title: G1-delta-H3K27me3-r2

description: Library name: G1-delta-H3K27me3-r2

data_processing:
Batch pre-processing of raw Cut&Run data from control and auxin-treated RanGAP1-AID cells synchronized in prometaphase or released for 5 hours to early G1 was performed using the nf-core/atacseq pipeline, version 2.1.0: https://github.com/nf-core/atacseq (Ewels et al. 2020). Adaptor-trimmed paired-end reads were mapped to the hg38 reference genome using bwa mem and filtered according to the standard pipeline for mapping quality, mitochondrial reads, PCR duplicates, and read length (< 2000 bp).
Coverage tracks were generated from read ends -/+ 25bp using BEDtools (Quinlan and Hall 2010), and scaled to 1 million mapped reads.
Assembly: hg38
Supplementary files format and content: BigWigs: mM_ = control prometaphase, mG1_ = control G1, pG1_ = delta RanGAP1 G1
Library strategy: CUT&Run

growth_protocol: Cells were synchronized and arrested in prometaphase and RanGAP1-AID was degraded 2 hours prior to release from nocodazole block for the 5h depletion.

extract_protocol:
"Nuclei" were isolated using 0.1%TX-100 and frozen.
Antibodies were bound overnight at 4C and pAG-MNase was bound at 4C for 1h. Libraries were prepared for sequencing using the NEBNext Multiplex Oligos for Ilumina (NEB E7600,E7780) and were amplified in PCR reactions for 14-18 cycles before sequencing on an Illumina NextSeq 2000 using the Paired End 50 bp module.

treatment_protocol: The CUT&RUN protocol was modified from Skene and Henikoff(Skene and Henikoff 2017) and applied to control or RanGAP1-depleted cell populations arrested in prometaphase or released for 5h into G1. Because of the use of mitotic cells all wash and buffer exchanges were done by spinning 600xg / 3minutes

value: cell line

value: delta, G1, replicate 2


title: G1-delta-H3K27me3-r1

status: Public on Nov 06 2025

type: SRA

city: Worcester

first: Allana

last: Schooley

state: MA

address: 368 Plantation St

department: Systems Biology

country: USA

institute: UMass Medical School

description: Library name: G1-delta-H3K27me3-r1

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: cell line

tag: tissue

tag: cell line

tag: cell type

tag: treatment

value: delta, G1, replicate 1


title: NAc, K20, Female, Naïve, Input

city: Portland

first: Marina

last: Guizzetti

state: OR

address: 3710 SW US Veterans Hospital Rd

department: Behavioral Neuroscience

institute: Oregon Health & Science University; Portland VA Research Service

description: Library name: K20FNNin

library_source: transcriptomic

data_processing:
Raw sequencing reads were quality assessed with FastQC v0.11.9
Sequencing reads were trimmed with Trimmomatic v0.39
Trimmed reads were aligned to the mouse reference genome from Ensembl (GRCm38) with the STAR aligner v2.7.10b
The Ensembl annotation gtf file GRCm38.99 was used during alignment to define gene regions and to obtain gene counts from the ReadsPerGene output files from STAR.
Assembly: GRCm38
Supplementary files format and content: comma separated file, read-counts per gene

molecule: total RNA

organism: Mus musculus

source_name: Nucleus accumbens

extract_protocol:
Translating Ribosome Affinity Purification (TRAP) was carried out on nucleus accumbens brain punches to isolate astrocyte translating RNA. An aliquot was saved prior to the TRAP procedure to serve as input samples which represents the bulk-tissue RNA.
RNA libraries were generated with Takara’s SMART-Seq PLUS kit according to manufacturers protocol.

treatment_protocol: Animals underwent the CIE-2BC protocol for 5 rounds of CIE for dependent animals.

value: Nucleus accumbens

tag: Sex

value: Female

tag: fraction

value: Input

tag: genotype

value: Naïve

tag: batch

value: K


title: NAc, K19, Male, Naïve, IP

description: Library name: K19MNNIP

value: Male

value: IP


title: G1-delta-CTCF-r1

description: Library name: G1-delta-CTCF-r1


title: G1-delta-H3K27ac-r2

description: Library name: G1-delta-H3K27ac-r2


title: NAc, K19, Male, Naïve, Input

description: Library name: K19MNNin


title: NAc, K18, Male, Dependent, IP

description: Library name: K18MVNIP

value: Dependent


title: DLD-1 cells, replicate 1, RanGAP1 KD, hour 0, 1 hour 4sU labeling

description:
Library name: rep1_p0
SLAM-seq, cell cycle arrested (pro-metaphase)

data_processing:
*library strategy: SLAM-seq
Adapter trimming was performed using trimmomatic ILLUMINACLIP with TruSeq3 adapter sequences. Replicate 1 fastq files were subsampled to median read depth of replicate 2 and replicate 3 samples using seqtk. Replicate 2 and 3 reads (2x150 PE reads) were trimmed to 100nt reads for concordance with replicate 1 (2x100 PE reads). fastq.gz files here are raw reads wtihout trimming or subsampling.
Adapter trimmed, subsampled/length trimmed reads were aligned to Ensembl GRCh38v95 with Hisat-3n v2.2.1-3n-0.0.3, specifying T>C conversions (--base-change T,C)
TPMs were calculated using Kallisto quant v0.48.0. TPM files here are computed from adapter-trimmed and subsampled (rep1) / length trimmed (rep2 and rep3) fastq files.
Assembly: Ensembl GRCh38v95
Supplementary files format and content: Tab-delimited text files include transcript lengths, effective lengths, estimated counts, and computed TPMs for total RNA.

extract_protocol:
Total RNA harvested in TRIzol reagent in DNA LoBind tubes. 10% 4sU-labeled and unlabeled ERCC spike-ins added proportional to harvested cell number. RNA extracted with Zymo RNA Clean & Concentrate columns.
3ug total RNA was taken into ribosomal RNA depletion (Z. Zhang et al., 2012). rRNA-depleted RNA was treated with 10mM iodoacetamide to alkylate 4sU bases (Herzog et al., 2017). 100ng rRNA-depleted, IAA-treated RNA per sample was used as input to NEBNext Ultra II directional RNA library prep kit and libraries were prepared according to manufacturer's recommendations. Library quality was assessed on Agilent TAPE station.

treatment_protocol: 1 hour of 1mM 4sU labeling where noted

value: colorectal adenocarcinoma

value: RanGAP1 knockdown (AID)

value: pro-metaphase cell cycle arrest

tag: time

value: hour 0


title: NAc, K16, Female, non-Dependent, IP

description: Library name: K16FCNIP

value: non-Dependent


title: NAc, K18, Male, Dependent, Input

description: Library name: K18MVNin


title: G1-delta-H3K4me3-r1

description: Library name: G1-delta-H3K4me3-r1


title: DLD-1 cells, replicate 1, RanGAP1 control, hour 2, 1 hour 4sU labeling

description:
Library name: rep1_m2
SLAM-seq, 2 hours post-arrest release

value: WT

value: hour 2


title: NAc, L24, Female, Naïve, IP

description: Library name: L24FNNIP

value: L


title: G1-delta-IgG-r1

description: Library name: G1-delta-IgG-r1

value: cell line

value: delta, G1, replicate 1


title: NAc, K16, Female, non-Dependent, Input

description: Library name: K16FCNin

value: Nucleus accumbens

value: Female


title: DLD-1 cells, replicate 1, RanGAP1 control, hour 1, 1 hour 4sU labeling

description:
Library name: rep1_m1
SLAM-seq, 1 hour post-arrest release

value: hour 1


title: G1-control-CTCF-r2

description: Library name: G1-control-CTCF-r2

value: control, G1, replicate 2


title: G1-delta-CTCF-r2

description: Library name: G1-delta-CTCF-r2

value: delta, G1, replicate 2


title: NAc, K15, Male, non-Dependent, Input

description: Library name: K15MCNin

value: Male

value: Input

value: K


title: NAc, K14, Male, Naïve, IP

description: Library name: K14MNNIP

value: IP

value: Naïve


title: G1-control-H3K27me3-r1

description: Library name: G1-control-H3K27me3-r1

value: control, G1, replicate 1


title: NAc, K14, Male, Naïve, Input

description: Library name: K14MNNin


title: G1-control-H3K27me3-r2

description: Library name: G1-control-H3K27me3-r2


title: G1-control-H3K27ac-r2

description: Library name: G1-control-H3K27ac-r2


title: NAc, K13, Female, Naïve, Input

description: Library name: K13FNNin


title: G1-control-H3K27ac-r1

description: Library name: G1-control-H3K27ac-r1


title: G1-delta-H3K27ac-r1

description: Library name: G1-delta-H3K27ac-r1


title: G1-control-H3K4me3-r2

description: Library name: G1-control-H3K4me3-r2


title: G1-control-H3K4me3-r1

description: Library name: G1-control-H3K4me3-r1


title: NAc, J11, Male, non-Dependent, IP

description: Library name: J11MCNIP

value: non-Dependent

value: J


title: G1-control-IgG-r2

description: Library name: G1-control-IgG-r2


title: G1-delta-IgG-r2

description: Library name: G1-delta-IgG-r2


title: G1-delta-H3K4me3-r2

description: Library name: G1-delta-H3K4me3-r2


title: G1-control-IgG-r1

description: Library name: G1-control-IgG-r1


title: NAc, J10, Male, Dependent, IP

description: Library name: J10MVNIP

value: Dependent


title: NAc, J11, Male, non-Dependent, Input

description: Library name: J11MCNin


title: NAc, K15, Male, non-Dependent, IP

description: Library name: K15MCNIP


title: NAc, J10, Male, Dependent, Input

description: Library name: J10MVNin


title: G1-control-CTCF-r1

description: Library name: G1-control-CTCF-r1


title: prometa-H3K27me3-r2

description: Library name: prometa-H3K27me3-r2

value: control, prometaphase, replicate 2


title: NAc, J09, Female, Dependent, IP

description: Library name: J09FVNIP


title: prometa-CTCF-r1

description: Library name: prometa-CTCF-r1

value: cell line

value: control, prometaphase, replicate 1


title: NAc, J09, Female, Dependent, Input

description: Library name: J09FVNin

value: Nucleus accumbens


title: prometa-CTCF-r2

description: Library name: prometa-CTCF-r2


title: NAc, K12, Female, non-Dependent, Input

description: Library name: K12FCNin

value: Female


title: NAc, K13, Female, Naïve, IP

description: Library name: K13FNNIP


title: prometa-H3K27me3-r1

description: Library name: prometa-H3K27me3-r1


title: NAc, J08, Female, Naïve, IP

description: Library name: J08FNNIP


title: prometa-H3K27ac-r2

description: Library name: prometa-H3K27ac-r2


title: NAc, J08, Female, Naïve, Input

description: Library name: J08FNNin


title: NAc, K12, Female, non-Dependent, IP

description: Library name: K12FCNIP


title: prometa-H3K27ac-r1

description: Library name: prometa-H3K27ac-r1


title: NAc, J07, Male, Naïve, Input

description: Library name: J07MNNin


title: NAc, J07, Male, Naïve, IP

description: Library name: J07MNNIP


title: NAc, J06, Female, Dependent, IP

description: Library name: J06FVNIP


title: prometa-IgG-r2

description: Library name: prometa-IgG-r2


title: prometa-IgG-r1

description: Library name: prometa-IgG-r1


title: NAc, J05, Male, Dependent, IP

description: Library name: J05MVNIP


title: NAc, J05, Male, Dependent, Input

description: Library name: J05MVNin


title: NAc, J04, Female, non-Dependent, IP

description: Library name: J04FCNIP


title: ctrl_mito_r2

data_processing:
data was mapped using bwa-mem and filtered in the nf-core/atacseq pipeline, version 2.1.0: https://github.com/nf-core/atacseq (Ewels et al. 2020)
single end files were generated using bedtools
bigWig files were created from ATAC-seq read ends coverage and normalised to 1000000
Assembly: hg38

Supplementary files format and content: bigWig files

growth_protocol: Cells were synchronized and arrested in prometaphase and RanGAP1-AID was degraded 2 hours prior to release from nocodazole block. Cells were collected in prometaphase block or 5h after release in G1 of the cell cycle.

extract_protocol:
Chromatin accessibility was investigated using omni ATACseq (Corces et al. 2017; Buenrostro et al. 2015)
Libraries were constructed using custom primers similar to (Buenrostro et al. 2013)

treatment_protocol: control RanGAP1-AID (ctrl) or IAA-treated RanGAP1-AID (deltaRG) DLD-1 cells

value: control, prometaphase

tag: replicate


title: NAc, J06, Female, Dependent, Input

description: Library name: J06FVNin


title: NAc, J04, Female, non-Dependent, Input

description: Library name: J04FCNin


title: 250718B tendon, IRAK4 inhibitor and IL1B treated

city: Hatfield

first: Debbie

last: Guest

state: Hertfordshire

address: Royal Veterinary College, Hawkshead Lane, North Mymms

department: Clinical Science and Services

country: United Kingdom

institute: Royal Veterinary College

description: Library name: 250718BBOTH

data_processing:
Standard quality control was performed using FASTQC (version 0.11.9; Babraham Bioinformatics, Cambridge, UK). Reads did not require trimming or filtering due to the high sequence quality and minimal adapter content
Reads were aligned to the Equus caballus transcriptome obtained from the National Centre for Biotechnology Information (NCBI) EquCab3.0 GCF_ 002863925.1 using the pseudoaligner Salmon (version 1.8) in Quasi-mapping-based mode with GC-bias correction
Tximport (version 1.24) [37] was used to import the quantified gene abundance data into R studio (version 4.2.1) and differential expression analysis was carried out using DESEq2 (version 1.36)
Genes with an adjusted p value (p-adj) of <0.05 and a log2 fold change (Log2FC) of ±1 were considered to be differentially expressed
Assembly: Equus caballus transcriptome obtained from the National Centre for Biotechnology Information (NCBI) EquCab3.0 GCF_ 002863925.1
Supplementary files format and content: Spreadsheet Count data_IRAK4_both (.xlsx) includes normalised counts of sequencing reads for each sample in a matrix table

molecule: polyA RNA

organism: Equus caballus

source_name: primary tendon cells

growth_protocol: Equine tendon cells were cultured in 3D collagen gels for 14 days. Growth media was DMEM supplemented with 10% fetal bovine serum, 2 mM L-glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin. Constructs were cultured at 37 °C, 5% CO2.

extract_protocol:
RNA was isolated using a RNeasy mini kit (Qiagen, Manchester, UK). Contaminating genomic DNA was removed using a DNA-free kit (Thermo Fisher). 1 µg of RNA was used for the construction of sequencing libraries.
mRNA libraries and transcriptome sequencing were performed by Novogene (Cambridge, UK) on an Illumina NovaSeq 6000 to generate 31.2 – 41.4 million 150 bp paired-end reads per sample

treatment_protocol: IL-1β was used at a dose of 17 ng/ml and was added every 3-4 days. The IRAK-4 inhibitor PF-06650833 was used at a concentration of 100 nM and added daily to the cultures.

value: primary tendon cells

value: IRAK4 inhibitor and IL1B treated


title: CD tendon, IRAK4 inhibitor and IL1B treated

description: Library name: CDTendonBOTH


title: ctrl_mito_r1


title: NAc, J03, Male, non-Dependent, IP

description: Library name: J03MCNIP

value: Male


title: NAc, J03, Male, non-Dependent, Input

description: Library name: J03MCNin

value: Input


title: deltaRG_mito_r2

value: Auxin-treated, prometaphase


title: 130911 tendon, IRAK4 inhibitor and IL1B treated

description: Library name: 130911BOTH


title: NAc, J02, Male, Naïve, Input

description: Library name: J02MNNin


title: 180412 tendon, IRAK4 inhibitor and IL1B treated

description: Library name: 180412BOTH


title: NAc, J02, Male, Naïve, IP

description: Library name: J02MNNIP

value: IP


title: prometa-H3K4me3-r2

description: Library name: prometa-H3K4me3-r2


title: NAc, J01, Female, Naïve, Input

description: Library name: J01FNNin

value: Naïve


title: ctrl_G1_r2

value: control, G1


title: deltaRG_mito_r1


title: CD tendon, IRAK4 inhibitor alone treated

description: Library name: CDTendonIRAK4

value: IRAK4 inhibitor alone


title: NAc, I16, Female, non-Dependent, IP

description: Library name: I16FCNIP

value: non-Dependent

value: I


title: prometa-H3K4me3-r1

description: Library name: prometa-H3K4me3-r1


title: NAc, J01, Female, Naïve, IP

description: Library name: J01FNNIP

value: J


title: NAc, I15, Male, Dependent, IP

description: Library name: I15MVNIP

value: Dependent


title: 090811 tendon, IRAK4 inhibitor and IL1B treated

description: Library name: 090811BOTH


title: NAc, I16, Female, non-Dependent, Input

description: Library name: I16FCNin


title: 250718B tendon, IRAK4 inhibitor alone treated

description: Library name: 250718BIRAK4


title: deltaRG_G1_r2

value: Auxin-treated, G1


title: NAc, I15, Male, Dependent, Input

description: Library name: I15MVNin

value: Nucleus accumbens


title: NAc, I14, Male, non-Dependent, Input

description: Library name: I14MCNin


title: 180412 tendon, IRAK4 inhibitor alone treated

description: Library name: 180412IRAK4


title: deltaRG_G1_r1


title: 130911 tendon, IRAK4 inhibitor alone treated

description: Library name: 130911IRAK4


title: NAc, I13, Female, Dependent, Input

description: Library name: I13FVNin

value: Female


title: NAc, I12, Female, non-Dependent, IP

description: Library name: I12FCNIP


title: Spleen infected 6

city: Manchester

first: Matthew

middle: Christopher

last: Sinton

state: Greater Manchester

address: Core Technology Facility

department: Division of Immunology, Immunity to Infection and Respiratory Medicine

institute: University of Manchester

description: Library name: SpI6

data_processing:
Raw sequencing data in fastq format were subject to quality filtering. Sequences that passed the quality filtering were mapped against IMGT database to find the best germline V(D)J gene matches. CDR sequences were then further characterized and analyzed.
Assembly: GRCm39
Supplementary files format and content: Comma-separated value files containing clone counts

source_name: Spleen

growth_protocol: Mice were group housed at room temperatire under 12h light 12h dark conditions

extract_protocol:
Qiagen Rneasy Kit
This was performed by Azenta Life Sciences. To leverage high-throughput sequencing for the characterization of B cell immunoglobulin repertoires and T cell receptor repertoires, total RNA is extracted from the isolated B/T lymphocytes and then reverse transcribed to cDNA. The complete 5’ end of BCR/TCR genes containing the variable regions are amplified by oligonucleotide primers against constant BCR/TCR constant regions. The resulting fragments were subject to final library preparation and next-generation sequencing.

treatment_protocol: Mice were infected with ~2,000 T. brucei parasites via intraperitoneal injection on day 0, and monitored until day 25, alongside naïve control mice

value: Spleen

value: B cells

value: female


title: NAc, I12, Female, non-Dependent, Input

description: Library name: I12FCNin


title: Spleen infected 5

description: Library name: SpI5


title: NAc, I11, Male, Dependent, Input

description: Library name: I11MVNin

value: Male


title: NAc, I10, Male, non-Dependent, Input

description: Library name: I10MCNin

value: Input


title: ctrl_G1_r1


title: Spleen infected 4

description: Library name: SpI4


title: Rosiglitazone-replicate4

city: Clemson

first: Subham

last: Dasgupta

state: South Carolina

address: 142 Long Hall

department: Biological Sciences

institute: Clemson University

description: Library name: Rosig_4

data_processing:
For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification(
Raw data (raw reads) in fastq format was firstly processed throughin-house perl scripts. In this step, clean data (clean reads) was obtainedbyremoving reads containing adapter, reads containing ploy-N and lowqualityreads from raw data. A
Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired-end clean reads were aligned to the referencegenome using Hisat2 v2.0.5
FeatureCounts v1.5.0-p3 was used to count the reads numbers mappedto each gene. Then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene.
Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired-end clean reads were aligned to the referencegenome using Hisat2 v2.0.5
Assembly: GRZ11
Supplementary files format and content: Excel file contains FPKM values for each sample

organism: Danio rerio

source_name: whole embryo

growth_protocol: Embryos were spawned and maintained in system water

extract_protocol:
At each time point, embryos were collected in RNA zol, homogenized and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit (Zymo). RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop.
After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.
For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification(

treatment_protocol: Embryos were exposed to 0.1% DMSO or 75 uM GW9662 or 25 uM Rosiglitazone from 6 to 24 hpf

value: whole embryo

value: wildtype

value: DMSO

value: 35 hpf


title: NAc, I09, Female, Dependent, IP

description: Library name: I09FVNIP

value: IP


title: NAc, I09, Female, Dependent, Input

description: Library name: I09FVNin


title: Spleen infected 3

description: Library name: SpI3

value: Naïve


title: Rosiglitazone-replicate3

description: Library name: Rosig_3

value: 34 hpf


title: NAc, I08, Female, non-Dependent, Input

description: Library name: I08FCNin

value: non-Dependent

value: I


title: NAc, I08, Female, non-Dependent, IP

description: Library name: I08FCNIP


title: NAc, I07, Male, Dependent, IP

description: Library name: I07MVNIP

value: Dependent


title: Rosiglitazone-replicate2

description: Library name: Rosig_2

value: 33 hpf


title: Spleen infected 2

description: Library name: SpI2


title: Rosiglitazone-replicate1

description: Library name: Rosig_1

value: 32 hpf


title: Spleen infected 1

description: Library name: SpI1

value: Spleen


title: NAc, I06, Male, non-Dependent, IP

description: Library name: I06MCNIP

value: Nucleus accumbens


title: NAc, I13, Female, Dependent, IP

description: Library name: I13FVNIP

value: Female


title: GW9662-replicate4

description: Library name: GW9662_4

value: TBBPA

value: 31 hpf


title: NAc, I06, Male, non-Dependent, Input

description: Library name: I06MCNin

value: Male

value: Input


title: 090811 tendon, IRAK4 inhibitor alone treated

description: Library name: 090811IRAK4

value: primary tendon cells

value: IRAK4 inhibitor alone


title: GW9662-replicate3

description: Library name: GW9662_3

value: whole embryo

value: wildtype

value: 30 hpf


title: NAc, I11, Male, Dependent, IP

description: Library name: I11MVNIP

value: IP


title: Spleen naïve 6

description: Library name: SpN6

value: B cells

value: Naïve

value: female


title: NAc, I05, Female, Dependent, Input

description: Library name: I05FVNin

value: Dependent

value: I


title: Spleen naïve 5

description: Library name: SpN5

value: Spleen


title: muscle_48yrs

type: genomic

city: Seoul

first: Hwan Young

last: Lee

address: 103, Daehak-ro, Jongno-gu

country: South Korea

institute: Seoul National University College of Medicine

description: genomic DNA from muscle of 2020_102_48_M

hyb_protocol: Bisulfite converted DNA was amplified, fagmented and hybridised to Infinium HumanMethylation EPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were scanned with an iScan Reader (Illumina) using standard recommended Illumina scanner setting

data_processing:
GenomeStudio software v. 2011.1 (Illumina)
Average Beta or normalized (provide the normalization method) Average Beta
Unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: Muscle

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using Qiagen DNA Mini Kit (Qiagen, Hilden, Germany) based on the manufacturers’ instructions

tag: age

tag: gender

value: male

value: Muscle

tag: ethnicity

value: Korean-Asian


title: GW9662-replicate2

description: Library name: GW9662_2

value: TBBPA

value: 29 hpf


title: NAc, I04, Female, non-Dependent, IP

description: Library name: I04FCNIP

value: Nucleus accumbens

value: Female

value: non-Dependent


title: Spleen naïve 4

description: Library name: SpN4


title: muscle_45yrs

description: genomic DNA from muscle of 2020_11_45_M


title: muscle_55yrs

description: genomic DNA from muscle of 2020_2_55_M


title: NAc, I04, Female, non-Dependent, Input

description: Library name: I04FCNin

value: Input


title: NAc, I03, Male, non-Dependent, IP

description: Library name: I03MCNIP

value: Male


title: Spleen naïve 2

description: Library name: SpN2


title: Spleen naïve 3

description: Library name: SpN3


title: DMSO- replicate4

description: Library name: Control_4

value: whole embryo

value: wildtype

value: DMSO

value: 27 hpf


title: GW9662-replicate1

description: Library name: GW9662_1

value: 28 hpf


title: sijunb-pbs-3

city: Albany

first: Ramon

last: Bossardi Ramos

state: Ny

address: 43 New Scotland Avenue

department: Department of Molecular and Cellular Physiology

institute: Albany Medical College

description: Library name: Sample_12

data_processing:
Sequencing adapters and low-quality bases were trimmed using Trim Galore (v0.6.10). Reads were aligned to the human genome (hg38) using STAR (v2.7.10a). Gene-level counts were quantified with featureCounts (Subread v2.0.3). Differential expression was analyzed using the limma-voom pipeline in R (v4.3.2), with genes filtered by CPM >1 in at least 3 samples and adjusted p-value < 0.05.
Assembly: hg38
Supplementary files format and content: tab-delimited text files log read counts values for each Sample

source_name: HUVEC

growth_protocol: Primary human umbilical vein endothelial cells (HUVECs) were cultured in EGM-2 medium at 37°C in a humidified incubator with 5% CO₂. Cells were used at passage 4–6 and seeded in 12-well plates at a density of 3.2 × 10⁵ cells/well.

extract_protocol:
Trizol
RNA-seq libraries were generated using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs), including polyA enrichment for mRNA. Libraries were barcoded, quantified by qPCR, and sequenced on an Illumina NovaSeq 6000 using 150 bp paired-end reads.

treatment_protocol: Cells were treated with recombinant human IL-6 (50 ng/mL) or PBS for 72 hours (first hit), with or without siRNA for the JunB gene

value: HUVEC

value: endothelial cells


title: Spleen naïve 1

description: Library name: SpN1

value: Spleen

value: B cells

value: Naïve

value: female


title: NAc, I03, Male, non-Dependent, Input

description: Library name: I03MCNin

value: I


title: NAc, I07, Male, Dependent, Input

description: Library name: I07MVNin

value: Nucleus accumbens

value: Dependent


title: sijunb-pbs-2

description: Library name: Sample_11


title: DMSO- replicate3

description: Library name: Control_3

value: 26 hpf


title: NAc, I02, Female, Dependent, IP

description: Library name: I02FVNIP

value: Female

value: IP


title: DMSO- replicate2

description: Library name: Control_2

value: whole embryo

value: 25 hpf


title: Dura mater infected 6

description: Library name: MI6

source_name: Dura mater

value: Dura mater


title: DMSO- replicate1

description: Library name: Control_1

value: wildtype

value: DMSO

value: 24 hpf


title: sijunb-pbs-1

description: Library name: Sample_10

value: HUVEC

value: endothelial cells


title: NAc, I02, Female, Dependent, Input

description: Library name: I02FVNin

value: Input


title: Dura mater infected 5

description: Library name: MI5

value: B cells

value: Naïve


title: sijunb-IL6-3

description: Library name: Sample_9


title: NAc, I01, Female, non-Dependent, IP

description: Library name: I01FCNIP

value: non-Dependent

value: I


title: NAc, I05, Female, Dependent, IP

description: Library name: I05FVNIP

value: Nucleus accumbens

value: Dependent


title: Dura mater infected 4

description: Library name: MI4

value: female


title: sijunb-IL6-2

description: Library name: Sample_8


title: RL19_HF_Chr

city: Houston

first: Mark

last: Herman

state: Texas

address: 1 Baylor Plaza

institute: Baylor College of Medicine

description: Library name: RL19_HF_Chr

data_processing:
Raw data (raw reads) in fastq format were processed through Novogene in-house perl scripts including the following steps: removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. All the downstream analyses were based on the cleaned data.
Kallisto was used to align cleaned data to Rat BN7.2, as well as to extract read / gene counts and normalization.
Assembly: Rat BN7.2
Supplementary files format and content: Tab-delimited text files, on for each sample, include estimated counts and TPM.

organism: Rattus norvegicus

source_name: Liver

extract_protocol:
RNA was harvested with phenol / chloroform
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dUTP  instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion to remove UTP-containing second strand cDNA, amplification, and purification.

value: Liver

value: anti-ChREBP GalNAc siRNA


title: sijunb-IL6-1

description: Library name: Sample_7


title: RL18_HF_NTC

description: Library name: RL18_HF_NTC

value: non-targeted control GALNac siRNA


title: PBS-si1-exp1

description: Library name: Sample_6


title: RL17_HF_NTC

description: Library name: RL17_HF_NTC


title: NAc, G22, Female, Dependent, Input

description: Library name: G22FVNin

value: Female

value: G


title: NAc, G22, Female, Dependent, IP

description: Library name: G22FVNIP

value: IP


title: Dura mater infected 1

description: Library name: MI1

value: Dura mater


title: PBS-NTS-exp3

description: Library name: Sample_5

value: HUVEC


title: PBS-NTS-exp2

description: Library name: Sample_4

value: endothelial cells


title: NAc, C17, Female, Dependent, IP

description: Library name: C17FVNIP

value: C


title: Dura mater naïve 6

description: Library name: MN6

value: B cells


title: RL13_HF_PBS

description: Library name: RL13_HF_PBS

value: PBS control


title: NAc, C17, Female, Dependent, Input

description: Library name: C17FVNin

value: Input


title: IL6-NTS-exp3

description: Library name: Sample_3


title: Dura mater naïve 5

description: Library name: MN5

value: Naïve


title: RL15_HF_NTC

description: Library name: RL15_HF_NTC


title: RL11_HF_PBS

description: Library name: RL11_HF_PBS


title: RL21_HF_Chr

description: Library name: RL21_HF_Chr


title: FGF21KO_Den

city: Tokyo

first: Lirong

last: Zheng

address: kanto

country: Japan

institute: The University of Tokyo

description: Library name: Sample4

data_processing:
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating 4GB data/Sample. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: Mus musculus GRCm39
Supplementary files format and content: tab-delimited text files include counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: TA muscle

extract_protocol:
Muscles were dissected, snap-frozen, and stored at -80°C. For each condition 4 muscles were pooled together. RNA was extracted using RNeasy kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols.

value: TA muscle

value: Denervation

value: 14 days


title: RL10_HF_PBS

description: Library name: RL10_HF_PBS

value: Liver


title: Dura mater naïve 4

description: Library name: MN4

value: female


title: FGF21KO_Sham

description: Library name: Sample3

value: Sham


title: Dura mater naïve 3

description: Library name: MN3


title: IL6-NTS-exp1

description: Library name: Sample_1


title: RL9_HF_PBS

description: Library name: RL9_HF_PBS


title: IL6-NTS-exp2

description: Library name: Sample_2


title: Dura mater infected 3

description: Library name: MI3


title: NAc, I01, Female, non-Dependent, Input

description: Library name: I01FCNin

value: Nucleus accumbens

value: Female

value: non-Dependent

value: I


title: WT_Den

description: Library name: Sample2

value: WT


title: Dura mater infected 2

description: Library name: MI2

value: Dura mater


title: PBS72h_W48h_LPS_3

description: Library name: Sample_18

source_name: Endothelium

treatment_protocol: Cells were treated with recombinant human IL-6 (50 ng/mL) or PBS for 72 hours (first hit), followed by a 48-hour washout phase in fresh media. Subsequently, cells were re-stimulated with LPS (1 μg/mL) or PBS for 6 hours (second hit). Samples were collected after each phase to capture acute and memory responses.

value: Endothelium

value: HuVEC

value: wt


title: Dura mater naïve 2

description: Library name: MN2

value: B cells


title: PBS72h_W48h_LPS_2

description: Library name: Sample_17


title: Dura mater naïve 1

description: Library name: MN1

value: Naïve


title: WT_Sham

description: Library name: Sample1

value: TA muscle


title: RL8_HF_NTC

description: Library name: RL8_HF_NTC

value: non-targeted control GALNac siRNA


title: RL7_HF_Chr

description: Library name: RL7_HF_Chr

value: anti-ChREBP GalNAc siRNA


title: RL6_HF_Chr

description: Library name: RL6_HF_Chr

value: Liver


title: BAT SCNx mouse 21℃ TRF ZT16 rep2

city: suzhou

first: Yizhun

last: Zeng

address: renai road NO.199

country: China

institute: schoow university

description: Library name: 16scnxtrf2

data_processing:
Raw binary base calling data were converted to sequence data. Sequencing data were compared to the mm10 reference genome at UCSC using Rsem (V1.2.8). Finally, FPKM values of the genes in each sample were calculated using Bowtie
Assembly: Mouse mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample, csv files include FPKM values for each Sample

source_name: interscapular brown adipose tissue

growth_protocol: The mice were housed in an SPF - level animal facility with ad libitum access to food and water, and the temperature of the animal room was maintained at 24±1℃.

extract_protocol:
RNA was harvested using Trizol reagent (Ambion) and chloroform. 2 ug of total RNA was usedfor the construction of sequencing libraries.
The library was constructed using the VAHTS mRNA Capture Beads（N401）+ VAHTS Universal V8 RNA-seq Library Prep Kit following the manufacturer's instructions.

treatment_protocol: SCNx and sham mice were either maintained on ad libitum feeding or subjected to TRF at 21℃. Their BAT was collected at ZT4 and ZT16 on the second day of TRF.

value: interscapular brown adipose tissue


title: PBS72h_W48h_LPS_1

description: Library name: Sample_16


title: shMTHFD2-3

city: Wuhan

first: Aikebaier

last: Tuohuti

state: Hubei

address: shuiguohu

institute: Zhongnan Hospital of Wuhan University

data_processing:
CLC Genomic Workbench v 11.0.1
Assembly: mm10
Supplementary files format and content: tab-delimited text  filie incluldes raw counts for each sample
Supplementary files format and content: tab-delimited text  filie incluldes FPKM for each sample

source_name: Tongue

growth_protocol: SCC-9 was cultured in DMEM/F12 with 10% FBS and 400 ng/mL hydrocortisone.

extract_protocol:
Before collecting the samples, ensure that the cell condition is good and free from microbial contamination. During sample collection, wash the cells twice with PBS, then add 1 mL of Trizol to the cell pellet of each group, and gently pipette to ensure complete cell lysis
The impact of RNA sequencing library construction protocols on transcriptomic profiling of tongue squamous cell carcinoma after MTHFD2 knockdown

treatment_protocol: MTHFD2 knockdown was achieved by using shRNAplasmids to SCC-9

value: Tongue

value: tongue squamous cell carcinoma cells


title: BAT SCNx mouse 21℃ TRF ZT16 rep3

description: Library name: 16scnxtrf3


title: PBS_72h_W48h_3

description: Library name: Sample_15


title: RL4_HF_PBS

description: Library name: RL4_HF_PBS

value: PBS control


title: shMTHFD2-1


title: BAT SCNx mouse 21℃ TRF ZT16 rep1

description: Library name: 16scnxtrf1


title: shNC3

value: control group


title: PBS_72h_W48h_2

description: Library name: Sample_14


title: RL3_HF_Chr

description: Library name: RL3_HF_Chr


title: BAT sham mouse 21℃ TRF ZT16 rep3

description: Library name: 16shamtrf3


title: PBS_72h_W48h_1

description: Library name: Sample_13


title: RL2_HF_NTC

description: Library name: RL2_HF_NTC


title: BAT sham mouse 21℃ TRF ZT16 rep2

description: Library name: 16shamtrf2


title: RL1_HF_Chr

description: Library name: RL1_HF_Chr


title: shNC2


title: PBS_72h_3

description: Library name: Sample_12


title: shNC1


title: PBS_72h_2

description: Library name: Sample_11


title: BAT sham mouse 21℃ TRF ZT16 rep1

description: Library name: 16shamtrf1


title: JKZ243_phd2phd3C19_RNA-seq_rep2

city: Shenzhen

first: Jian-Kang

last: Zhu

state: Guangdong

address: 1088 Xueyuan Blvd, Nanshan

department: Institute of Advanced Biotechnology, Institute of Homeostatic Medicine, and School of Medicine

institute: Southern University of Science and Technology

description: Library name: phd2phd3C19_rep2

data_processing:
Raw reads were processed using Fastp (default settings) to remove adapters and low-quality bases. Clean reads were aligned to the TAIR10 reference genome using TopHat2 with the “--b2-very-sensitive” option. The resulting BAM files were normalized and converted to BedGraph format using deepTools for visualization in IGV. Differential expression of protein-coding genes and transposable elements (TEs) was determined using Cuffdiff (Cufflinks) with the “-u -b <genome.fa>” option. Genes or TEs with FDR < 0.05 and absolute log2 fold change (log2FC) ≥ 1 were considered differentially expressed.
Assembly: Arabidopsis thaliana (Col-0) TAIR10 reference genome
Supplementary files format and content: tab-delimited bedGraph.gz files with normalized CPM values per genomic interval
Supplementary files format and content: tab-delimited TSV file containing CPM-normalized expression matrix (genes/TEs × samples)

organism: Arabidopsis thaliana

source_name: Seedling

growth_protocol: Arabidopsis thaliana (Col-0) plants were grown under long-day conditions (16 h light/8 h dark, 22°C). Seeds were surface-sterilized, stratified for 3 days at 4°C in darkness, germinated on 1/2 Murashige and Skoog (MS) medium with 2% sucrose and 0.8% agar. Fourteen-day-old seedlings were harvested for RNA extraction.

extract_protocol:
Total RNA was extracted from 100 mg of tissue using TRIzol reagent (Invitrogen) following manufacturer’s instructions.
Library construction was performed at the Genomics Core Facilities of the PSC (Shanghai Center for Plant Stress Biology, Shanghai, China) following Illumina protocols.

value: Seedling


title: JKZ243_phd2phd3C19_RNA-seq_rep1

description: Library name: phd2phd3C19_rep1


title: JKZ305_WGBS_phd3-1

description: Library name: JKZ305_WGBS_phd3-1

data_processing:
Adapters and low-quality sequences (Q < 20) were trimmed using Fastp (v0.23.4) with default settings unless otherwise specified. Clean reads were aligned to both strands of the TAIR10 reference genome using Bismark (v0.23.1) in Bowtie2 mode (--score_min L,0,-0.6), retaining the best alignment per read. PCR duplicates were removed with deduplicate_bismark, and reads containing ≥ 4 consecutive methylated CHH cytosines were discarded. Cytosine methylation levels were extracted with the --comprehensive --CX option and filtered to retain sites with ≥ 10× coverage across all samples. Strand-specific methylation ratios were converted into bedGraph and BigWig formats with bedGraphToBigWig for IGV visualization. Differentially methylated regions (DMRs) were identified using methylKit (v1.20.0) on 200-bp non-overlapping tiles with Fisher’s exact test (FDR < 0.01; minimum absolute methylation differences of 40% for CG, 20% for CHG, and 10% for CHH). DMRs were annotated with GenomicRanges against TAIR10 gene and transposable element models and classified as genic, TE-associated, promoter-proximal (±1 kb), or downstream (±1 kb).
Assembly: Arabidopsis thaliana (Col-0) TAIR10 reference genome
Supplementary files format and content: BigWig files contain per-cytosine DNA methylation ratios in CG, CHG, and CHH contexts. Each file represents genome-wide methylation levels for one sample and one context.

growth_protocol: Arabidopsis thaliana (Col-0) plants were grown under long-day conditions (16 h light/8 h dark, 22°C). Seeds were surface-sterilized, stratified for 3 days at 4°C in darkness, germinated on 1/2 Murashige and Skoog (MS) medium with 2% sucrose and 0.8% agar. Fourteen-day-old seedlings were harvested for DNA extraction.

extract_protocol:
Genomic DNA was extracted from plant tissue using the DNeasy Plant Maxi Kit (QIAGEN) according to the manufacturer’s instructions.
Bisulfite conversion, library construction, and sequencing were performed at the Genomics Core Facilities of the PSC (Shanghai Center for Plant Stress Biology, Shanghai, China) following Illumina protocols.


title: shMTHFD2-2


title: JKZ305_WGBS_phd2-1

description: Library name: JKZ305_WGBS_phd2-1


title: BAT SCNx mouse 21℃ ad libitum ZT16 rep2

description: Library name: 16scnxad2


title: PBS_72h_1

description: Library name: Sample_10


title: IL672h_W48h_LPS_3

description: Library name: Sample_9


title: BAT SCNx mouse 21℃ ad libitum ZT16 rep3

description: Library name: 16scnxad3


title: BAT sham mouse 21℃ ad libitum ZT16 rep3

description: Library name: 16shamad3


title: IL672h_W48h_LPS_2

description: Library name: Sample_8


title: JKZ305_WGBS_cpl2-2_rep2

description: Library name: JKZ305_WGBS_cpl2-2


title: JKZ305_WGBS_Col-0_rep2

description: Library name: JKZ305_WGBS_Col-0


title: JKZ243_phd2phd3C11_RNA-seq_rep1

description: Library name: phd2phd3C11_rep1


title: IL672h_W48h_LPS_1

description: Library name: Sample_7


title: BAT SCNx mouse 21℃ ad libitum ZT16 rep1

description: Library name: 16scnxad1


title: BAT sham mouse 21℃ ad libitum ZT16 rep2

description: Library name: 16shamad2


title: JKZ243_phd3-1_RNA-seq_rep2

description: Library name: phd3-1_rep2


title: IL6_72h_W48h_3

description: Library name: Sample_6


title: BAT sham mouse 21℃ ad libitum ZT16 rep1

description: Library name: 16shamad1


title: JKZ243_phd3-1_RNA-seq_rep1

description: Library name: phd3-1_rep1


title: JKZ248_WGBS_phd2phd3C19

description: Library name: JKZ248_WGBS_phd2phd3C19


title: JKZ248_WGBS_phd2phd3C11

description: Library name: JKZ248_WGBS_phd2phd3C11


title: IL6_72h_W48h_2

description: Library name: Sample_5


title: JKZ243_phd2-1_RNA-seq_rep2

description: Library name: phd2-1_rep2


title: BAT SCNx mouse 21℃ TRF ZT4 rep3

description: Library name: 4scnxtrf3


title: JKZ248_WGBS_cpl2-2_rep1

description: Library name: JKZ248_WGBS_cpl2-2


title: JKZ243_phd2-1_RNA-seq_rep1

description: Library name: phd2-1_rep1


title: IL6_72h_W48h_1

description: Library name: Sample_4


title: BAT SCNx mouse 21℃ TRF ZT4 rep2

description: Library name: 4scnxtrf2


title: IL6_72h_3

description: Library name: Sample_3


title: JKZ243_phd2phd3C11_RNA-seq_rep2

description: Library name: phd2phd3C11_rep2


title: BAT SCNx mouse 21℃ TRF ZT4 rep1

description: Library name: 4scnxtrf1


title: JKZ248_WGBS_Col-0_rep1

description: Library name: JKZ248_WGBS_Col-0


title: JKZ243_cpl2-2_RNA-seq_rep2

description: Library name: cpl2-2_rep2


title: BAT sham mouse 21℃ TRF ZT4 rep3

description: Library name: 4shamtrf3


title: IL6_72h_2

description: Library name: Sample_2


title: AT3 ER-Over Expression replicate 2

city: Barcelona

first: Toni

last: Celià-Terrassa

address: C/ del Dr. Aiguader, 88, Ciutat Vella,

country: Spain

institute: Hospital del Mar Research Institute

description: Library name: Sample 4

data_processing:
Quality checking of raw data (fastq files) was performed with FastQC software (v.0.11.9).
Estimation of ribosomal RNA in the raw data was obtained with riboPicker74.
Raw reads were trimmed using TrimGalore (v.0.6.6) with a quality cutoff of 30.
Quality reads were aligned with the STAR mapper to the Mus musculus genome GRCm39/mm39.
Quantification was done with featureCounts.
Assembly: GRCm39/mm39
Supplementary files format and content: _quantification.txt. Tab-delimited text file containing a quantification matrix done with Feature Counts. Genes as rows and samples as columns.

source_name: Breast

growth_protocol: Cells were mantained in DMEM media supplemented with 10% of Fetal Bovine Serum (FBS), 2mM L-Glutamine (Glu) and 1% Penicilin/Streptomycin (P/S).

extract_protocol:
Cells were lysed and RNA was extracted following Qiagen RNA extraction kit guidelines
Libraries were prepared using Poly-A selection for mRNA enrichement, followed by sequencing

value: Breast

value: Mammary carcinoma cell line

value: ER-OE


title: JKZ243_cpl2-2_RNA-seq_rep1

description: Library name: cpl2-2_rep1


title: IL6_72h_1

description: Library name: Sample_1

value: Endothelium

value: HuVEC


title: AT3 ER-Over Expression replicate 1

description: Library name: Sample 3


title: BAT sham mouse 21℃ TRF ZT4 rep2

description: Library name: 4shamtrf2


title: AT3 Wild Type replicate 1

description: Library name: Sample 1

value: WT


title: BAT sham mouse 21℃ TRF ZT4 rep1

description: Library name: 4shamtrf1


title: CRC Patient Derived Organoid (PDO127B) rep3

first: Lluis

last: Espinosa

state: Barcelona

address: Dr. Aiguader 88

department: Institut Municipal d'Investigacions Mèdiques, (IMIM)

institute: Hospital del Mar

description: Library name: 127B_3

data_processing:
Raw reads were trimmed to remove adapters presence with Trimgalore (v0.6.6) (Krueger et al., 2020). Default parameters were used except for a minimum quality of 15 (Phred score) and an adapter removal stringency of 3bp overlap.
Trimmed reads were aligned to reference genome (hg38 release 106 from Ensembl) with STAR aligner tool (v2.7.8). STAR was executed with default parameters except for the number of allowed mismatches which was set to 1.
Uniquely mapped reads were considered for further analysis. Raw gene expression was quantified using featureCounts tool from subRead software (v2.0.1) with exon as feature.
Raw counts matrix was imported into R Statistical software (v4.3.2). Prior to statistical analysis, those genes with less than 5 raw counts across the samples were discarded.
For visualization purposes, counts were normalized by variance-stabilizing transformation method as implemented in DESeq2 R package (v1.40.2)
Assembly: hg38
Supplementary files format and content: Tab-separated value file: RNAseq_NormCounts_RNAseq_PDOs_dataset.txt. Normalized expression levels including the expression of 32,071 genes (rows) per all individual samples. Normalization carried out with VST from DESeq2 (v1.40.2)
Supplementary files format and content: Tab-separated value file: RNAseq_RawCounts_RNAseq_PDOs_dataset.txt: RNAseq Raw expression levels for each gene (61,552 rows) in each individual sample as calculated using featureCounts. This data is prior to conducting any pre-filtering step.

growth_protocol: PDOs were cultured in matrigel at 37°C, 5% CO2 and medium was changed every week.

extract_protocol:
Tumor spheres were collected and total RNA was extracted from cells using Qiagen RNeasy Micro Kit (#74004) following manufacturer's instructions. RNA quality was measured by Nanodrop.
Library was prepared according to manufacturer's instructions (PE 50bp paired-end reads)

treatment_protocol: Treatment with 5-FU [1mg/mL] + Irinotecan [0.4 mg/mL] for 72 hours

value: Colorectal Patient-Derived Organoid

value: Untreated


title: CRC Patient Derived Organoid (PDO127B) rep2

description: Library name: 127B_2


title: Arabidopsis seedlings, RNA, pif457, 7-day-old, LRFR 25h, R3

city: Lausanne

first: Christian

last: Fankhauser

state: Vaud

address: Batiment Genopode

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

description: Library name: pif457_rna_LRFR25_R3

data_processing:
Reads were trimmed with Cutadapt (Martin, 2011)
Reads were filtered for ribosomal RNA with fastq_screen
reaper was used to further filter sequence reads for low complexity (Davis et al., 2013)
Reads were aligned to the A. thaliana reference genome (TAIR10) using STAR (Dobin et al., 2013)
Counts were extracted using htseq-count (Anders et al., 2015)
Assembly: TAIR10.39
Supplementary files format and content: tab-delimited text file with raw gene counts

source_name: seedling

growth_protocol: Seedlings were grown on 1/2 MS media without vitamins in HRFR until LRFR treatment.

extract_protocol:
Total Arabidopsis RNA was extracted using Qiagen Plant RNeasy kit according to the manufacturer’s instructions.
Libraries were generated with Illumina Stranded mRNA Prep

treatment_protocol: Exposure to 1h or 25h of LRFR

value: seedling

value: LRFR 25h


title: JKZ243_Col-0_RNA-seq_rep1

description: Library name: Col-0_rep1


title: AT3 Wild Type replicate 2

description: Library name: Sample 2


title: BAT SCNx mouse 21℃ ad libitum ZT4 rep3

description: Library name: 4scnxad3


title: Arabidopsis seedlings, RNA, pif457, 7-day-old, LRFR 25h, R2

description: Library name: pif457_rna_LRFR25_R2


title: CRC Patient Derived Organoid (PDO127B) rep1

description: Library name: 127B_1


title: BAT SCNx mouse 21℃ ad libitum ZT4 rep2

description: Library name: 4scnxad2


title: Arabidopsis seedlings, RNA, pif457, 7-day-old, LRFR 25h, R1

description: Library name: pif457_rna_LRFR25_R1


title: BAT SCNx mouse 21℃ ad libitum ZT4 rep1

description: Library name: 4scnxad1


title: CRC Patient Derived Organoid (PDO66) rep3

description: Library name: 66_3


title: CRC Patient Derived Organoid (PDO66) rep2

description: Library name: 66_2


title: Arabidopsis seedlings, RNA, hfr1, 7-day-old, LRFR 25h, R3

description: Library name: hfr1_rna_LRFR25_R3


title: Worker_pool_2

city: London

first: Christopher

middle: Douglas Robert

last: Wyatt

address: Gower street

institute: UCL

data_processing:
Raw reads quality filtered and mapped to genome (GCF_001313835.1), to remove reads not mapping to the genome
Quality trimming using TrimGalore
Tophat2 and STAR used to map reads to the genome (GCF_001313835.1)
featureCounts used to calculate normalized gene counts
Genome_build: GCF_001313835.1
Supplementary_files_format_and_content: .txt files with counts for each sample

organism: Polistes canadensis

source_name: Whole brain

extract_protocol:
All wasps were collected directly from their nests during the daytime, placed immediately into RNAlater (Ambion, Invitrogen) and stored at -20°C until further use. Total RNA was extracted using the RNeasy Universal Plus Mini kit (Qiagen, #73404)
RNA libraries were prepared for sequencing using standard Illumina Truseq kit protocols

tag: wasp id 1

value: WYYB

tag: wasp id 2

value: PGPG

tag: nest code

tag: nest code 2

tag: caste

value: Worker

tag: pooled or individual

value: Pool

tag: pre or post worker emergence nests

value: Post-worker emergence


title: BAT sham mouse 21℃ ad libitum ZT4 rep3

description: Library name: 4shamad3

tag: tissue

value: interscapular brown adipose tissue


title: Worker_pool_1

value: YPGP

value: PWWW


title: Worker_pool_3

value: PGBY

value: YWGB


title: CRC Patient Derived Organoid (PDO66) rep1

description: Library name: 66_1

tag: cell line

tag: cell type

tag: treatment


title: JKZ243_Col-0_RNA-seq_rep2

description: Library name: Col-0_rep2

value: Seedling

tag: genotype


title: Arabidopsis seedlings, RNA, hfr1, 7-day-old, LRFR 25h, R2

description: Library name: hfr1_rna_LRFR25_R2


title: BAT sham mouse 21℃ ad libitum ZT4 rep2

description: Library name: 4shamad2


title: Focal_Worker_2

value: PBPB

value: Ex-worker

value: Individual


title: CRC Patient Derived Organoid (PDO27) rep3

description: Library name: 27_3

value: Colorectal Patient-Derived Organoid

value: Untreated


title: BAT sham mouse 21℃ ad libitum ZT4 rep1

description: Library name: 4shamad1


title: Arabidopsis seedlings, RNA, hfr1, 7-day-old, LRFR 25h, R1

description: Library name: hfr1_rna_LRFR25_R1

value: seedling

value: LRFR 25h


title: CRC Patient Derived Organoid (PDO27) rep2

description: Library name: 27_2


title: Arabidopsis seedlings, RNA, Col-0, 7-day-old, LRFR 25h, R3

description: Library name: Col-0_rna_LRFR25_R3


title: L_75_endo

description: Library name: lung_Sample_26

data_processing:
Sequencing adapters and low-quality bases were trimmed using Trim Galore (v0.6.10). Reads were aligned to the human genome (hg38) using STAR (v2.7.10a). Gene-level counts were quantified with featureCounts (Subread v2.0.3). Differential expression was analyzed using the limma-voom pipeline in R (v4.3.2), with genes filtered by CPM >1 in at least 3 samples and adjusted p-value < 0.05.
Assembly: mm10
Supplementary files format and content: tab-delimited text files log read counts values for each Sample

source_name: Lung

growth_protocol: Male C57BL/6 mice (8–12 weeks old) were housed under specific pathogen-free conditions with ad libitum access to food and water. All procedures were approved by the Institutional Animal Care and Use Committee. Mice were randomly assigned to experimental groups.

extract_protocol:
Lung and kidney tissues were enzymatically digested into single-cell suspensions, and endothelial cells were enriched using anti-CD31 magnetic-microbeads according to the manufacturer’s protocol. CD31⁺ cells were lysed in Trizol reagent (Thermo Fisher Scientific), and total RNA was purified using RNeasy Micro columns (Qiagen) with on-column DNase digestion to eliminate genomic DNA contamination.
RNA-seq libraries were generated using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs), including polyA enrichment for mRNA. Libraries were barcoded, quantified by qPCR, and sequenced on an Illumina NovaSeq 6000 using 150 bp paired-end reads.

treatment_protocol: To model post-sepsis inflammatory memory, mice underwent cecal ligation and puncture (CLP) or sham surgery (first hit). After a recovery period, mice were challenged intranasally with either Streptococcus pneumoniae (1×10⁶ CFU) or PBS (second hit). Endothelial cells were isolated from lung and kidney tissues at defined timepoints corresponding to acute and memory phases of the response.

value: Lung

value: Endothelium

value: WT


title: Subordinate_pool_3

value: Worker

value: Pool

value: Post-worker emergence


title: CRC Patient Derived Organoid (PDO27) rep1

description: Library name: 27_1


title: Arabidopsis seedlings, RNA, Col-0, 7-day-old, LRFR 25h, R2

description: Library name: Col-0_rna_LRFR25_R2


title: L_74_endo

description: Library name: lung_Sample_25


title: CRC Patient Derived Organoid (PDO10) rep3

description: Library name: 10_3


title: Arabidopsis seedlings, RNA, Col-0, 7-day-old, LRFR 25h, R1

description: Library name: Col-0_rna_LRFR25_R1


title: Subordinate_pool_2


title: L_73_endo

description: Library name: lung_Sample_24


title: Subordinate_pool_1


title: Foundress_subordinate_3

value: YELLOW

value: Pre-worker emergence


title: L_67_endo

description: Library name: lung_Sample_23


title: Arabidopsis seedlings, RNA, pif457, 7-day-old, LRFR 1h, R3

description: Library name: pif457_rna_LRFR1_R3

value: LRFR 1h


title: Arabidopsis seedlings, RNA, pif457, 7-day-old, LRFR 1h, R2

description: Library name: pif457_rna_LRFR1_R2


title: Foundress_subordinate_2


title: CRC Patient Derived Organoid (PDO10) rep1

description: Library name: 10_1


title: Arabidopsis seedlings, RNA, pif457, 7-day-old, LRFR 1h, R1

description: Library name: pif457_rna_LRFR1_R1


title: Arabidopsis seedlings, RNA, hfr1, 7-day-old, LRFR 1h, R3

description: Library name: hfr1_rna_LRFR1_R3


title: CRC Patient Derived Organoid (PDO5) rep2

description: Library name: 5_2


title: Focal_Worker_3

value: GGBB


title: Focal_Subordinate_4


title: L_64_endo

description: Library name: lung_Sample_22


title: L_57_endo

description: Library name: lung_Sample_21


title: CRC Patient Derived Organoid (PDO10) rep2

description: Library name: 10_2


title: Focal_Worker_1

value: GYYY


title: CRC Patient Derived Organoid (PDO5) rep3

description: Library name: 5_3


title: CRC Patient Derived Organoid (PDO5) rep1

description: Library name: 5_1


title: L_48_endo

description: Library name: lung_Sample_19


title: Arabidopsis seedlings, RNA, hfr1, 7-day-old, LRFR 1h, R2

description: Library name: hfr1_rna_LRFR1_R2


title: CRC Patient Derived Organoid (PDO4) rep3

description: Library name: 4_3


title: Focal_Subordinate_3

value: Ex-worker


title: Arabidopsis seedlings, RNA, hfr1, 7-day-old, LRFR 1h, R1

description: Library name: hfr1_rna_LRFR1_R1


title: L_45_endo

description: Library name: lung_Sample_18


title: Arabidopsis seedlings, RNA, Col-0, 7-day-old, LRFR 1h, R3

description: Library name: Col-0_rna_LRFR1_R3


title: L_43_endo

description: Library name: lung_Sample_17


title: Focal_Subordinate_2

value: Individual


title: Focal_Subordinate_1


title: CRC Patient Derived Organoid (PDO4) rep1

description: Library name: 4_1

value: Colorectal Patient-Derived Organoid


title: Foundress_subordinate_1

value: GREEN


title: L_56_endo

description: Library name: lung_Sample_20


title: Subordinate_3


title: Arabidopsis seedlings, RNA, Col-0, 7-day-old, LRFR 1h, R1

description: Library name: Col-0_rna_LRFR1_R1

value: seedling


title: L_40_endo

description: Library name: lung_Sample_15


title: Arabidopsis seedlings, RNA, pif457, 7-day-old, HRFR, R3

description: Library name: pif457_rna_HRFR_R3

value: HRFR


title: Subordinate_2


title: CRC tumor tissue P24

city: Lille, Cedex

first: Bernadette

last: Neve

address: Bâtiment ONCOLille, Bld du Professeur Jules Leclercq

department: CANTHER

country: France

institute: ONCOLille

description:
Library name: P24
Fresh frozen Spatail transcriptome sequencing

data_processing:
Raw sequencing data were processed using the 10xGenomics SpaceRanger pipeline (version 1.3.1) to generate FASTQ files
sequences were aligned to GRCh38-2020-A using SpaceRanger
Ensembl-gene expression levels were quantified using SpaceRanger
Assembly: GRCh38-2020-A
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducial spots of the tissue image
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: high resolution image of tissue
Supplementary files format and content: tissue_lowres_image.png: low resolution 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: barcodes.tsv.gz: raw feature list of spatial barcodes
Supplementary files format and content: features.tsv.gz: raw feature list of gene Ids
Supplementary files format and content: matrix.mtx.gz: raw feature list of gene expression count data in Matrix Marker Exchange Format
Library strategy: spatial transcriptomics

source_name: CRC

extract_protocol:
Tumor tissues from CRC patients (OrgaRES consortium study, France) were cryopreserved by snap freeze in Tissue-TekR OCT-compound and 10µm cryosections were subjected to the 10x Visium gene expression analysis according to the manufacturer guidelines. The optimal tissue permeabilization time used was 30 min. A Hematoxylin-Eosin staining was done after the tissue section was deposited onto the Visium slide capture area, images were obtained by Axioscan (Zeiss)
Visium spatial gene expression Slide and Reagent kit (at the Go@L-GFS platform (PBLS - UAR2014 - US41, Lille France))
according to 10x Genomics guidelines;  The libraries were realized and sequenced on the NovaSeq 6000 system (Illumina).

value: CRC


title: Subordinate_1


title: L_39_endo

description: Library name: lung_Sample_14

value: Lung

value: Endothelium


title: Arabidopsis seedlings, RNA, pif457, 7-day-old, HRFR, R2

description: Library name: pif457_rna_HRFR_R2


title: CRC tumor tissue P17

description:
Library name: P17
Fresh frozen Spatail transcriptome sequencing


title: L_290

description: Library name: lung_Sample_13

value: WT


title: Foundress_subordinate_pool_3

value: PY

value: Worker

value: Pool


title: CRC Patient Derived Organoid (PDO4) rep2

description: Library name: 4_2

value: Untreated


title: CRC tumor tissue P15

description:
Library name: P15
Fresh frozen Spatail transcriptome sequencing


title: L_284

description: Library name: lung_Sample_12


title: Foundress_subordinate_pool_2

value: YELLOW

value: PG

value: Pre-worker emergence


title: Arabidopsis seedlings, RNA, hfr1, 7-day-old, HRFR, R3

description: Library name: hfr1_rna_HRFR_R3


title: CRC tumor tissue P13

description:
Library name: P13
Fresh frozen Spatail transcriptome sequencing


title: L_283

description: Library name: lung_Sample_11


title: Arabidopsis seedlings, RNA, hfr1, 7-day-old, HRFR, R2

description: Library name: hfr1_rna_HRFR_R2


title: Arabidopsis seedlings, RNA, Col-0, 7-day-old, LRFR 1h, R2

description: Library name: Col-0_rna_LRFR1_R2

value: LRFR 1h


title: L_42_endo

description: Library name: lung_Sample_16


title: L_271

description: Library name: lung_Sample_10


title: Queen_pool_3

value: Queen

value: Post-worker emergence


title: Arabidopsis seedlings, RNA, hfr1, 7-day-old, HRFR, R1

description: Library name: hfr1_rna_HRFR_R1


title: CRC tumor tissue P18

description:
Library name: P18
Fresh frozen Spatail transcriptome sequencing


title: CRC tumor tissue P10

description:
Library name: P10
Fresh frozen Spatail transcriptome sequencing


title: L_267

description: Library name: lung_Sample_9


title: Arabidopsis seedlings, RNA, Col-0, 7-day-old, HRFR, R3

description: Library name: Col-0_rna_HRFR_R3


title: L_265

description: Library name: lung_Sample_8


title: CRC tumor tissue P09

description:
Library name: P09
Fresh frozen Spatail transcriptome sequencing


title: L_240a

description: Library name: lung_Sample_7

value: sham


title: Arabidopsis seedlings, RNA, pif457, 7-day-old, HRFR, R1

description: Library name: pif457_rna_HRFR_R1

value: seedling


title: Focal_Queen_4

value: Ex-queen

value: Individual


title: CRC tumor tissue P05

description:
Library name: P05
Fresh frozen Spatail transcriptome sequencing

value: CRC


title: Focal_Queen_3


title: L_235a

description: Library name: lung_Sample_6

value: Lung

value: Endothelium


title: Arabidopsis seedlings, RNA, Col-0, 7-day-old, HRFR, R1

description: Library name: Col-0_rna_HRFR_R1

value: HRFR


title: L_229a

description: Library name: lung_Sample_5

value: WT


title: CRC tumor tissue P04

description:
Library name: P04
Fresh frozen Spatail transcriptome sequencing


title: pPXY::shy2-2-GR_DEX treatment_Bio3

city: ghent

first: Wei

last: Xiao

address: Technologiepark-Zwijnaarde 71 - 9052 Ghent - Belgium

country: Belgium

institute: VIB-UGent Center for Plant Systems Biology

data_processing:
using Galaxy Belgium platform
Trimmomatic
Salmon quant
tximport
Deseq2 to differentially expressed gened
Assembly: TAIR10 on Galaxy
Supplementary files format and content: tab-delimited file of count read for each sample

source_name: Root

growth_protocol: 1/2 MS  plates 22 Celsius degrees constant light 12d-old-root

extract_protocol:
1.5 cm of the upper part of the primary root. Rna extraction with Ronoklon kit
Illumina kit protocol

treatment_protocol: After 12-day, we transferred the plants to either Mock or DEX plates and harvested the samples after 24 hours treatment

value: Root

value: DEX (Dexamethasone)


title: Foundress_subordinate_pool_1

value: GREEN

value: WHITE

value: Worker

value: Pool


title: CRC tumor tissue P11

description:
Library name: P11
Fresh frozen Spatail transcriptome sequencing


title: Focal_Queen_2

value: BWYW


title: pPXY::shy2-2-GR_DEX treatment_Bio2


title: L_224a

description: Library name: lung_Sample_4

value: clp


title: CRC tumor tissue P02

description:
Library name: P02
Fresh frozen Spatail transcriptome sequencing


title: Focal_Queen_1

value: Post-worker emergence


title: dUCA1E2 +5-FU, series 2

data_processing:
European GALAXY platform
Raw paired-end sequencing reads were cleaned using Trimmomatic
ribosomal RNA reads were filtered out by SortMeRNA
Cleaned reads were aligned to the human Gencode reference (GRCh38.p13, v36  (Ensembl 102) ) using HISAT2
Transcriptome assembly and quantification was applied by StringTie
Normalization and differential expression analysis were performed using edgeR
Assembly: ftp___ftp.ebi.ac.uk_pub_databases_gencode_Gencode_human_release_36_gencode.v36.annotation.gtf.gz
Supplementary files format and content: Tab-delimeted file with edgeR normalized gene counts

growth_protocol: The HT29 cell-line was cultured in DMEM supplemented with 10% (v/v) FBS, and penicillin -streptomycin (100 U/mL-100 μg/mL) at 37°C in humidified air containing 5% CO2.

extract_protocol:
RNAs were isolated from 80%-confluent cultured cells using the NucleoSpin® miRNA kit (Macherey-Nagel).
librairies were prepared by Illumina TruSeq Stranded mRNA Library Prep
paired end RNA-seq

treatment_protocol: Cells treated for 72h with or without 2 µM 5-Fluorouracil (5-FU, Merck/Sigma-Aldrich).

value: colorectal cancer

value: UCA1 deleted exon 2

value: 2 µM 5-Fluorouracil


title: Queen_pool_2

value: Queen


title: pPXY::shy2-2-GR_DEX treatment_Bio1


title: L_213a

description: Library name: lung_Sample_3

value: Lung


title: Foundress_dominant_3

value: PINK

value: Individual

value: Pre-worker emergence


title: dUCA1E2, series 2


title: Queen_pool_1


title: CRC tumor tissue P07

description:
Library name: P07
Fresh frozen Spatail transcriptome sequencing

value: CRC


title: Arabidopsis seedlings, RNA, Col-0, 7-day-old, HRFR, R2

description: Library name: Col-0_rna_HRFR_R2

value: seedling

value: HRFR


title: L_211a

description: Library name: lung_Sample_2

value: Endothelium

value: WT


title: Foundress_dominant_2

value: GREEN


title: L_209a

description: Library name: lung_Sample_1


title: dUCA1E1 +5-FU, series 2

value: UCA1 deleted exon 1


title: pPXY::shy2-2-GR_Mock treatment_Bio2

value: Root

value: Mock


title: dUCA1E1, series 2

value: colorectal cancer


title: Foundress_dominant_1

value: BLUE


title: k_75_endo

description: Library name: kidney_Sample_27

source_name: Kidney

value: Kidney


title: pPXY::shy2-2-GR_Mock treatment_Bio1


title: Focal_Dominant_3

value: Ex-queen


title: Focal_Dominant_2


title: k_74_endo

description: Library name: kidney_Sample_26


title: ICP, series 2

value: Wt


title: pPER15::slr-GR_DEX treatment_Bio3

value: DEX (Dexamethasone)


title: dUCA1E2 +5-FU, series 1

value: UCA1 deleted exon 2

value: 2 µM 5-Fluorouracil


title: Focal_Dominant_1

value: Individual

value: Pre-worker emergence


title: pPER15::slr-GR_DEX treatment_Bio2


title: k_67_endo

description: Library name: kidney_Sample_24


title: k_73_endo

description: Library name: kidney_Sample_25


title: Dominant_3

value: Queen


title: k_65_endo

description: Library name: kidney_Sample_23

value: Endothelium


title: Dominant_2


title: pPER15::slr-GR_DEX treatment_Bio1


title: pPXY::shy2-2-GR_Mock treatment_Bio3


title: pPER15::slr-GR_Mock treatment_Bio3


title: dUCA1E2, series 1


title: dUCA1E1 +5-FU, series 1


title: pPER15::slr-GR_Mock treatment_Bio2


title: Foundress_dominant_pool_3

value: PINK

value: WHITE

value: Pool


title: k_64_endo

description: Library name: kidney_Sample_22

value: WT


title: dUCA1E1, series 1

value: UCA1 deleted exon 1


title: Foundress_dominant_pool_2

value: GREEN

value: UM


title: pPER15::slr-GR_Mock treatment_Bio1

value: Root

value: Mock


title: k_57_endo

description: Library name: kidney_Sample_21

value: Kidney


title: ICP +5-FU, series 2

value: colorectal cancer

value: Wt


title: ICP +5-FU, series 1

value: 2 µM 5-Fluorouracil


title: ICP, series 1


title: MCF-7 LSKAA replicate 1

description: Library name: Sample 9

data_processing:
Fastq files quality were checked with FastQC software. Reads were aligned with the bowtie2 mapper to release 27 of Homo sapiens Gencode version of the genome (GRCh38/hg38 assembly).
Quality of the mapped files (BAM format) was checked with QualiMap.
Peaks on individual samples were identified using the MACS2 software (narrow peaks with q<0.1 were initially selected).
Overlap of peaks across biological replicates were retrieved using the Bedtools.
To visualize the distribution of chromatin accessibility and transcription factor binding across genomic regions, we generated a heatmap using deepTools v3.5.5 (PMID: 27079975).
The computeMatrix scale-regions function was employed to process BigWig files corresponding to different experimental conditions (LCOR, LCOR+Fulvestrant, and LSKAA) relative to a set of predefined genomic regions.
Shared and condition-specific peaks were identified by finding overlaps within a 100 bp tolerance. Signal intensities were extracted from BigWig files using overlaps with peak regions, and the log2-transformed values were plotted. Peak categories (shared and exclusive) were color-coded, and regression lines were added to assess correlation. Gene annotation was performed using ChIPseeker and TxDb.Hsapiens.UCSC.hg38.knownGene, identifying transcription start site (TSS)-associated peaks.
Assembly: Homo sapiens genome GRCh38/hg38.
Supplementary files format and content: _.bw. BigWig files from each of the replicates of Fulvesrant+LCOR, LCOR and LSKAA.

extract_protocol:
Cells were grown in 150 mm2 plates, crosslinked for 10’ in 2% PFA and lysed. Cells were sonicated in 10 cycles of 30’’ ON/OFF using Bioruptor Pico Tubes (Diagenode) with sonication beads (Diagenode) in a Bioruptor sonicator (Diagenode). Sonicated chromatin was incubated with anti-HA antibody (ab9110, Abcam) at 4ºC in rotation o/n. Chromatin-antibody complexes were pulled down using Protein G dynabeads (ThermoFisher, 10003D) and magnetic rack. Isolated chromatin was decrosslinked at 65ºC for 4 h and DNA was purified with Qiagen DNA purification kit (Qiagen, 56304).
Repaired dA-tailing

value: Breast

value: Derived from human mammary adenocarcinoma


title: k_48_endo

description: Library name: kidney_Sample_19


title: deltaN93_5hG1_r2

city: Worcester

first: Allana

last: Schooley

address: 368 Plantation St

institute: UMass Medical School

data_processing:
Hi-C libraries were processed using the distiller-nf pipeline (Goloborodko et al. 2022), version 0.3.4
paired-end reads were mapped to hg38 human reference genome using bwa mem (Li 2013) in a single-sided fashion (-SP); read alignments were parsed and classified into pairwise interactions, or pairs, by parse from the pairtools package (Open2C et al. 2024b), version 1.0.2, additional `--walk-policy all` option was used in order to rescue multi-way interactions (walks); after the removal of duplicates, uniquely mapped and rescued pairs were further filtered according to their alignment quality (MAPQ > 30), and subsequently aggregated into binned contact matrices in the cooler format (Abdennur and Mirny 2020) at 1, 2, 5, 10, 25, 50, 100, 250, 500 and 1000 kb resolutions;  contact matrices were normalized using the iterative correction normalization (Imakaev et al. 2012) with the default parameters
Assembly: hg38
Supplementary files format and content: mcool (cooler) files for each replicate library and a pooled replicate mcool for each treatment/timepoint
Supplementary files format and content: 1D bed file: microcompartment domain (MCD) locations from Hi-C delta RanGAP1 data: 5hr_2X_enrichment.pixel_derived.signal_peaks.bed
Supplementary files format and content: 2D bedpe file: convergent CTCF loop anchors from Hi-C control data: mG1s_MEGA_10kb_wheader_CTCF_annotation.bedpe

source_name: cell line

growth_protocol: Cells were synchronized and arrested in prometaphase and either RanGAP1-AID or Nup93-AID was degraded 2 hours prior to release from nocodazole block. Cells were sorted in prometaphase, telophase, cytokinesis, and G1 of the cell cycle (5h). A G1 depletion was also performed 5h after mitotic release and cells were allowed to progress in G1 for a total of 10h (at5h-10h).

extract_protocol:
Cells were fixed with FA/DSG and digested with DdeI/DpnII according to Hi-C 3.0 (Lafontaine et al 2021)
Libraries were constructed using either Illumina TruSeq DNA LT Kit indexed adapters or NEBNext Multiplex Oligos

treatment_protocol: control Nup93-AID (ctrlN93) or IAA-treated Nup93-AID (deltaN93) or control RanGAP1-AID (ctrlRG) or IAA-treated RanGAP1-AID (deltaRG) DLD-1 cells

value: cell line

value: auxin-treated, 5h G1, replicate 2


title: k_56_endo

description: Library name: kidney_Sample_20

value: Endothelium


title: MCF-7 LCOR + Fulvestrant replicate 1

description: Library name: Sample 7


title: k_43_endo

description: Library name: kidney_Sample_17


title: deltaN93_5hG1_r1

value: auxin-treated, 5h G1, replicate 1


title: k_45_endo

description: Library name: kidney_Sample_18


title: sgALAS1 rep1

city: Melbourne

first: Emily

last: Gruber

state: VIC

address: 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

description:
Library name: AL-10_S19_R1_001.fastq.gz
Column name of raw_counts.txt: sgALAS1 rep1

data_processing:
Sequencing reads were de-multiplexed using bcl2fastq (v2.17.1.14)
Low quality reads (Q < 30) removed and trimmed using cutadapt (v1.14)
Reads were mapped to the human (hg19) reference genomes using HISAT2 (v2.0.4)
Reads were counted using featureCounts (-O) from subread (v 2.0.0)
Counts were filtered using filterByExpr from edgeR (v 3.34.0)82 with default parameters, quantile normalized using voom and differential gene expression performed using Limma (v 3.48.3)
Assembly: hg19
Supplementary files format and content: raw counts table output from featureCounts

extract_protocol:
Cells were lysed in Trizol reagent (Thermo Fisher) and RNA was extracted using the Direct-zol RNA Miniprep kit (Zymo Research).
RNAseq was performed at the Peter MacCallum Cancer Centre Molecular Genomics core facility. RNAseq libraries were generated using the QuantSeq 3¢ mRNA-seq Library Prep Kit for Illumina (Lexogen) and sequenced on an Illumina NextSeq500 to produce 75-100 bp single-end reads with a depth of 6-10x106 reads per sample.

treatment_protocol: OCI-AML3 cells transduced with sgRNAs were treated with doxycycline for 7 days to induce sgRNA expression. Additionally, OCI-AML3 cells were treated with vehicle or SA (500uM) for 6 days


title: sgALAS1 rep3

description:
Library name: AL-12_S21_R1_001.fastq.gz
Column name of raw_counts.txt: sgALAS1 rep3


title: deltaRG_10hG1_r2

value: auxin-treated, 10h G1, replicate 2


title: k_42_endo

description: Library name: kidney_Sample_16

value: WT


title: deltaRG_10hG1_r1

value: auxin-treated, 10h G1, replicate 1


title: MCF-7 LCOR replicate 2

description: Library name: Sample 6


title: sgSCR rep3

description:
Library name: AL-9_S36_R1_001.fastq.gz
Column name of raw_counts.txt: sgSCR rep3

value: sgSCR


title: MCF-7 LCOR replicate 1

description: Library name: Sample 5


title: k_40_endo

description: Library name: kidney_Sample_15


title: sgSCR rep2

description:
Library name: AL-8_S35_R1_001.fastq.gz
Column name of raw_counts.txt: sgSCR rep2


title: MCF-7 LSKAA replicate 2

description: Library name: Sample 10


title: deltaRG_at5h-10hG1_r1

value: auxin-treated, at5h 10h G1, replicate 1


title: Foundress_dominant_pool_1

value: BLUE

value: PINK

value: Queen

value: Pool

value: Pre-worker emergence


title: sgSCR rep1

description:
Library name: AL-7_S34_R1_001.fastq.gz
Column name of raw_counts.txt: sgSCR rep1


title: deltaRG_at5h10hG1_r2

value: auxin-treated, at5h 10h G1, replicate 2


title: MCF-7 Ctrl vector replicate 1

description: Library name: Sample 3

value: Breast


title: k_39_endo

description: Library name: kidney_Sample_14

value: Kidney


title: k_290

description: Library name: kidney_Sample_13


title: SA rep3

description:
Library name: AL-6_S33_R1_001.fastq.gz
Column name of raw_counts.txt: SA rep3

value: SA


title: deltaRG_5hG1_r2

value: cell line

value: auxin-treated, 5h G1, replicate 2


title: MCF-7 LCOR + Fulvestrant replicate 2

description: Library name: Sample 8

value: Derived from human mammary adenocarcinoma


title: k_284

description: Library name: kidney_Sample_12

value: Endothelium


title: sgALAS1 rep2

description:
Library name: AL-11_S20_R1_001.fastq.gz
Column name of raw_counts.txt: sgALAS1 rep2


title: SA rep2

description:
Library name: AL-5_S32_R1_001.fastq.gz
Column name of raw_counts.txt: SA rep2


title: deltaRG_5hG1_r1

value: auxin-treated, 5h G1, replicate 1


title: k_283

description: Library name: kidney_Sample_11

value: WT


title: MCF-7 Input repliate 1

description: Library name: Sample 1


title: k_271

description: Library name: kidney_Sample_10


title: deltaRG_cyto_r1

value: auxin-treated, cytokinesis, replicate 1


title: MDA-MB-231 LCOR over-expression cells

description: Library name: Sample 4

data_processing:
Quality checking of raw data (fastq files) was performed with FastQC software (v.0.11.9).
Estimation of ribosomal RNA in the raw data was obtained with riboPicker74.
Raw reads were trimmed using TrimGalore (v.0.6.6) with a quality cutoff of 30.
Quality reads were aligned with the STAR mapper to the Homo sapiens genome GRCh38/hg38.
The R/Bioconductor package DESeq2 (v.1.30.1) was used to assess differential expression between experimental groups (Wald statistical test plus false discovery rate (FDR) correction). Genes for which the sum of raw counts across all samples was <1 were discarded. Genes are considered differentially expressed if their absolute log2 fold change was >1 and their adjusted p-value < 0.05.
Assembly: Homo sapiens genome GRCh38/hg38.
Supplementary files format and content: results_.txt: Tab-delimited text file containing a Differential analysis results with the symbol, ensembl_id, baseMean, log2FoldChange, lfcSE, stat, pvalue and padj

value: Derived from metastatic mammary adenocarcinoma

value: LCOR-OE


title: SA rep1

description:
Library name: AL-4_S31_R1_001.fastq.gz
Column name of raw_counts.txt: SA rep1


title: MCF-7 Ctrl vector replicate 2

description: Library name: Sample 4


title: deltaRG_telo_r1

value: auxin-treated, telophase, replicate 1


title: k_267

description: Library name: kidney_Sample_9


title: Vehicle rep3

description:
Library name: AL-3_S30_R1_001.fastq.gz
Column name of raw_counts.txt: Vehicle rep3

value: Vehicle


title: Vehicle rep2

description:
Library name: AL-2_S29_R1_001.fastq.gz
Column name of raw_counts.txt: Vehicle rep2


title: MDA-MB-231 Wild Type cells

description: Library name: Sample 3


title: k_265

description: Library name: kidney_Sample_8


title: Vehicle rep1

description:
Library name: AL-1_S28_R1_001.fastq.gz
Column name of raw_counts.txt: Vehicle rep1


title: MCF-7 LCOR over-expression cells

description: Library name: Sample 2


title: deltaRG_mito_r2

value: auxin-treated, prometaphase, replicate 2


title: MCF-7 Wild Type cells

description: Library name: Sample 1


title: k_240a

description: Library name: kidney_Sample_7

value: sham


title: deltaRG_mito_r1

value: auxin-treated, prometaphase, replicate 1


title: DNMT3AR882H rep2

description:
Library name: 3RNA-AL-4_S22_R1_001.fastq.gz
Column title in raw_counts.txt: AL_4_R882H

data_processing:
Sequencing reads were de-multiplexed using bcl2fastq (v2.17.1.14)
Low quality reads (Q < 30) removed and trimmed using cutadapt (v1.14)
Reads were mapped to the mouse (mm10) reference genomes using HISAT2 (v2.0.4)
Reads were counted using featureCounts (-O) from subread (v 2.0.0)
Counts were filtered using filterByExpr from edgeR (v 3.34.0)82 with default parameters, quantile normalized using voom and differential gene expression performed using Limma (v 3.48.3)
Assembly: mm10
Supplementary files format and content: raw counts table output from featureCounts


title: MCF-7 Input repliate 2

description: Library name: Sample 2

value: Breast


title: k_235a

description: Library name: kidney_Sample_6

value: Kidney


title: ctrlN93_5hG1_r2

value: control, 5h G1, replicate 2


title: ctrlN93_5hG1_r1

value: cell line

value: control, 5h G1, replicate 1


title: k_229a

description: Library name: kidney_Sample_5


title: DNMT3AR882H rep1

description:
Library name: 3RNA-AL-3_S21_R1_001.fastq.gz
Column title in raw_counts.txt: AL_3_R882H


title: tratamiento_rep3

city: Mexico

first: Leticia

last: Vega

state: Mexico

address: Circuito Ext s/n

country: Mexico

institute: Universidad Nacional Autonoma de Mexico

description: Library name: Tratamiento 3

data_processing:
Illumina bcl2fastq software were used for basecalling
Reads were aligned to the GCA_000203895.1/ASM20389v1 genome assembly using smalt
The number of reads falling in the genes  were counted using coveragebed software and normalized with DESeq2 software
Assembly: GCA_000203895.1
Supplementary files format and content: tab-delimited text file include the differential expression results of DESeq2 and raw and normalized counts  for each sample.

organism: Paracoccus denitrificans PD1222

source_name: strain

growth_protocol: Paracoccus denitrificans PD1222 was initially grown aerobically in LB medium supplemented with 5 mM sodium nitrate and 10 mM calcium chloride. Cultures were grown in 4-L Erlenmeyer flasks containing 1 L working volume at 30 °C.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol. Genomic DNA contamination was removed by DNase I (RNase-free) treatment (Thermo Scientific). RNA concentration and purity were measured using a NanoDrop 200c spectrophotometer (Thermo Scientific), and RNA integrity was assessed with an Agilent 2100 Bioanalyzer. The resulting RNA samples were used for both RNA sequencing (RNA-seq) and reverse transcription quantitative PCR (RT-qPCR).
RNA-Seq was performed using total RNA extracted from Paracoccus denitrificans PD1222 grown with and without applied constant potential. Ribosomal RNA was depleted using the Ribo-Zero Plus Microbiome Depletion Kit (Illumina). The remaining mRNA was chemically fragmented to ~150–200 bp, and cDNA libraries were synthesized using the Illumina Stranded Total RNA Prep Kit (Illumina). Libraries were quantified using the Qubit dsDNA HS Assay Kit and a Qubit v4 fluorometer (Thermo Scientific). Sequencing was carried out at the UUSMB (Unidad Universitaria de Secuenciación Masiva y Bioinformática, UNAM, México) on an Illumina NextSeq 500 platform using a 2 × 75-cycle sequencing kit (NextSeq 500/550 Mid Output Kit, 150 cycles). Differential expression analysis was performed using DESeq2 (Anders and Huber, 2010). Genes with adjusted p-value < 0.05 and fold change > 1 were considered significantly differentially expressed.

treatment_protocol: Cells were harvested by centrifugation, washed with saline solution, and resuspended in a minimal medium supplemented with 7.5 mM nitrate and 3.5 mM succinate to an initial OD₈₀₀ of 0.6. Cultures were grown anaerobically in a 2-L bioreactor with a working volume of 1.5 L. The reactor was purged with nitrogen gas for 30 minutes to ensure anaerobiosis. After stabilization, an electrical potential of +200 mV (treatment) or 0 mV (control) was applied. Samples were collected after 6 hours based on previously determined growth curves.

value: strain


title: EV rep2

description:
Library name: 3RNA-AL-2_S20_R1_001.fastq.gz
Column title in raw_counts.txt: AL_2_EV

value: EV


title: k_224a

description: Library name: kidney_Sample_4

value: Endothelium

value: clp


title: EV rep1

description:
Library name: 3RNA-AL-1_S19_R1_001.fastq.gz
Column title in raw_counts.txt: AL_1_EV


title: ctrlRG_10hG1_r1

value: control, 10h G1, replicate 1


title: control_rep2

description: Library name: Control 2

value: WT

value: 0 mV


title: k_213a

description: Library name: kidney_Sample_3


title: DIN cells 5 days untreated (R882H on) rep2

description:
Library name: 5UT2_S60_R1_001.fastq.gz
Column name in raw_counts.txt: 5UT2_day5_R882H_on

source_name: cKit+/CD11b- DIN cells

value: cKit+/CD11b- DIN cells

value: Untreated


title: control_rep1

description: Library name: Control 1


title: ctrlRG_5hG1_r2


title: k_211a

description: Library name: kidney_Sample_2


title: DIN cells 5 days untreated (R882H on) rep1

description:
Library name: 5UT1_S59_R1_001.fastq.gz
Column name in raw_counts.txt: 5UT1_day5_R882H_on


title: DIN cells 5 days DOX (R882H off) rep1

description:
Library name: 5D1_S63_R1_001.fastq.gz
Column name in raw_counts.txt: 5D1_day5_R882H_off

value: Doxycycline


title: Elim_WT_lactate_with100nM_W_2

city: Athens

first: Michael

middle: W. W.

last: Adams

state: GA

address: 120 East Green St.

department: Molecular Biology and Biochemistry

institute: University of Georgia

data_processing:
Raw data was processed through fastp. Low quality reads and adapters and poly-N sequences were removed.
Rockhopper was used to identify novel genes, operon, and transcription start sites. Then, Time-Delay Neural Network was used to extract predictede promoters.
FeatureCounts was used to count the reads mapped to each gene.
Assembly: Bowtie2 was used to align reads to the reference genome and build an index.
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.
Supplementary files format and content: tab-delimited text file includes fpkm values for each sample.

organism: Eubacterium limosum

source_name: ATCC 8486

growth_protocol: The growth media for E. limosum contained 0.5 g/L yeast extract, 1 g/L cysteine, 10 mM 3-(N-morpholino)propanesulfonic acid (MOPS), 1 mM KH2PO4, 1X salts, vitamin mix, trace elements, 10 mM acetate, 100 nM (NH4)2MoO4.4H2O and 100 nM Na2WO4.2H2O. The pH of the medium was adjusted with 5 M NaOH to 7.0 and was filter sterilized using a 0.2 μM filter before use. For glucose grown cells, 28 mM glucose was added to the media. For lactate grown cells, 70 mM lactate was added to the media. E. limosum was grown anaerobically with a headspace of 20% CO2 and 80% N2 at 35°C with shaking.

extract_protocol:
E. limosum cells were grown in 50 mL serum bottles under glucose and lactate conditions, with and without 100 nM W added. At mid-log phase (OD600 = 0.3), 50 mL of cells were spun down for 15 minutes at 15,000g at 4 °C. The cells were resuspended in 0.5 mL of the supernatant and 2 mL RNAprotect Bacteria Reagent (Qiagen). The Qiagen RNeasy Mini Kit was used as suggested with an added lysozyme treatment and bead beater (model and parameters) was used to extract RNA. An additional on column DNase I treatment was performed as suggested with the kit. The RNA quality was assessed using A260/A280 on a Nanodrop and a Bioanalyzer RIN>7 (as suggested by Novogene). 1 µg of RNA was used for library preparation.
Ribosomal RNA was removed from total RNA, followed by ethanol precipitation. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer recommendations and index codes were added.

treatment_protocol: For the W limited medium, Milli-Q filtered water was used to make up the growth medium and Na2WO4.2H2O were not added to the trace elements solution.

tag: strain

value: ATCC 8486

value: Wild Type


title: Elim_WT_lactate_with100nM_W_3


title: T41S_1_H8

city: Leiden

first: Karamjit

middle: Singh

last: Dolt

address: Einthovenweg 20

department: Human Genetics

country: Netherlands

institute: LUMC

description: Library name: Sample-25

data_processing:
A Galaxy workflow consisting of the following tools were used to perform (reads to count) transcriptome analysis.
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2
toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna/2.1b.6
toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_dedup/umi_tools_dedup/1.1.2+galaxy2
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1+galaxy2
Assembly: mm10 full
Supplementary files format and content: FeatureCount output file in text file format containing raw counts.

source_name: Embryonic

growth_protocol: E14 cells were cultured in ES medium with serum at 5%CO2 and humidified incubator at 37 degree celcius

extract_protocol:
Total RNA isolation was performed using the RNAeasy mini kit (Qiagen) according to the manufacturer’s instructions.
the generation of cDNA and the RNA-seq library, we used the method that was described as mcSCRB-seq (PMID 30050112).

treatment_protocol: Respective Chiron treatment was performed for 48 hours

value: Embryonic

value: Embryonic Stem Cells

tag: duration

value: 48 Hours


title: k_209a

first: Ramon

last: Bossardi Ramos

address: 43 New Scotland Avenue

institute: Albany Medical College

description: Library name: kidney_Sample_1

value: Kidney


title: ctrlRG_5hG1_r1

value: cell line

value: control, 5h G1, replicate 1


title: ctrlRG_cyto_r1

value: control, cytokinesis, replicate 1


title: tratamiento_rep2

description: Library name: Tratamiento 2

value: strain


title: DIN cells 5 days DOX (R882H off) rep2

description:
Library name: 5D2_S55_R1_001.fastq.gz
Column name in raw_counts.txt: 5D2_day5_R882H_off


title: Elim_WT_lactate_with100nM_W_1


title: ctrlRG_mito_r2

value: control, prometaphase, replicate 2


title: T41I_2_A6

description: Library name: Sample-23


title: Elim_WT_lactate_without_W_3

value: W limited


title: ctrlRG_telo_r1

value: control, telophase, replicate 1


title: DIN cells 14 days untreated (R882H on) rep1

description:
Library name: 14UT1_S62_R1_001.fastq.gz
Column name in raw_counts.txt: 14UT1_day14_R882H_on


title: T41N_1_D3

description: Library name: Sample-24


title: tratamiento_rep1

description: Library name: Tratamiento 1

value: WT


title: ctrlRG_10hG1_r2

value: control, 10h G1, replicate 2


title: ctrlRG_mito_r1

value: control, prometaphase, replicate 1


title: DIN cells 14 days DOX (R882H off) rep4

description:
Library name: 14D4_S56_R1_001.fastq.gz
Column name in raw_counts.txt: 14D4_day14_R882H_off

value: cKit+/CD11b- DIN cells

value: Doxycycline


title: Elim_WT_lactate_without_W_2

value: ATCC 8486

value: Wild Type


title: T41I_1_B9

description: Library name: Sample-22

value: Embryonic

value: Embryonic Stem Cells


title: Elim_WT_lactate_without_W_1


title: DIN cells 14 days DOX (R882H off) rep3

description:
Library name: 14D3_S58_R1_001.fastq.gz
Column name in raw_counts.txt: 14D3_day14_R882H_off


title: T41A_2_E6

description: Library name: Sample-21

value: 48 Hours


title: T41A_1_C1

description: Library name: Sample-20


title: Elim_WT_glucose_with100nM_W_3


title: DIN cells 14 days DOX (R882H off) rep2

description:
Library name: 14D2_S61_R1_001.fastq.gz
Column name in raw_counts.txt: 14D2_day14_R882H_off


title: Elim_WT_glucose_with100nM_W_1


title: DNMT3AR882H + Hemin

description: Library name: AL4_S20_R1_001.fastq.gz

data_processing:
Raw sequencing reads were demultiplexed using bcl2fastq (v2.17.1.14)
adaptor sequences were removed using Trim Galore (-q 30) (v0.4.4)
reads aligned to the mouse genome (mm10) using Bowtie2 (v2.3.3) using default parameters
Samtools (v1.9) was used for processing SAM and BAM files.
Picard (v2.6.0) was used to remove duplicate reads
Peaks were called using Macs2 callpeak (v2.2.7.1) with default settings
bedtools intersect (v 2.31.1) used to exclude peaks that overlap with blacklisted regions (ENCODE).
Motif analysis was performed using Homer (v4.11)
Bigwig files were generated with deeptools (v 3.5.0) bamCoverage (-bl $blacklist --effectiveGenomeSize 2652783500 --binSize 10 --smoothLength 50 --normalizeUsing CPM --extendReads 200)
Assembly: mm10
Supplementary files format and content: bigwig

growth_protocol: 1.5x107 HoxB8 EV and DNMT3AR882H cells were seeded at 5x105 per ml in POG complete media.

extract_protocol:
Samples were fixed with formaldehyde solution (1% w/v) for 15mins with gentle rocking and quenched by adding 2.5M glycine for 5mins.  2x107 cells were washed twice in ice cold PBS and resuspended in 1ml of ChIP Lysis buffer (1% SDS (w/v), 10mM EDTA, 50mM Tris-HCl pH 8.0, cOmplete mini EDTA-free protease inhibitor cocktail (Sigma-Aldrich)). Each sample was sonicated using a Covaris S220 Focused Ultrasonicator for 40 cycles (30s on (5% duty cycle; intensity - 5200 cycles per burst), 20s off). 9ml of modified RIPA buffer (1% (v/v) TritonX100, 0.1% (v/v) deoxycholate, 90mM NaCl, 10mM Tris-HCl pH8, cOmplete mini EDTA-free protease inhibitor cocktail (Sigma-Aldrich)) was added to each sample. 5% from each sample was collected and pooled for an input sample. 2.5µg of Bach1 antibody (R&D systems #AF5777) was added to each sample with gentle rocking overnight at 4°C. Protein G Dynabeads (Theromo Fisher) were washed twice in modified RIPA buffer and added to each sample for 2hrs with gentle mixing at 4°C. Dynabeads were washed 3 times in wash buffer (0.1% (w/v) SDS, 1% (v/v) TritonX100 v/v, 2mM EDTA, 150mM NaCl, 20mM Tris-HCl pH 8) for 5 min.  Reverse crosslinking buffer: (1% (w/v) SDS, 100mM NaHCO3, 200mM NaCl, 300µg/ml Proteinase K) was added to each sample and incubated at 65°C for overnight. DNA was extracted with ChIP DNA Clean & Concentrator kit (Zymo Research).
Sequencing libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina kit (New England Biolabs) according to the manufacturer's protocol. Cleanup of adaptor ligated DNA was performed using AMPure XP beads. Purified DNA was amplified using PCR enrichment with 12 and 16 cycles for input and ChIP samples respectively. Libraries were sequenced on an Illumina Nextseq500 with 75bp single end reads to a depth of 21-35 million reads.

treatment_protocol: DNMT3AR882H cells were treated with DMSO (0.16% v/v) or hemin (40μM) for 24hrs.

value: DNMT3AR882H + Hemin

tag: chip antibody

value: R&D systems #AF5777


title: S45P_1_G5

description: Library name: Sample-19


title: DIN cells 14 days DOX (R882H off) rep1

description:
Library name: 14D1_S57_R1_001.fastq.gz
Column name in raw_counts.txt: 14D1_day14_R882H_off


title: DIN cells 14 days untreated (R882H on) rep2

description:
Library name: 14UT2_S64_R1_001.fastq.gz
Column name in raw_counts.txt: 14UT2_day14_R882H_on

value: Untreated


title: Elim_WT_glucose_with100nM_W_2


title: S45F_2_D9

description: Library name: Sample-18


title: Elim_WT_glucose_without_W_3


title: DNMT3AR882H

description: Library name: AL3_S19_R1_001.fastq.gz


title: Elim_WT_glucose_without_W_2


title: Empty vector (EV)

description: Library name: AL2_S18_R1_001.fastq.gz

value: EV


title: Elim_WT_glucose_without_W_1


title: S45F_1_C1

description: Library name: Sample-17


title: S37Y_1_A5

description: Library name: Sample-15


title: S37F_2_G1

description: Library name: Sample-14