title: F2 Embry.63 T CM WT 325Mu

value: 63 days post conception (dpc)


title: Veh-4b1

status: Public on Aug 31 2021

type: SRA

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

description:
2014_529_CTTGTA_L001
Veh, fourth, Biological replicate B, Technical replicate 1

library_source: transcriptomic

data_processing:
Illumina bcl2fastq 1.8.4 software used for demultiplexing.
The analyses were performed using the Eoulsan pipeline, including read filtering, mapping, alignment filtering, read quantification, normalisation and differential analysis: Before mapping, poly N read tails were trimmed, reads ≤11 bases were removed, and reads with quality mean ≤12 were discarded. Reads were then aligned against the Mus musculus genome (mm10 genome assembly from UCSC) using Bowtie (version 0.12.9, parameters -n 2 -l 34 -e 70 -k 2 –best). Alignments from reads matching more than once on the reference genome were removed using Java version of samtools. To compute gene expression, Mus musculus (mm10) GFF3 genome annotation from UCSC database was used. All overlapping regions between alignments and referenced exons were counted using HTSeq-count 0.5.3. The sample counts were normalized using DESeq 1.8.3. Statistical treatments and differential analyses were also performed using DESeq 1.8.3.
Genome_build: mm10 (UCSC)
Supplementary_files_format_and_content: tab-delimited text files include gene counting for each sample

molecule: total RNA

organism: Mus musculus

source_name: S129_Veh_Choroid plexus, 4th ventricle

extract_protocol:
RNA extracted directly from tissue with RNEasy Mini Kit (Qiagen)
Ribosomal RNA depletion was performed with the Ribo-Zero kit (Epicentre), using 0.5 (first run) or 1 µg (second run) of total RNA. Libraries were prepared using the strand specific RNA-Seq library preparation ScriptSeq V2 kit (Epicentre). Libraries were multiplexed by 6 on one flow cell lane for the first run, and by 8 on 2 flow cell lanes for the other run. A 50 bp read sequencing was performed on a HiSeq 1500 device (Illumina).

tag: strain

tag: genotype

value: Veh

tag: tissue

value: Choroid plexus, 4th ventricle


title: D65_NEG3

city: La Jolla

first: Karl

last: Wahlin

state: CA

address: 9415 Campus Point Dr., #0946

department: Ophthalmology

country: USA

institute: UC San Diego

data_processing:
Adapter and quality trimming using Trimmomatic
concatenate files using Galaxy Core utilities 'concatenate datasets' and FastQC for quality assessment.
Feature counts
Reads mapped to reference genome GRCh37.13(hg19) using HISAT2 (v2.1.0)
Differential sequence analysis performed using DESeq2 (v1.22.1) and EdgeR (v3.24.1)
Genome_build: GRCh37.13(hg19)

organism: Homo sapiens

source_name: Neural organoids

growth_protocol: Stem cells were maintained under hypoxic conditions in mTeSR1 media. Stem cells were differentiated into organoids using BE6.2-NIM (B27 + E6 at 2X concentration) (neural induction medium) consists of DMEM (#11965; Invitrogen) supplemented with 1% B27 vitamin A (-) (#12587010; Invitrogen) and 2X E6 supplement (38.8 mg/L insulin (#11376497001; Roche), +128mg/L L-ascorbic acid (#A8960; Sigma), 28μg/L selenium (#S5261; Sigma), 21.4 mg/L transferrin (#T0665; Sigma) and 38.8 mg/L NaHCO3). Osmolarity was raised +30mOsm to ~330-340mOsm) by adding 0.88 g/L NaCl (Ludwig, Bergendahl et al. 2006, Chen, Gulbranson et al. 2011). LTR (Long-Term Retina) medium was a 3:1 mix of high glucose DMEM:F12 (#11965, #11765; Invitrogen) supplemented with 1% B27 (#17504044; Invitrogen), 10% heat inactivated qualified-grade FBS (#16140071; Invitrogen), 1mM pyruvate (#11360; Invitrogen), 1xNEAA (#11140; Invitrogen), 1X Glutamax (#35050061; Invitrogen) and 1mM taurine (#T-8691; Sigma).

extract_protocol:
Organoids were harvested, stored at -80 and RNA extracted using a Zymopure RNA microprep kit
TruSeq Library Prep kit v3.0
RNA analyzed using a 4200 Tapestation System, RIN value greater than 8 used for library preparation

tag: cell type

value: human induced pluripotent stem cell-derived organoids

tag: fluorescence

value: SIX6 GFP negative

value: IMR90.4 SIX6-eGFP/POU4F2-tdTomato


title: Veh-Lb1

description:
2014_527_TTAGGC_L001
Veh, lateral, Biological replicate B, Technical replicate 1

source_name: S129_Veh_Choroid plexus, lateral ventricle

value: Choroid plexus, lateral ventricle


title: G_ME79_EV_CTTGTA_S38

city: Chapel Hill

first: Gregory

middle: James

last: Smith

state: North Carolina

address: 120 Mason Farm Road, 5070E Genetic Medicine Building

department: Genetics

institute: University of North Carolina

description:
pooled BALF from 3 mice
G_ME79_EV_CTTGTA_S38_L003

data_processing:
Read alignment, annotation, and quantification of reads were performed with miRquant 2.0
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: RPMMM = Read counts normalized to the total number of reads mapped to all miRNA/isomiR loci multiplied by 1 million.

source_name: bronchoalveolar lavage fluid extracellular vesicles

growth_protocol: Mice were housed on alpha-dri bedding with ad libitum food/water and a standard 12 hour light cycle.

extract_protocol:
Bronchoalveolar lavage fluid extracellular vesicle RNA was isolated using a QIAGEN ExoEasy Serum/Plasma midi kit according to the manufacturers protocol.
Libraries were prepared by the University of North Carolina High Throughput Sequencing Facility using the BioOScientific NEXT FlexRNA -v3 kit. Samples were sequenced on an Illunina HS4000; 50bp single end reads; 20 million reads/sample

treatment_protocol: Mice were exposed to Filtered Air (Control), 1 or 2 ppm Ozone in a whole body inhalation exposure chamber for 3 hours.

tag: exposure

value: 2 ppm Ozone

tag: age

value: 8 to 10 weeks


title: Veh-La1

description:
2014_526_ATCACG_L001
Veh, lateral, Biological replicate A, Technical replicate 1


title: F_ME79_EV_TAGCTT_S31

description:
pooled BALF from 4 mice
F_ME79_EV_TAGCTT_S31_L003

value: bronchoalveolar lavage fluid extracellular vesicles

value: Filtered Air


title: F2 Embry.63 T CM WT 321Mu

type: RNA

city: Dummerstorf

first: Siriluck

last: Ponsuksili

address: Wilhelm-stahl-allee 2

country: Germany

institute: FBN

description:
Gene expression data from skeletal muscle of 63 dpc of F2 population basedbreed Pi and DL.
Muscle samples of foetuses (F2) derived from the F1 sows were collected and evaluated at gestational day 63. Muscle (longissimus dorsi) samples were immediately frozen in liquid nitrogen and stored at -80°C until RNA extraction.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42 C on Affymetrix Porcine Snowball Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500.

label: biotin

organism: Sus scrofa

source_name: Musculus longissimus dorsi tissue from 63 dpc pig

label_protocol: biotin-labeled cRNAs were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated using TRI Reagent (Sigma, Taufkirchen, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was cleaned up using the RNeasy Kit (Qiagen, Hilden, Germany).

tag: breed

value: F2 based German Landrace (DL) x Pietrain (Pi)

value: Musculus longissimus dorsi


title: Cre-4b1

description:
2014_525_GGCTAC_L001
Cre, fourth, Biological replicate B, Technical replicate 1

source_name: S129_Cre_Choroid plexus, 4th ventricle

value: Cre


title: A_ME79_EV_ATCACG_S36

description:
pooled BALF from 3 mice
A_ME79_EV_ATCACG_S36_L003

value: 1 ppm Ozone


title: Otx2(+/-)-2

description:
2013_0259_TTAGGC_L001
Otx2 (+/-), Biological replicate B

source_name: B6D2_Otx2 (+/-)_Choroid plexus, 4th ventricle


title: Cre-Lb1

description:
2014_523_ACTTGA_L001
Cre, lateral, Biological replicate B, Technical replicate 1

source_name: S129_Cre_Choroid plexus, lateral ventricle


title: Otx2(+/AA )-2

description:
2013_0258_ATCACG_L001
Otx2(+/AA), Biological replicate B

source_name: B6D2_Otx2 (+/AA)_Choroid plexus, 4th ventricle

value: Otx2 (+/AA)


title: F2 Embry.63 T CM WT 326Mu


title: C_ME79_EV_TGACCA_S34

description:
pooled BALF from 3 mice
C_ME79_EV_TGACCA_S34_L003


title: F2 Embry.63 T CM WT 322Mu


title: EPI+SA+H_4

city: Leuven

first: Marino

last: Caruso

address: Herestraat 49

department: Oncology

country: Belgium

institute: KULeuven

description: mESCs were cultured in N2B27 medium supplemented with 12 ng/ml of bFGF and 20 ng/ml of activin for 48H on 15 μg/ml fibronectin-coated plates

data_processing:
Quality control of raw reads was performed with FastQC v0.11.7
Adapters were filtered with ea-utils fastq-mcf v1.05 (Erik Aronesty (2011)
Splice-aware alignment was performed with HiSAT2
BAM files were handled with Samtools v1.5
Quantification of reads per gene was performed with HT-seq Count v2.7.14
Genome_build: mouse reference genome mm10
Supplementary_files_format_and_content: Tab-delimited file with raw gene counts for every gene and every sample

source_name: ES-E14TG2a mESCs

growth_protocol: mESCs were cultured in N2B27 medium consisting in 1:1 mixture of DMEM/F12 and Neurobasal Medium supplemented with 1x N-2 Supplement, 1x B-27 Supplement, 1/100 penicillin-streptomycin, 1x MEM nonessential amino acids (NEAA), 1x GlutaMAX, 1x sodium-pyruvate and 0.1 mM β-mercaptoethanol on 0.2 % gelatin-coated plates

extract_protocol:
RNA was extracted  with the ReliaPrep™ RNA Tissue Miniprep System (Promega, Z6111) following manufacturer’s protocol for non-fibrous tissue by adding RNA lysis buffer on pelleted cells.
Sequence libraries were prepared with the Lexogen QuantSeq 3' mRNA-Seq library prep kit according to the manufacturer protocol. Samples were indexed to allow for multiplexing. Library quality and size range were assessed using a Bioanalyzer (Agilent Technologies) with the DNA 1000 kit (Agilent Technologies, California, USA).
Single-end reads of 50 bp length were produced with a minimum of 1M reads per sample

value: ES-E14TG2a mESCs

tag: model

value: EPI 48h

tag: treatment

value: 0.5 mM succinylacetone + 10uM Hemin 48h


title: B_ME79_EV_CGATGT_S39

description:
pooled BALF from 3 mice
B_ME79_EV_CGATGT_S39_L003


title: Cre-La1

description:
2014_522_TGACCA_L001
Cre, lateral, Biological replicate A, Technical replicate 1


title: F2 Embry.63 T CM WT 317Mu

value: 63 days post conception (dpc)


title: D_ME79_EV_ACAGTG_S33

description:
pooled BALF from 4 mice
D_ME79_EV_ACAGTG_S33_L003


title: Otx2(+/-)-1

description:
2013_0256_GCCAAT_L001
Otx2 (+/-), Biological replicate A

value: Choroid plexus, 4th ventricle


title: WT-2

description:
2013_0260_CAGATC_L001
WT, Biological replicate B

source_name: B6D2_Ot2 (+/+)_Choroid plexus, 4th ventricle


title: EPI+SA+H_2


title: EPI+SA+H_1


title: F2 Embry.63 T CM WT 316Mu


title: Otx2(+/AA)-1

description:
2013_0255_CGATGT_L001
Otx2 (+/AA), Biological replicate A


title: F2 Embry.63 T CM WT 319Mu


title: EPI+SA_4

value: 0.5 mM succinylacetone 48h


title: F2 Embry.63 T CM WT 315Mu


title: F2 Embry.63 T CM WT 318Mu


title: EPI+SA_3


title: WT_H3K27me3

city: Toon

first: Junpei

last: Suzuki

address: Shitukawa

department: Graduate School of Medicine

country: Japan

institute: Ehime University

library_source: genomic

data_processing:
Illumina Casava1.8.2 software used for basecalling.
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie (Galaxy Tool Version 1.1.2)
peaks were called using MACS (Galaxy Tool Version 1.0.1)
All ChIP-seq analysis was performed on Galaxy web site
Genome_build: mm9
Supplementary_files_format_and_content: wig

molecule: genomic DNA

source_name: WT_Splenic CD8 T cell

growth_protocol: Naïve CD8 T (CD44lowCD62Lhigh) cells were prepared from spleens of WT or Utx KO mice.  Naïve CD8 T cells were stimulated with an immobilized anti-TCR-β mAb (3 μg/ml, H57-597; BioLegend) and an anti-CD28 mAb (1 μg/ml, 37.5; BioLegend), and IL-2 (10 ng/ml, Cat.21-8021:Tonbo biosciences) for two days.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to NEB's instructions accompanying the NEBNext ChIP-Seq Library prep Master Mix Set for Illumina (E6240)

tag: strain background

tag: genotype/variation

value: wild type

value: spleen

value: Naive CD8 T (CD44lowCD62Lhigh) cells

tag: chip antibody


title: EPI+SA+H_3


title: F2 Embry.63 T CM WT 310Mu


title: WT-1

description:
2013_0257_CTTGTA_L001
WT, Biological replicate A


title: EPI+SA_1


title: EPI_4

value: Untreated


title: EPI+SA_2


title: Daxx F/F GMP 1 [3427]

city: Bonn

first: Paolo

last: Salomoni

address: Sigmund-Freud-Str. 27

institute: DZNE e.V.

description:
180829_GMP_NormalizedCounts_AllGenes.txt
180829_GMP_NormalizedCounts_TEtranscripts.txt
3427

data_processing:
Illumina Casava 1.8.4 for base calling and demultiplexing
Sequencing reads were adapter trimmed using Cutadapt 1.13 and aligned against mm10 (GENCODE release M14) using STAR aligner 2.5.3 with standard settings. For repeat element analysis STAR aligner was run with the following options: --outFilterMultimapNmax 100 --winAnchorMultimapNmax 100.
Reads mapping to rRNA, the mitochondrial genome and non-uniquely were removed. For repeat element expression analysis only reads mapping to the mitochondrial genome were removed.
Differentially expressed genes and repeat elements were obtained by running DESeq2 1.16.1.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file with DESeq2 normalized counts for each sample

source_name: Hematopoietic Progenitor Cell

extract_protocol:
Primary hematopoietic stem/progenitor cells were isolated form bone marrow and populations sorted by flow cytometry. Total RNA was extracted using Trizol reagent.
Illumina sequencing libraries were created with the Ovation SoLo RNA-seq kit from NuGEN Technologies according to the manufacturer's instructions.

value: Bone marrow

value: Daxx F/F Cre +/-


title: Daxx +/+ GMP 1 [3425]

description:
180829_GMP_NormalizedCounts_AllGenes.txt
180829_GMP_NormalizedCounts_TEtranscripts.txt
3425

value: Daxx +/+ Cre +/-


title: Daxx +/+ GMP 2 [3426]

description:
180829_GMP_NormalizedCounts_AllGenes.txt
180829_GMP_NormalizedCounts_TEtranscripts.txt
3426


title: Daxx F/F GMP 2 [3428]

description:
180829_GMP_NormalizedCounts_AllGenes.txt
180829_GMP_NormalizedCounts_TEtranscripts.txt
3428


title: Utx_KO_H3K27me3

source_name: Utx_KO_Splenic CD8 T cell

value: Utx KO


title: Daxx F/F KLS 2 [3424]

description:
180829_KLS_NormalizedCounts_AllGenes.txt
180829_KLS_NormalizedCounts_TEtranscripts.txt
3424

source_name: Hematopoietic Stem/Progenitor Cell


title: EPI_3


title: EPI_2


title: Daxx F/F KLS 1 [3423]

description:
180829_KLS_NormalizedCounts_AllGenes.txt
180829_KLS_NormalizedCounts_TEtranscripts.txt
3423


title: 2IL+SA+H_4

description: mESCs were cultured in N2B27 medium supplemented with with 103 U/ml of mLIF, 3 μM of GSK3 inhibitor (CHIR99021) and 1 μM of MEK inhibitor (PD0325901)

value: Naive 2IL


title: Daxx +/+ KLS 2 [3422]

description:
180829_KLS_NormalizedCounts_AllGenes.txt
180829_KLS_NormalizedCounts_TEtranscripts.txt
3422


title: F2 Embry.63 T CM WT 308Mu

description:
Gene expression data from skeletal muscle of 63 dpc of F2 population basedbreed Pi and DL.
Muscle samples of foetuses (F2) derived from the F1 sows were collected and evaluated at gestational day 63. Muscle (longissimus dorsi) samples were immediately frozen in liquid nitrogen and stored at -80°C until RNA extraction.

value: F2 based German Landrace (DL) x Pietrain (Pi)

value: Musculus longissimus dorsi


title: EPI_1

description: mESCs were cultured in N2B27 medium supplemented with 12 ng/ml of bFGF and 20 ng/ml of activin for 48H on 15 μg/ml fibronectin-coated plates

value: ES-E14TG2a mESCs


title: F2 Embry.63 T CM WT 314Mu


title: F2 Embry.63 T CM WT 304Mu


title: F2 Embry.63 T CM WT 306Mu


title: F2 Embry.63 T CM WT 309Mu


title: F2 Embry.63 T CM WT 302Mu


title: 2IL+SA+H_3


title: Daxx +/+ KLS 1 [3421]

description:
180829_KLS_NormalizedCounts_AllGenes.txt
180829_KLS_NormalizedCounts_TEtranscripts.txt
3421


title: F2 Embry.63 T CM WT 301Mu


title: F2 Embry.63 T CM WT 300Mu


title: 2IL+SA+H_2


title: F2 Embry.63 T CM WT 299Mu


title: Daxx F/F GMP 2

data_processing:
Illumina Casava 1.8.4 for base calling and demultiplexing
Sequencing reads were adapter trimmed using Cutadapt 1.13 and aligned against mm10 (GENCODE release M14) using STAR aligner 2.5.3 with the following options: --alignIntronMax 1 --alignMatesGapMax 1800.
Reads mapping to the the mitochondrial genome and non-uniquely were removed. In addition, read duplicates were removed and start position of reads was offset by +4 bp if mapping to the positive strand and -5 bp if mapping to the negative strand.
For peak calling the ENCODE ATAC-seq analysis pipeline 0.3.4 was used.
Peak files were sorted by coordinate and overlapping peaks were merged with bedtools merge.
Genome_build: mm10
Supplementary_files_format_and_content: Bed file with merged ATAC-seq peak positions

extract_protocol:
Primary hematopoietic stem/progenitor cells were isolated form bone marrow and populations sorted by flow cytometry.
ATAC-seq libraries were created as described in Buenrostro et al. 2015. Briefly, cells were lysed and treated with Tn5 Transposase from the Nextera Library Prep kit from Illumina for 30 min at 37°C. DNA was purified with Qiagen MinElute PCR purification kit and libraries were generated by PCR amplification using Nextera Index Primers from Illumina.


title: Daxx F/F GMP 1


title: F2 Embry.63 T CM WT 305Mu


title: F2 Embry.63 T CM WT 298Mu


title: 2IL+SA_4


title: Daxx +/+ GMP 1


title: 2IL+SA_3


title: PDLF_si-control_day0

city: Okayama

first: Shigeki

state: Okayama

address: 2-5-1 Shikata-cho, Kita-ku

department: Department of Operative Dentistry

institute: Okayama University

data_processing:
Adapter trimming was conducted with Trim galore with default setting and then aligned to a reference genome (hg38) using HISAT2. The gene expression at exons was quantified using `analyzeRepeast.pl ` command in HOMER using `-strand both` and `-count exons` to identify expressed genes.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all 4 samples in rpkm-Genes_ss1418_trimglore.txt

source_name: periodontal ligament fibroblasts

growth_protocol: PDLF cells were maintained in SCBM Stromal Cell Growth Basal Medium (Lonza Inc. CC-3204).

extract_protocol:
RNA was isolated from PDLF with RNAiso plus. Purified RNA was DNase-treated and further used for RNA-seq analyses.
Input RNA was converted to cDNA libraries using the NEBNExt poly(A) mRNA magnetic isolation module. Libraries were sequenced using 150-bp paired-end reads on an illumine Novaseq instruments.

treatment_protocol: PDLF cells were cultured in induction medium (low glucose DMEM with ascorbic acid (100 mg/ml) and beta-glecerophosphate (10 mM)). Medium was replaced every 3 days.

value: periodontal ligament

tag: supplier

value: Lonza

tag: knockdown

value: control

tag: day


title: PDLF_si-PPARg_day0

value: si-PPARg


title: 2IL+SA+H_1

value: 0.5 mM succinylacetone + 10uM Hemin 48h


title: PDLF_si-control_day6


title: PDLF_si-PPARg_day6


title: 2IL+SA_2

value: 0.5 mM succinylacetone 48h


title: Daxx F/F CMP 2


title: 2IL+SA_1


title: Daxx +/+ GMP 2


title: 2IL_4


title: 2IL_3


title: Daxx F/F LT.HSC 2

source_name: Hematopoietic Stem Cell


title: Daxx +/+ CMP 2


title: Daxx F/F CMP 1


title: Daxx +/+ LT.HSC 2


title: Daxx +/+ CMP 1


title: 2IL_1


title: Daxx F/F LT.HSC 1


title: PDLF_input2

description: inputDNA

data_processing:
Adapter trimming and quality check were conducted with Trim galore and then aligned to a reference genome (hg38) using Bowtie2 with `-seed` parameters to efficiently use multimap reads with assuring reproducibility. Tag directories were generated using `makeTagDirectory` command in HOMER and ChIP-seq peaks were identified using the `getDiffrentialPeaksReplicates.pl` command in HOMER, specifying `-style histone` to generate a high confidence set of peaks across duplicates. This HOMER command internally calls DESeq2 to calculate enrichment value for each peak using the individual raw counts and return only those peaks that pass 2-fold enrichment and a FDR-adjusted p-value of < 0.05. Input chromatin DNA was used as controls.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated by bamCoverage commond.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Cells used for ChIP-seq analysis were fixed with formaldehyde and ChIP was performed using the SimpleChIP plus enzymatic chromatin IP kit and magnetic beads (Cell Signaling Technologies) following the manufacturer’s protocol. Equal amounts of chromatin (estimated as chromatin obtained from 4 x 106 cells) were used for precipitation of protein-DNA complex with ChIP-validated anti-H3K27ac antibody (ab4729: Abcam). After reverse-crosslinking with proteinase K treatment, chromatin was eluted using ChIP DNA clean and concentrator (Zymo Research). Libraries were sequenced using 150-bp paired-end reads on an NovaSeq instrument to a depth of >10 million mapped reads.

tag: antibody

value: input

value: not provided


title: PDLF_si-control_duplicate1

description: ChIP-DNA

value: anti-H3K27ac antibody (ab4729)


title: PDLF_si-PPARg_duplicate1

description: ChIP-DNA

value: PPARg


title: PDLF_input1

description: inputDNA


title: PDLF_si-PPARg_duplicate2

description: ChIP-DNA


title: PDLF_si-control_duplicate2

description: ChIP-DNA


title: 2IL_2

value: Untreated


title: ChIP-seq-D-Pol2-SPT5AID7-shNEDD4-Vehicle

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

description: ChIP-seq Pol II

data_processing:
For ChIP-seq, single-end raw reads trimmed by Trimmomatic 0.33 (Bolger et al., 2014) were aligned to a concatenated genome comprised of human hg38 and mouse mm10 assemblies, using bowtie 2.2.6 (Langmead and Salzberg, 2012) with --sensitive option. The aligned reads with MAPQ ≥ 30 were extended to 150 bp and read counts were normalized to total reads aligned to spike-in genome. Metaplots of ChIP-seq signals were generated using deepTools 3.1.1 (Ramírez et al., 2016).
For PRO-seq, low-quality bases and adapters from 3’ ends of reads were removed using cutadapt 1.14 (Martin, 2011) requiring a read length of 16–36 bp. Reads derived from ribosomal RNA were filtered out by mapping reads on human and fly ribosomal DNA. The remaining reads were aligned using bowtie 2.2.6 with --very-sensitive option (Langmead and Salzberg, 2012), to a concatenated genome comprised of human hg38 and fly dm6 assemblies. The 5’ ends of aligned reads with MAPQ ≥ 30 were taken by bedtools genomecov 2.25 (Quinlan and Hall, 2010) with -strand and -5 options, and strands of the 5’ ends of reads were then swapped. Read counts were normalized to total reads aligned to the spike-in genome. Heatmaps and metaplots of PRO-seq signal were generated by deepTools 3.1.1 (Ramírez et al., 2016).
For TT-seq, single-end raw reads trimmed by Trimmomatic 0.33 (Bolger et al., 2014) were aligned to human genome hg38 assemblies, using bowtie 2.2.6 (Langmead and Salzberg, 2012) with --sensitive option. Heatmaps of ChIP-seq signals were generated using deepTools 3.1.1 (Ramírez et al., 2016).
Genome_build: hg38, mm10, dm6
Supplementary_files_format_and_content: bigWig files with normalized read counts were provided for all samples.

growth_protocol: Human DLD-1 cells that constitutively express OsTIR1 were cultured at 37°C in DMEM (Sigma #D6429) supplemented with 10% FBS (Sigma #F2442), 1% Pen-Strep (Gibco #15140-122) in CO2 incubators. Yeast cells were grown in YPAD medium

extract_protocol:
For ChIP-seq in human DLD1 cells, 20-50 million cells were crosslinked with 1% paraformaldehyde (Electron Microscopy Sciences) in PBS for 10 min at r.t. Spike-in mouse embryonic fibroblast fixed cells were added to samples as described previously (Orlando et al., 2014). Chromatin was sonicated with the Covaris E220 for 4 min with 10% duty cycle, 140 peak intensity power, 200 cycles per burst. Immunoprecipitations were carried out with antibodies and Dynabeads Protein G (Invitrogen). For ChIP-seq in yeast cells, cells were fixed with 2.2% formaldehyde for 15 min. PRO-seq sample preparation was performed according to the previously described qPRO-seq protocol (Judd et al., 2020). ~5 million DLD-1 nuclei mixed with spike-in Drosophila S2 nuclei were used for nuclear run-on assay. For pulse-chase nascdnt RNA labeling with TT-seq, cells were treated with 250 nM NVP-2 for 1 h, followed by nascent RNA labeling with 500 µM 4-thiouridin (Sigma # T4509) for 15 min.
For ChIP-seq, DNA libraries were prepared by the HTP Library Preparation Kit for Illimina (KAPA). For PRO-seq, adapter sequences previously described (Mahat et al., 2016) were used. PRO-seq libraries were prepared according to the previously described qPRO-seq protocol (Judd et al., 2020). TT-seq library was prepared as described previously (Schwalb et al., 2016; Rosencrance wt al., 2020).

treatment_protocol: o induce degradation of AID-tagged proteins, 500 µM auxin was added to culture. To induce anchor-away depletion, exponentially growing yeast cultures were treated with 1.0 ug/mL Rapamycin.

tag: cell line

value: Colorectal adenocarcinoma

value: SPT5-AID7 AtAFB2

value: RPB1 NTD (Cell signaling # 14958S)


title: ChIP-seq-D-Pol2-SPT5AID7-shNEDD4-Auxin

description: ChIP-seq Pol II

tag: genotype


title: Daxx +/+ LT.HSC 1

tag: strain

tag: tissue

value: Bone marrow

value: Daxx +/+ Cre +/-


title: F2 Embry.63 T CM WT 296Mu

value: F2 based German Landrace (DL) x Pietrain (Pi)

value: Musculus longissimus dorsi

value: 63 days post conception (dpc)


title: Con A + MSCs #2

city: Guangzhou

first: Yan

last: Xu

state: Guangdong

address: No. 600 Tianhe Road

country: China

institute: The Third Affiliated Hospital of Sun Yat-Sen University

data_processing:
RNA-seq reads were aligned to the mouse Ensembl transcriptome (mm10, v76) using bowtie2 (v2.2.1) and RSEM (v1.2.18)
mapped counts were GC-normalized using EDASeq (v2.0.0)
Genome_build: mm10
Supplementary_files_format_and_content: csv files containing ensembl gene accession number, gene name and normalised abundance estimates for each transcript

source_name: Con A + MSCs #2 liver

growth_protocol: C57BL/6J mice were housed under specific pathogenfree conditions. Experiments were performed with animals at 8-10 weeks of age under ethical conditions approved by the Institutional Animal Care and Use Committee of The Third Affiliated Hospital of Sun Yat-sen  University.

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction.
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase（RNase H-）. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and  library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina NovaSeq platform and 150 bp paired-end reads were generated.

treatment_protocol: A single dose of Con A (Sigma-Aldrich) was administrated at 15mg/kg through the tail vein. PBS or 2 × 106 hUC-MSCs suspended in 200 μL PBS were transplanted intravenously (i.v) 30 min after Con A injection  (N = 4/group). Liver tissues were collected 24 h later for further analysis.

value: liver

value: Con A + MSCs


title: ChIP-seq-D-Pol2-SPT5AID7-shCUL3-2-Vehicle

description: ChIP-seq Pol II

tag: cell type


title: ChIP-seq-D-Pol2-SPT5AID7-shCUL3-1-Auxin

description: ChIP-seq Pol II


title: Con A + MSCs #4

source_name: Con A + MSCs #4 liver


title: ChIP-seq-D-Pol2-SPT5AID7-shCUL3-1-Vehicle

description: ChIP-seq Pol II


title: ChIP-seq-D-Pol2-SPT5AID7-shCUL3-2-Auxin

description: ChIP-seq Pol II


title: Con A + MSCs #3

source_name: Con A + MSCs #3 liver


title: Con A + MSCs #1

source_name: Con A + MSCs #1 liver


title: F2 Embry.63 T CM WT 291Mu

source_name: Musculus longissimus dorsi tissue from 63 dpc pig


title: ChIP-seq-D-Pol2-SPT5AID7-shNT-Vehicle

description: ChIP-seq Pol II

value: shNT-Vehicle


title: Con A #4

source_name: Con A #4 liver

value: Con A


title: F2 Embry.63 T CM WT 286Mu


title: ChIP-seq-D-Pol2-SPT5AID7-shNT-Auxin

description: ChIP-seq Pol II

value: shNT-Auxin


title: Con A #3

source_name: Con A #3 liver


title: F2 Embry.63 T CM WT 295Mu


title: AnpKDH2AZKD2

city: Mississauga

first: iva

last: zovkic

state: ON

address: 3359 Mississauga road North

country: Canada

institute: University of Toronto Mississauga

data_processing:
raw sequencing data was aligned to mm10 genome using RNA-STAR
alignment files were read count normalized for visualization using deepTools bamCoverage
differential gene expression from alignment files using DESeq2
Genome_build: mm10

molecule: polyA RNA

source_name: mouse hippocampal neurons

growth_protocol: primary neurons were made from E16 embryos. Gentle dissociation with Trypsin was followed by manual dissociation and neurons were plated on Poly L lysine coated plates

extract_protocol:
RNA was collected using the Direct-zol RNA mini prep kit (Zymo research cat # R2051)
poly-A tail RNA selection, 250-300bp insert cDNA selection.

treatment_protocol: neurons were infected with AAVs to knock down Anp32e or Anp32e and H2A.Z

value: primary hippocampal neurons

tag: developmental stage

value: 9 DIV

tag: condition


title: AnpKDH2AZKD3


title: Scr1

value: shScr


title: F2 Embry.63 T CM WT 293Mu

tag: breed

tag: age


title: Scr4


title: Scr2


title: F2 Embry.63 T CM WT 279Mu


title: AnpKDH2AZKD1


title: AnpKDH2AZKD4


title: Scr3


title: Wild Type Teratoma 2 RNA-seq

first: Udit

last: Parekh

address: 9500 Gilman Drive, Room 353, Powell-Focht (EBU3A)

department: Bioengineering

institute: University of California, San Diego

description:
Bulk RNA-seq data from teratoma formed from wild type H1 hESCs
validation_tumors_counts.csv
WT_ter2_S122

data_processing:
Samples were sequenced on an Illumina NovaSeq 6000 platform
For scRNA-seq samples, fastq files were aligned, and cell barcodes and UMIs processed using cellranger count (Cell Ranger version 3.0.0). Lists of barcodes and features, and the feature-barcode matrix were generated by Cell Ranger v3.0.0. The reference genome used was combined hg19 and mm10.
For bulk RNA-seq the fastq files were aligned using STAR Aligner and read counts obtained with the --quantMode GeneCounts option, with the reference human genome GRCh38 and mapped to exons using Ensembl v99.
For barcodes amplified from genomic DNA, barcodes were aligned using Bowtie2 and counted using MAGeCK.
Genome_build: hg19
Supplementary_files_format_and_content: scRNA-seq processed data for each sample is comprised of three zipped, tab-separated files: list of cell barcodes (files ending in _barcodes.tsv.gz), list of genes/features (files ending in _features.tsv.gz) and a feature-barcode matrix file (files ending in _matrix.mtx.gz)
Supplementary_files_format_and_content: Genotype to cell dictionaries for scRNA-seq data consist of lists of cells mapped to each genotype (files ending in _genotype.csv)
Supplementary_files_format_and_content: Bulk RNA-seq processed data consists of read counts for each gene (validation_tumors_counts.csv)
Supplementary_files_format_and_content: Barcode counts from genomic DNA processed data consists of read counts for each barcode (files ending in _gDNA_BC_counts.txt)

source_name: Human tumor

growth_protocol: H1 human embryonic stem cells (hESCs) were maintained in feeder free culture in mTeSR1 and passaged with Versene.  For round 1 tumors: H1 hESCs were passaged with Accutase, transduced with lentiviral particles for driver overexpression the next day and maintained under hygromycin selection for up to 4 days. 6-8 million of these cells were then resuspended in a 1:1 mix of Matrigel and mTeSR1 and injected subcutaneously into immunodeficient mice for tumor formation. Tumors were grown for up to 11 weeks and then extracted and dissociated for single cell RNA-sequencing, bulk RNA-sequencing or barcode amplification from genomic DNA.  For round 2 tumors: 6-8 million dissociated cells from round 1 tumors were resuspended in matrigel and injected subcutaneously into immunodeficient mice for tumor formation. Tumors were grown for up to 11 weeks and then extracted and dissociated for single cell RNA-sequencing, bulk RNA-sequencing or barcode amplification from genomic DNA.

extract_protocol:
Teratomas and tumors were dissociated using the standard GentleMACS human tumor dissociation protocol. For scRNA-seq, dissociated cells were resuspended in PBS + 0.04% BSA and processed on the 10X Genomics Chromium system using standard protocols. For bulk RNA extraction, dissociated cells were pelleted, RNA extracted using a Qiagen RNeasy kit and RNA-seq libraries prepared. For barcode amplification from genomic DNA, dissociated cells were pelleted, genomic DNA extracted using the Qiagen DNeasy kit and barcodes were PCR amplified and prepared for sequencing.
scRNA-seq Libraries were constructed using the standard Chromium Single Cell 3ʹ Reagent Kits v3 workflow (10x Genomics). Bulk RNA-seq libraries were constructed using NEBNext Ultra RNA Library Prep Kit.

tag: genetic perturbation

value: wild type

tag: tumor round

value: Round 1


title: Con A #2

source_name: Con A #2 liver

tag: treatment


title: F2 Embry.63 T CM WT 282Mu


title: F2 Embry.63 T CM WT 284Mu


title: F2 Embry.63 T CM WT 289Mu


title: F2 Embry.63 T CM WT 280Mu


title: F2 Embry.63 T CM WT 287Mu


title: F2 Embry.63 T CM WT 294Mu


title: F2 Embry.63 T CM WT 277Mu


title: F2 Embry.63 T CM WT 288Mu


title: F2 Embry.63 T CM WT 290Mu


title: F2 Embry.63 T CM WT 285Mu


title: Wild Type Teratoma 1 RNA-seq

description:
Bulk RNA-seq data from teratoma formed from wild type H1 hESCs
validation_tumors_counts.csv
WT_ter1_S121


title: F2 Embry.63 T CM WT 292Mu


title: AnpKD3


title: F2 Embry.63 T CM WT 278Mu


title: AnpKD4


title: AnpKD2


title: MEK1 Round 2 Tumor 2 gDNA barcodes

description:
Driver barcode data from genomic DNA from Round 2 Tumor 2 formed from mix of H1 cells transduced with MEK1 (S218D/S222D) or mCherry
MEK_gDNA_BC_counts.txt
MEK1_Round2_ter2_gDNA_BC_S36

data_processing:
Library strategy: DNA-seq
Samples were sequenced on an Illumina NovaSeq 6000 platform
For scRNA-seq samples, fastq files were aligned, and cell barcodes and UMIs processed using cellranger count (Cell Ranger version 3.0.0). Lists of barcodes and features, and the feature-barcode matrix were generated by Cell Ranger v3.0.0. The reference genome used was combined hg19 and mm10.
For bulk RNA-seq the fastq files were aligned using STAR Aligner and read counts obtained with the --quantMode GeneCounts option, with the reference human genome GRCh38 and mapped to exons using Ensembl v99.
For barcodes amplified from genomic DNA, barcodes were aligned using Bowtie2 and counted using MAGeCK.
Genome_build: hg19
Supplementary_files_format_and_content: scRNA-seq processed data for each sample is comprised of three zipped, tab-separated files: list of cell barcodes (files ending in _barcodes.tsv.gz), list of genes/features (files ending in _features.tsv.gz) and a feature-barcode matrix file (files ending in _matrix.mtx.gz)
Supplementary_files_format_and_content: Genotype to cell dictionaries for scRNA-seq data consist of lists of cells mapped to each genotype (files ending in _genotype.csv)
Supplementary_files_format_and_content: Bulk RNA-seq processed data consists of read counts for each gene (validation_tumors_counts.csv)
Supplementary_files_format_and_content: Barcode counts from genomic DNA processed data consists of read counts for each barcode (files ending in _gDNA_BC_counts.txt)

value: 1:1 mix of H1 cells transduced with MEK1 (S218D/S222D) or mCherry

value: Round 2


title: MEK1 Round 2 Tumor 2 RNA-seq

description:
Bulk RNA-seq data from Round 2 Tumor 2 formed from mix of H1 cells transduced with MEK1 (S218D/S222D) or mCherry
validation_tumors_counts.csv
MEK1_Round2_ter2_RNA_Seq_S34


title: AnpKD1


title: Con A #1

source_name: Con A #1 liver


title: Ctrl #4

source_name: Ctrl #4 liver

value: Control


title: Ctrl #3

source_name: Ctrl #3 liver


title: RNA-seq B16 F1 cell line

city: Vancouver

first: Tully

middle: Michael

last: Underhill

state: British Columbia

address: 2222 Health Sciences Mall

department: Biomedical Research Centre

institute: University of British Columbia

data_processing:
Basecalls were made using RTA v2.1.
Demultiplexing was achieved using bcl2fastq2.
De-multiplexed read sequences were then aligned to the Mouse Genome mm10 reference sequence using TopHat splice junction mapper with Bowtie 2
Assembly and differential gene expression were estimated using Cufflinks
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: B16 F1 cell line, ATCC CRL-6323

growth_protocol: Cells were routinely cultured in high glucose DMEM (Sigma-Aldrich) supplemented with 8% FBS, utilized within 10 passages after thawing from liquid nitrogen, and regularly tested for mycoplasma.

extract_protocol:
Total RNA from subconfluent B16F0, F1, and F10 cell monolayers was isolated using the QIAshredder followed by RNeasy kit (Qiagen).  Sample integrity was tested on an Agilent Bioanalyzer 2100 RNA 6000 Nano chip (5067-1511)
TruSeq Stranded mRNA library kit (Illumina)

value: Derived from melanoma

tag: subclone


title: RNA-seq B16 F10 cell line

source_name: B16 F10 cell line, ATCC CRL-6475


title: RNA-seq B16 F0 cell line

source_name: B16 F0 cell line, ATCC CRL-6322


title: MEK1 Round 2 Tumor 1 gDNA barcodes

description:
Driver barcode data from genomic DNA from Round 2 Tumor 1 formed from mix of H1 cells transduced with MEK1 (S218D/S222D) or mCherry
MEK_gDNA_BC_counts.txt
MEK1_Round2_ter1_gDNA_BC_S35


title: MEK1 Round 2 Tumor 1 RNA-seq

description:
Bulk RNA-seq data from Round 2 Tumor 1 formed from mix of H1 cells transduced with MEK1 (S218D/S222D) or mCherry
validation_tumors_counts.csv
MEK1_Round2_ter1_RNA_Seq_S33


title: 20_ DKO_Ezetimibe

city: SOUTH SAN FRANCISCO

first: Tracy

last: Yamawaki

state: California

address: 1120 VETERANS BLVD.

institute: AMGEN, INC.

description: heart tissue from Ezetimibe treated ABCG5/8 DKO mouse

data_processing:
Alignment and quantification were performed using Oshell v10.0.1.111.
Reads were aligned to the OmicsoftGencode.V19 mouse reference based on GRCm38.
Quantile normalization of FPKM values was performed using the 70th percentile of gene expression.
Genome_build: GRCm38

source_name: heart tissue

extract_protocol:
total RNA was extracted using the Qiagen Rneasy kit
TruSeq Stranded mRNA Library Prep (Illumina)

value: heart

tag: gender

value: Male

value: Ezetimibe

value: ABCG5/8 DKO


title: Ctrl #2

source_name: Ctrl #2 liver

value: liver


title: Ctrl #1

source_name: Ctrl #1 liver


title: 19_ DKO_Ezetimibe


title: MEK1 Round 1 Tumor 2 gDNA barcodes

description:
Driver barcode data from genomic DNA from Round 1 Tumor 2 formed from mix of H1 cells transduced with MEK1 (S218D/S222D) or mCherry
MEK_gDNA_BC_counts.txt
MEK1_Round1_ter2_gDNA_BC_S100


title: MEK1 Round 1 Tumor 1 gDNA barcodes

description:
Driver barcode data from genomic DNA from Round 1 Tumor 1 formed from mix of H1 cells transduced with MEK1 (S218D/S222D) or mCherry
MEK_gDNA_BC_counts.txt
MEK1_Round1_ter1_gDNA_BC_S99


title: CLPS5

city: Burlington

first: Feng-Qi

last: Zhao

state: VT

address: #211 Terrill Building, 570 Main Street

department: Department of Animal and Veterinary Sciences

institute: University of Vermont

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to mm10 whole genome using using the STAR (v2.5) aligner.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using HTSeq (v0.6.1). Differential gene expression analysis was performed using the DESeq2 R package (v2_1.6.3).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited files include FPKM values for each Sample, DEGs

source_name: Mammary gland

extract_protocol:
Mammary gland were removed, flash frozen in liquid nitrogen, and RNA was isolated using RNeasy Mini Kit (Qiagen). NEBNext® UltraTM RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The left and right sides of the 4th pair of mouse mammary glands were alternatively injected with either lipopolysaccharide (LPS, E. coli 055: B5, 50 μL of 0.4 mg/mL) or sterile PBS through the teat meatus 3 days postpartum (n = 9). The 4th glands were individually collected at 12 h after the LPS injection and analyzed for gene expression changes by RNA sequencing

value: BALB/c

value: Mammary gland

value: Lactation day 3

value: LPS, 0.4 mg/mL, 50 µL


title: 18_ DKO_Ezetimibe


title: F2 Embry.63 T CM WT 276Mu

value: F2 based German Landrace (DL) x Pietrain (Pi)

value: Musculus longissimus dorsi

value: 63 days post conception (dpc)


title: Ctrl_2

city: Doha

first: Tanwir

last: Habib

address: Al Luqta Street

country: Qatar

institute: Weill Cornell Medicine Qatar

data_processing:
reads were mapped to the mouse genome mm10 using the Tophat version 2.0.12 with the reference annotation file mm10.
Cufflinks version 2.2.1 was used for transcript quantification and cuffdiff was used for differential expression analysis.
Fold change (FC) between p50 / wild type, HP / Control were calculated.
Genome_build: MM10
Supplementary_files_format_and_content: cuffdiff output in FPKM format

source_name: Gmacs from mice stomach

growth_protocol: H. pylori were grown in BHI media at 37°C and 10% CO2

extract_protocol:
Total RNA was isolated using Trizol and RNA integrity was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies).
Library preparation was performed using the Illumina TruSeq stranded mRNA Sample Preparation Kit. Samples were sequenced on the Illumina HiSeq 2500 using v3 SBS chemistry. Libraries were sequenced on a Single Read 50bp run at 30 million passing filter reads/sample.

treatment_protocol: Gastric Macrophage isolated from mice were infected with H. pylori at MOI of 1:10

value: stomach

value: macrophage

value: wildtype

tag: infection status

value: not infected


title: HP_2

source_name: Ex-vivo infected Gmacs from mice stomach with H. pylori

value: infected ex-vivo with H. pylori


title: HP_1


title: CLPS4


title: F2 Embry.63 T CM WT 275Mu

source_name: Musculus longissimus dorsi tissue from 63 dpc pig


title: 16_ DKO_Ezetimibe

value: heart


title: CLPS3


title: MEK1 Pre-injection gDNA barcodes

description:
Driver barcode data from genomic DNA from pre-injection mix of H1 cells transduced with MEK1 (S218D/S222D) or mCherry
MEK_gDNA_BC_counts.txt
MEK1_pre_inject_gDNA_BC_S98

value: 1:1 mix of H1 cells transduced with MEK1 (S218D/S222D) or mCherry

value: Pre-injection


title: NF-κB1(p50)_2

source_name: Gmacs from p50 knockout mice stomach

value: NF-kappaB1(p50) knockout


title: 15_ TKO_Ezetimibe

description: heart tissue from Ezetimibe treated ABCG5/8 NPC1L1 TKO mouse

value: Male

value: Ezetimibe

value: ABCG5/8 NPC1L1 TKO


title: Ctrl_1


title: 17_ DKO_Ezetimibe

value: ABCG5/8 DKO


title: CLPS2

value: BALB/c

value: Mammary gland

value: Lactation day 3

value: LPS, 0.4 mg/mL, 50 µL


title: 13_ TKO_Ezetimibe


title: MYC + AKT Round 2 Tumor 2 gDNA barcodes

description:
Driver barcode data from genomic DNA from Round 2 Tumor 2 formed from serially injected c-MYC+myr-AKT1/mCherry round 1 tumor cells
MYC_AKT_gDNA_BC_counts.txt
MYC-AKT_Round2_ter2_gDNA_BC_S46

value: 1:1 mix of H1 cells transduced with c-MYC+myr-AKT1 or mCherry

value: Round 2


title: MYC + AKT Round 2 Tumor 3 gDNA barcodes

description:
Driver barcode data from genomic DNA from Round 2 Tumor 3 formed from serially injected c-MYC+myr-AKT1/mCherry round 1 tumor cells
MYC_AKT_gDNA_BC_counts.txt
MYC-AKT_Round2_ter3_gDNA_BC_S47


title: MYC + AKT Round 2 Tumor 2 RNA-seq

description:
Bulk RNA-seq data from Round 2 Tumor 2 formed from serially injected c-MYC+myr-AKT1/mCherry round 1 tumor cells
validation_tumors_counts.csv
MYC_AKT_Round2_ter2_RNA_Seq_S120


title: Wt_2

source_name: Gmacs from wt mice stomach

value: stomach

value: macrophage

value: wildtype


title: 14_ TKO_Ezetimibe

value: heart


title: CPBS5

value: PBS, 50 µL


title: CLPS1


title: Wt_1


title: MYC + AKT Round 2 Tumor 1 gDNA barcodes

description:
Driver barcode data from genomic DNA from Round 2 Tumor 1 formed from serially injected c-MYC+myr-AKT1/mCherry round 1 tumor cells
MYC_AKT_gDNA_BC_counts.txt
MYC-AKT_Round2_ter1_gDNA_BC_S45

source_name: Human tumor


title: 12_ TKO_Ezetimibe


title: F2 Embry.63 T CM WT 273Mu

description:
Gene expression data from skeletal muscle of 63 dpc of F2 population basedbreed Pi and DL.
Muscle samples of foetuses (F2) derived from the F1 sows were collected and evaluated at gestational day 63. Muscle (longissimus dorsi) samples were immediately frozen in liquid nitrogen and stored at -80°C until RNA extraction.

value: F2 based German Landrace (DL) x Pietrain (Pi)

value: Musculus longissimus dorsi

value: 63 days post conception (dpc)


title: CPBS3


title: 10_ DKO_Vehicle

description: heart tissue from vehicle treated ABCG5/8 DKO mouse

value: Male

value: Vehicle


title: 11_ TKO_Ezetimibe

value: Ezetimibe

value: ABCG5/8 NPC1L1 TKO


title: CPBS2

value: BALB/c

value: Mammary gland


title: MYC + AKT Round 2 Tumor 1 RNA-seq

description:
Bulk RNA-seq data from Round 2 Tumor 1 formed from serially injected c-MYC+myr-AKT1/mCherry round 1 tumor cells
validation_tumors_counts.csv
MYC_AKT_Round2_ter1_RNA_Seq_S119


title: NF-κB1(p50)_1

source_name: Gmacs from  p50 knockout mice stomach

value: NF-kappaB1(p50) knockout


title: MYC + AKT Round 1 Tumor 3 gDNA barcodes

description:
Driver barcode data from genomic DNA from Round 1 Tumor 3 formed from mix of H1 cells transduced with c-MYC+myr-AKT1 or mCherry
MYC_AKT_gDNA_BC_counts.txt
MYC-AKT_Round1_ter3_gDNA_BC_S36

value: 1:1 mix of H1 cells transduced with c-MYC+myr-AKT1 or mCherry

value: Round 1


title: 9_ DKO_Vehicle

value: ABCG5/8 DKO


title: MYC + AKT Round 1 Tumor 2 gDNA barcodes

description:
Driver barcode data from genomic DNA from Round 1 Tumor 2 formed from mix of H1 cells transduced with c-MYC+myr-AKT1 or mCherry
MYC_AKT_gDNA_BC_counts.txt
MYC-AKT_Round1_ter2_gDNA_BC_S35


title: CPBS1

value: Lactation day 3


title: 8_ DKO_Vehicle


title: 7_ DKO_Vehicle


title: MYC + AKT Round 1 Tumor 2 RNA-seq

description:
Bulk RNA-seq data from Round 1 Tumor 2 formed from mix of H1 cells transduced with c-MYC+myr-AKT1 or mCherry
validation_tumors_counts.csv
MYC_AKT_Round1_ter2_RNA_Seq_S27


title: Daxx +/+ 24wpi H3K27me3 2

description:
DaxxWtWt_24wpi_H3K27me3_cov.bw
3386

data_processing:
Illumina Casava 1.8.4 for base calling and demultiplexing
Sequencing reads were adapter trimmed using Cutadapt 1.13 and aligned against mm10 (GENCODE release M14) using STAR aligner 2.5.3 with the following options: --alignIntronMax 1 --alignMatesGapMax 1800.
Reads mapping to the the mitochondrial genome and non-uniquely were removed. In addition, read duplicates were removed and start position of reads was offset by +4 bp if mapping to the positive strand and -5 bp if mapping to the negative strand.
For peak calling the ENCODE ATAC-seq analysis pipeline 0.3.4 was used.
Peak files were sorted by coordinate and overlapping peaks were merged with bedtools merge.
Identification of differentially accessible sites using diffreps with 600 bp window size.
Genome_build: mm10
Supplementary_files_format_and_content: Bed/NarrowPeak file with merged ATAC-seq peak positions and/or tab-delimited files with differentially accessible regions identified with diffreps

source_name: Hematopoietic Stem/Progenitor Cell

extract_protocol:
Primary hematopoietic stem/progenitor cells were isolated form bone marrow and Lineage-negative/c-Kit-positive (HSPCs) were enriched by MACS. Nuclei were isolated, washed and frozen in wash buffer according to the “Bench top CUT&Tag V.3” protocol (https://ww.protocols.io/view/bench-top-cut-amp-tag-bcuhiwt6).
For the actual CUT&Tag experiment, we followed the CUT&Tag-direct protocol described by Henikoff et al.74 using the CUTANA pAG-Tn5 enzyme (Epicypher). Briefly, aliquots of 30,000-45,000 native nuclei per reaction were bound to activated Concanavalin A beads. After successive incubations with primary antibody (overnight at 4°C) and secondary antibody (0.5-1 h) in wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine and 1x protease inhibitor), the beads were washed and resuspended in pAG-Tn5 (1:20 dilution) in 300-wash buffer (wash buffer containing 300 mM NaCl) for 1 h. Incubations were performed at room temperature, except when otherwise stated, in volumes of 25-50 ul in low-retention PCR tubes. Tagmentation was performed for 1 h in 300-wash buffer supplemented with 10 mM MgCl2. Following tagmentation, beads were washed in 50 ul TAPS buffer (10 mM TAPS pH8.5, 0.2 mM EDTA), resuspended in 5 ul SDS release buffer (0.1% SDS, 10 mM TAPS pH8.5) and incubated for 1 h at 58°C. SDS was neutralized with 15 ul of 0.67% Triton-X100, and 4 ul of dual indexed primers from the “IDT for Illumina Nextera DNA UD Indexes Set A” (Illumina) as well as 25 ul of NEBNext High-Fidelity 2x PCR Master mix (NEB) were added. Gap filling and 18 cycles of PCR were performed, followed by clean-up with 65 ul of SPRIselect beads (Beckman Coulter).
CUT&Tag

value: Bone marrow

value: Daxx +/+ Cre +/-

tag: chip antibody


title: CPBS4

value: PBS, 50 µL


title: Daxx +/+ 24wpi H3K9me3 2

description:
DaxxWtWt_24wpi_H3K9me3_cov.bw
3386


title: MYC + AKT Round 1 Tumor 1 RNA-seq

description:
Bulk RNA-seq data from Round 1 Tumor 1 formed from mix of H1 cells transduced with c-MYC+myr-AKT1 or mCherry
validation_tumors_counts.csv
MYC_AKT_Round1_ter1_RNA_Seq_S26


title: 6_ DKO_Vehicle

value: heart


title: MYC + AKT Pre-injection gDNA barcodes

description:
Driver barcode data from genomic DNA from pre-injection mix of H1 cells transduced with c-MYC+myr-AKT1 or mCherry
MYC_AKT_gDNA_BC_counts.txt
MYC-AKT_pre_inject_gDNA_BC_S37

value: Pre-injection


title: Daxx +/+ 24wpi Pu.1 2

description:
DaxxWtWt_24wpi_Pu1_cov.bw
3386


title: MYC + AKT Round 1 Tumor 1 gDNA barcodes

description:
Driver barcode data from genomic DNA from Round 1 Tumor 1 formed from mix of H1 cells transduced with c-MYC+myr-AKT1 or mCherry
MYC_AKT_gDNA_BC_counts.txt
MYC-AKT_Round1_ter1_gDNA_BC_S34


title: 5_ DKO_Vehicle


title: 4_ TKO_Vehicle

description: heart tissue from vehicle treated ABCG5/8 NPC1L1 TKO mouse


title: Daxx +/+ 24wpi H3.3 2

description:
DaxxWtWt_24wpi_H3.3_cov.bw
3386


title: 3_ TKO_Vehicle


title: Daxx +/+ 24wpi Pu.1 1

description:
DaxxWtWt_24wpi_Pu1_cov.bw
3320


title: AKT Round 2 Tumor 2 gDNA barcodes

description:
Driver barcode data from genomic DNA from Round 2 Tumor 2 formed from serially injected myr-AKT1/mCherry round 1 tumor cells
AKT_gDNA_BC_counts.txt
AKT_Round2_ter2_gDNA_BC_S33

value: 1:1 mix of H1 cells transduced with myr-AKT1 or mCherry

value: Round 2


title: Daxx +/+ 24wpi H3K27ac 2

description:
DaxxWtWt_24wpi_H3K27ac_cov.bw
3386


title: AKT Round 2 Tumor 2 RNA-seq

description:
Bulk RNA-seq data from Round 2 Tumor 2 formed from serially injected myr-AKT1/mCherry round 1 tumor cells
validation_tumors_counts.csv
AKT_Round2_ter2_RNA_seq_S25


title: AKT Round 2 Tumor 1 RNA-seq

description:
Bulk RNA-seq data from Round 2 Tumor 1 formed from serially injected myr-AKT1/mCherry round 1 tumor cells
validation_tumors_counts.csv
AKT_Round2_ter1_RNA_seq_S24


title: STZ4_rep1

city: Hsinchu

first: Yong Chun

last: Luo

address: Boai Street

country: Taiwan

institute: National Chiao Tung University

hyb_protocol: Total samples were hybridized using Phalanx OneArray Plus Protocol. Non-speciﬁc binding targets were washed away after 16 hours.

scan_protocol: The slides scanned using Agilent 0.1 XDR Protocol.

data_processing: GPR files were loaded into Rosetta Resolver® System (Rosetta Biosoftware) for data processing. The raw data normalized using the normalizeQuantiles function from 'limma' package (v. 3.30.7).

source_name: STZ-induced DM in 8 week mouse, replicate 1, sample 1

label_protocol: Fluorescent aRNA targets were prepared from 1 μg total RNA samples using OneArray® Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group, Taiwan) and Cy5 dye (GE Healthcare).

growth_protocol: The mice were used and growth for 8 weeks.

extract_protocol: Total RNA was extracted from the liver tissues using TRIzol Reagent through chloroform/isopropanol purification. RNA quantity and purity was assessed using NanoDrop ND-1000. Pass criteria for absorbance ratios are established as A260/A280 ≥ 1.8 and A260/A230 ≥ 1.5. RIN values are assessed and examined using Agilent RNA 6000 Nano assay to determine RNA integrity.

treatment_protocol: We administrated the MENS treatments by printed circuit board empowered by MENS device for 1 h/day, 5 days/week with 6 weeks.

value: liver

value: STZ

value: 8 weeks-old


title: 1_ TKO_Vehicle

value: Male

value: Vehicle

value: ABCG5/8 NPC1L1 TKO


title: STZ4_rep2

source_name: STZ-induced DM in 8 week mouse, replicate 2, sample 1


title: 2_ TKO_Vehicle


title: Daxx F/F Pu.1 F/F 8wpi H3K9me3 3

description:
DaxxFFPu1FF_8wpi_H3K9me3_cov.bw
H3K9me3_DaxxFFPu1FFvsDaxxWtWt_8wpi_diffsite.txt
3441

value: Daxx F/F Pu.1 F/F Cre +/-


title: STZ10_rep1

source_name: STZ-induced DM in 8 week mouse, replicate 1, sample 2


title: STZ10_rep2

source_name: STZ-induced DM in 8 week mouse, replicate 2, sample 2


title: Daxx F/F Pu.1 F/F 8wpi H3K27me3 2

description:
DaxxFFPu1FF_8wpi_H3K27me3_cov.bw
H3K27me3_DaxxFFPu1FFvsDaxxWtWt_8wpi_diffsite.txt
3394


title: Control6_rep2

source_name: No treatment in 8 week mouse, replicate 2, sample 2

value: Control


title: AKT Round 1 Tumor 3 gDNA barcodes

description:
Driver barcode data from genomic DNA from Round 1 Tumor 3 formed from mix of H1 cells transduced with myr-AKT1 or mCherry
AKT_gDNA_BC_counts.txt
AKT_Round1_ter3_gDNA_BC_S31

value: Round 1


title: MENS1_rep1

source_name: MENS treatment in 8 week STZ-induced DM mouse, replicate 1, sample 1

value: STZ+MENS


title: MENS6_rep2

source_name: MENS treatment in 8 week STZ-induced DM mouse, replicate 2, sample 2


title: MENS6_rep1

source_name: MENS treatment in 8 week STZ-induced DM mouse, replicate 1, sample 2


title: MENS1_rep2

source_name: MENS treatment in 8 week STZ-induced DM mouse, replicate 2, sample 1


title: hypg15_4

city: Zurich

first: Cora

middle: S.

last: Thiel

address: Winterthurerstrasse 190

department: Institute of Anatomy

country: Switzerland

institute: University of Zurich

data_processing:
Quaility and adapter trimming with TrimGalore! 0.6.5 in standard settings.
Read aligning with STAR aligner 2.7.8a.
featureCounts in standard settings, paired-end mode
Differential expression with DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: Read counts from featureCounts, against Ensembl Gene ID, csv table

source_name: ATCC Jurkat cells

growth_protocol: Grown in RPMI + 10% FCS + Penicillin/Streptomycin, split every second day, feeding every day

extract_protocol:
Cells were fixed by quickly releasing them into TRIzol. Cells were sheared with a needle and syringe. After chloroform extraction, 0.6ml RLT buffer was added to the aqueous supernatent. RNA was extracted with Quiagen Rneasy mini kit.
A standard polyA library was used

treatment_protocol: Jurkat cells were exposed to 15 minutes of hypergravity or to normal gravity

value: Jurkat T cells


title: Daxx F/F Pu.1 F/F 8wpi H3K9me3 2

description:
DaxxFFPu1FF_8wpi_H3K9me3_cov.bw
H3K9me3_DaxxFFPu1FFvsDaxxWtWt_8wpi_diffsite.txt
3394

value: Bone marrow


title: Control1_rep2

source_name: No treatment in 8 week mouse, replicate 2, sample 1


title: Control1_rep1

source_name: No treatment in 8 week mouse, replicate 1, sample 1


title: AKT Round 2 Tumor 1 gDNA barcodes

description:
Driver barcode data from genomic DNA from Round 2 Tumor 1 formed from serially injected myr-AKT1/mCherry round 1 tumor cells
AKT_gDNA_BC_counts.txt
AKT_Round2_ter1_gDNA_BC_S32


title: AKT Round 1 Tumor 2 gDNA barcodes

description:
Driver barcode data from genomic DNA from Round 1 Tumor 2 formed from mix of H1 cells transduced with myr-AKT1 or mCherry
AKT_gDNA_BC_counts.txt
AKT_Round1_ter2_gDNA_BC_S30


title: Control6_rep1

source_name: No treatment in 8 week mouse, replicate 1, sample 2


title: AKT Round 1 Tumor 1 gDNA barcodes

description:
Driver barcode data from genomic DNA from Round 1 Tumor 1 formed from mix of H1 cells transduced with myr-AKT1 or mCherry
AKT_gDNA_BC_counts.txt
AKT_Round1_ter1_gDNA_BC_S29


title: hypg15_3


title: Daxx F/F Pu.1 F/F 8wpi H3K27me3 3

description:
DaxxFFPu1FF_8wpi_H3K27me3_cov.bw
H3K27me3_DaxxFFPu1FFvsDaxxWtWt_8wpi_diffsite.txt
3441


title: Daxx +/+ 8wpi H3K27me3 3

description:
DaxxWtWt_8wpi_H3K27me3_cov.bw
3462

value: Daxx +/+ Cre +/-


title: 4T1-Luc met_Rep 1

city: Minneapolis

first: Rebecca

last: LaRue

state: MN

address: 117 Pleasant St SE

department: Department of Lab medicine and Pathology

institute: University of Minnesota

data_processing:
10x genomic CellRanger pipeline (version 3.0.2) was used to demultiplex, map and retrieve counts for all of the samples.
Analysis of sequencing data was performed using the Seurat R package (version 3.1.1).
Data was filtered to keep all genes expressed in >=5 cells and keep all cells with >=200 and <= 5000 genes expressed.
The global-scaling normalization method “LogNormalize” normalizes the gene expression measurements for each cell by the total expression, multiplies this by a scale factor (10,000), and log-transforms the result.
Genome_build: GRCm38
Supplementary_files_format_and_content: Seurat global-scaling normalization method “LogNormalize”

source_name: Lung

extract_protocol:
Lungs were harvested and collagenase digested. Macrophages were stained with surface markers and FACS sorted.
Libraries were prepared using the Chromium Single Cell 3’ Library and Reagent Kit v2

value: Balb/C

value: Lung

value: Macrophage

tag: tumor model

tag: timepoint

value: 5 weeks post transplant


title: hypg15_2


title: AKT Pre-injection gDNA barcodes

city: La Jolla

description:
Driver barcode data from genomic DNA from pre-injection mix of H1 cells transduced with myr-AKT1 or mCherry
AKT_gDNA_BC_counts.txt
AKT1_pre_inject_gDNA_BC_S11

source_name: Human tumor

tag: cell line

value: 1:1 mix of H1 cells transduced with myr-AKT1 or mCherry

value: Pre-injection


title: hypg15_1

tag: strain


title: scRNA-seq Sertoli

city: Pullman

first: Michael

last: Griswold

state: WA

address: Biotechnology Life Sciences

department: School of Molecular Biosciences; Center for Reproductive Biology

institute: Washington State University

description: scRAN-seq data from isolated Sertoli cells

data_processing:
Raw base call files were demultiplexed using the 10X Genomics Cell Ranger pipeline (v2.1.0) and aligned to the mouse mm10 transcriptome.
Transcriptomes were analyzed in R using the Seurat package (v3.2.2).
Low quality cell transcriptomes with over 25% mitochondrial gene representation were removed.
Resulting singe-cell transcriptomes were normalized, scale, and dimensionally reduced in Seurat using standard procedures.
Genome_build: Mus musculus mm10
Supplementary_files_format_and_content: Gene-Cell Matrix filled with Raw Read/Expression Values

source_name: Testis

extract_protocol:
Single cell suspensions of Amh-Cre;RFP male mouse testes were prepared and Sertoli cells isolated using FACS with an SH800 machine (Sony Biotechnology) gating for RFP+ cells. Live cells were loaded into a Chromium Controller (10X Genomics, Inc.).
Single-cell cDNA libraries were generated using v3 chemistry according to the manufacturer’s protocol (10X Genomics, Inc.).

value: Derived from C57BL/6 x 129s4/SvJae

tag: genotype

value: RFP heterozygote, Amh-Cre-positive

value: untreated


title: Daxx +/+ 8wpi H3K9me3 3

description:
DaxxWtWt_8wpi_H3K9me3_cov.bw
3462

source_name: Hematopoietic Stem/Progenitor Cell

tag: tissue


title: Pparg-/- (CMG_ID 11)

city: Indianapolis

first: Raymond

last: Konger

state: IN

address: 975 West Walnut Street

department: Pathology & Laboratory Medicine

institute: Indiana University School of Medicine

data_processing:
FASTQ files were aligned with STAR v.2.5.2b using parameter “--outSAMmapqUnique 60”
Aligned reads in BAM files were counted with featureCounts from the subread package v.1.5.1 with parameters “-s 2 –p –Q 10”
Counts were filtered to exclude genes with counts per million (CPM) <0.5 in a total number of samples larger than the smallest experimental group
Genome_build: UCSC mm10
Supplementary_files_format_and_content: A tab-separated text file containing gene annotation information and RAW unfiltered read counts for each sample

source_name: Skin

extract_protocol:
Dorsal epidermis was excised from euthanized mice.  The epidermis was snap frozen in liquid nitrogen.  The epidermis was scraped off using a curette until the subepidermal vascular bed was observed (pink color).  The scraped epidermis was placed into QIAzol lysis reagent (BioRad), then the RNA was further purified using a Qiagen RNeasy kit.
Library construction was done with 200 ng starting RNA using KAPA mRNA Hyperprep Kit (KK8581). Dual Index.

treatment_protocol: The epidermis was obtained from mice with no treatment.

tag: breeding

value: Pparg (flox/flox), Cytokeratin14 promoter-driven Cre+/-

value: Scraped frozen epidermis

tag: age (weeks)

value: Female

tag: rin


title: Daxx +/+ 8wpi H3K27me3 2

description:
DaxxWtWt_8wpi_H3K27me3_cov.bw
3461


title: Pparg-/- (CMG_ID 12)

value: Male


title: MYC Round 2 Tumor 3 RNA-seq

description:
Driver barcode data from genomic DNA from Round 2 Tumor 3 formed from serially injected c-MYC/mCherry round 1 tumor cells
MYC_gDNA_BC_counts.txt
MYC_Round2_ter3_gDNA_BC_S25

value: 1:1 mix of H1 cells transduced with c-MYC or mCherry

value: Round 2


title: Daxx +/+ 8wpi H3K9me3 2

description:
DaxxWtWt_8wpi_H3K9me3_cov.bw
3461

value: Bone marrow


title: Ctrl_4

tag: cell type

value: Jurkat T cells

tag: condition

value: Ctrl


title: 4T1-Luc met_Rep 2

value: Balb/C

value: Lung


title: Daxx +/+ 8wpi H3K27me3 1

description:
DaxxWtWt_8wpi_H3K27me3_cov.bw
3543

value: Daxx +/+ Cre +/-


title: Daxx +/+ 8wpi H3K9me3 1

description:
DaxxWtWt_8wpi_H3K9me3_cov.bw
3543


title: Ctrl_2


title: MYC Round 2 Tumor 1 gDNA barcodes

description:
Driver barcode data from genomic DNA from Round 2 Tumor 1 formed from serially injected c-MYC/mCherry round 1 tumor cells
MYC_gDNA_BC_counts.txt
MYC_Round2_ter1_gDNA_BC_S23

tag: genetic perturbation

tag: tumor round


title: Pparg-/- (CMG_ID 9)


title: Pparg-/- (CMG_ID 7)


title: Pparg-/- (CMG_ID 8)


title: Daxx F/F 3wpi H3K27ac 2

description:
DaxxFF_3wpi_H3K27ac_cov.bw
H3K27ac_DaxxFF_diffsite.txt
3660

value: Daxx F/F Cre +/-


title: MYC Round 2 Tumor 2 RNA-seq

description:
Bulk RNA-seq data from Round 2 Tumor 2 formed from serially injected c-MYC/mCherry round 1 tumor cells
validation_tumors_counts.csv
MYC_Round2_ter2_RNA_Seq_S17


title: Ctrl_1


title: MYC Round 2 Tumor 1 RNA-seq

description:
Bulk RNA-seq data from Round 2 Tumor 1 formed from serially injected c-MYC/mCherry round 1 tumor cells
validation_tumors_counts.csv
MYC_Round2_ter1_RNA_Seq_S16


title: CD34+ Undifferentiated  Donor 5

city: Didcot

first: Leonie

middle: Francina Hendrina

last: Fransen

state: Oxfordshire

address: CRCE

department: Toxicology

country: United Kingdom

institute: PHE

data_processing:
Raw sequence data was processed to remove adaptor sequences, contamination and low-quality reads.
Clean reads were annotated to human GRCh38 reference genome and counts processed for RPKM values and relative gene expression using CLC Genomics browser software
Statistically significant gene expression between CD34+ and differentiated lineages was established using Benjamin Hochberg adjusted p values < 0.05.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with RPKM values for every gene and sample

source_name: CD34+ hemopoietic stem cell

growth_protocol: CD34+ hempoietic stem cells obtained from 5 different donors were expanded using Stemspan medium containing 0.05% w/v serum albumin, 100 U/mL penicillin/streptomycin, 50 ng/mL FLT3L, 50 ng/mL TPO, 50 ng/mL SCF, 20 ng/mL IL6 and 20 ng/mL IL3. CD34+ cells were harvested or seeded at 5*104 cells/mL in 48 well plates and differentiated towards macrophages using IL6 (20 ng/mL), CSF1(50 ng/mL), CSF2(TGFb) and TGFb(2ng/mL) and towards dendritic cells using FLT3L (50 ng/mL), SCF(50 ng/mL), CSF2 (20 ng/mL) and IL4 (20 ng/mL).

extract_protocol:
RNA was extracted using an RNAeasy minikit (Qiagen) and quality determined using Agilent 2100 Bioanalyzer
TruSeq library preparation (Illumina)
RNA-seq (150 PE sequencing, Illumina HiSeq 2000)

value: CD34+ stem cells

tag: donor id

tag: Sex

tag: age (years)

tag: smoker

value: No


title: Daxx F/F 3wpi H3K9me3 2

description:
DaxxFF_3wpi_H3K9me3_cov.bw
H3K9me3_DaxxFF_diffsite.txt
3660

tag: chip antibody


title: CD34+ Undifferentiated  Donor 2


title: MYC Round 1 Tumor 2 gDNA barcodes

description:
Driver barcode data from genomic DNA from Round 1 Tumor 2 formed from mix of H1 cells transduced with c-MYC or mCherry
MYC_gDNA_BC_counts.txt
MYC_Round1_ter2_gDNA_BC_S21

value: Round 1


title: MYC Round 1 Tumor 3 gDNA barcodes

description:
Driver barcode data from genomic DNA from Round 1 Tumor 3 formed from mix of H1 cells transduced with c-MYC or mCherry
MYC_gDNA_BC_counts.txt
MYC_Round1_ter3_gDNA_BC_S22


title: Wildtype (CMG_ID 6)

value: Pparg (flox/flox), Cytokeratin14 promoter-driven Cre-/-

tag: gender


title: CD34+ Undifferentiated  Donor 4


title: Wildtype (CMG_ID 5)


title: Daxx F/F 3wpi Pu.1 2

description:
DaxxFF_3wpi_Pu1_cov.bw
Pu1_DaxxFF_3wpi_diffsite.txt
4022


title: Daxx F/F 3wpi H3.3 2

description:
DaxxFF_3wpi_H3.3_cov.bw
H3.3_DaxxFF_3wpi_diffsite.txt
4022


title: MYC Round 1 Tumor 2 Bulk RNA-seq

description:
Bulk RNA-seq data from Round 1 Tumor 2 formed from mix of H1 cells transduced with c-MYC or mCherry
validation_tumors_counts.csv
MYC_Round1_ter2_RNA_Seq_S15

tag: cell line


title: Wildtype (CMG_ID 4)

tag: strain


title: Ctrl_3


title: Pparg-/- (CMG_ID 10)

value: Pparg (flox/flox), Cytokeratin14 promoter-driven Cre+/-


title: Wildtype (CMG_ID 3)

value: Scraped frozen epidermis


title: Daxx F/F 3wpi H3K27ac 1

description:
DaxxFF_3wpi_H3K27ac_cov.bw
H3K27ac_DaxxFF_diffsite.txt
3659

tag: genotype


title: CD34+ Dendritic cells Donor 4

value: CD34+ derived dendritic cells

value: Female


title: CD34+ Dendritic cells Donor 5


title: Daxx F/F 3wpi H3K9me3 1

description:
DaxxFF_3wpi_H3K9me3_cov.bw
H3K9me3_DaxxFF_diffsite.txt
3659

tag: tissue


title: MYC Round 1 Tumor 1 gDNA barcodes

description:
Driver barcode data from genomic DNA from Round 1 Tumor 1 formed from mix of H1 cells transduced with c-MYC or mCherry
MYC_gDNA_BC_counts.txt
MYC_Round1_ter1_gDNA_BC_S20

value: 1:1 mix of H1 cells transduced with c-MYC or mCherry


title: CD34+ Dendritic cells Donor 2

value: Male


title: CD34+ Dendritic cells Donor 1


title: MYC Pre-injection gDNA barcodes

description:
Driver barcode data from genomic DNA from pre-injection mix of H1 cells transduced with c-MYC or mCherry
MYC_gDNA_BC_counts.txt
MYC_pre_inject_gDNA_BC_S10

value: Pre-injection


title: Wildtype (CMG_ID 2)

tag: breeding


title: Daxx F/F 3wpi Pu.1 1

description:
DaxxFF_3wpi_Pu1_cov.bw
Pu1_DaxxFF_3wpi_diffsite.txt
4020

value: Bone marrow


title: Wildtype (CMG_ID 1)

tag: age (weeks)


title: Driver Sub-library Round 2 Teratoma 2 cDNA barcodes

description: Driver barcode data from scRNA-seq of Round 2 Tumor 2, formed from serially injected driver sub-library teratoma cells

value: Driver sub-library without c-MYC and AKT1

value: Round 2


title: Daxx F/F 3wpi H3.3 1

description:
DaxxFF_3wpi_H3.3_cov.bw
H3.3_DaxxFF_3wpi_diffsite.txt
4020


title: Wild-type (Rubinstein-Taybi cohort) rep 7

city: Baltimore

first: Teresa

middle: Romeo

last: Luperchio

state: MD

address: 733 N Broadway

department: Department of Genetic Medicine

institute: Johns Hopkins School of Medicine

data_processing:
Reads were pseudo-aligned to a fasta file containing all mouse cDNA sequences obtained from ENSEMBL (http://uswest.ensembl.org/Mus_musculus/Info/Index, version 91, downloaded January 2018), using Salmon (v0.10)
Transcript quantifications were imported into R with the tximport R package, to obtain gene-level counts
Supplementary_files_format_and_content: The processed data files are expression matrices (in csv format), with rows corresponding to genes (each gene is associated with its unique ENSEMBL id), and columns to samples (each sample name contains information about genotype). The entries in the matrices are counts, as obtained using the "tximport" function from the tximport R package. One expression matrix (rna_genes_by_samples_matrix_Kabuki_cohort.csv) contains samples from Kabuki type 1/2 mutants and wild-type littermates, and the other expression matrix (rna_genes_by_samples_matrix_Rub_Taybi_cohort.csv) contains samples from Rubinstein-Taybi mutants and wild-type littermates.

source_name: CD19+ B cells

extract_protocol:
Peripheral blood was obtained from facial vein bleed and CD19+ cells were isolated by positive selection using magnetic microbeads (Miltenyi 130-052-201) per manufacturer protocols and placed on ice. 100k-500k cells were spun at 300-500g for 5 min at 4’, homogenized in Trizol (Invitrogen 15596018) and stored at -80 until extraction. RNA was phase separated using standard protocols followed by purification using the Direct-zol RNA microprep kit (Zymo R2060) with an on-column DNAse step per manufacturer directions. RNA was then quantified using Quant-iT RiboGreen RNA Assay Kit (ThermoFisher R11490) or Qubit RNA HS Assay Kit (ThermoFisher Q32852), and quality checked by Bioanalyzer with RNA 6000 Pico Kit (Agilent 5067-1513). mRNA was isolated using (NEBNext Poly(A) mRNA Magnetic Isolation Module; NEB #E7490).
Libraries were generated using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB E7760/E7765) per manufacturer protocols. Library size and quality were determined using BioAnalyzer with DNA High Sensitivity reagents (Agilent 5067-4626), and concentration was determined using Qubit dsDNA HS Assay Kit (ThermoFisher Q32851) and KAPA Library Quantification Kit for qPCR (KAPA KK4824).

value: CD19+ B cells from peripheral blood

tag: age (approximate)

value: 85 days

tag: disease state

value: Wild-type (Rubinstein-Taybi cohort)


title: MYC Round 2 Tumor 2 gDNA barcodes

description:
Driver barcode data from genomic DNA from Round 2 Tumor 2 formed from serially injected c-MYC/mCherry round 1 tumor cells
MYC_gDNA_BC_counts.txt
MYC_Round2_ter2_gDNA_BC_S24


title: Daxx +/+ 3wpi H3K27ac 1

city: Bonn

first: Paolo

address: Sigmund-Freud-Str. 27

institute: DZNE e.V.

description:
DaxxWtWt_3wpi_H3K27ac_cov.bw
3658

value: Daxx +/+ Cre +/-


title: CD34+ Macrophages Donor 5

tag: cell type

value: CD34+ derived macrophages

value: No


title: CD34+ Macrophages Donor 4


title: Daxx F/F Pu.1 F/F GMP 24wpi 2

description:
210215_GMP_24wpi_NormalizedCounts_Gene.txt
Mx1_TC.cntTable

data_processing:
Illumina Casava 1.8.4 for base calling and demultiplexing
Sequencing reads were adapter trimmed using Cutadapt 1.13 and aligned against mm10 (GENCODE release M14) using STAR aligner 2.5.3 with standard settings. For repeat element analysis STAR aligner was run with the following options: --outFilterMultimapNmax 100 --winAnchorMultimapNmax 100.
Reads mapping to rRNA, the mitochondrial genome and non-uniquely were removed. For repeat element expression analysis only reads mapping to the mitochondrial genome were removed.
Differentially expressed genes and repeat elements were obtained by running DESeq2 1.16.1.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file with DESeq2 normalized counts for each sample

source_name: Hematopoietic Progenitor Cell

extract_protocol:
Primary hematopoietic stem/progenitor cells were isolated form bone marrow and populations sorted by flow cytometry. Total RNA was extracted using Trizol reagent.
Illumina sequencing libraries were created with the Ovation SoLo RNA-seq kit from NuGEN Technologies according to the manufacturer's instructions.

tag: mouse line

value: Daxx F/F Pu.1 F/F Cre +/-

tag: time after end of induction

value: 24 wpi


title: Daxx +/+ 3wpi H3K9me3 1

description:
DaxxWtWt_3wpi_H3K9me3_cov.bw
3658


title: Driver Sub-library Round 2 Teratoma 2 scRNA-seq

description: scRNA-seq data from Round 2 Tumor 2, formed from serially injected driver sub-library teratoma cells

tag: genetic perturbation

tag: tumor round


title: Wild-type (Rubinstein-Taybi cohort) rep 4


title: Wild-type (Rubinstein-Taybi cohort) rep 5


title: Wild-type (Rubinstein-Taybi cohort) rep 6


title: Driver Sub-library Round 1 Teratoma 3 cDNA barcodes

description: Driver barcode data from scRNA-seq of Round 1 Teratoma 3, formed from H1 cells transduced with driver sub-library without c-MYC and AKT1

source_name: Human teratoma

value: Round 1


title: MYC Round 1 Tumor 1 RNA-seq

description:
Bulk RNA-seq data from Round 1 Tumor 1 formed from mix of H1 cells transduced with c-MYC or mCherry
validation_tumors_counts.csv
MYC_Round1_ter1_RNA_Seq_S14


title: Driver Sub-library Round 2 Teratoma 1 cDNA barcodes

description: Driver barcode data from scRNA-seq of Round 2 Tumor 1, formed from serially injected driver sub-library teratoma cells


title: Driver Sub-library Round 2 Teratoma 1 scRNA-seq

description: scRNA-seq data from Round 2 Tumor 1, formed from serially injected driver sub-library teratoma cells


title: CD34+ Macrophages Donor 2

tag: donor id

tag: Sex

tag: age (years)


title: Daxx F/F Pu.1 F/F GMP 24wpi 1


title: Wild-type (Rubinstein-Taybi cohort) rep 3


title: CD34+ Macrophages Donor 1

tag: smoker


title: Wild-type (Rubinstein-Taybi cohort) rep 2


title: Daxx F/F GMP 24wpi 1

value: Daxx F/F Cre +/-


title: Daxx F/F GMP 24wpi 2


title: Driver Sub-library Round 1 Teratoma 2 cDNA barcodes

description: Driver barcode data from scRNA-seq of Round 1 Teratoma 2, formed from H1 cells transduced with driver sub-library without c-MYC and AKT1

tag: cell line


title: pt5: Myelofibrosis

city: Florence

first: Paola

last: Chiarugi

state: Florence

address: Viale Morgagni 50

department: Department of Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

data_processing:
Reads were trimmed for low quality bases.  then mapped to GRCh38 whole genome using STAR v2.7.3a with default parameters
The feature count was perfomed by HTSeq (v0.11.1) with parameters --max-reads-in-buffer 80000000 -m intersection-nonempty -t gene --idattr gene_id --additional-attr gene_name -r pos -s reverse
The number of reads falling in the genes were normalized by the size of the library
Detection  of differentially expressed genes by DEseq2 (v1,26,0)
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Peripheral Blood

extract_protocol:
CD34 cells were immune magnetically isolated from Cord Blood and Bone Marrow of Calreticulin-mutated Myeloproliferative Neoplasms patients. Total RNA was extracted using Trizol Reagents. NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® was used with 1 ug of RNA for the construction od sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Myelofibrosis

value: Peripheral Blood


title: Driver Sub-library Round 1 Teratoma 3 scRNA-seq

description: scRNA-seq data from Round 1 Teratoma 3, formed from H1 cells transduced with driver sub-library without c-MYC and AKT1


title: CD34+ Macrophages Donor 3

value: Female


title: Daxx +/+ GMP 24wpi 2

last: Salomoni

tag: strain


title: Wild-type (Kabuki cohorts) rep 5

value: 82 days

value: Wild-type (Kabuki cohorts)


title: pt4: Myelofibrosis


title: pt3: Myelofibrosis


title: pt2: Myelofibrosis


title: Wild-type (Kabuki cohorts) rep 4

value: 74 days


title: Daxx +/+ GMP 24wpi 1

value: Bone marrow

tag: genotype


title: Daxx F/F Pu.1 F/F KLS 24wpi 2

description:
210215_KLS_24wpi_NormalizedCounts_Gene.txt
Mx1_TC.cntTable

tag: tissue


title: Driver Sub-library Round 1 Teratoma 1 cDNA barcodes

description: Driver barcode data from scRNA-seq of Round 1 Teratoma 1, formed from H1 cells transduced with driver sub-library without c-MYC and AKT1

value: Driver sub-library without c-MYC and AKT1


title: Wild-type (Kabuki cohorts) rep 2

value: CD19+ B cells from peripheral blood

value: 84 days


title: Daxx F/F Pu.1 F/F KLS 24wpi 1


title: Wild-type (Kabuki cohorts) rep 3

value: 98 days


title: Driver Sub-library Round 1 Teratoma 1 scRNA-seq

description: scRNA-seq data from Round 1 Teratoma 1, formed from H1 cells transduced with driver sub-library without c-MYC and AKT1


title: pt6: Myelofibrosis


title: Wild-type (Kabuki cohorts) rep 1


title: Driver Library Round 2 Teratoma 2 scRNA-seq

description: scRNA-seq data from Round 2 Tumor 2, formed from serially injected driver library teratoma cells

value: Full driver library

value: Round 2


title: Wild-type (Rubinstein-Taybi cohort) rep 1

value: 85 days

value: Wild-type (Rubinstein-Taybi cohort)


title: Daxx F/F KLS 24wpi 2

value: 24 wpi


title: pt1: Myelofibrosis


title: Rubinstein-Taybi syndrome type 1 rep 5

value: Rubinstein-Taybi syndrome type 1


title: P131430_J49

city: Montreal

first: Jean-Sebastien

last: Delisle

state: Quebec

address: 5415 Boulevard de l'Assomption

institute: Centre de recherche de l'Hôpital Maisonneuve-Rosemont

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to hg19 whole genome.
Basecalls were performed using CASAVA version 1.8.2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include rawcount values for each sample and normalized values determined by DESeq2 package on R plateform.

source_name: CD8+ T cells

growth_protocol: Cells were stimulated weekly with anti-CD3/CD28 beads at a 1:5 ratio (bead:cell) and cultured in complete media.

extract_protocol:
Cells were harvested and enriched for CD8+ T cells. RNA was isolated using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: number of stimulation

tag: total days in culture


title: Rubinstein-Taybi syndrome type 1 rep 4

tag: age (approximate)


title: Daxx F/F KLS 24wpi 1

value: Daxx F/F Cre +/-


title: Daxx +/+ KLS 24wpi 2

value: Daxx +/+ Cre +/-


title: Driver Library Round 2 Teratoma 1 scRNA-seq

description: scRNA-seq data from Round 2 Tumor 1, formed from serially injected driver library teratoma cells

data_processing:
Samples were sequenced on an Illumina NovaSeq 6000 platform
For scRNA-seq samples, fastq files were aligned, and cell barcodes and UMIs processed using cellranger count (Cell Ranger version 3.0.0). Lists of barcodes and features, and the feature-barcode matrix were generated by Cell Ranger v3.0.0. The reference genome used was combined hg19 and mm10.
For bulk RNA-seq the fastq files were aligned using STAR Aligner and read counts obtained with the --quantMode GeneCounts option, with the reference human genome GRCh38 and mapped to exons using Ensembl v99.
For barcodes amplified from genomic DNA, barcodes were aligned using Bowtie2 and counted using MAGeCK.
Genome_build: hg19
Supplementary_files_format_and_content: scRNA-seq processed data for each sample is comprised of three zipped, tab-separated files: list of cell barcodes (files ending in _barcodes.tsv.gz), list of genes/features (files ending in _features.tsv.gz) and a feature-barcode matrix file (files ending in _matrix.mtx.gz)
Supplementary_files_format_and_content: Genotype to cell dictionaries for scRNA-seq data consist of lists of cells mapped to each genotype (files ending in _genotype.csv)
Supplementary_files_format_and_content: Bulk RNA-seq processed data consists of read counts for each gene (validation_tumors_counts.csv)
Supplementary_files_format_and_content: Barcode counts from genomic DNA processed data consists of read counts for each barcode (files ending in _gDNA_BC_counts.txt)


title: P130898_J49


title: Driver Library Round 2 Teratoma 2 cDNA barcodes

description: Driver barcode data from scRNA-seq of Round 2 Tumor 2, formed from serially injected driver library teratoma cells


title: Driver Library Round 1 Teratoma 4 cDNA barcodes

description: Driver barcode data from scRNA-seq of Round 1 Teratoma 4, formed from H1 cells transduced with driver library

value: Round 1


title: Daxx +/+ KLS 24wpi 1


title: P13016_J35


title: Driver Sub-library Round 1 Teratoma 2 scRNA-seq

description: scRNA-seq data from Round 1 Teratoma 2, formed from H1 cells transduced with driver sub-library without c-MYC and AKT1


title: Driver Library Round 1 Teratoma 4 scRNA-seq

description: scRNA-seq data from Round 1 Teratoma 4, formed from H1 cells transduced with driver library


title: P131430_J7


title: Daxx F/F MPP4 2

description: 210215_MPP_3wpi_NormalizedCounts_Gene.txt

value: 3 wpi


title: Rubinstein-Taybi syndrome type 1 rep 2

tag: disease state


title: Rubinstein-Taybi syndrome type 1 rep 1

tag: cell type


title: Driver Library Round 1 Teratoma 3 cDNA barcodes

description: Driver barcode data from scRNA-seq of Round 1 Teratoma 3, formed from H1 cells transduced with driver library


title: Driver Library Round 2 Teratoma 1 cDNA barcodes

description: Driver barcode data from scRNA-seq of Round 2 Tumor 1, formed from serially injected driver library teratoma cells


title: Daxx F/F MPP4 1

tag: mouse line


title: Driver Library Round 1 Teratoma 3 scRNA-seq

description: scRNA-seq data from Round 1 Teratoma 3, formed from H1 cells transduced with driver library


title: P131164_J35


title: Daxx +/+ MPP4 2

tag: time after end of induction


title: P131164_J7


title: Daxx +/+ MPP4 1


title: P13016_J7


title: Kabuki syndrome type 2 rep 5

value: 72 days

value: Kabuki syndrome type 2


title: Kabuki syndrome type 2 rep 4

value: 82 days


title: Driver Library Round 1 Teratoma 2 scRNA-seq

description: scRNA-seq data from Round 1 Teratoma 2, formed from H1 cells transduced with driver library

tag: genetic perturbation


title: P131430_J0


title: Daxx F/F MPP3 2

value: Bone marrow


title: Driver Library Round 1 Teratoma 2  cDNA barcodes

description: Driver barcode data from scRNA-seq of Round 1 Teratoma 2, formed from H1 cells transduced with driver library

tag: tumor round


title: Daxx F/F MPP3 1


title: Rubinstein-Taybi syndrome type 1 rep 3

value: CD19+ B cells from peripheral blood


title: Kabuki syndrome type 2 rep 2


title: Driver Library Round 1 Teratoma 1 scRNA-seq

description: scRNA-seq data from Round 1 Teratoma 1, formed from H1 cells transduced with driver library


title: Kabuki syndrome type 2 rep 1


title: P13016_J0


title: Daxx +/+ MPP3 2


title: Kabuki syndrome type 1 rep 5

value: Kabuki syndrome type 1


title: P130898_J7


title: CaSki-P3

city: Seoul

first: SUYEON

last: KIM

address: IN-CHONRO 73

department: BIOCHEMISTRY

country: South Korea

institute: KOREA UNI.

description: Selected with KKM MART-1 specific CD8 T cell 3 times.

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence (using fastx_trimmer, bbmap), then mapped to hg19 whole genome using Tophat2.
Read count extraction and normalization were performed using edgeR.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *txt: Tab-delimited text files include read count values for each Sample.

source_name: CaSki cells

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen).
2 ug of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using TruSeq Stranded Total RNA Library Prep Kit standard protocols.

value: epidermoid cervical carcinoma


title: Pre-injection cDNA barcodes

description: Driver barcode data from scRNA-seq of pre-injected cells transduced with driver library

source_name: H1 human embryonic stem cells

extract_protocol:
Teratomas and tumors were dissociated using the standard GentleMACS human tumor dissociation protocol. For scRNA-seq, dissociated cells were resuspended in PBS + 0.04% BSA and processed on the 10X Genomics Chromium system using standard protocols. For bulk RNA extraction, dissociated cells were pelleted, RNA extracted using a Qiagen RNeasy kit and RNA-seq libraries prepared. For barcode amplification from genomic DNA, dissociated cells were pelleted, genomic DNA extracted using the Qiagen DNeasy kit and barcodes were PCR amplified and prepared for sequencing.
scRNA-seq Libraries were constructed using the standard Chromium Single Cell 3ʹ Reagent Kits v3 workflow (10x Genomics). Bulk RNA-seq libraries were constructed using NEBNext Ultra RNA Library Prep Kit.

value: Full driver library

value: Pre-injection


title: Pre-injection gDNA barcodes

description: Driver barcode data from genomic DNA of pre-injected cells transduced with driver library

data_processing:
Library strategy: DNA-seq
Samples were sequenced on an Illumina NovaSeq 6000 platform
For scRNA-seq samples, fastq files were aligned, and cell barcodes and UMIs processed using cellranger count (Cell Ranger version 3.0.0). Lists of barcodes and features, and the feature-barcode matrix were generated by Cell Ranger v3.0.0. The reference genome used was combined hg19 and mm10.
For bulk RNA-seq the fastq files were aligned using STAR Aligner and read counts obtained with the --quantMode GeneCounts option, with the reference human genome GRCh38 and mapped to exons using Ensembl v99.
For barcodes amplified from genomic DNA, barcodes were aligned using Bowtie2 and counted using MAGeCK.
Genome_build: hg19
Supplementary_files_format_and_content: scRNA-seq processed data for each sample is comprised of three zipped, tab-separated files: list of cell barcodes (files ending in _barcodes.tsv.gz), list of genes/features (files ending in _features.tsv.gz) and a feature-barcode matrix file (files ending in _matrix.mtx.gz)
Supplementary_files_format_and_content: Genotype to cell dictionaries for scRNA-seq data consist of lists of cells mapped to each genotype (files ending in _genotype.csv)
Supplementary_files_format_and_content: Bulk RNA-seq processed data consists of read counts for each gene (validation_tumors_counts.csv)
Supplementary_files_format_and_content: Barcode counts from genomic DNA processed data consists of read counts for each barcode (files ending in _gDNA_BC_counts.txt)


title: CaSki-P0


title: Kabuki syndrome type 1 rep 3


title: Kabuki syndrome type 1 rep 4


title: Kabuki syndrome type 2 rep 3

value: 84 days


title: Mac-453-Endo

city: Guildford

first: Fernando

middle: O

last: Martinez Estrada

state: Surrey

address: Stag Hill

department: Faculty of Health & Medical Sciences

institute: University of Surrey

data_processing:
Reads were aligned with HISAT2 to GRCh38.p3, sorted and duplicates marked using Sambamba and primary alignment reads counted at the exon and summarized at gene level using Feature Counts.
Differential expression analysis was performed on TPM (Transcripts per million) values.
Genome_build: GRCh38.p3
Supplementary_files_format_and_content: RNAseq Data Processed data.txt represents TPM (Transcripts per million) values.

source_name: Human Peritoneal Fluid

growth_protocol: Monocytes and macrophages for RNAseq analysis were isolated by Ficoll gradient followed by the Negative isolation Kit II from Miltenyi according to manufacturer instructions.

extract_protocol:
Total RNA was extracted using the Trizol and the Quiazol kit according to manufacturer’s instructions.
After verifying that the integrity of total RNA was above a RIN score of 8 on a Tape Station 2200 (Agilent), 200ng of total RNA was used as input for poly-A selection and Illumina library construction using the NEBNext Ultra Directional Library Kit (NEB) according to the manufacturer’s instructions.
Samples were sequenced on an Illumina NextSeq 500 platform with 42bp paired-end reads.

value: Endometriosis

value: Peritoneal Fluid

value: Peritoneal macrophages


title: Driver Library Round 1 Teratoma 1 cDNA barcodes

first: Udit

last: Parekh

state: CA

address: 9500 Gilman Drive, Room 353, Powell-Focht (EBU3A)

institute: University of California, San Diego

description: Driver barcode data from scRNA-seq of Round 1 Teratoma 1, formed from H1 cells transduced with driver library


title: Kabuki syndrome type 1 rep 2

value: 98 days


title: Pre-injection scRNA-seq

description: scRNA-seq data from pre-injected cells transduced with driver library


title: Pu.1 F/F GMP 2

description:
210215_GMP_Pu1FFvsWT_3wpi_NormalizedCounts_Gene.txt
Pu1singleKO_wt1.cntTable

value: Pu.1 F/F Cre +/-


title: Mac-451-Endo


title: P131164_J0


title: Pu.1 +/+ GMP 2


title: Pu.1 F/F GMP 1


title: Kabuki syndrome type 1 rep 1


title: Pu.1 F/F KLS 2

description:
210215_KLS_Pu1FFvsWT_3wpi_NormalizedCounts_Gene.txt
Pu1singleKO_wt1.cntTable


title: Mac-450-Endo


title: ChIP-seq-B-Pol2-SPT5AID-NVP2Auxin

city: Chicago

first: Ali

last: Shilatifard

address: 320 E Superior St

institute: Northwestern University Feinberg School of Medicine

description: ChIP-seq Pol II

data_processing:
For ChIP-seq, single-end raw reads trimmed by Trimmomatic 0.33 (Bolger et al., 2014) were aligned to a concatenated genome comprised of human hg38 and mouse mm10 assemblies, using bowtie 2.2.6 (Langmead and Salzberg, 2012) with --sensitive option. The aligned reads with MAPQ ≥ 30 were extended to 150 bp and read counts were normalized to total reads aligned to spike-in genome. Metaplots of ChIP-seq signals were generated using deepTools 3.1.1 (Ramírez et al., 2016).
For PRO-seq, low-quality bases and adapters from 3’ ends of reads were removed using cutadapt 1.14 (Martin, 2011) requiring a read length of 16–36 bp. Reads derived from ribosomal RNA were filtered out by mapping reads on human and fly ribosomal DNA. The remaining reads were aligned using bowtie 2.2.6 with --very-sensitive option (Langmead and Salzberg, 2012), to a concatenated genome comprised of human hg38 and fly dm6 assemblies. The 5’ ends of aligned reads with MAPQ ≥ 30 were taken by bedtools genomecov 2.25 (Quinlan and Hall, 2010) with -strand and -5 options, and strands of the 5’ ends of reads were then swapped. Read counts were normalized to total reads aligned to the spike-in genome.  Heatmaps and metaplots of PRO-seq signal were generated by deepTools 3.1.1 (Ramírez et al., 2016).
For TT-seq, single-end raw reads trimmed by Trimmomatic 0.33 (Bolger et al., 2014) were aligned to human genome hg38 assemblies, using bowtie 2.2.6 (Langmead and Salzberg, 2012) with --sensitive option. Heatmaps of ChIP-seq signals were generated using deepTools 3.1.1 (Ramírez et al., 2016).
Genome_build: hg38, mm10, dm6
Supplementary_files_format_and_content: bigWig files with normalized read counts were provided for all samples.

extract_protocol:
For ChIP-seq in human DLD1 cells, 20-50 million cells were crosslinked with 1% paraformaldehyde (Electron Microscopy Sciences) in PBS for 10 min at r.t. Spike-in mouse embryonic fibroblast fixed cells were added to samples as described previously (Orlando et al., 2014). Chromatin was sonicated with the Covaris E220 for 4 min with 10% duty cycle, 140 peak intensity power, 200 cycles per burst. Immunoprecipitations were carried out with antibodies and Dynabeads Protein G (Invitrogen). For ChIP-seq in yeast cells, cells were fixed with 2.2% formaldehyde for 15 min.    PRO-seq sample preparation was performed according to the previously described qPRO-seq protocol (Judd et al., 2020). ~5 million DLD-1 nuclei  mixed with spike-in Drosophila S2 nuclei were used for nuclear run-on assay.     For pulse-chase nascdnt RNA labeling with TT-seq, cells were treated with 250 nM NVP-2 for 1 h, followed by nascent RNA labeling with 500 µM 4-thiouridin (Sigma # T4509) for 15 min.
For ChIP-seq, DNA libraries were prepared by the HTP Library Preparation Kit for Illimina (KAPA). For PRO-seq, adapter sequences previously described (Mahat et al., 2016) were used. PRO-seq libraries were prepared according to the previously described qPRO-seq protocol (Judd et al., 2020). TT-seq library was prepared as described previously (Schwalb et al., 2016; Rosencrance wt al., 2020).

treatment_protocol: To induce degradation of AID-tagged proteins, 500 µM auxin was added to culture. To induce anchor-away depletion, exponentially growing yeast cultures were treated with 1.0 ug/mL Rapamycin.

value: Colorectal adenocarcinoma

value: SPT5-AID OsTIR1

tag: treatment

tag: antibody

value: RPB1 NTD (Cell signaling # 14958S)

tag: molecule subtype

value: genomic DNA


title: ChIP-seq-B-Pol2-SPT5AID-Auxin

description: ChIP-seq Pol II

value: Auxin


title: Pu.1 +/+ GMP 1

value: Bone marrow

value: 3 wpi


title: Daxx +/+ MPP3 1

value: Daxx +/+ Cre +/-


title: Mac-437-Endo


title: ChIP-seq-B-Pol2-SPT5AID-Vehicle

description: ChIP-seq Pol II

value: Vehicle


title: PRO-seq-SPT5AID-VCPiAuxin-Rep2

description: PRO-seq

data_processing:
Library strategy: PRO-seq
For ChIP-seq, single-end raw reads trimmed by Trimmomatic 0.33 (Bolger et al., 2014) were aligned to a concatenated genome comprised of human hg38 and mouse mm10 assemblies, using bowtie 2.2.6 (Langmead and Salzberg, 2012) with --sensitive option. The aligned reads with MAPQ ≥ 30 were extended to 150 bp and read counts were normalized to total reads aligned to spike-in genome. Metaplots of ChIP-seq signals were generated using deepTools 3.1.1 (Ramírez et al., 2016).
For PRO-seq, low-quality bases and adapters from 3’ ends of reads were removed using cutadapt 1.14 (Martin, 2011) requiring a read length of 16–36 bp. Reads derived from ribosomal RNA were filtered out by mapping reads on human and fly ribosomal DNA. The remaining reads were aligned using bowtie 2.2.6 with --very-sensitive option (Langmead and Salzberg, 2012), to a concatenated genome comprised of human hg38 and fly dm6 assemblies. The 5’ ends of aligned reads with MAPQ ≥ 30 were taken by bedtools genomecov 2.25 (Quinlan and Hall, 2010) with -strand and -5 options, and strands of the 5’ ends of reads were then swapped. Read counts were normalized to total reads aligned to the spike-in genome.  Heatmaps and metaplots of PRO-seq signal were generated by deepTools 3.1.1 (Ramírez et al., 2016).
For TT-seq, single-end raw reads trimmed by Trimmomatic 0.33 (Bolger et al., 2014) were aligned to human genome hg38 assemblies, using bowtie 2.2.6 (Langmead and Salzberg, 2012) with --sensitive option. Heatmaps of ChIP-seq signals were generated using deepTools 3.1.1 (Ramírez et al., 2016).
Genome_build: hg38, mm10, dm6
Supplementary_files_format_and_content: bigWig files with normalized read counts were provided for all samples.

value: VCPiAuxin

value: nuclear RNA


title: Mac-386-Endo


title: Mac-382-Endo


title: PRO-seq-SPT5AID-Auxin-Rep2

description: PRO-seq


title: Mac-388-Endo


title: PRO-seq-SPT5AID-VCPiAuxin-Rep1

description: PRO-seq


title: ChIP-seq-B-Pol2-SPT5AID-dCDK9Auxin

description: ChIP-seq Pol II


title: Mac-381-Endo


title: PRO-seq-SPT5AID-Vehicle-Rep2

description: PRO-seq


title: Mac-375-Endo


title: Mac-445-Control

value: Pain Only


title: Mac-365-Endo

value: Endometriosis


title: Mac-446-Endo

value: Peritoneal Fluid


title: Mac-443-Control

value: Peritoneal macrophages


title: Mac-432-Control


title: PRO-seq-SPT5AID-Auxin-Rep1

description: PRO-seq


title: Mac-379-Control


title: PRO-seq-SPT5AID-Vehicle-Rep1

description: PRO-seq


title: Mon-388-Endo

source_name: Human blood

value: Blood

value: Total monocytes


title: Mon-387-Endo


title: Daxx +/+ GMP 3wpi 2

description:
210215_GMP_3wpi_NormalizedCounts_Gene.txt
GMP_AllGenotypes.cntTable


title: Pu.1 +/+ KLS 1


title: Daxx +/+ GMP 3wpi 3


title: Daxx F/F Pu.1 F/F KLS 3wpi 2 Lo56

description:
210215_KLS_3wpi_NormalizedCounts_Gene.txt
KLS_DaxxFFPu1FFvsDaxxWt.cntTable

value: Daxx F/F Pu.1 F/F Cre +/-


title: Daxx F/F GMP 3wpi 1

value: Daxx F/F Cre +/-


title: Daxx F/F GMP 3wpi 3


title: Daxx F/F GMP 3wpi 2


title: Pu.1 +/+ KLS 2


title: Daxx F/F Pu.1 F/F GMP 3wpi 2


title: Daxx F/F Pu.1 F/F GMP 3wpi 1


title: ChIP-seq-A-NELFA-SPT5AID-Vehicle

description: ChIP-seq NELFA

value: Colorectal adenocarcinoma

value: SPT5-AID OsTIR1

value: NELF-A (Proteintech # 10456-1-AP)