title: Sample_33A (WTEE)

city: Coventry

first: Bruno

middle: G.

last: Frenguelli

state: Coventry

address: Gibbet Hill Road

department: School of Life Sciences

country: United Kingdom

institute: University of Warwick

data_processing:
Illumina software 1.9 used for basecalling.
Adaptor contamination was removed using Skewer (v0.2.2), with Illumina TruSeq v2 adapter lists, including reverse complements and theoretical PCR product. Fastq files were trimmed if the mean quality of bases dropped below 10 (4bp window) and only reads >50bp and with no multiple alignments were kept.The following Skewer parameters were used: -Q 10 -t 10 -x  -y -l 50 -z --compress
Paired trimmed reads for each sample were aligned to the mouse genome (GRCm38) using STAR aligner (v2.5), and annotated (GRCm38.87)
Counts for each gene were calculated using HTSeq counts based on exon mapping across all transcripts, disregarding reads that mapped ambiguously and that had an alignment score <10. The following parameters were used: -r pos -f bam -s no -a 10 -t exon -i gene_name -m union
DESeq design = ~condition
Genome_build: GRCm38
Supplementary_files_format_and_content: Sample text files: RNA fragment counts for each gene
Supplementary_files_format_and_content: JNeurosci_Privitera_et_al_dds_count_summary.txt: Tab delimited gene normalised counts for each gene, dds output from DESeq, column names are Gene_ID followed by each sample number

source_name: Whole hippocampus

extract_protocol:
Hippocampi were extracted and then rapidly homogenized in Trizol. Total RNA was precipitated using isopropanol following the manufacturer’s protocol and treated with DNaseI. RNA quality was checked using Nanodrop and a Qubit 4 fluorimeter (Invitrogen).
150bp paired-end mRNA libraries were prepared using the TruSeqv2 (Illumina, #RS-122-2001) LS protocol. Briefly, poly-A mRNA was pulled down using poly-T magnetic beads, fragmented, and primed with random hexamers before first-strand synthesis. Following second-strand synthesis, blunt end repair was performed with a 3’ to 5’ exonuclease, and 3’ ends adenylated. Adaptors were then ligated to the cDNA. All 24 library samples were quality checked on a Agilent 2100 bioanalyser and assayed on a Qubit 4 fluorimeter.

treatment_protocol: Environmental Enrichment (2 samples)

value: Whole hippocampus

value: 12 weeks post natal

tag: genotype

value: Wildtype


title: Sample_35A (WTEE)

status: Public on May 10 2020

type: SRA

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: tissue

tag: age


title: Sample_34B (KDEE)

description: Poor amplification and rRNA contamination

value: MSK1 kinase dead


title: RNA_KC-N_10wkNASH_rep2

city: La Jolla

first: Christopher

middle: K

last: Glass

state: CA

address: 9500 Gilman Drive

department: School of Medicine

country: USA

institute: University of California, San Diego

description:
processed data file: rna_raw_counts.txt
processed data file: rna_tpm_counts.txt

data_processing:
Preprocessing: FASTQ files from sequencing experiments were mapped to the mouse mm10 genome. STAR with default parameters was used to map RNA-seq experiments (Dobin et al., 2013). HOMER was used to convert aligned reads into “tag directories” for further analysis (Heinz et al., 2010).
Each experiment was quantified using the “analyzeRepeats” script of HOMER. To generate a table of raw read counts, the parameters -count exons -condenseGenes - noadj were used. To generate a table of TPM values, the parameters -count exons -tpm were used. Differentially expressed genes were identified using raw sequencing read counts by DESeq2 (Love et al., 2014) analysis through the “getDifferentialExpression” HOMER command. Gene ontology analysis was performed using Metascape (Tripathi et al., 2015).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: rna_raw_counts.txt: Tab-delimited text file includes table of unnormalized read counts.
Supplementary_files_format_and_content: rna_tpm_counts.txt: Tab-delimited text file includes table of  TPM values.

source_name: Sorted hepatic macrophages

extract_protocol:
Hepatic macrophages: Mice were humanely euthanized by exposure to CO2 and liver non-parenchymal cells processed for fluorescence activated cell sorting of Kupffer cells, with modifications from published methodology (Mederacke et al., 2015; Muse et al., 2018; Seki et al., 2007). In brief, livers were retrograde perfused for 3 min at a rate of 5-7 ml/min through the inferior vena cava with HBSS without Ca++ or Mg++ supplemented with 0.5 mM EGTA, 0.5 mM EDTA, and 20 mM HEPES. Perfusions were then switched to 40 ml of a digestion buffer, held at 37C, comprised of HBSS with Ca++ and Mg++ supplemented with 0.033 mg/ml of Liberase TM (Roche), 20 μg/ml DNaseI (Worthington), and 20 mM HEPES. Livers were then excised, minced, and digested for an additional 20 minutes in vitro at 37C with gentle rotation in 20 ml of fresh digestion buffer. The perfusion and digestion steps were performed in the presence of 1 μM flavopiridol to offset transcriptional changes associated with digestion. After tissue digestion, cells were passed through a 70-micron cell strainer and hepatocytes removed by 2 low-speed centrifugation steps at 50 X G for 2 min. Nonparenchymal cells in the supernatant were further separated from debris by pelleting for 15 min at 600 X G in 50 ml of 20% isotonic Percoll (Sigma Aldrich) at room temperature. Cells were then washed from Percoll containing buffer and suspended in 10 ml 28% OptiPrep (Sigma Aldrich) and carefully underlaid beneath 3 ml of wash buffer. The resulting gradient was centrifuged at 1,400 X G for 25 minutes at 4C with no break and cells enriched at the interface were saved and subjected to isotonic erythrocyte lysis. Enriched non-parenchymal cells were then washed, suspended in PBS, then stained for 10 minutes with Zombie NIR (BioLegend) and purified anti-CD16/32 (93, BioLegend) to label dead cells and block Fc receptors. Cells were then immunolabeled with specific antibodies of interest, washed, and sorted using a Beckman Coulter MoFlo Astrios EQ configured with spatially separated 355 nm, 405 nm, 488 nm, 561 nm, and 642 nm lasers.
Peripheral monocytes: Mice were humanely euthanized by exposure to CO2. Blood was collected from mice via cardiac puncture into K3EDTA tubes and subjected to RBC lysis (eBioscience). Cells were pelleted by centrifugation at 350 X G for 10 minutes at 4°C and washed, suspended in PBS, then stained for 10 minutes with Zombie NIR (BioLegend) and purified anti-CD16/32 (93, BioLegend) to label dead cells and block Fc receptors. Next, cells were stained in wash buffer for an additional 20 minutes with the antibodies listed in the Key Resource Table. Stained cells were washed twice and strained through a 30 μm strainer, then subjected to cell sorting using a Beckman Coulter MoFlo Astrios EQ configured with 355 nm, 405 nm, 488 nm, 561 nm, and 642 nm lasers. Each cell population was hierarchically gated using Beckman Coulter Summit software. Ly6CHi monocytes were defined as CD45PosCD11bHiCD115PosCD19NegCD90.2NegLy6GNegLy6CHi. Ly6CHi monocytes were further restricted to single particles by comparing height and area side scatter pulses, and dead cells were excluded by detecting the integration of the live/dead dye (Zombie NIR).
Whole liver tissue: Mice were humanely euthanized by exposure to CO2 and liver pieces were snap frozen for RNA-seq.
Performed as published previously (Gosselin et al., 2017; Oishi et al., 2016). Isolated cells were pelleted and put into 150 μl lysis/Oligo d(T) Magnetic Beads binding buffer and stored at -80°C until processing. mRNAs were enriched by incubation with Oligo d(T) Magnetic Beads (NEB, S1419S) and then fragmented/eluted by incubation at 94°C for 9 min. Poly A enriched mRNA was fragmented, in 2x Superscript III first-strand buffer with 10mM DTT (Invitrogen), by incubation at 94°C for 9 minutes, then immediately chilled on ice before the next step. The 10 μL of fragmented mRNA, 0.5 μL of Random primer (Invitrogen), 0.5 μL of Oligo dT primer (Invitrogen), 0.5 μL of SUPERase-In (Ambion), 1 μL of dNTPs (10 mM) and 1 μL of DTT (10 mM) were heated at 50°C for three minutes. At the end of incubation, 5.8 μL of water, 1 μL of DTT (100 mM), 0.1 μL Actinomycin D (2 μg/μL), 0.2 μL of 1% Tween-20 (Sigma) and 0.2 μL of Superscript III (Invitrogen) were added and incubated in a PCR machine using the following conditions: 25°C for 10 minutes, 50°C for 50 minutes, and a 4°C hold. The product was then purified with RNAClean XP beads according to manufacturer's instruction and eluted with 10 μL nuclease-free water. The RNA/cDNA double-stranded hybrid was then added to 1.5 μL of Blue Buffer (Enzymatics), 1.1 μL of dUTP mix (10 mM dATP, dCTP, dGTP and 20 mM dUTP), 0.2 μL of RNAse H (5 U/μL), 1.05 μL of water, 1 μL of DNA polymerase I (Enzymatics) and 0.15 μL of 1% Tween-20. The mixture was incubated at 16°C for 1 hour. The resulting dUTP-marked dsDNA was purified using 28 μL of Sera-Mag Speedbeads (Thermo Fisher Scientific), diluted with 20% PEG8000, 2.5M NaCl to final of 13% PEG, eluted with 40 μL EB buffer (10 mM Tris-Cl, pH 8.5) and frozen at -80°C. The purified dsDNA (40 μL) underwent end repair by blunting, A-tailing and adapter ligation as previously described (Heinz et al., 2010) using barcoded adapters (NextFlex, Bioo Scientific). Libraries were PCR-amplified for 9-14 cycles, size selected by gel extraction, quantified using a Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and sequenced on a Hi-seq 4000 or a NextSeq 500 (Illumina, San Diego, CA) according to the manufacturer's instructions.

tag: strain

tag: cell type

value: Sorted hepatic macrophages

tag: cell subtype

value: F4/80-Hi Tim4-Pos Kupffer cells

tag: treatment

value: NASH diet


title: Sample_36A (KDEE)


title: RNA_KC-N_10wkNASH_rep3


title: Sample_33B (WTEE)

description: Excessive sequence duplication and rRNA contamination


title: Sample_32A (KDEE)


title: Sample_31B (WTEE)


title: RNA_KC-N_10wkNASH_rep1


title: RNA_KC-H_grp0_rep2

value: Control diet


title: Sample_17 (WTEE)


title: Sample_16 (WTEE)


title: Sample_15 (WTSH)


title: RNA_KC-H_0WkNASH_rep2


title: RNA_KC-H_grp0_rep1


title: RNA_KC-H_0WkNASH_rep3


title: Sample_13 (WTSH)


title: Sample_14 (WTSH)


title: RNA_KC-H_0WkNASH_rep1


title: RNA_CreNeg_LXRaLXRb_flox20wkNASH_KN-RM_rep3

value: Cre neg LXRaLBRb flox

value: F4/80-Hi Tim4-Neg Kupffer niche recruited macrophages


title: Sample_12 (WTSH)


title: RNA_CreNeg_LXRaLXRb_flox20wkNASH_KN-RM_rep1


title: Sample_11 (WTSH)


title: RNA_CreNeg_LXRaLXRb_flox20wkNASH_KN-RM_rep2


title: RNA_Clec4fCrePos_LXRaLXRb_flox20wkNASH_KN-RM_rep2

value: Clec4f-cre pos LXRaLBRb flox


title: Sample_9 (KDEE)


title: Sample_8 (KDEE)


title: RNA_Clec4fCrePos_LXRaLXRb_flox20wkNASH_KN-RM_rep1


title: Sample_7 (KDEE)


title: Sample_5 (KDSH)


title: RNA_Clec4fCreDTRPos_4wkCDAHFD_WholeLiver_rep9

source_name: Whole liver

value: Clec4f-cre DTR pos

value: Whole liver

value: CDAHFD NASH diet


title: Sample_6 (KDSH)


title: Sample_4 (KDSH)


title: RNA_Clec4fCreDTRPos_4wkCDAHFD_WholeLiver_rep8


title: RNA_Clec4fCreDTRPos_4wkCDAHFD_WholeLiver_rep7


title: Sample_3 (KDSH)


title: RNA_Clec4fCreDTRPos_4wkCDAHFD_WholeLiver_rep6


title: RNA_Clec4fCreDTRPos_4wkCDAHFD_WholeLiver_rep4


title: RNA_Clec4fCreDTRPos_4wkCDAHFD_WholeLiver_rep5


title: Sample_1 (KDSH)


title: Sample_10 (WTSH)


title: RNA_Clec4fCrePos_LXRaLXRb_flox20wkNASH_KN-RM_rep3


title: RNA_Clec4fCreDTRPos_4wkCDAHFD_WholeLiver_rep3


title: RNA_Clec4fCreDTRPos_4wkCDAHFD_WholeLiver_rep1


title: RNA_Clec4fCreDTRPos_4wkCDAHFD_WholeLiver_rep2


title: Lm_EtOH_2 [18_wtLM]

city: Seattle

first: Hannah

last: Tabakh

state: WA

address: 750 Republican St Bldg F

department: Microbioloby

institute: University of Washington

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18.66.3 software
This was followed by 'demultiplexing' of indexed reads and generation of FASTQ files using Illumina's bcl2fastq Conversion Software v1.8.4
Reads determined by the RTA software to pass Illumina's default quality filters were concatenated for further analysis
The FASTQ files were aligned and analyzed using Rockhopper software (https://cs.wellesley.edu/~btjaden/Rockhopper/index.html)
Genome_build: https://www.ncbi.nlm.nih.gov/assembly/GCF_000168695.2
Supplementary_files_format_and_content: tab delimited file containing RPKM values for each gene in each sample (as indicated in the file name) and Rockhopper generated statistical significance of EtOH versus 4-HNE treatment RPKM difference

molecule: total RNA

organism: Listeria monocytogenes 10403S

growth_protocol: L. monocytogenes grown to mid-log (0.4-0.8 OD) in tryptic soy broth at 27C.

extract_protocol:
RNA was extracted using hot phenol and treated with DNase.
RNA was processed using the Ovation Complete Prokaryotic RNA-Seq Library System (NuGEN, #0363-32, 0326-32, 0327-32) per the manufacturer's instructions.

treatment_protocol: then a bolus of 640 micromolar 4-HNE or vehicle (ethanol) was added to midlog L.monocytogenes. Bacteria were exposed to 4-HNE for 20 minutes at 37C after which they were quenched with methanol and RNA was extracted for transcriptional analysis.

tag: phylum

value: Firmicute bacterium

tag: growth phase

value: vehicle (ethanol)


title: Lm_4HNE_2 [22_wtLM_HNE]


title: Lm_EtOH_1 [17_wtLM]


title: Lm_4HNE_1 [21_wtLM_HNE]


title: RNA_Clec4fCreDTRPos_4wkCDAHFD_WholeLiver_rep12


title: RNA_Clec4fCreDTRPos_4wkCDAHFD_WholeLiver_rep11


title: RNA_Clec4fCreDTRPos_4wkCDAHFD_WholeLiver_rep10


title: RNA_Clec4fCreDTRNeg_4wkCDAHFD_WholeLiver_rep9

value: Clec4f-cre DTR neg


title: Sample_2 (KDSH)

value: Whole hippocampus


title: NURF301_CUTandRUN

city: Ithaca

first: Julius

last: Judd

state: NY

address: 417 Biotechnology Bldg; 215 Tower Road

department: Molecular Biology and Genetics

institute: Cornell University

library_source: genomic

data_processing:
Library strategy: CUT&RUN
Adapters were trimmed and paired-end overlap correction was performed using fastp v0.20.0.
Reads were aligned to the dm6 genome assembly using bowtie2 v2.3.5.1.
Counts per million (CPM) bigWig coverage tracks of piled up fragments < 120 bp were generated using deepTools bamCoverage v3.1.3.
Genome_build: dm6
Supplementary_files_format_and_content: Counts per million (CPM) bigWig coverage tracks of piled up fragments < 120 bp.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: S2 cells

growth_protocol: Drosophila S2 cells were maintained in M3+BPYE medium supplemented with 10% FBS at 25 °C.

extract_protocol:
CUT&RUN was performed as previously described in Skene et al. 2017 (PMID: 28079019). Antibodies to GAF (lab made; 1:10) and NURF301 (Novus Biologicals Cat. No. 40360002; 1:10) were incubated with 10e6 permeabilized Drosophila S2 cells bound to concanavalinA coated beads, and proteinA-MNase cleavage was initiated by incubating on ice with calcium for 30 min. Cleaved fragments were recovered by phenol:chloroform extraction followed by ethanol precipitation.
Library preparation was completed using enzymes from NEB (T4 PNK, T4 DNA Polymerase, and Klenow fragment for end-repair; Klenow exo- for A-tailing; and T4 DNA ligase for adapter ligation) and lab-made Illumina forked TruSeq adapters synthesized by IDT. Libraries were amplified for 15 PCR cycles.

treatment_protocol: For CUT&RUN, no treatment was performed.

tag: cell line

tag: antibody


title: NURF301BAP170_RNAseq_Rep2

description:
10R
processed data file: NURF301BAP170_RNAseq_pooled_normalized_fwd.bw
processed data file: NURF301BAP170_RNAseq_pooled_normalized_rev.bw

data_processing:
Reads were trimmed of adapter and polyA sequences and UMIs were extracted using fastp v0.20.0.
Reads were aligned to a combined dm6/ERCC genome using STAR v2.7.0f_0328.
Alignments were PCR-deduplicated using umi_tools dedup v1.0.0.
bigWig strand-specific coverage tracks were generated from the 5' ends of alignments (so each read is only counted once in the signal tracks) using deepTools bamCoverage v3.1.3.
Genome_build: dm6
Supplementary_files_format_and_content: For each sample, there are strand-specific raw signal bigWig tracks of read 5' end positions. There are also replicate-pooled, spike-in normalized bigWig coverage tracks of read 5' end positions.

source_name: S2 Cells

extract_protocol:
For 3'RNA-seq, we counted and aliquoted 10e6 cells and added a fixed amount of ERCC polyadenylated spike-in RNA. We then isolated total RNA using TRIzol, followed by ethanol precipitation. RNA was removed using RNase-free DNase I.
Libraries were constructed from 325 ng total RNA using the QuantSeq 3’ mRNA-seq Library Prep Kit (Lexogen) with the UMI add-on kit per manufacturer instructions.

treatment_protocol: Growing S2 cells were diluted to 10e6 cells/mL in serum free media containing dsRNA complementary to the target transcript at final concentration 10 µg/mL. After 45 min at 25 °C, serum-containing media was added to a final serum concentration of 10%. After 2.5 days, cells were passaged 1:2 and more ds RNA was added to maintain the concentration. After a total of 5 days, flasks were harvested and pooled. Two independent knockdown replicates were performed for each target.

tag: dsrna


title: NURF301BAP170_RNAseq_Rep1

description:
9R
processed data file: NURF301BAP170_RNAseq_pooled_normalized_fwd.bw
processed data file: NURF301BAP170_RNAseq_pooled_normalized_rev.bw


title: NURF301_RNAseq_Rep2

description:
8R
processed data file: NURF301_RNAseq_pooled_normalized_fwd.bw
processed data file: NURF301_RNAseq_pooled_normalized_rev.bw


title: RNA_Clec4fCreDTRNeg_4wkCDAHFD_WholeLiver_rep7


title: BAP170_RNAseq_Rep2

description:
6R
processed data file: BAP170_RNAseq_pooled_normalized_fwd.bw
processed data file: BAP170_RNAseq_pooled_normalized_rev.bw


title: BAP170_RNAseq_Rep1

description:
5R
processed data file: BAP170_RNAseq_pooled_normalized_fwd.bw
processed data file: BAP170_RNAseq_pooled_normalized_rev.bw


title: NURF301_RNAseq_Rep1

description:
7R
processed data file: NURF301_RNAseq_pooled_normalized_fwd.bw
processed data file: NURF301_RNAseq_pooled_normalized_rev.bw


title: RNA_Clec4fCreDTRNeg_4wkCDAHFD_WholeLiver_rep6


title: LACZ_RNAseq_Rep2

description:
2R
processed data file: LACZ_RNAseq_pooled_normalized_fwd.bw
processed data file: LACZ_RNAseq_pooled_normalized_rev.bw

value: LACZ


title: GAF_RNAseq_Rep2

description:
4R
processed data file: GAF_RNAseq_pooled_normalized_fwd.bw
processed data file: GAF_RNAseq_pooled_normalized_rev.bw

value: GAF


title: RNA_Clec4fCreDTRNeg_4wkCDAHFD_WholeLiver_rep5


title: RNA_Clec4fCreDTRNeg_4wkCDAHFD_WholeLiver_rep4


title: NURF301BAP170_ATACseq_Rep1

description:
9A
processed data file: NURF301BAP170_ATACseq_pooled_normalized_HS.bw
processed data file: NURF301BAP170_ATACseq_pooled_normalized_MN.bw
processed data file: ATACseq_peaks_summits_macs2.bed

data_processing:
Reads were aligned to the dm6 genome assembly using bowtie2 v2.3.5.1.
Alignments were split into hypersensitive (HS; fragments < 120 bp) and mononucleosome (MN; fragments 130–200 bp) classes by PE alignment fragment size into bigWig files using deepTools bamCoverage v3.1.3.
Scale Factors were calculated using DESeq2 v1.26.0 (from total signal within all promoters (-1000–TSS)).
Peaks were called on a pool of all data using macs2 v2.1.0.20150731.
Genome_build: dm6
Supplementary_files_format_and_content: For each sample, there are bigWig files of raw signal in both HS (pileup of fragments < 120 bp) and MN (pileup of central 3 bp of each read with PE fragment size 130–200 bp). There is also a file of peak summits called using macs2 with all samples pooled as input.

extract_protocol:
For ATAC-seq, we counted and aliquoted 10e5 cells and washed them with ice-cold PBS. Cells were then lysed on ice for 3 min in ATAC-lysis buffer (10 mM Tris-Cl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, and 1x Pierce Protease Inhibitors). Nuclei were transposed with Illumina Nextera adapter sequences with 1.5 µL lab-made Tn5 transposase in TD buffer (10 mM Tris-Cl pH 7.4, 10% DMF, and 5 mM MgCl2) for 30 min at 37 °C, and transposed gDNA was recovered by phenol:chloroform extraction followed by ethanol precipitation.
Libraries were amplified for 11 PCR cycles using Illumina Nextera indexed primers.


title: NURF301BAP170_ATACseq_Rep2

description:
10A
processed data file: NURF301BAP170_ATACseq_pooled_normalized_HS.bw
processed data file: NURF301BAP170_ATACseq_pooled_normalized_MN.bw
processed data file: ATACseq_peaks_summits_macs2.bed


title: RNA_Clec4fCreDTRNeg_4wkCDAHFD_WholeLiver_rep8


title: LACZ_RNAseq_Rep1

description:
1R
processed data file: LACZ_RNAseq_pooled_normalized_fwd.bw
processed data file: LACZ_RNAseq_pooled_normalized_rev.bw


title: wounded seedlings (6H) WCM

type: RNA

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

description: 6 he wounded plant

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 the 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

organism: Calotropis procera

source_name: Whole plant tissue

label_protocol: The microarray hybridization and scanning were performed at the Agilent certified microarray facility of Genotypic Technology, Bengaluru, India. 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: Seeds of C. procera were germinated in pots filled with a mixture of soilrite and vermiculite (3:1, v/v) and germinated seedlings were transferred in pots for experimentation. For proper growth, seedlings were kept at 250C in green house with 16h/8h day light condition.  3-month-old whole seedlings were used for the experiments.

extract_protocol: RNA was prepared using standard TRIzol method.The concentration and purity of the RNA extracted were evaluated using the Nanodrop Spectrophotometer (Thermo Scientific; 1000).  The integrity of the extracted RNA were analysed on the Bioanalyzer (Agilent; 2100). We considered RNA to be of good quality based on the 260/280 values (Nanodrop), rRNA 28S/18S ratios and RNA integrity number (RIN) (Bioanalyzer).

treatment_protocol: For wound treatment, 3 months old greenhouse grown whole seedlings were pricked with sterile needle uniformly and harvested after 1h, 3h and 6h of wound stress and freeze in liq. nitrogen for the isolation of RNA.

value: Whole  tissue

tag: time point

value: 6 hr

tag: protocol

value: wounded


title: NURF301_ATACseq_Rep2

description:
8A
processed data file: NURF301_ATACseq_pooled_normalized_HS.bw
processed data file: NURF301_ATACseq_pooled_normalized_MN.bw
processed data file: ATACseq_peaks_summits_macs2.bed


title: GAF_CUTandRUN


title: GAF_RNAseq_Rep1

description:
3R
processed data file: GAF_RNAseq_pooled_normalized_fwd.bw
processed data file: GAF_RNAseq_pooled_normalized_rev.bw


title: wounded seedlings (3H) WBM

description: 3 hr wounded plant

value: 3 hr


title: K12_SLIPS

city: Hannover

first: Katharina

last: Doll

address: Carl-Neuberg-Str. 1

country: Germany

institute: Hannover Medical School

description:
processed data file:
NormalizedCounts_BF SLIPS vs Planktonic.txt
NormalizedCounts_BF Titanium vs BF SLIPS.txt

data_processing:
Image analysis and base calling were performed using the Illumina pipeline v 1.8
RNA Sequencing data were analyzed on the Galaxy platform (https://usegalaxy.org/, last access: October, 2018). Where not stated otherwise, default settings were used.
Data were trimmed using Trim Galore! (Galaxy Version 0.4.3.1; Adapter sequence to be trimmed: Illumina universal; Overlap with adapter sequence required to be trimmed: 5; Discard reads that became shorter than length N: 30) and quality controlled using FastQC (Galaxy Version 0.69; [Andrews S. FastQC A Quality Control tool for High Throughput Sequence Data.]).
Data were aligned to the genome of S. oralis ATCC 9811 using HISAT2 (Galaxy Version 2.1.0; [Kim D et al. HISAT: a fast spliced aligner with low memory requirements. Nat Methods 2015;12:357-360]).
To count aligned reads, htseq-count (Galaxy Version 0.9.1; Mode: Intersection (nonempty); Stranded: No; Feature type: gene; [Anders S et al. HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics 2015;31:166-169]) and the genome annotation for S. oralis ATCC 9811 were used.
Differently expressed genes were determined using DESeq2 (Galaxy Version 2.11.40.1; Output normalized count table: True; [Love MI et al. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 2014;15:550-014-0550-8]) comparing each pair of datasets separately (biofilm on titanium vs. planktonic, biofilm on SLIPS vs. planktonic, biofilm on SLIPS vs. biofilm on titanium).
Genome_build: GenBank Accession Number SSNB00000000; Genome was de novo sequenced and will be released together with this GEO data
Supplementary_files_format_and_content: tab-delimited text files include normalized mean counts for each Sample in the respective comparison

organism: Streptococcus oralis

source_name: Biofilm

growth_protocol: S. oralis was precultured in Tryptone Soy Broth (Oxoid Limited, Hampshire, UK) supplemented with 10% yeast extract (Carl Roth GmbH + Co. KG, Karlsruhe, Germany), at 37 °C for 18 h under anaerobic conditions. For flow chamber biofilm experiments, a bioreactor containing Brain Heart Infusion growth medium (Oxoid Limited, Hampshire, UK) supplemented with 10 µl/ml vitamin K (Oxoid Limited, Hampshire, UK) (BHI/vitamin K) and 5% sucrose (Carl Roth GmbH + Co. KG) was inoculated to a final optical density of 0.026 at 600 nm. According to standard plate counting, this corresponds to 5x106 CFU/ml for S. oralis.

extract_protocol:
RNA was isolated according to the protocol described by Szafranski et al., Functional biomarkers for chronic periodontitis and insights into the role of Prevotella nigrescens and Fusobacterium nucleatum; a metatranscriptome analysis. NPJ Biofilms Microbiomes 2015;1:1:15017
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Bacteria were grown in flow chamber system containing a bioreaktor feeding flow chambers with either a titanium or a SLIPS surface at 37 °C and a flow rate of 100 µl/min.

value: ATCC 9811

tag: obtained from

value: Flow chamber

tag: surface grown on

value: SLIPS


title: wounded seedlings (3H) WCM

description: 3 hr wounded plant


title: BAP170_ATACseq_Rep2

description:
6A
processed data file: BAP170_ATACseq_pooled_normalized_HS.bw
processed data file: BAP170_ATACseq_pooled_normalized_MN.bw
processed data file: ATACseq_peaks_summits_macs2.bed


title: NURF301_ATACseq_Rep1

description:
7A
processed data file: NURF301_ATACseq_pooled_normalized_HS.bw
processed data file: NURF301_ATACseq_pooled_normalized_MN.bw
processed data file: ATACseq_peaks_summits_macs2.bed


title: RNA_Clec4fCreDTRNeg_4wkCDAHFD_WholeLiver_rep2

description:
processed data file: rna_raw_counts.txt
processed data file: rna_tpm_counts.txt


title: wounded seedlings (1H) WCM

description: 1 hr wounded plant

value: 1 hr


title: wounded seedlings (1H) WBM

description: 1 hr wounded plant


title: wounded seedlings (6H) WBM

description: 6 he wounded plant


title: RNA_Clec4fCreDTRNeg_4wkCDAHFD_WholeLiver_rep3


title: BAP170_ATACseq_Rep1

description:
5A
processed data file: BAP170_ATACseq_pooled_normalized_HS.bw
processed data file: BAP170_ATACseq_pooled_normalized_MN.bw
processed data file: ATACseq_peaks_summits_macs2.bed


title: Control Seedlings BM

description: Control plant

value: Control


title: RNA_Clec4fCreDTRNeg_4wkCDAHFD_WholeLiver_rep1

value: Whole liver


title: K10_Planktonic

description:
processed data file:
NormalizedCounts_BF Titanium vs Planktonic.txt
NormalizedCounts_BF SLIPS vs Planktonic.txt

source_name: Planktonic Culture

value: Bioreactor


title: Control Seedlings CM

description: Control plant


title: LACZ_ATACseq_Rep2

description:
2A
processed data file: LACZ_ATACseq_pooled_normalized_HS.bw
processed data file: LACZ_ATACseq_pooled_normalized_MN.bw
processed data file: ATACseq_peaks_summits_macs2.bed


title: K11_Titanium

description:
processed data file:
NormalizedCounts_BF Titanium vs Planktonic.txt
NormalizedCounts_BF Titanium vs BF SLIPS.txt

value: Titanium


title: GAF_ATACseq_Rep1

description:
3A
processed data file: GAF_ATACseq_pooled_normalized_HS.bw
processed data file: GAF_ATACseq_pooled_normalized_MN.bw
processed data file: ATACseq_peaks_summits_macs2.bed


title: s_A2

city: New York

first: Rohit

last: Bose

address: 1275 York Ave

institute: Memorial Sloan Kettering Cancer Center

data_processing:
The reads were aligned to the human genome (hg19, build 37) using the program BWA51 (default parameters) within the PEMapper
analysed by the software MACS252 (-q 0.1 –m 20 100) for peak identification with data from ChIP input DNAs as controls
Genome_build: HG19, build 37
Supplementary_files_format_and_content: tab-delimited text files with enriched read counts

organism: Homo sapiens

source_name: VCaP

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody
DNA libraries were prepared for sequencing using standard Illumina protocols by MSKCC Integrated Genomics Operation core

tag: doxycycline

tag: chip antibody


title: K7_Planktonic


title: K8_Titanium


title: s_input2

description: input for AR and ERG ChIP -dox


title: BAP170_PROseq_Rep1

description:
5P
nuclear RNA
processed data file: BAP170_PROseq_pooled_normalized_fwd.bw
processed data file: BAP170_PROseq_pooled_normalized_rev.bw

data_processing:
Library strategy: PRO-seq
Adapters were trimmed, UMIs were extracted, and paired-end overlap correction was performed using fastp v0.20.0.
Spike-in reads were counted by alignment to a combined custom-masked human and Drosophila genome using bowtie2 v2.3.5.1.
Reads were aligned to the dm6 genome assembly using bowtie2 v2.3.5.1.
Strand specific bigWig coverage tracks of 3' positions were generated using deepTools bamCoverage v3.1.3.
Alignments were deduplicated using umi_tools dedup v1.0.0.
Genome_build: dm6
Supplementary_files_format_and_content: bigWig files of UMI-deduplicated strand-specific raw signal (3' ends of PE alignments) as well as bigWig files of UMI-deduplicated replicate-pooled strand-specific spike-in normalized signal.

extract_protocol:
For PRO-seq, we started with 2 × 10e7 cells per condition, and spiked in 2.7 × 10e5 human K562 cells to facilitate spike-in normalization immediately after harvest. Cells were pelleted at 4 °C and washed with ice-cold PBS, then with wash buffer (10 mM Tris-Cl pH 7.5, 10 mM Kcl, 150 mM Sucrose, 5 mM MgCl2, 0.5 mM CaCl2, 0.5 mM DTT, 1X Pierce Protease inhibitors, and SUPERase-In RNase inhibitor). Cells were then incubated for 5 min on ice in permeabilization buffer (10 mM Tris-Cl pH 7.5, 10 mM Kcl, 250 mM Sucrose, 5 mM MgCl2, 1 mM EGTA, 0.5 mM DTT, 0.05% Tween-20, 1X Pierce Protease inhibitors, and SUPERase-In RNase inhibitor) and > 99% permeabilization was observed using trypan blue staining. Nuclei were then washed twice with wash buffer, and snap frozen in freezing buffer (50 mM Tris-Cl pH 8.0, 40% Glycerol, 5 mM MgCl2, 0.1 mM EDTA, 0.5 mM DTT).
Run-on and PRO-seq library construction was performed as in Mahat et al. 2016 (PMID: 27442863) with some modification. The run-on reaction was performed with biotin-11-UTP and biotin-11-CTP, and ATP and GTP. We substituted MyOne C1 Streptavidin beads for the M280 beads recommended by the protocol, and used 5' and 3' adapters with 6N UMIs at the ligation junction. Libraries were amplified for 11 PCR cycles.


title: NURF301_PROseq_Rep1

description:
7P
nuclear RNA
processed data file: NURF301_PROseq_pooled_normalized_fwd.bw
processed data file: NURF301_PROseq_pooled_normalized_rev.bw


title: BAP170_PROseq_Rep2

description:
6P
nuclear RNA
processed data file: BAP170_PROseq_pooled_normalized_fwd.bw
processed data file: BAP170_PROseq_pooled_normalized_rev.bw


title: K5_Titanium


title: s_RB_input2

description: input for ERF ChIP +dox


title: NURF301BAP170_PROseq_Rep2

description:
10P
nuclear RNA
processed data file: NURF301BAP170_PROseq_pooled_normalized_fwd.bw
processed data file: NURF301BAP170_PROseq_pooled_normalized_rev.bw


title: NURF301BAP170_PROseq_Rep1

description:
9P
nuclear RNA
processed data file: NURF301BAP170_PROseq_pooled_normalized_fwd.bw
processed data file: NURF301BAP170_PROseq_pooled_normalized_rev.bw


title: GAF_PROseq_Rep2

description:
4P
nuclear RNA
processed data file: GAF_PROseq_pooled_normalized_fwd.bw
processed data file: GAF_PROseq_pooled_normalized_rev.bw


title: s_RB_input1

description: input for ERF ChIP -dox


title: s_RB_anti_EF_2


title: K4_Planktonic


title: NURF301_PROseq_Rep2

description:
8P
nuclear RNA
processed data file: NURF301_PROseq_pooled_normalized_fwd.bw
processed data file: NURF301_PROseq_pooled_normalized_rev.bw


title: s_G2

value: anti-ERG (ab92513)


title: GAF_PROseq_Rep1

description:
3P
nuclear RNA
processed data file: GAF_PROseq_pooled_normalized_fwd.bw
processed data file: GAF_PROseq_pooled_normalized_rev.bw


title: GAF_ATACseq_Rep2

description:
4A
processed data file: GAF_ATACseq_pooled_normalized_HS.bw
processed data file: GAF_ATACseq_pooled_normalized_MN.bw
processed data file: ATACseq_peaks_summits_macs2.bed


title: RNA_Clec4fCreDTRNeg_4wkCDAHFD_WholeLiver_rep10

value: Clec4f-cre DTR neg

tag: tissue

value: CDAHFD NASH diet


title: K6_SLIPS

description:
processed data file:
NormalizedCounts_BF SLIPS vs Planktonic.txt
NormalizedCounts_BF Titanium vs BF SLIPS.txt


title: K9_SLIPS


title: K3_SLIPS


title: LACZ_PROseq_Rep2

description:
2P
nuclear RNA
processed data file: LACZ_PROseq_pooled_normalized_fwd.bw
processed data file: LACZ_PROseq_pooled_normalized_rev.bw

value: LACZ


title: LACZ_ATACseq_Rep1

description:
1A
processed data file: LACZ_ATACseq_pooled_normalized_HS.bw
processed data file: LACZ_ATACseq_pooled_normalized_MN.bw
processed data file: ATACseq_peaks_summits_macs2.bed


title: K2_Titanium


title: LACZ_PROseq_Rep1

description:
1P
nuclear RNA
processed data file: LACZ_PROseq_pooled_normalized_fwd.bw
processed data file: LACZ_PROseq_pooled_normalized_rev.bw


title: s_RB_anti_EF_1


title: SK-MES-1_siSC_2

city: Granada

first: Pedro

last: Medina Vico

state: Granada

address: Avenida de Fuente Nueva, s/n

department: Biochemistry and Molecular Biology I

country: Spain

institute: University of Granada

description: Cell line was obtained from a 65-year-old Caucasian male

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data was exported from Illumina GenomeStudio software and processed using R (v 3.2.3) with the packages 'limma' and 'RankProducts'. For background correction, a normal-exponential convolution model using negative control probes was applied. Then, quantile normalization was performed including control probe data. The normalized data were log2-transformed. Probes with detection p-value > 0.05 in all samples were filtered out. For genes with more than one probe, the median expression value was calculated.

label: biotin

source_name: SK-MES-1 cell line, scrambled siRNA control

label_protocol: Biotinylated cRNA was prepared with the Ambion Illumina TotalPrep kit

growth_protocol: Cells were cultured in DMEM with 10% fetal bovine serum, and 1% P/S/A at 37ºC with 5% CO2, 95% O2 and 95% relative humidity

extract_protocol: RNA was extracted using the mirVana miRNA extraciton kit (Thermo Fisher)

treatment_protocol: Cells were subcultured 3 times before the treatment. They were transfected with anti-PKP1 siRNA (siPKP1) or scrambled siRNA (siSC) using Lipofectamine® RNAiMAX.

tag: transfection

value: siRNA

tag: tumor type

value: Lung squamous cell carcinoma

tag: source

value: Metastatic site (pleural effusion)


title: CUP36-F

status: Public on May 09 2020

city: Rochester

first: John

last: Mariani

address: 601 Elmwood Avenue

department: Neurology

institute: University of Rochester

data_processing:
Basecalls were performed using CASAVA version 1.8
Reads were demultiplexed via blctofastq version 1.8.4 and then trimmed and cleaned using Trimmomatic 0.32 with the following paramters: SLIDINGWINDOW:4:20 TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 MINLEN:15.
Reads were then aligned using STAR version 2.5.3a in 2-passes with quantMode set to TranscriptomeSAM to the GRCh38 genome with annotations derived from Ensembl release 91.
Gene and isoform abundances were estimated using RSEM version 1.3.0.
Gene abundances were imported into R via tximport 1.6.0.  Gene names and GC content were obtained via biomaRt 2.34.2.  Low expressing genes were removed if the median of both conditions’ expected counts were below 3.  GC content bias was removed via EDA-Seq 2.12.0.  A DESeq2 object was created using DESeqDataSetFromTximport where size normalized counts were then extracted.  A covariate of unwanted variance was then generated with the RUVs function from RUVSeq 1.12.0 with all genes set as in silico negative controls and k set to 1.  Differential expression between control and cuprizone diet hGPCs was then carried out using DESeq2 1.18.1 with the RUVSeq generated covariate included and betaPrior set to True.  Genes with an adjusted p-value less than 0.05 were deemed significant.  Finally, genes with low abundance were removed if both groups’ averages were below 5.
Genome_build: GRCh38

source_name: Glial Progenitor Cells

growth_protocol: Human fetal glial progenitor cells (PSA-NCAM-/A2B5+) were isolated via MACS from 18-22 week gestational age fetuses and maintained for 1-14 days in DMEM-F12/N1 with 10ng/ml bFGF and 20ng/ml PDGFαα.  Immunodeficient homozygous rag1-null mice were then transplanted with 200,000 hGPCs into their corpora callosa at P1.

extract_protocol:
Cells were lysed and prepared for library prep input via Prelude Direct Lysis Module
RNA libraries were prepared using Nugen Ovation V2 library prep kits

treatment_protocol: Mice were fed either a control diet for 36 weeks before sacrifice or a diet consisting of 0.2% cuprizone (w/w) beginning at 12 weeks until 24 weeks of age.  Mice were allowed to recover for 12 weeks on a control diet before sacrifice.  Corpora callosa of mice were extracted and pooled as pairs, dissociated, before FACS isolation of human glial progenitor cells defined by expression of human specific PDGFRα.

value: Glial Progenitor Cells

tag: diet

value: Cuprizone


title: CUP36-E


title: CUP36-B


title: CUP36-D


title: CUP36-C


title: CUP36-A


title: SK-MES-1_siPKP1_2

source_name: SK-MES-1 cell line, PKP1 inhibition by siRNA


title: SK-MES-1_siSC_1


title: CTR36-C


title: SK-MES-1_siPKP1_1


title: CTR36-D


title: CTR36-E


title: CTR36-F


title: CTR36-B


title: CTR36-A


title: ws998M18_H3K27ac_ChIPSeq

city: Saarbrücken

first: Tim

last: Kehl

address: Campus E2.1, P.O. box 151150

department: Center for Bioinformatics

institute: Saarland University

description: ChIP-Seq (H3K27ac) of primary Wilms tumor cells.

data_processing:
Base calling was performed using the Illumina HiSeq2500 build-in RTA (Real-Time Analysis) Software.
Low quality ends (phred score=20) of FastQ format reads were trimmed in addition to adapter removal using Trim Galore (version 0.3.3) [http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/].
Trimmed reads were aligned to the human reference genome (hs37d5) using GEM mapper (version 1.376 beta, doi: 10.1038/nmeth.2221).
Samtools (version 1.3, 10.1093/bioinformatics/btp352) was used to convert SAM to BAM format.
MarkDuplicate (version 1.115) from Picard tools [http://broadinstitute.github.io/picard/] was used to mark PCR duplications.
Peaks were called using the narrow option of MACS2 (version 2.1.1): Minimum FDR (q-value) cutoff for peak detection = 0.05.
Genome_build: hs37d5
Supplementary_files_format_and_content: BED and BEDGRAPH (.bdg) files were generated using the MACS2 peak caller. Output file formats are described on the MACS2 github page (https://github.com/taoliu/MACS).

source_name: Primary Wilms tumor cells

growth_protocol: All primary WT cell cultures were maintained in Dulbecco's Modified Eagle Medium supplemented with 10% fetal calf serum and 1% penicillin/streptomycin.

extract_protocol:
Chromatin preparation was performed using the NEXSON protocol (doi:10.1093/nar/gkv1495) with some modifications. Up to and including immunoprecipitation all buffers were supplemented with Complete Protease Inhibitor Cocktail (Roche) and 10 mM Sodiumbutyrate (Sigma-Aldrich, St. Louis, USA). Briefly, fixed cells were resuspended in 1 ml Farnham lab buffer (5 mM PIPES pH 8, 85 mM KCl, 0.1% Igepal CA-630) and sonicated in a Bioruptor NGS (Diagenode) with 3 cycles (15 s on and 30 s off) in high power mode using standard 1.5 ml tubes. After centrifugation nuclei were resuspended in shearing buffer (10 mM Tris-HCl (pH 8), 0.1% SDS, 1 mM EDTA) and chromatin was sonicated into fragments between 100 and 800 bp using 1.5 ml microtubes with caps (Diagenode, C30010016) for 6 cycles (30 s on and 30 s off) in high power mode. For each immunoprecipitation 10 µl protein G beads (Invitrogen) were combined either with 2 μg H3K4me3 (Diagenode, C15410003-50) or H3K27ac antibody (C15410196) and 5 μl BSA (NEB, 10 mg / ml) and rotated for 2 h at 4 °C. Then, 80 µl sheared chromatin (equal to approx. 106 cells) diluted with double volume dilution buffer (25 mM Tris-HCl (pH 8.0), 150 mM NaCl, 1 mM EDTA, 1 % Triton X-100, 0.75 % Glycerol) were added. After immunoprecipitation overnight beads were consecutively washed with 1 ml of WB1 (20 mM Tris-HCl, (pH 8.0), 150 mM NaCl, 2 mM EDTA, 1 % Triton X-100, 0.25 % SDS), twice WB2 (20 mM Tris-HCl (pH 8.0), 500 mM NaCl, 2 mM EDTA, 1 % Triton X-100, 0.25 % SDS), WB3 (10 mM Tris-HCl, (pH 8.0), 250 mM LiCl, 1 mM EDTA, 0.5 % Nonident P-40, 0.5 % Sodiumdesoxycholate) and twice Tris Buffer  (10 mM Tris-HCl (pH 8.0)) under rotation for 10 min at 4 °C.
Library construction was performed as previously described (doi:10.1038/nmeth.3542) with modifications. In brief, immunoprecipitated chromatin bound to beads was incubated in 25 µl tagmentation mix containing 1 µl Nextera Tn5 (Illumina, FC-121-1030) for 10 minutes at 37 °C. Beads were then washed twice with WB1 and TE/NaCl (10 mM Tris-HCl (pH 8.0), 50 mM NaCl, 1 mM EDTA) and eluted in 70 µl elution buffer (10 mM Tris-HCl (pH 8), 300 mM NaCl, 5 mM EDTA, 0.5 % SDS) containing 2 µl proteinase K (Sigma-Aldrich, P6556) over night at 65 °C. After magnetic separation eluates were transferred into fresh tubes, while the beads were resuspended in additional 30 µl elution buffer and incubated for 10 minutes at 65 °C. Eluates were combined, supplemented with 1 µl proteinase K and incubated for 1 hour at 55 °C. Tagmented DNA was purified using the MinElute PCR Purification Kit (Qiagen, 28004) and amplified using 1 X NEBNext® High-Fidelity PCR Master Mix (NEB, M0541S) and 0.2 µM of Nextera PCR primer 1 (AATGATACGGCGACCACCGAGATCTACACTCG TCGGCAGCGTCAGATGTG) and indexed primer 2 (CAAGCAGAAGACGGCATACGAGATNNNNNNNNGTCTCGTGGGCTC GGAGATGT) in a 50 µl reaction with the following PCR conditions: 72 °C for 5 min, 98 °C for 30 s, 12 cycles of 98 °C for 10 s, 63 °C for 30 s, 72 °C for 1 min and a final elongation at 72 °C for 7 min. Final library clean-up was performed with 1 X AMPure XP beads (Beckman Coulter). Libraries were sequenced 2x 50 bp using a v3 paired-end flowcell on a HiSeq2500 system (Illumina).

treatment_protocol: After fixation with 1% formaldehyde for 5 minutes, cross-linking was stopped by adding glycine to a final concentration of 125 mM and incubation for 5 minutes at room temperature. If not mentioned otherwise, samples were kept on ice or at 4° C and centrifugation was performed at 500 x g for 5 minutes at 4° C.

value: Wilms tumor

tag: cell type

value: Cell culture derived from a blastemal mouse xenograft of an originally triphasic tumor

tag: passages

value: H3K27ac (Diagenode, C15410196)


title: ws568li_H3K27ac_ChIPSeq

value: Cell culture derived from primary cells of an originally stromal tumor that shows mesenchymal characteristics


title: ws998M18_H3K4me3_ChIPSeq

description: ChIP-Seq (H3K4me3) of primary Wilms tumor cells.


title: ws568li_H3K4me3_ChIPSeq


title: WT_1: Adar1 Fl/Fl+Veh_rep1

city: Santiago de Compostela

first: Miguel

last: Fidalgo

state: A Coruña

address: Barcelona Avenue s/n-Campus Vida

department: Physiology

institute: Universidade de Santiago de Compostela

data_processing:
Sequences reads were aligned to mouse genome (GRCm38, mm10) with TopHat2 (v2.1.1) and Bowtie2 (v.2.3.0), providing a GTF reference genome for mapping (-G)
Transcript assembly and diferential expression analysis was performed by cufflinks (v.2.2.1) following default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files including FPKM values for each sample.

source_name: MEF+OSKM d7

extract_protocol:
Total RNA was extracted using TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols. Briefly, rRNA was removed using Ribo-Zero kit. RNA was fragmented randomly by adding fragmentation buffer and cDNA was synthesized. Finally, sequencing adaptor ligation was performed and the double-stranded cDNA library was completed through size selection and PCR enrichment.

tag: initial cell type

value: Mouse embryonic fibroblast

tag: reprogramming day


title: KO_2: Adar1 Fl/Fl+4OHT_rep2


title: WT_2: Adar1 Fl/Fl+Veh_rep2


title: KO_1: Adar1 Fl/Fl+4OHT_rep1


title: K2405

city: Philadelphia

first: Kathrin

last: Bernt

state: PA

address: 3501 Civic Center Boulevard,

institute: Children's Hospital of philadelphia

data_processing:
kallisto to get read counts
DEseq2 to normalize and detect DE genes
star aligner to align reads
star-fusion to detect gene fusion
Genome_build: mm10
Supplementary_files_format_and_content: read counts

source_name: Men1wt MN1-driven leukemic cells

growth_protocol: Men1-/- and Men1wt MN1-driven leukemic cells were isolated from the bone marrow of moribund mice. Cells were plated in methylcellulose.

extract_protocol:
After 7 days in culture, cells were harvested and mRNA was isolated using Qiagen Rneasy kit.
Isolated RNA was sent to Genewiz for library preparation and sequencing.

value: Men1wt MN1-driven leukemic cells


title: K2412


title: K2410


title: K2420

source_name: Men1-/- MN1-driven leukemic cells

value: Men1-/- MN1-driven leukemic cells


title: K2419


title: MUT: Adar1 Fl/E861A+4OHT


title: K2422


title: HET: Adar1 Fl/E861A+Veh


title: NC2

city: Hangzhou

first: xiaodong

last: jin

address: The First Affiliated Hospital

department: Department of Urology

country: China

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

data_processing:
Raw data (raw reads) were processed using Trimmomatic. The reads  containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the  clean reads were mapped to reference genome using hisat2
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count. DEGs were identified using the DESeq[6](2012) R package functions estimateSizeFactors and nbinomTest. Pvalue < 0.05 and foldChange >2 or  fold Change < 0.5 was set as the threshold for significantly differential expression.
Hierarchical cluster analysis of DEGs was performed to explore genes expression pattern. GO enrichment  and KEGG pathway enrichment analysis of DEGs were respectively performed using R  based on the hypergeometric distribution.
Transcript-level quantification, analysis of differentially expressed transcript (DEGs),  cluster analysis, GO and KEGG enrichment
The reads were reassembled using StringTie. Then gene structure extension and novel  transcripts identification were performed by comparing the reference genome and the known  annotated genes using cuffcompare software.
Genome_build: human NCBI genome
Supplementary_files_format_and_content: xlsx mRNA_reads_count

source_name: T24 bladder cancer cell lines

extract_protocol:
total RNA  was extracted with TRIzol® Reagent (Life technologies)
RNA sequencing libraries were prepared from 2μg of total RNA using the KAPA RNA HyperPrep Kit with RiboErase (HMR) for Illumina®（Kapa Biosystems, Inc., Woburn, MA）. Instead of purifying poly-A RNA using poly-dT primer beads, we removed ribosomal RNA using the Ribo-Zero rRNA Removal Kit (Illumina, Inc.). Linear RNA was removed using RNase R (Epicentre, Inc). Next, the  RNA was fragmented, and then first-strand and directional second-strand syntheses were performed. Subsequently, a tailing/adapter ligation approach was performed with the purified cDNA. Finally, the purified, adapter ligated DNA was amplified. Each library was diluted to 10 nM and pooled equimolar prior to clustering.All of the steps were performed according to the manufacturer's protocols.

tag: cell line


title: J82

data_processing:
The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15
TMM (trimmed mean of M-values) was used to normalize the gene expression. Differentially expressed genes were identified using the edgeR program. Genes showing altered expression with p < 0.05 and more than 1.5 fold changes were considered differentially expressed
For circRNA expression analysis, the reads were to mapped genome using the STAR and DCC was used to identify the cirRNA and to estimate the circRNA expression
Genome_build: hg19
Supplementary_files_format_and_content: xlsx circRNA_reads_count

source_name: bladder cancer cell lines


title: sh-circRIMS1-3


title: NC3


title: sh-circRIMS1-2


title: T24


title: SV-HUC-1

source_name: immortalized cell line from the urothelium


title: Z2G9V

first: Nathan

last: Lewis

address: 9500 Gilman Dr. MC 0760 BRF2 4a16

department: Pediatrics

institute: UC San Diego

data_processing:
Fastq files for each sample underwent quality control using FastQC (v0.33).
PolyA and adaptor-trimming were conducted using Trimmomatic
Reads were aligned to the gencode annotated (v25) human reference genome (GRCh38) using STAR (v2.4.0)
Alignments were processed to sorted SAM files using SAMtools (v1.7)
HTSeq (v0.6.1) was used to quantify reads
Genome_build: GRCh38
Supplementary_files_format_and_content: polyA_raw_counts: raw count expression matrix for polyA extracted samples; read_coverage_distribution.csv: transcript-wide average read coverage distributions for poly(A) and ribosomal depleted samples. The distribution of read coverage over each gene body was measured using 567 geneBody_coverage.py from the RSeQC (v3.0.0) package 57.

source_name: leukocytes

extract_protocol:
RNA was extracted using either poly(A) or ribosomal depletion
For 47 samples (from 16 individuals), mRNA was extracted using polyA selection with the TruSeq Stranded mRNA library preparation kit (Illumina). Ribosomal depletion was used to prepare an additional 52 samples. Ribosome depletion prepared samples used the TruSeq Stranded Total RNA with RiboZero Gold library preparation kit (Illumina). RNA Integrity Numbers (RIN) were measured using a NanoDrop ND-1000 (ThermoFisher). Poly-A selected samples were sequenced using 50-base pair single end sequencing on a HiSeq4000 (Illumina) to a depth of 25M reads. The ribo-depletion prepared libraries were sequenced using 100-base pair paired end sequencing on a HiSeq4000 (Illumina) to a depth of 50M reads.

value: isolated from whole blood

value: leukocytes

tag: freeze-thaw cycles

tag: rin

tag: fraction

value: ribosomal depleted RNA


title: U6H3B


title: Y2W7Y


title: V7Y3Z


title: S11

description:
read_coverage_distribution.csv
polyA_raw_counts.csv

source_name: industry standard (Clontech-2)

value: industry standard (Clontech-2)

value: polyA RNA


title: NC1


title: U5B9H


title: S1


title: Z3S5Y


title: S13


title: S12


title: V4A4U


title: mouse 4 single peptide

city: Rotterdam

first: Peter

middle: D

last: Katsikis

state: Zuid Holland

address: Dr Molewaterplein 40

department: Department of Immunology

country: Netherlands

institute: Erasmus University Medical Center

description:
RNA seq from purified murine splenocytes CD8+ T cells
m4_onexpep

data_processing:
Illumina Casava1.9 software used for basecalling.
Seuence reads were aligned to the GRCm38 asembly using STAR  2.5.3e with default settings configurations to obtain sorter bam files
Aligned files were annotated with FeatureCount 1.6.1 to obtain the processed files
All quality check, for sequencing, aligment and annotation, were done with MultiQC
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include r-log and RPKM and values for each sample

source_name: spleen

growth_protocol: CD8+ T cells were purified from spleens of OT-I mice by negative selection with magnetic beads (EasySep, Stemcell Technologies). In each well of a 24-well plate, 5x105 of the purified CD8+ T cells/ml were cultured in complete media (RPMI 1640, 10% FBS (Gibco), 1% 2mM L-glutamine (Life Technologies), 1% HEPES (Life Technologies), 1% 100nM Sodium Pyruvate (Life Technologies), 1% non-essential amino acides (Life Technologies), 100U/ml penicillin (Gibco) and 100µg/ml Streptomycin-sulfate (Gibco), 0.05mM Betamercaptoethanol (Sigma)) with IL-15 (5ng/ml,  Peprotech , Cat 210-15) and IL-7 (5ng/ml, Peprotech, Cat 210-07) with or without 10ng/ml OVA(257-264) peptide (Anaspec Cat AS-60193).

extract_protocol:
After 5 days, 1x10E6 live CD8+ T cells were sorted from the three different culture conditions and immediately lysed with TRIzol LS reagent (Life Technologies) and stored at -80°C. RNA was extracted according to manufacturer’s instructions and a bioanalyzer (Agilent) was used to determine the integrity of the extracted RNA. Barcoded sequencing libraries were generated using the KAPA RNA HyperPrep kit (Roche Diagnostics) with RiboErase (HMR) rRNA depletion.
RNA libraries were prepared for sequencing using standard Illumina protocols. Library quality was assessed with the bioanalyzer and KAPA qPCR was performed for quantification.

treatment_protocol: For single peptide stimulation, cells were cultured in the presence of OVA(257-264) peptide for 48 hours. The peptide was then removed by washing the cells two times with complete media. For the remaining 3 days, the cells were cultured in the complete media with cytokines. For repeat peptide stimulation, 10ng/ml OVA(257-264) peptide was added daily for five days. The cells were washed also on day 2 to allow for comparable culture conditions. Unstimulated control cells were cultured in media with cytokines but without adding peptide. Cells from all three conditions were checked daily, and when the cells were confluent, they were split and cultured with fresh complete media containing cytokines.

tag: strain

value: C57BL/6J-OT-I [Tg-(TcraTcrb)1100Mjb/J]

value: spleen

value: purified CD8+ T cells

tag: treatment

value: single OVA peptide stimulation


title: mouse 3 single peptide

description:
RNA seq from purified murine splenocytes CD8+ T cells
m3_onexpep


title: mouse 4 repeat peptide

description:
RNA seq from purified murine splenocytes CD8+ T cells
m4_multipep

value: repeat OVA peptide stimulation


title: mouse 3 no peptide

description:
RNA seq from purified murine splenocytes CD8+ T cells
m3_nopep

value: no stimulation


title: mouse 4 no peptide

description:
RNA seq from purified murine splenocytes CD8+ T cells
m4_nopep


title: sh-circRIMS1-1


title: mouse 3 repeat peptide

description:
RNA seq from purified murine splenocytes CD8+ T cells
m3_multipep


title: S14


title: mouse 2 single peptide

description:
RNA seq from purified murine splenocytes CD8+ T cells
m2_onexpep


title: S15


title: S16


title: Y5A9A


title: S17


title: mouse 2 repeat peptide

description:
RNA seq from purified murine splenocytes CD8+ T cells
m2_multipep


title: mouse 1 single peptide

description:
RNA seq from purified murine splenocytes CD8+ T cells
m1_onexpep


title: mouse 1 no peptide

description:
RNA seq from purified murine splenocytes CD8+ T cells
m1_nopep


title: mouse 2 no peptide

description:
RNA seq from purified murine splenocytes CD8+ T cells
m2_nopep


title: S3


title: S21


title: S19


title: UC.ACTIVE_97_LP [SNAP4]

city: Boston

first: Vanessa

last: Mitsialis

state: MA

address: 300 Longwood Avenue

institute: Boston Children's Hospital

description:
SNAP4
reads.Snap4_LAM_B_S2

data_processing:
For each NextSeq sequencing run, raw sequencing data was converted to demultiplexed FASTQ files using bcl2fastq2 based on Nextera N700 indices corresponding to individual samples/arrays. Reads were then aligned to Hg19 genome using the Galaxy portal maintained by the Broad Institute for Drop-Seq alignment using standard settings. Individual reads were tagged according to the 12-bp barcode sequenced and the 8-bp UMI contained in Read 1 of each fragment. Following alignment, reads were binned onto 12-bp cell barcodes and collapsed by their 8-bp UMI. Digital gene expression matrices (e.g. cells-by-genes tables) for each sample were obtained from quality filtered and mapped reads, with an automatically determined threshold for cell count. UMI-collapsed data was utilized as input into Seurat (https://github.com/satijalab/seurat) for further analysis.
Merging of datasets, clustering, and differential gene expression analyses were performed using Seurat v3.154 (https://satijalab.org/seurat/). In brief, the unique molecular identified (UMI) count matrices from the LP sequencing data of the 5 included subjects were read into Seurat objects. Each Seurat object was subsetted so that only those cells with at least 200 and no more than 2500 features (genes), and no more than 15% mitochondrial-specific genes, were included. Seurat objects were then merged. Count data was scaled using the default scale factor of 10000 and then log-normalized (natural log +1) as per Seurat v3.1 implementation. Then, the top 2000 differentially expressed genes were identified using the vst method and the data was scaled using a linear transformation to enable dimensionality reduction techniques such as PCA and t-SNE.
Genome_build: Hg19
Supplementary_files_format_and_content: .csv file with scaled and normalized count data (all 5 samples merged). Each row is a gene transcript, each column is a cell, labeled SNAP1-5 according to the sample it derived from.

source_name: Colonic lamina propria

extract_protocol:
Cryopreserved mucosal samples (2-3 biopsies/sample, or equivalently-sized pieces of resected surgical tissue, as described in Konnikova et al [PMID 30111863]) were thawed in a 37C rock bath. Biopsy bites were rinsed in 30 mL of ice-cold PBS (ThermoFisher 10010-049) and allowed to settle. Each individual bite was then transferred to 10 mL epithelial cell solution (HBSS Ca/Mg-Free, 10mM EDTA, 100U/ml penicillin, 100mg/mL streptomycin, 10mM HEPES, and 2% FCS [all ThermoFisher]) freshly supplemented with 100uL 0.5M EDTA. Separation of the epithelial layer from the underlying lamina propria was performed for 15min at 37oC at 140rpm in a dry shaking incubator. Samples were placed on ice for 10min, then shaken vigorously 15 times. Visual macroscopic inspection of the tube at this point yielded visible epithelial sheets, and microscopic examination confirmed the presence of single-layer sheets and crypt-like structures. The remnant lamina propria (LP) was carefully transferred into a large volume (30mL) of ice-cold PBS to rinse, and then into 10mL enzymatic digestion mix (Base: RPMI1640, 100U/ml penicillin, 100mg/mL streptomycin, 10mM HEPES, 2% FCS, and 50mg/mL gentamicin [all ThermoFisher]), supplemented with 100mg/mL Liberase TM [Roche] and 100mg/mL DNaseI [Roche]), at 37oC at 120rpm for 30min. During this 30-minute lamina propria (LP) digestion, the epithelial fraction was spun down at 400g for 7 minutes and resuspended in 500 uL of epithelial cell solution. Cells were resuspended in ACK lysis buffer [ThermoFisher A1049201] with gentle resuspension, incubated on ice for 4 minutes, and spun down at 300g for 4 minutes. This step removes red blood cells and was used even if no RBC contamination was visibly observed in order to maintain consistency across samples. Cells were resuspended in TrypLE express enzyme [ThermoFisher 12604013] for 4 minutes in a 37oC bath followed by gentle trituration with a P1000 pipette and filtering into a new conical tube through a 40um cell strainer [Falcon/VWR 21008-949]. Filter was washed with 20mL of ice-cold PBS. Cells were spun down at 300g for 4 minutes and resuspended in 1 mL of epithelial cell solution and placed on ice while final steps of LP dissociation occurred. The LP enzymatic dissociation was quenched with 1mL 100% FCS [ThermoFisher] and 80uL 0.5M EDTA and placed on ice x5min, followed by filtering through 40um cell strainer and rinsing with PBS to 30mL total volume. This tube was spun down at 400 g for 10 minutes and resuspended in 1 mL of ACK and placed on ice for 3 minutes. Cells were spun down at 400 g for 4 minutes and resuspended in 1 mL of epithelial cell solution and spun down at 400 g for 2 minutes and resuspended in 400uL of epithelial cell solution and placed on ice.
Lamina propria samples were run on separate Seq-Well arrays as described in Ordovas-Montanes et al [PMID 30135581] with the improved protocol for library preparation based on second-strand synthesis for cDNA  (S^3) from Hughes et al ("Highly Efficient, Massively-Parallel Single-Cell RNA-Seq Reveals Cellular States and Molecular Features of Human Skin Pathology", BioRx). Two arrays were sequenced per sequencing run with an Illumina 75 Cycle NextSeq500/550v2.5 kit on an Illumina NextSeq at a final concentration of 2.2 pM. The read structure was paired end with read 1 starting from a custom read 1 primer containing 20 bases with a 12-bp cell barcode and 8-bp unique molecular identified (UMI) and read 2 containing 50 bases of transcript information. Read alignment was performed as done previously (in Ordovas-Montanes et al and Hughes et al referenced above). Quality-filtered base calls were converted to demultiplexed FASTQ files and aligned to the Hg19 genome using Cell Ranger on the Galaxy portal maintained by the Broad Institute.

tag: subject status

value: active ulcerative colitis

tag: tissue/cell type

value: Colonic lamina propria


title: UC.ACTIVE_92_LP [SNAP5]

description:
SNAP5
reads.Snap5_LAM_B_S3


title: S20

tag: tissue


title: UC.ACTIVE_70_LP [SNAP3]

description:
SNAP3
reads.Snap3LAM_B_S4


title: S24


title: S23


title: PATU8988S_sgNEG

city: Cold Spring Harbor

middle: D D

last: Somerville

address: 1 Bungtown Road

department: CSHL

institute: Cold Spring Harbor Laboratory

description:
PATU8988S_sgNEG
processed data file:
GATA6_KO_in_PATU8988S.txt

data_processing:
Single-end 50bp or 76bp sequencing reads were mapped to the hg19 or hg38 genome using hisat2 with default settings.
Structural RNAs were masked
Differentially expressed genes were identified using Cuffdiff, normalized to total mapped reads.
Genome_build: hg19 or hg38
Supplementary_files_format_and_content: txt files generated from Cuffdiff

growth_protocol: Human PDA cells were cultured in RPMI with 10%FBS and P/S.

extract_protocol:
RNA was extracted using TRIzol following manufacture’s protocol. 2ug total RNA was used for constructing RNA-seq library
RNA-seq libraries were constructed using the Illumina TruSeq sample prep kit v2 following manufacture’s protocol. Briefly, RNA was polyA selected and enzymatically fragmented. cDNA was synthesized using Super Script II master mix, followed by end repair, A-tailing and PCR amplification.

tag: genotype/variation

value: PATU8988S-Cas9 cells infected with a control sgRNA

tag: treatment time

value: Day 20 post infection


title: UC.ACTIVE_62_LP [SNAP1]

description:
SNAP1
reads.Snap1LAM_B_S2


title: S25


title: PATU8988S_sgGATA6_3

description:
PATU8988S_sgGATA6_3
processed data file:
GATA6_KO_in_PATU8988S.txt

value: PATU8988S-Cas9 cells infected with sgRNA targeting GATA6


title: S26


title: PATU8988S_sgGATA6_2

description:
PATU8988S_sgGATA6_2
processed data file:
GATA6_KO_in_PATU8988S.txt


title: S27


title: S28


title: PATU8988S_sgGATA6_1

description:
PATU8988S_sgGATA6_1
processed data file:
GATA6_KO_in_PATU8988S.txt


title: S29


title: mouse 1 repeat peptide

description:
RNA seq from purified murine splenocytes CD8+ T cells
m1_multipep


title: S30

description:
read_coverage_distribution.csv
polyA_raw_counts.csv


title: S18


title: PANC0403_sgSTAT2_D3

description:
PANC0403_sgSTAT2_D3
processed data file:
STAT2_KO_in_PANC0403.txt

value: PANC0403-Cas9 cells infected with sgRNA targeting STAT2

value: Day 7 post infection


title: S22

value: isolated from whole blood

value: leukocytes


title: SUIT2_empty_ZBED2_2

description:
MTV_ZBED2_2_S3
processed data file:
GATA6_ZBED2_cDNA_expression_in_SUIT2.txt

value: lentivirally transduced with ZBED2 cDNA plus empty vector control


title: UC.ACTIVE_46_LP [SNAP2]

description:
SNAP2
reads.Snap2LAM_B_S2


title: SUIT2_empty_empty_2

description:
MTV_MTV_2_S1
processed data file:
GATA6_ZBED2_cDNA_expression_in_SUIT2.txt

value: lentivirally transduced with empty vector control


title: S31

value: polyA RNA


title: SUIT2_empty_ZBED2_1

description:
MTV_ZBED2_1_S2
processed data file:
GATA6_ZBED2_cDNA_expression_in_SUIT2.txt


title: S4


title: SUIT2_empty_empty_1

description:
MTV_MTV_1_S1
processed data file:
GATA6_ZBED2_cDNA_expression_in_SUIT2.txt


title: S33


title: SUIT2_GATA6_ZBED2_2

description:
GATA6_ZBED2_2_S4
processed data file:
GATA6_ZBED2_cDNA_expression_in_SUIT2.txt

value: lentivirally transduced with GATA6 cDNA plus ZBED2 cDNA


title: SUIT2_GATA6_ZBED2_1

description:
GATA6_ZBED2_1_S4
processed data file:
GATA6_ZBED2_cDNA_expression_in_SUIT2.txt


title: S35


title: SUIT2_GATA6_empty_2

description:
GATA6_MTV_2_S2
processed data file:
GATA6_ZBED2_cDNA_expression_in_SUIT2.txt

value: lentivirally transduced with GATA6 cDNA plus empty vector control


title: S34


title: S36


title: SUIT2_GATA6_empty_1

description:
GATA6_MTV_1_S3
processed data file:
GATA6_ZBED2_cDNA_expression_in_SUIT2.txt


title: S37


title: KO3

city: Ann Arbor

first: Ronald

middle: J

last: Koenig

state: MI

address: 1150 West Medical Center Dr

department: Metabolism, Endocrinology & Diabetes

institute: University of Michigan

description:
96510 clone5-2-4
log2RPKM_allSamples.txt

data_processing:
Illumina RTA2 for basecalling
TrimGalore (version 0.4.1) low-quality bases and adapters
STAR (version 2.5.3a) to align reads to the human reference genome
HTseq (version 0.11.2) to assemble aligned reads
edgeR to call differentially expressed genes (fold change > 2.0 and false-discovery rate < 0.05)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: BHT-101 anaplastic thyroid cancer cell line

growth_protocol: Cells were grown in DMEM plus 10% FBS, 1 mM NaPyruvate and Pen-Strep

extract_protocol:
Total RNA was isolated using a Qiagen RNeasy mini kit with DNase1 on-column digestion.
Illumina TruSeq RNA library prep kit, per manufacturer's protocol

tag: ash1l gene

value: premature stop codon after amino acid 2129 both alleles


title: PANC0403_sgSTAT2_D1

description:
PANC0403_sgSTAT2_D1
processed data file:
STAT2_KO_in_PANC0403.txt


title: S39


title: KO4

description:
96509 clone4-14
log2RPKM_allSamples.txt

value: premature stop codon after amino acid 2169 and 2174


title: S40


title: KO1

description:
96508 clone3-11
log2RPKM_allSamples.txt

value: premature stop codon after amino acid 413 both alleles


title: KO2

description:
96507 clone2-11
log2RPKM_allSamples.txt

value: premature stop codon after amino acid 610 both alleles


title: WT3

description:
96506 WT3
log2RPKM_allSamples.txt

value: wild type


title: S5


title: S38


title: S42


title: WT2

description:
96505 WT2
log2RPKM_allSamples.txt


title: WT1

description:
96504 WT1
log2RPKM_allSamples.txt


title: S43


title: S32


title: AsPC1_IRF1_ZBED2_ChIP

data_processing:
50bp single end sequencing reads were mapped to hg19 genome using Bowtie2 using default settings
PCR duplicates were removed from sequencing reads using SAM Tools rmdup.
MACS 1.4.2 was used to call peaks with input genomic DNA as control with other default parameters: 1e-05 Pvalue cutoff for peak detection, 10-30 within MFOLD range
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files converted from wiggle file generated from MACS peaks calling

source_name: AsPC1_ZBED2 cDNA

extract_protocol:
After cross-link, cells were incubated with cell lysis buffer (10mM Tris pH8.0, 10mM NaCl, 0.2% NP-40) and then resuspended and sonicated in nuclei lysis buffer (50mM Tris pH8.0, 10mM EDTA, 1%SDS) for 15mins, followed by ChIP
Library was constructed using Illumina TruSeq ChIP Sample Prep kit following manufacture’s protocol. Briefly, ChIP DNA was end repaired, followed by A tailing and size selection (250-500 bp) by gel electrophoresis. 15 PCR cycles were used for final library amplification and the library was analyzed on Bioanalyzer using high sensitivity DNA chip (Agilent) on Bio-analyzer.

treatment_protocol: Cell cultures were collected and cross-likned with formaldehyde at room temperature for 15 mins.

value: pancreatic ductal adenocarcinoma (PDA) cell line

value: lentivirally transduced with ZBED2 cDNA

tag: chip antibody

value: #8478, Cell Signaling


title: S41

tag: cell type


title: S45

value: industry standard (Clontech-2)


title: S46


title: AsPC1_IRF1_empty_IFNgamma_ChIP

source_name: AsPC1_empty vector and cultured overnight in the presence of 0.2ng/ul IFNgamma

value: lentivirally transduced with empty vector and cultured overnight in the presence of 0.2ng/ul IFNgamma


title: Input_for_AsPC1_IRF1_empty_IFNgamma_ChIP


title: AsPC1_IRF1_empty_control_ChIP

source_name: AsPC1_empty vector and cultured overnight in the presence of control

value: lentivirally transduced with empty vector and cultured overnight in the presence of control


title: Input_for_AsPC1_IRF1_empty_control_ChIP


title: S48

value: isolated from whole blood

value: leukocytes


title: S49


title: SUIT2_FLAG-ZBED2_ChIP

source_name: SUIT2_FLAG-ZBED2 cDNA

value: lentivirally transduced with FLAG-ZBED2 cDNA

value: F1804, Sigma-Aldrich


title: S50

value: polyA RNA


title: Input_for_SUIT2_FLAG-ZBED2_ChIP


title: AsPC1_ZBED2_IFNgamma_rep2

description: processed data file: AsPC1_ZBED2_IFN_treatments.txt

data_processing:
single 50bp sequencing reads were mapped to the hg19 or hg38 genomes using hisat2 with default settings.
Structural RNAs were masked
Differentially expressed genes were identified using Cuffdiff, normalized to total mapped reads.
Genome_build: hg19 or hg38
Supplementary_files_format_and_content: txt files generated from Cuffdiff

source_name: AsPC1_ZBED2 cDNA and cultured overnight in the presence of 0.2ng/ul IFNgamma

value: lentivirally transduced with ZBED2 cDNA and cultured overnight in the presence of 0.2ng/ul IFNgamma

value: 12 hour treatment


title: S51


title: S52


title: AsPC1_ZBED2_IFNgamma_rep1


title: S53


title: Input_for_AsPC1_IRF1_ZBED2_ChIP


title: S54


title: S55


title: AsPC1_ZBED2_IFNbeta_rep1

source_name: AsPC1_ZBED2 cDNA and cultured overnight in the presence of 0.2ng/ul IFNbeta

value: lentivirally transduced with ZBED2 cDNA and cultured overnight in the presence of 0.2ng/ul IFNbeta


title: AsPC1_ZBED2_control_rep2

source_name: AsPC1_ZBED2 cDNA and cultured overnight in the presence of control

value: lentivirally transduced with ZBED2 cDNA and cultured overnight in the presence of control


title: S44


title: AsPC1_ZBED2_IFNbeta_rep2


title: A3J9C

value: ribosomal depleted RNA


title: AsPC1_ZBED2_control_rep1


title: S47


title: AsPC1_empty_IFNgamma_rep1


title: AsPC1_empty_IFNbeta_rep2

source_name: AsPC1_empty vector and cultured overnight in the presence of 0.2ng/ul IFNbeta

value: lentivirally transduced with empty vector and cultured overnight in the presence of 0.2ng/ul IFNbeta


title: A5G5M


title: A8N8M


title: AsPC1_empty_IFNbeta_rep1

value: pancreatic ductal adenocarcinoma (PDA) cell line


title: S2


title: AsPC1_empty_control_rep2


title: B4Z9C


title: S6


title: S7


title: B8Z4F


title: AsPC1_empty_control_rep1


title: C4G5E


title: AsPC1_IRF1_rep1

description: processed data file: IRF1_cDNA_expression_in_AsPC1.txt

source_name: AsPC1_IRF1 cDNA

value: lentivirally transduced with IRF1 cDNA

value: Day 7 post infection


title: AsPC1_IRF1_rep2


title: C7Y3V


title: D8A3T


title: PANC0403_sgIRF1_A2

description: processed data file: IRF1_KO_in_PANC0403.txt

source_name: PANC0403_an sgRNA targeting IRF1 DNA binding domain

value: lentivirally transduced with an sgRNA targeting IRF1 DNA binding domain


title: E6X6M


title: PANC0403_sgIRF1_A1


title: PANC0403_sgNEG_2

source_name: PANC0403_control sgRNA

value: lentivirally transduced with control sgRNA


title: F2D5V


title: PANC0403_sgZBED2_B8

description: processed data file: ZBED2_KO_in_PANC0403.txt

source_name: PANC0403_an sgRNA targeting ZBED2 DNA binding domain

value: lentivirally transduced with an sgRNA targeting ZBED2 DNA binding domain


title: F3H4P

source_name: leukocytes

value: isolated from whole blood


title: PANC0403_sgZBED2_B7


title: S8

value: leukocytes


title: PANC0403_sgNEG


title: F9Z3U


title: G5F8D


title: CISH-KO rep2

first: Huang

last: Zhu

address: 2880 Torrey Pines Scenic Dr.

department: Medicine

institute: University of California-San Diego

data_processing:
Raw image data file from high-throughput sequencing (illumina) was transformed to Sequenced Reads(called Raw Data or Raw Reads) by CASAVA base recognition (Base calling)
Raw sequencing reads were filted as follow: (1) Remove reads containing adaptors;  (2) Remove reads containing N > 10% (N represents base that could not be determined);  (3) The Qscore (Quality value) of over 50% bases of the read is <= 5.
Clean reads were mapped to human genome using STAR software. In order to avoid losing a lot of effective junction reads,  we use STAR software to alignment for RNA-seq sequencing data analysis, the junction reads can be positioned precisely. Reads were mapped to exon, intron and intergenic.
Gene expression level was estimated by the abundance of transcripts(count of sequencing) that mapped to genome or exon. Reads count is proportional to be proportional to gene expression level, gene length and sequencing depth. FPKM (short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) is the most common method of estimating gene expression levels, which takes the effects into consideration of both sequencing depth and gene length on counting of fragments.(Mortazavi et al. 2008).
Genome_build: Homo_sapiens_hg38
Supplementary_files_format_and_content: FPKM values for all the samples

source_name: CISH-KO_NK cells derived from iPSC

growth_protocol: iPSC-NK cells were harvested after they reached maturity and co-cultured with irradiated K562-mbIL-21-4-1BB artificial antigen presenting cells (aAPCs) for expansion with media containing RPMI 1640 and 10% FBS supplemented with 50 units/mL of hIL-2 (Peprotech).

extract_protocol:
Total RNA was isolated from cells using the miRNeasy Kit (Qiagen) according to the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: iPSC derived NK cells

value: CISH-KO

tag: passage

tag: expansion method

value: using K562-41BB-mbIL21


title: CISH-KO rep1


title: F4Q8E


title: G7M9T


title: AsPC1_empty_rep2

source_name: AsPC1_empty vector control

value: lentivirally transduced with empty vector control


title: AsPC1_empty_rep1


title: D7L2Z


title: WT rep1

source_name: WT_NK cells derived from iPSC

value: wild type


title: C3U8Q


title: WT rep2


title: H5U5U


title: abdominal subcutaneous adipose tissue, sample 19

city: Worcester

first: Silvia

last: Corvera

address: 373 Plantation St

institute: University of Massachusetts Medical School

data_processing:
The following pre-processing steps where performed using the Fastx toolkit and PRINSEQ: 7 nt were clipped off from the 5’ end of every read. The reads were then filtered to remove all N-reads. The 3 ́ ends were then trimmed and the reads filtered to minimum Q25 and 50 bp length.
Reads were then mapped with tophat2 to the human genome GRCh38 Ensembl release 77
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample.

source_name: abdominal subcutaneous adipose tissue

extract_protocol:
Total RNA extraction was performed using TriPure Trizol reagent.  Trizol was added to the cells and incubated at room temperature for 5 minutes. Cells were collected into a GentleMACS M tube and dissociated using the GentleMACS Dissociator (Miltenyi Bio) Program RNA01.01. Tubes were centrifuged for 3 minutes at 800RPM and the mixture was transferred to a 2ml collection tube. Chloroform was added in a 1:5 ratio to the tripure/cell mix and tubes were inverted to mix, then incubated at room temperature for 3-5 minutes. Aqueous phase separation was performed, and the RNA-containing layer was mixed with an equal volume of 100% Isopropanol and incubated overnight at -20 degrees for precipitation. RNA was pelleted and washed with 80% ETOH and eluted in nuclease-free water.
cDNA library was prepared using  TruSeq® Stranded mRNA LT Sample Prep Kit according to the manufacturer’s instructions. For each clone, 1 ug of total RNA was used as input to synthesize cDNA which was subsequently amplified. All samples were processed concurrently during library preparation. Illumina sequencing indexes were added to the fragmented libraries and indexed libraries were amplified.

value: abdominal subcutaneous adipose tissue

value: saline


title: abdominal subcutaneous adipose tissue, sample 20

value: norepinephrine


title: H4Z3U

city: La Jolla

value: ribosomal depleted RNA


title: H6D3L


title: abdominal subcutaneous adipose tissue, sample 17


title: abdominal subcutaneous adipose tissue, sample 18


title: abdominal subcutaneous adipose tissue, sample 16


title: H7U8Q


title: J3A7M


title: J3N8R


title: L7C8J


title: AsPC1_empty_IFNgamma_rep2

value: pancreatic ductal adenocarcinoma (PDA) cell line

value: lentivirally transduced with empty vector and cultured overnight in the presence of 0.2ng/ul IFNgamma

value: 12 hour treatment


title: abdominal subcutaneous adipose tissue, sample 14


title: abdominal subcutaneous adipose tissue, sample 15


title: L8Y8V


title: S56

source_name: industry standard (Clontech-2)

value: industry standard (Clontech-2)

value: polyA RNA


title: abdominal subcutaneous adipose tissue, sample 12


title: abdominal subcutaneous adipose tissue, sample 13


title: M3U4G


title: M7J9T


title: abdominal subcutaneous adipose tissue, sample 11


title: supraclavicular adipose tissue, sample 10

source_name: supraclavicular adipose tissue

value: supraclavicular adipose tissue


title: M7Y3Q

value: isolated from whole blood


title: supraclavicular adipose tissue, sample 7


title: M9Q2D

value: leukocytes


title: supraclavicular adipose tissue, sample 8


title: N6D6M


title: supraclavicular adipose tissue, sample 5


title: supraclavicular adipose tissue, sample 9


title: supraclavicular adipose tissue, sample 6


title: Q3E8E


title: mouse 5 repeat peptide

description:
RNA seq from purified murine splenocytes CD8+ T cells
m5_multipep

source_name: spleen

value: C57BL/6J-OT-I [Tg-(TcraTcrb)1100Mjb/J]

value: spleen

value: purified CD8+ T cells

value: repeat OVA peptide stimulation


title: Q9R4U


title: S9

description:
read_coverage_distribution.csv
polyA_raw_counts.csv


title: N6W9J


title: supraclavicular adipose tissue, sample 4


title: supraclavicular adipose tissue, sample 3


title: supraclavicular adipose tissue, sample 2


title: R3N5A


title: R3N7U


title: R6W8B


title: supraclavicular adipose tissue, sample 1


title: hT1.2D_ZBED2

description: processed data file: ZBED2_cDNA_expression_in_15_PDA_cell_lines.txt

source_name: hT1.2D_ZBED2 cDNA

value: lentivirally transduced with ZBED2 cDNA

value: Day 7 post infection


title: hM6.2D_ZBED2

source_name: hM6.2D_ZBED2 cDNA


title: N3A2W


title: T3E8T


title: hM1.2D_empty

source_name: hM1.2D_empty vector control

value: lentivirally transduced with empty vector control


title: hM1.2D_ZBED2

source_name: hM1.2D_ZBED2 cDNA


title: PATU8988S_ZBED2

source_name: PATU8988S_ZBED2 cDNA


title: T5X2N


title: S10


title: PATU8988S_empty

source_name: PATU8988S_empty vector control


title: HPAFII_empty

source_name: HPAFII_empty vector control

value: HPAFII


title: HPAFII_ZBED2

source_name: HPAFII_ZBED2 cDNA


title: s2_plexed_4861: Multiplexed sample 2

city: Montreal

first: Hamed

middle: S

last: Najafabadi

state: QC

address: 740 Dr. Penfield Avenue, Room 7202

department: Human Genetics

country: Canada

institute: McGill University

description: Sample 2, multiplexed together with another sample on one lane of HiSeq 4000 and then demultiplexed by sample index.

data_processing:
Cell Ranger 3.0.0 was run with the default options on each of the four samples (two samples multiplexed on the same lane and the same two samples non-multiplexed).
A joined count table was created, containing the number of read counts observed in each sample for each unique combination of cell-gene-UMI.
Genome_build: hg38
Supplementary_files_format_and_content: Each row corresponds to a unique combination of cell barcode, gene, and UMI. For each sample, the number of read counts corresponding to each combination is reported.

source_name: Sample 2

extract_protocol: Single-cell RNA extraction and library construction was performed using 10X Genomics Chromium Single Cell 3’ Kit v2, according to manufacturers instructions.

tag: multiplexing

value: Multiplexed


title: s1_plexed_4861: Multiplexed sample 1

description: Sample 1, multiplexed together with another sample on one lane of HiSeq 4000 and then demultiplexed by sample index.

source_name: Sample 1


title: T8T3Y

source_name: leukocytes

value: ribosomal depleted RNA


title: s2_nonplexed_4741: Non-multiplexed sample 2

description: Sample 2, sequenced on a separate lane of HiSeq 4000.

value: Non-multiplexed


title: hT2.2D_ZBED2

source_name: hT2.2D_ZBED2 cDNA

tag: cell line

value: pancreatic ductal adenocarcinoma (PDA) cell line


title: S6K2X

tag: freeze-thaw cycles


title: hT2.2D_empty

source_name: hT2.2D_empty vector control


title: T8C6Q

tag: rin


title: s1_nonplexed_4741: Non-multiplexed sample 1

description: Sample 1, sequenced on a separate lane of HiSeq 4000.


title: CFPAC1_ZBED2

source_name: CFPAC1_ZBED2 cDNA


title: CFPAC1_empty

source_name: CFPAC1_empty vector control


title: Expt3_Input-KO clone 4

data_processing:
Illumina RTA2 for basecalling
TrimGalore (version 0.4.1) low-quality bases and adapters
Bowtie2 (version 2.2.9) to align reads to the human reference genome
MACS2 (version 1.1.14) to identify H3K36me2 peaks
Genome_build: hg38
Supplementary_files_format_and_content: broadPeak files were generated by MACS2

source_name: BHT-101 anaplastic thyroid cancer cell line

extract_protocol:
3x10^7 cells were cross-linked with 1% formaldehyde at room temperature for 10 min, quenched with 0.125 M glycine and resuspended in SDS lysis buffer. The cells were sheared twice with a 27-gauge needle and sonicated in a Bioruptor (Diagenode, Denville, NJ) to generate chromatin fragments of 200–600 bp, followed by ChIP using H3K36me2 antibody catalog #ab9049 from Abcam, Cambridge, MA.
The ChIP and input DNA samples were used for library construction (ThruPLEX library prep kit, Takara Bio, Mountain View, CA) and DNA sequencing on an Illumina HiSeq 4000 per the manufacturers’ protocols using 50 nt single-end reads. The wild type and 4 KO samples from three biological replicate experiments were barcoded and run together in five lanes.

value: premature stop codon after amino acid 2169 and 2174

tag: antibody


title: hT1.2D_empty

source_name: hT1.2D_empty vector control


title: Expt3_IP_KO clone 4

value: H3K36me2 antibody catalog #ab9049


title: S2X8A

tag: fraction


title: hM6.2D_empty

source_name: hM6.2D_empty vector control


title: PANC1_ZBED2

source_name: PANC1_ZBED2 cDNA


title: S8P3B


title: PANC1_empty

source_name: PANC1_empty vector control


title: Expt3_IP_KO clone 1

value: premature stop codon after amino acid 413 both alleles


title: MIAPaca2_ZBED2

source_name: MIAPaca2_ZBED2 cDNA


title: Expt3_Input-WT

value: wild type


title: MIAPaca2_empty

source_name: MIAPaca2_empty vector control


title: Expt2_Input-KO clone 4


title: Expt3_IP_WT


title: SUIT2_ZBED2

source_name: SUIT2_ZBED2 cDNA


title: Expt3_Input-KO clone 1


title: Expt2_IP_KO clone 4


title: hF3.2D_ZBED2

source_name: hF3.2D_ZBED2 cDNA


title: Expt2_IP_KO clone 1


title: Expt2_Input-KO clone 1


title: hF3.2D_empty

source_name: hF3.2D_empty vector control


title: CAPAN2_ZBED2

source_name: CAPAN2_ZBED2 cDNA


title: hF2.2D_empty

source_name: hF2.2D_empty vector control


title: CAPAN2_empty

source_name: CAPAN2_empty vector control


title: Expt1_IP_KO clone 4


title: Expt1_Input-KO clone 4


title: Expt2_IP_WT


title: Expt1_Input-KO clone 1


title: BxPC3_empty

source_name: BxPC3_empty vector control


title: Expt1_IP_KO clone 1


title: Expt2_Input-WT


title: AsPC1_ZBED2

source_name: AsPC1_ZBED2 cDNA


title: RTseq_7

city: West Lafayette

first: Damon

last: Lisch

state: IN

address: 915 West State Street

institute: Purdue University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and processed follow the Museq pipeline for TSD identification. Please refer to the following method paper for details: Cost-Effective Profiling of Mutator Transposon Insertions in Maize by Next-Generation Sequencing. Xinyan Zhang, Meixia Zhao and Damon Lisch. Methods in Molecular Biology, 2020, 2072: 39-50.).
For RT-PCR-based quantification of allele frequency, paired SNP-containing sequenced tags were searched against the fastq files for each samples.
Genome_build: AGPv4 B73
Supplementary_files_format_and_content: tab-delimited text files include TSD-coordinates and allele frequency of their nearby genes (counts of reads representing the expression products of either B73 or Mo17 copy in the hybrid plants)

organism: Zea mays

source_name: RT-PCR

extract_protocol:
amplicon-PCR and RT-PCR was perfromed followed by a regular culumn-purification step.
Libraries were prepared using an mRNA preparation kit (Illumina) following a standard protocol (https://www.purdue.edu/hla/sites/genomics/wi-deseq-2/)

value: shoot

tag: genotype

value: B73/Mo17 F1 hybrid

tag: age

value: 6-day-old seedlings


title: RTseq_8


title: RTseq_4


title: Expt1_Input-WT


title: RTseq_5


title: AsPC1_empty

source_name: AsPC1_empty vector control


title: SUIT2_empty

source_name: SUIT2_empty vector control


title: Expt1_IP_WT

source_name: BHT-101 anaplastic thyroid cancer cell line


title: RTseq_6


title: RTseq_2


title: RTseq_3


title: hF2.2D_ZBED2

source_name: hF2.2D_ZBED2 cDNA


title: RTseq_1


title: museq_8


title: BxPC3_ZBED2

source_name: BxPC3_ZBED2 cDNA


title: museq_7


title: ucd65brain scRNA-seq

city: Aurora

last: Kabos

state: CO

address: 12801 E. 17th Avenue

department: Division of Medical Oncology

institute: University of Colorado School of Medicine

data_processing:
UMI count matrices were generated using the 10x genomics CellRanger count (2.1.1) pipeline with default parameters.
The count matrices were combined and normalized using Seurat.
The combined matrix was then further filtered to exclude cells not passing the following QC measures: at least 500 genes detected (UMI > 0) and proportion of UMIs derived from mitochondia less than 7.5% (UCD46) or 15% (UCD4 and UCD65). Cell barcodes identified as murine cells or human-murine doublets after alignment to the mm10 genome were also, discarded, as were cell barcodes with more than 9000 (UCD46) or 8000 genes (UCD4 and UCD65) detected (likely human doublets).
After filtering, this matrix was normalized and used for tSNE projection and graph based clustering. Following cell-embeddings and clustering, the original UMI data was used for all analyses and are provided as per-model count_matrix.tsv.gz tables.
Genome_build: GRCh38
Supplementary_files_format_and_content: Count matrix with UMI counts per gene per cell.

source_name: UCD65 PDX Brain Metastasis

growth_protocol: Breast cancer PDX were derived in female NOD/SCID/ILIIrg−/− (NSG) mice. PDX were transduced with luciferase-gfp lentivirus, regrown into tumors, and processed into single cell suspensions. 1x10^6 viable cells suspended in 0.1 mL PBS were injected into the aorta of female NSG mice to model late stage metastases. For subcutaneous (primary) tumors, cells were placed into mammary fat pads suspended in 50% DMEM/50% Cultrex. Animals were monitored by IVIS imaging biweekly starting at 10 weeks post-injection, and sacrificed at 2-3 months post-injection or when moribund.

extract_protocol:
Single cell suspensions were prepared as described for viral transduction. Human PDX cells were enriched using a mouse cell depletion kit (Miltenyi Biotech). Isolated cells were loaded onto a 10x genomics (San Francisco, CA) controller per manufacturer instructions to generate barcoded single cell GEMs using the 10x genomics 3’ kit.
10x Genomics 3' end library kit

treatment_protocol: All animals were supplemented with subcutaneous silastic pellets containing 17β-estradiol.

tag: metastatic site

value: Brain

value: Human breast tumor


title: Lachit leaf control [24_S25]

city: Dusseldorf

first: Hans-Joerg

last: Mai

address: Universitaetsstrasse 1

department: Institute of Botany

institute: Heinrich Heine University

data_processing:
Basecalls were performed and demultiplexed using bcl2fastq2.
Sequenced reads were trimmed for adapter sequence and masked for low-complexity or low-quality sequence, then mapped to the IRGSP 1.0 reference transcriptome using kallisto.
TSV files with TPM (transcripts per million) values were generated using kallisto.
Average insert length information was extracted from the command line output of kallisto.
Genome_build: IRGSP 1.0
Supplementary_files_format_and_content: TSV files were generated using kallisto. Besides normalized TPM values they contain counts and length information.

organism: Oryza sativa

source_name: L2 leaves of 11-day old Lachit rice plants that were previously grown under control conditions for 2 days

growth_protocol: Plant growth was conducted in a controlled growth chamber, with a 16-hour light/ 8-hour dark cycle, 70 % humidity, a light intensity of 220 µmol*m-2*s-1, a day/night temperature of 26 °C. Rice seeds were disinfected using 1 % sodium hypochlorite for 15 min. Subsequently, seeds were soaked in water for one day at 4 °C and transferred for three days in the dark to 30 °C for germination. Homogenously grown seedlings were transplanted into 1 l pots filled with half-strength modified Hoagland solution for two days. Then, half-strength nutrient solution was replaced with a full-strength solution containing 1 mM calcium nitrate, 2.5 mM potassium nitrate, 2.86 mM ammonium nitrate, 1 mM potassium dihydrogen phosphate, 1 mM magnesium sulfate, 0.045 μM boric acid, 0.009 µM manganese chloride, 0.666 μM zinc sulfate, 0.4 μM copper sulfate, and 0.0176 μM sodium molybdate and 50 µM Fe sodium EDTA, pH 6.2, which also represented the control treatment condition. The nutrient solutions were renewed every second day.

extract_protocol:
RNA was isolated from 100 mg plant material using the RNeasy plant mini kit (Qiagen) according to the manufacturer‘s instructions.
Libraries were constructed with the TruSeq RNA Sample Prep Kit v2 (Illumina Technologies). Double-stranded cDNA was purified for end repair, adaptor ligation, and DNA fragment enrichment.

treatment_protocol: 9-days old plants were treated for two days with Fe stress with full-strength Hoagland medium plus 15 mM Fe sulfate at pH 5.2 was applied or plants were exposed to control conditions (50 µM Fe).

tag: line

value: Lachit (derived from a cross between CRM 13-3241 and Kalinga 2)

value: 11 days

tag: tissue

value: L2 leaves


title: ucd65tumor scRNA-seq

source_name: UCD65 PDX Primary Tumor

value: Primary Tumor


title: Lachit leaf control [23_S24]


title: Lachit leaf control [22_S23]


title: museq_6


title: ucd46tumor scRNA-seq

source_name: UCD46 PDX Primary Tumor


title: Lachit root control [21_S22]

source_name: Roots of 11-day old Lachit rice plants that were previously grown under control conditions for 2 days

value: whole root


title: museq_4


title: museq_3


title: museq_2


title: museq_5


title: ucd46liver scRNA-seq

source_name: UCD46 PDX Liver Metastasis

value: Liver


title: museq_1


title: Soybean leaf V3 rep1

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

data_processing:
The adapter sequences were trimmed from raw sequence reads, and then the RNA sequences were trimmed to the lengths between 18 and 50 nucleotides.
The reads were mapped to the Soy genome (version JGI version2 genome). We used Trimmomatic version for the removal of the adapter sequences.
Genome_build: SoyGenome (version JGI version2)
Supplementary_files_format_and_content: Text containing distinct smallRNAs with their raw abundance after removing the adapter sequences

organism: Glycine max

source_name: leaf

extract_protocol:
RNA-seq library constructed from soybean.
The RNA-seq library was constructed with Illumina TruSeq RNA preparation kit (not stranded)

value: leaf


title: Soybean leaf V3 rep2


title: sgs3-12-1: sgs3-12 mutants rep1

city: shanghai

first: junzhong

last: Liu

state: shanghai

address: 300 Feng Lin Road

department: National Key Laboratory of Plant Molecular Genetics

institute: Institute of Plant Physiology and Ecology, SIBS, CAS

data_processing:
Sequenced reads were trimmed for adaptor sequence, and get rid of ribosome RNA reads and low-quality sequence, then mapped to TAIR10 using Hisat2 (version 2.0.4)
The number of mapped reads of each gene were calculated using Stringtie (version:1.3.0), and normalized by TMM (trimmed mean of M values), and then the FPKM (Fragments Per Kilobase of exon model per Million mapped reads) for each gene were calculated.
Genome_build: TAIR10
Supplementary_files_format_and_content: A single excel include RPKM values and counts for all samples

organism: Arabidopsis thaliana

source_name: sgs3-12 mutants

growth_protocol: The seeds were plated on 1/2 Murashige and Skoog (MS) agar medium and placed at 4°C in darkness for 3 d, and then moved to a growth chamber and incubated at 22°C. One week later, the seedlings were transplanted to the soil and retained at 22°C or transferred to 30°C for heat treatment under long-day conditions (16-h light/8-h dark)

extract_protocol:
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Total RNA was isolated from 4-week-old 22ºC or 30ºC-grown plants.

value: sgs3-12 mutants

value: the fifth true leaves


title: Open flower, rep 1

source_name: flower

value: flower


title: Lachit root control [19_S20]


title: sgs3-12-2: sgs3-12 mutants rep2


title: C2nd-2: unstressed progeny of C30-22 (3rd generation) rep2


title: Hacha leaf control [17_S18]

source_name: L2 leaves of 11-day old Hacha rice plants that were previously grown under control conditions for 2 days

value: Hacha (derived from a cross of CRM 53 X IR 64)


title: Hacha leaf control [18_S19]


title: Unopened flower, rep 1


title: D2-2

city: New York

first: Li

last: Gan

address: 413 East 69th Street, 9th Floor BB904

department: Helen and Robert Appel Alzheimer’s Disease Research Institute

institute: Weill Cornell Medicine

data_processing:
The Illumina BCL output files were processed by the Cell Ranger software (3.1.0, 10x Genomics)
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv, features.tsv and matrix.mtx files were generated by Cell Ranger count.

source_name: microglia isolated from early microglial repopulation mice (switched to ctrl diet for 2d after 14d of PLX5622)

extract_protocol:
Whole brain was dissected, with the cerebellum removed, and homogenized. The homogenates were then processed for myelin depletion using myelin removal beads. The myelin-depleted fraction was incubated with a Cd11b antibody and then Sytox-blue live/dead stain. Live Cd11b+ fraction was sorted using FACS and used to make scRNAseq library.
Single-cell expression libraries were prepared using the 10x genomics Chromium single cell 3′ library and gel bead kit v3 reagents (10x Genomics, PN-1000075)

treatment_protocol: Six C57BL/6 mice (2 brains/sample) were treated with PLX diet (1200 mg/kg) for 14 days (D0). An additional six mice (2 brains/sample) were switched to a control diet for 2 days after PLX treatment (D2). Three age-matched non-treated mice were used as control (Ctrl).

tag: strain

tag: treatment

value: ctrl diet for 2d after 14d of PLX5622


title: D2-3


title: C2nd-1: unstressed progeny of C30-22 (3rd generation) rep1


title: D2-1


title: Hacha leaf control [16_S17]


title: Ovary, rep 1

source_name: Ovary

value: Ovary