title: C57BL/6 mouse, control, Day90, rep1

description:
Library name: Sample1
Mouse, Liver, Input, Control, Gavage, 90 days
S54


title: C57BL/6 mouse, control, Day90, rep2

status: Public on Apr 07 2025

type: SRA

city: Guangzhou

first: Hao

last: Huang

state: Guangdong

address: No. 1023 Shatai Road

country: China

institute: Southern Medical University

description:
Library name: Sample2
Mouse, Liver, Input, Control, Gavage, 90 days
S1035

library_source: transcriptomic

data_processing:
Following sequencing, paired-end reads were generated and subjected to quality control in accordance with the Q30 standard.
Adapters and low-quality reads were removed from the raw data using the Cutadapt program (v1.1.8).
The clean reads from all libraries were aligned to the reference genome using STAR (v2.7.1a), and duplicate reads were removed using Samtools (v1.3.1).
The differential m6A methylation peaks and genes were characterized and subjected to analysis utilising the Model-based Analysis of MACS (v2.1.1) and DESeq2 R package (v4.1.0), respectively. The peaks identified by the two software programs were then subjected to screening and annotation, with the objective of identifying those that overlapped with exons of mRNA.
The construction and sequencing of the RNA-seq libraries were conducted using the MeRIP-seq input libraries and the same methodology.
Assembly: mm10
Supplementary files format and content: Each processed data file type is an XLS file, and these include FPKM for each sample.

molecule: total RNA

organism: Mus musculus

source_name: Liver

growth_protocol: Male C57BL/6 mice aged between 6 and 8 weeks old were housed in a dedicated pathogen-free facility with controlled environmental conditions (room temperature maintained at 24±2℃, relative humidity between 40-60%, and a 12/12 h light/dark cycles), and the subjects had unlimited accessibility to food and water.

extract_protocol:
Total RNA was extracted from liver tissues using TRIzol reagent (Invitrogen, Grand Island, NY, USA).
After determining RNA concentration with Qubit (4.0) and assessing RNA quality by agarose gel electrophoresis techniques. An adequate quantity of RNA was interrupted to 200-500 bp using metal ions, then purified and solubilised. Next, an anti-m6A antibody (Danvers, MA, USA) was added for immunoprecipitation, which binds to the RNA fragments containing the m6A site. Subsequently, the immunoprecipitated RNA fragments (IP) and the unbound RNA fragments (Input) were subjected to library construction using the Ovation SoLo RNA-Seq System Core Kit (NuGEN, USA). The Illumina NovaSeq 6000 platform (Illumina, USA) was used to sequence the resulting libraries in PE150 sequencing mode.

treatment_protocol: The mice were randomly selected to either the control or the Cd exposure group, with each group comprising six individuals. In the groups exposed to Cd, mice were intragastric injected with 0/20 mg/kg CdCl2 daily for a period of 90 days. Stock solutions of cadmium chloride (CdCl2) were prepared by dissolving CdCl2 (Sigma-Aldrich, 439800) in deionized water for subsequent use.

tag: tissue

value: Liver

tag: genotype

value: WT

tag: treatment

value: 0 mg/kg/day CdCl2, Gavage

tag: time

value: Day 90

tag: batch


title: Il-17rc_replicate_3

city: Cambridge

first: Myriam

last: Heiman

state: Massachusetts

address: 43 Vassar St

country: USA

institute: Massachusetts Institute of Technology

description:
Library name: Rc-3
S1DZ cells expressing Il-17rc-driven Cre recombinase to induce the TRAP construct expression

data_processing:
FASTQ files of 100-bp paired-end sequencing reads were aligned to the Mus musculus genome using STAR_2.7.5c.
Read counts were generated by STAR using the-quantMode GeneCounts option, using the default options.
Assembly: The Mus musculus genome build GRCm38 and annotation build 98 (reference FASTA and GTF file)
Supplementary files format and content: TXT file containing raw count

molecule: cytoplasmic RNA

source_name: brain

extract_protocol:
The S1DZ tissue was homogenized with a glass/Teflon power-driven Potter-Elvehjem homogenizer in an ice-cold lysis buffer (150 mM KCl, 10 mM HEPES [pH 7.4], 5 mM MgCl2, 0.5mM dithiothreitol, 100 μg/mL cycloheximide, 20 U/µL SUPERaseIn RNase Inhibitor, 40 U/µL RNasin Plus Rnase Inhibitor, and EDTA-free protease inhibitors).  Following homogenization, samples were centrifuged at 2,000 x g at 4°C for 10 min and the supernatant was removed to a new tube.  NP-40 (final concentration 1%) and 1,2-Diheptanoyl-sn-glycero-3-phosphocholine (DHPC, final concentration 15 mM) were subsequently added and samples were incubated on ice for 5 min.  Samples were centrifuged at 13,000 x g at 4°C for 10 min and the supernatant was removed to a new tube.  Streptavidin Dynabeads (ThermoFisher Scientific, Waltham MA) coated with biotin-linked mouse anti-GFP antibodies were then added to this supernatant and the samples were incubated overnight at 4°C with end-over-end rotation.  Beads were collected on a magnetic rack and washed three times with wash buffer (350 mM KCl, 10 mM HEPES [pH 7.4], 5 mM MgCl2, 0.5 mM dithiothreitol, 100 μg/mL cycloheximide, 1% NP-40).  RNA was subsequently purified using the Absolutely RNA Isolation Nanoprep kit (Agilent Technologies, Santa Clara CA).
Libraries were constructed using the Takara Bio SMART-Seq v4 kit (Takara Bio USA, Inc.).

treatment_protocol: For TRAP purification, AAV5-EF1α-Flex-EGFPL10a (Addgene viral prep #98747-AAV5) was injected into the S1DZ of Il-17ra-Cre, Il-17rb-Cre, or Il-17rc-Cre mice. Viruses were incubated for 4 weeks after the surgery. Injections were performed using a pulled fine-glass capillary at 0.1 μl/min (400 nl/side).

value: brain


title: C57BL/6 mouse, control, Day90, rep3

description:
Library name: Sample3
Mouse, Liver, Input, Control, Gavage, 90 days
S94


title: Il-17rc_replicate_4

description:
Library name: Rc-4
S1DZ cells expressing Il-17rc-driven Cre recombinase to induce the TRAP construct expression


title: C57BL/6 mouse, cadmium-exposed, Day90, rep1

description:
Library name: Sample4
Mouse, Liver, Input, 20 mg/kg/day CdCl2, Gavage, 90 days
S37

value: 20 mg/kg/day CdCl2, Gavage


title: Il-17rc_replicate_2

description:
Library name: Rc-2
S1DZ cells expressing Il-17rc-driven Cre recombinase to induce the TRAP construct expression


title: Il-17rb_replicate_3

description:
Library name: Rb-4
S1DZ cells expressing Il-17rb-driven Cre recombinase to induce the TRAP construct expression


title: Il-17rb_replicate_1

description:
Library name: Rb-1
S1DZ cells expressing Il-17rb-driven Cre recombinase to induce the TRAP construct expression


title: Proliferating iMOPs, stranded RNA-seq, biol rep 1

city: Piscataway

first: Kelvin

middle: Y.

last: Kwan

state: NJ

address: 604 Allison Rd.

department: Cell Biology & Neuroscience

institute: Rutgers University

description: Library name: SG0920_S16_Sample4

data_processing:
Sequence reads were mapped to reference mouse genome (mm10) using HISAT2.
SAM files were converted, sorted, and indexed to generate sorted BAM files using Samtools
The featureCounts command from Rsubread was used to create a count matrix and differential expression was calculated using DEseq2.
To visualize RNA-seq read coverage at forward(+) and reverse(-) strands of the genome separately, employed Deeptools (3.4.3) bamCCoverage function (-normalizeUsing RPKM-filterRNAstrand forward/reverse) with sorted BAN files as input.
Assembly: mm10
Supplementary files format and content: comma separated values text files include raw counts for each sample
Supplementary files format and content: comma separated values text files include differential expression

source_name: iMOPs

growth_protocol: Proliferating iMOPs: DMEM/F12, 1XB27, 25 µg/ml carbenicillin and 20 ng/ml bFGF.iMOP-derived neurons: Neurobasal media, 1XN21, 2 mM L-glutamine, and 1 µM K03861.

extract_protocol:
Total RNA was extracted from 1-5x106 proliferating or neuronal iMOP cells using TRIzol Reagent following the manufacturer's protocol. Total RNA was treated with Dnase I and phenol-chloroform extraction was used to remove DNaseI. Ribosomal RNA was depleted from 500 ng of Dnase-treated total RNA using the NEBNext rRNA depletion kit.
Yielded RNA was used for stranded RNA-seq library preparation with the Takara SMARTer Stranded RNA-seq kit following the manufacturer's instructions. The average library size, including adaptors was ~300bp. Eight uniquely indexed libraries were normalized by concentration and pooled together. Pooled libraries were sequenced using Illumina Novaseq 6000 S4 platform (2x150bp) and resulted in ~2.5 billion total paired reads.

tag: cell line

value: iMOPs

tag: cell type

value: Proliferating iMOPs

value: wild-type


title: Il-17rb_replicate_2

description:
Library name: Rb-2
S1DZ cells expressing Il-17rb-driven Cre recombinase to induce the TRAP construct expression


title: Il-17ra_replicate_1

description:
Library name: Ra-1
S1DZ cells expressing Il-17ra-driven Cre recombinase to induce the TRAP construct expression


title: Il-17ra_replicate_2

description:
Library name: Ra-2
S1DZ cells expressing Il-17ra-driven Cre recombinase to induce the TRAP construct expression


title: E3.5 uterus, Atp11a KO8 [L002]

city: Calgary

last: Hemberger

address: 3330 Hospital Dr NW

country: Canada

institute: University of Calgary

data_processing:
Reads aligned using STAR aligner
Assembly: mm10
Supplementary files format and content: Ensembl gene ID, Ensembl transcript ID, number of reads

source_name: E3.5 pregnant uterus

extract_protocol: E3.5 uteri were dissected from psudo-pregnant feamles (mated with vasectomized males), then 1/4 of a uterine horn was cut and flash frozen, then proccesed using Trizol RNA extraction before sequencing.

value: E3.5 pregnant uterus


title: E3.5 uterus, Atp11a KO6 [L002]


title: E3.5 uterus, Atp11a KO7 [L002]


title: E3.5 uterus, Atp11a KO4 [L002]


title: E3.5 uterus, Atp11a KO3 [L002]


title: E3.5 uterus, Atp11a KO2 [L002]


title: E3.5 uterus, Atp11a HET5 [L002]


title: E3.5 uterus, Atp11a HET4 [L002]


title: E3.5 uterus, Atp11a HET3 [L002]


title: C57BL/6 mouse, cadmium-exposed, Day90, rep2

description:
Library name: Sample5
Mouse, Liver, Input, 20 mg/kg/day CdCl2, Gavage, 90 days
S28


title: E3.5 uterus, Atp11a KO1 [L002]


title: Il-17rc_replicate_1

description:
Library name: Rc-1
S1DZ cells expressing Il-17rc-driven Cre recombinase to induce the TRAP construct expression


title: E3.5 uterus, Atp11a HET2 [L002]


title: E3.5 uterus, Atp11a HET1 [L002]


title: E3.5 uterus, Atp11a WT6 [L002]


title: E3.5 uterus, Atp11a WT4 [L002]


title: E3.5 uterus, Atp11a WT3 [L002]


title: E3.5 uterus, Atp11a WT7 [L002]


title: E3.5 uterus, Atp11a WT5 [L002]


title: Il-17ra_replicate_3

description:
Library name: Ra-4
S1DZ cells expressing Il-17ra-driven Cre recombinase to induce the TRAP construct expression


title: E3.5 uterus, Atp11a WT1 [L002]


title: E3.5 uterus, Atp11a WT2 [L002]


title: E3.5 uterus, Atp11a KO9 [L001]


title: E3.5 uterus, Atp11a KO8 [L001]


title: E3.5 uterus, Atp11a KO9 [L002]


title: E3.5 uterus, Atp11a KO5 [L002]


title: E3.5 uterus, Atp11a KO7 [L001]


title: E3.5 uterus, Atp11a KO6 [L001]


title: E3.5 uterus, Atp11a KO5 [L001]


title: Breast epithelial, EV, rep2

city: Nijmegen

first: Cyriel

last: Huijer

address: Houtlaan 4

department: Molecular Developmental Biology

country: Netherlands

institute: Radboud University Nijmegen

description: Library name: 44103_CH_EV_0_38

data_processing:
Fastq files were mapped to the human genome hg38 through the Seq2science pipeline (https://github.com/vanheeringen-lab/seq2science, accessed 10 January 2024). Reads were aligned with STAR. QC was performed with the MultiQC report from Seq2science.
trimmer: fastp
Assembly: GRCh38.p14
Supplementary files format and content: MCF10A_GEO_tpm.csv: Trancripts per million, calculated by the seq2science pipeline in a csv file

organism: Homo sapiens

source_name: Breast

extract_protocol:
RNA was extracted using the Quick-RNA Microprep Kit (Cat# R1051, Zymo Research) according to the manufacturer’s protocol.
Libraries were prepared from 300 ng RNA with the KAPA RNA HyperPrep Kit with RiboErase (HMR) (Cat# KK8502, Kapa Biosystems). RNA fragmentation was performed for a desired library insert size of 200-300 bp by fragmentation for 6 min at 94 °C.  Library concentrations were determined using the Qubit HS kit (Cat# Q32854, Invitrogen). Library size distribution was determined using a High Sensititivy DNA analysis (Cat# 5067-4626, Agilent) on a Bioanalyzer 2100 (Agilent). Libraries with an average between 300-400 bp were loaded on the NextSeq 2000 system (Illumina).

value: Breast

value: Breast epithelial cells

value: Empty vector

value: no treatment


title: Breast epithelial, EV, rep3

description: Library name: 44104_CH_EV_0_39


title: pmo_WT_Ab_6_2

city: Chapel Hill

first: Todd

last: Cohen

state: NC

address: 115 Mason Farm Rd

institute: University of North Carolina at Chapel Hill

description:
Library name: Sample 12
TDPB_pmo_WT_Ab_6.0_2_1

data_processing:
The quality of the reads was assessed by FastQC (version 0.11.9). Low-quality reads and adapters were trimmed by using Trim Galore (version 0.6.7). The trimmed reads were mapped to the hg19 transcriptome (GENCODE release19) and quantified by Salmon. The estimated counts for each sample were summarized by using tximport (v. 1.28.0), and the normalized counts were estimated based on the size factors calculated by DESeq2.
Assembly: hg19 transcriptome (GENCODE release19)
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
Supplementary files format and content: Tab-delimited text file includes normalized counts for each sample

source_name: primary human monocyte derived marcrophages

growth_protocol: primary human monocyte derived macrophages were grown at 37C, 5% CO2 in complete DMEM (DMEM + 10% FBS + 1X penicillin/streptamycin)

extract_protocol:
RNA was harvested using RNeasy Mini Kit (QIAGEN). 500 ng of total RNA was used for the construction of sequencing libraries.
The depletion of ribosomal RNAs (rRNAs) and the generation of stranded RNA-seq libraries were performed using KAPA RNA HyperPrep with RiboErase kit following manufacturer’s instructions

treatment_protocol: primary human monocyte derived macrophages were stimulated with TDP-43 aggregates, amyloid beta oligomers, LPS, or vehicle (PBS) control for 12 hours (acutely) or 6 days (chronically) before RNA was harvested

value: white blood cell

value: Abeta

value: 6 days


title: E3.5 uterus, Atp11a KO4 [L001]


title: pmo_WT_Ab_6_1

description:
Library name: Sample 11
TDPB_pmo_WT_Ab_6.0_1_1

value: primary human monocyte derived marcrophages


title: pmo_WT_LPS_0.5_2

description:
Library name: Sample 10
TDPB_pmo_WT_LPS_0.5_2_1

value: WT

value: LPS

value: 12 hours


title: pmo_WT_LPS_0.5_1

description:
Library name: Sample 9
TDPB_pmo_WT_LPS_0.5_1_1


title: E3.5 uterus, Atp11a KO3 [L001]


title: pmo_WT_PBS_6_1

description:
Library name: Sample 7
TDPB_pmo_WT_PBS_6.0_1_1

value: PBS


title: E3.5 uterus, Atp11a WT9 [L002]


title: E3.5 uterus, Atp11a KO2 [L001]


title: pmo_WT_PBS_0.5_2

description:
Library name: Sample 6
TDPB_pmo_WT_PBS_0.5_2_1


title: E3.5 uterus, Atp11a WT8 [L002]


title: pmo_WT_PBS_0.5_1

description:
Library name: Sample 5
TDPB_pmo_WT_PBS_0.5_1_1


title: E3.5 uterus, Atp11a HET5 [L001]


title: E3.5 uterus, Atp11a KO1 [L001]


title: pmo_WT_TDP43_6_1

description:
Library name: Sample 3
TDPB_pmo_WT_TDP_6.0_1_1


title: pmo_WT_TDP43_0.5_2

description:
Library name: Sample 2
TDPB_pmo_WT_TDP_0.5_2_1


title: pmo_WT_TDP43_6_2

description:
Library name: Sample 4
TDPB_pmo_WT_TDP_6.0_2_1


title: pmo_WT_TDP43_0.5_1

description:
Library name: Sample 1
TDPB_pmo_WT_TDP_0.5_1_1


title: E3.5 uterus, Atp11a HET4 [L001]


title: E3.5 uterus, Atp11a HET3 [L001]


title: HD-D_Pos

city: Bethesda

first: Amanda

last: Henning

state: MD

address: 9000 Rockville Pike

institute: National Institutes of Health

data_processing:
Illumina BaseSpace Sequencing Hub applications were used for data processing. Specifically, alignment and transcript quantification was performed using the DRAGEN RNA application (v4.2.7). These analyses were conducted using the default parameters.
Assembly: hg38
Supplementary files format and content: *.quant is the transcript quantification output file

source_name: Blood

extract_protocol:
B cells were isolated from frozen PBMC via 3 different methods: positive MACS (EasySep Human CD19 Positive Selection Kit II; StemCell Tech), negative MACS (EasySep Human B cell Isolation kit; StemCell Tech), and FACS (sorted Live/CD19+ cells; MACSQuant Tyto Cell Sorter, Miltenyi). RNA was isolated via the RNeasy Plus Micro kit (Qiagen).
Libraries were prepared using the TruSeq Stranded mRNA library prep kit (Illumina) following manufacturer's protocol.

value: Blood

value: B cells

tag: isolation

value: Positive MACS


title: E3.5 uterus, Atp11a HET2 [L001]


title: HD-D_Neg

value: Negative MACS


title: HD-D_FACS

value: FACS


title: Breast epithelial, EV, rep1

description: Library name: 44102_CH_EV_0_37

value: Breast


title: HD-C_Pos


title: E3.5 uterus, Atp11a HET1 [L001]

value: E3.5 pregnant uterus


title: HD-C_FACS


title: HD-B_Neg


title: E3.5 uterus, Atp11a WT9 [L001]


title: pmo_WT_PBS_6_2

description:
Library name: Sample 8
TDPB_pmo_WT_PBS_6.0_2_1


title: Nexrutine, rep3

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

description: Library name: DP_MT_23b

data_processing:
Illumina bcl2fastq software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using Tophat algoritm (v2.0.8).
Gene count measurements were obtained using HTSeq-count
Assembly: mm9
Supplementary files format and content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

molecule: polyA RNA

source_name: prostate tumor tissue

extract_protocol:
Total RNA was extracted using TRIzol (Thermo Fisher) from tumor and quantified using nanodrop and Agilent bioanalyzer.
Total RNA samples  were used for sequencing library preparation according to Illumina stranded mRNA sample preparation guide. Each library was bar-coded and then pooled for sequencing run with 50bp single-read sequencing protocol.

treatment_protocol: Mice were maintained in a climate-controlled environment with a 12-hour light-dark cycle with diet and water provided ad libitum. Phellodendron amurense extract (Nexrutine) was supplied in the diet and running wheel was used as the exercise intervention. The control group mice were group housed had access to AIN-93 diet ad libitum and did not have access to running wheel

tag: mouse strain

value: Transgenic adenocarcinoma of the mouse prostate (TRAMP) mice in C57BL/6 background

value: prostate tumor tissue

value: Phellodendron amurense extract was supplied in the diet


title: E3.5 uterus, Atp11a WT8 [L001]


title: HD-B_Pos


title: HD-B_FACS


title: Nexrutine, rep2

description: Library name: DP_MT_022


title: HD-A_Neg


title: HD-A_Pos


title: Non-Niche

city: Ithaca

first: Noor

last: Bala

state: NY

address: 602 Tower Rd

institute: Cornell University

description:
Library name: Sample_152021_AAAJTVNHV_3_Non_PAC10
10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads for the mRNA libraries were processed into raw count matrices using CellRanger version 6.1.2 (10X Genomics) with the mm10 2020-A reference.
Assembly: Mouse mm10
Supplementary files format and content: HD5, compressed matrix files

source_name: Skin

extract_protocol:
Mice were euthanized, and their ears were excised. Ears was then split into ventral and dorsal sheets and placed in 1.5 ml of Liberase TL (0.4 mg/mL in RPMI; Sigma Aldrich) and 50ug of DNase I (Sigma Aldrich) per ear. Ears were minced and incubated with agitation for 1h at 37°C. Tissue digestion was quenched by adding complete media (RPMI 1640 supplemented with 10% fetal calf serum, Lonza), followed by mechanical disaggregation using program C on the GentleMACS dissociator (Miltenyi Biotec). Insoluble material was removed by filtration, and the pellet was washed twice with 2% neonatal calf serum in Hank’s balanced-salt solution (HBSS). Single cell suspensions were stained with Ghost Dye UV 450 or Violet 510 dead cell stain for 405 nm excitation (Tonbo Biosciences) at a 1:1000 dilution in PBS for 30 minutes at 4°C, followed by a wash with 2% NCS in HBSS.The cells were washed, filtered, and resuspended in FACS buffer containing 100μg/mL of DNase I. Live cells were collected using a FACSAria fusion (BD Biosciences) and single cell suspension were used for library construction.
Single-cell suspensions were submitted to the Cornell BRC Genomics Facility for processing and sequencing. The Chromium Next GEM Single Cell 3’ reagent kit v3 from 10X Genomics® protocol was used for FACS-sorted cell sequencing. A target of 10000 cells across runs were loaded for Gel Beads-in-emulsion (GEM) generation. According to the kit protocol first GEMs were generated, subsequently reverse transcription was performed, and cDNA was cleaned up, amplified, and size selected. Sample quality was confirmed using a Qubit (RNA HS kit; Thermo Fisher) to determine concentration and a Fragment Analyzer (Agilent) to determine RNA integrity. The libraries were sequenced with an Illumina NextSeq 2000.

value: Skin


title: Nexrutine, rep1

description: Library name: DP_MT_012


title: E3.5 uterus, Atp11a WT6 [L001]


title: Exercise, rep3

description: Library name: DP_MT_004

value: Mice  singularly housed and given access to a 15.5 cm diameter low-profile running wheel with activity recorded.


title: Perivascular Niche

description:
Library name: Sample_152020_AAAJTVNHV_2_PAC10
10x Genomics


title: E3.5 uterus, Atp11a WT5 [L001]


title: HD-C_Neg


title: Exercise, rep1

description: Library name: DP_MT_001


title: E3.5 uterus, Atp11a WT4 [L001]


title: Exercise, rep2

description: Library name: DP_MT_002


title: Ln, GC, GEX

city: Berlin

first: Frederik

middle: Richard

last: Heinrich

state: Berlin

address: Chariteplatz 1

department: Bioinformatics

country: Germany

description: 10x Genomics

data_processing:
Demultiplexing, mapping, detection of intact cells as well as quantification of gene expression was performed using Cell Ranger’s count pipeline in default parameter settings with an expected number of 3,000 cells per sample and refdata-cellranger-mm10-1.2.0 as reference.
Assembly: mm10A
Supplementary files format and content: .h5 or .csv

source_name: tracheal lymph node

extract_protocol:
On day 17, lungs were removed and bronchial lymph nodes were dissected from the lung tissue under a stereo microscope. Single-cell suspensions from lung tissue were prepared using the Miltenyi gentleMACS Dissociator and digested with 0.5 mg/ml collagenase D and 20 mg/ml DNase I for 25 min at 37°C. Antigen-specific B cells were first enriched for CD45.1 expressing cells by magnetic sorting. For higher purity, cells were sorted on a Becton Dickinson ARIA II or ARIA Fusion cell sorter as DAPI- CD4- CD8- CD19+ CD45.1+ CD45.2- total B cells or additionally as CD138- CD38low GL7+ geminal center (GC) B cells.
Library construction was performed according to 10x Genomics instructions. For samples 1 and 2, the Chromium Next GEM Single Cell 3' v2 Kit was used. For samples 3-6, the Chromium Next GEM Single Cell 5' v2 kit in combination with the Single Cell Mouse BCR Amplification Kit was used.

treatment_protocol: 1.25 x 10e5 Smarta T cells were co-transferred with 5 x 10e5 follicular B1-8i B cells (expressing CD45.1 as congenic marker) into C57BL/6NCrl mice by intravenous injection. To induce lung inflammation, mice were repeatedly challenged intranasally with 10 µg of cognate antigen (Smarta peptide and iodinated nitrophenol (NIP) coupled to mouse serum album as non-immunogenic carrier) and 5 µg of LPS as adjuvant on days 0, 1, 10, and 13. For details of the mouse model see Bauer and Hutloff, Meth Mol Biol (2021) 2285:91-98.

value: tracheal lymph node

tag: strain

value: GC B cell


title: Lung, GC, GEX

description: 10x Genomics

source_name: lung

value: lung

value: GC-like B cell


title: Lung, GC, BCR

description: 10x Genomics


title: sid2, 10dpi, rep4

city: Göttingen

first: Christiane

last: Gatz

state: Lower Saxony

address: Julia-Lermontowa-Weg 3

department: Plant Molecular Biology and Physiology

institute: Georg-August-University Göttingen

data_processing:
Sequence images were transformed with the Illumina BaseCaller software to BCL files, which were subsequently demultiplexed to FASTQ files with CASAVA (v1.8.2).
Using a Galaxy platform, alignment of reads to the Arabidopsis thaliana genome reference sequence (TAIR10 release-39; https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-39/fasta/arabidopsis_thaliana/) and counting of the aligned reads to the feature type “CDS” were carried out with RNA STAR (Galaxy version 2.5.2b-2;  Dobin et al., 2013).
Assembly: Arabidopsis thaliana (TAIR10 release-39; https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-51/fasta/arabidopsis_thaliana/)
Supplementary files format and content: tab-delimited text files include raw counts for each sample

organism:
Arabidopsis thaliana
Verticillium longisporum

source_name: Roots

growth_protocol:
Surface sterilized A. thaliana seeds were sown onto horizontal MS agar plates supplemented with 2% sucrose and kept at 4°C in darkness for 48–72 h. Subsequently, plates were transferred to short day conditions (8-h day/16-h night cycle) at 22°C, 60% relative humidity, and a photon flux density of 80–100 μmol m−2 s−1. After 14 days, plantlets were transferred onto a 1:1 mixture of sand (white, 1–2 mm grain size, Rosnerski, Königslutter, Germany) and twice-steamed soil (Fruhstorfer Erde, Spezial Substrat, Typ T, Str. 1 fein, HAWITA, Vechta, Germany) on a thin layer of Seramis (Westland Deutschland, Mogendorf, Germany) and grown for another 14 days under short day conditions at 120–140 μmol photons m−2 s−1. The sand–soil mixture was initially watered with 0.1% Wuxal Super (Manna, Ammerbuch-Pfäffingen, Germany) in dH2O. For the first week, plants were kept under a transparent hood. If genotyping was required, a single leaf was clipped from each plant during the first week of growth on the sand–soil mixture.
For plant infections, Verticillium longisporum VL43 was grown in Potato Dextrose Medium with 0.5 mg/L Cefotaxim for 14 days at 21°C, 90 rpm, in the dark. Spores were harvested by straining through a filter (Nucleo Bond Folded filters, Macherey-Nagel, Düren, Germany) and washed in sterile tap water. The spore concentration was determined with a hemocytometer.

extract_protocol:
Total RNA was extracted using Trizol; TruSeq RNA Library Prep Kit v2 (Illumina)
TruSeq RNA Library Prep Kit v2 (Illumina)

treatment_protocol: Plants were carefully uprooted from the sand–soil mixture and washed in tap water. Roots were then dipped in spore suspension (1*106 spores/mL tap water) or tap water (mock) for 45 min, after which plants were planted into individual pots containing steamed soil (Fruhstorfer Erde, Spezial Substrat, Typ T, Str. 1 fein, HAWITA, Vechta, Germany) soaked with 0.2% Wuxal Super, where plants were kept for a final 10 days in short day conditions at 120–140 μmol photons m−2 s−1 until harvest. During the first 2 days after transfer of plants to soil, they were kept under transparent hoods.

value: Roots

value: infection


title: Control, rep3

description: Library name: DP_MT_017

value: Control group without intervention


title: sid2, 10dpi, rep3


title: Control, rep2

description: Library name: DP_MT_014


title: E3.5 uterus, Atp11a WT3 [L001]


title: E3.5 uterus, Atp11a WT2 [L001]


title: sid2, 10dpi, rep2


title: E3.5 uterus, Atp11a WT1 [L001]


title: sid2, 10dpi, rep1


title: E3.5 uterus, Atp11a WT7 [L001]


title: coi1, 10dpi, rep4

value: outcrossed coi1-t from heterozygous COI1/coi1-t plants


title: coi1, 10dpi, rep3


title: Whole Ear Skin 2

description:
Library name: Sample_152019_AAAJTVNHV_1_total_ear2
10x Genomics


title: coi1, 10dpi, rep1


title: Whole Ear Skin 1

description:
Library name: Sample_152022_AAAJTVNHV_4_total_ear1
10x Genomics


title: Control, rep1

description: Library name: DP_MT_013


title: Transgenic, Barley, rep2

city: Uttarakhand

first: Harsh

last: Chauhan

state: Haridwar

address: Roorkee-Haridwar Highway, Roorkee

department: Department of Biosciences and Bioengineering

country: India

institute: Indian Institute of Technology Roorkee

data_processing:
NGSQC toolkit used for QC.
Alignment and mapping of reads was performed using STAR (Dobin et al., 2013; https://github.com/alexdobin/STAR) and Trinity platform (genome-guided) (Bowtie2) (Hass et al., 2013; https://github.com/trinityrnaseq/trinityrnaseq).
Abundance estimation was calculated  using RSEM (RNA-Seq by Expectation-Maximization) method (Li and Dewey, 2011) and differential gene expression analysis was  performed using DESeq2 (Mi et al., 2014; https://bioconductor.org/packages/release/bioc/html/DESeq2.html).
Assembly: MorexV3_pseudomolecules_assembly, INSDC Assembly GCA_904849725.1 (https://www.ebi.ac.uk/ena/browser/view/GCA_904849725.1)
Supplementary files format and content: Excel file having FPKM values for the samples

organism: Hordeum vulgare

source_name: Leaves

growth_protocol: Seeds of barley (Hordeum vulgare L.) Cv. Golden promise were germinated in a mixture of soil and soilrite (1:1) in greenhouse under control conditions of 18/16◦C (day/night) temperature and 16-hour photoperiod.

extract_protocol:
Leaves of three-week old non-transformed wild type (WT) and HvHSFA6a overexpression transgenic plants were used to extract the total RNA with RNeasy® plant mini kit (74904; Qiagen) as per the manufacturer’s instructions. During the total RNA extraction, RQ1 RNase-free DNase (M6101; Promega Corporation) was used to remove the genomic DNA. The RNA concentration was quantified by NanoDrop microvolume UV-Vis spectrophotometers (ND-ONE-W; Thermo Fisher Scientific), and total RNA (5µg) was separated on 1.2 % formaldehyde gel to determine concentration and integrity.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Transgenic lines and WT plants were grown in plant growth chamber under continuous moderate heat stress conditions of 34 oC, two-week old plants were used to assess the thermotolerance.

value: Leaves

tag: cultivar

value: Golden Promise

value: Heat stress at 42ºC for 30 minutes


title: coi1, 10dpi, rep2


title: Adult_superficialLV

city: Gyeonggi-do

first: Hokyung

last: Jin

address: 2066, Seobu-ro, Jangan-gu, Suwon-si

department: Otolaryngology

country: South Korea

institute: Sungkyunkwan University

description: Adult superficial cervical lymphatic system

data_processing:
For droplet-based sequencing, sequenced libraries were demultiplexed and aligned to the mouse reference genome GRCm39 (mm10), with the eGFP sequence added to the reference using Cell Range (version 8.0.1).
Raw expression matrices were constructed using Read10X function in the 'R' package Seurat (version 5.0.3)
Before clustering analysis, low-quality cells detected with fewer than 1,000 genes and putative dead cells with high mitochondrial percentage (>10% of reads mapped to mitochondrial genes) were discarded. Cells detexted with more than 6,000 genes were also considered as doublets and removed. For gene-based quality control, genes detected in fewer than three cells were removed from the raw expression matrix.
After quality control of unwanted cells and genes, expression matrices were normalized column-wise, dividing each gene’s unique molecular identifier (UMI) counts by the sum of UMI counts for a given cell. Then, scale factor 10,000 was multiplied, and log2 transformed to yield log counts per million equivalent values.
Assembly: mm10
Supplementary files format and content: Cell-gene expression matrix of log normalized UMI counts for adult and aged scLV

source_name: FVB/N

extract_protocol:
FACS sorted superficial cervical system cells were processed using Chromium Next GEM Single Cell 3p RNA library kit v3.1 (10X Genomics) following the manufacturer's protocol.
Using Chromium Next GEM Single Cell 3p RNA library kit v3.1 (10X Genomics), cDNA libraries were constructed.

value: FVB/N

tag: age

value: 12 weeks old


title: Ln, GC, BCR

description: 10x Genomics


title: WTcoi1, 10dpi, rep3

value: outcrossed wild-type from heterozygous COI1/coi1-t plants


title: Aged_superficialLV

description: Aged superficial cervical lymphatic system

value: 93 weeks old


title: Transgenic, Barley, rep1


title: WTcoi1, 10dpi, rep2


title: CgA-KO/hTau, rep6

city: La Jolla

first: Shandy

last: Shahabi

state: CA

address: 9500 Gilman Dr

department: Chemistry

institute: UCSD

data_processing:
RNA samples were assessed for sequencing quality by FASTQC and libraries with high quality reads were trimmed using Trimmomatic (v0.39).
Reads were mapped to the mm10 mouse reference genome using STAR (v2.7.10b) and transcripts were quantified by StringTie (v1.3.6).
Transcript counts were imported to R using prepDE.py3 for normalization and differential expression was analyzed by DESeq2 (v1.42.0).
Assembly: mm10
Supplementary files format and content: CSV file containing raw gene counts.

source_name: Prefrontal cortex

growth_protocol: WT, hTau, and CgA-KO/hTau B6C3F1/J mice were kept in a 12 hr dark/light cycle and fed a regular chow diet (NCD: 14% calorie from fat; LabDiet 5P00).

extract_protocol:
Total RNA was isolated from prefrontal cortex of 8-month old mouse using RNeasy kit (Qiagen).
Complementary DNA libraries were prepared from 500 ng of total RNA using the mRNA HyperPrep Kit (KAPA) according to manufacturer’s recommendations with Unique Dual-Indexed adapters (KAPA). Libraries were PCR-amplified for 10 cycles and quality was assessed by Tapestation. Libraries were then quantified by Qubit 2.0 fluorometer (Thermo), pooled, and analyzed by paired-end 100 sequencing on the NovaSeq 6000 platform (Illumina) at UCSD IGM Core.

value: Prefrontal cortex

value: CgA-KO/hTau


title: aos, 10dpi, rep4

value: outcrossed aos from heterozygous AOS/aos plants


title: CgA-KO/hTau, rep5


title: Wild type, Barley, rep1

value: Control


title: WTcoi1, 10dpi, rep1


title: CgA-KO/hTau, rep4


title: Hela Kyoto, Docetaxel, 3

city: Vienna

first: Alexis

middle: J.

last: LOMAKIN

address: Währinger Straße 10

department: Center for Pathobiochemistry & Genetics

country: Austria

institute: Medical University of Vienna

description: Library name: Kyoto_Docetaxel3_S131953

data_processing:
Illumina NovaSeq Control Software (NCS) 1.8.0 was used for the data acquisition on the sequencing instrument.
On-instrument base-calling was performed by the Illumina Real-Time Analysis (RTA) software 3.4.4.
BCL to BAM file conversion and demultiplexing with custom programmes (https://github.com/epigen/picard/) based on Picard tools 2.19.2 (https://broadinstitute.github.io/picard/)
Spliced genome alignments to GRCh38 (UCSC Genome Browser hg38) and Ensembl reference transcriptome e100 (April 2020) with STAR 2.7.9a and options recommended by the ENCODE project (--alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --outFilterMultimapNmax 20 --outFilterType BySJout)
Differential expression modelling with Bioconductor 3.16 package DESeq2 1.38.0, running under R 4.2.2.
Assembly: UCSC hg38 based on GRCh38
Supplementary files format and content: Per gene and sample raw (integer) counts and DESeq2-calculated FPKMs in tab-separated value (TSV) format

source_name: Uterus; cervix

growth_protocol: Hela Kyoto cells were grown in DMEM/F-12 at 37°C with 5% CO2, for 72 hours

extract_protocol:
RNA was exctracted following the protocol of RNeasy Plus Mini Kit from Qiagen
The amount of total RNA was quantified using the Qubit 2.0 Fluorometric Quantitation assay (Ther-mo Fisher Scientific, Waltham, MA, USA) and the RNA integrity number (RIN) was determined using the 2100 Bioanalyzer High-Resolution Automated Electrophoresis instrument (Agilent, Santa Clara, CA, USA). RNA-seq libraries were prepared with the NEBNext® Poly(A) mRNA Magnetic Isolation Module and the NEBNext® Ultra™ II Direction-al RNA sample preparation kit (New England Biolabs, Inc., Ipswich, MA, USA). NGS library concentra-tions were quantified with the Qubit 2.0 assay and the size distribution was assessed using the 2100 Bioanalyzer instrument. Before sequencing, sample-specific NGS libraries were diluted and pooled in equimolar amounts.

treatment_protocol: Growth for 72 hours in the mentioned media (Control), and for 72 hours with the addition of a clinically relevant concentration of chemotherapeutic agent (Docetaxel, 10nM)

value: Uterus; cervix

value: Hela Kyoto cell line

value: Endothelial cells

value: 72h Docetaxel

tag: Sex

value: female


title: CgA-KO/hTau, rep3


title: aos, 10dpi, rep2

value: Roots

value: infection


title: WTaos, 10dpi, rep4

value: outcrossed wild-type from heterozygous AOS/aos plants


title: CgA-KO/hTau, rep2


title: aos, 10dpi, rep1


title: Hela Kyoto, Docetaxel, 2

description: Library name: Kyoto_Docetaxel2_S131954


title: aos, 10dpi, rep3


title: WTaos, 10dpi, rep2


title: WTaos, 10dpi, rep1


title: Hela Kyoto, Docetaxel, 1

description: Library name: Kyoto_Docetaxel1_S131952


title: Proliferating iMOPs, input, ChIP

description: Library name: P_Input

library_source: genomic

data_processing:
CHD7 ChIP-seq seuencing reads were mapped to reference mouse genome (grcm38) using HISAT2/2.1.0.
SAM files created by HISAT2 were converted, sorted, and indexed to generate sorted BAM files using Samtools.
Reads aligned to ENCODE mouse (mm10) blacklist2 were removed from BAM files using bedtools.
MACS2 with parameter "--nomodel'' and ''--broad' was used for peak calling. Input libraries were used as control for MACS2 peak calling.
Peaks identified in biological replicas were merged using bedtools.
Assembly: mm10
Supplementary files format and content: bigwig
Supplementary files format and content: MACS2 peaks

molecule: genomic DNA

extract_protocol:
2x106 - 1x107 cells were used for a set of ChIP experiment.  Cells were incubated with primary antibodies against CHD7. DNA libraries were amplified using PCR and purified using Agencourt Ampure XP beads (Beckmann). Libraries were sequenced on illumina Genome Analyzer II.
ChIP-seq library prep was performed using KAPA Hyper Prep kit (Cat# KK8503) and HiFi Hotstart DNA Polymerase.

value: iMOPs

value: Proliferating iMOPs

value: wild-type


title: CgA-KO/hTau, rep1


title: iMOP-derived neurons, input, ChIP

description: Library name: N_Input

value: iMOP-derived neurons


title: Hela Kyoto, Control, 3

description: Library name: Kyoto_Control3_S131957

value: 72h untreated


title: hTau, rep6

value: Prefrontal cortex

value: hTau


title: Hela Kyoto, Control, 2

description: Library name: Kyoto_Control2_S131955


title: Wild type, Barley, rep2

value: Leaves

value: Golden Promise


title: hTau, rep5


title: iMOP-derived neurons, CHD7, ChIP, biol rep 3

description: Library name: N_CHD7_S4


title: Proliferating iMOPs, CHD7, ChIP, biol rep 4

description: Library name: P_CHD7_2


title: iMOP-derived neurons, CHD7, ChIP, biol rep 2

description: Library name: N_CHD7_S11


title: iMOP-derived neurons, CHD7, ChIP, biol rep 1

description: Library name: N_CHD7_S5


title: Proliferating iMOPs, CHD7, ChIP, biol rep 2

description: Library name: P_CHD7_S3


title: Proliferating iMOPs, CHD7, ChIP, biol rep 3

description: Library name: P_CHD7_3


title: Hela Kyoto, Control, 1

description: Library name: Kyoto_Control1_S131956

value: Uterus; cervix


title: WTaos, 10dpi, rep3


title: hTau, rep4


title: SW620 SM120-3

city: Montpellier cedex 5

first: Francoise

last: Macari

address: 208 avenue des Apothicaires

country: France

institute: INSERM

description:
Library name: SW620 SM120-3
column name : SM120_3

data_processing:
Image analysis and base calling were realized in real-time using the NovaSeq Control Software and the Real-Time Analysis 3 software respectively (Illumina, San Diego, CA, USA). Demultiplexing and FASTQ files generation were carried out using Illumina’s bcl2fastq software (v2.20.0.422). Adapter sequences were trimmed using Cutadapt (v3.4).
The quality control of raw data and demultiplexed reads was assessed using respectively Illumina’s Sequencing Analysis Viewer (SAV) software and the FastQC (v0.11.9) software from the Babraham Institute.Contaminant screening was performed using FastQ Screen (v0.14.0, Babraham Institute). Quality checks for each samples was summarised using MultiQC software (v1.10.1).
TopHat2 software (v2.1.1) was used to align the obtained reads on the human genome (hg38 version). FeatureCounts (v2.0.0) software was then used to obtain read counts per gene. Counts were normalized using DESeq2 (v1.26.0).
Assembly: Hg38 (UCSC)
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: Tab-delimited text file includes normalized counts for each Sample

growth_protocol: Cells were maintained in M11 medium (DMEMF12 (1:1) GlutaMAX medium, N2, Glucose 0.3%, insulin 20 µg/mL, hBasic-FGF 10 ng/mL, hEGF 20 ng/mL) in low attachement plates treated with Poly-HEME at 10 mg/mL. in humidified atmosphere with 5% CO2 37°C

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen) following manufacturer procedure
RNA-seq libraries were prepared using Universal Plus mRNA-seq kit from NuGEN according to manufacturer's protocols.

treatment_protocol: Cells were treated with or without SM, DSM at 120µM during 48h in corresponding medium.

value: Colon cancer cells

value: WT

value: treated with SM 120µM


title: Proliferating iMOPs, CHD7, ChIP, biol rep 1

description: Library name: P_CHD7_S10


title: Exp 2 Lung GC-like

description: Chudakov

data_processing:
Raw sequence reads were demultiplexed with MIGEC-1.2.4a Checkout -cute and assembled with AssembleBatch --force-collision-filter and --force-overseq of 3
Assembly: mm10
Supplementary files format and content: .tsv

extract_protocol:
On day 18, lungs were removed and bronchial lymph nodes were dissected from the lung tissue under a stereo microscope. Single-cell suspensions from lung tissue were prepared using the Miltenyi gentleMACS Dissociator and digested with 0.5 mg/ml collagenase D and 20 mg/ml DNase I for 25 min at 37°C. Antigen-specific B cells were first enriched for CD45.1 expressing cells by magnetic sorting. For higher purity, cells were sorted on a Becton Dickinson ARIA II cell sorter as DAPI- CD4- CD8- CD19+ CD45.1+ CD45.2- B cells and either as CD138- CD38low GL7+ geminal center (GC) B cells or CD19low CD138+ plasmablasts directly into Trizol LS. RNA was isolated using the Qiagen RNeasy Micro Kit.
Heavy chain immunoglobulin BCR libraries were prepared according to the protocol of Chudakov (Turchaninova et al., Nat Prot (2016) doi: 10.1038/nprot.2016.093).

treatment_protocol: 1.25 x 10e5 Smarta T cells were co-transferred with 5 x 10e5 follicular B1-8i B cells (expressing CD45.1 as congenic marker) into CD28 knock-out mice (on a C57BL/6NCrl background) mice by intravenous injection. To induce lung inflammation, mice were repeatedly challenged intranasally with 10 µg of cognate antigen (Smarta peptide and iodinated nitrophenol (NIP) coupled to mouse serum album as non-immunogenic carrier) and 5 µg of LPS as adjuvant on days 0, 1, 10, and 13. For details of the mouse model see Bauer and Hutloff, Meth Mol Biol (2021) 2285:91-98.

value: lung

value: GC-like B cell


title: Exp 2 Lung PB

description: Chudakov

value: Plasmablast


title: hTau, rep2


title: Exp 2 Ln PB

description: Chudakov

value: tracheal lymph node


title: SW620 0AB -3

description:
Library name: SW620 0AB -3
column name : 0AB_3

value: Non treated


title: hTau, rep1


title: Exp 2 Ln GC

description: Chudakov

value: GC B cell


title: SW620 SM120-2

description:
Library name: SW620 SM120-2
column name : SM120_2


title: Exp 1 Lung PB

description: Chudakov


title: Wild-type, rep5


title: Exp 1 Ln GC

description: Chudakov


title: SW620 DSM120-2

description:
Library name: SW620 DSM120-2
column name : DSM120_2

value: treated with DSM 120µM


title: Wild-type, rep4


title: HLF DMSO replicate 3

first: Jesse

last: Raab

address: 120 Mason Farm Rd

department: Genetics

institute: University of North Carolina Chapel Hill

description: Library name: HLF_DMSO_3

data_processing:
salmon 1.10.0 was used to generate count tables salmon quant  - l A --gcBias --seqBias --posBias
all processing steps are implemented in github.com/raab-lab/rnaseq
Assembly: hg38
Supplementary files format and content: TSV files of raw count fiels used for DESEq2

source_name: Liver tumor

growth_protocol: HLF and PLC/PRF5 cells are grown in DMEM + 10% FBS + penicillin and streptomycin.

extract_protocol: library was generated using Kapa mRNA Hyperprep kit

treatment_protocol: HLF and PLC/PRF5 cells were treated with 5uM SNDX-5613 or DMSO for 24 hours or menin KO cell lines were generated by CRISPR

value: Liver tumor

value: HLF

value: DMSO


title: Wild-type, rep3

value: Prefrontal cortex


title: SW620 0AB -2

description:
Library name: SW620 0AB -2
column name : 0AB_2


title: Exp 1 Ln PB

description: Chudakov


title: Wild-type, rep2


title: HLF menin KO replicate 2

description: Library name: HLF_MEN1-KO_2

value: menin-ko


title: hTau, rep3

value: hTau


title: SW620 DSM120-3

description:
Library name: SW620 DSM120-3
column name : DSM120_3


title: HLF menin KO replicate 1

description: Library name: HLF_MEN1-KO_1


title: SW620 DSM120-1

description:
Library name: SW620 DSM120-1
column name : DSM120_1


title: SW620 SM120-1

description:
Library name: SW620 SM120-1
column name : SM120_1


title: HLF SNDX replicate 3

description: Library name: HLF_SNDX_3

value: SNDX


title: sid2, mock, rep4

organism: Arabidopsis thaliana

value: Roots

value: water control


title: SW620 0AB -1

description:
Library name: SW620 0AB -1
column name : 0AB_1

value: Colon cancer cells

value: WT


title: HLF non targeting replicate 2

description: Library name: HLF_NTC_2


title: Exp 1 Lung GC-like

description: Chudakov

value: lung

value: GC-like B cell


title: sid2, mock, rep2


title: decidual tissue from healthy control who terminated their pregnancies for non-medical reasons  (HC)  -4

city: Jinan

first: Yu

last: Xia

state: Shandong

address: 324 Jingwu Street

department: Department of Central Laboratory

institute: Shandong Provincial Hospital affiliated to Shandong University

description: Library name: HC-4

data_processing:
Raw reads were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat 2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Assembly: hg38
Supplementary files format and content: csv files include FPKM values for each sample

source_name: decidua

extract_protocol:
Total RNA was extracted using using Trizol reagent following the manufacturer's protocol.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions.

value: decidua


title: HLF non targeting replicate 1

description: Library name: HLF_NTC_1


title: heart,MI3d,WT

city: Shanghai

first: Sheng

last: Xu

state: Shanghai

address: No. 301, Yanchang Middle Road

institute: The NO.10 People's Hospital of Shanghai

data_processing:
The 10× Cell Ranger (v3.1.0) was used to align the raw data to the mouse reference transcriptome (mm10) and generate gene-cell count matrices.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: left ventricular tissues

extract_protocol:
Left ventricular (LV) tissues were isolated 3 days after MI, minced and washed in ice-cold RPMI1640 and digested using Multi-tissue dissociation kit 2 (Miltenyi, 130-110-203) according to the manufacturer’s protocol. Digested cells were filtered and centrifuged to obtain a single-cell suspension. Cell debris  were removed using Debris Removal Solution (Miltenyi Biotec,130-109-398). Cells were washed in the RPMI1640 and then resuspended at 1×106 cells/ml in 1×PBS and 0.04%BSA.
Cells were loaded into Chromium microfluidic chips and barcoded within a 10x Chromium Controller (10x Genomics). The single-cell transcriptome was reverse-transcribed into a cDNA library which contain 10X cell barcodes and unique molecular identifiers constructed with reagents from the Chromium Next GEM Single Cell 5' Library & Gel Bead Kit v1.1 (10x Genomics,1000165) according to the manufacturer’s protocol.

value: left ventricular tissues

value: MI


title: HLF SNDX replicate 1

description: Library name: HLF_SNDX_1


title: decidual tissue from healthy control who terminated their pregnancies for non-medical reasons  (HC)  -3

description: Library name: HC-3


title: sid2, mock, rep1


title: HLF DMSO replicate 1

description: Library name: HLF_DMSO_1


title: heart,MI3d,KLF9-/-


title: decidual tissue from healthy control who terminated their pregnancies for non-medical reasons  (HC)  -2

description: Library name: HC-2


title: coi1, mock, rep4

value: outcrossed coi1-t from heterozygous COI1/coi1-t plants


title: decidual tissue from healthy control who terminated their pregnancies for non-medical reasons  (HC)  -1

description: Library name: HC-1


title: HLF DMSO replicate 2

description: Library name: HLF_DMSO_2

value: Liver tumor


title: Bone marrow, sorted LSK, Vav1-iCre Control x Jak2 V617F/+

city: Saint Louis

first: Stephen

last: Oh

state: MO

address: Room 8834, 320 S. Euclid Ave, CSRB building

institute: Washington University School of Medicine in St. Louis

description: 10x Genomics

data_processing:
CellRanger (10x Genomics, version 3.0.1) was used for transcript alignment, counting, and inter-library normalization of single cell samples.
Aggr function was used to merge genotype libraries into a single dataset, and initial visualization utilized LoupeBrowser version 6.0 (10x Genomics).
Seurat version 4.0.0: Cells with <500 or >7500 genes captured per cell were removed from analysis, as were cells with 10% or more mitochondrial transcripts.
RNA reads were normalized with LogNormalize and data were scaled using Seurat 4.0.0..
Unsupervised cell clustering was performed using an unanchored version of the uniform manifold approximation and projection (UMAP) algorithm in Seurat: See Fisher et al., 2023 Experimental Hematology, Complementary and countervailing actions of Jak2 and Ikk2 in hematopoiesis in mice.
Assembly: mm10-2020A (scRNA-Seq)
Supplementary files format and content: barcodes, features, and matrix files

source_name: Bone marrow

extract_protocol:
Bone marrow cells from 5 mice of each genotype were pooled, and Kit+ cells were purified using Cd117 microbead kit on AutoMACS separator (Miltenyi). Kit+ cells were flow sorted on MoFlo sorter (Beckman Coulter), to obtain LSK (Lin-Kit+Sca1+) cells. Sorted cells were resuspended at 1000/μL density in 1x PBS with 0.04% BSA. Cells were subjected to droplet bead capture, followed by cell lysis, reverse transcription, and amplification according to TotalSeqA protocol from 10X Genomics (Pleasanton, CA).
TotalSeqA protocol from 10X Genomics (Pleasanton, CA).

value: Bone marrow

value: Vav1-iCre (B6.Cg-Tg(Vav1-cre)A2Kio/J)/+ x Jak2 V617F/+

value: Flow sorted LSK (Lin-Sca-1+Kit+)

value: Vav1-iCre/+, Jak2 V617F flox/+

value: 8-12 weeks age mice, extracted bone marrow, Cd117+ bead purified, flow sorted for LSK


title: Bone marrow, sorted LSK, Vav1-iCre Control x Jak2 V617F/+, Ikk2-CA/+

description: 10x Genomics

value: Vav1-iCre (B6.Cg-Tg(Vav1-cre)A2Kio/J)/+ x Jak2 V617F/+, Ikk2-CA (R26StopFLikk2ca)/+

value: Vav1-iCre/+, Jak2 V617F flox/+, Ikk2-CA flox/+


title: Wild-type, rep1

value: Prefrontal cortex


title: HLF SNDX replicate 2

description: Library name: HLF_SNDX_2

value: HLF

value: SNDX


title: decidual tissue from obstetric antiphospholipid syndrome (OAPS) patient -4

description: Library name: OAPS-4


title: HLF menin KO replicate 3

description: Library name: HLF_MEN1-KO_3

value: menin-ko


title: Bone marrow, sorted LSK, Vav1-iCre x Ikk2-CA flox/+

description: 10x Genomics

value: Vav1-iCre (B6.Cg-Tg(Vav1-cre)A2Kio/J)/+ x Ikk2-CA (R26StopFLikk2ca)/+

value: Vav1-iCre/+, Ikk2-CA flox/+


title: coi1, mock, rep2

value: Roots

value: water control


title: coi1, mock, rep3

value: outcrossed coi1-t from heterozygous COI1/coi1-t plants


title: sid2, mock, rep3


title: HLF non targeting replicate 3

description: Library name: HLF_NTC_3

value: Liver tumor

value: WT


title: Bone marrow, sorted LSK, Vav1-iCre Control

description: 10x Genomics

value: Bone marrow

value: Vav1-iCre (B6.Cg-Tg(Vav1-cre)A2Kio/J)/+


title: PLC/PRF/5 3D Initial Rep 3

description:
Library name: MD0040
Other: amplicon sequencing containing gRNA
Columns for processed data file; id = Gene ID; Score_HLF_2D_vs_t0_818 = RRA for 2D vs initial HLF; Score_HLF_3D_vs_t0_818 = RRA for 3D vs initial HLF; Score_PLCPRF5_2D_vs_t0 = RRA for 2D vs initial PLCPRF5 ; Score_PLCPRF5_3D_vs_t0_0042 = RRA for 3D vs initial PLCPRF5; Score_PLCPRF5_2D_vs_3D_8440042 = RRA for 2D vs 3D end for PLCPRF5; Score_HLF_2D_vs_3D_818 = RRA for 2D vs 3D HLF end point; Score_HLF_SNDX_vs_T0_885 = RRA for SNDX vs T0 in HLF; Score_HLF_DMSO_vs_t0_885 = RRA for DMSO vs T0 in HLF; Score_HLF_SNDX_vs_DMSO_885 = RRA SNDX vs DMSO in HLF at endpoint. FDR_HLF_2D_vs_t0_818 = FDR for 2D vs initial HLF; FDR_HLF_3D_vs_t0_818 = FDR for 3D vs initial HLF;FDR_PLCPRF5_2D_vs_t0 = FDR for 2D vs initial PLCPRF5 ;FDR_PLCPRF5_3D_vs_t0_0042 = FDR for 3D vs initial PLCPRF5; FDR_PLCPRF5_2D_vs_3D_8440042 = FDR for 2D vs 3D end for PLCPRF5; FDR_HLF_2D_vs_3D_818 = FDR for 2D vs 3D HLF end point; FDR_HLF_SNDX_vs_T0_885 = FDR for SNDX vs T0 in HLF; FDR_HLF_DMSO_vs_t0_885 = FDR for DMSO vs T0 in HLF; FDR_HLF_SNDX_vs_DMSO_885 =FDR SNDX vs DMSO in HLF at endpoint.

library_source: other

data_processing:
Data were processed using the MaGeck Pipeline.
mageck count --norm-method none
mageck test --control-sgrna --norm-method control
Pipeline implemented in Nextflow at github.com/raab-lab/crispr-screens
Supplementary files format and content: processed files contain RRA and FDR values for each gene in library for each comparison.
Library strategy: CRISPR Screen

molecule: other

source_name: Liver cancer cells

growth_protocol: HLF cells were grown in DMEM + 10% FCS + penicillin and streptomycin. PLC/PRF/5 were grown in RPMI + 10% FCS + P/s. 2D growth was on normal tissue culture plastic dishes. 3D growth was media containin 0.75% methylcelluose and were grown on ultra-low attachment plasticware.

extract_protocol:
gDNA was harvested using
libraries were constructed using primers to amplify the gRNAs from genomic DNA and add indexes and illumina sequencing adapters as described in PMCID: PMC5526071

treatment_protocol: where indicated cells were treated with 5uM SNDX-5613

value: Liver cancer cells

value: None 3D


title: coi1, mock, rep1


title: decidual tissue from obstetric antiphospholipid syndrome (OAPS) patient -2

description: Library name: OAPS-2

value: decidua


title: WTcoi1, mock, rep4

value: outcrossed wild-type from heterozygous COI1/coi1-t plants


title: Pten- 4w

city: New York

first: Erik

last: Ladewig

state: New York

address: 435 East 65th Street

institute: MSKCC

description: 10x Genomics

library_source: genomic single cell

data_processing:
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
Supplementary files format and content: barcodes.tsv, features.tsv, matrix.mtx

source_name: prostate

growth_protocol: DMEM, 15% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
For scATAC-seq, dorsal-lateral lobes of mouse prostates from indicated age were freshly dissociated (described above), and flow sorted for live single cells using DAPI. Fresh nuclei were isolated before processing for 10X Genomics Chromium single cell multiome ATAC + gene expression sequencing following manufacture’s instructions.
Mouse prostates were harvested and subsequently digested with collagenase type II (Gibco) for 2 hrs at 37 °C, followed by TrypLE (Gibco) digestion at 37 °C until a single-cell suspension was obtained. Digestions were supplemented with Y-27632 (10 μM) to inhibit anoikis and filtered to obtain single cell suspension.
Murine prostate organoid culture was established and maintained under standard conditions as described previously122,123. Briefly, dissociated prostatic epithelial cells were embedded in 20-µl drops of Matrigel (Corning) and overlaid with mouse prostate organoid medium. Organoids were passaged by mechanical splitting by repetitively passing through a 200-µl pipette tip or by trypsinization using TryplE. For lineage marker analysis, organoids were trypsinized into single cells and seeded at 20,000-50,000 cells per well of a 12-well plate in the absence of EGF (counted as day 0). For EdU pulse-chase experiments, the organoid culture was incubated with EdU (10 µM, Theremo Fisher) for 2 hrs before harvesting (pulse) or wash-off and re-seeding (chase). To compare cell fate from reporter cells, basal and luminal cells were sorted based on single-positive reporter signals and seeded at equal cell number between sgNT and sgERG in the absence of EGF (counted as day 0). Basal cells were seeded at 20,000-50,000 cells per well of a 12-well plate; less luminal cells were seeded (5,000-10,000 per well) due to a low recovery from the sgERG group.

value: prostate

value: Pten-


title: PLC/PRF/5 3D Initial Rep 2

description:
Library name: MD0039
Other: amplicon sequencing containing gRNA
Columns for processed data file; id = Gene ID; Score_HLF_2D_vs_t0_818 = RRA for 2D vs initial HLF; Score_HLF_3D_vs_t0_818 = RRA for 3D vs initial HLF; Score_PLCPRF5_2D_vs_t0 = RRA for 2D vs initial PLCPRF5 ; Score_PLCPRF5_3D_vs_t0_0042 = RRA for 3D vs initial PLCPRF5; Score_PLCPRF5_2D_vs_3D_8440042 = RRA for 2D vs 3D end for PLCPRF5; Score_HLF_2D_vs_3D_818 = RRA for 2D vs 3D HLF end point; Score_HLF_SNDX_vs_T0_885 = RRA for SNDX vs T0 in HLF; Score_HLF_DMSO_vs_t0_885 = RRA for DMSO vs T0 in HLF; Score_HLF_SNDX_vs_DMSO_885 = RRA SNDX vs DMSO in HLF at endpoint. FDR_HLF_2D_vs_t0_818 = FDR for 2D vs initial HLF; FDR_HLF_3D_vs_t0_818 = FDR for 3D vs initial HLF;FDR_PLCPRF5_2D_vs_t0 = FDR for 2D vs initial PLCPRF5 ;FDR_PLCPRF5_3D_vs_t0_0042 = FDR for 3D vs initial PLCPRF5; FDR_PLCPRF5_2D_vs_3D_8440042 = FDR for 2D vs 3D end for PLCPRF5; FDR_HLF_2D_vs_3D_818 = FDR for 2D vs 3D HLF end point; FDR_HLF_SNDX_vs_T0_885 = FDR for SNDX vs T0 in HLF; FDR_HLF_DMSO_vs_t0_885 = FDR for DMSO vs T0 in HLF; FDR_HLF_SNDX_vs_DMSO_885 =FDR SNDX vs DMSO in HLF at endpoint.


title: Erg+Pten- 4w

description: 10x Genomics

value: Erg+Pten-


title: PLC/PRF/5 3D Initial Rep 1

description:
Library name: MD0038
Other: amplicon sequencing containing gRNA
Columns for processed data file; id = Gene ID; Score_HLF_2D_vs_t0_818 = RRA for 2D vs initial HLF; Score_HLF_3D_vs_t0_818 = RRA for 3D vs initial HLF; Score_PLCPRF5_2D_vs_t0 = RRA for 2D vs initial PLCPRF5 ; Score_PLCPRF5_3D_vs_t0_0042 = RRA for 3D vs initial PLCPRF5; Score_PLCPRF5_2D_vs_3D_8440042 = RRA for 2D vs 3D end for PLCPRF5; Score_HLF_2D_vs_3D_818 = RRA for 2D vs 3D HLF end point; Score_HLF_SNDX_vs_T0_885 = RRA for SNDX vs T0 in HLF; Score_HLF_DMSO_vs_t0_885 = RRA for DMSO vs T0 in HLF; Score_HLF_SNDX_vs_DMSO_885 = RRA SNDX vs DMSO in HLF at endpoint. FDR_HLF_2D_vs_t0_818 = FDR for 2D vs initial HLF; FDR_HLF_3D_vs_t0_818 = FDR for 3D vs initial HLF;FDR_PLCPRF5_2D_vs_t0 = FDR for 2D vs initial PLCPRF5 ;FDR_PLCPRF5_3D_vs_t0_0042 = FDR for 3D vs initial PLCPRF5; FDR_PLCPRF5_2D_vs_3D_8440042 = FDR for 2D vs 3D end for PLCPRF5; FDR_HLF_2D_vs_3D_818 = FDR for 2D vs 3D HLF end point; FDR_HLF_SNDX_vs_T0_885 = FDR for SNDX vs T0 in HLF; FDR_HLF_DMSO_vs_t0_885 = FDR for DMSO vs T0 in HLF; FDR_HLF_SNDX_vs_DMSO_885 =FDR SNDX vs DMSO in HLF at endpoint.


title: Pten- 3m

description: 10x Genomics


title: decidual tissue from obstetric antiphospholipid syndrome (OAPS) patient -1

description: Library name: OAPS-1


title: WTcoi1, mock, rep2


title: PLC/PRF/5 3D Final Rep 3

description:
Library name: MD0043
Other: amplicon sequencing containing gRNA
Columns for processed data file; id = Gene ID; Score_HLF_2D_vs_t0_818 = RRA for 2D vs initial HLF; Score_HLF_3D_vs_t0_818 = RRA for 3D vs initial HLF; Score_PLCPRF5_2D_vs_t0 = RRA for 2D vs initial PLCPRF5 ; Score_PLCPRF5_3D_vs_t0_0042 = RRA for 3D vs initial PLCPRF5; Score_PLCPRF5_2D_vs_3D_8440042 = RRA for 2D vs 3D end for PLCPRF5; Score_HLF_2D_vs_3D_818 = RRA for 2D vs 3D HLF end point; Score_HLF_SNDX_vs_T0_885 = RRA for SNDX vs T0 in HLF; Score_HLF_DMSO_vs_t0_885 = RRA for DMSO vs T0 in HLF; Score_HLF_SNDX_vs_DMSO_885 = RRA SNDX vs DMSO in HLF at endpoint. FDR_HLF_2D_vs_t0_818 = FDR for 2D vs initial HLF; FDR_HLF_3D_vs_t0_818 = FDR for 3D vs initial HLF;FDR_PLCPRF5_2D_vs_t0 = FDR for 2D vs initial PLCPRF5 ;FDR_PLCPRF5_3D_vs_t0_0042 = FDR for 3D vs initial PLCPRF5; FDR_PLCPRF5_2D_vs_3D_8440042 = FDR for 2D vs 3D end for PLCPRF5; FDR_HLF_2D_vs_3D_818 = FDR for 2D vs 3D HLF end point; FDR_HLF_SNDX_vs_T0_885 = FDR for SNDX vs T0 in HLF; FDR_HLF_DMSO_vs_t0_885 = FDR for DMSO vs T0 in HLF; FDR_HLF_SNDX_vs_DMSO_885 =FDR SNDX vs DMSO in HLF at endpoint.


title: WildType 3m

description: 10x Genomics

value: WildType


title: WTcoi1, mock, rep3


title: CD8 Donor 6 secretory lgA 20h

city: Silver Spring

first: Frederick

middle: Curtis

last: Mills

state: Maryland

address: 10903 New Hampshire Avenue

department: CDER/OPQR/OPQRIV

institute: FDA

description: 150 x 150 bp paired end reads

data_processing:
Sequencing reads were aligned to the Homo sapiens UCSC hg19 (RefSeq and Gencode gene annotations) using BaseSpace Onsite (Illumina). Gene level counts were determined using BaseSpace TopHat Alignment v1.0.1. Read mapping was done using TopHat 2 Aligner and FPKM estimation of reference genes and transcripts were performed using Cufflinks 2.
Assembly: hg19
Supplementary files format and content: Treg FPKM, CD8 FPKM  estimation of reference genes and transcripts were performed using Cufflinks 2.
Supplementary files format and content: Treg DGE TopGenes,CD8 DGE TopGenes .xlsx format, Genesretained if ≥1.5-fold induced by both stim AND p value ≤0.1 for both FCRL3 mAb Ab and secretory lgA stimulation

source_name: Peripheral blood

extract_protocol:
Cell pellets were stored at 4ºC with 50 μl of RNAlater (Invitrogen) until RNA purified using the RNAqueous-4PCR DNA-free RNA isolation kit following the provided protocol.  0.1-0.5 µg of total RNA pers sample was used after removal of ribosomal RNA using the Next rRNA depletion kit (New England Biolabs).
RNA samples passed quality control and proceeded to library preparation using TruSeq Stranded mRNA library prep kit (Illumina) with IDT for Illumina - TruSeq RNA UD indexes (Illumina, 20022371) following manufacturer’s protocol. Libraries were amplified using 12 cycles of PCR
RNA seq libraries were amplified using 12 cycles of PCR, pooled, and sequenced on Illumina NovaSeq 6000 with 150x150 bp paired-end reads

treatment_protocol: Sorted CD4+CD25hiCD127dim CD14- Treg cells or CD8+CCR7-CD45 RO- TTE cells  were incubated with 150 μg/mL biotinylated secretory lgA (Athens Research) or 20 µg/ml biotinylated FCRL3 mAb Ab clone 6F2 10 for 10 minutes at 4°C, then washed once.  secretory lgA and FCRL3 mAb Ab were biotinylated using EZ-Link Sulfo-NHS-LC-Biotin (Thermo Fisher).  Biotinylated reagents were crosslinked for 15 minutes at 37°C using 5 μg/mL streptavidin (Southern Biotech).  CD4+ Treg cells were cultured in X-Vivo 20 medium (Lonza), while CD8+ TTE cells were cultured in RPMI with 10% fetal calf serum, glutamine, nonessential amino acids, and sodium pyruvate for 4 hours or 20 hours at 37°C.

value: Peripheral blood

value: CD8 effector T

tag: individual

value: CD8 Donor 6

value: secretory lgA 20h


title: aos, mock, rep4

value: Roots

value: outcrossed aos from heterozygous AOS/aos plants

value: water control


title: Erg+Pten- 3m

description: 10x Genomics


title: decidual tissue from obstetric antiphospholipid syndrome (OAPS) patient -3

description: Library name: OAPS-3


title: CD8 Donor 6 FCRL3 mAb 20h

description: 150 x 150 bp paired end reads

value: FCRL3 mAb 20h


title: CD8 Donor 6 SA control 4h

description: 150 x 150 bp paired end reads

value: SA control 4h


title: aos, mock, rep3


title: Erg+Pten- 6m

description: 10x Genomics


title: PLC/PRF/5 3D Final Rep 1

description:
Library name: MD0041
Other: amplicon sequencing containing gRNA
Columns for processed data file; id = Gene ID; Score_HLF_2D_vs_t0_818 = RRA for 2D vs initial HLF; Score_HLF_3D_vs_t0_818 = RRA for 3D vs initial HLF; Score_PLCPRF5_2D_vs_t0 = RRA for 2D vs initial PLCPRF5 ; Score_PLCPRF5_3D_vs_t0_0042 = RRA for 3D vs initial PLCPRF5; Score_PLCPRF5_2D_vs_3D_8440042 = RRA for 2D vs 3D end for PLCPRF5; Score_HLF_2D_vs_3D_818 = RRA for 2D vs 3D HLF end point; Score_HLF_SNDX_vs_T0_885 = RRA for SNDX vs T0 in HLF; Score_HLF_DMSO_vs_t0_885 = RRA for DMSO vs T0 in HLF; Score_HLF_SNDX_vs_DMSO_885 = RRA SNDX vs DMSO in HLF at endpoint. FDR_HLF_2D_vs_t0_818 = FDR for 2D vs initial HLF; FDR_HLF_3D_vs_t0_818 = FDR for 3D vs initial HLF;FDR_PLCPRF5_2D_vs_t0 = FDR for 2D vs initial PLCPRF5 ;FDR_PLCPRF5_3D_vs_t0_0042 = FDR for 3D vs initial PLCPRF5; FDR_PLCPRF5_2D_vs_3D_8440042 = FDR for 2D vs 3D end for PLCPRF5; FDR_HLF_2D_vs_3D_818 = FDR for 2D vs 3D HLF end point; FDR_HLF_SNDX_vs_T0_885 = FDR for SNDX vs T0 in HLF; FDR_HLF_DMSO_vs_t0_885 = FDR for DMSO vs T0 in HLF; FDR_HLF_SNDX_vs_DMSO_885 =FDR SNDX vs DMSO in HLF at endpoint.

value: Liver cancer cells


title: PLC/PRF/5 2D Initial Rep 3

description:
Library name: PLCPRF5_CRISPR_d0_3
Other: amplicon sequencing containing gRNA
Columns for processed data file; id = Gene ID; Score_HLF_2D_vs_t0_818 = RRA for 2D vs initial HLF; Score_HLF_3D_vs_t0_818 = RRA for 3D vs initial HLF; Score_PLCPRF5_2D_vs_t0 = RRA for 2D vs initial PLCPRF5 ; Score_PLCPRF5_3D_vs_t0_0042 = RRA for 3D vs initial PLCPRF5; Score_PLCPRF5_2D_vs_3D_8440042 = RRA for 2D vs 3D end for PLCPRF5; Score_HLF_2D_vs_3D_818 = RRA for 2D vs 3D HLF end point; Score_HLF_SNDX_vs_T0_885 = RRA for SNDX vs T0 in HLF; Score_HLF_DMSO_vs_t0_885 = RRA for DMSO vs T0 in HLF; Score_HLF_SNDX_vs_DMSO_885 = RRA SNDX vs DMSO in HLF at endpoint. FDR_HLF_2D_vs_t0_818 = FDR for 2D vs initial HLF; FDR_HLF_3D_vs_t0_818 = FDR for 3D vs initial HLF;FDR_PLCPRF5_2D_vs_t0 = FDR for 2D vs initial PLCPRF5 ;FDR_PLCPRF5_3D_vs_t0_0042 = FDR for 3D vs initial PLCPRF5; FDR_PLCPRF5_2D_vs_3D_8440042 = FDR for 2D vs 3D end for PLCPRF5; FDR_HLF_2D_vs_3D_818 = FDR for 2D vs 3D HLF end point; FDR_HLF_SNDX_vs_T0_885 = FDR for SNDX vs T0 in HLF; FDR_HLF_DMSO_vs_t0_885 = FDR for DMSO vs T0 in HLF; FDR_HLF_SNDX_vs_DMSO_885 =FDR SNDX vs DMSO in HLF at endpoint.

value: None 2D


title: CD8 Donor 6 secretory lgA 4h

description: 150 x 150 bp paired end reads

value: secretory lgA 4h


title: Pten- 6m

description: 10x Genomics


title: aos, mock, rep2


title: aos, mock, rep1


title: CD8 Donor 6 FCRL3 mAb 4h

description: 150 x 150 bp paired end reads

value: FCRL3 mAb 4h


title: WTaos, mock, rep4

value: outcrossed wild-type from heterozygous AOS/aos plants


title: Pten- 3 months 2

description: 10x Genomics

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

extract_protocol:
For scRNA-seq, whole mouse prostates from indicated age were freshly dissociated (described above), and flow sorted for live single cells using DAPI, before processing for scRNA-seq using 10X Genomics Chromium following manufacture’s instructions.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: prostate

value: Pten-

value: 3 months old


title: Pten- 3 months 1

description: 10x Genomics


title: PLC/PRF/5 2D Initial Rep 1

description:
Library name: PLCPRF5_CRISPR_d0_1
Other: amplicon sequencing containing gRNA
Columns for processed data file; id = Gene ID; Score_HLF_2D_vs_t0_818 = RRA for 2D vs initial HLF; Score_HLF_3D_vs_t0_818 = RRA for 3D vs initial HLF; Score_PLCPRF5_2D_vs_t0 = RRA for 2D vs initial PLCPRF5 ; Score_PLCPRF5_3D_vs_t0_0042 = RRA for 3D vs initial PLCPRF5; Score_PLCPRF5_2D_vs_3D_8440042 = RRA for 2D vs 3D end for PLCPRF5; Score_HLF_2D_vs_3D_818 = RRA for 2D vs 3D HLF end point; Score_HLF_SNDX_vs_T0_885 = RRA for SNDX vs T0 in HLF; Score_HLF_DMSO_vs_t0_885 = RRA for DMSO vs T0 in HLF; Score_HLF_SNDX_vs_DMSO_885 = RRA SNDX vs DMSO in HLF at endpoint. FDR_HLF_2D_vs_t0_818 = FDR for 2D vs initial HLF; FDR_HLF_3D_vs_t0_818 = FDR for 3D vs initial HLF;FDR_PLCPRF5_2D_vs_t0 = FDR for 2D vs initial PLCPRF5 ;FDR_PLCPRF5_3D_vs_t0_0042 = FDR for 3D vs initial PLCPRF5; FDR_PLCPRF5_2D_vs_3D_8440042 = FDR for 2D vs 3D end for PLCPRF5; FDR_HLF_2D_vs_3D_818 = FDR for 2D vs 3D HLF end point; FDR_HLF_SNDX_vs_T0_885 = FDR for SNDX vs T0 in HLF; FDR_HLF_DMSO_vs_t0_885 = FDR for DMSO vs T0 in HLF; FDR_HLF_SNDX_vs_DMSO_885 =FDR SNDX vs DMSO in HLF at endpoint.


title: PLC/PRF/5 2D Initial Rep 2

description:
Library name: PLCPRF5_CRISPR_d0_2
Other: amplicon sequencing containing gRNA
Columns for processed data file; id = Gene ID; Score_HLF_2D_vs_t0_818 = RRA for 2D vs initial HLF; Score_HLF_3D_vs_t0_818 = RRA for 3D vs initial HLF; Score_PLCPRF5_2D_vs_t0 = RRA for 2D vs initial PLCPRF5 ; Score_PLCPRF5_3D_vs_t0_0042 = RRA for 3D vs initial PLCPRF5; Score_PLCPRF5_2D_vs_3D_8440042 = RRA for 2D vs 3D end for PLCPRF5; Score_HLF_2D_vs_3D_818 = RRA for 2D vs 3D HLF end point; Score_HLF_SNDX_vs_T0_885 = RRA for SNDX vs T0 in HLF; Score_HLF_DMSO_vs_t0_885 = RRA for DMSO vs T0 in HLF; Score_HLF_SNDX_vs_DMSO_885 = RRA SNDX vs DMSO in HLF at endpoint. FDR_HLF_2D_vs_t0_818 = FDR for 2D vs initial HLF; FDR_HLF_3D_vs_t0_818 = FDR for 3D vs initial HLF;FDR_PLCPRF5_2D_vs_t0 = FDR for 2D vs initial PLCPRF5 ;FDR_PLCPRF5_3D_vs_t0_0042 = FDR for 3D vs initial PLCPRF5; FDR_PLCPRF5_2D_vs_3D_8440042 = FDR for 2D vs 3D end for PLCPRF5; FDR_HLF_2D_vs_3D_818 = FDR for 2D vs 3D HLF end point; FDR_HLF_SNDX_vs_T0_885 = FDR for SNDX vs T0 in HLF; FDR_HLF_DMSO_vs_t0_885 = FDR for DMSO vs T0 in HLF; FDR_HLF_SNDX_vs_DMSO_885 =FDR SNDX vs DMSO in HLF at endpoint.


title: CD8 Donor 6 SA control 20h

description: 150 x 150 bp paired end reads

value: Peripheral blood

value: SA control 20h


title: WTaos, mock, rep3


title: CD8 Donor 5 secretory lgA 20h

description: 150 x 150 bp paired end reads

value: CD8 effector T

value: CD8 Donor 5


title: CD8 Donor 5 SA control 20h

description: 150 x 150 bp paired end reads


title: Erg+Pten- 3 months 2

description: 10x Genomics

value: Erg+Pten-


title: WTaos, mock, rep2

value: Roots


title: PLC/PRF/5 3D Final Rep 2

description:
Library name: MD0042
Other: amplicon sequencing containing gRNA
Columns for processed data file; id = Gene ID; Score_HLF_2D_vs_t0_818 = RRA for 2D vs initial HLF; Score_HLF_3D_vs_t0_818 = RRA for 3D vs initial HLF; Score_PLCPRF5_2D_vs_t0 = RRA for 2D vs initial PLCPRF5 ; Score_PLCPRF5_3D_vs_t0_0042 = RRA for 3D vs initial PLCPRF5; Score_PLCPRF5_2D_vs_3D_8440042 = RRA for 2D vs 3D end for PLCPRF5; Score_HLF_2D_vs_3D_818 = RRA for 2D vs 3D HLF end point; Score_HLF_SNDX_vs_T0_885 = RRA for SNDX vs T0 in HLF; Score_HLF_DMSO_vs_t0_885 = RRA for DMSO vs T0 in HLF; Score_HLF_SNDX_vs_DMSO_885 = RRA SNDX vs DMSO in HLF at endpoint. FDR_HLF_2D_vs_t0_818 = FDR for 2D vs initial HLF; FDR_HLF_3D_vs_t0_818 = FDR for 3D vs initial HLF;FDR_PLCPRF5_2D_vs_t0 = FDR for 2D vs initial PLCPRF5 ;FDR_PLCPRF5_3D_vs_t0_0042 = FDR for 3D vs initial PLCPRF5; FDR_PLCPRF5_2D_vs_3D_8440042 = FDR for 2D vs 3D end for PLCPRF5; FDR_HLF_2D_vs_3D_818 = FDR for 2D vs 3D HLF end point; FDR_HLF_SNDX_vs_T0_885 = FDR for SNDX vs T0 in HLF; FDR_HLF_DMSO_vs_t0_885 = FDR for DMSO vs T0 in HLF; FDR_HLF_SNDX_vs_DMSO_885 =FDR SNDX vs DMSO in HLF at endpoint.

value: None 3D


title: PLC/PRF/5 2D Final Rep 2

description:
Library name: PLCPRF5_CRISPR_2D_d28_DMSO2
Other: amplicon sequencing containing gRNA
Columns for processed data file; id = Gene ID; Score_HLF_2D_vs_t0_818 = RRA for 2D vs initial HLF; Score_HLF_3D_vs_t0_818 = RRA for 3D vs initial HLF; Score_PLCPRF5_2D_vs_t0 = RRA for 2D vs initial PLCPRF5 ; Score_PLCPRF5_3D_vs_t0_0042 = RRA for 3D vs initial PLCPRF5; Score_PLCPRF5_2D_vs_3D_8440042 = RRA for 2D vs 3D end for PLCPRF5; Score_HLF_2D_vs_3D_818 = RRA for 2D vs 3D HLF end point; Score_HLF_SNDX_vs_T0_885 = RRA for SNDX vs T0 in HLF; Score_HLF_DMSO_vs_t0_885 = RRA for DMSO vs T0 in HLF; Score_HLF_SNDX_vs_DMSO_885 = RRA SNDX vs DMSO in HLF at endpoint. FDR_HLF_2D_vs_t0_818 = FDR for 2D vs initial HLF; FDR_HLF_3D_vs_t0_818 = FDR for 3D vs initial HLF;FDR_PLCPRF5_2D_vs_t0 = FDR for 2D vs initial PLCPRF5 ;FDR_PLCPRF5_3D_vs_t0_0042 = FDR for 3D vs initial PLCPRF5; FDR_PLCPRF5_2D_vs_3D_8440042 = FDR for 2D vs 3D end for PLCPRF5; FDR_HLF_2D_vs_3D_818 = FDR for 2D vs 3D HLF end point; FDR_HLF_SNDX_vs_T0_885 = FDR for SNDX vs T0 in HLF; FDR_HLF_DMSO_vs_t0_885 = FDR for DMSO vs T0 in HLF; FDR_HLF_SNDX_vs_DMSO_885 =FDR SNDX vs DMSO in HLF at endpoint.


title: Wildtype 3 months

description: 10x Genomics

value: Wildtype


title: CD8 Donor 5 FCRL3 mAb 20h

description: 150 x 150 bp paired end reads

value: FCRL3 mAb 20h


title: PLC/PRF/5 2D Final Rep 1

description:
Library name: PLCPRF5_CRISPR_2D_d28_DMSO1
Other: amplicon sequencing containing gRNA
Columns for processed data file; id = Gene ID; Score_HLF_2D_vs_t0_818 = RRA for 2D vs initial HLF; Score_HLF_3D_vs_t0_818 = RRA for 3D vs initial HLF; Score_PLCPRF5_2D_vs_t0 = RRA for 2D vs initial PLCPRF5 ; Score_PLCPRF5_3D_vs_t0_0042 = RRA for 3D vs initial PLCPRF5; Score_PLCPRF5_2D_vs_3D_8440042 = RRA for 2D vs 3D end for PLCPRF5; Score_HLF_2D_vs_3D_818 = RRA for 2D vs 3D HLF end point; Score_HLF_SNDX_vs_T0_885 = RRA for SNDX vs T0 in HLF; Score_HLF_DMSO_vs_t0_885 = RRA for DMSO vs T0 in HLF; Score_HLF_SNDX_vs_DMSO_885 = RRA SNDX vs DMSO in HLF at endpoint. FDR_HLF_2D_vs_t0_818 = FDR for 2D vs initial HLF; FDR_HLF_3D_vs_t0_818 = FDR for 3D vs initial HLF;FDR_PLCPRF5_2D_vs_t0 = FDR for 2D vs initial PLCPRF5 ;FDR_PLCPRF5_3D_vs_t0_0042 = FDR for 3D vs initial PLCPRF5; FDR_PLCPRF5_2D_vs_3D_8440042 = FDR for 2D vs 3D end for PLCPRF5; FDR_HLF_2D_vs_3D_818 = FDR for 2D vs 3D HLF end point; FDR_HLF_SNDX_vs_T0_885 = FDR for SNDX vs T0 in HLF; FDR_HLF_DMSO_vs_t0_885 = FDR for DMSO vs T0 in HLF; FDR_HLF_SNDX_vs_DMSO_885 =FDR SNDX vs DMSO in HLF at endpoint.

value: Liver cancer cells


title: CD8 Donor 5 SA control 4h

description: 150 x 150 bp paired end reads

value: SA control 4h


title: HLF 3D Initial Rep 3

description:
Library name: HLF_CRISPR_3D_d0_3
Other: amplicon sequencing containing gRNA
Columns for processed data file; id = Gene ID; Score_HLF_2D_vs_t0_818 = RRA for 2D vs initial HLF; Score_HLF_3D_vs_t0_818 = RRA for 3D vs initial HLF; Score_PLCPRF5_2D_vs_t0 = RRA for 2D vs initial PLCPRF5 ; Score_PLCPRF5_3D_vs_t0_0042 = RRA for 3D vs initial PLCPRF5; Score_PLCPRF5_2D_vs_3D_8440042 = RRA for 2D vs 3D end for PLCPRF5; Score_HLF_2D_vs_3D_818 = RRA for 2D vs 3D HLF end point; Score_HLF_SNDX_vs_T0_885 = RRA for SNDX vs T0 in HLF; Score_HLF_DMSO_vs_t0_885 = RRA for DMSO vs T0 in HLF; Score_HLF_SNDX_vs_DMSO_885 = RRA SNDX vs DMSO in HLF at endpoint. FDR_HLF_2D_vs_t0_818 = FDR for 2D vs initial HLF; FDR_HLF_3D_vs_t0_818 = FDR for 3D vs initial HLF;FDR_PLCPRF5_2D_vs_t0 = FDR for 2D vs initial PLCPRF5 ;FDR_PLCPRF5_3D_vs_t0_0042 = FDR for 3D vs initial PLCPRF5; FDR_PLCPRF5_2D_vs_3D_8440042 = FDR for 2D vs 3D end for PLCPRF5; FDR_HLF_2D_vs_3D_818 = FDR for 2D vs 3D HLF end point; FDR_HLF_SNDX_vs_T0_885 = FDR for SNDX vs T0 in HLF; FDR_HLF_DMSO_vs_t0_885 = FDR for DMSO vs T0 in HLF; FDR_HLF_SNDX_vs_DMSO_885 =FDR SNDX vs DMSO in HLF at endpoint.

value: HLF


title: Wild type 0mM phosphate 4h Experiment 1 Replicate 3

first: Lori

middle: B

last: Huberman

address: 236 Tower Rd.

department: Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science

description: Library name: WT_0mM_Phosphate_4h_Exp1_Rep3

data_processing:
Illumina Casava1.8 software used for base calling
Sequenced reads were trimmed for adaptor sequence and aligned to the predicted transcripts from the N. crassa OR74A genome (v12) and TPMs were quantified with Salmon v. 1.4.0 with the --validateMappings setting.
Assembly: Neurospora crassa OR74A NC12
Supplementary files format and content: tab-deliminated text file with TPM values for each sample

organism: Neurospora crassa

source_name: Mycelia

growth_protocol: N. crassa conidia were inoculated into 3ml of Vogel's minimal media + 2% sucrose and incubated at 25C in constant light with constant shaking at 200rpm for 24h.

extract_protocol:
Mycelia were filtered using Whatman paper #1 and flash frozen using liquid nitrogen. RNA was isolated by beading beating in Trizol reagent and then cleaned up using the Qiagen RNeasy kit.
RNA were prepared for sequencing using poly-A enrichment and standard Illumina protocols

treatment_protocol: Mycelia were washed in 3ml Fries minimal media with 7mM phosphate (for 7mM phosphate) or Fries minimal media with 0mM phosphate (for 0mM phosphate) three times and then transferred to 3ml Fries minimal media with 7mM phosphate or 0mM phosphate as indicated and incubated at 25C in constant light with constant shaking at 200rpm for either 4h or 12h as indicated prior to harvesting for RNAseq.

value: Mycelia

value: FGSC 2489

value: Wild type mat A

value: 4h Fries minimal medium 0mM phosphate


title: 3T3_HiC_C5_rep1

city: Beijing

first: Jiacheng

last: Wang

address: No. 30 Shuangqing Road

institute: Tsinghua University

description: Hi-C on CBX7 overexpression stable cell line monoclone5 NIH3T3 cells

data_processing:
Paired-end RNA-seq reads were aligned to mm9 using HISAT2 v2.2.1 and FPKM value of each gene was calculated with StringTie v2.1.2.
The paired end ChIP-seq or CUT&Tag reads were mapped to mm9 using bowtie2 (version 2.2.5) with the parameters: -t -q -p 40 -N 1 -L 25 -X 2000 --no-mixed --no-discordant. The unmapped reads, not uniquely mapped, and duplicate reads were removed. Read coverages over the mm9 genome were calculated by bamCoverage from deepTools v3.3.1. The signal was then normalized by computing the number of reads per kilobase of bin per million reads sequenced (RPKM), followed by normalization using Z-score (whole genome 100bp bn with outliner regions excluded).
Hi-C data analysis was performed as previously described. Briefly, Hi-C libraries were aligned using HiCPro (version 2.10.0) with bowtie2 end-to-end algorithm and with the option ‘-very-sensitive’.
Assembly: mm9
Supplementary files format and content: Bigwig for ChIP-seq tracks, gene expression table for RNA-seq data, ValidPairs for Hi-C data

source_name: NIH 3T3

growth_protocol: NIH 3T3 cells were maintained in DMEM (SH30022.01, Hyclone) containing 5% FBS and 100 units/mL penicillin-100 ug/mL streptomycin solution (SV30010, HyClone).

extract_protocol:
sisHiC experiments were performed as previously described (Z. Du et al., 2017.). Briefly, 50,000-100,000 1% formaldehyde (Sigma) fixed cells were treated with 50 uL lysis buffer (10 mM Tris•HCl pH 7.4, 10 mM NaCl, 0.1 mM EDTA, 0.5 % NP-40 and freshly added ROCHE cOmplete protease inhibitor cocktail at 0.01 tablet/mL) in PCR tubes on ice for 50 min. Cell nucleus were pelleted through a centrifuge at 3000 rpm for 5 min. 10 uL 0.5% SDS was added and cells were incubated at 62°C for 10 min. 25 uL water and 5 uL 10% Triton X-100 were then added and cells were incubated at 37°C for 15 min. 5 uL NEBuffer 2 and 2 uL MboI were then added and digestion was performed overnight at 37°C with rotation. After chromatin digestion, biotin end repair, proximity ligation, and reverse crosslink were performed. The ligated DNA was then sheared and fragments with biotin were pulled down with straptavidin beads.
DNA was end-repaired, adenylated, and ligated to TruSeq sequencing adaptors. DNA was purified by AMPure beads or DNA purification kit according to the DNA amount. Library DNA was amplified by KAPA DNA polymerase. The amplified DNA was size selected using SPRI beads.

value: NIH 3T3

value: fibroblast

value: CBX7 OE


title: CD8 Donor 5 secretory lgA 4h

description: 150 x 150 bp paired end reads

value: Peripheral blood

value: CD8 effector T

value: secretory lgA 4h


title: Wild type 0mM phosphate 4h Experiment 1 Replicate 2

description: Library name: WT_0mM_Phosphate_4h_Exp1_Rep2


title: HLF 3D Intiial Rep 2

city: Chapel Hill

description:
Library name: HLF_CRISPR_3D_d0_2
Other: amplicon sequencing containing gRNA
Columns for processed data file; id = Gene ID; Score_HLF_2D_vs_t0_818 = RRA for 2D vs initial HLF; Score_HLF_3D_vs_t0_818 = RRA for 3D vs initial HLF; Score_PLCPRF5_2D_vs_t0 = RRA for 2D vs initial PLCPRF5 ; Score_PLCPRF5_3D_vs_t0_0042 = RRA for 3D vs initial PLCPRF5; Score_PLCPRF5_2D_vs_3D_8440042 = RRA for 2D vs 3D end for PLCPRF5; Score_HLF_2D_vs_3D_818 = RRA for 2D vs 3D HLF end point; Score_HLF_SNDX_vs_T0_885 = RRA for SNDX vs T0 in HLF; Score_HLF_DMSO_vs_t0_885 = RRA for DMSO vs T0 in HLF; Score_HLF_SNDX_vs_DMSO_885 = RRA SNDX vs DMSO in HLF at endpoint. FDR_HLF_2D_vs_t0_818 = FDR for 2D vs initial HLF; FDR_HLF_3D_vs_t0_818 = FDR for 3D vs initial HLF;FDR_PLCPRF5_2D_vs_t0 = FDR for 2D vs initial PLCPRF5 ;FDR_PLCPRF5_3D_vs_t0_0042 = FDR for 3D vs initial PLCPRF5; FDR_PLCPRF5_2D_vs_3D_8440042 = FDR for 2D vs 3D end for PLCPRF5; FDR_HLF_2D_vs_3D_818 = FDR for 2D vs 3D HLF end point; FDR_HLF_SNDX_vs_T0_885 = FDR for SNDX vs T0 in HLF; FDR_HLF_DMSO_vs_t0_885 = FDR for DMSO vs T0 in HLF; FDR_HLF_SNDX_vs_DMSO_885 =FDR SNDX vs DMSO in HLF at endpoint.


title: Wild type 0mM phosphate 4h Experiment 1 Replicate 1

description: Library name: WT_0mM_Phosphate_4h_Exp1_Rep1


title: CD8 Donor 4 SA control 20h

description: 150 x 150 bp paired end reads

value: CD8 Donor 4

value: SA control 20h


title: HLF 3D Initial Rep 1

description:
Library name: HLF_CRISPR_3D_d0_1
Other: amplicon sequencing containing gRNA
Columns for processed data file; id = Gene ID; Score_HLF_2D_vs_t0_818 = RRA for 2D vs initial HLF; Score_HLF_3D_vs_t0_818 = RRA for 3D vs initial HLF; Score_PLCPRF5_2D_vs_t0 = RRA for 2D vs initial PLCPRF5 ; Score_PLCPRF5_3D_vs_t0_0042 = RRA for 3D vs initial PLCPRF5; Score_PLCPRF5_2D_vs_3D_8440042 = RRA for 2D vs 3D end for PLCPRF5; Score_HLF_2D_vs_3D_818 = RRA for 2D vs 3D HLF end point; Score_HLF_SNDX_vs_T0_885 = RRA for SNDX vs T0 in HLF; Score_HLF_DMSO_vs_t0_885 = RRA for DMSO vs T0 in HLF; Score_HLF_SNDX_vs_DMSO_885 = RRA SNDX vs DMSO in HLF at endpoint. FDR_HLF_2D_vs_t0_818 = FDR for 2D vs initial HLF; FDR_HLF_3D_vs_t0_818 = FDR for 3D vs initial HLF;FDR_PLCPRF5_2D_vs_t0 = FDR for 2D vs initial PLCPRF5 ;FDR_PLCPRF5_3D_vs_t0_0042 = FDR for 3D vs initial PLCPRF5; FDR_PLCPRF5_2D_vs_3D_8440042 = FDR for 2D vs 3D end for PLCPRF5; FDR_HLF_2D_vs_3D_818 = FDR for 2D vs 3D HLF end point; FDR_HLF_SNDX_vs_T0_885 = FDR for SNDX vs T0 in HLF; FDR_HLF_DMSO_vs_t0_885 = FDR for DMSO vs T0 in HLF; FDR_HLF_SNDX_vs_DMSO_885 =FDR SNDX vs DMSO in HLF at endpoint.

value: None 3D


title: PLC/PRF/5 2D Final Rep 3

description:
Library name: PLCPRF5_CRISPR_2D_d28_DMSO3
Other: amplicon sequencing containing gRNA
Columns for processed data file; id = Gene ID; Score_HLF_2D_vs_t0_818 = RRA for 2D vs initial HLF; Score_HLF_3D_vs_t0_818 = RRA for 3D vs initial HLF; Score_PLCPRF5_2D_vs_t0 = RRA for 2D vs initial PLCPRF5 ; Score_PLCPRF5_3D_vs_t0_0042 = RRA for 3D vs initial PLCPRF5; Score_PLCPRF5_2D_vs_3D_8440042 = RRA for 2D vs 3D end for PLCPRF5; Score_HLF_2D_vs_3D_818 = RRA for 2D vs 3D HLF end point; Score_HLF_SNDX_vs_T0_885 = RRA for SNDX vs T0 in HLF; Score_HLF_DMSO_vs_t0_885 = RRA for DMSO vs T0 in HLF; Score_HLF_SNDX_vs_DMSO_885 = RRA SNDX vs DMSO in HLF at endpoint. FDR_HLF_2D_vs_t0_818 = FDR for 2D vs initial HLF; FDR_HLF_3D_vs_t0_818 = FDR for 3D vs initial HLF;FDR_PLCPRF5_2D_vs_t0 = FDR for 2D vs initial PLCPRF5 ;FDR_PLCPRF5_3D_vs_t0_0042 = FDR for 3D vs initial PLCPRF5; FDR_PLCPRF5_2D_vs_3D_8440042 = FDR for 2D vs 3D end for PLCPRF5; FDR_HLF_2D_vs_3D_818 = FDR for 2D vs 3D HLF end point; FDR_HLF_SNDX_vs_T0_885 = FDR for SNDX vs T0 in HLF; FDR_HLF_DMSO_vs_t0_885 = FDR for DMSO vs T0 in HLF; FDR_HLF_SNDX_vs_DMSO_885 =FDR SNDX vs DMSO in HLF at endpoint.

value: None 2D


title: 3T3_HiC_C3_rep1

description: Hi-C on CBX7 overexpression stable cell line monoclone3 NIH3T3 cells


title: CD8 Donor 5 FCRL3 mAb 4h

description: 150 x 150 bp paired end reads

value: CD8 Donor 5

value: FCRL3 mAb 4h


title: 3T3_HiC_WT_rep1

description: Hi-C on WT NIH3T3 cells

value: WT


title: HLF 3D Final SNDX-5613 Rep 3

description:
Library name: HLF_3D_d28_SNDX_3
Other: amplicon sequencing containing gRNA
Columns for processed data file; id = Gene ID; Score_HLF_2D_vs_t0_818 = RRA for 2D vs initial HLF; Score_HLF_3D_vs_t0_818 = RRA for 3D vs initial HLF; Score_PLCPRF5_2D_vs_t0 = RRA for 2D vs initial PLCPRF5 ; Score_PLCPRF5_3D_vs_t0_0042 = RRA for 3D vs initial PLCPRF5; Score_PLCPRF5_2D_vs_3D_8440042 = RRA for 2D vs 3D end for PLCPRF5; Score_HLF_2D_vs_3D_818 = RRA for 2D vs 3D HLF end point; Score_HLF_SNDX_vs_T0_885 = RRA for SNDX vs T0 in HLF; Score_HLF_DMSO_vs_t0_885 = RRA for DMSO vs T0 in HLF; Score_HLF_SNDX_vs_DMSO_885 = RRA SNDX vs DMSO in HLF at endpoint. FDR_HLF_2D_vs_t0_818 = FDR for 2D vs initial HLF; FDR_HLF_3D_vs_t0_818 = FDR for 3D vs initial HLF;FDR_PLCPRF5_2D_vs_t0 = FDR for 2D vs initial PLCPRF5 ;FDR_PLCPRF5_3D_vs_t0_0042 = FDR for 3D vs initial PLCPRF5; FDR_PLCPRF5_2D_vs_3D_8440042 = FDR for 2D vs 3D end for PLCPRF5; FDR_HLF_2D_vs_3D_818 = FDR for 2D vs 3D HLF end point; FDR_HLF_SNDX_vs_T0_885 = FDR for SNDX vs T0 in HLF; FDR_HLF_DMSO_vs_t0_885 = FDR for DMSO vs T0 in HLF; FDR_HLF_SNDX_vs_DMSO_885 =FDR SNDX vs DMSO in HLF at endpoint.

value: Liver cancer cells

value: HLF

value: SNDX 3D


title: 3T3_HiC_C4_rep1

description: Hi-C on CBX7 overexpression stable cell line monoclone4 NIH3T3 cells


title: Wild type 7mM phosphate 4h Experiment 1 Replicate 3

description: Library name: WT_7mM_Phosphate_4h_Exp1_Rep3

value: Mycelia

value: FGSC 2489

value: Wild type mat A

value: 4h Fries minimal medium 7mM phosphate


title: CD8 Donor 4 secretory lgA 20h

description: 150 x 150 bp paired end reads

value: Peripheral blood

value: secretory lgA 20h


title: HLF 3D Final SNDX-5613 Rep 2

description:
Library name: HLF_3D_d28_SNDX_2
Other: amplicon sequencing containing gRNA
Columns for processed data file; id = Gene ID; Score_HLF_2D_vs_t0_818 = RRA for 2D vs initial HLF; Score_HLF_3D_vs_t0_818 = RRA for 3D vs initial HLF; Score_PLCPRF5_2D_vs_t0 = RRA for 2D vs initial PLCPRF5 ; Score_PLCPRF5_3D_vs_t0_0042 = RRA for 3D vs initial PLCPRF5; Score_PLCPRF5_2D_vs_3D_8440042 = RRA for 2D vs 3D end for PLCPRF5; Score_HLF_2D_vs_3D_818 = RRA for 2D vs 3D HLF end point; Score_HLF_SNDX_vs_T0_885 = RRA for SNDX vs T0 in HLF; Score_HLF_DMSO_vs_t0_885 = RRA for DMSO vs T0 in HLF; Score_HLF_SNDX_vs_DMSO_885 = RRA SNDX vs DMSO in HLF at endpoint. FDR_HLF_2D_vs_t0_818 = FDR for 2D vs initial HLF; FDR_HLF_3D_vs_t0_818 = FDR for 3D vs initial HLF;FDR_PLCPRF5_2D_vs_t0 = FDR for 2D vs initial PLCPRF5 ;FDR_PLCPRF5_3D_vs_t0_0042 = FDR for 3D vs initial PLCPRF5; FDR_PLCPRF5_2D_vs_3D_8440042 = FDR for 2D vs 3D end for PLCPRF5; FDR_HLF_2D_vs_3D_818 = FDR for 2D vs 3D HLF end point; FDR_HLF_SNDX_vs_T0_885 = FDR for SNDX vs T0 in HLF; FDR_HLF_DMSO_vs_t0_885 = FDR for DMSO vs T0 in HLF; FDR_HLF_SNDX_vs_DMSO_885 =FDR SNDX vs DMSO in HLF at endpoint.


title: Erg+Pten- 3 months 1

description: 10x Genomics

value: prostate

value: Erg+Pten-

value: 3 months old


title: 3T3_CBX7_C5_rep1

description: ChIP-seq for CBX7 on CBX7 overexpression stable cell line monoclone5 NIH3T3 cells

extract_protocol:
CBX7 ChIP-seq for WT and CBX7-mCherry cell lines were performed as previously described with modifications (Y. Zhang et al., 2019.). Cells were centrifuged and resuspended in 1 × PBS containing 1 % formaldehyde (Sigma) for 10 min at room temperature for fixation. Glycine was then added to a final concentration of 0.14 M and incubated for 10 min at room temperature to quench fixation. Crude nuclei were purified and the lysate is sonicated using the program configured as power 10, cycle 12, 15 seconds sonication, and 45 seconds rest for every minute. For each ChIP assay, proteinA/G beads bond antibodies (3ug, ab21873) were added and incubated at 4◦C overnight. After washing, Chromatin was then reverse-crosslinked and purified by 2.5 × DNA beads (Vazyme).
Tru-seq library preparation was done using NEBNext® Ultra TM II DNA Library Prep Kit for Illumina® v1.0. The amplified DNA was size selected using SPRI beads.

value: NIH 3T3

value: fibroblast

value: CBX7 OE


title: CD8 Donor 4 FCRL3 mAb 20h

description: 150 x 150 bp paired end reads

value: CD8 effector T

value: CD8 Donor 4

value: FCRL3 mAb 20h


title: WTaos, mock, rep1

data_processing:
Sequence images were transformed with the Illumina BaseCaller software to BCL files, which were subsequently demultiplexed to FASTQ files with CASAVA (v1.8.2).
Using a Galaxy platform, alignment of reads to the Arabidopsis thaliana genome reference sequence (TAIR10 release-39; https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-39/fasta/arabidopsis_thaliana/) and counting of the aligned reads to the feature type “CDS” were carried out with RNA STAR (Galaxy version 2.5.2b-2;  Dobin et al., 2013).
Assembly: Arabidopsis thaliana (TAIR10 release-39; https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-51/fasta/arabidopsis_thaliana/)
Supplementary files format and content: tab-delimited text files include raw counts for each sample

extract_protocol:
Total RNA was extracted using Trizol; TruSeq RNA Library Prep Kit v2 (Illumina)
TruSeq RNA Library Prep Kit v2 (Illumina)

value: Roots

value: outcrossed wild-type from heterozygous AOS/aos plants

value: water control


title: Wild type 7mM phosphate 4h Experiment 1 Replicate 2

description: Library name: WT_7mM_Phosphate_4h_Exp1_Rep2

value: Mycelia

value: FGSC 2489


title: 3T3_CBX7_C4_rep1

description: ChIP-seq for CBX7 on CBX7 overexpression stable cell line monoclone4 NIH3T3 cells


title: HLF 3D Final SNDX-5613 Rep 1

description:
Library name: HLF_3D_d28_SNDX_1
Other: amplicon sequencing containing gRNA
Columns for processed data file; id = Gene ID; Score_HLF_2D_vs_t0_818 = RRA for 2D vs initial HLF; Score_HLF_3D_vs_t0_818 = RRA for 3D vs initial HLF; Score_PLCPRF5_2D_vs_t0 = RRA for 2D vs initial PLCPRF5 ; Score_PLCPRF5_3D_vs_t0_0042 = RRA for 3D vs initial PLCPRF5; Score_PLCPRF5_2D_vs_3D_8440042 = RRA for 2D vs 3D end for PLCPRF5; Score_HLF_2D_vs_3D_818 = RRA for 2D vs 3D HLF end point; Score_HLF_SNDX_vs_T0_885 = RRA for SNDX vs T0 in HLF; Score_HLF_DMSO_vs_t0_885 = RRA for DMSO vs T0 in HLF; Score_HLF_SNDX_vs_DMSO_885 = RRA SNDX vs DMSO in HLF at endpoint. FDR_HLF_2D_vs_t0_818 = FDR for 2D vs initial HLF; FDR_HLF_3D_vs_t0_818 = FDR for 3D vs initial HLF;FDR_PLCPRF5_2D_vs_t0 = FDR for 2D vs initial PLCPRF5 ;FDR_PLCPRF5_3D_vs_t0_0042 = FDR for 3D vs initial PLCPRF5; FDR_PLCPRF5_2D_vs_3D_8440042 = FDR for 2D vs 3D end for PLCPRF5; FDR_HLF_2D_vs_3D_818 = FDR for 2D vs 3D HLF end point; FDR_HLF_SNDX_vs_T0_885 = FDR for SNDX vs T0 in HLF; FDR_HLF_DMSO_vs_t0_885 = FDR for DMSO vs T0 in HLF; FDR_HLF_SNDX_vs_DMSO_885 =FDR SNDX vs DMSO in HLF at endpoint.

value: Liver cancer cells

value: HLF

value: SNDX 3D


title: Wild type 7mM phosphate 4h Experiment 1 Replicate 1

description: Library name: WT_7mM_Phosphate_4h_Exp1_Rep1

value: Wild type mat A

value: 4h Fries minimal medium 7mM phosphate


title: CD8 Donor 4 SA control 4h

description: 150 x 150 bp paired end reads

value: Peripheral blood

value: SA control 4h


title: CD8 Donor 4 FCRL3 mAb 4h

description: 150 x 150 bp paired end reads

value: FCRL3 mAb 4h


title: 3T3_CBX7_WT_rep1

description: ChIP-seq for CBX7 on WT NIH3T3 cells

value: NIH 3T3

value: fibroblast

value: WT


title: 3T3_CBX7_C3_rep1

description: ChIP-seq for CBX7 on CBX7 overexpression stable cell line monoclone3 NIH3T3 cells

value: CBX7 OE


title: HLF 3D Final DMSO Rep 2

description:
Library name: HLF_3D_d28_DMSO_2
Other: amplicon sequencing containing gRNA
Columns for processed data file; id = Gene ID; Score_HLF_2D_vs_t0_818 = RRA for 2D vs initial HLF; Score_HLF_3D_vs_t0_818 = RRA for 3D vs initial HLF; Score_PLCPRF5_2D_vs_t0 = RRA for 2D vs initial PLCPRF5 ; Score_PLCPRF5_3D_vs_t0_0042 = RRA for 3D vs initial PLCPRF5; Score_PLCPRF5_2D_vs_3D_8440042 = RRA for 2D vs 3D end for PLCPRF5; Score_HLF_2D_vs_3D_818 = RRA for 2D vs 3D HLF end point; Score_HLF_SNDX_vs_T0_885 = RRA for SNDX vs T0 in HLF; Score_HLF_DMSO_vs_t0_885 = RRA for DMSO vs T0 in HLF; Score_HLF_SNDX_vs_DMSO_885 = RRA SNDX vs DMSO in HLF at endpoint. FDR_HLF_2D_vs_t0_818 = FDR for 2D vs initial HLF; FDR_HLF_3D_vs_t0_818 = FDR for 3D vs initial HLF;FDR_PLCPRF5_2D_vs_t0 = FDR for 2D vs initial PLCPRF5 ;FDR_PLCPRF5_3D_vs_t0_0042 = FDR for 3D vs initial PLCPRF5; FDR_PLCPRF5_2D_vs_3D_8440042 = FDR for 2D vs 3D end for PLCPRF5; FDR_HLF_2D_vs_3D_818 = FDR for 2D vs 3D HLF end point; FDR_HLF_SNDX_vs_T0_885 = FDR for SNDX vs T0 in HLF; FDR_HLF_DMSO_vs_t0_885 = FDR for DMSO vs T0 in HLF; FDR_HLF_SNDX_vs_DMSO_885 =FDR SNDX vs DMSO in HLF at endpoint.

value: DMSO 3D


title: 3T3_H3K4me3_C5_rep1

description: CUT&Tag for H3K4me3 on CBX7 overexpression stable cell line monoclone5 NIH3T3 cells

data_processing:
Paired-end RNA-seq reads were aligned to mm9 using HISAT2 v2.2.1 and FPKM value of each gene was calculated with StringTie v2.1.2.
The paired end ChIP-seq or CUT&Tag reads were mapped to mm9 using bowtie2 (version 2.2.5) with the parameters: -t -q -p 40 -N 1 -L 25 -X 2000 --no-mixed --no-discordant. The unmapped reads, not uniquely mapped, and duplicate reads were removed. Read coverages over the mm9 genome were calculated by bamCoverage from deepTools v3.3.1. The signal was then normalized by computing the number of reads per kilobase of bin per million reads sequenced (RPKM), followed by normalization using Z-score (whole genome 100bp bn with outliner regions excluded).
Hi-C data analysis was performed as previously described. Briefly, Hi-C libraries were aligned using HiCPro (version 2.10.0) with bowtie2 end-to-end algorithm and with the option ‘-very-sensitive’.
Assembly: mm9
Supplementary files format and content: Bigwig for ChIP-seq tracks, gene expression table for RNA-seq data, ValidPairs for Hi-C data
Library strategy: CUT&tag

extract_protocol:
CUT&Tag experiments were performed as previously described with modifications (H. S. Kaya-Okur et al., 2019.). Briefly, cells suspended in washing buffer were Concanavalin A coated magnetic beads (Polyscience, 86057) for 10 min at room temperature. Cells were then incubated with primary antibody (H3K4me3, Active motif #39160; H3K27me3, Cell Signaling Technology 9733 C36B11; H2AK119ub, Cell Signaling Technology 8240s; H3K9me3, active motif #39161) at a ratio of 1:100 at 4°C for 2 h on a thermomixer at 400 rpm. After the removal of primary antibody, secondary antibody (Invitrogen, #SA5-10228) were added at a ratio of 1:100, and incubation was performed for 1 h at 4°C. After washing two times, beads were incubated with protein A-Tn5 (Vazyme, S603) at 4°C for 1 h. Tagmentation was performed at 37°C for 30 min after washing. SDS was then added to stripe Tn5 and tagmented DNA was purified with 3 × VAHTS DNA Clean Beads (Vazyme, N411).
PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing.