title: primBM2

city: Guangzhou

first: Xiaobing

last: Jiang

state: Guangdong Province

address: Sun Yat-Sen University

institute: Sun Yat-sen University Cancer Center

data_processing:
The CellRanger version 5.0.0 (10X Genomics) function ‘‘cellranger count’’ was used to process the raw data, demultiplex cellular barcodes, and map reads to the human reference genome GRCh38-2020 (10X Genomics). Then, the ‘‘cellranger aggr’’ function was used to generate normalized aggregate data across samples. The ‘‘cellranger aggr’’ function aggregates outputs from multiple runs of cellranger count, normalizing those runs to the same sequencing depth and then recomputing the feature-barcode matrices and analysis of the combined data. The aggr pipeline can be used to combine data from multiple samples into an experiment-wide feature-barcode matrix and analysis. These processes produced a raw unique molecular identifier count matrix that was converted into a Seurat object using the R package Seurat (version 4.1, https://github.com/satijalab/seurat). Cells whose gene number was less than 300, UMI count was less than 1000, or mitochondrial gene ratio was more than 20% were regarded as abnormal and filtered out. Finally, 26,949 cells remained. doubletFinder_v3 was utilized for the screening and removal of doublets in single-cell data. After quality control filtering, Seurat packages were used to perform log normalization on the UMI count matrix.
Assembly: GRCh38-2020 (10X Genomics)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

extract_protocol:
The tissue was washed with PBS and cut as small as possible. Then, 3 mL of 1640 culture medium was added to a 15 mL centrifuge tube, and 1350 μL of collagenase Ⅰ, 375 μL of collagenase Ⅳ and 180 μL of hyaluronidase were added in sequence and placed into a 37 °C water bath for 30 min with gentle inversion every 5 min. The resulting suspension was filtered through a 70 µm cell strainer to remove larger chunks of undigested tissue. Red blood cell lysis buffer (SAB, R1010) was added to the cells and incubated at 25 °C for 10 min to remove red blood cells. The obtained cell suspension is quality inspected using a cell counter, and samples that pass the quality requirements are labeled for use in experiments. Quality inspection requires cell viability to be greater than 85%, clustering rate to be less than 15%, and nuclear rate to be greater than 70%.
Using a single-cell 3' Library and Gel Bead Kit V3.1 (10x Genomics, 1000121) and Chromium Single Cell G Chip Kit (10x Genomics, 1000120) according to Manufacturer's protocol.


title: KOHypoxia4

status: Public on Sep 23 2024

type: SRA

city: La Jolla

first: Miguel

middle: Alejandro

last: Lopez-Ramirez

state: Ca

address: 9500 Gilman Dr

department: Medicine

country: USA

institute: University of California, San Diego

library_source: transcriptomic

data_processing:
Data was processed using the systempipeR workflow.
RNA reads were aligned to the GRCm39 genome assembly using hisat2.
Differential gene expression was calculated using EdgeR.
Assembly: GRCm39 release 104

molecule: total RNA

organism: Mus musculus

source_name: Brain

extract_protocol:
Brain tissue was harvested from animals and homogenized in TRIzol solution for RNAseq analysis according to the manufacturer’s instructions.
Following isolation, RNA quality was assessed using an Agilent Tapestation 4200. Only samples with with an RNA Integrity Number (RIN) greater than 8.0 were used to generate RNA sequencing libraries using the Illumina Stranded mRNA Prep according to the manufacturer’s insturctions.

treatment_protocol: Hypoxic conditions consisted of 12% O2,  for seven days and normoxic conditions consisted of 21% O2.

tag: tissue

value: Brain

tag: cell line

value: Male

tag: genotype

tag: treatment

value: Hypoxia


title: FloxNormoxia2

value: Pdcd10fl/fl; Aldh1l1-EGFP/Rpl10a

value: Normoxia


title: HCC_TMA_20210610_07_77035_ROI5_Vessel

city: Boston

first: Joseph

last: Franses

state: Massachusetts

department: Cancer Center

institute: Massachusetts General Hospital

description: (v1.0) Cancer Transcriptome Atlas

data_processing:
Raw sequencing data were processed using the GeoMx NGS Pipeline to generate fastq files followed by dcc files
Sequences were aligned to the Cancer Transcriptome Atlas probe set using default settings
Assembly: hg38
Supplementary files format and content: rawCounts.tsv: gene count matrix file in tsv format
Supplementary files format and content: qnormCounts.tsv: Q3 normalized gene count matrix file in tsv format
Library strategy: GeoMx Spatial Transcriptomics

organism: Homo sapiens

source_name: Liver cancer resection

extract_protocol:
We followed published experimental methods (NanoString) with modifications as noted below. Briefly, slides were baked at 60 °C for one hour, deparaffinized with CitriSolv (DECON), rehydrated, antigen-retrieved in 1x Tris-EDTA/pH 9 in a steamer for 15 min at 100 °C, proteinase K (Thermo Fisher Scientific, AM2548) digested at 0.1 ng/ml for 15 min at 37 °C, and postfixed in neutral-buffered formalin for 10 min, hybridized to UV-photocleavable barcode-conjugated RNA in situ hybridization probe set (CTA with 1,779 gene targets and 32 reference genes) overnight at 37 °C, washed to remove off-target probes and then counterstained with morphology markers for 2 h at room temperature. The morphology markers consisted of: 1:50 CD31 (Abcam, ab47063) and 1:50 Arginase-1 (Cell Signaling Technology, 93668S) in blocking buffer W (NanoString). The anti-CD31 antibody was conjugated using the Alexa Fluor 555 Lightning-Link kit (Abcam, ab269820) and the anti-Arginase-1 antibody with the Alexa Fluor 647 Lightning-Link kit (Abcam, ab269823). These two morphology markers allowed distinction between vessel areas of interest (AOIs) and tumor regions of interest (AOIs) within a microscopic region of interest (ROI). 22 Immunofluorescence images, ROI selection, segmentation into marker-specific AOIs and 23 spatially indexed barcode cleavage and collection were performed on a GeoMx DSP instrument 24 (NanoString). Typical exposure times were 400 ms for CD31 and 300 ms for Arg 1. Approximately 25 4 AOIs on average were collected per specimen (details in Table 1)
Library preparation was performed according to the manufacturer’s instructions and involved PCR amplification to add Illumina adapter sequences and unique dual sample indices. A minimum sequencing depth of 2 150–200 reads per square micron of illumination area was achieved by sequencing all CTA AOIs on a NovaSeq S2 (100 cycles, read 1: 27 nt, read 2: 27 nt, index 1: 8 nt, index 2: 8 nt).

value: Liver cancer resection

tag: slide name

tag: pool

tag: roi

tag: aoi type

value: Vessel

tag: area


title: Mouse9, 16s v3v4, After Stress

city: Shanghai

first: Xiaofei

last: Yu

address: 2005 Songhu Rd

country: China

institute: Fudan University

description:
F-A-9
16s_asv_table.tsv

library_source: genomic

data_processing:
Raw fastq files were imported into QIIME2 and trimmed by cutadapt
QIIME2 DADA2 were used to denoise and generate representative sequences. Pre-built QIIME2 classifier was used to classify the representitave sequences.
Shannon diversity and PCoA using unweighted Unifrac distance were calculated by QIIME2 and visualized using R package phyloseq (v1.36.0) and ggplot2 (v3.3.5).
Assembly: SILVA v138(NR99) for 16s v3v4 and UNITE v9 for ITS1-2
Supplementary files format and content: OTU count tables (tsv format)

molecule: genomic DNA

organism: feces metagenome

source_name: Fecal pellets

extract_protocol:
Fecal microbial DNA were extracted using the QIAamp PowerFecal Pro DNA Kit (Cat. 51804).
DNA sequencing library were constructed by KAPA High Throughput Library Preparation Kit (KK8234) per the manufacturer's guide.
DNA amplicon sequencing

treatment_protocol: Fecal pellets were collected from mice before and after 30-min restraint stress.

tag: animal id

tag: strain

value: After Stress

tag: region


title: primBM1

library_source: transcriptomic single cell


title: HCC_TMA_20210610_07_77035_ROI5_Tumor

description: (v1.0) Cancer Transcriptome Atlas

value: Tumor


title: Mouse8, 16s v3v4, After Stress

description:
F-A-8
16s_asv_table.tsv


title: FloxNormoxia1


title: SW1990R_RRBS

first: Boshi

last: Wang

address: No.800 Dongchuan Road

institute: Shanghai Cancer Institute

data_processing:
To process the RRBS data, initial quality control was performed using FastQC (v0.11.9).
Trim_galore (0.6.5-1) was applied for trimming the FASTQ files.
The trimmed files were aligned to the hg38 genome using bismark -bowtie2 (2.2.5).
The mCpG sites were identified using bismark_methylation_extractor.
For IGV visualization, bedGraphToBigWig (v4) was utilized to generate bigwig files.
Assembly: hg38
Supplementary files format and content: bigwig

source_name: pancreas

extract_protocol:
Genomic DNA was isolated from cells using the QIAamp DNA Mini and Blood Mini Kit (Qiagen, 51304).
The DNA samples were then assessed for quality and quantity through agarose gel electrophoresis, Nanodrop, and Qubit. After passing quality checks, Firstly, DNA samples were subjected to digestion by the methylation-insensitive restriction enzyme MspI. The resulting DNA fragments were subjected to end repair, A-tailing, and ligation of sequencing adaptors. Gel electrophoresis was then performed to select DNA fragments ranging from 40-220bp in length. Subsequent Bisulfite treatment was carried out using the EZ DNA Methylation Gold Kit from Zymo Research. Finally, PCR amplification was performed to obtain the final DNA library. After library construction, initial quantification was conducted using Qubit 2.0. The library was then diluted to a concentration of 1ng/μl. The insert fragment length of the library was examined using the 5400 Fragment Analyzer System.

value: pancreas

value: Gemcitabine-resistant


title: HCC_TMA_20210610_07_77035_ROI4_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: Mouse14, 16s v3v4, Before Stress

description:
F-B-14
16s_asv_table.tsv

value: Before Stress


title: SW1990_RRBS

value: Parental


title: KONormoxia4


title: HCC_TMA_20210610_07_77035_ROI4_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: SW1990R_RNAseq_rep2

data_processing:
Raw RNA-seq data were subjected to quality control using FastQC (v0.11.9) and trimmed using Trim_galore (0.6.5-1).
SortMeRNA (4.2.0) was used to remove rRNA reads to generate clean data.
The clean reads were aligned to the human reference genome (hg38) using the HISAT2 (version 2.2.1) aligner to generate BAM files.
The aligned reads (BAM files) were transformed into bigwig files using Deeptools software (v3.5.1)
Assembly: hg38
Supplementary files format and content: bigwig

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Life Technologies, CA, USA) according to the manufacturer's protocol, and RNA integrity was assessed using an Agilent Bioanalyzer 2100 (Agilent Technologies, CA, USA) to obtain RIN values. RNA with RIN values > 7 was purified using an RNAClean XP Kit (Beckman Coulter, Inc. CA, USA) and RNase-Free DNase Set (QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using a VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme, Nanjing, China), and sequencing was performed on an Illumina HiSeq 2500 system.


title: KONormoxia3


title: KONormoxia2


title: SW1990R_RNAseq_rep1


title: HCC_TMA_20210610_07_77035_ROI3_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: neoBM


title: HCC_TMA_20210610_07_69847_ROI2_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: SW1990_RNAseq_rep2


title: Mouse12, 16s v3v4, Before Stress

description:
F-B-12
16s_asv_table.tsv


title: KONormoxia1


title: HCC_TMA_20210610_07_77035_ROI3_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: Mouse11, 16s v3v4, Before Stress

description:
F-B-11
16s_asv_table.tsv


title: Mouse10, 16s v3v4, Before Stress

description:
F-B-10
16s_asv_table.tsv


title: c587ts;UAS-Stat92E,testis

city: Beijing

first: Ruiyan

last: Kong

address: 105 Xi San Huan Bei Lu, Haidian District, Beijing

institute: Capital Normal University

data_processing:
The reads had a quality score > 30, using Trimmomatic v0.38.0, discarding reads left with < 20 bp
Reads were aligned using Bowtie (version 1.1.2) to build version BDGP6 of the D. melanogaster genome.
MACS (version 1.4.1) was used to identify regions of ChIP-seq enrichment.
The density of reads in each region was normalized to reads per million(rpm).
BigWig files were generated for visualization using the R/Bioconductor package.
Assembly: BDGP6
Supplementary files format and content: bigWig

organism: Drosophila melanogaster

source_name: testis

extract_protocol:
The required adult testes were dissected and cross-linked with 1% formaldehyde for 15 minutes. After quenching and cell lysis, chromatin was sonicated using the Covaris system.
Most chromatin fragments occurred between 200-400bp. The process of dilution, antibody incubation, protein G pull down, beads washing, DNA complex elution, de-link,RNAse A/proteinase K digestion and DNA extraction are all performed according to standard protocols.

value: testis

tag: cell type

value: cyst cell

tag: chip antibody

value: Stat92E (a gift from Dr Yu Cai)

value: 1 day at 29℃


title: Mouse9, 16s v3v4, Before Stress

description:
F-B-9
16s_asv_table.tsv


title: HCC_TMA_20210610_07_69847_ROI2_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: Mouse13, 16s v3v4, Before Stress

description:
F-B-13
16s_asv_table.tsv


title: c587ts,testis

value: 2 days at 29℃


title: HCC_TMA_20210610_07_69847_ROI1_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: Mouse8, 16s v3v4, Before Stress

description:
F-B-8
16s_asv_table.tsv


title: c587ts;UAS-upd,testis


title: SW1990_RNAseq_rep1


title: HCC_TMA_20210610_07_69847_ROI1_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: 7_SW1990R_H3K27me3

data_processing:
The sequencing reads obtained from the Illumina platform were subjected to quality control using FastQC (v0.11.9) to assess the quality of the reads.
Adapter trimming and read filtering were performed using Trim-galore (0.6.5-1) with the following parameters: --phred33 --length 35 --stringency 3.
The filtered reads were then aligned to the human genome (UCSC hg38) using Bowtie2 version 2.2.6 with parameters: --local --very-sensitive --no-mixed --no-discordant --phred33.
The aligned reads were processed by MACS2 (v2.2.7.1) to call peaks and transformed to bigwig formatted files by bamCoverage function in Deeptools (v3.5.1) or .bedGraphToBigWig (v4) program.
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

extract_protocol:
The CUT&Tag experiments were performed using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme Biotech Co., Ltd., TD903) according to the manufacturer’s instructions.
The library was constructed by TruePrep® Index Kit V2 for Illumina kit and PCR amplification

tag: antibody

value: H3K27me3 ab6002 Abcam


title: 7_SW1990_H3K27me3


title: 6_SW1990_H3K9me3

value: H3K9me3 ab4729 Abcam


title: 24h_TLC-065_rep4 [C2.4]

city: Lausanne

first: Xiaoxu

last: Li

address: Station 15 - CH

country: Switzerland

institute: EPFL

data_processing:
After sequencing on the BGIseq-500 platform, the raw reads were filtered. Data filtering includes removing adaptor sequences, contamination and low-quality (phred quality < 20) reads from raw reads.
For the mouse hepatocyte samples, sequenced reads were mapped to the GRCm38 (mm10) primary assembly of the mouse genome using ensembl release 102 gene annotation with STAR aligner version 2.7.3a
For the human liver organoid samples, sequenced reads were mapped to the GRCh38 assembly of the human genome using ensembl release 109 gene annotation with STAR aligner version 2.7.3a
Read counts were generated using STAR aligner
Assembly: Mus_musculus.GRCm38.102, Homo_sapiens.GRCh38.109
Supplementary files format and content: xlsx file with counts per gene per sample

source_name: Liver

extract_protocol:
RNA was extracted in Trizol and purified using NucleoSpin RNA purification kit (MACHEREY-NAGEL). mRNA concentration was measured for all samples. All samples passed a quality check of purity (NanoDrop) and fragmentation (FragmentAnalyzer).
BGISEQ-500 library construction was performed by BGI

value: Liver

value: Primary hepatocytes


title: 5_SW1990R_H3K4me3

value: H3K4me3 ab8580 Abcam


title: 24h_TLC-065_rep3 [C2.3]


title: 24h_TLC-065_rep2 [C2.2]


title: 6_SW1990R_H3K9me3


title: Differentiated cells at d14, control, replicate 2

city: Segrate

first: Ingrid

last: Cifola

state: Milan

address: Via F.lli Cervi, 93

department: Institute for Biomedical Technologies (ITB)

country: Italy

institute: National Research Councill (CNR)

data_processing:
After fastq quality control by using FastQC tool, raw reads were trimmed to 100 bases and mapped to the human reference genome (HG38) using STAR aligner (v.2.7.10a).
Gene counts were calculated by HTSeq (v.1.99.2), using the HG38 Encode-Gencode GTF file (v43) as gene annotation file.
Differential gene expression analysis was performed by DESeq2 Bioconductor package (v.1.30.1), in R environment (v.4.0.5).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw gene counts for each sample

molecule: polyA RNA

growth_protocol: hiPSC were grown on MytC-treated mouse embryonic fibroblasts (MEF) in hiPSC medium supplemented with FGF and expanded by enzymatic dissociation with collagenase IV. hiPSC-NSC were grown on poly-L-ornithine/laminin coating in N2 medium supplemented with EGF and FGF and expanded by enzimatic dissociation with PBS-EDTA. For differentiation of hiPSC-NSC, cells were plated on Matrigel-coated dishes at a density of 20.000 cells/cm2 on Neuronal Differentiation Medium for 7 and 14 days. For the medium composition and culture refer to Meneghini, V. et al. Generation of Human Induced Pluripotent Stem Cell-Derived Bona Fide Neural Stem Cells for Ex Vivo Gene Therapy of Metachromatic Leukodystrophy. Stem Cells Transl Med 6, 352-368, doi:10.5966/sctm.2015-0414 (2017).

extract_protocol:
Total RNA samples were extracted using miRNeasy Mini Kit (Qiagen) and checked for integrity on TapeStation instrument (Agilent Technologies).
Poly-A+ RNA-seq libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina), according to manufacturer’s instructions, and sequenced on HiSeq2500 platform (Illumina) in 150-cycle paired-end run.

treatment_protocol: To generate SREBF1-deficient cells hiPSC were nucleofected with ribonucleoprotein Cas9 with a pool of sgRNA targeting exon 5 of the SREBF1 gene. After recovery, cells underwent clonal selection and expansion as reported in growth protocol. Control cells have been nucleofected with ribonucleoprotein Cas9 only and maintained as SREBF1-deficient cells.

value: Differentiated cells at d14

value: control


title: HCC_TMA_20210610_NA_ROINA_NA

description: (v1.0) Cancer Transcriptome Atlas

source_name: Control

value: Control

value: No Template Control


title: Differentiated cells at d14, control, replicate 3


title: 24h_TLC-065_rep1 [C2.1]


title: 24h_DMSO_rep4 [C1.4]


title: 5_SW1990_H3K4me3

value: pancreas


title: MAPseq barcodes

city: New York

first: Benjamin

last: Fait

state: NY

address: 1230 York Ave

institute: The Rockefeller University

library_source: other

data_processing:
*library strategy: MAP-seq
Raw sequences were first separated according to unique sample identifiers, corresponding to individual mice and dissected brain regions. Data was processed with custom MATLAB (RRID:SCR_001622) scripts. For each brain area with a given barcode and UMI combination, reads were tabulated according to empirically determined thresholds: two for the injection site and five for the target sites. Any barcodes with a hamming distance of no more than three (of thirty bp barcode length) were collapsed. After collapsing reads, data was further filtered to barcodes >50 counts in the injection area and > 5 counts in at least one projection area. Finally, counts were normalized according to the number of spike-in molecules in a given dissected region.
The theoretical estimation of the number of re-used barcodes within a 20 million barcode library is ~0.1%. The template switching rate induced during sample preparation was estimated to be 0.2%. For analysis, in contrast to previous MAPseq papers, barcode counts were normalized according to the relative number of counts in the injection site. This was because the standard method, in which the barcodes are normalized among several projection sites, was unsuitable due to the data of interest being distributed across only two. One of four samples was excluded from the analysis due to several-fold higher rates of ipsilateral projections, also apparent from the qPCR controls, which was thought to be likely due to contamination during dissection.
Assembly: NA
Supplementary files format and content: Matrix of barcode counts

molecule: other

source_name: Cortex, olfactory bulb, spinal cord

extract_protocol:
Libraries were prepared as described previously and in the MAPseq protocol (DOI: 10.17504/protocols.io.bsm9nc96):156 Tissue was homogenized in 400 μL TRIzol (Thermo Fisher Scientific, 15596026), and then brought to 1 mL total TRIzol. RNA was extracted according to the manufacturer’s protocol and dissolved into 13 μL RNAse-free water.
To begin reverse transcription, 4 μL of dissolved mRNA mixed in 6 μL nuclease-free water, 1 μL spike-in RNA (salt purification, IDT, GTCATGATCATAATACGACTCACTATAGGGGACGAGCTG TACAAGTAAACGCGTAATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNNNNNNNNNNNNNNNNNNNNNATCAGTCATCGGAGCGGCCGCTACCTAATTGCCGTCGTGAGGTACGACCACCGCTAGCTGTACA, where ATCAGTCA is the barcode tag of the spike-in and N indicates A, C, G, or T. Spike-in RNA was transcribed in vitro by T7 RNA polymerase and diluted into 103 molecules/ul for target sites and 105 molecules/μL for injection sites) (Integrated DNA Technologies), 1 μL of 10 μM RT primer (salt purification, IDT, CTTGGCACCCGAGAATTCCANNNNNNNNNNNNXXXXXXXXTGTACAGCTAGCGGTGGTCG, where N indicates A, C, G, or T and is the UMI and X is the sample identifier barcode) (Integrated DNA Technologies), and 1 μL of 10 uM dNTPs. The mixture of RNAs was denatured at 70° C for 10 minutes and cooled on ice for 5 minutes. To complete the reverse transcription, 1 μL SuperScript IV (Thermo Fisher Scientific, 18090010), 4 μL SuperScript IV buffer, 1 μL 0.1 M DTT, and 1 μL RNAsin Plus (Promega, N2611) were added into the mixture, and incubated for 10 minutes at 55°C and 10 minutes at 80°C. Samples were pooled and cleaned with 1.8X AMPure XP beads per the manufacturer’s instructions (Beckman Coulter, A63881).
For second strand synthesis, 17 μL cDNA was added to 2.4 μL SuperScript IV buffer, 0.6 μL 0.1M DTT, 5.6 μL second strand kit buffer (Thermo Fisher Scientific, A48571), 0.75 μL 10mM dNTPs, 0.25 μL e. coli DNA ligase, 1 μL DNA polymerase I, and 0.25 μL RNAseH. These were mixed well and incubated for two hours at 16°C, and then 1 μL T4 DNA Polymerase was added and the sample was incubated for 10 minutes again at 16°C. Second-strand products were cleaned with 1.8X AMPure XP beads (Beckman Coulter, A63881). Following second strand synthesis, 1 μL Exonuclease I (New England Biolabs, M0293S) was added per 16 μL bead-purified product, along with 2 μL of Exonuclease I buffer. The reaction was incubated for 1 hour at 37 °C and inactivated at 80 °C for 20 minutes. All injection sites were pooled together, as were all target sites for the following steps.
The reaction was then PCR amplified by adding 25 μL Accuprime Buffer (Thermo Fisher Scientific, 12346086), 25 μL 10 μM Nested1st gfpF primer (HPLC purified, IDT, CTGTACAAGTAAACGCGTAATG), 25 μL 10 μM Nested2nd R primer (salt purification, IDT, CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA), 2.5 μL Accuprime Pfx HF enzyme, and 152.5 μL water. The reaction was incubated at 95ºC for 2 minutes, followed by 15 cycles of 95ºC for 15 seconds and 68ºC for 2.5 minutes. The final extension was at 68ºC for 5 minutes. The samples were again exonuclease digested by adding 5 μL Exonuclease I, incubated at 37 °C for 30 minutes, and inactivated at 80 °C for 20 minutes. The products were diluted 10x for the following PCR steps.
For the final PCR, 2.5 μL of diluted product from the first PCR reaction was added to 2.5 μL Accuprime buffer, 2.5 μL 10 μM Sol I primer (salt purification, IDT, AATGATACGGCGACCACCGA), 2.5 μL 10 μM Sol II primer (salt purification, IDT, CAAGCAGAAGACGGCATACGA), 0.25 μL Accuprime Pfx HF enzyme (Thermo Fisher Scientific, 12346086), and 14.75 μL water. The final PCR cycles were determined by testing each sample in multiples of two cycles and running the resultant product on a gel. The minimal number of cycles to produce a visible and clean band at 230 bp was used. The reaction was incubated at 95ºC for 2 minutes, followed by the empirically determined number of cycles of 95ºC for 15 seconds and 68ºC for 2.5 minutes. The final extension was at 68ºC for 5 minutes.
The product was then cleaned with the Wizard SV Gel and PCR Clean-Up System (Promega, A9282) and eluted into 40 μL per 1 mL of initial pooled PCR product volume. Then, the purified product was loaded onto a 2% agarose gel, and the 230 bp band was cut and purified with a MinElute Gel Extraction Kit (Qiagen, 28604). The 230 bp product was analyzed on a DNA Bioanalyzer Chip (Agilent, 5067-1504) on a Bioanalyzer (Agilent) to confirm the size and concentration for sequencing and then sequenced on a NextSeq 500 (Illumina) on a high-output paired-end 36 bp run (Illumina, 20024906) with the SBS3T sequencing primer (ACACTCTTTCCCTACACGACGCTCTTCCGATCT, Illumina) for paired-end 1 and the Illumina small RNA sequencing primer 2 (CTTGGCACCCGAGAATTCCA, Illumina) for the second paired-end, resulting in 388 million reads passing Illumina standard quality control.

value: Cortex, olfactory bulb, spinal cord


title: 4_SW1990R_H3K4me2

value: Gemcitabine-resistant

value: H3K4me2 ab32356 Abcam


title: Differentiated cells at d14, SREBF1-KO, clone 15


title: Replicate 7 Contra Input

data_processing:
Binary base-call files were converted to Fastq with bcl2fast2 (version 2.20, RRID:SCR_015058). Sequences were aligned and converted to feature count matrices using a pipeline from Rockefeller University’s Bioinformatics Resource Center (https://github.com/RockefellerUniversity/RU_RNAseq.git).
Sequence and transcript coordinates for mouse mm10 UCSC genome and gene models were retrieved from the BSgenome.Mmusculus.UCSC.mm10 Bioconductor package (version 1.4.0; DOI: 10.18129/B9.bioc.BSgenome.Mmusculus.UCSC.mm10) and TxDb.Mmusculus.UCSC.mm10.knownGene (version 3.4.0; DOI: 10.18129/B9.bioc.TxDb.Mmusculus.UCSC.mm10.knownGene) Bioconductor libraries respectively. Reads were aligned to the genome with Rsubread's subjunc method161 (version 1.30.6; RRID:SCR_016945) and exported as bigWigs normalized to reads per million with the rtracklayer package (version 1.40.6; RRID:SCR_021325; 10.18129/B9.bioc.rtracklayer). Reads in genes were counted with the featurecounts function within the Rsubread package against the full gene bodies (Genebody.Counts) and gene exons (Gene.Counts). This resulted in a median of 87.1% mapped reads ranging from 80.3 to 91.4% per sample.
Assembly: mm10
Supplementary files format and content: Sample TPMS in a CSV file

source_name: Motor Cortex

extract_protocol:
Until reverse transcription steps, all work was completed with precautions against exogenous RNAses: equipment was cleaned with RNaseZap™ RNase Decontamination Solution (Invitrogen, AM9780) and rinsed with UltraPure™ water (Invitrogen, 10977015), all reagents were RNAse-free, and work completed on ice.
Seven replicates of three pooled mice were processed bilaterally for each region of interest. Both unprecipitated input RNA and polysome immunoprecipitated (IP) samples were prepared for a total of 28 libraries. Two libraries were excluded due to non-Layer 5b and non-neuronal marker expression, presumably due to failed pulldowns. Ultimately, two replicates from male mice and three from female mice were used for the analysis. All 15 spinal cords were cleared with CUBIC tissue clearing and imaged coarsely; however, because the tissue was not perfused with PBS, the autofluorescence from the remaining blood made the injection site less clear than in perfused tissue. An unused mouse was cleared, and the cortex and spinal cord were imaged thoroughly to ensure that the injection protocol produced unilateral expression and the previously observed cortical distribution.
Each mouse was rapidly decapitated, and the cortices ipsilateral and contralateral to the viral injection site were rapidly dissected in an ice-cold buffer consisting of 1X HBSS, 2.5 mM HEPES-KOH (pH = 7.4), 35 mM glucose (Sigma Aldrich, G7528-250G), 4 mM NaHCO3 (Sigma Aldrich, S6297-250G), and fresh 100 μg/ml cycloheximide (Sigma Aldrich, C7698-5G) in UltraPure™ water (Invitrogen, 10977015). Each tissue section was rewashed in the dissection buffer to remove excess blood. The triplicate hemicortices were then transferred to tissue homogenizers (DWK Life Sciences, K885510-0020) with 1 mL each of ice-cold homogenization buffer consisting of 10 mM HEPES-KOH (pH 7.4) (Thermo Fisher Scientific, AM9640G), 150 mM KCl (Thermo Fisher Scientific, AM9640G), 5 mM MgCl2 (Thermo Fisher Scientific, AM9530G), fresh 0.5 mM DTT (Sigma Aldrich, D9779-5G), 1 tablet per 10 mL  cOmplete™ EDTA-free Protease Inhibitor Cocktail (Roche, 11836170001), 400 Units/mL RNasin® Recombinant RNase Inhibitor (Promega, N2511), 200 Units/mL SUPERase•In™ RNase inhibitor (Invitrogen, AM2694), and 100 μg/ml cycloheximide (Sigma, C7698-5G) in UltraPure™ water (Invitrogen, 10977015). Tissues were homogenized with Teflon tissue homogenizing pestles (DWK Life Sciences, K886000-0019, 0.1–0.15mm clearance) using a lab stirrer (Yamato Scientific Co, 231349) for three strokes at 300 RPM. Then, the rotational speed was increased to 900 RPM for 12 additional strokes.
The homogenate was transferred into pre-chilled 1.5 mL centrifuge tubes, spun at 2000 x g for 10 minutes at 4°C, and then transferred to a fresh 1.5 mL centrifuge tube. The homogenate volume was measured at this point, and 1/9th of this volume of 10% NP-40/IGEPAL was added (Sigma, I8896-50ML). Based on the resultant volume of this addition, 1/9th a volume of 300 mM DHPC (Avanti Polar Lipids, 850306P) was added. The samples were gently mixed by inversion five times and incubated on ice for 5 minutes. Then, the samples were spun at 20,000 x g for 15 minutes at 4°C.
Ribosomal Pulldown:
TRAP was performed as previously,87 albeit with a low-yield protocol consisting of half the standard amount of antibodies and beads in anticipation of the potential for differing pulldown efficiencies between neurons of differing abundance. The rationale was that by pooling mice and restricting bead-antibody conjugates, the beads might saturate equally between the differing amounts of available GFP and yield equivalent pulldowns.
The magnetic beads were prepared during the previous day and in tandem with sample preparation. 150 μl for every sample of Streptavidin MyOne T1 Dynabeads (Invitrogen, 65601) were resuspended and washed 1X PBS. Each 500 μg vial of Pierce™ Biotinylated Protein L (Thermo Fisher Scientific, 29997) was resuspended on ice in 500 μl PBS. Each aliquot of beads was resuspended in 880 μl PBS and 120 μl Biotinylated Protein L and allowed to incubate at RT for 35 minutes with gentle end-to-end rotation. The beads were then washed five times with 1 mL 1X PBS containing 3% w/v nuclease-free BSA (Jackson Immunores. 001-000-162) and resuspended in 500 μl wash buffer containing 10 mM HEPES-KOH (pH = 7.4) (Fisher Scientific, AAJ16924AE), 150 mM KCl (Thermo Fisher, AM9640G), 5 mM MgCl2 (Thermo Fisher Scientific, AM9530G), 1% (v/v) IGEPAL® (Sigma Aldrich, I8896-50ML), 0.5 mM DTT (Sigma Aldrich, D9779-5G), 40 Units/mL RNasin® Recombinant RNase Inhibitor (Promega, N2511), 20 Units/mL SUPERase•In™ RNase inhibitor (Invitrogen, AM2694), and 100 μg/ml cycloheximide (Sigma Aldrich, C7698-5G) in UltraPure™ water (Invitrogen, 10977015). To this was added 50 μg total of mouse α-EGFP clones 19C8 and 19F7 mAb (25 μg each) (Memorial Sloan-Kettering Antibody and Bioresource Core Facility). The beads were then incubated with slow tilt rotation for >1 hr at RT. During the high-speed spin of the samples, the beads were washed thrice with 1 mL of the aforementioned 0.15 M KCl wash buffer and resuspended in 180 μl. 20 μl 300 mM DHPC (Avanti Polar Lipids, 850306P) was added to the resuspension.
After the high-speed spin, 30 μl of supernatant was removed as “input” samples mixed with 350 μl buffer containing 340 μl RLT and 10 μl βME from the RNeasy Plus Micro kit (Qiagen, 74034) and flash frozen for parallel purification with other samples. The remaining supernatant was placed in a chilled 1.5 mL tube, mixed with 200 μl bead and antibody solution, and incubated on gentle rotation at 4°C overnight.
The following morning, beads were magnetically collected on ice. 30 μl of supernatant was reserved as “unbound” RNA but ultimately not sequenced. The remaining supernatant was removed and washed four times with 1 mL of wash buffer containing 10 mM HEPES-KOH (pH = 7.4) (Fisher Scientific, AAJ16924AE), 350 mM KCl (Thermo Fisher Scientific, AM9640G), 5 mM MgCl2 (Thermo Fisher Scienific, AM9530G), 1% (v/v) IGEPAL® (Sigma Aldrich, I8896-50ML), 0.5 mM DTT (Sigma Aldrich, D9779-5G), 40 Units/mL RNasin® Recombinant RNase Inhibitor (Promega, N2511), and 100 μg/ml cycloheximide in UltraPure™ water (Invitrogen, 10977015). All samples, bound and unbound, were then suspended in 350 μl RLT-βME buffer as described above and incubated at room temperature on gentle end-over-end rotation for 10 minutes. The beads were magnetically separated, and the supernatant was removed and placed in fresh 1.5 mL tubes. RNA was purified with the RNeasy Plus Micro kit per the manufacturer’s instructions but eluted into UltraPure™ water (Invitrogen, 10977015) rather than the provided elution buffer (Qiagen, 74034). RNA was quantified, and RNA integrity was confirmed with a Nanodrop spectrophotometer as well as a TapeStation High-Sensitivity RNA ScreenTape (Agilent, 5067-5579).
Libraries were prepared using the Revelo™ RNA-Seq High Sensitivity library preparation kit (Tecan, 30201358) and associated SPIABoost™ Mouse reagents (Tecan, 30201371) and sequencing adapters (Tecan, S02317-FG) per manufacturer’s instructions. Library fragment distribution was analyzed with a TapeStation D1000 DNA ScreenTape (Agilent, 5067-5582). Libraries were sequenced on a NextSeq 500 (Illumina) on a high-output paired-end 75 base pair run (Illumina, 20024907). A median of 35,208,430 paired-end reads passed the filter, ranging from 5,524,727 to 77,421,692 reads per sample.

value: Motor Cortex

value: Corticospinal Neurons

tag: sample type

value: Contra Input


title: 24h_DMSO_rep3 [C1.3]


title: Replicate 7 Contra IP

value: Contra IP


title: Differentiated cells at d14, SREBF1-KO, clone 8


title: 4_SW1990_H3K4me2

value: Parental


title: Replicate 7 Ipsi IP

value: Ipsi IP


title: Differentiated cells at d7, control, replicate 3

value: Differentiated cells at d7


title: 24h_DMSO_rep2 [C1.2]

value: Liver

value: Primary hepatocytes


title: 3_SW1990R_H3K4me1

value: H3K4me1 ab176877 Abcam


title: Replicate 5 Contra Input


title: 24h_DMSO_rep1 [C1.1]


title: Differentiated cells at d14, SREBF1-KO, clone 34

value: Differentiated cells at d14


title: Differentiated cells at d7, control, replicate 2

value: control


title: Replicate 7 Ipsi Input

value: Ipsi Input


title: Replicate 5 Ipsi Input


title: 3_SW1990_H3K4me1

value: pancreas


title: Replicate 5 Contra IP


title: Differentiated cells at d7, control, replicate 1


title: 12h_TLC-065_rep3 [B2.3]


title: 12h_TLC-065_rep4 [B2.4]


title: Replicate 5 Ipsi IP


title: 2_SW1990_H3K27ac

value: H3K27ac ab4729 Abcam


title: 2_SW1990R_H3K27ac

value: Gemcitabine-resistant


title: 12h_TLC-065_rep2 [B2.2]


title: Differentiated cells at d7, SREBF1-KO, clone 34


title: Replicate 4 Contra Input


title: Differentiated cells at d14, control, replicate 1


title: 12h_TLC-065_rep1 [B2.1]


title: Differentiated cells at d7, SREBF1-KO, clone 15


title: Replicate 4 Ipsi Input


title: Differentiated cells at d7, SREBF1-KO, clone 8


title: 1_SW1990_IgG

value: IgG Abclonal AC005


title: 12h_DMSO_rep4 [B1.4]


title: Neural stem cells (NSCs) derived from human iPSCs, control, replicate 3


title: 12h_DMSO_rep3 [B1.3]


title: Replicate 4 Contra IP

value: Motor Cortex


title: Neural stem cells (NSCs) derived from human iPSCs, control, replicate 2


title: Replicate 4 Ipsi IP

value: Corticospinal Neurons


title: Replicate 2 Contra Input

value: Contra Input


title: AsPC1R_RNAseq_rep1_1


title: Neural stem cells (NSCs) derived from human iPSCs, control, replicate 1


title: 12h_DMSO_rep2 [B1.2]


title: 12h_DMSO_rep1 [B1.1]


title: Neural stem cells (NSCs) derived from human iPSCs, SREBF1-KO, clone 34


title: AsPC1_RNAseq_rep3_1


title: 1_SW1990R_IgG


title: Neural stem cells (NSCs) derived from human iPSCs, SREBF1-KO, clone 15


title: Replicate 2 Ipsi Input


title: 6h_TLC-065_rep4 [A2.4]


title: Neural stem cells (NSCs) derived from human iPSCs, SREBF1-KO, clone 8


title: Replicate 2 Contra IP

value: Contra IP


title: 6h_TLC-065_rep3 [A2.3]


title: AsPC1_RNAseq_rep2_1

value: Parental


title: AsPC1_RNAseq_rep1_1


title: Human induced pluripotent stem cells (iPSCs), control, replicate 3


title: AsPC1R_RNAseq_rep3_1


title: 6h_TLC-065_rep1 [A2.1]


title: 6h_TLC-065_rep2 [A2.2]


title: Human induced pluripotent stem cells (iPSCs), control, replicate 2


title: AsPC1R_RNAseq_rep2_1


title: Replicate 2 Ipsi IP

value: Ipsi IP


title: 6_AsPC1R_H3K27me3_R1

value: H3K27me3 ab6002 Abcam


title: Replicate 1 Ipsi Input


title: 6h_DMSO_rep4 [A1.4]

value: Liver


title: 6_AsPC1_H3K27me3_R1


title: Human induced pluripotent stem cells (iPSCs), control, replicate 1


title: 5_AsPC1R_H3K9me3_R1

value: H3K9me3 ab4729 Abcam


title: Replicate 1 Contra IP


title: Human induced pluripotent stem cells (iPSCs), SREBF1-KO, clone 34


title: 6h_DMSO_rep3 [A1.3]

value: Primary hepatocytes


title: 6h_DMSO_rep2 [A1.2]


title: 5_AsPC1_H3K9me3_R1


title: Replicate 1 Contra Input


title: Human induced pluripotent stem cells (iPSCs), SREBF1-KO, clone 15


title: 4_AsPC1R_H3K4me3_R1

value: H3K4me3 ab8580 Abcam


title: Replicate 1 Ipsi IP


title: Cultured cortical neurons Phf6 knock-out replicate 4

city: Parkville

first: Alexandra

last: Garnham

state: Victoria

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Base calling and quality scoring was performed by Illumina Real-Time Analysis (v2) software. FASTQ file generation and de-multiplexing was performed by bcl2fastq conversion software (v2.15.0.4).
Reads were aligned to the human genome by Rsubread version 1.21.12
Read counts were summarized by Entrez Gene ID using the Rsubread's featureCounts function and Rsubread's built-in NCBI annotation.
Assembly: mm10
Supplementary files format and content: tab-delimited text files (tsv). Columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene.

source_name: E16.5 cortex

growth_protocol: Dissected E16.5 cerebral cortices were incubated on ice in pancreatin trypsin (25 mg/ml pancreatin, Sigma, and 5 mg/ml trypsin; Gibco, in PBS) for 30 min, followed by a 5 min incubation at 37°C after removal of the pancreatin trypsin. Alternatively, cortices were incubated with trypsin-EDTA (Sigma-Aldrich, 59430C) and for 10 to 15 min in a 37°C water bath. After rinsing, cortices were dissociated in 2% FCS using a P1000 pipette, then filtered through a 40 µm sieve in a 0.2% BSA/PBS solution. Cells were centrifuged twice for 5 min at 140 × g, rinsing with 0.2% BSA/PBS in between, and resuspended in medium (DMEM, 5 mM HEPES, 13.4 mM NAHC03 , 0.6% D-glucose, 25 µg/mL insulin, 100 µg/mL apotransferrin, 9.6 µg/mL putrescine HCL (9.6 µg/mL, 2 mg/mL BSA, 1% FCS, 5.18 nM selenium and 6.3 ng/mL progesterone, 100 µg/mL streptomycin and 100 U/mL penicillin) and filtered again through a 40 µM sieve onto plates pre-coated with poly-L-lysine (Sigma). Alternatively, 50,000 cells/cm2 were plated on 8-well chamber slides (Ibidi, 80826) or 10,000 cells/cm2 on 13 mm coverslips, both pre-coated with 15 μg/ml poly-L-ornithine (Sigma-Aldrich, P4957) for 2 h at 37°C and 5% CO2, followed by 4.5 μg/ml laminin (Sigma-Aldrich, L2020) O/N at 37°C and 5% CO2, with a PBS wash in between coating solutions.

extract_protocol:
RNA was isolated using an RNeasy-mini kit (Qiagen).
cDNA libraries were constructed using the TruSeq Stranded RNA Library Prep Kit (Illumina), sequencing length of 80 bp.

treatment_protocol: Samples were not treated. Instead samples were isolated from mice of the following Phf6 mutant and control genotypes: (a) cortex was dissected and used without further treatment from Phf6+/Y and Phf6–/Y E15.5 mouse foetuses. (b) Cortical neurons isolated using the protocol above from Phf6+/Y;Nes-creTg/+ and Phf6lox/Y;Nes-creTg/+ E16.5 mouse foetuses.

value: E16.5 cortex

value: Cultured primary cortical neurons

value: Phf6 lox/Y NesCre T/+

tag: phf6 status

value: Deleted

tag: embryo stage

tag: litter


title: Human induced pluripotent stem cells (iPSCs), SREBF1-KO, clone 8

tag: cell line


title: 6h_DMSO_rep1 [A1.1]

tag: tissue

tag: treatment


title: 3_AsPC1R_H3K4me1_R1

value: pancreas

value: Gemcitabine-resistant

value: H3K4me1 ab176877 Abcam


title: 4_AsPC1_H3K4me3_R1


title: Neural stem cells (NSCs) differentiated from hiPSCs, HD2.2

data_processing:
After fastq quality control by using FastQC tool, raw reads were mapped to the human reference genome (hg19) using STAR aligner (v2.5.0a).
Gene counts were calculated by HTSeq (v.0.6.1), using the hg19 Encode-Gencode GTF file (v19) as gene annotation file.
Differential gene expression analysis was performed by DESeq2 Bioconductor package (v1.8.1), in R environment (v3.2.2).
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for all samples

growth_protocol: The hfNSC line was originally isolated from the fetal brain diencephalon; cells were expanded in mitogen-supplemented serum-free medium and used between passages 18 and 25 for RNA-seq and ChIP-seq analyses. The hiPSC clones were obtained by reprogramming of healthy skin fibroblasts from the Cell Line and DNA Bank of Patients affected by Genetic Diseases (Institute Gaslini, Genova, Italy) for HD1 (adult) or acquired from Invitrogen (C0045C/ Invitrogen) for HD2 (newborn).

extract_protocol:
Total RNA samples were extracted using miRNeasy Mini Kit (Qiagen) and checked for integrity by microcapillary electrophoresis on 2200 TapeStation instrument (Agilent Technologies).
Poly-A+ RNA-seq libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina), according to manufacturer’s instructions, and sequenced on HiSeq2500 platform (Illumina) in a 125-cycle paired-end run.

treatment_protocol: hiPSC-NSCs were differentiated from hiPSCs. Briefly, hiPSCs were detached with dispase and cultured as embryoid bodies (EBs) in EB medium. On day 4, EBs were plated on Matrigel dishes and grown in EB medium supplemented with NOGGIN (250 ng/ml, R&D Systems). At day 10, medium was replaced with EB medium supplemented with Sonic Hedgehog (SHH; 20 ng/ml, R&D Systems) and fibroblast growth factor 8 (FGF8; 100 ng/ml, R&D Systems). Upon appearance of rosette like structures (day 14), medium was changed to BASF medium (brain-derived neurotrophic factor [BDNF], ascorbic acid, SHH, and FGF8). On day 22, FGF8 was withdrawn, and cells were maintained in BAS medium (BDNF, ascorbic acid, and SHH). At day 29, cells were detached with Accutase solution and plated on poly-l-ornithine (20 μg/ml, Sigma-Aldrich)/laminin (10 μg/ml, Thermo Fisher Scientific Life Sciences)-coated dishes in hiPSC-NSC proliferation medium.

value: NSCs differentiated from newborn hiPSCs


title: HCT116, Valine deprivation, END-seq

first: Yu

last: Yuanyuan

address: No. 1239, Siping Road, Shanghai

institute: Tongji University

data_processing:
END-seq and ddC-S1-END-seq data were checked with FASTQC (v0.11.8) and trimmed using TrimGalore (v0.6.4)
END-seq and ddC-S1-END-seq reads were aligned to hg38 using Bowtie2 (v2.3.5.1) in single-end mode, and were further filtered with mapping quality of at least 20
bigWig files were generated by bamToBed and genomecov in bedtools(v2.28.0) and normalized as RPM
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: END-seq

extract_protocol:
4×106 HCT116 cells were plated in a 6 cm plate prior to the experiment. Cells were valine deprivation for 24 hrs and treated ddC (20 µM) for 20 hrs prior to harvest washed three times with cold PBS buffer Cells were collected and gently pipetted 5-10 times and transferred to a conical 15ml tube. Cells were neutralized with 10ml of cold PBS/EDTA 5mM/10% FBS buffer, then pelleted, resuspended in 1ml of neutralization buffer and transferred to an Eppendorf tube. They were then processed for END-seq or S1-END-seq. For S1-END-seq, cells were collected and embedded in 1% agarose plugs, lysed and digested with Proteinase K (1 hour at 50°C, followed by 7 hours at 37°C), washed with TE buffer, and then treated with RNAse A for 1 hour at 37°C. Plugs were then washed in EB and equilibrated in S1 nuclease buffer (40 mM sodium acetate pH 5.2, 300 mM NaCl, 2 mM ZnSO4) for 30 minutes. 1.8 U of S1 nuclease was added to 100 µL of S1 nuclease buffer per plug and incubated on ice for 15 minutes to allow for the enzyme to diffuse into the plug. The reaction mix was then placed at 37°C for 20 minutes before addition of EDTA (10 mM final concentration) to terminate the reaction
Finally, plugs were processed through the standard END-seq protocol

value: Valine deprivation


title: Neural stem cells (NSCs) differentiated from hiPSCs, HD2.3


title: Cultured cortical neurons Phf6 knock-out replicate 2

tag: genotype


title: HCT116, Valine deprivation, ddC-S1-END-seq

data_processing:
END-seq and ddC-S1-END-seq data were checked with FASTQC (v0.11.8) and trimmed using TrimGalore (v0.6.4)
END-seq and ddC-S1-END-seq reads were aligned to hg38 using Bowtie2 (v2.3.5.1) in single-end mode, and were further filtered with mapping quality of at least 20
bigWig files were generated by bamToBed and genomecov in bedtools(v2.28.0) and normalized as RPM
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: ddC-S1-END-seq


title: Cultured cortical neurons Phf6 knock-out replicate 3


title: Cultured cortical neurons Phf6 knock-out replicate 1


title: 3_AsPC1_H3K4me1_R1


title: HCT116, END-seq

value: Control


title: Cultured cortical neurons wild type replicate 3

value: Phf6 +/Y NesCre T/+

value: Intact


title: Neural stem cells (NSCs) differentiated from hiPSCs, HD1.1

value: NSCs differentiated from adult hiPSCs


title: 2_AsPC1_H3K27ac_R1

value: Parental

value: H3K27ac ab4729 Abcam


title: 2_AsPC1R_H3K27ac_R1


title: 1_AsPC1_IgG_R1

value: IgG Abclonal AC005


title: Cultured cortical neurons wild type replicate 2


title: Human induced pluripotent stem cells (hiPSCs) from newborn fibroblasts, HD2.3

value: hiPSCs obtained by reprogramming of healthy newborn fibroblasts acquired from Invitrogen (C0045C/Invitrogen)


title: EPCs，PCL-SE，Day3

city: 南充市

first: Cai-Ping

last: Yan

state: sichuan

address: No. 1 The South of Maoyuan Road

department: orthopedics

institute: North sichuan medical college

data_processing:
NanoDrop 2000 spectrophotometer: Detects RNA purity and concentration；Agient2100/LabChip GX detection: Accurate detection of RNA integrity.
The Qubit 3.0 fluorometric quantifier was used for preliminary quantification, and the concentration should reach more than 1ng/ul. Then, the Qsep400 high-throughput analysis system was used to detect the inserted fragments of the library. After the inserted fragments met the expectations, the effective concentration of the library (the effective concentration of the library was > 2nM) was accurately quantified by Q-PCR method
After the library was qualified, PE150 mode sequencing was performed using Illumina NovaSeq6000 sequencing platform.
After the sequencing data was unloaded, the bioinformatics analysis process provided by BMKCloud(www.biocloud.net) was used for data analysis.
FPKM=cDNAFragments/MappedFragments(Millions)∗TranscriptLength(kb).In the formula, cDNA Fragments represent the number of fragments that are compared to a transcript, that is, the number of double-ended Reads. Mapped Fragments (Millions) indicates the total number of fragments aligned to the transcript, in 10^6; Transcript Length(kb) : Length of the transcript, in units of 10^3 bases.
Assembly: mm10
Supplementary files format and content: tab-delimited file includes raw counts for each Sample
Supplementary files format and content: tab-delimited file includes FPKM values for each Sample

source_name: EPCs cell line

growth_protocol: 5% CO2 medium was added at 37 °C, incubated for complete DMEM medium containing 10% FBS was used as the medium of extraction

extract_protocol:
The cells were lysed with 1ml TRIzol to extract the RNA samples (n=3), and the specimens were subsequently analyzed
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacture's protocols

treatment_protocol: The complete DMEM medium containing 10% FBS was used as the medium of extraction, and the PCL scaffolds were added to it at an area/volume ratio of 1.25 cm2/ml and immersed for 72 h at 37 °C to prepare the solution for material extraction.

value: EPCs cell line

value: EPCs

value: WT

value: Angiogenic differentiation


title: Human induced pluripotent stem cells (hiPSCs) from newborn fibroblasts, HD2.2


title: Cultured cortical neurons wild type replicate 1

value: E16.5 cortex

value: Cultured primary cortical neurons


title: HCT116, Valine deprivation,ddC-S1-END-seq

data_processing:
ddC-S1-END-seq data were checked with FASTQC (v0.11.8) and trimmed using TrimGalore (v0.6.4)
ddC-S1-END-seq reads were aligned to hg38 using Bowtie2 (v2.3.5.1) in single-end mode, and were further filtered with mapping quality of at least 20
bigWig files were generated by bamToBed and genomecov in bedtools(v2.28.0) and normalized as RPM
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: ddC-S1-END-seq

value: shNC, Valine deprivation


title: HCT116, TDG-KD, ddC-S1-END-seq

value: TDG-KD

value: shTDG


title: Neural stem cells (NSCs) differentiated from hiPSCs, HD1.3


title: EPCs，PCL-E，Day3


title: Cortex Phf6 knock-out replicate 4

source_name: E15.5 cortex

value: E15.5 cortex

value: Phf6 -/Y

value: Deleted


title: Human induced pluripotent stem cells (hiPSCs) from adult fibroblasts, HD1.1

value: hiPSCs obtained by reprogramming of healthy skin adult fibroblasts from the Cell Line and DNA Bank of Patients affected by Genetic Diseases (Institute Gaslini, Genova, Italy)


title: TT_sHLO_TLC065_rep3 [TT_S_6]

source_name: Human liver organoids

value: Human liver organoids

value: GCKR rs1260326 TT


title: HCT116, TDG-KD, Valine deprivation, ddC-S1-END-seq

value: shTDG, Valine deprivation


title: Cortex Phf6 knock-out replicate 5


title: HCT116, ddC-S1-END-seq

value: shNC


title: EPCs，PCL-S，Day3

value: EPCs cell line


title: TT_sHLO_TLC065_rep1 [TT_S_4]


title: EPCs，PCL-O，Day3

value: EPCs


title: Human fetal neural stem cell (hfNSC) cell line, replicate 2

value: hfNSC line originally isolated from the fetal brain diencephalon


title: TT_sHLO_TLC065_rep2 [TT_S_5]


title: iPSC_D0_3

city: Brussels

first: Stefaan

last: Verhulst

address: Laarbeeklaan 103, D022

department: BMWE

country: Belgium

institute: Vrije Universiteit Brussel

data_processing:
Quality control was performed by FastQC followed by trimming using afterQC.
mapping of the reads to the reference genome (Homo Sapiens_GRCm38.p6)was performed using STAR
Assembly of genes and transcripts was performed using Python package StringTie.
Assembly: GRCm38.P6
Supplementary files format and content: raw counts as CSV (comma delimited)

source_name: 2D iPSC

growth_protocol: iPSC were maintained in Essential 8 Flex medium. IPSC were differentiated towards iHepatoblast, iHSC, iEndo and iMC/iMΦ using specific differen

extract_protocol:
RNA was extracted using ReliaPrep RNA Cell Miniprep System (Promega). RNA quality was assessed using a Bioanalyzer 6000 and samples with sufficient quality and a concentration of at least 10ng/µl were used.
Library preparation was done with the QuantSeq 3' mRNA-Seq Library Prep Kit of Lexogen (015.96)

value: iPSC derived

value: 2D cells

value: 2D iPSC


title: Cortex Phf6 knock-out replicate 2


title: Human fetal neural stem cell (hfNSC) cell line, replicate 1


title: iHep_D8_3

source_name: 2D iHepatoblast D8

value: 2D differentiated iPSC

value: 2D iHepatoblast D8


title: Cortex Phf6 knock-out replicate 1


title: Cortex Phf6 knock-out replicate 3


title: Human fetal neural stem cell (hfNSC) cell line, replicate 3


title: TT_sHLO_DMSO_rep3 [TT_S_3]

value: DMSO


title: Cortex wild type replicate 3

value: E15.5 cortex

value: Phf6 +/Y

value: Intact


title: TT_sHLO_DMSO_rep2 [TT_S_2]


title: Neural stem cells (NSCs) differentiated from hiPSCs, input

data_processing:
Raw reads were mapped against the human reference genome (build hg19) using Bowtie, allowing up to 2 mismatches (-v 2 option) and discarding multiple alignments (-m 1 option).
Each BAM file was then processed by using SAMtools and converted into a bed file using BEDTools. Quality of each sequenced sample was checked using cross-correlation analysis implemented in spp R package.
ChIP-seq peak calling was performed with MACS2 tool (with –broad and --qvalue 0.05 options), using each INPUT data to model the background noise.
bigwig files were generated using genomicRanges R package.
Assembly: hg19
Supplementary files format and content: bigwig files include coverage along genomic coordinates for each sample.

source_name: hiPSC-NSC

extract_protocol:
hiPSC, hiPSC-NSC and hfNSC were cross-linked for 10 min at RT with 1% methanol-free formaldehyde-containing medium and blocked with 0.125 M glycine. Cross-linked cells were washed with PBS containing protease and phosphatase inhibitors and stored at -80 until use. Nuclei were collected upon cell lysis using Cell lysis buffer and by nuclei release with B tight dounce. Nuclear extracts were sonicated on Diagenode 1.5 ml tubes with BioruptorPico in sonication buffer for 12 (for hiPSCs) or 15 (for hiPSC-NSCs and hfNSCs) cycles of 30 sec ON /30 sec OFF to obtain DNA fragments averaging 200 bp in length and then checked by microcapillary electrophoresis on 2200 TapeStation instrument (Agilent Technologies). Chromatin preclearing was performed using IgG isotype (1 ug IgG/106 cells)-Protein G Agarose coated beads (Thermo Scientific) mixed to chromatin. The equivalent of 3-6 x107 cells were precipitated overnight with 1 ug IgG/106 cells of rabbit antibody against H3K27ac (ab4729, Abcam). Before antibody precipitation, total chromatin was collected as INPUT. H3K27Ac chromatin was precipitated with precleared (RIPA Buffer + protease inhibitors; BSA at 0.5 ug/ul and S256 containing salmon sperm at 2.7 ug/ul overnight at 4°C)-Protein G Agarose coated beads for 2 hours on rotating wheel at 4°C. Beads were then washed with RIPA buffer, LiCl buffer and TE buffer. Chromatin was then eluted with Elution Buffer, reverse cross-linking was performed with 0.3M NaCl and Rnase A (10 mg/ml) for 4-5 hrs at 67°C. Chromatin was precipitated overnight on 100% ethanol with glycogen (5 mg/ml) at -20 °C. After protein digestion (PK Buffer and Proteinase K (20 mg/ml) 2 hrs at 45°C), DNA was purified with Qiaquick PCR purification kit (Qiagen, Germany).
ChIP-seq libraries were prepared from 10 ng of immunoprecipitated DNA (ChIP) and control DNA (INPUT: nuclear extracts sonicated but non-immunoprecipitated) using the ChIP-seq DNA sample preparation kit (Illumina). Libraries were checked by microcapillary electrophoresis on Bioanalyzer 2100 (Agilent Technologies), using with the High Sensitivity DNA Assay kit, and quantified with Quant-iT™ PicoGreen dsDNA Kit (Invitrogen) on Nanodrop Fluorometer. Each library was sequenced in one lane of a single-end 50-cycle Illumina run.

value: hiPSC-NSC

value: NSCs differentiated from adult hiPSCs

value: Input - nuclear extracts sonicated but non-immunoprecipitated


title: Human induced pluripotent stem cells (hiPSCs) from adult fibroblasts, HD1.3

value: hiPSCs obtained by reprogramming of healthy skin adult fibroblasts from the Cell Line and DNA Bank of Patients affected by Genetic Diseases (Institute Gaslini, Genova, Italy)


title: TT_sHLO_DMSO_rep1 [TT_S_1]

value: Human liver organoids

value: GCKR rs1260326 TT


title: iHep_D8_2


title: Cortex wild type replicate 2


title: Neural stem cells (NSCs) differentiated from hiPSCs, HD2.3, ChIP for H3K27ac

value: NSCs differentiated from newborn hiPSCs

value: Chromatin immunoprecipitation with rabbit antibody against H3K27ac (ab4729, Abcam)


title: iHep_D8_1

value: iPSC derived


title: Cortex wild type replicate 1


title: Neural stem cells (NSCs) differentiated from hiPSCs, HD2.2, ChIP for H3K27ac


title: TT_HLO_TLC065_rep3 [TT_H_6]


title: TT_HLO_TLC065_rep2 [TT_H_5]


title: iPSC_D0_2

value: 2D cells


title: pHep_0h_4

source_name: freshly isolated pHep

value: Liver

value: primary cell

value: freshly isolated primary human hepatocyte


title: iPSC_D0_1

value: 2D iPSC


title: Human induced pluripotent stem cells (hiPSCs), input

source_name: hiPSC

value: hiPSC

value: Input:nuclear extracts sonicated but non-immunoprecipitated


title: Neural stem cells (NSCs) differentiated from hiPSCs, HD1.1, ChIP for H3K27ac


title: Control SLEC RNA-seq Replicate 3

first: Martin

middle: Wallace

last: LaFleur

state: MA

address: 4 Blackfan Circle Room 140

institute: Harvard Medical School

data_processing:
Paired ends fastq files were mapped to the mm10 genome using STAR
Duplicate reads were removed with PICARD
edgeR was used to called differentially expressed genes
Assembly: mm10
Supplementary files format and content: RPKM values per sample
Supplementary files format and content: NA

source_name: Spleen

growth_protocol: Cells were extracted from C57BL6 mice (naïve or challenged with LCMV Armstrong OVA intraperitoneally).

extract_protocol:
RNA was extracted with a Qiagen Rneasy kit
SMART-seq v4 kit followed by Illumina NexteraXT kit

value: Spleen

tag: sample group

value: Control SLEC

value: CD8+ T cells

value: C57BL6J strain

value: Day 8


title: Control SLEC RNA-seq Replicate 1


title: TT_HLO_TLC065_rep1 [TT_H_4]

value: Human liver organoids


title: Control SLEC RNA-seq Replicate 2


title: Neural stem cells (NSCs) differentiated from hiPSCs, HD1.3, ChIP for H3K27ac

value: NSCs differentiated from adult hiPSCs


title: pHep_0h_2


title: Chd7 KO SLEC RNA-seq Replicate 3

value: Chd7 KO SLEC


title: Human induced pluripotent stem cells (hiPSCs) from newborn fibroblasts, HD2.3, ChIP for H3K27ac

value: hiPSCs obtained by reprogramming of healthy newborn fibroblasts acquired from Invitrogen (C0045C/Invitrogen)

value: Chromatin immunoprecipitation with rabbit antibody against H3K27ac (ab4729, Abcam)


title: TT_HLO_DMSO_rep3 [TT_H_3]

value: GCKR rs1260326 TT

value: DMSO


title: TT_HLO_DMSO_rep1 [TT_H_1]


title: Chd7 KO SLEC RNA-seq Replicate 1


title: Human induced pluripotent stem cells (hiPSCs) from newborn fibroblasts, HD2.2, ChIP for H3K27ac


title: CC_sHLO_TLC065_rep3 [CC_S_6]

value: GCKR rs1260326 CC


title: pHep_0h_1

value: Liver

value: primary cell

value: freshly isolated primary human hepatocyte


title: Human induced pluripotent stem cells (hiPSCs) from adult fibroblasts, HD1.3, ChIP for H3K27ac

value: hiPSCs obtained by reprogramming of healthy skin adult fibroblasts from the Cell Line and DNA Bank of Patients affected by Genetic Diseases (Institute Gaslini, Genova, Italy)


title: iPSC_D21_3

source_name: spheroids with iHepatoblast iHSC iEndo iMacro

value: iPSC derived

value: spheroids

value: differentiation and maturation in 3D


title: Control MPEC RNA-seq Replicate 3

value: Spleen

value: Control MPEC

value: CD8+ T cells

value: C57BL6J strain


title: CC_sHLO_TLC065_rep2 [CC_S_5]

value: Human liver organoids


title: pHep_0h_3


title: TT_HLO_DMSO_rep2 [TT_H_2]


title: iPSC_D21_2


title: CC_sHLO_TLC065_rep1 [CC_S_4]


title: Human induced pluripotent stem cells (hiPSCs) from adult fibroblasts, HD1.1, ChIP for H3K27ac


title: iPSC_D21_1


title: CC_sHLO_DMSO_rep2 [CC_S_2]


title: Control MPEC RNA-seq Replicate 1

value: Day 8


title: Control MPEC RNA-seq Replicate 2


title: Human fetal neural stem cell (hfNSC) cell line, input

source_name: hfNSC

value: hfNSC

value: hfNSC line originally isolated from the fetal brain diencephalon

value: Input:nuclear extracts sonicated but non-immunoprecipitated


title: Chd7 KO MPEC RNA-seq Replicate 3

value: Chd7 KO MPEC


title: Chd7 KO MPEC RNA-seq Replicate 2


title: iPSC_D1_3


title: Human fetal neural stem cell (hfNSC) cell line, ChIP for H3K27ac, replicate 2

value: Chromatin immunoprecipitation with rabbit antibody against H3K27ac (ab4729, Abcam)


title: Human fetal neural stem cell (hfNSC) cell line, ChIP for H3K27ac, replicate 3


title: Human fetal neural stem cell (hfNSC) cell line, ChIP for H3K27ac, replicate 1


title: CC_sHLO_DMSO_rep1 [CC_S_1]

value: GCKR rs1260326 CC

value: DMSO


title: iPSC_D1_1


title: iPSC_D1_2


title: CC_HLO_TLC065_rep3 [CC_H_6]


title: Chd7 KO MPEC RNA-seq Replicate 1


title: K-562 parental wildtype, replicate 1, expressing FLAG-TASOR2 transgene

city: Madison

first: Peter

last: Lewis

state: Wisconsin

address: 440 Henry Mall

department: Department of Biomolecular Chemistry

institute: University of Wisconsin-Madison

description:
WT_FLAGTASOR2_rep1
WT-T2_genes_sig.txt
TEtranscriptsWTvWT-T2_all.txt

data_processing:
RNA-seq reads were aligned to hg38 human genome using STAR-2.7.8 (--winAnchorMultimapNmax 200 --outFilterMultimapNmax 100) to allow for capture of multi-mapped repetitive elements.
Counts were anlayzed for differential expression using salmon and edgeR for host genes and TETranscripts and DEseq2 for repetitive transposable elements
Assembly: hg38
Supplementary files format and content: Differential expressed genes (logCPM > 1, logFC > +/-1, pvalue < 0.05) by salmon and edgeR in txt file
Supplementary files format and content: Differential expressed genes and transposable elements (logCPM > 1, logFC > +/-1, pvalue < 0.05) by TETranscripts and DEseq2 in txt file

growth_protocol: RPMI-1640, 10% fetal bocine serum, 1x Glutamax, 1x penicillin-streptomycin, grown at 37C at 5% CO2

extract_protocol:
RNA was extracted from cells using Zymo Zyppy RNA miniprep kit
total ribo-deplete RNA-seq libraries were prepared using the NEBNext rRNA Depletion kit and NEBNext Ultra RNA Library Prep Kit for Illumina and amplified with NEBNext Multiplex Oligos, Unique Dual Index Primer Pairs with 13 cycles. Post amplification libraries were purified using size selection Agencourt Ampure XP beads

treatment_protocol: K-562 cells were transfected with px458 GFP CRISPR/Cas9 sgRNA plasmids and sorted for GFP expressing cells as single colonies. Resulting clonal populations were verified for targeted knockout using gDNA sequencing and western blot analysis. Cells were transduced with lentivirus containing empty puromycin resistance vectors (negative control) or FLAG tagged transgenes of interest.

value: Human Lymphoblast

value: WT


title: Ctrl Day 0 RNA-seq Replicate 2

value: Ctrl Day 0

value: Day 0


title: CC_sHLO_DMSO_rep3 [CC_S_3]


title: Chd7 KO SLEC RNA-seq Replicate 2

value: Spleen

value: Chd7 KO SLEC


title: CC_HLO_TLC065_rep1 [CC_H_4]


title: Ctrl Day 0 RNA-seq Replicate 1

value: CD8+ T cells


title: PP_RC_003

type: RNA

city: Seongnam

first: WON SUK

last: LEE

address: 59 Yatap-ro

country: South Korea

institute: CHA Bundang Medical Center

description: Gene expression changes of peyer's patch after RC402 treatment

hyb_protocol: According to the manufacturer's protocol.

data_processing: See manufacturer's website (http://www.nanostring.com). The data were normalized against internal reference genes.

label: biotin

source_name: Peyer's patch

growth_protocol: We implanted 2 × 10^5 CT26 cells into the right flank of BALB/c mice.

extract_protocol: Total RNA from the whole tumor tissues using TRIzol.

treatment_protocol: Mice were orally administrated RC402 or the same volume of PBS daily when tumor volume exceeded 50 mm^3.

value: Peyer's patch


title: K-562 TASOR KO, replicate 2, expressing FLAG-TASOR transgene

value: TASOR KO


title: K-562 parental wildtype, replicate 2, expressing FLAG-TASOR2 transgene


title: PP_RC_002

scan_protocol: According to the manufacturer's protocol.


title: Chd7 KO Day 0 RNA-seq Replicate 3

value: Chd7 KO Day 0

value: C57BL6J strain


title: PP_RC_001

label_protocol: According to the manufacturer's protocol.


title: CC_HLO_DMSO_rep3 [CC_H_3]

value: Human liver organoids


title: Chd7 KO Day 0 RNA-seq Replicate 2


title: Chd7 KO Day 0 RNA-seq Replicate 1


title: K-562 TASOR KO, replicate 1, expressing FLAG-TASOR transgene

description:
TASOR_KO_FLAGTASOR_rep1
T1KO-T1_genes_sig.txt
TEtranscriptsWTvT1KO_T1_all.txt


title: K-562 TASOR KO, replicate 1

description:
TASOR_KO_rep1
T1KO_genes_sig.txt
TEtranscriptsWTvT1KO_all.txt


title: Control SLEC Replicate 3

data_processing:
Paired ends fastq files were mapped to the mm10 genome using Bowtie2
Peaks were called used MACS and annotated using HOMER
Assembly: mm10
Supplementary files format and content: RPKM values per sample

extract_protocol:
Incubation with Tagment DNA Buffer/Ezyme, Digitonin, and Tween-20 as in Patterson et al.
PCR amplification with indexed primers

value: Control SLEC

tag: strain background

value: Day 8


title: CC_HLO_DMSO_rep2 [CC_H_2]


title: LN_RC_003

description: Gene expression changes of lymph node after RC402 treatment

source_name: Lymph node

value: Lymph node


title: LN_RC_001


title: Control SLEC Replicate 2


title: CC_HLO_TLC065_rep2 [CC_H_5]

value: GCKR rs1260326 CC


title: CC_HLO_DMSO_rep1 [CC_H_1]

value: DMSO


title: K-562 parental wildtype, negative sgRNA replicate 2

value: Human Lymphoblast


title: rtt105 rad1 rep1

first: Xin

address: 300 Longwood Ave,

institute: Boston children's hospital

description: The library has the forward index: aac and reverse index:gag A total of  14496 colony number was in this library.

data_processing:
For local inversion insertion from MATa, you can find the corresponding code at: https://github.com/gucascau/iMMBIR.git. The codes utilized for characterizing inverted repeats resulting from ssDNA transformation have been made available at: https://github.com/gucascau/iDSBInvert.git. The code for large insertion detection can be accessed at the following GitHub repository: https://github.com/gucascau/iDSBins.git. The features related to large insertion analysis have been uploaded to a dedicated GitHub repository, which can be found here: https://github.com/gucascau/LargeInsertionFeature.git.
Reference: RPA and Rad27 limit templated and inverted insertions at DNA breaks
Assembly: saccharomyces_cerevisiae_R64-2-1_20150113
Supplementary files format and content: BED file that contain the single donor.  Each column represents : "Donor  Chromosome",  "Donor Start","Donor End", " CaseID", "Score", "Donor Strand ", and  "Representative Read"
Supplementary files format and content: BED file for poly insertions.  Each column represents : "Donor  Chromosome",  "Donor Start","Donor End", " CaseID", "Score", "Donor Strand ", and  "Representative Read"

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cells were grown overnight in YPD (1% yeast extract, 2% peptone, 2% dextrose), washed twice with YP-raffinose (1% yeast extract, 2% peptone, 2% raffinose) media, inoculated into 10 mL YP-raffinose media, and incubated at 30 °C overnight.

extract_protocol:
All colonies from YEP-Galactose plates were collected, pooled together and mixed vigorously. ~80 μl cells were spun down and the genomic DNA was extracted using standard glass beads and phenol chloroform. The genomic DNA was treated with RNase A overnight. The genomic DNA was dissolved with water and adjusted to a concentration of 10 ng/μl.
The construction of the amplicon sequencing library was adapted from Illumina’s protocol #15044223 Rev. B. Briefly, the sequencing libraries were constructed with two rounds of PCR using KAPA HiFi HotStart ReadyMix polymerase (Roche, 7958927001). For the first round of PCR, 3.2 μL genomic DNA and 0.5 μL 10 μM primers were used for a total volume of 25 μL. The forward and reverse primers targeting the MATa locus are located 11 bp upstream or 18 bp downstream of the HO cleavage site respectively, containing Illumina adapter sequence and 3 bases unique home index as described (7). The thermocycling conditions were: 95 °C for 5 min; 22 cycles of 98 °C for 20 s, 65 °C for 30 s, 72 °C for 3 min; 72 °C for 10 min. After the first round of PCR, 18μL PCR product was purified with an equal volume of AMPure XP beads (Beckman Coulter, A63880). The DNA was eluted with 52.5 μL of 10 mM Tris (pH 8.5) and used as the templates for the second round of PCR. For the second round of PCR, 5 μl template DNA, 5 μL index primer N7xx and 5 μL index primer S5xx from Nextera XT V2 Index kit (Illumina, FC-131-2001) were used for the total volume of 50 μL. The following conditions were used for the second round of PCR: 95 °C for 5 min; 8 cycles of 95 °C for 30 s, 55 °C for 30 s, 72 °C for 3 min; 72 °C for 10 min. Then, the PCR product was purified with 1.2x volume of AMPure XP beads and eluted with 10 mM Tris pH 8.5. The average size of each sample was measured with TapeStation and the DNA concentration was measured with Qubit dsDNA BR Assay Kit (ThermoFisher, Q32850). Then, the DNA was diluted to a concentration of 4 nM. An equal volume of DNA from ~20 samples was pooled into the library. The 0.2 M NaOH was used to denature the pooled library and PhiX library (Illumina, FC‐110‐3001). After diluting the libraries with pre-chilled HT1 to 12 pM, pooled library and PhiX library were mixed with the ratio 9:1, further denatured by incubating at 96 °C for 2 min and immediately put in an ice-water bath for 5 min.
The denatured combined library was loaded into the MiSeq Reagent Kit v3 (600 cycle) (Illumina, MS-102-3003) for amplicon sequencing.

treatment_protocol: When the cell density was about 2x107/mL, 500 µL cells were spread onto YP-galactose (1% yeast extract, 2% peptone, 2% galactose, 2.5% agar) plates to induce HO expression and the DSB at MATa locus, and incubated at 30 °C for 5 days.

value: S. cerevisiae haploid strain, mutant isogenic to JKM139

value: rtt105::hphMX rad1::klTRP1 DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO

value: Cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus at 30°C


title: K-562 parental wildtype, negative sgRNA replicate 1

value: WT


title: Tumor_RC_003

description: Gene expression changes of tumor after RC402 treatment

source_name: Tumor

value: Tumor


title: Control SLEC Replicate 1

value: Spleen

value: CD8+ T cells


title: rtt105 tel1 rep2

description: The library has the forward index: ttg and reverse index:ctg A total of  33280 colony number was in this library.

value: rtt105::hphMX tel1::TRP1 DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO


title: K-562 TASOR KO + FLAG-TASOR (-PIN), TASOR, ChIP

data_processing:
ChIP-seq reads were aligned to hg38 human genome using Bowtie2-2.3.5.1 (--no-mixed --no-discordant --maxins 500 --end-to-end) to allow for capture of multi-mapped repetitive elements.
Reads were normalized to mm9 genome from spike-in (1000000/number of reads aligned to the exogenous refernce genome(mm9))
Peaks were called using MACS2
Deeptools was used to generate bigwig files for visuallization
Assembly: hg38
Supplementary files format and content: bigwig (genome wide enrichment)

extract_protocol:
Cells were fixed with 1% formaldehyde at 37C for 10 minutes. After quenching and cell lysis, chromatin was treated with MNAse and sonication with Covaris S220, 80ug of human chromatin, with 1:40 mouse chromatin spike-in was used for ChIP.
ChIP-seq libraries were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina and amplified with NEBNext Multiplex Oligos, Unique Dual Index Primer Pairs with 13 cycles. Post amplification libraries were purified using size selection Agencourt Ampure XP beads

value: TASOR KO


title: K-562 TASOR KO, replicate 2


title: Tumor_RC_002


title: Chd7 KO SLEC Replicate 2

value: Chd7 KO SLEC

value: C57BL6J strain


title: K-562 TASOR KO + FLAG-TASOR(-PARP), TASOR, ChIP


title: rtt105 tel1 rep1

description: The library has the forward index: tgg and reverse index:cct A total of  46080 colony number was in this library.


title: LN_RC_002


title: Tumor_RC_001


title: rtt105 rad1 rep2

description: The library has the forward index: cag and reverse index:gtt A total of  14784 colony number was in this library.


title: Escherichia coli SAPYR treated, irradiated sample: replicate R5

city: Tuebingen

first: Stefan

last: Czemmel

address: Auf der Morgenstelle 10

department: University of Tuebingen

country: Germany

institute: Quantitative Biology Center (QBiC)

description:
Sample L+ R5
QPDAM070AC_EC-21-5

data_processing:
The Nextflow-based nf-core pipeline nf-core/rnaseq (version 1.4.2; https://github.com/nf-core/rnaseq) was used for the RNA-Seq bioinformatic analysis.
As part of this workflow, FastQC (version v0.11.8) was used to determine the quality of the FASTQ files (Andrews, 2010). Subsequently, adapter trimming was conducted with Trim Galore (version 0.6.4) (Krueger and Andrews, 2012). STAR aligner (version 2.6.1, (Dobin et al., 2012)) was used to map the reads that passed the quality control against the latest assembly (E. coli-strain K-12, DH10B (Build EB1)), downloaded from NCBI. The RNA-Seq data quality control was performed with RSeQC (version 3.0.1) (Wang et al., 2012) and read counting of the features (e.g. genes) with featureCounts (version 1.6.4) (Liao et al., 2014). An aggregation of the quality control for the RNA-Seq analysis was performed with MultiQC (version 1.7; http://multiqc.info/) (Ewels et al., 2016).
The analysis of the differential gene expression was performed in the R language (version 3.5.1) using DESeq2 (version 1.22) through the nextflow based workflow qbic-pipelines/rnadeseq (https://github.com/qbic-pipelines/rnadeseq, version 1.3.2). Table 1 shows the experimental groups that were compared. Genes were considered differentially expressed (DE) genes when the Benjamini-Hochberg multiple testing adjusted p-value (Benjamini and Hochberg, 1995) was smaller than 0.05 (padj ≤ 0.05).
Genes were further filtered for biological relevance if the log2 Fold Change (FC) in expression between the two considered groups  was above the threshold of 1.0 and less than -1.0.
EcoCyc database was used for pathway analysis (Keseler et al., 2017). All DE genes were included, and enrichment was calculated using Fisher'’s exact test and Benjamini-Hochberg multiple testing (p ≤ 0.05).
Assembly: E. coli-strain K-12, DH10B (Build EB1)), downloaded from NCBI
Supplementary files format and content: Raw counts as standard output from the featureCounts step of the nf-core pipeline nf-core/rnaseq (version 1.4.2; https://github.com/nf-core/rnaseq)  workflow, showing raw read count values for each gene as row in each sample as separate column.

organism: Escherichia coli

source_name: bacterial cell culture

growth_protocol: Gram-negative Escherichia coli (DSM 1103; ATCC 25922) was obtained from the German Collection of Microorganisms and Cell Cultures GmbH (DSMZ; Braunschweig, Germany) and was used as reference strain in this study. E. coli was grown in Tryptic Soy Broth (TSB) and on Mueller-Hinton (MH) agar plates. Planktonic cultures (5 mL) were grown aerobically overnight at 37 °C. Afterwards, suspensions were harvested by centrifugation (ROTINA 420 R, Hettich Lab Technology, Tuttlingen, Germany) and resuspended in TSB yielding an optical density (OD) of 2.0, as measured by means of a spectrophotometer at 600 nm (Ultrospec 3300 pro; Amersham Biosciences, Amersham, United Kingdom).

extract_protocol:
RNA extraction and sequencing were performed by the NGS Competence Center Tübingen (NCCT), the sequencing partner of the Quantitative Biology Center (QBiC), University of Tübingen, Germany. RNA of all samples was isolated with the RNeasy® Mini-Kit (Qiagen, Hilden, Germany). RNA extraction was followed by DNase I treatment in solution using the DNase I recombinant Kit (Roche, Basel, Switzerland) and purification and concentration of RNA using the RNA Clean & Concentrator-5 Kit (Zymo Research, Freiburg, Germany).
Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus Kit (Illumina, San Diego, CA, USA) with 100 ng total RNA. Sequencing was performed on the Illumina NextSeq 500 using a High Output Kit (version 2.5; 75 cycles) with 1% PhiX spike-in (Illumina, San Diego, CA, USA).

treatment_protocol: Samples were either incubated with 200 μL distilled water or 200 μL SAPYR (0.5 μM) in the dark for 5 min and then either illuminated for 10 min or kept in the dark for 10 min.

value: SAPYR

tag: irradiation

value: irradiated

value: L+


title: Escherichia coli SAPYR treated, irradiated sample: replicate R4

description:
Sample L+ R4
QPDAM069A9_EC-21-4


title: K-562 TASOR KO, TASOR, ChIP


title: Chd7 KO SLEC Replicate 1

value: Day 8


title: Control MPEC Replicate 3

value: Control MPEC


title: PP_Control_002

value: Peyer's patch


title: Escherichia coli SAPYR treated, irradiated sample: replicate R3

description:
Sample L+ R3
QPDAM068A1_EC-21-3


title: K-562 +FLAG-TASOR2, MPP8, ChIP

value: Human Lymphoblast


title: Control MPEC Replicate 2


title: LN_Control_003

value: Lymph node


title: Chd7 KO SLEC Replicate 3


title: K-562 +FLAG-TASOR, MPP8, ChIP


title: LN_Control_002


title: Escherichia coli SAPYR treated, irradiated sample: replicate R1

description:
Sample L+ R1
QPDAM066AJ_EC-21-1


title: K-562 TASORs dKO, MPP8, ChIP

value: TASOR and TASOR2 dKO


title: Escherichia coli SAPYR treated, not irradiated sample: replicate R5

description:
Sample L- R5
QPDAM065AB_EC-20-5

value: not irradiated

value: L-


title: PP_Control_003


title: Chd7 KO MPEC Replicate 2

value: Spleen

value: Chd7 KO MPEC


title: K-562 TASOR KO, MPP8, ChIP


title: K-562 TASOR2 KO, MPP8, ChIP

value: TASOR2 KO


title: Tumor_Control_003

value: Tumor


title: Chd7 KO MPEC Replicate 1

value: CD8+ T cells

value: Day 0


title: Tumor_Control_002


title: PP_Control_001


title: K-562 TASOR KO + FLAG-TASOR, TASOR, ChIP

value: TASOR KO


title: Escherichia coli SAPYR treated, not irradiated sample: replicate R3

description:
Sample L- R3
QPDAM063AT_EC-20-3

value: SAPYR


title: LN_Control_001


title: SPN_TIGR4_Dccn_3_BHI

city: Houston

first: Nicholas

last: De Lay

state: Texas

address: 6431 Fannin St

department: Microbiology and Molecular Genetics

institute: University of Texas Health Science Center

description: rRNA depleted

data_processing:
Adapters and low quality bases were trimmed using Cutadapt
Trimmed reads were mapped on the Streptococcus pneumoniae D39 using Bowtie2
Read counting was performed with HTSeq
Differential Gene expression analysis performed with DESeq2
Assembly: Streptococcus pneumoniae D39  (Genbank CP000410.1) genome and Streptococcus pneumoniae TIGR4 (Genbank AE005672.3) genome
Supplementary files format and content: WT_vs_ccn_DESeq2.xlsx: differentially expressed genes

organism: Streptococcus pneumoniae TIGR4

source_name: bacterial cell

growth_protocol: Strains were grown in Difco Brain Heart Infusion Broth alone or supplmented with 0.2 mM zinc sulfate at 37oC in atmosphere of 5% CO2 to an OD620 of 0.2

extract_protocol:
RNA was isolated from cells via the Fastprep blue kit (MPBiomedicals)
Library was generated  with NEBNext Ultra II RNA Library Prep Kit for library preparation after removing DNA by DNase treatment and depleting rRNA with FastSelect Bacteria kit for rRNA depletion.

treatment_protocol: BHI Broth at 37 degrees celsius under atmosphere of 5% carbon dioxide

value: bacterial cell

value: rpsL1 DccnABCDE

value: BHI


title: Escherichia coli SAPYR treated, irradiated sample: replicate R2

description:
Sample L+ R2
QPDAM067AR_EC-21-2

value: irradiated

value: L+


title: K-562 PPHLN1 KO, MPP8, ChIP

value: Human Lymphoblast

value: PPHLN1 KO


title: Escherichia coli SAPYR treated, not irradiated sample: replicate R2

description:
Sample L- R2
QPDAM062AL_EC-20-2

value: not irradiated


title: Ctrl Day 0 Replicate 2

value: Ctrl Day 0

value: C57BL6J strain


title: Control MPEC Replicate 1

value: Spleen

value: Control MPEC

value: Day 8


title: Tumor_Control_001

value: Tumor


title: Escherichia coli SAPYR treated, not irradiated sample: replicate R1

description:
Sample L- R1
QPDAM061AD_EC-20-1

value: L-


title: Ctrl Day 0 Replicate 1

value: CD8+ T cells

value: Day 0


title: Chd7 KO MPEC Replicate 3

value: Chd7 KO MPEC


title: K-562, MPP8, ChIP

value: WT


title: Escherichia coli control, irradiated sample: replicate R5

description:
Sample UC L+ R5
QPDAM060A5_EC-01-5

value: control

value: UC L+


title: Escherichia coli SAPYR treated, not irradiated sample: replicate R4

description:
Sample L- R4
QPDAM064A3_EC-20-4

value: SAPYR


title: SPN_TIGR4_Dccn_1_BHI

description: rRNA depleted

value: bacterial cell

value: rpsL1 DccnABCDE

value: BHI


title: K-562, ChIP input

value: Human Lymphoblast


title: Chd7 KO Day 0 Replicate 3

value: Chd7 KO Day 0

value: C57BL6J strain


title: Escherichia coli control, irradiated sample: replicate R4

description:
Sample UC L+ R4
QPDAM059A2_EC-01-4

value: irradiated


title: SPN_TIGR4_3_BHI

description: rRNA depleted


title: Ctrl Day 0 Replicate 3

value: Spleen

value: Ctrl Day 0


title: K-562 MPP8 KO, MPP8, ChIP

value: MPP8 KO


title: PANC1_3

city: Wenzhou

first: Bangjie

last: He

state: Zhejiang Province

address: Nanbaixiang Street

institute: the first affiliated hospital of wenzhou medical university

description: PANC-1 cells

data_processing:
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100).
And After removed the low quality bases and undetermined bases ,we used HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) to map reads to the genome (for example:Homo sapiens Ensembl v96),(command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam). The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam). Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64).
After the final transcriptome was generated, StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam).
The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by R package edgeR(https://bioconductor.org/packages/release/bioc/html/edgeR.html) or DESeq2(http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html),and then analysis GO enrichment and KEGG enrichment to the differentially expressed mRNAs.
Genome_build: Homo sapiens, Ensembl v96
Supplementary_files_format_and_content: FPKM and count values for each Sample.

source_name: PANC-1 cells

growth_protocol: PANC-1 cells were maintained in Dulbecco’s Modified Eagle Medium (Gibco, Grand Island, NY, USA), supplemented with 10% fetal bovine serum (Gibco, Grand Island, NY, USA), 100 µg/ml streptomycin, and 100 IU/ml penicillin (Invitrogen) at 37 ℃ in a 5% CO2 atmosphere.

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: PANC-1 cells were treated with 50  μM  D(+)-Raffinose pentahydrate


title: Escherichia coli control, irradiated sample: replicate R3

description:
Sample UC L+ R3
QPDAM058AS_EC-01-3


title: SPN_TIGR4_2_BHI

description: rRNA depleted


title: PANC1_2

description: PANC-1 cells


title: Chd7 KO Day 0 Replicate 2

value: CD8+ T cells


title: Chd7 KO Day 0 Replicate 1

value: Day 0


title: SPN_TIGR4_1_BHI

description: rRNA depleted


title: Escherichia coli control, irradiated sample: replicate R2

description:
Sample UC L+ R2
QPDAM057AK_EC-01-2


title: PANC1_1

description: PANC-1 cells


title: Embryonic meninges, E14.5, Foxc1 null, embryo 8

city: Edmonton

first: Serhiy

last: Havrylov

state: Alberta

address: 8-29 Medical Sciences Building

department: Medical Genetics

country: Canada

institute: University of Alberta

description: 43bp x 43bp

data_processing:
Data de-multiplexed using Illumina's bcl2fastq2. Illumina BaseSpace FASTQ generation version 1.0.0.
De-multiplexed read sequences aligned to the Mus musculus (mm10) reference sequence using STAR aligner. Illumina BaseSpace workflow version 1.1.0.
Assembly and differential expression was estimated using Cufflinks (http://cole-trapnell-lab.github.io/cufflinks/) through bioinformatics apps available on Illumina Sequence Hub. Illumina BaseSpace Cufflinks Assembly & DE version 2.1.0.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample. Cuffdiff defferential expression analysis results provided as comma separated values file.

source_name: meninges

growth_protocol: The embryos carrying Foxc1 delta/delta null mutation were generated by deletion of the entire Foxc1 open reading frame by crossing Foxc1 flox/flox mice to EIIa-cre mice as described previously (Sasman et al., 2012, PMID: 22522965).

extract_protocol:
Foxc1 null and wild-type embryos were harvested at E14.5 in cold PBS and dissected in RNALater solution (Thermo). RNA was isolated from meningeal tissue by RNeasy Mini Kit (Qiagen).
Library construction and sequencing was performed at the BRC Sequencing Core (University of British Columbia, Vancouver, BC). Sample quality was checked using the Agilent 2100 Bioanalyzer to ensure high RNA integrity. Samples were then prepped following the standard protocol for the NEBnext Ultra II Stranded mRNA (New England Biolabs).

value: meninges

value: Foxc1 null

tag: age


title: Embryonic meninges, E14.5, Foxc1 null, embryo 9

description: 43bp x 43bp


title: MH-S cells LPS+RCMNs treated replicate3

city: Chongqing

first: Haiyu

address: No. 61 Puguobao Road, Bicheng Street, Bishan District

institute: Chongqing University of Chinese medicine

data_processing:
The sequencing data was filtered with SOAPnuke by Removing reads containing sequencing adapter
Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%
Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format
Assembly: mm10
Supplementary files format and content: fpkm, TPM for each sample

source_name: MH-S Cells

extract_protocol:
Total RNA was extracted from tissues using TRlzol (lnvitrogen, Carlsbad, California, USA) according to manual instruction.The TRlzol was directly added to  the cell sample  with the amount 1 ml per 1 x 106 cells, followed by vortex mixing and standing for  5-minute.
Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China). A certain amount of RNA are denatured at suitable temperature to open the secondary structure, and mRNA is enriched by oligo (dT) attached magnetic beads.

value: MH-S Cells

value: treated LPS+RCMNs


title: Escherichia coli control, irradiated sample: replicate R1

description:
Sample UC L+ R1
QPDAM056AC_EC-01-1

value: control

value: UC L+


title: DR_PANC1_2

description: PANC-1 cells treated with  D(+)-Raffinose pentahydrate (50 uM) for 24 hours


title: Embryonic meninges, E14.5, Foxc1 null, embryo 7

description: 43bp x 43bp


title: Escherichia coli control, not irradiated sample: replicate R4

description:
Sample UC L- R4
QPDAM054AU_EC-00-4

value: not irradiated

value: UC L-


title: SPN_TIGR4_Dccn_2_BHI

description: rRNA depleted

value: bacterial cell

value: rpsL1 DccnABCDE

value: BHI


title: Escherichia coli control, not irradiated sample: replicate R5

description:
Sample UC L- R5
QPDAM055A4_EC-00-5


title: MH-S cells LPS+RCMNs treated replicate1


title: DR_PANC1_1

source_name: PANC-1 cells treated with  D(+)-Raffinose pentahydrate (50 uM) for 24 hours


title: MH-S cells LPS treated replicate2

value: treated LPS


title: Escherichia coli control, not irradiated sample: replicate R3

description:
Sample UC L- R3
QPDAM053AM_EC-00-3


title: Embryonic meninges, E14.5, Foxc1 null, embryo 6

description: 43bp x 43bp


title: Escherichia coli control, not irradiated sample: replicate R2

description:
Sample UC L- R2
QPDAM052AE_EC-00-2


title: Embryonic meninges, E14.5, Foxc1 +/+, embryo 4

description: 43bp x 43bp

value: Foxc1 +/+


title: MH-S cells LPS treated replicate1


title: ATCC 19606T after 1-week desiccation (second biological replicate)

city: Rome

first: Massimiliano

last: Lucidi

state: Rome

address: Viale Guglielmo Marconi 446

department: Sciences

institute: University of Roma Tre

description: ATCC 19606T desiccated cells (#2)

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Acinetobacter_baumannii_ATCC 19606 reference genome available on ENSEMBL using the Bowtie2 aligner v.2.2.6. BAM files were generated because of this step. Unique gene hit counts were calculated using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within gene regions were counted. After the extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed. The Wald test was used to generate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were defined as differentially expressed genes for each comparison.
Assembly: A. baumannii ATCC 19606T [NZ_CP058289.1]
Assembly: A. baumannii ACICU [NZ_CP031380.1]
Supplementary files format and content: Processed data: tab-delimited text files including raw counts for each sample
Supplementary files format and content: Raw data files: tab-delimited text files including RPKM values for each sample

organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841

source_name: A. baumannii [NZ_CP058289.1]

growth_protocol: ATCC 19606T and ACICU were grown in LB and incubated at 37°C under shaking for 18 h. Bacterial cultures were sub-cultured (1:100 dilution) in a flask and incubated at 37°C under shaking for 6 h.

extract_protocol:
RNA was purified with RNeasy MiniElute Cleanup Kit (Qiagen) and RNA samples were treated with TURBO DNase (Invitrogen) to remove genomic DNA.
The RNA-seq analysis, RNA quality assessment, library preparation, sequencing, and statistical analysis of the data were performed at the GENEWIZ Biotechnology Facility (GENEWIZ, Azenta Life Sciences Company, Leipzig, Germany), as previously described [doi: 10.1128/spectrum.00961-22].

treatment_protocol: ATCC 19606T and ACICU were washed, diluted in ultrapure distilled water to an OD600 of 1.0, and desiccated on glass Petri plates for 1 week. Before and after desiccation, samples were collected and mixed with 2 mL of RNA Protect Bacteria Reagent (Qiagen). Total RNA isolation was performed by using miRNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

value: wild-type; subline A [doi:10.1099/mgen.0.000749]

value: Total RNA extraction from cells harvested after 1-week desiccation (desiccated sample)


title: Embryonic meninges, E14.5, Foxc1 +/+, embryo 5

description: 43bp x 43bp


title: MH-S cells control replicate3

value: treated PBS


title: DR_PANC1_3


title: ATCC 19606T after 1-week desiccation (third biological replicate)

description: ATCC 19606T desiccated cells (#3)


title: MH-S cells LPS+RCMNs treated replicate2


title: ATCC 19606T after 1-week desiccation (first biological replicate)

description: ATCC 19606T desiccated cells (#1)


title: MH-S cells control replicate2


title: Embryonic meninges, E14.5, Foxc1 +/+, embryo 3

description: 43bp x 43bp


title: Embryonic meninges, E14.5, Foxc1 +/+, embryo 2

description: 43bp x 43bp


title: MH-S cells control replicate1


title: ATCC 19606T before desiccation (third biological replicate)

description: ATCC 19606T before desiccation (#3)

value: Total RNA extraction from cells harvested immediately after resuspension in ultrapure distilled water (before desiccation)


title: RB1311.5

city: Montreal

first: Alain

last: Pacis

state: QC

address: 1010 Sherbrooke #1800

institute: Canadian Centre for Computational Genomics (C3G)

data_processing:
Adapters and low-quality sequences (Phred score <30) were trimmed using Trimmomatic. The resulting reads were aligned to the C. elegans reference genome WBcel235 assembly using STAR. Read counts were obtained using HTSeq with parameters -m intersection-nonempty -stranded=reverse. For all downstream analyses, we excluded lowly expressed genes (average read count <10 across all samples). Raw counts were normalized using the edgeR’s TMM algorithm125 and transformed to log2-counts per million (log2CPM) using the voom function in the limma R package. To assess differences in gene expression, we fitted a linear model using the lmfit function with parameter method = "robust". Nominal p-values were corrected for multiple testing using the Benjamini-Hochberg method. Gene set enrichment analysis based on pre-ranked gene list by t-statistic was performed using the R package fgsea (http://bioconductor.org/packages/fgsea/)
Assembly: WBcel235
Supplementary files format and content: RNA-seq raw counts matrix are tab-delimited text files, with the genes in rows and the samples in columns.

organism: Caenorhabditis elegans

source_name: Strain RB1311

growth_protocol: ~50,000 synchronized L1s were hatched in 2-3 15-cm NGM plates with 2mL OP50 lawn and grown at 16C to gravidity and until embryos are laid on the plates.

extract_protocol:
Embryos were harvested with standard bleaching procedure, flash-frozen in liquid N2, and kept at -80C until RNA extraction. Embryo pellets were Dounce-homogenized and RNA was extracted using phenol(Trizol)/chloroform, treated with Turbo DNase, and pure RNA was extracted using chloroform/isopropanol and dissolved in water. RNA with RIN >8 was used for library preparation. Four independent biological replicates (denoted .2, .3, .4, .5) were used.
RNA-seq libraries were prepared using the TruSeq Stranded Total RNA Library Prep Gold (Illumina Cat#20020599) following manufacturer's protocol.

treatment_protocol: Each genotype was grown in parallel and no treatment was applied.

value: Strain RB1311

value: Mixed-stage embryos


title: ATCC 19606T before desiccation (second biological replicate)

description: ATCC 19606T before desiccation (#2)


title: ATCC 19606T before desiccation (first biological replicate)

description: ATCC 19606T before desiccation (#1)


title: Embryonic meninges, E14.5, Foxc1 +/+, embryo 1

description: 43bp x 43bp

value: meninges


title: RB1311.2