title: SWTX143 50mpk 24h 3

city: Leuven

first: Georg

last: Halder

address: Herestraat 49

department: VIB-KU Leuven Center for Cancer Biology

country: Belgium

institute: VIB-KU Leuven

data_processing:
Quality control and trimming of the sequencing reads was performed using FastQC and Cutadapt (-q 15 --minmum-length 80)
Trimmed sequence reads were mapped to hg19 using STAR v2.6.1d (with default mapping parameters).
Reads were counted with STAR --quantMode GeneCounts
Assembly: GRCh37/hg19
Supplementary files format and content: Tab-delimited text file with raw gene counts for every gene and every sample

growth_protocol: The human lung cancer cell line NCI-H226 was acquired from ATCC and cultured in RPMI1640 medium (HyClone; GE Healthcare Life Sciences, Logan, UT, USA) supplemented with 10% FBS (EXCELL Bio, Inc., China); Female BALB/c nude mice, purchased from GemPharmatech Co.,Ltd (Jiangsu, China), were subcutaneously inoculated in the mouse flank with 10x10E6 NCI-H226 cells in 0.2ml PBS mixed with 1:1 Matrigel (Corning Inc., NY, USA) for tumor development.

extract_protocol:
After tumor dissociation RNA was extracted using RNeasy Kit (Qiagen, # 74004) following the manufacturer recommendations
First poly-A containing mRNA molecules purification was performed using poly-T oligo-attached magnetic beads. Following purification, the mRNA was fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using DNA polymerase I and RNase H. These cDNA fragments underwent the addition of a single ‘A’ base and subsequent ligation of the adapter. The products were then purified and enriched through PCR amplification. We then quantified the PCR yield by Qubit and pooled the samples together to make a single strand DNA circle (ssDNA circle), which generated the final library. DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals during the sequencing process. The DNBs were loaded into the patterned nanoarrays, and pair-end reads of 100bp were read on the BGISEQ-500 platform for the following data analysis

treatment_protocol: When tumors reached about 170mm3, mice were randomized into groups and treated once daily with SWTX-143 (10, 25 and 50mg/kg) or vehicle for control group for 19 days. SWTX-143 was formulated in PEG-400 40%, 1,2-Propanediol 30% and H2O 30% and dosed orally (PO) at the indicated concentrations.

tag: treatment

value: SWTX143 50mpk

tag: time after_last_dose


title: Pt.2 Con

status: Public on Oct 04 2023

type: SRA

city: Toronto

first: YU XUAN

last: LUO

state: ON

address: 2075 Bayview Avenue

department: Biological sciences

country: Canada

institute: Sunnybrook research institute

library_source: transcriptomic

data_processing:
Ion Torrent sequencing was performed for 500 flows on an Ion S5XL Sequencer with Ion 540 Chips.
Ion Torrent platform-specific pipeline software (Torrent Suite version 5.12.1; ThermoFisher Scientific) was used to remove polyclonal, low quality and adapter dimer reads and then separate barcoded reads for each sample.
Ion Torrent platform-specific ampliSeqRNA plug-in (v5.12.0.1) was used to analyze the sequencing reads.
Reads were aligned to the human transcriptome reference and target regions flle (hg19_AmpliSeq_Transcriptome_21K_v1) With TMAP mapper in Torrent Suite version 5.12.1.
hg19 Human genome reference
Assembly: text files.  Raw read count and normalized reads count (RPM, reads per million).
Supplementary files format and content: tab-delimited text files includes raw counts for each sample
Supplementary files format and content: tab-delimited text files includes RPM values for each sample

molecule: total RNA

organism: Homo sapiens

source_name: blood

growth_protocol: Leukemia cells were purified from the blood and RNA was made immediately and frozen until used for RNAseq.

extract_protocol:
RNA was prepared using the RNeasy mini kit (Qiagen, Valencia, CA, USA), and cDNA was synthesized from 2 μg of RNA using Superscript II reverse transcriptase (Invitrogen), according to the instructions of the manufacturer.
Complementary DNA (cDNA) libraries were constructed from the total RNA using the Ion AmpliSeq Transcriptome Human Gene Expression kit (ThermoFisher Scientific) in accordance with the manufacturer’s manuals.

treatment_protocol: CLL cells were isolated from blood by negative selection with the Rosette Sep Human B cell enrichment cocktail (StemCell Technologies, Vancouver BC, Canada) and density centrifugation. This method yields percentages of CD19+ and CD19+/CD5+ cells of >98 and >96%, respectively. Aliquots were cryopreserved until used for RNAseq.

tag: tissue

value: blood

tag: cell type

value: CLL-B lymphocytes

value: Control

tag: time


title: MeT-5A.control.HA.2

city: Charlestown

first: Rui

last: Dong

state: MA

address: 149 13th Street

country: USA

institute: Massachusetts General Hospital

library_source: genomic

data_processing:
Reads were aligned to hg19 using bwa (Li and Durbin, 2009). Aligned reads were then filtered to exclude PCR duplicates.
Aligned reads were extended to 200 bp to approximate fragment sizes. Density maps were generated by counting the number of fragments overlapping each position using igvtools, and normalized to 10 million reads.
Assembly: hg19
Supplementary files format and content: bigWig files

molecule: genomic DNA

source_name: HA

extract_protocol:
Chromatin from formaldehyde-fixed cells (2-5 x 10^6 cells per epitope) was fragmented to a size range of 200 - 700 bases with a Branson 250 Sonifier. Solubilized chromatin was immunoprecipitated with the indicated antibodies and Protein G-Dynabeads (Life Technologies). Immunoprecipitated DNA was extracted with AMP Pure beads (Beckman Coulter) after crosslink reversal, RNase A and Proteinase K treatment.
ChIP DNA samples were used to generate Illumina sequencing libraries following standard protocols.

tag: cell line

value: untreated

tag: expression

value: control

tag: chip antibody

value: HA


title: LMDP_117int_W3_rep3

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

country: France

institute: Inserm U1085-Irset

description:
W3_P10_3
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat

data_processing:
16 bases are initially read, and all must have a quality score > 10. The unique sample-specific barcode corresponds to first 6 bp, and the unique molecular identifier (UMI) corresponds to the following 10 bp.
Human reference transcriptome from the UCSC website (release hg38) using BWA version 0.7.4.4  was used to align the second reads
Assembly: hg38
Supplementary files format and content: Expression file in dat format. Contains for each sample, the number of unique umis (unique molecular identifier) associated with the 28,307 genes detected.

molecule: polyA RNA

extract_protocol:
no extraction_cell lysates
Libraries were prepared using the Illumina DNA Prep kit (Illumina) according to the manufacturer’s guidelines.

value: no


title: L49293, normal

city: Phoenix

first: Nicholas

last: Banovich

state: AZ

address: 445 North Fifth Street

department: Integrated Cancer Genomics

institute: TGen - Translational Genomics Research Institute

library_source: transcriptomic single cell

data_processing:
CellRanger Count v5.0.2 (10x Genomics) was used to align reads to the GRCh38 (Ensembl 98) reference genome.
Assembly: GRCh38 (Ensembl 98)
Supplementary files format and content: Tab-separated values file containing cell barcodes
Supplementary files format and content: Tab-separated values file containing features
Supplementary files format and content: Matrix file containing counts
Supplementary files format and content: Appendiceal_Epithelial_infercnv_HMMi3.rds - Seurat object containing infercnv results in metadata for epithelial cell lineage
Supplementary files format and content: Appendiceal_integratedrpca_alllineages_final.rds - Seurat object integrated with rPCA, contains all cell lineages with annotations

source_name: Normal Appendix

extract_protocol:
Minced tissue (1-3 mm) was digested with 3 -5 ml RMPI medium containing 0.05mg/ml TM Liberase (Sigma Aldrich, 5401119001) and 0.02 mg/ml DNAaseI (ThermoFisher, EN0521) at 37 ° C for 30 mins with rotation at 150 rpm. Cells were filtered through a 70 µM and 37 µM cell strainer to isolate single cells. The cell suspension was centrifuged at 500xg for 10 mins and resuspended with 5 ml ACK lysis buffer (K.D Medical, RGF3015) at room temperature for 3 mins to remove red blood cells. Microbeads (Miltenyi Biotec, 130-090-101) were used for dead cell removal. Cell viability and number were detected using a TC Automated Cell Counter (Bio-Rad Laboratories), and samples with at least 70% cell viability were processed
Cells were captured on a Chromium controller (10xGenomics) using a single cell 3’ Reagent kit V3.1 (10X Genomics, PN-1000121) targeting ~5000-10000 cell/sample

value: Normal Appendix

tag: pathology reviewed

tag: pathology abbreviated

value: Normal

tag: pathology

tag: pathology 2

tag: pathology 3

value: Benign Appendix

tag: Sex

value: Female

tag: age

tag: ethnicity

value: Non-HISPANIC WHITE

tag: clinical diagnosis

tag: status


title: K28668, LGMA

source_name: Peritoneal metastasis

value: Peritoneal metastasis

value: Low-grade mucinous adenocarcinoma

value: LGMA

value: low grade mucinous adenocarcinoma

value: Low grade appendiceal adenocarcinoma

value: Male

value: Low grade Adenocarcinoma

value: Cancerous

tag: gemextra

value: GNAS(R201H); KRAS (G12D); Low (1mut/Mb), MSS

tag: vus

value: AHNAK2 (P3501L) Missense 5 AIRE (R494H) Missense 5 CASKIN2 (R217H) Missense 5 DYSF (T1870M) Missense 6 ELFN2 (T143M) Missense 5 GALNT1 (C497R) Missense 6 GATA4 (T280M) Missense 5 GRIN2A (R1316K) Missense 5 IGKV4- 1/IGKC Fused Genes (RNA) . KIF26B (V1113M) Missense 5 MXD3 (R148Q) Missense 5 NBPF3 (G281R) Missense 7 NUP88 (M332I) Missense 6 OVCH1 (L439F) Missense 7 PCDHA12 (S668L) Missense 6 PLD2 (R829W) Missense 6 PMEPA1 (C24Y) Missense 5 PRRG3 (R19H) Missense 11 SLC13A5 (V431M) Missense 5 ZNF521 (E454G) Missense 6 ZNF853 (L302F) Missense 5


title: SWTX143 50mpk 24h 2

tag: treatment

value: SWTX143 50mpk

tag: time after_last_dose


title: Pt.3 K

tag: tissue

value: blood

tag: cell type

value: CLL-B lymphocytes

value: 300 microg/ml of anakinra for 48h

tag: time


title: SWTX143 50mpk 24h 1

tag: cell line


title: SWTX143 50mpk 4h 3


title: K28667, normal

value: Normal Appendix

tag: pathology reviewed

tag: pathology abbreviated

value: Normal

value: Benign Appendix

value: HISPANIC WHITE

value: Control


title: MeT-5A.control.V5.5

value: untreated

tag: expression

value: control

tag: chip antibody


title: MeT-5A.control.V5.1


title: LMDP_117int_W3_rep2

description:
W3_P10_2
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat

value: no


title: MeT-5A.control.H3K27ac.6


title: SWTX143 50mpk 4h 2


title: L35152, normal

tag: pathology

tag: pathology 2

tag: pathology 3

tag: Sex

value: Female


title: LMDP_117int_W4_rep1

description:
W4_P10_1
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: MeT-5A.control.H3K27ac.5


title: L35149, normal

tag: age

tag: ethnicity

value: Non-HISPANIC WHITE

tag: clinical diagnosis

tag: status


title: LMDP_117int_W3_rep1

description:
W3_P10_1
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat

tag: treatment


title: LMDP_117hi_W5_rep5

description:
W5_P8_5
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: SWTX143 50mpk 4h 1

tag: time after_last_dose


title: MeT-5A.control.HA.1

value: HA


title: LMDP_117hi_W5_rep4

description:
W5_P8_4
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat

tag: cell type


title: MeT-5A.control.H3K27ac.4


title: MeT-5A.control.H3K27ac.3


title: SWTX143 25mpk 24h 3

value: SWTX143 25mpk


title: LMDP_117hi_W5_rep3

description:
W5_P8_3
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat

tag: time


title: JN-DSRCT1.wt.HiChIP

data_processing:
Illumina Casava v.2.19 software used for basecalling.
Paired-end HiC reads were aligned against the hg19 genome using HiC-Pro.
The hichipper tool (v 0.7.7) (Lareau et al., 2018) was used for loop calling within H3K27ac ChIP-seq peak (q-value < 0.00001) regions, by applying the following parameters: --max-distance 100000000 --read-length 100
Assembly: hg19
Supplementary files format and content: HiC all valid interaction read pairs (allValidPairs). Columns are: read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size.
Supplementary files format and content: HiChIP loop contacts (.bedpe). Intrachromosomal looping between anchor loci.
Library strategy: HiChIP

extract_protocol:
Genomic DNA/ChIP DNA was isolated from x-linked nuclei after Mbo1 restriction digestion, end filling with biotin-14ATP and following ligation, according to in-situ HiC protocol. H3K27ac antibody was used to pull-down ChIP following HiC and proceed to library construction.
Followed Next Gen DNA Library Kit & Next Gen Indexing Kit from Active Motif.

treatment_protocol: Untreated

tag: cell line

tag: antibody


title: SWTX143 25mpk 24h 2


title: MeT-5A.control.H3K27ac.2


title: LMDP_117hi_W5_rep2

description:
W5_P8_2
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: JN-DSRCT1.shGFP.HiChIP

tag: shRNA

value: shGFP


title: JN-DSRCT1.shEWSWT1.HiChIP


title: JN-DSRCT.WT1.2


title: MeT-5A.control.H3K27ac.1

tag: expression


title: SWTX143 25mpk 24h 1


title: LMDP_117hi_W5_rep1

description:
W5_P8_1
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: SWTX143 25mpk 4h 3


title: LMDP_117hi_W4_rep5

description:
W4_P8_5
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: JN-DSRCT.WT1.1

tag: chip antibody


title: C91_Untreated

city: Rochester

first: Saad

last: Kenderian

state: MN

address: 200 First Street SW

institute: Mayo Clinic

data_processing:
Binary base call data converted to fastq using Illumina bcl2fastq software
Check quality with FastQC, trim adapters with trimmomatic, and re-check quality with FastQC
Latest human reference genome GRCh38 was downloaded from NCBI and indexed using STAR
Paired end reads were mapped to the genome, and HTSeq was used to generate expression counts for each gene
DeSeq2 was used to calculate differential expression, and gene ontology was assessed using Enrichr
Assembly: CRCh38
Supplementary files format and content: tab-delimted text files contain the gene expression counts for each sample; csv is DeSeq2 dataset; text files with enriched GO terms from Enrichr

source_name: CART19 cells

extract_protocol:
RNA was isolated using miRNeasy Micro kit (Qiagen, Gaithersburg, MD, USA) and treated with RNase-Free DNase Set (Qiagen, Gaithersburg, MD, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CART19 cells from five biological replicates were thawed and stimulated with irradiated Jeko-1 cells (120 Gy) for 5 days. Each sample was treated with either 30 nM TP0903 (treated condition) or DMSO (untreated control). CART19 were isolated to a purity of 100% using CD19 microbeads (Miltenyi).

value: CART19 cells

tag: tp-0903 treatment

value: Untreated


title: SWTX143 25mpk 4h 2


title: C91_Treated

value: Treated


title: SWTX143 25mpk 4h 1


title: JN-DSRCT.shGFP.WT1.2.b


title: JN-DSRCT1_HiC

data_processing:
Illumina Casava v.2.19 software used for basecalling.
Paired-end HiC reads were aligned against the hg19 genome using HiC-Pro.
Default settings were used to control quality, align paired reads, identify valid interactions and generate interaction matrices. The Iterative Correction and Eigenvector decomposition (ICE) method (Imakaev et al., 2012) was performed for each sample.
Assembly: hg19
Supplementary files format and content: HiC all valid interaction read pairs (allValidPairs). Columns are: read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size
Supplementary files format and content: HiC 40kb resolution Interaction matrix files (.matrix). A matrix, stored as standard triplet sparse format (i.e. list format). Based on the observation that a contact map is symmetric and usually sparse, only non-zero values are stored for half of the matrix.

source_name: JN-DSRCT1 cells

growth_protocol: JN-DSRCT1 cells were grown in Dulbecco’s Modified Eagle Medium (DMEM/F12) supplemented with 10% Fetal Bovine Serum (FBS) and 1% Penicillin/Streptomycin. All cells were cultured at 37°C with 5% CO2. Cells were maintained and split every 2-4 days

extract_protocol:
Genomic DNA was isolated from x-linked nuclei after Mbo1 restriction digestion, end filling with biotin-14ATP and following ligation, according to in-situ HiC protocol.
Followed Next Gen DNA Library Kit & Next Gen Indexing Kit from Active Motif


title: C57_Untreated


title: JN-DSRCT.shGFP.WT1.2.a


title: SWTX143 10mpk 24h 3

value: SWTX143 10mpk


title: LMDP_117hi_W4_rep3

description:
W4_P8_3
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: SWTX143 10mpk 24h 2


title: C57_Treated


title: JN-DSRCT.shGFP.WT1.1


title: LMDP_117hi_W4_rep2

description:
W4_P8_2
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: C56_Untreated


title: LMDP_117hi_W4_rep4

description:
W4_P8_4
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: LMDP_117hi_W4_rep1

description:
W4_P8_1
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: SWTX143 10mpk 24h 1


title: C56_Treated


title: SWTX143 10mpk 4h 3


title: LMDP_117hi_W3_rep5

description:
W3_P8_5
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: JN-DSRCT.shGFP.H3K4me1.2


title: LMDP_117hi_W3_rep4

description:
W3_P8_4
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: SWTX143 10mpk 4h 2


title: JN-DSRCT.shGFP.INPUT.1

source_name: INPUT


title: C55_Untreated


title: C55_Treated


title: LMDP_117hi_W3_rep3

description:
W3_P8_3
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: SWTX143 10mpk 4h 1


title: CTRL 24h 3

value: vehicle


title: JN-DSRCT.shGFP.H3K27ac.2


title: C105_Untreated


title: LMDP_117hi_W3_rep2

description:
W3_P8_2
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: C105_Treated


title: CTRL 24h 2


title: JN-DSRCT.shGFP.INPUT.2


title: JN-DSRCT.shGFP.H3K27ac.1


title: AF5202: H9 shZEB2-3

city: Barcelona

first: Antonio

last: Postigo

state: BARCELONA

address: Casanova 143. Cellex 1B

country: Spain

institute: IDIBAPS/ICREA

description: Day 2 of CHIR treatment

data_processing:
RNA-seq reads were mapped against Homo sapiens reference genome with STAR (ENCODE parameters)
Genes were quantified with RSEM (default parameters)
Normalization and differential expression was performed with DESeq2
GO/KEGG enrichment analysis was performed with G:profiler
Genome_build: GRCm38
Supplementary_files_format_and_content: txt file containing RSEM expected counts

source_name: H9 shZEB2 day 2 Differentiation - Experiment 3

growth_protocol: H9 cells grown in matrigel-coated plates in E8 medium

extract_protocol:
Total RNA was isolated using Trizol
0.5ug RNA was subjected to library synthesis using TruSeq® Stranded mRNA LT Sample Prep Kit

treatment_protocol: 2 days of CHIR treatment and doxycycline supplemented medium to induce sh knock-down

value: Day 2 of differentiation protocol (2 days CHIR treated)

value: Cultured H9 cells

tag: genotype

value: H9 shZEB2


title: LMDP_117hi_W2_rep4

description:
W2_P8_4
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: CTRL 4h 3


title: AF5201: H9 shZEB2-2

description: Day 2 of CHIR treatment

source_name: H9 shZEB2 day 2 Differentiation - Experiment 2


title: LMDP_117hi_W2_rep3

description:
W2_P8_3
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: JN-DSRCT.shEWSWT1.WT1.2.b


title: JN-DSRCT.shEWSWT1.WT1.2.a


title: CTRL 24h 1


title: JN-DSRCT.shEWSWT1.WT1.1


title: JN-DSRCT.shGFP.H3K4me1.1


title: AF5200: H9 shZEB2-1

description: Day 2 of CHIR treatment

source_name: H9 shZEB2 day 2 Differentiation - Experiment 1


title: CTRL 4h 1


title: JN-DSRCT.shEWSWT1.INPUT.2


title: CTRL 4h 2


title: AF5199: H9 shZEB1-3

description: Day 2 of CHIR treatment

source_name: H9 shZEB1 day 2 Differentiation - Experiment 3

value: H9 shZEB1


title: LMDP_117hi_W3_rep1

description:
W3_P8_1
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: H226 SWTX143 3

data_processing:
Quality control and trimming of the sequencing reads was performed using FastQC and Cutadapt (-q 15 --minmum-length 20)
Trimmed sequence reads were mapped to hg19 using STAR v2.6.1d (with default mapping parameters).
Reads were counted with STAR --quantMode GeneCounts
Assembly: GRCh37/hg19
Supplementary files format and content: Tab-delimited text file with raw gene counts for every gene and every sample

growth_protocol: H226 and ACHN cells were seeded at 600.000 cells per well in 6-well culture plates and incubated with SWTX-143 overnight at 100nM in a 37°C incubator, 5% CO2

extract_protocol:
Cells were washed with cold PBS before RNA extraction using RNeasy Kit (Qiagen, # 74004) following the manufacturer recommendations
First poly-A containing mRNA molecules purification was performed using poly-T oligo-attached magnetic beads. Following purification, the mRNA was fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using DNA polymerase I and RNase H. These cDNA fragments underwent the addition of a single ‘A’ base and subsequent ligation of the adapter. The products were then purified and enriched through PCR amplification. We then quantified the PCR yield by Qubit and pooled the samples together to make a single strand DNA circle (ssDNA circle), which generated the final library. DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals during the sequencing process. The DNBs were loaded into the patterned nanoarrays, and pair-end reads of 100bp were read on the BGISEQ-500 platform for the following data analysis

value: SWTX143 100nM


title: AF5198: H9 shZEB1-2

description: Day 2 of CHIR treatment

source_name: H9 shZEB1 day 2 Differentiation - Experiment 2


title: LMDP_117int_W3_rep4

description:
W3_P10_4
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: LMDP_W1_rep4

description:
W1_P11_4
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat

source_name: LMDP

value: LMDP


title: AF5197: H9 shZEB1-1

description: Day 2 of CHIR treatment

source_name: H9 shZEB1 day 2 Differentiation - Experiment 1


title: H226 SWTX143 2


title: LMDP_W1_rep3

description:
W1_P11_3
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat

value: no


title: JN-DSRCT.shEWSWT1.INPUT.1

value: untreated


title: AF5196: H9 shCTL-3

description: Day 2 of CHIR treatment

source_name: H9 shCTL day 2 Differentiation - Experiment 3

value: H9 shCTL


title: JN-DSRCT.shEWSWT1.H3K4me1.2


title: H226 SWTX143 1


title: JN-DSRCT.shEWSWT1.H3K4me1.1


title: LMDP_117hi_W2_rep2

description:
W2_P8_2
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: LMDP_W1_rep2

description:
W1_P11_2
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: LMDP_117hi_W2_rep1

description:
W2_P8_1
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: LMDP_W1_rep1

description:
W1_P11_1
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: AF5195: H9 shCTL-2

description: Day 2 of CHIR treatment

source_name: H9 shCTL day 2 Differentiation - Experiment 2


title: H226 DMSO 3

value: DMSO


title: AF5194: H9 shCTL-1

description: Day 2 of CHIR treatment

source_name: H9 shCTL day 2 Differentiation - Experiment 1


title: JN-DSRCT.shEWSWT1.H3K27ac.2


title: H226 DMSO 2


title: JN-DSRCT.shEWSWT1.H3K27ac.1


title: HPC_W5_rep5

description:
W5_P15_5
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat

source_name: HPC

value: HPC


title: HPC_W5_rep4

description:
W5_P15_4
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: JN-DSRCT.INPUT


title: offspring (D28) kidney, maternal protein restriction sample, rep9

city: Tokyo

first: Xuguang

last: Li

address: 1-1-1 Yayoi, Bunkyo-ku

country: Japan

institute: Tokyo University

data_processing:
Quality control by Fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Mapping by Bismarck (reference BN/ SsNHsdMCW rat) (http://www.bioinformatics.babraham.ac.uk/projects/bismark/).
Alignment and Extraction of Methylation Site by SeqMonk (http://www.bioinformatics.bbsrc.ac.uk/projects/seqmonk/), and Reference Genome (Rnor_6.0, Rattus norvegicus (Norway rat).
For extracting DNA methylation sites, CpG sites were narrowed down using a cutoff of p < 0.1 in the windowed replication test, then genes in the vicinity of the sites were extracted.
Assembly: Rnor_6.0
Supplementary files format and content: tab-delimited text files include methylation level for each cytosine (chg, chh, cpg)

organism: Rattus norvegicus

source_name: offspring (D28) kidney of fetal exposure to maternal low-protein diet

extract_protocol:
DNA extraction was performed using the DNAiso Reagent (Takara Bio Inc., Shiga, Japan) according to the manufacturer’s instructions. DNA concentration was determined using a NanoDrop® 1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA), and quality was confirmed at OD260/280 > 1.8 and OD260/230 > 1.8. Electrophoresis (100 V, 20 min) using a 1.2% agarose gel was used to check for DNA degradation. DNA concentration was measured again using Qubit (Thermo Fisher Scientific, Waltham, MA, USA). Extracted DNA was kept at -80 °C until later analysis.
Whole-genome bisulfite sequencing was performed using the PBAT (Post-bisulfite adapter tagging) method. A DNA library was prepared according to the method of Miura et al., and indexed and read in the paired-end mode for 150 cycles ×2 using a large-scale sequencer (HiSeq X Ten; Illumina, San Diego, CA, USA) at the Macrogen Japan (Tokyo) sequencing laboratory.

tag: tissue

value: offspring (D28) kidney

value: offspring exposure to maternal low protein diet during fetal life


title: H226 DMSO 1


title: ACHN SWTX143 3

source_name: ACHN

value: ACHN


title: ACHN SWTX143 2


title: HPC_W5_rep3

description:
W5_P15_3
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: JN-DSRCT.H3K4me3


title: HPC_W5_rep1

description:
W5_P15_1
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: ACHN SWTX143 1


title: JN-DSRCT.H3K4me1


title: offspring (D28) kidney, maternal protein restriction sample, rep7


title: HPC_W5_rep2

description:
W5_P15_2
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: offspring (D28) kidney, maternal protein restriction sample, rep6


title: ACHN DMSO 3


title: HPC_W4_rep5

description:
W4_P15_5
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: HPC_W4_rep4

description:
W4_P15_4
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: JN-DSRCT.H3K27ac


title: JN-DSRCT.H3K27me3


title: offspring (D28) kidney, maternal protein restriction sample, rep5


title: offspring (D28) kidney, maternal protein restriction sample, rep4


title: ACHN DMSO 2


title: ACHN DMSO 1


title: offspring (D28) kidney, maternal protein restriction sample, rep10


title: offspring (D28) kidney, maternal protein restriction sample, rep3


title: DSRCT2.H3K9ac

value: Desmoplastic small round cell tumor (DSRCT)


title: JN-DSRCT.H3K9ac


title: DSRCT2.INPUT


title: offspring (D28) kidney, maternal protein restriction sample, rep8


title: offspring (D28) kidney, maternal protein restriction sample, rep2


title: DSRCT2.H3K4me3


title: DSRCT2.H3K4me1


title: HPC_W3_rep5

description:
W3_P15_5
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: offspring (D28) kidney, maternal protein restriction sample, rep1


title: SAMP8_16-weeks-old_rp2

type: RNA

city: つくば市

first: ミチタカ

last: フジワラ

state: 茨城県

institute: University of Tsukuba

description: Gene expression data from 16 weeks old SAMP8 mouse brain cortex

hyb_protocol: The cartridge array hybridization was performed using the Affymetrix Mouse Genome 430 PM array (Affymetrix, Santa Clara, CA, United States).

scan_protocol: Scanning was performed using GeneAtlas Fluidics and Imaging Station (ThermoFisher Scientific).

data_processing:
The raw data were normalized following the robust multi-chip analysis (RMA) algorithm. Further, gene-level analysis was performed using the Limma Bioconductor package. For differential expression analysis, a One-Way ANOVA followed by an empirical Bayes correction was performed. The detected above background (DABG) cutoff was set to 0.05. The positive vs negative area under the curve (AUC) value was set at greater than or equal to 0.7.
Signal intensity of all the samples derived from Transcriptome analysis console software (sheet 2 ). For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, Transcriptome Analysis Console software (CEL files). filter criteria was set as p value < 0.05 (one-way between-subjects ANOVA) and fold change > 1.1 (in linear space)

label: biotin

organism: Mus musculus

source_name: 16 weeks old SAMP8 mice

label_protocol: Biotinylated cRNA were prepared according to the standard WT PLUS Reagent Kit protocol (ThermoFisher Scientific) from 100 ng/ uL total RNA

growth_protocol: No growth protocols were used.

extract_protocol: Total RNA was extracted using ISOGEN (Nippon Gene Co., Ltd, Tokyo, Japan) following the manufacture’s instruction.

treatment_protocol: No treatment were given to the mice.

value: Brain cortex

value: 16 weeks


title: SAMP8_16-weeks-old_rp1


title: DSRCT2.H3K27me3


title: HPC_W4_rep3

description:
W4_P15_3
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: DSRCT2.H3K27ac


title: HPC_W3_rep2

description:
W3_P15_2
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: HPC_W4_rep2

description:
W4_P15_2
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: HPC_W3_rep3

description:
W3_P15_3
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: SAMP8_1-year-old_rp2

description: Gene expression data from 1 year old SAMP8 mouse brain cortex

source_name: 1 year old SAMP8 mice

value: 1 year


title: offspring (D28) kidney, control sample, rep8

source_name: offspring (D28) kidney of fetal exposure to maternal control diet

value: offspring exposure to maternal control diet during fetal life


title: offspring (D28) kidney, control sample, rep7


title: offspring (D28) kidney, control sample, rep9


title: offspring (D28) kidney, control sample, rep6


title: HPC_W3_rep1

description:
W3_P15_1
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: DSRCT1.H3K9ac


title: DSRCT1.H3K4m3


title: HPC_W4_rep1

description:
W4_P15_1
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: HPC_W2_rep4

description:
W2_P15_4
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: SAMP8_1-year-old_rp1


title: offspring (D28) kidney, control sample, rep10


title: DSRCT1.H3K4m1


title: SAMR1_16-weeks-old_rp1

description: Gene expression data from 16 weeks old SAMR1 mouse brain cortex

source_name: 16 weeks old SAMR1 mice


title: SAMR1_16-weeks-old_rp2


title: SAMR1_1-year-old_rp2

description: Gene expression data from 1 year old SAMR1 mouse brain cortex

source_name: 1 year old SAMR1 mice


title: offspring (D28) kidney, control sample, rep5


title: HPC_W2_rep3

description:
W2_P15_3
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: SAMR1_1-year-old_rp1


title: DSRCT1.H3K27me3


title: offspring (D28) kidney, control sample, rep4


title: DSRCT1.H3K27ac


title: offspring (D28) kidney, control sample, rep3


title: HPC_W2_rep2

description:
W2_P15_2
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: HPC_W2_rep1

description:
W2_P15_1
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: MeT-5A.xeno.EWSWT1+KTS-KTS.RNAseq.2

data_processing:
Illumina Casava v.2.19 software used for basecalling.
Sequenced reads were aligned to hg19 genome using STAR v.2.4.0h with default settings.
The aligned fragments quantification was computed by featureCounts, and FPKM expression values were calculated for hg19 RefSeq genes.
We also used kallisto (v0.43.0) for gene expression quantification.
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include raw gene expression counts for each sample.

extract_protocol:
Total RNA was isolated using NucleoSpin RNA (Clontech). 1 μg of total RNA was treated with Ribogold zero to remove ribosomal RNA. Remaining RNA was used to construct Illumina sequencing libraries with random primers according to manufacturer instructions using the TruSeq Stranded RNA LT Kit.
RNA samples were used to generate Illumina sequencing libraries following standard protocols.


title: offspring (D28) kidney, control sample, rep2


title: HPC_W1_rep4

description:
W1_P15_4
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: offspring (D28) kidney, control sample, rep1


title: HPC_W3_rep4

description:
W3_P15_4
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: MeT-5A.xeno.EWSWT1+KTS-KTS.RNAseq.1


title: DSRCT1.INPUT

source_name: INPUT


title: Sample 8_AU1038_STRSS4

first: Marc

last: Dabad

address: Baldiri i Reixac, 4-8

institute: CNAG

data_processing:
Trimming with trim_galore v0.6.6 --length 16 --stringency 10
Mapping with STAR v2.7.8a against GRCz11
Quantification with RSEM v1.3.0 using ensembl release 104
Assembly: GRCz11
Supplementary files format and content: TSV raw counts

organism: Danio rerio

source_name: larvae

extract_protocol: RNA was harvested using with Qiazol; a miRNeasy tissue kit (Qiagen). Only samples meeting the requirements (3 µg of RNA; RNA integrity number (RIN) > 8) were used in RNA-seq analysis.

value: larvae

value: WT

value: From parent chronically stressed (21 days)


title: HPC_W1_rep3

description:
W1_P15_3
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: MeT-5A.EWSWT1+KTS.RNAseq.3


title: HPC_W1_rep2

description:
W1_P15_2
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: HPC_W1_rep1

description:
W1_P15_1
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: Sample 7_AU1037_STRSS3


title: MeT-5A.EWSWT1-KTS.RNAseq.3


title: Sample 6_AU1036_STRSS2


title: CFT073 stimulated NLRP3 gRNA 6 hours rep2

city: örebro

first: isak

last: demirel

address: campus usö

country: Sweden

institute: örebro University

description: Gene expression after 6 hours of stimulation 5637

hyb_protocol: Labelled samples were hybridised onto G4851C SurePrint G3 Human Gene Expression v3 8x60K Microarray glass slides (Agilent)

scan_protocol: Microarrays were scanned with a G2565 CA array laser scanner (Agilent) followed by image analysis and data extraction with Feature Extraction Software version 10.7.3.1 (Agilent).

data_processing: 75th percentile shift normalisation and baseline adjusted

source_name: 5637 cell line

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using the low input quick amp labeling kit,one-color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The 5637cell line was cultured in Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine and 1 mM non-essential amino acids (all from Thermo Fisher Scientific, Waltham, MA, USA) at 37 °C in 5% CO2 atmosphere.

extract_protocol: Total RNA was isolated using the E.Z.N.A. Total RNA Kit I. RNA quality and integrity were evaluated using Agilent TapeS  tation 2200 platform (Agilent Technologies, Palo Alto, CA, USA) according to manufacturer in-structions. The RNA integrity number (RIN) was 10 for all RNA samples.

treatment_protocol: 5637 cells (Cas9 control and NLRP3-deficient) were stimulated with CFT073 MOI 10 for 6 h at 37 °C in 5% CO2 and the gene expression was evaluated.

value: NLRP3 gRNA knockout

value: CFT073 stimulated


title: CFT073 stimulated NLRP3 gRNA 6 hours rep3


title: Unstimulated NLRP3 gRNA 6 hours rep2

value: unstimulated


title: MeT-5A.EWSWT1+KTS.RNAseq.2

value: untreated


title: Unstimulated NLRP3 gRNA 6 hours rep3


title: HSC_W5_rep5

description:
W5_P13_5
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat

source_name: HSC

value: HSC

value: no


title: MeT-5A.EWSWT1-KTS.RNAseq.2


title: HSC_W5_rep4

description:
W5_P13_4
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: Sample 5_AU1035_STRSS1


title: CFT073 stimulated NLRP3 gRNA 6 hours rep1


title: MeT-5A.EWSWT1+KTS.RNAseq.1


title: Sample 4_AU1028_CTRL4

value: Control


title: HSC_W5_rep3

description:
W5_P13_3
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: Sample 3_AU1027_CTRL3


title: HSC_W5_rep2

description:
W5_P13_2
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: Sample 2_AU1026_CTRL2


title: HSC_W5_rep1

description:
W5_P13_1
W5.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: Unstimulated NLRP3 gRNA 6 hours rep1


title: MeT-5A.EWSWT1+KTS-KTS.RNAseq.3


title: Sample 1_AU1024_CTRL1


title: CFT073 stimulated Cas9 control 6 hours rep3

description: Gene expression after 6 hours of unstimulated 5637

value: Cas9 control


title: CFT073 stimulated Cas9 control 6 hours rep2


title: MeT-5A.EWSWT1+KTS-KTS.RNAseq.2


title: D4

city: QingDao

first: Kejin

last: Gao

state: Shan Dong

address: NO.59 hai er Rd, Qingdao, China

country: China

institute: The Affiliated Hospital of Qingdao University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip miRNA 4.0 Array in GeneChip Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: plasma exosomes of patients with CSVD

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: All subjects had fasting venous blood drawn within 24h of admission, and the blood specimens were immediately centrifuged and stratified (300 g, 4°C, 10 min). The upper layer of plasma was aspirated, diluted to 10 ml with PBS buffer, then stratified by high-speed centrifugation (2000 g, 4°C, 10 min), and the sediment at the bottom of the tube was discarded. The collected plasma was stored in a refrigerator at -80 ℃ pending extraction of exosomes.

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

treatment_protocol: Exosome was isolated using total exosome isolation (from plasma) reagent (cat no.4484451, Thermo Fisher Scientific, Inc.).Store the isolated exosomes in a refrigerator at -80 °C pending RNA extraction.

tag: sample type

value: circulating plasma exosomes


title: HSC_W4_rep5

description:
W4_P13_5
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: HSC_W4_rep4

description:
W4_P13_4
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: Unstimulated Cas9 control 6 hours rep3


title: M-TAF4b, rep 2

city: Providence

first: Megan

last: Gura

state: RI

address: 70 Ship St.

department: Molecular Biology, Cell Biology, and Biochemistry

institute: Brown University

data_processing:
Library strategy: CUT&RUN
The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were clustered on flowcells. After clustering, the flowcells were loaded on to the Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Raw sequence data (.bcl files) generated from Illumina HiSeq were converted into fastq files and de-multiplexed using bcl2fastq (v. 2.20). One mismatch was allowed for index sequence identification.
Reads were quality-trimmed and had adapters removed using Trim Galore! (v 0.5.0) with the parameter -q 10.
Samples before and after trimming were analyzed using FastQC (v 0.11.5) for quality and then aligned to the Ensemble GRCm39 using Bowtie2 (v 2.3.0). Fastq screen (v 0.13.0) was used to determine the percentage of reads uniquely mapped to the mouse genome in comparison to other species.
Resulting sam files were converted to bam files, then unmapped, duplicated reads, and low quality mapped were removed using Samtools (v1.9). Resulting bam files were split into size classes using a unix script.
For calling peaks, annotating peaks, and identifying coverage around TSSs, Homer (v 4.10) was used. For signal visualization, IGV was used.
Genome_build: GRCm39
Supplementary_files_format_and_content: Peaks called by Homer for male H3K4me3 replicate 1 with annotation
Supplementary_files_format_and_content: Peaks called by Homer for male TAF4b replicate 1 with annotation
Supplementary_files_format_and_content: Peaks called by Homer for male H3K4me3 repliate 2 with annotation
Supplementary_files_format_and_content: Peaks called by Homer for male TAF4b replicate 2 with annotation

source_name: prospermatogonia

extract_protocol:
Mice that were homozygous for an Oct4-EGFP transgene (The Jackson Laboratory: B6;129S4-Pou5f1tm2Jae/J) were mated for germ cell collections. Timed matings were estimated to begin at day 0.5 by evidence of a copulatory plug. To dissociate gonadal tissue into a single-cell suspension, embryonic gonads were harvested and placed in 0.25% Trypsin/EDTA and incubated at 37°C for 25 minutes, as previously described (Gura et al., 2020). Eppendorf tubes were flicked to dissociate tissue halfway through and again at the end of the incubation. Trypsin was neutralized with FBS. Cells were pelleted at 1,500 RPM for 5 minutes, the supernatant was removed, and cells were resuspended in 100 μL PBS. The cell suspension was strained through a 35 μm mesh cap into a FACS tube (Gibco REF # 352235). Propidium iodide (1:500) was added to the cell suspension as a live/dead distinguishing stain. Fluorescence-activated cell sorting (FACS) was performed using a Becton Dickinson FACSAria III in the Flow Cytometry and Cell Sorting Core Facility at Brown University. A negative control of a non-transgenic mouse gonad was used for each experiment to establish an appropriate GFP signal baseline. Dead cells were discarded and then cells were sorted at 4°C in PBS based on GFP signal into GFP+ or GFP- samples.
For library preparation, the KAPA HyperPrep kit (Roche Cat. No 07962363001) was used with New England Biolabs NEBNext Multiplex Oligos for Illumina (NEB #E7335). After library amplification through PCR, libraries were size selected through gel extraction (~150-650 bp) and cleaned up using the Qiagen QIAquick Gel Extraction Kit (Cat. # 28704). CUT&RUN libraries in EB buffer were shipped to GENEWIZ (GENEWIZ Inc., NJ) on dry ice. Sample QC, sequencing, and initial bioinformatics were done at GENEWIZ.

tag: strain

tag: age

tag: Sex

value: male


title: M-IgG, rep 2


title: Unstimulated Cas9 control 6 hours rep1


title: MeT-5A.EWSWT1-KTS.RNAseq.1


title: CFT073 stimulated Cas9 control 6 hours rep1


title: HSC_W4_rep3

description:
W4_P13_3
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: MeT-5A.control.RNAseq.3

value: control


title: D3


title: MeT-5A.control.RNAseq.2


title: MeT-5A.EWSWT1+KTS-KTS.RNAseq.1


title: M-IgG, rep 1


title: M-H3K4me3, rep 2


title: Unstimulated Cas9 control 6 hours rep2


title: JN-DSRCT1.shGFP.RNAseq.3

value: shGFP


title: MeT-5A.control.RNAseq.1


title: M-TAF4b, rep 1


title: HSC_W4_rep2

description:
W4_P13_2
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: HSC_W3_rep5

description:
W3_P13_5
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: D1


title: M-H3K4me3, rep 1


title: A4

source_name: plasma exosomes of controls


title: A3


title: HSC_W3_rep4

description:
W3_P13_4
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: HSC_W3_rep3

description:
W3_P13_3
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: A2


title: JN-DSRCT1.shGFP.RNAseq.1


title: E16.5_Taf4b-Def_rep7

data_processing:
Reads were quality-trimmed and had adapters removed using Trim Galore! (v 0.5.0) with the parameters -q 10 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Samples before and after trimming were analyzed using FastQC (v 0.11.5) for quality and then aligned to the Ensemble GRCm38 using HiSat2 (v 2.1.0) with the optional -dta setting enabled. (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/; Kim et al., 2019).
Resulting sam files were converted to bam files using Samtools (v 1.9) (Li et al., 2009).
To obtain transcripts per million (TPMs) for each sample, StringTie (v 1.3.3b) was used with the optional parameters -A and -e (Pertea et al., 2016).
To obtain count tables, featurecounts (Subread v 1.6.2) was used (Liao et al., 2014).
DESeq2 was  used for differential gene expression analysis, where the Subread count table was used as input (Love et al., 2014).
Genome_build: GRCm38
Supplementary_files_format_and_content: comma-delimited text file of E16.5 gene counts for each sample
Supplementary_files_format_and_content: comma-delimited text file of E16.5 TPMs and gene information for each sample
Supplementary_files_format_and_content: comma-delimited text file of E16.5 DESeq2 differential gene expression analysis
Supplementary_files_format_and_content: comma-delimited text file of E14.5 gene counts for each sample
Supplementary_files_format_and_content: comma-delimited text file of E14.5 TPMs and gene information for each sample
Supplementary_files_format_and_content: comma-delimited text file of E14.5 DESeq2 differential gene expression analysis

extract_protocol:
Mice that were homozygous for an Oct4-EGFP transgene (The Jackson Laboratory: B6;129S4-Pou5f1tm2Jae/J) and heterozygous for the Taf4b-deficiency mutation were mated for mRNA collections. Timed matings were estimated to begin at day 0.5 by evidence of a copulatory plug. To dissociate gonadal tissue into a single-cell suspension, embryonic gonads were harvested and placed in 0.25% Trypsin/EDTA and incubated at 37°C for 25 minutes, as previously described (Gura et al., 2020). Eppendorf tubes were flicked to dissociate tissue halfway through and again at the end of the incubation. Trypsin was neutralized with FBS. Cells were pelleted at 1,500 RPM for 5 minutes, the supernatant was removed, and cells were resuspended in 100 μL PBS. The cell suspension was strained through a 35 μm mesh cap into a FACS tube (Gibco REF # 352235). Propidium iodide (1:500) was added to the cell suspension as a live/dead distinguishing stain. Fluorescence-activated cell sorting (FACS) was performed using a Becton Dickinson FACSAria III in the Flow Cytometry and Cell Sorting Core Facility at Brown University. A negative control of a non-transgenic mouse gonad was used for each experiment to establish an appropriate GFP signal baseline. Dead cells were discarded and then cells were sorted at 4°C in PBS based on GFP signal into GFP+ or GFP- samples. These cells were then spun down at 1,500 RPM for 5 minutes, had PBS removed, and were then resuspended in Trizol (ThermoFisher # 1556026). If samples had roughly less than 50 µL of PBS in the tube, Trizol was added immediately. Samples were stored at -80°C.
Embryonic germ cells in Trizol were shipped to GENEWIZ (GENEWIZ Inc., NJ) on dry ice. Sample RNA extraction, sample QC, library preparation, sequencing, and initial bioinformatics were done at GENEWIZ. RNA was extracted following the Trizol Reagent User Guide (Thermo Fisher Scientific). Glycogen was added (1 µL, 10 mg/mL) to the supernatant to increase RNA recovery. RNA was quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked with TapeStation (Agilent Technologies, Palo Alto, CA, USA) to see if the concentration met the requirements.  SMART-Seq v4 Ultra Low Input Kit for Sequencing was used for full-length cDNA synthesis and amplification (Clontech, Mountain View, CA), and Illumina Nextera XT library was used for sequencing library preparation. The sequencing libraries were multiplexed and clustered on a lane of a flowcell. After clustering, the flowcell was loaded onto an Illumina HiSeq 4000 according to manufacturer’s instructions. The samples were sequenced using a 2x150 Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS) on the HiSeq instrument.  Raw sequence data (.bcl files) generated from Illumina HiSeq were converted into fastq files and de-multiplexed using bcl2fastq (v. 2.17). One mismatch was allowed for index sequence identification.

value: prospermatogonia

tag: litter date


title: E16.5_Taf4b-Def_rep8


title: D2


title: HSC_W3_rep2

description:
W3_P13_2
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat

tag: treatment


title: JN-DSRCT1.shEWSWT1.RNAseq.4


title: HSC_W3_rep1

description:
W3_P13_1
W3.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: HSC_W4_rep1

description:
W4_P13_1
W4.DGE-SciLicium-HuDeCA-Hemato.unq.refseq.umi_reduced.dat


title: JN-DSRCT1.shEWSWT1.RNAseq.3


title: E16.5_Taf4b-Def_rep6


title: JN-DSRCT1.shEWSWT1.RNAseq.2


title: HSC_W2_rep4

description:
W2_P13_4
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: Sham, Female, Day 7, 3

city: New Haven

first: Yuichi

last: Ohashi

state: CT

address: 10 Amistad Street #414J

department: Surgery

institute: Yale University School of Medicine

data_processing:
Samples were sequenced using 101 bp paired-end sequencing on an Illumina NovaSeq 6000 (Illumina, San Diego, CA, USA). Data generated during sequencing runs were simultaneously transferred to the YCGA high-performance computing cluster.
The FASTQ files of raw sequencing reads were imported into a computing cluster based on Red Hat Linux computing system and analyzed. For the purpose of quality control, poly A and poly T sequences, Illumina adaptor sequences and low-quality sequences in the reads were deleted using PRINSEQ v0.20.4 and Trimmomatic v0.39 software.
The trimmed sequencing data were aligned to the GRCm39 reference genome with the gene annotation information  (Ensembl release 106)] and expression values for each gene were counted using STAR v2.7.7a and RSEM v1.3.3 software.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each samples

source_name: inferior vena cava

extract_protocol:
10-week-old wild-type female and male C57BL/6J mice were purchased from Jackson Laboratory (Bar Harbor, ME, USA). Infrarenal aortocaval fistulae were created. Briefly, inhaled 2 - 2.5 % isoflurane in 1.0 L/min 02 was used for general anesthesia, and extended-release buprenorphine (Ethiqa XR; North Brunswick, NJ, USA) was administered subcutaneously with a dosage of 3.25 mg/kg body weight for intraoperative and postoperative analgesia. The abdominal aorta and the inferior vena cava (IVC) were exposed with a midline laparotomy; the bowels were gently retracted. After the vessels were clamped at an immediately caudal level of the origins of the left renal artery and vein, a fistula between the vessels was created by using a 25-gauge needle to puncture the aorta and IVC, from a left lateral side of the aorta into a lumen of the IVC at a level cranial to the aortic bifurcation. Hemostasis of the puncture site on the lateral aortic wall was achieved by a gentle compression with a surrounding retroperitoneal tissue. A pulsatile bright-red blood flow visible intraoperatively through the IVC wall was considered as a primary technical success of the AVF creation. Sham-operated mice underwent all the same steps except the needle puncture.
Preparation and sequencing of poly-A mRNA sequencing libraries were performed by the Yale Center for Genome Analysis (YCGA). RNA integrity was estimated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Samples with RNA integrity number (RIN) values of ≥ 8.0 were used for analysis.  Poly-A mRNA was purified from approximately 200 ng of total RNA and the stranded mRNA sequencing libraries were constructed using KAPA mRNA HyperPrep Kit for Illumina sequencing (Roche, Basel, Switzerland). Indexed libraries were quantified by qRT-PCR using KAPA Library Quantification Kits (Roche, Basal, Switzerland) and insert size distribution was determined using an Agilent 2100 Bioanalyzer. Samples with a yield of ≥ 0.5 ng/µL and a size distribution of 150 - 300 bp were sequenced. Sample concentrations were normalized to 1.2 nM and loaded onto an Illumina NovaSeq flow cell (Illumina, San Diego, CA, USA) at a concentration that yielded 25 million passing filter clusters per sample.

treatment_protocol: All animal experiments were performed in compliance with federal guidelines and with approval from the Institutional Animal Care and Use Committee of Yale University.

value: inferior vena cava

value: Female

tag: time point

value: Day 7

value: 10 wk

value: Sham


title: Sham, Female, Day 7, 2


title: Sham, Female, Day 7, 1


title: A1


title: JN-DSRCT1.shGFP.RNAseq.2


title: JN-DSRCT1.shEWSWT1.RNAseq.1


title: Sham, Male, Day 7, 2

value: Male


title: E16.5_Taf4b-Def_rep4


title: JN-DSRCT1.control.RNAseq.2


title: Sham, Male, Day 7, 1


title: HSC_W2_rep2

description:
W2_P13_2
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat

tag: cell type


title: AVF, Female, Day 7, 3

value: AVF


title: JN-DSRCT1.control.RNAseq.1

value: untreated


title: E16.5_Taf4b-Def_rep1


title: E16.5_Taf4b-Def_rep5


title: HSC_W2_rep1

description:
W2_P13_1
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat

value: HSC

tag: time


title: AVF, Female, Day 7, 2


title: CD8 cells, Day 7 FLICA Positive, Biological Replicate 2

city: Maywood

first: Edward

middle: M

last: Campbell

state: IL

address: 2160 S First Ave

department: Microbiology and Immunology

institute: Loyola University Chicago

data_processing:
Fast QC c0.11.8
dds/DESeq2 in R studio, genes with more than 10 counts retained
res filies show DEGs between two groups indicated.
res files ending with name include gene name in additional to ENSMUSG annotation
GOST files show gene ontology/pathway anaylsis between two indicated groups.
Assembly: STAR v2.7.1a alignment to GRCm38
Supplementary files format and content: csv

source_name: FACS sorted CD8 T cells

extract_protocol:
NucleoSpin RNA isolation kit (Machery-Nagel)
NovaSeq PE150

value: FACS sorted CD8 T cells

value: Transfer to allogeneic recipient Balb/C mouse


title: Sham, Male, Day 7, 3


title: E16.5_Taf4b-Het_rep8


title: HSC_W2_rep5

description:
W2_P13_5
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat

data_processing:
16 bases are initially read, and all must have a quality score > 10. The unique sample-specific barcode corresponds to first 6 bp, and the unique molecular identifier (UMI) corresponds to the following 10 bp.
Human reference transcriptome from the UCSC website (release hg38) using BWA version 0.7.4.4  was used to align the second reads
Assembly: hg38
Supplementary files format and content: Expression file in dat format. Contains for each sample, the number of unique umis (unique molecular identifier) associated with the 28,307 genes detected.

extract_protocol:
no extraction_cell lysates
Libraries were prepared using the Illumina DNA Prep kit (Illumina) according to the manufacturer’s guidelines.

value: no


title: CD8 cells, Day 7 FLICA Positive, Biological Replicate 3


title: HSC_W1_rep3

description:
W1_P13_3
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: E16.5_Taf4b-Def_rep3


title: E16.5_Taf4b-Het_rep9


title: HSC_W1_rep2

description:
W1_P13_2
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: AVF, Female, Day 7, 1


title: AVF, Male, Day 7, 3


title: CD8 cells, Day 7 FLICA Negative, Biological Replicate 3


title: CD8 cells, Day 7 FLICA Positive, Biological Replicate 1


title: E16.5_Taf4b-Het_rep6


title: HSC_W2_rep3

description:
W2_P13_3
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: CD8 cells, Day 7 FLICA Negative, Biological Replicate 2


title: HSC_W1_rep1

description:
W1_P13_1
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: AVF, Male, Day 7, 2


title: E16.5_Taf4b-Def_rep2


title: HSC_W1_rep4

description:
W1_P13_4
W1-2.DGE_SciLicium_HuDeCA_Hemato.unq.refseq.umi_reduced.dat


title: CD8 cells, Day 7 FLICA Negative, Biological Replicate 1


title: AVF, Male, Day 7, 1


title: E16.5_Taf4b-Het_rep5


title: E16.5_Taf4b-Het_rep4


title: CD4 cells, Day 7 FLICA Negative, Biological Replicate 3

source_name: FACS sorted CD4 T cells

value: FACS sorted CD4 T cells


title: mouse #342 NUT

city: Boston

first: Chris

last: French

address: 77 avenue louis Pasteur, NRB 652

department: Pathology

institute: Brigham and Women's Hospital

data_processing:
Reads were trimmed for adaptor sequences using trimmomatic v0.36 and then aligned to concatenated mm39/Genome Reference Consortium mouse Reference 39 (GRCm39) assembly of the human genome, using bowtie2 v2.3.1 with options --local --very-sensitive-local --no-unal --nomixed --no-discordant --phred33. Only reads with a MAPQ ≥ 30 were retained using samtools v1.3.1. PCR duplicates were removed with picard MarkDuplicates v2.9.2. Coverage-based tracks were generated with deepTools bamCoverage with options --binSize 1 -normalizingUsing RPGC --effectiveGenomeSize 2800000000 -extendReads --samFlagInclude 64. CUT&RUN profiles were then calibrated by spike-in normalization using the E. Coli DNA as the internal reference using a similar method as that done for ChIP-seq[25]. Specifically, the Occupancy Ratio (OR) was calculated as the product of IgG spike-in reads and immunocleaved (IC) human reads, divided by the product of IgG human reads and IC spike-in reads. Spike-in normalized tracks were generated with deepTools bamCoverage with options --binSize 1 --normalizeUsing RPGC --effectiveGenomeSize 2800000000 --extendReads --samFlagInclude 64 --scaleFactor OR.epic2 v0.0.52 was used for domain calling on the canonical human chromosomes with options --bin-size 200 --gaps-allowed 5 with the corresponding IgG library set as the control. Called domains were filtered by signal strength and by domain size using the ROSE algorithm (Rank Ordering of Super-Enhancers)[26]. Domains that exceeded both the signal cutoff and the size threshold were retained. We frequently observed closely spaced filtered domains that corresponded to larger domains based on CUT&RUN signal tracks. To span and capture these regions filtered domains within 25 kb of one another were combined. A high confidence list of “megadomains” was created by merging filtered domains identified in both logical replicates.
Supplementary files format and content: GRCm39/mm39

source_name: stomach tumor

growth_protocol: DMEM, 10% fetal bovine serum, 1x glutamax, 1% penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 0.1% formaldehyde for 1 minute. Tissue was fixed with 0.2% formaldehyde for 2 minutes. Cells were bound to Con-A beads and incubated overnight with target antibodies. Bead bound cells were washed and incubated with pAG-MNase for 60 minutes at 4degC before being washed and incubated with CaCl2 to activate MNase. Reaction was stopped with EGTA,EDTA containing buffer and incubated for 10minutes at 37degC to release DNA. SDS and proteinase K were added to each sample before overnight incubation at 55degC to reverse cross link. DNA was purified using oligo clean and concentrator. Yields were determined using Qubit 2.0 Fluorometer with 1x dsDNA HS assay kit
Immunoprecipitated DNA was quantified with Qubit 2.0 DNA HS Assay (ThermoFisher, Massachusetts, USA) and quality was assessed by Tapestation genomic DNA Assay (Agilent Technologies, California, USA). Library preparation was performed using KAPA Hyper Prep kit with PCR (Roche, Basel, Switzerland) per manufacturer’s recommendations. Library quality and quantity were assessed with Qubit 2.0 DNA HS Assay (ThermoFisher, Massachusetts, USA), Tapestation High Sensitivity D1000 Assay (Agilent Technologies, California, USA), and QuantStudio ® 5 System (Applied systems, California, USA). Illumina® 8-nt unique dual-indices were used. Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® NovaSeq X Plus 10B (Illumina, California, USA) with a read length configuration of 150 PE for 8M PE reads (4M in each direction).

value: stomach tumor

tag: cell line

value: Genetically engineered mouse model of NUT Carcinoma

tag: cut&run antibody


title: E16.5_Taf4b-Het_rep7

value: male


title: CD34hi/CD45RAhi/ITGB7pos/CD127- fraction (T/NK/ILC-Mono-Dendritic)

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
not applicable
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics)

tag: developmental stage

value: fetal (2nd trimester)


title: CD34hi/CD45RAhi/ITGB7neg-pos/CD127+ fraction (B lymphoid)

description: 10x Genomics


title: mouse #005 NUT

source_name: stomach tissue

value: stomach tissue


title: CD4 cells, Day 7 FLICA Negative, Biological Replicate 1


title: E16.5_Taf4b-Het_rep3

value: prospermatogonia


title: E16.5_Taf4b-Het_rep1


title: E16.5_Taf4b-Het_rep2


title: E16.5_Taf4b-Wt_rep7


title: mouse #004 NUT


title: mouse #005 H3K27ac


title: ARP1_DIM

city: 南京

first: yang

last: shu

state: 江苏

address: xianlin road

institute: Nanjin university of Chinese medicin

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Multiple myeloma cells

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Homo multiple myeloma cells

value: Dosing DIM


title: ARP1_T6

value: Dosing T6


title: Control CD8 cells, Day 0, Biological Replicate 2

value: Day 0


title: Control CD8 cells, Day 0, Biological Replicate 3


title: Control CD8 cells, Day 0, Biological Replicate 1


title: mouse #004 H3K27ac


title: CD34hi/CD45RAhi/ITGB7-/CD127- fraction (MPP/GMP/LMPP/MLP))

description: 10x Genomics

source_name: lymphoMonoDendriticCellProgenitors

value: lymphoMonoDendriticCellProgenitors


title: ARP1_F2

value: Dosing F2


title: E16.5_Taf4b-Wt_rep5


title: Control CD4 cells, Day 0 Biological Replicate 3


title: mouse #342 H3K27me3


title: ARP1_I3C

value: Dosing I3C


title: CD4 cells, Day 7 FLICA Negative, Biological Replicate 2

value: Day 7


title: mouse #342 H3K27ac


title: ARP1_WT

value: No dosing


title: E16.5_Taf4b-Wt_rep4


title: mouse #005 H3K27me3


title: mouse #004 H3K27me3


title: Control CD4 cells, Day 0 Biological Replicate 2


title: E16.5_Taf4b-Wt_rep3


title: CD34hiCD45RA-/int fraction (HSC/MPP)

description: 10x Genomics


title: E16.5_Taf4b-Wt_rep6


title: CD34+ HSPC replicate 2, C1 capture

city: Frankfurt

first: Jan-Henning

last: Klusmann

address: Theodor-Stern-Kai 7

department: Pediatric Hematology and Oncology

country: Germany

institute: Goehte University Frankfurt

data_processing:
Library strategy: NG Capture-C
Sequencing data were processed using the capC-MAP suite from Buckle, A., Gilbert, N., Marenduzzo, D. & Brackley, C.A. capC-MAP: software for analysis of Capture-C data. Bioinformatics 35, 4773-4775 (2019).
In silico DpnII restriction enzyme digest of the human reference genome hg38 was performed using the "capC-MAP genomedigest" command.
Adapter trimming (cutadapt), in silico restriction enzyme digestion, alignment (bowtie), PCR duplicate removal, and interaction mapping were all performed using the "capC-MAP run" command.
Replicates were combined using the "capC-MAP combinereps" command.
Each resulting track (bedGraph format) was capped at the 99th percentile and normalized to the maximum signal in R.
Genome_build: hg38
Supplementary_files_format_and_content: Custom bedGraph tracks (replicates combined, viewpoint excluded, signal capped at 99th percentile, normalized to max)

source_name: CD34+ HSPCs

extract_protocol:
Samples were prepared using the NG Capture-C protocol from Davies, J.O. et al. Multiplexed analysis of chromosome conformation at vastly improved sensitivity. Nat Methods 13, 74-80 (2016), with the following modifications: (1) Five to ten million cells were harvested per sample and the DpnII digestion reactions were scaled down accordingly. (2) DNA was sheared to 200 bp fragments using a Branson 450 Digital Sonifier (Marshall Scientific) (time 18 s, amplitude 20%, pulse 0.5 s, pause 1.5 s; repeat 5x). (3) All of the material from the first capture was used as input for the second round of oligonucleotide capture. (4) Two biological replicates were prepared per sample and pooled for the oligonucleotide capture steps (multliplexed library capture).
Illumina sequencing libraries were prepared using the NEBNext DNA Library Prep Reagent Set (E6040S/L). The libraries were sequenced by Novogene Company, Ltd. on an Illumina NovaSeq platform (150 bp paired-end reads).

treatment_protocol: Stable Cas9-expressing K562 and ML-2 cells were transduced with sgRNAs targeting either MYNRL15 cis-regulatory region C1 (sgC1.1) or the firefly luciferase gene (sgLUC; non-targeting control). Primary CD34+ HSPCs were thawn and expanded in vitro for 3 days.

value: CD34+ HSPCs

value: In vitro expansion


title: Control CD4 cells, Day 0 Biological Replicate 1

value: FACS sorted CD4 T cells


title: E16.5_Taf4b-Wt_rep1


title: CD34+ HSPC replicate 1, C1 capture


title: mouse #342 IgG

value: stomach tumor

value: Genetically engineered mouse model of NUT Carcinoma

value: IgG (EpiCypher, 13-0042K)


title: ML-2 sgC1.1 replicate 2, C1 capture

source_name: ML-2 cell line

value: Myelomonocytic leukemia

value: sgRNA against MYNRL15 C1


title: mouse #004 IgG

value: stomach tissue


title: mouse #005 IgG


title: TMS3

first: Alexander

last: Gimelbrant

address: 31A Iroquois St

institute: Altius Institute

data_processing:
Mapping: STAR v2.6.1d ; parameter - mismatch=2
Quantification: FeatureCounts v1.5.0-p3
Assembly: mm10
Supplementary files format and content: fpkm_sample.xls: Tab-delimited xls file. The file format: column1 = gene ID; column2 = sample 1; column3 = sample 2; …
Supplementary files format and content: readcount.xls: Tab-delimited xls file. Format: column1 = gene ID; column2 = sample 1; column3 = sample 2; …

source_name: BMDMs

growth_protocol: B6.Sst1S BMDM were maintained in DMEM F12 media supplemented with 10% FCS and 10 % L Cell Conditioned Medium (LCCM) in humidified atmosphere with 5 % CO2 at 37oC

extract_protocol:
RNA was harvested using Rnesay mini plus kit. A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: BMDM were treated with TNF (10 ng/mL) and different inhibitors for 3 days post-phagocytosis.

value: BMDMs

value: Primary cells

value: sst1 KO

value: TNF Mtb SP600125

value: Day 3


title: E16.5_Taf4b-Wt_rep2

value: prospermatogonia

value: male


title: E14.5_Taf4b-Def_rep4


title: TMS1


title: ML-2 sgC1.1 replicate 1, C1 capture


title: TMS2


title: E14.5_Taf4b-Def_rep3


title: 317E cell line NUT  rep 2

source_name: 317E cell line

value: 317E cell line


title: TMRS3

value: TNF Mtb RocA SP600125


title: ML-2 sgLUC replicate 2, C1 capture

value: sgRNA against LUC (control)


title: 317E cell line NUT  rep 1


title: E14.5_Taf4b-Def_rep2


title: TMRS2


title: E14.5_Taf4b-Def_rep1


title: TMRS1


title: 317E cell line H3K27ac  rep 2


title: K562 sgC1.1 replicate 2, C1 capture

source_name: K562 cell line

value: Erythroleukemia


title: ML-2 sgLUC replicate 1, C1 capture


title: E14.5_Taf4b-Wt_rep4


title: 317E cell line H3K27ac  rep 1


title: TMRI3

value: TNF Mtb RocA ISRIB


title: K562 sgC1.1 replicate 1, C1 capture


title: E14.5_Taf4b-Wt_rep3


title: 317E cell line H3K27me3  rep 2

value: Genetically engineered mouse model of NUT Carcinoma


title: K562 sgLUC replicate 2, C1 capture


title: 317E cell line H3K27me3  rep 1


title: TMRI1


title: TMRI2


title: E14.5_Taf4b-Wt_rep2


title: TMRb3

value: TNF Mtb RocA Batch 2


title: E14.5_Taf4b-Wt_rep1


title: 317E cell line IgG  rep 2

value: IgG (EpiCypher, 13-0042K)


title: TMRb2


title: Pik3cdE1020K/+ HDM

city: Bethesda

first: Tom

last: Hill

state: Maryland

address: NIHBC 10 - CLINICAL CENTER BG RM 11N244A, 10 CENTER DR

institute: NIAID

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PBMC

extract_protocol:
Samples 1-3 in each group are pooled and used in 10x genomics 3’ kit library prep
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: Cell extracted from spleen 20 days after exposure to HDM or to control substance.

value: PBMC

value: HDM


title: 317E cell line IgG  rep 1


title: ML-2 sgC2.2 replicate 2, day 6 post-transduction

description:
d6_ML-2_sgC2.2_R2
RNA-seq_I_genes.count.annot.xls

data_processing:
Raw reads were trimmed and filtered by Novogene Company, Ltd. using in-house scripts, then mapped to human reference genome hg38 using HISAT2.
Gene expression values (FPKM) were calculated using the featureCounts package in R.
Genome_build: hg38
Supplementary_files_format_and_content: Raw read counts in tab-separated format
Supplementary_files_format_and_content: Normalized read counts (FPKM) in tab-separated format

extract_protocol:
Transduced cells were sorted directly into RNA lysis buffer and extracted using the Zymo Quick-RNA Miniprep Kit with on-column DNase treatment (R1054).
Illumina sequencing libraries were prepared by Novogene Company, Ltd. using polyA-enriched total cellular RNA, and sequenced on an Illumina NovaSeq platform (150 bp paired-end reads).

treatment_protocol: Stable Cas9-expressing K562 and ML-2 cells were transduced with sgRNAs targeting the MYNRL15 cis-regulatory regions C1 (sgC1.1-2) and C2 (sgC2.1-2) or the firefly luciferase gene (sgLUC; non-targeting control).

value: Myelomonocytic leukemia

value: sgRNA against MYNRL15 C2


title: 311E cell line 9nM ABBV075 96hr NUT  rep 2

source_name: 311E cell line

value: 311E cell line


title: ML-2 sgC2.1 replicate 2, day 6 post-transduction

description:
d6_ML-2_sgC2.1_R2
RNA-seq_I_genes.count.annot.xls


title: TMRb1

value: BMDMs

value: Primary cells

value: sst1 KO


title: 311E cell line 9nM ABBV075 96hr NUT  rep 1


title: TMR3

value: TNF Mtb RocA

value: Day 3


title: ML-2 sgC2.1 replicate 1, day 6 post-transduction

description:
d6_ML-2_sgC2.1_R1
RNA-seq_I_genes.count.annot.xls


title: Wildtype Naïve

description: 10x Genomics

value: WT

value: Naïve


title: TMR2


title: 311E cell line 9nM ABBV075 96hr H3K27ac rep 2


title: ML-2 sgC1.2 replicate 2, day 6 post-transduction

description:
d6_ML-2_sgC1.2_R2
RNA-seq_I_genes.count.annot.xls

value: sgRNA against MYNRL15 C1


title: ML-2 sgC1.2 replicate 1, day 6 post-transduction

description:
d6_ML-2_sgC1.2_R1
RNA-seq_I_genes.count.annot.xls


title: K562 sgLUC replicate 1, C1 capture

value: Erythroleukemia

value: sgRNA against LUC (control)


title: 311E cell line 9nM ABBV075 96hr H3K27ac  rep 1

value: Genetically engineered mouse model of NUT Carcinoma


title: Hair matrix cells, cultured, biol rep 3 [MA_3 miRNA-seq]

city: lanzhou

first: zhang

last: xiaolan

address: Lanzhou Institute of Husbandry and Pharmaceutical Sciences

institute: Chinese Academy of Agricultural Sciences

data_processing:
Trimmomatic, 0.36
hisat2, 2.2.1.0, --rna-strandness rf --fr
DESeq, 1.20.0, qvalue<0.05, |log2FoldChange|>1
Assembly: Bosgru_v3.0
Supplementary files format and content: TPM values  for each Sample

organism: Bos grunniens

source_name: skin

growth_protocol: DPCs and HMCs were cultured in DMEM/F12 medium supplemented with 1% penicillin-streptomycin, 10 ng/mL IGF1, 20 ng/mL EGF , and 10% FBS in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA of DPCs and HMCs were extracted using Trizol reagent.
For mRNA sequencing, six libraries from DPCs (n=3) and HMCs (n=3) were constructed using TruSeq Stranded mRNA LT Sample Prep Kit. For miRNA sequencing, a total amount of 1 µg RNA per sample was used for the small RNA library construction using TruSeq Small RNA Sample Prep Kits.

value: skin

value: Hair matrix cells

value: epidermal cell

value: isolated and cultured


title: TMI3

value: TNF Mtb ISRIB


title: TMR1


title: ML-2 sgC1.1 replicate 2, day 6 post-transduction

description:
d6_ML-2_sgC1.1_R2
RNA-seq_I_genes.count.annot.xls

value: Myelomonocytic leukemia


title: Hair matrix cells, cultured, biol rep 2 [MA_2 miRNA-seq]


title: TMI2

value: BMDMs


title: 311E cell line 9nM ABBV075 96hr H3K27me3  rep 2

value: 311E cell line


title: Hair matrix cells, cultured, biol rep 1 [MA_1 miRNA-seq]


title: Dermal papilla cells, cultured, biol rep 3 [DP3 miRNA-seq]

value: Dermal papilla cells

value: dermal cell


title: ML-2 sgC2.2 replicate 1, day 6 post-transduction

description:
d6_ML-2_sgC2.2_R1
RNA-seq_I_genes.count.annot.xls

value: sgRNA against MYNRL15 C2


title: ML-2 sgC1.1 replicate 1, day 6 post-transduction

description:
d6_ML-2_sgC1.1_R1
RNA-seq_I_genes.count.annot.xls


title: TMI1

value: Primary cells

value: sst1 KO

value: Day 3


title: Wildtype HDM

description: 10x Genomics

value: PBMC

value: WT

value: HDM


title: 311E cell line 9nM ABBV075 96hr IgG  rep 2

value: Genetically engineered mouse model of NUT Carcinoma

value: IgG (EpiCypher, 13-0042K)


title: ML-2 sgLUC replicate 2, day 6 post-transduction

description:
d6_ML-2_sgLUC_R2
RNA-seq_I_genes.count.annot.xls

value: sgRNA against LUC (control)


title: Pik3cdE1020K/+ Naïve

description: 10x Genomics

value: Naïve


title: Dermal papilla cells, cultured, biol rep 2 [DP2 miRNA-seq]

value: skin

value: isolated and cultured


title: TMb3

value: BMDMs

value: TNF Mtb infected Batch 2


title: 311E cell line 1uM taz 96hr NUT  rep 2

value: 311E cell line


title: ML-2 sgLUC replicate 1, day 6 post-transduction

description:
d6_ML-2_sgLUC_R1
RNA-seq_I_genes.count.annot.xls

value: Myelomonocytic leukemia


title: Dermal papilla cells, cultured, biol rep 1 [DP1 miRNA-seq]

value: Dermal papilla cells

value: dermal cell


title: 311E cell line 1uM taz 96hr NUT  rep 1


title: TMb2

value: Primary cells

value: sst1 KO


title: TMb1

value: Day 3


title: ML-2 sgC2.2 replicate 2, day 3 post-transduction

description:
d3_ML-2_sgC2.2_R2
RNA-seq_I_genes.count.annot.xls

value: sgRNA against MYNRL15 C2


title: ML-2 sgC2.2 replicate 1, day 3 post-transduction

description:
d3_ML-2_sgC2.2_R1
RNA-seq_I_genes.count.annot.xls


title: 311E cell line 9nM ABBV075 96hr H3K27me3  rep 1


title: ML-2 sgC2.1 replicate 2, day 3 post-transduction

description:
d3_ML-2_sgC2.1_R2
RNA-seq_I_genes.count.annot.xls


title: 311E cell line 1uM taz 96hr H3K27ac  rep 1


title: ML-2 sgC2.1 replicate 1, day 3 post-transduction

description:
d3_ML-2_sgC2.1_R1
RNA-seq_I_genes.count.annot.xls


title: 311E cell line 1uM taz 96hr H3K27ac rep 2


title: 311E cell line 1uM taz 96hr H3K27me3  rep 1


title: C2_24h_bilirubin

city: Düsseldorf

first: Wasco

last: Wruck

address: Moorenstr. 5

institute: Universitätsklinikum Düsseldorf

description: replicate 1

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol for Affymetrix Clariom S Assay Gene Expression Array

data_processing: The data were normalised using RMA normalisation from R/Bioconductor

source_name: brain organoids derived from induced pluripotent stem cells

growth_protocol: The iPSCs were cultured on Matrigel coated culture dishes using mTeSR plus medium.  iPSCs were seeded to form embryoid bodies (EBs) with mTesR plus medium and 10 µM ROCK inhibitor Y-27632. The EBs were cultured  for 5 days with the neural induction medium (StemCell Technologies). At day 6, culture medium was changed to  organoid medium, which is composed of DMEM/F12 and the Neural Basal Medium (in 1:1 ratio), supplemented with 1:200 N2, 1:100 L-glutamine, 1:100 B27 w/o vitamin A, 100 U/mL   penicillin, 100 mg/mL streptomy-cin, 0.05 mM MEM NEAA, 0.05 mM β  -mercaptoethanol.  From day 9 onward, 0.5 µM of dorsomorphin and 5 µM SB431542  were added to the organoid medium.

extract_protocol: The RNA was extracted using TRIzol reagent (Thermo Fisher Scientific) and the manufactural protocol. The quality of the RNA was checked with a NanodropTM spectrophotometer (Thermo Scientific).

treatment_protocol: The day-20 cortical organoids were treated up to 72 h with 200 nM free bilirubin (BF) (purchased from Sigma-Aldrich), whileDMSO served as the control and the medium was refreshed every 24 h. In brief, DMSO was used to dissolve the free bilirubin to obtain a stock concentration of 100 mM and further diluted to 200 µM. For the treatment and control conditions, BF and DMSO were diluted (1:1000) in the culture medium (orgnaoid medium), respectively.

value: C2 bilirubin


title: ML-2 sgC1.2 replicate 2, day 3 post-transduction

description:
d3_ML-2_sgC1.2_R2
RNA-seq_I_genes.count.annot.xls

value: sgRNA against MYNRL15 C1


title: 311E cell line 1uM taz 96hr IgG  rep 2

value: Genetically engineered mouse model of NUT Carcinoma

value: IgG (EpiCypher, 13-0042K)


title: C2_24h_ctrl

description: replicate 1

value: C2 ctrl


title: 311E cell line 1uM taz 96hr H3K27me3  rep 2


title: T3

value: Uninfected TNF treated


title: UM51_72h_ctrl

description: replicate 1

value: UM51 ctrl


title: ML-2 sgC1.2 replicate 1, day 3 post-transduction

description:
d3_ML-2_sgC1.2_R1
RNA-seq_I_genes.count.annot.xls


title: ML-2 sgC1.1 replicate 2, day 3 post-transduction

description:
d3_ML-2_sgC1.1_R2
RNA-seq_I_genes.count.annot.xls


title: T2

value: BMDMs


title: UM51_72h_bilirubin

description: replicate 1

value: UM51 bilirubin


title: 311E cell line 1uM taz 96hr IgG  rep 1

value: 311E cell line


title: T1


title: 311E cell line DMSO 96hr NUT  rep 1


title: UM51_24h_bilirubin

description: replicate 1


title: UM51_24h_ctrl

description: replicate 1


title: TM3

value: TNF Mtb infected


title: ML-2 sgLUC replicate 2, day 3 post-transduction

description:
d3_ML-2_sgLUC_R2
RNA-seq_I_genes.count.annot.xls

value: Myelomonocytic leukemia

value: sgRNA against LUC (control)


title: ML-2 sgC1.1 replicate 1, day 3 post-transduction

description:
d3_ML-2_sgC1.1_R1
RNA-seq_I_genes.count.annot.xls


title: TM2

value: Primary cells


title: M3

value: sst1 KO

value: Untreated Mtb infected


title: TM1

value: Day 3


title: M2


title: C2_72h_bilirubin

description: replicate 1

value: C2 bilirubin


title: ML-2 sgLUC replicate 1, day 3 post-transduction

description:
d3_ML-2_sgLUC_R1
RNA-seq_I_genes.count.annot.xls


title: M1


title: 311E cell line DMSO 96hr H3K27ac  rep 1


title: K562 sgC2.2 replicate 2, day 7 post-transduction

description:
d7_K562_sgC2.2_R2
RNA-seq_I_genes.count.annot.xls

value: Erythroleukemia

value: sgRNA against MYNRL15 C2


title: 311E cell line DMSO 96hr NUT  rep 2

value: Genetically engineered mouse model of NUT Carcinoma


title: 311E cell line DMSO 96hr H3K27me3  rep 2


title: K562 sgC2.2 replicate 1, day 7 post-transduction

description:
d7_K562_sgC2.2_R1
RNA-seq_I_genes.count.annot.xls


title: UNTREAT2

value: Untreated uninfected


title: K562 sgC2.1 replicate 2, day 7 post-transduction

description:
d7_K562_sgC2.1_R2
RNA-seq_I_genes.count.annot.xls


title: K562 sgC2.1 replicate 1, day 7 post-transduction

description:
d7_K562_sgC2.1_R1
RNA-seq_I_genes.count.annot.xls


title: 311E cell line DMSO 96hr IgG  rep 1

value: IgG (EpiCypher, 13-0042K)


title: 311E cell line DMSO 96hr IgG  rep 2


title: UNTREAT1


title: 311E cell line DMSO 96hr H3K27ac rep 2


title: Ti-TMS-PEI _24h_D

city: Rostock

first: Dirk

last: Koczan

address: Schillingallee 70

department: Institute for Immunology

institute: University of Rostock

description: cell grown for 24h on amine-based polymer coating Ti-TMS-PEI

hyb_protocol: Hybridization was performed for 16 hours at 45 degrees celsius using the GeneChip Hybridization Oven 645 (Affymetrix, St. Clara, USA).

scan_protocol: Scanning was done using the GeneChip Scanner 3000/7G (Affymetrix, St. Clara, USA) with 0.7 micron resolution.

data_processing: Data were processed by SST-RMA (signal space transformation with robust multichip averaging) using TAC 4.0.3.14 (transcriptome analysis console; Applied Biosystems, Thermo Fisher Scientific Inc.)

source_name: Ti-TMS-PEI _24h

label_protocol: 200 ng total RNA was labeled as descriped in the WT-labeling protocol (Affymetrix/Thermofisher).

growth_protocol: MG-63 were growm in DMEM medium with 10% FCS at 37 °C with 5 % CO2.

extract_protocol: Extraction was done with the RNeasy kit (Qiagen, Hilden, Germany) according to the manufacturer`s instructions. A Dnase I digestion was included on the spin column during the first washing step.

treatment_protocol: Surface coating and growth time were variated.

value: MG-63 (ATCC® CRL-1427™, United States)

value: osteoblast-like cells

value: Ti-TMS-PEI _24h


title: C2_72h_ctrl

description: replicate 1

value: C2 ctrl


title: Ti-TMS-PEI _24h_A


title: K562 sgC1.2 replicate 2, day 7 post-transduction

description:
d7_K562_sgC1.2_R2
RNA-seq_I_genes.count.annot.xls

value: sgRNA against MYNRL15 C1


title: Cells treated with MMP3 recombinant protein, H3

first: Yihong

last: Ye

state: MD

address: 5 Center Drive

institute: NIH

data_processing:
Data quality check-a step where low confidence nucleotide base-calls can be identified and removed
Map data to reference genome – a suitable genome was chosen from publicly available genomic repositories, such as the NCBI/UCSC/Ensembl databases.
Differential gene expression analysis, where results visualize the distribution of differentially expressed genes across the samples using high-resolution and publication ready volcano plots and heatmaps.
Functional analysis by mapping the reads against publicly available protein databases, such as the Gene Ontology db (GO enrichment analysis), Kyoto Encyclopedia of Genes and Genomes db (KEGG enrichment analysis), or perform a Gene Set Enrichment Analysis (GSEA) and Protein-Protein interaction studies.
Supplementary files format and content: Excel file reporting counts and fpkms.

source_name: Brain

growth_protocol: Isolated astrocytes were cultured in a defined, serum-free base medium containing 50% neurobasal, 50% DMEM, 100 U/ml penicillin, 100 μg/ml streptomycin, 1 mM sodium pyruvate, 292 μg/ml L-glutamine, 1 x G5 supplement, and the astrocyte-required survival factor HBEGF at 5 ng/ml.

extract_protocol:
RNA isolation was performed using a RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA concentration was measured using Nanodrop-1000.
The polyA enrichment library preparation procedure is used for RNA library construction and it results in the construction of 250-300 bp insert cDNA library
PE150 bp strategy

treatment_protocol: Astrocytes were treated with tau PFF 200 nM together with the inhibitors specified in the sample section. Cells were incubated with a serum free medium containing 0.05% trypsin for 10 min at 25 °C. Cells were washed at least three times to remove the remaining tau. Cells were then incubated with a serum-free and protein-free medium at 37 °C in the incubator for the indicated time periods.

value: Brain

value: astrocyte

value: wt


title: Cells treated with MMP3 recombinant protein, H2


title: GEMM control tissue #3

data_processing:
Quality-controlled reads are aligned to the human genome (GRCh38/hg38) and to ERCC92 spike-in sequences using a splice-aware aligner (STAR89) with Ensembl. transcriptome annotations.
Differential expression (DE) analysis is performed using RUVSeq to identify unwanted variation followed by edgeR91 and/or DESeq2
Assembly: GRCm39/mm39 and GRCh38/hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: HBSS + 10% FBS + 1% pen/strep + 1x glutamax

extract_protocol:
RNA was harvested using RNAeasy (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries. ERCC92 spike-in RNA is added to normalize reads.
RNA libraries for RNA-seq were prepared using the Roche KAPA HyperPrep RNA RiboErase Kit following manufacturer's protocols.

value: SOX2-/-BRD4-NUTM1+/- esophgeal mucosa fresh tissue


title: K562 sgC1.2 replicate 1, day 7 post-transduction

description:
d7_K562_sgC1.2_R1
RNA-seq_I_genes.count.annot.xls


title: Ti-TMS-PEI _24h_B


title: GEMM control tissue #2


title: Cells treated with MMP3 recombinant protein, H1


title: K562 sgC1.1 replicate 2, day 7 post-transduction

description:
d7_K562_sgC1.1_R2
RNA-seq_I_genes.count.annot.xls


title: Ti-Ref_24h_C

description: cells grown for 24h on uncoated titanium surface

value: uncoated titanium surface


title: Tau PFF treatment with PF271, F3

value: Tau PFF+PF271


title: 311E cell line DMSO 96hr H3K27me3  rep 1

value: 311E cell line


title: K562 sgC1.1 replicate 1, day 7 post-transduction

description:
d7_K562_sgC1.1_R1
RNA-seq_I_genes.count.annot.xls

value: Erythroleukemia


title: Ti-Ref_24h_B


title: Ti-TMS-PEI _24h_C


title: Ti-Ref_24h_A


title: UNTREAT3

value: BMDMs

value: Primary cells

value: sst1 KO

value: Day 3


title: 317E tumor tissue

value: fresh GEMM tumor tissue from which 317E cell line was derived


title: K562 sgLUC replicate 2, day 7 post-transduction

description:
d7_K562_sgLUC_R2
RNA-seq_I_genes.count.annot.xls

value: sgRNA against LUC (control)


title: Ti-TMS-PEI _4h_D

description: cell grown for 4h on amine-based polymer coating Ti-TMS-PEI

source_name: Ti-TMS-PEI _4h

value: MG-63 (ATCC® CRL-1427™, United States)

value: osteoblast-like cells

value: Ti-TMS-PEI _4h


title: 317E cell line bio rep 3

value: 317E cell line

value: GEMM, esophagus mNC tumor


title: Ti-TMS-PEI _4h_B


title: 311E tumor tissue

value: fresh GEMM tumor tissue from which 311E cell line was derived


title: Ti-TMS-PEI _4h_C


title: Tau PFF treatment with PF271, F2

value: Brain

value: astrocyte

value: wt


title: Tau PFF treatment with PF271, F1

value: Tau PFF+PF271


title: GEMM control tissue #1

value: SOX2-/-BRD4-NUTM1+/- esophgeal mucosa fresh tissue


title: K562 sgC2.2 replicate 3, day 3 post-transduction

description:
d3_K562_sgC2.2_R3
RNA-seq_II_genes.count.annot.xls

value: Erythroleukemia

value: sgRNA against MYNRL15 C2


title: K562 sgC2.2 replicate 2, day 3 post-transduction

description:
d3_K562_sgC2.2_R2
RNA-seq_II_genes.count.annot.xls


title: 317E cell line bio rep 2


title: K562 sgLUC replicate 1, day 7 post-transduction

description:
d7_K562_sgLUC_R1
RNA-seq_I_genes.count.annot.xls


title: Tau PFF treatment with PDTC, E3

value: Tau PFF+PDTC


title: Ti-TMS-PEI _4h_A


title: Ti-Ref_4h_D

description: cells grown for 4h on uncoated titanium surface

value: uncoated titanium surface


title: 317E cell line bio rep 1


title: Tau PFF treatment with PDTC, E1


title: 311E,1uM taz + 9nM ABBV075 96hr bio rep 3

value: 311E cell line

value: 9nM ABBV075 + 1uM tazemetostat


title: K562 sgC2.2 replicate 1, day 3 post-transduction

description:
d3_K562_sgC2.2_R1
RNA-seq_II_genes.count.annot.xls


title: Tau PFF treatment with PI103, D3

value: Tau PFF+PI103


title: Ti-Ref_4h_C

value: MG-63 (ATCC® CRL-1427™, United States)

value: osteoblast-like cells


title: K562 sgC1.1 replicate 3, day 3 post-transduction

description:
d3_K562_sgC1.1_R3
RNA-seq_II_genes.count.annot.xls

value: sgRNA against MYNRL15 C1


title: B37-S1, Control group, Utah, Skin_rep6

city: Las Vegas

first: Sarah

last: Corey-Rivas

state: New Mexico

address: PO BOX 9000

department: Biology

institute: New Mexico Highlands University

data_processing:
Trimmomatic (ver. 0.33) was used to remove residual adapter/index sequences and quality trimming of paired reads.
Trinity (ver. 2.4.0) was used to de novo assemble trimmed read data from all forty-eight libraries. After filtering transcripts with lengths less than 500 bp from the primary assembly, the filtered transcriptome was used as the mapping reference for subsequent RNA-Seq analysis and as input for Blast analyses.
Trinity was used to align reads from each sample to the transcriptome with Bowtie2 and to determine count values using RSEM.
Supplementary files format and content: Tab-delimited txt file, raw count for each sample, from RSEM

organism: Anaxyrus boreas boreas

source_name: Skin

extract_protocol:
Tissue was harvested in RNA-later and stored at -80C. RNA was isolated from liver using the RNeasy Plus Mini Kit and isolated RNA from ventral skin using the RNeasy Fibrous Tissue Mini Kit (Qiagen, Germantown, MD) and homogenized tissue using a Polytron PT1600E (Kinematica AG, Bohemia, NY) or liquid nitrogen and mortar and pestle following the kit protocols. RNA quality was quantified using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) and verified a minimum RIN>8 and quantity >1ug.
Stranded sequence libraries were prepared from total RNA (KAPA Stranded mRNA-Seq kit, Kappa Biosystems) and fragmentation was performed to select for larger sized inserts.

treatment_protocol: Bd challenge group was innoculated with 10^6 Bd zoospores (JEL 275) for 24 hours in Holfreter’s solution and control animals were treated with Holfreter’s solution, alone, for 24 hours. The experiment ran for 34 days before tissue was collected from euthanized animals.

value: Skin

value: F

tag: location

value: Utah

value: Control


title: 311E,1uM taz + 9nM ABBV075 96hr bio rep 2

value: GEMM, esophagus mNC tumor


title: Ti-Ref_4h_B


title: Ti-Ref_4h_A


title: 311E, 9nM ABBV075 96hr bio rep 3

value: 9nM ABBV077


title: Tau PFF treatment with PDTC, E2

value: Brain

value: astrocyte

value: wt


title: Tau PFF treatment with MK2206, C3

value: Tau PFF+MK2206


title: B28-S1, Control group, Utah, Skin_rep5

value: M


title: K562 sgLUC replicate 3, day 3 post-transduction

description:
d3_K562_sgLUC_R3
RNA-seq_II_genes.count.annot.xls

value: Erythroleukemia

value: sgRNA against LUC (control)


title: Tau PFF treatment with PI103, D1

value: Tau PFF+PI103


title: K562 sgC1.1 replicate 2, day 3 post-transduction

description:
d3_K562_sgC1.1_R2
RNA-seq_II_genes.count.annot.xls


title: B21-S1, Control group, Utah, Skin_rep3


title: 311E,1uM taz + 9nM ABBV075 96hr bio rep 1

value: 311E cell line

value: 9nM ABBV075 + 1uM tazemetostat


title: K562 sgC1.1 replicate 1, day 3 post-transduction

description:
d3_K562_sgC1.1_R1
RNA-seq_II_genes.count.annot.xls

value: sgRNA against MYNRL15 C1


title: 311E, 9nM ABBV075 96hr bio rep 2

value: 9nM ABBV076


title: K562 sgLUC replicate 2, day 3 post-transduction

description:
d3_K562_sgLUC_R2
RNA-seq_II_genes.count.annot.xls


title: 311E, 9nM ABBV075 96hr bio rep 1

value: 9nM ABBV075


title: 311E, 1uM taz 96hr bio rep 3

value: 1uM tazemetostat


title: Tau PFF treatment with MK2206, C2


title: B18-S1, Control group, Utah, Skin_rep1

value: Skin

value: Utah

value: Control


title: B2-S1, Control group, Utah, Skin_rep2


title: Tau PFF treatment with MK2206, C1

value: Brain


title: B24-S1, Control group, Utah, Skin_rep4

value: F


title: B37-L1, Control group, Utah, Liver_rep6

source_name: Liver

value: Liver


title: K562 sgLUC replicate 1, day 3 post-transduction

description:
d3_K562_sgLUC_R1
RNA-seq_II_genes.count.annot.xls


title: Tau PFF treatment, B3

value: astrocyte

value: wt

value: Tau PFF+DMSO


title: ML-2 sgC1.1, CTCF CnR

data_processing:
Library strategy: CUT&RUN
Raw reads were processed using Trimmomatic v0.39 to remove adapter sequences. Parameters: -phred33 ILLUMINACLIP:Truseq3.PE.fa:2:15:4:4:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:25.
Kseq (Zhu et al., Genome Biol 2019) was to trim reads containing ≤6 bp of adapter sequence, which are not effectively handled by Trimmomatic.
Trimmed reads were aligned to human reference genome hg38 using bowtie v2.3.5.1 with the parameter --phred33.
Aligned reads were sorted and indexed using Samtools v1.3.1.
Normalized bigWig files were generated using bamCoverage from deepTools v3.5.1.
Genome_build: hg38
Supplementary_files_format_and_content: Raw pileups as bigWig tracks for each sample
Supplementary_files_format_and_content: Normalized (RPM) bigWig tracks for CTCF samples

extract_protocol:
We performed CUT&RUN as previously described (Meers et al., eLife 2019; Skene et al., Nat Protoc 2018). On day 3 post-transduction, 0.4 million cells were sorted and incubated overnight with the following antibodies: CTCF (1:50; Diagenode C15410210), rabbit IgG (Diagenode C15410206). pAG/MNase nuclease (Addgene 123461) was produced and purified as previously described, after removal of the HA tag.
Illumina libraries were constructed from the cleaved DNA as previously described (Meers et al., eLife 2019; Skene et al., Nat Protoc 2018), and sequenced by Novogene Company, Ltd. on an Illumina NovaSeq platform (150 bp paired-end reads).

treatment_protocol: Stable Cas9-expressing K562 and ML-2 cells were transduced with sgRNAs targeting either MYNRL15 cis-regulatory region C1 (sgC1.1) or the firefly luciferase gene (sgLUC; non-targeting control).

value: Myelomonocytic leukemia


title: 311E, 1uM taz 96hr bio rep 2

value: GEMM, esophagus mNC tumor


title: Tau PFF treatment, B2


title: ML-2 sgLUC, CTCF CnR

value: sgRNA against LUC (control)


title: B28-L1, Control group, Utah, Liver_rep5

value: M


title: 311E, 1uM taz 96hr bio rep 1

value: 311E cell line


title: Tau PFF treatment, B1


title: 311E, DMSO 96hr bio rep 3

value: DMSO


title: PBS treated control, A3

value: PBS


title: K562 sgC1.1, CTCF CnR

value: Erythroleukemia

value: sgRNA against MYNRL15 C1


title: ML-2, IgG control


title: B21-L1, Control group, Utah, Liver_rep3

value: Utah


title: 311E, DMSO 96hr bio rep 1


title: PBS treated control, A2


title: K562 sgLUC, CTCF CnR


title: B18-L2, Control group, Utah, Liver_rep1

value: Control


title: B2-L1, Control group, Utah, Liver_rep2


title: PBS treated control, A1

value: Brain


title: K562, IgG control