title: small RNA -  Embryos stage 8- stage 11 rep 4

value: Embryos stage 8- stage 11


title: PSO36B-04T-MF-17_N706-S508_S21_L003_R

status: Public on Sep 06 2021

type: SRA

city: San Francisco

first: Wilson

last: Liao

state: CA

address: 2340 Sutter St.

department: Dermatology

country: USA

institute: University of California, San Francisco

library_source: transcriptomic

data_processing:
Mapping to GRCh38 performed using STAR v2.4.2a
Raw gene counts calculated using HTSeq v0.6.1p1  on the GENCODE 25 annotation of GRCh38
Samples with < 1 million reads, < 10,000 detected genes, or < 60% mappable reads were excluded
Genes expressed at < 5 reads in fewer than 20% of samples were excluded
Genome_build: GRCh38
Supplementary_files_format_and_content: CountData_SecukinumabPsoRnaSeq_20210324.tsv  (Matrix table with raw gene counts for every gene and every sample)

molecule: polyA RNA

organism: Homo sapiens

source_name: skin

extract_protocol:
Sequencing libraries were constructed using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Clontech cat. 634894). Bulk RNA was extracted from whole skin tissue using Qiagen RNeasy fibrous tissue mini kit (cat. 74704). Reverse transcription was performed on poly-adenylated RNA from cell lysate for up to 1,000 cells followed by second strand synthesis to make full length cDNA. cDNA was then later amplified by PCR using cycle numbers determined by cell numbers. Amplified cDNA was purified by AMPure XP beads (Beckman Coulter) and followed by Qubit quantification.
Sequencing libraries were constructed using the Illumina Nextera DNA kit with 0.4 ng of amplified cDNA for sorted lymphocytes and 0.3 ng for cDNA synthesized from bulk skin RNA.

tag: sequencing batch

tag: sequencing lane

tag: cell type

value: Teff

tag: subject id

tag: tissue

value: lesion

tag: clinical status

tag: sorted cells

tag: used for analysis

value: FALSE


title: PSO36B-04T-MF-17_N705-S507_S20_L003_R

value: Treg

value: TRUE


title: small RNA -  Embryos stage 8- stage 11 rep 2

city: Mancheste

first: Llilians

last: Calvo

address: Oxford Rd

country: United Kingdom

institute: University of Manchester

data_processing:
small RNA:
Adaptors were removed and read ranging from 18 to 26 nucleotides were kepts using Cutadapt v. 1.18
tRNAs were predicted using tRNAscan-SE (v2.0; option -e)
Reads were mapped to tRNAs and rRNAs and only unmapped reads were kept using Bowtie (v1.1.1)
Reads were mapped to Parhyale predicted microRNAs using Bowtie (v1.1.1)
Quantification was performed using salmon quant from salmon (v0.14.1) (37) in alignment mode
polyA RNA
Paired-end RNA-seq reads from each developmental library were mapped to the Parhyale genome STAR (v2.7.2b)
To quantify mRNAs, reads mapped to the genome and to annotated Parhyale transcripts were quantified using salmon quant from salmon (v0.14.1) in mapping base mode
Genome_build: GCA_001587735.2 Phaw_5.0
Supplementary_files_format_and_content: Tab-delimited sf files include RPM (small RNA) or TPM values for each sample as generated from salmon

molecule: total RNA

organism: Parhyale hawaiensis

source_name: Parhyale hawaiensis pooled staged embryos

growth_protocol: Animals (Parhyale hawaiensis) were reared in standard plastic aquarium tanks containing artificial sea water (aquarium salt and deionised water) at a salinity of 30 PPT, and kept at ∼26◦C.

extract_protocol:
Embryos were extracted from females anaesthetised using clove oil (Sigma) diluted 1:10000 in sea water. Embryos were washed in filtered seawater and manually staged using a Leica Stereo Fluorescence microscope. Isolated embryos were stored in RNAlater (Sigma) and total RNA was then extracted using the SPLIT RNA Extraction Kit (Lexogen) following the manufacturer’s instructions.
Small RNA libraries (4 replicates per time-point) were built using the Small RNA-Seq Library Prep Kit (Lexogen). Long library fragments and linker-linker artefacts were removed using a purification module with magnetic beads (Lexogen). Long mRNA libraries (2 replicates per time-point) were built using the TruSeq Stranded mRNA HT Sample Prep Kit (Illumina).

tag: strain/genotype

value: laboratory strain - wild type

tag: age

tag: molecule subtype

value: small RNA


title: small RNA -  Embryos stage 8- stage 11 rep 3


title: PSO36A-04T-MF-17_N710-S511_S15_L002_R

value: bulk


title: PSO36A-04T-MF-17_N706-S508_S13_L002_R


title: small RNA -  Embryos stage 8- stage 11 rep 1


title: small RNA -  Embryos stage 6 rep 4

value: Embryos stage 6


title: PSO36A-04T-MF-17_N707-S510_S14_L002_R


title: PSO36A-04T-MF-17_N705-S507_S12_L002_R


title: small RNA -  Embryos stage 6 rep 2


title: small RNA -  Embryos stage 6 rep 3


title: small RNA -  Embryos stage 1- stage 4 rep 4

value: Embryos stage 1- stage 4


title: PSO36A-04T-MF-17_N703-S505_S10_L002_R


title: small RNA -  Embryos stage 6 rep 1


title: small RNA -  Embryos stage 1- stage 4 rep 1


title: PSO36A-04T-MF-17_N704-S506_S11_L002_R


title: PSO35_W4_Teff_S26_L004_R


title: PSO35_W4_bulk_S28_L004_R


title: PSO35_W4_Treg_S25_L004_R


title: PSO35_W4_CD8_S27_L004_R


title: PSO36A-04T-MF-17_N701-S502_S8_L002_R


title: small RNA -  Embryos stage 1- stage 4 rep 3


title: PSO35_W2_Treg_S21_L003_R


title: small RNA -  Embryos stage 1- stage 4 rep 2


title: PSO35_W2_Teff_S22_L003_R


title: BH72_MinusN_1

city: Bremen

first: Shanmugam

last: Solaiyappan Mani

address: Leobner strasse

department: Department of Microbe-Plant Interactions

country: Germany

institute: University of Bremen

description:
rRNA eliminated total RNA
A. olearius BH72 grown without ammonium chloride (N2-fixing) replicate 1
Sample 4

data_processing:
The Illumina sequencing reads were trimmed using the fastp tool based on the adapter sequence (AGATCGGAAGAGCACACGTCTGAACTCCAGTCA) and read quality. Reads with at least one “N” base or more than 10 bases with Phred score less than 10 were removed.From the 5’ and 3’ end of the reads, bases up to a 3 nucleotide window that had a mean quality score less than 10 were also dropped.
Processed reads were aligned to the genome sequence of Azoarcus olearius strain BH72 using the READemption tool with its default parameters. Only reads that mapped uniquely were considered for quantification.
Raw coverage values for the annotated CDSs were rounded and used for differential expression analysis using DEseq2 tool. The results were optimized for an FDR cutoff value of 0.05 by independent filtering of genes based on mean normalized counts.
Genes with Padj < 0.05 and Fold-change > 1.8 were considered to be differentially regulated
Genome_build: AM406670.1 Azoarcus olearius BH72, complete genome
Supplementary_files_format_and_content: Matrix table with raw gene counts for every CDS and every sample

organism: Azoarcus olearius

growth_protocol: Azoarcus olearius strain BH72 was grown in minimal SM medium ([Reinhold B, Hurek T, Fendrik I (1985) Strain-specific chemotaxis of Azospirillum spp. J Bacteriol 162: 190–195.]) microaerobically (0.3% O2) in a bioreactor (Minifors, infors HT) at 37 °C with constant stirring at 600 rpm.

extract_protocol:
30 mL of harvested culture was frozen in liquid N2. RNA was extracted from the frozen cells using Hot phenol method. Genomic DNA was eliminatedby using RNeasy Plus Mini Kit (Qiagen, Catalog no. 74134). Ribosomal RNA was depleted using the Ribo-Zero rRNA Removal Kit for bacteria (Illumina, Catalog no. MRZB12424).
The samples were fragmented by 4 pulses of ultrasound, 30 s each, at 4 °C. To aid in directional sequencing, 3’ Illumina TruSeq sequencing adapter, with barcodes, was ligated to the 3’ end of the fragmented RNA molecules. First-strand cDNA was synthesized using M-MLV reverse transcriptase and a primer binding to the adapter sequence. Synthesized cDNA was purified, and to its 3’ end the 5’ Illumina TruSeq sequencing adapter, also containing barcodes, was ligated. The cDNA was amplified through 13 cycles of PCR, using a high fidelity DNA polymerase, to obtain about 10-20 ng/µl of DNA. Amplified cDNA was purified using AgencourtAMPure XP kit (Beckman Coulter Genomics). The six samples were pooled in approximately equimolar amounts and size-fractionated using a preparative agarose gel to obtain the size range between 200 and 400 bp. The sample pool was sequenced on an Illumina NextSeq 500 system using 75 bp read length.

treatment_protocol: Three replicates supplemented with 10 mM ammonium chloride, three replicates without ammonium chloride

tag: strain

tag: nitrogen source

value: Without ammonium chloride


title: BH72_plusN_3

description:
rRNA eliminated total RNA
A. olearius BH72 grown with ammonium chloride (non-fixing) replicate 3
Sample 3

value: 10 mM ammonium chloride


title: BH72_MinusN_2

description:
rRNA eliminated total RNA
A. olearius BH72 grown without ammonium chloride (N2-fixing) replicate 2
Sample 5


title: BH72_MinusN_3

description:
rRNA eliminated total RNA
A. olearius BH72 grown without ammonium chloride (N2-fixing) replicate 3
Sample 6


title: PSO35_W2_CD8_S23_L003_R


title: BH72_plusN_2

description:
rRNA eliminated total RNA
A. olearius BH72 grown with ammonium chloride (non-fixing) replicate 2
Sample 2


title: PSO35_W2_bulk_S24_L003_R


title: PSO36A-04T-MF-17_N702-S503_S9_L002_R


title: BH72_plusN_1

description:
rRNA eliminated total RNA
A. olearius BH72 grown with ammonium chloride (non-fixing) replicate 1
Sample 1


title: PSO35_W12_Treg_S29_L004_R


title: PSO35_W12_Teff_S30_L004_R


title: LN KO 4-b

city: Paris

first: Anaïs

last: Levescot

address: 24 boulevard du Montparnasse

country: France

institute: INSERM Institut Imagine

data_processing:
base calling by bustard
Alignment using BWA to mouse assembly 9 (UCSC 2009).
The processed data is separated by sample barcode and aligned using Tophat version 2.0.10 (Kim et. al. 2013) with default settings.
Transcripts are quantified using the Cufflinks suite version 2.2.1 (Trapnell et. al. 2012).
Data are processed through CuffNorm if 50% of the reads align and there are at least 100,000 aligned pairs per sample. This filtering is done to ensure the quality of the normalization step.
Genome_build: Mouse assembly 9 (UCSC 2009)
Supplementary_files_format_and_content: csv file with log2 counts per million

organism: Mus musculus

source_name: Lymph node

extract_protocol:
RNA was extracted from sorted cells (5 × 10^4) using a Qiagen RNeasy Micro Kit. RNA-seq was performed using the Smart-Seq2 platform. Smart-Seq2 libraries were prepared by the Broad Technology Labs and sequenced by the Joint Biology Consortium– associated Broad Genomics Platform. Transcripts were quantified by the Broad computational pipeline using Cuffquant version 2.2.1
Illumina SmartSeq2 low-input RNA-seq

tag: strain background

value: BALB/c

tag: genotype/variation

value: post natal day 35

value: Lymph node


title: LN KO 3-b


title: PSO35_W12_CD8_S31_L004_R


title: LN WT 3-b

value: wild type


title: PSO35_W0_Teff_S18_L003_R


title: LN WT 4-b


title: LN KO 2-b


title: PSO35_W12_bulk_S32_L004_R


title: PSO35_W0_Treg_S17_L003_R


title: PSO34_W4_Treg_S105_L008_R


title: LN WT 1-b


title: PSO35_W0_CD8_S19_L003_R


title: PSO34_W4_CD8_S107_L008_R


title: LN KO 1-b


title: LN KO 3-a


title: PSO35_W0_bulk_S20_L003_R


title: LN WT 2-b


title: PSO34_W4_Teff_S106_L008_R


title: LN KO 2-a


title: LN KO 1-a


title: LN WT 3-a


title: PSO34_W4_bulk_S108_L008_R


title: PSO34_W2_Teff_S102_L007_R


title: PSO34_W2_Treg_S101_L007_R


title: E14-ATAC_2

city: Worcester

first: Thomas

middle: G

last: Fazzio

state: MA

address: 364 Plantation St., LRB 519

department: Department of Molecular, Cell and Cancer Biology

institute: University of Massachusetts Medical School

description: ATACpeaks.txt

library_source: genomic

data_processing:
Library strategy: Multi-CUT&Tag
Paired-end sequencing was performed on an Illumina NextSeq 500 using custom read and index primers (Sup. Table 1). The sequencing parameters were as follows: read 1—72 cycles, read 2—72 cycles, index 1—8 cycles, index 2—8 cycles (for bulk multi-CUT&Tag) or 16 cycles (for sc multi-CUT&Tag).
Paired-end reads from each sample were then split based on their antibody specific barcodes on both ends of the fragment using novoBarcode (http://www.novocraft.com/documentation/novobarcode/). The first 42 bases of the reads were trimmed to remove the Antibody barcodes and the bases common to all Tn5 adapter sequences.
The reads were then aligned to the mouse genome (mm10) using Bowtie2 with the parameters -N 1 and -X 2000.
Duplicates were removed using Picard (http://broadinstitute.github.io/picard/).
Reads with low quality scores (MAPQ < 10) were removed.
The remaining mapped reads were then processed using the HOMER software suite. Peaks were called using the “findPeaks” command.
Genome_build: mm10
Supplementary_files_format_and_content: Peakfiles.txt and bedGraph.gz

molecule: genomic DNA

growth_protocol: E14 mouse embryonic stem cells (ESCs) were grown DMEM-high glucose media (MilliporeSigma, D6546-500ML) containing 10% Fetal Bovine Serum (MilliporeSigma, F2442), 2 mM L-Glutamine (Corning, 25-005-CI), MEM Nonessential Amino Acids (Corning, 25-025-CI), β-mercaptoethanol (MilliporeSigma, M6250) and recombinant leukemia inhibitory factor. Trophoblast stem cells (TSCs) were grown in RPMI 1640 media (ThermoFisher, 11875093) supplemented with 20% Fetal Bovine Serum, 2 mM L-Glutamine, 100 uM β-mercaptoethanol containing 25 ng/mL FGF4 (Peprotech, 100-31) and 1 µg/mL heparin (Sigma, H3149). 70% of the the TSC media was pre-conditioned by growing on feeder cells before use. Both ESCs and TSCs were maintained on plates coated with 0.2% gelatin.

extract_protocol:
Mouse ESCs or TSCs were trypsinized and counted using a TC-20 cell counter (Biorad). 100,000 cells were washed and resuspended in wash buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1× Protease inhibitor cocktail) and used for bulk multi-CUT&Tag. 10 µL of Concanavalin A coated magnetic beads (Polysciences) were activated as described30 and added per sample and incubated at RT for 15 min. Bead-bound cells were resuspended in 100 µL Dig-wash Buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 0.05% Digitonin; 1× Protease inhibitor cocktail) containing 2 mM EDTA and XX µg of each differentially barcoded purified antibody-pA-Tn5 complex was added. The mixture was incubated overnight at 4 °C for antibodies to bind. Cells were washed thrice in Dig-med Buffer (20 mM HEPES, pH 7.5; 300 mM NaCl; 0.5 mM Spermidine; 0.05% Digitonin; 1× Protease inhibitor cocktail) by placing the tube on the magnet stand until the solution clears and removal of all of the liquid by pipetting. The cells were then resuspended in 300 µL Dig-med Buffer containing 10 mM MgCl2 and incubated at 37 °C for 1 h to activate tagmentation. To stop tagmentation, 10 µL of 0.5 M EDTA, 3 µL of 10% SDS and 1 µL of 20 mg/mL Proteinase K was added to each tube, which were incubated at 55 °C for 1 hour. DNA was extracted by performing one phenol:chloroform extraction followed by ethanol precipitation. The DNA pellet was resuspended in 22 µL of 10 mM Tris pH 8.
The libraries were then amplified by mixing 21 µL of DNA with 2µL each of (10 µM) barcoded i5 and i7 primers, using a different combination for each sample. 25 µL NEBNext HiFi 2× PCR Master mix (NEB) was added, and PCR was performed using the following cycling conditions: 72 °C for 5 min (gap filling); 98 °C for 30 s; 17 cycles of 98 °C for 10 s and 63 °C for 30 s; final extension at 72 °C for 1 min and hold at 4 °C. 1.1× volume of Ampure XP beads (Beckman Coulter) was incubated with libraries for 10 min room temperature to clean up the PCR mix. Bead bound DNA was purified by washing twice with 80% ethanol and eluting in 20 µL 10 mM Tris pH 8.0.

treatment_protocol: Unfixed nuclei were bound to Concanavalin A beads (Polysciences, Inc), washed, followed by successive addition of Antibody-proteinA-Tn5 complexes. Tagmentation was initiated by Magnesium addition and chelated by EDTA. Fragments were released and deep sequencing libraries were prepared.

tag: cell line

value: mouse embryonic stem cells

tag: secondary antibody

value: adapter loaded Tn5


title: PSO34_W2_bulk_S104_L007_R

tag: sequencing batch

value: lesion


title: LN WT 1-a


title: PSO34_W2_CD8_S103_L007_R

tag: sequencing lane

value: FALSE


title: PSO34_W12_Treg_S109_L008_R

tag: cell type

value: Treg


title: PSO34_W12_Teff_S110_L008_R

value: Teff

tag: subject id

value: TRUE


title: E14-RNAPII+IgG_2

tag: antibody used

value: Rpb1 Phospho-serine 2 (Cell Signaling Technology, 13499)+ IgG (Abcam, Ab37415)

value: adapter loaded proteinA-Tn5


title: LN WT 2-a

tag: tissue


title: PSO34_W12_CD8_S111_L008_R

tag: clinical status

tag: sorted cells


title: PSO34_W12_bulk_S112_L008_R

value: bulk

tag: used for analysis


title: PSO34_W0_Treg_S97_L007_R


title: PSO34_W0_Teff_S98_L007_R


title: PSO34_W0_CD8_S99_L007_R


title: E14-RNAPII+IgG_1


title: E14-H3K27me3+IgG_1

value: H3K27me3 (Invitrogen, MA5-11198)+ IgG (Abcam, Ab37415)


title: PSO34_W0_bulk_S100_L007_R


title: PSO33_W4_Treg_S48_L007_R


title: PSO33_W4_Teff_S49_L007_R


title: PSO33_W4_CD8_S50_L007_R


title: E14-H3K27me3-rep2

data_processing:
Library strategy: Multi-CUT&Tag
Paired-end sequencing was performed on an Illumina NextSeq 500 using custom read and index primers (Sup. Table 1). The sequencing parameters were as follows: read 1—72 cycles, read 2—72 cycles, index 1—8 cycles, index 2—8 cycles (for bulk multi-CUT&Tag) or 16 cycles (for sc multi-CUT&Tag).
Paired-end reads from each sample were then split based on their antibody specific barcodes on both ends of the fragment using novoBarcode (http://www.novocraft.com/documentation/novobarcode/). The first 42 bases of the reads were trimmed to remove the Antibody barcodes and the bases common to all Tn5 adapter sequences.
The reads were then aligned to the mouse genome (mm10) using Bowtie2 with the parameters -N 1 and -X 2000.
Duplicates were removed using Picard (http://broadinstitute.github.io/picard/).
Reads with low quality scores (MAPQ < 10) were removed.
The remaining mapped reads were then processed using the HOMER software suite. Peaks were called using the “findPeaks” command. BedGraph files were generated using the “makeUCSCfile” command.
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph files

source_name: E14-embryonic Stem Cells

growth_protocol: E14 mouse embryonic stem cells (ESCs) were grown DMEM-high glucose media (MilliporeSigma, D6546-500ML) containing 10% Fetal Bovine Serum (MilliporeSigma, F2442), 2 mM L-Glutamine (Corning, 25-005-CI), MEM Nonessential Amino Acids (Corning, 25-025-CI), β-mercaptoethanol (MilliporeSigma, M6250) and recombinant leukemia inhibitory factor. Trophoblast stem cells (TSCs) were grown in RPMI 1640 media (ThermoFisher, 11875093) supplemented with 20% Fetal Bovine Serum, 2 mM L-Glutamine, 100 uM β-mercaptoethanol containing 25 ng/mL FGF4 (Peprotech, 100-31) and 1 µg/mL heparin (Sigma, H3149). 70% of the TSC media was pre-conditioned by growing on feeder cells before use. Both ESCs and TSCs were maintained on plates coated with 0.2% gelatin.

value: E14 mouse embryonic stem cells

value: H3K27me3 (Invitrogen, MA5-11198)


title: PSO33_W4_bulk_S51_L007_R


title: E14-ATAC_1

description: ATACpeaks.txt


title: E14-RNAPII_1

value: Rpb1 Phospho-serine 2 (Cell Signaling Technology, 13499)


title: E14-H3K27ac_2

value: H3K27ac (Abcam, ab4729)


title: E14-H3K27ac+H3K27me3+RNAPII-rep2

data_processing:
library strategy: Multi-CUT&Tag
Paired-end sequencing was performed on an Illumina NextSeq 500 using custom read and index primers (Sup. Table 1). The sequencing parameters were as follows: read 1—72 cycles, read 2—72 cycles, index 1—8 cycles, index 2—8 cycles (for bulk multi-CUT&Tag) or 16 cycles (for sc multi-CUT&Tag).
Paired-end reads from each sample were then split based on their antibody specific barcodes on both ends of the fragment using novoBarcode (http://www.novocraft.com/documentation/novobarcode/). The first 42 bases of the reads were trimmed to remove the Antibody barcodes and the bases common to all Tn5 adapter sequences.
The reads were then aligned to the mouse genome (mm10) using Bowtie2 with the parameters -N 1 and -X 2000.
Duplicates were removed using Picard (http://broadinstitute.github.io/picard/).
Reads with low quality scores (MAPQ < 10) were removed.
The remaining mapped reads were then processed using the HOMER software suite. Peaks were called using the “findPeaks” command. BedGraph files were generated using the “makeUCSCfile” command
Genome_build: mm10
Supplementary_files_format_and_content: Peakfiles.txt

growth_protocol: E14 mouse embryonic stem cells (ESCs) were grown DMEM-high glucose media (MilliporeSigma, D6546-500ML) containing 10% Fetal Bovine Serum (MilliporeSigma, F2442), 2 mM L-Glutamine (Corning, 25-005-CI), MEM Nonessential Amino Acids (Corning, 25-025-CI), β-mercaptoethanol (MilliporeSigma, M6250) and recombinant leukemia inhibitory factor. Trophoblast stem cells (TSCs) were grown in RPMI 1640 media (ThermoFisher, 11875093) supplemented with 20% Fetal Bovine Serum, 2 mM L-Glutamine, 100 M β-mercaptoethanol containing 25 ng/mL FGF4 (Peprotech, 100-31) and 1 µg/mL heparin (Sigma, H3149). 70% of the the TSC media was pre-conditioned by growing on feeder cells before use. Both ESCs and TSCs were maintained on plates coated with 0.2% gelatin.

value: H3K27me3 (Invitrogen, MA5-11198), H3K27ac (Abcam, ab4729), Rpb1 Phospho-serine 2 (Cell Signaling Technology, 13499)


title: E14-RNAPII+H3K27me3-rep2

description:
processed data file:
DualAb_PM_H3K27me3_peaks.txt, DualAb_PM_RNAPII_peaks.txt, DualAb_PM_mixed_peaks.txt

value: H3K27me3 (Invitrogen, MA5-11198), Rpb1 Phospho-serine 2 (Cell Signaling Technology, 13499)


title: E14-H3K27ac+H3K27me3+RNAPII-rep1


title: E14-H3K27me3+IgG_2

value: mouse embryonic stem cells


title: E14-H3K27ac+RNAPII-rep2

description:
processed data file:
DualAb_AP_H3K27ac_peaks.txt, DualAb_AP_RNAPII_peaks.txt, DualAb_AP_mixed_peaks.txt

value: H3K27ac (Abcam, ab4729), Rpb1 Phospho-serine 2 (Cell Signaling Technology, 13499)


title: E14-H3K27ac+H3K27me3-rep2

description:
processed data file:
DualAb_AM_H3K27ac_peaks.txt, DualAb_AM_H3K27me3_peaks.txt, DualAb_AM_mixed_peaks.txt

value: H3K27me3 (Invitrogen, MA5-11198), H3K27ac (Abcam, ab4729)


title: PSO33_W2_Treg_S44_L006_R

value: lesion


title: E14-H3K27ac+H3K27me3-rep1


title: PSO33_W2_CD8_S46_L006_R


title: E14-RNAPII_2


title: PSO33_W12_CD8_S54_L007_R


title: E14-H3K27ac_1


title: E14-RNAPII+H3K27me3-rep1


title: ESC+TSC-H3K27ac+H3K27me3-single cell

source_name: E14-embryonic Stem Cells, Trophoblast stem cells

value: E14 mouse embryonic stem cells, Trophoblast stem cells


title: E14-H3K27ac+RNAPII-rep1


title: PSO33_W12_Teff_S53_L007_R

value: Teff


title: PSO33_W2_Teff_S45_L006_R

value: TRUE


title: PSO33_W2_bulk_S47_L006_R


title: PSO33_W0_bulk_S43_L006_R


title: kit_2dpi_1

city: Guangzhou

first: Yuchen

last: Yang

state: Guangdong

address: Xingangxi Road 135

country: China

institute: Sun Yat-sen University

description:
kit_2dpi_1_S2
processed data file: zebrafish_nonCM_kit_mutant_scRNA_raw_count_matrix.csv

data_processing:
I1 (8 bp sample barcode), R1 (16 bp feature barcode + 10 bp UMI) and R2 (reads); Qualities of de-barcoded raw sequence reads were checked by fastqc.
Raw sequencing data was demultiplexed, debarcoded, mapped to UCSC_DanRer10 genome, and counted by UNC TGL bioinformatic staff following the Cell Ranger/2.0.2 pipeline. The Cell Ranger output of collapsed UMI counts were then processed and analyzed in R.
Genome_build: UCSC_DanRer10
Supplementary_files_format_and_content: two csv files containing raw count values for each cell in the samples of wild type and kit mutant, respectively

organism: Danio rerio

growth_protocol: Zebrafish were raised and maintained under standard laboratory conditions.

extract_protocol:
Primary cells from zebrafish ventricles subjected to control operation or apex resection were isolated. Cardiomyocytes and non-cardiomyocytes were separated by 3 times of centrifugation at 200g for 5 minutes at 4°C. isolated non-cardiomyocytes from zebrafish ventricles subjected to control operation or apex resection at indicated time points were loaded into the Chromium controller (10X Genomics) and processed with Chromium Single Cell Reagent Kit v2 (10X Genomics).
Illumina libraries were prepared using NextSeq 500/550 kit v2.5.

treatment_protocol: Zebrafish were anesthetized by immersion with 0.04% tricaine and immobilized in a dampened foam with ventral side up. A small incision was made between the gills to expose the ventricle. About 20% of ventricular apex was resected using iridectomy scissors. After apex resection, fish were returned to a recovery tank with fresh system water.

value: kit mutant; kita(w34b2);kitb(sa15356)

tag: age

value: 4-6 month

tag: treatment/timepoint

value: uninjured

value: heart

value: cardiac non-cardiomyocytes (nonCMs)


title: E14-H3K27me3

value: E14 mouse embryonic stem cells

value: H3K27me3 (Invitrogen, MA5-11198)

value: adapter loaded proteinA-Tn5


title: PSO33_W0_CD8_S42_L006_R


title: PSO33_W0_Teff_S41_L006_R


title: kit_14dpi_2

description:
kit_14dpi_2_S1
processed data file: zebrafish_nonCM_kit_mutant_scRNA_raw_count_matrix.csv

value: 14 days post injury


title: PSO33_W12_Treg_S52_L007_R

value: Treg


title: PSO33_W0_Treg_S40_L006_R


title: kit_14dpi_1

description:
kit_14dpi_1_S1
processed data file: zebrafish_nonCM_kit_mutant_scRNA_raw_count_matrix.csv

value: 7 days post injury


title: PSO33_W12_bulk_S55_L007_R

value: bulk


title: kit_7dpi_2

description:
kit_7dpi_2_S2
processed data file: zebrafish_nonCM_kit_mutant_scRNA_raw_count_matrix.csv


title: kit_uninjuried

description:
kit_uninjuried_S2
processed data file: zebrafish_nonCM_kit_mutant_scRNA_raw_count_matrix.csv


title: wt_7dpi_2

description:
wt_7dpi_2_S1
processed data file: zebrafish_nonCM_wildtype_scRNA_raw_count_matrix.csv

value: wild type


title: PSO31_W2_Teff_S34_L005_R

value: lesion

value: FALSE


title: kit_2dpi_2

description:
kit_2dpi_2_S2
processed data file: zebrafish_nonCM_kit_mutant_scRNA_raw_count_matrix.csv

value: 2 days post injury


title: PSO31-04T_JJ_012_N704-S506_S4_L001_R

value: TRUE


title: wt_2dpi_1

description:
wt_2dpi_1_S1
processed data file: zebrafish_nonCM_wildtype_scRNA_raw_count_matrix.csv


title: PSO31_W2_bulk_S36_L005_R


title: wt_unjuried_2

description:
wt_unjuried_2_S2
processed data file: zebrafish_nonCM_wildtype_scRNA_raw_count_matrix.csv


title: PSO31-04T_JJ_012_N702-S503_S2_L001_R

value: Teff


title: PSO31_W0_CD8_S27_L004_R


title: PSO31_W0_bulk_S28_L004_R


title: wt_14dpi

description:
wt_14dpi_S2
processed data file: zebrafish_nonCM_wildtype_scRNA_raw_count_matrix.csv

value: 4-6 month


title: kit_7dpi_1

description:
kit_7dpi_1_S1
processed data file: zebrafish_nonCM_kit_mutant_scRNA_raw_count_matrix.csv

value: kit mutant; kita(w34b2);kitb(sa15356)


title: PSO3_W12_Teff_S17_L003_R


title: PSO3_W12_CD8_S18_L003_R


title: PSO3_W12_bulk_S22_L003_R


title: PSO25_W4_Teff_S45_L007_R


title: PSO25_W4_bulk_S50_L007_R


title: PSO31-04T_JJ_012_N703-S505_S3_L001_R


title: PSO25_W4_CD8_S46_L007_R


title: PSO25_W2_bulk_S587_L008_R


title: PSO31_W2_Treg_S33_L005_R


title: PSO31_W2_CD8_S35_L005_R


title: wt_2dpi_2

description:
wt_2dpi_2_S1
processed data file: zebrafish_nonCM_wildtype_scRNA_raw_count_matrix.csv

value: heart


title: PSO25_W12_bulk_S51_L007_R


title: PSO25_W0_CD8_S579_L007_R


title: PSO25_W0_Treg_S577_L007_R


title: PSO25_W0_Teff_S578_L007_R


title: PSO25_W4_Treg_S44_L007_R


title: wt_7dpi_1

description:
wt_7dpi_1_S1
processed data file: zebrafish_nonCM_wildtype_scRNA_raw_count_matrix.csv

value: cardiac non-cardiomyocytes (nonCMs)


title: PSO24_W4_bulk_S43_L006_R


title: PSO24_W4_CD8_S39_L006_R


title: PSO31_W0_Treg_S25_L004_R


title: PSO24_W2_Teff_S30_L005_R


title: PSO24_W4_Treg_S37_L006_R


title: PSO25_W12_Teff_S48_L007_R


title: PSO25_W2_Teff_S585_L008_R


title: PSO31_W0_Teff_S26_L004_R


title: PSO25_W2_Treg_S584_L008_R


title: PSO24_W12_CD8_S42_L006_R


title: PSO24_W12_Treg_S40_L006_R


title: wt_unjuried_1

description:
wt_unjuried_1_S1
processed data file: zebrafish_nonCM_wildtype_scRNA_raw_count_matrix.csv

value: uninjured


title: PSO24_W12_bulk_S36_L005_R


title: PSO31-04T_JJ_012_N701-S502_S1_L001_R


title: PSO24_W4_Teff_S38_L006_R


title: PSO24_W2_bulk_S32_L005_R


title: PSO24_W0_CD8_S25_L004_R


title: pso19_w2_cd8_S11_L002_R


title: PSO19_W4_bulk_S23_L003_R


title: pso19_w2_treg_S9_L002_R


title: PSO19_W4_CD8_S19_L003_R


title: GMP+CMP_donor3_H3K27ac

city: PHILADELPHIA

first: Zhendong

last: Cao

state: PA

address: BRB Rm620, 421 Curie Blvd

department: Cancer biology

institute: university of pennsylvania

data_processing:
Library strategy: CUT&RUN
CUT & RUN were aligned to the hg19 genome assembly using Bowtie2 (v2.3.5), following parameters --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700 -k1 -N1
PCR duplicated reads were removed using Picard tools v1.96 MarkDuplicates command
Bam files containing uniquely mapped reads were created using Samtools v1.1
Fragments with <40bp or >1000bp were filtered. Blacklist regions defined by ENCODE, random chromosomes and mitochondria were removed, and filtered bam files were used for downstream analysis
Read count per million (RPM) normalized bigwig files were created by bedGraphToBigWig (UCSC) and used to compare relative binding signals in dTAG-engineered cell lines with different treatments, cells overexpressing WT or mutant ZMYND8 cDNA ,or primary patient samples. For visualization purpuse, average background subtracted and scaled bigwig files were used to visualize binding signals
Peak calling was performed using MAC2 v2.1 using broad peak setting, different p-values were adjusted by sample background level
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files for binding signals

source_name: human CD34+/CD38+/CD135hi GMP+CMP populations

growth_protocol: MOLM-13, THP1 and HEL were cultured in RPMI 1640-Media with 25mM HEPES supplemented with 10% Bovine Calf Serum (FCS) and 1% Penicillin/ Streptomycin.  HUH7 was cultured in DMEM with high glucose supplemented with 10% Bovine Calf Serum and 1% Penicillin/ Streptomycin. Primary  AML samples were frozen in FCS and 10% DMSO in liquid nitrogen until used. CD34+ cells were cultured in StemSpan SFEM medium (StemCell Technologies) supplemented with 1x CC100  (StemCell Technologies) and 1% Penicillin/ Streptomycin.

extract_protocol:
1-5x105 cells were used for H3K27ac/H3K14ac/H3K27me3 antibodies, and 2 million cells were used for other antibodies. Digitonin was diluted at a final concentration of 0.1% (w/v) in the antibody buffer (150 mM NaCl, 20 mM HEPES-KOH, 0.5 mM Spermidine, 2 mM EDTA, protease inhibitor cocktail plus digitonin), and Dig-wash buffer (150 mM NaCl, 20 mM HEPES-KOH, 0.5 mM Spermidine, protease inhibitor cocktail plus digitonin). For primary patient samples from frozen vials and CD34+ HPSCs, live cells were purified with the Dead Cell Removal kit (MACS) before wash and a final concentration of 0.05% of Digitonin was used for subsequent steps. Cells were washed twice in Wash buffer (150 mM NaCl, 20 mM HEPES-KOH,0.5 mM Spermidine, 2 mM EDTA, protease inhibitor cocktail) and incubated with 20 µl of Concanavalin A-coated beads for 10 min with rotation at room temperature. Antibody buffer containing indicated antibodies was added to the cell-attached beads and incubation was at 4°C with rotation overnight. Beads were washed with Dig-wash buffer and incubated with 300 µl Dig-wash buffer containing ~700 ng/ml pA-MN at 4°C for 1 hr. Beads were washed twice with Dig-wash buffer and chilled on a heated block sitting on ice. Digestion was activated through adding CaCl2 and chromatin was digested for 60 min when applying ZMYND8 antibody (Bethyl), and 30 min for other antibodies. Equal volume of 2x Stop solution (340 mM NaCl, 4 mM EGTA, 20 mM EDTA, 50 µg/ml RNase A, 0.02% Digitonin, 50 µg/ml Glycogen, 2 pg/ml heterogenous spike-in DNA) was added and beads were incubated at 37°C for 10 min to release the digested chromatin. Supernatant was collected and DNA was extracted through Phenol-Chloroform extraction.
Library construction was prepared with NEBNext® Ultra™ II DNA Library Prep Kit for Illumina with small modifications. For H3K27ac, H3K14ac and H3K27me3, adapter was diluted on a ratio of 1:25, and repaired DNA was first selected with 25 µl Ampure Beads (Beckman) and second selected with 45 µl beads, followed by 9 cycles of PCR amplification. For chromatin regulators, library preparation was previously described (Liu et al., Cell., 2018). Adapter was diluted on a ratio of 1:50 and 10-12 cycles of PCR amplification was used.

treatment_protocol: Dead cells from primay AML blasts were removed by Dead Cell Removal Kit (MACS) prior to RNA isolation.

value: Primary human cells

tag: antibody


title: GMP+CMP_donor2_H3K27ac


title: pso19_w2_bulk_S12_L002_R


title: PSO19_W12_CD8_S22_L003_R


title: PSO24_W0_Treg_S23_L004_R


title: HSPC_donor2_H3K27ac

source_name: human CD34+ HSPC


title: PSO19_W4_Treg_S17_L003_R


title: PSO25_W12_CD8_S49_L007_R


title: PSO24_W12_Teff_S41_L006_R


title: PSO19_W4_Teff_S18_L003_R


title: GMP+CMP_donor3_ZMYND8

value: ZMYND8 (bethyl A302-089A)


title: pso19_w2_teff_S10_L002_R


title: PSO24_W2_CD8_S31_L005_R


title: Ethanol control 1

first: Min

last: ZHAO

state: France

address: 15 rue de l'Ecole de Médecine

institute: INSERM U1138, Centre de Recherche des Cordelier, University Paris Descartes

data_processing:
Quality of raw data has been evaluated with FastQC
Poor quality sequences has been trimmed or removed with Trimmomatic software to retain only good quality paired reads with following parameters : cutoff: '20' leading: '10' minlen: '50' slidingwindow: '4' trailing: '10'
Star v2.5.3a has been used to align reads on  reference genome using standard options
Quantification of gene and isoform abundances has been done with rsem 1.2.28
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including expecting counts, TPM and FPKM

source_name: iRPE cells

growth_protocol: Cells were seeded at P3 in cell culture plastic dishes. On day 35, one week prior to corticosteroids treatments, RDMw/oA medium was remove and iRPE cells were incubated in experimental corticosteroid-free medium (DMEM, high glucose, HEPES, no phenol red, 10% Fetal Bovine Serum, charcoal stripped).

extract_protocol:
Total RNA was isolated from iRPE cells using the RNeasy Mini Kit (QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: On day 42, iRPE cells were treated for 24 h with the following corticosteroids treatments: aldosterone (10-7 M), cortisol (10-7 M) and cortisol (10-7 M) plus RU-486 (10-5 M). As corticosteroids were dissolved in ethanol (EtOH) or methanol (MeOH) control cells were treated with 0.1% EtOH or MeOH in medium.

value: hiPSC-derived RPE cells

tag: treatment

value: ethanol 0,1% in culture medium


title: Aldosterone 1

value: Aldosterone 100nM


title: PSO13_W4_Teff_S17_L003_R


title: PSO13_W4_CD8_S18_L003_R


title: PSO24_W0_Teff_S24_L004_R


title: HSPC_donor2_ZMYND8


title: PSO25_W0_bulk_S580_L007_R

value: bulk


title: PSO13_W4_bulk_S22_L003_R


title: Methanol Control 4

value: methanol 0.1percent in culture medium


title: Methanol Control 3


title: PSO24_W0_bulk_S26_L004_R

value: lesion


title: pso19_w0_cd8_S3_L001_R


title: PSO13_W2_Teff_S10_L002_R


title: HSPC_donor3_H3K27ac


title: PSO25_W12_Treg_S47_L007_R

value: Treg


title: pso19_w0_bulk_S4_L001_R


title: PSO19_W12_Treg_S20_L003_R


title: PSO19_W12_Teff_S21_L003_R


title: Cortisol+RU486_4

value: Cortisol 100 nM+RU486 10µM


title: PSO13_W12_Treg_S19_L003_R

value: TRUE


title: Ethanol control 3


title: Cortisol+RU486_2


title: Aldosterone 3


title: Cortisol+RU486_1


title: Cortisol+RU486_3


title: PSO13_W12_bulk_S8_L001_R


title: pso19_w0_teff_S2_L001_R

value: Teff


title: HSPC_donor3_ZMYND8


title: Ethanol control 2


title: PSO13_W12_CD8_S21_L003_R


title: PSO19_W12_bulk_S24_L003_R


title: Cortisol 2

value: Cortisol 100 nM


title: pso19_w0_treg_S1_L001_R


title: PSO13_W0_CD8_S3_L001_R


title: Methanol Control 2


title: PSO13_W0_Teff_S2_L001_R


title: Methanol Control 1


title: Aldosterone 2


title: MOLM13_PWWPmut_ZMYND8

source_name: human AML MOLM-13 cell line

tag: infection

value: Cells were stably expressing sgRNA_resistant ZMYND8 (F308A/W311A), and collected on 5 days post infection of sgZMYND8_2


title: MOLM13_WT_IgG

value: IgG (Sigma I8140)

value: Cells were stably expressing sgRNA_resistant ZMYND8-WT, and collected on 5 days post infection of sgZMYND8_2


title: PSO13_W0_bulk_S4_L001_R

value: FALSE


title: PSO13_W2_CD8_S11_L002_R


title: PSO13_W4_Treg_S16_L003_R


title: PSO12_W2_Teff_S9_L002_R


title: PSO13_W2_Treg_S9_L002_R


title: MOLM13_PHDmut_ZMYND8

value: Cells were stably expressing sgRNA_resistant ZMYND8  (N107A/D108A), and collected on 5 days post infection of sgZMYND8_2


title: PSO12_W2_bulk_S11_L002_R


title: PSO13_W0_Treg_S1_L001_R


title: PSO13_W2_bulk_S12_L002_R


title: MOLM13_BRDmut_ZMYND8

value: ZMYND8 (bethyl A302-089A)

value: Cells were stably expressing sgRNA_resistant ZMYND8 (N248A), and collected on 5 days post infection of sgZMYND8_2


title: Cortisol 4

value: hiPSC-derived RPE cells


title: MOLM13_dZD8_IgG


title: PSO12_W12_Teff_S20_L003_R


title: PSO12_W12_CD8_S21_L003_R


title: PSO12_W2_CD8_S10_L002_R


title: PSO12_W12_bulk_S23_L003_R


title: MOLM13_dZD8_dTAG_BRD4

value: Cells were stably expressing sgZMYND8_2 and sgRNA_resistant ZMYND8-FKBP12-G36V

value: Four hour treatment with 500nM dTAG-47


title: PSO12_W0_Treg_S1_L001_R


title: MOLM13_dZD8_JQ1_BRD4

value: Four hour treatment with 2uM JQ1


title: PSO12_W0_Teff_S2_L001_R

value: lesion


title: PSO12_W0_bulk_S4_L001_R

value: bulk


title: PSO10_W4_Treg_S32_L005_R

value: Treg


title: PSO10_W4_Teff_S33_L005_R

value: TRUE


title: HSPC_donor1_IgG

value: Primary human cells


title: PSO10_W4_bulk_S35_L005_R


title: MOLM13_dZD8_DMSO_BRD4

value: Four hour treatment with 0.05% DMSO


title: MOLM13_WT_ZMYND8


title: PSO13_W12_Teff_S20_L003_R

value: Teff


title: Cortisol 3

value: Cortisol 100 nM


title: p6610_IgG

source_name: human primary AML blast #6610

value: IgG (Sigma I8140)


title: MOLM13_dZD8_DMSO_ZMYND8


title: MOLM13_dZD8_JQ1_ZMYND8


title: p6610_ZMYND8


title: PSO10_W2_CD8_S30_L004_R


title: PSO10_W2_bulk_S31_L004_R


title: p6527_ZMYND8

source_name: human primary AML blast #6527


title: HSPC_donor1_H3K27ac


title: MOLM13_dZD8_dTAG_ZMYND8


title: p6527_H3K27ac


title: PSO10_W12_bulk_S39_L005_R


title: PSO10_W12_CD8_S38_L005_R


title: PSO10_W12_Teff_S37_L005_R


title: PSO10_W2_Teff_S29_L004_R


title: p4943_H3K27ac

source_name: human primary AML blast #4943


title: PSO10_W2_Treg_S28_L004_R


title: p6610_H3K27ac


title: PSO10_W12_Treg_S36_L005_R

value: FALSE


title: HSPC_donor1_ZMYND8


title: PSO10_W0_Teff_S25_L004_R


title: p6527_IgG


title: HUH7_IgG

source_name: human liver cancer HUH7 cell line


title: PSO10_W0_bulk_S27_L004_R


title: PSO10_W4_CD8_S34_L005_R


title: HUH7_ZMYND8


title: NP4-04T-JJ-001_N714-S505_S49_L007_R


title: HEL_BRD4

source_name: human AML HEL cell line

value: HEL


title: Cortisol 1


title: p4943_ZMYND8

value: ZMYND8 (bethyl A302-089A)


title: PSO10_W0_CD8_S26_L004_R


title: NP4-04T-JJ-001_N715-S506_S50_L007_R


title: NP4-04T-JJ-001_N707-S510_S53_L007_R


title: PSO10_W0_Treg_S24_L004_R


title: HEL_ZMYND8


title: HEL_IgG


title: NP4-04T-JJ-001_N710-S511_S54_L007_R


title: NP4-04T-JJ-001_N705-S507_S51_L007_R


title: NP4-04T-JJ-001_N706-S508_S52_L007_R


title: NP4-04T-JJ-001_N715-S511_S58_L008_R


title: NP3-04T-AR-003_N712-S503_S61_L008_R


title: HUH7_BRD4


title: THP1_ZMYND8

source_name: human AML THP1 cell line


title: THP1_BRD4


title: MOLM13_IgG


title: MOLM13_H3K14ac

value: H3K14ac (MABE351)


title: MOLM13_H3K27ac


title: NP1-04T-JC-002_N707-S510_S46_L006_R


title: MOLM13_BRD4


title: NP1-04T-JC-002_N706-S508_S45_L006_R


title: MOLM13_H3K27me3


title: THP1_IgG


title: NP1-04T-JC-002_N701-S502_S40_L006_R


title: NP1-04T-JC-002_N704-S506_S43_L006_R


title: p6610_RNA-seq_rep3

data_processing:
sequencing reads for human cell lines upon ZMYND8 depletion/IRF8 degradation were aligned to human genome hg38,  and for primary patient samples, aligned to human genome hg19 using STAR Aligner. Raw read counts were generated via HTSeq-count. RPM-normalized bigwig files were generated using bedGraphToBigWig and were visualized in UCSC genome browser.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig, gene track

growth_protocol: Samples were frozen in FCS and 10% DMSO in liquid nitrogen until used.

extract_protocol:
RNA was isolated from 1-3 million cells with Direct-zol RNA Miniprep Plus kit (ZYMO).
RNA-seq libraries were constructed using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina. Briefly, 1 g of total RNA was poly-A selected and fragmented with NEBNext® Poly(A) mRNA Magnetic Isolation Module, followed by first and second strand cDNA synthesis. The libraries were end-repaired, linked with the Illumina adaptor, PCR amplified with 8 cycles.

treatment_protocol: Dead cells were removed by Dead Cell Removal Kit (MACS) prior to RNA isolation.

value: primary AML blast


title: p6610_RNA-seq_rep2


title: N4W4_CD8_S586_L008_R


title: MOLM13_ZMYND8


title: N4W4_Teff_S585_L008_R


title: MOLM13-4C_MYC_rep1

data_processing:
Library strategy: 4C-seq
Paired-end reads of each replicate were aligned to hg19 and processed as .hic file using juicer. Intrachromosomal contact matrices of chromosome 8 (for MYC) or 16 (for IRF8) were extracted using juicer tools ‘dump’ command at 5 kb resolution without normalization. For each replicate, contacts ± 350 kb around the viewpoint were summed up as total valid contacts. Contacts from the viewpoint were normalized by dividing total valid contacts times 1000.
Genome_build: hg19
Supplementary_files_format_and_content: hic file, interaction frequency

growth_protocol: MOLM-13 were cultured in RPMI 1640-Media with 25mM HEPES supplemented with 10% Bovine Calf Serum (FCS) and 1% Penicillin/ Streptomycin.

extract_protocol:
5-10 million cells were harvested and cross-linked as described in previously mentioned the ChIP-seq protocol. Cells were resuspended in lysis buffer (10mM Tris-HCl pH 8.0, 10mM NaCl, 0.2% NP-40 with protease inhibitor) at 4°C for 30 minutes with rotation. Isolated nuclei were washed with lysis buffer, and permeabilized with 200 µl 10% SDS at 62°C for 10 min, which was sequestered by 235 µl 2% Triton X-100 at 37°C for 15 minutes. Chromatin was digested with 15 µl of MboI (R0147) at 37°C for 2 hr, and an additional 5 µl of MboI was applied for 1 hr. MboI was then heat inactivated at 62°C for 20 minutes. Proximity ligation was performed using the ligation master mix (150µl 10X NEB T4 DNA ligase buffer, 125 µl 10% Triton X-100, 3µl 50mg/ml BSA, 4000U T4 DNA ligase, 660µl H2O) at room temperature for 4 hr with rotation, and an additional 4000U T4 DNA ligase was applied for 2 hr. The nuclei pellet was spun down at 2500 rcf at 4°C for 5 minutes, resuspended with 200 µl Proteinase K Buffer, and treated with 10 µl proteinase K at 55°C for 45min, then at 65°C overnight with 900 rpm shaking. The next day, 10 µl of RNase A was added and the mixture was incubated at 37°C for 10 minutes. DNA was precipitated with 3M NaAc and cold 100% ethanol, and eluted with 200 µl of Elution Buffer (EB) (10 mM Tris-HCl).
Samples underwent two rounds of PCR (20 cycles for the first round, and 15 for the second) and in each round, the 4C primer was paired with Illumia universal primer. The amplified 4C libraries were purified with 1x Ampure beads. For each viewpoint, two pairs of 4C primers were used and the libraries from the same viewpoint were equally pooled together.

value: AML

tag: viewpoint

value: MYC


title: MOLM13-4C-IRF8_rep1

tag: cell line


title: N4W3_Teff_S582_L007_R


title: p4943_IgG


title: N4W4_Treg_S587_L008_R


title: MOLM13-4C-IRF8_rep2


title: NP3-04T-AR-003_N714-S510_S57_L008_R


title: N4W3_Treg_S584_L008_R


title: p6527_RNA-seq


title: NP3-04T-AR-003_N711-S502_S60_L008_R


title: MOLM13-4C_MYC_rep3


title: MOLM13-4C-IRF8_rep3


title: NP1-04T-JC-002_N702-S503_S41_L006_R


title: MOLM13-4C_MYC_rep2


title: N4W3_CD8_S583_L007_R


title: NP1-04T-JC-002_N705-S507_S44_L006_R


title: MOLM13-dZD8_dTAG_rep2

data_processing:
Sequencing reads were aligned to human genome hg38, and for primary patient samples, aligned to human genome hg19 using STAR Aligner. Raw read counts were generated via HTSeq-count.
Genome_build: hg38
Supplementary_files_format_and_content: txt, raw read counts

extract_protocol:
Total RNA was isolated from 1~5 million cells using Direct-zol RNA Miniprep Plus kit (ZYMO) with DNase I treatment in column.
RNA-seq libraries were prepared using QuantSeq 3’ mRNA-seq Library Prep Kit (Lexogen) with 2 µg of total RNA according to the manufacturer's protocol. Library quality was checked by High Sensitivity Bioanalyzer (Agilent) and libraries with different barcodes were pooled and sequenced on the Nextseq 500 platform with 75 or 150 bp single-end reads.

treatment_protocol: Cells were treated with 500 dTAG-47 or DMSO (ctrl) for 4 hours

value: Four hour post treatment with 500nM dTAG-47


title: N4W0_Teff_N707-S504_S48_L007_R

value: lesion


title: NP1-04T-JC-002_N703-S505_S42_L006_R


title: p4943_RNA-seq


title: N4W0_CD8_S98_L001_R


title: N3W4_Teff_S96_L001_R


title: N3W4_CD8_S97_L001_R


title: MOLM13-dZD8_DMSO_rep1

value: Four hour post treatment with DMSO


title: MOLM13-dZD8_DMSO_rep2


title: N3W2_Teff_S93_L001_R


title: N3W4_Treg_S95_L001_R

value: Treg


title: MOLM13-dIRF8_dTAG_rep1


title: HUH7_sgZMYND8_1

growth_protocol: MOLM-13, MV4-11, THP1, NOMO1, HEL, OCI-AML3 and K562 were cultured in RPMI 1640-Media with 25mM HEPES supplemented with 10% Bovine Calf Serum (FCS) and 1% Penicillin/ Streptomycin.  HUH7 was cultured in DMEM with high glucose supplemented with 10% Bovine Calf Serum and 1% Penicillin/ Streptomycin.

treatment_protocol: MOLM-13, MV4;11, OCI-AML3, HEL, K562 and HUH7 cells were harvested on day 5 post infection of two independent sgZMYND8 or two sgNeg. NOMO-1 was harvested on day 6 post infection. THP-1 was harvested on day 9 post infection.

tag: post infection

value: day 5 after infection

tag: expression


title: N30_CD8_S38_L005_R

tag: sequencing batch

tag: sequencing lane

value: skin

value: Healthy

value: TRUE


title: N3W2_CD8_S94_L001_R

tag: cell type

tag: subject id


title: MOLM13-dIRF8_DMSO_rep3


title: HUH7_sgNeg2


title: MOLM13-dZD8_dTAG_rep1


title: MOLM13-dIRF8_dTAG_rep2


title: N3W0_Teff_S92_L001_R

value: Teff

tag: tissue


title: N3W2_Treg_S581_L007_R

tag: clinical status


title: HUH7_sgNeg1


title: MOLM13-dIRF8_dTAG_rep3


title: MOLM13-dIRF8_DMSO_rep2


title: N29_Teff_S29_L004_R

tag: sorted cells


title: N30_Teff_S37_L005_R

tag: used for analysis


title: p6610_RNA-seq_rep1


title: HUH7_sgZMYND8_2


title: N29_Treg_S31_L004_R


title: MOLM13-dIRF8_DMSO_rep1


title: K562_sgZMYND8_2

source_name: human CML K562 cell line


title: K562_sgNeg2


title: N30_bulk_S40_L005_R

value: bulk


title: N29_CD8_S30_L004_R


title: Hetero sample 2

city: Seoul

first: Kihoon

last: Han

address: 73, Inchon-ro, Seongbuk-gu

department: Neuroscience

country: South Korea

institute: Korea University College of Medicine

data_processing:
Transcript abundance was estimated with Salmon(v0.11.2) in Quasi-mapping-based mode onto the Mus musculus genome (GRCm38) with GC bias correction (--gcBias).
Quantified gene-level abundance data was imported to R (v.3.6.0) with tximport package and differential gene expression analysis was carried out using R/Bioconductor DEseq2 (v1.19.11).
The normalized read counts were computed by dividing the raw read counts by size factors and fit to a negative binomial distribution.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file include normalized read count metrix calculated by using DESeq2.

source_name: Brain

extract_protocol:
RNA samples were prepared for sequencing using a TruSeq Stranded mRNA LT Sample Prep Kit  (Illumina) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq Stranded mRNA Sample Preparation Guide)

tag: strain

value: Cortex

tag: developmental stage

value: embryo (E18.5)

tag: genotype

value: Cyfip2 Heterozygote


title: Knockout sample 1

value: Cyfip2 knockout


title: Knockout sample 2


title: N29_bulk_S32_L004_R

source_name: skin


title: Knockout sample 3


title: N30_Treg_S39_L005_R


title: N28_Treg_S14_L002_R


title: K562_sgZMYND8_1


title: Hetero sample 1


title: Wild type sample 3

value: WT


title: Wild type sample 1


title: N28_Teff_S12_L002_R


title: K562_sgNeg1


title: HEL_sgZMYND8_1

value: HEL


title: N28_CD8_S13_L002_R


title: HEL_sgNeg2


title: N27_Treg_S7_L001_R


title: HEL_sgZMYND8_2


title: HEL_sgNeg1


title: THP1_sgZMYND8_2

value: day 9 after infection


title: THP1_sgZMYND8_1


title: N27_Teff_S5_L001_R

value: FALSE


title: Wild type sample 2


title: N27_CD8_S6_L001_R


title: N27_bulk_S8_L001_R


title: THP1_sgNeg2


title: N26_CD8_S14_L002_R


title: N28_bulk_S15_L002_R


title: OCI-AML3_sgZMYND8_1

source_name: human AML OCI-AML3 cell line


title: OCI-AML3_sgNeg1


title: NOMO1_sgZMYND8_1

source_name: human AML NOMO1 cell line

value: day 6 after infection


title: THP1_sgNeg1


title: Hetero sample 3


title: N23_N706-S508_S56_L008_R


title: NOMO1_sgZMYND8_2


title: OCI-AML3_sgNeg2


title: OCI-AML3_sgZMYND8_2


title: N23_Treg_S15_L002_R


title: NOMO1_sgNeg1


title: NOMO1_sgNeg2


title: N23_CD8_S14_L002_R


title: MV4-11_sgZMYND8_2

source_name: human AML MV4-11 cell line


title: N22_Teff_S5_L001_R


title: N26_treg_S15_L002_R


title: N26_Teff_S13_L002_R


title: N23_Teff_S13_L002_R


title: N26_bulk_S16_L002_R


title: N22_Treg_S7_L001_R


title: N22_CD8_S6_L001_R


title: MV4-11_sgZMYND8_1


title: MV4-11_sgNeg2


title: N21_Teff_S588_L008_R


title: MV4-11_sgNeg1


title: N21_Treg_S590_L008_R


title: N21_CD8_S589_L008_R


title: MOLM13_sgZMYND8_1


title: MOLM13_sgZMYND8_2


title: N20_Treg_S583_L007_R


title: MOLM13_sgNeg2_rep2


title: MOLM13_sgMEF2D_2


title: N22_N705-S507_S55_L008_R


title: N1W7_Treg_S580_L007_R

value: lesion


title: MOLM13_sgMEF2D_1


title: MOLM13_input

data_processing:
Reads were aligned to human genome hg19 using Bowtie2 v2.3.5 , following parameters as previously suggested (Skene et al., 2018): --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700 -k1 -N1. Picard tools v1.96 was used to remove presumed PCR duplicates using the MarkDuplicates command. Bam files containing uniquely mapped reads were created using Samtools v1.1. Fragments of <40 bp or >1000 bp were filtered out. Blacklist regions defined by ENCODE, random chromosomes, and mitochondria were removed, and filtered bam files were used for downstream analysis. Read count per million (RPM)-normalized bigwig files were created by bedGraphToBigWig (UCSC).
Genome_build: hg19
Supplementary_files_format_and_content: bigwig, gene track

extract_protocol:
A total of 5x107 leukemia cells were harvested and supplemented with full culture media. Cross-linking was performed with 1% formaldehyde for 20 minutes at room temperature with rotation, and the sample was quenched with glycine for 10 minutes at a final concentration of 0.125 M. The cell pellet was washed with PBS, and lysed with cell lysis buffer (10 mM Tris, pH8.0, 10 mM NaCl, 0.2% NP-40, protease inhibitor) on ice for 10 min. The buffer was removed, and the cell pellet was split into 1x107 cell aliquots in 15 mL falcon tubes and incubated in 1mL of nuclear lysis buffer (50 mM Tris, pH 8.0, 10 mM EDTA, 1% SDS, protease inhibitor) for at least 10 minutes on ice. Lysed cells were sonicated with a bioruptor (Diagenode) for 5 min at 4°C, followed by centrifugation at 14,000 rpm for 15 minutes at 4°C. Supernatants were combined and diluted with 35 mL IP dilution buffer (20 mM Tris, pH 8.0, 2 mM EDTA, 150 mM NaCI, 1% Triton X-100, 0.01% SDS), 5 µg of IRF8 antibody (ab207418), and 40 µl of Protein A magnetic beads (Invitrogen). The mixture was incubated in rotation overnight at 4°C. The beads were subjected to a wash cycle with wash buffers in the following order: IP Wash I buffer (20 mM Tris-HCI pH 8.0, 2mM EDTA, 50 mM NaCI, 1% Triton X-100, 0.1% SDS), High salt buffer (20 mM Tris-HCI pH 8.0, 2 mM EDTA, 500 mM NaCI, 1% Triton X-100, 0.1% SDS) (twice), IP Wash II buffer (10 mM Tris-HCI pH 8.0, 1 mM EDTA, 0.2 M LiCI, 1% NP-40, 1% Nadeoxycholate), and TE pH 8.0 (twice). Fragmented chromatin was eluted with 200 µl elution buffer (50 mM Tris 8.0,10 mM EDTA, 1% SDS) with shaking at 600 rpm at 65°C for 15 minutes. The chromatin was reverse-crosslinked with 0.25 M NaCI overnight at 65°C, and non-DNA content was digested with RNase A for 1 hour at 65°C, and Proteinase K (0.2 mg/mL) for 2 hr at 42°C.
DNA was purified with QIAquick PCR purification kit following the manufacturer’s instructions. ChIP-seq library construction was prepared with NEBNext® Ultra™ II DNA Library Prep Kit for Illumina. Library quality was validated with a high sensitivity Bioanalyzer (Aligent) kit

tag: antibody


title: zCM_kit_14dpi1

data_processing:
Qualities of de-barcoded raw sequence reads were checked by fastqc.
The alignment was performed using BBMap/38.1213 against the reference zebrafish genome UCSC_DanRer10
Gene counts were obtained using featureCounts. The raw counts were normalized to sequencing depth using counts per million (CPM).
Genome_build: UCSC_DanRer10
Supplementary_files_format_and_content: tab-delimited text files containing CPM values for each sample

extract_protocol:
Total RNAs of isolated adult zebrafish cardiomyocytes from eight pooled ventricles were extracted using QIAGEN RNeasy Micro kit.
Illumina libraries were prepared using TrueSeq Standard mRNA Sample Preparation Kit.

tag: genotype/variation

value: kit mutant; kita(w34b2);kitb(sa15356)

tag: treatment/timepoint

value: 14 days post injury

tag: age

value: 4-6 month

value: heart

value: cardiomyocytes


title: MOLM13_sgNeg2_rep1

tag: post infection

value: day 5 after infection

tag: cell line


title: MOLM13_sgNeg1_rep2

tag: expression


title: N1W2_Treg_N706-S503_S5_L001_R

tag: sequencing batch

tag: sequencing lane

value: Treg


title: N1W2_Teff_N704-S503_S6_L001_R

tag: cell type

value: Teff

tag: subject id


title: N20_bulk_S3_L001_R

value: bulk

tag: tissue

value: skin

tag: clinical status

value: Healthy

value: TRUE


title: N20_CD8_S582_L007_R

tag: sorted cells

tag: used for analysis


title: N1W7_Teff_S578_L007_R


title: N1W2_CD8_N705-S503_S7_L001_R


title: N21_bulk_S19_L003_R


title: zCM_kit_7dpi2

value: 7 days post injury


title: zCM_kit_14dpi2


title: N1W7_CD8_S579_L007_R


title: VDR ko THP-1, 4 h EtOH, replicate 4

city: Frankfurt am Main

first: Timothy

last: Warwick

state: Hesse

address: Theodor-Stern-Kai 7

department: Institute for Cardiovascular Physiology

institute: Goethe Universität Frankfurt am Main

data_processing:
FastQC: assessed for quality, adapter content and duplication rates
STAR: alignment to reference genome with the parameter –quantMode GeneCounts for gene-level quantification and otherwise default parameters
DESeq2: computation of differential gene expression with standard parameters and an adjusted p-value cutoff of 0.05
Genome_build: hg19
Supplementary_files_format_and_content: VDR.KO.RNAseq.ResultsTables.4N_l.xlsx

source_name: human monocytic cell line THP-1

growth_protocol: THP-1 human monocytic leukemia cells were grown in RPMI 1640 supplemented with 10% fetal calf serum, 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin and the cells were kept at 37 °C in a humidified 95% air/ 5% CO2 incubator.

extract_protocol:
Total RNA was extracted with the Quick-RNA Miniprep Kit (Zymo Research).
with VAHTS Stranded mRNA-seq Library Prep Kit for Illumina V2 (Vazyme NR612, poly(A) enrichment)

treatment_protocol: VDR knockout or control cells were either treated with 100 nM of the natural VDR ligand 1,25-dihydroxyvitamin D3 (Sigma-Aldrich) or with vehicle (EtOH).

value: monocytic cell line THP-1

value: VDR knockout

tag: treatment

value: EtOH

tag: treatment time

value: 4 h


title: N20_Teff_S581_L007_R

data_processing:
Mapping to GRCh38 performed using STAR v2.4.2a
Raw gene counts calculated using HTSeq v0.6.1p1  on the GENCODE 25 annotation of GRCh38
Samples with < 1 million reads, < 10,000 detected genes, or < 60% mappable reads were excluded
Genes expressed at < 5 reads in fewer than 20% of samples were excluded
Genome_build: GRCh38
Supplementary_files_format_and_content: CountData_SecukinumabPsoRnaSeq_20210324.tsv  (Matrix table with raw gene counts for every gene and every sample)


title: VDR ko THP-1, 24 h EtOH, replicate 4


title: N18_Treg_S35_L005_R


title: VDR ko THP-1, 24 h 1,25(OH)2D3, replicate 4


title: N18_Teff_S33_L005_R


title: zCM_kit_5dpi1

value: kit mutant; kita(w34b2);kitb(sa15356)

value: 5 days post injury


title: zCM_kit_5dpi2

value: 4-6 month


title: VDR ko THP-1, 4 h 1,25(OH)2D3, replicate 4


title: MOLM13_sgNeg1_rep1


title: control THP-1, 4 h EtOH, replicate 4

value: non-targeting control gRNA-transduced


title: zCM_kit_2dpi2

value: 2 days post injury

value: heart

value: cardiomyocytes


title: N18_CD8_S34_L005_R


title: N1W0_CD8_S577_L007_R

value: lesion


title: MOLM13_IRF8_ChIP

tag: antibody


title: control THP-1, 24 h 1,25(OH)2D3, replicate 4


title: VDR ko THP-1, 4 h 1,25(OH)2D3, replicate 3


title: N17_CD8_S6_L001_R


title: N1W0_Teff_N707-S504_S59_L008_R

value: Teff

value: FALSE


title: zCM_wt_14dpi1

tag: genotype/variation

value: wild type

value: 14 days post injury


title: VDR ko THP-1, 24 h 1,25(OH)2D3, replicate 3


title: control THP-1, 24 h 1,25(OH)2D3, replicate 3


title: N15_Teff_S27_L004_R

value: skin

value: Healthy

value: TRUE


title: N17_Treg_S7_L001_R

value: Treg


title: zCM_kit_7dpi1

tag: treatment/timepoint

value: 7 days post injury


title: control THP-1, 4 h 1,25(OH)2D3, replicate 4

value: monocytic cell line THP-1

value: 4 h


title: N15_CD8_S28_L004_R


title: N17_bulk_S8_L001_R

value: bulk


title: zCM_kit_2dpi1

value: kit mutant; kita(w34b2);kitb(sa15356)

tag: age

value: 4-6 month


title: zCM_kit_untouched2

value: untouched

value: heart


title: control THP-1, 4 h 1,25(OH)2D3, replicate 3

value: non-targeting control gRNA-transduced


title: VDR ko THP-1, 24 h EtOH, replicate 3

value: VDR knockout

value: EtOH


title: control THP-1, 24 h EtOH, replicate 4


title: zCM_wt_2dpi1

value: wild type

value: 2 days post injury

value: cardiomyocytes


title: zCM_wt_14dpi2

value: 14 days post injury


title: VDR ko THP-1, 24 h EtOH, replicate 2


title: N17_Teff_S5_L001_R

value: Teff

value: skin

value: Healthy

value: TRUE


title: N11_CD8_S589_L008_R


title: control THP-1, 24 h EtOH, replicate 3

value: monocytic cell line THP-1


title: zCM_wt_5dpi1

value: 5 days post injury


title: zCM_kit_untouched1

value: kit mutant; kita(w34b2);kitb(sa15356)


title: zCM_wt_7dpi2

value: 7 days post injury

value: 4-6 month


title: N11_Treg_S590_L008_R

value: Treg


title: VDR ko THP-1, 4 h EtOH, replicate 3

value: 4 h


title: N15_bulk_S16_L003_R

value: bulk


title: VDR ko THP-1, 24 h 1,25(OH)2D3, replicate 2

value: VDR knockout


title: R_WT_ndb_819

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

data_processing:
trimmed with trim_galore version 0.6.4. Parameters: --length 26 --phred33
Get raw counts with kallisto quant version 0.4.6.
TPM abundance estimates, generated with kallisto quant 0.4.6
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: TPM abundance estimates and raw counts generated with kallisto.

source_name: Retina

extract_protocol:
Organs were removed, flash frozen in liquid nitrogen; RNA was isolated by Trizol method
RNA libraries were prepared for sequencing using standard BGISeq-500 protocols

value: Retina

tag: diabetic status

value: normal

tag: genotype

value: WT


title: VDR ko THP-1, 4 h EtOH, replicate 2

tag: cell line

value: EtOH


title: N11_Teff_S588_L008_R

tag: sequencing batch

value: Teff


title: zCM_wt_7dpi1

value: wild type

value: heart

value: cardiomyocytes


title: KURAMOCHI L778123 1

type: RNA

city: Tokyo

first: Yusuke

last: Kobayashi

state: Outside of the US

address: 35 Shinanomachi, Shinjuku-ku

department: Department of Obstetrics and Gynecology

country: Japan

institute: Keio University School of Medicine

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v3; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction software 11.5.1.1 (Agilent).

data_processing: The scanned images were analyzed with Feature Extraction software 11.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

source_name: KURAMOCHI, L778123

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: The total RNA was isolated from cells using RNeasy Mini Kits (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

value: Ovarian cancer cell line

value: KURAMOCHI


title: zCM_wt_2dpi2

value: 2 days post injury


title: R_WT_ndb_812


title: zCM_wt_5dpi2

value: 5 days post injury


title: KURAMOCHI L778123 2


title: KURAMOCHI Simvastatin 2

source_name: KURAMOCHI, Simvastatin

value: Simvastatin


title: R_WT_db_954

value: diabetic


title: N15_Treg_S29_L004_R

extract_protocol:
Sequencing libraries were constructed using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Clontech cat. 634894). Bulk RNA was extracted from whole skin tissue using Qiagen RNeasy fibrous tissue mini kit (cat. 74704). Reverse transcription was performed on poly-adenylated RNA from cell lysate for up to 1,000 cells followed by second strand synthesis to make full length cDNA. cDNA was then later amplified by PCR using cycle numbers determined by cell numbers. Amplified cDNA was purified by AMPure XP beads (Beckman Coulter) and followed by Qubit quantification.
Sequencing libraries were constructed using the Illumina Nextera DNA kit with 0.4 ng of amplified cDNA for sorted lymphocytes and 0.3 ng for cDNA synthesized from bulk skin RNA.

tag: sequencing lane

value: Treg

value: skin

value: Healthy

value: TRUE


title: control THP-1, 4 h EtOH, replicate 3

value: monocytic cell line THP-1

value: non-targeting control gRNA-transduced

value: 4 h


title: zCM_wt_untouched1

value: untouched

value: 4-6 month

tag: cell type


title: R_WT_ndb_852

value: Retina

value: normal

value: WT


title: VDR ko THP-1, 24 h 1,25(OH)2D3, replicate 1

value: VDR knockout


title: VDR ko THP-1, 4 h 1,25(OH)2D3, replicate 2


title: VDR ko THP-1, 24 h EtOH, replicate 1

value: EtOH


title: zCM_wt_untouched2

value: wild type

value: heart

value: cardiomyocytes


title: control THP-1, 24 h EtOH, replicate 2


title: VDR ko THP-1, 4 h 1,25(OH)2D3, replicate 1


title: control THP-1, 4 h 1,25(OH)2D3, replicate 2


title: R_WT_db_915

value: diabetic


title: OVSAHO Simvastatin 1

source_name: OVSAHO, Simvastatin

value: Ovarian cancer cell line

value: OVSAHO

value: Simvastatin


title: control THP-1, 24 h 1,25(OH)2D3, replicate 1

value: monocytic cell line THP-1


title: control THP-1, 24 h EtOH, replicate 1

value: non-targeting control gRNA-transduced


title: CT7.5 SCN cells run 3 (mmSCN11)

city: Cambridge

first: Emma

last: Morris

address: Francis Crick Avenue

department: Neurobiology

institute: MRC Laboratory of Molecular Biology

data_processing:
CellRanger mkfastq software was used for demultiplexing raw base call files generated by Illumina sequencers into FASTQ files
CellRanger count software was used for alignment (STAR), filtering, barcode counting and UMI counting.
CellRanger aggr software was used for aggregating cells from biologically replicate runs
Clustering of cells was performed by either graph-based clustering or k-means clustering methods
Cell Loupe Browser was used to visualise and analyse data
Genome_build: mm38
Supplementary_files_format_and_content: HDF5 files include filtered gene - barcode matrices for each sequencing run
Supplementary_files_format_and_content: Excel format files include abundance measurements of all genes in each cluster within CT7.5 (day) and CT15.5 (night) sequenced cells

source_name: Hypothalamic Cells

extract_protocol:
Brains were retrieved from mouse pups at p10-12 and cut into 300µm thick slices using a McIlwain Tissue Chopper. The slices were examined under a bright-light microscope to sort those containing optimal SCN preparations and trimmed accordingly. Single SCN cells were isolated by proteolytic enzymatic digestion using the Worthington Papain dissociation kit. To ensure the cells were properly dissociated the mixture was filtered through a 40µm mesh.
scRNASeq libraries were prepared using the Chromium Single Cell Controller. Cells were treated following the manufacturer's protocols using 10x Genomics ChromiumTM Single Cell 3' Library and Gel Bead Kit v2 and ChromiumTM Single Cell A Chip Kit. Final libraries were sequenced on one flow cell of an Illumina HiSeq 4000 with a read length of 26 bp for read 1 and 98 bp for read 2 to yield approximately 340 million reads per sample.

tag: strain

value: Brain Hypothalamus

value: Postnatal day 10-12


title: control THP-1, 4 h EtOH, replicate 2

value: 4 h


title: OVSAHO L778123 1

source_name: OVSAHO, L778123


title: R_KO_ndb_559

tag: tissue

value: Retina

value: KO


title: R_KO_db_591


title: control THP-1, 4 h 1,25(OH)2D3, replicate 1


title: KURAMOCHI Simvastatin 1

value: KURAMOCHI


title: R_WT_db_844

value: WT


title: R_WT_db_942


title: control THP-1, 24 h 1,25(OH)2D3, replicate 2


title: OVSAHO Simvastatin 2


title: CT7.5 SCN cells run 1 (mmSCN6)


title: R_KO_db_587


title: R_KO_db_588


title: smax1smxl2_2

city: Berlin

first: Henrik

last: Johansson

address: Albrecht-Thaer-Weg 6

institute: Freie Universität Berlin

data_processing:
base-calling was done with BGISEQ500, version 1.1.2.29164
After removal of adaptors and low quality reads, the obtained clean reads (approximately 23 million) were stored as FASTQ format   SOAPnuke, version v1.5.2, parameters: -I15 -q 0.5 -n0.1
The clean reads were mapped to the reference genome (TAIR10) using HISAT, version v2.0.4, parameters: -p8 --phred64 --sensitive -I 1 -X10000
For gene expression analysis clean reads were mapped to reference using Bowtie2, v2.2.5, parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k  200
Gene expression levels based on the FPKM method were quantified using RSEM v1.2.12, Parameters: default
Genome_build: TAIR10
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample

organism: Arabidopsis thaliana

source_name: whole seedling

growth_protocol: Seeds were surface sterilized, sown on half MS medium without sucrose and stratified in darkness for 2 days at 4°C. Seedlings were grown for 4  days in red light [80 µmol m-2 s-1] at 22 °C.

extract_protocol:
Total RNA was extracted from seedlings flash-frozen in liquid nitrogen using Phenol/Chloroform/Isoamylalcohol method, follwed by RNA cleanup and on-column DNAse treatment with the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany) as described in the user’s manual
RNA libraries were prepared by the BGISEQ-500 RNA-Seq Library Preparation Protocol. In brief, mRNA was purified with oligo(dt) magnetic beads, mRNA was chemically fragmented and cDNA was generated using random hexamer-primed reverse transcription. End-repair and 3'adenylation was done and adapters were ligated to the adenylated cDNA. adapter-ligated was amplified via PCR and purified with Ampure XP Beads (Agencourt). The library was validated on the Agilent Technologies 2100 bioanalyzer and the double stranded PCR products were denaturated and circularized.

value: whole seedling

tag: Stage

value: 4 days after germination

tag: growth

value: deetiolated/red light


title: ADAM10 KO CD8+ DC_sample 3

city: Mainz

first: Ronald

last: Backer

address: Obere Zahlbacher Str. 67

department: Institute for Molecular Medicine

institute: University Medical Center of the Johannes Gutenberg-University Mainz

description: Sample 18

data_processing:
Raw sequence reads were processed by the RASflow pipeline (DOI: 10.1186/s12859-020-3433-x)
The quality of raw sequence reads of all samples was analyzed with the FastQC tool 0.11.8 (Babraham Bioinformatics).
Raw sequence reads were mapped to the reference transcriptome GRCm38 to generate raw read counts and TPM values with salmon v0.14.1 (-l A –seqBias --useVBOpt –validateMappings) (DOI: 10.1038/nmeth.4197)
Genome_build: reference genome GRCm38
Supplementary_files_format_and_content: Matrix table with TPM values for every transcripts and every sample
Supplementary_files_format_and_content: Matrix table with raw transcript counts (abundance) for every transcript and every sample

source_name: dendritic cell

extract_protocol:
Spleens were cut in grain size pieces and digested with 200U/ml Collagenase Type IV + 0,5 U/ml Dnase for 30 min at 37 oC. CD11c+ cells were pre-enriched by MACS, followed by FACS-sorting for living CD11c+MHCII+CD8+ cDC1, CD11c+MHCII+CD4+ cDC2 and CD11c+MHCII+CD8-CD4- cDC2.
mRNA was purified from sorted splenic cDC subpopulations with the RNeasy Plus Micro kit according to manufacturer’s instructions (Qiagen). Barcoded mRNA-seq cDNA libraries were prepared from 50 ng of total mRNA using NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II RNA Library Prep Kit for Illumina according to the manual (New England BioLabs. Barcoded RNA-Seq libraries were onboard clustered using HiSeq Rapid SR Cluster Kit v2 using 8 pM and 59 bps reads were sequenced on the Illumina HiSeq2500 using the HiSeq Rapid SBS Kit v2 (50 Cycles).

value: spleen


title: K_WT_ndb_861

source_name: Kidney

value: Kidney

value: normal


title: bbx2021_3


title: smax1smxl2_1


title: CT15.5 SCN cells run 2 (mmSCN10)


title: R_KO_ndb_590


title: R_KO_ndb_582


title: bbx2021_1


title: Col-0 3


title: VDR ko THP-1, 4 h EtOH, replicate 1

value: VDR knockout

value: EtOH


title: WT CD8+ DC_sample 1

description: Sample 13


title: ADAM10 KO CD4- DC_sample 3

description: Sample 12


title: K_WT_ndb_812


title: K_WT_db_645

value: diabetic


title: Col-0 2


title: CT7.5 SCN cells run 2 (mmSCN7)


title: SK-N-AS BG-P-TAT (30 µM) Rep. TREATED-1_29

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

hyb_protocol: 16 h to Affymetrix Clariom S Human arrays

scan_protocol: Affymetrix Scanner 3000 7G using AGCC software.

data_processing: CEL files were summarized using the Gene Level-SST RMA algorithm in Transcriptome Analysis Console v4.0.1.36 (Affymetrix) and the normalized data were subjected to one-way ANOVA with a p-value less than 0.05 . A 2-fold change was used to select entities that were statistically and differentially expressed between any two conditions.

label: biotin

source_name: Neuroblastoma Primary cell line

label_protocol: Affymetrix Whole Transcript Sense Target labeling protocol

growth_protocol: Human Neuroblastoma cells  SKNFI  (ATCC , Manassas, VA, USA) and SKNAS  (as a gift from Children’s Oncology Group, Texas Tech University Health Sciences Center, Lubbock, TX, USA) were cultured in IMDM medium containing 10% FBS at 37°C and 5% CO2/95% O2.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells were treated with BG-P1600-TAT (30 µM) for 48 h. Control cells were exposed to PBS, pH 7.4, for the same period of time.

value: Neuroblastoma Primary cell line

tag: group

value: Treated


title: bbx2021_2


title: CT15.5 SCN cells run 1 (mmSCN5)

value: Brain Hypothalamus

value: Postnatal day 10-12


title: K_KO_ndb_582


title: OVSAHO L778123 2

value: Ovarian cancer cell line

value: OVSAHO

tag: treatment


title: control THP-1, 4 h EtOH, replicate 1

value: monocytic cell line THP-1

value: non-targeting control gRNA-transduced

tag: treatment time

value: 4 h


title: K_KO_ndb_560

value: KO


title: R_KO_ndb_560

value: Retina


title: ADAM10 KO CD8+ DC_sample 2

description: Sample 17

value: spleen


title: ADAM10 KO CD4- DC_sample 1

description: Sample 10


title: WT CD8+ DC_sample 2

description: Sample 14

value: WT


title: ADAM10 KO CD8+ DC_sample 1

description: Sample 16


title: K_WT_ndb_819

value: Kidney

value: normal


title: SK-N-AS BG-P-TAT (30 µM) Rep. TREATED-1_30


title: K_WT_db_844


title: WT CD4- DC_sample 2

description: Sample 8


title: smax1smxl2_3

value: whole seedling

value: 4 days after germination

value: deetiolated/red light


title: Col-0 1


title: WT CD4- DC_sample 3

description: Sample 9


title: K_WT_ndb_834


title: SK-N-AS UNTREATED Rep. Control 1_27

value: Neuroblastoma Primary cell line

value: Control


title: WT CD8+ DC_sample 3

description: Sample 15


title: K_WT_db_877

value: diabetic


title: WT CD4- DC_sample 1

description: Sample 7


title: K_WT_db_597


title: ADAM10 KO CD4+ DC_sample 2

description: Sample 5


title: ADAM10 KO CD4+ DC_sample 3

description: Sample 6


title: ADAM10 KO CD4- DC_sample 2

description: Sample 11


title: K_KO_db_591


title: K_KO_ndb_584


title: WT CD4+ DC_sample 3

description: Sample 3


title: K_KO_ndb_559


title: SK-N-AS UNTREATED Rep. Control 1_25


title: SK-N-AS BG-P-TAT (30 µM) Rep. TREATED-1_28

value: Treated


title: WT CD4+ DC_sample 1

description: Sample 1


title: SK-N-FI  TREATED (30 µM) BG-P1600-TAT Rep. Treated 2

source_name: Neuroblastoma  cell line

value: Neuroblastoma  cell line


title: ADAM10 KO CD4+ DC_sample 1

description: Sample 4


title: K_KO_db_588


title: K_KO_db_596


title: SK-N-AS UNTREATED Rep. Control 1_26


title: tag

status: Public on Sep 05 2021

city: Shinjuku

first: Kyoko

last: Komai

state: Tokyo

address: 35 Shinanomachi

department: Department of Microbiology and Immunology

institute: Keio University school f medecine

description: combined samples of tag5 to tag9

data_processing:
Adapter trimming of sequencing data was performed using cutadapt 2.10
Filtered cell barcode reads were annotated by Python script provided by BD Biosciences with minor modification for compatibility to Python 3.7
Reference RNA sequences were built by concatenating cDNA and ncRNA fasta files of the Ensembl database
Associated cDNA reads were mapped to reference RNA using bowtie2-2.4.2
Genome_build: GRCm38
Supplementary_files_format_and_content: Column names were named as "Hashtag_ID"_"sample ID"_"Cell barcode", and row names were gene symbols.

source_name: heart

extract_protocol:
Hearts were cut into small pieces with a razor blade and digested enzymatically using collagenaseⅡand DNase I (Sigma-Aldrich, St Louis, MO) for 60 min at 37°C. Cardiomyocyte and dead cell were removed by 40% Percoll (GE Healthcare, Buckinghamshire, UK) density separation.
For scRNA-seq, cDNA libraries and hashtag libraries were prepared combined by an BD Rhapsody system and TAS-Seq protocol (Shichino S. et al. BioRxiv 2021).
BD Rhapsody WTA

treatment_protocol: The transverse aorta was constricted with a 7-0 nylon suture across a 27-gauge blunt needle, which was removed after constriction

value: CD45+ cells

value: heart

tag: Sex

value: male

tag: model

value: TAC


title: cDNA

description: combined samples of tag5 to tag9


title: H3K27me3_Epi_Aebp2_KO2_rep1

city: Hangzhou

first: Dong

last: Fang

state: Zhejiang

address: 866 Yuhangtang Road

department: Life Sciences Institute

institute: Zhejiang University

data_processing:
Sequencing reads adaptor and low-quality bases were removed by Trim Galore (version 0.6.4) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore)
Filtered transcriptional SET-seq reads were mapped to the mouse reference genome mm9, which excluded mitochondria and random chromosomes, by STAR (version 2.5.4b)(Dobin et al., 2013)
Trimmed epigenomic SET-seq were then mapped to the mouse reference genome mm9 using Bowtie2(Langmead and Salzberg, 2012).PCR duplicates were removed by GATK4 (version 4.1.4.0) (https://github.com/broadinstitute/gatk) with the parameter ‘--REMOVE_DUPLICATES =true’.
Expression matrixes were counted by featureCounts(Liao et al., 2014) (version 2.0.0)
To get the single-cell gene expression matrixes, pipeline tool zUMIs(Parekh et al., 2018) (version 2.7.1c) was used to split reads into each cell by cell-specific barcode and map reads to mouse genome mm9, which excluded mitochondria and random chromosomes. The expression matrixes were analyzed by R package Seurat(Stuart et al., 2019) (version 3.2.1) using genes mapped to both of exons and introns.
Bedtools(Quinlan, 2014) (version 2.92.2) and bedGraphToBigWig (https://www.encodeproject.org/software/bedgraphtobigwig/) (version 4) were used to normalize mapped reads and calculate the coverage of features among the genome with the following parameters ‘genomecov --scaleFactor 10,000,000/mapped_reads_number’.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample of transcriptional SET-seq

source_name: Embryonic stem cells

growth_protocol: mESCs were cultured on 0.1% gelatin-coated plates in DMEM medium containing 15% Fetal Bovine Serum, 1% Penicillin/Streptomycin, 1% Glutamax, 0.1 mM 2-mercaptoethanol, 1% MEM nonessential amino acids, 1% sodium pyruvate, and 1,000 U/ml recombinant leukemia inhibitory factor (LIF).

extract_protocol:
The total RNA was extracted by UNIQ-10 Column Total RNA Purification kit (Sangon Biotech). Cells were harvested and then lysed in NE buffer (20 mM HEPES pH 7.5, 0.5 mM KCl, 0.5 mM Spermidine, 0.5% Triton X-100, 20% Glycerol, 1mM PMSF) on ice for 10min.
Bulk libraries preparation was described previously(Kaya-Okur et al., 2019a). Sc-libraries were constructed with a structure similar to True-seq libraries for pooling with other samples as described(Ai et al., 2019a).

treatment_protocol: A localized Wnt3a beads with mESCs were engineered in the 2 cm plates following previous method(Habib et al.). To achieve one cell and one bead contact, mESCs were sed at a low concentration before imaging or collecting. After seeding the cells and Wnt3a beads, samples were collected at around 12 hours.

value: untreated

tag: chip antibody

value: H3K27me3 (Cat# 9733, Cell Singaling Technology)


title: H3K27me3_Exp_Aebp2_KO2_rep2

tag: age


title: SK-N-FI UNTREATED Rep. Untreated 1


title: SK-N-FI  UNTREATED Rep. Untreated 2

source_name: Neuroblastoma cell line

value: Neuroblastoma cell line


title: SK-N-FI  TREATED (30 µM) BG-P1600-TAT Rep. Treated 1


title: H3K27me3_Epi_Aebp2_KO2_rep2


title: H3K27me3_Epi_Aebp2_KO1_rep2


title: Case18_remission_sequencing

city: Perugia

first: Danika

last: Di Giacomo

address: Piazzale Menghini 0

department: Medicine

country: Italy

institute: University of Perugia

description: Case_18 (UPN#148)

data_processing:
FASTQ sequencing files were uploaded to SOPHiA DDM® platform version 4 and, following adapter trimming and quality filtering, reads were aligned to the human reference genome (hg19 assembly) through the artificial SOPHiA™ intelligence.
Variant calling of the resulted alignments was then performed using an in-house somatic variant caller
Genome_build: hg19
Supplementary_files_format_and_content: None

extract_protocol:
DNA were extracted from bone marrow cells of patients using All Prep DNA/RNA Mini Kit (Qiagen).
Libraries were prepared using 200 ng of BM genomic DNA following manufacturer’s instructions (SOPHiA Genetics, Saint Sulpice, Switzerland).
probe-based targeted sequencing

value: Unsorted Bone Marrow Cells

tag: cytogenetics


title: Wnt beads H3K27me3 scSET-seq_Exp_10

description: Wnt_beads_H3K27me3_scSET-seq_Exp_counts_matrix.txt

value: treated with Wnt3a coated beads for 12 h


title: MGT_scATAC

data_processing:
Qualities of de-barcoded raw sequence reads were checked by fastqc.
Raw sequencing data was demultiplexed, debarcoded, mapped to Cell Ranger pre-built mm10 genome, and counted following the Cell Ranger ATAC v.1.1.0 pipeline. The Cell Ranger output of collapsed UMI counts were then processed and analyzed in R.
Genome_build: Cell Ranger pre-built mm10 reference
Supplementary_files_format_and_content: Two csv files containing peak status for cells in the two samples, respectively

source_name: cardiac fibroblast

growth_protocol: Mice were raised and maintained under standard laboratory conditions.

extract_protocol:
For direct cardiac reprogramming, pMXs retrovirus encoding Mef2c, Gata4, Tbx5, and LacZ were packaged by transfecting platE cells with Trans-IT as the manufacturer suggested. Viruses were collected from one 10-cm dish were resuspended in 100μl iCM medium(400ml DMEM, 100ml M199, and 50ml FBS). All virus transductions were performed in the iCM medium containing 4 μg/ml of polybrene. For single-cell ATAC-seq, cardiac fibroblasts were transduced with M, G, and T viruses for reprogramming sample or equal amounts of LacZ for mock sample.
Illumina libraries were prepared using Chromium Single Cell ATAC v1.0.
single-cell ATAC-seq

tag: genotype

value: wild type


title: Wnt beads H3K27me3 scSET-seq_Exp_5


title: Case17_remission_sequencing

description: Case_17 (UPN#150)


title: H3K27me3_Exp_Aebp2_KO1_rep2


title: Case17_diagnosis_sequencing

description: Case_17 (UPN#149)


title: H3K27me3_Exp_Aebp2_KO2_rep1


title: K_KO_db_587

value: Kidney

tag: diabetic status

value: KO


title: LacZ_scATAC


title: Wnt beads H3K27me3 scSET-seq_Exp_2


title: Wnt beads H3K27me3 scSET-seq_Exp_1


title: H3K27me3_Epi_Aebp2_KO1_rep1


title: Case11_remission_sequencing

description: Case_11 (UPN#261)


title: Case18_diagnosis_sequencing

description: Case_18 (UPN#147)


title: Case9_remission_sequencing

description: Case_9 (UPN#146)


title: WT CD4+ DC_sample 2

description: Sample 2

value: spleen

value: WT


title: Case16_diagnosis_sequencing

description: Case_16 (UPN#466)


title: H3K27me3_Exp_Aebp2_KO1_rep1


title: Wnt beads H3K27me3 scSET-seq_Exp_9


title: Wnt beads H3K27me3 scSET-seq_Exp_4


title: Wnt beads H3K27me3 scSET-seq_Exp_7


title: Wnt beads H3K27me3 scSET-seq_Exp_8


title: Wnt beads H3K27me3 scSET-seq_Epi_7


title: Wnt beads H3K27me3 scSET-seq_Epi_9


title: Wnt beads H3K27me3 scSET-seq_Exp_6


title: Wnt beads H3K27me3 scSET-seq_Epi_6


title: Case6_remission_sequencing

description: Case_6 (UPN#152)


title: Wnt beads H3K27me3 scSET-seq_Epi_4


title: Case4_remission_sequencing

description: Case_4 (UPN#142)


title: Case8_diagnosis_sequencing

description: Case_8 (UPN#143)


title: Wnt beads H3K27me3 scSET-seq_Exp_3


title: Case11_diagnosis_sequencing

description: Case_11 (UPN#260)


title: Wnt beads H3K27me3 scSET-seq_Epi_10


title: Case4_diagnosis_sequencing

description: Case_4 (UPN#141)


title: Case9_diagnosis_sequencing

description: Case_9 (UPN#145)


title: Wnt beads H3K4me3 scSET-seq_Exp_6

description: Wnt_beads_H3K4me3_scSET-seq_Exp_counts_matrix.txt


title: Wnt beads H3K27me3 scSET-seq_Epi_1


title: Wnt beads H3K27me3 scSET-seq_Epi_3


title: Case8_remission_sequencing

description: Case_8 (UPN#144)


title: Wnt beads H3K27me3 scSET-seq_Epi_8


title: Wnt beads H3K4me3 scSET-seq_Exp_1


title: Case6_diagnosis_sequencing

description: Case_6 (UPN#151)


title: Wnt beads H3K4me3 scSET-seq_Epi_6

value: H3K4me3 (Cat# ab8580, Abcam)


title: Wnt beads H3K27me3 scSET-seq_Epi_5


title: Wnt beads H3K4me3 scSET-seq_Epi_3


title: ns889 exposed to P. brevicompactum, replicate 3 [SW12_1]

city: New York

first: Sean

middle: William

last: Wallace

address: 1230 York Avenue Box 46

department: Laboratory of Developmental Genetics

institute: The Rockefeller University

data_processing:
Sequencing data was assessed for quality control using FastQC v0.11.12
fastq files were trimmed and aligned to WBcel235 using STAR v2.4a aligner with default parameters.
aligned reads were evaluated with Qualimap v2.2 to ensure consistent coverage, alignment rate and no obvious 5' or 3' bias
aligned reads were summarized through featureCounts on gene (Ensemble gene model Caenorhabditis_elegans.WBcel235.103.gtf and normalized through edgeR v 3.28.1
voom from limma v 3.42.2 was applied to estimate fold changes and BH-adjusted p-values
Genome_build: WBcel235
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Animals fgrown from L1 arrest to young adult stage (approx 48 hrs at 20 C on NMG plates with E. coli OP50)

extract_protocol:
Trizol LS treatment with freeze/thawing and vortexing, followed by chloroform extraction, RN easy column cleanup ans Dnase treatment
Illumina Truseq stranded mRNA-Seq library prep kit, with polyA selection (manufacturer's protocol)

treatment_protocol: Indicated samples also contained the mold P. brevicompacum on the plates

tag: agent

value: P. brevicompactum


title: Wnt beads H3K4me3 scSET-seq_Epi_2


title: Wnt beads H3K4me3 scSET-seq_Epi_1


title: WT exposed to P. brevicompactum, replicate 3 [SW10_1]


title: WT not exposed to P. brevicompactum, replicate 3 [SW9_2]


title: H3K27me3 scSET-seq_Epi_5


title: Wnt beads H3K4me3 scSET-seq_Epi_5


title: H3K27me3 scSET-seq_Epi_4


title: WT exposed to P. brevicompactum, replicate 3 [SW10_2]


title: ns889 exposed to P. brevicompactum, replicate 3 [SW12_2]


title: WT not exposed to P. brevicompactum, replicate 3 [SW9_1]


title: Wnt beads H3K4me3 scSET-seq_Exp_5


title: Wnt beads H3K4me3 scSET-seq_Epi_4


title: Wnt beads H3K4me3 scSET-seq_Exp_2


title: Wnt beads H3K4me3 scSET-seq_Exp_3


title: Wnt beads H3K4me3 scSET-seq_Exp_4


title: ns889 exposed to P. brevicompactum, replicate 2 [SW8_2]


title: H3K27me3 scSET-seq_Epi_1


title: ns889 not exosed to P. brevicompactum, replicate 3 [SW11_1]


title: H3K27me3 scSET-seq_Epi_3


title: H3K4me3 scSET-seq_Epi_5


title: H3K27me3 scSET-seq_Epi_2


title: Wnt beads H3K27me3 scSET-seq_Epi_2


title: ns889 not exosed to P. brevicompactum, replicate 2 [SW7_2]


title: ns889 not exosed to P. brevicompactum, replicate 3 [SW11_2]


title: ns889 not exosed to P. brevicompactum, replicate 2 [SW7_1]


title: WT exposed to P. brevicompactum, replicate 2 [SW6_2]


title: ns889 exposed to P. brevicompactum, replicate 2 [SW8_1]


title: WT not exposed to P. brevicompactum, replicate 2 [SW5_2]


title: H3K4me3 scSET-seq_Epi_1


title: H3K4me3 scSET-seq_Epi_3


title: Wnt H3K27me3 SET-seq_Epi_rep1

value: treated with WNT3a protein for 12h


title: WT not exposed to P. brevicompactum, replicate 2 [SW5_1]


title: H3K4me3 scSET-seq_Epi_2


title: Wnt H3K4me3 SET-seq_Epi_rep2


title: ns889 exposed to P. brevicompactum, replicate 1 [SW4]


title: Wnt H3K4me3 SET-seq_Epi_rep1


title: WT exposed to P. brevicompactum, replicate 2 [SW6_1]


title: Wnt H3K27me3 SET-seq_Epi_rep2


title: ns889 not exosed to P. brevicompactum, replicate 1 [SW3]


title: WT exposed to P. brevicompactum, replicate 1 [SW2]


title: WT not exposed to P. brevicompactum, replicate 1 [SW1]


title: H3K4me3 scSET-seq_Epi_4


title: H3K27me3 SET-seq 10^4 cells_Exp_rep2


title: H3K27me3 SET-seq 10^3 cells_Exp_rep2


title: H3K27me3 SET-seq 10^4 cells_Exp_rep1


title: H3K27me3 SET-seq 10^3 cells_Exp_rep1


title: H3K27me3 SET-seq 10^2 cells_Exp_rep1


title: H3K27me3 SET-seq 10^2 cells_Exp_rep2


title: H3K27me3 SET-seq 10^4 cells_Epi_rep2


title: H3K27me3 SET-seq 10^3 cells_Epi_rep2


title: H3K27me3 SET-seq 10^3 cells_Epi_rep1


title: PA6 3h mono-cultures BMP4 rep1

city: Candiolo

first: Davide

last: Cora'

state: TO

department: Dept. of Oncology

institute: Piemonte Orientale University and IRCCS Candiolo Cancer Institute

description: PA6 cell monolayers cultured for 3 hours in serum-free medium in presence of recombinant BMP4

hyb_protocol: 750 ng of cRNA was hybridized on MouseWG-6 v2.0 Expression BeadChip (Illumina Inc.). Array washes were performed using wash buffer

scan_protocol: Hybridized BeadChips were scanned using illumina Array reader

data_processing: Cubic Spline-normalized probe intensity data, togheter with detection p-values, were obtained using the GenomeStudio software v2011.01 (Illumina)

source_name: PA6 monolayers cultured in serum-free medium in presence of recombinant BMP4 for 3 hours

label_protocol: Bioinylated cRNA was prepared with Illumina TotalPrep RNA Amplification kit (Life Technologies)

growth_protocol: PA6 cells were cultured in 6-well plates until confluence; then PA6 mololayers were incubated in serum-free medium for 3 hours

extract_protocol: Total RNA was extracted from PA6 mono-cultures with Trizol reagent (Invitrogen) and purified using the RNeasy total RNA Isolation Kit (Qiagen).

treatment_protocol: For each biological replicate PA6 monolayers were treated as it follows: one well of PA6 monolayers untreated, one well of PA6 monolayers treated with 20 ng/ml of recombinant FGF2, one well of PA6 monolayers treated with 10 ng/ml of recombinant BMP4

tag: cell line

tag: growth factors

value: presence of recombinant BMP4


title: PA6 3h mono-cultures BMP4 rep2


title: H3K27me3 SET-seq 10^2 cells_Epi_rep2

tag: cell type

tag: strain


title: H3K27me3 SET-seq 10^2 cells_Epi_rep1


title: H3K27me3 SET-seq 10^4 cells_Epi_rep1


title: Brap-cKO__A3-B2-21

city: Bethesda

first: Yuanyi

last: Feng

state: MD

address: 4301 Jones Bridge Road

institute: UNIFORMED SERVICES UNIVERSITY OF THE HEALTH SCIENCES

description: BrapcKO

data_processing:
The quality of raw sequencing data was assessed using FastQC.
We obtained more than 30 million sequence reads per sample that are uniquely mapped to the mouse reference genome (build mm10).
After alignment of reads, expression levels of individual genes were quantified and estimated using subread::featureCounts.
With the removal of lowly expressed genes using the threshold at least 10 raw read counts, 14,276 out of 21,969 annotated, valid mouse genes were retained for further analysis.
Data were analyzed using several state-of-the-art tools, including DESeq2, edgeR, and Iimma, with a fold change ≥1.5 and FDR < 0.1. We collected overlapped differentially expressed mRNA genes detected with more than one method, and identified 811 differentially expressed genes between BrapcKO and control group.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: df.data.csv: Matrix table with raw gene counts for every gene and every sample.

source_name: cerebral cortex

extract_protocol:
Cerebral cortices were removed, flash frozen in liquid nitrogen, and RNA was extracted and purified using Trizol reagent followed by treatment with TURBO DNase. 1ug of total RNA was used for the construction of sequencing libraries using Illumina Ribo-Zero RNA Sample Prep Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: tissue

value: cerebral cortex

value: 3 month

value: Brapflox/ko Cre+


title: Brap-cKO__A3-B1-07

description: BrapcKO


title: PA6 7 days mono-cultures BMP4 rep3

description: PA6 cell monolayers cultured for 7 days in serum-free medium in presence of recombinant BMP4

source_name: PA6 mono-cultures cultured in serum-free medium in presence of recombinant BMP4 for 7 days

label_protocol: Bioinylated cRNA were prepared with Illumina TotalPrep RNA Amplification kit (Life Technologies)

growth_protocol: Murine ES cells were cultured into 6-well plates onto monolayers of stromal PA6 cells in serum-free medium for 7 days and in parallel, PA6 mono-cultures were cultured in serum-free medium for 7 days as well

extract_protocol: Total RNA was extracted from ES/PA6 co-cultures or from PA6 mono-cultures with Trizol reagent (Invitrogen) and purified using the RNeasy total RNA Isolation Kit (Qiagen).

treatment_protocol: For each biological replicate ES/PA6 co-cutlures or PA6 mono-cultures were treated as it follows: one well of ES/PA6 co-cultures and PA6 monocultures untreated, one well of ES/PA6 co-cultures and PA6 monocultures treated with 20 ng/ml of recombinant FGF2, one well of ES/PA6 co-cultures and PA6 monocultures treated with 10 ng/ml of recombinant BMP4

tag: cell lines

value: recombinant BMP4 for 3 days


title: PA6 3h mono-cultures FGF2 rep1

description: PA6 cell monolayers cultured for 3 hours in serum-free medium in presence of recombinant FGF2

source_name: PA6 monolayers cultured in serum-free medium in presence of recombinant FGF2 for 3 hours

value: presence of recombinant FGF2


title: PA6 7 days mono-cultures FGF2 rep3

description: PA6 cell monolayers cultured for 7 days in serum-free medium in presence of recombinant FGF2

source_name: PA6 mono-cultures cultured in serum-free medium in presence of recombinant FGF2 for 7 days

value: recombinant FGF2 for 3 days


title: PA6 7 days mono-cultures BMP4 rep2


title: Brap-cKO__A3-B1-06

description: BrapcKO

value: Brapflox/floxCre+


title: 53_PIK3CD

city: VILLEJUIF

first: christophe

last: desterke

address: 14-16 avenue Paul Vaillant Couturier

department: UFR medecine institute Andre Lwoff

institute: university Paris Sud11

description: tumor

hyb_protocol: WT plus Affymetrix chemistry

scan_protocol: scan of Clariom S mouse slide on affymetrix microarray station

data_processing: RMA normalization TAC 4.0 software

label_protocol: WT plus Affymetrix chemistry

growth_protocol: tranfection with empty vector (AAV) or with PIK3CD (PIK3CD)

extract_protocol: total RNA was extract from the cell culture and a quantity of 100 ng was investigated to start microarray probe synthesis

treatment_protocol: ex vivo  tumor analysis

value: tumor


title: PA6 7 days mono-cultures BMP4 rep1


title: PA6 7 days mono-cultures FGF2 rep2


title: PA6 3h mono-cultures control rep2

description: PA6 cell monolayers cultured for 3 hours in serum-free medium in absence of growth factors

source_name: PA6 monolayers cultured in serum-free medium in absence of growth factors for 3 hours


title: H3K4me3 SET-seq 10^4 cells_Exp_rep2

value: untreated


title: 52_PIK3CD

description: tumor


title: H3K4me3 SET-seq 10^4 cells_Exp_rep1


title: H3K4me3 SET-seq 10^3 cells_Exp_rep2


title: PA6 3h mono-cultures control rep1


title: PA6 3h mono-cultures FGF2 rep2


title: Brap-cKO__A3-B1-05

description: BrapcKO


title: 51_PIK3CD

description: tumor


title: Brap-CT__A3-B2-24

description: Control

value: Brapflox/flox Cre-


title: H3K4me3 SET-seq 10^3 cells_Exp_rep1


title: Brap-CT__A3-B2-23

description: Control

value: Brapflox/wt Cre-


title: H3K4me3 SET-seq 10^2 cells_Exp_rep2


title: Case18_SNParray

type: genomic

description: Case_18 (UPN#147)

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.

data_processing:
Protocol was supported by Affymetrix GeneChip Command Console (AGCC) software. Analysis was performed through Affymetrix Chromosome Analysis (ChAS) software with filters set at 200 Kb dimension for Copy Number Alterations (CNAs) and 10 Mb dimensions for copy neutral loss of heterozygosity (cnLOH). Our data refer to NetAffx Build 32.3 (hg19) database.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: Biotin

source_name: Unsorted Bone Marrow Cells

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA were extracted from bone marrow cells or periferichal blood cells of patients using All Prep DNA/RNA Mini Kit (Qiagen). DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, Bioanalyzer and/or Tapestation visualization (Agilent 2100 Bioanalyzer) and agarose gel electrophoresis.

value: bone marrow

tag: disease state

value: acute leukemia


title: H3K4me3 SET-seq 10^2 cells_Exp_rep1

tag: treatment


title: H3K4me3 SET-seq 10^4 cells_Epi_rep2

value: H3K4me3 (Cat# ab8580, Abcam)


title: Brap-CT__A3-B1-09

description: Control


title: Brap-CT__A3-B2-22

description: Control


title: 50_AAV

description: tumor

source_name: AAV

value: empty vector (AAV)


title: 49_AAV

description: tumor