title: PIT10_2nd_assay

value: Epimastigotes

value: PIT10 Second Assay


title: C57BL/6N mice,Control,C-1

status: Public on Apr 11 2023

type: SRA

city: Shijiazhuang

first: Zhimin

last: Wu

address: Zhongshan East Road

department: Department of phamarcy

country: China

institute: Hebei Medical University

library_source: transcriptomic

data_processing:
Raw data (or Raw reads) of fastq format were firstly processed through in-house perl scripts. Int his step, remove the adapter sequence and filter out low quality (low quality, the number of lines with astring quality value less than or equal to 25 accounts for more than 60% of the entire reading) and N (N means that the base information cannot be determined) ratio is greater than 5% reads to obtain clean reads that can be used for subsequent analysis.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software (http://daehwankimlab.github.io/hisat2/) to obtain mapped reads.
FeatureCounts (http://subread.sourceforge.net/) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Left ventricle

extract_protocol:
Total RNA was extracted from the heart tissue using TRIzol® Reagent according to the manufacturer’s instructions (Magen).
Paired-end libraries were prepared using an ABclonal mRNA-seq Lib Prep Kit (ABclonal, China) following the manufacturer’s instructions.

tag: tissue

value: Left ventricle

tag: Sex

value: male

tag: disease state

value: health

tag: treatment

value: Intraperitoneal injection of saline

tag: strain


title: COACHI_2nd_assay

type: genomic

city: São Paulo

first: José

middle: Franco

last: Da Silveira

state: São Paulo

address: Rua Botucatu, 862

department: Departamento de Microbiologia, Imunologia e Parasitologia

country: Brazil

institute: Universidade Federal de São Paulo

hyb_protocol: After assembling the chamber the Hybridization was performed into the oven rotator rack at 67 ºC, 20 rpm for 24 hours, according to the manufacturer's instructions.

scan_protocol: The Scanning of the microarray slides was performed in a Agilent G2565CA Microarray Scanning System following the manufacturer's steps described in Oligonucleotide Array-Based CGH for Genomic DNA Analysis - Enzymatic Labeling (Agilent).

data_processing:
Raw data was first normalized using Feature Extraction software (Agilent).
Agilent Genomic Workbench Standard Edition 6.5 was then used to perform CNV interval detection. The QC metrics motif of Workbench 6.5 ensured adequate quality control of the hybridization data. In our study, an array signal which met the requirements if intensity value >50 and signal-to-noise ratio >25 was included in the analysis. The Aberration Detection Method 2 algorithm was used with a threshold of 6 and bin size of 10 to identify genomic variation. Additionally, we applied a relatively stringent post-analysis filter (4 probes, 0.5 log ratio) to ignore small, spurious or low-quality
Logratio.xlsx: represents final processed data, contains the probes, gene name, genomic location, and log2 of (Cy5/Cy3)ratios.

molecule: genomic DNA

organism: Trypanosoma rangeli

source_name: Epimastigotes (test)

label_protocol: Fluorescent labeling of gDNA was performed with SureTag DNA Labeling kit (Agilent) following the manufacturer's instructions.

growth_protocol: Axenic cultures at 28 °C in liver-infusion tryptose medium (LIT) containing 10% fetal calf serum.

extract_protocol: Genomic DNA extraction was performed with the Dneasy Blood & Tissue kit (Qiagen) using 5x107 cells/mL according to the manufacturer's instructions.

value: Choachi

tag: Stage

tag: cell type

value: Axenic culture

tag: assay

value: Choachi Second Assay

organism: Trypanosoma cruzi

source_name: Epimastigotes (control)

value: CL brener

value: CLB Second Assay


title: CLB_2nd_assay


title: Wildtype-3

city: New York

first: Angad

last: Garg

state: New York

department: Molecular Biology

country: USA

institute: Memorial Sloan Kettering Cancer Center

description:
WT-3
GSM3767965

data_processing:
Base calls from Illumina NovaSeq 6000 or HiSeq 4000 (FASTQ files)
Each replicate processed separately
The FASTQ files were mapped to the S. pombe genome (current version, source: Pombase) using HISAT2_2.1.0
resulting SAM files were converted to BAM files using Samtools
Count files for individual replicates were generated with HTSeq-0.10.0 using exon annotations from Pombase (GFF annotations, genome-version ASM294v2; source ‘ensembl’)
Differential gene expression and fold change analysis was performed in DESeq2
Assembly: Schizosaccharomyces_pombe_all_chromosomes.fa (Reference sequence, ftp://ftp.pombase.org/pombe/genome_sequence_and_features/genome_sequence/Schizosaccharomyces_pombe_all_chromosomes.fa.gz)
Supplementary files format and content: Matrix file for raw HTSeq counts
Supplementary files format and content: DESeq output file

molecule: polyA RNA

organism: Schizosaccharomyces pombe

source_name: JS 77

growth_protocol: log phase cultures, 30ºC, YES medium

extract_protocol:
hot acid phenol RNA purification protocol
RNA-seq libraries were prepared from polyA+ RNA using the Illumina TruSeq stranded mRNA Kit according to the manufacturers protocol. Indexed libraries were normalized and pooled for paired-end sequencing performed using an Illumina NovaSeq 6000 or Illumina HiSeq 4000 instrument at the Weill Cornell Medical College Genome Core Facility (in New York).

value: JS 77

tag: growth phase

value: log phase growth

tag: growth medium

value: Yeast Extract Supplemented

tag: genotype

value: WT


title: WT_2_Cyto

city: Aurora

first: Kristen

last: Wells

state: CO

address: 1775 Aurora Ct,

department: Barbara Davis Center

institute: University of Colorado Anschutz

description: ZNT8 +/+ Rep 1 cytokine treated

data_processing:
Fastqc (version 0.11.7) was run on the raw fastq files to check quality
Cutadapt (version 1.16) was used to trim illumina sequencing adaptors from the raw fastq files. Cutadapt was run using the following parameters -m 20 -a 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'
STAR (version 2.5.2a) was used to align reads to the mouse GRCm38 genome post adaptor trimming. Star was run using the following parameters --outFilterMultimapNmax 10 --outFilterMismatchNmax 10 --outFilterMismatchNoverReadLmax 0.04 --tSAMmultNmax 1 --outMultimapperOrder Random --outSAMattrIHstart 0 --outSAMstrandField intronMotif
Reads were counted using featureCounts (version 1.6.2) from the subread package. FeatureCOunts was run with the following parameters --extraAttributes 'gene_name,gene_biotype' -s 1
rRNAs, snoRNAs, and snRNAs were filtered out of the count matrix and raw reads were loaded into the DESeq2 package (version 1.30.0). DESeq analysis was performed using the following design ~group + treatment + group:treatment to allow for interaction between the genotype and treatment.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab delimited text file of counts output by feature counts and tab delimited meta data file with sample information

source_name: Pancreatic islet

extract_protocol:
Islets were isolated from 17-week-old male mice (n=3) and digested by Cizyme RI (Vitacyte), followed by Lympholyte 1.1 (Cedarlane) gradient centrifugation. Islets were cultured in RPMI1640 media (10 % FBS, 1 % P/S) for overnight for stabilization. After stabilization, Islets were cultured RPMI 1640 or RPMI 1640 with cytokines (100 pg/ml TNF-alpha, 150 pg/ml IL-1beta, 10 pg/ml IFN-gamma) for 24 hours. After cytokine treatment, wash with PBS and extract RNA.
RNA was isolated with the RNeasy Micro kit (QIAGEN). Sequencing was performed using Illumina NovaSEQ6000.

value: Pancreatic islet

tag: age

value: 17 weeks

value: 100 pg/ml TNF-a, 150 pg/ml IL-1b, 10 pg/ml IFN-g, 24 hours


title: BAT, wildtype, ZT6, rep2

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

data_processing:
Reads were aligned using STAR v. 2.5.3a, against the GRCm38.p5 primary assembly and GENCODE Comprehensive gene annotations version 15 with the flags --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated set
Read summation onto genes was performed onto the same gene annotations as during mapping, by featureCounts v. 1.5.3 with the -p -B -C -t exon -g gene_id flags set
Quality was tested using fastqc v 0.11.5 and multiqc v 1.2
Assembly: GRCm38.p5
Supplementary files format and content: csv file with read counts for each sample

source_name: brown adipose tissue

extract_protocol:
Total RNA was extracted from tissues using TRI reagent (T9424, Sigma-Aldrich) and isolated using RNeasy Mini Kit (74106, Qiagen). From this, 500-1000 ng RNA was used for reverse transcription with the High Capacity cDNA Reverse Transcription kit (4368814, Applied Biosystems).
RNA sequencing libraries were prepared using the Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold protocol (Illumina)

value: NamptTM1Jtree line crossed with the Adiponectin-Cre mice (010803, Jackson Labs)

value: brown adipose tissue

value: wildtype

tag: timepoint

tag: replicate


title: Wildtype-2

description:
WT-2
GSM3767964


title: BAT, wildtype, ZT6, rep1

value: male


title: KO_4_Non

description: ZNT8 -/- Rep 3 not treated

growth_protocol: Islets were cultured in RPMI1640 media (10 % FBS, 1 % P/S) for overnight for stabilization.

treatment_protocol: 100 pg/ml TNF-a, 150 pg/ml IL-1b, 10 pg/ml IFN-g

value: islet cultured RPMI1640 media (no cytokines) 24 hours


title: Wildtype-1

description:
WT-1
GSM3767963


title: KO_3_Non

description: ZNT8 -/- Rep 2 not treated


title: BAT, wildtype, ZT22, rep4


title: CONORHINI_2nd_assay

organism: Trypanosoma conorhini

value: Epimastigotes

value: Cono Second Assay


title: R1625_1st_assay

value: Axenic culture

value: R1625 First Assay

value: CLB First Assay


title: WT_3_Cyto

description: ZNT8 +/+ Rep 2 cytokine treated


title: H14_1st_assay

value: H14 First Assay

value: CL brener


title: KO_2_Non

description: ZNT8 -/- Rep 1 not treated


title: SC_2nd_assay

value: SC58 Second Assay

value: CLB Second Assay


title: KO_4_Cyto

description: ZNT8 -/- Rep 3 cytokine treated

value: Pancreatic islet


title: BAT, wildtype, ZT22, rep3


title: BAT, wildtype, ZT22, rep2


title: BAT, wildtype, ZT22, rep1


title: KO_3_Cyto

description: ZNT8 -/- Rep 2 cytokine treated

value: 17 weeks


title: CONORHINI_1st_assay

value: Cono First Assay


title: KO_2_Cyto

description: ZNT8 -/- Rep 1 cytokine treated

value: 100 pg/ml TNF-a, 150 pg/ml IL-1b, 10 pg/ml IFN-g, 24 hours


title: COACHI_1st_assay

value: Choachi

value: Choachi First Assay


title: BAT, wildtype, ZT18, rep4

value: NamptTM1Jtree line crossed with the Adiponectin-Cre mice (010803, Jackson Labs)

value: brown adipose tissue

value: male

value: wildtype


title: BAT, wildtype, ZT18, rep3


title: SC_1st_assay

value: Epimastigotes

value: Axenic culture

value: SC58 First Assay


title: HE_4_Non

description: ZNT8 +/- Rep 3 not treated

value: islet cultured RPMI1640 media (no cytokines) 24 hours


title: HE_2_Non

description: ZNT8 +/- Rep 2 not treated


title: CLB_1st_assay

value: CL brener

value: CLB First Assay


title: BAT, wildtype, ZT18, rep2


title: WT_4_Non

description: ZNT8 +/+ Rep 3 not treated


title: PIT10_1st_assay

value: PIT10 First Assay


title: m6A IP sample

city: Coyoacan

first: V Miguel

last: Palomar

state: Mexico City

address: Circuito Exterior SN

department: Biochemistry

country: Mexico

institute: School of Chemistry, UNAM

description:
MeRIP_IP
We used the m6A antibody (D9D9W, cat #56593) from Abcam (Cambridge, UK).

data_processing:
Reads were adapter-trimmed with Trim-galore.
Mapping against the P. patens reference genome was done with Bowtie2.
Reads were PCR de-duplicated with PICARD tools.
Peak calling was performed using MACS2.
Assembly: Physcomitrium patens 318 v3
Supplementary files format and content: merip_peaks_narrowPeak.bed includes peaks.
Library strategy: MeRIP-seq

organism: Physcomitrium patens

source_name: protonema 18 d

growth_protocol: Protoplasts were grown in PRMB for 4 d, and them moved to PPNH4 medium for 8 d.

extract_protocol:
For meRIP-seq analysis, polyA+ RNA was extracted with Dynabeads mRNA direct purification kit (Thermo Fisher Scientific).
RNA libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina) following manufacturer's protocols.

treatment_protocol: NAA 1uM, 5 d; kinetin 1 uM, 1d.

value: protonema 18 d

value: Grandsen

value: Protoplast

value: WT

value: NAA 1uM, 5 d; kinetin 1 uM, 1d.

tag: antibody


title: BAT, wildtype, ZT18, rep1


title: HE_1_Non

description: ZNT8 +/- Rep 1 not treated

value: Pancreatic islet

value: 17 weeks


title: m6A input


title: HE_2_Cyto

description: ZNT8 +/- Rep 2 cytokine treated

value: 100 pg/ml TNF-a, 150 pg/ml IL-1b, 10 pg/ml IFN-g, 24 hours


title: HE_1_Cyto

description: ZNT8 +/- Rep 1 cytokine treated


title: BAT, wildtype, ZT10, rep2

value: NamptTM1Jtree line crossed with the Adiponectin-Cre mice (010803, Jackson Labs)

value: brown adipose tissue

value: male


title: BAT, wildtype, ZT10, rep4

value: wildtype


title: C23_1st_assay

value: Epimastigotes

value: Axenic culture

value: C23 First Assay


title: PA14_ctrl_3

city: Hanover

first: Thomas

middle: H.

last: Hampton

state: NH

address: Dewey Field Road, HB 7550

department: Microbiology and Immunology

institute: Geisel School of Medicine at Dartmouth

data_processing:
Raw reads were trimmed using CLC Genomics Workbench software (Qiagen).
Trimmed reads were aligned to the Pseudomonas earuginosa PA14 reference genome using CLC Genomics Workbench.
Assembly: UCBPP-PA14 NC_008463
Supplementary files format and content: csv file with counts for reads that aligned with the PA14 reference

organism: Pseudomonas aeruginosa

source_name: Pseudomonas aeruginosa

growth_protocol: P. aeruginosa strain PA14 were grown in Luria broth. Primary human airway epithelial cells from 3 donors were obtained from Dr. Scott Randell (University of North Carolina, Chapel Hill, NC) and cultured in BronchiaLife basal medium (Lifeline Cell Technology, Frederick, MD, Cat. # LM-0007) supplemented with the BronchiaLife B/T LifeFactors Kit (Lifeline Cell Technology, Cat. # LS-1047) as well as 10,000 U/ml Penicillin and 10,000 μg/ml Streptomycin (Sigma-Aldrich, Cat. # P4333). EVs were purified from cell culture supernatants (passages 4-8) using the ExoQuick-TC EV isolation kit (System Biosciences, Palo Alto, CA, Cat. # EXOTC50A-1).

extract_protocol:
Total RNA was isolated with the miRNeasy Mini Kit (Qiagen, Germantown, MD, Cat. # 217004), including the on-column DNA digestion. RNA was ribosome-depleted prior to library prep.
Sequencing libraries were prepared with an Illumina Stranded mRNA Prep kit (Illumina).
150-bp single-end reads were generated using an Illumina MiniSeq.

treatment_protocol: P. aeruginosa (1.5E+07 CFU) were exposed to PBS vehicle control or EVs (5E+09 EV/ml) for 6 h. To avoid possible carry-over of EVs (and miRNA) attached to the outside of the bacteria, the bacteria were washed with PBS and the bacterial outer membrane was lysed with EDTA to release periplasmic contents and factors associated with the bacterial outer membrane and periplasm (77-79). The cells were then washed again in PBS, and cytoplasmic RNA was harvested after lysis of bacterial cell wall and inner membrane.

value: PBS vehicle control

value: bacterial cell


title: PA14_ctrl_2


title: BAT, wildtype, ZT10, rep1


title: BAT, wildtype, ZT10, rep3


title: PA14_ctrl_1


title: embryo, replication2, scRNAseq

city: Shanghai

first: zixin

last: liu

address: 320 Yueyang road, Life Science Research Building A2112

institute: Center for Excellence in Molecular Cell Science

description:
10x Genomics
JHW3

library_source: transcriptomic single cell

data_processing:
The Cell Ranger pipeline version 6.1.1 (10x Genomics Inc.) was used for each scRNA-seq data set to perform the alignment against the mouse reference genome mm10, filter the alignment and count barcodes and UMIs.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: caudal tissues

extract_protocol:
Specific tissues of E8.5 embryos were pooled together in a low DNA bind Eppendorf tube and dissociated into single cell in 200μl TrypLE Express (Thermo Fisher Scientific, 12604013) for 15 mins at 37°C with agitation every 5 mins. 1ml 1xPBS + 0.4%BSA was added into the digestive buffer to quench the reaction. Then cells were centrifuged at 1200rpm for 5 mins and resuspended in 30μl PBS.
Single-cell RNA-seq libraries were prepared using 10× Genomics Chromium Single Cell 5′ Reagent Kits according to the manufacturer’s instructions. Brieﬂy, dissociated cells were resuspended to a ﬁnal cell concentration of ~1500 cells/μL with more than 85% viability as determined by Trypan Blue Solution (Thermo Fisher Scientific, 15250061). Cells were subjected to single-cell RNA sequencing aiming for a target cell recovery of up to 20,000 sequenced cells per sequencing library. After the reverse transcription step, emulsions were broken and barcoded-cDNA was puriﬁed with Dynabeads, followed by PCR ampliﬁcation. Ampliﬁed cDNA was then used for 5′ gene expression library construction.

value: caudal tissues

value: endoderm, mesoderm, ectoderm

value: wild type


title: smartseq2_Mature_Hand_161514

status: Public on Apr 10 2023

city: Vienna

first: Jingkui

last: Wang

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology (IMP)

description: RNA- expression for Differential Gene expression analysis regrading mature arm vs hand as different limb positions (intact Hand CT cells).

data_processing:
Smart-seq2 processing pipeline was adapted for axolotl genome from nf-core/rnaseq.
The raw reads were trimmed with trim_galore (v0.6.2) and mapped to axolotl genome (AmexG_v6,  Schloissnig et al., 2021) using hisat2 (v2.1.0).
Read counts at gene levels were quantified by featureCounts in subread (v2.0.1).
To identify segment-specific genes in mature samples, the read counts were normalized and pairwise comparisons were done with DESeq2 (v1.26.0)
Bigwig files were made with deeptools (v3.1.2)
Assembly: AmexG_6
Supplementary files format and content: bigwigs and genomic tracks

organism: Ambystoma mexicanum

source_name: Connective tissue cells

extract_protocol:
RNA was harvested using a total RNA isolation kit (in-house kit provided by Molecular Biology Services in Vienna BioCenter). Sequencing libraries were prepared by VBC NGS-Facility.
Smart-seq version 2

value: Connective tissue cells


title: smartseq2_Mature_UA_161512

description: RNA- expression for Differential Gene expression analysis regrading mature arm vs hand as different limb positions (intact Upper arm CT cells).


title: smartseq2_Mature_UA_161516


title: atac_Embryo_Stage44_distal_93321

description: To find ACRs in the developmental limb buds, the distal part of limb buds (stage 46/47) were isolated and used for ATAC-seq library preparation with in-house Tn5.

library_source: genomic

data_processing:
The pair-ended ATAC-seq reads were trimmed with cutadapt (v1.18) and aligned to axolotl genome (AmexG_v6) with bowtie2 (v2.3.5.1).
Multimappers and duplicated reads in the aligned bam files were discarded respectively with samtools (v1.10) and picard (v2.20.6). ATAC-seq narrow peaks were called by macs2 (v2.2.5) with default parameters.
The processing workflow was wrapped with nextflow. For the purpose of reproducibility, peaks were retained only if they were called in at least two biological replicates with p-value < 10^-6;
they were merged into a list of peak consensuses for all samples. Read counts were quantified within those peaks with feature counts from subread (v2.0.1).
After low-signal peaks were filtered with less than 50 read counts, the read counts within peaks across all samples were normalized using the scaling factors from DESeq2 (v1.26.0). These scaling factors were also used to make bigwig files with deeptools (v3.1.2) for the data visualization.
Assembly: AmexG_6
Supplementary files format and content: bigwigs and genomic tracks

source_name: Limb buds only distal part

extract_protocol:
The sample was performed from 20,000 cells isolated from transgenic animals. Limb connective tissue cells were used for FACS, and then used for library preparation immediately.
We performed ACR profiling analysis using data obtained from ATAC-seq libraries of developmental limb buds (stage 40/41, stage 46 proximal and distal parts), and mature limb at different segments (mature UA vs LA vs hand). Therefore, we also performed libraries from the mature arm and 5, 9, 13 dpa (13 dpa blastema data have two different positions like proximal and distal parts) regenerating arm blastema.

value: Limb buds only distal part

value: d/d strain

value: Cells were isolated and collected. OMNI-ATAC-seq protocol with in-house Tn5 was used for processing the tagmentation.


title: atac_Embryo_Stage44_proximal_93320

description: To find ACRs in the developmental limb buds, the proximal part of limb buds (stage 46/47) were isolated and used for ATAC-seq library preparation with in-house Tn5.

source_name: Limb buds only proximal part

value: Limb buds only proximal part


title: smartseq2_Mature_Hand_161517


title: atac_Embryo_Stage44_distal_93323


title: embryo,replication1, scRNAseq

description:
10x Genomics
JHW1


title: atac_Embryo_Stage40_93324

description: To find ACRs in the developmental limb buds, whole limb buds (stage 40/41) were isolated and used for ATAC-seq library preparation with in-house Tn5.

source_name: Whole limb buds

value: Whole limb buds


title: HE_4_Cyto

description: ZNT8 +/- Rep 3 cytokine treated

value: Pancreatic islet

value: 17 weeks

value: 100 pg/ml TNF-a, 150 pg/ml IL-1b, 10 pg/ml IFN-g, 24 hours


title: atac_Embryo_Stage40_93325


title: atac_BL_UA_5days_89543

description: To find ACRs in arm regenerating blastema cells (5 dpa blastema cells), ATAC-seq libray with FACSed Cherry positive cells was prepared with in-house Tn5.

source_name: UA 5 dpa BL

value: UA 5 dpa BL

value: Cells were isolated and FACSorted. OMNI-ATAC-seq protocol with in-house Tn5 was used for processing the tagmentation.


title: atac_BL_UA_5days_89542


title: atac_Mature_UA_102655

description: To find ACRs in mature limb cells, ATAC-seq library with FACSed Cherry positive cells was prepared with in-house Tn5.

source_name: Mature UA

value: Mature UA


title: atac_Mature_Hand_74940

source_name: Mature Hand

value: Mature Hand


title: atac_Mature_LA_102657

source_name: Mature LA

value: Mature LA


title: atac_Mature_Hand_102659


title: atac_Mature_LA_74939


title: Control microglia, biol rep 1

city: Boston

first: Zhuoran

last: Yin

state: Massachusetts

address: 60 Fenwood Road

department: Neurology

institute: Brigham and Women's Hospital

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v.4.0.0 (1st sequencing run) and v6.0.1 (2nd sequencing run) (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: Brain

extract_protocol:
The left hemisphere of the mouse brain was homogenized to form a single cell suspension, then resuspended and centrifuged in a 37%/70% Percoll Plus gradient at 800G, 23˚C, for 25 min with an acceleration of 3 and a deceleration of 1. Mononuclear cells were taken from the interface layer. The cells were stained with anti-CD11b PECy7 and CD45 PerCP. After staining cells were washed and sorted using BD FACSAriaTM II.
GEMs were generated according to the manufacturer’s protocol by combining barcoded Single Cell 3’ v3.1 Gel Beads, a Master Mix containing cells, and Partitioning Oil onto Chromium Next GEM Chip G (10X Genomics, USA) with targeted capture of 5000 cells per sample. Reverse transcription immediately followed GEM generation, producing barcoded, full-length cDNA from poly-adenylated mRNA. After incubation, GEMs were broken and pooled fractions of cDNA were recovered. Barcoded, full-length cDNA was amplified via PCR to generate sufficient mass for library construction.

value: Brain

value: Myeloid cells

value: Female

value: 4 months old


title: atac_Mature_UA_74938

value: Connective tissue cells


title: Deletion of miR-155 in microglia, biol rep 2

description: 10x Genomics

value: APP/PS1:miR-155 cKO


title: Control microglia, biol rep 2

description: 10x Genomics


title: Deletion of miR-155 in microglia, biol rep 1

description: 10x Genomics


title: atac_Embryo_Stage44_proximal_93322

value: d/d strain

value: Cells were isolated and collected. OMNI-ATAC-seq protocol with in-house Tn5 was used for processing the tagmentation.


title: Vero_KDM6A_KO_2

city: New Haven

first: Qin

last: Yan

email: qin.yan@yale.edu, craig.wilen@yale.edu

address: 310 Cedar St.

department: Pathology

institute: Yale University

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were trimmed of adapters using Trimmomatic v0.32
Trimmed reads were aligned to reference genome chlSab2, NCBI annotation release 100 using STAR aligner v2.7.3a with parameters –winAnchorMultimapNmax 200 –outFilterMultimapNmax 100 –quantMode GeneCounts
DEseq2 was used to determine differential gene expression using counts.
Assembly: chlSab2
Supplementary files format and content: tab (raw counts)

organism: Chlorocebus sabaeus

source_name: Vero-E6 cell line

growth_protocol: All Vero-E6 cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) with 10% heat-inactivated fetal bovine serum (FBS), and 1% Penicillin/Streptomycin

extract_protocol:
Samples were performed in biological duplicate and harvested by scraping. Total cellular RNA was extracted using the Direct-zol RNA MiniPrep Plus (Zymo Research)
Libraries were prepared using TruSeq stranded mRNA library prep kit (Illumina)

tag: cell line

value: Epithelial cell

value: KDM6A KO


title: Vero_KDM6A_KO_1


title: Vero_Ctrl_1

value: control


title: SK-N-DZ, lane 2, targeted gRNA library

city: Heidelberg

first: Umut

last: Yildiz

address: Meyerhofstraße 1

country: Germany

institute: European Molecular Biology Laboratory

description:
10x Genomics - gRNA enrichment library. Read1 contains cell barcode and UMI. Read2 contains gRNA sequence
lane2_gRNA

data_processing:
Single-cell reads were mapped to the GRCh 38 reference genome. Count matrices were generated using Cell Ranger (10X Genomoics, version 6.0.1). Single-cell sequencing data from the two lanes were combined using the aggregation function (cellranger aggr). Data normalization and downstream analysis were performed via Seurat (R package, version 4.0.1). Briefly, the count matrix was filtered for genes that were detected in at least 10 cells. UMI counts for each gene were divided by the total number of counts and multiplied by 10,000 and log-transformed. Guide RNA libraries were processed via fba. Briefly, cell barcode - gRNA assignments were made based on mapping the reads to the custom gRNA library and the whitelist of 10X barcode sequences thereby allowing two mismatches.
Assembly: GRCh 38
Supplementary files format and content: Comma-separated, tab-separated values files and matrix files
Library strategy: CROP-seq

organism: Homo sapiens

growth_protocol: Cells were maintained in DMEM (Gibco) with 10% FCS (Gibco), 1X HEPES (Gibco) and 100 U/ml penicillin/streptomycin at 37° C and 5 % CO2.

extract_protocol:
Ten days after transduction, puromycin-selected cells were washed twice with PBS and dissociated with accutase (37° C, 5 min). Cells were collected in PBS + 0.04 % BSA, counted and diluted to 10^6 cells/ml
Single-cell libraries were constructed following the manufacter’s instructions (10x Genomics, Single Cell Gene Expression v3.1 protocol). Briefly, 20,000 SK-N-DZ cells per lane were resuspended in the master mix and loaded alongside the gel beads and the partitioning oil into the chip (G) to generate the GEMs. Polyadenylated mRNA in every single GEM was reverse-transcribed to cDNA with a oligo(dT) primer, that contains the illumina TruSeq Read 1 primer sequence, the 10x Barcode and Unique Molecular Identifiers (UMIs). The barcoded cDNA was pooled and cleaned up with Silane DynaBeads. Full-legnth cDNA was amplified by PCR. AFter enzymatic fragmentation, end repair, A-tailing and ligation, the apropiated sized fragments were selected with SPRIselect beads for subsequent library construction. During the final library construction, the Illumina TruSeq Read 2 primer sequence was introduced alongside a sample index (four per lane). Forty nanogram of full-length cDNA was used as input for the construction of gRNA enrichment libraries following a previously published hemi-nested PCR strategy (Hill et al., 2018)

value: Neuroblastoma

value: SK-N-DZ

value: 2 years


title: CS3-N

city: Greenville

first: Weihua

last: Huang

state: North Carolina

address: 600 Moye Blvd, Brody 7S-24

institute: East Carolina University

description: depletion of human rRNA

data_processing:
bcl2fastq v2.20 was used for base-calling.
Kallisto pseudo-alignment to human Ensembl GRCh38 (v.87) transcriptome was used with 100 bootstraps for abundance measurement.
HISAT2 aligner was used for alignment to human UCSC hg19 genome, followed by SAMtools mpileup for variant calling.
Genome_build: human Ensembl GRCh38 (v.87) transcriptome; human UCSC hg19 genome
Supplementary_files_format_and_content: A csv file include TPM values for each sample

source_name: Heart

extract_protocol:
After removing the top 2-3 sections, the following ~5-10 sections were subjected to RNA extraction using Qiagen RNeasy FFPE kit.
After depletion of human rRNA with Illumina RiboZero Gold kit, RNA-seq libraries were prepared with Illumina TruSeq Stranded Total RNA Library Prep kit.

tag: condition

tag: specimen

value: FFPE


title: C4

description: depletion of human rRNA

value: lesion


title: CS1-L

description: depletion of human rRNA


title: C3

description: depletion of human rRNA


title: C1

description: depletion of human rRNA


title: C2

description: depletion of human rRNA


title: CS2-N

description: depletion of human rRNA


title: CS3-L

description: depletion of human rRNA


title: CS2-L

description: depletion of human rRNA


title: G1E CTCF [2628]

city: University Park

first: Ross

last: Hardison

state: PA

address: 303 Wartik Lab

institute: Pennsylvania State University

data_processing:
Basecalls using bcl2fastq-1.8.4, and parameters --no-eamss --mismatches 1
Mapping to reference genome mm10 canon with Bowtie 1.0.0 using parameters --chunkmbs 1024 -y -n 2  --best -k 1 --maxbts 800 -l 28 -e 80 --sam-nohead --sam
Wiggle and peaks called using MACS with parameters --format BAM --gsize 1870000000 --tsize 36 --bw 120 --mfold 12 --wig --space 1
Filter blacklist regions from peaks, and convert the *peaks.xls file from MACs to broadpeak format (see UCSC Genome Browser for format specs)
Assembly: mm10
Supplementary files format and content: bigWigs, signal from MACS

source_name: cell line

growth_protocol: G1E and G1E-ER4 cells were grown in IMDM media + 15% FBS, kit ligand, and erythropoietin in a standard tissue culture incubator at 37°C with 5% CO2.

extract_protocol:
Lysates were prepared from sonicated nuclei and protein-DNA complexes were isolated with antibody.
ChIP-seq samples were prepared by end repair, 3’ adenylation, and adaptor ligation using Illumina’s TruSeq ChIP-seq Sample Preparation Kit.

tag: chip antibody

value: CTCF


title: G1E input [1924]


title: G1E-ER4+E2 CTCF [1775]

value: To induce erythroid maturation, G1E-ER4 cells were treated with 10-8 mol/L β-estradiol for 24 hours (G1E-ER4+E2).


title: G1E-ER4+E2 CTCF [1776]


title: G1E-ER4+E2 input [1774]


title: Vero_Ctrl_2


title: Vehicle, biological replicate 1, scRNAseq

city: MEMPHIS

first: Richard

last: Chapple

state: Tennessee

address: 262 Danny Thomas Pl

institute: St Jude Children's Hospital

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Neuroblastoma tumor

extract_protocol:
Single cell suspensions of neuroblastoma cells were generated according to the manufacturer's instructions (Worthington Papain Dissociation System, CAS: 9035-81-1).  Breifly, minced neuroblastoma tissue is dissociated by incubation with activated papain at 37oC followed by trituration.  Papain dissociation is then halted with ovomucoid.  A single step discontinuous density gradient separates intact cells from cell membranes, and then the pelleted cells are resuspended for sequencing with 10X Genomics kits.
Library was performed according to the manufacter’s instructions (10x Genomics). Single cell suspensions of neuroblastoma cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

tag: tissue

value: Neuroblastoma tumor

value: adrenal neuroblastoma

value: Dbh-iCre;LSL-MYCN

value: DMSO


title: H3K4me1 iMK [1905]

data_processing:
Basecalls using bcl2fastq-1.8.4, and parameters --no-eamss --mismatches 1
Mapping to reference genome mm10 canon with Bowtie 1.0.0 using parameters --chunkmbs 1024 -y -n 2  --best -k 1 --maxbts 800 -l 28 -e 80 --sam-nohead --sam
Wiggle generated with MACS using parameters --nomodel --shiftsize=120--format BAM --gsize 2615371906 --tsize 36 --bw 120 --mfold 12 --wig --space 1
peaks were called with Sicer V1.1 using parameters mm10 1 200 150 0.74 600 0.01
Filter blacklist regions from peaks, and convert to broadpeak format (see UCSC Genome Browser for format specs)
Assembly: mm10
Supplementary files format and content: bigWig signal from MACS

source_name: bone marrow

value: bone marrow

value: bone marrow derived progenitor cells, specifically Immature megakaryocytes, abbreviated iMK

tag: target

tag: facs cell isolation sort markers


title: H3K27me3 iMK [1913]


title: H3K4me1 ERY adult [1911]

value: bone marrow derived erythroblasts, abbreviated ERY, adult


title: H3K4me1 iMK [1912]


title: Sample 11_Control_Phag

data_processing:
Samples were processed according to Smart-Seq2 protocol and sequenced on Illumina sequencers.
Reads in FASTQ were quantified at the transcript level using Salmon (v1.4) against the M. musculus Ensembl gene catalog (May 2020).
Differential expression analysis was conducted using R (v4.1.1) and DESeq2 (v1.34.0). Hypothesis testing was performed by using either DESeq2’s Wald test on appropriate variable contrasts or with a Likelihood Ratio Test (LRT) for models with greater than two variable conditions being tested.
Assembly: mm10
Supplementary files format and content: tar file of salmon outputs including plaint text  quantification file (quant.sf), transcripts used for quantification, parameter settings, version of Salmon, and estimated bias parameters

source_name: Microglia cells

extract_protocol:
Isolated Dead neuron+Ly6C–CD11b+Fcrls+ and Dead neuron-Ly6C–CD11b+Fcrls+ microglia were lysed in 5 ul TCL buffer +1% beta-mercaptoethanol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Microglia cells

value: Control

tag: treatment

value: Phag

tag: Sex

value: m


title: H3K27me3 iMK [1907]

tag: cell type


title: Sample 10_Control_Non_Phag


title: SK-N-DZ, lane 1, targeted gRNA library

description:
10x Genomics - gRNA enrichment library. Read1 contains cell barcode and UMI. Read2 contains gRNA sequence
lane1_gRNA

value: Neuroblastoma

value: Brain

tag: strain

value: SK-N-DZ


title: Sample 9_Control_Phag


title: Sample 8_Control_Non_Phag


title: H3K9me3 iMK [1906]


title: Sample 7_Control_Phag


title: CS1-N

description: depletion of human rRNA

value: control

value: FFPE


title: Sample 12_Control_Non_Phag


title: Sample 6_IfnKO_Non_Phag

value: IfnKO


title: Sample 3_IfnKO_Phag


title: Sample 2_IfnKO_Non_Phag


title: Sample 1_IfnKO_Phag


title: Sample 5_IfnKO_Phag


title: Sample 4_IfnKO_Non_Phag


title: APP/PS1-miR155cKO, replicate 3, scRNAseq

description: 10x Genomics

data_processing:
The gene counting and aggregation were made using the Cell Ranger software v7.0.0 combining all fastq files per sample together (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Barcodes, features and matrix file were imported into R using Seurat (v4.0.0)
Cells with more than 1000 reads used on only genes present in more than 3 cells.
Batch correction and dublets removed.
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
The left hemisphere of the mouse brain was homogenized to form a single cell suspension, then resuspended and centrifuged in a 37%/70% Percoll Plus gradient at 800G, 23˚C, for 25 min with an acceleration of 3 and a deceleration of 1. Mononuclear cells were taken from the interface layer. The cells were stained with anti-CD11b PECy7 and CD45 PerCP. After staining cells were washed and sorted using BD FACSAriaTM II.
Single cell RNA-Seq libraries was generated by the Single Cell Core at Harvard Medical School, Boston, according to the manufracturer's protocol of 10X Chromium Next GEM Single Cell 3' Reagent Kits v3.1

value: Micorglia cells

value: male

tag: batch


title: APP/PS1-miR155cKO, replicate 2, scRNAseq

description: 10x Genomics


title: APP/PS1, replicate 2, scRNAseq

description: 10x Genomics


title: APP/PS1, replicate 3, scRNAseq

description: 10x Genomics


title: APP/PS1-miR155cKO, replicate 1, scRNAseq

description: 10x Genomics


title: Sample 27_Non_phag_WT_IgG

tag: genotype

value: WT

value: IgG

tag: time


title: APP/PS1, replicate 1, scRNAseq

description: 10x Genomics

tag: age


title: Sample 26_Non_phag_WT_IgG


title: Sample 25_Non_phag_WT_IgG


title: Sample 24_Non_phag_WT_IgG


title: Sample 22_Non_phag_miR155cKO_IgG


title: Sample 23_Non_phag_miR155cKO_Blocker

value: Blocker


title: Sample 20_Non_phag_miR155cKO_IgG


title: Sample 21_Non_phag_miR155cKO_Blocker


title: Sample 19_Non_phag_miR155cKO_IgG


title: Sample 17_Non_phag_miR155cKO_IgG


title: Sample 16_Non_phag_miR155cKO_Blocker


title: Sample 18_Non_phag_miR155cKO_Blocker


title: Sample 14_Phagocytic_WT_IgG

source_name: Phagocytic

value: Phagocytic


title: Sample 15_Phagocytic_WT_IgG


title: Sample 13_Phagocytic_WT_IgG


title: Sample 12_Phagocytic_WT_IgG


title: Sample 10_Phagocytic_WT_IgG


title: Sample 7_Phagocytic_miR155cKO_Blocker


title: Sample 8_Phagocytic_miR155cKO_IgG


title: Sample 11_Phagocytic_WT_IgG


title: Sample 6_Phagocytic_miR155cKO_IgG


title: Sample 5_Phagocytic_miR155cKO_IgG


title: Sample 3_Phagocytic_miR155cKO_IgG


title: Sample 2_Phagocytic_miR155cKO_Blocker


title: Sample 4_Phagocytic_miR155cKO_Blocker


title: Differential gene expression in WT and AMPK deficient CD4 T cell [AKO1]

city: Gyeongsan

first: Jae

middle: Hoon

last: Chang

state: Gyeongsangbuk

address: 280, Daehak-ro

department: Pharmacy

country: South Korea

institute: Yeungnam University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: Spleen and Lymph nodes

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: CD4 T cell were isolated from the mouse spleen and lymph nodes and keep on resting for 1 hour in RPMI-1640 and followed by  cultured in vitro along with anti-CD3/CD28 antibody for 24 hours.

value: Spleen and Lymph nodes

value: CD4 T cell

value: Lymphocytes

value: anti-CD3/CD28 antibody


title: Differential gene expression in WT and AMPK deficient CD4 T cell [AKO2]


title: Differential gene expression in WT and AMPK deficient CD4 T cell [AKO3]


title: Differential gene expression in WT and AMPK deficient CD4 T cell [WT3]


title: Differential gene expression in WT and AMPK deficient CD4 T cell [WT1]


title: Differential gene expression in WT and AMPK deficient CD4 T cell [WT2]


title: RNA-sequencing of the CD4 T cell culture under the various conditioned media [DM+Met_DM]

source_name: Spleen and Lymph node

growth_protocol: CD4 T cell were isolated from the mouse spleen and lymph nodes and cultured in vitro along with anti-CD3/CD28 antibody

treatment_protocol: All the samples were cultured with anti-CD3/CD28 antibody. DM + Met samples were treated with 30 µM methionine.

value: Spleen and Lymph node

value: anti-CD3/CD28 antibody + Methionine


title: RNA-sequencing of the CD4 T cell culture under the various conditioned media [CD4_CM]


title: microglia, WT:miR-155 cKO, Male, 8 months old, H11

data_processing:
Samples were processed according to Smart-Seq2 protocol and sequenced on Illumina sequencers.
Reads in FASTQ were quantified at the transcript level using Salmon (v1.4) against the M. musculus Ensembl gene catalog (May 2020).
Differential expression analysis was conducted using R (v4.1.1) and DESeq2 (v1.34.0). Hypothesis testing was performed by using either DESeq2’s Wald test on appropriate variable contrasts or with a Likelihood Ratio Test (LRT) for models with greater than two variable conditions being tested.
Adjusted p-values were determined using the Benjamini-Hochberg procedure and significance cutoffs were set at 0.05.
Assembly: mm10
Supplementary files format and content: tar file of salmon outputs including plaint text  quantification file (quant.sf), transcripts used for quantification, parameter settings, version of Salmon, and estimated bias parameters

source_name: brain

extract_protocol:
1,000 isolated Ly6C–CD11b+Fcrls+ microglia were lysed in 5 ul TCL buffer +1% beta-mercaptoethanol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: brain

value: microglia

value: WT:miR-155 cKO

value: Male

value: 8 months old

tag: biological replicate

value: biol rep 16


title: microglia, WT:miR-155 cKO, Male, 8 months old, H12


title: microglia, WT:miR-155 cKO, Male, 8 months old, H09


title: microglia, WT:miR-155 cKO, Male, 8 months old, H10


title: microglia, WT:miR-155 cKO, Male, 8 months old, H07


title: microglia, WT:miR-155 cKO, Female, 8 months old, H06

value: Female

value: biol rep 15


title: microglia, WT:miR-155 cKO, Male, 8 months old, H08


title: Sample 9_Phagocytic_miR155cKO_IgG

value: Microglia cells

value: IgG


title: microglia, WT:miR-155 cKO, Female, 8 months old, H02


title: microglia, WT:miR-155 cKO, Female, 8 months old, H05


title: microglia, WT, Male, 8 months old, G01

value: WT

value: biol rep 14


title: Sample 1_Phagocytic_miR155cKO_Blocker

value: Phagocytic

value: Blocker


title: microglia, WT, Male, 8 months old, F08


title: microglia, WT, Male, 8 months old, F11


title: microglia, WT, Male, 8 months old, F09


title: microglia, WT, Male, 8 months old, F10


title: microglia, WT, Male, 8 months old, F12


title: microglia, WT, Female, 8 months old, F07

value: biol rep 13


title: RNA-sequencing of the CD4 T cell culture under the various conditioned media [CD4_DM]

value: Spleen and Lymph node

value: CD4 T cell

value: Lymphocytes

value: anti-CD3/CD28 antibody


title: microglia, WT, Female, 8 months old, F05

value: brain

value: microglia


title: microglia, WT, Female, 8 months old, F06

value: 8 months old


title: microglia, WT, Female, 8 months old, F04


title: microglia, WT, Female, 8 months old, F03


title: microglia, WT:miR-155 cKO, Male, 4 months old, D12

value: WT:miR-155 cKO

value: Male

value: 4 months old

value: biol rep 12


title: microglia, WT:miR-155 cKO, Female, 8 months old, H03

value: Female

value: biol rep 15


title: microglia, WT:miR-155 cKO, Male, 4 months old, D11


title: microglia, WT:miR-155 cKO, Male, 4 months old, D09


title: microglia, WT:miR-155 cKO, Male, 4 months old, D08


title: microglia, WT:miR-155 cKO, Male, 4 months old, D10


title: microglia, WT:miR-155 cKO, Female, 4 months old, D05

value: biol rep 11


title: microglia, WT:miR-155 cKO, Female, 4 months old, D02


title: microglia, WT:miR-155 cKO, Female, 8 months old, H04


title: microglia, WT:miR-155 cKO, Female, 4 months old, D04


title: microglia, WT, Male, 4 months old, B12

value: WT

value: biol rep 10


title: microglia, WT, Male, 4 months old, B11


title: microglia, WT:miR-155 cKO, Female, 4 months old, D06


title: microglia, WT:miR-155 cKO, Female, 4 months old, D01


title: microglia, WT, Male, 4 months old, B10


title: microglia, WT, Female, 8 months old, F02

value: biol rep 13


title: microglia, WT, Female, 4 months old, B06

value: biol rep 9


title: microglia, WT, Male, 4 months old, B09


title: microglia, WT, Female, 4 months old, B01


title: microglia, APP/PS1, Male, 8 months old, G11

value: biol rep 8


title: microglia, APP/PS1, Male, 8 months old, G12


title: microglia, WT, Female, 4 months old, B02


title: microglia, WT, Female, 4 months old, B03


title: microglia, APP/PS1, Male, 8 months old, G09


title: microglia, WT, Female, 4 months old, B05


title: microglia, WT, Male, 4 months old, B07


title: microglia, APP/PS1, Male, 8 months old, G10


title: microglia, WT:miR-155 cKO, Male, 4 months old, D07


title: microglia, WT:miR-155 cKO, Female, 4 months old, D03


title: microglia, WT, Female, 4 months old, B04


title: microglia, APP/PS1, Female, 8 months old, G03

value: biol rep 7


title: microglia, APP/PS1, Male, 8 months old, G08


title: microglia, APP/PS1, Female, 8 months old, G07


title: microglia, APP/PS1, Female, 8 months old, G06


title: microglia, APP/PS1, Female, 8 months old, G05


title: microglia, APP/PS1, Female, 8 months old, G02


title: microglia, APP/PS1:miR-155 cKO, Male, 8 months old, E12

value: APP/PS1:miR-155 cKO

value: biol rep 6


title: microglia, APP/PS1:miR-155 cKO, Male, 8 months old, F01

value: brain

value: microglia


title: microglia, APP/PS1:miR-155 cKO, Male, 8 months old, E11

value: 8 months old


title: microglia, APP/PS1:miR-155 cKO, Male, 8 months old, E10

value: Male


title: microglia, APP/PS1:miR-155 cKO, Male, 8 months old, E08


title: microglia, APP/PS1:miR-155 cKO, Male, 8 months old, E09


title: microglia, APP/PS1:miR-155 cKO, Female, 8 months old, E07

value: biol rep 5


title: microglia, WT, Male, 4 months old, B08

value: 4 months old


title: microglia, APP/PS1:miR-155 cKO, Female, 8 months old, E06

value: Female


title: microglia, APP/PS1:miR-155 cKO, Female, 8 months old, E05


title: microglia, APP/PS1:miR-155 cKO, Female, 8 months old, E04


title: microglia, APP/PS1:miR-155 cKO, Female, 8 months old, E01


title: microglia, APP/PS1, Male, 4 months old, C10

value: biol rep 4


title: microglia, APP/PS1, Male, 4 months old, C11


title: microglia, APP/PS1, Female, 4 months old, C06

value: biol rep 3


title: microglia, APP/PS1, Female, 4 months old, C05


title: microglia, APP/PS1, Female, 8 months old, G04


title: microglia, APP/PS1, Female, 4 months old, C04


title: microglia, APP/PS1, Female, 4 months old, C03


title: microglia, APP/PS1, Female, 4 months old, C01


title: microglia, APP/PS1:miR-155 cKO, Male, 4 months old, A11

value: biol rep 2


title: microglia, APP/PS1:miR-155 cKO, Male, 4 months old, A07


title: microglia, APP/PS1:miR-155 cKO, Male, 4 months old, A09


title: microglia, APP/PS1:miR-155 cKO, Female, 4 months old, A06

value: biol rep 1


title: microglia, APP/PS1:miR-155 cKO, Female, 4 months old, A02


title: microglia, APP/PS1:miR-155 cKO, Female, 4 months old, A04


title: microglia, APP/PS1:miR-155 cKO, Female, 4 months old, A03


title: microglia, APP/PS1, Male, 4 months old, C12


title: microglia, APP/PS1:miR-155 cKO, Female, 4 months old, A01


title: microglia, APP/PS1, Male, 4 months old, C09


title: microglia, APP/PS1, Female, 4 months old, C02


title: microglia, APP/PS1:miR-155 cKO, Female, 8 months old, E02


title: microglia, APP/PS1:miR-155 cKO, Female, 8 months old, E03


title: sh15.5K-2+Dox rep2

city: Guangzhou

first: Jian-Hua

last: Yang

address: No. 135, Xingang Xi Road

department: School of Life Sciences

institute: Sun Yat-sen University

data_processing:
Cutadapt (v2.8) was used to cut the adapters of the paired-end reads and single-end reads. These reads without adapter were subsequently mapped to the human reference genome (hg38) with STAR software with the following parameters: ‘--alignEndsType EndToEnd --outFilterType Normal --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 20 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.03  --outFilterScoreMin 0 --outFilterScoreMinOverLread 0 --outFilterMatchNmin 15  --outFilterMatchNminOverLread 0.8 --alignIntronMin 20 --alignIntronMax 1 --alignMatesGapMax 1000  --seedSearchStartLmax 15 --seedSearchStartLmaxOverLread 1 --seedSearchLmax 0 --seedMultimapNmax 20000 --seedPerReadNmax 1000 --seedPerWindowNmax 100 --seedNoneLociPerWindow 20 --alignSJDBoverhangMin 1000’. Reads mapping to more than twenty locations were discarded and only sequences in which both ends were aligned to the reference genomes were further analyzed.
We clustered the overlapping paired-end reads that mapped to the genomes. Specifically, we defined the start and end sites with the highest abundance in the cluster as the transcription start site (TSS) and transcription terminal site (TTS), respectively. The sequences between TSSs and TTSs co-occurring within 500 bp were extracted as candidate transcripts. Each candidate transcript with a precise TSS and TTS was input to kturnSeeker. A new software, kturnSeeker, was developed to discover ncRNAs with forward and backward kturn structure. kturnSeeker searches A•G, G•A and G-C basepairs (N-C stem), three-nucleotide bulge and a section of regular basepairing (C stem) step-by-step in candidate sequences, and scores the C stem with a strict score scheme (G-C pair is bonus 3, A-U pair is bonus 2 and mismatch minus 5). Only the total score (C stem) large than 7 was kept as candidate ktRNAs. To identify novel ktRNAs, ktRNAs overlapped known annotation were discarded.
The genome sequence of humans (hg38) was downloaded from the UCSC Genome Browser site. Human gene annotations were acquired from GENCODE on August 2018. The repeat elements in RepeatMasker were downloaded from the UCSC Genome Browser site. Sequences and annotation data for human snoRNAs were downloaded from snoRNA-LBME-db, deepBase, GENCODE, snoRNAome and Refseq in August 2018. All novel ktRNAs were intersected with these gene annotations using bedtools software.
Genome_build: hg38

source_name: 15.5K-knockdown (sh15.5K-2 HEK293T cells

growth_protocol: Negative control and 15.5K-knockdown HEK293T cells were cultured in DMEM (GIBCO, Thermo Scientific) supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin solution (Gibco), 1μg/mL puromycin (Invivogen) and 3 μM Doxycycline (Selleck) at 37°C under 5% CO2.

extract_protocol:
Total RNA was isolated from cells using RNAzol.
RNA was treated with RQ1 DNase (Promega) and purified by RNA Clean & Concentrator-5 (Zymo Research). The samples were then ligated to 3’ randomized RNA adaptor (/rApp/NNNNTGGAATTCTCGGGTGCCAAGG/3SpC3/) with T4 RNA ligase 2 truncated KQ (NEB) in 1× T4 RNA ligase reaction buffer supplemented with 12.5% PEG 8000 at 16 °C for 18 h. The excessive adaptors were digested with 100 U 5’ Deadenylase (NEB) at 30 °C for 1 h, incubated with 2 μg E. coli Single-strand DNA-binding protein (Promega) on ice for 30 min and followed by adding 60 U RecJf (NEB) for ssDNA digestion at 37 °C for another hour. The ligated RNA was ligated to 5’ randomized RNA adaptor (GUUCAGAGUUCUACAGUCCGACGAUCNNNN) using T4 RNA Ligase 1 (NEB) in 1× T4 RNA ligase reaction buffer supplemented with 1 mM ATP at 16 °C for 18 h. The ligated RNA was column-purified by RNA Clean & Concentrator-5 (Zymo Research) and subjected to RNase H-based ribosomal RNA depletion according to the standard protocol with some modification5. For rRNA probe digestion, DNase I was replaced by RecJf exonuclease to prevent the digestion of 3’ randomized RNA adaptor. After column-based purification, the rRNA-depleted RNA was reverse-transcribed using SuperScript IV reverse transcriptase (Invitrogen) in 1× RT buffer with truncated RT primer (GCCTTGGCACCCGAGAAT) to eliminate mispriming artifacts. The cDNA was amplified using Phusion High-Fidelity DNA Polymerase (Thermo Scientific) in 1× Phusion HF buffer (Thermo Scientific) with primers (RP1 forward primer and RPI-X reverse primer). The PCR-amplified cDNA was gel-purifed using a 4% NuSieve 3-1 Agarose gel (Lonza) to remove adapter dimers.

value: human colon cancer cell line


title: sh15.5K-2+Dox rep3

source_name: 15.5K-knockdown (sh15.5K-2) HEK293T cells


title: microglia, APP/PS1:miR-155 cKO, Male, 4 months old, A10


title: sh15.5K-1+Dox rep3

source_name: 15.5K-knockdown (sh15.5K-1) HEK293T cells


title: sh15.5K-2+Dox rep1


title: microglia, APP/PS1:miR-155 cKO, Female, 4 months old, A05


title: sh15.5K-1+Dox rep1


title: sh15.5K-1+Dox rep2


title: HEK293T_Np_rep4

data_processing:
Cutadapt (v2.8) was used to cut the adapters of the paired-end reads and single-end reads. These reads without adapter were subsequently mapped to the human reference genome (hg38) with STAR software with the following parameters: ‘--alignEndsType EndToEnd --outFilterType Normal --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 20 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.03  --outFilterScoreMin 0 --outFilterScoreMinOverLread 0 --outFilterMatchNmin 15  --outFilterMatchNminOverLread 0.8 --alignIntronMin 20 --alignIntronMax 1 --alignMatesGapMax 1000  --seedSearchStartLmax 15 --seedSearchStartLmaxOverLread 1 --seedSearchLmax 0 --seedMultimapNmax 20000 --seedPerReadNmax 1000 --seedPerWindowNmax 100 --seedNoneLociPerWindow 20 --alignSJDBoverhangMin 1000’. Reads mapping to more than twenty locations were discarded and only sequences in which both ends were aligned to the reference genomes were further analyzed.
We clustered the overlapping paired-end reads that mapped to the genomes. Specifically, we defined the start and end sites with the highest abundance in the cluster as the transcription start site (TSS) and transcription terminal site (TTS), respectively. The sequences between TSSs and TTSs co-occurring within 500 bp were extracted as candidate transcripts. Each candidate transcript with a precise TSS and TTS was input to kturnSeeker. A new software, kturnSeeker, was developed to discover ncRNAs with forward and backward kturn structure. kturnSeeker searches A-G, G-A and G-C basepairs (NC stem), three-nucleotide bulge and a section of regular basepairing (C stem) step-by-step in candidate sequences, and scores the C stem with a strict score scheme (G-C pair is bonus 3, A-U pair is bonus 2 and mismatch minus 5). Only the total score (C stem) large than 7 was kept as candidate ktRNAs. To identify novel ktRNAs, ktRNAs overlapped known annotation were discarded.
The genome sequence of humans (hg38) was downloaded from the UCSC Genome Browser site. Human gene annotations were acquired from GENCODE on August 2018. The repeat elements in RepeatMasker were downloaded from the UCSC Genome Browser site. Sequences and annotation data for human snoRNAs were downloaded from snoRNA-LBME-db, deepBase, GENCODE, snoRNAome and Refseq in August 2018. All novel ktRNAs were intersected with these gene annotations using bedtools software.
Genome_build: hg38

growth_protocol: Cells were cultured in complete medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin solution (Gibco) at 37°C under 5% CO2.

extract_protocol:
For subcellular RNA isolation, cells were trypsinized, centrifuged at 500 g for 3 min at 4 °C, washed with ice-cold PBS and recentrifuged. The cell pellet was resuspended in Hypotonic lysis buffer (10 mM Tris, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.3% NP-40 and 10% Glycerol) supplemented with 1 mM DTT, 100 U/mL RNase inhibitor and 400 μM RVC (NEB) and incubated on ice for 30 min. The resuspension was centrifuged at 1,000 g for 3 min at 4 °C. Approximately 70% volume of the supernatant was carefully removed without disturbing the nuclear pellet and precipitated by RNA precipitation solution (5% 3M sodium acetate, pH 5.5 and 95% ethanol), followed by RNA isolation using RNAzol; this was the cytoplasmic fraction. The remaining nuclear pellet was washed with Hypotonic lysis buffer three times. After centrifugation at 200 g for 2 min at 4 °C, the pellet was resuspended in Modified Wuarin-Schibler buffer (10 mM Tris, pH 7.0, 4 mM EDTA, 0.3 M NaCl, 1 M Urea and 1% NP-40) supplemented with 1 mM DTT, 100 U/mL RNase inhibitor and 400 μM RVC (NEB) and incubated on ice for 5 min. The sample was then centrifuged at 1,000g for 3 min at 4 °C and the supernatant was taken and precipitated by RNA precipitation solution, followed by RNA isolation using RNAzol; this was the nucleoplasmic fraction. For nucleoli isolation, the cell pellet volume was estimated for the next steps. The nuclear pellet was isolated and washed as described above. The pellet was resuspended in ten cell packed pellet volumes of ice-cold S1 buffer (0.25 M Sucrose, 10 mM MgCl2) supplemented with 1 mM DTT, 100 U/mL RNase inhibitor and 400 μM RVC (NEB) and then layered on ten cell packed pellet volumes of ice-cold S3 buffer (0.88 M Sucrose, 5 mM MgCl2) supplemented with 1 mM DTT, 100 U/mL RNase inhibitor and 400 μM RVC (NEB) and pelleted at 1,200g for 5 min at 4 °C. The pellet was then resuspended in ten cell packed pellet volumes of ice-cold S2 buffer (0.34 M Sucrose, 5 mM MgCl2) supplemented with 1 mM DTT, 100 U/mL RNase inhibitor and 400 μM RVC (NEB) and sonicated by using VibraCell Sonicator VCX130PB (Sonics & Materials, Inc.). The suspension was layered on ten cell packed pellet volumes of ice-cold S3 buffer (0.88 M Sucrose, 5 mM MgCl2) supplemented with 1 mM DTT, 100 U/mL RNase inhibitor and 400 μM RVC (NEB) and pelleted at 2,000g for 20 min at 4 °C. The supernatant was discarded, and the pellet was washed with S2 buffer and then centrifuged at 2,000g for 5 min at 4 °C. The pellet constituted the nucleolar fraction.
RNA was treated with RQ1 DNase (Promega) and purified by RNA Clean & Concentrator-5 (Zymo Research). The samples were then ligated to 3’ randomized RNA adaptor (/rApp/NNNNTGGAATTCTCGGGTGCCAAGG/3SpC3/) with T4 RNA ligase 2 truncated KQ (NEB) in 1× T4 RNA ligase reaction buffer supplemented with 12.5% PEG 8000 at 16 °C for 18 h. The excessive adaptors were digested with 100 U 5’ Deadenylase (NEB) at 30 °C for 1 h, incubated with 2 μg E. coli Single-strand DNA-binding protein (Promega) on ice for 30 min and followed by adding 60 U RecJf (NEB) for ssDNA digestion at 37 °C for another hour. The ligated RNA was ligated to 5’ randomized RNA adaptor (GUUCAGAGUUCUACAGUCCGACGAUCNNNN) using T4 RNA Ligase 1 (NEB) in 1× T4 RNA ligase reaction buffer supplemented with 1 mM ATP at 16 °C for 18 h. The ligated RNA was column-purified by RNA Clean & Concentrator-5 (Zymo Research) and subjected to RNase H-based ribosomal RNA depletion according to the standard protocol with some modification5. For rRNA probe digestion, DNase I was replaced by RecJf exonuclease to prevent the digestion of 3’ randomized RNA adaptor. After column-based purification, the rRNA-depleted RNA was reverse-transcribed using SuperScript IV reverse transcriptase (Invitrogen) in 1× RT buffer with truncated RT primer (GCCTTGGCACCCGAGAAT) to eliminate mispriming artifacts. The cDNA was amplified using Phusion High-Fidelity DNA Polymerase (Thermo Scientific) in 1× Phusion HF buffer (Thermo Scientific) with primers (RP1 forward primer and RPI-X reverse primer). The PCR-amplified cDNA was gel-purifed using a 4% NuSieve 3-1 Agarose gel (Lonza) to remove adapter dimers.

value: human embryonic kidney cell

tag: fraction

value: Nucleoplasm RNA


title: shNC+Dox rep3

source_name: HEK293T (shNC) cells

value: shNC


title: shNC+Dox rep1


title: shNC+Dox rep2


title: HEK293T_Np_rep3


title: HEK293T_15.5K_RIP_PEN_SHAPE_MaP_DMSO_rep4

data_processing:
Pre-processing of RIP-PEN-SHAPE-MaP sequencing data included removing adapters with Cutadapt (v3.4), merging pair-ended reads with FLASH2 and collapsing PCR duplicates utilizing the 6 nt barcodes from 5' and 3' ends of reads with the fastq tool from bio-playground package (https://github.com/martijnvermaat/bio-playground). The processed reads were aligned to a collection of reference sequences including all bktRNAs in addition to hg38 chromosomes (the original bktRNA loci were masked) using STAR software with the following parameters: --alignSJoverhangMin 1000  --scoreDelOpen -1 --scoreDelBase -1 --scoreInsOpen -1 --scoreInsBase -1 --outFilterMultimapScoreRange 1 --outFilterMultimapNmax 20 --outFilterMismatchNmax 30 --outFilterMismatchNoverLmax 0.3 --outFilterMismatchNoverReadLmax 1 --outFilterScoreMin 0 --outFilterScoreMinOverLread 0.3 --outFilterMatchNmin 25 --outFilterMatchNminOverLread 0. The alignments for individual bktRNAs were extracted and processed with shapemapper_mutation_parser, shapemapper_mutation_counter and python script "make_reactivity_profiles.py" from ShapeMapper2 to produce the reactivity profiles. Only the bktRNAs with a median effective coverage ≥ 200 over the transcript for both control and treated samples were kept.
Assembly: hg38
Supplementary files format and content: nucleotide SHAPE reactivity signal in text file

growth_protocol: HEK293T-FLAG-15.5K stable cells were cultured in DMEM (Gibico) with 10% fetal bovine serum (FBS, Gibico), 1% penicillin-streptomycin solution (Gibico) and 1μg/mL puromycine (MCE) at 37℃ at 5% CO2.

extract_protocol:
Cell lysate was prepared and incubated with anti-FLAG. Afterwards, the RNA-protein complexes were immunoprecipitated with Dynabeads protein G. Then the on-beads modification was performed with SHAPE reagent NAI-N3 or DMSO (negative control) with the SHAPE modification buffer (100 mM HEPES, pH8.0, 6 mM MgCl2, 150 mM NaCl). Thereafter, RNA fraction was extracted using RNAzol reagent.
After RNA isolation and DNase I-treatment, the 15.5K-interacted RNAs were ligated to 3’ and 5’ randomized RNA adaptors. Then the ligated products were subjected to rRNA, snRNA and some high-abundance snoRNA depletion utilizing an RNase H-based strategy. Following the reverse transcription under SHAPE-MaP conditions, the libraries were amplified with Illumina small RNA indexed PCR primers.

tag: cell line

value: Human embryonic kidney

value: FLAG-15.5K overexpression

value: DMSO


title: HEK293T_15.5K_RIP_PEN_SHAPE_MaP_DMSO_rep2


title: HEK293T_15.5K_RIP_PEN_SHAPE_MaP_DMSO_rep3


title: HEK293T_15.5K_RIP_PEN_SHAPE_MaP_NAI_N3_rep2


title: HEK293T_15.5K_RIP_PEN_SHAPE_MaP_NAI_N3_rep1


title: HEK293T_15.5K_RIP_PEN_SHAPE_MaP_NAI_N3_rep4


title: HEK293T_15.5K_RIP_PEN_SHAPE_MaP_NAI_N3_rep3


title: HEK293T_15.5K_RIP_PEN_SHAPE_MaP_DMSO_rep1


title: HEK293T_Np_rep2


title: HEK293T_No_rep3

value: Nucleolus RNA


title: HEK293T_No_rep2


title: HEK293T_Cyto_rep4

data_processing:
Cutadapt (v2.8) was used to cut the adapters of the paired-end reads and single-end reads. These reads without adapter were subsequently mapped to the human reference genome (hg38) with STAR software with the following parameters: ‘--alignEndsType EndToEnd --outFilterType Normal --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 20 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.03  --outFilterScoreMin 0 --outFilterScoreMinOverLread 0 --outFilterMatchNmin 15  --outFilterMatchNminOverLread 0.8 --alignIntronMin 20 --alignIntronMax 1 --alignMatesGapMax 1000  --seedSearchStartLmax 15 --seedSearchStartLmaxOverLread 1 --seedSearchLmax 0 --seedMultimapNmax 20000 --seedPerReadNmax 1000 --seedPerWindowNmax 100 --seedNoneLociPerWindow 20 --alignSJDBoverhangMin 1000’. Reads mapping to more than twenty locations were discarded and only sequences in which both ends were aligned to the reference genomes were further analyzed.
We clustered the overlapping paired-end reads that mapped to the genomes. Specifically, we defined the start and end sites with the highest abundance in the cluster as the transcription start site (TSS) and transcription terminal site (TTS), respectively. The sequences between TSSs and TTSs co-occurring within 500 bp were extracted as candidate transcripts. Each candidate transcript with a precise TSS and TTS was input to kturnSeeker. A new software, kturnSeeker, was developed to discover ncRNAs with forward and backward kturn structure. kturnSeeker searches A-G, G-A and G-C basepairs (N-C stem), three-nucleotide bulge and a section of regular basepairing (C stem) step-by-step in candidate sequences, and scores the C stem with a strict score scheme (G-C pair is bonus 3, A-U pair is bonus 2 and mismatch minus 5). Only the total score (C stem) large than 7 was kept as candidate ktRNAs. To identify novel ktRNAs, ktRNAs overlapped known annotation were discarded.
The genome sequence of humans (hg38) was downloaded from the UCSC Genome Browser site. Human gene annotations were acquired from GENCODE on August 2018. The repeat elements in RepeatMasker were downloaded from the UCSC Genome Browser site. Sequences and annotation data for human snoRNAs were downloaded from snoRNA-LBME-db, deepBase, GENCODE, snoRNAome and Refseq in August 2018. All novel ktRNAs were intersected with these gene annotations using bedtools software.
Genome_build: hg38

value: Cytoplasm RNA


title: HEK293T_No_rep4


title: HEK293T_Np_rep1


title: HEK293T_Cyto_rep2


title: HEK293T_Cyto_rep3


title: HEK293T_Cyto_rep1


title: HEK293T_No_rep1


title: HCT116_Np_rep3


title: HCT116_Np_rep2


title: HCT116 shZCRB1-2+Dox rep3

data_processing:
Adaptor sequences were trimmed from raw RNA-seq data using cutadapt (v2.0.dev0).
The clean reads were mapped to the reference genome (hg38) using the STAR software (2.7.1a) with the genome index built from GENCODE v32 annotation and additional parameters: --alignEndsType EndToEnd --outSAMstrandField intronMotif --outFilterMismatchNmax 5.
For each intron, the numbers of reads that either support the spliced isoform or the retained isoform were counted. Reads that skip the intron and span at least 10 bp at both exons are thought to support the spliced isoform, and reads that include the intron with at least 10 bp overlapping with exon side and intron side are thought to support the retained isoform. The read counts are normalized by effective length, defined as the number of possible positions for supporting reads, to estimate the abundance of the spliced isoform and the retained isoform.
The inclusion level was calculated as the abundance of the retained isoform divided by the abundance of both isoforms. The statistical method and codes from rMATS25 were utilized to look for introns with significant inclusion level difference between wild-type and knockout cells.
Genome_build: hg38

source_name: ZCRB1-knockdown (shZCRB1-2) HCT116 cells

growth_protocol: Negative control and ZCRB1-knockdown HCT116 cells were cultured in DMEM (GIBCO, Thermo Scientific) supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin solution (Gibco), 1μg/mL puromycin (Invivogen) and 3 μM Doxycycline (Selleck) at 37°C under 5% CO2.

extract_protocol:
Total RNA was isolated from cells using RNAzol. Three microgram total RNA was used for polyadenylated RNA enrichment by using VAHTS mRNA Capture Beads (Vayzme) following the manufacture’s protocol.
Standard protocol of NEBNext Ultra ™ II Directional RNA Library Prep Kit was followed for mRNA enrichment and library preparation.


title: HCT116 shNC+Dox rep2

source_name: HCT116 (shNC) cells


title: HCT116 shZCRB1-2+Dox rep2

source_name: ZCRB1-knockdown (shZCRB1-2 HCT116 cells


title: HCT116 shZCRB1-1+Dox rep1

source_name: ZCRB1-knockdown (shZCRB1-1) HCT116 cells


title: HCT116 shZCRB1-2+Dox rep1


title: HCT116 shNC+Dox rep3


title: HCT116_Cyto_rep1


title: HCT116_No_rep4


title: HCT116 shZCRB1-1+Dox rep2


title: HCT116_Cyto_rep4


title: HCT116_Cyto_rep3


title: HCT116_Cyto_rep2


title: HCT116_No_rep2


title: HCT116_No_rep1


title: HCT116_No_rep3


title: sh15.5K-2+Dox_rep3


title: sh15.5K-2+Dox_rep2


title: sh15.5K-1+Dox_rep3


title: sh15.5K-1+Dox_rep2


title: HCT116 shNC+Dox rep1


title: sh15.5K-1+Dox_rep1


title: HCT116_Np_rep4


title: shNC+Dox_rep3


title: HCT116_Np_rep1


title: shNC+Dox_rep2


title: HCT116 shZCRB1-1+Dox rep3


title: shNC+Dox_rep1


title: HEK293T_15.5K_RIP_PEN_seq_rep7

extract_protocol:
Cell lysate was prepared and incubated with anti-FLAG. Afterwards, the RNA-protein complexes were immunoprecipitated with Dynabeads protein G and the RNA fraction was extracted using RNAzol reagent.
For RIP-PEN-seq, RIP RNA was subjected to rRNA removal (Ribo-Zero rRNA Removal Kit, Illumina, MRZH11124) and further used to generate the library using the TruSeq Samll RNA sample preparation kit (Illumina) following the manufacturer’s instructions.

value: Stable overexpression of 15.5K

tag: antibody

value: anti-FLAG [Proteintech, cat# 66008-3-Ig]


title: HEK293T_15.5K_RIP_PEN_seq_rep8


title: HEK293T_15.5K_RIP_PEN_seq_rep5


title: HEK293T_15.5K_RIP_PEN_seq_rep4

data_processing:
Cutadapt (v2.8) was used to cut the adapters of the paired-end reads and single-end reads. These reads without adapter were subsequently mapped to the human reference genome (hg38) with STAR software with the following parameters: ‘--alignEndsType EndToEnd --outFilterType Normal --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 20 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.03  --outFilterScoreMin 0 --outFilterScoreMinOverLread 0 --outFilterMatchNmin 15  --outFilterMatchNminOverLread 0.8 --alignIntronMin 20 --alignIntronMax 1 --alignMatesGapMax 1000  --seedSearchStartLmax 15 --seedSearchStartLmaxOverLread 1 --seedSearchLmax 0 --seedMultimapNmax 20000 --seedPerReadNmax 1000 --seedPerWindowNmax 100 --seedNoneLociPerWindow 20 --alignSJDBoverhangMin 1000’. Reads mapping to more than twenty locations were discarded and only sequences in which both ends were aligned to the reference genomes were further analyzed.
We clustered the overlapping paired-end reads that mapped to the genomes. Specifically, we defined the start and end sites with the highest abundance in the cluster as the transcription start site (TSS) and transcription terminal site (TTS), respectively. The sequences between TSSs and TTSs co-occurring within 500 bp were extracted as candidate transcripts. Each candidate transcript with a precise TSS and TTS was input to kturnSeeker. A new software, kturnSeeker, was developed to discover ncRNAs with forward and backward kturn structure. kturnSeeker searches A•G, G•A and G-C basepairs (N-C stem), three-nucleotide bulge and a section of regular basepairing (C stem) step-by-step in candidate sequences, and scores the C stem with a strict score scheme (G-C pair is bonus 3, A-U pair is bonus 2 and mismatch minus 5). Only the total score (C stem) large than 7 was kept as candidate ktRNAs. To identify novel ktRNAs, ktRNAs overlapped known annotation were discarded.
The genome sequence of humans (hg38) was downloaded from the UCSC Genome Browser site. Human gene annotations were acquired from GENCODE on August 2018. The repeat elements in RepeatMasker were downloaded from the UCSC Genome Browser site. Sequences and annotation data for human snoRNAs were downloaded from snoRNA-LBME-db, deepBase, GENCODE, snoRNAome and Refseq in August 2018. All novel ktRNAs were intersected with these gene annotations using bedtools software.
Genome_build: hg38
Supplementary_files_format_and_content: RPM


title: sh15.5K-2+Dox_rep1


title: HEK293T_15.5K_RIP_PEN_seq_rep6


title: K562_rep1

data_processing:
Cutadapt (v2.8) was used to cut the adapters of the paired-end reads and single-end reads. These reads without adapter were subsequently mapped to the human reference genome (hg38) with STAR software with the following parameters: ‘--alignEndsType EndToEnd --outFilterType Normal --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 20 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.03  --outFilterScoreMin 0 --outFilterScoreMinOverLread 0 --outFilterMatchNmin 15  --outFilterMatchNminOverLread 0.8 --alignIntronMin 20 --alignIntronMax 1 --alignMatesGapMax 1000  --seedSearchStartLmax 15 --seedSearchStartLmaxOverLread 1 --seedSearchLmax 0 --seedMultimapNmax 20000 --seedPerReadNmax 1000 --seedPerWindowNmax 100 --seedNoneLociPerWindow 20 --alignSJDBoverhangMin 1000’. Reads mapping to more than twenty locations were discarded and only sequences in which both ends were aligned to the reference genomes were further analyzed.
We clustered the overlapping paired-end reads that mapped to the genomes. Specifically, we defined the start and end sites with the highest abundance in the cluster as the transcription start site (TSS) and transcription terminal site (TTS), respectively. The sequences between TSSs and TTSs co-occurring within 500 bp were extracted as candidate transcripts. Each candidate transcript with a precise TSS and TTS was input to kturnSeeker. A new software, kturnSeeker, was developed to discover ncRNAs with forward and backward kturn structure. kturnSeeker searches A•G, G•A and G-C basepairs (N-C stem), three-nucleotide bulge and a section of regular basepairing (C stem) step-by-step in candidate sequences, and scores the C stem with a strict score scheme (G-C pair is bonus 3, A-U pair is bonus 2 and mismatch minus 5). Only the total score (C stem) large than 7 was kept as candidate ktRNAs. To identify novel ktRNAs, ktRNAs overlapped known annotation were discarded.
The genome sequence of humans (hg38) was downloaded from the UCSC Genome Browser site. Human gene annotations were acquired from GENCODE on August 2018. The repeat elements in RepeatMasker were downloaded from the UCSC Genome Browser site. Sequences and annotation data for human snoRNAs were downloaded from snoRNA-LBME-db, deepBase, GENCODE, snoRNAome and Refseq in August 2018. All novel ktRNAs were intersected with these gene annotations using bedtools software.
Genome_build: hg38
Supplementary_files_format_and_content: human_ktRNA.csv

extract_protocol:
Total RNA was isolated from cells using RNAzol. For subcellular RNA isolation, cells were trypsinized, centrifuged at 500 g for 3 min at 4 °C, washed with ice-cold PBS and recentrifuged. The cell pellet was resuspended in Hypotonic lysis buffer (10 mM Tris, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.3% NP-40 and 10% Glycerol) supplemented with 1 mM DTT, 100 U/mL RNase inhibitor and 400 μM RVC (NEB) and incubated on ice for 30 min. The resuspension was centrifuged at 1,000 g for 3 min at 4 °C. Approximately 70% volume of the supernatant was carefully removed without disturbing the nuclear pellet and precipitated by RNA precipitation solution (5% 3M sodium acetate, pH 5.5 and 95% ethanol), followed by RNA isolation using RNAzol; this was the cytoplasmic fraction. The remaining nuclear pellet was washed with Hypotonic lysis buffer three times. After centrifugation at 200 g for 2 min at 4 °C, the pellet was resuspended in Modified Wuarin-Schibler buffer (10 mM Tris, pH 7.0, 4 mM EDTA, 0.3 M NaCl, 1 M Urea and 1% NP-40) supplemented with 1 mM DTT, 100 U/mL RNase inhibitor and 400 μM RVC (NEB) and incubated on ice for 5 min. The sample was then centrifuged at 1,000g for 3 min at 4 °C and the supernatant was taken and precipitated by RNA precipitation solution, followed by RNA isolation using RNAzol; this was the nucleoplasmic fraction. For nucleoli isolation, the cell pellet volume was estimated for the next steps. The nuclear pellet was isolated and washed as described above. The pellet was resuspended in ten cell packed pellet volumes of ice-cold S1 buffer (0.25 M Sucrose, 10 mM MgCl2) supplemented with 1 mM DTT, 100 U/mL RNase inhibitor and 400 μM RVC (NEB) and then layered on ten cell packed pellet volumes of ice-cold S3 buffer (0.88 M Sucrose, 5 mM MgCl2) supplemented with 1 mM DTT, 100 U/mL RNase inhibitor and 400 μM RVC (NEB) and pelleted at 1,200g for 5 min at 4 °C. The pellet was then resuspended in ten cell packed pellet volumes of ice-cold S2 buffer (0.34 M Sucrose, 5 mM MgCl2) supplemented with 1 mM DTT, 100 U/mL RNase inhibitor and 400 μM RVC (NEB) and sonicated by using VibraCell Sonicator VCX130PB (Sonics & Materials, Inc.). The suspension was layered on ten cell packed pellet volumes of ice-cold S3 buffer (0.88 M Sucrose, 5 mM MgCl2) supplemented with 1 mM DTT, 100 U/mL RNase inhibitor and 400 μM RVC (NEB) and pelleted at 2,000g for 20 min at 4 °C. The supernatant was discarded, and the pellet was washed with S2 buffer and then centrifuged at 2,000g for 5 min at 4 °C. The pellet constituted the nucleolar fraction.
RNA was treated with RQ1 DNase (Promega) and purified by RNA Clean & Concentrator-5 (Zymo Research). The samples were then ligated to 3’ randomized RNA adaptor (/rApp/NNNNTGGAATTCTCGGGTGCCAAGG/3SpC3/) with T4 RNA ligase 2 truncated KQ (NEB) in 1× T4 RNA ligase reaction buffer supplemented with 12.5% PEG 8000 at 16 °C for 18 h. The excessive adaptors were digested with 100 U 5’ Deadenylase (NEB) at 30 °C for 1 h, incubated with 2 μg E. coli Single-strand DNA-binding protein (Promega) on ice for 30 min and followed by adding 60 U RecJf (NEB) for ssDNA digestion at 37 °C for another hour. The ligated RNA was ligated to 5’ randomized RNA adaptor (GUUCAGAGUUCUACAGUCCGACGAUCNNNN) using T4 RNA Ligase 1 (NEB) in 1× T4 RNA ligase reaction buffer supplemented with 1 mM ATP at 16 °C for 18 h. The ligated RNA was column-purified by RNA Clean & Concentrator-5 (Zymo Research) and subjected to RNase H-based ribosomal RNA depletion according to the standard protocol with some modification5. For rRNA probe digestion, DNase I was replaced by RecJf exonuclease to prevent the digestion of 3’ randomized RNA adaptor. After column-based purification, the rRNA-depleted RNA was reverse-transcribed using SuperScript IV reverse transcriptase (Invitrogen) in 1× RT buffer with truncated RT primer (GCCTTGGCACCCGAGAAT) to eliminate mispriming artifacts. The cDNA was amplified using Phusion High-Fidelity DNA Polymerase (Thermo Scientific) in 1× Phusion HF buffer (Thermo Scientific) with primers (RP1 forward primer and RPI-X reverse primer). The PCR-amplified cDNA was gel-purifed using a 4% NuSieve 3-1 Agarose gel (Lonza) to remove adapter dimers.
small RNA-seq

value: human erythroleukemic cell line

tag: rna fraction

value: total RNA


title: K562_rep2


title: HepG2_rep1

value: human liver cancer cell line


title: HEK293T_15.5K_RIP_PEN_seq_rep3


title: Hela_rep2

source_name: Hela

value: Hela

value: human cervical carcinoma cell line


title: FBL_CLASH_rep2

data_processing:
Cutadapt (v2.8) was used to cut the adapters of the paired-end reads with the following parameters: cutadapt -a TGGAATTCTCGGGTGCCAAGG -A GATCGTCGGACTGTAGAACTCTGAAC -m 15 -e 0.15. The paired-end reads without adapters were further merged using FLASH software (v1.2.11) with following parameters: -z -m 10 -M 135 -x 0.25. fastx_collapser software was used to collapse the reads with the default parameters for removing PCR duplicates. Reads with fully identical sequences, including the same barcode and insert fragment, were marked as PCR duplicates, and only one of the identical sequences was retained for subsequent analysis. Reads shorter than 30 nucleotides were removed.
The processing CLASH reads were aligned to human genome and transcriptome with STAR software with following parameters: --alignEndsType EndToEnd --outFilterType BySJout --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 30 --outFilterMismatchNmax 15 --outFilterMismatchNoverLmax 0.1 --outFilterScoreMin 0 --outFilterScoreMinOverLread 0 --outFilterMatchNmin 15 --outFilterMatchNminOverLread 0.8 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --seedSearchStartLmax 15 --seedSearchStartLmaxOverLread 1 --seedSearchLmax 0 --seedMultimapNmax 20000 --seedPerReadNmax 1000 --seedPerWindowNmax 100 --seedNoneLociPerWindow 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts.
The mapped reads were discarded and the unmapped reads were further aligned to all bktRNAs by using bowtie2 software with following local alignment parameters: -p 16 -t --no-unal --norc --local --reorder -D 200 -R 3 -N 0 -L 10 -i S,1,0.5 --score-min G,10,5 --mp 4,2 . The aligned reads located within with bktRNAs were further aligned to genome for identifying bktRNA-target chimeras using STAR program with chimeric parameters: --outFilterType Normal --outFilterMultimapNmax 30 --outFilterMultimapScoreRange 0 --alignIntronMin 3 --scoreGapNoncan -2 --scoreGapATAC -2 --scoreGapGCAG -2 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimMultimapNmax 30 --chimMultimapScoreRange 2 --chimScoreJunctionNonGTAG -8 --alignSJoverhangMin 15 --alignSJDBoverhangMin 10 --chimOutType Junctions --outSAMtype BAM SortedByCoordinate. The chimeric reads were folded to identify complementary regions between bktRNAs and their targets using RNAduplex program.
Genome_build: hg38

growth_protocol: HEK293T-FLAG-15.5K and HEK293T-FLAG-FBL stable cells were cultured in DMEM (Gibico) with 10% fetal bovine serum (FBS, Gibico), 1% penicillin-streptomycin solution (Gibico) and 1μg/mL puromycine (MCE) at 37℃ at 5% CO2.

extract_protocol:
Cell lysate was prepared and incubated with anti-FLAG. Afterwards, the RNA-protein complexes were immunoprecipitated with Dynabeads protein G and the RNA fraction was extracted using RNAzol reagent.
HEK293T-FLAG-15.5K and HEK293T-FLAG-FBL cells grown on a 150 mm dish were rinsed with ice-cold PBS and crosslinked with 0.4 J/cm2 of 254 nm UV light. Crosslinked cells were harvested and snap frozen in liquid nitrogen and stored at -80°C. Frozen cell pellets were lysed directly in 6 volumes of ice-cold CLASH lysis buffer (50 mM Tris, pH 7.5, 100 mM NaCl, 0.1% SDS, 0.5% Sodium deoxycholate and 1% NP-40) supplemented with 1× protease inhibitor cocktail (Roche) on ice for 30 min. After sonication by using Bioruptor (Dieagenode) and then centrifugation at 15,000 g for 15 min at 4°C, the supernatant was treated with 60 U RQ1 DNase (Promega) at 37°C for 10 min, followed by adding 600 U S1 Nuclease for RNA digestion at 30°C for 15 min and stopped by addition of 80 μl 0.5 M EDTA. The lysate was precleared with Dynabeads Protein G (Invitrogen) at 4°C for 1 h and then subjected to FLAG antibody-bound beads for immunoprecipitation at 4°C overnight. After incubation, immunoprecipitaes were washed consecutively with once High-stringency buffer (20 mM Tris, pH 7.5, 120 mM NaCl, 5 mM EDTA, 25 mM KCl, 0.5% Sodium deoxycholate and 1% Triton X-100), once High-salt buffer (50 mM Tris, pH 7.5, 1 M NaCl, 0.1% SDS, 0.5% Sodium deoxycholate and 1% NP-40), once Low-salt buffer (50 mM Tris, pH 7.5, 5 mM EDTA) and twice NT2 buffer (50 mM Tris, pH 7.5, 150 mM NaCl, 0.0005% NP-40 and 1 mM MgCl2). The immunoprecipitated material was digested with S1 Nuclease in final concentration of 4 U/µL at 30°C for 15 min and subsequently treated with T4 RNA Ligase 1 (NEB) for intramolecular ligation in an Eppendorf Thermomixer at 16 °C overnight, 15 s 1,400 r.p.m., 90 s rest in a 30 µL reaction. The beads were resuspended in 500 µL NT2 buffer and washed twice with High-salt buffer and twice with NT2 buffer. Then immunoprecipitaes were 3’-end ligated to IRdye-800CW-DBCO labeled preA-DNA adaptor with T4 RNA ligase 2 truncated KQ (NEB) in an Eppendorf Thermomixer at 16 °C overnight, 15 s 1,400 r.p.m., 90 s rest. (preA-DNA adaptor: /rApp/AGATCGGAAGAGCGGTTCAGAAAAAAAAAAAA/iAzideN/AAAAAAAAAAAA/3Bio/, /iAzideN/ site directly conjugated to IRdye-800CW-DBCO). The following day, beads were recovered and resuspended in 1× LDS sample buffer + reducing agent, and the RNA-protein complexes are run on NuPAGE™ 4-12% Bis-Tris Protein Gels and transferred to nitrocellulose membranes, and the region (30~120 nt of RNA for 15.5K and 50~130 nt of RNA for FBL) above the protein molecular weight is excised and Proteinase K (Thermo Fisher) treated to isolate RNA. The RNA was then reverse transcribed by using SuperScript IV reverse transcriptase (Invitrogen) and RT primer (ACACGACGCTCTTCCGATCT). After digestion of excessive RT primers, the cDNA was ligated to a 3’ DNA adaptor (/5Phos/AGATCGGAAGAGCACACGTCTG/3SpC3/) using T4 RNA Ligase 1 (NEB). Next, the generated DNA was ampliﬁed by PCR that utilized 2 × Q5 PCR Master Mix (NEB) and corresponding illumina PCR primers. Ampliﬁed library was puriﬁed from 6% native acrylamide gel and sequenced on an Illumina HiSeq X ten platform.

value: Stable overexpression of FBL


title: HepG2_rep2


title: FBL_CLASH_rep3


title: Hela_rep1


title: U-87 MG_rep2

source_name: U-87 MG

value: U-87 MG

value: human primary glioblastoma cell line


title: HEK293T_rep1

value: human embryonic kidney cell


title: HCT116_rep2

value: human colon cancer cell line


title: HCT116_rep3

data_processing:
Cutadapt (v2.8) was used to cut the adapters of the paired-end reads and single-end reads. These reads without adapter were subsequently mapped to the human reference genome (hg38) with STAR software with the following parameters: ‘--alignEndsType EndToEnd --outFilterType Normal --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 20 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.03  --outFilterScoreMin 0 --outFilterScoreMinOverLread 0 --outFilterMatchNmin 15  --outFilterMatchNminOverLread 0.8 --alignIntronMin 20 --alignIntronMax 1 --alignMatesGapMax 1000  --seedSearchStartLmax 15 --seedSearchStartLmaxOverLread 1 --seedSearchLmax 0 --seedMultimapNmax 20000 --seedPerReadNmax 1000 --seedPerWindowNmax 100 --seedNoneLociPerWindow 20 --alignSJDBoverhangMin 1000’. Reads mapping to more than twenty locations were discarded and only sequences in which both ends were aligned to the reference genomes were further analyzed.
We clustered the overlapping paired-end reads that mapped to the genomes. Specifically, we defined the start and end sites with the highest abundance in the cluster as the transcription start site (TSS) and transcription terminal site (TTS), respectively. The sequences between TSSs and TTSs co-occurring within 500 bp were extracted as candidate transcripts. Each candidate transcript with a precise TSS and TTS was input to kturnSeeker. A new software, kturnSeeker, was developed to discover ncRNAs with forward and backward kturn structure. kturnSeeker searches A•G, G•A and G-C basepairs (N-C stem), three-nucleotide bulge and a section of regular basepairing (C stem) step-by-step in candidate sequences, and scores the C stem with a strict score scheme (G-C pair is bonus 3, A-U pair is bonus 2 and mismatch minus 5). Only the total score (C stem) large than 7 was kept as candidate ktRNAs. To identify novel ktRNAs, ktRNAs overlapped known annotation were discarded.
The genome sequence of humans (hg38) was downloaded from the UCSC Genome Browser site. Human gene annotations were acquired from GENCODE on August 2018. The repeat elements in RepeatMasker were downloaded from the UCSC Genome Browser site. The genome sequence of humans (hg38) was downloaded from the UCSC Genome Browser site. Human gene annotations were acquired from GENCODE on August 2018. The repeat elements in RepeatMasker were downloaded from the UCSC Genome Browser site. Sequences and annotation data for human snoRNAs were downloaded from snoRNA-LBME-db, deepBase, GENCODE, snoRNAome and Refseq in August 2018. All novel ktRNAs were intersected with these gene annotations using bedtools software.
Genome_build: hg38
Supplementary_files_format_and_content: human_ktRNA.csv


title: HCT116_rep1


title: 15.5K_CLASH_rep3


title: 15.5K_CLASH_rep1


title: 15.5K_CLASH_rep2


title: KO-4_rep3

source_name: bktRNA1-deficient (KO-4) HCT116 cells

growth_protocol: Wild-type and bktRNA1-deficient HCT116 cells were cultured in DMEM (GIBCO, Thermo Scientific) supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin solution (Gibco) at 37°C under 5% CO2.


title: KO-4_rep2


title: KO-4_rep1


title: KO-3_rep3

source_name: bktRNA1-deficient (KO-3) HCT116 cells


title: KO-3_rep2


title: KO-3_rep1


title: U-87 MG_rep1


title: HEK293T_rep2


title: FBL_CLASH_rep1


title: KO-2_rep2

source_name: bktRNA1-deficient (KO-2) HCT116 cells


title: KO-2_rep1


title: KO-2_rep3


title: KO-1_rep3

source_name: bktRNA1-deficient (KO-1) HCT116 cells


title: WT_rep3

source_name: wild-type HCT116 (WT) cells

value: wild type


title: KO-1_rep2


title: KO-1_rep1


title: XT-GR-20

city: Villejuif

first: Felix

last: Blanc-Durand

address: 114 rue Edouard Vaillant

department: Medical Oncology

country: France

institute: Institut Gustave Roussy

data_processing:
Alignment BWA-MEM v-0.7.12
Alignment correction: Samtools v-1.2; Picard-tools v-1.139
Variant calling: GATK Haplotype v-3.4-46;MutaCaller-1.7
Assembly: hg19
Supplementary files format and content: variants, vcf format

source_name: Tumor Tissue

extract_protocol:
QIAsymphony DSP DNA Kits (QIAGEN)
SureSelect XT HS Target Enrichment System (Agilent Technologies) : large pan-cancer panel

treatment_protocol: FFPE treated and bisulfite-conversion + ddPCR

value: Tumor Tissue

value: Ovarian cancer

tag: cell subtype

value: High-grade serous

value: Myriad MyChoice CDx Positive

value: Before chemotherapy


title: XT-GR-34

tag: tissue

value: After chemotherapy


title: XT-GR-68

value: Myriad MyChoice CDx Negative


title: XT-GR-38


title: XT-GR-82


title: XT-GR-58


title: XT-GR-65


title: XT-GR-21


title: XT-GR-33


title: XT-GR-78


title: XT-GR-30


title: XT-GR-73


title: XT-GR-39


title: XT-GR-47


title: XT-GR-60


title: XT-GR-62


title: XT-GR-51


title: XT-GR-12


title: XT-GR-27


title: XT-GR-32


title: WT_rep2


title: XT-GR-9


title: XT-GR-89

value: High-grade endometrioid


title: WT_rep1


title: XT-GR-23


title: XT-GR-19


title: XT-GR-69


title: XT-GR-44


title: XT-GR-7


title: XT-GR-52


title: XT-GR-41


title: XT-GR-81


title: XT-GR-13


title: XT-GR-28


title: XT-GR-5


title: XT-GR-67


title: XT-GR-97

value: Undifferentiated


title: XT-GR-24


title: XT-GR-14


title: male, iron deficient + choline, rep4

city: Minneapolis

first: Phu

middle: V

last: Tran

state: MN

address: 516 Delaware St., SE

department: Department of Pediatrics

institute: University of Minnesota

data_processing:
Raw reads were processed with CHURP-PURR pipeline (https://doi.org/10.1145/3332186.3333156). Each library was searched for contamination from ribosomal RNA using a representative rRNA sequence list from the SILVA database release 132. Reads were summarized with FastQC, adapter-trimmed (Trimmomatic) and aligned to the reference genome with HISAT2.
Alignments were processed with the featureCounts tool from the subread package. Fragments were counted in a strand-specific manner. Both mates of a read pair were required to map to a feature to be counted.
Assembly: Rnor_6.0
Supplementary files format and content: Tab delimited text files with raw counts. Column names correspond to samples and row names to genes.

organism: Rattus norvegicus

source_name: Hippocampus

extract_protocol:
RNAqueous RNA isolation kit (Ambion)
TruSeq RNA v2 kit (Illumina). Libraries were size- selected to have approximatelly 200-bp inserts and sequenced as a 50-bp pair end

value: Sprague-Dawley

value: Hippocampus

value: male

tag: diet

value: IDch

tag: age (days)

tag: seq batch

value: I


title: XT-GR-85

tag: treatment


title: male, iron deficient + choline, rep3

tag: Sex


title: male, iron deficient + choline, rep2

tag: strain


title: male, iron deficient + choline, rep1


title: XT-GR-70

tag: cell type


title: XT-GR-61

tag: genotype


title: male, iron deficient, rep4

value: ID


title: XT-GR-48


title: XT-GR-17


title: male, iron deficient, rep3


title: XT-GR-43


title: male, iron deficient, rep2


title: male, iron deficient, rep1


title: XT-GR-22


title: male, iron sufficient + choline, rep4

value: ISch


title: XT-GR-64


title: male, iron sufficient + choline, rep3


title: XT-GR-16


title: male, iron sufficient + choline, rep2


title: XT-GR-11


title: XT-GR-96

value: Clear-cell


title: male, iron sufficient + choline, rep1


title: XT-GR-46

value: Tumor Tissue


title: male, iron sufficient, rep3

value: IS


title: XT-GR-76

value: Ovarian cancer

value: High-grade serous


title: male, iron sufficient, rep2


title: XT-GR-80


title: male, iron sufficient, rep1


title: XT-GR-56

value: Myriad MyChoice CDx Positive

value: Before chemotherapy


title: XT-GR-100

value: Myriad MyChoice CDx Negative


title: WT Normoxia 105

first: Vamsi

last: Mootha

state: MA

address: 185 Cambridge Street 6th Floor

institute: Massachusetts General Hospital

description:
unstranded 150bp; 2 lanes 350M raw reads per lane
ercc1_rna-seq.raw_counts.csv.gz
ercc1_rna-seq.sample_metadata.csv.gz
ercc1_rna-seq.gene_metadata.csv.gz

data_processing:
Reads were aligned to the mm10 mouse genome assembly with the STAR aligner (v. 2.7.5a).
For reads that aligned equally well to both the mtDNA and a known NUMT, the mtDNA alignment was set as the primary alignment in the BAM file.
Duplicate reads were removed using Picard MarkDuplicates (GATK v4.1.5.0-9-g227bef6-SNAPSHOT, Picard v2.21.9).
Reads were mapped to genes using featureCounts (Subread v2.0.1) with GENCODE vM24 genome annotation for the mm10 assembly, and with options "-t exon -p -M --primary".
The featureCounts output was parsed and assembled into an annotated data matrix (AnnData v0.7.5) for downstream analysis.
Assembly: mm10
Supplementary files format and content: ercc1_rna-seq.raw_counts.csv.gz is a comma-delimited file that contains the raw read count data for each sample and gene. ercc1_rna-seq.sample_metadata.csv.gz is a comma-delimited file that contains the metadata for each sample. Note that sample WT Normoxia 101 was an outlier in PCA and had excessive Cook's distance on many genes based on DESeq2 analysis, so was excluded from our analysis. ercc1_rna-seq.gene_metadata.csv.gz is a comma-delimited file that contains the metadata for each gene, including Ensembl gene ID, the gene common name, and the transcript length as reported in the featureCounts output (for use in TPM normalization of the counts).

source_name: bulk cerebellum

extract_protocol:
RNA was extracted and polyA-selected by Genewiz (now Azenta Life Sciences, South Plainfield, NJ)
Unstranded RNA-seq libraries were prepared by Genewiz (now Azenta Life Sciences, South Plainfield, NJ)

treatment_protocol: Hypoxia treament = at age 4 weeks (time of weaning) mice were placed in continuous 11% oxygen (normobaric at sea level, achived with dilution of air with nitrogen) for the remainder of the experiment. All mice were hybrid C57BL/6 and FVB.

value: M

value: bulk cerebellum

value: WT

value: Normoxia (21%)

tag: time (age_in_weeks)


title: XT-GR-1


title: WT Normoxia 104

value: F


title: XT-GR-57

value: After chemotherapy


title: WT Normoxia 102


title: WT Normoxia 103


title: WT Hypoxia 110

value: Hypoxia (11%)


title: XT-GR-18


title: XT-GR-79


title: XT-GR-26


title: WT Normoxia 101


title: XT-GR-45


title: WT Hypoxia 109


title: XT-GR-99


title: male, iron sufficient, rep4

value: Sprague-Dawley

value: Hippocampus

value: male

value: I


title: WT Hypoxia 108


title: XT-GR-49

value: Tumor Tissue


title: XT-GR-90

value: Ovarian cancer


title: XT-GR-98

value: High-grade endometrioid


title: WT Hypoxia 107


title: WT Hypoxia 104


title: WT Hypoxia 106


title: WT Hypoxia 105


title: XT-GR-93

value: High-grade serous


title: XT-GR-59

value: Myriad MyChoice CDx Positive

value: Before chemotherapy


title: WT Hypoxia 103


title: WT Hypoxia 102


title: WT Hypoxia 101

value: M


title: XT-GR-6


title: XT-GR-25


title: KO Normoxia 106

value: bulk cerebellum

value: Ercc1 [delta]/-


title: XT-GR-54

value: Myriad MyChoice CDx Negative


title: KO Normoxia 105

value: F

value: Normoxia (21%)


title: KO Normoxia 104


title: XT-GR-72

value: Undifferentiated

value: After chemotherapy


title: KO Normoxia 103


title: XT-GR-83


title: XT-GR-87


title: XT-GR-92


title: XT-GR-77


title: KO Hypoxia 106

value: Hypoxia (11%)


title: XT-GR-31


title: KO Normoxia 101


title: KO Normoxia 102


title: KO Hypoxia 105


title: XT-GR-3


title: XT-GR-2


title: XT-GR-10


title: KO Hypoxia 104


title: KO Hypoxia 102


title: XT-GR-40


title: KO Hypoxia 101


title: XT-GR-63


title: XT-GR-55


title: XT-GR-74