title: Sample NE3 technical replicate d [2018_509d]

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

institute: IBENS

description: Non dependent rat 3 technical replicate d

data_processing:
Illumina bcl2fastq 2.18.0.12 software used for basecalling.
RNA-Seq data analysis was done using the Eoulsan software version 2.3. Before mapping, reads ≤40 bases were removed, and reads with quality mean ≤30 were discarded. Reads were then aligned against the Rattus norvegicus genome (rnor6 genome assembly from Ensembl version 84) using the STAR mapper (version 2.6.1b, with –outSAMunmapped Within parameter). Alignments from reads matching more than once on the genome were removed. Rattus norvegicus GFF3 genome annotation from Ensembl version84. All overlapping regions between alignments and referenced exons were counted with HTSeq-count 0.5.3.
Genome_build: rnor6 version Ensembl 84
Supplementary_files_format_and_content: *.tsv:Tb-delimited text files include transcripts counting for each Sample.

source_name: Nucleus accumbens

extract_protocol:
Total RNA was extracted from bilateral nucleus accumbens and caudate putamen with RNeasy Qiagen mini kit according to the lipid tissue protocol of the manufacturer (Qiagen, Courtaboeuf, France).
Messenger (polyA+) RNAs were purified from 300 ng of total RNA using oligo(dT). Libraries were prepared using the strand specific RNA-Seq library preparation TruSeq Stranded mRNA kit (Illumina).

treatment_protocol: Rats received either a challenge dose of cocaine (5 mg/kg i.p; cocaine treated rats), or saline (control group) and their preference was immediately measured in the CPP apparatus for 18 min.

tag: genetic background

value: 8 weeks

tag: phenotype

value: Non dependent Rat (non CPP-E)

value: 4 cocaine injections (1 per day), withdrawal 15 days, 1 cocaine injection

value: Nucleus accumbens


title: ChIP_N1

status: Public on Mar 11 2024

type: SRA

city: Little Rock

first: Kimberly

middle: E

last: Stephens

state: AR

address: 4301 W. Markham St Slot 510

department: Neuroscience

country: USA

institute: University of Arkansas for Medical Sciences

library_source: genomic

data_processing:
Casava v1.8.2 used for base calling
Reads trimmed for adapter sequence
reads mapped to rn6 genome using Bowtie2
Assembly: rn6
Supplementary files format and content: Align reads shifted 4 nucleotides upstream for 5' and 5 nucleotides downstream for 3' end; insertion sites identified by trimming to the 5'end. Insertion site extended in both directions by 75bp; Reads downsampled; peaks called by MACS2; limma used to count reads for CCI versus Naive.

molecule: genomic DNA

organism: Rattus norvegicus

source_name: DRG

extract_protocol:
Dorsal root ganglion (L4-L6) harvested and homogenized
ATAC-seq with Illumina TDE1 enzyme after nuclei isolation

treatment_protocol: Chronic Constriction Injury and Naïve groups

tag: group

value: naive

tag: Sex

value: Female

tag: strain

value: Sprague-Dawley


title: Naive-H9_ATACseq_rep3

city: Tianjin

first: Niannian

last: Li

state: Tianjin

address: No. 94 Weijin Road, Nankai District, Tianjin

department: college of Life Sciences

country: China

institute: Nankai University

data_processing:
ChiLin pipeline 2.0.0  (Qin et al., 2016) is used for QC and preprocess of the ATAC-seq.
We use Burrows-Wheeler Aligner (BWA)  as a read mapping tool, and Model-based Analysis of ChIP-Seq (MACS2)  as a peak caller, with a q-value (FDR) threshold of 0.01
Deeptools is used for the heatmap plots
Differential peaks between Naive and Primed were identified by DEseq2 with adjusted P ≤0.05, |log2fold change| ≥ 1.
Assembly: hg38
Supplementary files format and content: ATACseq peak bigwig files

organism: Homo sapiens

growth_protocol: The naive hESCs (also named as prEpiSCs) were derived from the LTR7-GFP hESC_H9 cell line. The basal culture medium (500 ml) is prepared as follows, 240 ml DMEM/F12 (Thermo Fisher Scientific, catalog. no. 21331020), 240 ml Neurobasal medium (Thermo Fisher Scientific, catalog. no. 21103049), 2 mM L-glutamine (Thermo Fisher Scientific, catalog. no. 25030081), non-essential amino acids (Thermo Fisher Scientific, catalog. no. 11140050), 1% N2 supplement (Thermo Fisher Scientific, catalog. no. 17502048), 2% B27 supplement (Thermo Fisher Scientific, catalog. no. 12587010, minus vitamin A), 100 mg/ml Vitamin C (Sigma, catalog no. A4403), 50 ng/ml Bovine Albumin Fraction V (Thermo Scientific, cat. no. 15260-037), 20 ng/ml IL6 (PeproTech, catalog. no. AF-200-06), 20 ng/ml sIL-6R (PeproTech, catalog. no. 200-06R), 0.1 mM β-mercaptoethanol (Thermo Fisher Scientific, catalog. no. 21985023), Primocin (InvivoGen, catalog. no. ant-pm-2). The naive/prEpiSCs were cultured in the advanced GIX medium (basal culture medium plus chemical cocktail [0.2 μM Trametinib (GSK112022, Selleck S2673), 0.3 μM PD0325901, 2.0 μM XAV939, 0.5 μM Go6983]).IL6, IL-6R, Trametinib, PD0325901, XAV939, Go6983

extract_protocol:
the sample used to perform RNA-seq, ATAC-seq, CUT&Tag-seq are prepared based on the commonly used method.
AS for ATAC-seq, Cells were harvested and counted. Number of 500~1000 cells were used for ATAC-seq. The number of cells at this step is crucial, as the transposase-to-cell ratio determines the distribution of DNA fragments generated. Sample with 500~ 1000 cells was centrifuged for 5 min at 500 × g at 4 °C. Supernatant was removed and discarded. Cells were washed once with 50 μl of cold PBS buffer, centrifuged for 5 min at 500 × at 4 °C, and supernatant removed and discarded. The cell pellet in 50 μl of cold lysis buffer was resuspended by gently pipetting up and down and lysed for 10 min on ice, followed by centrifugation immediately for 10 min at 500 × g at 4 °C. The supernatant was discarded, and immediately continued to transposition reaction. Lysis buffer used was, 10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.5% NP-40.For transposition reaction and purification, TruePrep® DNA Libraryaf Prep Kit V2 for Illumina (Vazyme, TD502, 5ng) for tagmentation was used. After tagmentation reaction, AMP XP beads for purifying was used. In preparation, AMPure XP beads were equilibrated at room temperature for 30 minutes and mixed well. 25 μl (0.6x) beads were pipetted into the 50 μl PCR product, gently pipetted and mixed, and incubated at room temperature for 5 min (to remove long fragments). The reaction tube was centrifuged briefly and placed on a magnetic stand. After clarification, the supernatant (75 μl) was transferred to a new tube (be careful to mark the tube cap and tube body), and the magnetic beads discarded. 60 μl (1.2x) beads were pipetted into the supernatant, mixed by pipetting, and incubated at room temperature for 5 min (magnetic beads can be added to the new EP tube during the first incubation). The reaction tube was centrifuged briefly and placed on a magnetic stand. After clarification, the supernatant was removed, the tube was kept on the magnetic stand.  200 μl of freshly prepared 80% ethanol was added to rinse the magnetic beads, incubated at room temperature for 30 s, and the supernatant carefully removed. The rinse was repeated three times. The tube was kept on the magnetic stand, the lid left open and dry (not too dry, no alcohol residue at the bottom of the tube). The tube was taken out of the magnetic stand, 25 μl of sterile ultrapure water added, the magnetic beads smashed from the wall, mixed well, and incubated at room temperature for 5 min. The reaction tube was dentrifuged briefly and placed on a magnetic stand. After clarification, 20 μl of supernatant was carefully transferred to a new tube and stored at −20°C.Library was constructed as follow. TruePrep TM Index V4 for Illumina (Vazyme TD204) was used to enrich DNA and PCR amplification. The PCR products were purified with VAHTS DNA Clean Beads (Vazyme N411). At last, DNA fragments of preferentially about 300 bp in length were selected, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA)

treatment_protocol: The medium was changed every other day. The dome-shaped colonies were dissociated with Accutase (Thermo Fisher Scientific, catalog. no. A1110501) into single cells, and then passaged onto new Matrigel- or feeder-coated plates every 3 - 4 days.

tag: cell line

tag: cell type

value: ESC

tag: genotype

value: WT

tag: treatment

value: navie induced medium


title: Sample NE3 technical replicate b [2018_509b ]

country: France

description: Non dependent rat 3 technical replicate b

library_source: transcriptomic

molecule: total RNA

tag: age

tag: tissue


title: Primed-H9_ATACseq_rep3

value: Primed medium (E8)


title: Naive-H9_Cuttagseq_H3K9ac_rep1

data_processing:
Use FastQC v0.11.9 for quality control of raw sequencing readings.
Using TrimGalore v0.6.6 to remove raw readings from low-quality base and linker sequences
Clean reads of  were mapped to hg38 using Bowtie2(2.3.1) The options are: --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700
Use the sorting function of samtools v1.13 to sort aligned bam files based on chromosome coordinates
Use the genomecov function of bedtools v2.30 to summarize the sorted bam files into a bedgraph file (Quinlan et al., 2010).
Peak calling on all bedgraph files using SEACR v1.3 by selecting the top 1% of the call peak.
Assembly: hg38
Supplementary files format and content: cut&tag peak bigwig files

extract_protocol:
the sample used to perform RNA-seq, ATAC-seq, CUT&Tag-seq are prepared based on the commonly used method.
as for CUT&Tag, 20000~50000 cells per sample replicate were washed in Wash Buffer [1 mL 1 M HEPES pH 7.5 (Sigma–Aldrich, H3375), 1.5 mL 5 M NaCl (Sigma–Aldrich, S5886-1KG), 12.5 μL 2 M Spermidine (MCE, HY-B1776), Roche Complete Protease Inhibitor EDTA-Free tablet (Sigma–Aldrich, 4693132001), and bring the final volume to 50 mL with dH2O], then immobilized on 10 ul of Concanavalin A-coated beads (Bangs Laboratories, BP531). Cells were cleared on a magnetic rack, then permeabilized with cold Antibody buffer [20 mM HEPES pH 7.5, 150 mM NaCl, 2mM EDTA, 0.1% BSA, 0.5 mM Spermidine and 1× protease inhibitor cocktail containing 0.05% Digitonin (AbMole, M5020-100mg)] on ice. The cells were then incubated with anti-H3K9me3(Abcam, ab8898, 1:100 dilution), anti-H3K9ac (Abcam, ab32129, 1:100 dilution), anti-H3K27me3(Millipore, 07-449, 1:100 dilution), H3K27ac (Abcam, ab177178, 1:100 dilution), anti-CTCF (Millipore, ab128873,1:100 dilution) for 2h at RT on a shaker. The primary antibody was cleared on a magnetic rack. Goat anti-Rabbit IgG secondary antibody (Millipore, 07-449) was diluted 1:100 in Dig-wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine and 1× protease inhibitor cocktail containing 0.05% Digitonin) and incubated at RT for an hour. Cells were cleared on a magnetic rack and washed three times with 700ul of Dig-wash buffer. A 1:100 diluted of pA-Tn5 adapter complex combining adapter primers (Table S3) and pA-Tn5 according to the manufacturer’s instructions (Vazyme, S603-01) was prepared in Dig-300 Buffer [20 mM HEPES pH 7.5, 300 mM NaCl, 0.5 mM Spermidine and 1× protease inhibitor cocktail containing 0.05% Digitonin]. Cells were cleared on a magnetic rack and incubated by adding 100 ul of pA-Tn5 at RT for 1 h. Cells were washed with 700ul of Dig-300 buffer, resuspended in 300 ul of Tagmentation buffer [10 mM MgCl2 in Dig-300 Buffer], and incubated at 37 °C for 1 h. 10 ul of 0.5 M EDTA, 3 ul of 10% SDS, and 2.5 ul of 20 mg/mL Proteinase K was added to each reaction to stop the tagmentation at 37 °C overnight. DNA was purified using phenol/chloroform/isoamyl alcohol (PCI) extraction followed by chloroform extraction and precipitated with glycogen and ethanol. DNA was pelleted with a high-speed spin at 4 °C, washed, air dried for 5 min and resuspended in 25 ul of double-distilled water (ddH2O) containing 100ug/ml RNase. The DNA was then PCR amplified using TruePrep Index Kit V4 for Illumina (Vazyme, TD204), and cleaned up with VAHTS DNA Clean Beads (Vazyme, N411-01).


title: Sample NE3 technical replicate a [2018_509a ]

description: Non dependent rat 3 technical replicate a


title: ChIP_CCI1

value: CCI


title: ATAC_N2


title: ATAC_N1


title: ATAC_CCI2


title: Sample NE3 technical replicate c [2018_509c ]

description: Non dependent rat 3 technical replicate c


title: Sample NE1 technical replicate b [2018_507b ]

description: Non dependent rat 1 technical replicate b


title: Sample NE1 technical replicate d [2018_507d ]

description: Non dependent rat 1 technical replicate d


title: Sample NE2 technical replicate d [2018_508d ]

description: Non dependent rat 2 technical replicate d


title: Sample NE2 technical replicate c [2018_508c ]

description: Non dependent rat 2 technical replicate c


title: Sample NE2 technical replicate a [2018_508a ]

description: Non dependent rat 2 technical replicate a


title: DMSO (1) - control (48 h)

type: genomic

city: Oviedo

first: Rene

last: Rodriguez

state: Asturias

address: Av. Hospital Universitario s/n

country: Spain

institute: Health Research Institute of Asturias (ISPA)

hyb_protocol: The processed DNA samples were then hybridised to Infinium MethylationEPIC BeadChips following the Illumina Infinium HD Methylation Assay protocol.

scan_protocol: The arrays were scanned with iScan (Illumina) in accordance with the manufacturer's protocol.

data_processing: IDAT files were processed using the R/Bioconductor package minfi and differentially methylated probes were extracted with the R/Bioconductor package limma. Background correction was applied with the ssNOOB method. Probe signals were further corrected using the BMIQ algorithm. Sex chromosome, SNP-overlapping and multi-mapping probes were filtered out.

label: Cy3, Cy5

source_name: cell line

label_protocol: Labelling was performed automatically during the post-amplification xStain process and is achieved using Biotin and DNP labelled antibodies

growth_protocol: T-CDS17#1 chondrosarcoma cell line were growth in high glucose DMEM suplemented with 10% fetal bovine serum (FBS)

extract_protocol: Genomic DNA was extracted using the QIAmp DNA Mini Kit (Qiagen, Germany) following the manufacturing´s intructions.

treatment_protocol: T-CDS17#1 chondrosarcoma cell line was treated with 20 uM of enasidenib and DMSO (control) for 48 h

value: chondrosarcoma cells

value: IDH2 mutant

value: DMSO

tag: time


title: Sample NE2 technical replicate b [2018_508b ]

description: Non dependent rat 2 technical replicate b


title: Sample E2 technical replicate c [2018_505c ]

description: Dependent 2 technical replicate c

value: Dependent Rat (CPP-E)


title: ENASIDENIB (2) -treated (48 h)

value: ENASIDENIB 20 uM


title: Sample E3 technical replicate c [2018_506c ]

description: Dependent 3 technical replicate c

value: 8 weeks


title: Primed-H9_ATACseq_rep2


title: Sample NE1 technical replicate a [2018_507a ]

description: Non dependent rat 1 technical replicate a

value: Non dependent Rat (non CPP-E)


title: Sample E3 technical replicate a [2018_506a ]

description: Dependent 3 technical replicate a

value: 4 cocaine injections (1 per day), withdrawal 15 days, 1 cocaine injection


title: Sample NE1 technical replicate c [2018_507c ]

description: Non dependent rat 1 technical replicate c

value: Nucleus accumbens


title: Sample E2 technical replicate d [2018_505d ]

description: Dependent 2 technical replicate d


title: Sample E1 technical replicate b [2018_504b ]

description: Dependent 1 technical replicate b


title: DMSO (2) - control (48 h)


title: Sample E3 technical replicate b [2018_506b ]

description: Dependent 3 technical replicate b


title: DMSO (3) - control (48 h)


title: Sample E3 technical replicate d [2018_506d ]

description: Dependent 3 technical replicate d


title: ENASIDENIB (1) -treated (48 h)


title: Sample E2 technical replicate a [2018_505a ]

description: Dependent 2 technical replicate a


title: Sample E2 technical replicate b [2018_505b ]

description: Dependent 2 technical replicate b


title: Sample E1 technical replicate d [2018_504d ]

description: Dependent 1 technical replicate d


title: Sample E1 technical replicate c [2018_504c ]

description: Dependent 1 technical replicate c


title: Sample E1 technical replicate a [2018_504a ]

description: Dependent 1 technical replicate a


title: Sample S3 technical replicate d [2018_503d ]

description: Saline rat 3 technical replicate d

value: Saline Rat

value: 4 physiological serum injections, withdrawal 15 days, 1 physiological serum injection


title: Sample S2 technical replicate b [2018_502b ]

description: Saline rat 2 technical replicate b

value: Sprague-Dawley


title: ENASIDENIB (3) -treated (48 h)


title: Sample S3 technical replicate c [2018_503c ]

description: Saline rat 3 technical replicate c


title: Sample S2 technical replicate d [2018_502d ]

description: Saline rat 2 technical replicate d


title: Sample S2 technical replicate a [2018_502a ]

description: Saline rat 2 technical replicate a


title: Sample S1 technical replicate b [2018_501b ]

description: Saline rat 1 technical replicate b


title: Sample NV1 technical replicate d [2016_239d ]

description:
2016_239d
Non Vulnerable rat 1 technical replicate d

data_processing:
Illumina bcl2fastq 2.17.1.14 software used for basecalling.
RNA-Seq data analysis was done using the Eoulsan software version 2.0-beta4. Before mapping, reads ≤40 bases were removed, and reads with quality mean ≤30 were discarded. Reads were then aligned against the Rattus norvegicus genome (rnor6 genome assembly from Ensembl version 84) using the STAR mapper (version 2.4.0k, with --outSAMunmapped Within parameter). Alignments from reads matching more than once on the genome were removed. Rattus norvegicus GFF3 genome annotation from Ensembl version84. All overlapping regions between alignments and referenced exons were counted with HTSeq-count 0.5.3.
Genome_build: rnor6 version Ensembl 84
Supplementary_files_format_and_content: *.tsv: Tab-delimited text files include transcripts counting for each Sample.

extract_protocol:
Total RNA was extracted from bilateral nucleus accumbens and caudate putamen with RNeasy Qiagen mini kit according to the lipid tissue protocol of the manufacturer (Qiagen, Courtaboeuf, France).
Messenger (polyA+) RNAs were purified from 500 ng of total RNA using oligo(dT). Libraries were prepared using the strand specific RNA-Seq library preparation TruSeq Stranded mRNA kit (Illumina).

treatment_protocol: On the morning of the first conditioning day, animals were treated with saline and placed in one of the conditioning environments individually for 20 min. After 6 h, the animals were given cocaine (20 mg/kg, i.p.) in the opposite compartment and this sequence alternated during the next 3 days. Control animals received saline twice a day and were submitted to the same alternated sequence between the 2 compartments. Testing phase was conducted the day after the last conditioning session and was identical to the preconditioning phase.

value: Non Vulnerable

value: 4 cocaine injections


title: Sample NV3 technical replicate a [2016_241a ]

description:
2016_241a
Non Vulnerable rat 3 technical replicate a


title: Sample S1 technical replicate a [2018_501a ]

description: Saline rat 1 technical replicate a


title: Sample NV3 technical replicate d [2016_241d]

description:
2016_241d
Non Vulnerable rat 3 technical replicate d


title: Sample S1 technical replicate c [2018_501c ]

description: Saline rat 1 technical replicate c


title: Sample NV2 technical replicate c [2016_240c ]

description:
2016_240c
Non Vulnerable rat 2 technical replicate c


title: Sample NV3 technical replicate b [2016_241b ]

description:
2016_241b
Non Vulnerable rat 3 technical replicate b


title: Sample NV1 technical replicate a [2016_239a ]

description:
2016_239a
Non Vulnerable rat 1 technical replicate a


title: Sample NV3 technical replicate c [2016_241c ]

description:
2016_241c
Non Vulnerable rat 3 technical replicate c


title: Sample NV1 technical replicate c [2016_239c ]

description:
2016_239c
Non Vulnerable rat 1 technical replicate c


title: Sample S3 technical replicate d [2016_238d ]

description:
2016_238d
Saline rat 3 technical replicate d

value: 4 physiological serum injections


title: Sample NV1 technical replicate b [2016_239b ]

description:
2016_239b
Non Vulnerable rat 1 technical replicate b


title: Sample NV2 technical replicate b [2016_240b ]

description:
2016_240b
Non Vulnerable rat 2 technical replicate b


title: Sample S3 technical replicate c [2016_238c ]

description:
2016_238c
Saline rat 3 technical replicate c


title: Sample S3 technical replicate b [2016_238b ]

description:
2016_238b
Saline rat 3 technical replicate b


title: Sample NV2 technical replicate a [2016_240a ]

description:
2016_240a
Non Vulnerable rat 2 technical replicate a


title: Sample S2 technical replicate c [2018_502c ]

description: Saline rat 2 technical replicate c


title: Sample S2 technical replicate d [2016_237d ]

description:
2016_237d
Saline rat 2 technical replicate d


title: Sample S3 technical replicate a [2018_503a ]

description: Saline rat 3 technical replicate a


title: Sample S3 technical replicate b [2018_503b ]

description: Saline rat 3 technical replicate b


title: Sample S2 technical replicate c [2016_237c ]

description:
2016_237c
Saline rat 2 technical replicate c


title: Sample S1 technical replicate d [2018_501d ]

description: Saline rat 1 technical replicate d


title: Sample S2 technical replicate b [2016_237b ]

description:
2016_237b
Saline rat 2 technical replicate b


title: Sample S2 technical replicate a [2016_237a ]

description:
2016_237a
Saline rat 2 technical replicate a


title: Sample NV2 technical replicate d [2016_240d ]

description:
2016_240d
Non Vulnerable rat 2 technical replicate d


title: Sample S1 technical replicate c [2016_236c ]

description:
2016_236c
Saline rat 1 technical replicate c


title: Sample S1 technical replicate d [2016_236d ]

description:
2016_236d
Saline rat 1 technical replicate d


title: Sample S1 technical replicate a [2016_236a ]

description:
2016_236a
Saline rat 1 technical replicate a


title: Sample V3 technical replicate b [2016_235b ]

description:
2016_235b
Vulnerable rat 3 technical replicate b

value: Vulnerable


title: Sample V3 technical replicate d [2016_235d ]

description:
2016_235d
Vulnerable rat 3 technical replicate d


title: Sample V2 technical replicate d [2016_234d ]

description:
2016_234d
Vulnerable rat 2 technical replicate d


title: Sample V3 technical replicate a [2016_235a ]

description:
2016_235a
Vulnerable rat 3 technical replicate a


title: Sample V2 technical replicate b [2016_234b ]

description:
2016_234b
Vulnerable rat 2 technical replicate b


title: Sample V2 technical replicate a [2016_234a ]

description:
2016_234a
Vulnerable rat 2 technical replicate a


title: Sample V1 technical replicate c [2016_233c ]

description:
2016_233c
Vulnerable rat 1 technical replicate c


title: Sample V1 technical replicate d [2016_233d ]

description:
2016_233d
Vulnerable rat 1 technical replicate d


title: Sample V1 technical replicate a [2016_233a ]

description:
2016_233a
Vulnerable rat 1 technical replicate a


title: Sample V1 technical replicate b [2016_233b ]

description:
2016_233b
Vulnerable rat 1 technical replicate b


title: Sample S3 technical replicate a [2016_238a ]

description:
2016_238a
Saline rat 3 technical replicate a


title: WT, P21, VNO, replicate 1, scRNAseq

city: Albany

first: Paolo

middle: Emanuele

last: Forni

state: NY

address: 1400 Washington Avenue

department: Biology

institute: University at Albany

description:
Sample 1  - WT_P21_VNO
10x genomics; single cell transcriptome

library_source: transcriptomic single cell

data_processing:
Our lab used cellranger count (version4)to perform alignment, filtering, barcode counting, and UMI counting on the fastq files of 6 separate libraries.
We used filtered processed files as input and Seurat 4.3.0 package in R studio to do quality control and downstream cell clustering analysis. Cells with mitochondrial read rate >5% and expressed < 200 genes were  filtered out from our data set.
Assembly: mm10
Supplementary files format and content: tsv and mtx files containing cell barcodes and gene count matrix

organism: Mus musculus

source_name: Whole Postnatal VNO

extract_protocol:
2 VNOs that were harvested at 21 days postnatal were isolated and dissociated into single-cell suspension using neural isolation enzyme/papain (NIE/Papain in Neurobasal Medium with 0.5mg/mL Collagenase A, 1.5mM L-cysteine and 100U/mL DNAse I) incubated at 37ºC. The dissociated cells were then washed with HBSS and reconstituted in cell freezing medium (90% FBS, 10% DMSO). Cells were frozen from room temperature to -80°C at a -1°C/min freeze rate. The single cell suspension was sent to the Center of Functional Genomics (CFG) , generating datasets and high-throughput single-cell gene expression profiling using the 10x Genomics Chromium Platform.
Single cell library preparation and sequencing were conducted by the Center of Functional Genomics (CFG) (https://www.albany.edu/genomics/ngs.html, Albany, NY) and Singulomics Corporation (https://singulomics.com/, Bronx, NY). Cryopreserved, viable single cell suspensions were thawed, washed, resuspended in cell culture media with 0.04% BSA, and counted. Viable cell suspensions were then loaded into the Chromium Controller (10x Genomics, Pleasanton, CA) to generate gel beads-in-emulsion (GEM) with each GEM containing a single cell as well as barcoded oligonucleotides. We targeted 10,000 cells to be captured per sample for a total of 5 samples. Next, the GEMs were placed in the SimpliAmp 96-well Thermal Cycler (Thermo Fisher Scentific, Wilmington, DE) and reverse transcription was performed in each GEM (GEM-RT). After the reaction, the complementary cDNA was amplified and cleaned using Silane DynaBeads (10X Genomics, Pleasanton, CA) and the SPRIselect Reagent kit (Beckman Coulter, Indianapolis, IN). Amplified full-length cDNAs from poly-adenylated mRNA were then used to generate 3ʹ Gene Expression library (Chromium Next GEM 3’ Single Cell Reagent kits v3.1, dual index), following the manufacturer’s instructions (10x Genomics, Pleasanton, CA). Amplified cDNAs and the libraries were measured by Qubit dsDNA HS assay (Thermo Fisher Scientific, Wilmington, DE) and quality assessed by BioAnalyzer (Agilent Technologies, Santa Clara, CA).

value: Whole Postnatal VNO

value: Postnatal day 21


title: 2DG_aPDL1

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
Preprocessing of scRNA-seq data was done using CellRanger Suite (v3.1.0, https://support.10xgenomics.com) with refdata-cellranger-mm10-3.0.0 transcriptome as a reference
Assembly: mm10
Supplementary files format and content: standard cellranger output

molecule: polyA RNA

source_name: lymph node

extract_protocol:
Single cell droplets were generated using the Chromium next gem single cell 3' kit v3.1 (10x Genomics)
cDNA synthesis and amplification, library preparation and indexing were done using the 10x Genomics Library Preparation kit (10x Genomics)
10x genomics single cell RNA-seq

value: lymph node

value: Treatment, 2-Deoxy-D-glucose (2DG) _ aPDL1


title: Sample S1 technical replicate b [2016_236b ]

description:
2016_236b
Saline rat 1 technical replicate b


title: 2FF_aPDL1

value: Treatment, 2F-Peracetyl-Fucose (2FF) _ aPDL1


title: aPDL1

value: Treatment, aPDL1


title: 2DG

value: Treatment, 2-Deoxy-D-glucose (2DG)


title: Sample V3 technical replicate c [2016_235c ]

description:
2016_235c
Vulnerable rat 3 technical replicate c

value: 8 weeks


title: Sample V2 technical replicate c [2016_234c ]

description:
2016_234c
Vulnerable rat 2 technical replicate c


title: V5-GFP

type: protein

city: Mainz

first: Emil

last: Karaulanov

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology

description: Array ID: 0000088750

hyb_protocol: The protein microrrays (ProtoArray v5.1, Invitrogen) were incubated for 1 h at 4 °C in Blocking Buffer I (PBS, 0.1 % Tween-20, 1 % BSA). The arrays were washed three times at 4 °C in Blocking Buffer II (TBS supplemented with 0.5 % Triton X-100, 1 mM β-mercaptoethanol, 5 % Glycerol, 2 mM MgCl2, 1 % BSA), placed at room temperature and incubated for 1 h with 600 µl of ~ 0.5 µM of immunopurified V5-DDX39, V5-DDX56 or V5-GFP. The arrays were then washed twice in Blocking Buffer II at 4 °C and incubated with 1:1000 α-V5 tag monoclonal antibody (Thermo Fisher, R960-25) for 2 h at 4 °C. After three additional washes in Blocking Buffer II, the microarrays were incubated with anti-mouse secondary antibody Alexa Fluor 680 (Thermo Fisher) for 1 h at 4 °C and washed again three times. Finally, the arrays were rinsed 3 times in water and dried by spinning at 300 g for 5 min.

scan_protocol: The microarrays were scanned in an Odyssey scanner (LI-COR) using the following parameters: Channel 700, Grid = 8x3, 21.17, Intensity = 5, Offset = 0.

data_processing: ProtoArray signal data was determined with GenePix Pro v5.0.0.49 (Molecular Devices) and then processed following the manufacturer's recommendations using ProtoArray Prospector v5.2 (Invitrogen) with default settings.

label: Alexa Fluor 680

molecule: protein

source_name: V5-tagged GFP protein purified from HEK293T cells

label_protocol: Anti-mouse secondary antibody Alexa Fluor 680 (Thermo Fisher).

growth_protocol: HEK293T cells were grown in 15 cm2 dishes at 37°C with 5% CO2 in DMEM medium supplemented with 10% fetal calf serum, 2 mM L-Glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin.

extract_protocol: Cells were lysed in 50 mM HEPES-KOH, pH 7.7, 1 mM MgCl2, 300 mM NaCl, 0.8 % Triton X-100, 5 mM NaF, 0.1 % Sodium deoxycholate, 2 mM β-mercaptoethanol, 1x protease inhibitor mixture tablet (Roche). Cleared lysates were immunoprecipitated using anti-V5 agarose beads (Roche) at 4 °C for 3 h. Beads were washed in TBS-T supplemented with 1 mM MgCl2, 2 mM β-mercaptoethanol and 1x protease inhibitor mixture tablet (Roche), followed by elution in the same buffer using 200 µg/ml V5 peptide.

treatment_protocol: HEK293T cells were transfected with 15 µg of the respective expression constructs using Calcium phosphate.

tag: recombinant protein expression

value: Negative control


title: ctrl

value: control


title: V5-DDX56

description: Array ID: 0000088692

source_name: V5-tagged DDX56 protein purified from HEK293T cells


title: None Cartilage Dahup None Sept_2021 [Dahup149JZ_S21_L002]

city: Cambridge

first: Alberto

last: Rosello-Diez

address: Physiology building. Downing St.

department: Physiology, Development and Neuroscience

country: United Kingdom

institute: University of Cambridge

data_processing:
umi-tools (v 0.5.5) and bbmap (v. 38.81) were used to demultiplex the samples based on barcodes from the multiplexed data
Read alignment via STAR (v 2.7.9a) --outFilterMultimapNmax 20 --outFilterMismatchNmax 5 --outFilterScoreMinOverLread 0 --outFilterScoreMinOverLread 0
featureCounts() function from the R/Bioconductor package Rsubread (v 2.10.4) was used to generate the gene count matrix for the aligned reads with following parameters; allowMultiOverlap = TRUE, minOverlap = 1, fracOverlap = 0, fracOverlapFeature = 0
Assembly: mm39 (GRCm39)
Supplementary files format and content: .tab with raw gene counts

source_name: Hind limb cartilage

extract_protocol: Total RNA was extracted using the Monarch Total RNA Miniprep Kit (New England Biolabs), following manufacturer instructions. From this, RNA-Seq of messenger RNAs (mRNAs) was performed using a custom in-house multiplex method, which allowed us to sequence up to 24 different samples in the same sequencing lane. Briefly, samples were given a unique i7 index (together with UMI) during individual polyA-priming and first-strand synthesis, which also added a template-switch sequence to the 5’ end. Samples were then pooled and amplified using P7 and an oligo which binds the template-switch sequence. Final library construction was completed by tagmentation and addition of P5 (with i5 index) by PCR.

value: Hind limb cartilage

tag: condition

tag: Stage

value: Normalisation


title: None Cartilage Dahup None Sept_2021 [Dahup149JZ_S21_L001]


title: 2FF

value: Treatment, 2F-Peracetyl-Fucose (2FF)


title: None Cartilage Dahup None Sept_2021 [Dahup150JZ_S22_L002]


title: Right Cartilage 489 Exp Sept_2021 [489R_S10_L002]

value: Exp


title: Ventral tissue at E12.5, biological rep 4

type: RNA

city: Paris

first: Charles

last: Durand

address: 9, quai saint-Bernard

department: Laboratory of Developmental Biology

institute: Sorbonne University

description: Gene expression data from ventral aortic  tissue at E12.5

hyb_protocol: After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® Mouse Gene 2.0 ST (Affymetrix) at 45°C for 17 hours.

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G.

data_processing: The scanned images are then analyzed with Expression Console software (Affymetrix) to obtain raw data (cel files) and metrics for Quality Controls. The observations of some of these metrics and the study of the distribution of raw data show no outlier experiment. RMA normalization is performed using R with Version 21 of Entrezgene CDF brain array.

label: biotin

source_name: Ventral tissue at E12.5

label_protocol: Between 200 and 1000 pg of total RNA was reverse transcribed following the Ovation Pico V2 system (Nugen) and the resulting double strand cDNA was used for amplification based on SPIA technology. After purification according to Nugen protocol, sens target DNA was fragmented and biotin labelled using Encore Biotin Module kit (Nugen).

growth_protocol: Embryos were collected from pregnant C57B/6 mice at embryonic day 12.5.

extract_protocol: Microdissected tissues were collected on appropriate caps and then proceeded for RNA extraction using Acturus Picopure RNA isolation kit. RNAs were eluted in a final volume of 13 μl and their concentrations and integrity quantified on a bioanalyzer (Agilent).

treatment_protocol: Unfixed embryos were embedded in OCT medium in presence of isopentane cooled at -65°C. Twenty μm cryostat sections were then prepared and stained before laser micro-dissection. The dorsal tissue localized in between the notochord and the roof of the aorta and the ventral tissue underneath the aorta were isolated from the same embryos.

value: ventral aortic tissue

tag: isolation

value: Tissue isolated by laser microdissection

tag: developmental stage


title: Ventral tissue at E12.5, biological rep 1


title: Ventral tissue at E12.5, biological rep 2


title: Right Cartilage 489 Exp Sept_2021 [489R_S10_L001]


title: Dorsal tissue at E12.5, biological rep 2

description: Gene expression data from dorsall aortic  tissue at E12.5

source_name: Dorsal tissue at E12.5

value: dorsal aortic tissue


title: Dorsal tissue at E12.5, biological rep 4


title: Ventral tissue at E10.5, biological rep 4

description: Gene expression data from ventral aortic  tissue at E10.5

source_name: Ventral tissue at E10.5

growth_protocol: Embryos were collected from pregnant C57B/6 mice at embryonic day 10.5.


title: Left Cartilage 489 Exp Sept_2021 [489L_S9_L001]


title: Dorsal tissue at E12.5, biological rep 1


title: Dorsal tissue at E12.5, biological rep 3


title: Left Cartilage 489 Exp Sept_2021 [489L_S9_L002]


title: Dorsal tissue at E10.5, biological rep 4

description: Gene expression data from dorsall aortic  tissue at E10.5

source_name: Dorsal tissue at E10.5


title: Ventral tissue at E10.5, biological rep 2


title: None Cartilage Dahup None Sept_2021 [Dahup150JZ_S22_L001]


title: recovCVS608(MTA-1_0)

city: Duesseldorf

first: Birgit

last: Knebel

address: Auf'm Hennekamp 65

department: Cinical Biochemistry and Pathobiochemistry

institute: German Diabetes Center

description: RNA expression value derived from Expression Console software

hyb_protocol: Amplified cDNA was hybridized on Affymetrix Mouse MTA arrays (Affymetrix)

scan_protocol: Detection of probe intensities was performed using a GeneChip scanner 3000 7G (GDAS 1.4 package, Affymetrix).

data_processing: The data were analyzed with Affymetrix Expression  Console v4.0 using default analysis settings for combined RMA analyses dabg .CHP files.

label_protocol: 150 ng total RNAwas amplified using the  WT Expression Kit and the WT Terminal Labeling Kit (Thermofisher, Darmstadt, Germany).

growth_protocol: C57/Bl6 male mice were bred and maintained in a regular 12h light/dark cycle (22°C ± 1°C, 50% ± 5% humidity). All mice were group housed (max. 5 mice per cage) with ad libitum access to standard chow (58% carbohydrates, 9% fat, 33% protein, R/M-H Extrudat, ssniff Spezialdiäten GmbH, Soest, Germany) and tap water. Animal protocols were approved by the Landesamt für Natur, Umwelt und Verbraucherschutz (LANUV), NRW, Germany (81-02.04.2017.A421) and performed according to the ‘Principle of laboratory animal care’ (NIH publication No. 85-23, revised 1996) and the German law on the protection of animals.

extract_protocol: Total RNA extraction from liver tissue was made with RNeasy mini kit (Qiagen, Hilden, Germany) including DNAse digestion according to the manufacturer's instructions. RNA quality was evaluated using an Agilent 2100 Bioanalyzer and only high quality RNA (RIN > 8) was used for microarray analysis.

treatment_protocol: The mice were stressed with our Cvs protocol as previously described (doi:https://doi.org/10.1016/j.molmet.2018.06.012). In brief,  the  Cvs protocoll consists of five different stressors (warm swim, cold exposure, shaking, restraint and overnight isolation) applied in a random manner 2 per day for 15 days. the first cohort was analysed immediately after the stress protocoll, a recovery cohor was analysed 3 month later. Age matched unstressed animals were used as control pe cohort.

value: Male

value: Cvs

value: liver


title: Right Cartilage 488 Ctrl Sept_2021 [488R_S8_L002]

value: Ctrl


title: Ventral tissue at E12.5, biological rep 3


title: recovCVS598(MTA-1_0)


title: Left Cartilage 488 Ctrl Sept_2021 [488L_S7_L001]


title: Dorsal tissue at E10.5, biological rep 2


title: Dorsal tissue at E10.5, biological rep 3


title: Right Cartilage 487 Exp Sept_2021 [487R_S6_L002]


title: Right Cartilage 488 Ctrl Sept_2021 [488R_S8_L001]


title: recovCtrl533(MTA-1_0)


title: acuteCVS270(MTA-1_0)


title: Ventral tissue at E10.5, biological rep 1


title: Right Cartilage 487 Exp Sept_2021 [487R_S6_L001]


title: Left Cartilage 487 Exp Sept_2021 [487L_S5_L001]


title: acuteCVS269(MTA-1_0)


title: acuteCVS267(MTA-1_0)


title: Right Cartilage 485 Ctrl Sept_2021 [485R_S4_L002]


title: Left Cartilage 485 Ctrl Sept_2021 [485L_S3_L001]


title: acuteCVS268(MTA-1_0)


title: acuteCVS266(MTA-1_0)


title: Ventral tissue at E10.5, biological rep 3


title: Left Cartilage 485 Ctrl Sept_2021 [485L_S3_L002]


title: Left Cartilage 487 Exp Sept_2021 [487L_S5_L002]


title: Left Cartilage 488 Ctrl Sept_2021 [488L_S7_L002]


title: Right Cartilage 484 Exp Sept_2021 [484R_S2_L001]


title: recovCVS606(MTA-1_0)


title: acuteCtrl299(MTA-1_0)


title: recovCtrl652r(MTA-1_0)


title: acuteCtrl300(MTA-1_0)


title: Right Cartilage 485 Ctrl Sept_2021 [485R_S4_L001]


title: Right Cartilage 484 Exp Sept_2021 [484R_S2_L002]


title: acuteCtrl289(MTA-1_0)


title: Left Cartilage 484 Exp Sept_2021 [484L_S1_L001]


title: Dorsal tissue at E10.5, biological rep 1


title: acuteCtrl283(MTA-1_0)


title: recovCtrl651(MTA-1_0)


title: Left Cartilage 484 Exp Sept_2021 [484L_S1_L002]


title: Right Cartilage 482 Ctrl Sept_2021 [482R_S20_L002]


title: Right Cartilage 482 Ctrl Sept_2021 [482R_S20_L001]


title: acuteCtrl284(MTA-1_0)


title: Left Cartilage 482 Ctrl Sept_2021 [482L_S19_L001]


title: Left Cartilage 482 Ctrl Sept_2021 [482L_S19_L002]


title: Right Cartilage 481 Exp Sept_2021 [481R_S18_L002]


title: TSk-2

city: Lanzhou

first: jinqiang

last: huang

address: Yintanlu Stress

institute: Gansu Agricultural University

data_processing:
Reads obtained from the sequencing machines included raw reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered according to the following rules: 1) Removing reads containing adapters; 2) Removing reads consisting of all A bases; 3) Removing reads containing more than 10% of unknown nucleotides (N); 4) Removing low quality reads containing more than 50% of low quality (Q-value≤20) bases
Short reads alignment tool Bowtie2 (2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads were then removed. The remaining reads were further used in assembly and analysis of transcriptome.
The rRNA removed reads of each sample were then mapped to reference genome by TopHat2 (version 2.1.1), respectively. The alignment parameters were as follows: 1) Maximum read mismatch is 2 2) Disables the coverage based search for junctions 3) The distance between mate-pair reads is 50bp 4) The standard deviation for the distribution on inner distance between mate-pair reads is 80bp
After aligned with reference genome, unmapped reads (or mapped very poorly) were then re-aligned with Bowtie2, the enriched unmapped reads were split into smaller segments which were then used to find potential splice sites. The section and the section position of these short segments were predicted as well. A set of splice sites was built with initial unmapped reads by TopHat2 without relying on the known genes annotation. Not only be used for identifying expressed genes and their quantitative expression, the sequence alignment will also be helpful to find alternative splicing and new transcripts.
Assembly: Oncorhynchus mykiss USDA_OmykA_1.1
Supplementary files format and content: tab-delimited text files include counts, FPKM values, TPM values for each Sample

organism: Oncorhynchus mykiss

source_name: skin tissues

extract_protocol:
The samples were collected immediately, then flash-frozen in liquid nitrogen,and total RNA was extracted using Trizol reagent.
RNA/miRNA libraries were prepared for sequencing using standard Illumina protocols

value: skin tissues

value: wild-type

tag: infection

value: IHNV


title: CSk-3


title: TSk-1


title: CSk-2


title: CSk-1


title: Left Cartilage 481 Exp Sept_2021 [481L_S17_L002]


title: Right Cartilage 481 Exp Sept_2021 [481R_S18_L001]


title: Left Cartilage 481 Exp Sept_2021 [481L_S17_L001]


title: Left Cartilage 401 Exp Sept_2021 [401L_S15_L002]


title: Right Cartilage 401 Exp Sept_2021 [401R_S16_L002]


title: Right Cartilage 401 Exp Sept_2021 [401R_S16_L001]


title: Right Cartilage 400 Ctrl Sept_2021 [400R_S14_L002]


title: Right Cartilage 400 Ctrl Sept_2021 [400R_S14_L001]


title: TSk-3


title: Left Cartilage 401 Exp Sept_2021 [401L_S15_L001]


title: Left Cartilage 400 Ctrl Sept_2021 [400L_S13_L001]


title: R1-NHP-55-N-H3K9me3

city: STANFORD

first: Katja

last: Pekrun

state: CA

address: 269 Campus Drive

department: Pediatrics & Genetics

institute: Stanford School of Medicine

data_processing:
Reads were trimmed with Trimmomatic-0.39 program for classical Illumina adapters. Aligned using Bowtie2 version 2.2.5 (https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.5/) with options: --local --very-sensitive-local --nounal --no-mixed --no-discordant --phred33 -I 10 -X 700; mapping was performed using the mm10 build of the mouse genome, merged with viral genome sequence (gAAV).
PCR duplicates were eliminated with “MarkDuplicates” command of Picard version 2.23 (https://broadinstitute.github.io/picard/index.html).
Tracks were made as bedgraph files of normalized counts, using deeptools 3.3 (https://deeptools.readthedocs.io/en/develop/content/list_of_tools.html) bamCoverage with options: --binSize 1, --normalizeUsing CPM; track plots were made with R package Gviz 4.1. Coverage was calculated as SUM[(normalized count*(end-start position+1))/gAAV size] for each dataset. Importantly, ITR regions were removed from the calculation, as their coverage is overrepresented in all samples, perhaps due to recognition of ITRs from ssDNA.
Assembly: Mmul_1
Supplementary files format and content: Bedgraph

organism: Macaca mulatta

source_name: liver

extract_protocol:
Macaques were euthanized 3.5 months after rAAV injection and liver tissue from 4 lobes was flash-frozen. Frozen liver tissue was pulverized on dry ice and aliquoted. Equal amounts of pulverized liver tissue from each lobe were combined and ~100 mg of this pool were homogenized in RINO 1.5-ml Screw-Cap tubes filled with stainless steel beads and 1mL of NE buffer using a bead homogenizer (Next Advance Bullet Blender Storm - BBY24M) at speed 8 for 6 minutes. The homogenate was transferred into to a 50mL tube with 12mL of NE buffer and incubated on ice for 10 min. Nuclei were pelleted by a 5 min centrifugation at 600g, the supernatant was decanted, and the pellet was resuspended in 1mL of NE buffer. After passing nuclei through a 0.45um cell strainer quantitation was performed after Trypan Blue staining using an automated cell counter (Countess, Thermo Fisher) and diluted accordingly. 1e5 nuclei per target protein were used for Cut&Tag.
Nuclei were mixed with activated Concanavalin A beads. After successive incubations with primary antibody (overnight) and secondary antibody (for 30 min) in antibody and Digitonin150 buffer respectively, the beads were washed with Digitonin150 buffer and resuspended in Digitonin300 buffer with 2.5uL of pA(G)-Tn5 for 1 hr and washed with the same buffer. Incubations were performed at room temperature in low-retention PCR strip tubes (Epicypher). Tagmentation was performed for 1 hr at 37C in Tagmentation buffer that provides MgCl2. Beads were washed with TAPS buffer and DNA material was released by adding SDS Release Buffer and incubating at 58C for 1hr. Quenching of SDS was performed by adding SDS Quench buffer and PCR was performed directly on this material. Universal P5 and indexed P7 primer solutions were used (see Supplemental Table 3 for sequences), and 17 cycles of PCR were performed. Clean-up was performed with AMPure beads, eluted in 15uL 0.1x TE buffer. Qubit and Bioanalyzer were used to verify library qualities before pooling samples for sequencing. The barcoded libraries were mixed to achieve equimolar representation aiming for a 10nM final concentration.
Cut & Tag. Sequencing of the same library was performed twice (R1, R2), once with Illumina HiSeq 4000 and once with Illumina NovaSeq SP100, 150 cycles total per lane, 2x75 paired-end reads, depth of >15M reads per sample.

treatment_protocol: Rhesus macaques were intravenously infused with rAAV packaged using different capsids. The rAAV vector expressed CpG depleted, codon-optimized huFIX under control of a liver-specific promoter.


title: R1-NHP-55-N-H3K4me3


title: R1-NHP-57-N-H3K27ac


title: R1-NHP-55-N-H3K27ac


title: R1-NHP-55-N-H3K27me3


title: R1-NHP-57-N-H3K27me3


title: R1-NHP-57-N-H3K9me3


title: R1-NHP-57-N-H3K4me3


title: Left Cartilage 400 Ctrl Sept_2021 [400L_S13_L002]


title: R1-NHP-42-N-H3K4me3


title: R1-NHP-42-N-H3K9me3


title: R1-NHP-42-N-H3K27me3


title: R1-NHP-13-N-H3K9me3


title: Left Cartilage 399 Exp Sept_2021 [399L_S11_L001]


title: R1-NHP-42-N-H3K27ac


title: R1-NHP-13-N-H3K27me3


title: None Cartilage Dahup None Nov_2021 [Dahup149_S12_L001]


title: Left Cartilage 399 Exp Sept_2021 [399L_S11_L002]


title: Right Cartilage 680 Exp Nov_2021 [680R_S13_L001]


title: None Cartilage Dahup None Nov_2021 [Dahup150_S24_L001]


title: R1-NHP-13-N-H3K4me3


title: R1-NHP-04-N-H3K9me3


title: R1-NHP-13-N-H3K27ac


title: Left Cartilage 680 Exp Nov_2021 [680L_S11_L001]


title: R1-NHP-04-N-H3K4me3


title: R1-NHP-04-N-H3K27me3


title: Right Cartilage 677 Ctrl Nov_2021 [677R_S23_L001]


title: Left Cartilage 677 Ctrl Nov_2021 [677L_S22_L001]


title: R1-NHP-04-N-H3K27ac


title: Right Cartilage 675 Ctrl Nov_2021 [675R_S19_L001]


title: R1-NHP-02-N-H3K9me3


title: Right Cartilage 399 Exp Sept_2021 [399R_S12_L001]


title: Right Cartilage 399 Exp Sept_2021 [399R_S12_L002]


title: Left Cartilage 675 Ctrl Nov_2021 [675L_S18_L001]


title: Right Cartilage 676 Ctrl Nov_2021 [676R_S21_L001]


title: Left Cartilage 676 Ctrl Nov_2021 [676L_S20_L001]


title: R1-NHP-02-N-H3K27me3


title: Right Cartilage 674 Exp Nov_2021 [674R_S17_L001]


title: R1-NHP-02-N-H3K27ac


title: R1-NHP-02-N-H3K4me3


title: Right Cartilage 673 Exp Nov_2021 [673R_S15_L001]


title: Left Cartilage 673 Exp Nov_2021 [673L_S14_L001]


title: Right Cartilage 480 Exp Nov_2021 [480R_S10_L001]


title: Left Cartilage 480 Exp Nov_2021 [480L_S9_L001]


title: RC162DF, 541-15, replicate2

city: New York

first: Ming-Ting

middle: Kessler

last: Tsai

address: 408 E 69th Street Z1619

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
The output data (FASTQ files) were trimmed and filtered using CutAdapt (cutadapt-1.6). Adapters were trimmed with minimum overlap of 10 bases and reads of less than half original read length were filtered out.
Filtered reads were mapped to the target genome UCSC HG19 using the STAR aligner (STAR-2.5.0a) that maps reads genomically and resolves reads across splice junctions.
After mapping we post process the output SAM files using the PICARD tools to add read groups, AddOrReplaceReadGroups which in additional sort the file and coverts it to the compressed BAM format.
Expression count matrix was computed using HTSeq (HTSeq-0.5.3.) Parameters set were: -m intersection-strict -s reverse -t exon.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each samples

source_name: Rectum

growth_protocol: UD monolayers were maintained in hW-CMGF+ medium and DF monolayers were maintained in differentiation medium for 5 days in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA were harvested using Qiagen RNeasy Mini Kit with DNase treatment according to manufacturer’s protocols.
285-500 ng of total RNA with RIN values of 8.5-10 were underwent polyA selection and library preparation using Illumina TruSeq Stranded mRNA LT Kit according to manufacturer’s instructions.

treatment_protocol: Medium were changed to CMGF- with 10%FBS before treatment. Both UD and DF monolayers were left untreated (NT) or colonized with AIEC 541-15 or non-AIEC T75 at MOI of 10, 37°C for 4 hours.

value: Rectum

value: Organoid derived Monolayer

value: Differentiated


title: Right Cartilage 479 Ctrl Nov_2021 [479R_S8_L001]

value: Hind limb cartilage


title: Left Cartilage 479 Ctrl Nov_2021 [479L_S7_L001]


title: Right Cartilage 474 Exp Nov_2021 [474R_S6_L001]


title: Left Cartilage 474 Exp Nov_2021 [474L_S5_L001]


title: ASC161DF, 541-15, replicate2

source_name: Ascending colon

value: Ascending colon


title: RC162DF, 541-15, replicate1


title: ASC161DF, 541-15, replicate1


title: ASC103DF, 541-15, replicate2


title: Right Cartilage 473 Ctrl Nov_2021 [473R_S4_L001]


title: Left Cartilage 674 Exp Nov_2021 [674L_S16_L001]


title: ASC103DF, 541-15, replicate1


title: RC162DF, T75, replicate1

value: non-AIEC T75


title: Right Cartilage 478 Exp Nov_2021 [478R_S2_L001]

value: Exp


title: ASC161DF, T75, replicate2


title: RC162DF, T75, replicate2


title: WT, replicate 4, scRNAseq

description: 10x genomics

source_name: Whole Embryonic Nose

extract_protocol:
5 embryonic noses at embryonic day 14.5 CD1 IGS mice and 1 embryonic nose at embryonic day 14.5 ProKR2iCre/R26tdTomato were isolated and dissociated into single-cell suspension using neural isolation enzyme/papain (NIE/Papain in Neurobasal Medium with 0.5mg/mL Collagenase A, 1.5mM L-cysteine and 100U/mL DNAse I) incubated at 37ºC. The dissociated cells were then washed with HBSS and reconstituted in cell freezing medium (90% FBS, 10% DMSO). Cells were frozen from room temperature to -80ºC at a -1°C/min freeze rate.
The single cell suspension of the ProKR2iCre/R26tdTomato was sent to SingulOmics to perform FACS, generating sorted and unsorted datasets and high-throughput single-cell gene expression profiling using the 10x Genomics Chromium Platform.
Single cell library preparation and sequencing were conducted by the Center of Functional Genomics (CFG) (https://www.albany.edu/genomics/ngs.html, Albany, NY) and Singulomics Corporation (https://singulomics.com/, Bronx, NY). Cryopreserved, viable single cell suspensions were thawed, washed, resuspended in cell culture media with 0.04% BSA, and counted. Viable cell suspensions were then loaded into the Chromium Controller (10x Genomics, Pleasanton, CA) to generate gel beads-in-emulsion (GEM) with each GEM containing a single cell as well as barcoded oligonucleotides. We targeted 10,000 cells to be captured per sample for a total of 5 samples. Next, the GEMs were placed in the SimpliAmp 96-well Thermal Cycler (Thermo Fisher Scentific, Wilmington, DE) and reverse transcription was performed in each GEM (GEM-RT). After the reaction, the complementary cDNA was amplified and cleaned using Silane DynaBeads (10X Genomics, Pleasanton, CA) and the SPRIselect Reagent kit (Beckman Coulter, Indianapolis, IN). Amplified full-length cDNAs from poly-adenylated mRNA were then used to generate 3ʹ Gene Expression library (Chromium Next GEM 3’ Single Cell Reagent kits v3.1, dual index), following the manufacturer’s instructions (10x Genomics, Pleasanton, CA). Amplified cDNAs and the libraries were measured by Qubit dsDNA HS assay (Thermo Fisher Scientific, Wilmington, DE) and quality assessed by BioAnalyzer (Agilent Technologies, Santa Clara, CA).

value: Whole Embryonic Nose

value: CD1 IGS

value: Embryonic day 14.5


title: C.crescentus, ∆alkB, exponential growth (fast5)

city: Amherst

first: Maxwell

middle: B

last: Campbell

state: MA

address: 240 Thatcher Way

department: Molecular and Cellular Biology

institute: UMass Amherst

description: R9.5 pores

data_processing:
Samples were de-multiplexed, and unique molecular identifiers (UMIs) were added during PCR steps removed using Je
The clipped reads were mapped to the Caulobacter crescentus NA1000 genome (NCBI Reference Sequence: NC011916.1) using bwa and sorted with samtools.
Duplicate transposon reads removed by Je and indexed with samtools.
Genome positions are assigned to the 5′ position of transposon insertions using bedtools genomecov.
bedtools map is used to count either the total number of transposon insertions per gene using the bedtools map -o sum argument or the unique number of insertions using the bedtools map -o count argument
Assembly: NCBI Reference Sequence: NC011916.1
Supplementary files format and content: tab delimited text files include raw total or unique insertion counts for each gene.

organism: Caulobacter vibrioides NA1000

source_name: bacteria

growth_protocol: Transposon mutagenesis libraries were thawed and recovered in PYE or PYE + %0.2 Xylose overnight at saturating concentrations to minimize growth during recovery. Only for dnaK-NI library, overnights were recovered in saturating Xylose concentrations (%0.2), and treatment and T24 control conditions were grown in minimal Xylose concentrations. (%0.002)

extract_protocol:
Following overnight growth, 1 ml of saturated culture from each Tn library was pelleted at 8000xg for 2 minutes. Genomic DNA was extracted by Monarch Genomics DNA Preparation Kit (NEB) according to the manufacturer’s protocol.
The sequencing libraries for Next-generation sequencing were prepared using a customized three-step PCR protocol. Genomic DNA input was normalized to a concentration of 100 ng/μl. The initial transposon junction amplification (PCR1) was carried out using an arbitrary PCR amplification method. This step utilized a forward primer designed to align with one end of the transposon and three reverse arbitrary primers. The PCR1 process employed a 2-step cycling protocol with annealing temperatures set at 42°C and 58°C, and number of cycles at 6 and 15, respectively.  Subsequently, the second PCR step (PCR2) involved the addition of 16S adapters for Illumina indexing, along with unique molecular identifiers (UMI), and amplification of the library for 36 cycles. Post-PCR2 cleanup was performed using Aline PCRClean DX magnetic beads. The final PCR step (PCR3) incorporated NexteraXT indexing in accordance with the manufacturer's protocol. Post-indexed library (PCR3) cleanup was carried out using Aline PCRClean DX magnetic beads.

treatment_protocol:
Control condition: Libraries were back diluted to OD 0.008 into 7 ml of PYE or PYE+0.002% xylose and grown overnight until they reached saturation at OD ∼1.6.
Heat stress: Libraries diluted to OD of 1 and heat-stressed at low, medium, or high (37, 42, 43.8◦C, respectively) for 45 minutes in a Biorad Thermocycler. After 45 minutes, cells diluted back to a final OD of 0.008 in 7 ml media for 24-hour growth.
Oxidative stress: Libraries were directly diluted back to OD of 0.008 in 7 ml media that contains low, medium, or high (0.025mM, 0.05mM, 0.1mM) level hydrogen peroxide. Cells were grown for 24 hours in these chronic stress conditions.
L-canavanine stress: Libraries were directly diluted back to OD of 0.008 in 7 ml media that contains low, medium, or high (25ug/ml, 50ug/ml, 100ug/ml) levels of L-canavanine. Cells were grown for 24 hours in these chronic stress conditions.

value: delta-alkB

tag: development stage

value: exponential

value: bacteria


title: C.crescentus, ∆alkB, exponential growth (fastq)

description: R9.5 pores


title: C.crescentus, wild-type, exponential growth (fast5)

description: R9.5 pores


title: C.crescentus, ∆lon, exponential growth (fast5)

description: R9.5 pores

value: delta-lon


title: Left Cartilage 473 Ctrl Nov_2021 [473L_S3_L001]

value: Ctrl


title: C.crescentus, wild-type, exponential growth (fastq)

description: R9.5 pores

value: wild-type


title: C.crescentus, ∆lon, exponential growth (fastq)

description: R9.5 pores


title: Left Cartilage 478 Exp Nov_2021 [478L_S1_L001]


title: ASC161DF, T75, replicate1


title: WT, replicate 3, scRNAseq

description: 10x genomics


title: ASC103DF, T75, replicate1


title: ASC103DF, T75, replicate2


title: WT, replicate 1, scRNAseq

description: 10x genomics


title: WT, replicate 2, scRNAseq

description: 10x genomics


title: RC162DF, NT, replicate2

value: untreated


title: ll1_2355_43_clp1lat

city: London

first: Shaimaa

last: Hassan

address: Gower Street, Darwin Building London

department: Bioscience

institute: UCL

description: Biological replicate 2 of 2 clp1Δ yeast treated with LatrunculinA

hyb_protocol: Hybridization was performed at 49°C in a buffer containing 48% formamide using LifterSlips (Erie Scientific) and a hybridisation oven with humid chamber (Boekel Scientific).

scan_protocol: Microarrays were scanned using a GenePix 4000 B laser scanner, and fluorescence signals were analysed using GenePix Pro software (Axon Instruments).

data_processing: The signal ratios used for normalization correspond to the median of all pixel-by-pixel ratios of signals minus median local background for each pixel of a given spot (called 'median of ratios' in GenePix Pro).

organism: Schizosaccharomyces pombe

source_name: LatA-treated clp1Δ repeat2

label_protocol: 10–20 μg of total RNA was reverse transcribed into cDNA with Superscript enzyme (GibcoBRL) and an oligo-dT17 primer in the presence of Cy3- or Cy5-dCTP (PerkinElmer). The labelled cDNAs were purified using AutoSeq G-50 columns (Amersham) and precipitation

growth_protocol: cells were grown in yeast extract (YE) at 32˚C

extract_protocol: Total RNA wase extracted using a hot phenol method followed by phenol-chloroform extractions, precipitation, and purification using Qiagen RNe- asy columns.

value: clp1Δ  pombe treated with LatrunculinA

source_name: clp1Δ cells treated with DMSO repeat2

value: clp1Δ cells treated with DMSO repeat2


title: ll1_2355_38_clp1lat

description: Biological replicate 1of 2.of  clp1Δ yeast treated with LatrunculinA

source_name: LatA-treated clp1Δ repeat 1


title: RC162DF, NT, replicate1

value: Rectum

value: Organoid derived Monolayer

value: Differentiated


title: ll1_2355_41_WT_lat

description: Biological replicate 2 of 2 wild type treated with LatrunculinA

source_name: LatA-treated wildtype cells  repeat 2

value: h- wild type pombe treated with LatrunculinA

source_name: wildtype h- Pombe wreated with DMSO repeat2


title: ASC161DF, NT, replicate2

value: Ascending colon


title: WT, replicate 5, scRNAseq

description: 10x genomics

value: Whole Embryonic Nose


title: ASC161DF, NT, replicate1


title: ll1_2370_45_clp1C286S

description: Biological replicate 2 of 2.of clp1 mutants compared to wildtype

source_name: clp1-C286S repeat 2

value: h- pombe with clp1 single mutation

source_name: wildtype h- pombe repeat2

value: wildtype h- pombe repeat2


title: ASC103DF, NT, replicate2


title: RC162UD, 541-15, replicate3

value: Undifferentiated


title: ll1_2339_48_clp1KO_2_635

description: Biological replicate 1 of 2.of clp1Δ compared to wildtype

source_name: clp1Δ repeat1

value: h- pombe with clp1 deletion mutant

source_name: wildtype h- pombe repeat1

value: wildtype h- pombe repeat1


title: RC162UD, 541-15, replicate2


title: ASC161UD, 541-15, replicate4


title: aerial parts, H1, 8day, rep1

city: Shanghai

first: Huiming

last: Zhang

address: No. 3888 Chenhua Road

institute: Shanghai Center for Plant Stress Biology, and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences

data_processing:
raw data was preprocessed by fastp v 0.19.3, and the clean reads were then aligned to the reference genome using HISAT v2.1.0. The reference genome of coriander was downloaded from CGDB (http://cgdb.bio2db.com/). FeatureCounts v1.6.2 were used to calculate the gene alignment.
Assembly: CGDB: (bio2db.com)
Supplementary files format and content: TXT files contain raw counts for each sample

organism: Coriandrum sativum

source_name: aerial parts

extract_protocol:
total RNA was extracted using the Eastep Super Total RNA Extraction Kit (Promega)
A total amount of 1 μg RNA per sample was used as input material for the library preparations using the NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB) following manufacturer’s recommendations.

value: aerial parts

value: 8 day


title: aerial parts, H1,8day, rep2


title: ll1_2389_6_clp1C286S

description: Biological replicate 1 of 2.of clp1 mutants compared to wildtype

source_name: clp1-C286S  repeat 1


title: RC162UD, 541-15, replicate1


title: ASC161UD, 541-15, replicate2


title: ASC161UD, 541-15, replicate5


title: aerial parts, H1, 8day, rep3


title: ASC161UD, 541-15, replicate3


title: ASC161UD, 541-15, replicate1


title: aerial parts, Mock, 8day, rep1

value: Mock


title: ASC103UD, 541-15, replicate3


title: Male 2018, control line, ambient temp, fish 11

city: Québec

first: Kyle

last: Wellband

state: QC

address: 1030 avenue de la Médecine

department: Institut de biologie intégrative et des systèmes

country: Canada

institute: Université Laval

data_processing:
Raw reads were adaptor trimmed and filtered using fastp
Trimmed reads were mapped with bwa-meth
Duplicates were removed using MarkDuplicates from the Piacrd Tools suite
Methylation pileups were generated using methylDackel
Assembly: SaNama_1.0 (RefSeq: GCF_016432855.1)
Supplementary files format and content: bedGraph files with methylated and non-methylated base coverage counts

organism: Salvelinus fontinalis

source_name: milt/sperm

extract_protocol:
Genomic DNA was extracted using a salt-precipitation based protocol (Aljanabi and Martinez 1997, NAR. doi:10.1093/nar/25.22.4692).
Whole-genome bisulfite sequencing libraries were prepared using the NEB Ultra II library prep protocol.
Libraries were pooled and sequenced across 20 lanes on the HiSeq X platform with between two and four samples per lane and an expected total sequencing effort of one half lane per sample.

value: milt/sperm

value: Male

value: control line, ambient temp


title: aerial parts, Mock, 8day, rep2


title: Male 2018, control line, ambient temp, fish 10


title: ASC103UD, 541-15, replicate2


title: ASC103UD, 541-15, replicate1


title: ll1_2370_49_clp1_635

description: Biological replicate 2 of 2.of clp1Δ compared to wildtype

source_name: clp1Δ repeat 2


title: RC162UD, T75, replicate3

source_name: Rectum

value: Rectum

value: non-AIEC T75


title: ASC103DF, NT, replicate1

source_name: Ascending colon

value: Organoid derived Monolayer

value: Differentiated

value: untreated


title: Male 2018, control line, warm temp, fish 08

value: control line, warm temp


title: RC162UD, T75, replicate2


title: RC162UD, T75, replicate1


title: Male 2018, selected line, ambient temp, fish 08

value: selected line, ambient temp


title: Male 2018, selected line, ambient temp, fish 07


title: ASC161UD, T75, replicate4

value: Ascending colon


title: Male 2018, control line, ambient temp, fish 07


title: Male 2018, control line, ambient temp, fish 08


title: aerial parts, Mock, 8day, rep3


title: ASC161UD, T75, replicate3

value: Undifferentiated


title: Male 2018, control line, warm temp, fish 06


title: Male 2018, selected line, ambient temp, fish 06


title: ASC161UD, T75, replicate2


title: ASC103UD, T75, replicate3


title: Male 2018, control line, ambient temp, fish 06


title: ASC161UD, T75, replicate1


title: ASC103UD, T75, replicate2


title: Male 2018, selected line, ambient temp, fish 05


title: Male 2018, control line, warm temp, fish 05


title: Male 2018, control line, ambient temp, fish 09


title: ASC161UD, T75, replicate5


title: Male 2018, control line, warm temp, fish 07


title: RC162UD, NT, replicate3


title: R1-M-46-KP

data_processing:
Reads were trimmed with Trimmomatic-0.39 program for classical Illumina adapters. Aligned using Bowtie2 version 2.2.5 (https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.5/) with options: --local --very-sensitive-local --nounal --no-mixed --no-discordant --phred33 -I 10 -X 700; mapping was performed using the Mmul_1 build of the rhesus macaque genome, merged with viral genome sequence (gAAV).
PCR duplicates were eliminated with “MarkDuplicates” command of Picard version 2.23 (https://broadinstitute.github.io/picard/index.html).
Tracks were made as bedgraph files of normalized counts, using deeptools 3.3 (https://deeptools.readthedocs.io/en/develop/content/list_of_tools.html) bamCoverage with options: --binSize 1, --normalizeUsing CPM; track plots were made with R package Gviz 4.1. Coverage was calculated as SUM[(normalized count*(end-start position+1))/gAAV size] for each dataset. Importantly, ITR regions were removed from the calculation, as their coverage is overrepresented in all samples, perhaps due to recognition of ITRs from ssDNA.
Assembly: mm10
Supplementary files format and content: Bedgraph

source_name: liver

extract_protocol:
Mice were sacrificed 10 weeks after rAAV injection and liver tissue was pulverized and flash-frozen in aliquots. Liver tissue (~100 mg) was homogenized in RINO 1.5-ml Screw-Cap tubes filled with stainless steel beads and 1mL of NE buffer using a bead homogenizer (Next Advance Bullet Blender Storm - BBY24M) at speed 8 for 4 minutes. The homogenate was transferred into to a 50mL tube with 12mL of NE buffer and incubated on ice for 10 min. Nuclei were pelleted by a 5 min centrifugation at 600g, the supernatant was decanted, and the pellet was resuspended in 1mL of NE buffer. Nuclei were quantitated after Trypan Blue staining using an automated cell counter (Countess, Thermo Fisher) and diluted accordingly. 1e5 nuclei per target protein were used for Cut&Tag.
Total gDNA was extracted using a QIAamp DNA Mini kit (Qiagen) including RNAse treatment. The protocol for Illumina DNA prep was followed as per manufacturer’s instructions with 100ng of DNA as input, 30min tagmentation and 8 cycles of PCR. The same indexed primers as for Cut&Tag were used for PCR amplification.
Illumina DNA prep kit. Sequencing was performed with Illumina NovaSeq 6000, 150 cycles total per lane (2 lanes total), 2x75 paired-end reads, depth of >15M reads per sample.

treatment_protocol: Mice were intravenously injected with rAAV packaged using the KP1 capsid. The rAAV vector expressed CpG depleted, codon-optimized huFIX under control of a liver-specific promoter.

value: liver


title: Male 2018, selected line, ambient temp, fish 04


title: Male 2018, selected line, ambient temp, fish 03


title: Male 2018, control line, warm temp, fish 03


title: Male 2018, control line, warm temp, fish 04


title: Male 2018, selected line, warm temp, fish 02

value: selected line, warm temp


title: ASC161UD, NT, replicate2


title: RC162UD, NT, replicate1


title: HPC-7-shYY1-SMC3-2

city: Madison

first: Xuan

last: Pan

state: WI

address: 4470 Veterinary Medicine Building

institute: University of Wisconsin

data_processing:
CUT&Tag FASTQ files were first processed by removing the adapter ‘CTGTCTCTTATACACATCT’ using the Cutadapt software (version 4.5) and then aligned to the mouse genome (version mm10) by Bowtie2 (version 2.5.1). Duplicated fragments were marked and removed by Picard (version 3.1.1). Peaks were called by MACS2 (version 2.2.9.1) for each replicate under a q-value cutoff of 10-6. Only peaks from Chromosome 1-19, X, or Y, and not overlapping with any of the ENCODE problematic genomic regions (https://www.encodeproject.org/files/ENCFF547MET/) were kept.
Assembly: mm10
Supplementary files format and content: gzipped TSV files of CUT&Tag peaks and bigWig files of CUT&Tag signals
Library strategy: CUT&Tag

extract_protocol:
The library was constructed following the published protocol (Li, Yuefeng et al. “Chromatin and transcription factor profiling in rare stem cell populations using CUT&Tag.” STAR protocols vol. 2,3 100751. 19 Aug. 2021). Around 150,000 cells were used per each reaction with antibodies against IgG (Invitrogen 10500C), H3K4me3 (Abcam ab213224), YY1 (Active Motif 61780) and SMC3 (Abcam ab9263). To ensure reproducibility, three biological replicates were obtained for each reaction.
The library is amplified with barcoded i5 and i7 primer using NEBNext High-Fidelity 2X PCR Master Mix (M0541). The quality of the tagmented DNA library is assessed using Bioanalyzer High Sensitivity DNA Analysis (Agilent).

value: Early haematopoietic cell line derived from ES cells

tag: group


title: HPC-7-shYY1-SMC3-3


title: Male 2018, control line, ambient temp, fish 02

tag: Sex


title: Male 2018, control line, warm temp, fish 02


title: ASC161UD, NT, replicate1


title: ASC103UD, T75, replicate1


title: Male 2018, selected line, warm temp, fish 01


title: HPC-7-shYY1-SMC3-1


title: ASC103UD, NT, replicate3


title: Male 2018, selected line, ambient temp, fish 01


title: Male 2018, control line, warm temp, fish 01


title: ASC103UD, NT, replicate2


title: HPC-7-WT-YY1-3

value: WT


title: R1-M-48-KP


title: Male 2018, control line, ambient temp, fish 01


title: Male 2017, control line, ambient temp, fish 12


title: ll1_2355_40_WT_lat

description: Biological replicate 1 of 2.of wild type treated with LatrunculinA

source_name: LatA-treated wildtype cells  repeat 1

value: h- wild type pombe treated with LatrunculinA

source_name: wildtype h- Pombe wreated with DMSO repeat1


title: RC162UD, NT, replicate2


title: HPC-7-WT-YY1-2


title: Male 2017, selected line, warm temp, fish 08

value: milt/sperm


title: ASC103UD, NT, replicate1


title: Male 2018, selected line, ambient temp, fish 02

value: Male


title: Male 2017, selected line, warm temp, fish 07


title: Male 2017, selected line, warm temp, fish 06


title: Male 2017, control line, ambient temp, fish 06

value: control line, ambient temp


title: HPC-7-WT-SMC3-3


title: HPC-7-WT-YY1-1


title: Male 2017, control line, ambient temp, fish 05


title: A-T to G-C base editing efficiency at VEGFA gene site in HEK295T cell line

city: Guangzhou

first: Kechen

last: Chen

state: Guangdong

address: Shatai South Road

institute: Southern Medical University

description: VEGFA

data_processing:
Sample indexes were removed by trim_galore(0.6.10).
BAM files were generated by alignment to the reference genomic regions using the Bowtie2(2.5.1).
The substitution at each base was calculated with CRISPResso(2.2.12).
Assembly: hg38
Supplementary files format and content: Quantification of A to G substitution at each target position.

source_name: HEK293T cell line

growth_protocol: HEK293T cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin.

extract_protocol:
The HEK293T transfected cells were washed with 1x PBS, and harvested by addition of lysis buffer with proteinase K, 55℃ overnight. And then the genomic DNA was extracted with the steps of ethanol precipitation.
The targeted genome regions of interest were amplified with the first round PCR by Gold Medal Mix to add unique indexes for each sample. Each sample was then amplified by the second round PCR using P5 and P7 primers. All PCR products were mixed into one pot and purified by DNA Clean Beads.

treatment_protocol: In 24-well plates, HEK293T cells were transfected with 16ng gRNA plasmids and 484ng dCas12f-ABE or Cas12f-ABE plasmids.

value: HEK293T cell line

value: Human embryonic Kidney


title: A-T to G-C base editing efficiency at GS1 gene site in HEK293T cell line


title: Male 2017, selected line, warm temp, fish 05


title: HPC-7-WT-SMC3-2


title: Male 2017, selected line, warm temp, fish 03


title: hCSF-72h-C4, SM10, 72 hrs

city: Columbia

first: Rajiv

middle: R

last: Mohan

state: Missouri

address: 1520 East Rollins University of Missouri

department: Department of Veterinary Medicine and Surgery

institute: University of Missouri

data_processing:
Galaxy europe server, version 23.1.rc1 and R-programming
Sequence reads were trimmed for adaptors/low sequence reads using Cutadapt (Number of bases to average across =4, Average quality required=20)
Trimmed sequences were aligned with human genome GRCh37 using HISAT2 with default parameters.
gene counts were extracted using srtingtie and noramalized gene counts were obtained from DESeq2 using default parameters
Assembly: GRCh37
Supplementary files format and content: tab-delimited normalized gene counts from DESeq2 for all samples

source_name: Human corneal stromal fibroblast

growth_protocol: Human corneal stromal fibroblasts were maintained in with or without 10% serum media in humidified atmosphere  with 5% CO2 at 37C

extract_protocol:
RNA was extracted using RNeasy Mini Kit_QIAGEN . 2ug total RNA was used for construction of sequencing libraries
RNA libraries for RNA-seq were prepared using KAPA Stranded RNA-Seq Library Prep Kit (Roche) following the manufacturer's protocols.

treatment_protocol:
Human corneal stromal fibroblasts were  kept in serum-free media for 72 hrs to get human corneal stromal fibroblasts
Human corneal stromal fibroblasts were treated with 5ng/ml TGF-beta in serum-free media for 72 hrs to get human corneal stromal myofibroblasts.
Human corneal stromal fibroblasts were treated with 10% serum media to get  nutrient enriched  Human corneal stromal fibroblasts

value: Human corneal stromal fibroblast

value: Serum media 10%

value: 72 hrs


title: HPC-7-WT-SMC3-1


title: Male 2017, selected line, warm temp, fish 04


title: Male 2017, selected line, ambient temp, fish 04


title: Male 2017, selected line, warm temp, fish 02


title: hCSF-72h-C3,  SM10, 72 hrs


title: hCSF-72h-C2, SM10, 72 hrs


title: HPC-7-WT-H3K4me3-3


title: hCSF-72h-C1, SM10, 72 hrs


title: Male 2017, control line, warm temp, fish 01

value: control line, warm temp


title: Male 2017, control line, ambient temp, fish 01


title: HPC-7-WT-H3K4me3-1


title: HPC-7-WT-H3K4me3-2


title: ARPE-19, TCP [miRNA-Seq]

city: Tübingen

first: Lasse

last: Wolfram

address: Elfriede-Aulhorn-Straße 7

institute: Department for Ophthalmology, Eberhard Karls University of Tübingen

data_processing:
TrueQuant UMI-based PCR bias elimination
Data analysis using omiRas webtool (Müller, S. et al. omiRas: a Web server for differential expression analysis of miRNAs derived from small RNA-Seq data. Bioinformatics 29, 2651–2652 (2013).)
Supplementary files format and content: comma-separated values (CSV) files

source_name: retinal pigment epithelium

extract_protocol:
Extraction was performed using MN NucleoSpin miRNA kit (Protocol for animal tissue and cultured cells) with a separate elution of small RNAs and large RNAs. Following DNAse I digestion using beta-mercaptoethanol (ß-ME), the RNA concentration was measured with the Qubit RNA HS Assay Kit on a Qubit Fluorometer (Life Technologies, USA). RNA quality was determined with the Bioanalyzer (Agilent, USA).
The preparation of smallRNA Sequencing libraries was carried out by GenXPro GmbH.

value: retinal pigment epithelium

value: retinal pigment epithelial cells

value: standard tissue culture plastic


title: ARPE-19, stiff PA gel [miRNA-Seq]

value: stiff polyacrylamide gel


title: hCMF-72h-B4, TGF-Beta, 72 hrs

source_name: Human corneal stromal myofibroblast

value: Human corneal stromal myofibroblast

value: TGF-Beta


title: ARPE-19, soft PA gel [miRNA-Seq]

value: soft polyacrylamide gel


title: ARPE-19, TCP

data_processing:
Illumina sequence reads were processed with an in-house analysis pipeline (GenXPro), including TrueQuant PCR bias elimination and mapping against the human reference genome.
genome build: hg19
Supplementary files format and content: comma-separated values (CSV) files
Library strategy: RNA-Seq (MACE)

extract_protocol:
Extraction was performed using MN NucleoSpin miRNA kit (Protocol for animal tissue and cultured cells) with a separate elution of small RNAs and large RNAs. Following DNAse I digestion using the Baseline-ZERO kit (Epicentre, USA), the RNA concentration was measured with the Qubit RNA HS Assay Kit on a Qubit Fluorometer (Life Technologies, USA). RNA quality was determined with the RNA Pico Sensitivity Assay on a LabChip GXII Touch (PerkinElmer, USA) as described in Boneva, S. et al. 3′ MACE RNA-sequencing allows for transcriptome profiling in human tissue samples after long-term storage. Laboratory Investigation 100, 1345–1355 (2020).
The preparation of massive analysis of cDNA ends (MACE) libraries was carried out by GenXPro GmbH using 1 µg of total RNA following GenXPro MACE-Seq Protocol (2014-2016), as described in Lange, C. A. K. et al. Increased expression of hypoxia-inducible factor-1 alpha and its impact on transcriptional changes and prognosis in malignant tumours of the ocular adnexa. Eye 32, 1772–1782 (2018) and Zajac, B., Amendt, J., Horres, R., Verhoff, M. & Zehner, R. De novo transcriptome analysis and highly sensitive digital gene expression profiling of Calliphora vicina (Diptera: Calliphoridae) pupae using MACE (Massive Analysis of cDNA Ends). Forensic Science International: Genetics 15, 137–146 (2015).


title: ARPE-19, stiff PA gel


title: HPC-7-WT-IgG-3

description: shLUC-IgG-FA

value: Early haematopoietic cell line derived from ES cells

value: WT

value: IgG


title: HPC-7-WT-IgG-2

description: shLUC-IgG-CI


title: hCMF-72h-B3, TGF-Beta, 72 hrs


title: hCMF-72h-B2, TGF-Beta, 72 hrs


title: ARPE-19, soft PA gel


title: IgG_rep1

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
Low-quality reads were removed using Sickle.
Reads were aligned to mm10 by bowtie2 (v2.3.4.3) with the single-end or paired-end mode.
Non-uniquely mapped and mitochondrial DNA reads were removed using a combination of SAMtools functions.
PCR duplicates were removed using Picard (‘MarkDuplicates’, v2.8.0).
Bigwig files were generated using deepTools (‘bamCoverage’, v3.0.2).
Assembly: mm10
Supplementary files format and content: *.bw: bigwig files

source_name: Thymus

extract_protocol:
Cells were cross-linked with 1% formaldehyde and then lysed for 10 min on ice in RadioImmunoPrecipitation Assay (RIPA) buffer supplemented with complete protease inhibitor cocktail (Roche). Chromatin was fragmented using Covaris for 15 min (duty cycle 2%, intensity 3, cycle/burst 200) and the sheared material was cleared by a 10-min centrifugation at 13,000 rpm at 4 °C. The cleared material was immunoprecipitated overnight at 4 °C with Pol II Ab conjugated to magnetic Protein-G beads (Life Technologies, Dynabeads), followed by extensive washing of the beads with ice-cold RIPA, high-salt RIPA, LiCl. Chromatin was eluted from the beads, treated with 1µg DNase-free RNase (Roche) for 30 min at 37°C and then treated with Proteinase K (Roche) for 2 hrs at 37°C.
Chromatin was reverse cross-linked by incubating at 65°C overnight. DNA from reverse cross-linked material was purified with SPRI beads (Agencourt AMPure XP beads, Beckman Coulter); and then subject to sequential steps of end-repair, A-base addition, adaptor-ligation and PCR amplification. DNA was PCR amplified for 15 cycles. Libraries were size-selected for 200–500-bp fragments with SPRI beads.

treatment_protocol: mTECs were isolated by collagenase and dispase digestion, CD45+ cells depletion using magnetic beads, fluorescent antibodies staining, and flow sorting.

value: Thymus

value: mTEChi

tag: chip antibody

value: Rabbit IgG (#2729, Cell Signaling)

value: 4-6 weeks old

value: Female

tag: strain


title: WT_Spermidine_ZDNA_rep2

tag: cell type

value: Z22 (Ab00783-23.0, Absolute Antibody)

value: Spermidine ip injection


title: hCMF-72h-B1, TGF-Beta, 72 hrs

value: 72 hrs


title: Male 2017, control line, ambient temp, fish 03

value: milt/sperm

value: Male

value: control line, ambient temp


title: HPC-7-WT-IgG-1

description: shLUC-IgG-AF

tag: cell line

tag: genotype


title: WT_ZDNA_rep1

tag: age

tag: treatment


title: hCSF-72h-A4, untreated, 72 hrs

value: Human corneal stromal fibroblast

value: NT

tag: time


title: WT_ZDNA_rep2

tag: tissue


title: hCSF-72h-A3, untreated, 72 hrs


title: Liver, PLIN5, DMBA, western, rep3 [30_PM]

city: Zagreb

first: Paula

last: Štancl

state: Grad Zagreb

address: Horvatovac 102a

department: Department of Biology

country: Croatia

institute: Faculty of Science

description:
30_PM_S30_R1_001
raw_counts.txt

data_processing:
Quality control was performed with FastQC v0.11.9.
Sequencing reads were mapped to mm10.GRCm38.GCA_000001635.2 using STAR (version 2.7.3a) with parameters --outFilterScoreMinOverLread 0.25 --outFilterMatchNminOverLread 0.25 --alignSoftClipAtReferenceEnds “No”
Read count extraxction were performed using featureCounts (version 2.0.0)  with parameter --primary
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for multiple Samples

extract_protocol:
Total RNA was extracted with phenol-chloroform and precipitated with isopropanol. DNAse digestion and RNA subsequent cleaning was performed with PureLink® RNA Mini Kit (Invitrogen, Thermo Fisher Scientific, Darmstadt, Germany) following manufacturing instructions. 500 ng of total RNA was used for library preparation.
Libraries were prepared using 36x Colibri 3’ mRNA Library Preparation kit (Invitrogen) following manufacturer's instructions.

treatment_protocol: 4-5 days-old mice were treated with 50 µL of 0.5% of DMBA or acetone as control, applied on the dorsal surface of the neck area.Pups were returned to their mothers until weaning. Mice were randomly assigned to a normal diet or a western diet and fed for 30 weeks. Mice treated with acetone represented the NAFLD model, while mice additionally treated with DMBA served as the model for NAFLD-induced HCC.

value: liver

value: PLIN5 knockdown

value: DMBA

tag: diet

value: western

tag: disease

value: NAFLD-HCC

value: male


title: Liver, PLIN5, DMBA, western, rep2 [29_PM]

description:
29_PM_S29_R1_001
raw_counts.txt


title: Liver, WT, DMBA, western, rep3 [24_PM]

description:
24_PM_S24_R1_001
raw_counts.txt

value: WT


title: Liver, WT, DMBA, western, rep2 [23_PM]

description:
23_PM_S23_R1_001
raw_counts.txt


title: LPS1

first: Yongyi

last: Ye

address: No.250, Changgang East Road

department: the Second Affiliated Hospital of Guangzhou Medical University

data_processing:
The clean reads were obtained after removal of reads containing adapter, ploy-N and at low quality from raw data.
HISAT2 was used to align the clean reads to the mouse reference genome mm10 with default parameters.
HTSeq was subsequently employed to convert aligned short reads into read counts for each gene model.
Assembly: mm10
Supplementary files format and content: comma-separated values (CSV) file including raw counts for each sample

source_name: primary microglia

extract_protocol:
Total RNA was isolated from cells/tissues using the Magzol Reagent (Magen, China)according to the manufacturer’s protocol.
The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit(Thermo Fisher Scientific, USA). The libraries were sequenced by Illumina (Illumina, USA) with paired-end 150bp at Ribobio  Co. Ltd (Ribobio, China).

value: primary microglia

value: mesenchymal stem cells

tag: genotype:

value: LPS


title: LPS3

institute: the Second Affiliated Hospital of Guangzhou Medical University


title: WT3

value: control


title: hCSF-72h-A2, untreated, 72 hrs

value: 72 hrs


title: LPS2


title: WT2


title: Liver, WT, DMBA, western, rep1 [22_PM]

description:
22_PM_S22_R1_001
raw_counts.txt


title: Liver, WT, DMBA, control, rep3 [21_PM]

description:
21_PM_S21_R1_001
raw_counts.txt


title: hCSF-72h-A1, untreated, 72 hrs


title: Liver, WT, DMBA, control, rep2 [20_PM]

description:
20_PM_S20_R1_001
raw_counts.txt


title: WT1


title: NSLA_72

city: daejeon

first: Seung-Jin

last: Park

address: gwahakro

country: South Korea

institute: KRIBB

data_processing:
STAR mapping (2.9.10) with GeneCount function Assembly: GRCh38 Supplementary files format and content: Genecounts as text formats
Assembly: GRCh38
Supplementary files format and content: txt

source_name: Lung

extract_protocol:
Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light. Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.
We used the TruSeq DNA Library Prep Kit (Illumina, San Diego, CA, USA) for TruSeq Stranded Total RNA Sample Preparation Kit (Illumina) for stranded total RNA-seq library, following the manufacturer’s instructions. For paired-end sequencing was performed using an Illumina NovaSeq 6000 sequencing instrument, the constructed library was sequenced using a HiSeq 4000 sequencing system, resulting in 2× 100 bp sequencing reads.

value: Lung

tag: subject status

value: Never-Smoker Lung Adenocarcinoma Patients without EGFR or ALK Alterations

value: NSCLC

tag: Stage

tag: gender

value: FEMALE


title: Liver, PLIN5, acetone, western, rep2 [11_PM]

description:
11_PM_S11_R1_001
raw_counts.txt

value: acetone

value: NAFLD


title: Liver, WT, DMBA, control, rep1 [19_PM]

description:
19_PM_S19_R1_001
raw_counts.txt

value: liver


title: WT_Spermidine_ZDNA_rep1

value: Thymus

value: mTEChi

value: Z22 (Ab00783-23.0, Absolute Antibody)

value: 4-6 weeks old

value: Female

value: Spermidine ip injection


title: BSseq_XX_d4_r2

city: Berlin

first: Till

last: Schwämmle

state: Berlin

address: Ihnestrasse 63

department: Otto-Warburg-Laboratory

institute: Max Planck Institute for Molecular Genetics

data_processing:
Adaptor and quality trimming was performed using Trim Galore (v0.6.4)
Reads were aligned to mm10 using BSMAPz.
.bam files were sorted with samtools (v1.10) and duplicate reads removed using Picard (v2.7.1)
.bedGraph files were generated using Methyldackel (v0.3.0) [extract –minDepth 2]
Lastly, blackliseted regions and mitochondrial reads were removed.
Assembly: mm10
Supplementary files format and content: .bedGraph files containing per-base CpG methylation (merged or biological replicates)

source_name: XX ESCs

growth_protocol: Cells were kept on gelatine, without feeders in 2i/LIF + Serum conditions.

extract_protocol:
gDNA extraction and bisulfite conversion
Whole-Genome Bissulfite sequencing

treatment_protocol: Cells were differentiated for the indicated days using 2i/LIF-withdrawal.

value: XX ESCs

value: TX1072 XXdXic

value: Cast x B6


title: NSLA_699


title: NSLA_698


title: Liver, PLIN5, acetone, western, rep1 [10_PM]

description:
10_PM_S10_R1_001
raw_counts.txt

value: PLIN5 knockdown

value: western

value: male


title: BSseq_XX_d4_r1


title: Liver, PLIN5, DMBA, western, rep1 [28_PM]

description:
28_PM_S28_R1_001
raw_counts.txt

value: DMBA

value: NAFLD-HCC


title: Liver, WT, acetone, western, rep3 [06_PM]

description:
06_PM_S6_R1_001
raw_counts.txt

value: WT

value: acetone


title: Liver, WT, acetone, western, rep2 [05_PM]

description:
05_PM_S5_R1_001
raw_counts.txt

value: liver

value: NAFLD


title: NSLA_693

value: Lung

value: Never-Smoker Lung Adenocarcinoma Patients without EGFR or ALK Alterations

value: NSCLC

value: FEMALE


title: NSLA_696


title: Liver, WT, acetone, control, rep3 [03_PM]

description:
03_PM_S3_R1_001
raw_counts.txt

value: control


title: BSseq_XX_d2_r1

value: XX ESCs


title: Liver, WT, acetone, control, rep1 [01_PM]

description:
01_PM_S1_R1_001
raw_counts.txt


title: Liver, WT, acetone, control, rep2 [02_PM]

description:
02_PM_S2_R1_001
raw_counts.txt


title: NSLA_682


title: BSseq_XX_d0_r2

value: TX1072 XXdXic


title: HiC_ESC_BPTFko_rep2

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

data_processing:
Illumina RTA 2.4.1 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing. Hi-C data was processed using the distiller-nf pipeline (https://github.com/open2c/distiller-nf ). Briefly, reads were mapped to mm10 using BWA (ver. 0.7.17)  with default parameters "bwa mem -SP5M ".
Hi-C pairs contacts were extracted from mapped files and processed using pairtools (10.5281/zenodo.5214125), specifically with the parse (with --add-columns mapq --walks-policy all additional arguments), sort and dedup (with max_mismatch_bp: 1 setting).
Deduplicated pairs were then filtered to retain pairs with both sides mapping with high confidence (mapq>=30) and converted to cooler format using cooler ver. 0.9.0 using the ‘cload pairs’ function with default parameters. Matrices were then zoomified to produce multiresolution cooler (.mcool) files, and they were balanced with the –cis-only flag.
Assembly: mm10
Supplementary files format and content: Contact matrix in multiple cool format.

source_name: embryonic stem cells

extract_protocol:
DNA was purified using AMPure XP beads
Sequencing libraries were prepared using the NEBNext Ultra Library Preparation Kit (NEB) with 12 PCR amplification cycles for Ips and 5 PCR amplification cycles for inputs.

value: embryonic stem cells

value: BPTF knock-out


title: HiC_ESC_wt_rep2

value: wild-type


title: HiC_ESC_BPTFko_rep1


title: NSLA_680


title: HiC_ESC_wt_rep1


title: BSseq_XX_d0_r1

value: Cast x B6


title: Liver, PLIN5, acetone, western,rep 3 [12_PM]

description:
12_PM_S12_R1_001
raw_counts.txt

value: PLIN5 knockdown

value: western

value: male


title: NSLA_679


title: CUTandRUN_ESC_IgG_Bptfko_rep2

data_processing:
Illumina RTA 2.4.1 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing. Reads were mapped to mm10 using QuasR (Gaidatzis et al, Bioinformatics 2015) with default parameters, allowing only for uniquely mapping reads.
wig files were generated using the qExportWig function from the QuasR package with scaling=1e6 . The scores in the wig file represent the number of fragment midpoints per 100bp window and per million reads in the library.
Assembly: mm10
Supplementary files format and content: wig
Library strategy: Cut&Run

extract_protocol:
DNA was purified using the MinElute PCR Purification Kit (Qiagen).
Sequencing libraries were prepared using the NEBNext Ultra Library Preparation Kit (NEB) .

value: Bptf knock-out


title: NSLA_677


title: Treg Met 2

city: Tel Aviv

first: Neta

last: Erez

address: TAU

department: Pathology

country: Israel

institute: Tel Aviv University

data_processing:
Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1
Sequencing data was then trimmed using fastp 0.20.0 and aligned to the GRCm38 assembly using STAR 2.6.0c
DESeq2 1.30.1 and R 3.6 were used for normalization of count data and for statistical analysis of differential gene expression.
Assembly: Reads were mapped to the Mus musculus genome (mm10) using STAR.
Supplementary files format and content: Tab-delimited text files include RPKM values for each Sample

source_name: Bone metastatic lesion

extract_protocol:
EZ-RNA Total RNA Isolation Kit
MARS-seq protocol was used to generate libraries

value: Bone metastatic lesion

value: CD4+CD25+ T reg

value: Late met stage


title: CUTandRUN_ESC_Snf2h_Bptfko_rep2


title: Liver, WT, acetone, western, rep1 [04_PM]

description:
04_PM_S4_R1_001
raw_counts.txt

value: liver

value: WT

value: acetone

value: NAFLD


title: Treg Met 3


title: Treg Met 1


title: CUTandRUN_ESC_Snf2h_Bptfko_rep1


title: CUTandRUN_ESC_IgG_SNF2Hko_rep2

value: Snf2h knock-out


title: CUTandRUN_ESC_IgG_Bptfko_rep1


title: CUTandRUN_ESC_IgG_SNF2Hko_rep1


title: CUTandRUN_ESC_Snf2h_SNF2Hko_rep2


title: NSLA_689

value: Lung

value: Never-Smoker Lung Adenocarcinoma Patients without EGFR or ALK Alterations

value: NSCLC

value: FEMALE


title: Treg Periph 3

source_name: bone marrow

value: bone marrow


title: Treg Periph 2


title: CUTandRUN_ESC_Snf2h_SNF2Hko_rep1

value: embryonic stem cells


title: NSLA_672


title: CUTandRUN_ESC_IgG_wt_rep2

value: wild-type


title: CUTandRUN_ESC_Snf2h_wt_rep1


title: CUTandRUN_ESC_Snf2h_wt_rep2


title: NSLA_667


title: Treg Premet 4

value: Early met stage


title: ATACseq_ESC_cecr2_ko_D_rep3

data_processing:
Illumina RTA 2.4.1 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing. Reads were mapped to mm10 using QuasR (Gaidatzis et al, Bioinformatics 2015) with default parameters, allowing only for uniquely mapping reads.
wig files were generated using the qExportWig function from the QuasR package with scaling=1e6 . The scores in the wig file represent the number of fragment midpoints per 100bp window and per million reads in the library.
Assembly: mm10
Supplementary files format and content: wig

extract_protocol:
DNA was purified using the MinElute PCR Purification Kit (Qiagen).
PCR amplification with Nextera compatible primers

value: cecr2 knock-out


title: NSLA_674


title: NSLA_666


title: ATACseq_ESC_acf1_ko_D_rep3

value: acf1 knock-out


title: Treg Periph 1

value: CD4+CD25+ T reg


title: NSLA_675


title: Treg Premet 1


title: ATACseq_ESC_acf1_ko_D_rep2


title: NSLA_663


title: Treg Normal 4

value: Normal


title: ATACseq_ESC_cecr2_ko_D_rep2


title: NSLA_66


title: ATACseq_ESC_acf1_ko_D_rep1


title: ATACseq_ESC_wt_D_rep3

value: wt


title: ATACseq_ESC_wt_D_rep2


title: Treg Normal 3


title: CUTandRUN_ESC_IgG_wt_rep1


title: ATACseq_ESC_snf2h_ko_C_rep2

value: snf2h knock-out


title: ATACseq_ESC_wt_C_rep2


title: ATACseq_ESC_cecr2_ko_D_rep1


title: Treg Premet 2


title: Treg Normal 1


title: NSLA_653


title: ATACseq_ESC_snf2h_ko_C_rep1


title: NSLA_654


title: NSLA_657


title: ATACseq_ESC_wt_C_rep1


title: NSLA_665


title: ATACseq_ESC_bptf_ko_B_rep1

value: bptf knock-out


title: ATACseq_ESC_wt_B_rep2


title: CD8 Met 2

value: Bone metastatic lesion

value: CD8+ T cytotoxic

value: Late met stage


title: ATACseq_ESC_bptf_ko_B_rep2


title: NSLA_649

value: Lung

value: Never-Smoker Lung Adenocarcinoma Patients without EGFR or ALK Alterations


title: ATACseq_ESC_wt_B_rep1


title: NSLA_632

value: NSCLC

value: FEMALE


title: ATACseq_ESC_wstf_ko_A_rep2

value: embryonic stem cells

value: wstf knock-out


title: CD8 Periph 2

value: bone marrow


title: CD8 Met 1


title: ATACseq_ESC_wstf_ko_A_rep1


title: NSLA_631


title: ATACseq_ESC_tip5_ko_A_rep1

value: tip5 knock-out


title: CD8 Periph 1


title: ATACseq_ESC_tip5_ko_A_rep2


title: NSLA_626


title: ATACseq_ESC_rsf_ko_A_rep2

value: rsf knock-out


title: Treg Normal 2

value: CD4+CD25+ T reg


title: CD8 Premet 4

value: Early met stage


title: ATACseq_ESC_wt_D_rep1

value: wt


title: ATACseq_ESC_rsf_ko_A_rep1


title: NSLA_616


title: ATACseq_ESC_wt_A_rep2


title: NSLA_611


title: MNaseSeq_ESC_wt_C_rep2

data_processing:
Illumina RTA 2.4.1 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing. MNase-seq reads were mapped to mm10 using QuasR (Gaidatzis et al, Bioinformatics 2015) with default parameters, allowing only for uniquely mapping reads.
wig files were generated using the qExportWig function from the QuasR package with scaling=1e6 . The scores in the wig file represent the number of fragment midpoints per 100bp window and per million reads in the library.
Assembly: mm10
Supplementary files format and content: wig

extract_protocol:
DNA was purified using AMPure XP beads
Sequencing libraries were prepared from 500ng of MNase digested DNA using the NEBNext Ultra Library Preparation Kit (NEB) with 5 PCR amplification cycles.

value: acf1 knock-out


title: NSLA_61


title: ATACseq_ESC_wt_A_rep1


title: MNaseSeq_ESC_wt_C_rep1


title: CD8 Premet 2


title: NSLA_608


title: MNaseSeq_ESC_wt_B_rep3


title: MNaseSeq_ESC_wt_B_rep2


title: MNaseSeq_ESC_wt_A_rep2

value: cecr2 knock-out


title: MNaseSeq_ESC_wt_B_rep1


title: CD8 Normal 4

value: Normal


title: CD8 Premet 1

value: CD8+ T cytotoxic


title: NSLA_6


title: MNaseSeq_ESC_wt_A_rep1


title: CD8 Normal 3


title: MNaseSeq_ESC_wstf_ko_A_rep2


title: NSLA_598


title: CD8 Normal 2


title: MNaseSeq_ESC_tip5_ko_A_rep2


title: MNaseSeq_ESC_tip5_ko_A_rep1

value: bptf knock-out


title: CD8 Normal 1


title: MNaseSeq_ESC_rsf1_ko_A_rep2


title: CD8 Premet 3


title: MNaseSeq_ESC_rsf1_ko_A_rep1


title: CD4 Met 3

value: Bone metastatic lesion

value: CD4+ T helper

value: Late met stage


title: NSLA_589

value: Lung

value: Never-Smoker Lung Adenocarcinoma Patients without EGFR or ALK Alterations

value: NSCLC

value: FEMALE


title: MNaseSeq_ESC_cecr2_ko_B_rep2

value: embryonic stem cells

value: wstf knock-out


title: CD4 Met 2


title: MNaseSeq_ESC_cecr2_ko_B_rep3


title: NSLA_587