title: 786-O-ACSS2i-24h-n2

city: Nashville

first: Zachary

last: Bacigalupa

state: TN

address: 1161 21st Ave S

institute: Vanderbilt University Medical Center

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
After investigating the quality of the raw data, sequencing adapters and low-quality bases were trimmed using Trimmomatic 0.38. Cleaned reads were then aligned to reference genome hg38 using bowtie2. Aligned reads were filtered using samtools 1.9 to keep alignments that (1) have a minimum mapping quality of 30, (2) were aligned concordantly, and (3) were the primary called alignments. PCR or optical duplicates were marked using Picard 2.18.26 and removed. Prior to peak calling, reads mapping to mitochondria (mt) were called and filtered, and reads mapping to unplaced contigs were removed.
MACS2 2.1.2 was used for peak calling to identify open chromatin regions. Valid peaks from each group or condition were then merged and peaks called in at least 66% of samples were kept for downstream analyses. For each pair-wise comparison, peaks from condition A and condition B were merged and peaks found in either condition were kept for downstream analyses. Reads falling beneath peaks were counted in all samples, and these counts were used for differential peak analyses using the R package Diffbind.
To explore the ATAC signals across the genome, we use the python package deeptools (v3.5.0). Briefly, the bam files from Genewiz were first transformed to bigwig files using the command ‘bamCoverage’ with parameters ‘-bs 10 --normalizeUsing CPM’. Then command ‘computeMatrix’ and ‘plotHeatmap’ were used to generate heatmaps of ATAC signal 5kb around the accessible regions from the bigwig files. The peaks called from different groups are merged with bedtools and used as the reference regions in the heatmap.
Assembly: hg38
Supplementary files format and content: Illumina Hi-Seq 4000 cleaned reads and filtered removal of reads mapped to mitochondria prior to peak calling:  filtered.peaks.txt.gz

growth_protocol: 768-O cells were cultured using Gibco RPMI-1640 supplemented with 10% FBS, 1% L-glutamine (Sigma), and 10 mL/L penicillin/streptomycin (Sigma) and maintained at 37°C in a 5% CO2 incubator.

extract_protocol:
Live cell samples were thawed, washed, and treated with DNAse I (Life Tech, Cat. #EN0521) to remove genomic DNA contamination. Live cell samples were quantified and assessed for viability using a Countess Automated Cell Counter (ThermoFisher Scientific, Waltham, MA, USA).
After cell lysis and cytosol removal, nuclei were treated with Tn5 enzyme (Illumina, Cat. #20034197) for 30 minutes at 37°C and purified with Minelute PCR Purification Kit (Qiagen, Cat. #28004) to produce tagmented DNA samples. Tagmented DNA was barcoded with Nextera Index Kit v2 (Illumina, Cat. #FC-131-2001) and amplified via PCR prior to a SPRI Bead cleanup to yield purified DNA libraries. The sequencing libraries were clustered on a single lane of a flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration.

treatment_protocol: Cells were grown to approximately 70% confluency and fresh growth media was provided. The cells were then treated with either 1:2000 DMSO (equal volume) or 5 µM ACSS2i and returned to the incubator for 24 hours. After 24 hours, cells were washed with PBS, pelleted and frozen for shipment to Azenta Life Sciences.

tag: cell line

value: Human clear cell renal cell carcinoma


title: MM-expr01-plate01-020

status: Public on May 26 2023

type: SRA

city: Seattle

first: Chengxiang

last: Qiu

state: WA

address: William H. Foege Hall, 3720 15th Ave NE

department: Genome Sciences

country: USA

institute: University of Washington

description: sci-RNA-seq3 library

library_source: transcriptomic

data_processing:
Base calls were converted to fastq format using Illumina’s bcl2fastq/v2.20 and demultiplexed based on PCR i5 and i7 barcodes using maximum likelihood demultiplexing package deML (Renaud et al. 2015) with default settings. Downstream sequence processing and single cell digital expression matrix generation were similar to sci-RNA-seq (Cao et al. 2017) except that RT index was combined with hairpin adaptor index, and thus the mapped reads were split into constituent cellular indices by demultiplexing reads using both the RT index and ligation index (Levenshtein edit distance (ED) < 2, including insertions and deletions).
Briefly, demultiplexed reads were filtered based on RT index and ligation index (ED < 2, including insertions and deletions) and adaptor-clipped using trim_galore/v0.6.5 with default settings. Trimmed reads were mapped to the mouse reference genome (mm10) for mouse embryo nuclei, using STAR/v2.6.1d (Dobin et al. 2013) with default settings and gene annotations (GENCODE VM12 for mouse). Uniquely mapping reads were extracted, and duplicates were removed using the unique molecular identifier (UMI) sequence (ED < 2, including insertions and deletions), reverse transcription (RT) index, hairpin ligation adaptor index and read 2 end-coordinate (i.e. reads with UMI sequence less than 2 edit distance, RT index, ligation adaptor index and tagmentation site were considered duplicates).
Finally, mapped reads were split into constituent cellular indices by further demultiplexing reads using the RT index and ligation hairpin (ED < 2, including insertions and deletions). To generate digital expression matrices, we calculated the number of strand-specific UMIs for each cell mapping to the exonic and intronic regions of each gene with python/v2.7.13 HTseq package (Anders, Pyl, and Huber 2015). For multi-mapped reads, reads were assigned to the closest gene, except in cases where another intersected gene fell within 100 bp to the end of the closest gene, in which case the read was discarded. For most analyses we included both expected-strand intronic and exonic UMIs in per-gene single-cell expression matrices.
Assembly: mm10
Supplementary files format and content: Processed data files include a cell annotation csv  file, gene annotation csv file, and a gene count sparse matrix file

molecule: polyA RNA

organism: Mus musculus

source_name: mouse embryos

growth_protocol: The mutants were generated through conventional gene editing tools and breeding or tetraploid aggregation and collected at the embryonic stage E13.5, calculated from the day of vaginal plug (noon= E0.5). Collection and whole embryo dissection was performed as previously described (Kraft et al. 2015). The embryos were immediately snap-frozen in liquid nitrogen. Each wildtype and mutant was collected consistent within the background strain (either all male or half male half female).

extract_protocol:
The snap frozen embryos were processed as previously described (Cao et al. 2019). Briefly, the frozen embryos were cut into small pieces with a blade and further dissected by resuspension in 1 ml ice cold cell lysis buffer (CLB) in a 6 cm dish. adding another 3ml CLB, the sample was strained (40 µm) into a 15 ml Falcon tube and centrifuged to a pellet (500g, 5 min). Resuspending the sample with another 1 ml CLB, the isolation of nuclei was ensured. Pelleting the isolated nuclei again (500g, 5 min) was followed by a washing step by fixation in 10 ml 4% Paraformaldehyde (PFA) for 15 minutes on ice. The fixed nuclei were pelleted (500g, 3 min) and washed twice in the nuclei suspension buffer (NSB) (500g, 5 min). The nuclei finally were resuspended in 500µl NSB and split into 2 tubes, each containing 250 µl sample. The tubes were flash frozen in liquid nitrogen, until further use for library preparation. The embryo preparation was preceded randomly for nuclei isolation in order to avoid batch effects.
The library preparation proceeded as previously described (Cao et al. 2019). In short, the fixed nuclei were permeabilized, sonicated and washed. Nuclei from each mouse embryo were then distributed into several individual wells into 4 96-well plates. We split samples into four batches (~25 samples randomly selected in each batch) for sci-RNA-seq3 processing. The ID of the reverse transcription well was linked to the respective embryo for downstream analysis. In a first step the nuclei were then mixed with oligo-dT primers and dNTP mix, denatured and placed on ice, afterwards they were proceeded for reverse transcription including a grading incubation step. After reverse transcription, the Nuclei from all wells were pooled with the nuclei dilution buffer, spun down and redistributed into 96-well plates containing the reaction mix for ligation. The ligation was proceeded for 3 h at 16 °C. Afterwards, nuclei again were pooled with nuclei suspension buffer, spun down and washed and filtered. Next, the nuclei were counted and recistributed for second strand synthesis, which was was carried out at 16 °C for 3h. Afterwards tagmentation mix was added to each well and  tagmentation was carried out for 5 minutes. Stopping the reaction, DNA binding buffer was added and the sample was incubated for another 5 minutes. Following an elution step  using AMPure XP beads and elution mix, the samples were PCR amplified. Finally after PCR amplification, the nuclei were pooled and purified using AMPure XP beads. The library was analyzed by electrophoresis and the concentration was calculated using Qubit (Invitrogen). The library was sequenced on the NovaSeq platform (Illumina) (read 1: 34 cycles, read 2: 52 cycles, index 1: 10 cycles, index 2: 10 cycles).

tag: developmental stage

value: mouse embryo (E13.5)

tag: strain

value: C57BL/6, BALB/C, FVB, G4

tag: genotype

value: multiplexed sample:WT and mutant


title: WT 3 0h [0hWT3]

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

data_processing:
FASTQ files were aligned to Genome data base using STAR software [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530905/],and read counts obtained for each gene
Differential Expression was estimated using DESeq2 [https://www.ncbi.nlm.nih.gov/pubmed/25516281] and edgeR [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2796818/]
Genome_build: Mus_musculus.GRCm38.94.gtf
Supplementary_files_format_and_content: A matrix is generated as a plain text file (*.txt), in which each column is a sample, each row is a gene (ensembl_ID), and in each cell indicates the number of raw counts obtained by STAR per sample and gene.

molecule: total RNA

source_name: CD4+ T cells from spleen of WT #3 control

growth_protocol: Culture in RP10 between 0 and 24 h

extract_protocol:
The CD4+ T cells were washed with PBS and pelleted. Then the cells were resuspended in RLT buffer from the RNeasy Mini kit (Qiagen) and from there we followed the protocol of the kit.
Sequencing libraries were prepared following the protocol "TruSeqStrandedmRNASamplePreparationGuide(Part#15031047Rev.E)" with the "TruSeq stranded mRNAseq library preparation kit” (Illumina Inc., Cat.#RS-122-2101orRS-122-2102(SetAorB,respectively))
mRNA stranded library sequencing

treatment_protocol: Stimulation with anti-CD3/CD28 between 0 h and 24 h

tag: strain background

tag: genotype/variation

value: WT

tag: treatment

value: control

tag: tissue

value: spleen

tag: cell type

value: CD4+ T cells


title: 786-O-ACSS2i-24h-n1

department: Medicine

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens


title: WT 4 0h [0hWT4]

source_name: CD4+ T cells from spleen of WT #4 control


title: 786-O-DMSO-n2

value: DMSO


title: WT 1 0h [0hWT1]

source_name: CD4+ T cells from spleen of WT #1 control


title: MM-expr01-plate01-018

description: sci-RNA-seq3 library


title: NN-0009

city: Raleigh

first: Nirav

middle: M

last: Amin

state: NC

address: 1060 William Moore Drive

department: Molecular Biomedical Sciences

institute: North Carolina State University

description:
NNY13
Processed data file: raw_read_counts_per_gene.txt
Processed data file: normalized_read_counts_per_gene.csv

data_processing:
Trimmomatic (downloaded 2014-07-17 with Trinity Package) was used to trim low quality reads and adapter sequences using the following parameters: ILLUMINACLIP:2:30:10 MAXINFO:40:0.2
Trimmed reads were mapped to reference transcriptome (see below) using Bowtie2 (2.1.0) and default parameters (for mapping).
Samtools (v0.1.19) was used to sort .bam files from bowtie mapping, index and count reads uniquely mapping to reference transcriptome from bowtie2 alignment.
Read counts were compiled in a matrix and analyzed using DESeq (Bioconductor release 3.5).
Genome_build: A de novo transcriptome was generated from the RNA-seq data using Trinity. Bowtie2 was used to build a reference to which reads were mapped.
Supplementary_files_format_and_content: raw_read_counts_per_gene.txt: Tab-delimited text file; raw read counts.
Supplementary_files_format_and_content: normalized_read_counts_per_gene.csv: Comma-separated text file; normalized read counts (DESeq output).
Supplementary_files_format_and_content: Lepido_10_9_14.fasta: Fasta file of the de novo transcriptome assembly.

organism: Lepidobatrachus laevis

source_name: Gosner stage 19 left stomach

extract_protocol:
Stomach halves were dissected in 10% Holtfretter's solution and transferred with forceps to Trizol. DirectZol RNA extraction kit (Zymo Research) was used to purify RNA (standard protocol, incorporating DNase-on-column digestion step).
Libraries were constructed by NCSU Genomic Services Laboratory for NNY1-10 and HudsonAlpha Genomic Services Lab for NNY11-14 using strand-specific RNA library synthesis kits.

tag: strain/background

value: Wild-caught

value: Wild-type

tag: Stage

value: Stomach

tag: left/right

value: Left


title: MM-expr01-plate01-017

description: sci-RNA-seq3 library


title: Glu2

city: Belfast

first: Andrew

last: Marshall

state: Select...

address: 19 Chlorine Gardens

country: United Kingdom

institute: Queen's University Belfast

data_processing:
Differential gene expression analysis was carried out by mapping the sequenced reads to the C. difficile R20291 reference genome (https://www.ncbi.nlm.nih.gov/nuccore/FN545816.1). Reads were filtered by using the trimming pipeline, which filtered low sequencing score and reads aligned to adapter sequences. Raw reads were trimmed against adaptors and then reads were quality trimmed by skewer. Reads that passed the filter were then mapped onto the reference genome by the hisat2 mapping tool. Mapped reads were then counted by using the “featurecounts” tool (http://subread.sourceforge.net/) to determine the number of uniquely and correctly aligned reads per gene. Normalised read counts (RPKM) for a given gene were determined by normalising the exon space of a gene against the total number of mapped reads (excluding rRNA and reads not uniquely mapped according to their mapping quality score [MAPQ] using MAPQ20) in an alignment file and against the total length of the gene’s exon space. Differentially expressed genes were then determined using the DESeq package, which analyses the variance between biological replicates within the RNA-seq analysis in order to better model the expression values of individual genes within the group of replicates. DESeq then determines differentially expressed genes for each comparison by using, p value= ≤ 0.05.
Assembly: FN545816.1
Supplementary files format and content: Excel file shows transcripts per million (TPM) which is equivalent to RPKM

organism: Clostridioides difficile R20291

growth_protocol: BHIS overnight R20291 cultures of each were sub-cultured to an OD600 of 0.05 in 25 mL of DMM supplemented with either 20 mM glucose, 10 mM trehalose or 20 mM glucose and 10 mM trehalose. These were grown to mid-logarithmic phase (strain dependent 4-6 h), mixed with an equal volume of ice-cold 1:1 ethanol: acetone mix and stored at -80oC.

extract_protocol:
The cell suspension was thawed on ice, centrifuged at 5 000 x g for 10 min at 4oC, supernatant decanted and the pellet resuspended in 5 mL 1% beta-mercaptoethanol. The suspension was then centrifuged once more at 10 000 x g for 5 min at 4oC. RNA isolation was carried out using a Qiagen RNeasy Mini Kit (Qiagen, Manchester, UK ). Cells were resuspended in 200 µL TE buffer (10 mM Tris-HCl, 1 mM EDTA pH 8.0) containing 15 mg/mL lysozyme and 1.5 mg/ml Proteinase K (Qiagen, Manchester, UK) and incubated for 10 min at room temperature followed by the addition of 700 µL buffer RLT with 1% beta-mercaptoethanol. Cells were then transferred to a 2 mL Lysing Matrix B tube (MP Biomedicals, Cambridge, UK) and treated in a FastPrep-24 instrument (MP Biomedicals, Cambridge, UK) at a setting of 6.0 m/s for 45 s. The lysate was then centrifuged at 13 000 x g for 10 min and the supernatant added to 500 µL of 98% ethanol before RNA isolation and clean-up using a RNeasy column by following the manufacturer’s instructions. The protocol was modified to include an initial on-column DNA digestion step using the RNase-free DNase set (Qiagen, Manchester, UK) according to the manufacturer’s instructions.
RNA integrity was assessed using the Agilent 4200 TapeStation and the Agilent RNA ScreenTape Assay (Agilent, SantaClara, USA) with RNA samples of RIN > 8.0 being used for subsequent procedures. Ribodepletion was performed on 500 ng of total RNA, using the Qiagen FastSelect-5S/16S/23S ribodepletion kit (Qiagen, Manchester, UK) using the protocol: FastSelect-5S/16S/23S with NEBNext Ultra II Directional Library Prep Kit. Indexed sequencing libraries were then prepared using the NEBNext Ultra II Directional RNA Library Preparation Kit for Illumina (New England BioLabs, Ipswich, UK) and NEBNextMultiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) (New England Bio Labs, Ipswich, UK). Libraries were quantified using the Qubit Fluorometer and the Qubit dsDNA HS Kit (Thermo Fisher Scientific, Massachusetts, USA). Library fragment-length distributions were analysed using the Agilent TapeStation 4200 and the Agilent High Sensitivity D1000 ScreenTape Assay (Agilent, Santa Clara, USA). Libraries were pooled in equimolar amounts and final library quantification performed using the KAPA Library Quantification Kit for Illumina (Roche; Diagnostics, UK). The library pool was sequenced on the Illumina NextSeq 500 on a NextSeq500 High Output 300 cycle kit (Illumina, San Diego, USA), to generate over 10 million pairs of 150-bp paired-end reads per sample.

tag: growth phase

value: mid-logarithmic phase

value: Glucose grown


title: 786-O-DMSO-n1


title: Glu3


title: NN-0010

description:
NNY14
Processed data file: raw_read_counts_per_gene.txt
Processed data file: normalized_read_counts_per_gene.csv

source_name: Gosner stage 19 right stomach

value: Right


title: AIM2-/- 4 0h [0hKO4]

source_name: CD4+ T cells from spleen of Aim2 KO #4 control


title: MM-expr01-plate01-023

description: sci-RNA-seq3 library


title: NN-0007

description:
NNY11
Processed data file: raw_read_counts_per_gene.txt
Processed data file: normalized_read_counts_per_gene.csv


title: NN-0008

description:
NNY12
Processed data file: raw_read_counts_per_gene.txt
Processed data file: normalized_read_counts_per_gene.csv


title: AIM2-/- 2 0h [0hKO2]

source_name: CD4+ T cells from spleen of Aim2 KO #2 control


title: AIM2-/- 1 24h [24hKO1]

source_name: CD4+ T cells from spleen of Aim2 KO #1 24h stimulation

value: 24h stimulation with anti-CD3/CD28


title: MM-expr01-plate01-016

description: sci-RNA-seq3 library


title: MM-expr01-plate01-015

description: sci-RNA-seq3 library


title: Glu1


title: 97H-SMS2_2

city: Shanghai

first: Wenqing

last: Tang

address: 180 Fenglin Road, Xuhui District

country: China

institute: Department of Gastroenterology and Hepatology, Shanghai Institute of Liver Disease, Zhongshan Hospital, Fudan University

data_processing:
The raw paired end reads were trimmed and quality controlled by SeqPrep and Sickle with default  parameters.
Clean reads were separately aligned to reference genome with orientation mode  using HISAT2.
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
Assembly: hg18
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample

source_name: Adult hepatocellular carcinoma

extract_protocol:
RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 2.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Adult hepatocellular carcinoma


title: MM-expr01-plate01-019

description: sci-RNA-seq3 library

value: mouse embryo (E13.5)


title: AIM2-/- 1 0h [0hKO1]

source_name: CD4+ T cells from spleen of Aim2 KO #1 control


title: 97H-SMS2_1


title: MM-expr01-plate01-013

description: sci-RNA-seq3 library

value: C57BL/6, BALB/C, FVB, G4


title: 97H-Ctrl_3

value: Wild type


title: MM-expr01-plate01-014

description: sci-RNA-seq3 library

value: multiplexed sample:WT and mutant


title: 97H-Ctrl_2


title: MM-expr01-plate01-012

description: sci-RNA-seq3 library


title: TDP-43 KD, Rep 7

city: Tübingen

first: Vikas

last: Bansal

state: BW

address: Otfried Müller Strasse 23

country: Germany

institute: German Center for Neurodegenerative Diseases (DZNE)-Tübingen

data_processing:
RNA-sequencing quality was evaluated by utilizing raw reads using the FastQC quality control tool version 0.10.1
Bowtie2 v2.0.2 using RSEM version 1.2.29 with default parameters was utilized to align sequence reads (single-end 50 bp) to human reference genome (hg38)
Ensembl annotations (version 84.38) with rsem-prepare-reference from RSEM software was used to index the human reference genome
Furthermore, sequence alignment of sequence reads and gene quantity was obtained through the use of rsem-calculate-expression. Rsem-calculate-expression resulted in sequence read count and TPM value (transcripts per million) for individual genes.
DESeq2 package was used to carry out differential expression analysis. Finally, genes with less than 5 reads (baseMean) were filtered, while genes with an adjusted p-value < 0.01 were classified as differentially expressed.
Assembly: hg38
Supplementary files format and content: Tab-delimited excel files (xlsx) include DESeq2 normalized values for each Sample

source_name: HUVEC

growth_protocol: HUVEC were purchased from PromoCell (Heidelberg, Germany) and cultured in 50% Endothelial Cell Basal Medium (PromoCell, Heidelberg, Germany) and 50% Medium 199 (Life Technologies, Carlsbad, CA, USA) with 20%FCS.

extract_protocol:
The cells were subsequently washed twice with ice cold PBS and further processed with TRIZOL for RNA analysis.
Total RNA was isolated using Tri-Reagent. RNA quality was assessed using Nanodrop 2000 (Thermo Fisher Scientific, GmbH) and RNA integrity number (RIN) was evaluated by using the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., USA). RNA was reverse transcribed to cDNA using Transcriptor High Fidelity cDNA synthesis kit (Roche Diagnostics Deutschland GmbH, Mannheim, Germany)  RNA-Seq libraries were obtained using TruSeq RNA Sample Preparation v2 kit (Illumina, Inc., San Diego, USA). To analyze the library quality, Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, USA) was used and the concentration was measured by a QubitR dsDNA HS Assay kit (Thermo Fisher Scientific Inc., Waltham, USA).

treatment_protocol: For virus transduction, cells were grown to 80 confluence and detached with Trypsin/EDTA. They were seeded and transduced with virus containing either the sequence coding for shCtr, shTARDBP#1, or shTARDBP#2 on the following day with 25 ml virus mix per 10ml culture volume in a 10cm dish.

value: HUVEC

value: endothelial cells

value: TDP-43 KD


title: 97H-SMS2_3


title: TDP-43 KD, Rep 6


title: MM-expr01-plate01-011

description: sci-RNA-seq3 library


title: TDP-43 KD, Rep 8


title: 97H-Ctrl_1


title: 3-prime-rnaseq-log2

city: Bethesda

first: Philip

last: Adams

state: MD

address: 9000 Rockville Pike

department: NICHD

institute: National Institutes of Health

description:
3-prime-rnaseq-log-forward.1bp.narrowPeak
3-prime-rnaseq-log-reverse.1bp.narrowPeak

data_processing:
library strategy: 3′RNA-seq (term-seq)
Raw sequence reads were processed using lcdb-wf (lcdb.github.io/lcdb-wf/) according to the following steps, as previously performed (Adams et al., 2021). Raw sequence reads were trimmed with cutadapt 2.3 (Martin, 2011) to remove any adapters while performing light quality trimming with parameters “-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -q 20 –minimum-length=25.” Sequencing library quality was assessed with fastqc v0.11.8 with default parameters. The presence of common sequencing contaminants was evaluated with fastq_screen v0.13.0 with parameters “–subset 100000 –aligner bowtie2.” Trimmed reads were mapped to the B. burgdorferi reference genome (GCF_000008685.2_ASM868v2) using BWA-MEM. Multimapping reads were filtered using samtools (Li et al., 2009). Uniquely aligned reads were then mapped using subread featureCounts v1.6.4 with default parameters to gene features made from the union of NCBI B. burgdorferi B31 gene annotations GCF_000008685.2 and the updated sRNA annotation. BedGraph files were generated using deepTools (Ramírez et al., 2016) on reads from each strand separately.  An initial set of termination peaks was called per sample on the uniquely aligned reads using a novel signal processing approach combined with a statistically-informed method of combining multiple replicates. Briefly, the scipy.signal Python package was used to call peaks on each replicate in a manner which handled high, sharp peaks as found in Term-seq data, using the scipy.signal.find_peaks function with a width of (1, None), a prominence of (None, None), and a relative height of 0.75. Peaks for each replicate were then combined using the IDR framework (Landt et al., 2012) into a set of peaks that were reproducible across replicates. The code for this can be found at https://github.com/NICHD-BSPC/termseq-peaks and can be used in general for Term-seq peak-calling in other bacteria. Termination peaks were subsequently curated according to the following criteria. The single-bp peak coordinate was set to the strongest signal nucleotide within the boundary of the initial broader peak using multiBigWigSummary from deepTools 3.2.1. The most downstream position, relative to the peak orientation, was chosen when several positions were equally strong. Scores from peaks within a distance of up to 100 bp were assessed to select the peak with the highest score among the cluster for further analysis.
Assembly: GCF_000008685.2_ASM868v2
Supplementary files format and content: narrowPeak files of filtered termination peaks

organism: Borreliella burgdorferi

source_name: B31 (lab strain number: PA003)

growth_protocol: B. burgdorferi were cultivated in liquid Barbour-Stoenner-Kelly (BSK) II medium supplemented with gelatin and 6% rabbit serum.  Three biological replicates of B. burgdorferi B31 (lab strain number: PA003) were grown in BSKII to mid-logarithmic phase (3.75e7 – 5.5e7 cells/ml) at 35°C, the culture split for RNA isolation or temperature shifted (TS) to bench (~23°C) and then back to 35°C and grown to stationary phase (~3.2e8 cells/ml).

extract_protocol:
RNA was isolated using TRIzol.
RNA was prepared for sequencing as described previously (Adams et al., 2021). Any contaminating DNA in the samples was removed by treating 15 µg of RNA with 10 U of DNase I (Roche) for 15 min at 37˚C in the presence of 80 U of recombinant RNase inhibitor (Takara Bio). Next, RNA was purified by mixing the sample with an equal volume of phenol stabilized:chloroform:isoamyl alcohol (25:24:1) and centrifugation at maximum speed in Heavy Phase Lock Gel tubes (5 PRIME). A volume of chloroform, equal to the original sample volume, was added to the same Heavy Phase Lock Gel tubes and spun again. The aqueous layer was removed and ethanol precipitated. RNA pellets were reconstituted in 10 µl DEPC H2O and analyzed using an Agilent 4200 TapeStation System to ensure DNase-treated RNA was at high quality. Term-seq libraries were prepared using a modified version of the RNAtag-seq methodology (Shishkin et al., 2015), based on the previously published Term-seq methodology (Dar et al., 2016). 1.5 µg of DNA-free RNA was first ligated at the 3′ end with 150 µM barcoded oligonucleotide adapters which were 5′phosphorylated and dideoxycytidine 3′ terminated. RNA and 3′ adapters were incubated at 22˚C for 2.5 hr with 51 U of T4 RNA Ligase I (NEB) and 12 U of recombinant RNase inhibitor (Takara Bio) in 1X T4 RNA Ligase Buffer (NEB), 9% DMSO, 20% PEG 8000, and 1 mM ATP. 3′ ligated RNA was cleaned by incubating with 2.5X volume of RNAClean XP beads (Beckman Coulter) and 1.5X volume of isopropanol for 15 min, before separation on a magnetic rack. Bead-bound RNA was washed with 80% ethanol, air dried, and resuspended in DEPC H2O. RNA-containing-supernatants were removed and the same RNAClean XP bead cleanup protocol was repeated, with a final DEPC H2O elution of 9.5 µl. RNA was fragmented by incubating 9 µl of cleaned-up RNA with 1X Fragmentation Reagent (Invitrogen) for 2 min at 72˚C, followed by an addition of 1X Stop Solution (Invitrogen). Samples were stored on ice following individual fragmentation of each sample. Fragmented-RNA was pooled together and cleaned using the RNA Clean and Concentrator-5 kit (Zymo) according to the manufacturer’s instructions. Library construction continued following the bacterial-sRNA adapted, RNAtag-seq methodology starting at the rRNA removal step (Melamed et al., 2018). Term-seq RNA libraries were analyzed on a Qubit 3 Fluorometer (Thermo Fisher Scientific) and an Agilent 4200 TapeStation System prior to paired-end sequencing using the HiSeq 2500 system (Illumina).

value: B31 (lab strain number:PA003)

value: log

tag: seq type


title: 3-prime-rnaseq-TS-stationary3

description:
3-prime-rnaseq-TS-stationary-forward.1bp.narrowPeak
3-prime-rnaseq-TS-stationary-reverse.1bp.narrowPeak

value: TS-stationary


title: 3-prime-rnaseq-TS-stationary2


title: 3-prime-rnaseq-log1


title: MM-expr01-plate01-010

description: sci-RNA-seq3 library


title: 3-prime-rnaseq-TS-stationary1


title: 3-prime-rnaseq-log3


title: BCM-plus-rnaseq2

data_processing:
Raw sequence reads were processed using lcdb-wf (lcdb.github.io/lcdb-wf/) according to the following steps, as previously performed (Adams et al., 2021). Raw sequence reads were trimmed with cutadapt 2.3 (Martin, 2011) to remove any adapters while performing light quality trimming with parameters “-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -q 20 –minimum-length=25.” Sequencing library quality was assessed with fastqc v0.11.8 with default parameters. The presence of common sequencing contaminants was evaluated with fastq_screen v0.13.0 with parameters “–subset 100000 –aligner bowtie2.” Trimmed reads were mapped to the B. burgdorferi reference genome (GCF_000008685.2_ASM868v2) using BWA-MEM. Multimapping reads were filtered using samtools (Li et al., 2009). Uniquely aligned reads were then mapped using subread featureCounts v1.6.4 with default parameters to gene features made from the union of NCBI B. burgdorferi B31 gene annotations GCF_000008685.2 and updated sRNA annotations. BedGraph files were generated using deepTools (Ramírez et al., 2016) on reads from each strand separately. Sequencing reads from untreated and BCM treated samples were aligned to the GCF_000008685.2_ASM868v2 genome by following the same procedures as 3′RNA-seq data analysis for QC, adaptor removal and sequencing read mapping. The approximate Rho-dependent transcription termination sites were predicted by identifying the locations of transcriptional readthrough in the BCM treated sample using rhoterm-peaks ((Adams et al., 2021), available at https://github.com/gbaniulyte/rhoterm-peaks). The ratio of the read count in a 800 nt region upstream (BCM_us) and downstream (BCM_ds) of each position was compared to the same ratios at the same position in the untreated sample (Untreated_us, Untreated_ds) (R(BCM/untreated) =  (BCM_ds/BCM_us)/(Untreated_ds/Untreated_us) ). The ratio R(BCM/Untreated) threshold for termination sites was set to ≥ 2.0.
Assembly: GCF_000008685.2_ASM868v2
Supplementary files format and content: narrowPeak files of filtered termination peaks

growth_protocol: B. burgdorferi were cultivated in liquid Barbour-Stoenner-Kelly (BSK) II medium supplemented with gelatin and 6% rabbit serum. Two cultures of B. burgdorferi B31 (lab strain number: PA003) spirochetes were grown in BSKII to a cell density of 2.75e7 – 4.0e7 cells/ml, the cultures divided and half treated with 100 μg/ml of bicyclomycin benzoate (MedChemExpress) for 6 h.

extract_protocol:
RNA was isolated using TRIzol.
Total RNA-seq library construction was carried out based on the RNAtag-seq methodology (Shishkin et al., 2015), which was adapted to capture bacterial sRNAs (Melamed et al., 2018).

value: B. burgdorferi B31 (lab strain number:PA003)

value: BCM


title: RFG6

description:
NNY10
Processed data file: raw_read_counts_per_gene.txt
Processed data file: normalized_read_counts_per_gene.csv

value: Wild-caught

value: Wild-type

value: Stomach


title: LFG6

description:
NNY9
Processed data file: raw_read_counts_per_gene.txt
Processed data file: normalized_read_counts_per_gene.csv

value: Left


title: MM-expr01-plate01-009

description: sci-RNA-seq3 library


title: MM-expr01-plate01-008

description: sci-RNA-seq3 library


title: BCM-plus-rnaseq1

source_name: B. burgdorferi B31 (lab strain number: PA003)


title: BCM-minus-rnaseq2

value: control


title: MM-expr01-plate01-007

description: sci-RNA-seq3 library

value: mouse embryo (E13.5)


title: RFG5

description:
NNY8
Processed data file: raw_read_counts_per_gene.txt
Processed data file: normalized_read_counts_per_gene.csv

value: Right


title: LFG5

description:
NNY7
Processed data file: raw_read_counts_per_gene.txt
Processed data file: normalized_read_counts_per_gene.csv


title: Thyroid, PolyA RNA

city: Planegg-Martinsried

first: Irina

last: Solovei

address: Großhaderner Str. 2

institute: LMU Munich

data_processing:
Basecalling was performed using Guppy 6.4.6
Read quality was checked using pycoQC 2.5.2
Sequence alignment to the mm10 genome was performed using minimap2 (parameters: -ax splice)
Genome coverage was processed using Bedtools (v2.30.0) genomecov (parameters: -trackline -bg -split -ibam)
Assembly: mm10
Supplementary files format and content: BedGraph file

source_name: Thyroid

extract_protocol:
RNA was extracted from freshly dissected thyroids which were immediately placed in ice cold TriZol and homogenized using an ultra-turrax dispersing tool (IKA).
The sequencing library was created using the cDNA-PCR Sequencing Kit (Oxford Nanopore Technologies)  according to the manufacter’s instructions

value: Thyroid

value: Thyrocytes


title: MM-expr01-plate01-006

description: sci-RNA-seq3 library

value: C57BL/6, BALB/C, FVB, G4

value: multiplexed sample:WT and mutant


title: bulk-rna-seq-TS-stationary3

data_processing:
Raw sequence reads were processed using lcdb-wf (lcdb.github.io/lcdb-wf/) according to the following steps, as previously performed (Adams et al., 2021). Raw sequence reads were trimmed with cutadapt 2.3 (Martin, 2011) to remove any adapters while performing light quality trimming with parameters “-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -q 20 –minimum-length=25.” Sequencing library quality was assessed with fastqc v0.11.8 with default parameters. The presence of common sequencing contaminants was evaluated with fastq_screen v0.13.0 with parameters “–subset 100000 –aligner bowtie2.” Trimmed reads were mapped to the B. burgdorferi reference genome (GCF_000008685.2_ASM868v2) using BWA-MEM. Multimapping reads were filtered using samtools (Li et al., 2009). Uniquely aligned reads were then mapped using subread featureCounts v1.6.4 with default parameters to gene features made from the union of NCBI B. burgdorferi B31 gene annotations GCF_000008685.2 and the updated sRNA annotation. BedGraph files were generated using deepTools (Ramírez et al., 2016) on reads from each strand separately.
Assembly: GCF_000008685.2_ASM868v2
Supplementary files format and content: TXT file tab-separated of featurecounts gene counts

value: bulk-rnaseq


title: BCM-minus-rnaseq1


title: H23S

city: Madrid

first: Carlos

last: Rodriguez Antolin

address: Paseo de la Castellana

department: Genetics

institute: Hospital La Paz Institute for Health Research

data_processing:
The trimmed reads (length >= 15 nt and adapters removal) were aligned to the human pre-miRNA in miRBase 21 using novoalign software. For miRNA alignment, the maximum mismatch was 1. Reads with counts less than 2 were discarded when calculating the miRNA expression.
Assembly: miRBase 21
Supplementary files format and content: Tab-delimited text files include annotations and read counts (number of transcripts per million, TPM) of all mature miRNA variants (miRBase21) in each sample

source_name: Lung cancer sensitive cell line

growth_protocol: All cell lines were maintained in RPMI or DMEM supplemented with 10% exosome-depleted FBS, according to manufacturer’cifications. FBS was depleted of bovine exosomes by ultracentrifugation at 100,000 x g 16 h at 4 C.

extract_protocol:
RNA was extracted using miRCURY RNA Isolation Kit - Cell and Plant (Exiqon, Denmark)
Total RNA of each sample was sequentially ligated to 3’ and 5’ small RNA adapters. cDNA was then synthesized and amplified using Illumina’s proprietary RT primers and amplification primers. Subsequently, ~130-150 bp PCR amplified fragments were extracted and purified from the PAGE gel. Sequencing was performed on Illumina HiSeq 2000 using Truseq Rapid SBS Kits, according to the manufacturer's instructions.

treatment_protocol: The Cisplatin (CDDP) resistant variants H23R and A2780R were established by exposing cells to increasing doses of  cisplatin,and selected after a final exposure to 0.2 and 0.5 µ respectively, showing approximately four times more drug resistance than the matched parental cell line (4.07 and 3.89 resistant index; P<0.001 and P<0.002). The CDDP sensitive and resistant ovarian cancer cell lines 41M and 41MR were kindly provided by Dr. Kelland (UK) and maintained in DMEM supplemented with 10% exosome-depleted FBS, showing a similar CDDP resistant-index of 4.8; P<0.001.

tag: biological source

value: Lung

tag: chemoterapy drug

value: cisplatin

tag: phenotype

value: Sensitive


title: H23R

source_name: Lung cancer resistant cell line

tag: cell line

value: Resistant


title: A2780S

source_name: Ovarian cancer sensitive cell line

value: Ovary


title: bulk-rna-seq-TS-stationary2

value: B. burgdorferi B31 (lab strain number:PA003)

value: TS-stationary


title: A2780R

source_name: Ovarian cancer resistant cell line


title: Control, Rep 2

value: HUVEC

value: endothelial cells

value: Control


title: Control, Rep 1


title: TDP-43 KD, Rep 5

description: note from submitter: we did not use the KD1 sample to calculate p-value. But we provide raw data for this sample for transparency purposes.

value: TDP-43 KD


title: Control, Rep 3


title: bulk-rna-seq-log3

value: log


title: Control, Rep 4


title: LFG3

description:
NNY5
Processed data file: raw_read_counts_per_gene.txt
Processed data file: normalized_read_counts_per_gene.csv

value: Wild-caught

value: Wild-type

value: Stomach

value: Left


title: Right-Gut

description:
NNY4
Processed data file: raw_read_counts_per_gene.txt
Processed data file: normalized_read_counts_per_gene.csv

value: Right


title: Left-Gut

description:
NNY3
Processed data file: raw_read_counts_per_gene.txt
Processed data file: normalized_read_counts_per_gene.csv


title: RFG3

description:
NNY6
Processed data file: raw_read_counts_per_gene.txt
Processed data file: normalized_read_counts_per_gene.csv


title: MM-expr01-plate01-005

description: sci-RNA-seq3 library

source_name: mouse embryos

tag: developmental stage

value: mouse embryo (E13.5)

value: C57BL/6, BALB/C, FVB, G4

value: multiplexed sample:WT and mutant


title: Right-Foregut

description:
NNY2
Processed data file: raw_read_counts_per_gene.txt
Processed data file: normalized_read_counts_per_gene.csv


title: 41MS

value: cisplatin

value: Sensitive


title: bulk-rna-seq-log2

tag: strain

value: B. burgdorferi B31 (lab strain number:PA003)

value: bulk-rnaseq


title: 41MR

value: Ovary

value: Resistant


title: bulk-rna-seq-log1


title: Left-Foregut

description:
NNY1
Processed data file: raw_read_counts_per_gene.txt
Processed data file: normalized_read_counts_per_gene.csv


title: MM-expr01-plate01-002

description: sci-RNA-seq3 library

tag: genotype


title: MM-expr01-plate01-003

description: sci-RNA-seq3 library


title: MM-expr01-plate01-001

description: sci-RNA-seq3 library


title: MM-expr01-plate01-004

description: sci-RNA-seq3 library


title: bulk-rna-seq-TS-stationary1

value: TS-stationary


title: GNT-iPSCs#1_rep2

status: Public on May 25 2023

city: Beijing

first: Jianyong

last: Han

address: 2rd, Yuanmingyuan West Road

department: State Key Laboratory of Agrobiotechnology

institute: China Agricultural University

data_processing:
For the all paired-end libraries from public data and our data, trim_garole(Martin, 2011) (v-0.6.6) software was used for quality control with the parameters: “-q 25 -j 8 --phred33 --length (reads length)/2 -e 0.1 --stringency 4 --paired”. Then, high quality reads from 12 RNA-seq libraries of our data were mapped to the reference pig genome(Sscrofa 11.1) using HISAT2(Pertea et al., 2016) (v-2.1.0) with default parameters. Expression levels of all genes were quantified as reads counts using FeatureCounts(Liao et al., 2014) (v-2.0.1) and only genes containing exons were counted, with the reference annotation Sus_scrofa.Sscrofa11.1.105.gtf downloaded from Ensembl (http://dec2021.archive.ensembl.org/index.html) that mitochondrial genes were removed.
Assembly: Sscrofa 11.1
Supplementary files format and content: tab-delimited text files include read counts for each Sample

organism: Sus scrofa

source_name: Reprogrammed from pig ear fibroblast

growth_protocol: Pig iPSCs were induced and maintained on MEF feeder layers in 3i/LAF culture medium under 20% O2 and 5% CO2. The basal medium of 3i/LAF consists of following components per 500 mL: 227.5 mL DMEM/F12 (Thermo Fisher Scientific, 10565-018), 227.5 mL neurobasal (Thermo Fisher Scientific, 21103-049), 2.5 mL N2 supplement (Thermo Fisher Scientific, 17502-048), 5 mL B27 supplement (Thermo Fisher Scientific, 12587-010), 2.5 mL GlutaMAX (Thermo Fisher Scientific, 35050-061), 5 mL nonessential amino acids (Thermo Fisher Scientific, 11140-050), 500 μL β-mercaptoethanol (Thermo Fisher Scientific, 21985-023), 5 mL penicillin-streptomycin (Thermo Fisher Scientific, 15140-122), 25 mL knockout serum replacement (KOSR, Thermo Fisher Scientific, A3181502), and 50 μg/mL ascorbic acid (Vc, Sigma-Aldrich, A4544). Cytokines and small molecules in 3i/LAF contained recombinant FGF-basic(154aa) (10 ng/mL, PeproTech, 100-18-B), recombinant human Activin A (25ng/mL, PeproTech, 120-14E), recombinant human LIF (10ng/ml, PeproTech, 300-05), CHIR99021 (1 μM, Selleckchem, S1263), IWR-1 (2.5 μM, Selleckchem, S7086), WH-4-023 (1 μM, Selleckchem, S7565). 10 μM Y-27632 (Selleckchem, S1049) was added when passaging, and 2 μM for routinely maintenance.

extract_protocol:
Around 1×106 cells GNT-iPSCs, pMX-iPSCs and epi-iPSCs were collected per replicate. The cells were lysed in Trizol (Invitrogen). RNA-seq library was constructed using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® (Vazyme, NR604-02). PCR production was purified using VAHTSTM DNA Clean Beads (Vazyme, N411-03).
RNA-seq library was constructed using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® (Vazyme, NR604-02) following manufacturer's protocols.

value: Reprogrammed from pig ear fibroblast

value: iPSC

value: Reprogrammed by retroviral vector

value: GFP insertion, NANOG-tdTomato knock in, TYR-/-

tag: passage

value: Passage 31


title: P6-M1-Bulk

city: Brisbane

first: Alexander

last: Walsh

state: Queensland

address: QBI Building 79, University of Queensland, St Lucia

country: Australia

institute: University of Queensland

description: small RNA sequencing

data_processing:
Adapter sequences were removed from small RNA sequencing data and remaining reads were filtered by size (>18 bp) using fastp (ver 0.20.0).
Trimmed reads were mapped to mature mouse miRNAs downloaded from mIRBase and remaining reads were aligned to the mouse reference genome (mm10/GRCm38) using mirDeep2 with default settings (ver 0.1.3).
Candidate novel miRNAs detected by miRDeep2 with a miRDeep2 score > 4 and randfold p value < 0.05 were included in downstream analysis.
Supplementary files format and content: mm10
Supplementary files format and content: delimited text file containing matrix of raw read counts generated from mirdeep2 for all samples

source_name: Whole brain

extract_protocol:
Whole brain was extracted from male and female WTC57Bl/6 mice at appropriate ages. Brain was digested to a single cell suspension, and CD45+ microglia were isolated using CD45+ immunopanning (antibody, Jackson ImmunoResearch Laboratories, Inc, 112-005-167). Cd45- Bulk CNS cells were also collectedand sequenced for comparative analysis. Cells were collected into Qiazol and total RNA was extracted using the miRNeasy mini kit (Qiagen) in accordance with manufacturers protocol.
small RNA libraries were prepared using the MGIEasy Small RNA library prep chemistry (MGI).

value: Whole brain

value: WT/Male


title: P6-M4-Bulk

description: small RNA sequencing


title: P6-M5-Bulk

description: small RNA sequencing


title: P6-M2-Bulk

description: small RNA sequencing


title: P6-M3-Bulk

description: small RNA sequencing


title: P6-M6-Bulk

description: small RNA sequencing


title: epi-iPSCs#8_rep1

source_name: Reprogrammed from pig embryonic fibroblast

value: Reprogrammed by episomal vector

value: wt

value: Passage 21


title: pMX-iPSCs#6_rep2

value: Reprogrammed from pig embryonic fibroblast

value: Passage 15


title: GNT-iPSCs#3_rep1

value: Passage 30


title: pMX-iPSCs#10_rep1

value: Passage 16


title: GNT-iPSCs#3_rep2


title: epi-iPSCs#5_rep2


title: pMX-iPSCs#10_rep2

value: Passage 17


title: epi-iPSCs#8_rep2

value: Passage 22


title: pMX-iPSCs#6_rep1

value: Passage 14


title: P6-F5-Bulk

description: small RNA sequencing

value: WT/Female


title: P6-F6-Bulk

description: small RNA sequencing


title: epi-iPSCs#5_rep1

value: iPSC


title: P6-F2-Bulk

description: small RNA sequencing


title: P6-F1-Bulk

description: small RNA sequencing


title: P15-M6-Bulk

description: small RNA sequencing


title: P15-M5-Bulk

description: small RNA sequencing


title: P15-M4-Bulk

description: small RNA sequencing


title: P15-M2-Bulk

description: small RNA sequencing


title: GNT-iPSCs#1_rep1

value: Reprogrammed from pig ear fibroblast

value: Reprogrammed by retroviral vector


title: P6-F3-Bulk

description: small RNA sequencing


title: 8W-M6-Bulk

description: small RNA sequencing

value: 8 weeks


title: P15-F3-Bulk

description: small RNA sequencing

value: Whole brain


title: P15-F4-Bulk

description: small RNA sequencing


title: 8W-M5-Bulk

description: small RNA sequencing

value: WT/Male


title: P15-F2-Bulk

description: small RNA sequencing


title: 8W-M2-Bulk

description: small RNA sequencing


title: 8W-M3-Bulk

description: small RNA sequencing


title: 8W-F4-Bulk

description: small RNA sequencing


title: 8W-F3-Bulk

description: small RNA sequencing


title: P6-M5-CD45

description: small RNA sequencing


title: 8W-M1-Bulk

description: small RNA sequencing


title: 8W-F6-Bulk

description: small RNA sequencing


title: 8W-F2-Bulk

description: small RNA sequencing


title: 8W-F5-Bulk

description: small RNA sequencing


title: P15-M3-Bulk

description: small RNA sequencing


title: 8W-M4-Bulk

description: small RNA sequencing


title: 8W-F1-Bulk

description: small RNA sequencing


title: P6-M1-CD45

description: small RNA sequencing


title: P6-M3-CD45

description: small RNA sequencing


title: P6-M4-CD45

description: small RNA sequencing


title: P6-M2-CD45

description: small RNA sequencing


title: P15-M1-Bulk

description: small RNA sequencing


title: P15-F6-Bulk

description: small RNA sequencing


title: P6-F3-CD45

description: small RNA sequencing


title: P15-F5-Bulk

description: small RNA sequencing


title: P6-F5-CD45

description: small RNA sequencing


title: P15-F1-Bulk

description: small RNA sequencing


title: P6-F2-CD45

description: small RNA sequencing


title: P6-M6-CD45

description: small RNA sequencing


title: P15-M6-CD45

description: small RNA sequencing


title: P6-F1-CD45

description: small RNA sequencing


title: P15-M5-CD45

description: small RNA sequencing


title: 8W-M6-CD45

description: small RNA sequencing


title: P15-M4-CD45

description: small RNA sequencing


title: P15-F2-CD45

description: small RNA sequencing


title: P15-F3-CD45

description: small RNA sequencing


title: P15-F4-CD45

description: small RNA sequencing


title: P15-M1-CD45

description: small RNA sequencing


title: P15-M2-CD45

description: small RNA sequencing


title: P15-F5-CD45

description: small RNA sequencing


title: 8W-M3-CD45

description: small RNA sequencing


title: 8W-M1-CD45

description: small RNA sequencing


title: 8W-M5-CD45

description: small RNA sequencing


title: 8W-M2-CD45

description: small RNA sequencing


title: P6-F6-CD45

description: small RNA sequencing


title: 8W-F4-CD45

description: small RNA sequencing


title: 8W-F6-CD45

description: small RNA sequencing


title: 8W-F3-CD45

description: small RNA sequencing


title: 8W-F1-CD45

description: small RNA sequencing


title: 8W-F2-CD45

description: small RNA sequencing


title: P6-M6

description: mRNA sequencing

data_processing:
Adapter sequences were removed from RNA sequencing data using fastp (ver 0.20.0)
mRNA sequencing data was mapped to the mouse reference genome (mm10/GRCm38) using STAR with default settings (ver 2.7.3).
Gene read counts were generated using the featureCounts pipeline in Subread with the following flags (-T 8 -s 2 -p -a) (ver 2.0.0).
Assembly: mm10
Supplementary files format and content: tab-delimited text file matrix containing gene counts derived from Subread featurecounts.

extract_protocol:
Whole brain was extracted from male and female WTC57Bl/6 mice at three different ages (P6, P15, 8 weeks). Brain was digested to a single cell suspension, and CD45+ microglia were isolated using CD45+ immunopanning (antibody, Jackson ImmunoResearch Laboratories, Inc, 112-005-167).  CD45+ cells were collected into Qiazol and total RNA was extracted using the miRNeasy mini kit (Qiagen) in accordance with manufacturers protocol.
mRNA libraries were prepared using MGIEasy RNA Directional RNA library prep chemistry (MGI)


title: P6-M5

description: mRNA sequencing


title: P6-M4

description: mRNA sequencing


title: P15-M3-CD45

description: small RNA sequencing


title: P15-F1-CD45

description: small RNA sequencing


title: P6-M3

description: mRNA sequencing


title: P6-M1

description: mRNA sequencing


title: P15-F6-CD45

description: small RNA sequencing


title: 8W-M4-CD45

description: small RNA sequencing


title: 8W-F5-CD45

description: small RNA sequencing


title: P15-M3

description: mRNA sequencing


title: P6-F1

description: mRNA sequencing


title: P15-M4

description: mRNA sequencing


title: P6-F3

description: mRNA sequencing


title: P15-M2

description: mRNA sequencing


title: P15-F5

description: mRNA sequencing


title: P15-M1

description: mRNA sequencing


title: P6-F2

description: mRNA sequencing


title: P15-F6

description: mRNA sequencing


title: P15-F3

description: mRNA sequencing


title: P15-M5

description: mRNA sequencing


title: P15-F4

description: mRNA sequencing


title: P15-F2

description: mRNA sequencing


title: P15-M6

description: mRNA sequencing


title: P6-F5

description: mRNA sequencing


title: 8W-M6

description: mRNA sequencing


title: P15-F1

description: mRNA sequencing


title: 8W-M5

description: mRNA sequencing


title: 8W-M4

description: mRNA sequencing


title: P6-F6

description: mRNA sequencing


title: P6-M2

description: mRNA sequencing


title: 8W-M3

description: mRNA sequencing


title: 8W-M2

description: mRNA sequencing


title: 8W-M1

description: mRNA sequencing


title: 8W-F6

description: mRNA sequencing


title: 8W-F3

description: mRNA sequencing


title: 8W-F4

description: mRNA sequencing


title: 8W-F5

description: mRNA sequencing


title: 8W-F2

description: mRNA sequencing


title: 8W-F1

description: mRNA sequencing


title: PBMC, BioCAP, replicate 2

city: Sydney

first: Allegra

last: Angeloni

state: NSW

address: 384 Victoria St Darlinghurst

department: Genomics and Epigenetics Division

institute: Garvan Institute of Medical Research

data_processing:
BioCAP reads were trimmed using trimmomatic (ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 SLIDINGWINDOW:5:20 LEADING:3 TRAILING:3 MINLEN:25) (Bolger et al., 2014) and aligned to the petMar3 reference genome using bowtie2 (-p 10 -N 1 --very-sensitive -X 2000 --no-mixed --no-discordant) (Langmead & Salzberg, 2012). The resulting alignments in BAM format were deduplicated using Picard MarkDuplicates (REMOVE_DUPLICATES=true) (https://github.com/broadinstitute/picard). NMIs were called using the macs2 callpeak function (Zhang et al., 2008). Bigwig (log2 IP/input) files were generated using deepTools bamCompare (--ignoreDuplicates --binSize 50 --centerReads --extendReads) (Ramirez et al., 2014).
Assembly: petMar3
Supplementary files format and content: bigWig, narrowPeak (except for Input samples)

organism: Petromyzon marinus

source_name: PBMC

extract_protocol:
For DNA extraction, lamprey embryos were lysed in buffer containing 20 mM Tris, pH 8.0, 100 mM NaCl, 15 mM EDTA, 1% SDS and 0.5 mg/ml proteinase K for 3 h at 55 °C. Lysis was followed by two phenol:chloroform:isoamyl alcohol (25:24:1) extractions and subsequent centrifugation (5 min at 17,949g). DNA was then precipitated by adding 0.2 volumes of 4 M ammonium acetate and 3 volumes of 96% ethanol. The reaction was left on ice for a minimum of 30 min. The DNA precipitate was centrifuged for 20 min at 4 °C (17,949g), and the pellet was washed with 500 μl of 70% ethanol and centrifuged for 5 min (17,949g) at room temperature. The pellet was then resuspended in 200 μl of TE buffer, and 1 μl of RNase A (20 μg/μl) was added. The reaction was left to proceed for 30 min at room temperature, after which time the DNA was precipitated with 0.1 volumes of 4 M ammonium acetate and 1 volume of isopropanol on ice for 2 h. The reaction was then centrifuged for 30 min at 4 °C (17,949g), and the pellet was resuspended in TE buffer.
BioCAP was performed on genomic DNA in replicate and with input controls, using methods described in Long et al. Methods Mol Biol 2018. Briefly, genomic DNA was sonicated to approximately 200 base pairs and incubated with biotinylated zinc-finger CxxC protein domain from human KDM2B. NMIs were eluted in buffer containing 700mM-1M NaCl, 0.1% Triton X-100, 20 mM HEPES pH 7.9 and 12.5% v/v glycerol, then DNA was purified using the Wizard SV Gel and PCR Clean-Up System (Promega) according to manufacturer instructions. Library preparation was performed on BioCAP samples using TruSeq ChIP Sample Preparation (Illumina) according to manufacturer instructions. Libraries were amplified using 18 PCR cycles and quantified using KAPA qPCR Library Quantification Kit (KAPA Biosystems) according to manufacturer instructions. Libraries were sequenced on the Illumina NovaSeq 6000 (150 bp, paired-end), generating 34M-307M read pairs per sample.
BioCAP-seq

value: PBMC

value: Adult


title: PBMC, BioCAP, replicate 1


title: Brain, BioCAP, replicate 2

source_name: Brain

value: Brain


title: Muscle, BioCAP, replicate 2

source_name: Muscle

value: Muscle


title: Day 1, BioCAP, input

source_name: Day 1

value: Day 1

value: Embryonic day 1


title: Day 1, BioCAP, replicate 1


title: Day 2, BioCAP, replicate 1

source_name: Day 2

value: Day 2

value: Embryonic day 2


title: Brain, BioCAP, replicate 1


title: Brain, BioCAP, input


title: Muscle, BioCAP, replicate 1


title: Day 1, BioCAP, replicate 2


title: Sperm, BioCAP, replicate 2

source_name: Sperm

value: Sperm


title: Sperm, BioCAP, input


title: Day 2, BioCAP, replicate 2


title: Day 2, BioCAP, input


title: 14D_M_2928

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

tag: age


title: 14D_M_2926


title: 14D_M_2923


title: 14D_M_2924


title: 14D_M_2925


title: 14D_M_2922


title: Sperm, BioCAP, replicate 1

tag: tissue


title: 14D_M_2927


title: 14D_M_2929


title: 14D_M_2921


title: Muscle, BioCAP, input


title: 14D_M_2920


title: 14D_M_2917


title: 14D_M_2919


title: 14D_M_2916


title: 14D_M_2915


title: 14D_M_2911


title: 14D_M_2910


title: 14D_M_2907


title: 14D_M_2904


title: 14D_M_2906


title: 14D_M_2905


title: 14D_M_2908


title: 14D_M_2913


title: 14D_M_2901


title: 14D_M_2902


title: 14D_M_2903


title: 14D_M_2898


title: 14D_M_2897


title: 14D_M_2895


title: 14D_M_2900


title: 14D_M_2892


title: 14D_M_2896


title: 14D_M_2891


title: 14D_M_2899


title: 14D_M_2893


title: 14D_M_2914


title: 14D_M_2890


title: 14D_M_2886


title: 14D_M_2887


title: 14D_M_2889


title: 14D_M_2909


title: 14D_M_2888


title: 14D_M_2912


title: 14D_M_2885


title: 14D_M_2884


title: 14D_M_2877


title: 14D_M_2876


title: 14D_M_2875


title: 14D_M_2880


title: 14D_M_2881


title: 14D_M_2883


title: 14D_M_2894


title: 14D_M_2871


title: 14D_M_2873


title: 14D_M_2869


title: 14D_M_2868


title: 14D_M_2878


title: 14D_M_2867


title: 14D_M_2879


title: 14D_M_2872


title: 14D_M_2866


title: 14D_M_2882


title: 14D_M_2799


title: 14D_M_2874


title: 14D_M_2801


title: 14D_M_2800


title: 14D_M_2797


title: 14D_M_2794


title: 14D_M_2790


title: 14D_M_2793


title: 14D_M_2791


title: 14D_M_2798


title: 14D_M_2870


title: 14D_M_2773


title: 14D_M_2788


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title: 14D_M_2778


title: 14D_M_2777


title: 14D_M_2781


title: 14D_M_2780


title: 14D_M_2789


title: 14D_M_2787


title: 14D_M_2775


title: 14D_M_2779


title: 14D_M_2776


title: 14D_M_2782


title: 14D_M_2784


title: 14D_M_2786


title: 14D_M_2774


title: 14D_M_2772


title: 14D_M_2767


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title: 14D_M_2769


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title: 14D_M_2761


title: 14D_M_2762


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title: 14D_M_2764


title: 14D_M_2756


title: 14D_M_2757


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title: 14D_M_2748


title: 14D_M_2609


title: 14D_M_2746


title: 14D_M_2742


title: 14D_M_2753


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title: 14D_M_2608


title: 14D_M_2755


title: 14D_M_2738


title: 14D_M_2745


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title: 14D_M_2739


title: 14D_M_2747


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title: 14D_M_2605


title: 14D_M_2603


title: 14D_M_2602


title: 14D_M_2604


title: 14D_M_2607


title: 14D_M_2600


title: 14D_M_2599


title: 14D_M_2759


title: 14D_M_2743


title: 14D_M_2598


title: 14D_M_2597


title: 14D_M_2595


title: 14D_M_2594


title: 14D_M_2591


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title: 14D_M_2561


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title: 14D_M_2559


title: 14D_M_2552


title: 14D_M_2546


title: 14D_M_2551


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title: 14D_M_2548


title: 14D_M_2481


title: 14D_M_2478


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title: 14D_M_2445


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title: 14D_M_2352


title: 14D_M_2429


title: 14D_M_2424


title: 14D_M_2340


title: 14D_M_2347


title: 14D_M_2337


title: 14D_M_2335


title: 14D_M_2345


title: 14D_M_2344


title: 14D_M_2343


title: 14D_M_2334


title: 14D_M_2336


title: 14D_M_2339


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title: 14D_M_2323


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title: 14D_M_2325


title: 14D_M_2327


title: 14D_M_2326


title: 14D_M_2321


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title: 14D_M_2320


title: 14D_M_2333


title: 14D_M_2332


title: 14D_M_2341


title: 14D_M_2315


title: 14D_M_2319


title: 14D_M_2318


title: 14D_M_2317


title: 14D_M_2316


title: 14D_M_2324


title: 14D_M_2309


title: 14D_M_2311


title: 14D_M_2307


title: 14D_M_2305


title: 14D_M_2314


title: 14D_M_2294


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title: 14D_M_2212


title: 14D_M_2199


title: 14D_M_2198


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title: 14D_M_2209


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title: 14D_M_2172


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title: 14D_M_2174


title: 14D_M_2180


title: 14D_M_2173


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title: 14D_M_2168


title: 14D_M_2167


title: 14D_M_2166


title: 14D_M_2165


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title: 14D_M_2163


title: 14D_M_1969


title: 14D_M_2162


title: 14D_M_1968


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title: 14D_M_1965


title: 14D_M_1966


title: 14D_M_1963


title: 14D_M_1961


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title: 14D_M_1964


title: 14D_M_1960


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title: 14D_M_1959


title: 14D_M_2169


title: 14D_M_1958


title: 14D_M_1957


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title: 14D_M_1947


title: 14D_M_1948


title: 14D_M_1955


title: 14D_M_1952


title: 14D_M_1956


title: 14D_M_1943


title: 14D_M_1940


title: 14D_M_1937


title: 14D_M_1944


title: 14D_M_1938


title: 14D_M_1939


title: 14D_M_1942


title: 14D_M_1936


title: 14D_M_1941


title: 14D_M_1929


title: 14D_M_1933


title: 14D_M_1935


title: 14D_M_1930


title: 14D_M_1934


title: 14D_M_1931


title: 14D_M_1927


title: 14D_M_1928


title: 14D_M_1950


title: 14D_M_1925


title: 14D_M_1926


title: 14D_M_1945


title: 14D_M_1946


title: 14D_M_1924


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title: 14D_M_1914


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title: 14D_M_1835


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title: 14D_M_1460


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title: 14D_M_1527


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title: 14D_M_1458


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