title: HUVECs_PA_Sample 1

first: Xiao-Hui

last: Tan

address: 8, Xishiku Street, Xicheng District

institute: Peking University First Hospital

data_processing:
Illumina Casava1.7 software
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt (version 2.7)
Trimmed sequence reads were mapped to GRCh38.102/hg38 (human) and Rnor_6.0.102/rn6 (Rat) using Hisat2 (version 2.0.5).
The output SAM (sequencing alignment/map) files were converted to BAM (binary alignment/map) files and sorted using SAM tools (version 1.3.1).
Gene abundance was expressed as fragments per kilobase of exon per million reads mapped (FPKM). Stringtie software was used to count the fragment within each gene, and TMM algorithm was used for normalization.
Assembly: hg38, rn6
Supplementary files format and content: Matrix table with FPKM values and counts for each sample

source_name: Primary cells

growth_protocol: HUVECs and RCCECs were maintained in endothelial cell medium (ScienCell) supplemented with 5% fetal bovine serum (FBS), endothelial cell growth supplement, and antibiotics in a humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
The total RNA from primary cells was extracted using Trizol (Invitrogen) following the manufacturer's procedure. The quality and integrity of each sample were checked using the Agilent BioAnalyzer 2100 (Agilent RNA 6000 nano kit) and a NanoDrop ND-1000 spectrophotometer (NanoDrop Technology, Rockland, DE). 1 mg of RNA was used as input material for the RNA sample preparations.
Paired-end libraries were synthesized by using the mRNA-seq Lib Prep Kit for Illumina (ABclonal, Wuhan, Hubei, China).

treatment_protocol: Endothelial dysfunction was induced by treatment of 24-h post confluent cells with palmitic acid.

value: Primary cells

tag: cell type

value: Human umbilical vein endothelial cells

value: palmitic acid


title: MV4;11_MEN1-WT_DMSO_Menin-ChIP_SNDX5613_0.1uM

status: Public on Dec 01 2022

type: SRA

city: Hannover

first: Florian

last: Perner

address: Carl-Neuberg-Str. 1

department: Hematology, Hemostasis, Oncology and Stem Cell Transplantation

country: Germany

institute: Hannover Medical School

description:
MV411_ChIP_MEN1_SNDX_100nM_4d_REP1_220115_TTAGGC_S2
MV4;11_MEN1-WT-vs-M327I_TSS-signals.xlsx
MV4;11_MEN1-WT-vs-M327I_Alignment-rmdup_STATs.zip

library_source: genomic

data_processing:
Raw Illumina sequencer output was converted to FASTQ format using bcl2fastq (v2.20.0.422).
Reads (paired-end 37-mers) were aligned to the human(Gencode GRCh38/hg38) genome using STAR (v2.7.5a; params --alignIntronMax 1 --alignEndsType EndToEnd --alignM  atesGapMax 2000 for ChIPseq analysis), sorted and duplicates marked/removed with picard pipeline tools (v2.9.4).
Final “deduped” .BAM files were indexed using SAMtools (v1.95).
ChIP-seq data visualizations were produced using IGVtools (TDF signal pileups; v2.3.75) and ngs.plot (pileup heatmaps). ChIPseq peaks were called using MACS2 with appropriate input samples used as controls.
TSS signals were assessed using the bedtools coverage function. Signal values were normalized based on the ratio of hg38-aligning reads in treated and control samples, after deduplication.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Sample signal files for visualization in IGV (.tdf), MACS peak calling output (.xls) and summary bedtools TSS signal intensities (xlsx)

molecule: genomic DNA

organism: Homo sapiens

source_name: MLL-AF4 rearranged human leukemia cell line (MV4;11)

growth_protocol: MV4;11 cells were cultured in PRMI1640 media supplemented with 10% Fetal bovine serum (v/v) (Gibco), 1x penicillin/streptomycin (Gibco), plasmocin (ThermoFisher). For the treatment the cells were plated at 2x10^5 cells/ml in T75 tissue culture treated flasks. Cryo-conserved PDX material was transplanted into non-conditioned NOG mice (250.000 cells per mouse) and harvested from bone marrow of tibias, femurs, iliac crests and lumbar spine after 14 days of drug- or vehicle-treatment.

extract_protocol:
PDX-derived human leukemia cells from the bone marrow were depleted for mouse cells using magnetic cell sorting (mouse cell depletion kit, Milteny). The cells were collected and washed twice in ice-cold PBS followed by crosslinking in 1% formaldehide (methanol free) for 5 minutes. Excess of formaldehyde was quenched by addition of Tris pH 8.0 to 100nM final and Glycine 125 mM final. Chromatin was cheared using Covaris E220 for 20 min with power 140; duty 5; bursts 200/sec. We then used 5ul aliquote of sherared chromatin to decrosslink in order to test completeness of shearing. Chromatin was considered passed QC if fragments 100-600bp were >90%. For immunoprecipitation we used aproximately chromatin from 1-10x10^6 cells, 5-10ug of specific antibody and 10-20ul of Protein-A/G magnetic beads (Dynal). In 16 hours the immune complexes were wased in Mixed Micelle Buffer, buffer 500, LiCl/detergent solution and TE buffers. DNA was eluted from the beads using 100mM NaHCO3 100mM NaCl 1% SDS and purified using AmpureXP beads.
1-10 ng of ChIP'ed DNA was used for Illumina compatibl library generation using ThruPlex DNA-seq kit with 12 to 14 cycles of amplification with single or paired end barcodes

treatment_protocol: ChIPseq for Menin and MLL1 was performed in MV4;11 cells harboring a MEN1-M327I mutation and in an MLL-AF10 rearranged PDX with MEN1-T349M as well as the respective isogenic WT controls. Drug treatments were performed for 4 days in vitro for with different doses of SNDX-5613 (0.1uM, 1uM, 5uM) or DMSO control. Treatment of the MLL-AF10 PDX CBAM44728 was performed by oral exposure in vivo using 0.1% VTP-50469 supplemented rodent diet for 14 days.

tag: cell line

tag: chip-antibody

value: anti-Menin (Rb)

tag: antibody manufacturer

value: Bethyl laboratories

tag: antibody catalog number

tag: treatment molecule

tag: treatment timepoint

tag: treatment dose


title: HUVECs_PA_Sample 3

city: Beijing

country: China

library_source: transcriptomic

molecule: total RNA

tag: treatment


title: Cerebellum WT 26wk replicate 4

city: Minneapolis

first: Christine

middle: M.

last: Henzler

state: MN

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

country: USA

institute: University of Minnesota, Twin Cities (Minneapolis, MN, US)

data_processing:
Illumina bcl2fastq2 v2.20.0 software used for basecalling.
FASTQ files were trimmed, aligned to the mouse reference genome (GRCm38), sorted, and counted using the Bulk RNAseq Analysis Pipeline from the Minnesota Supercomputing Institute’s Collection of Hierarchical UMII/RIS Pipelines (v0.2.0 was used for 26-week-old data. v0.2.2 was used for the 10-week-old data). Component steps for read trimming, aligning and counting are as follows:
Reads were trimmed with Trimmomatic v.0.33 using illumina adapters, seedMismatches=4,palindromeClipThreshold=15, simpleClipThreshold=7, minAdapterLength=2 and keepBothReads=true
Trimmed reas were aligned to GRCm38 using hisat v.2.1.0 using the parameters --rna-strandedness RF and --no-mixed (suppress unpaired alignments for paired reads).
Aligned reads were assinged to genes using the featureCounts function of Subread v.1.6.2 with the parameters -B -p -Q10 -s2 and the Ensembl GRCm38 v.97 annotation gtf.
Assembly: GRCm38
Supplementary files format and content: subread_counts_10wk.txt is a matrix of gene counts for each sample at 10 weeks of age
Supplementary files format and content: subread_counts_26wk.txt is a matrix of gene counts for each sample at 26 weeks of age

organism: Mus musculus

source_name: cerebellum

extract_protocol:
Collected tissue was stored in RNAlater solution (Thermo Fisher Scientific). Total RNA was isolated using TRIzol reagent (Thermo Fisher Scientific) following the manufacturer’s protocol. Quality control involved quantification using fluorimetry via RiboGreen assay kit (Thermo Fisher Scientific) and RNA integrity was assessed via capillary electrophoresis using an Agilent BioAnalyzer 2100 to generate an RNA integrity number (RIN).
Library creation was completed using oligo-dT purification of polyadenylated RNA, which was reverse transcribed to create cDNA. cDNA was fragmented, blunt ended, and ligated to barcode adaptors. Libraries were size selected to 320 bp ± 5% to produce average inserts of approximately 200 bp, and size distribution was validated using capillary electrophoresis and quantified using fluorimetry (PicoGreen, Thermo Fisher Scientific) and qPCR. Libraries were then normalized, pooled, and sequenced on an S4 flow cell by an Illumina NovaSeq 6000 using a 150-nucleotide, paired-end read strategy. Libraries were prepared and sequenced in two batches based on mouse age; 10-week mice were sequenced to a minimum of 70 million reads/sample, while 26-week mice were sequenced to  a minimum pf 40 million reads/sample.

tag: tissue

value: cerebellum

tag: gender

value: male

tag: age

value: post natal week 26

tag: genotype

value: WT

tag: strain


title: h3.3ko_G24h_2

first: Zhang

last: Huairen

address: No. 1 West Beichen Road

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

data_processing:
Adapter trimming was performed and low quality reads were filtered with fastp version 0.20.1
Reads were mapped to the Arabidopsis genome (TAIR10) with Botiew2 version 2.4.2
Reads were filtered for duplicated reads by using Picard version 2.24.0 MarkDuplicates
bigwig coverage files were generated using deepTools utility bamCoverage with a bin size of 10bp and normalized to sequencing depth using RPKM
Average ATAC-seq profiles were generated using deepTools utility plotProfile
Supplementary files format and content: TAIR10
Supplementary files format and content: *.bw, normlized ATAC-seq coverage files

organism: Arabidopsis thaliana

source_name: imbibed seeds

growth_protocol: Mature seeds, seeds imbibed for different time periods, seedlings

extract_protocol:
Seeds at different germination stages or 10-day-old seedlings were chopped in lysis buffer (15 mM Tris-HCl pH 7.5, 20 mM NaCl, 80 mM KCl, 0.5 mM Spermine, 0.2% Triton X-100, 5 mM β-ME, protease inhibitor cocktail). After being filtered with a 30μm filter (CellTrics), nuclei were stained with DAPI and subjected to fluorescence-activated cell sorting (FACS). 50,000 nuclei per sample were collected and mixed with Tn5 transposase (Mei5bio, MF650-01), after 20 minutes of incubation at 37°C, tagmented DNA was recovered with ChIP DNA Clean & Concentrator kit (ZYMO, D5205).
After PCR amplification, sequencing libraries were purified with VAHTS DNA Clean Beads (Vazyme N411)

value: imbibed seeds

value: seeds subject to germination for 24 hours


title: HUVECs_PA_Sample 2


title: HTR5-GFP_MS_2_input

data_processing:
Adapter trimming was performed and low quality reads were filtered with fastp version 0.20.1
Reads were mapped to the Arabidopsis genome (TAIR10) with Botiew2 version 2.4.2
Reads were filtered for duplicated reads by using Picard version 2.24.0 MarkDuplicates
bigwig coverage files were generated using deepTools utility bamCoverage with a bin size of 10bp and normalized to input or sequencing depth using RPKM
Average ChIP-seq profiles were generated using deepTools utility plotProfile
Assembly: TAIR10
Supplementary files format and content: *.bw, normlized ChIP-seq coverage files

source_name: mature seeds

growth_protocol: Mature seeds, seeds imbibed for different time periods

extract_protocol:
Materials were ground with liquid nitrogen into fine powder and immediately fixed with 1% formaldehyde. Nuclei were extracted and mononucleosomes were generated with micrococcal nuclease (MNase) (Sigma, N5386) digestion as previously described. Immunoprecipitation was conducted with anti-GFP (Thermo Fisher Scientific, A-11122) or anti-H2A.Z. After antibody incubation, Protein A Dynabeads (Thermo Fisher Scientific, 10002D) were added to collect the immunocomplexes.
After washing, elution, reverse cross-linking and DNA purification, recovered DNA was subjected to library preparation with VAHTS universal DNA library prep kit for Illumina (Vazyme, ND607) according to the manufacture’s instruction

value: HTR5-GFP mature seeds

value: mature seeds

tag: chip antibody

value: input


title: MV4;11_MEN1-WT_DMSO_Menin-ChIP_SNDX5613_1uM

description:
MV411_ChIP_MEN1_SNDX_1uM_4d_REP1_220115_TGACCA_S3
MV4;11_MEN1-WT-vs-M327I_TSS-signals.xlsx
MV4;11_MEN1-WT-vs-M327I_Alignment-rmdup_STATs.zip


title: MV4;11_MEN1-WT_DMSO_Menin-ChIP_SNDX5613_5uM

description:
MV411_ChIP_MEN1_SNDX_5uM_4d_REP1_220115_ACAGTG_S4
MV4;11_MEN1-WT-vs-M327I_TSS-signals.xlsx
MV4;11_MEN1-WT-vs-M327I_Alignment-rmdup_STATs.zip


title: h3.3ko_G24h_1


title: h3.3ko_Mature Seeds_2

description:
Accessibility_decreased_in_h3.3ko.bed
Accessibility_increased_in_h3.3ko.bed


title: Striatum 175Q 10wk replicate 1

source_name: striatum

value: striatum

value: female

value: post natal week 10


title: HUVECs_NC_Sample 1

value: Primary cells

value: untreated


title: HUVECs_NC_Sample 3

value: Human umbilical vein endothelial cells


title: MV4;11_MEN1-WT_DMSO_Menin-ChIP_DMSO

description:
MV411_ChIP_MEN1_DMSO_4d_REP1_220115_CGATGT_S1
MV4;11_MEN1-WT-vs-M327I_TSS-signals.xlsx
MV4;11_MEN1-WT-vs-M327I_Alignment-rmdup_STATs.zip

value: anti-Menin (Rb)

value: DMSO


title: HUVECs_NC_Sample 2


title: Col_Seedling_2

source_name: seedlings

value: seedlings

value: Col

value: 10-day-old seedlings


title: Striatum 175QK772T 10wk replicate 4

value: male


title: MV4;11_MEN1-WT_DMSO_MLL1-ChIP_DMSO

description:
MV411_ChIP_MLL1_DMSO_4d_REP1_220115_TAGCTT_S9
MV4;11_MEN1-WT-vs-M327I_TSS-signals.xlsx
MV4;11_MEN1-WT-vs-M327I_Alignment-rmdup_STATs.zip

value: anti-MLL1 (Rb)

value: Bethyl laboratories


title: h3.3ko_Mature Seeds_1


title: Striatum 175QK772T 10wk replicate 3


title: MV4;11_MEN1-WT_DMSO_IgG-ChIP

description:
MV411_ChIP_IgG_DMSO_4d_REP1_220115_GTGAAA_S17
MV4;11_MEN1-WT-vs-M327I_TSS-signals.xlsx
MV4;11_MEN1-WT-vs-M327I_Alignment-rmdup_STATs.zip

value: Rabbit polyclonal IgG

value: Abcam


title: MV4;11_MEN1-WT_DMSO_ChIP-input

description:
MV411_ChIP_input_DMSO_4d_REP1_220115_GTTTCG_S19
MV4;11_MEN1-WT-vs-M327I_TSS-signals.xlsx
MV4;11_MEN1-WT-vs-M327I_Alignment-rmdup_STATs.zip


title: Striatum 175QK772T 10wk replicate 2


title: Col_Seedling_1


title: oocyte, auto, patient7

city: DIJON

first: Bastien

last: Ducreux

address: Batiment B3, 15 boulevard Maréchal de Lattre de Tassigny

country: France

institute: Inserm U1231

library_source: transcriptomic single cell

data_processing:
We carried out sequencing quality checks with FastQC (Andrews et al. 2010), and the trimming of adapters and low-quality sequences was done using TrimGalore! (Krueger et al. 2012). Paired-end reads were aligned onto Human reference genome (hg38) with STAR (v2.5.2) (Dobin et al. 2013) reporting randomly one position, allowing 6% of mismatches. Repeat annotation was downloaded from RepeatMasker and merged with gene annotation from Gencode v29 (Frankish et al. 2021). The combined file was used as input for quantification with featureCounts (Liao et al. 2014), as recommended in Teissandier et al. (2019).
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Oocyte

extract_protocol:
The free-zona pellucida oocyte (after using acidic Tyrode’s solution) was individually placed in a lysis buffer containing MgCl2 (4379878, Applied Biosystems), DTT, Nonidet P-40 (11332473001, Roche), SUPERase-In (AM2694, Ambion) and RNase-inhibitor (AM2682, Ambion). Then, we performed a reverse transcription reaction (SuperScript III reverse transcriptase - 18080-044, Invitrogen) and a poly(A) tailing to the 3’ end of the first-strand cDNA (by using terminal deoxynucleotidyl transferase - 10533-073, Invitrogen). After the second-strand cDNA synthesis, 20 cycles of PCR were performed to amplify the oocyte cDNA using the TaKaRa ExTaq HS (TAKRR006B, Takara) and IS PCR primer (IDT).
The library preparation (KAPA Hyper Plus Library prep kit) and the sequencing of the scRNA-seq was performed by the ICGex - NGS platform (Curie Institute) on NovaSeq 6000 Illumina sequencer for 100-bp paired-end sequencing.

treatment_protocol:
The controlled ovarian hyperstimulation and oocyte retrieval were performed as previously described (Barberet et al. 2019).
On the day of oocyte retrieval, after removing the cumulus cells (hyaluronidase treatment plus mechanical pipetting), oocytes were classified as mature (Metaphase II) or immature (Germinal Vesicle or Metaphase I oocyte). When more than one immature oocyte was present, they were cultured in Global culture media (Global, LifeGlobal) in a time-lapse incubator (EmbryoScope, Unisense FertiliTech), at 37.0°C, 6%CO2, 5%O2 for a maximum period of 24 hours.
MII were vitrified in a closed system (Rapid-ITM, Vitrolife) using the RapidVitTM Oocyte kit (Vitrolife) containing ethylene glycol and propanediol, which are permeable cryoprotectants, and sucrose, acting as an extracellular cryoprotectant. The vitrification procedure was performed according to the manufacturer’s protocol.
MII oocytes were vitrified in the semi-automated vitrification group using GAVI®, as previously described by Roy et al. (2017).

value: Oocyte

tag: vitrification

value: yes

tag: vitrification type

value: auto

tag: patient

tag: in vitro_maturation


title: oocyte, fresh, patient6

tag: cell type

value: no

value: fresh


title: Striatum WT 10wk replicate 4

value: striatum

value: post natal week 10

value: WT


title: Striatum 175QK772T 10wk replicate 1

value: female


title: PDX3_MLL-AF10_MEN1-T349M_VTP50469_rep.1

description:
CBAM44728_iMENINres_RNA_VTP_chow_14d_REP1_210713_CGTACG_S16
PDX3_MLL-AF10_raw_gene-counts_sorted_rmdup.csv
PDX3_MLL-AF10_MEN1-WT-vs-T349M_DESeq2_diffExp_summary.xlsx
PDX3_MLL-AF10_MEN1-WT-vs-T349M_DESeq2_rlog-expression_normalized_counts.csv
PDX3_MLL-AF10_MEN1-WT-vs-T349M_DESeq2_rlog-expression_z-scores.csv

data_processing:
Raw Illumina sequencer output was converted to FASTQ format using bcl2fastq (v2.20.0.422).
Reads (paired-end 37-mers) were aligned to the human (Gencode GRCh38/hg38) using STAR (v2.7.5a, sorted and duplicates marked/removed with picard pipeline tools (v2.9.4).
Final “deduped” .BAM files were indexed using SAMtools (v1.95).
RNA-seq data visualizations were produced using IGVtools (TDF signal pileups; v2.3.75).
Raw per-gene counts calculated with HTSeq (htseq-count, v0.6.1pl).
Differential RNA-seq expression was calculated using the BioConductor DESeq2 package (v1.24,0), using raw unnormalized per-gene counts from deduplicated BAMs.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: IGVtools tiled data file (TDF)
Supplementary_files_format_and_content: raw gene counts_HTseq (csv)
Supplementary_files_format_and_content: differentially expressed genes_DESeq2 (xlsx)
Supplementary_files_format_and_content: rlog_normalized gene counts_DESeq2 (csv)
Supplementary_files_format_and_content: z-scores_from rlog counts_DESEq2 (csv)

molecule: polyA RNA

source_name: MLL-AF10 rearranged human leukemia PDX (CBAM44728)

extract_protocol:
1Mio MV4;11 cells were lysed in 350 µl of RLT buffer and RNA was isolated using the RNeasy Mini Kit (Qiagen) according to manufacturers instructions for cell ine experiments. PDX-derived human leukemia cells from the bone marrow were depleted for mouse cells using magnetic cell sorting (mouse cell depletion kit, Milteny)
Poly-A tail selection and library preparation were performed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA).
Sequencing was done using the Illumina Next Gen Sequencing NextSeq platform (Illumina, San Diego, CA) with 37bp, paired-end reads.

treatment_protocol: RNAseq was performed in MV4;11 cells harboring a MEN1-M327I mutation and in an MLL-AF10 rearranged PDX with MEN1-T349M as well as the respective isogenic WT controls. Drug treatments were performed for 5 days in vitro for with different doses of SNDX-5613 (0.1uM, 1uM, 5uM) or DMSO control. Treatment of the MLL-AF10 PDX CBAM44728 was performed by oral exposure in vivo using 0.1% VTP-50469 supplemented rodent diet for 14 days.

tag: cell line

value: 0.1% drug supplemented diet


title: PDX3_MLL-AF10_MEN1-T349M_VTP50469_rep.2

description:
CBAM44728_iMENINres_RNA_VTP_chow_14d_REP2_210713_GAGTGG_S17
PDX3_MLL-AF10_raw_gene-counts_sorted_rmdup.csv
PDX3_MLL-AF10_MEN1-WT-vs-T349M_DESeq2_diffExp_summary.xlsx
PDX3_MLL-AF10_MEN1-WT-vs-T349M_DESeq2_rlog-expression_normalized_counts.csv
PDX3_MLL-AF10_MEN1-WT-vs-T349M_DESeq2_rlog-expression_z-scores.csv


title: PDX3_MLL-AF10_MEN1-T349M_VTP50469_rep.3

description:
CBAM44728_iMENINres_RNA_VTP_chow_14d_REP3_210713_GGTAGC_S18
PDX3_MLL-AF10_raw_gene-counts_sorted_rmdup.csv
PDX3_MLL-AF10_MEN1-WT-vs-T349M_DESeq2_diffExp_summary.xlsx
PDX3_MLL-AF10_MEN1-WT-vs-T349M_DESeq2_rlog-expression_normalized_counts.csv
PDX3_MLL-AF10_MEN1-WT-vs-T349M_DESeq2_rlog-expression_z-scores.csv


title: Col_G24h_2

value: imbibed seeds

value: Col

value: seeds subject to germination for 24 hours


title: oocyte, manual, patient7

value: manual


title: Col_S48h_2

value: seeds stratified for 48 hours


title: oocyte, fresh, patient7


title: Striatum WT 10wk replicate 1


title: Col_G24h_1


title: Col_S48h_1


title: PDX3_MLL-AF10_MEN1-T349M_vehicle_rep.3

description:
CBAM44728_iMENINres_RNA_vehicle_14d_REP3_210713_TCGGCA_S15
PDX3_MLL-AF10_raw_gene-counts_sorted_rmdup.csv
PDX3_MLL-AF10_MEN1-WT-vs-T349M_DESeq2_diffExp_summary.xlsx
PDX3_MLL-AF10_MEN1-WT-vs-T349M_DESeq2_rlog-expression_normalized_counts.csv
PDX3_MLL-AF10_MEN1-WT-vs-T349M_DESeq2_rlog-expression_z-scores.csv

value: vehicle

value: regular rodent diet


title: Hippocampus 175Q 10wk replicate 4

source_name: hippocampus

value: hippocampus

value: male


title: PDX3_MLL-AF10_MEN1-T349M_vehicle_rep.2

description:
CBAM44728_iMENINres_RNA_vehicle_14d_REP2_210713_AGTTCC_S14
PDX3_MLL-AF10_raw_gene-counts_sorted_rmdup.csv
PDX3_MLL-AF10_MEN1-WT-vs-T349M_DESeq2_diffExp_summary.xlsx
PDX3_MLL-AF10_MEN1-WT-vs-T349M_DESeq2_rlog-expression_normalized_counts.csv
PDX3_MLL-AF10_MEN1-WT-vs-T349M_DESeq2_rlog-expression_z-scores.csv


title: oocyte, manual, patient3

value: Oocyte

value: yes


title: Striatum WT 10wk replicate 3


title: Striatum WT 10wk replicate 2


title: oocyte, auto, patient3

value: auto


title: PDX3_MLL-AF10_MEN1-T349M_vehicle_rep.1

description:
CBAM44728_iMENINres_RNA_vehicle_14d_REP1_210713_AGTCAA_S13
PDX3_MLL-AF10_raw_gene-counts_sorted_rmdup.csv
PDX3_MLL-AF10_MEN1-WT-vs-T349M_DESeq2_diffExp_summary.xlsx
PDX3_MLL-AF10_MEN1-WT-vs-T349M_DESeq2_rlog-expression_normalized_counts.csv
PDX3_MLL-AF10_MEN1-WT-vs-T349M_DESeq2_rlog-expression_z-scores.csv


title: PDX3_MLL-AF10_MEN1-WT_VTP50469_rep.3

description:
CBAM44728_RNA_VTP_chow_14d_REP3_210713_GCCAAT_S6
PDX3_MLL-AF10_raw_gene-counts_sorted_rmdup.csv
PDX3_MLL-AF10_MEN1-WT-vs-T349M_DESeq2_diffExp_summary.xlsx
PDX3_MLL-AF10_MEN1-WT-vs-T349M_DESeq2_rlog-expression_normalized_counts.csv
PDX3_MLL-AF10_MEN1-WT-vs-T349M_DESeq2_rlog-expression_z-scores.csv


title: PDX3_MLL-AF10_MEN1-WT_VTP50469_rep.2

description:
CBAM44728_RNA_VTP_chow_14d_REP2_210713_ACAGTG_S5
PDX3_MLL-AF10_raw_gene-counts_sorted_rmdup.csv
PDX3_MLL-AF10_MEN1-WT-vs-T349M_DESeq2_diffExp_summary.xlsx
PDX3_MLL-AF10_MEN1-WT-vs-T349M_DESeq2_rlog-expression_normalized_counts.csv
PDX3_MLL-AF10_MEN1-WT-vs-T349M_DESeq2_rlog-expression_z-scores.csv


title: Col_Mature Seeds_2

value: mature seeds


title: oocyte, auto, patient2


title: Col_Mature Seeds_1


title: oocyte, auto, patient6


title: Col_MS_2

data_processing:
Adapter trimming was performed and low quality reads were filtered with fastp version 0.20.1
Reads were mapped to the Arabidopsis genome (TAIR10) with Botiew2 version 2.4.2
Reads were filtered for duplicated reads by using Picard version 2.24.0 MarkDuplicates
bigwig coverage files were generated using deepTools utility bamCoverage with a bin size of 10bp and normalized to sequencing depth using RPKM
Average ATAC-seq profiles were generated using deepTools utility plotProfile
Assembly: TAIR10
Supplementary files format and content: *.bw, normlized ATAC-seq coverage files

source_name: seeds

growth_protocol: Mature seeds

extract_protocol:
Mature seeds were chopped in lysis buffer (15 mM Tris-HCl pH 7.5, 20 mM NaCl, 80 mM KCl, 0.5 mM Spermine, 0.2% Triton X-100, 5 mM β-ME, protease inhibitor cocktail). After being filtered with a 30μm filter (CellTrics), nuclei were stained with DAPI and subjected to fluorescence-activated cell sorting (FACS). 50,000 nuclei per sample were collected and mixed with Tn5 transposase (Mei5bio, MF650-01), after 20 minutes of incubation at 37°C, tagmented DNA was recovered with ChIP DNA Clean & Concentrator kit (ZYMO, D5205).
After PCR amplification, sequencing libraries were purified with VAHTS DNA Clean Beads (Vazyme N411)

value: seeds


title: oocyte, manual, patient6


title: PDX3_MLL-AF10_MEN1-WT_VTP50469_rep.1

description:
CBAM44728_RNA_VTP_chow_14d_REP1_210713_TGACCA_S4
PDX3_MLL-AF10_raw_gene-counts_sorted_rmdup.csv
PDX3_MLL-AF10_MEN1-WT-vs-T349M_DESeq2_diffExp_summary.xlsx
PDX3_MLL-AF10_MEN1-WT-vs-T349M_DESeq2_rlog-expression_normalized_counts.csv
PDX3_MLL-AF10_MEN1-WT-vs-T349M_DESeq2_rlog-expression_z-scores.csv


title: oocyte, auto, patient5


title: Hippocampus 175Q 10wk replicate 2

value: post natal week 10


title: h2a.z_MS_1

value: h2a.z mature seeds


title: Hippocampus 175QK772T 10wk replicate 4


title: oocyte, manual, patient5


title: Hippocampus 175Q 10wk replicate 1

value: female


title: PDX3_MLL-AF10_MEN1-WT_vehicle_rep.3

description:
CBAM44728_RNA_vehicle_14d_REP3_210713_CACTCA_S3
PDX3_MLL-AF10_raw_gene-counts_sorted_rmdup.csv
PDX3_MLL-AF10_MEN1-WT-vs-T349M_DESeq2_diffExp_summary.xlsx
PDX3_MLL-AF10_MEN1-WT-vs-T349M_DESeq2_rlog-expression_normalized_counts.csv
PDX3_MLL-AF10_MEN1-WT-vs-T349M_DESeq2_rlog-expression_z-scores.csv


title: h2a.z_MS_2


title: Hippocampus 175Q 10wk replicate 3


title: Hippocampus 175QK772T 10wk replicate 2


title: PDX3_MLL-AF10_MEN1-WT_vehicle_rep.1

description:
CBAM44728_RNA_vehicle_14d_REP1_210713_ATCACG_S1
PDX3_MLL-AF10_raw_gene-counts_sorted_rmdup.csv
PDX3_MLL-AF10_MEN1-WT-vs-T349M_DESeq2_diffExp_summary.xlsx
PDX3_MLL-AF10_MEN1-WT-vs-T349M_DESeq2_rlog-expression_normalized_counts.csv
PDX3_MLL-AF10_MEN1-WT-vs-T349M_DESeq2_rlog-expression_z-scores.csv


title: Mnase_spt6ldeltatSH2_rep2

city: Guangzhou

first: Chen

last: Chen

state: Guangdong

address: 723 Xinke Rd.

institute: South China Botanical Garden, Chinese Academy of Science

data_processing:
adapters were removed from raw sequencing reads with cutadapt (version 3.4, -m 10)
ChIP-seq reads were mapped to the Arabidopsis genome (TAIR10) by Bowtie2 with default settings
PCR duplicates were removed by using samtools (for pair-end reads) or running the MACS2-filterdup program (for single-end reads)
To identify read-enriched regions (peaks), the MACS2 program was employed to perform peak calling with the following settings (-g 135000000, -nomodel, and -p 0.01).
Highly confident peaks were generated by running idr (2.0.3) (--idr-threshold 0.01) with biological replicates
bigWig files were generated using bamCoverage with RPGC normalization
The nucleosome positions were determined by applying the improved nucleosome-positioning algorithm iNPS with default settings. The smoothed bigwig files across biological replicates were generated by using dpos function in DANPOS3. Finally, MNase-seq data among samples were normalized by applying quantile normalization methods to normalize occupancy with Wiq function in DANPOS3
Assembly: TAIR10
Supplementary files format and content: Bigwig files.

growth_protocol: Seeds were stratified in the dark at 4°C for 3 days before being sown on agar plates containing 2.22 g/L Murashige and Skoog basal medium with vitamins mix (Cat. M519, PhytoTech LABS), 1.5% sucrose (pH 5.75), and 0.8% agar. Plant growth was in long-day photoperiod (16h light/8h dark cycles) at 22°C

extract_protocol:
plants were crosslinked with 1% formaldehyde for 20 min under vacuum at room temperature and quenched with 0.125 M glycine under vacuum for an additional 5 min. Approximately 500 milligrams of tissues were used for each ChIP assay. The chromatin was sonicated using a Covaris M220 sonicator (peak power: 75; duty factor: 20; cycles/burst: 200) for 210 s at 6°C. The lysates were centrifuged at 18,000 g for 10 min at 4°C to remove debris. 10 µL of supernatant was used as the input sample, whereas the remaining supernatant was kept for the downstream procedure. 10 µL of Dynabeads Protein A (Cat. 10002D, ThermoFisher SCIENTIFIC) were added to each sample to prewash for 1 h at 4°C with gentle rotating. ChIP was carried out using antibodies as follows: anti-GFP (Cat. ab290, Abcam) and anti-Pol II CTD repeat YSPTSPS (Cat. ab817, Abcam). 40 µL of Dynabeads Protein A were mixed with 4 µL of antibodies and incubated for approximately 6 h on a rotator at 4°C to form antibody-bead complexes. Finally, ChIP-DNA were recovered by Phenol/chloroform extraction. Approximately 400 milligrams of seedlings were used per sample. Additionally, equal amounts of spike-in nuclei extracted from Saccharomyces cerevisiae were added to each sample before MNase treatment, which worked as the internal control among samples. For MNase treatment, the prepared nuclei were resuspended in prewarmed MNase digestion buffer, followed by the addition of 8 units of MNase (Cat. 2910A, TaKaRa) and incubation (15 min at 37°C with periodic agitation). Finally, the mono-nucleosomal DNA was isolated from 2% agarose gels and quantified by the Qubit dsDNA HS assay kit (Cat. Q32851, ThermoFisher SCIENTIFIC).
ChIP libraries were prepared by using the NEBNext® Ultra™ DNA Library Prep Kit (E7370S) following the manufacturer’s instructions, and subsequently used for Illumina

treatment_protocol: 10-day old seedlings

value: seedlings


title: Hippocampus 175QK772T 10wk replicate 3


title: MV4;11_MEN1-M327I_SNDX5613_5uM_rep.2

description:
MV411-MEN1-M327I_RNA_SNDX_5uM_5d_REP2_211221_GAGTGG_S23
MV4;11_MEN1-WT-vs-M327I_raw_gene-counts_sorted_rmdup.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_diffExp_summary.xlsx
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_normalized_counts.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_z-scores.csv


title: PDX3_MLL-AF10_MEN1-WT_vehicle_rep.2

description:
CBAM44728_RNA_vehicle_14d_REP2_210713_CGATGT_S2
PDX3_MLL-AF10_raw_gene-counts_sorted_rmdup.csv
PDX3_MLL-AF10_MEN1-WT-vs-T349M_DESeq2_diffExp_summary.xlsx
PDX3_MLL-AF10_MEN1-WT-vs-T349M_DESeq2_rlog-expression_normalized_counts.csv
PDX3_MLL-AF10_MEN1-WT-vs-T349M_DESeq2_rlog-expression_z-scores.csv


title: oocyte, fresh, patient4

value: no

value: fresh


title: oocyte, manual, patient4

value: manual


title: Mnase_spt6l_rep2


title: oocyte, fresh, patient3


title: MNase_WT

value: wild type


title: oocyte, auto, patient4


title: MV4;11_MEN1-M327I_SNDX5613_5uM_rep.1

description:
MV411-MEN1-M327I_RNA_SNDX_5uM_5d_REP1_211221_CGTACG_S22
MV4;11_MEN1-WT-vs-M327I_raw_gene-counts_sorted_rmdup.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_diffExp_summary.xlsx
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_normalized_counts.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_z-scores.csv


title: Hippocampus WT 10wk replicate 4

value: WT


title: Mnase_spt6l_rep1


title: Hippocampus WT 10wk replicate 2


title: MV4;11_MEN1-M327I_SNDX5613_1uM_rep.3

description:
MV411-MEN1-M327I_RNA_SNDX_1uM_5d_REP3_211221_GTCCGC_S18
MV4;11_MEN1-WT-vs-M327I_raw_gene-counts_sorted_rmdup.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_diffExp_summary.xlsx
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_normalized_counts.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_z-scores.csv


title: MV4;11_MEN1-M327I_SNDX5613_1uM_rep.2

description:
MV411-MEN1-M327I_RNA_SNDX_1uM_5d_REP2_211221_GTAGAG_S17
MV4;11_MEN1-WT-vs-M327I_raw_gene-counts_sorted_rmdup.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_diffExp_summary.xlsx
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_normalized_counts.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_z-scores.csv


title: Hippocampus 175QK772T 10wk replicate 1


title: MV4;11_MEN1-M327I_SNDX5613_5uM_rep.3

description:
MV411-MEN1-M327I_RNA_SNDX_5uM_5d_REP3_211221_GGTAGC_S24
MV4;11_MEN1-WT-vs-M327I_raw_gene-counts_sorted_rmdup.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_diffExp_summary.xlsx
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_normalized_counts.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_z-scores.csv


title: Hippocampus WT 10wk replicate 1


title: BRM-GFP spt6l input


title: oocyte, fresh, patient2


title: oocyte, auto, patient1


title: BRM-GFP spt6l rep2

value: anti-GFP (Abcam, ab290)


title: Mnase_spt6ldeltatSH2_rep1


title: Col_MS_1

value: Col


title: MV4;11_MEN1-M327I_SNDX5613_1uM_rep.1

description:
MV411-MEN1-M327I_RNA_SNDX_1uM_5d_REP1_211221_CCGTCC_S16
MV4;11_MEN1-WT-vs-M327I_raw_gene-counts_sorted_rmdup.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_diffExp_summary.xlsx
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_normalized_counts.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_z-scores.csv


title: Hippocampus WT 10wk replicate 3

value: hippocampus


title: oocyte, manual, patient2

value: Oocyte


title: Cortex 175Q 10wk replicate 4

source_name: cortex

value: cortex

value: male


title: MV4;11_MEN1-M327I_SNDX5613_100nM_rep.3

description:
MV411-MEN1-M327I_RNA_SNDX_100nM_5d_REP3_211221_CTTGTA_S12
MV4;11_MEN1-WT-vs-M327I_raw_gene-counts_sorted_rmdup.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_diffExp_summary.xlsx
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_normalized_counts.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_z-scores.csv


title: Cortex 175Q 10wk replicate 3


title: BRM-GFP spt6l rep1


title: MV4;11_MEN1-M327I_SNDX5613_100nM_rep.2

description:
MV411-MEN1-M327I_RNA_SNDX_100nM_5d_REP2_211221_GGCTAC_S11
MV4;11_MEN1-WT-vs-M327I_raw_gene-counts_sorted_rmdup.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_diffExp_summary.xlsx
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_normalized_counts.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_z-scores.csv


title: THP1, SGOL1-AS1 KD, Rep1

city: Aldereley Park

first: Georges

last: Lacaud

address: University of Manchester

country: United Kingdom

institute: Cancer Research UK Manchester Institute

data_processing:
Alignments and gene counts were calculated by STAR v2.5.1b
Counts were normalised by DeSeq2
Assembly: GrCh38
Supplementary files format and content: Normalised Count file

extract_protocol:
Qiagen Rneasy Plus Mini
NEBNext Ultra II

value: Targeting ASO


title: SYD-GFP spt6ldeltatSH2 rep1


title: THP1, SGOL1-AS1 KD, Rep2


title: Cortex 175QK772T 10wk replicate 4


title: Cortex 175Q 10wk replicate 2


title: oocyte, fresh, patient1


title: SYD-GFP spt6ldeltatSH2 rep2


title: THP1, Non Targeting, Rep2

value: Non Targeting ASO


title: SYD-GFP spt6ldeltatSH2 input


title: MV4;11_MEN1-M327I_DMSO_rep.3

description:
MV411-MEN1-M327I_RNA_DMSO_5d_REP3_211221_GCCAAT_S6
MV4;11_MEN1-WT-vs-M327I_raw_gene-counts_sorted_rmdup.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_diffExp_summary.xlsx
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_normalized_counts.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_z-scores.csv

value: DMSO


title: Cortex 175QK772T 10wk replicate 3

value: post natal week 10


title: MV4;11_MEN1-M327I_DMSO_rep.2

description:
MV411-MEN1-M327I_RNA_DMSO_5d_REP2_211221_ACAGTG_S5
MV4;11_MEN1-WT-vs-M327I_raw_gene-counts_sorted_rmdup.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_diffExp_summary.xlsx
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_normalized_counts.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_z-scores.csv


title: MV4;11_MEN1-M327I_SNDX5613_100nM_rep.1

description:
MV411-MEN1-M327I_RNA_SNDX_100nM_5d_REP1_211221_TAGCTT_S10
MV4;11_MEN1-WT-vs-M327I_raw_gene-counts_sorted_rmdup.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_diffExp_summary.xlsx
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_normalized_counts.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_z-scores.csv


title: SYD-GFP rep1


title: SYD-GFP rep2


title: THP1, Non Targeting, Rep1


title: oocyte, manual, patient1

value: yes


title: RNA_CR_186

city: Lausanne

first: kevin

last: perez

address: rue du Bugnon 27

country: Switzerland

institute: University of Lausanne

data_processing:
Alignment: STAR aligner (v2.7.9a) with '--sjdbOverhang 100'.
Counting: featureCounts, Subread package (v2.0.3).
Assembly: GRCh38
Supplementary files format and content: Raw matrix table representing the number of transcripts per gene

source_name: Peripheral blood mononuclear cells

extract_protocol:
PBMCs were isolated from whole blood using histopaque.
RNA libraries were constructed using standard Illumina protocols

value: Peripheral blood mononuclear cells

value: F


title: Cortex 175QK772T 10wk replicate 1

value: female


title: RNA_CR_185

value: M


title: MV4;11_MEN1-M327I_DMSO_rep.1

description:
MV411-MEN1-M327I_RNA_DMSO_5d_REP1_211221_TGACCA_S4
MV4;11_MEN1-WT-vs-M327I_raw_gene-counts_sorted_rmdup.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_diffExp_summary.xlsx
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_normalized_counts.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_z-scores.csv


title: Cortex 175Q 10wk replicate 1


title: SYD-GFP input

value: seedlings


title: RNA_CR_184


title: SYD-GFP spt6l rep2


title: RNA_CR_183


title: MV4;11_MEN1-WT_SNDX5613_5uM_rep.3

description:
MV411_RNA_SNDX_5uM_5d_REP3_211221_GTTTCG_S21
MV4;11_MEN1-WT-vs-M327I_raw_gene-counts_sorted_rmdup.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_diffExp_summary.xlsx
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_normalized_counts.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_z-scores.csv


title: MV4;11_MEN1-WT_SNDX5613_5uM_rep.2

description:
MV411_RNA_SNDX_5uM_5d_REP2_211221_GTGGCC_S20
MV4;11_MEN1-WT-vs-M327I_raw_gene-counts_sorted_rmdup.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_diffExp_summary.xlsx
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_normalized_counts.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_z-scores.csv


title: MV4;11_MEN1-WT_SNDX5613_5uM_rep.1

description:
MV411_RNA_SNDX_5uM_5d_REP1_211221_GTGAAA_S19
MV4;11_MEN1-WT-vs-M327I_raw_gene-counts_sorted_rmdup.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_diffExp_summary.xlsx
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_normalized_counts.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_z-scores.csv


title: SYD-GFP spt6l rep1


title: RNA_CR_182


title: Cortex WT 10wk replicate 4

value: WT


title: Cortex WT 10wk replicate 3


title: SPT6L-GFP syd-5 rep2

value: anti-GFP (Abcam, ab290)


title: Cortex 175QK772T 10wk replicate 2


title: Cortex WT 10wk replicate 1


title: SPT6L-GFP syd-5 rep1


title: MV4;11_MEN1-WT_SNDX5613_1uM_rep.3

description:
MV411_RNA_SNDX_1uM_5d_REP3_211221_ATGTCA_S15
MV4;11_MEN1-WT-vs-M327I_raw_gene-counts_sorted_rmdup.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_diffExp_summary.xlsx
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_normalized_counts.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_z-scores.csv


title: MV4;11_MEN1-WT_SNDX5613_1uM_rep.1

description:
MV411_RNA_SNDX_1uM_5d_REP1_211221_AGTCAA_S13
MV4;11_MEN1-WT-vs-M327I_raw_gene-counts_sorted_rmdup.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_diffExp_summary.xlsx
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_normalized_counts.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_z-scores.csv


title: Brainstem 175Q 10wk replicate 4

source_name: brainstem

value: brainstem


title: MV4;11_MEN1-WT_SNDX5613_1uM_rep.2

description:
MV411_RNA_SNDX_1uM_5d_REP2_211221_AGTTCC_S14
MV4;11_MEN1-WT-vs-M327I_raw_gene-counts_sorted_rmdup.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_diffExp_summary.xlsx
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_normalized_counts.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_z-scores.csv


title: RNA_CR_181


title: RNA_CR_180


title: RNA_CR_178


title: MV4;11_MEN1-WT_SNDX5613_100nM_rep.3

description:
MV411_RNA_SNDX_100nM_5d_REP3_211221_GATCAG_S9
MV4;11_MEN1-WT-vs-M327I_raw_gene-counts_sorted_rmdup.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_diffExp_summary.xlsx
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_normalized_counts.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_z-scores.csv


title: SPT6L-GFP syd-5 input


title: Brainstem 175Q 10wk replicate 3


title: Cortex WT 10wk replicate 2


title: Brainstem 175Q 10wk replicate 1


title: RNA_CR_177


title: RNA_CR_179


title: Brainstem 175QK772T 10wk replicate 4


title: SPT6L-GFP input


title: SPT6L-GFP rep1


title: MV4;11_MEN1-WT_SNDX5613_100nM_rep.1

description:
MV411_RNA_SNDX_100nM_5d_REP1_211221_CAGATC_S7
MV4;11_MEN1-WT-vs-M327I_raw_gene-counts_sorted_rmdup.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_diffExp_summary.xlsx
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_normalized_counts.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_z-scores.csv


title: MV4;11_MEN1-WT_SNDX5613_100nM_rep.2

description:
MV411_RNA_SNDX_100nM_5d_REP2_211221_ACTTGA_S8
MV4;11_MEN1-WT-vs-M327I_raw_gene-counts_sorted_rmdup.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_diffExp_summary.xlsx
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_normalized_counts.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_z-scores.csv


title: SPT6L-GFP rep2


title: SYD-GFP spt6l input


title: RNA_CR_176


title: Brainstem 175QK772T 10wk replicate 2


title: MV4;11_MEN1-WT_DMSO_rep.2

description:
MV411_RNA_DMSO_5d_REP2_211221_CGATGT_S2
MV4;11_MEN1-WT-vs-M327I_raw_gene-counts_sorted_rmdup.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_diffExp_summary.xlsx
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_normalized_counts.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_z-scores.csv


title: MV4;11_MEN1-WT_DMSO_rep.1

description:
MV411_RNA_DMSO_5d_REP1_211221_ATCACG_S1
MV4;11_MEN1-WT-vs-M327I_raw_gene-counts_sorted_rmdup.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_diffExp_summary.xlsx
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_normalized_counts.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_z-scores.csv


title: Pol II WT rep1

value: wild type

value: anti-Pol II (Abcam ab817)


title: RNA_CR_174


title: Brainstem 175Q 10wk replicate 2


title: hiPSC_day+40_2

city: Boston

first: Jyoti

last: Rao

state: Massachusetts

address: 60 Fenwood road

department: Pathology/Genetics

institute: Brigham and Women’s Hospital/Harvard Medical School

description:
Single-cell RNA-Seq (inDrops)
processed data files:
D+20-40_matrix.csv
D+20-40_CellData.csv
D+20-40_GeneData.csv

data_processing:
Single-cell RNA-seq data were generated using inDrop version 3. Raw sequencing FASTQ files were demultiplexed and processed using a custom python pipeline as previously described (see Zilionis et al., Nature Protocols 2017) Also available at github.com/indrops/indrops. Default parameters were applied (for Trimmomatic, LEADING: "28", SLIDINGWINDOW: "4:20", MINLEN: "16"; for UMI quantification, m: 10, u: 1, d: 600, split-ambigs: False, min_non_polyA: 15; for low complexity filter, max_low_complexity_fraction: 0.50; for output: output_unaligned_reads_to_other_fastq: False, filter_alignments_to_softmasked_regions: False).
Sequencing reads were first sorted according to sample of origin.  Each library is associated with 4 reads - R1, R2, R3 and R4.  R1 is the biological read, R2 carries the first half of the hydrogel bead barcode (8 bp), R3 carries the library index (8 bp), and R4 carries the second half of the hydrogel bead barcode (8 bp), followed by the UMI (6 bp).
Cell-specific barcodes for each cDNA read were then matched against a set of pre-determined barcodes.
cDNA reads were then aligned to a reference transcriptome using Bowtie (version 1.2.2, parameters: -n 1 -l 15 -e 100 -m 200 -best -strata -a).  Reference transcriptomes were built from Homo_sapiens.GRCh38.94 and Mus_musculus.GRCm38.94 genome assembly. Mapped reads were then processed into counts of UMI-filtered transcripts per gene.
UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads.  This determination was made by inspecting a weighted histogram of UMI counts for each cell barcode and thresholds were set manually for each sample. We excluded the cells with less than 250 genes expressed, and exclude the genes if they were expressed in less than 3 cells. Fraction of counts due to mitochondrial genes (n) was determined and cells with n= 0.2 were removed. Cells with less than 250 genes expressed were removed. Genes expressed in less than 3 cells were filtered out. Fraction of counts due to mitochondrial genes (n) was determined and cells with n= 0.2 were removed.
Genome_build: Homo_sapiens.GRCh38.94 and Mus_musculus.GRCm38.94
Supplementary_files_format_and_content: X.csv: Raw UMI-filtered counts.  Matrix columns are transcripts, rows are single cells.
Supplementary_files_format_and_content: CellData.csv: Identifiers for single cells corresponding to the rows of X.csv.  Unique cell identifiers are in the following format: LibraryName_CellBarcodePart1_CellBarcodePart2.  Numbers of UMIS and genes detected and clustering assignments are included for each cell
Supplementary_files_format_and_content: GeneData.csv: Gene names corresponding to the columns of X.csv

source_name: human iPSC NCRM1

extract_protocol:
Single cell analysis of differentiating iPSCs and mouse embryos cells was performed using inDrops as previously reported (Klein et al.). UCP1-mCherry iPSC line was differentiated into brown adipocytes as described above. Cultures were harvested on day 6, 10, 15, 20, 30 of the primary differentiation and day 20 and 40 after replating.  The cultures were washed with PBS and dissociated into single cells using 2.5mg/ml Collagenase and 0.05% Trypsine EDTA in PBS for 5-15 minutes at 37ºC. Dissociated cells were run through 70µm cell strainer followed by 30µm cell strainer, spun at 300g for 5 minutes and resuspended in DMEM supplemented with 5% fetal bovine serum. Cells were again spun at 300g for 5 minutes and resuspended in DMEM + 5% fetal bovine serum, this was repeated 2-3 times to remove debris. Final resuspension was made in PBS + 0.1% bovine serum albumin. Cell density was adjusted to 200,000 cells/ml. For day 6, 10, 15 and 20, 2500 cells were collected from each sample. For samples 30 day, 20 day after replating and 40 day after replating, at least 3000 cells were collected from each sample from two independent differentiations. For analyzing mouse embryonic tissues, embryos were collected on embryonic day 13.5, 14.5 and 15.5 from wildtype CD1 IGS mice. For each stage, back tissue dorsal to rib cage at the level of forelimb was dissected out. Neural tube/spinal cord and dorsal root ganglion were removed wherever possible. For E15.5, epidermis and underlying dermis was removed before dissociating the tissue. Dissected tissues were washed several times in Hanks' Balanced Salt Solution. Tissues were transferred to microfuge tube with 200µl of 2.5mg/ml Collagenase and 0.05% Trypsine EDTA in PBS, chopped into small pieces using scissors and incubated at 37ºC for 15 minutes with intermittent shaking. Tissues were mechanically dissociated by triturating several times using wide-bore 1ml pipette. The resulting cell suspension was mixed with HBBS + 10% FBS, filtered through a 30µm cell strainer and spun at 300g for 5 minutes. To remove red blood cells, cell pellet was resuspended and incubated with RBC Lysis Solution for 5 minutes at room temperature. Cells were washed with HBSS + 10% FBS for 2-3 times to remove debris. Final suspension was made in PBS + 0.1% BSA. Cell density was adjusted to 200,000/ml. For each stage, cells were collected from two littermate embryos. For E13.5-14.5  embryo, 3000 cells were encapsulated and sequenced from each embryo. For E15.5, 5000 cells were collected and sequenced from each embryo.
Single-cell RNA-Seq libraries were prepared using a protocol customized for the inDrops platform (see Zilionis et al., Nature Protocols 2017)

value: human iPSC derived brown adipocytes

value: UCP1-mCherry reporter

tag: library name


title: RNA_CR_175


title: Pol II syd-5 rep2


title: Pol II syd-5 rep1


title: RNA_CR_172


title: Brainstem WT 10wk replicate 4

value: male


title: hiPSC_day+40_1


title: Brainstem 175QK772T 10wk replicate 1


title: Pol II WT rep2


title: Brainstem 175QK772T 10wk replicate 3


title: Pol II brm-1 syd-5 rep1


title: RNA_CR_173


title: Brainstem WT 10wk replicate 2


title: MV4;11_MEN1-WT_DMSO_rep.3

description:
MV411_RNA_DMSO_5d_REP3_211221_TTAGGC_S3
MV4;11_MEN1-WT-vs-M327I_raw_gene-counts_sorted_rmdup.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_diffExp_summary.xlsx
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_normalized_counts.csv
MV4;11_MEN1-WT-vs-M327I_DESeq2_rlog-expression_z-scores.csv

tag: treatment molecule


title: Brainstem WT 10wk replicate 3


title: Pol II brm-1 syd-5 rep2


title: hiPSC_day+20_2


title: RNA_CR_171


title: hiPSC_day+20_1


title: RNA_CR_170


title: Pol II brm-1


title: RNA_CR_169


title: RNA_CR_168


title: Cerebellum 175Q 10wk replicate 3

value: cerebellum


title: Cerebellum 175Q 10wk replicate 4


title: RNA_CR_167


title: hiPSC_day30_2b

description:
Single-cell RNA-Seq (inDrops)
processed data files:
D6-D30_matrix.csv
D6-D30_CellData.csv
D6-D30_GeneData.csv


title: CHIP_RVE5-MYC_rep1

city: hangzhou

first: wei

last: li

address: Yuhangtang Road 866 ,Zijingang Campus, Zhejiang University

institute: zhejiang univeisity

data_processing:
Basecalls performed using CASAVA version 1.4.
ChIP-seq reads were aligned to the tair10 genome assembly using EasyAlign version 3.2.
Peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Genome_build: TAIR10
Supplementary_files_format_and_content: *.Final.peaks.txt: Tab-delimited text files include peaks.

growth_protocol: Seedlings grow under long day (LD) conditions (16/8 h light / dark cycle at 22˚C).

extract_protocol:
Sampled for fixation with 1% formaldehyde for 15 min, which was stopped by adding 0.15 M Glycine. After sonication in 0.8% SDS buffer, the mix was immunoprecipitated with anti-MYC antibody (Abmart).
Libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Seedlings grow under long day (LD) conditions (16/8 h light / dark cycle at 29˚C).

value: 14 days

value: 29C for 12h

value: RVE5-MYC overexpression

value: anti-MYC antibody


title: hiPSC_day30_2a


title: Cerebellum 175Q 10wk replicate 2

value: post natal week 10


title: hiPSC_day30_1a


title: RNA_CR_166

value: Peripheral blood mononuclear cells


title: hiPSC_day30_1b


title: CHIP_RVE5-MYC_rep3


title: hiPSC_day20


title: Cerebellum 175Q 10wk replicate 1

value: female


title: Cerebellum 175QK772T 10wk replicate 4


title: Cerebellum 175QK772T 10wk replicate 3


title: RNA_CR_164

value: M


title: RNA_CR_163


title: hiPSC_day15


title: RNA_CR_165

value: F


title: Brainstem WT 10wk replicate 1

value: WT


title: hiPSC_day10


title: Cerebellum 175QK772T 10wk replicate 2


title: hiPSC_day6


title: BPA-IP

city: Hefei

first: Danyang

last: Li

address: No. 193 Tunxi Road

institute: Hefei university of technology

data_processing:
Illumina Novaseq 6000 sequencer
Paired-end reads were harvested from Illumina Novaseq 6000 sequencer. 3’ adaptor-trimming and low-quality reads removing by cutadapt software (v1.9.3).
Clean reads of input libraries were aligned to reference genome (UCSC RN5) by STAR software.
Reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4).
Assembly: UCSC RN5
Supplementary files format and content: Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA. GO and Pathway enrichment analysis were performed by the differentially methylated protein coding genes.

organism: Rattus norvegicus

source_name: Brain(Hippocampus )

growth_protocol: Hippocampi were dissociated by enzymatic digestion in 0.03% trypsin for 19min at 37 °C and then triturated with a fire-polished Pasteur pipette. Neurons were plated on poly-L-lysine (0.5mg/ml; Sigma P-2636)-treated 25mm glass coverslips at a density of 100,000 cells per coverslip. Change 70% of media to neurobasal on DIV (day in vitro) 2 and change half the media with neurobasal on DIV7 with Ara-C (1 μL/ml from 4mM stock, sigma C6645-25MG).

extract_protocol:
Total RNA was extracted using RNA isolater Total RNA Extraction Reagent (R401-01, Vazyme, China) according to the manufacturer’s instructions.
m6A RNA immunoprecipitation was performed with the GenSeqTM m6A-MeRIP Kit (GenSeq Inc., China) by following the manufacturer’s instructions. The library was used for RNA-seq library generation with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA).

treatment_protocol: Neurons were exposed to BPA for 48hrs on DIV 12-14

value: Brain(Hippocampus )

tag: antibody

value: Primary hippocampal neurons

value: Exposed to BPA with 1mM for 48h on DIV 12-14


title: BPA-Input

value: Exposed to BPA with 1mM for 48h on DIV 12-13


title: Ctrl-IP


title: RNA_CR_161


title: Ctrl-Input


title: CHIP_RVE5-MYC_rep2

value: seedlings


title: Cerebellum WT 10wk replicate 4

value: male


title: Cerebellum 175QK772T 10wk replicate 1

value: cerebellum


title: RCCECs_PA_Sample 3

value: Primary cells

value: Rat corpus cavernosum endothelial cells

value: palmitic acid


title: RCCECs_PA_Sample 2


title: MS_8

city: Pieve Emanuele

first: Elvezia

middle: Maria

last: Paraboschi

address: via Rita Levi Montalcini 4

department: Department of Biomedical Sciences

country: Italy

institute: Humanitas University

description: circular RNA

data_processing:
Reads were mapped to the human genome (hg19) using STAR (version 2.5.2)
circRNA quantification from chimeric reads was performed using DCC software, retaining only those circRNAs with at least 5 reads in 10 samples
Differential expression analysis was carried out using R and the edgeR package
Genome_build: hg19 (GRCh37), transcripts annotations from Ensembl database
Supplementary_files_format_and_content: tab-delimited text files include raw reads counts

source_name: blood

extract_protocol:
Peripheral blood mononuclear cells were isolated by centrifugation on a Lympholyte Cell separation medium (Cedarlane, Burlington, Ontario, Canada) gradient and total RNA was extracted using the miRNeasy Mini Kit (Qiagen, Hilden, Germany).
One µg of RNA was treated with 3 units of RNase R for 15 minutes at 37°C. After phenol-chloroform purification, the entire elution volume of each RNA was used for the library preparation, using the TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA, USA). Samples were sequenced using the NextSeq 500 platform (Illumina) to obtain 150-nt-long paired-end reads.

value: blood

value: peripheral blood mononuclear cells

tag: disease state

value: MS case


title: MS_9

description: circular RNA


title: RNA_CR_159

value: Peripheral blood mononuclear cells


title: input DNA

value: 14 days

tag: treatment

value: 29C for 12h

value: RVE5-MYC overexpression


title: Cerebellum WT 10wk replicate 2

tag: tissue

value: post natal week 10

value: WT


title: MS_10

description: circular RNA


title: MS_7

description: circular RNA


title: Cerebellum WT 10wk replicate 3

tag: gender

value: female


title: RCCECs_PA_Sample 1

source_name: Primary cells


title: RNA_CR_160

tag: age

value: M


title: MS_6

description: circular RNA


title: RCCECs_NC_Sample 2

value: untreated


title: RNA_CR_158


title: RNA_CR_157


title: RNA_CR_162


title: RCCECs_NC_Sample 1


title: RNA_CR_156


title: MS_5

description: circular RNA


title: RCCECs_NC_Sample 3


title: RNA_CR_154


title: RNA_CR_155


title: Kidney_W_12M_Rep7 [W87]

city: Lexington

first: Yuan

last: Wen

state: Kentucky

address: 760 Press Ave

institute: University of Kentucky

data_processing:
Sequenced reads were mapped to mRatBN7.2 rat genome assembly using STAR 2.7.2a with default parameters.
Aligned reads were quantified for gene counts using featureCounts from subread 1.6.4
Assembly: mRatBN7.2
Supplementary files format and content: raw gene counts

source_name: Kidney

extract_protocol:
Total RNA was isolated from kidney tissue following the recommendations of TRIzol reagent (Invitrogen, Carlsbad, CA). Briefly, tissue was homogenized using Polytron power homogenizer. After homogenization, RNA was isolated with the assistance of the Phase Lock Gel (Heavy) Kit. RNA was treated in-column with DNAse and eluted in nuclease-free water before being stored at -80°C. The total RNA concentration and purity were assessed by measuring the optical density (230, 260, and 280 nm) with the Nanodrop One Spectrophotometer (ThermoFisher Scientific, Wilmington, DE). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
RNA sequencing libraries were constructed at NovoGene

tag: metal

value: W

tag: time

value: Kidney


title: Cerebellum WT 10wk replicate 1

source_name: cerebellum

value: cerebellum

tag: genotype

tag: strain


title: MS_2

description: circular RNA


title: Kidney_W_12M_Rep6 [W86]


title: BA-Nac neurons, Cre, rep3

city: Biberach an der Riss

first: Gregorio

last: Alanis-Lobato

address: Birkendorfer Str 65

department: Global Computational Biology and Digital Sciences

institute: Boehringer Ingelheim Pharma

data_processing:
Sequencing reads were mapped to the Mus musculus reference genome (mm10) using STAR v2.5.2b allowing for soft clipping of adapter sequences. An average of 20 million reads per sample was obtained, from which approximately 10 million reads were assigned to genomic features. Transcript quantification was conducted with RSEM v1.3.0 and featureCounts v1.5.1. QC, and downstream bioinformatic analyses were conducted with R v4.1.0 and Bioconductor v3.12 tools.
Assembly: mm10
Supplementary files format and content: 2021_1055_CNS_CSS_BA-NAc_reward_neuron_exp_III_Pryce_SE.rds: R data storage file (rds) with a SummarizedExperiment object containing all sample metadata, gene metadata, raw and normalized gene expression matrices

source_name: Basal amygdala

extract_protocol:
Naive mice (n=12) underwent stereotactic surgery and were allocated to either the experimental group BA TeTxLC x NAc retro-Cre (n=6, BW=31.3.±1.5g) or the control group BA TeTxLC x NAc retro-mCherry (n=6, BW=33.0±3.2 g). At 15 days post-surgery mice were deeply anaesthetised and perfused with PBS at RT for 1 min. The brain was removed and placed in a cryo-mould (E6032-1CS, Sigma) containing embedding medium (Tissue-TEK OCT Compound, Sysmex). The cryo-mould was then placed on powdered dry ice for 10 min, wrapped in aluminium foil, placed in a polythene bag and stored at -80°C, prior to laser capture microdissection. Frozen brains were processed using RNA- and RNAse-free conditions throughout. Using a cryostat set at -17 to -20°C, coronal sections that included the BA at AP -1.6 to -2.0 mm were cut at 10 µm and mounted (3 sections per slide) on RNAse-free PET membrane slides (50102, Molecular Machines & Industries, MMI). Sections then underwent fixation and dehydration and were placed on their edge in a covered dark box at RT for 10 min or until completely dried, and then in a capped 50 ml Falcon tube for either immediate cell collection or stored at -80°C for 7 days maximum. Fluorescent reporter protein-labelled tissue was collected from coronal sections at bregma AP -1.6 to -2.0 using a laser capture microdissection system (CellCut, MMI). Fluorescence settings were optimized for visualization of mCherry+ tissue at wavelength 570 nm (channel TRITC).  The membrane slide was positioned and using 40x magnification, BA tissue areas that were mCherry+ were each encircled at Ø = 35 µm using the MMI CellTools software. There were 40-60 such areas per BA hemisphere and these were encircled for both hemispheres for each of the 3 sections on the membrane slide. A MMI Universal UV laser (355 nm, 2 µJ, 4 kHz frequency with 500 pico-s Pulse-Duration) at 40-50% laser power was activated (velocity = 54 µm/sec, focus = 27 µm) and the designated tissue areas were collected on the adhesive cap of an MMI Isolation tube (0.5 ml). The procedure was conducted with 2 membrane slides (6 sections) and isolation tubes per mouse, giving a total of 500-510 tissue samples per mouse. Following tissue collection, tissue lysis was conducted by adding QIAzol® (100 µl/tube; BA-NAc neuron tetanus toxin experiment) to the tube, triturating the tissue on the cap with 20 µl volumes and returning this volume to the tube. The tube was closed, inverted for 15 min at RT, and vortexed for 1 min, inverted for 5 min and centrifuged for 5 sec. The tube was then sealed with Parafilm and frozen at -80°C until RNA extraction. Lysate aliquots (2-3 x 100 µl per sample) from the same sample were pooled, and if required QIAzol was added, to give a final lysis volume of 300 µL. Samples were transferred to 2 mL PhaseLock tubes (QuantaBio) and half volume of chloroform:isoamyl alcohol (24:1 v:v) was added before shaking, a 3 min RT incubation and centrifugation at 4°C. The aqueous phase was then transferred to a 1.5 mL Eppendorf tube and mixed with a 1.5 volume of isopropanol (Sigma). After thorough pipette mixing, the isopropanol mixture was applied to an RNeasy MinElute spin column and total RNA was extracted using the miRNeasy Micro Kit (Qiagen) with a DNase treatment. Samples were eluted in 14 µL nuclease-free water. RNA samples were assessed both quantitatively and qualitatively using the High Sensitivity Total RNA 15nt Analysis DNF-472 Kit on a 48-channel Fragment Analyzer (Agilent). Total RNA yield was 1.45±0.51 ng. RNA integrity could often not be computed due to low input.
Up to 1.6 ng of total RNA was used for cDNA synthesis, conducted with the SMART-Seq® v4 Ultra Low Input RNA kit (Takara Bio). Depending on the input amount, 12-15 amplification cycles were conducted. After clean-up, up to 10 ng of cDNA was used to generate the final sequencing libraries with the tagmentation-based DNA Prep Kit (#20018705) and the IDT® DNA/RNA UD Indexes Set A (#20026121), both Illumina®. The index PCR was conducted with 9 or 10 cycles depending on cDNA amount, while the final library was eluted in 30 µL EB Buffer. Low input mRNA libraries were then quantified using the High Sensitivity dsDNA Quanti-iT Assay Kit (ThermoFisher) on a Synergy HTX (BioTek). Library molarity averaged at 21 nM. Libraries were also assessed for size distribution and adapter dimer presence (<0.5%) by the High Sensitivity NGS Fragment DNF-474 Kit on a 48-channel Fragment Analyzer (Agilent). All sequencing libraries were then normalized on the MicroLab STAR (Hamilton), pooled and spiked in with PhiX Control v3 (Illumina). The library pools was subsequently clustered on an SP Flow Cell and sequenced on a NovaSeq 6000 Sequencing System (Illumina) with dual index, paired-end reads at 2 x 100 bp length (Read parameters: Rd1: 101, Rd2: 10, Rd3: 10, Rd4: 101), reaching an average depth of 26 million Pass-Filter reads per sample (18.2% CV).

treatment_protocol: Basal amygdala (BA) of N=6 mice was infused with an AAV vector for floxed tetanus toxin light chain (TeTxLC) and their Nucleus Accumbens (NAc) with a Cre recombinase-expressing retrograde AAV vector. TeTxLC expression resulted in cleavage of the vesicle-associated membrane protein 2 (VAMP2), causing reduction of the vesicular glutamate release in the BA neurons projecting to the NAc. Control mice (N=6) were infused with the floxed TeTxLC vector in the BA, but only with a non-Cre expressing control vector in the NAc. Samples were collected 15 days after infusion.

value: Basal amygdala

value: Glutamatergic neuron

tag: experiment group

value: Glutamate neurotransmission inhibition

value: Cre mCherry x TeTxLC


title: RNA_CR_153


title: BA-Nac neurons, Cre, rep5


title: BA-Nac neurons, Cre, rep6


title: BA-Nac neurons, control, rep6, ExpIII

value: Control

value: mCherry x TeTxLC


title: Kidney_W_12M_Rep5 [W85]


title: BA-Nac neurons, Cre, rep4


title: BA-Nac neurons, Cre, rep2


title: RNA_CR_151

value: Peripheral blood mononuclear cells

value: F


title: CTR_10

description: circular RNA

value: blood

value: peripheral blood mononuclear cells

value: healthy control


title: RNA_CR_150


title: RNA_CR_152


title: Kidney_W_12M_Rep3 [W83]


title: Kidney_W_12M_Rep8 [W88]


title: Kidney_W_12M_Rep2 [W82]


title: CTR_9

description: circular RNA


title: Kidney_W_12M_Rep4 [W84]


title: CTR_7

description: circular RNA


title: BA-Nac neurons, control, rep4, ExpIII

value: mCherry x TeTxLC


title: MS_4

description: circular RNA

value: MS case


title: BA-Nac neurons, Cre, rep1


title: RNA_CR_149

value: M


title: MS_3

description: circular RNA


title: RNA_CR_148


title: Kidney_W_12M_Rep1 [W81]

value: W


title: CTR_8

description: circular RNA


title: Kidney_Ta_12M_Rep8 [T80]

value: Ta

value: Kidney


title: MS_1

description: circular RNA


title: RNA_CR_147


title: Kidney_Ta_12M_Rep6 [T78]


title: Kidney_Ta_12M_Rep7 [T79]


title: BA-Nac neurons, control, rep3, ExpIII

value: Basal amygdala


title: CTR_5

description: circular RNA


title: RNA_CR_146


title: BA-Nac neurons, control, rep2, ExpIII

value: Glutamatergic neuron


title: RNA_CR_145


title: Amygdala tissue, CTB neurons, rep4

data_processing:
Sequencing reads were mapped to the Mus musculus reference genome (mm10) using STAR v2.5.2b allowing for soft clipping of adapter sequences. An average of 20 million reads per sample was obtained, from which approximately 10 million reads were assigned to genomic features. Transcript quantification was conducted with RSEM v1.3.0 and featureCounts v1.5.1. QC, and downstream bioinformatic analyses were conducted with R v4.1.0 and Bioconductor v3.12 tools.
Assembly: mm10
Supplementary files format and content: 2020_1011_CNS_CSS_BA-NAc_reward_neuron_exp_I_Pryce_SE.rds: R data storage file (rds) with a SummarizedExperiment object containing all sample metadata, gene metadata, raw and normalized gene expression matrices

extract_protocol:
On day 16 after treatment, mice were deeply anaesthetized and then perfused with PBS at RT for 1 min. The brain was removed and placed in a cryo-mould (E6032-1CS, Sigma) with embedding medium (Tissue TEK OCT Compound). The cryo-mould was then placed on powdered dry ice for 10 min, wrapped in aluminium foil, placed in a polythene bag and stored at -80°C, prior to laser capture microdissection. Frozen brains were processed using RNA- and RNAse-free conditions throughout. Using a cryostat set at -17 to -20°C, coronal sections that included the BA at AP -1.6 to -2.0 mm were cut at 10 µm and mounted (3 sections per slide) on RNAse-free PET membrane slides (50102, Molecular Machines & Industries, MMI). Sections then underwent fixation and dehydration and were placed on their edge in a covered dark box at RT for 10 min or until completely dried, and then in a capped 50 ml Falcon tube for either immediate cell collection or stored at -80°C for 7 days maximum. Fluorescent reporter protein-labelled tissue was collected from coronal sections at bregma AP -1.6 to -2.0 using a laser capture microdissection system (CellCut, MMI). Fluorescence settings were optimized for visualization of CTB-555+ tissue (channel TRITC). The membrane slide was positioned and using 40x magnification, BA tissue areas that were CTB-555+ were each encircled at Ø = 35 µm using the MMI CellTools software. There were 40-60 such areas per BA hemisphere and these were encircled for both hemispheres for each of the 3 sections on the membrane slide. A MMI Universal UV laser (355 nm, 2 µJ, 4 kHz frequency with 500 pico-s Pulse-Duration) at 40-50% laser power was activated (velocity = 54 µm/sec, focus = 27 µm) and the designated tissue areas were collected on the adhesive cap of an MMI Isolation tube (0.5 ml). The procedure was conducted with 2 membrane slides (6 sections) and isolation tubes per mouse, giving a total of 500-510 tissue samples per mouse. Following tissue collection, tissue lysis was conducted by adding RLT buffer with DTT (100 µl) to the tube, triturating the tissue on the cap with 20 µl volumes and returning this volume to the tube. The tube was closed, inverted for 15 min at RT, and vortexed for 1 min, inverted for 5 min and centrifuged for 5 sec. The tube was then sealed with Parafilm and frozen at -80°C until RNA extraction. Lysate aliquots (2-3 x 100 µl per sample) from the same sample were pooled, and if required RLT was added, to give a final lysis volume of 300 µL. Samples were transferred to 2 mL PhaseLock tubes (QuantaBio). For RLT lysates specifically, a half volume of phenol:chloroform:isoamyl alcohol (25:24:1 v:v:v; Sigma) was added before brief shaking and centrifuging at 4°C. Half volume of chloroform:isoamyl alcohol (24:1 v:v) was added before shaking, a 3 min RT incubation and centrifugation at 4°C. The aqueous phase was then transferred to a 1.5 mL Eppendorf tube and mixed with a 1.5 volume of isopropanol (Sigma). After thorough pipette mixing, the isopropanol mixture was applied to an RNeasy MinElute spin column and total RNA was extracted using the miRNeasy Micro Kit (Qiagen) with a DNase treatment. Samples were eluted in 14 µL nuclease-free water. RNA samples were assessed both quantitatively and qualitatively using the High Sensitivity Total RNA 15nt Analysis DNF-472 Kit on a 48-channel Fragment Analyzer (Agilent). Total RNA yield was 0.31±0.11 ng (mean±SD). RNA integrity could often not be computed due to low input.
Up to 1.6 ng of total RNA was used for cDNA synthesis, conducted with the SMART-Seq® v4 Ultra Low Input RNA kit (Takara Bio). Depending on the input amount, 12-15 amplification cycles were conducted. After clean-up, up to 10 ng of cDNA was used to generate the final sequencing libraries with the tagmentation-based DNA Prep Kit (#20018705) and the IDT® DNA/RNA UD Indexes Set A (#20026121), both Illumina®. The index PCR was conducted with 9 or 10 cycles depending on cDNA amount, while the final library was eluted in 30 µL EB Buffer. Low input mRNA libraries were then quantified using the High Sensitivity dsDNA Quanti-iT Assay Kit (ThermoFisher) on a Synergy HTX (BioTek). Library molarity averaged at 21 nM. Libraries were also assessed for size distribution and adapter dimer presence (<0.5%) by the High Sensitivity NGS Fragment DNF-474 Kit on a 48-channel Fragment Analyzer (Agilent). All sequencing libraries were then normalized on the MicroLab STAR (Hamilton), pooled and spiked in with PhiX Control v3 (Illumina). The library pools was subsequently clustered on an SP Flow Cell and sequenced on a NovaSeq 6000 Sequencing System (Illumina) with dual index, paired-end reads at 2 x 100 bp length (Read parameters: Rd1: 101, Rd2: 10, Rd3: 10, Rd4: 101), reaching an average depth of 26 million Pass-Filter reads per sample (18.2% CV).

treatment_protocol: The Nucleus Accumbens (NAc) of C57BL/6 mice was infused with the cholera toxin beta (CTB) retrograde neuroanatomical tracer. 14 days later, after recovery and tracing, one cohort (Chronic Social Stress or CSS mice) were exposed to dominant CD1 mice including brief daily attacks for a time period of 15 days. A second cohort (Control mice) were maintained in brother pairs and handled daily. Following the 15 day time period, the brains of both CSS and CON mice were collected on day 16.

value: Amygdala with CTB neurons


title: CTR_4

description: circular RNA


title: Kidney_Ta_12M_Rep5 [T77]


title: BA-Nac neurons, control, rep1, ExpIII


title: BA-Nac neurons, control, rep5, ExpIII


title: CTR_1

description: circular RNA


title: Kidney_Ta_12M_Rep4 [T76]


title: Amygdala tissue, no CTB neurons, rep4

value: Amygdala without CTB neurons


title: Kidney_Ta_12M_Rep3 [T75]


title: RNA_CR_144


title: CTR_6

description: circular RNA


title: Amygdala tissue, CTB neurons, rep3


title: Kidney_Ta_12M_Rep2 [T74]


title: CTR_2

description: circular RNA


title: RNA_CR_142


title: Amygdala tissue, no CTB neurons, rep3


title: Amygdala tissue, CTB neurons, rep2


title: RNA_CR_143


title: Amygdala tissue, no CTB neurons, rep2


title: RNA_CR_141


title: RNA_CR_140


title: RNA_CR_139


title: Kidney_Pb_12M_Rep6 [P135]

value: Pb


title: RNA_CR_137


title: Wild type cells 2

city: Stockholm

first: Shreekara

last: Gopalakrishna

state: Solna

address: Solnavägen 9

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

data_processing:
Library strategy: Ribo-seq
Adaptor sequences were trimmed using the FASTX-Toolkit
Trimmed reads mapping to nuclear-encoded rRNA were discarded
The remaining reads were mapped sequentially to mitochondrial rRNA (mt-rRNA); mitochondrial tRNA (mt-tRNA); and mitochondrial mRNA (mt-mRNA) using bowtie version 1, with parameters -v 2 --best (i.e. maximum two mismatches, report best match)
When calculating the expression levels of mitochondrial genes, to normalise for different library sizes, counts for a given library were expressed as reads per million (RPM) mapped in the positive-sense orientation to nuclear-encoded mRNA in that library
Regions of coding sequence (CDS) that overlap (ATP8/ATP6 and ND4L/ND4) were excluded due to ambiguous CDS assignment
Mitochondrial ribosome-protected fragments (mtRPFs) with 5' ends mapping within 15 nt of the start codon or 45 nt of the stop codon were excluded
The reference genome assembly used for read mapping was from GenBank, accession number: GQ472310.1
Genome_build: GQ472310.1
Supplementary_files_format_and_content: Tab-delimited text file including normalized counts per gene as Ensemble Gene ID for each sample

source_name: Human Embryonic Kidney_Flp-In™ 293 T-REx

growth_protocol: Flp-In T-Rex human embryonic kidney 293T (HEK293T, Invitrogen) cells (wildtype and mtIF3 KO) were cultured in DMEM (Dulbecco´s modified eagle medium) supplemented with 10% (v/v) tetracycline-free fetal bovine serum (FBS), 2 mM GlutaMax (Gibco), 1x Penicillin/Streptomycin (Gibco), 50 μg/ml uridine, 100 μg/ml Zeocin (Invitrogen) and 10 μg/ml blasticidin (Gibco) at 37°C under 5% CO2 humidified atmosphere

extract_protocol:
200 μl aliquots of cell lysates were treated with 7.5 μl RNase 1 (100 units/μl) at 28°C. The reaction was layered onto a 10–30% sucrose gradient as described above for ‘Analysis of mitochondrial ribosome integrity’. Subsequently, all fractions containing mitochondrial monosomes, ascertained by western blotting, were pooled and digested with proteinase K (200 μg/ml) for 30 min at 42°C. RPFs were recovered by extracting twice with pre-warmed (65°C) acidic phenol:chloroform and once with chloroform (1:1, v/v, buffered with 10 mM Tris pH 7.5, 0.1 mM EDTA) followed by ethanol precipitation
RPFs (1 μg) were separated on 15% denaturing polyacrylamide gels and RNA species migrating between 10 and 50 nt were harvested. RNA was eluted from the gel slices and ethanol precipitated. The RNA samples from above were heated at 80°C for 2 min, cooled and the 3’ phosphate group removed using T4 polynucleotide kinase (New England Biolabs) for 2 hr at 37°C in a 20 μl reaction. The RNA was concentrated by ethanol precipitation, resuspended in 10 mM Tris-HCl (pH 7.5) and ligated in a 20 μl reaction overnight at 14°C to a preadenylated 3’-adaptor using T4 RNA Ligase 2 (New England Biolabs). RNA was precipitated, loaded into a 15% denaturing polyacrylamide gel and ligated RNA fragments migrating between 10 and 50 nt were excised. The RNA was eluted, precipitated, resuspended as above, and 5’ phosphorylated using T4 PNK in the presence of 1 mM ATP for 2 hr at 37°C. RNA was concentrated by ethanol precipitation, resuspended in 10 mM Tris-HCl (pH 7.5) and ligated to a 5’ RNA adaptor overnight at 14°C using T4 RNA Ligase (New England Biolabs). The fully adapted RNAs were recovered by ethanol precipitation, dissolved in 6 μl 10 mM Tris-HCl (pH 7.5), and ligated product annealed to an RT primer for 5 min at 65°C. The RNA was subsequently reverse transcribed for 50 min at 55°C in using SuperScript III according to manufacturer’s instructions, followed by heat inactivation for 5 min at 85°C. Standard PCR reactions were used to prepare amplicons using forward primer RP1 and RPIX as reverse primer, where X is primer number (1-24). PCR reactions were loaded onto 10% non-denaturing polyacrylamide-TBE gels and products of ~150 bp were excised from the gel and eluted. These amplicon libraries were ethanol precipitated and resuspended in 15 μl 10 mM Tris-HCl (pH 7.5)
Ribosomal RNA was depleted from MitoRibo-Seq samples at the library amplicon stage; 12 µL of the relevant MitoRibo-Seq library was mixed with 4 µL of 4 × hybridization buffer (200 mM HEPES pH 7.5 and 2 M NaCl) and denatured at 98°C for 2 min. DNA was re-annealed for 5 hr at 68°C prior to addition of 2 µL of 10 × DSN master buffer and 2 µL of DSN (four units, Evrogen). Digestion was allowed to proceed for 25 min at 68°C, before addition of 20 µL 10 mM EDTA and incubation for a further 5 min at 68°C. DNA was recovered by a single extraction with phenol–chloroform (1:1, vol/vol) followed by ethanol precipitation and resuspended in 4 µL 10 mM Tris–HCl pH 7.5. The treated amplicon library was subjected to another round of PCR (as above) and the resulting library subjected to a second round of DSN treatment.

treatment_protocol: Generation of HEK293T knockout cell line for mtIF3 was performed using CRISPR/Cas9 system. Briefly, guide RNAs (gRNAs) designed to generate an out-of-frame deletion in exon 1 were cloned into pSpCas9(BB)-2A-Puro (pX459) V2.0 vector. mtIF3 targeting pX459 vectors were transfected to cells using Lipofectamine 3000 according to the manufacturer’s instructions. After 48 h of puromycin (1.5 μg/ml) selection, cells were serially diluted to plate single cells in each well of a 96-well plate. Resultant clones were screened by PCR and Western blotting. Loss of mtIF3 in selected clones was confirmed by Sanger sequencing

value: Wildtype


title: Wild type cells 1


title: mtIF3 KO cells 2

value: mtIF3 -/-


title: CTR_3

description: circular RNA


title: Kidney_Ta_12M_Rep1 [T73]


title: Amygdala tissue, CTB neurons, rep1


title: Kidney_Pb_12M_Rep7 [P136]


title: Kidney_Pb_12M_Rep4 [P132]


title: RNA_CR_135

value: Peripheral blood mononuclear cells


title: mtIF3 KO cells 1


title: VROH3

city: apex

first: Lyle

last: Burgoon

state: nc

address: 216 kelly west dr

department: Environmental Laboratory

institute: US Army Engineer Research and Development Center

data_processing:
Our RNA-sequencing analysis pipeline is focused on measuring the abundance of gene transcripts, giving us a measure of gene expression. We start by using Salmon to align and measure the number of RNA molecules. Gene-specific transcript abundance is then calculated using the tximport package in R. We narrowed down the genes to those represented in our Adverse Outcome Pathway Networks for steatosis, energy balance, cell cycle, and cell death. We focused on these networks as they serve as the precursor for liver tumor formation (tumorigenesis) and cancer (carcinogenesis), as well as yields insights into energy availability, which may impact fitness and population health.
Genome_build: GRCh38
Supplementary_files_format_and_content: Table/matrix where first column is the gene symbol, subsequent columns are the sites where water samples were obtained. CONTROL is a control water sample from a reference laboratory.

growth_protocol: HepG2 cells (ATCC, Manassas, VA) were cultivated at 37 °C in a humidified 5% CO2 atmosphere as monolayer cultures in Dulbecco's modified Eagle's medium (DMEM, Fisher Scientific, Pittsburgh, PA) supplemented with 100 units/mL penicillin, 100 g/mL streptomycin, 15 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES, Fisher Scientific), and 10% (v/v) heat inactivated fetal bovine serum (FBS, Atlanta Biological, Atlanta, GA). To prepare HepG2 cells for exposure, two T225 flasks of cells were harvested after they reached 80-90% confluence. Cells were combined and evenly distributed to 88 6-cm dishes (there were 4 biological replicates for each of 16 sampling locations, 16 replicates for the laboratory controls, and 8 spare dishes) for precultivation in 5% CO2 at 37 °C for 72 hours.

extract_protocol:
After the 48-hour exposure, cells were harvested with RNALater (Sigma-Aldrich, St. Louis, MO). Briefly, exposure medium was quickly removed from the culture dish and 1 mL RNALater was added to each dish. The cells were detached from the dish bottom with a cell lifter and transferred to a 2-mL centrifuge tube. The harvested cells were kept at 4 °C for 2 hours before stored at -80 °C.
RNA was shipped to BioSpyder for sequencing using their TempO-Seq platform. We received FASTQ files from BioSpyder that contained our sequencing results.

treatment_protocol: For cell exposure experiments, exposure medium was prepared by mixing stock medium with the field-collected grab samples. Specifically, a DMEM with a four-fold higher concentration (4x stock) was prepared with all above supplements, plus 0.4 mg/mL normocin (Invivogen, San Diego, CA). This 4x stock medium was mixed in a ratio of 1:3 with a filtered (0.7 µm) water sample from each field site, or with purified water (ultrapure type 1, 18.2 MΩ.cm, 0.1-µm filtered, Aqua Solutions, Jasper, GA) that served as the laboratory control. The final concentrations of environmental samples in the exposure medium were 75% of the initial field-collected water samples. Cells were then incubated in 5% CO2 at 37 °C for 48 hours before quench.

value: hepatoma cell line

tag: surface water site

value: VROH

tag: protocol

value: TempO-Seq


title: RNA_CR_138

tag: cell type


title: Kidney_Pb_12M_Rep2 [P130]


title: SRMI4

tag: cell line

value: SRMI


title: Amygdala tissue, no CTB neurons, rep1


title: VROH1


title: BA-NAc neurons, CSS, rep14

value: CSS

value: Chronic social stress


title: VROH4


title: BA-NAc neurons, Control, rep9

value: Control


title: BA-NAc neurons, CSS, rep13


title: Kidney_Pb_12M_Rep5 [P134]


title: BA-NAc neurons, CSS, rep16


title: Kidney_Pb_12M_Rep1 [P129]


title: RNA_CR_132

value: M


title: BA-NAc neurons, Control, rep8


title: Kidney_DU_12M_Rep8 [D144]

value: DU

value: Kidney


title: RNA_CR_131

value: F


title: RNA_CR_133


title: VROH2


title: BA-NAc neurons, CSS, rep15

value: Basal amygdala

value: Glutamatergic neuron


title: BA-NAc neurons, Control, rep7


title: Kidney_Pb_12M_Rep3 [P131]

value: Pb


title: SRMI2


title: BA-NAc neurons, CSS, rep12


title: RNA_CR_134


title: RRMI4

value: RRMI


title: RRMI3


title: SRMI3


title: BA-NAc neurons, CSS, rep11


title: RNA_CR_136


title: RNA_CR_128


title: Kidney_DU_12M_Rep7 [D143]


title: RNA_CR_129


title: SRMI1


title: RNA_CR_130


title: RRMI2


title: Kidney_DU_12M_Rep5 [D141]


title: Kidney_DU_12M_Rep3 [D139]


title: RNA_CR_127


title: RNA_CR_126


title: Kidney_DU_12M_Rep2 [D138]


title: BA-NAc neurons, CSS, rep8


title: BA-NAc neurons, CSS, rep9


title: Kidney_DU_12M_Rep1 [D137]


title: BA-NAc neurons, CSS, rep10


title: BA-NAc neurons, CSS, rep7


title: Kidney_DU_12M_Rep4 [D140]


title: Kidney_Co_12M_Rep6 [C102]

value: Co


title: ORNY4

value: ORNY


title: RNA_CR_125

value: Peripheral blood mononuclear cells


title: ORNY3

value: hepatoma cell line


title: RRMI1

value: TempO-Seq


title: MROH4

value: MROH


title: Kidney_DU_12M_Rep6 [D142]


title: ORNY1


title: MROH3


title: BA-NAc neurons, Control, rep5


title: MROH2


title: Kidney_Co_12M_Rep3 [C99]


title: BA-NAc neurons, CSS, rep3

value: CSS


title: RNA_CR_124


title: Kidney_Co_12M_Rep8 [C104]


title: ORNY2


title: BA-NAc neurons, CSS, rep6

value: Chronic social stress


title: RNA_CR_123


title: Kidney_Co_12M_Rep7 [C103]


title: Kidney_Co_12M_Rep2 [C98]


title: BA-NAc neurons, CSS, rep5


title: Kidney_Co_12M_Rep1 [C97]


title: RNA_CR_121


title: BA-NAc neurons, Control, rep6

value: Control


title: RNA_CR_120

value: M


title: Kidney_Co_12M_Rep4 [C100]


title: MROH1


title: RNA_CR_118


title: RNA_CR_122


title: RNA_CR_115


title: MIWI1

value: MIWI


title: RNA_CR_119


title: Kidney_Al_12M_Rep7 [A127]

value: Al

value: Kidney


title: BA-NAc neurons, Control, rep2

value: Basal amygdala


title: BA-NAc neurons, Control, rep4

value: Glutamatergic neuron


title: Kidney_Co_12M_Rep5 [C101]


title: RNA_CR_117


title: BA-NAc neurons, Control, rep3


title: BA-NAc neurons, Control, rep1


title: MIWI4


title: MIWI3


title: RNA_CR_116


title: BA-NAc neurons, CSS, rep4


title: Kidney_Al_12M_Rep8 [A128]


title: BA-NAc neurons, CSS, rep2


title: BA-NAc neurons, CSS, rep1


title: MAWI2

value: MAWI


title: RNA_CR_114


title: Kidney_Al_12M_Rep6 [A126]


title: MAWI4


title: MAWI1


title: LRMN4

value: LRMN


title: LOVO si-SRSF11 3

city: xuzhou

first: Yao-Jie

last: Pan

address: 209 Tong Shan Road, Xuzhou, Jiangsu, P. R. China

institute: xuzhou medical university

data_processing:
RNA quantification and qualification
Library preparation for Transcriptome sequencing
Clustering and sequencing (Genchem Experimental Department)
Quality control
Reads mapping to the reference genome;Novel transcripts prediction;Quantification of gene expression level;Differential expression analysis;GO and KEGG enrichment analysis of differentially expressed genes;SNP analysis;AS analysis;PPI analysis of differentially expressed genes
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: cell

extract_protocol:
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.  Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse  Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

value: LOVO

tag: transfection


title: CD8WT_TGACCA

city: GOSSELIES

first: Abdulkader

last: AZOUZ

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

description: CD8 T cells WT

data_processing:
Adapters were removed with Trimmomatic-0.36
Reads were mapped to the reference genome mm10 using STAR_2.5.3 software with default parameters
Read counts were obtained using HTSeq-0.9.1.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include CPM values for each Sample

source_name: CD8 T cells

extract_protocol:
We extracted RNA from 2x105 sorted WT CD8+ T cells mice (in duplicates), and RNA from 2x105  sorted CD8 T cells KO PHD2  (in triplicate) using  RNeasy Plus Mini kit according to manufacturer’sinstructions (Qiagen)
Libraries were prepared using Ovation SoLo RNA-Seq System (NuGEN Technologies) and  underwent paired-end sequencing

value: CD8 T cells

value: WT


title: CD8WT_ACAGTG

description: CD8 T cells WT


title: Kidney_Al_12M_Rep5 [A125]


title: RNA_CR_113

value: Peripheral blood mononuclear cells


title: CD8CP_GTTTCG

description: CD8 T cells KO PHD2


title: Kidney_Al_12M_Rep4 [A124]


title: CD8CP_GTGGCC

description: CD8 T cells KO PHD2


title: LRMN2

value: hepatoma cell line

value: TempO-Seq


title: LRMN1


title: RNA_CR_112


title: Kidney_Al_12M_Rep3 [A123]


title: LRMN3


title: LOVO si-nc 2

value: si-nc


title: LOVO si-SRSF11 2


title: LOVO si-nc 3


title: LOVO si-SRSF11 1


title: Kidney_Al_12M_Rep1 [A121]


title: d_14d_2_samll

city: Shanghai

last: Xiao

address: No.197, Rui Jin Er Road

department: Department of Pediatrics

institute: Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine,

description:
miRNA_normalizedcounts.txt
miRNA_raw_counts.txt

data_processing:
Illumina Bustard used for basecalling.
For lncRNA sequences, the clean reads were aligned to the rat reference genome (rattus norvegicus genome obtained from Ensembl Rnor_6.0) with the software Hisat2 (version 2.0.5; main parameter: --no-unal -t --phred33 --rna-strandness RF --dta-cufflinks --un-conc-gz). For small RNA sequences, the small RNA tags were mapped to reference sequence by Bowtie (version 0.12.9; main parameter: -v 0 -k 1) and miRBase20.0 (rattus norvegicus) was used as reference.
Quantification of the transcripts was performed using StringTie software and Fragments Per Kilobase of transcript per Millions base pairs sequenced (FPKM) was use to determine the expression level of mRNAs and lncRNAs. miRNA and circRNA expression levels were estimated by transcript per million (TPM) through the following criteria: Normalization formula: Normalized expression = mapped readcount/Total reads*1000000.
Genome_build: rattus norvegicus genome obtained from Ensembl (Rnor_6.0) and miRBase20.0 (rattus norvegicus)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values of mRNA and lncRNA for each Sample; tab-delimited text files include TPM values of miRNA and circRNA for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: proximal tibia growth plate

extract_protocol:
The proximal tibia growth plates were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded Total RNA Library Prep Plant/Gold/Globin +NEBNext® Ultra Directional RNA Library Prep Kit (Cat#RS-122-2303) was used with total RNA for the construction of lncRNA sequencing libraries. NEB Next® Multiplex Small RNA Library Prep Set for Illumina® (Set 1) (Cat#E7300) was used with total RNA for the construction of small RNA sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: SD rats at postnatal 14 days were treated with 2 mg/kg/d of dexamethasone for 7 or 14 days (intraperitoneal injection), after which growth plate tissue was obtained from the rat proximal tibia. Control rats received the same volume of saline.

value: Sprague-Dawley

value: proximal tibia growth plate

value: post natal day 28

value: dexamethasone intraperitoneal injection at a dose of 2.0 mg/kg/d for 14 days


title: MAWI3


title: C2B5

city: Blacksburg

first: Honglin

last: Jiang

state: VA

address: Litton Reaves Hall

department: School of Animal Sciences

institute: Virginia Tech

data_processing:
Raw sequencing reads were first filtered with Trimmomatic to remove low quality reads and reads containing adaptors. Clean reads were mapped to the mouse reference genome (mm10) using the STAR (v2.5) program. The uniquely mapped reads were used in quantification of gene expression level, which was done using the HTSeq v0.6.1 program.
Assembly: mm10
Supplementary files format and content: Excell file for gene counts

source_name: C2C12 cells

growth_protocol: cells were cultured in growth medium consisting of DMEM and 10% FBS and 1% antibiotics

extract_protocol:
Total RNA was extracted using TRIzol
RNA-seq library was constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina.

treatment_protocol: Myogenic differentation was induced by changing growth meidum to ifferentiation medium consisting of DMEM and 2% horse serum and 1% antibiotics.

tag: Stage

value: differentiating


title: LOVO si-nc 1


title: JRMI3

value: JRMI


title: Patient AC439 replicate 1

city: Villeurbanne

first: Audric

last: Cologne

address: 43 Bd du 11 Novembre 1918

institute: CNRS

description:
AC439-1
kissDE_table.tab header: F2

data_processing:
Reads aligned with STAR v2.0.7a with --quantMode TranscriptomeSAM for RSEM quantification
Genes quantification with RSEM v1.3.1 with --seed 12345 and –strandedness reverse
Genes differential expression between WT and mutated samples with DESeq2 v1.32.0, genes with a TPM sum across all condition < 10 were discarded
Intron quantification with IRFinder v1.2.5
Differential intron retentions with kissDE v1.15.0
Genome_build: hg38
Supplementary_files_format_and_content: genes.results files are RSEM result files containing TPM and FPKM values for each sample, tab delimited
Supplementary_files_format_and_content: TPM.tab is a matrix of RSEM results containing only the TPM value for each gene and sample, tab delimited
Supplementary_files_format_and_content: IRFinder-IR-dir.txt files are IRFinder result files containing introns, junctions and PSI quantification for each sample, tab delimited
Supplementary_files_format_and_content: DESeq2.WtvsMut.csv is DESeq2 result file with baseMean, FDR and log2(FC) metrics, csv file
Supplementary_files_format_and_content: kissDE_table.tab is a matrix of IRFinder result files formated for kissDE usage, tab delimited
Supplementary_files_format_and_content: kissDE.IR.WtvsMut.tab is kissDE result file with FDR and deltaPSI metrics, tab delimited

source_name: Patient AC439

extract_protocol:
Whole cell extracts were prepared from harvested cells and total RNA was extracted using TriReagent.
Libraries are prepared with NEBNextUltra II mRNA-Seq Library Prep Kit for Illumina protocol according supplier recommendations. The purification of polyA+ containing mRNA molecules was done using poly-T oligo attached magnetic beads from 100ng total RNA

tag: condition

value: Microcephalic osteodysplastic primordial dwarfism type 1 (MOPD1)

tag: individual

value: Patient AC439

value: lymphoblastoid cell line

value: MOPD1 patient-derived immortalized lymphoblasts

tag: genotype/variation


title: c_14d_2_samll

tag: tissue

tag: treatment

value: saline intraperitoneal injection at a dose of 2.0 mg/kg/d for 14 days


title: C2B2


title: JRMI1


title: CD8CP_GCCAAT

description: CD8 T cells KO PHD2

value: CD8 T cells


title: d_14d_1_samll

tag: age


title: d_14d_3_samll


title: C2B4


title: C2B3


title: Kidney_Al_12M_Rep2 [A122]

tag: metal

value: Al

value: Kidney


title: IHIN4

value: hepatoma cell line

value: IHIN


title: Patient AC438 replicate 1

description:
AC438-1
kissDE_table.tab header: F1

source_name: Patient AC438

value: Patient AC438


title: d_7d_2_samll

value: Sprague-Dawley

value: post natal day 21

value: dexamethasone intraperitoneal injection at a dose of 2.0 mg/kg/d for 7 days


title: d_7d_3_samll

value: proximal tibia growth plate


title: JRMI4

value: TempO-Seq


title: IHIN2


title: JRMI2

value: JRMI


title: c_14d_3_samll

value: post natal day 28


title: d_7d_1_samll


title: Patient AC439 replicate 2

description:
AC439-2
kissDE_table.tab header: F4

value: Microcephalic osteodysplastic primordial dwarfism type 1 (MOPD1)

value: Patient AC439


title: Control C702 replicate 1

description:
C702-1
kissDE_table.tab header: F5

source_name: Control C702

value: control

value: Control C702

value: lymphoblastoid cell line

value: RNU4ATAC g.WT;g.WT


title: IHIN1


title: Patient AC438 replicate 2

description:
AC438-2
kissDE_table.tab header: F3

value: MOPD1 patient-derived immortalized lymphoblasts


title: C2A3

value: before differentiation


title: C2B1

value: differentiating


title: IHIN3

value: hepatoma cell line

value: IHIN


title: c_14d_1_samll

value: Sprague-Dawley

value: saline intraperitoneal injection at a dose of 2.0 mg/kg/d for 14 days


title: Control C702 replicate 2

description:
C702-2
kissDE_table.tab header: F6


title: C2A4


title: C2A5


title: GRNY4

value: GRNY


title: c_7d_2_samll

value: proximal tibia growth plate

value: post natal day 21

value: saline intraperitoneal injection at a dose of 2.0 mg/kg/d for 7 days


title: C2A1


title: GRNY3

value: TempO-Seq


title: RNA-Seq H1299-R213X5FUR-5

city: Utrecht

first: Sebastiaan

last: van Heesch

address: Heidelberglaan 25

country: Netherlands

institute: Princess Maxima Center

data_processing:
use cutadapt v3.4 to trim the data to 29 NT and remove low-quality reads with the following parameters:
STAR v2.7.8a with reference assembly ensembl 102 and the following parameters: --outFilterMismatchNmax 6; --outFilterMultimapNmax 10; --alignSJoverhangMin 10 --outFilterScoreMinOverLread 0.75
run FeatureCount v2.0.2 with the following parameters: -t "CDS"  -g "gene_id" -O  -s 1
use cutadapt v3.4 with --hardtrim5 29 to trim RNA-seq reads to ribo-seq length and follow ribo-seq data processing protocol
Genome_build: hg38
Supplementary_files_format_and_content: count files with raw gene counts for all data generated by FeatureCount

source_name: epithelial

growth_protocol: H1299 human lung adenocarcinoma parental cells (ATCC, USA), which are p53 null, were stably transfected with R213X nonsense mutant TP53, Empty Vector (EV) as a control, or other plasmid constructs as described (Zhang et al., Front Oncol 2018). Stably transfected cells were cultured in RPMI-1640 medium (Hyclone, USA) supplemented with 25 mM HEPES Buffer solution (Gibco, USA) and 10% fetal bovine serum (Gibco, USA).

extract_protocol:
Total RNA was isolated from 200 µl of lysate using 750 µl of TRIzol LS and purified using the Zymo RNA Clean and Concentrator-5 kit with modifications to the manufacturer's instructions: Recovered RNA was treated with DNAse I at 37°C for 10 min prior to addition of RNA Binding Buffer, and isolated RNA was eluted in 15 µl nuclease-free water. Prior to library preparation, purified RNA was quantified and checked for RNA integrity with Agilent Bioanalyzer 2100 using the RNA 6000 Nano kit according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were seeded at a density of 0.3 x 106 cells/15 cm dish for non-treated and G418-treated conditions or at a density of 2.3 x 106 cells/15 cm dish for FUr-treated condition in a final volume of 32 ml. One day after seeding the cells, they were treated with 100 µM of G418 or 3 µM of 5-Fluorouridine for 72h, respectively, using four replicate treatments per condition. Next, medium was aspirated, cells were washed once with 5 ml of ice-cold Dulbecco’s Phosphate Buffered Saline (DPBS), and plates were snap frozen with liquid nitrogen.

tag: vector

value: FUr


title: C2A2


title: c_7d_3_samll