title: Mus musculus liver from mice in Equal light, recieving a LFD diet, at timepoint ZT8 [0101_61]


title: Mus musculus liver from mice in Long light, recieving a HFD diet, at timepoint ZT16 [0101_58]

status: Public on Sep 09 2023

type: SRA

city: Copenhagen

first: Lewin

last: Small

address: Blegdamsvej 3B

department: CBMR

country: Denmark

institute: University of Copenhagen

library_source: transcriptomic

data_processing:
Data were aligned to mm10_GRCm38_release99 using star/2.7.2b, counted using subread/1.6.2.
Star setting were: STAR --runThreadN 40 --outReadsUnmapped Fastx --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated  --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat
featureCounts settings were: featureCounts -p -B -C -T $threads -t exon -g gene_id
Assembly: mm10 GRC 38

molecule: total RNA

organism: Mus musculus

source_name: Liver

extract_protocol:
Trizol+ Qiagen Rneasy according to manufacturers instructions
Messenger RNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA protocol (Illumina). Poly-A containing mRNAs were purified by poly-T attached magnetic beads, fragmented, and cDNA was synthesized using SuperScript III Reverse Transcriptase (Thermo Fisher Scientific). cDNA was adenylated to prime for adapter ligation and after a clean-up using AMPure beads (Beckman coulter), DNA fragments were amplified using PCR followed by a final clean-up.
Libraries were quality-controlled using a Bioanalyzer instrument (Agilent Technologies) and subjected to 52-bp paired-end sequencing on a NovaSeq6000 (Illumina).

tag: tissue

value: Liver

tag: timepoint

tag: photoperiod

value: Long light

tag: diet

value: HFD


title: Mus musculus liver from mice in Equal light, recieving a HFD diet, at timepoint ZT12 [0101_57]

value: Equal light


title: Mus musculus liver from mice in Short light, recieving a HFD diet, at timepoint ZT0 [0101_56]

value: Short light


title: Mus musculus liver from mice in Long light, recieving a LFD diet, at timepoint ZT16 [0101_59]

value: LFD


title: Mus musculus liver from mice in Long light, recieving a LFD diet, at timepoint ZT12 [0101_55]


title: Mus musculus liver from mice in Short light, recieving a LFD diet, at timepoint ZT20 [0101_79]


title: Mus musculus liver from mice in Equal light, recieving a LFD diet, at timepoint ZT12 [0101_54]


title: Mus musculus liver from mice in Short light, recieving a HFD diet, at timepoint ZT16 [0101_52]


title: Mus musculus liver from mice in Equal light, recieving a LFD diet, at timepoint ZT16 [0101_51]


title: Mus musculus liver from mice in Equal light, recieving a LFD diet, at timepoint ZT12 [0101_50]


title: Mus musculus liver from mice in Equal light, recieving a LFD diet, at timepoint ZT20 [0101_5]


title: Mus musculus liver from mice in Equal light, recieving a HFD diet, at timepoint ZT16 [0101_64]


title: Mus musculus liver from mice in Short light, recieving a LFD diet, at timepoint ZT0 [0101_49]


title: FUSWT 5c

city: Pittsburgh

first: Dhivyaa

last: Rajasundaram

state: PA

address: 4401 Penn Avenue

department: Pediatrics

country: USA

institute: University of Pittsburgh

data_processing:
Profiling was performed on 1 µg of total RNA using BGI’s DNBSEQ™ small RNA sequencing platform
Reads were mapped to the human reference genome and to other sRNA databases using Bowtie2, and gene expression levels were calculated using Transcripts Per Kilobase Million (TPM)
Differentially expressed small RNAs were screened by DESeq2 based on the negative binomial distribution, and the significance of gene expression differences was calculated using an adjusted P value of ≤ 0.1 and the absolute value of Log2Ratio ≥1.
RNAhybrid, miRanda, or TargetScan were used to predict the small RNA targets
Assembly: human reference genome (hg19) and to other sRNA databases (mirBase 22)
Supplementary files format and content: count, TPM

organism: Homo sapiens

growth_protocol: HEK293T (ATCC® CRL-3216™) and Drosha KO HEK293 cells were cultured in Advanced DMEM supplemented with 10% FBS and 1% Glutamax at 37°C and 5% CO2.

extract_protocol:
HEK293T and DKO cells were transfected with FUSWT and R521C for 24 hours with Turbofect (Invitrogen), and total RNA was isolated using MagMAX™ mirVana™ Total RNA Isolation Kit (Applied Biosystems™) by following the manufacturer's instructions.
18–30 nt RNA segments were separated by PAGE gel, followed by adaptor ligation and RT-PCR amplification of cDNAs. All the contaminant adaptors or tags were removed, and the length distribution of clean reads (between 18 nt and 30 nt) was summarized.

tag: genotype

value: FUSWT

tag: cell line

tag: cell type

value: Human Embryonic kidney


title: FUSWT 5b


title: FUSR521C 6b


title: FUSR521C 6a


title: Mus musculus liver from mice in Short light, recieving a LFD diet, at timepoint ZT8 [0101_47]


title: Mus musculus liver from mice in Short light, recieving a LFD diet, at timepoint ZT0 [0101_48]


title: control 4c (DKO ctrl)

value: control  (DKO ctrl)


title: Mus musculus liver from mice in Equal light, recieving a HFD diet, at timepoint ZT20 [0101_46]


title: control 4a (DKO ctrl)


title: control 4b (DKO ctrl)


title: FUSR521C 3c


title: Mus musculus liver from mice in Equal light, recieving a HFD diet, at timepoint ZT4 [0101_45]


title: Mus musculus liver from mice in Equal light, recieving a LFD diet, at timepoint ZT0 [0101_44]


title: FUSR521C 3b


title: Mus musculus liver from mice in Long light, recieving a LFD diet, at timepoint ZT0 [0101_43]


title: FUSR521C 3a


title: Mus musculus liver from mice in Equal light, recieving a LFD diet, at timepoint ZT4 [0101_42]


title: Mus musculus liver from mice in Equal light, recieving a HFD diet, at timepoint ZT4 [0101_53]


title: FUSWT 2b


title: FUSWT 2c


title: FUSR521C 6c


title: Mus musculus liver from mice in Equal light, recieving a LFD diet, at timepoint ZT0 [0101_40]


title: FUSWT 2a


title: Mus musculus liver from mice in Equal light, recieving a LFD diet, at timepoint ZT4 [0101_4]


title: FUSWT 5a


title: control 1c (HEK control)

value: control


title: Mus musculus liver from mice in Short light, recieving a LFD diet, at timepoint ZT0 [0101_36]


title: Mus musculus liver from mice in Equal light, recieving a LFD diet, at timepoint ZT16 [0101_38]


title: Mus musculus liver from mice in Short light, recieving a HFD diet, at timepoint ZT4 [0101_37]


title: Mus musculus liver from mice in Short light, recieving a LFD diet, at timepoint ZT12 [0101_39]


title: control 1a (HEK control)


title: WT met1-3 F2 2

city: Berkeley

first: Ben

last: Williams

state: CA

address: 2151 Berkeley Way

institute: UC Berkeley

description: 150x 150

library_source: genomic

data_processing:
FastQC was used to examine read quality. Low quality reads were removed with trim_galore with parameters --clip_R1 8, --clip_R2 8, --stringency 3, -q 25, -r1 32, -r2 32 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/, version from 16 July 2014).
Libraries were mapped using Bismark 0.20.1 permitting one mismatch (all other parameters default).
PCR duplicate reads were removed using Bismark.
censor reads with 3 or more consecutive unconverted CHHs in a row, which likely indicate read was not fully converted
Bismark methylation extractor and custom scripts previously described were used to obtain per base methylation and to identify DMRs.
Assembly: Araport11 and spike in Genome (Control DNA CpG methylated pUC19 and Control DNA Unmethylated Lambda)
Supplementary files format and content: Methylation level at single base resolution in CHH, CHG, and CG context for met1 heterozygous and WT segregated offpsirng
Supplementary files format and content: tab-delimited text
Library strategy: Methyl-Seq

molecule: genomic DNA

organism: Arabidopsis thaliana

growth_protocol: Plants were grown in a growth chamber (Percival) in long-day conditions (16 hours light, 8 hours dark) at 22℃ and 50% relative humidity.

extract_protocol:
DNA was extracted using a CTAB method
Leaf tissue from 28-day old plants was collected and flash frozen in liquid nitrogen. Two leaves per sample were ground using a Qiagen TissueLyser II and immediately after 200 µl of CTAB was added and heated to 65°C for approximately 20 minutes. This was followed by the addition of 200 µl chloroform, 10 minute centrifugation and ethanol washes to isolate total genomic DNA. The DNA concentration was quantified using a Qubit Flex fluorometer, and a diluted spike-in was added according to NEB recommendations (1 µl diluted pUC19 (0.001 ng) control DNA and 1 µl diluted unmethylated lambda DNA (0.02 ng) in 0.1X TE, pH 8.0 per 10–200 ng plant sample DNA). Genomic DNA samples with added spike-ins were sonicated to an average fragment size of 300bp using a Covaris S220 Focused Ultrasonicator (80s treatment, 140 peak power, 10 duty factor 200 cycles/burst). Subsequently, samples were incubated with an RNAse cocktail and RNAse was removed using a Qiagen spin column. EM-seq libraries were constructed following the NEBNext® Enzymatic Methyl-seq Kit protocol. Library quality was verified with a KAPA Library Quant Kit and fragment analyzer. The samples were pooled to a concentration of 4 ng/µl and 19.2 nM and sequenced using an Illumina NextSeq 2000 (paired-end 150 x 150 bp) 11 million average reads/sample.

treatment_protocol: met1-3 segregating WT plants methylation was compared with heterozygous parental line

value: Rosette leaf

tag: age

value: 28 day old leaf

value: met1-3 segregating WT

tag: treatment

value: grown under long day (16L8D)


title: Mus musculus liver from mice in Long light, recieving a HFD diet, at timepoint ZT16 [0101_35]


title: het met1-3 F2

description: 150x 150

value: heterozygous parental line


title: Mus musculus liver from mice in Short light, recieving a LFD diet, at timepoint ZT16 [0101_34]


title: Mus musculus liver from mice in Long light, recieving a HFD diet, at timepoint ZT12 [0101_41]


title: Mus musculus liver from mice in Equal light, recieving a LFD diet, at timepoint ZT12 [0101_32]


title: WT met1-3 F3 2a

description: 150x 150


title: WT met1-3 F2 3

description: 150x 150


title: Mus musculus liver from mice in Long light, recieving a LFD diet, at timepoint ZT4 [0101_31]


title: WT met1-3 F3 1a

description: 150x 150


title: control 1b (HEK control)


title: WT met1-3 F3 3a

description: 150x 150


title: Mus musculus liver from mice in Short light, recieving a HFD diet, at timepoint ZT8 [0101_30]


title: WT met1-3 F2 1

description: 150x 150


title: Miapaca-2 cells,TPL3

city: NanJing

first: Jianxiang

last: GU

state: JiangSu

address: 321 Zhongshan Road

department: Department of Gastroenterology

country: China

institute: Nanjing Drum Tower Hospital Clinical College of Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine

data_processing:
ensemble
Raw data (or Raw reads) of fastq format were firstly processed through in-house perl scripts. Inthis step, remove the adapter sequence and filter out low quality (low quality, the number of lines with a string quality value less than or equal to 25 accounts for more than 60% of the entire reading) and N (N means that the base information cannot be determined) ratio is greater than 5% reads to obtain clean reads that can be used for subsequent analysis.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software to obtain mapped reads
FeatureCounts was used to count the reads numbers mapped to each gene
Assembly: 104
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: pancreas

extract_protocol:
Total RNA was extracted from the pancreas using TRIzol Reagent according the Magen.RNA samples were detected based on the A260/A280 absorbance ratio with a Nanodrop ND-2000 system(Thermo Scientific,USA),and the RIN of RNA was determined by an Agilent Bioanalyzer 4150 system(Agilent Technologies,CA,USA).
Paired-end libraries were prepared using a ABclonal mRNA-seq Lib Prep Kit (ABclonal, China) following the manufacturer’s instructions. The mRNA was purified from 1 μg total RNA using oligo (dT) magnetic beads followed by fragmentation carried out using divalent cations at elevated temperatures in ABclonal First Strand Synthesis Reaction Buffer. Subsequently, first-strand cDNAs were synthesized with random hexamer primers and Reverse Transcriptase (RNase H) using mRNA fragments as templates, followed by second-strand cDNA synthesis using DNA polymerase I, RNAseH, buffer, and dNTPs. The synthesized double stranded cDNA fragments were then adapter ligated for preparation of the paired-end library.Adaptor-ligated cDNA were used for PCR amplification. PCR products were purified (AMPure XP system) and library quality was assessed on an Agilent Bioanalyzer 4150 system. Finally, the library preparations were sequenced on an Illumina Novaseq 6000 (or MGISEQ-T7) and 150 bp paired-end reads were generated.

value: pancreas

value: Pancreatic ductal adenocarcinoma cells

value: WT

value: treatment with 10nM TPL with24h


title: Mus musculus liver from mice in Long light, recieving a HFD diet, at timepoint ZT20 [0101_3]

value: Liver

value: Long light

value: HFD


title: Mus musculus liver from mice in Long light, recieving a LFD diet, at timepoint ZT12 [0101_33]

value: LFD


title: Mus musculus liver from mice in Equal light, recieving a HFD diet, at timepoint ZT0 [0101_29]

value: Equal light


title: Miapaca-2 cells,TPL2


title: Mus musculus liver from mice in Long light, recieving a HFD diet, at timepoint ZT4 [0101_28]


title: Miapaca-2 cells,TPL1


title: Miapaca-2 cells,NC3


title: Mus musculus liver from mice in Long light, recieving a LFD diet, at timepoint ZT12 [0101_27]


title: Miapaca-2 cells,NC2


title: A549-IL1B timecourse-MAP3K8 Control-6 hours-sample2

type: RNA

city: London

first: William

last: Cookson

address: Dovehouse Street

country: United Kingdom

institute: Imperial College London

hyb_protocol: Hybridization was performed for 16 h on GeneTitanTM Instrument.

scan_protocol: GeneChips were scanned on a GeneTitan system (Affymetrix Ltd.).

data_processing: The Robust Multichip Analysis (RMA) algorithm, as implemented in Affymetrix Power Tools (APT, version 1.15.0), was utilized for the generation of normalized transcript cluster signal values. Systematic variation in expression between time points and conditions was modeled using LIMMA. Three contrast matrices were generated, first extracting contrasts between time-points under control conditions, second extracting contrasts between time-points under knockdown conditions, and third identifying transcript clusters that respond differently over time between the two conditions. P-values were adjusted using Benjamini and Hochberg's method in order to control the false discovery rate (FDR). Universally low expressed transcript clusters (i.e. those expressed below the median across all 48 arrays) were excluded.

label: Biotin

source_name: MAP3K8 Control-6 hours

label_protocol: Total RNA was converted to labelled cDNA for hybridization onto the gene expression chips using the AmbionTM WT Expression Kit. The single-stranded DNA was fragmented and labelled using Affymetrix GeneChipTM WT Terminal Labelling Kit *.

extract_protocol: RNA was extracted using the Qiagen RNeasy mini kit (Qiagen, Crawley, UK).

tag: genotype/variation

value: Control

tag: agent

tag: time

value: 6 hrs


title: A549-IL1B timecourse-MAP3K8 Knockdown-8 hours-sample3

source_name: MAP3K8 Knockdown-8 hours

value: MAP3K8 Knockdown

value: 8 hrs


title: A549-IL1B timecourse-MAP3K8 Control-1 hours-sample3

source_name: MAP3K8 Control-1 hours

value: 1 hrs


title: A549-IL1B timecourse-MAP3K8 Control-8 hours-sample3

source_name: MAP3K8 Control-8 hours


title: A549-IL1B timecourse-MAP3K8 Knockdown-6 hours-sample4

source_name: MAP3K8 Knockdown-6 hours


title: A549-IL1B timecourse-MAP3K8 Control-4 hours-sample2

source_name: MAP3K8 Control-4 hours

value: 4 hrs


title: A549-IL1B timecourse-MAP3K8 Control-6 hours-sample3


title: A549-IL1B timecourse-MAP3K8 Knockdown-4 hours-sample1

source_name: MAP3K8 Knockdown-4 hours


title: A549-IL1B timecourse-MAP3K8 Knockdown-0 hours-sample2

source_name: MAP3K8 Knockdown-0 hours

value: control

value: 0 hrs


title: A549-IL1B timecourse-MAP3K8 Control-2 hours-sample4

source_name: MAP3K8 Control-2 hours

value: 2 hrs


title: Miapaca-2 cells,NC1

value: pancreas

value: Pancreatic ductal adenocarcinoma cells


title: A549-IL1B timecourse-MAP3K8 Control-0 hours-sample2

source_name: MAP3K8 Control-0 hours


title: A549-IL1B timecourse-MAP3K8 Knockdown-12 hours-sample1

source_name: MAP3K8 Knockdown-12 hours

value: 12 hrs


title: A549-IL1B timecourse-MAP3K8 Knockdown-0 hours-sample3


title: A549-IL1B timecourse-MAP3K8 Control-0 hours-sample1


title: Mus musculus liver from mice in Short light, recieving a LFD diet, at timepoint ZT8 [0101_25]

value: Liver

value: Short light


title: A549-IL1B timecourse-MAP3K8 Knockdown-4 hours-sample3


title: i706_i505

city: cambridge

first: Kendig

last: Sham

state: england

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

department: MRC Cambridge Stem Cell Institute

institute: University of Cambridge

description: DNMT3A WT

data_processing:
STAR alignment parameters: --outFilterMultimapNmax 1 –outSAMstrandField intronMotif –outSAMattributes All –outSAMtype BAM SortedByCoordinate
Picard AddOrReplaceReadGroups with parameters: RGID=4 RGLB=lib1 RGPL=illumina RGPU=unit1 RGSM=20
Picard ValidateSamFile with parameters: MODE=SUMMARY
Picard MarDuplicates -REMOVE_DUPLICATES true
HTSeq was used to ount reads mapped to each gene with parameters: -s no -f bam
Assembly: GRCh38
Supplementary files format and content: raw_counts.txt.gz

source_name: mobilised peripheral blood

growth_protocol: single HSC/MPPs (CD19-/CD33-/CD34+/CD45dim/CD38-/CD45RA-) and single GMPs (CD19-, CD33-, CD34+, CD45dim, CD38+, CD7/CD10-, CD45RA+)  were cultured for 21 days in media promoting HSC/MPP differentiation: StemPro base media supplemented with Nutrients , Pen/Strep (1%), L-Glu (1%), human LDL (50ng/ml)  in addition to the following cytokines: SCF (100ng/ml), Flt-3L (20ng/ml), TPO (100ng/ml), EPO (3 units/ml), IL-6 (50ng/ml), IL-3 (10ng/ml) and GM-CSF (20ng/ml), IL-11 (50ng/ml), IL-2 (10ng/ml), IL-7 (20ng/ml).

extract_protocol:
Qiagen RNA extraction kit
Library preparation was performed based on the protocol from Picelli et al. (doi: 10.1038/nprot.2014.006) modified as follows: 1) using a set input of 500pg for each sample in 2uL volume 2) starting protocol at reverse transcription step 3) number of preamplification cycles changed from 21 to 16 4) cDNA input amount for library prep step with Illumina Nextera XT kit was 0.2ng 5) library pooling and clean up step modified by quantifying each sample individually and making an equimolar pool for sequencing.

value: mobilised peripheral blood

value: Single haematopoietic granulocyte macrophage progenitor cell derived colonies

value: DNMT3A WT

value: 21 day culture in MEM medium


title: A549-IL1B timecourse-MAP3K8 Knockdown-2 hours-sample2

source_name: MAP3K8 Knockdown-2 hours


title: Mus musculus liver from mice in Equal light, recieving a HFD diet, at timepoint ZT8 [0101_24]

value: Equal light

value: HFD


title: A549-IL1B timecourse-MAP3K8 Knockdown-6 hours-sample3

value: MAP3K8 Knockdown

value: 6 hrs


title: A549-IL1B timecourse-MAP3K8 Knockdown-6 hours-sample2


title: i705_i511

description: DNMT3A mut

value: DNMT3A mut


title: Mus musculus liver from mice in Short light, recieving a HFD diet, at timepoint ZT20 [0101_26]


title: Mus musculus liver from mice in Short light, recieving a HFD diet, at timepoint ZT8 [0101_23]


title: A549-IL1B timecourse-MAP3K8 Control-4 hours-sample1

value: Control

value: 4 hrs


title: A549-IL1B timecourse-MAP3K8 Knockdown-4 hours-sample2


title: A549-IL1B timecourse-MAP3K8 Control-12 hours-sample1

source_name: MAP3K8 Control-12 hours


title: A549-IL1B timecourse-MAP3K8 Control-2 hours-sample2

value: 2 hrs


title: i703_i507

description: DNMT3A mut


title: i704_i507

description: DNMT3A WT


title: Mus musculus liver from mice in Equal light, recieving a HFD diet, at timepoint ZT4 [0101_22]


title: i702_i508

description: DNMT3A mut


title: Mus musculus liver from mice in Short light, recieving a LFD diet, at timepoint ZT16 [0101_21]

value: LFD


title: i702_i507

description: DNMT3A mut


title: Mus musculus liver from mice in Short light, recieving a LFD diet, at timepoint ZT8 [0101_20]


title: Mus musculus liver from mice in Short light, recieving a LFD diet, at timepoint ZT4 [0101_2]


title: Mus musculus liver from mice in Short light, recieving a HFD diet, at timepoint ZT20 [0101_19]


title: ESCA20T

city: Shanghai

first: Shenglin

last: Huang

address: 270 Dongan

institute: Fudan University

data_processing:
The raw data after quality control was aligned to human reference genome  (GRCh38) by STAR
gene expression were qualified by featureCounts (version 1.6.2) with Genecode(version 29)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: esophagus tissue

extract_protocol:
Total RNAs (500 ng) from ESCC tissues and matched normal tissues were extracted by Trizol® Reagent (Thermo, USA) and treated with DNase I (NEB) to remove DNA before constructing the RNA-seq libraries.
QIAseq FastSelect reagent was added to the RNA sample to fragment the RNA at 85°C for 6 minutes and then stepwise cool the reaction from 75°C to 25°C for 14 minutes. First- and second-strand cDNA was synthesized with random hexamer primers, treated with DNA End Repair Kit (Qiagen) to repair the ends, then modified with Klenow to add an A at the 3’ end of the DNA fragments, and finally ligated to adapters. Purified dsDNA was further subjected to 11 cycles of PCR amplification. The libraries were quality controlled with Qubit (Thermo Fisher Scientific, USA) and Qsep100 (BiOptic, China)

tag: disease state

value: Early Esophageal Squamous Cell Carcinoma

value: esophagus tissue

value: tumor


title: ESCA19T


title: Mus musculus liver from mice in Short light, recieving a HFD diet, at timepoint ZT4 [0101_18]

source_name: Liver

value: Liver

value: Short light


title: ESCA18T


title: Mus musculus liver from mice in Equal light, recieving a LFD diet, at timepoint ZT0 [0101_17]


title: A549-IL1B timecourse-MAP3K8 Knockdown-6 hours-sample1


title: ESCA17T


title: A549-IL1B timecourse-MAP3K8 Control-6 hours-sample4


title: A549-IL1B timecourse-MAP3K8 Knockdown-4 hours-sample4


title: Mus musculus liver from mice in Short light, recieving a HFD diet, at timepoint ZT0 [0101_16]


title: A549-IL1B timecourse-MAP3K8 Control-12 hours-sample2

value: 12 hrs


title: A549-IL1B timecourse-MAP3K8 Control-4 hours-sample4


title: A549-IL1B timecourse-MAP3K8 Control-1 hours-sample1

value: 1 hrs


title: A549-IL1B timecourse-MAP3K8 Knockdown-2 hours-sample3


title: A549-IL1B timecourse-MAP3K8 Knockdown-1 hours-sample1

source_name: MAP3K8 Knockdown-1 hours


title: ESCA16T


title: A549-IL1B timecourse-MAP3K8 Knockdown-1 hours-sample3


title: A549-IL1B timecourse-MAP3K8 Control-4 hours-sample3


title: A549-IL1B timecourse-MAP3K8 Knockdown-2 hours-sample1


title: A549-IL1B timecourse-MAP3K8 Control-0 hours-sample3

value: control

value: 0 hrs


title: A549-IL1B timecourse-MAP3K8 Control-8 hours-sample1

value: 8 hrs


title: A549-IL1B timecourse-MAP3K8 Control-2 hours-sample1


title: Mus musculus liver from mice in Long light, recieving a LFD diet, at timepoint ZT20 [0101_15]

value: Long light


title: A549-IL1B timecourse-MAP3K8 Knockdown-8 hours-sample1

value: MAP3K8 Knockdown


title: Mus musculus liver from mice in Short light, recieving a HFD diet, at timepoint ZT12 [0101_14]

value: HFD


title: ESCA14T


title: A549-IL1B timecourse-MAP3K8 Control-2 hours-sample3

value: Control


title: Mus musculus liver from mice in Long light, recieving a LFD diet, at timepoint ZT8 [0101_13]


title: A549-IL1B timecourse-MAP3K8 Knockdown-12 hours-sample3


title: ESCA10T


title: A549-IL1B timecourse-MAP3K8 Knockdown-8 hours-sample2


title: A549-IL1B timecourse-MAP3K8 Control-1 hours-sample2


title: A549-IL1B timecourse-MAP3K8 Knockdown-0 hours-sample1


title: A549-IL1B timecourse-MAP3K8 Knockdown-2 hours-sample4


title: ESCA15T


title: Mus musculus liver from mice in Short light, recieving a LFD diet, at timepoint ZT20 [0101_122]


title: Mus musculus liver from mice in Long light, recieving a HFD diet, at timepoint ZT0 [0101_120]


title: Mus musculus liver from mice in Short light, recieving a HFD diet, at timepoint ZT8 [0101_123]


title: Mus musculus liver from mice in Equal light, recieving a HFD diet, at timepoint ZT16 [0101_121]

value: Equal light


title: ESCA19N

value: adjacent normal


title: ESCA20N


title: ESCA01T


title: PERK -/-  Veh Replicate 3

city: La Jolla

first: R.

middle: Luke

last: Wiseman

address: 10550 N Torrey Pines Rd

department: Dept. of Molecular Medicine

institute: The Scripps Research Institute

data_processing:
Alignment using DNAstar Lasergene SeqManPro
Read counts generated using ArrayStar 12.2 with QSeq
Differential expression calculations using DESeq 2 v. 1.34
Assembly: GRCm39
Supplementary files format and content: 2023-02-27 ISR Activators read counts.txt

source_name: MEF

extract_protocol:
QuickRNA mini kit (Zymo)
DNBSEQ Eukaryotic Strand-specific
ribosomal depletion, mRNA selection

value: MEF

value: Mouse Embroyonic Fibroblast

value: PERK -/-

value: DMSO


title: PERK -/-  Veh Replicate 2


title: ESCA07T

value: Early Esophageal Squamous Cell Carcinoma

value: esophagus tissue

value: tumor


title: A549-IL1B timecourse-MAP3K8 Knockdown-1 hours-sample2

value: 1 hrs


title: A549-IL1B timecourse-MAP3K8 Control-12 hours-sample3

value: 12 hrs


title: ESCA18N


title: Dissociated antral cells sorted as live, EPCAM-negavie population

city: Berlin

first: Cornelius

last: Fischer

state: Berlin

address: Robert-Rössle-Straße 10

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrück Center for Molecular Medicine (MDC)

description: Cellranger output files (multiple flies)

data_processing:
HiSeq 4000 data was demultiplexed using bcl2fastq v2.20.0
Fastq data from different lanes and appropriate indexes was merged.
Alignment, filtering, UMI counting, barcode counting and gene-barcode matrix generation was done with Cell Ranger (3.1.0, 10X Genomics).
Seurat version 3 was used for downstream analysis.
Genome_build: mm10 (Ensembl, GRCm38.93)
Supplementary_files_format_and_content: Cell Ranger output

molecule: polyA RNA

source_name: murrine stomach antrum

growth_protocol: The stomach was opened along the lesser curvature and whole antrum and transitional zone were removed and washed in PBS. Epithelial cells were removed by incubating tissue in calcium and magnesium-free DMEM (Gibco) containing 10 mM EDTA for 20 min at 37 °C with gentle agitation. Next, stomach pieces were washed and incubated in DMEM (Gibco) containing Liberase TL (1 unit/ml; Roche) and DNase I (1 unit/ml; Invitrogen) at 37 °C. After 20 min, the digested fraction was collected and put on ice. This cycle was repeated two more times for a total digestion time of 60 min. The remaining stomach fragments were collected, filtered through a 100-μm mesh and mixed with the collected supernatants. Cells were then stained againast EPCAM and EPCAM negative cells were supnitted for ScRNAseq

extract_protocol:
Libraries were prepared as per manufacturer's insturctions provided by 10X Genomics platform for the Single Cell 3-prime Gene Expression v3.1 workflow.
scRNA seq

value: stomach antrum


title: PERK -/-  Tg Replicate 3

value: Thapsigargin


title: A549-IL1B timecourse-MAP3K8 Control-6 hours-sample1

source_name: MAP3K8 Control-6 hours

value: 6 hrs


title: A549-IL1B timecourse-MAP3K8 Control-8 hours-sample2

source_name: MAP3K8 Control-8 hours

value: 8 hrs


title: Mus musculus liver from mice in Short light, recieving a HFD diet, at timepoint ZT20 [0101_119]

value: Liver

value: Short light

value: HFD


title: PERK -/-  Tg Replicate 2


title: A549-IL1B timecourse-MAP3K8 Knockdown-12 hours-sample2

value: MAP3K8 Knockdown


title: Mm_CD4_chronic_II

description:
Cellranger output files (multiple files)
SP008_chronic_2

data_processing:
HiSeq 4000 data was demultiplexed using bcl2fastq v2.20.0
Fastq data from different lanes and appropriate indexes was merged.
Alignment, filtering, UMI counting, barcode counting and gene-barcode matrix generation was done with Cell Ranger (3.0.2, 10X Genomics).
Cellbender v1 (remove-background)
Seurat version 3 was used for downstream analysis (min cells 5 per gene, min features per cell 300). Non-T-cell contamination removed. SCT regression (cell-cycle and mtRNA)
Genome_build: mm10 (Ensembl, GRCm38.93)
Supplementary_files_format_and_content: HDF5 feature-barcode matrixes

source_name: immune cells

growth_protocol: To induce EAE in mice, 125 µg MOG35-55 (Charité Universitätsmedizin Berlin) emulsified in 400 µg M. tuberculosis H-37Ra and complete Freund´s adjuvant (Sigma-Aldrich) was injected subcutaneously followed by 2 intraperitoneal injections of 300 ng pertussis toxin reconstituted in Phosphate Buffered Saline (PBS) (Gibco) at 2 and 24 hours post immunization. Mice were monitored, weighed and scored on a daily basis.

extract_protocol:
At the designated chronic or acutetimepoint mice received a lethal dose of a Ketamine-Xylazine mixture (Ketamine320 mg/kg; Xylazine 5 mg/kg) i.p. and were transcardially perfused with 50ml ofice cold PBS. spinal cord tissue was removed and placed in a small petri dishand fully covered with ice cold D-PBS (with Ca2+, Mg2+,glucose and pyruvate, Gibco). Now under sterile conditions, tissues werechopped into smaller pieces and transferred into C-tubes® containing enzyme mix 1 and 2 (for furtherdetails please refer to manufactures protocol). The tissue was homogenized onthe gentleMACS® Octo Dissociator with Heaters (Miltenyi), program 37C_ABDK_01. Followinghomogenization, C-tubes® containing homogenate were briefly centrifuged, resuspendedin 10 ml of cold D-PBS then passed through a 100 µm cell strainer placed on anew 50 ml tube. The cell suspension was centrifuged at 300 x g and 4 °C for[TC1] 10 min. The supernatant was completely aspirated and the cell pelletwas at first resuspended with 3.1 ml cold D-PBS and 900 µl Percoll®, transferredinto a new 15 ml tube and then overlaid with 4 ml cold D-PBS. To remove most ofthe cell debris and myelin a density gradient centrifugation step was performedat 3,000 x g and 4 °C for 10 min with a soft acceleration and brake. The twotop phases were aspirated, the 15 ml tube was filled with cold D-PBS, gentlyinverted, centrifuged at 1,000 x g and 4 °C for 10 min with full accelerationand brake. Again, the supernatant was aspirated and now an erythrolysis wasperformed by adding 10 ml of 1X Red Blood Cell Removal Solution® followed by anincubation of 10 min at 4 °C. The lysis was stopped by adding 10 ml of coldD-PBS/BSA buffer (0.5 % BSA, pH 7.2). A final washing step at 300 x g and 4 °Cfor 10 min prepared the single cell suspension for the following immunostainingprocedure.
Libraries were prepared as per manufacturer's insturctions provided by 10X Genomics platform for the Single Cell 3-prime Gene Expression v3 workflow.
scRNA seq

treatment_protocol: To induce a remission in animals, corticosteroids (1.6 mg Methylprednisolone in 200 µl 0.9 % NaCl) were administered interperitoneally on 3-5 consecutive days at the peak of the disease (Chan et al, 2008; Schmidt et al, 2000).

value: CD4 T cells

tag: strain

value: immune cells

value: chronic autoimmune encephalomyelitis


title: Mm_CD4_chronic_I

description:
Cellranger output files (multiple files)
SP008_chronic_1


title: Mm_CD4_acute_I

description:
Cellranger output files (multiple files)
SP008_acute_1

value: acute autoimmune encephalomyelitis


title: ESCA17N

value: Early Esophageal Squamous Cell Carcinoma

value: adjacent normal


title: Mm_CD4_acute_II

description:
Cellranger output files (multiple files)
SP008_acute_2


title: Mus musculus liver from mice in Equal light, recieving a LFD diet, at timepoint ZT8 [0101_118]

value: Equal light

value: LFD


title: PERK -/-  Halofuginone + Tg Replicate 3

value: MEF

value: Mouse Embroyonic Fibroblast

value: PERK -/-

value: Halofuginone + Thapsigargin


title: ESCA16N

value: esophagus tissue


title: PERK -/-  Halofuginone + Tg Replicate 1


title: Mus musculus liver from mice in Short light, recieving a LFD diet, at timepoint ZT20 [0101_12]

value: Liver


title: PERK -/-  Veh Replicate 1

value: DMSO


title: Mus musculus liver from mice in Long light, recieving a LFD diet, at timepoint ZT8 [0101_117]

value: Long light


title: PERK -/-  Halofuginone Replicate 3

value: Halofuginone


title: ESCA15N


title: PERK -/-  Halofuginone Replicate 1


title: PERK -/-  Halofuginone + Tg Replicate 2


title: Mus musculus liver from mice in Short light, recieving a LFD diet, at timepoint ZT4 [0101_116]

value: Short light


title: ESCA14N


title: Mus musculus liver from mice in Long light, recieving a LFD diet, at timepoint ZT4 [0101_115]


title: PERK -/-  BtdCPU + Tg Replicate 2

value: BtdCPU + Thapsigargin


title: PERK -/-  Halofuginone Replicate 2


title: PERK -/-  Tg Replicate 1

value: Thapsigargin


title: Mus musculus liver from mice in Long light, recieving a LFD diet, at timepoint ZT16 [0101_114]


title: PERK -/-  BtdCPU + Tg Replicate 1


title: Mus musculus liver from mice in Long light, recieving a HFD diet, at timepoint ZT12 [0101_113]

value: HFD


title: PERK -/-  BtdCPU Replicate 2

value: BtdCPU


title: Mus musculus liver from mice in Long light, recieving a LFD diet, at timepoint ZT0 [0101_112]


title: ESCA01N

value: Early Esophageal Squamous Cell Carcinoma

value: adjacent normal


title: PERK -/- BtdCPU Replicate 1


title: PERK WT Veh Replicate 3

value: WT


title: PERK WT Veh Replicate 2

value: MEF


title: Mus musculus liver from mice in Short light, recieving a LFD diet, at timepoint ZT20 [0101_111]

value: LFD


title: Multiple myeloma cancer stem cells-SKO-007 CSC_rep3

city: Beijing

first: Ying

last: Li

state: AL

address: Beijing Chaoyang Hospital

institute: 首都医科大学附属北京朝阳医院

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. The clean reads were mapped to GRCh38 whole genome using HISAT2.
Gene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped(FPKM).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: Multiple myeloma cancer stem cells

growth_protocol: Parental U266 and SKO-007 cells were cultured in RPMI 1640 with 10% FBS, 2 mM glutamine and 1% P/S. The reprogrammed multiple myeloma cancer stem cells were cultured in Expansion Medium (mTeSR containing 2% FBS, 10 μl ml-1 B27, 0.1% PVA, 0.1% Glycerol, 0.1 mM cAMP, and 1% P/S). Cells were cultured at 37℃ and 5% CO2.

extract_protocol:
Total RNA from cells was extracted using TRIzol
The cDNA library was constructed following the manufacturer’s instructions of NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, E7530) and NEBNext Multiplex Oligos for Illumina (NEB, E7500). The enriched mRNA was fragmented into approximately 200nt RNA inserts, which were used to synthesize the first-strand cDNA and the second cDNA. The double-stranded cDNA were performed end-repair/dA-tail and adaptor ligation. The suitable fragments were isolated by Agencourt AMPure XP beads (Beckman Coulter, Inc.), and enriched by PCR amplification. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 and qPCR. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kitv3-cBot-HS(Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform at Biomarker Technologies(Beijing, China) and pair-end reads were generated.

treatment_protocol: To determine the efect of dihydroartemisinin on the global transcriptional profiles of the reprogrammed MMSCs(U266-CSCs), U266-CSCs were treated with vehicle or dihydroartemisinin (5 μM) for 48 h.

value: Multiple myeloma cancer stem cells

value: untreated


title: PERK WT Tg Replicate 2

value: Mouse Embroyonic Fibroblast


title: PERK WT Veh Replicate 1


title: Mus musculus liver from mice in Long light, recieving a LFD diet, at timepoint ZT20 [0101_110]

value: Liver


title: PERK WT Tg Replicate 3


title: Multiple myeloma cancer stem cells-SKO-007 CSC_rep2

institute: 首都医科大学附属北京朝阳医院


title: Multiple myeloma cancer stem cells-SKO-007 CSC_rep1

institute: 首都医科大学附属北京朝阳医院


title: Multiple myeloma cancer cells-SKO-007_rep3

institute: 首都医科大学附属北京朝阳医院

source_name: Multiple myeloma cells

value: Multiple myeloma cells


title: PERK WT Halofuginone + Tg Replicate 3

value: Halofuginone + Thapsigargin


title: ESCA10N

value: esophagus tissue


title: PERK WT Tg Replicate 1


title: PERK -/-  BtdCPU + Tg Replicate 3

value: PERK -/-


title: Mus musculus liver from mice in Equal light, recieving a LFD diet, at timepoint ZT16 [0101_11]

value: Equal light


title: Mus musculus liver from mice in Equal light, recieving a LFD diet, at timepoint ZT12 [0101_109]


title: PERK -/-  BtdCPU Replicate 3


title: NSCs-passage10 treated with ESC-sEVs rep-4

first: zhifeng

last: deng

address: 600 yishan road

institute: shanghai 6th people's hospital

description:
total RNA from primary cultured NSCs treated with ESC-sEV at passage10 rep-4
NSC6P10exo

data_processing:
Purified libraries were quantified by Qubit® 2.0 Fluorometer (Life Technologies) and validated by Agilent 4200 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced by using the Next Generation Sequencing (NGS) on the Illumina HiSeq 2500.
Raw Reads were checked Seqtk to select the clean Reads. Genome mapping was carried out by using Hisat2 (version: 2.0.4)
Using Stringtie (version:1.3.0) to calculate genes's fragments, and perl was used to calculate Fragments Per Kilobase of exon model per Million mapped reads (FPKM) of every gene
Genome_build: perl was used to calculate Fragments Per Kilobase of exon model per Million mapped reads (FPKM) of every gene
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene

source_name: NSCs

growth_protocol: NSCs were cultured in complete H-NSCs medium: DMEM/F12 medium supplemented with 2% B27 (Gibco Life Technologies), 1% penicillin/streptomycin (Gibco Life Technologies), 20 ng/ml epidermal growth factor (EGF, ProSpec), 20 ng/ml basic fibroblast growth factor (bFGF, ProSpec), and 5 μg / ml heparin (Sigma-Aldrich)

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany). Paired-end libraries were synthesized by using the TruSeq™ RNA Sample Preparation Kit (Illumina, USA) following TruSeq™ RNA Sample Preparation Guide. The poly-A containing mRNA molecules were purified using Poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under 94°C for 8 min. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: ESC-sEVs or an equal volume of PBS from passage 2 to passage 10

value: hippocampus

value: wild type


title: PERK WT Halofuginone + Tg Replicate 2


title: ESCA07N


title: Mus musculus liver from mice in Short light, recieving a LFD diet, at timepoint ZT4 [0101_108]

value: Short light


title: Multiple myeloma cancer cells-SKO-007_rep1

institute: 首都医科大学附属北京朝阳医院


title: NSCs-passage10 treated with ESC-sEVs rep-3

description:
total RNA from primary cultured NSCs treated with ESC-sEV at passage10 rep-3
NSC5P10exo


title: NSCs-passage10 treated with ESC-sEVs rep-2

description:
total RNA from primary cultured NSCs treated with ESC-sEV at passage10 rep-2
NSC4P10exo


title: Mus musculus liver from mice in Equal light, recieving a HFD diet, at timepoint ZT8 [0101_107]

value: HFD


title: NSCs-passage10 treated with ESC-sEVs rep-1

description:
total RNA from primary cultured NSCs treated with ESC-sEV at passage10 rep-1
NSC1P10exo


title: Mus musculus liver from mice in Short light, recieving a LFD diet, at timepoint ZT16 [0101_106]


title: Multiple myeloma cancer stem cells-U266 CSC DHA10_rep3

institute: 首都医科大学附属北京朝阳医院

value: treated with DHA


title: Multiple myeloma cancer stem cells-U266 CSC DHA10_rep2

institute: 首都医科大学附属北京朝阳医院


title: NSCs-passage10 treated with PBS rep-4

description:
total RNA from primary cultured NSCs treated with PBS at passage10 rep-4
NSC6P10


title: PERK WT Halofuginone Replicate 3

value: WT

value: Halofuginone


title: NSCs-passage10 treated with PBS rep-3

description:
total RNA from primary cultured NSCs treated with PBS at passage10 rep-3
NSC5P10


title: Mus musculus liver from mice in Long light, recieving a LFD diet, at timepoint ZT8 [0101_105]

value: Long light

value: LFD


title: Mus musculus liver from mice in Equal light, recieving a LFD diet, at timepoint ZT8 [0101_104]


title: PERK WT Halofuginone Replicate 1

value: MEF


title: PERK WT BtdCPU + Tg Replicate 3

value: Mouse Embroyonic Fibroblast

value: BtdCPU + Thapsigargin


title: Multiple myeloma cancer stem cells-U266 CSC DHA10_rep1

institute: 首都医科大学附属北京朝阳医院

value: Multiple myeloma cancer stem cells


title: Multiple myeloma cancer cells-SKO-007_rep2

institute: 首都医科大学附属北京朝阳医院

value: Multiple myeloma cells

value: untreated


title: NSCs-passage10 treated with PBS rep-1

description:
total RNA from primary cultured NSCs treated with PBS at passage10 rep-1
NSC1P10


title: Mus musculus liver from mice in Equal light, recieving a HFD diet, at timepoint ZT8 [0101_103]

value: Liver


title: PERK WT Halofuginone + Tg Replicate 1

value: Halofuginone + Thapsigargin


title: PERK WT BtdCPU + Tg Replicate 2


title: Mus musculus liver from mice in Long light, recieving a LFD diet, at timepoint ZT4 [0101_102]


title: NSCs-passage2 rep-4

description:
total RNA from primary cultured NSCs at passage2 rep-4
NSC6P2

value: hippocampus


title: Multiple myeloma cancer stem cells-U266 CSC_rep1

institute: 首都医科大学附属北京朝阳医院


title: PERK WT BtdCPU + Tg Replicate 1


title: Multiple myeloma cancer stem cells-U266 CSC_rep2

institute: 首都医科大学附属北京朝阳医院


title: Multiple myeloma cells-U266_rep3

institute: 首都医科大学附属北京朝阳医院


title: PERK WT BtdCPU Replicate 3

value: BtdCPU


title: Mus musculus liver from mice in Long light, recieving a LFD diet, at timepoint ZT20 [0101_101]


title: Mus musculus liver from mice in Short light, recieving a HFD diet, at timepoint ZT8 [0101_100]

value: Short light


title: NSCs-passage2 rep-2

description:
total RNA from primary cultured NSCs at passage2 rep-2
NSC4P2

value: wild type


title: Multiple myeloma cells-U266_rep2

institute: 首都医科大学附属北京朝阳医院


title: NSCs-passage2 rep-3

description:
total RNA from primary cultured NSCs at passage2 rep-3
NSC5P2


title: PERK WT BtdCPU Replicate 2


title: Mus musculus liver from mice in Short light, recieving a HFD diet, at timepoint ZT4 [0101_10]

value: HFD


title: PERK WT Halofuginone Replicate 2

value: WT


title: NSCs-passage2 rep-1

description:
total RNA from primary cultured NSCs at passage2 rep-1
NSC1P2


title: NSCs-passage10 treated with PBS rep-2

description:
total RNA from primary cultured NSCs treated with PBS at passage10 rep-2
NSC4P10


title: Multiple myeloma cancer stem cells-U266 CSC_rep3

institute: 首都医科大学附属北京朝阳医院


title: PERK WT BtdCPU Replicate 1


title: Multiple myeloma cells-U266_rep1

institute: 首都医科大学附属北京朝阳医院


title: Mus musculus liver from mice in Long light, recieving a HFD diet, at timepoint ZT20 [0101_1]


title: RNAPol2-Ser5_YAP1_Glutathione_low_(230801_SH_Mm_P2S5_Ypl_0727)

status: Public on Sep 08 2023

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: Test of Biomag Plus Amine and Pierce Gluathione magnetic beads, see FFPE_beadtest.pdf

data_processing:
Genome_build: mm10
1. We used cutadapt 2.9 with parameters "-j 8 --nextseq-trim 20 -m 20 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -Z" to trim adapters from 50bp paired-end reads. 2. We used Bowtie2 2.4.4 with options "--very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 1000" to map the paired-end 50bp reads to the repeat-masked mm10 Mus musculus reference sequence obtained from UCSC. 3. We used samtools 1.14 "view" to extract properly paired reads from the mm10 alignments. 4. We used bedtools 2.30.0 "genomecov" to make a normalized count mm10 track which is the fraction of counts at each base pair scaled by the size of the mm10 reference sequence (2725537669) so that if the counts were uniformly distributed across the reference sequence there would be one at each position (Supplementary file .mm10.bw)

source_name: FFPE-CUTAC

extract_protocol:
FFPE_beadtest.pdf
CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID:31036827

tag: antibody

value: RNAP2Ser5P Cell Signaling Technology cat# 13523

value: mouse brain tumor FFPE


title: RNAPol2-Ser5_YAP1_Glutathione_high_(230801_SH_Mm_P2S5_Yph_0727)


title: RNAPol2-Ser5_RELA_onslide_5micron47_(230801_SH_Mm_P2S5s_5R4_0727)

description: Biological replicate with on-slide dissection, see FFPE_onslide.pdf

extract_protocol:
FFPE_onslide.pdf
CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID:31036827


title: RNAPol2-Ser5_RELA_onslide_5micron27_(230801_SH_Mm_P2S5s_5R2_0727)


title: RNAPol2-Ser5_RELA_onslide_5micron37_(230801_SH_Mm_P2S5s_5R3_0727)


title: RNAPol2-Ser5_RELA_onslide_57_(230801_SH_Mm_P2S5s_R5_0727)


title: RNAPol2-Ser5_RELA_onslide_67_(230801_SH_Mm_P2S5s_R6_0727)


title: RNAPol2-Ser5_RELA_onslide_52_(230801_SH_Mm_P2S5s_R5_0722)


title: RNAPol2-Ser5_RELA_onslide_47_(230801_SH_Mm_P2S5s_R4_0727)


title: RNAPol2-Ser5_YAP1_Biomag-amine_low_(230801_SH_Mm_P2S5_Ybl_0727)


title: RNAPol2-Ser5_RELA_onslide_37_(230801_SH_Mm_P2S5s_R3_0727)


title: RNAPol2-Ser5_RELA_onslide_32_(230801_SH_Mm_P2S5s_R3_0722)


title: RNAPol2-Ser5_RELA_onslide_22_(230801_SH_Mm_P2S5s_R2_0722)


title: RNAPol2-Ser5_RELA_onslide_17_(230801_SH_Mm_P2S5s_R1_0727)


title: RNAPol2-Ser5_RELA_onslide_42_(230801_SH_Mm_P2S5s_R4_0722)


title: RNAPol2-Ser5_RELA_onslide_12_(230801_SH_Mm_P2S5s_R1_0722)


title: RNAPol2-Ser5_PDGFB_onslide_80_(230801_SH_Mm_P2S5_P8_0720)


title: RNAPol2-Ser5_RELA_onslide_27_(230801_SH_Mm_P2S5s_R2_0727)


title: RNAPol2-Ser5_PDGFB_onslide_70_(230801_SH_Mm_P2S5_P7_0720)


title: RNAPol2-Ser5_PDGFB_onslide_10_(230801_SH_Mm_P2S5_P1_0720)


title: RNAPol2-Ser5_PDGFB_onslide_60_(230725_SH_Mm_P2S5_P6_0720)


title: RNAPol2-Ser5_Normal_brain_onslide_9_(230801_SH_Mm_P2S5_N7_0720)


title: RNAPol2-Ser5_PDGFB_onslide_30_(230801_SH_Mm_P2S5_P3_0720)


title: RNAPol2-Ser5_Normal_brain_onslide_8_(230801_SH_Mm_P2S5_N6_0720)


title: RNAPol2-Ser5_Normal_brain_onslide_7_(230801_SH_Mm_P2S5_N5_0720)


title: RNAPol2-Ser5_Normal_brain_onslide_6_(230801_SH_Mm_P2S5_N3_0720)


title: RNAPol2-Ser5_Normal_brain_onslide_4_(230801_SH_Mm_P2S5_N1_0720)


title: RNAPol2-Ser5_Normal_brain_onslide_2_(230801_SH_Mm_P2S5s_N2_0722)


title: RNAPol2-Ser25_YAP1_onslide_2_(230801_SH_Mm_P2S25s_Y2_0727)

value: RNAP2,5p Cell Signaling Technology cat# 13523


title: RNAPol2-Ser5_Normal_brain_onslide_10_(230725_SH_Mm_P2S5_N8_0720)


title: RNAPol2-Ser25_YAP1_onslide_3_(230801_SH_Mm_P2S25s_Y3_0727)


title: RNAPol2-Ser5_Normal_brain_onslide_1_(230801_SH_Mm_P2S5s_N1_0722)


title: RNAPol2-Ser25_YAP1_Glutathione_low_(230801_SH_Mm_P2S25_Ypl_0727)


title: RNAPol2-Ser5_Normal_brain_Biomag-amine_low_(230801_SH_Mm_P2S5_Nbl_0727)


title: RNAPol2-Ser25_YAP1_onslide_4_(230801_SH_Mm_P2S25s_Y4_0727)


title: RNAPol2-Ser5_Normal_brain_onslide_3_(230801_SH_Mm_P2S5s_N3_0722)


title: RNAPol2-Ser25_YAP1_onslide_1_(230801_SH_Mm_P2S25s_Y1_0727)


title: RNAPol2-Ser25_YAP1_Glutathione_high_(230801_SH_Mm_P2S25_Yph_0727)


title: RNAPol2-Ser25_Normal_brain_onslide_4_(230801_SH_Mm_P2S25s_N4_0727)


title: RNAPol2-Ser25_Normal_brain_onslide_2_(230801_SH_Mm_P2S25s_N2_0727)


title: RNAPol2-Ser25_Normal_brain_onslide_3_(230801_SH_Mm_P2S25s_N3_0727)


title: RNAPol2-Ser25_Normal_brain_Biomag-amine_low_(230801_SH_Mm_P2S25_Nbl_0727)


title: RNAPol2-Ser5_PDGFB_onslide_40_(230801_SH_Mm_P2S5_P4_0720)


title: RNAPol2-Ser25_YAP1_Biomag-amine_low_(230801_SH_Mm_P2S25_Ybl_0727)


title: RNAPol2-Ser25_Normal_brain_onslide_1_(230801_SH_Mm_P2S25s_N1_0727)


title: RNAPol2-Ser5_PDGFB_onslide_50_(230801_SH_Mm_P2S5_P5_0720)


title: RNAPol2-Ser5_Normal_brain_onslide_5_(230801_SH_Mm_P2S5_N2_0720)


title: Triton_95_P2S5p_(221206_SH_Mm_P2S5p_FF_TX95_1204)

description: Optimization of CUT&Tag for FFPEs: Harsher pre-treatments, see FFPE_heating_series_20221204.pdf

extract_protocol:
FFPE_heating_series_20221204.pdf
CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID:31036827


title: Triton_85_P2S5p_(221206_SH_Mm_P2S5p_FF_TX85_1204)


title: Triton_90_P2S5p_(221206_SH_Mm_P2S5p_FF_TX90_1204)


title: Triton_95_K27me3_(221206_SH_Mm_K27m3_FF_TX95_1204)

value: H3K27me3 Cell Signaling Technology cat# 9733


title: Triton_90_K27me3_(221206_SH_Mm_K27m3_FF_TX90_1204)


title: Triton_80_P2S5p_(221206_SH_Mm_P2S5p_FF_TX80_1204)


title: Triton_80_K27me3_(221206_SH_Mm_K27m3_FF_TX80_1204)


title: Triton_75_P2S5p_(221206_SH_Mm_P2S5p_FF_TX75_1204)


title: Triton_75_K27me3_(221206_SH_Mm_K27m3_FF_TX75_1204)


title: Triton_79_K27me3_(221206_SH_Mm_K27m3_FF_TX70_1204)


title: Triton_70_P2S5p_(221206_SH_Mm_P2S5p_FF_TX70_1204)


title: Triton_65_P2S5p_(221206_SH_Mm_P2S5p_FF_TX65_1204)


title: RNAPol2-Ser5_YAP3_high_(230512_SH_Mm_P2S5_Y3H_0506)

description: Biological replicates at 85oC with 4:1 post-tagmentation splits, see FFPE_85deg.pdf

extract_protocol:
FFPE_85deg.pdf
CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID:31036827


title: Triton_65_K27me3_(221206_SH_Mm_K27m3_FF_TX65_1204)


title: RNAPol2-Ser5_YAP3_1_(230410_SH_Mm_P2S5_Y3_0330)

description: Biological replicates and double (except pAG-Tn5), see FFPE_90deg.pdf

extract_protocol:
FFPE_90deg.pdf
CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID:31036827


title: RNAPol2-Ser5_YAP3_low_(230512_SH_Mm_P2S5_Y3l_0506)


title: RNAPol2-Ser5_YAP2_low_(230512_SH_Mm_P2S5_Y2l_0506)


title: RNAPol2-Ser5_YAP2_high_(230512_SH_Mm_P2S5_Y2H_0506)


title: RNAPol2-Ser5_YAP1_5_(230503_SH_Mm_P2S5_Y85-12_0429)

description: Testing mineral oil extraction followed by 80oC or 85oC pre-incubations, see FFPE_temp_mineraloil.pdf

extract_protocol:
FFPE_temp_mineraloil.pdf
CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID:31036827


title: RNAPol2-Ser5_YAP1_1_(230404_SH_Mm_P2S5_Y1_0330)


title: RNAPol2-Ser5_YAP1_4_(230503_SH_Mm_P2S5_Y85-4_0429)


title: RNAPol2-Ser5_YAP1_3_(230503_SH_Mm_P2S5_Y90-2_04295)


title: Triton_85_K27me3_(221206_SH_Mm_K27m3_FF_TX85_1204)


title: RNAPol2-Ser5_Ser25_YAP1_1_(230410_SH_Mm_P2S525_Y1_0330)


title: RNAPol2-Ser5_YAP2_1_(230404_SH_Mm_P2S5_Y2_0330)


title: RNAPol2-Ser5_Ser25_RELA_1_(230404_SH_Mm_P2S525_R_0330)


title: RNAPol2-Ser5_YAP1_low_(230512_SH_Mm_P2S5_Y1l_0506)


title: RNAPol2-Ser5_YAP1_2_(230503_SH_Mm_P2S5_Y95-2_0429)


title: RNAPol2-Ser5_Ser25_YAP3_1_(230410_SH_Mm_P2S525_Y3_0330)


title: RNAPol2-Ser5_Ser25_Normal_brain_1_(230410_SH_Mm_P2S525_N1_0330)

value: mouse normal brain FFPE


title: RNAPol2-Ser5_YAP1_6_(230503_SH_Mm_P2S5_Y80-12_0429)


title: RNAPol2-Ser5_RELA_high_(230512_SH_Mm_P2S5_RH_0506)


title: RNAPol2-Ser5_Ser25_PDGFB_1_(230410_SH_Mm_P2S525_P_0330)


title: RNAPol2-Ser5_RELA_3_(230321_SH_Mm_P2S5_RS_0319)

description: Xylene->HITE and epitope retrieval test, see Epitope_retrieval.pdf

extract_protocol:
Epitope_retrieval.pdf
CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID:31036827


title: RNAPol2-Ser5_PDGFB_low_(230512_SH_Mm_P2S5_Pl_0506)


title: RNAPol2-Ser5_PDGFB_high_(230512_SH_Mm_P2S5_PH_0506)


title: RNAPol2-Ser5_PDGFB_4_(230428_SH_Mm_P2S5_P80_0422)


title: RNAPol2-Ser5_PDGFB_5_(230428_SH_Mm_P2S5_P85_0422)


title: RNAPol2-Ser5_PDGFB_1_(230410_SH_Mm_P2S5_P_0330)


title: RNAPol2-Ser5_Normal_brain_7_(230503_SH_Mm_P2S5_N80-4_0429)


title: RNAPol2-Ser5_Normal_brain_8_(230503_SH_Mm_P2S5_N80-12_0429)


title: RNAPol2-Ser5_YAP1_high_(230512_SH_Mm_P2S5_Y1H_0506)


title: RNAPol2-Ser5_Normal_brain_6_(230503_SH_Mm_P2S5_N85-12_0429)


title: RNAPol2-Ser5_Normal_brain_5_(230503_SH_Mm_P2S5_N85-4_0429)


title: RNAPol2-Ser5_Normal_brain_4_(230503_SH_Mm_P2S5_N90-2_0429)


title: RNAPol2-Ser5_Normal_brain_3_low_(230512_SH_Mm_P2S5_N3l_0506)


title: RNAPol2-Ser5_Normal_brain_3_high_(230512_SH_Mm_P2S5_N3H_0506)


title: RNAPol2-Ser5_Normal_brain_3_(230503_SH_Mm_P2S5_N95-12_0429)


title: RNAPol2-Ser5_RELA_low_(230512_SH_Mm_P2S5_Rl_0506)


title: RNAPol2-Ser5_Normal_brain_1_high_(230512_SH_Mm_P2S5_N1H_0506)


title: RNAPol2-Ser5_Normal_brain_2_high_(230512_SH_Mm_P2S5_N2H_0506)


title: RNAPol2-Ser525_liver_C12_(230612_RP_Mm_20230520_FFPE_6541_C12)

description: CUTAC for FFPEs

extract_protocol:
https://www.protocols.io/view/cutac-for-ffpes-14egn292zg5d/v1
CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID:31036827

value: RNAP2,5p + Ser5p Cell Signaling Technology cat# 13523

value: mouse normal liver FFPE


title: RNAPol2-Ser5_Normal_brain_2_(230503_SH_Mm_P2S5_N95-2_0429)


title: RNAPol2-Ser5_Normal_brain_1_(230410_SH_Mm_P2S5_N1_0330)


title: RNAPol2-Ser525_liver_B10_(230612_RP_Mm_20230520_FFPE_6541_B10)

description: CUTAC for FFPEs


title: RNAPol2-Ser525_liver_B12_(230612_RP_Mm_20230520_FFPE_6541_B12)

description: CUTAC for FFPEs


title: RNAPol2-Ser525_liver_A12_(230612_RP_Mm_20230520_FFPE_6541_A12)

description: CUTAC for FFPEs


title: RNAPol2-Ser525_cholangiocacinoma_H1_(230612_RP_Mm_20230524_FFPE_O651_H1)

description: CUTAC for FFPEs

value: mouse liver tumor FFPE


title: RNAPol2-Ser525_cholangiocacinoma_G1_(230612_RP_Mm_20230524_FFPE_O651_G1)

description: CUTAC for FFPEs


title: RNAPol2-Ser525_cholangiocacinoma_F1_(230612_RP_Mm_20230524_FFPE_O651_F1)

description: CUTAC for FFPEs


title: RNAPol2-Ser525_liver_A10_(230612_RP_Mm_20230520_FFPE_6541_A10)

description: CUTAC for FFPEs


title: RNAPol2-Ser525_cholangiocacinoma_G3_(230612_RP_Mm_20230526_FFPE_O652_G3)

description: CUTAC for FFPEs


title: RNAPol2-Ser525_YAP3_low_(230512_SH_Mm_P2S525_Y3l_0506)


title: RNAPol2-Ser525_cholangiocacinoma_C3_(230612_RP_Mm_20230526_FFPE_O652_C3)

description: CUTAC for FFPEs


title: RNAPol2-Ser525_YAP2_high_(230512_SH_Mm_P2S525_Y2H_0506)


title: RNAPol2-Ser525_YAP1_(230512_SH_Mm_P2S525_Y1_0506)


title: RNAPol2-Ser525_RELA_low_(230512_SH_Mm_P2S525_Rl_0506)


title: RNAPol2-Ser525_YAP1_high_(230512_SH_Mm_P2S525_Y1H_0506)


title: RNAPol2-Ser5_Normal_brain_2_low_(230512_SH_Mm_P2S5_N2l_0506)


title: RNAPol2-Ser525_YAP2_low_(230512_SH_Mm_P2S525_Y2l_0506)


title: RNAPol2-Ser525_PDGFB_low_(230512_SH_Mm_P2S525_Pl_0506)


title: RNAPol2-Ser525_PDGFB_high_(230512_SH_Mm_P2S525_PH_0506)


title: RNAPol2-Ser525_RELA_high_(230512_SH_Mm_P2S525_RH_0506)


title: RNAPol2-Ser525_Normal_brain_2_high_(230512_SH_Mm_P2S525_N2H_0506)


title: RNAPol2-Ser525_liver_C10_(230612_RP_Mm_20230520_FFPE_6541_C10)

description: CUTAC for FFPEs


title: RNAPol2-Ser525_Normal_brain_1_high_(230512_SH_Mm_P2S525_N1H_0506)


title: RNAPol2-Ser525_Normal_brain_3_low_(230512_SH_Mm_P2S525_N3l_0506)


title: RNAPol2-Ser525_cholangiocacinoma_H3_(230612_RP_Mm_20230526_FFPE_O652_H3)

description: CUTAC for FFPEs


title: RNAPol2-Ser525_Normal_brain_1_low_(230512_SH_Mm_P2S525_N1l_0506)


title: RNAPol2-Ser25_YAP2_high_(230512_SH_Mm_P2S25_Y2H_0506)


title: RNAPol2-Ser25_YAP2_low_(230512_SH_Mm_P2S25_Y2l_0506)


title: RNAPol2-Ser25_YAP1_low_(230512_SH_Mm_P2S25_Y1l_0506)


title: RNAPol2-Ser25_YAP3_low_(230512_SH_Mm_P2S25_Y3l_0506)


title: RNAPol2-Ser25_YAP1_high_(230512_SH_Mm_P2S25_Y1H_0506)


title: RNAPol2-Ser25_YAP3_high_(230512_SH_Mm_P2S25_Y3H_0506)


title: RNAPol2-Ser525_cholangiocacinoma_D3_(230612_RP_Mm_20230526_FFPE_O652_D3)

description: CUTAC for FFPEs


title: RNAPol2-Ser25_RELA_high_(230512_SH_Mm_P2S25_RH_0506)


title: RNAPol2-Ser25_RELA_1_(230308_SH_Mm_P2S25_Rx8_0225)


title: RNAPol2-Ser25_RELA_5_(230417_SH_Mm_P2S25_RLo_0408)

description: Testing 80oC pre-incubation, see FFPE_80deg.pdf

extract_protocol:
FFPE_80deg.pdf
CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID:31036827


title: RNAPol2-Ser25_PDGFB_low_(230512_SH_Mm_P2S25_Pl_0506)


title: RNAPol2-Ser25_PDGFB_high_(230512_SH_Mm_P2S25_PH_0506)


title: RNAPol2-Ser25_PDGFB_6_(230428_SH_Mm_P2S25_P85_0422)


title: RNAPol2-Ser25_PDGFB_1_(230308_SH_Mm_P2S25_Px8_0225)


title: RNAPol2-Ser25_Normal_brain_3_high_(230512_SH_Mm_P2S25_N3H_0506)


title: RNAPol2-Ser25_Normal_brain_3_low_(230512_SH_Mm_P2S25_N3l_0506)


title: RNAPol2-Ser25_Normal_brain_2_high_(230512_SH_Mm_P2S25_N2H_0506)


title: RNAPol2-Ser25_Normal_brain_1_low_(230512_SH_Mm_P2S25_N1l_0506)


title: RNAPol2-Ser25_Normal_brain_1_high_(230512_SH_Mm_P2S25_N1H_0506)


title: K27ac_RELA_1_(230308_SH_Mm_K27ac_Px8_0225)


title: K27ac_PDGFB_2_(230308_SH_Mm_K27ac_Rx8_0225)


title: K27ac_PDGFB_1_(230301_SH_Mm_KacL_PD-B5_0219)


title: H3K27ac_YAP1_high_(230512_SH_Mm_K27ac_Y1H_0506)

value: H3K27ac Abcam cat# ab4729


title: H3K27ac_YAP1_low_(230512_SH_Mm_K27ac_Y1l_0506)


title: RNAPol2-Ser25_RELA_low_(230512_SH_Mm_P2S25_Rl_0506)


title: H3K27ac_YAP1_11_(230410_SH_Mm_K27ac_Y11_0401)


title: H3K27ac_YAP2_low_(230512_SH_Mm_K27ac_Y2l_0506)


title: H3K27ac_YAP1_1_(230404_SH_Mm_K27ac_Y1_0330)


title: H3K27ac_RELA_low_(230512_SH_Mm_K27ac_Rl_0506)


title: H3K27ac_YAP1_2_(230404_SH_Mm_K27ac_Y2_0330)


title: H3K27ac_YAP1_14_(230410_SH_Mm_K27ac_Y14_0401)


title: H3K27ac_YAP1_18_(230410_SH_Mm_K27ac_Y18_0401)


title: H3K27ac_YAP1_3_(230404_SH_Mm_K27ac_Y3_0330)


title: H3K27ac_YAP3_high_(230512_SH_Mm_K27ac_Y3H_0506)


title: H3K27ac_RELA_8_(230410_SH_Mm_K27ac_R8_0401)


title: H3K27ac_RELA_3_(230404_SH_Mm_K27ac_R_0330)


title: H3K27ac_PDGFB_low_(230512_SH_Mm_K27ac_Pl_0506)


title: H3K27ac_YAP1_12_(230410_SH_Mm_K27ac_Y12_0401)


title: RNAPol2-Ser525_YAP3_high_(230512_SH_Mm_P2S525_Y3H_0506)


title: H3K27ac_RELA_1_(230410_SH_Mm_K27ac_R1_0401)


title: H3K27ac_RELA_high_(230512_SH_Mm_K27ac_RH_0506)


title: H3K27ac_PDGFB_Triton_(230321_SH_Mm_K27ac_PT_0319)


title: H3K27ac_RELA_4_(230410_SH_Mm_K27ac_R4_0401)


title: H3K27ac_PDGFB_SDS_(230321_SH_Mm_K27ac_PS_0319)


title: H3K27ac_PDGFB_3_(230404_SH_Mm_K27ac_P_0330)


title: H3K27ac_PDGFB_high_(230512_SH_Mm_K27ac_PH_0506)


title: H3K27ac_YAP2_high_(230512_SH_Mm_K27ac_Y2H_0506)


title: H3K27ac_Normal_brain_2_low_(230512_SH_Mm_K27ac_N2l_0506)


title: H3K27ac_Normal_brain_1_low_(230512_SH_Mm_K27ac_N1l_0506)


title: H3K27ac_Normal_brain_2_(230410_SH_Mm_K27ac_N21_0401)


title: H3K27ac_Normal_brain_1_high_(230512_SH_Mm_K27ac_N1H_0506)


title: H3K27ac_Normal_brain_3_low_(230512_SH_Mm_K27ac_N3l_0506)


title: H3K27ac_Normal_brain_2_high_(230512_SH_Mm_K27ac_N2H_0506)


title: H3K27ac_Normal_brain_mineraloil_(230428_SH_Mm_K27ac_N80m_0425)


title: H3K27ac_Normal_brain_1_(230404_SH_Mm_K27ac_N1_0330)


title: H3K27ac_RELA_2_(230410_SH_Mm_K27ac_R2_0401)


title: 3T3_H3K4me2_3T3_nuclei_(230417_SH_Mm_K4m2_3T3_0405)

description: CUT&Tag-direct for whole cells, see CUTnTag-direct_v4_whole-cells.pdf

extract_protocol:
CUTnTag-direct_v4_whole-cells.pdf
CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID:31036827

value: H3K4me2 Epicypher cat#13-0027

value: mouse NIH 3T3 fibroblast cells


title: 3T3_H3K36me3_3T3_nuclei_(230417_SH_Mm_K36m3_3T3_0405)

value: H3K36me3 Thermo MAS-24687


title: 3T3_H3K27me3_3T3_nuclei_(230417_SH_Mm_K27m3_3T3_0405)


title: K562_H3K4me3_40k_whole-cell_(230421_SH_Hs_K4m3_Kl_0405)

description: H3K4me3 CUT&Tag-direct_v4 40k K562 cells

data_processing:
Genome_build: hg19
1. We used cutadapt 2.9 with parameters "-j 8 --nextseq-trim 20 -m 20 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -Z" to trim adapters from 50bp paired-end reads. 2. We used Bowtie2 2.4.4 with options "--very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 1000" to map the paired-end 50bp reads to the repeat-masked hg19 Homo sapiens reference sequence obtained from UCSC. 3. We used samtools 1.14 "view" to extract properly paired reads from the hg19 alignments. 4. We used bedtools 2.30.0 "genomecov" to make a normalized count hg19 track which is the fraction of counts at each base pair scaled by the size of the hg19 reference sequence (3095693983) so that if the counts were uniformly distributed across the reference sequence there would be one at each position (Supplementary file .hg19.bw)

extract_protocol:
https://www.protocols.io/view/cut-amp-tag-direct-for-whole-cells-with-cutac-x54v9mkmzg3e/v4
CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID:31036827

value: H3K4me3 Active Motif 39159

value: K562 human immortalised myelogenous leukemia cell line


title: K562_H3K4me3_100k_whole-cell_(230421_SH_Hs_K4m3_Kh_0405)

description: H3K4me3 CUT&Tag-direct_v4 100k K562 cells


title: 3T3_H3K4me3_3T3_nuclei_(230417_SH_Mm_K4m3_3T3_0405)


title: 3T3_RNAPol2-Ser5_3T3_nuclei_(230417_SH_Mm_P2S5_3T3_0405)


title: IVV8_10

city: Gainesville

first: Zongliang

last: Jiang

state: FL

address: 2033 Mowry Rd

department: Animal Sciences

institute: University of Florida

description: TPM.txt

data_processing:
Multiplexed sequencing reads that passed filters were trimmed to remove low quality reads and adaptors. The quality of reads after filtering was examined using fastQC, followed by alignment to the bovine reference genome by STAR (2.5.3a) with default parameters. Individual mapped reads were quantified to calculate TPM (transcript per Million) values using RefSeq genes as reference. Data was analyzed using principal component analysis, Leiden clustering analysis, UMAP plotting.
Assembly: ARS-UCD1.2
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Bos taurus

source_name: Embryo

extract_protocol:
Prior to dissociation and single cell collection, embryos were manipulated to remove approximately half of the TE to enrich the cell population for ICM cells
The RNA-seq libraries were generated from individual cells by using the Smart-seq2 v4 Ultra Low Input RNA Kit and Nextera XT DNA Library Prep Kit and multiplexed by Nextera XT indexes (Illumina).

value: Embryo

value: Embryonic cells

value: Blastocyst


title: Hspa5_IP_2

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniquely mapped reads were remained. One more reads with the same start and end position, only one is considered.
After reads were aligned onto the genome, we analysed the unique reads binding regions of HSPA5 on genome using “ABLIRC” strategy.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include peak information for each group.

source_name: HeLa cell

growth_protocol: HeLa cells were first lysed in ice-cold lysis buffer (10 mM HEPES, pH 7.0, 100 mM KCl, 5 mM MgCl2, 0.5% NP-40, 10 mM DTT) with 200 U/ml RNase inhibitor (Promega) and a protease inhibitor (Roche) on ice for 5 min

extract_protocol:
The beads were washed 6 times with lysis buffer and then divided into two groups, one for RNA isolation from HSPA5-RNA complexes and another for the western blotting assay for HSPA5 immunoprecipitation.The HSPA5-bound RNAs were isolated from the immunoprecipitate of monoclonal Flag antibody (Sigma), followed by the preparation of the Illumina Truseq pair-end libraries.
The reverse transcription was performed with RT primers harboring 3′ adaptor sequence and random hexamer. The generated cDNAs were PCR-amplified and the 200–500 bp products were purified

treatment_protocol: The supernatant was pre-cleared with 100 μl of DynaBeads protein G (Life Technologies) at 4 °C for 30 min. The pre-cleared supernatant was incubated with DynaBeads protein G conjugated with monoclonal Flag antibody (Sigma) or Input at 4℃ for 30 min.

value: HeLa


title: Hspa5_input_2


title: Hspa5_input_1


title: H3K27ac_Normal_brain_3_high_(230512_SH_Mm_K27ac_N3H_0506)


title: IVV8_9

description: TPM.txt


title: Hspa5_IP_1


title: IVV8_7

description: TPM.txt


title: IVV8_8

description: TPM.txt


title: IVV8_5

description: TPM.txt


title: IVV8_4

description: TPM.txt


title: IVV8_6

description: TPM.txt


title: H3K27ac_Normal_brain_3_(230404_SH_Mm_K27ac_N3_0330)


title: IVV8_3

description: TPM.txt


title: IVV8_1

description: TPM.txt


title: IVV8_2

description: TPM.txt


title: IVV7_9

description: TPM.txt


title: IVV7_10

description: TPM.txt


title: H1_H3K4me3_whole-cell_(230421_SH_Hs_K4m3_H1_0405)

description: H3K4me3 CUT&Tag-direct_v4 H1 cells

tag: H1 human embryonic cell line


title: IVV7_7

description: TPM.txt


title: IVV6_10

description: TPM.txt


title: IVV7_6

description: TPM.txt


title: IVV6_8

description: TPM.txt


title: IVV7_4

description: TPM.txt


title: IVV7_1

description: TPM.txt


title: IVV6_9

description: TPM.txt


title: IVV7_2

description: TPM.txt


title: IVV7_3

description: TPM.txt


title: IVV6_4

description: TPM.txt


title: IVV6_3

description: TPM.txt


title: IVV6_6

description: TPM.txt


title: IVV6_7

description: TPM.txt


title: IVV5_6

description: TPM.txt


title: IVV6_5

description: TPM.txt


title: IVV5_8

description: TPM.txt


title: IVV5_10

description: TPM.txt


title: IVV7_8

description: TPM.txt


title: IVV5_7

description: TPM.txt


title: IVV7_5

description: TPM.txt


title: IVV5_9

description: TPM.txt


title: IVV5_5

description: TPM.txt


title: IVV5_4

description: TPM.txt


title: IVV5_3

description: TPM.txt


title: IVV4_10

description: TPM.txt


title: IVV5_2

description: TPM.txt


title: IVV5_1

description: TPM.txt


title: IVV4_9

description: TPM.txt


title: IVV4_8

description: TPM.txt


title: IVV4_6

description: TPM.txt


title: IVV4_7

description: TPM.txt


title: IVV4_5

description: TPM.txt


title: IVV4_3

description: TPM.txt


title: IVV6_1

description: TPM.txt


title: IVV6_2

description: TPM.txt


title: IVV4_2

description: TPM.txt


title: IVV3_10

description: TPM.txt


title: IVV4_1

description: TPM.txt


title: IVV3_9

description: TPM.txt


title: IVV3_8

description: TPM.txt


title: IVV3_6

description: TPM.txt


title: IVV3_5

description: TPM.txt


title: IVV3_4

description: TPM.txt


title: IVV3_7

description: TPM.txt


title: IVV3_2

description: TPM.txt


title: IVV3_1

description: TPM.txt


title: IVV2_10

description: TPM.txt


title: IVV2_9

description: TPM.txt


title: IVV2_7

description: TPM.txt


title: IVV2_8

description: TPM.txt


title: IVV2_6

description: TPM.txt


title: IVV2_5

description: TPM.txt


title: IVV4_4

description: TPM.txt


title: IVV2_4

description: TPM.txt


title: IVV2_1

description: TPM.txt


title: IVV2_2

description: TPM.txt


title: IVR8_10

description: TPM.txt


title: IVR8_11

description: TPM.txt


title: IVV2_3

description: TPM.txt


title: IVR8_12

description: TPM.txt


title: IVR8_8

description: TPM.txt


title: IVR8_9

description: TPM.txt


title: IVR8_4

description: TPM.txt


title: IVR8_5

description: TPM.txt


title: IVR8_2

description: TPM.txt


title: IVR8_1

description: TPM.txt


title: IVR8_7

description: TPM.txt


title: IVV3_3

description: TPM.txt


title: IVR7_7

description: TPM.txt


title: IVR7_6

description: TPM.txt


title: IVR7_10

description: TPM.txt


title: IVR7_4

description: TPM.txt


title: IVR7_3

description: TPM.txt


title: IVR7_2

description: TPM.txt


title: IVR7_1

description: TPM.txt


title: IVR5_8

description: TPM.txt


title: IVR5_7

description: TPM.txt


title: IVR5_5

description: TPM.txt


title: IVR5_6

description: TPM.txt


title: IVR8_13

description: TPM.txt


title: IVR8_6

description: TPM.txt


title: IVR5_3

description: TPM.txt


title: IVR4_5

description: TPM.txt


title: IVR8_3

description: TPM.txt


title: IVR4_1

description: TPM.txt


title: IVR3_14

description: TPM.txt


title: IVR3_13

description: TPM.txt


title: IVR7_9

description: TPM.txt


title: IVR4_2

description: TPM.txt


title: IVR3_12

description: TPM.txt


title: IVR4_3

description: TPM.txt


title: IVR5_2

description: TPM.txt


title: IVR3_10

description: TPM.txt


title: IVR3_9

description: TPM.txt


title: IVR4_4

description: TPM.txt


title: IVR3_8

description: TPM.txt


title: IVR3_7

description: TPM.txt


title: IVR3_6

description: TPM.txt


title: IVR3_5

description: TPM.txt


title: IVR3_4

description: TPM.txt


title: IVR3_2

description: TPM.txt


title: IVR1_14

description: TPM.txt


title: IVR3_3

description: TPM.txt


title: IVR1_13

description: TPM.txt


title: IVR1_12

description: TPM.txt


title: IVR4_6

description: TPM.txt


title: IVR1_11

description: TPM.txt


title: IVR3_15

description: TPM.txt


title: IVR1_9

description: TPM.txt


title: IVR1_8

description: TPM.txt


title: IVR3_11

description: TPM.txt


title: IVR1_7

description: TPM.txt


title: IVR1_6

description: TPM.txt


title: IVR1_4

description: TPM.txt


title: IVR1_3

description: TPM.txt


title: IVR1_5

description: TPM.txt


title: IVR1_1

description: TPM.txt


title: IVR1_2

description: TPM.txt


title: IVC6_9

description: TPM.txt


title: IVC6_10

description: TPM.txt


title: IVC6_7

description: TPM.txt


title: IVC6_8

description: TPM.txt


title: IVC6_6

description: TPM.txt


title: IVC6_5

description: TPM.txt


title: IVC6_3

description: TPM.txt


title: IVC6_4

description: TPM.txt


title: IVC6_1

description: TPM.txt


title: IVR3_1

description: TPM.txt


title: IVC6_2

description: TPM.txt


title: IVC5_12

description: TPM.txt


title: IVC5_9

description: TPM.txt


title: IVC5_10

description: TPM.txt


title: IVC5_8

description: TPM.txt


title: IVC5_5

description: TPM.txt


title: IVC5_7

description: TPM.txt


title: IVC5_4

description: TPM.txt


title: IVC5_3

description: TPM.txt


title: IVC5_2

description: TPM.txt


title: IVC4_10

description: TPM.txt


title: IVC5_1

description: TPM.txt


title: IVC4_9

description: TPM.txt


title: IVC4_7

description: TPM.txt


title: IVC4_8

description: TPM.txt


title: IVC4_6

description: TPM.txt


title: IVC4_4

description: TPM.txt


title: IVC4_2

description: TPM.txt


title: Cortex_Cont-STZ-Pio_5

city: Grand Forks

first: Junguk

last: Hur

state: ND

address: 1301 N. Columbia Rd. Stop 9037

department: Biomedical Sciences

institute: University of North Dakota

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then processed using the Tuxedo suite of sequence analysis programs. Reads were mapped to the NCBI reference mouse transcriptome (NCBI 37) to identify transcripts.
Mapped reads were processed using the Cufflinks algorithm to calculate fragments per kilobase of exon per million mapped reads (FPKM), as presented in Trapnell et al., Nature Protocol 2012, which accurately reflects the RNA transcript number normalized for RNA length and total number of mapped reads.
Assembly: NCBI37/mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

source_name: kidney cortex

extract_protocol:
Tissues [sciatic nerve (SCN), dorsal root ganglia (DRG), kidney glomerui, and kidney cortex] were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq mRNA Sample Prep v2 kit (Catalog #s RS‐122‐2001, RS‐122‐2002; Illumina, San Diego, CA, USA) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: kidney cortex

tag: pioglitazone-treatment

value: Yes

tag: diabetes-type

value: db+ with STZ


title: IVC3_14

description: TPM.txt

tag: tissue


title: IVC3_13

description: TPM.txt


title: IVC3_11

description: TPM.txt


title: IVC3_12

description: TPM.txt


title: IVC4_1

description: TPM.txt


title: Cortex_Cont-STZ-Pio_3


title: Cortex_Cont-STZ-Pio_2


title: Cortex_Cont-STZ-Pio_4


title: IVC3_8

description: TPM.txt


title: Cortex_Cont-STZ_6

value: No


title: Cortex_Cont-STZ_5


title: Cortex_Cont-STZ_4


title: Cortex_Cont-STZ_3


title: IVC3_6

description: TPM.txt


title: IVC3_7

description: TPM.txt


title: IVC3_4

description: TPM.txt


title: Cortex_Cont-STZ-Pio_1


title: Cortex_Cont-STZ_2


title: IVC4_5

description: TPM.txt


title: IVC3_3

description: TPM.txt


title: IVC4_3

description: TPM.txt


title: IVC3_5

description: TPM.txt


title: Cortex_Cont-STZ_1


title: Glom_Cont-STZ-Pio_6

source_name: kidney glomeruli

value: kidney glomeruli


title: IVC3_2

description: TPM.txt


title: Glom_Cont-STZ-Pio_5


title: IVC2_25

description: TPM.txt


title: Cortex_Cont-STZ-Pio_6


title: IVC2_24

description: TPM.txt


title: Glom_Cont-STZ-Pio_3


title: Glom_Cont-STZ-Pio_4


title: IVC2_22

description: TPM.txt


title: Glom_Cont-STZ-Pio_2


title: IVC2_18

description: TPM.txt


title: IVC2_23

description: TPM.txt


title: IVC2_17

description: TPM.txt


title: Glom_Cont-STZ_6


title: Glom_Cont-STZ_5


title: IVC2_14

description: TPM.txt


title: IVC2_13

description: TPM.txt


title: Glom_Cont-STZ_4


title: IVC2_12

description: TPM.txt


title: Glom_Cont-STZ_2


title: Glom_Cont-STZ_1


title: IVC3_1

description: TPM.txt


title: Glom_Cont-STZ_3


title: IVC2_11

description: TPM.txt


title: IVC1_10

description: TPM.txt


title: IVC1_9

description: TPM.txt


title: IVC2_10

description: TPM.txt


title: IVC2_9

description: TPM.txt


title: DRG_Cont-STZ-Pio_6

source_name: dorsal root ganglia

value: dorsal root ganglia


title: DRG_Cont-STZ-Pio_4


title: DRG_Cont-STZ-Pio_3


title: DRG_Cont-STZ-Pio_5


title: IVC1_8

description: TPM.txt


title: DRG_Cont-STZ-Pio_2


title: Glom_Cont-STZ-Pio_1


title: IVC1_7

description: TPM.txt


title: IVC1_5

description: TPM.txt


title: IVC1_4

description: TPM.txt


title: IVC1_6

description: TPM.txt


title: DRG_Cont-STZ_5


title: DRG_Cont-STZ_6


title: IVC1_3

description: TPM.txt


title: IVC1_2

description: TPM.txt


title: DRG_Cont-STZ_2


title: IVC1_1

description: TPM.txt


title: DRG_Cont-STZ_1


title: DRG_Cont-STZ_4


title: Tspan8+ Basal cells, biol rep 3 [P7_3]

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Libraries were sequenced on an Illumina NextSeq 500, generating 80 bp paired-end reads.
Reads pairs from each sample were aligned to the mouse genome with Bowtie2. Technical replicates were merged with samtools merge.
Bam files were processed with FixMateInformatrion and MarkDuplicates from Picard tools.
Read pairs were filtered for artefacts using R package diffHic v1.26.0 and then counted into 50 kB bin pairs.
Assembly: mm10
Supplementary files format and content: Processed data files give the number of reads supporting each interaction, where an interaction corresponds to a pair of 50 kB bins. The .mtx files are space-delimited text files in Matrix Market Exchange format with integer entries. The first two columns give the indices of the two interacting genomic bins and the third column gives the read count. Bin pairs with no reads are omitted. The indices correspond to rows of the BED format file GenomicRegions.bed. The processed data files can be read into R using the readMTX2IntSet function of the diffHic package or the readMM function of the Matrix package.

source_name: Mammary epithelial cells

extract_protocol:
Chromatin was crosslinked with formaldehyde and in situ digested with DNase followed by proximity ligation and introduction of capture beads.
Proximity ligated DNA was decrosslinked, end repaired and sequencing adapters added before capture of successfully re-ligated material and sequencing, following the manufacturer's protocol, Doveltail Omni-CTM.

value: Mammary epithelial cells

value: Tspan8+ myoepithelial (quiescent basal, QBa)

value: FVB/N mice

tag: developmental stage

value: adult (9-10 weeks of age)

tag: Sex

value: female

tag: mouse pool


title: Tspan8+ Basal cells, biol rep 2 [P7_2]


title: SCN_Cont-STZ-Pio_5

source_name: sciatic nerve

value: sciatic nerve


title: Tspan8- Basal cells, biol rep 3 [P6_3]

value: Tspan8- myoepithelial (active basal, ABa)


title: SCN_Cont-STZ-Pio_3


title: Tspan8- Basal cells, biol rep 2 [P6_2]


title: SCN_Cont-STZ-Pio_2


title: SCN_Cont-STZ-Pio_1


title: SCN_Cont-STZ-Pio_4


title: SCN_Cont-STZ_6


title: DRG_Cont-STZ-Pio_1


title: Tspan8- Basal cells PolII bio rep 2 [P6_PolII_2]

data_processing:
Libraries were sequenced on an Illumina NextSeq 500, generating 80 bp paired-end reads.
Reads were aligned to the mouse genome mm10 by Bowtie2 with duplicates removed with Picard tools MarkDuplicates command.
Bam files for technical replicates were merged using samtools post-mapping.
BigWig files were generated with BamCoverage from Deeptools with bamCoverage --normalizeUsing RPKM.
Assembly: mm10
Supplementary files format and content: *.bw: BigWig, a coverage track generated from the mapped read fragments. The coverage is calculated as the number of reads per 50 bp bin. Coverage was normalization by reads Per Kilobase per Million mapped reads (RPKM).
Library strategy: CUT&Tag

extract_protocol:
Whole cells were captured on ConA beads and genomic DNA treated with pA-Tn5 followed by overnight antibody incubation.
Libraries were constructed as per Kaya-Okur et al. 2019.

tag: chip antibody

value: PolII (Merck Cat#05-623)


title: Tspan8- Basal cells PolII bio rep 1 [P6_PolII_1]

tag: cell type


title: SCN_Cont-STZ_5


title: Tspan8- Basal cells muIgG bio rep 2 [P6_muIgG_2]

value: IgG (Merck Cat#12-371)


title: SCN_Cont-STZ_4


title: Tspan8- Basal cells muIgG bio rep 1 [P6_muIgG_1]


title: Tspan8- Basal cells H3K27ac bio rep 2 [P6_H3K27ac_2]

value: H3K27ac (abcam Cat#4729)


title: DRG_Cont-STZ_3


title: Tspan8- Basal cells H3K27ac bio rep 1 [P6_H3K27ac_1]


title: SCN_Cont-STZ_3


title: SCN_Cont-STZ_2


title: SCN_Cont-STZ_1


title: SCN_Cont-STZ-Pio_6


title: Tspan8- Basal cells H3K9me3 bio rep 2 [P6_H3K9me3_2]

value: H3K9me3 (abcam Cat#8898)


title: Tspan8+ Basal cells, biol rep 1 [P7_1]


title: TP53-R277K_rep2

city: Amsterdam

first: Max

middle: D

last: Wellenstein

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Sequences were generated by the Illumina Hiseq 2000 genome analyser (using 65 bp reads), and aligned to the Mouse Reference Genome (assembly mm10) using BWA.
Reads with a BWA alignment quality score less than 20 were removed.
Peaks were called over input with MACS2.0 with a q-value cutoff of 0.01
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak

source_name: Breast cancer cells

growth_protocol: DMEM + 10%FCS + 1%Pen/Strep

extract_protocol:
Cells were fixed in 1% formaldehyde,  followed by sonication. Protocol was done according to Schmidt et al., 2009). 5 µg of p53 antibody (1C12, Cell Signaling Technologies) and 50 µL of Protein G magnetic beads (Invitrogen) were used for each ChIP
Immunoprecipitated DNA was processed for library preparation (Part# 0801-0303, KAPA biosystems kit).

treatment_protocol: No treatment

tag: genotype

value: Wap-cre;Cdh1F/F;AktE17K ;Trp53 R277K

value: p53 (1C12) Mouse mAb - #2524 - Cell Signaling


title: Tspan8- Basal cells H3K9me3 bio rep 1 [P6_H3K9me3_1]


title: Tspan8- Basal cells H3K9me2 bio rep 2 [P6_H3K9me2_2]

value: H3K9me2 (abcam Cat#1220)


title: TP53-R246S_rep2

value: Wap-cre;Cdh1F/F;AktE17K ;Trp53 R246S


title: TP53-R270H_rep2

value: Wap-cre;Cdh1F/F;AktE17K ;Trp53 R270H


title: Tspan8- Basal cells, biol rep 1 [P6_1]


title: Tspan8- Basal cells H3K9ac bio rep 2 [P6_H3K9ac_2]

value: H3K9ac (abcam Cat#4441)


title: Tspan8- Basal cells H3K9ac bio rep 1 [P6_H3K9ac_1]

value: Mammary epithelial cells


title: TP53-R245W_rep2

value: Wap-cre;Cdh1F/F;AktE17K ;Trp53 R245W


title: TP53-G242S_rep2

value: Wap-cre;Cdh1F/F;AktE17K ;Trp53 G242S


title: TP53-Y217C_rep2

value: Wap-cre;Cdh1F/F;AktE17K ;Trp53 Y217C


title: Tspan8- Basal cells H2AK119ub bio rep 2 [P6_H2AK119ub_2]

value: FVB/N mice

value: adult (9-10 weeks of age)

value: female

value: H2AK119ub (CST Cat#8240)


title: TP53-R172H_rep2

value: Wap-cre;Cdh1F/F;AktE17K ;Trp53 R172H


title: TP53-WT_rep2


title: TP53-KO_rep2

value: Wap-cre;Cdh1F/F;AktE17K ;Trp53 KO


title: Tspan8- Basal cells H2AK119ub bio rep 1 [P6_H2AK119ub_1]

value: Tspan8- myoepithelial (active basal, ABa)


title: Tspan8- Basal cells H3K36me3 bio rep 2 [P6_H3K36me3_2]

value: H3K36me3 (Active Motif Cat#61021)


title: Tspan8- Basal cells H3K36me3 bio rep 1 [P6_H3K36me3_1]


title: Tspan8- Basal cells H3K4me3 bio rep 1 [P6_H3K4me3_1]

value: H3K4me3 (Merck Cat#07-473)


title: TP53-R270H_rep1

value: p53 (1C12) Mouse mAb - #2524 - Cell Signaling


title: Tspan8- Basal cells H3K4me3 bio rep 2 [P6_H3K4me3_2]


title: TP53-R245W_rep1


title: Tspan8- Basal cells H3K4me1 bio rep 2 [P6_H3K4me1_2]

value: H3K4me1 (abcam Cat#8895)


title: Tspan8- Basal cells H3K9me2 bio rep 1 [P6_H3K9me2_1]

value: H3K9me2 (abcam Cat#1220)


title: TP53-R246S_rep1

value: Wap-cre;Cdh1F/F;AktE17K ;Trp53 R246S


title: Tspan8- Basal cells H3K4me1 bio rep 1 [P6_H3K4me1_1]

value: Mammary epithelial cells


title: Tspan8- Basal cells H3K27me3 bio rep 2 [P6_H3K27me3_2]


title: TP53-R172H_rep1


title: Tspan8+ Basal cells PolII bio rep 2 [P7_PolII_2]

value: Tspan8+ myoepithelial (quiescent basal, QBa)

value: PolII (Merck Cat#05-623)


title: TP53-KO_rep1


title: TP53-Y217C_rep1

value: Wap-cre;Cdh1F/F;AktE17K ;Trp53 Y217C


title: Tspan8- Basal cells H3K27me3 bio rep 1 [P6_H3K27me3_1]

value: FVB/N mice


title: genomic DNA from Whole Blood [MN59001]

type: genomic

city: Provo

first: Timothy

middle: G

last: Jenkins

state: UT

address: 4005 Life Sciences Building

department: Cell Biology and Physiology

institute: Brigham Young University

description: Tissue Specific Aging Between Tissue Types

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation850K Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Data was processed using the minfi R package, and normalized using SWAN normalization.

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: not provided

tag: gender

value: Male

tag: sample type

value: Blood

value: Oligozoospermia


title: TP53-WT_rep1


title: Tspan8+ Basal cells H3K27ac bio rep 2 [P7_H3K27ac_2]

value: adult (9-10 weeks of age)

value: female

value: H3K27ac (abcam Cat#4729)


title: genomic DNA from Sperm [Z8SP010]


title: genomic DNA from Sperm [ZA43007]

value: Sperm


title: genomic DNA from Whole Blood [Z8SP010]


title: Tspan8+ Basal cells H3K27ac bio rep 1 [P7_H3K27ac_1]


title: Tspan8+ Basal cells muIgG bio rep 1 [P7_muIgG_1]

value: IgG (Merck Cat#12-371)


title: TP53-R277K_rep1

value: Wap-cre;Cdh1F/F;AktE17K ;Trp53 R277K

value: p53 (1C12) Mouse mAb - #2524 - Cell Signaling


title: Tspan8+ Basal cells H3K9me3 bio rep 2 [P7_H3K9me3_2]

value: H3K9me3 (abcam Cat#8898)


title: Tspan8+ Basal cells H3K9me3 bio rep 1 [P7_H3K9me3_1]


title: TP53-G242S_rep1

value: Wap-cre;Cdh1F/F;AktE17K ;Trp53 G242S


title: Tspan8+ Basal cells muIgG bio rep 2 [P7_muIgG_2]

value: Mammary epithelial cells


title: Tspan8+ Basal cells H3K9me2 bio rep 2 [P7_H3K9me2_2]

value: Tspan8+ myoepithelial (quiescent basal, QBa)

value: H3K9me2 (abcam Cat#1220)


title: Tspan8+ Basal cells H3K9me2 bio rep 1 [P7_H3K9me2_1]


title: genomic DNA from Sperm [641J019]


title: genomic DNA from Sperm [CV79013]


title: genomic DNA from Whole Blood [YB94011]


title: genomic DNA from Sperm [8ZY8008]


title: Tspan8+ Basal cells H3K9ac bio rep 2 [P7_H3K9ac_2]

value: H3K9ac (abcam Cat#4441)


title: Tspan8+ Basal cells H3K9ac bio rep 1 [P7_H3K9ac_1]

value: FVB/N mice


title: Tspan8+ Basal cells PolII bio rep 1 [P7_PolII_1]

value: PolII (Merck Cat#05-623)


title: Tspan8+ Basal cells H2AK119ub bio rep 2 [P7_H2AK119ub_2]

value: H2AK119ub (CST Cat#8240)


title: Tspan8+ Basal cells H2AK119ub bio rep 1 [P7_H2AK119ub_1]


title: Tspan8+ Basal cells H3K36me3 bio rep 2 [P7_H3K36me3_2]

value: H3K36me3 (Active Motif Cat#61021)


title: genomic DNA from Whole Blood [5VW6016]

value: Male

value: Oligozoospermia


title: genomic DNA from Whole Blood [4Z36010]

value: Blood


title: Tspan8+ Basal cells H3K36me3 bio rep 1 [P7_H3K36me3_1]

value: adult (9-10 weeks of age)

value: female


title: genomic DNA from Sperm [T8IJ018]


title: genomic DNA from Sperm [TD6B016]


title: genomic DNA from Whole Blood [SX6G010]

value: Sperm


title: genomic DNA from Whole Blood [T8IJ018]


title: genomic DNA from Sperm [Q21N007]


title: Tspan8+ Basal cells H3K4me3 bio rep 1 [P7_H3K4me3_1]

value: H3K4me3 (Merck Cat#07-473)


title: genomic DNA from Whole Blood [T5TA023]

value: Normozoospermia


title: Tspan8+ Basal cells H3K27me3 bio rep 2 [P7_H3K27me3_2]


title: Drrp6_Ysh1AA_R1

first: Richard

middle: James

last: Mitter

state: LONDON

address: 1 Midland Road

department: Bioinformatics & Biostatistics

institute: The Francis Crick Institute

data_processing:
Reads were trimmed of their Illumina TruSeq single index adapter sequences using Cutadapt v2.10 allowing for reads with a minimal length of 20bp to remain (--minimum-length 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA).
Trimmed reads were aligned against the Saccharomyces cerevisiae R64-1-1 genome assembly using STAR v2.7.6a with default settings.  Low quality, multi-mapping alignments were removed from the downstream analysis using Samtools v1.12 (-q 255).
Per-million scaled, strand-specific BedGraph files representing read-depth coverage of the most 3’ transcribed base of reads from each sample were created from the filtered BAM files using BEDTools v2.27.1’s genomecov function (-bg -5 –strand [+-] –scale [scale factor]).  Note that due to the library preparation being “reverse” it was necessary to request the 5' base from genomecov.  Scale factors were calculated as 1,000,000 divided by the total number of mapped reads.  BedGraph files were subsequently converted to Bigwig format using Kent Tools bedGraphToBigWig function.
Assembly: Saccharomyces cerevisiae R64-1-1
Supplementary files format and content: Per-million scaled, strand-specific bigwig files representing coverage derived from the most 3' transcribed base of filtered reads.

organism: Saccharomyces cerevisiae

growth_protocol: S.cerevisiae cells grow in YPD medium

extract_protocol:
RNAs were prepared with hot phenol extraction method.
400 μg RNA was incubated with MTESA biotin-XX linker (Biotium, BT90066) in the biotinylation buffer (10mM Tris pH7.4-7.5, 1mM EDTA, 400ug RNA, 40ug MTSEA biotin-XX linker) in the dark at 24 °C for 30min with 750 rpm shaking. After biotinylation, Chloroform/Isoamyl alcohol (24:1) was applied to remove excess MTSEA biotin-XX liner. After purification, 200 μL of μMACS streptavidin MicroBeads (Miltenyi Biotec, 130-074-101) was added to bind biotin labelled RNAs and isolate them. The RNAs eluted from streptavidin beads were further cleaned up by RNeasy minElute kit (Qiagen, 74204). To efficiently capture <200 nt fragments from the MinElute spin columns, the amount of ethanol added to the RNA and RLT buffer was increased compared to the manufacturer’s recommendation. For a 200 μL sample, 700 μL of RLT buffer and 1,050 μL of 100% ethanol was added, mixed well and applied to the minElute spin columns over three rounds. The remaining protocol was as recommended by Qiagen. The RNA was eluted in 20 μL. Where relevant, in vitro polyadenylation was performed by using E. coli polyA polymerase (EPAP) (NEB, M0276L). Ribosome RNAs were depleted by using RiboMinus Transcriptome Isolation Kit (Thermo Fisher Scientific, 10388792). Library of 3’ end sequencing was prepared by using Lexogen QuantSeq 3′ mRNA-Seq Library Prep Kit REV (Lexogen, 16.24) for Illumina and sequenced with single end 75bp reads by NextSeq 500/550 Mid Output Kit v2.5 (150 Cycles) with advanced sequencing science technology platform (STP) at the Francis Crick institute.

treatment_protocol: Rapamycin (final concentration at 0.1 μg/ml) was added to anchor away Rat1 or Ysh1 for one hour. Then, 4TU (2 M stock in DMSO) was added to the media at a final concentration of 5 mM, and cells were harvested after 6 min of labelling.

tag: cell line

value: rrp6[delta]::His5 (s.pombe) in Ysh1 FRB

tag: treatment


title: Drrp6_R2

value: rrp6[delta]::His5 (s.pombe) in HHY168

value: Rapamycin (final concentration at 0.1 μg/ml)


title: Drrp6_Rat1AA_R1

value: rrp6[delta]::His5 (s.pombe) in Rat1 FRB


title: Tspan8+ Basal cells H3K4me1 bio rep 2 [P7_H3K4me1_2]

value: Mammary epithelial cells

value: Tspan8+ myoepithelial (quiescent basal, QBa)

value: H3K4me1 (abcam Cat#8895)


title: genomic DNA from Whole Blood [TG9L005]

tag: disease state


title: Drrp6_R1


title: genomic DNA from Whole Blood [8ZY8008]


title: Tspan8+ Basal cells H3K4me3 bio rep 2 [P7_H3K4me3_2]

tag: strain

value: FVB/N mice


title: Drrp6_Rat1AA_R2


title: Drrp6_Ysh1AA_R2


title: genomic DNA from Sperm [41SF007]


title: genomic DNA from Whole Blood [R6H8016]


title: genomic DNA from Sperm [P3G6026]


title: genomic DNA from Sperm [R6H8016]


title: Ysh1AA_R2

value: Ysh1 FRB, HHY168 YSH1-FRB::KAN


title: genomic DNA from Whole Blood [CU0R012]

value: Male


title: genomic DNA from Sperm [T5TA023]


title: genomic DNA from Whole Blood [SP04018]


title: genomic DNA from Sperm [5VW6016]

value: Oligozoospermia


title: Ysh1AA_R1


title: Tspan8+ Basal cells H3K27me3 bio rep 1 [P7_H3K27me3_1]


title: Tspan8+ Basal cells H3K4me1 bio rep 1 [P7_H3K4me1_1]


title: genomic DNA from Whole Blood [Q21N007]


title: genomic DNA from Whole Blood [B8XV006]

value: Blood


title: genomic DNA from Sperm [SP04018]


title: Tspan8+ Basal cells, biol rep 1 [P7_ATAC_1]

data_processing:
Libraries were sequenced on an Illumina NextSeq 500, generating 80 bp paired-end reads.
Fastq files for technical replicates were merged and reads were aligned to the mouse genome mm10 by Bowtie2 with duplicates removed with Picard tools MarkDuplicates command and mitochondrial reads excluded.
BigWig files were generated with BamCoverage from Deeptools with bamCoverage --normalizeUsing RPKM.
Assembly: mm10
Supplementary files format and content: *.bw: BigWig, a coverage track generated from the mapped read fragments. The coverage is calculated as the number of reads per 50 bp bin. Coverage was normalization by reads Per Kilobase per Million mapped reads (RPKM).

extract_protocol: Transposed genomic DNA was extracted and amplified for sequencing as per Buenrostro et al. 2015.

value: adult (9-10 weeks of age)


title: genomic DNA from Sperm [CU0R012]


title: genomic DNA from Sperm [B8XV006]


title: genomic DNA from Whole Blood [B8EG014]


title: genomic DNA from Whole Blood [SG4S020]


title: genomic DNA from Sperm [SG4S020]


title: genomic DNA from Whole Blood [8MM6018]


title: ML cells, biol rep 2 [ML2]

data_processing:
Libraries were sequenced on an Illumina NextSeq 500, technical replicate 1 was sequenced at 150 bp and 2/3 were 80 bp paired-end reads.
Reads pairs from each sample were aligned to the mouse genome with Bowtie2. Technical replicates were merged with samtools merge.
Bam files were processed with FixMateInformatrion and MarkDuplicates from Picard tools.
Read pairs were filtered for artefacts using R package diffHic v1.26.0 and then counted into 50 kB bin pairs.
Assembly: mm10
Supplementary files format and content: Processed data files give the number of reads supporting each interaction, where an interaction corresponds to a pair of 50 kB bins. The .mtx files are space-delimited text files in Matrix Market Exchange format with integer entries. The first two columns give the indices of the two interacting genomic bins and the third column gives the read count. Bin pairs with no reads are omitted. The indices correspond to rows of the BED format file GenomicRegions.bed. The processed data files can be read into R using the readMTX2IntSet function of the diffHic package or the readMM function of the Matrix package.

value: mature luminal

value: female


title: Tspan8+ Basal cells, biol rep 2 [P7_ATAC_2]


title: genomic DNA from Whole Blood [PI07002]


title: Rat1AA_R2

value: Rat1 FRB, HHY168 RAT1-FRB::KAN


title: Tspan8- Basal cells, biol rep 1 [P6_ATAC_1]

value: Tspan8- myoepithelial (active basal, ABa)


title: genomic DNA from Sperm [8MM6018]

value: Sperm

value: Normozoospermia


title: wt_R1

value: HHY168, MATalpha tor1-1 fpr1::NAT RPL13A-2xFKB12::TRP1

value: Rapamycin (final concentration at 0.1 μg/ml)


title: genomic DNA from Sperm [8KF7001]


title: ML cells, biol rep 1 [ML1]

value: Mammary epithelial cells


title: wt_R2


title: genomic DNA from Sperm [B8EG014]


title: genomic DNA from Sperm [PI07002]


title: Rat1AA_R1


title: LP cells, biol rep 2 [LP2]

value: luminal progenitor


title: Tspan8- Basal cells, biol rep 2 [P6_ATAC_2]


title: genomic DNA from Whole Blood [K8J7003]


title: LP cells, biol rep 1 [LP1]


title: EPAP_Drrp6_R2

value: Rrp6 knockout

value: with in vitro polyadenylation by E.coli polyA polymerase (EPAP)


title: EPAP_Drrp6_R3


title: genomic DNA from Whole Blood [LZ6J015]


title: EPAP_Drrp6_R1


title: genomic DNA from Sperm [K8J7003]


title: Basal cells, biol rep 2 [Ba2]

value: myoepithelial

value: FVB/N mice


title: genomic DNA from Whole Blood [8BZT004]

value: Male


title: EPAP_wt_R3

value: WT


title: Basal cells, biol rep 1 [Ba1]

value: adult (9-10 weeks of age)


title: genomic DNA from Sperm [ZY67011]


title: genomic DNA from Whole Blood [8AR0004]

value: Blood


title: genomic DNA from Sperm [8AR0004]


title: genomic DNA from Whole Blood [ZY67011]


title: EPAP_wt_R1


title: genomic DNA from Whole Blood [GU82013]


title: ML cells PolII biol rep 2 [ML_PolII_2]

value: mature luminal

value: female

tag: antibody

value: PolII (Merck Cat#05-623)


title: nonEPAP_Drrp6_R2

value: without in vitro polyadenylation by E.coli polyA polymerase (EPAP)


title: ML cells PolII biol rep 1 [ML_PolII_1]


title: genomic DNA from Sperm [7N6J004]

value: Sperm

value: Normozoospermia


title: ML cells IgG biol rep 2 [ML_muIgG_2]

value: IgG (Merck Cat#12-371)


title: genomic DNA from Whole Blood [7N6J004]


title: ML cells IgG biol rep 1 [ML_muIgG_1]

value: Mammary epithelial cells


title: nonEPAP_Drrp6_R3


title: genomic DNA from Sperm [GU82013]


title: genomic DNA from Whole Blood [XH9R013]


title: nonEPAP_Drrp6_R1


title: genomic DNA from Sperm [XH9R013]


title: genomic DNA from Sperm [K53P003]


title: genomic DNA from Sperm [FI18012]


title: EPAP_wt_R2


title: ML cells H3K27ac biol rep 2 [ML_H3K27ac_2]

value: H3K27ac (abcam Cat#4729)


title: genomic DNA from Whole Blood [3CM1011]


title: nonEPAP_wt_R2


title: genomic DNA from Whole Blood [V14J016]


title: nonEPAP_wt_R3


title: genomic DNA from Whole Blood [FI18012]


title: ML cells H3K27ac biol rep 1 [ML_H3K27ac_1]


title: genomic DNA from Sperm [V14J016]


title: ML cells H3K9me3 biol rep 2 [ML_H3K9me3_2]

value: H3K9me3 (abcam Cat#8898)


title: genomic DNA from Sperm [3CM1011]


title: nonEPAP_wt_R1


title: genomic DNA from Whole Blood [FD99018]


title: genomic DNA from Whole Blood [28AS014]