title: Sperm_ATAC_untreated_NoSomaticLysis_rep2


title: H119754-15 Tumor biopsy

status: Public on Aug 12 2023

type: SRA

city: Frankfurt am Main

first: Florian

last: Greten

address: Paul-Ehrlich-Str. 42-44

department: Institute for Tumor Biology and Experimental Therapy

country: Germany

institute: Georg-Speyer-Haus

description: pretherapeutic

library_source: transcriptomic

data_processing:
Sequence reads trimmed by Trimmomatic Software v.0.36
Reads mapped by STAR aligner v.2.5.2b
Hit counts calculated by Subread packages v.1.5.2
Differential gene expression by DESeq2
GSEA software for enrichment analysis
Genome_build: Human NCBI genome build GRCh38
Supplementary_files_format_and_content: Raw counts in txt file format

molecule: total RNA

organism: Homo sapiens

source_name: Biopsy

extract_protocol:
Qiagen Rneasy FFPE kit (Qiagen; #73504)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: FFPE material of Patients with advanced rectal cancer treated with neoadjuvant chemoradiotherapy

tag: tissue

value: Tumor

tag: disease state

value: Rectal cancer

tag: Stage


title: Trp53_p53CGmut_p53mNGreen_pWZ455_DNA

city: New York

first: Weimin

last: Zhang

state: NY

address: 435 E 30th street

department: Institute for Systems Genetics

country: USA

institute: NYU Langone Health

description:
Assemblon BAC DNA  seq
FCHFC7TBGXB

library_source: other

data_processing:
Sequencing reads were demultiplexed using bcl2fastq v2.20, and subsequently trimmed using Trimmomatic v0.39. Trimmed reads were aligned to references using BWA v0.7.17. Duplicates were marked using samblaster v0.1.24.
Coverage depth tracks and quantification was generated using BEDOPS v2.4.35. Sequencing data were visualized using UCSC genome browser.
The sequencing processing pipeline is available at https://github.com/mauranolab/mapping.
Assembly: mm10, hg38
Supplementary files format and content: bigwig files mapping to genome references (hg38 and/or mm10)
Supplementary files format and content: txt files for UMI numbers

molecule: other

organism: Mus musculus

source_name: E. coli

growth_protocol: All sequenced mESC clones were from the feeder-independent condiftion. Culture medium consisted of 80% of 2i basal medium supplement with 3 µM CHIR99021 and 1 µM PD0325901, 20% of feeder-dependent ES medium (85% (v/v) KnockOut DMEM (Fisher Scientific, 10829018), 15% (v/v) Fetal Bovine Serum (Hyclone, SH30070.03), 0.5 mg/ml Penicillin-Streptomycin-Glutamine (Gibco, 10378016), 7 μL 2-Mercaptoethanol (Sigma-Aldrich, M6250), 0.1 mM MEM Non-Essential Amino Acids (Gibco, 11140050) and 1 U/ml LIF (EMD Millipore, ESG1107)). Tissue culture treated plates were coated with 0.1% gelatin solution before use. All cells were grown in a humidified tissue culture incubator at 37°C supplied with 5% CO2. E. coli cells were grown in standard LB medium supplemented with 12.5 ug/ml chloramphenical, or 50 ug/ml kanamycin.

extract_protocol:
1-3 million of feeder-independent mESCs were harvested for genomic DNA extraction by using a QIAamp DNA Mini Kit (QIAGEN, 51306). Plasmid DNA were extracted by using a NucleoBond Xtra BAC kit (Takara, 740436.25)
Approximately 100 ng DNA was used for the library construction using the NEBNext Ultra II FS DNA library prep kit (E7805). AMPure XP beads (Beckman Coulter, A63881) were used for DNA purification on a magnetic stand. DNA libraries were loaded on a ZAG DNA analyzer (Agilent) for quality control.

tag: strain

tag: cell type

value: E. coli


title: H112683-12 Tumor biopsy

description: pretherapeutic


title: 22082R-05-14

city: Atlanta

first: Srikant

last: Rangaraju

state: GA

address: 615 Michael St

department: Neurology

institute: Emory University

data_processing:
RNA-seq analysis was conducted to identify genes exhibiting differential expression. The counts data provided information on the abundance of reads mapped to the reference genome or the number of fragments assigned to each gene. The primary objective was to identify systematic changes between the conditions of interest, specifically Control vs Treatment. The analysis utilized the Deseq2 package, developed by Michael I. Love, Simon Anders, and Wolfgang Huber (Package Authors). A Deseq2DataSetFromMatrix object was created, and the design parameter was set to ~Treatment, which captured the information on how the traits file was structured. For instance, in the case of n=4 Control vs n=4 LPS, the design matrix reflected these conditions.
To ensure data quality, the raw counts data were aligned to the traits file, following the documentation guidelines. Lowly expressed genes were filtered out based on the criterion of rowSums(counts(dds)) ≥ 30, meaning that only genes with 30 reads in total across all samples (5 X 6 samples = 30) were retained. This step was performed to remove genes with insufficient expression levels. Additionally, if required by the dataset, Ensembl IDs were converted to gene names for ease of downstream analysis. The control condition was designated as the reference for comparison, and genes exhibiting differential expression were identified using the criteria of adjusted p-value < 0.05 and log2 fold change (LFC > 0 for upregulated genes and LFC < 0 for downregulated genes).
It should be noted that in the comparison of Bulk RNA-seq on responder BV2 cells, the LPS samples were contrasted against the control (n = 4), deviating from the general protocol. Principal component analysis (PCA) was employed as an initial analysis step to identify patterns, relationships, and important variables in the high-dimensional dataset.
Assembly: Next generation sequencing
Supplementary files format and content: comma separated file includes raw counts for each sample

source_name: Extracellular Vesicles

extract_protocol:
Total RNA was extracted from BV2 cells and BV2 cell-derived extracellular vesicles using the Qiagen miRNeasy Mini Kit (Cat. No. 217004). 20 µL of EV fraction was resuspended in 700 µL of trizol lysis buffer. BV2 cell pellets were harvested in 700 μL of trizol lysis buffer. Added 140ul of chloroform was added to each sample and shook vigorously. Samples were then centrifuged for 15 min at 12,000 x g at 4°C. After centrifugation, the sample separated into 3 phases: an upper, colorless, aqueous phase containing RNA; a white interphase; and a lower, red, organic phase.
The top aqueous phase was carefully isolated without disturbing the other phases. The top aqueous phase was transferred to a new collection tube and 1.5 volumes of 100% ethanol was added and mixed by pipetting up and down. 700 μL of the sample was added to the provided spin column in collection tubes. Samples were spin at ≥8000 x g for 15 s at room temperature and the flow-through was discarded. This was repeated for the rest of the sample.
Bound RNA was washed 2 times using the included wash solution (Buffer RPE). Finally, a preheated elution solution (RNase-free water) was used to elute the RNA in 40 uL volume for cells and 20 uL for extracellular vesicles.
cDNA Libraries were prepared  using the SMART-Seq v4 and Nextera XT kit. A total of 18 cycles of PCR were carried out to obtain a good yield of cDNA from cells and EVs. Final library quality was verified with Qbit and bioanalyzer. Negative (no RNA) and positive controls provided expected results. Next-generation RNA sequencing was performed using a HiSeq X Illumina 2x150, 40M total reads per sample (20M each direction) at Admera Health.

treatment_protocol: BV2 cells were treated with either TGF-β (50 ng/mL), IL-10 (50 ng/mL), and LPS (100 ng/mL) for 72 hours

value: Extracellular Vesicles

tag: cell line

value: BV2 Cells

value: Microglia

tag: treatment

value: Control


title: H109499-14 Tumor biopsy

description: pretherapeutic

value: Not applicable


title: 22082R-05-19


title: H10843-17 Tumor biopsy

description: pretherapeutic


title: H06621-17 Tumor biopsy

description: pretherapeutic


title: Trp53_RP23-51O13_RepoBAC

description:
BAC DNA seq
FCH7J2JBGXB


title: Sperm_ATAC_MNase

city: Boston

first: Qiangzong

last: Yin

state: MA

address: 3 Blackfan St, CLS building 440A

department: Medicine

institute: BIDMC/Harvard Medical School

library_source: genomic

data_processing:
Paired-end ATAC-seq reads were adapter-trimmed and aligned to the mm10 genome using Bowtie2 (Version 2.3.2) with the parameters: -t -q -N 1 -L 25 -X 2000 no-mixed no-discordant.
All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed. MACS2 (Zhang et al. 2008) was used for peak calling with parameters: --nolambda --nomodel.
Reads with insert size larger than 150 bp were separated and used for nucleosome positioning analysis.
TSS enrichment analysis was done using Homer annotatePeaks (Heinz et al. 2010)
Assembly: mm10
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: Sperm

extract_protocol:
About 100,000 sperm were on-ice lysed with hypotonic lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin) for 10 min.
Sperm were then resuspended in Tagmentation buffer (10 mM TAPS-NaOH pH 8.5, 5 mM MgCl2, 10% DMF, 0.05% Digitonin) and tagmentation was conducted by adding Tn5 transposase (Diagenode, C01070012) at 1:20 and incubated at 37C for 30min. Reaction was stopped by SDS and proteinase K and incubated at 55°C  overnight. SDS was quenched by tween-20 and library amplification was done with 1x NEBNext High-Fidelity PCR Master Mix containing 0.5 mM indexed primers using the following PCR conditions: 72°C for 5 min; 98°C for 3 min; and 14 cycles at 98°C for 15 s, 63°C for 30 s, and 72°C for 1 min.

value: Sperm

tag: genotype

value: WT

value: Tn5 transposase (Diagenode, C01070012)


title: 22082R-05-13


title: 22082R-05-12

source_name: Cells

value: Cells

value: TGFB


title: H02336-17 Tumor biopsy

description: pretherapeutic


title: 22082R-05-11


title: Trp53_p53CGmut_p53mNGreen_pWZ457_DNA

description:
Assemblon BAC DNA  seq
FCHFC7TBGXB


title: 180kACE2testis_1-H3K27ac

data_processing:
Sequencing reads were demultiplexed using bcl2fastq v2.20, and subsequently trimmed using Trimmomatic v0.39. Trimmed reads were aligned to references using BWA v0.7.17. Duplicates were marked using samblaster v0.1.24.
Coverage depth tracks and quantification was generated using BEDOPS v2.4.35. Sequencing data were visualized using UCSC genome browser.
The sequencing processing pipeline is available at https://github.com/mauranolab/mapping.
Assembly: mm10, hg38
Supplementary files format and content: bigwig files mapping to genome references (hg38/mm10)
Library strategy: CUT&RUN

source_name: testis

growth_protocol: Mice were maintained in the NYU Langone Health BSL1 barrier facility. Testes were dissected from ~36 weeks old male mice.

extract_protocol:
After washing in a 6 cm dish with PBS, testes were cut into small pieces to expose the seminiferous tubules. Seminiferous tubules were transferred to a 15 mL tube containing 5 mL dissociation buffer [DMEM with 10% FBS, 1% Pen/Strep, 0.25 mg/mL collagenase/dispase (Roche, 10269638001)] for 30 min incubation at 37°C. Tubes were inverted every 5 min. Seminiferous tubule fragments were collected and washed with PBS by centrifugation at 300 x g for 5 min at room temperature. Seminiferous tubule fragments were passed through a 70 μm cell strainer, and then washed with PBS twice. Testicular cell density and viability were evaluated by using an automated cell counter. 500,000 testicular cells were used for each CUT&RUN reaction by following vendor’s instructions (EpiCypher, 14-1048).
Sequencing libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit (E7645L).

value: testis

tag: chip antibody

tag: Sex

value: Male

tag: genetic modifications


title: Sperm_ATAC_DNase_NoSomaticLysis


title: Sperm_ATAC_ExoV


title: 180kACE2testis_2-H3K27ac


title: Cauda_epididymis_ATAC


title: 22082R-05-15


title: 22082R-05-10


title: H00373-14 Tumor biopsy

description: pretherapeutic


title: Sperm_ATAC_untreated_NoSomaticLysis_rep1


title: 22082R-05-09


title: 116kACE2testis_2-H3K27ac


title: Lytic_AKATA_IP2

city: PHILADELPHIA

first: Fengchao

last: Lang

state: PA

address: 3610 Hamilton Walk

institute: University of Pennsylvania

description: peak Lytic AKATA

data_processing:
After sequencing, the first step is quality and adapter trimming. Trimming was conducted by Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove adapter sequences and low-quality bases (bases with < 20 quality score will be removed). After trimming, the MeRIP-seq reads were aligned to EBV reference genome by the aligner HISAT2 [39] with the annotation of the splice sites (the EBV reference genome and annotation were downloaded from https://www.ncbi.nlm.nih.gov/nuccore/NC_007605.1). The m6A peaks were called by a graphical model-based peak calling method – MeTPeak [40], with the parameters of window width = 50, sliding step = 50 and read length = 50. The peaks were visualized in IGV (http://www.broadinstitute.org/igv).
Genome_build: EBV genome NC_007605.1
Supplementary_files_format_and_content: peka, rpkm

organism: human gammaherpesvirus 4

source_name: EBV-positive Burkitt's lymphoma cell line

growth_protocol: LCL cells were generated in our laboratory. These B-cell lines and PBMC were cultured in RPMI 1640 media (Hyclone, Logan, UT) with 10% BGS (HyClone Bovine Growth Serum).

extract_protocol:
The total RNA extraction was performed using Trizol reagent (Invitrogen, Inc., Carlsbad, CA) and treated with DNase I (Invitrogen, Inc., Carlsbad, CA). cDNA was prepared with Superscript II reverse transcriptase kit (Invitrogen, Inc., Carlsbad, CA) according to the manufacturer’s protocol.
The library was prepared using the TruSeq stranded mRNA kit (Illumina, San Diego, CA) according to the manufacturer’s protocol. First, the elute-frag-prime stage was done at 80°C for 2 min to allow annealing without causing fragmentation [12]. RNA was reverse transcribed into first strand cDNA using reverse transcriptase and random primers. This was followed by the second strand cDNA synthesis using DNA Polymerase I and RNase H. The cDNA fragments were used for end repair process with the addition of a single ‘A’ base followed by ligation of adapters. The products were then purified and enriched by PCR amplification for 12 cycles to generate the final RNA-seq library. cDNA libraries were quantified and pooled and subsequent sequencing on an Illumina HiSeq3000 platform 50 bp single read sequencing module.

treatment_protocol: To reactivate EBV, TPA (20 ng/ml) and Butyric acid (BA, 2.5 mM) were used to treat the cells for 48 hours.

tag: passage

tag: rip antibody


title: H00146-14 Tumor biopsy

description: pretherapeutic


title: Trp53_p53CGmut_p53mNGreen_pWZ454_DNA

description:
Assemblon BAC DNA  seq
FCHFC7TBGXB


title: 116kACE2testis_1-H3K27ac


title: Lytic_AKATA_IP1

description: peak Lytic AKATA

value: EBV-positive Burkitt's lymphoma cell line


title: WTtestis_2-H3K27ac


title: 22082R-05-08


title: Lytic_AKATA_input2

value: non


title: 22082R-05-07


title: H04068-13 Tumor biopsy

description: pretherapeutic

value: Tumor


title: WTtestis_1-H3K27ac


title: 9794-08 Tumor biopsy

description: pretherapeutic

value: Rectal cancer


title: Lytic_AKATA_input1


title: 9554-13 Tumor biopsy

description: pretherapeutic


title: 22082R-05-05

value: LPS


title: 180kACE2testis_1-H3K4me3


title: 91232-11 Tumor biopsy

description: pretherapeutic


title: 8597-12 Tumor biopsy

description: pretherapeutic


title: AKATA_IP1

description: peak AKATA


title: 22082R-05-04


title: AKATA_input2


title: 22082R-05-03


title: 116kACE2testis_2-H3K4me3


title: 8535-12 Tumor biopsy

description: pretherapeutic


title: AKATA_input1


title: 116kACE2testis_1-H3K4me3


title: 22082R-05-02


title: 99514-10 Tumor biopsy

description: pretherapeutic


title: WTtestis_2-H3K4me3


title: 22082R-05-06


title: WTtestis_1-H3K4me3


title: Lytic_LCL_IP2

description: peak Lytic LCL

value: EBV transformed lymphoblastoid cell lines


title: 75693-12 Tumor biopsy

description: pretherapeutic


title: 180kACE2testis_2-H3K4me3


title: 76228-13 Tumor biopsy

description: pretherapeutic


title: Lytic_LCL_IP1

description: peak Lytic LCL

source_name: EBV transformed lymphoblastoid cell line


title: AKATA_IP2

description: peak AKATA


title: Lytic_LCL_input2


title: 22082R-05-01

value: BV2 Cells


title: 7081-III Tumor biopsy

description: pretherapeutic


title: IL-10 Evs Tx_3

extract_protocol:
Total RNA was extracted from BV2 cells using the Qiagen miRNeasy Mini Kit (Cat. No. 217004). BV2 cell pellets were harvested in 700 μL of trizol lysis buffer. Added 140ul of chloroform was added to each sample and shook vigorously. Samples were then centrifuged for 15 min at 12,000 x g at 4°C. After centrifugation, the sample separated into 3 phases: an upper, colorless, aqueous phase containing RNA; a white interphase; and a lower, red, organic phase.
The top aqueous phase was carefully isolated without disturbing the other phases. The top aqueous phase was transferred to a new collection tube and 1.5 volumes of 100% ethanol was added and mixed by pipetting up and down. 700 μL of the sample was added to the provided spin column in collection tubes. Samples were spin at ≥8000 x g for 15 s at room temperature and the flow-through was discarded. This was repeated for the rest of the sample. Bound RNA was washed 2 times using the included wash solution (Buffer RPE). Finally, a preheated elution solution (RNase-free water) was used to elute the RNA in 40 uL volume for cells.
cDNA Libraries were prepared using the SMART-Seq v4 and Nextera XT kit. A total of 18 cycles of PCR were carried out to obtain a good yield of cDNA from cells. Final library quality was verified with Qbit and bioanalyzer. Negative (no RNA) and positive controls provided expected results. Next-generation RNA sequencing was performed using a HiSeq X Illumina 2x150, 40M total reads per sample (20M each direction) at Admera Health.

value: Microglia

value: IL10 EVs


title: 180kACE2testis_1-IgG

value: IgG


title: 180kACE2testis_2-IgG


title: 68433-06 Tumor biopsy

description: pretherapeutic


title: IL-10 Evs Tx_1


title: 116kACE2testis_2-IgG


title: LCL_IP2

description: peak LCL


title: 64809-10 Tumor biopsy

description: pretherapeutic


title: LCL_IP1

description: peak LCL


title: TGF-B Evs Tx_3

value: TGFB EVs


title: 116kACE2testis_1-IgG


title: TGF-B Evs Tx_2


title: WTtestis_2-IgG


title: 63926-13 Tumor biopsy

description: pretherapeutic


title: LCL_input2


title: TGF-B Evs Tx_1


title: WTtestis_1-IgG


title: LCL_input1


title: IL-10 Evs Tx_2


title: 6207 Tumor biopsy

description: pretherapeutic


title: 6110-1 Tumor biopsy

description: pretherapeutic


title: Bl6 smallintestine 116khACE2 2

data_processing:
Sequencing reads were demultiplexed using bcl2fastq v2.20, and subsequently trimmed using Trimmomatic v0.39. Trimmed reads were aligned to references using BWA v0.7.17. Duplicates were marked using samblaster v0.1.24.
Coverage depth tracks and quantification was generated using BEDOPS v2.4.35. Sequencing data were visualized using UCSC genome browser.
The sequencing processing pipeline is available at https://github.com/mauranolab/mapping.
Assembly: mm10, hg38
Supplementary files format and content: bigwig files mapping to genome references (hg38/mm10)

source_name: Small intestine

growth_protocol: Mice were maintained in the NYU Langone Health BSL1 barrier facility. Small intestines were harvested from ~25 week old mice

extract_protocol:
After washing with PBS, intestines were opened and spread on a bilulous paper. Following two washes using PBS, the intestines were cut into small pieces using a blade, and transferred to 10 mL dissociation buffer [DMEM with 5% FBS, 1% Pen/Strep, 0.25 mg/mL collagenase/dispase (Roche, 10269638001), 0.25 U/mL DNaseI (Thermo Scientific, EN0521), 8 mM EDTA, 0.5 mM DTT] for 30 min incubation at 4°C with gentle shaking. Tissue fragments were collected by removing the supernatant after settling down at room temperature. 10 mL wash buffer (DMEM with 5% FBS, 1% Pen/Strep) was added to the tissue fragment pellet, and followed by firmly shaking up and down for 8 times. After tissue fragment settled, supernatant containing crypts was transferred to a new 15 mL tube for centrifugation at 300 x g for 5 min at 4°C. Crypts were resuspended in 1 mL ACK lysis buffer (Gibco, A1049201) for 3 min incubation at room temperature. 4 mL wash buffer was added to stop the lysing, crypts were collected by centrifugation at 300 x g for 5 min at 4°C. Crypts were digested with 1 mL 0.25% trypsin-EDTA (Gibco, 25200056) at 37°C for 5 min, and the digested was stopped by adding 4 mL wash buffer. Crypts were passed through a 70 μm cell strainer, and intestinal cells were washed in cold PBS twice. Intestinal cell number and viability were evaluated by using an automated cell counter.
Approximately 50,000 intestinal cells were collected and washed once with cold PBS at 500 x g for 5 min, 4°C. Cell pellet was resuspended in 50 μL cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630), and immediately span down at 500 x g for 10 min, 4°C. Tn5 transposase was used for the tagmentation reaction (Illumina, 20034197) at 37°C for 30 min. Fragmented DNAs were purified using a cleanup column (Zymo Research, D4013) and eluted in 10 μL water. All eluted DNA was used as template for a 10 cycles PCR using KAPA-HiFi polymerase (Kapa Biosystems, KK2602) in a 50 μL reaction.

value: Small intestine


title: TMPRSS2_humanization_80kb_pWZ693_DNA

description:
Assemblon BAC DNA  seq
FCH52MCBGXJ

value: E. coli


title: 61088-14 Tumor biopsy

description: pretherapeutic


title: LPS Evs Tx_1

value: Cells

value: LPS EVs


title: LPS Evs Tx_2


title: Bl6 smallintestine 180khACE2 1


title: Lytic_LCL_input1


title: 6551-II Tumor biopsy

description: pretherapeutic


title: 6057-12 Tumor biopsy

description: pretherapeutic


title: Bl6 smallintestine 116khACE2 1


title: control Evs Tx_3

value: Control EVs


title: LPS Evs Tx_3


title: Bl6 smallintestine 180khACE2 2


title: TMPRSS2_CH17-339H2_RepoBAC

description:
BAC DNA seq
FCHNC3CBGXH


title: 6007-11 Tumor biopsy

description: pretherapeutic


title: TMPRSS2_humanization_80kb_pWZ691_DNA

description:
Assemblon BAC DNA  seq
FCH52MCBGXJ


title: ACE2_CH17-449P15_RepoBAC

description:
BAC DNA seq
FCHNJC7BGXG


title: Bl6 smallintestine WT

description: FCHTMHJBGXN


title: 5763-13 Tumor biopsy

description: pretherapeutic


title: 56233-11 Tumor biopsy

description: pretherapeutic


title: control Evs Tx_1

value: Control Evs


title: ACE2_CH17-203N23_RepoBAC

description:
BAC DNA seq
FCHNJC7BGXG


title: 55726-08 Tumor biopsy

description: pretherapeutic


title: iPSC-derived neural stem cells, C9KO_rep2

city: Los Angeles

first: Justin

last: Ichida

state: California

address: 1425 San pablo Street, BCC Room 209

institute: USC

description:
28_3_11_2_S28
Frameshit mutation induced by CRISPR/Cas9 to deplete endogenous C9ORF72 levels to generate the 3-11 cell line; iPSC-derived neural stem cells

data_processing:
Reads were aligned against human hg38 transcriptome using HISAT2 (v.2.1.0).
A gene count table was obtained using Partek E/M with Partek® Flow® software, v10.0
Differential expression analysis was performed using DESeq2 (v.1.18.1).
Pathway enirchment analysis was performed using Enrichr
Computations were performed on the High Performing-Computing Cluster supported by the University of Southern California.
Assembly: hg38
Supplementary files format and content: Normalized_counts.xlsx

source_name: neural

growth_protocol: iPSC-derived neural stem cells were cultured in DMEM/F12, 1x B27 supplement (Thermo Fisher, cat no. 17504044), 1x N2 supplement, 1x NEAA, 1x Glutamax, 10 ng/ml EGF (R&D Systems, cat. no. 236-EG-200), and 10 ng/ml FGF (R&D Systems, cat. no. 3718-FB-025)

extract_protocol:
Day 10 neural stem cells were enriched using a PSA-NCAM MACs and sorted into Qiagen's RLT buffer and sent to Amaryllis Nucleics for processing
3'-Digital Gene Expression RNAseq Library Kit (3’-DGE)
3' RNA-seq libraries were generated using the3'-Digital Gene Expression RNAseq Library Kit at Amaryllis Nucleics. Libraries were sequenced at Amaryllis Nucleics on a NextSeq 500 SR75 sequencer. A total of 6 million to 19 million 150-bp, single-end reads were obtained for samples.

value: neural

value: Neural stem cells

value: C9ORF72 knockout


title: iPSC-derived neural stem cells, C9KO_rep3

description:
41_3_11_S41
Frameshit mutation induced by CRISPR/Cas9 to deplete endogenous C9ORF72 levels to generate the 3-11 cell line; iPSC-derived neural stem cells


title: Melatonin_rep4

city: Wuhan

first: changjiu

last: he

state: Hubei

address: 1 Shizishan street, Hongshan District

department: College of Animal Science and Technology

country: China

institute: Huazhong Agricultural University

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. 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.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample .

source_name: Type 7-8 follicles

extract_protocol:
Type 7-8 follicles were isolated from the ovaries, flash frozen on dry ice, and RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina® was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Kunming

value: ovary

tag: age

value: postnatal day 21

tag: treament

value: 24h after PMSG and melatonin injection


title: small intestine, male, control diet, metformin, biological replicate 3

city: Riga

first: Monta

last: Brīvība

address: Ratsupites 1

country: Latvia

institute: Latvian Biomedical Research and Study Centre

data_processing:
The reads were trimmed with Trimmomatic 0.39 using window size 5, minimal read length 30 bp and quality threshold 25.
Sequencing reads were mapped against mouse reference genome GRCm38 release 90 and read counts were calculated with STAR 2.5.3a.
Assembly: GRCm38
Supplementary files format and content: Text file containing RNA-Seq read counts per gene for all samples claculated with STAR 2.5.3a.

source_name: distal part of small intestine/ileum

extract_protocol:
RNA extraction from intestinal tissue was performed using AllPrep DNA/RNA Mini Kit (QIAGEN, Germany) according to the manufacturer’s instructions.
For rRNA depletion 200 ng of total RNA was processed using MGIEasy rRNA depletion kit (MGI Tech Co. Ltd, China). Complementary DNA library preparation was performed with MGIEsy RNA Directional Library Prep Set (MGI Tech Co. Ltd, China). Sequencing was done using DNBSEQ-G400RS High-throughput Sequencing Set (FCL PE100) (MGI Tech Co. Ltd., China).

treatment_protocol: Each tissue sample was collected in 1.5 mL of RNAlater solution (ThermoFisher Scientific, USA) and stored at -80°C until further processing.

value: distal part of small intestine/ileum

value: male

value: healthy

value: control diet (CD:10 kcal percent fat, D12450J, Research Diets), metformin 50 mg/kg body mass/day


title: small intestine, female, control diet, biological replicate 3

value: female

value: control diet (CD:10 kcal percent fat, D12450J, Research Diets)


title: 5166-09 Tumor biopsy

description: pretherapeutic

value: Tumor

value: Rectal cancer


title: Melatonin_rep3


title: iPSC-derived neural stem cells, C9KO_rep1

description:
27_3_11_1_S27
Frameshit mutation induced by CRISPR/Cas9 to deplete endogenous C9ORF72 levels to generate the 3-11 cell line; iPSC-derived neural stem cells


title: iPSC-derived neural stem cells, Iso_C1_rep3

description:
38_c1_S38
CRISPR/Cas9 removal of the C9ORF72 repeat expansion from parental line 6769 to generate the C1 isogenic line; iPSC-derived neural stem cells

value: Isogenic control; corrected


title: Melatonin_rep2


title: small intestine, female, high-fat diet, metformin, biological replicate 3

value: obese

value: high-fat diet (HFD:60 kcal percent fat, D12492, Research Diets), metformin 50 mg/kg body mass/day


title: 5023 Tumor biopsy

description: pretherapeutic


title: Melatonin_rep1


title: 4973 Tumor biopsy

description: pretherapeutic


title: small intestine, female, high-fat diet, biological replicate 3

value: high-fat diet (HFD:60 kcal percent fat, D12492, Research Diets)


title: 50132-09 Tumor biopsy

description: pretherapeutic


title: Control _rep3

value: 24h after PMSG and normal saline injection


title: small intestine, male, high-fat diet, metformin, biological replicate 3


title: small intestine, male, control diet, biological replicate 3


title: Control _rep4

value: Kunming


title: control Evs Tx_2

value: Cells

value: BV2 Cells

value: Microglia

value: Control EVs


title: iPSC-derived neural stem cells, C9_12100_rep3

description:
33_12100_S33
C9-FTD/ALS iPSC-derived neural stem cells

value: neural

value: Neural stem cells


title: iPSC-derived neural stem cells, Iso_C1_rep2

description:
10_c1_2_S10
CRISPR/Cas9 removal of the C9ORF72 repeat expansion from parental line 6769 to generate the C1 isogenic line; iPSC-derived neural stem cells


title: iPSC-derived neural stem cells, Iso_C1_rep1

description:
09_c1_1_S9
CRISPR/Cas9 removal of the C9ORF72 repeat expansion from parental line 6769 to generate the C1 isogenic line; iPSC-derived neural stem cells


title: Control _rep2

value: ovary

value: postnatal day 21


title: 4790-13 Tumor biopsy

description: pretherapeutic


title: small intestine, male, high-fat diet, biological replicate 3

value: distal part of small intestine/ileum

value: male


title: iPSC-derived neural stem cells, C9_12100_rep2

description:
18_12100_2_S18
C9-FTD/ALS iPSC-derived neural stem cells


title: Control _rep1


title: small intestine, female, control diet, metformin, biological replicate 3

value: female

value: healthy

value: control diet (CD:10 kcal percent fat, D12450J, Research Diets), metformin 50 mg/kg body mass/day


title: 465 Tumor biopsy

description: pretherapeutic

value: Tumor

value: Rectal cancer


title: small intestine, female, control diet, metformin, biological replicate 2


title: 44561-14 Tumor biopsy

description: pretherapeutic


title: small intestine, male, control diet, metformin, biological replicate 2


title: iPSC-derived neural stem cells, C9_10689_rep3

description:
36_10689_S36
C9-FTD/ALS iPSC-derived neural stem cells


title: iPSC-derived neural stem cells, C9_12100_rep1

description:
17_12100_1_S17
C9-FTD/ALS iPSC-derived neural stem cells


title: small intestine, female, control diet, biological replicate 2

value: control diet (CD:10 kcal percent fat, D12450J, Research Diets)


title: 4362-II Tumor biopsy

description: pretherapeutic


title: spleen,replicate3

city: NYC

first: Denis

last: Loredan

address: 550 1st Ave

department: Microbiology

institute: New York University Grossman Medical school

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The sequenced data were processed using Cell Ranger (version 6.0) to demultiplex the libraries. The reads were aligned to Mus musculus mm10 and SCV2 (MN985325.1) genomes to generate count tables that were further analyzed using Seurat (version 4.1.2). Data are displayed as uniform manifold approximation and projection (UMAP). Some plots were generated using the Loupe Cell Browser application from 10X Genomics
Supplementary files format and content: Tab-separated values files and matrix files

source_name: spleen

extract_protocol:
Livers were chopped and incubated in RPMI + 10% FBS with collagenase VIII (100U/mL; Sigma Aldrich)and DNase I (150 µg/mL; Sigma Aldrich) for 45 minutes at 37° C and then passed through a 70-µm cell strainer (Fisher Scientific). Leukocytes were enriched for by density-gradient centrifugation over a 40/80% Percoll (GE Healthcare) gradient, and remaining red blood cells were lysed with ACK lysis buffer (Lonza) and washed in PBS. Spleens were removed and placed in RPMI + 10%FBS. Spleens were then passed through a 70-µm cell strainer (Fisher Scientific). Red blood cells were lysed with ACK lysis buffer (Lonza) and washed in PBS.
For both tissues, cells were sorted on singlet cells, live cells, CD45+ cells, DumpNEG (CD11b+, CD11c+, CD49b+, CD19+, CD8+) cells, CD3+ cells, CD4+ cells. Cells were isolated from 2 mice and pooled together, with equal numbers of cells pooled from each animal used. 12,000 cells from each tissue were loaded on a 10X Genomics Next GEM chip and single-cell GEMs were generated on a 10X Chromium Controller. Subsequent steps to generate cDNA and sequencing libraries were performed following 10X Genomics’ protocol. Libraries were pooled and sequenced using Illumina NovaSeq SP 100 cycle as per 10X sequencing  recommendations.

value: spleen cells

value: spleen


title: 3857-14 Tumor biopsy

description: pretherapeutic


title: iPSC-derived neural stem cells, C9_10689_rep2

description:
22_10689_2_S22
C9-FTD/ALS iPSC-derived neural stem cells


title: small intestine, male, control diet, biological replicate 2


title: iPSC-derived neural stem cells, C9_10689_rep1

description:
21_10689_1_S21
C9-FTD/ALS iPSC-derived neural stem cells


title: spleen,replicate2

description: 10x Genomics


title: 31285-08 Tumor biopsy

description: pretherapeutic


title: 30948-12 Tumor biopsy

description: pretherapeutic


title: iPSC-derived neural stem cells, C9_12099_rep3

description:
34_12099_S34
C9-FTD/ALS iPSC-derived neural stem cells


title: 278 Tumor biopsy

description: pretherapeutic


title: spleen,replicate1

description: 10x Genomics


title: small intestine, female, high-fat diet, metformin, biological replicate 2

value: obese

value: high-fat diet (HFD:60 kcal percent fat, D12492, Research Diets), metformin 50 mg/kg body mass/day


title: small intestine, male, high-fat diet, metformin, biological replicate 2


title: 2676-12 Tumor biopsy

description: pretherapeutic


title: liver,replicate4

description: 10x Genomics

source_name: liver

value: liver cells

value: liver


title: small intestine, female, high-fat diet, biological replicate 2

value: high-fat diet (HFD:60 kcal percent fat, D12492, Research Diets)


title: liver,replicate3

description: 10x Genomics


title: spleen,replicate4

description: 10x Genomics


title: 2674-12 Tumor biopsy

description: pretherapeutic


title: iPSC-derived neural stem cells, C9_6769_rep3

description:
35_6769_S35
C9-FTD/ALS iPSC-derived neural stem cells

value: neural

value: Neural stem cells


title: small intestine, male, high-fat diet, biological replicate 2

value: distal part of small intestine/ileum


title: liver,replicate1

description: 10x Genomics


title: 23493-13 Tumor biopsy

description: pretherapeutic


title: small intestine, male, control diet, metformin, biological replicate 1

value: male


title: small intestine, female, control diet, metformin, biological replicate 1

value: female


title: cWZ395-untreated-2

description:
S2 100 cycle flow cell v1.5
Doxorubicin_cts_norm.csv

data_processing:
Adapters and low-quality bases were trimmed using Trimmomatic (v0.36).
Sequencing reads were mapped to the mouse reference genome (mm10) using the STAR aligner (v2.7.3). Alignments were guided by a Gene Transfer Format (GTF) file.
The mean read insert sizes and their standard deviations were calculated using Picard tools (v.2.18.20).
The genes-samples counts matrix was generated using featureCounts (v1.6.3), normalized based on their library size factors using DEseq2, and differential expression analysis was performed. The Read Per Million (RPM) normalized BigWig files were generated using deepTools (v.3.1.0). Data were visualized using GraphPad Prism or Rstudio.
Assembly: mm10, hg38, SARS-CoV-2
Supplementary files format and content: Raw count txt files
Supplementary files format and content: Normalized csv file

source_name: mESC

growth_protocol:
For mice, Ten to fifteen weeks old mice were transferred to the NYU Langone Health BSL3 facility for the SARS-CoV-2 infection. All mice were settled for at least two days prior to infection.
mESC culture medium consisted of 80% of 2i basal medium supplement with 3 µM CHIR99021 and 1 µM PD0325901, 20% of feeder-dependent ES medium (85% (v/v) KnockOut DMEM (Fisher Scientific, 10829018), 15% (v/v) Fetal Bovine Serum (Hyclone, SH30070.03), 0.5 mg/ml Penicillin-Streptomycin-Glutamine (Gibco, 10378016), 7 μL 2-Mercaptoethanol (Sigma-Aldrich, M6250), 0.1 mM MEM Non-Essential Amino Acids (Gibco, 11140050) and 1 U/ml LIF (EMD Millipore, ESG1107)). Tissue culture treated plates were coated with 0.1% gelatin solution before use. All cells were grown in a humidified tissue culture incubator at 37°C supplied with 5% CO2.

extract_protocol:
One lobe of lung was immersed in 1 ml Trizol solution (Invitrogen, 15596018) in Lysing Matrix A homogenization tubes (MP Biomedicals) immediately after dissecting from euthanized mice, and total RNAs were extracted from Trizol following the standard protocol.
Total RNA from mESCs were extracted using A RNeasy miniplus kit (QIAGEN, 74136)
Lung total RNA quality and quantity were examined using a Bioanalyzer (Agilent 2100, RNA 6000 nano kit). Sequencing libraries were constructed using a TruSeq Stranded Total RNA Library Prep Gold kit (Illumina, 20020599).

treatment_protocol:
Mice were anesthetized with intraperitoneal injection of 150 μL ketamine (10 mg/mL)/xylazine (1 mg/mL) solution. 1x10^3 or 1x10^5 PFU of SARS-CoV-2 were administered intranasally in a total volume of 50 μL PBS per mouse, delivered to both nostrils equally. All infection experiments were performed in the NYU BSL3 facility.
mESCs were treated with 250 nM doxorubicin for 20 hours before total RNA extraction.

value: mESC

value: Untreated control


title: iPSC-derived neural stem cells, C9_12099_rep1

description:
15_12099_1_S15
C9-FTD/ALS iPSC-derived neural stem cells


title: 20536-13 Tumor biopsy

description: pretherapeutic

value: Tumor


title: iPSC-derived neural stem cells, C9_6769_rep1

description:
19_6769_1_S19
C9-FTD/ALS iPSC-derived neural stem cells


title: small intestine, male, high-fat diet, metformin, biological replicate 1


title: iPSC-derived neural stem cells, Control_5280_rep3

description:
30_5280_S30
Control iPSC-derived neural stem cells

value: Control


title: iPSC-derived neural stem cells, C9_12099_rep2

description:
16_12099_2_S16
C9-FTD/ALS iPSC-derived neural stem cells


title: MK6-untreated-2


title: 19482-14 Tumor biopsy

description: pretherapeutic

value: Rectal cancer


title: cWZ395-untreated-1


title: 18419-09 Tumor biopsy

description: pretherapeutic


title: small intestine, female, high-fat diet, biological replicate 1


title: small intestine, male, high-fat diet, biological replicate 1


title: 18290-09 Tumor biopsy

description: pretherapeutic


title: iPSC-derived neural stem cells, Control_5280_rep1

description:
03_5280_1_S3
Control iPSC-derived neural stem cells


title: small intestine, female, control diet, biological replicate 1

value: healthy

value: control diet (CD:10 kcal percent fat, D12450J, Research Diets)


title: liver,replicate2

description: 10x Genomics


title: 17645-13 Tumor biopsy

description: pretherapeutic


title: iPSC-derived neural stem cells, Control_00184_rep3

description:
31_00184_S31
Control iPSC-derived neural stem cells


title: cWZ395-DOXOtreated-2

value: 250nM doxorubicin treated for 20h


title: cWZ395-DOXOtreated-1


title: 17424-I2 Tumor biopsy

description: pretherapeutic


title: iPSC-derived neural stem cells, C9_6769_rep2

description:
20_6769_2_S20
C9-FTD/ALS iPSC-derived neural stem cells


title: MK6-DOXOtreated-2


title: iPSC-derived neural stem cells, Control_00184_rep2

description:
06_00184_2_S6
Control iPSC-derived neural stem cells


title: small intestine, female, high-fat diet, metformin, biological replicate 1

value: obese

value: high-fat diet (HFD:60 kcal percent fat, D12492, Research Diets), metformin 50 mg/kg body mass/day


title: 1731-14 Tumor biopsy

description: pretherapeutic


title: MK6-DOXOtreated-1


title: iPSC-derived neural stem cells, Control_5280_rep2

description:
04_5280_2_S4
Control iPSC-derived neural stem cells


title: iPSC-derived neural stem cells, Control_3719_rep3

description:
29_3719_S29
Control iPSC-derived neural stem cells


title: 1649 Tumor biopsy

description: pretherapeutic


title: iPSC-derived neural stem cells, Control_3719_rep2

description:
02_3719_2_S2
Control iPSC-derived neural stem cells


title: hd2bhd2c,heat,rep2,RNAseq

first: Xiangsong

last: Chen

address: Bayi Road

institute: Wuhan university

data_processing:
reads from each sample were mapped to the TAIR10 genome using Hisat2 v2.1.0 (Kim et al., 2019)
The unique mapped reads were then extracted through in-house script for futher analysis.
Gene level expression was calculated using featureCount v2.0.3 (Liao et al., 2014) with parameters -p -t exon.
Assembly: TAIR10
Supplementary files format and content: txt files include raw counts for each Sample

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: A. thaliana plants were growth on 1/2X MS agar (0.6%) + 1% sucrose  at 22 degree under a 16-h-light/8-h-dark photoperiod.

extract_protocol:
RNA isolated with Trizol （ThermoFisher, 15596026),following the manufacturer’s instructions
RNA library was construbuted by using the Fast RNA-seq lib prep kit V2(Abclonal,RK20306),following manufacterers' instructions

treatment_protocol: 6 day seedling were treated at 44 degrees for 3 hours

value: seedling

tag: developmental stage

value: 6 day seedling

value: hd2b hd2c knockout

value: 44 degrees heat shock for 3 hours

tag: time

value: 3 hours


title: MK6-untreated-1

tag: tissue


title: hd2bhd2c,heat,rep3,RNAseq


title: 116kb-hACE2-Female2-uninfected

description:
SP 100 Cycle Flow Cell v1.5
SARS-CoV-2_cts_norm.csv

source_name: Lung

value: Lung

value: Uninfected control


title: 116kb-hACE2-Female1-uninfected


title: 16386 Tumor biopsy

description: pretherapeutic

source_name: Biopsy

tag: disease state


title: 16013-12 Tumor biopsy

description: pretherapeutic

tag: Stage


title: K18-hACE2-Female-uninfected

tag: strain


title: iPSC-derived neural stem cells, Control_3719_rep1

description:
01_3719_1_S1
Control iPSC-derived neural stem cells

value: neural

tag: cell type

value: Neural stem cells


title: hd2bhd2c,heat,rep1,RNAseq


title: iPSC-derived neural stem cells, Control_3231_rep3

description:
32_3231_S32
Control iPSC-derived neural stem cells

tag: cell line


title: small intestine, male, control diet, biological replicate 1

value: distal part of small intestine/ileum

value: male

tag: treatment


title: hd2bhd2c,normal,rep3,RNAseq

tag: genotype

value: normal

value: 0 hours


title: K18-hACE2-Male-uninfected


title: 15760-11 Tumor biopsy

description: pretherapeutic

value: Tumor

value: Rectal cancer


title: hd2bhd2c,normal,rep2,RNAseq


title: 14997-10 Tumor biopsy

description: pretherapeutic


title: hd2bhd2c,normal,rep1,RNAseq


title: iPSC-derived neural stem cells, Control_3231_rep2

description:
08_3231_2_S8
Control iPSC-derived neural stem cells

value: Control


title: WT-Female2-uninfected


title: 116647-13 Tumor biopsy

description: pretherapeutic


title: iPSC-derived neural stem cells, Control_00184_rep1

description:
05_00184_1_S5
Control iPSC-derived neural stem cells


title: iPSC-derived neural stem cells, Control_3231_rep1

description:
07_3231_1_S7
Control iPSC-derived neural stem cells


title: WT-Female1-uninfected


title: 11081-14 Tumor biopsy

description: pretherapeutic


title: 116kb-hACE2-Female-infected

value: 10^5 PFU SARS-CoV-2, 3dpi


title: 10971-13 Tumor biopsy

description: pretherapeutic


title: WT,heat,rep2,RNA-seq

value: seedling

value: WT


title: WT,heat,rep3,RNA-seq

value: 6 day seedling


title: Rbpj_P2_Rbpj-Olig2 cko_2

city: Shanghai

first: Zhejun

last: Xu

address: Room B4-029, 131 Dong'an Road, Xuhui

institute: Fudan University

data_processing:
Seqtk-1.4 (https://github.com/lh3/seqtk)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome (version:GRCm38) using Hisat2 (version:2.0.4)
Stringtie (vetrsion: 1.3.0) was used to count the read numbers mapped to each gene, and standardrized the counts using TMM (Trimmed mean of M values)
edgeR was used to find the differential expression genes. To identify most differentially expressed genes, we ranked genes according to their size and sequencing coverage normalized FPKM (fragments per kilo base of exon per million). The log2 fold changes of gene FPKM between two genotypes were tested statistically to determine whether an individual gene expression was altered significantly or not.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample.

source_name: cortex

extract_protocol:
Cortices were dissected from Olig2-Cre, RbpjF/F, H2B-GFP F/+ mice (n=2) and littermate controls (Olig2-Cre, Rbpj F/+, H2B-GFP F/+, n=3) at P2. Tissues were dissociated into single cells and fluorescent cells were sorted and collected by flow cytometry.
The total mRNAs were extracted and performed quality control using Qubit 2.0 Fluorometer, cDNAs were generated and amplified using the SMART-Seq HT kit (Cat, 634437, Takara) according to the manufacturer's protocol followed by quality control using Agilent2100. The libraries were generated using the Ovation Ultralow Library System V2 liabrary kit (0347, Nugen)

value: cortex

value: Rbpj-Olig2 cko


title: Rbpj_P2_Rbpj-Olig2 cko_1


title: WT,heat,rep1,RNA-seq

value: 44 degrees heat shock for 3 hours

value: 3 hours


title: 1095-04-11 Tumor biopsy

description: pretherapeutic


title: Rbpj_P2_control_3


title: 116kb-hACE2-Male-infected

value: Lung


title: K18-hACE2-Female-infected


title: WT,normal,rep3,RNA-seq


title: 10859-10 Tumor biopsy

description: pretherapeutic


title: WT,normal,rep2,RNA-seq


title: WT,normal,rep1,RNA-seq


title: K18-hACE2-Male-infected


title: 1067-13 Tumor biopsy

description: pretherapeutic


title: WT-Female-infected


title: Rbpj_P2_control_1


title: Rbpj_cko_scRNA

description: 10X Genomics

data_processing:
High quality sequences (clean reads) were obtained by removing low quality sequences and joints. The clean reads were then processed with Cell Ranger software to obtain quantitative information on gene expression.
Genes expressed in>3 cells and cells with>750 detected genes were filtered out. Cells with [10% mitochondrial genes were also filtered out. A global-scaling normalization method ‘‘Log Normalize’’ was applied to the raw read counts generated by 10X Cell Ranger to normalize the gene expression measurements for each cell by the total expression.
The log-transformed normalized single-cell expression values were used for differential expression tests. Potential sources of variation, which may include technical noise, batch effects, and biological sources of variation such as cell-cycle stage, were regressed out to improve downstream dimensionality reduction and clustering.
We regressed gene expression on the number of detected molecules per cell and the cell-cycle stage score. The scaled z-scored residuals were used for principal component analysis (PCA). Statistically significant principal components determined by a resampling test were kept for uniform manifold approximation and projection (UMAP) analysis.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include UMI values for each sample.

extract_protocol:
Mouse brains were dissected out and immediately submerged in fresh ice-cold Hanks balanced salt solution (Gibco 12175-095). The cortex was then cut into pieces and dissociated into a single-cell suspension using a Papain Cell Dissociation Kit (Miltenyi Biotec, catalog no. 130-092-628) according to the manufacturer’s instructions. CellTrace Yellow labeled single-cells were sorted using a BD FACSAriaII.
The Chromium droplet-based sequencing platform (10× Genomics) was employed to generate scRNA-Seq libraries, following the manufacturer’s instructions (manual document part number: CG00052 Rev C).

value: Rbpj cko


title: 103306-17 Tumor biopsy

description: pretherapeutic


title: WT-Male-infected


title: slr1-Input

status: Public on Aug 11 2023

first: Qi

last: Li

address: Lion Rock Street

department: Hongshan District

data_processing:
TrimGalore (version 0.6.6) was used to trim the adaptors and remove low quality reads from the raw reads.
Clean reads were mapped to the rice genome (MSU7.0) by Bowtie2 (version 2.4.4).
The bigwig files were generated using bamCoverage with the parameters “-bam -binSize 10 –normalize Using RPKM” in deepTools (version 3.5.0).
MACS2 (version 2.2.7.1) was used to call histone modification peaks with the parameters (-g 4.01e8 --broad --broad-cutoff 0.1 -B), and input sample was used as control.
Assembly: MSU version 7.0 rice genome
Supplementary files format and content:bigWig, broadPeak(except for Input sample)

organism: Oryza sativa Japonica Group

growth_protocol: Seedlings were grown in one-half-strength Murashige and Skoog medium under 14-h light/10-h dark cycles at 28/24 °C

extract_protocol:
Chromatin fragments were incubated with antibody-coated beads overnight, after extensive washing, immunoprecipitated chromatin was de-cross-linked and retrieved for sequencing.
ChIP DNA libraries were prepared using a TruSeq DNA Sample Preparation Kit v2 (Illumina, San Diego, CA, USA)

treatment_protocol: In chemical treatment experiments, 100 uM GA (Sigma, G1025) was supplied to seedlings through the roots for various durations.

value: SLR1 knockout

tag: chip antibody


title: slr1-H3K27me3-1


title: GA-H3K27me3-1

value: GA


title: GA-H3K27me3-2


title: CK-H3K27me3-2

value: control


title: CK-H3K27me3-1


title: GP5d, nanoNOMe

city: Helsinki

first: Konsta

last: Karttunen

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

data_processing:
The GP5d nanopore data was basecalled with Guppy 5.0.17 with the super-accurate basecalling model and a minimum q-score of 10.
Basecalled reads were aligned to the reference genome with minimap2 2.16 (minimap2 –x map-ont –a).
Alignment and quality controls were performed with nanoplot 1.20.0 and Samtools 1.9.
After alignment, methylation was called with nanopolish v.0.11.1. The cpggpc_new_train branch (https://github.com/jts/nanopolish/tree/cpggpc_new_train) was used to call both CpG and GpC methylation (nanopolish call-methylation -q cpggpc).
The resulting table was processed to a BED format (mtsv2bedGraph.py -q cpggpc --nome) and to methylation frequency table formats for CpG and GpC methylation (parseMethylbed.py frequency -v -m cpg and parseMethylbed.py frequency -v -m gpc) with scripts from https://github.com/isaclee/nanopore-methylation-utilities
The resulting methylation tables were converted to bedGraph and bigwig formats with a self-made script (mfreq_to_bw.R), utilizing bedGraphToBigWig v377.
The CpG methylation frequency tables were loaded into R and smoothed with bsseq v.1.28.0 (BSmooth ns = 50, h = 1000, maxGap = 100000).
Assembly: hg38
Supplementary files format and content: Methylation frequency tables in in the same format as Bismark cytosine reports.
Library strategy: NaNoME-seq

growth_protocol: GP5d cells were grown in DMEM supplemented with 10% FBS, 2 mM L-glutamine and 1% penicillin-streptocmycin. Cells were checked for mycoplasma contamination and were passaged at 80% confluency.

extract_protocol:
Genomic DNA was from GC methylated nuclei by using phenol chloroform extraction protocol.
NaNoME-seq library was prepared as described previously (Sahu et al., Oncogene 2021).

treatment_protocol: GP5d cell nuclei was isolated and treated with GC methylase M.CviPI as described earlier (Sahu et al., Oncogene 2021).

value: Colon adenocarcinoma


title: Rbpj_P2_control_2


title: HepG2, nanoNOMe

value: Hepatocellular carcinoma


title: hmi32Fibroblast.Prom

city: Perth

first: Ryan

last: Lister

state: WA

address: 35 Stirling Highway

country: Australia

institute: The University of Western Australia

data_processing: Fast5 reads with a Phred score ≥ 10 were basecalled with Guppy (version 5.0.11).

source_name: stem cell

growth_protocol: On day 8, the cells were switched to primed, naive, naive-to-primed (NtP) or transient-naive-treatment (TNT) reprogramming protocols. For primed: Cells were transient primed essential8 (E8) culture media after the initial 7 days culturing in fibroblast media. For Naive: Naive hiPSCs colonies were established through extended naive culturing. For TNT: cells were transient naive culture for 5 days after the initial 7 days culturing in fibroblast media, followed by culturing in primed E8 media. For NtP: Naive hiPSCs colonies were established through extended naive culturing and then transitioned the cells to a primed pluripotent state in E8 media to give rise to naive-to-primed hiPSCs.

extract_protocol:
Circulomics Nanobind CBB kit
ONT DNA-seq libraries were prepared with the ONT CS9109 largely according to the kit's guidelines. performed according to the ONT Cas9 enrichment guidelines. We increased the starting amount of DNA to 5µg, and the dephosphorylation and cleavage incubation times to 2 hours and 24 hours, respectively. Additionaly, the starting fibrobast population was also prepped for WGS with the ONT LSK109 kit according to the manufacturer's guidelines. All samples were sequenced on R9.4 flowcell chemistry.
ONT DNA-seq

treatment_protocol: To generate human primed and naïve iPSCs used for this study, somatic cell reprogramming with the Cytotune 2.0 kit, experiments were performed according to the manufacturer’s instructions (Invitrogen). Briefly, human dermal fibroblast (adult) were seeded at ~5x104 cells per well of a 6-well plate in fibroblast medium containing DMEM (Gibco), 10% FBS (Hyclone), 1% nonessential amino acids (Gibco), 1mM GlutaMAX (Gibco), Pen-strep (Gibco), 0.1mM 2-mercaptoethanol (Gibco) and 1mM sodium pyruvate (Gibco) . After 2 days, cells were transduced with Sendai viruses in fibroblast medium with multiplicity of infections (MOIs) as follows, KOS MOI=5, c-MYC MOI=15, KLF4 MOI=6. After 24 hours, the medium was replaced with fresh fibroblast medium and media were changed every other day thereafter. On day 7, cells were trypsinized and seeded onto a layer of iMEF feeders at ~0.5x105~1x105 per flask in fibroblast medium. The next day, the cells were switched to primed or naive media. 21-24 days after transduction, cells were passaged and expanded. Reprogramming intermediates were collected at the indicated time and isolated by FACS.

tag: background

value: Fibroblast

tag: culture medium

value: fibroblast media

value: stem cell


title: slr1-H3K27me3-2

value: seedling


title: NIP-Input

value: WT


title: Chem_NonGliaBAC_2

city: London

first: Vassilis

last: Pachnis

state: London

address: 1 Midland Road

department: Development and Homeostasis of the Nervous System Laboratory

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
The RSEM package (version 1.3.0) in conjunction with the STAR alignment algorithm (version 2.5.2)  was used for the mapping and subsequent gene-level counting of the sequenced reads with respect to Ensembl GRCm38-release-89 transcriptome
Differential expression analysis was performed with the DESeq2 package (version 1.10.1) within the R programming environment (version 3.3.2)
Assembly: GRCm38
Supplementary files format and content: Tab delimited text files containing TMM normalised data. Rows represent ensembl gene identifiers and columns represent individual samples.

growth_protocol: Mice used in this study were maintained according to standard practices and all procedures were approved by The Francis Crick Institute Animal Ethics Committee and conformed to UK Home Office requirements (ASPA 1986) and the ARRIVE guidelines.

extract_protocol:
For isolation of EGCs, the longitudinal smooth muscle layer and associated myenteric plexus were peeled off the wall of the smal intestineand subjected to enzymatic digestion to prepare a single-cell suspension. Single-cell suspensions were subjected to fluorescence activated cell sorting and live EGCs were isolated based on tdT expression DAPI exclusion. Cells were sorted directly into Trizol. Total RNA was isolated using PureLink RNA Micro Kit (Invitrogen #12183016) according to the manufacturer’s instructions.
Double stranded full-length cDNA was generated using the Ovation RNA-Seq System V2 (NuGen Technologies). Following quantification on a Qubit 3.0 fluorometer (Thermo Fisher Scientific), cDNA was fragmented to 200bp by acoustic shearing using Covaris E220 instrument (Covaris) at standard settings. The fragmented cDNA was then normalized to 100ng, which was used for sequencing library preparation using the Ovation Ultralow System V2 1-96 protocol (NuGen Technologies). A total of 7 PCR cycles were used for library amplification. The quality and quantity of the final libraries were assessed with TapeStation D1000 Assay (Agilent Technologies). The libraries were then normalized to 2,5 nM, pooled and loaded onto a HiSeq4000 (Illumina) to generate 75bp single-end reads.

treatment_protocol: All mice were injected with tamoxifen on two consecutive days 10 days prior cell isolation and some mice were treated with BAC 48 hours prior cell isolation.

value: non-glia cells (tdT-)


title: Chem_NonGliaBAC_4


title: Chem_NonGliaCtrl_4


title: Chem_NonGliaBAC_3


title: Chem_NonGliaCtrl_1


title: Y1, yki tumor,Day8 (re-analysis)

first: Wei

last: Song

email: rocwsong@gmail.com, songw@whu.edu.cn

state: Massachusetts

address: 77 Ave Louis Pasteur, NRB 336

department: Department of Genetics

institute: Harvard Medical School

data_processing:
Samples were multiplexed  in each lane, which yields target number of pair-end 100-bp reads for each sample, as a fraction of 180 million reads for the whole lane.
After trimming, sequence reads were mapped to the Drosophila genome (FlyBase genome annotation version r6.39) using Tophat.
With the uniquely mapped reads, gene expression was quantified using Cufflinks (FPKM values) and HTseq (read counts per gene).
We test for differentially expressed genes under various conditions using DEseq. It is an R package based on a negative binomial distribution that models the number reads from RNA-seq experiments and test for differential expression.
Non
Assembly: Drosophila genome (FlyBase genome annotation version r6.39)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Drosophila melanogaster

source_name: Malpighian tubules

growth_protocol: All flies were grown on the food containing 5.5 g agar, 65 g maltose, 25 g dry yeast, 65 g cornmeal, 4 mL propionic acid, and 1.25 g Methylparaben (dissolved in 95% ethanol) per liter under standard laboratory conditions

extract_protocol:
80 Malpighian tubules of each genotype were lysed with Trizol (ThermoFisher, 15596018) for RNA extraction. After assessing RNA quality with Agilent Bioanalyzer (RIN > 7), mRNAs were enriched by poly-A pull-down.
Sequencing libraries were prepared with Illumina Truseq RNA preparation kits and were sequenced using Illumina HiSeq 2000 by Benagen (Wuhan, China).

treatment_protocol: Virgin progenies were maintained at 18_x0001_C for 6-8 days and then switched to 29_x0001_C to induce transgenes for 8 days.

value: Malpighian tubules

value: 29 degree induction for 8 days


title: YT3, yki+ITP-i tumor, Day8


title: W3, control, Day8 (re-analysis)

value: esg-Gal4, tub-Gal80ts, UAS-GFP/+


title: Y2, yki tumor, Day8 (re-analysis)


title: Y3, yki tumor, Day8 (re-analysis)


title: YT2, yki+ITP-i tumor, Day8


title: Chem_NonGliaBAC_1


title: W2, control, Day8 (re-analysis)


title: YT1, yki+ITP-i tumor, Day8


title: Chem_GliaCtrl_4

value: enteric glia cells (EGCs, tdT+)


title: Chem_GliaCtrl_2


title: Chem_GliaCtrl_3


title: Chem_GliaCtrl_1


title: Chem_GliaBAC_4


title: Chem_GliaBAC_3


title: Chem_GliaBAC_2


title: KMC005

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

data_processing:
Counts and TPM values were obtained using kallisto v0.46 against the Ensembl mouse transcriptome (v97)
Assembly: mm10
Supplementary files format and content: tab-delimited files contain counts and TPM values

extract_protocol:
Total RNA from a 20 mg piece of the large lobe of the liver was purified from one mouse per strain of the HMDP, and from 3 mice per diet group in the C57BL6J Control study, using the Qiagen miRNeasy Mini kit (Qiagen cat#217004) per the manufacturer’s instructions. RNA preparation was as previously described (Ma, Fuqua et al. 2019) except that samples were homogenized in QIAzol using a TissueLyzer (Qiagen). All samples had RINe values greater than 8.
RNA sequencing libraries were prepared as described previously (Ma, Fuqua et al. 2019) using the KAPA Stranded mRNA-Seq Kit (cat #KK8421, KAPA Biosystems, Wilmington, MA).

value: liver

tag: Sex

value: male

tag: diet

value: chow


title: Chem_GliaBAC_1


title: KMC002


title: Chem_NonGliaCtrl_2


title: Chem_NonGliaCtrl_3


title: KMC003


title: W1, control, Day8 (re-analysis)


title: KMC012

value: sufficient iron (50 ppm)


title: KMC016


title: KMC010


title: KMC019

value: elevated iron (500 ppm)


title: D13_plus_10_32F_SmithR_to_E8

data_processing:
Sequencing adapters were trimmed with BBduk with the options mink = 3, qtrim = r, trimq = 10 minlength = 20 before alignment to hg19 with Bowtie and BSseeker2 with the option -n 1. PCR duplicates were removed using Sambamba and DNA methylation levels at base resolution calculated using CGmap tools. The non–conversion rate was calculated using the DNA methylation levels for the spiked–in lambda phage genome. When DNA methylation levels were calculated for regions such as promoters, enhancers, DMRs or ICRs, the methylation level was calculated as a coverage–weighted average by summing the number of methylated C calls (mCG) and dividing that by the total number of reads with either a C or T call (CG). This is represented in the figures and text as mCG/CG. To calculate methylation in CH contexts (where H = A, T or C), the level of methylation was calculated as above (mCH/CH) with the non–conversion rate subtracted from this value. When CH methylation was calculated for individual contexts, for example CA methylation, the non–conversion rate for that context was subtracted from the calculated methylation levels. For CA methylation browser tracks, mCA/CA was calculated for 5kb sliding windows (1kb slide), with the CA methylation non–conversion rate for that library subtracted from each window. To calculate per-read methylation, reads classified as methylated had methylation calls at every CG position in the read; unmethylated reads had zero methylation calls at CG positions; partially methylated reads had at least one CG methylation call  and one non-methylated CG call.
Genome_build: hg19
Supplementary_files_format_and_content: CGmap file generated with CGmap tools. File has 8 columns: [1]chromosome [2] nucleotide on Watson (+) strand [3] position [4] context (CG/CHG/CHH) [5] dinucleotide-context (CA/CC/CG/CT) [6] methylation-level = #_of_C / (#_of_C + #_of_T) [7] #_of_C (methylated C, the count of reads showing C here) [8] = #_of_C + #_of_T (all Cytosines, the count of reads showing C or T here).

source_name: Human pluripotent stem cells

growth_protocol: To generate human primed and naïve iPSCs used for this study, somatic cell reprogramming with the Cytotune 2.0 kit, experiments were performed according to the manufacturer’s instructions (Invitrogen). Briefly, human dermal fibroblast (adult) were seeded at ~5x104 cells per well of a 6-well plate in fibroblast medium containing DMEM (Gibco), 10% FBS (Hyclone), 1% nonessential amino acids (Gibco), 1mM GlutaMAX (Gibco), Pen-strep (Gibco), 0.1mM 2-mercaptoethanol (Gibco) and 1mM sodium pyruvate (Gibco) . After 2 days, cells were transduced with Sendai viruses in fibroblast medium with multiplicity of infections (MOIs) as follows, KOS MOI=5, c-MYC MOI=15, KLF4 MOI=6. After 24 hours, the medium was replaced with fresh fibroblast medium and media were changed every other day thereafter. On day 7, cells were trypsinized and seeded onto a layer of iMEF feeders at ~0.5x105~1x105 per flask in fibroblast medium. The next day, the cells were switched to primed or naive media. 21-24 days after transduction, cells were passaged and expanded. Reprogramming intermediates were collected at the indicated time and isolated by FACS.

extract_protocol:
Genomic DNA was isolated with the Qiagen Blood and Tissue Kit according to manufacturer's instructions. 0.5% (w/w) of unmethylated lambda phage DNA (Promega) was added to the sample genomic DNA for the purpose of an unmethylated control to measure the bisulfite non-conversion frequency in each sample.
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to methylated Illumina TruSeq adapters, and subjected to PCR amplification with KAPA HiFi Uracil+ DNA polymerase (KAPA Biosystems). Single-end sequencing was performed on a HiSeq1500, NextSeq500 or NovaSeq.

treatment_protocol: On day 8, the cells were switched to primed, naive, naive-to-primed (NtP) or transient-naive-treatment (TNT) reprogramming protocols. For primed: Cells were transient primed essential8 (E8) culture media after the initial 7 days culturing in fibroblast media. For Naive: Naive hiPSCs colonies were established through extended naive culturing. For TNT: cells were transient naive culture for 5 days after the initial 7 days culturing in fibroblast media, followed by culturing in primed E8 media. For NtP: Naive hiPSCs colonies were established through extended naive culturing and then transitioned the cells to a primed pluripotent state in E8 media to give rise to naive-to-primed hiPSCs.


title: KMC028

value: 2% carbonyl iron (20,000 ppm)


title: D13_plus_10_38F_SmithR_to_E8


title: KMC017


title: P11_plus_10_38F_SmithR_to_E8_rep1


title: RL412: Naive_hiPSC_P10_32F

value: Human pluripotent stem cells


title: P11_plus_10_32F_SmithR_to_E8_rep1


title: KMC024


title: KMC025


title: RL411: Naive_hiPSC_P3_32F


title: P3_plus_14_32F_Smith_C_OKSM

description:
RL700
Primed-to-Naïve-hiPSC reprogrammed from primary fibroblasts
WGBS

data_processing:
Sequencing adapters were trimmed with BBduk with the options mink = 3, qtrim = r, trimq = 10 minlength = 20 before alignment to hg19 with Bowtie and BSseeker2 with the option -n 1. PCR duplicates were removed using Sambamba and DNA methylation levels at base resolution calculated using CGmap tools.
Assembly: hg19
Supplementary files format and content: CGmap file generated with CGmap tools. File has 8 columns: [1]chromosome [2] nucleotide on Watson (+) strand [3] position [4] context (CG/CHG/CHH) [5] dinucleotide-context (CA/CC/CG/CT) [6] methylation-level = #_of_C / (#_of_C + #_of_T) [7] #_of_C (methylated C, the count of reads showing C here) [8] = #_of_C + #_of_T (all Cytosines, the count of reads showing C or T here).

value: Primed-to-Naïve-hiPSC

tag: pluripotent state

value: Primed


title: P3_plus_12_32F_Smith_C_Klf4

description:
RL699
Primed-to-Naïve-hiPSC reprogrammed from primary fibroblasts
WGBS


title: P12_plus_10_38F_SmithR_to_E8


title: M0767

value: A/J


title: RL418: Primed_hiPSC_P10_32F


title: RL414: Day_13_Naive_32F

source_name: Human reprogramming intermediate cells

value: Human reprogramming intermediate cells


title: RL417: Primed_hiPSC_P3_32F


title: M0754


title: RL416: Day_13_Primed_32F


title: RL413: Day_3_32F


title: RL399: Day_7_32F


title: KMC032


title: RL415: Day_0_32F

source_name: Cultured human fibroblasts

value: Cultured human fibroblasts

value: Fibroblast


title: M0741

value: NON/ShiLtJ


title: Biological rep#3, Cells transfected with HDR-CRISPR, HSPC

city: Freiburg

first: Claudio

last: Mussolino

address: Breisacherstr. 115

institute: Institute for Transfusion Medicine and Gene Therapy

data_processing:
demultiplexing: BCL2FASTQ v 2.0
Alignment: CRISPResso2 v2.0.20b
INDELs were counted from CRISPResso2 results included in report named "Allele frequency table around the cleavage site"
Library strategy: Amplicon Sequencing

growth_protocol: CD34+ were isolated from mobilized PBMC using the CD34 MicroBead Kit UltraPure (Miltenyi Biotec). Cultured in CellGenix GMP SCGM (CellGenix) supplemented with human SCF (300 ng/ml; Immunotools), Flt3-L (300 ng/ml; Immunotools), TPO (100 ng/ml; Immunotools) and IL-3 (60 ng/ml; Preprotech) for 72h before electroporation at a density of 0.5x106 cells/ml in a 24-well plate.

extract_protocol:
Cells were harvested 2 days post electroporation and their genomic DNA was extracted using the NucleoSpin® Tissue gDNA extraction kit (Machery Nagel) following the manufacture’s procedure and resuspended in 40 L of Nuclease-free water.
Libraries were prepared according to manufacturers guidlines (NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®)

treatment_protocol: Cells were electroporated 3 days post activation using the P3 Primary Cell 4D-Nucleofector Kit (Lonza) and the CA-137 program

value: Electroporated with HDR-CRISPR expressing IVT mRNA + sgRNA


title: Biological rep#2, Cells transfected with HDR-CRISPR, HSPC


title: Biological rep#2, Cells transfected with Cas9, HSPC

value: Electroporated with Cas9 expressing IVT mRNA + sgRNA


title: M0738


title: RL698: Day_21_Naive_32F


title: Biological rep#3, Cells transfected with Cas9, HSPC


title: M0726


title: Biological rep#2, Untreated Control, HSPC

value: Untreated


title: M0733

value: liver

value: PL/J


title: Biological rep#1, Cells transfected with HDR-CRISPR, HSPC


title: M0759

value: male


title: M0721


title: Biological rep#3, Untreated Control, HSPC


title: Ago-APP in neuroblasts_3

city: Marseille

first: christophe

last: beclin

state: Bouches du Rhone

address: campus de Luminy, case 907

department: Aix-Marseille université

country: France

institute: CNRS

data_processing:
Reads were trimmed at 3' and 5' ends for illumina adaptors and 4 additional nucleotides using Trim-Galore tool (default parameters) provided by useGalaxy.org website
BAM files were generated using "Map with BWA" tool (default parameters) provided by useGalaxy.org website.
micro-RNAs reads were counted in R using the summarizeOverlaps function of GenomicAlignments package
Counts were normalized between samples using the "counts per million" method
Assembly: dm6
Supplementary files format and content: A single Excel file containing normalized data for all samples

source_name: brain

extract_protocol:
Ago-APP
Truseq small RNA library prep modified according to Kim et al. (2019)

value: brain

value: neuroblasts

value: L3 larvae

value: Ago-APP


title: Ago-APP in neuroblasts_1


title: Biological rep#1, Cells transfected with Cas9, HSPC


title: M0709

value: 2% carbonyl iron (20,000 ppm)


title: RL697: Day_21_Primed_32F


title: M0703


title: M0756


title: Ago-APP in glial cells_3

value: glial cells


title: Ago-APP in glial cells_2


title: Ago-APP in glial cells_1


title: Ago-APP in neuronal cells_3

value: neuronal cells


title: M0697


title: M0695


title: Ago-APP in neuronal cells_2


title: Ago-APP in neuronal cells_1


title: M0693


title: Biological rep#1, Untreated Control, HSPC


title: M0675


title: Ago-APP in neuroblasts_2


title: PII-A3, GeoMx Seq

city: Rangsit

first: Sasin

last: Charoensuksira

state: Pathum Thani

address: 99 Moo 18 Klong Luang

country: Thailand

institute: Thammasat University

description:
PFI-A3
Q3_normalized count above LOQ.xlsx

data_processing:
save-interim-files=false
quality-trim-score=20
2color-trimming=True
adapter1=AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
adapter2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
adapter-trim-match-length=10
adapter-trim-max-mismatch=3
barcode-max-mismatch=1
stitching-max-mismatch=2
dedup-hd=1
threads=4
Assembly: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform, see attached PKC file (Hs_R_NGS_WTA_v1.0.pkc)
Supplementary files format and content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Supplementary files format and content: xlsx file includes normalized counts for each Sample. The final list of detectable genes was obtained by dropping genes with a limit of quantification (LOQ) of 1% coverage within replicates. Analyzed counts represent the upper quartile normalized collapsed counts across the study after removing QC flagged segments and features.
Library strategy: GeoMx Spatial Transcriptomics

source_name: Scalp tissue

extract_protocol:
Samples were incubated with DNA-oligo barcoded RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with flourescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Each collection of oligo tags from one well (representing an ROI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR.  After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.

tag: slide id

tag: roi number

tag: segment type

tag: disease

value: Androgenetic alopecia

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

value: Scalp tissue

value: Immune CD45+ cells


title: M0674

tag: tissue

tag: strain


title: M0690

tag: Sex

value: RIIIS/J

tag: diet


title: PII-A1, GeoMx Seq

description:
PFI-A1
Q3_normalized count above LOQ.xlsx

tag: slide id

tag: cell type


title: M0667


title: PII-C1, GeoMx Seq

description:
PFI-C1
Q3_normalized count above LOQ.xlsx

tag: roi number

tag: segment type

value: Normal scalp


title: NHEK_rep2

description:
RL3246
Keratinocytes
WGBS

source_name: Keratinocytes

growth_protocol: To generate human primed and naïve iPSCs used for this study, somatic cell reprogramming with the Cytotune 2.0 kit, experiments were performed according to the manufacturer’s instructions (Invitrogen). Briefly, human dermal fibroblast (adult) were seeded at ~5x10^4 cells per well of a 6-well plate in fibroblast medium containing DMEM (Gibco), 10% FBS (Hyclone), 1% nonessential amino acids (Gibco), 1mM GlutaMAX (Gibco), Pen-strep (Gibco), 0.1mM 2-mercaptoethanol (Gibco) and 1mM sodium pyruvate (Gibco). After 2 days, cells were transduced with Sendai viruses in fibroblast medium with multiplicity of infections (MOIs) as follows, KOS MOI=5, c-MYC MOI=15, KLF4 MOI=6. After 24 hours, the medium was replaced with fresh fibroblast medium and media were changed every other day thereafter. On day 7, cells were trypsinized and seeded onto a layer of iMEF feeders at ~0.5x10^5~1x10^5 per flask in fibroblast medium. The next day, the cells were switched to primed or naive media. 21-24 days after transduction, cells were passaged and expanded. Reprogramming intermediates were collected at the indicated time and isolated by FACS.

extract_protocol:
Genomic DNA was isolated with the Qiagen Blood and Tissue Kit according to manufacturer's instructions. 0.5% (w/w) of unmethylated lambda phage DNA (Promega) was added to the sample genomic DNA for the purpose of an unmethylated control to measure the bisulfite non-conversion frequency in each sample.
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to methylated Illumina TruSeq adapters, and subjected to PCR amplification with KAPA HiFi Uracil+ DNA polymerase (KAPA Biosystems).

tag: treatment

value: Keratinocyte

tag: background

value: NHEK

tag: pluripotent state

value: Somatic


title: PII-C2, GeoMx Seq

description:
PFI-C2
Q3_normalized count above LOQ.xlsx

tag: disease

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads


title: NB19_NHEK_TNTtoKSR_rep2

description:
RL3243
TNT-hiPSC reprogrammed from keratinocytes
WGBS

value: TNT-hiPSC

value: Primed


title: NB19_NHEK_TNTtoKSR_rep3

description:
RL3244
TNT-hiPSC reprogrammed from keratinocytes
WGBS


title: NB19_NHEK_TNTtoKSR_rep1

description:
RL3242
TNT-hiPSC reprogrammed from keratinocytes
WGBS


title: med28_2ctrl

city: Berkeley

first: Benjamin

last: Cole

state: CA

address: 1 Cyclotron Road

department: Biosciences

institute: Lawrence Berkeley National Laboratory

description: 10x Genomics Chromium

data_processing:
For single-nuclei samples, 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: Medicago truncatula MedtrA17_4.0, Rhizophagus irregularis Rir_HGAP_ii_V2 (DAOM 181602, DAOM 197198)
Supplementary files format and content: barcodes.tsv.gz:  list of spatial barcodes
Supplementary files format and content: features.tsv.gz:  list of gene IDs
Supplementary files format and content: matrix.mtx.gz:  gene expresion count data in Matrix Market Exchange Format

molecule: polyA RNA

organism: Medicago truncatula

source_name: root

growth_protocol: Seeds of Medicago truncatula Gaertn, cv Jemalong A17 (Noble Foundation) were scarified in concentrated sulfuric acid for 5-10 min and rinsed with distilled water, sterilized in 3.75% sodium hypochlorite solution, then rinsed five times with sterile distilled water and placed on 1â„2 Murashige and Skoog medium, 1% agar plates at 4C or RT for 48h. Germinated seedlings were transplanted to the top fine sand layer of inoculated and non-inoculated sand cones. Plants were grown in 22-24 ËšC 16 h day/ 8 h night, with 300 Î¼mol m-2 s-1 light intensity, and 60% relative humidity.

extract_protocol:
150 mg of roots growing in inoculated fine sand layer was weighed out and placed in the lid of a petri dish and chopped rapidly with a razor blade for three minutes in 600ÂµL NIBAM: 1x NIB (Sigma CELLYTPN1-1KT), 4% BSA, 1 mM DTT, 0.4 U/ÂµL Superase RNAse inhibitor (Sigma), 1:100 Protease Inhibitor Cocktail for plant tissues (Sigma). NIBAM-root slurry was strained through 40 Âµm and 20 Âµm filters (CellTrics). SYBR Green (1:10000) was used to visualize nuclei during purification on the Influx Flow Cytometer.
Library was performed according to the manufacterâ€™s instructions (Chromium Next GEM Automated Single Cell 3' cDNA Kit v3.1 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: To inoculate seedlings with Rhizophagus irregularis (BÅ‚aszk., Wubet, Renker and Buscot) C. Walker and A. SchÃ¼ÃŸler: 50 mL Agtiv Field Crops liquid mycorrhizal inoculant (PremierTech, RiviÃ¨re-du-Loup, QuÃ©bec, Canada) spores were captured on a 40 Âµm filter, rinsed with distilled water and resuspended in 50 mL distilled water. 1 mL of resuspended spores was applied to the horticultural sand layer and an additional 300 ÂµL applied to the fine play sand layer.

value: root

value: not inoculated

tag: timepoint

tag: genotype

value: WT


title: med38

description: 10x Genomics Chromium

tag: tissue

value: inoculated with Rhizophagus irregularis DAOM 181602, DAOM 197198

tag: strain

value: Medicago truncatula Gaertn, cv Jemalong A17


title: med21ctrl

description: 10x Genomics Chromium


title: med38ctrl

description: 10x Genomics Chromium


title: M0649

value: liver

tag: Sex

value: male

tag: diet

value: 2% carbonyl iron (20,000 ppm)


title: M0632


title: NB19_NHEK_D8toKSR_rep2

description:
RL3240
Primed-hiPSC reprogrammed from keratinocytes
WGBS

value: Primed-hiPSC


title: med21

description: 10x Genomics Chromium


title: NB19_NHEK_D8toKSR_rep1

description:
RL3239
Primed-hiPSC reprogrammed from keratinocytes
WGBS


title: MSC2_rep2

description:
RL3162
Mesenchymal stem cells
WGBS

source_name: Mesenchymal stem cells

value: MSC


title: med28_2

description: 10x Genomics Chromium


title: PII-A2, GeoMx Seq

description:
PFI-A2
Q3_normalized count above LOQ.xlsx

tag: slide id

value: Androgenetic alopecia

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

value: Scalp tissue

tag: cell type

value: Immune CD45+ cells


title: NHEK_rep3

description:
RL3247
Keratinocytes
WGBS

tag: treatment

value: Keratinocyte

tag: background

value: NHEK

tag: pluripotent state


title: MSC2_rep1

description:
RL3161
Mesenchymal stem cells
WGBS

value: Somatic


title: MSC_D8toKSR_rep3

description:
RL3160
Primed-hiPSC reprogrammed from mesenchymal stem cells
WGBS

value: Primed


title: M0629


title: MSC_D8toKSR_rep2

description:
RL3159
Primed-hiPSC reprogrammed from mesenchymal stem cells
WGBS


title: med28_1

description: 10x Genomics Chromium

value: root


title: M0659


title: MSC_D8toKSR_rep1

description:
RL3158
Primed-hiPSC reprogrammed from mesenchymal stem cells
WGBS


title: MSC_TNTtoKSR_rep3

description:
RL3157
TNT-hiPSC reprogrammed from mesenchymal stem cells
WGBS

value: TNT-hiPSC


title: MSC_TNTtoKSR_rep2

description:
RL3156
TNT-hiPSC reprogrammed from mesenchymal stem cells
WGBS


title: M0613


title: TNTKSR

value: Naive

tag: culture medium

value: KSR

value: stem cell


title: M0598

value: liver


title: MSC_TNTtoKSR_rep1

description:
RL3155
TNT-hiPSC reprogrammed from mesenchymal stem cells
WGBS


title: NB19_NHEK_D8toKSR_rep3

description:
RL3241
Primed-hiPSC reprogrammed from keratinocytes
WGBS


title: 38F_NB3_p28_p2n2p_p10_rep3

description:
RL3078
PNP-hiPSC reprogrammed from primary fibroblasts
WGBS

value: Primed-Naive-Primed-hiPSC


title: 38F_NB3_p28_p2n2p_p10_rep2

description:
RL3077
PNP-hiPSC reprogrammed from primary fibroblasts
WGBS


title: TNTE8


title: M0591

value: male

value: 2% carbonyl iron (20,000 ppm)


title: D8KSR


title: M0588


title: 38F_NB3_p28_p2n2p_p10_rep1

description:
RL3076
PNP-hiPSC reprogrammed from primary fibroblasts
WGBS


title: M0582

value: SEA/GnJ


title: 32F_NB3_p28_p2n2p_p10_rep2

description:
RL3074
PNP-hiPSC reprogrammed from primary fibroblasts
WGBS


title: 32F_NB3_p28_p2n2p_p10_rep1

description:
RL3073
PNP-hiPSC reprogrammed from primary fibroblasts
WGBS


title: M0624


title: 32F_NB3_p28_p2n2p_p10_rep3

description:
RL3075
PNP-hiPSC reprogrammed from primary fibroblasts
WGBS


title: D8E8


title: NB18_32F_D8toKSR_556_rep3

description:
RL3072
Primed-hiPSC reprogrammed from primary fibroblasts
WGBS

value: Primed-hiPSC


title: hmi32Fibroblast.CasEnr

value: Fibroblast

value: fibroblast media


title: NB18_32F_D8toKSR_556_rep2

description:
Primed-hiPSC reprogrammed from secondary fibroblasts
RL3071

growth_protocol: To generate human primed and naïve iPSCs used for this study, somatic cell reprogramming with the Cytotune 2.0 kit, experiments were performed according to the manufacturer’s instructions (Invitrogen). Briefly, human dermal fibroblast (adult) were seeded at ~5x104 cells per well of a 6-well plate in fibroblast medium containing DMEM (Gibco), 10% FBS (Hyclone), 1% nonessential amino acids (Gibco), 1mM GlutaMAX (Gibco), Pen-strep (Gibco), 0.1mM 2-mercaptoethanol (Gibco) and 1mM sodium pyruvate (Gibco). After 2 days, cells were transduced with Sendai viruses in fibroblast medium with multiplicity of infections (MOIs) as follows, KOS MOI=5, c-MYC MOI=15, KLF4 MOI=6. After 24 hours, the medium was replaced with fresh fibroblast medium and media were changed every other day thereafter. On day 7, cells were trypsinized and seeded onto a layer of iMEF feeders at ~0.5x10^5~1x10^5 per flask in fibroblast medium. The next day, the cells were switched to primed or naive media. 21-24 days after transduction, cells were passaged and expanded. Reprogramming intermediates were collected at the indicated time and isolated by FACS.


title: GRPR-AngII3

city: Heifei

first: Gao

address: Meishan Road

institute: The First Affiliated Hospital of Anhui Medical University

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

source_name: kidney

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

value: kidney

value: CDH16 Cre+/GRPRfl/fl

value: AngII


title: NB18_32F_D8toKSR_556_rep1

description:
Primed-hiPSC reprogrammed from secondary fibroblasts
RL3070

value: Primed


title: ROCY1-eCLIP_repC

city: Indianapolis

first: Michael

middle: James

last: Holmes

state: IN

address: 635 Barnhill Drive

department: Pharmacology & Toxicology

institute: Indiana University School of Medicine

description:
TgPRUΔKu80ΔHXGPRT::FLAG-ROCY1
ROCY1_eCLIP_forward_strand.bigwig
ROCY1_eCLIP_reverse_strand.bigwig
ROCY1_binding_regions.bed

data_processing:
library strategy: eCLIP
sequencing adapters from read2 were removed with CutAdapt (5'adapt: CTCTTCCGATCT, 3'adapt:GATCGTCGGACT); UMI extracted with UMI-tools (pattern "NNNNNNNNNN" located at 3'end)
mapped with RNA-STAR to TgME49 genome (v58). Settings: –outFilterMismatchNoverLmax=0.1, –outFilterScoreMinOverLread=0.75, –outFilterMatchNminOverLread=0.75, –outFilterMultimapNmax=1, –alignIntronMax=1
mapped reads deduplicated with UMI-tools
peaks called with PureCLIP. Settings -dm50, -nim3 with background control experiment from input
Assembly: TGME49 v58 (toxodb.org)
Supplementary files format and content: ROCY1 binding profiles across genome (bigwig)
Supplementary files format and content: ROCY1 enriched peaks (bed)

organism: Toxoplasma gondii

source_name: PRU

growth_protocol: Freshly lysed tachyzoites were innoculated on confluent HFFs and grown under bradyzoite-inducing conditions (RPMI HEPES pH8.3, ambient CO2) for 48h

extract_protocol:
monolayers were rinsed with PBS, UV-crosslinked 2x 175mJ/cm2 with 254nm.  Monolayers were syringe lysed and parasites were pelleted twice with PBS washes. Parasites were lysed in (50mM Tris pH7.4, 100mM NaCl, 1% NP40, 0.1% SDS, 0.5% sodium deoxycholate) and FLAG tag was immunoprecipated for 6h after saving an aliquot for size-matched input
library was generated according to eCLIP protocol PMID: 27018577

tag: cell line

value: PRU

value: bradyzoite

value: 48h pH8.3, ambient CO2

tag: sample type


title: NB18_32F_D8toKSR_553_rep3

description:
Primed-hiPSC reprogrammed from secondary fibroblasts
RL3069


title: GRPR-AngII1

tag: tissue

tag: genotype


title: NB18_32F_D8toKSR_553_rep2

description:
Primed-hiPSC reprogrammed from secondary fibroblasts
RL3068


title: CDH16KO-AngII3

value: CDH16 Cre+/Tmemfl/fl


title: NHEK_rep1

description:
RL3245
Keratinocytes
WGBS

value: Keratinocyte

value: NHEK

value: Somatic


title: ROCY1-eCLIP_repB


title: M0572

source_name: liver

value: liver

tag: Sex

value: male

tag: strain


title: M0568

value: BALB/cJ

tag: diet

value: 2% carbonyl iron (20,000 ppm)


title: NB18_32F_D8toKSR_553_rep1

description:
Primed-hiPSC reprogrammed from secondary fibroblasts
RL3067

value: Primed-hiPSC


title: M0565


title: CDH16KO-AngII2


title: ROCY1-eCLIP_repA


title: CDH16KO-AngII1


title: M0549


title: AngII3

value: Tmemfl/fl


title: NB18_32F_TNTtoKSR_556_rep2

description:
TNT-hiPSC reprogrammed from secondary fibroblasts
RL3065

value: TNT-hiPSC


title: size-matched-input_repA

description:
TgPRUΔKu80ΔHXGPRT::FLAG-ROCY1
input_forward_strand.bigwig
input_reverse_strand.bigwig
ROCY1_binding_regions.bed

value: size-matched-input


title: NB18_32F_TNTtoKSR_556_rep1

description:
TNT-hiPSC reprogrammed from secondary fibroblasts
RL3064


title: M0560


title: M0576


title: size-matched-input_repC


title: NB18_32F_TNTtoKSR_556_rep3

description:
TNT-hiPSC reprogrammed from secondary fibroblasts
RL3066


title: GRPR-AngII2

value: kidney

value: CDH16 Cre+/GRPRfl/fl

value: AngII


title: AngII2


title: NB18_32F_TNTtoKSR_553_rep3

description:
TNT-hiPSC reprogrammed from secondary fibroblasts
RL3063

value: Primed


title: GA-RNA_seq-3

data_processing:
The RNA-seq clean data were mapped against the rice genome(MSU version 7.0) with the corre_x0002_sponding annotation by hisat2 using default parameters
FeatureCounts (version 2.0.0) and DESeq2 (version 1.38.3) were used to calculate DEGs
Assembly: MSU version 7.0 rice genome
Supplementary files format and content:output from DESeq

source_name: seedling

extract_protocol:
Total RNA was extracted from the indicated tissues using TRIzol reagent (Invitrogen, USA) according to the manufac_x0002_turer’s protocol.
RNA-seq libraries were prepared using the Illumina TruSeq RNA Sample Preparation Kit and sequenced (paired-end, 2 x 150 bp).

value: seedling

value: WT

value: GA


title: AngII1


title: M0536


title: M0526


title: GA-RNA_seq-2


title: NB18_32F_TNTtoKSR_553_rep2

description:
TNT-hiPSC reprogrammed from secondary fibroblasts
RL3062


title: M0527


title: M0523


title: NB18_32F_TNTtoKSR_553_rep1

description:
TNT-hiPSC reprogrammed from secondary fibroblasts
RL3061


title: GA-RNA_seq-1


title: CK-RNA_seq-3

value: control


title: p47plus13_H9_ESC

description:
Human embryonic stem cell line
RL2351

source_name: Human embryonic stem cells

value: hESC


title: M0521

value: liver

value: SWR/J


title: size-matched-input_repB

value: PRU

value: bradyzoite

value: 48h pH8.3, ambient CO2


title: MCF7-CTCF

city: Saint Louis

first: Li

last: Ding

state: MO

address: 660 S. Euclid Avenue

institute: Washington University in St. Louis

data_processing:
To process the CUT&RUN reads, we first performed quality control using FastQC to assess read quality (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Then we used Trimmomatic95. The resulting trimmed reads were subsequently mapped to the human genome (UCSC hg38) utilizing Bowtie296 with the dovetail setting. Finally, to eliminate any duplicated reads, the aligned reads were subjected to duplicate removal via Picard (http://broadinstitute.github.io/picard/). To call peaks, we used MACS2 using an IgG bam file as a control. Then for resulting peaks, we applied the same filtering steps as for the peak calling on snATAC-seq data.
Assembly: UCSC hg38
Supplementary files format and content: tab separated files
Library strategy: CUT&RUN

extract_protocol: Caki-1, MCF7, and U251 cell lines were cultured under designated conditions according to information on the American Type Culture Collection (ATCC) website (https://www.atcc.org/). When cells reached the desired confluence and numbers, the CUT&RUN Kit (14-1048, EpiCypher, USA) and CUT&RUN Library Prep Kit (14-1002, EpiCyher, USA) were applied following the manufacturer's protocols.


title: U251-CTCF


title: CAKI1-CTCF


title: CK-RNA_seq-2

institute: Huazhong Agricultural University


title: OVCAR8, Input_for_H3K4me3

first: Jianfeng

state: Shanghai

address: 270 Dong'an Road

institute: Fudan University Shanghai Cancer Center

data_processing:
Raw reads were filtered and cleaned by fastp software.
Aliments were performed followed by bowtie2 and STAR instruction
MACS2 were used for the binding profile
IGV and R were used for visualization
Supplementary files format and content: hg19
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

growth_protocol: OVCAR8 cellls were cultured in RPMI1640 medium supplemented with 10% FBS and 1% P/S.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared according to NEB ChIP-Seq Library Prep Kit (E6240).

value: Human high grade serous ovarian cancer

tag: chip antibody

value: no antibody


title: OVCAR8, H3K4me3


title: slr1-RNA_seq-3

value: SLR1 knockout


title: M0517

value: male

value: 2% carbonyl iron (20,000 ppm)


title: Cornea_AffectedSib_Rep1

city: Ann Arbor

first: William

last: Presley

state: MI

address: 1137 Catherine St

department: Human Genetics

institute: University of Michigan

data_processing:
Reads were timmed with CutAdapt
Quality control was performed with FastQC
Reads were alighed to GRCh38 reference genome with STAR v2.7.8a
Reads were recoreded in count matrices with RSEM v1.3.3
Assembly: GRCh38
Supplementary files format and content: Text file contains raw sequencing read values from sample

source_name: Corneal Epithelium

extract_protocol:
Corneal tissue was stored in RNAlater before RNA was extracted using Rneasy kit (Qiagen)
RNA underwent Poly(A) enrightment via the NEBNext Poly(A) mRNA Magnetic Isolation Module, and cDNA library genetation with the xGen Broad-Range RNA Library Prep kit using xGen Normalase UDI primers

value: Corneal Epithelium

value: 13q12 Microdeletion


title: U251-NRF1


title: M0502

value: CE/J


title: M0509


title: M0514


title: CK-RNA_seq-1

value: seedling

value: WT


title: RPE1, non-methylated, replicate 2

data_processing:
FastQC v.0.11.9 was used for quality control and determination of read lengths of raw data.
Two technical replicates were combined before alignment.
Raw reads were mapped with bowtie2 v.2.4.1 (bowtie2 --maxins 1000) to the reference genome.
Picard v.2.23.4 was used to remove duplicates (MarkDuplicates -REMOVE_DUPLICATES false -ASSUME_SORTED true)
Samtools v.1.7 was used to filter non-concordant reads and reads with a MAPQ of smaller than 20 (samtools view -F 1024 -b -q 20).
Peaks were called with MACS2 v.2.2.7.1 with the STARR input library as control (macs2 callpeak -f BAMPE -g hs).
Peaks overlapping with ENCODE blacklisted regions were removed from the narrowPeak and summit files with bedtools v.2.29.2 (bedtools subtract -A).
Genome read coverage was calculated with bedtools v.2.29.2 (bedtools coverage –pc -bg) and bedGraphToBigWig v377 was used to create a bigwig file.
A RPKM normalized bigwig file was created with deepTools v.3.5.0 (bamCoverage --binSize 50 --normalizeUsing RPKM --effectiveGenomeSize 2913022398).
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak
Library strategy: STARR-seq

growth_protocol: As described in (Sahu et al., Nat. Gen. 2022).

extract_protocol:
Extraction was performed as described in (Sahu et al., Nat. Gen. 2022).
Library was prepared as described in (Sahu et al., Nat. Gen. 2022).

value: Retinal pigment epithelium