title: Muscle SPRITE 12

description: MM14 mouse skeletal myoblast cells, differentiation for 60 hours Replicate 12

value: mouse skeletal myoblasts

value: 2% horse serum supplemented with insulin


title: PDGFRα+ cells, AR C&R, biol rep3

status: Public on Mar 28 2024

type: SRA

city: Toon

first: Hiroshi

last: Sakai

state: Ehime

address: Shitsukawa

department: Proteo-Science Center

country: Japan

institute: Ehime University

library_source: genomic

data_processing:
Paired-end reads were trimmed with Trim Galore and mapped to mm10 using Bowtie2 (v2.4.5) with the following options: --no-mixed --no-discordant. Multi or no mate reads were removed with samtools (v1.10) view (-q 4 -F 0x2).
To identify AR peaks across samples, BAM files were merged across biological replicates (n = 2) to call peaks with MACS2 (v2.2.7.1) (-q 0.05). H3K4me3 peaks were called on individual BAM files using MACS2 (-q 0.0001).
Merged BAM files for AR and IgG were used for downstream analysis (2 merged BAM files for AR and 1 merged BAM file for IgG).
Motif enrichment analysis of AR peaks was performed with HOMER (v4.11) findMotifs with -size 200 -mask options and AR peaks were annotated to mm10 genes using annotatePeaks (-size 200 -mask) from MACS2 summit files.
To generate bigwig files, merged (AR or IgG) or individual (H3K4me3) BAM files were converted to CPM-normalized bigwig files using deepTools (v3.5.1) bamCoverage (--binSize 100 --normalizeUsing CPM).
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&RUN

molecule: genomic DNA

organism: Mus musculus

source_name: Hindlimb muscles

extract_protocol:
The nuclei were prepared with ChIC/CUT&RUN Assay Kit (Active Motif, Cat# 53180) following the manufacturer’s protocol.
The library was prepared using NEBNext Ultra II for DNA Library Preparation for Illumina (New England Biolabs, Cat# E7645L) with some modifications according to the Active Motif's instruction.

treatment_protocol: To induce AR signaling, dihydrotestosterone (DHT, 2.5 mg/mouse), dissolved in absolute ethanol and diluted in 0.3% w/v hydroxypropyl cellulose in PBS, was injected subcutaneously at 2 hours before sampling.

tag: tissue

value: Hindlimb muscles

tag: cut&run antibody

value: AR (Abcam, Cat# ab108341)

tag: cell type

value: mesenchymal progenitors

tag: strain

tag: treatment

value: DHT for 2h


title: Human H1 DNA SPRITE 1

city: Pasadena

first: Mitchell

last: Guttman

state: CA

address: 1200 E. California Blvd

department: Biology and Biological Engineering

country: USA

institute: California Institute of Technology

description: H1 human embryonic stem cells Replicate 1

data_processing:
Adapters were trimmed from raw paired-end fastq files using Trim Galore! v0.6.2 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and assessed with Fastqc v0.11.9. Subsequently, the DPM (GATCGGAAGAG) and RPM (ATCAGCACTTA) sequences are trimmed using Cutadapt v2.5 from the 5’ end of Read 1 along with the 3’ end DPM sequences that result from short reads being read through into the barcode. The additional trimming helps improve read mapping in the end-to-end alignment mode. The SPRITE barcodes of trimmed reads are identified with Barcode ID v1.2.0 (https://github.com/GuttmanLab/sprite2.0-pipeline) and the ligation efficiency is assessed. Reads with an RPM or a DPM barcode are split into two separate files, to process RNA and DNA reads individually downstream, respectively.
RNA reads were aligned to GRCm38.p6 with the Ensembl GRCm38 v95 gene model annotation using Hisat2 v2.1.01 with a high penalty for soft-clipping --sp 1000,1000. Unmapped and reads with a low MapQ score (samtools view -bq 20) were filtered out for downstream realignment. Mapped reads were annotated for gene exons and introns with the featureCounts tool from the subread package v1.6.4 using Ensembl GRCm38 v95 gene model annotation and the Repeat and Transposable element annotation from the Hammel lab. Filtered reads were subsequently realigned to our custom collection of repeat sequences using Bowtie v2.3.5, only keeping mapped and primary alignment reads. For the H1 dataset, hg38 genome annotation was used.
DNA reads were aligned to GRCm38.p6 using Bowtie2 v2.3.5, filtering out unmapped and reads with a low MapQ score (samtools view -bq 20). Data generated in F1 hybrid cells (pSM33: C57BL/6 × 129SV-Jae or pSM44: 129 × castaneous) were assigned the allele of origin using SNPsplit v0.3.4. RepeatMasker defined regions with milliDev <= 140 along with blacklisted v2 regions were filtered out using Bedtools v2.29.0. For the H1 dataset, hg38 genome assembly was used.
RNA and DNA reads were merged, and a cluster file was generated for all downstream analysis. MultiQC v1.6 was used to aggregate all reports.
Assembly: mm10 and hg38
Supplementary files format and content: Each cluster occupies one line of the .clusters text file. A cluster corresponds to all reads with a shared series of tags and is identified by the barcode name and genomic alignments of contained reads.
Supplementary files format and content: Config files contain the SPRITE tag sequence strings and sample identifiers which were embedded in the DPM tag.

organism: Homo sapiens

source_name: H1 hESC

growth_protocol: MM14 mouse skeletal myoblasts were passaged at 50-60% confluency every 1-2 days using the Wold lab protocol: (https://www.encodeproject.org/documents/a5f5c35a-cdda-4a45-9742-22e69ff50c9c/@@download/attachment/C2C12_Wold_protocol.pdf). Undifferentiated myoblasts grow in growth medium (20% fetal bovine serum). H1 hESC cells were maintained on matrigel matrix (Corning, 354277) in feeder free media using mTeSR1 (Stemcell Tech, 85850). Every 4-5 days cells were passaged using ReLeSR reagent (Stemcell tech, 05872).

extract_protocol:
SPRITE crosslinking, lysis, and DNA fragmentation.
SPRITE library construction as previously described in Quinodoz et al 2022 and Quinodoz et al 2021.

treatment_protocol: Myogenic differentiation was initiated upon reaching confluence by switching MM14 cells to medium containing 2% horse serum supplemented with insulin. Differentiation was performed for 60 hours by rinsing fully confluent cells once with PBS and adding 25mL of low-serum differentiation medium. Fresh differentiation medium was changed every 24 hours up to the 48h timepoint and 12 hours afterward were crosslinked using SPRITE crosslinking procedures.

tag: cell line

value: H1 hESC

value: H1 human embryonic stem cells


title: GL261-GSCs-rep1

city: Salamanca

first: Arantxa

last: Tabernero

address: Pintor Fernando Gallego 1

department: INCyL

country: Spain

institute: Universidad de Salamanca

library_source: transcriptomic

data_processing:
Sequences were aligned to the mm10 genome using Space Ranger's default settings
Assembly: mm10
Supplementary files format and content: SmartSeq_processed.h5ad

molecule: total RNA

source_name: Brain

growth_protocol: Single-cell RNA-sequencing (scRNA-Seq) of GL261 and GL261-GSCs

extract_protocol:
Fresh frozen brains were OCT embedded and 10 μm sections were cut with cryostat
Preparation of lysis plates, FACS sorting, cDNA synthesis using the Smart-Seq2 protocol (Picelli, et al. 2013; Darmanis, et al. 2015), library preparation using an in-house version of Tn5 (Picelli, et al. 2014; Hennig, et al. 2018), library pooling and quality control, and sequencing.

value: Brain


title: GL261-rep2


title: GL261-rep1


title: IPF (before PFD) [DK21068_03]

city: Chiba

first: Takeshi

last: Kawasaki

address: 1-8-1, Inohana, Chuoku

department: Respirology

institute: Chiba University

description:
DK21068_03
3' RNA-seq

data_processing:
Removal of poly A tail and adapter sequences were performed using BBDuk (BBMap version 38.96) with the following settings (k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20).
Trimmed reads were mapped to hg38 using STAR version 2.7.6a with the following settings (--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000).
Read counts for each gene were obtained using HTSeq-count version 1.99.2 with the following settings (-m intersection-nonempty -s yes).
Assembly: hg38
Supplementary files format and content: xlsx files include raw counts for each sample.
Supplementary files format and content: xlsx files include RPM values for each sample.

source_name: PBMC

extract_protocol:
RNA was harvested using ISOGEN reagent (Life Technologies, Carlsbad, CA, USA).
Purified total RNA (200 ng) was used for RNA library preparation, according to the instructions of the Quant Seq 3' mRNA-seq library preparation kit FWD of Illumina (Lexogen, Vienna, Austria). The RNA libraries were sequenced on an Illumina NextSeq 500 system with 75-nt-long reads.

tag: disease

value: Idiopathic Pulmonary Fibrosis

value: PBMC

tag: age

tag: Sex

value: Male

tag: race

value: Asian


title: Mouse GL261-GSC glioblastoma TMZ 28d rep2

data_processing:
Demultiplexing, barcode processing, gene counting and aggregation were made using Cell Ranger software
Assembly: mm10
Supplementary files format and content: 10xnuclei_annotated.h5ad: annotated file in h5ad format

growth_protocol: GL261-GSCs were intracranially injected into the brains of C57BL/6 mice

extract_protocol:
Brains were fresh-frozen and nuclei were obtained from tissue blocks
Single nuclei were processed using the 10x Multiome ATAC + Gene Expression kit according to manufacturer's instructions

treatment_protocol: 100 μM Tat-Cx43266-283 or 250 μM TMZ were intracranially injected in 1 μl of physiological saline together with the cells. For 28-day experiments, 4 nmol/g Tat-Cx43266–283 or 10 nmol/g TMZ were intraperitonially injected twice per week, starting on day 8 and until the end of the experiment. An equivalent amount of saline was injected to control mice.

tag: time point

value: TMZ


title: Mouse GL261-GSC glioblastoma TMZ 28d rep3


title: IPF (before PFD) [DK22190_01]

description:
DK22190_01
3' RNA-seq


title: Muscle SPRITE 11

description: MM14 mouse skeletal myoblast cells, differentiation for 60 hours Replicate 11


title: Muscle SPRITE 10

description: MM14 mouse skeletal myoblast cells, differentiation for 60 hours Replicate 10


title: Healthy control [DK21222_17]

description:
DK21222_17
3' RNA-seq

value: Healthy


title: Mouse GL261-GSC glioblastoma peptide 28d rep1

value: Peptide


title: Muscle SPRITE 9

description: MM14 mouse skeletal myoblast cells, differentiation for 60 hours Replicate 9


title: Mouse GL261-GSC glioblastoma control 28d rep2

value: Control


title: Mouse GL261-GSC glioblastoma control 28d rep1


title: GL261-rep3


title: Muscle SPRITE 7

description: MM14 mouse skeletal myoblast cells, differentiation for 60 hours Replicate 7

value: mouse skeletal myoblasts


title: GL261-GSCs rep2


title: Healthy control [DK22269_03]

description:
DK22269_03
3' RNA-seq


title: GL261-GSCs rep3


title: Healthy control [DK22269_04]

description:
DK22269_04
3' RNA-seq


title: Muscle SPRITE 6

description: MM14 mouse skeletal myoblast cells, differentiation for 60 hours Replicate 6

value: 2% horse serum supplemented with insulin


title: Muscle SPRITE 8

description: MM14 mouse skeletal myoblast cells, differentiation for 60 hours Replicate 8


title: Healthy control [DK22269_01]

description:
DK22269_01
3' RNA-seq


title: Healthy control [DK21222_19]

description:
DK21222_19
3' RNA-seq


title: Muscle SPRITE 5

description: MM14 mouse skeletal myoblast cells, differentiation for 60 hours Replicate 5


title: GL261-GSCs rep1


title: GL261 cells rep1


title: Muscle SPRITE 4

description: MM14 mouse skeletal myoblast cells, differentiation for 60 hours Replicate 4


title: Muscle SPRITE 3

description: MM14 mouse skeletal myoblast cells, differentiation for 60 hours Replicate 3


title: GL261 cells rep2


title: GFI1B-Q287*

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

department: RIMLS

country: Netherlands

institute: Radboud University

library_source: transcriptomic single cell

data_processing:
Reads were aligned to the GrCH38 reference genome using CelLRanger v6.0.0.
Raw count matrices were filtered using emptydrops from DopletUtils v1.12.3
Droplets with high mitochondrial gene content were filtered based on UMAP clustering. Dimensional reduction on all non-empty droplets was performed for every sample and cells were clustered using resolution 1.6 in Seurat 4.1.0. Mitochondrial gene content was plotted and clusters with high mitochondrial gene content were selected. Differential gene expression analysis on these clusters was performed to establish whether non-mitochondrial genes are expressed in these clusters. If that is the case, the clusters were retained for analysis, otherwise they were removed.
Cell doublets were filtered using DoubletFinder v2.0.3. Parameters were chosen based on sample (wildt ype = PCs = 1:15, pK = 0.005, pN = 0.25, nExp = 393, sct = FALSE, reuse.pANN = FALSE; LSD1i = PCs = 1:10, pK = 0.23, pN = 0.25, nExp = 190, sct = FALSE, reuse.pANN = FALSE; Q287* = PCs = 1:10, pK = 0.3, pN = 0.25, nExp = 69, sct = FALSE, reuse.pANN = FALSE)
Filtered cells from all samples were regressed for cell cycle genes and integrated using SCT integration with 3000 most variable features, normalization.method = "SCT", default parameters. Clusters were identified using FindNeighbors with reduction = "pca"and dims = 1:10 and FindClusters with algorithm = 1, resolution = 0.3 and random.seed = 0.
Assembly: GRCh38
Supplementary files format and content: The barcode.tsv file contains a list of all barcodes that are present in a sample.
Supplementary files format and content: The features.tsv file contains all features that were present in a sample. This is identical for all samples.
Supplementary files format and content: The matrix.mtx file contains the counts for each feature in each barcode (features as rows and barcodes as columns)

molecule: polyA RNA

source_name: GPS

growth_protocol: Induced pluripotent stem cells were maintained according to previously described protocols (doi:10.1016/j.scr.2016.12.004; doi:10.1016/j.scr.2017.10.008) on Matrigel (Corning), E8 medium (Thermofisher Scientific), and mTESR1 medium (Stemcell Technologies)

extract_protocol: Libraries were constructed using the Chromium Single Cell 3’ kit (v3.1 Chemistry; 10X genomics) according to protocol.

treatment_protocol: Wild type IPSCs were treated with 4µM GSK-LSD1 (Merck) inhibitor for 24 hours.

value: GPS

tag: genotype

value: GFI1B wt/Q287*


title: Muscle SPRITE 2

description: MM14 mouse skeletal myoblast cells, differentiation for 60 hours Replicate 2


title: Healthy control [DK22269_14]

description:
DK22269_14
3' RNA-seq


title: Wild type

value: GFI1B wild type


title: GL261-GSCs-rep4

data_processing:
Demultiplexing, barcode processing, gene counting and aggregation were made using Cell Ranger software
Assembly: mm10
Supplementary files format and content: 10xcells_processed.h5ad: annotated file in h5ad format

growth_protocol: GL261 cells were grown in FCS-containing differentiation medium. GL261-GSCs were grown in defined GSC medium.

extract_protocol:
Cells and neurospheres were dissociated using Accutase and lysed in lysis buffer containing 0.3% IGEPAL® CA-630
Single cells or nuclei were captured in droplet emulsions using the Chromium instrument (10x Genomics) and scRNA-seq libraries were constructed as per the 10x Genomics protocol using GemCode Single-Cell 5’ Bead and Library kit.

value: Glioblastoma stem cell


title: Mouse GL261-GSC glioblastoma TMZ 28d rep1


title: LSD1i


title: MEG01, GFI1B-Q287*, rep3

data_processing:
Reads were filtered, trimmed and QC'd using trim_galore v0.4.4 with fastqc v0.11.8 and citadapt v1.18. Trim_galore was run with --fastqc --paired and standard input.
Reads were aligned to the reference genome using STAR v2.7.5a with --readFIleCommand zcat, --outSAMtype BAM unsorted --twopassMode Basic --outSAMstrandField intronMotif --limitOutSJcollapsed 2000000.
STAR output was quantified using htseq v0.11.0 with bam files as input and htseq-count -s "\$s"
Gene modules for GFI1B variant data (GFP, GFI1B, GFI1B-T174N, GFI1B-H181Y, GFI1B-R184P, GFI1B-Q278*) were identified using Weighted Gene Co-expression Network analysis (v1.71), with varience stabilised counts generated by DESeq2 (v1.32) as input. Weighted Gene Co-expression Network analysis softpower threshold was set to 12 and and the networks were calculated using signed-hybrid networks. Resulting modules were merged using a cutting height of 0.2.
Assembly: Hg38
Supplementary files format and content: the processed data files contain the htseq output files. Each .txt file contains the number of reads that are aligned to a gene.

growth_protocol: MEG01 cells were cultured at 5% CO2 and at 37°C in RPMI supplemented with 10% heat-inactivated foetal calf serum.

extract_protocol:
RNA was isolated using the NucleoSpin RNA plus kit (Macherey-Nagel) and 100ng was used for sequencing.
Library generation was performed using KAPA RNA HyperPrep Kit with RiboErase (HMR;Kapa Biosystems), with an RNA fragmentation of approximately 300 bp fragments for 6 min at 94 °C.

treatment_protocol: MEG01 cells were treated with 4µM GSK-LSD1 (Merck) inhibitor for 4 days.

value: wild type

value: GFI1B-Q287 retroviral overexpression


title: Control 28d

library_source: other

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to mm10 genome to gene expression count using Space Ranger
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue spots
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: 10xVisium_annotated.h5ad: annotated file in h5ad format
Library strategy: Spatial transcriptomics

molecule: other

extract_protocol:
Brains were fresh-frozen and sections were obtained with a cryostat and methanol-fixed
Library preparation was performed according to manufacturer's instructions

value: Brain


title: GL261-GSCs-rep3


title: Muscle SPRITE 1

description: MM14 mouse skeletal myoblast cells, differentiation for 60 hours Replicate 1


title: MEG01, GFI1B-Q287*, rep2


title: MEG01, GFI1B-R184P, rep1

value: GFI1B-R184P retroviral overexpression


title: MEG01, GFI1B-Q287*, rep1


title: AC16 Clone 9B4, MKK6-EE

city: Charlottesville

first: Kevin

middle: A.

last: Janes

state: VA

address: Box 800759 Health System

department: Department of Biomedical Engineering

institute: University of Virginia

data_processing:
Reads were aligned with HISAT2 v2.1.0 using the downstream transcriptome assembly option and the RF paired-end stranded option. An artificial chromosome was added to the GRCh38 release 99 reference genome containing open reading frames of the integrated pSLIK CVB3 A67G plasmid: positive and negative strand “genes” for CVB3, neomycin resistance gene, reverse tetracycline-controlled transactivator (rtTa), hygromycin resistance gene, and ampicillin resistance gene. SV40 genes (small t [exon 1 and 2], large T [exon 1 and 2], agnoprotein, VP1, and VP2) were also included in the artificial chromosome because SV40 was involved in creating the AC16 cell line. Transcripts were assembled and counted with Stringtie v2.1.0, restricting assembly to the reference genome and associated artificial chromosome. The prepDE.py3 script provided by Stringtie was used to extract count information for downstream differential expression.
Assembly: GRCh38 + SV40 + CVB3
Supplementary files format and content: Tab separated matrix containing raw output counts from the Stringtie prepDE.py script.

growth_protocol: iPSCs: iCell Cardiomyocytes² Maintenance Medium as recommended by the manufacturer and plated in iCell Cardiomyocytes² Plating Medium for two days (asynchronous beating) or four days (synchronous beating). AC16 cells: DMEM/F12 medium (Gibco Cat#11330-032) + 12.5% fetal bovine serum + 1% pen/strep + 10 mg/ml blasticidin (AC16-CAR only) + 100 µg/ml hygromycin (AC16 CVB3+ clones only) + 2 µg/ml puromycin (IkBa-SR, MKK6-EE, and IKK2-EE only).

extract_protocol:
iPSCs, AC16-CAR cells, and unperturbed AC16 clones: lysed with buffer RLT and mRNA extracted with the RNeasy Mini Kit. Perturbed AC16 clones: lysed with buffer RLT and mRNA extracted with the RNeasy Plus Mini Kit.
iPSCs, AC16-CAR cells, and unperturbed AC16 clones: prepared with the TruSeq stranded mRNA library prep kit. Perturbed AC16 clones: strand-specific sequencing libraries, after poly(A) pulldown, were prepared by Novogene.

treatment_protocol: iPSCs and AC16-CAR cells: infected with wildype CVB3 (MOI 10 for 8 hours) or encapsidation-deficient CVB3 (VP4 A67G - MOI of 3 for 16 hours). All AC16 cells: terminally quiesced by shSV40 lentivirus and serum withdrawal. AC16 CVB3+ clones: stably transfected with encapsidation-deficient pSLIK CVB3 (VP4 A67G) and clonally isolated. Perturbed AC16 clones: transduced with retrovirus encoding pBABE FLAG-IKK2-EE puro, pBABE 3xHA-MKK6-EE puro, pBABE IκBα-SR puro, or empty pBABE puro then selected with 2 µg/ml puromycin for 3 days, and replated at equivalent cell density. Transduced AC16 clones were treated with 5 µM BIRB796 or 0.05% DMSO while undergoing the quiescence protocol.

tag: modifications

value: CVB3+ Clone 9B4


title: MEG01, GFI1B-R184P, rep3


title: AC16 Clone 9B4, pBABE-DMSO

value: pBABE-DMSO


title: GL261-rep1

value: Glioblastoma cell


title: A10_SCLC28

city: Erlangen

first: Lydia

last: Meder

state: Bavaria

address: Glückstr. 6

department: Experimentelle Medizin 1

country: Germany

description: sclc_gene_counts_16_17_23_28_30_31_N3_ITGB1KO.xlsx

data_processing:
Trasnfering gene counts to CPM using GENAVi
GSEA using VolcaNoiseR
Assembly: mm10
Supplementary files format and content: comma seperated value (.csv); comma as seperator.xlsx-file

source_name: lung origin

growth_protocol: The cell lines were cultured under conditions of 5% CO2 and 37°C. The cell culture media RPMI medium 1640 (Thermo Fisher Scientific Inc., USA) was supplemented with 10% FBS (PAN-Biotech, Aidenbach, Germany), 50U/ml Penicillin, 50μg/ml Streptomycin.

extract_protocol:
RNA was harvested using the RNeasy Mini Kit (Qiagen N.v., Netherlands) according to manufacturer’s instruction.
RNA libraries for RNASeq are generated using TruSeq total RNA. 1µg of total RNAwas used for library preparation.

treatment_protocol: In murine derived SCLC liver metastasis cells a RNA-guided Cas9 ITGB1 Knock-out (KO) was achieved applying the Santa Cruz CRISPR construct transfectionaccording to manufacturer’s advices, follwoed by puromycin selection and GFP based cell sorting.

value: lung origin

value: RBP1578 ITGB1KO clone 2

value: SCLC liver metastasis


title: A10_SCLC23

value: RBP1578 ITGB1KO clone 1


title: A10_SCLC30

value: RBP1578 ITGB1KO clone 3


title: A10_SCLC17

value: RBP1578 WT clone 2


title: MEG01, GFI1B-H181Y, rep3

value: GFI1B-H181Y retroviral overexpression


title: GL261-GSCs-rep2


title: A10_SCLC31

value: RBP1578 WT clone 3


title: GL261-rep2


title: Protocol 3 HMGB1 biol rep 3

city: Manhasset

first: Mark

last: Mizrachi

state: NY

address: 350 Community Drive

department: Institute of Molecular Medicine

institute: Feinstein Institutes for Medical Research

data_processing:
Messenger RNA (mRNA) was isolated from total RNA using magnetic beads with attached poly-T oligos. cDNA was synthesized, and the directional library underwent end repair, A-tailing, adapter ligation, size selection, and purification. Quantification and size distribution were confirmed using Qubit, real-time PCR, and a bioanalyzer.
Raw fastq data was processed to remove adapters, poly-N sequences, and low-quality reads. Metrics such as Q20, Q30, and GC content were computed.
Using Hisat2 v2.0.5, an index of the reference genome was built, and paired-end clean reads were aligned to it.
Reads mapped to each gene were quantified using featureCounts v1.5.0-p3.

extract_protocol:
RNA was extracted using Qiagen RNeasy Mini Kit.
RNA libraries for RNA seq were constructed using EBNext Ultra™ II RNA Library Prep Kit using manufacturer's instructions

value: Microglia


title: GL261-GSCs-rep1

value: Glioblastoma stem cell


title: CNS-Tconv from EAE-induced Ctrl mice

city: Lyon

first: Yenkel

last: Grinberg-Bleyer

address: 28 rue Laennec

department: Immunity, viruses and inflammation

country: France

institute: Cancer Research Center of Lyon

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing and gene counting were made using the Cell Ranger v7.0.0.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Central nervous system

extract_protocol:
FACS sorted T cells were encapsulated using the Single Cell Controller (10x Genomics, Pleasanton, CA)
N/A
Chromium Single Cell 3′Library & Gel Bead v3.1 kit

value: Central nervous system

value: CD4+ T cells

value: Ctrl


title: MEG01, GFI1B-H181Y, rep1

value: wild type


title: CNS-Tconv from EAE-induced Rel-cKO mice

description: 10x Genomics

value: Rel-cKO


title: CNS-Tconv from EAE-induced Rela-cKO mice

description: 10x Genomics

value: Rela-cKO


title: Protocol 3 HMGB1 biol rep 2

value: Brain


title: AC16 Clone 9B4, IkBa-SR

value: CVB3+ Clone 9B4

value: IkBa-SR


title: AC16 Clone 9B4, BIRB796


title: A10_SCLC16

value: lung origin

value: RBP1578 WT clone 1

value: SCLC liver metastasis


title: MEG01, GFI1B-R184P, rep2

value: GFI1B-R184P retroviral overexpression


title: MEG01, GFI1B-H181Y, rep2

value: GFI1B-H181Y retroviral overexpression


title: DLN-Tconv from EAE-induced Rela-cKO mice

description: 10x Genomics

source_name: Central nervous system-draining lymph nodes


title: Protocol 3 HMGB1 biol rep 1


title: MEG01, GFI1B-T174N, rep3

value: GFI1B-T174N retroviral overexpression


title: AC16 Clone 7G5, pBABE-DMSO

value: CVB3+ Clone 7G5

value: pBABE-DMSO


title: DLN-Tconv from EAE-induced Ctrl mice

description: 10x Genomics

value: Central nervous system-draining lymph nodes


title: Protocol 3 Control biol rep 3

value: Microglia

value: Control


title: MEG01, GFI1B-T174N, rep1

value: wild type


title: MEG01, GFI1B, rep3

value: GFI1B retroviral overexpression


title: Protocol 3 Control biol rep 2


title: MEG01, GFI1B-T174N, rep2


title: DLN-Tconv from EAE-induced Rel-cKO mice

description: 10x Genomics

value: CD4+ T cells

value: Rel-cKO


title: TIL-Tconv from B16OVA-bearing Ctrl mice

description: 10x Genomics

source_name: Tumor

value: Tumor

value: Ctrl


title: Protocol 3 Control biol rep 1

value: Brain


title: AC16 Clone 7G5, MKK6-EE


title: AC16 Clone 7G5, IkBa-SR

value: IkBa-SR


title: MEG01, GFI1B, rep2


title: MEG01, GFI1B, rep1


title: TIL-Tconv from B16OVA-bearing Rel-icKO mice

description: 10x Genomics

value: Rel-icKO


title: AC16 Clone 7G5, BIRB796


title: Protocol 2 HMGB1 biol rep 3


title: DLN-Tconv from B16OVA-bearing Ctrl mice

description: 10x Genomics

source_name: Tumor draining lymph nodes

value: Tumor draining lymph nodes


title: Protocol 2 HMGB1 biol rep 1


title: AC16 Clone 7F4, MKK6-EE

value: CVB3+ Clone 7F4


title: MEG01, GFP, rep1

value: GFP retroviral overexpression


title: Protocol 2 Control biol rep 3


title: Protocol 2 HMGB1 biol rep 2


title: MEG01, GFP, rep2


title: Ctrl mouse Tconv cells, rep. 3

data_processing:
Bcl files were converted to fastq using Bcl2fastq (2.20.0).
Gene expression was quantified using Salmon (1.1.0) and the annotation of protein coding genes from gencode vm24.
Transcription matrix was done using R package tximport on the salmon results.
Assembly: mm10
Supplementary files format and content: tab delimited file with samples in columns, genes in rows, and estimated raw counts.

source_name: Spleen+lymph nodes

extract_protocol:
RNA was isolated with Nucleospin RNA extraction kits (Macherey Nagel)
libraries were prepared using an Illumina TruSeq Library Kit

value: Spleen+lymph nodes

value: CD4+CD25- T cells

value: WT


title: DLN-Tconv from B16OVA-bearing Rel-icKO mice

description: 10x Genomics


title: AC16 Clone 7G5, IKK2-EE

value: CVB3+ Clone 7G5


title: AC16 Clone 7F4, IkBa-SR


title: Ctrl mouse Tconv cells, rep. 4


title: MEG01, LSD1i, rep3

value: 4µM GSK-LSD1


title: Protocol 2 Control biol rep 2

value: Microglia

value: Control


title: Protocol 2 Control biol rep 1


title: Ctrl mouse Tconv cells, rep. 1


title: Ctrl mouse Tconv cells, rep. 2


title: Protocol 1C HMGB1 biol rep 3


title: AC16 Clone 7F4, BIRB796


title: AC16 Clone 7F4, pBABE-DMSO

value: pBABE-DMSO


title: MEG01, LSD1i, rep2

value: wild type


title: AC16 Clone 7E7, pBABE-DMSO

value: CVB3+ Clone 7E7


title: MEG01, LSD1i, rep1


title: Rel-KO mouse Tconv cells, rep. 4

value: Rel-cKO


title: AC16 Clone 7E7, MKK6-EE


title: MEG01, GFP, rep3


title: Rel-KO mouse Tconv cells, rep. 3


title: Protocol 1C HMGB1 biol rep 1

value: Brain


title: AC16 Clone 7F4, IKK2-EE


title: AC16 Clone 7E7, IKK2-EE


title: Rel-KO mouse Tconv cells, rep. 2


title: MEG01, Non Treated, rep2

value: NT


title: Protocol 1C Control biol rep 3


title: AC16 Clone 7E7, IkBa-SR

value: IkBa-SR


title: MEG01, Non Treated, rep1


title: Protocol 1C Control biol rep 2


title: DTCs, IAV_2

city: Frankfurt am Main

first: Benjamin

middle: Florian

last: Koch

address: Theodor-Stern-Kai 7

department: Nephrology

institute: Goethe University Hospital

data_processing:
Basecalls performed using CASAVA version 1.4 and
Illumina BCL files were converted to FASTQ by bcl-convert.
Next FASTQ reads were aligned to a human reference genome (GRCh38.p12 cDNA) index by kallisto (version 0.46.1).
Afterwards sleuth (version 0.30.0) was employed for differential expression analysis using the Wald test (adjusted p-value (q-value) <0.05).
Genome_build: hg38
Supplementary_files_format_and_content: Tab-separated (tsv) value files containing kallisto TPM -and gene counts for each sample
Supplementary_files_format_and_content: The sleuth output file from differential expression analysis (xslx).

source_name: Primary distal tubular cells

growth_protocol: Distal tubular cells (DTC) were isolated from human kidney tissue using magnetic cell separation technology using a mAb recognizing Tamm Horsfall glycoprotein (THG, clonotype no. 109, purified supernatant from hybridoma established in our laboratory), a speciﬁc antigen of the thick ascending limb of Henle’s loop and the early distal convoluted tubule. DTC were maintained in M199 medium (Sigma-Aldrich, Germany) supplemented with 10% fetal bovine serum (FBS, Biochrom, Germany).

extract_protocol:
Total RNA was extracted 12 hours post infection from the H1N1(pdm09)-infected / non-infected DTC by Qiagen RNeasy Maxi Kit (Qiagen, Hilden, Germany), including on-column removal of DNA by digestion with rDNase for 15 min at room temperature, and 500 ng (each showing a RIN score from >9) were used for library preparation.
After depletion of ribosomal RNA (QIAseq FastSelect RNA Removal Kit, Qiagen, Hilden, Germany) directional libraries were prepared with a NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® sequencing (#E7420S, New England Biolabs, Frankfurt, Germany).

treatment_protocol: DTC grown in 6-well plates were either left uninfected or were infected with H1N1(pdm09) at a MOI = 1

value: Primary distal tubular cells (DTCs)

tag: infection

value: influenza A virus (IAV)


title: Rel-KO mouse Tconv cells, rep. 1


title: AC16 Clone 7E7, BIRB796


title: Rela-KO mouse Tconv cells, rep. 4

value: Rela-cKO


title: AC16 Clone 7E11, pBABE-DMSO

value: CVB3+ Clone 7E11


title: DTCs, IAV_1


title: Rela-KO mouse Tconv cells, rep. 3

value: Spleen+lymph nodes

value: CD4+CD25- T cells


title: AC16 Clone 9B4, IKK2-EE

value: CVB3+ Clone 9B4


title: Protocol 1C HMGB1 biol rep 2


title: DTCs, mock_2

value: untreated


title: Protocol 1B HMGB1 biol rep 2

value: Microglia


title: AC16 Clone 7E11, IKK2-EE


title: Protocol 1B HMGB1 biol rep 3


title: MEG01, Non Treated, rep3


title: DTCs, mock_1


title: AC16 Clone 7E11, MKK6-EE


title: Protocol 1B HMGB1 biol rep 1


title: RNA-Seq - Treg WT ex vivo 3

city: Philadelphia

first: Matthew

middle: C

last: Pahl

state: PA

address: 3615 Civic Center Blvd

institute: Children's Hospital of Philadelphia

data_processing:
Bases were called using Illumina bcl2fastq2 conversion v2.29
The pair-end fastq files were mapped to genome assembly mm9 by STAR (v2.6.0c) for each replicate.
htseq-count (v0.6.1)39 with parameter settings -f bam -r pos -s reverse -t exon -m union
The gene features annotated as rRNAs were removed from the final sample-by-gene read count matrix.
The raw reads on genes features with total CPM (read counts per million) value of less than 3.66 (the bottom 25% gene features when comparing the highest count per condition across all samples) were removed from differential analysis. The trimmed mean of M-values (TMM) method were used to calculate normalization scaling factors and quasi-likelihood negative binomial generalized log-linear (glmQLFit) approach was applied to the count data and through pairwise comparisons of stimulated and unstimulated IK cko and WT. The differential expression genes (DEGs) between were identified with cut-off FDR < 0.05 and absolute logFC>1.
TPM values were calculated
Assembly: mm9
Supplementary files format and content: tab-delimited text files include TPM for each sample

source_name: Children’s Hospital of Philadelphia

extract_protocol:
Total CD4+ T cells isolated from individual WT YFP Cre+ and Ikzf1-Treg-cko mice (3 biological replicates) were sorted for YFP+ Tregs on a FACS Jaz sorter. For stimulation, Tregs were activated with plate bound anti-CD3 and anti-CD28 (1 ug/ml each) for 4 hrs. Total RNA was isolated from the unstimulated and stimulated Tregs using Direct-zol RNA micro prep kit (Zymo Research).
RNA samples were depleted of rRNA using the QIAseq FastSelect RNA Removal Kit then processed into libraries using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina according to manufacturer’s instructions. Quality and quantity of the libraries was measured using the Bioanalyzer 2100 DNA chip and Qubit Fluorometer. Libraries were pooled and sequenced on the NovaSeq 6000 platform using paired-end 51bp reads at the Center for Spatial and Functional Genomics at CHOP.
Ribosomal RNA was depleted from the total RNA using QIAseq fast select multi-RNA removal kit for mouse RNA(Qiagen) and then RNAseq libraries were made using NEB Next Ultra II Directional RNA library prep kit for Illumina.

value: WT

value: unstimulated

value: Tregs dervived from spleen


title: Blimp1 KO rep3

city: Pittsburgh

last: Shlomchik

address: The Assembly, 5051 Centre Avenue

department: Department of Immunology

institute: University of Pittsburgh

description: germinal centers sorted from 50/50 mixed bone marrow chimera (Prdm1 flox/flox CD19 Cre/+ CD45.2/2 and Prdm1 wt/wt CD19 Cre/+ CD45.1/1) day 12 post immunization with NP-CGG in alum

data_processing:
Raw reads quality and adapter sequences were checked using fastqc (v. 0.11.9).
Filtered adaptor and poor quality sequences respectively, using trimgalore(v.0.6.5 )
The reference genome (mm10) based alignment of clean reads were performed using STAR (v.2.7.9a) (Dobin et al., 2013).
Gene-level counts were determined using featureCounts packgae by subread/2.0.1 (Liao et al. 2014).
Raw counts were analyzed for differential expression using the “voom” method (Law et al. 2014) in the “limma” R package (Ritchie et al. 2015).
Assembly: Mus musculus reference genome (mm10).
Supplementary files format and content: tab-delimited text files include log2 normalized expression values for each Sample.

source_name: spleen

extract_protocol:
RNA purification was performed using the Qiagen RNeasy Micro Plus Kit. Libraries were generated using the SMART-Seq v4 Ultra Low Input RNA kit followed by Nextera FLEX using UDI set B indexes. Samples were sequenced using NovaSeq 6000 or NextSeq 2000 flowcells to obtain 20M 2x75 bp reads. Some samples were sequenced as 2x101 bp reads. Cells were collected via FACS, washed twice in PBS + 1% FCS, resuspended in 350 ul RLT Plus Buffer (Qiagen) with 1% 2-Me, and frozen at -80 ⁰C. RNA purification was performed using the Qiagen RNeasy Micro Plus Kit.
Libraries were generated using the SMART-Seq v4 Ultra Low Input RNA kit followed by Nextera FLEX using UDI set B indexes. Samples were sequenced using NovaSeq 6000 or NextSeq 2000 flowcells to obtain 20M 2x75 bp reads. Some samples were sequenced as 2x101 bp reads.

treatment_protocol: Cells were surfaced stained using antibodies for flow cytometry and sorted on BD FacsAria.

value: Prdm1 flox/flox CD19 Cre/+

value: spleen

value: Germinal Center B cells


title: Rela-KO mouse Tconv cells, rep. 1


title: AC16 Clone 7E11, BIRB796


title: Protocol 1B Control biol rep 3

value: Brain

value: Control


title: RNA-Seq - Treg WT ex vivo 2

department: Center for Spatial and Functional Genomics


title: Protocol 1B Control biol rep 2


title: Blimp1 KO rep2


title: Blimp1 KO rep1


title: Protocol 1C Control biol rep 1


title: RNA-Seq - Treg WT ex vivo 1


title: AC16 Clone 7C2, MKK6-EE

value: CVB3+ Clone 7C2


title: Rela-KO mouse Tconv cells, rep. 2


title: Protocol 1A HMGB1 biol rep 3


title: Blimp1 WT rep3

value: CD19 Cre/+


title: RNA-Seq - Treg WT ex vivo stimulated 3

value: stimulated


title: Protocol 1A HMGB1 biol rep 2


title: RNA-Seq - Treg WT ex vivo stimulated 2


title: Blimp1 WT rep2


title: AC16 Clone 7C2, IkBa-SR

value: IkBa-SR


title: Blimp1 WT rep1


title: RNA-Seq - Treg WT ex vivo stimulated 1


title: AC16 Clone 7C2, BIRB796


title: Protocol 1A HMGB1 biol rep 1


title: AC16 Clone 7E11, IkBa-SR

value: CVB3+ Clone 7E11


title: RNA-Seq - Treg Ikzf1 conditional knockout ex vivo 3

value: Ikzf1 conditional knockout


title: Protocol 1A Control biol rep 3


title: Ka539 hsc-lipo 2

city: Hangzhou

first: Li

last: jinxin

address: 1369 West Wenyi Road

country: China

institute: Zhejiang University

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data were trimmed by Trimmomatic (v0.39).
Clean data were aligned to the mouse reference genome mm10 by HISAT2 (v2.1.0) with default setting.
htseq-count (v0.13.5) was used to calculate genes counts with parameter “--mode intersection-strict --stranded no --minaqual 1”.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each Sample .

growth_protocol: Ka539 cells were mouse B-cell leukemia/lymphoma mixed cell line cultured in 45% DMEM +45% IMDM +10% FBS+β-Me medium. C1498, a mouse acute myeloid leukemia cell line, was cultured with DMEM+10% FBS and passed every 72 hours.

extract_protocol: Total RNA was extracted by trizol method, and RNA was extracted by isopropyl alcohol, and washed with 75% alcohol.

treatment_protocol: About 100 0,000 cells were inoculated in each hole of the flat bottom 6-well plate.Cells were harvested 24 hours after treatment with the drug.

value: lymphocyte


title: Ka539 hsc-lipo 1


title: RNA-Seq - Treg Ikzf1 conditional knockout ex vivo 2


title: AC16 Clone 6E8, pBABE-DMSO

value: CVB3+ Clone 6E8

value: pBABE-DMSO


title: RNA-Seq - Treg Ikzf1 conditional knockout ex vivo 1


title: Ka539 lipo 2

value: WT


title: Protocol 1B Control biol rep 1

value: Microglia


title: Protocol 1A Control biol rep 2


title: AC16 Clone 7C2, pBABE-DMSO


title: AC16 Clone 6E8, MKK6-EE


title: AC16 Clone 6E8, IKK2-EE


title: Protocol 1A Control biol rep 1


title: Ka539 lipo 1


title: AC16 Clone 7C2, IKK2-EE


title: RNA-Seq - Treg Ikzf1 conditional knockout ex vivo stimulated 3

value: Tregs dervived from spleen


title: Tumor_sgCda_5

city: Leuven

first: Sandrine

last: Da Cruz

state: Flemish Brabant

address: ON 5 Herestraat 49

department: KU Leuven Department of Neurosciences

country: Belgium

institute: VIB-KU Leuven Center for Brain and Disease Research

data_processing:
FastQC v0.11.5
adapter removal using fastxtoolkit- fastx_clipper v0.0.13
aligning using tophat2.0.10-bowtie2
gene expression matrix generation using HTSeq v07.2
Genome_build: mm10.ensembl
Supplementary_files_format_and_content: Collated count matrix derived from raw data files

source_name: tumor

growth_protocol: 4x10e6 sgNT and sgCda Panc02 cells were injected subcutaneously (s.c.) in the right flank of the C57BL/6J mouse in a final suspension of 200 μL PBS. Tumor volumes were measured at least three times per week. At day 16 after injection, tumor-bearing mice were sacrificed by cervical dislocation

extract_protocol:
Tumor-bearing mice were sacrificed by cervical dislocation and RNA was isolated from tumor tissue using TRIzol (Life Technologies). KAPA Stranded mRNA Sequencing Kit (Roche) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: s.c.Panc02 tumor

value: wild type


title: AC16 Clone 6E8, IkBa-SR


title: C1498 hsc-lipo 1

value: Myeloid cell


title: AC16 Clone 6E8, BIRB796


title: RNA-Seq - Treg Ikzf1 conditional knockout ex vivo stimulated 2


title: RNA-Seq - Treg Ikzf1 conditional knockout ex vivo stimulated 1


title: C1498 hsc-lipo 2


title: Tumor_sgCda_4


title: Tumor_sgNT_5


title: C1498 lipo 2


title: AC16 Clone 2E3, pBABE-DMSO

value: CVB3+ Clone 2E3


title: Tumor_sgNT_4


title: AC16 Clone 2E3, MKK6-EE


title: Treg from WT mice ex vivo 3 H3K27ac_input

data_processing:
Bases were called using Illumina bcl2fastq2 conversion v2.29
Reads were aligned to mm9 using bowtie2 and duplicated reads were marked using Picard with parameters VALIDATION_STRINGENCY=LENIENT and ASSUME_SORTED=true and removed samtools.
Peaks were called using MACS2 with the parameters -g mm9 –nomodel –p 0.01 –keep-dup_all with the – extsize estimated fragment size from the strand cross correlation for each replicate of H3K27ac, Ikzf1, or Foxp3 with matching input sample.
Within condition peaks were filtered to ones found in at least two replicates.
bigwig files were generated using deeptools (v 3.30) bamCoverage function with the parameters --normalizeUsing RPGC --effectiveGenomeSize 2304947926 --binSize 10 --extendReads
Assembly: mm9
Supplementary files format and content: bigwig files

extract_protocol:
5x10^6 purified cells were fixed in medium for 15 minutes at room temperature using complete cell fixative solution prepared using formaldehyde and cell fixative solution from the kit. The reaction was stopped by adding 1/20 media volume of stop solution, cells were washed with ice-cold PBS and a cell pellet was stored at -80C  for later use or cells were lysed in chromatin preparation buffer cells as described in the protocol. The cell pellet was resuspended in ChIP buffer and chromatin was sonicated by a QSonica Q800R sonicator with settings: amplitude 20%, pulse for 30 seconds on, 30 second off, for a total of 30 cycles. For input DNA preparation, 25 ul of the sonicated sample was removed and DNA was isolated as suggested in the protocol. An agarose (1%) gel electrophoresis was performed for DNA isolated from the input fraction to determine the sonication efficiency. 5x106 purified cells were fixed in medium for 15 minutes at room temperature using complete cell fixative solution prepared using formaldehyde and cell fixative solution from the kit. The reaction was stopped by adding 1/20 media volume of stop solution, cells were washed with ice-cold PBS and a cell pellet was stored at -80C  for later use or cells were lysed in chromatin preparation buffer cells as described in the protocol. The cell pellet was resuspended in ChIP buffer and chromatin was sonicated by a QSonica Q800R sonicator with settings: amplitude 20%, pulse for 30 seconds on, 30 second off, for a total of 30 cycles. For input DNA preparation, 25 ul of the sonicated sample was removed and DNA was isolated as suggested in the protocol. An agarose (1%) gel electrophoresis was performed for DNA isolated from the input fraction to determine the sonication efficiency. 5x106 purified cells were fixed in medium for 15 minutes at room temperature using complete cell fixative solution prepared using formaldehyde and cell fixative solution from the kit. The reaction was stopped by adding 1/20 media volume of stop solution, cells were washed with ice-cold PBS and a cell pellet was stored at -80C  for later use or cells were lysed in chromatin preparation buffer cells as described in the protocol. The cell pellet was resuspended in ChIP buffer and chromatin was sonicated by a QSonica Q800R sonicator with settings: amplitude 20%, pulse for 30 seconds on, 30 second off, for a total of 30 cycles. For input DNA preparation, 25 ul of the sonicated sample was removed and DNA was isolated as suggested in the protocol. An agarose (1%) gel electrophoresis was performed for DNA isolated from the input fraction to determine the sonication efficiency. For all ChIP-seq experiments, 3 biological replicates of cells isolated from 3 individual mice were used. Chromatin immunoprecipitations were performed using ChIP-IT high-sensitivity kits (cat #53040, Active Motif) following the manufacturer’s instructions. Briefly, 5x106 purified cells were fixed in medium for 15 minutes at room temperature using complete cell fixative solution prepared using formaldehyde and cell fixative solution from the kit. The reaction was stopped by adding 1/20 media volume of stop solution, cells were washed with ice-cold PBS and a cell pellet was stored at -80C  for later use or cells were lysed in chromatin preparation buffer cells as described in the protocol. The cell pellet was resuspended in ChIP buffer and chromatin was sonicated by a QSonica Q800R sonicator with settings: amplitude 20%, pulse for 30 seconds on, 30 second off, for a total of 30 cycles. For input DNA preparation, 25 ul of the sonicated sample was removed and DNA was isolated as suggested in the protocol. An agarose (1%) gel electrophoresis was performed for DNA isolated from the input fraction to determine the sonication efficiency.  ChIP-validated anti-mouse Ikaros antibody (cat #39355) and H3K27Ac antibody (cat #39133) were purchased from Active Motif. For Foxp3 ChIP-seq, eBioscience anti-mouse monoclonal antibody (cat#14-5773-82) was purchased from ThermoFisher Scientific.
The volume of the sheared chromatin was adjusted to 200 ul using ChIP buffer, and to which was added 5 ul of Protease inhibitor, and a mix containing ChIP antibody (4 ug) and 5 ul of blocker, mixed and pre-incubated at room temperature for a minute. Final volume of the ChIP reaction was 240 ul, which was incubated at 4C overnight on a rotator. Antibody precipitated chromatin immune complexes were collected using washed protein G agarose beads and immune complexes were washed 5X in ChIP filtration columns using wash buffer, and eluted the DNA with elution buffer. The eluted DNA was reverse cross linked and further purified through DNA purification columns. ChIP’d DNA was eluted from the column using 30 ul of DNA purification elution buffer. All ChIP-seq and input DNA libraries were made using ThruPLEX DNA-Seq kit (cat #R400674, Takara Bio, USA) following the manufacturer’s instructions. In brief, the fragmented DNA obtained from ChIP reaction or input DNA was end repaired to generate blunt ends, to which stem-loop adaptors with blocked 5’ ends are ligated. Libraries were amplified through high fidelity amplification buffer mix and Takara dual indexing primers (cat# R400407). Finally, the amplified dual indexed libraries were purified using AMpure XP beads (Beckman Coulter, Cat # A63880) at 1:1 ratio. The purified DNA was recovered from the beads using 20 ul of TE buffer. The library quality was checked on a bioanalyzer using high sensitivity DNA Chip. Library DNA concentration was determined using Qubit. Dual-indexed ChIP-seq libraries were pooled and sequenced on a the Illumina NovaSeq 6000 platform.

value: Tregs derived from spleen

tag: antibody

value: input


title: C1498 lipo 1


title: Tumor_sgCda_3


title: Treg from WT mice ex vivo 2 H3K27ac_input


title: AC16 Clone 2E3, IKK2-EE


title: AC16 Clone 2E3, IkBa-SR


title: Treg from WT mice ex vivo 1 H3K27ac_input


title: Tumor_sgNT_3


title: Panc02_sgCda_3

growth_protocol: sgNT and sgCda PancO2 cells were treated for seven days with or without doxycycline (2.5ug/mL, Sigma-Aldrich) to induce Cas9 expression and grown for seven more days without doxycycline before being used

extract_protocol:
RNA was isolated using TRIzol (Life Technologies). Starting from total RNA, poly-adenylated fragments were isolated, reverse transcribed and converted into indexed sequencing libraries using the KAPA stranded mRNA-seq kit (Sopachem, Eke, Belgium)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: with doxycicline


title: Treg from WT mice ex vivo 3 H3K27ac_chip


title: AC16 Clone 1C2, pBABE-DMSO

value: CVB3+ Clone 1C2


title: Tumor_sgCda_2


title: AC16 Clone 1C2, MKK6-EE


title: Tumor_sgCda_1


title: Panc02_sgNT_3

treatment_protocol: with or without doxycycline (2.5ug/mL, Sigma-Aldrich)


title: AC16 Clone 2E3, BIRB796


title: 6A3, CK2

city: Yangzhou

first: Mingnan

last: Qu

state: Jiangsu

address: Pazhou Dadao Rd, 17-19

institute: Yangzhou Univerisity

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to Oryza MSU7.0 database using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork.
Assembly: Oryza MSU7.0 database
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample.

organism: Oryza sativa

source_name: leaves

growth_protocol: Seedlings were cultivated in glass test tubes using 0.5× Murashige and Skoog (½ MS) solid medium, at 26 °C under a photoperiod of 13h/11h (light/dark).

extract_protocol:
the total RNA was isolated from the leaf tissue using the RNA extraction kit (Huayueyang, China).
The RNA-Seq library construction was performed using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, Ispawich, USA) following the manufacturer’s instructions.

value: leaves

value: Control


title: Panc02_sgNT_2

value: without doxycicline


title: Panc02_sgCda_2


title: Tumor_sgNT_2


title: Naïve CD4 T cell from WT mice ex vivo 3 H3K27ac_chip

value: Naïve CD4 Tcells


title: Treg from WT mice ex vivo 1 H3K27ac_chip


title: K3, CK2

value: WT (K3)


title: Panc02_sgNT_1


title: Panc02_sgCda_1


title: PancO2_PD1_70

extract_protocol:
At end-stage, tumor-bearing mice were sacrificed by cervical dislocation and RNA was isolated from tumor tissue using TRIzol (Life Technologies). Starting from total RNA, poly-adenylated fragments were isolated, reverse transcribed and converted into indexed sequencing libraries using the Illumina TruSeq RNA sample preparation kit V2 according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: After tumor injection, mice were randomized and treated intraperitoneally (i.p.) with 10 mg/kg α-PD-1 (BioXcell) or α-CTLA4 or control IgG from rat serum (Sigma-Aldrich)

value: s.c.PancO2 tumor

value: 10 mg/kg α-PD-1


title: Panc02_sgNT_4


title: Naïve CD4 T cell from WT mice ex vivo 3 H3K27ac_input

value: WT


title: Tumor_sgNT_1


title: AC16 Clone 1C2, IKK2-EE


title: PancO2_PD1_68


title: AC16 Clone 1C2, IkBa-SR

value: IkBa-SR


title: Naïve CD4 T cell from WT mice ex vivo 2 H3K27ac_input


title: Naïve CD4 T cell from WT mice ex vivo 1 H3K27ac_input


title: Panc02_sgCda_4


title: 6A3, CK1


title: AC16 Clone 1C2, BIRB796


title: Treg Ikzf1cko mice ex vivo 3 H3K27ac_input


title: Treg Ikzf1cko mice ex vivo 1 H3K27ac_input


title: PancO2_PD1_71


title: Treg from WT mice ex vivo 2 H3K27ac_chip


title: PancO2_CTLA_58

value: 10 mg/kg α-CTLA4


title: Human H1 RD SPRITE

description: H1 human embryonic stem cells

data_processing:
Adapters were trimmed from raw paired-end fastq files using Trim Galore! v0.6.2 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and assessed with Fastqc v0.11.9. Subsequently, the DPM (GATCGGAAGAG) and RPM (ATCAGCACTTA) sequences are trimmed using Cutadapt v2.5 from the 5’ end of Read 1 along with the 3’ end DPM sequences that result from short reads being read through into the barcode. The additional trimming helps improve read mapping in the end-to-end alignment mode. The SPRITE barcodes of trimmed reads are identified with Barcode ID v1.2.0 (https://github.com/GuttmanLab/sprite2.0-pipeline) and the ligation efficiency is assessed. Reads with an RPM or a DPM barcode are split into two separate files, to process RNA and DNA reads individually downstream, respectively.
RNA reads were aligned to GRCm38.p6 with the Ensembl GRCm38 v95 gene model annotation using Hisat2 v2.1.01 with a high penalty for soft-clipping --sp 1000,1000. Unmapped and reads with a low MapQ score (samtools view -bq 20) were filtered out for downstream realignment. Mapped reads were annotated for gene exons and introns with the featureCounts tool from the subread package v1.6.4 using Ensembl GRCm38 v95 gene model annotation and the Repeat and Transposable element annotation from the Hammel lab. Filtered reads were subsequently realigned to our custom collection of repeat sequences using Bowtie v2.3.5, only keeping mapped and primary alignment reads. For the H1 dataset, hg38 genome annotation was used.
DNA reads were aligned to GRCm38.p6 using Bowtie2 v2.3.5, filtering out unmapped and reads with a low MapQ score (samtools view -bq 20). Data generated in F1 hybrid cells (pSM33: C57BL/6 × 129SV-Jae or pSM44: 129 × castaneous) were assigned the allele of origin using SNPsplit v0.3.4. RepeatMasker defined regions with milliDev <= 140 along with blacklisted v2 regions were filtered out using Bedtools v2.29.0. For the H1 dataset, hg38 genome assembly was used.
RNA and DNA reads were merged, and a cluster file was generated for all downstream analysis. MultiQC v1.6 was used to aggregate all reports.
Assembly: mm10 and hg38
Supplementary files format and content: Each cluster occupies one line of the .clusters text file. A cluster corresponds to all reads with a shared series of tags and is identified by the barcode name and genomic alignments of contained reads.
Supplementary files format and content: Config files contain the SPRITE tag sequence strings and sample identifiers which were embedded in the DPM tag.

extract_protocol:
SPRITE crosslinking, lysis, and DNA fragmentation.
SPRITE library construction as previously described in Quinodoz et al 2022 and Quinodoz et al 2021.

value: H1 hESC

value: H1 human embryonic stem cells


title: Treg Ikzf1cko mice ex vivo 3 H3K27ac_chip


title: K3, CK1


title: PancO2_CTLA_57

value: wild type


title: Treg Ikzf1cko mice ex vivo 1 H3K27ac_chip

value: Tregs derived from spleen


title: Naïve CD4 T cell from WT mice ex vivo 1 H3K27ac_chip


title: PancO2_CTRL_54

value: 10 mg/kg IgG


title: Treg Ikzf1cko mice ex vivo 2 H3K27ac_input

value: input


title: Naïve CD4 T cell from Treg Ikzf1cko mice ex vivo 3 H3K27ac_input


title: PancO2_PD1_64


title: MCF10A DBF4-deficient clone30 Replicate 1

type: genomic

city: PARIS

first: Chrystelle

last: Maric

address: 15 rue Hélène Brion

department: UMR7592 Institut Jacques-Monod

institute: CNRS

description: Biological replicate 1 of 2 MCF10A isogenic DBF4-30 deficient cells

hyb_protocol: The hybridization was performed according to the manufacturer instructions on 4× 180K human microarray.

scan_protocol: Microarrays were scanned with an Agilent's High-Resolution C Scanner using a resolution of 3 µm and the autofocus option.

data_processing: Feature extraction was performed with the Feature Extraction 9.1 software (Agilent technologies). For each experiment, the raw data sets were automatically normalized by the Feature extraction software. Analysis was performed with the START-R software.

source_name: MCF10A isogenic DBF4-deficient breast epithelial cells

label_protocol: Microarray hybridization requires a minimum of 1000 ng of DNA. To obtain sufficient specific immunoprecipited DNA, whole genome amplification (WGA) was conducted (Seq-plex, Sigma). To be sure that this step does not introduce bias, an after WGA qPCR was performed to confirm the specific enrichment in each fractions S1 and S2. After amplification, early and late neo-synthesized DNA were labeled with Cy3 and Cy5 ULS molecules (Genomic DNA labeling Kit, Agilent) as recommended by the manufacturer.

growth_protocol: MCF10A cells were cultured using DMEM supplemented with 5% (v/v) horse serum, 25 ng/ml cholera toxin, 10 μg/ml insulin, 20 ng/ml epidermal growth factor (Peprotech), 500 ng/ml hydrocortisone, 50 U/ml penicillin and 50 μg/ml streptomycin.

extract_protocol: Cells were incubated with 50µM BrdU at 37°C for 90 min. Cells were then collected, washed three times in PBS, fixed in 75% final cold EtOH and stored at -20°C. BrdU labelled cells were incubated with 80 μg/mL Propidium Iodide and with 0.4 mg/ml RNaseA for 1 hr at room temperature. 150,000 cells were sorted in early (S1) and late (S2) S-phase fractions using a Fluorescence Activated Cell Sorting system (FACS Aria Fusion, BD). Immunoprecipitation of neo-synthesized DNA was performed using an anti-BrdU antibody (10 μg, purified mouse Anti-BrdU, BD Biosciences, #347580). Control quantitative PCRs (qPCRs) were performed using oligonucleotides specific of early (BMP1 gene) or late (DPPA2 gene) replicating regions.

treatment_protocol: XL413 (synthesised in-house) was used at a concentration of 10 μM.

tag: gender

value: female

tag: tumor stage

value: non tumorigenic

tag: sample type

value: Nascent DNA from Early S-phase

tag: sampel type

value: Nascent DNA from late S-phase


title: PancO2_CTLA_62

tag: tissue


title: MCF10A DBF4-deficient clone11 Replicate 1

description: Biological replicate 1 of 2 MCF10A isogenic DBF4-11 deficient cells


title: Naïve CD4 T cell from Treg Ikzf1cko mice ex vivo 2 H3K27ac_input

value: Naïve CD4 Tcells


title: PancO2_CTLA_61

tag: strain


title: PancO2_CTRL_49

tag: treatment


title: Treg Ikzf1cko mice ex vivo 2 H3K27ac_chip


title: Naïve CD4 T cell from Treg Ikzf1cko mice ex vivo 1 H3K27ac_input


title: PancO2_CTRL_51

tag: cell line


title: Naïve CD4 T cell from Treg Ikzf1cko mice ex vivo 3 H3K27ac_chip


title: CT26_PD1_42

value: BALB/c

value: s.c.CT26 tumor


title: CT26_PD1_46

value: 10 mg/kg α-PD-1


title: Naïve CD4 T cell from Treg Ikzf1cko mice ex vivo 1 H3K27ac_chip


title: PancO2_CTRL_48

value: s.c.PancO2 tumor


title: Treg WT ex vivo 3 Ikaros_input

value: WT


title: Naïve CD4 T cell from Treg Ikzf1cko mice ex vivo 2 H3K27ac_chip


title: Riftia_trophosome_sample_HS_noN_HO_biological_replicate_3

city: Cambridge

first: Jessica

last: Mitchell

state: Massachusetts

address: 16 Divinity St, Biolabs # 3102

department: Department of Organismic and Evolutionary Biology

institute: Harvard University

description:
Riftia pachyptila/Candidatus Endoriftia persephone
1310j_RSEMbt2.genes.results (column names of processed data file Endoriftia_rsem_gene_count.matrix.txt)

data_processing:
raw, unfiltered sequencing reads was assessed using FastQC
adapter sequences were removed with TrimGalore!
overrepresented reads were removed (https://github.com/harvardinformatics/TranscriptomeAssemblyTools) and rRNA was filtered out using the silva rRNA database.
Assembly: transcript abundances were quantified with RSEM, using the Candidatus Endoriftia persephone genome (GCF_023733635.1) as a reference.
expression estimates were normalized using the TMM method in limma-voom
Using  limma-voom, comparisons between pairs of conditions of interest were then performed by extracting linear contrasts for these comparisons. Differentially expressed genes were determined using a false discovery rate (FDR) cut-off of ≤ 0.05
Coexpression analysis was done using the Weighted Gene Co-Expression Network Analysis (WGCNA) package in R
Supplementary files format and content: A count .matrix file with transcript abundance estimates for each sample corresponding to genes in the Endoriftia genome (GCF_023733635.1)
Supplementary files format and content: A .csv file containing the results of the differential expression analysis for each pairwise comparison
Supplementary files format and content: A text file containg edge weights for each node (gene) in the coexpression network built with WGCNA in R, made to be imported into Cytoscape
Supplementary files format and content: A text file containg node information in the coexpression network built with WGCNA in R, made to be imported into Cytoscape
Supplementary files format and content: A .csv file conatining the module membership (MM) and gene significance (GS) for the conditions sulfide and oxygen, from the WGCNA analysis in R

organism: Candidatus Endoriftia persephonae

source_name: Symbiont-bearing trophosome tissue from R. pachyptila

growth_protocol: Symbiont bearing trophosome sampled from Riftia pachyptila maintained at high pressures in flow through aquaria in seawater amended with sulfide (or hydrogen), oxygen, carbon dioxide and nitrate for ~2-3 days prior to sampling.

extract_protocol:
RNA was extracted using the Direct-Zol RNA MiniPrep (Zymo research Inc), following manufacturer's instructions and quality checked using an Agilent Bioanalyzer 2100
cDNA libraries were constructed from 0.5 to 1 µg of RNA using a modified RNAtag-seq protocol (Shishkin, A. A. et al. Simultaneous generation of many RNA-seq libraries in a single reaction. Nat Methods 12, 323–325 (2016))

treatment_protocol: Treatments varied by sulfide, oxygen, hydrogen and nitrate. For a list of treatments and their abbreviations, see README.txt

tag: host

value: Riftia pachyptila


title: Naïve CD4 T cell from WT mice ex vivo 2 H3K27ac_chip


title: CT26_PD1_41

tag: age


title: MCF10A DBF4-deficient clone11 Replicate 2

description: Biological replicate 2 of 2 MCF10A isogenic DBF4-11 deficient cells


title: MCF10A DBF4-deficient clone30 Replicate 2

description: Biological replicate 2 of 2 MCF10A isogenic DBF4-30 deficient cells


title: MCF10A XL413 treated Replicate 2

description: Biological replicate 2 of 4 MCF10A XL413 treated cells

source_name: MCF10A breast epithelial cells


title: MCF10A XL413 treated Replicate 3

description: Biological replicate 3 of 4 MCF10A XL413 treated cells


title: MCF10A DMSO treated Replicate 4

description: Biological replicate 4 of 4 MCF10A DMSO treated cells


title: Treg WT ex vivo 2 Ikaros_input


title: CT26_PD1_40


title: Riftia_trophosome_sample_HS_noN_HO_biological_replicate_1

description:
Riftia pachyptila/Candidatus Endoriftia persephone
1294j_RSEMbt2.genes.results (column names of processed data file Endoriftia_rsem_gene_count.matrix.txt)

value: Symbiont-bearing trophosome tissue from R. pachyptila


title: MCF10A XL413 treated Replicate 1

description: Biological replicate 1 of 4 MCF10A XL413 treated cells


title: CT26_CTLA_35

value: 10 mg/kg α-CTLA4


title: Riftia_trophosome_sample_HS_N_HO_biological_replicate_2

description:
Riftia pachyptila/Candidatus Endoriftia persephone
127j_RSEMbt2.genes.results (column names of processed data file Endoriftia_rsem_gene_count.matrix.txt)


title: MCF10A DMSO treated Replicate 3

description: Biological replicate 3 of 4 MCF10A DMSO treated cells


title: Treg WT ex vivo 1 Ikaros_input


title: MCF10A DMSO treated Replicate 2

description: Biological replicate 2 of 4 MCF10A DMSO treated cells


title: Riftia_trophosome_sample_HS_N_LO_biological_replicate_3

description:
Riftia pachyptila/Candidatus Endoriftia persephone
119j_RSEMbt2.genes.results (column names of processed data file Endoriftia_rsem_gene_count.matrix.txt)


title: CT26_CTLA_32

value: wild type


title: CT26_CTLA_34


title: Riftia_trophosome_sample_HS_noN_HO_biological_replicate_2

description:
Riftia pachyptila/Candidatus Endoriftia persephone
1300j_RSEMbt2.genes.results (column names of processed data file Endoriftia_rsem_gene_count.matrix.txt)


title: Treg WT ex vivo 2 Ikaros_chip

value: Tregs derived from spleen


title: CT26_CTLA_36


title: NSCLC 5mCAdpBS-Seq Library 04

city: Los Angeles

first: Jordan

last: Cheng

institute: UCLA

description: 5mCAdpBS-Seq (Pre Tag Bisulfite Conversion)

data_processing:
Demultiplexed using SRSLYumi; SRSLYumi (0.4 version), Claret Bioscience
Merge paired end reads; bbmap (38.94)
Fastq trimmed with fastp; fastp (0.23.1 version)
Align with bwa mem or Bsbolt; BWA-mem (0.7.17) or bsbolt (1.6.0)
sam to bam and indexing with Samtools; Samtools (1.9 version)
Quality Cotrol using Qualimap; Qualimap (2.2.2c version)
Move UMI tags with SRSLYumi (srslyumi-bamtag); SRSLYumi (0.4 version), Claret Bioscience
Mark UMI with umi-tools; umi-tools (11.2 version)
Remove duplicates with Picard; Picard (2.27.0 version)
Files split by alignmentsieve (uscfDNA 40-70 and mncfDNA 125-250) with alignmentsieve in deep tools; DeepTools (3.31 version).
Methylation Call; bsbolt (1.6.0)
Assembly: hg38
Supplementary files format and content: CGmap.gz

source_name: Plasma

extract_protocol:
Qiagen Circulating Nucleic Acid Extraction Kit
SRSLYTM PicoPlus DNA NGS Library Preparation  CBS-K250B-24

treatment_protocol: No treatment

value: Plasma

value: NSCLC

tag: molecule type

value: Cell-free DNA


title: NSCLC 5mCAdpBS-Seq Library 03


title: Naïve CD4 T cell from WT mice ex vivo 3 Ikaros_input

value: input


title: Riftia_trophosome_sample_HS_N_HO_biological_replicate_1

description:
Riftia pachyptila/Candidatus Endoriftia persephone
121j_RSEMbt2.genes.results (column names of processed data file Endoriftia_rsem_gene_count.matrix.txt)


title: CT26_CTRL_29

value: 10 mg/kg IgG


title: Naïve CD4 T cell from WT mice ex vivo 2 Ikaros_input


title: Riftia_trophosome_sample_H2_N_HO_biological_replicate_3

description:
Riftia pachyptila/Candidatus Endoriftia persephone
94j_RSEMbt2.genes.results (column names of processed data file Endoriftia_rsem_gene_count.matrix.txt)


title: Treg WT ex vivo 1 Ikaros_chip


title: CT26_CTRL_27


title: NSCLC 5mCAdpBS-Seq Library 02


title: Naïve CD4 T cell from WT mice ex vivo 1 Ikaros_input


title: Riftia_trophosome_sample_H2_noN_LO_biological_replicate_3

description:
Riftia pachyptila/Candidatus Endoriftia persephone
78j_RSEMbt2.genes.results (column names of processed data file Endoriftia_rsem_gene_count.matrix.txt)


title: MCF10A DMSO treated Replicate 1

description: Biological replicate 1 of 4 MCF10A DMSO treated cells

value: female

value: non tumorigenic

value: Nascent DNA from Early S-phase

value: Nascent DNA from late S-phase


title: CT26_CTRL_28

value: BALB/c

value: s.c.CT26 tumor


title: NSCLC 5mCAdpBS-Seq Library 01


title: Riftia_trophosome_sample_HS_N_LO_biological_replicate_2

description:
Riftia pachyptila/Candidatus Endoriftia persephone
115j_RSEMbt2.genes.results (column names of processed data file Endoriftia_rsem_gene_count.matrix.txt)


title: Naïve CD4 T cell from WT mice ex vivo 3 Ikaros_chip

value: Naïve CD4 Tcells

value: WT


title: MCA38_PD1_19

value: s.c.MC38 tumor

value: 10 mg/kg α-PD-1


title: CT26_CTRL_24

value: wild type


title: Riftia_trophosome_sample_H2_noN_LO_biological_replicate_2

description:
Riftia pachyptila/Candidatus Endoriftia persephone
72j_RSEMbt2.genes.results (column names of processed data file Endoriftia_rsem_gene_count.matrix.txt)

value: Riftia pachyptila

value: Symbiont-bearing trophosome tissue from R. pachyptila


title: Naïve CD4 T cell from WT mice ex vivo 2 Ikaros_chip


title: 5mCAdpBS-Seq Library 04

value: Plasma

value: Non-cancer


title: MCA38_PD1_18


title: MCA38_PD1_17


title: Naïve CD4 T cell from WT mice ex vivo 1 Ikaros_chip


title: Treg WT ex vivo 3 Foxp3_input

value: Tregs derived from spleen

value: input


title: Riftia_trophosome_sample_H2_N_LO_biological_replicate_3

description:
Riftia pachyptila/Candidatus Endoriftia persephone
56j_RSEMbt2.genes.results (column names of processed data file Endoriftia_rsem_gene_count.matrix.txt)


title: 5mCAdpBS-Seq Library 03

value: Cell-free DNA


title: 5mCAdpBS-Seq Library 02


title: Riftia_trophosome_sample_H2_N_LO_biological_replicate_2

description:
Riftia pachyptila/Candidatus Endoriftia persephone
54j_RSEMbt2.genes.results (column names of processed data file Endoriftia_rsem_gene_count.matrix.txt)


title: Treg WT ex vivo 2 Foxp3_input


title: MCA38_PD1_16


title: MCA38_CTLA_14

value: 10 mg/kg α-CTLA4


title: 5mCAdpBS-Seq Library 01


title: Treg WT ex vivo 1 Foxp3_input


title: BS-Seq Library 05

description: BS-Seq (Post Tag Bisulfite Conversion)


title: Riftia_trophosome_sample_LS_N_HO_biological_replicate_3

description:
Riftia pachyptila/Candidatus Endoriftia persephone
36j_RSEMbt2.genes.results (column names of processed data file Endoriftia_rsem_gene_count.matrix.txt)


title: Riftia_trophosome_sample_H2_noN_LO_biological_replicate_1

description:
Riftia pachyptila/Candidatus Endoriftia persephone
69j_RSEMbt2.genes.results (column names of processed data file Endoriftia_rsem_gene_count.matrix.txt)


title: MCA38_CTLA_11


title: Treg WT ex vivo 3 Foxp3_chip


title: Riftia_trophosome_sample_H2_noN_HO_biological_replicate_3

description:
Riftia pachyptila/Candidatus Endoriftia persephone
1876j_RSEMbt2.genes.results (column names of processed data file Endoriftia_rsem_gene_count.matrix.txt)


title: BS-Seq Library 03

description: BS-Seq (Post Tag Bisulfite Conversion)


title: MCF10A XL413 treated Replicate 4

description: Biological replicate 4 of 4 MCF10A XL413 treated cells

value: female

value: non tumorigenic

value: Nascent DNA from Early S-phase


title: Treg Ikzf1 conditional knockout ex vivo 3 Foxp3_input

value: Ikzf1 conditional knockout


title: Riftia_trophosome_sample_H2_noN_HO_biological_replicate_2

description:
Riftia pachyptila/Candidatus Endoriftia persephone
1871j_RSEMbt2.genes.results (column names of processed data file Endoriftia_rsem_gene_count.matrix.txt)


title: Treg WT ex vivo 2 Foxp3_chip


title: MCA38_CTLA_8


title: Riftia_trophosome_sample_HS_N_LO_biological_replicate_1

description:
Riftia pachyptila/Candidatus Endoriftia persephone
112j_RSEMbt2.genes.results (column names of processed data file Endoriftia_rsem_gene_count.matrix.txt)


title: BS-Seq Library 01

description: BS-Seq (Post Tag Bisulfite Conversion)


title: MCA38_CTRL_4

value: 10 mg/kg IgG


title: BS-Seq Library 02

description: BS-Seq (Post Tag Bisulfite Conversion)


title: 5mCAdpBS-Seq Library 05


title: MCA38_CTRL_3


title: Riftia_trophosome_sample_LS_N_HO_biological_replicate_2

description:
Riftia pachyptila/Candidatus Endoriftia persephone
28j_RSEMbt2.genes.results (column names of processed data file Endoriftia_rsem_gene_count.matrix.txt)


title: MCA38_CTRL_7


title: retina explant, CRISPRi, donor 011

city: Iowa City

first: Nathaniel

middle: Kevin

last: Mullin

state: IA

address: 375 Newton Road

institute: University of Iowa

data_processing:
An index for the human transcriptome was generated from the human genome assembly GRCh38 using Salmon’s index function (Version 1.10.1). FASTQ quality was confirmed using FastQC (Version 0.11.9) and reads from samples passing initially quality control were quantified against the above index using Salmon’s quant function (Version 1.10.1) with the following settings: --validateMappings --seqBias --gcBias.
Assembly: GRCh38
Supplementary files format and content: Salmon quant output files used for downstreatm differential gene expression analysis.

source_name: retinal explant

extract_protocol:
RNA was isolated using the NucleoSpin RNA kit (Takara Bio, San Jose, CA). RNA was DNase-treated using RQ1 RNase-Free DNase according to manufacturer’s instructions (Promega Corporation, Madison, WI).
Sequencing libraries were prepared by the Genomics Division of the Iowa Institute of Human Genetics. The TruSeq Stranded mRNA library kit was used (Illumina).

treatment_protocol: Human donor eyes were obtained from the Iowa Lions Eye Bank (Coralville, IA) within 4-6 h of death (Table 2) and prepared for explant culture as previously described (27). 10 µl AAV5-RHOp-CRISPR-dSaCas9 (1 x 1012 vg/ml) were applied directly beneath explants and 10 µl were added to the culture medium beneath transwell inserts (20 µl vector per well). Untransduced explants were cultured as controls. Human explants were cultured for seven days in the presence of virus.

value: retinal explant


title: MCA38_CTLA_10

value: s.c.MC38 tumor


title: Riftia_trophosome_sample_HS_N_HO_biological_replicate_3

description:
Riftia pachyptila/Candidatus Endoriftia persephone
136j_RSEMbt2.genes.results (column names of processed data file Endoriftia_rsem_gene_count.matrix.txt)


title: Treg Ikzf1 conditional knockout ex vivo 3 Foxp3_chip


title: human primary T cell lymphoma MR14

city: San Francisco

first: Huimin

last: Geng

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

institute: UCSF

description: total RNA

data_processing:
Raw image data were converted into base calls and fastq files via the Illumina pipeline CASAVA version 1.8 with default parameters. All 50-bp-long paired-end reads were mapped to the reference human genome sequence, hg19, using Tophat2 aligner (Daehwan et al, Genome Biology 2013,14:R36) with the default parameters. The mRNA expression level for each gene was represented as FPKM (fragments per kilobase of transcript per million fragments mapped), called by Cufflinks (Trapnell et al, Nat Biotech 2010, 28: 511–515) in the Tophat2 package.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM values

source_name: human primary T cell lymphoma

growth_protocol: No cultered cells were used.

extract_protocol:
Libraries were prepared according to a version of Illumina's mRNA-Seq protocol (Illumina, CA)
Libraries were prepared according to Illumina's TruSeq RNAseq protocol (Illumina, CA)

tag: cell type

value: Peripheral T-Cell Lymphoma (PTCL)


title: Riftia_trophosome_sample_H2_noN_HO_biological_replicate_1

description:
Riftia pachyptila/Candidatus Endoriftia persephone
1750j_RSEMbt2.genes.results (column names of processed data file Endoriftia_rsem_gene_count.matrix.txt)


title: Treg Ikzf1 conditional knockout ex vivo 1 Foxp3_input


title: Riftia_trophosome_sample_LS_noN_HO_biological_replicate_3

description:
Riftia pachyptila/Candidatus Endoriftia persephone
1369j_RSEMbt2.genes.results (column names of processed data file Endoriftia_rsem_gene_count.matrix.txt)


title: Riftia_trophosome_sample_SW_noN_HO_biological_replicate_3

description:
Riftia pachyptila/Candidatus Endoriftia persephone
1353j_RSEMbt2.genes.results (column names of processed data file Endoriftia_rsem_gene_count.matrix.txt)


title: REL-KO human Tconv, donor 4

data_processing:
Bcl files were converted to fastq using Bcl2fastq (2.20.0).
Gene expression was quantified using Salmon (0.14.1) and the annotation of protein coding genes from gencode v29.
Transcription matrix was done using R package tximport on the salmon results.
Assembly: hg38
Supplementary files format and content: tab delimited file with samples in columns, genes in rows, and estimated raw counts.

source_name: Human blood

value: Human blood

tag: individual

value: donor 4

value: CD4+CD25- T cells

value: REL-/-


title: retina explant, untreated, donor 004

value: untreated control


title: Treg Ikzf1 conditional knockout ex vivo 2 Foxp3_input

value: Tregs derived from spleen

tag: genotype


title: Riftia_trophosome_sample_LS_N_HO_biological_replicate_1

description:
Riftia pachyptila/Candidatus Endoriftia persephone
16j_RSEMbt2.genes.results (column names of processed data file Endoriftia_rsem_gene_count.matrix.txt)

value: Riftia pachyptila

value: Symbiont-bearing trophosome tissue from R. pachyptila


title: MCA38_CTRL_2

value: wild type


title: REL-KO human Tconv, donor 3

value: donor 3


title: retina explant, untreated, donor 011


title: human primary T cell lymphoma MR11

description: total RNA


title: Treg Ikzf1 conditional knockout ex vivo 1 Foxp3_chip


title: human primary T cell lymphoma MR13

description: total RNA


title: Riftia_trophosome_sample_LS_noN_HO_biological_replicate_2

description:
Riftia pachyptila/Candidatus Endoriftia persephone
1330j_RSEMbt2.genes.results (column names of processed data file Endoriftia_rsem_gene_count.matrix.txt)


title: Treg Ikzf1 conditional knockout ex vivo 2 Foxp3_chip


title: human primary T cell lymphoma MR12

description: total RNA


title: REL-KO human Tconv, donor 1

value: donor 1


title: Riftia_trophosome_sample_LS_noN_HO_biological_replicate_1

description:
Riftia pachyptila/Candidatus Endoriftia persephone
1324j_RSEMbt2.genes.results (column names of processed data file Endoriftia_rsem_gene_count.matrix.txt)


title: ATAC-Seq - Treg WT ex vivo 3

data_processing:
Bases were called using Illumina bcl2fastq2 conversion v2.29
Reads were aligned using bowtie2 implimented in the ENCODE pipeline. Reads alignment by offsetting +4bp for all the reads aligned to the forward strand, and -5bp for all the reads aligned to the reverse strand
Open chromatin regions (OCRs) were called using MACS2 implimented in the ENCODE pipeline with the following parameters -p 0.01 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits. The encode blacklist regions (wgEncodeDacMapabilityConsensusExcludable.bed.gz) were removed from called peaks.
Assembly: mm9
Supplementary files format and content: comma deliminated files

extract_protocol:
One hundred thousand cells were lysed with 50 ul of cold lysis buffer (10mM Tris pH 7.4, 10 mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630) and centrifuged at 550g for 10 minutes at 4C. Supernatants were discarded and nuclear pellets were subjected to Tn5 transposition using Nextera DNA preparation kits (cat #1502812). DNA was purified from transposition reaction using Qiagen Min-Elute PCR purification kits.
Transposed DNA fragments were PCR amplified and indexed using Nextera index kits. PCR reaction products were size selected using AMpure-XP beads and DNA fragments were re-suspended in 10 mM Tris-HCl. DNA concentration was determined by Qubit, and ATAC seq library quality was checked on a bioanalyzer. Dual indexed libraries were sequenced on the Illumina NovaSeq 6000 platform.

value: WT

value: unstimulated

value: Tregs dervived from spleen


title: human primary T cell lymphoma MR09

description: total RNA


title: Riftia_trophosome_sample_H2_N_HO_biological_replicate_2

description:
Riftia pachyptila/Candidatus Endoriftia persephone
106j_RSEMbt2.genes.results (column names of processed data file Endoriftia_rsem_gene_count.matrix.txt)


title: Riftia_trophosome_sample_SW_noN_HO_biological_replicate_2

description:
Riftia pachyptila/Candidatus Endoriftia persephone
1347j_RSEMbt2.genes.results (column names of processed data file Endoriftia_rsem_gene_count.matrix.txt)


title: Riftia_trophosome_sample_SW_noN_HO_biological_replicate_1

description:
Riftia pachyptila/Candidatus Endoriftia persephone
1346j_RSEMbt2.genes.results (column names of processed data file Endoriftia_rsem_gene_count.matrix.txt)


title: ATAC-Seq - Treg WT ex vivo 2


title: REL-KO human Tconv, donor 2

extract_protocol:
RNA was isolated with Nucleospin RNA extraction kits (Macherey Nagel)
libraries were prepared using an Illumina TruSeq Library Kit

value: donor 2


title: ATAC-Seq - Treg WT ex vivo 1


title: human primary T cell lymphoma MR10

description: total RNA


title: ATAC-Seq - Treg WT ex vivo stimulated 3

value: stimulated


title: RELA-KO human Tconv, donor 3

value: RELA-/-


title: human primary T cell lymphoma MR07

description: total RNA

value: Anaplastic Large cell lymphoma (ALCL)


title: human primary T cell lymphoma MR06

description: total RNA


title: human primary T cell lymphoma MR08

description: total RNA


title: human primary T cell lymphoma MR05

description: total RNA


title: RELA-KO human Tconv, donor 1

value: Human blood


title: RELA-KO human Tconv, donor 2

value: CD4+CD25- T cells


title: ATAC-Seq - Treg WT ex vivo stimulated 1


title: BS-Seq Library 04

description: BS-Seq (Post Tag Bisulfite Conversion)

value: Plasma

value: Non-cancer

value: Cell-free DNA


title: ATAC-Seq - Treg Ikzf1 conditional knockout ex vivo 3

value: Ikzf1 conditional knockout


title: Control human Tconv, donor 4

value: donor 4


title: ATAC-Seq - Treg Ikzf1 conditional knockout ex vivo 2


title: RELA-KO human Tconv, donor 4


title: human primary T cell lymphoma MR04

description: total RNA


title: ATAC-Seq - Treg WT ex vivo stimulated 2


title: ATAC-Seq - Treg Ikzf1 conditional knockout ex vivo 1


title: Riftia_trophosome_sample_H2_N_HO_biological_replicate_1

description:
Riftia pachyptila/Candidatus Endoriftia persephone
103j_RSEMbt2.genes.results (column names of processed data file Endoriftia_rsem_gene_count.matrix.txt)

value: Riftia pachyptila

value: Symbiont-bearing trophosome tissue from R. pachyptila


title: Arabinose treated, biological replicate 3

city: Newcastle upon Tyne

first: Curtis

last: Cottam

address: The Medical School, Newcastle University, Framlington Place

department: Biosciences Institute

country: United Kingdom

institute: Newcastle University

data_processing:
To estimate transcript abundance, SALMON was used under the default parameters for the mapping of reads to the E. coli O157:H7 strain EDL933 reference sequence (Accession GCA_000006665), retrieved from Ensembl. Transcript level counts outputted from SALMON were then summarised at the gene-level using tximport
Assembly: ASM666v1
Supplementary files format and content: txt files with transcript level counts

organism: Escherichia coli O157:H7

source_name: bacterial cell

growth_protocol: Cells were grown in MEM-HEPES and supplemented with or without 1mg/ml L-arabinose.

extract_protocol:
RNA from samples was prepared using a Monarch Total RNA Miniprep kit (New England Biolabs) following the manufacturer’s instruction and treated with TURBO DNAse. Concentrations and quality were assessed using Qubit (ThermoFisher Scientific).
Ribosomal depletion and library assembly of DNA-free total RNA samples was carried out using an Illumina Ribo-Zero Tru-seq kit according to the manufacturer’s specifications.

value: bacterial cell

value: Arabinose


title: Arabinose treated, biological replicate 2


title: Arabinose treated, biological replicate 1


title: human primary T cell lymphoma MR03

description: total RNA


title: Control, biological replicate 3

value: Control


title: ATAC-Seq - Treg Ikzf1 conditional knockout ex vivo stimulated 3

value: Tregs dervived from spleen


title: Riftia_trophosome_sample_H2_N_LO_biological_replicate_1

description:
Riftia pachyptila/Candidatus Endoriftia persephone
58j_RSEMbt2.genes.results (column names of processed data file Endoriftia_rsem_gene_count.matrix.txt)


title: ATAC-Seq - Treg Ikzf1 conditional knockout ex vivo stimulated 2


title: Control human Tconv, donor 2

value: donor 2

value: WT


title: human primary T cell lymphoma MR02

description: total RNA


title: Control human Tconv, donor 1

value: donor 1


title: ATAC-Seq - Treg Ikzf1 conditional knockout ex vivo stimulated 1

value: stimulated


title: Treg WT ex vivo 1 Foxp3_chip

value: Tregs derived from spleen


title: Control, biological replicate 1


title: Control human Tconv, donor 3

value: Human blood

value: donor 3

value: CD4+CD25- T cells


title: human primary T cell lymphoma MR01

description: total RNA

value: Anaplastic Large cell lymphoma (ALCL)


title: NP69T_Hi-C

status: Public on Mar 27 2024

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

institute: Chiba University

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
Hi-C reads were processed using HiC-Pro.
Assembly: hg19+NC007605.1
Supplementary files format and content: hic

source_name: nasopharyngeal epithelial cell lines

growth_protocol: NP69T was cultured in keratinocyte serum-free medium (Gibco, Carlsbad, CA). C666-1 was cultured in RPMI-1640 medium with 10% FBS (HyClone SH30910.03, GE Healthcare, Chicago, IL) and Penicillin-Streptomycin (Sigma-Aldrich, St. Louis, MO). These cells were incubated in a humidified atmosphere containing 5% CO2 at 37 ℃.

extract_protocol: Hi-C experiment were conducted in biological replicates using MboI, according to the protocol published by Suhas S.P. Rao et al. Cell 2014 (PMID: 25497547).  DNA libraries were prepared during Hi-C protocol according to experimental procedures described in Suhas S.P. Rao et al. Cell 2014 (PMID: 25497547).

value: nasopharyngeal epithelial cell lines

tag: restriction enzyme

value: MboI


title: IPH3_FBY2789_2

city: Namur

first: Carlo

last: Yague-Sanz

address: 61 rue de Bruxelles

department: Medecine

institute: Namur University

data_processing:
Reads were mapped using HISAT2 (Kim et al, 2015) with option --no-splice-alignment on a concatenate genome containing the S. pombe (version ASM294v2.26) and S. cerevisiae chromosomes. Normalization factors were computed based on the proportion of reads mapped to the S. cerevisiae genome as previously described (Larochelle et al, 2018) while the average fragment size was estimated using MACS2 predicted function (Zhang et al, 2008). Based on the normalization factors and averaged fragment size, we used deepTools (Ramirez et al, 2016) to generate normalized coverage files (.bigwig) with options bamCoverage --smoothlength 20 --centerReads -e [average_fragment_size] --scaleFactor [size_factor] -bs 1 -of bigwig. If no spike-in was available (as it is the case for the Pcf11-myc and Set2-TAP ChIP data), the option --normalizeUsing RPKM was used instead of --scale factor.
Assembly: ASM294v2.26
Supplementary files format and content: genome coverage files in bigWig format are provided

organism: Schizosaccharomyces pombe

source_name: S. pombe cells

growth_protocol: For each condition (IP), 50 mL of cell cultures were grown to an OD600nm of ∼0.5 at 30 °C in YES .

extract_protocol:
After quenching the solution with glycine (final concentration of 360 mM), cells were washed twice with a cold Tris-buffer saline (20 mM Tris-HCl [pH 7.5] and 150 mM NaCl) and frozen in liquid nitrogen. Cell pellets from 50 ml cultures were thawed and resuspended in 500 µL of cold lysis buffer (50 mM HEPES-KOH [pH 7.5], 140 mM NaCl, 1 mM EDTA pH 8.0, 1% Triton X-100 and 0.1% Na-deoxycholate) that was supplemented with a protease inhibitor cocktail (1X PMSF and 1X PLAAC) and disrupted vigorously with glass beads in a FastPrep-24TM (MP biomedical) for 3 cycles of 30 sec at 6.5 m/s. Then, 150 µL of cold lysis buffer with proteases was added to increase the volume and samples were sonicated for 12 cycles of 10 sec at 20% amplitude with a Branson digital sonifier. Sonicated chromatin was then incubated overnight at 4 °C with 50 µl of magnetic beads IgG Dynabeads (Life Technologies, 11041) in the case of TAP tagged proteins, or Dynabeads M-280 Sheep Anti-Rabbit IgG (Invitrogen, 11203D) beads coupled with 2 ug of rabbit anti-Histone H3 total (ab1791, abcam), H3K36me3 (ab9050, abcam) or H3K9ac (06-942, Millipore Sigma). Beads were then washed twice for 4 minutes at 4oC with 1 mL of cold lysis buffer, twice with 1 mL of cold lysis buffer with 500 mM NaCl, twice with 1 mL of cold wash buffer (10 mM Tris-HCl [pH 8.0], 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate and 1 mM EDTA), and once with 1 mL of cold Tris-EDTA (TE: 10 mM Tris-HCl [pH 8.0] and 1 mM EDTA [pH8.0]). Bound material was eluted by resuspending the beads in 50 µl elution buffer (50 mM Tris-HCl [pH 8.0], 10 mM EDTA and 1% SDS) at 65 °C for 15 min at 1200 rpm in an Eppendorf Thermomixer. After a short centrifugation, reverse-crosslinking was performed by incubating eluted chromatin with 120 µl of TE and 1% SDS or 5 µl of WCE in 165 µl of TE with 1% SDS at 65 °C overnight. For ChIP-Seq experiments, reverse-crosslinking was perfomed by incubating eluted chromatin with 20 µl of WCE in 150 µl of TE and 1% SDS. Samples were treated with a proteinase K mix (150 mg proteinase K, 60 mg glycogen in TE) and DNA was extracted twice with phenol-chloroform-isoamyl alcohol (25:24:1, [pH8.0], Invitrogen) and once with chloroform (Bioshop). Following ethanol precipitation, pellets were resuspended in 30 µl of TE plus 10 µg of RNAse A and incubated 1 h i at 37 °C. RNase-treated DNA was then purified with a QIAGEN PCR purification kit. The input DNA was diluted 400 times while the coimmunoprecipitated DNA was diluted 100 times in water. DNA were analyzed on a LightCycler 96 Instrument system (Roche) with the addition of the 2X SYBR Green in the presence of 0.15 μM of gene-specific oligonucleotide
ChIP-sequencing libraries were prepared using the SPARQ DNA Sample Prep Kit Illumina Platform (Quantabio) according to the manufacturer's instructions.

treatment_protocol: Cultures were cross-linked with 1% formaldehyde for 20 min at room temperature with manual shaking every 5 min.

tag: fraction

value: H3 IP

tag: spike-in

value: 5 % S. cerevisiae strain mixed before the crosslink

value: h+ lsk1::ura4 ura4-D18

value: S. pombe cells


title: WCE_FBY2789_2

value: input


title: IPH3_FBY2789_1


title: IPH3K36me3_FBY2789_2

value: H3K36me3 IP


title: IPH3K9ac_FBY2789_2

value: H3K9ac IP


title: IPH3K9ac_FBY2567_2

value: h- rpb1-S2A::kanR


title: IPH3_FBY2567_1


title: IPH3_FBY2567_2


title: IPH3K36me3_FBY2567_2


title: Treg WT ex vivo 3 Ikaros_chip

tag: antibody

value: WT


title: IPH3K36me3_FBY2567_1


title: Control, biological replicate 2

value: bacterial cell

value: Control


title: IPH3_FBY2566_2

value: h-


title: WCE_FBY2567_1


title: WCE_FBY2567_2


title: IPH3K36me3_FBY2566_2


title: WCE_FBY2566_2


title: IPTAP_FBY2733_2

value: lsk1D Set2-TAP

value: Set2-TAP IP

value: h+ lsk1::ura4 set2-TAP-hphR ura4-D18


title: IPH3K9ac_FBY2566_2


title: IPH3_FBY2566_1


title: WCE_FBY2733_2


title: IPH3K36me3_FBY2566_1


title: WCE_FBY2566_1


title: IPH3K36me3_FBY2789_1


title: IPTAP_FBY2732_2

value: S2A Set2-TAP

value: h- rpb1 S2A-kanR set2-TAP-hphR


title: WCE_FBY2789_1


title: WCE_FBY2731_2

value: WT Set2-TAP

value: h- Set2-TAP::HphR


title: WCE_FBY2732_1


title: IPTAP_FBY2733_1


title: IPTAP_FBY2732_1


title: WCE_FBY2731_1


title: retina explant, CRISPRi, donor 004

value: retinal explant


title: WCE_FBY2733_1

value: S. pombe cells


title: IPFLAG_FBY2830_1

value: S2A Pcf11-myc Rpb3-flag

value: Rpb3-flag IP

value: h- Rpb3-3flag::hygMX6 Pcf11-myc ::natMX6 CTD S2A-kanR


title: IPFLAG_FBY2830_2


title: WCE_FBY2830_2

value: input


title: IPFLAG_FBY2829_2

value: WT Pcf11-myc Rpb3-flag

value: h- Rpb3-3flag::hygMX6 Pcf11-myc ::natMX6


title: IPFLAG_FBY2829_1


title: WCE_FBY2830_1


title: IPMYC_FBY2830_1

value: Pcf11-myc IP


title: IPMYC_FBY2829_2


title: WCE_FBY2829_2


title: IPMYC_FBY2829_1


title: IPTAP_FBY2731_2


title: WCE_FBY2732_2


title: H3K9K14Ac, HDC1 KO mutant complemented with full length HDC1 gene sequence, control media

city: Bearsden

first: Pawel

last: Herzyk

address: Wolfson Wohl Cancer Research Centre, Garscube Estate

department: College of Medical, Veterinary and Life Sciences

institute: University of Glasgow

description: HDC1c AC ctrl

data_processing:
Fastq files were generated with bcl2fastq v.1.8.4 Illumina software
The raw fastq files were pre-processed to trim the 3’ end adapter and to trim the low quality reads using Cutadapt (version 1.9.2) and Sickle (version 0.940; flags -q 10 -l 54), respectively.
ChIP-seq reads were aligned to the TAIR10 genome using Bowtie version 0.12.7. Only uniquely mapping reads with at most two mismatches in the first 54 bp were retained.
The alignment files were then sorted, and the duplicated reads of the same orientation were removed using Samtools (version 0.1.19). The locations of the mapped ChIP-seq reads were shifted in the 3'end direction by half of the sample-specific mean fragmernt length to represent the centres of sequenced fragments. Reads were then counted in 200 bp long windows and resulting raw counts stored in WIG files.
For each sample the aligned reads positions were shifted in the 3’end direction by half of the sample-specific mean fragment length to represent the centres of sequenced fragments, counted in 200-bp long windows using Sicer (version 1.03)(Zang et al., 2009) and resulting profiles stored in WIG files,
Assembly: TAIR10
Supplementary files format and content: WIG

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Seeds were sterilised with 50% bleach solution, wash with dH2O water three times and stored at 4C for two days.

extract_protocol:
ChIP assays were performed on 2g of tissue as described previously with minor modifications (Sani et al., 2013). A Bioruptor sonicator (Diagenode, B01020001) was used to shear the chromatin using the following settings: 20 cycles x 30 sec ON, 30 sec OFF at high power.
ChIP-seq libraries were prepared using the NEBNext Ultra DNA Prep Kit according to the manufacturer’s protocol, size selected with SPRIselect Beads and amplified by PCR.

treatment_protocol: Sterilized seeds were then sown on 1/2 MS 1% sucrose plates with or without 100 mM NaCl. At day 3 after sowing the seeds were harvested and and snap-frozen with liquid N2.

value: 3 days old

value: seedlings

value: control

tag: chip antibody

value: Anti-H3K9K14Ac (Diagenode pAb-005-050 )


title: IPTAP_FBY2731_1

value: Set2-TAP IP


title: H3K9K14Ac, HDC1 KO mutant complemented with full length HDC1 gene sequence, 100 mM NaCl

description: HDC1c AC salt

value: 100 mM NaCl


title: HDC1 KO mutant expressing RXT3 sequence of HDC1, 100mM NaCl, replicate 3

description: RXT3, S, 3

data_processing:
Fastq files were generated with bcl2fastq v.1.8.4 Illumina software
The raw fastq files were pre-processed to trim the 3’ end adapter and to trim the low quality reads using Cutadapt (version 1.5) and Sickle (version 0.940; flags -q 10 -l 54), respectively.
Transcript expression quantification was performed using Kallisto (version 0.43.0) against the TAIR10 transcriptome.
Read counts related to TAIR10 transcripts were collected, rounded, and summarized into gene-specific read counts.
Differential gene expression was analysewd using DESeq2 (version 1.24.0).
Assembly: TAIR10
Supplementary files format and content: Comma-delimited text fille containing raw gene-count for each sample separately

extract_protocol:
RNA was extracted using hot phenol method and treated with DNAse I. 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruSeq stranded mRNA kit following manufacturer's protocols.

treatment_protocol:
Sterilized seeds were then sown on 1/2 MS 1% sucrose plates with or without 100 mM NaCl.
At day 3 after sowing the seeds were harvested and and snap-frozen with liquid N2.

value: HDC1 KO mutant expressing RXT3-like domain


title: HDC1 KO mutant expressing RXT3 sequence of HDC1, 100mM NaCl, replicate 2

description: RXT3, S, 2


title: NRCFs, miR-142-3p antagomiR-3

city: Nanjing

first: Kun

last: Zhao

address: 101Longmian Avenue

institute: Nanjing Medical University

data_processing:
Quality control was conducted using FastQC. Adapters and low-quality reads were filtered out using Cutadapt . The samples were then aligned to the mRatBN7.2 genome with HISAT2. Quantification of genes expression was achieved through HTSeq. Differentially expressed  were determined using edgeR.
Assembly: mRatBN7.2
Supplementary files format and content: tab delimited text file with FPKM expression

organism: Rattus norvegicus

source_name: Heart

growth_protocol: Primary CFs were isolated from 1- to 2-day-old newborn SD rats (Vital River Biological Co., Ltd.). Briefly, the heart was excised and digested through agitations in buffer containing collagenase type II (Worthington Biochemical Corp., NJ, USA) and pancreatin (Sigma, MO, USA). The atria and great vessels were discarded. The ventricles were cut into small pieces and digested with collagenase type II and pancreatin. Cells from digestion were collected, cultured in complete Dulbecco’s modified Eagle’s medium (DMEM; Biochannel Biotechnology Co., Ltd.) for 2-4 hours to allow for the preferential attachment of CFs. Then, the medium containing cardiomyocytes were removed to enrich CFs. The CFs were cultured at 37°C with 5% CO2 and 95% air. CFs that reached 70%–80% confluency were incubated in the serum-free DMEM medium for overnight starvation.

extract_protocol:
paired-end illumina preparation: Illumina Hiseq 2x150bp configuration single index per lane, RNA library preparation with polyA enrich
Total RNA was extracted using TriPure (Roche), cDNA synthesis was made with Ovation RNA-seq System V2 (NuGEN), Library prep was made with TruSeq  Sample Preparation Kit (Illumina), Hiseq PE Cluster Kit (Illumina) and Hiseq SBS Kit (Illumina) was used for clustering and sequencing

treatment_protocol: We treated cardiac fibroblasts with NC or miR-142-3p antagomiR (n=3).Briefly, 50nM miR-142-3p antagomir or NC was transfected into CFs using Lipofectamine RNAiMAX (Invitrogen, Carlsbad, CA, USA) following the manufacturers’ instructions.

value: Heart

value: NRCFs

value: cardiac fibroblasts

value: miR-142-3p antagomiR

value: miR-142-3p knockdown


title: H3K9K14Ac, HDC1 KO mutant, control medium

description: hdc1-1 AC ctrl

value: HDC1 KO mutant


title: NRCFs, NC-2

value: NC


title: NRCFs, NC-1


title: NRCFs, miR-142-3p antagomiR-1


title: HDC1 KO mutant complemented with full length HDC1 gene sequence, 100 mM NaCl, replicate 3

description: HDC1c, S, 3


title: HDC1 KO mutant expressing RXT3 sequence of HDC1, control media, replicate 1

description: RXT3, C, 1


title: NRCFs, NC-3


title: HDC1 KO mutant expressing RXT3 sequence of HDC1, control media, replicate 3

description: RXT3, C, 3


title: HDC1 KO mutant expressing RXT3 sequence of HDC1, control media, replicate 2

description: RXT3, C, 2


title: HDC1 KO mutant complemented with full length HDC1 gene sequence, 100 mM NaCl, replicate 2

description: HDC1c, S, 2