title: untreated_replicate_2 [SAM24371014]


title: Tuft cells, congenic, untreated [UG11]

status: Public on Nov 04 2022

type: SRA

city: Seattle

first: Jakob

middle: Helmuth

last: von Moltke

state: Washington

address: 750 Republican Street

department: Immunology

country: USA

institute: University of Washington

library_source: transcriptomic

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina).
Reads were processed using workflows managed on the Galaxy platform; reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0)
FastqMcf (v1.1.2) was used to remove any remaining adapter sequence.
Trimmed sequence reads were mapped to GrCM39/mm39 using Kallisto
Rmarkdown file with all further data processing and analysis is included as _Congenic_RNAseq.html
Assembly: mm39
Supplementary files format and content: comma-delimited text files include log2 transformed CPM values for each Sample

molecule: total RNA

organism: Mus musculus

extract_protocol:
Cells were sorted directly into buffer from SMART-Seq4 and cDNA was prepared according to manufacturers protocol
Libraries were prepared using NexteraXT DNA Library kit according to manufacturer's protocol
Barcoded libraries were pooled and quantified using a Qubit® Fluorometer (Life Technologies). Single-read sequencing of the pooled libraries was carried out on a HiSeq2500 sequencer (Illumina) for 74 cycles, using TruSeq v3, and SBS kits (Illumina). Target read depths were ~5-10 million raw reads per sample.

treatment_protocol:
N/A
N/A

tag: cell line

tag: cell type

value: small intestine tuft cells

tag: genotype

value: Congenic Strain 3

tag: treatment


title: AML2910 (scRNA-seq)

city: New York

first: Bettina

last: Nadorp

state: NY

address: 500 1st Ave

department: Medicine/Pathology

institute: NYU Langone Health

description: Chromium Single Cell 5’ polyA RNA

data_processing:
Indexed BAM files containing position-sorted reads aligned to the genome.
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment to GRCh38 (version 5.0.1) was performed with 10x Genomics Cell Ranger Single Cell Gene Expression Software (version 2020-A).
HTOs each cell were normalized using a centered log ratio (CLR) transformation across cells.
Samples were demultiplexed based on HTOs using the HTODemux function in Seurat.
3' libraries were filtered for incorrectly assigned hash tags using Souporcell, doublet filtered using scDblFinder, and ambient RNA contamination was removed using SoupX.  Please see publication for detailed processing steps.
Genome_build: hg38
Supplementary_files_format_and_content: Processed data files for Single Cell RNAseq, CITEseq, TCR-seq:
feature reference
metadata
processed ADT counts
processed RNA counts
filtered barcodes
filtered features
filtered gene-barcode matrix
clonotypes
feature reference file 5 prime
filtered contig annotations
filtered count matrix

molecule: polyA RNA

organism: Homo sapiens

source_name: bone marrow

extract_protocol:
Cryopreserved bone marrow aspirates were obtained from Ohio State University’s sample bank (adult AML samples), from St. Jude Children’s Research Hospital AML16 clinical trial (pediatric AML samples) or from the Children’s Oncology Group AML cell bank (pediatric AML sample). All subjects provided written consent for banking and research use of these specimens, in accordance with the regulations of the institutional review boards of all participating institutes. Cryopreserved primary human bone marrow mononuclear cells were obtained from STEMCELL Technologies or from StemExpress. Frozen human bone marrow samples were thawed and transferred into 50mL conical tubes containing PBS + 2% fetal bovine serum (FBS). Cell suspensions were centrifuged at 350 x g for 5 minutes at 4C, and the supernatant was discarded. Samples were then subjected to dead cell depletion, using a dead cell removal kit (Miltenyi Biotec, 130-090-101), or stained with DAPI (0.5mg/mL) and sorted for live cells (DAPIlow), using a FACSAria IIu SORP cell sorter (BD Biosciences). For cell sorting, all samples were gated based on forward and side scatter, followed by doublet exclusion, and then gated on DAPIlow for viable cells. Samples were sorted into 5mL poly-propylene tubes containing 300mL ice-cold PBS + 2% FBS. Following cell sorting, samples were centrifuged at 350 x g for 5 minutes at 4C. For CITE-seq, enriched live cells were first tagged with cell-hashing oligo-tagged antibodies (Biolegend) according to the manufacturer’s instructions. Samples were than counted, and a maximum of 10e5 cells for each sample was pooled together and stained with a CITE-Seq antibody cocktail (Biolegend) according to the manufacturer’s instructions. For scTCR-Seq, T cells were enriched using a pan T cell isolation kit (Miltenyi Biotec, 130-096-535) or sorted for live CD45+ CD3+ cells. For cell sorting, samples were stained with PerCP-conjugated anti-human CD45 (1:400, Biolegend, 304025), FITC-conjugated anti-human CD3 (1:100, Biolegend,  300452). And DAPI (0.5mg/mL). Sorted samples were gated based on forward and side scatter, followed by doublet exclusion and then gated on DAPIlow for viable cells. CD45+ CD3+ cells were sorted into 5mL poly-propylene tubes containing 300mL ice-cold PBS + 2% FBS. Following cell sorting, samples were centrifuged at 350 x g for 5 minutes at 4C. Libraries were prepared using the Chromium Single Cell 3’ Reagent Kits (v3 and v3.1, CITE-Seq) or the Chromium Single Cell Immune Profiling Kits (v1.1 and v2, scTCR-Seq, 10x Genomics).  Hashtag and antibody-derived tag (ADT) libraries were prepared according to the New York Genome Center CITE-Seq and hashing protocol (https://citeseq.files.wordpress.com/2019/02/cite-seq_and_hashing_protocol_190213.pdf). Libraries were run on an Illumina NovaSeq 6000.
Chromium Single Cell 3’ Reagent Kits (v3 )

tag: disease state

value: Acute Myeloid Leukemia

tag: tissue

value: Bone Marrow

value: mononuclear cells

tag: assay

value: Chromium Single Cell 5’ polyA RNA


title: Quadriceps AR100Q Rep2

city: Trento

first: Alessandro

last: Romanel

state: TN

address: Via Sommarive 9

country: Italy

institute: University of Trento

data_processing:
Data was processed by ROSALIND® (https://rosalind.onramp.bio/), with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA).
Reads were trimmed using cutadapt
Reads were aligned to the Mus musculus genome (mm10) using STAR
Individual sample reads were quantified using HTseq and normalized via Relative Log Expression (RLE) using DEseq2
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

source_name: Quadriceps

extract_protocol:
Quadriceps were isolated, flash frozen in liquid nitrogen. RNA was extracted using Trizol, following manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols. (TruSeq Stranded mRNA)

tag: strain

value: Quadriceps

value: Saline

tag: library prep

value: polyA-enriched


title: Quadriceps AR100Q Rep3


title: Tuft cells, B6, untreated [UG10]

value: WT C57BL/6J


title: AML2975 (scRNA-seq)

description: Chromium Single Cell 5’ polyA RNA


title: Tuft cells, Balb, untreated [UG9]

value: WT Balb/cJ


title: Quadriceps AR100Q Rep1


title: AML1133 (scRNA-seq)

description: Chromium Single Cell 5’ polyA RNA


title: day 7, IL6_replicate 3

city: SOUTH SAN FRANCISCO

first: Kobe

last: Yuen

state: California

address: 1 DNA WAY

department: Oncology Biomarker Development

institute: Genentech

data_processing:
RNA-sequencing data were analyzed using HTSeqGenie in BioConductor. Reads with low nucleotide qualities (70% of bases with quality <23) or rRNA and adapter contamination were removed
Filtered reads were aligned to the reference genome GRCm38 using GSNAP
Gene expression levels were quantified as Reads Per Kilobase of exon model per Million mapped reads normalized by size factor (nRPKM)
Assembly: GRCm38
Supplementary files format and content: RPKM

source_name: spleen

growth_protocol: Spleens from 8 week-old female C57BL/6J OT-I mice were mashed through sterile 70um filters and plated in flat-bottom 96 well plates at 0.2 million per well and pulsed with 100 ng/ml SIINFEKL peptide. After 2 days, a portion of the expanded cells were used to sort CD8 T cells. The remaining cells were washed to remove peptide and maintained with recombinant human IL-2 (10 ng/ml) for 3 days. On day 5, cells were restimulated with anti-CD3/CD28 antibodies, and on day 7 CD8 T cells were isolated by FACS for RNA extraction.

extract_protocol:
Total RNA was extracted using the RNEasy Mini kit (Qiagen)
0.1 μg of total RNA was used for library preparation using TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA). Libraries were multiplexed and sequenced on Illumina HiSeq4000 (Illumina, San Diego, CA) to generate 30 million single-end 50 basepair reads.

value: CD8 T cell

tag: agent


title: Tuft cells, B6, untreated [UG8]


title: untreated_replicate_1 [SAM24371013]

data_processing:
RNA-sequencing data were analyzed using HTSeqGenie in BioConductor. Reads with low nucleotide qualities (70% of bases with quality <23) or rRNA and adapter contamination were removed
Filtered reads were aligned to the reference genome GRCm38 using GSNAP
Gene expression levels were quantified as Reads Per Kilobase of exon model per Million mapped reads normalized by size factor (nRPKM)
Assembly: GRCm38
Supplementary files format and content: RPKM_matrix

growth_protocol: Spleens from 8 week-old female C57BL/6J mice were mashed through sterile 70um filters and naïve CD8+ T cells were isolated by FACS (Thy1+ CD8A+ CD62L+ CD44-).

treatment_protocol: T cells were plated in RPMI + 10% FCS and either IL-6 (10ng/ml), plate-bound anti-CD3/CD28 antibodies + IL-2 (10 ng/ml), or plate-bound anti-CD3/CD28 antibodies + IL-2 + IL-6. Cells were spun for 1 minute at 500g to synchronize contact with plate-bound antibodies, incubated at 37° C, and harvested after 4 hours for RNA extraction.

value: naive CD8 T cell


title: AML0693 (scRNA-seq)

description: Chromium Single Cell 5’ polyA RNA


title: day 7, IL6_replicate 2


title: Tuft cells, Balb, untreated [UG12]


title: Quadriceps WT Rep4

value: wt

value: no


title: Tuft cells, congenic, untreated [UG7]


title: Quadriceps WT Rep3


title: AML0102 (scRNA-seq)

description: Chromium Single Cell 5’ polyA RNA


title: Quadriceps WT Rep2


title: AML0134 (scRNA-seq)

description: Chromium Single Cell 5’ polyA RNA


title: day 7, IL6_replicate 1


title: day 7, anti-IL6R_replicate 3


title: Tuft cells, Balb, untreated [UG5]


title: Control0005_AML009 (scRNA-seq)

description: Chromium Single Cell 5’ polyA RNA

value: Acute Myeloid Leukemia and Healthy Control


title: day 7, anti-IL6R_replicate 2


title: Tuft cells, Balb, untreated [UG4]


title: Quadriceps WT Rep1


title: Tuft cells congenic, untreated [UG3]


title: day 7, anti-IL6R_replicate 1


title: AML051 (scRNA-seq)

description: Chromium Single Cell 5’ polyA RNA


title: day 7, IgG_replicate 3


title: day 7, IgG_replicate 2


title: Spermatogonial stem cells KO2

city: jinan

first: Junchao

last: Qin

address: 44 Wenhua Xi Road

country: China

institute: Shandong University

data_processing:
An Oligo-dT primer was introduced to the reverse transcription reaction for first-strand cDNA synthesis, followed by PCR amplification to enrich the cDNA and magbeads purification step to clean up the production
Then the cDNA production was checked by Qubit® 3.0 Flurometer and Agilent 2100 Bioanalyzer to ensure the expected production with length around 1~2kbp.
Then the cDNA was sheared randomly by ultrasonic waves for Illumina library preparation protocol including DNA fragmentation, end repair, 3’ ends A-tailing, adapter ligation, PCR amplification and library validation.
After library preparation, PerkinElmer LabChip® GX Touch and Step OnePlus™ Real-Time PCR System were introduced for library quality inspection.
Qualified libraries were then loaded on Illumina Hiseq platform for PE150 sequencing
Genome_build: mm10
Supplementary_files_format_and_content: Transform into original sequencing sequence (Sequenced Reads) by bcl2fastq software

source_name: Spermatogonial stem cells

extract_protocol:
THY1+/c-KIT-spermatogonial stem cells were separated by flow cytometry from P4 mouse testis tissue through a two-step enzymatic digestion method
The single-cell samples were collected and amplification by the Smart-Seq2 method.
Smart-Seq2

treatment_protocol: Enzymatic digestion into single cells and flow sorting

value: Testis

tag: age

value: post natal day 4


title: day 7, IgG_replicate 1


title: Tuft cells, congenic, untreated [UG1]

value: small intestine tuft cells

value: Congenic Strain 3


title: Spermatogonial stem cells KO1


title: Tuft cells, B6, untreated [UG6]


title: ID216_RNAseq

city: Birmingham

first: Peter

last: Keane

address: Vincent Drive

department: Institute for Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

data_processing:
Low-quality reads and sequencing adapters were removed using Trimmomatic
Processed reads were then aligned to the human genome (version hg38) using Hisat2
Read counts were calculated using featureCounts from the SubRead package
Assembly: hg38
Supplementary files format and content: Tab-separated table with geneID and corresponding read counts

source_name: CD34+ AML cells

growth_protocol: Patient cells were cultured at the concentration of 1x106 cell/mL in StemSpanTM Serum-Free Expansion Medium II (SFEM II) (STEMCELL Technologies) supplemented with 10% StemSpanTM CD34+ Expansion Supplement and 175nM UM171 (STEMCELL Technologies). Other patient cells were grown in SFEM II supplemented with 100 ng/mL thrombopoietin, 10 ng/mL FMS-like tyrosine kinase 3 ligand, 750 nM Stem Regenin 1 (SRI), 10 ng/mL Interleukin 3, 10 ng/mL human granulocyte/macrophage colony stimulating factor, 150 ng/mL Stem Cell Factor (SCF) (all Peprotech) and UM729 (STEMCELL Technologies). Patient CD34+ or CD117+ hematopoietic progenitors were isolated with CD34 MicroBead Kit, human or CD117 MicroBead Kit, human (Miltenyi-Biotech) as described in PMID:30420649

extract_protocol:
Total RNA was extracted with NucleoSpin RNA (Machery-Nagel) and 1 ug of nucleic acid was retrotranscribed using SuperScriptTM II Reverse Transcriptase kit (Thermo Fisher) and 0.5 μg of Oligo(dT) primers (Promega), according to the manufacturer’s instruction.
RNA-seq libraries were prepared with a Total RNA Ribo-zero library preparation kit (with ribosomal RNA depletion) (Illumina, USA) according to manufacturer’s instructions with the following alterations: 15 cycles of PCR was undertaken to amplify the library and adaptors for multiplexing were used at a 1:4 dilution. Library quality was checked by running the samples on a Bioanalyser and libraries were quantified using a Kapa library quantification kit (Kapa Biosystems, USA) and run on a NextSeq 500 with 75bp paired-end reads

value: CD34+ AML cells

value: CEBPA double mutant

tag: disease

value: Acute Myeloid Leukemia


title: day 2, IL6_replicate 3


title: Control4003b (scRNA-seq)

description: Chromium Single Cell 5’ polyA RNA

value: Healthy Control

value: Bone Marrow

value: mononuclear cells

value: Chromium Single Cell 5’ polyA RNA


title: Spermatogonial stem cells WT3

value: wild type


title: Control0182b (scRNA-seq)

description: Chromium Single Cell 5’ polyA RNA


title: Control0182a (scRNA-seq)

description: Chromium Single Cell 5’ polyA RNA


title: Spermatogonial stem cells WT2


title: CEHRB31-005_RNAseq


title: Control0082 (scRNA-seq)

description: Chromium Single Cell 5’ polyA RNA


title: day 2, IL6_replicate 2

value: CD8 T cell


title: Spermatogonial stem cells WT1


title: 2273_RNAseq


title: Spermatogonial stem cells KO3


title: AML052 (scRNA-seq)

description: Chromium Single Cell 5’ polyA RNA


title: day 2, IL6_replicate 1


title: Tuft cells, B6, untreated [UG2]

value: WT C57BL/6J


title: ACCCA, rep2

city: Paris

first: David

last: Bikard

address: 28 rue du Dr Roux

country: France

institute: Institut Pasteur

library_source: genomic

data_processing:
Trimming, Fastp v.0.20.1
Alignment, Bowtie2 v.2.3.4
Sorting and indexing, samtools v.1.9
Peak calling, MACS3 v.3.0.0b1
Assembly: NC_000913
Supplementary files format and content: bed files with peak summits and score

molecule: genomic DNA

organism: Escherichia coli

growth_protocol: LB +  1 nM aTc + 50ug/ml Kanamycin + 25ug/ml chloramphenicol at 30°C

extract_protocol:
To enable immune-precipitation, a C-terminal 3x FLAG tag was added to dCas9 and the gene cloned under the control of a ptet promoter on plasmid pLC133. Samples were prepared from E. coli MG1655 harboring pLC133 and psgRNAcos plasmids with 3 different guide RNAs, a control guide targeting lacZ, the AGGAA_non1 guide or the ACCCA_non1 guide. Cells were grown at 30 degree and induced with aTc when OD600 reaches 0.2. When OD600 reaches 1.0, formaldehyde (final concentration: 1%) was added to fix the cells. After that, glycine was added to block formaldehyde. Samples were further washed with PBS and pelleted.   Samples were then resuspended in 1 ml of IP lysis buffer (50 mM Hepes pH 7.5, 0.4 M NaCl, 1 mM EDTA, 1 mM DTT, 0.5% Triton-X100, 10% Glycerol), 20 μl 0.1 M phenylmethylsulfonyl fluoride, 20 μl complete protease inhibitor (50x), 5 μl RNase inhibitor (40 U/ul). Cell lysis was performed using a covaris sonicator (S220), 10x (10 sec on, 10 sec off, Amplitude 15 μm) until the samples appeared clear. Samples were centrifuged and the supernatant mix with Anti-Flag M2 Affinity Gel (Sigma-Aldrich) beads and incubated overnight at 4 °C on a rotating wheel. After that, the beads were washed 5 times with IP lysis buffer, then eluted in Chip-Seq elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1.0% SDS). Bead pellets were incubated at 65°C in a water bath for 1 hour, then spun at 14,000 rpm for 3 minutes. The supernatant, which contains the Chipped DNA was then collected.
Samples were column purified to remove RNA, then fragment ends were repaired and phosphorylated with T4 polymerase and T4 PNK. After that, an A was added to 3’ end of repaired ends, then the DNA fragments with 3’ A overhang was ligated with illumina TrueSeq Adaptors. Samples were PCR amplified using primers (LC1504_TruSeq_P5 5’- AATGATACGGCGACCACCGAGATCTACAC-’3, LC1505_TruSeq_P7 5’- CAAGCAGAAGACGGCATACGAGAT-’3).

tag: guide rna

value: ACCCA

tag: antibody

value: Anti-Flag


title: Control4003a (scRNA-seq)

description: Chromium Single Cell 5’ polyA RNA


title: 2240_RNAseq


title: 2192_RNAseq


title: Control0004 (scRNA-seq)

description: Chromium Single Cell 5’ polyA RNA


title: ACCCA, rep3


title: AML0114c (CITE-seq)

description: Chromium Single Cell 3’ Reagent Kits (CITE-Seq)

data_processing:
Library strategy: CITE-Seq
Indexed BAM files containing position-sorted reads aligned to the genome.
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment to GRCh38 (version 5.0.1) was performed with 10x Genomics Cell Ranger Single Cell Gene Expression Software (version 2020-A).
HTOs each cell were normalized using a centered log ratio (CLR) transformation across cells.
Samples were demultiplexed based on HTOs using the HTODemux function in Seurat.
3' libraries were filtered for incorrectly assigned hash tags using Souporcell, doublet filtered using scDblFinder, and ambient RNA contamination was removed using SoupX.  Please see publication for detailed processing steps.
Genome_build: hg38
Supplementary_files_format_and_content: Processed data files for Single Cell RNAseq, CITEseq, TCR-seq:
feature reference
metadata
processed ADT counts
processed RNA counts
filtered barcodes
filtered features
filtered gene-barcode matrix
clonotypes
feature reference file 5 prime
filtered contig annotations
filtered count matrix

molecule: other

value: Chromium Single Cell 3’ polyA RNA and surface protein


title: 1316_RNAseq


title: day 2, anti-IL6R_replicate 2


title: day 2, anti-IL6R_replicate 3


title: day 2, anti-IL6R_replicate 1


title: day 2, IgG_replicate 2


title: AML0114a (CITE-seq)


title: AGGAA, rep2

value: AGGAA


title: AGGAA, rep3


title: day 2, IgG_replicate 3


title: ID216_DNaseI

data_processing:
Sequencing adapters and low-quality reads and were removed using Trimmomatic
Reads were then mapped to the human genome version hg38 using Bowtie v2.2.3
PCR duplicated reads were removed using the MarkDuplicates funtion Picard tools
Open chromatin regions (peaks) were identified using MACS2 and bedGraph files were generated by including the options -B --trackline
Assembly: hg38
Supplementary files format and content: bedGraph files of read pileups generated by MACS2
Library strategy: Dnase-Hypersensitivity

extract_protocol:
DNase I digestions of permeabilized cells were performed briefly as follows: live cells were added directly to a solution of DNase I (DPFF, Worthington) in dilute Nonidet P40, digested for 3 min at 22oC, and the reactions then terminated by addition of SDS to 0.5%. DNase I was typically used in the range of 2-6 μg/ml using a final 1.5 x 107 cells/ml.  DNase I (DPFF) was obtained from Worthington Biochemical Corporation and typically used in the range of 2-6 μg/ml using a final 1.5 x 107 cells/ml. The DNA digestion extent was comparable in all the generated samples as measured by RT-PCR. DNase-Seq libraries were then prepared. Levels of DNase I digestion were assessed using quantitative real-time PCR, measuring the ratio of the presence of known DNase I hypersensitive regions compared to a more resistant inactive region. Sequences of the PCR primers used for this purpose were, for the active region, TBP promoter 5´- CTGGCGGAAGTGACATTATCAA and 5´- GCCAGCGGAAGCGAAGTTA; and for the inactive region, a region of chromosome 18: 5´- ACTCCCCTTTCATGCTTCTG and 5´- AGGTCCCAGGACATATCCATT.
DNase-Seq samples were generated from a size selection of DNase I-digested DNA fragments comprised within a range of 100 to 250 bp (not including linkers) and subjected to library preparation as per manufacturer´s instruction (Illumina).


title: day 2, IgG_replicate 1


title: AML0114b (CITE-seq)


title: AML3730 (CITE-seq)


title: KO52_RUNX1_ChIP

data_processing:
Raw sequencing reads were trimmed to remove low-quality sequences and adaptors using Trimmomatic.
Processed reads were then aligned to the human genome version hg38 using Bowtie2 v2.2.3, with only uniquely aligned reads retained for further analysis.
PCR duplicated reads were identified and removed from the alignments using the MarkDuplicates function in Picards tools.
Peaks were called using MACS2 with settings -B --trackline.
Assembly: hg38
Supplementary files format and content: bedGraph files of read pileups generated by MACS2

growth_protocol: Patient cells were cultured at the concentration of 1x10^6 cell/mL in StemSpanTM Serum-Free Expansion Medium II (SFEM II) (STEMCELL Technologies) supplemented with 10% StemSpanTM CD34+ Expansion Supplement and 175nM UM171 (STEMCELL Technologies). Other patient cells were grown in SFEM II supplemented with 100 ng/mL thrombopoietin, 10 ng/mL FMS-like tyrosine kinase 3 ligand, 750 nM Stem Regenin 1 (SRI), 10 ng/mL Interleukin 3, 10 ng/mL human granulocyte/macrophage colony stimulating factor, 150 ng/mL Stem Cell Factor (SCF) (all Peprotech) and UM729 (STEMCELL Technologies). Patient CD34+ or CD117+ hematopoietic progenitors were isolated with CD34 MicroBead Kit, human or CD117 MicroBead Kit, human (Miltenyi-Biotech) as described in PMID:30420649. KO52 were cultured in Alpha MEM (Lonza) supplemented with 10% FCS (Gibco), 5% Pen-Strep, 5% L-Glu.

extract_protocol:
Up to 2x10^7 cells (depending on the antibody used and the expression level of the TF of interest) were washed 3 times in PBS and resuspended in 10 mL of PBS. To achieve protein- protein cross-linking, cells were incubated with 0.25M Di(N-succinimidyl) glutarate (DSG) (Sigma-Aldrich) for 45 min on rotation at RT. Cross-linked cells were pelleted and washed 3 times with 10 mL of PBS, spinning at 300xg for 5 min at 4°C between washes.  For single crosslinking the pellet was resuspended in 10 mL of PBS. Proteins were fixed to chromatin by adding 16% formaldehyde (Pierce) to a final 1% concentration and incubating on rotation for 10 min at RT. To quench the cross-linking reaction, cells were incubated on ice for 5 min with 0.4M glycine (Sigma-Aldrich). Cross-linked cells were pelleted and washed twice with 50 mL of ice-cold PBS, spinning at 300xg for 5 min at 4°C between washes.  Cell pellets were resuspended in 10 mL of ice-cold lysis buffer A (10 mM HEPES pH 8.0, 10 mM EDTA pH 8.0, 0.5 mM MEGTA pH 8.0, 0.25% Triton-X 100) with the addition of 1x Protein Inhibitor Cocktail (PIC) (Sigma-Aldrich) and incubated on rotation for 10 min at 4°C. Residual nuclei were pelleted at 500xg for 10 min at 4°C, resuspended in 10 mL of ice-cold Buffer B (10 mM HEPES pH 8.0, 200 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM MEGTA pH 8.0, 0.01% Triton-X 100) with the addition of 0.1x PIC and incubated on rotation for 10 min at 4°C. Chromatin was pelleted at 500xg for 5 min at 4°C and resuspended to a final concentration of 5x10^6 cells/300 μL of ice-cold IP Buffer I (25 mM Tris-HCl, pH 8.0, 150 mM NaCl, 2 mM EDTA, pH 8.0, 1% Triton-X 100, 0.25% SDS) with the addition of 0.1x PIC.  A maximum of 300 μL of chromatin suspension were aliquoted in Bioruptor tubes (Diagenode) and fragmented by using a Bioruptor Pico Sonicator (Diagenode). For each cell type, the number of sonication cycles was optimized to obtain chromatin fragment ranging between 200 and 1000 bp. Each cycle was 30 sec long with a 30 sec break. Sonicated chromatin was spun down at 16000xg for 15 min at 4°C and resuspended in 2 volumes of IP Buffer II (25 mM Tris-HCl, pH 8.0, 150 mM NaCl, 2 mM EDTA, pH 8.0, 1% Triton-X 100, 7.5% Glycerol) with the addition of 1x PIC. Separated reactions were pooled and 10% of the chromatin suspension was stored as input control.  The following IP protocol is optimized for a maximum input of 5x10^6 cells, and multiple reactions were set up for experiments requiring a greater number of cells. For each IP, 10 μL of Dynabeads Protein G (Thermo Fisher) were washed once with 200 μL of 0.1M citrate phosphate pH 5.0 and twice with 200 μL of 100 mM NaH2 pH 8.0 phosphate buffer. 4 μg of C/EBPα antibody (sc-1662587), RUNX1 antibody (Ab23980) or c-Fos antibody (MA5-15055, Invitrogen) were added to 5 μL of 100 mM NaH2 pH 8.0 phosphate buffer, 0.5% BSA and incubated with Dynabeads Protein G on rotation for 2 hours at 4°C.  Chromatin was incubated with the antibody-beads mixture for 4 h (C/EBPα and RUNX-1 IPs) or overnight (c-FOS IPs) on rotation at 4°C. Beads were washed once with Wash Buffer I (20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 2mM EDTA pH 8.0, 1% Triton-X 100, 0.1% SDS), twice with Wash Buffer II (20 mM Tris-HCl, pH 8.0, 500 mM NaCl, 2mM EDTA pH 8.0, 1% Triton-X 100, 0.1% SDS), once with Lithium Chloride (LiCl) Buffer (10 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1mM EDTA pH 8.0, 0.5% NP-40, 0.5% Na-Deoxycholate) and twice with TE/NaCl Buffer (10 mM Tris-HCl, pH 8.0, 50 mM NaCl, 1 mM EDTA pH 8.0). Chromatin was eluted from beads in 100 μL of freshly prepared Elution Buffer (EB) (100 mM NaHCO3, 1% SDS) incubating on a shaker for 30 minutes at RT. Samples, including the input control, were incubated overnight at 65°C in 500 mM NaCl and 500 μg/ml proteinase K (Roche) to reverse crosslinks and digest proteins. After this step, multiple reactions were pooled together.  For quality control, samples were incubated with 1.8x volumes of AMPure XP beads (Beckman Coulter) for 30 minutes at RT. After washing beads twice with 200 μL of ethanol, chromatin was eluted in 50 μL of 0.1x TE pH 8.0.  The quality of the ChIP was assessed by qPCR. The immunoprecipitated DNA and the input control were amplified using primers specific for both putative binding sites of the TF in exam as well as non-bounding sites (Table 2.8) and the enrichment of the target sequences was measured over the input.
ChIP library preparation was performed by using the KAPA Hyper Prep Kit (Roche) with a 200-450 bp library size selection.

tag: chip antibody

value: Abcam Ab23980

tag: target


title: lacZ, rep3

value: lacZ


title: KO52_cFOS_ChIP

value: Invitrogen MA5-15055

value: cFOS


title: lacZ, rep2


title: ACCCA, rep1


title: WT replicate C [FTC]

city: Rochester

first: Wenqian

last: Hu

state: Minnesota

address: 200 First St SW, GU16-01A

department: Biochemistry and Molecular Biology

institute: Mayo Clinic

data_processing:
Basecalls performed using CASAVA version 1.4
The sequenced reads were trimmed for adaptor sequence, then mapped to mm10 whole genome using hisat2 with default parameters. The resulting sam file is converted into bam file using samtools. The uniquely mapped reads were isolated using samtools.
The raw count file was generated from Rsubread
Genome_build: mm10
Supplementary_files_format_and_content: The csv file contains raw counts from each of the samples

source_name: mouse embryonic stem cells (mESCs)

growth_protocol: All the mESCs used in this study were cultured on 0.5% gelatin-coated tissue culture plates in the 2i + Lif medium (DMEM/F-12, 2% FBS, 2mM L-Glutamine, 0.1mM MEM NEAA, 1% Penicillin-Streptomycin, 0.1 mM β-mercaptoethanol and 1000 U/mL mLIF, 1 x N2N27, 3 uM CHIR99021 and 1 uM PD0325901).

extract_protocol:
Total RNA were isolated from mESCs via Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

value: FLAG-Trim71 mESCs

tag: genetic background

tag: molecule type

value: oligo(dT) selected RNA


title: AML3948 (CITE-seq)

value: Acute Myeloid Leukemia

tag: cell type


title: KO52_CEBPA_ChIP

tag: cell line

tag: genotype

value: CEBPA double mutant

value: Santa Cruz sc-1662587

value: CEBPA


title: AML0693 (CITE-seq)

tag: disease state

value: Bone Marrow

value: mononuclear cells


title: WT replicate B [FTB]


title: CEHRB31-005_DNaseI

value: CD34+ AML cells


title: ID216_RUNX1_ChIP


title: AML001 (CITE-seq)

tag: tissue


title: WT replicate A [FTA]


title: ID216_CEBPA_ChIP


title: Control0005_AML009b (CITE-seq)

value: Healthy Control

tag: assay


title: AGGAA, rep1

tag: strain

value: Anti-Flag


title: PAO1_skin_TnSeq_H2O4

city: Vancouver

first: Robert

middle: E. W.

last: Hancock

state: British Columbia

address: 2259 - Lower Mall Research Station

department: Department of Microbiology & Immunology

country: Canada

institute: University of British Columbia

data_processing:
Read quality was assessed using FastQC v0.11.6
Read alignment 1: BioTraDIS was run using default parameters to align reads using SMALT and determine insertion counts per gene.
Read alignment 2: Transit was run using TPP pre-processing tool to align reads using BWA V0.7.17 with default parameters to tabulate counts of reads mapped per TA site. The read counts were passed through the Gumbel method to calculate the probability of essentiality for each gene.
Any genes predicted to be essential by BioTraDIS or Gumbel in at least four of five replicates for experimental conditions or two of three replicates for the baseline T0 pool were compiled into a final list of "essential" genes.
Assembly: Pseudomonas aeruginosa PAO1 downloaded from Pseudomonas Genome database v17.1 (accession GCF_000006765.1; PseudoCap version 138)
Supplementary files format and content: BioTradis (CSV): Comma-delimited files containing a list of all PAO1 genes, along with statistics of the number of sequencing reads mapped to a given gene by BioTradis (eg. "read count", "insertion count", etc).
Supplementary files format and content: Transit (WIG): Number of reads aligned at each TA site in the PAO1 genome, as calculated by Transit.

organism: Pseudomonas aeruginosa PAO1

source_name: P. aeruginosa transposon insertion mutant cell pool

growth_protocol: A TnSeq pool was constructed in Pseudomonas aeruginosa PAO1 strain H103 using the mariner Himar1 transposon vector pBT20 until at least 200,000 mutants were collected. Total genomic DNA was extracted from TnSeq pool at baseline prior to growth under various testing conditions. Tested growth conditions included LB (planktonic), Mueller-Hinton Broth (MHB), RPMI supplemented with MHB (RPMI), RPMI supplemented with MHB and human serum (Serum), in-vivo murine skin abscess model that was left untreated (Abs_unt), and air-liquid interface human N/TERT skin organoid model (skin).

extract_protocol:
Genomic DNA was extracted using the Dneasy Blood and Tissue kit (Qiagen). Concentration and purity was measured using a NanoDrop 2000 (ThermoFisher).
Four replicate PCR reactions were used to amplify the transposon-genome junctions and were pooled together. Two-sided size selection was performed with Agencourt AMPure XP magnetic beads. Illumina Nextera Index Kit v2 SetA was used for indexing.

tag: growth condition

value: Air-liquid interface skin model using N/TERT keratinocyte cells (skin)

tag: condition

value: skin


title: R783H replicate C [783C]

value: FLAG-Trim71 (R783H) mESCs


title: AML026_AML051 (CITE-seq)

value: Chromium Single Cell 3’ polyA RNA and surface protein


title: R783H replicate B [783B]


title: 2273_RUNX1_ChIPseq

value: Abcam Ab23980


title: 2273_CEBPA_ChIP


title: R783H replicate A [783A]


title: lacZ, rep1

value: lacZ


title: 2240_RUNX1_ChIPseq


title: PAO1_skin_TnSeq_H2O1

value: P. aeruginosa transposon insertion mutant cell pool


title: PAO1_skin_TnSeq_H2O2


title: AML4897 (CITE-seq)


title: AML0024 (CITE-seq)


title: Trim71(R783H) CLIPseq in mESCs 1

description: Trim71(R783H) bound mRNA

data_processing:
Basecalls performed using CASAVA version 1.4
For CLIPseq, sequenced reads were trimmed for adaptor sequence, then mapped to mm10 whole genome using hisat2 with parameters--mp 6,2. The resulting sam file is converted into bam file using samtools. The uniquely mapped reads were isolated using samtools.
For small RNAseq, sequenced reads were trimmed for adapter sequence using cutadapt. The resulting reads with a minimal length of 15nt were retained for mapping by HISAT2 (v2.1.0).
The CLIPseq peak calling were performed by the Piranha, iCount, and CLIPper. The common peaks from these 3 programs were retained as Trim71(R783H)-binding regions
Genome_build: mm10
Supplementary_files_format_and_content: The csv file contains Trim71(R783H)-binding regions from the CLIPseq

extract_protocol:
Total RNA were isolated from mESCs via Trizol reagent
The Trim71(R783H) CLIP-seq was performed using the previously established HITS-CLIP protocol (Moore et al., 2014).
CLIP-seq

value: FLAG-M2 (Sigma)


title: Trim71(R783H) CLIPseq in mESCs 2

description: Trim71(R783H) bound mRNA


title: AML1371_AML4340b (CITE-seq)

value: Acute Myeloid Leukemia


title: 2240_CEBPA_ChIPseq

value: CEBPA double mutant


title: 1316_RUNX1_ChIPseq


title: Abs_unt_5

value: Subcutaneous injection and 18 hour abscess growth on Mus musculus CD-1 (Abscess_untreated)


title: input B

value: input


title: Abs_unt_4


title: input A


title: AML1371_AML4340a (CITE-seq)

value: Bone Marrow


title: Control4003c (CITE-seq)

value: mononuclear cells


title: PAO1_skin_TnSeq_H2O3


title: Control0005_AML009a (CITE-seq)


title: 1316_CEBPA_ChIPseq

value: CD34+ AML cells

value: Santa Cruz sc-1662587

value: CEBPA


title: Control4003b (CITE-seq)

value: Healthy Control


title: Abs_unt_2


title: Control4003a (CITE-seq)


title: 2240_ATACseq

data_processing:
Sequencing adapters and low-quality reads and were removed using Trimmomatic
Reads were then mapped to the human genome version hg38 using Bowtie v2.2.3
PCR duplicated reads were removed using the MarkDuplicates funtion Picard tools
Open chromatin regions (peaks) were identified using MACS2 and bedGraph files were generated by including the options -B --trackline
Assembly: hg38
Supplementary files format and content: bedGraph files of read pileups generated by MACS2

extract_protocol: ATAC libraries were generated following the Omni-ATAC protocol from Corces et al, 2017 (PMID:28846090)


title: 2273_ATACseq


title: spleen, anti-IL6R_2

data_processing:
RNA-sequencing data were analyzed using HTSeqGenie in BioConductor
reads with low nucleotide qualities (70% of bases with quality <23) or rRNA and adapter contamination were removed
Filtered reads were aligned to the reference genome GRCm38 using GSNAP
Gene expression levels were quantified as Reads Per Kilobase of exon model per Million mapped reads normalized by size factor (nRPKM)
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix with raw counts for every gene and every sample (txt format)

growth_protocol: Splenocytes were isolated by mashing spleens through sterile 70 um filters. Red blood cells were lysed using ACK buffer. 0.2 million splenocytes were seeded in T cell medium in flat-bottom 96-well plates and stimulated with 100 ng/ml SIINFEKL peptide for 2 days. Cells were then washed and cultured for a further 3 days in T cell medium with recombinant human IL-2 (10 ng/ml). Cells were stimulated with plate-bound anti-CD3 (clone 145-2C11; 5 ug/ml) and anti-CD28 (clone 37.51; 2.5 ug/ml) antibodies and collected for RNA extraction on day 7.

extract_protocol:
Total RNA extracted using RNEasy mini kit (Qiagen) according to manufacturer instructions
0.1 μg of total RNA was used as an input material for library preparation using TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA). Size of the libraries was confirmed using 4200 TapeStation and High Sensitivity D1K screen tape (Agilent Technologies, Santa Clare, CA) and their concentration was determined by a quantitative PCR-based method using Library quantification kit (KAPA Biosystems, Wilmington, MA). The libraries were multiplexed and sequenced on Illumina HiSeq4000 (Illumina, San Diego, CA) to generate 30 million single-end 50 base pair reads.

treatment_protocol: T cells cultured in the presence or absence of recombinant mouse IL-6 (10 ng/ml; R&D Systems), recombinant mouse hyper-IL-6 (20 ng/ml; R&D Systems), mouse IgG2A isotype control antibody (in-house, 5 ug/ml), or mouse IgG2A anti-IL6R antibody clone MR16-1 (in-house, 5 ug/ml).

value: OT-I (C57BL/6-Tg(TcraTcrb)1100Mjb/J)

value: spleen

value: CD8+ T cells

tag: treatment

value: anti-IL6R (5 ug/ml)


title: spleen, anti-IL6R_1


title: 2234_ATACseq

tag: disease


title: AML2123b (CITE-seq)

value: Chromium Single Cell 3’ polyA RNA and surface protein


title: 2192_ATACseq


title: Serum_3

value: P. aeruginosa transposon insertion mutant cell pool

value: RPMI-1640 supplemented with 5% MHB and 20% human serum (Serum)

value: Serum


title: 1316_ATACseq

value: CEBPA double mutant

value: Acute Myeloid Leukemia


title: Abs_unt_3

value: Subcutaneous injection and 18 hour abscess growth on Mus musculus CD-1 (Abscess_untreated)


title: Serum_5


title: Serum_4


title: Serum_2


title: spleen, IgG_2

value: isotype IgG (5 ug/ml)


title: spleen, anti-IL6R_3


title: spleen, hyper-IL6_3

value: hyper-IL6 (20 ng/ml)


title: AML2123a (CITE-seq)

value: Bone Marrow

value: mononuclear cells


title: spleen, IgG_3


title: RPMI_5

value: RPMI-1640 supplemented with 5% MHB (RPMI)

value: RPMI


title: Control0082_AML052_AML022a (CITE-seq)

value: Acute Myeloid Leukemia and Healthy Control


title: Serum_1


title: Abs_unt_1


title: KO52_EV_RNAseq_rep2

growth_protocol: KO52 were cultured in Alpha MEM (Lonza) supplemented with 10% FCS (Gibco), 5% Pen-Strep, 5% L-Glu.

treatment_protocol: The doxycycline inducible pCW57.1-dnC/EBP plasmid was generated using Gateway Gene Cloning (Thermo Fisher Scientific), according to manufacturer’s instructions. The CMV500 A- C/EBP plasmid containing the dnC/EBP insert was a gift from Charles Vinson, National Cancer Institute, Bethesda, USA 1. dnC/EBP cDNA was PCR amplified (with Phusion DNA polymerase (New England Biolabs) using primers containing SalII and NotI restriction enzymes overhangs and cloned into pENTR-IRES-GFP (a modification of the Invitrogen pENTR plasmid constructed by Benjamin Edginton-White, University of Birmingham, UK) digested with 30 units of SalI-HF (New England Biolabs), 30 units of NotI-HF (New England Biolabs). The dnC/EBP insert was then transferred into the Tet-on pCW57.1 backbone (Addgene plasmid #41393) by using the Gateway Gene Cloning System. The pCW57.1 containing the dnFOS insert was generated by Dr Sandeep Potluri (University of Birmingham) following the same protocol. Lentiviral particles containing pCW57.1-dnC/EBP / dnFOS or the empty vector were generated in HEK293T cells using calcium-phosphate transfection. Cells were cultured in DMEM supplemented with 10% foetal calf serum (FCS), 5% Penicillin-Streptomycin (Pen-Strep), 5% L-Glutamine (L-Glu) and 5% Sodium Pyruvate and seeded to achieve about 30-40% confluency at the time of transfection. 12 μg of pCW57.1-dnC/EBP or empty vector were transfected with 0.6 ug of REV, 0.6 ug of GAG/POL, 1.2 ug of VSV-G and 0.6 ug of TAT packaging plasmids. Viral supernatant was harvested at 24, 36, 48, 60 and 72h and concentrated with Centricon Plus- 70 columns (Merk-Millipore) using manufacturer’s instructions. Concentrated viral particles were filtered through 0.45 um filter and stored at -80°C or immediately used to infect recipient cells. To carry out the spin infection, 1 x 10^6 Kasumi-1 or KO52 cells were plated in 17 6-well plates with the viral supernatant and 8 ug/mL of polybrene, and centrifuged for 1h 30m at 1500 x g at 32°C. After infection cells were incubated at 37 °C for 12 hours and then resuspended in fresh media. Few days after infection, cells were cultured in medium supplemented with puromycin 1.5 ug/mL and 2ug/mL for 5 days, allowing the selection of cells positive for pCW57.1-dnC/EBP. Single clones were then isolated from the bulk Kasumi-1 population, expanded and tested for leakiness and induction of dnC/EBP measuring both GFP and FLAG expression through both FACS and RT-qPCR. Despite several attempts, it was not possible to expand KO52 single cell clones with either vector and the bulk population was used for downstream experiments. Dominant negative peptides expression was induced by adding 2 μg/mL of doxycycline to culture medium.

value: Empty Vector


title: AML3266 (scRNA-seq)

description: Chromium Single Cell 3’ Reagent Kits

value: Chromium Single Cell 3’ polyA RNA


title: KO52_dnFOS_RNAseq_rep1

value: dnFOS


title: spleen, hyper-IL6_2

value: OT-I (C57BL/6-Tg(TcraTcrb)1100Mjb/J)

value: spleen

value: CD8+ T cells


title: Control0082_AML052_AML022c (CITE-seq)

value: Chromium Single Cell 3’ polyA RNA and surface protein


title: KO52_EV_RNAseq_rep1

value: CEBPA double mutant


title: RPMI_4

value: P. aeruginosa transposon insertion mutant cell pool


title: AML0048-c2 (CITE-seq)

value: Acute Myeloid Leukemia


title: RPMI_3


title: spleen, hyper-IL6_1


title: spleen, IL6_3

value: IL6 (10 ng/ml)


title: spleen, IgG_1

value: isotype IgG (5 ug/ml)


title: KO52_dnCEBP_RNAseq_rep2

value: dnCEBP


title: AML0048-c1 (CITE-seq)

value: Bone Marrow

value: mononuclear cells


title: RPMI_2

value: RPMI-1640 supplemented with 5% MHB (RPMI)

value: RPMI


title: spleen, IL6_2


title: RPMI_1


title: Control0082_AML052_AML022b (CITE-seq)

value: Acute Myeloid Leukemia and Healthy Control


title: spleen, IL6_1


title: AML012_AML005_AML055_AML048a (CITE-seq)


title: KO52_dnFOS_RNAseq_rep2


title: KO52_EV_ATAC_rep2

value: Empty Vector


title: MHB_4

value: Mueller-Hinton broth (MHB)

value: MHB


title: KO52_dnCEBP_RNAseq_rep1


title: spleen, control_3

value: OT-I (C57BL/6-Tg(TcraTcrb)1100Mjb/J)

value: spleen

value: control


title: KO52_dnFOS_ATAC_rep2

value: CEBPA double mutant

value: dnFOS


title: KO52_EV_ATAC_rep1


title: MHB_5

value: P. aeruginosa transposon insertion mutant cell pool


title: MHB_3


title: spleen, control_2

value: CD8+ T cells


title: KO52_dnFOS_ATAC_rep1


title: AML073_AML006_AML025_AML003a (CITE-seq)

value: Acute Myeloid Leukemia

value: Chromium Single Cell 3’ polyA RNA and surface protein


title: spleen, control_1


title: AML073_AML006_AML025_AML003b (CITE-seq)

value: Bone Marrow


title: MHB_2


title: KO52_dnCEBP_ATAC_rep2

value: dnCEBP


title: AML038_AML008_AML043_AML028_AML057b (CITE-seq)

value: mononuclear cells


title: AML012_AML005_AML055_AML048b (CITE-seq)


title: AML038_AML008_AML043_AML028_AML056a (CITE-seq)


title: Liver_SASP_3

city: Zhengzhou

first: Yucheng

last: Li

address: Jinshui East 156

institute: Henan University of Chinese Medicine

data_processing:
Cutadapt was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases, sequence quality was verified using FastQC.
We used Bowtie2  and topaht2 to map reads to the genome of mouse.The mapped reads of each sample were assembled using StringTie
all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts.
After the final transcriptome was generated, StringTie  and Ballgown was used to estimate the expression levels of all transcripts.
StringTie was used to perform expression level for mRNAs by calculating FPKM. The mRNA with a fold change >1.5 and P<0.05 were considered to be the DEGs.
Genome_build: GRCm38.p5

source_name: liver, sulfasalazine-treated

growth_protocol: Forty male ICR mice weighing 18-22 g were obtained from Hunan Slac Animal Center. Mice were housed ten per cage under a 12-h light/dark cycle with 23-25 ℃ and 40-60% of humidity. After arrival, mice were acclimatized for 1 week with access to water and food.

extract_protocol:
Total RNA was extracted from liver tissue using TRIZol reagent. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 μg of total RNA representing a specific adipose type was used to deplete ribosomal RNA according to the manuscript of the Epicentre Ribo-Zero Gold Kit.
Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA)

treatment_protocol: After one week of adaption, forty mice were randomly divided into four experimental groups (n = 10): control group and SASP groups (250, 500, 1000 mg/kg). SASP (98% of purity, Aladdin, Shanghai, China) was dissolved in 0.1% dimethyl sulfoxide (DMSO) and were administered by oral gavage in a volume of 10 mL/kg for 4 weeks. Control group received equal volume of 0.1% DMSO.

value: ICR

tag: age

value: 8 weeks

tag: Sex

value: male

value: liver


title: MHB_1

value: Mueller-Hinton broth (MHB)

value: MHB


title: KO52_dnCEBP_ATAC_rep1


title: Liver_SASP_2


title: PAO1_TnSeq

value: T0 LB (planktonic)


title: Liver_SASP_1


title: Control0058_PAXMIJ_PAUMTZb (CITE-seq)

value: Acute Myeloid Leukemia and Healthy Control


title: ID216_Blast_and_LSC_scRNAseq

description: Blast and LSC populations sorted from bulk primary cells and pooled to form a single library

library_source: transcriptomic single cell

data_processing:
Reads from single-cell RNA-Seq experiments were aligned to the human genome (version hg38) and quantified using the count function in CellRanger v3.1.0 from 10x Genomics and using gene models from Ensembl as the reference transcriptome.
Unique Molecular Identifier (UMI) count data was filtered for low quality cells by removing cells with less than 500 and more than 5000 detectable genes.
Assembly: hg38
Supplementary files format and content: Tab-separated table of cell barcodes with corresponding cluster and cell-type assignments from Seurat analysis
Supplementary files format and content: HDF5 feature barcode matrix files generated using CellRanger Count

source_name: Sorted leukemic stem cells and blasts pooled

extract_protocol: Library generation for scRNA-Seq was performed by the genomics Birmingham sequencing facility using the Chromium Single Cell 3' library and gel bead kit v3 (10x Genomics). Libraried were paired-end sequenced on an Illumina NextSeq 500 using the cycle parameters recommended by 10x Genomics

value: CEBPA double mutant


title: ID216_LSC

source_name: Leukemic Stem Cells

value: Leukemic Stem Cells


title: PAO1_B

value: P. aeruginosa transposon insertion mutant cell pool


title: Liver_Con_2

source_name: liver, control


title: ID216_Blast

source_name: Leukemic Blasts

value: Leukemic Blasts


title: Control0058_PAXMIJ_PAUMTZa (CITE-seq)


title: AML2451_Control0004 (CITE-seq)


title: PAO1_A


title: Liver_Con_3


title: Control0058_PAXMIJ_PAUMTZc (CITE-seq)


title: Mammary gland macrophages replicate 3

city: Heidelberg

first: Joschka

last: Hey

state: Deutschland

address: Im Neuenheimer Feld 280

department: Cancer epigenomics

institute: DKFZ

description:
meth.tsv
cov.tsv

data_processing:
WGBS data were processed by the Omics IT and Data Management Core Facility (DKFZ, Heidelberg). Preprocessing of sequencing reads was performed as described earlier by Delacher et al 2017. Reads were aligned using an updated pipeline published by Wang et al. 2013, implemented as a Roddy Workflow (https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows) in the automated One Touch Pipeline. Briefly, adaptor sequences of raw reads were trimmed using Trimmomatic. Sequencing reads were then in silico bisulfite-converted 65 (C>T for the first read in the pair, G>A for the second). The software BWA-MEM was used with default parameters to align the converted reads to the in silico bisulfite-converted reference genome mm10, extended with the PhiX and lambda phage sequences. After alignment, reads were converted back to their original state, considering reads with a mapping quality ≥25 and nucleotides with a Phred-scaled quality score ≥25. PCR duplicate removal was performed per sequencing library using Picard. Methylation calling and M-bias QC were performed using MethylDackel  v0.4.0 and the parameters --OT 6,0,6,140 --OB 2,145,12,150, according to the M-bias quality control plots.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text files include methylation levels and coverages

source_name: Normal mammary fat pad

growth_protocol: 8 to 13 weeks-old mice housed at the Weizmann Institute animal facility under specific pathogen-free conditions.

extract_protocol:
Normal mammary fat pad: Tissue was minced using scissors and placed and disrupted for 25 min at 37oC in a gentleMACS C tube using gentleMACS dissociator, in the presence of enzymatic digestion solution containing 1 mg ml-1 collagenase II, 1 mg ml-1collagenase IV and 70 unit ml-1 DNase. Primary tumor: Tissue was minced using scissors and treated with enzymatic digestion solution containing 3 mg ml-1 collagenase A and 70 unit ml-1 DNase in RPMI 1640 for 20 min at 37oC, with pipetting every 3 min. Foe BMDM extraction the Tibia and Femur leg bones were dissected Bones were flushed with MACS buffer using a 5 ml syringe with a 25 G needle. The flushed cells from the bone marrow were centrifuged at 500 g for 5 min and resuspended in red blood cell lysis buffer  cells were washed with PBS and resuspended in macs buffer.
Post bisulfite adaptor tagging protocol by Clark et al 2017: WGBS libraries from low input material were prepared using a PBAT protocol initially developed for single-cell bisulfite sequencing. As input, 6 ng of purified DNA or 1,000 cells, which were lysed in RLT Plus buffer (Qiagen), were used. A total of 10 µl of cell suspension was applied to the protocol, including the following changes: A single preamplification step was performed for 90 min at 37°C. Fourteen cycles of library amplification were conducted with default PCR parameters. Libraries were purified by applying twice a 0.7x SPRI selection using AMPure XP beads (Agencourt, Indianapolis, IN, USA). The libraries’ molarities were calculated based on concentrations measured with the Qubit dsDNA Assay (Thermo Fisher Scientific) and fragment size distribution measured with the high sensitivity D5000 Assay for the Agilent Tapestation (Agilent Technologies Germany GmbH & Co. KG, Waldbronn, Germany). Libraries were sequenced one lane per sample on a HiSeq X sequencer using the 150 base pairs (bp), paired-end mode (Illumina, San Diego, CA, USA) at the DKFZ Genomics and Proteomics Core Facility.

treatment_protocol: 8 weeks old BALB/c females were injected under anaesthesia with 100,000 4T1-luc cells suspended in PBS, directly into the lower left mammary fat pad. To obtain TAMs from primary tumors, mice were sacrificed and tumors were immediately excised post mortem.

value: BALB/c

value: Normal mammary fat pad

value: Mammary gland macrophages

tag: selection marker

tag: mouse age

value: 13 weeks


title: Liver_Con_1


title: ID216-LSC

source_name: Leukemic Stem Cell

value: Leukemic Stem Cell

value: Acute Myeloid Leukemia


title: Mammary gland macrophages replicate 2

description:
meth.tsv
cov.tsv

value: 12 weeks


title: Mammary gland macrophages replicate 1

description:
meth.tsv
cov.tsv


title: S. maltophilia K279a chpA del, LB broth rep2

first: Melissa

middle: Skye

last: McDaniel

state: AL

address: 845 19th St S BBRB 744

department: Microbiology

institute: University of Alabama at Birmingham

data_processing:
Raw reads were trimmed using Trim Galore! (v. 0.4.4) and Cutadapt (v. 1.9.1) and were evaluated for quality with FastQC
Reads were aligned to the published genome of S. maltophilia K279a or the Mus musculus genome build GRCm39/mm39 using the STAR aligner (v. 2.7.3a)
Read counts were obtained via Subread FeatureCounts
Differential expression analysis was performed with DESeq2
Assembly: GRCm39/mm39
Supplementary files format and content: tab-delimited text files include gene counts from FeatureCounts and differential expression values as calculated using DESeq2

organism: Stenotrophomonas maltophilia

source_name: bacteria

extract_protocol:
For RNA isolation from the lung, BALB/cJ mice (8-10 weeks old) were obtained from Jackson laboratories (Bar Harbor, ME).  Mice were anesthetized with isoflurane and intratracheally infected with either S. maltophilia, P. aeruginosa, or both (~107 CFU each in 100 µL PBS). Mice were euthanized 24 hours post-infection, and lungs were inflated with RNA-later to preserve RNA integrity. Whole lungs were homogenized, and cells were lysed by bead beating (0.1 mm silica) in Trizol reagent (Invitrogen), and a full lung RNA extraction was performing using a standard protocol (50). Extracted RNA samples were sent to GENEWIZ (South Plainfield, NJ) for DNase treatment, host and bacterial rRNA depletion (Ribo-Zero Gold rRNA Removal Kit (Epidemiology), Illumina), and library preparation using standard protocols. For bacterial RNA-seq, single-end directional samples were DNase treated (DNase I, NEB) using a standard protocol, before being run through a second Trizol extraction to purify the sample of enzyme.
Sequencing libraries were constructed using the directional RNA Library Prep Kit (NEB) and tagged for multiplexing via the NE Next Multiplex Oligos for Illumina (NEB).
For in vivo bacterial samples, a pathogen-specific probe list for S. maltophilia was generated using previously published methods (28). Briefly, 100 bp probes were generated to cover annotated coding sequences of S. maltophilia, with 15 bp spacer sequences added on either end to allow for amplification of the probe library.   5’ SPACER : ATCGCACCAGCGTGT  3’ SPACER: CACTGCGGCTCCTCA  Probes completely covered the sense strand of each gene and were also generated to tile every other 100 bp of the antisense strand for a total of 68,704 probe sequences Figure S1). Probes with significant homology to the mouse genome or to bacterial non-coding RNAs (P <0.05 with BLAST analysis) were manually removed from the list. The resulting oligo pool was synthesized by Genscript (Piscataway, NJ). Before hybridization, DNA oligos were amplified and then transcribed (MEGAshortscript T7 Transcription Kit, Ambion), with added biotin-16-UTP (Roche) to generate biotinylated RNA probes.   Prepared cDNA libraries were hybridized to the generated pathogen-specific RNA probes using previously described methods (28) with a few modifications. Briefly, the synthesized probes and the prepared cDNA library were incubated in hybridization buffer for 24 hours at 68°C. Blocking primers were modified for compatibility with NEB multiplexing primers and a 3’ ddc’ modification was added to maintain barcoding.   Hybridization primer FWD:   AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT/3ddC/  Hybridization primer REV:  CAAGCAGAAGACGGCATACGAGATNNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT/3ddC/  Hybridized cDNA was isolated via streptavidin beads and then eluted. Enriched samples were amplified using universal primers that maintained sample barcoding before sequencing.

value: bacteria

value: del chpA (smlt3670)

value: Overnight growth in LB broth


title: Tumor-associated macophages replicate 2

description:
meth.tsv
cov.tsv

source_name: Tumor microenvironment of breast cancer

value: Breast cancer

value: Tumor-associated macrophages

value: Orthotopic injection of 4T1-luc cells into the mammary fat pad

value: 8 weeks


title: Bone marrow-derived monocytes from healthy mice replicate 4

description:
meth.tsv
cov.tsv

source_name: Bone marrow of healthy mice

value: Bone marrow

value: Bone marrow-derived monocytes

value: CD11b+ Gr+ F4/80low


title: PAWWEEc (CITE-seq)

source_name: bone marrow

extract_protocol:
Cryopreserved bone marrow aspirates were obtained from Ohio State University’s sample bank (adult AML samples), from St. Jude Children’s Research Hospital AML16 clinical trial (pediatric AML samples) or from the Children’s Oncology Group AML cell bank (pediatric AML sample). All subjects provided written consent for banking and research use of these specimens, in accordance with the regulations of the institutional review boards of all participating institutes. Cryopreserved primary human bone marrow mononuclear cells were obtained from STEMCELL Technologies or from StemExpress. Frozen human bone marrow samples were thawed and transferred into 50mL conical tubes containing PBS + 2% fetal bovine serum (FBS). Cell suspensions were centrifuged at 350 x g for 5 minutes at 4C, and the supernatant was discarded. Samples were then subjected to dead cell depletion, using a dead cell removal kit (Miltenyi Biotec, 130-090-101), or stained with DAPI (0.5mg/mL) and sorted for live cells (DAPIlow), using a FACSAria IIu SORP cell sorter (BD Biosciences). For cell sorting, all samples were gated based on forward and side scatter, followed by doublet exclusion, and then gated on DAPIlow for viable cells. Samples were sorted into 5mL poly-propylene tubes containing 300mL ice-cold PBS + 2% FBS. Following cell sorting, samples were centrifuged at 350 x g for 5 minutes at 4C. For CITE-seq, enriched live cells were first tagged with cell-hashing oligo-tagged antibodies (Biolegend) according to the manufacturer’s instructions. Samples were than counted, and a maximum of 10e5 cells for each sample was pooled together and stained with a CITE-Seq antibody cocktail (Biolegend) according to the manufacturer’s instructions. For scTCR-Seq, T cells were enriched using a pan T cell isolation kit (Miltenyi Biotec, 130-096-535) or sorted for live CD45+ CD3+ cells. For cell sorting, samples were stained with PerCP-conjugated anti-human CD45 (1:400, Biolegend, 304025), FITC-conjugated anti-human CD3 (1:100, Biolegend,  300452). And DAPI (0.5mg/mL). Sorted samples were gated based on forward and side scatter, followed by doublet exclusion and then gated on DAPIlow for viable cells. CD45+ CD3+ cells were sorted into 5mL poly-propylene tubes containing 300mL ice-cold PBS + 2% FBS. Following cell sorting, samples were centrifuged at 350 x g for 5 minutes at 4C. Libraries were prepared using the Chromium Single Cell 3’ Reagent Kits (v3 and v3.1, CITE-Seq) or the Chromium Single Cell Immune Profiling Kits (v1.1 and v2, scTCR-Seq, 10x Genomics).  Hashtag and antibody-derived tag (ADT) libraries were prepared according to the New York Genome Center CITE-Seq and hashing protocol (https://citeseq.files.wordpress.com/2019/02/cite-seq_and_hashing_protocol_190213.pdf). Libraries were run on an Illumina NovaSeq 6000.
Chromium Single Cell 3’ Reagent Kits (v3 )

value: Bone Marrow

value: mononuclear cells

value: Chromium Single Cell 3’ polyA RNA and surface protein


title: Tumor-associated macophages replicate 1

description:
meth.tsv
cov.tsv

value: BALB/c


title: ID216-Blast

source_name: Leukemic Blast

value: Leukemic Blast

value: CEBPA double mutant


title: S. maltophilia K279a chpA del, LB broth rep1


title: Bone marrow-derived monocytes from healthy mice replicate 3

description:
meth.tsv
cov.tsv

value: 12 weeks


title: Control1_Control2_Control3_Control4d (CITE-seq)

value: Healthy Control


title: Control5_AML2910_AML3050_AML0361b (CITE-seq)

value: Acute Myeloid Leukemia and Healthy Control


title: Control5_AML2910_AML3050_AML0361a (CITE-seq)


title: Control1_Control2_Control3_Control4b (CITE-seq)


title: PAWWEEa (CITE-seq)

value: Acute Myeloid Leukemia


title: Bone marrow-derived monocytes from healthy mice replicate 2

description:
meth.tsv
cov.tsv


title: CML cells from PDX mouse treated with ISRIB and Imatinib – rep3

city: Warsaw

first: Katarzyna

last: Piwocka

address: Pasteur 3

country: Poland

institute: Nencki Institute of Experimental Biology

data_processing:
We inspected the quality of raw data in FASTQ format from RNA-Seq experiments with FastQC (“Babraham Bioinformatics - FastQC A Quality Control tool for High Throughput Sequence Data,” n.d.). Because of observed high quality of the raw data, no further processing of reads was performed.
We utilized the SQuIRE (Yang et al., 2019) pipeline for analyzing the RNA-Seq data. Human genome hg38 and corresponding refseq gene annotations were downloaded from UCSC (https://genome.ucsc.edu/; (Haeussler et al., 2019) with SQuIRE. STAR version 2.5.3a (Dobin et al., 2013), StringTie version 1.3.3b (Pertea et al., 2015), and DESeq2 version 1.16.1 (Love et al., 2014) were used within the SQuIRE pipeline for alignment of reads, transcript assembly and quantification, and differential gene expression analysis respectively.
Differentially expressed genes with false discovery rate (FDR) < 0.05 were considered for further analysis.
Genome_build: hg38
Supplementary_files_format_and_content: tab separated text files with gene abundance measurements for each sample
Supplementary_files_format_and_content: tab separated text files containing DESeq2 output for differential expression of genes between each treatment conditions

source_name: CML cells

growth_protocol: CML CD34+ cells were obtained from the Institute of Hematology and Blood Transfusion in Warsaw, Poland, in accordance with the Declaration of Helsinki and with patients’ consent and approval of the local Ethical Committee (Ethical and Bioethical Committee UKSW, Approval No.WAW2/059/2019 and WAW2/51/2016, Approval No. KEiB-19/2017). The characteristics of patient is detailed in the Supplementary Information. Peripheral blood mononuclear cells (PBMC) were isolated by density gradient centrifugation and CD34+ cells were separated using EasySep human CD34+ selection cocktail (StemCell Technologies, Inc.). CD34+ cells were short-term cultured in IMDM medium (Invitrogen) with 10% FBS, 1 ng/ml of granulocyte-macrophage colony-stimulating factor (GM-CSF), 1 ng/ml of stem cell factor (SCF), 2 ng/ml of interleukin-3 (IL-3). Cells were cryopreserved and kept in -180C until usage.

extract_protocol:
Total RNA was extracted using TRI Reagent (Sigma #T9424) or by Renozol (Genoplast #BMGPB1100-2) followed by Total RNA Mini column purification kit (A&A Biotechnology #031-100). 2 µg of RNA was subjected to reverse transcription using M-MLV enzyme (Promega #M1705), dNTP mix 100 mM each (BLIRT #RP65) and oligo (dT)18 primers (Bioline #BIO-38029). The RT-qPCR reaction was performed using SensiFAST SYBR Hi-ROX Kit (Bioline #BIO-92020) on the StepOnePlus™ platform (Thermo Fisher Scientific) according to MIQE guideline. Primers sequences are listed in the Supplementary Information. The comparative 2-ΔΔCt method was used to determine the relative mRNA level using StepOnePlus software. 18SrRNA was used as a reference control.
The library was prepared using NEB Next Ultra II Directional RNA library Prep kit for Illumina (#E7335S/L).

treatment_protocol: Experiments were performed using immunodeficient NOD.Cg-PrkdcscidIl2rgtm1WjL/SzJ mice, in accordance with the Animal Protection Act in Poland (Directive 2010/63/EU) and approved by the Second Local Ethics Committee (Permission No. WAW/51/2016). Cells (106) were injected subcutaneously or into tail vain. Mice were treated with: imatinib - twice a day (50 mg/kg); GSK157 - once a day (20 mg/kg); ISRIB - once a day (2 mg/kg) or in combination with the same doses, as indicated.

tag: cancer model

value: patient derived xenograft mouse

value: chronic myeloid leukemia

value: Imatinib and ISRIB

value: CD34+ chronic myeloid leukemia cells


title: CML cells from PDX mouse treated with ISRIB and Imatinib – rep2


title: PAWWEEb (CITE-seq)


title: CML cells from PDX mouse treated with ISRIB and Imatinib – rep1


title: Control1_Control2_Control3_Control4c (CITE-seq)


title: CML cells from PDX mouse treated with ISRIB – rep3

value: ISRIB


title: CML cells from PDX mouse treated with ISRIB – rep2


title: CML cells from PDX mouse treated with ISRIB – rep1


title: KGN-siYT+8Br-cAMP

type: RNA

city: Eiheiji

first: Tetsuya

last: Mizutani

state: Fukui

address: 4-1-1 Kenjojima

country: Japan

institute: Fukui Prefectural University

description: RMA expression value derived from Expression Console software

hyb_protocol: Following fragmentation, 15µg of cRNA were hybridized for 16 hr at 45ﾟC on GeneChip Human Genome U133 Plus 2.0 Array.

scan_protocol: The samples were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Raw gene expression data was normalized using RMA in Affymetrix Expression Console.

label: biotin

source_name: KGN cells

label_protocol: One hundred ng of total RNA was used to synthesize cRNA with a GeneChip 3’ IVT Express Kit (Affymetrix).

growth_protocol: KGN cells were cultured in DMEM/F12 supplemented with 10% FBS, and 1% penicillin/streptomycin.

extract_protocol: The total RNA was isolated from the cells using the PureLink RNA Mini Kit (Thermo Fisher Scientific) with DNase I treatment, followed by RNA integrity number (RIN) measured using the Agilent 2100 Bioanalyzer.

treatment_protocol: Cells were transfected with YT- (5 nM ea), NC- (10 nM) siRNA. At 48 h after transfection, media with or without 8Br-cAMP (0.5 mM) were replaced, and the cells were further incubated for 24 h.

value: KGN

value: Human granulosa cell line

tag: sirna

value: YAP/TAZ

value: 8Br-cAMP treatment (0.5 mM, 24 h)


title: KGN-siYT

tag: cell type

value: no treatment


title: S. maltophilia K279a, LB broth

value: bacteria

value: WT

value: Overnight growth in LB broth


title: KGN-siNC+8Br-cAMP

tag: cell line

value: Control


title: KGN-siNC


title: Bone marrow-derived monocytes from healthy mice replicate 1

description:
meth.tsv
cov.tsv

value: BALB/c

value: Bone marrow

value: Bone marrow-derived monocytes

value: CD11b+ Gr+ F4/80low

value: 12 weeks


title: CML cells from PDX mouse treated with Imatinib – rep3

value: patient derived xenograft mouse

tag: genotype

value: chronic myeloid leukemia

value: Imatinib


title: Bone marrow-derived monocytes from tumor-bearing mice replicate 3

description:
meth.tsv
cov.tsv

source_name: Bone marrow of tumor bearing mice

value: Orthotopic injection of 4T1-luc cells into the mammary fat pad

value: 8 weeks


title: CML cells from Control PDX mouse – rep1

tag: disease state

value: untreated

value: CD34+ chronic myeloid leukemia cells


title: Bone marrow-derived monocytes from tumor-bearing mice replicate 4

description:
meth.tsv
cov.tsv

tag: tissue


title: CML cells from PDX mouse treated with Imatinib – rep2


title: AML0612_AML3762_AML0160_AML0310_AML3133a (CITE-seq)

value: Acute Myeloid Leukemia

value: Bone Marrow

value: mononuclear cells

tag: assay

value: Chromium Single Cell 3’ polyA RNA and surface protein


title: HK_replicate4

status: Public on Nov 03 2022

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

data_processing:
Twenty mRNA samples were pooled and sequenced on 4 lanes of HiSeq3000 with Illumina hiseq 3000/4000 chemistry.
Both reads of each sample was trimmed for adapters and low quality bases using Trimmomatic software and aligned with reference Mouse mm10 genome and gencode vM9 transcripts using star software.
Quantification was carried out with RSEM using transcriptome bam file created by star and genecode vM9 transcriptome as index for RSEM.
Basecalling was performed by RTA (version 1.18.66.3).
Demultiplexing and FASTQ generation was performed using bcl2fastq (version 2.17) allowing 1 mismatch.
Trimming of adapters and low-quality bases was performed using Trimmomatic (version 0.36).
Alignment of reads to the mm10 reference genome was performed using STAR (version 2.5.1) with parameters: STAR --genomeDir $star_genome --readFilesIn R1_trimmed.fastq R2_trimmed.fastq --outTmpDir /logs/star --outSAMunmapped Within -- outFilterType BySJout --outFilterMultimapNmax 20 -- outFilterMismatchNmax999 --outFilterMismatchNoverLmax0.04 -- alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 -- sjdbScore 1 --runThreadN 8 --genomeLoad NoSharedMemory -- outSAMtype BAM Unsorted --quantMode TranscriptomeSAM
Gene-level expression quantificiation and library size normalization in counts-per-million was performed using RSEM (version 1.2.22) and the mm10 vM9 gene annotation.
Quantile-normalization and differential expression was performed using limma-voom (version 3.34.5).
Assembly: mm10
Supplementary files format and content: Comma-Separated Values (.csv) file containing filtered raw counts produced by RSEM

source_name: mouse primary keratinocytes

growth_protocol: Primary mouse keratinocytes and hair follicle buds were isolated from newborn pups and cultured in modified Eagle's medium (EMEM, Lonza 06-174G), 8% Chelex-treated FBS (Gemini Bio Products 100-106), and 0.05 mmol/L calcium unless otherwise indicated.

extract_protocol:
mRNA was extracted using standard protocols.
Illumina TruSeq® Stranded mRNA Library Prep (Illumina Inc., CA)

treatment_protocol: The Cre recombinase (Cre) was introduced into primary keratinocytes using an adenoviral construct driven by a cytomegalovirus promoter.

tag: strain


title: Bone marrow-derived monocytes from tumor-bearing mice replicate 2

description:
meth.tsv
cov.tsv


title: HK_replicate1


title: AML0612_AML3762_AML0160_AML0310_AML3135c (CITE-seq)


title: Control1_Control2_Control3_Control4a (CITE-seq)

value: Healthy Control


title: CML cells from Control PDX mouse – rep2


title: HK_replicate3


title: CML cells from PDX mouse treated with Imatinib – rep1


title: Bone marrow-derived monocytes from tumor-bearing mice replicate 1

description:
meth.tsv
cov.tsv

value: BALB/c


title: HK_replicate2


title: Ho_replicate4

tag: genotype/variation

value: LSL-HrasG12D mice


title: AML0612_AML3762_AML0160_AML0310_AML3134b (CITE-seq)


title: Ho_replicate2


title: Ho_replicate1


title: Ho_replicate3


title: Hras_replicate3


title: Hras_replicate2


title: KGN-siYT

hyb_protocol: RNA samples were hybridized to Human Clariom S Gene Chip according to standardized protocols from Affymetrix.

data_processing:
Raw gene expression data was normalized using RMA in Affymetrix Expression Console.
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

label_protocol: RNA samples were labeled to the Clariom S Human Array according to standardized protocols from Affymetrix..

value: KGN

value: Human granulosa cell line

value: YAP/TAZ

value: no treatment


title: KGN-siNC

value: Control


title: Hras_replicate4


title: KGN-siYT+8Br-cAMP

value: 8Br-cAMP treatment (0.5 mM, 24 h)


title: KGN-siNC+8Br-cAMP


title: WT_replicate4


title: Kras_replicate4

value: LSL-KrasG12D mice


title: WT_replicate2


title: Hras_replicate1


title: Kras_replicate2


title: Kras_replicate3


title: Kras_replicate1


title: WT_replicate3


title: WT_replicate1


title: Female Osteoclast 3

city: Cheney

first: Jason

middle: W

last: Ashley

state: WA

address: Eastern Washington University, SCI154

department: Biology

institute: Eastern Washington University

data_processing:
Adaptor sequences removed with Trimmomatic v. 0.36
Reads mapped to Mus musculus GRCm38 reference genome using STAR aligner
Unique exons hits calculated with Feature counts
Assembly: mm10
Supplementary files format and content: tab-delimited text files include gene name, chromosome, start, end, strand, length, and counts for each sample

source_name: Bone Marrow

growth_protocol: Mouse long bones were flushed with minimum essential medium with 10% FBS and cultured overnight in treated culture dishes. Non-adherent cells were cultured with 25ng/mL MCSF for 2 days to induce macrophage differentiation.

extract_protocol:
Total RNA was extracted using the Zymo Direct-Zol RNA miniprep kit. More than 2ug RNA was provided to GeneWiz/Azenta for library preparation, sequencing, and data processing
mRNA was isolated through polyA selection and library was prepared with Illumina TruSeq RNA Library Prep Kit

treatment_protocol: Macrophages were maintained in minimum essential medium wit 10% FBS and 25ng/mL MCSF for 3 days; osteoclasts were differentiated by culutring macrophages with 25ng/mL and 100ng/mL RANKL for 3 days.

value: Female

value: Osteoclast

value: WT

value: 25ng/mL MCSF + 100ng/mL RANKL


title: Female Osteoclast 2

value: Bone Marrow


title: Female Macrophage 1

value: Macrophage

value: 25ng/mL MCSF


title: Female Macrophage 2


title: Male Osteoclast 1

value: Male


title: Female Macrophage 3


title: Male Osteoclast 2


title: Male Osteoclast 3


title: Female Osteoclast 1


title: Male Macrophage 3


title: Male Macrophage 2


title: Male Macrophage 1


title: l, ESC, XHOM, RS10.1

city: Prague

first: Filip

last: Horvat

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR

data_processing:
Raw RNA-seq reads were mapped to mouse (mm10) genome using STAR 2.7.3a with following parameters:  STAR --readFilesIn ${FILE}.fastq.gz --genomeDir ${GENOME_INDEX} --runThreadN 12 --genomeLoad NoSharedMemory --limitBAMsortRAM 20000000000 --readFilesCommand unpigz –c --outFileNamePrefix ${FILENAME} --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --outFilterMultimapNmax 20  --outFilterMultimapScoreRange 0 --outFilterMismatchNoverLmax 0.05 --sjdbScore 2
Genome browser coverage tracks in bigWig format were produced using bedtools v2.29.2 and wigToBigWig v 4 from UCSC:  genomeCoverageBed -ibam ${FILE} -bg -split > ${FILE}.bedGraph  wigToBigWig ${FILE}.bedGraph chrNameLength.txt ${FILE}.bw
Genome_build: mm10
Supplementary_files_format_and_content: coverage genome browser tracks files:  - .bigWig format  - generated in a non-stranded mode.   - not normalized for library size

source_name: mouse ESC

growth_protocol: Mouse ESCs were cultured in 2i-LIF media: KnockOut-DMEM (ThermoFisher) supplemented with 15% fetal calf serum (Sigma), 1x L-Glutamine (Sigma), 1x non-essential amino acids (ThermoFisher), 50 µM β-Mercaptoethanol (ThermoFisher), 1000 U/mL LIF (Isokine), 1 µM PD0325901, 3 µM CHIR99021 (Selleck Chemicals), penicillin (100 U/mL), and streptomycin (100 µg/mL). All plastic was coated with 1% gelatin (Sigma) in PBS.

extract_protocol:
Cells were plated on 6-well plates and grown to 70 % density. Cells were washed with PBS, and total RNA was isolated using the RNeasy mini kit (Qiagen) according to the manufacturer’s protocol. RNA quality was verified by Agilent 2100 Bioanalyzer. Ribosomal RNA was removed from total RNA using Illumina Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat) according to the manufacturer’s protocol. Ribo Depleted RNA was fragmented for 15 min. at 94°C.
Libraries were constructed using NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer's protocol.

value: Dicer X/X

value: ESC

tag: replicate


title: l, ESC, WT, RS7.2

value: Dicer wt/wt


title: l, ESC, WT, RS7.1


title: l, ESC, XHOM, RS10.2


title: 201800470026_R03C01

type: genomic

city: Titusville

first: Qingqin

middle: S

state: NJ

address: 1125 Trenton-Harbourton Road

institute: Janssen R&D, LLC

hyb_protocol: Infinium® HD Assay Methylation Protocol

scan_protocol: Infinium® HD Assay Methylation Protocol

data_processing:
Illumina® GenomeStudio
normalized (dasen) Average Beta
Unmethylated and methylated signal intensities

label: Cy3 and Cy5

source_name: blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from blood samples

tag: diagnosis

tag: gender

value: M

tag: nk

tag: bcell

tag: mono

tag: gran

tag: eos

tag: subject

tag: cohort

value: Cohort 1


title: MF_lung_e17_2

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent

description:
F4/80+ cells on embryonic day 17
F4/80+ cells on embryonic day 17

hyb_protocol: standard Affymetrix protocol

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Samples were analyzed using R/limma: Robust Multi-array Average (RMA) procedure was used to normalize data within arrays (probeset summarization, background correction and log2-transformation) and between arrays (quantile normalization). Only probesets that uniquely mapped to an EntrezID were kept.

organism: Mus

source_name: Lung

label_protocol: standard Affymetrix protocol

extract_protocol: Cells were sorted into 500ul RLT buffer (QIAGEN). RNA was isolated using the RNeasy micro kit (QIAGEN) and sent to the Nucleomics facility, VIB Leuven, Belgium where the microarrays were performed using the GeneChip Mouse Gene 1.0 ST arrays (Affymetrix).

tag: metadata info


title: Pre_AMF_dob_4

description:
Pre-alveolar macrophages on day of birth
Pre-alveolar macrophages on day of birth


title: Pre_AMF_dob_1


title: MF_lung_e17_3


title: 201800470015_R07C01

tag: age


title: MF_lung_e19_4

description:
F4/80+ cells on embryonic day 19
F4/80+ cells on embryonic day 19


title: MF_lung_e15_3

description:
F4/80+ cells on embryonic day 15
F4/80+ cells on embryonic day 15


title: MF_lung_e19_2


title: Pre_AMF_dob_3


title: MF_lung_e19_3


title: AMF_pbs_pnd9_2

description:
Alveolar macrophages on post natal day 9 treated with PBS
Alveolar macrophages on post natal day 9


title: MF_lung_e15_2


title: MF_lung_e19_1


title: 201800470041_R04C01


title: Pre_AMF_dob_5


title: MF_lung_e17_1


title: AMF_pbs_pnd9_3


title: Pre_AMF_dob_2


title: MF_Gm_csfKO_pnd9_2

description:
GM-CSF KO macrophages on post natal day 9
GM-CSF KO macrophages on post natal day 9 treated with PBS


title: MF_Gm_csfKO_treated_pnd9_2

description:
GM-CSF KO macrophages on post natal day 9 treated with GM-CSF
GM-CSF KO macrophages on post natal day 9 treated with GM-CSF


title: MF_Gm_csfKO_pnd9_5


title: MF_Gm_csfKO_pnd9_1


title: MF_Gm_csfKO_treated_pnd9_1


title: MF_Gm_csfKO_treated_pnd9_3


title: MF_Gm_csfKO_treated_pnd9_4


title: AMF_pbs_pnd9_1


title: MF_lung_e15_1


title: MF_Gm_csfKO_pnd9_3


title: 201800470045_R04C01

value: HC


title: 201800470041_R05C01


title: 201800470015_R06C01


title: 201800470045_R03C01


title: 201800470041_R01C01


title: 201800470026_R02C01


title: 201800470041_R06C01


title: 201800470045_R02C01


title: 201800470041_R02C01


title: 201800470041_R03C01


title: 201810150049_R04C01


title: 201800470054_R05C01


title: 201800470011_R04C01


title: 201800470026_R05C01


title: 201800470026_R04C01


title: 201800470048_R05C01


title: 201800470045_R01C01


title: 201800470024_R02C01


title: 201800470054_R04C01


title: 201800470011_R05C01


title: 201800470024_R01C01


title: 201502870060_R06C01


title: 201502870060_R07C01


title: 201800470033_R08C01


title: 201800470015_R08C01


title: 201502860018_R07C01


title: 201502860023_R07C01


title: 201800470033_R07C01


title: 201800470044_R08C01


title: 201502870060_R08C01


title: 201800470035_R02C01


title: 201800470013_R06C01


title: 201800470035_R03C01


title: 201800470035_R01C01


title: 201800470051_R05C01

value: F


title: 201800470047_R08C01


title: 201502860018_R06C01


title: 201800470035_R04C01


title: 201800470013_R07C01


title: 201800470047_R07C01


title: 201800470040_R06C01


title: 201502860018_R08C01


title: 201800470032_R04C01


title: MF_Gm_csfKO_pnd9_4


title: 201800470040_R07C01


title: 201800470040_R02C01


title: 201800470050_R02C01


title: 201800470050_R04C01


title: 201810150049_R03C01


title: 201800470050_R03C01


title: 201800470050_R06C01


title: 201800470050_R05C01


title: 201800470040_R01C01


title: 201800470032_R06C01


title: 201800470051_R07C01


title: 201800470040_R05C01


title: 201800470051_R08C01


title: 201800470051_R06C01


title: 201800470026_R06C01


title: 201800470015_R04C01


title: 201800470051_R04C01


title: 201800470040_R04C01


title: 201800470024_R05C01


title: 201800470051_R02C01


title: 201800470041_R07C01


title: 201800470032_R05C01


title: 201502860023_R02C01


title: 201800470032_R03C01


title: 201800470032_R01C01


title: 201800470044_R02C01


title: 201800470032_R02C01


title: 201800470018_R05C01


title: 201800470013_R08C01


title: 201800470044_R04C01


title: 201800470045_R05C01


title: 201800470044_R03C01


title: 201800470038_R04C01


title: 201800470038_R06C01


title: 201800470045_R08C01


title: 201800470041_R08C01


title: 201800470026_R07C01


title: 201810150027_R04C01


title: 201800470050_R08C01


title: 201810150027_R03C01


title: 201800470025_R07C01


title: 201800470011_R07C01


title: 201810150049_R02C01


title: 201800470045_R06C01


title: 201800470027_R05C01


title: 201800470038_R08C01


title: 201800470014_R04C01


title: 201800470024_R03C01


title: 201800470027_R07C01


title: 201800470054_R06C01


title: 201800470027_R04C01


title: 201800470025_R02C01


title: 201800470025_R05C01


title: 201800470025_R08C01


title: 201800470050_R01C01


title: 201800470025_R04C01


title: 201800470018_R04C01


title: 201800470040_R08C01


title: 201800470018_R07C01


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title: 201800470024_R07C01


title: 201800470011_R03C01


title: 201800470011_R08C01


title: 201502860030_R01C01


title: 201800470025_R01C01


title: 201800470027_R03C01


title: 201800470038_R02C01


title: 201800470026_R08C01


title: 201502860030_R02C01


title: 201800470044_R05C01


title: 201800470025_R03C01


title: 201502860023_R05C01


title: 201502860023_R06C01


title: 201800470044_R06C01


title: 201800470016_R03C01


title: 201800470011_R06C01


title: 201800470045_R07C01


title: 201502860030_R05C01


title: 201502860023_R04C01


title: 201800470018_R06C01


title: 201800470048_R04C01


title: 201810150049_R05C01


title: 201800470011_R02C01


title: 201502860030_R03C01


title: 201800470025_R06C01


title: 201800470051_R03C01


title: 201800470038_R05C01


title: 201800470047_R02C01


title: 201502870060_R03C01


title: 201800470015_R02C01


title: 201800470014_R02C01


title: 201800470038_R03C01


title: 201800470032_R08C01


title: 201800470024_R06C01


title: 201810150027_R05C01


title: 201502860030_R06C01


title: 201800470048_R01C01


title: 201502860023_R03C01


title: 201800470054_R01C01


title: 201800470044_R07C01


title: 201800470014_R05C01


title: 201800470027_R01C01


title: 201800470040_R03C01


title: 201800470018_R01C01


title: 201800470016_R05C01


title: 201800470035_R08C01


title: 201800470035_R07C01


title: 201800470031_R02C01


title: 201502860023_R01C01


title: 201800470027_R06C01


title: 201800470018_R08C01


title: 201502860030_R07C01


title: 201800470016_R02C01


title: 201800470031_R06C01


title: 201800470050_R07C01


title: 201800470054_R03C01


title: 201502860018_R04C01


title: 201800470038_R07C01


title: 201800470016_R04C01


title: 201800470018_R03C01


title: 201502870060_R01C01


title: 201800470015_R03C01


title: 201800470027_R02C01


title: 201800470024_R04C01


title: 201502860006_R05C01


title: 201502870060_R04C01


title: 201800470047_R03C01


title: 201800470044_R01C01


title: 201800470035_R05C01


title: 201800470014_R03C01


title: 201800470013_R02C01


title: 201502860018_R05C01


title: 201502860018_R03C01


title: 201800470028_R06C01


title: 201800470047_R04C01


title: 201800470014_R06C01


title: 201800470015_R05C01


title: 201800470048_R02C01


title: 201800470054_R02C01


title: 201502870060_R05C01


title: 201502860006_R04C01


title: 201800470018_R02C01


title: 201800470016_R01C01


title: 201800470035_R06C01


title: 201800470013_R05C01


title: 201800470013_R04C01


title: 201810150049_R07C01


title: 201810150012_R02C01


title: 201502870060_R02C01


title: 201800470011_R01C01


title: 201800470028_R05C01


title: 201800470027_R08C01


title: UKN1_SBAD2_Teriflunomide_Low_RNA [57]

city: Dortmund

first: Jan

middle: Georg

last: Hengstler

address: Ardeystraße 67

department: Toxikologie / Systemtoxikologie

country: Germany

institute: Leibniz-Institut für Arbeitsforschung an der TU Dortmund

hyb_protocol: The samples were purified using magnetic beads and fragmented. 12,5 μg of fragmented RNA samples were hybridized on Affymetrix Human Genome U133 Plus 2.0 arrays (Affymetrix, Santa Clara, CA, USA). The microarray hybridization step was performed in an Affymetrix GeneChip Hybridization Oven-645 for 16 h at 45 °C and 60 rpm. Washing and staining of the hybridized arrays was completed using the GeneChip HWS Kit (Affymetrix, High Wycombe, United Kingdom) and Affymetrix GeneChip Fluidics Station-450.

scan_protocol: Stained arrays were scanned with Affymetrix Gene-Chip Scanner-3000-7G and evaluated for quality control with Affymetrix GCOS software

data_processing: All analyses were conducted using the statistical software R, version 4.0.5. Pre-processing of the data consists of the three steps background correction, normalization, and summarization, using the frozen robust multi-array average (fRMA) algorithm. This yields expression values for 54675 probe sets. The R-packages affy, frma and hgu133plus2frmavecs were used.

source_name: SBAD2 iPS cells

label_protocol: The samples were amplified and labelled with biotin using GeneChip 3′ IVT Express Kit per the manufacturer’s instructions (Affymetrix, High Wycombe, UK).

growth_protocol: The differentiation of SBAD2 hiPSCs to neuroepithelial precursor cells was performed using the UKN1 protocol (Chambers et al. 2009) with minor changes. Briefly, hiPSCs were seeded in 1 ml pluripotent stem cell (PSC) medium (spiked with a Rho-kinase inhibitor (ROCKi)) per well on extracellular matrix protein-coated 12-well-plates at a density of 12,000 - 24,000 cells/cm² on day -3. On day  2 and day  1, the PSC medium was refreshed. On days 0, 1 and 2, medium was changed to differentiation medium, which was spiked with 21.6 µM SB431542, 0.64 µM dorsomorphin, 35 ng/ml noggin and 0.1% DMSO to induce neural differentiation. On day 4, medium was changed to a mixed medium of 75% differentiation medium / 25% N2-S and the same concentrations of SB431542, dorsomorphin and noggin as given above. On day 6, cells were collected for RNA extraction. A more detailed method description is given in the supplemental information.

extract_protocol: Total RNA was isolated from sonicated cell lysates with the ExtractMe Total RNA-Kit (Blirt, Poland). The concentration and purity of the RNA were determined with a NanoDrop2000 (ThermoFisher Scientific, Germany).

treatment_protocol: On days 0, 1 and 2, differentiating cells were incubated (5 % CO2, 37 °C) with the test compounds at 1-fold Cmax and 1.67-, 10- or 20 fold Cmax concentration for a total of 96 h, as well as the vehicle alone (0.1% DMSO). The compounds leflunomide and teriflunomide were tested at a DMSO concentration of 0.5 % and compared to a 0.5% DMSO vehicle control.

value: male

tag: agent


title: UKN1_SBAD2_Favipiravir_High_RNA [51]


title: UKN1_SBAD2_9-cis retinoic acid_High_RNA [49]

value: 9-cis retinoic acid_High_RNA


title: UKN1_SBAD2_Leflunomide_Low_RNA [56]


title: UKN1_SBAD2_Phenytoin_Low_RNA [54]


title: UKN1_SBAD2_Carbamazepine_Low_RNA [52]


title: UKN1_SBAD2_Retinol_Low_RNA [46]


title: UKN1_SBAD2_9-cis retinoic acid_Low_RNA [48]

value: 9-cis retinoic acid_Low_RNA


title: UKN1_SBAD2_Favipiravir_Low_RNA [50]


title: 201800470047_R05C01


title: 201800470028_R01C01


title: 201800470031_R08C01


title: UKN1_SBAD2_Carbamazepine_High_RNA [53]


title: 201502860006_R06C01


title: 201800470013_R03C01


title: 201502860018_R02C01


title: 201502860006_R03C01


title: 201800470016_R06C01


title: UKN1_SBAD2_Vismodegib_Low_RNA [55]


title: UKN1_SBAD2_Untreated 0.5 % DMSO_Ctrl_RNA [40]

value: Untreated 0.5 % DMSO_Ctrl_RNA


title: 201502860030_R04C01


title: UKN1_SBAD2_Retinol_High_RNA [47]


title: UKN1_SBAD2_Untreated_Ctrl_RNA [39]


title: UKN1_SBAD2_Diphenhydramine_High_RNA [45]


title: UKN1_SBAD2_Diphenhydramine_Low_RNA [44]


title: UKN1_SBAD2_Acitretin_High_RNA [43]


title: UKN1_SBAD2_Acitretin_Low_RNA [42]


title: 201800470015_R01C01


title: 201800470028_R03C01


title: 201800470013_R01C01


title: 201800470028_R02C01


title: 201800470038_R01C01


title: 201800470047_R06C01


title: 201800470031_R07C01


title: 201800470016_R07C01


title: 201800470031_R04C01


title: 201810150049_R01C01


title: 201810150012_R01C01


title: 201810150049_R08C01


title: 201800470028_R04C01


title: UKN1_SBAD2_Favipiravir_Low_RNA [31]


title: 201810150012_R03C01


title: 201800470028_R08C01


title: UKN1_SBAD2_Favipiravir_High_RNA [32]


title: UKN1_SBAD2_Teriflunomide_Low_RNA [38]


title: UKN1_SBAD2_Vismodegib_Low_RNA [36]


title: UKN1_SBAD2_Leflunomide_Low_RNA [37]


title: 201172200058_R06C01

value: MDD

value: Cohort 2


title: UKN1_SBAD2_9-cis retinoic acid_Low_RNA [29]


title: 201502860006_R07C01


title: 201172200059_R02C01


title: UKN1_SBAD2_Retinol_Low_RNA [27]


title: 201810150048_R06C01


title: 201810150076_R04C01


title: UKN1_SBAD2_Diphenhydramine_High_RNA [26]


title: UKN1_SBAD2_Acitretin_High_RNA [24]


title: UKN1_SBAD2_Phenytoin_Low_RNA [35]


title: UKN1_SBAD2_Carbamazepine_Low_RNA [33]


title: UKN1_SBAD2_Diphenhydramine_Low_RNA [25]


title: UKN1_SBAD2_Acitretin_Low_RNA [23]


title: UKN1_SBAD2_Untreated_Ctrl_RNA [20]


title: 201810150079_R07C01


title: UKN1_SBAD2_Untreated 0.5 % DMSO_Ctrl_RNA [21]


title: 201800470007_R04C01


title: UKN1_SBAD2_Retinol_High_RNA [28]


title: 201810150076_R05C01


title: 201502870005_R04C01


title: 201502870015_R07C01


title: 201502870014_R02C01


title: 201172200036_R01C01


title: 201172200022_R08C01


title: 201172200053_R04C01


title: 201502870014_R03C01


title: UKN1_SBAD2_9-cis retinoic acid_High_RNA [30]


title: 201502870048_R03C01


title: UKN1_SBAD2_Teriflunomide_Low_RNA [19]


title: 201810150079_R05C01


title: 201502870048_R06C01


title: UKN1_SBAD2_Leflunomide_Low_RNA [18]


title: 201502870005_R05C01


title: UKN1_SBAD2_Retinol_Low_RNA [12]


title: 201172200053_R03C01


title: UKN1_SBAD2_9-cis retinoic acid_Low_RNA [14]


title: 201502870015_R03C01


title: UKN1_SBAD2_Phenytoin_Low_RNA [16]


title: UKN1_SBAD2_Carbamazepine_High_RNA [34]


title: 201810150075_R06C01


title: UKN1_SBAD2_Retinol_High_RNA [13]


title: 201810150071_R02C01


title: 201172200019_R03C01


title: UKN1_SBAD2_Carbamazepine_Low_RNA [10]


title: UKN1_SBAD2_Vismodegib_Low_RNA [17]


title: 201502870014_R07C01


title: UKN1_SBAD2_9-cis retinoic acid_High_RNA [15]


title: 201172200059_R03C01


title: UKN1_SBAD2_Diphenhydramine_Low_RNA [8]


title: UKN1_SBAD2_Favipiravir_Low_RNA [4]


title: UKN1_SBAD2_Acitretin_Low_RNA [6]


title: 201502870011_R05C01


title: 201172200005_R03C01


title: 201502870015_R08C01


title: UKN1_SBAD2_Untreated_Ctrl_RNA [1]


title: 201172200022_R07C01


title: UKN1_SBAD2_Carbamazepine_High_RNA [11]


title: 201810150079_R03C01


title: UKN1_SBAD2_Acitretin_High_RNA [7]


title: UKN1_SBAD2_Diphenhydramine_High_RNA [9]


title: 201502870018_R07C01


title: 201502870048_R04C01


title: UKN1_SBAD2_Untreated_Ctrl_RC' [25.DO_292_M29_UKN1_U_6_Tage_(HG-U133_Plus_2).CEL]


title: 201810150057_R06C01


title: UKN1_SBAD2_Entinostat (MS-275)_Low_RC [27.DO_294_M29_UKN1_MS_1x_6_Tage_(HG-U133_Plus_2).CEL]

value: Entinostat (MS-275)_Low_RC


title: UKN1_SBAD2_Untreated 0.5 % DMSO_Ctrl_RNA [2]


title: UKN1_SBAD2_Favipiravir_High_RNA [5]


title: UKN1_SBAD2_Lithiumchloride_Low_RC [28.DO_295_M29_UKN1_LiCl_1x_6_Tage_(HG-U133_Plus_2).CEL]


title: UKN1_SBAD2_Sucralose_High_RC [23.DO_291_D57_Sucra_20x_(HG-U133_Plus_2).CEL]


title: UKN1_SBAD2_Methylmercury_Low_RC [20.DO_288_D57_MeHg_1x_(HG-U133_Plus_2).CEL]


title: 201502870018_R06C01


title: UKN1_SBAD2_Trichostatin A_Low_RC [26.DO_293_M29_UKN1_TSA_1x_6_Tage_(HG-U133_Plus_2).CEL]

value: Trichostatin A_Low_RC


title: 201800470008_R05C01


title: UKN1_SBAD2_Sucralose_Low_RC [22.DO_290_D57_Sucra_1x_(HG-U133_Plus_2).CEL]


title: UKN1_SBAD2_Untreated_Ctrl_RC [19.DO_287_D57_U_(HG-U133_Plus_2).CEL]


title: UKN1_SBAD2_Methylmercury_High_RC [21.DO_289_D57_MeHg_20x_(HG-U133_Plus_2).CEL]


title: 201502870034_R08C01


title: UKN1_SBAD2_Trichostatin A_Low_RB [17.DO_286_D56_UKN1_DoD_6_TSA_1x_(HG-U133_Plus_2).CEL]

value: Trichostatin A_Low_RB


title: 201172200005_R02C01


title: 201810150057_R03C01


title: UKN1_SBAD2_Sucralose_Low_RB [12.DO_281_D56_UKN1_DoD_6_Sucra_1x_(HG-U133_Plus_2).CEL]


title: UKN1_SBAD2_Methylmercury_Low_RB [14.DO_283_D56_UKN1_DoD_6_MeHg_1x_(HG-U133_Plus_2).CEL]


title: 201810150079_R04C01


title: UKN1_SBAD2_Entinostat (MS-275)_Low_RB [16.DO_285_D56_UKN1_DoD_6_MS_1x_(HG-U133_Plus_2).CEL]

value: Entinostat (MS-275)_Low_RB


title: 201810150070_R02C01


title: 201810150079_R08C01


title: 201810150068_R06C01


title: 201502870015_R04C01


title: UKN1_SBAD2_Lithiumchloride_Low_RB [11.DO_280_D56_UKN1_DoD_6_LiCl_1x_(HG-U133_Plus_2).CEL]


title: UKN1_SBAD2_Methylmercury_High_RA [7.DO_277_D55_UKN1_Tag_6_MeHg_20x_(HG-U133_Plus_2).CEL]


title: UKN1_SBAD2_Lithiumchloride_Low_RA [8.DO_278_D55_UKN1_Tag_6_LiCl_1x_(HG-U133_Plus_2).CEL]


title: UKN1_SBAD2_Sucralose_High_RB [13.DO_282_D56_UKN1_DoD_6_Sucra_20x_(HG-U133_Plus_2).CEL]


title: UKN1_SBAD2_Methylmercury_Low_RA [6.DO_276_D55_UKN1_Tag_6_MeHg_1x_(HG-U133_Plus_2).CEL]


title: 201502870027_R06C01


title: 201502870034_R07C01


title: 201800470033_R05C01


title: 201172200021_R02C01


title: 201502870005_R08C01


title: UKN1_SBAD2_Sucralose_Low_RA [4.DO_274_D55_UKN1_Tag_6_Sucra_1x_(HG-U133_Plus_2).CEL]


title: UKN1_SBAD2_Sucralose_High_RA [5.DO_275_D55_UKN1_Tag_6_Sucra_20x_(HG-U133_Plus_2).CEL]


title: UKN1_SBAD2_Entinostat (MS-275)_Low_RA [2.DO_272_D55_UKN1_Tag_6_MS_1x_(HG-U133_Plus_2).CEL]

value: Entinostat (MS-275)_Low_RA


title: 201810150068_R05C01


title: UKN1_SBAD2_Trichostatin A_Low_RA [3.DO_273_D55_UKN1_Tag_6_TSA_1x_(HG-U133_Plus_2).CEL]

value: Trichostatin A_Low_RA


title: UKN1_SBAD2_L-Thyronine_High_RC [27.DO_270_D52_Tri_20x_(HG-U133_Plus_2).CEL]


title: 201810150075_R07C01


title: UKN1_SBAD2_L-Thyronine_Low_RC [26.DO_269_D52_Tri_1x_(HG-U133_Plus_2).CEL]


title: UKN1_SBAD2_Levothyroxine_High_RC [25.DO_261_D52_Levo_20X_(HG-U133_Plus_2).CEL]


title: UKN1_SBAD2_Dextrometorphan_High_RC [23.DO_259_D52_Dex_20x_(HG-U133_Plus_2).CEL]


title: 201800470052_R08C01


title: 201810150025_R04C01


title: UKN1_SBAD2_Levothyroxine_Low_RC [24.DO_260_D52_Levo_1x_(HG-U133_Plus_2).CEL]


title: 201502870048_R05C01


title: 201502870058_R06C01


title: 201172200058_R04C01


title: 201800470033_R04C01


title: 201172200008_R02C01


title: 201502870055_R08C01


title: 201810150048_R04C01


title: 201800470017_R01C01


title: 201810150075_R04C01


title: 201172200013_R03C01


title: UKN1_SBAD2_Untreated_Ctrl_RB [10.DO_279_D56_UKN1_DoD_6_U_(HG-U133_Plus_2).CEL]


title: 201800470017_R02C01


title: 201172200024_R07C01


title: 201810150070_R01C01


title: UKN1_SBAD2_Untreated_Low_RC [19.DO_252_D52_U_(HG-U133_Plus_2).CEL]


title: UKN1_SBAD2_Ranitidine_High_RC [21.DO_257_D52_Ran_20x_(HG-U133_Plus_2).CEL]


title: UKN1_SBAD2_Dextrometorphan_Low_RB [17.DO_249_M20_Dextro_1x_(HG-U133_Plus_2).CEL]


title: UKN1_SBAD2_Levothyroxine_Low_RB [15.DO_247_M20_Levo_1x_(HG-U133_Plus_2).CEL]


title: UKN1_SBAD2_Dextrometorphan_High_RB [18.DO_250_M20_Dextro_20x_(HG-U133_Plus_2).CEL]


title: UKN1_SBAD2_Ranitidine_Low_RB [13.DO_241_M20_Ran_1x_(HG-U133_Plus_2).CEL]


title: UKN1_SBAD2_Dextrometorphan_Low_RC [22.DO_258_D52_Dex_1x_(HG-U133_Plus_2).CEL]


title: UKN1_SBAD2_Ranitidine_Low_RC [20.DO_256_D52_Ran_1x_(HG-U133_Plus_2).CEL]


title: 201172200036_R06C01


title: UKN1_SBAD2_Levothyroxine_High_RB [16.DO_248_M20_Levo_20x_(HG-U133_Plus_2).CEL]


title: 201172200055_R04C01


title: UKN1_SBAD2_Ranitidine_High_RB [14.DO_242_M20_Ran_20x_(HG-U133_Plus_2).CEL]


title: 201800470052_R02C01


title: 201172200012_R05C01


title: UKN1_SBAD2_L-Thyronine_High_RB [12.DO_238_M20_Triiodo_1x_(HG-U133_Plus_2).CEL]


title: UKN1_SBAD2_Dextrometorphan_Low_RA [6.DO_224_D51_Dextro_1x_(HG-U133_Plus_2).CEL]


title: UKN1_SBAD2_L-Thyronine_High_RA [5.DO_220_D51_Triiodo_20x_(HG-U133_Plus_2).CEL]


title: 201172200027_R02C01


title: 201800470052_R07C01


title: 201172200058_R05C01


title: 201172200045_R05C01


title: 201502870058_R08C01


title: 201810150038_R02C01


title: 201172200016_R07C01


title: 201502870011_R06C01


title: UKN1_SBAD2_Untreated_Low_RB [10.DO_233_M20_U_(HG-U133_Plus_2).CEL]


title: UKN1_SBAD2_Dextrometorphan_High_RA [7.DO_225_D51_Dextro_20x_(HG-U133_Plus_2).CEL]


title: 201810150040_R03C01


title: UKN1_SBAD2_Levothyroxine_Low_RA [8.DO_226_D51_Levo_1x_(HG-U133_Plus_2).CEL]


title: 201172200008_R05C01


title: 201172200022_R06C01


title: UKN1_SBAD2_L-Thyronine_Low_RB [11.DO_237_M20_Triiodo_1x_(HG-U133_Plus_2).CEL]


title: UKN1_SBAD2_Ranitidine_High_RA [3.DO_217_D51_Ran_20x_(HG-U133_Plus_2).CEL]


title: UKN1_SBAD2_Untreated_Low_RA [1.DO_214_D51_U_(HG-U133_Plus_2).CEL]


title: UKN1_SBAD2_Methotrexate_Low_RD [112]


title: UKN1_SBAD2_Paroxetine_Low_RD [110]


title: UKN1_SBAD2_Valproic acid_High_RD [108]

value: Valproic acid_High_RD


title: UKN1_SBAD2_L-Thyronine_Low_RA [4.DO_220_D51_Triiodo_1x_(HG-U133_Plus_2).CEL]


title: 201800470017_R03C01

value: M