title: OregonR_M_D30_WB_rep2

city: Gainesville

first: Lei

last: Zhou

state: FL

department: Molecular Genetics and Microbiology

institute: University of Florida

data_processing:
Mapped to Dm6.43, TPM obtained with Slamon
Assembly: Dm6.43
Supplementary files format and content: Excel file, first two colomns are FBgn and Gene_Symbol, followed by TPM for sample columns.

organism: Drosophila melanogaster

source_name: Male, D30, whole body

growth_protocol: 25C normal diet

extract_protocol:
Flies or tissues are homogenized in Trizol, total RNA is then extracted with standard protocol.
Standard Illumina library construction

value: Whole Body

value: OregonR


title: WT D60 H3K9me3 Replicate 2

status: Public on Apr 17 2024

type: SRA

city: Saint Louis

first: Kristen

last: Kroll

state: MO

address: 320 McDonnell Sciences/660 S. Euclid Ave.

department: Developmental Biology

country: USA

institute: Washington University School of Medicine

library_source: genomic

data_processing:
Raw reads were processed using AIAP (v1.1) for trimming, alignment, bigWig generation and peak calling
Assembly: hg38
Supplementary files format and content: bigWig density file
Supplementary files format and content: narrowPeak or broadPeak file containing output from MACS2 peakcalling
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Homo sapiens

source_name: matured cortical interneurons

growth_protocol: Embryonic stem cells were mainatined in mTeSR media on Vitronectin coated cultureware.

extract_protocol:
Genomic DNA was processed using CUT&Tag (Epicypher) and isolated using phenol-chloroform follow by the NucleoSpin® Gel and PCR Clean-Up kit (Macherey-Nagel).
After PCR amplification samples with unique dual-end indexes were pooled in equimolar concentrations.

tag: cell type

value: matured cortical interneurons

tag: stem cell_source

value: H9 hESC

tag: passage

tag: timepoint

tag: antibody


title: WT D60 H3K4me3 Replicate 3


title: CADASIL brain arteries (12 months) rep3

city: Paris

first: Anne

last: JOUTEL

address: 102 rue de la Sante

country: France

institute: Inserm

library_source: transcriptomic

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.20.0.422.
Reads were preprocessed using cutadapt version 1.10 in order to remove adapter, polyA and low-quality sequences (Phred quality score below 20) and reads shorter than 40 bases were discarded for further analysis. Reads mapping to rRNA were also discarded (this mapping was performed using bowtie version 2.2.8).
Reads were then mapped onto the mm39 assembly of mouse genome using STAR version 2.5.3a.
Gene expression was quantified using htseq-count version 0.6.1p1 and gene annotations from Ensembl release 106.
Assembly: mm39
Supplementary files format and content: tab-delimitated text file includes raw count for each sample

molecule: total RNA

organism: Mus musculus

source_name: brain arteries

extract_protocol:
Brain arteries were homogenized on ice in lysis buffer using a polytron homogenizer, and total RNA was extracted following the manufacturer’s protocol (RNeasy MicroKit, Quiagen).
libraries were generated from 150 ng of total RNA using Illumina Stranded mRNA Prep, Ligation kit and IDT for Illumina RNA UD Indexes Ligation (Illumina, San Diego, USA) according to manufacturer's instructions. Following polyA selection, mRNAs were fragmented at 94°C for 8 minutes. DNA libraries were amplified using 13 cycles of PCR. Surplus PCR primers were further removed by two successive purifications using SPRIselect beads (Beckman-Coulter, Villepinte, France). The final libraries were checked for quality and quantified using Bioanalyzer 2100 system (Agilent technologies, Les Ulis, France).

tag: tissue

value: brain arteries

tag: age

value: 12 months

tag: genotype

tag: treatment


title: SCNn+a, S289

city: Zurich

first: Csaba

last: Földy

state: Zurich

address: Winterthurerstrasse 190

department: Brain Research Institute

country: Switzerland

institute: University of Zurich

description:
Data-sce-count.txt
Data-sce-normed.txt
Data-sce-log.txt

library_source: transcriptomic single cell

data_processing:
Base calling was done using Illumina RTA2
Illumina bc12fastq v2.20 was used for demultiplexing and fastq file generation
Reads were aligned using STAR aligner to GRCm38.p4  to get gene counts (Data-sce-count.txt)
Cells that passed quality control were normalized (Data-sce-normed.txt, Lab-Sara-sce-log.txt)
Differential gene expression was analyzed using DESeq2.
Assembly: GRCm38.p4
Supplementary files format and content: Data-sce-count.txt; raw counts
Supplementary files format and content: Data-sce-normed.txt; normalized counts
Supplementary files format and content: Data-sce-log.txt; log of normalized counts

source_name: interneurons of the suprachiasmatic nucleus

extract_protocol:
single cell extraction via patch pipette
Nextera XT DNA Library Preparation kit

tag: time of_day

value: night

tag: electrophysiology

value: active

tag: cfos expression

value: cFOS+


title: SCNn-a, S287

value: interneurons of the suprachiasmatic nucleus

value: cFOS-


title: SCNn-s, S288

value: silent


title: WT D60 H3K4me3 Replicate 2


title: Sedentary_ATMs_Biological_rep_1

type: RNA

city: Guangzhou

first: Wenbai

last: Huang

state: Guangdong

address: 601 Huangpu Ave. Tianhe Dist.

department: School of Physical Education

country: China

institute: Jinan University

description: adipose tissue macrophages of mice with 8-week inactivity

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

scan_protocol: After staining, the microarray chip was scanned using a GeneChip Scanner 3000 7G

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

label: biotin

source_name: 15-week male mouse post 8-week inactivity

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

growth_protocol: 6-week- old male C57BL/6 mice were housed individually in ventilated caging system under a 12:12-hour light-dark cycle at 23±2℃ and 45%–55% humidity.

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

treatment_protocol: Forty male C57BL/6 mice were randomly assigned to either a sedentary (S) or an exercise (E) group. The S group remained inactive, while the E group underwent a one-week treadmill adaptation, followed by an 8-week aerobic treadmill exercise protocol (60 min/ day, 5 days/ week, at 65%-75% VO2max). ATMs harvested from visceral adipose tissues.

tag: gender

value: male

value: adipose tissue

tag: strain


title: OregonR_M_D5_WB_rep2

source_name: Male, D5, whole body


title: Sedentary_ATMs_Biological_rep_2


title: OregonR_M_D5_WB_rep1


title: WT D60 H3K4me3 Replicate 1


title: CADASIL brain arteries (12 months) rep1


title: SCNn+a, S285


title: WT D60 H3K27me3 Replicate 3


title: OregonR_F_D30_WB_rep2

source_name: Female, D30, Whole body


title: WT D60 H3K27me3 Replicate 2


title: Notch3KO brain arteries (3 months) rep8

value: 3 months


title: SCNn+a, S283


title: Sedentary_ATMs_Biological_rep_3


title: OregonR_F_D5_WB_rep2

source_name: Female, D5, whole body


title: WT D60 H3K27ac Replicate 3


title: Notch3KO brain arteries (3 months) rep6


title: CADASIL brain arteries (12 months) rep2


title: SCNn+a, S282


title: Notch3KO brain arteries (3 months) rep5


title: SCNn+s, S281


title: WT D60 H3K27ac Replicate 2


title: SCNn-s, S279


title: SCNn-d, S286

value: depolarized


title: w1118_M_D45_Gut_rep1

source_name: Male, D45, Whole guts

value: Whole Gut


title: WT D60 H3K27ac Replicate 1


title: w1118_M_D30_Gut_rep3

source_name: Male, D30, Whole guts


title: Notch3KO brain arteries (3 months) rep4


title: OregonR_F_D5_WB_rep1

value: Whole Body


title: WT D35 IgG Replicate 3

source_name: immature cortical interneurons

value: immature cortical interneurons

value: IgG


title: OregonR_F_D30_WB_rep1

value: OregonR


title: SCNd+a, S275

value: day


title: OregonR_M_D30_WB_rep1


title: Notch3KO brain arteries (3 months) rep7

value: brain arteries


title: SCNn+s, S284

value: night


title: WT D60 H3K27me3 Replicate 1

value: matured cortical interneurons

value: H9 hESC


title: w1118_M_D30_Gut_rep2


title: WT D35 IgG Replicate 2


title: Notch3KO brain arteries (3 months) rep2


title: Notch3KO brain arteries (3 months) rep3


title: w1118_M_D30_Gut_rep1


title: SCNd-a, S273

value: interneurons of the suprachiasmatic nucleus

value: active


title: Notch3KO brain arteries (3 months) rep1


title: WT D35 IgG Replicate 1


title: w1118_M_D5_Gut_rep3

source_name: Male, D5, Whole guts


title: Wildtype brain arteries (3 months) rep8


title: SCNd+s, S274

value: silent

value: cFOS+


title: Wildtype brain arteries (3 months) rep7


title: SCNn-a, S270

value: cFOS-


title: WT D35 H3K9me3 Replicate 3


title: w1118_M_D5_Gut_rep1


title: Wildtype brain arteries (3 months) rep6

value: 3 months


title: Exercise_ATMs_Biological_rep_2

description: adipose tissue macrophages of mice with 8-week moderate aerobic exercise

source_name: 15-week male mouse post 8-week exercise

value: male

value: adipose tissue


title: WT D35 H3K9me3 Replicate 2


title: Wildtype brain arteries (3 months) rep5


title: SCNd-s, S272


title: WT D35 H3K9me3 Replicate 1


title: w1118_F_D45_Gut_rep1

source_name: Female, D45,  Whole guts

value: Whole Gut


title: w1118_F_D45_Gut_rep2


title: WT D35 H3K4me3 Replicate 4

value: immature cortical interneurons


title: Wildtype brain arteries (3 months) rep4


title: SCNn-s, S264


title: w1118_F_D30_Gut_rep3

source_name: Female, D30,  Whole guts


title: WT D35 H3K4me3 Replicate 3


title: SCNn-s, S267


title: SCNn-s, S263


title: Wildtype brain arteries (3 months) rep3


title: w1118_F_D30_Gut_rep2


title: WT D35 H3K9me3 Replicate 4


title: w1118_M_D5_Gut_rep2


title: Wildtype brain arteries (3 months) rep2


title: Wildtype brain arteries (3 months) rep1


title: WT D35 H3K4me3 Replicate 2


title: SCNn+a, S260


title: WT D35 H3K4me3 Replicate 1


title: w1118_F_D5_Gut_rep3

source_name: Female, D5,  Whole guts


title: w1118_F_D5_Gut_rep2


title: SCNn-a, S258


title: Fth1△/△,HSC,rep4

first: Qiang

last: Zhan

address: 601 W.Huangpu Avenue

description:
b4
Fth1△/△

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.4 and paired- end clean reads were aligned to the reference genome using Hisat2 v2.0.4.
HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: GRCm38
Supplementary files format and content: *.txt: Tab-delimited text file includes FPKM values of each sample.

molecule: polyA RNA

source_name: Bone marrow

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

value: Bone marrow

value: Hematopoietics stem cell

value: 2 months


title: Fth1△/△,HSC,rep3

description:
b3
Fth1△/△


title: SCNn+s, S257


title: w1118_F_D5_Gut_rep1


title: SCNn+a, S265


title: Fth1△/△,HSC,rep2

description:
b2
Fth1△/△


title: SCNn-a, S256


title: WT D35 H3K27ac Replicate 4


title: SCNn-s, S255


title: Fth1△/△,HSC,rep1

description:
b1
Fth1△/△


title: w1118_M_D45_FB_rep1

source_name: Male, D45, Fat body

value: Fat body


title: Fth1fl/fl,HSC,rep3


title: w1118_M_D30_FB_rep3

source_name: Male, D30, Fat body


title: SCNn-s, S254

value: night


title: w1118_F_D30_Gut_rep1


title: WT D35 H3K27ac Replicate 3


title: WT D35 H3K27ac Replicate 2


title: w1118_M_D30_FB_rep1


title: SCNn+d, S262

value: depolarized


title: Fth1fl/fl,HSC,rep2


title: Fth1fl/fl,HSC,rep1


title: SCNn+s, S253-2


title: w1118_M_D5_FB_rep3

source_name: Male, D5, Fat body


title: SCNn-a, S253

source_name: interneurons of the suprachiasmatic nucleus


title: WT D35 H3K27ac Replicate 1

value: H9 hESC


title: WT D15-D IgG Replicate 4

source_name: dorsally patterned neuronal precursors

value: dorsally patterned neuronal precursors

value: IgG


title: SCNn-a, S252

value: interneurons of the suprachiasmatic nucleus

value: active


title: LLC JAG2KO2

city: Tampa

first: Paulo

last: Rodriguez

state: Florida

address: 3011 W. Holly Drive, MRC, 2067

institute: H. Lee Moffitt Cancer Center

description: Lewis Lung Carcinoma Jagged2KO2

data_processing:
STAR v2.7.7a
HTSeq v0.11.2
Supplementary files format and content: Raw counts using HTSeq

source_name: Tumor

extract_protocol:
Qiagen Rneasy
single index

value: Tumor

tag: cell line

value: Lewis Lung Carcinoma

value: Lung


title: LLC JAG2KO3

description: Lewis Lung Carcinoma Jagged2KO3


title: SCNn+a, S251

value: cFOS+


title: WT D15-D IgG Replicate 3


title: w1118_M_D5_FB_rep2


title: w1118_M_D5_FB_rep1


title: LLC JAG2KO1

description: Lewis Lung Carcinoma Jagged2KO1


title: WT D15-D IgG Replicate 2


title: SCNn-a, S249

value: cFOS-


title: LLC Scramble3

description: Lewis Lung Carcinoma Scramble3

value: Scramble


title: SCNn+a, S248


title: w1118_F_D45_FB_rep1

source_name: Female, D45, Fat body


title: w1118_M_D30_FB_rep2


title: w1118_F_D30_FB_rep3

source_name: Female, D30, Fat body


title: LLC Scramble2

description: Lewis Lung Carcinoma Scramble2


title: SCNn-d, S247


title: WT D15-D H3K9me3 Replicate 4


title: SCNn+a, S246


title: WT D15-D H3K9me3 Replicate 3


title: LLC Scramble1

description: Lewis Lung Carcinoma Scramble1


title: w1118_F_D30_FB_rep1


title: WT D15-D H3K9me3 Replicate 2


title: SCNn-s, S245

value: silent


title: 75Gy_6w [3143]

city: Seodaemun-gu

first: Jaeho

last: Cho

state: Seoul

address: Yonsei-ro

department: Department of Radiation Therapy

country: South Korea

institute: Yonsei University

data_processing:
not provided
Assembly: GRCm38.p6
Supplementary files format and content: raw_gene_count.txt: Tab-delimited text file includes raw counts.

source_name: lung

growth_protocol: 6-week-old mice weighing 20-25g were acclimatised for a week before irradiation.

extract_protocol:
Total RNA were isolated from collected lung tissue using RNeasy Mini Kit according to manufacturer's instructions.
Library were constructed using TruSeq Stranded mRNA LT Sample Prep Kit according to manufacturer's instructions.

treatment_protocol: Single dose of 65 or 75Gy were delivered to left lung in a single fraction using image guided small-animal irradiator.

tag: Sex

value: male

value: wild-type

value: lung

value: 75Gy radiation

tag: time point

value: collected after 6 weeks


title: 75Gy_6w [3142]


title: WT D15-D H3K9me3 Replicate 1

tag: cell type

value: H9 hESC


title: w1118_F_D5_FB_rep3

source_name: Female, D5, Fat body

value: Fat body


title: w1118_F_D5_FB_rep2


title: SCNn+d, S242

value: night

value: depolarized


title: SCNn-a, S241

value: interneurons of the suprachiasmatic nucleus

value: active


title: w1118_F_D5_FB_rep1


title: WT D15-D H3K4me3 Replicate 4

value: dorsally patterned neuronal precursors

tag: stem cell_source


title: SCNn-a, S240


title: 75Gy_6w [3141]


title: WT D15-D H3K4me3 Replicate 2

tag: passage


title: 65Gy_6w [3138]

value: 65Gy radiation


title: w1118_M_D45_WB_rep2

source_name: Male, D45, whole body

value: Whole Body


title: SCNn-s, S239

value: cFOS-


title: w1118_M_D45_WB_rep3


title: 65Gy_6w [3140]


title: w1118_F_D30_FB_rep2


title: WT D15-D H3K4me3 Replicate 1

tag: timepoint


title: WT D15-D IgG Replicate 1

tag: antibody

value: IgG


title: w1118_M_D45_WB_rep1

tag: tissue


title: SCNn-a, S238


title: WT D15-D H3K4me3 Replicate 3


title: WT D15-D H3K27me3 Replicate 4


title: con_6w [3136]

value: no radiation


title: con_6w [3137]

value: male


title: SCNn+a, S237

value: cFOS+


title: con_6w [3135]

value: wild-type

value: lung


title: SCNn-a, S236


title: WT D15-D H3K27me3 Replicate 3


title: 75Gy_2w [3134]

value: 75Gy radiation

value: collected after 2 weeks


title: WT D15-D H3K27me3 Replicate 2

value: H9 hESC


title: w1118_M_D30_WB_rep1

source_name: Male, D30, whole body


title: w1118_M_D30_WB_rep2


title: SCNn+a, S235

value: night


title: WT D15-D H3K27me3 Replicate 1


title: SCNn+s, S234

value: silent


title: 75Gy_2w [3132]


title: SCNn+d, S233

value: interneurons of the suprachiasmatic nucleus

value: depolarized


title: WT D15-D H3K27ac Replicate 4

value: dorsally patterned neuronal precursors


title: 65Gy_2w [3131]

value: 65Gy radiation


title: w1118_F_D45_WB_rep2

source_name: Female, D45, Whole body

value: Whole Body


title: WT D15-D H3K27ac Replicate 3


title: 65Gy_2w [3130]


title: w1118_F_D45_WB_rep1


title: WT D15-D H3K27ac Replicate 2


title: SCNn-a, S231

value: active

value: cFOS-


title: w1118_F_D30_WB_rep2

source_name: Female, D30, Whole body


title: 65Gy_2w [3129]


title: WT D15-D H3K27ac Replicate 1


title: SCNd-a, S206

value: day


title: w1118_F_D30_WB_rep1


title: con_2w [3128]

value: male

value: no radiation


title: w1118_M_D5_WB_rep2

source_name: Male, D5, whole body


title: 75Gy_2w [3133]

value: wild-type


title: WT D15-V IgG Replicate 3

source_name: ventrally patterned neuronal precursors

value: ventrally patterned neuronal precursors

value: IgG


title: SCNd-a, S205


title: w1118_M_D5_WB_rep1


title: con_2w [3127]

value: lung

value: collected after 2 weeks


title: WT D15-V IgG Replicate 2

value: H9 hESC


title: con_2w [3126]


title: WT D15-V IgG Replicate 1


title: SCNd+a, S202

value: cFOS+


title: SCNn+s, S232

value: interneurons of the suprachiasmatic nucleus

value: night

value: silent


title: polsFC5.8_rep2

city: Cuernavaca

first: Jose

last: Utrilla

state: Morelos

address: Av. Universidad sn

department: Centro de Ciencias Genómicas

country: Mexico

institute: Universidad Nacional Autonoma de México

data_processing:
Base-calling was performed in the Illumina by Novogene Company.
Reads were processed for adapter trimming and quality control filtering using Trim Galore (v.0.6.6).
Reads were aligned using R package Rsubread (v.2.2.6) and mapped to the reference genome (GCF_000005845.2).
Read counts were obtained using the function featureCounts from Rsubread package.
Batch correction and normalization were perfomed with ARSyseq and TMM, respectively.  respectively.
The differential expression analysis was performed using DESeq2 (v.1.28.1)
Assembly: Reference genome GCF_000005845.2
Supplementary files format and content: counts_raw.txt, text file includes table with the number of sequence reads that are mapped to a particular gene.
Supplementary files format and content: Differential_gene_expression_analysis.xlsx, Spreadsheet file includes DEGs tables for each comparison.

organism: Escherichia coli

source_name: Culture Cells

growth_protocol: E. coli K12pSEVA, and K12pOlsFC cells were pre-grown at 37°C in 25 mL of MOPS minimal medium with 4 g/L glucose overnight. The cells were washed three-time and cultured in MES/glucose medium and during exponential growth (11h)

extract_protocol:
Total RNA was prepared using the RNeasy mini kit (QIAGEN, Hildesheim, Germany)
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: mRNA of exponentially growing (11h) E. coli mutants in MOPS pH 7.4  and M9 pH 5.4 minimal medium supplemented with glucose

value: Culture Cells


title: WT D15-V H3K9me3 Replicate 3


title: polsFC5.8_rep1


title: Setd7 WT Kidney - Diabetic 374

city: Melbourne

first: Assam

last: El-Osta

address: 75 Commercial Road

country: Australia

institute: Baker Heart and Diabetes Institute

data_processing:
library strategy: DROP-seq
Drop-Seq:
The primary sequence data was generated using the Illumina bcl2fastq 1.8 pipeline.
Fastq files were processed into a count matrix using Drop-seq tools v2.1, retain top 3000 cell barcodes
RNA-Seq:
The primary sequence data was generated using the Illumina bcl2fastq 1.8 pipeline.
Low-quality bases (Q score < 10) were removed from the 3 end with Skewer 0.2.2 (Jiang et al., 2014)
Mouse genome cDNA sequences were retrieved from Ensembl version 96 (Cunningham et al., 2019). Reads were mapped to transcripts using Kallisto v0.45.0 (Bray et al., 2016). Transcript counts were aggregated to gene-level counts with the sum function in R. Genes with an average of fewer than 10 reads per sample were omitted from downstream analysis
Genome_build: GRCm38
Supplementary_files_format_and_content: RNA-seq gene level count matrix; Single Cell count matrix (gene ~ cell-barcode)

extract_protocol:
Drop-Seq. Kidney cortex was dissected and homogenized by pressing though a 100uM sieve and glomerular fraction collected using 70uM sieve. Glomerular fraction was dissociated using cold active protease (subtilisin A, Sigma). Single cell RNA was captured using the drop-seq method (Macosko 2015)
Drop-Seq. Sequencing libraries were created from barcoded cDNA (Drop-seq) using the illumina Nextera XT library prep kit (Illumina) as adapted in the Drop-Seq protcol (Macosko 2015)
RNA-Seq. Kidneys were homogenized TRIzol solution. RNA was extracted using the Directzol RNA mini-prep kit according to the manufacturer’s protocol, with DNase I treatment in the column to remove genomic DNA contamination (Zymo Research, Irvine, CA, USA). RNA was eluted in 30 μl TE buffer, and the quantity and quality of RNA examined on a MultiNA bioanalyzer (Shimadzu, Tokyo, Japan).
RNA-Seq. A NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA) was used to enrich mRNA from 1 μg of total RNA. The NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® was then used to generate barcoded libraries according to the manufacturer’s protocol, and these libraries were then quantified on the MultiNA bioanalyzer and pooled to equimolar ratios for sequencing.

tag: strain background

tag: genotype/variation

value: Apoe-/-

tag: condition

value: diabetic

value: Kidney


title: SCNd-a, S197

tag: time of_day

value: day

value: active

value: cFOS-


title: SCNd+s, S196

tag: electrophysiology


title: Setd7 WT Kidney - Diabetic 373


title: WT D15-V H3K9me3 Replicate 2


title: polsFC7.4_rep2

tag: genotype

tag: treatment


title: WT D15-V H3K9me3 Replicate 1


title: SCNd+a, S194

tag: cfos expression


title: polsFC7.4_rep1


title: WT D15-V H3K4me3 Replicate 4


title: pSEVA5.8_rep2

value: wild type


title: w1118_F_D5_WB_rep1

source_name: Female, D5, whole body

value: Whole Body


title: w1118_F_D5_WB_rep2


title: SCNd-s, S192


title: Setd7 KO Kidney - Diabetic 567

source_name: Apoe-/- Setd7 -/-_diabetic_kidney

value: Apoe-/- Setd7 -/-


title: SCNd-s, S199


title: WT D15-V H3K4me3 Replicate 3

value: ventrally patterned neuronal precursors


title: Setd7 WT Kidney - Control 370

value: control


title: pSEVA5.8_rep1


title: SCNd+a, S191


title: SCNd-a, S190


title: pSEVA7.4_rep2


title: WT D15-V H3K4me3 Replicate 1

value: H9 hESC


title: Setd7 KO Kidney - Control 562

source_name: Apoe-/- Setd7 -/-_control_kidney


title: WT D15-V H3K4me3 Replicate 2


title: Setd7 WT Kidney - Control 372


title: Setd7 KO Kidney - Control 561


title: D140-JGH-805

city: Sejong

first: Sinwoo

last: Park

address: Sejongro

institute: Korea Universiy

data_processing:
Low qaulity of reads in the raw reads were trimmed using the Trimmomatic (v0.39)
Trimmed reads were align using HISAT2 (v2.2.1)
FeatureCounts (v2.0.3) was used for the quantification of aligned reads.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.

source_name: blood

extract_protocol:
For Illumina NovaSeq 6000, total RNA was extracted using TruSeq Stranded Total RNA LT Sample Prep Kit (Globin). For MGISEQ-2000RS, total RNA was isolated from tissue using TRI-reagent based method. Total RNA (500 ng) was processed for  preparing whole transcriptome sequencing library.
For Illumina NovaSeq 6000, libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Sample Prep Guide, Part # 15031048 Rev. E, For MGISEQ-2000RS,  Enrichment of whole transcriptome RNA by depleting  ribosomal RNA (rRNA) was processed for preparing whole transcriptome sequencing library using MGIEasy RNA Directional Library Prep Kit (MGI) according to manufacturer’s instruction.

value: blood

value: M

tag: disease

value: COPD


title: NTC/T1 null cells, sgERO1α-3

city: Anhui Province

first: zixi

last: wang

address: Hefei City, Anhui Province

institute: Anhui Medical University

description:
208T-62-3
raw counts.xlsx

data_processing:
mRNA-seq reads were trimmed from 3' end until the final base had a quality score > 20, using seqtk v1.0-r82-dirty, discarding reads left with < 25 bp
Trimmed sequence reads were mapped to GrCM38/mm10 using Hisat2(version:2.0.4)
The number of Fragments of each gene after Hisat2 comparison was counted by Stringtie (version:1.3.0), and then normalized by the original mean of M Values (TMM) method. Finally, the FPKM value of each gene was calculated by Perl script.
Assembly: GRCm38.p4 (mm10)
Supplementary files format and content: Excel file includes count values and FPKMs for each Sample

source_name: NTC/T1 null

growth_protocol: NTC/T1 null cells were cultured in DMEM Medium (BOSTER, Wuhan, China) supplemented with 10% fetal bovine serum (Gibco, CA, USA) and 1% penicillin and streptomycin (Beyotime, Jiangsu, China).

extract_protocol:
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018 ， Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany)
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® following manufacturers' protocols

treatment_protocol: Using CRISPR-Cas9 to knockout ERO1α.

tag: cell line

value: NTC/T1 null

value: mouse embryonic fibroblasts

value: ERO1alpha knockout


title: SCNn+a, S181

source_name: interneurons of the suprachiasmatic nucleus

value: night

value: cFOS+


title: Setd7 KO Kidney - Diabetic 562

value: diabetic

value: Kidney


title: SCNn-s, S185

value: interneurons of the suprachiasmatic nucleus

value: silent

value: cFOS-


title: NTC/T1 null cells, sgERO1α-2

description:
208T-62-2
raw counts.xlsx


title: D139-YSH-356

tag: Sex

value: F


title: SCNn-a, S177

tag: cell type

value: active


title: NTC/T1 null cells, sgERO1α-1

description:
208T-62-1
raw counts.xlsx


title: D138-MJI-951


title: NTC/T1 null cells, sgCtrl-3

description:
208T-C1-3
raw counts.xlsx

value: WT


title: WT D15-V H3K27ac Replicate 3

value: ventrally patterned neuronal precursors

tag: stem cell_source

value: H9 hESC


title: SCNn-a, S176


title: D137-PHJ-451

value: blood

value: M


title: SCNn+a, S175


title: WT D15-V H3K27ac Replicate 1

tag: passage


title: WT D15-V H3K27ac Replicate 2

tag: timepoint


title: D136-HIP-572

value: COPD


title: NTC/T1 null cells, sgCtrl-2

description:
208T-C1-2
raw counts.xlsx

value: NTC/T1 null

value: mouse embryonic fibroblasts


title: pSEVA7.4_rep1

value: Culture Cells

value: wild type


title: SCNn+a, S172

value: night

value: cFOS+


title: D135-PYC-633


title: NTC/T1 null cells, sgCtrl-1

description:
208T-C1-1
raw counts.xlsx


title: SCNn-s, S189

value: interneurons of the suprachiasmatic nucleus


title: D133-CJH-153


title: H9 WT D0 IgG Replicate 3

source_name: embryonic stem cells

value: embryonic stem cells

tag: antibody

value: IgG


title: SCNn+a, S163


title: SCNn-s, S169

value: silent

value: cFOS-


title: NS_11_rep1

city: Moscow

first: Alexander

last: Modestov

address: 8-2 Trubetskaya str.

country: Russia

institute: I.M. Sechenov First Moscow State Medical University

data_processing:
RNA sequencing FASTQ files were processed with STAR aligner in ‘GeneCounts’ mode with the Ensembl human transcriptome annotation (Build version GRCh38 and transcript annotation GRCh38.89).
Assembly: hg38
Supplementary files format and content: comma-delimited file includes raw counts for each sample

source_name: Brain

extract_protocol:
Solid tissue samples were either immediately stabilized in RNAlater (Qiagen, Germany) and then stored at −70 °C or fixed in formalin and embedded in paraffin blocks. RNA extraction was performed immediately before the preparation of sequencing libraries using QIAGEN RNeasy Kit (Qiagen) or Direct-zol™ RNA MiniPrep (Zymo Research) with TRI Reagent (MRC) for tissues in RNAlater and the RecoverAll™ RNeasy FFPE Kit (Qiagen), following the manufacturer’s protocol.
RNA Integrity Number (RIN) was measured using Agilent 2100 bioanalyzer. Agilent RNA 6000 Nano or Qubit RNA Assay Kits were used to measure RNA concentration. KAPA RNA Hyper with RiboErase (KAPA Biosystem) Kit was used for further depletion of ribosomal RNA and library preparation. Different adaptors were used for multiplexing samples in one sequencing run. Library concentrations and quality were measured using Qubit ds DNA HS Assay kit (Life Technologies) and Agilent Tapestation (Agilent).

tag: tissue

value: Brain

value: Glioblastoma

tag: age

value: Temozolomide


title: NS_7

value: F


title: NS_11_rep2

value: M


title: SCNn+a, S162

value: active


title: SCNn-a, S166


title: D132-HYJ-841

value: blood

value: COPD


title: H9 WT D0 IgG Replicate 2

value: H9 hESC


title: D130-LSR-896


title: H9 WT D0 IgG Replicate 1


title: H9 WT D0 H3K9me3 Replicate 1


title: NS_4


title: H9 WT D0 H3K9me3 Replicate 3


title: SCNn-a, S157


title: D131-KDH-684


title: H9 WT D0 H3K9me3 Replicate 2


title: D128-CDR-935


title: SCNd+a, S149

value: day


title: SCNd+a, S144


title: D127-KJM-754


title: D129-SEJ-617


title: SCNn+s, S136

value: night


title: H9 WT D0 H3K4me3 Replicate 5


title: SCNn+a, S132

value: cFOS+


title: D124-KJO-020


title: SCNn+s, S130

value: interneurons of the suprachiasmatic nucleus


title: D122-KCH-393


title: H9 WT D0 H3K4me3 Replicate 2

value: embryonic stem cells


title: SCNn-s, S128


title: D123-SMH-524


title: SCNn-a, S126


title: H9 WT D0 H3K4me3 Replicate 1


title: D121-KNJ-947


title: SCNn+s, S123


title: H9 WT D0 H3K27me3 Replicate 5


title: D120-JYB-981


title: H9 WT D0 H3K4me3 Replicate 6


title: D118-YYW-502


title: SCNd+s, S97


title: D126-LGB-767


title: SCNn+s, S122


title: H9 WT D0 H3K27me3 Replicate 4


title: D119-CTY-971


title: SCNd+a, S96


title: D117-LCG-858


title: H9 WT D0 H3K4me3 Replicate 4


title: H9 WT D0 H3K27me3 Replicate 2


title: H9 WT D0 H3K27me3 Replicate 1


title: SCNd+a, S95


title: D116-AHR-518


title: H9 WT D0 H3K27ac Replicate 5


title: SCNd-a, S94


title: D115-LJS-367


title: H9 WT D0 H3K4me3 Replicate 3


title: D114-PMH-948


title: SCNd-s, S93


title: H9 WT D0 H3K27ac Replicate 4


title: SCNd+a, S92


title: H9 WT D0 H3K27ac Replicate 2


title: SCNd+a, S90


title: H9 WT D0 H3K27ac Replicate 3


title: D113-KJW-109


title: D112-KHR-807


title: H9 WT D0 H3K27me3 Replicate 3


title: SCNd-s, S87


title: D111-CST-893


title: H9 WT D0 H3K27ac Replicate 1


title: D110-JDY-686


title: SCNd-s, S81


title: H9 WT D60 RNAseq Replicate 3

data_processing:
Raw reads for RNAseq samples were quality trimmed using cutadapt (v3.4) and aligned using STAR (v2.5.4b).
Aligned reads were quantified using featureCounts (v1.4.6-p4) from the subreads package.
Assembly: hg38
Supplementary files format and content: tab-deliminated text file containing raw counts for each sample

source_name: matrued cortical interneurons

extract_protocol:
RNA was extracted using the NucleoSpin® RNA kit (Takara Bio)
RNA-seq library preparation was performed using the KAPA RNA HyperPrep Kit with RiboErase (Roche) per the manufacturer’s instructions.

value: matrued cortical interneurons


title: D109-CJY-794


title: SCNn-a, S72


title: H9 WT D60 RNAseq Replicate 1


title: H9 WT D35 RNAseq Replicate 4

source_name: immature cortical interneurons

value: immature cortical interneurons


title: SCNn+s, S71

value: silent


title: H9 WT D60 RNAseq Replicate 2


title: H9 WT D35 RNAseq Replicate 3


title: D108-LJH-189


title: SCNd+s, S68


title: D106-LSI-299


title: D107-PDW-845


title: SCNn-s, S70

value: cFOS-


title: D105-KGP-644


title: SCNd+a, S62


title: SCNd-s, S66


title: D100-KBG-949


title: sample_6138

city: Columbus

first: Alessandro

last: La Ferlita

state: OH

department: The James Comprehensive Cancer Center

institute: The Ohio State University

data_processing:
Raw sequencing reads in FASTQ format were quality trimmed, and adapters were removed using Trim Galore (v.0.6.6).
Trimmed reads were then mapped to the human genome (HG38 assembly) using Bowtie2 (v. 2.4.5), allowing up to 100 alignments per read (-k 100).
Afterward, the mapped reads in SAM format were converted into BAM format, sorted (for coordinates), and indexed using Samtools (v. 1.6).
Finally, HERV quantification was performed using Telescope (v. 1.0.3) with its GTF annotation file.
Assembly: HG38
Supplementary files format and content: tab-delimited text file reporting telescope output of HERVs for each sample

source_name: normal

extract_protocol:
RNA was extracted using TRIzol reagent (Thermo Fisher) following the standard protocol.
Samples with acceptable RNA quality (RIN > 7; assessed with Agilent 6000 RNA Nano chip) and quantity (200ng or more; assessed with Invitrogen Qubit High Sensitivity RNA assay) were used in library preparation. NEBNext® Ultra™ II Directional (stranded) RNA Library Prep Kit for Illumina (NEB #E7760L) was used as the core kit and coding genes were enriched using the NEBNext Poly (A) mRNA Magnetic Isolation Module (NEB #E7490). RNA fragmentation time: 10 min. PCR cycles: 12. NEBNext Multiplex Oligos for Illumina Unique Dual Index Primer Pairs (NEB #6446/L) were used to index each sample for multiplexing purposes. Final libraries were quantified using Qubit High Sensitivity DNA assay and pooled to yield ~20 million clusters/sample. mRNA-seq libraries were sequenced using Illumina NovaSeq 6000 flow cell with Paired-End 100 bp format to ~20 million clusters/sample.

value: B-cells

value: CTRL


title: sample_6140


title: D104-DMH-870


title: SCNd-s, S58


title: D099-KCB-644


title: D098-HHJ-528

value: F


title: sample_6131


title: H9 WT D35 RNAseq Replicate 2


title: sample_2353

source_name: indolent; VH: 96%; NK


title: sample_2355

source_name: aggressive, VH: 100%; NK


title: SCNn-a, S36


title: D097-LIY-038

value: M


title: H9 WT D35 RNAseq Replicate 1


title: SCNn-s, S29


title: D096-PYJ-011


title: sample_2351


title: SCNd+a, S65

value: active


title: SCNn+a, S33


title: SCNd+a, S64


title: sample_2349


title: SCNn+s, S28


title: sample_2347


title: D095-YCY-061

value: blood


title: D094-KIC-319

value: COPD


title: D101-NDS-236


title: SCNn+s, S26


title: D091-KJJ-282


title: sample_2341

source_name: aggressive, VH: 100%; T12


title: sample_6136


title: SCNn-s, S24


title: SCNn-a, S38


title: D092-OKH-451


title: sample_2337


title: D090-JKH-065


title: SCNn+a, S23


title: sample_2317

source_name: indolent; VH: 94%; 13q del


title: D089-KSH-546


title: SCNn-a, S16


title: D088-ASS-751


title: sample_2241

source_name: indolent; VH: 92.3%; NK


title: SCNn-s, S15


title: sample_2240

source_name: indolent; VH: 91.7%; NK


title: D087-NTH-248


title: sample_2234

source_name: indolent; VH: 93%; NK


title: D086-SCH-342


title: D084-SKH-788


title: sample_2221


title: SCNn+s, S27


title: sample_2219

source_name: indolent; VH: 92.2%; T12


title: scRNA-seq_LLC JAG2KO2

description: Lewis Lung Carcinoma Jagged2KO2

data_processing:
10x
Seurat
Assembly: GRCm38/mm10
Supplementary files format and content: txt file

source_name: Tumor

extract_protocol:
10x
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: Tumor

value: Lewis Lung Carcinoma

value: Lung


title: scRNA-seq_LLC Scramble3

description: Lewis Lung Carcinoma Scramble3

value: Scramble


title: D083-PPS-522

source_name: blood


title: scRNA-seq_LLC JAG2KO1

description: Lewis Lung Carcinoma Jagged2KO1


title: scRNA-seq_LLC Scramble2

description: Lewis Lung Carcinoma Scramble2


title: sample_2218

source_name: indolent; VH: 91.8%; T12


title: SC2_C, RCAS-GFP-SOCS2 uninjected

city: Shenyang

first: Xiaoping

last: Li

address: 120 Dongling Rd.

institute: Shenyang Agricultural University

data_processing:
Reads from mRNA-seq data were aligned to Ensembl chicken genome (GRCg6a.release96) using HISAT2 version 2.2.1.
Transcript assembly by StringTie v2.1.7
Use prepDE.py3 script of StringTie to get raw counts and TPM counts
Assembly: GRCg6a.release96
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 TPM values for each Sample

organism: Gallus gallus

source_name: forelimb bud

growth_protocol: A chicken with overexpressed SOCS2 was selected to perform mRNA-Seq.

extract_protocol:
Total RNA was extracted using the RNeasy micro kit (Qiagen, Hilden, Germany), with on-column DNase to remove contaminating genomic DNA. RNA concentration and purity were measured using NanoDrop 2000. (Thermo Fisher Scientific, Wilmington, DE). RNA integrity was assessed using the RNA Nano 6000 Assay Kit from the Agilent Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.

treatment_protocol: RNA was extracted separately from the injected right wing and uninjected (control) left wing of the same individual 5 days after infection (HH 34)

value: forelimb bud

value: uninjected


title: SC2_R, RCAS-GFP-SOCS2 injected

value: injected


title: D081-KWB-134


title: sample_2192

source_name: aggressive, VH: 100%; T12 and13q del


title: scRNA-seq_LLC Scramble1

description: Lewis Lung Carcinoma Scramble1


title: Hi-C: scc-1 coh-1 TEV replicate 2

city: Bern

first: Peter

last: Meister

state: Schweiz

address: Baltzerstrasse 4

department: Institute of Cell Biology

institute: University of Bern

description: NovaSeq 6000 iSeq 100

data_processing:
Data was processed with HiC-Pro using min_mapq=10 and ligation_site = GATCGATC,GANTGATC,GANTANTC,GATCANTC and bin_size=2000
HiCPro matrix was converted to cooler format with the HiCPro conversion tool
Supplementary files format and content: Processed data file (.cool) are contact frequency matrices at 2 kb resolution, in cooler format.

organism: Caenorhabditis elegans

source_name: Whole animals

growth_protocol: Gravid adults were bleached and eggs were left to hatch overnight at room temperature with agitation. L1 animals were then put to grow for 3 hours on OP50. Plates were heat-shocked at 34°C for 30 minutes in a waterbath, and grown for an additional 19 hours before recovering the animals in M9 buffer. Recovered animals were washed 3 times in M9 before snap-freezing in liquid nitrogen.

extract_protocol: Libraries were constructed according to the supplier's recommendations (Arima HiC kit)

treatment_protocol: L1 sync. animals were grown 3 hours at 22°C, then heat-shocked for 30 min at 34°C before additional 19 hours of growth

value: Whole animals

tag: strain

value: coh-1(ubs26[TEVcs]) X scc-1(ubs19[TEVcs]) II ubsSi20[hsp-16.2p::TEV Cb unc-119+ @ ttTi5605] II


title: sample_2176

source_name: aggressive, VH: 100%; 11q del


title: D080-KYH-237


title: Hi-C: scc-1 coh-1 TEV replicate 1

description: NovaSeq 6000 iSeq 100


title: D079-YJC-840


title: sample_2168


title: Hi-C: sdc-3AID auxin replicate 2

data_processing:
HiC-Pro pipeline (Servant et al. 2015), version 3.0.0.
Hicpro matrices were converted to cool format using the hicpro2higlass.sh utility from hicpro.
Assembly: ce11
Supplementary files format and content: Cool files with a bin size of 2000bp.

source_name: L3 animals

extract_protocol:
Hi-C was done as in Jimenez et al. 2021, with minor modifications. In short, the frozen worm pellet was resuspended in 2% formaldehyde prepared in M9 buffer and incubated for 30 mins in the rotator. Formaldehyde was quenched with glycine at 125 mM (final) and incubated for 5 mins. The worms were pelleted, washed with M9 and about 100 ul of the packed animals were transferred to 1.5 ml microcentrifuge tubes. Each tube with the worms were washed with 1 ml 1x PBS and protease inhibitors, washed again with 1 ml 1x PBS, snap frozen in liquid nitrogen and stored at -80°C. Cross-linked frozen worms were ground using a SPEX 6775 freezer/mill at 5 cycles per second for 1 minute with a total of 2 cycles. The ground worm powder was dissolved in 5 ml 1x PBS and immediately cross-linked with 500 μl TC buffer (100 mM NaCl, 1mM EDTA, 0.5 mM EGTA, 50 mM Hepes pH 8.0, 22% formaldehyde), to a final concentration of 2% formaldehyde for 20 minutes at room temperature. Cross-linking was stopped by addition of 289 ul of Stop Solution 1 (provided in the Arima Hi-C kit) and 5 minutes incubation at RT. Samples were pelleted at 2000g for 15 mins at RT and resuspended in 5 ml 1x PBS before 10 aliquots were distributed into 1.5 ml microcentrifuge tubes. The amount of DNA acquired from a single aliquot was estimated and accordingly the subsequent Hi-C experiment was done as per the manufacturer’s instructions.
Modified protocol from Arima Genomics for the KAPA Hyper Prep Kit was used.

treatment_protocol: Synchronised L1 animals are seeded on NGM plates, incubated for 3 hours at 22℃, heat-shocked for 30 mins at 34℃. Then they are incubated again for 19 hours at 22℃. The degron strain was seeded on 1mM auxin plates and heat-shocked as described earlier. All animals were collected by washing thrice with M9 buffer, pelleted and stored at -80°C.

value: whole body

value: Exposure to 1mM auxin, heat-shock for 30 min at 34C

value: L3 larvae

value: ubsSi20[hsp-16.2p::TEV::unc-54 3'UTR; Cbr-unc-119(+)] II; xeSi376[eft-3p::TIR1::mRuby::unc-54 3'UTR, cbr-unc-119(+)] III; sdc-3(ubs20[N-term AID]) V.


title: sample_2157

source_name: indolent; VH: 90.6%; 13q del

value: B-cells


title: sample_2233

source_name: indolent; VH: 91%; NK


title: ATAC-seq in fish 16 hpf rhombomeres replicate 1

city: Geneva

first: Aurelie

last: Hintermann

address: 30 quai Ernest-Ansermet

department: Genetics and Evolution

institute: University of Geneva

data_processing:
All scripts necessary to reproduce the analyses are available at https://github.com/AurelieHintermann/HintermannBoltEtAl2024.
Raw ATAC-seq paired-end reads were processed with CutAdapt version 4.1 (-a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA -q 30 -m 15) to remove Nextera adapters and bad quality bases.
Filtered reads were mapped on mm39 for mouse samples and danRer11 where alternative contigs were removed for fish samples with bowtie2 version 2.4.5 with the following parameters: --very-sensitive --no-unal --no-mixed --no-discordant --dovetail -X 1000. Only pairs mapping concordantly outside of mitochondria were kept (Samtools v1.16.1)
PCR duplicates were removed by Picard version 3.0.0 (http://broadinstitute.github.io/picard/index.html). BAM files were converted to BED with bedtools version 2.30.0. Peaks were called and coverage was generated by MACS2 version 2.2.7.1 with --nomodel --keep-dup all --shift -100 --extsize 200 --call-summits -B. Coverages were normalized to million mapped reads.
Assembly: mm39
Assembly: danRer11
Supplementary files format and content: *narrowPeak.gz: peaks from MACS2
Supplementary files format and content: *bw: coverage from MACS2 normalized to million mapped reads

organism: Danio rerio

source_name: rhombomeres

extract_protocol:
Mouse and fish tissues were isolated and placed into 1x PBS containing 10% FCS on ice. Collagenase (Sigma-Aldrich C9697) was added to 50ug/ml and incubated at 37º for 20 minutes with shaking at 900rpm.
Cells were washed 3x in 1x PBS. The number of cells was counted and viability confirmed to be greater than 90%. An input of 50000 cells was then processed according to previous description.

value: rhombomeres

tag: Stage

value: 16 hpf

value: wild type

value: AB, Tu, TL


title: Hi-C: sdc-3AID auxin replicate 1


title: sample_2153

source_name: indolent; VH: 93.3%; 13q del


title: Hi-C: coh-1cs TEV replicate 2

value: Heat-shock for 30 min at 34C

value: ubsSi20[hsp-16.2p::TEV::unc-54 3'UTR; Cbr-unc-119(+)] II; coh-1(ubs26[FLAG-TEVcs]) X.


title: ATAC-seq in fish 16 hpf anterior trunk replicate 1

source_name: anterior trunk

value: anterior trunk


title: D076-HKS-423

value: blood

value: M

value: COPD


title: AsiSI-ER 4OHT HDAC1 replicate 3

city: Oxford

first: Kamal

last: Ajit

address: South Parks Road

country: United Kingdom

institute: Sir William Dunn School of Pathology

data_processing:
Reads were trimmed using Cutadapt
The trimmed reads were then mapped to hg19 genome following the standard ChIP seq-pipeline.
The classic ChIP-seq pipeline consists of BWA (http://bio-bwa.sourceforge.net/) for alignment and samtools (http://www.htslib.org/) for duplicate removal (rmdup), sorting (sort) and indexing (index)
Coverage was computed using Deeptools BamCoverage and the data was exported in BigWig format (.bw)
Assembly: hg19

growth_protocol: DMEM, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Diagenode Bioruptor.
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: 4hr 400nm 4OHT or equivalent DMSO

value: osteosarcoma

tag: chip antibody


title: Hi-C: coh-1cs TEV replicate 1


title: ATAC-seq in fish 16 hpf posterior trunk replicate 1

source_name: posterior trunk

value: posterior trunk


title: ATAC-seq in fish 30 hpf head replicate 1

source_name: head

value: head

value: 30 hpf


title: AsiSI-ER 4OHT GATAD2B replicate 3


title: D075-KTM-382


title: D082-JTC-859


title: AsiSI-ER 4OHT input replicate 3


title: Hi-C: scc-1cs TEV replicate 2

value: whole body

value: L3 larvae

value: scc-1(ubs19[FLAG-TEVcs]), ubsSi20[hsp-16.2p::TEV::unc-54 3'UTR Cbr-unc-119(+)] II.


title: ATAC-seq in fish 16 hpf head replicate 1


title: D073-SCH-274


title: AsiSI-ER DMSO HDAC1 replicate 3

value: DMSO


title: Hi-C: scc-1cs TEV replicate 1


title: Hi-C: kle-2cs TEV replicate 2

value: ubsSi20[hsp-16.2p::TEV::unc-54 3'UTR; Cbr-unc-119(+)] II; kle-2(ubs14[FLAG-TEVcs]) III.


title: D072-LYJ-764


title: D078-JGH-279


title: HCT116_PCHiC_Nut1h-Rad21_BR2

city: Badalona

first: Biola

middle: M

last: Javierre

state: Barcelona

address: Ctra de Can Ruti, Camí de les Escoles , s/n

country: Spain

institute: Josep Carreras Leukaemia Research Institute

data_processing:
Hi-C: Various steps were taken to process the Hi-C data, including read quality control, mapping, interaction detection, filtering, and matrix normalization using the TADbit pipeline
PCHiC: Raw reads were processed using HiCUP with default parameters Captured reads were selected using hicup_capture function Interactions were called using CHiCAGO R package with default parameters Significant interactions were selected with a CHiCAGO score <= 5
Assembly: hg19
Supplementary files format and content: Hi-C: matrices .abc.gz
Supplementary files format and content: PCHiC: Ibed
Library strategy: PCHiC

extract_protocol:
Hi-C: Cells were fixed in DMEM medium supplemented with 10% FBS and 2% methanol-free formaldehyde for 10 minutes rotating at room temperature. After quenching the formaldehyde with 0.125M glycine and washing the cells with 1X PBS, nuclei were extracted by lysing the cells in 10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% IGEPAL CA630 (SIGMA-ALDRICH #18896-50ML), 1× cOmplete EDTA-free protease inhibitor cocktail. Chromatin was digested overnight with HindIII enzyme and the cohesive restriction fragment ends were filled-in with dCTT, dTTP, dGTP and biotin-14-dATP(Invitrogen #19524-016) nucleotides. After blunt-end ligating the restriction fragment ends, the chromatin was decrosslinked by incubating overnight with proteinase K and purified by phenol:chloroform:isoamyl alcohol 25:24:1 (SIGMA-ALDRICH #P3803-100ML) extraction.Non-informative biotin at restriction fragment ends was removed by incubating the samples with dATP and T4 DNA polymerase (New England Biolabs#M0203S). After purifying the DNA again with a phenol:chloroform:isoamyl alcohol extraction, 10µg of the chromatin was sheared using a Covaris M220 focused ultrasonicator in 130µl cuvettes using the following parameters: 20% duty factor, 50 peak incident power, 200 cycles per burst, 65 seconds. The ends were end-repaired and dATP-tailed, followed by a biotin-pulldown using Dynabeads MyOne streptavidin C1 paramagnetic beads (Thermo Fisher #65001) to enrich for those DNA fragments which contain information of a chromatin loop. PE Illumina adapters(Supplementary Data 9) were ligated to the sample and the library was amplified for 8 cycles. Finally, the library was purified using a SPRI bead double-sided selection (0.4-1 volumes). Size and concentration of the finished Hi-C libraries was assessed by DNA ScreenTape Analysis (Agilent #5067-5582) on an Agilent 2200 Tapestation.
PCHiC: Cells were fixed in DMEM medium supplemented with 10% FBS and 2% methanol-free formaldehyde for 10 minutes rotating at room temperature. After quenching the formaldehyde with 0.125M glycine and washing the cells with 1X PBS, nuclei were extracted by lysing the cells in 10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% IGEPAL CA630 (SIGMA-ALDRICH #18896-50ML), 1× cOmplete EDTA-free protease inhibitor cocktail. Chromatin was digested overnight with HindIII enzyme and the cohesive restriction fragment ends were filled-in with dCTT, dTTP, dGTP and biotin-14-dATP(Invitrogen #19524-016) nucleotides. After blunt-end ligating the restriction fragment ends, the chromatin was decrosslinked by incubating overnight with proteinase K and purified by phenol:chloroform:isoamyl alcohol 25:24:1 (SIGMA-ALDRICH #P3803-100ML) extraction.Non-informative biotin at restriction fragment ends was removed by incubating the samples with dATP and T4 DNA polymerase (New England Biolabs#M0203S). After purifying the DNA again with a phenol:chloroform:isoamyl alcohol extraction, 10µg of the chromatin was sheared using a Covaris M220 focused ultrasonicator in 130µl cuvettes using the following parameters: 20% duty factor, 50 peak incident power, 200 cycles per burst, 65 seconds. The ends were end-repaired and dATP-tailed, followed by a biotin-pulldown using Dynabeads MyOne streptavidin C1 paramagnetic beads (Thermo Fisher #65001) to enrich for those DNA fragments which contain information of a chromatin loop. PE Illumina adapters(Supplementary Data 9) were ligated to the sample and the library was amplified for 8 cycles. Finally, the library was purified using a SPRI bead double-sided selection (0.4-1 volumes). Size and concentration of the finished Hi-C libraries was assessed by DNA ScreenTape Analysis (Agilent #5067-5582) on an Agilent 2200 Tapestation.
PCHi-C: libraries, 500-1000ng of Hi-C library were captured using the SureSelectXT Target Enrichment System for the Illumina Platform (Agilent Technologies) as instructed by the manufacturer. Captured library was amplified a total of 4 cycles, and the size and concentration of the finished PCHi-C libraries was assessed by high-sensitivity DNA ScreenTape Analysis (Agilent #5067-5584) on an Agilent 2200 Tapestation.

value: Nutlin3a 1h + degron Rad21 KD 6h


title: AsiSI-ER DMSO GATAD2B replicate 3


title: HCT116_PCHiC_Nut1h-Rad21_BR1


title: D077-JGM-054


title: D071-LJW-870


title: Hi-C: kle-2cs TEV replicate 1


title: AsiSI-ER DMSO input replicate 3


title: HCT116_HiC_washout_BR2

data_processing:
Hi-C: Various steps were taken to process the Hi-C data, including read quality control, mapping, interaction detection, filtering, and matrix normalization using the TADbit pipeline
PCHiC: Raw reads were processed using HiCUP with default parameters Captured reads were selected using hicup_capture function Interactions were called using CHiCAGO R package with default parameters Significant interactions were selected with a CHiCAGO score <= 5
Assembly: hg19
Supplementary files format and content: Hi-C: matrices .abc.gz
Supplementary files format and content: PCHiC: Ibed

value: Nutlin3a 24h + washout


title: Hi-C: dpy-26cs TEV replicate 2

value: Heat-shock for 30 min at 34C

value: ubsSi20[hsp-16.2p::TEV::unc-54 3'UTR; Cbr-unc-119(+)] II; dpy-26(ubs4[FLAG-TEVcs]) IV.


title: D070-LJW-621


title: AsiSI-ER 4OHT HDAC1 replicate 2


title: Hi-C: dpy-26cs TEV replicate 1


title: HCT116_HiC_washout_BR1


title: D069-KKM-715


title: D074-SJH-810


title: D068-PHD-970


title: HCT116_PCHiC_Nut10h_BR2

data_processing:
Raw reads were processed using HiCUP with default parameters
Captured reads were selected using hicup_capture function
Interactions were called using CHiCAGO R package with default parameters
Significant interactions were selected with a CHiCAGO score <= 5
Assembly: hg19
Supplementary files format and content: ibed
Library strategy: PCHi-C

extract_protocol:
Cells were fixed in DMEM medium supplemented with 10% FBS and 2% methanol-free formaldehyde for 10 minutes rotating at room temperature. After quenching the formaldehyde with 0.125M glycine and washing the cells with 1X PBS, nuclei were extracted by lysing the cells in 10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% IGEPAL CA630 (SIGMA-ALDRICH #18896-50ML), 1× cOmplete EDTA-free protease inhibitor cocktail. Chromatin was digested overnight with HindIII enzyme and the cohesive restriction fragment ends were filled-in with dCTT, dTTP, dGTP and biotin-14-dATP(Invitrogen #19524-016) nucleotides. After blunt-end ligating the restriction fragment ends, the chromatin was decrosslinked by incubating overnight with proteinase K and purified by phenol:chloroform:isoamyl alcohol 25:24:1 (SIGMA-ALDRICH #P3803-100ML) extraction.Non-informative biotin at restriction fragment ends was removed by incubating the samples with dATP and T4 DNA polymerase (New England Biolabs#M0203S). After purifying the DNA again with a phenol:chloroform:isoamyl alcohol extraction, 10µg of the chromatin was sheared using a Covaris M220 focused ultrasonicator in 130µl cuvettes using the following parameters: 20% duty factor, 50 peak incident power, 200 cycles per burst, 65 seconds. The ends were end-repaired and dATP-tailed, followed by a biotin-pulldown using Dynabeads MyOne streptavidin C1 paramagnetic beads (Thermo Fisher #65001) to enrich for those DNA fragments which contain information of a chromatin loop. PE Illumina adapters(Supplementary Data 9) were ligated to the sample and the library was amplified for 8 cycles. Finally, the library was purified using a SPRI bead double-sided selection (0.4-1 volumes). Size and concentration of the finished Hi-C libraries was assessed by DNA ScreenTape Analysis (Agilent #5067-5582) on an Agilent 2200 Tapestation.
For PCHi-C libraries, 500-1000ng of Hi-C library were captured using the SureSelectXT Target Enrichment System for the Illumina Platform (Agilent Technologies) as instructed by the manufacturer. Captured library was amplified a total of 4 cycles, and the size and concentration of the finished PCHi-C libraries was assessed by high-sensitivity DNA ScreenTape Analysis (Agilent #5067-5584) on an Agilent 2200 Tapestation.

value: Nutlin3a 10h


title: Hi-C: TEV control replicate 2


title: AsiSI-ER 4OHT input replicate 2


title: HCT116_PCHiC_Nut10h_BR1


title: Hi-C: TEV control replicate 1


title: CNA-050

value: blood


title: HCT116_PCHiC_Nut1h_BR2

value: Nutlin3a 1h


title: AsiSI-ER DMSO HDAC1 replicate 2


title: CNA-049

value: M

value: COPD


title: AsiSI-ER 4OHT GATAD2B replicate 2

value: osteosarcoma


title: Hi-C: wild-type replicate 2

value: untreated

value: wildtype


title: HCT116_PCHiC_Nut1h_BR1


title: CNA-048


title: Ribozero total RNA seq: scc-1cs TEV

data_processing:
Reads were trimmed with Cutadapt v2.5 to remove adaptors.
Bigwigs were obtained by aligning trimmed reads to the WS275 C. elegans genome using STAR v2.7.9a with the options --outSAMmultNmax 1 --alignIntronMax 5000 --quantMode GeneCounts --outSAMtype BAM SortedByCoordinate --outMultimapperOrder Random --outWigType wiggle --outWigStrand Stranded --outWigNorm RPM. Wig files were converted to bigwigs with the wigToBigWig v2.8 from UCSCtools. After visual inspection, bigWigs of technical replicates were averaged using Ensemble WiggleTools mean command for each strand separately. The bigwigs of the two strands were then summed using the Ensembl tool bigWigMerge v2.
Assembly: WS275
Supplementary files format and content: The bigwig files contain the pileup of reads from both strands in RPM, averaged over different sequencing lanes.

extract_protocol:
RNA was extracted using Trizol, treated with DNase and cleaned using RNeasy MinElute Cleanup Kit.
To enrich for non-coding RNAs, total RNA was sequenced after depletion of ribosomal RNA with the Illumina Ribo-Zero kit.

treatment_protocol: Synchronised L1 animals are seeded on NGM plates, incubated for 3 hours at 22℃, heat-shocked for 30 mins at 34℃. Then they are incubated again for 19 hours at 22℃. All animals were collected by washing thrice with M9 buffer.

value: whole body


title: AsiSI-ER DMSO input replicate 2


title: AsiSI-ER 4OHT HDAC1 replicate 1


title: Ribozero total RNA seq: kle-2cs TEV

value: L3 larvae


title: CNA-047


title: HCT116_PCHiC_Nut0h_BR1


title: CNA-046


title: Ribozero total RNA seq: dpy-26cs TEV


title: Ribozero total RNA seq: TEV control


title: AsiSI-ER DMSO GATAD2B replicate 2


title: AsiSI-ER DMSO GATAD2B replicate 1


title: CNA-045


title: HCT116_RAD21_input_Nut1h_BR2

data_processing:
ENCODE standards were followed to process paired-end reads.
Sequencing adapters were trimmed using Trim Galore! (0.6.6).
Reads were then mapped to the reference genome (GRCh37.p13) using bowtie2 (2.3.2)88 in the --very-sensitive mode. Low-quality reads, reads overlapping the ENCODE blacklist, and duplicate reads were filtered out using samtools
Genome-wide coverage was computed using the function bamCoverage from deepTools (3.2.1)  to obtain bigwig files for visualization purposes. Macs2 (2.2.7.1) was used for peak calling in the narrow mode for H3K27ac and broad mode for H3K4me1, using an input sample as control, with default parameters. The signal of this set of regions was then quantified for each sample by counting the number of reads falling into each region using the function regionCounts from R package csaw (1.30.1)
Consensus peaks were computed for each condition using Macs2 with all replicates and their respective input samples as control, setting the parameter --scale-to small.For quantification, a set of non-redundant enriched regions were defined by taking the union of peaks from all datasets. The signal of this set of regions was then quantified for each sample by counting the number of reads falling into each region using the function regionCounts from R package csaw (1.30.1)
Normalization and differential analysis were performed using R package DESeq2 (1.36.0) Library size factors for normalization were calculated based on the background signal. This background signal was quantified per sample, excluding the set of previously defined non-redundant enriched regions. Specifically, this signal was quantified on fragment counts over genomic bins of 10kb using the function windowCounts from R package csaw
Library statistics were assessed using FastQC and MultiQC
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak, broadPeak (except for Input sample)

extract_protocol:
Cells were crosslinked in 1X PBS supplemented with 1% methanol-free formaldehyde (Thermo Fisher #28908) for 10 minutes rotating at room temperature. After quenching the formaldehyde with 0.125M glycine for 5 minutes rotating at room temperature. After washing the cells with 1X PBS, pelleted cells were lysed in 1% SDS (AppliChem #A0676,0250), 10mM EDTA (Invitrogen #AM9260G), 50mM Tris-Cl pH 8'1 (Invitrogen #AM9855G) at 4ºC for 20 minutes. Samples were sonicated using a Covaris M220 focused ultrasonicator at a concentration of 20·106 cells/ml using the following parameters: 10% duty factor, 75 peak incident power, 200 cycles per burst, 15 minutes. After centrifuging the samples at 14000rpm to remove cell debris and recovering the chromatin-containing supernatant, 33µl of sonicated chromatin were prepared for immunoprecipitation by adding 267µl of buffer containing 1% Triton (AppliChem #A4975,0100), 1'2mM EDTA, 16'7mM Tris pH 8, 167mM NaCl (Invitrogen #AM9760G), 1X cOmplete protease inhibitor cocktail (Merck cat. #11873580001) and the appropriate amount of antibody (1ug ofα-H3K27ac and 0.5ug ofα-H3K4me1; Diagenode #C15410196and#C15410194respectively). Samples were incubated rotating at 4ºC overnight. Chromatin was immunoprecipitated by adding 10µl of both protein A and protein G-conjugated paramagnetic beads (Invitrogen #1001D and #1003D, respectively) and incubated at 4ºC for 1h. After washing the beads, chromatin was decrosslinked overnight at 65ºC using proteinase K (ThermoFisher Scientific #EO0491)and purified using 1.1 volumes of SPRI beads according to the manufacturer’s instructions (CleanNA #CNGS-0050). For ChIP inputs, an equivalent amount of sonicated chromatin was directly decrosslinked and purified as before.
ChIP-seq libraries were performed using the KAPA HyperPrep Kit (Roche #07962363001) according to the manufacturer’s instructions using Truseq Illumina adapters and PCR primers describedinSupplementary Data 9. Samples were sequenced to reach a minimum number of either 20M or 45M valid paired-read for H3K27ac and H3K4me1 histone marks respectively.

value: input


title: HCT116_RAD21_input_Nut1h_BR1


title: AsiSI-ER 4OHT input replicate 1


title: AsiSI-ER DMSO HDAC1 replicate 1

value: DMSO


title: CNA-044


title: HCT116_RAD21_input_Nut0h_BR2


title: RNA-seq: TEV auxin control replicate 2, BATCH 3

data_processing:
Reads were trimmed with Cutadapt v2.5 to remove adaptors.
Counts per transcript tables were obtained by aligning trimmed reads to the WS275 version of the C. elegans protein coding transcriptome using Salmon v1.5.2 in quant mode using –seqBias –gcBias and --numBootstraps 100 options
Bigwigs were obtained by aligning trimmed reads to the WS275 C. elegans genome using STAR v2.7.9a with the options --outSAMmultNmax 1 --alignIntronMax 5000 --quantMode GeneCounts --outSAMtype BAM SortedByCoordinate --outMultimapperOrder Random --outWigType wiggle --outWigStrand Stranded --outWigNorm RPM. Wig files were converted to bigwigs with the wigToBigWig v2.8 from UCSCtools. After visual inspection, bigWigs of technical replicates and then biological replicates from each batch were averaged using Ensemble WiggleTools mean command for each strand separately. Finally the bigwigs of the two strands were summed using the Ensembl tool bigWigMerge v2.
Assembly: WS275
Supplementary files format and content: Salmon quant.sf files contain 5 columns: Name, Length, EffectiveLength, TPM, NumReads and one row for each transcript.
Supplementary files format and content: The bigwig files contain the pileup of reads from both strands in RPM, averaged over technical and biological replicates.

extract_protocol:
RNA was extracted using Trizol, treated with DNase and cleaned using RNeasy MinElute Cleanup Kit.
Illumina Stranded mRNA preparation kit.

treatment_protocol: Synchronised L1 animals are seeded on NGM plates, incubated for 3 hours at 22℃, heat-shocked for 30 mins at 34℃. Then they are incubated again for 19 hours at 22℃. The degron strains were seeded on 1mM auxin plates and heat-shocked as described earlier. For the auxin control, the animals were seeded on plates without auxin but with ethanol. All animals were collected by washing thrice with M9 buffer.

value: Exposure to 1mM auxin, heat-shock for 30 min at 34C


title: RNA-seq: TEV auxin control replicate 3, BATCH 3


title: CNA-043

data_processing:
Low qaulity of reads in the raw reads were trimmed using the Trimmomatic (v0.39)
Trimmed reads were align using HISAT2 (v2.2.1)
FeatureCounts (v2.0.3) was used for the quantification of aligned reads.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.


title: AsiSI-ER 4OHT GATAD2B replicate 1


title: HCT116_RAD21_input_Nut0h_BR1


title: RNA-seq: TEV auxin control replicate 1, BATCH 3


title: AsiSI-ER DMSO input replicate 1


title: CNA-042


title: HCT116_PCHiC_Nut0h_BR2


title: RNA-seq: TEV TIR1 auxin control replicate 3, BATCH 3

value: ubsSi20[hsp-16.2p::TEV::unc-54 3'UTR; Cbr-unc-119(+)] II; xeSi376[eft-3p::TIR1::mRuby::unc-54 3'UTR, cbr-unc-119(+)] III.


title: HCT116_RAD21_H3K27ac_Nut1h_BR2


title: CNA-041


title: RNA-seq: TEV TIR1 auxin control replicate 2, BATCH 3


title: HCT116_RAD21_H3K27ac_Nut1h_BR1


title: CNA-040


title: HCT116_RAD21_H3K27ac_Nut0h_BR2


title: CNA-039


title: RNA-seq: TEV TIR1 auxin control replicate 1, BATCH 3


title: HCT116_RAD21_H3K27ac_Nut0h_BR1


title: CNA-038


title: RNA-seq: dpy-26cs sdc-3AID auxin replicate 2, BATCH 3

value: ubsSi20[hsp-16.2p::TEV::unc-54 3'UTR; Cbr-unc-119(+)] II; xeSi376[eft-3p::TIR1::mRuby::unc-54 3'UTR, cbr-unc-119(+)] III; dpy-26(ubs4[FLAG-TEVcs]) IV; sdc-3(ubs20[N-term AID]) V.


title: CNA-037


title: RNA-seq: dpy-26cs sdc-3AID auxin replicate 1, BATCH 3


title: CNA-036


title: CNA-035


title: HCT116_input_Nut10h_BR2


title: HCT116_input_Nut1h_BR1


title: RNA-seq: sdc-3AID control replicate 2, BATCH 4

value: Heat-shock for 30 min at 34C

value: ubsSi20[hsp-16.2p::TEV::unc-54 3'UTR; Cbr-unc-119(+)] II; xeSi376[eft-3p::TIR1::mRuby::unc-54 3'UTR, cbr-unc-119(+)] III; sdc-3(ubs20[N-term AID]) V.


title: CNA-034


title: HCT116_input_Nut0h_BR2


title: CNA-033


title: RNA-seq: sdc-3AID control replicate 1, BATCH 4


title: RNA-seq: sdc-3AID control replicate 3, BATCH 4


title: HCT116_input_Nut0h_BR1


title: RNA-seq: sdc-3AID auxin replicate 3, BATCH 4


title: CNA-032


title: BRC patient P3, tumour breast tissue, MNase-assisted H3 ChIP-seq

city: Colchester

first: Vladimir

middle: B

last: Teif

address: Wivenhoe Park

department: School of Life Sciences

institute: University of Essex

data_processing:
Breast tissue samples for patients P1-P3 were sequenced on Illumina NovaSeq S4, TruSeq ChIP Library Prep Kit (IP-202-1012), 2 x 100 bp paired-end mode. cfDNA samples for patients P1 and P3 were sequenced as above, but in 2 x 150 bp paired-end mode. Samples for patient P4 were sequenced on Illumina HiSeq 2500 sequencer, 2 x 75 bp paired-end mode, using NEBNext Ultra II Kit from NEB for library preparation. Paired-end sequenced reads were mapped with Bowtie  to human genome hg19, considering only uniquely mapped reads and allowing up to one mismatch. This resulted in ~500 million mapped reads per sample (see details in Supplementary Table S1). NucTools pipeline was used to obtain BED files with mapped nucleosomal DNA fragments including information about DNA fragment sizes. A set of Perl scripts called cfDNAtools developed for the next steps of analysis reported here is available at https://github.com/TeifLab/cfDNAtools. cfDNAtools script extract_nuc_sizes.pl  was used to extract fractions with DNA fragments with sizes between 100-120 bp, 120-140 bp, 140-160 bp, 160-180 bp and 180 -200 bp. Intersections between regions of interest were done using BEDTools (Quinlan, 2014).
DNA fragments with sizes 120-180bp are included in this dataset
Assembly: hg19
Supplementary files format and content: BED files containing all mapped reads within size range 120-180bp. The FED file contains the following columns: chromosome, start coordinate, end coordinate, fragment size (bp)
Supplementary files format and content: BigWig files for visualisation in the genome browser

source_name: breast

extract_protocol:
MNase-seq and MNase-assisted histone H3 ChIP-seq  Chromatin extraction. Paired normal and tumour breast tissues extracted during surgery were stored at -80  ͦC. Frozen tissue was first ground into fine powder in liquid nitrogen. It was further homogenized by manual douncing in 5 ml ice-cold Buffer I (0.3 M Sucrose in 60 mM KCl, 15 mM NaCl, 5mM MgCl2, 0.1 mM EGTA, 15 mM Tris-HCl (pH 7.5) with freshly added 0.5 mM DTT, 0.1 mM PMSF and 1XProtease Inhibitor Cocktail, Thermo Scientific Halt Protease Inhibitor Single-use Cocktail (100X). The homogenized cell suspension was centrifuged in a 15 ml Falcon conical centrifuge tube at 6000 g for 10 minutes at 4  ͦC. The precipitated cells were re-suspended in 500 µL of Buffer I, then 500 µL of Buffer II (same as Buffer I, but with freshly added 0.4 % (v/v) IGEPAL CA-630) was gently added on top and the lysate was incubated on ice for 3 minutes, followed by centrifugation at 3000 g for 3 minutes at 4  ͦC. The pellet was re-suspended in 1 ml of ice-cold NBR Buffer (85 mM NaCl, 5.5 % Sucrose, 10 mM Tris-HCl pH 7.5, 3 mM MgCl2, 1.5 mM CaCl2 with freshly added 0.2 mM phenylmethylsulfonyl fluoride (PMSF) and 1 mM DTT) and centrifuged at 3000 g for 3 minutes at 4  ͦC. The pellet then was re-suspended in 200 µl of NBR buffer. Samples were treated with 1 µl RNAseA (10 mg/ml) per 100 µl of nuclear lysate for 5 minutes at room temperature.     MNase digestion. MNase restriction enzyme (Sigma, Cat No: N5386-500UN) was diluted to 1U (Sigma Boehringer Units) in MNase buffer (50 % Glycerol, 10 mM Tris p H7.6 and 50 mM NaCl). The pellets re-suspended in 200 µl of NBR buffer in the chromatin extraction step were digested with MNase enzyme as follows. Chromatin derived from paired normal and tumour tissue was diluted with NBR buffer to keep the same concentration in both preparations.  A 20 µl aliquot of purified nuclei was test digested with 1 µl MNase for 7 min at room temperature to assess the optimal digestion time and enzyme concentrations. 1 µg of chromatin was digested with 1U of MNase for 7 minutes at room temperature to achieve 80:20 relative abundance of mono- and di-nucleosome fractions on agarose gel. The MNase digestion was stopped by addition of equal volume (NBR:STOP, 1:1) of STOP Buffer (215  mM NaCl, 10 mM TrisHCl pH 8, 20 mM EDTA, 5.5 % Sucrose, 2 % TritonX 100 with freshly added 0.2 mM PMSF, 1 mM DTT and 2X Protease Inhibitors). After digestion, chromatin was incubated on ice in the fridge at 4  ͦC overnight to release the digested chromatin.     Chromatin Immunoprecipitation (ChIP). 10 µl of Protein A beads (DynabeadsTM Protein A; Invitrogen) equivalent to 10 µl bed volume of slurry were prepared per each ChIP reaction. Bead storage buffer was aspirated, and the beads were washed twice in 500 µl in Block solution (0.5 % BSA (w/v) in PBS supplemented with 0.1 mM PMSF). Beads sufficient for 4 ChIP samples were all combined and dissolved in 600 µl of Block solution with addition of 5 µg of anti-H3 antibody Abcam AB1791 per ChIP reaction (20 µg for 40 µl of beads for 4 ChIP samples). The antibody-bead solution was incubated on a slow rotating wheel at 4  ͦC for two hours. After incubation, the beads were again washed in 600 µl block solution to remove un-bound antibody. The chromatin incubated overnight after MNase digestion, was then centrifuged for 10 minutes at max speed 9800 g at 4  ͦC. The supernatant with released chromatin was collected and stored at -20  ͦC and used for ChIP experiment. 5 % of chromatin volume used for MNase-assisted ChIP-seq was frozen at -20  ͦC as Input and used for MNase-seq. 300 µl of chromatin was incubated with the antibody bound Protein A beads for 3 hours on a rotating wheel at 4  ͦC. Unbound chromatin was washed 4 times  in 1 ml volume of ChIP-Wash buffer (150 mM NaCl, 10 mM Tris-HCl pH 8, 2 mM EDTA, 1 % NP40, 1 % Nadeoxycholate with freshly added 0.5 mM DTT, 0.1 mM PMSF and 1XProtease Inhibitor Cocktail). The initial wash of bound beads was done by gently mixing beads in the ChIP-Wash buffer for one min. For subsequent 3 washes: the tube was rotated for 5 minutes at 4  ͦC on a rotating wheel, then placed in magnetic rack for 1 min at 4  ͦC and then the supernatant was withdrawn.  After two washes the beads with wash buffer were transferred to new tubes. And as a final step, the beads were washed with 1 ml of filtered 1x TE buffer (10 mM Tris-HCl containing 1 mM EDTA) at room temperature, after which the TE buffer was removed as above. The elution of bound chromatin was performed with 100 µl of Elution buffer (0.1 M NaHCO3, 1 % SDS) supplemented with 2 µl of Proteinase K per ChIP sample tube. The beads were incubated with the elution buffer for 6-12 hours at 55  ͦC. Similarly, 2 µl of Proteinase K were added to Input material and incubated at 55  ͦC for 6-12 hours. The incubated beads were briefly vortexed and supernatant collected by placing the tubes in a magnetic rack. The beads were additionally washed in 20 µl of elution buffer and supernatant collected as above. The eluants were further purified with PCR purification columns according to manufacturer’s instructions and eluted in 20 µl volume of elution buffer of the kit. These final eluants were stored at -20  ͦC ready for library preparation step.   cfDNA extraction. Cell-free DNA was extracted from 500 µl of blood plasma or serum as detailed below, following the instructions of the purification kits. For patient P1, cfDNA was extracted from 500 µl of blood serum using Plasma/serum Cell-Free Circulating DNA purification Mini Kit  (Norgen Biotek Corp). For patient P2, cfDNA was extracted from 500 µl
The libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, NEB #E7103) according to the manufacturer’s instructions.
NEBNext Ultra II DNA Library Prep Kit (New England Biolabs, NEB #E7103)

value: breast

tag: condition

value: tumour

value: histone H3


title: CNA-031

extract_protocol:
For Illumina NovaSeq 6000, total RNA was extracted using TruSeq Stranded Total RNA LT Sample Prep Kit (Globin). For MGISEQ-2000RS, total RNA was isolated from tissue using TRI-reagent based method. Total RNA (500 ng) was processed for  preparing whole transcriptome sequencing library.
For Illumina NovaSeq 6000, libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Sample Prep Guide, Part # 15031048 Rev. E, For MGISEQ-2000RS,  Enrichment of whole transcriptome RNA by depleting  ribosomal RNA (rRNA) was processed for preparing whole transcriptome sequencing library using MGIEasy RNA Directional Library Prep Kit (MGI) according to manufacturer’s instruction.

value: blood

value: M


title: RNA-seq: dpy-26cs sdc-3AID auxin replicate 3, BATCH 3

tag: genotype


title: RNA-seq: sdc-3AID auxin replicate 2, BATCH 4

tag: treatment


title: CNA-030

value: COPD


title: BRC patient P3, normal breast tissue, MNase-seq

value: normal


title: RNA-seq: sdc-3AID auxin replicate 1, BATCH 4


title: HCT116_H3K4me1_Nut1h_BR2

value: Nutlin3a 1h


title: HCT116_input_Nut10h_BR1

value: Nutlin3a 10h


title: HCT116_input_Nut1h_BR2


title: RNA-seq: scc-1cs coh-1cs TEV replicate 3, BATCH 2

value: whole body

value: L3 larvae

value: scc-1(ubs19[FLAG-TEVcs]), ubsSi20[hsp-16.2p::TEV::unc-54 3'UTR; Cbr-unc-119(+)] II; coh-1(ubs26[FLAG-TEVcs]) X.


title: BRC patient P3, normal breast tissue, MNase-assisted H3 ChIP-seq


title: CNA-029


title: HCT116_H3K4me1_Nut1h_BR1


title: CNA-028


title: BRC patient P3, cfDNA rep2

source_name: cfDNA from blood plasma

value: cfDNA from blood plasma


title: CNA-027


title: RNA-seq: scc-1cs coh-1cs TEV replicate 1, BATCH 2


title: BRC patient P3, tumour breast tissue, MNase-seq


title: HCT116_H3K4me1_Nut0h_BR2

value: DMSO


title: BRC patient P3, cfDNA rep1


title: RNA-seq: coh-1cs TEV replicate 3, BATCH 2

value: ubsSi20[hsp-16.2p::TEV::unc-54 3'UTR; Cbr-unc-119(+)] II; coh-1(ubs26[FLAG-TEVcs]) X.


title: CNA-026


title: HCT116_H3K4me1_Nut10h_BR2


title: HCT116_H3K27ac_Nut10h_BR2


title: HCT116_H3K4me1_Nut0h_BR1


title: HCT116_H3K4me1_Nut10h_BR1


title: CNA-025

value: F


title: RNA-seq: coh-1cs TEV replicate 2, BATCH 2

value: Heat-shock for 30 min at 34C


title: BRC patient P1, tumour breast tissue, MNase-seq

value: breast


title: HCT116_H3K27ac_Nut10h_BR1


title: CNA-024


title: RNA-seq: coh-1cs TEV replicate 1, BATCH 2


title: RNA-seq: scc-1cs TEV replicate 4, BATCH 1

value: scc-1(ubs19[FLAG-TEVcs]), ubsSi20[hsp-16.2p::TEV::unc-54 3'UTR Cbr-unc-119(+)] II.


title: HCT116_H3K27ac_Nut1h_BR2


title: CNA-023


title: BRC patient P1, tumour breast tissue, MNase-assisted H3 ChIP-seq

value: tumour

value: histone H3


title: RNA-seq: scc-1cs coh-1cs TEV replicate 2, BATCH 2


title: CNA-022

value: blood

value: M


title: HCT116_H3K27ac_Nut1h_BR1


title: BRC patient P2, normal breast tissue, MNase-seq

value: normal


title: BRC patient P1, normal breast tissue, MNase-seq


title: RNA-seq: scc-1cs TEV replicate 2, BATCH 1


title: BRC patient P2, tumour breast tissue, MNase-seq


title: CNA-021

value: COPD


title: BRC patient P1, normal breast tissue, MNase-assisted H3 ChIP-seq


title: HCT116_H3K27ac_Nut0h_BR1


title: RNA-seq: scc-1cs TEV replicate 1, BATCH 1


title: BRC patient P1, cfDNA rep1


title: RNA-seq: kle-2cs TEV replicate 4, BATCH 1

value: ubsSi20[hsp-16.2p::TEV::unc-54 3'UTR; Cbr-unc-119(+)] II; kle-2(ubs14[FLAG-TEVcs]) III.


title: HCT116_RNA_Nut10h_BR2

data_processing:
ENCODE standards were followed to process paired-end reads. Sequencing adapters were trimmed using Trim Galore! (0.6.6).
Reads were then mapped to the reference genome (GRCh37.p13) using STAR (2.7.0f) with parameters recommended by ENCODE. Read counts were quantified using featureCounts from subread (2.0.0)
Normalization and differential analysis were performed using R package DESeq2 (1.36.0)
Library statistics were assessed using FastQC and MultiQC
Assembly: hg19
Supplementary files format and content: raw count, DESeq2 output

extract_protocol:
RNA was extracted from 200,000 frozen cell pellets using the RNAeasy Mini Kit (Qiagen #74104) following the manufacturer’s instructions. otal RNA’s integrity and concentration was assessed using RNA ScreenTape Analysis (Agilent #5067-5576) on an Agilent 2200 Tapestation
Samples were sequenced to reach a minimum number of 30M unique valid paired reads.

value: Nutlin3a 10h


title: CNA-019


title: CNA-020


title: ARTEMIS #6

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

institute: CIBEREHD

description: arTreg low expansion: sample 19

data_processing:
Mapping of the reads were obtained using the STAR program against hg38 and the quantification of genes and transcripts were done with STAR using option GeneCount option using Ensembl annotation
We use quantile method and limma-voom transformation from rounded expected counts to normalize the non biological variability
Assembly: Homo Sapiens (HG38)
Supplementary files format and content: STAR GeneCount

source_name: Peripheral blood Tregs

extract_protocol:
Cells were sorted into Trizol and extracted using Direct-zol RNA extraction kit from Zymo per manufacture's instructions.
Paired-ended sequencing was performed on Illumina platform.

treatment_protocol: FACS purification

tag: group

value: arTreg low expansion


title: HCT116_RNA_Nut10h_BR1


title: RNA-seq: kle-2cs TEV replicate 3, BATCH 1

value: whole body

value: L3 larvae


title: ARTEMIS #2

description: arTreg medium expansion: sample 18

value: arTreg medium expansion


title: HCT116_RNA_Nut1h_BR2

value: Nutlin3a 1h


title: CNA-018

source_name: blood

tag: disease


title: HCT116_RNA_Nut1h_BR1

tag: cell line


title: RNA-seq: kle-2cs TEV replicate 2, BATCH 1


title: ARTEMIS #5

description: arTreg low expansion: sample 17


title: RNA-seq: scc-1cs TEV replicate 3, BATCH 1


title: CNA-016

tag: Sex


title: RNA-seq: kle-2cs TEV replicate 1, BATCH 1


title: Post-KTx #5

description: PolyTreg medium expansion: sample 16

value: PolyTreg medium expansion


title: HCT116_RNA_Nut0h_BR2

value: DMSO


title: HCT116_H3K27ac_Nut0h_BR2


title: RNA-seq: dpy-26cs TEV replicate 4, BATCH 1

value: Heat-shock for 30 min at 34C

value: ubsSi20[hsp-16.2p::TEV::unc-54 3'UTR; Cbr-unc-119(+)] II; dpy-26(ubs4[FLAG-TEVcs]) IV.


title: Post-KTx #1

description: arTreg high expansion: sample 15

value: arTreg high expansion


title: CNA-015


title: HCT116_RNA_Nut0h_BR1


title: CNA-017


title: Post-KTx #6

description: PoyTreg low expansion: sample 14

value: PoyTreg low expansion


title: RNA-seq: dpy-26cs TEV replicate 3, BATCH 1


title: HCT116_HiC_Nut24h_BR2

data_processing:
Various steps were taken to process the Hi-C data, including read quality control, mapping, interaction detection, filtering, and matrix normalization using the TADbit pipeline
Assembly: GRCh37.p13
Supplementary files format and content: HiC matrices .abc.txt

extract_protocol: Cells were fixed in DMEM medium supplemented with 10% FBS and 2% methanol-free formaldehyde for 10 minutes rotating at room temperature. After quenching the formaldehyde with 0.125M glycine and washing the cells with 1X PBS, nuclei were extracted by lysing the cells in 10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% IGEPAL CA630 (SIGMA-ALDRICH #18896-50ML), 1× cOmplete EDTA-free protease inhibitor cocktail. Chromatin was digested overnight with HindIII enzyme and the cohesive restriction fragment ends were filled-in with dCTT, dTTP, dGTP and biotin-14-dATP(Invitrogen #19524-016) nucleotides. After blunt-end ligating the restriction fragment ends, the chromatin was decrosslinked by incubating overnight with proteinase K and purified by phenol:chloroform:isoamyl alcohol 25:24:1 (SIGMA-ALDRICH #P3803-100ML) extraction.Non-informative biotin at restriction fragment ends was removed by incubating the samples with dATP and T4 DNA polymerase (New England Biolabs#M0203S). After purifying the DNA again with a phenol:chloroform:isoamyl alcohol extraction, 10µg of the chromatin was sheared using a Covaris M220 focused ultrasonicator in 130µl cuvettes using the following parameters: 20% duty factor, 50 peak incident power, 200 cycles per burst, 65 seconds. The ends were end-repaired and dATP-tailed, followed by a biotin-pulldown using Dynabeads MyOne streptavidin C1 paramagnetic beads (Thermo Fisher #65001) to enrich for those DNA fragments which contain information of a chromatin loop. PE Illumina adapters(Supplementary Data 9) were ligated to the sample and the library was amplified for 8 cycles. Finally, the library was purified using a SPRI bead double-sided selection (0.4-1 volumes). Size and concentration of the finished Hi-C libraries was assessed by DNA ScreenTape Analysis (Agilent #5067-5582) on an Agilent 2200 Tapestation.

value: Nutlin3a 24h


title: CNA-013

value: blood

value: M


title: RNA-seq: dpy-26cs TEV replicate 2, BATCH 1


title: RNA-seq: dpy-26cs TEV replicate 1, BATCH 1


title: Pre-KTx #2

description: arTreg high expansion: sample 13


title: ARTEMIS #3

description: arTreg low expansion: sample 12


title: CNA-012

value: COPD


title: HCT116_HiC_Nut10h_BR2


title: RNA-seq: TEV control replicate 3, BATCH 2


title: HCT116_HiC_Nut24h_BR1


title: CNA-011


title: HCT116_HiC_Nut10h_BR1


title: ARTEMIS #4

description: arTreg high expansion: sample 11


title: HCT116_HiC_Nut7h_BR2

value: Nutlin3a 7h


title: CNA-009


title: RNA-seq: TEV control replicate 1, BATCH 2


title: CNA-010


title: RNA-seq: TEV control replicate 2, BATCH 2


title: Post-KTx #3

description: PolyTreg medium expansion: sample 9


title: CNA-014


title: HCT116_HiC_Nut7h_BR1


title: ARTEMIS #10

description: arTreg low expansion: sample 8


title: RNA-seq: TEV control replicate 4, BATCH 1


title: CNA-008


title: HCT116_HiC_Nut4h_BR2

value: Nutlin3a 4h


title: Post-KTx #2

description: arTreg low expansion: sample 7

value: arTreg low expansion


title: RNA-seq: TEV control replicate 3, BATCH 1

value: whole body


title: RNA-seq: TEV control replicate 2, BATCH 1

value: L3 larvae


title: HCT116_HiC_Nut4h_BR1


title: CNA-006


title: CNA-005


title: Pre-KTx #1

description: arTreg high expansion: sample 6


title: RNA-seq: TEV control replicate 1, BATCH 1


title: T1D #2

description: PolyTreg high expansion: sample 10

value: PolyTreg high expansion


title: CNA-003


title: WT_WW_7

city: Grugliasco

first: IVAN

last: VISENTIN

state: Seleziona uno Stato

address: Largo Braccini 2

department: DISAFA

country: Italy

institute: University of Turin

data_processing:
Clean reads were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were mapped to the reference genome (SL3.0) using the HISAT2 software.
HTSeq was used to count the read numbers mapped of each gene, including known and novel genes; then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: ITAG SL3.0
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Solanum lycopersicum

source_name: Leaf

growth_protocol: Seeds were sterilized in 4% (v/v) sodium hypochlorite containing 0.02% (v/v) Tween 20, rinsed thoroughly with sterile water, and then placed for 48 h on moistened filter paper at 25°C in darkness. Germinated seedlings were grown for two weeks in a walk-in climate chamber (16/8h light/dark 25°C, 65% humidity, and 200 µmol s–1 m–2 of photosynthetic photon flux density) in a seedbed with standard soil (Terra Nature, NPK 12:14:24) and then moved into 1-liter pots filled with vermiculite and kept under the same conditions.

extract_protocol:
Total RNA was extracted from leaves using the Spectrum Plant Total RNA Kit (Sigma Aldrich). After digestion of contaminant DNA by DNAse I (ThermoScientific) at 37°C for 30 min, RNA quantity and quality were determined with a Nanodrop 2000 spectrophotometer (Thermo Fisher Scientific Inc., Wilmington, DE, United States).
cDNA libraries were prepared from 1 µg total RNA using NEBnext Ultra TM RNA Library Prep Kit for Illumina (NEB, USA) following the manufacturer’s recommendations. A total of 21 libraries (three each for wt and SL- leaves, plus wt treated with GR245DS) were constructed and quantified using a Qubit 2.9 fluorometer (Life Technologies) and sequenced on an Illumina platform to generate paired-end reads.

treatment_protocol: Time-course experiments were performed by gently uprooting plants of both wt and SL- genotypes, transferring them in vermiculite hydrated with only 20 ml of water (stressed group), or transferred in wet vermiculite (well-watered controls). After having completely recovered, the stressed plants were subjected to a second identical cycle of dehydration and rewatering. Unstressed, well-watered controls were sampled before transfer to new wet substrates. GR245DS treatment was carried out by leaf spraying of a 5 uM solution until drip-off 24 h before sampling, which corresponded with the beginning of the drought time-course (hence, untreated irrigated wt plants are an appropriate control group for this condition as well).

tag: cultivar

value: Leaf

value: WT

value: Well-watered

tag: time


title: HCT116_HiC_Nut0h_BR2

value: DMSO


title: CNA-004


title: HCT116_HiC_Nut1h_BR1

value: Nutlin3a 1h


title: ARTEMIS #7

description: arTreg medium expansion: sample 4

value: arTreg medium expansion


title: WT_WW_14


title: HCT116_HiC_Nut0h_BR1


title: T1D #4

description: PolyTreg medium expansion: sample 3

value: PolyTreg medium expansion


title: WT_WW_6


title: CNA-002


title: T1D #3

description: PolyTreg medium expansion: sample 2


title: CNA-007


title: WTTR2411

value: GR24 5DS treated


title: CNA-001

value: blood


title: CTCF_d80_170_adult_C-CTCF_2

first: Natalia

last: Klimenko

address: 34/5 Vavilova Street

institute: Institute of Gene Biology (IGB) of the Russian Academy of Sciences

data_processing:
Adapters, poly-N and poly-A read ends were removed using cutadapt software (Martin 2011). Cutadapt was also used for trimming low-quality ends (quality threshold was set to 20, reads with the length less than 20 bp after trimming were discarded).
The remaining reads were aligned to build version dm6 of the Drosophila melanogaster genome using Bowtie version 2 (Langmead and Salzberg 2012). Only reads that aligned concordantly exactly one time were passed to further analysis.
After alignment, read duplicates were removed using Picard MarkDuplicates function (http://broadinstitute.github.io/picard/). Also, peaks overlapping with blacklist regions were discarded (blacklist regions were previously converted from dm3 to dm6 genome built version) (https://sites.google.com/site/anshulkundaje/projects/blacklists)
Chip-seq coverage tracks (BedGraph) were obtained using deepTools (Ramírez et al. 2014) bamCoverage function with bin width 50 bp and RPKM normalization.
Assembly: dm6
Supplementary files format and content: Processed data was obtained by deeptools bamCoverage (bedGraph)

source_name: whole organism

growth_protocol: Drosophila strains were maintained on standard medium at 25°C and 50-60% humidity.

extract_protocol:
After 3 rounds of washing with lysis buffer supplemented with 500 mM NaCl, and TE buffer (10 mM Tris-HCl, pH 8; 1 mM EDTA), the DNA was eluted with elution buffer (50 mM Tris-HCl, pH 8.0; 1 mM EDTA, 1% SDS), the cross-links were reversed, and the precipitated DNA was extracted by the ChIP DNA Clean &Concentrator kit (Zymoresearch).
Libraries were prepared according to manufacturers recommendations with small modifications. In short, 1-10ng of purified, RNase treated, and reverse cross-linked genomic DNA was end-repaired and terminal adenosine residues were added using the NEBNext reagents. Custom-made indexed adapters were ligated, after which the material was size selected at ~200-600 bp with Ampure XP beads (Beckman Coulter). PCR amplification was performed using PE1.0 and PE2.0 primers (custom-made) for 12 cycles for Input samples and 14 to 15 cycles for IP-ed samples using the Q5 Hot Start HiFi PCR Master Mix (NEB). The PCR-amplified library was purified using Ampure XP beads and its quality was assessed on a Bioanalyzer 2100 system (Agilent). The libraries were sequenced on aNovaSeq 6000 (Illumina) in pair-end mode.

treatment_protocol: Chromatin was prepared from two- to three-day-old adult flies. A 1 g of adult flies was ground in a mortar in liquid nitrogen and resuspended in 20 mL of buffer A (15 mM HEPES-KOH, pH 7.6, 60 mM KCl, 15 mM NaCl, 13 mM EDTA, 0.1 mM EGTA, 0.15 mM spermine, 0.5 mM spermidine, 0.5% NP-40, 0.5 mM DTT) supplemented with 0.5 mM PMSF and Calbiochem Cocktail V. The suspension was then homogenized subsequently in a Potter and Dounce homogenizer with tight pestle, filtered through 100 µm Nylon Cell Strainer (Miltenyi Biotec, United States), and cross-linked with 1% formaldehyde for 15 min at room temperature. Cross-linking was stopped by adding glycine to a final concentration of 125 mM. The nuclei were washed with three 10-mL portions of wash buffer (15 mM HEPES-KOH, pH 7.6, 60 mM KCl, 15 mM NaCl, 1 mM EDTA, 0.1 mM EGTA, 0.1% NP-40, protease inhibitors), one 5-mL portion of nuclear lysis basic buffer (15 mM HEPES, pH 7.6, 140 mM NaCl, 1 mM EDTA, 0.1 mM EGTA, 1% Triton X-100, 0.5 mM DTT, 0.1% sodium deoxycholate, protease inhibitors) and resuspended in 1 mL of nuclear lysis buffer (15 mM HEPES, pH 7.6, 140 mM NaCl, 1 mM EDTA, 0.1 mM EGTA, 1% Triton X-100, 0.5 mM DTT, 0.1% sodium deoxycholate, 0.5% SLS, 0.1% SDS, protease inhibitors). The suspension was sonicated in a Covaris ME220 focused-ultrasonicator (40 alternating 15-s ON and 45-s OFF intervals, peak power 75, duty % factor 25), and 50-µL aliquots were used to test extent of sonication and to measure DNA concentration. Debris was removed by centrifugation at 14 000 g, 4°C, for 10 min, and chromatin was pre-cleared with Protein A Dynabeads (Invitrogen). Corresponding antibodies were incubated for 1 hour at room temperature with 20 µL aliquots of Protein A (anti-CTCF C, 1:200) or G (anti-CP190, 1:200) Dynabeads (Invitrogen) mixed with 200 µL of PBST. Then antibodies-Dynabeads complexes and anti-HA Magnetic beads (Pierce) were washed and equilibrated in nuclear lysis buffer. Chromatin samples containing 10–20 µg of DNA equivalent in 200 µL of nuclear lysis buffer (2 µL aliquots of such pre-cleared chromatin being stored as input material) were incubated overnight, at 4°C, with antibodies-Dynabeads complexes.

tag: development stage

value: adult

tag: protein

value: dCTCF

tag: antibody source

value: rabbit

value: Oregon-R


title: Post-KTx #4

description: PolyTreg high expansion: sample 1


title: PI_HA_adult

description: Preimmune control

value: PI

value: HA

value: dCTCFwt


title: WTTR24_9

tag: tissue


title: RSEM_siNC_3

city: Memphis

first: William

middle: C.

last: Wright

state: Tennessee

address: 262 Danny Thomas Pl

department: Computational Biology

institute: St. Jude Children's Research Hospital

data_processing:
Raw sequence files were merged across lanes according to sample and subjected to a first round of quality control using the FastQC tool (www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Illumina universal adapters were trimmed from all samples using Trim Galore ([www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and samples were then subjected to a second round of quality control
Reads were mapped to the human Hg38 reference genome using Bowtie2
The edgeR package with Limma/Voom was used for linear modeling, empirical Bayes smoothing, TMM normalization, generation of Log2(CPM), and statistical analysis
Genome_build: Hg38
Supplementary_files_format_and_content: Log2(Normalized Counts per Million + 1)

growth_protocol: All cells were maintained according to respective ATCC recommended culture conditions

extract_protocol:
Total RNA was extracted from each cell line using the Maxwell 16 LEV automation system and simplyRNA purification kit (Promega, Cat. No. 1280) according to the manufacturer’s protocol. The extracted RNA was quantified by spectrophotometry using a NanoDrop 8000 (ThermoFisher Scientific, Waltham, MA) to ensure a reading of OD260/OD280 between 1.8 and 2.0.
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA Library Preparation Kit (Illumina)

treatment_protocol: Cells were not drug treated

tag: cell type

value: pancreatic cancer cell line

value: cancer

value: Pancreas

tag: genotype/variation

value: siNC


title: ARTEMIS #8

description: arTreg low expansion: sample 5

value: arTreg low expansion


title: CTCF_wt_2_adult_HA_2

tag: strain


title: WTTR24_8

value: Leaf

value: WT


title: RSEM_siNC_2


title: WT_S2_9

value: Water recovery 2


title: PI_rabbit_adult

description: Preimmune control


title: HCT116_HiC_Nut1h_BR2

value: Nutlin3a 1h


title: RSEM_siNC_1


title: CTCF_wt_2_adult_HA_1