title: ss8_P1F9, scRNAseq

extract_protocol:
EGFP+ single cells were individually collected by FACS into 96 well plates.
Libraries were prepared following SmartSeq2 NexteraXT indications.
single cell RNA seq


title: Replicate 2: mRNA-derived cDNA

status: Public on Jul 06 2022

type: SRA

city: Houston

first: Jlenia

last: Guarnerio

state: TX

address: 6767 Bertner Ave

department: Genetics

country: USA

institute: MD Anderson Cancer Center

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA

library_source: transcriptomic

data_processing:
The Cell Ranger pipeline from 10X Genomics was used to align, filter, and count reads from FASTQ data, generating count matrices for both gene expression and HTO barcodes.
Seurat package (v4) for R was used to demultiplex sample identity based on oligo hashtags, and to filter for doublets and dead cells. Following preprocessing, Seurat was used to perform dimensionality reduction, clustering, and differential expression analysis.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix_sarc001__ccne1-REP1.h5: Feature count data as sparse matrix (ouput from 10x Genomics "cellranger count" pipeline)
Supplementary files format and content: Sarcoma1_hash_idents.csv: original sample ID of each single-cell barcode corresponding to a high-quality cell.
Supplementary files format and content: filtered_feature_bc_matrix_sarc002__ccne1-REP2.h5: Feature count data as sparse matrix (ouput from 10x Genomics "cellranger count" pipeline)
Supplementary files format and content: Sarcoma2_hash_idents.csv: original sample ID of each single-cell barcode corresponding to a high-quality cell.
Library strategy: CITE-Seq

molecule: polyA RNA

organism: Mus musculus

source_name: Whole tumor (sarcoma)

growth_protocol: Soft-tissue sarcoma cells were generated as transformed mesenchymal stem cells (bearing p53 KO and Ccne1 overexpression, allowed to form subcutaneous tumors in primary recipient mice).

extract_protocol:
Mouse tumors were digested into single-cell suspensions using the Mouse Tumor Dissociation Kit and gentleMACS dissociator (Miltenyi). CD45+ cells were enriched from each sample with magnetic beads. Enriched samples were individually hashtagged with a unique oligonucleotide barcodes (TotalSeq-A, Biolegend) and then pooled together in equal proportions at a concentration of 1000 cells/uL. Single cells were partitioned for RNA capture using 10X Chromium Controller.
mRNA and TotalSeq HTO libraries were prepared with the 10X Genomics Single Cell 3' Gene Expression kit v3 using standard manufacturer protocols, pooled together (5% for HTO library), and sequenced on the NovaSeq 6000 as 400M paired-end reads.

tag: tissue

value: Whole tumor (sarcoma)

tag: cell type

value: Tumor and immune cells

tag: cell line

value: Mouse sarcoma p53-/- Ccne1+

tag: library type

value: mRNA

tag: antibodies/tags


title: mm_atac_immatureb_kmac.1

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

description: Ex Vivo Sorted Kappa-macroself immature B cells

library_source: genomic

data_processing:
RNA-seq: Raw reads were aligned to reference genome mm9 in a splice aware manner using STAR (Dobin et al., 2013; Dobin and Gingeras, 2015). Gene expression was quantified using featureCounts within the RSubread R package (Liao et al., 2019) against UCSC genes with Ensembl Ig genes from mm10 converted to mm9 coordinates with UCSC liftOver. GTF file is included in the submission.
ATAC-seq: Raw reads were aligned to the reference genome using BWA MEM, and apparent PCR duplicates removed using Picard MarkDuplicates. Read alignments were first adjusted to account for TAC transposon binding: +4 bp for +strand alignments, −5 bp for −strand alignments. The open chromatin enrichment track was generated by first creating a bedGraph from the raw reads using bedtools genomcov, then converted to bigWig using UCSC tool bedGraphToBigWig; tracks were normalized by the sum of alignment lengths over 1 billion. Open chromatin peaks were called using Macs2 (Zhang et al., 2008) with no model set and no background provided; peaks with a score of >5 were retained.
Genome_build: mm9
Supplementary_files_format_and_content: GTF formatted file: gene annotations used for RNA-seq. UCSC genes for mm9 + Ig genes from Ensembl mm10, lifted over to mm9
Supplementary_files_format_and_content: BED formatted file: peak calls for ATAC-seq
Supplementary_files_format_and_content: BigWig formatted file: normalized enrichment of open chromatin for ATAC-seq
Supplementary_files_format_and_content: Tab-delimited text formatted file: unnormalized counts per gene

molecule: genomic DNA

growth_protocol: B cell progenitors (B220+IgM−) from WT, Igkdel , k-mac mice were isolated from BM with a MACS separation column (Miltenyi Biotec) and cultured in complete Opti-MEM containing 10% (v/v) FBS and IL-7 (16 ng ml−1) for 5 d.

extract_protocol:
RNA-seq: FACS sorted cells from small pre-B and immature B cells isolated from WT, Igkdel k-mac, k-mac CXCR4fl/fl and k-mac CXCR4fl/fl mb1-cre+ mice and total RNA isolated using Trizol (15596026, Invitrogen) following the protocol described by the Immunological Genome Project (Immgen.org).
RNA-seq: Libraries were generated TruSeq® Stranded mRNA Sample Prep” kit from Illumina and the associated user manual
ATAC-seq: 1.2x105 small pre-B and immature B cells sorted from WT, Igkdel k-mac, k-mac CXCR4fl/fl and k-mac CXCR4fl/fl mb1-cre+ mice were used for ATAC-seq. Cells were centrifuged at 500g at 4°C for 5 minutes, washed with 1X PBS, and centrifuged again. Cells were resuspended in lysis buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630) and immediately centrifuged at 500g at 4°C for 10 minutes. Pellet was resuspended in transposition reaction buffer (25ml 2x Tagment Buffer (FC-121-1030, Illumina), 2.5ml Tagment DNA Enzyme, 22.5ml nuclease free H2O) for 30 minutes at 37°C.
ATAC-seq: DNA was purified with a Qiagen MinElute Kit and amplified with Nextera PCR Primers (Illumina Nextera Index Kit) and NEBNext PCR Master Mix (M0541, New England BioLabs) for 11 cycles. Amplified DNA was purified with a Qiagen PCR cleanup kit. Libraries were sequenced on a NextSeq 550 sequencer at University of Chicago Genomics Facility.

treatment_protocol: After growth phase cells were cultured for 72 hours with 16 ng ml−1 IL-7 (+IL-7), 0.2 ng ml−1 IL-7 (−IL-7) or 0.2 ng ml−1 IL-7 with 100 ng CXCL12 (−IL-7+CXCL12).

tag: sample group

value: ImmatureB K-Macroself


title: Tomato Interface Day 14b

city: University Park

first: Michael

middle: J

last: Axtell

state: PA

address: 280 Mueller Lab

department: Biology

institute: Pennsylvania State University

data_processing:
Adapters were trimmed using CutAdapt v3.0 (Martin, 2010) using parameters -m 1 -j 4 -o
Using Bowtie, reads that mapped to the Solanum lycopersicum genome were removed using parameters -p 8 -v 0 --un
Remaining reads were aligned to the Cuscuta campestris genome using ShortStack V3.8.5 using default parameters and a --locifile corresponding to known interface-induced MIRNA loci.
Genome_build: Cuscuta campestris genome assembly v0.32 as downloaded from https://www.plabipd.de/project_cuscuta2/start.ep in mid-2020. Described by Vogel et al. (2018) doi: 10.1038/s41467-018-04344-z
Supplementary_files_format_and_content: .tsv file. Raw counts of trans-species miRNAs. Columns are sRNA-seq libraries, rows are trans-species miRNAs

molecule: total RNA

organism: Solanum lycopersicum

source_name: Solanum lycopersicum / Cuscuta campestris haustorial interface

growth_protocol: Solanum lycopersicum was grown at 18-20°C and illuminated with fluorescent tubing supplemented with far-red LED lights for 16 hours.  Cuscuta campestris seed coats were dissolved with sulfuric acid for 1 hour, washed with distilled water 5-6 times, and placed in a growth chamber set to 30°C for 3 days to germinate.

extract_protocol:
RNA was extracted using TRI-reagent (sigma: 93289-100ML) using the manufacturer's protocol.  An additional step of sodium acetate cleanup / ethanol precipitation was also used.
Libraries were constructed using randomized splint ligation as specified in Maguire et al.,2020 https://doi.org/10.1093/nar/gkaa480

treatment_protocol: Cuscuta campestris seedlings were placed at the base of Solanum lycopersicum hypocotyls and allowed to attach. Day 0 is defined when seedlings have successfully wraped around the hypocotyl.

tag: day

value: Solanum lycopersicum hypocotyls and Cuscuta campestris haustoria

tag: agent

value: Cuscuta campestris


title: Tomato Interface Day 14a


title: shSCR-1, Mif-WT

data_processing:
FASTQ files were trimmed with Trimmomatic.
Transcript abundances were quantified using salmon quant with the --gcBias flag set.
Assembly: mm10
Supplementary files format and content: Transcript abundance matrix (output from salmon)

source_name: Whole mouse tumor (sarcoma)

growth_protocol: Soft-tissue sarcoma cells were generated as transformed mesenchymal stem cells (bearing p53 KO and Ccne1 overexpression, allowed to form subcutaneous tumors in primary recipient mice). Then, transformed cells were additionally transduced with an sg- or shRNA against Mif or non-targeting control. sgRNA samples were transduced with Cas9. These cells were transplanted subcutaneously and allowed to grow tumors in secondary recipients.

extract_protocol: Total RNA was extracted from FACS-purified tumor cells using TRIzol (Invitrogen) according to the manufacturer's instructions.

value: Whole mouse tumor (sarcoma)

value: tumor cells ex vivo

tag: strain

tag: genotype

value: Mif-wildtype


title: Tomato Interface Day 14c


title: shMif-2, Mif-KD

value: Mif-knockdown


title: Tomato Interface Day 13c


title: shMif-1, Mif-KD


title: Csalc 2

city: Beijing

first: zhongyi

last: wang

state: Beijing

address: No.2 Yuanmingyuan Xi Lu

country: China

institute: CAU(China Agricultural University)

data_processing:
Analyses of the transcriptome data were performed on the BMKCloud platform  (www.biocloud.net).
HISAT2 software used to compare the sequenced Reads to the reference genome (Kim D, Langmead B, Salzberg S L. HISAT: a fast spliced aligner with low memory requirements[J]. Nature methods, 2015, 12(4): 357-360.).
Differentially expressed genes (DEGs) were calculated using DESeq2 (Love MI, Huber W and Anders S (2014). “Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.” Genome Biology, 15, pp. 550. doi:10.1186/s13059-014-0550-8.). The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. The false discovery rate (FDR) less than 0.05 and the fold change larger than 2 as were set as the threshold.
Genome_build: ChineseLong_v2
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample

organism: Cucumis sativus

source_name: stigma at anthesis

extract_protocol:
The RNA of the sample was harvested using Trizol reagent. Illumina NEBNext® Ultra™ RNA Library Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: Stage

value: at anthesis

value: Csalc-/-

value: cucumber stigma and style


title: Csalc 1


title: ss8_P1F6, scRNAseq

city: London

first: Andrea

last: Streit

address: Guys Hospital, Great Maze Pond

department: Centre for Craniofacial & Regenerative Biology

country: United Kingdom

institute: Kings College London

data_processing:
All data was processed using a custom Nextflow pipeline available at https://github.com/alexthiery/otic-reprogramming. All packages and versions are containerised in Docker images called by the pipeline. Full documentation of pipeline parameters and how to reproduce the analysis is available at https://alexthiery.github.io/otic-reprogramming/
Adaptor sequences were trimmed using cutadapt v2.10, aligned using hisat2 v2.2.1, sorted using samtools v1.10, and read counts obtained using htseq v0.12.4.
RNA velocity counts were obtained using Velocyto v0.17.17.
Genome_build: galgal6
Supplementary_files_format_and_content: assayData.csv (raw counts)
phenoData.csv (sample metadata)
gfpData.csv (raw gfp counts)
onefilepercell_ss8-TSS_P2_C10_75_and_others_TVIUH.loom (raw velocyto counts)

organism: Gallus gallus

source_name: Pax2+ cells

growth_protocol: Chick embryos were electroporated and grown at 38°C until reaching the desired stage.

treatment_protocol: Chick embryos were electroporated at head fold stage with pTK-Pax2E1-EGFP plasmids.

value: Pax2+ cells


title: sgSCR-2, Mif-WT


title: ss8_P1F4, scRNAseq


title: sgMif-2, Mif-KO

value: Mif-knockout


title: ss8_P1F5, scRNAseq


title: ss8_P1F3, scRNAseq


title: 2_500nM

city: Ann Arbor

first: Rachel

middle: Orion

last: Niederer

state: MI

address: 1150 W. Medical Center Dr

department: Biological Chemistry

institute: University of Michigan

data_processing:
Library strategy: RNA Bind-N-Seq
Illumina software was used for basecalling
reads were trimmed for adaptor with cutadapt and aligned to custom genomic file containing all the synthetic sequences with STAR. PCR duplicates were discared from the final file using 10N random barcode with a custom python script
sequences with less then 1 rpm in any input library and 2 raw reads in any other library was discarded from further analysis
Genome_build: "JK_pool.fasta", custom genome based on synthetic sequences
Supplementary_files_format_and_content: matrix of raw counts for each TL (transcript leader)

organism: synthetic construct

source_name: yeast (Saccharomyces cerevisiae) 5'-UTRs, synthetic pool

growth_protocol: T7 RNA polymerase transcribed RNA

extract_protocol:
Proteinase K treatment, phenol:chlorophorm extraction
reverse transcription, ligation of 5'-linker, PCR amplification.

treatment_protocol: Incubated with various amounts of purified eIF3

tag: replicate

tag: treatment

value: 500 nM eIF3

tag: rna extraction

value: passed through nitrocellulose filter, RNA extracted from filter

tag: fraction

value: eIF3-bound RNA


title: 2_input

value: 0 nM eIF3

value: RNA directly extracted

value: input RNA


title: 2_in500


title: ss8_P1F8, scRNAseq


title: Tomato Interface Day 13b

value: Solanum lycopersicum hypocotyls and Cuscuta campestris haustoria


title: ss8_P1F2, scRNAseq


title: 2_1500nM

value: 1500 nM eIF3


title: Tomato Interface Day 12c

value: Cuscuta campestris


title: Tomato Interface Day 12b


title: sgSCR-1, Mif-WT

value: Whole mouse tumor (sarcoma)

value: Mouse sarcoma p53-/- Ccne1+

value: tumor cells ex vivo


title: 2_166nM

value: 166 nM eIF3


title: sgMif-1, Mif-KO


title: Replicate 2, mRNA-derived cDNA

data_processing:
The Cell Ranger pipeline from 10X Genomics was used to align, filter, and count reads from FASTQ data, generating count matrices for both gene expression and HTO barcodes.
Seurat package (v4) for R was used to demultiplex sample identity based on oligo hashtags, and to filter for doublets and dead cells. Following preprocessing, Seurat was used to perform dimensionality reduction, clustering, and differential expression analysis.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix_sarc006-REP1.h5: Feature count data as sparse matrix (ouput from 10x Genomics "cellranger count" pipeline)
Supplementary files format and content: SarcomaMIF-REP1_hash_idents.csv: original sample ID of each single-cell barcode corresponding to a high-quality cell.
Supplementary files format and content: filtered_feature_bc_matrix_sarc006-REP2.h5: Feature count data as sparse matrix (ouput from 10x Genomics "cellranger count" pipeline)
Supplementary files format and content: SarcomaMIF-REP2_hash_idents.csv: original sample ID of each single-cell barcode corresponding to a high-quality cell.
Library strategy: CITE-Seq

growth_protocol: Soft-tissue sarcoma cells were generated as transformed mesenchymal stem cells (bearing p53 KO and Ccne1 overexpression, allowed to form subcutaneous tumors in primary recipient mice), which were subsequently transduced with Cas9 and either sgCTR or sgMif.

extract_protocol:
Mouse tumors were digested into single-cell suspensions using the Mouse Tumor Dissociation Kit and gentleMACS dissociator (Miltenyi). CD45+ cells were enriched from each sample with magnetic beads. Enriched samples were individually hashtagged with a unique oligonucleotide barcodes (TotalSeq-A, Biolegend) and then pooled together in equal proportions at a concentration of 1000 cells/uL. Single cells were partitioned for RNA capture using 10X Chromium Controller.
mRNA and TotalSeq HTO libraries were prepared with the 10X Genomics Single Cell 3' Gene Expression kit v3 using standard manufacturer protocols, pooled together (5% for HTO library), and sequenced on the NovaSeq 6000 as 800M paired-end reads.

value: Whole tumor (sarcoma)

value: Tumor and immune cells

value: Mouse sarcoma p53-/- Ccne1+, transduced with sgCTR or sgMif

value: mRNA


title: Replicate 2, HTO-derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)

library_source: other

molecule: protein

value: HTO

value: Biolegend TotalSeqA mouse hashtags 1, 2, 3, 4, 12


title: Tomato Interface Day 12a


title: ss8_P1F12, scRNAseq

value: Pax2+ cells


title: ss8_P1F11, scRNAseq


title: 2_19nM

value: 19nM eIF3

value: passed through nitrocellulose filter, RNA extracted from filter

value: eIF3-bound RNA


title: Tomato Interface Day 11c

value: Solanum lycopersicum hypocotyls and Cuscuta campestris haustoria


title: ss8_P1F1, scRNAseq


title: Replicate 1, HTO-derived cDNA


title: 2_55nM

value: 55 nM eIF3


title: Tomato Interface Day 13a

value: Cuscuta campestris


title: 1_input

value: 0 nM eIF3

value: RNA directly extracted

value: input RNA


title: 2_0nM


title: Replicate 1, mRNA-derived cDNA


title: ss8_P1F10, scRNAseq


title: ss8_P1E9, scRNAseq


title: Tomato Interface Day 10c


title: 1_500nM

value: 500 nM eIF3


title: TMF2

city: Shanghai

first: Xiaonan

last: Chen

state: Shanghai

address: 639 Zhizaoju Road

department: Department of Cardiology

institute: Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

description: MTRG2 HFPEF FEMALE

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include readcount and fpkm values for each Sample ...

source_name: cardiomyocytes

extract_protocol:
Using Langendorff to isolate cardiomyocytes, and RNA was harvested using Trizol reagen. Illumina NEBNext® UltraTM RNA Library Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: heart

tag: age

value: post natal week 16

value: second generation TERC-/-

tag: Sex

value: female

tag: diet

value: HFPEF


title: 1_1500nM

value: 1500 nM eIF3


title: ss8_P1E8, scRNAseq

tag: cell type

value: Pax2+ cells


title: Tomato Interface Day 11a

tag: tissue


title: ss8_P1E7, scRNAseq


title: TMF1

description: MTRG2 HFPEF FEMALE


title: TMF3

description: MTRG2 HFPEF FEMALE


title: 1_55nM


title: TCF3

description: MTRG2 CHOW FEMALE

value: chow


title: Tomato Interface Day 11b


title: Tomato Interface Day 10b


title: 1_19nM

value: 19nM eIF3

value: passed through nitrocellulose filter, RNA extracted from filter


title: TCF2

description: MTRG2 CHOW FEMALE


title: 1_0nM

value: eIF3-bound RNA


title: ss8_P1E6, scRNAseq


title: Tomato Interface Day 9b

value: Solanum lycopersicum hypocotyls and Cuscuta campestris haustoria


title: ss8_P1E3, scRNAseq


title: Tomato Interface Day 8c

value: Cuscuta campestris


title: ss8_P1E4, scRNAseq


title: G2333_Pph_BR2

city: Davis

first: Cristian

last: Jacob

state: CA

address: 3800 Solano Park CR., Apt. 4022

department: Plant Sciences

institute: University of California, Davis

data_processing:
Sequence reads were subjected to a multi-phase quality control regime as follows: raw reads were trimmed with fastx_trimmer using a minimum quality threshold of 13 and minimum length of 32 bases. Subsequently, reads were filtered with a fastq_quality_filter with a quality cut-off of 13 and minimum percentage of 90. Mitochondrial and plastid genome reads and repeat elements were further filtered out using the bowtie-based TopHat suite (Trapnell et al. 2009). Reads that passed quality control were mapped to the genome of Pph 1448A (GenBank assembly accession: GCA_000012205.1) to remove bacterial sequences, and to the current P. vulgaris reference genome assembly v2.1 (https://phytozome.jgi.doe.gov) using the default parameters of the STAR RNA-Seq aligner version 2.5.2b (Dobin et al. 2013). For each biological replicate, an average of 15 million reads were mapped to the P. vulgaris genome.
Supplementary_files_format_and_content: spreadsheet, fold change

organism: Phaseolus vulgaris

growth_protocol: Seeds of the P. vulgaris landrace G2333 were kept on water-soaked filter paper for three days to ensure uniform germination at room temperature. Seedlings were transplanted to individual 42 mm peat moss pellets (Jiffy-7®) and kept at 28  2°C, 100 ± 10 µmol.m-2.sec-1 with a 12-hour photoperiod, and 60 ± 10% air relative humidity. Two-week old plants were used in the experiments detailed below.

extract_protocol:
Total RNA was extracted with the TRIzol reagent (Thermo Fisher Scientific, Rockford, IL) following the manufacturer’s recommendations.
RNA was quantified using a NanoDrop spectrophotometer (Thermo Fisher Scientific, Rockford, IL). RNA quality was evaluated with a BioAnalyzer 2100 (Agilent, Santa Clara, CA). RNA-seq libraries were prepared with 2 µg of total RNA with the TruSeq RNA v2 kit (Illumina, Inc., San Diego, CA), according to the manufacturer’s protocol. The concentration of the libraries was measured with the Qubit fluorometer (Invitrogen, Carlsbad, CA) and fragment sizes were determined using the Agilent High Sensitivity DNA kit on a BioAnalyzer 2100 (Agilent Technologies, Waldbronn, Germany). RNA sequences (1 × 100 bases) were obtained with a HiSeq 2000 system (Illumina Inc., San Diego, CA) at the DNA Core Facility, University of Missouri, USA.

treatment_protocol: Pseudomonas syringae pv. phaseolicola (Burkn.) Downs (Pph) strain NPS3121 was streaked from frozen glycerol culture stock on low-salt Luria Bertani (LSLB) agar plates (10 g/L tryptone, 5 g/L yeast extract, 5 g/L NaCl, pH 7.0, 12 g/L agar), supplemented with 100 μg.mL-1 rifampicin, and incubated at 30°C for 2 to 3 days. A single colony was placed in 100 mL of LSLB liquid medium with 100 μg.mL-1 rifampicin and incubated in an orbital shaker (30°C and 200 rpm). The bacterial culture was grown until it reached the optical density at a wavelength of 600 nm (OD600) between 0.8–1.0. The volume of the bacterial solution reached an inoculum concentration of 1 × 106 CFU.mL-1 and was then centrifuged at room temperature at 1,200 ×g for 20 min. The supernatant was discarded and the bacterial cell pellet was resuspended in sterile distilled water to make the inoculum. Fully expanded primary leaves were syringe-infiltrated with bacterial inoculum or water as a mock control. After inoculation, plants were grown under the same conditions as described above until the time of sampling. Leaflets from the same plant were collected at each time point, 6 and 12 hours post inoculation (hpi), flash frozen in liquid nitrogen, and stored at -80°C until processing. Leaves collected at 6 and 12 hpi were pooled for total RNA extraction, and RNA from two different plants were pooled for RNA sequencing. The experiment was repeated twice, resulting in four biological replicates and two replicates were pooled for RNA-sequencing.

value: Bacteria inoculated

value: Leaf tissue


title: 1_166nM

value: 166 nM eIF3


title: Tomato Interface Day 9a


title: G2333_Pph_BR1


title: WMF3

description: WT HFPEF FEMALE

value: wild type


title: Tomato Interface Day 8b


title: Tomato Interface Day 10a


title: ss8_P1E5, scRNAseq


title: G2333_Mock_BR1

value: Mock inoculated


title: WMF2

description: WT HFPEF FEMALE

value: heart

value: post natal week 16


title: ss8_P1E2, scRNAseq


title: ss8_P1E12, scRNAseq


title: WMF1

description: WT HFPEF FEMALE

value: female


title: ss8_P1E11, scRNAseq


title: WCF2

description: WT CHOW FEMALE


title: Tomato Interface Day 9c


title: Ctrl_35

city: HELSINKI

first: Chunguang

last: Wang

address: BIOMEDICUM Helsinki 2U, Tukholmankatu 8

department: Cardiovascular Research Unit

country: Finland

institute: Minerva Foundation Institute for Medical Research

data_processing:
bcl2fastq2 Conversion Software was used to convert BCL files to FASTQ file format and demultiplex samples. All samples were sequenced on two sequencing runs and the resulting sequence files were combined with "cat" -command.
Sequenced reads were trimmed for adapter sequence, and masked for low-complexity or low-quality sequence using Trimmomatic. Parameters used: :2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Trimmed reads were mapped to GRCh38.p13 whole genome using STAR aligner with parameters  --runThreadN 20 --chimSegmentMin 12 --chimJunctionOverhangMin 12 --chimSegmentReadGapMax 3 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJstitchMismatchNmax 5 -1 5 5 --outFilterType BySJout --outFilterMismatchNmax 999 --outSAMattributes NH HI NM MD AS nM jM jI XS --outSAMtype BAM SortedByCoordinate --outSAMmapqUnique 60 --quantMode GeneCounts --twopassMode Basic
Counts per gene were calculated using featureCounts software. Parameters used: -s 2 -T 20 -t exon -g gene_id -a gencode.v33.annotation.gtf
Differential expression analysis used the DESeq2 software in R environment. Procedures included: Normalization of count values between samples using a geometric mean, estimation of samples-wise factors to correct for library size variability (for example), estimation of dispersion (i.e. variance, scatter) of gene-wise values between conditions, negative binomial linear model and Wald test to produce p-values, removal of low-expression outliers (using Cook's distance)  to optimize for p-value adjustment and finally, multiple testing adjustment of p-values with Benjamini-Hochberg procedure.
Assembly: GRCh38.p13 genome and annotations from GENCODE Release v.33
Supplementary files format and content: Raw count matrix of sequencing reads asMS .xlsx

organism: Homo sapiens

source_name: Heart, Left ventricle

extract_protocol:
About 50 mg of snap-frozen left ventricle were cut into pieces on dry ice and homogenized with OMNI Bead Ruptor for 30s (6m/s) in 0.7 ml of QIAzol reagent (Qiagen). After removing debris with centrifugation, the lysate was transferred to a fresh tube and proceeded to RNA isolation using the miRNeasy Mini Kit (Qiagen).
NEBNext Ultra II Directional RNA after rRNA depletion
Illumina NextSeq High Output 1 x 75 bp (2 sequencing runs)

value: Heart, Left ventricle


title: G2333_Mock_BR2


title: ss8_P1E1, scRNAseq


title: ss8_P1D9, scRNAseq


title: Tomato Interface Day 8a


title: WCF3

description: WT CHOW FEMALE


title: TMM2

description: MTRG2 HFPEF MALE

value: second generation TERC-/-

value: male

value: HFPEF


title: Tomato Interface Day 5a


title: TCF1

description: MTRG2 CHOW FEMALE

value: chow


title: Tomato Interface Day 7c


title: Ctrl_43


title: Ctrl_9


title: TCM3

description: MTRG2 CHOW MALE


title: Tomato Interface Day 7b


title: WCF1

description: WT CHOW FEMALE


title: ss8_P1E10, scRNAseq

value: Pax2+ cells


title: Ctrl_20


title: ss8_P1D8, scRNAseq


title: Tomato Interface Day 7a


title: TMM1

description: MTRG2 HFPEF MALE


title: Ctrl_19


title: Tomato Interface Day 4c


title: ss8_P1D5, scRNAseq


title: Tomato Interface Day 4d


title: TCM1

description: MTRG2 CHOW MALE


title: TX_30


title: ss8_P1D6, scRNAseq


title: WMM3

description: WT HFPEF MALE


title: Ctrl_3


title: Tomato Interface Day 3c


title: Tomato Interface Day 3b


title: Ctrl_1


title: Tomato Interface Day 4b


title: TCM2

description: MTRG2 CHOW MALE


title: TMM3

description: MTRG2 HFPEF MALE


title: Tomato Interface Day 4a


title: ss8_P1D4, scRNAseq


title: ss8_P1D3, scRNAseq


title: ss8_P1D7, scRNAseq


title: WMM2

description: WT HFPEF MALE


title: ss8_P1D1, scRNAseq


title: TX_28


title: TX_34


title: TX_24


title: TX_25


title: WMM1

description: WT HFPEF MALE


title: Tomato Interface Day 2c


title: ss8_P1D12, scRNAseq


title: TX_14


title: WCM2

description: WT CHOW MALE


title: TX_5


title: Tomato Interface Day 2a


title: TX_19


title: ss8_P1D10, scRNAseq


title: Tomato Interface Day 2b


title: ss8_P1D11, scRNAseq


title: WCM3

description: WT CHOW MALE


title: Tomato Interface Day 2d


title: WCM1

description: WT CHOW MALE


title: ss8_P1D2, scRNAseq


title: FXR KO_GW4064_3

city: Hwasun-gun, Jeollanam-do

first: Dong-Hyun

last: Kim

state: Not Applicable

address: 264, Seoyang-ro, Hwasun-eup,

country: South Korea

institute: Medispan

data_processing:
Aligned reads are generated after mapping to the reference genome using the HISAT2 program that considers splice for reads that have undergone pre-processing.
Using the reference-based aligned reads information, the transcript assembly is performed through the StringTie program.
Raw data were calculated as FPKM (Fragments Per Kilobase of exon model per Millon mapped fragments) of each transcript in each sample by cufflinks software.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM    TPM

source_name: Kidney

extract_protocol:
Kidneys were removed, and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded Total RNA LT Sample Prep Kit (Gold) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq Stranded Total RNA Sample Prep Guide, Part #15031048 Rev. E)

value: Kidney

value: GW4064 for 6h


title: Tomato Interface Day 1c

value: Solanum lycopersicum hypocotyls and Cuscuta campestris haustoria

value: Cuscuta campestris


title: Tomato Interface Day 3a


title: ss8_P1C9, scRNAseq


title: FXR KO_GW4064_2


title: ss8_P1C6, scRNAseq


title: FXR KO_Veh_3

value: Vehicle


title: ss8_P1C8, scRNAseq


title: Tomato Interface Day 1b


title: Tomato Interface Day 0a


title: FXR KO_GW4064_1


title: ss8_P1C7, scRNAseq


title: FXR KO_Veh_1


title: Tomato hypocotyl only

source_name: Solanum lycopersicum hypocotyl only

value: host only

value: Solanum lycopersicum hypocotyls


title: ss8_P1C3, scRNAseq


title: ss8_P1C2, scRNAseq


title: Tomato Interface Day 0c


title: ss8_P1C5, scRNAseq


title: WT_GW4064_1


title: FXR KO_Veh_2


title: ss8_P1C1, scRNAseq


title: Tomato Interface Day 1a


title: ss8_P1C4, scRNAseq


title: Arabidopsis thaliana / Cuscuta campestris interface Day 14b

data_processing:
Adapters were trimmed using CutAdapt v3.0 (Martin, 2010) using parameters -m 1 -j 4 -o
Using bowtie, reads that mapped to the Arabidopsis thaliana genome (TAIR10) were removed using parameters -p 8 -v 0 --un
Remaining reads were aligned to the Cuscuta campestris genome using ShortStack V3.8.5 using default parameters and a --locifile corresponding to known interface-induced MIRNA loci.
Genome_build: Cuscuta campestris genome assembly v0.32 as downloaded from https://www.plabipd.de/project_cuscuta2/start.ep in mid-2020. Described by Vogel et al. (2018) doi: 10.1038/s41467-018-04344-z
Supplementary_files_format_and_content: .tsv file. Raw counts of trans-species miRNAs. Columns are sRNA-seq libraries, rows are trans-species miRNAs

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana / Cuscuta campestris haustorial interface

growth_protocol: Arabidopsis thaliana was grown at 18-20°C and illuminated with fluorescent tubing supplemented with far-red LED lights for 16 hours.  Cuscuta campestris seed coats were dissolved with sulfuric acid for 1 hour, washed with distilled water 5-6 times, and placed in a growth chamber set to 30°C for 3 days to germinate.

treatment_protocol: Cuscuta campestris seedlings were placed at the base of Arabidopsis thaliana inflorescence stems and allowed to attach. Day 0 is defined when seedlings have successfully wraped around the inflorescence.

value: Arabidopsis thaliana stems and Cuscuta campestris haustoria


title: WT_GW4064_3


title: WT_GW4064_2


title: Arabidopsis thaliana / Cuscuta campestris interface Day 14a


title: WT_Veh_3


title: ss8_P1B9, scRNAseq


title: Arabidopsis thaliana / Cuscuta campestris interface Day 12c


title: ss8_P1B8, scRNAseq


title: Arabidopsis thaliana / Cuscuta campestris interface Day 13b


title: Arabidopsis thaliana / Cuscuta campestris interface Day 13c


title: WT_Veh_2


title: ss8_P1C12, scRNAseq


title: ss8_P1C11, scRNAseq


title: Arabidopsis thaliana / Cuscuta campestris interface Day 12a


title: WT_Veh_1


title: Arabidopsis thaliana / Cuscuta campestris interface Day 13a


title: ss8_P1C10, scRNAseq


title: Arabidopsis thaliana / Cuscuta campestris interface Day 12d


title: ss8_P1B5, scRNAseq


title: MOC2K17KOEX1Bulk, 28

city: Madison

first: Huy

last: Dinh

state: WI

address: 1111 Highland Avenue

institute: University of Wisconsin-Madison

data_processing:
Read quality was QC using FastQC 0.11.7
Read mapping was done by Rsubread 1.30.5
Read count was calculated using FeatureCount 1.22.2 and edgeR 1.30.5
Genes with at least 2 samples with CPM>1 were kept for downstream analysis.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: read_count.txt: tab-delimited text file includes read count for each samples (Column names: Gene ID, 7 samples)

source_name: Tumor

extract_protocol:
Fresh tumors were snap frozen in liquid nitrogen, placed into tissueTUBE (Covaris) and pulverized Cryoprep Pulverizer (Covaris).
Total RNA was isolated by addition of 1ml or TRizol (Thermo Fisher Scientific) using RNA-binding columns (Qiagen RNA isolation kit). On column-bound RNA was treated with RQ1 RNase-free DNase (Promega) for 30 min at room temperature, washed with washing buffers, and eluted in RNase-free water. Pooled libraries were sequenced on Illumina NovaSeq 6000. RNA-Seq analysis was done using R and Bioconductor analysis framework.

tag: cell line

value: K17-expressing murine HNC cell line MOC2

value: K17KO (using CRISPR)

value: injected K17KO MOC2 cells into C57BL/6 mice

value: K17KO MOC2 tumors

tag: disease state

value: head and neck cancer mouse model


title: Arabidopsis thaliana / Cuscuta campestris interface Day 11b


title: Arabidopsis thaliana / Cuscuta campestris interface Day 12b


title: MOC2, 27

value: control

value: injected parental MOC2 cells into C57BL/6 mice

value: parental MOC2 tumors


title: ss8_P1B6, scRNAseq

value: Pax2+ cells


title: ss8_P1B7, scRNAseq


title: MOC2, 26


title: MOC2K17KO_rep2

data_processing:
Raw reads were aligned to the mm10 reference genome, UMI (unique molecular identifier) counting was performed using Cell Ranger v.2.1.1 (10X Genomics)
Genome_build: mm10
Supplementary_files_format_and_content: HDF5 Feature Barcode Matrix Format

extract_protocol:
Tumors were collected and sorted for 150,000 live CD45+ cells per sample. Duplicate tumors were collected for each genotype. Around 6000 cells per sample were captured for library preparation, and sequenced on Illumina NovaSeq at the UW-Madison Biotechnology Center
10x Chromium Single Cell 3ʹ Reagent Kits User Guide (v2 or v3)
RNA-Seq(size fractionation)

value: tumors sorted for CD45+ cells


title: ss8_P1B2, scRNAseq


title: ss8_P1B4, scRNAseq


title: Arabidopsis thaliana / Cuscuta campestris interface Day 11c


title: MOC2K17KOEX1Bulk, 29


title: MOC2K17KOEX5Bulk, 25


title: MOC2_rep2


title: Arabidopsis thaliana / Cuscuta campestris interface Day 11a


title: MOC2, 23


title: Arabidopsis thaliana / Cuscuta campestris interface Day 10c


title: MOC2_rep1


title: ss8_P1B3, scRNAseq


title: MOC2K17KO_rep1


title: ss8_P1B12, scRNAseq


title: Arabidopsis thaliana / Cuscuta campestris interface Day 10b


title: Arabidopsis thaliana / Cuscuta campestris interface Day 9c


title: ss8_P1B1, scRNAseq


title: ss8_P1B10, scRNAseq


title: MOC2, 24


title: ss8_P1B11, scRNAseq


title: Arabidopsis thaliana / Cuscuta campestris interface Day 9b


title: Arabidopsis thaliana / Cuscuta campestris interface Day 10d


title: ss8_P1A9, scRNAseq


title: Arabidopsis thaliana / Cuscuta campestris interface Day 9a


title: patient 4 untreated

city: Torino

first: Ivan

last: Molineris

state: TO

address: Via Nizza 52

department: Life Science and System Biology

country: Italy

institute: University of Turin

data_processing:
Sequencing reads were aligned to human reference genome (version GRCh38.p13) using STAR v2.7.7a0 [PMID:23104886] (with parameters --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04) and providing a list of known splice sites extracted from GENCODE comprehensive annotation (version 32)
Read that align on ribosomal gene or ribosomal repeated sequences in the genome are removed
Gene expression levels were quantified with featureCounts v1.6.3 [PMID:24227677] (options: -t exon -g gene_name) using GENCODE gene annotation (version 32 basic). Multi-mapped reads were excluded from quantification.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: raw gene count

source_name: sorted CD34+ cells

growth_protocol: Mononuclear cells (MNCs) were isolated from both BM and PB using Ficoll-Hypaque (Sigma Aldrich, Milan, Italy). Then, CML CD34+ cells were positively isolated by immunomagnetic separation (MACS, Miltenyi Biotec, Italy) and cultured in serum-free stemMACS media (Miltenyi Biotec, Italy) with recombinant human Flt3L (100ng/mL), SCF (100ng/mL), IL3 (20ng/mL), and TPO (20ng/mL). All of the ex vivo experiments were performed on CML CD34+ population as CML stem/progenitor cells.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen), according to the manufacturer’s protocol. Quantity and quality of the starting RNA were checked by Qubit and Bioanalyzer (Agilent
Libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina) following the manufacturer’s instructions

treatment_protocol: CML CD34+ cell lines were seeded 10,000 cells/well and incubated at 37°C with Meds433 for 72 hours at indicated concentrations or DMSO, as the vehicle


title: patient 5 untreated


title: mm_rna_DM.2

description:
Cultured Small pre B cells from IgK deleted
rna_counts.txt
mm9_plus_ig.gtf

source_name: KDEL -IL7.2

tag: sample group

value: KDEL -IL7


title: mm_rna_DT.2

source_name: KDEL -IL7+CXCL12.2

value: KDEL -IL7+CXCL12


title: mm_rna_DM.1

source_name: KDEL -IL7.1


title: patient 3 untreated


title: mm_rna_DT.1

source_name: KDEL -IL7+CXCL12.1


title: ss8_P1A8, scRNAseq


title: Arabidopsis thaliana / Cuscuta campestris interface Day 10a

value: Cuscuta campestris

tag: day


title: ss8_P1A7, scRNAseq


title: mm_rna_DP.2

source_name: KDEL +IL7.2

value: KDEL +IL7


title: Arabidopsis thaliana / Cuscuta campestris interface Day 8b

tag: agent


title: patient 1 untreated


title: patient 2 untreated


title: ss8_P1A6, scRNAseq


title: ss8_P1A5, scRNAseq


title: patient 5 treated

value: three days of treatment with Meds433 100nM


title: mm_rna_MM.3

description:
Cultured Small pre B cells from Kappa-macroself mice
rna_counts.txt
mm9_plus_ig.gtf

source_name: KMAC -IL7.3

value: KMAC -IL7


title: Arabidopsis thaliana / Cuscuta campestris interface Day 7c

value: Arabidopsis thaliana stems and Cuscuta campestris haustoria


title: mm_rna_DP.1

source_name: KDEL +IL7.1


title: Arabidopsis thaliana / Cuscuta campestris interface Day 8a


title: patient 4 treated


title: ss8_P1A4, scRNAseq


title: Arabidopsis thaliana / Cuscuta campestris interface Day 7a


title: ss8_P1A3, scRNAseq


title: ss8_P1A2, scRNAseq


title: Arabidopsis thaliana / Cuscuta campestris interface Day 7b


title: mm_rna_MM.2

source_name: KMAC -IL7.2


title: mm_rna_MM.1

source_name: KMAC -IL7.1


title: patient 2 treated


title: mm_rna_MT.3

source_name: KMAC -IL7+CXCL12.3

value: KMAC -IL7+CXCL12


title: ss8_P1A1, scRNAseq

source_name: Pax2+ cells


title: Arabidopsis thaliana / Cuscuta campestris interface Day 8c


title: Arabidopsis thaliana / Cuscuta campestris interface Day 6d


title: ss8_P1A12, scRNAseq


title: patient 3 treated


title: mm_rna_immatureb.2

description:
Ex Vivo Sorted WT immature B cells
rna_counts.txt
mm9_plus_ig.gtf

value: ImmatureB


title: ss8_P1A11, scRNAseq


title: Arabidopsis thaliana / Cuscuta campestris interface Day 6b


title: mm_atac_spreb_2

description: Ex Vivo Sorted WT immature B cells

value: small Pre-B


title: mm_rna_MT.1

source_name: KMAC -IL7+CXCL12.1


title: Arabidopsis thaliana / Cuscuta campestris interface Day 5c


title: ss8_P1A10, scRNAseq


title: mm_atac_spreb_1

description: Ex Vivo Sorted WT immature B cells


title: mm_rna_MP.2

source_name: KMAC +IL7.2

value: KMAC +IL7


title: Arabidopsis thaliana / Cuscuta campestris interface Day 5b


title: mm_rna_immatureb.1


title: patient 1 treated


title: Arabidopsis thaliana / Cuscuta campestris interface Day 6a


title: Control_rep3, RNAseq

data_processing:
Data was processed and aligned using the NF-core RNAseq v2.0 pipeline (doi: 10.5281/zenodo.1400710).
Reads were trimmed using Trim Galore! Reads were aligned using Star. Read counts were obtained using featureCounts.
Genome_build: galgal6

source_name: Head ectoderm cells

growth_protocol: Chick embryos were electroporated ex ovo and grown at 38°C for 16-24hrs.

extract_protocol:
mCherry+EGFP double positive cells were collected into 20ul of lysis buffer by FACS
Libraries were prepared following Nextera Sample low input kit (Illumina, 15028212) indications.

treatment_protocol: Chick embryos were electroporated at head fold stages with a combination of either pCES-Sox8-mCherry + pTK-Lmx1aE1-EGFP or pCES-mCherry + pCES-EGFP plasmids. Heads were collected, the endogenous otic placode was removed and tissues were lysed in lysis buffer.

value: Head ectoderm cells

value: mCherry and EGFP tagged cells


title: mm_rna_MP.3

source_name: KMAC +IL7.3


title: Control_rep1, RNAseq


title: CHIP-seq with M2 mouse anti-Flag antibody

city: Wynnewood

first: Xuanmao

last: Jiao

address: 100 E Lancaster Ave, LIMR R234

department: Pennsylvania Cancer and Regenerative Medicine Research Center

institute: Baruch S. Blumberg Institute

data_processing:
Peak locations were determined using the MACS algorithm. These files were analyzed using Genpathway proprietary software that provides comprehensive information on genomic annotation, peak metrics and sample comparisons for all peaks (intervals). The MACs algorithm comparing cyclin D1/FLAG with IgG (cut off p=10e-5); 3231 peaks were identified, 9 of which had a corresponding peak in the IgG sample (using a threshold of fragment density >8).
To view genomic peaks the BED files were uploaded to the Integrated Genome Browser (Affymetrix) to generate and visualize genomics regions bound by cyclin D1.

source_name: Embyonic

growth_protocol: Cyclin D1 knock-out Mouse embryonic fibroblasts (Ccnd1-/- MEFs) stable transfected with flag-cyclin D1 were maintained in Dulbecco's modified Eagle's media (DMEM). supplemented with 10% FBS, 2 mmol/L glutamine, 100 units/mL penicillin, and 100 μg/mL streptomycin in humidified atmosphere containing 5% CO2 at 37°C.

extract_protocol:
Cyclin D1-/- 3T3s transduced with MSCV-FLAG/Cyclin D1 cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding 5-10 ml lysis buffer containing PIPES, Igepal, PMSF and Protease Inhibitor Cocktail, followed by disruption with a Dounce homogenizer. Samples were pelleted by centrifugation and resuspended in buffer containing Na deoxycholate, SDS, and Triton X-100. Lysates were sonicated using a Misonix Sonicator 3000 equipped with a microtip in order to shear the DNA to an average length of 300-500 bp. Lysates were cleared by centrifugation and the chromatin suspensions were transferred to new tubes and stored at -80 C. Prior to use in ChIP, protein G agarose beads (Invitrogen) were preblocked using blocking proteins and nucleic acids for 3 hr. For each ChIP reaction, an aliquot of chromatin (20-30 ug) was precleared with 30 ul preblocked protein G agarose beads for 1-2 hr. ChIP reactions were set up using precleared chromatin and antibody (mouse IgG, anti-FLAG M2) in a buffer containing Na deoxycholate and incubated overnight at 4 C. Preblocked protein G agarose beads were added and incubation at 4 C was continued for another 3 hr. Agarose beads containing the immune complexes were washed two times each with a series of buffers consisting of the deoxycholate sonication buffer, high salt buffer, LiCl buffer, and TE buffer. An SDS-containing buffer was added to elute the immune complexes from the beads, and the eluents were subjected to RNase treatment at 37 C for 20 min and proteinase K treatment at 37 C for 3 hr. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNAs were purified by phenol-chloroform extraction and ethanol precipitation. ChIP DNA was amplified using the Illumina ChIPSeq DNA Sample Prep Kit. In brief, DNA ends were polished and 5’-phosphorylated using T4 DNA polymerase, Klenow polymerase and T4 polynucleotide kinase. After addition of 3’-A to the ends using Klenow fragment (3’-5’ exo minus), Illumina genomic adapters were ligated and the sample was size-fractionated (~250 bp) on a 2% agarose gel. After a final PCR amplification step (18 cycles, Phusion polymerase), the resulting DNA libraries were quantified and tested by QPCR at the same specific genomic regions as the original ChIP DNA to assess quality of the amplification reactions.
DNA libraries were sequenced on a Genome Analyzer II. Sequences (36 nt reads) were aligned to the mouse genome (NCBI Build 37.1/mm9) using Eland (Illumina pipeline) software. Aligned sequence fragments were extended in silico at their 3’-ends to a length of 160 bp, which is the average genomic fragment length in the size selected library, and assigned to 32-nt bins along the genome. The resulting histograms were stored in BAR (Binary Analysis Results) files.

treatment_protocol: No treatment

value: Embyonic

value: Fibroblast

value: CCND1-/-  Flag-CCND1

tag: chip antibody

value: Monoclonal ANTI-FLAG M2,  Sigma-Aldrich


title: Arabidopsis thaliana / Cuscuta campestris interface Day 6c

source_name: Arabidopsis thaliana / Cuscuta campestris haustorial interface


title: Sox8OE_rep3, RNAseq

value: Sox8OE and Lmx1aE1 tagged cells


title: Arabidopsis thaliana / Cuscuta campestris interface Day 4c


title: Arabidopsis thaliana / Cuscuta campestris interface Day 4b


title: mm_rna_MT.2

data_processing:
RNA-seq: Raw reads were aligned to reference genome mm9 in a splice aware manner using STAR (Dobin et al., 2013; Dobin and Gingeras, 2015). Gene expression was quantified using featureCounts within the RSubread R package (Liao et al., 2019) against UCSC genes with Ensembl Ig genes from mm10 converted to mm9 coordinates with UCSC liftOver. GTF file is included in the submission.
ATAC-seq: Raw reads were aligned to the reference genome using BWA MEM, and apparent PCR duplicates removed using Picard MarkDuplicates. Read alignments were first adjusted to account for TAC transposon binding: +4 bp for +strand alignments, −5 bp for −strand alignments. The open chromatin enrichment track was generated by first creating a bedGraph from the raw reads using bedtools genomcov, then converted to bigWig using UCSC tool bedGraphToBigWig; tracks were normalized by the sum of alignment lengths over 1 billion. Open chromatin peaks were called using Macs2 (Zhang et al., 2008) with no model set and no background provided; peaks with a score of >5 were retained.
Genome_build: mm9
Supplementary_files_format_and_content: GTF formatted file: gene annotations used for RNA-seq. UCSC genes for mm9 + Ig genes from Ensembl mm10, lifted over to mm9
Supplementary_files_format_and_content: BED formatted file: peak calls for ATAC-seq
Supplementary_files_format_and_content: BigWig formatted file: normalized enrichment of open chromatin for ATAC-seq
Supplementary_files_format_and_content: Tab-delimited text formatted file: unnormalized counts per gene

source_name: KMAC -IL7+CXCL12.2


title: CHIP-seq with normal mouse IgG as control

tag: genotype

value: Normal mouse IgG1, Santa Cruz Biotech


title: Arabidopsis thaliana / Cuscuta campestris interface Day 5a

value: Cuscuta campestris


title: mm_rna_WM.1

description:
Cultured Small pre B cells from WT mice
rna_counts.txt
mm9_plus_ig.gtf

source_name: WT -IL7.1

value: WT -IL7


title: mm_rna_WM.2

source_name: WT -IL7.2


title: Arabidopsis thaliana / Cuscuta campestris interface Day 4a


title: mm_rna_MP.1

source_name: KMAC +IL7.1


title: Sox8OE_rep1, RNAseq


title: Arabidopsis thaliana / Cuscuta campestris interface Day 3c


title: Sox8OE_rep2, RNAseq


title: Control_rep2, RNAseq


title: Sox3U3_rep3, RNAseq

data_processing:
Data was processed and aligned using the NF-core RNAseq v2.0 pipeline (doi: 10.5281/zenodo.1400710).
Reads were trimmed using Trim Galore! Reads were aligned using Star. Read counts were obtained using featureCounts.
Genome_build: galgal6
Supplementary_files_format_and_content: featurecounts.merged.counts.tsv (raw counts)

source_name: Sox3U3 tagged epibranchial cells

growth_protocol: Chick embryos were electroporated in ovo and grown at 38°C until reaching the desired stage (ss18-21).

extract_protocol:
Lmx1aE1-EGFP and Sox3U3-EGFP positive cells were collected into 20ul of lysis buffer.
Libraries were prepared following Nextera Sample low input kit (Illumina, 15028212).

treatment_protocol: Chick embryos were electroporated in ovo at ss3-5 with either Lmx1aE1-EGFP or SoxU3-EGFP plasmids. Cells were dissociated and collected by FACS.

value: Epibranchial placode cells

tag: Stage

value: Sox3U3 tagged


title: mm_rna_WT.2

source_name: WT -IL7+CXCL12.2

value: WT -IL7+CXCL12


title: Arabidopsis thaliana / Cuscuta campestris interface Day 3a

value: Arabidopsis thaliana stems and Cuscuta campestris haustoria


title: Sox3U3_rep2, RNAseq


title: mm_rna_WM.3

source_name: WT -IL7.3


title: Sox3U3_rep4, RNAseq


title: Arabidopsis thaliana / Cuscuta campestris interface Day 3b


title: mm_rna_WP.2

source_name: WT +IL7.2

value: WT +IL7


title: mm_rna_WP.1

source_name: WT +IL7.1


title: mm_rna_WT.3


title: MY_XR4

type: RNA

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

hyb_protocol: A total of 600 ng Cy3-labeled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 microL containing 0.5x Agilent fragmentation buffer and 2x Agilent gene expression blocking agent following the manufacturers instructions.  On completion of the fragmentation reaction, 25 microL of 2× Hi-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint GE3 Mouse 8x60k v2 gene expression microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were rinsed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), and dried by slowly removing from Wash buffer 2.

scan_protocol: Following posthybridization rinses, arrays were scanned using an Agilent SureScan microarray Scanner at 3 micron, and hybridization intensity data extracted from the scanned images using Agilent’s Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

data_processing: Raw microarray data were log transformed to yield z-scores. The z-ratio was calculated as the difference between the observed gene z-scores for the experimental and the control comparisons, and dividing by the standard deviation associated with the distribution of these differences. Z-ratio values of ± 1.5 were used as cut-off values and calculated using a 5% false discovery rate (FDR) threshold. The complete set was tested for gene set enrichment using parametric analysis of gene set enrichment. For each pathway z-score, a p-value was computed using JMP 6.0 software to test for the statistical significance.

source_name: Gastronemius_5 mo_XR4

label_protocol: Cy3-labeled cRNA was prepared from 200 ng of total RNA using the Agilent Low-Input Quick Amp Labeling Kit and was purified and quantitated according to the manufacturer’s instructions.

growth_protocol: Male C57BL/6J mice at either 5 months (young group) or 24 months (old group) of age were obtained from the National Institute on Aging (NIA) Aged Rodent Colony (Charles Rivers Laboratories, Germantown, MD, USA). Mice were kept on a standard mouse diet (house chow 2018SX, Envigo, Frederick, MD, USA) with ad libitum access to food and water. Mice were single-housed in conventional micro-isolator cages (Lab Products, Seaford, DE, USA) on a light:dark 12:12-h schedule and maintained between 20–22 °C at 30-70% humidity. Mice were randomized to one of three experimental groups, namely sedentary control, HIIT, and MICT (n=9 for each age group). Animal procedures, housing, and diets were in accordance with the guidelines issued by the Intramural Research Program of the National Institutes of Health (Animal Study Protocol 415-TGB-2018).

extract_protocol: After collection of physiological measurements, mice were let to rest for 12 h and were then euthanized by cervical dislocation, and gastrocnemius muscle was excised, and snap-frozen in liquid nitrogen for storage. Total Gastrocnemius RNA was isolated using a RNeasy Mini kit (Qiagen, Germantown, MD, USA).Total RNA quantity and quality were evaluated using the Bioanalyzer RNA 6000 Chip (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Mice were trained daily (between 5:00-6:00 PM) for 4 consecutive weeks using an exercise treadmill (Columbus Instruments, Columbus, OH, USA). Two training protocols were tested: 1) HIIT, essentially an anaerobic exercise fueled mostly by stored carbohydrates in the form of glycogen, consisted of three short runs (2 min each) at 27 m/min with a one-min recovery (5 m/min) between bouts, and 2) MICT, an aerobic exercise dependent on oxygen consumption and fueled mostly by stored fat, consisted of a single 45-min run at 13 m/min. Sedentary control mice were brought to the room daily where the exercise training was performed and were exposed to the treadmill turned off to ensure the same stress adaptation for all mice.

value: muscle

tag: muscle name

value: Gastrocnemius

value: MICT - moderate-intensity continuous training

value: M

value: 6 months

tag: strain


title: MY_CON3

source_name: Gastronemius_5 mo_Control

tag: treatment

value: Control


title: MY_XR3

source_name: Gastronemius_5 mo_XR3


title: mm_rna_WP.3

source_name: WT +IL7.3

extract_protocol:
RNA-seq: FACS sorted cells from small pre-B and immature B cells isolated from WT, Igkdel k-mac, k-mac CXCR4fl/fl and k-mac CXCR4fl/fl mb1-cre+ mice and total RNA isolated using Trizol (15596026, Invitrogen) following the protocol described by the Immunological Genome Project (Immgen.org).
RNA-seq: Libraries were generated TruSeq® Stranded mRNA Sample Prep” kit from Illumina and the associated user manual
ATAC-seq: 1.2x105 small pre-B and immature B cells sorted from WT, Igkdel k-mac, k-mac CXCR4fl/fl and k-mac CXCR4fl/fl mb1-cre+ mice were used for ATAC-seq. Cells were centrifuged at 500g at 4°C for 5 minutes, washed with 1X PBS, and centrifuged again. Cells were resuspended in lysis buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630) and immediately centrifuged at 500g at 4°C for 10 minutes. Pellet was resuspended in transposition reaction buffer (25ml 2x Tagment Buffer (FC-121-1030, Illumina), 2.5ml Tagment DNA Enzyme, 22.5ml nuclease free H2O) for 30 minutes at 37°C.
ATAC-seq: DNA was purified with a Qiagen MinElute Kit and amplified with Nextera PCR Primers (Illumina Nextera Index Kit) and NEBNext PCR Master Mix (M0541, New England BioLabs) for 11 cycles. Amplified DNA was purified with a Qiagen PCR cleanup kit. Libraries were sequenced on a NextSeq 550 sequencer at University of Chicago Genomics Facility.


title: Arabidopsis thaliana / Cuscuta campestris interface Day 2d

extract_protocol:
RNA was extracted using TRI-reagent (sigma: 93289-100ML) using the manufacturer's protocol.  An additional step of sodium acetate cleanup / ethanol precipitation was also used.
Libraries were constructed using randomized splint ligation as specified in Maguire et al.,2020 https://doi.org/10.1093/nar/gkaa480


title: mm_rna_WT.1

source_name: WT -IL7+CXCL12.1


title: Sox3U3_rep1, RNAseq


title: MY_AC4

source_name: Gastronemius_5 mo_AC4

value: HIIT - high-intensity intermittent training


title: MY_XR1

source_name: Gastronemius_5 mo_XR1


title: Arabidopsis thaliana / Cuscuta campestris interface Day 2c

source_name: Arabidopsis thaliana / Cuscuta campestris haustorial interface


title: MY_CON4


title: MY_AC3

source_name: Gastronemius_5 mo_AC3


title: Arabidopsis thaliana / Cuscuta campestris interface Day 1b


title: Papillary renal cancer cells -UOK345-SNX2112_rep1

city: BETHESDA

first: Ramaprasad

last: Srinivasan

state: MD

address: 1-W-5888, 10 center drive

department: Urologic Oncology Branch

institute: National Cancer Institute – NIH

description:
U345_SNX_1
Metastatic renal cancer cells derived from patient pleural effusion.

data_processing:
Basecalling was performed using RTA version 1.18.64.
Demultiplexing and FASTQ generation was performed using bcl2fastq (version 2.17) allowing 1 mismatch.
Trimming of adapters and low-quality bases was performed using CutAdapt (v.1.16).
Mapping to the human genome (hg38) was performed using STAR 2.5.2b.
The following parameters were used: "--outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField None --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 clip3pAdapterSeq - --readFilesCommand zcat --runThreadN 32 --outSAMtype BAM Unsorted --chimSegmentMin 20"
Gene-level expression quantification was performed using subread (version 1.4.6).
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: NormalizedGeneExression.txt: Tab-delimited text file of normalized gene expression of differentially expressed genes.

source_name: Papillary renal cancer cells

growth_protocol: PRCC cell line UOK342 was derived from ascites and UOK345 was derived from pleural effusion of metastatic sporadic type 1 PRCC patient. The cells were cultured in high glucose DMEM containing pyruvate, glutamine and supplemented with 10% FBS.

extract_protocol:
High-quality RNA was harvested from treated and control cell lines using Qiagen kit. The quality of total RNA was evaluated using the Agilent RNA Screen 2200 Tape Station system (G2964AA). Only samples with a 28S/18S ribosomal peak ratio of 1.8–2.0 and a RIN number >8.0 were considered suitable for sequencing.
RNA-seq libraries were prepared using Illumina® TruSeq mRNA Prep Kit RS-122-2101 and were sequenced using Illumina® HiSeq3000/4000 to obtain 76-bp paired-end reads. The sequencing depth for each sample was >20 million reads.

treatment_protocol: UOK345 and UOK342 cells were treated with SNX2112 (50nM) or vehicle for 48h.

value: Treated with SNX2112

value: germline MET mutation (p.H1112R)


title: Papillary renal cancer cells -UOK345_Control_rep2

description:
U345_Control_2
Metastatic renal cancer cells derived from patient pleural effusion.

value: Untreated


title: MY_CON2


title: Arabidopsis thaliana / Cuscuta campestris interface Day 1a

value: Cuscuta campestris


title: Papillary renal cancer cells -UOK342_Control_rep3

description:
U342_Control_3
Metastatic renal cancer cells derived from patient ascites.

value: wild type MET gene with gain of chromosome 7


title: Lmx1aE1_rep3, RNAseq

source_name: Lmx1aE1 tagged otic cells

value: Otic placode cells

value: Lmx1aE1 tagged


title: MY_CON1


title: Papillary renal cancer cells -UOK345_Control_rep1

description:
U345_Control_1
Metastatic renal cancer cells derived from patient pleural effusion.


title: Arabidopsis thaliana / Cuscuta campestris interface Day 1c


title: Lmx1aE1_rep2, RNAseq


title: Arabidopsis thaliana / Cuscuta campestris interface Day 2a


title: Papillary renal cancer cells -UOK345-SNX2112_rep2

description:
U345_SNX_2
Metastatic renal cancer cells derived from patient pleural effusion.


title: Arabidopsis thaliana / Cuscuta campestris interface Day 0d


title: Papillary renal cancer cells -UOK342_Control_rep2

description:
U342_Control_2
Metastatic renal cancer cells derived from patient ascites.


title: Arabidopsis thaliana / Cuscuta campestris interface Day 0c


title: Arabidopsis thaliana / Cuscuta campestris interface Day 2b


title: Lmx1aE1_rep4, RNAseq


title: Papillary renal cancer cells -UOK342_Control_rep1

description:
U342_Control_1
Metastatic renal cancer cells derived from patient ascites.


title: NPt1

city: Shenyang

first: Jianhua

state: Liaoning

address: No.120 Dongling Road, Shenhe District

institute: Shenyang Agricultural University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Hisat2 tools soft were used to map with reference genome.
Gene function was annotated based on the following databases:Nr (NCBI non-redundant protein sequences)；Nt (NCBI non-redundant nucleotide sequences)；Pfam (Protein family)；KOG/COG (Clusters of Orthologous Groups of proteins)；Swiss-Prot (A manually annotated and reviewed protein sequence database)；KO (KEGG Ortholog database)；GO (Gene Ontology).
Picard - tools v1.41 and samtools v0.1.18 were used to sort, remove duplicated reads and merge the bam alignment results of each sample. GATK2 or Samtools software was used to perform SNP calling. Raw vcffiles were filtered with GATK standard filter method and other parameters ( clusterWindowSize: 10; MQ0 >= 4 and (MQ0/(1.0*DP)) > 0.1; QUAL < 10; QUAL < 30.0 or QD < 5.0 or HRun > 5), and only SNPs with distance > 5 were retained.
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.
Differential expression analysis of two samples was performed using the edgeR.The FDR < 0.01 & Fold Change ≥2 was set as the threshold for significantly differential expression.
Genome_build: Analysis Name: Prunus sibirica F106 Whole Genome v1.0 Assembly & Annotation.  Source: (F106) PacBio,BioNano and Hi-C.
Supplementary_files_format_and_content: All_gene_fpkm.list include FPKM values for each sample.

organism: Prunus sibirica

source_name: Flower buds

extract_protocol:
Flower buds were grinned under liquid nitrogen to fine powder using cooled mortar and pestle. Samples were placed in Eppendorf tubes. Total RNA was extracted from flower buds by EASYspin Plant microRNA Kit.
The six RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: tag

value: Prunus sibirica clone

value: Flower buds

tag: treatment group

value: normal pistil


title: MY_AC2

source_name: Gastronemius_5 mo_AC2

value: muscle

tag: Sex

tag: age


title: APt3

value: abortive pistil


title: NPt3


title: Papillary renal cancer cells -UOK342-SNX2112_rep3

description:
U342_SNX_3
Metastatic renal cancer cells derived from patient ascites.


title: NPt2


title: APt2


title: MO_XR4

source_name: Gastronemius_24 mo_XR4

value: Gastrocnemius

value: MICT - moderate-intensity continuous training

value: 25  months


title: Papillary renal cancer cells -UOK342-SNX2112_rep2

description:
U342_SNX_2
Metastatic renal cancer cells derived from patient ascites.


title: Arabidopsis thaliana / Cuscuta campestris interface Day 0a

value: Arabidopsis thaliana stems and Cuscuta campestris haustoria


title: MY_AC1

source_name: Gastronemius_5 mo_AC1

value: HIIT - high-intensity intermittent training

value: M

value: 6 months


title: MO_XR3

source_name: Gastronemius_24 mo_XR3


title: MO_XR2

source_name: Gastronemius_24 mo_XR2


title: APt1


title: MO_XR1

source_name: Gastronemius_24 mo_XR1


title: Arabidopsis thaliana stem only

source_name: Arabidopsis thaliana inflorescence stem only

value: Host only

value: Arabidopsis thaliana stems


title: Papillary renal cancer cells -UOK342-SNX2112_rep1

description:
U342_SNX_1
Metastatic renal cancer cells derived from patient ascites.

value: Treated with SNX2112

value: wild type MET gene with gain of chromosome 7


title: Arabidopsis thaliana / Cuscuta campestris interface Day 0b

value: Cuscuta campestris


title: FFUL674.3vsCBS138.2

city: Aveiro

first: Ana

last: Soares

address: Campus de Santiago

country: Portugal

institute: University of Aveiro

hyb_protocol: Six hundred nanograms of labelled cDNA were hybridized in the microarray. Hybridizations were carried out using Agilent gasket slides in a rotating oven for 17 h at 65°C.

scan_protocol: Slides were then washed following manufacturer’s instructions and scanned in an Agilent G2565AA microarrays scanner. Probes signal values were extracted using Agilent Feature Extraction Software.

data_processing: Data were normalized using median centering of signal distribution with Biometric Research Branch BRB-Array tools v3.4.o software 36. Final statistical analysis was carried out using LIMMA package in MeV software (MultiExperiment Viewer 4.8.0) 36 with a cut-off p-value of 0.1.

organism: Nakaseomyces glabratus

label_protocol: cDNA synthesis, hybridization, and scanning were performed using the Agilent protocol for two-color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling v6.9 (Agilent Technologies), according to the manufacturer’s instructions. One hundred nanograms of total RNA of each isolate were used to synthesize labeled cDNA (with Cyanine 3-CTP and cyanine 5-CTP), using Agilent T7 Promoter Primer and T7 RNA polymerase Blend (Agilent Technologies, Cat.5190–2305).

growth_protocol: For the transcriptomic profiling an individual colony of the FFUL443, FFUL674 and ISTB218 isolates was inoculated in YPD at 30 ºC with orbital agitation (250 rpm) overnight and then re-inoculated (at an initial OD600nm of 0.1) in 150 mL of RPMI with FLC (32mg/L) and left to grow at 30 ºC and 250 rpm orbital shake.

extract_protocol: RNA extraction was performed using the hot-phenol method. RNA extraction was performed using RiboPureTM RNA Isolation Kit (Ambion, Life Technologies, CA). The quality and integrity of the purified RNA was confirmed in a Bioanalyzer, and only samples with an RNA integrity number (RIN) > 7 were used.

treatment_protocol: When the OD600nm of the cultures achieved 2 (corresponding to mid-exponential phase) cells were harvested by centrifugation and immediately frozen at -80ºC until further use.

tag: carbon source

value: glucose 20g/L


title: FFUL674.2vsCBS138.2


title: FFUL443.3vsCBS138.2


title: MO_CON1

source_name: Gastronemius_24 mo_Control

tag: tissue

value: Control


title: MO_CON3


title: Er60_OX_TR2

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

hyb_protocol: Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

scan_protocol: Scanned using Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Data extraction from Images was done using Feature Extraction software  and Normalization of the data was done in GeneSpring GX  : 75th percentile shift  method.

source_name: whole plant (shoot and root tissue)

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). The total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Arabidopsis plants were grown in the MS media under controlled conditions in growth chamber

extract_protocol: RNA Extraction was performed using QIAamp Circulating Nucleic Acid Kit as per the manufacturer's recommendations.

value: seedlings

value: 2 weeks after germination


title: MO_CON2

value: muscle


title: Er60_OX_TR1


title: Occm30, 2cycles, PTH, rep3

city: Chengdu

first: Tiancheng

last: Li

address: No. 14, 3rd section of Renmin South Road

institute: West China Hospital of Stomatology, Sichuan University

description: Gene expression after 2 cylces of 100 ng/ml PTH.

hyb_protocol: The labeled cRNAs were hybridized onto the Mouse LncRNA Array v 3.0 (8 x 60K, Arraystar).

scan_protocol: After washing the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies, Palo Alto, CA, USA). Differentially expressed lncRNAs and mRNAs with statistical significance were identified through volcano plot filtering. The threshold used to screen up- or down-regulated lncRNAs in this study was fold change > 1.5 and P value < 0.05. Hierarchical clustering was performed using the Agilent Gene Spring GX software (version 11.5.1).

source_name: OCCM-30 cells, 2 cycles, PTH

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: OCCM-30 cells were maintained in Dulbecco’s modified Eagle medium (DMEM) with 5% fetal bovine serum (FBS), 100 U/ml penicillin G, and 100 μg/ml streptomycin (Gibco, Grand Island, NY, USA).

extract_protocol: Total RNA from OCCM-30 cells was extracted using TRIzol Reagent (Invitrogen, Carlsbad, CA, USA). The RNA purification was performed on the RNA-containing aqueous phase with RNeasy minikit (Qiagen, Duesseldorf, Germany). After elution with RNase-free water and treatment with turbo DNase (Ambion, Thermo Fisher Scientific, San Jose, CA), the RNA was ready for use. Quantification and quality check were performed with Nanodrop and Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), respectively.

treatment_protocol: Concerning the administration of intermittent PTH, OCCM-30 cells at 80% confluence were treated with 100 ng/ml PTH (dissolved in 0.1% acetic acid), while the control group was treated with 0.1% acetic acid. The treatment of PTH or acetic acid lasted for the first 6 hours in each cycle (one cycle represented 24 hours), then OCCM-30 cells were treated with fresh medium containing no PTH or acetic acid during the subsequent 18 hours in each cycle. After 2 cycles of PTH treatment, cells were harvested and tested.

tag: cell line

tag: cell type

value: cementoblast-like cell

value: PTH


title: FFUL443.2vsCBS138.2


title: MO_CON4

value: Gastrocnemius

value: 25  months


title: MO_AC4

source_name: Gastronemius_24 mo_AC

value: HIIT - high-intensity intermittent training


title: ISTB218.3vsCBS138.2


title: ISTB218.2vsCBS138.2


title: MO_AC3

value: M


title: MO_AC1


title: MO_AC2


title: Er60_mutant_TR2


title: WT_TR2


title: Occm30, 2cycles, PTH, rep2


title: Occm30, 2cycles, CON, rep2

description: Gene expression after 2 cylces of 0.1% acetic acid.

source_name: OCCM-30 cells, 2 cycles, CON

value: acetic acid


title: Er60_mutant_TR1


title: WT_TR1


title: Occm30, 2cycles, CON, rep1


title: H460 T3 rep1

status: Public on Jul 05 2022

city: Dublin

first: Rory

last: Johnson

address: Belfield

country: Ireland

institute: UCD Conway Institute for Biomolecular and Biomedical Research

description:
lncRNA targeted CRISPR/Cas9 pgRNA library
H460_counts_table.txt
H460_pro_T3vsT0.txt

data_processing:
library strategy: PCR amplicon sequencing
The raw sequencing reads were analysed by using CASPR.
After the mapping step, the obtained counts per million (cpm) for each pgRNA were filtered to remove sequences with 3>cpm>666.
Low scoring guides were removed by GuideScan, and a batch effect correction was applied using MageckFlute.
Assembly: hg19 (GENCODE release 19)
Supplementary files format and content: *_counts_table.txt: filtered read counts per million
Supplementary files format and content: CASPR output (incl. log2FoldChange)

extract_protocol:
Genomic DNA (gDNA) was isolated using the Blood & Cell Culture DNA Midi (5e6–3e07 cells) (Qiagen, cat. no. 13343), or Mini (<5e6 cells) Kits (Qiagen, cat. no. 13323) as per the manufacturer’s instructions.
For PCR amplification, gDNA was divided into 100 μl reactions such that each well had at most 4 μg of gDNA. Each well consisted of 66.5 μl gDNA plus water, 23.5 μl PCR master mix (20 μl Buffer 5X, 2 μl dNTPs 10 μM, 1.5 μl GoTaq; Promega, cat. no. M3001), and 5 μl of Forward universal primer, and 5 μl of a uniquely barcoded P7 primer (both stock at 10 μM concentration). PCR cycling conditions: an initial 2 min at 95 °C; followed by 30 s at 95 °C, 40 s at 60 °C, 1 min at 72 °C, for 22 cycles; and a final 5 min extension at 72 °C.

tag: tumor type

value: non-small cell lung cancer (NSCLC)

tag: disease subtype

value: large cell carcinoma

tag: expresses

tag: timepoint

value: T3 (21 days)


title: H460 T0 rep2

description:
lncRNA targeted CRISPR/Cas9 pgRNA library
H460_counts_table.txt
H460_cis_T3_10uMvsT0.txt
H460_cis_T3_2uMvsT0.txt
H460_pro_T3vsT0.txt


title: H460 T3 rep2


title: H460 T2 rep2

description:
lncRNA targeted CRISPR/Cas9 pgRNA library
H460_counts_table.txt

value: T2 (14 days)


title: H460 T2 rep1


title: H460 T0 rep1


title: Occm30, 2cycles, PTH, rep1


title: H460 CFSE high rep1

description:
lncRNA targeted CRISPR/Cas9 pgRNA library
H460_counts_table.txt
H460_pro_CFSE_HvsL.txt


title: H460 CFSE high rep2


title: A549 NM 1R rep2

description:
lncRNA targeted CRISPR/Cas9 pgRNA library
Migration_counts_table.txt
A549_mig_NMvsMIG.txt

value: adenocarcinoma

value: 48h after T0


title: A549 MIG 1R rep2


title: A549 T3 cis 25uM rep3

description:
lncRNA targeted CRISPR/Cas9 pgRNA library
A549_counts_table.txt
A549_cis_T3_25uMvsT0.txt

value: cisplatin

tag: dose


title: A549 CTR MIG 1R rep2

description:
lncRNA targeted CRISPR/Cas9 pgRNA library
Migration_counts_table.txt


title: Occm30, 2cycles, CON, rep3


title: A549 T2 cis 25uM rep2

description:
lncRNA targeted CRISPR/Cas9 pgRNA library
A549_counts_table.txt


title: A549 T3 rep2

description:
lncRNA targeted CRISPR/Cas9 pgRNA library
A549_counts_table.txt
A549_pro_T3vsT0.txt


title: H460 CFSE low rep2


title: H460 CFSE low rep1


title: A549 T2 cis 6.5uM rep2


title: A549 T0 rep3

description:
lncRNA targeted CRISPR/Cas9 pgRNA library
A549_counts_table.txt
A549_cis_DeathvsT0.txt
A549_cis_T3_25uMvsT0.txt
A549_cis_T3_6.5uMvsT0.txt
A549_pro_T3vsT0.txt


title: A549 CFSE high rep2

description:
lncRNA targeted CRISPR/Cas9 pgRNA library
A549_counts_table.txt
A549_pro_CFSE_HvsL.txt


title: A549 T2 rep2


title: A549 T0 rep2


title: A549 T3 cis 25uM rep2


title: A549 CFSE low rep2


title: A549 T2 rep3


title: H 240 ASO3 rep2

description:
RNAseq, antisense oligonucleotide targeting candidate240 ("CHiLL2") with ASO 3
ASO_TPM_table.csv
H_240_ASO3_vs_CTR_gene_DE_Table.tsv

data_processing:
Libraries were sequenced in paired-end 150 format to a depth of 30M reads/sample.
Transcript quantification was performed using Kallisto v0.46.0116 against GENCODE v36.
Differential expression analysis was performed using Sleuth v0.30.
Assembly: hg38 (GENCODE release 36)
Supplementary files format and content: gene level expression (TPM)
Supplementary files format and content: differential gene expression

extract_protocol:
RNA was extracted using the Quick-RNA MiniPrep kit (Ref R1055, ZymomResearch) according to manufacturer's protocol.
Libraries were prepared using the NEBNext® Ultra RNA Library Prep Kit.

value: 24h after ASO transfection

value: antisense oligonucleotide


title: H 42 ASO5 rep2

description:
RNAseq, antisense oligonucleotide targeting candidate42 ("CHiLL1") with ASO 5
ASO_TPM_table.csv
H_42_ASO5_vs_CTR_gene_DE_Table.tsv


title: H 42 ASO3 rep2

description:
RNAseq, antisense oligonucleotide targeting candidate42 ("CHiLL1") with ASO 3
ASO_TPM_table.csv
H_42_ASO3_vs_CTR_gene_DE_Table.tsv


title: H 240 ASO1 rep2

description:
RNAseq, antisense oligonucleotide targeting candidate240 ("CHiLL2") with ASO 1
ASO_TPM_table.csv
H_240_ASO1_vs_CTR_gene_DE_Table.tsv


title: H CTR ASO rep2

description:
RNAseq, antisense oligonucleotide with Qiagen neutral control ASO Control A
ASO_TPM_table.csv
H_240_ASO1_vs_CTR_gene_DE_Table.tsv
H_240_ASO3_vs_CTR_gene_DE_Table.tsv
H_42_ASO3_vs_CTR_gene_DE_Table.tsv
H_42_ASO5_vs_CTR_gene_DE_Table.tsv


title: A549 T3 cis 6.5uM rep2

description:
lncRNA targeted CRISPR/Cas9 pgRNA library
A549_counts_table.txt
A549_cis_T3_6.5uMvsT0.txt


title: H 240 ASO1 rep1


title: A 240 ASO3 rep5

description:
RNAseq, antisense oligonucleotide targeting candidate240 ("CHiLL2") with ASO 3
ASO_TPM_table.csv
A_240_ASO3_vs_CTR_gene_DE_Table.tsv


title: H CTR ASO rep1


title: A 240 ASO1 rep5

description:
RNAseq, antisense oligonucleotide targeting candidate240 ("CHiLL2") with ASO 1
ASO_TPM_table.csv
A_240_ASO1_vs_CTR_gene_DE_Table.tsv


title: H 42 ASO5 rep1


title: A 42 ASO3 rep5

description:
RNAseq, antisense oligonucleotide targeting candidate42 ("CHiLL1") with ASO 3
ASO_TPM_table.csv
A_42_ASO3_vs_CTR_gene_DE_Table.tsv


title: H 240 ASO3 rep1


title: A 240 ASO3 rep4


title: A CTR ASO rep5

description:
RNAseq, antisense oligonucleotide with Qiagen neutral control ASO Control A
ASO_TPM_table.csv
A_240_ASO1_vs_CTR_gene_DE_Table.tsv
A_240_ASO3_vs_CTR_gene_DE_Table.tsv
A_42_ASO3_vs_CTR_gene_DE_Table.tsv
A_42_ASO5_vs_CTR_gene_DE_Table.tsv


title: A 42 ASO5 rep5

description:
RNAseq, antisense oligonucleotide targeting candidate42 ("CHiLL1") with ASO 5
ASO_TPM_table.csv
A_42_ASO5_vs_CTR_gene_DE_Table.tsv


title: H 42 ASO3 rep1


title: A CTR ASO rep4


title: A 240 ASO3 rep3


title: A549 Death rep2

description:
lncRNA targeted CRISPR/Cas9 pgRNA library
A549_counts_table.txt
A549_cis_DeathvsT0.txt

value: after T0 every 24h for 5 days, pooled


title: A 42 ASO5 rep3


title: A 42 ASO3 rep4


title: A 240 ASO1 rep3


title: A 42 ASO3 rep3


title: CH04 Amplicon

city: New York

first: Neville

last: Dusaj

state: NY

institute: Weill Cornell Medicine

data_processing:
10x data was processed using Cell Ranger 3.0.1 using default parameters. RNA reads were aligned to the human or mouse referece genome, or human and mouse reference concatenation for species mixing experiment.
Amplicon reads was processed following steps: 1) Identification of reads with proper priming, 2) Identification of cell barcodes (CB) that match with the whitelisted CB, 3) Replacement of CB that are not perfectly matched with the whitelist CB, 4) Deduplication of reads, 5) Analyze reads with CB that are also observed in the 10x scRNA-seq data, 6) Collapse networks of closely related UMIs within CBs to correct for sequencing error, 7) Matching of CB/UMI pairs found in 10x scRNA-seq data, discarding those matching non-DNMT3A genes and those matching no gene below a supporting read threshold.
Genome_build: hg19
Supplementary_files_format_and_content: Processed 10X data is matrix table of gene counts per cell for each sample
Supplementary_files_format_and_content: Output matrices processed from amplicon data have three columns: barcodes (BC), number of wildtype calls (num.WT.call), and number of mutant calls (num.MUT.call).

source_name: GCSF mobilized stem cells from patient

extract_protocol:
Cryopreserved patient samples approved by the Institutional Review Board of Dana Farber Cancer Institute were thawed and stained using standard procedures (10 min, 4°C) with the surface antibody CD34-PE-Vio770 (clone AC136, Miltenyi Biotec) and DAPI (Sigma-Aldrich). Cells were then sorted for DAPI-negative, CD34+ and CD34-negative cells using BD Influx.
The standard 10x Genomics Chromium v.3 protocol was carried out according to manufacturer’s recommendations (10x Genomics, Pleasanton, CA) until after emulsion breakage and recovery of first strand cDNA. A gene-specific DNMT3A primer was spiked into 10x primer mix at 1% of the concentration of the cDNA amplification primers for the initial cDNA PCR step. Then, during the amplification step, the 10x cDNA library underwent an extra cycle of PCR beyond the manufacturer’s recommended number of cycles. After cleanup with SPRIselect, a small portion of the cDNA library, 3 µL (~10% of total) was aliquoted for targeted genotyping, and the remaining cDNA underwent the standard 10x protocol. The cDNA set aside for GoT was amplified for 3 to 4 additional cycles using KAPA HiFi HotStart ReadyMix (KAPABiosystems) and 10x primer mix to provide sufficient material for the enrichment step. After clean-up, locus-specific reverse primers and the generic forward SI-PCR were used to amplify the site of interest of the cDNA template using ~10 PCR cycles. The locus-specific reverse primers contain a partial Illumina read 2 handle, a stagger to increase the complexity of the library for optimal sequencing and a gene specific region to allow specific priming. The SI-PCR oligo (10x) anneals to the partial Illumina read 1 sequence at the 3’ end of the molecule, preserving the cell barcode (CB) and UMI. After the initial amplification and SPRI purification to remove unincorporated primers, a second PCR was performed with a generic forward PCR primer (P5_generic) to retain the CB and UMI together with an RPI-x primer (Illumina) to complete the P7 end of the library and add a sample index. The targeted amplicon library was subsequently sequenced separately. The cycle settings were as follows: 28 cycles for read 1, 98 or 130 cycles for read 2, and 8 cycles for sample index.
Single-cell RNA-seq (10X) with targeted amplification of a mutation of interest.

value: Blood


title: A CTR ASO rep3


title: Lmx1aE1_rep1, RNAseq

city: London

first: Andrea

institute: Kings College London

value: Otic placode cells

tag: Stage

value: Lmx1aE1 tagged


title: NJA9_MD_Cult_3

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

data_processing:
Sequenced reads were quality-tested using FASTQC v0.11.8
The genome index was constructed using the gene annotation supplied with the mm10 Illumina iGenomes collection and sjdbOverhang value of 100.
Reads were aligned to the mm10 mouse genome using the STAR aligner version 2.5.3a. Mapping was carried out using default parameters, filtering non-canonical introns and allowing up to 10 mismatches per read and only keeping uniquely mapped reads.
Raw or FPKM (fragments per kilobase per million mapped reads) gene expression was quantified across all gene exons with HOMER v4.10.4 analyzeRepeats.pl with mm10 annotation v5.10 and parameters -strand + -count exons -condenseGenes (top-expressed isoform as proxy for gene expression)
Differential gene expression was carried out on the raw counts with HOMER getDiffExpression.pl that runs DESeq2 v1.14.1 using replicates to compute within-group dispersion. BMP6 treatment samples were adjusted for mouse-specific batch effects using the -batch flag. Differentially expressed genes were defined as having FDR<0.05, FC>1.5, and FPKM>1, when comparing two experimental conditions.
Genome_build: mm10
Supplementary_files_format_and_content: Excel table of FPKM values

source_name: astrocyte

growth_protocol: See overall study design

extract_protocol:
RNA was extracted using the RNEasy Micro Plus kit (Qiagen 74034).
For RNA sequencing RNA libraries were prepared with TrueSeq Stranded mRNA Library Prep Kit (Illumina), from on average 0.8ug total RNA. Poly(A) mRNA was isolated from total RNA samples, followed by mRNA fragmentation, first strand cDNA synthesis, second cDNA synthesis and adaptor ligation, and isolation and amplification of cDNA fragments. Illumina HiSeq 2500 instrument was used for sequencing, with a read length of 50bp single-end, and an average of 36 million reads per sample.

treatment_protocol: See overall study design

tag: condition

value: MD cultured

tag: batch


title: CH04 10X


title: NJA4_IP_Cult_2

value: Immunopanned cultured


title: NJA5_IP_Cult_4


title: NJA8_MD_Cult_2


title: NJA7_MD_Cult_1


title: GM23225_NPC_Supt4-kd

city: Stanford

first: Stanley

middle: N.

last: Cohen

address: 300 Pasteur Drive, Lane Bldg, Rm L-314

institute: Stanford University

data_processing:
Reads were then aligned to the Human (hg19) genome using STAR version 2.5.1b with splice junctions being defined in GTF file (obtained from UCSC for hg19).
Expression at gene level was determined by calculating reads per kilobase per million aligned reads (FPKM) as well as raw count using RSEM (version 1.2.30).
Gene expression change as fold change was further calculated by DEseq version 1.10.1 for these two conditions (Untreated and Supt4h kd).
Genome_build: hg19
Supplementary_files_format_and_content: summary_gene_count_table.txt  (Matrix table with raw gene counts for every gene and every sample)
Supplementary_files_format_and_content: summary_gene_FPKM_table.txt  (Matrix table with FPKM for every gene and every sample)

source_name: Neural progenitor cells

growth_protocol: The NPC were differentiated from iPSC GM23225 by 7 days of induction in differentiation medium made with 15% KnockOut Serum Replacement (ThermoFisher Scientific), 1% Glutamax, 1% Non-Essential Amino Acids Solution, 1% GibcoTM 2-Mercaptoethanol, 10µM SB431542 and 500ng/ml Noggin in KnockOut DMEM (ThermoFisher Scientific). Medium was changed daily.

extract_protocol:
Total RNA was extracted using RNeasy kit (Qiagen) according to the manufacturer’s instructions.
ScriptSeq v2 RNA-seq kit (Epicenter) was used following the manufacturer’s instructions. The workflow includes rRNA removal (RiboZero technology) followed by RNA fragmentation, ligation-free cDNA synthesis for preparing directional RNA-seq libraries. The final amplified libraries were further purified by gel excision and extraction. The libraries were analyzed using an Illumina HiSeq 2000 sequencer.

treatment_protocol: Lentivirus carrying human Supt4h shRNA (clone ID: TRCN0000019645 from Dharmacon having the mature antisense sequence TTAAAGTTACTGACTCGCTGC) was introduced into the iPSC cell line GM23225 (Coriell Institute). Puromycin was used to select shRNA positive cells. Knocking down of Supt4h was confirmed by Realtime PCR for mRNA and by Western blotting for protein.

value: iPSC-derived neuronal progenitor cells

value: GM23225 (Coriell Institute)

tag: genotype

value: Supt4h knockdown


title: NJA6_IP_Cult_7


title: NJA1_IP_Acute_2

value: Immunopanned acute


title: GM23225_NPC_unt

value: untreated


title: NJA3_IP_Acute_7


title: A 240 ASO1 rep4

value: non-small cell lung cancer (NSCLC)

tag: treatment


title: A 42 ASO5 rep4

value: adenocarcinoma


title: RBG26066_Plate_3_WT [SLX.14258.i726_i517]

city: Cambridge

first: Hugo

middle: P.

last: Bastos

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

department: Haematology

institute: Wellcome - MRC Cambridge Stem Cell Institute

data_processing:
RNA-seq reads were aligned to mm10 + ERCC92 using GSNAP (version 2018-03-25) with parameters (-B 5 -t 24 -n 1 -Q -N 1).
Reads in features were counted with htseq-count (HTSeq version 0.9.1) with the parameter (-s no).
Genome_build: GRCm38.81
Supplementary_files_format_and_content: Processed files are cell gene count matrices, both raw and filtered and normalized and associated cell metadata

source_name: bone marrow

extract_protocol:
Bone marrow cells were harvested from STAT1KO and WT control mice, single ESLAM HSCs was FACS sorted into 2.3ul 0.2% Triton-100 containg RNAse inhibitor
Tagmentation is carried out using the Illumina Nextera XT DNA sample preparation kit. The protocol is based on the Tagmentation protocol from Fluidigm.

value: ESLAM

value: WT

value: bone marrow


title: RBG26070_Plate_3_KO [SLX.14258.i716_i518]

value: KO


title: RBG26067_Plate_3_WT [SLX.14258.i727_i517]


title: RBG26071_Plate_3_KO [SLX.14258.i718_i518]


title: RBG26064_Plate_3_WT [SLX.14258.i723_i517]


title: RBG26065_Plate_3_WT [SLX.14258.i724_i517]


title: RBG26069_Plate_3_WT [SLX.14258.i729_i517]


title: RBG26074_Plate_3_KO [SLX.14258.i721_i518]


title: RBG26075_Plate_3_KO [SLX.14258.i722_i518]


title: RBG26072_Plate_3_KO [SLX.14258.i719_i518]


title: NJA2_IP_Acute_4


title: RBG26078_Plate_3_WT [SLX.14258.i726_i518]


title: RBG26079_Plate_3_WT [SLX.14258.i727_i518]


title: RBG26073_Plate_3_KO [SLX.14258.i720_i518]


title: RBG26082_Plate_3_KO [SLX.14258.i716_i520]


title: RBG26080_Plate_3_WT [SLX.14258.i728_i518]


title: RBG26076_Plate_3_WT [SLX.14258.i723_i518]


title: RBG26085_Plate_3_KO [SLX.14258.i720_i520]


title: RBG26086_Plate_3_KO [SLX.14258.i721_i520]


title: RBG26084_Plate_3_KO [SLX.14258.i719_i520]


title: RBG26081_Plate_3_WT [SLX.14258.i729_i518]


title: RBG26087_Plate_3_KO [SLX.14258.i722_i520]


title: RBG26083_Plate_3_KO [SLX.14258.i718_i520]


title: RBG26091_Plate_3_WT [SLX.14258.i727_i520]


title: RBG26068_Plate_3_WT [SLX.14258.i728_i517]


title: RBG26092_Plate_3_WT [SLX.14258.i728_i520]


title: RBG26089_Plate_3_WT [SLX.14258.i724_i520]


title: RBG26090_Plate_3_WT [SLX.14258.i726_i520]


title: RBG26094_Plate_3_KO [SLX.14258.i716_i521]


title: RBG26032_Plate_3_WT [SLX.14258.i728_i513]


title: RBG26095_Plate_3_KO [SLX.14258.i718_i521]


title: RBG26077_Plate_3_WT [SLX.14258.i724_i518]


title: RBG26034_Plate_3_KO [SLX.14258.i716_i515]


title: RBG26088_Plate_3_WT [SLX.14258.i723_i520]


title: RBG26035_Plate_3_KO [SLX.14258.i718_i515]


title: RBG26093_Plate_3_WT [SLX.14258.i729_i520]


title: RBG26037_Plate_3_KO [SLX.14258.i720_i515]


title: RBG26033_Plate_3_WT [SLX.14258.i729_i513]


title: RBG26036_Plate_3_KO [SLX.14258.i719_i515]


title: RBG26040_Plate_3_WT [SLX.14258.i723_i515]


title: RBG26039_Plate_3_KO [SLX.14258.i722_i515]


title: RBG26038_Plate_3_KO [SLX.14258.i721_i515]


title: RBG26042_Plate_3_WT [SLX.14258.i726_i515]


title: RBG26044_Plate_3_WT [SLX.14258.i728_i515]


title: RBG26041_Plate_3_WT [SLX.14258.i724_i515]


title: RBG26046_Plate_3_KO [SLX.14258.i716_i516]


title: RBG26045_Plate_3_WT [SLX.14258.i729_i515]


title: RBG26048_Plate_3_KO [SLX.14258.i719_i516]


title: RBG26047_Plate_3_KO [SLX.14258.i718_i516]


title: RBG26049_Plate_3_KO [SLX.14258.i720_i516]


title: RBG26051_Plate_3_KO [SLX.14258.i722_i516]


title: RBG26050_Plate_3_KO [SLX.14258.i721_i516]


title: RBG26053_Plate_3_WT [SLX.14258.i724_i516]


title: RBG26055_Plate_3_WT [SLX.14258.i727_i516]


title: RBG26056_Plate_3_WT [SLX.14258.i728_i516]


title: RBG26052_Plate_3_WT [SLX.14258.i723_i516]


title: RBG26054_Plate_3_WT [SLX.14258.i726_i516]


title: RBG26057_Plate_3_WT [SLX.14258.i729_i516]


title: RBG26059_Plate_3_KO [SLX.14258.i718_i517]


title: RBG26058_Plate_3_KO [SLX.14258.i716_i517]


title: RBG26061_Plate_3_KO [SLX.14258.i720_i517]


title: RBG26043_Plate_3_WT [SLX.14258.i727_i515]


title: A549 T3 cis 6.5uM rep3

value: T3 (21 days)

value: cisplatin


title: RBG26006_Plate_2_WT [SLX.14258.i711_i521]


title: RBG26062_Plate_3_KO [SLX.14258.i721_i517]


title: RBG26005_Plate_2_WT [SLX.14258.i710_i521]


title: RBG26003_Plate_2_KO [SLX.14258.i706_i521]


title: RBG26004_Plate_2_WT [SLX.14258.i707_i521]


title: RBG26000_Plate_2_KO [SLX.14258.i703_i521]


title: RBG26014_Plate_2_KO [SLX.14258.i705_i522]


title: RBG26001_Plate_2_KO [SLX.14258.i704_i521]


title: RBG26013_Plate_2_KO [SLX.14258.i704_i522]


title: RBG26015_Plate_2_KO [SLX.14258.i706_i522]


title: RBG26012_Plate_2_KO [SLX.14258.i703_i522]


title: RBG26002_Plate_2_KO [SLX.14258.i705_i521]


title: RBG26010_Plate_2_KO [SLX.14258.i701_i522]


title: RBG26011_Plate_2_KO [SLX.14258.i702_i522]


title: RBG26008_Plate_2_WT [SLX.14258.i714_i521]


title: RBG26009_Plate_2_WT [SLX.14258.i715_i521]


title: RBG26060_Plate_3_KO [SLX.14258.i719_i517]


title: RBG26063_Plate_3_KO [SLX.14258.i722_i517]


title: RBG26023_Plate_3_KO [SLX.14258.i718_i513]


title: RBG26019_Plate_2_WT [SLX.14258.i712_i522]


title: RBG26007_Plate_2_WT [SLX.14258.i712_i521]


title: RBG26018_Plate_2_WT [SLX.14258.i711_i522]


title: RBG26022_Plate_3_KO [SLX.14258.i716_i513]


title: RBG26031_Plate_3_WT [SLX.14258.i727_i513]


title: RBG26030_Plate_3_WT [SLX.14258.i726_i513]


title: RBG26017_Plate_2_WT [SLX.14258.i710_i522]


title: RBG26016_Plate_2_WT [SLX.14258.i707_i522]


title: RBG26021_Plate_2_WT [SLX.14258.i715_i522]


title: RBG26028_Plate_3_WT [SLX.14258.i723_i513]


title: RBG26029_Plate_3_WT [SLX.14258.i724_i513]


title: RBG26026_Plate_3_KO [SLX.14258.i721_i513]


title: RBG26025_Plate_3_KO [SLX.14258.i720_i513]


title: RBG25975_Plate_2_KO [SLX.14258.i702_i518]


title: RBG25972_Plate_2_WT [SLX.14258.i714_i517]


title: RBG25974_Plate_2_KO [SLX.14258.i701_i518]


title: RBG25968_Plate_2_WT [SLX.14258.i707_i517]


title: RBG25970_Plate_2_WT [SLX.14258.i711_i517]


title: A549 T3 rep3


title: RBG25981_Plate_2_WT [SLX.14258.i710_i518]


title: RBG25980_Plate_2_WT [SLX.14258.i707_i518]


title: RBG25982_Plate_2_WT [SLX.14258.i711_i518]


title: RBG25969_Plate_2_WT [SLX.14258.i710_i517]


title: RBG26027_Plate_3_KO [SLX.14258.i722_i513]


title: RBG25983_Plate_2_WT [SLX.14258.i712_i518]


title: RBG26020_Plate_2_WT [SLX.14258.i714_i522]


title: A549 T2 cis 6.5uM rep3

value: T2 (14 days)


title: RBG25977_Plate_2_KO [SLX.14258.i704_i518]


title: RBG25976_Plate_2_KO [SLX.14258.i703_i518]


title: RBG25978_Plate_2_KO [SLX.14258.i705_i518]


title: RBG25979_Plate_2_KO [SLX.14258.i706_i518]


title: RBG25989_Plate_2_KO [SLX.14258.i704_i520]


title: RBG25987_Plate_2_KO [SLX.14258.i702_i520]


title: RBG25988_Plate_2_KO [SLX.14258.i703_i520]


title: RBG25990_Plate_2_KO [SLX.14258.i705_i520]


title: RBG26024_Plate_3_KO [SLX.14258.i719_i513]


title: RBG25986_Plate_2_KO [SLX.14258.i701_i520]


title: RBG25991_Plate_2_KO [SLX.14258.i706_i520]


title: RBG25985_Plate_2_WT [SLX.14258.i715_i518]


title: RBG25984_Plate_2_WT [SLX.14258.i714_i518]


title: RBG25973_Plate_2_WT [SLX.14258.i715_i517]


title: RBG25996_Plate_2_WT [SLX.14258.i714_i520]


title: RBG25998_Plate_2_KO [SLX.14258.i701_i521]


title: RBG25999_Plate_2_KO [SLX.14258.i702_i521]


title: RBG25993_Plate_2_WT [SLX.14258.i710_i520]


title: RBG25995_Plate_2_WT [SLX.14258.i712_i520]


title: RBG26202_Plate_4_KO [SLX.14258.i716_i511]


title: RBG25994_Plate_2_WT [SLX.14258.i711_i520]


title: RBG26203_Plate_4_KO [SLX.14258.i718_i511]


title: RBG26201_Plate_4_WT [SLX.14258.i729_i510]


title: RBG25992_Plate_2_WT [SLX.14258.i707_i520]


title: RBG26206_Plate_4_KO [SLX.14258.i721_i511]


title: RBG26200_Plate_4_WT [SLX.14258.i728_i510]


title: RBG26207_Plate_4_KO [SLX.14258.i722_i511]


title: RBG26205_Plate_4_KO [SLX.14258.i720_i511]


title: RBG26204_Plate_4_KO [SLX.14258.i719_i511]


title: RBG26195_Plate_4_KO [SLX.14258.i722_i510]


title: RBG26199_Plate_4_WT [SLX.14258.i727_i510]


title: RBG26198_Plate_4_WT [SLX.14258.i726_i510]


title: RBG26192_Plate_4_KO [SLX.14258.i719_i510]


title: RBG25997_Plate_2_WT [SLX.14258.i715_i520]


title: RBG26196_Plate_4_WT [SLX.14258.i723_i510]


title: RBG26197_Plate_4_WT [SLX.14258.i724_i510]


title: RBG26211_Plate_4_WT [SLX.14258.i727_i511]


title: RBG26169_Plate_4_KO [SLX.14258.i720_i507]


title: RBG26193_Plate_4_KO [SLX.14258.i720_i510]


title: RBG26208_Plate_4_WT [SLX.14258.i723_i511]


title: RBG26212_Plate_4_WT [SLX.14258.i728_i511]


title: RBG26209_Plate_4_WT [SLX.14258.i724_i511]


title: RBG26168_Plate_4_KO [SLX.14258.i719_i507]


title: RBG26171_Plate_4_KO [SLX.14258.i722_i507]


title: RBG26194_Plate_4_KO [SLX.14258.i721_i510]


title: RBG26172_Plate_4_WT [SLX.14258.i723_i507]


title: RBG26175_Plate_4_WT [SLX.14258.i727_i507]


title: RBG26174_Plate_4_WT [SLX.14258.i726_i507]


title: RBG26170_Plate_4_KO [SLX.14258.i721_i507]


title: RBG26163_Plate_4_WT [SLX.14258.i727_i506]


title: RBG26173_Plate_4_WT [SLX.14258.i724_i507]


title: RBG26210_Plate_4_WT [SLX.14258.i726_i511]


title: RBG26160_Plate_4_WT [SLX.14258.i723_i506]


title: RBG26213_Plate_4_WT [SLX.14258.i729_i511]