed by fastq-multx tool from ea-util, then adaptor sequence was further trimmed with SeqPrep utility.
Pre-processed reads were then mapped to customized mm9 (for CSR) or mm10 (for chromosomal V(D)J recombination) genome using Bowtie2. The best-path searching algorithm (related to YAHA; G. G. Faust, et al. Bioinformatics 28, 2417-2424 (2012)) was used to identify optimal sequence alignments from Bowtie2-reported top alignments (alignment score > 50).
The reads were then filtered to exclude mis-priming events, germline (unmodified) sequence, sequential joints, and duplicated reads. A “duplicate read” is defined by bait and prey alignment coordinates within 2 nt of another read’s bait and prey alignments. Since signal joint reads number was very low after applying deduplication filter, this filter was not used for SJ analysis. For SJ deletion analyses, the deletion size was capped at 1,000 bp. Since some switch region sequences are very repetitive, the alignments in those regions were filtered out by the mappability filter. But they do unequivocally map to an individual switch region, so to plot all the switch region junctions, we added the ones filtered out by the mappability filter back after deduplication (J. Dong, et al. Nature 525, 134-139 (2015)). MHs are defined as regions of 100% homology between the bait and prey-break site. Insertions are defined as regions containing nucleotides that map to neither the bait nor prey-break site. Blunt junctions are considered to have no MHs or insertions.
Assembly: For SJ analysis, to specifically study the DNA repair junctions on the pMX-INV substrate we added the substrate sequence as an additional chromosome (chrP) on top of the mm10 genome during the alignment process. For CSR analysis, the IgH switch region (from JH4 to the last Cα exon, chr12 114, 494, 415–114, 666, 816; C57/BL6) of customized mm9 genome (mm9sr) was replaced by the corresponding region of 129 strain in NCBI gene accession sequence AJ851868.3.
Supplementary files format and content: .xlsx files generated from tab-delimited text files after analysis for reads distribution.
Library strategy: HTGTS

growth_protocol: For SJ analysis, V-abl transformed B cells from mice were cultured in DMEM medium. For CSR analysis, purified splenic B (CD43-) cells from mice were cultured in RPMI medium with cytokines (anti-CD40 (1 µg/mL; BD Pharmingen) and IL-4 (20 ng/mL; R&D)).

extract_protocol:
Genomic DNA was extracted from treated B cells on day 3 for SJ HTGTS analysis and day 4 for CSR analysis.
For SJ analysis, sonicated DNA was linearly amplified with primer (/5Bios/GGCAGCCTACCAAGAACAAC) and nested amplified with primer (5′-CGGTGGTACCTCACCCTTA-3′). Germline sequence was removed with EcoRI (NEB) digestion. For CSR analysis, libraries were prepared according to the protocol in (Hu J, et al. Nat Protoc 11:853–871 (2016)). Linear amplifications were performed using Sμ-specific biotin primer (/5Bios/CAGACCTGGGAATGTATGGT) and followed by nesting PCR with (5′-CACACAAAGACTCTGGACCTC-3′). AflII was used to remove germline sequence.
high-throughput genome translocation sequencing (HTGTS). Sequenced with MiSeq 500v

treatment_protocol: For SJ analysis, V-abl transformed B cells with integrated pMX-INV substrate were treated with STI571 (3 µM; Novartis Pharmaceuticals) for 3 days to arrest cells in G1 phase and induce RAG recombinase expression, generating breaks for V(D)J recombination of the substrate. Cells were analyzed via flow cytometry before DNA extraction. For CSR analysis, cells were cultured for 4 days and analyzed via flow cytometry before DNA extraction.

value: Spleen

value: anti-CD40 and IL-4 activated B cell

value: B cells

value: anti-CD40 and IL-4 for 4 days


title: RHT6129: B1_cLVX+

value: 100ng/ml lipopolysaccharide

value: Levofloxacin (25 uM)


title: MG1655, PEG Planktonic, 24 hr, rep 2

city: Amherst

first: Lauren

last: Andrews

state: Massachusetts

address: 240 Thatcher Rd Life Sciences Laboratories N265

department: Chemical Engineering

institute: University of Massachusetts Amherst

description:
PE2L; Planktonic cell growth in stationary liquid media for PEG experiment 2
gRNA_counts_all.csv
PEG_Planktonic_fitnesses.csv

library_source: other

data_processing:
Base calling and demultiplexing was performed automatically by Illumina Basespace (Illumina.BaseSpace.NativeApp.Core v0.9.0.2, Illumina.BaseSpace.NativeApp.Host v0.9.0.1) and FASTQ files generated by Illumina BaseSpace using Workflow v1.37.0 via GenerateFASTQ v1.1.0.64
Raw reads from the FASTQ files were filtered for an average quality of at least 20 using a custom Python (v3.9) script
For each sample, the counts for each gRNA design in the CRISPRi library were determined using a custom Python script (v3.9) by matching the 20 nucleotide sequence between ACAATTG and GTTTTA (or the reverse complement, if the read is in the reverse direction) to the sequence of a gRNA spacer seqeunce in the designed library, if possible
gRNA with fewer than 20 total counts in the combined four initial library count data were filtered out from downstream analysis
Relative frequencies for each gRNA design in all four initial library samples, the replicates of each selective condition (biomaterial and stiffness or planktonic growth above a biomaterial), and the duplicates of each selective condition were calculated using a custom Python (v3.9) script with a single pseudocount for each gRNA design. Specifically, relative frequency for the four combined initial library samples or a single replicate of a selective condition was calculated as the number of counts of a design in the sample divided by the total number of counts in that sample, with a +1 pseudocount for each gRNA design. Relative frequency for duplicates of a selective condition were calculated as the geometric mean of relative frequencies of both replicates.
Using a custom Python (v3.9) script, gRNA fitness for each gRNA design in each selective condition was then calculated as the log2-fold change in relative frequencies between the combined four initial library samples and the selective condition, normalized to median log2-fold change in relative frequencies for the non-targeting negative control gRNA in that selective condition. This was calculated for both individual replicates and duplicates of a selective condition using the appropriate relative frequency value.
Assembly: Not applicable
Supplementary files format and content: comma-delimited CSV file containing raw counts for all gRNA designs (34,315) and samples (20)
Supplementary files format and content: comma-delimited CSV files containing calculated gRNA fitness values of each replicate and the geometric mean of both replicates for each selective condition (biomaterial and stiffness or planktonic growth)
Library strategy: CRISPRi selection

molecule: other

organism: Escherichia coli

growth_protocol: The MG1655 CRISPRi library was grown in M9 media (6.78 g/L Na2HPO4, 3 g/L KH2PO4, 1 g/L NH4Cl, 0.5 g/L NaCl, 2 µM MgSO4, 0.1 mM CaCl2, 0.2% casamino acids, 0.34 g/L thiamine hydrochloride, 0.4% D-glucose) with 50 µg/mL kanamycin from a starting OD600 of 0.1 A for 2.5 hours at 250 rpm and 37C. A sample of culture was taken as an initial time point ("initial library") and then approximately 1.6X10^8 cells of this culture used to inoculate M9 media with 50 ug/mL kanamycin, 1 mM isopropyl ß-D-1-thiogalactopyranoside (IPTG), and 0.25 ng/mL anhydrotetracycline (aTc) above a biomaterial in a 6-well plate to a total volume of 8 mL. Cultures were then incubated in a stationary incubator at 37C for 24 hours.

extract_protocol:
Plasmid DNA from each cell library sample was extracted using the Qiagen QIAPrep Spin Miniprep kit according to the manufacturer's protocol
The gRNA spacer region of each plasmid pool sample was amplified using custom primers with variable lengths and sequences at the 5′ end to increase nucleotide diversity while maintaining a total amplicon length of 92 base pairs. Amplification was performed using Q5 polymerase (New England Biolabs, NEB) according to the manufacturer's protocol with 18 cycles. Amplicons were then digested using DpnI (NEB) for 8 hours and the PCR products purified using the GenCatch PCR purification kit according to the manufacturer's protocol. The 20 amplicon samples were then prepared for NGS using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) according to the manufacturer's protocol with 500 ng of starting material and purification of the adaptor-ligated DNA with 0.80X ratio of AMPure XP beads (Beckman Coulter) to for each reaction mixture. NEBNext Multiplex Oligos for Illumina Set 1 or Set 2 primers (NEB) were used to amplify (for 3 cycles) and barcode each sample. DNA concentration was quantified using a Qubit 4 Fluorometer with dsDNA High Sensitivity Quantification assays. All 20 samples were then pooled together in equal mass ratios and sequenced using an Illumina NexSeq500 System with a Mid-150 cycle kit (75 bp X 2 paired end reads) and a 10% PhiX spike-in.

treatment_protocol: Initial library samples were taken prior to inoculating media above biomaterials for selections (time 0 hours). After 24 hours of growth, samples of selections for cellular adhesion were obtained by gently washing biomaterials to remove loosely adhered cells from the surface and harvesting the adhered cells from a 2 cm^2 area on the biomaterial surface using a cell lifter. For each experiment, samples for selection of planktonic growth in stationary media above each biomaterial chemistry were obtained by carefully removing equal volumes of media above each biomaterial (Soft, Medium, and Stiff) in the 6-well plate, being careful to not disturb the biofilm formed on the surface.

tag: selection

value: Planktonic cell growth in stationary liquid media above biomaterials

tag: biomaterial chemistry

value: Not applicable

tag: biomaterail stiffness

tag: time

value: 24 hr

tag: biological replicate


title: RHT6128: B1_cLVX-

tag: cell types in culture

value: iHep + iKC co-culture


title: MG1655, Stiff PEG, 24 hr, rep 2

description:
PE2St
gRNA_counts_all.csv
PEG_St_fitnesses.csv

tag: cell line

value: Cellular adhesion

value: PEG

value: Stiff


title: N.furzeri brain/Proteasome Inhibition - Rep3

value: Brain

tag: treatment

value: Bortezomib


title: CSR_SAPPKHL-2

tag: tissue

tag: genotype


title: CSR_SAPPKHL-1


title: MG1655, Medium PEG, 24 hr, rep 2

description:
PE2Int
gRNA_counts_all.csv
PEG_Med_fitnesses.csv

value: Medium


title: liver_MYC_non-tumor_18months_Mice2

description: Gene expression data from non-tumor liver of MYC transgenic mice aged of 18 months

value: non tumor liver


title: RHT6127: B1_cTVX+

tag: lps stimulation

tag: drug treatment

value: Trovafloxacin (25 uM)


title: RHT6126: B1_cTVX-

value: Untreated


title: liver_MYC_non-tumor_18months_Mice3

source_name: non-tumor liver of MYC transgenic mice aged of 18 months


title: MG1655, Soft PEG, 24 hr, rep 2

description:
PE2So
gRNA_counts_all.csv
PEG_So_fitnesses.csv

tag: strain

value: Soft


title: CSR_PKHL-2

description:
Class Switch Recombination junctions
Pool_PKHL_240610_IgH_putback added.xlsx

value: Spleen

value: anti-CD40 and IL-4 activated B cell

value: B cells

value: DNA-PKcs-/-HLK/K

value: anti-CD40 and IL-4 for 4 days


title: RHT6125: B1_cVeh+

value: 100ng/ml lipopolysaccharide

value: Vehicle (0.2% DMSO)


title: N.furzeri brain/Proteasome Inhibition - Rep1


title: CSR_PKHL-1


title: liver_MYC_non-tumor_18months_Mice4


title: MG1655, Initial PEG, 0 hr, rep 2

description:
PE20; Initial library for PEG replicate 2 experiment
gRNA_counts_all.csv

value: Initial library

value: Not applicable

value: 0 hr


title: CSR_HL-2

description:
Class Switch Recombination junctions
Pool_HL_240610_IgH_putback added.xlsx

value: HLK/K


title: MG1655, PEG Planktonic, 24 hr, rep 1

description:
PE1L; Planktonic cell growth in stationary liquid media for PEG experiment 1
gRNA_counts_all.csv
PEG_Planktonic_fitnesses.csv

value: Planktonic cell growth in stationary liquid media above biomaterials

value: 24 hr


title: RHT6124: B1_cVeh-

value: iHep + iKC co-culture


title: colon tissues,DSS+AP4

city: Changsha

first: Xing

last: Wu

address: 138 Tongzipo Road, Changsha, Hunan 410013, P.R. China

department: Department of Gastroenterology

institute: The Third Xiangya Hospital of Central South University

data_processing:
Data filtering: The raw data was filtered with SOAPnuke (v1.5.2) by 1) Removing reads containing adapters (adapter contamination); 2) Removing reads whose unknown base ('N' base) ratio is more than 10%; 3) Removing reads whose low-quality base ratio (Base quality less than or equal to 15) is more than 50%, afterwards clean reads were obtained and stored in FASTQ format.
Reference genome mapping：The clean data were mapped to the reference genome by HISAT (v2.1.0)
Reference gene mapping: The clean data were mapped to the assembled unique gene by Bowtie2 (v2.2.5).The expression level of genes was calculated by RSEM (v1.2.8)
The reference mice genome was GCF_000001635.26_GRCm38.p6
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

source_name: Colon

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep kit following manufacture's  protocols.

value: Colon


title: colon tissues,DSS+AP2


title: liver_MYC_non-tumor_18months_Mice1

value: non tumor liver


title: colon tissues,DSS+AP3


title: MG1655, Stiff PEG, 24 hr, rep 1

description:
PE1St
gRNA_counts_all.csv
PEG_St_fitnesses.csv

value: Cellular adhesion

value: PEG

value: Stiff


title: colon tissues,DSS+AP1


title: RHT6121: B1_mTVX+

value: iHep mono-culture

value: Trovafloxacin (25 uM)


title: RHT6122: B1_mLVX-

value: Untreated

value: Levofloxacin (25 uM)


title: CSR_SAP-2

description:
Class Switch Recombination junctions
Pool of SAP_2280_3833_7282_CSR_putback.xlsx

value: Spleen

value: anti-CD40 and IL-4 activated B cell

value: B cells

value: anti-CD40 and IL-4 for 4 days


title: N.furzeri brain/Proteasome Inhibition - Rep4

value: Brain

value: Bortezomib


title: MG1655, Medium PEG, 24 hr, rep 1

description:
PE1Int
gRNA_counts_all.csv
PEG_Med_fitnesses.csv

value: Medium

value: 24 hr


title: CSR_SAP-3

description:
Class Switch Recombination junctions; Pooled 2 biological replicates
Pool of SAP_2280_3833_7282_CSR_putback.xlsx


title: N.furzeri brain/Proteasome Inhibition - Rep2


title: MG1655, Soft PEG, 24 hr, rep 1

description:
PE1So
gRNA_counts_all.csv
PEG_So_fitnesses.csv

value: Soft


title: colon tissues,DSS4

value: Colon


title: RHT6120: B1_mTVX-


title: CSR_SAP-1


title: colon tissues,DSS3


title: RHT6119: B1_mVeh+

value: 100ng/ml lipopolysaccharide

value: Vehicle (0.2% DMSO)


title: MG1655, Initial PEG, 0 hr, rep 1

description:
PE10; Initial library for PEG replicate 1 experiment
gRNA_counts_all.csv

value: Initial library

value: Not applicable

value: 0 hr


title: colon tissues,DSS2


title: RHT6123: B1_mLVX+

value: iHep mono-culture


title: RHT6118: B1_mVeh-

value: Untreated


title: CSR_WT-2

description:
Class Switch Recombination junctions
Pool of wt_3821_3831_CSR_putback.xlsx

value: Spleen

value: WT


title: CSR_HL-1

value: anti-CD40 and IL-4 activated B cell

value: B cells

value: HLK/K


title: CSR_WT-1

value: anti-CD40 and IL-4 for 4 days


title: MG1655, PDMS Planktonic, 24 hr, rep 2

description:
PD2L; Planktonic cell growth in stationary liquid media for PDMS experiment 2
gRNA_counts_all.csv
PDMS_Planktonic_fitnesses.csv

value: Planktonic cell growth in stationary liquid media above biomaterials


title: colon tissues,DSS1


title: MG1655, Stiff PDMS, 24 hr, rep 2

description:
PD2St
gRNA_counts_all.csv
PDMS_St_fitnesses.csv

value: Cellular adhesion

value: PDMS

value: Stiff

value: 24 hr


title: SJ_SAPPK-2

description: Signal Join junctions on the chromosomal V(D)J recombination substrate pMX-INV

source_name: Bone marrow

value: Bone marrow

value: v-abl transformed B cell

value: STI571 for 3 days


title: MAH022420_006

data_processing:
Raw reads were aligned to human reference genome hg38 using STAR (Dobin et al., 2013). ENSEMBL genes were quantified using FeatureCounts (Liao, Smyth, & Shi, 2014). Differential expression statistics were computed using edgeR (McCarthy, Chen, & Smyth, 2012; Robinson, McCarthy, & Smyth, 2010) on raw expression counts with the exactTest function. P-values were adjusted for multiple testing using the false discovery rate (FDR) correction of Benjamini and Hochberg (Benjamini & Hochberg, 1995).
Genome_build: hg38
Supplementary_files_format_and_content: Table of raw counts per gene – tabular text file

extract_protocol:
RNA was isolated and analyzed for integrity using Agilent 4200 TapeStation and RNA Screen Tape
RNA-seq libraries were prepared using a Universal Plus mRNASeq kit, and library fragment size distribution was confirmed by electrophoresis using a 2200 TapeStation system with D1000
Sequencing was carried out on NovaSeq 6000, SP flowcell, 2x50 nt reads. General quality-control metrics were obtained using FastQC and raw reads were aligned to human reference genome hg38 using STAR and BWA MEM. ENSEMBL genes were quantified using FeatureCounts, and differential expression statistics were computed using edgeR. Specific gene expression was measured and verified using qPCR.

treatment_protocol: HCT-116 colon cancer cells were grown and maintained and treated with a combination of Vitamin D2 and D3 and all trans-retinoic acid (ATRA) at 1 µM for four hours.

value: Treatment


title: SJ_SAPPK-1


title: MAH022420_005


title: MG1655, Soft PDMS, 24 hr, rep 2

description:
PD2So
gRNA_counts_all.csv
PDMS_So_fitnesses.csv

value: Soft


title: SJ_PK-2

description: Signal Join junctions on the chromosomal V(D)J recombination substrate pMX-INV; Pooled 3 biological replicates

value: DNA-PKcs-/-


title: MAH022420_003

value: Control


title: MG1655, PDMS Planktonic, 24 hr, rep 1

description:
PD1L; Planktonic cell growth in stationary liquid media for PDMS experiment 1
gRNA_counts_all.csv
PDMS_Planktonic_fitnesses.csv

value: Not applicable


title: MG1655, Medium PDMS, 24 hr, rep 2

description:
PD2Int
gRNA_counts_all.csv
PDMS_Med_fitnesses.csv

value: Medium


title: MG1655, Initial PDMS, 0 hr, rep 2

description:
PD20; Initial library for PDMS replicate 2 experiment
gRNA_counts_all.csv

value: Initial library

value: 0 hr


title: smf12_Mn_5min R1

city: Montreal

first: Adnane

last: Sellam

address: 5000, rue Bélanger

country: Canada

institute: Universite de Montreal

description: Library name: smf12_Mn_5min_R1

data_processing:
Sequencing reads were filtered with fastp version 0.23.2
Filtered reads were mapped to the reference genome sequence of strain SC5314 with STAR version 2.7.9a
The number of reads mapping on each of the genes was calculated by featurecount version 2.0.1
Differential gene expression was calculated with DESeq2 version 1.26.0.
Assembly: GCF_000182965.3
Supplementary files format and content: Tab-delimited file with normalized read counts for each sample

organism: Candida albicans

growth_protocol: Overnight cultures of WT (SN148-CIp20) strain and smf12 mutant were diluted to an OD600 of 0.1 in 60 ml of fresh SC-Mn medium and grown at 30°C under agitation (200 rpm) to early logarithmic phase (OD600=0.4).

extract_protocol:
Total RNA was extracted using an RNAeasy purification kit (Qiagen) and glass bead lysis in a Biospec Mini 24 bead-beater
The NEBNext UltraTM II RNA Library Prep Kit for Illumina was used to construct the RNA-seq library following the manufacturer’s instruction.

treatment_protocol: Cultures were then either left untreated or exposed to 1 mM MnCl2 and incubated at 30°C for 5 and 90 min. For RNA-seq profiling of Mn excess, overnight cultures of WT cells were diluted to an OD600 of 0.1 in fresh 100 ml YPD and incubated with shaking at 30°C to an OD600 of 0.8 and split into 50-ml cultures. MnCl2 was added to the experimental culture to a final concentration of 7.5 mM, while an equal volume of sterile water was added to the control culture and incubated for 30 min. Cells were harvested by centrifugation and were quick-frozen and stored at -80°C.

value: Yeast cells

value: 90 min in SC+MN


title: smf12_Mn_5min R2

description: Library name: smf12_Mn_5min_R2


title: SJ_SAP-2

city: New York

value: B cells


title: smf12_YNB_5min R1

description: Library name: smf12_YNB_5min_R1

value: 90 min in SC-MN


title: MAH022420_004


title: smf12_YNB_5min R2

description: Library name: smf12_YNB_5min_R2


title: WT_Mn_5min R2

description: Library name: WT_Mn_5min_R2

value: WT


title: SJ_SAP-1


title: WT_Mn_5min R1

description: Library name: WT_Mn_5min_R1


title: MG1655, Soft PDMS, 24 hr, rep 1

description:
PD1So
gRNA_counts_all.csv
PDMS_So_fitnesses.csv

value: Cellular adhesion

value: PDMS

value: 24 hr


title: SJ_PK-1

value: Bone marrow

value: v-abl transformed B cell

value: STI571 for 3 days


title: WT_YNB_5min R2

description: Library name: WT_YNB_5min_R2


title: MAH022420_002


title: MG1655, Stiff PDMS, 24 hr, rep 1

description:
PD1St
gRNA_counts_all.csv
PDMS_St_fitnesses.csv

value: Stiff