title: HSD, ICHD7, 2, HSPC

city: Taiepi

first: Che-Feng

last: Chang

address: No. 1, Sec. 1, Jen-Ai Rd.

country: Taiwan

institute: National Taiwan University College of Medicine

data_processing:
Sequencing reads were aligned to the mouse reference (mm10) using Rsubread aligner (v.1.32.4) and mapped reads were quantified by gene-level using featureCounts
Genes with counts above 10 counts per million in at least three samples went through further analysis
Trimmed Mean of M-values method was performed for normalization using edgeR (v3.24.3)
Assembly: mm10
Supplementary files format and content: Comma separated files include CPM values for each sample

source_name: Bone marrow

extract_protocol:
Total RNA was isolated using miRNeasy Micro Kit (Qiagen). RNA quality was assessed by Qsep100 (BiOptic Inc.) and Qubit 3 fluorometer (Thermo Fisher Scientific)
RNA sequencing libraries were generated using a SMART-Seq Stranded Kit (Takara Bio) according to the manufacturer's instructions.

value: Bone marrow

value: hematopoietic stem and progenitor cells

tag: diet

value: high salt diet

value: Intracerebral blood injection


title: RNAseq_2C_doubke_KD_rep1

status: Public on Aug 29 2023

type: SRA

city: Shinjuku

first: Haruhiko

last: Siomi

state: Tokyo

address: 35 Shinanomachi

department: Department of Molecular Biology

country: Japan

institute: Keio University School of Medicine

library_source: transcriptomic

data_processing: Base calling was performed using bcl2fastq v2.20 to generate raw reads.  Quality control and adapter trimming was done using fastp (Chen et al., 2018) v0.23.2.  For RNA-seq, quality controlled reads were aligned to GRCm38.p6 reference genome using STAR (Dobin et al., 2013) v2.7.9a with default arguments. Reads were counted against GRCm38.p6 comprehensive gene annotation (Frankish et al., 2020) and mm10 repeats from UCSC RepeatMasker using FeatureCounts (Liao et al., 2014) v2.0.1 with multi mapping reads discard for non-TE features and count fractionally for TEs. For CUT&RUN-seq, quality controller reads were aligned to GRCm38.p6 reference genome using Bowtie2 (Langmead and Salzberg, 2012) v2.4.1 with default arguments.  For CUT&RUN, Peaks were called in each biological replicated using MACS3 (Zhang et al., 2008) v3.0.0a6 callpeak function (-f BAMPE). Quantitative histone modification analysis with replicated samples was performed using MAnorm2 (Tu et al., 2021) v1.2.0.  For visualization of CUT&RUN results, alignment tracks were generated using deepTools (Ramírez et al., 2016) v3.5.1 bamCoverage function (--binSize 10 --normalizeusing CPM --smoothLength 30). Visualization of genomic tracks was performed using trackplot (Pohl and Beato, 2014) v1.3.10.

molecule: total RNA

organism: Mus musculus

source_name: emrbyo

growth_protocol: Eight-weeks old female and male B6D2F1 (BDF1) mice were purchased from the Japan SLC, Inc. All animal experiments were reviewed and approved by the Institutional Animal Care and Use Committee (protocol no. 09105-(10) and 11045-(6)) at Keio University, where mice were maintained and fed ad libitum with standard diet and water in a temperature- and light-controlled room (23℃±3℃, 14/10 hour light/dark cycle).

extract_protocol:
For RNA-seq of embryos, 30 middle-2C embryos were collected 20 hours after microinjection in each independent biological replicates. Zona pellucida was removed by treating the embryos with Acidic Tyrode’s solution. For RNA-seq of culture cells, total RNA was prepared using RNeasy Kit according to the manufacturer’s instruction. The RNA solution was subjected to TURBO DNase treatment according to the manufacturer’s instructions to remove genomic DNA carryover. For CUT&RUN, 1×105 culture cells freshly prepared by trypsin digestion were used to perform CUT&RUN assay with CUT&RUN Assay Kit (Cell Signaling Technology, 86652) according to the manufacturer’s instructions.
For RNA-seq of embryos, libraries were constructed with SMART-Seq Stranded Kit (TaKaRa, 634442) and indexed with SMARTer RNA Unique Dual Index Kit (TaKaRa, 634451) according to the manufacturer’s instructions. For RNA-seq of culture cells, libraries were constructed using 1µg total RNA with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, E7760L) and indexed with NEBNext Multiplex Oligos for Illumina (NEB, E6440S) according to the manufacturer’s instructions. For CUT&RUN, enriched DNAs were subjected to library construction using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645L) with the adapter ligation step performed at 50°C instead of 65°C to prevent denature of small DNA inserts. The libraries were indexed with NEBNext Multiplex Oligos for Illumina according to the manufacturer’s instructions.

treatment_protocol: 8-weeks-old BDF1 female mice were injected with 150µL CARD HyperOva (Kyudo Co., Ltd.). After 48 hours, the female mice were injected with 5IU hCG (ASKA Animal Health Co., Ltd.) and mated with BDF1 male mice. After 22 hours, PN3 zygotes were collected. Cumulus cells were removed by briefly culture the zygotes in KSOM medium (Merck, MR-101-D) supplemented with 0.3µg/µL hyaluronidase (Merck, H4272). Embryos were cultured in KSOM medium drops covered with liquid paraffin (Nacalai Tesque, 26137-85) under 5% CO2 at 37°C. After 4 hours, PBS containing either 40µM scramble ASO, 20µM anti-Dux ASO, 20µM anti-Obox4 ASO, 40µM equal molar anti-Dux/anti-Obox4 ASO mixture, or 40µM equal molar anti-Dux/anti-Obox4 ASO mixture with 100ng/μL codon-optimized Obox4 mRNA were microinjected into male pronuclei of zygotes using FemtoJet 4i microinjector (Eppendorf, 5252000013).

tag: tissue

value: emrbyo

tag: cell type

value: 2C embryo

tag: genotype

value: WT

tag: treatment

value: Dux/Obox4 double KD

tag: background strain


title: HSD, ICHD7, 3, HSPC

department: Physiology


title: X15_OGD-TIA

city: Berlin

first: Ria

last: Göttert

address: Charitéplatz 1

department: experimental Neurology

country: Germany

institute: Charité

data_processing:
quality control checks on raw sequence data was performed using FastQC
spliced sequence alignment was performed using STAR
Estimation of gene and isoform expression was performed using eXpress
Differential gene expression was performed using DESeq2
Assembly: Mus_musculus.GRCm38.92.gtf
Supplementary files format and content: csv  (comma-separated values) file includes TMM and FPKM values for each sample

source_name: primary cortical neurons

growth_protocol: Cells were seeded in 6-well plates containing neurobasal medium supplemented with B27, Pen/strep, L-glutamine and glutamate (2.5 ml medium, 1.5x10^6 cells per well). The cells were incubated at 37 °C with 5% CO2 and were fed every 3–4 days in vitro (DIV) with fresh medium without glutamate.

extract_protocol:
The total RNA was extracted at 6 hours after OGD using the NucleoSpin® XS Kit following manufacturer’s guidelines (MACHEREY-NAGEL GmbH & Co. KG).
Libraries were prepared from total RNA using Illumina TruSeq Stranded mRNA Library Prep Kit and sequenced with 50 single-end reads. 18 - 23 million reads per sample were aligned to the reference genome.

treatment_protocol: Primary cortical neurons at 8 DIV were pretreated with vehicle or 10 μM TIA. 24 hours later; the cells were subjected to SHAM or 3 h-OGD followed by 6 hours of reoxygenation.

value: primary cortical neurons

value: wt

value: OGD-Tianeptine


title: sunflower stem, ZT5, lit side, rep2

city: Davis

first: Stacey

last: Harmer

state: California

address: One Shields Ave

department: Plant Biology

country: USA

institute: University of California Davis

data_processing:
Reads were filtered for quality using fastx toolkit so that at least 95 percent of bases must have a score of 20
Read counts were generated using salmon-1.4.0 against a transcriptome biult using cufflinks v2.2.1 gffread using the Ha412HOv2.0 genome and the Eugene annotation (HAN412_Eugene_curated_v1)
Counts were then normalized using edgeR TMM method and counts-per-million were extracted
Assembly: Ha412HOv2.0 genome and the Eugene annotation (HAN412_Eugene_curated_v1)  from the sunflower genome database
Supplementary files format and content: phototropism_counts.csv, contains the raw Salmon generated counts of the phototropism data
Supplementary files format and content: phototropism_cpm.csv, contains the edgeR normalized counts-per-million of the phototropism data
Supplementary files format and content: Heliotropism_counts.csv, contains the raw Salmon generated counts of the heliotropism data
Supplementary files format and content: Heliotropism_cpm.csv, contains the edgeR normalized counts-per-million of the heliotropism data

molecule: polyA RNA

organism: Helianthus annuus

source_name: stem

growth_protocol: Sunflower seeds (HA412-HO) were obtained from USDA North Central Regional Plant Introduction Station (USDA Germplasm Resources Information Network ID: PI 603993). Seeds were germinated in flats (filled with SunGro® Sunshine® mix #1) covered with a lid for two days. Lids were then removed and plants were grown in controlled environment chambers in 16 light:8 dark with 180 µmol m–2  s–1 fluorescent light at constant 25 °C.

extract_protocol:
RNA was extracted according to the high-throughput method found in "A High-Throughput Method for Illumina RNA-seq Library Preparation" from Kumar et al. 2012.
RNA-seq libraries were prepared according to the high-throughput method found in "A High-Throughput Method for Illumina RNA-seq Library Preparation" from Kumar et al. 2012.

treatment_protocol: For phototropism experiments, two-week old chamber-grown sunflowers were placed in front of unidirectional blue lights (Yescom 225 Blue LEDs Grow Light Ultrathin Panel, 280 µmol  m–2  s–1) in a growth chamber at constant 25 °C. Plants were placed in front of the lights and ZT3 and tissue was collected from the shaded and lit sides of stems at 9 different timepoints from ZT3 to ZT21

value: stem

tag: strain

value: Lit side

tag: time

tag: experiment

value: phototropism


title: HSD, ICHD7, 1, HSPC


title: ND, ICHD7, 3, HSPC

value: normal diet


title: sunflower stem, ZT5, lit side, rep1


title: ND, ICHD7, 2, HSPC


title: RNAseq_2C_rescue_KD_rep2

value: Dux/Obox4 double KD rescued by Obox4 mRNA


title: X12_OGD-VEH

value: OGD-Untreated


title: sunflower stem, ZT5, shaded side, rep5

value: Shaded side


title: ND, ICHD7, 1, HSPC

value: Bone marrow

value: hematopoietic stem and progenitor cells


title: sunflower stem, ZT5, shaded side, rep6


title: sunflower stem, ZT5, shaded side, rep4


title: HSD, 3, HSPC

value: high salt diet


title: X10_OGD-VEH


title: X16_OGD-TIA


title: X11_OGD-VEH


title: sunflower stem, ZT5, shaded side, rep3


title: X14_OGD-TIA


title: HSD, 2, HSPC


title: sunflower stem, ZT5, shaded side, rep2


title: X8_CONTROL-TIA

value: Control-Tianeptine


title: X9_OGD-VEH


title: BF638R_WT Low iron + oxygen exposure Rep2

type: RNA

city: Greenville

first: Edson

middle: R

last: Rocha

state: NC

address: 600 Moye Blvd.

department: M

institute: East Carolina University Brody School of Medicine

description: This sample is of the Bacteroides fragilis 638R fur deletion mutant second of two independent biological replicates from two separate cultures in low iron conditions.

hyb_protocol: Hybridization was performed by at the FSU NimbleGen Microarray Facility, using standard protocols as described previously (Sund et al., 2008, Mol. Microbiol. 67:129-142)

scan_protocol: Scanning was performed by at the FSU NimbleGen Microarray Facility, using standard protocols as described previously (Sund et al., 2008, Mol. Microbiol. 67:129-142)

data_processing:
Raw data (pair files) were subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185) using NimbleGen Systems DEVA 1.1 software as described on their web site. The RMA processed data was averaged and log2 transformed (see *.calls files).
Raw data (pair files) were subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185) using NimbleGen Systems DEVA 1.1 software as described on their web site. The RMA processed data was averaged and log2 transformed (see *.calls files).

organism: Bacteroides fragilis 638R

source_name: Bacteroides fragilis 638R Wild type

label_protocol: Labeling was peformed by at the FSU Nimblegen Microarray Facility using standard protocols as described previously (Sund et al., 2008, Mol Microbiol. 67:129-142).

growth_protocol: Overnight cultures of Bacteroides fragilis 638R wild type or mutant strains were diluted into minimal defined media supplemented with 5 microgram/ml protoporphyrin IX containing 100 micromolar iron sulfate or 50 micromomolar 2,2-bipyridyl and exposed to atmospheric air (oxygen exposure) for 1 hour.

extract_protocol: Total RNA was isolated by the hot phenol method and treatd as described by Sund et al., 2008, Mol. Microbiol. 67:129-142.

treatment_protocol: Bacterial cultures were grown to mid-logarithmic phase (O.D. 550 nm of 0.3-0.4), exposed to oxygen for 1h, and submitted to total RNA extract by the hot phenol method.

value: Wild type


title: BF638R_fur_mut Low iron + oxygen exposure Rep1

description: This sample is of the Bacteroides fragilis 638R wild type first of two independent biological replicates from two separate cultures in high heme conditions.

source_name: Bacteroides fragilis 638R fur deletion mutant

value: fur deletion mutant


title: X13_OGD-TIA


title: X7_CONTROL-TIA


title: BF638R_fur_mut Low iron + oxygen exposure Rep2

description: This sample is of the Bacteroides fragilis 638R wild type second of two independent biological replicates from two separate cultures in high heme conditions.


title: sunflower stem, ZT5, shaded side, rep1

value: WT


title: BF638R_WT Low iron + oxygen exposure Rep1

description: This sample is of the Bacteroides fragilis 638R fur deletion mutant first of two independent biological replicates from two separate cultures in low iron conditions.


title: BF638R_fur_mut High iron + oxygen exposure Rep2

description: This sample is of the Bacteroides fragilis 638R fur deletion mutant second of two independent biological replicates from two separate cultures in high iron conditions.


title: sunflower stem, ZT4, lit side, rep6


title: ND, 2, HSPC


title: BF638R_fur_mut High iron + oxygen exposure Rep1

description: This sample is of the Bacteroides fragilis 638R fur deletion mutant first of two independent biological replicates from two separate cultures in high iron conditions.


title: ND, 1, HSPC


title: BF638R_WT High iron + oxygen exposure Rep2

description: This sample is of the Bacteroides fragilis 638R wild type swecond of two independent biological replicates from two separate cultures in low iron conditions.

source_name: Bacteroides fragilis 638R wild type


title: X5_CONTROL-TIA

value: primary cortical neurons


title: X6_CONTROL-TIA

value: wt


title: sunflower stem, ZT4, lit side, rep5


title: BF638R_WT High iron + oxygen exposure Rep1

description: This sample is of the Bacteroides fragilis 638R wild type first of two independent biological replicates from two separate cultures in low iron conditions.


title: wt.7d_6

city: Cologne

first: Ulrike

last: Göbel

state: NRW

address: Joseph Stelzmann Strasse, 26

department: Bioinformatics Core Facility

institute: CECAD Research Center

data_processing:
Trimming: Cutadapt version 2.10 was used to iteratively trim (1) the Illumina Reverse Read2 Sequencing Primer and (2) 3’ polyA runs of length >= 18.
Mapping: Trimmed reads were mapped to a concatenation of the mouse genome (Mus_musculus.GRCm38.dna.chromosome.*.fa.gz, downloaded from ftp://ftp.ensembl.org/pub/release-100/fasta/mus_musculus/dna/) and the ERCC92 Spike In sequences (downloaded from https://assets.thermofisher.com/TFS-Assets/LSG/manuals/ERCC92.zip), using subread-align version v2.0.1 with parameters -t 0 -d 50 -D 600 --multiMapping -B 5.
Counting: Genomic matches were counted using featureCounts v2.0.1 with parameters -F "GTF" -t "exon" -g "gene_id" --minOverlap 20 -M --primary -O --fraction -J -Q 30 -T 4. The genome annotation used was Mus_musculus.GRCm38.100.gtf (downloaded from ftp://ftp.ensembl.org/pub/release-100/gtf/mus_musculus/), augmented by entries for the ERCC92 Spike Ins.
Normalization: Counts Per Million (CPM) were computed according to the measure’s definition, using R version 4.0.0.
Assembly: mm10 (chromosome sequences from ftp://ftp.ensembl.org/pub/release-100/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.chromosome.*.fa.gz, annotation from ftp:  //ftp.ensembl.org/pub/release-100/gtf/mus_musculus/Mus_musculus.GRCm38.100.chr.gtf.gz).
Supplementary files format and content: A comma-separated values (csv) file is a delimited text file that uses a comma to separate values. Each line of the file is a data record. Each record consists of one or more fields, separated by commas (definition from https://en.wikipedia.org/wiki/). Here, each record except the first one corresponds to a gene. The first record is a header containing names for the comma-separated fields (=column names). The first comma separated field in each record holds the Ensembl ID of the corresponding gene, and the second field holds the gene symbol. All subsequent fields are numerical and hold read counts per gene in the samples indicated by the column names. The counts are the direct output of featureCounts in “raw_readcounts.csv”, and have been normalized to Counts Per Million in “CPM_readcounts.csv”.

source_name: proximal small intestinal tissue

extract_protocol:
Small intestinal tissues were disrupted using Precellys 24 tissue homogenizer. Isolation of RNA from small intestinal tissues was performed using a NucleoSpin RNA isolation kit from Macherey Nagel according to manufacturer’s instructions. RNA quality was evaluated based on RNA integrity number (RIN) and OD260/280 and OD260/230 ratios. RIN value was determined using TapeStation4200 and RNA Screen Tapes from Agilent Technologies.
Lexogen 3' QuantSeq Kit (FWD protocol).

value: proximal small intestinal tissue

tag: time point


title: BF638R_WT High iron anaerobic control Rep2

description: This sample is of the Bacteroides fragilis 638R wild type second of two independent biological replicates from two separate cultures in high iron conditions.


title: HSD, 1, HSPC


title: wt.7d_5


title: sunflower stem, ZT4, lit side, rep3

value: stem


title: X3_CONTROL-VEH

value: Control-Untreated


title: wt.7d_4


title: BF638R_WT High iron anaerobic control Rep1

description: This sample is of the Bacteroides fragilis 638R wild type first of two independent biological replicates from two separate cultures in high iron conditions.


title: X2_CONTROL-VEH


title: sunflower stem, ZT4, lit side, rep1

value: Lit side

value: phototropism


title: wt.7d_3


title: ND, 3, HSPC

value: normal diet


title: X1_CONTROL-VEH


title: sunflower stem, ZT4, lit side, rep2


title: group1-3

city: 上海

first: 建港

last: 郭

address: 浦江智谷25号楼

country: China

institute: 欧易生物

data_processing:
CLC Genomics Workbench v 11.0
Assembly: NCBI_GRCh38.p13
Supplementary files format and content: tab-delimited text file includes FPKM for each Sample

organism: Homo sapiens

extract_protocol:
RNA was harvested usinge TRIzol reagent (Invitrogen, CA, USA). 13 ug of total RNA was used for the construction of seduencina libraries
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-seq Library Prep kit folowing manufacturer's protocols.

tag: cell line

value: YTHDC2 knockout


title: group2-1


title: group2-2


title: group2-3


title: wt.7d_2


title: NC-Foxc2-KO

city: Chicago

first: Pieter

middle: Russell

last: Norden

state: IL

address: 303 E Superior Street

department: Feinberg Cardiovascular and Renal Research Institute

institute: Northwestern University Feinberg School of Medicine

data_processing:
Sequencing data was demultiplexed using Cell Ranger mkfastq version 4.0.0
FASTQ files were aligned and counted to mm10 (10X Genomics transcript version 1.2.0) using Cell Ranger version 4.0.0
Matrix files were analyzed using the browser-based tool BIOMEX 1.0-5 (Taverna et al, 2020, Nucelic Acid Res)
Genome_build: mm10
Supplementary_files_format_and_content: Filtered and compiled matrix output file following BIOMEX 1.0-5 analysis
Supplementary_files_format_and_content: tab-delimited matrix output files from Cell Ranger count
Supplementary_files_format_and_content: cloupe files from Cell Ranger output

source_name: anterior eye segment

extract_protocol:
For single-cell RNA sequencing, eyes were pooled from 4 –6 individuals of both 3 –4 week old Foxc2fl/flcontrol and NC-Foxc2-/-mice. The anterior segment from each eye was dissected in ice-cold dye-free DMEM containing 10% FBS and the iris was gently removed using fine forceps. Pooled tissues from each group were then chopped with Vannas Scissors in ice-cold DMEM, then digested in DMEM containing 10% FBS, 1 mg/mL Collagenase A (Millipore Sigma), and 10 μM Y-27632 (R&D Systems) for 2 hours at 37°C. Tissues were then washed in 1X PBS solution, then further digested in 0.25% Trypsin solution containing 10 μM Y-27632 and 0.2 mg/mL DNAse I (Sigma) at 37°C for 25 minutes with shaking and gentle trituration using a P1000 pipettor and wide-bore pipette tips. Following dissociation, the tissues were centrifuged and the supernatant was removed. Pelleted cells were washed and re-suspended in warm DMEM containing 10% FBS, then passed through a Flowmi 40 μm cell strainer before repeating centrifugation. Washing and centrifugation was repeated once more to pellet cells, which were then resuspended in 100  μL of ice-cold Hank’s balanced salt solution (HBSS) containing 1% BSA. Cell viability was assessed using the Cellometer Auto 2000 Cell Viability Counter. Cell viabilityof 70% was used as a minimum threshold.
Single cell 3’ gene expression libraries were constructed from samples using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics, Pleasonton, CA, USA) according to the manufacturer’s instructions. Libraries were then assessed for quality (TapeStation 4200, Agilent, Santa Clara, CA, USA) and then processed for paired-end sequencing on an Illumina HiSeq 4000 platform (Illumina, San Diego, CA, USA). 10,000 cells were targeted for each sample with a sequencing depth of 20,000 read pairs per cell.

value: anterior eye segment

value: mixed

value: Foxc2 flox/flox;Wnt1Cre+

tag: age

value: 4 weeks-old


title: group1-2


title: sunflower stem, ZT4, lit side, rep4


title: sunflower stem, ZT4, shaded side, rep5

value: Shaded side


title: group1-1


title: wt.7d_1


title: X4_CONTROL-VEH


title: sunflower stem, ZT4, shaded side, rep4


title: Control

value: Foxc2 flox/flox


title: AV_AATBC_3

city: Munich

first: Stefan

last: Kotschi

address: Max-Lebsche-Platz 30

department: Institute for Cardiovascular Prevention

institute: Klinikum der Universitaet Muenchen

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were mapped to the reference genome using HISAT2 software. HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome. These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads.
Because transcriptome annotations are still incomplete, most RNA-seq studies will reveal novel genes and transcripts. The Stringtie was used to assemble the set of transcript isoforms of each bam file obtained in the mapping step. gffcompare can compare Strintie assemblies to reference annotation files and help sort out new genes from known ones.
Featurecounts was used to count the read numbers mapped of each gene, including known and novel genes. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. RPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: grch38
Supplementary files format and content: xls with samples in columns

source_name: hMADS

growth_protocol: Human multipotent adipose derived stem (hMADS) cells were kept until confluency in proliferation medium (Dulbecco’s Modified Eagle’s Medium (DMEM), (Lonza, Switzerland # BE12-707F) supplemented with 10 % FBS (Sigma, Germany), 10 mmol/l 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) (Gibco, Germany #15630056), 2.5 ng/ml human fibroblast growth factor-basic (hFGF2) (PeproTech, Germany #100-18B), 50 mg/ml penicillin, and 50 mg/ml streptomycin (Gibco, Germany #15140122), followed by 48 h of incubation without hFGF2. The induction of the differentiation towards adipocytes was started (d0) using a cocktail of DMEM/Ham’s F12 (Lonza, Switzerland # BE12-615F) supplemented with 10 mg/ml apo-transferrin (Sigma, Germany # T1428), 10 nM insulin (Sigma, Germany # I 9278), 100 nM rosiglitazone (Cayman, Germany #71740), 0.2 nM triiodothyronine (T3) (Sigma, Germany #6893-02-3), 1 mmol/l dexamethasone (DEX) (Sigma, Germany # D4902), 1 mM 3-isobutyl-1-methylxanthine (IBMX) (Sigma, Germany #28822-58-4). After 48h the induction medium was replaced by the differentiation medium containing DMEM/Ham’s F12, 10mg/ml transferrin, 10nM insulin, 0.2nM triiodothyronine and 1μM rosiglitazone. Until day 9, the medium was changed every other days. At day 9, thermogenic differentiated hMADS cells were obtained with chronic rosiglitazone treatment until day of completion of the experiment (d14).

extract_protocol:
RNA of cells and tissues were extracted using TRIzol (Invitrogen, #15596026) and NucleoSpin® RNA kit (Macherey-Nagel, #740955.250) according to the manufacturer’s instruction.
NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA)

treatment_protocol: The expression of AATBC was modulated in vitro using antisense oligonucleotide-mediated knockdown (ASO, Exiqon, #634048-6, #634048-4), siRNA-mediated knockdown (Lincode Human AATBC (Horizon Discovery, #284837) and adenovirus (AV) mediated overexpression (VectorBuilder, #AVM (VB150925-10024) + GFP). White hMADS were transfected at day 12 of differentiation with 30 nmol of siRNA or ASO at day 10 using LipofectamineTM RNAiMAX transfection reagent (Thermo Scientific, #13778075) according to the manufacturer’s protocol. For overexpression, white hMADS cells were infected with 200 particles of virus per cell. 24 h later, the transfection medium was removed and replaced by the suitable differentiation medium. 48 h after transfection cells were harvested.

value: hMADS

value: human mesenchymal stem cells

value: AV AATBC


title: tg.7d_6

value: tg


title: sunflower stem, ZT4, shaded side, rep3

value: WT


title: tg.7d_5

value: proximal small intestinal tissue


title: AV_AATBC_2


title: sunflower stem, ZT4, shaded side, rep6

value: stem


title: tg.7d_4


title: sunflower stem, ZT4, shaded side, rep2


title: AV_AATBC_1


title: tg.7d_3


title: sunflower stem, ZT4, shaded side, rep1


title: tg.7d_2


title: AV_GFP_2

value: AV GFP control


title: sunflower stem, ZT3, lit side, rep5

value: Lit side

value: phototropism


title: AV_GFP_3


title: sunflower stem, ZT3, lit side, rep6


title: AV_GFP_1


title: tg.7d_1


title: wt.3d_7

value: wt


title: si_AATBC_4

value: siRNA AATBC


title: sunflower stem, ZT3, lit side, rep4


title: si_AATBC_3


title: sunflower stem, ZT3, lit side, rep3


title: BA_rep2

city: Shanghai

first: Junfeng

last: Wang

address: 399 Wanyuan Road

department: Department of Pediatric Surgery

institute: Chlidren's Hospital of Fudan University

description: Gene expression in the biliary atresia livers

hyb_protocol: The labeled cRNA was then used as probes to hybridized onto microarray.

scan_protocol: The arrays were scanned by Agilent Scanner G2505C (Agilent Technologies).

data_processing:
As for the data analysis, raw data of the array images was primarily acquired using feature extraction software (version10.7.1.1, Agilent Technologies), and analyzed by GeneSpring. Subsequently, the raw data were normalized with the quantile algorithm.
Differentially expressed genes (DEGs) were then identified with a fold change more than 2.0 and a P value less than 0.05 using unpaired 2-tailed t-test.

label_protocol: Total RNA was transcribed into double strand cDNA, and synthesized into cRNA labeled with Cyanine-3-CTP.

extract_protocol: The total RNA was isolated from liver tissues, and was quantified by the NanoDrop ND-2000 (Thermo Scientific) and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: The harvested liver samples were immediately frozen at -80℃ for further treatments.

value: liver

tag: gender

value: male


title: BA_rep3

value: female


title: BA_rep1


title: sunflower stem, ZT3, lit side, rep2


title: CTRL_rep3

description: Gene expression in the control livers


title: CTRL_rep2

description: Gene expression in the control livers


title: 7C-Ablation-p63-P2+16-d19-220824

city: Hannover

first: Lara

last: Gentemann

address: Welfengarten 1

department: Institute of Quantum Optics

institute: Leibniz University Hannover

data_processing:
BCL files were converted to FASTQ files using bcl2fastq Conversion Software version v2.20.0.422 (Illumina).
Raw data processing was conducted by use of nfcore/rnaseq (version 1.4.2) which is a bioinformatics best-practice analysis pipeline used for RNA sequencing data at the National Genomics Infrastructure at SciLifeLab Stockholm, Sweden. The pipeline uses Nextflow, a bioinformatics workflow tool. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results. The genome reference and annotation data were taken from GENCODE.org (Mus musculus; GRCm38.p6).
Normalization and differential expression analysis was performed on the internal Galaxy (version 20.05) instance of the RCU Genomics, Hannover Medical School, Germany with DESeq2 (Galaxy Tool Version 2.11.40.6) with default settings except for “Output normalized counts table”, which was set to “Yes” and all additional filters were disabled (“Turn off outliers replacement”, “Turn off outliers filtering”, and “Turn off independent filtering” set “Yes”). The different conditions were selected as primary factor whereas the batch was used as secondary factor in DESeq2 analyses (two factor design).
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited txt file with DESeq2 normalized counts and results

source_name: lung; proximal airways

growth_protocol: Airway epithelial cells isolated from adult C57BL/6J wt mouse lungs were embedded into Cultrex basement membrane extract, covered with conditioned medium (DMEM, high glucose, GlutaMAX™, pyruvate with 50 % L-WRN-supernatant (ATCC® CRL3276™ in DMEM, high glucose, GlutaMAX™, pyruvate plus 10 % fetal calf serum), 1x N2, 1× B27, 50 ng/μL recombinant mouse epidermal growth factor, 10 μM Y-27632, 1× Cellshield) and kept at 37 °C, 5 % CO2 and a humidified atmosphere. Organoid formation was observed within 7 days of culture.

extract_protocol:
Organoid harvest was carried out using Trevigen Cultrex 3-D Cell Harvesting Kit. Organoids were stored in 1x RNA Shield at -80°C until RNA isolation (maximum storage time: 3 weeks). RNA of all samples was isolated in one run using ZYMO Quick-DNA/RNA Microprep Plus Kit.
Library generation, quality control, and quantification:  150ng of total RNA per sample were utilized as input for mRNA enrichment procedure with ‘NEBNext® Poly(A) mRNA Magnetic Isolation Module’ (E7490L; New England Biolabs) followed by stranded cDNA library generation using ‘NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina’ (E7760L; New England Biolabs). All steps were performed as recommended in user manualE7760 (Version 1.0_02-2017; NEB) except that all reactions were downscaled to 2/3 of initial volumes.  cDNA libraries were barcoded by dual indexing approach, using ‘NEBNext Multiplex Oligos for Illumina – 96 Unique Dual Index Primer Pairs’ (6440S; New England Biolabs). All generated cDNA libraries were amplified with 10 cycles of final pcr.  One additional purification step was introduced at the end of the standard procedure, using 1.2x ‘Agencourt® AMPure® XP Beads’ (#A63881; Beckman Coulter, Inc.). Fragment length distribution of individual libraries was monitored using ‘Bioanalyzer High Sensitivity DNA Assay’ (5067-4626; Agilent Technologies). Quantification of libraries was performed by use of the ‘Qubit® dsDNA HS Assay Kit’ (Q32854; ThermoFisher Scientific).   Library denaturation and Sequencing run:  Equal molar amounts of individually barcoded libraries were pooled for a common sequencing run in which each analyzed library constituted 16.7% of overall flowcell / run capacity. The library pool was denatured with NaOH and was finally diluted to 1.8pM according to the Denature and Dilute Libraries Guide (Document # 15048776 v02; Illumina). 1.3ml of the denatured pool was loaded on an Illumina NextSeq 550 sequencer using a Mid Output Flowcell (130M cluster) for 2x75bp paired-end reads (20024904; Illumina). Sequencing was performed with the following settings: Sequence reads 1 and 2 with 76 bases each; Index reads 1 and 2 with 8 bases each.

treatment_protocol: 45 organoids were tranferred into fresh Cultrex the day before experiment. Medium was changed to unsupplemented Fluorobrite DMEM 1 h before femtosecond laser treatment, by which 10 neighboring cells of each organoid were ablated. No cells were ablated in control samples. Organoids were harvested 4.5 hours post laser treatment.

value: lung; proximal airways

value: organoids derived from primary airway epithelial cells

tag: genetic modification

value: lentivirally transduced with expression vector coding for Histone2A-mCherry fusion protein under control of p63 promoter

value: control/no treatment


title: si_AATBC_2

value: hMADS

value: human mesenchymal stem cells


title: CTRL_rep1

description: Gene expression in the control livers


title: sunflower stem, ZT3, lit side, rep1

value: WT


title: si_AATBC_1


title: 7-Ablation-p63-P2+16-d19-220824

value: fs laser-based ablation of 10 cells


title: wt.3d_2

value: proximal small intestinal tissue


title: sunflower stem, ZT3, shaded side, rep6

value: stem

value: Shaded side


title: 6-Ablation-p63-P2+16-d18-220823


title: wt.3d_3


title: sunflower stem, ZT3, shaded side, rep5

value: phototropism


title: si_scramble_3

value: siRNA scramble


title: 4-Ablation-p63-P2+15-d14-220726


title: 5C-Kontrolle-p63-P2+15-d15-220727


title: sunflower stem, ZT3, shaded side, rep4


title: 6C-Ablation-p63-P2+16-d18-220823


title: wt.3d_1

value: wt


title: wt.3d_5


title: wt.3d_4


title: 4C-Ablation-p63-P2+15-d14-220726


title: sunflower stem, ZT3, shaded side, rep3


title: si_scramble_2


title: tg.3d_7

value: tg


title: tg.3d_6


title: si_scramble_1


title: sunflower stem, ZT3, shaded side, rep2


title: 1C-Kontrolle-p63-P2+14-d14-220708


title: 3C-Kontrolle-p63-P2+14-d20-220714


title: sunflower stem, ZT3, shaded side, rep1


title: si_scramble_4


title: LCS9172_NK92_WT_RAJI_2

city: West Lafayette

first: Marxa

middle: Leao

last: Figueiredo

state: IN

address: 625 Harrison St

department: Basic Medical Sciences

institute: Purdue University

description: NK92 wild-type cocultured with RAJI

data_processing:
Cutadaptand perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases, followed by sequence quality verification using FASTQC.
HISAT2 was used to map reads to the human genome.
The mapped reads of each sample were assembled using StringTie. All transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare. After the ﬁnal transcriptome was generated, StringTie and ballgown was used to estimate the expression levels of all transcripts.
StringTie was used to perform expression level for mRNAs by calculating FPKM. mRNAs differential expression analysis were performed by R package DESeq2.
Assembly: GRCh38 (Ensembl release-101)
Supplementary files format and content: Tab delimited text file containing raw counts for each sample

source_name: Blood

growth_protocol: Natural Killer 92 (NK-92) cells were maintained in serum free X-VIVO 10 media (Lonza, Cologne, Germany) containing 5% human heat inactivated AB plasma (Brazilian Blood Donation Service of Hemocentro de Ribeirao Preto), supplemented with 500 IU/ml IL-2 (Clinigen), as previously described (17,18) . Human leukemia cell lines K562, Raji and NALM-6 were cultured in RPMI medium (ThermoFisher Scientific) supplemented with 10% Fetal Bovine Serum (FBS). All cell lines were tested negative for mycoplasma using the MycoAlertPLUS Mycoplasma Detection Kit (Lonza) (reference value < 1.0).

extract_protocol:
Total RNA from NK cells was isolated from two biological replicates. In short, RNA was isolated using RNeasy kit (Qiagen) according to manufacturer's protocol. Poly(A) RNA sequencing library was prepared following Illumina's TruSeq-stranded-mRNA protocol and conducted by LC Sciences (Houston, TX, USA). Poly(A) tail-containing mRNAs were purified using oligo-dT Briefly, magnetic beads with two rounds of purification, and fragmented using divalent cation buffer at elevated temperature. Quality control analysis and quantification of the sequencing library were performed using an Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip.
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol. RNA integrity was checked with Agilent Technologies 2100 Bioanalyzer. Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification. After purification, poly(A) RNA was fragmented using divalent cation buffer in elevated temperature. The DNA library construction is shown in the following workflow. Quality control analysis and quantification of the sequencing library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip.

treatment_protocol: NK cells were cocultured with Raji cell 10:1 ratio (E:T) for 24h at 37°C, enough time to eliminate target cells.

value: Blood

value: Natural Killer


title: LCS9172_NK92_WT_RAJI_1

description: NK92 wild-type cocultured with RAJI


title: 5-Ablation-p63-P2+15-d15-220727

value: lung; proximal airways


title: tg.3d_3


title: tg.3d_2


title: 3-Ablation-p63-P2+14-d20-220714

value: organoids derived from primary airway epithelial cells


title: tg.3d_1


title: wt.3d_6


title: 1-Ablation-p63-P2+14-d14-220708

value: lentivirally transduced with expression vector coding for Histone2A-mCherry fusion protein under control of p63 promoter


title: LCS9172_NK92_WT_1

description: NK92 wild-type


title: LCS9172_NK92_CAR_RAJI_2

description: NK92 transducted with Lv_CAR specific for CD19 (CAR.19) and cocultured with RAJI


title: LCS9172_NK92_WT_2

description: NK92 wild-type


title: LCS9172_NK92_CAR_IL15RA_RAJI_2

description: NK92 transducted with Lv_CAR specific for CD19 (CAR.19), a P2A and IL-15 and IL15Ra and cocultured with RAJI


title: TIAL1_iCLIP_B cells

city: Toulouse

first: Manuel

middle: D

last: Diaz-Munoz

address: CHU Purpan, BP3028

country: France

institute: INSERM

data_processing:
See Konig et al. for all details (Nature Structural & Molecular Biology 17, 909–915 (2010)). Raw sequence reads were trimmed to remove both barcodes and adapters. AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT and CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
Remaining sequences were mapped to the mouse mm10 genome (Ensembl59 genome annotation) using Bowtie (Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).).
Deduplication and identification of unique cDNA counts was performed based on the  random bases present in the 5' barcode.
Position -1 of uniquely annotated reads to the genome was annotated as the crosslink site.
Peak enrichment analysis of Tial1 binding sites was performed. Unique Tia1 crosslink sites were identified as previously described (See Konig et al. for all details (Nature Structural & Molecular Biology 17, 909–915 (2010)). Briefly, 15 nucleotide windows flanking the crosslink site were generated, 100 permutations were allowed and multiple test correction of p-values (Benjamini-Hochberg) was performed to calculate FDR.
Assembly: mm10
Supplementary files format and content: tsv file contain the annotation of unique nucleotide crosslinks

source_name: Spleen

growth_protocol: Follicular B cells isolated using magenetic beads (Miltenyi) were stimulated with anti-IgM, anti-CD40 and rmIL4 for 48h.

extract_protocol:
RIPA buffer and sonication (10s, x3) was used for cell lysate and clarification. Protein:RNA complexes were immunoprecipitated for RNA extraction and small RNA library preparation
L3-ATT-App DNA Linker (/5rApp/WN ATT AGA TCG GAA GAG CGG TTC AG/3Bio/) linker primer and irCLIP_ddRT primer_19 (/5Phos/WWW GTATT NNNN AGA TCG GAA GAG CGT CGT GAT/iSp18/GGA TCC/iSp18/TAC TGA ACC GC) or irCLIP_ddRT primer_13 (/5Phos/WWW CCGGA NNNN AGA TCG GAA GAG CGT CGT GAT/iSp18/GGA TCC/iSp18/TAC TGA ACC GC) were used for library preparation as previously described for iCLIP

treatment_protocol: Stimulation with anti-IgM, anti-CD40 and rmIL4 for 48h. The, cells were washed with ice-cold PBS and irradiated with UV light (600 mJ/cm2, Stratalinker 2400).

value: Spleen

value: Primary B cells

value: B cell

value: anti-IgM, anti-CD40 and rmIL4 for 48h.


title: TIA1_iCLIP_B cells


title: LCS9172_NK92_CAR_RAJI_1


title: synovium from rat (rat ID #24) with medial meniscus transection surgery 6 weeks post-surgery

city: La Jolla

first: Padma

last: Natarajan

state: CA

address: 10550 N.Torrey Pines Road

department: CCBB

institute: The Scripps Research Institute

data_processing:
The high throughput RNA-seq data was initially processed with in-house custom scripts using BBTools (https://sourceforge.net/ projects/bbmap/) to obtain demultiplexed reads for each sample based on the inline barcodes. The 5’-end 10-base barcodes and 3’-end 12-base UMI information from read1 fastq were first incorporated into read2 fastq as part of sequence ID using UMI-tools. The read2 sequences (from the pre-deduplicated dataset) were analyzed using nf-core/RNA-seq pipeline v1.4.2 (implemented on Nextflow v20.07.1), which is an open-source and available at https://github.com/nf-core/rnaseq as part of the nf-core project. Reads2s were trimmed for adapters using trimGalore! V0.6.4 (https://www.bioinformatics.babraham.ac.uk/projects/trim_ galore/) and aligned to the rat genome (Rattus norvegicus) ENSEMBL build Rnor 6.0 using STAR v2.6.1d. Gene-level assignment was then performed using featurecounts v1.6.4. The gene expression matrix with raw gene counts was then used for differential gene expression analysis using the Bioconductor DESeq2 R package v1.20.0. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate (FDR). Genes with an adjusted P-value (padj) < 0.05 found by DESeq2 were assigned as significantly differentially expressed genes (DEGs). The uniquely mapped alignments resulting from alignments to the reference genome were deduplicated removing the PCR duplicates. The transcript UMI for each gene was counted for each sample using UMI-tools.
Assembly: Rattus norvegicus (Rnor 6.0)
Supplementary files format and content: gene counts matrix, FPKM matrix, TPM matrix

organism: Rattus norvegicus

source_name: synovium

extract_protocol:
Rats were euthanized 2 (n=8), 4 (n=8), or 6 (n=8) weeks after MMT. Cartilage from both the medial and lateral sides of tibial plateaus and femoral condyles, medial and lateral menisci, and synovium of both knees were collected. All visible synovium tissue was collected from the medial and lateral sides of the joint capsule and femoral condyles, distal to the meniscus and directly adjacent to the tibial plateau at all time points. Due to the very thin layer of synovium, it was not possible to collect exclusively the lining layer without some sub synovial adipose tissue. Tissues were homogenized with 350 uL TRIZOL using a homogenizer, for three 30 s intervals interrupted b y3 min breaks. The homogenized tissue was added to 70 uL ethanol. This mixture was vortexed, and the 100 uL supernatant was collected, centrifuged, and added to the mRNeasy Mini kit column (Qiagen) following manufacturer's instructions. Total RNA was eluted in 12 uL RNase-free water. The RNA integrity was determined using and Agilent Bioanalyzer and only samples with values >5 were used for RNA-seq.
The high throughput RNA-seq assay used was part of an early access kit from iGenomX Inc. Briefly, total RNA (50 ng) was placed in a solution containing 1.4X First Strand Buffer and barcode oligo dT primer and incubated at 80C for 10 min in 7 uL total volume, subsequently added was 4.5 mM DTT, barcoded template-switching oligonucleotide, 1.8 U/uL RNaseOUT (ThermoFisher), dNTP mix and Reverse Transcriptase in 11 uL final volume. Reactions were incubated 50 min at 42C, followed by 5 min at 85C. This was followed by addition of 2 uL reaction clean-up mix and incubated at 37C for 30 min and 80C for 20 min. Samples were pooled together, and cDNA products were purified by 1.2X SPRI bead clean-up procedure with SPRI bead mixture. cDNA products were taken directly into a PCR reaction containing 1X KAPA HiFi reaction mixture and 0.5 uM barcoded PCR primers of Illumina p5 and p7 sequences in 100 uL final volume. PCR products were first cleaned using 1X SPRI bead clean-up mix, and then separated on 2% agarose gels. Products approximately 350 bp-800 bp were excised and isolated using agarose gel dissolving buffer and clean-up and concentrator column (Zymo Research). Purified PCR products were quantified using Qubit dsDNA HS assay kit, analyzed on Agilent Tapestation, and sequenced on 100 cycle P2 flow cells with an Illumina NextSeq2000 sequencing instrument using paired-end sequencing (read1: 26 bases, read2: 94 bases, i5 and i8 indexes used 8 base reads).

treatment_protocol: All animal procedures were approved by the Scripps Research Institutional Animal Care and Use Committee. Male Lewis rats (n=42 total) were assigned to the following groups: 24 rats with MMT surgery on the right and sham surgery (SS) on the left knee for knee tissue collection and RNA sequencing at 2, 4 and 6 weeks (n=8 animals per time point); 18 rats with MMT surgery on the right and sham surgery on the left knee for knee histology at 2, 4 and 6 weeks (n=6 animals per time point). Animals were anesthetized with ketamine/xylazine cocktail (50 mg/kg Ketaved – Henry Schein, and 5 mg/kg Xylazine – AniSed respectively) by intraperitoneal injection, administered appropriate analgesics (Flunixin, 5 mg/kg subcutaneous injection), and the surgical site shaved and disinfected. A small incision was made on the medial right hind knee to expose the collateral ligament. The collateral ligament was transected, and the joint capsule opened sufficiently to expose the medial meniscus. The meniscus was transected completely, then the skin incision was closed, and pressure applied to the wound to prevent hematoma development. Animals were allowed to recover on a heated blanket and were returned to their home cage. Sham procedures were carried out in a similar fashion except the medial meniscus was not cut.

value: synovium

tag: timepoint

value: 6 weeks

tag: disease state

value: Medial Meniscus Transection


title: mESC_Obox4_KO_PlaB_plus_H3K27me3_rep2

description: CUT&RUN-enriched DNA

library_source: genomic

data_processing:
Library strategy: CTU&RUN
Base calling was performed using bcl2fastq v2.20 to generate raw reads.
Quality control and adapter trimming was done using fastp (Chen et al., 2018) v0.23.2.
For RNA-seq, quality controlled reads were aligned to GRCm38.p6 reference genome using STAR (Dobin et al., 2013) v2.7.9a with default arguments. Reads were counted against GRCm38.p6 comprehensive gene annotation (Frankish et al., 2020) and mm10 repeats from UCSC RepeatMasker using FeatureCounts (Liao et al., 2014) v2.0.1 with multi mapping reads discard for non-TE features and count fractionally for TEs.  For CUT&RUN-seq, quality controller reads were aligned to GRCm38.p6 reference genome using Bowtie2 (Langmead and Salzberg, 2012) v2.4.1 with default arguments.
For CUT&RUN, Peaks were called in each biological replicated using MACS3 (Zhang et al., 2008) v3.0.0a6 callpeak function (-f BAMPE). Quantitative histone modification analysis with replicated samples was performed using MAnorm2 (Tu et al., 2021) v1.2.0.
For visualization of CUT&RUN results, alignment tracks were generated using deepTools (Ramírez et al., 2016) v3.5.1 bamCoverage function (--binSize 10 --normalizeusing CPM --smoothLength 30). Visualization of genomic tracks was performed using trackplot (Pohl and Beato, 2014) v1.3.10.
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq reads (.csv)
Supplementary_files_format_and_content: CUT&RUN peaks (.narrowPeak or .broadPeak)
Supplementary_files_format_and_content: CUT&RUN read coverage (.bigwig)

molecule: genomic DNA

source_name: Obox4 KO mESC

extract_protocol:
For RNA-seq of embryos, 30 middle-2C embryos were collected 20 hours after microinjection in each independent biological replicates. Zona pellucida was removed by treating the embryos with Acidic Tyrode’s solution.  For RNA-seq of culture cells, total RNA was prepared using RNeasy Kit according to the manufacturer’s instruction. The RNA solution was subjected to TURBO DNase treatment according to the manufacturer’s instructions to remove genomic DNA carryover.  For CUT&RUN, 1×105 culture cells freshly prepared by trypsin digestion were used to perform CUT&RUN assay with CUT&RUN Assay Kit (Cell Signaling Technology, 86652) according to the manufacturer’s instructions.
For RNA-seq of embryos, libraries were constructed with SMART-Seq Stranded Kit (TaKaRa, 634442) and indexed with SMARTer RNA Unique Dual Index Kit (TaKaRa, 634451) according to the manufacturer’s instructions.  For RNA-seq of culture cells, libraries were constructed using 1µg total RNA with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, E7760L) and indexed with NEBNext Multiplex Oligos for Illumina (NEB, E6440S) according to the manufacturer’s instructions.  For CUT&RUN,  enriched DNAs were subjected to library construction using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645L) with the adapter ligation step performed at 50°C instead of 65°C to prevent denature of small DNA inserts. The libraries were indexed with NEBNext Multiplex Oligos for Illumina according to the manufacturer’s instructions.

value: culture cell (ESC)

tag: developmental stage

value: pladienolide B


title: mESC_Obox4_KO_PlaB_plus_H3K27me3_rep3

description: CUT&RUN-enriched DNA


title: meniscus from rat (rat ID #24) with medial meniscus transection surgery 6 weeks post-surgery

source_name: meniscus

value: meniscus


title: LCS9172_NK92_CAR_IL15RA_RAJI_1


title: mESC_Obox4_KO_PlaB_plus_H3K27me3_rep1

description: CUT&RUN-enriched DNA


title: tg.3d_5

value: proximal small intestinal tissue


title: LCS9172_NK92_CAR_IL15_RAJI_2

description: NK92 transducted with Lv_CAR specific for CD19 (CAR.19), a P2A and IL-15 anc coculture with RAJI


title: cartilage from rat (rat ID #24) with medial meniscus transection surgery 6 weeks post-surgery

source_name: cartilage

value: cartilage


title: tg.3d_4

value: tg


title: mESC_Obox4_KO_PlaB_plus_H3K27ac_rep3

description: CUT&RUN-enriched DNA


title: synovium from rat (rat ID #24) with sham surgery 6 weeks post-surgery

value: Sham Surgery


title: Human WAT, patient 4

data_processing:
Single read sequencing was carried out using Illumina/Solexa HiSeq 2000.
High-throughput sequencing was conducted by the Biomedical Sequencing Facility, Vienna. RNAseq alignment, long non-coding quantification and differential expression analysis were performed as follows:
Raw sequencing reads were aligned against the human hg38 genome using STAR aligner with default parameters.
The mapped reads were assigned to genes using featureCount from the Bioconductor package Rsubread. All annotated lncRNAs were quantified across each condition, using hg38 annotation.
Normalization and differential expression analysis were performed using the R/Bioconductor package DESeq2. Significance was assumed for an adjusted p-value < 0.01.
Assembly: hg38
Supplementary files format and content: xlsx with samples in columns. mRNA read counts
Supplementary files format and content: xlsx with samples in columns. lncRNA read counts

source_name: metabolically healthy donor  white adipose tissue

growth_protocol: Human BAT and WAT were removed from the same incision site in the supraclavicular localization, BAT being fluorodeoxyglucose-positron emission tomography (FDG-PET)-positive scan sites and WAT being not. The Study protocol was approved by the ethics committee of the Hospital District of Southwestern Finland, and subjects provided written informed consent following the committee's instructions. The study was conducted according to the principles of the Declaration of Helsinki. All potential subjects who donated BAT were screened for metabolic status, and only those with normal glucose tolerance and normal cardiovascular status (as assessed based on electrocardiograms and measured blood pressure) were included. The age range of the subjects was 23–49 years. We studied a group of 5 healthy volunteers (3 females, 2 males).

extract_protocol:
RNA of tissues were extracted using TRIzol (Invitrogen, #15596026) and NucleoSpin® RNA kit (Macherey-Nagel, #740955.250) according to the manufacturer’s instruction.
TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) was usedto generate cDNA libraries according to the manufacturer’s protocol


title: Human BAT, patient 5

source_name: metabolically healthy donor  brown adipose tissue


title: meniscus from rat (rat ID #24) with sham surgery 6 weeks post-surgery


title: LCS9172_NK92_CAR_IL15_RAJI_1

value: Blood

value: Natural Killer


title: mESC_Obox4_KO_PlaB_plus_H3K27ac_rep2

description: CUT&RUN-enriched DNA


title: Human WAT, patient 3

value: metabolically healthy donor  white adipose tissue


title: Human WAT, patient 5


title: cartilage from rat (rat ID #24) with sham surgery 6 weeks post-surgery


title: Human BAT, patient 3

value: metabolically healthy donor  brown adipose tissue


title: synovium from rat (rat ID #23) with medial meniscus transection surgery 6 weeks post-surgery


title: Human WAT, patient 2


title: mESC_Obox4_KO_PlaB_plus_H3K4me3_rep3

description: CUT&RUN-enriched DNA


title: mESC_Obox4_KO_PlaB_plus_H3K27ac_rep1

description: CUT&RUN-enriched DNA


title: mESC_Obox4_KO_PlaB_plus_H3K4me3_rep2

description: CUT&RUN-enriched DNA


title: Human BAT, patient 2


title: cartilage from rat (rat ID #23) with medial meniscus transection surgery 6 weeks post-surgery


title: meniscus from rat (rat ID #23) with medial meniscus transection surgery 6 weeks post-surgery


title: mESC_Obox4_KO_PlaB_plus_H3K4me3_rep1

description: CUT&RUN-enriched DNA


title: LCS9172_NK92_CAR_IL15_1

description: NK92 transducted with Lv_CAR specific for CD19 (CAR.19), a P2A and IL-15


title: LCS9172_NK92_CAR_2

description: NK92 transducted with Lv_CAR specific for CD19 (CAR.19)

value: CAR


title: LCS9172_NK92_CAR_IL15_2


title: synovium from rat (rat ID #23) with sham surgery 6 weeks post-surgery


title: LCS9172_NK92_CAR_1


title: Human WAT, patient 1


title: Human BAT, patient 4


title: Human BAT, patient 1


title: mESC_Obox4_KO_PlaB_plus_IgG

description: CUT&RUN-enriched DNA

source_name: EB3 mESC


title: LCS9172_NK92_CAR_IL15RA_2

description: NK92 transducted with Lv_CAR specific for CD19 (CAR.19), a P2A and IL-15 and IL15Ra


title: BM065

city: New York

first: Meri

last: Rogava

state: New York

address: 650 W 168th St, New York, NY 10032

department: Hematology Oncology

institute: Columbia University

description:
Bulk RNA
RNAseq_normalized_counts_human.tsv
RNAseq_raw_counts_human.csv

data_processing:
Samples were multiplexed in each lane, which yielded targeted number of paired-end 100bp reads for each sample. We used RTA (Illumina) for base calling and bcl2fastq2 (v 2.19) for converting BCL to fastq conversion, coupled with adaptor trimming.
We performed a pseudoalignment to a kallisto index created from Human transcriptomes GRCh38 using kallisto (0.44.0).
Genome_build: GRCh38

source_name: uveal

extract_protocol: For Bulk RANseq We used poly-A pull-down to enrich mRNAs from total RNA samples, then proceed with library construction using Illumina TruSeq chemistry. Libraries were then sequenced using Illumina NovaSeq 6000 at Columbia Genome Center.

value: Patient sample

tag: pertubation/treatment

value: FFPE_Liver Mets

tag: sample origin

value: patient samples_FFPE


title: Brain, AAV-ORF3a, rep6

city: Bethesda

first: Richard

middle: L

last: Proia

state: MD

address: 10 Center Drive Room 9D11

department: National Institute of Diabetes and Digestive and Kidney Diseases

institute: National Institutes of Health

data_processing:
Raw reads in FASTQ format were first processed to remove adapters, reads containing poly-N, and low-quality reads using fastp.
high-quality clean reads were mapped to reference genome mm10 (GRCm38) using hisat2 2.0.5.
Gene-expression quantification was performed using featureCounts 1.5.0-p3  and differential analysis performed using DESeq2 1.20.0
Pathway enrichment Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed using clusterProfiler 3.8.1 with corrected p-value set to <0.05 for significant enrichment.
Gene Set Enrichment Analysis (GSEQ) was performed using the local version of the GSEA analysis tool http://www.broadinstitute.org/gsea/index.jsp
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Brain

growth_protocol: Healthy mice were obtained from The Jackson Laboratory

extract_protocol:
Total RNA from 1 brain hemisphere each was isolated using miRNeasy Mini Kit(Qiagen).
3 ug of total RNA was used for the construction of sequencing libraries using NEBNext Ultra II RNA with PolyA Selection Kit (New England Biolab).

treatment_protocol: AAV-ORF3a and AAV-Control were injected using Retro-orbital injections. Brain tissue were harvested two weeks post injuection.

tag: tissue

value: Brain

tag: cell type

value: WT


title: mESC_WT_PlaB_plus_H3K27me3_rep3

description: CUT&RUN-enriched DNA

value: culture cell (ESC)

tag: treatment


title: meniscus from rat (rat ID #23) with sham surgery 6 weeks post-surgery

value: 6 weeks


title: mESC_WT_PlaB_plus_H3K27me3_rep2

description: CUT&RUN-enriched DNA

tag: background strain

value: pladienolide B


title: LCS9172_NK92_CAR_IL15RA_1


title: cartilage from rat (rat ID #23) with sham surgery 6 weeks post-surgery


title: Brain, AAV-ORF3a, rep5

tag: genotype


title: Brain, AAV-ORF3a, rep4


title: synovium from rat (rat ID #22) with medial meniscus transection surgery 6 weeks post-surgery

value: synovium

value: Medial Meniscus Transection


title: mESC_WT_PlaB_plus_H3K27me3_rep1

description: CUT&RUN-enriched DNA


title: mESC_WT_PlaB_plus_H3K27ac_rep3

description: CUT&RUN-enriched DNA


title: BM059


title: BM063


title: meniscus from rat (rat ID #22) with medial meniscus transection surgery 6 weeks post-surgery

value: meniscus


title: Brain, AAV-ORF3a, rep3


title: BM058


title: mESC_WT_PlaB_plus_H3K27ac_rep1

description: CUT&RUN-enriched DNA


title: mESC_WT_PlaB_plus_H3K27ac_rep2

description: CUT&RUN-enriched DNA


title: cartilage from rat (rat ID #22) with medial meniscus transection surgery 6 weeks post-surgery

value: cartilage


title: synovium from rat (rat ID #22) with sham surgery 6 weeks post-surgery

value: Sham Surgery


title: meniscus from rat (rat ID #22) with sham surgery 6 weeks post-surgery


title: Brain, AAV-ORF3a, rep1


title: cartilage from rat (rat ID #22) with sham surgery 6 weeks post-surgery


title: BM052


title: Brain, AAV-Control, rep6

value: AAV-Control


title: BM064


title: mESC_WT_PlaB_plus_H3K4me3_rep2

description: CUT&RUN-enriched DNA


title: mESC_WT_PlaB_plus_H3K4me3_rep3

description: CUT&RUN-enriched DNA


title: synovium from rat (rat ID #21) with medial meniscus transection surgery 6 weeks post-surgery


title: BM050


title: BM048


title: mESC_WT_PlaB_plus_H3K4me3_rep1

description: CUT&RUN-enriched DNA


title: mESC_WT_PlaB_plus_IgG

description: CUT&RUN-enriched DNA


title: Brain, AAV-Control, rep4


title: BM047


title: meniscus from rat (rat ID #21) with medial meniscus transection surgery 6 weeks post-surgery


title: Brain, AAV-ORF3a, rep2


title: cartilage from rat (rat ID #21) with medial meniscus transection surgery 6 weeks post-surgery


title: Brain, AAV-Control, rep3


title: BM057


title: BM062

source_name: cutaneous


title: Brain, AAV-Control, rep2


title: mESC_Obox4_KO_PlaB_minus_H3K27me3_rep2

description: CUT&RUN-enriched DNA


title: synovium from rat (rat ID #21) with sham surgery 6 weeks post-surgery


title: BM061


title: meniscus from rat (rat ID #21) with sham surgery 6 weeks post-surgery


title: Brain, AAV-Control, rep1


title: mESC_Obox4_KO_PlaB_minus_H3K27me3_rep1

description: CUT&RUN-enriched DNA


title: Brain, AAV-Control, rep5


title: BM055


title: mESC_Obox4_KO_PlaB_minus_H3K27ac_rep3

description: CUT&RUN-enriched DNA


title: HCmel12_Parental_Insulin_125ng/ml_4h_replicate 3

description: bulk RNA

data_processing:
data processing steps were performed as described previously (Doench et al., 2016). CRISPR–Cas9 screens were analyzed using software packages MAGeCK and MAGeCKFlute. MAGeCK allows to analyze CRISPR/Cas9 screen data, and performs quality control, read count generation and normalization, calculated beta score to evaluate gene selection performance. MAGeCK’s robust rank aggregation (RRA) method was used to identify significantly enriched or depleted CRISPR-screen hits in cells and tumors. MAGeCKFlute R package was used for data analysis and visualization.
For RNAseq data analysis the tximeta R package (Love et al. 2020) was used to import transcript-level quantification data quantified with Salmon package (Patro et al. 2017). Reads were mapped to mouse reference - Mus_musculus.GRCm38.97 and DESeq2 package was applied to generate normalized data.
Genome_build: Mus_musculus.GRCm38.97

source_name: mouse melanoma cell line

growth_protocol: Mouse melanoma cell line HCmel12 (gift from Prof. Thomas Tueting, Magdeburg, Germany) were grown in ‘complete’ RPMI-1640 medium (Gibson Bioscience) supplemented with 10%FBS (Gibco™ 10437028), 10mM non-essential amino acids, 1mM HEPES (all from Life Technologies), 20 µM 2-mercaptoethanol (Sigma), 100 IU per ml penicillin and 100 µg/ml-1 streptomycin (Invitrogen). Cell lines were routinely tested for mycoplasma contamination using Lonza MycoAlert Kit (Cat. # LT07-318).

extract_protocol:
Cells (~2x106) were lysed using RLT buffer and RNA was extracted using Qiagen kit (74136).
Illumina standard library construction protocol.

treatment_protocol: Parental and Pip4k2c KO cells were placed in 6-well plates in starvation media (-FBS) overnight, next day cells were treated with insulin (125ng/ml) for four hours. Experiment contained three biological replicates for each condition, total of 12 samples.

value: no treatment

value: in vitro cells


title: BM060


title: HCmel12_Pip4k2c_KO _Insulin_125ng/ml_4h_replicate 3

description: bulk RNA

value: Insulin


title: BM053

value: Patient sample


title: synovium from rat (rat ID #20) with medial meniscus transection surgery 6 weeks post-surgery


title: mESC_Obox4_KO_PlaB_minus_H3K27ac_rep2

description: CUT&RUN-enriched DNA


title: HCmel12_Pip4k2c_KO _Insulin_125ng/ml_4h_replicate 2

description: bulk RNA


title: cartilage from rat (rat ID #21) with sham surgery 6 weeks post-surgery


title: HCmel12_Parental_Insulin_125ng/ml_4h_replicate 2

description: bulk RNA


title: mESC_Obox4_KO_PlaB_minus_H3K27me3_rep3

description: CUT&RUN-enriched DNA


title: cartilage from rat (rat ID #20) with medial meniscus transection surgery 6 weeks post-surgery


title: Grovers_9

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

data_processing:
Quality control and adaptor trimming were performed on sequence reads form the RNA-Seq data. STAR alignment was used to align the reads to the reference genome (GRCh37), and HTSeq was used for gene quantification.
Assembly: GRCh37
Supplementary files format and content: gene by sample read count matrix

source_name: lesional skin

extract_protocol: RNA was isolated from 10 um sections of formalin-fixed paraffin embedded blocks from 11 Darier disease, 7 Hailey-Hailey disease, and 10 Grover’s disease samples. RNA was isolated using the E.N.Z.A. FFPE RNA Kit (Omega Bio-tek). Samples were prepared using the Lexogen 3’ QuantSeq mRNA-Seq Library Prep Kit FWD and sequences on the Illumina NovaSeq 6000 System

value: lesional skin

tag: condition

value: Grovers


title: mESC_Obox4_KO_PlaB_minus_H3K4me3_rep3

description: CUT&RUN-enriched DNA


title: Grovers_8


title: HCmel12_Pip4k2c_KO_Insulin_125ng/ml_4h_replicate 1

description: bulk RNA


title: mESC_Obox4_KO_PlaB_minus_H3K27ac_rep1

description: CUT&RUN-enriched DNA


title: meniscus from rat (rat ID #20) with medial meniscus transection surgery 6 weeks post-surgery


title: synovium from rat (rat ID #20) with sham surgery 6 weeks post-surgery


title: Grovers_7


title: HCmel12_Parental_Insulin_125ng/ml_4h_replicate 1

description: bulk RNA


title: mESC_Obox4_KO_PlaB_minus_H3K4me3_rep2

description: CUT&RUN-enriched DNA


title: mESC_Obox4_KO_PlaB_minus_H3K4me3_rep1

description: CUT&RUN-enriched DNA


title: Grovers_6


title: HCmel12_Pip4k2c_KO _no treatment_replicate 3

description: bulk RNA


title: meniscus from rat (rat ID #20) with sham surgery 6 weeks post-surgery


title: HCmel12_Parental_no treatment_replicate 3

description: bulk RNA


title: cartilage from rat (rat ID #20) with sham surgery 6 weeks post-surgery


title: Grovers_5


title: HCmel12_Pip4k2c_KO _no treatment_replicate 2

description: bulk RNA


title: synovium from rat (rat ID #19) with medial meniscus transection surgery 6 weeks post-surgery


title: mESC_WT_PlaB_minus_H3K27me3_rep2

description: CUT&RUN-enriched DNA


title: NN_31

value: control


title: HCmel12_Parental_no treatment_replicate 2

description: bulk RNA


title: meniscus from rat (rat ID #19) with medial meniscus transection surgery 6 weeks post-surgery


title: mESC_WT_PlaB_minus_H3K27me3_rep1

description: CUT&RUN-enriched DNA


title: cartilage from rat (rat ID #19) with medial meniscus transection surgery 6 weeks post-surgery


title: HCmel12_Pip4k2c_KO _no treatment_replicate 1

description: bulk RNA


title: Grovers_3


title: mESC_WT_PlaB_minus_H3K27ac_rep3

description: CUT&RUN-enriched DNA


title: Dariers_29

value: Dariers


title: HCmel12_Parental_no treatment_replicate 1

description: bulk RNA


title: Dariers_28


title: meniscus from rat (rat ID #19) with sham surgery 6 weeks post-surgery


title: mESC_WT_PlaB_minus_H3K27ac_rep1

description: CUT&RUN-enriched DNA

value: culture cell (ESC)


title: mESC_WT_PlaB_minus_H3K27ac_rep2

description: CUT&RUN-enriched DNA


title: pDNA_Brie_mouse kinome_Broad_reference_library_03

description: plasmid

extract_protocol:
Genomic DNA from cells (edited for 10, 14, 21, 28, 35, 42, 49 and 52 days) and mouse tissue (primary tumor, lung, liver, lymph node), was extracted using Qiagen kit for DNeasy Blood & Tissue Kit (69506,Qiagen).
The procedure of amplifying pooled sgRNA library was based on the protocol described previously (Doench et al., 2016). Sequencing libraries were constructed as previously described (Doench et al., 2016) and sequenced on an Illumina HiSeq2500 Instrument.
sgRNA enrichment sequencing

treatment_protocol: HCmel12-Cas9 melanoma cells were transduced at a MOI < 0.1 with lentivirus produced from a kinome-wide lentiviral mouse CRISPR knockout guide library containing 2,852 sgRNAs (Brie, Addgene # 75316) with at least 1000-fold representation (cells per construct) in each infection replicate. Spin-infected ~30 million HCmel12_Cas9 cells with the kinome CRISPR lentivirus library at MOI =0.1 in multiple 6-well plates at Day 0, and transferred the cells into T75 flasks at Day 2. Blasticidin selection (10 µg/ml) started at Day 2, and cells were harvested at Day 7. Puromycin selection stated at day 2 and lasted the entire experiment. On day 14 tumor cells were harvested and used for in vivo screening experiment. In parallel to in vivo screening experiment, cells were kept in culture and continued to edit for 21, 28, 35, 42, 49 and 52 days, the entire duration in parallel to in vivo editing. In vitro edited cells were palleted and used for downstream gDNA extraction and library preparations. For in vivo screening, 3x106 of library-transduced HCmel12-Cas9 cells were injected into the right flank or lateral tail vein of the mice. Tumor growth and signs of sickness was monitored over time. Mice were euthanized after 4 weeks and tumors, lungs, lymph node and liver were evaluated for metastasis presence, lesions dissected for gDNA isolation, amplification of the sgRNA region, and sequencing.

value: Broad Plasmid control


title: mESC_Obox4_KO_PlaB_minus_IgG

description: CUT&RUN-enriched DNA


title: Dariers_27


title: Grovers_4


title: pDNA_Brie_mouse kinome_Broad_reference_library_02

description: plasmid


title: mESC_WT_PlaB_minus_H3K27me3_rep3

description: CUT&RUN-enriched DNA


title: mESC_WT_PlaB_minus_H3K4me3_rep3

description: CUT&RUN-enriched DNA


title: synovium from rat (rat ID #18) with medial meniscus transection surgery 6 weeks post-surgery

value: 6 weeks


title: cartilage from rat (rat ID #19) with sham surgery 6 weeks post-surgery


title: Dariers_25


title: Dariers_26


title: library pDNA(100pg)_Brie mouse kinome_03

description: plasmid

value: Library Brie HMS


title: pDNA_Brie_mouse kinome_Broad_reference_library_01

description: plasmid


title: mESC_WT_PlaB_minus_H3K4me3_rep2

description: CUT&RUN-enriched DNA


title: Dariers_24


title: library pDNA(100pg)_Brie mouse kinome_02

description: plasmid


title: mESC_WT_PlaB_minus_H3K4me3_rep1

description: CUT&RUN-enriched DNA


title: synovium from rat (rat ID #19) with sham surgery 6 weeks post-surgery

value: synovium


title: synovium from rat (rat ID #18) with sham surgery 6 weeks post-surgery


title: Dariers_23


title: library pDNA(100pg)_Brie mouse kinome_01

description: plasmid


title: meniscus from rat (rat ID #18) with sham surgery 6 weeks post-surgery

value: meniscus


title: meniscus from rat (rat ID #18) with medial meniscus transection surgery 6 weeks post-surgery

value: Medial Meniscus Transection


title: Dariers_21


title: Dariers_22


title: cartilage from rat (rat ID #18) with sham surgery 6 weeks post-surgery

value: cartilage

value: Sham Surgery


title: HEamiRNA5_Male_placenta [17_a5_Male]

city: Bryan

first: Rajesh

last: Miranda

address: 8447 Riverside Parkway

institute: Texas A&M University

data_processing:
Trimmomatic read trimmer was used to evaluate and trim all adapter sequences and low quality bases. Reads were scanned with a sliding window of 5, cutting when the average quality per base drops below 20, then trimming reads at the beginning and end if base quality drops below 25, and then if the read length is less than 35.
HISAT2 was used for read mapping
HTSeq generated transcript-wise counts
DESeq2 was used for normalizing counts, calculating fold change, and differential analysis.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

source_name: HEamiRNAs_Male_Placenta (non-decidual)

growth_protocol: Adult C57BL/6J mice were purchased from Envigo and breeding was done in house to produce fetuses for experiments.

extract_protocol:
On gestational day 18, animals were anesthized using isoflurane vapor.  Placentas were removed and the nondecidual portion was microdissected, flash frozen in liquid nitrogen, and stored at -80 degrees Celcius. RNA was isolated using the Qiagen RNeasy Mini Kit.
RNA quantity was assessed using an Agilent TapeStation RNA assay.  Total RNA concentration was quantified via Qubit Fluorometric assay and subsequently all samples were normalized to an equivalent starting concentration. Sequencing libraries were prepared using the TruSeq Stranded Total RNA with Ribo-Zero Library Preparation kit (Illumina; San Diego, CA). Each sample was uniquely indexed (barcoded) to allow for pooling of all samples in a single sequencing run. Library size and quality were then assessed with an Agilent TapeStation D1000 DNA assay. Samples were normalized to ~4nM and pooled equally. Sequencing was performed on an Illumina NovaSeq 6000running with a 150 cycle, paired‐end (2x150) sequencing run to generate approximately 50 million read pairs per sample.

treatment_protocol: Pregnant dams were distributed between treatment groups, pooled HEamiRNAs or scrambled miRNAs as control, and received treatment by tail vein injection on gestational day 10 while under isoflurane anesthesia.

tag: strain background

value: Placenta (non-decidual)

value: Gestational Day 18

value: HEamiRNAs

tag: Sex

value: Male


title: HEamiRNA6_Male_placenta [18_a6_Male]


title: synovium from rat (rat ID #17) with medial meniscus transection surgery 6 weeks post-surgery


title: HEamiRNA6_Female_placenta [19_a6_Female]

value: Female


title: meniscus from rat (rat ID #17) with medial meniscus transection surgery 6 weeks post-surgery


title: neg_1

description: gDNA

tag: cell line

value: Negative


title: neg_2

description: gDNA


title: Dariers_20

value: lesional skin


title: BRN_R12

description: gDNA

value: Brain Metastasis


title: cartilage from rat (rat ID #18) with medial meniscus transection surgery 6 weeks post-surgery


title: mESC_WT_PlaB_minus_IgG

city: Shinjuku

first: Haruhiko

last: Siomi

address: 35 Shinanomachi

institute: Keio University School of Medicine

description: CUT&RUN-enriched DNA

value: culture cell (ESC)


title: cartilage from rat (rat ID #17) with medial meniscus transection surgery 6 weeks post-surgery


title: HEamiRNA4_Male_placenta [15_a4_Male]

tag: age


title: Grovers_2

value: Grovers


title: BRN_R11

description: gDNA


title: HEamiRNA4_Female_placenta [16_a4_Female]


title: BRN_R10

description: gDNA


title: HEamiRNA3_Female_placenta [14_a3_Female]


title: synovium from rat (rat ID #17) with sham surgery 6 weeks post-surgery

value: 6 weeks


title: Dariers_19

value: Dariers


title: Hailey_Hailey_18

value: Hailey-Hailey


title: BRN_R9

description: gDNA


title: meniscus from rat (rat ID #17) with sham surgery 6 weeks post-surgery

value: meniscus


title: HEamiRNA3_Male_placenta [13_a3_Male]


title: Hailey_Hailey_16


title: HEamiRNA2_Male_placenta [12_a2_Male]


title: cartilage from rat (rat ID #17) with sham surgery 6 weeks post-surgery


title: BRN_R8

description: gDNA


title: BRN_R7

description: gDNA


title: Hailey_Hailey_15


title: synovium from rat (rat ID #16) with medial meniscus transection surgery 4 weeks post-surgery

value: synovium

value: 4 weeks

value: Medial Meniscus Transection


title: HEamiRNA1_Female_placenta [11_a1_Female]

value: Placenta (non-decidual)


title: Hailey_Hailey_14


title: meniscus from rat (rat ID #16) with medial meniscus transection surgery 4 weeks post-surgery


title: BRN_R6

description: gDNA


title: Hailey_Hailey_13


title: Control5_Female_placenta [09_c5_Female]

source_name: Scrambled miRNA (control)_Female_Placenta (non-decidual)

value: Gestational Day 18

value: Scrambled miRNA (control)


title: cartilage from rat (rat ID #16) with medial meniscus transection surgery 4 weeks post-surgery

value: cartilage


title: Hailey_Hailey_11


title: Hailey_Hailey_12


title: BRN_R3

description: gDNA


title: Control4_Female_placenta [07_c4_Female]

value: Female


title: Grovers_10


title: BRN_R2

description: gDNA


title: meniscus from rat (rat ID #16) with sham surgery 4 weeks post-surgery

value: Sham Surgery


title: cartilage from rat (rat ID #16) with sham surgery 4 weeks post-surgery


title: Control4_Male_placenta [06_c4_Male]

source_name: Scrambled miRNA (control)_Male_Placenta (non-decidual)

value: Male


title: Grovers_1

value: lesional skin


title: synovium from rat (rat ID #15) with medial meniscus transection surgery 4 weeks post-surgery


title: Control3_Female_placenta [05_c3_Female]


title: BRN_R1

description: gDNA

value: Brain Metastasis


title: meniscus from rat (rat ID #15) with medial meniscus transection surgery 4 weeks post-surgery


title: 786-0 SETD2 KO cell, Day26, DAC100nM+BMN10nM, rep2

city: Los Angeles

first: Xinyi

last: Zhou

address: 1441 Eastlake Ave.

institute: Keck School of Medicine

description: Partek_xz_533_Alingment_of_76_samples_Jul2021_STAR_Aligned_reads/H8.bam

data_processing:
Raw *.fq.gz files were checked by fastqc on linux terminal
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic on linux terminal
Trimmed sequence reads were checked by fastqc on linux terminal and aligned using Partek Flow
Read count extraction from *.bam files were performed by featureCounts on linux terminal
Assembly: Homo_sapiens.GRCh38.104.gtf
Supplementary files format and content: tab-delimited .tsv text files include raw counts for each Sample

source_name: renal

extract_protocol:
1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA RNA HyperPrep Kit (#KK8563) following manufacturer's protocols.

value: renal

value: clear cell renal cell carcinoma

value: SETD2 KO


title: HEamiRNA1_Male_placenta [10_a1_Male]

value: HEamiRNAs


title: BRN_R5

description: gDNA


title: Control3_Male_placenta [04_c3_Male]


title: Control2_Female_placenta [03_c2_Female]


title: LN14_R3W2

description: gDNA

value: Lymph node


title: 786-0 SETD2 KO cell, Day16, DAC100nM+BMN10nM, rep2

description: Partek_xz_533_Alingment_of_76_samples_Jul2021_STAR_Aligned_reads/H5.bam


title: synovium from rat (rat ID #16) with sham surgery 4 weeks post-surgery

value: synovium


title: 786-0 SETD2 KO cell, Day26, DAC100nM, rep1

description: Partek_xz_533_Alingment_of_76_samples_Jul2021_STAR_Aligned_reads/H7.bam


title: cartilage from rat (rat ID #15) with medial meniscus transection surgery 4 weeks post-surgery

value: 4 weeks


title: BRN_R4

description: gDNA


title: Control5_Male_placenta [08_c5_Male]


title: Control1_Female_placenta [02_c1_Female]


title: synovium from rat (rat ID #15) with sham surgery 4 weeks post-surgery


title: LN14_R3B1

description: gDNA


title: LN14_R2

description: gDNA


title: 786-0 SETD2 KO cell, Day5, DAC100nM+BMN10nM, rep2

description: Partek_xz_533_Alingment_of_76_samples_Jul2021_STAR_Aligned_reads/H2.bam


title: LN14_R1B2

description: gDNA


title: 786-0 SETD2 KO cell, Day16, DAC100nM, rep1

description: Partek_xz_533_Alingment_of_76_samples_Jul2021_STAR_Aligned_reads/H4.bam


title: meniscus from rat (rat ID #15) with sham surgery 4 weeks post-surgery

value: meniscus


title: cartilage from rat (rat ID #15) with sham surgery 4 weeks post-surgery


title: 786-0 SETD2 KO cell, Day5, DAC100nM, rep1

description: Partek_xz_533_Alingment_of_76_samples_Jul2021_STAR_Aligned_reads/H1.bam


title: RNAseq_mTOR_KI_500nM AZD_3

city: Cincinnati

first: Yi

last: Zheng

state: OH

address: 3333 Burnet Ave MLC7013

department: Experimental Hematology and Cancer Biology

institute: CINCINNATI CHILDRENS HOSP MED CTR

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence.
Reads mapped to mm10 whole genome by Tophat with default options
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks with default options. Outputs from Cufflinks are provided as supplementary files as a tab-delimited text file.
Genome_build: mm10
Supplementary_files_format_and_content: fpkm_tracking (contains the estimated expression values produced by Cufflinks)

source_name: cultured mTOR KI mutant HSC cells

growth_protocol: HSC cells from poly(I:C)-treated WT control and mTOR KI mice were sorted by FACS and then cultured in StemSpan SFEM medium.

extract_protocol:
RNA were extracted using miRNeasy Micro Kit (Qiagen, 217084).
RNA-seq libraries were prepared using Illumina TruSeq Stranded Total RNA Sample Preparation Kit

treatment_protocol: HSC cells were treated with DMSO, or 200nM AZD2014 or 500nM AZD2014 respectively and then followed by RNA-seq.

value: HSC cells

value: Adult

value: 500nM AZD


title: LN14_R1W

description: gDNA


title: RNAseq_mTOR_KI_500nM AZD_2


title: synovium from rat (rat ID #14) with medial meniscus transection surgery 4 weeks post-surgery

source_name: synovium

value: Medial Meniscus Transection


title: 786-0 SETD2 KO cell, Day26, BMN10nM, rep2

description: Partek_xz_533_Alingment_of_76_samples_Jul2021_STAR_Aligned_reads/G8.bam


title: LN14_R1B1

description: gDNA


title: LN14_R3B2

description: gDNA

value: Luymph node


title: meniscus from rat (rat ID #14) with medial meniscus transection surgery 4 weeks post-surgery


title: RNAseq_mTOR_KI_500nM AZD_1


title: 786-0 SETD2 WT cell, Day26, DAC100nM+BMN10nM, rep1

description: Partek_xz_533_Alingment_of_76_samples_Jul2021_STAR_Aligned_reads/G7.bam

value: SETD2 WT


title: cartilage from rat (rat ID #14) with medial meniscus transection surgery 4 weeks post-surgery

value: cartilage


title: RNAseq_mTOR_KI_200nM AZD_3

value: 200nM AZD


title: LNG14_R5

description: gDNA

value: Lung


title: 786-0 SETD2 KO cell, Day16, BMN10nM, rep2

description: Partek_xz_533_Alingment_of_76_samples_Jul2021_STAR_Aligned_reads/G5_L1_1.bam

value: renal


title: synovium from rat (rat ID #14) with sham surgery 4 weeks post-surgery

value: Sham Surgery


title: LNG14_R4

description: gDNA


title: 786-0 SETD2 WT cell, Day16, DAC100nM+BMN10nM, rep1

description: Partek_xz_533_Alingment_of_76_samples_Jul2021_STAR_Aligned_reads/G4_L1_1.bam

value: clear cell renal cell carcinoma


title: LNG14_R6

description: gDNA


title: RNAseq_mTOR_KI_200nM AZD_2


title: Control1_Male_placenta [01_c1_Male]

value: Placenta (non-decidual)

value: Gestational Day 18

value: Scrambled miRNA (control)

value: Male


title: RNAseq_mTOR_KI_200nM AZD_1


title: cartilage from rat (rat ID #14) with sham surgery 4 weeks post-surgery

value: 4 weeks


title: RNAseq_mTOR_KI_DMSO_3

value: HSC cells

value: DMSO


title: LNG14_R2

description: gDNA


title: RNAseq_mTOR_KI_DMSO_2

value: Adult


title: meniscus from rat (rat ID #14) with sham surgery 4 weeks post-surgery

value: meniscus


title: LNG14_R3

description: gDNA


title: 786-0 SETD2 WT cell, Day5, DAC100nM+BMN10nM, rep1

description: Partek_xz_533_Alingment_of_76_samples_Jul2021_STAR_Aligned_reads/G1_L1_1.bam


title: synovium from rat (rat ID #13) with medial meniscus transection surgery 4 weeks post-surgery

value: synovium

value: Medial Meniscus Transection


title: LNG14_R1

description: gDNA


title: 786-0 SETD2 KO cell, Day26, DAC100nM, rep2

description: Partek_xz_533_Alingment_of_76_samples_Jul2021_STAR_Aligned_reads/F8.bam

value: SETD2 KO


title: LIV14_R7

description: gDNA

value: Liver Metastasis


title: meniscus from rat (rat ID #13) with medial meniscus transection surgery 4 weeks post-surgery


title: RNAseq_mTOR_WT_500nM AZD_3

source_name: cultured mTOR WT Control HSC cells

value: 500nM AZD


title: cartilage from rat (rat ID #13) with medial meniscus transection surgery 4 weeks post-surgery

value: cartilage


title: RNAseq_mTOR_KI_DMSO_1


title: LIV14_R6

description: gDNA


title: 786-0 SETD2 KO cell, Day5, BMN10nM, rep2

description: Partek_xz_533_Alingment_of_76_samples_Jul2021_STAR_Aligned_reads/G2_L1_1.bam

value: renal


title: synovium from rat (rat ID #13) with sham surgery 4 weeks post-surgery

value: Sham Surgery


title: 786-0 SETD2 WT cell, Day16, BMN10nM, rep1

description: Partek_xz_533_Alingment_of_76_samples_Jul2021_STAR_Aligned_reads/F4_L1_1.bam

value: clear cell renal cell carcinoma

value: SETD2 WT


title: LIV14_R5.2

description: gDNA


title: meniscus from rat (rat ID #13) with sham surgery 4 weeks post-surgery

source_name: meniscus


title: RNAseq_mTOR_WT_200nM AZD_3

value: 200nM AZD


title: RNAseq_mTOR_WT_500nM AZD_1


title: cartilage from rat (rat ID #13) with sham surgery 4 weeks post-surgery

source_name: cartilage


title: LIV14_R5.1

description: gDNA


title: 786-0 SETD2 KO cell, Day5, DAC100nM, rep2

description: Partek_xz_533_Alingment_of_76_samples_Jul2021_STAR_Aligned_reads/F2_L1_1.bam


title: 786-0 SETD2 WT cell, Day5, BMN10nM, rep1

description: Partek_xz_533_Alingment_of_76_samples_Jul2021_STAR_Aligned_reads/F1.bam


title: RNAseq_mTOR_WT_200nM AZD_1


title: LIV14_R4.1

description: gDNA


title: 786-0 SETD2 WT cell, Day26, BMN10nM, rep1

description: Partek_xz_533_Alingment_of_76_samples_Jul2021_STAR_Aligned_reads/F7.bam


title: 786-0 SETD2 WT cell, Day26, DAC100nM+BMN10nM, rep2

description: Partek_xz_533_Alingment_of_76_samples_Jul2021_STAR_Aligned_reads/E8.bam


title: RNAseq_mTOR_WT_DMSO_3


title: LIV14_R3.6

description: gDNA


title: synovium from rat (rat ID #12) with medial meniscus transection surgery 4 weeks post-surgery


title: meniscus from rat (rat ID #12) with medial meniscus transection surgery 4 weeks post-surgery


title: 786-0 SETD2 WT cell, Day26, DAC100nM, rep1

description: Partek_xz_533_Alingment_of_76_samples_Jul2021_STAR_Aligned_reads/E7_L1_1.bam


title: cartilage from rat (rat ID #12) with medial meniscus transection surgery 4 weeks post-surgery


title: 786-0 SETD2 KO cell, Day16, DAC100nM, rep2

description: Partek_xz_533_Alingment_of_76_samples_Jul2021_STAR_Aligned_reads/F5_L1_1.bam


title: 786-0 SETD2 WT cell, Day16, DAC100nM+BMN10nM, rep2

description: Partek_xz_533_Alingment_of_76_samples_Jul2021_STAR_Aligned_reads/E5.bam


title: LIV14_R3.5

description: gDNA


title: RNAseq_mTOR_WT_500nM AZD_2


title: RNAseq_mTOR_WT_DMSO_2


title: synovium from rat (rat ID #12) with sham surgery 4 weeks post-surgery


title: 786-0 SETD2 WT cell, Day16, DAC100nM, rep1

description: Partek_xz_533_Alingment_of_76_samples_Jul2021_STAR_Aligned_reads/E4_L1_1.bam


title: LIV14_R3.4

description: gDNA


title: RNAseq_mTOR_WT_DMSO_1


title: meniscus from rat (rat ID #12) with sham surgery 4 weeks post-surgery


title: LIV14_R3.3

description: gDNA


title: RNAseq_mTOR_WT_200nM AZD_2


title: LIV14_R4

description: gDNA


title: 786-0 SETD2 WT cell, Day5, DAC100nM, rep1

description: Partek_xz_533_Alingment_of_76_samples_Jul2021_STAR_Aligned_reads/E1.bam


title: 786-0 SETD2 WT cell, Day5, DAC100nM+BMN10nM, rep2

description: Partek_xz_533_Alingment_of_76_samples_Jul2021_STAR_Aligned_reads/E2_L1_1.bam


title: cartilage from rat (rat ID #12) with sham surgery 4 weeks post-surgery


title: LIV14_R3.2

description: gDNA


title: synovium from rat (rat ID #11) with medial meniscus transection surgery 4 weeks post-surgery


title: 786-0 SETD2 WT cell, Day26, BMN10nM, rep2

description: Partek_xz_533_Alingment_of_76_samples_Jul2021_STAR_Aligned_reads/D8.bam


title: meniscus from rat (rat ID #11) with medial meniscus transection surgery 4 weeks post-surgery


title: B_L6_166-F37-DI-SW-98_S119_L002

city: Ås

first: Byron

last: Morales Lange

address: Arboretveien 6

country: Norway

institute: Norwegian University of Life Sciences

data_processing:
nf-core rnaseq v3.3
Fragment mapping was counted using featureCounts (subread v1.5.1).
Differentially expressed genes (DEGs) were estimated using the SARTools R package (v1.7.3). Significant DEGs were determined when the adjusted p-value (padj) was < 0.05.
Assembly: SSAL_v3.1 (GenBank assembly accession: GCA_905237065.2).
Supplementary files format and content: Count files / Counts for each Sample.

organism: Salmo salar

source_name: Distal Intestine

extract_protocol:
Total RNA was extracted from each sample using RNeasy Mini Kit (Qiagen) following the supplier’s instructions. Then, RNA samples were quantified using a NanoDrop™ 8000 spectrophotometer and RNA integrity was measured by Agilent Bioanalyzer 2100. All samples showed an RNA integrity number ≥ 7).
RNA libraries for RNA-seq were prepared by the Norwegian Sequencing Center (UiO, Norway).

value: Distal Intestine

tag: FISH group

value: B

tag: diet

value: hydrolyzed Debaryomyces hansenii

tag: water stage

value: Seawater


title: SPLN_R1

description: gDNA


title: LIV14_R3.1

description: gDNA


title: cartilage from rat (rat ID #11) with medial meniscus transection surgery 4 weeks post-surgery

tag: timepoint

value: 4 weeks

tag: disease state


title: B_L6_167-F37-DI-SW-103_S108_L002


title: B_L6_165-F37-DI-SW-97_S166_L002


title: 786-0 SETD2 KO cell, Day0, control, rep2

description: Partek_xz_533_Alingment_of_76_samples_Jul2021_STAR_Aligned_reads/D1_L1_1.bam

value: control


title: 786-0 SETD2 WT cell, Day5, BMN10nM, rep2

description: Partek_xz_533_Alingment_of_76_samples_Jul2021_STAR_Aligned_reads/D2_L1_1.bam


title: LIV14_R1

description: gDNA

tag: pertubation/treatment


title: B_CD_159-F37-DI-SW-79_S104_L002

value: Control Diet

value: Control


title: LIV14_R2

description: gDNA

tag: sample origin


title: 786-0 SETD2 WT cell, Day26, DAC100nM, rep2

description: Partek_xz_533_Alingment_of_76_samples_Jul2021_STAR_Aligned_reads/C8.bam

tag: tissue


title: B_CD_160-F37-DI-SW-80_S151_L002


title: LN10_R3B

description: gDNA

value: Lymph node


title: B_L6_168-F37-DI-SW-104_S165_L002


title: B_CD_148-F37-DI-SW-45_S150_L002


title: 786-0 SETD2 WT cell, Day16, DAC100nM, rep2

description: Partek_xz_533_Alingment_of_76_samples_Jul2021_STAR_Aligned_reads/C5.bam

tag: cell type


title: cartilage from rat (rat ID #11) with sham surgery 4 weeks post-surgery


title: B_CD_147-F37-DI-SW-43_S128_L002

tag: treatment


title: synovium from rat (rat ID #10) with medial meniscus transection surgery 4 weeks post-surgery

value: synovium

value: Medial Meniscus Transection


title: LN10_R3W

description: gDNA


title: 786-0 SETD2 WT cell, Day5, DAC100nM, rep2

description: Partek_xz_533_Alingment_of_76_samples_Jul2021_STAR_Aligned_reads/C2_L1_1.bam


title: LN10_R2

description: gDNA


title: 786-0 SETD2 WT cell, Day16, BMN10nM, rep2

description: Partek_xz_533_Alingment_of_76_samples_Jul2021_STAR_Aligned_reads/D5_L1_1.bam


title: meniscus from rat (rat ID #10) with medial meniscus transection surgery 4 weeks post-surgery

value: meniscus


title: 786-0 SETD2 WT cell, Day0, control, rep2

description: Partek_xz_533_Alingment_of_76_samples_Jul2021_STAR_Aligned_reads/C1.bam

value: renal


title: A_L6_164-F37-DI-SW-92_S120_L002

value: A


title: A_L6_163-F37-DI-SW-91_S183_L002


title: LN10_R1.1

description: gDNA


title: synovium from rat (rat ID #11) with sham surgery 4 weeks post-surgery

value: Sham Surgery


title: LN10_R1.2

description: gDNA


title: A_L6_152-F37-DI-SW-57_S143_L002


title: 786-0 SETD2 KO cell, Day16, DAC100nM+BMN10nM, rep1

description: Partek_xz_533_Alingment_of_76_samples_Jul2021_STAR_Aligned_reads/B5_L1_1.bam

value: clear cell renal cell carcinoma

value: SETD2 KO


title: cartilage from rat (rat ID #10) with medial meniscus transection surgery 4 weeks post-surgery

value: cartilage


title: 786-0 SETD2 KO cell, Day26, DAC100nM+BMN10nM, rep1

description: Partek_xz_533_Alingment_of_76_samples_Jul2021_STAR_Aligned_reads/B8_L1_1.bam


title: meniscus from rat (rat ID #11) with sham surgery 4 weeks post-surgery


title: meniscus from rat (rat ID #10) with sham surgery 4 weeks post-surgery


title: synovium from rat (rat ID #10) with sham surgery 4 weeks post-surgery


title: A_L6_151-F37-DI-SW-55_S147_L002

value: Distal Intestine


title: LNG10_R6

description: gDNA

value: Lung


title: A_CD_140-F37-DI-SW-20_S154_L002

value: Seawater


title: 786-0 SETD2 KO cell, Day0, control, rep1

description: Partek_xz_533_Alingment_of_76_samples_Jul2021_STAR_Aligned_reads/B1.bam


title: cartilage from rat (rat ID #10) with sham surgery 4 weeks post-surgery

value: 4 weeks


title: 786-0 SETD2 KO cell, Day5, DAC100nM+BMN10nM, rep1

description: Partek_xz_533_Alingment_of_76_samples_Jul2021_STAR_Aligned_reads/B2.bam


title: A_CD_139-F37-DI-SW-19_S156_L002


title: 786-0 SETD2 KO cell, Day26, BMN10nM, rep1

description: Partek_xz_533_Alingment_of_76_samples_Jul2021_STAR_Aligned_reads/A8.bam


title: synovium from rat (rat ID #9) with medial meniscus transection surgery 4 weeks post-surgery


title: meniscus from rat (rat ID #9) with medial meniscus transection surgery 4 weeks post-surgery


title: A_CD_134-F37-DI-SW-2_S105_L002


title: LNG10_R5.1

description: gDNA


title: 786-0 SETD2 KO cell, Day16, BMN10nM, rep1

description: Partek_xz_533_Alingment_of_76_samples_Jul2021_STAR_Aligned_reads/A5.bam


title: LNG10_R4

description: gDNA


title: A_CD_133-F37-DI-SW-1_S159_L002


title: LNG10_R3.2

description: gDNA


title: cartilage from rat (rat ID #9) with medial meniscus transection surgery 4 weeks post-surgery


title: synovium from rat (rat ID #9) with sham surgery 4 weeks post-surgery


title: LNG10_R7

description: gDNA


title: LNG10_R3.1

description: gDNA


title: meniscus from rat (rat ID #9) with sham surgery 4 weeks post-surgery


title: 786-0 SETD2 WT cell, Day0, control, rep1

description: Partek_xz_533_Alingment_of_76_samples_Jul2021_STAR_Aligned_reads/A1_L1_1.bam

value: SETD2 WT

value: control


title: LNG10_R2

description: gDNA


title: cartilage from rat (rat ID #9) with sham surgery 4 weeks post-surgery


title: B_L6_239-F37-LIV-SW-103_S261_L003

source_name: Liver

value: Liver

value: B

value: hydrolyzed Debaryomyces hansenii


title: B_L6_238-F37-LIV-SW-98_S242_L003


title: THP6, CDC73, shETS1-2, 1

first: Brian

last: Magnuson

address: 1500 East Medical Center Drive

data_processing:
Data processing was performing using Chipseq ATACseq Pipelines 1.0.1 (https://github.com/russell-ryan-lab/ChIPseq_ATACseq_pipelines).
Paired-end reads were aligned to using BWA 0.7.17.
Read duplicates were removed using Picard 2.22.3 and multimapping reads were also removed.
Peak calling was performed using Homer 4.10 findPeaks (“style -factor” for human CDC73 amd "style -histone” for mouse H3K27ac). Peaks falling within ENCODE exclusion / problematic regions were removed (https://github.com/Boyle-Lab/Blacklist).
Coverage/signal files (bigWig) were produced using DeepTools 3.4.3 bamCoverage.
H2K120Ub1 was quantified over genes defined in the GENCODE M15 mouse annotation (basic GTF). Raw counts and RPKM-normalized counts were computed using Homer 4.10 analyzeRepeats.pl in a strand-insensitive manner using parameters: (-raw or -rpkm) -gid -count genes -strand both.
Assembly: mm10, hg19
Supplementary files format and content: H2K120Ub1 quantification files (read coverage over genes) are tab-delimited text files with headers and include gene annotations, raw counts (0.5 per read in paired-end data, as per Homer analyzeRepeats.pl), and RPKM.  Sample matrices fir counts and RPKM are also included for H2K120Ub1 data.

source_name: T-cell acute lymphoblastic leukemia

growth_protocol: T-ALL cell lines were grown in RPMI 1640 (Invitrogen) supplemented with 10% fetal bovine serum (Hyclone or Gibco), 2 mM L-glutamine, 2-mercaptoethanol (0.0005% (v/v), Sigma), penicillin and streptomycin.

extract_protocol:
Cells were crosslinked for most samples by addition of 1% formaldehyde to media at 37 C for 10 minutes, followed by glycine quenching and 2x washing in PBS. For Ets1. For H3K27ac and H2K120ub1, cells were crosslinked with 1% formaldehyde at room temperature. Nuclei were isolated by hypotonic buffer lysis, and chromatin was fragmented with a QSonica Q800 bath sonicator in 0.3% SDS-containing lysis buffer. Samples were diluted 1:3.3 and chromatin complexes containing the target of interest were isolated by immunoprecipitation, followed by reverse crosslinking and DNA purification by SPRI. For input samples (vehicle-treated only), 1:8 diluted sonicated chromatin (whole cell extract) was added directly to the reverse crosslinking step without immunoprecipitation.
Purified ChIP or input DNA was end-repaired and A-tailed. Illumina barcoded adaptors were ligated and PCR amplified. Final library was isolated by double SPRI purification (sequential reverse and forward SPRI) and paired-end sequenced on the Illumina NextSeq 550 (38 bp reads) or on the Illumina NovaSeq 6000 (151 bp reads) .

treatment_protocol: Murine T-ALL cells were treated with EtOH or OHT at 6nM for 30 hours prior to harvesting. THP-6 T-ALL cells were lentivirally transduced with pLKO.1-type shRNA for 2 days  and then selected with puromycin for 2 days prior to harvesting.

value: T-cell acute lymphoblastic leukemia

tag: chip-seq antibody

value: CDC73/Parafibromin (Bethyl A300-171A)


title: THP6, CDC73, shETS1-2, 2

tag: genotype


title: LNG10_R5.2

description: gDNA


title: B_L6_237-F37-LIV-SW-97_S256_L003


title: synovium from rat (rat ID #8) with medial meniscus transection surgery 2 weeks post-surgery

value: synovium

value: 2 weeks

value: Medial Meniscus Transection


title: LNG10_R1

description: gDNA


title: B_CD_232-F37-LIV-SW-80_S282_L003

value: Control Diet

value: Control


title: THP6, CDC73, shETS1-3, 2


title: meniscus from rat (rat ID #8) with medial meniscus transection surgery 2 weeks post-surgery

value: meniscus


title: THP6, CDC73, shETS1-3, 1


title: B_CD_231-F37-LIV-SW-79_S225_L003


title: THP6, CDC73, shControl, 2

value: shControl


title: cartilage from rat (rat ID #8) with medial meniscus transection surgery 2 weeks post-surgery

value: cartilage


title: 786-0 SETD2 KO cell, Day5, BMN10nM, rep1

description: Partek_xz_533_Alingment_of_76_samples_Jul2021_STAR_Aligned_reads/A2.bam

value: renal

value: clear cell renal cell carcinoma

value: SETD2 KO


title: B_L6_240-F37-LIV-SW-104_S258_L003

value: Seawater


title: LIV10_R3

description: gDNA

value: Liver Metastasis