title: RP27N

value: biopsy of normal

value: ModeratelyDifferentiated


title: 4g1a (18 months, male)

status: Public on Sep 20 2023

type: SRA

city: Saarbruecken

first: Gilles

last: Gasparoni

state: Saarland

address: Campus

department: Genetics Department

country: Germany

institute: Saarland University

description: ATAC-seq

library_source: genomic

data_processing:
after a quality control with FastQC (www.bioinformatics.bbsrc.ac.uk/projects/fastqc/), reads were adapter-trimmed (Q < 20) with Trim Galore! version 0.4.2 (www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
reads were aligned to mm10 assembly with the GEM mapper.
duplicated reads were identified using Picard tools (v1.115).
reads were downscaled to avoid any bias in the downstream analysis due to variations in sequencing depth.
nucleosome depleted regions (NDRs) were called using MACS2 (v2.1.0) using the following settings: -shift -100, -extsize 200, -nomodel, -keep-dup all.
peaks which overlap with the black regions as defined by ENCODE (https://doi.org/10.1038/s41598-019-45839-z) were excluded.
Assembly: mm10
Supplementary files format and content: bed file with ATAC peak call positions.

molecule: genomic DNA

organism: Mus musculus

source_name: brain

extract_protocol:
Cerebral endothelial cells were sorted into FACS buffer (1X PBS, 2%FCS and 2mM EDTA) at 4°C and the assay for transposa-se-accessible chromatin sequencing (ATAC-seq) was performed according to a protocol adapted from Buenrostro et al57. 50,000 endothelial cells were spun down (500g, 5 minutes, 4°C), supernatant was removed and the cell pellet was resuspended in cold DNase inhibiting buffer (1 M KCl, 5 M NaCl, 1 M Tris-HCl, 0.5 M EGTA and 0.5 M Spermidine) containing prote-ase inhibitor cocktail (Roche). 0.1% IGEPAL® CA-630 (Sigma) was added to the suspension followed by gently inverting the tube 3-4 times and incubation on ice for 5 minutes. The nuclei were spun down (500g, 5 minutes, 4°C), supernatant was removed and resuspended in the DNase inhibiting buffer. The nuclei were again centrifuged (500g, 9 minutes, 4°C), the superna-tant was removed, and the pellet was resuspended in 50 µL reaction mixture, containing 25 µL 2X TD buffer, 22.5 µL nuclease-free water, and 2.5 µL Tn5 transposase enzyme (Nextera DNA Library Preparation Kit, Illumina, FC-121-1030). The tagmentation reaction was performed at 37 °C for 30 min followed by purification of library using MinElute PCR Purification Kit (Qiagen). The library was eluted in 26 µL elution buffer (Qiagen) and stored at –80°C until amplification. For amplification, 20 µL library was added to 30 µL PCR mix containing 25 µL NEB Next High Fidelity 2X Master Mix (New England Biolabs), 1 µL each Nextera i5 and i7 indexed primers as forward and reverse primers, and 3 µL nuclease-free water. The amplification was carried out in following steps – one cycle of 72°C for 5 minutes and 98°C for 30 seconds, 12 cycles of 98°C for 10 seconds, 63°C for 30 seconds and 72°C for 1 minute and one cycle of 72°C for 5 minutes. The amplified library was cleaned using 0.8x volume (40 µL) of Ampure beads XP (Beckman Coulter) according to the manufacturer’s instruction and eluted in 20 µL of 0.1X TE buffer. Six animals (3 males and 3 females) belonging to each of the age-groups of 2, 6, 12 and 18 months (total n = 24) were used for the ATAC-seq study. The quality of the ATAC library was analyzed with Bioanalyzer High-Sensitivity DNA Analysis kit (Agilent) and the concentration of the library was determined using the Qubit HS DNA kit (Life Technologies). The ATAC libraries were sequenced on an Illumina HiSeq2500 sequencing system at the University of Saarland, Saarbrücken and generated approx. 50 million 100 bp paired end reads for each sample.
endothelial cells from brain were FACS enriched.
native nuclei were tagmented with Tn5 transposase which was preloaded with Nextera NGS adaptors. After column-based purification, fragmented were amplified by PCR.

treatment_protocol: all animals were wildtype, several subgroups of female and males with four different ages.

tag: tissue

value: brain

tag: Sex

value: male

tag: age

value: 18 months

tag: genotype

value: WT

tag: strain

tag: cell type

value: FACS enriched brain endothelial cells


title: 12a9 (12 months, female)

description: ATAC-seq

value: female

value: 12 months


title: mRNA CRISPRi Dgcr8 experiment

city: Basel

first: Antonio

middle: Jose

last: Santinha

address: Mattenstrasse 26

department: D-BSSE

country: Switzerland

institute: ETH Zurich

description:
P2281_NGS_238
10x Genomics
arrayed_CRISPRi_hSyn.rds

library_source: transcriptomic

data_processing:
The demultiplexing, barcodes processing, gene counting, and aggregation were made using Cell Ranger software v5.0.1 (10xGenomics.). gRNA counting, gRNA-nucleus association, and downstream analyses were done with custom-made scripts in R.
Assembly: GRCm38
Supplementary files format and content: rds

molecule: polyA RNA

source_name: Prefrontal cortex of adult mice

extract_protocol:
Nuclei isolation was performed with mechanical and chemical tissue dissociation procedures using a tissue grinder (Sigma-Aldrich, D8938) and ice-cold nuclei isolation buffer (Sigma-Aldrich, NUC101-1KT). Isolated nuclei solutions were spiked with 2 mL/mL of Vybrant DyeCycle Ruby Stain (ThermoFisher, V10273) and sorted in a MA900 apparatus (Sony).
Nuclei were sequenced with a Chromium Single Cell 5ʹ Reagent Kit v1 (10x Genomics). To capture gRNA molecules, we altered the reverse transcription (RT) reaction to additionally include a gRNA-constant-region-targeting RT primer. After cDNA amplification, gene expression and gRNA expression cDNA fractions were separated. The gene expression library was constructed accordingly with the manufacturer’s instructions. The gRNA expression library was subjected to a sample indexing PCR and sequenced alongside the gene expression library with an Illumina NovaSeq 100 cycle kit.
Chromium Single Cell 5ʹ Reagent Kit v1 with altered reverse transcription reaction to additionally include a gRNA-constant-region-targeting RT primer.

value: Prefrontal cortex of adult mice

value: Mouse brain cells

value: dCas9-KRAB +/+


title: scMAb-ID library (index 10)

city: Utrecht

first: Robin H.

last: van der Weide

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description:
scMAbID_countMatrix_100kb_hg19.MM
scMAbID_countMatrix_100kb_mm10.MM

data_processing:
Reads of the raw sequencing output conform to a MAb-ID specific layout of 5'-[3 nt UMI][4 nt SBC part 1][3 nt UMI][4 nt SBC part 2]AGGGCCGC[8 nt ABBC][genomic sequence]-3'. Raw R1-reads were demultiplexed on the expected barcode-sequences using CutAdapt 3.047, with the following custom settings. First, we only allow matches with at least a 29 nt overlap and only keep reads directly starting with the adapter (i.e., an anchored 5’ adapter). The maximum error rate setting of 2 makes it possible to retain reads with 1) two mismatches in the specified adapter-sequence (ignoring the UMI) and 2) a one nucleotide insertion or deletion (indel) at the start of the read due to digestion-ligation or sequencing(-library) errors. Demultiplexed reads are parsed through a custom script to classify reads on correct adapter-structures on a 7-tiered range. Reads in class-1 adhere perfectly to the barcode-expectations, while class-7 reads only contain the AGGGCCGC-sequence at the expected location. Reads typically fall into class 1 (average for figure 1: 95%). This classification allows fine control on which reads should be retained. For this manuscript, we only allow classes 1 and 2 (1 nucleotide indel in the first UMI) to ensure the highest possible quality. Finally, the script creates a fastq.gz-file, adding the UMI-sequences to the read-ID for downstream processing and removing the adapter sequence. Custom pipelines and scripts are available on https://github.com/KindLab.
Demultiplexed and filtered reads were processed in a similar fashion to Rooijers et al.13, with the additional flexibility to set the selected restriction site motif. Briefly, reads are aligned using Bowtie version 2.4.148 in unpaired mode, using default end-to-end parameters. We used the UCSC hg19 reference genome for K562 samples and the NCBI mm10 reference genome for mESC/mEN-samples (both references were downloaded from https://benlangmead.github.io/aws-indexes). Alignments with a mapping quality lower than 10 or not at the expected ligation-site (5’ for the MboI-motif or 5’+ 1 for the MseI-motif) were discarded. For reads originating from mixed sorting single-cell samples (e.g., K562 and mESC), a new hybrid reference genome was built by concatenating hg19 and mm10. Aligned reads to this reference were subsequently mapped to the individual references for further downstream processing by Bowtie using the --very-sensitive -N 1 parameters. Mouse allele-specific reads were assigned by mapping mm10-reads to 129/Sv and Cast/Eij reference genomes. We designated reads to one of the genotypes if it mapped better (i.e., lower edit-distance or higher alignment-score) to one of the references.
Aligned reads are UMI-flattened and counted per restriction site, like in the scDamID-protocol. We allowed up to 1000 UMI’s per site in the bulk analyses and up to 2 UMI’s per site in the single-cell analyses. UMI-counts per sample were binned (5kb, 20kb, and 100kb), loaded into R and stored into singleCellExperiment-containers. Counts in bins overlapping regions of known problematic nature (i.e., blacklist-regions55) or low mappability are set to zero. Normalization of the data was performed by calculating RPKM-values for both samples and control (see eq. 1) and calculating the fold-change over control with a pseudocount of 1.
Assembly: UCSC hg19 and NCBI mm10
Supplementary files format and content: bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of UMI's at a given genomic coordinate.
Supplementary files format and content: MM files are sparse matrices and generated using the Matrix R package. Columns denote single cells, rows denote 100kb genomic bins, and values denote the number of UMI-flattened counts.
Library strategy: MAb-ID

organism:
Homo sapiens
Mus musculus

source_name: mESC, NPC_d6, K562

growth_protocol: All cell lines were grown in a humidified chamber at 37 °C in 5% CO2, and were routinely tested for mycoplasma. K562 cells were cultured in suspension on 10-cm dishes in Roswell Park Memorial Institute 1640 (RPMI 1640, Gibco, 61870010) supplemented with 10% FBS (Sigma, F7524, lot BCBW6329) and 1% Pen/Strep (Gibco, 15140122). Cells were passaged every 2-3 days. Mouse F1 hybrid Cast/EiJ x 129SvJae embryonic stem cells (mESCs; a gift from the Joost Gribnau laboratory) were cultured on 6-well plates with irradiated primary mouse embryonic fibroblasts (MEFs) in mESC culture media (CM) defined as follows: Glasgow's MEM (G-MEM, Gibco, 11710035) supplemented with 10% FBS, 1% Pen/Strep, 1x GlutaMAX (Gibco, 35050061), 1x MEM non-essential amino acids (Gibco, 11140050), 1 mM sodium pyruvate (Gibco, 11360070), 0.1 mM β-mercaptoethanol (Sigma, M3148) and 1000 U/mL ESGROmLIF (EMD Millipore, ESG1107). mESCs were alternatively cultured in feeder-free conditions on gelatin coated plates (0.1% gelatin, in house) in 60%-BRL medium, defined as a mix of 40% CM medium (as defined) and 60% conditioned CM medium (incubated 1 week on Buffalo Rat Liver cells), supplemented with 10% FBS, 1% Pen/Strep, 1x GlutaMAX, 1x MEM non-essential amino acids, 0.1 mM β-mercaptoethanol and 1000 U/mL ESGROmLIF. Cells were split every 2-3 days and medium was changed every 1-2 days. This mESC cell line does not contain a Y chromosome. To harvest, cells were washed once with Phosphate Buffered Saline (PBS, in house) and incubated with TrypLE Express Enzyme (Gibco, 12605010) for 3 minutes at 37 °C. Cells were dissociated by pipetting and TrypLE was inactivated by diluting cells five-fold in CM medium, before proceeding with fixation and permeabilization as described.

extract_protocol:
Cells were harvested (~10 x 106 cells) and washed once with PBS. All centrifugation steps were at 200 g for 4 minutes at 4 °C. Cells were fixated in 1% formaldehyde (Sigma, F8875) in PBS for 5 minutes, before quenching the reaction with 125 mM final concentration of glycine (Sigma, 50046) and placing the cells on ice. All subsequent steps were performed on ice or at 4⁰C. Cells were washed three times with PBS before resuspension in Wash buffer 1 (20mM HEPES pH 7.5 (Gibco, 15630-056), 150 mM NaCl, 66.6 µg/mL Spermidine (Sigma, S2626), 1X cOmplete™ protease inhibitor cocktail (Roche, 11697498001), 0.05% Saponin (Sigma, 47036), 2mM EDTA) and transferred to a 1.5 mL protein LoBind Eppendorf tube (Eppendorf, EP0030108116-100EA). Cells were permeabilized for 30 minutes at 4 ⁰C on a tube roller. Bovine Serum Albumin (BSA, Sigma, A2153) was added to 5 mg/mL final concentration and incubated for another 60 minutes at 4 ⁰C on a tube roller. Permeabilized nuclei were used for antibody incubation.
Samples ligated with unique SBC adapters were pooled, either 2-4 1000 nuclei samples or a full 384-well plate were pooled for combined in vitro transcription (IVT). To reduce batch effects, controls (secondary antibody-conjugates without primary antibody incubation) were pooled with their corresponding samples whenever possible. For 384-well plates, mineral oil was removed by spinning the sample for 2 minutes at 2000 g and transferring the liquid phase to a clean tube, which was repeated three times. After pooling, samples were incubated for 10 minutes with 1.0 volume CleanNGS magnetic beads (CleanNA, CPCR-0050), diluted 1:4 to 1:10 in bead binding buffer (20% PEG 8000, 2.5 M NaCl, 10 mM Tris–HCl, 1 mM EDTA, 0.05% Tween 20, pH 8.0 at 25 °C). The bead dilution ratio depended on the total volume, 1:4 for 1000 nuclei samples and 1:10 for a full 384-well plate. Samples were placed on a magnetic rack (DynaMag™-2, ThermoFisher, 12321D) to collect beads on the side of the tube. Beads were washed two times with 80% ethanol and briefly allowed to dry before resuspending in 8 µL water. In vitro transcription was performed by adding 12 µL IVT mix from the MEGAScript T7 kit (Invitrogen, AM1334) for 14 hours at 37 ⁰C before holding at 4 ⁰C. Library preparation was subsequently performed as described previously 13,46, using 5 µL of aRNA and 8 to 11 PCR cycles, depending on the aRNA yield. Purified aRNA from different IVT reactions (with unique SBC adapters) can be pooled before proceeding with cDNA synthesis to reduce batch effects. Libraries were run on the Illumina NextSeq500 platform with high output 1x75 bp, the Illumina NextSeq2000 platform with high output 1x100 bp or the Illumina NextSeq2000 platform with high output 2x100 bp.

treatment_protocol: For differentiation towards the neural lineage, mESCs were taken in culture on MEFs and subsequently passaged 3 times in feeder-free conditions in 60%-BRL medium. On day 0 of the differentiation, mESCs were plated on gelatin-coated 6-well plates (0.15% gelatin, Sigma, G1890) at a density of 2.5 x 104 cells per cm2 in N2B27 medium defined as follows: 0.5x Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12 (DMEM-F12, Gibco, 11320033), 0.5x Neurobasal medium (Gibco, 21103049), 15mM HEPES (Gibco, 15630080), 0.5x N-2 supplement (Gibco, 17502048), 0.5x B-27 serum-free supplement (Gibo, 17504044) and 0.1 mM β-mercaptoethanol. From day 3 of differentiation, cells were washed daily with DMEM-F12 medium and refreshed with N2B27 medium. To harvest on day 5 of differentiation, cells were washed once with DMEM-F12 and incubated for 1 minute at room temperature with Accutase Enzyme Detachment Medium (Invitrogen, 00-4555-56). Cells were dissociated by pipetting and Accutase was inactivated by diluting cells ten-fold in DMEM-F12 or N2B27 medium, before proceeding with fixation and permeabilization as described.

tag: cell line

value: mESC, NPC_d6, K562

tag: cell count

tag: antibody

value: H3K9me3, H3K36me3, Lamin B1, H3K27me3, H3K27ac, H3K4me1


title: scMAb-ID library (index 18)


title: 12a8 (12 months, female)

description: ATAC-seq


title: RP27M

city: Kalyani

first: Partha

middle: P.

last: Majumder

state: West Bengal

country: India

institute: National Institute of Biomedical Genomics

data_processing:
Raw sequencing reads were converted to FASTQ files; data quality was assessed using FASTQC (https://qubeshub.org/resources/fastqc). Low quality reads and adapter sequences were removed. RNA-sequence data were processed in accord with the TCGA mRNA Analysis pipeline (https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/).
Assembly: hg19 (NCBI 37)
Supplementary files format and content: TXT

molecule: total RNA

organism: Homo sapiens

source_name: biopsy of margin

extract_protocol:
total RNA was extracted using RNeasy kit (QIAGEN)
RNA sequencing libraries were generated using TruSeq RNA Library Prep Kit v2 (Illumina), following the manufacturer’s protocol

value: biopsy of margin

tag: patient id

tag: recurrence

value: R

tag: survival

value: DIED

value: Male

tag: tobacco

value: NO

tag: grade


title: 12a6 (12 months, female)

description: ATAC-seq

value: brain


title: mRNA LgDel +/- 1

description:
P1875_NGS_227
10x Genomics
lgdel_model.rds

value: LgDel +/-


title: scMAb-ID library (index 9)


title: mRNA LgDel +/+ 3

description:
P1875_NGS_226
10x Genomics
lgdel_model.rds

value: LgDel +/+


title: mRNA CRISPRi SH control experiment

description:
P2281_NGS_237
10x Genomics
arrayed_CRISPRi_hSyn.rds


title: RP20T

source_name: biopsy of tumor

value: biopsy of tumor

value: YES

value: ModeratelyDifferentiated


title: scMAb-ID library (index 20)


title: RP20M


title: mRNA LgDel +/+ 2

description:
P1875_NGS_225
10x Genomics
lgdel_model.rds


title: mRNA LgDel +/+ 1

description:
P1875_NGS_224
10x Genomics
lgdel_model.rds


title: UnfertilizedOvule stage WholeSeed RNA-seq (L49)

city: Saskatoon

first: Peng

last: Gao

state: Saskatchewan

address: 107 Science Place

country: Canada

institute: Agriculture and Agri-Food Canada

data_processing:
Illumina Casava software used for basecalling.
Trimming the adaptor sequences, filtering low-quality reads  and eliminating short reads using Trimmomatic.
Filtered reads were mapped to the lentil genome (Lens culinaris Medik. CDC Redberry Genome Assembly v2.0).
Read counting was carried out with FeatureCounts.
Normalized counts were obtained from R DESeq2 package.
Assembly: lentil genome (Lens culinaris Medik. CDC Redberry Genome Assembly v2.0)
Supplementary files format and content: Matrix table files include normalized counts for each sample

organism: Lens culinaris

source_name: WholeSeed

growth_protocol: Plants were grown in growth chambers under long-day conditions of 16 h light, 22°C and 8 h dark, 20 °C; light intensity was set to 100 to 120 μmol m−2 s−1 for whole life cycle.

extract_protocol:
Embryo and seed coat tissue isolation were performed using a dissecting microscope, fine forceps and needles in a 4.8% Sucrose solution that contained 0.1% RNALater solution.For seed coat isolation, the embryos were manually removed, and the remaining seed coat was kept. Total RNA was extracted from each stage embryo sample following the protocol of RNAqueous-micro kit.
RNA-seq libraries were prepared using the NEBNext Single Cell/Low Input RNA library Prep Kit for Illumina.

treatment_protocol: Flowers were emasculated and pollinated at the flower stage, to ensure sufficient and developmentally coordinated seed production for embryo isolation.

value: WholeSeed

tag: Stage

value: UnfertilizedOvule

tag: ecotype

value: CDC Gold

tag: replicate


title: mRNA Gnb1l array experiment

description:
P1829_NGS_222
10x Genomics
arrayed_screen_hSyn.rds

tag: tissue

value: Prefrontal cortex of adult mice

value: Mouse neurons

value: LSL-Cas9 +/+


title: RP14T

value: NR

value: ALIVE

tag: Sex

value: PoorlyDifferentiated


title: Mature stage WholeSeed RNA-seq (L48)

value: Mature


title: 20b3 (6 months, male)

description: ATAC-seq

value: male

tag: age

value: 6 months

value: WT

value: FACS enriched brain endothelial cells


title: 13a1 (12 months, male)

description: ATAC-seq

value: brain

value: 12 months

tag: genotype


title: mRNA Dgcr8 array experiment

description:
P1829_NGS_221
10x Genomics
arrayed_screen_hSyn.rds


title: RP14N

source_name: biopsy of normal

value: biopsy of normal

value: Male

value: YES


title: Mature stage SeedCoat RNA-seq (L46)

source_name: SeedCoat

value: SeedCoat

value: CDC Gold


title: RP14M

value: biopsy of margin


title: 20b2 (6 months, male)

description: ATAC-seq

tag: strain


title: RP20N

value: R

value: DIED

value: ModeratelyDifferentiated


title: 18b5 (6 months, female)

description: ATAC-seq

value: female

tag: cell type


title: mRNA Dgcr14 array experiment

description:
P1829_NGS_220
10x Genomics
arrayed_screen_hSyn.rds

value: Prefrontal cortex of adult mice

value: Mouse neurons

value: LSL-Cas9 +/+


title: 18b6 (6 months, female)

description: ATAC-seq

value: 6 months

value: WT


title: mRNA SH control array experiment

description:
P1829_NGS_219
10x Genomics
arrayed_screen_hSyn.rds


title: 19b11 (6 months, female)

description: ATAC-seq

value: brain

value: FACS enriched brain endothelial cells


title: Mature stage SeedCoat RNA-seq (L45)

value: Mature


title: 13a3 (12 months, male)

description: ATAC-seq

value: male

value: 12 months


title: P13_lenti_3

city: Chengdu

first: Fanyuan

last: Yu

state: Sichuan

address: No.14, 3rd Section, Ren Min Nan Rd

department: Endodontics

country: China

institute: State Key Laboratory of Oral Diseases, West China Hospital of Stomatology

description:
we infected p1 hDPCs with control-lentivirus, and then culture and passage cells to p13
adult human dental pulp stromal cells

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index ofthe reference genome was builtusing Hisat2 v2.0.5 andpaired-endcleanreadswerealignedtothereferencegenomeusingHisat2v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: Homo_sapiens_Ensemble_94.fa
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: hDPCs infected with lentivirus

extract_protocol:
total RNA was extracted using the RNeasy mini kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol.
Libraries were prepared according to Illumina's instructions of RNA sample. Paired-end method was adopted for further processes.

tag: treatment

value: control-lentivirus

value: dental pulp stromal cells


title: gRNA 22q11.2 pooled screen 9

description:
P1318_NGS_121_gRNA
10x Genomics
pooled_screen_CBh.rds

library_source: other

molecule: other

value: Mouse brain cells


title: 19e_6 (2 months, female)

description: ATAC-seq

value: 2 months


title: Mature stage Embryo RNA-seq (L44)

source_name: Embryo

value: Embryo

value: CDC Gold


title: P13_lenti_2


title: UnfertilizedOvule stage WholeSeed RNA-seq (L50)

value: WholeSeed

value: UnfertilizedOvule


title: Mature stage Embryo RNA-seq (L43)


title: Mature stage WholeSeed RNA-seq (L47)


title: P13_2SA_2

description:
we infected p1 hDPCs with YAP2SA-lentivirus, and then culture and passage cells to p13
adult human dental pulp stromal cells


title: P13_2SA_1


title: gRNA 22q11.2 pooled screen 7

description:
P1318_NGS_119_gRNA
10x Genomics
pooled_screen_CBh.rds

value: Prefrontal cortex of adult mice


title: gRNA 22q11.2 pooled screen 6

description:
P1318_NGS_118_gRNA
10x Genomics
pooled_screen_CBh.rds

value: LSL-Cas9 +/+


title: 19e_5 (2 months, female)

description: ATAC-seq

value: female


title: P13_lenti_1


title: 15b4 (2 months, male)

description: ATAC-seq

value: WT


title: P13_2SA_3


title: 19e_4 (2 months, female)

description: ATAC-seq

value: brain


title: LateBent stage WholeSeed RNA-seq (L42)

value: LateBent


title: gRNA 22q11.2 pooled screen 5

description:
P1318_NGS_117_gRNA
10x Genomics
pooled_screen_CBh.rds


title: gRNA 22q11.2 pooled screen 4

description:
P1318_NGS_116_gRNA
10x Genomics
pooled_screen_CBh.rds


title: 6f8 (18 months, female)

city: Oxford

first: Kshitij

last: Mohan

address: CVMed, Level 5, John Radcliffe Hospital

department: Radcliffe Department of Medicine

country: United Kingdom

institute: University of Oxford

data_processing:
The preliminary quality control checks on the raw RNA-seq data were performed using FASTQC (v0.11.4). The 3҆ adapter sequence were trimmed using Cutadapt66 (v1.15) and quality control checks were again performed on the trimmed reads with FASTQC. The trimmed reads were then aligned to the mouse genome (GRCm38/mm10) using STAR aligner (v2.5.2b). The parameter quantMode was set to GeneCounts for the calculation of counts per gene. A comprehensive quality report for all the samples was generated with MultiQC68 (v1.7) (https://multiqc.info/). The counts obtained after STAR alignment was used to study differential expression analysis using DESeq269 (v1.24.0). Linear regression analysis was performed on TPM (transcripts per million) values, calculated by normalizing the raw read counts to the gene length and sequencing depth in each sample, to study the age-associated changes in gene expression. A gene was considered to be significantly dysregulated with age if it had an adjusted p-value less than 0.05 (p.value.age.fdr < 0.05) in the linear regression analysis.
Assembly: mm10
Supplementary files format and content: tab delimited text files (.tab) with raw counts for each sample.  Column 1: gene ID, column 2: counts for unstranded RNA-seq (htseq-count option --stranded no), column 3: counts for the 1st read strand aligned with RNA (htseq-count option, --stranded yes), column 4: counts for the 2nd read strand aligned with RNA (htseq-count option --stranded reverse).

source_name: Brain

extract_protocol:
Full-length cDNA libraries were prepared with the SMART-Seqv4 Ultra Low Input RNA kit (TaKaRa) and the libraries for sequencing were prepared using Nextera XT DNA Library Prep (Illumina) according to the manufacturer’s instructions.
The libraries from 24 samples were sequenced on Illumina NovaSeq6000 sequencing system and generated 50 bp paired end reads (PE50). Libraries from the other 6 samples were sequenced on Illumina HiSeq 2500 SR50 single end reads.

value: 18 months

value: Brain

tag: cell line

value: Primary cells

value: Endothelial cells


title: LateBent stage SeedCoat RNA-seq (L39)

value: SeedCoat


title: gRNA 22q11.2 pooled screen 8

description:
P1318_NGS_120_gRNA
10x Genomics
pooled_screen_CBh.rds

value: Mouse brain cells


title: LateBent stage SeedCoat RNA-seq (L40)


title: KO CFL1_2

city: Guangzhou

first: Rui

last: Li

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

description:
KO CFL1_2
CFL1KOvsControl_DEseq2_result.txt

data_processing:
Raw data was cleaned with cutadapt and subjected to QC analyses with FastQC tool, all clean reads were mapped to the hg19 genome using STAR
The expression of genes was assembled and quantified using RSEM with the following parameters: -paired-end, -star
differentially expressed genes (DEGs) were identified by R package DEseq246 (|log2 Fold Change| ≥ 0.26 and P ≤ 0.05 was considered as DEGs)
Assembly: hg19
Supplementary files format and content: txt

extract_protocol:
The RNA samples were quantified by measuring absorbance at 260 nm with a UV spectrophotometer, and only analytes with an RNA integrity number (RIN) ≥ 7.0 were used in further experiments.
Total RNA extracted from PANC-1 cells with or without CFL1 knockout was subjected to RNA sequencing (Novegene, Illumina Novaseq6000).

treatment_protocol: Total RNA from tissues or cell lines was isolated by using Trizol reagent (Invitrogen).

value: Human PDAC cell lines

value: KO CFL1


title: LateBent stage WholeSeed RNA-seq (L41)

value: CDC Gold


title: 6f6 (18 months, female)


title: 6f7 (18 months, female)


title: LateBent stage Embryo RNA-seq (L38)

value: Embryo


title: gRNA 22q11.2 pooled screen 3

description:
P1318_NGS_115_gRNA
10x Genomics
pooled_screen_CBh.rds


title: gRNA 22q11.2 pooled screen 2

description:
P1318_NGS_114_gRNA
10x Genomics
pooled_screen_CBh.rds


title: KO CFL1_1

description:
KO CFL1_1
CFL1KOvsControl_DEseq2_result.txt


title: LateBent stage Embryo RNA-seq (L37)


title: control2

description:
control2
CFL1KOvsControl_DEseq2_result.txt


title: EarlyBent stage WholeSeed RNA-seq (L36)

value: WholeSeed

value: EarlyBent


title: gRNA 22q11.2 pooled screen 1

description:
P1318_NGS_113_gRNA
10x Genomics
pooled_screen_CBh.rds

value: Prefrontal cortex of adult mice

value: LSL-Cas9 +/+


title: 5e4 (18 months, male)

value: male

value: WT


title: mRNA 22q11.2 pooled screen 9

description:
P1318_NGS_121_mRNA
10x Genomics
pooled_screen_CBh.rds


title: control1

description:
control1
CFL1KOvsControl_DEseq2_result.txt


title: YTHDC2, rep3

data_processing:
Raw reads were cleaned using cutadapt and aligned to the hg19 genome using Bowtie2
PCR duplicates were removed using picard MarkDuplicates. Genome coverage files for UCSC genome browser were generated by deepTools
Peaks were called by MACS2 and annotated by annotatePeaks.pl in Homer
Visualization of the genomic regions was performed with IGV.
Assembly: hg19
Supplementary files format and content: bigwig
Library strategy: CUT&TAG

growth_protocol: The CUT&Tag was performed by Jiayin Biotechnology Ltd. (Shanghai, China)

extract_protocol:
Bead-bound cells were suspended by dig wash buffer with 1:50 dilution of anti-MLL1, RNAPII, YTHDC2 or H3K4me3 antibody incubated on a roating platform overnight at 4 °C.After removing primary antibodies, the corresponding secondary antibody was diluted 1:100 in dig wash buffer and cells were incubated for 60 min. Then cells were washed using dig wash buffer. A 1:100 dilution of pA-Tn5 adapter complex was prepared in dig-med buffer and incubated with cells for 1 h. Cells were washed with Dig-med buffer. Then cells were resuspended in tagmentation buffer (10mM MgCl2 in Dig-med Buffer) and incubated at 37 °C for 1 h. DNA was purified using phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation.
Sequencing was performed in the Illumina Novaseq 6000 using 150bp paired-end.

treatment_protocol: PANC-1 cells (1×106) were incubated with 10μL Concanavalin A coated magnetic beads (Bangs Laboratories) for 10 min.

tag: chip antibody


title: EarlyBent stage WholeSeed RNA-seq (L35)


title: EarlyBent stage Embryo RNA-seq (L32)


title: YTHDC2, rep2


title: 5e3 (18 months, male)


title: mRNA 22q11.2 pooled screen 6

description:
P1318_NGS_118_mRNA
10x Genomics
pooled_screen_CBh.rds


title: EarlyBent stage SeedCoat RNA-seq (L33)


title: EarlyBent stage SeedCoat RNA-seq (L34)


title: mRNA 22q11.2 pooled screen 8

description:
P1318_NGS_120_mRNA
10x Genomics
pooled_screen_CBh.rds


title: exp3_regen_gfp

city: Vancouver

first: Jordan

middle: W

last: Squair

state: BC

address: 818 West 10th Avenue

institute: University of British Columbia

description: 10x v3

data_processing:
Reads were aligned using Cellranger v.4.0.0
Data were analyzed using Seurat v3
Assembly: mm10-1.2.0 (GRCm38.93)
Supplementary files format and content: tab-delimited text files include UMI values for each cell with tab delimeters

source_name: Low thoracic spinal cord

extract_protocol:
We performed single-nucleus dissociation of the mouse spinal cord according to our previously described procedures. Following euthanasia by isoflurane inhalation and cervical dislocation, the low thoracic spinal cord site was immediately dissected and frozen on dry ice. We denounced spinal cords in 500 µl sucrose buffer (0.32 M sucrose, 10 mM HEPES [pH 8.0], 5 mM CaCl2, 3 mM Mg acetate, 0.1 mM EDTA, 1 mM DTT) and 0.1% Triton X-100 with the Kontes Dounce Tissue Grinder. 2 mL of sucrose buffer was then added and filtered through a µm cell strainer. The lysate was centrifuged at 3200 g for 10 min at 4°C. The supernatant was decanted, and 3 mL of sucrose buffer added to the pellet and incubated for 1 min. The pellet was homogenized using an Ultra-Turrax and 12.5 mL of density buffer (1 M sucrose, 10 mM HEPES [pH 8.0], 3 mM Mg acetate, 1 mM DTT) was added below the nuclei layer. The tube was centrifuged at 3200 g at 4°C and supernatant poured off. Nuclei on the bottom half of the tube wall were collected with 100 µl PBS with 0.04% BSA and 0.2 U/µl RNase inhibitor. Resuspended nuclei were filtered through a 30 µm strainer, and adjusted to 1000 nuclei/µl. For projection-specific snRNA-seq experiments the nuclei were first resuspended in 500 µl Pre-FACS buffer (1× PBS with 1% BSA, 0.2 U/µl SUPERaseIn RNase Inhibitor), and filtered through a 35 µm cell strainer. Samples were processed on a Sony SH800 Cell Sorter with a 100 mm sorting chip.
We used single-nucleus RNA sequencing (snRNA-seq) to profile the low thoracic spinal cord of mice. We devised three experiments to identify and target the molecularly defined neuronal subpopulations involved in natural spinal cord repair.

value: spinal cord

tag: condition

value: regen

value: wild type


title: Torpedo stage WholeSeed RNA-seq (L30)

value: Torpedo


title: exp2_hemi1

description: 10x v3

value: hemisection


title: mRNA 22q11.2 pooled screen 5

description:
P1318_NGS_117_mRNA
10x Genomics
pooled_screen_CBh.rds


title: exp2_hemi2

description: 10x v3


title: Torpedo stage WholeSeed RNA-seq (L29)


title: RNAPII, rep3

value: RNAPII


title: RNAPII, rep1


title: 5e6 (18 months, male)

value: 18 months

value: Brain

value: Primary cells

value: Endothelial cells


title: exp2_uninjured_control

description: 10x v3

value: uninjured


title: mRNA 22q11.2 pooled screen 3

description:
P1318_NGS_115_mRNA
10x Genomics
pooled_screen_CBh.rds

value: Mouse brain cells


title: RNAPII, rep2

value: Human PDAC cell lines


title: mRNA 22q11.2 pooled screen 4

description:
P1318_NGS_116_mRNA
10x Genomics
pooled_screen_CBh.rds

value: Prefrontal cortex of adult mice


title: exp1_healthy2_nogfp

description:
10x v3
GFP denotes traced neurons


title: exp1_healthy2_gfp

description:
10x v3
GFP denotes traced neurons


title: YTHDC2, rep1


title: EarlyBent stage Embryo RNA-seq (L31)

value: Embryo

value: EarlyBent

value: CDC Gold


title: mRNA 22q11.2 pooled screen 7

description:
P1318_NGS_119_mRNA
10x Genomics
pooled_screen_CBh.rds

value: LSL-Cas9 +/+


title: Torpedo stage SeedCoat RNA-seq (L28)

value: SeedCoat


title: MLL1, siYTHDC2_2

description: YTHDC2KOvsControl_MLL1_YTHDC2KO_merge.RPKM.bw


title: MLL1, siYTHDC2_1


title: MLL1, WT2

description: YTHDC2KOvsControl_MLL1_Control_merge.RPKM.bw


title: mRNA 22q11.2 pooled screen 1

description:
P1318_NGS_113_mRNA
10x Genomics
pooled_screen_CBh.rds


title: Torpedo stage SeedCoat RNA-seq (L27)


title: exp1_healthy1_gfp

description:
10x v3
GFP denotes traced neurons

value: spinal cord

value: wild type


title: exp1_healthy1_nogfp

description:
10x v3
GFP denotes traced neurons


title: MLL1, WT1


title: mRNA 22q11.2 pooled screen 2

description:
P1318_NGS_114_mRNA
10x Genomics
pooled_screen_CBh.rds


title: MS-444_Rep2 [EK6]

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

data_processing:
For RNA pair-end raw data, we first trimmed the adaptor sequences and low-quality reads with BBmap (version 38.16), then aligned to the mm9 reference genome using Hisat2 (version 4.8.2) (Pertea et al., 2016) with default parameters
Gene expression FPKM was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) using the RefSeq database from the UCSC genome browser. Sequencing depth was normalized.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample

source_name: 2-cell stage embryos

growth_protocol: Two-cell stage embryos were cultured in KSOM medium with 75 μM MS-444 or 0.1% DMSO.

extract_protocol:
16 embryos cells were lysed by freeze-thaw and reverse-transcription reactions were performed using Minus Reverse Transcriptase (Invitrogen, Carlsbad, CA, USA).
All samples were pooled together and the cDNA was purified using a purification kit (Zymo Research, Irvine, CA, USA). Full-length cDNA was amplified using the Terra PCR Direct Polymerase Mix buffer (Clontech, Mountain View, CA, USA). Sequencing libraries were constructed using TruePrep DNA Library Prep Kit (Vazyme, Nanjin, China), in accordance with the manufacturer’s instructions.

value: ICR

value: 2-cell stage embryos


title: H3K4me3, siYTHDC2_2

description: YTHDC2KOvsControl_H3K4me3_YTHDC2KO_merge.RPKM.bw


title: Torpedo stage Embryo RNA-seq (L25)

value: Torpedo


title: MS-444_Rep3 [EK7]


title: gRNA 22q11.2 pooled screen 12

description:
P1188_NGS_100_gRNA
10x Genomics
pooled_screen_CBh.rds


title: gRNA 22q11.2 pooled screen 11

description:
P1188_NGS_099_gRNA
10x Genomics
pooled_screen_CBh.rds


title: MS-444_Rep1 [EK5]


title: Heart stage WholeSeed RNA-seq (L24)

value: WholeSeed

value: Heart


title: gRNA 22q11.2 pooled screen 10

description:
P1188_NGS_098_gRNA
10x Genomics
pooled_screen_CBh.rds


title: Heart stage WholeSeed RNA-seq (L23)


title: H3K4me3, siYTHDC2_1


title: H3K4me3, NC4

description: YTHDC2KOvsControl_H3K4me3_Control_merge.RPKM.bw


title: mRNA 22q11.2 pooled screen 12

description:
P1188_NGS_100_mRNA
10x Genomics
pooled_screen_CBh.rds


title: Heart stage SeedCoat RNA-seq (L22)


title: mRNA 22q11.2 pooled screen 11

description:
P1188_NGS_099_mRNA
10x Genomics
pooled_screen_CBh.rds


title: DMSO_Rep2 [EK3]

value: DMSO


title: Heart stage SeedCoat RNA-seq (L21)


title: DMSO_Rep1 [EK1]


title: Heart stage Embryo RNA-seq (L20)


title: H3K4me3, siCFL1_1

description: CFLKOvsControl_H3K4me3_CFL1KO_merge.RPKM.bw


title: H3K4me3, siCFL1_2


title: Globular stage WholeSeed RNA-seq (L17)

value: Globular


title: H3K4me3, NC3


title: ESB_0331p15

city: Lausanne

first: Candice Megan

last: Young

state: Vaud

address: Rue du Bugnon 25A

department: SV

institute: EPFL

data_processing:
Raw sequences were aligned to a merged mouse+human genome, quality controlled, and subjected to peak calling by the nf-core/chipseq v1.2.2 workflow
Scaling factors were computed according to the total library size of the human spike in
Bigwig files and normalized counts were generated using these scaling factors
Data visualization was performed using pyGenomeTracks and deepTools
Assembly: GRCm38/mm10 + GrCh38 (for spike in)

source_name: Mammary

growth_protocol: Cells were grown in DMEM containing 10% FBS, 20 mM Hepes (pH 7.4), and 1% pen/strep

extract_protocol:
Cells were fixed with 1% methanol-free PFA, then sheared with micrococcal nuclease for 20 mins. Nuclei were disrupted using the diagenode Bioruptor.
7.5% of human chromatin was added to the mouse chromatin as a spike in control
Library preparation was performed with the NEBNext Ultra II DNA library kit according to the manufacturer's protocol. Minimum input DNA was 4 ng per sample.

treatment_protocol: Cells were treated for 48 hours in either Vehicle, 5 mM Acetate, 50 µM Etomoxir, 50 µM SB204990, or the indicated combinations prior to sample collection

value: Mammary

value: breast cancer

value: WT

value: SB204990 + Etomoxir

tag: antibody


title: Globular stage WholeSeed RNA-seq (L18)


title: DMSO_Rep3 [EK4]


title: ESBA_0331p15

value: SB204990 + Etomoxir + Acetate


title: Torpedo stage Embryo RNA-seq (L26)

value: Embryo

value: CDC Gold


title: Abl1_RRBS_high_5azadC_rep1

city: Boston

first: Saumya

last: Gupta

state: MA

address: 450 Brookline Ave

department: Cancer Biology

country: USA

institute: Dana-Farber Cancer Institute

description: Cell line Abl.1, in growth medium with 10µM 5-aza-dC, cells collected on Day 2, Library preparation replicate 1

data_processing:
Reference preparation: we created two custom parental genomes (“pseudogenomes” (Crowley et al., 2015; Zou et al., 2014); or “pseudocontigs” when we have phasing by contigs) for each organism, we used a custom script (all custom software tools mentioned are available on Github https://github.com/gimelbrantlab/QCumber). We also created a vcf-file with one allele considered as a reference (maternal 129S1 or first phased allele) and the other as an alternative allele. Only heterozygous sites were used.
RRBS reads were aligned to the mouse mm10 genome using BSmap3 with flags -v 0.05 -s 16 -w 100 -S 1 -p 8 –u.
Custom scripts written in Perl were used to calculate the methylation percentage for CpGs covered by 4 or more reads at locations of known SNPs between parental genomes. Briefly, VCF files containing SNPs between 129 and Cast strains were filtered to exclude calls that did not pass minimum requirements as well as C->T or G->A calls. For each SNP, RRBS reads that overlapped that SNP were extracted, and the methylation status of genomic cytosines was calculated by dividing the number of unconverted (methylated) cytosines (C) by the total number of unconverted (C) or converted (T) cytosines.
methylation status of all cytosines on reads overlapping a SNP were aggregated by SNP status to create a methylation average for the reference and alternate genotype.
Genome_build: mm10
Supplementary_files_format_and_content: bed files

growth_protocol: Immortalised B-cell llines  were cultured in Roswell Park Memorial Institute medium (Gibco), containing 15% FBS (Sigma), 1X L-Glutamine (Gibco), 1X Penicillin/Streptomycin (Gibco) and 0.1% β-mercaptoethanol (Sigma).

extract_protocol:
2x10^5  cells were spun down, washed using PBS and flash frozen on dry ice for DNA extractions for RRBS. Dead cells were removed from these samples by sucrose gradient centrifugation. (Histopaque®-1077, Sigma, Cat 10771), before sample preparation using conditions specified by the manufacturer.
Libraries were generated from 50ng input DNA using a scaled-down (half reactions) of the NuGEN Ovation RRBS Methyl-Seq System (Tecan) following the manufacturer's recommendation. Libraries were PCR amplified for 11 cycles.

treatment_protocol: 5-aza-2'-deoxycytidine (Sigma, A3656) was diluted in DMSO at a concentration of 10mM. Cells were grown in grown in growth media containing 0.2μM, 2μM and 10μM of 5-aza-2'-deoxycytidine. On Day 2, live cells were collected after sucrose gradient centrifugation (Histopaque®-1077, Sigma, Cat 10771), and genomic DNA was prepared for RRBS.

value: 129S1/SvImJ x CAST/EiJ F1

value: immortalised B cells

tag: drug treatment

value: treated

tag: library replicates

value: female


title: Abl1_RRBS_high_5azadC_rep2

description: Cell line Abl.1, in growth medium with 10µM 5-aza-dC, cells collected on Day 2, Library preparation replicate 2


title: E_0331p15

value: Etomoxir


title: KO MLL1, rep2

description:
KO MLL1, rep2
ATAC_MLL1_SI12.merge.RPKM.bw

data_processing:
Raw sequencing fastq files were assessed for quality, adapter content and duplication rates with FastQC, and duplicated mapped reads were further removed using picard MarkDuplicates.
Clean reads were aligned with STAR to the human genome using hg19 versions.
Accessible regions were identified by peak calling using MACS2
Diffbind was used for differential accessibility analysis, ATAC sites were considered as differentially accessibility sites if meeting |log2 Fold Change| > 0.5 and with FDR < 0.05.
Assembly: hg19

growth_protocol: ATAC-seq was performed by Shanghai Jiayin Biotechnology Ltd. on Illumina Novaseq 6000 using PE150 according to the published protocol

extract_protocol: After Samples were PCR-amplified using 1X NEBNext High-Fidelity PCR Master Mix (New England Biolabs, MA). Subsequent libraries were purified with the MinElute PCR Purification Kit (Qiagen) and subjected to sequencing

treatment_protocol:
cells were harvested from cell culture and lysed in lysis buffer. The Nextera DNA Library Preparation Kit (Illumina) was used to perform the transposition
50 000 nuclei were pelleted and resuspended with transposase, for 30 minutes at 37 °C. The transposed DNA fragments were purified immediately after with a MinElute PCR Purification Kit (Qiagen)

value: Human PDAC cell lines

value: KO MLL1


title: EA_0331p15

value: Etomoxir + Acetate


title: Abl1_RRBS_med_5azadC_rep3

description: Cell line Abl.1, in growth medium with 2µM 5-aza-dC, cells collected on Day 2, Library preparation replicate 3


title: H3K4me3, NC2

description: CFLKOvsControl_H3K4me3_Control_merge.RPKM.bw


title: H3K4me3, NC1


title: A_0331p15

value: Acetate


title: Abl1_RRBS_med_5azadC_rep1

description: Cell line Abl.1, in growth medium with 2µM 5-aza-dC, cells collected on Day 2, Library preparation replicate 1


title: Abl1_RRBS_med_5azadC_rep2

description: Cell line Abl.1, in growth medium with 2µM 5-aza-dC, cells collected on Day 2, Library preparation replicate 2


title: mRNA 22q11.2 pooled screen 10

description:
P1188_NGS_098_mRNA
10x Genomics
pooled_screen_CBh.rds

value: Prefrontal cortex of adult mice

value: Mouse brain cells

value: LSL-Cas9 +/+


title: KO MLL1, rep1

description:
KO MLL1, rep1
ATAC_MLL1_SI12.merge.RPKM.bw


title: Globular stage SeedCoat RNA-seq (L16)

value: SeedCoat

value: Globular


title: Heart stage Embryo RNA-seq (L19)

value: Heart


title: Globular stage SeedCoat RNA-seq (L15)


title: V_0331p15

value: Mammary

value: breast cancer

value: WT

value: Vehicle


title: Abl1_RRBS_low_5azadC_rep2

description: Cell line Abl.1, in growth medium with 0.2µM 5-aza-dC, cells collected on Day 2, Library preparation replicate 2

value: 129S1/SvImJ x CAST/EiJ F1

value: immortalised B cells

value: treated


title: Globular stage Embryo RNA-seq (L14)

value: Embryo

value: CDC Gold


title: Globular stage Embryo RNA-seq (L13)


title: ESB_0327p19

value: SB204990 + Etomoxir


title: KO YTHDC2, rep2

description:
KO YTHDC2, rep2
ATAC_YTHDC2_SI12.merge.RPKM.bw

value: Human PDAC cell lines

value: KO YTHDC2


title: Quadrant stage WholeSeed RNA-seq (L12)

value: WholeSeed

value: Quadrant


title: KO YTHDC2, rep1

description:
KO YTHDC2, rep1
ATAC_YTHDC2_SI12.merge.RPKM.bw


title: E_0327p19

value: Etomoxir


title: KO CFL1, rep2

description:
KO CFL1, rep2
ATAC_CFL1_SI12.merge.RPKM.bw

value: KO CFL1


title: ESBA_0327p19

value: SB204990 + Etomoxir + Acetate


title: P3436

city: Be'er Sheva

first: Nataly

last: Makarenkov

address: David Ben Gurion Blvd 1

country: Israel

institute: Ben Gurion University

data_processing:
adapter trimming with cutadapt AACTGTAGGCACCATCAAT - leaving only reads above 17 bp
running miRGE3
Supplementary files format and content: .txt file with counts (not normalized) matrix for all samples

source_name: Plasma

extract_protocol:
small RNA was extracted from the plasma using mirneasy serum/plasma advanced kit (Qiagen) (Cat No. 217204)
libraries were constructed using QIAseq™ miRNA Library Kit (Qiagen, Cat # 331505)

value: Plasma

tag: patient number

tag: group low_/_int_/_high

value: low


title: Abl1_RRBS_DMSO_rep2

description: Cell line Abl.1, in growth medium with 1% DMSO (control), cells collected on Day 2, Library preparation replicate 2

value: control

value: female


title: EA_0327p19

value: Mammary

value: breast cancer

value: WT

value: Etomoxir + Acetate


title: KO CFL1, rep1

description:
KO CFL1, rep1
ATAC_CFL1_SI12.merge.RPKM.bw


title: P3435


title: Abl1_RRBS_DMSO_rep1

description: Cell line Abl.1, in growth medium with 1% DMSO (control), cells collected on Day 2, Library preparation replicate 1

value: 129S1/SvImJ x CAST/EiJ F1

value: immortalised B cells


title: Quadrant stage WholeSeed RNA-seq (L11)

tag: Stage

tag: ecotype

value: CDC Gold


title: control, rep1

description:
control, rep1
ATAC_NC12.merge.RPKM.bw

value: Human PDAC cell lines

value: Control


title: P3434

tag: tissue

value: int


title: Quadrant stage SeedCoat RNA-seq (L9)

value: SeedCoat

value: Quadrant

tag: replicate


title: Quadrant stage SeedCoat RNA-seq (L10)


title: oligodendroglioma, ATAC

city: Heidelberg

first: Sevin

last: Turcan

address: Im Neuenheimer Feld 460

institute: Heidelberg University Hospital

description: 10x Genomics

data_processing:
Raw sequencing data of all samples were processed using the Cell Ranger workflow (v3.1.0). Further data analysis was carried out using the R (v3.6.1) package Seurat (v3.1.0)
To remove droplets, a two-step quality control cutoff was applied regarding to the number of unique mRNAs per nucleus (Unique Molecular Identifier, UMI), the number of genes per nucleus, and the percentage of mitochondrial RNA in the nuclei. Nuclei with less than 1000 UMIs/nucleus or 500 genes/nucleus were removed from the analysis. Nuclei with more than 5% of mitochondrial RNA were also excluded.
Assembly: hg38
Supplementary files format and content: Tab-delimited tsv files include raw or normalized counts for all samples. Annotation files contain the metadata of the seurat objects.The rds files contain the Seurat R objects. Matrix table (.mtx) with raw or normalized counts for all samples

source_name: Glioma

extract_protocol:
Fresh frozen tissue samples were cut into small pieces and homogenized using a dounce homogenizer in EZ lysis buffer (Sigma Aldrich). The tissue was homogeneized 20 times with pestle A and 20 times with pestle B. This was followed by centrifugation, filtration and buffer-mediated gradient centrifugation to derive pure single nuclei.
Nuclei were counted using a hemocytometer and the concentration adjusted if needed to meet the optimal range for loading on the 10X Chromium chip. The nuclei were then loaded into the 10X Chromium system using the Single Cell 3′ Reagent Kit v3 (for snRNAseq)  according to the manufacturer’s protocol. We aimed to load ~20,000 nuclei for each snRNAseq run. Following library construction, libraries were sequenced on  the Illumina NovaSeq 6000 system.

value: Glioma

tag: tumor type

value: astrocytoma

value: IDH1 mutant

tag: disease stage

value: primary


title: A_0327p19

tag: genotype

value: Acetate


title: Abl1_RRBS_low_5azadC_rep1

description: Cell line Abl.1, in growth medium with 0.2µM 5-aza-dC, cells collected on Day 2, Library preparation replicate 1

tag: strain

value: treated

tag: Sex

value: female


title: V_0327p19

value: Mammary

tag: cell line

tag: cell type

value: breast cancer

value: WT

tag: treatment

value: Vehicle


title: P3409

value: Plasma

value: high


title: 160.Insr.KO 3

city: Toronto

first: Vuk

last: Stambolic

state: Ontario

address: 101 College Street

institute: University of Toronto/University Health Network

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trim_galore! (v. 0.6.6)
Trimmed sequence reads were mapped to GrCM38/mm10 using STAR (v. 2.7.9a)
High-quality, single-mapping reads were counted to gene exons using FeatureCounts (subread v. 2.0.1)
Assembly: mm10
Supplementary files format and content: tab-delimited text file of raw gene-level counts

growth_protocol: Luminal Comma1D cells were cultured on DMEM/F12 with 5% FBS, 1% penicillin/streptomycin, 20ng/ml EGF, 0.5mg/ml hydrocortisone,100ng/ml Cholera Toxin, 10ug/ml Insulin.

extract_protocol:
RNA was isolated using RNeasy minikit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA was sent to Novogene Inc for mRNA isolation, library preparation, and sequencing.

treatment_protocol: Luminal Comma1D cells were transfected with px463 INSR sg1 using the polyjet transfection reagent. After 48hours of transfection, cells were selected with 5ug/mL puromycin for 48hrs and were allowed to grow until colonies formed.

value: Luminal

value: Insr KO


title: control, rep2

description:
control, rep2
ATAC_NC12.merge.RPKM.bw

value: Human PDAC cell lines

value: Control


title: Quadrant stage Embryo RNA-seq (L8)

value: Embryo

value: Quadrant

value: CDC Gold


title: astrocytoma, ATAC

description: 10x Genomics

value: Glioma

value: astrocytoma

value: IDH1 mutant

value: primary


title: 160.Insr.KO 2


title: Quadrant stage Embryo RNA-seq (L7)


title: P3406


title: 160.Insr.KO 1


title: astrocytoma, counts

description: 10x Genomics

molecule: nuclear RNA

extract_protocol:
Fresh frozen tissue samples were cut into small pieces and homogenized using a dounce homogenizer in EZ lysis buffer (Sigma Aldrich). The tissue was homogeneized 20 times with pestle A and 20 times with pestle B. This was followed by centrifugation, filtration and buffer-mediated gradient centrifugation to derive pure single nuclei.
Nuclei were counted using a hemocytometer and the concentration adjusted if needed to meet the optimal range for loading on the 10X Chromium chip. The nuclei were then loaded into the 10X Chromium system using the Single Cell 3′ Reagent Kit v3 (for snRNAseq)  according to the manufacturer’s protocol. We aimed to load ~20,000 nuclei for each snRNAseq run. Following library construction, libraries were sequenced on  the Illumina NovaSeq 6000 system.
snRNA-seq


title: paired astrocytoma, counts

description: 10x Genomics

value: paired primary and recurrent


title: Zygote stage WholeSeed RNA-seq (L6)

value: WholeSeed

value: Zygote


title: P3401


title: OVCAR8 FAPKD 4-DAY_3

city: Gainesville

first: Shuang

last: Huang

state: FL

address: 2033 mowry road

institute: University of Florida

data_processing:
Samples were analyzed using STAR-htseqcount-deseq2 packages
in galaxy all at default settings (https://usegalaxy.org/)
Supplementary files format and content: tabular file created by galaxy using deseq2
Supplementary files format and content: KD vs. EV differential genes

growth_protocol: OVCAR8 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Cells were treated with virus and RNA was collected after four day treatment

value: mesenchymal cells

value: WT

value: shFAPKD


title: Zygote stage WholeSeed RNA-seq (L5)


title: 87.Insr.KO 1

value: Luminal


title: OVCAR8 FAPKD 4-DAY_2


title: 65.Insr.WT 3


title: P3403

value: Plasma

value: high


title: 87.Insr.KO 3

value: Insr KO


title: oligodendroglioma, counts

description: 10x Genomics

value: oligodendroglioma


title: Zygote stage SeedCoat RNA-seq (L4)

value: SeedCoat


title: OVCAR8 FAPKD 4-DAY_1


title: P3405


title: Zygote stage Embryo RNA-seq (L1)

value: Embryo

value: CDC Gold


title: Zygote stage Embryo RNA-seq (L2)


title: OVCAR8 EV 4-DAY_3

value: shEV


title: 87.Insr.KO 2


title: Mixed scRNA-seq Trichoplax adhaerens and  Hoilungia hongkongensis 2 clicktags

city: Barcelona

first: Arnau

last: Sebe-Pedros

address: Dr. Aiguader 88

department: Systems Biology

country: Spain

institute: Centre for Genomic Regulation

description:
Clicktags to demultiplex single-cells from H1 and H13. See Readme_ClickTag_demultiplexing.xlsx for details.
Tadh.umimatrix.cell_annotations.tsv
Tadh.umimatrix.genes.tsv
Tadh.umimatrix.mtx.gz
Hhon.umimatrix.cell_annotations.tsv
Hhon.umimatrix.genes.tsv
Hhon.umimatrix.mtx.gz

library_source: transcriptomic single cell

data_processing:
scRNA-seq: We used CellRanger 6.1.1 (10X Genomics) to map reads and count unique molecular identifiers (UMIs) per gene per cell. We used the --force-cells flat to set a constant number of 20,000 per experiment (well in excess of the expected number cells for each case, as we intended to remove non-cells from the dataset using our own procedure; see below). We used whole gene bodies to guide the mapping of reads to the genome (--transcriptome flag). We also extended gene ranges to include proximal scRNA-seq peaks located downstream of each gene (in the region 5 kbp downstream of each gene, or less if another gene was closer to that peak). For details on clicktag barcode demultiplexing see Readme_ClickTag_demultiplexing.xlsx file.
ATAC-seq: Reads were mapped using bwa 0.7.17, using the mem algorithm. The resulting BAM files were filtered using the alignmentSieve utility from the deeptools 3.5.1 package, in order to filter out weak alignments (with minimum mapping quality or MAPQ = 30) and shifting the left and right ends of reads according to usual ATAC specifications (+4/−5 bp in the positive and negative strands, activated with the --ATACshift flag in deeptools). Duplicated reads were removed using biobambam2 2.0.87, and the resulting alignments were coordinate-sorted with the same tool. Then, we concatenated all the ATAC-seq libraries for each species. bigWig files were generated with deepTools v3.5.2 bamCoverage function.
ChIP-seq: The ChIP-seq libraries corresponding to H3K4me2 and H3K4me3 were mapped to their corresponding species with bwa mem, using the same procedure as described for ATAC-seq (except for the adjustment of read end coordinates specific to ATAC libraries).
Assembly: Trichoplax adhaerens: GCA_000150275.1
Assembly: Trichoplax sp. H2: GCA_003344405.1
Assembly: Hoilungia honkgongensis: https://bitbucket.org/molpalmuc/hoilungia-genome/src/master/
Assembly: Cladtertia collaboinventa: https://www.frontiersin.org/articles/10.3389/fevo.2022.1016357/full
Supplementary files format and content: For ATAC-seq and ChIP-seq: bigWig coverage files (bw extension)
Supplementary files format and content: For scRNA_seq: TSV file with CellIDs and associated metadata (in the same order as in the UMI matrix)
Supplementary files format and content: For scRNA_seq: TSV file with gene names associated to the UMI matrix
Supplementary files format and content: For scRNA_seq: MTX file containin gene x cell UMI counts

organism:
Trichoplax adhaerens
Hoilungia hongkongensis

source_name: Whole adult specimens

extract_protocol:
Cells were fixed using the ACME protocol (10.1186/s13059-021-02302-5), FACS sorted, and processed with the 10X Genomics Chromium Single Cell 3' scRNAseq v3.1 kit.
Adult specimens were fixed, dissociated and pooled before sorting single-cells for scRNAseq. The same procedure was followed for chromatin profiling experiments, except that cells were used fresh for ATAC-seq and fixed with 1% formaldehyde (10 min) for ChIP-seq

value: Whole adult specimens

value: Wild type


title: P3383

value: low


title: P3362


title: 44.Insr.WT 2


title: Zygote stage SeedCoat RNA-seq (L3)


title: Mixed scRNA-seq Trichoplax adhaerens and  Hoilungia hongkongensis 1 clicktags


title: Human Bone MSC, S3

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values and counts for each Sample

source_name: Senile hBMSC from 21y old donor at passage 9

growth_protocol: Cells were cultured in hBMSC-specific medium of OriCell® Adult Bone Marrow Mesenchyaml Stem Cell Complete Medium (Cyagen, Cat#HUXMA-90011).

extract_protocol:
Cells were harvested at 80% confluence.  Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were passaged at the confluence of 90%~95%.

tag: individual

value: 21y old donor

value: Senile hBMSC at passage 9


title: 65.Insr.WT 1


title: P3363


title: Trichoplax sp. H2 H3K4me2 ChIP-seq

organism: Trichoplax sp. H2

extract_protocol:
ChIP-seq was performed as described in 10.1038/s41559-018-0575-6.
Adult specimens were fixed, dissociated and pooled before sorting single-cells for scRNAseq. The same procedure was followed for chromatin profiling experiments, except that cells were used fresh for ATAC-seq and fixed with 1% formaldehyde (10 min) for ChIP-seq

tag: chip antibody

value: ChIP-seq ab32356, Abcam


title: Human Bone MSC, S1


title: P3396


title: Human Bone MSC, Y2

source_name: young hBMSC from 21y old donor at passage 2

value: young hBMSC at passage 2


title: P3329


title: Human Bone MSC, Y1


title: Mixed scRNA-seq Trichoplax adhaerens and  Cladtertia collaboinventa 1 clicktags

description:
Cladtertia collaboinventa
Clicktags to demultiplex single-cells from H1 and H23. See Readme_ClickTag_demultiplexing.xlsx for details.
Tadh.umimatrix.cell_annotations.tsv
Tadh.umimatrix.genes.tsv
Tadh.umimatrix.mtx.gz
HoiH23.umimatrix.cell_annotations.tsv
HoiH23.umimatrix.genes.tsv
HoiH23.umimatrix.mtx.gz

organism:
Trichoplax adhaerens
Hoilungia sp. H23


title: p28 enthesis, replicate 1, scRNAseq

city: chang sha

first: zhang

last: tao

address: xiangya street

institute: xiangya hospital

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10; GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: tendon enthesis

extract_protocol:
The humeral head- supraspinatus tendon samples were dissected from the left shoulders of C57/BL6 mice at embryonic day-15.5, postnatal day-1, day-7, day-14, and day-28. In general, samples were harvested from pooled sibling limbs of two litters (five to six limbs per pool). Following dissection, all the samples were minced immediately and digested in type I collagenase (1mg/ml, Gibico) and type II collagenase (1mg/ml, Gibico) diluted in low-glucose DMEM (Gibco) solution at 37 °C for 30-40 min.  Cell suspensions were stained with antibodies including Ter119-Alexa700 and Cd45- Alexa700 (Biolengend) to remove blood cells. DAPI (BD) stain was used to exclude dead cells.
8000-10,000 cells were loaded for each age group by Chromium instrument and its chemistry kit V3 (10X Genomics) according to the manufacturer’s guidance. Each cell was encapsulated with a barcoded Gel Bead in a single partition, then amplified to generate single-cell cDNA libraries and sequenced on an Illumina NovaSeq 6000 platform at a sequencing depth of ~500 million reads. The Cellranger pipeline (version 6.1.1) was used to align the raw reads to the mouse reference genome GRCm38 and to generate feature-barcode matrices.

value: tendon enthesis

tag: age

value: postnatal day 28

value: wild type


title: scRNA-seq of Trichoplax. sp H2 Notch drugs clicktags

description:
Clicktags to demultiplex single-cells from different treatments. See Readme_ClickTag_demultiplexing.xlsx for details.
TrH2_notch_drugs.umimatrix.cell_annotations.tsv
TrH2_notch_drugs.umimatrix.genes.tsv
TrH2_notch_drugs.umimatrix.mtx.gz


title: p28 enthesis, replicate 3, scRNAseq

description: 10x Genomics


title: P3399

value: Plasma

tag: patient number

value: high


title: 44.Insr.WT 3

value: Luminal

value: WT


title: p7 enthesis, scRNAseq

description: 10x Genomics

value: postnatal day 7


title: p1 enthesis, scRNAseq

description: 10x Genomics

value: postnatal day 1


title: P3290

tag: group low_/_int_/_high


title: 65.Insr.WT 2


title: Trichoplax sp. H2 scRNA-seq 3

description:
TrH2.umimatrix.cell_annotations.tsv
TrH2.umimatrix.genes.tsv
TrH2.umimatrix.mtx.gz


title: Trichoplax sp. H2 scRNA-seq 2


title: P3385


title: P3289


title: P3384

value: int


title: OVCAR8 EV 4-DAY_2

value: mesenchymal cells

value: shEV


title: OVCAR8 EV 4-DAY_1


title: 44.Insr.WT 1


title: Mixed scRNA-seq Trichoplax adhaerens and  Hoilungia hongkongensis 2

description:
Tadh.umimatrix.cell_annotations.tsv
Tadh.umimatrix.genes.tsv
Tadh.umimatrix.mtx.gz
Hhon.umimatrix.cell_annotations.tsv
Hhon.umimatrix.genes.tsv
Hhon.umimatrix.mtx.gz

value: Whole adult specimens

value: Wild type


title: P3358


title: P3287


title: Human Bone MSC, Y3

value: 21y old donor


title: Human Bone MSC, S2

value: Senile hBMSC at passage 9


title: Cladtertia collaboinventa scRNA-seq 3

description:
Cladtertia collaboinventa
HoiH23.umimatrix.cell_annotations.tsv
HoiH23.umimatrix.genes.tsv
HoiH23.umimatrix.mtx.gz

organism: Hoilungia sp. H23


title: P3338


title: Mixed scRNA-seq Trichoplax adhaerens and  Hoilungia hongkongensis 1


title: P3339


title: Trichoplax sp. H2  ATAC

extract_protocol:
ATAC-seq was performed using the Omni-ATAC protocol (10.1038/nmeth.4396) and using custom Tn5 enzyme
Adult specimens were fixed, dissociated and pooled before sorting single-cells for scRNAseq. The same procedure was followed for chromatin profiling experiments, except that cells were used fresh for ATAC-seq and fixed with 1% formaldehyde (10 min) for ChIP-seq


title: Trichoplax sp. H2  H3K4me3 ChIP-seq

value: ChIP-seq antibody 07-473, Millipore


title: snRNA-seq  4 weeks BAT Flox

city: Shenyang

first: Wei

last: Shen

state: Liaoning

address: No. 77 Puhe Road, Shenyang North New Area

department: School of Public Health

institute: China Medical University

description: 10x Genomics

data_processing:
The 10x Genomics Cell ranger analysis pipeline (Version 3.0.0) was used for demultiplexing and generating the FeatureBarcode Matrices. Briefly, cellranger mkfastq was used to convert the raw base call (BCL) files of snRNA-seq into FASTQ files. Then cellranger count was used for alignment with reference genome mm10, filtering, and processing barcode data to create the feature-barcode matrices for each sample.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Brown adipose tissue

extract_protocol:
The BAT  was rinsed with pre-cooled RNase-free saline to remove blood stains and dirt, and non-necessary tissues were removed. After blotting the water stains, BAT was taken and cut into small pieces (operation on ice). The cut tissue blocks were placed together into 2.0 mL RNase-free EP tubes stored at -80℃.
The snRNA-seq was performed with the assistance of the UNMC Genomics Core. The core operates a 10x Genomics Chromium instrument for isolation of single nucleus and generation of Illumina compatible sequencing libraries (10x Genomics, Pleasanton, CA). The instrument captures individual nucleus using a gel bead in emulsion (GEM) technology. The droplets contain the reagents for reverse transcription and all transcripts within each nucleus are uniquely barcoded (all transcripts within a given cell contain the same barcode for cell identification) and Illumina compatible cDNA libraries created are for each nucleus within the given sample. The single‐nucleus suspensions were diluted to the working concentration required to 8000 target nuclei captured. The pooled nuclei were captured, lysed, RNA reverse transcribed and barcoded using Chromium Single Cell 3’ Reagent Kits v3 reagents. Libraries are quantified by qPCR using the KAPA Library Quant Kit (Illumina) from KAPA Biosystems (Roche, Pleasonton, CA) and paired-end sequenced (PE150) on Illumina Novaseq6000 according to the standard protocols.

value: Brown adipose tissue

value: Flox


title: snRNA-seq  4 weeks BAT KO

description: 10x Genomics

value: KO


title: P3321

value: Plasma


title: Cladtertia collaboinventa H3K4me2 ChIP-seq

description: Cladtertia collaboinventa

value: ChIP-seq ab32356, Abcam


title: p28 enthesis, replicate 2, scRNAseq

description: 10x Genomics

value: tendon enthesis

value: postnatal day 28

value: wild type


title: scRNA-seq of Trichoplax. sp H2 Notch drugs

description:
TrH2_notch_drugs.umimatrix.cell_annotations.tsv
TrH2_notch_drugs.umimatrix.genes.tsv
TrH2_notch_drugs.umimatrix.mtx.gz

value: Control sample, Yhhu, DAPT, LY411575


title: p14 enthesis, scRNAseq

description: 10x Genomics

value: postnatal day 14


title: P3304

value: low


title: P3303


title: Mixed scRNA-seq Trichoplax adhaerens and  Cladtertia collaboinventa 1

description:
Cladtertia collaboinventa
Tadh.umimatrix.cell_annotations.tsv
Tadh.umimatrix.genes.tsv
Tadh.umimatrix.mtx.gz
HoiH23.umimatrix.cell_annotations.tsv
HoiH23.umimatrix.genes.tsv
HoiH23.umimatrix.mtx.gz


title: e15 enthesis, scRNAseq

description: 10x Genomics

value: embryonic day 15.5


title: Cladtertia collaboinventa H3K4me3 ChIP-seq

description: Cladtertia collaboinventa

value: Whole adult specimens


title: Cladtertia collaboinventa scRNA-seq 2

value: Wild type


title: B. subtilis 9407 derived strain, active PNPase, PNPase group

city: Beijing

first: Xiaofei

last: Gu

state: China

address: NO 2 Yuanmingyuan West Road , Haidian District, Beijing

institute: China Agricultural University

data_processing:
Raw sequencing data were filtered using Trimmomatic (version 0.36) to discard low-quality reads and trim reads contaminated with adaptor sequences.
The de-duplicated consensus sequences were mapped to the reference genome of B. subtilis 9407, which was obtained from NCBI's GenBank database (https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/835/225/GCF_002835225.1_ASM283522v1/) and aligned using STAR software (version 2.5.3a) with default parameters.
The RSeQC (version 2.6) was used for analyzing read distribution.
The exomePeak (Version 3.8) software was used for peak calling with a more stringent significance threshold (FDR < 0.05 and log2 FC ≥ 2).
Peaks were annotated using Bedtools (Version 2.25.0). DeepTools (Version 2.4.1) was used for analyzing peak distribution.
Assembly: GCA_002835225.1
Supplementary files format and content: D493A_peaks.tsv: Peaks of D493A group in tsv format
Supplementary files format and content: D493A_peaks_anno.tsv: Gene Annotation information of D493A group in tsv format
Supplementary files format and content: PNPase_peaks.tsv: Peaks of PNPase group in tsv format
Supplementary files format and content: PNPase_peaks_anno.tsv: Gene Annotation information of PNPase group in tsv format

organism: Bacillus subtilis

source_name: B. subtilis 9407

extract_protocol:
Target mRNAs were extracted using TRIzol reagent (Invitrogen), followed by determination of RNA concentration and quality analysis conducted by Seqhealth Technology Co., Ltd (Wuhan, China).
The stranded RNA sequencing library was constructed using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Seqhealth) following the manufacturer's instruction. The library products corresponding to 200-500 bps were enriched, quantified, and finally sequenced using the PE150 model on a Novaseq 6000 sequencer (Illumina).

value: Bacteria

value: Overexpressed

tag: rip antibody

value: Anti-6X His tag monoclonal rabbit antibodies (Abcam, #ab200537)

value: Control


title: Cladtertia collaboinventa scRNA-seq 1


title: 3c9 (24 months, female)

data_processing:
The preliminary quality control checks on the raw RNA-seq data were performed using FASTQC (v0.11.4). The 3҆ adapter sequence were trimmed using Cutadapt66 (v1.15) and quality control checks were again performed on the trimmed reads with FASTQC. The trimmed reads were then aligned to the mouse genome (GRCm38/mm10) using STAR aligner (v2.5.2b). The parameter quantMode was set to GeneCounts for the calculation of counts per gene. A comprehensive quality report for all the samples was generated with MultiQC68 (v1.7) (https://multiqc.info/). The counts obtained after STAR alignment was used to study differential expression analysis using DESeq269 (v1.24.0). Linear regression analysis was performed on TPM (transcripts per million) values, calculated by normalizing the raw read counts to the gene length and sequencing depth in each sample, to study the age-associated changes in gene expression. A gene was considered to be significantly dysregulated with age if it had an adjusted p-value less than 0.05 (p.value.age.fdr < 0.05) in the linear regression analysis.
Assembly: mm10
Supplementary files format and content: tab delimited text files (.tab) with raw counts for each sample.  Column 1: gene ID, column 2: counts for unstranded RNA-seq (htseq-count option --stranded no), column 3: counts for the 1st read strand aligned with RNA (htseq-count option, --stranded yes), column 4: counts for the 2nd read strand aligned with RNA (htseq-count option --stranded reverse).

extract_protocol:
Full-length cDNA libraries were prepared with the SMART-Seqv4 Ultra Low Input RNA kit (TaKaRa) and the libraries for sequencing were prepared using Nextera XT DNA Library Prep (Illumina) according to the manufacturer’s instructions.
The libraries from 24 samples were sequenced on Illumina NovaSeq6000 sequencing system and generated 50 bp paired end reads (PE50). Libraries from the other 6 samples were sequenced on Illumina HiSeq 2500 SR50 single end reads.

value: female

value: 24 months

value: Brain

value: Primary cells

value: Endothelial cells

value: WT


title: Cladtertia collaboinventa ATAC

description: Cladtertia collaboinventa


title: Trichoplax sp. H2 scRNA-seq 1


title: P3281

value: Plasma

value: high


title: 3c8 (24 months, female)


title: 4b2 (24 months, male)

value: male


title: 3c5 (24 months, female)


title: P3284

value: low


title: P3283


title: ET87

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description: rm.m.results.csv.gz

data_processing:
Basic read quality was verified using summaries produced by FastQC. Trimmomatic was used to remove low quality reads and bases
The reads for each sample were mapped to the GCF_019320065.1 elk genome using Bowtie2.
The mapped read files were then converted to sorted BAM files using SAMtools
The MEDIPS R package was used to calculate differential coverage between sample groups. To identify DMR, the reference genome was broken into 1000 bp windows. The edgeR p-value was used to determine the relative difference between the two sample groups for each genomic window. Windows with an edgeR p-value less than an arbitrarily chosen threshold were considered DMR. The DMR edges were extended until no genomic window with an edgeR p-value less than 0.1 remained within 1000 bp of the DMR.
The selected DMR were then summarized and annotated.
Assembly: GCF_019320065.1
Supplementary files format and content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window and other summary values.
Library strategy: MeDIP-Seq

organism: Cervus canadensis

source_name: Tendon

growth_protocol: Lower limbs from TAHD-suspect and apparently normal elk and associated metadata were solicited from state, federal, and tribal collaborators for TAHD surveillance conducted during 2018-2020. Elk were harvested, culled for management purposes, or found recently deceased. As such, the study was exempt from review by an Institutional Animal Care and Use Committee. Ecotype was inferred from location of collection. Age class of elk was assigned as adult (>2 years old), juvenile (<2 years old), or unknown.

extract_protocol:
Frozen elk tendon samples were thawed for analysis. Genomic DNA from tendon samples was prepared as follows: DNA was isolated from tendon samples by cutting a 2mm x 2mm x 2mm cube of tendon and rinsing twice in 1 ml PBS followed by centrifugation at 13,000g for 1 min to remove the Allprotect Tissue Reagent™. Each sample was minced and incubated with 1 mg/ml collagenase I in 1 ml PBS at 37° with rotation overnight.  Samples were then processed using the DNeasy Blood and Tissue Kit™ (Qiagen) to extract DNA, following the manufacturer’s protocols. DNA concentration was measured using the Nanodrop (Thermo Fisher, Waltham, MA). Methylated DNA Immunoprecipitation (MeDIP) with genomic DNA was performed as follows: individual DNA samples (2-4 ug of total DNA) were diluted to 130 μl with 1x Tris-EDTA (TE, 10 mM Tris, 1 mM EDTA) and sonicated with the Covaris M220 using the 300 bp setting. Fragment size was verified on a 2% E-gel agarose gel. The sonicated DNA was transferred from the Covaris tube to a 1.7 ml microfuge tube, and the volume was measured. The sonicated DNA was then diluted with TE buffer (10mM Tris HCl, pH7.5; 1mM EDTA) to 400 μl, heat-denatured for 10 min at 95 C, then immediately cooled on ice for 10 min. Then 100 μl of 5X IP buffer and 5 μg of antibody (monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006) were added to the denatured sonicated DNA. The DNA-antibody mixture was incubated overnight on a rotator at 4 C. The following day magnetic beads (Dynabeads M-280 Sheep anti-Mouse IgG; 11201D) were pre-washed as follows: The beads were resuspended in the vial, then the appropriate volume (50 μl per sample) was transferred to a microfuge tube. The same volume of Washing Buffer (at least 1 mL 1XPBS with 0.1% BSA and 2mM EDTA) was added and the bead sample was resuspended. The tube was then placed into a magnetic rack for 1-2 min and the supernatant was discarded. The tube was removed from the magnetic rack and the beads were washed once. The washed beads were resuspended in the same volume of 1xIP buffer (50 mM sodium phosphate ph7.0, 700 mM NaCl, 0.25% TritonX-100) as the initial volume of beads. 50μl of beads were added to the 500μl of DNA-antibody mixture from the overnight incubation, then incubated for 2 hours on a rotator at 4 C. After the incubation, the bead-antibody-DNA complex was washed three times with 1X IP buffer as follows: The tube was placed into a magnetic rack for 1-2 min and the supernatant was discarded, then the magnetic bead antibody pellet was washed with 1xIP buffer 3 times. The washed bead antibody DNA pellet was then resuspended in 250 μl digestion buffer with 3.5 μl Proteinase K (20mg/ml). The sample was incubated for 2-3 hours on a rotator at 55 C, then 250 μl of buffered Phenol-Chloroform- Isoamylalcohol solution was added to the sample, and the tube was vortexed for 30 sec and then centrifuged at 14,000rpm for 5 min at room temperature. The aqueous supernatant was carefully removed and transferred to a fresh microfuge tube. Then 250 μl chloroform were added to the supernatant from the previous step, vortexed for 30 sec and centrifuged at 14,000rpm for 5 min at room temperature. The aqueous supernatant was removed and transferred to a fresh microfuge tube. To the supernatant 2μl of glycoblue (20mg/ml), 20μl of 5M NaCl and 500μl ethanol were added and mixed well, then precipitated in -20 C freezer for 1 hour to overnight. The precipitate was centrifuged at 14,000rpm for 20 min at 4 C and the supernatant was removed, while not disturbing the pellet. The pellet was washed with 500μl cold 70% ethanol in -20 C freezer for 15 min then centrifuged again at 14,000rpm for 5 min at 4 C and the supernatant was discarded. The tube was spun again briefly to collect residual ethanol to the bottom of the tube and as much liquid as possible was removed with gel loading tip. The pellet was air-dried at RT until it looked dry (about 5 min) then resuspended in 20μl H2O or TE. DNA concentration was measured in Qubit (Life Technologies) with ssDNA kit (Molecular Probes Q10212).
The MeDIP DNA samples (50 ng of each) were used to create libraries for next generation sequencing (NGS) using the NEBNext Ultra RNA Library Prep Kit for Illumina (San Diego, CA) starting at step 1.4 of the manufacturer’s protocol to generate double stranded DNA. After this step the manufacturer’s protocol was followed. Each sample received a separate index primer.

treatment_protocol: Frozen lower limbs (-20) were submitted to the Washington Disease Diagnostic Laboratory (WADDL) for TAHD diagnosis and sample collection. Feet were thawed, grossly examined, and sampled under the direction of a board-certified veterinary pathologist. Tissue samples used to determine TAHD status were placed in formalin and processed for histologic examination with H&E and Warthin Starry silver stains. Cases that exhibited characteristic gross lesions with inflammation and spirochetes on histologic examination were diagnosed as TAHD positive. An approximately 1 cm section of the superficial or deep flexor tendon at about the level of the fetlock was collected from one foot from each elk for epigenetic analysis. Tendon appeared grossly normal and was collected proximal to the location of TAHD lesions. The sample was placed in AllProtect Tissue Reagent™ (Qiagen, Germantown, Maryland) storage solution and frozen at -80 until use.

tag: subspecies

value: nelsoni

tag: group

value: tahd negative

value: Tendon


title: P3280

tag: tissue


title: B. subtilis 9407 derived strain, inactive PNPase, D493A group 1

value: Bacteria

value: Treatment 1


title: B. subtilis 9407 derived strain, inactive PNPase, D493A group 2

value: Overexpressed

value: Anti-6X His tag monoclonal rabbit antibodies (Abcam, #ab200537)

value: Treatment 2


title: 3b3 (24 months, male)

value: 24 months


title: LagPhase_Rep3_240min

city: Basel

first: Kazuki

last: Nosho

address: Spitalstrasse 41

department: Biozentrum

institute: University of Basel

data_processing:
Sequencing of the cDNA libraries was performed by MPGC (Cologne, Germany) or D-BSSE genomics facilty (Basel, Switzerland)
Sequence reads were trimmed for adaptor sequence/short sequence (<35 nt) using Trimmomatic v0.39
Trimmed sequence reads were mapped to B. subtilis NCIB3610 genome and plasmid (NCBI Accession number: NZ_CP020102 and NZ_CP020103) using HISAT2 v2.2.1 in single-end mode.
Reads mapped to all cetegory of genes (CDS, ncRNA, tmRNA, signal recognition particle RNA, ribonuclease P RNA, tRNA, rRNA) were counted using featureCounts v2.0.1 with fractional counting for multi-mapping and multi-overlapping reads (-OM --fraction) in a strand-specific manner (-s 2). Of those, reads mapped in tRNA and rRNA were removed and the remaining reads were used for the downstream analysis.
All genes for which there were at least 2 samples with a read count of at least 10 were used for the downstream analysis. Samples with remaining reads of < 1 million reads were excluded and the rest of the samples were used for normalization using edgeR (version 3.6.1) and transformed (log2).
Supplementary files format and content: comma-separated files include mapped read count data for each sample
Supplementary files format and content: comma-separated files include edgeR-normalized log2 count data for each of the samples at expansion phase
Supplementary files format and content: comma-separated files include edgeR-normalized log2 count data for each of the samples at lag and expansion phase

source_name: cells, 240 min after inoculation on soft-agar, rep.3

growth_protocol: Bacterial cells were spotted onto the center of a 9 cm petri dish filled with LB soft-agar (0.5% agar) medium and incubated at 30°C for swarm expansion.

extract_protocol:
RNA was isolated by the hot phenol method (Jahn et al, J Microbiol Methods, 2008) with some modifications. Prepared RNA was DNase-digested and cleaned up using RNACleanXP. Depletion of ribosomal RNA was performed using DIY method (Culviner et al, mBio, 2020). Integrity of the prepared RNA was tested using a TapeStation.
Directional cDNA libraries were prepared using the NEBNext Ultra II Directional RNA Libary Prep Kit for Illumina (NEB, E7760) according to the manufacturers instructions. Quality of the prepared libraries was tested using a TapeStation.

treatment_protocol: Cells that started swarm expansion were collected into the lysis buffer by our custom sampling robot. Cells before swarm expansion (lag phase) were collected by being suspened in the lysis buffer.

value: WT chromosome; comI_Q12L in natual plasmid

tag: time after_inoculation_(min)


title: LagPhase_Rep3_225min

source_name: cells, 225 min after inoculation on soft-agar, rep.3


title: ET85

description: rm.m.results.csv.gz

value: tahd positive


title: P3275


title: P3277


title: ET84

description: rm.m.results.csv.gz


title: 13a9 (12 months, female)

value: female

value: 12 months

value: Brain

value: Primary cells

value: Endothelial cells


title: LagPhase_Rep3_210min

source_name: cells, 210 min after inoculation on soft-agar, rep.3


title: LagPhase_Rep3_195min

source_name: cells, 195 min after inoculation on soft-agar, rep.3


title: 13a7 (12 months, female)

source_name: Brain

value: WT


title: P3271

value: Plasma

value: int


title: 13a6 (12 months, female)


title: LagPhase_Rep3_180min

source_name: cells, 180 min after inoculation on soft-agar, rep.3


title: 12a2 (12 months, male)

value: male


title: P3263

value: low


title: P3267


title: P3262


title: LagPhase_Rep3_150min

source_name: cells, 150 min after inoculation on soft-agar, rep.3

value: Bacteria


title: ET86

description: rm.m.results.csv.gz

value: nelsoni

value: Tendon


title: 3a3 (24 months, male)


title: ET83

description: rm.m.results.csv.gz

value: tahd negative


title: 9a1 (12 months, male)


title: ET81

description: rm.m.results.csv.gz


title: ET82

description: rm.m.results.csv.gz


title: LagPhase_Rep3_120min

source_name: cells, 120 min after inoculation on soft-agar, rep.3


title: ET80

description: rm.m.results.csv.gz


title: ET79

description: rm.m.results.csv.gz


title: 12a1 (12 months, male)


title: LagPhase_Rep3_90min

source_name: cells, 90 min after inoculation on soft-agar, rep.3


title: HTO iAT2 wild-type and ADGRG6-kd (hashed)

first: Pushpinder

last: Bawa

state: Massachusetts

address: 670 Albany St

department: Boston University Medical Campus

institute: Center for Regenerative Medicine

description: 10x Genomics

data_processing:
The sample was processed using the standard Cellranger v.2 pipeline
Reads were mapped to GRCh38 with TdTomato reporter
Downstream analysis and QC done on Seurat
Differential expression using MAST models
Assembly: GRCh38 with TdTomato reporter
Supplementary files format and content: the processed files are the standard output from the cellranger count pipeline: filtered feature-barcode matrices in HDF5 format

source_name: Cell line

growth_protocol: To generate iAT2s, we performed PSC directed differentiation via definitive endoderm into NKX2-1 lung progenitors using methods we have previously described (Hawkins et al., JCI 2017; Jacob et al., Cell Stem Cell 2017; Jacob et al., Nat Protoc 2019). In brief, cells maintained in mTeSR1 media were differentiated into definitive endoderm using the STEMdiff Definitive Endoderm Kit (StemCell Technologies) for 3 days (day 0-3) and after the endoderm-induction stage, cells were dissociated with gentle cell dissociation reagent and passaged into 6-well dishes pre-coated with growth factor reduced Matrigel in ‘‘DS/SB’’ anteriorization media, consisting of complete serum-free differentiation media (cSFDM) base as previously described (Jacob et al., Cell Stem Cell 2017; Jacob et al., Nat Protoc 2019), supplemented with 2 µM Dorsomorphin (‘‘DS’’; Stemgent) and 10 µM SB431542 (‘‘SB’’; Tocris). For the first 24 hour after passaging, 10 µM Y-27632 was added to the media. After anteriorization in DS/SB media for 3 days (day 3-6), cells were cultured in ‘‘CBRa’’ lung progenitor-induction media until day 15, as we have previously published (Jacob et al., Cell Stem Cell 2017). ‘‘CBRa’’ media consists of cSFDM base supplemented with 3 µM CHIR99021 (Tocris), 10 ng/ml recombinant human BMP4 (rhBMP4, R&D Systems), and 100 nM retinoic acid (RA, Sigma). On day 15 of differentiation, live cells were sorted on a high-speed cell sorter (MoFlo Legacy or MoFlo Astrios EQ) to isolate NKX2-1+ lung progenitors based on CD47hi/CD26neg gating (Hawkins et al., JCI 2017). Sorted lung progenitors were resuspended in undiluted growth factor reduced 3D Matrigel (Corning) at a concentration of approximately 400 cells/µl and distal/alveolar differentiation of cells was performed in CK+DCI media, consisting of cSFDM base supplemented with 3 µM CHIR99021, 10 ng/mL rhKGF (CK), and 50 nM dexamethasone (Sigma), 0.1 mM 8-Bromoadenosine 30,50-cyclic monophosphate sodium salt (Sigma) and 0.1 mM 3-Isobutyl-1-methylxanthine (IBMX; Sigma) (DCI).

extract_protocol: 10X Chromium system

value: Cell line

value: BU3 NGST CRISPRi line

value: iPSC-derived AT2

value: CK+DCI media +/- doxycyline


title: 20b6 (6 months, female)

first: Kshitij

last: Mohan

address: CVMed, Level 5, John Radcliffe Hospital

institute: University of Oxford

value: female

value: 6 months


title: 20b4 (6 months, female)

value: Brain

value: Primary cells


title: SK-Hep-1 cells, sh1089-2

city: Jinan

first: Tao

last: Su

state: Shandong

address: 440 Jiyan Rd

institute: Shandong Cancer Hospital and Institute

description: FPKM.txt

data_processing:
FastQC was used to cut off sequencing connectors and low-quality fragments of sequencing data
The clean data were mapping to reference genome (GRCh38)
The expression of known genes (FPKM) was analyzed by StingTie and gffmerge
The alternative splicing (AS) was analyzed by StringTie, gffcompare, and ASprofile
New transcripts were annotated by StingTie and gffcompare
Assembly: GRCh38
Supplementary files format and content: FPKM of known mRNAs
Supplementary files format and content: FPKM.txt

source_name: liver

extract_protocol:
Total RNA was extracted using the Trizol method
After quality control of the total RNA, mRNA enrichment was performed.Strand-specific library was constructed, and the library quality was tested.

value: liver

value: knockdown of LINC01089


title: ET78

description: rm.m.results.csv.gz


title: GEX iAT2 wild-type and ADGRG6-kd (hashed)

description: 10x Genomics


title: ET77

description: rm.m.results.csv.gz


title: LagPhase_Rep3_30min

source_name: cells, 30 min after inoculation on soft-agar, rep.3

value: WT chromosome; comI_Q12L in natual plasmid


title: SK-Hep-1 cells, sh1089-1

description: FPKM.txt


title: 16a6 (6 months, female)

city: Oxford

value: Endothelial cells

value: WT


title: LagPhase_Rep3_0min

source_name: cells, 0 min after inoculation on soft-agar, rep.3

value: Bacteria


title: ET76

description: rm.m.results.csv.gz

value: nelsoni

value: male


title: 12e3 (6 months, male)


title: SK-Hep-1 cells, shNC

description: FPKM.txt

value: negative control


title: ET75

description: rm.m.results.csv.gz

value: tahd negative

value: Tendon


title: LagPhase_Rep2_240min

source_name: cells, 240 min after inoculation on soft-agar, rep.2


title: ET74

value: tahd omit


title: ET73

description: rm.m.results.csv.gz


title: 12e2 (6 months, male)


title: 12e1 (6 months, male)


title: LagPhase_Rep2_225min

source_name: cells, 225 min after inoculation on soft-agar, rep.2


title: 18c8 (2 months, female)

value: 2 months


title: ET72

value: tahd suspected positive


title: 18c6 (2 months, female)

value: female


title: LagPhase_Rep2_210min

source_name: cells, 210 min after inoculation on soft-agar, rep.2


title: LagPhase_Rep3_60min

source_name: cells, 60 min after inoculation on soft-agar, rep.3


title: ET71

description: rm.m.results.csv.gz

source_name: Tendon


title: LagPhase_Rep2_180min

source_name: cells, 180 min after inoculation on soft-agar, rep.2


title: LagPhase_Rep2_195min

source_name: cells, 195 min after inoculation on soft-agar, rep.2


title: A549_Con_3

first: Shaohua

last: Wang

address: No 12 Middle Wulumuqi Road

institute: Department of Thoracic Surgery

data_processing:
Solexa pipeline version 1.8 (Off-Line Base Caller software, version 1.8) used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Bioconductor DESeq2 (V1.6.3) used for differential analysis
Assembly: GRCh37
Supplementary files format and content: xlsx file for differential gene expression information for OE_1/2/3 vs con_1/2/3

source_name: Mock transfected A549

growth_protocol: A549 cells were cultured in Dulbecco's modified eagle medium (DMEM)  supplemented with 10% Fetal Bovine Serum (FBS), 100 U/mL penicillin and 100 µg/mL streptomycin.

extract_protocol:
mRNA was isolated from total RNA using NEB Next poly (A) mRNA Magnetic Isolation Module (NEB, MA, USA) and rRNA was removed using RiboZero Magnetic Gold Kit (Epicentre NY, USA).
RNA library was prepared using KAPA Stranded RNA-SEQ Library Prep Kit (illumina, CA, USA) according to instruction manual prior to subject to sequencing using illumina NovaSeq 6000.

value: Mock transfected A549

value: Lung adenocarcinoma (LUAD)

value: untreated


title: A549_Con_2


title: 18c5 (2 months, female)

source_name: Brain

value: Brain

value: Primary cells


title: ET70


title: LagPhase_Rep2_150min

source_name: cells, 150 min after inoculation on soft-agar, rep.2

value: WT chromosome; comI_Q12L in natual plasmid


title: A549_Con_1


title: ET69

description: rm.f.results.csv.gz

value: tahd positive


title: 18c4 (2 months, male)

value: Endothelial cells

value: WT


title: LagPhase_Rep2_120min

source_name: cells, 120 min after inoculation on soft-agar, rep.2

value: Bacteria


title: 18c3 (2 months, male)

value: male


title: ZmRPN1-Mutator-aa-rep3

first: Luguang

last: Jiang

state: Beijing

address: No.2 Yuanmingyuan West Road, Haidian, Beijing

description:
ZmRPN1 knockout
RPN1-AA-aa-genecounts.txt

data_processing:
Sequencing reads were processed with trimmomatic-0.39 to remove adaptor sequence and low-quality sequence, and then mapped to B73 RefGen_v4 reference genome (https://ftp.ebi.ac.uk/ensemblgenomes/pub/release-50/plants/fasta/zea_mays/dna/) using HISAT2 (version: 2.2.1).
Uniquely mapped reads were kept for subsequent gene expression quantification using featureCounts (v1.6.4).
DEGs analysis was performed using the DESeq2 R package.
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated using stringtie (version: 1.3.6).
Assembly: B73 RefGen_v4 reference genome
Supplementary files format and content: tab-delimited text files include read counts for each sample

organism: Zea mays

source_name: anther (S3-S5 stage)

extract_protocol:
Total RNA was extracted using RNAprep Pure Plant Plus kit,treated with RNase-free DNaseI and purified using the RNAclean Kit.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep kit following manufacturer's protocols.

value: anther (S3-S5 stage)

value: ZmRPN1 knockout


title: A549_OE_3

source_name: c-Jun overexpression plasmid transfected A549


title: A549_OE_2

value: c-Jun overexpression plasmid transfected A549


title: ET68

description: rm.f.results.csv.gz

value: nelsoni

value: Tendon


title: LagPhase_Rep2_90min

source_name: cells, 90 min after inoculation on soft-agar, rep.2


title: 18c1 (2 months, male)

value: 2 months


title: A549_OE_1


title: ZmRPN1-Mutator-aa-rep2


title: LagPhase_Rep2_60min

source_name: cells, 60 min after inoculation on soft-agar, rep.2


title: ZmRPN1-Mutator-aa-rep1


title: Cav1 knockout (KO) week 70 aging brain rep1

city: Columbia

first: Susanta

middle: K.

last: Behura

state: Missouri

address: 920 East Campus Drive

department: Division of Animal Sciences

institute: Univeristy of Missouri

description: Illumina

data_processing:
The quality of raw sequences was checked with FastQC followed by trimming the adaptors from the sequence reads by cutadapt. The trimmomatic tool was used to perform base quality trimming (Phred score >30) by sliding window scan (4 nucleotides). The quality reads were then mapped to the mouse reference genome GRCm38 using Hisat2 aligner.
Read counting from the alignment data was performed by FeatureCounts. The feature count data was then analyzed by edgeR to determine significance of differential expression of KO compared to WT brain.
Assembly: GRCm39
Supplementary files format and content: comma separated file

source_name: whole brain

extract_protocol:
Total RNA was isolated from day 15 fetal brain of WT and KO mice, in three biological replicates, using an AllPrep DNA/RNA Mini Kit (Qiagen, Cat No./ID: 80204) following the manufacturer’s instruction. Sample was homogenized with 500 ul -1 ml RLT buffer (Qiagen, Cat No./ID: 79216) supplemented with 5μl of 2-mercaptoethanol. The homogenate was transferred to a fresh tube and centrifuged for 1 minute at ≥ 8000 x g. From the supernatant, 750μl was transferred to fresh tube and mixed with 1 volume 70% ethanol to precipitate RNA. RNA was eluted in 30μl nuclease-free water twice to a total volume of 60μl. Concentration of RNA was determined using Nanodrop 1000 spectrophotometer (Thermo Fisher Scientific). RNA Integrating Number (RIN) was determined (using Agilent2100).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: whole brain

value: week 70

value: Cav1 KO


title: ET66

description: rm.f.results.csv.gz

value: female


title: ZmRPN1-WT-AA-rep3

description:
WT
RPN1-AA-aa-genecounts.txt


title: LagPhase_Rep2_30min

source_name: cells, 30 min after inoculation on soft-agar, rep.2


title: ET65

description: rm.f.results.csv.gz


title: Wildtype (W) day 15 fetal brain rep3

description: Illumina

value: day 15 fetus


title: ET64

description: rm.f.results.csv.gz

value: tahd negative


title: ZmRPN1-WT-AA-rep2

description:
WT
RPN1-AA-aa-genecounts.txt