title: NeuronKCL_RNAseq_female_rep5

city: Old Westbury

first: Ying-Tao

last: Zhao

state: NY

address: Riland building, Room 024 Northern Boulevard, P.O. Box 8000

department: Biomedical Sciences

institute: New York Institute of Technology

data_processing:
FASTQ files were aligned to mouse mm10 genome using STAR 2.7.7a with the following parameters: ‘–runThreadN 40 –outFilterMultimapNmax 1 –outFilterMismatchNmax 3 –outFilterScoreMinOverLread 0.25 –outFilterMatchNminOverLread 0.25’. A Perl script was used to calculate the total number of mapped reads and the number of reads that aligned to the exons of each gene. The table of raw read counts was normalized, and the top 1000 variable genes were selected to perform the principal component analysis by DESeq2 and to perform the distance between variables by pheatmap. The edgeR and the Genewise Negative Binomial Generalized Linear Models with Quasi-likelihood Tests (glmQLFTest) were used to compare the gene expression levels between the groups. The false discovery rate (FDR) < 0.05 was used as the cutoff to identify differentially expressed genes (DEGs).
Assembly: mm10
Supplementary files format and content: bigwig format files including the tracks for the data
Supplementary files format and content: tab-delimited text files include raw read count values for each sample

source_name: DRG neurons, DIV3, female

growth_protocol: DRG neurons were prepared as previously described [35]. Briefly, thoracic DRG were harvested from 3-week-old mice and dissociated in collagenase (5mg/ml) and dispase (1mg/ml) at 37°C for 70 minutes, and then cultured in 6-well plates coated with Poly-D-lysine (100μg/ml) and laminin (10μg/ml). DRG neurons were plated at a density of 5x104 cells/well in Neurobasal media containing B27 (200mM), NGF (50 ng/ml), GDNF (2ng/ml) and AraC (10μM).

extract_protocol:
Cells were lysed and total RNAs were harvested for RNA sequencing. Supernatants were collected for secretome analysis by LC-MS/MS.
RNA samples were quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) and RNA integrity was checked with 4200 TapeStation (Agilent Technologies, Palo Alto, CA, USA). Samples were initially treated with TURBO DNase (Thermo Fisher Scientific, Waltham, MA, USA) to remove DNA contaminants. rRNA depletion sequencing library was prepared by using QIAGEN FastSelect rRNA HMR Kit (Qiagen, Hilden, Germany). RNA sequencing library preparation uses NEBNext Ultra II RNA Library Preparation Kit for Illumina by following the manufacturer’s recommendations (NEB, Ipswich, MA, USA). Briefly, enriched RNAs are fragmented for 15 minutes at 94 °C. First strand and second strand cDNA are subsequently synthesized. cDNA fragments are end-repaired and adenylated at 3’ends, and universal adapters are ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR.

treatment_protocol: After 3 days of axonal outgrowth, DRG neurons were incubated in HEPES solution containing 75mM KCL for 60 minutes.

value: spinal cord

value: Primary DRG neurons

tag: gender

value: female

value: KCL


title: NeuronKCL_RNAseq_female_rep2

status: Public on Sep 20 2023

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell type

tag: treatment

tag: strain


title: NeuronKCL_RNAseq_female_rep4


title: NeuronKCL_RNAseq_male_rep3

source_name: DRG neurons, DIV3, male

value: male


title: NeuronKCL_RNAseq_male_rep5


title: NeuronKCL_RNAseq_male_rep4


title: NeuronKCL_RNAseq_female_rep1


title: Fresh1 hour (10xx21YW_X_C03_S12)

city: Pitscataway

first: Shuo

last: Xiao

state: NJ

address: 170 Frelinghuysen Rd, Room 404

department: Pharmacology & Toxicology

institute: Rutgers University

data_processing:
Sequenced reads were uploaded into Partek Flow software for data analyses. We first filtered out potential rDNA and mtDNA contaminants using Bowtie 2. Filtered reads were aligned to the whole mouse genome assembly-mm10 using the HISAT 2 aligner. Raw read counts were obtained by quantifying aligned reads to Ensembl Transcripts release 99 using the Partek EM algorithm. Raw read counts were then normalized based on the Transcripts Per Million (TPM) method, and differential expression analysis was performed by using the DESeq2(R).
Assembly: Ensembl Transcripts release 99
Supplementary files format and content: Raw_counts.txt contains the raw read counts that were obtained by quantifying aligned reads to Ensembl Transcripts release 99 using the Partek EM algorithm.
Supplementary files format and content: Log2(TPM+1).txt contains the log2 transformed normalized counts  based on the Transcripts Per Million (TPM) method

source_name: Ovarian follicle

growth_protocol: Vitrified and fresh follicles with intact morphology were encapsulated in 0.5% (w/v) alginate and cultured in 96-well plates, with each well containing one bead and 100 μl growth media. The growth media consisted of 50% αMEM Glutamax (Thermo Fisher Scientific) and 50% F-12 Glutamax (Thermo Fisher Scientific) supplemented with 3 mg/ml bovine serum albumin (BSA; Sigma-Aldrich), 10 mIU/ml recombinant follicle stimulating hormone (rFSH; gifted by Organon, Jersey City, NJ, USA), 1 mg/ml bovine fetuin (Sigma-Aldrich), and 5 μg/ml insulin-transferrin-selenium (ITS, Sigma-Aldrich). Follicles were cultured for 8 days at 37 °C in a humidified environment of 5% CO2 .in air.

extract_protocol:
RNA was extracted using the RNEasy Plus Micro Kit (Qiagen) according to the manufacturers recommendations.
Smart-Seq2 cDNA synthesis was performed on isolated follicle RNA with Maxima H Minus reverse transcriptase (ThermoFisher). Whole transcriptome amplified (WTA) product was purified with AMPure XP beads (Beckman Coulter), quantified with Quanit-iT PicoGreen dsDNA Assay (ThermoFisher), normalized and used for preparing paired-end sequencing libraries with Nextera XT (Illumina, #FC-131) according to the manufacturer’s instructions.
Illumina NextSeq500/550

treatment_protocol: On day 8 of eIVFG, mature follicles with diameter at 300-350 μm were removed from alginate beads by incubation in L15 media containing 1% FBS and 10 IU/ml alginate lyase from Flavobacterium multivorum (Sigma-Aldrich) at 37 °C for 20 minutes. Follicles were then transferred to the maturation media and ovulation was induced by incubation in the maturation media containing 50% αMEM Glutamax and 50% F-12 Glutamax supplemented with 10%FBS, 1.5 IU/ml hCG (Sigma-Aldrich], 10 ng/ml epidermal growth factor (EGF; BD Biosciences), and 10 mIU/ml rFSH. At 0, 1, 4, and 8 hours post-hCG treatment,  follicles were collected and washed in 1X phosphate buffered saline (PBS; Invitrogen) three times .

value: Ovarian follicle

value: Fresh

tag: genotype

value: WT

value: hCG

tag: time

value: 1 hour


title: Fresh8 hours (10xx21YW_X_B08_S8)

value: 8 hours


title: Fresh4 hours (10xx21YW_X_A06_S6)

value: 4 hours


title: NeuronKCL_RNAseq_male_rep1


title: Fresh4 hours (10xx21YW_X_A03_S3)


title: heart, CBD3, biological rep3

city: London

first: Daniel

middle: B

last: Hardy

state: Ontario

address: 1151 Richmond St

department: Physiology & Pharmacology

country: Canada

institute: Western University

description:
C3_3.1
C3_3.1

data_processing:
All reads were aligned and annotated with the latest ENSEMBL rat genome release available (mRatBN7.2) using the R package Rsubread with default settings
Raw counts were generated using the Rsubread sub package featureCounts
To correct for batch effects, the R package ComBat_seq was used
Normalization and differential expression analysis were done using the edgeR R package
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Rattus norvegicus

source_name: heart

extract_protocol:
Collected and flash frozen hearts from 3-week-old male offspring were sent to Genome Quebec (Montreal, Quebec, Canada) for total Trizol-phenol RNA extraction. Quality of RNA was assessed using the RNA integrity number (RIN), with all samples having a RIN score ≥ 7.0.
Libraries were generated from RNA as follows: mRNA enrichment was performed using Illumina Stranded mRNA Prep (Illumina); adapters and PCR primers were purchased from IDT; libraries were quantified using the KAPA Library Quantification Kits - Complete kit (Universal) (Kapa Biosystems).

value: heart

value: CBD 3 mg/kg


title: heart, CBD3, biological rep6

description:
C3_3.2
C3_3.2


title: heart, CBD30, biological rep1

description:
C30_1.1
C30_1.1

value: CBD 30 mg/kg


title: heart, CBD30, biological rep4

description:
C30_3.2
C30_3.2


title: heart, vehicle, biological rep7

description:
V_3.2
V_3.2

value: Vehicle


title: heart, CBD30, biological rep3

description:
C30_1.2
C30_1.2


title: heart, CBD3, biological rep5

description:
C3_2.2
C3_2.2


title: heart, CBD3, biological rep4

description:
C3_1.2
C3_1.2


title: heart, CBD30, biological rep5

description:
C30_4.2
C30_4.2


title: heart, CBD3, biological rep1

description:
C3_1.1
C3_1.1


title: heart, CBD30, biological rep2

description:
C30_2.1
C30_2.1


title: heart, CBD3, biological rep2

description:
C3_2.1
C3_2.1


title: NeuronKCL_RNAseq_male_rep2


title: LDP124

city: Tampa

first: Alexander

last: Starushchenko

state: FL

address: 560 Channelside Dr

department: Molecular Pharmacology & Physiology

institute: University of South Florida, College of medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website 2 directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: reference genome was built using Hisat2 v2.0.5 a
Supplementary files format and content: excel file with FPKM

extract_protocol:
RNA was extracted using the Trizol reagent according to the manufacturer's protocol
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification). The library was checked with Qubit and real-time PCR for quantification and a bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: Kidney

tag: time point


title: LDP84


title: LDP121

value: Homo


title: LDP86


title: heart, vehicle, biological rep6

description:
V_2.2
V_2.2


title: NeuronKCL_RNAseq_female_rep3

value: spinal cord

value: Primary DRG neurons


title: heart, vehicle, biological rep5

description:
V_1.2
V_1.2


title: heart, vehicle, biological rep4

description:
V_4.1
V_2.1


title: LDP87

value: Het


title: LDP116

value: male


title: LDP78


title: heart, vehicle, biological rep2

description:
V_2.1
V_4.1


title: LDP122


title: heart, vehicle, biological rep3

description:
V_3.1
V_1.1


title: heart, vehicle, biological rep1

description:
V_1.1
V_3.1


title: LDP123


title: LDP120


title: LDP58


title: LDP119


title: LDP109


title: LDP56


title: LDP57


title: LDP100


title: LDP62


title: LDP64


title: LDP67


title: LDP61


title: LD122


title: LDP55


title: LDP131


title: LDP138


title: LDP60


title: LDP21


title: LDP63


title: LDP22


title: LDP48


title: LDP65


title: LDP161


title: LDP68


title: LDP149


title: LDP54


title: LDP130


title: LDP148


title: LDP23


title: LDP108


title: LDP66


title: LDP110


title: LDP104


title: LDP98


title: LDP42


title: WKY_3

city: Fuzhou

first: Jun

last: Peng

state: Fujian

address: 1 Qiuyang Road, Minhou Shangjie

department: Academy of Integrative Medicine

country: China

institute: Fujian University of Traditional Chinese Medicine

description: WKY rat with 10-week double distilled water treatment

data_processing:
Data were filtered using the following specifications fastq software，The filtering standards from raw data to clean reads are:：  Check the sample for contamination and, if there is pollution, remove it  If the reads contains a joint sequence, the joint sequence is cut off first  a base having an average base mass of less than 15 on both ends of the readth window is cut with four base lengths as a sliding window;  Remove the number of threads with a high N content. If the N content in a read is more than 5%, the whole read is removed, and the read pair with high low-quality base content is removed. If the low-quality base in one read (the mass value is not higher than the base of 20) exceeds 30%, the whole pair of the reads is removed;  if the truncated read length is less than 50 bp, the entire read is removed  Remove unmatched reads  Q30，Q20 explanation：  Q30 indicates that the sequencing error rate of the base is 0.1%.  Q20 indicates that the sequencing error rate of the base is 1%.
Using String Tie for readcount and FPKM calculation.
Differential expression analyses were performed using the limma package.
Assembly: RGSC6.0/RN6 (UCSC)
Supplementary files format and content: tab_delimited text files include FPKM values for each Sample

source_name: kidney

extract_protocol:
The renal tissues were dissected and  stored in RNA later.Total RNA was extracted with Trizol (Tiangen, Beijing, China). RNA integrity was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and RNA concentration was measured by Qubit RNA Assay Kit in a Qubit Fluorometer (Invitrogen, CA, USA).
A total amount of 1 μg RNA per sample was used. In brief, the NEBNext rRNA Depletion Kit was used to remove rRNA from the total RNA. The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, Beijing, China) was used to construct the libraries for sequencing following the manufacturer’s instructions.

value: WKY

value: kidney

value: double distilled water

tag: group


title: SHR_5

description: SHR  with 10-week  double distilled water  treatment

value: SHR


title: Iso_2

description: SHR  with 10-week Iso (5mg/kg/d) treatment

value: Isoliensinine

value: SHR+Iso


title: Iso_6


title: Iso_1


title: WKY_4


title: WKY_2


title: Iso_5


title: SHR_1


title: SHR_3


title: SHR_2


title: SHR_4


title: WKY_1


title: Iso_3


title: SHR_6


title: R145

city: Milan

first: Luca

middle: Vittorio Carlo

last: Valenti

address: via Francesco Sforza 35

department: Transfusion Medicine and Haematology

country: Italy

institute: Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico

data_processing:
After the primary analysis step including reads quality check (FastQC software, Babraham Bioinformatics, Cambridge, UK) and low-quality reads trimming, raw reads were mapped against GRCh37/hg19 reference genome using STAR mapper
Reads count (ENSEMBL human transcript reference assembly version 75) was performed using RSEM package
Counts were normalized using DESeq2 packag
To quantify isoform expression, per transcript reads count and normalization in transcript per million was performed exploiting RSEM package
Assembly: GRCh37/hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes normalized counts for each sample

organism: Homo sapiens

source_name: Liver

extract_protocol:
Total RNA was extracted from liver tissue using miRNeasy mini-kit (Qiagen, Hulsterweg, Germany). RNA quality was assessed through Agilent 2100 Bioanalyzer and samples with RNA integrity numbers greater than or equal to 7 were used for library preparation.
Library preparation were performed by Novogene (UK) Company Limited (Cambridge, United Kingdom)

tag: disease state

value: Obese

value: Liver

tag: pnpla3 rs738409

value: CG

tag: Sex

value: F

tag: age

tag: steatosis grade

tag: nash

value: yes


title: R144

value: CC

value: no


title: R135


title: R146

value: M


title: R134


title: R138


title: R136


title: R137


title: Iso_4


title: WKY_6


title: WKY_5


title: R127


title: R143


title: R126


title: R114


title: R111


title: R113


title: R112


title: R107


title: R101


title: R108


title: R125


title: R110

value: GG


title: R106


title: R103


title: R104


title: R109


title: R99


title: R93


title: R90


title: R98


title: R89


title: R97


title: R96


title: R95


title: R94


title: LDP20

value: Kidney

value: Het


title: R92


title: R86


title: R91


title: R82


title: R80


title: R75


title: R77


title: R88


title: R76


title: R105


title: R87


title: R102


title: R72


title: R84


title: R85


title: R83


title: R78


title: R81


title: R79


title: R74


title: R66


title: R63


title: R71


title: R61


title: R70


title: R68


title: R58


title: R56


title: R69


title: R65


title: R67


title: R57


title: R62


title: R53


title: R60


title: R52


title: R54


title: R55


title: R47


title: R48


title: R73


title: R59


title: R42


title: R50


title: R51


title: R46


title: R39


title: R41


title: R49


title: R64


title: R40


title: R45


title: R43


title: R36


title: R37


title: R33


title: R34


title: R31


title: R32


title: R28


title: R30


title: R44


title: R29


title: R26


title: R25


title: R38


title: R24


title: R35


title: R27


title: R23


title: R21


title: R22


title: R20


title: R16


title: R19


title: B.I.1_2

city: Bethesda

first: Julie

middle: E

last: Niemela

state: MD

address: 10 Center Dr.

department: Dept. of Lab. Medicine

institute: NIH Clinical center

data_processing:
Alignment and mapping analyses were performed by the Takara Cogent NGS Analysis Pipeline v1.5.0 (also known as CogentAP).
Differential gene expression analysis was performed by DESeq2 v1.32.0 [Bioconductor version: Release (3.15)].
Assembly: hg38
Supplementary files format and content: csv-delimited gene matrix of gene counts for each sample (in duplicate), with the genes in the rows and samples in the columns

source_name: Peripheral blood

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using SMARTer Stranded Total RNA-Seq Kit v3 – Pico Input Mammalian Components (Takara San Jose, CA) following manufacturer's protocols.

tag: cell line

value: Peripheral blood

value: EBV-immortalized B-cells

value: WT


title: C.II.1_2

value: AIOLOS E82K heterozygous


title: C.III.1_2


title: R14


title: R15


title: B.II.2_2


title: HC3_2


title: R18


title: R17


title: R13


title: R12


title: HC2_2


title: C.III.1_1


title: HC1_2


title: R10


title: C.II.1_1


title: R11


title: R8


title: B.I.1_1


title: B.II.2_1


title: R7


title: R6


title: R5


title: R4


title: R9


title: HC1_1


title: R3


title: HC3_1


title: MAbID library Pol2Ser5P (H3+H3K27me3+Pol2Ser5P)

city: Utrecht

first: Robin H.

last: van der Weide

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description:
Pol2Ser5P (H3+H3K27me3+Pol2Ser5P)
crosstalk_Pol2_noK36.bw
MAbID library

library_source: genomic

data_processing:
Reads of the raw sequencing output conform to a MAb-ID specific layout of 5'-[3 nt UMI][4 nt SBC part 1][3 nt UMI][4 nt SBC part 2]AGGGCCGC[8 nt ABBC][genomic sequence]-3'. Raw R1-reads were demultiplexed on the expected barcode-sequences using CutAdapt 3.047, with the following custom settings. First, we only allow matches with at least a 29 nt overlap and only keep reads directly starting with the adapter (i.e., an anchored 5’ adapter). The maximum error rate setting of 2 makes it possible to retain reads with 1) two mismatches in the specified adapter-sequence (ignoring the UMI) and 2) a one nucleotide insertion or deletion (indel) at the start of the read due to digestion-ligation or sequencing(-library) errors. Demultiplexed reads are parsed through a custom script to classify reads on correct adapter-structures on a 7-tiered range. Reads in class-1 adhere perfectly to the barcode-expectations, while class-7 reads only contain the AGGGCCGC-sequence at the expected location. Reads typically fall into class 1 (average for figure 1: 95%). This classification allows fine control on which reads should be retained. For this manuscript, we only allow classes 1 and 2 (1 nucleotide indel in the first UMI) to ensure the highest possible quality. Finally, the script creates a fastq.gz-file, adding the UMI-sequences to the read-ID for downstream processing and removing the adapter sequence. Custom pipelines and scripts are available on https://github.com/KindLab.
Demultiplexed and filtered reads were processed in a similar fashion to Rooijers et al.13, with the additional flexibility to set the selected restriction site motif. Briefly, reads are aligned using Bowtie version 2.4.148 in unpaired mode, using default end-to-end parameters. We used the UCSC hg19 reference genome for K562 samples and the NCBI mm10 reference genome for mESC/mEN-samples (both references were downloaded from https://benlangmead.github.io/aws-indexes). Alignments with a mapping quality lower than 10 or not at the expected ligation-site (5’ for the MboI-motif or 5’+ 1 for the MseI-motif) were discarded. For reads originating from mixed sorting single-cell samples (e.g., K562 and mESC), a new hybrid reference genome was built by concatenating hg19 and mm10. Aligned reads to this reference were subsequently mapped to the individual references for further downstream processing by Bowtie using the --very-sensitive -N 1 parameters. Mouse allele-specific reads were assigned by mapping mm10-reads to 129/Sv and Cast/Eij reference genomes. We designated reads to one of the genotypes if it mapped better (i.e., lower edit-distance or higher alignment-score) to one of the references.
Aligned reads are UMI-flattened and counted per restriction site, like in the scDamID-protocol. We allowed up to 1000 UMI’s per site in the bulk analyses and up to 2 UMI’s per site in the single-cell analyses. UMI-counts per sample were binned (5kb, 20kb, and 100kb), loaded into R and stored into singleCellExperiment-containers. Counts in bins overlapping regions of known problematic nature (i.e., blacklist-regions55) or low mappability are set to zero. Normalization of the data was performed by calculating RPKM-values for both samples and control (see eq. 1) and calculating the fold-change over control with a pseudocount of 1.
Assembly: UCSC hg19 and NCBI mm10
Supplementary files format and content: bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of UMI's at a given genomic coordinate.
Supplementary files format and content: MM files are sparse matrices and generated using the Matrix R package. Columns denote single cells, rows denote 100kb genomic bins, and values denote the number of UMI-flattened counts.
Library strategy: MAb-ID

molecule: genomic DNA

growth_protocol: All cell lines were grown in a humidified chamber at 37 °C in 5% CO2, and were routinely tested for mycoplasma. K562 cells were cultured in suspension on 10-cm dishes in Roswell Park Memorial Institute 1640 (RPMI 1640, Gibco, 61870010) supplemented with 10% FBS (Sigma, F7524, lot BCBW6329) and 1% Pen/Strep (Gibco, 15140122). Cells were passaged every 2-3 days. Mouse F1 hybrid Cast/EiJ x 129SvJae embryonic stem cells (mESCs; a gift from the Joost Gribnau laboratory) were cultured on 6-well plates with irradiated primary mouse embryonic fibroblasts (MEFs) in mESC culture media (CM) defined as follows: Glasgow's MEM (G-MEM, Gibco, 11710035) supplemented with 10% FBS, 1% Pen/Strep, 1x GlutaMAX (Gibco, 35050061), 1x MEM non-essential amino acids (Gibco, 11140050), 1 mM sodium pyruvate (Gibco, 11360070), 0.1 mM β-mercaptoethanol (Sigma, M3148) and 1000 U/mL ESGROmLIF (EMD Millipore, ESG1107). mESCs were alternatively cultured in feeder-free conditions on gelatin coated plates (0.1% gelatin, in house) in 60%-BRL medium, defined as a mix of 40% CM medium (as defined) and 60% conditioned CM medium (incubated 1 week on Buffalo Rat Liver cells), supplemented with 10% FBS, 1% Pen/Strep, 1x GlutaMAX, 1x MEM non-essential amino acids, 0.1 mM β-mercaptoethanol and 1000 U/mL ESGROmLIF. Cells were split every 2-3 days and medium was changed every 1-2 days. This mESC cell line does not contain a Y chromosome. To harvest, cells were washed once with Phosphate Buffered Saline (PBS, in house) and incubated with TrypLE Express Enzyme (Gibco, 12605010) for 3 minutes at 37 °C. Cells were dissociated by pipetting and TrypLE was inactivated by diluting cells five-fold in CM medium, before proceeding with fixation and permeabilization as described.

extract_protocol:
Cells were harvested (~10 x 106 cells) and washed once with PBS. All centrifugation steps were at 200 g for 4 minutes at 4 °C. Cells were fixated in 1% formaldehyde (Sigma, F8875) in PBS for 5 minutes, before quenching the reaction with 125 mM final concentration of glycine (Sigma, 50046) and placing the cells on ice. All subsequent steps were performed on ice or at 4⁰C. Cells were washed three times with PBS before resuspension in Wash buffer 1 (20mM HEPES pH 7.5 (Gibco, 15630-056), 150 mM NaCl, 66.6 µg/mL Spermidine (Sigma, S2626), 1X cOmplete™ protease inhibitor cocktail (Roche, 11697498001), 0.05% Saponin (Sigma, 47036), 2mM EDTA) and transferred to a 1.5 mL protein LoBind Eppendorf tube (Eppendorf, EP0030108116-100EA). Cells were permeabilized for 30 minutes at 4 ⁰C on a tube roller. Bovine Serum Albumin (BSA, Sigma, A2153) was added to 5 mg/mL final concentration and incubated for another 60 minutes at 4 ⁰C on a tube roller. Permeabilized nuclei were used for antibody incubation.
Samples ligated with unique SBC adapters were pooled, either 2-4 1000 nuclei samples or a full 384-well plate were pooled for combined in vitro transcription (IVT). To reduce batch effects, controls (secondary antibody-conjugates without primary antibody incubation) were pooled with their corresponding samples whenever possible. For 384-well plates, mineral oil was removed by spinning the sample for 2 minutes at 2000 g and transferring the liquid phase to a clean tube, which was repeated three times. After pooling, samples were incubated for 10 minutes with 1.0 volume CleanNGS magnetic beads (CleanNA, CPCR-0050), diluted 1:4 to 1:10 in bead binding buffer (20% PEG 8000, 2.5 M NaCl, 10 mM Tris–HCl, 1 mM EDTA, 0.05% Tween 20, pH 8.0 at 25 °C). The bead dilution ratio depended on the total volume, 1:4 for 1000 nuclei samples and 1:10 for a full 384-well plate. Samples were placed on a magnetic rack (DynaMag™-2, ThermoFisher, 12321D) to collect beads on the side of the tube. Beads were washed two times with 80% ethanol and briefly allowed to dry before resuspending in 8 µL water. In vitro transcription was performed by adding 12 µL IVT mix from the MEGAScript T7 kit (Invitrogen, AM1334) for 14 hours at 37 ⁰C before holding at 4 ⁰C. Library preparation was subsequently performed as described previously 13,46, using 5 µL of aRNA and 8 to 11 PCR cycles, depending on the aRNA yield. Purified aRNA from different IVT reactions (with unique SBC adapters) can be pooled before proceeding with cDNA synthesis to reduce batch effects. Libraries were run on the Illumina NextSeq500 platform with high output 1x75 bp, the Illumina NextSeq2000 platform with high output 1x100 bp or the Illumina NextSeq2000 platform with high output 2x100 bp.

treatment_protocol: For differentiation towards the neural lineage, mESCs were taken in culture on MEFs and subsequently passaged 3 times in feeder-free conditions in 60%-BRL medium. On day 0 of the differentiation, mESCs were plated on gelatin-coated 6-well plates (0.15% gelatin, Sigma, G1890) at a density of 2.5 x 104 cells per cm2 in N2B27 medium defined as follows: 0.5x Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12 (DMEM-F12, Gibco, 11320033), 0.5x Neurobasal medium (Gibco, 21103049), 15mM HEPES (Gibco, 15630080), 0.5x N-2 supplement (Gibco, 17502048), 0.5x B-27 serum-free supplement (Gibo, 17504044) and 0.1 mM β-mercaptoethanol. From day 3 of differentiation, cells were washed daily with DMEM-F12 medium and refreshed with N2B27 medium. To harvest on day 5 of differentiation, cells were washed once with DMEM-F12 and incubated for 1 minute at room temperature with Accutase Enzyme Detachment Medium (Invitrogen, 00-4555-56). Cells were dissociated by pipetting and Accutase was inactivated by diluting cells ten-fold in DMEM-F12 or N2B27 medium, before proceeding with fixation and permeabilization as described.   Mice with the C57BL/6NCrl genotype were used for bone marrow isolations, 4 female littermates of 9 weeks old were sacrificed. To isolate bone marrow cells, the tibia and femur bones from the hindlegs were removed. The top of the bone was removed and the marrow was flushed out using a syringe with HBSS buffer (Gibco, 14025092). Cells were isolated from the marrow by pipetting up and down several times and poured through a 70 μm cell strainer (Greiner, 542070) before diluting in 25 mL HBSS buffer. Cells were centrifuged for 10 minutes at 300 g at 4 °C. Supernatant was removed, cells were resuspended in 10 mL PBS and centrifuged at 500g for 5 min.  After removing the supernatant, cells were counted using a TC20™ Automated Cell Counter (BioRad, 1450102) and diluted in 300 μL PBS per 1 x 106 cells. Per 300 μL PBS, 700 μL ice-cold Ethanol (100%, Boom, 84028185) was added dropwise while vortexing the suspension, to reach a 70% Ethanol final concentration. Cells were fixed for 1 hour at -20 °C. After fixation completed, cells were washed with Wash buffer 1 (20mM HEPES pH 7.5 (Gibco, 15630-056), 150 mM NaCl, 66.6 μg/mL Spermidine (Sigma, S2626), 1X cOmplete™ protease inhibitor cocktail (Roche, 11697498001), 0.05% Tween20 (Sigma, P9416), 2mM EDTA).  Finally, cells were stored in Wash buffer 1 containing 10% DMSO (Calbiochem, 317275) and frozen at -80 °C.

tag: cell count


title: R2


title: YTHDC1, rep1

city: Guangzhou

first: Rui

last: Li

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

data_processing:
adaptors, low-quality bases and reads shorted than 17 nucleotides were trimmed by cutadapt
Sequence-based removal of PCR duplicates was discarded with samtools and picard
Reads were then mapped to human genome (hg19) with STAR
CLIP peaks were called using Piranha
Assembly: hg19
Supplementary files format and content: bigwig
Library strategy: PAR-CLIP-Seq

growth_protocol: After treatment with 4-thiouridine (200 µM) for 14 h, PANC-1 cells were subjected to UV crosslinking and lysed on ice.

extract_protocol:
After end repair using T4 PNK (NEB), the bead-antibody-RNA complexes were treated with proteinase K, and the bound RNA was purified by acidic phenol/chloroform extraction and ethanol precipitation.
For PAR-CLIP sequencing, the purified RNAs were utilized for library construction using the NEBNext small RNA library prep kit (E7330S) and sequenced on an Illumina HiSeq4000

treatment_protocol: Cell lysate was then sonicated, digested with DNase I and RNase I for 15 min at 37 °C and incubated with Dynabeads protein A/G (Millipore) conjugated with anti-CFL1/METTL3/YTHDC2 antibody overnight at 4 °C.

value: Human PDAC cell lines

tag: chip antibody


title: MAbID library Pol2Ser5P (H3+H3K36me3+Pol2Ser5P)

description:
Pol2Ser5P (H3+H3K36me3+Pol2Ser5P)
crosstalk_Pol2_noK27.bw
MAbID library


title: MAbID library H3K36me3 (H3+H3K27me3+H3K36me3)

description:
H3K36me3 (H3+H3K27me3+H3K36me3)
crosstalk_K36_noPol2.bw
MAbID library


title: R1

tag: tissue


title: MAbID library Pol2Ser5P (H3+H3K27me3+H3K36me3+Pol2Ser5P)

description:
Pol2Ser5P (H3+H3K27me3+H3K36me3+Pol2Ser5P)
crosstalk_Pol2_all.bw
MAbID library


title: YTHDC1, rep3

tag: cell type


title: YTHDC1, rep2


title: YTHDC2, rep3

molecule: nuclear RNA


title: MAbID library H3K36me3 (H3+H3K27me3+H3K36me3+Pol2Ser5P)

description:
H3K36me3 (H3+H3K27me3+H3K36me3+Pol2Ser5P)
crosstalk_K36_all.bw
MAbID library


title: MAbID library H3K36me3 (H3+H3K36me3+Pol2Ser5P)

description:
H3K36me3 (H3+H3K36me3+Pol2Ser5P)
crosstalk_K36_noK27.bw
MAbID library


title: MAbID library H3K27me3 (H3+H3K27me3+Pol2Ser5P)

description:
H3K27me3 (H3+H3K27me3+Pol2Ser5P)
i39_H3K27me3.H3-K27-Pol2_merged_Log2OE.bw
MAbID library


title: YTHDC2, rep2


title: MAbID library H3K27me3 (H3+H3K27me3+H3K36me3)

description:
H3K27me3 (H3+H3K27me3+H3K36me3)
i39_H3K27me3.H3-K27-K36_merged_Log2OE.bw
MAbID library


title: MAbID library SUZ12

description:
Suz12
Suz12.bw
MAbID library


title: MAbID library H3K27me3 (H3+H3K27me3+H3K36me3+Pol2Ser5P)

description:
H3K27me3 (H3+H3K27me3+H3K36me3+Pol2Ser5P)
i39_H3K27me3.H3-K27-K36-Pol2_merged_Log2OE.bw
MAbID library


title: METTL3, rep3


title: YTHDC2, rep1


title: HC2_1


title: METTL3, rep1


title: MAbID library CTCF

description:
CTCF
CTCF.bw
MAbID library


title: CFL1, rep3


title: CFL1, rep2


title: CFL1, rep1


title: WA_WR_0726_10

city: Boston

first: Pushpinder

last: Bawa

state: Massachusetts

address: 670 Albany St

department: Boston University Medical Campus

institute: Center for Regenerative Medicine

description: Total RNA with ribosomal reduction

data_processing:
Reads were mapped to GRCh38 with TdTomato reporter
Counts per gene were summarized using the featureCounts function from the subread package
edgeR package was used to import and filter the counts
Differential expression using MAST models
The limma package with its voom method, namely, linear modelling and empirical Bayes moderation was used to test differential expression (moderate t-test). P-values were adjusted for multiple testing using Benjamini-Hochberg correction (false discovery rate-adjusted p-value; FDR). Differentially expressed genes for each comparison were visualized using Glimma package, and FDR<0.05 was set as the threshold for determining significant differential gene expression. Enrichment analyses were carried out using Fgsea package.
Assembly: GRCh38 with TdTomato reporter
Supplementary files format and content: Tab separated file having raw read count for each sample in singular file

molecule: polyA RNA

source_name: ADGRG6 gRNA +dox 5% smoke 8hr_biol rep 1

growth_protocol: To generate iAT2s, we performed PSC directed differentiation via definitive endoderm into NKX2-1 lung progenitors using methods we have previously described (Hawkins et al., JCI 2017; Jacob et al., Cell Stem Cell 2017; Jacob et al., Nat Protoc 2019). In brief, cells maintained in mTeSR1 media were differentiated into definitive endoderm using the STEMdiff Definitive Endoderm Kit (StemCell Technologies) for 3 days (day 0-3) and after the endoderm-induction stage, cells were dissociated with gentle cell dissociation reagent and passaged into 6-well dishes pre-coated with growth factor reduced Matrigel in ‘‘DS/SB’’ anteriorization media, consisting of complete serum-free differentiation media (cSFDM) base as previously described (Jacob et al., Cell Stem Cell 2017; Jacob et al., Nat Protoc 2019), supplemented with 2 µM Dorsomorphin (‘‘DS’’; Stemgent) and 10 µM SB431542 (‘‘SB’’; Tocris). For the first 24 hour after passaging, 10 µM Y-27632 was added to the media. After anteriorization in DS/SB media for 3 days (day 3-6), cells were cultured in ‘‘CBRa’’ lung progenitor-induction media until day 15, as we have previously published (Jacob et al., Cell Stem Cell 2017). ‘‘CBRa’’ media consists of cSFDM base supplemented with 3 µM CHIR99021 (Tocris), 10 ng/ml recombinant human BMP4 (rhBMP4, R&D Systems), and 100 nM retinoic acid (RA, Sigma). On day 15 of differentiation, live cells were sorted on a high-speed cell sorter (MoFlo Legacy or MoFlo Astrios EQ) to isolate NKX2-1+ lung progenitors based on CD47hi/CD26neg gating (Hawkins et al., JCI 2017). Sorted lung progenitors were resuspended in undiluted growth factor reduced 3D Matrigel (Corning) at a concentration of approximately 400 cells/µl and distal/alveolar differentiation of cells was performed in CK+DCI media, consisting of cSFDM base supplemented with 3 µM CHIR99021, 10 ng/mL rhKGF (CK), and 50 nM dexamethasone (Sigma), 0.1 mM 8-Bromoadenosine 30,50-cyclic monophosphate sodium salt (Sigma) and 0.1 mM 3-Isobutyl-1-methylxanthine (IBMX; Sigma) (DCI).

extract_protocol: Qiagen RNeasy Kit

value: Cell line

value: BU3 NGST CRISPRi line

value: iPSC-derived AT2

tag: treatment

value: CK+DCI media +doxycyline; smoke-exposed


title: WA_WR_0726_9

description: Total RNA with ribosomal reduction

source_name: ADGRG6 gRNA -dox 5% smoke 8hr_biol rep 3

value: wildtype

value: CK+DCI media -doxycyline; smoke-exposed


title: WA_WR_0726_8

description: Total RNA with ribosomal reduction

source_name: ADGRG6 gRNA -dox 5% smoke 8hr_biol rep 2


title: Superovulation, biological replicate 4

city: Philadelphia

first: Scott

middle: Michael

last: Gordon

state: PA

address: 3615 Civic Center Blvd

department: Neonatology

institute: Children's Hospital of Philadelphia

data_processing:
After demultiplexing, sequence data was checked for overall quality and yield. Then, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens reference genome GRCh38 available on ENSEMBL.
Assembly: Homo sapiens GRCh38

source_name: sort purified NK cells CD45+CD3-CD56+

extract_protocol:
RNA library preparations and sequencing reactions were conducted at GENEWIZ, LLC. (South Plainfield, NJ, USA). RNA samples received were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA)
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).
The sequencing libraries were clustered on a single lane of a flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification

value: sort purified NK cells CD45+CD3-CD56+

value: Superovulation


title: WA_WR_0726_7

description: Total RNA with ribosomal reduction

source_name: ADGRG6 gRNA -dox 5% smoke 8hr_biol rep 1


title: WA_WR_0726_6

description: Total RNA with ribosomal reduction

source_name: ADGRG6 gRNA +dox Air_biol rep 3

value: CK+DCI media +doxycyline; air-exposed


title: Natural implantation window, biological replicate 5

value: Natural


title: WA_WR_0726_4

description: Total RNA with ribosomal reduction

source_name: ADGRG6 gRNA +dox Air_biol rep 1


title: WA_WR_0726_5

description: Total RNA with ribosomal reduction

source_name: ADGRG6 gRNA +dox Air_biol rep 2


title: WA_WR_0726_3

description: Total RNA with ribosomal reduction

source_name: ADGRG6 gRNA -dox Air_biol rep 3

value: CK+DCI media -doxycyline; air-exposed


title: Superovulation, biological replicate 1


title: Superovulation, biological replicate 2


title: Natural implantation window, biological replicate 3


title: Natural implantation window, biological replicate 4


title: Superovulation, biological replicate 3


title: METTL3, rep2


title: WA_WR_0726_2

description: Total RNA with ribosomal reduction

source_name: ADGRG6 gRNA -dox Air_biol rep 2


title: WA_WR_0726_11

description: Total RNA with ribosomal reduction

source_name: ADGRG6 gRNA +dox 5% smoke 8hr_biol rep 2


title: WA_WR_0726_12

description: Total RNA with ribosomal reduction

source_name: ADGRG6 gRNA +dox 5% smoke 8hr_biol rep 3


title: Natural implantation window, biological replicate 2


title: MAb-ID bulk TTAA K562 control

treatment_protocol: For differentiation towards the neural lineage, mESCs were taken in culture on MEFs and subsequently passaged 3 times in feeder-free conditions in 60%-BRL medium. On day 0 of the differentiation, mESCs were plated on gelatin-coated 6-well plates (0.15% gelatin, Sigma, G1890) at a density of 2.5 x 104 cells per cm2 in N2B27 medium defined as follows: 0.5x Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12 (DMEM-F12, Gibco, 11320033), 0.5x Neurobasal medium (Gibco, 21103049), 15mM HEPES (Gibco, 15630080), 0.5x N-2 supplement (Gibco, 17502048), 0.5x B-27 serum-free supplement (Gibo, 17504044) and 0.1 mM β-mercaptoethanol. From day 3 of differentiation, cells were washed daily with DMEM-F12 medium and refreshed with N2B27 medium. To harvest on day 5 of differentiation, cells were washed once with DMEM-F12 and incubated for 1 minute at room temperature with Accutase Enzyme Detachment Medium (Invitrogen, 00-4555-56). Cells were dissociated by pipetting and Accutase was inactivated by diluting cells ten-fold in DMEM-F12 or N2B27 medium, before proceeding with fixation and permeabilization as described.


title: MAb-ID bulk 4-mer TTAA K562 primary conjugate: Pol II CTD Ser5P, 1.5K

description: sce_multi_Pol_II_Ser5P_multi_TTAA11.5k.bw

tag: antibody

value: Pol II CTD Ser5P


title: MAb-ID bulk GATC K562 control


title: Superovulation, biological replicate 5


title: NY3_A549_D3L3A_48h_3

city: San Francisco

first: Mehdi

last: Bouhaddou

state: CA

institute: University of California San Francisco

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adapter sequence using Trimmomatic.
Reads were mapped to Homo_sapiens ensembl_release-101 genome using HISAT2.
Counts of reads mapped to protein coding genes were extracted using featureCount and are reported.
Assembly: Not relevant
Supplementary files format and content: count values for each Sample

source_name: epithelial lung cancer cells

extract_protocol:
Total RNA was extracted from 10^6 cells using the Qiagen RNeasy Kit after inactivating the virus post infection.
The chosen method of rRNA removal was rRNA depletion for mRNA and long noncoding species. RNA was primed with random hexamers for first-strand cDNA synthesis and then second-strand cDNA synthesis. All samples were sequenced on HiSeq 4000.

tag: sars-cov-2 voc

tag: collection time point

tag: additional conditions

tag: experiment group


title: MAb-ID bulk 4-mer TTAA K562 primary conjugate: Pol II CTD Ser5P, 2.5K

description: sce_multi_Pol_II_Ser5P_multi_TTAA12.5k.bw


title: NY3_A549_D3L3A_48h_2


title: NY3_A549_D3L3A_48h_1


title: NY3_A549_WT_48h_3


title: MAb-ID bulk 4-mer GATC or TTAA K562 primary conjugate: Pol II CTD Ser5P, 2.5K

description: sce_multi_Pol_II_Ser5P_multi_GATCorTTAA_2.5k.bw


title: NY3_A549_WT_48h_2


title: MAb-ID bulk 4-mer GATC or TTAA K562 primary conjugate: Pol II CTD Ser5P, 1.5K

description: sce_multi_Pol_II_Ser5P_multi_GATCorTTAA_1.5k.bw


title: WA_WR_0726_1

description: Total RNA with ribosomal reduction

source_name: ADGRG6 gRNA -dox Air_biol rep 1

tag: genotype


title: NY3_A549_WT_48h_1


title: MAb-ID bulk 4-mer TTAA K562 primary conjugate: H3K36me3, 2.5K


title: NY3_A549_Mock_48h_1

value: Mock


title: NY3_A549_Mock_48h_2


title: MAb-ID bulk 4-mer TTAA K562 primary conjugate: H3K36me3, 1.5K


title: NY3_A549_D3L3A_24h_3


title: NY3_A549_D3L3A_24h_1


title: MAb-ID bulk 4-mer GATC or TTAA K562 primary conjugate: H3K36me3, 1.5K

description: sce_multi_H3K36me3_multi_GATCorTTAA_1.5k.bw


title: MAb-ID bulk 4-mer TTAA K562 primary conjugate: H3K27me3, 2.5K


title: MAb-ID bulk 4-mer GATC or TTAA K562 primary conjugate: H3K36me3, 2.5K

description: sce_multi_H3K36me3_multi_GATCorTTAA_2.5k.bw


title: MAb-ID bulk 4-mer TTAA K562 primary conjugate: H3K27me3, 1.5K


title: NY3_A549_WT_24h_2


title: MAb-ID bulk 4-mer GATC or TTAA K562 primary conjugate: H3K27me3, 2.5K

description: sce_multi_H3K27me3_multi_GATCorTTAA_2.5k.bw


title: NY3_A549_WT_24h_3


title: NY3_A549_WT_24h_1


title: NY3_A549_Mock_24h_3


title: NY3_A549_Mock_24h_1


title: MAb-ID bulk 4-mer TTAA K562 primary conjugate: H3, 2.5K


title: NY3_A549_Mock_24h_2


title: UK8_Calu3_BA.5_Rux_48h_3

value: Omicron (BA.5)

value: Ruxolitinib treatment


title: MAb-ID bulk 4-mer GATC and TTAA K562 primary conjugate: Pol II CTD Ser5P

description: sce_multi_Pol_II_Ser5P_multi_GATCandTTAA_3.5k.bw


title: MAb-ID bulk 4-mer GATC and TTAA K562 primary conjugate: H3K27me3

description: sce_multi_H3K27me3_multi_GATCandTTAA_3.5k.bw


title: UK8_Calu3_BA.5_Rux_48h_2


title: NY3_A549_Mock_48h_3


title: UK8_Calu3_BA.5_Rux_48h_1


title: MAb-ID bulk K562 6-mer primary conjugate: Lamin B1

value: Lamin B1


title: MAb-ID bulk 4-mer GATC and TTAA K562 primary conjugate: H3K36me3

description: sce_multi_H3K36me3_multi_GATCandTTAA_3.5k.bw


title: NY3_A549_D3L3A_24h_2


title: MAb-ID bulk 4-mer TTAA K562 primary conjugate: H3, 1.5K


title: UK8_Calu3_BA.4_Rux_48h_2

value: Omicron (BA.4)


title: UK8_Calu3_BA.4_Rux_48h_3


title: MAb-ID bulk 4-mer GATC or TTAA K562 primary conjugate: H3K27me3, 1.5K

description: sce_multi_H3K27me3_multi_GATCorTTAA_1.5k.bw


title: MAb-ID bulk K562 6-mer primary conjugate: H3K9me3


title: MAb-ID bulk K562 6-mer primary conjugate: H3K4me1


title: MAb-ID bulk K562 6-mer primary conjugate: H3K27me3

description: sce_fig3_primMulti_merged_H3K27me3.5k.bw


title: UK8_Calu3_BA.4_Rux_48h_1


title: MAb-ID bulk K562 6-mer primary conjugate: H3K36me3

description: sce_fig3_primMulti_merged_H3K36me3.5k.bw


title: UK8_Calu3_BA.2_Rux_48h_3

value: Omicron (BA.2)


title: UK8_Calu3_BA.2_Rux_48h_2


title: UK8_Calu3_BA.1_Rux_48h_3

value: Omicron (BA.1)


title: UK8_Calu3_BA.2_Rux_48h_1


title: MAb-ID bulk K562 6-mer primary conjugate: H3K27ac


title: MAb-ID bulk 4-mer GATC or TTAA K562 primary conjugate: H3, 2.5K


title: MAb-ID bulk K562 primary conjugate: Lamin B1 rep 2


title: MAb-ID bulk K562 primary conjugate: H3K9me3 rep 2


title: MAb-ID bulk 4-mer GATC or TTAA K562 primary conjugate: H3, 1.5K


title: MAb-ID bulk K562 primary conjugate: H3K4me3 rep 2


title: MAb-ID bulk K562 primary conjugate: H3K36me3 rep 2


title: UK8_Calu3_BA.1_Rux_48h_2


title: MAb-ID bulk K562 primary conjugate: H3K4me1 rep 2


title: UK8_Calu3_Delta_Rux_48h_3


title: MAb-ID bulk K562 primary conjugate: H3K27ac rep 2


title: MAb-ID bulk K562 primary conjugate: H3K27me3 rep 2


title: UK8_Calu3_Delta_Rux_48h_1


title: UK8_Calu3_Alpha_Rux_48h_3


title: UK8_Calu3_Delta_Rux_48h_2


title: MAb-ID bulk K562 primary conjugate: Lamin B1 rep 1


title: MAb-ID bulk K562 primary conjugate: H3K9me3 rep 1


title: UK8_Calu3_Alpha_Rux_48h_2


title: UK8_Calu3_Alpha_Rux_48h_1


title: UK8_Calu3_IC19_Rux_48h_2


title: UK8_Calu3_IC19_Rux_48h_3


title: UK8_Calu3_Mock_Rux_48h_3


title: MAb-ID bulk K562 primary conjugate: H3K4me1 rep 1


title: UK8_Calu3_IC19_Rux_48h_1


title: UK8_Calu3_BA.1_Rux_48h_1


title: UK8_Calu3_Mock_Rux_48h_2


title: MAb-ID bulk K562 primary conjugate: H3K27me3 rep 1


title: MAb-ID bulk K562 4-mer secondary conjugate: Pol II CTD Ser5P

description: sce_fig2_merged_Pol_II_Ser5P_multi.5k.bw


title: MAb-ID bulk K562 primary conjugate: H3K27ac rep 1


title: MAb-ID bulk K562 primary conjugate: H3K36me3 rep 1


title: MAb-ID bulk K562 4-mer secondary conjugate: H3K27me3


title: UK8_Calu3_BA.5_48h_3


title: UK8_Calu3_Mock_Rux_48h_1


title: MAb-ID bulk K562 4-mer secondary conjugate: H3K36me3


title: UK8_Calu3_BA.5_48h_1


title: UK8_Calu3_BA.5_48h_2


title: MAb-ID bulk K562 4-mer secondary conjugate: H3


title: MAb-ID bulk K562 secondary conjugate: Lamin B1 rep 2


title: MAb-ID bulk K562 secondary conjugate: Pol II CTD Ser5P rep 2


title: MAb-ID bulk K562 secondary conjugate: H3K9me3 rep 2


title: MAb-ID bulk K562 secondary conjugate: H3K9me2 rep 2


title: UK8_Calu3_BA.4_48h_1


title: MAb-ID bulk K562 primary conjugate: H3K4me3 rep 1


title: MAb-ID bulk K562 secondary conjugate: H3K4me3 rep 2


title: UK8_Calu3_BA.2_48h_3


title: UK8_Calu3_BA.2_48h_2


title: UK8_Calu3_BA.2_48h_1


title: MAb-ID bulk K562 secondary conjugate: H3K36me3 rep 2


title: MAb-ID bulk K562 secondary conjugate: H3K27me3 rep 2


title: UK8_Calu3_BA.1_48h_2


title: UK8_Calu3_Delta_48h_2


title: UK8_Calu3_BA.1_48h_1


title: MAb-ID bulk K562 secondary conjugate: H3K9me3 rep 1


title: MAb-ID bulk K562 secondary conjugate: Lamin B1 rep 1


title: MAb-ID bulk K562 secondary conjugate: Pol II CTD Ser5P rep 1


title: MAb-ID bulk K562 secondary conjugate: H3 rep 2


title: UK8_Calu3_BA.4_48h_3


title: MAb-ID bulk K562 secondary conjugate: H3K9me2 rep 1


title: MAb-ID bulk K562 secondary conjugate: H3K4me3 rep 1


title: UK8_Calu3_Alpha_48h_2


title: UK8_Calu3_Alpha_48h_3


title: MAb-ID bulk K562 secondary conjugate: H3K4me1 rep 2


title: UK8_Calu3_Alpha_48h_1


title: MAb-ID bulk K562 secondary conjugate: H3K4me1 rep 1


title: MAb-ID bulk K562 secondary conjugate: H3K36me3 rep 1


title: MAb-ID bulk K562 secondary conjugate: H3K27me3 rep 1


title: UK8_Calu3_BA.4_48h_2


title: UK8_Calu3_IC19_48h_1


title: UK8_Calu3_IC19_48h_3


title: MAb-ID bulk K562 secondary conjugate: H3K27ac rep 1


title: UK8_Calu3_BA.1_48h_3


title: MAb-ID bulk K562 secondary conjugate: H3K27ac rep 2


title: MAb-ID bulk K562 secondary conjugate: H3 rep 1


title: UK8_Calu3_IC19_48h_2


title: UK8_Calu3_Delta_48h_3


title: UK8_Calu3_Delta_48h_1


title: UK8_Calu3_Mock_48h_2


title: UK8_Calu3_Mock_48h_3


title: UK8_Calu3_Mock_48h_1


title: UK8_Calu3_BA.5_24h_3


title: UK8_Calu3_BA.5_24h_2


title: UK8_Calu3_BA.5_24h_1


title: UK8_Calu3_BA.4_24h_3


title: Rep3_Lib92_e-100

city: Basel

first: Kazuki

last: Nosho

address: Spitalstrasse 41

department: Biozentrum

country: Switzerland

institute: University of Basel

data_processing:
Sequencing of the cDNA libraries was performed by MPGC (Cologne, Germany) or D-BSSE genomics facilty (Basel, Switzerland)
Sequence reads were trimmed for adaptor sequence/short sequence (<35 nt) using Trimmomatic v0.39
Trimmed sequence reads were mapped to B. subtilis NCIB3610 genome and plasmid (NCBI Accession number: NZ_CP020102 and NZ_CP020103) using HISAT2 v2.2.1 in single-end mode.
Reads mapped to all cetegory of genes (CDS, ncRNA, tmRNA, signal recognition particle RNA, ribonuclease P RNA, tRNA, rRNA) were counted using featureCounts v2.0.1 with fractional counting for multi-mapping and multi-overlapping reads (-OM --fraction) in a strand-specific manner (-s 2). Of those, reads mapped in tRNA and rRNA were removed and the remaining reads were used for the downstream analysis.
All genes for which there were at least 2 samples with a read count of at least 10 were used for the downstream analysis. Samples with remaining reads of < 1 million reads were excluded and the rest of the samples were used for normalization using edgeR (version 3.6.1) and transformed (log2).
Supplementary files format and content: comma-separated files include mapped read count data for each sample
Supplementary files format and content: comma-separated files include edgeR-normalized log2 count data for each of the samples at expansion phase
Supplementary files format and content: comma-separated files include edgeR-normalized log2 count data for each of the samples at lag and expansion phase

organism: Bacillus subtilis

source_name: cells, 6.70 h after swarm expansion, 12938 µm distance from the swarm center (= point of inoculation)

growth_protocol: Bacterial cells were spotted onto the center of a 9 cm petri dish filled with LB soft-agar (0.5% agar) medium and incubated at 30°C for swarm expansion.

extract_protocol:
RNA was isolated by the hot phenol method (Jahn et al, J Microbiol Methods, 2008) with some modifications. Prepared RNA was DNase-digested and cleaned up using RNACleanXP. Depletion of ribosomal RNA was performed using DIY method (Culviner et al, mBio, 2020). Integrity of the prepared RNA was tested using a TapeStation.
Directional cDNA libraries were prepared using the NEBNext Ultra II Directional RNA Libary Prep Kit for Illumina (NEB, E7760) according to the manufacturers instructions. Quality of the prepared libraries was tested using a TapeStation.

treatment_protocol: Cells that started swarm expansion were collected into the lysis buffer by our custom sampling robot. Cells before swarm expansion (lag phase) were collected by being suspened in the lysis buffer.

value: Bacteria

value: WT chromosome; comI_Q12L in natual plasmid

tag: strain

tag: time after expansion (h)

tag: position (um)


title: Rep3_Lib90_e-98

source_name: cells, 6.70 h after swarm expansion, 2674 µm distance from the swarm center (= point of inoculation)


title: Rep3_Lib93_e-101

source_name: cells, 6.70 h after swarm expansion, 17854 µm distance from the swarm center (= point of inoculation)


title: Rep3_Lib95_e-103

source_name: cells, 6.70 h after swarm expansion, 27685 µm distance from the swarm center (= point of inoculation)


title: Rep3_Lib96_e-104

source_name: cells, 6.70 h after swarm expansion, 32601 µm distance from the swarm center (= point of inoculation)


title: Rep3_Lib91_e-99

source_name: cells, 6.70 h after swarm expansion, 8023 µm distance from the swarm center (= point of inoculation)


title: Rep3_Lib89_e-97

source_name: cells, 6.38 h after swarm expansion, 29302 µm distance from the swarm center (= point of inoculation)


title: Rep3_Lib88_e-96

source_name: cells, 6.38 h after swarm expansion, 24814 µm distance from the swarm center (= point of inoculation)


title: UK8_Calu3_BA.2_24h_3


title: Rep3_Lib87_e-94

source_name: cells, 6.38 h after swarm expansion, 15840 µm distance from the swarm center (= point of inoculation)


title: Rep3_Lib86_e-93

source_name: cells, 6.38 h after swarm expansion, 11355 µm distance from the swarm center (= point of inoculation)


title: Rep3_Lib85_e-92

source_name: cells, 6.38 h after swarm expansion, 6878 µm distance from the swarm center (= point of inoculation)


title: UK8_Calu3_BA.1_24h_3


title: UK8_Calu3_BA.1_24h_2


title: UK8_Calu3_BA.2_24h_1


title: Rep3_Lib84_e-91

source_name: cells, 6.38 h after swarm expansion, 2293 µm distance from the swarm center (= point of inoculation)


title: UK8_Calu3_BA.1_24h_1


title: Rep3_Lib83_e-90

source_name: cells, 6.06 h after swarm expansion, 27112 µm distance from the swarm center (= point of inoculation)


title: Rep3_Lib94_e-102

source_name: cells, 6.70 h after swarm expansion, 22770 µm distance from the swarm center (= point of inoculation)


title: Rep3_Lib82_e-89

source_name: cells, 6.06 h after swarm expansion, 23548 µm distance from the swarm center (= point of inoculation)


title: UK8_Calu3_Delta_24h_3

source_name: epithelial lung cancer cells


title: UK8_Calu3_Delta_24h_2


title: Rep3_Lib81_e-88

source_name: cells, 6.06 h after swarm expansion, 19984 µm distance from the swarm center (= point of inoculation)


title: UK8_Calu3_Delta_24h_1


title: Rep3_Lib80_e-87

source_name: cells, 6.06 h after swarm expansion, 16419 µm distance from the swarm center (= point of inoculation)


title: UK8_Calu3_BA.4_24h_2


title: Rep3_Lib79_e-86

source_name: cells, 6.06 h after swarm expansion, 12856 µm distance from the swarm center (= point of inoculation)


title: UK8_Calu3_Alpha_24h_3


title: UK8_Calu3_BA.4_24h_1


title: Rep3_Lib78_e-85

source_name: cells, 6.06 h after swarm expansion, 9292 µm distance from the swarm center (= point of inoculation)


title: UK8_Calu3_IC19_24h_3


title: UK8_Calu3_BA.2_24h_2


title: Rep3_Lib77_e-83

source_name: cells, 6.06 h after swarm expansion, 1910 µm distance from the swarm center (= point of inoculation)


title: UK8_Calu3_Alpha_24h_1


title: Rep3_Lib76_e-82

source_name: cells, 5.73 h after swarm expansion, 22082 µm distance from the swarm center (= point of inoculation)


title: Rep3_Lib75_e-81

source_name: cells, 5.73 h after swarm expansion, 19165 µm distance from the swarm center (= point of inoculation)


title: UK8_Calu3_IC19_24h_2


title: UK8_Calu3_IC19_24h_1


title: Rep3_Lib74_e-80

source_name: cells, 5.73 h after swarm expansion, 16246 µm distance from the swarm center (= point of inoculation)


title: Rep3_Lib73_e-78

source_name: cells, 5.73 h after swarm expansion, 10413 µm distance from the swarm center (= point of inoculation)


title: UK8_Calu3_Mock_24h_3


title: UK8_Calu3_Mock_24h_2


title: UK8_Calu3_Mock_24h_1


title: UK8_Calu3_BA.5_10h_3


title: Rep3_Lib72_e-77

source_name: cells, 5.73 h after swarm expansion, 7497 µm distance from the swarm center (= point of inoculation)


title: Rep3_Lib71_e-76

source_name: cells, 5.73 h after swarm expansion, 4585 µm distance from the swarm center (= point of inoculation)


title: UK8_Calu3_BA.5_10h_2


title: UK8_Calu3_BA.5_10h_1


title: Rep3_Lib70_e-75

source_name: cells, 5.73 h after swarm expansion, 1529 µm distance from the swarm center (= point of inoculation)


title: Rep3_Lib68_e-72

source_name: cells, 5.38 h after swarm expansion, 16538 µm distance from the swarm center (= point of inoculation)


title: UK8_Calu3_BA.4_10h_3


title: Rep3_Lib69_e-73

source_name: cells, 5.38 h after swarm expansion, 19529 µm distance from the swarm center (= point of inoculation)


title: Rep3_Lib66_e-70

source_name: cells, 5.38 h after swarm expansion, 10557 µm distance from the swarm center (= point of inoculation)


title: Rep3_Lib64_e-68

source_name: cells, 5.38 h after swarm expansion, 4584 µm distance from the swarm center (= point of inoculation)


title: Rep3_Lib65_e-69

source_name: cells, 5.38 h after swarm expansion, 7568 µm distance from the swarm center (= point of inoculation)


title: UK8_Calu3_BA.4_10h_2

source_name: epithelial lung cancer cells


title: UK8_Calu3_BA.2_10h_3


title: UK8_Calu3_BA.4_10h_1


title: UK8_Calu3_Alpha_24h_2


title: Rep3_Lib63_e-67

source_name: cells, 5.38 h after swarm expansion, 1528 µm distance from the swarm center (= point of inoculation)


title: UK8_Calu3_BA.2_10h_1


title: Rep3_Lib62_e-65

source_name: cells, 5.04 h after swarm expansion, 15655 µm distance from the swarm center (= point of inoculation)


title: Rep3_Lib61_e-64

source_name: cells, 5.04 h after swarm expansion, 12887 µm distance from the swarm center (= point of inoculation)


title: UK8_Calu3_BA.1_10h_3


title: Rep3_Lib58_e-61

source_name: cells, 5.04 h after swarm expansion, 4584 µm distance from the swarm center (= point of inoculation)


title: UK8_Calu3_BA.2_10h_2


title: UK8_Calu3_BA.1_10h_2


title: UK8_Calu3_Delta_10h_3


title: Rep3_Lib60_e-63

source_name: cells, 5.04 h after swarm expansion, 10119 µm distance from the swarm center (= point of inoculation)


title: Rep3_Lib55_e-58

source_name: cells, 4.70 h after swarm expansion, 14377 µm distance from the swarm center (= point of inoculation)


title: Rep3_Lib56_e-59

source_name: cells, 4.70 h after swarm expansion, 16565 µm distance from the swarm center (= point of inoculation)


title: Rep3_Lib59_e-62

source_name: cells, 5.04 h after swarm expansion, 7351 µm distance from the swarm center (= point of inoculation)


title: Rep3_Lib57_e-60

source_name: cells, 5.04 h after swarm expansion, 1528 µm distance from the swarm center (= point of inoculation)


title: UK8_Calu3_Delta_10h_2


title: UK8_Calu3_Delta_10h_1


title: UK8_Calu3_IC19_10h_3


title: Rep3_Lib67_e-71

source_name: cells, 5.38 h after swarm expansion, 13546 µm distance from the swarm center (= point of inoculation)


title: Rep3_Lib54_e-57

source_name: cells, 4.70 h after swarm expansion, 12189 µm distance from the swarm center (= point of inoculation)


title: UK8_Calu3_Alpha_10h_2


title: UK8_Calu3_IC19_10h_1


title: Rep3_Lib50_e-52

source_name: cells, 4.70 h after swarm expansion, 1146 µm distance from the swarm center (= point of inoculation)


title: UK8_Calu3_Alpha_10h_1


title: Rep3_Lib53_e-56

source_name: cells, 4.70 h after swarm expansion, 10001 µm distance from the swarm center (= point of inoculation)


title: UK8_Calu3_Mock_10h_3


title: Rep3_Lib51_e-53

source_name: cells, 4.70 h after swarm expansion, 3438 µm distance from the swarm center (= point of inoculation)


title: Rep3_Lib52_e-55

source_name: cells, 4.70 h after swarm expansion, 7813 µm distance from the swarm center (= point of inoculation)


title: Rep3_Lib49_e-51

source_name: cells, 4.38 h after swarm expansion, 14380 µm distance from the swarm center (= point of inoculation)


title: UK8_Calu3_Mock_10h_2

source_name: epithelial lung cancer cells


title: Rep3_Lib48_e-50

source_name: cells, 4.38 h after swarm expansion, 12192 µm distance from the swarm center (= point of inoculation)


title: UK8_Calu3_Alpha_10h_3


title: UK8_Calu3_Mock_10h_1


title: UK8_Calu3_IC19_10h_2


title: UK7_Calu3_AlphaWT_24h_3


title: UK8_Calu3_BA.1_10h_1


title: UK7_Calu3_AlphaWT_24h_2


title: UK7_Calu3_AlphaWT_24h_1


title: UK7_Calu3_Wu203204_2 _24h_3

value: Wuhan


title: Rep3_Lib43_e-44

source_name: cells, 4.06 h after swarm expansion, 11480 µm distance from the swarm center (= point of inoculation)


title: Rep3_Lib45_e-47

source_name: cells, 4.38 h after swarm expansion, 5627 µm distance from the swarm center (= point of inoculation)


title: Rep3_Lib42_e-43

source_name: cells, 4.06 h after swarm expansion, 9946 µm distance from the swarm center (= point of inoculation)


title: Rep3_Lib46_e-48

source_name: cells, 4.38 h after swarm expansion, 7815 µm distance from the swarm center (= point of inoculation)


title: UK7_Calu3_Wu203204_2 _24h_2


title: Rep3_Lib44_e-46

source_name: cells, 4.38 h after swarm expansion, 3439 µm distance from the swarm center (= point of inoculation)


title: UK7_Calu3_Wu203204_1 _24h_3


title: Rep3_Lib41_e-41

source_name: cells, 4.06 h after swarm expansion, 6880 µm distance from the swarm center (= point of inoculation)


title: UK7_Calu3_Wu203204_1 _24h_2


title: Rep3_Lib39_e-39

source_name: cells, 4.06 h after swarm expansion, 3818 µm distance from the swarm center (= point of inoculation)


title: UK7_Calu3_Wu203204_2 _24h_1


title: UK7_Calu3_Wu203204_1 _24h_1


title: Rep3_Lib40_e-40

source_name: cells, 4.06 h after swarm expansion, 5348 µm distance from the swarm center (= point of inoculation)


title: UK7_Calu3_WuWT_24h_3


title: Rep3_Lib38_e-38

source_name: cells, 4.06 h after swarm expansion, 2291 µm distance from the swarm center (= point of inoculation)


title: Rep3_Lib37_e-37

source_name: cells, 4.06 h after swarm expansion, 763 µm distance from the swarm center (= point of inoculation)


title: Rep3_Lib36_e-36

source_name: cells, 3.57 h after swarm expansion, 9932 µm distance from the swarm center (= point of inoculation)


title: UK7_Calu3_WuWT_24h_1


title: Rep3_Lib47_e-49

source_name: cells, 4.38 h after swarm expansion, 10004 µm distance from the swarm center (= point of inoculation)


title: UK7_Calu3_WuWT_24h_2


title: UK7_Calu3_Mock_24h_3


title: Rep3_Lib33_e-33

source_name: cells, 3.57 h after swarm expansion, 5348 µm distance from the swarm center (= point of inoculation)


title: Rep3_Lib32_e-32

source_name: cells, 3.57 h after swarm expansion, 3820 µm distance from the swarm center (= point of inoculation)


title: Rep3_Lib34_e-34

source_name: cells, 3.57 h after swarm expansion, 6877 µm distance from the swarm center (= point of inoculation)


title: UK6_Calu3_Omicron1_24h_3

source_name: epithelial lung cancer cells


title: Rep3_Lib31_e-31

source_name: cells, 3.57 h after swarm expansion, 2291 µm distance from the swarm center (= point of inoculation)


title: UK7_Calu3_Mock_24h_2


title: Rep3_Lib30_e-30

source_name: cells, 3.57 h after swarm expansion, 764 µm distance from the swarm center (= point of inoculation)


title: Rep3_Lib35_e-35

source_name: cells, 3.57 h after swarm expansion, 8404 µm distance from the swarm center (= point of inoculation)


title: UK6_Calu3_Omicron1_24h_2


title: UK6_Calu3_Omicron1_24h_1


title: Rep3_Lib29_e-29

source_name: cells, 3.27 h after swarm expansion, 9166 µm distance from the swarm center (= point of inoculation)


title: UK7_Calu3_Mock_24h_1


title: UK6_Calu3_DeltaA_24h_3


title: Rep3_Lib28_e-28

source_name: cells, 3.27 h after swarm expansion, 7638 µm distance from the swarm center (= point of inoculation)


title: Rep3_Lib27_e-27

source_name: cells, 3.27 h after swarm expansion, 6111 µm distance from the swarm center (= point of inoculation)


title: UK6_Calu3_DeltaA_24h_2


title: UK6_Calu3_AlphaA_24h_3


title: UK6_Calu3_DeltaA_24h_1


title: Rep3_Lib26_e-26

source_name: cells, 3.27 h after swarm expansion, 4583 µm distance from the swarm center (= point of inoculation)


title: UK6_Calu3_AlphaA_24h_2


title: Rep3_Lib24_e-24

source_name: cells, 3.27 h after swarm expansion, 1528 µm distance from the swarm center (= point of inoculation)


title: Rep3_Lib23_e-23

source_name: cells, 2.97 h after swarm expansion, 7641 µm distance from the swarm center (= point of inoculation)


title: 1309-21_Untransduced

city: Chicago

first: Hananeh

last: Fonoudi

state: IL

address: 320 E Superior st.,

department: Pharmacology

institute: Northwestern University

data_processing:
Using SOAPnuke, sequence files were trimmed for adaptors, low-quality reads, and N reads.
Clean sequencing reads were mapped to the GRCh38 reference genome using STAR and counted using RSEM.
Supplementary files format and content: Organized .xlsx files include TPM values for each sample

source_name: Primary Cells

extract_protocol:
RNA was extracted using 300 µL/well of TRIzol Reagent. RNA was then purified using the Direct-zol RNA MicroPrep kit, including on-column Dnase digestion to remove genomic DNA.
RNA libraries for RNA-seq were prepared using DNBSEQ Eukaryotic strand-specific mRNA library protocol.

value: Primary Cells

value: Cardiac Fibroblasts

value: WT

value: Untransduced


title: 1309-21

value: Transduced


title: UK6_Calu3_AlphaA_24h_1


title: 1289-20_Untransduced


title: Rep3_Lib22_e-22

source_name: cells, 2.97 h after swarm expansion, 6113 µm distance from the swarm center (= point of inoculation)


title: 1289-20


title: UK6_Calu3_IC19_24h_3


title: 1274-20_Untransduced


title: Lower arm Cz amp, 5dpa

city: Dresden

first: Tatiana

last: Sandoval-Guzmán

state: Saxony

address: Fetscherstrasse 74

department: Department of Internal Medicine III, Center for Healthy Aging, Medical Faculty Carl Gustav Carus

country: Germany

institute: Technische Universität Dresden

description: Fresh frozen spatial transcriptome sequencing using 10x Genomics Visium

data_processing:
Gene expression quantification of the Visium dataset was done using kallisto (v0.48.0) and bustools (v0.41.0).
Cells were filtered using emptyDrops and defaultDrops functions in the DropletUtils R package (v1.12.3).
SpaceRanger (v2.0.0) was used to match the Visium spots to the tissue slice.
Assembly: AmexG_v6_DD
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: list of spatial barcodes
Supplementary files format and content: list of gene IDs
Supplementary files format and content: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned fiducials of the tissue image
Supplementary files format and content: image of tissue and spots
Supplementary files format and content: scalefactors in json format
Supplementary files format and content: his-res image of tissue
Supplementary files format and content: low-res image of tissue
Supplementary files format and content: list of spatial barcodes and the coordinated specifying the spots
Library strategy: Spatial Transcriptomics

organism: Ambystoma mexicanum

source_name: 5 dpa regenerating lower arm

extract_protocol:
Tissue was processed according to the 10x Visium Spatial transcriptomics kit.  10μm tissue sections were cut with the cryostat and the permeabilization time used was 20 min.
RNA libraries for RNA-seq were prepared using 10x GEX Library Prep following manufacturer's protocols.
Spatial Transcriptomics, slide PN: 2000233, SN: V10M09-105

treatment_protocol: 8.5cm ST animal was amputated in the lower arm and collected 5 days post-amputation by embedding directly in OCT and freezing in a chilled isopentane bath. Tissues were kept at -80 until sectioning.

value: 5 dpa regenerating lower arm

value: DD

value: CZ lower arm amputation


title: UK6_Calu3_IC19_24h_2


title: Rep3_Lib21_e-21

source_name: cells, 2.97 h after swarm expansion, 4585 µm distance from the swarm center (= point of inoculation)


title: 1274-20


title: Rep3_Lib20_e-20

source_name: cells, 2.97 h after swarm expansion, 3056 µm distance from the swarm center (= point of inoculation)


title: UK6_Calu3_IC19_24h_1


title: primary ATRT, ATRT48

type: genomic

city: Paris

first: Mamy

middle: Jean de Dieu

last: ANDRIANTERANAGNA

state: Ile de France

address: 26 rue d'Ulm

department: Centre de Recherche

country: France

institute: Institut Curie

hyb_protocol: please refer to GEO:GSE175892

scan_protocol: please refer to GEO:GSE175892

data_processing:
Re-analysis: RnBeads Bioconductor R package version 1.6.1 (Assenov et al., 2014; doi: 10.1038/nmeth.3115) was used to re-process the data from IDAT files.   All samples and all probes were kept after quality control. Probe intensities were normalized using the rnb.execute.normalization() function with the “illumina” method. Probes outside CpG context (2991 probes), targeting single nucleotide polymorphisms (17369 probes) or targeting X and Y chromosomes (19457 probes) were respectively filtered out before subsequent analysis.
beta-value; processed file matrix in a separate file: matrix_LobonIglesias2023_DNAmethylation_EPICarray_reanalysed_primaryATRT.csv; sample ID correspondance with Andrianteranagna et al., 2021 paper is given in a separate file: LobonIglesias2023_Andrianteranagna2021_sampleIDs.csv

label: cy3, cy5

source_name: primary tumor

label_protocol: please refer to GEO:GSE175892

growth_protocol: please refer to GEO:GSE175892

extract_protocol: please refer to GEO:GSE175892

treatment_protocol: please refer to GEO:GSE175892

tag: anatomic location

tag: age at diagnosis


title: primary ATRT, ATRT51

value: Spinal Cord


title: primary ATRT, ATRT47

value: MCP/ICV


title: primary ATRT, ATRT45

value: Cranial Nerves


title: primary ATRT, ATRT46


title: UK6_Calu3_VIC_24h_3

tag: cell line


title: Rep3_Lib19_e-19

source_name: cells, 2.97 h after swarm expansion, 1528 µm distance from the swarm center (= point of inoculation)


title: Rep3_Lib25_e-25

source_name: cells, 3.27 h after swarm expansion, 3056 µm distance from the swarm center (= point of inoculation)


title: primary ATRT, ATRT43


title: UK6_Calu3_VIC_24h_2

source_name: epithelial lung cancer cells


title: primary ATRT, ATRT28


title: UK6_Calu3_VIC_24h_1


title: Rep3_Lib18_e-18

source_name: cells, 2.67 h after swarm expansion, 6113 µm distance from the swarm center (= point of inoculation)


title: primary ATRT, ATRT29

value: Cerebellar Anterior Lobe


title: Rep3_Lib17_e-17

source_name: cells, 2.67 h after swarm expansion, 4584 µm distance from the swarm center (= point of inoculation)


title: primary ATRT, ATRT26


title: primary ATRT, ATRT24


title: Rep3_Lib15_e-15

source_name: cells, 2.67 h after swarm expansion, 1528 µm distance from the swarm center (= point of inoculation)


title: primary ATRT, ATRT23

value: Basal Ganglia


title: UK6_Calu3_Mock_24h_2

value: Mock


title: primary ATRT, ATRT21


title: primary ATRT, ATRT22

value: Septum


title: primary ATRT, ATRT20


title: Rep3_Lib14_e-14

source_name: cells, 2.37 h after swarm expansion, 4585 µm distance from the swarm center (= point of inoculation)

value: Bacteria

value: WT chromosome; comI_Q12L in natual plasmid


title: UK6_Calu3_Mock_24h_1


title: primary ATRT, ATRT19


title: UK6_Calu3_Omicron1_10h_3

value: Omicron (BA.1)


title: primary ATRT, ATRT14


title: UK6_Calu3_Omicron1_10h_2


title: primary ATRT, ATRT16

value: Intraventricular


title: primary ATRT, ATRT27


title: primary ATRT, ATRT12


title: Rep3_Lib12_e-12

source_name: cells, 2.37 h after swarm expansion, 1529 µm distance from the swarm center (= point of inoculation)


title: primary ATRT, ATRT18


title: primary ATRT, ATRT05


title: primary ATRT, ATRT04


title: Rep3_Lib11_e-11

source_name: cells, 2.07 h after swarm expansion, 4583 µm distance from the swarm center (= point of inoculation)


title: Rep3_Lib10_e-10

source_name: cells, 2.07 h after swarm expansion, 3056 µm distance from the swarm center (= point of inoculation)


title: UK6_Calu3_Mock_24h_3


title: Rep3_Lib16_e-16

source_name: cells, 2.67 h after swarm expansion, 3056 µm distance from the swarm center (= point of inoculation)


title: primary ATRT, ATRT02


title: Rep3_Lib9_e-9

source_name: cells, 2.07 h after swarm expansion, 1528 µm distance from the swarm center (= point of inoculation)


title: UK6_Calu3_Omicron1_10h_1


title: UK6_Calu3_DeltaA_10h_2


title: DNA from SW620 cell line

city: Santiago de Compostela

first: Angel

last: Diaz-Lagares

state: A Coruña

address: C/ Choupana s/n

department: ONCOMET

country: Spain

institute: Health Research Institute of Santiago (IDIS)

description: DNA from SW620 cell line

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to human Infinium MethylationEPIC BeadChip (Illumina) using standard Illumina protocol

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

data_processing: GenomeStudio (V2011.1) Methylation Module (1.9.0) software

label: Cy5 and Cy3

source_name: SW620 cell line

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from cell lines samples using  a standard high salt method based on SDS/Proteinase K.

tag: gender

value: Male

tag: disease

value: Colorectal adenocarcinoma (Metastasis, lymph node)


title: Rep3_Lib8_e-8

source_name: cells, 1.77 h after swarm expansion, 3057 µm distance from the swarm center (= point of inoculation)


title: DNA from COLO205 cell line (Passage 4)

description: DNA from COLO205 cell line

source_name: COLO205 cell line (P4)

value: Colorectal adenocarcinoma (Metastasis, ascytic fluid)


title: DNA from COLO205 cell line (Passage 3)

description: DNA from COLO205 cell line

source_name: COLO205 cell line (P3)


title: Rep3_Lib13_e-13

source_name: cells, 2.37 h after swarm expansion, 3057 µm distance from the swarm center (= point of inoculation)


title: DNA from COLO205 cell line (Passage 2)

description: DNA from COLO205 cell line

source_name: COLO205 cell line (P2)


title: Rep3_Lib7_e-7

source_name: cells, 1.77 h after swarm expansion, 1529 µm distance from the swarm center (= point of inoculation)


title: UK6_Calu3_AlphaA_10h_3

source_name: epithelial lung cancer cells


title: Rep3_Lib6_e-6

source_name: cells, 1.47 h after swarm expansion, 3056 µm distance from the swarm center (= point of inoculation)


title: DNA from CTC-MCC-41 cell line (Passage 13)

description: DNA from CTC-MCC-41 cell line

source_name: CTC-MCC-41 cell line (P13)

value: Colorectal adenocarcinoma (Circulating Tumor Cell from peripheral blood)


title: UK6_Calu3_AlphaA_10h_2


title: DNA from RKO cell line

description: DNA from RKO cell line

source_name: RKO cell line

value: Unknown

value: Colorectal carcinoma (Primary tumor)

value: RKO


title: primary ATRT, ATRT03

source_name: primary tumor

value: MCP/ICV


title: DNA from Caco2 cell line

description: DNA from Caco2 cell line

source_name: Caco2 cell line

value: Colorectal adenocarcinoma (Primary tumor)


title: Rep3_Lib5_e-5

source_name: cells, 1.47 h after swarm expansion, 1528 µm distance from the swarm center (= point of inoculation)


title: UK6_Calu3_DeltaA_10h_3


title: UK6_Calu3_AlphaA_10h_1


title: DNA from CTC-MCC-41 cell line (Passage 14)

description: DNA from CTC-MCC-41 cell line

source_name: CTC-MCC-41 cell line (P14)


title: DNA from HCT116 cell line

description: DNA from HCT 116 cell line

source_name: HCT116 cell line


title: UK6_Calu3_IC19_10h_2


title: DNA from HT29 cell line (Passage 3)

description: DNA from HT29 cell line

source_name: HT29 cell line (P3)

value: Female


title: Rep3_Lib3_e-3

source_name: cells, 1.17 h after swarm expansion, 1527 µm distance from the swarm center (= point of inoculation)


title: Rep3_Lib4_e-4

source_name: cells, 1.17 h after swarm expansion, 3056 µm distance from the swarm center (= point of inoculation)


title: UK6_Calu3_DeltaA_10h_1


title: PA047

city: Homburg (Saar)

first: Marc

last: Remke

state: Saarland

address: Kirrberger Straße 100, Gebäude 9

department: Pediatric Translational Oncology Lab

institute: Universitätsklinikum des Saarlandes

hyb_protocol: Bisulphite converted DNA from the samples were hybridised to the Illumina Infinium MethylationEPIC Kit array.

scan_protocol: not provided

data_processing:
Matrix_processed.txt: Normalized Average Beta
Matrix_signal_intensities.txt: Unmethylated and methylated signal intensities

label: not provided

source_name: brain tumor

label_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium EPIC chip according to standard protocol.

extract_protocol: Genomic DNA was extracted and purified from cell culture samples using Qiagen DNeasy Kit according to standard instructions.

value: Pilocytic Astrocytoma

tag: tissue

value: Brain tumor

tag: tissue status

value: FFPE


title: PA046


title: Rep3_Lib2_e-2

source_name: cells, 0.87 h after swarm expansion, 1527 µm distance from the swarm center (= point of inoculation)

tag: cell type

value: Bacteria


title: Rep3_Lib1_e-1

source_name: cells, 0.57 h after swarm expansion, 1528 µm distance from the swarm center (= point of inoculation)

value: WT chromosome; comI_Q12L in natual plasmid


title: PA043


title: PA040


title: UK6_Calu3_VIC_10h_3


title: PA065


title: Rep2_Lib96_c-103

source_name: cells, 6.14 h after swarm expansion, 27535 µm distance from the swarm center (= point of inoculation)


title: DNA from CTC-MCC-41 cell line (Passage 12)

description: DNA from CTC-MCC-41 cell line

source_name: CTC-MCC-41 cell line (P12)


title: UK6_Calu3_IC19_10h_3

source_name: epithelial lung cancer cells


title: DNA from HT29 cell line (Passage 4)

description: DNA from HT29 cell line

source_name: HT29 cell line (P4)


title: UK6_Calu3_VIC_10h_2


title: PA037


title: DNA from HT29 cell line (Passage 2)

description: DNA from HT29 cell line

source_name: HT29 cell line (P2)


title: Rep2_Lib95_c-102

source_name: cells, 6.14 h after swarm expansion, 23920 µm distance from the swarm center (= point of inoculation)


title: UK6_Calu3_VIC_10h_1


title: PA050


title: UK6_Calu3_IC19_10h_1


title: Rep2_Lib94_c-101

source_name: cells, 6.14 h after swarm expansion, 20307 µm distance from the swarm center (= point of inoculation)


title: PA051


title: UK6_Calu3_Mock_10h_2

value: Mock


title: PA036


title: Rep2_Lib92_c-99

source_name: cells, 6.14 h after swarm expansion, 13084 µm distance from the swarm center (= point of inoculation)


title: PA067


title: PA060


title: PA045


title: UK6_Calu3_Mock_10h_3


title: Rep2_Lib91_c-98

source_name: cells, 6.14 h after swarm expansion, 9405 µm distance from the swarm center (= point of inoculation)


title: PA059


title: UK6_Calu3_Mock_10h_1


title: PA038


title: PA001

value: FrFr


title: PA020


title: Rep2_Lib90_c-97

source_name: cells, 6.14 h after swarm expansion, 5731 µm distance from the swarm center (= point of inoculation)


title: PA017


title: UK6_Calu3_Omicron1_2h_2

value: Omicron (BA.1)


title: Rep2_Lib89_c-96

source_name: cells, 6.14 h after swarm expansion, 1911 µm distance from the swarm center (= point of inoculation)


title: PA034


title: UK6_Calu3_Omicron1_2h_1


title: PA019


title: UK6_Calu3_DeltaA_2h_3


title: Rep2_Lib87_c-94

source_name: cells, 5.80 h after swarm expansion, 20673 µm distance from the swarm center (= point of inoculation)


title: Rep2_Lib88_c-95

source_name: cells, 5.80 h after swarm expansion, 24427 µm distance from the swarm center (= point of inoculation)


title: PA010


title: PA009


title: PA008


title: UK6_Calu3_DeltaA_2h_2


title: PA031


title: UK6_Calu3_DeltaA_2h_1


title: Rep2_Lib86_c-92

source_name: cells, 5.80 h after swarm expansion, 13227 µm distance from the swarm center (= point of inoculation)


title: PA026

source_name: brain tumor


title: Rep2_Lib85_c-91

source_name: cells, 5.80 h after swarm expansion, 9477 µm distance from the swarm center (= point of inoculation)


title: PA032


title: PA023


title: PA024


title: Rep2_Lib84_c-90

source_name: cells, 5.80 h after swarm expansion, 5730 µm distance from the swarm center (= point of inoculation)


title: UK6_Calu3_AlphaA_2h_3


title: PA022


title: UK6_Calu3_Omicron1_2h_3


title: PA021


title: Rep2_Lib82_c-88

source_name: cells, 5.48 h after swarm expansion, 23391 µm distance from the swarm center (= point of inoculation)


title: Rep2_Lib83_c-89

source_name: cells, 5.80 h after swarm expansion, 1910 µm distance from the swarm center (= point of inoculation)


title: PA013


title: PA011


title: UK6_Calu3_IC19_2h_3

source_name: epithelial lung cancer cells


title: Rep2_Lib81_c-87

source_name: cells, 5.48 h after swarm expansion, 19858 µm distance from the swarm center (= point of inoculation)


title: PA012


title: PA030


title: PA018


title: PA028


title: PA016


title: PA015


title: Rep2_Lib80_c-86

source_name: cells, 5.48 h after swarm expansion, 16326 µm distance from the swarm center (= point of inoculation)


title: UK6_Calu3_IC19_2h_1


title: Rep2_Lib79_c-85

source_name: cells, 5.48 h after swarm expansion, 12794 µm distance from the swarm center (= point of inoculation)


title: UK6_Calu3_AlphaA_2h_2


title: PA033


title: UK6_Calu3_VIC_2h_3


title: Rep2_Lib78_c-84

source_name: cells, 5.48 h after swarm expansion, 9262 µm distance from the swarm center (= point of inoculation)


title: PA039


title: PA041


title: PA048


title: Rep2_Lib77_c-83

source_name: cells, 5.48 h after swarm expansion, 5730 µm distance from the swarm center (= point of inoculation)


title: Rep2_Lib76_c-82

source_name: cells, 5.48 h after swarm expansion, 1910 µm distance from the swarm center (= point of inoculation)


title: PA064


title: UK6_Calu3_AlphaA_2h_1


title: UK6_Calu3_VIC_2h_2


title: UK6_Calu3_VIC_2h_1


title: Rep2_Lib75_c-81

source_name: cells, 5.13 h after swarm expansion, 21685 µm distance from the swarm center (= point of inoculation)


title: PA062


title: UK6_Calu3_IC19_2h_2


title: UK6_Calu3_Mock_2h_3


title: PA061


title: PA058


title: Rep2_Lib74_c-80

source_name: cells, 5.13 h after swarm expansion, 18834 µm distance from the swarm center (= point of inoculation)


title: PA057


title: PA056


title: UK6_Calu3_Mock_2h_2


title: PA053


title: UK6_Calu3_Mock_2h_1


title: Rep2_Lib72_c-78

source_name: cells, 5.13 h after swarm expansion, 13131 µm distance from the swarm center (= point of inoculation)


title: PA029


title: Rep2_Lib71_c-77

source_name: cells, 5.13 h after swarm expansion, 7431 µm distance from the swarm center (= point of inoculation)


title: PA035


title: UK5_Calu3_PolyIC_24h_3

value: Poly I:C stimulation


title: PA004


title: PA005


title: PA002


title: UK5_Calu3_PolyIC_24h_2


title: PA063


title: PA003


title: Rep2_Lib70_c-75

source_name: cells, 5.13 h after swarm expansion, 4583 µm distance from the swarm center (= point of inoculation)


title: T28_Blm6

city: PARMA

first: Barbara

last: Montanini

state: PR

address: Parco Area delle Scienze 23/A

department: Department of Chemistry, Life Sciences and Environmental Sustainability

institute: University of Parma

data_processing:
Data processing steps were conducted following the LeXogen suggested pipeline https://www.lexogen.com/quantseq-data-analysis/
The adapter contamination, polyA read through, and low quality tails were removed using bbduk
Reads were aligned to the Rattus norvegicus genome (v. 6) using STAR (v. 2.5) with parameters: --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000
Counts were generated using HTSeq (v 0.10)
Assembly: rn6

source_name: Lung

extract_protocol:
Fresh right lungs were immediately collected in RNAlater™ (Sigma, USA) for the next homogenization in QIAzol® Lysis Reagent (QIAGEN, Netherlands) with gentleMACS™ Dissociator (Miltenyi Biotec, Germany). RNA was extracted using the QIAcube robotic workstation with the miRNeasy Mini Kit (QIAGEN, Netherlands), including DNase digestion protocol.
Libraries for massive parallel RNA sequencing (RNA-seq) were prepared with the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD (Lexogen) and sequenced, in two runs, with the use of an Illumina NextSeq500 platform, which generated at least 30 million reads/sample (75 bp Single End).

value: Sprague Dawley

tag: treatment

value: Bleomycin 2U/Kg - IT administration (day 0 and day 4)

tag: termination day

value: Day 28

value: Total Right Lung Homogenate


title: UK5_Calu3_AlphaAplusRux_24h_3

tag: sars-cov-2 voc

tag: collection time point

value: Ruxolitinib treatment


title: UK5_Calu3_PolyIC_24h_1

tag: additional conditions

tag: experiment group


title: T28_Sal7

tag: strain

value: Saline Solution - IT administration (day 0 and day 4)


title: Rep2_Lib68_c-72

source_name: cells, 4.77 h after swarm expansion, 16571 µm distance from the swarm center (= point of inoculation)

tag: genotype

tag: time after expansion (h)


title: Rep2_Lib67_c-71

source_name: cells, 4.77 h after swarm expansion, 14382 µm distance from the swarm center (= point of inoculation)

tag: position (um)


title: UK5_Calu3_AlphaAplusRux_24h_2


title: T21_Blm6

value: Day 21


title: T21_Sal6


title: T21_Blm5


title: Rep2_Lib66_c-70

source_name: cells, 4.77 h after swarm expansion, 12193 µm distance from the swarm center (= point of inoculation)


title: UK5_Calu3_AlphaAplusRux_24h_1


title: T14_Sal5

value: Day 14


title: T28_Sal6


title: UK5_Calu3_Delta2AplusTPCA_24h_3

value: TPCA treatment


title: PA007

source_name: brain tumor

value: Pilocytic Astrocytoma

value: Brain tumor


title: T14_Blm7


title: Rep2_Lib64_c-68

source_name: cells, 4.77 h after swarm expansion, 7815 µm distance from the swarm center (= point of inoculation)

value: Bacteria


title: Rep2_Lib65_c-69

source_name: cells, 4.77 h after swarm expansion, 10004 µm distance from the swarm center (= point of inoculation)

value: WT chromosome; comI_Q12L in natual plasmid


title: UK5_Calu3_Delta2AplusTPCA_24h_2

source_name: epithelial lung cancer cells


title: Rep2_Lib69_c-74

source_name: cells, 5.13 h after swarm expansion, 1528 µm distance from the swarm center (= point of inoculation)


title: T56_Sal6

value: Day 56


title: UK5_Calu3_Delta2AplusTPCA_24h_1


title: T56_Blm7


title: T56_Sal7


title: UK5_Calu3_Delta2AplusRux_24h_3


title: Rep2_Lib63_c-66

source_name: cells, 4.77 h after swarm expansion, 3439 µm distance from the swarm center (= point of inoculation)


title: Rep2_Lib62_c-65

source_name: cells, 4.77 h after swarm expansion, 1146 µm distance from the swarm center (= point of inoculation)


title: T28_Sal5


title: T28_Blm7


title: Rep2_Lib61_c-64

source_name: cells, 4.48 h after swarm expansion, 14915 µm distance from the swarm center (= point of inoculation)


title: UK5_Calu3_Delta2AplusRux_24h_2


title: T28_Blm5


title: T21_Sal8


title: T21_Sal5


title: T14_Sal8


title: UK5_Calu3_AlphaWT_24h_2


title: Rep2_Lib59_c-62

source_name: cells, 4.48 h after swarm expansion, 10323 µm distance from the swarm center (= point of inoculation)


title: T14_Sal7


title: T14_Blm5


title: T21_Blm7


title: T0_Naïve3-2

value: Day 0


title: T07_Sal8

value: Day 7


title: UK5_Calu3_Delta2AplusRux_24h_1


title: Rep2_Lib57_c-60

source_name: cells, 4.48 h after swarm expansion, 5732 µm distance from the swarm center (= point of inoculation)


title: T56_Blm6


title: T14_Blm6


title: Rep2_Lib58_c-61

source_name: cells, 4.48 h after swarm expansion, 8027 µm distance from the swarm center (= point of inoculation)


title: Rep2_Lib56_c-59

source_name: cells, 4.48 h after swarm expansion, 3438 µm distance from the swarm center (= point of inoculation)


title: T07_Sal5


title: T07_Blm8


title: T07_Blm6


title: UK5_Calu3_AlphaWT_24h_1


title: UK5_Calu3_AlphaOrf6KO_24h_3


title: T0_Naïve3


title: T0_Naïve6


title: UK5_Calu3_AlphaOrf6KO_24h_2


title: UK5_Calu3_AlphaOrf6KO_24h_1


title: Rep2_Lib52_c-55

source_name: cells, 4.17 h after swarm expansion, 12010 µm distance from the swarm center (= point of inoculation)


title: UK5_Calu3_AlphaWT_24h_3


title: HeLa Hi-Mid GFP rep2

city: Amsterdam

first: Kaspar

last: Bresser

address: Plesmanlaan 125

department: Hematopoeisis

institute: Sanquin

description: HeLa.HiMi.B

data_processing:
Sequencing adapters were trimmed using cutadapt using the settings -n 2, -e 0.2 and -M 62.
aligned to the UTR library using bowtie2 in local mode
PCR hybrids that were generated during library amplification were removed from the alignment file using a custom script
Read counts were obtained using htseq-count
sequence motifs detected with less than 10 reads across all samples were excluded from the analysis, and individual libraries were normalized to 10,000 reads
Assembly: Not applicable
Library strategy: Amplicon sequencing

source_name: HeLa cells

extract_protocol:
Retroviral library was produced by transfecting 4.5 ug of the library plasmid DNA into FLYRD18 retroviral packaging cells, as described above. HEK and HeLa cells were cultured to a density of 60% prior to addition of virus-containing supernatants, and subsequently expanded for 10 days. PBMCs were activated with αCD3/ αCD28 and spinfected with virus-containing supernatants, as described above, and expanded for 10 days in RPMI supplemented with 10% fetal bovine serum (FBS; Bodinco), 2 mM L-glutamine, 20 IU/mL penicillin G sodium salts, 20 μg/mL streptomycin sulfate (all Sigma Aldrich), Non-Essential Amino Acids (Gibco), Sodium pyruvate (Gibco), 50 IU/mL recombinant human (rh) IL-2 (Proleukin, Novartis), 5 ng/mL rhIL-15 (Peprotech), and 10 ng/mL rhIL7 (Miltenyi). Transduction efficiencies were kept between 5-10% in order to minimize multiple transgene integrations. After expansion cells were harvested and stained with Near-IR live/dead marker (Life Technologies) for dead cell exclusion, in addition to anti-CD8-AF700 (Biolegend) and anti-CD4-BV510 (Biolegend) in the case of the T cell assay. The top and bottom 15% GFP expressing cells, in addition to the full GFP-positive fraction, were sorted on a FACS Aria II (BD Biosciences). The sorted cells were subsequently pelleted and resuspended in 1 µl DirectPCR Lysis Reagent (Viagen) per 2,500 cells, supplemented with 0.5 mg/ml proteinase K (Viagen). The obtained lysate was incubated at 55 C for 3 hours, followed by 85 C for 45 minutes, and 95 C for 5 minutes.
An initial pre-amplification of the synthetic 3’UTRs was performed on 20 µl lysate (±50,000 cells) in a 100 µl reaction volume using the NEBnext kit (NEB) and 10 µM forward (5’-AAAGACCCCAACGAGAAGC-3’) and reverse (5’-AGTCTATAGCTACTAGGCG-3’) primers. An initial touchdown stage was performed dropping the annealing temperature 1 C per cycle from 58 C to 50 C (8 cycles), followed by 12 cycles at 50 C. Extension time was kept at 20 seconds. This initial PCR was performed in duplicate for each sample, as a technical control. Excess primers were removed from each reaction by incubating 20 µl of the initial PCR volume with 40 U Exonuclease I (NEB) at 37 C for 15 minutes, followed by a heat-inactivation at 80 C for 15 minutes. Each of these samples were subsequently used as template for a second PCR, with primers (Forward: 5’-ACACTCTTTCCCTACACGACGCTCTTCCGATCTAGACCCCAACGAGAAGCGCGATCAC-3’, Reverse: 5’-GACTGGAGTTCAGACGTGTGCTCTTCCGATCTAGTCTATAGCTACTAGGCGATA-3’) designed to amplify the product and attach partial Illumina adapters. This second PCR was performed using the NEBnext kit (NEB), and consisted of 16 cycles with a constant annealing temperature of 65 C and extension time of 30 seconds. Correct products (±275 base pairs) were purified from a 2% agarose gel using the Monarch® DNA Gel Extraction Kit (NEB). Purified products were sequenced using the Amplicon-EZ service from Genewiz (Azenta Life Sciences).

value: HeLa cells


title: Rep2_Lib54_c-57

source_name: cells, 4.17 h after swarm expansion, 16295 µm distance from the swarm center (= point of inoculation)


title: HeLa Low-Low GFP rep2

description: HeLa.LoLo.B


title: UK5_Calu3_AlphaOrf9bKO_24h_2


title: Rep2_Lib51_c-54

source_name: cells, 4.17 h after swarm expansion, 9867 µm distance from the swarm center (= point of inoculation)


title: HeLa Hi-Hi GFP rep2

description: HeLa.HiHi.B


title: Rep2_Lib55_c-58

source_name: cells, 4.48 h after swarm expansion, 1146 µm distance from the swarm center (= point of inoculation)


title: HeLa Low-Mid GFP rep2

description: HeLa.LoMi.B


title: UK5_Calu3_AlphaOrf9bKO_24h_3


title: Rep2_Lib50_c-53

source_name: cells, 4.17 h after swarm expansion, 7725 µm distance from the swarm center (= point of inoculation)


title: UK5_Calu3_AlphaOrf9bKO_24h_1


title: HEK all GFP+ rep2

description: HEK.GFP.B

source_name: Human Embryonic Kidney

value: Human Embryonic Kidney


title: HeLa Hi-Hi GFP rep1

description: HeLa.HiHi.A


title: HEK bottom 15% GFP rep2

description: HEK.Bot.B


title: HEK top 15% GFP rep2

description: HEK.Top.B


title: HeLa Low-Mid GFP rep1

description: HeLa.LoMi.A


title: HeLa Hi-Mid GFP rep1

description: HeLa.HiMi.A


title: Rep2_Lib49_c-52

source_name: cells, 4.17 h after swarm expansion, 5582 µm distance from the swarm center (= point of inoculation)


title: Rep2_Lib48_c-50

source_name: cells, 4.17 h after swarm expansion, 1147 µm distance from the swarm center (= point of inoculation)


title: Rep2_Lib53_c-56

source_name: cells, 4.17 h after swarm expansion, 14153 µm distance from the swarm center (= point of inoculation)


title: HeLa Low-Low GFP rep1

description: HeLa.LoLo.A


title: UK5_Calu3_GammaP1B_24h_2

source_name: epithelial lung cancer cells

value: Gamma (P.1)


title: HEK top 15% GFP rep1

description: HEK.Top.A


title: HEK all GFP+ rep1

description: HEK.GFP.A


title: Rep2_Lib47_c-49

source_name: cells, 3.89 h after swarm expansion, 11242 µm distance from the swarm center (= point of inoculation)


title: UK5_Calu3_Delta2A_24h_3


title: HEK bottom 15% GFP rep1

description: HEK.Bot.A


title: UK5_Calu3_GammaP1B_24h_1


title: UK5_Calu3_Delta2A_24h_2


title: Microbiota of adrenal gland from subject ACC4

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

institute: University of Florence

description: 16s rRNA v3-v4 sequencing of human adrenal gland biopsy

data_processing:
from raw to demultiplexed fastq files please contact IGA Technology Services (Udine, Italy)
qiime cutadapt trim-paired --i-demultiplexed-sequences demux-paired-end.qza --p-front-f CCTACGGGNGGCWGCAG --p-front-r GACTACNVGGGTWTCTAATCC --p-cores 7 --o-trimmed-sequences trimmed-seqs.qza --p-discard-untrimmed --p-minimum-length 100 --verbose
qiime demux summarize  --i-data trimmed-seqs.qza --o-visualization demux.qzv
qiime dada2 denoise-paired --i-demultiplexed-seqs trimmed-seqs.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 275 --p-trunc-len-r 168 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza --p-n-threads 7
bowtie2 -x ~/GRCh38_noalt_as -U filtered_dna-sequences.fasta  -S bowtie2_SAM_output.txt -f -p 4
qiime feature-classifier classify-sklearn --i-classifier SILVA_138_V3V4_BayesClassifier.qza --i-reads filtered_dna-sequences.qza --o-classification taxonomy.qza
R software (see the relative script publicly available at github.com/LeandroD94)
Assembly: NA
Supplementary files format and content: filtered_dna-sequences.fasta: text containing every processed ASV code and sequence retained after off-target reads decontamination
Supplementary files format and content: feature_table.csv: CSV text file containing the abundance table (after off-target reads decontamination)
Supplementary files format and content: taxonomy.tsv: TSV text file containing the complete taxonomic classification of the reference sequences
Library strategy: paired-end (2x300) amplicon sequencing

source_name: Adrenal gland

extract_protocol:
Genomic DNA was extracted using the DNeasy PowerSoil Pro Kit (Qiagen, Hilden, Germany)
Illumina 16S Metagenomic Sequencing Library Preparation protocol ( see https://emea.support.illumina.com)

value: Adrenal gland

value: F

tag: age

tag: condition

value: ACC

tag: acc stage

value: I-II

tag: secretion

tag: fastq id

tag: sequencing batch