title: atxr5;atxr5;atxr6hyp;atxr6c-1_H3K36me3 rep1

description: Library name: atxr5;atxr5;atxr6hyp;atxr6c-1_H3K36me3_rep1


title: 8-month WT female mouse thyroid-3

status: Public on Jan 29 2026

type: SRA

city: Shanghai

first: Junjie

last: Gao

address: 600 Yishan Road

country: China

institute: Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

library_source: transcriptomic

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include FPKM and count values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: thyroid

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

tag: strain

tag: tissue

value: thyroid

tag: genotype

value: wild type


title: Col_input rep2

city: Beijing

first: Xiaoyi

last: Li

address: west beichen

department: Chinese Academy of Sciences

institute: Institute of Genetics and Developmental Biology

description: Library name: Col_input_rep2

library_source: genomic

data_processing:
Adapter trimming was performed and low quality reads were filtered with fastp version 0.20.1
Reads were mapped to the Arabidopsis (TAIR10) genome with Botiew2 version 2.4.2
Duplicate reads were filtered using Picard version 2.24.0 MarkDuplicates (https://github.com/broadinstitute/picard)
H3K36me3 peaks in WT Col were called using MACS2 version 2.1.2 with default parameters. Only peaks identified in both biological replicates were retained
For data visualization, data from two biological replicates were merged, and bigwig coverage files were generated using deepTools utility bamCoverage with a bin size of 10bp
Assembly: TAIR10
Supplementary files format and content: bigwig

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: leaves of 3-week-old Arabidopsis plants

growth_protocol: Plants were grown under long day conditions (16h light/8h dark) at 22°C

extract_protocol:
Materials were ground with liquid nitrogen into fine powder and fixed with 1% formaldehyde.To profile H3K36me3, nuclei were extracted and mononucleosomes were generated with micrococcal nuclease (MNase)(Sigma, N5386) digestion. Immunoprecipitation was conducted with  anti-H3K36me3 (Abcam, ab9050). After antibody incubation, Protein A Dynabeads (Life technologies, 10002D) were added to collect the immunocomplexes, followed by elution, reverse cross-linking and DNA purification.
Immunoprecipitated DNA were subjected to library preparation with the VAHTS universal DNA library prep kit for Illumina (Vazyme, ND607-02) according to the manufacturer’s instruction

treatment_protocol: ChIP-seq was performed using leaves from 3-week-old Arabidopsis plants

value: leaves of 3-week-old Arabidopsis plants

value: WT


title: 2-month WT male mouse thyroid-5


title: 2-month WT male mouse thyroid-4


title: RNA library from E18.5 Natural male placenta 1 [Natural_F2_E185_placenta_Male_1]

city: Philadelphia

first: Eric

middle: Alejandro

last: Rhon Calderon

state: Pennsylvania

address: 3400 Civic Center Blvd, Bldg 421, Floor 9-175

department: Cell and Developmental Biology

country: USA

institute: University of Pennsylvania

description: Library name: Natural_F2_E185_placenta_Male_1

data_processing:
RNA-seq reads were trimmed for quality using Trimmomatic (version 0.32). Illumina TruSeq3-PE primers, leading and trailing low-quality (below quality 3) and N base calls were trimmed, and reads were scanned using a 4-bp sliding window and trimmed when the average quality per base dropped below 15. Reads of at least 30-bp in length following this quality control process were retained and used for subsequent analyses.
The resulting reads were then aligned to mm10 reference genome assembly using STAR (version 2.3.0e), allowing read pairs to align no farther than 2000-bp apart and keeping alignments with a mapping quality score (MAPQ) greater than 1 for genome-wide transcript counting.
FeatureCounts (version 1.5.0) was used to generate a matrix of mapped fragments per RefSeq annotated gene.
Analysis for differential gene expression was performed using DESeq2 with the cutoff of FDR < 0.05. Clustering and heatmaps of differentially expressed genes were generated using heatmaply R package. Chord plots were done using complexheatmap, clusterprofiler and circlize packages in R. WGCNA was done using the WGCNA package for R.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: F2 E185 Placenta

growth_protocol: All animals were housed in polysulfone cages containing drinking water and chow (Laboratory Irradiated Rodent Diet 5LG4, LabDiet) ad libitum.

extract_protocol:
For tissue: RNA was extracted using Rneasy mini plus kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries. For single oocytes and cumulus cells: a modified SMART-seq extraction protocol was used using TCL and BME for cell lysis
For tissue: RNA libraries for RNA-seq were prepared using KAPA Stranded mRNA-Seq Kit (Illumina Platforms) and KAPA Single-Indexed adapter kit following manufacturer's protocols. For single oocytes and cumulus cells: Nextera Library prep and Nextera sequencing indexes (Illumina) were used.

treatment_protocol: E18.5 ovaries, 12 weeks ovaries, 39 weeks ovaries, 12 weeks single oocytes, 39 weeks single oocytes, 12 cumulus cells pools, 39 weeks cumulus cells pools, F2 12 weeks testis, F2 12 weeks male livers, F2 12 weeks ovaries, F2 weeks female livers awere collected, snap frozen in liquid nitrogen and stored at -80C for RNA extraction.

value: F2 E185 Placenta

tag: Sex

value: Male

tag: treatment

value: Natural


title: AML_patient_sample_352

city: Milan

first: Serena

last: Ghisletti

address: Via Adamello 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology

description: Library name: sample_352

data_processing:
After demultiplexing with bcl2fastq v2.20 (Illumina, Inc.), raw data quality checks were performed with FastQC v0.11.8. Adapters removal and dynamic trimming of low-quality bases were performed using Trimmomatic v0.39 with parameters “ILLUMINACLIP:adapters.fa:2:30:10, LEADING:30, MAXINFO:50:0.7, MINLEN:40. Paired-end reads were aligned to the UCSC hg38 human genome using STAR v2.7 22 with parameters “--outSAMtype BAM SortedByCoordinate, --outFilterMultimapNmax 20. Uniquely mapped pairs were selected for downstream analysis using SAMtools v1.9. Alignments quality controls were carried out using Qualimap v2.2.2a 23. Gene-level quantification was performed using featureCounts of the Rsubread package v1.34 according to Human GRChg38 annotation. Gene-level counts were then processed with the edgeR  R-package 24 to perform sample normalization using the ‘relative-log-expression’ (RLE) method.
Assembly: GRCh38 assembly version
Supplementary files format and content: Gene raw count matrix and log-normalized CPM (Counts per Million) matrix are provided in compressed tab-delimited format.

molecule: polyA RNA

organism: Homo sapiens

source_name: Bone marrow-CD34+

extract_protocol:
Human bone marrow aspirates were obtained from in accordance with the Italian laws and the policies and practices of the Ethical Committee of Humanitas Research Hospital. Patients were classified following the updated WHO classification of tumors and lymphoid tissues guidelines 1 and stratified by risk of evolution following the IPSS-R parameters. Bone marrow mononuclear cells (BMNCs) were isolated by density gradient separation with Lympholyte®-H Cell Separation Media (Cedarlane corporation, Burlington, USA) according to manufacturer’s instructions, frozen in fetal bovine serum (FBS) (Lonza, Basel, Switzerland) containing 10% DimethylSulfoxide (DMSO) (Sigma Aldrich, St. Louis, Missouri, USA) and cryopreserved in liquid nitrogen. Bone marrow HSPCs were isolated based on CD34+ surface marker using the MACS CD34 microbead kit on autoMACS (Miltenyi Biotech Inc, San Diego, CA). MDS-L cells were kindly provided by Dr. Daniel Starczynowski, Cincinnati Children's Hospital Medical Center and were cultured in RPMI-1640 medium supplemented with 10% heat-inactivated FBS and 1% P/S and 10ng/mL of hrIL-3 (PeproTech, Paisley, UK). Cells were grown at 37°C and 5%CO2 and treated with 3uM DB2115 (Cat. No. HY-124676A Medchem, NJ, USA) for the specified time.
Libraries for CD34+ mRNA sequencing were prepared by using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech-Takara). Libraries for MDS-L mRNA sequencing were prepared by using the Illumina Stranded mRNA Prep (Illumina). All samples were sequenced at an average of 40 million 50-bp pair-end reads with Novaseq 6000.
All RNA-seq data sets were processed in paired-end.

tag: cell type

value: Bone marrow-CD34+

tag: disease state

value: AML


title: AML_patient_sample_353

description: Library name: sample_353

growth_protocol: Human bone marrow aspirates were obtained from in accordance with the Italian laws and the policies and practices of the Ethical Committee of Humanitas Research Hospital. Patients were classified following the updated WHO classification of tumors and lymphoid tissues guidelines 1 and stratified by risk of evolution following the IPSS-R parameters. Bone marrow mononuclear cells (BMNCs) were isolated by density gradient separation with Lympholyte®-H Cell Separation Media (Cedarlane corporation, Burlington, USA) according to manufacturer’s instructions, frozen in fetal bovine serum (FBS) (Lonza, Basel, Switzerland) containing 10% DimethylSulfoxide (DMSO) (Sigma Aldrich, St. Louis, Missouri, USA) and cryopreserved in liquid nitrogen. Bone marrow HSPCs were isolated based on CD34+ surface marker using the MACS CD34 microbead kit on autoMACS (Miltenyi Biotech Inc, San Diego, CA).


title: Col_H3K36me3 rep2

description: Library name: Col_H3K36me3_rep2


title: RNA library from E13.5 IVF 100 primordial germ cells 4 [IVF_E13.5_100cells_PGCs_4]

description: Library name: IVF_E13.5_100cells_PGCs_4

source_name: E13.5 primordial germ cells

value: E13.5 primordial germ cells

value: Female

value: IVF


title: RNA library from E13.5 IVF 100 primordial germ cells 5 [IVF_E13.5_100cells_PGCs_5]

description: Library name: IVF_E13.5_100cells_PGCs_5


title: Col_H3K36me3 rep1

description: Library name: Col_H3K36me3_rep1


title: RNA library from E13.5 IVF 100 primordial germ cells 3 [IVF_E13.5_100cells_PGCs_3]

description: Library name: IVF_E13.5_100cells_PGCs_3


title: 8-month WT female mouse thyroid-2


title: atxr5;atxr5;atxr6hyp;atxr6c-1_H3K36me3 rep2

description: Library name: atxr5;atxr5;atxr6hyp;atxr6c-1_H3K36me3_rep2


title: AML_patient_sample_350

description: Library name: sample_350


title: h2a.z;HTA11-FLAG #1_Input rep2

description: Library name: h2a.z;HTA11-FLAG #1_Input rep2

data_processing:
Adapter trimming was performed and low quality reads were filtered with fastp version 0.20.1. Reads were mapped to the Arabidopsis (TAIR10) genome with Botiew2 version 2.4.2.
Duplicate reads were filtered using Picard version 2.24.0 MarkDuplicates (https://github.com/broadinstitute/picard).
For data visualization, data from two biological replicates were merged, and bigwig coverage files were generated using deepTools utility bamCoverage with a bin size of 10bp.
Average ChIP-seq profiles were generated using deepTools utility plotProfile.
Assembly: TAIR10
Supplementary files format and content: bigwig

source_name: Seedlings

extract_protocol:
Chromatin was resuspended with ChIP lysis buffer and sheared to generate 200 bp-500 bp fragments.Sheared chromatin was diluted four times with ChIP dilution buffer.Immunoprecipitation was conducted with anti-FLAG (Proteintech, 20543-1-AP).
The input DNA and immunoprecipitated DNA were subjected to library preparation with VAHTS universal DNA library prep kit for illumina (Vazyme, ND607-02) according to the manufacturer’s instruction.

treatment_protocol: ChIP-seq was performed using 10-day-old seedlings, which were fixed with 1% formaldehyde.

value: Seedlings


title: h2a.z;HTA11 K to R-FLAG #1_Input rep1

description: Library name: h2a.z;HTA11 K to R-FLAG #1_Input rep1


title: h2a.z;HTA11 K to R-FLAG #1_Input rep2

description: Library name: h2a.z;HTA11 K to R-FLAG #1_Input rep2


title: RNA library from E13.5 IVF 100 primordial germ cells 2 [IVF_E13.5_100cells_PGCs_2]

description: Library name: IVF_E13.5_100cells_PGCs_2


title: 8-month FAD4T female mouse thyroid-2


title: AML_patient_sample_351

description: Library name: sample_351


title: AML_patient_sample_348

description: Library name: sample_348


title: 8-month WT female mouse thyroid-1


title: RNA library from E13.5 IVF 100 primordial germ cells 1 [IVF_E13.5_100cells_PGCs_1]

description: Library name: IVF_E13.5_100cells_PGCs_1


title: 8-month FAD4T female mouse thyroid-3


title: AML_patient_sample_349

description: Library name: sample_349


title: h2a.z;HTA11-FLAG #1_Input rep1

description: Library name: h2a.z;HTA11-FLAG #1_Input rep1


title: RNA library from E13.5 Natural 100 primordial germ cells 3 [Natural_E13.5_100cells_PGCs_3]

description: Library name: Natural_E13.5_100cells_PGCs_3


title: 8-month WT male mouse thyroid-3


title: 8-month WT male mouse thyroid-2


title: h2a.z;HTA11 K to R-FLAG #1_IP rep2

description: Library name: h2a.z;HTA11 K to R-FLAG #1_IP rep2


title: RNA library from E13.5 Natural 100 primordial germ cells 2 [Natural_E13.5_100cells_PGCs_2]

description: Library name: Natural_E13.5_100cells_PGCs_2


title: RNA library from E13.5 Natural 100 primordial germ cells 4 [Natural_E13.5_100cells_PGCs_4]

description: Library name: Natural_E13.5_100cells_PGCs_4


title: RNA library from E13.5 Natural 100 primordial germ cells 1 [Natural_E13.5_100cells_PGCs_1]

description: Library name: Natural_E13.5_100cells_PGCs_1


title: h2a.z;HTA11 K to R-FLAG #1_IP rep1

description: Library name: h2a.z;HTA11 K to R-FLAG #1_IP rep1


title: AML_patient_sample_345

description: Library name: sample_345


title: 8-month WT male mouse thyroid-1


title: h2a.z;HTA11-FLAG #1_IP rep2

description: Library name: h2a.z;HTA11-FLAG #1_IP rep2


title: AML_patient_sample_346

description: Library name: sample_346


title: 8-month FAD4T male mouse thyroid-3


title: 8-month FAD4T female mouse thyroid-1


title: AML_patient_sample_343

description: Library name: sample_343


title: h2a.z;HTA11-FLAG #1_IP rep1

description: Library name: h2a.z;HTA11-FLAG #1_IP rep1


title: RNA library from 39 weeks IVF cumulus cells 1 [IVF_39wks_cumulus_cells_1]

description: Library name: IVF_39wks_cumulus_cells_1

source_name: 39 week cumulus cells

value: 39 week cumulus cells


title: AML_patient_sample_344

description: Library name: sample_344


title: 8-month FAD4T male mouse thyroid-2


title: 8-month FAD4T male mouse thyroid-1


title: fve-4_27C rep1

description: Library name: fve-4_27C rep1

data_processing:
Adapter trimming was performed and low quality reads were filtered with fastp version 0.20.1
Reads were aligned to the Arabidopsis genome (TAIR10) using Hisat2 version 2.1.10
Transcripts per million (TPM) values were generated using R
Differential gene expression analysis was performed using DESeq2 version 1.26.0
Genes were considered as differentially expressed if they exhibited a fold change greater than two and a P adjust value < 0.05
Assembly: TAIR10
Supplementary files format and content: *.txt: TPM values for all samples

growth_protocol: Plants were germinated and grown under short day conditions (8h light/16h dark) at 21°C until day 7

extract_protocol:
Total RNA was extracted with Eastep Super Total RNA Extraction Kit (Promega, LS1040)
Sequencing libraries were prepared with the NEBNext Ultra RNA library prep kit for Illumina (NEB, 7530L) according to the manufacturer’s instruction

treatment_protocol: 7-day-old seedlings grown at 21°C were shifted to 27°C or kept at 21°C with or without mannitol treatment at ZT1, and seedlings were collected at ZT13.

value: fve


title: AML_patient_sample_347

description: Library name: sample_347


title: fve-4_27C rep2

description: Library name: fve-4_27C rep2


title: AML_patient_sample_341

description: Library name: sample_341


title: fve-4_27C rep3

description: Library name: fve-4_27C rep3


title: AML_patient_sample_342

description: Library name: sample_342


title: RNA library from 39 weeks Natural cumulus cells 2 [Natural_39wks_cumulus_cells_2]

description: Library name: Natural_39wks_cumulus_cells_2


title: RNA library from 39 weeks IVF cumulus cells 2 [IVF_39wks_cumulus_cells_2]

description: Library name: IVF_39wks_cumulus_cells_2


title: Col_27C rep3

description: Library name: Col_27C rep3

value: Wild type Columbia


title: 2-month WT female mouse thyroid-2


title: 2-month WT female mouse thyroid-1


title: RNA library from 12 weeks Natural cumulus cells 2 [Natural_12wks_cumulus_cells_2]

description: Library name: Natural_12wks_cumulus_cells_2

source_name: 12 week cumulus cells

value: 12 week cumulus cells


title: RNA library from 39 weeks Natural cumulus cells 1 [Natural_39wks_cumulus_cells_1]

description: Library name: Natural_39wks_cumulus_cells_1


title: 2-month WT female mouse thyroid-3

value: thyroid


title: AML_patient_sample_340

description: Library name: sample_340


title: RNA library from 12 weeks IVF cumulus cells 2 [IVF_12wks_cumulus_cells_2]

description: Library name: IVF_12wks_cumulus_cells_2


title: 2-month FAD4T female mouse thyroid-2


title: AML_patient_sample_338

description: Library name: sample_338


title: AML_patient_sample_337

description: Library name: sample_337


title: 2-month FAD4T female mouse thyroid-1


title: AML_patient_sample_339

description: Library name: sample_339


title: 2-month FAD4T female mouse thyroid-3


title: Col_27C rep2

description: Library name: Col_27C rep2


title: RNA library from 12 weeks IVF cumulus cells 1 [IVF_12wks_cumulus_cells_1]

description: Library name: IVF_12wks_cumulus_cells_1


title: RNA library from 39 weeks IVF single oocyte 10 [IVF_39wks_single_oocyte_10]

description: Library name: IVF_39wks_single_oocyte_10

source_name: 39 week single oocyte

value: 39 week single oocyte


title: fve-4_21C rep1

description: Library name: fve-4_21C rep1


title: AML_patient_sample_334

description: Library name: sample_334


title: 2-month WT male mouse thyroid-1

value: wild type


title: Col_27C rep1

description: Library name: Col_27C rep1


title: Col_21C rep2

description: Library name: Col_21C rep2


title: RNA library from 39 weeks IVF single oocyte 9 [IVF_39wks_single_oocyte_9]

description: Library name: IVF_39wks_single_oocyte_9


title: fve-4_21C rep3

description: Library name: fve-4_21C rep3


title: AML_patient_sample_336

description: Library name: sample_336


title: AML_patient_sample_335

description: Library name: sample_335


title: RNA library from 12 weeks Natural cumulus cells 1 [Natural_12wks_cumulus_cells_1]

description: Library name: Natural_12wks_cumulus_cells_1


title: RNA library from 39 weeks IVF single oocyte 7 [IVF_39wks_single_oocyte_7]

description: Library name: IVF_39wks_single_oocyte_7


title: RNA library from 39 weeks IVF single oocyte 8 [IVF_39wks_single_oocyte_8]

description: Library name: IVF_39wks_single_oocyte_8


title: 2-month WT male mouse thyroid-3


title: h3.3ko;HTR5_G34W_BS_rep2

description: Library name: h3.3ko;HTR5_G34W_BS_rep2

data_processing:
Adapter trimming was performed and low-quality reads were filtered with fastp version 0.20.1 (Chen et al., 2018).
Reads were mapped to the Arabidopsis genome (TAIR10) with BS-Seeker2 version 2.1.8 using default parameters (Guo et al., 2013)
Duplicated reads were filtered with Picard version 2.24.0 MarkDuplicates (https://github.com/broadinstitute/picard).
For data visualization, data from two biological replicates were merged. CG, CHG, and CHH methylation levels were calculated with CGmaptools (version 0.1.2) (Guo et al., 2018)
Methylation data were visualized with ggplot2 in R (version 1.1.1106).
Assembly: TAIR10
Supplementary files format and content: CGmap.txt

extract_protocol:
Genomic DNA was extracted from 10-day-old seedlings with Quick-DNA Plant/Seed Miniprep Kit (ZYMO, D6020)
200ng fragmented genomic DNA (200bp-500bp) was used for library preparation with VAHTS universal Pro DNA library prep kit for Illumina (Vazyme, ND608),NEBNext Multiplex Oligos for Illumina (NEB, E7535) were used for adapter ligation. After purification with VAHTS DNA Clean Beads (Vazyme N411), bisulfite conversion was performed with EZ DNA Methylation-Gold Kit (ZYMO, D5005), followed by DNA purification and PCR amplification

treatment_protocol: BS-seq was performed using 10-day-old seedlings.

value: h3.3ko;HTR5 G34W


title: fve-4_21C rep2

description: Library name: fve-4_21C rep2


title: AML_patient_sample_332

description: Library name: sample_332


title: AML_patient_sample_331

description: Library name: sample_331


title: AML_patient_sample_333

description: Library name: sample_333


title: Col_21C rep3

description: Library name: Col_21C rep3


title: AML_patient_sample_330

description: Library name: sample_330


title: S_Ahyb_R3

city: Irapuato

first: Alfredo

middle: Heriberto

last: Herrera

state: Guanajuato

address: Libr.  Norte Carr. Leon Km 9.6

department: LANGEBIO

country: Mexico

institute: LANGEBIO

description:
Library name: SAMPLE 15
Raw_Counts_AhybrEs.txt
Column names in Raw_Counts .txt file:AhybSR3

data_processing:
EdgeR package
The overrepresented sequences (OVERrepseq1.fasta) and the quality of the raw reads were determined using the FASTQC program (Andrews 2010). Low-quality reads (QC<20) and overrepresented sequences were trimmed with TRIMMOMATIC
Transcriptome assemblies of A. hybridus and A. hypochondriacus were obtained using TRINITY v2.1.1 with –normalize_reads and --trimmomatic default parameters. Transcripts redundancy from trinity “genes” was filtered with CD-HIT at 90% of identities on the sequences
High-quality reads of each library were mapped using (BOWTIE v2.3.0 very sensitive parameters to the transcriptome of A. hybridus or A. hypochondriacus, respectively. An in-house script was used to count unique reads from the SAM files. A table count reads matrix was constructed in an R environment and used to obtain the differentially expressed genes (DEG) Pairwise analysis of stressed (drought or salinity) plant samples vs control plant samples.
Assembly: Transcrptome assembly in this project for both species
Supplementary files format and content: tab-delimited text file includes raw counts for each samples

organism: Amaranthus hybridus

source_name: Leaves

growth_protocol: Amaranthus hypochondriacus cv. Nutrisol and Amaranthus hybridus lines were obtained from the National Institute of Forestry, Agricultural and Livestock Research (INIFAP), Texcoco, Mexico. Seeds were placed on a sterile wet substrate (BM2 Germination Mix, Berger, CA) at 4 °C for 12 h. Subsequently, they were transferred to a growth chamber at 25 °C and cycles of 12 h light/dark cycles. After 11 days in the growth chamber, the seedlings were transferred to a greenhouse in plastic pots 10 cm in diameter and 20 cm high; 12-15 plants per species were placed for each of the three experimental groups: control, drought, and salinity

extract_protocol:
Total RNA samples were extracted from three biological replicates of leaves stressed (salinity or drought) and non-stressed (watered) plants using the TRIZol protocol specified by the manufacturer (Invitrogen, GIBCO-BLR)
TruSeq libraries of all samples were sequenced by the Illumina NextSeq 500 1x75 HIGH at the LANGEBIO facilities

treatment_protocol: Control plants were watered every third day during the 19 days after entering the greenhouse (until they were one month old), and treatments were started. For saline stress, 100 ml of 0.15 M NaCl was applied daily for 7 days, 100 ml of 0.3 M NaCl for the next four days, and 100 ml of 0.5 M NaCl during the last three days. The plants subjected to water stress were kept without irrigation during the 14 days of the treatment. Three biological replicates of mature non-senescent leaves were collected (leaves 5, 6, and 7 from the plant´s apex).

value: Leaves

value: Wild Type

value: Drought


title: 2-month FAD4T male mouse thyroid-2


title: RNA library from 39 weeks IVF single oocyte 6 [IVF_39wks_single_oocyte_6]

description: Library name: IVF_39wks_single_oocyte_6


title: Col_21C rep1

description: Library name: Col_21C rep1


title: 2-month WT male mouse thyroid-2


title: AML_patient_sample_329

description: Library name: sample_329

value: Bone marrow-CD34+


title: 2-month FAD4T male mouse thyroid-3


title: AML_patient_sample_328

description: Library name: sample_328

value: AML


title: RNA library from 39 weeks IVF single oocyte 5 [IVF_39wks_single_oocyte_5]

description: Library name: IVF_39wks_single_oocyte_5


title: 2-month FAD4T male mouse thyroid-1


title: S_Ahyb_R1

description:
Library name: SAMPLE 13
Raw_Counts_AhybrEs.txt
Column names in Raw_Counts .txt file:AhybSR1


title: RNA library from 39 weeks IVF single oocyte 2 [IVF_39wks_single_oocyte_2]

description: Library name: IVF_39wks_single_oocyte_2


title: efs_BS_rep2

description: Library name: efs_BS_rep2

value: efs


title: SA_Ahyb_R3

description:
Library name: SAMPLE 9
Raw_Counts_AhybrEs.txt
Column names in Raw_Counts .txt file:AhybSAR3

value: Salinity


title: AML_patient_sample_326

description: Library name: sample_326


title: AML_patient_sample_327

description: Library name: sample_327


title: h3.3ko;HTR5_G34R_BS_rep2

description: Library name: h3.3ko;HTR5_G34R_BS_rep2

value: h3.3ko;HTR5 G34R


title: h3.3ko;HTR5_G34W_BS_rep1

description: Library name: h3.3ko;HTR5_G34W_BS_rep1

value: Seedlings


title: h3.3ko;HTR5_G34R_BS_rep1

description: Library name: h3.3ko;HTR5_G34R_BS_rep1


title: RNA library from 39 weeks IVF single oocyte 1 [IVF_39wks_single_oocyte_1]

description: Library name: IVF_39wks_single_oocyte_1

value: Female

value: IVF


title: RNA library from 39 weeks IVF single oocyte 4 [IVF_39wks_single_oocyte_4]

description: Library name: IVF_39wks_single_oocyte_4


title: AML_patient_sample_325

description: Library name: sample_325


title: SA_Ahyb_R1

description:
Library name: SAMPLE 7
Raw_Counts_AhybrEs.txt
Column names in Raw_Counts .txt file:AhybSAR1


title: h3.3ko;HTR5_K36A_BS_rep1

description: Library name: h3.3ko;HTR5_K36A_BS_rep1

value: h3.3ko;HTR5 K36A


title: S_Ahyb_R2

description:
Library name: SAMPLE 14
Raw_Counts_AhybrEs.txt
Column names in Raw_Counts .txt file:AhybSR2


title: RNA library from 39 weeks IVF single oocyte 3 [IVF_39wks_single_oocyte_3]

description: Library name: IVF_39wks_single_oocyte_3


title: AML_patient_sample_322

description: Library name: sample_322


title: efs_BS_rep1

description: Library name: efs_BS_rep1


title: h3.3ko;HTR5_BS_rep2

description: Library name: h3.3ko;HTR5_BS_rep2


title: h3.3ko;HTR5_K36A_BS_rep2

description: Library name: h3.3ko;HTR5_K36A_BS_rep2


title: RNA library from 39 weeks Natural single oocyte 9 [Natural_39wks_single_oocyte_9]

description: Library name: Natural_39wks_single_oocyte_9

value: Natural


title: RNA library from 39 weeks Natural single oocyte 4 [Natural_39wks_single_oocyte_4]

description: Library name: Natural_39wks_single_oocyte_4


title: Mnase_Seq_KD_6_28days

city: Heidelberg

first: Jaime

last: Diaz-Larrosa

state: Baden Württemberg

address: INF 580

department: Epigenetics

country: Germany

institute: DKFZ

description:
Library name: Mnase_Seq_sample10
Column name: KD6

data_processing:
Raw reads were aligned using bwa and downstream analysis was performed using NucTools (Vanishtein 2017)
After producing bed files, NucTools was used for extending the reads to 150 bp (Extend_PE_reads.pl) and calculate occupancy per scaffold (bed2occupancy_average.pl) generating .occ files. Using the default normalisation method
Using the .occ files, fuzziness and stability were calculated (stable_nucs_replicates.pl) using rel. error >1.5 and <0.2 for determining fuzzy and stable nucleosomes respectively
Assembly: pvir_genome_ncbi_v1.0
Supplementary files format and content: Occupancy file across all the scaffolds. Tab separated.

organism: Procambarus virginalis

source_name: Hemolymph

extract_protocol:
28 days post injection with dsGFP and dsDNMT1, 4 control and 6 KD animals were bled. Hemocytes were subject to a Micrococcal Nuclease incubation, covaris sonication and anti-H3 pulldown to capture the Nucleosomes wrapping DNA. After reverse crosslinking, the resulting DNA was sequenced.
Performed following the instructions from Watchmaker DNA Library Prep Kit, #7K0102-024

treatment_protocol: dsRNA for control (GFP) or Dnmt1 were injected into the hemolymph stream of crayfish animals

value: Hemolymph

value: Hemocytes

value: Dnmt1 Knockdown

value: dsDnmt1 injection


title: RNA library from 39 weeks Natural single oocyte 6 [Natural_39wks_single_oocyte_6]

description: Library name: Natural_39wks_single_oocyte_6

value: 39 week single oocyte


title: Ahyb_R1

description:
Library name: SAMPLE 1
Raw_Counts_AhybrEs.txt
Column names in Raw_Counts .txt file:AhybR1

value: Leaves

value: Wild Type

value: Control


title: RNA library from 39 weeks Natural single oocyte 8 [Natural_39wks_single_oocyte_8]

description: Library name: Natural_39wks_single_oocyte_8


title: AML_patient_sample_323

description: Library name: sample_323

value: Bone marrow-CD34+

value: AML


title: RNA library from 39 weeks Natural single oocyte 7 [Natural_39wks_single_oocyte_7]

description: Library name: Natural_39wks_single_oocyte_7


title: RNA library from 39 weeks Natural single oocyte 5 [Natural_39wks_single_oocyte_5]

description: Library name: Natural_39wks_single_oocyte_5


title: h3.3ko;HTR5_T31A_BS_rep2

description: Library name: h3.3ko;HTR5_T31A_BS_rep2

value: h3.3ko;HTR5 T31A


title: AML_patient_sample_324

description: Library name: sample_324


title: RNA library from 39 weeks Natural single oocyte 3 [Natural_39wks_single_oocyte_3]

description: Library name: Natural_39wks_single_oocyte_3


title: SA_Ahyb_R2

description:
Library name: SAMPLE 8
Raw_Counts_AhybrEs.txt
Column names in Raw_Counts .txt file:AhybSAR2

value: Salinity


title: h3.3ko;HTR5_T31A_BS_rep1

description: Library name: h3.3ko;HTR5_T31A_BS_rep1

value: Seedlings


title: Mnase_Seq_KD_5_28days

description:
Library name: Mnase_Seq_sample9
Column name: KD5


title: AML_patient_sample_321

description: Library name: sample_321


title: Ahyb_R3

description:
Library name: SAMPLE 3
Raw_Counts_AhybrEs.txt
Column names in Raw_Counts .txt file:AhybR3


title: Mnase_Seq_KD_4_28days

description:
Library name: Mnase_Seq_sample8
Column name: KD4


title: Col_BS_rep1

description: Library name: Col_BS_rep1

value: WT (Col)


title: h3.3ko;HTR5_T31A_input_replicate2

description: Library name: h3.3ko;HTR5_T31A_input_rep2

extract_protocol:
Nuclei were extracted, and mononucleosomes were generated using micrococcal nuclease (NEB, M0247S) digestion.Immunoprecipitation was conducted with anti-H3K27me1 ( (Abclonal, A22170).
The input DNA and immunoprecipitated DNA were subjected to library preparation with VAHTS universal DNA library prep kit for illumina (Vazyme, ND607-02) according to the manufacturer’s instruction.

tag: chip antibody

value: H3K27me1 (Abclonal, A22170)


title: AML_patient_sample_320

description: Library name: sample_320


title: Col_BS_rep2

description: Library name: Col_BS_rep2


title: Mnase_Seq_KD_3_28days

description:
Library name: Mnase_Seq_sample7
Column name: KD3


title: Ahyb_R2

description:
Library name: SAMPLE 2
Raw_Counts_AhybrEs.txt
Column names in Raw_Counts .txt file:AhybR2


title: AML_patient_sample_319

description: Library name: sample_319


title: RNA library from 39 weeks Natural single oocyte 2 [Natural_39wks_single_oocyte_2]

description: Library name: Natural_39wks_single_oocyte_2

value: Female


title: AML_patient_sample_317

description: Library name: sample_317


title: AML_patient_sample_314

description: Library name: sample_314


title: RNA library from 12 weeks IVF single oocyte 10 [IVF_12wks_single_oocyte_10]

description: Library name: IVF_12wks_single_oocyte_10

source_name: 12 week single oocyte

value: 12 week single oocyte

value: IVF


title: AML_patient_sample_316

description: Library name: sample_316


title: h3.3ko;HTR5_input_replicate1

description: Library name: h3.3ko;HTR5_input_rep1


title: h3.3ko;HTR5_BS_rep1

description: Library name: h3.3ko;HTR5_BS_rep1


title: AML_patient_sample_315

description: Library name: sample_315


title: RNA library from 39 weeks Natural single oocyte 1 [Natural_39wks_single_oocyte_1]

description: Library name: Natural_39wks_single_oocyte_1

value: Natural


title: RNA library from 12 weeks IVF single oocyte 11 [IVF_12wks_single_oocyte_11]

description: Library name: IVF_12wks_single_oocyte_11


title: Mnase_Seq_Control_3_28days

description:
Library name: Mnase_Seq_sample3
Column name: Ctrl3

value: Hemolymph

value: Hemocytes

value: dsGFP injection


title: AML_patient_sample_313

description: Library name: sample_313


title: RNA library from 12 weeks IVF single oocyte 7 [IVF_12wks_single_oocyte_7]

description: Library name: IVF_12wks_single_oocyte_7


title: Mnase_Seq_KD_2_28days

description:
Library name: Mnase_Seq_sample6
Column name: KD2

value: Dnmt1 Knockdown

value: dsDnmt1 injection


title: Col_input_replicate1

description: Library name: Col_input_rep1


title: Mnase_Seq_KD_1_28days

description:
Library name: Mnase_Seq_sample5
Column name: KD1


title: AML_patient_sample_312

description: Library name: sample_312


title: RNA library from 12 weeks IVF single oocyte 5 [IVF_12wks_single_oocyte_5]

description: Library name: IVF_12wks_single_oocyte_5


title: AML_patient_sample_311

description: Library name: sample_311


title: Col_input_replicate2

description: Library name: Col_input_rep2


title: Mnase_Seq_Control_4_28days

description:
Library name: Mnase_Seq_sample4
Column name: Ctrl4

value: Control


title: h3.3ko;HTR5_input_replicate2

description: Library name: h3.3ko;HTR5_input_rep2


title: AML_patient_sample_318

description: Library name: sample_318

value: Bone marrow-CD34+


title: RNA library from 12 weeks IVF single oocyte 6 [IVF_12wks_single_oocyte_6]

description: Library name: IVF_12wks_single_oocyte_6


title: AML_patient_sample_310

description: Library name: sample_310

value: AML


title: Sting controls - Replicate 4

city: Ghent

first: Bruno

last: Verstraeten

state: Oost-Vlaanderen

address: Technologiepark 71

country: Belgium

institute: Ghent University

description: Library name: Sample 22

data_processing:
The quality of the reads was verified with FastQC (version 0.11.9).
Reads were mapped using STAR (version 2.7.11a) with the following parameters: readFilesCommand zcat, outFilterMultimapNmax 1 and outSAMtype BAM SortedByCoordinate using the GRCm39 genome build.
umi sequences were extracted from the reads (first six nucleotides before the TATA spacer) and deduplication was performed with UMI-tools (version 1.1.4).
A count table was made using the following R packages: GenomicFeatures (version 1.44.2) to convert the GRCm39 GTF file into a Granges object, and GenomicAlignments (version 1.28.0) for the summarizeOverlaps function to create the count table. The following options were used for counting: mode = ’Union’, singleEnd = TRUE and ignore.strand = FALSE.
Assembly: GRCm39
Supplementary files format and content: csv file with raw counts.

source_name: skin tissue

growth_protocol: Mice were housed in individually ventilated cages at the VIB-UGent Center for Inflammation Research in a specific pathogen-free facility according to national and institutional guidelines for animal care.

extract_protocol:
Total RNA from FACS-sorted cells was extracted using RNeasy Micro kit (74004, Qiagen) with on-column DNase I digestion, according to the manufacturer’s instructions.
RNA integrity was tested using an Agilent RNA 6000 Pico kit (50671513; Agilent). Sequencing libraries were prepared using a Quantseq 3' mRNA ligation kit (Lexogen). Sequencing of the libraries was performed using an Aviti System (Element Biosciences).

treatment_protocol: Pieces of shaved mouse skin were isolated from mice of the indicated genotypes. Subcutaneous fat and muscle were removed by mechanical scraping with a scalpel. Subsequently, the skin was carefully placed in 0.4 mg/mL dispase II (4492078001, Roche) with the dermal side facing down for 2 h at 37 °C. Epidermis was separated from the dermis with forceps, cut into fine pieces and incubated in 2 ml enzymatic solution containing 1.5 mg/mL collagenase type IV (LS004188, Worthington) and 0.5 mg/mL DNase I (10104159001, Roche) for 20 min at 37 °C with shaking. After neutralization with 2% FCS RPMI medium, the cell suspension was filtered through a 70-µm cell strainer to obtain a single-cell suspension. Single-cell suspensions were first stained with anti-mouse CD16/CD32 (Fc block; 553142, BD Biosciences) and dead cells were excluded with Fixable Viability Dye eFluor506 (65-0866-14, Thermo Fisher Scientific) for 30 min at 4 °C in PBS. Next, cell surface markers were stained for 30 min at 4 °C in FACS buffer (PBS, 5% FCS, 1 mM EDTA and 0.05% sodium azide). Cells were sorted on a FACSAria II cell sorter (BD BioSciences), LSR Fortessa (BD Biosciences) or a FACSymphony (BD Biosciences). Data were analysed with FlowJo software (Tree Star). The total number of cells was counted on a FACSVerse (BD Biosciences). Sorted cells were centrifuged for 5 minutes at 500x g at 4°C and the pellet was snap frozen on dry ice before storage at -80°C.

value: skin tissue

value: Sting WT


title: RNA library from 12 weeks IVF single oocyte 8 [IVF_12wks_single_oocyte_8]

description: Library name: IVF_12wks_single_oocyte_8


title: h3.3ko;HTR5_T31A_H3K27me1_replicate2

description: Library name: h3.3ko;HTR5_T31A_H3K27me1_rep2

value: Seedlings

value: h3.3ko;HTR5 T31A


title: h3.3ko;HTR5_T31A_input_replicate1

description: Library name: h3.3ko;HTR5_T31A_input_rep1

value: H3K27me1 (Abclonal, A22170)


title: h3.3ko;HTR5_T31A_H3K27me1_replicate1

description: Library name: h3.3ko;HTR5_T31A_H3K27me1_rep1


title: RNA library from 12 weeks IVF single oocyte 9 [IVF_12wks_single_oocyte_9]

description: Library name: IVF_12wks_single_oocyte_9

value: Female


title: Mnase_Seq_Control_1_28days

description:
Library name: Mnase_Seq_sample1
Column name: Ctrl1


title: h3.3ko;HTR5_H3K27me1_replicate2

description: Library name: h3.3ko;HTR5_H3K27me1_rep2


title: Sting controls - Replicate 3

description: Library name: Sample 21


title: RNA library from 12 weeks IVF single oocyte 4 [IVF_12wks_single_oocyte_4]

description: Library name: IVF_12wks_single_oocyte_4

value: 12 week single oocyte


title: Sting controls - Replicate 2

description: Library name: Sample 20


title: RNA library from 12 weeks IVF single oocyte 3 [IVF_12wks_single_oocyte_3]

description: Library name: IVF_12wks_single_oocyte_3

value: IVF


title: Mnase_Seq_Control_2_28days

description:
Library name: Mnase_Seq_sample2
Column name: Ctrl2


title: AML_patient_sample_308

description: Library name: sample_308


title: h3.3ko;HTR5_H3K27me1_replicate1

description: Library name: h3.3ko;HTR5_H3K27me1_rep1


title: AML_patient_sample_309

description: Library name: sample_309


title: Sting controls - Replicate 1

description: Library name: Sample 19


title: Col_H3K27me1_replicate2

description: Library name: Col_H3K27me1_rep2

value: WT (Col)


title: RNA library from 12 weeks IVF single oocyte 2 [IVF_12wks_single_oocyte_2]

description: Library name: IVF_12wks_single_oocyte_2


title: AML_patient_sample_306

description: Library name: sample_306


title: RNA library from 12 weeks IVF single oocyte 1 [IVF_12wks_single_oocyte_1]

description: Library name: IVF_12wks_single_oocyte_1


title: efs_rep3

description: Library name: efs_rep3

extract_protocol:
Total RNA was extracted using Minibest plant RNA extraction kit (Takara)
Sequencing libraries were prepared with the NEBNext Ultra RNA library prep kit for Illumina (NEB, 7530L) according to the manufacturer’s instruction

treatment_protocol: Total RNA was extracted from 10-day-old seedlings

value: efs


title: RNA library from 12 weeks Natural single oocyte 7 [Natural_12wks_single_oocyte_7]

description: Library name: Natural_12wks_single_oocyte_7

value: Natural


title: Ripk1 EKO Sting EKO - Replicate 1

description: Library name: Sample 15

value: Ripk1 EKO Sting EKO


title: RNA library from 12 weeks Natural single oocyte 6 [Natural_12wks_single_oocyte_6]

description: Library name: Natural_12wks_single_oocyte_6


title: Ripk1 EKO Sting EKO - Replicate 3

description: Library name: Sample 17


title: Ripk1 EKO Sting EKO - Replicate 4

description: Library name: Sample 18


title: efs_rep2

description: Library name: efs_rep2


title: AML_patient_sample_303

description: Library name: sample_303


title: AML_patient_sample_305

description: Library name: sample_305


title: AML_patient_sample_307

description: Library name: sample_307


title: efs_rep1

description: Library name: efs_rep1


title: Ripk1 EKO Sting EKO - Replicate 2

description: Library name: Sample 16


title: h3.3ko;HTR5_K36A_rep3

description: Library name: h3.3ko;HTR5_K36A_rep3

value: h3.3ko;HTR5 K36A


title: AML_patient_sample_301

description: Library name: sample_301


title: Ripk1 controls - Replicate 3

description: Library name: Sample 13

value: Ripk1 WT


title: Ripk1 controls - Replicate 4

description: Library name: Sample 14


title: RNA library from 12 weeks Natural single oocyte 5 [Natural_12wks_single_oocyte_5]

description: Library name: Natural_12wks_single_oocyte_5


title: h3.3ko;HTR5_K36A_rep2

description: Library name: h3.3ko;HTR5_K36A_rep2


title: RNA library from 12 weeks Natural single oocyte 2 [Natural_12wks_single_oocyte_2]

description: Library name: Natural_12wks_single_oocyte_2


title: Ripk1 controls - Replicate 1

description: Library name: Sample 11


title: Col_H3K27me1_replicate1

description: Library name: Col_H3K27me1_rep1


title: RNA library from 12 weeks Natural single oocyte 3 [Natural_12wks_single_oocyte_3]

description: Library name: Natural_12wks_single_oocyte_3


title: AML_patient_sample_302

description: Library name: sample_302


title: h3.3ko;HTR5_T31A_rep3

description: Library name: h3.3ko;HTR5_T31A_rep3


title: Ripk1 EKO non lesional - Replicate 5

description: Library name: Sample 10

value: Ripk1 EKO


title: RNA library from 12 weeks Natural single oocyte 4 [Natural_12wks_single_oocyte_4]

description: Library name: Natural_12wks_single_oocyte_4


title: RNA library from 12 weeks Natural single oocyte 1 [Natural_12wks_single_oocyte_1]

description: Library name: Natural_12wks_single_oocyte_1


title: AML_patient_sample_297

description: Library name: sample_297

value: Bone marrow-CD34+


title: AML_patient_sample_300

description: Library name: sample_300

value: AML


title: RNA library from 39 weeks IVF ovary 4 [IVF_39wks_ovary_4]

description: Library name: IVF_39wks_ovary_4

source_name: 39 weeks ovary

value: 39 weeks ovary


title: RNA library from 12 weeks Natural single oocyte 8 [Natural_12wks_single_oocyte_8]

description: Library name: Natural_12wks_single_oocyte_8


title: RNA library from 39 weeks IVF ovary 3 [IVF_39wks_ovary_3]

description: Library name: IVF_39wks_ovary_3


title: AML_patient_sample_304

description: Library name: sample_304


title: Ripk1 EKO non lesional - Replicate 2

description: Library name: Sample 7

value: skin tissue


title: RNA library from 39 weeks IVF ovary 5 [IVF_39wks_ovary_5]

description: Library name: IVF_39wks_ovary_5


title: AML_patient_sample_299

description: Library name: sample_299


title: AML_patient_sample_295

description: Library name: sample_295


title: AML_patient_sample_294

description: Library name: sample_294


title: RNA library from 39 weeks IVF ovary 2 [IVF_39wks_ovary_2]

description: Library name: IVF_39wks_ovary_2


title: Ripk1 EKO non lesional - Replicate 1

description: Library name: Sample 6


title: AML_patient_sample_298

description: Library name: sample_298


title: Ripk1 controls - Replicate 2

description: Library name: Sample 12


title: Ripk1 EKO non lesional - Replicate 4

description: Library name: Sample 9


title: Col_rep3, rna-seq

description: Library name: Col_rep3

value: Seedlings


title: h3.3ko;HTR5_T31A_rep2

description: Library name: h3.3ko;HTR5_T31A_rep2

value: h3.3ko;HTR5 T31A


title: h3.3ko;HTR5_T31A_rep1

description: Library name: h3.3ko;HTR5_T31A_rep1


title: Ripk1 EKO lesional - Replicate 4

description: Library name: Sample 4


title: Ripk1 EKO non lesional - Replicate 3

description: Library name: Sample 8


title: AML_patient_sample_292

description: Library name: sample_292


title: Ripk1 EKO lesional - Replicate 3

description: Library name: Sample 3


title: lung tissue, from APP infected pig 3, scRNAseq

city: Changchun

first: Liancheng

last: Lei

state: Jilin

address: 5333, Xi'an Road

institute: Jilin university

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Sscrofa11
Supplementary files format and content: Tab-separated values files and matrix files

organism: Sus scrofa

source_name: Lung tissue

extract_protocol:
Lungs were washed with cold PBS three times and minced into 1 mm pieces by sterilized scissors. Tissue pieces were dissolved with 1640 medium containing 25 U/mL DNase I, 300 U/mL collagenase type VIII, and 10% fetal bovine serum (FBS) in a 50 mL tube for 20 min at 37 °C. The suspension was mechanically dissociated and filtered through a 70 μm cell strainer. Cells suspensions were pelleted by centrifuging at 350 g for 7 min at 4 °C. Red blood cell lysis buffer (Solarbio, China) was then applied to remove red cells by incubating for 4 min and quenching with 10 ml PBS. The cell suspension was centrifuged at 350 g for 7 min at 4 °C, and the supernatant was decanted. After removing the dead cells using OptiPrep medium (Axis-Shield, Scotland), the cells were counted and immediately analysed by scRNA-seq.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Lung tissue

tag: age

value: 45 days old

value: APP infected


title: RNA library from 39 weeks Natural ovary 3 [Natural_39wks_ovary_3]

description: Library name: Natural_39wks_ovary_3

value: Female


title: Col_rep2, rna-seq

description: Library name: Col_rep2

value: WT (Col)


title: AML_patient_sample_291

description: Library name: sample_291


title: RNA library from 39 weeks Natural ovary 5 [Natural_39wks_ovary_5]

description: Library name: Natural_39wks_ovary_5

source_name: 40 weeks ovary

value: 40 weeks ovary


title: lung tissue, from APP infected pig 1, scRNAseq

description: 10x Genomics


title: lung tissue, from control pig 3, scRNAseq

description: 10x Genomics

value: PBS treatment


title: Ripk1 EKO lesional - Replicate 5

description: Library name: Sample 5


title: h3.3ko;HTR5_K36A_rep1

description: Library name: h3.3ko;HTR5_K36A_rep1


title: RNA library from 39 weeks Natural ovary 2 [Natural_39wks_ovary_2]

description: Library name: Natural_39wks_ovary_2

value: Natural


title: AML_patient_sample_296

description: Library name: sample_296


title: lung tissue, from control pig 2, scRNAseq

description: 10x Genomics


title: AML_patient_sample_288

description: Library name: sample_288


title: RNA library from 39 weeks IVF ovary 1 [IVF_39wks_ovary_1]

description: Library name: IVF_39wks_ovary_1

value: IVF


title: RNA library from 12 weeks IVF ovary 5 [IVF_12wks_ovary_5]

description: Library name: IVF_12wks_ovary_5

source_name: 12 weeks ovary

value: 12 weeks ovary


title: AML_patient_sample_293

description: Library name: sample_293


title: Bioreactor hepatocytes, gDNA Day 10

city: Berlin

first: Anja

last: Hess

email: ahess@molgen.mpg.de, anja.hess@mail.de

address: Ihnestrasse 63-67

institute: Max-Planck-Institut für molekulare Genetik

description:
Library name: Bioreactor-hepatocytes_gDNA_D10
PromethION 2 Solo

data_processing:
ONT signal data were base-called with dorado (v. 0.8.3, '5mCG_5hmCG' model and sup mode). Reads were aligned to human chm13v.2 with minimap2 (v. 2.26), with options minimap2 --secondary=no -2 -a -y -t 32 -K 2G -x map-ont.
Methylation bed files were generated with modkit’s pileup command using --cpg --combine-strands --threads 40 --filter-threshold 0.8 --ignore h to analyse individual replicates or --cpg --combine-strands --threads 40 --filter-percentile 0.21 --ignore h for aligned bam files of replicates previously merged with samtools. Analyses were restricted to autosomes, only CpGs covered by a minimum of 3 and a maximum of 150 reads passed criteria for downstream analyses.
Assembly: chm13.v2
Supplementary files format and content: filtered.bed - bedgraph files with methylation calls, coverage 3-150X, autosomes only
Supplementary files format and content: filtered.bw - bigwig files of filteres bedgraph methylation call files for IGV exploration
Supplementary files format and content: H5AD - AnnData matrix of methylation calls
Supplementary files format and content: TSV - methylation call table
Supplementary files format and content: Table of mean 1kb tile CpG methylation, related to all chm13 ONT-Seq files: Bioreactor-hepatocytes_1kb_tiles_averages_shared.tsv
Supplementary files format and content: Table of mean hepatocyte enhancer CpG methylation, related to all chm13 ONT-Seq files: Bioreactor-hepatocytes_hep-enhancers-ES-filtered.tsv
Supplementary files format and content: Table of mean hepatocyte enhancer CpG methylation, related to all chm13 ONT-Seq files: Bioreactor-hepatocytes_hep-enhancers-ES-filtered_anno.tsv

source_name: Nanopore-Seq, gDNA

growth_protocol: FSPS13B hiPSCs were aggregated in 3D differentiated into bioreactor hepatocytes as described (Tomaz et al., eLife, 2022), with slight modifications to the protocol: cells were cultured in 3D bioreactors (ReproCell ABLE Biott, ABBWVS03A-6), culture was fully xeno- and Matrigel-free, and Doxycyclin was removed at day 10.

extract_protocol:
Supernatants were treated with Proteinase K (Jena, 845-CH-0010030, stock concentration 22 mg/mL) for 1 hour or overnight at 37°C at 8.3 µl per 100 µl medium, and purified with the DNA Clean & Concentrator Kit (Zymo, D4004) mixing SN with DNA binding buffer at ratio 1:5. Genomic DNA was isolated with the PureLink Genomic DNA kit (Invitrogen,  K182001) according to manufacturer’s instructions.
Cell-free DNA libraries were prepared from 19-127 ng cell-free DNA with the Native Barcoding Kit 24 V14 (Oxford Nanopore, SQK-NBD114.24) according to the manufacturer’s recommendations (https://nanoporetech.com/document/ligation-sequencing-v14-human-cfdna-multiplex-sqk-nbd114-24). Four to five samples per pool were sequenced on a FLO-PRO114M flow cell (Oxford Nanopore). Genomic DNA reference libraries were prepared from 100-300 ng genomic DNA, sheared with the Megaruptor3 (Diagenode, B06010003) using the native Barcoding Kit 96 V14 (Oxford Nanopore, SQK-NBD114.96, https://nanoporetech.com/document/ligation-sequencing-gdna-native-barcoding-v14-sqk-nbd114-96), according to the manufacturer’s recommendations, but doubling the initial input DNA amount to a total of 24 µl and adjusting downstream volumes. Four to eight samples per pool were sequenced on a FLO-PRO114M flow cell (Oxford Nanopore).

treatment_protocol: Day 0-9: Doxycylin at 1µg/ml

tag: cell line

value: human 3D bioreactor hepatocytes (bioreactor)

tag: batch


title: lung tissue, from control pig 1, scRNAseq

description: 10x Genomics


title: RNA library from 39 weeks Natural ovary 4 [Natural_39wks_ovary_4]

description: Library name: Natural_39wks_ovary_4


title: RNA library from 12 weeks IVF ovary 4 [IVF_12wks_ovary_4]

description: Library name: IVF_12wks_ovary_4


title: Bioreactor hepatocytes, gDNA Day 0

description:
Library name: Bioreactor-hepatocytes_gDNA_D0
PromethION 2 Solo

value: human 3D induced pluripotent cells (bioreactor)

value: Doxycycline


title: AML_patient_sample_290

description: Library name: sample_290

value: Bone marrow-CD34+

value: AML


title: AML_patient_sample_286

description: Library name: sample_286


title: AML_patient_sample_289

description: Library name: sample_289


title: AML_patient_sample_287

description: Library name: sample_287


title: DBY8268 hog1Δ, 5% (v/v) ethanol (30 min), replicate 3

city: Fayetteville

first: Carson

middle: Len

last: Stacy

state: AR

address: 850 W. Dickson St. Rm 601

department: Biological Sciences

institute: University of Arkansas

description:
Library name: DBY8268_hog1del_EtOH_rep3
Column name in HOG1_RSEM_raw_gene_counts.tsv: DBY8268_hog1del_EtOH_rep3

data_processing:
Raw reads were trimmed and filtered using TrimGalore (version 0.6.7), a wrapper for cutadapt (version 3.4), with default settings to remove Illumina adapters. Reads with phred quality scores <20 or a post-trimming length <20 bp were discarded. Trimmed reads were mapped to the S288C genome (SacCer3 R64-1-1, Ensembl accession GCA_000146045.2) using STAR (version 2.7.10a) [62] implemented through the nf-core/rnaseq (v 3.10.1) pipeline [63]. Alignment used  a GTF containing only chromosomal protein-coding genes. Gene counts were generated using RSEM (version 1.3.1, [64]). A median of approximately 17 million reads (range: 12.4-69.5 million) were successfully mapped per sample, representing over 95% of trimmed reads successfully mapped.
Differential expression analysis was performed in edgeR (v. 4.4.2) with a negative binomial quasi likelihood (QL) generalized linear model [65,66], following TMM normalization. Genes with fewer than 10 counts across all samples were excluded from subsequent analysis. The QL model included sample type (e.g., M22 hog1∆ unstressed, M22 hog1∆ NaCl stressed, M22 hog1∆ ethanol stressed, etc.) and biological replicate as factors. Contrasts of interest included comparisons of wild-type vs hog1∆ mutants and the stress response (stress vs. unstressed) for each strain individually (e.g., the S288C wild-type NaCl response, the S288c hog1∆ NaCl response), as well as comparisons of strain stress responses (e.g., S288C wild-type NaCl response vs the S288c hog1∆ NaCl response). Genes were considered differentially expressed if they met a Benjamini-Hochberg false discovery rate (FDR) cutoff of < 0.01 and at least a ±1.5-fold change in expression. To identify Hog1-affected genes across all strains, all replicates were used. Counts for each sample were subsampled down to lowest read depth of any sample and samples were then subset to biological triplicate.
Assembly: SacCer3 R64-1-1
Supplementary files format and content: Tab separated values (tsv) file containing a matrix of raw fractional counts for all samples.

organism: Saccharomyces cerevisiae

growth_protocol: Saccharomyces cerevisiae strains were grown at 30°C with orbital shaking (270 rpm) in YPD (1% yeast extract, 2% peptone, 2% dextrose). ~5 unique colonies per replicate experiment were grown overnight to saturation in YPD. Cells were then sub-cultured for at least 8 generations (~16 hours) to mid-log phase (OD600 0.3 - 0.6 on a Unico spectrophotometer).

extract_protocol:
RNA was extracted using the ‘hot phenol’ method, with a detailed protocol available on protocols.io DOI 10.17504/protocols.io.inwcdfe. Phenol-extracted RNA was treated with DNaseI (Ambion), and then purified with a Quick-RNA MiniPrep Plus Kit (Zymo Research) including the optional on-column DNase step. RNA quantity was measured using a Qubit fluorometer (Fisher), and all samples were confirmed to have a RIN > 9 as assessed by an Agilent 2200 Tapestation.
RNA-seq libraries were prepared using the KAPA mRNA HyperPrep Kit (Roche) and KAPA Single-Indexed Adapter Set A + B, according to manufacturer specifications with minor modifications. Starting samples consisted of 500 ng, which were then polyA-enriched, fragmented to an average size of 200-300 nucleotides, and then cDNA libraries were amplified for 9 PCR cycles. A detailed protocol is available on protocols.io DOI 10.17504/protocols.io.uueewte.

treatment_protocol: For each biological replicate, an unstressed control sample was collected, and then the culture was split and exposed to stress media with final concentrations: 0.4 M NaCl, 5% (v/v) ethanol, or 0.4 mM H2O2. Cells were incubated in the stress for either 30 min (ethanol and H2O2) or 45 min (NaCl), timepoints which encompass the peak response for each stressor. Unstressed and stressed samples were collected by centrifugation at 1,500 x g for 1 min, flash frozen in liquid nitrogen, and stored at -80°C until RNA extraction.

value: budding yeast cells

value: hog1 KO (hog1/hog1)

value: 5% (v/v) ethanol (30 min)


title: Bioreactor hepatocytes, gDNA Day 20

description:
Library name: Bioreactor-hepatocytes_gDNA_D20
PromethION 2 Solo


title: AML_patient_sample_284

description: Library name: sample_284


title: Ripk1 EKO lesional - Replicate 2

description: Library name: Sample 2

value: skin tissue

value: Ripk1 EKO


title: RNA library from 12 weeks IVF ovary 2 [IVF_12wks_ovary_2]

description: Library name: IVF_12wks_ovary_2

value: Female


title: Ripk1 EKO lesional - Replicate 1

description: Library name: Sample 1


title: single cells from 3 WT mice

city: Hangzhou

first: Zhang

middle: Zhou

last: melanoma

state: China

address: 西湖大学医学院

institute: Westlake University

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.2.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest/getting-started)
Assembly: GRCm39
Supplementary files format and content: matrix files in .h5 format

source_name: Epidermis of back skin

extract_protocol:
The tissue was incubated in a digestion buffer consisting of 0.1% collagenase II (Gibco 17101015), 0.2% collagenase IV (Worthington LS004189), and 50 μg/ml DNase I in a 5% FBS-PBS solution at 37 °C for 80 minutes on a shaker. After centrifugation, the pellets were digested using 0.25% trypsin at 37 °C for 10 minutes. A single-cell suspension was obtained by filtering through 70-μm and 40-μm filters, followed by centrifugation at 500g at 4 °C for 10 minutes
Library preparation was performed using 10x Genomics Chromium Next GEM Single Cell 5' Kit v2 reagents according to the manufacturer’s instructions

value: Epidermis of back skin

value: Mixture

value: WT

value: No treatment


title: single cells from control 3 mice

value: CNO


title: Bioreactor hepatocytes, cell-free DNA Day 0

description:
Library name: Bioreactor-hepatocytes_cfDNA_D0
PromethION 2 Solo

library_source: other

molecule: other

source_name: Nanopore-Seq, Cell-free DNA


title: RNA library from 39 weeks Natural ovary 1 [Natural_39wks_ovary_1]

description: Library name: Natural_39wks_ovary_1

value: 39 weeks ovary

value: Natural


title: RNA library from 12 weeks Natural ovary 4 [Natural_12wks_ovary_4]

description: Library name: Natural_12wks_ovary_4

value: 12 weeks ovary


title: Bioreactor hepatocytes, cell-free DNA Day 20

description:
Library name: Bioreactor-hepatocytes_cfDNA_D20
PromethION 2 Solo

value: human 3D bioreactor hepatocytes (bioreactor)


title: RNA library from 12 weeks IVF ovary 3 [IVF_12wks_ovary_3]

description: Library name: IVF_12wks_ovary_3

value: IVF


title: Bioreactor hepatocytes, cell-free DNA Day 10

description:
Library name: Bioreactor-hepatocytes_cfDNA_D10
PromethION 2 Solo


title: RNA library from 12 weeks IVF ovary 1 [IVF_12wks_ovary_1]

description: Library name: IVF_12wks_ovary_1


title: AML_patient_sample_282

description: Library name: sample_282

source_name: Bone marrow-CD34+

value: Bone marrow-CD34+

value: AML


title: Col_rep1, rna-seq

description: Library name: Col_rep1

value: Seedlings

value: WT (Col)


title: DBY8268 hog1Δ, 0.4 mM H2O2 (30 min), replicate 1

description:
Library name: DBY8268_hog1del_H2O2_rep1
Column name in HOG1_RSEM_raw_gene_counts.tsv: DBY8268_hog1del_H2O2_rep1

value: budding yeast cells

value: hog1 KO (hog1/hog1)


title: lung tissue, from APP infected pig 2, scRNAseq

description: 10x Genomics

value: Lung tissue

value: 45 days old

value: APP infected


title: efs_input_rep2

description: Library name: efs_input_rep2

extract_protocol:
Nuclei were extracted, and mononucleosomes were generated using micrococcal nuclease (NEB, M0247S) digestion.Immunoprecipitation was conducted with anti-H3K36me3 (Abcam, ab9050).
The input DNA and immunoprecipitated DNA were subjected to library preparation with VAHTS universal DNA library prep kit for illumina (Vazyme, ND607-02) according to the manufacturer’s instruction.

value: efs

value: H3K36me3 (Abcam, ab9050)


title: DBY8268 hog1Δ, 5% (v/v) ethanol (30 min), replicate 2

description:
Library name: DBY8268_hog1del_EtOH_rep2
Column name in HOG1_RSEM_raw_gene_counts.tsv: DBY8268_hog1del_EtOH_rep2

value: 5% (v/v) ethanol (30 min)


title: single cells from SN suppressed 3 mice

value: Epidermis of back skin

value: Mixture

value: DBHCre; R26-LSL-Gi-DREADD

value: CNO


title: DBY8268 hog1Δ, 0.4 M NaCl (45 min), replicate 3

description:
Library name: DBY8268_hog1del_NaCl_rep3
Column name in HOG1_RSEM_raw_gene_counts.tsv: DBY8268_hog1del_NaCl_rep3

value: 0.4 M NaCl (45 min)


title: AML_patient_sample_283

description: Library name: sample_283

value: Bone marrow-CD34+


title: AML_patient_sample_285

description: Library name: sample_285

value: AML


title: AML_patient_sample_279

description: Library name: sample_279


title: h3.3ko;HTR5_K36A_input_rep1

description: Library name: h3.3ko;HTR5_K36A_input_rep1

value: Seedlings

value: h3.3ko;HTR5 K36A


title: DBY8268 hog1Δ, 0.4 mM H2O2 (30 min), replicate 3

description:
Library name: DBY8268_hog1del_H2O2_rep3
Column name in HOG1_RSEM_raw_gene_counts.tsv: DBY8268_hog1del_H2O2_rep3

value: budding yeast cells


title: RNA library from E18.5 IVF ovary 5 [IVF_ovary_E185_5]

description: Library name: IVF_ovary_E185_5

source_name: E18.5 ovary

value: E18.5 ovary

value: Female

value: IVF


title: RNA library from 12 weeks Natural ovary 3 [Natural_12wks_ovary_3]

description: Library name: Natural_12wks_ovary_3

value: 12 weeks ovary

value: Natural


title: AML_patient_sample_280

description: Library name: sample_280


title: DBY8268 hog1Δ, 0.4 mM H2O2 (30 min), replicate 2

description:
Library name: DBY8268_hog1del_H2O2_rep2
Column name in HOG1_RSEM_raw_gene_counts.tsv: DBY8268_hog1del_H2O2_rep2

value: hog1 KO (hog1/hog1)


title: AML_patient_sample_277

description: Library name: sample_277


title: AML_patient_sample_275

description: Library name: sample_275


title: DBY8268 hog1Δ, 5% (v/v) ethanol (30 min), replicate 1

description:
Library name: DBY8268_hog1del_EtOH_rep1
Column name in HOG1_RSEM_raw_gene_counts.tsv: DBY8268_hog1del_EtOH_rep1

value: 5% (v/v) ethanol (30 min)


title: RNA library from E18.5 IVF ovary 6 [IVF_ovary_E185_6]

description: Library name: IVF_ovary_E185_6


title: DBY8268 hog1Δ, unstressed control (0 min), replicate 1

description:
Library name: DBY8268_hog1del_CTRL_rep1
Column name in HOG1_RSEM_raw_gene_counts.tsv: DBY8268_hog1del_CTRL_rep1

value: unstressed control (0 min)


title: h3.3ko;HTR5_T31A_input_rep1

description: Library name: h3.3ko;HTR5_T31A_input_rep1

source_name: Seedlings

value: h3.3ko;HTR5 T31A

value: H3K36me3 (Abcam, ab9050)


title: RNA library from 12 weeks Natural ovary 2 [Natural_12wks_ovary_2]

description: Library name: Natural_12wks_ovary_2


title: AML_patient_sample_276

description: Library name: sample_276


title: AML_patient_sample_278

description: Library name: sample_278


title: RNA library from E18.5 IVF ovary 2 [IVF_ovary_E185_2]

description: Library name: IVF_ovary_E185_2


title: h3.3ko;HTR5_K36A_input_rep2

description: Library name: h3.3ko;HTR5_K36A_input_rep2


title: DBY8268 wild-type, 5% (v/v) ethanol (30 min), replicate 3

description:
Library name: DBY8268_WT_EtOH_rep3
Column name in HOG1_RSEM_raw_gene_counts.tsv: DBY8268_WT_EtOH_rep3

value: wild-type (HOG1/HOG1)


title: AML_patient_sample_274

description: Library name: sample_274


title: RNA library from E18.5 IVF ovary 1 [IVF_ovary_E185_1]

description: Library name: IVF_ovary_E185_1


title: DBY8268 hog1Δ, unstressed control (0 min), replicate 3

description:
Library name: DBY8268_hog1del_CTRL_rep3
Column name in HOG1_RSEM_raw_gene_counts.tsv: DBY8268_hog1del_CTRL_rep3


title: AML_patient_sample_281

description: Library name: sample_281


title: efs_input_rep1

description: Library name: efs_input_rep1

value: efs


title: h3.3ko;HTR5_T31A_input_rep2

description: Library name: h3.3ko;HTR5_T31A_input_rep2


title: h3.3ko;HTR5_input_rep2

description: Library name: h3.3ko;HTR5_input_rep2


title: h3.3ko;HTR5_input_rep1

description: Library name: h3.3ko;HTR5_input_rep1


title: DBY8268 hog1Δ, 0.4 M NaCl (45 min), replicate 1

description:
Library name: DBY8268_hog1del_NaCl_rep1
Column name in HOG1_RSEM_raw_gene_counts.tsv: DBY8268_hog1del_NaCl_rep1

value: 0.4 M NaCl (45 min)


title: RNA library from 12 weeks Natural ovary 1 [Natural_12wks_ovary_1]

description: Library name: Natural_12wks_ovary_1


title: DBY8268 hog1Δ, 0.4 M NaCl (45 min), replicate 2

description:
Library name: DBY8268_hog1del_NaCl_rep2
Column name in HOG1_RSEM_raw_gene_counts.tsv: DBY8268_hog1del_NaCl_rep2


title: AML_patient_sample_272

description: Library name: sample_272

value: Bone marrow-CD34+

value: AML


title: DBY8268 wild-type, 5% (v/v) ethanol (30 min), replicate 1

description:
Library name: DBY8268_WT_EtOH_rep1
Column name in HOG1_RSEM_raw_gene_counts.tsv: DBY8268_WT_EtOH_rep1


title: RNA library from E18.5 IVF ovary 4 [IVF_ovary_E185_4]

description: Library name: IVF_ovary_E185_4


title: DBY8268 hog1Δ, unstressed control (0 min), replicate 2

description:
Library name: DBY8268_hog1del_CTRL_rep2
Column name in HOG1_RSEM_raw_gene_counts.tsv: DBY8268_hog1del_CTRL_rep2


title: AML_patient_sample_273

description: Library name: sample_273


title: DBY8268 wild-type, 0.4 mM H2O2 (30 min), replicate 2

description:
Library name: DBY8268_WT_H2O2_rep2
Column name in HOG1_RSEM_raw_gene_counts.tsv: DBY8268_WT_H2O2_rep2


title: DBY8268 wild-type, 0.4 mM H2O2 (30 min), replicate 3

description:
Library name: DBY8268_WT_H2O2_rep3
Column name in HOG1_RSEM_raw_gene_counts.tsv: DBY8268_WT_H2O2_rep3


title: RNA library from E18.5 Natural ovary 4 [Natural_ovary_E185_4]

description: Library name: Natural_ovary_E185_4


title: Col_input_rep1

description: Library name: Col_input_rep1

value: Seedlings

value: WT (Col)


title: h3.3ko;HTR5_K36A_H3K36me3_rep2

description: Library name: h3.3ko;HTR5_K36A_H3K36me3_rep2

value: h3.3ko;HTR5 K36A


title: RNA library from E18.5 IVF ovary 3 [IVF_ovary_E185_3]

description: Library name: IVF_ovary_E185_3

value: E18.5 ovary

value: Female


title: Col_input_rep2

description: Library name: Col_input_rep2


title: DBY8268 wild-type, 5% (v/v) ethanol (30 min), replicate 2

description:
Library name: DBY8268_WT_EtOH_rep2
Column name in HOG1_RSEM_raw_gene_counts.tsv: DBY8268_WT_EtOH_rep2

value: budding yeast cells


title: DBY8268 wild-type, 0.4 mM H2O2 (30 min), replicate 1

description:
Library name: DBY8268_WT_H2O2_rep1
Column name in HOG1_RSEM_raw_gene_counts.tsv: DBY8268_WT_H2O2_rep1


title: Maize_leaf, CR-Hap1_infected, rep3

city: Köln

first: Gunther

last: Doehlemann

address: Zülpicher Straße 47a

institute: University of Cologne/ Universität zu Köln

description:
Library name: C3
3dpi, CR-Hap1, rep3

data_processing:
Trimmomatic (0.39) was used for quality filtering of the paired-end reads.
bowtie2 (2.3.5.1) was used for the mapping of the quality-filtered reads to the reference genome of maize.
samtools (1.9) were used to dort the BAM files.
Htseq-count (2.0.1) was used to count the mapped reads.
edgeR (3.36.0) was used for the differential gene expression analysis.
Assembly: Zea mays reference genome Zm-B73-REFERENCE-NAM-5.0
Supplementary files format and content: Gzipped text files containing transcript counts for all samples

organism: Zea mays

source_name: leaf

extract_protocol:
RNA was harvested from frozen and homogenized samples using TRIzol reagent (Invitrogen, Darmstadt, Germany). The Turbo DNA-Free Kit from Ambion (Ambion Life TechnologiesTM, Carlsbad, USA) was used to exclude DNA contamination.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: leaf

value: EGB

value: U. maydis_SG200_CR-hap1

tag: time point


title: efs_H3K36me3_rep2

description: Library name: efs_H3K36me3_rep2


title: DBY8268 wild-type, 0.4 M NaCl (45 min), replicate 3

description:
Library name: DBY8268_WT_NaCl_rep3
Column name in HOG1_RSEM_raw_gene_counts.tsv: DBY8268_WT_NaCl_rep3


title: RNA library from E18.5 Natural ovary 2 [Natural_ovary_E185_2]

description: Library name: Natural_ovary_E185_2

value: Natural


title: AML_patient_sample_271

description: Library name: sample_271


title: AML_patient_sample_270

description: Library name: sample_270


title: h3.3ko;HTR5_T31A_H3K36me3_rep1

description: Library name: h3.3ko;HTR5_T31A_H3K36me3_rep1

value: h3.3ko;HTR5 T31A


title: DBY8268 wild-type, 0.4 M NaCl (45 min), replicate 2

description:
Library name: DBY8268_WT_NaCl_rep2
Column name in HOG1_RSEM_raw_gene_counts.tsv: DBY8268_WT_NaCl_rep2


title: Maize_leaf, CR-Hap1_infected, rep2

description:
Library name: C2
3dpi, CR-Hap1, rep2


title: AML_patient_sample_268

description: Library name: sample_268


title: RNA library from E18.5 Natural ovary 3 [Natural_ovary_E185_3]

description: Library name: Natural_ovary_E185_3


title: AML_patient_sample_266

description: Library name: sample_266


title: efs_H3K36me3_rep1

description: Library name: efs_H3K36me3_rep1

value: H3K36me3 (Abcam, ab9050)


title: h3.3ko;HTR5_K36A_H3K36me3_rep1

description: Library name: h3.3ko;HTR5_K36A_H3K36me3_rep1


title: RNA library from E18.5 Natural ovary 1 [Natural_ovary_E185_1]

description: Library name: Natural_ovary_E185_1


title: Maize_leaf, CR-Hap1_infected, rep1

description:
Library name: C1
3dpi, CR-Hap1, rep1


title: DBY8268 wild-type, 0.4 M NaCl (45 min), replicate 1

description:
Library name: DBY8268_WT_NaCl_rep1
Column name in HOG1_RSEM_raw_gene_counts.tsv: DBY8268_WT_NaCl_rep1

value: wild-type (HOG1/HOG1)


title: h3.3ko;HTR5_T31A_H3K36me3_rep2

description: Library name: h3.3ko;HTR5_T31A_H3K36me3_rep2


title: AML_patient_sample_267

description: Library name: sample_267


title: AML_patient_sample_265

description: Library name: sample_265


title: h3.3ko;HTR5_H3K36me3_rep2

description: Library name: h3.3ko;HTR5_H3K36me3_rep2


title: AML_patient_sample_269

description: Library name: sample_269


title: Maize_leaf, SG200-infected, rep2

description:
Library name: B2_1
3dpi, SG200 treatment, rep2

value: U. maydis_SG200


title: h3.3ko;HTR5_H3K36me3_rep1

description: Library name: h3.3ko;HTR5_H3K36me3_rep1


title: AML_patient_sample_264

description: Library name: sample_264


title: Maize_leaf, SG200-infected, rep3

description:
Library name: B3
3dpi, SG200 treatment, rep3


title: DBY8268 wild-type, unstressed control (0 min), replicate 2

description:
Library name: DBY8268_WT_CTRL_rep2
Column name in HOG1_RSEM_raw_gene_counts.tsv: DBY8268_WT_CTRL_rep2

value: unstressed control (0 min)


title: Maize_leaf, SG200-infected, rep1

description:
Library name: B1
3dpi, SG200 treatment, rep1


title: Maize_leaf, Mock-infected, rep3

description:
Library name: A3_1
3dpi, water control, rep3

value: water


title: AML_patient_sample_263

description: Library name: sample_263

value: Bone marrow-CD34+

value: AML


title: DBY8268 wild-type, unstressed control (0 min), replicate 3

description:
Library name: DBY8268_WT_CTRL_rep3
Column name in HOG1_RSEM_raw_gene_counts.tsv: DBY8268_WT_CTRL_rep3


title: DBY8268 wild-type, unstressed control (0 min), replicate 1

description:
Library name: DBY8268_WT_CTRL_rep1
Column name in HOG1_RSEM_raw_gene_counts.tsv: DBY8268_WT_CTRL_rep1


title: Col_H3K36me3_rep2

description: Library name: Col_H3K36me3_rep2

value: Seedlings

value: WT (Col)


title: Col_H3K36me3_rep1

description: Library name: Col_H3K36me3_rep1


title: AML_patient_sample_261

description: Library name: sample_261


title: HTR5_T31A_input_rep1

description: Library name: HTR5_T31A_input_rep1

extract_protocol:
Nuclei were extracted, and mononucleosomes were generated using micrococcal nuclease (NEB, M0247S) digestion.Immunoprecipitation was conducted with anti-GFP (Thermo Fisher Scientific, A11122).
The input DNA and immunoprecipitated DNA were subjected to library preparation with VAHTS universal DNA library prep kit for illumina (Vazyme, ND607-02) according to the manufacturer’s instruction.

value: GFP (Thermo Fisher Scientific, A11122)


title: M22 hog1Δ, 5% (v/v) ethanol (30 min), replicate 4

description:
Library name: M22_hog1del_EtOH_rep4
Column name in HOG1_RSEM_raw_gene_counts.tsv: M22_hog1del_EtOH_rep4

value: hog1 KO (hog1/hog1)

value: 5% (v/v) ethanol (30 min)


title: AML_patient_sample_262

description: Library name: sample_262


title: AML_patient_sample_260

description: Library name: sample_260


title: Normal_growth_tooth

city: Qingdao

first: Xianwei

last: Yang

address: Hengyushan Road

institute: BGI-Qingdao

description: Library name: NG

data_processing:
The sequence reads were demultiplexed and mapped to the reference genome GRCr8 (GCF_036323735.1) using Stereo-seq Analysis Workflow (SAW, version 8.1.1)
Assembly: GRCr8
Supplementary files format and content: tissue.gef: gene expression count data in gef format (Stereo-seq)
Library strategy: Spatial Transcriptomics

organism: Rattus norvegicus

source_name: tooth

extract_protocol:
10 μm tissue sections were mounted onto Stereo-seq chips (1 cm2 size, generated by BGI, China). which feature capture spots with 220 nm diameter and 500 nm spacing. After fixation (pre-chilled methanol) and staining (Qubit ssDNA dye, Thermo Fisher, USA), tissues were permeabilized using 0.1% pepsin (Sigma, USA) at 37℃. In situ RNA was reverse transcribed into cDNA using the capture probes (containing 10 bp MID and 25 bp CID barcodes). The cDNA was released, amplified using cDNA HIFI PCR mix (MGI), and fragmented (400-600 bp)
Stereo-seq transcriptomic library preparation and sequencing were performed following the protocol previously described by 10.1016/j.cell.2022.04.003

value: tooth


title: M22 hog1Δ, 5% (v/v) ethanol (30 min), replicate 3

description:
Library name: M22_hog1del_EtOH_rep3
Column name in HOG1_RSEM_raw_gene_counts.tsv: M22_hog1del_EtOH_rep3

value: budding yeast cells


title: Maize_leaf, Mock-infected, rep1

description:
Library name: A1_1
3dpi, water control, rep1

value: leaf

value: EGB


title: AML_patient_sample_259

description: Library name: sample_259

extract_protocol:
Human bone marrow aspirates were obtained from in accordance with the Italian laws and the policies and practices of the Ethical Committee of Humanitas Research Hospital. Patients were classified following the updated WHO classification of tumors and lymphoid tissues guidelines 1 and stratified by risk of evolution following the IPSS-R parameters. Bone marrow mononuclear cells (BMNCs) were isolated by density gradient separation with Lympholyte®-H Cell Separation Media (Cedarlane corporation, Burlington, USA) according to manufacturer’s instructions, frozen in fetal bovine serum (FBS) (Lonza, Basel, Switzerland) containing 10% DimethylSulfoxide (DMSO) (Sigma Aldrich, St. Louis, Missouri, USA) and cryopreserved in liquid nitrogen. Bone marrow HSPCs were isolated based on CD34+ surface marker using the MACS CD34 microbead kit on autoMACS (Miltenyi Biotech Inc, San Diego, CA). MDS-L cells were kindly provided by Dr. Daniel Starczynowski, Cincinnati Children's Hospital Medical Center and were cultured in RPMI-1640 medium supplemented with 10% heat-inactivated FBS and 1% P/S and 10ng/mL of hrIL-3 (PeproTech, Paisley, UK). Cells were grown at 37°C and 5%CO2 and treated with 3uM DB2115 (Cat. No. HY-124676A Medchem, NJ, USA) for the specified time.
Libraries for CD34+ mRNA sequencing were prepared by using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech-Takara). Libraries for MDS-L mRNA sequencing were prepared by using the Illumina Stranded mRNA Prep (Illumina). All samples were sequenced at an average of 40 million 50-bp pair-end reads with Novaseq 6000.
All RNA-seq data sets were processed in paired-end.


title: iron_deficiency_anemia_tooth

description: Library name: IDA


title: HTR5_K36A_input_rep1

description: Library name: HTR5_K36A_input_rep1


title: HTR5_K36A_input_rep2

description: Library name: HTR5_K36A_input_rep2


title: M22 hog1Δ, 0.4 mM H2O2 (30 min), replicate 4

description:
Library name: M22_hog1del_H2O2_rep4
Column name in HOG1_RSEM_raw_gene_counts.tsv: M22_hog1del_H2O2_rep4


title: AML_patient_sample_258

description: Library name: sample_258


title: AML_patient_sample_257

description: Library name: sample_257


title: M22 hog1Δ, 0.4 mM H2O2 (30 min), replicate 3

description:
Library name: M22_hog1del_H2O2_rep3
Column name in HOG1_RSEM_raw_gene_counts.tsv: M22_hog1del_H2O2_rep3


title: M22 hog1Δ, 5% (v/v) ethanol (30 min), replicate 2

description:
Library name: M22_hog1del_EtOH_rep2
Column name in HOG1_RSEM_raw_gene_counts.tsv: M22_hog1del_EtOH_rep2


title: UC1, ulcerative colitis patient 4, ALI monolayer cells, day 14

city: Vancouver

first: Irvin

last: Ng

state: BC

address: 950 West 28th Avenue Room #211 Room #211

country: Canada

institute: BC Children's Hospital Research Institute

description:
Library name: Treatment_D2
Column name in salmon.merged.gene_counts.tsv: Treatment_D2

data_processing:
Raw reads were trimmed for adaptor sequence and low-quality sequences using Trim Galore v.0.6.5
Genome contaminant sequences were removed using BBSplit.sh from the BBMap suite v39.06
Ribosomal rRNA sequences were removed using SortMeRNA v4.3.7
Reads were aligned using STAR v2.7.11b to GRCh38.p14
Gene quantification was conducted using Salmon v1.10.2 and tximport was used to scale counts to library size and average transcript length
Assembly: GRCh38.p14
Supplementary files format and content: TSV file containing the normalized gene counts for all samples

source_name: sigmoid colon organoids

growth_protocol: Sigmoid colon organoids were grown for 10 days, then converted to submerged monolayers for 7 days, followed by removing the top transwell media to generate an air-liquid interface, where cells were grown until day 14. Cells were maintained in monolayer media (DMEM/F12, WRN, N2, B27, mEGF, and rock inhibitor Y-27632) at 37oC with 5% CO2.

extract_protocol:
RNA was harvested using RNAzol according to the manufacturers instructions.
Sample quality control was performed using the Agilent 2100 Bioanalyzer or the Agilent 4200 Tapestation. Samples that passed quality control were then prepared for sequencing following the standard Illumina stranded mRNA prep protocol.

value: sigmoid colon organoids

value: ulcerative colitis

value: intestinal epithelial cells

tag: time

value: day 14

value: air-liquid interface monolayers


title: Maize_leaf, Mock-infected, rep2

description:
Library name: A2_1
3dpi, water control, rep2

value: water


title: M22 hog1Δ, 5% (v/v) ethanol (30 min), replicate 1

description:
Library name: M22_hog1del_EtOH_rep1
Column name in HOG1_RSEM_raw_gene_counts.tsv: M22_hog1del_EtOH_rep1


title: HTR5_T31A_GFP_IP_rep2

description: Library name: HTR5_T31A_GFP_IP_rep2


title: UC3, ulcerative colitis patient 3, ALI monolayer cells, day 14

description:
Library name: Treatment_B3
Column name in salmon.merged.gene_counts.tsv: Treatment_B3


title: M22 hog1Δ, 0.4 mM H2O2 (30 min), replicate 2

description:
Library name: M22_hog1del_H2O2_rep2
Column name in HOG1_RSEM_raw_gene_counts.tsv: M22_hog1del_H2O2_rep2


title: HTR5_GFP_input_rep2

description: Library name: HTR5_GFP_input_rep2


title: UC4, ulcerative colitis patient 2, ALI monolayer cells, day 14

description:
Library name: Treatment_B2
Column name in salmon.merged.gene_counts.tsv: Treatment_B2


title: M22 hog1Δ, 0.4 mM H2O2 (30 min), replicate 1

description:
Library name: M22_hog1del_H2O2_rep1
Column name in HOG1_RSEM_raw_gene_counts.tsv: M22_hog1del_H2O2_rep1


title: HTR5_T31A_GFP_IP_rep1

description: Library name: HTR5_T31A_GFP_IP_rep1


title: HTR5_T31A_input_rep2

description: Library name: HTR5_T31A_input_rep2


title: HTR5_K36A_GFP_IP_rep2

description: Library name: HTR5_K36A_GFP_IP_rep2


title: M22 hog1Δ, 0.4 M NaCl (45 min), replicate 4

description:
Library name: M22_hog1del_NaCl_rep4
Column name in HOG1_RSEM_raw_gene_counts.tsv: M22_hog1del_NaCl_rep4

value: 0.4 M NaCl (45 min)


title: CART19-Ramos-IDC-Con

city: Saint Louis

first: Li

last: Ding

state: MO

address: 660 S. Euclid Avenue

institute: Washington University in St. Louis

description:
Library name: Sample 5
10X Genomics

data_processing:
For each sample, we obtained the unfiltered feature-barcode matrix per sample by passing the demultiplexed FASTQs to Cell Ranger v.6.0.1 ‘count’ command using default parameters and the prebuilt GRCh38 genome reference v.3.0.0 (GRCh38-2020-A) (1, 2). All subsequent processing was performed using Seurat v. 5.0.1. Finally, a series a quality control filters were utilized to filter cell barcodes including: nFeature_RNA > 200,  nFeature_RNA < 10,000, nCount_RNA > 1000, nCount RNA < 80,000 and perent.mito < 10%. After filtering data underwent SCTranformation (vars.to.regress=”nCountRNA”,”percent.mito”), followed by RunPCA, RunUMAP, FindNeighbors, and FindClusters. After each sample was processed, we performed UpdateSeuratObject before merging all the samples and performing downstream integration as suggested in the Seurat tutorial. Briefly, each RNA assay was split by experimental condition (or sample), followed by SCTransform (vars.to.regress=”nCountRNA”,”percent.mito”; vst.flavor = "v2"), RunPCA (npcs=20), NormalizeData, FindVariableFeatures ScaleData and RunPCA. To integrate samples all three methods including CCAIntegration, RPCAIntegration and HarmonyIntegration were run. Finally, FindNeighbors, FindClusters and RunUMAP was run to determine clusters. Layers were joined using JoinLayers, followed by Azimuth annotation for intiial cell typing (reference=”pbmcref”). One cluster of doublets was identified exhibiting reduced and relatively similar expression of all cell type markers (CAR-T cell markers: CD4, CD8A, CD8B; pMC markers: CD86, CD80, CD83; RamosCG markers: CD79A CD19, MS4A1) along with mixed cell identities from the Azimuth reference. Suspected doublet clusters were removed and FindNeighbors, FindClusters and RunUMAP was run to create final object use for downstream analysis. PrepSCTIntegration was run before any subsequent differential gene expression analysis.
Assembly: GRCh38-2020-A
Supplementary files format and content: Gene Expression Matrices

source_name: CART, Ramos, IDC

growth_protocol: Human T cells isolated from PBMC were activated with human anti-CD3/CD28 Dynabeads (Gibco; bead: cell ratio 3:1, 2 days) were cultured in RPMI-1640, 10% FBS, 1% GlutaMAX, 1% penicillin/ streptomycin, 50µM β-mercaptoethanol (Gibco), 20 mM HEPES (Corning), 50U/mL IL-2, 10ng/mL IL-15, and 10ng/mL IL-7 (PeproTech). Cells were transduced on day +1 with anti-CD19 lentivirus. CAR positive cells were sorted with CD34-PE and anti-PE beads on a an AutoMACS. Positive fraction contains CART19 cells. For generating primed myeloid cells (pMC), monocytes of matched donor were cultured in RPMI-1640, 1%MEM Non-Essential Amino Acids, 1 mM Sodium Pyruvate, 50µM β-mercaptoethanol, 2mmol/L L-glutamine, 1% penicillin/ streptomycin, 10% FBS, 0.4µg/mL human IL-4 and 0.2µg/mL GM-CSF (PeproTech). Day 5 pMCs were used in assays. Tumor cells are Ramos cells expressing luciferase GFP (RamosCG) cultured in complete RMPI-1640 media.

extract_protocol:
Cells from each experimental groups are washed with PBS and cell pellet containing ~50,000 cells were analyzed for scRNA sequencing.
3’ V3.1 – Dual Index Kit - 10x Genomics

treatment_protocol: CART19, RamosCG, and primed myeloid cells (pMC), were co-cultured for 24hrs with DMSO control or 1000 nM duvelisib or 1000nM ruxolitinib

value: CART, Ramos, IDC

value: Untreated


title: UC2, ulcerative colitis patient 1, ALI monolayer cells, day 14

description:
Library name: Treatment_B1
Column name in salmon.merged.gene_counts.tsv: Treatment_B1


title: N3, non-IBD patient 3, ALI monolayer cells, day 14

description:
Library name: Control_C1
Column name in salmon.merged.gene_counts.tsv: Control_C1

value: non-IBD


title: CART19-Ramos-IDC-Duv

description:
Library name: Sample 6
10X Genomics

value: Duvelisib


title: CART19-Ramos-IDC-Rux

description:
Library name: Sample 7
10X Genomics

value: Ruxolitinib


title: N2, non-IBD patient 2, ALI monolayer cells, day 14

description:
Library name: Control_A2
Column name in salmon.merged.gene_counts.tsv: Control_A2


title: CART19-Ramos-Duv

description:
Library name: Sample 4
10X Genomics

source_name: CART, Ramos

value: CART, Ramos


title: HTR5_K36A_GFP_IP_rep1

description: Library name: HTR5_K36A_GFP_IP_rep1

value: Seedlings

value: GFP (Thermo Fisher Scientific, A11122)


title: M22 hog1Δ, 0.4 M NaCl (45 min), replicate 3

description:
Library name: M22_hog1del_NaCl_rep3
Column name in HOG1_RSEM_raw_gene_counts.tsv: M22_hog1del_NaCl_rep3

value: budding yeast cells

value: hog1 KO (hog1/hog1)


title: HTR5_GFP_input_rep1

description: Library name: HTR5_GFP_input_rep1


title: M22 hog1Δ, 0.4 M NaCl (45 min), replicate 1

description:
Library name: M22_hog1del_NaCl_rep1
Column name in HOG1_RSEM_raw_gene_counts.tsv: M22_hog1del_NaCl_rep1


title: N1, non-IBD patient 1, ALI monolayer cells, day 14

description:
Library name: Control_A1
Column name in salmon.merged.gene_counts.tsv: Control_A1

value: sigmoid colon organoids


title: CART19-IDC-cont

description:
Library name: Sample 2
10X Genomics

source_name: CART, IDC

value: CART, IDC


title: CART19-IDC-Duv

description:
Library name: Sample 3
10X Genomics


title: HTR5_GFP_IP_rep1

description: Library name: HTR5_GFP_IP_rep1


title: CD4+ T cells, MLR MAX.16H5, biol rep5

city: Leipzig

first: Kristina

last: Roth

state: Outside USA

address: Perlickstraße 1

institute: Fraunhofer IZI

data_processing:
Reads were demultiplexed by Illumina’s bcl-convert (v3.7.5).
Adapter sequences were removed from reads using adapter removal (v2.3.1) using parameters –trimns, –trimqualities, –minquality ‘20’, and –minlength ‘30’).
Read alignment by HISAT2 (v2.1.0) with parameters –fr and rna-strandness: RF
Read counting by htseq-count (v0.11.2) using parameters –mode intersection-strict, –stranded reverse and –type exon
All steps were orchestrated by the workflow-manager uap
Assembly: human genome hg38 (Gencode v36)
Supplementary files format and content: htseq_counts.txt files contain raw reads per gene for a given sample
Supplementary files format and content: .csv file contains matrix table with vst normalized gene counts for every gene and every sample

source_name: CD4+ T cells

growth_protocol: Human CD4+ T cells were isolated by Ficoll density gradient centrifugation from peripheral blood and stimulated in a one-way mixed lymphocyte reaction (MLR) with irradiated CD3-depleted PBMCs in RPMI 1640 medium (Gibco) supplemented with 10% FBS (heat-inactivated) (Responder/Stimulator ratio = 1:4). Cells were cultured at 37°C in a humidified atmosphere at 5% CO2 for three days. CD4+ T cells were isolated out of the cocultures by magnetic isolation (Miltenyi).

extract_protocol:
Total RNA extraction (Qiagen,  RNeasy Mini Kit) with double DNAse digestion (TURBO DNA free Kit, Ambion)
TruSeqStranded mRNA Illumina

treatment_protocol:
Untreated Condition: CD4+ responder T cells were left untreated before getting added to the MLR cocultures.
MAX.16H5 Treatment: CD4+ responder T cells were pre-incubated with excess anti-CD4 antibody MAX.16H5 (humanized, IgG4 isotype, 1.2 – 1.5 µg mAb per 106 cells) for 2 h. To remove unbound antibodies, cells were washed twice before getting added to the MLR cocultures.
Cyclosporin A Treatment:  Cyclosporin A (Sandimmun® Optoral, Novartis) was added directly into the MLR cocultures to reach a final concentration of 200 ng/mL.

value: CD4+ T cells

value: anti-human CD4 mAb (MAX.16H5 IgG4)


title: IDC

description:
Library name: Sample 1
10X Genomics

source_name: IDC

value: IDC


title: M22 hog1Δ, unstressed control (0 min), replicate 4

description:
Library name: M22_hog1del_CTRL_rep4
Column name in HOG1_RSEM_raw_gene_counts.tsv: M22_hog1del_CTRL_rep4

value: unstressed control (0 min)


title: SETD3_KO2 rep3

city: Be'er Sheva

first: Dan

last: Levy

address: David Ben Gurion Blvd 1

country: Israel

institute: Ben-Gurion University

description: Library name: Sample 18

data_processing:
Raw sequences were quality trimmed and filtered using Trim Galore (version 0.4.5) (quality cutoff=25, length cutoff=25) and cutadapt (version 1.15)
Alignment of the reads to the human genome (Homo_sapiens.GRCh38) was done with RSEM (version 1.2.28 option ‘bowtie2’) and calculation of number of reads per gene per sample was also done with RSEM
Assembly: GRCH38
Supplementary files format and content: Count Matrix for all samples

growth_protocol: HCT116  were maintained in Dulbecco’s modified Eagle’s medium with 10% fetal bovine serum (FBS), penicillin-streptomycin , 2 mg/ml L-glutamine and non-essential amino acids.

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA Kit (Macherey-Nagel)
mRNA library preparation (poly A enrichment)

value: SETD3 KO


title: h3.3ko;HTR5_G34W_rep3

description: Library name: h3.3ko;HTR5_G34W_rep3

value: h3.3ko;HTR5 G34W


title: M22 hog1Δ, unstressed control (0 min), replicate 3

description:
Library name: M22_hog1del_CTRL_rep3
Column name in HOG1_RSEM_raw_gene_counts.tsv: M22_hog1del_CTRL_rep3


title: SETD3_KO2 rep2

description: Library name: Sample 17


title: CD4+ T cells, MLR Untreated, biol rep5

value: Untreated


title: M22 hog1Δ, unstressed control (0 min), replicate 2

description:
Library name: M22_hog1del_CTRL_rep2
Column name in HOG1_RSEM_raw_gene_counts.tsv: M22_hog1del_CTRL_rep2


title: SETD3_KO2 rep1

description: Library name: Sample 16


title: h3.3ko;HTR5_G34W_rep2

description: Library name: h3.3ko;HTR5_G34W_rep2


title: CD4+ T cells, MLR MAX.16H5, biol rep4


title: CD4+ T cells, MLR Cyclosporin A, biol rep4

value: Cyclosporin A


title: h3.3ko;HTR5_G34W_rep1

description: Library name: h3.3ko;HTR5_G34W_rep1


title: SETD3_KO1 rep3

description: Library name: Sample 15


title: M22 hog1Δ, unstressed control (0 min), replicate 1

description:
Library name: M22_hog1del_CTRL_rep1
Column name in HOG1_RSEM_raw_gene_counts.tsv: M22_hog1del_CTRL_rep1


title: h3.3ko;HTR5_G34R_rep3

description: Library name: h3.3ko;HTR5_G34R_rep3

value: h3.3ko;HTR5 G34R


title: M22 hog1Δ, 0.4 M NaCl (45 min), replicate 2

description:
Library name: M22_hog1del_NaCl_rep2
Column name in HOG1_RSEM_raw_gene_counts.tsv: M22_hog1del_NaCl_rep2

value: 0.4 M NaCl (45 min)


title: CD4+ T cells, MLR Untreated, biol rep4


title: M22 wild-type, 5% (v/v) ethanol (30 min), replicate 4

description:
Library name: M22_WT_EtOH_rep4
Column name in HOG1_RSEM_raw_gene_counts.tsv: M22_WT_EtOH_rep4

value: wild-type (HOG1/HOG1)

value: 5% (v/v) ethanol (30 min)


title: SETD3_KO1 rep2

description: Library name: Sample 14


title: CD4+ T cells, MLR Cyclosporin A, biol rep3


title: M22 wild-type, 5% (v/v) ethanol (30 min), replicate 3

description:
Library name: M22_WT_EtOH_rep3
Column name in HOG1_RSEM_raw_gene_counts.tsv: M22_WT_EtOH_rep3


title: SETD3_KO1 rep1

description: Library name: Sample 13


title: h3.3ko;HTR5_G34R_rep1

description: Library name: h3.3ko;HTR5_G34R_rep1

value: Seedlings


title: Col_wildtype_rep3

description: Library name: Col_rep3

value: WT (Col)


title: M22 wild-type, 5% (v/v) ethanol (30 min), replicate 2

description:
Library name: M22_WT_EtOH_rep2
Column name in HOG1_RSEM_raw_gene_counts.tsv: M22_WT_EtOH_rep2

value: budding yeast cells


title: SETD3_CT rep2

description: Library name: Sample 11

value: SETD3 Control


title: Col_wildtype_rep2

description: Library name: Col_rep2


title: CD4+ T cells, MLR Cyclosporin A, biol rep2


title: M22 wild-type, 0.4 mM H2O2 (30 min), replicate 4

description:
Library name: M22_WT_H2O2_rep4
Column name in HOG1_RSEM_raw_gene_counts.tsv: M22_WT_H2O2_rep4


title: SETD3_CT rep3

description: Library name: Sample 12


title: CD4+ T cells, MLR Untreated, biol rep3


title: CD4+ T cells, MLR Cyclosporin A, biol rep5


title: CD4+ T cells, MLR MAX.16H5, biol rep2


title: CD4+ T cells, MLR Untreated, biol rep2


title: h3.3ko;HTR5_rep3

description: Library name: h3.3ko;HTR5_rep3


title: SETD3_CT rep1

description: Library name: Sample 10


title: h3.3ko;HTR5_G34R_rep2

description: Library name: h3.3ko;HTR5_G34R_rep2


title: M22 wild-type, 0.4 mM H2O2 (30 min), replicate 2

description:
Library name: M22_WT_H2O2_rep2
Column name in HOG1_RSEM_raw_gene_counts.tsv: M22_WT_H2O2_rep2


title: ACTB-mut rep3

description: Library name: Sample 9

value: Actin mut over-expression


title: ACTB-mut rep2

description: Library name: Sample 8


title: Col_wildtype_rep1

description: Library name: Col_rep1


title: h3.3ko;HTR5_rep2

description: Library name: h3.3ko;HTR5_rep2


title: CD4+ T cells, MLR MAX.16H5, biol rep3

value: CD4+ T cells


title: M22 wild-type, 0.4 mM H2O2 (30 min), replicate 1

description:
Library name: M22_WT_H2O2_rep1
Column name in HOG1_RSEM_raw_gene_counts.tsv: M22_WT_H2O2_rep1


title: CD4+ T cells, MLR Cyclosporin A, biol rep1


title: M22 wild-type, 0.4 mM H2O2 (30 min), replicate 3

description:
Library name: M22_WT_H2O2_rep3
Column name in HOG1_RSEM_raw_gene_counts.tsv: M22_WT_H2O2_rep3


title: h3.3ko;HTR5_rep1

description: Library name: h3.3ko;HTR5_rep1


title: CD4+ T cells, MLR MAX.16H5, biol rep1

value: anti-human CD4 mAb (MAX.16H5 IgG4)


title: ACTB-mut rep1

description: Library name: Sample 7


title: M22 wild-type, 0.4 M NaCl (45 min), replicate 4

description:
Library name: M22_WT_NaCl_rep4
Column name in HOG1_RSEM_raw_gene_counts.tsv: M22_WT_NaCl_rep4


title: M22 wild-type, 5% (v/v) ethanol (30 min), replicate 1

description:
Library name: M22_WT_EtOH_rep1
Column name in HOG1_RSEM_raw_gene_counts.tsv: M22_WT_EtOH_rep1


title: ACTB-WT rep3

description: Library name: Sample 6

value: Actin WT over-expression


title: CD4+ T cells, MLR Untreated, biol rep1


title: Col_wildtype rep3

description: Library name: Col_rep3


title: M22 wild-type, 0.4 M NaCl (45 min), replicate 1

description:
Library name: M22_WT_NaCl_rep1
Column name in HOG1_RSEM_raw_gene_counts.tsv: M22_WT_NaCl_rep1


title: Col_wildtype rep1

description: Library name: Col_rep1