title: InSPI2 Ciprofloxacin 0.1 (Biological replicate 1)

city: Liverpool

first: Jonathan

middle: Paul

last: Bollback

address: Crown Street

institute: University of Liverpool

data_processing:
Quality checks and demultiplexing of sequenced reads were performed
Sequenced reads were then processed using AdapterRemoval (v2) (Schubert et al. 2016) to trim regions with low quality bases (q<30), merge overlapping read pairs, remove Illumina adapter sequences, and remove reads containing ambiguous bases (Ns).
The sequenced reads were then mapped to the custom built reference genome using the defaults local alignment parameter in Bowtie2 (Version 2.4.4) (Langmead et al., 2009). The mapped SAM files were converted to BAM format and the corresponding BAM files were sorted using Samtools (Tools for Alignment in SAM format) (Version 1.13) (Li et al., 2009).
Read depths at each nucleotide position were calculated using depth function of Samtools (Version 1.13) (Li et al., 2009). Nucleotide depths were converted to gene frequencies by calculating the median of depths obtained for every gene using the R software (Version 4.0.0). All steps of the sequencing data processing were performed on Ubuntu 16.04.5 LTS (GNU/Linux 4.15.0-52-generic x86_64).
Supplementary files format and content: The csv files contain the read depth at each nucleotide position for each gene and the plasmid.
Library strategy: DNA-seq

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74

source_name: Bacteria

growth_protocol: For each of the four infection relevant environments, 100ml volume of cultures were grown in 200ml conical flasks, except InSPI2 Hypoxic, where cultures were filled up to the brim of 50ml conical tubes, capped with rubber septum, and further sealed using parafilm. Gene expression was induced by the addition of 4ng/ml aTc, and 50 µg/ml Ampicillin was used for maintenance of pZS* plasmids carrying the transferred genes. The flasks were incubated at 37℃ and 250 rpm and grown to OD600 0.4. For the InSPI2 Hypoxic environment, cultures were grown on static at 37℃ to OD600 0.2.

extract_protocol:
Plasmid DNA was extracted from the total culture volume using InvitrogenTM PureLinkTM HiPure Plasmid Midiprep Kit (Catalog number: K210004).
DNA was first fragmented by sonication using Qsonica 800R, followed by construction for Illumina compatible sequencing libraries using the Kapa Hyperprep kit following manufacturer’s protocols. Sequencing libraries were generated using PCR with Illumina-specific barcoded primers and dual index approach was used to allow multiplexing.

value: end point (OD600 0.4)

value: Bacteria

value: Pool of 44 mutants and a WT

value: gene expression induced using 4ng/ml inducer aTc


title: InSPI2 Ciprofloxacin 0.1 (Biological replicate 2)

status: Public on Jan 27 2023

type: SRA

country: United Kingdom

library_source: other

molecule: other

tag: time

tag: strain

tag: cell type

tag: genotype

tag: treatment


title: InSPI2 Hypoxic (Biological replicate 4)

value: end point (OD600 0.2)


title: WT_3m_RNA_rep3

city: Tianjin

first: Jiayuan

last: Chen

state: State...

address: Heping

country: China

institute: Tianjin Medical University

library_source: transcriptomic

data_processing:
Sequence reads were aligned to the mm10 reference genome sequence using STAR (2.7.4a).
The aligned reads were sorted using samtools (1.12).
Read counts per gene were obtained from mapped reads using FeatureCount (1.6.0).
Differentially expressed genes were identified by DESeq2 (1.26.0) algorithms.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include raw count values for each sample.

molecule: polyA RNA

organism: Mus musculus

source_name: primary cholangiocytes

extract_protocol:
Total RNAs were extracted from primary cholangiocytes using TRIzol (Invitrogen, 15596018) according to the manufacturer’s instructions.
For RNA samples from WT or PLD mice 3 months after tamoxifen induction, libraries were constructed and sequenced on the BGISEQ-500 platform.

treatment_protocol: In brief, the livers of WT or PLD mice were perfused through inferior cava vein with 50 mL solution A (140 mM NaCl, 5.4 mM KCl, 0.8 mM Na2HPO4, 25 mM HEPES, 0.5 mM EGTA, 1 mM MgCl2, pH 7.4) at 37°C, followed by 30 mL solution B (140 mM NaCl, 5.4 mM KCl, 0.8 mM Na2HPO4, 25 mM HEPES, 5mM CaCl2, 0.5mg/mL collagenase II (Worthington, LS004176), pH 7.4) at 37°C. Through mechanical dissociation, shaking and microdissection, the adherent parenchymal cells were removed leaving an intact biliary tree. The biliary tree was finely minced, and digested in digestion solution [RPMI medium containing 0.32 mg/mL collagenase XI (Sigma C7657), 0.4 mg/mL hyaluronidase (Sigma H3506) and 40 U/mL DNase I (Sigma D4513)] with shaking for 60 min at 37°C. Single-cell suspension was collected using a 70-μm cell strainer (Corning, 352350) and then washed three times with RPMI medium. Cholangiocytes were then purified by immunomagnetic isolation. Briefly, Cholangiocytes cell suspensions were incubated with anti-EpCAM antibody (DSHB, G8.8) with rotation for 45 min at 4°C. Dynabeads Protein G (Thermo Fisher Scientific, 10004D) were added into the cell suspensions and continued the rotation for another 45 min at 4°C. After washing three times with PBS, cholangiocytes were collected using a magnetic separator. The purity of cholangiocytes was assessed by staining for cytokeratin-19 (CK19).

value: primary cholangiocytes

value: WT


title: InSPI2 Hypoxic (Biological replicate 3)


title: InSPI2 Hypoxic (Biological replicate 1)


title: InSPI2 Hypoxic (Biological replicate 2)


title: InSPI2 Ciprofloxacin 0.1 (Biological replicate 4)


title: Tumor_Pretreatment_Rep 5

type: RNA

city: New York

first: Navin

middle: K

last: Chintala

state: NY

address: 417 E 68th Street, 4th Flr, Room 427D

department: Surgery

country: USA

institute: MSKCC

data_processing: nSolver Analysis software (v4) and nCounter® Advanced Analysis Software (v2)

label: Nanostring reporter probe

molecule: total RNA

organism: Homo sapiens

source_name: tumor biopsy_Pre

extract_protocol: Total RNA was extracted from FFPE tumor biopsies using Qiagen All prep DNA/RNA mini kit according to manufacturers instructions.

treatment_protocol: Tumor biopsies were collected Pre- or Post- treatment with Olvi-Vec (Vaccinia Virus) agent

tag: pathology

value: meso - epitheloid

tag: cohort

tag: dose


title: Tumor_Pretreatment_Rep 2

value: meso - biphasicd


title: Tumor_Pretreatment_Rep 4


title: InSPI2 Ciprofloxacin 0.1 (Biological replicate 3)


title: Tumor_Pretreatment_Rep 3


title: AGS_control_biological_rep3

city: Zhengzhou

first: Yuan

last: Yuan

state: Henan

address: No. 3, Fukang Front Street, Erqi District, Zhengzhou, Henan Province

institute: The Fifth Affiliated Hospital of Zhengzhou University

description: Gene expression for control

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent  Human  lncRNA  Microarray  2018 Version（4*180k, Design ID: 085630） for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Genespring(version 13.1, Agilent Technologies) were employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm. The probes that at least 1 conditions out of 2 conditions have flags in “P” were chosen for further data analysis. Differentially expressed genes or lncRNAs were then identified through fold change. The threshold set for up- and down-regulated genes was a fold change>= 2.0. Afterwards, GO analysis and KEGG analysis were applied to determine the roles of these differentially expressed mRNAs. Finally, Hierarchical Clustering was performed to display the distinguishable genes' expression pattern among samples.

source_name: Human gastric cancer, empty AGS control cell line,replicate 3

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

growth_protocol: The cells were cultured in F12k culture medium (100 U/ml penicillin and 100 µg/ml streptomycin) containing 10% fetal bovine serum (Hangzhou Sijiqing Bioengineering Materials Co., Ltd.) under 5% CO2 in a 37℃ incubator.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Cells were seeded in 6-well plates (1.0 × 105 cells per well) and incubated overnight until 60–70% confluence. Transfection was performed using Lipofectamine 2000 (Thermo Fisher Scientific) according to the manufacturer’s instructions. The experiments were divided into the small interference RNA negative control group (si-NC), small interference RNA EGFR knockdown group (si-EGFR), overexpression negative control group (OE-NC), and the overexpression E-cadherin group (OE-E-cadherin). After 6 hours of transfection, transfection medium was removed and replaced with completed medium. After 36 hours of incubation, the subsequent experiments were performed.

tag: tissus

value: human gastric cancer AGS cell

value: control


title: AGS_EGFR knockdown_biological_rep1

description: Gene expression after EGFR knockdown

source_name: Human gastric cancer, the EGFR low expression AGS cell line,replicate 1

value: EGFR knockdown


title: AGS_E-cadherin overexpression_biological_rep1

description: Gene expression after E-cadherin overexpression

source_name: Human gastric cancer, The E-cadherin-overexpressing AGS cell line ,replicate 1

value: E-cadherin overexpression


title: MGH66_persister1

city: Cambridge

first: Peijun

last: Ma

state: MA

address: 415 Main Street

department: Infectious Disease and Microbiome program

institute: The Broad Institute of MIT and Harvard

library_source: genomic

data_processing:
bcl2fastq2-v2.20.0 was used to generate fastq files
Sequencing reads were trimed and sorted using fastp-0.20.0
Alignment was using BWA
Pilon was used for mutation detection of the WGS data
Supplementary files format and content: text files containing mutations detected by pilon.
Supplementary files format and content: Excel spreadsheet summarizing mutations from 6 persister strains and the ancestor strain.

molecule: genomic DNA

organism: Klebsiella pneumoniae

growth_protocol: 37ºC, regular laboratory condition

extract_protocol:
gDNA was extracted using Qiagen DNeasy Blood & Tissue
Library was contructed using Illumina Nextera XT

tag: method

value: Nextera XT

value: Persister derived from MGH66

value: untreated


title: InSPI2 Low Mg (Biological replicate 4)


title: AGS_EGFR knockdown_biological_rep3

description: Gene expression after EGFR knockdown

source_name: Human gastric cancer, the EGFR low expression AGS cell line,replicate 3


title: AGS_control_biological_rep2

description: Gene expression for control

source_name: Human gastric cancer, empty AGS control cell line,replicate 2


title: AGS_EGFR knockdown_biological_rep2

description: Gene expression after EGFR knockdown

source_name: Human gastric cancer, the EGFR low expression AGS cell line,replicate 2


title: AGS_E-cadherin overexpression_biological_rep3

source_name: Human gastric cancer, The E-cadherin-overexpressing AGS cell line ,replicate 3


title: InSPI2 Low Mg (Biological replicate 1)


title: AGS_control_biological_rep1

description: Gene expression for control

source_name: Human gastric cancer, empty AGS control cell line,replicate 1


title: AGS_E-cadherin overexpression_biological_rep2

source_name: Human gastric cancer, The E-cadherin-overexpressing AGS cell line ,replicate 2


title: InSPI2 (Biological replicate 4)


title: InSPI2 Low Mg (Biological replicate 3)


title: Tumor_Olvi-vec_Rep 14

source_name: tumor biopsy_Post


title: Tumor_Olvi-vec_Rep 15


title: InSPI2 (Biological replicate 3)


title: InSPI2 Low Mg (Biological replicate 2)


title: Tumor_Olvi-vec_Rep 12


title: InSPI2 (Biological replicate 2)


title: Tumor_Olvi-vec_Rep 10


title: Tumor_Olvi-vec_Rep 13


title: Starting frequency (Technical replicate 2)

value: start point of experiment


title: InSPI2 (Biological replicate 1)

value: end point (OD600 0.4)


title: Tumor_Pretreatment_Rep 1

value: NSCLC - SCC


title: Tumor_Olvi-vec_Rep 11


title: Tumor_Olvi-vec_Rep 9

value: TNBC


title: Tumor_Olvi-vec_Rep 6


title: Starting frequency (Technical replicate 1)

value: Bacteria

value: Pool of 44 mutants and a WT


title: Tumor_Olvi-vec_Rep 8

value: meso - sarcomatoid


title: Tumor_Olvi-vec_Rep 3


title: Tumor_Olvi-vec_Rep 5


title: Tumor_Olvi-vec_Rep 1


title: IgG12_SPL_mB_2

city: Noda

first: Hiroyasu

last: Aoki

state: Chiba

address: 2669 Yamazaki

department: Research Institute for Biomedical Sciences

country: Japan

institute: Tokyo University of Science

description:
Bulk IgH-seq
messenger RNA

data_processing:
Only read2 contained the sequence of IgHs. Adapter trimming and quality filtering of sequencing data were performed using Cutadapt-3.2 (Martin, 2011) and PRINSEQ-0.20.4 (Schmieder, 2011). Sequencing data were processed using MiXCR-3.0.5 (Bolotin, 2015). In MiXCR, filtered reads were aligned to reference mouse IgH V/D/J sequences registered in the international ImMunoGeneTics (IMGT) information system, and then identical sequences were assembled and grouped into clones with PCR and sequencing error correlation, memory B cell or plasma cell clones were determined as IgH reads with the same V segment, J segment, and CDR3 nucleotide sequence. The similarity of IgH repertoire between samples were quantified by calculating MorisitaHorn index using VDJtools (Shugay, 2015).
Assembly: IMGT reference sequences of mouse IGH.
Supplementary files format and content: Text files in VDJtools format include read count and frequency, complementarity determining region 3 (CDR3) nucleotide and amino acid sequences, Variable(V)/ Diversity(D)/ Joining(J) segment names, and V, D and J segment boundaries within CDR3 nucleotide sequence of individual clones.

source_name: Spleen

extract_protocol:
Splenic or mediastinal LN cells were prepared by the standard method. Lungs were cut into small pieces and digested for 30 minutes at 37°C with 0.6 mg/ml collagenase D and 0.1 mg/ml DNase I (Roche), then the exudate cells were filtered to prepare single cell suspensions.
Red blood cells and naive B cells were removed from splenic or lung cells by negative sorting using biotinylated Abs against IgD and Ter119 (Biolegend), the iMag system (BD Biosciences) and MACS system (Miltenyi Biotec).
IgD- cells from a spleen, lungs or medLNs were stained with FcγR-blocking mAb (2.4G2) and then fluorophore-conjugated mAbs against mouse surface markers.
IgD- IgM- CD138- GL7- CD38+ CD19+ class-switched memory B cells and CD19- CD98+ CD138+ plasma cells from spleen, medLNs or lungs were sorted using FACS Aria III (BD Biosciences). Dead cells were excluded by fixable viability dye (eBioscience) staining.
Transcriptome libraries were prepared on cell lysate resolved in lysis buffer. PolyA RNAs were isolated using Dynabeads M-270 Streptavidin (Thermo Fisher Scientific) conjugated with biotin-3’ WTA-EcoP-dT25 according to the previous report with some modifications (GSE110711) (Shichino, 2019). To perform reverse transcription, beads were then suspended in 10 μL of RT mix [1× First Strand buffer (Thermo Fisher Scientific), 1 mM dNTP, 2.5 mM DTT (Thermo Fisher Scientific), 1 M betaine (Sigma-Aldrich), 9 mM MgCl2 (NIPPON GENE), 1 U/µL RNaseIn Plus RNase Inhibitor (Promega, Madison, WI), 10 U/µL Superscript II (Thermo Fisher Scientific), and 1 µM of trP1-TSO], and incubated for 60 min at 42ºC, and immediately cooled on ice. Beads were washed once with B&W-T buffer [5 mM Tris-HCl (pH 8.0) (Nippon Gene, Tokyo, Japan), 1 M NaCl (Merck), 1 mM EDTA (Nippon Gene) and 0.05% Tween-20 (Merck)], and once with Tris-HCl (pH 8.0). To amplify the total cDNA, beads containing cDNA were resuspended with 25 μL of WTA (whole transcript amplification) PCR mix [0.4 μM of trP1 primer, 0.4 μM of primer (NH2-3’ WTA), and 1x KAPA Hifi Hotstart ReadyMix], and the thermal cycling was performed as following condition: for 3 min at 95°C, 12 cycles of 20 sec at 98°C, 15 sec at 65°C, and 5 min at 72°C, followed by 5 min at 72°C, and hold at 4°C. The WTA PCR products were purified by AmPure XP beads (Beckman-Coulter) at a 0.6:1 ratio of reagents to sample and eluted with 20 μL of nuclease-free water.
To amplify the heavy chain of IgH cDNA, nested PCR of the IgH locus was performed as follows. Purified WTA PCR products were used as template in 25 µL of first PCR mixture [0.4 μM of primers (i5-trP1, mIghE_1st, mIghG1/2b/2c_1st, and mIghG3_1st), and 1x KAPA Hifi Hotstart ReadyMix (KAPA Biosystems, Wilmington, MA)], and the thermal cycling was performed as the following condition: denaturation at 95°C for 3 min, 10 cycles of denaturation for 20 sec at 98°C, annealing for 15 sec at 65°C and extension for 30 sec at 72°C, followed by a final extension at 72°C for 2 min. Then, 1.0µL of first PCR product was mixed with the 9 μL of second PCR mixture [0.35 μM of primers (Illumina i5_2nd and i7-BC_mIghE or G1/2b/2c or G3), and 1x KAPA Hifi Hotstart ReadyMix], and the thermal cycling was performed under the same condition as first PCR except that the number of cycles was 15. The second-PCR products were purified by an Agencort AM Pure XP kit (Beckman Coulter, CA) at a 0.7:1 ratio of beads to sample and eluted with 12 μL of 10 mM Tris-HCl (pH 8.0). To amplify IgH libraries and to add adaptor sequences for the next-generation sequencer, the third PCR was performed with i5_UDI and i7_UDI primers after pooling equal amounts of the IgH libraries obtained in the 2nd PCR. The third-PCR products were purified as were the second PCR products. The products were pooled and then purified and subjected to dual size selection using the ProNex size-selective purification system (Promega) and eluted with 25 μL of 10 mM Tris-HCl (pH 8.5). Primer sequences used for IgH library preparation were shown in Supplemental Table 1.

tag: age

value: 10 weeks

tag: Sex

value: female

tag: isotype

value: IgG1, IgG2b, IgG2c


title: IgG12_SPL_PC_1

description:
Bulk IgH-seq
messenger RNA

value: CD19- CD98+ CD138+ plasma cells

value: 12 weeks


title: IgG12_SPL_mB_3

description:
Bulk IgH-seq
messenger RNA

value: IgD- IgM- CD138- GL7- CD38+ CD19+ class-switched memory B cells

value: 11 weeks

value: male


title: Tumor_Olvi-vec_Rep 2


title: Tumor_Olvi-vec_Rep 4

value: meso - epitheloid


title: RPGE2-OX rep3

city: Daejeon

first: Namuk

last: Kim

address: Daehakro 291

country: South Korea

institute: KAIST

data_processing:
Sequencing platform was Nextseq500 with 75bp reads and insert size was 80bp to 380bp (main 130bp).
Basecalling software was CASAVA (Version 1.8.2).
Sequenced reads were mapped to TAIR10 Arabidopsis whole genome using Tophat.
Mapped BAM files were processed with cufflinks/cuffmerge/cuffdiff pipeline for the differential expression.
Assembly: TAIR10
Supplementary files format and content: Tab-delimited text file with DEG analysis result including  |log2(Fold-change)| value and q-value for each genes.

organism: Arabidopsis thaliana

source_name: Seedling

growth_protocol: Seeds were spotted on 1/2MS plate and cold (4°C) stratified for 3 days. Seeds were treated continuous white light (50 μmol/m2s, 22°C) for 7 days.

extract_protocol:
The Spectrum Plant Total RNA Kit (STRN250, Sigma-Aldrich) was used to isolate total RNA.
1 ug of total RNA was processed for preparing mRNA-sequencing library using Truseq stranded total RNA prep kit (Plant leaf). RNA libraries were generated and sequenced on the Illumina NextSeq500.

tag: ecotype

value: 7 days grown under white light

value: RPGE2 overexpression

tag: tissue

value: whole seedlings


title: IgG12_SPL_PC_2

description:
Bulk IgH-seq
messenger RNA


title: RPGE2-OX rep2


title: IgG12_SPL_mB_1

description:
Bulk IgH-seq
messenger RNA


title: Tumor_Olvi-vec_Rep 7


title: IgG12_medLN_PC_1

description:
Bulk IgH-seq
messenger RNA

source_name: Mediastinal lymph node


title: IgG12_medLN_PC_2

description:
Bulk IgH-seq
messenger RNA


title: IgG12_medLN_PC_3

description:
Bulk IgH-seq
messenger RNA


title: IgG12_SPL_PC_3

description:
Bulk IgH-seq
messenger RNA


title: RPGE2-OX rep1


title: glk12 rep2

value: glk1/glk2 double mutant


title: IgG12_medLN_mB_3

description:
Bulk IgH-seq
messenger RNA


title: glk12 rep1


title: glk12 rep3


title: WT rep2

value: wild type


title: WT rep3


title: IgG12_medLN_mB_2

description:
Bulk IgH-seq
messenger RNA


title: WT rep1


title: IgG12_Lung_PC_3

description:
Bulk IgH-seq
messenger RNA

source_name: Lung


title: IgG12_Lung_mB_3

description:
Bulk IgH-seq
messenger RNA


title: IgG12_Lung_mB_2

description:
Bulk IgH-seq
messenger RNA


title: IgG12_Lung_PC_2

description:
Bulk IgH-seq
messenger RNA


title: IgG12_Lung_PC_1

description:
Bulk IgH-seq
messenger RNA


title: IgG12_medLN_mB_1

description:
Bulk IgH-seq
messenger RNA


title: IgG3_SPL_PC_2

description:
Bulk IgH-seq
messenger RNA


title: IgG12_Lung_mB_1

description:
Bulk IgH-seq
messenger RNA


title: IgG3_SPL_PC_3

description:
Bulk IgH-seq
messenger RNA


title: IgG3_SPL_PC_1

description:
Bulk IgH-seq
messenger RNA


title: IgG3_SPL_mB_2

description:
Bulk IgH-seq
messenger RNA


title: IgG3_SPL_mB_1

description:
Bulk IgH-seq
messenger RNA


title: IgG3_SPL_mB_3

description:
Bulk IgH-seq
messenger RNA


title: IgG3_medLN_PC_2

description:
Bulk IgH-seq
messenger RNA


title: IgG3_medLN_PC_1

description:
Bulk IgH-seq
messenger RNA


title: IgG3_medLN_mB_3

description:
Bulk IgH-seq
messenger RNA


title: IgG3_medLN_PC_3

description:
Bulk IgH-seq
messenger RNA


title: IgG3_medLN_mB_2

description:
Bulk IgH-seq
messenger RNA


title: atscl26 cortical cells 2hr KNO3 nitrogen treated, biological rep2

city: Coventry

first: Miriam

last: Gifford

address: Gibbet Hill Road

department: School of Life Sciences

institute: University of Warwick

description: NimbleGen gene expression array data for custom-design array based on the TAIR10 release of the Arabidopsis thaliana genome

hyb_protocol: Following fragmentation, 4 ug of cRNA was hybridized for 16 hr at 42oC on a NimbleGen.

scan_protocol: Slides were scanned using an MS 200 microarray scanner and associated NimbleGen software using only the 480 nm laser with gain calculated using the autogain feature of NimbleScan, based on a representative region of the slide (an area covering around half an array found to have average intensity based on a prescan at lower resolution), as per manufacturer’s instructions. Grids were aligned automatically to each microarray image and manually veriﬁed, ensuring reference spots in each corner and in the centre of the array were aligned to the grid and the alignment score minimised.

data_processing: Data were obtained using NimbleScan and normalised by robust multichip averaging (RMA) (quantile normalisation, taking into account outlier probes per gene) and summarised to gene level by median polish.

source_name: 12 day old Arabidopsis atscl26  root cortical cells, 2 hr 5mM KNO3 nitrogen treated

label_protocol: RNA samples were amplified using Ovation Pico WTA System V2 kit (NuGEN Technologies Inc., San Carlos, CA, USA) as per the manufacturer’s ‘quick’ protocol. Post-ampliﬁcation puriﬁcation of cDNA was performed using the QIAquick PCR Puriﬁcation Kit (Qiagen) as manufacturer’s guidelines. RNA was labelled with the Cy3 dye according to NimbleGen protocols.

growth_protocol: Plants were grown for 9 days in long day (16hr light/8hr dark) 22 oC conditions in a Sanyo growth chamber (MLR251).  Plants were grown vertically on plates on basal MS containing no nitrogen, supplemented with 0.1mM KNO3 and 30mM sucrose.

extract_protocol: FACS samples were collected in RLT lysis buffer (Qiagen) with 1 % (v:v) β-mercaptoethanol, then total RNA extracted using the Qiagen plant RNeasy kit.

treatment_protocol: At dawn on the 9th day plants were either transferred to 5mM KNO3-containing plates (High N) or moved to fresh 0.1mM KNO3 (Low N) plates. Whole roots were harvested then prototplast generation and Fluorescence-Activated Cell Sorting (FACS) used to isolate epidermal or cortical cells (following methods in Gifford et al 2008 PNAS).

tag: organ

value: root

value: cortex


title: IgG3_medLN_mB_1

description:
Bulk IgH-seq
messenger RNA


title: atscl26 epidermal cells 2hr KNO3 nitrogen treated, biological rep3

source_name: 12 day old Arabidopsis atscl26  root epidermal cells, 2 hr 5mM KNO3 nitrogen treated

value: epidermis


title: atscl26 epidermal cells 2hr KNO3 nitrogen treated, biological rep2


title: IgG3_Lung_PC_3

description:
Bulk IgH-seq
messenger RNA


title: atscl26 cortical cells 2hr KNO3 nitrogen treated, biological rep1


title: Col0 cortical cells 2hr KNO3 nitrogen treated, biological rep2

source_name: 12 day old Arabidopsis Col0  root cortical cells, 2 hr 5mM KNO3 nitrogen treated

value: wildtype

tag: cultivar


title: Col0 cortical cells 2hr KCl control treated, biological rep1

source_name: 12 day old Arabidopsis Col0  root cortical cells, 2 hr 5mM KCl control treated


title: IgG3_Lung_PC_1

description:
Bulk IgH-seq
messenger RNA

value: female


title: IgG3_Lung_PC_2

description:
Bulk IgH-seq
messenger RNA

value: 10 weeks


title: Col0 cortical cells 2hr KNO3 nitrogen treated, biological rep1


title: Col0 cortical cells 2hr KCl control treated, biological rep2


title: atscl26 cortical cells 2hr KCl control treated, biological rep1

source_name: 12 day old Arabidopsis atscl26  root cortical cells, 2 hr 5mM KCl control treated


title: atscl26 cortical cells 2hr KNO3 nitrogen treated, biological rep3


title: atscl26 cortical cells 2hr KCl control treated, biological rep2


title: Col0 epidermal cells 2hr KNO3 nitrogen treated, biological rep3

source_name: 12 day old Arabidopsis Col0  root epidermal cells, 2 hr 5mM KNO3 nitrogen treated


title: atscl26 epidermal cells 2hr KCl control treated, biological rep1

source_name: 12 day old Arabidopsis atscl26  root epidermal cells, 2 hr 5mM KCl control treated


title: IgG3_Lung_mB_3

description:
Bulk IgH-seq
messenger RNA


title: atscl26 epidermal cells 2hr KCl control treated, biological rep2


title: atscl26 epidermal cells 2hr KNO3 nitrogen treated, biological rep1


title: IgE_SPL_PC_1

description:
Bulk IgH-seq
messenger RNA

value: CD19- CD98+ CD138+ plasma cells

value: IgE


title: Col0 cortical cells 2hr KCl control treated, biological rep3


title: Col0 epidermal cells 2hr KNO3 nitrogen treated, biological rep2


title: IgG3_Lung_mB_1

description:
Bulk IgH-seq
messenger RNA

value: IgD- IgM- CD138- GL7- CD38+ CD19+ class-switched memory B cells

value: 12 weeks


title: TSLP treated Treg1

city: Chiba

first: Shigeru

last: Tanaka

address: 1-8-1 Inohana

department: Allergy and Clinical Immunology

institute: Chiba University

data_processing:
The sequences which passed QC were mappted to mm10 using Hisat2.
Htseq was used to obtain gene expression counts.
DESeq2 was used to normalize gene counts.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every sample.

source_name: regulatory T cells

growth_protocol: regulatory T cells were collected from lymphoid tissues of Foxp3yfpCre mice.

extract_protocol:
Total RNA was extracted using Rneasy mini kit.
The libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.

treatment_protocol: Regulatory T cells were stimulated with PBS or TSLP for 3hours.

value: TSLP


title: Col0 epidermal cells 2hr KCl control treated, biological rep3

source_name: 12 day old Arabidopsis Col0  root epidermal cells, 2 hr 5mM KCl control treated


title: IgG3_Lung_mB_2

description:
Bulk IgH-seq
messenger RNA


title: IgE_SPL_PC_3

description:
Bulk IgH-seq
messenger RNA

value: 11 weeks

value: male


title: PBS treated Treg2

value: PBS


title: TSLP treated Treg2


title: IgE_SPL_PC_2

description:
Bulk IgH-seq
messenger RNA


title: PBS treated Treg1


title: Col0 epidermal cells 2hr KNO3 nitrogen treated, biological rep1


title: Col0 epidermal cells 2hr KCl control treated, biological rep2


title: atscl26 cortical cells 2hr KCl control treated, biological rep3


title: Col0 epidermal cells 2hr KCl control treated, biological rep1


title: K562_pool2, insulators, RNA, rep2_2

city: Saint Louis

first: Barak

last: Cohen

state: MO

address: 4515 Mckinley Ave

institute: Washington University in St. Louis

description: Stable cell line containing 'landing pads' at multiple genomic locations

data_processing:
We first filtered for reads that contained barcodes in the correct sequence context. Barcodes were then counted to generate the counts.txt file. The barcodes were then corrected according to the corresponding mapping file for that pool to generate the corrected.txt files.
Assembly: hg38
Supplementary files format and content: Mapping files: bed file containing location of each barcode. The start and end positions are the same and indicate the base immediately 3' of the landing pad.
Supplementary files format and content: DNA and RNA barcode files: counts.txt files contain the barcodes and corresponding read count for each barcode. The corrected.txt contains the corrected barcodes and corresponding read count for each barcode.
Library strategy: barcode sequencing

growth_protocol: K562 cells were grown in IMDM (Isocove's Modified Dulbecco's Medium) supplemented with 10% fetal bovine serum (FBS), 1% non-essential amino acids (NEAA) and 1% penicillin/streptomycin (pen/strep).

extract_protocol:
Genomic DNA and RNA was extracted using TRIzol according to manufacturer's instructions.
Genomic DNA: Barcodes were amplified from DNA using custom primers. RNA: Extracted RNA was treated with DNase and reverse transcribed using Superscript IV with oligo-d(T) primers. Barcodes were then amplified from cDNA with custom primers. For both genomic DNA and RNA, sequencing adapters were added to the amplified barcodes for Illumina sequencing.

treatment_protocol: Cell containing genome-wide landing pads were transfected with BxbI and phiC31 recombinases together with the insulator library. The cells were allowed to grow for  a week before genomic DNA and RNA extraction.

tag: cell line

value: chronic myelogenous leukemia

value: Transfected with insulator library


title: IgE_medLN_PC_2

description:
Bulk IgH-seq
messenger RNA

tag: strain


title: IgE_medLN_PC_3

description:
Bulk IgH-seq
messenger RNA

tag: cell type


title: IgE_medLN_mB_3

description:
Bulk IgH-seq
messenger RNA

tag: genotype


title: IgE_SPL_mB_1

description:
Bulk IgH-seq
messenger RNA


title: IgE_SPL_mB_3

description:
Bulk IgH-seq
messenger RNA


title: K562_pool2, insulators, RNA, rep1_1

tag: treatment


title: K562_pool2, insulators, RNA, rep1_2


title: Lung_C_14

city: Oxford

first: Amy

middle: Rachael

last: Cross

address: John Radcliffe Hospital

department: NDS

institute: University of Oxford

data_processing:
Library strategy: GeoMx Seq
save-interim-files = false
quality-trim-score = 20
2color-trimming = True
adapter1 = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
adapter2 = AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
adapter-trim-match-length = 10
adapter-trim-max-mismatch = 3
barcode-max-mismatch = 1
stitching-max-mismatch = 2
dedup-hd = 1
threads = 4
Quality control and initial data exploration was conducted using the GeoMx DSP Analysis Suite.  Sequencing quality per AOI was examined and an under-sequenced area (B_04) with zero deduplicated reads was excluded.  Expression of each transcript was measured by 5 or more probes; outlier probes (geomean probe in all AOI/geomean of all probes for a transcript = <0.1; or probe failure in the Grubbs outlier test in over 20% AOIs) were excluded and the remaining probes combined to generate a single (post “biological probe QC”) expression value per gene target per AOI.
Genome_build: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform, see attached PKC files (Alpha_CTA_v2.0.pkc, and GeoMx_COVID19_v1.0.pkc)
Supplementary_files_format_and_content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode). Png files show the immunofluorescent microscopy image corresponding to each sample, including a white line border around the acquired areas of interest (AOIs).  The multichannel rendered images show DNA in blue, CD45 in red, PanCK in green and CD68 in yellow.
Supplementary_files_format_and_content: [value definition]  Values represented in the 'TargetCountMatrix' sheet of the ‘Post Biological Probe QC.xlsx’ are the geometric mean of the probes for a given target--in the case that multiple probes were used-- and excludes any targets flagged as outliers. A single sample (Cun4_2_004) was removed for sequencing failure and the absence of detected RawReads and AlignedReads. Analyzed counts in 'qn.exprs.tsv' represent quantile normalized collapsed counts for each sample in the study.  Analyzed counts in 'qn.exprs.corrected.tsv' represent quantile normalized collapsed counts for each sample in the study and corrected for batch effects using the Limma "removeBatchEffect" function.

source_name: Rapid biopsy post-morterm lung tissue Donor CUN6/C

extract_protocol:
Samples were incubated with DNA-oligo barcoded RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with fluorescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Each collection of oligo tags from one well (representing an ROI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR.  After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: molecule

value: Oligonucleotide

tag: individual

value: donor CUN6/C

value: post-morterm lung

tag: disease state

tag: morphology

value: Geometric; Alveolar morphology

tag: severity

tag: sample name

tag: sample name_2

tag: slide id

tag: roi number

tag: segment type

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: severity binary

value: Mild

tag: proximal sars-cov-2 nucleocapsid protein

value: No


title: K562_pool2, insulators, DNA, rep2_2

tag: cell line

tag: cell type

tag: treatment


title: IgE_medLN_mB_1

description:
Bulk IgH-seq
messenger RNA

tag: strain

tag: genotype

tag: age

tag: Sex

value: female

tag: isotype


title: IgE_medLN_PC_1

description:
Bulk IgH-seq
messenger RNA

value: CD19- CD98+ CD138+ plasma cells


title: IgE_Lung_PC_3

description:
Bulk IgH-seq
messenger RNA

value: IgE


title: K562_pool2, insulators, DNA, rep1_2


title: IgE_SPL_mB_2

description:
Bulk IgH-seq
messenger RNA

value: IgD- IgM- CD138- GL7- CD38+ CD19+ class-switched memory B cells

value: 10 weeks


title: IgE_medLN_mB_2

description:
Bulk IgH-seq
messenger RNA


title: K562_pool2, insulators, DNA, rep1_1


title: Lung_C_12

tag: molecule

tag: individual

tag: tissue

tag: disease state

tag: morphology

tag: severity

tag: sample name

tag: sample name_2

tag: slide id

tag: roi number

tag: segment type

tag: area

tag: roi x coordinate

tag: roi y coordinate

value: Severe


title: K562_pool2, insulators, DNA, rep2_1

tag: cell line

tag: cell type

tag: treatment


title: MethylationEPIC_786O_KO_Day15

type: genomic

city: Grand Rapids

first: Hyo Sik

last: Jang

state: Michigan

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

hyb_protocol: A total of 1 ug DNA was bisulfite converted using the EZ DNA Methylation-Lightning Kit (Zymo research, Cat# D5030) and hybridised to Illumina Infinium MethylationEPIC BeadChip

scan_protocol: Illumina iScan with Tecan Freedom EVO

data_processing: Illumina iScan with Tecan Freedom EVO

label: Cy3 and Cy5

source_name: kidney cancer cell line

label_protocol: Standard Illumina Protocol

growth_protocol: 786-O (ATCC Cat# CRL-1932, RRID:CVCL_1051) was cultured in RPMI 1640 medium (Corning). All media were supplemented with 10% heat-inactivated FBS (Corning) and 1% Penicillin-Streptomycin (Genesee Scientific).

extract_protocol: Genomic DNAs were purified using phenol–chloroform extraction and ethanol precipitation.

treatment_protocol: Cells were seeded in 10 cm dishes and treated with 300 nM DAC for 24 hrs and harvested days after treatment as labeled.

tag: genotype

value: 300nM DAC


title: K562_pool2, insulators, RNA, rep2_1


title: K562_pool1, insulators, RNA, rep2_2


title: Lung_C_13

tag: molecule

tag: individual

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: severity binary

tag: proximal sars-cov-2 nucleocapsid protein


title: MethylationEPIC_786O_KO_Day0


title: IgE_Lung_PC_1

description:
Bulk IgH-seq
messenger RNA

tag: strain

tag: age

value: 12 weeks

tag: Sex

tag: isotype


title: Lung_C_11

tag: tissue

tag: disease state

tag: morphology

tag: severity

tag: sample name

tag: sample name_2

tag: slide id

tag: roi number

tag: segment type

tag: area

tag: roi x coordinate

tag: roi y coordinate


title: IgE_Lung_PC_2

description:
Bulk IgH-seq
messenger RNA

tag: genotype

tag: cell type


title: Lung_C_10

tag: molecule

tag: individual

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: severity binary

tag: proximal sars-cov-2 nucleocapsid protein


title: K562_pool1, insulators, RNA, rep2_1

tag: cell line

tag: treatment


title: IgE_Lung_mB_3

description:
Bulk IgH-seq
messenger RNA

tag: strain

tag: age

value: 11 weeks

tag: Sex

value: male

tag: isotype


title: MethylationEPIC_786O_KO_Day5

tag: genotype


title: K562_pool1, insulators, RNA, rep1_2

tag: cell type

value: chronic myelogenous leukemia

value: Transfected with insulator library


title: MethylationEPIC_786O_EV_Day5

value: WT


title: Lung_C_08

tag: molecule

value: Oligonucleotide

tag: individual

value: donor CUN6/C

tag: tissue

value: post-morterm lung

tag: disease state

tag: morphology

tag: severity

tag: sample name

tag: sample name_2

tag: slide id

tag: roi number

tag: segment type

tag: area

tag: roi x coordinate

tag: roi y coordinate


title: MethylationEPIC_786O_EV_Day15

tag: cell line

tag: treatment


title: Lung_C_04

value: Geometric; Alveolar morphology

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: severity binary

value: Mild

tag: proximal sars-cov-2 nucleocapsid protein

value: No


title: Lung_C_09

tag: molecule

tag: individual

tag: tissue

tag: disease state

tag: morphology

tag: severity

tag: sample name

tag: sample name_2

value: Yes


title: MethylationEPIC_786O_KO_Day39

tag: cell line

tag: genotype

tag: treatment


title: Lung_C_02

tag: slide id

tag: roi number

tag: segment type

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads


title: Lung_C_07

tag: molecule

tag: individual

tag: tissue

tag: disease state

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: severity binary

tag: proximal sars-cov-2 nucleocapsid protein


title: K562_pool1, insulators, DNA, rep2_1

tag: cell line

tag: cell type

tag: treatment


title: Lung_C_01

tag: morphology

tag: severity

tag: sample name

tag: sample name_2

tag: slide id

tag: roi number

tag: segment type

tag: area

tag: roi x coordinate


title: IgE_Lung_mB_1

description:
Bulk IgH-seq
messenger RNA

tag: strain

tag: genotype

value: IgD- IgM- CD138- GL7- CD38+ CD19+ class-switched memory B cells

tag: age

tag: Sex

value: female

tag: isotype

value: IgE


title: Lung_C_05

tag: molecule

tag: individual

tag: tissue

tag: disease state

value: Severe

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: severity binary

tag: proximal sars-cov-2 nucleocapsid protein


title: MethylationEPIC_786O_EV_Day0

tag: cell line

tag: genotype

tag: treatment


title: Lung_C_06

tag: morphology

tag: severity

tag: sample name

tag: sample name_2

tag: slide id

tag: roi number

tag: segment type

tag: area

tag: roi x coordinate


title: ChIRP_Odd_probes

city: Duarte

first: Zhipeng

last: Fang

address: 1500 E Duarte Rd

institute: City of Hope

data_processing:
The ChIRP reads were aligned to the mm10 genome assembly by Novoalign (v4.02.02)
The bam files were sorted and indexed by SAMtools/1.9-foss-2018b
MACS2 was used for Peak calling
Assembly: mm10
Supplementary files format and content: bigWig
Supplementary files format and content: peak text files
Library strategy: ChIRP-seq

source_name: mouse primary hepatocytes

extract_protocol:
Fresh isolated primary hepatocytes were fixed with 3% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor (Diagenode).
The libraries were constructed using the KAPA HyperPrep kit following the user manual.

tag: cell type

value: mouse primary hepatocytes

tag: probes

value: Gm19619-targeting Odd probes (Biosearch Technologies)


title: K562_pool1, insulators, DNA, rep2_2


title: PLD_3m_RNA_ML324_rep2

source_name: primary cholangiocytes

extract_protocol:
Total RNAs were extracted from primary cholangiocytes using TRIzol (Invitrogen, 15596018) according to the manufacturer’s instructions.
For RNA samples from WT or PLD mice 1 month and 2 months after tamoxifen induction, libraries were constructed and sequenced on the Illumina NovaSeq platform. For RNA samples from PLD mice treated with CPTH6 or ML324, libraries were constructed and sequenced on the Illumina NovaSeq platform.

value: primary cholangiocytes

value: PLD


title: Lung_A_13

source_name: Rapid biopsy post-morterm lung tissue Donor CUN5/A

tag: molecule

tag: individual

value: donor CUN5/A

tag: tissue

tag: disease state

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: K562_pool1, insulators, RNA, rep1_1

tag: cell line

value: chronic myelogenous leukemia

tag: treatment

value: Transfected with insulator library


title: Lung_A_12

value: Oligonucleotide

tag: morphology

tag: severity

tag: sample name

tag: sample name_2

tag: slide id

tag: roi number

tag: segment type

tag: area

tag: severity binary

tag: proximal sars-cov-2 nucleocapsid protein


title: PLD_3m_RNA_ML324_rep3

tag: cell type

tag: genotype


title: MethylationEPIC_786O_EV_Day39

value: WT

value: 300nM DAC


title: Lung_C_03

tag: molecule

tag: individual

value: donor CUN6/C

tag: tissue

value: post-morterm lung

tag: disease state

value: Geometric; Alveolar morphology

value: Mild

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads


title: PLD_3m_RNA_CPTH6_rep3

tag: treatment


title: K562_pool2, GWLP mapping, rep4

description:
Stable cell line containing 'landing pads' at multiple genomic locations
P2_combined_unique.bed

data_processing:
Mapping files: We first filtered for reads that contained barcodes in the correct sequence context. Barcodes were associated with their corresponding integration site sequence, which was then aligned to the reference genome with BWA (v0.7.17) using default parameters. We only kept barcodes where the reads for one location represented at least 80% of all the locations for that barcode. To generate the combined_unique.bed files for each pool, we only kept the most abundant barcode for each location. To generate all other bed files, we kept all the barcodes associated with any given location.
DNA and RNA barcode files: We first filtered for reads that contained barcodes in the correct sequence context. Barcodes were then counted to generate the counts.txt file. The barcodes were then corrected according to the corresponding mapping file for that pool to generate the corrected.txt files.
Assembly: hg38
Supplementary files format and content: Mapping files: bed file containing location of each barcode. The start and end positions are the same and indicate the base immediately 3' of the landing pad.
Supplementary files format and content: DNA and RNA barcode files: counts.txt files contain the barcodes and corresponding read count for each barcode. The corrected.txt contains the corrected barcodes and corresponding read count for each barcode.
Library strategy: barcode sequencing

treatment_protocol: For mock transfected or recombinase transfected samples, cells were either electroporated with no plasmid (mock) or with BxbI and phiC31 recombinases (recombinase) in a 1:1 ratio. The cells were then allowed to grow for a week before DNA/RNA extraction.

tag: cell line

value: No treatment


title: K562_pool2, GWLP mapping, rep3


title: Lung_A_09

tag: morphology

tag: severity

tag: sample name

tag: sample name_2

tag: slide id

tag: roi number

tag: segment type

tag: area

tag: stitchedreads

tag: sequencingsaturation

value: No


title: PLD_3m_RNA_ML324_rep1

tag: cell type

tag: genotype


title: PLD_3m_RNA_CPTH6_rep2


title: K562_pool1, insulators, DNA, rep1_2


title: Lung_A_16

tag: molecule

tag: individual

tag: tissue

tag: disease state

value: Geometric; Bronchiolar epithelium

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: proximal sars-cov-2 nucleocapsid protein


title: Lung_A_17

tag: morphology

tag: severity

tag: sample name

tag: sample name_2

tag: slide id

tag: deduplicatedreads

tag: trimmedreads


title: Lung_A_06

value: Severe

tag: roi number

tag: segment type

tag: area

tag: stitchedreads

tag: sequencingsaturation

tag: severity binary


title: Lung_A_15

tag: molecule

tag: individual

tag: tissue

tag: disease state

tag: roi x coordinate

tag: roi y coordinate


title: IgE_Lung_mB_2

description:
Bulk IgH-seq
messenger RNA

tag: strain

tag: genotype

tag: cell type

value: IgD- IgM- CD138- GL7- CD38+ CD19+ class-switched memory B cells

tag: age

value: 10 weeks

tag: Sex

value: female

tag: isotype

value: IgE


title: ChIRP_Even_probes

value: mouse primary hepatocytes

tag: probes

value: Gm19619-targeting Even probes (Biosearch Technologies)


title: Lung_A_10

value: Oligonucleotide

value: donor CUN5/A

tag: morphology

tag: severity

tag: sample name

tag: sample name_2

tag: slide id

tag: roi number

tag: segment type

tag: area

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: proximal sars-cov-2 nucleocapsid protein


title: Lung_A_14

tag: molecule

tag: individual

tag: tissue

tag: disease state

tag: roi x coordinate

tag: roi y coordinate

tag: stitchedreads

tag: sequencingsaturation

tag: severity binary


title: Lung_A_08

tag: morphology

tag: severity

tag: sample name

tag: sample name_2

tag: slide id

tag: roi number


title: R29d180PBMC VDJ

city: Berlin

first: Benedikt

last: Obermayer

address: Chariteplatz 1

department: Core Unit Bioinformatics

country: Germany

institute: Berlin Institute of Health

data_processing:
Sequencing libraries for gene expression and TCR was jointly processed using cellranger multi (v6.0.0) and the GRCh38 genome annotation
clonotypes in bulk TCR sequencing were characterized IMSEQ software
Assembly: GRCh38
Supplementary files format and content: cellranger h5 output (gene expression, CITEseq) and contig table (VDJ)
Supplementary files format and content: IMSEQ output table (bulk TCR)
Library strategy: VDJ profiling

source_name: blood

extract_protocol:
PBMC were isolated from up to 20ml whole blood using density gradient centrifugation. PBMC were then freshly frozen according to standard procedures and stored in liquid nitrogen. The samples were thawed and stained with 4',6- diamidino-2-phenylindole (DAPI). We sorted for alive lymphocytes using a FACSAria Fusion cell sorter (Becton Dickinson, Franklin Lakes, NJ, USA).
Samples were treated individually, using one 10x lane per sample. Alive cells were incubated with 5 μl Human TruStain FcX™ per 1x106 cells for 10 min, then stained with nucleotide‑labeled TotalSeqCTM antibodies (Biolegend, San Diego, USA) for 30min. To avoid antibody aggregates, labeled cells were washed 3 times with 1 ml PBS/BSA with centrifugation at 300 g for 5 min. Cells were then resuspended in 50 μl PBS/BSA and counted using the Neubauer chamber. We aimed for a calculated amount of ~16.500 cells of each sample for droplet encapsulation on separate lanes of the Chromium Controller (10x Genomics, Pleasanton, CA, USA). Single-cell capturing and library construction were performed with the Chromium Next GEM Single Cell V(D)J Reagent Kit v2 (10x Genomics, Pleasanton, CA, USA) according to manufacturer’s instructions. Essentially, single-cell gel beads-in-emulsion (GEMs) are formed, each containing a single cell and 10x chemistry for cell lysis, barcoding and reverse transcription of contained RNA within each GEM. The resulting cDNA including the single-cell barcodes is then amplified using standard polymerase-chain reaction (PCR). We constructed We constructed TCR libraries with the 10x T-cell V(D)J Enrichment Kits (PN-1000252)
single-cell immune profiling (totalSeq: scRNAseq, CITEseq, single-cell VDJ sequencing), bulk TCR

value: blood

tag: donor

tag: cell type

value: PBMC

tag: treatment


title: R29d90PBMC VDJ

value: day +90


title: WT_1m_RNA_rep3

value: primary cholangiocytes

tag: genotype

value: WT


title: R16d180PBMC VDJ

tag: tissue


title: K562_pool1, insulators, DNA, rep1_1

tag: cell line

value: chronic myelogenous leukemia

value: Transfected with insulator library


title: Lung_A_07

tag: molecule

tag: individual

value: post-morterm lung

tag: disease state

value: Geometric; Alveolar morphology

tag: segment type

tag: area

tag: roi x coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: proximal sars-cov-2 nucleocapsid protein

value: No


title: Lung_A_11

tag: morphology

tag: severity

value: Severe

tag: sample name

tag: sample name_2

tag: slide id

tag: roi number

tag: roi y coordinate

tag: stitchedreads

tag: sequencingsaturation

tag: severity binary


title: Lung_A_05

tag: molecule

tag: individual

tag: tissue

tag: disease state

tag: segment type

tag: area


title: PLD_3m_RNA_CPTH6_rep1

tag: cell type

tag: genotype

value: PLD

tag: treatment


title: D16postPBMC VDJ

tag: donor

value: post G-CSF


title: Lung_A_03

tag: morphology

tag: severity

tag: sample name

tag: sample name_2

tag: roi x coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: proximal sars-cov-2 nucleocapsid protein


title: Lung_B_15

source_name: Rapid biopsy post-morterm lung tissue Donor CUN4/B

tag: molecule

tag: individual

value: donor CUN4/B

tag: tissue

tag: disease state

tag: slide id

tag: roi number

tag: roi y coordinate

tag: stitchedreads

tag: sequencingsaturation

tag: severity binary

value: Yes


title: Lung_A_01

value: Oligonucleotide

tag: morphology

tag: severity

tag: sample name

tag: sample name_2

tag: segment type

tag: area


title: WT_1m_RNA_rep1

tag: cell type

tag: genotype


title: D29postPBMC VDJ

tag: donor

tag: treatment


title: Lung_B_11

tag: molecule

tag: individual

tag: tissue

tag: disease state

tag: roi x coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: proximal sars-cov-2 nucleocapsid protein


title: Lung_B_14

tag: morphology

tag: severity

tag: sample name

tag: sample name_2

tag: slide id

tag: roi number

tag: roi y coordinate

tag: stitchedreads

tag: sequencingsaturation

tag: severity binary


title: Lung_B_13

tag: molecule

tag: individual

tag: tissue

tag: disease state

tag: segment type

tag: area


title: Lung_B_10

tag: roi x coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: proximal sars-cov-2 nucleocapsid protein


title: D16prePBMC VDJ

tag: donor

tag: cell type

tag: treatment

value: pre G-CSF


title: WT_1m_RNA_rep2

tag: genotype


title: Lung_A_04

value: donor CUN5/A

tag: morphology

tag: severity

tag: sample name

tag: sample name_2

tag: slide id

tag: roi number

tag: roi y coordinate

tag: stitchedreads

tag: sequencingsaturation

tag: severity binary


title: PLD_1m_RNA_rep2


title: PLD_1m_RNA_rep3


title: Lung_B_16

tag: molecule

tag: individual

tag: tissue

tag: disease state

tag: segment type

tag: area

tag: roi x coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads


title: PLD_1m_RNA_rep1

tag: cell type

tag: genotype


title: R10d180PBMC VDJ

value: blood

tag: donor

value: PBMC

tag: treatment


title: D10prePBMC VDJ


title: D10postPBMC VDJ


title: Lung_B_09

tag: morphology

tag: severity

value: Mild

tag: sample name

tag: sample name_2

tag: slide id

tag: roi number

tag: roi y coordinate

tag: trimmedreads

tag: stitchedreads

tag: proximal sars-cov-2 nucleocapsid protein


title: Lung_A_02

tag: molecule

tag: individual

tag: tissue

tag: disease state

tag: segment type

tag: area

tag: roi x coordinate

tag: rawreads

tag: sequencingsaturation

tag: severity binary


title: R16d90PBMC VDJ

tag: donor

tag: cell type

tag: treatment

value: day +90


title: WT_2m_RNA_rep3

value: primary cholangiocytes

tag: genotype

value: WT


title: Lung_B_07

value: post-morterm lung

tag: morphology

tag: severity

tag: sample name

tag: sample name_2

tag: slide id

tag: roi number

tag: roi y coordinate

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads


title: Lung_B_06

tag: molecule

tag: individual

tag: tissue

tag: disease state

value: Geometric; Alveolar morphology

tag: segment type

tag: area

tag: roi x coordinate

tag: rawreads

tag: stitchedreads

tag: proximal sars-cov-2 nucleocapsid protein


title: WT_2m_RNA_rep2

tag: cell type

tag: genotype


title: Lung_B_04

description: Sample failed sequencing.

tag: morphology

tag: severity

tag: sample name

tag: sample name_2

tag: slide id

tag: roi number

tag: sequencingsaturation

tag: severity binary


title: R26d90PBMC VDJ

tag: tissue

tag: donor

tag: treatment


title: Lung_B_05

tag: molecule

tag: individual

tag: disease state

tag: segment type

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads


title: Lung_B_03

tag: morphology

tag: severity

tag: sample name

tag: sample name_2

tag: slide id

tag: rawreads

tag: stitchedreads

tag: proximal sars-cov-2 nucleocapsid protein


title: PLD_2m_RNA_rep3

tag: cell type

tag: genotype


title: WT_2m_RNA_rep1


title: Lung_B_02

tag: molecule

tag: individual

tag: tissue

tag: disease state

tag: roi number

tag: segment type

tag: sequencingsaturation

tag: severity binary


title: Lung_B_12

tag: morphology

tag: severity

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads


title: MGH66_ciprofloxacin_BacDrop_replicate2

description:
BacDrop_MGH66_replicate2
Replicate 2

data_processing:
bcl2fastq2-v2.20.0 was used to generate fastq files
Sequencing reads were trimed and sorted using fastp-0.20.0
Cell barcodes were extracted using UMI-Tools package installed in Python-3.6
Alignment was using BWA
FeatureCounts was used to assign reads to gene, count transcripts and generate counts tables.
Assembly: Counts matrix from BacDrop experiments were generated using UMI-Tools

extract_protocol: Trizol RNA extraction for Bulk RNAseq data

tag: strain

tag: method

value: BacDrop

tag: genotype

value: Clinical isolate

tag: treatment

value: ciprofloxacin


title: D26postPBMC VDJ

tag: tissue

tag: donor

tag: cell type

value: post G-CSF


title: Lung_B_01

tag: molecule

tag: individual

value: donor CUN4/B

tag: disease state

value: Severe

tag: sample name

tag: sample name_2

tag: slide id

tag: roi number

tag: segment type

tag: rawreads

tag: stitchedreads

tag: sequencingsaturation

tag: proximal sars-cov-2 nucleocapsid protein


title: MGH66_meropenem_BacDrop_replicate2

description:
BacDrop_MGH66_replicate2
Replicate 2

tag: strain

tag: method

tag: genotype

value: meropenem


title: D26prePBMC VDJ

tag: tissue

tag: donor

tag: treatment

value: pre G-CSF


title: PLD_2m_RNA_rep1

tag: cell type

value: PLD


title: PLD_2m_RNA_rep2


title: Lung_B_08

tag: molecule

value: Oligonucleotide

tag: individual

tag: disease state

tag: morphology

tag: severity

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: severity binary

value: No


title: MGH66_gentamicin_BacDrop_replicate2

description:
BacDrop_MGH66_replicate2
Replicate 2

tag: strain

tag: method

tag: genotype

value: gentamicin


title: WT_3m_H3K27ac_rep2

data_processing:
Paired-end reads from ATAC-seq were aligned by the Bowtie2 (2.3.5.1) algorithm against the mouse reference genome mm10.
Picard “mark duplicates” (2.25.1) command was applied to remove PCR duplicates and reads aligned to mtDNA were removed.
Deeptools (3.4.3) was used for generating bigWig file.
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
Briefly, primary cholangiocytes were divided into 100,000 cells per tube, and the samples were kept on ice or at 4°C. Cells were lysed in 19 μL lysis buffer (0.5% NP-40, 0.5% Tween-20, 0.1% SDS and cOmplete Protease Inhibitor Cocktail), and then incubated with 19 μL MNase buffer (100 mM Tris-HCl pH 8.0 and 2 mM CaCl2) containing 0.02 U MNase (Sigma, N3755) at 37°C for 5 min. Digestion was terminated by adding 5 μL stop buffer (110 mM Tris-HCl pH 8.0 and 55 mM EDTA). Each sample was incubated with 45 μL 2x RIPA buffer (280 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.2% sodium deoxycholate, 5 mM EGTA and cOmplete Protease Inhibitor Cocktail) for 10 min before centrifuged at 14500 rpm for 15 min. The supernatant was transferred to a new tube, and then added with 40 μL RIPA buffer (10 mM Tris-HCl pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate and 1 mM EDTA). For IP samples, each sample was incubated overnight with 1 μg antibody of H3K9ac (Abcam, ab4441), H3K9me3 (Abcam, ab8898), H3K4me3 (Millipore, 05-745R), H3K4me1 (Abcam, ab8895) or H3K27ac (Abcam, ab4729), and followed by immunoprecipitation with Dynabeads Protein G (Thermo Fisher Scientific, 10004D). And then samples were centrifuged and the collected-beads were washed five times with 150 μL RIPA buffer and rinsed once with 150 μL LiCl buffer (10 mM Tris-HCl pH 8.0, 0.5% NP-40, 1 mM EDTA, 0.5% sodium deoxycholate and 250 mM LiCl). Beads were finally resuspended with 30 μL elution buffer containing 1 μL proteinase K (TransGen Biotech, GE201-01), and followed by shaking at 55°C for 90 min. The supernatant was transferred to a new tube, and proteinase K was inactivated by heated at 72°C for 40 min. For Input samples, each sample was treated with 1 μL proteinase K, followed by shaking at 55°C for 90 min, and then DNA was purified using DNA Extraction Reagent (Solarbio, P1012).
Library construction was performed using a VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme, ND607). Sequencing was performed on the Illumina platform.

tag: chip antibody

value: H3K27ac (Abcam, #ab4729)


title: R36d90PBMC VDJ

tag: tissue

value: blood

tag: donor

tag: cell type

value: PBMC

tag: treatment

value: day +90


title: R26d180PBMC VDJ


title: D36prePBMC VDJ


title: MGH66_gentamicin_Bulk3 [G3]

data_processing:
bcl2fastq2-v2.20.0 was used to generate fastq files
Sequencing reads were trimed and sorted using fastp-0.20.0
Cell barcodes were extracted using UMI-Tools package installed in Python-3.6
Alignment was using BWA
FeatureCounts was used to assign reads to gene, count transcripts and generate counts tables.
Counts matrix from BacDrop experiments were generated using UMI-Tools
Genome_build: NOT PROVIDED
Supplementary_files_format_and_content: Counts matrix

source_name: Antibiotic susceptible clinical isolate

value: RNAtag-seq

tag: accession no.


title: MGH66_gentamicin_Bulk2 [G2]


title: MGH66_ciprofloxacin_Bulk2 [C2]


title: Kp_BacDrop

description: Kp

source_name: A K. pneumoniae clinical isolate, susceptible to carbapenems, resistant to ciprofloxacin and gentamicin

value: untreated

value: BacDrop


title: MGH66_ciprofloxacin_Bulk3 [C3]

value: ciprofloxacin


title: MGH66_untreated_BacDrop_replicate2

description:
BacDrop_MGH66_replicate2
Replicate 2

value: Clinical isolate


title: WT_3m_H3K27ac_rep1

value: primary cholangiocytes

value: WT


title: R29d180PBMC CITEseq

data_processing:
Sequencing libraries for gene expression and TCR was jointly processed using cellranger multi (v6.0.0) and the GRCh38 genome annotation
clonotypes in bulk TCR sequencing were characterized IMSEQ software
Assembly: GRCh38
Supplementary files format and content: cellranger h5 output (gene expression, CITEseq) and contig table (VDJ)
Supplementary files format and content: IMSEQ output table (bulk TCR)
Library strategy: CITEseq

molecule: protein

extract_protocol:
PBMC were isolated from up to 20ml whole blood using density gradient centrifugation. PBMC were then freshly frozen according to standard procedures and stored in liquid nitrogen. The samples were thawed and stained with 4',6- diamidino-2-phenylindole (DAPI). We sorted for alive lymphocytes using a FACSAria Fusion cell sorter (Becton Dickinson, Franklin Lakes, NJ, USA).
Samples were treated individually, using one 10x lane per sample. Alive cells were incubated with 5 μl Human TruStain FcX™ per 1x106 cells for 10 min, then stained with nucleotide‑labeled TotalSeqCTM antibodies (Biolegend, San Diego, USA) for 30min. To avoid antibody aggregates, labeled cells were washed 3 times with 1 ml PBS/BSA with centrifugation at 300 g for 5 min. Cells were then resuspended in 50 μl PBS/BSA and counted using the Neubauer chamber. We aimed for a calculated amount of ~16.500 cells of each sample for droplet encapsulation on separate lanes of the Chromium Controller (10x Genomics, Pleasanton, CA, USA). Single-cell capturing and library construction were performed with the Chromium Next GEM Single Cell V(D)J Reagent Kit v2 (10x Genomics, Pleasanton, CA, USA) according to manufacturer’s instructions. Essentially, single-cell gel beads-in-emulsion (GEMs) are formed, each containing a single cell and 10x chemistry for cell lysis, barcoding and reverse transcription of contained RNA within each GEM. The resulting cDNA including the single-cell barcodes is then amplified using standard polymerase-chain reaction (PCR). We constructed gene expression libraries with 10x 5’ Library Kits (PN-1000263/5, PN-1000190, PN-1000286, PN-1000215)
single-cell immune profiling (totalSeq: scRNAseq, CITEseq, single-cell VDJ sequencing), bulk TCR


title: MGH66_ciprofloxacin_Bulk1 [C1]


title: WT_3m_H3K9me3_rep1

value: H3K9me3 (Abcam, #ab8898)


title: WT_3m_H3K9me3_rep2


title: WT_3m_H3K9ac_rep2

value: H3K9ac (Abcam, #ab4441)


title: R29d90PBMC CITEseq


title: MGH66_meropenem_Bulk2 [M2]

value: meropenem


title: D36postPBMC VDJ

value: post G-CSF


title: D29postPBMC CITEseq


title: MGH66_meropenem_Bulk1 [M1]


title: MGH66_meropenem_Bulk3 [M3]


title: MGH66_gentamicin_Bulk1 [G1]


title: MGH66_untreated_Bulk3 [U3]


title: WT_3m_H3K9ac_rep1


title: MGH66_untreated_Bulk2 [U2]


title: MGH66_untreated_Bulk1 [U1]


title: WT_3m_H3K4me3_rep2

value: H3K4me3 (Millipore, #05-745R)


title: BIDMC35_untreated_BacDrop

source_name: Multi-drug resistant clinical isolate


title: WT_3m_H3K4me3_rep1


title: R16d90PBMC CITEseq


title: MGH66_ciprofloxacin_BacDrop


title: D16postPBMC CITEseq


title: MGH66_meropenem_BacDrop


title: MGH66_untreated_BacDrop


title: WT_3m_H3K4me1_rep2

value: H3K4me1 (Abcam, #ab8895)


title: D16prePBMC CITEseq

value: pre G-CSF


title: R10d180PBMC CITEseq

value: blood


title: D10prePBMC CITEseq

value: PBMC


title: R26d180PBMC CITEseq


title: WT_3m_Input_rep2


title: R16d180PBMC CITEseq


title: D10postPBMC CITEseq


title: K562_pool6, insulators, DNA, rep1_2

tag: cell line

value: chronic myelogenous leukemia

value: Transfected with insulator library


title: K562_pool6, insulators, RNA, rep2_1


title: K562_pool6, insulators, RNA, rep1_1


title: K562_pool6, insulators, RNA, rep1_2


title: PLD_3m_H3K27ac_rep2

value: H3K27ac (Abcam, #ab4729)

value: PLD


title: K562_pool6, insulators, RNA, rep2_2


title: WT_3m_H3K4me1_rep1


title: K562_pool5, insulators, RNA, rep2_2


title: K562_pool5, insulators, RNA, rep2_1


title: K562_pool6, insulators, DNA, rep2_2


title: K562_pool5, insulators, RNA, rep1_1


title: MGH66_gentamicin_BacDrop

value: gentamicin

value: BacDrop


title: PLD_3m_H3K9me3_rep2

value: primary cholangiocytes


title: D26postPBMC CITEseq


title: PLD_3m_H3K27ac_rep1


title: PLD_3m_H3K9me3_rep1


title: K562_pool5, insulators, DNA, rep2_2


title: R26d90PBMC CITEseq

value: day +90


title: K562_pool6, insulators, DNA, rep1_1


title: K562_pool6, insulators, DNA, rep2_1


title: K562_pool5, insulators, DNA, rep2_1


title: WT_3m_Input_rep1

value: WT


title: R36d90PBMC CITEseq


title: K562_pool5, insulators, DNA, rep1_2


title: K562_pool4, insulators, RNA, rep2_1


title: D36prePBMC CITEseq


title: PLD_3m_H3K4me3_rep2


title: K562_pool4, insulators, DNA, rep2_2


title: K562_pool4, insulators, RNA, rep2_2


title: PLD_3m_H3K9ac_rep1

value: H3K9ac (Abcam, #ab4441)


title: R29d180PBMC scRNAseq

library_source: transcriptomic single cell

data_processing:
Sequencing libraries for gene expression and TCR was jointly processed using cellranger multi (v6.0.0) and the GRCh38 genome annotation
clonotypes in bulk TCR sequencing were characterized IMSEQ software
Assembly: GRCh38
Supplementary files format and content: cellranger h5 output (gene expression, CITEseq) and contig table (VDJ)
Supplementary files format and content: IMSEQ output table (bulk TCR)


title: PLD_3m_H3K9ac_rep2


title: PLD_3m_H3K4me1_rep2


title: K562_pool5, insulators, DNA, rep1_1


title: PLD_3m_H3K4me1_rep1


title: K562_pool4, insulators, RNA, rep1_2


title: K562_pool4, insulators, RNA, rep1_1


title: PLD_3m_Input_rep2


title: R16d180PBMC scRNAseq


title: K562_pool3, insulators, RNA, rep1_2


title: K562_pool3, insulators, DNA, rep2_2


title: K562_pool3, insulators, DNA, rep1_2


title: D26prePBMC CITEseq


title: PLD_3m_ATAC_ML324_rep2

data_processing:
Paired-end reads from ATAC-seq were aligned by the Bowtie2 (2.3.5.1) algorithm against the mouse reference genome mm10.
Picard “mark duplicates” (2.25.1) command was applied to remove PCR duplicates and reads aligned to mtDNA were removed.
MACS3 (3.0.0a4) was used for each sample using fragment sizes obtained from the alignments and a p-value cutoff of 0.05.
Then IDR (2.0.4.2) was applied to identify reproducible peaks between biological replicates of the same condition. The IDR passed peaks were used for further analysis.
Deeptools (3.4.3) was used for generating bigWig file.
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
100,000 primary cholangiocytes were lysed in cold ATAC lysis buffer (10 mM Tris–HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) igepal CA-630) for 20 min on ice before centrifuged at 500 g for 10 min. The cell nuclei were collected and incubated with 50 μL transposition reaction buffer (3 μL TruePrep Tagment Enzyme, 10 μL TruePrep Tagment Buffer L from Vazyme TD501) at 37°C for 60 min.
DNA was purified using the QIAquick PCR Purification Kit (QIAGEN, 28106) according to the manufacturer’s instructions. After DNA fragmentation and purification, library construction was performed with TruePrepTM DNA Library Prep Kit V2 for Illumina (Vazyme, TD501) according to the manufacturer’s instructions.


title: PLD_3m_H3K4me3_rep1


title: K562_pool3, insulators, RNA, rep2_1


title: K562_pool1, GWLP expression, recombinase transfected, RNA2

value: Transfected with BxbI and phiC31 recombinases


title: K562_pool4, insulators, DNA, rep1_1


title: K562_pool1, GWLP expression, recombinase transfected, RNA1


title: D16prePBMC scRNAseq


title: K562_pool3, insulators, RNA, rep2_2


title: D29postPBMC scRNAseq

value: post G-CSF


title: K562_pool1, GWLP expression, recombinase transfected, DNA


title: D10postPBMC scRNAseq


title: D10prePBMC scRNAseq


title: R29d90PBMC scRNAseq


title: K562_pool4, insulators, DNA, rep2_1


title: K562_pool1, GWLP expression, mock transfected, DNA, rep1

value: Mock transfected


title: K562_pool1, GWLP mapping, recombinase transfected, rep6


title: K562_pool4, insulators, DNA, rep1_2


title: R26d180PBMC scRNAseq


title: K562_pool3, insulators, DNA, rep2_1


title: D36postPBMC CITEseq


title: K562_pool1, GWLP mapping, recombinase transfected, rep4


title: K562_pool1, GWLP mapping, recombinase transfected, rep5


title: K562_pool3, insulators, DNA, rep1_1


title: D16postPBMC scRNAseq


title: R10d180PBMC scRNAseq


title: K562_pool1, GWLP expression, mock transfected, DNA, rep2


title: PLD_3m_Input_rep1


title: K562_pool1, GWLP expression, mock transfected, RNA, rep1_3


title: R16d90PBMC scRNAseq


title: K562_pool1, GWLP expression, mock transfected, RNA, rep2


title: K562_pool1, GWLP expression, mock transfected, RNA, rep1_2


title: K562_pool5, insulators, RNA, rep1_2


title: PLD_3m_ATAC_CPTH6_rep2


title: PLD_3m_ATAC_CPTH6_rep1


title: K562_pool3, insulators, RNA, rep1_1


title: PLD_3m_ATAC_ML324_rep1


title: WT_1m_ATAC_rep2


title: PLD_1m_ATAC_rep2


title: WT_1m_ATAC_rep1


title: D26prePBMC scRNAseq


title: K562_pool1, GWLP expression, mock transfected, RNA, rep1_1


title: R36d90PBMC scRNAseq


title: K562_pool6, GWLP expression, DNA

value: No treatment


title: K562_pool5, GWLP expression, DNA


title: D26postPBMC scRNAseq


title: K562_pool1, GWLP mapping, recombinase transfected, rep3


title: PLD_2m_ATAC_rep2


title: PLD_1m_ATAC_rep1


title: K562_pool4, GWLP expression, RNA


title: K562_pool4, GWLP expression, DNA


title: D36postPBMC scRNAseq


title: K562_pool1, GWLP mapping, recombinase transfected, rep2


title: K562_pool5, GWLP expression, RNA


title: K562_pool1, GWLP mapping, recombinase transfected, rep1


title: PLD_2m_ATAC_rep1


title: K562_pool3, GWLP expression, RNA


title: WT_2m_ATAC_rep2


title: K562_pool6, GWLP expression, RNA


title: WT_2m_ATAC_rep1


title: WT_3m_ATAC_rep2


title: K562_pool2, GWLP expression, RNA


title: K562_pool3, GWLP expression, DNA


title: R26d90PBMC scRNAseq


title: D36prePBMC scRNAseq

value: pre G-CSF


title: TotalRNAseq_769P_Day25_Rep2

data_processing:
ChIP-seq reads were trimmed with Trim Galore to remove adapter sequences and aligned to the hg38 genome using bwa (bwa mem) . Duplicate reads were removed from aligned reads using Picard MarkDuplicates. Reproducible histone peaks (broad peaks for H3K36me3, H3K27me3 & narrow peaks for H3K4me3, H3K9me3, H3K27ac) were identified by using MACS2 followed by IDR identification and filtering using idr-threshold < 0.05.
The reads from total RNA-seq libraries were trimmed for adapter sequences and aligned to the hg38 genome using HISAT2 with proper capture of RNA strand orientation. The bam files were normalized into CPM bedgraph files using deeptools "bamCoverage" command.
Assembly: hg38
Supplementary files format and content: Total RNAseq are processed and presented as CPM normalized bedgraph files. For ChIP-seq, MACS2-identified peaks are presented as bed files.

growth_protocol: 786-O (ATCC Cat# CRL-1932, RRID:CVCL_1051) and 769-P (ATCC Cat# CRL-1933, RRID:CVCL_1050) were cultured in RPMI 1640 medium (Corning). A-498 (ATCC Cat# HTB-44, RRID:CVCL_1056), A-704 (ATCC Cat# HTB-45, RRID:CVCL_1065) were cultured in EMEM medium (ATCC), and ACHN (ATCC Cat# CRL-1611, RRID:CVCL_1067). Caki-1 (ATCC Cat# HTB-46, RRID:CVCL_0234) and Caki-2(ATCC Cat# HTB-47, RRID:CVCL_0235) were cultured in McCoy's 5A Medium (Millipore Sigma). All media were supplemented with 10% heat-inactivated FBS (Corning) and 1% Penicillin-Streptomycin (Genesee Scientific).

extract_protocol:
Total RNA was extracted using RNeasy kit (Qiagen) followed by on-column DNase I digestion according to the manufacturer’s protocol. Genomic DNAs were purified using phenol–chloroform extraction and ethanol precipitation.
Sequencing libraries were prepared using the KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche, Cat# 08098140702). ChIP assays were performed following the native ChIP protocol. ChIP assays were performed following the native ChIP protocol (Ohtani et al., 2018) with minor modifications.
Total RNA-seq 786-O EV/KO Rep1 were sequenced 75 bp single end.  Total RNA-seq  769-P Day 0 Rep1 and Rep2 were sequenced 75bp paired-end. Total RNA-seq 786-O EV/KO Rep2 and other kidney cancer cell line total RNA-seq libraries were sequenced 50 bp paired-end. All ChIP-seq libraries were sequenced 50 bp paired-end.

value: 300nM DAC


title: WT_3m_ATAC_rep1


title: K562_pool2, GWLP expression, DNA


title: K562_pool6, GWLP mapping, rep2

description:
Stable cell line containing 'landing pads' at multiple genomic locations
P6_combined_unique.bed


title: K562_pool1, GWLP expression, RNA


title: PLD_3m_ATAC_rep2


title: K562_pool5, GWLP mapping, rep2

description:
Stable cell line containing 'landing pads' at multiple genomic locations
P5_combined_unique.bed


title: PLD_3m_ATAC_rep1


title: piC C

city: SALT LAKE CITY

first: Anna

middle: E

last: Beaudin

state: Utah

institute: University of Utah

description: flkswitch x WT fetus

data_processing:
Raw UMI-based data files were mapped against the mm10 reference genome using the scRNAseq tool from the bioinformatics pipeline snakePipes, with the 10xV3 mode (Bhardwaj et al., 2019).
STARsolo was used to i) map, ii) UMI-deduplicate and iii) count reads, to create the BAM files and a Seurat object with the gene counts (Dobin et al., 2013). The quality of this data was checked by running Deeptools QC (Ramírez et al., 2016).
After the preprocessing of data, R package Seurat was used to perform the single-cell RNA-seq analysis (Satija et al., 2015). The Seurat object was imported, and a cell filtering was performed, selecting the cells which i) contained more than 75,000 counts and ii) those that expressed above 2,000 genes to avoid empty droplets. Moreover, low-quality and dying cells with a percentage of mitochondrial mRNA higher than 20% were filtered out.
A log-normalization and scaling of the data was applied prior to the linear dimension reduction with the Principal Component Analysis (PCA).
After applying the JackStraw and Elbow plot procedures from Seurat, a clustering analysis was performed selecting the first 20 PCs, resulting in cell communities that were visualized with the Uniform Manifold Approximation and Projection (UMAP) technique (McInnes et al., 2018). From those, three clusters were filtered out based on the doublets scoring calculated with the doubletCells function from scran package (Lun et al., 2016), the enrichment of LSK and LS-K signatures described previously (Klimmeck et al., 2014) applying the AddModuleScore function and the presence of differentiated cells markers, detected with the FindAllMarkers function (min.pct = 0, logfc.threshold = 0.15)
Genome_build: mm10
Supplementary_files_format_and_content: Highly expressed genes in each cluster
Supplementary_files_format_and_content: Cell numbers

source_name: Hematopoietic Stem and Progenitor Cells

extract_protocol:
Cells were sorted and frozen in FBS and 15% DMSO. Cells were thawed and preped for 10X Chromium instrument V3. Loaded chip assuming concentration above with targeted recovery of 10,000. cells. 11 cycles cDNA amplification followed by Qubut and QC via bioanalyzer.
12 Cycles of library amplification followed by 1x bead clean-up on final libraries then resuspended in 80 uL. Quality control was performed via bioanalyzer.

tag: age

value: Fetal Liver

tag: agent

value: pIC


title: TotalRNAseq_769P_Day5_Rep2


title: TotalRNAseq_769P_Day0_Rep2


title: K562_pool5, GWLP mapping, rep1

value: chronic myelogenous leukemia


title: K562_pool3, GWLP mapping, rep1

description:
Stable cell line containing 'landing pads' at multiple genomic locations
P3_combined_unique.bed


title: pIC A

description: flkswitch x WT fetus


title: TotalRNAseq_769P_Day15_Rep2


title: K562_pool4, GWLP mapping, rep1

description:
Stable cell line containing 'landing pads' at multiple genomic locations
P4_combined_unique.bed


title: TotalRNAseq_769P_Day5_Rep1


title: TotalRNAseq_769P_Day25_Rep1


title: pIC B

description: flkswitch x WT fetus

value: piC


title: TotalRNAseq_769P_Day15_Rep1


title: TotalRNAseq_769P_Day0_Rep1


title: K562_pool1, GWLP mapping, mock transfected, rep6

description:
Stable cell line containing 'landing pads' at multiple genomic locations
P1_combined_unique.bed


title: K562_pool1, GWLP mapping, mock transfected, rep5


title: K562_pool4, GWLP mapping, rep2


title: Saline C

description: flkswitch x WT fetus

value: Saline


title: K562_pool2, GWLP mapping, rep1


title: K562_pool3, GWLP mapping, rep2


title: Saline A

description: flkswitch x WT fetus


title: K562_pool1, GWLP mapping, mock transfected, rep4


title: K562_pool6, GWLP mapping, rep1


title: K562_pool2, GWLP mapping, rep2


title: K562_pool1, GWLP mapping, mock transfected, rep2


title: K562_pool1, GWLP expression, DNA


title: K562_pool1, GWLP mapping, mock transfected, rep3


title: K562_pool1, GWLP mapping, mock transfected, rep1


title: TotalRNAseq_A704_Day15_Rep2


title: TotalRNAseq_A704_Day25_Rep2


title: piC 2

description: flkswitch x WT fetus

data_processing:
The mouse GRCm38 FASTA and GTF files were downloaded from Ensembl release 98.
The reference database was created using STAR version 2.7.2c with splice junctions optimized for 150 base pair reads.
Optical duplicates removed from NovaSeq runs via Clumpify v38.34
Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3
Non-coding features, histones, and ribosomal RNAs were removed and differentially expressed genes were identified using a 5% false discovery rate with DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: FeatureCounts output files combined into a single tab-delimited matrix

source_name: Hematopoietic Stem and Cells

extract_protocol:
Sorted cells were processed cDNA was generated using the RNeasy minikit
RNA libraries were generated with 20-25M 150PE reads using (polyA tail selection) for NovaSeq S4.


title: K562_pool1, GWLP mapping, rep2


title: TotalRNAseq_A704_Day5_Rep2


title: Saline B

description: flkswitch x WT fetus


title: K562_pool1, GWLP mapping, rep1


title: pIC 1

description: flkswitch x WT fetus


title: K562_eco2_pool7, A2, rBC DNA counts

data_processing:
Control barcode files: We first filtered for reads that contained barcodes in the correct sequence context, then tabulated the counts of each barcode.
Recombined barcode files: We first filtered for reads that contained barcodes in the correct sequence context, and the number of rBC/gBC pairs were tabulated. Only barcode pairs with >5 reads were kept for the analysis.
Assembly: hg38
Supplementary files format and content: Control barcode files: barcodes and corresponding read count for each barcode.
Supplementary files format and content: Recombined barcode files: barcodes and corresponding read count for each barcode pair.
Library strategy: barcode sequencing

extract_protocol:
Genomic DNA and RNA was extracted using TRIzol according to manufacturer's instructions.
Genomic DNA: Barcodes were amplified from DNA using custom primers. Sequencing adapters were added to the amplified barcodes for Illumina sequencing.

treatment_protocol: The no insulator and A2 constructs contain libraries of diverse random barcodes. For the samples that were recombined with either the no insulator or A2 constructs, cells containing genome-wide landing pads were transfected with BxbI, phiC31 and the respective construct library to allow recombination of the constructs into the landing pads. The cells were allowed to grow for a week before genomic DNA extraction.

value: Recombined with A2 construct carrying random barcodes


title: K562_eco2_pool8, A2, rBC DNA counts


title: K562_eco2_pool8, no insulator, rBC DNA counts

value: Recombined with no insulator construct carrying random barcodes


title: K562_eco2_pool7, no insulator, rBC DNA counts


title: Saline 1

description: flkswitch x WT fetus


title: TotalRNAseq_A704_Day25_Rep1


title: TotalRNAseq_A704_Day15_Rep1


title: K562_eco2_pool7, DNA counts


title: Input_ChIP_786O_KO_Combined_Rep1

growth_protocol: 786-O (ATCC Cat# CRL-1932, RRID:CVCL_1051) was cultured in RPMI 1640 medium (Corning). A-498 (ATCC Cat# HTB-44, RRID:CVCL_1056), A-704 (ATCC Cat# HTB-45, RRID:CVCL_1065) were cultured in EMEM medium (ATCC), and ACHN (ATCC Cat# CRL-1611, RRID:CVCL_1067). Caki-1 (ATCC Cat# HTB-46, RRID:CVCL_0234) and Caki-2(ATCC Cat# HTB-47, RRID:CVCL_0235) were cultured in McCoy's 5A Medium (Millipore Sigma). All media were supplemented with 10% heat-inactivated FBS (Corning) and 1% Penicillin-Streptomycin (Genesee Scientific).

extract_protocol:
Total RNA was extracted using RNeasy kit (Qiagen) followed by on-column DNase I digestion according to the manufacturer’s protocol. Genomic DNAs were purified using phenol–chloroform extraction and ethanol precipitation.
Sequencing libraries were prepared using the KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche, Cat# 08098140702). ChIP assays were performed following the native ChIP protocol. ChIP assays were performed following the native ChIP protocol (Ohtani et al., 2018) with minor modifications.
Total RNA-seq 786-O EV/KO Rep1 were sequenced 75 bp single end.  Total RNA-seq 786-O EV/KO Rep2 and other kidney cancer cell line total RNA-seq libraries were sequenced 50 bp paired-end. All ChIP-seq libraries were sequenced 50 bp paired-end.


title: Input_ChIP_786O_KO_Combined_Rep2


title: TotalRNAseq_A704_Day5_Rep1


title: Input_ChIP_786O_EV_Combined_Rep2


title: GFP_High

organism: Escherichia coli

value: BacDrop

value: E. coli expressing a GFP reporter driven by the promoter of rpsM

value: untreated


title: GFP_Low

value: E. coli expressing a GFP reporter driven by the promoter of spy


title: K562_eco2_pool8, DNA counts


title: Input_ChIP_786O_EV_Combined_Rep1

value: WT


title: H3K36me3_ChIP_786O_KO_Day23_Rep2

value: H3K36me3 (Cell Signaling Technology Cat# 4909, RRID:AB_1950412)


title: GFP_Mid

value: E. coli expressing a GFP reporter driven by the promoter of rpoH


title: H3K36me3_ChIP_786O_KO_Day5_Rep2


title: TotalRNAseq_Caki2_Day15_Rep2


title: TotalRNAseq_Caki2_Day25_Rep2


title: Saline 2

description: flkswitch x WT fetus


title: PAH-PASMC_Si-HNRNPA2B1_03

city: los angeles

first: Gregoire

last: Ruffenach

state: california

address: 650 charles E young street BH 550

department: Anesthesiology

institute: UCLA

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic
Trimmed sequence reads were mapped to GrCM38/mm10 using hisat 2
Read count extraction and normalization were performed using Stringtie
Assembly: GRCh38.84
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: primary cultured

growth_protocol: PAH-PASMC were grown in Medium 231 with Smooth muscle growth supplement (thermofisher)

extract_protocol:
RNA was harvested using trizol followed by column RNA purification
Libraries for RNA-seq were prepared by the Technology center for genomics & bioinformatics at UCLA

treatment_protocol:
Cells were transfected with lipofectamine for 48h
1uM dexamethasone (Sigma), and 0.5mM isobutylmethylxanthine (Sigma) in the presence of 10% FBS until day 2. Cells were then fed with DMEM supplemented with 10% FBS and 10ug/ml insulin for 2 days, after which they were fed every other day with DMEM containing 10% FBS

value: primary cultured

value: pulmonary arterial smooth muscle cells

tag: time

value: 2 days treatment


title: TotalRNAseq_A704_Day0_Rep1


title: Ec_BacDrop

description: Ec

source_name: E. coli strain from NEB


title: H3K36me3_ChIP_786O_KO_Day0_Rep2


title: Aggregates of  FACS d4.5 RA+ mCherry (d30)

city: Munich

first: Gianluca

last: Santamaria

state: Germany

address: Ismaninger Strasse 22

department: Department of Medicine I

institute: Klinikum rechts der Isar – Technical University Munich

data_processing:
Cell Ranger workflow using the DropletUtils was used to generate FASTQ and bam files
Genome_build: hg19
Supplementary_files_format_and_content: Cell Ranger output

source_name: Cardiomyocytes & non-myocytic cardiac cell types

growth_protocol: Human embryonic stem cells were differentiated as described in methods of Zawada et al., (2021) using a stepwise growth-factor based protocol  to direct hESCs towards CMs through defined developmental stages of primitive-like cells and early cardiovascular progenitor cells.

extract_protocol:
For scRNASeq at d1.5, cells were washed two times with PBS, dissociated with Accutase (3-5 min, 37°C), centrifuged at 1200 rpm for 5 min, resuspended in 0.04% BSA in PBS, filtered through a 40 μm filter and counted. For scRNASeq at d4.5 of differentiation, cells were subjected to sorting procedure as described in methods of Zawada et al. (2021). Cells were sorted based on mCherry and eGFP expression and collected into 10% FCS in PBS. Then cells were centrifuged, washed in 0.04% BSA in PBS, centrifuged again, filtered through a 40 μm filter and resuspended in 0.04% BSA in PBS for counting. For scRNA-Seq at d30 of differentiation of aggregates, aggregates were dissociated with papain as described in methods of Zawada et al. (2021), filtered through 40 μm filter, centrifuged at 1000 rpm for 3 min and resuspended in 0.04% BSA in PBS for counting. After counting, 10 000 cells for each sample were processed using Chromium Single Cell 3’ Library & Gel Bead Kit v3.1 (1000075, 10x Genomics) Chromium Single Cell B Chip Kit (1000073, 10x Genomics) and Chromium i7 Multiplex Kit (220103, 10x Genomics) to generate Gel Bead-In-EMulsions (GEMs) and single cell sequencing libraries.
10 000 cells per sample were processed using Chromium Single Cell 3’ Library & Gel Bead Kit v3.1 (1000075, 10x Genomics) Chromium Single Cell B Chip Kit (1000073, 10x Genomics) and Chromium i7 Multiplex Kit (220103, 10x Genomics) to generate Gel Bead-In-EMulsions (GEMs) and single cell sequencing libraries. Libraries were pooled and sequenced using the NextSeq 500/500 (Ilumina; High Output v2 kit 75 cycles v2.5 flow cell) with 28 cycles in read1 for the 10x barcodes and UMIs in and 8 cycles i7 index read and 58 cycles for cDNA in read2 with a read depth of at least 20 000 pair reads per cell.

treatment_protocol: Two versions of protocol were applied: without RA (RA-) between 40h (d1.5) and d5.5 or with 0.5 µM RA for 4 days between 40h (d1.5) and d5.5 (RA+)

value: in vitro differentiated human embryonic stem cells (hESC)

tag: pluripotent stem cell line

value: a double reporter hESC-03 line expressing eGFP and mCherry under the control of the endogenous NKX2-5 and TBX5 locus respectively

value: version of protocol:0.5 uM RA, 4 days


title: H3K36me3_ChIP_786O_EV_Day23_Rep2

value: 300nM DAC


title: TotalRNAseq_Caki2_Day5_Rep2


title: TotalRNAseq_A704_Day0_Rep2


title: PAH-PASMC_Si-HNRNPA2B1_02


title: Aggregates of  FACS d4.5 RA+ eGFP+ (d30)


title: Aggregates of  FACS d4.5 RA+ mCherry+ eGFP+ (d30)


title: TotalRNAseq_Caki2_Day0_Rep2


title: Cardiovascular progenitor cells (FACS d4.5 RA- eGFP+) (d30)

value: version of protocol:RA-


title: Primitive streak-like cells (d1.5)

source_name: Primitive-streak-like cells

value: before treatment was applied


title: PAH-PASMC_Si-Scrm_03

value: Si-Scrm


title: Cardiovascular progenitor cells (FACS d4.5 RA+ mCherry+ eGFP+)

source_name: Cardiovascular progenitor cells


title: PAH-PASMC_Si-Scrm_02


title: Cardiovascular progenitor cells (FACS d4.5 RA- eGFP+)


title: Cardiovascular progenitor cells (FACS d4.5 RA+ mCherry+)


title: Cardiovascular progenitor cells (FACS d4.5 RA+ eGFP+)


title: TotalRNAseq_Caki2_Day5_Rep1


title: PAH-PASMC_Si-Scrm_01


title: TotalRNAseq_Caki2_Day15_Rep1


title: Plasma_F2009198

city: Luxembourg

first: Yvan

last: Devaux

address: 120 route d'Arlon

country: Luxembourg

institute: LIH

data_processing:
Data reconstruction of FASTQ files and quantification againts the WTA-miRNA panel were obtained by the HTG Parser software.
Samples with high number of reads in negative control (over 150 CPM) were flagged as QC failure and removed from the analysis.
Differential expression analysis was performed using Limma R pacakge with quantile normalisation.
Genome_build: miRbase v20
Supplementary_files_format_and_content: csv files including CPM values for each sample

source_name: Plasma

growth_protocol: EDTA

extract_protocol:
HTG EdgeSeq miRNA whole transcriptome targeted sequencing kit
HTG EdgeSeq miRNA whole transcriptome targeted sequencing kit Barcoding was performed using Hemo KlenTaq (MO332S, NEB) enzyme

tag: patients

tag: timepoint

value: Last bleeding


title: Plasma_F2009196


title: Plasma_F2009192


title: Plasma_F2009191


title: Plasma_F2009194


title: TotalRNAseq_Caki2_Day0_Rep1

source_name: kidney cancer cell line


title: Plasma_F2009189


title: TotalRNAseq_786O_KO_Day15_Rep2


title: TotalRNAseq_Caki2_Day25_Rep1


title: Plasma_F2009188


title: Plasma_F2009187


title: TotalRNAseq_786O_KO_Day5_Rep2


title: MG1655_CmR_sum

city: Moscow

first: Anastasiia

last: Okhtienko

address: Akademika Kurchatova square 2

country: Russia

institute: Institute of Molecular Genetics, Russian Academy of Sciences

data_processing:
All libraries were quality checked before further processing using FastQC (v0.11.9).
Trimmomatik (v0.39) was used to remove adapters, eliminate reads shorter than 30
Reads were aligned onto the reference genome E.coli (MG1655 Refseq: NC_000913.3 with insertion of cat gene) and plasmids (pBAD_CbAgo_lacI_full, pDE351) via bowtie (v1.3.1) allowing zero mismatches and unique alignment
Alligned .sam files were converted to binary .bam, sorted using samtools (v. 1.15)
Reads from individual clones were aligned on reference genome only. The E. coli  genome was divided into intervals of length 200bp using custom Python script. bedtools (v2.30.0) was used to intersect the resulted bed file with the bam file.  Reads from “+” and “-” strands were selected with samtools view –F/ -f 16. For them, the coverage was calculated separately according to the method described above.
Assembly: NC_000913.3 / CP009273.1 with manually added cat gene and its promoter(366428-367335)
Supplementary files format and content: tsv files include count values for 200bp genome intervals (both strands and + / - separately, aligned on genome )
Library strategy: DNA-seq (gDNA)

growth_protocol: Cells for gDNA were grown overnight at 37 °C in LB containing 1% glucose and chloramphenicol 25 mkg/ml.

extract_protocol:
Genomic DNA was purified using Sigma kit NA2120 from total bacterial culture after 6 passage at 43 °C and from 2 separate single clones spectinomycin sensitive chloramphenicol resistant from this bacterial culture.
500 ng purified gDNA were treated with NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina E7805S and barcoded using NEBNext Multiplex Oligos for Illumina® (Dual Index Primers Set 1) E7600. gDNA libraries were sequenced using the HiSeq2500 platform (Illumina) in the rapid run mode (50-nucleotide single-end reads).

value: F-, lambda-, rph-1

tag: plasmid

tag: second plasmid


title: TotalRNAseq_786O_KO_Day0_Rep2


title: MG1655_CmR_SpS_clone1

tag: strain


title: MG1655_CmR_SpS_clone2

tag: genotype


title: Plasma_F2009185


title: PAH-PASMC_Si-HNRNPA2B1_01


title: Plasma_F2009195


title: Plasma_F2009184


title: TotalRNAseq_786O_KO_Day15_Rep1


title: TotalRNAseq_786O_KO_Day23_Rep1


title: SP+_8_C

city: New York

first: Sofie

last: Delbare

address: 435 East 30th Street

institute: NYU Langone

data_processing:
Read trimming: Sequencing adaptors were removed using Trimmomatic (version 0.39), which was also used to trim low quality bases at the 5’ end of reads (using parameters TRAILING:20 and SLIDINGWINDOW:5:20). Reads with a minimum length of 30 bases were retained.
Alignment: STAR (version 2.7.5a)
Read counting on gene-level: HTSeq (version 0.11.2); Read counting on exon level: scripts provided as part of R package DEXSeq (Anders et al. 2012).
Each sample was sequenced five times. We used PCA to verify the absence of a sequencing lane effect, after which we merged all five fastq files of each sample and repeated alignment and read counting based on the merged fastq files.
Gene-level filtering: Raw counts were filtered to keep only genes with at least three counts per million in at least three samples and genes encoded in mitochondrial DNA were removed. We removed three samples that were outliers in PCA (C_V_6, C_SP+_2 and C_SP+_3). Exon-level filtering: As a first filtering step, we only kept exons from genes that were analyzed in the gene-level analysis and removed exons that could not be unambiguously assigned to only one gene. For the second filtering step, after normalization (see below), we removed 20% of exons with the lowest normalized counts. Finally, we removed exons that are shared across all transcript isoforms of their gene, or that are present in a gene that has only one annotated transcript isoform. As for the gene-level analysis, we removed three outlier samples (C_V_6, C_SP+_2 and C_SP+_3).
Gene-level normalization: counts per million were calculated in edgeR, using TMM normalization. Exon-level normalization: exons were normalized as recommended in Soneson et al. 2016.
Batch effect correction: to correct for high immune gene expression in a random subset of samples, Combat-seq was applied to both gene and exon counts.
Assembly: dm6 version r6.24 for gene-level alignment; BDGP6.32 for exon-level alignment
Supplementary files format and content: Matrix table with raw gene-level and exon-level read counts. Both gene and exon read counts were corrected for batch effects using ComBat-seq.

organism: Drosophila melanogaster

source_name: head

growth_protocol: Flies were maintained on yeast/glucose food at 25⁰C on a 12h light/dark cycle (lights on at 8 AM)

extract_protocol:
Flash frozen flies were vortexed to dislodge heads. Heads were collected in Trizol. RNA was extracted and DNA was removed using the Directzol RNA microprep kit (Zymo).
Poly(A)-selected, stranded libraries were made using the NEBnext Ultra II Directional RNA library prep kit and the Poly(A) mRNA magnetic isolation module (New England Biolabs, MA).

treatment_protocol: Females were mated to a wildtype of Sex Peptide null male within a 3 hour window in the morning (8 AM - 11 AM) and were frozen at their designated time point after mating. Virgin females were frozen in parallel.

value: head

value: mated to wildtype male

value: Canton-S


title: TotalRNAseq_786O_KO_Day23_Rep2


title: Plasma_F2009179

value: First bleeding


title: SP+_12_C


title: Plasma_F2009183


title: Plasma_F2009180


title: Plasma_F2009177


title: SP+_6_C


title: Plasma_F2009176


title: Plasma_F2009175


title: SP+_4_C


title: SP+_5_C


title: SP+_24_C


title: Plasma_F2009171


title: SP+_3_C


title: Plasma_F2009173


title: TotalRNAseq_786O_EV_Day15_Rep2

value: WT


title: TotalRNAseq_786O_EV_Day23_Rep2


title: TotalRNAseq_786O_KO_Day0_Rep1


title: Plasma_F2009178


title: Plasma_F2009170


title: Plasma_F2009182


title: SP+_2_C


title: TotalRNAseq_786O_KO_Day5_Rep1


title: Plasma_F2009168


title: SP+_1_C


title: Plasma_F2009166


title: TotalRNAseq_786O_EV_Day0_Rep2


title: Plasma_F2009169


title: TotalRNAseq_786O_EV_Day5_Rep2


title: SP+_0.5_C


title: TotalRNAseq_786O_EV_Day15_Rep1


title: SP+_24_B


title: Plasma_F2009174


title: Plasma_F2009172


title: Plasma_F2009163


title: Plasma_F2009165


title: Plasma_F2009161


title: SP+_12_B


title: Plasma_F2009162


title: SP+_8_B


title: Plasma_F2009158


title: Plasma_F2009159


title: Plasma_F2009157


title: TotalRNAseq_786O_EV_Day23_Rep1


title: Plasma_F2009156


title: Plasma_F2009160


title: TotalRNAseq_786O_EV_Day5_Rep1


title: SP+_6_B


title: TotalRNAseq_786O_EV_Day0_Rep1


title: Plasma_F2009164


title: SP+_5_B


title: TotalRNAseq_A498_Day15_Rep2


title: TotalRNAseq_A498_Day5_Rep2


title: Plasma_F2009155


title: Plasma_F2009154


title: SP+_4_B


title: SP+_3_B


title: TotalRNAseq_A498_Day15_Rep1


title: Plasma_F2009152


title: Plasma_F2009150


title: Plasma_F2009153


title: TotalRNAseq_A498_Day5_Rep1


title: Plasma_F2009149


title: SP+_2_B


title: Plasma_F2009151