title: AML_U-14-1295_500_Cells

value: No DNA isolation


title: WTCHG_129187_07: cortex-Pep1-rep3

status: Public on Aug 10 2020

type: SRA

city: Coventry

first: Patrick

last: Schafer

address: Gibbet Hill Road

department: Life Sciences

country: United Kingdom

institute: University of Warwick

library_source: transcriptomic

data_processing:
Sequenced reads were mapped to Arabidopsis TAIR10 whole genome using tophat v2.0.14 with default parameters --library-type unstranded
Read counts were counted using htseq-count -f bam -s no -i Parent -t mRNA
Genome_build: Arabidopsis thaliana TAIR10
Supplementary_files_format_and_content: read counts from htseq-count

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Root cortex - Pep1 treated

growth_protocol: Arabidopsis thaliana marker lines for 3 cell types, epidermis, cortex and pericycle (list constructs) plants were grown for 10 days on plates

extract_protocol:
For RNA-extraction, GFP-expressing protoplasts were sorted into Qiagen RLT  lysis  buffer  containing  1%  (v:v)  β-mercaptoethanol, mixed, and immediately frozen at -80 °C. At least 10,000 GFP-expressing protoplasts were sorted per experiment and treatment condition.  Sorting times were kept below 25 min.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Marker lines were treated with 1mM flg22, Pep1 or H2O as a mock and incubated for 1 hr

tag: tissue

value: Root cortex

tag: treatment

value: Pep1 treated


title: AML_U-12-0958_500_Cells

city: Columbus

first: Eileen

middle: Yifan

last: Hu

state: OH

address: Rm 449, 410 West 12th Ave

country: USA

institute: The Ohio State University

library_source: genomic

data_processing:
Data were collected and analyzed using the Torrent Server (4462616) with Torrent Suite 5.0 version and 5.6.0.
Variant alleles were called using a combination of the following software:  Variant Caller v.5.0.28 and v.5.6.8-1, IGV v5.01 (0), Ion Reporter v.4.6, Samtools v1.6, Bcftools v1.31 and Ensembl Variant Effect Predictor (VEP) v.92.03.
Genome_build: hg19
Supplementary_files_format_and_content: BAM and VCF files were generated for each sample with Torrent Suite versions 5.0 and 5.6.0 using a combination of the following software: Variant Caller v.5.0.28 and v.5.6.8-1, IGV v5.01 (0), Samtools v1.6, Bcftools v1.31 and Ensembl Variant Effect Predictor (VEP) v.92.03. Excel files showing quanitites of all variant allele frequencies wthin each sample were generated utilizing Ion Reproter version 4.6.

molecule: genomic DNA

organism: Homo sapiens

source_name: CD34+/CD38+ tumor cells sorted from blood

growth_protocol: Blood from CLL and AML patients were collected at The Ohio State University Comprehensive Cancer Center (Columbus, OH, USA). PBMCs were isolated using Ficoll density-gradient centrifugation, Ficoll-Paque Plus (GE Healthcare, Uppsala, Sweden) and cryopreserved. Cryopreserved patient primary PBMCs were thawed and briefly cultured in 37oC and 5% CO2 in RPMI 1640 supplemented with 10% heat-inactivated fetal bovine serum (FBS), 2mM L-Glutamine (Invitrogen, Carlsbad, CA, USA), 56U/mL penicillin, and 56ug/mL streptomycin (Invitrogen) post isolation and before sorting. Cell sorting was performed using a BD Bioscience BD FACSAria™ Fusion flow cytometer with a blue, red, yellow-green, violet, and UV laser (BD Biosciences, San Jose, CA, USA). PBMCs from CLL and AML patients were selected and sorted for with the following antibody cocktail: Brilliant Violet 510 anti-human CD19 (Clone HIB19; #302242, Biolegend, San Diego, CA, USA), Alexa Fluor 700 anti-human CD3 (Clone UCHT1; #344822, Biolegend), PE/Cy7 anti-human CD5 (Clone UCHT2; #364008, Biolegend), PE anti-human CD45 (Clone HI30l; #555483, BD Biosciences), APC anti-human CD45 (Clone HI30; #561864, BD Biosciences), Pacific Blue anti-human Lineage Cocktail (#348805, Biolegend), and LIVE/DEAD Fixable Near-IR Dead Cell Stain (#L34975, Invitrogen, Carlsbad, CA, USA). CLL cells were identified as live, CD3-, CD45+, CD19+, and CD5+ cells. AML leukemic blasts were defined as CD45+ and Lin- cells. Briefly, cryopreserved or fresh mononuclear cells from CLL or AML patients were stained with antibody cocktail on ice for half an hour before being washed once and resuspended in DPBS at a concentration of 5 million cells/mL (Gibco, Grand Island, NY, USA). Cells were sorted through an 85um nozzle at a sheath pressure of 45 psi and a drop drive frequency of 60-70 kHz. A highly pure sorting modality (single-cell sorting for FACSAria Fusion) was used for cell numbers less than 1000 into PCR strip tubes. 4-way purity sorting was used for bulk samples (defined as >20000 cells) into 1.5mL Eppendorf tubes.

extract_protocol:
For bulk tumor samples DNA was extracted from isolated CLL and AML cells using the Puregene Core kit A DNA extraction kit (# 158667, Qiagen, Maryland, USA) according to manufacturer recommendations for <1 million cells (Gentra Puregene Handbook).  DNA was quantified using spectrophotometric methods (Nanodrop 2000 from Thermo Scientific) using standard 260/280 OD ratios. 10ng of DNA from bulk samples are used for first step amplification. For low cell number samples (defined as <1000 sorted cells) DNA was prepared from sorted cells using the Single Cell Lysis Kit (#4458235, Invitrogen). Briefly, 9uL of Single Cell Lysis solution (no Dnase I) was directly added to sorted cell droplet. After incubating for 5 minutes at room temperature 1uL of Stop Solution was added to the reaction for 2 minutes at room temperature. 5uL of the total reaction is used for first step amplification.
Libraries were prepared with Ion AmpliSeq Library kit2.0 (4475345) with a custom designed panel of AmpliSeq primers (CLL: IAD14429, 304 amplicons, 2 pools, 31.66kb panel size, 99.63% coverage; AML: IAD145356, 129 amplicons, 2 pools, 15.32kb panel size, coverage 100%; Supplementary Table 1, 2). To run multiple samples on the same chip we used IonExpress barcode adapters (kit#4471250 and #4474009). Libraries were constructed by first amplifying genomic DNA preparations with individual primer pools. Amplification was completed on the GeneAmp PCR system 9700 Dual 96-well thermal cycler from Applied Biosystems, using the following protocol: Initial Hold 99oC-2min followed by 21 cycles for the CLL panel (99oC-15sec, 60oC-4min), 20 cycles for the AML panel (99oC-15sec, 60oC-4min), and a final hold of 10oC. Corresponding PCR product pools were then combined and barcoded with IonExpress barcode adapters. Barcoded PCR products were purified with Agencourt AMPure XP kit (A63881 Beckman Coulter, Indianapolis, Indiana). While bulk extracted DNA libraries were eluted with low TE at this point and directly quantified, libraries constructed with <1000 cells underwent an additional amplification cycle to equalize library amounts using the following protocol: Initial hold of 98oC-2min followed by 5 cycles  (99oC-15sec, 64oC-1min) and a final hold of 10oC. All libraries were quantified using real time PCR with Ion Library TAQMAN Quantitation kit 44688022 on the Applied Biosystems ViiA7 Real Time PCR System instrument to allow for optimal final dilution of library for template preparation.

value: Blood

tag: tumor type

value: acute myeloid leukemia

tag: cell type

tag: cell number

tag: extract protocol


city: Charlottesville

first: Stephen

last: Turner

state: VA

address: 1670 Discovery Drive

institute: Signature Science, LLC

description: total RNA-seq from sample S11 CS status C. scindens (ATCC(R) 35704)  Mus musculus

data_processing:
Transcript-level quantitation with Salmon
Gene level summarization with txImport
Normalization with DESeq2
Differential expression with DESeq2
Genome_build: Ensembl GRCm38
Supplementary_files_format_and_content: normalized gene level counts for GRCm38 genes

organism: Mus musculus

source_name: Granulocyte macrophage progenitors

growth_protocol: Five week old male CBA/J mice (Jackson Laboratories or RAG 1 KO mice (Jackson Laboratories) were housed in a specific pathogen?free facility in micro isolator cages and provided autoclaved food (Lab diet 5010) and water ad libitum. Specific pathogen free status was monitored quarterly. A sentinel mouse was removed from each room and was humanely euthanized for serologic evaluation, examination of pelage for fur mites, and examination of cecal contents for pinworms. The serologic assays, conducted in-house using CRL reagents, are MHV, EDIM, GD-7, MVM, MPV, and MNV, (Sendai, PVM, RPV/ KRV/H-1, M. pulmonis). In the final quarter, a comprehensive serology was performed which included the above agents plus K-virus, MCMV, MTV, LCM, Ectromelia, Polyomavirus, Reovirus-3, and mouse adenoviruses (K87 and FL). All procedures were approved by the Institutional Animal Care and Use Committee of the University of Virginia. All experiments were performed according to provisions of the USA Animal Welfare Act of 1996 (Public Law 89.544).

extract_protocol:
RNA was isolated  from approximately 17,000 sorted GMPs  utilizing the Qiagen RNeasy Micro Kit.
Ribosomal reduction was performed to concentrate for mRNA. Directional cDNA libraries were generated and samples sequenced in multiplex (50PE reads) using the Illumina HiSeq v4 platform. For library prep, the NEBNext(R) Ultra? Directional RNA Library Prep Kit for Illumina(R) and NEBNext(R) rRNA Depletion Kit (Human/Mouse/Rat) and alternate protocol for  low yield RNA and 15 PCR cycles of amplification was utilized. For sequencing, libraries were sequenced with the NGS NextSeq kit - 150 cycle High Output Kit, paired end 75x75 bp read.

treatment_protocol: CBA/J mice were colonized with bile acid 7?-dehydroxylating bacteria C. scindens (ATCC(R) 35704) over three weeks prior to intracecal infection with E. histolytica. Mice were gavaged with 100ul of overnight culture at an optical density of 1.4 at 600nm or media control (BHI, Anerobe Systems, AS-872) once per week.

tag: agent

value: C. scindens (ATCC(R) 35704)

tag: strain

value: CBA/J

tag: Sex

value: male


title: CLL_24569_500_Cells

source_name: CD5+/CD19+ tumor cells sorted from blood

value: chronic lymphocytic leukemia


title: WTCHG_129190_01: cortex-Pep1-rep1


title: sample S09 CS status none

description: total RNA-seq from sample S09 CS status none Mus musculus


title: WTCHG_129190_03: cortex-Pep1-rep2


title: CLL_24569_100_Cells

value: CD5+/CD19+ tumor cells sorted from blood


description: total RNA-seq from sample S10 CS status C. scindens (ATCC(R) 35704)  Mus musculus


title: CLL_24569_300_Cells


title: WTCHG_129189_03: cortex-flg22-rep2

source_name: Root cortex - flg22 treated

value: flg22 treated


title: sample S08 CS status none

description: total RNA-seq from sample S08 CS status none Mus musculus


title: CLL_24569_Bulk_Cells

value: DNA isolated with Purgene Core Kit A


title: sorted germcell ChIPseq_St5NC_ScmGLKD_In

city: Baltimore

first: Allan

middle: C

last: Spradling

state: MD

address: 3520 San Martin Dr.

department: Embryology

institute: Carnegie Institution/HHMI

description:
processed data file:
4state_enrichment_counts.txt

data_processing:
RNAseq: reads mapped with Hisat2.1.0, processed with Stringtie1.3.5
RNAseq: raw read counts per gene extracted with htseq0.10.0
ChIPseq: reads mapped with bowtie2.3.2
ChIPseq: MAPQ30 filtered with samtools1.6
ChIPseq: RPM normalized (additionally normalized to spike in if applicaple)
Genome_build: RNAseq: dmel6.02, Ensembl 81; ChIPseq: dmel6.02 (no spike in), dmel6.02/dpse3.0 (D. pseudoobscura spike-in), or dmel6.02/mm10 (mouse spike-in)
Supplementary_files_format_and_content: RNAseq: htseq are text files with raw readcounts, polyA_RNAseq_stringtieO.txt is txt file with TPMs for all genes/samples from stringtie

organism: Drosophila melanogaster

source_name: sorted germcell ChIPseq_FACS purified germ cell

growth_protocol: flies were grown on standard food plus wet yeast paste for 3-6 days

extract_protocol: FACS-purified Drosophila melanogaster germ cells were mixed with either FACS purified Drosophila pseudoobscura follicle cells, mouse embryonic fibroblasts, or in some cases, no spike-in. Sequences were mapped to the D.mel6.02 genome or a hybrid genome of D.mel6.02/D.pse3.0 or D.mel /M.m10 and MAPQ 30 filtered. The ratio of Spike-in to D.mel reads was used to normalize enrichment between IP samples and normalized genome wide read coverage was calculated with Bedtools and supplied as a bigWig file for each sample. Normalized read depth was also was also calculated for overlapping 5kb bins annotated with a 3 or 4 state chromatin model and supplied as a modified bed file.

tag: uas-rnai

value: Scm

value: otu-Gal4, mata-gal4, nos-gal4, UASz-tdTomato

tag: developmental stage

value: 3-6 day old adult

tag: tissue/cell type

value: FACS-purified 64C germ cells

tag: chip antibody

value: Input

tag: spike-in normalization

tag: library construction

value: DNA libraries prepared with Takara Bio ThruPLEX DNA seq


title: Input-2-BN3_S2

city: Indianapolis

first: Mark

middle: H

last: Kaplan

state: IN

address: 635 Barnhill Dr. MS 420

department: Microbiology and Immunology

institute: Indiana University

data_processing:
Libraries were sequenced with 2×75bp paired-end configuration on an Illumina NextSeq 500
Illumina adapter sequences and low-quality base calls were trimmed off the paired-end reads with Trim Galore v0.4.3.
The resulting high-quality reads were aligned to the mouse reference genome mm10 using bowtie2.
Peaks were detected with MACS2 (version 2.1.0) with parameters "-f BAMPE --keep-dup all -B -q 0.01", peaks overlapped with the mm10 blacklist were removed.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: narrowPeak BED files were generated from MACS2

growth_protocol: Naïve T cells culture under Th9 and Th17 condition

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: antibody


title: CLL_24569_50_Cells

value: No DNA isolation


title: sample S07 CS status none

description: total RNA-seq from sample S07 CS status none Mus musculus


title: WTCHG_129189_01: cortex-flg22-rep1

value: Root cortex


title: CLL_24306_500_Cells

value: Blood


title: CLL_24306_Bulk_Cells


description: total RNA-seq from sample S06 CS status C. scindens (ATCC(R) 35704)  Mus musculus


title: CLL_24306_300_Cells


title: sorted germcell ChIPseq_St5NC_ScmGLKD_Pse_H3K27me3

value: H3K27me3 (Cell Signaling C36B11 (#139619) Lot 14)

value: Drosophila pseudoobscura follicle cells


title: WTCHG_129187_05: cortex-mock-rep3

source_name: Root cortex - mock treated

value: mock treated


description: total RNA-seq from sample S04 CS status C. scindens (ATCC(R) 35704)  Mus musculus

value: C. scindens (ATCC(R) 35704)

value: CBA/J

value: male


title: sorted germcell ChIPseq_St5NC_PclGLKD_Pse_H3K27me3

value: Pcl


title: WTCHG_129187_03: cortex-mock-rep2


title: sorted germcell ChIPseq_St5NC_ScmGLKD_Pse_In


title: sorted germcell ChIPseq_St5NC_ScmGLKD_H3K27me3


title: WTCHG_129187_01: cortex-mock-rep1


title: WTCHG_129189_05: cortex-flg22-rep3

value: flg22 treated


title: sample S03 CS status none

description: total RNA-seq from sample S03 CS status none Mus musculus


title: sample S02 CS status none

description: total RNA-seq from sample S02 CS status none Mus musculus


title: sorted germcell ChIPseq_St5NC_PclGLKD_Pse_In


title: CLL_23779_500_Cells

value: chronic lymphocytic leukemia

value: CD5+/CD19+ tumor cells sorted from blood


title: CLL_23779_Bulk_Cells

value: DNA isolated with Purgene Core Kit A


title: CLL_24306_50_Cells


title: CLL_23779_300_Cells


title: sorted germcell ChIPseq_GSC_PclGLKD_Pse_H3K27me3

value: nos-Gal4, UASp-NLS-GFP

value: bam ovary

value: FACS-purified germ cells


description: total RNA-seq from sample S05 CS status C. scindens (ATCC(R) 35704)  Mus musculus


title: sample S01 CS status none

description: total RNA-seq from sample S01 CS status none Mus musculus


title: CLL_23779_100_Cells

value: No DNA isolation


title: CLL_24306_100_Cells


title: CLL_23779_50_Cells


title: sorted germcell ChIPseq_GSC_PclGLKD_Pse_In

value: Input

value: DNA libraries prepared with Takara Bio ThruPLEX DNA seq


title: sorted germcell ChIPseq_GSC_Pse_H3K27me3

value: H3K27me3 (Cell Signaling C36B11 (#139619) Lot 14)


title: sorted germcell ChIPseq_GSC_Pse_In

value: Drosophila pseudoobscura follicle cells


title: CLL_23461_Bulk_Cells

value: Blood


title: Mouse_Con_skin

city: Iowa City

first: Ali

last: Jabbari

state: IA

address: 500 Newton Road

department: Dermatology

institute: University of Iowa

data_processing:
Basecalls were converted into FASTQs using the Illumina bcl2fastq software by the University of Iowa Genomics Division
10x data was processed with the Cell Ranger pipeline, version 3.1
Genome_build: mm10 and GRCh38
Supplementary_files_format_and_content: tab-delimited tsv files for genes and cell barcodes, mtx single-cell expression matrix, csv of CDR3 contig sequences

molecule: polyA RNA

source_name: CD45+ Immune Cells

extract_protocol:
CD45+ immune cell populations were flow sorted in parallel. Single-cell suspensions were processed with the Chromium Single Cell 5-prime Library & Gel Bead Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: skin

tag: condition

value: Control


title: Mouse_Con_lymphnode

tag: tissue

value: lymphnode


title: CLL_23461_500_Cells


title: PcGGLKD RNAseq_bam_E(z)GLKD_3

description:
processed data file:
polyA_RNAseq_stringtieO.txt
ezGLKD_bam_3_TPM

source_name: PcGGLKD RNAseq_whole ovary

extract_protocol: Total RNA prepared from whole ovaries expressing germline-specific RNAi, or from FACS-purified germline stem cells. Sequences were mapped to dmel 6.02 with Hisat2. Whole gene TPMs from Stringtie were aggregated into polyA_RNAseq_stringtieO.txt. For differential analysis, raw read counts from htseq-count were processed with DEseq2 and custom annotation, code at: github.com/ciwemb/polycomb-development

value: E(z)

value: 7-10 day-old adult

value: whole bam ovary

value: polyA-enriched mRNA libraries prepared with Illumina TRUseq v2


title: Mouse_AA_lymphnode

value: AA


title: PcGGLKD RNAseq_bam_E(z)GLKD_2

description:
processed data file:
polyA_RNAseq_stringtieO.txt
ezGLKD_bam_2_TPM


title: Mouse_AA_skin


title: RAD21 Stag1-KO Rep2

city: Chapel Hill

first: Jill

last: Dowen

state: NC

address: 250 Bell Tower Drive

institute: University of North Carolina at Chapel Hill

description: Samples were split across two lanes on the sequencer. These were treated as technical replicates and "L1" and "L2" were concatenated for each sample.

data_processing:
Any samples that were split scross sequencing lanes were treated as technical replicates and "L1" and "L2" were concatenated for each sample. If the sample was paired-end, only the first read of the pair was used for analysis (samples with "R1"). If more than 50bp reads were acquired, only the first 50bp were used in analysis.
Alignment: reads were aligned to a hybrid mm10+hg38 genome with  bowtie v 1.2.2 with parameters -v 2 -p 24 -S -m 1 --best --strata
PCR Duplicate Removal: duplicates removed with samtools v 1.9 fixmate -m followed by markdup -r -s
Peak Calling: peaks were called using MACS (v 2016-02-15) with parameters -f BED -g mm -q 0.01
Spike-In Normalization Factor: reads mapping to each genome (mouse and human) were counted. Normalization factor = 1/(number human reads / 1,000,000)
Coverage File Generation: bigwig files were generated using bedtools (v 2.26) genomecov with parameters -bga -g mm10.chrom.sizes -scale (Normalization Factor) followed by ucsctools (v 320) bedGraphToBigWig
Genome_build: Custom built bowtie index of Mus musculus build mm10 plus Homo sapiens build hg38
Supplementary_files_format_and_content: For each ChIP sample, a BigWig coverage track of merged replicates is provided for viewing in UCSC genome browser.

source_name: mESC v6.5_RAD21 Stag1-KO

growth_protocol: Murine embryonic stem cells (v6.5, male) were grown on gelatinized tissue culture dishes under standard ESC conditions as previously described (Whyte et al., 2012).

extract_protocol:
mESCs were crosslinked in 1% formaldehyde for 5 minutes before quenching with 2.5M glycine. Before chromatin extraction, 5% of HEK293T cells was added to the mESC samples to be later used as a spike-in normalization for the indicated experiments. Crosslinked cells were lysed using Lysis Buffer 1 and Lysis Buffer 2 before washing and resuspension in Shearing Buffer. Sonication of nuclei was performed on a Covaris E220 with the following settings: Duty Factor 5, PIP/W 140, and 200 cycles per burst for 12 minutes. Chromatin fragments of 200-1000 base pairs were generated. The antibodies were incubated with 30uL Protein G Dynabeads for 6 hours prior to addition of chromatin. The chromatin in shearing buffer was spiked with NaCL and Triton X-100 to be in a ChIP buffer. Chromatin from 1 x 10^7 cells was added to antibody conjugated beads and incubated rotating overnight at 4C. Beads were then washed with ChIP Buffer and Wash Buffers 1, 2, and 3. Chromatin was eluted and crosslinks were reversed overnight via incubation at 65C and addition of 5ul Proteinase K. The next day, DNA was purified using a Zymo ChIP DNA Clean and Concentrate kit. Sequencing libraries were prepared using Kapa Hyper Prep Kit.
Sequencing libraries were prepared using Kapa Hyper Prep Kit (Kapa Biosystems, Wilmington, MA).

treatment_protocol: As indicated, cells were counted and 5 x 10^5 were plated per well in 6-well plates. Each well was treated with 50nM of siRNA or siGLO transfection control using DharmaFECT (Dharmacon, Lafayette, CO) transfection reagent following manufacturer’s instructions: siGLO (D-001630-01-0) and siStag1 (M-041989-01-0005). Cell were harvested after 48 hours for crosslinking.

tag: cell line

value: Mouse embryonic stem cells

tag: genotype/variation

value: Stag1 knockout

value: Abcam ab992


title: PcGGLKD RNAseq_bam_E(z)GLKD_1

description:
processed data file:
polyA_RNAseq_stringtieO.txt
ezGLKD_bam_1_TPM


title: CLL_23461_300_Cells

tag: tumor type

value: chronic lymphocytic leukemia

tag: cell type

value: CD5+/CD19+ tumor cells sorted from blood

value: No DNA isolation


title: CLL_23461_100_Cells

tag: cell number

tag: extract protocol


title: CLL_23461_50_Cells


title: RAD21 Stag1-KO Rep1


title: CLL_22341_Bulk_Cells

value: DNA isolated with Purgene Core Kit A


title: PcGGLKD RNAseq_bam_5

description:
processed data file:
polyA_RNAseq_stringtieO.txt
control_bam_8_TPM


title: RAD21 Stag2-KO Rep2

source_name: mESC v6.5_RAD21 Stag2-KO

value: Stag2 knockout


title: PcGGLKD RNAseq_bam_6

description:
processed data file:
polyA_RNAseq_stringtieO.txt
control_bam_9_TPM


title: Liver_8weeks_EtOH_rep1

type: RNA

city: Beijing

first: Jing

last: Lu

address: Beijing, Fengtai District,100071, China

country: China

institute: Academy of Military Medical Sciences

description:
Gene expression after 8weeks EtOH-fed
C4T_8weeks

hyb_protocol: Add 500μL of nuclease-free water to the vial containing lyophilized 10X Blocking  Agent. Mix by gently vortexing. Equilibrate water bath to 60°C. For each microarray, add each of the components as indicated in the tables as below  to a 1.5mL nuclease-free microfuge tube. Mix well but gently on a vortex mixer. Incubate at 60°C for exactly 30 minutes to fragment RNA. Add 2x GEx Hybridization Buffer HI-RPM to the array to stop the fragmentation  reaction. Mix well by careful pipetting. Take care to avoid introducing bubbles. Do not mix on a vortex mixer; mixing on a vortex mixer introduces bubbles. Spin for 1 minute at room temperature at 13,000 rpm in a microcentrifuge to drive the  sample off the walls and lid and to aid in bubble reduction. Place sample on ice and load onto the array as soon as possible. Load a clean gasket slide into the Agilent SureHyb chamber base with the label facing up and aligned with the rectangular section of the chamber base. Ensure that  the gasket slide is flush with the chamber base and is not ajar. Slowly dispense the volume of hybridization sample onto the gasket well in a “drag  and dispense” manner. Slowly place an array “active side” down onto the SureHyb gasket slide, so that the “Agilent”-labeled barcode is facing down and the numeric barcode is facing up. Verify that the sandwich-pair is properly aligned. Place the SureHyb chamber cover onto the sandwiched slides and slide the clamp  assembly onto both pieces. Hand-tighten the clamp onto the chamber. Vertically rotate the assembled chamber to wet the gasket and assess the mobility of  the bubbles. Place assembled slide chamber in rotisserie in a hybridization oven set to 65°C. Set your hybridization rotator to rotate at 10rpm. Hybridize at 65°C for 17 hours.

scan_protocol: Assemble the slides into an slide holder. Place assembled slide holders into scanner carousel. Verify scan settings for one-color scans. Click Scan Slot m-n on the Scan Control main window where the letter m represents the Start slot where the first slide is located and the letter n represents the End slot where the last slide is located.

data_processing: Open the Agilent Feature Extraction (FE) software.Add the images (.tif) to be extracted to the FE Project. Set FE Project Properties. Check the Extraction Set Configuration. Save the FE Project (.fep) by selecting File > Save As and browse for desired location. Select Project > Start Extracting and export data to txt.

source_name: Liver, 8weeks, EtOH, replicate1

label_protocol: Add 200ng of total RNA (2.5μL) to a 1.5mL microcentrifuge tube. Add 0.8 μL of T7 Promoter Primer. Add 2 μL of Spike Mix. Denature the primer and the template by incubating the reaction at 65°C in a circulating water bath for 10 minutes. Place the reactions on ice and incubate for 5 minutes. Immediately prior to use, gently mix the components listed in the following table for the cDNA Master Mix by adding in the order indicated, and put the reaction solution on ice.Briefly spin each sample tube in a microcentrifuge to drive down the contents from  the tube walls and the lid. Return the tubes to ice. Add 4.7μL of cDNA Master Mix to each sample tube and mix by pipetting up and  down. Incubate samples at 40°C in a circulating water bath for 2 hours.  Move samples to a 70°C circulating water bath and incubate for 15 minutes. Move samples to ice. Incubate for 5 minutes. Spin samples briefly in a microcentrifuge to drive down tube contents from the tube  walls and lid. Immediately prior to use, gently mix the components listed in the following table in the  order indicated for the Transcription Master Mix by pipetting at room temperature. Add 6μL of Transcription Master Mix to each sample tube. Gently mix by pipetting.   Incubate samples in a circulating water bath at 40°C for 2 hours.

extract_protocol: Incubate at 37°C for 30 minutes.Add 350μl Buffer RLT, and mix well.Add 250μl ethanol (96–100%) to the diluted RNA, and mix well by pipetting. Do not  centrifuge. Proceed immediately to step 5.Transfer the sample (700μl) to an RNeasy Mini spin column placed in a 2ml collection  tube. Close the lid gently, and centrifuge for 15s at ≥8000 x g (≥10,000 rpm).Discard the flow-through.Add 500μl Buffer RPE to the RNeasy spin column. Close the lid gently, and centrifuge  for 15s at≥8000 x g (≥10,000 rpm) to wash the spin column membrane. Discard the flow-through. Add 500μl Buffer RPE to the RNeasy spin column. Close the lid gently, and centrifuge  for 2min at ≥8000 x g (≥10,000 rpm) to wash the spin column membrane. Place the RNasy spin column in a new 2ml collection tube, and discard the old  collection tube with the flow-through. Close the lid gently, and centrifuge at full speed  for 1min. Place the RNeasy spin column in a new 1.5ml collection tube. Add appropriate RNase-free water (please see report “RNA-QC”) directly to the spin column  membrane. Close the lid gently, and centrifuge for 1min at ≥8000 x g (≥10,000 rpm) to elute the RNA. RNA quantification and quality control (Passed-please see report “RNA-QC”)

treatment_protocol: After the mice were executed, the liver was taken and the liquid nitrogen was quickly frozen

tag: strain

value: Liver

value: male

tag: age

tag: feeding treatment

value: Ethanol

tag: weeks post gavage


title: Liver_4weeks_EtOH_rep1

description:
Gene expression after 4weeks EtOH-fed
C4T_4weeks

source_name: Liver, 4weeks, EtOH, replicate1

tag: Sex


title: CLL_22341_500_Cells

value: Blood


title: Liver_6weeks_EtOH_rep1

description:
Gene expression after 6weeks EtOH-fed
C4T_6weeks

source_name: Liver, 6weeks, EtOH, replicate1


title: PcGGLKD RNAseq_bam_4

description:
processed data file:
polyA_RNAseq_stringtieO.txt
control_bam_7_TPM

tag: uas-rnai

tag: developmental stage

tag: tissue/cell type


title: Liver_6weeks_TH1_rep1

description:
Gene expression after 6weeks TH1-fed
C3T_6weeks

source_name: Liver, 6weeks, TH1, replicate1

value: fed with Klebsiella pneumoniae strain TH1


title: PcGGLKD RNAseq_bam_3

description:
processed data file:
polyA_RNAseq_stringtieO.txt
control_bam_6_TPM

value: 7-10 day-old adult

tag: spike-in normalization

tag: library construction


title: RAD21 WT Rep2

source_name: mESC v6.5_RAD21 WT

value: wild type

tag: chip antibody


title: RAD21 WT Rep1

tag: cell line


title: CLL_22341_100_Cells

tag: tissue


title: Liver_8weeks_TH1_rep1

description:
Gene expression after 8weeks TH1-fed
C3T_8weeks

source_name: Liver, 8weeks, TH1, replicate1


title: PcGGLKD RNAseq_bam_2

description:
processed data file:
polyA_RNAseq_stringtieO.txt
control_bam_5_TPM

value: whole bam ovary

value: polyA-enriched mRNA libraries prepared with Illumina TRUseq v2


title: CLL_22341_300_Cells

tag: tumor type


title: NEU_B

city: Cincinnati

first: Xiaoting

last: Zhu

address: 3333 burnet avenue,MLC7024

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Fastq files were processed using the standard 10x Genomics pipeline.
In brief the propiertary software uses the STAR aligner to align against the reference genome and transcriptome
Reads are then grouped by the cellular barcode. Gene-level counts are finally computed based on unique molecular indentifiers using 10X Genomics Cellranger version3.0.2 with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: tsv files contain barcodes and genes for each sample, the combined files contain the merged data from all samples
Supplementary_files_format_and_content: mtx files contain UMI counts per gene and cell for each sample, the combined files contain the merged data from all samples

source_name: MMTV-Neu driven tumor

growth_protocol: Tumor cells derived from primary tumors were cultured in DMEM/F12 supplemented with 10% FBS, 10ng/ml EGF, 20μgml insulin and 50units/ml penicillin-streptomycin. 4T1 cells were obtained from ATCC and cultured in DMEM supplemented with 10% FBS. 4T1 cells were transduced with pLenti-GFP (LTV-400, Cell Biolabs) before transplantation experiments. FF99WT cells were derived from an autochthonous MMTV-PyMT tumor with FIP200 floxed alleles62 (essentially wild-type without Cre recombinase). FF99WT cells were used to generate the PyMT transplant tumor that was analyzed by scRNA-seq. N148 cells were derived from the autochthonous MMTV-Neu tumor with FIP200 floxed alleles (essentially wild-type without Cre recombinase) that was analyzed by sc-RNAseq.

extract_protocol:
Dissected primary tumors were cut and minced and then incubated in DMEM/F12 supplemented with 5% FBS, 1x antibiotic-antimycotics, gentamycin (20 µg/mL) (all from Invitrogen), collagenase (300 units/mL), and hyaluronidase (100 units/mL) (Worthington Biomedical) for 2 hours at 37 oC. They were then centrifuged at 400 g for 5 minutes, and the pellets were washed with PBS, and suspended in 0.05% trypsin/0.025% EDTA (Invitrogen) before incubated for 5 minutes at 37 oC. An equal volume of DMEM/F12 containing 5% FBS and DNase I (20 units/ml, Roche) was then added to stop the digestion.  After filtering through a 40µm nylon mesh (BD Biosciences), the cells were collected by centrifugation at 400g for 5 min and re-suspended in ACK lysis buffer (Invitrogen) to lyse red blood cells. Tumor single-cell suspensions were incubated with CD24-PE (553262, BD Biosciences), CD31-APC (102410, Biolegend), CD45-APC (103112, Biolegend), Ter119-APC (116212, Biolegend) according to manufacturer’s instructions for 20 minutes at 40C. Following that, cells were then rinsed and resuspended in HBSS before sorting or analysis by FACSAria or FACSCanto instruments (BD Biosciences). For isolation of CD14+ cells, CD14-APC/Cy7 (123317, Biolegend) antibody was used.
Single-cell cDNA libraries were prepared using the 10x Chromium single-cell kit (3’ gene expression platform version 2 chemistry) according to manufacturer’s instructions for each tumor separately.

value: Adult

tag: breast tumor model

value: MMTV-Neu driven tumor

value: Mammary gland tumor

value: FVB/NJ


title: Liver_8weeks_W14_rep1

description:
Gene expression after 8weeks W14-fed
C2T_8weeks

source_name: Liver, 8weeks, W14, replicate1

value: fed with Klebsiella pneumoniae strain W14


title: RAD21 Stag2-KO Rep1

tag: cell type

value: Mouse embryonic stem cells

tag: genotype/variation

value: Abcam ab992


title: CLL_22341_50_Cells

value: chronic lymphocytic leukemia

value: CD5+/CD19+ tumor cells sorted from blood

tag: cell number

tag: extract protocol

value: No DNA isolation


title: PcGGLKD RNAseq_bam_1

description:
processed data file:
polyA_RNAseq_stringtieO.txt
control_bam_4_TPM


title: Liver_6weeks_W14_rep1

description:
Gene expression after 6weeks W14-fed
C2T_6weeks

source_name: Liver, 6weeks, W14, replicate1

tag: strain

value: Liver

value: male

tag: age

tag: feeding treatment


title: Liver_4weeks_W14_rep1

description:
Gene expression after 4weeks W14-fed
C2T_4weeks

source_name: Liver, 4weeks, W14, replicate1

tag: Sex

tag: weeks post gavage


title: HFD Libramed ZT12 Replicate 3

city: irvine

first: Siwei

last: Chen

state: CA

address: 66304 Verano Road South

department: Computer Science

institute: University of California, Irvine

description:
Libramed ZT12_3
HFD Libramed ZT12 Replicate 3
processed data file: Genes.FPKM.tsv

data_processing:
RNA sequencing result aligned to reference assembly mm10 using Tuxedo tophat.
Alignment result quantified by Tuxedo cuffquant.
Read counting for each gene and normalization to FPKM values performed using Tuxedo cuffnorm.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Gene expression results (FPKM values) of the standard RNAseq analysis are reported in the tsv format.

source_name: Liver

extract_protocol:
Total RNA was isolated from liver at the indicated circadian times using TRIzol reagent.
Libraries were prepared from three biological replicates according to the TruSeq RNA Library Prep Kit v2.

treatment_protocol: Mice were treated with vehicle or Libramed for 2 weeks.

value: C57BL/6J background

value: Male

tag: diet

value: High fat

tag: treatment

value: Libramed

tag: time of harvest


title: Liver_8weeks_0_rep1

description:
Gene expression after 8weeks control-fed
C1T_8weeks

source_name: Liver, 8weeks, 0, replicate1

value: negative control (fed with ordinary food)


title: FF99WT_B

source_name: MMTV-PyMT driven tumor

tag: developmental stage

value: Adult

value: MMTV-PyMT driven tumor


title: CLL_20_PostIbrutinib

source_name: CD5+/CD19+ tumor cells sorted from blood

value: Blood

tag: treatment/time-point

value: Post-Ibrutinib


title: Liver_4weeks_0_rep1

description:
Gene expression after 4weeks control-fed
C1T_4weeks

source_name: Liver, 4weeks, 0, replicate1

tag: tissue


title: BRCA1_B

source_name: BRCA1null mammary tumor

value: BRCA1null mammary tumor

value: Mammary gland tumor

value: FVB/NJ


title: CLL_20_PreIbrutinib

tag: tumor type

value: chronic lymphocytic leukemia

value: Pre-Ibrutinib


title: Liver_6weeks_0_rep1

description:
Gene expression after 6weeks control-fed
C1T_6weeks

source_name: Liver, 6weeks, 0, replicate1


title: HFD Libramed ZT12 Replicate 1

description:
Libramed ZT12_1
HFD Libramed ZT12 Replicate 1
processed data file: Genes.FPKM.tsv


title: PcGGLKD RNAseq_ScmGLKD_2

description:
processed data file:
polyA_RNAseq_stringtieO.txt
scmGLKD_Ovary_2_TPM

source_name: PcGGLKD RNAseq_whole ovary

tag: uas-rnai

value: Scm

value: otu-Gal4, mata-gal4, nos-gal4

value: 3-6 day-old old adult, up to stage14

tag: tissue/cell type

value: whole ovary

tag: spike-in normalization

tag: library construction

value: polyA-enriched mRNA libraries prepared with Illumina TRUseq v2


title: PcGGLKD RNAseq_ScmGLKD_1

description:
processed data file:
polyA_RNAseq_stringtieO.txt
scmGLKD_Ovary_1_TPM


title: HFD Control ZT12 Replicate 3

description:
Cntrl ZT12_3
HFD Control ZT12 Replicate 3
processed data file: Genes.FPKM.tsv

value: C57BL/6J background

value: Male

value: Liver

value: High fat

value: Vehicle


title: PcGGLKD RNAseq_ScmGLKD_3

description:
processed data file:
polyA_RNAseq_stringtieO.txt
scmGLKD_Ovary_3_TPM


title: FF99WT_A

data_processing:
Read1 (27bp) and Read2 (147bp) and Index (8bp).
Fastq files were processed using the standard 10x Genomics pipeline.
In brief the propiertary software uses the STAR aligner to align against the reference genome and transcriptome
Reads are then grouped by the cellular barcode. Gene-level counts are finally computed based on unique molecular indentifiers using 10X Genomics Cellranger version 2.2.0 with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: tsv files contain barcodes and genes for each sample, the combined files contain the merged data from all samples
Supplementary_files_format_and_content: mtx files contain UMI counts per gene and cell for each sample, the combined files contain the merged data from all samples

growth_protocol: Tumor cells derived from primary tumors were cultured in DMEM/F12 supplemented with 10% FBS, 10ng/ml EGF, 20μgml insulin and 50units/ml penicillin-streptomycin. 4T1 cells were obtained from ATCC and cultured in DMEM supplemented with 10% FBS. 4T1 cells were transduced with pLenti-GFP (LTV-400, Cell Biolabs) before transplantation experiments. FF99WT cells were derived from an autochthonous MMTV-PyMT tumor with FIP200 floxed alleles (essentially wild-type without Cre recombinase). FF99WT cells were used to generate the PyMT transplant tumor that was analyzed by scRNA-seq. The Neu and BRCA1-null tumors were endogeneous spontaneous mammary tumors for MMTV-Neu and Brca1 F/F; Trp53 F/F; K14-Cre mice respectively.

extract_protocol:
Dissected primary tumors were cut and minced and then incubated in DMEM/F12 supplemented with 5% FBS, 1x antibiotic-antimycotics, gentamycin (20 µg/mL) (all from Invitrogen), collagenase (300 units/mL), and hyaluronidase (100 units/mL) (Worthington Biomedical) for 2 hours at 37 oC. They were then centrifuged at 400 g for 5 minutes, and the pellets were washed with PBS, and suspended in 0.05% trypsin/0.025% EDTA (Invitrogen) before incubated for 5 minutes at 37 oC. An equal volume of DMEM/F12 containing 5% FBS and DNase I (20 units/ml, Roche) was then added to stop the digestion.  After filtering through a 40µm nylon mesh (BD Biosciences), the cells were collected by centrifugation at 400g for 5 min and re-suspended in ACK lysis buffer (Invitrogen) to lyse red blood cells. Tumor single-cell suspensions were incubated with CD24-PE (553262, BD Biosciences), CD31-APC (102410, Biolegend), CD45-APC (103112, Biolegend), Ter119-APC (116212, Biolegend) according to manufacturer’s instructions for 20 minutes at 40C. Following that, cells were then rinsed and resuspended in HBSS before sorting or analysis by FACSAria or FACSCanto instruments (BD Biosciences). CD24+ Lin- (Ter119-, CD31-, CD45-) were sorted for single-cell analysis.
Single-cell cDNA libraries were prepared using the 10x Chromium single-cell kit (3’ gene expression platform version 2 chemistry) according to manufacturer’s instructions for each tumor separately.

treatment_protocol: Tumors were not treated and were harvested when the size was about 1000mm3.

value: Adult

tag: breast tumor model

value: MMTV-PyMT driven tumor


title: NEU_A

value: MMTV-Neu driven tumor

tag: strain


title: CLL_19_PreIbrutinib

value: Blood

tag: cell type

value: CD5+/CD19+ tumor cells sorted from blood

tag: cell number

tag: extract protocol

value: No DNA isolation


title: HFD Control ZT12 Replicate 1

description:
Cntrl ZT12_1
HFD Control ZT12 Replicate 1
processed data file: Genes.FPKM.tsv

tag: Sex


title: BRCA1_A

value: BRCA1null mammary tumor

value: Mammary gland tumor

value: FVB/NJ


title: CLL_19_PostIbrutinib

value: chronic lymphocytic leukemia

value: Post-Ibrutinib


title: CLL_18_PostIbrutinib


title: PcGGLKD RNAseq_Jarid2GLKD_2

description:
processed data file:
polyA_RNAseq_stringtieO.txt
jarid2GLKD_Ovary_2_TPM

value: otu-Gal4, mata-gal4, nos-gal4

value: 3-6 day-old old adult, up to stage14

value: whole ovary

value: polyA-enriched mRNA libraries prepared with Illumina TRUseq v2


title: PcGGLKD RNAseq_Jarid2GLKD_1

description:
processed data file:
polyA_RNAseq_stringtieO.txt
jarid2GLKD_Ovary_1_TPM


title: HFD Libramed ZT0 Replicate 3

description:
Libramed ZT0_3
HFD Libramed ZT0 Replicate 3
processed data file: Genes.FPKM.tsv

value: C57BL/6J background

value: Male

value: Liver

tag: diet

value: High fat

value: Libramed


title: CLL_17_PostIbrutinib

value: Blood


title: PcGGLKD RNAseq_SceGLKD_3

description:
processed data file:
polyA_RNAseq_stringtieO.txt
sceGLKD_Ovary_3_TPM

value: Sce


title: CLL_18_PreIbrutinib

value: Pre-Ibrutinib

value: CD5+/CD19+ tumor cells sorted from blood

value: No DNA isolation


title: HFD Control ZT12 Replicate 2

description:
Cntrl ZT12_2
HFD Control ZT12 Replicate 2
processed data file: Genes.FPKM.tsv

tag: treatment

value: Vehicle


title: PcGGLKD RNAseq_Jarid2GLKD_3

description:
processed data file:
polyA_RNAseq_stringtieO.txt
jarid2GLKD_Ovary_3_TPM


title: HFD Libramed ZT12 Replicate 2

description:
Libramed ZT12_2
HFD Libramed ZT12 Replicate 2
processed data file: Genes.FPKM.tsv

tag: time of harvest


title: Sample_16: TOP2A+/- Nalm 6 - a B cell precusor RNA-seq

city: Newcastle

first: John

last: Casement

address: Framlington Place

department: Bioinformatics Support Unit

institute: Newcastle University

data_processing:
Quality assessment with FastQC Version 0.11.2
Read trimming with FASTX-Trimmer from FASTX-Toolkit version 0.0.13
TPM abundances calculated using Salmon, with index created from GRCh37 release 75 transcripts
Genome_build: GRCh37 release 75
Supplementary_files_format_and_content: A matrix of TPM values for each transcript as a tab delimited text file. TPMs in the matrix are not normalized.

source_name: TOP2A+/- Nalm 6 - a B cell precusor

growth_protocol: Growth in RPMI medium with 10% FBS and 1% penicillin and streptomycin

extract_protocol:
Total RNA extraction using Qiagen RNeasy kit
Illumina's stranded mRNA kit for 100bp paired end reads

value: B cell precursor

tag: genotype

value: TOP2A+/- Nalm 6


title: PcGGLKD RNAseq_SceGLKD_2

description:
processed data file:
polyA_RNAseq_stringtieO.txt
sceGLKD_Ovary_2_TPM

value: otu-Gal4, mata-gal4, nos-gal4

tag: developmental stage


title: PcGGLKD RNAseq_SceGLKD_1

description:
processed data file:
polyA_RNAseq_stringtieO.txt
sceGLKD_Ovary_1_TPM

value: 3-6 day-old old adult, up to stage14


title: 4T1

source_name: 4T1 mammary tumor

value: Adult

value: 4T1 mammary tumor

tag: tissue

value: Mammary gland tumor

value: BALB/C


title: Sample_13: TOP2A+/- Nalm 6 - a B cell precusor RNA-seq


title: CLL_17_PreIbrutinib

tag: tumor type

value: chronic lymphocytic leukemia

tag: treatment/time-point


title: HFD Control ZT0 Replicate 2

description:
Cntrl ZT0_2
HFD Control ZT0 Replicate 2
processed data file: Genes.FPKM.tsv

value: C57BL/6J background

value: Male

value: Liver

value: High fat


title: PcGGLKD RNAseq_PcGLKD_3

description:
processed data file:
polyA_RNAseq_stringtieO.txt
pcGLKD_Ovary_3_TPM

tag: uas-rnai

value: Pc

tag: tissue/cell type

value: whole ovary

value: polyA-enriched mRNA libraries prepared with Illumina TRUseq v2


title: CLL_16_PostIbrutinib

value: Blood

value: Post-Ibrutinib

value: CD5+/CD19+ tumor cells sorted from blood

value: No DNA isolation


title: CLL_16_PreIbrutinib

value: Pre-Ibrutinib


title: CLL_15_PostIbrutinib


title: Sample_14: TOP2A+/- Nalm 6 - a B cell precusor RNA-seq

value: B cell precursor

value: TOP2A+/- Nalm 6


title: Sample_12: TOP2B-/- Nalm 6 - a B cell precursor RNA-seq

source_name: TOP2B-/- Nalm 6 - a B cell precursor

value: TOP2B-/- Nalm 6


title: PcGGLKD RNAseq_PcGLKD_1

description:
processed data file:
polyA_RNAseq_stringtieO.txt
pcGLKD_Ovary_1_TPM

value: otu-Gal4, mata-gal4, nos-gal4

value: 3-6 day-old old adult, up to stage14

tag: spike-in normalization

tag: library construction


title: Sample_11: TOP2B-/- Nalm 6 - a B cell precursor RNA-seq


title: HFD Control ZT0 Replicate 3

description:
Cntrl ZT0_3
HFD Control ZT0 Replicate 3
processed data file: Genes.FPKM.tsv

tag: strain

value: C57BL/6J background

value: Vehicle


title: B16F10-NTC cells implanted tumor-Mouse 2 [RNA-seq]

city: La Jolla

last: Li

state: California

address: 9500 Gilman Dr

department: Pediatrics

institute: University of California, San Diego

description: NTC_2 (RNA-Seq)_S6_L002

data_processing:
Basecalls performed using FastQC v0.11.8
RNA-seq reads and MeRIP reads were aligned to the mm10 genome assembly using STAR aligner version 2.6.
Data were filtered using cutadapt: Phred quality score > 30 and remove adapters
peaks were called using m6A viewer and MACS2 using the following configuration: m6Aviewer: p-value 0.05, min enrichment 2, fdr 0.05, Peak de-convolution running mode ; MACS2: fdr 0.05 with --call-summit option
Raw read gene counts are generated using htseq-count; normalized read gene counts are generated by DESeq2.
Genome_build: GRCm38
Supplementary_files_format_and_content: txt format: contains raw gene counts for RNA-seq samples, xlsx: contains normailzed gene expression by DESeq2; bigBed: contains common peaks detecting by both peak-calling tools

source_name: B16F10-NTC cells implanted tumor-mouse

extract_protocol:
For mice tumors, the freshly dissected tumors were weighed and immediately put into TRIzol Reagent (Thermo Fisher Scientific) for homogenization. The lysates were centrifuged, and the supernatant were proceeded for RNA isolation using Direct-zol RNA Miniprep Plus kit (ZYMO RESEARCH). All the RNAs were treated with DNaseI to avoid DNA contamination.
Total RNA, the immunoprecipitated m6A- containing RNAs and the input RNAs were proceeded for library generation by TruSeq mRNA library prep kit (Illumina).

treatment_protocol: Cancer immunotherapy by PD-1 antibody and GVAX in mice

tag: strain background

tag: genotype/variation

value: B16F10-NTC knockout

value: mouse melanoma cells

tag: passages

value: Mouse tumor after immunotherapy


title: PcGGLKD RNAseq_PcGLKD_2

description:
processed data file:
polyA_RNAseq_stringtieO.txt
pcGLKD_Ovary_2_TPM

value: Pc

value: whole ovary


title: HFD Libramed ZT0 Replicate 1

description:
Libramed ZT0_1
HFD Libramed ZT0 Replicate 1
processed data file: Genes.FPKM.tsv

tag: Sex

value: Male

value: Liver

value: High fat

value: Libramed


title: CLL_14_PostIbrutinib

value: Blood

value: chronic lymphocytic leukemia

value: Post-Ibrutinib

tag: cell type

value: CD5+/CD19+ tumor cells sorted from blood

tag: cell number

tag: extract protocol

value: No DNA isolation


title: B16F10-NTC cells implanted tumor-Mouse 1 [RNA-seq]

description: NTC_1 (RNA-Seq)_S5_L002


title: CLL_14_PreIbrutinib

value: Pre-Ibrutinib


title: HFD Control ZT0 Replicate 1

description:
Cntrl ZT0_1
HFD Control ZT0 Replicate 1
processed data file: Genes.FPKM.tsv

value: C57BL/6J background

tag: diet

tag: treatment

tag: time of harvest


title: B16F10-Fto knockout cells implanted tumor-Mouse 2 [RNA-seq]

description: FTO_2 (RNA-Seq)_S10_L002

source_name: B16F10-Fto knockout cells implanted tumor-mouse

value: B16F10-Fto knockout


title: Sample_10: TOP2B-/- Nalm 6 - a B cell precursor RNA-seq

value: B cell precursor

tag: genotype

value: TOP2B-/- Nalm 6


title: PcGGLKD RNAseq_PclGLKD_2

description:
processed data file:
polyA_RNAseq_stringtieO.txt
pclGLKD_Ovary_2_TPM

value: Pcl

value: otu-Gal4, mata-gal4, nos-gal4

tag: developmental stage

value: 3-6 day-old old adult, up to stage14

value: polyA-enriched mRNA libraries prepared with Illumina TRUseq v2


title: control_siRNA

city: Nagoya

first: Akio

last: Masuda

state: Aichi

address: 65 tsurumai-cho, Showa-ku

country: Japan

institute: Nagoya University Graduate School of Medicine

hyb_protocol: Samples were hybridized with GeneChip mouse exon 1.0 ST Arrays (Affymetrix) and scanned accoding to the manufacture's protocol.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip 3000 7G

data_processing:
The data were background corrected and normalized using the robust multiarray average (RMA) procedure implemented in the Affymetrix Expression Console software. probe group file: MoEx-1_0-st-v1.r2.pgf meta-probeset file: MoEx-1_0-st-v1.r2.dtl.mm9.full.ps
RMA expression value derived from Expression Console software; full-exon analysis

label: biotin

source_name: N2A cells transfected with control siRNA

label_protocol: 100ng of total RNA were used to generate labeled cDNA. Biotinylated DNA probes were prepared using Affymetrix WT Expression kit for Affymetrix Whole Transcript Sense Expression arrays and Affymetrix geneChip WT Terminal Labeling kit according to the manufacture's protocol.

growth_protocol: N2A mouse neuroblastoma cells were grown in MEM with 10% fetal bovine serum at 37 ˚C in 5% CO2.

extract_protocol: Total RNA was harvested from N2A cells in a 10-cm dish transfected with siRNA using Quickgene RNA cultured cell kit (Kurabo) according to the manufacturer’s instructions.

treatment_protocol: N2A cells were transfected with siRNA using Lipofectamine RNAiMAX (Life Technologies) according to the manufacturer’s instructions.

tag: cell line

value: neuroblastoma cell line N2A

tag: sirna

value: control


title: siRNA_FET_2

source_name: N2A cells transfected with siRNA_Fus_2, Ewsr1_2 and Taf15_2

value: Fus_2, Ewsr1_2, and Taf15_2


title: CLL_12_PostIbrutinib

tag: tissue

value: Blood

tag: tumor type

tag: treatment/time-point


title: B16F10-Alkbh5 knockout cells implanted tumor-Mouse 2 [RNA-seq]

description: ALK_2 (RNA-Seq)_S8_L002

source_name: B16F10-Alkbh5 knockout cells implanted tumor-mouse

tag: strain background

value: B16F10-Alkbh5 knockout

tag: tissue/cell type

value: mouse melanoma cells

value: Mouse tumor after immunotherapy


title: Sample_9: TOP2B-/- Nalm 6 - a B cell precursor RNA-seq


title: B16F10-Alkbh5 knockout cells implanted tumor-Mouse 1 [RNA-seq]

description: ALK_1 (RNA-Seq)_S7_L002

tag: genotype/variation

tag: passages


title: PcGGLKD RNAseq_PclGLKD_1

description:
processed data file:
polyA_RNAseq_stringtieO.txt
pclGLKD_Ovary_1_TPM

tag: uas-rnai

value: whole ovary

tag: spike-in normalization

tag: library construction


title: CLL_13_PostIbrutinib

value: chronic lymphocytic leukemia

value: Post-Ibrutinib

tag: cell type

value: CD5+/CD19+ tumor cells sorted from blood

tag: cell number

tag: extract protocol

value: No DNA isolation


title: Sample_8: WT Nalm6 - a B cell precursor  RNA-seq

source_name: WT Nalm6 - a B cell precursor

value: B cell precursor

tag: genotype

value: WT Nalm6


title: CLL_13_PreIbrutinib

value: Pre-Ibrutinib


title: PcGGLKD RNAseq_E(z)GLKD_3

description:
processed data file:
polyA_RNAseq_stringtieO.txt
ezGLKD_YoungOvary_3_TPM

value: E(z)

value: otu-Gal4, mata-gal4, nos-gal4

tag: developmental stage

value: 0-6 hour old adult, up to stage6


title: Sample_7: WT Nalm6 - a B cell precursor  RNA-seq


title: B16F10-Fto knockout cells implanted tumor-Mouse 1 [RNA-seq]

description: FTO_1 (RNA-Seq)_S9_L002

value: B16F10-Fto knockout


title: PcGGLKD RNAseq_E(z)GLKD_2

description:
processed data file:
polyA_RNAseq_stringtieO.txt
ezGLKD_YoungOvary_2_TPM

value: polyA-enriched mRNA libraries prepared with Illumina TRUseq v2


title: CLL_11_PostIbrutinib

value: Blood


title: B16F10-NTC cells implanted tumor-Mouse 2 [IP MeRIP-Seq]

value: B16F10-NTC knockout

tag: merip antibody

value: anti-m6A polyclonal antibody (ab151230, abcam)

tag: experiment type

value: IP MeRIP-Seq


title: siRNA_Fus_1

source_name: N2A cells transfected with siRNA_Fus_1

tag: cell line

value: neuroblastoma cell line N2A

tag: sirna


title: Sample_6: WT Nalm6 - a B cell precursor  RNA-seq


title: CLL_11_PreIbrutinib

tag: tissue

tag: tumor type

value: chronic lymphocytic leukemia

tag: treatment/time-point


title: siRNA_FET_1

source_name: N2A cells transfected with siRNA_Fus_1, Ewsr1_1 and Taf15_1

value: Fus_1, Ewsr1_1, and Taf15_1


title: CLL_12_PreIbrutinib

value: CD5+/CD19+ tumor cells sorted from blood


title: Sample_5: WT Nalm6 - a B cell precursor  RNA-seq


title: VKOR_activity_Exp5

city: Seattle

first: Douglas

last: Fowler

state: WA

address: 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

data_processing:
Library strategy: barcoded variant screen
Libraries were sequenced on NextSeq 500 instruments (Illumina) and base called using the instruments' Real Time Analysis software.
Sequencing reads were converted to fastq format and de-multiplexed with bcl2fastq. Barcode paired sequencing reads for all VKOR abundance and activity replicates were joined using PEAR software (https://cme.h-its.org/exelixis/web/software/pear/). FASTQ files from technical replicate amplification were concatenated for analysis with Enrich2.
The abundance and activity scores for VKOR were calculated as follows: The count for each variant in a bin was divided by the sum of counts recorded in that bin to obtain the frequency of each variant within that bin. This calculation was repeated for every bin in each replicate experiment. The summed counts of each variant in all four bins of an experiment was divided by the summed counts of all variants in all four bins of an experiment to obtain the total frequency value for each variant for each experiment. This total frequency value was used for filtering low-frequency variants out of the subsequent calculations. Next, a weighted average (w_ave) was calculated for each variant, with all weighted average values ranged from a value of 0.25 to 1. Finally, for each experiment, an abundance or activity score for each variant was obtained by subjecting the weighted average of each variant to min-max normalization, using the weighted average value of synonymous variants, which was given a score of 1, and the median weighted average value for non-terminal nonsense variants at positions 21 through 142, which was given an abundance score of 0. The final activity or abundance score for each variant was calculated by taking the mean of the min-max normalized scores across the replicate experiments in which it could have been observed. Only variants which were scored in two or more replicate experiments were retained in the analysis. A standard error for each score was calculated by dividing the standard deviation of the min-max normalized values for each variant by the square root of the number of replicate experiments in which it was observed. Lastly, the lower bound of the 95% confidence interval was calculated by multiplying the standard error with the 97.5 percentile value of a normal distribution and subtracting this product from the abundance score. The upper bound of the 95% confidence interval was calculated by instead adding the product with the score.
Genome_build: NONE
Supplementary_files_format_and_content: The VKOR_barcode_map.tsv.gz  processed data file is in gzip-compressed tab-separated text file format, containing the variant-barcode map determined by subassembly.

source_name: Human-derived cultured cell line

growth_protocol: HEK 293 and HEK293T TetBxb1BFP cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum, 100 U/mL penicillin, 0.1 mg/mL streptomycin, and 2.5 μg/mL doxycycline.

extract_protocol:
Cells were collected, pelleted by centrifugation and stored at −20 °C. Genomic DNA was prepared using a DNEasy kit, according to the manufacturer’s instructions (Qiagen), with the addition of a 30 min incubation at 37 °C with RNAse in the re-suspension step.
Eight 50 μl first-round PCR reactions were each prepared with a final concentration of ~50 ng μl−1 input genomic DNA, 1 × Q5 High-Fidelity Master Mix and 0.25 μM of the KAM499/VKORampR 1.1 primers. The reaction conditions were 98 °C for 30 s, 98°C for 10 s, 65°C for 20 s, 72°C for 60 s, repeat 5 times, 72°C for 2 min, 4°C hold. Eight 50 μl reactions were combined, bound to AMPure XP (Beckman Coulter), cleaned and eluted with 21 μl water. Forty percent of the eluted volume was mixed with Q5 High-Fidelity Master Mix; VKOR_indexF_1.1 and one of the indexed reverse primers, PTEN_seq_R1a through PTEN_seq_R2a, were added at 0.25 μM each. These reactions were run with Sybr Green I on a BioRad MiniOpticon; reactions were denatured for 3 minutes at 95°C and cycled 20 times at 95°C for 15s, 60°C for 15s, 72°C for 15s with a final 3 min extension at 72°C. The indexed amplicons were mixed based in relative fluorescence units and run on a 1% agarose gel with Sybr Safe and gel extracted using a freeze and squeeze column (Bio-Rad). The product was quantified using Kapa Illumina Quant kit.

value: HEK 293 TetBxb1BFP


title: B16F10-NTC cells implanted tumor-Mouse 3 [IP MeRIP-Seq]

tag: strain background

tag: genotype/variation

tag: tissue/cell type

value: mouse melanoma cells

value: Mouse tumor after immunotherapy


title: PcGGLKD RNAseq_E(z)GLKD_1

description:
processed data file:
polyA_RNAseq_stringtieO.txt
ezGLKD_YoungOvary_1_TPM

tag: uas-rnai

value: whole ovary

tag: spike-in normalization


title: VKOR_activity_Exp4

tag: cell type


title: CLL_10_PostIbrutinib

source_name: CD5+/CD19+ tumor cells sorted from blood

value: Post-Ibrutinib

tag: cell number

value: No DNA isolation


title: VKOR_activity_Exp6


title: B16F10-Fto knockout cells implanted tumor-Mouse 2 [IP MeRIP-Seq]

tag: passages


title: CLL_10_PreIbrutinib

value: Pre-Ibrutinib

tag: extract protocol


title: VKOR_activity_Exp3


title: CLL_09_PostIbrutinib


title: B16F10-Alkbh5 knockout cells implanted tumor-Mouse 2 [IP MeRIP-Seq]

value: B16F10-Alkbh5 knockout


title: VKOR_activity_Exp2


title: B16F10-Fto knockout cells implanted tumor-Mouse 1 [IP MeRIP-Seq]

value: B16F10-Fto knockout


title: HFD Libramed ZT0 Replicate 2

description:
Libramed ZT0_2
HFD Libramed ZT0 Replicate 2
processed data file: Genes.FPKM.tsv

source_name: Liver

tag: strain

value: C57BL/6J background

tag: Sex

value: Male

value: Liver

tag: diet

value: High fat

tag: treatment

value: Libramed

tag: time of harvest


title: CLL_09_PreIbrutinib

tag: tissue

value: Blood

value: chronic lymphocytic leukemia


title: B16F10-NTC cells implanted tumor-Mouse 3 [Input_MeRIP-Seq]

value: B16F10-NTC knockout

tag: experiment type


title: B16F10-Alkbh5 knockout cells implanted tumor-Mouse 1 [IP MeRIP-Seq]

tag: merip antibody

value: anti-m6A polyclonal antibody (ab151230, abcam)

value: IP MeRIP-Seq


title: Sample_26_RA0401-_NETs-48h-2

city: Bethesda

middle: R

last: Brooks

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

data_processing:
Reads were demultiplexed and converted to FastQ using Casava 1.8.2 and then mapped to hg19 using Tophat 2.1.0.  RPKM (reads per kilobase million mapped reads) was calculated using Partek GS 6, ANOVA comparisons were computed on Log2 transformed RPKM with a 0.1 offset also using Partek GS.
Genome_build: hg19
Supplementary_files_format_and_content: ANOVA results in Excel format
Supplementary_files_format_and_content: RPKM table in Excel format

source_name: Fibroblast-like synoviocytes

extract_protocol:
Human FLS were isolated from synovial tissue by arthroplasty or synovectomy from OA or RA joints. Cells were treated with NETs for 48 hours and RNA was isolated using Direct-zol RNA Miniprep kit.
cDNA libraries were prepared with poly(A) tail enrichment using NEBNext Ultra II RNA Library Prep Kit following manufacturer instructions (New England Biolabs Ipswich, MA).
RNA-Seq libraries were sequenced on an Illumina Hiseq 3000 as single end with 50 base reads.

value: Fibroblast-like synoviocytes

tag: agent

value: NETs


title: B16F10-NTC cells implanted tumor-Mouse 1 [IP MeRIP-Seq]

tag: strain background

tag: genotype/variation

value: mouse melanoma cells

value: Mouse tumor after immunotherapy


title: VKOR_abundance_Exp7

value: HEK 293T TetBxb1BFP


title: CLL_08_PostIbrutinib

tag: tumor type

tag: treatment/time-point

value: Post-Ibrutinib

value: CD5+/CD19+ tumor cells sorted from blood

value: No DNA isolation


title: VKOR_activity_Exp1

tag: cell type

value: HEK 293 TetBxb1BFP


title: Sample_25_RA0401-_NETs-48h-1


title: Sample_24_RA0401-48h-2


title: CLL_08_PreIbrutinib

value: Pre-Ibrutinib

tag: cell number


title: siRNA_Fus_2

source_name: N2A cells transfected with siRNA_Fus_2

tag: cell line

value: neuroblastoma cell line N2A

tag: sirna


title: Liver_4weeks_TH1_rep1

description:
Gene expression after 4weeks TH1-fed
C3T_4weeks

source_name: Liver, 4weeks, TH1, replicate1

tag: strain

value: Liver

value: male

tag: age

tag: feeding treatment

value: fed with Klebsiella pneumoniae strain TH1

tag: weeks post gavage


title: VKOR_abundance_Exp6


title: B16F10-NTC cells implanted tumor-Mouse 1 [Input_MeRIP-Seq]

value: B16F10-NTC knockout

tag: tissue/cell type

tag: passages


title: VKOR_abundance_Exp5


title: CLL_07_PreIbrutinib

tag: tissue

value: Blood

value: chronic lymphocytic leukemia

tag: extract protocol


title: CLL_07_PostIbrutinib


title: VKOR_abundance_Exp4


title: B16F10-Fto knockout cells implanted tumor-Mouse 1 [Input_MeRIP-Seq]

value: B16F10-Fto knockout

tag: experiment type


title: CLL_06_PostIbrutinib


title: VKOR_abundance_Exp2


title: CLL_06_PreIbrutinib


title: VKOR_abundance_Exp3


title: B16F10-Alkbh5 knockout cells implanted tumor-Mouse 2 [Input_MeRIP-Seq]

tag: strain background

value: B16F10-Alkbh5 knockout


title: B16F10-NTC cells implanted tumor-Mouse 2 [Input_MeRIP-Seq]

tag: genotype/variation

value: mouse melanoma cells


title: VKOR_abundance_Exp1


title: CLL_05_PostIbrutinib

tag: tumor type


title: onco-RNF43/TP53KO w/o Wnt3a-0.2% Rspo rep3

city: Utrecht

first: Madelon

middle: M

last: Maurice

state: Utrecht

address: Heidelberglaan 100

department: Cell Biology

country: Netherlands

institute: UMC Utrecht

data_processing:
Single-end reads of 75 bp were aligned to GRCh37 with STAR [PMID: 23104886] with parameters outSJfilterIntronMaxVsReadN, chimJunctionOverhangMin and chimSegmentMin set to 10000000, 15 and 15, respectively.
Gene expression was quantified with edgeR with the human Ensembl transcript database version 74. Differential gene expression analysis was performed with DESeq2 [25516281], and its ‘rlogTransformation’ function was used for variance stabilization of gene expression data.
Genome_build: GRCh37
Supplementary_files_format_and_content: abundance measurements

source_name: Colon

growth_protocol: Normal human colon organoids were cultured in advanced DMEM/F12 medium (Invitrogen), supplemented with B27 (Invitrogen), Nicotinamide (Sigma-Aldrich), N-acetylcysteine (Sigma-Aldrich), EGF (Peprotech), TGF-β type I receptor inhibitor A83-01 (Tocris), P38 inhibitor SB202190 (Sigma-Aldrich), Wnt3a-CM (50%), Noggin-CM (10%), Rspo1-CM (20%). Mutant TP53 organoids were cultured in the presence of 5 µM Nutlin-3 (Cayman Chemical).

extract_protocol:
Organoids lines were lysed in RLT lysis buffer (Qiagen). RNA was obtained using the Qiagen QiaSymphony SP (Qiagen) according to the manufacturer’s protocol.
RNA-sequencing (RNA-seq) libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s protocol.

treatment_protocol: Organoids were grown in full medium or medium without Wnt and 0.2% Rspo medium for 48h

value: Colon

tag: source

value: Colon organoids


title: Sample_23_RA0401-48h-1

tag: cell type

value: Fibroblast-like synoviocytes

tag: agent


title: CLL_05_PreIbrutinib

extract_protocol:
For bulk tumor samples DNA was extracted from isolated CLL and AML cells using the Puregene Core kit A DNA extraction kit (# 158667, Qiagen, Maryland, USA) according to manufacturer recommendations for <1 million cells (Gentra Puregene Handbook).  DNA was quantified using spectrophotometric methods (Nanodrop 2000 from Thermo Scientific) using standard 260/280 OD ratios. 10ng of DNA from bulk samples are used for first step amplification. For low cell number samples (defined as <1000 sorted cells) DNA was prepared from sorted cells using the Single Cell Lysis Kit (#4458235, Invitrogen). Briefly, 9uL of Single Cell Lysis solution (no Dnase I) was directly added to sorted cell droplet. After incubating for 5 minutes at room temperature 1uL of Stop Solution was added to the reaction for 2 minutes at room temperature. 5uL of the total reaction is used for first step amplification.
Libraries were prepared with Ion AmpliSeq Library kit2.0 (4475345) with a custom designed panel of AmpliSeq primers (CLL: IAD14429, 304 amplicons, 2 pools, 31.66kb panel size, 99.63% coverage; AML: IAD145356, 129 amplicons, 2 pools, 15.32kb panel size, coverage 100%; Supplementary Table 1, 2). To run multiple samples on the same chip we used IonExpress barcode adapters (kit#4471250 and #4474009). Libraries were constructed by first amplifying genomic DNA preparations with individual primer pools. Amplification was completed on the GeneAmp PCR system 9700 Dual 96-well thermal cycler from Applied Biosystems, using the following protocol: Initial Hold 99oC-2min followed by 21 cycles for the CLL panel (99oC-15sec, 60oC-4min), 20 cycles for the AML panel (99oC-15sec, 60oC-4min), and a final hold of 10oC. Corresponding PCR product pools were then combined and barcoded with IonExpress barcode adapters. Barcoded PCR products were purified with Agencourt AMPure XP kit (A63881 Beckman Coulter, Indianapolis, Indiana). While bulk extracted DNA libraries were eluted with low TE at this point and directly quantified, libraries constructed with <1000 cells underwent an additional amplification cycle to equalize library amounts using the following protocol: Initial hold of 98oC-2min followed by 5 cycles  (99oC-15sec, 64oC-1min) and a final hold of 10oC. All libraries were quantified using real time PCR with Ion Library TAQMAN Quantitation kit 44688022 on the Applied Biosystems ViiA7 Real Time PCR System instrument to allow for optimal final dilution of library for template preparation.

tag: treatment/time-point

value: CD5+/CD19+ tumor cells sorted from blood

tag: cell number


title: TP53KO w/o Wnt3a-0.2% Rspo rep3


title: CLL_04_PostIbrutinib_5_2

value: Post-Ibrutinib

value: No DNA isolation


title: WT w/o Wnt3a-0.2% Rspo rep3


title: R52A_MNase-seq_Rep2

city: Oakland

first: Mitchell

middle: Alden

last: Ellison

state: PA

address: Langley Hall

department: Biological Sciences

institute: University of Pittsburgh

description:
R52A_MNase-seq_CombinedReps.bw
R52AvsWT_l2fc_MNase-seq_CombinedReps.bw

data_processing:
Reads contained in FASTQ files were aligned to the genome of the organism used as a spike in using HISAT2.
Reads that did not align to the spike-in genome were aligned to S. cerevisiae genome using HISAT2.
Quality filtering, sorting and file conversion (SAM to BAM) of spike in and S. cerevisiae reads was performed with the SAMtools suite
Spike-in normalization was performed during conversion to bigwig format using deepTools2 as described in Orlando et al. (2014) where the reference adjusted reads-per-million normaliztion method is described.
Data processing and visualization were performed with DANPOS (MNase-seq), deepTools2 (ChIPseq, RNA-seq, 4tU-seq), IGV2.4.13, Prism8 and R Studio.
Genome_build: sacCer3
Supplementary_files_format_and_content: Values presented in bigWig files represent spike-in normalized abundance of RNA/DNA fragments mapped to a particular locus or log 2 fold change (l2fc in file name) values for mutant verses wild-type comparisons.

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae cells

growth_protocol:
cells were grown to mid log phase in SC-W
Yeast strains and media: Saccharomyces cerevisiae strains used in this study are isogenic to FY2, a GAL2+ derivative of S288C. Strains were derived by genetic crosses followed by tetrad dissection or by transformation. S. cerevisiae strains were grown in rich medium (YPD) supplemented with 400 µM tryptophan or synthetic complete (SC) media lacking uracil or the specified amino acids. Unless otherwise noted, transformations were performed with yeast strains lacking endogenous copies of the genes encoding histones H3 and H4 and containing a URA3-marked, wild-type H3-H4 plasmid. By selection on SC-Trp medium containing 0.1% 5-fluoroorotic acid (FOA), URA3 plasmids were shuffled with TRP1-marked CEN/ARS plasmids expressing alanine-substituted histones H3 and H4 (hht2-HHF2 or HHT2-hhf2, respectively) or a TRP1-marked plasmid expressing the wild-type HHT2-HHF2 cassette. Complete plasmid shuffling was ensured by sequential passaging of transformants three times on SC-Trp + 5-FOA media.

extract_protocol:
RNA-seq: Total RNA was isolated from a 9:1 ratio of S. cerevisiae to S. pombe cells by hot acid phenol extraction. RNA was DNase treated (Invitrogen, Carlsbad, CA, AM1907) and sent to the Health Sciences Sequencing Core at UPMC Children’s Hospital for RiboZero (Illumina) treatment, library preparation, and sequencing.
4tU-seq: A RiboPure Yeast RNA extraction kit (Ambion, Austin, TX, AM1926) was used to isolate total RNA from a 9:1 mixture of 4tU-labeled S. cerevisiae and S. pombe cells. After isolation, 4tU-labeled RNA was biotinylated with 1 mg/mL MTSEA Biotin-XX (Biotium, Fremont, CA, #90066) for 30 min at room temperature in biotinylation buffer (20 mM HEPES, 1 mM EDTA). Meanwhile, streptavidin beads (Invitrogen, #65001) were washed in a high salt wash buffer (100 mM Tris, 10 mM EDTA, 1 M NaCl, 0.05% Tween-20) and blocked (high salt wash buffer, 40 ng/uL glycogen) for one hour prior to use. A phenol chloroform extraction was used to quench biotinylation reactions by removing unincorporated biotin. Isopropanol precipitated RNA was resuspended in 100 µL nuclease-free water and incubated with blocked streptavidin beads for 15 min. Supernatant was removed and set aside as unlabeled RNA. Beads were washed twice with elution buffer (100 mM DTT, 20 mM HEPES, 1 mM EDTA, 100 mM NaCl, and 0.05% Tween-20) and samples were pooled for concentration via MinElute columns (Qiagen, #74204).
ChIP-seq: ChIPs were performed on plasmid shuffled derivatives of KY3232 as described above with an antibody against the FLAG epitope (Sigma-Aldrich, 30 µL A2220) to immunoprecipitate FLAG-Rpb3. After immunoprecipitation, crosslink reversal, and pronase digestion, DNA was column purified (Qiagen, Hilden, Germany, #28106) and analyzed by qPCR with Maxima 2X SYBR Master Mix (Thermo Fisher, K0221). After purification of ChIP DNA, S. cerevisiae was mixed 9:1 with FLAG-immunoprecipitated DNA from a K. lactis strain expressing FLAG-tagged Rpb3 from the endogenous locus
MNase-seq: Mononucleosomes were prepared using 100 mL of cells resuspended in FA buffer (50 mM HEPES/KOH, pH 8.0, 150 mM NaCl, 2.0 mM EDTA, 1.0% Triton X-100, and 0.1% sodium deoxycholate), and lysed by bead beating. Cell extracts containing chromatin were pelleted and resuspended in NP-S buffer (0.5 mM spermidine, 0.075% IGEPAL, 50 mM NaCl, 10 mM Tris–Cl, pH 7.5, 5 mM MgCl2, 1 mM CaCl2), and then subjected to digestion by MNase (Thermo Fisher, #88216). Mononucleosomal DNA was purified using agarose gel electrophoresis and Freeze N’ Squeeze Columns (BioRad, #7326166). As a spike-in control, MNase-treated K. lactis DNA, purified in the same manner as S. cerevisiae DNA, was added to achieve a 9:1 ratio of S. cerevisiae DNA to K. lactis DNA.
RNA-seq libraries were built by the UPMC Children’s Hospital Health Sciences Sequencing Core following rRNA depletion. MNase-seq and ChIP-seq libraries were built prior to sample submission to the sequencing core. Libraries were prepared using the NEBNext Ultra II kit (New England Biolabs, Ipswitch, MA; DNA – E7645, RNA – E7770) and NEBNext Ultra sequencing indexes (NEB; E7335, E7500, E7710) according to manufacturer’s instructions. 4tU-seq libraries were built using a custom SoLo RNA-seq library preparation kit (TECAN, Redwood City, CA; 0516-32) with custom primers targeting S. cerevisiae rRNAs for depletion. All RNA and DNA libraries were quantified using Qubit and TapeStation and pooled for paired-end sequencing on an Illumina NextSeq 500 (UPMC Children’s Hospital Health Sciences Sequencing Core).

treatment_protocol:
Cells were formaldehyde crosslinked at a final concentration of 1% formaldehyde
RNA-seq: S. cerevisiae and S. pombe cells were grown separately to log phase (OD600 = 0.8 – 1.0) and mixed in a 9:1 ratio enabling the use of mapped S. pombe reads as an internal spike-in control for RNA-seq analysis.
4tU-seq: S. cerevisae and S. pombe nascent RNA was labeled with 4-thiouracil (4tU). Briefly, 4tU was added to log phase cultures (OD600 = 0.8 – 1.2) to a final concentration of 0.65 mg/mL. Cultures were incubated for 5 min at room temperature with constant agitation. 10 OD units of cells were poured into a half volume of dry-ice cold methanol to rapidly halt metabolic labeling of RNAs. The resultant mixtures were pelleted for 3 min at 3000 rpm at 4°C, and supernatant was removed prior to snap-freezing the pellets in liquid nitrogen.
ChIP-seq and Mnase-seq: S. cerevisiae or K. lactis cells were grown in SC medium to OD600 = 0.8 and crosslinked with formaldehyde at a final concentration of 1%.

tag: strain

tag: genotype

value: (hht1-hhf1)[delta]::LEU2 (hht2-hhf2)[delta]::KanMXhis3[delta]200 lys2-128-del leu2[delta]1 ura3-52 trp1[delta]63

tag: plasmid

tag: mnase treatment

value: 2.5 Units

tag: spike in species

value: Kluyveromyces lactis

tag: spike in type

value: DNA

tag: spike in to sample ratio


title: R52A_MNase-seq_Rep1


title: Sample_15: TOP2A+/- Nalm 6 - a B cell precusor RNA-seq

source_name: TOP2A+/- Nalm 6 - a B cell precusor

value: B cell precursor

value: TOP2A+/- Nalm 6


title: B16F10-Fto knockout cells implanted tumor-Mouse 2 [Input_MeRIP-Seq]

tag: tissue/cell type

tag: passages

value: Mouse tumor after immunotherapy


title: CLL_04_PostIbrutinib_5_1

data_processing:
Data were collected and analyzed using the Torrent Server (4462616) with Torrent Suite 5.0 version and 5.6.0.
Variant alleles were called using a combination of the following software:  Variant Caller v.5.0.28 and v.5.6.8-1, IGV v5.01 (0), Ion Reporter v.4.6, Samtools v1.6, Bcftools v1.31 and Ensembl Variant Effect Predictor (VEP) v.92.03.
Genome_build: hg19
Supplementary_files_format_and_content: BAM and VCF files were generated for each sample with Torrent Suite versions 5.0 and 5.6.0 using a combination of the following software: Variant Caller v.5.0.28 and v.5.6.8-1, IGV v5.01 (0), Samtools v1.6, Bcftools v1.31 and Ensembl Variant Effect Predictor (VEP) v.92.03. Excel files showing quanitites of all variant allele frequencies wthin each sample were generated utilizing Ion Reproter version 4.6.

tag: tissue

value: Blood

value: chronic lymphocytic leukemia

tag: extract protocol


title: onco-RNF43/TP53KO Full medium rep3


title: B16F10-Alkbh5 knockout cells implanted tumor-Mouse 1 [Input_MeRIP-Seq]

tag: strain background

tag: genotype/variation

value: B16F10-Alkbh5 knockout

tag: experiment type


title: WT_MNase-seq_Rep2


title: WT_MNase-seq_Rep1


title: CLL_04_PostIbrutinib_4_2

tag: tumor type

tag: cell type


title: CLL_04_PostIbrutinib_4_1

tag: treatment/time-point

tag: cell number


title: CLL_04_PostIbrutinib_3_2


title: WT Full medium rep3

tag: source


title: onco-RNF43/TP53KO w/o Wnt3a-0.2% Rspo rep2


title: R52A_noFLAG-Rpb3-ChIP-seq

growth_protocol:
cells were grown to mid log phase in YPD
Yeast strains and media: Saccharomyces cerevisiae strains used in this study are isogenic to FY2, a GAL2+ derivative of S288C. Strains were derived by genetic crosses followed by tetrad dissection or by transformation. S. cerevisiae strains were grown in rich medium (YPD) supplemented with 400 µM tryptophan or synthetic complete (SC) media lacking uracil or the specified amino acids. Unless otherwise noted, transformations were performed with yeast strains lacking endogenous copies of the genes encoding histones H3 and H4 and containing a URA3-marked, wild-type H3-H4 plasmid. By selection on SC-Trp medium containing 0.1% 5-fluoroorotic acid (FOA), URA3 plasmids were shuffled with TRP1-marked CEN/ARS plasmids expressing alanine-substituted histones H3 and H4 (hht2-HHF2 or HHT2-hhf2, respectively) or a TRP1-marked plasmid expressing the wild-type HHT2-HHF2 cassette. Complete plasmid shuffling was ensured by sequential passaging of transformants three times on SC-Trp + 5-FOA media.

tag: strain

tag: genotype

value: RPB3-3xFLAG::KanMX KanMX::GAL1p-YLR454W HA-SPT15 (hht1-hhf1)[delta]::LEU2 (hht2-hhf2)[delta]::KanMX his3[delta]200 lys2-128-del leu2[delta]1 ura3-52 trp1[delta]63

tag: plasmid

value: R52A SHIMA library plasmid

tag: chip antibody

value: FLAG epitope (Sigma-Aldrich, 30 µL A2220)


title: R52A_FLAG-Rpb3-ChIP-seq_Input

tag: spike in species

tag: spike in type

tag: spike in to sample ratio


title: CLL_04_PostIbrutinib_3_1

tag: tissue


title: CLL_04_PostIbrutinib_2_2

tag: extract protocol


title: R52A_FLAG-Rpb3-ChIP-seq_Rep2

description:
R52A_FLAG-Rpb3-ChIP-seq_CombinedReps.bw
R52AvsWT_l2fc_FLAG-Rpb3-ChIP-seq_CombinedReps.bw


title: CLL_04_PostIbrutinib_2_1


title: TP53KO Full medium rep3

value: Colon

value: Colon organoids


title: WT w/o Wnt3a-0.2% Rspo rep2


title: R52A_FLAG-Rpb3-ChIP-seq_Rep1


title: WT_FLAG-Rpb3-ChIP-seq_Input


title: CLL_04_PostIbrutinib_1_2

value: Post-Ibrutinib

value: CD5+/CD19+ tumor cells sorted from blood


title: onco-RNF43/TP53KO Full medium rep2


title: TP53KO Full medium rep2


title: CLL_04_PostIbrutinib_1_1

value: No DNA isolation


title: CLL_04_PreIbrutinib_1_2

value: Pre-Ibrutinib


title: WT_FLAG-Rpb3-ChIP-seq_Rep2

description:
WT_FLAG-Rpb3-ChIP-seq_CombinedReps.bw
R52AvsWT_l2fc_FLAG-Rpb3-ChIP-seq_CombinedReps.bw

value: Kluyveromyces lactis


title: WT_noFLAG-Rpb3-ChIP-seq

value: DNA


title: CLL_15_PreIbrutinib


title: Cells from human pancreatic islets of Langerhans [7471147042_R05C01]

type: genomic

city: Bruxelles

first: Jean-Valery

last: Turatsinze

address: Route de Lennik 808 CP618

department: Faculté de Medecine

country: Belgium

institute: Université Libre de Bruxelles

description:
7471147042_R05C01
Pancreatic islet cells

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing: GenomeStudio software v2010.2, Methylation module v1.7.0.

label: Cy5 and Cy3

source_name: Pancreatic islets of Langerhans

label_protocol: Standard Illumina protocol.

growth_protocol: After isolation, islets were incubated at 37°C in CMRL 1066 medium with 10% fetal calf serum for 24 h prior to shipment at room temperature in the same culture medium. Upon arrival, samples were recultured at 37°C in Ham's F-10 medium containing 10% fetal bovine serum (FBS), 2 mM GlutaMAX, 50 U/ml penicillin and 50 μg/ml streptomycin (GIBCO), 6.1 mM glucose, 50 μM 3-isobutyl-1-methylxanthine, 1% BSA (Sigma).

extract_protocol: Genomic DNA was extracted and purified from primary pancreatic cells using Qiagen QiaAMP Kit according to standard instructions. The recommended RNase treatment was performed.

treatment_protocol: Dissociation of human islets was achieved by incubation with accutase (Millipore) supplemented with 5 U/ml of DNase 1 at 37°C for 10-15 min. The dissociated cells were washed with 1% BSA in PBS and cultured in islet standard medium and followed by Newport Green labeling.

value: Dispersed primary pancreatic islet cells


title: Cells from human pancreatic islets of Langerhans [7471147042_R06C01]

description:
7471147042_R06C01
Pancreatic islet cells


title: TP53KO w/o Wnt3a-0.2% Rspo rep2


title: CLL_04_PreIbrutinib_1_1

city: Columbus

last: Hu

address: Rm 449, 410 West 12th Ave

institute: The Ohio State University


title: onco-RNF43/TP53KO w/o Wnt3a-0.2% Rspo rep1


title: TP53KO w/o Wnt3a-0.2% Rspo rep1


title: WT Full medium rep2


title: Cells from human pancreatic islets of Langerhans [7471147042_R03C02]

description:
7471147042_R03C02
Pancreatic islet cells


title: T45A_RNA-seq_Rep2

description:
T45A_RNA-seq_CombinedReps.bw
T45AvsWT_l2fc_RNA-seq_CombinedReps.bw
T45A_RNA-seq_CombinedReps_crick_denovoAnnotation.bed
T45A_RNA-seq_CombinedReps_watson_denovoAnnotation.bed

growth_protocol:
cells were grown to mid log phase in SC
Yeast strains and media: Saccharomyces cerevisiae strains used in this study are isogenic to FY2, a GAL2+ derivative of S288C. Strains were derived by genetic crosses followed by tetrad dissection or by transformation. S. cerevisiae strains were grown in rich medium (YPD) supplemented with 400 µM tryptophan or synthetic complete (SC) media lacking uracil or the specified amino acids. Unless otherwise noted, transformations were performed with yeast strains lacking endogenous copies of the genes encoding histones H3 and H4 and containing a URA3-marked, wild-type H3-H4 plasmid. By selection on SC-Trp medium containing 0.1% 5-fluoroorotic acid (FOA), URA3 plasmids were shuffled with TRP1-marked CEN/ARS plasmids expressing alanine-substituted histones H3 and H4 (hht2-HHF2 or HHT2-hhf2, respectively) or a TRP1-marked plasmid expressing the wild-type HHT2-HHF2 cassette. Complete plasmid shuffling was ensured by sequential passaging of transformants three times on SC-Trp + 5-FOA media.

treatment_protocol:
RNA-seq: S. cerevisiae and S. pombe cells were grown separately to log phase (OD600 = 0.8 – 1.0) and mixed in a 9:1 ratio enabling the use of mapped S. pombe reads as an internal spike-in control for RNA-seq analysis.
4tU-seq: S. cerevisae and S. pombe nascent RNA was labeled with 4-thiouracil (4tU). Briefly, 4tU was added to log phase cultures (OD600 = 0.8 – 1.2) to a final concentration of 0.65 mg/mL. Cultures were incubated for 5 min at room temperature with constant agitation. 10 OD units of cells were poured into a half volume of dry-ice cold methanol to rapidly halt metabolic labeling of RNAs. The resultant mixtures were pelleted for 3 min at 3000 rpm at 4°C, and supernatant was removed prior to snap-freezing the pellets in liquid nitrogen.
ChIP-seq and Mnase-seq: S. cerevisiae or K. lactis cells were grown in SC medium to OD600 = 0.8 and crosslinked with formaldehyde at a final concentration of 1%.

value: (hht1-hhf1)[delta]::LEU2 (hht2-hhf2)[delta]::KanMXhis3[delta]200 lys2-128-del leu2[delta]1 ura3-52 trp1[delta]63

value: T45A SHIMA library plasmid

value: Schizosaccharomyces pombe

value: cell


title: Cells from human pancreatic islets of Langerhans [7471147042_R06C02]

description:
7471147042_R06C02
Pancreatic islet cells


title: Cells from human pancreatic islets of Langerhans [7471147042_R04C02]

description:
7471147042_R04C02
Pancreatic islet cells


title: WT w/o Wnt3a-0.2% Rspo rep1


title: CLL_03_PostIbrutinib_5_2

value: Blood

value: chronic lymphocytic leukemia


title: T45A_RNA-seq_Rep1


title: Cells from human pancreatic islets of Langerhans [6929742038_R02C02]

description:
6929742038_R02C02
Pancreatic islet cells


title: R52A_RNA-seq_Rep2

description:
R52A_RNA-seq_CombinedReps.bw
R52AvsWT_l2fc_RNA-seq_CombinedReps.bw
R52A_RNA-seq_CombinedReps_crick_denovoAnnotation.bed
R52A_RNA-seq_CombinedReps_watson_denovoAnnotation.bed

value: R52A SHIMA library plasmid


title: CLL_03_PostIbrutinib_5_1


title: Cells from human pancreatic islets of Langerhans [6929742038_R04C02]

description:
6929742038_R04C02
Pancreatic islet cells


title: onco-RNF43/TP53KO Full medium rep1


title: CLL_03_PostIbrutinib_4_2


title: R52A_RNA-seq_Rep1


title: TP53KO Full medium rep1


title: Cells from human pancreatic islets of Langerhans [7471147042_R03C01]

description:
7471147042_R03C01
Pancreatic islet cells


title: Cells from human pancreatic islets of Langerhans [7471147042_R02C01]

description:
7471147042_R02C01
Pancreatic islet cells


title: CLL_03_PostIbrutinib_4_1


title: Cells from human pancreatic islets of Langerhans [7471147042_R01C02]

description:
7471147042_R01C02
Pancreatic islet cells


title: Cells from human pancreatic islets of Langerhans [7471147046_R05C01]

description:
7471147046_R05C01
Pancreatic islet cells


title: Cells from human pancreatic islets of Langerhans [6929742038_R03C01]

description:
6929742038_R03C01
Pancreatic islet cells


title: Cells from human pancreatic islets of Langerhans [7471147046_R06C02]

description:
7471147046_R06C02
Pancreatic islet cells


title: WT_RNA-seq_Rep1

description:
WT_RNA-seq_CombinedReps.bw
WT_RNA-seq_CombinedReps_crick_denovoAnnotation.bed
WT_RNA-seq_CombinedReps_watson_denovoAnnotation.bed


title: CLL_03_PostIbrutinib_3_1


title: T45A_4tU-seq_Rep2

description:
T45A_4tU-seq_CombinedReps.bw
T45vsWT_l2fc_4tU-seq_CombinedReps.bw

data_processing:
Library strategy: 4tU-seq
Reads contained in FASTQ files were aligned to the genome of the organism used as a spike in using HISAT2.
Reads that did not align to the spike-in genome were aligned to S. cerevisiae genome using HISAT2.
Quality filtering, sorting and file conversion (SAM to BAM) of spike in and S. cerevisiae reads was performed with the SAMtools suite
Spike-in normalization was performed during conversion to bigwig format using deepTools2 as described in Orlando et al. (2014) where the reference adjusted reads-per-million normaliztion method is described.
Data processing and visualization were performed with DANPOS (MNase-seq), deepTools2 (ChIPseq, RNA-seq, 4tU-seq), IGV2.4.13, Prism8 and R Studio.
Genome_build: sacCer3
Supplementary_files_format_and_content: Values presented in bigWig files represent spike-in normalized abundance of RNA/DNA fragments mapped to a particular locus or log 2 fold change (l2fc in file name) values for mutant verses wild-type comparisons.

treatment_protocol:
4-thiouracil was added to log-phase cultures at a concentration of 0.65 mg/mL and rapidly chilled in a half volume of dry-ice-cold methanol.
RNA-seq: S. cerevisiae and S. pombe cells were grown separately to log phase (OD600 = 0.8 – 1.0) and mixed in a 9:1 ratio enabling the use of mapped S. pombe reads as an internal spike-in control for RNA-seq analysis.
4tU-seq: S. cerevisae and S. pombe nascent RNA was labeled with 4-thiouracil (4tU). Briefly, 4tU was added to log phase cultures (OD600 = 0.8 – 1.2) to a final concentration of 0.65 mg/mL. Cultures were incubated for 5 min at room temperature with constant agitation. 10 OD units of cells were poured into a half volume of dry-ice cold methanol to rapidly halt metabolic labeling of RNAs. The resultant mixtures were pelleted for 3 min at 3000 rpm at 4°C, and supernatant was removed prior to snap-freezing the pellets in liquid nitrogen.
ChIP-seq and Mnase-seq: S. cerevisiae or K. lactis cells were grown in SC medium to OD600 = 0.8 and crosslinked with formaldehyde at a final concentration of 1%.


title: CLL_03_PostIbrutinib_2_2


title: CLL_03_PostIbrutinib_2_1


title: Cells from human pancreatic islets of Langerhans [7471147046_R04C02]

description:
7471147046_R04C02
Pancreatic islet cells


title: WT_RNA-seq_Rep2


title: Cells from human pancreatic islets of Langerhans [6929742038_R02C01]

description:
6929742038_R02C01
Pancreatic islet cells


title: CLL_03_PostIbrutinib_1_2


title: co-incubated CD14 cells S21

city: Marburg

first: Leon

middle: Nicolas

last: Schulte

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute for Lung Research

country: Germany

institute: Philipps-Universität Marburg

description: co-incubated CD14 cells (rep 3

data_processing:
RTA version 2.4.11 was used for basecalling
bcl2fastq version 2.18.0.2 was used for demultiplexing
Reads were mapped using the CLC genomics workbench version 10.01 and the GRCh38 human genome annotation with standard settings: mismatch cost = 2; insertion cost = 3; deletion cost = 3; length fraction = 0.8; similarity fraction = 0.8.
RPKMs were calculated for genes using the CLC genomics worbench version 10.01
Genome_build: hg38
Supplementary_files_format_and_content: text file with genes and abundance

source_name: Peripheral blood leukocytes

growth_protocol: PBMCs’ isolated monocytes from buffy-coats (1.8x105), diluted in 500 µL of cRPMI, were routinely seeded per well (day 0) on treated Costar 24-well plates and let adhere for 24h before adding 500 µL CSC-H460 (0.2x105 cells), thus starting day 1 of experimental time-lapse for assaying fusion event. Cells were recovered after four days (d4, 96 hours) by gently tip-scraping of wells and posterior measurement of surface markers expression by FACS was done.

extract_protocol:
High-Pure RNA isolation kit (Roche) was used to isolate total RNA from sorted fractions (co-cultured CD14+ monocytes, co-CD14; GFP+ tumour cells, GFP; CD14+GFP+ hybrids, CD14/GFP) and parallel PBMCs’ adherence-isolated monocytes, naïve-CD14.
Libraries were prepared using Vertis Biotech mRNA library generation protocols

treatment_protocol: Puromycin-dependent GFP-expressing H460 cells were achieved by infection with pGIPZ-shRNAmir-NS lentiviral vector. CSC-H460 were obtained by culture in non-treated Costar plates with selective DMEM/F-12 supplemented with 2 mmol/L L-Glutamine, 5 mmol/L Hepes, 0.4% BSA, N2 supplement and 20 ng/mL of EGF and bFGF.

value: macrophage

tag: precursor

value: CD14+ monocyte

tag: donor

value: healthy, unknown


title: CD14/GFP double-positive cells S23

description: CD14/GFP double-positive cells (rep 3

source_name: New specimen

value: new specimen

value: parental precursors


title: R52A_4tU-seq_Rep2

description:
R52A_4tU-seq_CombinedReps.bw
R52vsWT_l2fc_4tU-seq_CombinedReps.bw


title: Cells from human pancreatic islets of Langerhans [7471147046_R06C01]

description:
7471147046_R06C01
Pancreatic islet cells


title: Cells from human pancreatic islets of Langerhans [6929742038_R01C02]

description:
6929742038_R01C02
Pancreatic islet cells


title: CLL_03_PostIbrutinib_3_2

value: Post-Ibrutinib

value: CD5+/CD19+ tumor cells sorted from blood

value: No DNA isolation


title: CLL_03_PostIbrutinib_1_1


title: Cells from human pancreatic islets of Langerhans [7471147018_R06C01]

description:
7471147018_R06C01
Pancreatic islet cells


title: R52A_4tU-seq_Rep1


title: T45A_4tU-seq_Rep1


title: Cells from human pancreatic islets of Langerhans [7471147018_R05C02]

description:
7471147018_R05C02
Pancreatic islet cells


title: WT_4tU-seq_Rep2


title: GFP-positive tumour cells S22

description: GFP-positive tumour cells (rep 3

source_name: H460 tumour cell line

value: cancer stem cell

value: GFP+ CSC-H460 line

value: H460 tumour cell line, caucasian


title: WT Full medium rep1

value: Colon

value: Colon organoids


title: CD14/GFP double-positive cells S19

description: CD14/GFP double-positive cells (rep 2)


title: WT_4tU-seq_Rep1

value: (hht1-hhf1)[delta]::LEU2 (hht2-hhf2)[delta]::KanMXhis3[delta]200 lys2-128-del leu2[delta]1 ura3-52 trp1[delta]63

value: Schizosaccharomyces pombe

value: cell


title: CLL_03_PreIbrutinib_1_1

value: Blood

value: chronic lymphocytic leukemia

value: Pre-Ibrutinib


title: co-incubated CD14 cells S17

description: co-incubated CD14 cells (rep 2)

value: macrophage

value: CD14+ monocyte

value: healthy, unknown


title: CLL_02_PostIbrutinib_4_2

value: Post-Ibrutinib


title: RCC_13-CD8_68T

city: Nashville

first: Jeff

last: Rathmell

state: TN

address: 1211 Medical Center Drive

department: PMI

institute: Vanderbilt University Medical Center

data_processing:
cell ranger2.2 (scRNAseq)
seurat/phate/monocle (scRNAseq)
fastqc for read quality (bulk RNAseq)
salmon quant (bulk RNAseq)
edgeR (bulk RNAseq)
fgsea (bulk RNAseq)
Genome_build: hg19 (scRNAseq)
Genome_build: hg38 (bulk RNAseq)
Supplementary_files_format_and_content: sparse matrix (scRNAseq)
Supplementary_files_format_and_content: quant.sf (bulk RNAseq)

source_name: ccRCC CD8 T cell

extract_protocol:
10x Genomics Single Cell Protocols
Chromium Single Cell 5'
5' capture

value: ccRCC tumor

value: CD8 T cell

tag: treatment


title: GFP-positive tumour cells S18

description: GFP-positive tumour cells (rep 2)

value: cancer stem cell


title: RCC_13-CD8_68B

source_name: peripheral CD8 T cell

value: PMBC


title: Cells from human pancreatic islets of Langerhans [6929793129_R02C02]

description:
6929793129_R02C02
Pancreatic islet cells

value: Dispersed primary pancreatic islet cells


title: Cells from human pancreatic islets of Langerhans [6929806060_R06C02]

description:
6929806060_R06C02
Pancreatic islet cells


title: CLL_03_PreIbrutinib_1_2

first: Eileen

tag: tumor type

value: CD5+/CD19+ tumor cells sorted from blood

value: No DNA isolation


title: naive CD14 cells S16

description: naive CD14 cells (rep 2)

tag: cell type


title: WT_FLAG-Rpb3-ChIP-seq_Rep1

description:
WT_FLAG-Rpb3-ChIP-seq_CombinedReps.bw
R52AvsWT_l2fc_FLAG-Rpb3-ChIP-seq_CombinedReps.bw

value: RPB3-3xFLAG::KanMX KanMX::GAL1p-YLR454W HA-SPT15 (hht1-hhf1)[delta]::LEU2 (hht2-hhf2)[delta]::KanMX his3[delta]200 lys2-128-del leu2[delta]1 ura3-52 trp1[delta]63

value: FLAG epitope (Sigma-Aldrich, 30 µL A2220)

value: Kluyveromyces lactis

value: DNA


title: Cells from human pancreatic islets of Langerhans [6929742057_R02C01]

description:
6929742057_R02C01
Pancreatic islet cells


title: co-incubated CD14 cells S13

description: co-incubated CD14 cells (rep 1)


title: Cells from human pancreatic islets of Langerhans [7471147018_R04C02]

description:
7471147018_R04C02
Pancreatic islet cells


title: CLL_02_PostIbrutinib_3_2

value: Blood

value: chronic lymphocytic leukemia

tag: treatment/time-point


title: Cells from human pancreatic islets of Langerhans [6929742057_R02C02]

description:
6929742057_R02C02
Pancreatic islet cells


title: Cells from human pancreatic islets of Langerhans [7471147018_R05C01]

description:
7471147018_R05C01
Pancreatic islet cells


title: RCC_13-CD8_59T


title: CD14/GFP double-positive cells S15

description: CD14/GFP double-positive cells (rep 1)

value: new specimen

value: parental precursors


title: CLL_02_PostIbrutinib_3_1

tag: cell number


title: RCC_13-CD8_59B


title: GFP-positive tumour cells S14

description: GFP-positive tumour cells (rep 1)

value: GFP+ CSC-H460 line

value: H460 tumour cell line, caucasian


title: RCC_13-CD8_54T

value: ccRCC tumor


title: naive CD14 cells S12

description: naive CD14 cells (rep 1)

value: macrophage

value: CD14+ monocyte

value: healthy, unknown


title: CLL_02_PostIbrutinib_2_2

value: Post-Ibrutinib


title: RCC_13-CD8_54B

value: PMBC

value: CD8 T cell


title: CLL_02_PostIbrutinib_2_1

value: CD5+/CD19+ tumor cells sorted from blood

value: No DNA isolation


title: Cells from human pancreatic islets of Langerhans [6929742057_R03C01]

description:
6929742057_R03C01
Pancreatic islet cells

value: Dispersed primary pancreatic islet cells


title: RCC_13-CD8_51T


title: Rp2

city: Wuhan

first: Dong

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

description: total RNA after removing rRNA

data_processing:
bcl2fastq(v2.16.0.10) were used for base calling
Raw reads were first discarded if containing more than 2-N bases, then reads were processed by clipping adaptor, removing low quality bases, and discarding too short reads (less than 16nt). FASTX-Toolkit (Version 0.0.13) was used to get the clean reads.
After that, clean reads were aligned to the human GRCH38 genome by tophat2 (Kim et al., 2013). Aligned reads with more than one genome location were discarded due to their ambiguous location.
Uniquely localized reads were used to calculate reads number and FPKM value (FPKM represents fragments per kilobase and per million) for each gene according to reads and genes genome location.
Genome_build: GRCh38.p2
Supplementary_files_format_and_content: tab-separate text file,the gene expression FPKM and Reads file

source_name: Retinal neovascular proliferative membrane

extract_protocol:
Total RNA was extracted from tissue or cell samples by using TRIzol Reagent (Ambion) following the manufacturer’s instructions. RQ1 DNase (promega) was added to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260 nm/280 nm (A260/A280) using smartspec plus (BioRad). RNA integrity was further verified by 1.5% Agarose gel electrophoresis.
For each sample，50ng of total RNA was used for RNA-seq library preparation. Ribosomal RNAs were depleted with Ribo-Zero™ rRNA depletion kit for human (Epicentre) before used for directional RNA-seq library preparation. Purified RNA was fragmented ，and Reverse transcription was performed with random primer harboring adaptor sequence and a randomized hexamer，then synthesized DNA with Terminal-Tagging oligo cDNA using ScriptSeq™ v2 RNA-Seq Library Preparation Kit(epicentre). The cDNAs were purified and amplified. PCR products corresponding to 300-500 bps were purified, quantified and stored at -80°C until used for sequencing.

tag: disease

value: retinal periphlebitis


title: Rp1

description: total RNA after removing rRNA


title: Cells from human pancreatic islets of Langerhans [6929742057_R01C02]

description:
6929742057_R01C02
Pancreatic islet cells


title: RCC_13-CD8_51B


title: Cells from human pancreatic islets of Langerhans [6929742057_R04C01]

description:
6929742057_R04C01
Pancreatic islet cells


title: CLL_02_PostIbrutinib_1_1

value: Blood


title: RCC_13-CD8_48T