title: hEnSCs_n3_JAZF1_8

first: Maria

last: Vila de Mucha

address: 72 Huntley Street

institute: UCL Cancer Institute

data_processing:
ChIP-Seq for FLAG tagged proteins data was aligned to a concatenated genome sequence of mouse (mm10) and spike-in of human (hg19) using bowtie2 [1] with --very-sensitive option. Uniquely mapped reads were extracted using samtools [2] and were used for the downstream analysis. Endogenous (mouse) and exogenous (human) reads were segregated into two bam files per sample using samtools. Spike-in calibration was performed according to the methodology suggested by Fursova et. al [3]. The two replicates for the endogenous and exogenous data were merged separately and peaks were called on the merged bams using MACS2[4] --broad option and --broad-cutoff = 0.001. A combined peak-set was created from the merged peaks from all the factors at the three time-points using DiffBind [5] in R with default parameters. Read counts were obtained for individual replicates for the combined peak-set using dba.count function in DiffBind. For the spike-in calibration, peaks present in all 12 samples were used and the normalisation was performed utilizing the methods described in Fursova et. Al. ChIP-Seq for H3K27me3 and H4ac data was aligned to a concatenated genome sequence of mouse (mm10) and spike-in of drosophila (BDGP5.25) using bowtie2 with --very-sensitive option. Uniquely mapped reads were extracted and separated in to exogenous (drosophila) and endogenous (mouse) reads using samtools.
RNA-seq data were processed using the Nextflow core RNA-seq pipeline with default settings (Ewels et al., 2020). In brief, reads were filtered to remove adaptors and low-quality bases using Trim Galore, aligned to GRCh38 using the STAR aligner (Dobin et al., 2013), and read counts generated using featureCounts (Liao et al., 2014).
Genome_build: mm10, hg19 and BDGP5.25
Supplementary_files_format_and_content: bigwigs

source_name: hEnSC

growth_protocol: Mouse embryonic stem cells Suz12GT/GT were cultured in 0.1% gelatin coated dishes using KO-DMEM (Thermofisher, 10829018) supplemented with 10% FBS validated for mouse embryonic stem cell culture (Thermofisher, 16141079), 5% knockout serum replacement (Thermofisher, 10828028), non-essential amino acids (Thermofisher, 11140035), L-glutamine 2 mM (Thermofisher, 25030-024), 2-mercaptoethanol 50uM (Thermofisher, 31350010), penicillin-streptomycin 100 U/mL (Thermofisher, 15140-122), sodium pyruvate 1 mM (Thermofisher, 11360039) and 1000 U/ml leukemia inhibitory factor (03-0011-100, Stemgent). mESCs were differentiated to form embryoid bodies as described previously (Brien et al., 2012). Briefly, mESCs were cultured and reseeded twice prior to forming EBs. Before seeding, cells were filtered using a 70 um cell strainer, and washed twice with LIF-free mESCs media. Afterwards, cells were seeded in ultra low attachment T75 flasks (Corning, 3814) in a single cell suspension of 2x106 cells per flask. LIF-free media was changed every second day and EBs were harvested at days 4 and 8. The collection of endometrial biopsies was approved by the NHS National Research Ethics - Hammersmith and Queen Charlotte's & Chelsea Research Ethics Committee (REC reference: 1997/5065) and Tommy’s National Reproductive Health Biobank (REC reference: 18/WA/0356). Samples were obtained using a Wallach Endocell sampler 5 to 10 days after the pre-ovulatory luteinizing hormone (LH) surge. hEnSC were harvested as previously described (Barros et al., 2016). Briefly, endometrial biopsies were subjected to enzymatic digestion using 500 µg/ml collagenase type Ia (Sigma-Aldrich,) and 100 µg/mL DNase I (Lorne Laboratories Ltd) for 1 hr at 37°C. Digested tissue was filtered through a 40 µm cell strainer to remove glandular cell clumps, and the flow-through collected and cultured in DMEM/F12 (Thermo Scientific, 31330038) containing 10% dextran-coated charcoal-treated foetal bovine serum (DCC-FBS), 1 × antibiotic-antimycotic mix (ThermoFisher, 15240062), 10 µM L-glutamine, 1 nM estradiol (Sigma, E2758) and 2 μg/mL insulin (Santa Cruz, sc-360248) .   Cells were reseeded at a 1:2 or 1:3 ratio when confluence was reached. All experiments were carried out before reaching the 10th passage. hEnSC were seeded at a confluency of 105 cells/well in 6 well plates and 1.5 ml of concentrated retrovirus added to each well in the presence of 8 μg/ml polybrene (Merck, TR-1003-G). Cells were then spinoculated at 500 x g for 1 hr at RT and incubated for 12 hrs. Cells were washed with fresh media and, after 3 days, selected with 5 g/ml blasticidin until they reached near confluency and no cells were found in the non-transduced control plate. Cells were reseeded and, at confluency two days later, decidualised for up to 8 days in DCC media with 2% DCC FBS supplemented with antibiotic antimycotic solution, l-glutamine, 50 M 8-Bromoadenosine 3’, 5’ cyclic mono-phosphate (8-Br-cAMP, Merck B5386) and 1 M medroxyprogesterone acetate (MPA, Sigma M1629), with the media changed every second day. Samples were taken at 0 and 8 days during decidualisation.

extract_protocol:
ChIP was performed as described, with minor modifications (Kanhere et al., 2012). Briefly, cells were trypsinised, resuspended in PBS and then crosslinked by adding 1/10 of cross-linking solution (11% formaldehyde, 0.1 M NaCl, 1mM EDTA pH 8, 0.5 mM EGTA pH 8, 50 mM HEPES pH 8) for 15 min in suspension. Formaldehyde was quenched by adding glycine to a final concentration of 1.25 mM. Cells were then washed twice with ice-cold PBS, centrifuging at 290G at 4 C for 10 min. After last wash, cells were flash-frozen and stored at -80 C. To carry out ChIP, cells were thawed in 5 ml per 3x107 lysis buffer 1 (50 mM HEPES pH 7.5, 140 mM NaCl, 1 mM EDTA, 10 % glycerol, 0.5 % IGEPAL CA-630, 0.25 % Triton X-100). Then cells were incubated at 4°C for 10 min with rocking. Cells were recovered by centrifuging at 290 C for 10 min at 4 C. Supernatant was discarded, and nuclei were resuspended in the same volume of lysis buffer 2 (10 mM Tris pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, supplemented with 0.1 DTT and complete protease inhibitor) and incubated at 4°C for 10 min with rocking. Nuclei were pelleted again at 290 G for 10 min at 4°C, and resuspended in 100 ml of lysis buffer 3 (10mM Tris pH 8, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% sodium deoxycholate, 0.5% N-lauryl sarcosine, 0.2 % SDS, supplemented with 0.1 DTT and complete protease inhibitor) per 5x106 cells. Cells were incubated for 30 min on ice, to allow lysis. Afterwards, lysates were sonicated for 15 cycles of 30s on and 30s off, using a Diagenode Bioruptor Pico. For EB processing, the same protocol was followed, except using the resulting EB formed by 2 plates per timepoint.  DNA was then quantified using Qubit dsDNA HS Assay kit (Thermofisher) and ChIP was performed using 45 mg of mouse chromatin, with 5 mg of human chromatin extracted from human immortalised fibroblasts (hTERT) cells stably expressing FLAG-tagged SUZ12 for factor, or 5 ug of Drosophila chromatin for histone modifications were added as calibration control for downstream analysis (Furzova et al 2019). The resulting mix of mouse and human chromatin was topped up to 900ul per IP. Then, 100 ml of Triton X-100 10% solution was added, and insoluble material was span down at 17,000 G for 20 mins at 4oC. 2% of the lysate was stored at -20oC to be used as input and whole cell extract and the remaining lysate was incubated overnight at 4oC with 50 ml Protein G Dynabeads preincubated for at least 4 hr with 2.5 mg of FLAG antibody (Sigma, A8592), H3K27me3 (Abcam, ) or H4 pan acetyl (Thermofisher, PA5-40083). Beads were washed and bound complexes were incubated in elution buffer () to reverse crosslinks by heating at 65oC for 1 h. IP and input DNA were then treated with 0.5 mg/ml RNAseA and  mg/ml of proteinase K (Ambion, ), and immunoprecipitated DNA was purified using Kapa Pure beads (Roche, KK8000) using manufacturers recommendations. DNA was resuspended in 60 ml of 10 mM Tris pH 8 and quantified using ds DNA HS Qubit kit (Thermofisher, Q32851). Total RNA was purified from hEnSC using TRIsure (Bioline, BIO-38033), treated with DNaseTurbo (Ambion, AM2238),  quantified with a Qubit RNA High Sensitivity assay kit (Invitrogen, Q32855) and its quality assessed using the Agilent RNA 6000 Pico Kit (Agilent, 5067-1513).
DNA libraries were generated using NEBNext Ultra II DNA library prep (NEB) using 1.2 ng of DNA and 9 cycles of PCR. Quality and distribution of all libraries was assessed using 2100 Bioanalyzer High Sensitivity DNA Kit (Agilent, 5067-4626) followed by qPCR quantification with Kapa Library Quant Kit (Roche, KK4824).  Sequencing was performed as 75 bp single end reads on Illumina NEXTseq 550 platform for FLAG immunoprecipitation and 138 bp single single end reads on  Novaseq plataform for histones modifications immunoprecipitation, using biological duplicates. For primary hEnSCs, RNA-seq libraries were prepared with 100 ng of total RNA using the KAPA Stranded RNA-Seq Kit with RiboErase (Roche, KR1151) following the manufacturer’s instructions and were sequenced on Illumina Nextseq 2000 to generate 2x50 bp paired-end reads.

value: Endometrial biopsy

tag: treatment/genotype

value: Day 8 decidualisation (cAMP/MPA)


title: hEnSCs_n3_JAZF1-SUZ12_8

status: Public on Apr 25 2022

type: SRA

city: London

country: United Kingdom

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: sample type


title: hEnSCs_n3_JAZF1_0

value: Day 0 decidualisation (cAMP/MPA)


title: WT rep1

city: Daejeon

first: Kwang-Soo

last: Shin

department: Life Science

country: South Korea

institute: Daejeon University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to Aspergillus fumigatus whole genome using Bowtie2
Read count extraction using bedtools.
Genome_build: Aspergillus fumigatus
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

organism: Aspergillus fumigatus

source_name: Asexual spore and mycelium

growth_protocol: Incubate 1-2 day in liquid media

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: Freeze-dry

tag: strain

tag: genotype

value: Wild type

tag: sample

value: conidia and mycelium


title: hEnSCs_n3_SUZ12D93_0


title: hEnSCs_n3_JAZF1-SUZ12_0


title: hEnSCs_n3_SUZ12D93_8


title: hEnSCs_n3_SUZ12_8


title: hEnSCs_n2_JAZF1_8


title: hEnSCs_n2_JAZF1_0


title: hEnSCs_n3_GFP_0


title: hEnSCs_n2_SUZ12D93_8


title: hEnSCs_n3_GFP_8


title: hEnSCs_n2_JAZF1-SUZ12_8


title: HDM1g-3

value: 1g12332 deletion mutant


title: hEnSCs_n2_JAZF1-SUZ12_0


title: hEnSCs_n2_SUZ12_8


title: hEnSCs_n2_GFP_0


title: hEnSCs_n1_JAZF1_8


title: hEnSCs_n2_GFP_8


title: hEnSCs_n2_SUZ12D93_0


title: hEnSCs_n1_JAZF1-SUZ12_8


title: hEnSCs_n1_SUZ12D93_8


title: hEnSCs_n1_JAZF1_0


title: hEnSCs_n1_SUZ12_0


title: hEnSCs_n1_SUZ12D93_0


title: hEnSCs_n1_SUZ12_8


title: hEnSCs_n1_JAZF1-SUZ12_0


title: hEnSCs_n1_GFP_0


title: hEnSCs_n1_GFP_8


title: input, shHuR cells

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

country: USA

institute: The Wistar Institute

description:
shH.inp
input

data_processing:
RNA-Seq data analysis was done with rsem (ver. 1.2.3) and hg19 genome with ensemble transcriptome information.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: HuR_RIPseq.txt: Processed data file contains the raw counts for each gene.

source_name: IMR90 cell line

extract_protocol:
Anti-HuR RNA-IP was carried out with a Magna RIP RNA-Binding Protein Immunoprecipitation Kit (Millipore, Cat. No. 17-700). Briefly, for each immunoprecipitation, 2 X 10^7 cells were harvested and lysed in 100 ul RIP Lysis Buffer with RNase and protease inhibitors. The lysate was subjected to immunoprecipitation using 5 ug anti-HuR antibody (Millipore, Cat. No. 03-102). The immunoprecipitated RNAs were extracted using phenol : chloroform : isoamyl alcohol (Thermo Fisher, Cat. No. AM9720) followed by quantitative PCR and RNA-seq.
The RNA library was prepared using KAPA RNA HyperPrep kit (Roche, Cat. No. 07962312001).

tag: cell line

tag: condition

value: shHuR

tag: antibody


title: hEnSCs_n2_SUZ12_0


title: input, shControl cells

description:
shc.inp
input

value: shControl


title: hEnSCs_n3_SUZ12_0


title: RNA-IP, shADAR1 cells

description:
shA.RIP
RNA-IP

value: Anti-HuR


title: input, shADAR1 cells

description:
shA.inp
input


title: RNA-IP, shHuR cells

description:
shH.RIP
RNA-IP


title: RNA-IP, shControl cells

description:
shc.RIP
RNA-IP


title: B.1.351-10μg-2_LN [bulk VDJ-seq]

city: West Haven

first: Sidi

last: Chen

state: CT

address: 850 West Campus Drive

institute: Yale University

description:
SA10-2_LN
VDJ Sequencing
LNP-mRNA vaccine

data_processing:
Bulk VDJ sequencing data had adapters trimmed by Trimmomatic v0.39 in single-end mode, clipping Illumina TruSeq adapters with default settings and filtering reads with an average quality score < 30 (Bolger et al., 2014).
Clonotypes were called using MiXCR v2.1.5 with the recommended settings for 5’ RACE (RNA alignment to V gene transcripts with P region) using the mm10 VDJ reference (Bolotin et al., 2015).
Assembly: mm10 VDJ reference
Supplementary files format and content: Tab-delimited text files contain the exported clonotype information from MiXCR.
Library strategy: VDJ-seq

organism: Mus musculus

source_name: Lymph node

extract_protocol:
Blood, draining lymph nodes, and spleens were collected from mice that were treated with either LNP-mRNA or PBS. The cell suspension was centrifuged for 5 min with 400 g at 4 °C. Erythrocytes were lysed briefly using ACK lysis buffer (Lonza) with 1mL per spleen for 1~2 mins before adding 10 mL PBS containing 2% FBS to restore iso-osmolarity. The single-cell suspensions were filtered through a 40 μm cell strainer (BD Falcon, Heidelberg, Germany). mRNA of lymphocytes from the three tissues were extracted using a commercial RNeasy® Plus Mini Kit (Qiagen).
Bulk BCR and TCR are prepared using SMARTer Mouse BCR IgG H/K/L Profiling Kit and SMARTer Mouse TCR a/b profiling kit separately (Takara). Based on the extracted mRNA amount of each sample, the input RNA amounts for bulk BCR libraries were as follows: lymphocytes from blood (100 ng), lymphocytes from lymph node (1000 ng), and lymphocytes from spleen (1000 ng). The input RNA amounts for bulk TCR libraries were as follows: lymphocytes from blood (100 ng), lymphocytes from lymph node (500 ng), and lymphocytes from spleen (500 ng). All procedures followed the standard protocol of the manufacturer. The pooled library was sequenced using MiSeq (Illumina) with 2*300 read length.

tag: tissue

value: Lymph node

tag: cell type

value: Lymphocyte

value: WT

tag: treatment

value: PBS


title: B.1.351-1μg-1_Blood [bulk VDJ-seq]

description:
SA1-1_Blood
VDJ Sequencing
LNP-mRNA vaccine

source_name: Blood

value: Blood


title: B.1.351-10μg-1_Spleen [bulk VDJ-seq]

description:
SA10-1_Spleen
VDJ Sequencing
LNP-mRNA vaccine

source_name: Spleen

value: Spleen


title: B.1.351-10μg-3_LN [bulk VDJ-seq]

description:
SA10-3_LN
VDJ Sequencing
LNP-mRNA vaccine


title: B.1.351-1μg-2_LN [bulk VDJ-seq]

description:
SA1-2_LN
VDJ Sequencing
LNP-mRNA vaccine

value: WA1 10ug


title: B.1.351-1μg-3_Spleen [bulk VDJ-seq]

description:
SA1-3_Spleen
VDJ Sequencing
LNP-mRNA vaccine

value: WA1 1ug


title: B.1.351-1μg-2_Blood [bulk VDJ-seq]

description:
SA1-2_Blood
VDJ Sequencing
LNP-mRNA vaccine


title: B.1.351-1μg-1_LN [bulk VDJ-seq]

description:
SA1-1_LN
VDJ Sequencing
LNP-mRNA vaccine


title: B.1.351-10μg-2_Blood [bulk VDJ-seq]

description:
SA10-2_Blood
VDJ Sequencing
LNP-mRNA vaccine


title: R95A mutant, treated, replicate 3

type: RNA

city: Doha

first: Dindial

last: Ramotar

state: Qatar

address: Education City, Qatar Foundation

department: Division of Biological and Biomedical Sciences, College of Health and Life Sciences

country: Qatar

institute: Hamad Bin Khalifa University

description: R95A Mutant Yeast Strain treated with rapamycin

hyb_protocol: 5 µg of fragmented aRNA from yeast cells was used in a 100-µl hybridization cocktail containing added hybridization controls followed by hybridization of 80 µl of mixture on arrays for 16 h at 45°C. Standard post-hybridization wash and double-stain protocols (FS450_0003; GeneChip HWS kit, Affymetrix) were used on an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Affymetrix GeneChip scanner 3000 7G.

data_processing: The Affymetrix raw data “.CEL” files were imported into the FlexArray (version 1.6.3) followed by execution of robust multi-array average (RMA), which performs the background correction and quantile normalization.

label: Biotin

organism: Saccharomyces cerevisiae

source_name: R95A mutant, treated, Yeast Strain

label_protocol: Total RNA from yeast cells was processed for use on Affymetrix GeneChip Yeast Genome 2.0 Arrays, according to the manufacturer’s GeneChip 3’ IVT Express kit user manual. Briefly, 100 ng of total RNA containing spiked in Poly-A RNA controls was used in a reverse transcription reaction using GeneChip 3’ IVT Express Kit to generate first-strand cDNA. Followed by second-strand synthesis using double-stranded cDNA in a 16h in vitro transcription (IVT) reaction to generate aRNA using GeneChip 3’ IVT Express Kit. Size distribution of the aRNA and fragmented aRNA, respectively, were assessed using an Agilent 2100 Bioanalyzer.

growth_protocol: Exponential Wild Type and Mutant Yeast cultures (50 ml of OD600 = 0.7) were either untreated or treated with rapamycin (200 ng/ml for 30 mins), cells harvested (4,000 rpm (3220 x g) for 2 min), resuspended in 6 ml of ice-cold sterile H2O, immersed into liquid nitrogen to snap freeze the cell pellet followed by immediate storage at -80°C.

extract_protocol: Total RNA isolation was performed using the hot-phenol method according to the published protocol (Koher & Domdey, 1991, Methods in Enzymology 194:398-405).

treatment_protocol: Yeast Cells were harvested by centrifugation using a benchtop centrifuge (4000 rpm, 5 min, 0ºC), washed with cold sterile distill water, immediately frozen in liquid nitrogen, and stored at -80ºC until RNA extraction.

value: R95A mutant

tag: agent

value: rapamycin


title: B.1.351-1μg-2_Spleen [bulk VDJ-seq]

description:
SA1-2_Spleen
VDJ Sequencing
LNP-mRNA vaccine


title: R95A mutant, treated, replicate 1


title: R95A mutant, untreated, replicate 3

description: R95A Mutant Yeast Strain untreated

source_name: R95A mutant, untreated, Yeast Strain

value: untreated


title: Wild Type, untreated, replicate 2

description: Wild Type untreated Yeast Strain

source_name: Wild Type, untreated, Yeast Strain

value: Wild Type


title: B.1.351-1μg-3_Blood [bulk VDJ-seq]

description:
SA1-3_Blood
VDJ Sequencing
LNP-mRNA vaccine


title: B.1.351-10μg-2_Spleen [bulk VDJ-seq]

description:
SA10-2_Spleen
VDJ Sequencing
LNP-mRNA vaccine


title: B.1.351-1μg-1_Spleen [bulk VDJ-seq]

description:
SA1-1_Spleen
VDJ Sequencing
LNP-mRNA vaccine


title: B.1.351-1μg-3_LN [bulk VDJ-seq]

description:
SA1-3_LN
VDJ Sequencing
LNP-mRNA vaccine


title: Wild Type, untreated, replicate 3

description: Wild Type untreated Yeast Strain


title: Wild Type, treated, replicate 3

description: Wild Type Yeast Strain treated with rapamycin

source_name: Wild Type, treated, Yeast Strain


title: R95A mutant, treated, replicate 2


title: Wild Type, treated, replicate 2


title: R95A mutant, untreated, replicate 2

description: R95A Mutant Yeast Strain untreated


title: B.1.351-10μg-3_Blood [bulk VDJ-seq]

description:
SA10-3_Blood
VDJ Sequencing
LNP-mRNA vaccine


title: Wild Type, treated, replicate 1


title: Wild Type, untreated, replicate 1

description: Wild Type untreated Yeast Strain

source_name: Wild Type, untreated Yeast Strain


title: R95A mutant, untreated, replicate 1

description: R95A Mutant Yeast Strain untreated


title: B.1.351-10μg-3_Spleen [bulk VDJ-seq]

description:
SA10-3_Spleen
VDJ Sequencing
LNP-mRNA vaccine


title: PBS-2_Spleen [bulk VDJ-seq]

description:
PBS-2_Spleen
VDJ Sequencing
LNP-mRNA vaccine


title: PBS-4_LN [bulk VDJ-seq]

description:
PBS-4_LN
VDJ Sequencing
LNP-mRNA vaccine


title: PBS-1_Spleen [bulk VDJ-seq]

description:
PBS-1_Spleen
VDJ Sequencing
LNP-mRNA vaccine


title: PBS-1_Blood [bulk VDJ-seq]

description:
PBS-1_Blood
VDJ Sequencing
LNP-mRNA vaccine


title: PBS-3_Spleen [bulk VDJ-seq]

description:
PBS-3_Spleen
VDJ Sequencing
LNP-mRNA vaccine


title: B.1.351-10μg-1_Blood [bulk VDJ-seq]

description:
SA10-1_Blood
VDJ Sequencing
LNP-mRNA vaccine


title: PBS-2_LN [bulk VDJ-seq]

description:
PBS-2_LN
VDJ Sequencing
LNP-mRNA vaccine


title: B.1.617-1μg-3_LN [bulk VDJ-seq]

description:
In1-3_LN
VDJ Sequencing
LNP-mRNA vaccine


title: PBS-3_Blood [bulk VDJ-seq]

description:
PBS-3_Blood
VDJ Sequencing
LNP-mRNA vaccine


title: B.1.617-1μg-3_Blood [bulk VDJ-seq]

description:
In1-3_Blood
VDJ Sequencing
LNP-mRNA vaccine


title: PBS-1_LN [bulk VDJ-seq]

description:
PBS-1_LN
VDJ Sequencing
LNP-mRNA vaccine


title: PBS-3_LN [bulk VDJ-seq]

description:
PBS-3_LN
VDJ Sequencing
LNP-mRNA vaccine


title: B.1.617-1μg-2_Spleen [bulk VDJ-seq]

description:
In1-2_Spleen
VDJ Sequencing
LNP-mRNA vaccine


title: ATRA+BEZ, t=3h, biological replicate1

city: Jena

first: Sven

last: Stengel

address: Am Klinikum 1

department: Clinic for Internal Medicine IV

country: Germany

institute: Jena University Hospital

description: Gene expression data from MV4-11 cells, treated with 100 nM ATRA + 100 nM NVP-BEZ238 for 3 hours replicate 1

hyb_protocol: Following fragmentation and labeling, 2.3 ug of ss cDNA were hybridized for 16 hr at 45°C at 60 rpm in a GeneChip Hybridization Oven. GeneChips were washed and stained on a GeneChip Fluidics Station 450 using the GeneChip Expression Hybridization Controls and the GeneTitan® Hybridization, Wash, and Stain Kit for WT Array Plates.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: Gene Array data was analyzed using Bioconductor version 3.11 and the R statistical programming language version 4.0.0. Thereby, RMA background correction and normalization was done using simpleaffy package version 2.66.0. For quality control we used the packages affyPLM version 1.66.0. Differentially expressed genes were identified using Limma package version 3.46.0 and annotated by the use of the hugene10sttranscriptcluster.db package version 8.7.0 and the annotate package version 1.68.0.

source_name: MV4-11 cells 100 nM ATRA + 100 nM NVP-BEZ238 t=3h

label_protocol: Biotinylated second cycle single stranded cDNA synthesis was carried out using the GeneChip® WT PLUS Reagent Kit in combination with the GeneChip® Eukaryotic Poly-A RNA Controls and 200 ng of total RNA. After that, second cycle ss-cDNA was fragmented and labeled by the use of the GeneChip WT Terminal Labeling Kit (Affymetrix reagents and protocols).

growth_protocol: MV4-11 cells were seeded in 6 well plates (1mio cells per well)  and  cultivated in RPMI-1640 medium (Biochrom AG, Germany) (4 ml per well) supplemented with 10% fetal bovine serum (FBS; Pan Biotech, Germany) and 1% L-Glutamine–Penicillin–Streptomycin solution (GPS; Sigma-Aldrich, USA). Cells were incubated at 37°C in 5% CO2 and 95% relative humidity.

extract_protocol: Following treatment, cells were washed in PBS and total RNA was isolated using the ZR RNA MiniPrep Kit (Zymo Research). We assessed the concentration and quality of the total RNA by spectrophotometry (NanoDrop, Thermo Scientific) and by using an Agilent 2100 BioAnalyzer (Agilent Technologies).

treatment_protocol: Cells were treated with the following agents: ATRA: 100 nM all-trans-retinoic acid (ATRA, Sigma), BEZ: 100 nM NVP-BEZ-235 (Selleck Chemicals), ATRA+BEZ: 100 nM all-trans-retinoic acid (ATRA, Sigma) + BEZ: 100 nM NVP-BEZ-235 (Selleck Chemicals). Treatment time was 3h, 12h and 24h.

value: 100 nM ATRA + 100 nM NVP-BEZ238

tag: time point


title: ATRA+BEZ, t=3h, biological replicate2

description: Gene expression data from MV4-11 cells, treated with 100 nM ATRA + 100 nM NVP-BEZ238 for 3 hours replicate 2


title: ATRA+BEZ, t=24h, biological replicate2

description: Gene expression data from MV4-11 cells, treated with 100 nM ATRA + 100 nM NVP-BEZ238 for 24 hours replicate 2

source_name: MV4-11 cells 100 nM ATRA + 100 nM NVP-BEZ238 t=24h


title: ATRA+BEZ, t=12h, biological replicate1

description: Gene expression data from MV4-11 cells, treated with 100 nM ATRA + 100 nM NVP-BEZ238 for 12 hours replicate 1

source_name: MV4-11 cells 100 nM ATRA + 100 nM NVP-BEZ238 t=12h


title: ATRA+BEZ, t=24h, biological replicate1

description: Gene expression data from MV4-11 cells, treated with 100 nM ATRA + 100 nM NVP-BEZ238 for 24 hours replicate 1


title: BEZ, t=12h, biological replicate2

description: Gene expression data from MV4-11 cells, treated with 100 nM NVP-BEZ238 for 12 hours replicate 2

source_name: MV4-11 cells 100 nM NVP-BEZ238 t=12h

value: 100 nM NVP-BEZ238


title: BEZ, t=12h, biological replicate1

description: Gene expression data from MV4-11 cells, treated with 100 nM NVP-BEZ238 for 12 hours replicate 1


title: ATRA+BEZ, t=12h, biological replicate2

description: Gene expression data from MV4-11 cells, treated with 100 nM ATRA + 100 nM NVP-BEZ238 for 12 hours replicate 2


title: BEZ, t=3h, biological replicate2

description: Gene expression data from MV4-11 cells, treated with 100 nM NVP-BEZ238 for 3 hours replicate 2

source_name: MV4-11 cells 100 nM NVP-BEZ238 t=3h


title: B.1.617-1μg-2_Blood [bulk VDJ-seq]

description:
In1-2_Blood
VDJ Sequencing
LNP-mRNA vaccine


title: B.1.617-1μg-3_Spleen [bulk VDJ-seq]

description:
In1-3_Spleen
VDJ Sequencing
LNP-mRNA vaccine


title: BEZ, t=24h, biological replicate2

description: Gene expression data from MV4-11 cells, treated with 100 nM NVP-BEZ238 for 24 hours replicate 2

source_name: MV4-11 cells 100 nM NVP-BEZ238 t=24h


title: B.1.617-1μg-1_LN [bulk VDJ-seq]

description:
In1-1_LN
VDJ Sequencing
LNP-mRNA vaccine


title: B.1.617-1μg-1_Blood [bulk VDJ-seq]

description:
In1-1_Blood
VDJ Sequencing
LNP-mRNA vaccine


title: B.1.617-10μg-3_LN [bulk VDJ-seq]

description:
In10-3_LN
VDJ Sequencing
LNP-mRNA vaccine


title: PBS-4_Blood [bulk VDJ-seq]

description:
PBS-4_Blood
VDJ Sequencing
LNP-mRNA vaccine


title: B.1.351-10μg-1_LN [bulk VDJ-seq]

description:
SA10-1_LN
VDJ Sequencing
LNP-mRNA vaccine


title: B.1.617-10μg-3_Blood [bulk VDJ-seq]

description:
In10-3_Blood
VDJ Sequencing
LNP-mRNA vaccine


title: BEZ, t=3h, biological replicate1

description: Gene expression data from MV4-11 cells, treated with 100 nM NVP-BEZ238 for 3 hours replicate 1


title: B.1.617-1μg-1_Spleen [bulk VDJ-seq]

description:
In1-1_Spleen
VDJ Sequencing
LNP-mRNA vaccine


title: ATRA, t=12h, biological replicate2

description: Gene expression data from MV4-11 cells, treated with 100 nM ATRA for 12 hours replicate 2

source_name: MV4-11 cells 100 nM ATRA t=12h

value: 100 nM ATRA


title: ATRA, t=24h, biological replicate1

description: Gene expression data from MV4-11 cells, treated with 100 nM ATRA for 24 hours replicate 1

source_name: MV4-11 cells 100 nM ATRA t=24h


title: B.1.617-10μg-2_Spleen [bulk VDJ-seq]

description:
In10-2_Spleen
VDJ Sequencing
LNP-mRNA vaccine


title: B.1.617-10μg-1_Spleen [bulk VDJ-seq]

description:
In10-1_Spleen
VDJ Sequencing
LNP-mRNA vaccine


title: B.1.617-10μg-2_Blood [bulk VDJ-seq]

description:
In10-2_Blood
VDJ Sequencing
LNP-mRNA vaccine


title: B.1.617-10μg-1_LN [bulk VDJ-seq]

description:
In10-1_LN
VDJ Sequencing
LNP-mRNA vaccine


title: ATRA, t=3h, biological replicate2

description: Gene expression data from MV4-11 cells, treated with 100 nM ATRA for 3 hours replicate 2

source_name: MV4-11 cells 100 nM ATRA t=3h


title: ATRA, t=12h, biological replicate1

description: Gene expression data from MV4-11 cells, treated with 100 nM ATRA for 12 hours replicate 1


title: ATRA, t=24h, biological replicate2

description: Gene expression data from MV4-11 cells, treated with 100 nM ATRA for 24 hours replicate 2


title: B.1.617-10μg-1_Blood [bulk VDJ-seq]

description:
In10-1_Blood
VDJ Sequencing
LNP-mRNA vaccine


title: B.1.617-10μg-2_LN [bulk VDJ-seq]

description:
In10-2_LN
VDJ Sequencing
LNP-mRNA vaccine

source_name: Lymph node


title: PBS-2_Blood [bulk VDJ-seq]

description:
PBS-2_Blood
VDJ Sequencing
LNP-mRNA vaccine

source_name: Blood


title: Untreated control, t=24h, biological replicate2

description: Gene expression data from MV4-11 cells, left untreated for 24 hours replicate 2

source_name: MV4-11 cells untreated t=24h


title: ATRA, t=3h, biological replicate1

description: Gene expression data from MV4-11 cells, treated with 100 nM ATRA for 3 hours replicate 1


title: RNA-seq_WT_3

city: washington dc

first: Shaoqi

last: Zhu

state: District of Columbia

address: 725 21st st nw

institute: The George Washington University

data_processing:
The sequencing quality of RNA-Seq libraries were assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
RNA-Seq libraries were mapped to mouse genome using Tophat (v2.1.0, Trapnell et al., Bioinformatics). UCSC genes for mouse mm10 from iGenome(http://support.illumina.com/sequencing/sequencing_software/igenome.html) were used for gene annotation.
Mapped reads were then processed by Cuffdiff (v2.2.1, Trapnell et al., Nature biotechnology) to estimate expression levels of all genes and identify differentially expressed genes (FDR = 0.05). The expression level of a gene is expressed as a gene-level Fragments Per Kilobase of transcripts per Million mapped reads (FPKM) value.
Assembly: mm9
Supplementary files format and content: FPKM

source_name: WT stim CD8 RNAseq rep3

extract_protocol:
Naive CD8+ T cells were allowed to undergo homeostatic poliferation of 72 hrs in vivo, then sort-purified, and total RNA was extracted using standard Qiagen RNeasy columns.
RNA-seq libraries were prepared for sequencing using stardard Illumina protocol. The resulting libraries were seqeunced with Illumina Hiseq-2000 platform.

value: wild type

value: splenocytes

value: CD8 T cells

tag: cell phenotype


title: Untreated control, t=3h, biological replicate2

description: Gene expression data from MV4-11 cells, left untreated for 3 hours replicate 2

source_name: MV4-11 cells untreated t=3h


title: Untreated control, t=12h, biological replicate1

description: Gene expression data from MV4-11 cells, left untreated for 12 hours replicate 1

source_name: MV4-11 cells untreated t=12h


title: RNA-seq_DKO_2

source_name: Tcf1/Lef1-deficient stim CD8 RNAseq rep3


title: BEZ, t=24h, biological replicate1

description: Gene expression data from MV4-11 cells, treated with 100 nM NVP-BEZ238 for 24 hours replicate 1


title: E_coli_rpoC-flag_3end_seq_LB_total

city: Berlin

first: Lydia

last: Herzel

address: Takustr. 6

department: Biology, Chemistry and Pharmacy

institute: Freie Universität

data_processing:
RNA-seq and Rend-seq data processing and mapping was done as described in (Lalanne et al., Cell 2018; Parker et al., Cell Systems 2020). For 3’ end-seq in analogy to Rend-seq, 3’ end linker sequences were trimmed. To deal with non-template addition during reverse transcription, all reads were further trimmed with the fastx_trimmer of the fastxtoolkit/0.0.13 by 1nt at their 5’end and only reads of 15nt length or longer were kept for mapping with bowtie/1.2 using the options -v 0 -k 1. For further data analysis mapped data were transformed into bam-format and bedgraph-format using samtools/1.5 and bedtools/2.25.0. Coverage data include 3’ terminal single nucleotide counts per read. To identify 3’adenylated transcript ends, the unmapped reads were trimmed using cutadapt/1.16. First, 3’terminal CCAs were removed with the following settings: -a "CCA$" --minimum-length 15 -O 3 --trimmed-only. Second, A-tails of any length were trimmed (-a "A{38}" --minimum-length 15 -O 1 --trimmed-only). These trimmed reads were mapped and further converted with the same settings and code as untrimmed reads above. For total RNA 3’ end analysis mapped trimmed (i.e. A-tailed) and untrimmed 3’ end coverage profiles were summed.
Assembly: E. coli NC_000913.2, B. subtilis NC_000964.3
Supplementary files format and content: bedgraph-files, 3' most read position recorded in coverage files

organism: Escherichia coli

source_name: Bacteria

growth_protocol: E. coli cells were grown in LB, MOPS Complete or MOPS Minimal media supplemented with 0.2% Glucose. B. subtilis cells were grown in MCCG media (Parker et al., Cell Systems 2020). To harvest cells in exponential growth, cells were backdiluted from overnight cultures into the respective growth media to enable ~10 doublings at 37°C prior to harvest at an OD600 smaller or equal to 0.3 (Sezonov et al. J Bac 2007). To harvest cells in early stationary growth, cells were harvested shortly after growth had plateaued (harvest at OD600 2.8 for MOPS Complete and at OD600 2.26 for MOPS Minimal). For Kasugamycin treatment, Kasugamycin was added at a final concentration of 1mg/ml to cells at OD600 0.22 grown in MOPS Complete media. After 15 min treated and untreated cells were harvested for total RNA analysis.

extract_protocol:
Samples have been either extracted by RNAsnap (Stead et al., NAR 2012), Hot Phenol, RiboPure (ThermoFisher/Ambion), RNeasy (Qiagen) or Trizol, precipitated, Dnase treated and cleaned uo with RNA clean & concentrator columns (Zymo research).
RNA-seq for E. coli Δpnp, Δrnb, ΔpcnB and MG1655 wildtype was executed as described in (Parker et al., Cell Systems 2020). Rend-seq libraries were prepared as described in (Lalanne et al., Cell 2018) with 25s RNA fragmentation. For 3’ end sequencing the Rend-seq protocol was modified in a way that 3’ end ligation (5'_App/CTGTAGGCACCATCAAT/3ddC_3') was done preceding fragmentation for 2min. Final libraries were sequenced on Illumina HiSeq 2000 or NextSeq500 machines.
single-end RNA-seq

treatment_protocol: For total RNA analysis, 5ml of cells were transferred into 0.55ml of ice-cold stop solution (95:5 Ethanol:Phenol) in a 15ml conical tube, quickly inverted and spun at 3220g at 4°C for 5-10min. The supernatant was discarded and cell pellets flash-frozen in liquid nitrogen and stored at -80C until lysis and RNA extraction. For nascent RNA and polysome analysis, 250ml of cells were filter harvested at 37°C and scraped into liquid nitrogen (Johnson and Li, 2018). The cell paste was kept at -80°C until lysis and RNA extraction.

value: K-12 MG1655, rpoC-flag,kan


title: E_coli_rpoC-flag_3end_seq_LB_nascent

description: nascent RNA


title: RNA-seq_DKO_1

source_name: Tcf1/Lef1-deficient stim CD8 RNAseq rep2


title: RNA-seq_DKO_0

source_name: Tcf1/Lef1-deficient stim CD8 RNAseq rep1


title: E_coli_WT2_3end_seq_LB

data_processing:
RNA-seq and Rend-seq data processing and mapping was done as described in (Lalanne et al., Cell 2018; Parker et al., Cell Systems 2020). For 3’ end-seq in analogy to Rend-seq, 3’ end linker sequences were trimmed. To deal with non-template addition during reverse transcription, all reads were further trimmed with the fastx_trimmer of the fastxtoolkit/0.0.13 by 1nt at their 5’end and only reads of 15nt length or longer were kept for mapping with bowtie/1.2 using the options -v 0 -k 1. For further data analysis mapped data were transformed into bam-format and bedgraph-format using samtools/1.5 and bedtools/2.25.0. Coverage data include 3’ terminal single nucleotide counts per read. To identify 3’adenylated transcript ends, the unmapped reads were trimmed using cutadapt/1.16. First, 3’terminal CCAs were removed with the following settings: -a "CCA$" --minimum-length 15 -O 3 --trimmed-only. Second, A-tails of any length were trimmed (-a "A{38}" --minimum-length 15 -O 1 --trimmed-only). These trimmed reads were mapped and further converted with the same settings and code as untrimmed reads above. For total RNA 3’ end analysis mapped trimmed (i.e. A-tailed) and untrimmed 3’ end coverage profiles were summed.
Genome_build: E. coli NC_000913.2, B. subtilis NC_000964.3
Supplementary_files_format_and_content: bedgraph-files

extract_protocol:
Samples have been either extracted by RNAsnap (Stead et al., NAR 2012), Hot Phenol, RiboPure (ThermoFisher/Ambion), RNeasy (Qiagen) or Trizol, precipitated, Dnase treated and cleaned uo with RNA clean & concentrator columns (Zymo research).
RNA-seq for E. coli Δpnp, Δrnb, ΔpcnB and MG1655 wildtype was executed as described in (Parker et al., Cell Systems 2020). Rend-seq libraries were prepared as described in (Lalanne et al., Cell 2018) with 25s RNA fragmentation. For 3’ end sequencing the Rend-seq protocol was modified in a way that 3’ end ligation (5'_App/CTGTAGGCACCATCAAT/3ddC_3') was done preceding fragmentation for 2min. Final libraries were sequenced on Illumina HiSeq 2000 or NextSeq500 machines.

value: wildtype


title: RNA-seq_CTCF_KO_3

source_name: CTCF-deficient stim CD8 RNAseq rep3

value: CTCF-/-


title: E_coli_WT2_3end_seq_LB_Trizol


title: E_coli_WT_3end_seq_LB_RiboPure


title: Untreated control, t=3h, biological replicate1

description: Gene expression data from MV4-11 cells, left untreated for 3 hours replicate 1


title: Untreated control, t=24h, biological replicate1

description: Gene expression data from MV4-11 cells, left untreated for 24 hours replicate 1


title: PDAC10 ribo-

city: nanjing

first: Guodong

last: Shi

state: Jiangsu

address: guangzhou road 300

country: China

institute: the First Affliated Hospital of Nanjing Medical University

description: frozen pancreatic tissue

data_processing:
Illumina Casava1.7 software used for basecalling.
Quality control and filtering of the raw fastq data was performed by using fastp tool with default parameters.
Bowtie1/2 index and transcriptome index were first established with Bowtie1 (version 1.0.0) and Bowtie2 (version 2.1.0) software for TopHat-Fusion and TopHat2, respectively. Ribo- RNA-seq fragments were then mapped to the human genome GRCh37/hg19 assembly with known gene annotations by TopHat2 (version 2.1.1). Tophat2-unmapped fragments were next mapped to the same reference genome using TopHat-Fusion in TopHat2 (version 2.1.0).
CIRCexplorer2 (version 2.3.8) was used for subsequent circRNA quantification. CIRCexplorer3-CLEAR was performed for generating the CIRCscore and FPBcirc from processed CIRCexplorer2 output files.
Supplementary files format and content: ciri,circexplorer2_circularRNA_known.txt and find_circ.candidates.bed for each Sample were  output files from three popular circRNAs detection algorithms (CIRI2 v2.0.6, CIRCexplorer2 v2.3.8, and find_circ v1.2), respectively. Chimeric.out.sam.result.as.txt and Chimeric.out.sam.result.circ.txt for each Sample output files were generated from CircSplice. CIRCexplorer3_quant.txt for each Sample was computed from CIRCexplorer3-CLEAR.

source_name: PDAC ribo-

extract_protocol:
Total RNAs were isolated from 10 patients with T4 pathological stage using TRIzol Reagent (Invitrogen, CA, USA).
After passing the assessment of RNA purity and RNA integrity (RIN), ribosomal RNAs were removed from total RNAs using Epicentre Ribo-Zero rRNA Removal Kit (illumina, USA), The purified library products were sequenced on Illumina HiSeq 2000 (huayin health, China).

value: frozen pancreatic tissue

tag: gender

value: Female

tag: age

tag: pre-operative ca199

tag: location

value: body/tail

tag: tumor dimension

tag: ajcc8th pathological stage

value: III

tag: t stage

tag: the total number of lymph nodes removed and pathologically assessed for disease

tag: the number of positive lymph nodes

tag: neural invasion

value: no

tag: vital status

value: ALIVE

tag: overall survival (month)

tag: genome build


title: PDAC8 ribo-

description: frozen pancreatic tissue

tag: tissue

value: Male

value: yes


title: PDAC9 ribo-

description: frozen pancreatic tissue

value: head


title: PDAC7 ribo-

description: frozen pancreatic tissue


title: RNA-seq_WT_1

source_name: WT stim CD8 RNAseq rep1

tag: genotype

tag: cell type


title: RNA-seq_WT_2

source_name: WT stim CD8 RNAseq rep2

tag: cell phenotype


title: PDAC6 ribo-

description: frozen pancreatic tissue

tag: gender


title: RNA-seq_CTCF_KO_2

source_name: CTCF-deficient stim CD8 RNAseq rep2


title: RNA-seq_CTCF_KO_1

source_name: CTCF-deficient stim CD8 RNAseq rep1


title: Untreated control, t=12h, biological replicate2

description: Gene expression data from MV4-11 cells, left untreated for 12 hours replicate 2

tag: treatment

value: untreated

tag: time point


title: PDAC4 ribo-

description: frozen pancreatic tissue

tag: age

tag: pre-operative ca199

tag: location

value: DEAD


title: PDAC1 ribo-

description: frozen pancreatic tissue

tag: tumor dimension

tag: ajcc8th pathological stage

tag: t stage


title: PDAC2 ribo-

description: frozen pancreatic tissue

tag: the total number of lymph nodes removed and pathologically assessed for disease

tag: the number of positive lymph nodes

tag: neural invasion


title: Untreated_Male_liver

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

description: 10x Genomics single nuclei RNA, polyA-selected

data_processing:
Raw fastq sequencing files were processed using CellRanger (v3.1.0) to align sequence reads to mouse reference genome mm10. We used a custom Gene Transfer Format (GTF) file comprised of 76,102 mouse genes for use with the Cellranger mkref pipeline. This reference GTF file consists of mouse mm10 gene coordinates for RefSeq protein coding genes (n = 20,960), mitochondrial genes (n = 13), a set of mouse liver-expressed lncRNAs genes (n = 48,261), RefSeq non-coding genes (NR accession numbers) that do not overlap with the set of 48,261 lncRNAs (n = 2,077), Ensembl non-coding lncRNAs that do not overlap either the RefSeq NR gene set or the 48,261 lncRNA gene set (n =4,697), 3 other lncRNAs with interesting liver functions (lnc-LFAR1, LeXis, Lnclgr), and 91 ERCC sequences. The UCSC genome browser liftOver tool (https://genome.ucsc.edu/cgi-bin/hgLiftOver) was used to convert the original set of mouse liver lncRNAs, discovered using mm9 reference genome, to mm10 coordinates. A GTF file comprised of gene coordinates from the full gene body, including all exonic and all intronic regions of each gene, was used when analyzing snRNA-seq data to enable Cellranger to capture the many unspliced RNAs found in nuclei, including those derived from lncRNAs, in addition to partially processed and mature RNAs, many of which are abundant in the nucleoplasm. As reads from genomic regions that overlap each other on the same strand are excluded by Cellranger, we made the following change for 4,352 overlapping genes that we identified in order to minimize the impact of the exclusion of overlap regions from Cellranger counting. For those 4,352 genes, we modified the full gene body GTF file to include all exons (regardless of whether they overlap another gene) plus all non-exonic regions that were unique to each gene. Sequencing data for all six samples was combined using CellRanger aggr, which enabled batch effect correction to be performed on the data set as a whole. A normalized integrated count matrix was generated by dividing the unique molecular identifier (UMI) count for each gene by the total number of UMIs in each cell, followed by log-transformation. To fully integrate the data sets, Harmony was applied to further remove unwanted variance by embedding and integrating shared cell types that are present across all six samples, by using the normalized integrated count matrix. Graph-based clustering of the cells based on their gene expression profiles was performed using the FindClusters function in Seurat. Nuclei with >5% of UMIs mapping to mitochondrial genes were considered low quality (e.g., due to mitochondrial contamination associated with apoptotic cell death or tissue necrosis) (n= 6,059 nuclei across the six liver groups analyzed) and were removed. Additionally, a small cluster of 1,316 nuclei with higher expression of mitochondrial genes than the other remaining clusters was removed. An additional 2,563 nuclei predicted to be multiplets, comprised of at least two nuclei each, were identified using DoubletFinder and removed (analysis parameters: top 10 principal components and 5% doublet formation rate). These steps filtered out a total of 9,937 nuclei from an initial total of 42,131 nuclei across the six samples, leaving 32,194 nuclei for our analysis. Of these, 31,896 nuclei mapped to nine clusters identified in the processed data file provided (G183M1M2M3M4_G185M1M2_M_F_TCPO_cGH.cloupe), where the final data set was re-integrated using Harmony and UMAPs were generated and are presented for downstream analysis with the Loupe Browser, available for download from 10X Genomics (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest?).
Genome_build: mm10
Supplementary_files_format_and_content: Cloupe file of final integrated set of approx 32,000 nuclei obtained from the 6 independent groups analyzed, for use with the 10X Genomics Loupe Browser.

source_name: liver tissue_nuclear RNA

extract_protocol:
The following buffers were prepared fresh daily in advance and kept on ice for up to 2 h: Base Solution, 10 mM Tris-Cl, pH 7.4, 146 mM NaCl, 1 mM CaCl2 21 mM MgCl2; Lysis Buffer, Base Solution containing 0.1% Triton X-100 (Cat. #T8787, Sigma), with 80 U/mL Protector RNase Inhibitor (Cat # 3335402001, Roche) added just prior to use; BSA Wash Buffer, 1X PBS containing 2% BSA and 0.02% Tween-20, with 80 U/mL Protector RNase Inhibitor added just prior to use. Due to the high cost of 10x Genomics library preparation, we prepared a single sequencing library for each of the 6 treatment groups studied, each of which was comprised of single nuclei extracted from four individual mouse livers (biological replicates) for each of the 6 groups: vehicle-treated male liver, 27-hr TCPOBOP-treated male liver, vehicle-treated female liver, 27-hr TCPOBOP-treated female liver, untreated male liver (marked Male-1 in the figures), and continuous GH (cGH)-infused male liver. Thus, each of our snRNA-seq samples represent single cell gene expression profiles from a population of four mice, rather than a single individual, minimizing the impact of individual variation on the single cell and differential expression transcriptomic profiles and datasets obtained. To minimize premature tissue thawing and RNA degradation, a 50-100 mg piece of each liver was cut and stored in an Eppendorf tube on dry ice until ready for processing. For this protocol, all pipette tips used were RNase and DNase free (Cat. #76322-132, 76322-134, 76322-150, 76322-154, VWR).    The frozen pre-cut pieces of liver (from all livers in the group) were transferred to a 3 mL glass-on-glass dounce homogenizer with 1 ml of Lysis Buffer, on ice. Keeping the homogenizer on ice, the sample was dounced for 10 strokes with pestle A (loose fit) followed by 10 strokes with pestle B (tight fit) until fully homogenized. BSA Wash Buffer (1 ml) was then added, pipetted up and down a few times to mix, and the sample was then passed through a 40 µm cell strainer into a 50 ml conical tube on ice. Three additional washes of BSA Wash Buffer (1 ml) was used to rinse the homogenizer and pestles on ice, passed through the same 40 µm cell strainer and then added to the homogenized sample in the conical tube. The homogenizer and pestles were then washed with MilliQ water on ice three times before processing the next sample. Homogenized samples were kept on ice until all samples were ready to proceed to the next stage. Each homogenized sample was divided into three 1.5 ml Eppendorf tubes, which were centrifuged at 500g in a swinging bucket centrifuge for 5 min at 4° C to pellet the lysed cells. The supernatant was discarded and the nuclei were reconstituted in 1 mL BSA Wash Buffer, pooling all three tubes back into a single sample. Half of the sample, 500 µL, was transferred to a new 1.5 mL Eppendorf tube, and diluted with 500 µL BSA Wash Buffer before pelleting at 500g for 5 min at 4° C. The supernatant was discarded and the pellet was resuspended in 1 mL BSA Wash Buffer then passed through a 20 µm cell strainer on ice (Cat # 43-50020-03, PluriSelect).  The strained sample was transferred to LoBind 1.5 mL Eppendorf tubes (Cat # 022431021, Eppendorf) on ice, quantified using a Cellometer (Nexcelom) and diluted to a final concentration of 1.2 x 106 nuclei/mL in BSA Wash Buffer. Samples were kept on ice from this point until they were used for library generation.
Libraries were constructed by the Boston University Single Cell Sequencing Core facility following the manufacturer's instructions for 10x Genomics Single Cell 3' Sequencing (Version 3 chemistry).
Single nucleus RNA-seq (snRNA-seq)

treatment_protocol: For male and female mice treated with vehicle or TCPOBP: Male and female CD-1 mice (strain Crl:CD1(ICR)), approx 7-8 weeks of age, were purchased from Charles River Laboratories (Wilmington, Massachusetts). TCPOBOP (1,4-bis(2-(3,5-dichloropyridyloxy))benzene) (purchased from Santa Cruz Biotechnology; Chem Cruze, Cat. #SC-203291) was dissolved in DMSO at 7.5 mg/ml, and then diluted 10-fold into corn oil, followed by IP injection at 4 µl per gram body weights (final dose: 3 mg TCPOBOP and 4 µl of 10% DMSO in corn oil, per kg body weight). Injections of TCPOBOP, or corn oil control, were performed at 8 AM. After 27 hr, at 11 AM, mice were euthanized under CO2 by cervical dislocation. For untreated male and 7-day continuous GH-infused male mice: These are the same livers described in Ling et al, Mol Cell Biol 2010 (PMID: 20876297). Briefly, approx. 7-8-week old male CD-1 mice were implanted with a subcutaneous Alzet model 1007D micro-osmotic pump to deliver 20 ng of rat GH per hr per gram body weight for 7 days before being euthanized under CO2 by cervical dislocation. Livers were excised and flash frozen in liquid nitrogen then stored at -80° C.

tag: strain

tag: Sex

value: 8 weeks

value: Untreated


title: Vehicle_Male_liver

value: Vehicle control


title: Tcf1/Lef1-deficient stim CD8 RNAseq rep3

data_processing:
The sequencing quality of RNA-Seq libraries were assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
RNA-Seq libraries were mapped to mouse genome using Tophat (v2.1.0, Trapnell et al., Bioinformatics). UCSC genes for mouse mm10 from iGenome(http://support.illumina.com/sequencing/sequencing_software/igenome.html) were used for gene annotation.
Mapped reads were then processed by Cuffdiff (v2.2.1, Trapnell et al., Nature biotechnology) to estimate expression levels of all genes and identify differentially expressed genes (FDR = 0.05). The expression level of a gene is expressed as a gene-level Fragments Per Kilobase of transcripts per Million mapped reads (FPKM) value.
Genome_build: mm9
Supplementary_files_format_and_content: CD8-HP_CuffDiff_Summary202005.xlsx

source_name: CD8 T cells

extract_protocol:
Naïve CD8+ T cells were sort-purified from the spleen, stimulated with IL-7 and IL-15 for 72 hrs in vitro, and total RNA was extracted using standard Qiagen RNease columns.
RNA-seq libraries were prepared for sequencing using stardard Illumina protocol. The resulting libraries were seqeunced with Illumina Hiseq-2000 platform.

tag: genotypes

tag: tissue

value: splenocytes

value: GFP+ TCRbeta+ CD62Lhi CD44lo-med CD8+


title: Tcf1/Lef1-deficient stim CD8 RNAseq rep2

tag: cell phenotype


title: TCPOBOP_Male_liver

value: TCPOBOP treatment (27 h)


title: Vehicle_Female_liver


title: TCPOBOP_Female_liver


title: cGH_Male_liver

value: Continuous Growth Hormone infusion for 7 days


title: PDAC5 ribo-

description: frozen pancreatic tissue

value: frozen pancreatic tissue

tag: gender

tag: vital status

tag: overall survival (month)

tag: genome build


title: Tcf1/Lef1-deficient stim CD8 RNAseq rep1


title: WT stim CD8 RNAseq rep2

value: wild type


title: PDAC9 poly(A)-/ribo- plus RNase R-treated

description: frozen pancreatic tissue

data_processing:
Illumina Casava1.7 software used for basecalling.
Quality control and filtering of the raw fastq data was performed by using fastp tool with default parameters.
The circRNAs were identified by 3 popular algorithms, including CIRI2 (version 2.0.6),CIRCexplorer2 (version 2.3.8) and find_circ (version 1.2).
R packages DEGseq and DEseq were used to identify DEcircRNAs from the gene expression values of RNA-seq data. In the DEGexp function of package DEGseq, we established argument method as "MARS" that represents MA-plot-based method with Random Sampling model. CircRNAs selection criteria were fold change (FC) >= 2, and Signature(p-value < 0.001)=TRUE. In the estimateDispersions function of package DEseq, we set parameter values, including "method='pooled' ", "sharingMode='maximum' ", and "fitType='local' ". CircRNAs selection criteria was fold change (FC) >= 2, and p-value<0.05.
Supplementary files format and content: ciri,circexplorer2_circularRNA_known.txt and find_circ.candidates.bed for each Sample were  output files from three popular circRNAs detection algorithms (CIRI2 v2.0.6, CIRCexplorer2 v2.3.8, and find_circ v1.2), respectively. Chimeric.out.sam.result.as.txt and Chimeric.out.sam.result.circ.txt for each Sample output files were generated from CircSplice. CIRCexplorer3_quant.txt for each Sample was computed from CIRCexplorer3-CLEAR.

source_name: PDAC poly(A)-/ribo- plus RNase R-treated

extract_protocol:
Total RNAs were isolated from 10 patients with T4 pathological stage using TRIzol Reagent (Invitrogen, CA, USA).
After passing the assessment of RNA purity and RNA integrity (RIN), total RNAs were separated into polyadenylated and nonpolyadenylated fraction by oligo(dT) magnetic beads (Invitrogen). Ribosomal RNAs were then removed from nonpolyadenylated fraction using Ribo-Zero rRNA Removal Kit. Poly(A)-/ribo- RNAs were further treated with RNase R (Epicentre, USA) and fragmented to approximately 200bp. The purified library products were sequenced on Illumina HiSeq 2000 (huayin health, China).

tag: age

tag: pre-operative ca199

value: III


title: WT stim CD8 RNAseq rep1


title: WT stim CD8 RNAseq rep3


title: PDAC8 poly(A)-/ribo- plus RNase R-treated

description: frozen pancreatic tissue

tag: location

value: body/tail

tag: tumor dimension


title: PDAC6 poly(A)-/ribo- plus RNase R-treated

description: frozen pancreatic tissue

value: Female

tag: ajcc8th pathological stage

tag: t stage

value: ALIVE


title: PDAC7 poly(A)-/ribo- plus RNase R-treated

description: frozen pancreatic tissue

value: Male

tag: the total number of lymph nodes removed and pathologically assessed for disease

tag: the number of positive lymph nodes

value: yes


title: PDAC10 poly(A)-/ribo- plus RNase R-treated

description: frozen pancreatic tissue

tag: neural invasion

value: no


title: Oxalate_late_8

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: ETH/University of Zurich

data_processing:
bcl2Fastq v2.19 software used for demultiplexing + basecalling.
reads trimmed with trimmomatic, options: ILLUMINACLIP:adapters.fa:1:20:7:5:true AVGQUAL:10 MINLEN:20
reads mapped with STAR  v2.7.1, options: --sjdbOverhang 150 --twopassMode None --runThreadN 8 --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --outMultimapperOrder Random --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif --outSAMattributes All --outStd BAM_Unsorted --outSAMtype BAM Unsorted
count: FeatureCounts (Bioconductor), options: allowMultiOverlap = true; countPrimaryAlignmentsOnly= true; minFeatureOverlap=10; minMapQuality= 10 ; keepMultiHits=true
differential expression analysis: EdgeR, options: normMethod = TMM; backgroundExpression =10; testMethod = glm; deTest =QL
Genome_build: Mus musculus GRCh38.p5
Supplementary_files_format_and_content: tad-delimited, raw counts

source_name: Oxalate late

extract_protocol:
TruSeq RNA stranded
PolyA, TruSeq RNA Kit

tag: treatment

value: Alkali therapy


title: PDAC5 poly(A)-/ribo- plus RNase R-treated

description: frozen pancreatic tissue

value: DEAD


title: PDAC4 poly(A)-/ribo- plus RNase R-treated

description: frozen pancreatic tissue

value: head


title: PDAC3 poly(A)-/ribo- plus RNase R-treated

description: frozen pancreatic tissue


title: PDAC3 ribo-

description: frozen pancreatic tissue


title: PDAC2 poly(A)-/ribo- plus RNase R-treated

description: frozen pancreatic tissue


title: PDAC1 poly(A)-/ribo- plus RNase R-treated

description: frozen pancreatic tissue


title: Oxalate_late_2


title: B.1.617-10μg-3_Spleen [bulk VDJ-seq]

description:
In10-3_Spleen
VDJ Sequencing
LNP-mRNA vaccine

source_name: Spleen

value: Spleen

tag: cell type

value: Lymphocyte

tag: genotype

value: WT

value: PBS


title: Oxalate_late_30


title: Oxalate_40

source_name: Oxalate

value: Untreated


title: Oxalate_39


title: JCe0042b

city: Lausanne

last: Gfeller

address: Bugnon 25A

department: Department of Oncology

institute: University of Lausanne

description: TCR beta sequencing

data_processing:
library strategy: TCR-seq
Deep sequencing of the TCR alpha and beta chain was performed on Illumina instrument
fastq reads were demultiplexed, assembled and aligned to databases of TCRa and TCRb with MIGEC (v1.2.9)
Assembly: IMGT human TCR genes
Supplementary files format and content: MIGEC CdrBlast (.txt) including V and J genes, CDR3 sequences, counts

extract_protocol:
mRNA was extracted using the Dynabeads mRNA DIRECT Purification Kit according to the manufacturer instruction
Libraries were prepare using targeted TCR amplification (Bobisse et al, Nat Commun. 2018 Mar 15;9(1):1092.)

tag: multimer

tag: donor


title: JCe0046b

description: TCR beta sequencing

value: effector CD8


title: JCe0045b

description: TCR beta sequencing


title: JCe0044b

description: TCR beta sequencing


title: Oxalate_32


title: JCe0051b

description: TCR beta sequencing

value: naive CD8


title: JCe0054b

description: TCR beta sequencing


title: JCe0047b

description: TCR beta sequencing


title: Control_late_7

source_name: Control late


title: Oxalate_12


title: Control_late_37


title: Oxalate_late_5


title: JC0034b

description: TCR beta sequencing


title: Control_late_1


title: JCe0044a

description: TCR alpha sequencing


title: JC0035b

description: TCR beta sequencing


title: Control_late_27


title: Oxalate_late_33


title: JCe0042a

description: TCR alpha sequencing


title: Control_35

source_name: Control


title: JCe0046a

description: TCR alpha sequencing


title: Oxalate_3


title: Control_26


title: JCe0045a

description: TCR alpha sequencing


title: Control_9


title: Control_late_4


title: MEF-cre-GDC500-3

city: New York

first: Erik

last: Ladewig

state: New York

address: 435 East 65th Street

institute: MSKCC

data_processing:
FASTQ files were first trimmed for quality (Phred score=5) and sequencing adaptors by trim_galore (v0.6.1) powered by Cutadapt.
The sequenced reads in the FASTQ files were aligned to the appropriate mouse or human transcriptome (GRCm38_M22 and GRCh38 version 30, respectively) obtained from Gencode.
Transcripts and genes were quantified using the Salmon Aligner (v1.2.1).
Salmon quantified files were imported with txImport (v1.16.1) using default parameters.
For each cell line all samples were normalized together and differential gene expression was called using DESeq2 (v1.28.1)
Genome_build: GRCh38_v30 or GRCm38_m22
Supplementary_files_format_and_content: count text files

source_name: H1047R PIK3CA Replicate 3 GDC0032 (500nM) PI3Ka inhibitor treatment

growth_protocol: Isogenic parental and PIK3CA H1047R heterozygous mutant were purchased from Horizon. MEFs were obtained via an MTA24  and infected with adenoviral GFP (parental cells) or adenoviral Cre to obtain homozygous PIK3CA H1047R mutation (mutant cells).

extract_protocol:
RNA was isolated using the QIAGEN RNeasy Kit and retrotranscription was performed using the iScript cDNA synthesis kit from Bio-Rad, following manufacturer’s instructions. cDNA was amplified by real time quantitative PCR in a ViiA 7 Real-Time PCR system, using SYBR Select Master Mix from Applied Biosystems
RNA from MCF10A cells was sequenced using Illumina HiSeq 2000 instrument at 2 X 150 nucleotide paired-end reads.  RNA from MEF cells were sequenced using Illumina HISeq 2000 instrument at 2 x 100 nucleotide paired-end reads.

treatment_protocol: Where indicated, cells were treated with DMSO as control or alpelisib (BYL719)  at 1uM or GDC500 at 500 nM.

tag: cell line

value: MEF

tag: condition

value: mutant

value: homozygous PIK3CA H1047R mutation


title: MEF-cre-GDC500-1

source_name: H1047R PIK3CA Replicate 1 GDC0032 (500nM) PI3Ka inhibitor treatment


title: JCe0051a

description: TCR alpha sequencing


title: Control_13


title: PBS-4_Spleen [bulk VDJ-seq]

description:
PBS-4_Spleen
VDJ Sequencing
LNP-mRNA vaccine

tag: tissue


title: JCe0054a

description: TCR alpha sequencing


title: JCe0048b

description: TCR beta sequencing


title: MEF-Ad-cre-2

source_name: H1047R PIK3CA Replicate 2 DMSO

value: DMSO


title: Control_19


title: MEF-Ad-cre-3

source_name: H1047R PIK3CA Replicate 3 DMSO


title: JC0035a

description: TCR alpha sequencing


title: JCe0047a

description: TCR alpha sequencing


title: MCF10A-KI-BYL719-10

source_name: MCF10A PIK3CA R1 KnockIn BYL719 4 hours

value: PIK3CA H1047R heterozygous mutant


title: MEF-cre-GDC500-2

source_name: H1047R PIK3CA Replicate 2 GDC0032 (500nM) PI3Ka inhibitor treatment


title: MCF10A-KI-BYL719-12

source_name: MCF10A PIK3CA R3 KnockIn BYL719 4 hours


title: MCF10A-KI-BYL719-11

source_name: MCF10A PIK3CA R2 KnockIn BYL719 4 hours


title: MEF-Ad-CMV-GFP-3

source_name: Wild type PIK3CA Replicate 3 DMSO

value: parental

value: wildtype


title: B.1.617-1μg-2_LN [bulk VDJ-seq]

description:
In1-2_LN
VDJ Sequencing
LNP-mRNA vaccine

source_name: Lymph node

value: Lymph node


title: MEF-Ad-cre-1

source_name: H1047R PIK3CA Replicate 1 DMSO


title: MEF-Ad-CMV-GFP-2

source_name: Wild type PIK3CA Replicate 2 DMSO


title: JCe0048a

description: TCR alpha sequencing


title: MEF-Ad-CMV-GFP-1

source_name: Wild type PIK3CA Replicate 1 DMSO


title: MCF10A-KI-DMSO-8

source_name: MCF10A PIK3CA R2 KnockIn DMSO 4 hours


title: MCF10A-KI-DMSO-7

source_name: MCF10A PIK3CA R1 KnockIn DMSO 4 hours


title: MEF-Ad-CMV-GDC500-3

source_name: Wild type PIK3CA Replicate 3 GDC0032 (500nM) PI3Ka inhibitor treatment


title: MCF10A-parental-BYL719-6

source_name: MCF10A Parental R3 BYL719 4 hours


title: MEF-Ad-CMV-GDC500-2

source_name: Wild type PIK3CA Replicate 2 GDC0032 (500nM) PI3Ka inhibitor treatment


title: MEF-Ad-CMV-GDC500-1

source_name: Wild type PIK3CA Replicate 1 GDC0032 (500nM) PI3Ka inhibitor treatment


title: genomic DNA from whole blood - 203257030005_R03C01

type: genomic

first: Stephan

last: Beck

department: Department of Cancer Biology

description: Whole Blood sample

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC array using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (Illumina iScan) using standard recommended Illumina scanner setting

data_processing:
Raw IDAT files were processed using R package minfi with SWAN normalisation. Methylation beta values were called as quantitative percentage of methylated signals over both unmethylated and methylated signals ranging from 0 to 1, with “0” indicating lack of methylation and “1” full methylation. We excluded measurements from non-CG probes (i.e. SNP targetting probes).
The processed_data.tsv contains SWAN normalized Average Beta
The signal_intensities.tsv contains Unmethylated and methylated signal intensities

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: For each sample, 500ng high-quality DNA was bisulphite converted using the EZ DNA methylation kit (Zymo Research), using alternative incubation conditions recommended for Illumina methylation arrays.

extract_protocol: Genomic DNA was extracted from whole blood samples using the QIAamp DNA Blood Mini Kit (Qiagen)

tag: Sex

value: Male

tag: age

value: whole blood

tag: batch


title: MCF10A-parental-BYL719-4

source_name: MCF10A Parental R1 BYL719 4 hours


title: MCF10A-parental-DMSO-3

source_name: MCF10A Parental R3 DMSO 4 hours


title: genomic DNA from whole blood - 203239580020_R08C01

description: Whole Blood sample


title: MCF10A-parental-DMSO-2

source_name: MCF10A Parental R2 DMSO 4 hours


title: MCF10A-parental-BYL719-5

source_name: MCF10A Parental R2 BYL719 4 hours


title: MCF10A-parental-DMSO-1

source_name: MCF10A Parental R1 DMSO 4 hours


title: genomic DNA from whole blood - 203239580020_R07C01

description: Whole Blood sample

value: Female


title: genomic DNA from whole blood - 203219760168_R03C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203219760168_R05C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810025_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810095_R02C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810095_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203219760166_R08C01

description: Whole Blood sample


title: WT stim CD8, DNase seq, rep1

library_source: genomic

data_processing:
The sequencing quality of DNase-Seq libraries were assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Bowtie2 (v2.2.5, Langmead et al., Nature Methods) was used to align the sequencing reads to the mouse genome. UCSC genes for mouse mm9 from iGenome (http://support.illumina.com/sequencing/sequencing_software/igenome.html) were used for gene annotation.
For Dnase-Seq libraries, MACS2 (v2.1.1, Zhang et al., Genome Biol) was used for peaks calling. We used the criteria of q val < 0.05, 4 fold change at peak summit as identified binding sites.
Genome_build: mm9
Supplementary_files_format_and_content: narrowPeak

source_name: CD8 T cells

extract_protocol:
Naïve CD8+ T cells were sort-purified from the spleen, and stimulated with IL-7 and IL-15 in vitro for 72 hrs, and then  lyzed and treated with DNase I
DNase-Seq libraries were prepared for sequencing using stardard Illumina protocol. The resulting libraries were sequenced on HiSeq 2500.

value: wild type

value: splenocytes

tag: cell phenotype

value: GFP+ TCRbeta+ CD62Lhi CD44lo-med CD8+


title: genomic DNA from whole blood - 203219760166_R07C01

description: Whole Blood sample


title: Tcf1/Lef1-deficient stim CD8, DNase seq, rep2


title: mouse_heart_sham_THZ1_rep4

city: South San Francisco

first: Saptarsi

last: Haldar

state: CA

address: 1120 Veterans Blvd

institute: Amgen

description: Mice were placed on a temperature-controlled small-animal surgical table to help maintain body temperature (37°C) during surgery. Mice were anesthetized with 1-3% isoflurane, mechanically ventilated (Harvard Apparatus), and subjected to thoracotomy. To perform transverse aortic artery constriction (TAC) aortic arch was exposed and constricted between the left common carotid and the brachiocephalic arteries using a 7-0 silk suture and a 27-gauge needle. Mice in sham group went through the same procedures except the constriction placement.

data_processing:
Each RNA-seq sample was aligned independently with the following procedure. The raw RNA-seq reads from each sample were aligned with TopHat v2.1.1 with options “-p 8 -r 300 --library-type fr-firststrand --no-coverage-search”. Each sample was aligned either against the mm9 or rn5 reference genome as appropriate for the sample.
After alignment, we quantified the number of mapped reads per gene per sample using htseq-counts. Each application of htseq-counts was run with the following options: ”-s reverse –f bam”. Each sample was quantified against the GENCODE mm9 transcript reference or the UCSC rn5 transcript reference, depending on the source of the sample.
We identified differentially expressed genes using DeSeq2. We imported the quantifications from htseq-count into DeSeq2, and we analyzed all samples from the same organism together in one analytical run. Replicate samples were grouped by their type (e.g., baseline, THZ1-treated) in order to better estimate the sample-level variance for comparison across samples. We ran the standard DeSeq2 workflow without modifications, and we used an adjusted p-value of 0.1 (10% FDR) as the cutoff threshold for identifying our differentially expressed genes throughout the paper (with the specific comparison between samples noted in the paper).
Genome_build: mm9
Supplementary_files_format_and_content: Table of normalized RNA-seq expression values by gene and by sample

source_name: heart

extract_protocol:
A 10–20 mg piece of mouse heart ventricles was mechanically homogenized in PureZOL (BioRad) on a TissueLyser (QIAGEN) using stainless steel beads (QIAGEN). Total RNA was purified using the Aurum total RNA purification kit (Bio-Rad 732-6830).
RNA libraries were prepared by using TruSeq Stranded mRNA Library Prep Kit (Illumina)

treatment_protocol: Four groups: 1. Sham+Vehicle; 2. TAC+Vehicle; 3. TAC+THZ1(10mg/kg b.i.d.); 4. Sham+THZ1 (10mg/kg b.i.d.); (Intraperitoneal injections of THZ1 were started on postoperative day 1 (10mg/kg b.i.d.) until postoperative day 60.)

tag: stain

value: heart ventricles

value: post natal week 10-12 (at the start of the experientment)


title: Tcf1/Lef1-deficient stim CD8, DNase seq, rep1


title: mouse_heart_sham_THZ1_rep3


title: F4KOorgans

city: TianJin

first: xiaomin

last: su

address: WeiJin Road

institute: Nankai University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: intestinal  organoids

growth_protocol: Mice intestina crypts were incubated for 15 minutes at room temperature (RT) in gentle cell dissociation reagent, then crypts were passed through 70μm cell strainer and collected the crypts by centrifugation at 100×g for 5 minutes. The crypts were embedded with Matrigel and plated. Carefully transfer the plate to a 37℃ incubator. Incubate at 37℃ for 10 minutes to allow domes to polymerization. After polymerization of matrigel, the crypts were added specifically IntestiCultTM medium and placed plate in incubate at 37℃ and 5% carbon dioxide for 6 days.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: The culture medium should be fully exchanged 3 times per week.

value: intestinal  organoids

value: FABP4 knockdown

value: in vitro cultured

tag: time

value: Day 6


title: WTorgans

value: WT


title: genomic DNA from whole blood - 203219760166_R02C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203219760166_R01C01

description: Whole Blood sample


title: mouse_heart_sham_THZ1_rep1


title: genomic DNA from whole blood - 203219760168_R04C01

description: Whole Blood sample


title: WT stim CD8, DNase seq, rep2


title: genomic DNA from whole blood - 203219760166_R04C01

description: Whole Blood sample


title: mouse_heart_TAC_THZ1_rep3


title: genomic DNA from whole blood - 203219760166_R05C01

description: Whole Blood sample


title: mouse_heart_TAC_THZ1_rep2


title: genomic DNA from whole blood - 203219760134_R08C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203219760166_R03C01

description: Whole Blood sample


title: mouse_heart_TAC_THZ1_rep1


title: mouse_heart_TAC_veh_rep4


title: genomic DNA from whole blood - 203219760134_R03C01

description: Whole Blood sample


title: mouse_heart_TAC_veh_rep3


title: mouse_heart_TAC_veh_rep2


title: mouse_heart_sham_THZ1_rep2


title: genomic DNA from whole blood - 203219760134_R04C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203219760134_R05C01

description: Whole Blood sample


title: mouse_heart_sham_veh_rep4


title: genomic DNA from whole blood - 203239810223_R06C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203219760134_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810223_R05C01

description: Whole Blood sample


title: mouse_heart_TAC_THZ1_rep4


title: genomic DNA from whole blood - 203219760166_R06C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810223_R04C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810223_R02C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810223_R03C01

description: Whole Blood sample


title: mouse_heart_sham_veh_rep1


title: mouse_heart_sham_veh_rep3


title: mouse_heart_sham_veh_rep2


title: genomic DNA from whole blood - 203239810223_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810223_R08C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810152_R08C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810152_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810249_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203219760134_R06C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239690268_R02C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810249_R02C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810249_R05C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810249_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239690268_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810249_R06C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810249_R08C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810249_R04C01

description: Whole Blood sample


title: mouse_heart_TAC_veh_rep1


title: genomic DNA from whole blood - 203239810249_R03C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810270_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810270_R05C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810270_R03C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810270_R06C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810270_R08C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810270_R04C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203219760013_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239690269_R04C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239690269_R05C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203219760013_R03C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239690269_R03C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810025_R02C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810025_R04C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203219760013_R02C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810025_R05C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810025_R03C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810078_R02C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810025_R08C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239690269_R02C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810078_R05C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810078_R08C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810078_R04C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810025_R06C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203219760168_R08C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239580019_R02C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810078_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810078_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239580019_R05C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239580019_R04C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239580019_R06C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810078_R03C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239580020_R02C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239580020_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239580019_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239580019_R08C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239580020_R03C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239580020_R04C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239580020_R06C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203219760088_R06C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810078_R06C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239580020_R05C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203219760133_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239580019_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239580019_R03C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203219760133_R06C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203219760088_R05C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203219760134_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203219760134_R02C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203219760168_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203219760168_R06C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203219760013_R06C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239690269_R08C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203219760013_R04C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810270_R02C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203219760013_R05C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239690269_R06C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810270_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203219760088_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239690269_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810094_R02C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810094_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203219760133_R08C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203219760133_R03C01

description: Whole Blood sample


title: MCF10A-KI-DMSO-9

source_name: MCF10A PIK3CA R3 KnockIn DMSO 4 hours

value: mutant

value: DMSO

value: PIK3CA H1047R heterozygous mutant


title: genomic DNA from whole blood - 203239810094_R04C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810094_R03C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810094_R06C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810094_R05C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810127_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810127_R06C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810127_R08C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810127_R05C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810137_R02C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810137_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203219760013_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810137_R04C01

description: Whole Blood sample


title: JC0034a

description: TCR alpha sequencing


title: genomic DNA from whole blood - 203219760013_R08C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203219760088_R02C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810127_R04C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203219760088_R03C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810127_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810127_R02C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810094_R08C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810127_R03C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810137_R03C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810094_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810151_R08C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810151_R06C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810152_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203219760133_R02C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203219760133_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810152_R02C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810152_R03C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203257030110_R05C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203257030110_R08C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203257030110_R04C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203257030110_R06C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203257030110_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810151_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203257030162_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203257030162_R04C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203257030162_R05C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203219760088_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203257030162_R03C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203257030162_R08C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203257030005_R05C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203219760088_R04C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203257030162_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203257030062_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203257030005_R06C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203257030005_R04C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203257030005_R08C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203257030005_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203257030162_R06C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810151_R04C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810151_R02C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810151_R05C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203219760088_R08C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810151_R03C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810151_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203257030162_R02C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810137_R06C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810137_R08C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810137_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810137_R05C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810152_R05C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810152_R04C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810152_R06C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810223_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203257030110_R02C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203257030110_R03C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810025_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203257030110_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203257030062_R08C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203257030062_R03C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203257030062_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203257030062_R02C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203257030062_R06C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203257030062_R05C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203257030005_R01C01

description: Whole Blood sample


title: LM2 pool of 10 WBC at 22h from mouse 2200_1

first: Francesc

last: Castro-Giner

address: Otto-Stern-Weg 7

institute: ETH Zurich

data_processing:
Basecalls performed using CASAVA version 1.4
Trim Galore (v0.6.5; parameters : –q 20 –length 20).
Trimmed reads were aligned to human (GRCh38) genome reference using STAR (v.2.7.3a; parameters: --twopassMode Basic --outSAMmapqUnique 60 --sjdbGTFfile) with splice junctions from the human GENCODE annotation (release 35). To eliminate residual contamination from mouse RNA, reads derived from xenograft models were also aligned to mouse (GRCm38) genome reference using STAR (v.2.7.3a; parameters: --twopassMode Basic --outSAMmapqUnique 60 --sjdbGTFfile) , with splice junctions from the mouse GENCODE annotation (release M25), and assigned to either human or mouse using Disambiguate (v1.0.0).
The gene-level expression counts were computed with featureCounts (v.2.0.1; parameters: -t exon -g gene_id --minOverlap 10 -Q 10) using the human gene annotations from GENCODE (release 35).
Genome_build: GRCh38
Supplementary_files_format_and_content: raw_counts.txt.gz are tab-delimited files containing per sample raw counts as obtained from featureCounts.

molecule: polyA RNA

extract_protocol:
Using the CellCelector, an automated single-cell picking system (ALS), single CTCs, CTC clusters and CTC-WBC clusters were collected and immediately transferred into individual tubes (Axygen, 321-032-501) containing 2.5 μl RLT Plus lysis buffer and 1U SUPERase IN RNAse inhibitor (Invitrogen, AM2694). Samples were immediately frozen and kept at 800C until further processing.
cDNA was amplifiead and libraries prepared according to the Smart-seq2 protocol.

tag: cancer type

value: breast

tag: origin

value: xenograft

tag: sample type

tag: number of ctcs

tag: number of wbcs attached

tag: timepoint

tag: zeitgeber time


title: LM2 pool of 10 WBC at 18h from mouse 1800_2

tag: donor


title: genomic DNA from whole blood - 203249020021_R08C01

description: Whole Blood sample

value: Male

value: whole blood


title: LM2 pool of 10 WBC at 10h from mouse 1000_3


title: LM2 pool of 10 WBC at 18h from mouse 1800_1


title: genomic DNA from whole blood - 203249020021_R06C01

description: Whole Blood sample


title: LM2 pool of 10 WBC at 10h from mouse 1000_2


title: LM2 pool of 10 WBC at 10h from mouse 1000_1


title: genomic DNA from whole blood - 203249020005_R07C01

description: Whole Blood sample


title: LM2 pool of 10 single CTC at 22h from mouse 2200_1


title: genomic DNA from whole blood - 203249020021_R05C01

description: Whole Blood sample


title: LM2 pool of 10 single CTC at 18h from mouse 1800_1


title: genomic DNA from whole blood - 203257030005_R02C01

description: Whole Blood sample

value: Female


title: genomic DNA from whole blood - 203257030062_R04C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203249020021_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203249020021_R03C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203249020021_R02C01

description: Whole Blood sample


title: LM2 pool of 10 single CTC at 10h from mouse 1000_2


title: genomic DNA from whole blood - 203249020005_R05C01

description: Whole Blood sample


title: LM2 pool of 10 single CTC at 10h from mouse 1000_3


title: genomic DNA from whole blood - 203249020005_R08C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203249020005_R06C01

description: Whole Blood sample


title: LM2 pool of 10 single CTC at 10h from mouse 1000_1


title: LM2 pool of 10 single CTC at 18h from mouse 1800_2


title: LM2 pool of 10 single CTC at 02h from mouse 0200_2


title: genomic DNA from whole blood - 203249020021_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203249020005_R04C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203219760133_R05C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203249020005_R02C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203249020021_R04C01

description: Whole Blood sample


title: LM2 pool of 10 WBC at 02h from mouse 0200_1


title: genomic DNA from whole blood - 203249020005_R01C01

description: Whole Blood sample


title: LM2 pool of 10 CTC clusters at 18h from mouse 1800_2


title: genomic DNA from whole blood - 203249020005_R03C01

description: Whole Blood sample


title: LM2 pool of 10 CTC clusters at 18h from mouse 1800_1


title: LM2 pool of 10 CTC clusters at 22h from mouse 2200_1


title: LM2 pool of 10 CTC clusters at 10h from mouse 1000_3


title: LM2 pool of 10 CTC clusters at 10h from mouse 1000_2


title: genomic DNA from whole blood - 203239810248_R08C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810248_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810248_R06C01

description: Whole Blood sample


title: LM2 pool of 10 single CTC at 06h from mouse 0600_1


title: LM2 pool of 10 CTC clusters at 10h from mouse 1000_1


title: genomic DNA from whole blood - 203239810248_R05C01

description: Whole Blood sample


title: LM2 pool of 10 CTC clusters at 02h from mouse 0200_2


title: genomic DNA from whole blood - 203239810248_R04C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810076_R02C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810248_R03C01

description: Whole Blood sample


title: LM2 pool of 10 single CTC at 02h from mouse 0200_1


title: LM2 pool of 10 CTC clusters at 02h from mouse 0200_1


title: genomic DNA from whole blood - 203239810076_R03C01

description: Whole Blood sample


title: Bulk_ciPOD_rep2

city: Nijmegen

first: Martijn

last: Broek

address: Geert Grooteplein 24, route 846

department: Molecular Biology

country: Netherlands

institute: Radboud university - RIMLS Science

data_processing:
Read 1 was used to identify the Illumina library index and CEL-Seq sample barcode. Read 2 was aligned to the hg19 human RefSeq transcriptome using BWA (68). Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script1. Samples were normalized using RPM normalization.
Genome_build: GRCh38 for single-cell and hf19 for bulk RNA sequencing
Supplementary_files_format_and_content: barcodes.tsv.gz = barcodes present in input data
Supplementary_files_format_and_content: features.tsv.gz = a bed file contains genes corresponding to row indices. For each gene, its gene ID and name are stored in the first and second column of the gene.tsv file, respectively
Supplementary_files_format_and_content: matrix.mtx.gz = a count matrix with Market Exchange Format (MEX). The first line contains the type code and the second line includes format and cell-ranger versions. Number of peaks, barcodes, and non-zero entries can be found in the third line.  The rest of the lines represent  nonzero entries with the first two numbers corresponding to peak and barcode indices and the last one corresponding to  the number of cut sites.
Supplementary_files_format_and_content: ReadCounts.tsv = Count matrix containing gene IDs and corresponding counts. Each column represents another sample (3x mutant (iPS134) and 3x repaired (iPS19))
Supplementary_files_format_and_content: counts.txt = Count matrix containing ENSEMBLE Ids and corresponding counts

source_name: Conditionally immortalized podocyte cell line

growth_protocol: The conditionally immortalized podocyte cell line (ciPOD) used in this study was kindly provided by Prof. Saleem (Bristol, UK). ciPODs were cultured using uncoated 75 cm2 culture flasks (Greiner) at 33⁰C with 5% (v/v) CO2 in DMEM/F12 (Gibco) supplemented with 5 µg/mL insulin, 5 µg/mL transferrin, 5 ng/mL selenium (Sigma-Aldrich, Zwijndrecht, the Netherlands), 10% heat inactivated FCS (Gibco)  and 1% (v/v) penicillin/streptomycin (Gibco). Passaging and seeding of cells was performed by washing cells with PBS and subsequently detaching them using accutase (Sigma-Aldrich). For sequencing, ciPODs were seeded at 62,500/cm2 in 6-wells plates (Greiner) for total RNA isolation and incubated at 37⁰C with 5% (v/v) CO2, which initiated differentiation of the ciPODs. Extraction Protocol: Total RNA was extracted using RNAeasy (Qiagen, Germantown, Maryland).

extract_protocol: Total RNA was extracted using RNAeasy (Qiagen, Germantown, Maryland). Library construction protocol: Sequencing was performed at Single Cell Discoveries, a (single cell) sequencing provider located in the Netherlands using an adapted version of the CEL-seq protocol. mRNA was processed as described previously, following an adapted version of the single-cell mRNA seq protocol of CEL-Seq. Briefly, samples were barcoded with CEL-seq primers during a reverse transcription and pooled after second strand synthesis. The resulting cDNA was amplified with an overnight In vitro transcription reaction. From this amplified RNA, sequencing libraries were prepared with Illumina Truseq small RNA primers. Paired-end sequencing was performed on the Illumina Nextseq500 platform.

tag: cell type

value: Conditionally immortalized podocytes


title: genomic DNA from whole blood - 203239810076_R04C01

institute: UCL Cancer Institute

description: Whole Blood sample


title: Bulk_ciPOD_rep1