title: MD, brain cells, Mut, replicate 2, scRNAseq

first: Shaonan

last: Wen

address: Beijing 100875, China

institute: Beijing Normal University

data_processing:
The demultpexna, barcoded processing,gene counting and acgregation were made using the Cell Ranger software v6.2.1 (he demultpexna. barcoded processing counting and acgregation were made using the Cell Ranger software v2.1.1 (htios:/support 10xcenomics com/sindle-cel-aene-expression/software/pipelines/latest/what-is-cel-ranger).
Assembly: ASM1176430v1.1
Supplementary files format and content: Tab-separated values files and matrix files

organism: Mustela putorius furo

source_name: brain

extract_protocol:
Somatosensory cortices were dissected carefully from fresh-frozen tissues stored in liquid nitrogen. Samples were minced into pieces <5 mm and then homogenized using a glass dounce tissue grinder (Sigma, D8938) in 2 mL of Nuclei EZ lysis buffer (Sigma, NUC-101) on ice. After two incubations on ice (with 4 mL of lysis buffer and 5 min each time), the homogenate was filtered through a 70 µm strainer, and then we used Debris Removal Solution (Miltenyi Biotech, 130-109-398) to perform density gradient centrifugation to clean the nuclear suspension according to the manufacturer’s protocol. Isolated nuclei were resuspended and washed with nuclei suspension buffer (NSB, consisting of 1× PBS, 0.1% BSA and 0.4 U/µL Ambion™ RNase inhibitor (Thermo Fisher, AM2684)) and filtered through a 35 µm cell strainer. Nuclei were counted using a hemocytometer and diluted to 1000 nuclei/μL for optimal 10× loading. Approximately 8000 nuclei were targeted and captured for each reaction.
All the libraries were prepared on a 10X GENOMICS platform following the RNA library preparation protocols. Cells were partitioned into nanoliter-scale Gel Bead-In EMulsions (GEMs) using 10x GemCode Technology, where a common 10x Barcode labeled all the cDNA produced from the same cell. Primers containing an Illumina R1 sequence (read1 sequencing primer), a 16-bp 10x Barcode, a 10-bp randomer, and a poly-dT primer sequence were released and mixed with cell lysate and Master Mix upon dissolution of the single cell 30 gel bead in a GEM. The GEMs were incubated, and barcoded, full-length cDNA was generated from poly-adenylated mRNA by reverse transcription. Then the GEMs were broken, and the leftover biochemical reagents and primers were removed with silane magnetic beads. Before constructing the library, the cDNA amplicon size was optimized by enzymatic fragmentation and size selection. After that, P5, P7, a sample index, and R2 (read 2 primer sequence) were added to each selected cDNA during end repair and adaptor ligation. P5 and P7 primers were used in Illumina bridge amplification of the cDNA (http://10xgenomics.com). Finally, 150-bp paired-end reads were sequenced from each library using the Illumina HiSeq4000. Concerning the update of the Single Cell 3’ Regent Kits version, two libraries were prepared with Single Cell 3’ Regent Kits V3.

value: brain

tag: tissue region

value: deeper band of cortex

value: DCX knockout


title: LT2_Fur_Fe_1

status: Public on Aug 04 2023

type: SRA

city: La Jolla

first: Ye

last: Gao

address: 9500 Gilman Dr.

country: USA

institute: UCSD

library_source: genomic

data_processing:
Library strategy: ChIP-exo
The base calling was done using Illumina’s Real-Time Analysis (RTA) v2.7.7; data was converted to fastq and demultiplexed using Illumina’s bcl2fastq2 Conversion Software v2.20;
Sequence reads generated from ChIP-exo were mapped onto the each reference genome using bowtie with default options to generate SAM output files
MACE program was used to define peak candidates from biological duplicates for each experimental condition with sequence depth normalization.
To reduce false-positive peaks, manual curation was performed based on the signal-to-noise(S/N) ratio value.
The calculation of S/N ratio resembles the way to calculate ChIP-chip peak intensity where IP signal was divided by Mock signal. Then, each peak was assigned to the nearest gene.
Genome_build: Each genome ( MG1655 =  NC_000913.2 / W3110 = NC_007779.1 / W  = NC_017635.1 , NC_017636.1 , NC_017637.1 / KO11FL = NC_017660.1 , NC_017661.1 / 042 = NC_017626.1 , NC_017627.1 / BL21 = NC_012971.2 / Crooks = NC_010468.1  / Sakai  = NC_002695.1 , NC_002127.1 , NC_002128.1  / CFT073 = NC_004431.1 / LT2 = NC_003197.2 , NC_003277.2 )
Supplementary_files_format_and_content: Tab-delimited text files in gff format which has 8 columns: sequence id, source(empty), feature (+/- strand), start position, end position, intensity score, strand(+/-), frame(.), attribute(.).

molecule: genomic DNA

organism: Salmonella enterica

source_name: bacteria cells

growth_protocol: glycerol stocks of E. coli and S. Typhimurium LT2 strains were inoculated into M9 minimal media with 0.2% (w/v) glucose. The culture was incubated at 37 oC overnight with agitation, and then was used to inoculate the fresh media (1/200 dilution). The volume of the fresh media was 150 mL for each biological replicate. The fresh culture was incubated at 37 oC with agitation to the mid-log phase (OD600 ≈ 0.5).

extract_protocol:
Lysates were clarified from sonicated uncharacterized transcripton factors-DNA complexes were isolated with myc antibody.
ChIP-exo experiment was performed following the procedures:  to identify each TF candidate binding maps in vivo, we isolated the DNA bound to each TF candidate from formaldehyde cross-linked E. coli cells by chromatin immunoprecipitation (ChIP) with the specific antibodies that specifically recognizes myc tag (9E10, Santa Cruz Biotechnology), and Dynabeads Pan Mouse IgG magnetic beads (Invitrogen) followed by stringent washings as described previously [42]. ChIP materials (chromatin-beads) were used to perform on-bead enzymatic reactions of the ChIP-exo method [11]. Briefly, the sheared DNA of chromatin-beads was repaired by the NEBNext End Repair Module (New England Biolabs) followed by the addition of a single dA overhang and ligation of the first adaptor (5’-phosphorylated) using dA-Tailing Module (New England Biolabs) and NEBNext Quick Ligation Module (New England Biolabs), respectively. Nick repair was performed by using PreCR Repair Mix (New England Biolabs). Lambda exonuclease- and RecJf exonuclease-treated chromatin was eluted from the beads and the protein-DNA cross-link was reversed by overnight incubation at 65oC. RNAs- and Proteins-removed DNA samples were used to perform primer extension and second adaptor ligation with following modifications. The DNA samples incubated for primer extension as described previously [12] were treated with dA-Tailing Module (New England Biolabs) and NEBNext Quick Ligation Module (New England Biolabs) for second adaptor ligation. The DNA sample purified by GeneRead Size Selection Kit (Qiagen) was enriched by polymerase chain reaction (PCR) using Phusion High-Fidelity DNA Polymerase (New England Biolabs). The amplified DNA samples were purified again by GeneRead Size Selection Kit (Qiagen) and quantified using Qubit dsDNA HS Assay Kit (Life Technologies). Quality of the DNA sample was checked by running Agilent High Sensitivity DNA Kit using Agilent 2100 Bioanalyzer (Agilent) before sequenced using HiSeq (Illumina) in accordance with the manufacturer’s instructions. Each modified step was also performed in accordance with the manufacturer’s instructions. ChIP-exo experiments were performed in biological duplicate.

treatment_protocol: For iron-replete condition, M9 minimal media was supplemented with 0.1 mM FeCl2 ; for iron-depleted condition, M9 minimal media was supplemented with 0.2 mM 2,2’-dipyridyl at early-log phase and continue to culture at 37 oC for additional 2h with vigorous agitation; for regulatory condition, M9 minimal media was supplemented with 1 mL trace element solution (100X) containing 1 g EDTA, 29 mg ZnSO4.7H2O, 198 mg MnCl2.4H2O, 254 mg CoCl2.6H2O, 13.4 mg CuCl2, and 147 mg CaCl2.

tag: strain

value: Typhimurium LT2

tag: myc-tagging

value: Fur myc-tagging cells

tag: chip-exo antibody

value: c-myc(9E10) mouse monoclonal IgG1,sc-40, lot#J2413, Santa Cruz Biotechnology


title: LT2_WT_Fe_2

library_source: transcriptomic

data_processing:
The base calling was done using Illumina’s Real-Time Analysis (RTA) v2.7.7; data was converted to fastq and demultiplexed using Illumina’s bcl2fastq2 Conversion Software v2.20;
Sequence reads generated from RNA-seq were mapped onto each reference genome using bowtie with the maximum insert size of 2000 bp, and 2 maximum mismatches after trimming 3 bp at 3’ ends
SAM files generated from bowtie, then, were then used for DESeq(https://bioconductor.org/packages/release/bioc/html/DESeq.html)
Cufflinks was run with default options with the library type of dUTP RNA-seq and the default normalization method (classic-fpkm)
Genome_build: The reference genomes used in this study are shown as below,  MG1655 =  NC_000913.2 / W3110 = NC_007779.1 / W  = NC_017635.1 , NC_017636.1 , NC_017637.1 / KO11FL = NC_017660.1 , NC_017661.1 / 042 = NC_017626.1 , NC_017627.1 / BL21 = NC_012971.2 / Crooks = NC_010468.1  / Sakai  = NC_002695.1 , NC_002127.1 , NC_002128.1  / CFT073 = NC_004431.1 / LT2 = NC_003197.2 , NC_003277.2
Supplementary_files_format_and_content: tab-delimited text files containing TPM values for each sample

molecule: total RNA

extract_protocol:
Three milliliters of cells from mid-log phase culture were mixed with 6 ml RNAprotect Bacteria Reagent (Qiagen), mixed immediately by vortexing for 5 seconds, incubated for 5 minutes at room temperature, and then centrifuged at 5000g for 10 minutes. The supernatant was decanted and any residual supernatant was removed, then samples were frozen at -80℃. Next, RNA was harvested using RNeasy Plus Mini kit (Qiagen) in accordance with the manufacturer’s instruction. Illumina Ribo-Zero rRNA removal kit (bacteria) (MRZMB126) was used with 1 ug of total RNA for the removal of rRNA procedure. Then KAPA RNA HyperPrep kits(Cat.No.08098107702) was used with rRNA-depleted RNA samples for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: medium

value: glucose M9 minimal

tag: phase

value: mid-log phase

tag: genotype

value: wild type


title: N2-iPSC, rep 1

city: Taipei

first: Yu-Hui

last: Wong

state: Taiwan

address: (NYCU) No. 155, Sec. 2, Linong St., Beitou Dist.

country: Taiwan

institute: National Yang Ming Chiao Tung University

data_processing:
The fastq format reads underwent quality filter (score >= Q15, qualified percentage > 60%) and adapter trimming using fastp (0.20.1).
The remain reads were mapped to Human Genome Reference GRCh38 using STAR (2.7.5a) to generate output in the BAM file format.
Expected counts were then estimated using RSEM (1.3.1).
Downstream analysis of the expected counts was performed in R Statistical Software (v4.2.1; R Core Team 2022) using DESeq2 (1.36.0).
Assembly: Human Genome Reference GRCh38
Supplementary files format and content: tab-delimited text file includes expected counts for each samples

organism: Homo sapiens

growth_protocol: Human iPSCs are maintained in Essential 8™ mediumor StemFlex™ medium (Gibco).

extract_protocol:
Total RNA of iRGCs from days 7, 14 and 28 were extracted using RNA Mini Kit (Geneaid).
1 μg of total RNA was used for following library preparation. The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.

treatment_protocol:
Human iPSCs for RGC differentiation are infected with lentiviruses encoding ubiquitously driven reverse tetracycline transactivator (rtTA) and Tet-On promoter driven ATOH7, BRN3B and SOX4 sequentially.
The differentiation process was started by addition of 2 μg/mL doxycycline, defined as day 0. Cells were then cultured in Medium-1: DMEM/F12 (Gibco) supplemented with N-2 (Gibco), 0.1 mM NEAA and 200 ng/mL mouse laminin (Gibco) with various other supplementary substances, namely brain-derived neurotrophic factor (BDNF, 10 μg/mL, PeproTech), ciliary neurotrophic factor (CNTF, 10 μg/mL, PeproTech), basic fibroblast growth factor (bFGF, 5 μg/mL, PeproTech), and forskolin (10 μM, Sigma-Aldrich). On day 1, Medium-1 was refreshed and 1 μg/mL puromycin and 2 μg/mL zeocin were added to allow selection of successfully induced cells.
On day 2, the cells were then dissociated using 0.5 mM EDTA in DPBS and replated onto poly-L-lysine- and laminin-coated culture plates for culture in Medium-2: DMEM/F12 + Neurobasal (1:1) supplemented with N-2, B-27, GlutaMAX (Gibco) and 200 ng/mL mouse laminin (Gibco) with supplementary substances. Zeocin selection was continued until day 6. On day 4 after doxycycline induction, Medium-2 was refreshed with 25 μM AraC to inhibit proliferation of undifferentiated cells.
On day 6, after 48 hrs of AraC treatment, Medium-2 was replaced by Medium-3: Neurobasal supplemented with N-2, B27 and GlutaMAX with supplementary substances. Hereafter, the cells were cultured in Medium-3 and medium was half refreshed every 3-4 days until day 15 or day 20, when the cells were used for downstream applications.The supplementary substances included doxycycline (2 μg/mL), brain-derived neurotrophic factor (BDNF, 10 μg/mL, PeproTech), ciliary neurotrophic factor (CNTF, 10 μg/mL, PeproTech), neurotrophin-3 (NT-3, 10 μg/mL, PeproTech), basic fibroblast growth factor (bFGF, 5 μg/mL, PeproTech), insulin (5 μg/mL, PeproTech) and forskolin (10 μM, Sigma-Aldrich)

tag: cell line

tag: cell type

value: hiPSC


title: LT2_WT_Fe_1


title: NR2F2 ChIP-seq on GD3.5 uteri replicate A

status: Public on Aug 03 2023

city: RTP

first: Franco

last: Demayo

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

data_processing:
The raw reads were trimmed by trim_galore (v0.4.4) (quality score < 20),
mapped with genome mm10.
The duplicate reads were removed using the MarkDuplicates tool in picard-tools-1.96.
The retained read alignments were sorted by coordinates, extended to 300 bases
Assembly: mm10

organism: Mus musculus

source_name: uterus

growth_protocol: C57B6/J female mice were mated at 8 weeks old whose uterus were collected at Pregnancy day 3.5

extract_protocol:
The uterus were frozen and sent to Active motif for ChIP-Seq analysis
NEXTflex Rapid DNA-Seq kit (Perkin Elmer)

treatment_protocol: No treatment

tag: tissue

value: uterus

tag: pregnancy day

value: Gestation day 3.5

tag: antibody

value: Polyclonal NR2F2 / COUP2 antibody Active Motif 61213


title: NR2F2 ChIP-seq on GD3.5 uteri replicate B


title: MU, brain cells, Mut, replicate 1, scRNAseq

city: Beijing

country: China

library_source: transcriptomic single cell

molecule: polyA RNA

value: upper band of cortex


title: Input-Seq for NR2F2 ChIP-seq

value: input


title: H3K4me1 ChIP-seq on GD3.5 uterus ChIP-seq

value: Polyclonal Histone H3K4me1 antibody Active Motif 39298


title: Adult male 1 liver (NYU, RNA)

city: New York

first: Paul

last: Frazel

state: NY

address: 435 E 30th St

institute: NYU Langone Medical Center

description:
final.gtf
S.Teguina_genome_st1.fasta

data_processing:
10xGenomics Multiomics libraries were processed using CellRanger  (v3.0.1) with custom premrna transcriptome
Supplementary files format and content: processed files include 10X genomics h5 gene expression file, genome file (fasta), gene annotation file (gtf)

organism: Scotinomys teguina

source_name: Adult male liver

extract_protocol:
scRNAseq: Single Index Illumina libraries were prepared following 10xGenomics Multiome instructions. Bulk RNAseq: libraries were processed on automated platform, see manuscript. Genomic DNA libraries: manufacturer's instructions were followed for each sequencing approach (see protocol column).
Qiagen DNA or RNA kits; Trizol

value: liver


title: Adult female liver (NYU, RNA)

description:
final.gtf
S.Teguina_genome_st1.fasta

source_name: Adult female liver


title: Adult male 2 brain2 (NYU, RNA)

description:
final.gtf
S.Teguina_genome_st1.fasta

source_name: Adult male forebrain

value: forebrain


title: Adult female brain1 (NYU, RNA)

description:
final.gtf
S.Teguina_genome_st1.fasta

source_name: Adult female forebrain


title: Adult male 2 liver (NYU, RNA)

description:
final.gtf
S.Teguina_genome_st1.fasta


title: Adult male 2 brain1 (NYU, RNA)

description:
final.gtf
S.Teguina_genome_st1.fasta


title: Adult male 1 brain1 (NYU, RNA)

description:
final.gtf
S.Teguina_genome_st1.fasta


title: Mouse_P21_2

city: Singapore

first: Lih Feng

last: Cheow

address: 4 Engineering Drive 3

department: Biomedical Engineering

country: Singapore

institute: National University of Singapore

data_processing:
UMI processed using umi-tools version 0.5.4
Unmethylation, methylation, and hydroxymethylation reads were separated and the tags were removed using Cutadapt version 1.5
Reads were aligned to the human genome using bowtie2 version 2.3.4.1
PCR duplicates were removed using umi-tools version 0.5.4
Assembly: hg38
Supplementary files format and content: bed files containing chromosome, start, end, 5C ratio, 5mC ratio, 5hmC ratio and coverage for each CCGG site
Library strategy: LM-PCR WGA

extract_protocol:
For bulk samples, DNA was extracted using Qiagen Dneasy Blood and Tissue kit. Single cells were stained with Calcein-AM dye and isolated into tubes.
Bulk samples undergo DARESOME protocol and single cells undergo scDARESOME. Cells were lysed and protease treated prior to HpaII digestion. Digested unmethylated sites were ligated with unmethylation-tag (U-tag) adapters. Excess adapters were then removed using NEB Thermolabile USER II enzyme. This was followed by the second round of digestion with MspI and NlaIII enzymes. Hydroxymethylation-tag (H-tag) and Nla-tag (N-tag) adapters were ligated with the digested fragments. Excess adapters and oligonucleotides were removed with Thermolabile USER. 5hmC CCGG sites were glucosylated by glusyl transferese. The samples then undergo MspI digestion, methylated CCGG sites are digested and liagated to Methylated-tag (M-tag). The Read1 and Read2 Illumina sequencing adapters were added through PCR. The amplified library was size selected using BluePippin and quantified using Kapa Library Quantification kit.

value: Cerebellum


title: N1-iPSC, rep 1


title: Mouse_32weeks_2


title: LT2_Fur_Fe_2


title: Adult male forebrain for 10X snRNAseq

description:
filtered_feature_bc_matrix.h5
S.Teguina_genome_st1.fasta


title: Adult male liver (UT, RNA)

description:
final.gtf
S.Teguina_genome_st1.fasta


title: Adult male liver for Promethion

description:
final.gtf
S.Teguina_genome_st1.fasta

extract_protocol:
High molecular weight gDNA libraries prepared according to manufacturer's instructions (PromethION long-read machine; Oxford Nanopore, August 2018)
Qiagen DNA or RNA kits; Trizol


title: Adult male gonads (UT, RNA)

description:
final.gtf
S.Teguina_genome_st1.fasta

source_name: Adult male gonads

value: gonads


title: Adult male forebrain (UT, RNA)

description:
final.gtf
S.Teguina_genome_st1.fasta


title: Mouse_32weeks_1


title: Adult male liver for Pacbio

description:
final.gtf
S.Teguina_genome_st1.fasta

extract_protocol:
High molecular weight gDNA libraries prepared according to manufacturer's instructions (SEQUEL long-read machine; Pacific Biosciences, December 2017)
Qiagen DNA or RNA kits; Trizol


title: Adult female brain2 (NYU, RNA)

description:
final.gtf
S.Teguina_genome_st1.fasta


title: PBMC, Atezo-carbo-nabP, Post-Treatment [G2]

city: Sacramento

first: Tianhong

last: Li

address: 2700 Stockton Blvd

institute: UC Davis Health

data_processing:
Reads mapped to hg38 with Salmon v1.6.0
Extracted read counts and Transcripts Per Million with DESeq2
Immune cell proportions estimated using CIBERSORTx
Assembly: hg38
Supplementary files format and content: tab-delimited text files include transcript per million values for each sample

source_name: PBMC

growth_protocol: PBMC isolated by Ficoll Gradient.

extract_protocol:
RNA was isolated from 1 million of PBMCs using the RNeasy mini kit (Qiagen).
Novogene Corporation Inc. constructed RNA libraries for RNAseq using TruSeq Stranded Total RNA Sample Prep Kit (Illumina).

value: PBMC

tag: treatment


title: PBMC, KN495, Post-Treatment [H2]

value: Combination ICI


title: PBMC, Ipi-Nivo, Pre-Treatment [I1]

value: Ipilimumab, Nivolumab


title: PBMC, Atezo-carbo-nabP, Pre-Treatment [G1]


title: Adult male 1 brain2 (NYU, RNA)

description:
final.gtf
S.Teguina_genome_st1.fasta


title: PBMC, KN495, Pre-Treatment [H1]


title: APRIL KO LPS #4

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

data_processing:
RNA-seq data were aligned with STAR  against the Mm10 reference genome. Aligned BAM files  were quantified as exon-exon junction-level RPKM  using AltAnalyze version 2.1.4 using the Ensembl 72 database (Emig, Salomonis et al. 2010). Differential gene expression analysis was performed in AltAnalyze using an empirical Bayes t-test p<0.05 and fold >1.5. Prioritized gene expression patterns were obtained using the MarkerFinder algorithm in AltAnalyze. Gene set enrichment analysis was performed in both AltAnalyze (Pathway Commons database) and ToppGene (Chen, Bardes et al. 2009).
Assembly: mm10
Supplementary files format and content: Gene-level RPKM estimates.

source_name: Macrophages

extract_protocol:
RNA from bone marrow derived macrophages was isolated using the mirVANA RNA isolation kit.  To measure the library concentration, NEBNext Ultra II Directional RNA Library Prep kit  (New England BioLabs) was used.
Library construction was performed using the TruSeq RNA Library Prep Kit (Illumina) according to the manufacturer's protocols. RNA-seq was performed using the Illumina NextSeq 550 with the sequencing setting of single read 85 bp to generate ∼20 M reads per sample.

treatment_protocol: Bone Marrow derived Macrophages from C57BL/6 (WT), BAFF KO and APRIL KO where stimulated with LPS (10ng/ml) for 4 hours.

value: Bone marrow macrophages

value: APRIL KO

tag: time point

value: Preterm birth (day 16 gestation)

value: LPS

tag: perturbation


title: PBMC, Atezo-carbo-nabP, Post-Treatment [F2]


title: PBMC, CK-9LA, Post-Treatment [E2]

value: Ipilimumab, Nivolumab, Chemotherapy


title: Adult male skeletal muscle  (UT, RNA)

description:
final.gtf
S.Teguina_genome_st1.fasta

source_name: Adult male skeletal muscle

value: skeletal muscle


title: PBMC, CK-9LA, Pre-Treatment [E1]


title: APRIL KO LPS #1


title: Adult male liver for Illumina

description:
final.gtf
S.Teguina_genome_st1.fasta

extract_protocol:
Two Illumina gDNA libraries were created: a fragmentation library consisting of 170, 400, and 900 bp segments (PE Barcode+2x100, 3 lanes = 510M reads requested) and a mate-pair library with a 3KB insert size (PE Barcode+2x100, 1 lane=170M reads requested).
Qiagen DNA or RNA kits; Trizol


title: PBMC, Ipi-Nivo, Post-Treatment [D2]


title: APRIL KO No stimulated #1


title: BAFF KO LPS #4

value: BAFF KO


title: PBMC, Ipi-Nivo, Pre-Treatment [D1]


title: BAFF KO LPS #3


title: APRIL KO LPS #3


title: BAFF KO LPS #2


title: APRIL KO LPS #2


title: PBMC, PEM, Post-Treatment [B2]

value: Pembrolizumab


title: PBMC, KN495, Post-Treatment [C2]


title: BAFF KO LPS #1


title: PBMC, PEM, Pre-Treatment [B1]


title: BAFF KO No stimulated #2


title: MAC CD80 high

city: Washington

first: Xiaolong

last: Cheng

state: DC

address: 7144 13th Place NW

institute: Children's National

data_processing:
Read count table generated by MAGeCK 0.5.9.4
MAGeCK count command was used to collect read count from the fastq file
Assembly: hg38
Supplementary files format and content: tab-delimited text files include normalized counts for each Sample

source_name: iMAC

growth_protocol: THP-1 cells were maintained in RPMI1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃. Human iPSCs were cultured in mTeSR medium (85852, STEMCELL Technologies) with Matrigel Matrix (354277, Corning) coated plates.

extract_protocol:
The genomic DNA of cells was isolated using TIANamp Micro DNA Kit.
The libraries were prepared using VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme).
Indexing of genomic DNA by sequencing

treatment_protocol: Macrophages were stimulated by LPS (50 ng/mL) plus IFN-γ (50 ng/mL) for 24 h. The stimulated cells were harvested and stained with anti-human CD80-FITC (305206, BioLegend) for 15 min at room temperature. The CD80-high and CD80-low cells were separated by flow cytometry sorting.

value: iMAC

value: macrophage

value: LPS and  IFN-γ stimulation

tag: sorted cells

value: MAC CD80 high


title: PBMC, Atezo-carbo-nabP, Pre-Treatment [F1]


title: PBMC, PEM, Post-Treatment [A2]


title: MAC CD80 low

value: MAC CD80 low


title: MAC presort

value: MAC presort


title: WT LPS #4

value: WT


title: WT LPS #2


title: THP1 CD80 high

value: THP1 CD80 high


title: WT LPS #3


title: APRIL KO No stimulated #2


title: THP1 CD80 low

value: THP1 CD80 low


title: WT LPS #1

value: Bone marrow macrophages


title: THP1 presort

value: THP1 presort


title: WT No stimulated #1

value: Preterm birth (day 16 gestation)


title: 4 days post EBV infection, Replicate 2

city: Kolkata

first: Samaresh

last: Malik

state: West Bengal

address: Street-358, Action Area-1, Newtown

department: Institute of Health Sciences

country: India

institute: Presidency University

data_processing:
High-quality reads were processed through Trimmomatic v0.35 to eliminate adapter sequences
The trimmed sequences were then aligned to the Human reference genome (Homo sapiens.GRCh37) using BWA v0.7.12 with default parameters.
Read counts were determined using featureCounts v2.0.3, followed by differential expression analysis conducted with DESeq v1.8.1
Assembly: hg38
Supplementary files format and content: Excel sheets containing DESeq output
Supplementary files format and content: .xlsx

source_name: PBMCs

extract_protocol:
RNA was extracted using the PureZOL™ RNA Isolation Reagent (Bio-Rad, USA).
A total of 5µg of RNA that passed quality control (QC) was utilized for library preparation employing the Illumina TruSeq standard mRNA sample prep kit.

value: PBMCs

tag: time

value: 4 day

value: Infected


title: 4 days post EBV infection, Replicate 1


title: WT No stimulated #2


title: CTC_MCC_41.5G_S2_TR2

city: Leiden

first: Danijela

last: Koppers-Lalic

address: Albinusdreef 2

department: Medical Oncology & Medical Microbiology

country: Netherlands

institute: Leiden University Medical Center

description: Sample 2 Co-incubate indirect  with CTC-MCC-41.5G

data_processing:
The pre-processing step includes the concatenation of the technical replicates per sample and was performed with Concatenate datasets tail-to-head tool (version 0.1.1) and adapters were removed with TrimGalore (version 0.6.7) on Galaxy Platform
Reads mapped to Ensemble gene set (GRCh38.103) with Hisat2 (version 2.1.0) and read counts were extracted with FeatureCounts (version 2.0.1) on Galaxy Platform
Normalization and differential expression differential analysis was performed with the EdgeR package (version 3.38.1) in R (version 4.0.1)
Assembly: hg38
Supplementary files format and content: Read counts: Data_matrix.txt

source_name: Blood

growth_protocol: Cells were grown in suspension under normoxia using RPMI 1640 (Eurobio ref: CM1RPM00-01 supplemented with 10%  fetal calf serum, insulin-transferrin-selenium L-glutamine epidermal growth factor, and beta fibroblast growth factor. Before platelets were added, CTCs were cultured in the serum-free medium (conditioned medium) for 24 hours. Also, the control serum-free media was incubated for the same time as the CTCs.

extract_protocol:
Total RNA isolation of platelets was performed using mirVana miRNA isolation kit (Ambion, Thermo Scientific ref: AM1560)
RNA libraries for RNA-seq were prepared using SMARTer Stranded Total RNA-seq kit (Pico Input Mammalian User Manual, TakaraBio, Kyoto, Japan)

value: Blood

value: platelets

value: Sample 2 Co-incubate  with CTC-MCC-41.5G


title: Uninfecetd PBMCS, Control

value: 0 day

value: Uninfected


title: CTC_MCC_41.5G_S1_TR1

description: Sample 1 Co-incubate  indirect with CTC-MCC-41.5G

value: Sample 1 Co-incubate  with CTC-MCC-41.5G


title: CTC_MCC_41.5G_S2_TR1


title: CTC_MCC_41.5G_S1_TR2


title: 2 days post EBV infection, Replicate 2

value: 2 day


title: 2 days post EBV infection, Replicate 1


title: BAFF KO No stimulated #1

value: BAFF KO


title: D8 hTSC-organoids infected with ZIKV at MOI 10

city: Suzhou

first: Hang-Yu

last: Zhou

state: Jiangsu

address: 100 Chongwen Road

institute: Institute of Systems Medicine, Chinese Academy of Systems Medicine

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Primary placenta derived hTSC

extract_protocol:
The Day 8 hTSC-organoids were removed from Matrigel using Cell Recovery Solution at 4℃ for 30 minutes (min). The free hTSC-organoids were further digested using TrypLE Express Enzyme in a shaker at 37℃ for 20 min, and pipetted every 5 min. The cells were collected by centrifugation and filtered through a 40 μm Cell Strainer. The cell viability was detected using trypan blue staining.
The construction of transcriptome libraries was performed following the standard protocol of 10x Genomics (v3). Briefly, the cDNA was purified after GEM generation, barcode addition, GEM-RT reaction and bead cleanup. The GEX libraries were generated following the protocol of 10x Genomics Chromium Single Cell 3’ Reagent Kits (v3). The concentration of each library was accurately detected for 10x Genomics sequencing.

value: Primary placenta derived hTSC

value: infected with ZIKV at MOI 10

tag: age

value: 8 days


title: CTC_MCC_41.4_S2_TR2

description: Sample 2 Co-incubate  indirect with CTC-MCC-41.4

value: Sample 2 Co-incubate  with CTC-MCC-41.4


title: CTC_MCC_41.4_S1_TR2

description: Sample 1 Co-incubate indirect with CTC-MCC-41.4

value: Sample 1 Co-incubate  with CTC-MCC-41.4


title: BT549_NCsi2

city: Adelaide

first: Katherine

middle: Anne

last: Pillman

state: SA

address: North Terrace

department: Centre for Cancer Biology

country: Australia

institute: Adelaide University

description: Replicate 2

data_processing:
Reads were mapped using the STAR (v2.6.1d) spliced alignment algorithm (Dobin et al., 2013) with parameters --twopassMode basic and --quantMode GeneCounts and otherwise default parameters. For each sample, a gene count file was produced containing the number of reads mapping to each gene.
From experiment-wide matrix (BT549_gene_counts.tsv), the Gene Count file for each sample, the third column column of counts (representing strand-specific gene counts) was selected and collated to form a table. Extra rows (N_unmapped, N_multimapping, N_noFeature, N_ambiguous) were excluded.
Assembly: Human reference genome (build hg19) using the iGenomes UCSC Refseq gene annotations
Supplementary files format and content: Raw STAR output gene count files (*ReadCounts.tsv).
Supplementary files format and content: BT549_gene_counts.tsv: collated tab-separated file containing strand-specific gene counts for all samples

growth_protocol: BT549 cells were grown at 37°C with 5% CO2 and maintained in RPMI media + 10%FCS

extract_protocol:
RNA was extracted using Trizol as per manufacturer's protocol.
RNA libraries for mRNAseq were started by using NEBNext® Poly(A) mRNA Magnetic Isolation Module to enrich the polyA RNA from total RNA, then library prep with KAPA RNA HyperPrep Kits according to the manufacturer’s guidelines

treatment_protocol: Cells were transfected with 20nM control or BNC2 siRNAs (obtained from GenePharma) using Lipofectamine 2000. Media was changed 6 hours post transfection. Sequencing was perfomed 6 days after transfection.

value: mesenchymal

value: WT

value: siRNA transfection with negative control siRNA


title: CTC_MCC_41_S2_TR2

description: Sample 2 Co-incubate  indirect with CTC-MCC-41

value: Sample 2 Co-incubate  with CTC-MCC-41


title: D8 hTSC-organoids

description: 10x Genomics


title: CTC_MCC_41.4_S1_TR1

description: Sample 1 Co-incubate  indirect with CTC-MCC-41.4

value: Blood


title: CTC_MCC_41_S2_TR1

value: platelets


title: BT549_BNC2si3

description: Replicate 3

value: siRNA transfection with BNC2 siRNA


title: BT549_NCsi1

description: Replicate 1


title: BT549_NCsi3

description: Replicate 3


title: CTC_MCC_41_S1_TR1

description: Sample 1 Co-incubate indirect  with CTC-MCC-41

value: Sample 1 Co-incubate  with CTC-MCC-41


title: BT549_BNC2si1

description: Replicate 1


title: CTC_MCC_41_S1_TR2

description: Sample 1 Co-incubate indirect with CTC-MCC-41


title: BT549_BNC2si2

description: Replicate 2


title: HD24_S2_TR2

description: Sample 2 control t=24h

value: Sample 2 control t=24h


title: HD24_S2_TR1

description: Sample 2 control t=24h


title: HD24_S1_TR2

description: Sample 1 control t=24h

value: Sample 1 control t=24h


title: Mouse_Kidney_C

city: Seoul

first: Junseok

last: Jeon

state: Seoul

address: 81, Irwon-ro, Gangnam-gu

department: Internal Medicine

country: South Korea

institute: Samsung Medical Center, Sungkyunkwan University School of Medicine

description: 10x Genomics

data_processing:
Both reads were aligned to the mm10-2020-A mouse genome reference sequence and quantified using CellRanger (version 5.0.1-dirty).
Assembly: mm10

source_name: Kidney

extract_protocol:
Each cell suspension was processed for the generation of scRNA-seq libraries using the Chromium Next Gem Single cell 5′ kit v2 (10x Genomics, USA, 1000263) according to the manufacturer’s protocol
Sequencing libraries were generated using Illumina HiSeq2500 according to the manufacturer’s instructions (Illumina).

treatment_protocol: JPI-289 100 mg/kg (n = 1) or saline (n = 1) was injected into the peritoneal cavity immediately before reperfusion during bilateral renal ischemia-reperfusion surgery.

value: Kidney

tag: stain

value: C57BL/6 mice

tag: Sex

value: Male

value: Saline


title: Mouse_Kidney_P

description: 10x Genomics


title: D8 hTSC-organoids infected with ZIKV at MOI 1

description: 10x Genomics

value: Primary placenta derived hTSC

value: infected with ZIKV at MOI 1

value: 8 days


title: HD24_S1_TR1

description: Sample 1 control t=24h


title: CTC_MCC_41.4_S2_TR1

value: Sample 2 Co-incubate  with CTC-MCC-41.4


title: Ginkgetin, replicate3

city: Wuhan

first: Chaoyang

last: Wang

address: Jiefang Avenue #1277

institute: Wuhan Union Hospital

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

source_name: liver tissue

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: liver tissue

value: treated with ginkgetin


title: Ginkgetin, replicate1


title: Ginkgetin, replicate2


title: HD0_S2_TR2

description: Sample 2 control t=0

value: Sample 2 control t=0


title: HD0_S1_TR2

description: Sample1 control t=0

value: Blood

value: Sample1 control t=0


title: Control, replicate3

value: treated with vehicle


title: HD0_S2_TR1

description: Sample 2 control t=0

value: platelets


title: Control, replicate1


title: HD0_S1_TR1

description: Sample1 control t=0


title: HO107

city: Rochester

first: Cheng

last: Zhang

state: MN

address: 200 1st street SW

institute: Mayo Clinic

data_processing:
Fastq files of pair-end RNA-Seq reads were aligned with STAR 2.6.0a to the reference genome GRCh38 with two-pass mode.
Gene level counts were obtained using featureCounts 1.4.6 from the subRead package.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw gene-level counts in csv file

source_name: Liver Metastasis

extract_protocol:
mRNA extracted using the Qiagen Rneasy Micro Kit. 200 ng of total RNA according to manufacturers instructions for Illumina TruSeq Stranded mRNA Sample Prep Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: Pancreatic Ductal Adenocarcinoma

value: Untreated

tag: tumor stage

value: Stage 4

value: Liver Metastasis


title: HO44

source_name: Primary Tumor

value: Stage 2

value: Primary Tumor


title: Ginkgetin, replicate3

first: Huanzhang

last: Niu

address: Jiefang Avenue 1277#

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

value: NASH mice


title: Ginkgetin, replicate2


title: Ginkgetin, replicate1


title: HO161

source_name: Patient-Derived Xenograft

value: Stage 1/2

value: Patient-Derived Xenograft


title: HO160


title: Control, replicate3


title: Control, replicate2


title: Control, replicate1


title: HO163


title: HO165


title: WT_M9_37_st_rep2

city: Warszawa

first: Adam

last: Kawałek

address: Pawinskiego 5A

department: Department of Microbial Biochemistry

country: Poland

institute: Institute of Biochemistry and Biophysics, PAS

data_processing:
Sequencing data were quality-checked and filtered using FASTP version 0.20.0.
Reads were mapped to P. aeruginosa PAO1161 genome (CP032126) using Bowtie2 version 2.3.4.3 using default settings.
Obtained *.sam files were sorted (samtools sort -n), run through samtools fixmate with the -m option, again sorted (samtools sort) and duplicates were marked with samtools markdup. Samtools ver. 1.9 was used.
The files were indexed and used to generate coverage *.bigwig files, normalized to 1× sequencing depth (RPGC), without binning and smoothing using the bamCoverage tool ver 3.3.0 included in deepTools.
Assembly: CP032126
Supplementary files format and content: Processed files in bigwig format represent normalized coverages of individual base pairs in the P. aeruginosa PAO1161 genome. Reference genome is enclosed in fasta format (CP032126.fa) and the annotation used is enclosed as a .bed (CP032126.bed). A modified .bed file with PAO1161 feature names changed to the names of corresponding PAO1 genes (PA… format) is included for convenience of data browsing e.g. using IGV (CP032126_PA_names.bed).

organism: Pseudomonas aeruginosa

source_name: bacterial cell

growth_protocol: P. aeruginosa PAO1161 strains were freshly  streaked from glycerol stocks kept at -80°C. Two independent overnight cultures from each strain were inoculated from single colonies and grown overnight with shaking at 37°C. After that they were diluted 1:200 in LB (DifcoTM L Broth, Lennox, BD) and grown with shaking at 37°C until reaching exponential phase with optical density about 0.5 (OD600) or stationary phase (24h). For cultures growing in M9 + 0.5% glucose, 100µg/ml leucine was added, overnight cultures were diluted 1:100, and cells were harvested at OD600nm of 0.25 (log) or after 36 hours of culturing (stationary).

extract_protocol:
Chromatin immunoprecipitation (ChIP) protocol was based on the method described earlier (Kawalek et al, 2018; Nucleic Acids Res. 46:9, 4592-4606; Modrzejewska et al, 2021; mSystems 6:4, e0001521). Two cultures of each strain with similar OD600 were combined, formaldehyde was added from a 37% stock to a final concentration of 1%, and the cultures were kept for 10 min at room temperature with gentle inverting. Glycine was added to a final concentration of 0.5 M and the cultures were incubated for 5 min at room temperature with gentle rotation. Cells were then harvested by centrifugation (20 min, 3000 x g, 25 mL of culture in 50 mL conical tubes, 4 tubes per strain), washed twice with ice-cold Tris-buffered saline (25 mM Tris-HCl, 150 mM NaCl, pH=7.6), resuspended in 1 mL of TBS, transferred to a fresh 1.5 mL tube and centrifuged (2 min, 6000 x g). The cell pellets were frozen at -70oC. The pellets were thawed on ice, suspended in 0.5 mL of lysis buffer [10 mM Tris-HCl, 20% (w/v) sucrose, 50 mM NaCl, 10 mM ethylenediaminetetraacetic acid (EDTA), pH=8.0] supplemented with 10 µl of Protease Inhibitor Cocktail (Sigma, PA8849) and 125 µL of lysozyme (20 mg/mL) and incubated for 30 min at 37oC. Four samples for each strain were combined in 15 mL. Subsequently, 1.5 mL of IP-buffer [50 mM Tris-HCl, pH=7.5, 150 mM NaCl, 1 mM EDTA, 1% (v/v) Triton X-100, 0.1% (m/v) sodium deoxycholate], 30 µL protease inhibitor cocktail, PMSF (phenylmethanesulfonyl fluoride) to a final concentration of 2 mM, SDS (sodium dodecyl sulphate) to a final concentration of 0.1% were added to each sample. The samples were sonicated 20 times for 20 s each with 1 min break on ice using a Microson ultrasonic cell disruptor Xl2000 (Misonix) with 5-mm tip and 90% of output power to obtain DNA fragments of an average length of 250-350 bp. DNA fragmentation was checked by agarose gel electrophoresis. After sonication, samples were aliquoted (1 mL in 1.5 mL tubes) and stored at -70oC. Sonicated lysate was thawed on ice and 150 μL of each strain variant was incubated with 20 μL of magnetic beads coupled with protein A (Dynabeads Protein A, Invitrogen, 10001D) previously separated from original suspension using Magnetic Separation Stand. Such pre-clearing step was performed for minimum 1 hour at 4oC with rotation of the mixtures. In the meantime 50 μL of magnetic beads were prepared for each reaction by separating from the suspension as above. It was then mixed with anti-ParB antibodies (3 μg,  diluted in 200 μL of PBS with 0.05% Tween-20. Mixtures of magnetic beads and antibodies were incubated for 10 minutes at 4oC with gentle rotation. Beads with bound antibodies were then separated from the supernatant, washed once with 200 μL of the PBS with 0.05% Tween-20 solution and stored on ice. Pre-cleared lysate was separated from the beads used for pre-incubation and added to the beads coated with antibodies. Mixture containing lysate and magnetic beads with antibodies was incubated at 4oC for 20 minutes with mixing on rotator. Beads were then collected and washed. Elution was performed twice for 15 minutes in 50 μL at 65oC in thermoblock with shaking (1400 rpm). All 100 μL of obtained eluates were incubated with 1 μL of RNase A (100 mg/mL, Qiagen, 19101) for 30 min at 65oC. Then, 5 μL of Proteinase K (20 mg/mL, Qiagen, 19133) was added and the samples were incubated for 1 h at 50oC followed by overnight incubation at 65oC. Such prepared probes were stored on ice and 3 μL of 3 M sodium acetate (pH=5) was added. DNA purification was performed using Qiaquick Qiagen PCR purification Kit according to manufacturer’s instructions. The DNA was stored at -20oC.
NGS library was constructed using QiaSeq Ultralow Input Library kit. Sample was further quality checked on 1% agarose gel and concentration was measured using qPCR KAPA Library Quantification Kit.

tag: strain

value: PAO1161 leu-

value: WT

tag: growth phase

value: M9 37oC stationary phase of culture growth

value: bacterial cell

tag: chip antibody

value: Anti-ParB (rabbit, polyclonal)


title: HO153


title: HO145


title: HO133


title: WT_M9_37_st_rep1

tag: genotype

tag: cell type


title: HO159

tag: tissue


title: Control, replicate2

value: liver tissue


title: HO228


title: WT_M9_37_log_rep2

value: M9 37oC log phase of culture growth


title: HO231


title: HO227


title: WT_M9_30_st_rep2

value: M9 30oC stationary phase of culture growth


title: WT_M9_37_log_rep1


title: WT_M9_30_log_rep2

value: M9 30oC log phase of culture growth


title: WT_M9_30_st_rep1


title: 2_C, Ishikawa cells, JWG-071

city: Sabadell

first: IDOIA

middle: BOLINAGA

last: AYALA

state: Barcelona

address: CARRER DE JESUS, 8, 2

department: Bioquímica, biología molecular facultad de medicina

country: Spain

institute: UNIVERSIDAD AUTONOMA DE BARCELONA

data_processing:
Dr Tom BGI Software
Sequencing Platform：DNBSEQ-G400
Sequencing length：PE100
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Dr Tom BGI Software. This project uses the filtering software SOAPnuke developed by BGI independently for filtering (parameter- Remove the reads containing the adaptor(adaptor pollution); Remove reads whose N content is greater than 5%; Remove low-quality reads (we define reads with bases with a quality score less than 15 as the proportion of total bases in the reads that are greater than 20% as low-quality reads).
After getting clean reads, we used HISAT to align the clean reads to the reference genome GCF_000001405.38_GRCh38.p12.
Assembly: Read count extraction and normalization were performed using DR Tom BGI Software
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Endometroid

growth_protocol: Ishikawa cells were maintained in MEM supplemented with 5% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol: RNA was purified from Ishikawa cells using RNeasy kit (Qiagen). RNA quality was evaluated using a Bioanalyzer 2100 (Agilent), and samples with a RIN value higher than 7 were selected

treatment_protocol: Ishikawa cells were treated with either vehicle or JWG-071 for 24 h

value: Endometroid

tag: cell line

value: Ishikawa

value: Epithelial


title: 2_A, Ishikawa cells, JWG-071

tag: treatment


title: HO219

value: Adenosquamous Pancreatic Ductal Adenocarcinoma

value: Untreated

value: Stage 2


title: 2_B, Ishikawa cells, JWG-071


title: HO222


title: 1_B, Ishikawa cells, control

value: DMSO


title: 1_C, Ishikawa cells, control


title: 1_A, Ishikawa cells, control


title: WT_LB_37_st_rep2

value: LB 37oC stationary phase of culture growth


title: WT_LB_37_st_rep1

value: PAO1161 leu-


title: OP2

city: guangzhou

first: Ruiqiang

last: Yan

address: 黄埔大道西601号

institute: Jinan University

data_processing:
Raw data were trimmed by Trim galore v0.4.1 to produce clean data (clean reads).
The clean reads were processed by Bismark v0.15.0 for genome alignment (Rat6) and the PCR duplicates were removed.The information of cytosine (C), CpG C and methylated CpG C (5mC), as well as their distribution and frequency, can be extracted from the information of genome alignment.
The methylation level of 5mC  is calculated by C/C+T(frequency).
The reads with more than 10X read depth were then processed by R methylkit v0.9.5 to indicate the details of the read depth and methylation level of all 5mC.
The methylation level of 5mC between groups were compared and annotated by DSS Bioconductor package, and the 5mC with mean methylation level difference > 10% and p < 0.05 between groups was considered to be differentially methylated site (DMS).
Genome_build: Rat6
Supplementary_files_format_and_content: text files

organism: Rattus norvegicus

source_name: OP_Colonic epithelia

extract_protocol:
Colonic epithelia (>95%) were obtained by scraping at 4 0C . Genome DNA was extracted with gDNA Extraction Kit (Omega Bio-Tek Research，USA) and sheared to fragments of 150-200 bp (Covaris E-series instrument, Australia).
DNA libraries were prepared with Agilent SureSelectXT Methyl-seq Library Pre kit and then hybridized with hybridization reagents, blocking agents and the SureSelect capture library.

tag: strain background

value: SD

value: female

tag: rat group

value: osteoporotic rat

value: colon

tag: tissue/cell type

value: Colonic epithelia


title: OP3


title: LSK, FLT3-ITD/ITD Llgl1-/- Mx1+, Rep2

city: Hannover

first: Tina

middle: M.

last: Schnoeder

address: Carl-Neuberg-Str. 1

country: Germany

institute: Hannover Medical School

description: alternative name for the analysis: 282_ITD_Cre_Llgl1_b2

data_processing:
Batch effect was corrected using the FLT3-ITD/ITD; Llgl1+/+; Mx1-Cre- samples (= sample271.fq.gz; sample236.fq.gz; AS-311282-LR-41637_R1.fastq.gz; AS-311280-LR-41637_R1.fastq.gz)
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v0.39
Trimmed sequence reads were aligned to the UCSC mm10 genome using STAR v2.7.10a
Read count extraction was performed using featureCounts v2.0.1
Normalization and differential gene expression analysis were performed using the DESeq2 R package
Assembly: mm10
Supplementary files format and content: abundance data in tab-delimited matrix table (.txt) and Excel formats

source_name: BM

growth_protocol:
Cells were obtained from isolated BM cells sorted for LSK (Lin- Sca-1+ cKit+) cells from FLT3-ITD/ITD; Llgl1-/-; Mx1-Cre+,  FLT3-ITD/ITD; Llgl1+/+; Mx1-Cre- and FLT3-ITD/ITD; Llgl1+/+; Mx1-Cre+ animals (FLT3-ITD animals from gifted from Prof. Benjamin L. Ebert (Harvard Medical School, Boston, MA, USA) conferring to the Lee et al., 2007 animal model; Mx1-Cre-recombinase was obtained from Jackson Laboratories (Strain 03556); Llgl1-flox/flox animals are described in Klezovitch et al., 2004)
Samples were processed at different timepoints (TP) TP1: sample271.fq.gz; sample236.fq.gz; sample270.fq.gz; sample273.fq.gz; sample274.fq.gz  and TP2: AS-311281-LR-41637_R1.fastq.gz; AS-311276-LR-41636_R1.fastq.gz; AS-311278-LR-41636_R1.fastq.gz; AS-311282-LR-41637_R1.fastq.gz; AS-311280-LR-41637_R1.fastq.gz

extract_protocol:
RNA isolation was perfomed using Arcturus PicoPuroe RNA Isolation Kit (Thermo Fisher Scienficif) or TRIzol (Thermo Fisher Scientific) according to the manufacturer's instruction.
RNA libraries for RNA-seq were prepared for TP1 using NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) following manufacturer's instruction, assessed for size and quantified using the 2100 Bioanalyzer (Agilent Technologies) and Kapa Library Quantification Kit (Illumina) prior to sequencing on the Illumina NextSeq500 platform (75bp single end) and TP2 using SmarTer Ultra Low Input RNA v4 (Takara Bio) and NEBNext ChIP-Seq Library Prep Kit for Illumina (New England Biolabs) following manufacturer's instruction, prior to sequencing on the Illumina HiSeq2000 platform (51bp single end).

treatment_protocol: Mice were injected two times i.p.  with poly(I):poly(C) (pIpC) at 4 weeks of age to induce the Mx1-Cre-recombinase

value: BM

value: LSK

value: FLT3-ITD/ITD; Llgl1-/-; Mx1-Cre+

value: pIpC


title: LSK, FLT3-ITD/ITD Llgl1-/- Mx1+, Rep3

description: alternative name for the analysis: 283_ITD_Cre_Llgl1_b2


title: OP1


title: WT_LB_37_log_rep2

value: WT

value: LB 37oC log phase of culture growth

value: bacterial cell

value: Anti-ParB (rabbit, polyclonal)


title: LSK, FLT3-ITD/ITD Llgl1+/+ Cre-, Rep3

description: alternative name for the analysis: 281_ITD_b2

value: FLT3-ITD/ITD; Llgl1+/+; Mx1-Cre-


title: GD3.5 mouse uterine transcriptome, Nr2f2 deficiency in Pgr-expressing cells,  Replicate 3

city: RTP

first: Franco

last: Demayo

address: 111 TW Alexander Drive

institute: NIEHS

data_processing:
Filter reads of Qual score <20
Remove reads carrying adaptor sequences using cutadapt (v1.12).
Agilgn reads to mm10 genome using STAR aligner (V2.5.2b)
Count reads mapped to each gene using featureCounts ( v1.5.0-p1) function in Subread program
Assembly: mm10
Supplementary files format and content: FPKM was calculated for each gene in each sample by using Cufflinks version 2.0.2.

source_name: Uterus

extract_protocol:
RNA was extracted using TRIzol according to manufacturer's instructions
RNA libraries were prepared for sequencing using  Illumina TruSeq RNA Library Prep kit v2.

tag: pregnancy day

value: Gestation day 3.5

value: uterus


title: GD3.5 mouse uterine transcriptome, Nr2f2 deficiency in Pgr-expressing cells,  Replicate 4


title: CTL3

source_name: CTL_Colonic epithelia

value: control rat


title: LSK, FLT3-ITD/ITD Llgl1+/+ Cre-, Rep4

description: alternative name for the analysis: 278_ITD_b2


title: GD3.5 mouse uterine transcriptome, Nr2f2 deficiency in Pgr-expressing cells,  Replicate 2


title: WT_M9_30_log_rep1

value: PAO1161 leu-

value: M9 30oC log phase of culture growth


title: CTL2

value: SD

value: female


title: GD3.5 mouse uterine transcriptome, Nr2f2 deficiency in Pgr-expressing cells,  Replicate 1


title: GD3.5 mouse uterine transcriptome, control 4


title: WT_LB_30_st_rep2

value: LB 30oC stationary phase of culture growth


title: WT_LB_30_st_rep1


title: GD3.5 mouse uterine transcriptome, control 3


title: GD3.5 mouse uterine transcriptome, control 2


title: LSK, FLT3-ITD/ITD Llgl1-/- Mx1+, Rep4

description: alternative name for the analysis: 287_ITD_Cre_Llgl1_b2

value: BM


title: GD3.5 mouse uterine transcriptome, control 1


title: WT_LB_30_log_rep2

value: LB 30oC log phase of culture growth


title: APS3

source_name: APS_Colonic epithelia

value: Astragalus polysaccharides (APS)-treated osteoporotic rat

value: colon

value: Colonic epithelia


title: Bovine Milk Cultured Cells

city: Ithaca

first: Gerlinde

middle: R.

last: Van de Walle

address: 235 Hungerford Hill Rd

department: Baker Institute for Animal Health

institute: Cornell University

description: 10X Genomics

data_processing:
Demultiplexing, barcoded processing, gene counting and aggregation using cellranger v6.1.1
Assembly: Bos taurus ARS-UCD1.2
Supplementary files format and content: Tab separated values and matrices

organism: Bos taurus

source_name: Milk

growth_protocol: Dulbecco’s Modified Eagle Medium (DMEM)/F12 (50/50), supplemented with 10% FBS, 2% B27, 10 ng/mL basic-fibroblast growth factor (bFGF) , 10 ng/mL epidermal growth factor (EGF) and 2% Antibiotic/Antimycotic, 37C, 5% CO2

extract_protocol:
Freshly collected milk from a healthy Holstein-Fresian cow was centrifuged to pellet cells, cells were washed and cultured on plastic and allowed to expand for ~8 days with daily medium changes, removing non-adherent cells.
According to manufacturer instructions, single cell 3' v3.1 protocol (10X Genomics)

value: Milk

value: MiDC

value: Milk-derived adherent cells

value: WT


title: APS2


title: P19 cells, DMSO, 48h, rep 2

city: Durham

first: Marcos

last: Morgan

address: 111 TW Alexander Dr

description:
Direct RNA-seq
DMSO_48_2

data_processing:
Base calling was done with Guppy version 5.0.10.
Demultiplexing of barcoded oligos was done with Deeplexicon.
The alignment to the reference transcriptome was done with Minimap2 version 2.20.
The poly (A) tail length was determined with Nanopolish version 0.13.3.
Supplementary files format and content: Comma separated value file wih polyA tail length, mapping transcript and replicate information for each read.

growth_protocol: P19 cells were grown in Dulbecco's modified Eagle's medium with 4,500 mg/L of glucose supplemented with 100 units/mL penicillin/streptomycin (Life Technologies) and 10% fetal bovine serum (FBS, Gemini Bio-Products).

extract_protocol:
Total RNA was extracted with TRIzol. Poly(A) RNAs were purified with oligoT beads.
Total RNA libraries were prepared with the Nanopre direct RNA-seq kit.
Libraries were run on a Nanopore R9 chip on a GridIon instrument.

treatment_protocol: The day after seeding, undifferentiated P19 cells were treated with 10 µM final concentration of MHY1485 (Selleckchem) for 24 hours, or 48 hours with media changed every 24 hours containing fresh MHY1485 solution. Cells exposed to the same amount of DMSO were used as control.

value: Embryonal carcinoma

value: DMSO

tag: time


title: P19 cells, MHY, 48h, rep 2

description:
Direct RNA-seq
MHY_48_2

value: MHY


title: APS1


title: WT_LB_30_log_rep1

value: PAO1161 leu-

value: bacterial cell

value: Anti-ParB (rabbit, polyclonal)


title: P19 cells, MHY, 48h, rep 1

description:
Direct RNA-seq
MHY_48_1


title: WT_LB37_log_INPUT

value: LB 37oC log phase of culture growth


title: WT_LB_37_log_rep1


title: P19 cells, MHY, 24h, rep 2

description:
Direct RNA-seq
MHY_24_2


title: CTL1

value: SD

value: female

value: control rat


title: P19 cells, DMSO, 24h, rep 2

description:
Direct RNA-seq
DMSO_24_2


title: P19 cells, MHY, 24h, rep 1

description:
Direct RNA-seq
MHY_24_1


title: parS1-4_M9_37_st_rep2

value: M9 37oC stationary phase of culture growth


title: P19 cells, DMSO, 48h, rep 1

description:
Direct RNA-seq
DMSO_48_1


title: P19 cells, siLarp1, 48h, rep 2

description:
Direct RNA-seq
siLarp1_48_2

treatment_protocol: Undifferentiated P19 cells were transfected with 50 nanomoles of the Larp1 siRNA (Dharmacon, J-063706-09-0010) using Lipofectamine 3000 (Invitrogen) according to the manufacturer's instructions. A pool of scrambled siRNAs (Dharmacon, D-001810-10-20) with no significant homology to the human, mouse, or rat genome was used as negative control. After transfection, cells were incubated at 37°C for 24 hours. To study the long-term effect at 48 hours, an additional transfection using the same conditions was performed 24 hours after the initial knock-down.

value: siRNA against Larp1


title: parS1-4_M9_37_log_rep2

value: M9 37oC log phase of culture growth


title: P19 cells, DMSO, 24h, rep 1

description:
Direct RNA-seq
DMSO_24_1


title: P19 cells, siCtl, 48h, rep 2

description:
Direct RNA-seq
siCtl_48_2

value: Scrambled siRNA


title: At, C_NoCa3

city: Singapore

first: Daisuke

last: Urano

address: 1 Research Link

institute: Temasek Lifescience Laboratory

description: Raw read counts_At.csv

data_processing:
STAR (v.2.5.3a) with default settings
Genome_build: Marchantia polymorpha MpTak1_V5.1 reference genome. Arabidopsis thaliana (TAIR10) reference genome. Lettuce Lsat_Salinas_v7_genomic
Supplementary_files_format_and_content: Raw read counts
Lists_of_DEGs.xlsx: lists of differentially expressed genes (DEGs) obtained from the following types of comparisons. 1) Comparisons between genotypes and treatments in the experiment involving M. polymorpha gemmalings of wild type Tak-1 and the knockout mutant gpb1-2 under two conditions (2 mM Ca and 0 mM Ca); 2) Comparisons between treatments in the experiment with Arabidopsis Col-0 seedlings under two conditions (2 mM Ca and 0 mM Ca); 3) Comparisons between treatments in the experiment with Lettuce wildtype under two conditions (2 mM Ca and 0.15 mM Ca).

organism: Arabidopsis thaliana

source_name: Shoot

growth_protocol: M. polymorpha Tak-1 and gpb1-2 gemma was grown in liquid Yamagami media with 1% sucrose for 6 days under continuous light (50 – 60 µmol m-2s-1) at 22°C. Arabidopsis thaliana Col-0 were grown on 1/2 MS media with 1% sucrose, 0.05% MES, 1% plant agar pH5.8 for six days under long-day condition (16 hr light / 8 hr darkness, 100 µmol/m2/sec and 22°C). Lettuce var. Little Gem were grown on water agar (1%) for 4 days under continuous light (50 – 60 µmol m-2s-1) at 22°C.

extract_protocol:
M. polymorpha gemmalings were collected through filtering through Miracloth. Arabidopsis and lettuce shoots were excised. All plant samples were immediately frozen in liquid nitrogen and followed by RNA extraction using Rneasy Plant Mini Kit. (Qiagen)
RNA libraries were prepared for sequencing using standard novaseq protocols

treatment_protocol: M. polymorpha 6-day old gemmalings were transferred to liquid Yamagami media with 1% sucrose, and with 0 mM of calcium chloride and treated for 48 hours. Arabidopsis 6-day old seedlings were transferred to Yamagami media with 1% sucrose, 1% plant agar, pH 5.8, with 2 mM CaCl2 or 0 mM CaCl2. Lettuce 4-day old seedlings were transferred to Yamagami media with 1% sucrose, 1% plant agar, pH 5.8 with 2 mM CaCl2 or 0.15mM CaCl2.

value: Shoot

tag: age

value: 6-day old

value: Col-0, WT

tag: stress

value: calcium deficient condition


title: parS1-4_M9_37_log_rep1


title: At, C_NoCa2

description: Raw read counts_At.csv


title: parS1-4_M9_37_st_rep1


title: P19 cells, siLarp1, 48h, rep 1

description:
Direct RNA-seq
siLarp1_48_1

value: Embryonal carcinoma

value: WT


title: P19 cells, siLarp1, 24h, rep 3

description:
Direct RNA-seq
siLarp1_24_3


title: At, C_NoCa1

description: Raw read counts_At.csv


title: parS1-4_M9_30_st_rep2

value: PAO1161 leu-

value: M9 30oC stationary phase of culture growth


title: P19 cells, siCtl, 48h, rep 1

description:
Direct RNA-seq
siCtl_48_1


title: At, C_Ca4

description: Raw read counts_At.csv

value: control condition


title: P19 cells, siLarp1, 24h, rep 2

description:
Direct RNA-seq
siLarp1_24_2


title: P19 cells, siLarp1, 24h, rep 1

description:
Direct RNA-seq
siLarp1_24_1


title: P19 cells, siCtl, 24h, rep 3

description:
Direct RNA-seq
siCtl_24_3


title: At, C_Ca2

description: Raw read counts_At.csv


title: At, C_NoCa4

description: Raw read counts_At.csv


title: P19 cells, siCtl, 24h, rep 2

description:
Direct RNA-seq
siCtl_24_2


title: parS1-4_M9_30_log_rep2

value: M9 30oC log phase of culture growth

value: bacterial cell

value: Anti-ParB (rabbit, polyclonal)


title: P19 cells, siCtl, 24h, rep 1

description:
Direct RNA-seq
siCtl_24_1


title: At, C_Ca1

description: Raw read counts_At.csv


title: parS1-4_M9_30_log_rep1


title: parS1-4_LB_37_st_rep2

value: LB 37oC stationary phase of culture growth


title: parS1-4_LB_37_st_rep1


title: SKBR3 cells, VIRMA-overexpressing IP replicate 2

city: Camperdown

first: RENHUA

last: SONG

state: NSW

address: Charles Perkins Centre - D17, Level 4 West. The University of Sydney Johns Hopkins Drive

institute: Centenary Institute

description:
IP_201_B.bw
201_B_peaks.narrowPeak

data_processing:
For all sequencing data, the raw reads were subject to quality check using FastQC.Adapter and poor-quality sequences were removed using Trimmomatic (version 0.39) with default settings.
For the analysis of m6A-RIP-sequencing data, only uniquely mapped were selected by samtools for downstream analysis. m6A peaks enriched in immunoprecipitation over corresponding input samples were identified by MACS2 (version 2.1.0.20150731).
The effective genome size was calculated by the reference annotation. Significant (FDR-adjusted p < 0.05, |fold change between IP and input | ≥ 2, and a minimum peak read count of 10 across replicates and conditions) peaks were considered.
To identify high confident or consensus m6A peaks, peaks were intersected in a pair-wise fashion among two replicates using the BedTools package with a setting of ‘-f 0.5’.
bigWig files were generated using Bamcoverage.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Breast cancer

growth_protocol: SKBR3 cells were seeded in a 6-well plate to 80-90% confluency, with AeraSeal™ film covering the plate in place of a lid for more efficient gas transfer. The plate was then placed in the hypoxic gas mixer (chamber) within a standard humidi-fied cell culture 37ºC incubator with 5% CO2 for up to 24 hours.

extract_protocol:
Freshly collected DC and Si8 from RedMUC298trTg mice were flushed with ice-cold HBSSwo (Mg2+/Ca2+ free supplemented with 10mM HEPES, pH 7.2) to remove luminal content. The tissue was inverted and inflated by injection of HBSSwo. Epithelial isolation was performed by incubation of tissue with pre-digestion buffer (HBSSwo, 5 mM EDTA, 5% v/v FCS, 1 mM DTT) in a shaking incubator. The isolated epithelial cells were resuspended in digestion buffer (HBSS with Mg2+/Ca2+ supplemented with 2 mg/ml collagenase type I and 40 U/ml DNase I) and incubated at 37 °C for 30 min. Cells were washed and re-suspended in PBS and stained with a Viability Dye, washed and resuspended in FACS buffer (HBSSwo, 2% v/v FCS, 5mM EDTA). Alive GCs were sorted using a FACS Jazz (Becton Dickinson) according to the presence or absence of mCherry signal using a C57Bl6 mouse as negative control. Goblet cells were washed in HBSS-/- and resuspended in HBSS-/- supplemented with 0.04% w/v BSA.
Library preparation was performed using the SMARTER Stranded Total RNA Seq kit v2-Pico Input Mammalian kit (Takara Bio cat #634411) according to the manufacturers’ instructions. Libraries were sequenced using HiSeq2500 (Illumina) at Novogene (China) to obtain at least 20 million paired-end reads per sample. Sequencing was performed in duplicates for each condition.

treatment_protocol:
5 μg total RNA was fragmented into ~200 nucleotide long fragments via incubation with ZnCl2 at 70˚C for 3 minutes. Fragmented RNA was precipitated, and the RNA size distribution was assessed using RNA 6000 Nano Bioanalyzer kit.After setting aside 500 ng of fragmented RNA as input control, the rest of the RNA was subjected to two rounds of immunoprecipitation, each for 2 hours, using anti-m6A antibody conjugated to protein-A and –G magnetic beads.
Extensive washing was performed on immunoprecipitated RNA and elution from beads was carried out using RLT buffer and RNeasy mini kit.

value: Breast cancer


title: 1703803_human_bone marrow_HMOX-1_KO

city: Tarrytown

first: Wei Keat

last: Lim

address: 777 Old Saw Mill River Rd

institute: Regeneron

description:
10x 5prime NextGEM v2
10x Chromium

data_processing:
CellRanger (v.6.1.1, 10X Genomics) with GRCh38 reference was performed on the processed cells to compute gene expression levels and to generate analysis-ready data.
We checked the quality of the data (Number of cells, mean reads per cell, median genes per cell, median UMI counts per cell, etc.) to filter out artifacts, empty droplets, and multiplets. In each sample, cells with the total number of molecules detected within a cell higher than 30,000 and lower than 1,000 were filtered out.
Then Python module Scanpy (v1.7.1) was used to normalize the data. The normalization was done as following: 1. Transformation of total counts so each cell sums to 10,000. 2. Log1p of the transformed counts. 3.Unit Scaling of the gene expression counts across all cells to ensure a mean of zero and a max value of 10.
Lastly, R Seurat package (v4.3.0.1) was utilized to generate UMAP plots and to run clustering. In each cluster, we identified markers based on differentially expressed genes, and cell types were given to the clusters based on the top markers. Cell type percentages were calculated by [the number of cells for the cell type x 100 / the total number of cells in the condition].
Assembly: GRCh38 & GRCm38
Supplementary files format and content: Tab-separated matrix files

source_name: bone marrow

extract_protocol:
The generation of knock-in mice encoding human SIRPa, human M-CSF, human CD47, and Rag2/IL-2Rg deletions were created by Velocigene technology. Mice were maintained on a sulfa diet (LabDiet, St. Louis, MO) in a MPF facility, and were intra-bred for about 5-10 generations. Mouse and human CD45+ cell fractions were collected from the tissues of human HSC-engrafted HMOX-1+/+ and HMOX-1-/- hSIRPa/hM-CSF/hCD47/Rag2-/-/IL-2Ryc-/- mice. Cells were isolated by positive magnetic enrichment using either mouse CD45 or human CD45 microbeads (Miltenyi).
Library was performed according to the manufacter's insturction (10x 5prime NextGEM v2)

value: bone marrow

value: hCD45+ cells


title: parS1-4_LB_37_log_rep2

value: LB 37oC log phase of culture growth


title: SKBR3 cells, VIRMA-overexpressing IP replicate 1

description:
IP_201_A.bw
201_A_peaks.narrowPeak


title: parS1-4_LB_37_log_rep1


title: 1703799_human_spleen_HMOX-1_KO

description:
10x 5prime NextGEM v2
10x Chromium

source_name: spleen

value: spleen


title: 1693167_human_bone marrow_HMOX-1_WT

description:
10x 5prime NextGEM v2
10x Chromium


title: parS1-4_LB_30_st_rep2

value: LB 30oC stationary phase of culture growth


title: parS1-4_M9_30_st_rep1


title: 1703802_human_bone marrow_HMOX-1_WT

description:
10x 5prime NextGEM v2
10x Chromium


title: SKBR3 cells, VIRMA-overexpressing Input replicate 2

description:
IN_201_B.bw
201_B_peaks.narrowPeak


title: 1693159_human_spleen_HMOX-1_WT

description:
10x 5prime NextGEM v2
10x Chromium


title: PROseq_C_aU_permeabilized

city: Vienna

first: Dominik

last: Handler

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA-Institute of Molecular Biotechnology of Austrian Academy of Sciences

description: PROseq from wt OSCs - premeabilized cells labelled with biotin-11-CTP + biotin-11-UTP

data_processing:
Reads have been prepared by first clipping of the 3' adaptor sequence (AGATCGGAAGAGCACACGTCT) and then trimming 4nt from the 5' and the 3' end to remove random nucleotides contained in the adaptors.
1st mate of paired-end reads was removed from the analysis to capture the true position of the polymerase
reads were mapped to the Drosophila melanogaster TE consensus using Bowtie (release 1.3.0) with 0 mismatches for genome wide analysis
reads mapping to annotated rRNA, tRNA, snRNA, snoRNA loci and the mitochondrial genome were excluded from analyses
reads were normalized to 10Mio genome uniquely mapping reads
Assembly: dm6
Supplementary files format and content: all mapping and unique mapping bigwig files for sense and antisense
Library strategy: PRO-seq

molecule: nuclear RNA

organism: Drosophila melanogaster

source_name: OSC

growth_protocol: OSC culture according to Niki et al., PNAS, 2006

extract_protocol:
Pro-seq library was generated according to Mahat et al. Nature Protocols, 2016.
Library was generated according to Mahat et al. Nature Protocols, 2016 except 3' and 5' adaptors containing 4 random nucleotides at the ends to reduce ligation biases have been used.

treatment_protocol: nuclear isolation, 3' run on with biotin-11-CTP+biotin-11-UTP - permeabilized cells, triple biotin purification

value: OSC


title: 1703798_human_spleen_HMOX-1_WT

description:
10x 5prime NextGEM v2
10x Chromium


title: At, C_Ca3

description: Raw read counts_At.csv

value: Shoot

value: 6-day old

value: Col-0, WT


title: SKBR3 cells, VIRMA-overexpressing Input  replicate 1

description:
IN_201_A.bw
201_A_peaks.narrowPeak


title: 1693168_human_bone marrow_HMOX-1_KO

description:
10x 5prime NextGEM v2
10x Chromium


title: 1686418_human_bone marrow_HMOX-1_WT

description:
10x 5prime NextGEM v2
10x Chromium


title: 1686419_human_bone marrow_HMOX-1_KO

description:
10x 5prime NextGEM v2
10x Chromium


title: 1693160_human_spleen_HMOX-1_KO

description:
10x 5prime NextGEM v2
10x Chromium


title: SKBR3 cells, eGFP control IP replicate 2

description:
IP_CTR_B.bw
CTR_B_peaks.narrowPeak


title: 1686410_human_spleen_HMOX-1_WT

description:
10x 5prime NextGEM v2
10x Chromium


title: parS1-4_LB_30_st_rep1

value: PAO1161 leu-


title: parS1-4_LB_30_log_rep2

value: LB 30oC log phase of culture growth


title: SKBR3 cells, eGFP control Input replicate 2

description:
IN_CTR_B.bw
CTR_B_peaks.narrowPeak


title: MRC5_VA cells, + UV, 24 h after release

city: Guangzhou

first: Yuming

state: Guangdong

address: Room 512, Anatomy Building

department: School of Basic Medical Science

institute: Guangzhou medical university

description:
UV_24h
FPKMs_allsamples.xlsx

data_processing:
Raw reads were pre-processed with sequence grooming tool FASTQC followed by sequence alignment using HISAT2. Transcript levels were quantified as fragments per kilobase of transcript per million mapped reads (FPKM) generated by TopHat/Cufflinks.
Transcript levels were converted to the log-space by taking the logarithm to the base 2.
R studio (ggplot2 and gplots packages) was used to run custom R scripts to perform box plots, principal component analysis (PCA), dendrograms, and heatmaps.
Samples were analyzed through DESeq2 to obtain log2 fold change and its respective p value. Differentially expressed transcripts have been identified on these transformed values by using the criteria of log2(fold change) > 1 and padj < 0.05. Gene ontology analysis of DEGs (differentially expressed genes) was performed using clusterProfiler.
Assembly: hg38
Supplementary files format and content: excel files include FPKM values for each sample.

growth_protocol: MRC5_VA cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total RNA was harvested with Rneasy mini kit (Qiagen), 2.0 ug of total RNA per sample was used for the construction of sequencing libraries.
Ribosome RNA was removed from the purified total RNA using Epicentre Ribo-Zero™ rRNA Removal Kit (Epicentre), and the remaining RNA was used for library preparation using TruSeq Stranded Total RNA Sample Prep Kit (Illumina). Libraries were quantified fluorometrically using Qubit® dsDNA HS Assay Kits (Thermo Fisher Scientific) on a Qubit 2.0 Fluorometer (Thermo Fisher Scientific). All libraries (> 2 nM/μl) were sequenced on an Illumina Novaseq 6000 (PE150 run) according to the manufacturer’s instruction to a depth of 220-340 million reads on average.

treatment_protocol: synchronized in G1/S phase with double thymidine block method, UV-C irradiated (10 J/m2) followed by release from G1/S block in fresh media.

value: human fibroblast cells

value: WT

value: UV-C irradiated 10J/m2

value: 24 h after release


title: MRC5_VA cells, + UV, 48 h after release

description:
UV_48h
FPKMs_allsamples.xlsx

value: 48 h after release


title: SKBR3 cells, eGFP control IP replicate 1

description:
IP_CTR_A.bw
CTR_A_peaks.narrowPeak

value: Breast cancer


title: SKBR3 cells, eGFP control Input replicate 1

description:
IN_CTR_A.bw
CTR_A_peaks.narrowPeak


title: MRC5_VA cells, + UV, 9 h after release

description:
UV_9h
FPKMs_allsamples.xlsx

value: 9 h after release


title: MRC5_VA cells, + UV, 72 h after release

description:
UV_72h
FPKMs_allsamples.xlsx

value: 72 h after release


title: MRC5_VA cells, + UV, 96 h after release

description:
UV_96h
FPKMs_allsamples.xlsx

value: 96 h after release


title: parS1-4_LB_30_log_rep1

value: bacterial cell

value: Anti-ParB (rabbit, polyclonal)


title: MRC5_VA cells, + UV, 12 h after release

description:
UV_12h
FPKMs_allsamples.xlsx

value: 12 h after release


title: MRC5_VA cells, + UV, 6 h after release

description:
UV_6h
FPKMs_allsamples.xlsx

value: 6 h after release


title: 1686411_human_spleen_HMOX-1_KO

description:
10x 5prime NextGEM v2
10x Chromium

value: spleen

value: hCD45+ cells


title: Ribo-seq SKBR3 cells, VIRMA-overexpressing replicate 3

data_processing:
For all sequencing data, the raw reads were subject to quality check using FastQC.
Adapter and poor-quality sequences were removed using Trimmomatic (version 0.39) with default settings
Trimed reads were filtered for mitochondrial DNA and ribosomal RNA using Bowtie2
Pair-end clean reads were then mapped to the human reference genome hg38 (EN-SEMBL 86 release, GRCm38) using STAR (version 2.5.2a)
Read counts for reads overlapping genomic regions were quantified with FeatureCounts from the Subread package.
Differential enrichment of mRNA transcripts in the polysome fraction was determine using DESeq2
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Library strategy: Ribo-seq

extract_protocol:
Polysome fractions were collected using an LC-MS/MS-based ribo Mega-Sec approach as previously described. Total RNA was extracted from the eluted polysome fractions using TRIzol LS.
Ribosomal RNA depleted library 1 μg total RNA using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus Kit (Illumina), according to the manufacturers’ instructions. A total of 25 million 150 bp paired-end strand-specific reads were sequenced per sample on an Illumina HiSeq® 2500 Platform (Illumina).

treatment_protocol:
The oxygen concentration in the hypoxic gas mixer (chamber) was maintained at 95% nitrogen, <0.05% O2 and 5% CO2 as monitored with Profiling oxygen microsensor (PM-PSt7, PreSens) connected to a compact oxygen transmitter (OXY-1 ST, PreSens)
After hypoxia treatment, the existing supernatant was immediately aspirated and the cells were subjected to 1× PBS wash and aspirated. Then 150-200 μL RIPA buffer  with 1× Protease Inhibitor Cocktail and 1× PhosSTOP (Sigma, cat# 4906845001) were add-ed to each well and cell scrapers were used to detach cells. The lysate was mix well and placed on ice for 15-30 minutes, centrifuged at 16000 g for 5 minutes at 4ºC and trans-ferred to a new 1.5 mL tube.

tag: genotype/variation

value: VIRMA overexpressed


title: ParBR94C_LB_37_log_rep1

value: PAO1161 leu-

value: LB 37oC log phase of culture growth


title: MRC5_VA cells, no UV, 12 h after release

description:
No UV_12h
FPKMs_allsamples.xlsx

value: human fibroblast cells

value: WT

value: no treatment


title: MRC5_VA cells, + UV, 3 h after release

description:
UV_3h
FPKMs_allsamples.xlsx

value: UV-C irradiated 10J/m2

value: 3 h after release


title: MRC5_VA cells, no UV, 24 h after release

description:
No UV_24h
FPKMs_allsamples.xlsx

value: 24 h after release


title: ParBR94C_LB_37_log_rep2


title: ParBA97T_LB_37_log_rep1


title: MRC5_VA cells, no UV, 9 h after release

description:
No UV_9h
FPKMs_allsamples.xlsx

value: 9 h after release


title: Ribo-seq SKBR3 cells, VIRMA-overexpressing replicate 2

value: Breast cancer


title: MRC5_VA cells, no UV, G1/S synchronized

description:
No UV_syn
FPKMs_allsamples.xlsx

value: 0 h after release


title: MRC5_VA cells, no UV, 6 h after release

description:
No UV_6h
FPKMs_allsamples.xlsx


title: Ribo-seq SKBR3 cells, VIRMA-overexpressing replicate 1


title: ParB1-283_LB_37_log_rep2

value: bacterial cell

value: Anti-ParB (rabbit, polyclonal)


title: MRC5_VA cells, no UV, 3 h after release

description:
No UV_3h
FPKMs_allsamples.xlsx


title: Ribo-seq SKBR3 cells, eGFP control replicate 3

value: Control


title: ParB1-283_LB_37_log_rep1


title: MRC5_VA cells, ZFAS1-sh2, + UV, 24 h recovery [RNA-seq]

treatment_protocol: UV-C irradiated (10 J/m2) and recovered for the indicated time intervals prior to total RNA extraction.

value: ZFAS1 knockdown

value: 24 h after irradiation


title: MRC5_VA cells, ZFAS1-sh2, + UV, 3 h recovery [RNA-seq]

value: 3 h after irradiation


title: ParBA97T_LB_37_log_rep2

value: PAO1161 leu-


title: MRC5_VA cells, ZFAS1-sh2, no UV [RNA-seq]

value: 0 h


title: Ribo-seq SKBR3 cells, eGFP control replicate 2


title: Ribo-seq SKBR3 cells, eGFP control replicate 1


title: MRC5_VA cells, ZFAS1-sh1, + UV, 24 h recovery [RNA-seq]

value: human fibroblast cells


title: MRC5_VA cells, ZFAS1-sh1, + UV, 3 h recovery [RNA-seq]


title: half-parS25_LB_37_log_rep2

value: LB 37oC log phase of culture growth


title: MRC5_VA cells, ZFAS1-sh1, no UV [RNA-seq]

value: no treatment


title: RNA-seq SKBR3 cells, VIRMA-overexpressing replicate 2

data_processing:
mRNA-sequencing was performed for each biological duplicates of samples by Novogene (China). For all sequencing data, the raw reads were subject to quality check using FastQC.
Adapter and poor-quality sequences were removed using Trimmomatic (version 0.39) with default settings
Pair-end clean reads were then mapped to the human reference genome hg38 (EN-SEMBL 86 release, GRCm38) using STAR (version 2.5.2a)
Read counts for reads overlapping genomic regions were quantified with FeatureCounts from the Subread package. Differentially expressed genes were determined using the R package DESeq2 with reads per kilo base per million (RPKM)>1, a Benjamini-Hochberg (BH)-adjusted P < 0.05 and an absolute value of a fold change > 2.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Poly-A-enriched mRNA libraries were prepared from 1 μg total RNA
RNA libraries for RNA-seq were prepared using the TruSeq® Stranded Library Preparation Kit (Illumina), according to the manufacturers’ instructions

value: VIRMA overexpressed


title: MRC5_VA cells, + UV, 24 h recovery [RNA-seq]

value: WT

value: UV-C irradiated 10J/m2


title: half-parS25_LB_37_log_rep1


title: RNA-seq SKBR3 cells, VIRMA-overexpressing replicate 1


title: RNA-seq SKBR3 cells, eGFP control replicate 2


title: MRC5_VA cells, no UV [RNA-seq]


title: MRC5_VA cells, + UV, 3 h recovery [RNA-seq]


title: MRC5_VA cells, + UV, replicate 2, even probe, ChIRP

data_processing:
Basecalls were performed using bcl2fastq v2.17 for NovaSeq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v3.36, discarding reads left with < 20bp.
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragment, renormalized and reformatted in the bigWig file format.
Peaks were called using MACS v1.4.2 with the significance cut-off p-value < 1e-5.
bigWig files were generated usign the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate.
Assembly: hg38

extract_protocol:
Cells were harvested by trypsin-treatment and fixed with 1% formaldehyde for 10 min. After quenching and cell lysis, nuclear lysate was sheared by sonication, fragmented chromatin was extracted.
2 ng of ChIRPed DNA and input samples were used for standard ChIP-Seq library preparation by using NEBNext Ultra DNA Library prep kit (NEB, E7103) and sequenced under Illumina NovaSeq 6000 system, resulting in the production of 150 bp paired-end reads.

treatment_protocol: UV-C irradiated (10 J/m2) followed by recovery for the indicated time intervals prior to cell extraction.

tag: chirp antibody

value: ZFAS1 even probe pool


title: dparB_M9_37_log

tag: strain

value: {delta}parB

value: M9 37oC log phase of culture growth


title: RNA-seq SKBR3 cells, eGFP control replicate 1

value: Breast cancer


title: dparB_M9_37_st

tag: growth phase

value: M9 37oC stationary phase of culture growth

value: bacterial cell

value: Anti-ParB (rabbit, polyclonal)


title: dparB_M9_30_st

value: M9 30oC stationary phase of culture growth

tag: chip antibody


title: MRC5_VA cells, + UV, replicate 2, Input (for ChIRP)

tag: genotype


title: MRC5_VA cells, + UV, replicate 2, odd probe, ChIRP

tag: cell type

value: ZFAS1 odd probe pool


title: MRC5_VA cells, + UV, Input (for ChIRP)


title: MRC5_VA cells, + UV, even probe, ChIRP


title: dparB_M9_30_log

value: PAO1161 leu-

value: M9 30oC log phase of culture growth


title: MRC5_VA cells, + UV, odd probe, ChIRP

value: human fibroblast cells


title: dparB_LB_37_st

value: LB 37oC stationary phase of culture growth


title: Gonads, male, 3

city: Milwaukee

first: Allison

last: Abbott

state: WI

address: 1428 W. Clybourn St.

department: Biological Sciences

institute: Marquette University

data_processing:
Galaxy
Adapters of small RNA seq reads were trimmed with Triommatic.
Reads were aligned to the reference genome assembly Ce10 with Bowtie2
The aligned reads were annotated with miRbase22 with htseq-count.
Differential expression analysis was performed with DESeq2
Assembly: Ce10
Supplementary files format and content: tabular files include raw counts for each sample
Supplementary files format and content: tsv file includes normalized counts for each sample

organism: Caenorhabditis elegans

source_name: gonads

extract_protocol:
total RNA was extracted with DirectZol RNA microprep kit
RNA library was prepared withTruSeq Small RNA Library kit. 1ug of total RNA was used for construction of sequencing library.

tag: tissue

value: gonads

value: germline

value: male


title: MRC5_VA cells, no UV, even probe, ChIRP

tag: cell line

value: WT

value: no treatment


title: MRC5_VA cells, no UV, Input (for ChIRP)

tag: treatment


title: MRC5_VA cells, shZFAS1, + UV, 12 h recovery, Input

data_processing:
Basecalls were performed using bcl2fastq v2.17 for NovaSeq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v3.36, discarding reads left with < 20bp.
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragment, renormalized and reformatted in the bigWig file format.
Peaks were called using MACS v1.4.2 with the significance cut-off q-value <=0.01.
bigWig files were generated usign the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Cells were harvested by trypsin-treatment and fixed with 1% formaldehyde for 15 min. After quenching and cell lysis, nuclear lysate was sheared by sonication, fragmented chromatin was extracted.
1 ng of ChIPed DNA and input samples were used for standard ChIP-Seq library preparation by using NEBNext Ultra DNA Library prep kit (NEB, E7103) and sequenced under Illumina NovaSeq 6000 system, resulting in the production of 150 bp paired-end reads.

value: ZFAS1 knockdown

value: UV-C irradiated 10J/m2


title: MRC5_VA cells, shZFAS1, + UV, 12 h recovery, RNAPII-Ser5P, ChIP

value: CTD Ser5P (Millipore, 04-1572)


title: MRC5_VA cells, shZFAS1, + UV, 12 h recovery, RNAPII-Ser2P, ChIP

value: CTD Ser2P (Millipore, 04-1571)


title: Gonads,hermaphrodite,3

value: hermaphrodite


title: MRC5_VA cells, no UV, odd probe, ChIRP


title: Exp2_halfparS25_Rep3

description:
RNAseq_WT_halfparS25_raw_counts.csv
Exp2_halfparS25_vs_WT_gene_expression_changes_All.csv

data_processing:
base calling: bcl2fastq v2.20 (Illumina)
Sequencing data were quality-checked and filtered using FASTP version 0.22.0.
Reads were mapped to P. aeruginosa PAO11161 genome (CP032126) using Bowtie2 version 2.2.5 using default settings.
The number of reads mapping to individual genes was counted using FeatureCounts v 2.0.3 (with the -s2 option).
Differential expression analysis was conducted using edgeR ver 3.40.2.
Assembly: CP032126
Supplementary files format and content: Raw counts of sequencing (FeatureCounts output summarized for all samples) (RNAseq_WT_halfparS25_raw_counts.csv).
Supplementary files format and content: A table with DE data for all genes and normalized abundance measurements (EdgeR output, separately for the two experiments) (Exp1_halfparS25_vs_WT_gene_expression_changes_All.csv and Exp2_halfparS25_vs_WT_gene_expression_changes_All.csv).

growth_protocol: P. aeruginosa PAO1161 (WT) as well as half-parS25 strains were grown overnight in LB broth (DifcoTM L Broth, Lennox, BD), diluted 1:200 in fresh medium and cells were harvested at logarithmic phase of growth (OD 600nm of 0.5). Culturing was performed in 20ml of medium in 100ml flask, closed with a cotton plug with shaking 200 rpm, at  37oC.

extract_protocol:
Total RNA was isolated from three independent replicates of each strain. 2 ml of cultures which reached optical density 0.4-0.6 at 600 nm were mixed with 4 ml of RNAprotect Bacteria Reagent (Qiagen). RNA was isolated with an RNeasy mini-kit (Qiagen) according to the manufacturer’s protocol. Total RNA was digested with DNase (TURBO DNA-free Kit, Ambion) to eliminate genomic DNA.
rRNA was depleted using Ribo-Zero rRNA Removal Kit (Bacteria) (MRZMB126, Illumina) according to manufacturer instructions. Libraries were prepared according to instructions accompanying the NEBNext Ultra DirectionalRNA Library Prep Kit for Illumina (NEB, E7420). Libraries were sequenced using standard Illumina protocols.

value: LB 37oC log phase of culture growth

value: bacterial cell


title: Gonads,hermaphrodite,1


title: Exp2_halfparS25_Rep2


title: MRC5_VA cells, shZFAS1, + UV, 3 h recovery, RNAPII-Ser2P, ChIP


title: aub_GLKD_pA_ee_new

description: total RNA (polyA selected) from MTD-Gal4 aubergine-sh KD

data_processing:
reads were prepared by removal of the adaptor sequences and base-clipping to keep nucleotides 6-50
reads mapping to the Drosophila melanogaster rRNA precursor and the mitochondrial genome using STAR (2.7.10b) with 0 mismatches were excluded
reads were mapped to the Drosophila melanogaster genome using STAR (2.7.10b)
reads mapping to rRNA, tRNA, mitoRNA were excluded
gene expression was quantified using Salmon (1.5.1) on Flybase r6.40 transcripts with transoposon sequences added and normalization by the GeTMM method implemented in edgeR (3.34)
Assembly: dm6
Supplementary files format and content: all mapping and unique mapping bigwig files for sense and antisense
Supplementary files format and content: gene expression table showing GeTMM expression values

source_name: embryo

growth_protocol:
25˚C, 12h dark/light, ovary dissection into 1x PBS on ice, snap frozen in Trizol
parents were kept in cages at 25˚C, 12h dark/light, embryos collected on applejuice agar plates, bleached, rinsed with water and 1xPBS 0.05% x-100 Triton, snap frozen in Trizol

extract_protocol:
RNA was extracted using Trizol
Libraries were prepared using a NEBNext Ultra Directional library prep kit (NEB) or NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB)

value: embryo

value: 0-1 hour old

value: MTD-GAL4/w1118;MTD-GAL4/+; MTD-GAL4/aub sh parents


title: Gonads, male, 2


title: Exp2_halfparS25_Rep1

value: PAO1161 leu-


title: MRC5_VA cells, shZFAS1, no UV, Input

value: human fibroblast cells


title: MRC5_VA cells, shZFAS1, no UV, RNAPII-Ser5P, ChIP


title: MRC5_VA cells, shZFAS1, + UV, 6 h recovery, Input


title: MRC5_VA cells, + UV, 12 h recovery, Input


title: Gonads, male, 1

value: gonads


title: dparB_LB_37_log

data_processing:
Sequencing data were quality-checked and filtered using FASTP version 0.20.0.
Reads were mapped to P. aeruginosa PAO1161 genome (CP032126) using Bowtie2 version 2.3.4.3 using default settings.
Obtained *.sam files were sorted (samtools sort -n), run through samtools fixmate with the -m option, again sorted (samtools sort) and duplicates were marked with samtools markdup. Samtools ver. 1.9 was used.
The files were indexed and used to generate coverage *.bigwig files, normalized to 1× sequencing depth (RPGC), without binning and smoothing using the bamCoverage tool ver 3.3.0 included in deepTools.
Assembly: CP032126
Supplementary files format and content: Processed files in bigwig format represent normalized coverages of individual base pairs in the P. aeruginosa PAO1161 genome. Reference genome is enclosed in fasta format (CP032126.fa) and the annotation used is enclosed as a .bed (CP032126.bed). A modified .bed file with PAO1161 feature names changed to the names of corresponding PAO1 genes (PA… format) is included for convenience of data browsing e.g. using IGV (CP032126_PA_names.bed).

extract_protocol:
Chromatin immunoprecipitation (ChIP) protocol was based on the method described earlier (Kawalek et al, 2018; Nucleic Acids Res. 46:9, 4592-4606; Modrzejewska et al, 2021; mSystems 6:4, e0001521). Two cultures of each strain with similar OD600 were combined, formaldehyde was added from a 37% stock to a final concentration of 1%, and the cultures were kept for 10 min at room temperature with gentle inverting. Glycine was added to a final concentration of 0.5 M and the cultures were incubated for 5 min at room temperature with gentle rotation. Cells were then harvested by centrifugation (20 min, 3000 x g, 25 mL of culture in 50 mL conical tubes, 4 tubes per strain), washed twice with ice-cold Tris-buffered saline (25 mM Tris-HCl, 150 mM NaCl, pH=7.6), resuspended in 1 mL of TBS, transferred to a fresh 1.5 mL tube and centrifuged (2 min, 6000 x g). The cell pellets were frozen at -70oC. The pellets were thawed on ice, suspended in 0.5 mL of lysis buffer [10 mM Tris-HCl, 20% (w/v) sucrose, 50 mM NaCl, 10 mM ethylenediaminetetraacetic acid (EDTA), pH=8.0] supplemented with 10 µl of Protease Inhibitor Cocktail (Sigma, PA8849) and 125 µL of lysozyme (20 mg/mL) and incubated for 30 min at 37oC. Four samples for each strain were combined in 15 mL. Subsequently, 1.5 mL of IP-buffer [50 mM Tris-HCl, pH=7.5, 150 mM NaCl, 1 mM EDTA, 1% (v/v) Triton X-100, 0.1% (m/v) sodium deoxycholate], 30 µL protease inhibitor cocktail, PMSF (phenylmethanesulfonyl fluoride) to a final concentration of 2 mM, SDS (sodium dodecyl sulphate) to a final concentration of 0.1% were added to each sample. The samples were sonicated 20 times for 20 s each with 1 min break on ice using a Microson ultrasonic cell disruptor Xl2000 (Misonix) with 5-mm tip and 90% of output power to obtain DNA fragments of an average length of 250-350 bp. DNA fragmentation was checked by agarose gel electrophoresis. After sonication, samples were aliquoted (1 mL in 1.5 mL tubes) and stored at -70oC. Sonicated lysate was thawed on ice and 150 μL of each strain variant was incubated with 20 μL of magnetic beads coupled with protein A (Dynabeads Protein A, Invitrogen, 10001D) previously separated from original suspension using Magnetic Separation Stand. Such pre-clearing step was performed for minimum 1 hour at 4oC with rotation of the mixtures. In the meantime 50 μL of magnetic beads were prepared for each reaction by separating from the suspension as above. It was then mixed with anti-ParB antibodies (3 μg,  diluted in 200 μL of PBS with 0.05% Tween-20. Mixtures of magnetic beads and antibodies were incubated for 10 minutes at 4oC with gentle rotation. Beads with bound antibodies were then separated from the supernatant, washed once with 200 μL of the PBS with 0.05% Tween-20 solution and stored on ice. Pre-cleared lysate was separated from the beads used for pre-incubation and added to the beads coated with antibodies. Mixture containing lysate and magnetic beads with antibodies was incubated at 4oC for 20 minutes with mixing on rotator. Beads were then collected and washed. Elution was performed twice for 15 minutes in 50 μL at 65oC in thermoblock with shaking (1400 rpm). All 100 μL of obtained eluates were incubated with 1 μL of RNase A (100 mg/mL, Qiagen, 19101) for 30 min at 65oC. Then, 5 μL of Proteinase K (20 mg/mL, Qiagen, 19133) was added and the samples were incubated for 1 h at 50oC followed by overnight incubation at 65oC. Such prepared probes were stored on ice and 3 μL of 3 M sodium acetate (pH=5) was added. DNA purification was performed using Qiaquick Qiagen PCR purification Kit according to manufacturer’s instructions. The DNA was stored at -20oC.
NGS library was constructed using QiaSeq Ultralow Input Library kit. Sample was further quality checked on 1% agarose gel and concentration was measured using qPCR KAPA Library Quantification Kit.

value: {delta}parB

value: Anti-ParB (rabbit, polyclonal)


title: dparB_LB_30_st

value: LB 30oC stationary phase of culture growth


title: dparB_LB_30_log

value: LB 30oC log phase of culture growth


title: MRC5_VA cells, + UV, 6 h recovery, Input

value: WT


title: MRC5_VA cells, shZFAS1, no UV, RNAPII-Ser2P, ChIP

value: ZFAS1 knockdown

value: no treatment


title: spnE30_GLKD_pA_ov_old

description: total RNA (polyA selected) from MTD-Gal4 spindle-E-sh KD

source_name: ovary

value: ovary

value: 4-6 days old


title: MRC5_VA cells, + UV, 6 h recovery, RNAPII-Ser2P, ChIP

value: UV-C irradiated 10J/m2

value: CTD Ser2P (Millipore, 04-1571)


title: Exp2_WT_Rep3

value: LB 37oC log phase of culture growth

value: bacterial cell


title: wcon_GLKD_pA_ov_old

description: total RNA (polyA selected) from MTD-Gal4 control KD

value: MTD-GAL4/w1118;MTD-GAL4/+; MTD-GAL4/+


title: MRC5_VA cells, + UV, 6 h recovery, RNAPII-Ser5P, ChIP

value: CTD Ser5P (Millipore, 04-1572)


title: Exp1_halfparS25_Rep2

description:
RNAseq_WT_halfparS25_raw_counts.csv
Exp1_halfparS25_vs_WT_gene_expression_changes_All.csv

value: PAO1161 leu-


title: Gonads,hermaphrodite,2

value: gonads

value: germline

value: hermaphrodite


title: MRC5_VA cells, shZFAS1, + UV, 6 h recovery, RNAPII-Ser5P, ChIP

value: human fibroblast cells


title: MRC5_VA cells, shZFAS1, + UV, 6 h recovery, RNAPII-Ser2P, ChIP


title: Methylated_array_15:1_techrep3

city: San Francisco

first: Megan

last: Ostrowski

state: CA

address: 1700 Owens

institute: Gladstone Institutes

description: Nonanucleosome DNA in a plasmid was purified by Gigaprep, isolated via restriction enzyme sites, and purified with Sephacryl S1000 super fine gel filtration. Histone octamers (Luger et al., 1999) were assembled onto purified DNA via salt gradient dialysis.

data_processing:
Demultiplexing subreads BAM files with lima (v2.6.0)
Generating circular concensus sequences (CCS) using ccs
Aligning subreads to nonanucleosomal molecule reference
Assembly: mm10
Supplementary files format and content: *_full.pickle: Python pickle files containing IPD measurements for each base in the forward and reverse strands per CCS read
Library strategy: SAMOSA

organism: unidentified plasmid

source_name: CTCF site 1 from Mus Musculus amplified, gibson cloned, isolated, and histone assembled

growth_protocol: N/A (in vitro samples)

extract_protocol:
CTCF site 1 was purified using a GigaPrep kit (Qiagen), restriction enzyme digested, and purified by size exclusion chromatography. Chromatin was assembled using salt gradient dialysis
Library preparation included DNA damage repair, end repair, blunt-end SMRTbell® ligation, Exonuclease treatment, and Ampure PB cleanup according to manufacturer’s instruction. Library quality was assessed with Agilent Bioanalyzer High Sensitivity DNA kit or Agilent Tapestation D5000 Assay.
PacBio SMRTbell® library preparation

treatment_protocol:
N/A (in vitro samples)
N/A (in vitro samples)

tag: remodeler

tag: remodeler concentration

tag: remodeling turnover_conditions

value: unremodeled

tag: remodeling time

tag: remodeling atp/adp_conditions

tag: histone

value: dna ratio:15:1 ratio

tag: ecogii methylation

value: EcoGII Methylated

tag: sample type

value: in vitro (plasmid insert)


title: MRC5_VA cells, + UV, 3 h recovery, Input

value: WT


title: MRC5_VA cells, shZFAS1, + UV, 3 h recovery, Input

value: ZFAS1 knockdown


title: MRC5_VA cells, shZFAS1, + UV, 3 h recovery, RNAPII-Ser5P, ChIP

value: UV-C irradiated 10J/m2