title: WT_P-69696.87

city: Vienna

first: Magdalena

last: Paolino

address: Dr.-Bohr-Gasse 9

country: Austria

institute: Institute of Molecular Biotechnology

data_processing:
Reads mapping to mouse rRNA transcripts were removed using bwa/0.7.12 alignment and samtools/1.3.1. Remaining reads were aligned to Mus musculus genome mm10 using TopHat v2.1.1 (GTF annotation file mm10, RefSeq from UCSC, 2015/02). Reads in genes were counted with htseq-count v0.6.1.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with per gene read counts

source_name: Gonadal white adipose tissue

extract_protocol:
Total RNA was extracted from the tissue using the RNAeasy Mini Kit (Qiagen) and included DNase I digestion to avoid potential DNA contamination
QuantSeq RNA-Seq Library preparation Kit (Lexogen)
3' RNA-Seq (Quantseq)

tag: developmental stage

value: pregnant E17.5

value: Tnfrsf11a (Rank) Foxn1 Cre- (wildtype)

value: Vehicle

value: Gonadal white adipose tissue


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C3_ad001

status: Public on Oct 05 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

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

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

tag: brain region

value: DG

tag: Sex

value: male

tag: age

tag: strain


title: WT_P-69692.76

library_source: transcriptomic

molecule: total RNA

tag: genotype

tag: treatment

tag: tissue


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C3_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C2_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C2_ad007


title: WT_P-67758.86


title: KO_Ptr-69698.77

value: Tnfrsf11a (Rank) Foxn1 Cre + (Knock-out)

value: Treg


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C2_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C2_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C12_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C12_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C12_ad001


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C12_ad007


title: KO_Ptr-69693.67


title: KO_Ptr-67755.74


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C4_ad001


title: KO_Ptr-67754.68


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C12_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C3_ad004


title: KO_P-67761.89


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C11_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C2_ad008


title: WT_P-67762.91


title: KO_P-67763.92


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C11_ad010


title: KO_P-67757.80


title: KO_P-67752.61


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C2_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C11_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C11_ad001


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C11_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C11_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C10_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C10_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C10_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C12_ad006


title: Hyalocytes sample 9 lane 3

city: Freiburg

first: Clemens

last: Lange

address: Kilianstraße 5

department: Klinik für Augenheilkunde

country: Germany

institute: Uniklinik Freiburg

data_processing:
Quality control FastQC Galaxy Version 0.72
Reads were mapped to the human reference genome (hg38, gencode, release 31) with RNA STAR Galaxy Version 2.6.0b-2 (default parameters) using the Gencode annotation file (Gencode 31, release June 2019)
Samples were then checked for contamination with rRNA using SortMeRNA Galaxy Version 2.1b.6 as well as with non-human reads (bacteria, virus, funghi, arachea and protozoa) using RNA STAR Galaxy Version 2.6.0b-2. Reference genomes were downloaded from NCBI FTP server (ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/, Download between 6th and 13th July 2019).
Three BAM files for each sample (one for each lane) were combined in one BAM file per sample using Convert, Merge, Randomize BAM datasets Galaxy Version 2.4.0
Reads mapped to the human reference genome were counted using featureCounts Galaxy Version 1.6.4 (default parameters) using the aforementioned annotation file.
Samples with less than 10 mio. assigned reads were excluded from further analysis.
Differential gene expression was analyzed using DESeq2 Galaxy Version 2.11.40.6 (default parameters)
The output of DESeq2 was imported to RStudio (Version 1.2.1335, R Version 3.5.3). Genesymbols and genetypes were determined based on ENSEMBL (download: 22.09.2019). Genes without a hit in the ENTREZ Gene (NCBI) search were removed from analysis.
Genome_build: hg38

organism: Homo sapiens

extract_protocol:
Vitreous tissue samples collected in vitrectomy collection bags were immediately placed on ice in the operating theatre and processed for cell isolation within two hours of surgical resection. The content of each vitrectomy bag was centrifuged for 10 min at 250x g at 15°C. After removing the supernatant, the pellet was transferred to FACS tubes by washing with phosphate-buffered saline (PBS) buffer (PAN) and Hank’s balanced salt solution (HBSS, Gibco) and again centrifuged for 10 min at 250x g at 15°C. The vitreous pellet was digested with Collagenase D (5 mg/mL, Roche) and DNase I (1 mg/mL, Roche) in HBSS for 20 min at 37°C. Cells were then filtered through a 70 µm cell strainer. Following another centrifugation step (7 min at 250x g at RT), 0.5 µL of Fixable Viability Dye (eFluor™ 780, eBioscience™) per 1 mL of cells was added. The pellet was stained for CD45 BV421 (anti-human, 1:100, BioLegend®), CD11b FITC (anti-human, 1:100, BioLegend®), CX3CR1 PE-Cy7 (anti-human, 1:200, BioLegend®). To exclude any potential contamination with blood-derived monocytes due to possible surgically induced micro bleedings which may influence the results, we further used the Anti-Human Mature Macrophages (MatMac) Antibody, an ED2-like (ectodermal dysplasia 2) marker for resident macrophages, which is absent in monocytes 8 (eFluor660, anti-human, 1:100, eBioscience™). After an incubation step of 20 min at 4°C the cells were re-suspended in FACS buffer and processed for sorting on the MoFlo Asrios EQ Cytometer (Beckman Coulter). Sorted cells were stored in RNAprotect Cell Reagent (QIAGEN) at 2-8 °C until sequencing was performed.  RNA extraction, library preparation and RNA sequencing were performed at the Genomics Core Facility “KFB - Center of Excellence for Fluorescent Bioanalytics” (University of Regensburg, Regensburg, Germany; www.kfb-regensburg.de). In brief, total RNA was extracted from isolated hyalocytes and stabilized in RNAprotect Cell Reagent according to the RNeasy Plus Micro Kit protocol (QIAGEN). After pelleting, the RNAprotect buffer was removed and replaced by RLT Plus and the samples homogenized by vortexing for 30 sec. Genomic DNA contamination was eliminated using gDNA Eliminator spin columns. Next, ethanol was added and the samples were applied to RNeasy MinElute spin columns followed by several wash steps. Finally, total RNA was eluted in 12 μl of nuclease-free water.
In total 13 samples were analyzed using RNA-sequencing. The SMARTer Ultra Low Input RNA Kit for Sequencing v4 (Clontech Laboratories, Inc.) was used to generate first strand cDNA from 750 pg total-RNA. Double-stranded cDNA was amplified by LD PCR (12 cycles) and purified via magnetic bead clean-up. Library preparation was carried out as described in the Illumina Nextera XT Sample Preparation Guide (Illumina, Inc.). 150 pg of input cDNA were tagmented (tagged and fragmented) by the Nextera XT transposome. The products were purified and amplified via a limited-cycle PCR program to generate multiplexed sequencing libraries. For the PCR step 1:5 dilutions of index 1 (i7) and index 2 (i5) primers were used. The libraries were quantified using the KAPA SYBR FAST ABI Prism Library Quantification Kit (Kapa Biosystems, Inc.). Equimolar amounts of each library were pooled, and the pools then used for cluster generation on the cBot with the Illumina TruSeq SR Cluster Kit v3. The sequencing run was performed on a HiSeq 1000 instrument using the indexed, 50 cycles single-read (SR) protocol and TruSeq SBS v3 Reagents according to the Illumina HiSeq 1000 System User Guide. Image analysis and base calling resulted in bcl files, which were converted into fastq files with the bcl2fastq v2.18 software. The sequence data have been submitted to the Gene Expression Omnibus database under accession number GSE147449. The password is available from the corresponding author upon request.

tag: cell type

value: Hyalocyte


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C10_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C10_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C11_ad012


title: Hyalocytes sample 9 lane 2


title: Hyalocytes sample 9 lane 1


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C11_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C1_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C1_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C1_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C1_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C1_ad001


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C1_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B9_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B9_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B9_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B9_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B9_ad001


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B9_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B9_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C10_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C10_ad001


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C10_ad006


title: Hyalocytes sample 6 lane 3


title: Hyalocytes sample 6 lane 1


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C1_ad012


title: Hyalocytes sample 6 lane 2


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B8_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B8_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B8_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B8_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B8_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B8_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B8_ad001


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B7_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B7_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B7_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B7_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B7_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B7_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B8_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B9_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B7_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B7_ad001


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B6_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B6_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B6_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B6_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B5_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B5_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B5_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B6_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B5_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B5_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B5_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B5_ad001


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B4_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B4_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B4_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B4_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B4_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B4_ad006


title: CRC organoid L3

city: Shanghai

first: He

last: Li

address: 26Qiu yue

country: China

institute: The Interdisciplinary Research Center on Biology and Chemistry

data_processing:
Sequence quality was examined using the FastQC software.
Sequencing reads were mapped to the reference genome Rnor_6.0 from ensembl with STAR-2.6.0 by default parameter.
HTSeq (v0.6.0) was used to count the reads numbers mapped to each gene. And then fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differentially expressed genes in paired organoids and tissue samples were identified using the DESeq2 package (1.10.1).
Genome_build: Rnor_6.0 from ensembl
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Patient 13

extract_protocol:
Total RNA was extracted from organoids 4-6 days after passaging and organoid-matching tumors using an AllPrep DNA/RNA Mini Kit (Qiagen). A total amount of 1 µg RNA per sample was used for sequencing library preparation. The quality of each sample was measured using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies). PolyA-tailed RNAs were selected by NEB Next Poly(A) mRNA Magnetic Isolation Module (NEB), followed by the library prep using NEB Next Ultra RNA library Prep Kit for Illumina according to manufacturers instruction (NEB). The quantification was performed by qRT-PCR with a reference to a standard library. The libraries were pooled together in equimolar amounts to a final 2 nM concentration. The normalized libraries were denatured with 0.1 M NaOH (Sigma, USA). Pooled libraries were sequenced on the illumina Xten platforms with PE150 (illumina, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subject status

value: colorectal cancer (CRC) patient

tag: subject id

value: Patient 13

tag: tumor stage

value: IV

value: CRC organoid derived from liver metastases from CRC


title: CRC organoid L4


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B3_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B4_ad002


title: CRC organoid L1


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B6_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B3_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B3_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B3_ad006


title: CRC organoid b4

value: CRC organoid derived from CRC tissue


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B6_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B3_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B3_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B3_ad001


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B2_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B2_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B2_ad007


title: CRC organoid b2


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B2_ad012


title: CRC organoid b1


title: CRC organoid a4


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B2_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B2_ad002


title: CRC organoid a3


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B2_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B2_ad001


title: CRC organoid L2


title: ALL bone marrow 6

city: Atlanta

first: Samuel

middle: Spence

last: McCachren

state: GA

address: 1760 Haygood Dr. NE

institute: Emory University

description: BM single cell RNA seq_1277

data_processing:
Reads were aligned, filtered, de-duplicated, and converted into a digital count matrix using Cell Ranger 1.2 (10X Genomics)
Additional quality control (QC) was performed using Seurat [Satija et al. Nat Biotech 33, 495-502 (2015)]. Outlier cells were identified and filtered based on (1) anomalously high mitochondrial gene expression (cells with >10% mitochondrial content were removed) and (2) potential doublets/multiplets, as identified by comparing the number of expressed genes detected by per cell versus the number of unique molecular identifiers (UMIs) detected per cell (cells with greater than 7000 expressed genes were removed). In addition, we removed clusters of plasma (cells expressing CD138) and erythroid cells (cells expressing hemoglobin).
To co-analyse all samples, a log-normalized aggregate digital expression matrix was produced using Seurat, and then the above steps were carried out.
The processed files are combined digital expression matrix divided in three files for each of the sample. The matrix.mtx file contains the values, barcodes.tsv contains the cell barcodes detected, and features.tsv contains the list of genes detected. The three files for each sample are copied in one folder, and this folder was read-in using the Seurat package.
For Seurat to work correctly the prefix for each file has to be removed.
Genome_build: hg38
Supplementary_files_format_and_content: The processed files are combined digital expression matrix divided in three files for each of the sample. The matrix.mtx file contains the values, barcodes.tsv contains the cell barcodes detected, and features.tsv contains the list of genes detected. The three files for each sample are copied in one folder, and this folder was read-in using the Seurat package.

source_name: ALL bone marrow

growth_protocol: Bone marrow sample from a healthy donor, AML patient, or ALL patient was thawed; tumor samples were sorted to decrease tumor cell abundance.

extract_protocol:
To prepare the libraries for sequencing, the Chromium Gel Bead and Library Kit (10X Genomics) and Chromium instrument (10X Genomics) were used following manufacturer’s protocol. Further, the barcoded libraries were sequenced using HiSeq2500.
10X Genomics manufacturer protocol

tag: disease state

value: Acute lymphoblastic leukemia

value: Bone Marrow Immune Cells


title: ALL bone marrow 7

description: BM single cell RNA seq_1209


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B3_ad012


title: CRC organoid a2


title: ALL bone marrow 5

description: BM single cell RNA seq_1281


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B12_ad010


title: CRC organoid a1


title: CRC organoid b3


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B12_ad001


title: Normal colon tissue

value: Normal colon tissue


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B12_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B12_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B12_ad002


title: ALL bone marrow 4

description: BM single cell RNA seq_1308


title: ALL bone marrow 3

description: BM single cell RNA seq_1167


title: CRC tissue L

value: Liver metastases from CRC


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B12_ad004


title: CRC tissue b

value: CRC tissue


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B12_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B11_ad008


title: ALL bone marrow 2

description: BM single cell RNA seq_1199


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B11_ad001


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B11_ad002


title: ALL bone marrow 1

description: BM single cell RNA seq_1236


title: CRC tissue a


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B11_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B11_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B11_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B10_ad012


title: AML bone marrow 7

description: BM single cell RNA seq_1249

source_name: AML bone marrow

value: Acute myeloid leukemia


title: p65_sh rep1

city: Guangzhou

first: Ziyang

last: Wang

state: Guangdong

address: 58 Zhongshan Second Road

institute: The First Affiliated Hospital, Sun Yat-sen University

data_processing:
Skewer (v0.2.2) software was used to remove the adapter sequence of raw data(Fastq) and the reads whose length is longer than 75bp were selected after adapters were removed.
The reads were mapped to the human (Homo sapiens) genome (version hg19) using STAR (v2.4.2a) software.
Expression estimation of gene and transcript was performed by using RSEM (V1.2.29) software. Then edgeR (v3.8.5) package in R was used to perform TMM (trimmed mean of M values) and CPM (count per million) normalization for the the gene expression. TMM is mainly used to normalize the depth of sequencing in different samples and estimate the expression level for each sample. CPM is used to normalize the amount of read count expression between samples.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TMM and CPM normalized values for each Sample ...

source_name: HCT116_p65 knockdown

extract_protocol:
Total RNA was extract using Trizol reagent. mRNA was extracted from total RNA using magnetic beads and used Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: HCT116 cells were infected with shNC, TEX10 knockdown or p65 knockdown lentiviruses for 24 h, and then screened by puromycin for 3 days.

tag: cell line

value: Human colorectal cell line

tag: genotype/variation

value: p65 knockdown


title: AML bone marrow 8

description: BM single cell RNA seq_1528


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B10_ad010

value: DG

value: male


title: shNC2 rep1

value: shNC


title: AML bone marrow 6

description: BM single cell RNA seq_1260


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B10_ad007


title: shNC2 rep2


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B10_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B10_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B10_ad001


title: AML bone marrow 5

description: BM single cell RNA seq_1323


title: AML bone marrow 4

description: BM single cell RNA seq_1258


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B10_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B10_ad004


title: TEX10_sh rep2

source_name: HCT116_TEX10 knockdown

value: TEX10 knockdown


title: AML bone marrow 3

description: BM single cell RNA seq_1210


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B1_ad012


title: p65_sh rep2


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B1_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B1_ad010


title: TEX10_sh rep3


title: AML bone marrow 2

description: BM single cell RNA seq_1197


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B1_ad002


title: shNC1 rep3


title: AML bone marrow 1

description: BM single cell RNA seq_1150


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B1_ad001


title: healthy donor bone marrow 4

description: BM single cell RNA seq_7903

source_name: healthy donor bone marrow

value: healthy


title: shNC1 rep2


title: healthy donor bone marrow 3

description: BM single cell RNA seq_5286


title: shNC1 rep1


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A9_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A9_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A9_ad002


title: healthy donor bone marrow 2

description: BM single cell RNA seq_3958


title: healthy donor bone marrow 1

description: BM single cell RNA seq_0064


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A9_ad001


title: TEX10_sh rep1


title: RNA-seq over-expression from MdoR sample replicate 3

city: Edinburgh

first: Sander

last: Granneman

address: Mayfield Road, Kings Buildings, Waddington building, room 3.06

department: Centre for Synthetic and Systems Biology

country: United Kingdom

institute: University of Edinburgh

data_processing:
Raw sequencing reads in fastq files were processed using a pipeline developed by Sander Granneman, which uses tools from the pyCRAC package (Webb et al., 2014a). The entire pipeline is available at https://bitbucket.org/sgrann/). The CRAC_pipeline_PE.py pipeline first demultiplexes the data using pyBarcodeFilter.py and the in-read barcode sequences found in the L5 5’ adapters. Flexbar then trims the reads to remove 3’-adapter sequences and poor quality nucleotides (Phred score <23). Using the random nucleotide information present in the L5 5’-adaptor sequences, the reads were collapsed to remove potential PCR duplicates. The reads were then mapped to the Escherichia coli MG1655 genome with Novoalign (www.novocraft.com). To determine which genes the reads overlapped with we generated an annotation file in the Gene Transfer Format (GTF). This file contains the start and end positions of each gene on the chromosome as well as what genomic features (i.e. sRNA, protein- coding, tRNA) it belongs to. To generate this file, we used the Rockhopper software (Tjaden, 2015) on E. coli  rRNA-depleted total RNA-seq data (generated by Christel Sirocchi), a minimal GTF file obtained from ENSEMBL (without UTR information). The resulting GTF file contained information not only on the coding sequences, but also complete 5’ and 3’ UTR coordinates. PyReadCounters then used the novoalign output file and the GTF file to count the total number of unique cDNAs that mapped to each gene.
Genome_build: Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.22
Supplementary_files_format_and_content: text file with raw counts or TPM, DESeq output for empty vector vs MdoR overexpression.  GTF and FASTA files are available on the SuperSeries.

organism: Escherichia coli

source_name: Escherichia coli grown in LB

growth_protocol: Cells were grown in standard LB medium to the desired optical density (OD600).

extract_protocol:
Total RNA was extracted using the Guanidium thiocyanate phenol method. RNA integrity was assessed with the Prokaryote Total RNA Nano assay on a 2100 Bioanalyzer (Agilent). Genomic DNA was removed by incubating 10 μg of total RNA with 2U Turbo DNase (Ambion) in a 50 μl final volume for 30 minutes at 37°C in the presence of 10 U SuperaseIn RNase Inhibitor (Ambion). RNA was subsequently phenol-chloroform extracted and purified by ethanol-precipitation.
For RNA-seq: Ribosomal RNA was removed with the Ribo-Zero rRNA Removal Kit (Gram-Negative Bacteria) (Illumina) according to the manufacturer’s instructions. Successful rRNA depletion was verified on the Agilent 2100 Bioanalyzer. The RNA was fragmented for 5 min at 95°C in the presence of Superscript III buffer (Invitrogen) followed by a five minute incubation on ice. Reverse-transcription (RT) was performed with Superscript III (Invitrogen) in 20 μl reactions according to manufacturer’s procedures using 250 ng of ribosomal RNA depleted RNA and 2.5 μM random hexamers (PE_solexa_hexamer, oligo 73, Table S7). The RNA and free primers were degraded using 20U of Exonuclease I (NEB) and 50U RNaseIf (NEB) and the cDNA was purified with the DNA Clean & Concentrator 5 kit (Zymo Research). Ligation of the 5’ adapter (P5_phospho_adapter, oligo 39) to the cDNA was performed using CircLigase II (EpiCentre) for 6 hours at 60ºC, followed by a 10 minute inactivation at 80ºC. The cDNA was purified with the DNA Clean & Concentrator 5 kit (Zymo Research). Half of the cDNA library was PCR amplified using Pfu polymerase (Promega) using the P5 forward PCR oligonucleotide and barcoded BC reverse oligonucleotides (200 nM; Table S7; 95°C for 2 min, 95°C for 20s, 52°C for 30s and 72°C for 1 min, and a final extension of 72°C for 5 min. 20 cycles of amplification). The PCR products were treated with Exonuclease 1 (NEB) for 1 h at 37ºC and purified by ethanol precipitation. Libraries were resolved on a 2% MetaPhor agarose (Lonza) gel 200-500 bp fragments were gel-extracted using the MinElute kit (Qiagen). All libraries were quantified on a 2100 Bionalyzer using the High-Sensitivity DNA assay. Individual libraries were pooled in equimolar amounts. Paired-end sequencing (75 bp) was performed by Edinburgh Genomics on a Illumina HiSeq 4000 platform.

treatment_protocol: For pulse-overexpression studies overnight MG1655 cultures containing pBAD::MdoR and empty pBAD control plasmids were inoculated in fresh LB-ampicillin medium at a starting OD600 of 0.05, and grown aerobically at 37  C to OD600 0.4. Pre-induction (0 min) and 15 minutes post-induction samples were harvested.  This series includes only the post-induction samples.

value: over-expression from MdoR

tag: optical density

value: not measured


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A8_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_B1_ad004


title: RNA-seq over-expression from MdoR sample replicate 2


title: RNA-seq over-expression from MdoR sample replicate 1


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A8_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A8_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A8_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A8_ad007


title: Input_Growing_3

city: Cambridge

first: Ioana

last: Olan

state: Cambridgeshire

address: Robinson Way

department: Cancer Research UK Cambridge Institute

institute: University of Cambridge

data_processing:
Fastq files were quality checked using FastQC [Babraham Institute, Simon Andrews], trimmed using cutadapt 2.0 [https://doi.org/10.14806/ej.17.1.200] with -m 20 --match-read-wildcards -q 28,28 -b GATCGGAAGAGCACACGTCTGAACTCCAGTCAC (paired-end experiments were trimmed simultaneously).
Reads were aligned with bowtie2 [Langmead and Salzberg 2012, Nature Methods] using default parameters and samtools [Li et al. 2009, Bioinformatics] was used for selecting only uniquely mapping reads and removing duplicates.
Alignment files corresponding to multiple lanes were merged using samtools [Li et al. 2009, Bioinformatics].
Peak calling was performed using macs2 [Zhang et al 2008, Genome Biology] in two stages, one with default parameters and one with insert sizes calculated using ChIPQC [Caroll et al. Frontiers in Genetics and R Bioconductor].
BigWig files were obtained by using THOR [Alhoff et al. 2016, Nucleic Acids Research] which performs input subtraction and library normalisation, as well as differential binding analysis.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig (THOR-normalised signal with Input subtracted)

growth_protocol: IMR90 and WI38 cells (ATCC) were cultured in DMEM supplemented with 10% FBS. Cells were maintained in physiological 5% O2.

extract_protocol:
Fixed cells were lysed and sonicated to generate 200-400 bp chromatin fragments before immunoprecipitation.
Libraries were prepared using the NEBnext ultra II DNA-library prep kit for Illumina (E7645) according to manufacturers instructions except that size selection was performed during the final bead purification step using SPRIselect beads (B23319, Beckman Coulter)

treatment_protocol: For RIS samples,IMR90 ER:HRAS(G12V) cells were treated for 6 days with 100nM 4OHT.

tag: vector

value: No

tag: chip antibody

tag: passage


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A8_ad002

tag: brain region

tag: Sex


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A8_ad001

tag: age

tag: strain


title: RNA-seq over-expression from empty plasmid control replicate 3

tag: genotype

value: empty plasmid control


title: Input_RIS_2

value: Yes, 6 days


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A9_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A7_ad012


title: Input_Growing_2


title: RNA-seq over-expression from empty plasmid control replicate 2


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A9_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A7_ad007


title: RNA-seq over-expression empty plasmid control replicate 1


title: Input_RIS_1


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A7_ad006


title: Input_Growing_1


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A7_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A6_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A7_ad001


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A6_ad012


title: PolII_RIS_4

value: Pol II (C13B9)


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A6_ad010


title: Input_RIS_3


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A6_ad007


title: PolII_Growing_4


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A6_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A6_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A6_ad001


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A5_ad012


title: PolII_RIS_3


title: NEGATIVE-2

city: Los Angeles

first: Emily

middle: Diane

last: Howard

state: Ca

address: 1450 Biggy St, NRT 5509

department: MMI

institute: University of Southern California

data_processing:
Illumina Casava1.7 software used for basecalling, algorithm: bcl2fastq-v2.17.1.14
RNAseq data were analyzed using Partek® Flow® software, version 7.0 Copyright ©; 2018
Raw reads were first trimmed based on Quality Score (min quality level 20, trim from both ends, min read length 25)
Trimmed reads were aligned to mm10 with Gencode M19 as guidance using STAR 2.5.3a
Aligned reads were quantified to Gencode M16 genes using Partek E/M. Normalized reads counts were tested for differential expression using Partek's GSA algorithm.
Genome_build: mm10
Supplementary_files_format_and_content: gene counts, normalized counts

source_name: pulmonary IL-10-negative ILC2s

extract_protocol:
Total RNA was isolated using MicroRNAeasy (Qiagen). 10ng of input RNA was used to produce cDNA for downstream library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Freshly sorted ILC2s after three intranasal administrations of rm-IL-33 (0.5 µg per mouse), were incubated (5 x 104 per mL) with rm-IL-2 (10 ng.mL-1), rm-IL-7 (10 ng.mL-1) and rm-IL-4 (10 ng.mL-1) for 48 h. IL-10-negative and IL-10 producing ILC2s were then again sorted into two separate populations for RNA sequencing.

tag: strain background

value: 8 weeks

tag: tissue

value: Lungs

value: freshly sorted ILC2s


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A5_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A5_ad007


title: NEGATIVE-1

tag: cell type


title: PolII_RIS_2


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A5_ad010


title: PolII_Growing_2


title: PolII_Growing_3


title: NEGATIVE-3


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A5_ad004


title: IL-10 GFP_3

source_name: pulmonary IL-10-producing ILC2s


title: 5_6Nx_heart_mRNA

type: RNA

city: fukuoka

first: naoya

last: matsunaga

address: maidashi 3-1-1, higashi-ku

country: Japan

institute: kyushu university

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K v2; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

source_name: 5/6 heart

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: The ventricle was prepared from mouse heart at 8 weeks after operation.

extract_protocol: The total RNA was isolated from cells using ReliaPrep TM  RNA Cell Miniprep System (Promega) according to the manufacturer's instructions.

value: ICR

value: 5/6 heart


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A5_ad002


title: 5_6_monocytes

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K v2 ; Agilent Technologies) according to the manufacturer's instructions.

source_name: 5/6 nephrectomized, splenic monocytes

growth_protocol: The monocytes was prepared from mouse spleen at 8 weeks after operation by flowcytemetry. Cells labeled anti-CD11b antibody and ant-Ly6c antibody.

value: icr

value: splenic monocytes


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A5_ad001

value: DG

value: male


title: PolII_RIS_1


title: sham_heart_mRNA

source_name: sham heart

value: sham heart


title: IL-10 GFP_2


title: PolII_Growing_1


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A4_ad012


title: sham_monocytes

source_name: sham mouse,  splenic monocytes

treatment_protocol: The monocytes was prepared from mouse spleen at 8 weeks after operation by flowcytemetry. Cells labeled anti-CD11b antibody and ant-Ly6c antibody.


title: IL-10 GFP_1


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A4_ad010


title: cHiC_RIS_1

description:
cHi-C
Capture HiC RAS-induced senescence Replicate 1

data_processing:
Fastq files were quality-checked with FastQC, aligned with the HiC-Pro pipeline [Servant et al. 2015, Genome Biology] using default parameters in the configuration file.
Artefacts and duplicates were removed using HiC-Pro and raw matrices as well as ICE-normalised ones were obtained at several resolutions using HiC-Pro.
Hi-C matrices at 40kb resolution (bin size), as well as cHiC matrices at 10kb resolution are provided, as well as the coordinates of the bins they correspond to.
Genome_build: hg19
Supplementary_files_format_and_content: BED: coordinates of the genomic bins
Supplementary_files_format_and_content: TXT: interaction matrix.txt in triplet sparse format

extract_protocol: Hi-C was carried out according to the in-nucleus ligation protocol detailed in (Nagano et al. 2015 Comparison of Hi-C results using in-solution versus in-nucleus ligation, Genome Biol, 16: 175). Capture Hi-C was carried out with SureSelect target enrichment (Agilent Technologies), using a custom-designed biotinylated RNA bait library targetting regions of interest in the human genome and custom paired-end blockers according to the manufacturer’s instructions (Agilent Technologies).

treatment_protocol: IMR90 cells were stably infected with an ER:RAS G12V containing construct. To induce RAS-induced senescence (RIS/Sen), cells were treated with 100nM 4-hydroxytamoxifen (4OHT) for 6 days.

tag: tamoxifen


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A4_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A4_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A5_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A4_ad008


title: cHiC_Growing_2

description:
cHi-C
Capture HiC Growing Replicate 2


title: H3K27me3_TSA

city: Moscow

first: Natalia

last: Klimenko

address: 34/5 Vavilova Street

country: Russia

institute: Institute of Gene Biology (IGB) of the Russian Academy of Sciences

data_processing:
Read adapters and poly-A tails were removed using cutadapt software. Trimming of low-quality tails was performed using sickle in paired-end mode, reads with the length less than 20 bp after trimming were discarded.
The remaining reads were aligned to build version danRer11 of the Danio rerio genome using Bowtie version 2 in paired-end mode (with enabling options --no-discordant --no-mixed). Only reads that aligned exactly one time concordantly were passed to further analysis.  After alignment read duplicates were removed using Picard MarkDuplicates function.
The coverage track (bedGraph) was obtained by calculation enrichment of each test signal against appropriate IgG control signal with deeptools2 bamCompare tool (with options --operation=ratio --extendReads) for merged replicates bam file.
The tracks signal was averaged using 500bp windows.
Genome_build: danRer11
Supplementary_files_format_and_content: Processed data was obtained by deeptools2 bamCompare and includes: values of ratio between sample and corresponding IgG averaged using 500 bp windows (bedGraph).

organism: Danio rerio

source_name: fibroblasts

growth_protocol: Zebrafish fibroblasts AB.9 were received from American Type Culture Collection (ATCC, CRL2298). The cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 15% fetal bovine serum (FBS) at 28°C under 5% CO2. For HDAC inhibition experiments cells were treated with increasing concentrations (0,1, 1, 5, 10, 20 µM) of trichostatin A (TSA) for 24 h.

extract_protocol:
Cells were harvested and nuclei were prepared by incubation in buffer, containing 10 mM Tris–HCl (pH, 8.0), 100 mM NaCl, 50 mM KCl, 0.32 M sucrose, 0.5 mM CuSO4 and 1 % Triton X-100. All solutions contained protease inhibitor cocktail (Bimake), and for histone panacetylation analysis 5 mM sodium butyrate was included to inhibit histone deacetylase activity. After 15 min of incubation on ice, the nuclei were pelleted and then resuspended in the same buffer without CuSO4. Next, the nuclei were washed twice with digestion buffer (50 mM Tris–HCl [pH 8.0], 3 mM MgCl2, 1 mM CaCl2, 0.3 M sucrose, and 100 mM NaCl) and treated with 60 U/μl micrococcal nuclease (Thermo Fisher Scientific) for 10 min at 28 °C. The reactions were stopped by the addition of EDTA to a final concentration of 10 mM. The solubilized chromatin was extracted with hypotonic buffer (1 mM Tris–HCl [pH 8.0], 1 mM EDTA). After purification and concentration with Amicon Ultra 30K centrifugal filter devices (Millipore), the chromatin was used for further analysis. Immunoprecipitation reactions were performed overnight at 4 °C in 1 ml of solution containing 50 mM NaCl, 20 mM Tris–HCl (pH 8.0), 5 mM EDTA, 20 mM sodium butyrate, protease inhibitor cocktail and 5 μg of rabbit polyclonal antibodies against modified histones. Histone  H3ac (pan-acetyl) antibody (Active Motif, # 39139), histone H4ac (pan-acetyl) antibody (Active Motif, # 39243) and histone H3K27me3 antibody (Active Motif, # 39155) were used. Rabbit IgG (Jackson ImmunoResearch, #011-000-002) was used as a negative ChIP control. Immune complexes were collected using magnetic beads coated with immobilized protein G (Thermo Fisher Scientific). Immobilized complexes were washed two times for 10 min at 4◦C in low salt buffer (20 mM Tris–HCl, pH 8.0, 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100) and high salt buffer (20 mM Tris–HCl, pH 8.0, 500 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100). Samples were incubated with RNase A (Thermo Fisher Scientific) for 30 min at 37°C. The DNA was eluted from the beads by proteinase K digestion overnight at 55◦C and purified using phenol/chloroform extraction.
ChIP samples containing 10 ng of precipitated DNA were prepared for next-generation sequencing using a standard protocol including DNA end repair, A-tailing, and Illumina Y-adapter ligation.

treatment_protocol: For HDAC inhibition experiments Danio rerio fibroblasts were treated with increasing concentrations (0,1, 1, 5, 10, 20 µM) of trichostatin A (TSA) for 24 h.

value: fibroblast

tag: treatment

value: TSA

tag: antibody


title: cHiC_Growing_1

description:
cHi-C
Capture HiC Growing Replicate 1

tag: cell line


title: HiC_RIS_1

description:
Hi-C
HiC RAS-induced senescence Replicate 1


title: wt_dhpg_rna_rep3

city: Worcester

first: Annie

last: Hien

state: MA

address: 373 Plantation Street

department: Molecular Medicine

institute: UMass Medical School Worcester

description: ca1.rep1-3.rna.rsem.gene.summary.counts.txt

data_processing:
reads mapped to rRNA and tRNA genes were removed using Bowtie2(Langmead and Salzberg, 2012) with parameter -N 1
remaining reads were mapped to the mm10 genome using TopHat2(Kim et al., 2013)
Uniquely mapped reads were then used as input to RSEM (Li and Dewey, 2011) for quantification of gene expression and mapped to RefSeq (v69) mm10.
We used log transformed TPM expression values to correct for batch effects using ComBat following a full model (Leek et al., 2012) (v3.18.0).
Corrected values were transformed back to read counts using the expected size of each transcript informed by RSEM.
Batch-corrected counts were used to identify differentially translated/expressed genes with DESeq2 (Love et al., 2014, p. 2)
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited files include a summary of counts from RSEM quantification of all mm10 genes.

source_name: mouse hippocampal slice

growth_protocol: Animals were given ad libitum access to food and water and reared on a 12-hour light-dark cycle. P28-42 male mice were used.

extract_protocol:
Trizol LS was used to extract RNA for library preparation.
RNA-Seq libraries were prepared using NEXTflex poly(A) beads (Bioo Scientific, #512980) and the NEXTFlex Rapid Directional qRNA-Seq kit (Bioo Scientific, # NOVA-5130-03D) according to manufacturer’s instructions

treatment_protocol: Hippocampal slices were treated with DHPG (100 µM) (Tocris) or ACSF (vehicle) for 5 min. Slices were then treated with cycloheximide (100 µg/ml) in ACSF, 4°C, snap-frozen on dry ice/EtOH bath, and stored at -80°C.

value: wild-type

value: DHPG

tag: experiment

value: RNA-seq


title: wt_dhpg_rna_rep1


title: wt_bas_rna_rep3

value: vehicle


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A4_ad001


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A4_ad002


title: HiC_Growing_2

description:
Hi-C
HiC Growing Replicate 2

value: No


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A3_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A3_ad008


title: wt_bas_rna_rep2


title: wt_bas_rna_rep1


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A3_ad007


title: RIS_Input_3

description: Input RAS-induced senescence Replicate 3

value: Yes, 6 days


title: C. albicans phagocytosed by BAPTA-AM-treated macrophages Replicate 5

city: Jena

first: Lydia

last: Kasper

address: Adolf-Reichwein-Straße 23

department: Microbial Pathogenicity Mechanisms

institute: Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute (HKI)

description:
log-phase Candida albicans in YPD complex medium
BAPTA_5

hyb_protocol: Gene Expression Hybridization kit (Agilent) was used according to the manufacturer's instructions

scan_protocol: Arrays were scanned on a GenePix 4200AL scanner (GenePix Pro 6.1; 635 and 594 nm; automatically determined photomultiplier tube [PMT] gains; pixel size 5 nm). Images were quantified using Agilent Feature Extraction Software (version 12.0).

data_processing:
Agilent Feature Extraction Software (v 12.0) was used for background subtraction and LOWESS normalization.
File matrix_6kORFs_log2_Cy5_Cy3_ratios.txt (linked as a supplementary file on the Series record) reports log2-normalized values for ~6k individual orfs (after combining array's different IDs that belong to the same orf).

organism: Candida albicans

source_name: Fungal cells (test)

label_protocol: One‐color QuickAmp labelling kit (Agilent) was used to generate cRNA with fluorescently labelled CTP (Cy5-CTP or Cy3-CTP; GE Healthcare, United Kingdom) from 1 µg of high‐quality total fungal RNA. Labelled cRNA was purified using the RNeasy Minikit (Qiagen), and sufficient dye incorporation was verified using a NanoDrop instrument (specific activity >7 pmol/µg).

growth_protocol: C. albicans was cultivated in complex YPD medium (in a shaking flask, 180 rpm, 37°C, 3 h), in DMEM-FBS (4x10e6 C. albicans cells/well, in 6-well plates, 37°C, 5% CO2, 3 h) , or co-incubated with murine bone-marrow-derived macrophages (BMDMs) in presence of DMSO vehicle or BAPTA-AM (4x10e6 C. albicans cells and 2x10e6 BMDMs/well 6-well plates, 37°C, 5% CO2, 3 h)

extract_protocol: Samples were lysed with 650 µL RLT buffer (Qiagen) containing 1% beta-mercaptoethanol and frozen in liquid nitrogen. After thawing, fungal and macrophage cells were collected using a cell scraper. Yeast were isolated from lysed macrophages by centrifugation (20,000 x g, 12 min, 4°C). Yeasts from six 6-well plates were pooled and resuspended in 440 µL AE-SDS buffer (50 mM sodium acetate, pH 5.3, 10 mM EDTA, 10% sodium dodecyl sulfate). Samples were vortexed for 30s and 440 uL Phenol:Chloroform:Isoamyl alcohol (25:24:1, v/v, ThermoFisher Scientific) was added. Samples were incubated for 5 min at 65°C followed by 10 min incubation at -80°C. The heating-freezing cycle was repeated once. After centrifugation (20,000 x g, 10 min, 4°C), the aqueous phase containing fungal RNA was collected and RNA was precipitated with isopropyl alcohol/sodium acetate. Precipitated RNA was collected by centrifugation (20,000 x g, 12 min, 4°C), washed in 70% ethanol and resuspended in RNase-free water.

treatment_protocol: Treatment with 20 µM DMSO or BAPTA-AM

tag: time

value: 3 h

value: cultivation with Macrophages (BMDMs) in DMEM-FBS + BAPTA-AM

source_name: Fungal cells (reference)

value: 6 h


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A3_ad006

source_name: C57BL/6J Male P56 Mouse Brain


title: C. albicans phagocytosed by BAPTA-AM-treated macrophages Replicate 4

description:
log-phase Candida albicans in YPD complex medium
BAPTA_4


title: tsc_dhpg_rna_rep3


title: tsc_dhpg_rna_rep2


title: wt_dhpg_rna_rep2


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A3_ad004


title: C. albicans phagocytosed by BAPTA-AM-treated macrophages Replicate 3

description:
log-phase Candida albicans in YPD complex medium
BAPTA_3


title: C. albicans phagocytosed by BAPTA-AM-treated macrophages Replicate 1

description:
log-phase Candida albicans in YPD complex medium
BAPTA_1


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A3_ad002


title: C. albicans phagocytosed by BAPTA-AM-treated macrophages Replicate 2

description:
log-phase Candida albicans in YPD complex medium
BAPTA_2


title: CTCF_RIS_3

description: CTCF RAS-induced senescence Replicate 3

tag: vector


title: tsc_dhpg_rna_rep1


title: Growing_Input_3

description: Input Growing Replicate 3


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A3_ad001


title: HiC_Growing_1

description:
Hi-C
HiC Growing Replicate 1


title: tsc_bas_rna_rep2


title: C. albicans phagocytosed by vehicle-treated macrophages Replicate 5

description:
log-phase Candida albicans in YPD complex medium
DMSO_5

value: cultivation with Macrophages (BMDMs) in DMEM-FBS + DMSO


title: RIS_Input_2

description: Input RAS-induced senescence Replicate 2


title: CTCF_Growing_3

description: CTCF Growing Replicate 3

tag: chip antibody


title: tsc_bas_rna_rep3


title: tsc_bas_rna_rep1


title: CTCF_RIS_2

description: CTCF RAS-induced senescence Replicate 2

tag: passage


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A2_ad006

tag: brain region


title: C. albicans phagocytosed by vehicle-treated macrophages Replicate 4

description:
log-phase Candida albicans in YPD complex medium
DMSO_4


title: Growing_Input_2

description: Input Growing Replicate 2


title: C. albicans phagocytosed by vehicle-treated macrophages Replicate 3

description:
log-phase Candida albicans in YPD complex medium
DMSO_3


title: RNA-seq_high_MYC_replicate2

city: Bethesda

first: David

last: Levens

state: MD

address: 10 Center Drive

institute: NCI

description:
primary cells
FPK_after_normalization.txt

data_processing:
RNA-seq: ChIP-seq and TACh-seq: After trimming bases on both ends with quality scores below 20, reads were aligned to the mouse genome (mm10) using Bowtie2. ChIP-seq peaks were called using SICER.
Genome_build: mm10
Supplementary_files_format_and_content: tdf format

source_name: Mouse embryo

growth_protocol: Primary MEFs were cultured in DMEM medium supplemented with 10% FBS, 100 units/mL of penicillin and 100 µg/mL of streptomycin for within 3 passages.

extract_protocol:
RNA-seq: After sorting, the low-MYC and high-MYC cells were seeded overnight. Considering the effects of MYC on global gene expression, external RNA spike-in control was added to cells in proportion to cell count before total RNA extraction. The mRNA libraries were prepared using TruSeq Stranded mRNA (Illumina) and sequenced on a NextSeq sequencer. ChIP-seq: Primary MEFs were cross-linked with 1% formaldehyde for 8 min (FUBP1 ChIP) and the cross-linking was terminated by adding glycine to a final concentration of 0.125M. After harvesting cells, the cell pellets were resuspended in RIPA buffer supplemented with protease inhibitors. Samples were sonicated to produce chromatin fragments of 300 bp on average, and subjected to immunoprecipitation. Five μg of rabbit monoclonal anti-FUBP1 antibody were used for the immunoprecipitation. The immunoprecipitated samples were subjected to library preparation and sequencing. TACh-seq: MEFs were lysed in hypertonic lysis buffer and digested with Cyanase (RiboSolutions) for 3 min at 37 degree. Reactions were terminated by the addition of EDTA (10 mM final) and SDS (0.75% final). After RNA and protein digestion, DNA was purified and the fragments of 100- 600 bp were selected by gel electrophoresis.
Libraries were prepared using the manufacturer's protocols.
RNA-seq:After trimming bases on the 3’ end with quality scores below 20, reads were aligned to the mouse transcriptome (mm10) using TopHat. For each ERCC RNA, the number of reads mapping to that transcript was divided by the transcript length to yield RPK (reads per kilobase of transcript). From the top 50 expressed transcripts as measured by average RPK over all samples, a set of 10 highly correlated transcripts was used to represent the quantity of spike-in RNA in each sample. The normalization score for each sample was then calculated as the geometric mean of the expression (FPK) of those 10 genes in that sample. Reads mapped to the transcriptome were quantified using the Partek E/M algorithm. For each transcript, the number of reads quantified to that transcript was divided by the transcript length to yield RPK, then divided by the normalization score for that sample to normalized to the number of cells. The normalized FPK of low-MYC and high-MYC cells were compared. ChIP-seq, TACh-seq

treatment_protocol: siRNA transfection: Wildtype and Fubp1 knockout MEFs were transfected with 100 nM of mouse Fubp2, or non-target siRNAfor 48 h using Dharmacon transfection reagents. Cell sorting: Primary MEFs from Myc-Egfp+/+ mice were treated with 20 µM of MG-132 for 6 h to inhibit proteasome degradation of MYC and therefore enhance the MYC-GFP signal, and then sorted for low- and high-GFP cells.

value: primary

tag: developmental stage

value: embryo

tag: cell name

value: mouse embryonic fibroblast


title: C. albicans phagocytosed by vehicle-treated macrophages Replicate 2

description:
log-phase Candida albicans in YPD complex medium
DMSO_2

tag: strain


title: RIS_Input_1

description: Input RAS-induced senescence Replicate 1


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A2_ad002

value: DG

tag: Sex

value: male

tag: age


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A2_ad004


title: CTCF_Growing_2

description: CTCF Growing Replicate 2


title: RNA-seq_high_MYC_replicate1


title: C. albicans phagocytosed by vehicle-treated macrophages Replicate 1

description:
log-phase Candida albicans in YPD complex medium
DMSO_1


title: RNA-seq_low_MYC_replicate2


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A2_ad001


title: Growing_Input_1

description: Input Growing Replicate 1


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A2_ad008


title: RNA-seq_low_MYC_replicate1


title: CTCF_RIS_1

description: CTCF RAS-induced senescence Replicate 1


title: TACh-seq_kokd_replicate2

description:
primary cells
wt1-peak.txt


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A12_ad010


title: C. albicans in DMEM-FBS cell culture medium Replicate 5

description:
log-phase Candida albicans in YPD complex medium
DMEM_5

value: cultivation with DMEM-FBS


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A12_ad002


title: C. albicans in DMEM-FBS cell culture medium Replicate 2

description:
log-phase Candida albicans in YPD complex medium
DMEM_2


title: CTCF_Growing_1

description: CTCF Growing Replicate 1


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A12_ad008


title: 2M_rep1

city: Zagreb

first: Tomislav

last: Domazet-Loso

state: Grad Zagreb

address: Bijenička cesta 54

department: Division of Molecular Biology

country: Croatia

institute: Institut Rudjer Bošković

data_processing:
The sequence quality and read coverage were checked using FastQC V0.11.7.
The RNA sequences were mapped onto the reference genome using BBMap V37.66.
The SAMtools package V1.6 was used to generate, sort and index BAM files.
Subsequent RNAseq data processing was performed in R V3.4.2.
Mapped reads were quantified per each Bacillus subtilis open reading frame using the R rsamtools package V1.30.0.
Raw counts for open reading frames were retrieved using the GenomicAlignments R package V1.14.2.
Genome_build: Bacillus subtilis NCIB3610 NCBI genome aaccession: ASM205596v1, GenBank assembly accession: GCA_002055965.1.
Supplementary_files_format_and_content: The processed data file contains a matrix of raw count values for each replicate and each mapped gene.

organism: Bacillus subtilis

source_name: biofilm

growth_protocol: The LC sample was grown in liquid LB medium at 30 ℃ for 24h, while the other samples were grown on MSgg agar plates at 30 ℃ for various time-periods.

extract_protocol:
The harvested biofilm samples were kept in RNAprotect Bacteria Reagent (Qiagen) until RNA extraction. The total RNA was extracted applying a modified version of the RNeasy Protect Mini Kit (Qiagen) protocol. The RNA quantification was performed using a NanoDrop 2000 spectrophotometer (ThermoFisher Scientific). The RNA was stored at -80 °C until sequencing.
The library was constructed according to the standard RNAseq library procotol at the EMBL Genomics Core Facility (Heidelberg, Germany).

value: NCIB 3610

value: late biofilm

value: 2 months after innoculation onto agar plate


title: 1M_rep3

value: 1 month after innoculation onto agar plate


title: TACh-seq_wt2_replicate2

description:
primary cells
wt1-peak.txt


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A12_ad001


title: TACh-seq_wt_replicate1

description:
primary cells
wt1-peak.txt


title: C. albicans in DMEM-FBS cell culture medium Replicate 1

description:
log-phase Candida albicans in YPD complex medium
DMEM_1


title: 1M_rep1


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A12_ad007


title: 1M_rep2


title: C. albicans in DMEM-FBS cell culture medium Replicate 3

description:
log-phase Candida albicans in YPD complex medium
DMEM_3


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A12_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A12_ad006


title: C. albicans in DMEM-FBS cell culture medium Replicate 4

description:
log-phase Candida albicans in YPD complex medium
DMEM_4


title: C. albicans in YPD complex medium Replicate 5

description:
log-phase Candida albicans in YPD complex medium
YPD_5

value: cultivation with YPD


title: HDE_E14.5_rep2

city: Lausanne

first: Lucille

last: Lopez-Delisle

address: Station 19

country: Switzerland

institute: EPFL

data_processing:
All scripts are available in https://github.com/lldelisle/scriptsForFernandezGuerreroEtAl2020
Adapters and bad-quality bases were removed with Cutadapt version 1.16 options -m 15 -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA -q 30.
Reads were further mapped using bowtie2 version 2.3.5 options --very-sensitive --no-mixed –no-discordant --dovetail -X 1000.
Only pairs with MAPQ30, concordant and in chromosomes which are not chrM were kept. Duplicates were removed with picard and the bam file was converted to bed with bedtools.
Peak calling and coverage were obtained with macs2 version 2.1.1.20160309 with options --nomodel --keep-dup all --shift -100 --extsize 200.
For each dataset, summit positions were extended 500bp each side and merged and the number of reads falling into these regions was used to normalize the coverage.
Mean of normalized coverage was performed between duplicates of ectoderm samples
Genome_build: mm10
Supplementary_files_format_and_content: bw: for each sample, the coverage from macs2 (not normalized)
Supplementary_files_format_and_content: normalized_ATAC_E13_FB.bw: normalized coverage for the forebrain E13.5 sample
Supplementary_files_format_and_content: normalized_*_neq2.bw : mean of normalized coverage
Supplementary_files_format_and_content: narrowPeak.gz : narrowPeak from macs2

source_name: Hindlimb distal ectoderm

extract_protocol:
For E14.5 ectoderm samples, the ectoderms were first isolated from the subjacent mesoderm by trypsin digestion and then dissociated to single cell suspension by pipetting up and down. For E13.5 forebrain sample, skull cartilage was removed with forceps and the forebrain portion was removed. The sample was digested in PBS with 10% FCS and digested with collagenase at 37ºC at 400rpm for 20 minutes.
ATAC-seq was performed as described in Buenrostro et al., 2016.

tag: tissue

value: Hindlimb distal ectoderm


title: 14D_rep3

value: mid biofilm

value: 14 days after innoculation onto agar plate


title: C. albicans in YPD complex medium Replicate 2

description:
log-phase Candida albicans in YPD complex medium
YPD_2

value: 3 h


title: HDE_E14.5_rep1


title: C. albicans in YPD complex medium Replicate 3

description:
log-phase Candida albicans in YPD complex medium
YPD_3

value: 6 h


title: TACh-seq_kokd_replicate1

description:
primary cells
wt1-peak.txt

tag: cell type


title: C. albicans in YPD complex medium Replicate 4

description:
log-phase Candida albicans in YPD complex medium
YPD_4


title: DU145 OE rep3

first: Jianming

last: Lu

address: No.253, Industrial Avenue Middle

department: Department of Urology

institute: Zhujiang Hospital of Southern Medical University

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Prostate

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the following the vendor's recommended protocol construct a computerized library.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: circCSPP1 overexpression

value: Prostate


title: 14D_rep2


title: FDE_E14.5_rep2

source_name: Forelimb distal ectoderm

value: Forelimb distal ectoderm


title: C. albicans in YPD complex medium Replicate 1

description:
log-phase Candida albicans in YPD complex medium
YPD_1

tag: treatment


title: DU145 OE rep1


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A11_ad012

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

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


title: 7D_rep3

value: 7 days after innoculation onto agar plate


title: FDE_E14.5_rep1


title: DU145 NC rep3

value: normal


title: GM26_70 TCDD, HFD

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

data_processing:
bcl files were processed into fastq files with bcl2fastq v.2.17.1.14
Fastq files were processed with the manufacturer's script generate_reference.R and pete.star.script_3.0.R where tables of feature counts were generated for each samples.
Genome_build: Human TempO-Seq® whole mouse transcriptome custom probe annotation
Supplementary_files_format_and_content: table of probe counts for each sample

source_name: Islets

extract_protocol:
Isolated islets were stored in RNAlater (Qiagen) and then frozen at -80C. RNA was extracted using the Qiagen RNeasyMicro kit.
The TempO-Seq® Assay User Guide was used to build the TempO-Seq libraries for the mouse whole transcription panel. Following amplification, libraries were pooled and purified using the Macherey-Nagel NucleoSpin Gel and PCR Cleanup Kit with modifications outlined in the TempO-Seq® User Guide. Pooled, purified libraires were quantified using the KAPA Biosystemd qPCR library quantification kit and diluted to 4 nM for denaturation and dilution for sequencing.
Human TempO-Seq® mouse whole transcription panel and libraries were sequenced using an Illumina NextSeq500.

value: M

tag: chemical

value: TCDD

tag: diet

value: HFD

tag: species


title: DU145 NC rep2

tag: cell line


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A11_ad010

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

value: DG

value: male


title: 7D_rep1

value: NCIB 3610


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A12_ad004


title: GM26_58 TCDD, HFD


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A11_ad002


title: GM26_44 TCDD, HFD


title: HS_07_2018-06-29

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

data_processing:
data processing including quality control, read alignment and gene quantification were conducted using the 10X Cell Ranger software
Seurat was then used for normalization, data integration, and clustering analysis
Genome_build: GRCh37
Supplementary_files_format_and_content: 10X read count files

source_name: skin biopsy

extract_protocol:
Skin was harvested via punch biopsy from HS patients
Samples were incubated overnight in 0.4% dispase (Life Technologies) in Hank’s Balanced Saline Solution (Gibco) at 4°C. scRNA-seq was performed by the University of Michigan Advanced Genomics Core on the 10 Chromium system. Libraries were sequencing on the Illumina NovaSeq 6000 sequencer.
single cell RNA-seq

tag: condition

value: Lesional skin of HS


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A11_ad008

city: La Jolla


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A11_ad001


title: 5D_rep3

value: 5 days after innoculation onto agar plate


title: GM26_52 TCDD, HFD


title: 5D_rep2

value: mid biofilm


title: 14D_rep1

value: 14 days after innoculation onto agar plate


title: HSDerm190115

value: Dermal layer of HS lesional skin


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A11_ad004


title: DU145 OE rep2


title: GM26_31 TCDD, HFD

value: F


title: 3D_rep3

value: 3 days after innoculation onto agar plate


title: GM26_28 TCDD, HFD


title: HSDerm190103


title: 7D_rep2


title: 3D_rep2


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A10_ad012


title: HSEpi190103

value: Epidermal layer of HS lesional skin


title: DU145 NC rep1

value: Prostate


title: GM26_4 TCDD, HFD


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A10_ad002


title: 3D_rep1


title: 181009_HS_lesional_dermis


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A11_ad006


title: GM26_51 TCDD, Chow

value: Chow


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A10_ad001


title: GM26_37 TCDD, HFD


title: 2D_rep3

value: 2 days after innoculation onto agar plate


title: 181009_HS_lesional_epi


title: GM26_26 TCDD, Chow


title: 2D_rep2


title: HS2


title: GM26_10 TCDD, Chow


title: 2D_rep1


title: HSEpi190115


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A10_ad004


title: 5D_rep1


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A10_ad006


title: HS1


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A1_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A1_ad010


title: GM26_12 TCDD, Chow


title: 1D_rep3

value: early biofilm

value: 1 day after innoculation onto agar plate


title: GM26_8 TCDD, Chow

value: TCDD


title: 1D_rep2


title: GM26_63 Corn oil, HFD

value: M

value: Corn oil

value: HFD


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A1_ad007

value: DG

value: male


title: Cremer-2019-RepliSeq001

city: Houston

first: Suhas

last: Rao

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description: Cremer-2019-RepliSeq001_HCT-RAD21-AUX-STD-CTRL-E1_S40

data_processing:
Reads were aligned to the hg19 reference genome with bowtie2, deduplicated with samtools, and the log-2 ratio between early and late time points was calculated as described in Marchal, et al Nature Protocols 2018.
Genome_build: hg19
Supplementary_files_format_and_content:
*.hic file contains contact matrices at various resolutions in an easy to visualize and access format (Durand, Robinson, et al Cell Systems 2016)
Bedgraph containing deduplicated counts (early and late bedgraphs) or log-2 ratios of early to late binned at 5kb or 50kb resolution (ELratio bedgraph)

source_name: HCT-116 cmvOsTIR1 RAD21-mAC

extract_protocol:
cells were incubated with 20 µM Lovastatin (Mevinolin) (LKT Laboratories M1687) for 24 hours to synchronize in G1. 500 µM auxin or DMSO was added 6 hours before release from lovastatin block. To release from G1 block, lovastatin was washed away with 3 washes of PBS and warm media plus 2 mM Mevalonic acid (Sigma-Aldrich M4667) and 500 μM Auxin or DMSO. Cells were released for 10, 14, 18, and 22 hours. 2 hours before the time point 100 μM BrdU was added to label nascent replication. After fixation, equal numbers of cells from each release time point were pooled together for early/late repli-seq processing
standard Illumina library construction protocol, Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 8-12 cycles and library fragments of 400-600 bp (insert plus adaptor and PCR primer sequences) were purified using SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the NovaSeq following the manufacturer's protocols

tag: cell line background

tag: genotype/variation

value: cmvOsTIR1, RAD21-mAC

value: 20uM lovastatin for 24hrs


title: 1D_rep1

value: NCIB 3610


title: GM26_60 Corn oil, HFD


title: H3K27ac_TNFa

description: H3K27ac TNFa

value: TNFa

tag: chip antibody

tag: passage


title: 12H_rep3

tag: developmental stage

value: 12 hours after innoculation onto agar plate


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A1_ad006

tag: brain region

tag: strain


title: 12H_rep2

tag: age


title: H3K27ac_Growing

description: H3K27ac Growing


title: GM26_73 Corn oil, HFD

tag: Sex


title: WI38_SMC3_pBabe_v

description: WI38 cells SMC3 pBabe vector Replicate 1

tag: vector

value: pBabe vector


title: GM26_16 Corn oil, HFD

value: F


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A1_ad001


title: WI38_SMC3_pBabe_RAS

description: WI38 cells SMC3 pBabe RAS Replicate 1

value: pBabe RAS


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A1_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A1_ad002


title: 12H_rep1


title: GM26_19 Corn oil, HFD


title: 6H_rep3

value: 6 hours after innoculation onto agar plate


title: SMC3_TNFa_2

description: SMC3 with TNFa treatment Replicate 2


title: GM26_20 Corn oil, HFD


title: GM26_65 Corn oil, Chow

value: Chow


title: 6H_rep2

value: early biofilm


title: CEMBA190214_11F_1_CEMBA190214_11F_2_A1_ad008


title: Cremer-2019-RepliSeq002

description: Cremer-2019-RepliSeq002_HCT-RAD21-AUX-STD-KD-E1_S38

value: 20uM lovastatin for 24hrs, 500uM IAA, 6hrs


title: RNA-Sequencing VapC21 deletion Rep2

city: Bangalore

first: Munmun

last: Bhasin

state: Karnataka

address: CV Raman Rd

department: Molecular Biophysics Unit

country: India

institute: Indian Institute of Science

data_processing:
Data was subjected to quality control check by FastQC_v0.11.8
Reads were mapped to H37Rv and Erdman genome by TopHat v2.1.1
Abundance calculations (FPKM) by Cufflink
Differential expression analysis by Cuffdiff
Visuaization of results by R
Genome_build: ASM19595v2 (H37Rv) and ASM35020v1 (Erdman)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for VapC21 overexpression study.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for VapC21 deletion study.

organism: Mycobacterium tuberculosis

source_name: Microbe

growth_protocol: For overexpression studies, early log phase cultures were induced were anhydrotetracycline addition for 24 hrs. For deletion strains, total RNA was isolated from mid log phase culture grown in 7H9 media.

extract_protocol:
Total RNA was extracted using Qiagen RNeasy minikit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Erdman

value: VapC21 deletion


title: RNA-Sequencing VapC21 deletion Rep1


title: 6H_rep1


title: SMC3_Growing_3

description: SMC3 Growing Replicate 3 (matched with the DRB/TNFa samples)


title: GM26_62 Corn oil, Chow

value: M

value: Corn oil


title: RNA-Sequencing Control Cells Rep2 (deletion study)

value: Control


title: GM26_74 Corn oil, Chow


title: SMC3_pBabe_v

description: SMC3 pBabe vector Replicate 1


title: LC_rep3

source_name: bacterial liquid culture

value: liquid culture

value: 24 hours after innoculation into liquid culture


title: LC_rep2

value: NCIB 3610


title: RNA-Sequencing Control Cells Rep1 (deletion study)


title: SMC3_pBabe_RAS

description: SMC3 pBabe RAS Replicate 1


title: RNA-Sequencing VapC21 overexpression Rep3


title: GM26_11 Corn oil, Chow


title: RNA-Sequencing VapC21 overexpression Rep2


title: SMC3_RIS_3

description: SMC3 RAS-induced senescence Replicate 3 (matched with the DRB/TNFa samples)

value: Yes, 6 days


title: SMC3_TNFa_1

description: SMC3 with TNFa treatment Replicate 1

value: TNFa


title: GM26_33 Corn oil, Chow


title: GM26_30 Corn oil, Chow


title: LC_rep1


title: SMC3_RIS_DRB_1

description: SMC3 RAS-induced senescence with DRB treatment Replicate 1

value: DRB


title: RNA-Sequencing Control Cells Rep3 (overexpression study)

value: pTetR-Int Vector only


title: RAD21_TNFa_2

description: RAD21 with TNFa treatment Replicate 2

value: Rad21 (gift from Shirahige lab)


title: SMC3_RIS_DRB_2

description: SMC3 RAS-induced senescence with DRB treatment Replicate 2


title: RNA-Sequencing VapC21 overexpression Rep1


title: RAD21_TNFa_1

description: RAD21 with TNFa treatment Replicate 1


title: wt_dhpg_rpf_rep2

description: ribosome protected RNA footprint

data_processing:
reads were separated based on sample barcode sequences using in-house codes
known 3’ adapter sequences and low quality bases were removed with Cutadapt(Martin, 2011) using parameters -O 2 -q 15 -a “TGGAATTCTCGGGTGCCAAGGAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG”
reads mapped to rRNA and tRNA genes were removed using Bowtie2(Langmead and Salzberg, 2012) with parameter -N 1
remaining reads were mapped to the mm10 genome using TopHat2(Kim et al., 2013)
For ribosome profiling, PCR duplicates were removed based on Unique Molecular Identifier sequences using in-house codes.
Uniquely mapped reads were then used as input to RSEM (Li and Dewey, 2011) for quantification of gene expression and mapped to RefSeq (v69) mouse coding sequences (RPF).
We used log transformed TPM expression values to correct for batch effects using ComBat following a full model (Leek et al., 2012) (v3.18.0).
Corrected values were transformed back to read counts using the expected size of each transcript informed by RSEM.
Batch-corrected counts were used to identify differentially translated/expressed genes with DESeq2 (Love et al., 2014, p. 2)
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited files include a summary of counts from RSEM quantification of all mm10 genes.

extract_protocol:
Trizol LS was used to extract RNA for library preparation.
Ribosome profiling and RNA-seq libraries were prepared following published protocols(Heyer et al., 2015)
ribosome profiling and RNA-seq

tag: genotype

value: wild-type

value: DHPG

tag: experiment

value: ribosome profiling


title: wt_dhpg_rpf_rep3

description: ribosome protected RNA footprint

tag: treatment


title: RNA-Sequencing Control Cells Rep2 (overexpression study)


title: RNA-Sequencing Control Cells Rep1 (overexpression study)


title: GM26_50 Corn oil, Chow

tag: chemical

tag: diet

value: Chow


title: RAD21_Growing_4

description: RAD21 Growing Replicate 4 (matched with the DRB/TNFa samples)

data_processing:
Fastq files were quality checked using FastQC [Babraham Institute, Simon Andrews], trimmed using cutadapt 2.0 [https://doi.org/10.14806/ej.17.1.200] with -m 20 --match-read-wildcards -q 28,28 -b GATCGGAAGAGCACACGTCTGAACTCCAGTCAC (paired-end experiments were trimmed simultaneously).
Reads were aligned with bowtie2 [Langmead and Salzberg 2012, Nature Methods] using default parameters and samtools [Li et al. 2009, Bioinformatics] was used for selecting only uniquely mapping reads and removing duplicates.
Alignment files corresponding to multiple lanes were merged using samtools [Li et al. 2009, Bioinformatics].
Peak calling was performed using macs2 [Zhang et al 2008, Genome Biology] in two stages, one with default parameters and one with insert sizes calculated using ChIPQC [Caroll et al. Frontiers in Genetics and R Bioconductor].
BigWig files were obtained by using THOR [Alhoff et al. 2016, Nucleic Acids Research] which performs input subtraction and library normalisation, as well as differential binding analysis.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig (THOR-normalised signal with Input subtracted)

extract_protocol:
Fixed cells were lysed and sonicated to generate 200-400 bp chromatin fragments before immunoprecipitation.
Libraries were prepared using the NEBnext ultra II DNA-library prep kit for Illumina (E7645) according to manufacturers instructions except that size selection was performed during the final bead purification step using SPRIselect beads (B23319, Beckman Coulter)

tag: cell line


title: wt_dhpg_rpf_rep1

description: ribosome protected RNA footprint


title: wt_bas_rpf_rep3

description: ribosome protected RNA footprint

value: vehicle


title: RAD21_RIS_DRB_2

description: RAD21 RAS-induced senescence with DRB treatment Replicate 2


title: RAD21_RIS_DRB_1

description: RAD21 RAS-induced senescence with DRB treatment Replicate 1


title: tsc_dhpg_rpf_rep3

description: ribosome protected RNA footprint


title: SMF sample1

city: shanghai

first: liu

last: yan

address: yueyang road 320

institute: shanghai institute of biochemistry and cell biology

data_processing:
After quality filteration and removing the sequencing adapters with Trimmomatic (version 0.36), the RNA-seq reads were aligned to mouse genome (mm10) using HISAT2, and only reads hitting no more than 2 genomic loci were used to quantify gene expressions with StringTie.
The gtf file of mouse genes was downloaded from GENCODE (vM12).
The gene expressions were normalized as FPKM.
The fold change and p-value of all the detected genes were estimated by Ballgown.

source_name: CD8+ T cells from spleen

extract_protocol:
All the RNA was extracted using Trizol reagent, purified and checked for integrity using an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US). Libraries were generated for sequencing using the SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian (Illumina).
RNA libraries were prepared for sequencing using standard illumina protocols

tag: cell subpopulations

value: CD8+ T cells

tag: tissue

value: spleen

value: static magnetic field


title: Control sample2

value: control


title: Cortex_NEIL1_WT_SHAM_REPLICATE2

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

hyb_protocol: A total of 600 ng Cy3-labeled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 microL containing 0.5x Agilent fragmentation buffer and 2x Agilent gene expression blocking agent following the manufacturers instructions.  On completion of the fragmentation reaction, 25 microL of 2× Hi-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint GE3 Mouse 8x60k v2 gene expression microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), and dried by slowly removing from Wash buffer 2.

scan_protocol: Following posthybridization rinses, arrays were scanned using an Agilent SureScan microarray Scanner at 5 micron, and hybridization intensity data extracted from the scanned images using Agilent’s Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

data_processing: Raw microarray hybridization intensity data were filtered to remove undetected and array control probes, before computing log z-score for each sample to identify and exclude possible outlying samples via clustering, scatter plots, and principal components analysis. After removal of the outlying samples, a sample-specific quantile normalization of the filtered raw average signal was employed to yield quantile normalized log scale z-scores. These quantile z-scores were used to ensure a standard normal distribution in further statistical analysis, including ANOVA, t- and z-testing. Z-ratio values of ± 1.5 were used as cut-off values and calculated using a combination of thresholds, including p<value 0.05, 30% false discovery rate (FDR), and average signal intensity of comparison >0. The gene expression change z-ratio values were then used as input to perform Parametric Analysis of Gene Set Enrichment (PAGE) testing. For each gene set change, an aggregate z-score, and p-value with false discovery change was calculated and reported for statistical significance.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng total RNA using the Low-Input Quick Amp Labeling Kit (Agilent, Santa Clara, CA) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were evaluated with the NanoDrop ND-1000 Spectrophotometer (Wilmington, DE).

growth_protocol: All mice were maintained in the in a constant-temperature facility with a 12 h light/12 h dark cycle and given food and water ad libitum. The mice were a generous gift from Steven Lloyd (Oregon Health and Science University, Portland, OR). The mice were backcrossed on a C57BL/6 background. Male littermate wild type (28-42 weeks old) and male Neil1-/- mice were used for all experiments. All procedures were approved by the Animal Care and Use Committee of the National Institute on Aging Intramural Research Program.

extract_protocol: RNA was purified from mouse cerebral cortex with PureLinkTM RNA isolation kit  according to the manufacturers instructions (Thermo).

treatment_protocol: Mice were subjected to whole body gamma irradiation in a Nordion Gammacell 40 Exactor Irradiator. Mice were placed in a stereotaxic cube box and exposed to gamma irradiation or not irradiated (sham). Radiation (6 Gy) was delivered at a rate of 0.74 Gy/min on day 0. After exposure, mice were returned to home cages.  BrdU (Sigma) was dissolved in 0.9% NaCl and sterile filtered at 0.2 µm.  Mice were administered intraperitoneally BrdU injection (100mg/Kg) before and after 2 h of IR exposure. Mice were sacrificed at 20 h or four weeks after IR.

tag: strain background info

tag: genotype/variation

value: 28-42 weeks

value: SHAM

tag: post-treatment timepoint

value: 20 hours

value: Brain; cortex


title: Control sample1


title: wt_bas_rpf_rep1

description: ribosome protected RNA footprint


title: Cortex_NEIL1_WT_SHAM_REPLICATE4


title: H3K27me3_Growing

first: Ioana

last: Olan

address: Robinson Way

institute: University of Cambridge

description: H3K27me3 Growing Replicate 1

tag: chip antibody

tag: passage


title: Unstimulated sample1

tag: strain

value: unstimulated


title: tsc_dhpg_rpf_rep2

description: ribosome protected RNA footprint


title: Cortex_NEIL1_WT_IRRADIATED_REPLICATE3

tag: age

value: IRRADIATED


title: Cortex_NEIL1_WT_IRRADIATED_REPLICATE1


title: Cortex_NEIL1_WT_SHAM_REPLICATE3


title: CTCF_TNFa_2

description: CTCF TNFa treatment Replicate 2

value: TNFa


title: tsc_dhpg_rpf_rep1

description: ribosome protected RNA footprint


title: RAD21_RIS_5

description: RAD21 RAS-induced senescence Replicate 5 (matched with the DRB/TNFa samples)

value: Yes, 6 days

value: Rad21 (gift from Shirahige lab)


title: wt_bas_rpf_rep2

description: ribosome protected RNA footprint

value: wild-type


title: Cortex_NEIL1_WT_IRRADIATED_REPLICATE2


title: SMF sample2


title: Cortex_NEIL1_WT_SHAM_REPLICATE1


title: Cortex_NEIL1_WT_IRRADIATED_REPLICATE4


title: CTCF_TNFa_1

description: CTCF TNFa treatment Replicate 1


title: tsc_bas_rpf_rep3

description: ribosome protected RNA footprint

value: ribosome profiling


title: H3K27me3_RIS

description: H3K27me3 RAS-induced senescence Replicate 1


title: Cortex_NEIL1KO_SHAM_REPLICATE3


title: tsc_bas_rpf_rep2

description: ribosome protected RNA footprint


title: Unstimulated sample2


title: Cortex_NEIL1KO_SHAM_REPLICATE2


title: CTCF_RIS_4

description: CTCF RAS-induced senescence Replicate 4 (matched with the DRB/TNFa samples)


title: tsc_bas_rpf_rep1

description: ribosome protected RNA footprint


title: CTCF_Growing_4

description: CTCF Growing Replicate 4 (matched with the DRB/TNFa samples)


title: CTCF_RIS_DRB_2

description: CTCF RAS-induced senescence with DRB treatment Replicate 2

value: DRB


title: FUBP1 binding to MYC

description: primary cells

data_processing:
After trimming bases on both ends with quality scores below 20, reads were aligned to the mouse genome (mm10) using Bowtie2. ChIP-seq peaks were called using SICER.
Genome_build: MM10
Supplementary_files_format_and_content: tdf format

source_name: MEF

growth_protocol: MEFs were cultured in DMEM containing 10% fetal bovine serum.

extract_protocol:
Lysates were clarified from sonicated nuclei and FUBP1-DNA complex  were isolated with antibody.
Libraries were prepared using the manufacturer's protocols.

treatment_protocol: MEFs at steady-state were examined.

tag: cell type

value: primary

tag: developmental stage

value: embryo

tag: cell name

value: mouse embryonic fibroblast


title: CTCF_RIS_DRB_1

description: CTCF RAS-induced senescence with DRB treatment Replicate 1

tag: vector


title: Cortex_NEIL1KO_SHAM_REPLICATE1

tag: treatment


title: Cortex_NEIL1KO_SHAM_REPLICATE4


title: PV_Strd_IP_biorep1

status: Public on Oct 04 2020

city: Boston

first: Michael

middle: E.

last: Greenberg

address: 220 Longwood Ave

department: Neurobiology

institute: Harvard Medical School

description:
DIFFL-EXPN_edgeR__Lynn_Rb-HIP-mm_ka-6hr.vs.0hr_in.IP__4-PV.IP_6hr_vs_4-PV.IP_0hr__mm10.cd_f.ge.4__6862-UP
DIFFL-EXPN_edgeR__Lynn_Rb-HIP-mm_ka-6hr.vs.0hr_in.IP__4-PV.IP_6hr_vs_4-PV.IP_0hr__mm10.cd_f.ge.4__7033-DN

data_processing:
Raw sequencing reads ≤ 75 bp in length were 3′-trimmed to a uniform 70 bp (ignoring the ~ 0.1% of reads that were shorter than this) and filtered for quality control. These were then mapped strand-nonspecifically to the mm10 genome (GRCm38) using the Burrows-Wheeler Aligner (bwa), allowing up to 2 mismatches and no gaps. In addition to the usual assembled chromosomes, alignment targets included mitochondrial DNA and a library of ~7 million short splice-junction sequences. Typically, 75–80% of reads were mappable; nonuniquely mapped reads were discarded, as were any that mapped to loci of rRNA genes (from RepeatMasker).
Genic features were based on exonic loci from the NCBI RefSeq annotation for mm10. Mean expression density across a gene’s exons was taken as a proxy for its expression level. (However, noncoding genes, some of which expressed quite highly and variably from one sample to the next, were excluded from these analyses.) The splice-junction target sequences for each gene comprised subsequences of minimal length of all possible concatenations of two or more ordered exons such that their boundaries would be crossed by 70 bp reads. This provided an exhaustive, nonredundant set of predictable exon-junction-spanning loci which typically accounted for ~ 20% of all exonic reads from mature messages.
Differential expression analyses employed edgeR to compare transcript levels in all biological-replicate samples at 6h of KA stimulation to the unstimulated samples. A gene’s expression level was flagged as significantly changed if (a) the Benjamini-Hochberg-corrected p value (q value) for the change, as calculated by edgeR, was consistent with a false discovery rate of 0.005, and (b) it passed a modest background filter (total number of reads ≥ 4 across all compared samples).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each gene for every sample with differential gene expression analyses (EdgeR)

molecule: cytoplasmic RNA

extract_protocol:
Hippocampal CA1 tissue was rapidly dissected from mice and subsequently Dounce homogenized; lysates were used directly for immunoprecipitation.
All RNA samples (20 ng for CaMK2a; 2.5 ng for PV) with sufficient integrity as analyzed by 2100 Bioanalyzer were SPIA-amplified with the Ovation RNA-seq System V2 (NuGEN). Subsequently, SPIA-amplified cDNA (1 ug) was fragmented to a length of ~400 bp using a Covaris S2 sonicator (Acoustic Wave Instruments). Fragmented cDNA (100 ng) was used to generate Illumina-compatible sequencing libraries using the Ovation Ultralow System V2 (NuGEN). Libraries were sequenced on a NextSeq 500 for 75 bp single-end reads to a depth of 20-40 million reads per sample.

value: 3-4 weeks

tag: genotype

value: PV-Cre/+; LSL-Rpl22-HA/+

value: 6-hour PBS

value: CA1 region of hippocampus

tag: antibody

value: anti-HA antibody (Sigma HA-7, H3663, 12 ug/IP)


title: PV_Strd_IP_biorep3


title: PV_Strd_IP_biorep2


title: PV_Strd_input_biorep2

description:
DIFFL-EXPN_edgeR__Lynn_Rb-HIP-mm_ka-6hr.vs.0hr_in.IP__4-PV.in_6hr_vs_4-PV.in_0hr__mm10.cd_f.ge.4__6780-UP
DIFFL-EXPN_edgeR__Lynn_Rb-HIP-mm_ka-6hr.vs.0hr_in.IP__4-PV.in_6hr_vs_4-PV.in_0hr__mm10.cd_f.ge.4__7206-DN


title: PV_Strd_IP_biorep4


title: PV_Strd_input_biorep3


title: PV_Strd_input_biorep4


title: PV_KA_IP_biorep4

value: 6-hour kainic acid


title: PV_KA_IP_biorep3


title: PV_KA_input_biorep4

description:
DIFFL-EXPN_edgeR__Lynn_Rb-HIP-mm_ka-6hr_IP-vs-in__4-PV.6hr_IP_vs_4-PV.6hr_in__mm10.cd_f.ge.4__6975-UP
DIFFL-EXPN_edgeR__Lynn_Rb-HIP-mm_ka-6hr_IP-vs-in__4-PV.6hr_IP_vs_4-PV.6hr_in__mm10.cd_f.ge.4__7058-DN


title: Cortex_NEIL1KO_IRRADIATED_REPLICATE3

value: 28-42 weeks

value: 20 hours

value: Brain; cortex


title: Cortex_NEIL1KO_IRRADIATED_REPLICATE1

value: IRRADIATED


title: Cortex_NEIL1KO_IRRADIATED_REPLICATE4


title: Cortex_NEIL1KO_IRRADIATED_REPLICATE2


title: PV_KA_input_biorep1


title: PV_KA_input_biorep2


title: PV_KA_IP_biorep1


title: CaMK2a_Strd_IP_biorep3

description:
DIFFL-EXPN_edgeR__Lynn_Rb-HIP-mm_ka-6hr.vs.0hr_in.IP__3-CaMKII.IP_6hr_vs_3-CaMKII.IP_0hr__mm10.cd_f.ge.4__6598-DN
DIFFL-EXPN_edgeR__Lynn_Rb-HIP-mm_ka-6hr.vs.0hr_in.IP__3-CaMKII.IP_6hr_vs_3-CaMKII.IP_0hr__mm10.cd_f.ge.4__6786-UP

value: CaMK2a-Cre/+; LSL-Rpl22-HA/+


title: PV_KA_input_biorep3


title: CaMK2a_Strd_IP_biorep1


title: CaMK2a_Strd_input_biorep3

description:
DIFFL-EXPN_edgeR__Lynn_Rb-HIP-mm_ka-6hr.vs.0hr_in.IP__3-CaMKII.in_6hr_vs_3-CaMKII.in_0hr__mm10.cd_f.ge.4__6774-UP
DIFFL-EXPN_edgeR__Lynn_Rb-HIP-mm_ka-6hr.vs.0hr_in.IP__3-CaMKII.in_6hr_vs_3-CaMKII.in_0hr__mm10.cd_f.ge.4__6984-DN


title: CaMK2a_Strd_IP_biorep2


title: PV_KA_IP_biorep2


title: PV_Strd_input_biorep1


title: CaMK2a_Strd_input_biorep2


title: CaMK2a_Strd_input_biorep1


title: CaMK2a_KA_IP_biorep3


title: CaMK2a_KA_input_biorep1

description:
DIFFL-EXPN_edgeR__Lynn_Rb-HIP-mm_ka-6hr_IP-vs-in__3-CaMKII.6hr_IP_vs_3-CaMKII.6hr_in__mm10.cd_f.ge.4__6470-UP
DIFFL-EXPN_edgeR__Lynn_Rb-HIP-mm_ka-6hr_IP-vs-in__3-CaMKII.6hr_IP_vs_3-CaMKII.6hr_in__mm10.cd_f.ge.4__7157-DN


title: CaMK2a_KA_IP_biorep2


title: CaMK2a_KA_input_biorep2


title: TPC-1-shSHCBP1_rep3

city: Yiwu

first: Qiang

last: Sun

state: Zhejiang

address: No. N1, Shangcheng Avenue

institute: Zhejiang University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Gene Expression Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).

data_processing: The data were analyzed with Robust multi-array average (RMA) using a non-linear correction based upon a convolution model.

label: biotin

source_name: cells transfected with SHCBP1 shRNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (GeneChip Expression Analysis Technical Manual, Affymetrix).

growth_protocol: TPC-1 cells were maintained in RPMI1640.The media were supplemented with 10% fetal bovine serum in an incubator with 5% CO2 at 37°C.

extract_protocol: Total RNA from control and RNAi DLD1 was prepared with TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.

treatment_protocol: Cells were transfected with control-shRNA-expressing lentivirus or SHCBP1-shRNA-expressing lentivirus.

tag: cell line

value: transfected with SHCBP1 shRNA