title: HiChIP H3K4me3 neural retina, biological replicate 2

city: Sevilla

first: Pedro Manuel

last: Martínez-García

state: Sevilla

address: Ctra. de Utrera, km. 1, 41013 Montequinto, Sevilla

institute: CSIC

description:
one technical replicate
HiChIP_H3K4me3_retina_combined.hic

data_processing:
Reads from biological replicates were pooled and aligned using GEM
Ligation events were detected using TADbit and filtered for non-ligated and self-ligated events
Binary multiresolution hic files were generated using Juicer Tools Pre
Assembly: Homo sapiens (hg38/GRCh38)
Supplementary files format and content: multiresolution hic files
Library strategy: Hi-ChIP

source_name: Neural retina

extract_protocol:
Post-mortem human neural retina and RPE/choroid mixtures were obtained through the Tissue Bank of Ghent University Hospital and Antwerp University Hospital under ethical approval of the Ethics Committee of Ghent University (2018/1072, B670201837286). Eye globes were provided with a description of time and cause of death, post-mortem circulation time, age and sex. None of the 6 donors had a prior known ophthalmological condition.  The eye globes were dissected on ice, followed by extraction of the neural retina and the retinal pigment epithelium/choroid. The resulting tissues were resuspended in 1XPBS supplemented with 10% Fetal Bovine Serum. The samples were processed according to Matelot & Noordermeer (2016) and cross-linking of nuclei was performed using 2% formaldehyde. Finally, the obtained nucleai were aliquoted per 10 million and snap frozen after supernatant removal. Samples were stored at -80°C. Extracted nuclei were processed for HiChIP preparation as previously described (Mumbach et al. 2016). Briefly, chromatin was digested with DpnII, fragment-ends were blunted and marked with dATP-biotin, followed by proximity ligation. Chromatin was sonicated in a Covaris M220 sonicator for fragments around 300 bp and immunoprecipitated with anti-H3K4me3 (abcam). DNA was extracted after cross-link reversal and biotinylated products were recovered with streptavidin-coated beads, TAGmented with Tn5 transposase and purified for library preparation.
Preparation of HiChIP libraries was performed as described for ATAC-seq assays in Buenrostro et al., 2015

value: Neural retina

tag: developmental stage

value: Adult

value: wild-type

value: H3K4me3 (Abcam, #ab8580)


title: single-Jk5-Sis-KO_v-Abl_Jk5_rep1

status: Public on Apr 08 2024

type: SRA

city: Boston

first: Frederick

last: Alt

state: MA

address: 1 Blackfan Circle

department: Program in Cellular and Molecular Medicine

country: USA

institute: Boston Children's Hospital / Harvard Medical School

description: aligned to AJ851868/mm9 hybrid genome

library_source: genomic

data_processing:
Standard basecalling formats for Miseq reads
Nextseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively
Reads were mapped to the indicated reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the reads composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp
Assembly: mm9 genome, AJ851868/mm9 hybrid genome and indicated custom genomes
Supplementary files format and content: Tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paired end read (Qlen); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)
Library strategy: HTGTS-V(D)J-seq

molecule: genomic DNA

organism: Mus musculus

source_name: v-Abl transformed pro-B cell line

growth_protocol: v-Abl cell lines were cultured in RPMI1640 media with 15% FBS

extract_protocol:
DNA was lysed overnight at 56degC in a lysis buffer containing: 200mM NaCl, 0.2% SDS, 10mM Tris-HCl pH7.4, 2mM EDTA pH8.0, 200ug/ml proteinase K, precipitated by isopropanol and dissolved in buffer containing 10mM Tris-HCl pH7.4, 0.5mM EDTA pH8.0
HTGTS-V(D)J-seq libraries were prepared using linear-amplification PCR-mediated high-throughput genome-wide translocation sequencing protocol with indicated bait primers

treatment_protocol:
Pre-B cells were isolated from mouse bone marrow by FACS sorting for B220+ CD43low IgM- cells
RAG complementation was performed by infecting v-Abl cell lines with RAG1 and/or RAG2 retrovirus followed by selection with blasticidin or puromycin
G1-arrest was performed by treating v-Abl cell lines with 3uM STI for 4 days
WAPL-depletion was performed by treating WAPL-degron v-Abl cell lines with 150uM IAA and 2mg/ml Dox for 3 days, starting on day 1 of G1-arrest

tag: cell line

value: v-Abl transformed pro-B cell line

tag: strain

tag: genotype

value: Rag2-/-, Emu-Bcl2, single Jk5-Sis KO

tag: treatment

value: RAG2 complementation, G1-arrest


title: HiChIP H3K4me3 neural retina, biological replicate 1

country: Spain

organism: Homo sapiens

tag: tissue

tag: chip antibody

value: untreated


title: RPMI 8226 cells, KO (rep 1)

city: Geneva

first: Rafael

last: Rincon Perez

state: Geneva

address: Rue Michel Servet 1, 1221, Genève

country: Switzerland

institute: Université de Genève

library_source: transcriptomic

data_processing:
After sequencing quality control (FastQC), the reads were aligned to the GRCh38 Ensembl human genome reference with STAR v.2.7.4.
The aligned reads were assessed for gene features with HTSeq v0.9.1 and the matrix of counts per genes was produced.
The differential expression analysis was performed with the statistical analysis R/Bioconductor package edgeR 1.34.1.
After normalization, the poorly detected genes were filtered out and out of 60,666 total genes, 21,394 genes with a count above 10 were kept.
Among them, only those genes with a fold change 2 threshold and a p-value < 0.05 (with a false discovery rate of 5%) were considered as differentially expressed.
Assembly: GRCh38
Supplementary files format and content: Microsoft Excel worksheet (xlsx) including raw counts for all samples
Supplementary files format and content: Microsoft Excel worksheet (xlsx) including normalized counts (cpm) for all samples
Supplementary files format and content: Microsoft Excel worksheet (xlsx) including differentially expressed genes (DEG, FC > 2, FDR 5%) between HDAC6 KO and WT cell lines
Supplementary files format and content: Microsoft Excel worksheet (xlsx) including differentially expressed genes (DEG, FC > 2, FDR 5%) between HDAC6 RY and WT cell lines

molecule: total RNA

source_name: RPMI 8226

growth_protocol: RPMI 8226 multiple myeloma cell lines were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) and antibiotics in humified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Aurum™ total RNA mini kit (Bio-Rad)
Library TruSeq HT stranded

value: RPMI 8226

tag: cell type

value: Multiple myeloma

value: HDAC6 KO


title: single-Jk5-Cer-KO_v-Abl_Jk5_rep4

description: aligned to AJ851868/mm9 hybrid genome

value: Rag2-/-, Emu-Bcl2, single Jk5-Cer KO


title: sMPTP_ACSA2 cells_MPTP4 Str

city: Pamplona

first: Maria S.

last: Aymerich

state: Navarra

address: Calle Irunlarrea, 1

department: Biochemistry and Genetics

institute: Universidad de Navarra

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to mm10 genome using Kallisto
Calculate raw counts with Kallisto
Assembly: mm10
Supplementary files format and content: abundance files from Kallisto

molecule: polyA RNA

source_name: Striatum

extract_protocol:
Samples were prepared with the Illumina TruSeq Stranded mRNA kit following manufacturer’s indications and sequenced as reverse paired-end (50 bp) runs on the Nextseq sequencer
Truseq mRNA (Illumina)
full length strand specific mRNA sequencing

value: Striatum

value: ACSA2+ cells


title: sMPTP_CD11b cells_Ctrl1 Mdb

source_name: Midbrain

value: Midbrain

value: CD11b+ cells


title: RPMI 8226 cells, WT (rep 2)

value: WT


title: single-Jk5-Cer-KO_v-Abl_Jk5_rep3

description: aligned to AJ851868/mm9 hybrid genome


title: RPMI 8226 cells, WT (rep 1)


title: sMPTP_CD11b cells_MPTP1 Mdb


title: single-Jk5-Cer-KO_v-Abl_Jk5_rep2

description: aligned to AJ851868/mm9 hybrid genome


title: HiChIP H3K4me3 RPE/choroid, biological replicate 1

description:
three technical replicates
HiChIP_H3K4me3_RPE_combined.hic

source_name: RPE/choroid

value: RPE/choroid


title: sMPTP_ACSA2 cells_MPTP3 Str


title: sMPTP_ACSA2 cells_MPTP2 Str


title: oxldl_siMCT43

city: Nanjing

first: Hong

last: Jiang

address: Longmian Road No.101

country: China

institute: Nanjing Medical University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: MCT4 deficiency


title: single-Jk5-Cer-KO_v-Abl_Jk5_rep1

description: aligned to AJ851868/mm9 hybrid genome


title: oxldl_siMCT42


title: C57BL/6J  mice, T3, ZnPP (20mg/kg)+OA (295.5 mg/kg)

city: Zunyi

first: Shaoyu

last: Zhou

state: Guizhou

address: Xinpu Campus, No.6 West Xuefu Road, Xinpu District, Zunyi City, Guizhou, China

institute: Zunyi Medical University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM and count values for each Sample

source_name: Liver

growth_protocol: All animals were kept under temperature-controlled (22-25℃) at conditions. And all mice were housed in recyclable individually ventilated cages in the SPF grade animal house on a 12 h light/dark cycle. Mice were fed a normal chow diet (protein, 20.6%; fat, 12.0%; carbohydrates, 67.4%; 1010088; Jiangsu Xietong, China) and sterile water, except for fasting period.

treatment_protocol: Protoporphyrin IX zinc (ZnPP) (Sigma) was intraperitoneally administrated at dose of 20 mg/kg or equal volume of 0.9% normal saline. After 2 hours, OA group and Znpp+OA group were gavaged OA (295.92 mg/kg, Sigma), whereas the contral groups received the same volume of corn oil intragastrically. Collect samples after four consecutive days.

value: Liver

value: ZnPP (Intraperitoneal injection, 20mg/kg)+OA (intragastrical administration, 295.5 mg/kg)


title: sMPTP_ACSA2 cells_Ctrl3 Str


title: Igh-Igk-hybrid_v-Abl_JH1-4_rep3

description: aligned to AJ851868/mm9 hybrid genome

value: v-Abl transformed pro-B cell line

value: Rag2-/-, Emu-Bcl2, Igh-Igk hybrid


title: C57BL/6J  mice, T2, ZnPP (20mg/kg)+OA (295.5 mg/kg)


title: oxldl_3

value: control


title: sMPTP_ACSA2 cells_Ctrl2 Str


title: Igh-Igk-hybrid_v-Abl_JH1-4_rep2

description: aligned to AJ851868/mm9 hybrid genome

value: RAG2 complementation, G1-arrest


title: C57BL/6J  mice, T1, ZnPP (20mg/kg)+OA (295.5 mg/kg)


title: sMPTP_ACSA2 cells_Ctrl1 Str


title: HiChIP H3K4me3 RPE/choroid, biological replicate 2

value: Adult

value: wild-type

value: H3K4me3 (Abcam, #ab8580)

value: untreated


title: C57BL/6J  mice, M3, OA (295.5 mg/kg)

value: OA (intragastrical administration, 295.5 mg/kg)


title: oxldl_2


title: sMPTP_CD11b cells_MPTP3 Str

value: Striatum


title: C57BL/6J  mice, M2, OA (295.5 mg/kg)


title: Igh-Igk-hybrid_v-Abl_Jk5_rep3

description: aligned to AJ851868/mm9 hybrid genome


title: C57BL/6J  mice, M1, OA (295.5 mg/kg)


title: sMPTP_CD11b cells_MPTP2 Str


title: Igh-Igk-hybrid_v-Abl_Jk5_rep2

description: aligned to AJ851868/mm9 hybrid genome


title: sMPTP_CD11b cells_MPTP1 Str


title: C57BL/6J  mice, C3, Corn oil

value: Corn oil (intragastrical administration)


title: SW620_mRNA-seq_Rep2

city: Shenzhen

first: Zhenzhen

last: Wang

address: 97 Buxin Road

institute: Chinese Academy of Agricultural Sciences

data_processing:
Sequence reads are mapped to h38 using HISTAT2(version 2.2.1) with default parameters
Raw counts for the feature of genes were extracted by featureCounts (version 2.0.3).
BigWig files were generated by using deepTools (version 3.5.1)
Assembly: GRCh38
Supplementary files format and content: BigWig format

extract_protocol:
Nucleic acid was extracted by SDS
gDNA library, mRNA library and mRNA&gDNA library were constructed by extracting whole nucleic acid from cells. RNase A enzyme is used to remove RNA from gDNA library. Genome DNA was removed by digested with DNase I in mRNA library while retained in mRNA&gDNA library as internal reference. mRNA was reverse-transcribed with oligo(dT) as the primer to synthesis the first strand of the complementary DNA (cDNA). To reduce bias and simplify our pipeline, fragmented cDNA without second strand synthesis and gDNA were denatured by heat following library preparation using a high-efficient ssDNA ligation technique, Adaptase from Accel-NGS 1S Plus DNA Library Kit (Swift Accel-NGS).

tag: molecule type

value: mRNA

value: untreatment


title: sMPTP_CD11b cells_Ctrl3 Str

value: CD11b+ cells


title: C57BL/6J  mice, C2, Corn oil

value: WT


title: single-Jk5-INV_v-Abl_Jk5_rep4

description: aligned to AJ851868/mm9 hybrid genome

value: Rag2-/-, Emu-Bcl2, single Jk5-INV


title: oxldl_siMCT41

value: MCT4 deficiency


title: SW620_mRNA_gDNA-seq_Rep2

library_source: other

molecule: other

value: mRNA  gDNA


title: sMPTP_CD11b cells_Ctrl2 Str


title: CON-5

city: Corvallis

first: Susan

middle: C.

last: Tilton

state: OR

address: 1007 ALS Bldg

department: AG Envr & Molec Toxicology

institute: Oregon State University

data_processing:
Reads were annotated and mapped to the human genome assembly GRCh38.p12 using HISAT
Differential expression (q<0.05) was determined in DESeq2  compared to vehicle control.
Assembly: GRCh38.p12
Supplementary files format and content: Processed data files are normalized read counts with corresponding Entrez Gene ID after DESeq2 analysis

source_name: primary bronchial epithelial cells differentiated at air-liquid interface

growth_protocol: Primary HBEC (Lonza) were expanded and transferred to transwell inserts for differentiation at the air-liquid interface in 24-well plates each containing 500 uL of assay medium utilizing the PnuemaCult™ ALI medium kit (STEMCELL Technologies, Vancouver, CA).   Cells were cultured at 37C, 5% CO2 with media changes every 48 to 72 hours.  On day 10, 10 ug/mL interleukin-13 was added to media for cells to induce an asthmatic phenotype.  IL-13 was included in every media change after day 10 for cells to induce an asthmatic phenotype.

extract_protocol:
Total RNA was isolated from HBEC (n=4) using RNeasy Mini Kits (Qiagen) and was quantified on a Synergy HTX plate reader equipped with a Take3 module (BioTek).  RNA quality was evaluated based on 260/280 ratio (acceptable range 2.0-2.1) and by examining 18S and 28S peaks (Bioanalyzer 2100, Agilent, Santa Clara, CA). Acceptable RNA quality was based on RIN ≥ 8.5.
mRNA was poly-A selected, and libraries were prepared as previously described (Dasgupta et al., 2022.

treatment_protocol: On day 25, inserts were washed with DPBS (pH 7.0 -- 7.3) and then exposed on the apical surface for 48 hours to either 25 uL 1% dimethyl sulfoxide (DMSO) with a DPBS vehicle or BAP (1 – 40 ug/mL) in DMSO with a DPBS vehicle.

value: vehicle control (PBS with 1% DMSO)


title: C57BL/6J  mice, C1, Corn oil

value: Liver


title: SW620_mRNA_gDNA-seq_Rep1


title: sMPTP_CD11b cells_Ctrl1 Str


title: single-Jk5-INV_v-Abl_Jk5_rep2

description: aligned to AJ851868/mm9 hybrid genome

value: v-Abl transformed pro-B cell line

value: RAG2 complementation, G1-arrest


title: Microglia 1% B3

city: Houston

first: Wei

last: Cao

state: Texas

address: 6431 Fannin St

department: Anesthesiology

institute: UT Health Houston

data_processing:
Quality control:  Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality
Reads mapping to the reference genome:  Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 2 reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level:  featureCounts v1.5.0-p3 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. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: mm39
Supplementary files format and content: text file includes first raw counts for each sample and then fpkm counts for each sample

source_name: Primary cultured microglia

extract_protocol:
RNA was harvested using Direct-zol RNA Microprep Kits
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

value: Primary cultured microglia

value: 1% O2 for 8h


title: single-Jk5-INV_v-Abl_Jk5_rep3

description: aligned to AJ851868/mm9 hybrid genome


title: SK-OV-3_mRNA-seq_Rep2


title: Igh-Igk-hybrid_v-Abl_JH1-4_rep1

description: aligned to AJ851868/mm9 hybrid genome

value: Rag2-/-, Emu-Bcl2, Igh-Igk hybrid


title: oxldl_1

value: control


title: Microglia 1% B2


title: thymus wt 2211 biol rep 03

city: Prague

first: Filip

last: Horvat

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR

data_processing:
Small RNA-seq reads were trimmed in two rounds using fastx-toolkit version 0.0.14 (http://hannonlab.cshl.edu/fastx_toolkit) and cutadapt version 1.8.3 (31). First, 4 random bases were trimmed from left side: fastx_trimmer -f 5 -i {INP}.fastq -o {TMP}.fastq
Next, NEXTflex adapters were trimmed. Additionally, the N-nucleotides on ends of reads were trimmed and reads containing more than 10% of the N-nucleotides were discarded: cutadapt --format="fastq" --front=”GTTCAGAGTTCTACAGTCCGACGATCNNNN” --adapter=”NNNNTGGAATTCTCGGGTGCCAAGG” --error-rate=0.075 --times=2 --overlap=14 --minimum-length=12 --max-n=0.1 --output=”${TRIMMED}.fastq" --trim-n --match-read-wildcards ${TMP}.fastq
Trimmed reads were mapped to the mouse (mm10) genome with added pCag-EGFP MosIR sequence with following parameters: STAR --readFilesIn ${TRIMMED}.fastq.gz --runThreadN 4 --genomeDir ${GENOME_INDEX} --genomeLoad LoadAndRemove --readFilesCommand unpigz -c --readStrand Unstranded --limitBAMsortRAM 20000000000 --outFileNamePrefix ${FILENAME} --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 99999 --outFilterMismatchNoverLmax 0.1 --outFilterMatchNminOverLread 0.66 --alignSJoverhangMin 999 --alignSJDBoverhangMin 999
Genome browser coverage tracks in bigWig format were produced using bedtools v2.26.0 and wigToBigWig v4 from UCSC: genomeCoverageBed -ibam ${FILENAME}.bam -bg -split > ${FILENAME}.bedGraph wigToBigWig ${FILENAME}.bedGraph chrNameLength.txt ${FILENAME}.bw
Assembly: mm10
Supplementary files format and content: .bigWig
Supplementary files format and content: coverage genome browser tracks files: - bigWig format - generated in a non-stranded mode - not normalized for library size

source_name: thymus

extract_protocol:
Organs from adult mice (9-13 w) were homogenized in Qiazol lysis reagent (Qiagen) and total RNA was isolated by phenol–chloroform extraction according to the manufacturer's protocol.
Small-RNA libraries were prepared using the NextFlex Small-RNA-seq v3 kit (Amplicon) according to the manufacturer’s protocol; 3′ adapter ligation was performed overnight at 20 °C, 15-18 cycles were used for PCR amplification and gel purification was performed for size selection. For gel purification, libraries were separated on a 2.5% agarose gel using 1× lithium borate buffer and visualized with ethidium bromide. The 140-160 bp fraction was cut off the gel and DNA was isolated using the MinElute Gel Extraction Kit (Qiagen). Final libraries were sequenced by 75-nucleotide single-end reading using the Illumina NextSeq500/550 platform

value: thymus

value: Dicerwt/wt

tag: age

value: adult

tag: expt month_year

tag: replicate


title: single-Jk5-INV_v-Abl_Jk5_rep1

description: aligned to AJ851868/mm9 hybrid genome


title: thymus wt 2211 biol rep 02


title: Igh-Igk-hybrid_v-Abl_Jk5_rep1

description: aligned to AJ851868/mm9 hybrid genome


title: SK-OV-3_mRNA-seq_Rep1

value: mRNA

value: untreatment


title: Microglia 1% B1


title: SK-OV-3_mRNA_gDNA-seq_Rep2


title: DJH-INV_v-Abl_WAPL-depleted_JH4_rep3

description: aligned to mm9_DQ52JH4 genome

value: Rag1-/-, Emu-Bcl2, OsTIR1, WAPL-degron, single Igh, DJH-INV

value: RAG1&2 complementation, G1-arrest, WAPL-depletion


title: SW620_mRNA-seq_Rep1


title: thymus wt 2211 biol rep 01


title: SK-OV-3_mRNA_gDNA-seq_Rep1


title: DJH-INV_v-Abl_WAPL-depleted_JH4_rep2

description: aligned to mm9_DQ52JH4 genome


title: thymus DicerSOMhet PKRnull MosIR 2306 biol rep 03

value: DicerSOM/wt Pkr-/- Tg(MosIR)


title: Microglia 5% A3

value: 5% O2 for 8h


title: DJH-INV_v-Abl_WAPL-depleted_JH4_rep1

description: aligned to mm9_DQ52JH4 genome


title: NCl-H226_mRNA-seq_Rep2


title: thymus DicerSOMhet PKRnull MosIR 2306 biol rep 02


title: Microglia 5% A2


title: NCl-H226_mRNA-seq_Rep1


title: Microglia 5% A1


title: NCl-H226_mRNA_gDNA-seq_Rep2

value: mRNA  gDNA


title: thymus DicerSOMhet PKRnull MosIR 2306 biol rep 01


title: thymus DicerDHEL1het PKRnull MosIR 2211 biol rep 03

value: Dicer{delta}HEL1/wt Pkr-/- Tg(MosIR)


title: DJH-WT_v-Abl_WAPL-depleted_JH4_rep2

description: aligned to mm9_DQ52JH4 genome

value: v-Abl transformed pro-B cell line

value: Rag1-/-, Emu-Bcl2, OsTIR1, WAPL-degron, single Igh, DJH-WT


title: DJH-WT_v-Abl_WAPL-depleted_JH4_rep1

description: aligned to mm9_DQ52JH4 genome


title: single-Jk1-allele_v-Abl_Jk1_rep3

description: aligned to AJ851868/mm9 hybrid genome

value: Rag2-/-, Emu-Bcl2, single Jk1 allele

value: RAG2 complementation, G1-arrest


title: NCl-H226_mRNA_gDNA-seq_Rep1


title: Microglia 21% B4

value: Primary cultured microglia

value: 21% O2 for 8h


title: Microglia 21% B3


title: MDA-MB-468_mRNA-seq_Rep2


title: single-Jk1-allele_v-Abl_Jk1_rep2

description: aligned to AJ851868/mm9 hybrid genome


title: Microglia 21% B2


title: thymus DicerDHEL1het PKRnull MosIR 2211 biol rep 02

value: thymus


title: MDA-MB-468_mRNA-seq_Rep1


title: thymus DicerDHEL1het PKRnull MosIR 2211 biol rep 01


title: single-Jk1-allele_v-Abl_Jk1_rep1

description: aligned to AJ851868/mm9 hybrid genome


title: Microglia 21% B1


title: Microglia 5% A4


title: MDA-MB-468_mRNA_gDNA-seq_Rep2


title: thymus DicerDHEL1het PKRhet MosIR 2211 biol rep 03

value: Dicer{delta}HEL1/wt Pkr+/- Tg(MosIR)


title: MDA-MB-468_mRNA_gDNA-seq_Rep1


title: thymus DicerDHEL1het PKRhet MosIR 2211 biol rep 01

value: adult


title: Microglia 21% A3


title: thymus DicerDHEL1het PKRhet MosIR 2211 biol rep 02


title: Microglia 21% A2


title: single-Jk5-Vk-INV_v-Abl_Jk5_rep1

description: aligned to AJ851868/mm9 hybrid genome

value: Rag2-/-, Emu-Bcl2, single Jk5-Vk INV


title: DU145_mRNA-seq_Rep1

value: mRNA

value: untreatment


title: spleen wt 2211 biol rep 02

source_name: spleen

value: spleen

value: Dicerwt/wt


title: single-Jk5-allele_v-Abl_Jk5_rep7

description: aligned to AJ851868/mm9 hybrid genome

value: Rag2-/-, Emu-Bcl2, single Jk5 allele


title: Microglia 21% A1


title: spleen wt 2211 biol rep 03


title: single-Jk5-allele_v-Abl_Jk5_rep6

description: aligned to AJ851868/mm9 hybrid genome


title: DU145_mRNA-seq_Rep2


title: DU145_mRNA_gDNA-seq_Rep2

value: mRNA  gDNA


title: Astrocytes 1% B3

source_name: Primary cultured astrocytes

value: Primary cultured astrocytes

value: 1% O2 for 8h


title: single-Jk5-allele_v-Abl_Jk5_rep5

description: aligned to AJ851868/mm9 hybrid genome

value: v-Abl transformed pro-B cell line


title: spleen DicerSOMhet PKRnull MosIR 2101 biol rep 03

value: DicerSOM/wt Pkr-/- Tg(MosIR)


title: spleen DicerSOMhet PKRnull MosIR 2101 biol rep 02


title: Astrocytes 1% B4


title: single-Jk5-allele_v-Abl_Jk5_rep4

description: aligned to AJ851868/mm9 hybrid genome

value: RAG2 complementation, G1-arrest


title: DU145_mRNA_gDNA-seq_Rep1


title: spleen wt 2211 biol rep 01


title: single-Jk5-Vk-INV_v-Abl_Jk5_rep3

description: aligned to AJ851868/mm9 hybrid genome


title: A498_mRNA-seq_Rep2


title: Astrocytes 1% B1


title: Astrocytes 1% B2


title: single-Jk5-allele_v-Abl_Jk5_rep3

description: aligned to AJ851868/mm9 hybrid genome


title: A498_mRNA-seq_Rep1


title: single-Jk5-Vk-INV_v-Abl_Jk5_rep2

description: aligned to AJ851868/mm9 hybrid genome


title: A498_mRNA_gDNA-seq_Rep1


title: A498_mRNA_gDNA-seq_Rep2


title: spleen DicerSOMhet PKRhet MosIR 2101 biol rep 03

value: DicerSOM/wt Pkr+/- Tg(MosIR)


title: single-Igk-allele_v-Abl_Jk5_rep4

description: aligned to AJ851868/mm9 hybrid genome

value: Rag2-/-, Emu-Bcl2, single Igk allele


title: Astrocytes 5% A4

value: 5% O2 for 8h


title: Astrocytes 5% A1


title: spleen DicerSOMhet PKRhet MosIR 2101 biol rep 02


title: spleen DicerSOMhet PKRnull MosIR 2101 biol rep 01


title: single-Igk-allele_v-Abl_Jk5_rep3

description: aligned to AJ851868/mm9 hybrid genome


title: single-Jk5-allele_v-Abl_Jk5_rep2

description: aligned to AJ851868/mm9 hybrid genome


title: spleen DicerSOMhet PKRhet MosIR 2101 biol rep 01


title: spleen DicerDHEL1het PKRnull MosIR 2101 biol rep 03

value: Dicer{delta}HEL1/wt Pkr-/- Tg(MosIR)


title: UMSCC74B cells, PRMT5 KD-1

city: ALBUQUERQUE

first: Viswanathan

last: Palanisamy

state: New Mexico

address: MSC01 1230 1 Univ of NM

department: Division of Molecular Medicine

institute: University of New Mexico Health Sciences Center

description: instrument model: Singular Genomics G4

data_processing:
nfcore rnaseq v 3.12.0
Read quality was checked for each sample using FastQC.
Sequence reads were trimmed for adapter sequence using Trim Galore.
Trimmed sequence reads were mapped to GRCh38 using STAR aligner
Read count extraction was done using Salmon and normalization performed using DESeq2.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: UMSCC74Bcells were grown to 70% confluency in  DMEM containing 10% FBS, 100 U/mL P/S, and 1X non-essential amino acids.

extract_protocol:
The mRNA and protein expression of PRMT5 was assessed by Realt time quantitative PCR and immunoblot.
RNA libraries for RNASeq were prepared using the NEBNext Ultra II Directional RNA Library Prek Kit for Illumina from New England BioLabs

treatment_protocol: Cells were washed with PBS and transfected using trasfection medium having ShRNA control and ShRNA PRMT5 plasmids independently and grown without antibiotic for 72 h.

value: HNSCC

value: PRMT5 KD

value: ShRNA


title: UMSCC74B cells, PRMT5 KD-2

description: instrument model: Singular Genomics G4


title: single-Igk-allele_v-Abl_Jk5_rep2

description: aligned to AJ851868/mm9 hybrid genome


title: Astrocytes 21% B3

value: 21% O2 for 8h


title: spleen DicerDHEL1het PKRnull MosIR 2101 biol rep 02

value: spleen

value: adult


title: UMSCC74B cells, Control-1

description: instrument model: Singular Genomics G4

value: WT

value: CONTROL


title: spleen DicerDHEL1het PKRnull MosIR 2101 biol rep 01


title: single-Igk-allele_v-Abl_Jk5_rep1

description: aligned to AJ851868/mm9 hybrid genome


title: UMSCC74B cells, Control-2

description: instrument model: Singular Genomics G4


title: Vk-INV_BM-preB_Jk5_rep7

description: aligned to AJ851868/mm9 hybrid genome

source_name: bone marrow pre-B cells

value: bone marrow pre-B cells

value: Vk-INV

value: pre-B cell isolation from mouse bone marrow


title: spleen DicerDHEL1het PKRhet MosIR 2211 biol rep 03

value: Dicer{delta}HEL1/wt Pkr+/- Tg(MosIR)


title: Astrocytes 5% A3

value: Primary cultured astrocytes


title: Astrocytes 21% B2


title: Alice_3

city: New York

first: Li

last: Gan

state: NY

address: 413 East 69th Street, 9th Floor BB904

department: Helen and Robert Appel Alzheimer’s Disease Research Institute

institute: Weill Cornell Medicine

description: mRNA expression in human iPSC-derived neurons

data_processing:
Gene counts were obtained by aligning reads to the human genome (hg38) with Cell Ranger software (v.6.1.2) (10x Genomics).
Cell Ranger 6.1.2 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 3 cells, cells with a unique gene count over 9000 or less than 300, cells with UMI counts over 50000, and cells with a high fraction of mitochondrial reads (>30%).
Potential doublet cells were predicted and removed using DoubletFinder for each sample.
SoupX was used to identify and remove ambient RNA from the dataset (Young et al., 2020)
Seurat v4.0.0 R package used for analysis
Assembly: hg38 genome
Supplementary files format and content: barcodes.tsv.gz: cellular barcodes present in datase
Supplementary files format and content: features.tsv.gz: IDs of quantified genes
Supplementary files format and content: matrix.mtx.gz: a matrix of count values, where rows are associated with the gene IDs above and columns correspond to the cellular barcodes.

source_name: iPSC-derived neurons

extract_protocol:
Neuronal dissociation was performed based on established protocols (Jerber et al., 2021; Tian et al., 2019).
10x Genomics 3’ library construction was prepared with Chromium Single Cell 3’ Reagent Kits v3.1 (10x Genomics, PN-1000268) according to the manufacturer’s protocol.

value: iPSC-derived neurons


title: single-Jk5-allele_v-Abl_Jk5_rep1

description: aligned to AJ851868/mm9 hybrid genome

value: v-Abl transformed pro-B cell line

value: Rag2-/-, Emu-Bcl2, single Jk5 allele

value: RAG2 complementation, G1-arrest


title: Astrocytes 21% B1


title: Astrocytes 5% A2

value: 5% O2 for 8h


title: Vk-INV_BM-preB_Jk5_rep5

description: aligned to AJ851868/mm9 hybrid genome


title: Astrocytes 21% A3


title: Vk-INV_BM-preB_Jk5_rep6

description: aligned to AJ851868/mm9 hybrid genome


title: Astrocytes 21% B4


title: spleen DicerDHEL1het PKRhet MosIR 2211 biol rep 02


title: Alice_2


title: Astrocytes 21% A4


title: 4R_P301S_plus_K18_4

description: mRNA expression in iPSC-derived neurons

data_processing:
The raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing. Paired-end reads were cleaned by trimming adapter sequences and low-quality bases using cutadapt v1.18 (Martin, 2011) and aligned and mapped to the human genome (GRCh38) using STAR v2.5.2 (Dobin et al., 2013).
The transcriptome reconstruction was performed by Cufflinks v2.1.2, and the abundance of transcripts was measured with Cufflinks in Fragments Per Kilobase of exon model per Million mapped reads (FPKM) (Trapnell et al., 2010).
Raw read counts per gene were extracted using HTSeq-count v0.11.2 (Anders et al., 2015).
DEGs were identified using the RStudio DESeq2 package (Love et al., 2014), and plots were generated with the ggplot2 package v3.4.1.
Gene Ontology analysis was performed using Gene Set Enrichment Analysis software on the four conditions using the Molecular Signatures Database C5 ontology gene sets (Liberzon et al., 2011; Subramanian et al., 2005).
Assembly: hg38 genome
Supplementary files format and content: csv: read counts

extract_protocol:
Total RNA was extracted from the samples using QuickRNA MicroPrep Kit (Zymo Research).
Preparation of the RNA sample library and RNA-seq were performed by the Genomics Core Laboratory at Weill Cornell Medicine using Illumina Stranded mRNA Sample Library Preparation kit (Illumina), according to the manufacturer’s protocol.


title: Vk-INV_BM-preB_Jk5_rep4

description: aligned to AJ851868/mm9 hybrid genome


title: spleen DicerDHEL1het PKRhet MosIR 2211 biol rep 01


title: 4R_P301S_plus_K18_3

description: mRNA expression in iPSC-derived neurons


title: Vk-INV_BM-preB_Jk5_rep3

description: aligned to AJ851868/mm9 hybrid genome


title: 4R_P301S_plus_K18_2

description: mRNA expression in iPSC-derived neurons


title: Vk-INV_BM-preB_Jk5_rep2

description: aligned to AJ851868/mm9 hybrid genome


title: liver wt 2201 biol rep 01

source_name: liver

value: liver

value: Dicerwt/wt


title: liver wt 2201 biol rep 03


title: Neuron 1% B4

source_name: Primary cultured neurons

value: Primary cultured neurons

value: 1% O2 for 8h


title: Vk-INV_BM-preB_Jk5_rep1

description: aligned to AJ851868/mm9 hybrid genome


title: 4R_P301S_plus_K18_1

description: mRNA expression in iPSC-derived neurons


title: liver DicerSOMhet PKRnull MosIR 2201 biol rep 03

value: DicerSOM/wt Pkr-/- Tg(MosIR)

value: adult


title: Neuron 1% B3


title: WT_BM-preB_Jk5_rep7

description: aligned to AJ851868/mm9 hybrid genome

value: WT


title: 4R_P301S_5

description: mRNA expression in iPSC-derived neurons

value: Vehicle


title: Neuron 1% B2


title: liver DicerSOMhet PKRnull MosIR 2201 biol rep 02


title: Alice_1

value: control


title: 4R_P301S_4

description: mRNA expression in iPSC-derived neurons


title: Astrocytes 21% A2

value: 21% O2 for 8h


title: WT_BM-preB_Jk5_rep6

description: aligned to AJ851868/mm9 hybrid genome

value: bone marrow pre-B cells

value: pre-B cell isolation from mouse bone marrow


title: Neuron 1% B1


title: Neuron 5% A4


title: 4R_P301S_3

description: mRNA expression in iPSC-derived neurons

value: iPSC-derived neurons


title: Astrocytes 21% A1

value: Primary cultured astrocytes


title: WT_BM-preB_Jk5_rep5

description: aligned to AJ851868/mm9 hybrid genome


title: WT_BM-preB_Jk5_rep4

description: aligned to AJ851868/mm9 hybrid genome


title: 4R_P301S_2

description: mRNA expression in iPSC-derived neurons


title: liver DicerSOMhet PKRnull MosIR 2201 biol rep 01


title: liver DicerSOMhet PKRhet MosIR 2201 biol rep 03

value: DicerSOM/wt Pkr+/- Tg(MosIR)


title: liver DicerSOMhet PKRhet MosIR 2201 biol rep 02


title: liver wt 2201 biol rep 02


title: 4R_P301S_1

description: mRNA expression in iPSC-derived neurons


title: Neuron 5% A3


title: liver DicerSOMhet PKRhet MosIR 2201 biol rep 01


title: Neuron 5% A2


title: 4R_plus_K18_5

description: mRNA expression in iPSC-derived neurons


title: WT_BM-preB_Jk5_rep3

description: aligned to AJ851868/mm9 hybrid genome


title: WT_BM-preB_Jk5_rep2

description: aligned to AJ851868/mm9 hybrid genome


title: WT_BM-preB_Jk5_rep1

description: aligned to AJ851868/mm9 hybrid genome


title: liver DicerDHEL1het PKRnull MosIR 2201 biol rep 03

value: Dicer{delta}HEL1/wt Pkr-/- Tg(MosIR)


title: 4R_plus_K18_4

description: mRNA expression in iPSC-derived neurons


title: liver DicerDHEL1het PKRnull MosIR 2201 biol rep 02


title: Neuron 21% B4


title: barcoded_v-Abl_Jk5_rep4

description: aligned to AJ851868/mm9 hybrid genome

value: v-Abl transformed pro-B cell line

value: RAG2 complementation, G1-arrest


title: 4R_plus_K18_3

description: mRNA expression in iPSC-derived neurons


title: Neuron 21% B3


title: liver DicerDHEL1het PKRnull MosIR 2201 biol rep 01

value: liver


title: 4R_plus_K18_2

description: mRNA expression in iPSC-derived neurons


title: Neuron 21% B2

value: Primary cultured neurons


title: barcoded_v-Abl_Jk5_rep3

description: aligned to AJ851868/mm9 hybrid genome


title: liver DicerDHEL1het PKRhet MosIR 2201 biol rep 03

value: Dicer{delta}HEL1/wt Pkr+/- Tg(MosIR)


title: barcoded_v-Abl_Jk5_rep2

description: aligned to AJ851868/mm9 hybrid genome


title: 4R_plus_K18_1

description: mRNA expression in iPSC-derived neurons


title: barcoded_v-Abl_Jk5_rep1

description: aligned to AJ851868/mm9 hybrid genome


title: Sample_8, C

city: Campinas

first: Mônica

last: Barbosa de Melo

state: Sao Paulo

address: Avenue Candido Rondon, 400. Cidade Universitária

department: Center for Molecular Biology and Genetic Engineering - CBMEG

country: Brazil

institute: Campinas University

data_processing:
Read quality was assessed by FastQC v0.11.5
Sequence reads were mapped to GRCh38.88 using STAR version 2.5.2
Read count extraction were performed using FeatureCounts algorithm from Rsubread
Assembly: GRCh38.88
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: ECFC, without ischemic stroke

extract_protocol:
RNA was harvested using Trizol Reagent (Ambion Life Technologies, Carlsbad CA, USA), and a commercial RNeasy mini Kit (Qiagen GmbH, Hilden, Germany), according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using Illumina TruSeq RNA-Seq v2 kit (Illumina, San Diego, CA, USA) according to manufacturer’s protocol.

value: peripheral blood

value: Endothelial colony-forming cell

value: SCA without IS


title: 4R_4

description: mRNA expression in iPSC-derived neurons

value: Vehicle


title: liver DicerDHEL1het PKRhet MosIR 2201 biol rep 02

value: adult


title: Neuron 21% A4

value: 21% O2 for 8h


title: Neuron 21% A3


title: Neuron 21% B1


title: Neuron 5% A1

value: 5% O2 for 8h


title: 4R_5

description: mRNA expression in iPSC-derived neurons


title: Sample_7, C


title: heart wt 2110 biol rep  02

source_name: heart

value: heart

value: Dicerwt/wt


title: Sample_6, C


title: heart wt 2110 biol rep  01


title: Neuron 21% A1


title: Neuron 21% A2


title: Sample_5, C


title: 4R_2

description: mRNA expression in iPSC-derived neurons

value: iPSC-derived neurons


title: 4R_1

description: mRNA expression in iPSC-derived neurons


title: 4R_3

description: mRNA expression in iPSC-derived neurons


title: PBS control 5

city: Beijing

first: jiabao

last: cao

address: Beichen west road

institute: Institute of microbiology, Chinese academy of science

data_processing:
Raw RNA-seq reads contaminated with adapters and reads with low-quality bases were discarded to obtain the clean reads, and then clean reads were mapped against Ensembl mouse reference GRC38 using Hisat2, and uniquely mapped reads were counted using FeatureCounts.
Assembly: Mus musculus (GRCm38)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: digit tips

growth_protocol: 9-day-old neonatal mice were mock-treated with PBS and vaseline ointment in a 10 μL volume (n > 5)

extract_protocol:
10 digits of the hind limbs from one mouse were amputated at the proximal level and collected together for RNA extraction and RNA-seq (5 dpi)
Libraries were prepared according to KAPA mRNA capture Kit and KAPA RNA HyperPrep Kit（for Illumina platform）

treatment_protocol: 9-day-old neonatal mice were infected with 10^4 TCID50 Coxsackievirus A10 in a 10 μL volume (n > 5) and vaseline or CHIR ointment

value: digit tips

value: WT

value: PBS control


title: Sample_4, IS

source_name: ECFC, ischemic stroke

value: SCA with IS


title: heart DicerSOMhet PKRnull MosIR 2110 biol rep  03

value: DicerSOM/wt Pkr-/- Tg(MosIR)


title: heart wt 2110 biol rep  03


title: PBS control 4


title: HSPC high endocytosis, scRNAseq

city: Los Angeles

first: Júlia

last: Aguadé-Gorgorió

state: California

address: 615 Charles E Young Drive South

department: Molecular, Cell and Developmental Biology

institute: University of California Los Angeles

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Sequencing was performed on the Illumina NovaSeq 6000 system.
Sequence data was mapped to the human reference genome (refdata-cellranger-GRCh38-1.2.0) using cellranger count.
Assembly: GRCh38
Supplementary files format and content: Annotated sequence data that contain cell barcodes (tsv), features (tsv) and gene expression matrix (mtx). Processed data files for the aggregated data of all samples is also provided (“aggregatedAll_”).

source_name: cord blood

growth_protocol: Human HSPCs were cultured in serum-free conditions with StemSpan SFEM II (StemCell Technologies, 9655) supplemented with 1% Pen/Strep, 1% L-glutamine, human FLT3-L (100 ng/mL, human TPO (50 ng/mL), human SCF (100 ng/mL) (Thermofisher Scientific15140122, 25030081 PHC9411, PHC9513, and PHC2113), human low-density lipoprotein (10 μg/mL), SR1 (500 nM) and UM171 (35 nM) (StemCell Technologies 2698, 72352, and 72914). Cells were cultured at 37 °C and 5% CO2, re-plated as necessary to maintain a cell density of ≤ 1x10^6/mL, and half media changes were performed every other day.

extract_protocol:
CB HSPCs were sorted after thawing (7AAD- CD34+ CD38- CD90+) and cultured for 96 hours. The cells were sorted again for HSPC phenotype (DAPI- CD34+ CD38- CD90+ EPCR+) in 3 fractions based on the intensity of internalized fluorescent dextran (20% lowest, mid, 20% highest). Cells were sorted into PBS 0.04% Ultrapure BSA (Thermofisher Scientific AM2616) using a BD FACS Aria cell sorter.
A Chromium single cell instrument (10x genomics) was used for the generation of single-cell gel beads in emulsion. In brief, single-cell suspension of cells in 0.4% BSA-PBS were added to each channel on the 10X chip. Cells were partitioned with Gel Beads into emulsion in the Chromium instrument where cell lysis and barcoded reverse transcription of RNA occurred following amplification. scRNA-seq libraries were prepared by using the Chromium single-cell 3′ library and gel bead kit v3 (10x Genomics).

value: cord blood

value: HSPC

value: 96h culture


title: liver DicerDHEL1het PKRhet MosIR 2201 biol rep 01

value: liver

value: Dicer{delta}HEL1/wt Pkr+/- Tg(MosIR)


title: heart DicerSOMhet PKRnull MosIR 2110 biol rep  02


title: PBS control 3


title: heart DicerSOMhet PKRnull MosIR 2110 biol rep  01


title: HSPC low endocytosis, scRNAseq

description: 10x Genomics


title: heart DicerSOMhet PKRhet MosIR 2110 biol rep  03

value: DicerSOM/wt Pkr+/- Tg(MosIR)


title: PBS control 2


title: HSPC mid endocytosis, scRNAseq

description: 10x Genomics


title: Sample_2, IS

value: peripheral blood

value: Endothelial colony-forming cell


title: heart DicerSOMhet PKRhet MosIR 2110 biol rep  02

value: adult


title: KO-d21 rep2

city: Chuo-ku

first: Mitsuhiro

last: Machitani

state: Tokyo

address: 5-1-1 Tsukiji

country: Japan

institute: National Cancer Center Research Institute

data_processing:
Sequencing data were analyzed to obtain the read counts for each sgRNA and to generate a maximum-likelihood estimation (mle) of gene essentiality score (beta score) for each gene using MAGeCK algorithm.
Assembly: Human Brunello CRISPR knockout pooled library (Addgene)
Supplementary files format and content: tab-delimited Excel files include counts for each Sample

source_name: hTERT-CRISPR clone

growth_protocol: U2OS cells or the hTERT-CRISPR clone (10^8 cells) were infected with the pooled lentivirus library at a multiplicity of infection (MOI) of ∼0.4 and >500-fold coverage of the library. Forty-eight hours postinfection, cells were selected with puromycin (2 μg/mL). After 48 h selection, 4 × 10^7 cells were collected as a control sample (day 0 timepoint), and the others were seeded to start the screen. Every 3 days, 4 × 10^7 cells were passaged (~500-fold coverage of the library). After 21 days of culture, 4 × 10^7 cells were harvested.

extract_protocol:
Genomic DNAs were isolated from the cell pellets using the Blood & Cell Culture DNA Maxi Kit (Qiagen) according to the manufacturer's instructions.
sgRNA sequences were amplified from 200 μg of gDNA by 20 parallel PCR reactions (10 μg of gDNA/ tube) using Q5 High-Fidelity DNA Polymerase (New England Biolabs, Ipswich, MA, USA). The resulting amplicons were mixed and purified by gel extraction using Wizard SV Gel and PCR Clean-Up System (Promega).

value: hTERT-CRISPR clone

value: osteosarcoma cell

value: hTERT +/-


title: heart DicerSOMhet PKRhet MosIR 2110 biol rep  01

value: heart


title: BT-549/tet-NEAT1siRNA_Rep3

first: Atrayee

last: Bhattacharya

state: Massachusetts

address: 450 Brookline Avenue, Boston 02215

institute: Dana Farber Cancer Institute, Harvard Medical School

data_processing:
Raw sequencing reads were aligned to the human genome (GRCh38.74) using STAR.
Raw feature counts were normalized and differential expression analysis using DESeq2.
Differential expression rank order was utilized for subsequent Gene Set Enrichment Analysis (GSEA), performed using the fgsea (v1.8.0) package in R.
Gene sets queried included those from the Hallmark Gene Sets available through the Molecular Signatures Database (MSigDB).

source_name: Breast

growth_protocol: BT-549 cells (American Type Culture Collection (ATCC), Manassas, VA, USA) were cultured in RPMI1640 medium (Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% fetal bovine serum (FBS; GEMINI Bio-Products, West Sacramento, CA, USA) and Insulin.

extract_protocol:
Total RNA from cells cultured in triplicates was isolated using RNeasy Plus Mini Kit.
TruSeq Stranded mRNA (Illumina, San Diego, CA, USA) was used for library preparation.

treatment_protocol: Cells were transfected with CsiRNA and NEAT1siRNa for 48 hours before RNA isolation

value: Breast

value: Breast Cancer

value: siRNA


title: BT-549/tet-NEAT1siRNA_Rep2


title: heart DicerDHEL1het PKRnull MosIR 2110 biol rep  03

value: Dicer{delta}HEL1/wt Pkr-/- Tg(MosIR)


title: Treat with agonist 5

value: digit tips

value: WT

value: Treat with agonist


title: BT-549/tet-NEAT1siRNA_Rep1


title: KO-d21 rep1


title: KO-d0 rep2


title: BT-549/tet-NEAT1CsiRNA_Rep3


title: Sample_3, IS

value: SCA with IS


title: Treat with agonist 3


title: KO-d0 rep1


title: Treat with agonist 4


title: heart DicerDHEL1het PKRnull MosIR 2110 biol rep  02


title: BT-549/tet-NEAT1CsiRNA_Rep2


title: Treat with agonist 2


title: U2OS-d21 rep2

value: hTERT +/+


title: Treat with agonist 1


title: heart DicerDHEL1het PKRnull MosIR 2110 biol rep  01


title: Sample_1, IS


title: heart DicerDHEL1het PKRhet MosIR 2110 biol rep  03

value: Dicer{delta}HEL1/wt Pkr+/- Tg(MosIR)


title: PBS control 1

value: PBS control


title: U2OS-d21 rep1


title: U2OS-d0 rep2


title: ST-7270 PDAC primary rep2

city: PORTLAND

first: JUNGSUN

last: KIM

address: KCRB 5001.51, 2720 SW Moody Ave

institute: Oregon Health & Science University

data_processing:
Reads with adapter sequences, reads with low quality (<Q20), short reads (<35bp), or reads with too many Ns (>5) were removed ( Trimmomatic 0.39)
Trimmed sequence reads were mapped to reference genome GRCh38.p13 using Spliced Transcripts Alignment to Reference (STAR) software.
Read count extraction were performed using featurecounts software
Raw counts were normalized with DESeq2 version 1.36.0 R package
Assembly: p13
Supplementary files format and content: Comma-separated values (CSV) text file includes DESeq2-normalized counts and gene annotation for each sample
Supplementary files format and content: Comma-separated values (CSV) text file includes raw countsfor each sample

source_name: pancreas

growth_protocol:
Human pancreatic ductal adenocarcinoma (PDAC) cell lines Panc-1 (ATCC # CRL-1469) and  CFPAC-1 (ATCC # CRL-1918) were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Thermo Fisher Scientific # 10569010) and  Iscove's modified Dulbecco’s medium (IMDM ATCC # 30-2005) respectively supplemented with 10% fetal bovine serum (FBS) in a humidified incubator with 5% CO2 at 37C.
Establish primary cell cultures (ST-7599, ST-14490  and ST-7270) were maintained in completed PDAC media (Completed Defined K-SFM medium (Thermo Fisher Scientific #10744-019) supplemented with 5 ng/ml human EGF (BD Bioscience #354052), 50 ng/ml cholera toxin (Sigma, St. Louis, MO #C8052) and 50 ug/ml bovine pituitary extract (Thermo Fisher Scientific, #13028014) under physiological conditions (37°C, 5% O₂, 5% CO₂).

extract_protocol:
RNA was prepared from frozen cells using the QIAGEN RNeasy kit. RNA quality was tested using the Bioanalyzer 2100 (Agilent) and concentration was determined using the Life Technologies Qubit.
RNA libraries were prepared for sequencing with NEBNext Ultra II non-directional RNA Library Prep kit.

value: pancreas

value: primary cell

value: pancreatic ductal adenocarcinoma

value: no treatment


title: heart DicerDHEL1het PKRhet MosIR 2110 biol rep  02

value: adult


title: ST-7270 PDAC primary rep3


title: heart DicerDHEL1het PKRhet MosIR 2110 biol rep 01

value: heart


title: Treat with virus 4

value: Treat with virus


title: U2OS-d0 rep1

value: osteosarcoma cell


title: ST-7270 PDAC primary rep1


title: Treat with virus 3


title: brain wt 2211 biol rep 03

source_name: brain

value: brain

value: Dicerwt/wt


title: ST-14490 PDAC primary rep3


title: brain wt 2211 biol rep 02


title: Treat with virus 2

value: digit tips


title: Treat with virus 1

value: WT


title: brain wt 2211 biol rep 01


title: brain DicerSOMhet PKRnull MosIR 2306 biol rep 03

value: DicerSOM/wt Pkr-/- Tg(MosIR)


title: Treat with virus 5


title: ST-14490 PDAC primary rep1


title: 8483

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

data_processing:
The quality of reads was first assessed using fastqc v. 0.11.8 and reads were trimmed using bbduk.
Cleaned reads were aligned to the mm10 reference genome and ENSEMBL annotation v. 89 using STAR v. 2.7.8a in 2-pass mode and the BAM files were sorted and indexed using  Samtools v. 1.9
featureCounts v. 2.0.1 was used to generate count matrix and an overall quality control assessment was then performed using multiqc v. 1.9
The genes in the count matrix were filtered by requiring at least 10 samples to have count greater than 10 and DESeq2 v. 1.40.2  was used for differential gene expression analysis.
The apeglm method was used for visualization and ranking and genes with adjusted p-value less than 0.05 were considered significant.
Assembly: mm10
Supplementary files format and content: Text files with counts

source_name: kidney

extract_protocol:
50mg of kidney tissue was weighed, resuspended in cold TRIzol™ Reagent (Invitrogen Life Technologies), and homogenized in a TissueLyser (Qiagen). After RT incubation, a 1:5 volume of chloroform was added to the trizol homogenates, shaken vigorously, and incubated again at RT for 5 minutes. Samples were then centrifuged at 12000g for 15 minutes to allow phase separation. Downstream steps for RNA isolation were carried out automatically on a QIACube by using the spin column kit RNAeasy Plus (Qiagen) according to manufacturers instructions.
total RNA samples (750 ng) were processed into cDNA sequencing libraries with the SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian kit, and unique dual-indexed PCR primers for amplification were used following manufacturer instructions (Takara Bio USA, Inc).

value: kidney

value: 25 months

value: Fed

tag: Sex

value: Female


title: 74B bio rep IP  eCLIP

city: Albuquerque

state: NM

address: 2325 Camino de Salud NE,

department: Internal Medicine

institute: University of New Mexico

data_processing:
Immuno precipitation of UV crosslinked FXR1 using specific antibody
IP RNA end epair and 3' adapter ligation
Libraries generated using the eCLIP-seq method are typically sequenced using standard SE50 or SE75 conditions on the Illumina HiSeq
eCLIP-Seq of 20M reads per datasets
Assembly: hg38
Supplementary files format and content: BW, Bed only for IP samples

molecule: protein

source_name: UMSCC 74B

growth_protocol: DMEM, 10% FBS with 1% penn/strep, grown the cells to 70% confluency at 37 C at 5% CO2

extract_protocol:
Immunoprecipitation
eCLIP

treatment_protocol: UV irradiation

value: UMSCC 74B

value: Head and Neack squamous cell carcinoma cell line

value: UV Cross linked


title: SM POS CON INPUT eCLIP


title: brain DicerSOMhet PKRnull MosIR 2306 biol rep 02


title: ST-7599 PDAC primary rep3

value: pancreas

value: primary cell

value: pancreatic ductal adenocarcinoma

value: no treatment


title: BT-549/tet-NEAT1CsiRNA_Rep1

city: Boston

value: Breast

value: Breast Cancer

value: siRNA


title: 6936


title: SM POS CON IP  eCLIP


title: ST-14490 PDAC primary rep2


title: 74B bio rep INPUT eCLIP


title: S16 slice 13

city: Hang Zhou

first: Tao

last: cheng

state: Zhe Jiang

address: 886 Yuhangtang Road

department: Institute of genetics

institute: Zhejiang University

data_processing:
Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 (GRCz11) using STAR v2.7.1a, and the aligned reads were assigned to each gene using featureCounts v1.6.0.
For each embryo, gene counts of each slice were merged into a count matrix, and the genes that received more than 0.5 counts per million reads (CPM) in at least 3 slices were retained.
The count matrixes with slice position information were constructed into DGEList objects using edgeR, which were saved in rds format.
Assembly: GRCz11
Supplementary files format and content: rds  files include count matrixes and slice position information after running the processing steps.

organism: Danio rerio

source_name: embryonic cells

growth_protocol: Zebrafish embryos were raised in 0.3x Danieau buffer, and were then embedded in OCT at the required developmental stages of 10 hpf, 12hpf and 16 hpf.

extract_protocol:
RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol.
Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.

treatment_protocol: Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.

value: embryonic cells

value: AB

value: 16 hpf


title: brain DicerDHEL1het PKRnull MosIR 2211 biol rep 02

value: brain

value: Dicer{delta}HEL1/wt Pkr-/- Tg(MosIR)

value: adult


title: brain DicerSOMhet PKRnull MosIR 2306 biol rep 01

value: DicerSOM/wt Pkr-/- Tg(MosIR)


title: 8482

value: kidney

value: 25 months

value: WT

value: Fed

value: Female


title: ST-7599 PDAC primary rep2

value: pancreas

value: primary cell

value: pancreatic ductal adenocarcinoma


title: 8073


title: 74B INPUT eCLIP

value: UMSCC 74B

value: Head and Neack squamous cell carcinoma cell line

value: UV Cross linked


title: ST-7599 PDAC primary rep1

value: no treatment


title: Panc-1 PDAC cell line rep2


title: brain DicerDHEL1het PKRnull MosIR 2211 biol rep 03


title: S16 slice 12

value: embryonic cells

value: AB

value: 16 hpf


title: Panc-1 PDAC cell line rep3


title: S16 slice 11


title: 74B IP eCLIP


title: CFPAC-1 PDAC cell line rep3


title: brain DicerDHEL1het PKRhet MosIR 2211 biol rep 03

value: brain

value: Dicer{delta}HEL1/wt Pkr+/- Tg(MosIR)

value: adult


title: S16 slice 10


title: Panc-1 PDAC cell line rep1


title: 4075

value: kidney

value: 25 months

value: Male


title: brain DicerDHEL1het PKRhet MosIR 2211 biol rep 02


title: 4074

value: WT

value: Fed


title: 8357

value: Female


title: 5281


title: brain DicerDHEL1het PKRhet MosIR 2211 biol rep 01


title: CFPAC-1 PDAC cell line rep1

value: pancreas

value: pancreatic ductal adenocarcinoma


title: 5438


title: 15965

value: 4 months


title: brain DicerDHEL1het PKRnull MosIR 2211 biol rep 01

value: Dicer{delta}HEL1/wt Pkr-/- Tg(MosIR)


title: 5437


title: S16 slice 7


title: 15963


title: UMI-4C in human RPE/choroid, ABCA4 Interacting Region 4 (IR4) as viewpoint, RPE_3_R_ABCA4_UMI_7

city: Sevilla

first: Pedro Manuel

last: Martínez-García

address: Ctra. de Utrera, km. 1, 41013 Montequinto, Sevilla

institute: CSIC

data_processing:
Raw fastq files were mapped, and viewpoints were demultiplexed using the R package umi4cpackage (https://bitbucket.org/tanaylab/umi4cpackage)
Contact profiles and domainograms were generated using 'p4cNewProfile' and 'plot.p4cProfile' function of the umi4cpackage with the default parameters and a min_win_cov=30
Bedgraph files were generated using 'p4cExportBedGraph' function of the umi4cpackage with default parameters and min_win_cov (Smoothing parameter) of 30
Bedgraph files in hg19 were converted into hg38 using the LiftOver executable (UCSC)
Assembly: Homo sapiens (hg38/GRCh38)
Supplementary files format and content: bedgraph files with contact data
Library strategy: UMI-4C

source_name: RPE/choroid

extract_protocol:
Post-mortem human neural retina and RPE/choroid mixtures were obtained through the Tissue Bank of Ghent University Hospital and Antwerp University Hospital under ethical approval of the Ethics Committee of Ghent University (2018/1072, B670201837286). Eye globes were provided with a description of time and cause of death, post-mortem circulation time, age and sex. None of the 6 donors had a prior known ophthalmological condition.  The eye globes were dissected on ice, followed by extraction of the neural retina and the retinal pigment epithelium/choroid. The resulting tissues were resuspended in 1XPBS supplemented with 10% Fetal Bovine Serum. The samples were processed according to Matelot & Noordermeer (2016) and cross-linking of nuclei was performed using 2% formaldehyde. Finally, the obtained nucleai were aliquoted per 10 million and snap frozen after supernatant removal. Samples were stored at -80°C. The generation of the 3C template was performed according to Schwartzman et al. 2016. Briefly, around 5 million cross-linked nuclei were digested overnight using 400 U DpnII (NEB). After digestion, ligation was performed overnight using 4,000 U of T4 DNA ligase (NEB), followed by the addition of proteinase K (BIOzymTC). Efficiency of digestion and ligation were evaluated via agarose gel electrophoresis. Next, samples were de-crosslinked, followed by purification of samples using AMPure XP beads (Agencourt). Subsequently, 4 µg of the 3C template was sheared on a Covaris M220 focused ultrasonicator to get 300 bp DNA fragments. The UMI-4C sequencing library preparation was obtained using the NEBNext Ultra II Library Prep Kit (NEB). Library amplification was performed by nested PCR. In the first PCR, 100ng of library were amplified using an upstream (US) forward primer and a universal reverse primer using the KAPA2G Robust HotStart ReadyMix (Roche). The resulting product was amplified using a downstream (DS) forward primer and the same universal reverse primer.
Preparation of libraries was performed as described for UMI-4C libraries assays in Schwartzman et al., 2016, using the NEBNext Ultra II Library Prep Kit (NEB)

tag: donor

value: Human donor 3 (Right eye)

value: RPE/choroid

value: Adult

value: wild-type

value: untreated


title: S16 slice 6

value: embryonic cells

value: AB

value: 16 hpf


title: CFPAC-1 PDAC cell line rep2

value: no treatment


title: S16 slice 5


title: Immunity 60hr (scRNAseq)

city: Melbourne

first: Ian

last: Parish

state: VIC

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

description:
matrix.mtx.gz
features.tsv.gz
barcodes.tsv.gz

data_processing:
The reads were originally paired-end, with read two containing the UMI and cell barcode. The UMI and cell barcodes have been transferred to the sequence ID lines in the read 1 FASTQ. The read 2 data can be recovered by splitting the sequenced ID strings into fields separated by the ‘-‘ character. The last field is the UMI, the 2nd last field is the cell barcode, the 4th last field is the Phred+33 quality score for the UMI, and the 5th last field is the Phred+33 quality score for the cell barcode.
From the list of cell barcodes (these can be found in sample_info.tsv), a whitelist was constructed containing all sequences within one nucleotide edit distance from a valid barcode. This was used with Umi-tools (v0.5.3) to assign each read to a valid cell barcode and remove reads with invalid barcodes.
Reads were then trimmed using Trimmomatic (v0.38) with the following settings: clip Nextera adaptors, LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, MINLEN:36.
Reads were aligned to mouse genome GRCm38, with ERCC sequences appended, using STAR (v2.6.1a).
Umi-tools (v0.5.3) was used to count the UMIs for each gene and cell.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: matrix.mtx.gz contains a gene by cell matrix of UMI counts. features.tsv.gz contains the matrix rownames and barcodes.tsv.gz contains the matrix column names.
Supplementary_files_format_and_content: sample_info.tsv contains cell metadata. The Well_ID field matches the matrix column names. This file contains sequencing, batch and treatment details and flourenscent intensity values from FACS.

source_name: T cells

extract_protocol:
Cells were sorted into 384 well plates with lysis buffer and indexing primers within each well
Libraries were prepared using the published MARS-seq scRNAseq approach

treatment_protocol: Various treatment conditions were used to activate cells in mice as described above. OT-I cells were enriched from pooled spleen and lymph nodes by magnetic bead enrichment, and then CD90.1+CD8+ cells were index sorted. CD45.1+CD8+ P14 cells were index sorted directly from spleen without enrichment.

value: CD90.1+ OT-I CD8+ T cells

value: 5x104 CTV labelled CD90.1+ OT-I cells were injected into mice then infected with OVA transgenic Listeria monocytogenes.

tag: timepoint

value: 60 hours post infection.


title: Arm/Cl13 D20 #1 (scRNAseq)

value: CD45.1+ P14 CD8+ T cells

value: 5x103 CD45.1+ P14 cells were injected into mice then infected with LCMV Armstrong (2x105 pfu i.p.) or Clone 13 (2x106 pfu i.v.)

value: 20 days post infection.


title: 15964

value: kidney

value: 4 months

value: WT

value: Fed

value: Female


title: Immunity 12hr (scRNAseq)

value: 12 hours post infection.


title: UMI-4C in human RPE/choroid, ABCA4 promoter as viewpoint, RPE_4_R_ABCA4_UMI_1

state: Sevilla

value: Human donor 4 (Right eye)

value: RPE/choroid

value: Adult

value: wild-type

value: untreated


title: 16664


title: S16 slice 3

value: embryonic cells

value: AB

value: 16 hpf


title: Arm/Cl13 D20 #2 (scRNAseq)

value: CD45.1+ P14 CD8+ T cells


title: UMI-4C in human RPE/choroid, ABCA4 Interacting Region 12 (IR12) as viewpoint, RPE_3_R_ABCA4_UMI_4

value: Human donor 3 (Right eye)


title: UMI-4C in human RPE/choroid, ABCA4 promoter as viewpoint, RPE_3_R_ABCA4_UMI_1


title: Naive 12hr (scRNAseq)

value: CD90.1+ OT-I CD8+ T cells

value: 5x104 CTV labelled CD90.1+ OT-I cells were injected into mice


title: Tolerance 60hr (scRNAseq)

value: RIP-OVAhi transgenic C57BL/6

value: 60 hours post infection.


title: S16 slice 9


title: S16 slice 4


title: 15994

value: kidney

value: 4 months

value: WT

value: Fed


title: S16 slice 2


title: 15984

value: Male


title: UMI-4C in human RPE/choroid, ABCA4 Interacting Region 7 (IR7) as viewpoint, RPE_3_R_ABCA4_UMI_5

value: RPE/choroid

value: Adult


title: Tolerance 36hr (scRNAseq)

value: 36 hours post infection.


title: Tolerance 12hr (scRNAseq)

value: 12 hours post infection.


title: 15996


title: S16 slice 1

value: embryonic cells

value: AB


title: UMI-4C in human RPE/choroid, ABCA4 Interacting Region 5 (IR5) as viewpoint, RPE_3_L_ABCA4_UMI_3

value: Human donor 3 (Left eye)

value: wild-type

value: untreated


title: 15997


title: UMI-4C in human RPE/choroid, ABCA4 Interacting Region 12 (IR12) as viewpoint, RPE_3_L_ABCA4_UMI_4


title: UMI-4C in human RPE/choroid, ABCA4 promoter as viewpoint, RPE_3_L_ABCA4_UMI_1


title: 15962


title: wild type-biol rep 5

city: St. Louis

first: James

middle: B

last: Skeath

state: Missouri

address: 4515 Couch building, 4523 Clayton Ave

department: Genetics

institute: Washington University School of Medicine

description: RNA-seq performed on indexed total RNA

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5.
Assembly: dm6
Supplementary files format and content: Each sample has its own tab-delimited file. Column 1: Feature. Column 2: Chromosome. Column 3: Start position. Column 4: End position. Column 5: Strand. Column 6: Length. Column 7: Count. Column 8: CPM. Column 9: RPKM.

organism: Drosophila melanogaster

source_name: Central nervous system

growth_protocol: Larvae were raised at 25 degree until late third instar when the CNS was dissected.

extract_protocol:
RNA was extracted using the Invitrogen RNAqueous-Micro Total RNA Isolation Kit (AM1931).
RNA was indexed by sample and pooled for sequencing.

value: Central nervous system


title: S12 slice 10

value: 12 hpf


title: UMI-4C in human RPE/choroid, ABCA4 Interacting Region 11 (IR11) as viewpoint, RPE_2_R_ABCA4_UMI_8

value: Human donor 2 (Right eye)


title: UMI-4C in human RPE/choroid, ABCA4 Interacting Region 11 (IR11) as viewpoint, RPE_3_L_ABCA4_UMI_8


title: wild type-biol rep 4

description: RNA-seq performed on indexed total RNA


title: wild type-biol rep 3

description: RNA-seq performed on indexed total RNA


title: 15961

value: kidney


title: TSK, scRNAseq

city: los angeles

first: Sandra

last: Orsulic

state: california

address: 10833 Le conte ave

department: OBGYN

institute: UCLA

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.1 (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: subcutaneous tumor

extract_protocol:
Subcutaneous Tumors collected from the flanks fof WT and TSK mice were pooled and minced into 1mm pieces. Tissue was further dissociated by enzymatic digestion by rotating at 37°C for 30 minutes with 1 mg/ml Collagenase/Hyaluronidase (STEMCELL), DNAse and trypsin (0.01%). After dissociation, the suspension was strained (70 micron strainer) followed by centrifugation (8 minutes at 300g). Red blood lysis buffer (Thermo Fisher) was used followed by dead cell removal (STEMCELL) to deplete the samples of erythrocytes and dead cells, respectively according to the manufacturer’s instructions. Finally, cells were resuspended in 0.04% BSA-PBS solution at a concentration of 700-1000 cells/microliter without selection for specific cell types.
Library construction was performed according to the manufacturer’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs 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 appropriate-sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, single-end constructs were added

value: subcutaneous tumor

value: TSK

value: Female

value: 6-8 weeks old


title: UMI-4C in human RPE/choroid, ABCA4 promoter as viewpoint, RPE_2_R_ABCA4_UMI_1

value: RPE/choroid


title: UMI-4C in human RPE/choroid, ABCA4 Interacting Region 4 (IR4) as viewpoint, RPE_1_R_ABCA4_UMI_7

value: Human donor 1 (Right eye)

value: Adult


title: S12 slice 8


title: wild type-biol rep 2

description: RNA-seq performed on indexed total RNA


title: WT, scRNAseq

description: 10x Genomics

value: WT


title: Immunity 36hr (scRNAseq)

value: CD90.1+ OT-I CD8+ T cells

value: 5x104 CTV labelled CD90.1+ OT-I cells were injected into mice then infected with OVA transgenic Listeria monocytogenes.

value: 36 hours post infection.


title: S12 slice 12

value: embryonic cells

value: AB


title: wild type-biol rep 1

description: RNA-seq performed on indexed total RNA

value: Central nervous system

value: wild-type


title: D4_H3K27me3_2

city: Schwerzenbach

first: Adhideb

last: Ghosh

address: Schorenstrasse 16

department: Health Sciences and Technology

institute: ETH Zurich

data_processing:
TrimGalore v0.6.6 used for trimming low quality bases + adapter sequences
Bowtie2 v2.4.4 used for read mapping
samtools v1.13 used for sorting bam files
bedtools v2.30 used for converting sorted bam files into bedgraph files
SEACR v1.3 used for calling peaks
Assembly: GRCm39
Supplementary files format and content: tab delimited called peak regions for each sample
Library strategy: Cut&Tag

source_name: post-ischemia hind limb recruited macrophages

extract_protocol:
To isolate macrophages, calf muscle from the ischemic limb was collected and digested in 2 mg/ml Collagenase IV (Thermo Fisher Scientific, 17104019) / Dispase II (Sigma-Aldrich, D4693-1G) for 1 h at 37°C. After filtration and washing steps, red blood cells were removed with ACK Lysis buffer (Gibco, A1049201).  CD45+CD11b+F4/80+CD64+ macrophages were stained and sorted (Sony Cell sorter SH800S) . The used antibodies were the following: PE anti-mouse CD45 (Biolegend [30-F11], 103106), PerCP/Cy5.5 anti-mouse/human CD11b (Biolegend [M1/70], 101228), Alexa Fluor® 488 anti-F4/80 mouse Monoclonal Antibody (Biolegend [clone: 30-F11], 103122), APC anti-CD64 mouse Monoclonal Antibody (Biolegend [clone: X54-5/7.1], 139306).  CUT&Tag was performed as described earlier starting from nuclei (Galle et al., 2022). Nuclei were isolated from the sorted macrophages. In short, the macrophages were centrifuged for 5 min at 4°C, 500 rpm, supernatant was removed, and the cells were lysed on ice in 1 mL of nucleus extraction buffer (1× prelysis buffer from the EpiGentek EpiQuick Total Histone Extraction Kit, OP-0006-100). To stop the lysis reaction, 1 mL of PBS+1%BSA was added, and nuclei were collected through centrifugation for 5 min at 4°C, 500 rpm. The supernatant was removed, the nuclei were resuspended in PBS+1% BSA, and a sample was visually inspected for viability, purity, and abundance of nuclei under the microscope. Next, CUT&Tag libraries were created according to the published CUT&Tag protocol [29] for nuclei. All buffers were supplemented with 5 mM sodium-butyrate (Sigma, 303410) and 1X complete protease inhibitor (Merck, 1187358000). Protein lo-bind tubes (Eppendorf, EP0030108116) were used to reduce sample loss. Antibodies against H3K18la (PTM-Bio, PTM-1406), H3K4me3 (Abcam, ab8580), H3K27me3 (Cell Signaling Technology, C36B11) and H3K27ac (Abcam, ab4729) were used in this study.
PCR was performed using Kapa HiFi plus dNTPs (Roche Diagnostics, #07958846001) with the following PCR settings: 72˚C 5 minutes, 98˚C 30 seconds, 15 cycles of 98˚C 10 seconds, 63˚C 30 seconds, 72˚C final extension for 1 minute, hold at 4˚C. Libraries were indexed using Nextera Indexes, and 150-bp paired-end sequencing was performed on Illumina Novaseq instruments.

value: macrophages

value: C57BL6J wild type

tag: histone

value: hind limb ischemia

tag: time

value: macrophages recruited to the hind limb muscle 4 days after ischemia induction profiled for H3K27me3


title: UMI-4C in human RPE/choroid, ABCA4 Interacting Region 7 (IR7) as viewpoint, RPE_1_R_ABCA4_UMI_5

tag: developmental stage

value: untreated


title: S12 slice 11

value: 12 hpf


title: S12 slice 6


title: UMI-4C in human RPE/choroid, ABCA4 promoter as viewpoint, RPE_1_R_ABCA4_UMI_1

value: RPE/choroid


title: UMI-4C in human RPE/choroid, ABCA4 Interacting Region 11 (IR11) as viewpoint, RPE_1_L_ABCA4_UMI_8

value: Human donor 1 (Left eye)


title: S12 slice 5


title: ifc mutant-biol rep 4

description: RNA-seq performed on indexed total RNA

value: ifc-/- mutant


title: D4_H3K27me3_1

value: post-ischemia hind limb recruited macrophages


title: D2_H3K27me3_2

value: macrophages recruited to the hind limb muscle 2 days after ischemia induction profiled for H3K27me3


title: UMI-4C in human RPE/choroid, ABCA4 Interacting Region 12 (IR12) as viewpoint, RPE_1_L_ABCA4_UMI_4

value: Adult


title: S12 slice 9


title: S12 slice 4


title: D2_H3K27me3_1


title: ifc mutant-biol rep 3

description: RNA-seq performed on indexed total RNA


title: UMI-4C in human RPE/choroid, ABCA4 Interacting Region 5 (IR5) as viewpoint, RPE_1_L_ABCA4_UMI_2


title: S12 slice 3


title: S12 slice 2


title: ifc mutant-biol rep 1

description: RNA-seq performed on indexed total RNA


title: UMI-4C in human RPE/choroid, ABCA4 promoter as viewpoint, RPE_1_L_ABCA4_UMI_1


title: S12 slice 7


title: S16 slice 8

value: 16 hpf


title: D4_H3K27ac_1

value: macrophages recruited to the hind limb muscle 4 days after ischemia induction profiled for H3K27ac


title: D4_H3K27ac_2


title: S12 slice 1

value: embryonic cells

value: AB


title: ifc mutant-biol rep 2

description: RNA-seq performed on indexed total RNA

value: Central nervous system


title: D2_H3K27ac_2

value: macrophages

value: macrophages recruited to the hind limb muscle 2 days after ischemia induction profiled for H3K27ac


title: UMI-4C in human neural retina, ABCA4 promoter as viewpoint, Ret_5_R_ABCA4_UMI_1

source_name: Neural retina

value: Human donor 5 (Right eye)

value: Neural retina

value: wild-type


title: Dhps<fl/fl>;Vil1<cre/+> + C. rodentium 16

city: Nashville

first: guoqiang

last: Gu

state: Tennessee

address: 9415D Medical Research Building IV

department: Department of Cell and Developmental Biology

institute: Vanderbilt University Medical Center

description:
10987-AG-16
CreCitroS16

data_processing:
STAR (v2.7.11a)
Reads were trimmed to remove adapter sequences using Cutadapt v4.5
Reads were aligned to the Gencode GRCm38.p6 genome using STAR (v2.7.11a). Gencode vM24 gene annotations were provided to STAR to improve the accuracy of mapping.
Quality control on both raw reads and adaptor-trimmed reads was performed using FastQC (v0.12.1) (www.bioinformatics.babraham.ac.uk/projects/fastqc).
featureCounts (v2.0.6) was used to count the number of mapped reads to each gene.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

source_name: colonic mucosa

extract_protocol:
Total RNA from colonic tissues was isolated using the RNeasy Mini kit (Qiagen)
NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (BioLabs, Inc.)

treatment_protocol: Mice were infected or not with Citrobacter rodentium for 14 days

value: colonic mucosa

value: epithelial cells

tag: infection

value: C. rodentium


title: S10 slice 28

tag: strain

value: 10 hpf


title: ifc mutant-biol rep 5

description: RNA-seq performed on indexed total RNA

tag: genotype

value: ifc-/- mutant


title: Dhps<fl/fl> + C. rodentium 14

description:
10987-AG-14
FloxCitroS14

value: Dhps<fl/fl>


title: Dhps<fl/fl>;Vil1<cre/+> + C. rodentium 15

description:
10987-AG-15
CreCitroS15


title: D2_H3K27ac_1

value: post-ischemia hind limb recruited macrophages

value: C57BL6J wild type

tag: treatment

value: hind limb ischemia


title: S10 slice 26

tag: tissue

value: embryonic cells


title: UMI-4C in human neural retina, ABCA4 Interacting Region 11 (IR11) as viewpoint, Ret_3_R_ABCA4_UMI_8

value: Human donor 3 (Right eye)

value: Adult

value: untreated


title: UMI-4C in human neural retina, ABCA4 promoter as viewpoint, Ret_4_R_ABCA4_UMI_1

value: Human donor 4 (Right eye)


title: S10 slice 27

value: AB


title: UMI-4C in human neural retina, ABCA4 Interacting Region 4 (IR4) as viewpoint, Ret_3_R_ABCA4_UMI_7

value: Neural retina


title: D4_H3K4me3_1

value: macrophages

value: macrophages recruited to the hind limb muscle 4 days after ischemia induction profiled for H3K4me3


title: Dhps<fl/fl> + C. rodentium 13

description:
10987-AG-13
FloxCitroS13

value: colonic mucosa

value: epithelial cells


title: UMI-4C in human neural retina, ABCA4 Interacting Region 12 (IR12) as viewpoint, Ret_3_R_ABCA4_UMI_4

value: wild-type


title: S10 slice 24

value: 10 hpf


title: Dhps<fl/fl> + C. rodentium 12

description:
10987-AG-12
FloxCitroS12

value: Dhps<fl/fl>

value: C. rodentium


title: UMI-4C in human neural retina, ABCA4 Interacting Region 5 (IR5) as viewpoint, Ret_3_R_ABCA4_UMI_3


title: S10 slice 23


title: Dhps<fl/fl>;Vil1<cre/+> + C. rodentium 11

description:
10987-AG-11
CreCitroS11


title: D2_H3K4me3_2

value: post-ischemia hind limb recruited macrophages

value: C57BL6J wild type

value: macrophages recruited to the hind limb muscle 2 days after ischemia induction profiled for H3K4me3


title: UMI-4C in human neural retina, ABCA4 Interacting Region 5 (IR5) as viewpoint, Ret_3_R_ABCA4_UMI_2

value: Human donor 3 (Right eye)


title: D2_H3K4me3_1

value: hind limb ischemia


title: UMI-4C in human neural retina, ABCA4 promoter as viewpoint, Ret_3_R_ABCA4_UMI_1

value: Adult

value: untreated


title: Dhps<fl/fl>;Vil1<cre/+> + C. rodentium 10

description:
10987-AG-10
CreCitroS10


title: Dhps<fl/fl>;Vil1<cre/+> + C. rodentium 9

description:
10987-AG-09
CreCitroS9


title: D4_H3K18la_2

value: macrophages recruited to the hind limb muscle 4 days after ischemia induction profiled for H3K18la


title: S10 slice 22

value: embryonic cells

value: AB


title: S10 slice 21


title: UMI-4C in human neural retina, ABCA4 Interacting Region 1 (IR1) as viewpoint, Ret_2_R_ABCA4_UMI_6

value: Human donor 2 (Right eye)

value: Neural retina


title: D4_H3K18la_1

value: macrophages


title: S10 slice 20


title: Dhps<fl/fl> + C. rodentium 8

description:
10987-AG-08
FloxCitroS8

value: colonic mucosa

value: epithelial cells


title: UMI-4C in human neural retina, ABCA4 Interacting Region 7 (IR7) as viewpoint, Ret_2_R_ABCA4_UMI_5

value: wild-type


title: D4_H3K4me3_2

value: macrophages recruited to the hind limb muscle 4 days after ischemia induction profiled for H3K4me3


title: D2_H3K18la_2

value: post-ischemia hind limb recruited macrophages

value: macrophages recruited to the hind limb muscle 2 days after ischemia induction profiled for H3K18la


title: S10 slice 25

value: 10 hpf


title: D2_H3K18la_1

value: C57BL6J wild type


title: UMI-4C in human neural retina, ABCA4 Interacting Region 12 (IR12) as viewpoint, Ret_2_R_ABCA4_UMI_4


title: Dhps<fl/fl> + C. rodentium 7

description:
10987-AG-07
FloxCitroS7

value: Dhps<fl/fl>

value: C. rodentium


title: D7_3

data_processing:
TrimGalore v0.6.6 used for trimming low quality bases + adapter sequences
HISAT2 v2.2.1 used for read mapping
subread v2.0.1 used for gene quantification
edgeR used for count normalization and differential expression analysis
Assembly: GRCm39
Supplementary files format and content: tab-delimited raw count matrix of all samples

extract_protocol:
To isolate macrophages, calf muscle from the ischemic limb was collected and digested in 2 mg/ml Collagenase IV (Thermo Fisher Scientific, 17104019) / Dispase II (Sigma-Aldrich, D4693-1G) for 1 h at 37°C. After filtration and washing steps, red blood cells were removed with ACK Lysis buffer (Gibco, A1049201). Total RNA for each sample was extracted using RNeasy micro kit (QIAGEN,  74106). Quantification of total RNA was performed using the Tecan microplate reader (DKSH). Quality control of RNA was performed with the Tapestation system (Agilent). 50-100 ng of RNA was used as an input for the Smart-seq2/3 protocol (Picelli et al, 2013, 2014; Hagemann-Jensen et al, 2020) including cDNA synthesis (quantified with the Qubit system for further steps), pre-amplification, tagmentation, and enrichement step.
In short, RNA libraries were prepared by performing reverse transcription and template switching using Maxima H Minus reverse transcriptase (ThermoFisher, #EP0753), a template switch oligo and an oligodT primer to generate full length cDNA. cDNA was amplified using the Kapa Hotstart 2x ReadyMix (Roche Diagnostics, #7958935001). 1-3 ng cDNA were then tagmentated using 1.3 µg Tn5 and amplified using Kapa HiFi plus dNTPs (Roche Diagnostics, #07958846001) and the following PCR settings: 72˚C 5 minutes, 98˚C 30 seconds, 10 cycles of 98˚C for 10 seconds, 63˚C for 30 seconds, 72˚C for 1 minute, hold at 4˚C. Libraries were quantified using the KAPA library quantification kit (Roche Diagnostis, #079602), and sequenced at PE150 on a NovaSeq 6000 at Novogene.

treatment_protocol: hind-limb ischemia

value: hind limb ischemia

value: macrophages recruited to the hind limb muscle 7 days after ischemia induction


title: Dhps<fl/fl> 6

description:
10987-AG-06
FloxS6

value: untreated


title: UMI-4C in human neural retina, ABCA4 Interacting Region 5 (IR5) as viewpoint, Ret_2_R_ABCA4_UMI_3

value: Adult


title: S10 slice 17

value: embryonic cells

value: AB


title: D7_2

value: macrophages


title: UMI-4C in human neural retina, ABCA4 Interacting Region 5 (IR5) as viewpoint, Ret_2_R_ABCA4_UMI_2

value: Human donor 2 (Right eye)

value: Neural retina


title: Dhps<fl/fl> 4

description:
10987-AG-04
FloxS4

value: colonic mucosa

value: epithelial cells


title: D7_1

value: post-ischemia hind limb recruited macrophages


title: S10 slice 16


title: UMI-4C in human neural retina, ABCA4 promoter as viewpoint, Ret_2_R_ABCA4_UMI_1

value: wild-type


title: D4_3

value: macrophages recruited to the hind limb muscle 4 days after ischemia induction


title: Dhps<fl/fl>;Vil1<cre/+> 3

description:
10987-AG-03
CreS3


title: UMI-4C in human neural retina, ABCA4 Interacting Region 11 (IR11) as viewpoint, Ret_2_L_ABCA4_UMI_8

value: Human donor 2 (Left eye)


title: S10 slice 15

value: 10 hpf


title: Dhps<fl/fl>;Vil1<cre/+> 2

description:
10987-AG-02
CreS2


title: S10 slice 19


title: S10 slice 14


title: D4_2

value: C57BL6J wild type


title: UMI-4C in human neural retina, ABCA4 Interacting Region 4 (IR4) as viewpoint, Ret_2_L_ABCA4_UMI_7


title: Dhps<fl/fl>;Vil1<cre/+> 1

description:
10987-AG-01
CreS1


title: S10 slice 13


title: D4_1

value: hind limb ischemia


title: D2_3

value: macrophages recruited to the hind limb muscle 2 days after ischemia induction


title: UMI-4C in human neural retina, ABCA4 promoter as viewpoint, Ret_2_L_ABCA4_UMI_1

value: untreated


title: CAF-200-3

city: Seoul

first: Young-Ho

last: Ahn

address: 25 Magokdong-ro 2-gil, Gangseo-gu

department: College of Medicine

country: South Korea

institute: Ewha Womans University

data_processing:
RNA-seq data qulity was checked using Fastqc, and sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt and Trimmomatic.
Trimmed sequence reads were mapped to GrCM38/mm10 using STAR.
Read count extraction, normalization, and differntial expression were performed using RSEM and edgeR.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include the Trimmed Mean of the M-values (TMM) values for each sample

source_name: lung

growth_protocol: CAFs were cultured in alpha-MEM containing 10% FBS, penicillin/streptomycin, 2 mM L-glutamine, and 1 mM sodium pyruvate at 37 °C in the presence of 5% CO2.

extract_protocol:
Total RNAs were isolated from CAF-VEC and CAF-200 using an AccuPrep Universal RNA Extraction Kit (Bioneer, Korea).
After checking the quantity and integrity of the total RNA, an RNA library was constructed from 1 μg of total RNA using an Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA).
Paired-end (2 × 100 bp) sequencing of the indexed library was performed using Illumina NovaSeq (Illumina).

treatment_protocol: miR-200b/a/429_pLVX-Neo was introduced into CAFs by lentiviral infection. CAFs were infected with lentiviruses produced from 293T cells co-transfected with the lentiviral vectors, pMD2.G, and psPAX2 for 2–3 days and then selected with G418 for more than 2 weeks.

value: lung

tag: cell line

value: CAF

value: miR-200 overexpression


title: UMI-4C in human neural retina, ABCA4 Interacting Region 1 (IR1) as viewpoint, Ret_1_L_ABCA4_UMI_6

value: Human donor 1 (Left eye)

value: Adult


title: S10 slice 18

value: embryonic cells

value: AB


title: D2_2

tag: cell type

value: macrophages


title: S10 slice 12


title: Dhps<fl/fl> 5

description:
10987-AG-05
FloxS5

value: colonic mucosa

value: epithelial cells

value: Dhps<fl/fl>


title: S10 slice 11


title: UMI-4C in human neural retina, ABCA4 Interacting Region 7 (IR7) as viewpoint, Ret_1_L_ABCA4_UMI_5

value: Neural retina

value: wild-type


title: UMI-4C in human neural retina, ABCA4 Interacting Region 12 (IR12) as viewpoint, Ret_1_L_ABCA4_UMI_4


title: D2_1

value: post-ischemia hind limb recruited macrophages

value: C57BL6J wild type


title: CAF-200-1


title: S10 slice 9

value: 10 hpf


title: UMI-4C in human neural retina, ABCA4 Interacting Region 5 (IR5) as viewpoint, Ret_1_L_ABCA4_UMI_3

value: untreated


title: S10 slice 10


title: D1_2

value: hind limb ischemia

value: macrophages recruited to the hind limb muscle 1 day after ischemia induction


title: CAF-VEC-1

value: lung

value: CAF

value: WT control


title: S10 slice 8

value: embryonic cells


title: D1_3


title: UMI-4C in human neural retina, ABCA4 Interacting Region 5 (IR5) as viewpoint, Ret_1_L_ABCA4_UMI_2

value: Human donor 1 (Left eye)

value: Adult


title: LMOVA_rep3 (RNAseq)

description: rawcounts.csv

data_processing:
Illumina Casava1.8.2 software used for basecalling
Reads were trimed using bbduk (v38.90) to remove adapter sequences and poor quality ends.
trimmed reads were aligned using STAR (v2.7.5b) to the mouse reference genome (mm10)
Aligned reads were counted using featurecounts (v2.0.1)
Assembly: mm10
Supplementary files format and content: csv file include raw count (non-normalized) values for each sample

source_name: OT-I CD8+ T cell

extract_protocol:
RNA was harvested using the Qiagen MinElute RNAeasy kit. All isolated RNA was then used for library construction.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep with PolyA Selection following manufacturer's protocols.

treatment_protocol:
CTV labelled CD45.1+ OT-I cells were injected i.v. into RIP-OVAhi mice that were untreated B6 mice (Tolerance), injected i.p. with OVA protein (OVAp), LM-33 infected i.p. (LM-33) or LM-OVA infected i.p. (LM-OVA)
60h after transfer, divided CD45.1+ OT-I cells were sorted from pooled sacral and pancreatic LNs. As a control for naïve OT-I cells, naïve (CD44loCD62Lhi) CD8+ cells were sorted from CD45.1+ OT-I mice.

value: OT-I CD8+ T cell

value: CD45.1+ OT-I TCR transgenic

value: 2x10^6 CTV labelled CD45.1+ OT-I cells were injected i.v. into RIP-OVAhi transgenic B6 mice that were simultaneously infected i.p. with 2x10^6 cfu LM-OVA


title: D1_1

value: macrophages


title: UMI-4C in human neural retina, ABCA4 promoter as viewpoint, Ret_1_L_ABCA4_UMI_1

value: Neural retina

value: wild-type


title: S10 slice 7

value: AB


title: CD11b+ myeloid cells, mtD2pos_3

city: Shanghai

first: Peng

last: Ding

address: No.600, Yishan Road

department: Orthopaedics

institute: Shanghai Jiao Tong University Affiliated Sixth People’s Hospital

data_processing:
After sequencing, generated reads were filtered and mapped to the reference genome using HISAT2 (v2.0.4)and assembled using StringTie (v1.3.4d) with default parameters.
All transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (v0.9.8) and the expression levels of all transcripts were calculated by Stringtie and ballgown.
Differential gene analysis was performed by DESeq2 software and then subjected to enrichment analysis of GO functions.
Assembly: Mus_musclus.GRCm38 V99
Supplementary files format and content: Excel file includes count and FPKM values for each Sample

source_name: bone marrow

growth_protocol: MtD2pos and mtD2neg CD11b+ myeloid cells were separated from Prx1creMitodendra+/+  mouse bone marrow

extract_protocol:
The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent,CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
Following purification, mRNA library was constructed, fragmented, amplified and loaded into the nanoarray and sequencing was performed on Illumina Novaseq™ 6000 platform following the vendor’s recommender protocol.

treatment_protocol: Using flow cytometry to sort targeted CD11b+ myeloid cells  by green fluorescence.

value: bone marrow

value: CD11b+ myeloid cells

tag: cell status


title: LMOVA_rep2 (RNAseq)

description: rawcounts.csv


title: CAF-200-2

value: miR-200 overexpression


title: S10 slice 6

tag: age

value: 10 hpf


title: HiC neural retina, replicate 4

data_processing:
Paired-end reads were processed into multiresolution .hic files using Juicer (v1.6) with BWA-MEM mapping (v0.7.17).
Paired contacts from individual replicates were merged using Juicer "mega" to create combined .hic files for each tissue.
Assembly: Homo sapiens (hg38/GRCh38)
Supplementary files format and content: multiresolution hic files

extract_protocol:
Post-mortem human neural retina and RPE/choroid mixtures were obtained through the Tissue Bank of Ghent University Hospital and Antwerp University Hospital under ethical approval of the Ethics Committee of Ghent University (2018/1072, B670201837286). Eye globes were provided with a description of time and cause of death, post-mortem circulation time, age and sex. None of the 6 donors had a prior known ophthalmological condition.  The eye globes were dissected on ice, followed by extraction of the neural retina and the retinal pigment epithelium/choroid. The resulting tissues were resuspended in 1XPBS supplemented with 10% Fetal Bovine Serum. The samples were processed according to Matelot & Noordermeer (2016) and cross-linking of nuclei was performed using 2% formaldehyde. Finally, the obtained nuclei were aliquoted per 10 million and snap frozen after supernatant removal. Samples were stored at -80°C.
Crosslinked nuclei from four neural retina and four RPE/choroid samples were used to construct Hi-C libraries, following the in situ Hi-C protocol adopted by the 4D Nucleome consortium with a few adaptations. Briefly, for each replicate ~5 million pre-lysed, crosslinked nuclei were digested overnight using 250 U DpnII restriction enzyme (New England Biolabs, R0543L). DNA ends were marked by incorporating biotin-14-dATP (Life Technologies, 19524-016) and ligated for 4 hours using 2000 U T4 DNA ligase (New England Biolabs, M0202L). Subsequently, crosslinks were reversed overnight using proteinase K (Qiagen, 19131) and Hi-C template DNA was purified using 1x AMPure XP beads (Beckman Coulter, A63881) and stored at 4°C until library preparation. Hi-C template DNA was sheared to a size of 300-500 bp using microTUBE snap-caps (Covaris, 520045) in a Covaris M220 sonicator and MyOne Streptavidin T1 beads (Life Technologies, 65601) were used to pull down biotinylated ligation junctions. Next, samples were split into 5 µg aliquots for sequencing library preparation using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs, E7645L) and NEBNext Multiplex Oligos (New England Biolabs, E7335L). Amplified libraries were purified and size selected using 0.55x and 1.2x AMPure XP beads (Beckman Coulter, A63881). Pooled libraries were sequenced on an Illumina NovaSeq 6000 using 100 bp paired-end reads to a depth of ~500 million reads per sample.
in situ Hi-C

value: untreated


title: OVAp_rep3 (RNAseq)

description: rawcounts.csv

value: 2x10^6 CTV labelled CD45.1+ OT-I cells were injected i.v. into RIP-OVAhi transgenic B6 mice that were simultaneously injected i.p. with 2mg purified OVA protein


title: CAF-VEC-2

value: lung

value: CAF

value: WT control


title: S10 slice 5

value: embryonic cells


title: S10 slice 3


title: HiC neural retina, replicate 2

value: Adult


title: LMOVA_rep1 (RNAseq)

description: rawcounts.csv

value: OT-I CD8+ T cell

value: CD45.1+ OT-I TCR transgenic


title: HiC neural retina, replicate 3


title: CD11b+ myeloid cells, mtD2neg_3


title: S10 slice 4


title: CD11b+ myeloid cells, mtD2pos_1


title: OVAp_rep2 (RNAseq)

description: rawcounts.csv


title: HiC RPE/choroid, replicate 4

value: RPE/choroid