title: dLNs_HA_24h_rep6


title: Embryo_10 PS and derivative [DNA_batch1_sc10]

status: Public on Mar 24 2023

type: SRA

city: Beijing

first: Fan

last: Guo

state: Beijing

address: 1 Beichen West Road, Chaoyang District

department: The State Key Laboratory of Stem Cell and Reproductive Biology

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

library_source: genomic

data_processing:
Processing of the scChaRM-seq DNA data:Trim Galore (v0.4.4) was used to remove random primer sequences, low-quality bases and adaptor sequences from the single-cell bisulfite data. Only reads longer than 50 bp after trimming were retained for alignment. Then, clean reads were mapped to the monkey reference genome mf5 by Bismark (v0.7.6) in paired-end mode, and unmapped reads were re-aligned to the reference genome in single-end mode. Duplicate reads from PCR were removed by the SAMtools (v0.1.18) command “samtools rmdup”, and only nonduplicate reads were used to perform the downstream analysis. The GCH (G=A, T or C) and WCG (W=A or T) sites (≥1× sequencing depth) in each single cell were summed. Then, the chromatin accessibility and DNA methylation level were calculated as the average GCH or WCG level, respectively.
Genome_build: mf5
Supplementary_files_format_and_content: bedgraph files；RNAid_DNAid_celltype.csv
Assembly: mf5
Supplementary files format and content: bedgraph files;csv files

molecule: genomic DNA

organism: Macaca fascicularis

source_name: in vitro

growth_protocol: The creation of cynomolgus monkey embryos including oocyte retrieval, intracytoplasmic sperm injection, and pre-implantation embryo culture were performed as described by Yamasaki et al (Nakamura et al., 2016). Briefly, female cynomolgus monkeys 7-10 years old with a successful reproductive history were used for mature oocyte collection by super-ovulation with follicle-stimulation hormone. The day collected oocytes were artificially fertilized by sperm injection was designated as embryonic day (E) 0. When the embryos developed to E6-E7, embryos with an  expanded blastocoel (>75% volume of the embryo) were selected for further culture .

extract_protocol:
The single-cell isolation procedures were performed according to the protocol previously described (Ma et al., 2019a). In brief, the pIVC cynomolgus embryos were  dissected by removing the extraembryonic tissues, then the inner embryonic bodies were digested with 500 μL of 1 × TrypLE for 15 min at 37°C and dissociated into single cells by mouth pipetting. Advanced DMEM/F12 containing 10% FBS was added to terminate the enzymatic reaction and the cells were centrifuged at 300 g for 5 min at room temperature, followed by the resuspension with 100 μL pre-cold 0.1% BSA/PBS.
Single cells were individually picked into ice-cold lysis buffer under stereoscopic microscope. single cells were picked of each stage and then the subjected to construct scChaRM-seq library. The method of library construction was described in our recently published method (Yan et al., 2021). In brief, in vitro CpG methylation was performed by M.CviPI (New England Biolabs, NEB) supplemented with S-adenosyl-methionine (SAM;NEB) and terminated by adding RLT buffer (QIAGEN). Then the genome DNA and mRNA were separated by capturing mRNA with oligo(dT) primers conjugated beads (Invitrogen), the supernatant containing genomic DNA was transferred into another PCR tube to bisulfite conversion (Zymo Research) and DNA library construction using previously descried TAILS method (Gu et al., 2019). The captured mRNA was subjected correspondingly to cDNA synthesis, PCR amplification and library construction (Gu et al., 2019).

tag: cell line

value: in vitro

tag: cell type

value: Embryo

tag: genotype

value: WT

tag: time


title: PLM5c_scRNA-seq

city: Muenster

first: Hyun-Woo

last: Jeong

state: NRW

department: Dept. Tissue Morphogenesis

country: Germany

institute: Max-Planck-Institute for Molecular Biomedicine

library_source: transcriptomic

data_processing:
illumina bcl2fastq (v2.19.1.403) used for basecalling and demultiplexing
BD Rhapsody WTA Analysis Pipeline (version 1.0) on SevenBridges Genomics online platform (SevenBridges) was used for alignment and sample de-multiplexing
Genome_build: GRCh38
Supplementary_files_format_and_content: txt files include UMI counts for each cell barcode and genes

molecule: polyA RNA

organism: Homo sapiens

source_name: PBMC

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from whole blood by a standard Ficoll-Paque (GE Healthcare, Uppsala, Sweden) density gradient centrifugation, frozen in freezing media, and stored in liquid nitrogen tank until use.
Freshly frozen PBMCs were thawed in a water bath at 37oC for 1 min, transferred to a 50-ml tube, and ten volumes of warm RPMI 1640 medium with 10% FCS and 0.1mg/ml DNase I were added slowly, followed by centrifugation at 300g for 5 min. The cell pellet was collected and cell number and viability were determined using trypan blue on Luna-II automated cell counter (Logos Biosystems). Each PBMC sample was labelled with respective sample multiplexing antibody (Single-Cell multiplex kit - Human; BD Biosciences) and then up to 6 samples were pooled together at equal numbers of 10,000 cells to make up 60,000 cells in total and loaded on a microwell cartridge of the BD Rhapsody Express system (BD Biosciences). Single cell whole transcriptome analysis libraries were prepared according to the manufacturer’s instructions using BD Rhapsody WTA Reagent kit (BD, 633802).

tag: cohort

tag: disease state

tag: gender

value: male

tag: group

value: longitudinal

value: PBMC


title: RT112_siF-1_siZ-1_rep1 [D763T38]

city: paris

first: Elodie

last: chapeaublanc

address: 26 rue d'ulm

department: UMR 144

country: France

institute: Institut Curie

description:
Sample 17
RT112 Bladder Cancer Cell line treated with siFOXA1 number 1 and siZBED2 number 1 replicate 1

data_processing:
Sequencer: NovaSeq - S1
Read length: 100bp
STAR: STAR_2.6.1a_08-27
GTF Annotation: gencode.v29.annotation.gtf
Index Adapters: Lexogen-Unique Dual index (96 Indexes)
Genome_build: human hg38
Supplementary_files_format_and_content: FOXA1_ZBED2_KD_tablecounts_raw.csv: Matrix table with raw counts for every gene and every sample.
Supplementary_files_format_and_content: FOXA1_ZBED2_KD_tablecounts_tpm.csv: Matrix table with TPM normalized counts for all samples and all genes.
Supplementary_files_format_and_content: pipeline_config.txt
Supplementary_files_format_and_content: adapter_list.txt
Supplementary_files_format_and_content: index_list.txt

molecule: total RNA

growth_protocol: RT112 were cultured in RPMI +10% FBS, SCaBER in DMEM + 10% FBS. See paper for more details.

extract_protocol:
RNA extraction was performed using RNeasy kit (Qiagen). See paper for more details.
3' mRNA-Seq library Prep Kit - FWD-Lexogen.

treatment_protocol: Cells were transfected using Lipfectamine RNAi Max. See paper for more details.

tag: treatment

value: siFOXA1.1 and siZBED2.1

tag: experiment batch replicate


title: PLM5a_scRNA-seq


title: Embryo_10 PS and derivative [DNA_batch1_sc1]


title: Embryo,E18,RNA_batch44

library_source: transcriptomic single cell

data_processing:
Processing of the single-cell RNA-seq data ：The raw data was trimmed with Cutadapt (v1.15). Clean reads for individual cells were then classified according to the cell barcodes on Read#2. Then, Read#1 was mapped to the mf5 genome using STAR (v2.6.0a) with the default parameters. The transcript copy number of each gene was determined with HTseq (v0.10.0) after de-duplication based on unique molecular identifiers (UMIs). Then, cells with low complexity (fewer than 500 detected genes) were excluded. High-quality data containing 3,682 cells from scChaRM-seq were retained for further analyses.
Genome_build: mf5
Supplementary_files_format_and_content:  counts.csv: Count matrix in tab-separated value files; meta.csv: annotations of cells processed by scChaRM-seq.
Assembly: mf5
Supplementary files format and content: tab-delimited text files include counts for each cell

extract_protocol:
The single-cell isolation procedures were performed according to the protocol previously described (Ma et al., 2019a). In brief, the pIVC cynomolgus embryos were  dissected by removing the extraembryonic tissues, then the inner embryonic bodies were digested with 500 μL of 1 × TrypLE for 15 min at 37°C and dissociated into single cells by mouth pipetting. Advanced DMEM/F12 containing 10% FBS was added to terminate the enzymatic reaction and the cells were centrifuged at 300 g for 5 min at room temperature, followed by the resuspension with 100 μL pre-cold 0.1% BSA/PBS.
An RNA-seq library was prepared by following the instruction manual of the NEBNext UltraII DNA Library Prep Kit for Illumina (New England Biolabs)


title: RT112_siFOXA1-1_rep1 [D763T37]

description:
Sample 16
RT112 Bladder Cancer Cell line treated with siFOXA1 number 1 replicate 1


title: PMF3_scRNA-seq

value: female

value: mild/moderate


title: Embryo,E18,RNA_batch43


title: RT112_siZBED2-1_rep1 [D763T35]

description:
Sample 14
RT112 Bladder Cancer Cell line treated with siZBED2 number 1 replicate 1


title: PLM5b_scRNA-seq


title: dLNs_HA_24h_rep5

type: RNA

city: Gothenburg

first: Ali

last: Harandi

address: Box 435

department: Department of Microbiology and Immunology

country: Sweden

institute: University of Gothenburg

hyb_protocol: Quantity and labelling efficiency were verified before hybridization to mouse whole genome microarrays (Agilent Technologies).

scan_protocol: Scanned on an Agilent Scanner G2505B. Image analysis was performed with Feature Extraction software (version 6.1.1, Agilent Technologies)

data_processing: Data were processed, quantile normalized and analyzed using the R package Limma (Ritchie et al (2015). Nucleic Acids Research, 43(7), pp. e47)

organism: Mus musculus

source_name: dLNs, HA, 24h

label_protocol: RNA was labeled with the Fluorescent Linear Amplification Kit (Agilent Technologies) following manufacturer’s instructions.

extract_protocol: RNA was extracted from lymph nodes using the RNeasy Mini QIAcube kit (Qiagen).

treatment_protocol: Anesthesized neonate mice were injected subcutaneously with 100 microliter antigen alone or together with adjuvant.

tag: tissue

value: dLNs

tag: timepoint

value: HA


title: PLM4d_scRNA-seq


title: Embryo,E18,RNA_batch42


title: RT112_siZBED2-2_rep1 [D763T36]

description:
Sample 15
RT112 Bladder Cancer Cell line treated with siZBED2 number 2 replicate 1


title: dLNs_HA_24h_rep4


title: RT112_siCt2_rep1 [D763T34]

description:
Sample 13
RT112 Bladder Cancer Cell line treated with siControl number 2 replicate 1


title: PLM4c_scRNA-seq


title: Embryo,E18,RNA_batch41


title: dLNs_HA_7d_rep2

source_name: dLNs, HA, 7d


title: dLNs_HA/CAF01_24h_rep4

source_name: dLNs, HA/CAF01, 24h


title: Embryo,E18,RNA_batch40


title: SCaBER_siF-1_siZ-2_rep2 [D763T33]

description:
Sample 12
SCaBER Bladder Cancer Cell line treated with siFOXA1 number 1 and siZBED2 number 2 replicate 2

value: SCaBER

value: siFOXA1.1 and siZBED2.2


title: PLM4a_scRNA-seq


title: SCaBER_siF-1_siZ-1_rep2 [D763T32]

description:
Sample 11
SCaBER Bladder Cancer Cell line treated with siFOXA1 number 1 and siZBED2 number 1 replicate 2


title: dLNs_HA/GLA-SE_24h_rep3

source_name: dLNs, HA/GLA-SE, 24h

value: HA/GLA-SE


title: PLM3d_scRNA-seq


title: Embryo,E20RNA_batch39


title: dLNs_HA_24h_rep3


title: PLM3c_scRNA-seq


title: SCaBER_siFOXA1-1_rep2 [D763T31]

description:
Sample 10
SCaBER Bladder Cancer Cell line treated with siFOXA1 number 1 replicate 2


title: SCaBER_siZBED2-2_rep2 [D763T30]

description:
Sample 9
SCaBER Bladder Cancer Cell line treated with siZBED2 number 2 replicate 2


title: dLNs_HA/GLA-SE_7d_rep3

source_name: dLNs, HA/GLA-SE, 7d


title: Embryo,E20RNA_batch37


title: SCaBER_siZBED2-1_rep2 [D763T29]

description:
Sample 8
SCaBER Bladder Cancer Cell line treated with siZBED2 number 1 replicate 2


title: dLNs_HA/CAF01_24h_rep3


title: PLM3b_scRNA-seq


title: PLM3a_scRNA-seq


title: PLM4b_scRNA-seq


title: dLNs_HA_24h_rep2


title: dLNs_HA/GLA-SE_24h_rep2


title: Embryo,E20RNA_batch35


title: PLM2c_scRNA-seq


title: SCaBER_siF-1_siZ-2_rep1 [D763T27]

description:
Sample 6
SCaBER Bladder Cancer Cell line treated with siFOXA1 number 1 and siZBED2 number 2 replicate 1


title: SCaBER_siF-1_siZ-1_rep1 [D763T26]

description:
Sample 5
SCaBER Bladder Cancer Cell line treated with siFOXA1 number 1 and siZBED2 number 1 replicate 1


title: PLM2b_scRNA-seq


title: Embryo,E20RNA_batch34


title: PLM2a_scRNA-seq


title: Embryo,E22,RNA_batch33


title: Embryo,E20RNA_batch38


title: dLNs_HA/GLA-SE_7d_rep2


title: Embryo,E22,RNA_batch32


title: PLM1d_scRNA-seq


title: Embryo,E20RNA_batch36


title: Embryo,E22,RNA_batch31


title: SCaBER_siZBED2-2_rep1 [D763T24]

description:
Sample 3
SCaBER Bladder Cancer Cell line treated with siZBED2 number 2 replicate 1


title: SCaBER_siCt2_rep2 [D763T28]

description:
Sample 7
SCaBER Bladder Cancer Cell line treated with siControl number 2 replicate 2


title: PLM1c_scRNA-seq


title: SCaBER_siZBED2-1_rep1 [D763T23]

description:
Sample 2
SCaBER Bladder Cancer Cell line treated with siZBED2 number 1 replicate 1


title: PLM1b_scRNA-seq


title: dLNs_HA/CAF01_7d_rep2

source_name: dLNs, HA/CAF01, 7d


title: SCaBER_siCt2_rep1 [D763T22]

description:
Sample 1
SCaBER Bladder Cancer Cell line treated with siControl number 2 replicate 1


title: dLNs_HA/CAF01_24h_rep2


title: Embryo,E22,RNA_batch30


title: dLNs_HA/CAF01_7d_rep1


title: Embryo,E22,RNA_batch29


title: dLNs_HA/GLA-SE_7d_rep1


title: dLNs_HA/CAF01_24h_rep1


title: RT112_F_22 [D373T24]

description:
Sample 16
RT112 bladder cancer cell line treated CrispR FOXA1 guide 1 clone F_22

data_processing:
Sequencer: NovaSeq - S1
Read length: 100bp
STAR: STAR_2.6.1a_08-27
GTF Annotation: gencode.v29.annotation.gtf
Index Adapters: Lexogen-Unique Dual index (96 Indexes)
Genome_build: human hg38
Supplementary_files_format_and_content: CrispR_FOXA1_tablecounts_raw.csv: Matrix table with raw counts for every gene and every sample.
Supplementary_files_format_and_content: CrispR_FOXA1_tablecounts_tpm.csv: Matrix table with TPM normalized counts for all samples and all genes.
Supplementary_files_format_and_content: pipeline_config.txt
Supplementary_files_format_and_content: adapter_list.txt
Supplementary_files_format_and_content: index_list.txt

growth_protocol: RT112 were cultured in RPMI +10% FBS, SD48 in DMEM + 10% FBS.

extract_protocol:
RNA extraction was performed using RNeasy kit (Qiagen).
3' mRNA-Seq library Prep Kit - FWD-Lexogen.

treatment_protocol: See paper for more details.

value: CrispR FOXA1

tag: sgrna


title: PLM1a_scRNA-seq


title: SCaBER_siFOXA1-1_rep1 [D763T25]

description:
Sample 4
SCaBER Bladder Cancer Cell line treated with siFOXA1 number 1 replicate 1


title: Tonsil, Infected Macaque (day 14)

city: Paris

last: Segura

address: 156 rue de Vaugirard

department: INSERM U1151

institute: INSERM

description: 10x Genomics

data_processing:
Sequencing reads were aligned to the UCSC Macaca fascicularis (v1.0) transcriptome using the Cell Ranger suite with default parameters.
Assembly: Macaca fascicularis (v1.0)
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: tonsil

extract_protocol:
Cellular suspension (3000 cells) was loaded on a 10X Chromium instrument (10X Genomics) according to manufacturer’s protocol. Single-cell RNA-Seq libraries were prepared using Chromium Single Cell 3’ v3.1 Reagent Kit (10X Genomics) according to manufacturer’s protocol.
Indexed libraries were equimolarly pooled and sequenced on an Illumina NovaSeq 6000 using paired-end 26x91bp as sequencing mode.

value: tonsil

tag: infection

value: Influenza virus (day 14)

value: antigen presenting cells


title: RT112_F_14 [D373T22]

description:
Sample 15
RT112 bladder cancer cell line treated CrispR FOXA1 guide 1 clone F_14


title: dLNs_HA_7d_rep1


title: Embryo,E22,RNA_batch27

value: in vitro

value: Embryo


title: PLF10d_scRNA-seq


title: Tonsil, Infected Macaque (day 5)

description: 10x Genomics

value: Influenza virus (day 5)


title: PLF10c_scRNA-seq

value: longitudinal


title: dLNs_HA_24h_rep1


title: dLNs_HA/GLA-SE_24h_rep1


title: Tonsil, Naive Macaque

description: 10x Genomics

value: Naive


title: PLF10b_scRNA-seq

value: PBMC


title: RT112_F_10 [D373T20]

description:
Sample 13
RT112 bladder cancer cell line treated CrispR FOXA1 guide 1 clone F_10


title: S.islandicus.REY15A.cbp1.ChIP-seq.TFB1.replicate2

city: London

first: Finn

last: Werner

address: Gower Street

department: Institute of Structural and Molecular Biology

country: United Kingdom

institute: University College London

data_processing:
Paired-end reads were mapped using Bowtie v1.1.2 [30] with parameters -v 2 -m 1 --fr over the first 50 nt allowing only for uniquely mapped  read pairs to be included
We sampled from the alignments to obtain a defined fragment size distribution (normal distribution, mean 120 bp, sd 18 bp) using a custom R script (https://github.com/fblombach/ChIP-seq/blob/master/read_sampling.R)
Coverage normalized to input ("normRatio") was calculated using deeptools bamCompare with SES scaling (10,000 bins, 200 bp bin width)
Assembly: NC_017276.1
Supplementary files format and content: bigwig files with occupancy normalised against the chromatin input samples, scaled by the Signal Extraction Scaling method

organism: Saccharolobus islandicus REY15A

source_name: microbial cells

growth_protocol: Strains were grown in Brock medium supplemented with 0.2% sucrose, 0.2% tryptone, and 20 µg/ml uracil at 75 °C in Erlenmeyer shake flasks at 150 rpm

extract_protocol:
Qiagen QIAquick PCR purification
NEBNext Ultra II DNA library prep kit for Illumina

value: cbp1, pyrEF, lacS

tag: chip antibody

value: microbial cells


title: Embryo,E21,RNA_batch25

value: WT


title: RT112_C_C5 [D373T16]

description:
Sample 12
RT112 bladder cancer cell line treated CrispR control scramble clone C_C5

value: CrispR control

value: Scramble


title: S.islandicus.REY15A.cbp1.ChIP-seq.TFB1.replicate1


title: Embryo,E24,RNA_batch26


title: RT112_C_C4 [D373T15]

description:
Sample 11
RT112 bladder cancer cell line treated CrispR control scramble clone C_C4


title: Embryo,E21,RNA_batch24


title: PLF9d_scRNA-seq

value: female


title: S.islandicus.REY15A.E234.ChIP-seq.TFB1.replicate2

value: E234 (pyrEF, lacS)


title: PLF9c_scRNA-seq


title: Embryo,E22,RNA_batch28


title: PLF9b_scRNA-seq


title: S.islandicus.REY15A.E234.ChIP-seq.TFB1.replicate1


title: Embryo,E25,RNA_batch22


title: RT112_C_C1 [D373T13]

description:
Sample 10
RT112 bladder cancer cell line treated CrispR control scramble clone C_C1


title: Embryo,E24,RNA_batch21


title: SD48_F_310 [D373T12]

description:
Sample 9
SD48 bladder cancer cell line treated CrispR FOXA1 guide 1 and guide 2 clone F_310

value: CrispR FOXA1


title: RT112_F_13 [D373T21]

description:
Sample 14
RT112 bladder cancer cell line treated CrispR FOXA1 guide 1 clone F_13


title: PLF9a_scRNA-seq


title: Embryo,E24,RNA_batch20


title: SD48_F_301 [D373T11]

description:
Sample 8
SD48 bladder cancer cell line treated CrispR FOXA1 guide 1 and guide 2 clone F_301


title: PLF8d_scRNA-seq


title: PLF10a_scRNA-seq


title: lreu-1000x-lpla-1x_ctr-mup_r1_m_r_v2

city: Solna

first: Vicent

last: Pelechano

address: Nobels väg 16

department: MTC

institute: ScilifeLab - Karolinska Institutet

description: Mixture ratio of RNA prior RNA ligation: 1000x(L. reuteri):1x(L. plantarum)

data_processing:
Adapter and quality trimming with the bbduk program of the BBTools suite, with options {qtrim=r, ktrim=r, hdist=3, hdist2=2, K=20, mink=14, trimq=16, minlen=30, maq=16}, using BBTools default adapter set and polyG or polyA sequences for short reads.
Deduplication of reads with both identical unique molecular identifier (UMI) and insert sequence using the dedupe program of the BBTools suite with its default parameters.
UMI sequences found in the first eight bases of each read were extracted using UMI-tools (version 1) with default options (using --bc-pattern NNNNNNNN).
Alignment was performed with the bbmap program of the BBTools suite, with the {32bit=t -da -eoom k=11 strictmaxindel=10 intronlen=0 t=16 trd=t minid=0.94 nzo=t} parameters. Alignment files were sorted and indexed with SAMtools.
Deduplication based on UMIs was then performed with UMI-tools (version 1) with options { --soft-clip-threshold 1 --edit-distance 2 --method unique}.
In selected samples, a dual undex strategy was used (sequencing runs v17). In brief, in addition of the Illumina indexes with dedicated reads used in HT-5Pseq, an additional index sequence is added before the UMI sequence. This is introduced during the ssRNA ligation space using anoligo with the following structure Illumina compatible-CCCCCC-NNNNNNNN. Please see dual_index_demultiplexing.txt for details on demultiplexing strategy for those samples.
Bedgraphs for read 5' positions for forward (fwd) and reverse (rev) strands were generated with BEDTools genomecov program with options {-bg -strand [+/-] -5}.
Genome_build: The genome used for alignment is indicated in the processed file names with the G-xxxx patterns. Those correspond to the following NCBI accessions and builds: G-bamy (Bacillus amyloliquefaciens: GCF_000196735.1), G-bsub (Bacillus subtilis: GCF_000009045.1), G-cvib (Caulobacter vibrioides/crescentus: GCF_000006905.1), G-ecol (Escherichia coli: GCF_000005845.2), G-spcc (Synechocystis sp. PCC 6803: GCF_000009725.1), G-lpla (Lactobacillus plantarum: GCF_000203855.3), G-lreu (Lactobacillus reuteriGCF_000016825.1), G-zymo (mix of the following genomes [Bacillus subtilis: GCF_000009045.1, Enterococcus faecalis: GCF_000007785.1, Escherichia coli: GCF_000005845.2, Lactobacillus fermentum: GCF_000010145.1, Listeria monocytogenes: GCF_000196035.1, Pseudomonas aeruginosa: GCF_000006765.1, Salmonella enterica: GCF_000006945.2, Staphylococcus aureus: GCF_000013425.1]), G-46genera (genomes from 46 genera listed in the Supplementary file).
Genome_build: Reference indiced for individual bacterial species and custom mixtures were built with the bbmap program of the BBTools suite, with default options (and k=10). See details in the supplementary file "46genera.xls". In Brief: Akkermansia muciniphila ATCC BAA-835 (GCF_000020225.1); Alistipes finegoldii DSM 17242 (GCF_000265365.1); Alistipes obesi (GCF_000311925.1); Alistipes putredinis DSM 17216 (GCF_000154465.1); Alistipes shahii WAL 8301 (GCF_000210575.1); Anaerobutyricum hallii DSM 3353 (GCF_000173975.1); Atopobium vaginae DSM 15829 (GCF_000159235.2); Bacillus amyloliquefaciens DSM 7 = ATCC 23350 (GCF_000196735.1); Bacillus subtilis subsp. subtilis str. 168 (GCF_000009045.1); Bacillus subtilis subsp. subtilis str. 168 (GCF_000009045.1); Bacteroides caccae (GCF_002222615.2); Bacteroides cellulosilyticus (GCF_001318345.1); Bacteroides coprocola DSM 17136 (GCF_000154845.1); Bacteroides coprophilus DSM 18228 = JCM 13818 (GCF_000157915.1); Bacteroides faecichinchillae JCM 17102 (GCF_000614145.1); Bacteroides fluxus YIT 12057 (GCF_000195635.1); Bacteroides fragilis YCH46 (GCF_000009925.1); Bacteroides ovatus (GCF_001314995.1); Bacteroides plebeius DSM 17135 (GCF_000187895.1); Bacteroides salanitronis DSM 18170 (GCF_000190575.1); Bacteroides salyersiae WAL 10018 = DSM 18765 = JCM 12988 (GCF_000381365.1); Bacteroides stercoris ATCC 43183 (GCF_000154525.1); Bacteroides thetaiotaomicron VPI-5482 (GCF_000011065.1); Bacteroides uniformis ATCC 8492 (GCF_000154205.1); Bilophila wadsworthia ATCC 49260 (GCF_000701705.1); Caulobacter vibrioides CB15 (GCF_000006905.1); Clostridium phoceensis (GCF_001244495.1); Collinsella aerofaciens ATCC 25986 (GCF_000169035.1); Coprobacter fastidiosus NSB1 (GCF_000473955.1); Coprococcus comes ATCC 27758 (GCF_000155875.1); Culturomica massiliensis (GCF_900091655.1); Desulfovibrio fairfieldensis (GCF_001553605.1); Dorea formicigenerans ATCC 27755 (GCF_000169235.1); Dorea longicatena DSM 13814 (GCF_000154065.1); Enterococcus faecalis V583 (GCF_000007785.1); [Clostridium] innocuum 2959 (GCF_000371425.1); [Clostridium] saccharogumia DSM 17460 (GCF_000686665.1); Escherichia coli str. K-12 substr. MG1655 (GCF_000005845.2); Escherichia coli str. K-12 substr. MG1655 (GCF_000005845.2); Eubacterium ventriosum ATCC 27560 (GCF_000153885.1); Faecalibacterium prausnitzii A2-165 (GCF_000162015.1); Flavobacterium johnsoniae UW101 (GCF_000016645.1); Flavobacterium saccharophilum (GCF_900142735.1); Fusicatenibacter saccharivorans (GCF_001405555.1); Gardnerella vaginalis 409-05 (GCF_000025205.1); Synechocystis sp. PCC 6803 (cyanobacteria) (GCF_000009725.1); Gemmiger formicilis (GCF_900167555.1); Intestinimonas butyriciproducens (GCF_001454945.1); Lactobacillus plantarum WCFS1 (GCF_000203855.3); Lactobacillus reuteri DSM 20016 (GCF_000016825.1); Lactobacillus crispatus ST1 (GCF_000091765.1); Lactobacillus iners DSM 13335 (GCF_000160875.1); Lactobacillus fermentum IFO 3956 (GCF_000010145.1); Lactococcus lactis subsp. lactis Il140 (GCF_000006865.1); Lacunisphaera limnophila (GCF_001746835.1); Listeria monocytogenes EGD-e (GCF_000196035.1); Mediterranea massiliensis (GCF_900128475.1); Megasphaera genomosp. type_1 str. 28L (GCF_000177555.1); Microbacterium barkeri 2011-R4 (GCF_000299315.2); Mucilaginibacter gossypiicola (GCF_900110105.1); Odoribacter splanchnicus DSM 20712 (GCF_000190535.1); Parabacteroides distasonis ATCC 8503 (GCF_000012845.1); Parabacteroides goldsteinii DSM 19448 = WAL 12034 (GCF_000969835.1); Prevotella amnii DSM 23384 = JCM 14753 (GCF_000378745.1); Prevotella bivia DSM 20514 (GCF_000262545.1); Prevotella buccalis ATCC 35310 (GCF_000177075.1); Prevotella timonensis 4401737 = DSM 22865 = JCM 15640 (GCF_000455445.1); Pseudomonas fluorescens F113 (GCF_000237065.1); Pseudomonas protegens CHA0 (GCF_000397205.1); Pseudomonas aeruginosa PAO1 (GCF_000006765.1); Rhodanobacter fulvus Jip2 (GCF_000264315.1); Romboutsia timonensis (GCF_900106845.1); Roseburia hominis A2-183 (GCF_000225345.1); Roseburia inulinivorans DSM 16841 (GCF_000174195.1); Ruthenibacterium lactatiformans (GCF_000949455.1); Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (GCF_000006945.2); Sneathia sanguinegens (GCF_001517935.1); Staphylococcus aureus subsp. aureus NCTC 8325 (GCF_000013425.1); Streptococcus salivarius (GCF_000785515.1); Streptococcus thermophilus JIM 8232 (GCF_000253395.1); [Eubacterium] rectale ATCC 33656 (GCF_000020605.1); [Eubacterium] siraeum DSM 15702 (GCF_000382085.1) and  Ureaplasma parvum serovar 3 str. ATCC 27815 (GCF_000019345.1).
Supplementary_files_format_and_content: Processed files are bedgraphs containing read 5' counts on reverse (_rev) and forward (_fwd) strands of genomes indicated with _G-xxxx pattern. The genomes corresponding to each pattern are described in the genome build entry above.

organism:
Lactiplantibacillus plantarum
Limosilactobacillus reuteri

source_name: Individual Liquid culture of Lactobacillus plantarum (ATCC 8014) and Lactobacillus reuteri (DSM17938.

growth_protocol: Bacteria were grown according to their requirements. Overnight Cultures were diluted to OD600 0.05-0.07, growth was continued and cells were harvested in log-phase by centrifugation. Resulting pellet was shock-frozen in Dry ice/Ethanol bath and stored for RNA analysis

extract_protocol:
Microbial cell pellets were resuspended in equal volume of LET (25 mM Tris pH 8.0, 100 mM LiCl, 20 mM EDTA) and water saturated Phenol pH 6.6 (Thermo Fisher),  lysed with acid washed glass beads (Sigma-Aldrich) and vortexing for three minutes in MultiMixer. Lysates were supplemented  with equal volumes of phenol/chloroform isoamyl alcohol pH 4.5 (25:24:1) and nuclease free water, l two-minute vortexing followed by centrifugation. Resulting aqueous phase was purified in two steps using phenol-chloroform isoamyl alcohol (25:24:1) followed by chloroform. After centrifugation, the clean aqueous phase was precipitated with sodium acetate-ethanol.
Standard and random fragmented 5PSeq libraries were generated as described in PMID: 26046441 with minor modifications using 150-9000ng total RNA as an input. To prepare random fragmented samples (negative controls), ribosomal RNA was depleted from DNA-free RNA and subsequent fragmented by incubating five minutes at 80 ̊C in fragmentation buffer (40mM Tris Acetate pH 8.1, 100mM KOAc and 30mM MgOAc). Reaction was purified using 2 volumes of RNACleanXP beads (Beckman Coulter) as recommended by the manufacturer. Free 5’OH sites were re-phosphorylated using 5 Units of T4 Polynucleotide kinase (PNK, NEB) and incubated at 37 ̊C for 60 minutes as recommended by the manufacturer. Re-phosphorylated fragmented RNA was purified using Phenol:Chloroform: Isoamyl Alcohol (24:25:1), followed by sodium acetate-ethanol precipitation. From this step forward, procedures for random fragmented and standard 5PSeq library preparation merge. RNA was Ligated to either rP5_RND or rP5_RNA oligo (specified in characteristics protocol).    containing unique molecular identifiers). Ribosomal RNA was depleted using Ribozero rRNA removal kit (Illumina) suitable for Bacteria and Yeast. rRNA depleted sample was purified using 1.8V of Ampure beads (Abcam), fragmented using heat (80˚C) for 5 min in 5x Fragmentation Buffer (200mM Tris Acetate pH 8.1,500mM KOAc,150mM MgOAc) and reverse transcribed using random hexamers to prime. Resulting cDNA was bound to streptavidin beads (M-280), subjected to enzymatic reactions of DNA end repair, fill-in of adenine to 5’ protruding ends of DNA fragments using Klenow Fragment (NEB). Common adaptor (P7-MPX) was ligated and 5PSeq Libraries were amplified by PCR (15- 17 cycles). Purified samples were quantified using Qubit (Thermo Fisher), library size was estimated from bioanalyzer traces. 5PSeq Libraries were pooled by mixing equal amounts of each sample, following enrichment of fragments of the length between 300-500nt.   HT-5PSeq Libraries were generated as recently described (bioRxiv 2020.06.22.165134; doi: https://doi.org/10.1101/2020.06.22.165134). In brief, DNA-free RNA was ligated with RNA oligos containing unique molecular identifiers. Ligated RNA was reverse transcribed priming with oligos containing a random hexamer and an Illumina compatible region. RNA was eliminated by addition of NaOH. Ribosomal RNA was depleted by adding in-house rRNA DNA oligo depletion mixes (table 2) to the cDNA and performing a duplex-specific nuclease (DSN, Evrogen) treatment. rRNA depleted cDNA was PCR amplified (15-17 cycles). Depletion of ribosomal RNA with Ribozero Illumina (for bacteria and yeast) was done after the single-stranded RNA ligation step. Ribosomal depleted RNA was purified and reverse transcribed using the same oligos as stated above, and then amplified by PCR. Libraries were quantified by fluorescence (Qubit, Thermo Fisher), size estimated using an Agilent Bioanalyzer and sequence using a NextSeq500 Illumina sequencer.
5PSeq that captures  transcripts with free 5' phospahte (without cap)

treatment_protocol: As for Chloramphenicol (CAM) treatment, Bacterial cells were incubated with Chloramphenicol (100µg/ml final) for 5 minutes at 37˚C with aeration and harvested at 4˚C on ice supplemented with Chloramphenicol (~100µg/ml final).   Mupirocin (MUP) was added to bacterial culture at a final concentration of 65µg/ml and incubated for 10 minutes at 37˚C with aeration.   Cultures for stationary growth phase samples were inoculated with single colony and harvested at indicated times post-inoculation.   Salt stress samples were generated as described in PMID: 28290514 with minor modifications Salt stress was initiated by mixing equal volumes of bacterial growth culture and 2M NaCl (~5.8% NaCl). Bacterial cells were exposed to salt stress for 10 minutes at room temperature and harvested by centrifugation.   Cultures for stationary growth phase samples were inoculated with single colony and harvested at indicated times post-inoculation.   Heat shock experiments were setup the following. Lactobacillus plantarum (ATCC 8014) growth culture was harvested by centrifugation and heat shock was induced by resuspending cell pellet in prewarmed broth media following 15-minute incubation at 60˚C.   To generate low nutrient samples, actively growing Lactobacillus plantarum (ATCC 8014) culture was harvested by centrifugation. Low nutrient stress was induced for 15 minutes beginning with excessive washing of the cell pellet with Low nutrient media (0.5x LB broth), followed by centrifugation. Washed cell pellet was resuspended in 0.5x LB broth, incubated at 37˚C for the remaining time.   Polyribosome fractions were generated as described in PMID: 27146487 with minor modifications. For short, exponentially grown bacterial cells were harvested by centrifugation (5 minutes) at 4˚C on ice supplemented with 100µg/ml Chloramphenicol. Lysis was done in 1xTN buffer (50mM TRIS/HCl pH 7.4,150mM NaCl, 1mM DTT, 100μg/ml CAM and Complete EDTA Free Protease inhibitor tablet) using glass beads and of vortexing (2minutes) followed by resting of sample on ice (5 minutes).  Vortexing/resting cycle was repeated two more times. Lysate was cleared by centrifugation at 1500g for 5 minutes at 4˚C. Resulting supernatant was loaded on to a 15-50% sucrose gradient with a 80% cushion and sedimentation was accomplished by ultracentrifugation for 90 minutes at 36,000rpm. Fractions were collected and A254 value was monitored. Subsequently, RNA was extracted from sucrose fractions by adding equal volumes of phenol/chloroform isoamyl alcohol pH 4.5 (25:24:1) and nuclease free water followed by 2-minute vortexing and centrifugation. Aqueous phase was further cleaned up by the addition of Chloroform, vortexing and centrifugation. Resulting aqueous phase was sodium acetate-ethanol precipitated.

value: Untreated/65microg/ml Mupirocin incubated for 5 minutes at 37

tag: culture conditions

value: lreu_ctr_rep2 OD600 0.56 and lpla_mup_technical _rep _of _rep2 OD600 0.47

tag: library protocol

value: Standard 5PSeq, RNA rP5_RND oligo for RNA ligation

tag: ribosomal rna delpetion strategy

value: Ribo-Zero rRNA Removal Kit (Bacteria) Illumina


title: lreu-10000x-lpla-1x_ctr-mup_r1_m_r_v2

description: Mixture ratio of RNA prior RNA ligation: 10000x(L. reuteri):1x(L. plantarum)


title: SD48_F_132 [D373T10]

description:
Sample 7
SD48 bladder cancer cell line treated CrispR FOXA1 guide 1 clone F_132

tag: cell line


title: PLF8c_scRNA-seq

tag: cell type


title: Embryo,E21,RNA_batch18

value: in vitro

value: Embryo

tag: genotype

tag: time


title: SD48_F_122 [D373T07]

description:
Sample 6
SD48 bladder cancer cell line treated CrispR FOXA1 guide 1 clone F_122


title: Embryo,E21,RNA_batch23


title: SD48_F_114 [D373T06]

description:
Sample 5
SD48 bladder cancer cell line treated CrispR FOXA1 guide 1 clone F_114


title: PLF8b_scRNA-seq

tag: cohort

tag: disease state

value: longitudinal


title: Embryo,E25,RNA_batch17


title: PLF8a_scRNA-seq

tag: gender

tag: group


title: lreu-1x-lpla-1x_ctr-ctr_r1_m_r_v1

description: Mixture ratio of RNA prior RNA ligation:1x(L. reuteri):1x(L. plantarum)

tag: treatment

value: Untreated/Untreated

value: lreu_ctr_rep2 OD600 0.56 and lpla_ctr_rep2 OD600 0.47

value: Standard 5PSeq


title: Embryo,E25,RNA_batch16


title: SD48_F_110 [D373T05]

description:
Sample 4
SD48 bladder cancer cell line treated CrispR FOXA1 guide 1 clone F_110


title: PLF7d_scRNA-seq

value: PBMC


title: lreu-1x-lpla-1x_ctr-cam_r1_m_r_v1

value: Untreated/ Chloramphenicol incubated for 5 minutes at 37C

value: lreu_ctr_rep2 OD600 0.56 and lpla_cam_rep2 OD600 0.47


title: SD48_C_021 [D373T03]

description:
Sample 3
SD48 bladder cancer cell line treated CrispR control scramble clone C_021

value: CrispR control

value: Scramble


title: lreu-10x-lpla-1x_ctr-mup_r1_m_r_v1

description: Mixture ratio of RNA prior RNA ligation: 10x(L. reuteri):1x(L. plantarum)

value: lreu_ctr_rep2 OD600 0.56 and lpla_mup_rep2 OD600 0.47


title: Embryo,E25,RNA_batch15

value: WT


title: PLF7c_scRNA-seq

value: female


title: PLF7b_scRNA-seq


title: Embryo,E21,RNA_batch19


title: lreu-1x-lpla-1x_ctr-mup_r1_m_r_v1

value: Untreated/65microg/ml Mupirocin incubated for 5 minutes at 37


title: SD48_C_003 [D373T01]

description:
Sample 1
SD48 bladder cancer cell line treated CrispR control scramble clone C_003


title: Embryo,E25,RNA_batch14


title: PLF7a_scRNA-seq


title: lreu-100x-lpla-1x_ctr-mup_r1_m_r_v1

description: Mixture ratio of RNA prior RNA ligation: 100x(L. reuteri):1x(L. plantarum)

value: Untreated/65microg/ml Mupirocin incubated for 5 minutes at 37C


title: Embryo,E23,RNA_batch13


title: lreu-10x-lpla-1x_ctr-cam_r1_m_r_v1

value: Untreated/100microg/ml  Chloramphenicol incubated for 5 minutes at 37C

value: Ribo-Zero rRNA Removal Kit (Bacteria) Illumina


title: Embryo,E23,RNA_batch12

value: in vitro

value: Embryo


title: lreu-100x-lpla-1x_ctr-ctr_r1_m_r_v1

value: Untreated/Untreated


title: RT112_siFOXA1-2_rep2 [D373T64]

description:
Sample 16
RT112 cell line treated with siFOXA1 num 2 replicate 2

data_processing:
Sequencer: NovaSeq - S1
Read length: 100bp
STAR: STAR_2.6.1a_08-27
GTF Annotation: gencode.v29.annotation.gtf
Index Adapters: Lexogen-Unique Dual index (96 Indexes)
Genome_build: human hg38
Supplementary_files_format_and_content: FOXA1KD_tablecounts_raw.csv: Matrix table with raw counts for every gene and every sample.
Supplementary_files_format_and_content: FOXA1KD_tablecounts_tpm.csv: Matrix table with TPM normalized counts for all samples and all genes.
Supplementary_files_format_and_content: pipeline_config.txt
Supplementary_files_format_and_content: adapter_list.txt
Supplementary_files_format_and_content: index_list.txt

treatment_protocol: Cells were transfected using Lipfectamine RNAi Max and 10nM of siRNA. See paper for more details.

tag: experiment batch replicate


title: PLF6d_scRNA-seq

value: longitudinal


title: RT112_siFOXA1-1_rep2 [D373T63]

description:
Sample 15
RT112 cell line treated with siFOXA1 num 1 replicate 2


title: Embryo,E23,RNA_batch11


title: lreu-100x-lpla-1x_ctr-cam_r1_m_r_v1

value: Untreated/100microg/ml Chloramphenicol incubated for 5 minutes at 37C

value: Standard 5PSeq


title: S.islandicus.REY15A.cbp1.ChIP-seq.CreN7.replicate2

value: cbp1, pyrEF, lacS

value: microbial cells


title: Embryo,E23,RNA_batch10


title: PLF6b_scRNA-seq

value: PBMC


title: PLF6c_scRNA-seq


title: RT112_siCt-1_rep2 [D373T61]

description:
Sample 13
RT112 cell line treated with siControl num 1 replicate 2


title: lreu-10x-lpla-1x_ctr-ctr_r1_m_r_v1

value: lreu_ctr_rep2 OD600 0.56 and lpla_ctr_rep2 OD600 0.47


title: PLF6a_scRNA-seq


title: SD48_C_010 [D373T02]

description:
Sample 2
SD48 bladder cancer cell line treated CrispR control scramble clone C_010

value: CrispR control

value: Scramble


title: S.islandicus.REY15A.cbp1.ChIP-seq.CreN7.replicate1


title: S.islandicus.REY15A.E234.ChIP-seq.CreN7.replicate2

value: E234 (pyrEF, lacS)


title: RT112_siFOXA1-2_rep1 [D373T60]

description:
Sample 12
RT112 cell line treated with siFOXA1 num 2 replicate 1


title: Embryo,E23,RNA_batch9

value: WT


title: Embryo,E23,RNA_batch8


title: PLF5d_scRNA-seq

value: female


title: PLF5c_scRNA-seq


title: RT112_siFOXA1-1_rep1 [D373T59]

description:
Sample 11
RT112 cell line treated with siFOXA1 num 1 replicate 1


title: Embryo,E16,RNA_batch7


title: S.islandicus.REY15A.E234.ChIP-seq.CreN7.replicate1


title: Embryo,E16,RNA_batch6


title: RT112_siCt2_rep1 [D373T58]

description:
Sample 10
RT112 cell line treated with siControl num 2 replicate 1


title: PLF5b_scRNA-seq


title: S.solfataricus.P2.ChIP-seq.Cbp1.replicate1

description:
13834X2
HiSeq 125 Cycle Paired-End Sequencing v4

data_processing:
Paired-end reads were mapped using Bowtie v1.1.2 [30] with parameters -v 2 -m 1 --fr over the first 50 nt allowing only for uniquely mapped  read pairs to be included
We sampled from the alignments to obtain a defined fragment size distribution (normal distribution, mean 120 bp, sd 18 bp) using a custom R script (https://github.com/fblombach/ChIP-seq/blob/master/read_sampling.R)
Coverage normalized to input ("normRatio") was calculated using deeptools bamCompare with SES scaling (10,000 bins, 200 bp bin width), chromatin input samples for these IPs were previously deposited at NCBI GEO (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE141286)
Assembly: NC_002754.1
Supplementary files format and content: bigwig files with occupancy normalised against the chromatin input samples, scaled by the Signal Extraction Scaling method

organism: Saccharolobus solfataricus P2

growth_protocol: S. solfataricus P2 was grown in Brock medium supplemented with 0.2% glucose, 0.1% tryptone, and 20 µg/ml uracil at 75 °C in Erlenmeyer shake flasks at 150 rpm


title: RT112_siCt2_rep2 [D373T62]

description:
Sample 14
RT112 cell line treated with siControl num 2 replicate 2


title: Embryo,E16,RNA_batch5


title: RT112_siCt-1_rep1 [D373T57]

description:
Sample 9
RT112 cell line treated with siControl num 1 replicate 1


title: PLF5a_scRNA-seq


title: SCaBER_siFOXA1-1_rep2 [D373T52]

description:
Sample 8
SCaBER cell line treated with siFOXA1 num 1 replicate 2

value: SCaBER


title: S.islandicus.REY15A.cbp1.Cappable-seq.replicate2

data_processing:
library strategy: Cappable-seq
In order to remove poly(A)-tails and adaptors, we trimmed the reads using the program Cutadapt in two rounds with the following settings to prevent trimming of naturally occurring A-rich RNAs due to the low GC-content of the S. islandicus REY15A genome: (i) -a “A{15}” -e 0 -m 15 to remove all poly(A) stretches of at least 15 nt length plus downstream regions and (ii) -a “A{15}”X -e 0 -O 5 to terminal shorter poly(A) stretches of minimum 5 nt length.
Trimmed and untrimmed reads were split into separate fastq files using awk.
Both fastq files were aligned to the S. islandicus REY15A genome using bowtie v1.2.2 61 (parameters -v 1 -m 1 –-best –-strata -S) with untrimmed 75 nt reads shortened to 71 nt (-3 4)
The bam file output was merged, sorted and indexed using SAMtools
Read 5'-end coverage  per strand was calculated using bedtools genomecov
Assembly: NC_017276.1
Supplementary files format and content: Big wig file with read 5'-end coverage per strand

extract_protocol:
15 ml cell culture was rapidly mixed with 30 ml pre-cooled RNAprotect Bacteria Reagent (Qiagen) placed in an ice bath. Cells were harvested by centrifugation (5 min at 4000 x g at 4 ºC). Pellets were immediately subjected to RNA isolation using the mirVana miRNA isolation kit (Ambion) with an initial resuspension buffer volume of 200 µl following the protocol for small RNAs (20-200 nt length).
Library preparation and deep sequencing was conducted at Vertis Biotechnologie (Germany). In brief, 5’-triphosporylated RNA was capped with 3’-desthiobiotin-TEG-GTP (NEB)) using the Vaccinia virus Capping enzyme (NEB) and biotinylated RNA species were subsequently enriched by affinity purification using streptavidin beads yielding 0.6 to 1.3% of the sRNA preparation. The eluted RNA was poly-adenylated using E. coli Poly(A) polymerase and 5’-ends were converted to mono-phosphates by incubation with RNA 5’ Pyrophosphohydrolase (NEB). Subsequently, an RNA adapter was ligated to the newly formed 5'-monophosphate structures. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and the M- MLV reverse transcriptase at 42 ºC. The resulting cDNA was finally PCR-amplified (12 cycles) with TruSeq Dual Index sequencing primers (Illumina).


title: PLF4d_scRNA-seq


title: SCaBER_siFOXA1-2_rep2 [D373T51]

description:
Sample 7
SCaBER cell line treated with siFOXA1 num 2 replicate 2


title: Embryo,E16,RNA_batch3


title: Embryo,E16,RNA_batch4


title: S.islandicus.REY15A.cbp1.Cappable-seq.replicate1


title: PLF4c_scRNA-seq


title: SCaBER_siCt2_rep2 [D373T48]

description:
Sample 6
SCaBER cell line treated with siControl num 2 replicate 2


title: SCaBER_siCt1_rep2 [D373T47]

description:
Sample 5
SCaBER cell line treated with siControl num 1 replicate 2


title: Embryo,E16,RNA_batch2


title: S.islandicus.REY15A.E234.Cappable-seq.replicate1


title: Embryo,E16,RNA_batch1


title: PLF4b_scRNA-seq


title: PLF4a_scRNA-seq


title: SCaBER_siFOXA1-2_rep1 [D373T42]

description:
Sample 4
SCaBER cell line treated with siFOXA1 num 2 replicate 1


title: PLF3d_scRNA-seq


title: SCaBER_siFOXA1-1_rep1 [D373T41]

description:
Sample 3
SCaBER cell line treated with siFOXA1 num 1 replicate 1


title: S.solfataricus.P2.ChIP-seq.Cbp1.replicate2

description:
13834X10
HiSeq 125 Cycle Paired-End Sequencing v4


title: SCaBER_siCt2_rep1 [D373T38]

description:
Sample 2
SCaBER cell line treated with siControl num 2 replicate 1


title: ecol_hs_abx_02_v17 [mixed sample]

description: Culture: cultured in LB Broth at 37˚C to late-log growth phase, CAM & MUP cultures were supplemented with 100µg/ml Chloramphenicol or 65µg/ml Mupirocin for 10 minutes incubated for 10 min at 37˚C while 2ml of HS culture was centrifuged and pellet was resuspended in 65˚C pr-warmed LB, incubated for 10 minutes at 65˚C and harvested by centrifugation; Library: HT-5PSeq using indexed rP5_RNA (rP5_MPX_RNA) Adapters (CrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrU rXrXrXrXrXrX rNrNrNrNrNrNrNrN) carrying a sample barcode (rX) and unique molecular identifiers (rN) which were removed from the reads into the read headers. rRNA removal:  in-house Bacterial rRNA Depletion MIX for Cultures , oVP670

data_processing:
library strategy:  5PSeq that captures  transcripts with free 5' phospahte (without cap)
Adapter and quality trimming with the bbduk program of the BBTools suite, with options {qtrim=r, ktrim=r, hdist=3, hdist2=2, K=20, mink=14, trimq=16, minlen=30, maq=16}, using BBTools default adapter set and polyG or polyA sequences for short reads.
Deduplication of reads with both identical unique molecular identifier (UMI) and insert sequence using the dedupe program of the BBTools suite with its default parameters.
UMI sequences found in the first eight bases of each read were extracted using UMI-tools (version 1) with default options (using --bc-pattern NNNNNNNN).
Dual index fastq samples were processed as described in supplementary file dual_index_demultiplexing.txt
Alignment was performed with the bbmap program of the BBTools suite, with the {32bit=t -da -eoom k=11 strictmaxindel=10 intronlen=0 t=16 trd=t minid=0.94 nzo=t} parameters. Alignment files were sorted and indexed with SAMtools.
Deduplication based on UMIs was then performed with UMI-tools (version 1) with options { --soft-clip-threshold 1 --edit-distance 2 --method unique}.
In selected samples, a dual undex strategy was used (sequencing runs v17). In brief, in addition of the Illumina indexes with dedicated reads used in HT-5Pseq, an additional index sequence is added before the UMI sequence. This is introduced during the ssRNA ligation space using anoligo with the following structure Illumina compatible-CCCCCC-NNNNNNNN. Please see dual_index_demultiplexing.txt for details on demultiplexing strategy for those samples.
Bedgraphs for read 5' positions for forward (fwd) and reverse (rev) strands were generated with BEDTools genomecov program with options {-bg -strand [+/-] -5}.
Assembly: The genome used for alignment is indicated in the processed file names with the G-xxxx patterns.  Those correspond to the NCBI accessions and builds indicated in the Supplementary file.
Supplementary files format and content: Reference indiced for individual bacterial species and custom mixtures were built with the bbmap program of the BBTools suite, with default options (and k=10).
Supplementary files format and content: Processed files are bedgraphs containing read 5' counts on reverse (_rev) and forward (_fwd) strands of genomes indicated with _G-xxxx pattern. The genomes corresponding to each pattern are described in the genome build entry above.

organism: Escherichia coli

source_name: A mixed sample of 5 cultures: ecol_ctr_r2-1_s_o_v17; ecol_hs_r2_s_o_v17; ecol_ctr_r2-2_s_o_v17; ecol_cam_r2_s_o_v17; ecol_mup_r2_s_o_v17

growth_protocol: Bacteria were grown according to their requirements. Overnight Cultures were diluted to OD600 0.01-0.07, growth was continued and cells were harvested in log-phase by centrifugation. Resulting pellet was shock-frozen in Dry ice/Ethanol bath and stored for RNA analysis

extract_protocol:
Microbial cell pellets were resuspended in equal volume of LET (25 mM Tris pH 8.0, 100 mM LiCl, 20 mM EDTA) and water saturated Phenol pH 6.6 (Thermo Fisher),  lysed with acid washed glass beads (Sigma-Aldrich) and vortexing for three minutes in MultiMixer. Lysates were supplemented  with equal volumes of phenol/chloroform isoamyl alcohol pH 4.5 (25:24:1) and nuclease free water, l two-minute vortexing followed by centrifugation. Resulting aqueous phase was purified in two steps using phenol-chloroform isoamyl alcohol (25:24:1) followed by chloroform. After centrifugation, the clean aqueous phase was precipitated with sodium acetate-ethanol.
Standard and random fragmented 5PSeq libraries were generated as described in PMID: 26046441 with minor modifications using 150-9000ng total RNA as an input. To prepare random fragmented samples (negative controls), ribosomal RNA was depleted from DNA-free RNA and subsequent fragmented by incubating five minutes at 80 ̊C in fragmentation buffer (40mM Tris Acetate pH 8.1, 100mM KOAc and 30mM MgOAc). Reaction was purified using 2 volumes of RNACleanXP beads (Beckman Coulter) as recommended by the manufacturer. Free 5’OH sites were re-phosphorylated using 5 Units of T4 Polynucleotide kinase (PNK, NEB) and incubated at 37 ̊C for 60 minutes as recommended by the manufacturer. Re-phosphorylated fragmented RNA was purified using Phenol:Chloroform: Isoamyl Alcohol (24:25:1), followed by sodium acetate-ethanol precipitation. From this step forward, procedures for random fragmented and standard 5PSeq library preparation merge. RNA was Ligated to either rP5_RND or rP5_RNA oligo (specified in characteristics protocol).    containing unique molecular identifiers). Ribosomal RNA was depleted using Ribozero rRNA removal kit (Illumina) suitable for Bacteria and Yeast. rRNA depleted sample was purified using 1.8V of Ampure beads (Abcam), fragmented using heat (80˚C) for 5 min in 5x Fragmentation Buffer (200mM Tris Acetate pH 8.1,500mM KOAc,150mM MgOAc) and reverse transcribed using random hexamers to prime. Resulting cDNA was bound to streptavidin beads (M-280), subjected to enzymatic reactions of DNA end repair, fill-in of adenine to 5’ protruding ends of DNA fragments using Klenow Fragment (NEB). Common adaptor (P7-MPX) was ligated and 5PSeq Libraries were amplified by PCR (15- 17 cycles). Purified samples were quantified using Qubit (Thermo Fisher), library size was estimated from bioanalyzer traces. 5PSeq Libraries were pooled by mixing equal amounts of each sample, following enrichment of fragments of the length between 300-500nt.   HT-5PSeq Libraries were generated as recently described (bioRxiv 2020.06.22.165134; doi: https://doi.org/10.1101/2020.06.22.165134). In brief, DNA-free RNA was ligated with RNA oligos containing unique molecular identifiers. Ligated RNA was reverse transcribed priming with oligos containing a random hexamer and an Illumina compatible region. RNA was eliminated by addition of NaOH. Ribosomal RNA was depleted by adding in-house rRNA DNA oligo depletion mixes (table 2) to the cDNA and performing a duplex-specific nuclease (DSN, Evrogen) treatment. rRNA depleted cDNA was PCR amplified (15-17 cycles). Depletion of ribosomal RNA with Ribozero Illumina (for bacteria and yeast) was done after the single-stranded RNA ligation step. Ribosomal depleted RNA was purified and reverse transcribed using the same oligos as stated above, and then amplified by PCR. Libraries were quantified by fluorescence (Qubit, Thermo Fisher), size estimated using an Agilent Bioanalyzer and sequence using a NextSeq500 Illumina sequencer.

value: wild type

value: Untreated (UT) or Heat shock at 65˚C for 10 minutes (HS)  or 100µg/ml Chloramphenicol incubated for 10 minutes at 37˚C (CAM) or 65µg/ml Mupirocin for 10 minutes at 37˚C (MUP)

tag: molecule subtype

value: total RNA, 5' monophosphorylated


title: ecol_hs_abx_03_v17 [mixed sample]

source_name: A mixed sample of 5 cultures: ecol_ctr_r3-1_s_o_v17; ecol_hs_r3_s_o_v17; ecol_ctr_r3-2_s_o_v17; ecol_cam_r3_s_o_v17; ecol_mup_r3_s_o_v17


title: PLF3b_scRNA-seq


title: PLF3c_scRNA-seq


title: ecol_hs_abx_01_v17 [mixed sample]

source_name: A mixed sample of 5 cultures: ecol_ctr_r1-1_s_o_v17; ecol_hs_r1_s_o_v17; ecol_ctr_r1-2_s_o_v17; ecol_cam_r1_s_o_v17; ecol_mup_r1_s_o_v17


title: SCaBER_siCt1_rep1 [D373T37]

description:
Sample 1
SCaBER cell line treated with siControl num 1 replicate 1


title: PLF3a_scRNA-seq


title: S.islandicus.REY15A.E234.Cappable-seq.replicate2


title: 0.1 Dox rep 3

city: Middletown

first: Joseph

last: Coolon

state: CT

address: 52 Lawn Avenue

department: Biology

country: USA

institute: Wesleyan University

data_processing:
FASTQC
Bowtie 2
CuffDiff
Assembly: Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa
Supplementary files format and content: Table1.xlsx (Cuffdiff output)

organism: Saccharomyces cerevisiae

source_name: Cell pellet

extract_protocol:
Promega SV total RNA extraction Kit
Truseq barcoded library prep

tag: tissue

value: Cell pellet

value: yeast cell

tag: growth phase

value: log phase growth

value: pRAP1::kanR-tetO7-TATA URA3::CMV-tTA MATa his3-1 leu2-0 met15-0

value: 0.1 μg/mL Dox


title: ecol_mup_r3_s_o_v17

description: Culture: ecol_mup_r3_s_o_v17 was cultured in LB Broth at 37˚C to late-log growth phase, culture was supplemented with 65µg/ml Chloramphenicol and incubated for 10 min at 37˚C and harvested by centrifugation ; Library: HT-5PSeq using indexed rP5_RNA (rP5_MPX_RNA) Adapters (CrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrU rXrXrXrXrXrX rNrNrNrNrNrNrNrN) carrying a sample barcode (rX) and unique molecular identifiers (rN) which were removed from the reads into the read headers. rRNA removal:  in-house Bacterial rRNA Depletion MIX for Cultures , oVP670

source_name: Liquid culture of Escherichia coli MG1655

value: 65µg/ml Mupirocin for 10 minutes at 37˚C


title: HNP210929

city: Taipei

first: Chih-Hung

last: Chung

address: No.155, Sec.2, Linong Street, Taipei, 112 Taiwan (ROC)

department: Institute of Clinical Medicine

country: Taiwan

institute: National Yang Ming Chiao Tung University

data_processing:
For Single-cell RNA sequencing, libraries were sequenced on Illumina NovaSeq 6000, with 150 bases from read 1 and read 2, and at a depth of 618 million reads per sample.
The data was processed with the cellranger pipeline (version 6.1.1, 10X Genomics) and mapped to the GRCH38 v98 genome assembly.
Genome_build: GRCh38 v98
Supplementary_files_format_and_content: Tab-delimited text files containing genes by barcode counts matrices, barcode file and gene list.

source_name: HNSCC Patient

extract_protocol:
The single-cell suspension from tumor with the viability over 80% was loaded onto the 10 × Genomics Next GEM Chip G for target capture of ~8,000 cells/chip.
Libraries were prepared using a Chromium Next GEM Single Cell 3' Reagent Kit (v3.1 kit) following the directions of the manufacturer. RNA libraries were prepared for sequencing using standard Illumina protocols.
10X Single-cell RNA sequencing platform

treatment_protocol: We collected HNSCC primary tumor from head and neck squamous cell carcinoma patients at the Taipei Veterans General Hospital (TVGH), according to the current TVGH-IACUC regulations. IRB approval number : 2017-05-013AC.

tag: tumor

value: Primary Tumor

tag: unique patient number (upn)


title: PLF2d_scRNA-seq

value: longitudinal

value: PBMC


title: ecol_ctr_r3-2_s_o_v17

description: Culture: ecol_ctr_r3-2_s_o_v17 was cultured in LB Broth at 37˚C and harvested in late-log growth phase  ; Library: HT-5PSeq using indexed rP5_RNA (rP5_MPX_RNA) Adapters (CrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrU rXrXrXrXrXrX rNrNrNrNrNrNrNrN) carrying a sample barcode (rX) and unique molecular identifiers (rN) which were removed from the reads into the read headers. rRNA removal:  in-house Bacterial rRNA Depletion MIX for Cultures , oVP670

value: Untreated


title: ecol_cam_r3_s_o_v17

description: Culture: ecol_cam_r3_s_o_v17 was cultured in LB Broth at 37˚C to late-log growth phase, culture was supplemented with 100µg/ml Chloramphenicol and incubated for 10 min at 37˚C and harvested by centrifugation; Library: HT-5PSeq using indexed rP5_RNA (rP5_MPX_RNA) Adapters (CrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrU rXrXrXrXrXrX rNrNrNrNrNrNrNrN) carrying a sample barcode (rX) and unique molecular identifiers (rN) which were removed from the reads into the read headers. rRNA removal:  in-house Bacterial rRNA Depletion MIX for Cultures , oVP670

value: 100µg/ml Chloramphenicol incubated for 10 minutes at 37˚C


title: 0.5 Dox rep 1

value: 0.5 μg/mL Dox


title: 0.5 Dox rep 3


title: 0.1 Dox rep 1


title: 0.1 Dox rep 2


title: PLF2c_scRNA-seq

value: female


title: PLF2b_scRNA-seq


title: 0.01 Dox rep 3

value: 0.01 μg/mL Dox


title: 0.5 Dox rep 2


title: 0.01 Dox rep 2


title: PLF2a_scRNA-seq


title: ecol_ctr_r3-1_s_o_v17

description: Culture: ecol_ctr_r3-1_s_o_v17 was cultured in LB Broth at 37˚C and harvested in mid-log growth phase  ; Library: HT-5PSeq using indexed rP5_RNA (rP5_MPX_RNA) Adapters (CrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrU rXrXrXrXrXrX rNrNrNrNrNrNrNrN) carrying a sample barcode (rX) and unique molecular identifiers (rN) which were removed from the reads into the read headers. rRNA removal:  in-house Bacterial rRNA Depletion MIX for Cultures , oVP670

value: wild type


title: G122_D3_Adjacent

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

institute: Queen Mary University of London

data_processing:
RNA-Seq reads were quality trimed and mapped to the human genome (hg38, Genome Reference Consortium GRCh38)  using STAR.
Number of reads aligned to the exonic region of each gene were counted using rsem-count based on the Ensembl annotation.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file of rsem gene counts  for each sample

source_name: adjacent normal omenum

growth_protocol: Metastatic ovarian omental tissues were decellularized. Sliced disks of decellularized tissues were added into 96-well culture plate. Freshly isolated blood-derived monocytes were seeded onto decellularized at density of 2x10^5 per well and cultured for 14 days in DMEM 10% human AB serum 1% P/S, chaning media every 3 days or when neccessary.

extract_protocol:
RNA was extracted from the cultures using the Qiagen RNeasyMicro kit according to manufacturer instructions
Extracted RNA samples were sent to the Oxford Genomics Centre for processing. Library preps were made with polyadenylated transcript enrichment and strand specific library preparation was completed using NEBNext Ultra II mRNA kit.

tag: blood donor

tag: tissue donor

value: adjacent normal omenum


title: G122_D4_Adjacent


title: 0.01 Dox rep 1

tag: cell line


title: PLF1c_scRNA-seq

source_name: PBMC

tag: cell type


title: control rep 3

tag: genotype

value: control


title: G122_D2_Adjacent


title: ecol_cam_r2_s_o_v17

description: Culture: ecol_cam_r2_s_o_v17 was cultured in LB Broth at 37˚C to late-log growth phase, culture was supplemented with 100µg/ml Chloramphenicol and incubated for 10 min at 37˚C and harvested by centrifugation; Library: HT-5PSeq using indexed rP5_RNA (rP5_MPX_RNA) Adapters (CrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrU rXrXrXrXrXrX rNrNrNrNrNrNrNrN) carrying a sample barcode (rX) and unique molecular identifiers (rN) which were removed from the reads into the read headers. rRNA removal:  in-house Bacterial rRNA Depletion MIX for Cultures , oVP670

value: total RNA, 5' monophosphorylated


title: HNP210915


title: control rep 2

value: Cell pellet

value: yeast cell


title: G122_D1_Adjacent


title: G145_D4_Adjacent


title: PLF1a_scRNA-seq


title: ecol_mup_r2_s_o_v17

description: Culture: ecol_mup_r2_s_o_v17 was cultured in LB Broth at 37˚C to late-log growth phase, culture was supplemented with 65µg/ml Chloramphenicol and incubated for 10 min at 37˚C and harvested by centrifugation ; Library: HT-5PSeq using indexed rP5_RNA (rP5_MPX_RNA) Adapters (CrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrU rXrXrXrXrXrX rNrNrNrNrNrNrNrN) carrying a sample barcode (rX) and unique molecular identifiers (rN) which were removed from the reads into the read headers. rRNA removal:  in-house Bacterial rRNA Depletion MIX for Cultures , oVP670


title: ecol_ctr_r2-2_s_o_v17

description: Culture: ecol_ctr_r2-2_s_o_v17 was cultured in LB Broth at 37˚C and harvested in late-log growth phase  ; Library: HT-5PSeq using indexed rP5_RNA (rP5_MPX_RNA) Adapters (CrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrU rXrXrXrXrXrX rNrNrNrNrNrNrNrN) carrying a sample barcode (rX) and unique molecular identifiers (rN) which were removed from the reads into the read headers. rRNA removal:  in-house Bacterial rRNA Depletion MIX for Cultures , oVP670


title: control rep 1

value: log phase growth

value: pRAP1::kanR-tetO7-TATA URA3::CMV-tTA MATa his3-1 leu2-0 met15-0


title: ecol_hs_r3_s_o_v17

description: Culture: ecol_hs_r3_s_o_v17 was cultured in LB Broth at 37˚C to log growth phase, 2 ml of culture was centrifuged and pellet was resuspended in 65˚C pr-warmed LB, incubated for 10 minutes at 65˚C on Heatblock and harvested by centrifugation;  ; Library: HT-5PSeq using indexed rP5_RNA (rP5_MPX_RNA) Adapters (CrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrU rXrXrXrXrXrX rNrNrNrNrNrNrNrN) carrying a sample barcode (rX) and unique molecular identifiers (rN) which were removed from the reads into the read headers. rRNA removal:  in-house Bacterial rRNA Depletion MIX for Cultures , oVP670

value: Heat shock at 65˚C for 10 minutes


title: ecol_hs_r2_s_o_v17

description: Culture: ecol_hs_r2_s_o_v17 was cultured in LB Broth at 37˚C to log growth phase, 2 ml of culture was centrifuged and pellet was resuspended in 65˚C pr-warmed LB, incubated for 10 minutes at 65˚C on Heatblock and harvested by centrifugation;  ; Library: HT-5PSeq using indexed rP5_RNA (rP5_MPX_RNA) Adapters (CrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrU rXrXrXrXrXrX rNrNrNrNrNrNrNrN) carrying a sample barcode (rX) and unique molecular identifiers (rN) which were removed from the reads into the read headers. rRNA removal:  in-house Bacterial rRNA Depletion MIX for Cultures , oVP670


title: CM5_scRNA-seq

value: healthy control

value: healthy

value: male


title: G145_D3_Adjacent


title: PLF1b_scRNA-seq

value: longitudinal

value: PBMC


title: ecol_rnja-ctr_r2_s_r_v2

description: Culture: ecol_rnja-ctr_r2_s_r_v2 was cultured in LB Broth supplemented with 25µg/ml Kanamycin at 37˚C and harvested in log growth phase ; Standard 5PSeq  ; rRNA removal: Ribo-Zero rRNA Removal Kit (Bacteria)

source_name: Liquid culture of one shot Top10 Ecoli cells transformed with  pEC622 plasmid expressing RNase J1 for complementation in Spyogenes on its native promoter

value: wild type + plasmid exprssing RNaseJ1

value: 100µg/ml Chloramphenicol incubated for 5 minutes at 37˚C


title: CM4_scRNA-seq


title: ecol_mup_r1_s_o_v17

description: Culture: ecol_mup_r1_s_o_v17 was cultured in LB Broth at 37˚C to late-log growth phase, culture was supplemented with 65µg/ml Chloramphenicol and incubated for 10 min at 37˚C and harvested by centrifugation ; Library: HT-5PSeq using indexed rP5_RNA (rP5_MPX_RNA) Adapters (CrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrU rXrXrXrXrXrX rNrNrNrNrNrNrNrN) carrying a sample barcode (rX) and unique molecular identifiers (rN) which were removed from the reads into the read headers. rRNA removal:  in-house Bacterial rRNA Depletion MIX for Cultures , oVP670

value: 65µg/ml Mupirocin for 10 minutes at 37˚C


title: G306_D1_Adjacent


title: G145_D2_Adjacent


title: ecol_rnja-ctr_r1_s_r_v2

description: Culture: ecol_rnja-ctr_r1_s_r_v2 was cultured in LB Broth supplemented with 25µg/ml Kanamycin at 37˚C and harvested in log growth phase ; Standard 5PSeq  ; rRNA removal: Ribo-Zero rRNA Removal Kit (Bacteria)


title: G145_D1_Adjacent


title: ecol_cam_r1_s_o_v17

description: Culture: ecol_cam_r1_s_o_v17 was cultured in LB Broth at 37˚C to late-log growth phase, culture was supplemented with 100µg/ml Chloramphenicol and incubated for 10 min at 37˚C and harvested by centrifugation; Library: HT-5PSeq using indexed rP5_RNA (rP5_MPX_RNA) Adapters (CrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrU rXrXrXrXrXrX rNrNrNrNrNrNrNrN) carrying a sample barcode (rX) and unique molecular identifiers (rN) which were removed from the reads into the read headers. rRNA removal:  in-house Bacterial rRNA Depletion MIX for Cultures , oVP670

value: wild type

value: 100µg/ml Chloramphenicol incubated for 10 minutes at 37˚C


title: CM3_scRNA-seq


title: ecol_rnja-cam_r2_s_r_v2

description: Culture: ecol_rnja-cam_r2_s_r_v2 was cultured in LB Broth supplemented with 25µg/ml Kanamycin at 37˚C to log growth phase, 100µg/ml Chloramphenicol was added  and incubated for 5min at 37˚C , harvested on ice containing 100µg/ml Chloramphenicol  ; Standard 5PSeq  ; rRNA removal: Ribo-Zero rRNA Removal Kit (Bacteria)


title: CM2_scRNA-seq


title: G198_D4_Adjacent

value: adjacent normal omenum


title: ecol_ctr_r1-2_s_o_v17

description: Culture: ecol_ctr_r1-2_s_o_v17 was cultured in LB Broth at 37˚C and harvested in late-log growth phase  ; Library: HT-5PSeq using indexed rP5_RNA (rP5_MPX_RNA) Adapters (CrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrU rXrXrXrXrXrX rNrNrNrNrNrNrNrN) carrying a sample barcode (rX) and unique molecular identifiers (rN) which were removed from the reads into the read headers. rRNA removal:  in-house Bacterial rRNA Depletion MIX for Cultures , oVP670

value: Untreated

value: total RNA, 5' monophosphorylated


title: G198_D3_Adjacent


title: ecol_rnja-cam_r1_s_r_v2

description: Culture: ecol_rnja-cam_r1_s_r_v2 was cultured in LB Broth supplemented with 25µg/ml Kanamycin at 37˚C to log growth phase, 100µg/ml Chloramphenicol was added  and incubated for 5min at 37˚C , harvested on ice containing 100µg/ml Chloramphenicol  ; Standard 5PSeq  ; rRNA removal: Ribo-Zero rRNA Removal Kit (Bacteria)


title: CM1_scRNA-seq


title: G198_D2_Adjacent


title: ecol_hs_r1_s_o_v17

description: Culture: ecol_hs_r1_s_o_v17 was cultured in LB Broth at 37˚C to log growth phase, 2 ml of culture was centrifuged and pellet was resuspended in 65˚C pr-warmed LB, incubated for 10 minutes at 65˚C on Heatblock and harvested by centrifugation;  ; Library: HT-5PSeq using indexed rP5_RNA (rP5_MPX_RNA) Adapters (CrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrU rXrXrXrXrXrX rNrNrNrNrNrNrNrN) carrying a sample barcode (rX) and unique molecular identifiers (rN) which were removed from the reads into the read headers. rRNA removal:  in-house Bacterial rRNA Depletion MIX for Cultures , oVP670


title: CF7_scRNA-seq

value: female


title: ecol_ctr_r2-1_s_o_v17

description: Culture: ecol_ctr_r2-1_s_o_v17 was cultured in LB Broth at 37˚C and harvested in mid-log growth phase  ; Library: HT-5PSeq using indexed rP5_RNA (rP5_MPX_RNA) Adapters (CrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrU rXrXrXrXrXrX rNrNrNrNrNrNrNrN) carrying a sample barcode (rX) and unique molecular identifiers (rN) which were removed from the reads into the read headers. rRNA removal:  in-house Bacterial rRNA Depletion MIX for Cultures , oVP670


title: ecol_ctr_r1-1_s_o_v17

description: Culture: ecol_ctr_r1-1_s_o_v17 was cultured in LB Broth at 37˚C and harvested in mid-log growth phase  ; Library: HT-5PSeq using indexed rP5_RNA (rP5_MPX_RNA) Adapters (CrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrU rXrXrXrXrXrX rNrNrNrNrNrNrNrN) carrying a sample barcode (rX) and unique molecular identifiers (rN) which were removed from the reads into the read headers. rRNA removal:  in-house Bacterial rRNA Depletion MIX for Cultures , oVP670


title: CF6_scRNA-seq


title: CF5_scRNA-seq


title: ecol_frag_r3_s_r_v1

source_name: Liquid culture of DH5α (Invitrogen cat-no.18265017.

tag: culture conditions

value: ecol_frag_rep3 was grown in LB broth at 37C and harvested at exponential growth OD600 0.7.

tag: library protocol

value: random fragmented ( 5PSeq)

tag: ribosomal rna delpetion strategy

value: Ribo-Zero rRNA Removal Kit (Bacteria) Illumina


title: ecol_frag_r1_s_r_v1

value: ecol_frag_rep1 was grown in LB broth at 37C and harvested at exponential growth OD600 0.88.


title: ecol_ctr_r2_s_r_v1

value: ecol_ctr_rep2 was grown in LB broth at 37C and harvested at exponential growth OD600 0.89.

value: Standard 5PSeq


title: ecol_frag_r2_s_r_v1

value: ecol_frag_rep2 was grown in LB broth at 37C and harvested at exponential growth phase OD600 0.89.


title: ecol_mup_r2_s_o_v15

data_processing:
Adapter and quality trimming with the bbduk program of the BBTools suite, with options {qtrim=r, ktrim=r, hdist=3, hdist2=2, K=20, mink=14, trimq=16, minlen=30, maq=16}, using BBTools default adapter set and polyG or polyA sequences for short reads.
Deduplication of reads with both identical unique molecular identifier (UMI) and insert sequence using the dedupe program of the BBTools suite with its default parameters.
UMI sequences found in the first eight bases of each read were extracted using UMI-tools (version 1) with default options (using --bc-pattern NNNNNNNN).
Alignment was performed with the bbmap program of the BBTools suite, with the {32bit=t -da -eoom k=11 strictmaxindel=10 intronlen=0 t=16 trd=t minid=0.94 nzo=t} parameters. Alignment files were sorted and indexed with SAMtools.
Deduplication based on UMIs was then performed with UMI-tools (version 1) with options { --soft-clip-threshold 1 --edit-distance 2 --method unique}.
In selected samples, a dual undex strategy was used (sequencing runs v17). In brief, in addition of the Illumina indexes with dedicated reads used in HT-5Pseq, an additional index sequence is added before the UMI sequence. This is introduced during the ssRNA ligation space using anoligo with the following structure Illumina compatible-CCCCCC-NNNNNNNN. Please see dual_index_demultiplexing.txt for details on demultiplexing strategy for those samples.
Bedgraphs for read 5' positions for forward (fwd) and reverse (rev) strands were generated with BEDTools genomecov program with options {-bg -strand [+/-] -5}.
Assembly: The genome used for alignment is indicated in the processed file names with the G-xxxx patterns.  Those correspond to the NCBI accessions and builds indicated in the Supplementary file.
Assembly: Reference indiced for individual bacterial species and custom mixtures were built with the bbmap program of the BBTools suite, with default options (and k=10).
Supplementary files format and content: Processed files are bedgraphs containing read 5' counts on reverse (_rev) and forward (_fwd) strands of genomes indicated with _G-xxxx pattern. The genomes corresponding to each pattern are described in the genome build entry above.

source_name: Liquid culture of DH5α (Invitrogen cat-no.18265017)

extract_protocol:
Microbial cell pellets were resuspended in equal volume of LET (25 mM Tris pH 8.0, 100 mM LiCl, 20 mM EDTA) and water saturated Phenol pH 6.6 (Thermo Fisher),  lysed with acid washed glass beads (Sigma-Aldrich) and vortexing for three minutes in MultiMixer. Lysates were supplemented  with equal volumes of phenol/chloroform isoamyl alcohol pH 4.5 (25:24:1) and nuclease free water, l two-minute vortexing followed by centrifugation. Resulting aqueous phase was purified in two steps using phenol-chloroform isoamyl alcohol (25:24:1) followed by chloroform. After centrifugation, the clean aqueous phase was precipitated with sodium acetate-ethanol.
Standard and random fragmented 5PSeq libraries were generated as described in PMID: 26046441 with minor modifications using 150-9000ng total RNA as an input. To prepare random fragmented samples (negative controls), ribosomal RNA was depleted from DNA-free RNA and subsequent fragmented by incubating five minutes at 80 ̊C in fragmentation buffer (40mM Tris Acetate pH 8.1, 100mM KOAc and 30mM MgOAc). Reaction was purified using 2 volumes of RNACleanXP beads (Beckman Coulter) as recommended by the manufacturer. Free 5’OH sites were re-phosphorylated using 5 Units of T4 Polynucleotide kinase (PNK, NEB) and incubated at 37 ̊C for 60 minutes as recommended by the manufacturer. Re-phosphorylated fragmented RNA was purified using Phenol:Chloroform: Isoamyl Alcohol (24:25:1), followed by sodium acetate-ethanol precipitation. From this step forward, procedures for random fragmented and standard 5PSeq library preparation merge. RNA was Ligated to either rP5_RND or rP5_RNA oligo (specified in characteristics protocol).    containing unique molecular identifiers). Ribosomal RNA was depleted using Ribozero rRNA removal kit (Illumina) suitable for Bacteria and Yeast. rRNA depleted sample was purified using 1.8V of Ampure beads (Abcam), fragmented using heat (80˚C) for 5 min in 5x Fragmentation Buffer (200mM Tris Acetate pH 8.1,500mM KOAc,150mM MgOAc) and reverse transcribed using random hexamers to prime. Resulting cDNA was bound to streptavidin beads (M-280), subjected to enzymatic reactions of DNA end repair, fill-in of adenine to 5’ protruding ends of DNA fragments using Klenow Fragment (NEB). Common adaptor (P7-MPX) was ligated and 5PSeq Libraries were amplified by PCR (15- 17 cycles). Purified samples were quantified using Qubit (Thermo Fisher), library size was estimated from bioanalyzer traces. 5PSeq Libraries were pooled by mixing equal amounts of each sample, following enrichment of fragments of the length between 300-500nt.   HT-5PSeq Libraries were generated as recently described (bioRxiv 2020.06.22.165134; doi: https://doi.org/10.1101/2020.06.22.165134). In brief, DNA-free RNA was ligated with RNA oligos containing unique molecular identifiers. Ligated RNA was reverse transcribed priming with oligos containing a random hexamer and an Illumina compatible region. RNA was eliminated by addition of NaOH. Ribosomal RNA was depleted by adding in-house rRNA DNA oligo depletion mixes (table 2) to the cDNA and performing a duplex-specific nuclease (DSN, Evrogen) treatment. rRNA depleted cDNA was PCR amplified (15-17 cycles). Depletion of ribosomal RNA with Ribozero Illumina (for bacteria and yeast) was done after the single-stranded RNA ligation step. Ribosomal depleted RNA was purified and reverse transcribed using the same oligos as stated above, and then amplified by PCR. Libraries were quantified by fluorescence (Qubit, Thermo Fisher), size estimated using an Agilent Bioanalyzer and sequence using a NextSeq500 Illumina sequencer.
other: 5PSeq that captures  transcripts with free 5' phospahte (without cap)

value: 65ug/ml Mupirocin incubated for 10 minutes at 37˚C

value: ecol_mup_r2 was cultured in LB Broth at 37˚C and Mupirocin was added in mid-log growth phase  for 10 minutes

tag: ribosomal rna depletion strategy

value: in-house Bacterial rRNA Depletion MIX for Cultures , oVP670


title: CF4_scRNA-seq

tag: cohort

value: healthy control

tag: disease state

value: healthy

tag: gender

tag: group

value: PBMC


title: G150_D4_Tumour

source_name: Tumour

tag: tissue

value: tissue from ovarian high grade serous omental metastasis


title: ecol_ctr_r3_s_r_v1

tag: treatment

value: Untreated

value: ecol_ctr_rep3 was grown in LB broth at 37C and harvested at exponential growth phase OD600 0.7.


title: ecol_ctr_r2_s_o_v15

value: ecol_ctr_r2 was cultured in LB Broth at 37˚C and harvested in  mid-log growth phase


title: CF3_scRNA-seq

value: female


title: ecol_mup_r1_s_o_v15

value: ecol_mup_r1  was cultured in LB Broth at 37˚C and Mupirocin was added in mid-log growth phase  for 10 minutes


title: G150_D3_Tumour


title: G150_D2_Tumour


title: ecol_ctr_r1_s_r_v1

value: ecol_ctr_rep1 was grown in LB broth at 37C and harvested at exponential growth phase OD600 0.88.

value: Ribo-Zero rRNA Removal Kit (Bacteria) Illumina


title: ecol_ctr_r1_s_o_v15

value: ecol_ctr_r1 was cultured in LB Broth at 37˚C and harvested in  mid-log growth phase


title: ecol_cam_r2_s_o_v15

value: 100ug/ml Chloramphenicol for 10 minutes at 37˚C

value: ecol_cam_r2 was cultured in LB Broth at 37˚C and Chloramphenicol was added in mid-log growth phase for 10 minutes


title: G150_D1_Tumour


title: ecol_cam_r3_s_r_v1

value: 100microg/ml Chloramphenicol for 5 minutes at 37C

value: ecol_cam_rep3 was grown in LB broth at 37C. Chloramphenicol treatment was initiated at exponential growth OD600 0.7.

value: Standard 5PSeq


title: G198_D1_Adjacent

value: adjacent normal omenum


title: G164_D4_Tumour


title: CF1_scRNA-seq

value: healthy control

value: healthy


title: ecol_cam_r2_s_r_v1

value: ecol_cam_rep2 was grown in LB broth at 37C. Chloramphenicol treatment  was initiated at exponential growth phase OD600 0.89.


title: ecol_cam_r1_s_o_v15

value: ecol_cam_r1 was cultured in LB Broth at 37˚C and Chloramphenicol was added in mid-log growth phase for 10 minutes

value: in-house Bacterial rRNA Depletion MIX for Cultures , oVP670


title: G164_D3_Tumour

value: tissue from ovarian high grade serous omental metastasis


title: IgG_Ctrl

city: BOSTON

first: Julie

last: Ng

state: MA

address: 75, Francis Street

institute: Brigham and Women's Hospital

data_processing:
Library strategy: CUT&RUN
Adaptors were trimmed using TrimGalore! (v0.6.6) and Cutadapt (v1.8.1).
Sequences were aligned using Bowtie2 (v2.4.1) to the mm10 mouse reference genome.
SAM files were converted to BAM files using samtools (v1.4.1).
Sorted BAM files were converted to bigwig files using bamCoverage, part of the deepTools suite (v3.1.2)
Quality was assessed using the ChIPQC R package. Peaks were called using MACS2 (v2.1)45 and the concordance of peak calls between replicates was assessed using the Irreproducibility Discovery Rate framework46 (v2.0.3). Replicates were combined using BEDtools (v2.26.0), and genes were annotated using the ChIPseeker R package using the full genome sequences for mus musculus (UCSC version mm10). Functional enrichment of the obtained gene annotations for peak calls for Gene Ontology biological processes and KEGG pathways was performed using the clusterProfiler R package.
Assembly: mm10
Supplementary files format and content: bigWig files

source_name: Bone marrow c-kit+ hematopoietic stem cell

growth_protocol: Male 6–8-week-old CD45.1 expressing CByJ.SJL(B6)-Ptprca/J mice (Strain # 006584) were purchased from Jackson Laboratory (Bar Harbor, ME, USA). CD45.1 lineage negative c-kit+ cells were isolated from compact bones by negative selection using biotinylated anti-mouse CD3 (Biolegend clone 145-2C11), B220 (Biolegend clone RA3-6B2), GR-1 (Biolegend clone RB6-8C5), CD11b (Biolegend clone M1/70), NKp46 (Biolegend clone 29A1.4), and TER-119 (Biolegend TER-119) with anti-biotin microbeads (Miltenyi Biotec) through an LD magnetic column (Miltenyi Biotec), followed by positive selection with PE anti-mouse c-kit (Biolegend clone 2B8) with anti-PE microbeads (Miltenyi Biotec) through an MS magnetic column (Miltenyi Biotec). The purity of c-kit+ cells were confirmed to be >90% by flow cytometry using a MACSQuant Analyzer 10 flow cytometer and analyzed using FlowJo software (Tree Star Inc). C-kit+ cells were cultured for 48 hours ex vivo in StemSpan SFEM II (STEMCELL Technologies) supplemented with 50ng/mL thrombopoietin (PeproTech), 100ng/mL stem cell factor (PeproTech) and 30% of either 1) MSC CdM (3x105 cell equivalent), 2) CpG-MSC CdM (3x105 cell equivalent), or 3) alpha-MEM media control at 37°C with 5% CO2. Recipient CD45.2 expressing 8-week-old male BALB/cByJ mice (Strain # 000651) were purchased from Jackson Laboratories (Bar Harbor, ME, USA) and lethally irradiated with 9Gy radiation in 2 doses spaced 12 hours apart using a Gammacell 40 Exactor Cesium-137 dual-source irradiator (Best Theratronics). 1.5-2x105 c-kit+ cells in 150µL PBS25 from one of the described three conditions were transplanted by retro-orbital injection.

extract_protocol:
Live c-kit+ cells from chimeric mice were stained using Zombie Violet fixable viability kit (Biolegend) and APC-c-kit (Biolegend clone 2B8). Sorting for live c-kit+ cells was performed using a FACSAria III cell sorter (BD Biosciences). CUT&RUN was performed on equal numbers of c-kit+ cells from each group of chimeric mice using the CUT&RUN Assay Kit (Cell Signaling, Kit #86652) per manufacturer’s protocol. Chromatin associated with H3K4me3 (Cell Signaling clone C42D8), and rabbit IgG negative isotype control (Cell Signaling clone DA1E) were isolated. Technical replicates were performed in duplicate.
CUT&RUN libraries were prepared using Swift S2 Acel reagents on a Beckman Coulter Biomek i7 liquid handling platform from approximately 1ng of DNA according to manufacturer’s protocol and 14 cycles of PCR amplification.  Subsequently, libraries were sequenced on a NovaSeq with 150bp paired-end reads.

treatment_protocol: No treatments were applied prior to preparation

tag: bone marrow transplant

value: Control

tag: strain

value: Balb/cByJ

tag: cut&run antibody

value: H3K4me3 (Cell Signaling, Clone C42D8)


title: bsub-str168_cam-ps_r6_s_o_v7

organism: Bacillus subtilis

source_name: Liquid culture of Bacillus subtilis 168 trpC2.

value: 100microg/ml Chloramphenicol for 5 minutes at 4C

value: bsub-str168_cam_ps_rep6 was grown in LB broth and harvested at exponential growth phase on ice supplemented with CAM OD600 0.628


title: H3K4me3_Ctrl_Rep2

value: Ctrl-BM


title: G164_D2_Tumour

tag: blood donor

tag: tissue donor


title: bsub-str168_cam-ms_r6_s_o_v7

value: bsub-str168_cam-ms_rep6 was grown in LB broth and harvested at exponential growth phase on ice supplemented with CAM OD600 0.628


title: G164_D1_Tumour


title: NIH3T3 cells, EV_MIY-D6_C3

city: Munich

first: Vanessa

last: Arfelli

state: Bavaria

address: Max-Lebsche-Platz 30

department: Medical Clinic and Polyclinic III

institute: Munich University Hospital, Ludwig-Maximilians University (LMU)

data_processing:
Raw Fastq data were processed with the pipeline zUMIs, version 0.2.0 (Parekh et al., 2018)
cDNA reads were mapped to the mouse genome mm10 using the software STAR (Dobin et al., 2013).
Gene annotations were obtained from Ensembl (GRCm38.75)
Assembly: Mouse: mm10
Supplementary files format and content: Sample (columns) and gene (rows) -wise UMI expression table

growth_protocol: The cells used in this study were cultivated at 37 ºC and 5% CO2 in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% of fetal bovine serum (FBS) and 1% of the antibiotics penicillin-streptomycin

extract_protocol:
Libraries were constructed using a bulk RNA-seq method named Prime-seq, which uses direct cell lysis, bead cleanup, cDNA synthesis and pre-aplification with KAPA HiFi Polymerase (see Janjic et al, 2021)
The cells were counted by Vi-Cell XR (Beckman Coulter, Brea, CA, USA) and 1x104 cells were harvested in microtubes containing 100 µl of DPBS 1x. After 5 minutes of centrifugation at 1500 rpm, cells were resuspended in 100 µl of Buffer RLT Plus, RNeasy Plus Lysis Buffer (Qiagen, Hilden, Germany) supplemented with 1% b-mercapoethanol.
Prime-seq (Janjic et al, 2021 -  https://doi.org/10.1101/2021.09.27.459575)

treatment_protocol: NIH3T3 cells were transduced with retroviral particles carrying either shRNA-UHMK1 sequences (shUHMK1#1, shUHMK1#2, shUHMK1#3 and scrambled control) or the rat Uhmk1 coding sequence, in frame with a Flag peptide in the 5’, N-terminal of the protein (and the respective empty vector control, MIY).

tag: cell line

tag: replicate number

value: Control - empty vector

tag: transduction

value: portion of the empty vector MIY


title: bsub-str168_cam-ps_r4_s_o_v7

tag: culture conditions

value: bsub-str168_cam_ps_rep4 was grown in LB broth and harvested at exponential growth phase on ice supplemented with CAM OD600 0.58

tag: library protocol


title: G302_D4_Tumour


title: NIH3T3 cells, UHMK1_WT_Uhmk1-D5_C4

tag: genotype

value: UHMK1 WT overexpression

value: rat Uhmk1 wild type coding sequence


title: H3K4me3_Ctrl_Rep1


title: bsub-str168_cam-ms_r4_s_o_v7

value: bsub-str168_cam-ms_rep4 was grown in LB broth and harvested at exponential growth phase on ice supplemented with CAM OD600 0.58

tag: ribosomal rna delpetion strategy


title: NIH3T3 cells, UHMK1_WT_Uhmk1-D6_G3


title: G302_D3_Tumour


title: H3K4me3_MSC_Rep2

value: MSC-BM


title: H3K4me3-MSC_Rep1


title: CF2_scRNA-seq

data_processing:
illumina bcl2fastq (v2.19.1.403) used for basecalling and demultiplexing
BD Rhapsody WTA Analysis Pipeline (version 1.0) on SevenBridges Genomics online platform (SevenBridges) was used for alignment and sample de-multiplexing
Genome_build: GRCh38
Supplementary_files_format_and_content: txt files include UMI counts for each cell barcode and genes

tag: cohort

value: healthy control

tag: disease state

value: healthy

value: female

tag: cell type

value: PBMC


title: NIH3T3 cells, EV_MIY-D5_H3


title: G302_D2_Tumour

tag: tissue

value: tissue from ovarian high grade serous omental metastasis


title: bsub-str168_cam-ps_r5_s_o_v7

tag: treatment

value: bsub-str168_cam_ps_rep5  was grown in LB broth and harvested at exponential growth phase on ice supplemented with CAM OD600 0.821

value: in-house Bacterial rRNA Depletion MIX for Cultures , oVP670


title: G302_D1_Tumour


title: H3K4me3-CpG_Rep1

tag: bone marrow transplant

value: CpG-BM

value: Balb/cByJ

value: H3K4me3 (Cell Signaling, Clone C42D8)


title: bsub-str168_stat-d8_r3_s_o_v7

value: Stationary growth phase 8 days post-inoculation

value: bsub-str168_stat-d8_rep2 was grown in 2xYT broth at 37C and collected 8 days post inoculation.


title: ecol_cam_r1_s_r_v1

value: 100microg/ml Chloramphenicol for 5 minutes at 37C

value: ecol_cam_rep1 was grown in LB broth at 37C. Chloramphenicol treatment  was initiated at exponential growth OD600 0.88.

value: Standard 5PSeq

value: Ribo-Zero rRNA Removal Kit (Bacteria) Illumina


title: bsub-str168_stat-d8_r2_s_o_v7


title: KB3

city: Toon

first: Yuuki

last: Imai

state: Ehime

address: Shitsukawa

department: Proteo-Science Center

country: Japan

institute: Ehime University

data_processing:
Sequence data were mapped on the mouse genome (mm10) using Tophat and analyzed by Cufflinks.
Genome_build: mm10

source_name: Tfam cKO rep3

growth_protocol: Humeral bone at postnatal 6 days were excised and thoroughly flushed out the bone marrow with PBS

extract_protocol:
Total RNA was extracted with Isogen (Nippon gene, Japan) and RNeasy spin column kit (Qiagen, USA). 50 ng of RNA samples with RNA integrity number (RIN) greater than 6.7 were used for library prepairation.
RNA-Seq libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina kit, NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Multiplex Oligos for Illumina according to the manufacturer's instructions and subsequently validated for an average size of about 375-390 bp using a 2100 Bioanalyzer and the Agilent DNA1000 kit for the construction of sequencing libraries.

tag: strain

value: humeral bone

tag: age

value: postnatal 6 days

value: Tfam cKO


title: NIH3T3 cells, EV_MIY-D4_D4

value: Control - empty vector

value: portion of the empty vector MIY


title: NIH3T3 cells, UHMK1_WT_Uhmk1-D3_E3

value: UHMK1 WT overexpression

value: rat Uhmk1 wild type coding sequence


title: G276_D3_Tumour

tag: blood donor

value: tissue from ovarian high grade serous omental metastasis


title: G276_D4_Tumour

tag: tissue donor


title: bsub-str168_stat-d8_r1_s_o_v7

value: bsub-str168_stat-d8_rep1 was grown in 2xYT broth at 37C and collected 8 days post inoculation.

value: in-house Bacterial rRNA Depletion MIX for Cultures , oVP670


title: KB2

source_name: Tfam cKO rep2


title: NIH3T3 cells, EV_MIY-D3_A3

tag: cell line


title: KB1

source_name: Tfam cKO rep1


title: H3K4me3-CpG_Rep2

value: CpG-BM

value: Balb/cByJ

tag: cut&run antibody

value: H3K4me3 (Cell Signaling, Clone C42D8)


title: bsub-str168_stat-48_r3_s_o_v7

value: Stationary growth phase 48 hours post-inoculation

value: bsub-str168_stat-48_rep3 was grown in 2xYT broth at 37C and collected 48 hours post inoculation.


title: G276_D2_Tumour


title: NIH3T3 cells, UHMK1_WT_Uhmk1-D2_E4

tag: replicate number

tag: transduction


title: CB2

source_name: Control rep2

value: Control


title: G306_D4_Adjacent

value: adjacent normal omenum


title: CB3

source_name: Control rep3

value: humeral bone


title: bsub-str168_stat-48_r1_s_o_v7

tag: culture conditions

value: bsub-str168_stat-48_rep1 was grown in 2xYT broth at 37C and collected 48 hours post inoculation.

tag: library protocol


title: NIH3T3 cells, UHMK1_WT_Uhmk1-D1_B3

tag: genotype


title: NIH3T3 cells, EV_MIY-D2_F3


title: bsub-str168_stat-48_r2_s_o_v7

value: bsub-str168_stat-48_rep2 was grown in 2xYT broth at 37C and collected 48 hours post inoculation.

tag: ribosomal rna delpetion strategy


title: NIH3T3 cells, UHMK1_WT_Uhmk1-D4_D3


title: bsub-str168_cam-ms_r5_s_o_v7

value: 100microg/ml Chloramphenicol for 5 minutes at 4C

value: bsub-str168_cam_ms_rep5 was grown in LB broth and was harvested at exponential growth phase on ice supplemented with CAM OD600 0.821


title: G276_D1_Tumour


title: CB1

source_name: Control rep1

value: postnatal 6 days


title: G306_D3_Adjacent


title: NIH3T3 cells, EV_MIY-D1_F4

value: Control - empty vector

value: portion of the empty vector MIY


title: G306_D2_Adjacent


title: NIH3T3 cells, sh#3_1836-D3_A4

value: UHMK1 knockdown

value: shUHMK1#3 (sh#3) sequence


title: HNP210804

description: Primary Tumor

extract_protocol:
The single-cell suspension from tumor with the viability over 90% was loaded onto the 10 × Genomics single-cell-A chip for target capture of ~10,000 cells/chip. Libraries were prepared using a Chromium Single Cell 3' Reagent Kit (10X Genomics, v3 kit) following the directions of the manufacturer. RNA libraries were prepared for sequencing using standard Illumina protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols
10X Single-cell RNA sequencing platform

tag: diesase

value: head and neck squamous carcinoma (HNSCC)

tag: unique patient number (upn)


title: IL_4_01185AAC_ACTGAT_batch2

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona

data_processing:
FastQ files were aligned against the mm10 reference genome using STAR 2.5.2b using default options.
Gene counts wer generated with the featureCounts function from the RSubread package version 1.32.4 with options: annot.inbuilt='mm10',allowMultiOverlap=TRUE,countMultiMappingReads=FALSE,minMQS=1,ignoreDup=FALSE
Genome_build: mm10
Supplementary_files_format_and_content: Excel XLSX

source_name: epidermal cells

growth_protocol: Mice were aged in our animal facilities until treatment was performed at 73 weeks of age

extract_protocol:
Trizol and Rneasy Mini kit
Libraries were prepared using the TruSeq stranded mRNA Library Prep (96 samples ref. 20020595 or 48 samples ref. 20020594) according to the manufacturer's protocol,  to convert total RNA into a library of template molecules of known strand origin and suitable for subsequent cluster generation and DNA sequencing.  Briefly, 1000-500 ng of total RNA were used for poly(A)-mRNA selection using poly-T oligo attached magnetic beads using two rounds of purification. During the second  elution of the poly-A RNA, the RNA was fragmented under elevated temperature and primed with random hexamers for cDNA synthesis.  Then, the cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase (SuperScript II, ref. 18064-014, Invitrogen) and random primers. The  addition of Actinomycin D to the First Stand Synthesis Act D mix (FSA) prevents spurious DNA-dependent synthesis, while allowing RNA-dependent synthesis, improving  strand specificity.  After that, second strand cDNA was synthesized, removing the RNA template and synthesizing a replacement strand, incorporating dUTP in place of dTTP to generate ds  cDNA using DNA Polymerase I and RNase H.  These cDNA fragments, then had the addition of a single 'A' base to the 3’ends of the blunt fragments to prevent them from ligating to one another during the adapter  ligation. A corresponding single T nucleotide on the 3’ end of the adapter provides a complementary overhang for ligating the adapter to the fragments ensuring a low rate  of chimera (concatenated template) formation. Subsequent ligation of the multiple indexing adapter to the ends of the ds cDNA.  Finally, PCR selectively enriched those DNA fragments that had adapter molecules on both ends and to amplify the amount of DNA in the library. The PCR was performed with a PCR Primer Cocktail that anneals to the ends of the adapters.  Final libraries were analyzed using Bioanalyzer DNA 1000 or Fragment Analyzer Standard Sensitivity (ref: 5067-1504 or ref: DNF-473, Agilent) to estimate the quantity and   validate the size distribution, and were then quantified by qPCR using the KAPA Library Quantification Kit KK4835 (REF. 07960204001, Roche) prior to the amplification with Illumina’s cBot.

treatment_protocol: Mice were injected intraperitoneally with blocking antibodies for IL-17A/F 3 times a week for 12 weeks

tag: cell type

value: epidermal cells

value: 73 weeks

value: IL-17A/F blocking antibodies

tag: sequencing batch


title: NIH3T3 cells, sh#2_1137-D3_E1

value: shUHMK1#2 (sh#2) sequence


title: bsub-str168_stat-24_r2_s_o_v7

tag: treatment

value: Stationary growth phase 24 hours post-inoculation

value: bsub-str168_stat-24_rep2 was grown in 2xYT broth at 37C and collected 24 hours post inoculation.

value: in-house Bacterial rRNA Depletion MIX for Cultures , oVP670


title: bsub-str168_salt_r3_s_o_v7

value: Salt stress, 1M NaCl incubated for 10 minutes

value: bsub-str168_saltstress_rep3(6) was grown in 2xYT broth at 37C and salt stress was induced at exponential growth OD600 0.39


title: NIH3T3 cells, sh#1_907-D3_C1

value: shUHMK1#1 (sh#1) sequence


title: IL_4_01185AAC_ACTGAT_batch1

tag: strain


title: NIH3T3 cells, shCTRL_SCR3-D3_F2

value: Control - scramble

value: scrambled shRNA-UHMK1 sequence (shCTRL) which has target gene


title: bsub-str168_salt_r2_s_o_v7

value: Salt stress, 1M NaCl for 10 minutes

value: bsub-str168_saltstress_rep2(5) was grown in 2xYT broth at 37C and salt stress was induced at exponential growth phase OD600 0.31


title: IL_3_01184AAC_GTCCGC_batch2

tag: age


title: IL_2_01183AAC_ATGTCA_batch2


title: IL_3_01184AAC_GTCCGC_batch1


title: NIH3T3 cells, shCTRL_SCR2-D3_A2


title: bsub-str168_salt_r1_s_o_v7

value: bsub-str168_saltstress_rep1(4) was grown in 2xYT broth at 37C and salt stress was induced at exponential growth phase OD600 0.2


title: bsub-str168_stat-24_r3_s_o_v7

value: bsub-str168_stat-24_rep3 was grown in 2xYT broth at 37C and collected 24 hours post inoculation.


title: NIH3T3 cells, shCTRL_SCR1-D3_G1


title: bsub-str168_ctr_r3_s_o_v7

value: Untreated

value: bsub-str168_ctr_rep6 was grown in 2xYT broth at 37C and harvested at exponential growth phase OD600 0.39.


title: NIH3T3 cells, sh#3_1836-D2_G2

value: UHMK1 knockdown

value: shUHMK1#3 (sh#3) sequence


title: bsub-str168_stat-24_r1_s_o_v7

value: bsub-str168_stat-24_rep1 was grown in 2xYT broth at 37C and collected 24 hours post inoculation.


title: NIH3T3 cells, sh#2_1137-D2_A1

value: shUHMK1#2 (sh#2) sequence


title: bsub-str168_ctr_r1_s_o_v7

value: bsub-str168_ctr_rep4 was grown in 2xYT broth at 37C and harvested at exponential growth phase OD600 0.2


title: IL_2_01183AAC_ATGTCA_batch1

value: epidermal cells

value: 73 weeks

value: IL-17A/F blocking antibodies


title: NIH3T3 cells, sh#1_907-D2_B2

value: shUHMK1#1 (sh#1) sequence


title: IL_1_01182AAC_GATCAG_batch1


title: bsub-str168_ctr_r2_s_o_v7

value: bsub-str168_ctr_rep5 was grown in 2xYT broth at 37C and harvested at exponential growth phase OD600 0.31

value: in-house Bacterial rRNA Depletion MIX for Cultures , oVP670


title: NIH3T3 cells, shCTRL_SCR3-D2_E2

value: Control - scramble

value: scrambled shRNA-UHMK1 sequence (shCTRL) which has target gene


title: c_4_01181AAC_CAGATC_batch2

value: Control IgG


title: NIH3T3 cells, shCTRL_SCR2-D2_C2


title: Iron deprivation time 9h Rep3

city: Montpellier

first: Sandrine

last: Ruffel

address: 2 Place Viala

department: Montpellier University

institute: INRA

description: Gene expression data from 10 days Arabidopsis roots on full nutrient medium + 9hours on an iron deprived medium

hyb_protocol: Following fragmentation, 5.5ug of cDNA were hybridized for 16 hr at 48C on GeneChip 1.1ST Array Strip. GeneChips were washed and stained in the Affymetrix GeneAtlas Fluidics Station.

scan_protocol: Array strips were scanned using the Affymetrix GeneAtlas Imaging Station.

data_processing: The data quality analysis was done with the Affymetrix Expression Console software. The normalization of the raw data was done with the Affymetrix Transcriptome Analysis Console software using the GCRMA method.

label: biotin

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana 10 Days old

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (GeneChip® WT PLUS Reagent Kit Manual Target Preparation for GeneChip® Whole Transcript (WT) Expression Arrays).

growth_protocol: Arabidopsis Columbia-0 plants were grown on a growth medium containing 1mM Pi

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: One part of the plants was transferred to a nutrient medium not containing Pi (0Pi)  for 3, 6 and 9 h. One part of the plants was transferred to a nutrient medium not containing Fe (0Fe)  for 3, 6 and 9 h and one part was tranferred to a nutrient medium not containing Pi (0Pi) and Fe (0Fe)  for 3, 6 and 9 h.

tag: tissue

value: Roots

tag: ecotype

value: 10 days


title: bsub-str168_frag_r2_s_r_v2

value: Untreated

value: bsub-str168_frag_rep2 was grown in 2xYT broth at 37C and harvested at exponential growth phase OD600 0.621

value: random fragmented ( Standard 5PSeq), RNA rP5_RND oligo for RNA ligation

value: Ribo-Zero rRNA Removal Kit (Bacteria) Illumina


title: bsub-str168_frag_r3_s_r_v2

value: bsub-str168_frag_rep3 was grown in 2xYT broth at 37C and harvested at exponential growth OD600 0.6