title: dataset3_BMPi_LDN_RFP

city: Charlottesville

first: Delai

last: Huang

state: VA

address: University of Virginia

institute: UVA

data_processing:
We built a zebrafish STAR genome index using Lawson Lab zebrafish transcriptome annotation (46) plus manually annotated entries for mCherry transcript, filtered for protein-coding genes. Final cellular barcodes and Unique Molecular Identifiers (UMIs) were determined using Cell Ranger 6.0.1 (10X Genomics) and cells were filtered to include only high-quality cells. Cell Ranger defaults for selecting cell-associated barcodes versus barcodes associated with empty partitions were used.
Assembly: GRCz11
Supplementary files format and content: bam and monocle3 RDS

organism: Danio rerio

source_name: dorsal fin

extract_protocol:
Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips.
Cells were captured in a Chromium controller (10X Genomics). Single-cell mRNA libraries were prepared using the single-cell 3’ solution V3 kit (10X Genomics). Quality control and quantification assays were performed using a Qubit fluorometer (ThermoFisher) and a 2100 Bioanalyzer (Agilent). Libraries were sequenced on an Illumina NextSeq 550 using 75-cycle, high output kits (read 1: 26 cycles, i7 Index: 8 cycles, read 2: 57 cycles).

value: dorsal fin

value: wild type

value: LDN


title: MCF-7 PR-2 cells

status: Public on Jan 30 2025

type: SRA

city: WASHINGTON

first: Wenge

last: Zhu

state: DC

address: 800 22ND ST NW, Room 8480, Science & Engineering Hall

department: Biochemistry and Molecular Medicine

country: USA

institute: George Washington University

library_source: transcriptomic

data_processing:
GLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork
Read cout extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file include raw counts for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: Breast

growth_protocol: All cells were maintained in DMEM supplemented with 10% FBS at 37 °C with 5% CO2.

extract_protocol:
Total RNA was harvested using Rneasy mini plus kit (Qiagen). 2ug of the total RNA was used for the construction of sequencing libraries
Total RNA was extracted and prepared for cDNA libraries within Illumina TruSeq Stranded mRNA sample preparation kit

tag: tissue

value: Breast

tag: cell line

value: MCF-7 PR

tag: cell type

value: Breast cancer cells

tag: genotype

value: PR

tag: treatment

value: Palbociclib


title: AL03, scTCR-seq

city: Seodaemun-gu

first: Insuk

last: Lee

state: Seoul

address: 50 Yonsei-ro

department: Biotechnology

country: South Korea

institute: Yonsei University

description: 10x Genomics

data_processing:
scRNA-seq: Barcoded processing, gene counting and aggregation were made using CellRanger v6.1.1. scTCR-seq: barcoded processing, V(D)J sequences and annotations were made using the CellRanger v7.0.0. scATAC-seq: barcoded processing, CellRanger ATAC v2.0.0 for scATAC-seq
Assembly: GRCh38
Supplementary files format and content: raw and filtered matrix file for scRNA-seq, filtered contigs for scTCR-seq, filtered peaks, cell list, peak list, and fragments for scATAC-seq

source_name: Lung

extract_protocol:
We collected fresh tumor tissues which was mechanically and enzymatically dissociated using a gentleMACS dissociator (Miltenyi Biotec, Gladbach Bergisch, Germany, Cat#130-093-235) and the Human Tumor Dissociation Kit (Miltenyi Biotec, Cat#130-095-929) following the manufacturer's instructions. After incubation for 1 h at 37℃, the resuspended samples were filtered through a 70-µm MACS SmartStrainer (Miltenyi Biotec, Cat# 130-098-462) into RPMI-1640 medium (Corning, Inc. Corning, NY, USA) supplemented with 10% fetal bovine serum (Biowest, Riverside, MO, USA) and centrifuged at 300 ×g for 10 min.
Single-cell RNA and TCR libraries were generated using the Chromium controller in accordance with the 10x Chromium Next GEM Single Cell 5-v2_CellSurfaceProtein_UserGuide (CG000330). Cell suspensions were initially diluted with nuclease-free water to a target concentration of 10,000 cells. These suspensions were then combined with the master mix, Single Cell 5′ Gel Beads, and Partitioning Oil, and loaded into a Next GEM Chip K. Within the droplets, RNA transcripts from individual cells were barcoded and reverse-transcribed. The resulting cDNA was pooled and subjected to PCR enrichment. Following amplification, the cDNA was size-selected to generate three distinct library types: 5ʹ Gene Expression, V(D)J Enriched, and Cell Surface Protein. For the Cell Surface Protein Library, the cDNA pool underwent further enrichment using index PCR. The V(D)J Enriched Library required two rounds of amplification with specific primers. The 5’ Gene Expression Library was processed through end repair, addition of a single ‘A’ base, adapter ligation, and subsequent purification and PCR enrichment. Quantification of the purified libraries was performed using qPCR as outlined in the qPCR Quantification Protocol Guide (KAPA), and quality assessment was conducted using the Agilent Technologies 4200 TapeStation. Finally, sequencing was carried out on the HiSeq platform (Illumina) according to the read length specifications provided in the user guide. Single-cell ATAC Libraries were generated using the Chromium controller in accordance with the 10x Single Cell ATAC protocol (CG000168). Initially, nuclei were isolated and incubated with Transposase in a Transposition Mix. These transposed nuclei were then combined with master mix, Single Cell ATAC gel beads, and Partitioning Oil in a Chip E, where DNA fragments are barcoded in droplets during thermal incubation. The resulting barcoded DNA fragments were pooled and underwent sample index PCR. Quantification of the purified libraries was performed using qPCR as described in the qPCR Quantification Protocol Guide (KAPA), and quality assessment was conducted with the Agilent Technologies 4200 TapeStation. Finally, sequencing was carried out on the HiSeq platform (Illumina) following the read length specifications provided in the user guide.

value: Lung

value: Total

tag: tumor type

value: WT LUAD


title: dataset3_BMPi_LDN_no RFP

library_source: transcriptomic single cell


title: dataset3_BMPi_DMSO_RFP

value: DMSO


title: AL05, scATAC-seq

description: 10x Genomics

library_source: genomic

molecule: genomic DNA

value: ALK-positive LUAD


title: AL12, scRNA-seq

description: 10x Genomics


title: dataset3_BMPi_DMSO_no RFP


title: dataset2_positions_edge


title: AL06, scRNA-seq

description: 10x Genomics


title: AL08, scRNA-seq

description: 10x Genomics


title: dataset1_stages_rep4


title: dataset2_positions_base


title: dataset1_stages_rep3


title: AL04, scRNA-seq

description: 10x Genomics


title: dataset1_stages_rep2


title: AL05, scRNA-seq

description: 10x Genomics


title: MCF-7 PR-3 cells


title: dataset1_stages_rep1


title: AL03, scRNA-seq

description: 10x Genomics


title: AL02, scTCR-seq

description: 10x Genomics


title: mRNA_ded1-ΔN_Rap_3

city: Bethesda

first: Alan

middle: G

last: Hinnebusch

state: Maryland

address: Building 6, 6 Center Drive, Room  233

department: SNCGE

institute: NICHD

data_processing:
For ribo-seq samples, Fastq records are trimmed with fastxtoolkit (version 0.0.14) to remove adapters sequences. rRNA sequence was removed with Bowtie2 (version 2-2.3.5.1) then mapped to yeast genome (sacCer3) with tophat (version 2.1.1). Perfect reads were extracted with samtools (version 1.9) for downstream analysis. Normalized wiggle files and reads counts are generated with RiboSeq tools (https://github.com/hzhanghenry/RiboProR). For RNA-seq, the same protocol mentioned above for ribo-seq analysis was followed.
Assembly: sacCer3
Supplementary files format and content: Processed data (txt) files contain raw reads for each file. For Ribo and parallel RNA-Sequencing, each file contains five columns providing: systemmatic gene name (Gene_ID), total reads (trx), reads in CDS, reads in 5' UTR and reads in 3' UTR.

organism: Saccharomyces cerevisiae

source_name: BY4741 H5437 [MATa his3Δ1 leu2Δ0 lys2Δ0 met15Δ0 ura3Δ0 ded1Δ::kanMX4 pSG34 (ded1-Δ2–90-myc LEU2)]

growth_protocol: Yeast cells were generally grown to an OD600 of 0.4-0.5  in YPD medium at 30°C. They were then grown further for 2 hr with or without rapamycin (200ng).

extract_protocol: For RNA-seq library preparation, total RNA was extracted and purified from aliquots of the same snapped-frozen cells described above using hot phenol-chloroform extraction. Libraries for mRNA-Seq were prepared by the NHLBI DNA Sequencing and Genomics Core at NIH (Bethesda, MD). Illumina TruSeq stranded mRNA kits were utilized, followed by sequencing with SR100 to prepare libraries from total RNA.

treatment_protocol: Cells were treated with 200 ng/mL rapamycin for 2 hours prior to harvesting.

value: Whole cells


title: mRNA_ded1-ΔN_2

treatment_protocol: No additional treatment


title: AL02, scRNA-seq

description: 10x Genomics


title: RNAseq HT115 treated with M60

city: Boston

first: Zhixin

last: Li

state: Massachusetts

address: 450 Brookline Avenue, D742

institute: Dana-Farber cancer institute

data_processing:
Raw sequence quality was assessed using fastp v0.23.4
More than 35 million reads of each RNA-seq sample were aligned to human genome assembly GRCh38 using STAR v2.7.11
Only unique alignments to the genome were allowed. Read counts for each gene is generate by RSEM v1.3.3
Assembly: hg38
Supplementary files format and content: Rdata that includes the raw count, scaled CPM value and meta data of each sample

growth_protocol: All cell lines were maintained at 37 °C with 5% CO2. The human colorectal cancer cell lines (HT115, HT29 (HTB-38) and LS180 (CL-187)) and HEK293T were obtained from CCLE core facility at the Broad Institute, MIT and used at early passage for the experiments. Cells were maintained in DMEM medium supplemented with 10% FBS and 1% penicillin/streptomycin. Mycoplasma testing was performed every 3 months and found to be negative on each check.

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen 74004) and cDNA was synthesized using the iScriptTM Reverse Transcription Supermix for RT-qPCR (Bio-Rad 1708840).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq library prep Kit following manufacturer's protocols.

treatment_protocol: Cells were treated by either DMSO, M60a 2 µM, M60i 2 µM, and Romidepsin 0.005 nM for 48 hours.

tag: disease state

value: colorectal cancer (CRC)

value: epithelial cells

value: MRK60 48 hours


title: mRNA_ded1-ΔN_Rap_2


title: RNAseq LS180 treated with DMSO

value: DMSO 48 hours


title: mRNA_ded1-ΔN_Rap_1


title: AL11, scRNA-seq

description: 10x Genomics


title: mRNA_ded1-ΔN_1


title: AL10, scRNA-seq

description: 10x Genomics


title: RNAseq HT115 treated with DMSO


title: mRNA_ded1-ΔC_Rap_3

source_name: BY4741 H5438 [MATa his3Δ1 leu2Δ0 lys2Δ0 met15Δ0 ura3Δ0 ded1Δ::kanMX4 pSG35 (ded1-Δ562–604-myc LEU2)]


title: RNAseq LS180 treated with M60


title: human cells sampling at carnegie stage 10

city: Beijing

first: Zhengyang

last: Xu

address: 8th Dongda street, Fengtai district

country: China

institute: Fifth Medical  Center of Chinese PLA General Hospital,

data_processing:
The raw data were aligned to the Mmul_10 and hg19 reference genome using cellranger count (Version 3.0), and the hashed cells were demultiplexed using HTODemux function in Seurat 3, the cells aligned to doublet and negative group were removed from further analysis.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every  cell

molecule: polyA RNA

source_name: human embryonic cs 10

extract_protocol: Single-cell RNA-seq library was prepared and performed on the Chromium platform(10X Genomics), using the single cell expression 3’ profiling chemistry combined with cell hashing. Cell-hashing antibody (HTO)-labeled cells from 2~3 tissues were pooled together and washed with RPMI-1640 immediately before loading on the 10X controller.Then library was constructed following the manufacturer’s protocol, with some additional steps for the amplification of HTO barcodes.

tag: developmental stage

value: Week 4


title: mRNA_ded1-ΔC_Rap_2


title: human cells sampling at carnegie stage 15

source_name: human embryonic cs 15

value: Week 5


title: mRNA_ded1-ΔC_Rap_1


title: CA235, WT

first: Ana

middle: B

last: Villasenor Altamirano

state: MA

address: 60 Fenwood Rd

department: Pulmonary and Critical Care

institute: Brigham and Women's Hospital, Harvard Medical School

data_processing:
Data were preprocessed with Cell Eanger and reads demultiplexed with DemuxEM. Reads were aligned to mm10 mouse reference genome.  Nuclei with genes lower than 350 or genes in less than 10 nulei were removed then we followed Seurat pipeline
Assembly: mm10
Supplementary files format and content: H5ad files with raw counts and logcounts

organism: Mus musculus

source_name: Hippocampus brain

extract_protocol:
By using a biopsy punch,  fresh-frozen hippocampal brain region from mice were placed into lysis buffer and dounced in pestles to extract the nuclei. Then, the nuclei were washed, incubated on ice, resuspended in buffer and blocked with albumin for being hased using biolegend antibodies. Samples were pooled and loaded onto Chromium single-cell V3 3'chip (10x Genomics)
Nuclei were hashed and pooled and loaded based onto a Chromium single-cell V3 3'chip (10x Genomics) following manufater's protocol for GEM formation

value: Hippocampus brain

value: Whole tissue

value: Cardiac arrest induced with potassium chloride


title: CA218, WT


title: mRNA_ded1-ΔC_3


title: mRNA_ded1-ΔC_2


title: mRNA_ded1-ΔC_1


title: CA223, CD1d KO


title: mES cells, mt2, d3 [RNA-Seq]

city: Paris

first: Guillaume

last: Velasco

address: 35 rue Hélène Brion

department: UMR7216 Epigenetics and Cell Fate

country: France

institute: Université Paris Cité

data_processing:
Paired end (2 × 75) sequencing was performed on an Illumina NextSeq 500 platform, demultiplexing and quality control were performed with the AOZAN software (based on bcl2fastq v2.20 and FastQC modules / v0.11.5).
The quality of raw data has been evaluated with FastQC. Poor quality sequences have been trimmed or removed with Trimmomatic software. Star v2.5.3a has been used to align reads on reference genome (mm10/hg38) using standard options.
Quantification of gene and isoform abundances has been done with rsem 1.2.28, prior to normalisation on library size with DESEq2 bioconductor R package. Finally, differential analysis has been conducted with edgeR bioconductor R package.
Assembly: mm10 or hg38
Supplementary files format and content: bigWig files for visualization of RNA-seq tracks

source_name: ESCs

growth_protocol: mESCs  were maintained in the absence of feeder cells, on plates coated with 1x Laminin in serum-free 2i medium containing  Dulbecco’s modified Eagle’s medium (DMEM) F12 Glutamax supplemented with  50% Neurobasal medium , N2 and B27 Supplements, penicillin/streptomycin, non-essential amino acids, 2-mercaptoethanol, CHIR99201, PD032552 inhibitors and Leukemia Inhibitory Factor. Cells were passaged every two days and maintained at 37ºC with 8% CO2 in a humidified chamber. Human Lymphoblastoid Cell Lines (LCLs) from healthy donors and ICF2 patients were cultured in RPMI 1640 supplemented with 15% FCS and antibiotics.

extract_protocol:
Total RNAs from cell lines were isolated using TRI Reagent according to manufacturer’s instructions. Contaminant genomic DNA was eliminated with TURBO DNA-free Kit . RNA quality was verified using the Bioanalyzer RNA 6000 Nano kit.
The libraries were prepared following the TruSeq Stranded Total RNA protocol from Illumina, starting from 1 µg of high-quality total RNA (RIN > 7)

treatment_protocol: For in vitro differentiation, mESCs were grown in bacteriological Petri dish with differentiation medium containing 25% Advanced DMEM, 25% DMEM/F12 GlutaMAX, 50% Neurobasal medium, penicilline/streptavidin, β-mercatoethanol and 11% of knock out serum, at 37ºC with 5% CO2. The differentiation medium was changed every day and embryoid bodies were collected by centrifugation and resuspended in fresh medium.

value: ESCs

value: embryonic stem cells

value: ZBTB24 mutant

value: ESCs differentiation

tag: time

value: Day 3

tag: strain

tag: Sex

value: Male


title: CA207, CD1d KO


title: mRNA_WT Ded1_Rap_3

source_name: BY4741 H5404 [MATa his3Δ1 leu2Δ0 lys2Δ0 met15Δ0 ura3Δ0 ded1Δ::kanMX4 pSG1 (DED1-myc LEU2)]


title: mES cells, mt1, d3 [RNA-Seq]


title: mRNA_ded1-ΔN_3


title: mRNA_WT Ded1_Rap_1


title: mRNA_WT Ded1_3


title: mRNA_WT Ded1_2


title: pTh17_cells, ORAI 1/2/3 TKO, 48h, biorep3

city: Los Angeles

first: Yousang

last: Gwack

state: CA

address: 10833 Le Conte Ave

institute: Univeristy of California-Los Angeles

description:
Library name: Sample9
Column names in raw_count file: Orai1-2-3TKO-1-1-pTh17_S7, Orai1-2-3TKO-1-2-pTh17_S8, Orai1-2-3TKO-1-3-pTh17_S9 (technical replicates)

data_processing:
Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq v2.19.1.403 software
The reads were mapped by STAR 2.7.9a and read counts per gene were quantified using the mouse Ensembl GRCm39.105 GTF file.
In Partek Flow, read counts were normalized by CPM +1.0E-4.
Assembly: mm10
Supplementary files format and content: tab-delimited files include RAW and CPM normalized counts for each sample

source_name: Lymph nodes, Spleen

growth_protocol: Naive CD4+ T-cells were isolated and purified from wild-type (control), ORAI 2/3 DKO, and ORAI 1/2/3 TKO mice. Naïve CD4+ T cells were enriched by magnetic sorting from single-cell suspensions generated by mechanical disruption of spleens and lymph nodes of adult mice using MagniSort naïve CD4+ T cell enrichment kit (catalog # 8804-6824-74,ThermoFisher Scientific). For effector T cell differentiation, cells were stimulated with anti-CD3 antibody (1452C11, Bio X Cell) and anti-CD28 antibody (Clone 37.51, Bio X Cell) for 48 hours on a plate coated with rabbit anti-hamster antibody (MP Biomedicals). CD4 + CD25 - T cells were cultured with anti-IL-4 antibody (Peprotech) and 10 μg/ml anti-IFN-γ antibody, 30 ng/ml IL-6 (Peprotech), 10 ng/ml IL-23 (R&D Systems) and 10 ng/ml IL-1β (R&D Systems) for pathogenic Th17 differentiation and cultured in T cell medium. At 48 hrs post isolation, ~3 million control, ORAI 2/3 DKO and ORAI 1/2/3 TKO pathogenic Th17 cells were harvested in TriZol reagent (Invitrogen) for RNA preparation.

extract_protocol:
~3 million control and ORAI 2/3 DKO and ORAI 1/2/3 TKO Pathogenic  Th17 cells were harvested in TriZol reagent (Invitrogen) for RNA preparation.  3 Biological replicates per genotype were pooled after harvesting and divided into 3 technical replicates per condition. RNA was isolated using RNA purification kit (ThermoFisher Scientific), quantified and used for purification of mRNA, cDNA synthesis and library preparation using  KAPA stranded RNA seq-kit Sample following manufacturer’s instructions.
Libraries for RNA-Seq were prepared with KAPA Stranded mRNA-Seq Kit. The workflow consists of mRNA enrichment and fragmentation, first strand cDNA synthesis using random priming followed by second strand synthesis converting cDNA:RNA hybrid to double-stranded cDNA (dscDNA), and incorporates dUTP into the second cDNA strand. cDNA generation is followed by end repair to generate blunt ends, A-tailing, adaptor ligation and PCR amplification. Different adaptors were used for multiplexing samples in one lane. Sequencing was performed on Illumina Hiseq 3000 for a SE 1x50 run. Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq v2.19.1.403 software.

treatment_protocol: Wild-type vs ORAI 2/3 DKO vs ORAI 1/2/3 TKO

value: Lymph nodes, Spleen

tag: age

value: Female

value: ORAI 1/2/3 KO

tag: batch


title: mES cells, mt2, 2i [RNA-Seq]

value: Day 0


title: mES cells, WT2, d3 [RNA-Seq]

value: WT


title: mES cells, WT2, 2i [RNA-Seq]


title: pTh17_cells, ORAI 1/2/3 TKO, 48h, biorep1

description:
Library name: Sample7
Column names in raw_count file: Orai1-2-3TKO-1-1-pTh17_S7, Orai1-2-3TKO-1-2-pTh17_S8, Orai1-2-3TKO-1-3-pTh17_S9 (technical replicates)


title: mES cells, WT1, d3 [RNA-Seq]


title: mES cells, WT1, 2i [RNA-Seq]


title: pTh17_cells, ORAI 2/3 DKO, 48h, biorep3

description:
Library name: Sample6
Column names in raw_count file: Orai2-3DKO-1-pTh17_S4, Orai2-3DKO-2-pTH17_S5, Orai2-3DKO-3-pTH17_S6  (technical replicates)

value: ORAI 2/3 KO


title: mRNA_WT Ded1_1

value: Whole cells


title: Ribo_ded1-ΔN_Rap_3

description: Ribosome protected RNA 25-34 nt

data_processing:
For ribo-seq samples, Fastq records are trimmed with fastxtoolkit (version 0.0.14) to remove adapters sequences. rRNA sequence was removed with Bowtie2 (version 2-2.3.5.1) then mapped to yeast genome (sacCer3) with tophat (version 2.1.1). Perfect reads were extracted with samtools (version 1.9) for downstream analysis. Normalized wiggle files and reads counts are generated with RiboSeq tools (https://github.com/hzhanghenry/RiboProR). For RNA-seq, the same protocol mentioned above for ribo-seq analysis was followed.
Assembly: sacCer3
Supplementary files format and content: Processed data (txt) files contain raw reads for each file. For Ribo and parallel RNA-Sequencing, each file contains five columns providing: systemmatic gene name (Gene_ID), total reads (trx), reads in CDS, reads in 5' UTR and reads in 3' UTR.
Library strategy: Ribo-seq

extract_protocol: Ribosome profiling (Rnase I footprinting, size selection, RNA extraction, preadenylated linker ligation, reverse transcription, cDNA circularization, PCR amplification) was done as described in "“Reprogramming of translation in yeast cells impaired for ribosome recycling favors short, efficiently translated mRNAs” Gaikwad et al. eLife 2021;10:e64283.


title: pTh17_cells, ORAI 1/2/3 TKO, 48h, biorep2

description:
Library name: Sample8
Column names in raw_count file: Orai1-2-3TKO-1-1-pTh17_S7, Orai1-2-3TKO-1-2-pTh17_S8, Orai1-2-3TKO-1-3-pTh17_S9 (technical replicates)


title: Ribo_ded1-ΔN_Rap_2

description: Ribosome protected RNA 25-34 nt


title: mES cells, WT2, d3, ZBTB24

data_processing:
Sequencing was done using a NextSeq 500 instrument (Illumina) in paired-end mode (2x75 cycles). After sequencing, a primary analysis based on AOZAN software  was applied to demultiplex and control the quality of the raw data (based on bcl2fastq v2.20 and FastQC modules / v0.11.5).
Quality of raw data has been evaluated with FastQC. Poor quality sequences have been trimmed or removed with Trimmomatic software.
ChIP-seq reads were mapped to the reference genomes (mm10/hg38) using Bowtie2 v2.3.4.3 with the option -k 2. Then, peaks were called with Macs2 v2.2.4  using the input as control, an FDR of 0.01 and keeping all the duplicates. Peaks from multiple replicates were combined by taking regions covered by at least 2 replicates.
Peak annotation was performed with ChiPseeker v1.18.0  and Bedtools intersect v2.28.0 was used to annotate peaks with repeated elements obtained on the repeatmasker website, enhancers obtained on FANTOM5 and genome segmentation from ENCODE data.
Assembly: mm10 or hg38
Supplementary files format and content: bigWig files for visualization of ChIP-seq tracks

growth_protocol: mESCs  were maintained in the absence of feeder cells, on plates coated with 1x Laminin in serum-free 2i medium containing  Dulbecco’s modified Eagle’s medium (DMEM) F12 Glutamax supplemented with  50% Neurobasal medium , N2 and B27 Supplements, penicillin/streptomycin, non-essential amino acids, 2-mercaptoethanol, CHIR99201, PD032552 inhibitors and Leukemia Inhibitory Factor. Cells were passaged every two days and maintained at 37°C with 8% CO2 in a humidified chamber. Human Lymphoblastoid Cell Lines (LCLs) from healthy donors and ICF2 patients were cultured in RPMI 1640 supplemented with 15% FCS and antibiotics.

extract_protocol:
Mouse ESCs and LCLs were crosslinked with 1% formaldehyde for 10min at room temperature (RT) and the reaction was quenched by adding glycine at a final concentration of 0.125M for 5min at RT. Fixed cells were washed and adherent cells were harvested with phosphate-buffered saline (PBS). Cell nuclei were isolated using a cell lysis buffer (5mM Pipes pH8.0, 85mM KCl, 0.5% NP40, Complete protease inhibitor cocktail) for 20min, at 4°C. Nuclei were then pelleted by centrifugation and lysed in a nuclei lysis buffer (50mM Tris HCl pH8.1, 150mM NaCl, 10mM EDTA, 1% SDS, Complete protease inhibitor cocktail) for 20min, 4°C. Chromatin was subjected to sonication with a Bioruptor (Diagenode) yielding genomic DNA fragments with a bulk size of 150- 300 bp.
ChIP-seq libraries were prepared using the MicroPlex Library Preparation Kit v2 (Diagenode) according to the manufacturer’s protocol. After adapters ligation, fragments were amplified with Illumina primers for 10 cycles. Libraries were purified using AMPure XP beads protocol (Beckman Coulter) and quantified using the Qubit fluorometer (Thermo Fisher Scientific). Libraries’ size distribution was assessed using the Bioanalyzer High Sensitivity DNA chip (Agilent Technologies). Libraries were normalized and pooled at 2nM and spike-in PhiX Control v3 (Illumina) was added.

treatment_protocol: For in vitro differentiation, mESCs were grown in bacteriological Petri dish with differentiation medium containing 25% Advanced DMEM, 25% DMEM/F12 GlutaMAX, 50% Neurobasal medium, penicilline/streptavidin, β-mercatoethanol and 11% of knock out serum, at 37°C with 5% CO2. The differentiation medium was changed every day and embryoid bodies were collected by centrifugation and resuspended in fresh medium.

tag: chip antibody

value: ZBTB24 (MBL life science, #PM085)


title: mES cells, mt1, 2i [RNA-Seq]


title: pTh17_cells, ORAI 2/3 DKO, 48h, biorep1

description:
Library name: Sample4
Column names in raw_count file: Orai2-3DKO-1-pTh17_S4, Orai2-3DKO-2-pTH17_S5, Orai2-3DKO-3-pTH17_S6  (technical replicates)


title: pTh17_cells, ORAI 2/3 DKO, 48h, biorep2

description:
Library name: Sample5
Column names in raw_count file: Orai2-3DKO-1-pTh17_S4, Orai2-3DKO-2-pTH17_S5, Orai2-3DKO-3-pTH17_S6  (technical replicates)


title: mES cells, WT1, d3, ZBTB24


title: pTh17_cells, Control/Wild-type, 48h, biorep2

description:
Library name: Sample2
Column names in raw_count file: Control_1_pTh17_S1,  Control_2_pTh17_S2, Control_3_pTh17_S3 (technical replicates)

value: Wild-type


title: pTh17_cells, Control/Wild-type, 48h, biorep3

description:
Library name: Sample3
Column names in raw_count file: Control_1_pTh17_S1,  Control_2_pTh17_S2, Control_3_pTh17_S3 (technical replicates)


title: Ribo_ded1-ΔN_3

description: Ribosome protected RNA 25-34 nt


title: mES cells, WT2, 2i, ZBTB24


title: mRNA_WT Ded1_Rap_2


title: Ribo_ded1-ΔN_2

description: Ribosome protected RNA 25-34 nt


title: HUVEC_PK-45H exosome_48h_rep1

type: RNA

city: Hirosaki

first: Mitsuru

last: Chiba

state: Aomori

address: 66-1 Hon-cho

department: Graduate School of Health Sciences

country: Japan

institute: Hirosaki University

description: gene expression in HUVEC

hyb_protocol: Cy3-labeled cRNA (600 ng) was fragmented at 60°C for 30 minutes in a reaction volume of 25 μL containing 1× Agilent fragmentation buffer and 2× Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μL of 2× Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE microarray 8×60K (Agilent Technologies) for 17 hours at 65°C in a rotating hybridization oven (Agilent Technologies). After hybridization, microarrays were washed at room temperature for 1 min with GE Wash Buffer 1 (Agilent Technologies) and at 37°C for 1 min with GE Wash buffer 2 (Agilent Technologies), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the SureScan Microarray Scanner (G4900DA) (Agilent Technologies) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 2 μm high sensitivity, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5 (Agilent Technologies) using default parameters (protocol GE1_1105_Oct12 and Grid: 039494_D_F_20140813).

source_name: exosome_48 h

label_protocol: Cyanine 3 (Cy3)-labeled cRNA was synthesized from 40 ng of total RNA using a Low Input Quick Amp Labeling Kit (Agilent Technologies), according to the manufacturer’s instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The human pancreatic cancer cell line PK-45H (RCB1973) derived from liver metastasis was kindly provided by the Riken BRC as a part of the National Bio-Resource Project of the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan. HUVECs were purchased from PromoCell GmbH (Heidelberg, Germany). PK-45H cells were cultured in RPMI-1640 medium (Wako, Tokyo, Japan) supplemented with 10% foetal bovine serum (Thermo Fisher Scientific), 100 U/mL penicillin and 100 µg/mL streptomycin (Wako). HUVECs were cultured in Endothelial Cell Media 2 (PromoCell GmbH) at 37 °C under a humidified atmosphere with 5% CO2.

extract_protocol: Total RNAs from HUVECs treated or not with 10 ng/µL of exosomes released from PK-45H cells for 24 h or 48 h were extracted using Isogen II reagent (NipponGene, Tokyo, Japan). A NanoDrop spectrophotometer (NanoDrop Technologies) assessed the quality and concentration of total RNAs. All RNA samples demonstrated 260/280-nm absorbance ratios of 1.8–2.0. An Agilent 2100 Bioanalyzer and an Agilent RNA 6000 Pico Kit (Agilent Technologies) confirmed the peaks of total RNAs, following the manufacturer’s instructions.

treatment_protocol: The cell culture media of PK-45H cells were collected and exosomes were isolated by a multistep centrifugation protocol. Exosomes from cell culture medium were collected by ultracentrifugation. The collected exosomes were suspended in Dulbecco’s phosphate-buffered saline. HUVECs were treated or not with 10 ng/µL of exosomes released from PK-45H cells for 24 h or 48 h.

tag: gender

value: HUVEC


title: mES cells, WT1, 2i, ZBTB24


title: Ribo_ded1-ΔN_1

description: Ribosome protected RNA 25-34 nt


title: HUVEC_control_48h_rep1

description: gene expression in HUVEC

source_name: control_48 h


title: Ribo_ded1-ΔC_Rap_3

description: Ribosome protected RNA 25-34 nt


title: MYb11_WT, liquid, rep5

city: Kiel

first: Hinrich

last: Schulenburg

address: Am Botanischen Garten 9

department: Evolutionary Ecology and Genetics

country: Germany

institute: Kiel University

description:
Library name: Sample40
Column name in rpkm_allSamples.csv: WT_liquid_5_S44

data_processing:
Adapter trimming was achieved with Trimmomatic in paired-end mode (version 0.39, phred33, adaptersUsed=TruSeq3-PE-2.fa, seedMismatches=2, palindromeClipThreshold=30, simpleClipThreshold=10, minimumadapterlength =2, lengthHeadcrop=5, lengthMin=36).
Read mapping and read counting were performed with EDGE-pro (v1.3.1) set for paired-end reads.
Assembly: Reference genome (NZ_CP023272.1) and files for Pseudomonas lurida MYb11 (Pseudomonas_lurida_MYb11_6243.csv.gz) were obtained from Pseuomonas.com.
Supplementary files format and content: csv file contains rpkm values for all samples

organism: Pseudomonas lurida

source_name: Prokaryote

growth_protocol: Bacteria were cultured on tryptic soy agar (TSA; 20°C, 72 hours) and tryptic soy broth (TSB; 28°C, 150 rpm, overnight).

extract_protocol:
1 ml of liquid cultures were centrifuged at 6000 rpm for 5 min, and pellets or colonies were resuspended in 800 µl TRI-zol™ reagent (ThermoFisher), frozen and stored (-80°C). RNA was isolated using the Direct-zol RNA Miniprep Kit (Zymo Research).
RNA libraries for RNA-seq were prepeared using Illumina stranded total RNA library preparation.

treatment_protocol: For the liquid treatment, a starter culture was prepared in 50 ml Falcon tubes. 10 ml TSB were inoculated with 100 µl of a MYb11 overnight culture and cultivated (28°C, 150 rpm) to OD600=1.8. A single colony was taken from the TSA plates for the solid treatment.

value: Prokaryote

value: liquid


title: MYb11_WT, liquid, rep4

description:
Library name: Sample39
Column name in rpkm_allSamples.csv: WT_liquid_4_S43


title: MYb11_WT, liquid, rep3

description:
Library name: Sample38
Column name in rpkm_allSamples.csv: WT_liquid_3_S17


title: mES cells, WT1, d3, input

value: ESCs

value: embryonic stem cells


title: Ribo_ded1-ΔN_Rap_1

description: Ribosome protected RNA 25-34 nt


title: MYb11_WT, liquid, rep2

description:
Library name: Sample37
Column name in rpkm_allSamples.csv: WT_liquid_2_S46


title: mES cells, WT2, 2i, input

value: ESCs differentiation


title: HUVEC_control_24h_rep1

description: gene expression in HUVEC

source_name: control_24 h


title: mES cells, WT2, d3, input

value: Day 3


title: Ribo_ded1-ΔC_Rap_1

description: Ribosome protected RNA 25-34 nt


title: Ribo_ded1-ΔC_Rap_2

description: Ribosome protected RNA 25-34 nt


title: MYb11_WT, colony, rep2

description:
Library name: Sample32
Column name in rpkm_allSamples.csv: WT_colony_2_S51

value: colony


title: MYb11_WT, liquid, rep1

description:
Library name: Sample36
Column name in rpkm_allSamples.csv: WT_liquid_1_S40


title: MYb11_WT, colony, rep5

description:
Library name: Sample35
Column name in rpkm_allSamples.csv: WT_colony_5_S34


title: HUVEC_PK-45H exosome_24h_rep1

description: gene expression in HUVEC

source_name: exosome_24 h


title: MYb11_WT, colony, rep4

description:
Library name: Sample34
Column name in rpkm_allSamples.csv: WT_colony_4_S33


title: TGF_KD_CM3

city: Changsha

first: Yubin

last: Chen

state: Hunan

address: Furong Road

department: Department of Cardiovascular Surgery

institute: Xiangya Hospital, Central South University

description: Library name: samples12

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLCgenomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomicbenchwork (parameters- mismath cost. 2 insertion cost. 3 deletion cost. 3 length fraction.0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text flles include FPKM and counts values for each Sample

source_name: cardiac fibroblasts

growth_protocol: Primary mouse CFs were cultured in DMEM containing 10% FBS and 1% penicillin-streptomycin.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Oiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: CFs were starved for 12 h, then treated with different CM for 24 h.

value: cardiac fibroblasts

value: TGF-beta1 and CM of adipocyte infected with hsa-miR-550ay inhibition lentivirus


title: A3_3_CD09_G

city: Evanston

first: Jubao

last: Duan

state: IL

address: 1001 University Place

department: Center for Psychiatric Genetics

institute: NorthShore University HealthSystem

data_processing:
Raw fastq files (pair-end) were aligned to human GRCh38.p13 genome using STAR 2.7.11 with GENCODE 35 annotations.
Counts were collected from the output of each STAR run and merged into one count matrix
Assembly: hunan GRCh38.p14 (hg38)
Supplementary files format and content: FASTQ
Supplementary files format and content: tab-delimited text included raw counts per sample

source_name: iPS-derived microglia

growth_protocol: The hiPSCs were maintained in mTeSRPlus (StemCell #100-0276) with primocin (Invitrogen #ant-pm-1) on tissue culture plates coated with matrigel (Fisher Scientific #08-774-552) or geltrex (Fisher Scientific #A1413202) throughout the mutagenesis process. The Institutional Review Board (IRB) of NorthShore University HealthSystem approved study.

extract_protocol:
Total RNA was extracted using Qiagen RNEasy mini spin columns and the concentrations verified by NanoDrop
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. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.Sequencing was performed on NovaX with 2x150 bp paired read

treatment_protocol: The cell culture, DNA base editing/sgRNA transfection, and cell sorting for LoF mutagenesis were performed in batches, each containing 23 genes and a non-transfected control (NTC) on a 24-well plate format. The base editor system (pEF-AncBE4max, pEF-BFP, and pDT-sgRNA) contains a reporter gene that makes cells that have undergone C to T editing turn from blue to green . LipofectamineSTEM was used for cell transfection.  After cell transfection for 72 hrs, single hiPSC from the post-transfection culture were sorted into 96-well plates with one cell per well using a BD FACSAria Fusion Flow Cytometer in the presence of CEPT cocktail (1:10,000 chroman 1, emricasan, and transISRIB; 1:1,000 polyamine supplement) (Tristan et al., 2023). The sorted single cells were cultured on a 96-well plate with media changes every other day for 10-14 days until colonies appeared with an appropriate size to pick for Sanger sequencing genotyping.

value: iPS-derived microglia

value: microglia


title: A3_2_CD09_G


title: pTh17_cells, Control/Wild-type, 48h, biorep1

description:
Library name: Sample1
Column names in raw_count file: Control_1_pTh17_S1,  Control_2_pTh17_S2, Control_3_pTh17_S3 (technical replicates)

value: Lymph nodes, Spleen

value: Female


title: Ribo_ded1-ΔC_2

description: Ribosome protected RNA 25-34 nt

value: Whole cells


title: mES cells, WT1, 2i, input

value: WT

value: Day 0

value: Male


title: MYb11_WT, colony, rep1

description:
Library name: Sample31
Column name in rpkm_allSamples.csv: WT_colony_1_S15

value: Prokaryote


title: Ribo_ded1-ΔC_1

description: Ribosome protected RNA 25-34 nt


title: TGF_KD_CM2

description: Library name: samples11

value: TGF-beta1 and CM of adipocyte infected with hsa-miR-549ay inhibition lentivirus


title: A3_1_CD09_G


title: MYb11_wspF, liquid, rep5

description:
Library name: Sample30
Column name in rpkm_allSamples.csv: wspF_liquid_5_S24

value: liquid


title: A1_3_CD09_A


title: Ribo_WT Ded1_Rap_3

description: Ribosome protected RNA 25-34 nt


title: TGF_KD_CM1

description: Library name: samples10

value: TGF-beta1 and CM of adipocyte infected with hsa-miR-548ay inhibition lentivirus


title: Ribo_ded1-ΔC_3

description: Ribosome protected RNA 25-34 nt


title: MYb11_WT, colony, rep3

description:
Library name: Sample33
Column name in rpkm_allSamples.csv: WT_colony_3_S47


title: MYb11_wspF, liquid, rep4

description:
Library name: Sample29
Column name in rpkm_allSamples.csv: wspF_liquid_4_S38


title: TGF_VEC_CM2

description: Library name: samples8

value: TGF-beta1 and CM of adipocyte infected with vector lentivirus


title: Ribo_WT Ded1_Rap_2

description: Ribosome protected RNA 25-34 nt


title: Ribo_WT Ded1_Rap_1

description: Ribosome protected RNA 25-34 nt


title: MYb11_wspF, liquid, rep2

description:
Library name: Sample27
Column name in rpkm_allSamples.csv: wspF_liquid_2_S31


title: MYb11_wspF, liquid, rep3

description:
Library name: Sample28
Column name in rpkm_allSamples.csv: wspF_liquid_3_S42


title: A1_2_CD09_A


title: G3_3_CD04_A


title: Ribo_WT Ded1_3

description: Ribosome protected RNA 25-34 nt


title: TGF_VEC_CM1

description: Library name: samples7


title: OE_CM3

description: Library name: samples6

value: CM of adipocyte infected with hsa-miR-550ay overexpression lentivirus


title: G3_2_CD04_A


title: MYb11_wspF, liquid, rep1

description:
Library name: Sample26
Column name in rpkm_allSamples.csv: wspF_liquid_1_S35


title: Ribo_WT Ded1_2

description: Ribosome protected RNA 25-34 nt


title: MYb11_wspF, colony, rep5

description:
Library name: Sample25
Column name in rpkm_allSamples.csv: wspF_colony_5_S49

value: colony


title: Ribo_WT Ded1_1

description: Ribosome protected RNA 25-34 nt


title: MS67, H3K4me3

city: Durham

first: Yiran

last: Guo

state: North Carolina

address: 3 Genome Ct

institute: Duke University

data_processing:
Fastq files were mapped to the reference genome (GRCh38/hg38 for human genome GRCm38/mm10 for mouse genome) using bowtie2.3.5. The non-primary alignment, PCR duplicates and blacklist regions were removed by Samtools (v1.9), Picard “MarkDuplicates” function (ver 2.20.4), and bedtools (v2.28.0), respectively. Peak calling was performed using MACS2 (macs2 callpeak -f BAMPE -g mm --keep-dup 1). Distribution of peaks was calculated by “annotatePeak” function of HOMER (Hypergeometric Optimization of Motif Enrichment). Deeptools (v3.3.0) was used to make bigwig files (--normalizeUsing RPKM), heatmaps, and averaged plotting of CUT&Tag signals. Genomic binding profiles were generated using the deepTools “bamCompare” functions.
To calibrate ChIP-seq and CUT&Tag signals, the spike-in control genome was used to quantitatively compare the genomic profiles, and a scale factor is calculated based on reads of each sample mapped to sample genome and spike-in genome, which is used for normalization.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: bone marrow

growth_protocol: 748T murine leukemia cell lines were maintained in Iscove’s modified Dulbecco’s medium (IMDM) supplemented with 15–20% fetal bovine serum (FBS), 100 mM L-glutamine and 100 µg/mL penicillin/streptomycin.

extract_protocol: 100,000 murine leukemia cells, added with 1% of spike-in control cells (human 293 cells stably expressed with GFP-H2B), were harvested and centrifuged for 3 min at 600g at room temperature. Pellets were washed with Wash buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1× Protease inhibitor cocktail). Concanavalin A coated magnetic beads were activated in Beads Activation buffer (20 mM HEPES, pH 7.9, 10 mM KCl, 1 mM CaCl2 and 1 mM MnCl2) and 10 µl of activated beads were added per sample and incubated at room temperature for 10 min. The unbound supernatant was removed, and bead-bound cells were resuspended in Digitonin 150 buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1× Protease inhibitor cocktail; 0.01% Digitonin) containing 2 mM EDTA and a 1:50 dilution of the appropriate primary antibody. Primary antibody incubation was performed on a rotating platform overnight at 4 °C. The next day, samples were incubated with appropriate secondary antibody (diluted 1:50 in Digitonin 150 buffer) at room temperature for 30 min. Cells were washed using the magnet stand with Digitonin 150 buffer to remove unbound antibodies. A 1:200 dilution of pA-Tn5 adapter complex was prepared in Digitonin 300 buffer (0.01% Digitonin, 20 mM HEPES, pH 7.5, 300 mM NaCl, 0.5 mM Spermidine, 1× Protease inhibitor cocktail). After added to the sample, sample was incubated at RT for 1 h. Samples were washed in Digitonin 300 buffer to remove unbound pA-Tn5 protein. Next, cells were resuspended in Tagmentation buffer (10 mM MgCl2 in Digitonin 300 buffer) and incubated at 37 °C for 1 h. To stop tagmentation, 2.25 µL of 0.5 M EDTA, 2.75 µL of 10% SDS and 0.5 µL of 20 mg/mL Proteinase K was added to 50 µL of sample, which was incubated at 55 °C for 30 min, and then at 70 °C for 20 min to inactivate Proteinase K. DNA was purified with Ampure XP beads following manufacture’s instruction and eluted in 10 mM Tris pH 8.0.  To amplify libraries, eluted DNA was mixed with a universal i5 and a uniquely barcoded i7 primer, with a different barcode for each sample and 2x PCR master mix. Post-PCR clean-up was performed using 0.9x volume of Ampure XP beads, and libraries were eluted in 30 µL 10 mM Tris pH 8.0. Sequencing was conducted using an Illumina Nextseq 550 High Output Kit v2.5.

value: bone marrow

value: precursor T-cell


title: OE_CM1

description: Library name: samples4

value: cardiac fibroblasts

value: CM of adipocyte infected with hsa-miR-548ay overexpression lentivirus


title: A5_2_CD04_G

value: iPS-derived microglia

value: microglia


title: MYb11_wspF, colony, rep3

description:
Library name: Sample23
Column name in rpkm_allSamples.csv: wspF_colony_3_S32


title: MS67, H3K27ac


title: MYb11_wspF, colony, rep2

description:
Library name: Sample22
Column name in rpkm_allSamples.csv: wspF_colony_2_S26


title: A1_1_CD09_A


title: MS67, Mll1


title: VEC_CM3

description: Library name: samples3

value: CM of adipocyte infected with vector lentivirus


title: A5_1_CD04_G


title: VEC_CM2

description: Library name: samples2


title: MS67, V5-NP23


title: MYb11_wspF, colony, rep1

description:
Library name: Sample21
Column name in rpkm_allSamples.csv: wspF_colony_1_S45


title: 24

city: New York

first: Matthew

last: Smith-Raska

state: NY

address: 1300 York Ave.

department: Pediatrics

institute: Weill Cornell Medicine

description:
Library name: Sample 12
oocyte small rna adjusted.xlsx

data_processing:
For each small RNA library, reads were mapped to rRNAs, miRbase, murine tRNAs, piRNA clusters, to Repeatmasker and Refseq using Bowtie 2.
Assembly: mm10
Supplementary files format and content: normalized small RNA reads (reads per million)

source_name: Oocyte

extract_protocol:
Oocytes were extracted from unstimulated ovaries manually.  Small RNAs were isolated using the PicoPure RNA Isolation kit (Thermo).
Library was constructed according to the NEXTFLEX Small RNA Sample Preparation protocol

value: Oocyte

value: Wild type from Khdc3-null grandfathers


title: MYb11_wspE, liquid, rep5

description:
Library name: Sample20
Column name in rpkm_allSamples.csv: wspE_liquid_5_S54


title: VEC_CM1

description: Library name: samples1


title: MYb11_wspE, liquid, rep4

description:
Library name: Sample19
Column name in rpkm_allSamples.csv: wspE_liquid_4_S48


title: DMSO, H3K4me3

value: DMSO


title: 23

description:
Library name: Sample 11
oocyte small rna adjusted.xlsx


title: OE_CM2

description: Library name: samples5

value: CM of adipocyte infected with hsa-miR-549ay overexpression lentivirus


title: MYb11_wspE, liquid, rep3

description:
Library name: Sample18
Column name in rpkm_allSamples.csv: wspE_liquid_3_S37

value: Prokaryote


title: A5_3_CD04_G


title: DMSO, Mll1


title: MYb11_wspE, liquid, rep2

description:
Library name: Sample17
Column name in rpkm_allSamples.csv: wspE_liquid_2_S16

value: liquid


title: 22

description:
Library name: Sample 10
oocyte small rna adjusted.xlsx


title: MYb11_wspF, colony, rep4

description:
Library name: Sample24
Column name in rpkm_allSamples.csv: wspF_colony_4_S18


title: DMSO, V5-NP23


title: 21

description:
Library name: Sample 9
oocyte small rna adjusted.xlsx


title: mpk4-2

first: Jen

last: Sheen

address: 185 Cambridge st. CPZN7620

department: Molecular Biology

institute: Massachusetts General Hospital

data_processing:
Total RNA (500 ng) was used for making the library. The library was prepared using Illumina TruSeq RNA sample Prep Kit v2 according to the manufacture's  guidelines. The libraries were sequenced for 50 cycles on an Illumina HiSeq 2500 rapid mode using two lanes of a flow cell.
51 nucleotide reads from single-end sequncing in fastq files were aligned to the Arabidopsis genome, TAIR10, with the Tophat aligner.
htseq-count from the HTSeq python library was used to determine numbers of reads per gene
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files contain the counts table output of HTseq analysis

organism: Arabidopsis thaliana

source_name: Adult plants (shoot)

growth_protocol: Plants were grown in a chamber with 12 h light /12 h dark (75 µmol m-2 s-1) at 23°C/20°C light/dark temperature, and 65 % relative humidity.  For experimental design 1) and 2), seedlings were grown in 0.5 X MS liquid media, 0.5 % Sucrose, pH5.8 in 6-well tissue culture plate (Falcon, USA) (8 seedlings per ml per well). For experimental design 3), plants  were grown in Jiffy Quick Soil Mix (QSM) pellets (Jiffy) (one plant per jiffy pellet).

extract_protocol:
Eight seedlings were pooled and total RNA was isolated using Trizol (Invitrogen).
The library was prepared for sequencing using standrad protocols of Illumina TruSeq RNA sample Prep Kit v2.

treatment_protocol: For experimental design 1) 7-d-old wild type seedlings grown in liquid medium were treated with 100nM flg22 and harvested at various time points. For experimental design 2) 7-d-old seedlings of wild type, impk36, and impk4 grown in liquid medium was pretreated with 0.1 % DMSO (Mock treatment) or 10 uM 3MBiP for 15 min. Then various stimuli signals (2 nM flg22 peptide, 100 nM pep3 peptide, 20 uM ABA, 50 uM MeJA, mechanical wounding by forceps, 40W UVB, 10 mM H2O2) were applied and incubated for 1 h before harvest. For experimental design 3) 4-week-old plants were sprayed with 1 % DMSO or 100 uM 3MBiP and harvested at various time points.

value: shoot

value: no treatment


title: MYb11_wspE, liquid, rep1

description:
Library name: Sample16
Column name in rpkm_allSamples.csv: wspE_liquid_1_S30


title: 1% water agar (WAT) hyphal knot + 7.5h; replica 3

city: Szeged

first: Botond

last: Hegedüs

state: Csongrád-Csanád

address: Temesvári krt. 62

department: Institute of Biochemistry

country: Hungary

institute: Biological Research Center

description:
Library name: HK_plus_7_5_3
QuantSeq 3′ mRNA-Seq library

data_processing:
The raw reads were trimmed using the BBduk.sh script from BBtools 38.92 and then mapped to the reference genome using STAR version 2.6.1a_08-27. The trimming and mapping parameters were set according to the manufacturer’s recommendations (https://www.lexogen.com/quantseq-data-analysis/).
The number of reads overlapping the transcript annotations was determined using the featureCounts function of the Rsubread package version 2.6.4
Assembly: CopciAB_V2_genome.fasta
Supplementary files format and content: Genome sequence of the Corinopsis cinerea AmutBmut V2 strain used for read alignment (CopciAB_V2_genome.fasta).
Supplementary files format and content: GTF-formatted annotation file of the Coprinopsis cinerea AmutBmut V2 strain, which was used to determine the read count values (CopciAB_V2_annotation.gtf).
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample (CopciAB_V2_rawCounts.tsv)
Supplementary files format and content: Text file includes detailed description of the growth conditions (growth_protocol.pdf).

organism: Coprinopsis cinerea AmutBmut pab1-1

source_name: Hyphal knot

growth_protocol: A detailed description of the growth conditions can be found in the document growth_protocol.pdf

extract_protocol:
RNA was extracted using Quick-RNA Miniprep kit (Zymo Research, USA, catalog number: R1054), following the manufacturer’s instructions.
The libraries were generated using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, Vienna). To begin, 100 ng of total RNA was used as input for first strand cDNA generation with an oligo-dT primer, followed by RNA removal. Next, second strand synthesis was initiated with random priming and the resulting products were purified with magnetic beads. Finally, the libraries were amplified and barcoded using PCR. The Agilent 4200 TapeStation (Agilent) was used to assess all libraries for the formation of adapter dimers during PCR. The QuantSeq libraries were sequenced on the Illumina NextSeq550 platform, producing 75 bp single-end reads.

value: Hyphal knot


title: 14

description:
Library name: Sample 8
oocyte small rna adjusted.xlsx


title: MYb11_wspE, colony, rep5

description:
Library name: Sample15
Column name in rpkm_allSamples.csv: wspE_colony_5_S39

value: colony


title: 1% water agar (WAT) hyphal knot + 7.5h; replica 2

description:
Library name: HK_plus_7_5_2
QuantSeq 3′ mRNA-Seq library


title: mpk4-1


title: 13

description:
Library name: Sample 7
oocyte small rna adjusted.xlsx


title: MYb11_wspE, colony, rep4

description:
Library name: Sample14
Column name in rpkm_allSamples.csv: wspE_colony_4_S53


title: impk4_3MBiP_24h-3

value: 100 uM 3MBiP


title: DMSO, H3K27ac

value: bone marrow

value: precursor T-cell


title: 12

description:
Library name: Sample 6
oocyte small rna adjusted.xlsx


title: TGF_VEC_CM3

description: Library name: samples9

value: cardiac fibroblasts

value: TGF-beta1 and CM of adipocyte infected with vector lentivirus


title: 11

description:
Library name: Sample 5
oocyte small rna adjusted.xlsx


title: MYb11_wspE, colony, rep3

description:
Library name: Sample13
Column name in rpkm_allSamples.csv: wspE_colony_3_S52


title: MYb11_wspE, colony, rep2

description:
Library name: Sample12
Column name in rpkm_allSamples.csv: wspE_colony_2_S21


title: mpk4-3


title: 20

description:
Library name: Sample 4
oocyte small rna adjusted.xlsx

value: Wild type from wild type ancestors


title: impk4_3MBiP_24h-1


title: impk4_3MBiP_12h-3


title: 1% water agar (WAT) hyphal knot ; replica 3

description:
Library name: HK_3
QuantSeq 3′ mRNA-Seq library


title: 1% water agar (WAT) hyphal knot ; replica 2

description:
Library name: HK_2
QuantSeq 3′ mRNA-Seq library


title: impk4_3MBiP_12h-2


title: MYb11_wspE, colony, rep1

description:
Library name: Sample11
Column name in rpkm_allSamples.csv: wspE_colony_1_S50


title: 1% water agar (WAT) hyphal knot ; replica 1

description:
Library name: HK_1
QuantSeq 3′ mRNA-Seq library


title: MYb11_rph, liquid, rep5

description:
Library name: Sample10
Column name in rpkm_allSamples.csv: rph_liquid_5_S29


title: 1% water agar (WAT) hyphal knot - 7.5h; replica 3

description:
Library name: a_7_5_3
QuantSeq 3′ mRNA-Seq library


title: 16

description:
Library name: Sample 2
oocyte small rna adjusted.xlsx


title: impk4_3MBiP_12h-1


title: MYb11_rph, liquid, rep4

description:
Library name: Sample9
Column name in rpkm_allSamples.csv: rph_liquid_4_S23


title: 1% water agar (WAT) hyphal knot + 7.5h; replica 1

description:
Library name: HK_plus_7_5_1
QuantSeq 3′ mRNA-Seq library


title: 15

description:
Library name: Sample 1
oocyte small rna adjusted.xlsx


title: MYb11_rph, liquid, rep3

description:
Library name: Sample8
Column name in rpkm_allSamples.csv: rph_liquid_3_S22


title: 1% water agar (WAT) hyphal knot - 7.5h; replica 2

description:
Library name: a_7_5_2
QuantSeq 3′ mRNA-Seq library


title: impk4_3MBiP_6h-3


title: 1% water agar (WAT) hyphal knot - 7.5h; replica 1

description:
Library name: a_7_5_1
QuantSeq 3′ mRNA-Seq library


title: Atg7-fl/fl;Cx3cr1-CreERT2_female_20mo_bio_rep3

city: St Louis

first: Zhangying

last: Cai

state: MO

address: 425 S Euclid Ave

institute: Washington University in St. Louis

description: Library name: KO3

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read.  RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32. Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.5.23.  Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 4.04.
Assembly: GRCm39
Supplementary files format and content: "all.gene_count.tsv" tab-delimed text file includes un-normalized gene counts of each sample

source_name: Brain

extract_protocol:
Cells were isolated from the cortex of 20-month-old mice (3 Atg7fl/fl, 3 Atg7ΔMG) and stained for CD45, CD11b and DAPI. Live CD45intCD11b+ microglia were FACS-sorted into RLT lysis buffer (provided in QIAGEN RNeasy Plus Micro Kit). More than 20k microglia were collected from each mouse. RNA was extracted by QIAGEN RNeasy Plus Micro Kit.
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 10ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags.

value: Brain

value: Microglia


title: impk4_3MBiP_6h-2


title: Atg7-fl/fl;Cx3cr1-CreERT2_female_20mo_bio_rep2

description: Library name: KO2


title: MYb11_rph, liquid, rep2

description:
Library name: Sample7
Column name in rpkm_allSamples.csv: rph_liquid_2_S36


title: 1% water agar (WAT) hyphal knot - 15h; replica 3

description:
Library name: a_15_3
QuantSeq 3′ mRNA-Seq library


title: 17

description:
Library name: Sample 3
oocyte small rna adjusted.xlsx

value: Oocyte


title: impk4_3MBiP_24h-2


title: Atg7-fl/fl;Cx3cr1-CreERT2_female_20mo_bio_rep1

description: Library name: KO1


title: impk4_3MBiP_6h-1


title: 1% water agar (WAT) hyphal knot - 15h; replica 2

description:
Library name: a_15_2
QuantSeq 3′ mRNA-Seq library


title: 1% water agar (WAT) hyphal knot - 15h; replica 1

description:
Library name: a_15_1
QuantSeq 3′ mRNA-Seq library


title: MYb11_rph, colony, rep5

description:
Library name: Sample5
Column name in rpkm_allSamples.csv: rph_colony_5_S19


title: impk4_3MBiP_3h-3


title: Atg7-fl/fl_female_20mo_bio_rep3

description: Library name: WT3


title: MYb11_rph, colony, rep4

description:
Library name: Sample4
Column name in rpkm_allSamples.csv: rph_colony_4_S28


title: impk4_3MBiP_3h-2


title: 1% water agar (WAT) hyphal knot - 22.5h; replica 3

description:
Library name: a_22_5_3
QuantSeq 3′ mRNA-Seq library


title: Atg7-fl/fl_female_20mo_bio_rep2

description: Library name: WT2


title: MYb11_rph, colony, rep3

description:
Library name: Sample3
Column name in rpkm_allSamples.csv: rph_colony_3_S27


title: impk4_3MBiP_3h-1


title: Atg7-fl/fl_female_20mo_bio_rep1

description: Library name: WT1


title: impk4_Mock_24h-3

value: 1% DMSO


title: MYb11_rph, colony, rep2

description:
Library name: Sample2
Column name in rpkm_allSamples.csv: rph_colony_2_S41


title: 1% water agar (WAT) hyphal knot - 22.5h; replica 2

description:
Library name: a_22_5_2
QuantSeq 3′ mRNA-Seq library


title: 1% water agar (WAT) hyphal knot - 22.5h; replica 1

description:
Library name: a_22_5_1
QuantSeq 3′ mRNA-Seq library


title: Atg7-fl/fl; Cx3cr1-CreERT2; 5xFAD_bio_rep3

description: Library name: AD_KO3

data_processing:
Cell Ranger Software Suite (v6.0.1) from 10xGenomics was used for sample demultiplexing, barcode processing, and single-cell counting. The reference genome GRCm39 were used for alignment. Seurat (v4.0) package in R (v4.1.0) was used for downstream analysis.
Assembly: GRCm39
Supplementary files format and content: Output of CellRanger: filtered matrix of gene by cell expression, file with barcodes and file with expressed genes. Files are ready to be imported to Seurat package.

extract_protocol:
Mice were perfused with cold PBS, and cortices were dissociated. CD45+ cells were sorted into 0.04% BSA in PBS.
library construction is performed by using 10x Genomics Chromium Single Cell 3’ v3 Gene Expression Kit.

value: Atg7-fl/fl; Cx3cr1-CreERT2; 5xFAD


title: MYb11_rph, colony, rep1

description:
Library name: Sample1
Column name in rpkm_allSamples.csv: rph_colony_1_S20

value: Prokaryote


title: Atg7-fl/fl; Cx3cr1-CreERT2; 5xFAD_bio_rep2

description: Library name: AD_KO2


title: MYb11_rph, liquid, rep1

description:
Library name: Sample6
Column name in rpkm_allSamples.csv: rph_liquid_1_S25

value: liquid


title: impk4_Mock_24h-2

value: shoot


title: impk4_Mock_24h-1


title: 1% water agar (WAT) hyphal knot - 30h; replica 2

description:
Library name: a_30_2
QuantSeq 3′ mRNA-Seq library


title: ExM-MOK20015-WT3

city: Hinxton

first: MorPhiC

last: Consortium

address: Wellcome Genome Campus

country: United Kingdom

institute: EMBL-EBI

description:
Library name: ISL1_WT_3_GT23-12146_AACAGGTT-CTTGGTAT_S23
KOLF2.2J differentiated to the trophoblast lineage and favoring mesenchymal cell formation

data_processing:
Reads are aligned to the reference genome using STAR aligner, count matrices are built with Salmon
Assembly: GRCh38 gencode.v44.primary_assembly
Supplementary files format and content: study1_featureCounts.csv study1_genesCounts.csv study1_genesRawCounts.csv study1_genesTPM.csv study1_stats.csv study1_txCounts.csv study1_txRawCounts.csv study1_txTPM.csv

extract_protocol:
Arcturus PicoPure RNA isolation Kit Applied biosystems
KAPA RNA HyperPrep Kit with RiboErase (HMR) Illumina NovaSeq X

value: iPSC

tag: editing strategy

value: Not Applicable

tag: altered gene_symbol

value: Not applicable

tag: altered locus

value: day 6

tag: model system

value: fibroblast of villous mesenchyme (CL:0002558)

tag: condition

tag: parental cell_line


title: ExM-MOK20015-WT2

description:
Library name: ISL1_WT_2_GT23-12145_GCGCTCTA-GTCGGAGC_S29
KOLF2.2J differentiated to the trophoblast lineage and favoring mesenchymal cell formation

tag: cell line

tag: cell type


title: impk4_Mock_12h-3

tag: tissue

tag: genotype

tag: treatment


title: ExM-MOK20015-WT1

description:
Library name: ISL1_WT_1_GT23-12144_ATATCTCG-ACTAAGAT_S33
KOLF2.2J differentiated to the trophoblast lineage and favoring mesenchymal cell formation

tag: time


title: impk4_Mock_12h-2


title: impk4_Mock_12h-1


title: 1% water agar (WAT) hyphal knot - 30h; replica 1

description:
Library name: a_30_1
QuantSeq 3′ mRNA-Seq library

value: Hyphal knot


title: ExM-MOK20015P-D10

description:
Library name: ISL1_PTC_D10_GT23-12155_AGCTCGCT-GATTCTGC_S32
KOLF2.2J derived knockout cell line, ISL1 PTC, differentiated to the trophoblast lineage and favoring mesenchymal cell formation

value: Termination codon


title: Trichoderma grown with Copci, just meeting; control is DM_60h; replica 2

description:
Library name: CTMP_2
QuantSeq 3′ mRNA-Seq library

source_name: Vegetative mycelium

value: Vegetative mycelium


title: Atg7-fl/fl; Cx3cr1-CreERT2_bio_rep3

description: Library name: KO3

value: Atg7-fl/fl; Cx3cr1-CreERT2


title: ExM-MOK20015P-C12

description:
Library name: ISL1_PTC_C12_GT23-12154_GATCTATC-AGCCTCAT_S21
KOLF2.2J derived knockout cell line, ISL1 PTC, differentiated to the trophoblast lineage and favoring mesenchymal cell formation


title: Trichoderma grown with Copci, just meeting; control is DM_60h; replica 1

description:
Library name: CTMP_1
QuantSeq 3′ mRNA-Seq library


title: Atg7-fl/fl; Cx3cr1-CreERT2_bio_rep2

description: Library name: KO2

value: Brain


title: impk4_Mock_6h-3


title: impk4_Mock_6h-2


title: 1% water agar (WAT) hyphal knot - 30h; replica 3

description:
Library name: a_30_3
QuantSeq 3′ mRNA-Seq library


title: impk4_Mock_6h-1


title: Atg7-fl/fl; Cx3cr1-CreERT2_bio_rep1

description: Library name: KO1


title: ExM-MOK20015C-D01

description:
Library name: ISL1_CE_D01_GT23-12152_TGCGGCGT-TACCGAGG_S15
KOLF2.2J derived knockout cell line, ISL1 CE, differentiated to the trophoblast lineage and favoring mesenchymal cell formation

value: Critical exon


title: ExM-MOK20015P-A10

description:
Library name: ISL1_PTC_A10_GT23-12153_CATAATAC-CGTTAGAA_S20
KOLF2.2J derived knockout cell line, ISL1 PTC, differentiated to the trophoblast lineage and favoring mesenchymal cell formation


title: Atg7-fl/fl; Cx3cr1-CreERT2; 5xFAD_bio_rep1

description: Library name: AD_KO1


title: Trichoderma and Copci grown over each other for 60hrs; control is DM_108h; replica 2

description:
Library name: CTGT_2
QuantSeq 3′ mRNA-Seq library


title: impk4_Mock_3h-3


title: Trichoderma and Copci grown over each other for 60hrs; control is DM_108h; replica 1

description:
Library name: CTGT_1
QuantSeq 3′ mRNA-Seq library


title: Atg7-fl/fl_bio_rep2

description: Library name: WT2


title: Trichoderma grown with Copci, just meeting; control is DM_60h; replica 3

description:
Library name: CTMP_3
QuantSeq 3′ mRNA-Seq library


title: impk4_Mock_3h-2


title: ExM-MOK20015C-B05

description:
Library name: ISL1_CE_B05_GT23-12151_CACGAGCG-TGGCAGAT_S27
KOLF2.2J derived knockout cell line, ISL1 CE, differentiated to the trophoblast lineage and favoring mesenchymal cell formation


title: Voriconazole - antifungal, 0,5ug/ml for 48h; control is LoKo; replica 3

description:
Library name: Vor_3
QuantSeq 3′ mRNA-Seq library


title: Atg7-fl/fl_bio_rep3

description: Library name: WT3


title: Atg7-fl/fl; 5xFAD_bio_rep1

description: Library name: AD_WT1

value: Atg7-fl/fl; 5xFAD


title: ExM-MOK20015C-A06

description:
Library name: ISL1_CE_A06_GT23-12150_GTTCGCCG-CAATGAGC_S24
KOLF2.2J derived knockout cell line, ISL1 CE, differentiated to the trophoblast lineage and favoring mesenchymal cell formation


title: impk4_Mock_3h-1

value: 1% DMSO


title: Atg7-fl/fl; 5xFAD_bio_rep2

description: Library name: AD_WT2


title: Voriconazole - antifungal, 0,5ug/ml for 48h; control is LoKo; replica 2

description:
Library name: Vor_2
QuantSeq 3′ mRNA-Seq library


title: Atg7-fl/fl_bio_rep1

description: Library name: WT1


title: ExM-MOK20015W-F04

description:
Library name: ISL1_KO_F04_GT23-12149_TGGTGGCA-TTACAGGA_S17
KOLF2.2J derived knockout cell line, ISL1 KO, differentiated to the trophoblast lineage and favoring mesenchymal cell formation

value: Full coding length


title: impk4_Mock_0h-3

value: no treatment


title: WTPP_7

description: Library name: WTPP_7_S27

data_processing:
Adapter and quality trimming of sequencing reads were performed using cutadapt
HISAT2 was used for aligning sequncing reads against the mouse genome GRCm38
Gene quantification was done using feature-counts
DESeq2 was used for normalization and differential gene expression analysis
Assembly: GRCm38
Supplementary files format and content: excel file of log2 normalized counts

source_name: Liver

extract_protocol:
RNA was isolated using the Qiagen RNeasy Lipid Tissue RNA Kit
NEB Ultra II Directional RNA Library Prep

value: Liver

value: Hepatocyte

value: Wild Type descended frrom Khdc3-null grandfathers


title: Voriconazole - antifungal, 0,5ug/ml for 48h; control is LoKo; replica 1

description:
Library name: Vor_1
QuantSeq 3′ mRNA-Seq library


title: impk4_Mock_0h-2

value: shoot


title: Trichoderma and Copci grown over each other for 60hrs; control is DM_108h; replica 3

description:
Library name: CTGT_3
QuantSeq 3′ mRNA-Seq library


title: ExM-MOK20015W-D04

description:
Library name: ISL1_KO_D04_GT23-12148_CAACAATG-CCGTGAAG_S3
KOLF2.2J derived knockout cell line, ISL1 KO, differentiated to the trophoblast lineage and favoring mesenchymal cell formation

value: iPSC

value: Not applicable


title: Copper stress 2mM CuSO4 for 6h; control is LoKo; replica 3

description:
Library name: Cu_3
QuantSeq 3′ mRNA-Seq library


title: ExM-MOK20015W-A02

description:
Library name: ISL1_KO_A02_GT23-12147_GGTGAACC-TCCAACGC_S5
KOLF2.2J derived knockout cell line, ISL1 KO, differentiated to the trophoblast lineage and favoring mesenchymal cell formation

value: day 6

value: fibroblast of villous mesenchyme (CL:0002558)


title: WTPP_3

description: Library name: WTPP_3_S25


title: PrS-MOK20026-WT3

description:
Library name: PPARG_WT_3_GT23-11447_TAAGTGGT-GGCTTAAG_S55
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: Not Applicable

value: primitive syncytium


title: impk4_Mock_0h-1


title: Copper stress 2mM CuSO4 for 6h; control is LoKo; replica 2

description:
Library name: Cu_2
QuantSeq 3′ mRNA-Seq library

value: Vegetative mycelium


title: WTPP_2

description: Library name: WTPP_2_S24


title: PrS-MOK20026-WT2

description:
Library name: PPARG_WT_2_GT23-11446_CTACGACA-TTGGACTC_S42
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: Calcium stress 200mM Ca2+ for 24h; control is LoKo; replica 3

description:
Library name: Calci_3
QuantSeq 3′ mRNA-Seq library


title: PrS-MOK20026-WT1

description:
Library name: PPARG_WT_1_GT23-11445_TCGTAGTG-CCAAGTCT_S43
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: Copper stress 2mM CuSO4 for 6h; control is LoKo; replica 1

description:
Library name: Cu_1
QuantSeq 3′ mRNA-Seq library


title: B4_impk4_3MBiP_H2O2-2

source_name: Seedlings

value: Seedlings

value: 10 uM 3MBiP/ H2O2 10 mM


title: WTMM_8

description: Library name: WTMM_8_S22

value: Wild Type descended frrom Khdc3-null grandmothers


title: PrS-MOK20026P-E12

description:
Library name: PPARG_PTC_E12_GT23-11456_ACCTTGGC-ATGAGGCC_S45
KOLF2.2J derived knockout cell line, PPARG PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: Termination codon

value: PPARG


title: WTMM_9

description: Library name: WTMM_9_S23


title: WTMM_7

description: Library name: WTMM_7_S21


title: B4_impk4_3MBiP_H2O2-1


title: WTPP_6

description: Library name: WTPP_6_S26


title: Calcium stress 200mM Ca2+ for 24h; control is LoKo; replica 2

description:
Library name: Calci_2
QuantSeq 3′ mRNA-Seq library


title: Calcium stress 200mM Ca2+ for 24h; control is LoKo; replica 1

description:
Library name: Calci_1
QuantSeq 3′ mRNA-Seq library


title: PrS-MOK20026P-D10

description:
Library name: PPARG_PTC_D10_GT23-11455_GTTCCAAT-GCAGAATT_S63
KOLF2.2J derived knockout cell line, PPARG PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: B4_impk36_3MBiP_H2O2-3


title: WTMM_6

description: Library name: WTMM_6_S20


title: PrS-MOK20026P-A10

description:
Library name: PPARG_PTC_A10_GT23-11454_GCAATGCA-AACGTTCC_S54
KOLF2.2J derived knockout cell line, PPARG PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: Control for Calci, Cu and Vor; replica 3

description:
Library name: LoKo_3
QuantSeq 3′ mRNA-Seq library


title: 120

description: Library name: 120_S4

value: Wild Type (WT)


title: PrS-MOK20026C-H05

description:
Library name: PPARG_CE_H05_GT23-11453_ATGGCATG-GGTACCTT_S62
KOLF2.2J derived knockout cell line, PPARG CE, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: Critical exon


title: Control for Calci, Cu and Vor; replica 2

description:
Library name: LoKo_2
QuantSeq 3′ mRNA-Seq library


title: B4_impk4_3MBiP_H2O2-3


title: 118

description: Library name: 118_S3

value: Liver

value: Hepatocyte


title: 117

description: Library name: 117_S2


title: Control for Calci, Cu and Vor; replica 1

description:
Library name: LoKo_1
QuantSeq 3′ mRNA-Seq library


title: PrS-MOK20026C-G05

description:
Library name: PPARG_CE_G05_GT23-11452_GGAGCGTC-GCACGGAC_S48
KOLF2.2J derived knockout cell line, PPARG CE, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: B4_WT_3MBiP_H2O2-2

value: WIld type


title: B4_WT_3MBiP_H2O2-3


title: 116

description: Library name: 116_S1


title: KO_star-29

data_processing:
Adapter and quality trimming of sequencing reads were performed using cutadapt
HISAT2 was used for aligning sequncing reads against the mouse genome GRCm38
Gene quantification was done using feature-counts
DESeq2 was used for normalization and differential gene expression analysis
Assembly: GRCm38
Supplementary files format and content: tab-delimited file with normalized gene counts for each sample

extract_protocol:
RNA was isolated using the Qiagen RNeasy Lipid Tissue RNA Kit
Libraries were prepared with Illumina Stranded Total RNA Prep with Ribo-Zero Plus


title: B4_WT_3MBiP_H2O2-1


title: starvation response, colonies put from YMG to water agar; 24h; control is DM60h, replica 2

description:
Library name: SWAT24h_2
QuantSeq 3′ mRNA-Seq library


title: PrS-MOK20026W-H02

description:
Library name: PPARG_KO_H02_GT23-11450_GCGCAAGC-CGGCGTGA_S40
KOLF2.2J derived knockout cell line, PPARG KO, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: iPSC

value: Full coding length


title: starvation response, colonies put from YMG to water agar; 24h; control is DM60h, replica 3

description:
Library name: SWAT24h_3
QuantSeq 3′ mRNA-Seq library


title: B4_impk36_3MBiP_H2O2-2


title: B4_WT_3MBiP-3

value: 10 uM 3MBiP


title: starvation response, colonies put from YMG to water agar; 24h; control is DM60h, replica 1

description:
Library name: SWAT24h_1
QuantSeq 3′ mRNA-Seq library


title: starvation response, colonies put from YMG to water agar; 16h; control is DM60h, replica 3

description:
Library name: SWAT16h_3
QuantSeq 3′ mRNA-Seq library


title: PrS-MOK20026W-E02

description:
Library name: PPARG_KO_E02_GT23-11448_CGGACAAC-AATCCGGA_S60
KOLF2.2J derived knockout cell line, PPARG KO, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: day 6

value: Not applicable


title: B4_WT_3MBiP-2


title: KO_star-17


title: PrS-MOK20026W-G02

description:
Library name: PPARG_KO_G02_GT23-11449_ATATGGAT-TAATACAG_S50
KOLF2.2J derived knockout cell line, PPARG KO, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: primitive syncytium


title: KO_star-16


title: starvation response, colonies put from YMG to water agar; 16h; control is DM60h, replica 2

description:
Library name: SWAT16h_2
QuantSeq 3′ mRNA-Seq library

value: Vegetative mycelium


title: B4_WT_3MBiP-1

value: Seedlings


title: PrS-MOK20022-WT3

description:
Library name: GCM1_WT_3_GT23-11435_CTTGGTAT-GGACTTGG_S41
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: Not Applicable


title: B4_impk36_3MBiP_H2O2-1

value: 10 uM 3MBiP/ H2O2 10 mM


title: KO_star-14


title: KO_star-13


title: starvation response, colonies put from YMG to water agar; 16h; control is DM60h, replica 1

description:
Library name: SWAT16h_1
QuantSeq 3′ mRNA-Seq library


title: PrS-MOK20022-WT2

description:
Library name: GCM1_WT_2_GT23-11434_GTCGGAGC-TTATAACC_S46
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: starvation response, colonies put from YMG to water agar; 8h; control is DM60h, replica 3

description:
Library name: SWAT8h_3
QuantSeq 3′ mRNA-Seq library


title: KO_star-12


title: B3_impk4_3MBiP_UVB-2

value: 10 uM 3MBiP/ UVB


title: PrS-MOK20026C-D08

description:
Library name: PPARG_CE_D08_GT23-11451_AAGATACT-ATGTAAGT_S61
KOLF2.2J derived knockout cell line, PPARG CE, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: PPARG


title: PrS-MOK20022-WT1

description:
Library name: GCM1_WT_1_GT23-11433_ACTAAGAT-CCGCGGTT_S57
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: starvation response, colonies put from YMG to water agar; 8h; control is DM60h, replica 2

description:
Library name: SWAT8h_2
QuantSeq 3′ mRNA-Seq library


title: B3_impk4_3MBiP_UVB-1


title: PrS-MOK20022P-E11

description:
Library name: GCM1_PTC_E11_GT23-11444_GATTCTGC-CTCTCGTC_S47
KOLF2.2J derived knockout cell line, GCM1 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: Termination codon


title: B3_impk36_3MBiP_UVB-3


title: PrS-MOK20022P-B12

description:
Library name: GCM1_PTC_B12_GT23-11443_AGCCTCAT-TCTCTACT_S51
KOLF2.2J derived knockout cell line, GCM1 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: WT_star-34


title: B3_impk36_3MBiP_UVB-2


title: WT_star-33


title: PrS-MOK20022P-A11

description:
Library name: GCM1_PTC_A11_GT23-11442_CGTTAGAA-GACCTGAA_S52
KOLF2.2J derived knockout cell line, GCM1 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: PrS-MOK20022C-G08

description:
Library name: GCM1_CE_G8_GT23-11441_TACCGAGG-AGTTCAGG_S44
KOLF2.2J derived knockout cell line, GCM1 CE, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: Critical exon


title: B3_impk36_3MBiP_UVB-1


title: B3_impk4_3MBiP_UVB-3


title: B3_WT_3MBiP_UVB-3


title: starvation response, colonies put from YMG to water agar; 4h; control is DM60h, replica 3

description:
Library name: SWAT4h_3
QuantSeq 3′ mRNA-Seq library


title: WT_star-20

value: Liver


title: starvation response, colonies put from YMG to water agar; 4h; control is DM60h, replica 1

description:
Library name: SWAT4h_1
QuantSeq 3′ mRNA-Seq library


title: PrS-MOK20022C-G06

description:
Library name: GCM1_CE_G6_GT23-11440_AATGCCTC-TGGATCGA_S59
KOLF2.2J derived knockout cell line, GCM1 CE, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: B3_WT_3MBiP_UVB-2


title: KO-32

value: Hepatocyte

value: KO


title: starvation response, colonies put from YMG to water agar; 2h; control is DM60h, replica 3

description:
Library name: SWAT2h_3
QuantSeq 3′ mRNA-Seq library


title: KO-31


title: PrS-MOK20022W-G04

description:
Library name: GCM1_KO_G4_GT23-11438_TTACAGGA-GCTTGTCA_S53
KOLF2.2J derived knockout cell line, GCM1 KO, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: iPSC


title: B3_WT_3MBiP_UVB-1

value: WIld type


title: starvation response, colonies put from YMG to water agar; 2h; control is DM60h, replica 2

description:
Library name: SWAT2h_2
QuantSeq 3′ mRNA-Seq library


title: KO-30


title: B3_WT_3MBiP-3

value: 10 uM 3MBiP


title: starvation response, colonies put from YMG to water agar; 8h; control is DM60h, replica 1

description:
Library name: SWAT8h_1
QuantSeq 3′ mRNA-Seq library


title: starvation response, colonies put from YMG to water agar; 2h; control is DM60h, replica 1

description:
Library name: SWAT2h_1
QuantSeq 3′ mRNA-Seq library


title: PrS-MOK20022W-E04

description:
Library name: GCM1_KO_E4_GT23-11437_CCGTGAAG-ATCCACTG_S56
KOLF2.2J derived knockout cell line, GCM1 KO, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: Full coding length

value: day 6


title: WT-28

value: WT


title: B3_WT_3MBiP-2


title: PrS-MOK20022W-C01

description:
Library name: GCM1_KO_C1_GT23-11436_TCCAACGC-AAGTCCAA_S58
KOLF2.2J derived knockout cell line, GCM1 KO, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: primitive syncytium

value: Not applicable


title: Mycelium was cut with a knife, incubated for 3h; control is DM_84h; replica 3

description:
Library name: Scratchy_3
QuantSeq 3′ mRNA-Seq library

value: Vegetative mycelium


title: WT_star-21


title: PrS-MOK20017-WT

description:
Library name: KOLF2_FOSB_1_GT23-10493_GACCTGAA-CTCACCAA_S32
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: Not Applicable


title: B3_WT_3MBiP-1

value: Seedlings


title: starvation response, colonies put from YMG to water agar; 4h; control is DM60h, replica 2

description:
Library name: SWAT4h_2
QuantSeq 3′ mRNA-Seq library


title: PrS-MOK20017P-C11

description:
Library name: FOSB_PTC_C11_GT23-10485_AAGTCCAA-TACTCATA_S21
KOLF2.2J derived knockout cell line, FOSB PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: FOSB


title: B2_impk4_3MBiP_Wounding-3

value: 10 uM 3MBiP/ Mechanical wounding


title: WT-27


title: WT-26


title: Mycelium was cut with a knife, incubated for 3h; control is DM_84h; replica 2

description:
Library name: Scratchy_2
QuantSeq 3′ mRNA-Seq library


title: Mycelium was cut with a knife, incubated for 3h; control is DM_84h; replica 1

description:
Library name: Scratchy_1
QuantSeq 3′ mRNA-Seq library


title: WT-25


title: B2_impk4_3MBiP_Wounding-2


title: PrS-MOK20017P-B09

description:
Library name: FOSB_PTC_B09_GT23-10486_ATCCACTG-ACGCACCT_S41
KOLF2.2J derived knockout cell line, FOSB PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: Termination codon


title: PrS-MOK20022C-D06

description:
Library name: GCM1_CE_D6_GT23-11439_GGCATTCT-CAAGCTAG_S49
KOLF2.2J derived knockout cell line, GCM1 CE, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: Critical exon


title: WT 3

data_processing:
The quality of the sequenced reads was assessed with FastQC v0.11.7 and QoRTs v1.3.0
Sequencing reads were aligned with default parameters to the mouse reference genome (GRCm38.p6) using STAR 2.6.0c.
Gene expression estimates were obtained with featureCounts v1.6.2 using composite gene models (union of the exons of all transcript isoforms per gene) from Gencode (version M16).
Assembly: GRCm38.p6
Supplementary files format and content: Excel file with RPKM values for each sample

extract_protocol:
Oocytes were manually dissected from ovaries.  RNA was isolated with PicoPure RNA Isolation Kit (Thermo)
RNA libraries for RNA-Seq were prepared using NEB Ultra II Directional RNA Library Prep

value: Oocyte

value: Wild Type


title: B2_impk4_3MBiP_Wounding-1


title: PrS-MOK20017P-A10

description:
Library name: FOSB_PTC_A10_GT23-10487_GCTTGTCA-GTATGTTC_S28
KOLF2.2J derived knockout cell line, FOSB PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: iPSC


title: Sclerotium - slight mycelium contamination is possible, it was growing for 4 weeks; control is DM_132h; replica 2

description:
Library name: Sclero_2
QuantSeq 3′ mRNA-Seq library


title: KO 3

value: Knockout


title: PrS-MOK20017C-D07

description:
Library name: FOSB_CE_D07_GT23-10484_GGACTTGG-CGTCTGCG_S22
KOLF2.2J derived knockout cell line, FOSB CE, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: Sclerotium - slight mycelium contamination is possible, it was growing for 4 weeks; control is DM_132h; replica 1

description:
Library name: Sclero_1
QuantSeq 3′ mRNA-Seq library


title: KO 2


title: B2_impk4_3MBiP_FLG22_1H-3

value: 10 uM 3MBiP/ 2nM Flg22


title: B2_impk4_3MBiP_FLG22_1H-2


title: WT 2


title: PrS-MOK20017C-C08

description:
Library name: FOSB_CE_C08_GT23-10482_CCGCGGTT-CTAGCGCT_S36
KOLF2.2J derived knockout cell line, FOSB CE, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: PrS-MOK20017C-C05

description:
Library name: FOSB_CE_C05_GT23-10483_TTATAACC-TCGATATC_S27
KOLF2.2J derived knockout cell line, FOSB CE, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: cold stress, 4°C for 4h; control is DM_84h; replica 2

description:
Library name: Cold_2
QuantSeq 3′ mRNA-Seq library


title: KO 1


title: cold stress, 4°C for 4h; control is DM_84h; replica 3

description:
Library name: Cold_3
QuantSeq 3′ mRNA-Seq library


title: B2_impk4_3MBiP_FLG22_1H-1


title: WT 1


title: B2_impk4_3MBiP_FLG22_30M-2


title: Sclerotium - slight mycelium contamination is possible, it was growing for 4 weeks; control is DM_132h; replica 3

description:
Library name: Sclero_3
QuantSeq 3′ mRNA-Seq library


title: B2_impk4_3MBiP_FLG22_30M-3


title: PrS-MOK20017W-E04

description:
Library name: FOSB_KO_E04_GT23-10488_CAAGCTAG-CGCTATGT_S20
KOLF2.2J derived knockout cell line, FOSB KO, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: Full coding length


title: PrS-MOK20017W-C02

description:
Library name: FOSB_KO_C02_GT23-10489_TGGATCGA-TATCGCAC_S1
KOLF2.2J derived knockout cell line, FOSB KO, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: day 6


title: PrS-MOK20017W-B04

description:
Library name: FOSB_KO_B04_GT23-10490_AGTTCAGG-TCTGTTGG_S16
KOLF2.2J derived knockout cell line, FOSB KO, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: Control for Hyp; replica 3

description:
Library name: HypK_3
QuantSeq 3′ mRNA-Seq library


title: HDAC1fl/fl Cd4 Cre pTh2 cells, after 48h in culture, sample 3

city: Vienna

first: Nicole

last: Boucheron

address: Lazarettgasse 19

country: Austria

institute: Institute of Immunology

data_processing:
Illumina NovaSeq Control Software (NCS) 1.8.1 was used for the data acquisition on the sequencing instrument and on-instrument base-calling performed by the Illumina Real-Time Analysis (RTA) software 3.4.4.
BCL to BAM file conversion and demultiplexing with custom programmes (https://github.com/epigen/picard/) was based on Picard tools 2.19.2 (https://broadinstitute.github.io/picard/)
NGS reads in unaligned BAM files were converted into FASTQ format with samtools, NGS adapter sequences were removed via fastp (0.23.2, GTCTCGTGGGCTCGG) and the reads were aligned to the GRCm38 (UCSC Genome Browser mm10) assembly with Bowtie2 (2.4.5, --very-sensitive, --no-discordant, --maxins 2000), before deduplicating with samblaster (0.1.24).
Alignment statistics and mitochondrial read fractions were collected with samtools. Peaks were called with MACS2 (2.2.7.1, --no-model, --keep-dup auto, –extsize 147) and both, peak annotation and motifs discovery was performed with Homer (4.11). UCSC Track hubs allowed for visual inspection of results. A consensus peak set was compiled and all peaks in mm10 assembly regions blacklisted by the ENCODE project were removed.
Assembly: GRCm38 (UCSC Genome Browser mm10)
Supplementary files format and content: MACS2 peak calls in tav-spearated value (TSV) format (_peaks.xls)
Supplementary files format and content: Consensus regions in UCSC BED format (consensus_regions.bed.gz)
Supplementary files format and content: Consensus counts in comma-separated value (CSV) format (consensus_counts.csv.gz)

source_name: Cell culture from Spleen/Lymph nodes

extract_protocol:
Cells were harvested, counted and 50000 cells centrifuged at 500 g for 5 min at 4°C. Cell pellets were resuspended in a tagmentation-mix containing Tagment DNA buffer, Tagment DNA Enzyme (Illumina), Digitonin (Promega) and Proteinase K (Roche). The lysate was incubated for 30min at 37°C with shaking (300rpm). The reaction was stopped by incubating the samples on ice. DNA was isolated using the MinElute PCR Purification Kit (Qiagen) according to the manufacturer’s instructions and eluted into 12 μl of elution buffer.
1 µl eluate was used in a quantitative PCR (qPCR) reaction to estimate the optimal number of cycles for library amplification. The remaining 10 µl of each tagmented sample was then amplified corresponding to the Cqvalue (i.e., the cycle number at which fluorescence has increased above background levels) in the presence of custom Nextera primers. PCR amplification was followed by SPRI (Beckman Coulter, Brea, CA, USA) size selection to exclude fragments larger than 1,200 bp. The DNA concentration of each library was assessed with a Qubit 2.0 Fluorometric Quantitation system (Life Technologies, Carlsbad, CA, USA), before pooling in equimolar amounts.

value: Cell culture from Spleen/Lymph nodes

value: primary cell culture material

value: KO

value: anti-CD3/anti-CD28 activation with IL-4, anti-GITR agonist, TSLP. anti-IFNg, anti-TGFb1

tag: Sex

value: female

value: 6-12 weeks


title: B2_impk4_3MBiP_FLG22_30M-1

value: Seedlings

tag: age


title: HDAC1fl/fl Cd4 Cre Th2 cells, after 48h in culture, sample 3

value: anti-CD3/anti-CD28 activation with IL-4, anti-IFNg, anti-TGFb1


title: Control for Hyp; replica 2

description:
Library name: HypK_2
QuantSeq 3′ mRNA-Seq library

value: Vegetative mycelium


title: B2_impk4_3MBiP-3

value: 10 uM 3MBiP


title: PrS-MOK20012-WT3-nor

description:
Library name: WT_3__Normoxia_GT23-11290_GGACTTGG-CGTCTGCG_S36
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation in 20% oxygen

value: Not Applicable

value: Not applicable

value: primitive syncytium

value: normoxia


title: HDAC1fl/fl pTh2 cells, after 48h in culture, sample 3

value: WT


title: Incubated in hypoxia bags for 24h; control is HypK; replica 3

description:
Library name: Hyp_3
QuantSeq 3′ mRNA-Seq library


title: HDAC1fl/fl Th2 cells, after 48h in culture, sample 3


title: Control for Hyp; replica 1

description:
Library name: HypK_1
QuantSeq 3′ mRNA-Seq library


title: PrS-MOK20012-WT2-nor

description:
Library name: WT_2__Normoxia_GT23-11289_TTATAACC-TCGATATC_S27
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation in 20% oxygen

value: iPSC


title: B2_impk4_3MBiP-1


title: Incubated in hypoxia bags for 24h; control is HypK; replica 2

description:
Library name: Hyp_2
QuantSeq 3′ mRNA-Seq library


title: cold stress, 4°C for 4h; control is DM_84h; replica 1

description:
Library name: Cold_1
QuantSeq 3′ mRNA-Seq library


title: HDAC1fl/fl Cd4 Cre pTh2 cells, after 24h in culture, sample 3


title: PrS-MOK20012P-G09-nor

description:
Library name: PTC_G09__Normoxia_GT23-11299_CTCTCGTC-AGGTTATA_S23
KOLF2.2J derived knockout cell line, EPAS1 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 20% oxygen

value: Termination codon

value: day 6


title: B2_impk36_3MBiP_Wounding-3

value: 10 uM 3MBiP/ Mechanical wounding


title: HDAC1fl/fl Cd4 Cre Th2 cells, after 24h in culture, sample 3

value: Cell culture from Spleen/Lymph nodes

value: primary cell culture material

value: KO


title: Incubated in hypoxia bags for 24h; control is HypK; replica 1

description:
Library name: Hyp_1
QuantSeq 3′ mRNA-Seq library


title: B2_impk36_3MBiP_Wounding-2


title: PrS-MOK20012P-D10-nor

description:
Library name: PTC_D10__Normoxia_GT23-11298_TCTCTACT-GAACCGCG_S32
KOLF2.2J derived knockout cell line, EPAS1 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 20% oxygen


title: cell wall stress, 3h in 1% congo red dye; control is LoKoLiquide; replica 3

description:
Library name: CR_3
QuantSeq 3′ mRNA-Seq library


title: PrS-MOK20012P-A09-nor

description:
Library name: PTC_A09__Normoxia_GT23-11297_GACCTGAA-CTCACCAA_S16
KOLF2.2J derived knockout cell line, EPAS1 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 20% oxygen


title: cell wall stress, 3h in 1% congo red dye; control is LoKoLiquide; replica 2

description:
Library name: CR_2
QuantSeq 3′ mRNA-Seq library


title: PrS-MOK20012C-H06-nor

description:
Library name: CE_H06__Normoxia_GT23-11296_AGTTCAGG-TCTGTTGG_S20
KOLF2.2J derived knockout cell line, EPAS1 CE, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 20% oxygen

value: Critical exon


title: B2_impk36_3MBiP_Wounding-1

value: Seedlings


title: HDAC1fl/fl Th2 cells, after 24h in culture, sample 3

value: anti-CD3/anti-CD28 activation with IL-4, anti-IFNg, anti-TGFb1

value: female

value: 6-12 weeks


title: B2_impk36_3MBiP_FLG22_1H-3

value: 10 uM 3MBiP/ 2nM Flg22


title: HDAC1fl/fl Cd4 Cre pTh2 cells, after 48h in culture, sample 2

value: anti-CD3/anti-CD28 activation with IL-4, anti-GITR agonist, TSLP. anti-IFNg, anti-TGFb1


title: B2_impk4_3MBiP-2

value: 10 uM 3MBiP


title: osmotic stress, 2h in 10% sorbitol; control is LoKoLiquide; replica 3

description:
Library name: Sor_3
QuantSeq 3′ mRNA-Seq library

value: Vegetative mycelium


title: PrS-MOK20012C-G07-nor

description:
Library name: CE_G07__Normoxia_GT23-11295_TGGATCGA-TATCGCAC_S25
KOLF2.2J derived knockout cell line, EPAS1 CE, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 20% oxygen

value: primitive syncytium

value: normoxia


title: HDAC1fl/fl Cd4 Cre Th2 cells, after 48h in culture, sample 2


title: PrS-MOK20012C-E06-nor

description:
Library name: CE_E06__Normoxia_GT23-11294_CAAGCTAG-CGCTATGT_S35
KOLF2.2J derived knockout cell line, EPAS1 CE, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 20% oxygen

value: iPSC


title: osmotic stress, 2h in 10% sorbitol; control is LoKoLiquide; replica 2

description:
Library name: Sor_2
QuantSeq 3′ mRNA-Seq library


title: HDAC1fl/fl pTh2 cells, after 48h in culture, sample 2

value: WT


title: PrS-MOK20012-WT1-nor

description:
Library name: WT_1__Normoxia_GT23-11288_CCGCGGTT-CTAGCGCT_S39
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation in 20% oxygen

value: Not Applicable

value: Not applicable

value: day 6


title: B2_impk36_3MBiP_FLG22_30M-3


title: HDAC1fl/fl pTh2 cells, after 24h in culture, sample 3

value: Cell culture from Spleen/Lymph nodes

value: primary cell culture material


title: B2_impk36_3MBiP_FLG22_30M-2

value: Seedlings


title: HDAC1fl/fl Th2 cells, after 48h in culture, sample 2

value: anti-CD3/anti-CD28 activation with IL-4, anti-IFNg, anti-TGFb1


title: HDAC1fl/fl Cd4 Cre pTh2 cells, after 24h in culture, sample 2

value: KO

value: female


title: PrS-MOK20012W-B01-nor

description:
Library name: KO_B01__Normoxia_GT23-11292_ATCCACTG-ACGCACCT_S24
KOLF2.2J derived knockout cell line, EPAS1 KO, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 20% oxygen

value: Full coding length


title: B2_impk36_3MBiP_FLG22_30M-1

value: 10 uM 3MBiP/ 2nM Flg22


title: PrS-MOK20012W-A03-nor

description:
Library name: KO_A03__Normoxia_GT23-11291_AAGTCCAA-TACTCATA_S31
KOLF2.2J derived knockout cell line, EPAS1 KO, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 20% oxygen


title: HDAC1fl/fl Cd4 Cre Th2 cells, after 24h in culture, sample 2

value: 6-12 weeks


title: B2_impk36_3MBiP-3

value: 10 uM 3MBiP


title: alkaline stress 3h; control is LoKoLiquide; replica 1

description:
Library name: pH_9_1
QuantSeq 3′ mRNA-Seq library

value: Vegetative mycelium


title: cell wall stress, 3h in 1% congo red dye; control is LoKoLiquide; replica 1

description:
Library name: CR_1
QuantSeq 3′ mRNA-Seq library


title: acidic stress 3h; control is LoKoLiquide; replica 3

description:
Library name: pH_4_3
QuantSeq 3′ mRNA-Seq library


title: B2_impk36_3MBiP-2


title: PrS-MOK20012-WT2-hyp

description:
Library name: WT_2__Hypoxia_GT23-11301_TTGGACTC-CTGCTTCC_S37
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation in 3% oxygen

value: primitive syncytium

value: hypoxia


title: B2_impk36_3MBiP_FLG22_1H-2


title: B2_impk36_3MBiP-1


title: alkaline stress 3h; control is LoKoLiquide; replica 3

description:
Library name: pH_9_3
QuantSeq 3′ mRNA-Seq library


title: PrS-MOK20012-WT1-hyp

description:
Library name: WT_1__Hypoxia_GT23-11300_CCAAGTCT-TCATCCTT_S29
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation in 3% oxygen

value: iPSC


title: PrS-MOK20012W-B02-nor

description:
Library name: KO_B02__Normoxia_GT23-11293_CTGCTTCC-GATCTATC_S63
KOLF2.2J derived knockout cell line, EPAS1 KO, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 20% oxygen

value: normoxia


title: acidic stress 3h; control is LoKoLiquide; replica 2

description:
Library name: pH_4_2
QuantSeq 3′ mRNA-Seq library


title: B2_impk36_3MBiP_FLG22_1H-1


title: HDAC1fl/fl Th2 cells, after 24h in culture, sample 2

value: WT


title: HDAC1fl/fl Cd4 Cre pTh2 cells, after 48h in culture, sample 1

value: anti-CD3/anti-CD28 activation with IL-4, anti-GITR agonist, TSLP. anti-IFNg, anti-TGFb1

value: male


title: B2_WT_3MBiP_Wounding-3

value: Wild type

value: 10 uM 3MBiP/ Mechanical wounding


title: PrS-MOK20012P-G09-hyp

description:
Library name: PTC_G09__Hypoxia_GT23-11311_ATGAGGCC-CAATTAAC_S28
KOLF2.2J derived knockout cell line, EPAS1 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 3% oxygen

value: Termination codon

value: day 6


title: acidic stress 3h; control is LoKoLiquide; replica 1

description:
Library name: pH_4_1
QuantSeq 3′ mRNA-Seq library


title: oxidative stress reaction, 3h in 1mM H2O2; control is LoKoLiquide; replica 3

description:
Library name: H2O2_3
QuantSeq 3′ mRNA-Seq library


title: B2_WT_3MBiP_Wounding-2

value: Seedlings


title: PrS-MOK20012P-D10-hyp

description:
Library name: PTC_D10__Hypoxia_GT23-11310_GCAGAATT-TGGCCGGT_S22
KOLF2.2J derived knockout cell line, EPAS1 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 3% oxygen


title: HDAC1fl/fl Cd4 Cre Th2 cells, after 48h in culture, sample 1

value: Cell culture from Spleen/Lymph nodes

value: primary cell culture material

value: KO

value: anti-CD3/anti-CD28 activation with IL-4, anti-IFNg, anti-TGFb1


title: alkaline stress 3h; control is LoKoLiquide; replica 2

description:
Library name: pH_9_2
QuantSeq 3′ mRNA-Seq library

value: Vegetative mycelium


title: HDAC1fl/fl pTh2 cells, after 24h in culture, sample 2

value: female

value: 6-12 weeks


title: PrS-MOK20012-WT3-hyp

description:
Library name: WT_3__Hypoxia_GT23-11302_CAGTAGGC-ATTCGTCA_S34
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation in 3% oxygen

value: iPSC

value: Not Applicable

value: Not applicable

value: primitive syncytium

value: hypoxia


title: B2_WT_3MBiP_Wounding-1

value: Wild type


title: PrS-MOK20012P-A09-hyp

description:
Library name: PTC_A09__Hypoxia_GT23-11309_AACGTTCC-AGTACTCC_S30
KOLF2.2J derived knockout cell line, EPAS1 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 3% oxygen


title: oxidative stress reaction, 3h in 1mM H2O2; control is LoKoLiquide; replica 2

description:
Library name: H2O2_2
QuantSeq 3′ mRNA-Seq library


title: HDAC1fl/fl Th2 cells, after 48h in culture, sample 1

value: WT

value: male


title: PrS-MOK20012C-H06-hyp

description:
Library name: CE_H06__Hypoxia_GT23-11308_GGTACCTT-GACGTCTT_S19
KOLF2.2J derived knockout cell line, EPAS1 CE, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 3% oxygen

value: Critical exon

value: day 6


title: B2_WT_3MBiP_FLG22_1H-3

value: Seedlings

value: 10 uM 3MBiP/ 2nM Flg22