title: KO SEN 2

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

country: Spain

institute: IRB Barcelona

data_processing:
Single-end reads were aligned to the mouse genome version mm10 using STAR (v.2.5.2b).
SAM files were converted to BAM files and sorted using sambamba.
The count matrix was generated with Rsubread with the built-in annotation for mm10.
Assembly: mm10
Supplementary files format and content: featureCounts.tsv is a tab-delimited text file that contains the number of reads mapped to each gene (rows) for each sample (columns).

growth_protocol: Panc02 cells were maintained in Roswell Park Memorial Institute medium (Gibco) supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin in a humidified atmosphere and 5% CO2 at 37° C.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen).  1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the kits NEBNext® Poly(A) mRNA Magnetic Isolation Module (Cat# E7490) and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (Cat#E7770), following manufacturer´s instructions and 10 cycles of library amplification.

treatment_protocol: PD-L2-WT and PD-L2-KO Panc02 cells were treated with 200 nM doxorubicin for 48 h or treated with vehicle (water)

value: pancreatic adenocarcinoma cells

value: Doxorubicin

tag: phenotype

value: senescent


title: gut tissue from patient IMM48

status: Public on Oct 19 2022

type: SRA

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

library_source: genomic

data_processing:
library strategy: paired-end amplicon sequencing
demultiplexing: from raw to demultiplexed fastq files please contact IGA Technology Services (Udine, Italy)
pair merging: micca mergepairs -i pair1.fastq -r pair2.fastq -o out.joined.fastq -l 30 -d 3
primer check and trimming: micca trim -i out.joined.fastq -o out.trimmed.fastq -w CCTACGGGNBGCWSCAG -r GACTACHVGGGTATCTAATCC -W -R -c
quality check: micca filter -i out.trimmed.fastq -o out.hiqual.fastq -e 0.5 -m 350 -f fastq
read merging: micca merge -i *.hiqual.fastq -o merged.fastq -f fastq
OTU table creation by clustering: micca otu -m denovo_greedy -i merged.fasta -o otudata -d 0.97 -c -t 20
taxonomic assignment (RDP): micca classify -m rdp -i otudata/otus.fasta -o otudata/taxa.txt
further analyses: R phyloseq package (see https://github.com/matteoramazzotti/papers/tree/main/2021celiac)

molecule: genomic DNA

organism: Homo sapiens

source_name: 16S rRNA V3-V4 sequencing of an intestinal mucosal sample of a celiac patient

growth_protocol: Mucosa biopsies were stored at -80°C

extract_protocol:
Genomic DNA was extracted using the DNeasy PowerSoil Pro Kit (Qiagen, Hilden, Germany)
Illumina 16S Metagenomic Sequencing Library Preparation protocol ( see https://emea.support.illumina.com)

tag: status

value: celiac

tag: age

tag: Sex

value: F

tag: anti-ttg iga (u/ml)

tag: anti-ema-iga

value: Positive

tag: histology(grade marsh)


title: KO SEN 3

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: Day 6 differentiating adipocytes Input Rep2 WT

city: Bethesda

first: Michael

last: Bustin

state: MD

address: Building 37, Room 3122

department: NCI

country: USA

institute: NIH

data_processing:
Basecalling was performed using RTA version 2.4.6
Demultiplexing and FASTQ generation was performed using bcl2fastq (version 2.17) allowing 1 mismatch.
Trimming of adapters and low-quality bases was performed using CutAdapt (v.1.18).
Reads were mapped to UCSC mm10 reference genome using BWA 07.17
Peak detection of enriched binding regions was performed using MACS2 v. 2.1.1.20160309 with the default settings
Genome_build: mm10
Supplementary_files_format_and_content: Predicted peak files in narrowPeak format

source_name: Inguinal white adipose tissue

growth_protocol: Preadipocytes were isolated from inguinal white adipose tissue of WT and DKO mice and cultured on collagen coated plates.

extract_protocol:
Cells for fixed in tissue culture plates with methonol free 1% paraformaldehyde and then collected.
ChIP libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Proliferating preadipocytes were replated and grown until confluency. Two days after reaching confulency,  Preadipocytes were treated to differentiate into adipocytes using differentiation media (Insulin (0.5 μg/ml), dexamethasone (5 μM), IBMX (0.5 mM), T3 (1 nM), Rosiglitazone (1 μM)) for 4 days and maintained in maintenance medium (Insulin (0.5 μg/ml), T3 (1 nM)) for 4 days.

tag: strain

value: Wild type


title: Succinate_1

city: Rehovot

first: Roi

last: Avraham

address: Herzl St 234

country: Israel

institute: Weizmann Institute of Science

data_processing:
Fastq reads were demultiplex to their respective sample by using fastq-multx (version 1.3.1) and aligned to a composite genome of S.Tm 14028S and mouse (mm10) using STAR (version 2.5.3a).
For S.Tm read counts, R2 reads were calculated by HTSeq.
Data of each organism was normalized to a library size factor. Factors were calculated by dividing the total number of reads from each sample to the median of the total number of reads across all samples.
Data was transformed to log scale after DESeq2 normalization.
Genome_build: composite genome of S.Tm 14028S and mouse (mm10)
Supplementary_files_format_and_content: tab-delimited text files include normalized number of reads (log scale) for each sample

organism: Salmonella enterica subsp. enterica serovar Typhimurium

growth_protocol: Culture of WT S.Tm strain was grown in Luria-Bertani (LB) medium at 37 °C shaken for 16 h (overnight culture).  Cells were washed and diluted to OD 600 of 0.005 in 3ml LPM medium (glycerol) or modified LPM medium (without glycerol supplemented with 10mM succinate) and were grown for 16 hours at 37°C without shaking (oxygen-limited conditions).

extract_protocol:
Bacterial pellets were washed with PBS and resuspended in RLT buffer.  Pellets were freeze and thawed for efficient cell lysis and RNA was extracted using the RNeasy mini kit (QIAGEN) with DNase I-treatment (45 minutes at 23°C) (QIAGEN).
RNAtag-seq cDNA libraries was done as previously described in Avraham et al (2016) (Avraham et al., 2016). Bacterial rRNA was depleted using the RiboZero Gold (Bacteria) kit (Illumina) according to the manufacturer’s guidelines. Strand-specific cDNA libraries were prepared and sequenced as Paired-end (R1: 30, R2: 50) using Miniseq machine and 300 mid output kit with total coverage of ~10.5M and mean of ~380K reads per library, ranges from ~35K to ~1.3M. For each condition, biological triplicates were analyzed.

value: succinate

tag: replicate


title: Glycerol_2

value: glycerol


title: KO SEN 1


title: KO NS 4

value: Vehicle

value: control


title: Glycerol_1


title: gut tissue from patient IMM40


title: Day 6 differentiating adipocytes Input Rep1 WT


title: KO SEN 4


title: gut tissue from patient IMM41


title: Day 3 differentiating adipocytes Input Rep2 DKO

value: Hmgn1-/- and Hmgn2-/-


title: manZ_No_2DG_3

growth_protocol: Cultures of WT ∆manZ S.Tm strains were grown in Luria-Bertani (LB) medium at 37 °C shaken for 16h (overnight culture). Cells were washed and diluted to OD 600 of 0.005 in 3ml acidic minimal medium low in phosphate and magnesium (LPM) untreated or treated with 1mM 2-DG (Sigma D8375-5G) and were grown for 16h at 37°C with shaking

tag: bacteria status

value: manZ

tag: 2-dg status

value: without 2-DG


title: Day 3 differentiating adipocytes Input Rep1 DKO


title: KO NS 3


title: manZ_No_2DG_2


title: gut tissue from patient IMM31


title: KO NS 2


title: manZ_No_2DG_1


title: Day 3 differentiating adipocytes Input Rep1 WT


title: KO NS 1


title: Day 6 differentiating adipocytes Input Rep1 DKO


title: WT SEN 4


title: gut tissue from patient IMM26


title: Preadipocytes Input Rep2 DKO


title: gut tissue from patient IMM27

value: Weakly positive


title: Preadipocytes Input Rep1 DKO


title: gut tissue from patient IMM35


title: manZ_2DG_1

value: with 2-DG


title: WT SEN 2


title: gut tissue from patient IMM11

value: M


title: WT SEN 1

value: pancreatic adenocarcinoma cells


title: WT_No_2DG_3

value: WT


title: WT_No_2DG_2


title: Day 3 differentiating adipocytes Input Rep2 WT


title: gut tissue from patient IMM109


title: Preadipocytes Input Rep1 WT


title: Brown-like adipocytes H3K27ac ChIP seq DKO3


title: WT_No_2DG_1


title: WT NS 3


title: manZ_2DG_3


title: WT_2DG_3


title: Brown-like adipocytes H3K27ac ChIP seq DKO2


title: WT NS 2


title: Brown-like adipocytes H3K27ac ChIP seq DKO1


title: WT SEN 3

value: Doxorubicin

value: senescent


title: WT NS 1


title: manZ_2DG_2


title: Preadipocytes Input Rep2 WT


title: Brown-like adipocytes H3K27ac ChIP seq WT3


title: WT NS 4


title: WT_2DG_1


title: Liver Fnip2T/T (YFN 659) 4

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

institute: CNIO

description:
Liver Fnip2T/T (YFN 659)
RNA958

data_processing:
RNA-seq processing:
Eightysix-base-pair single-end reads were preprocessed to remove possible traces of rRNA, adapters and polyA tails. The resulting reads were analysed with the nextpresso pipeline as follows: sequencing quality was checked with FastQC v0.11.9 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were aligned to the mouse genome (GRCm39) with Hisat2. SAMtools v1.12 was used to convert Hisat2 SAM output files to their corresponding sorted BAM files. The Gencode vM26 gene annotation was used to get read counts with HTSeq. Read count normalization and differential expression was performed with DESeq2, after removing all genes where the sum of raw counts was < 10 across all the samples. Finally, those genes that had an adjusted p-value below 0.05 FDR were selected. GSEAPreranked was used to perform gene set enrichment analysis for the selected gene signatures on a pre-ranked gene list, setting 1000 gene set permutations. Only those gene sets with significant enrichment levels (FDR q-value < 0.25) were considered.
Assembly: GRCm39
Supplementary files format and content: Normalized counts obtained with DESeq2

source_name: Liver

extract_protocol:
RNA was extracted using RNeasy Mini kit (QIAGEN)
Total RNA samples (250 ng for liver samples and 500 ng for adipose tissue samples) were converted into cDNA sequencing libraries with the "QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 015). Briefly, library generation is initiated by reverse transcription with oligodT priming, followed by a random-primed second strand synthesis. Primers from both steps contain Illumina-compatible sequences. Libraries were completed by PCR and sequenced on an Illumina NextSeq 550 (with v2.5 reagent kits) by following manufacturer's protocols. This library preparation kit generates directional libraries stranded in the sense orientation, the read1 (the only read in single read format) has the sense orientation.
Quantseq 3’UTR

tag: tissue

value: Liver

tag: feeding state

value: Ad libitum acces to food and drink

value: Female


title: Liver Fnip2T/T (YFN 659) 3

description:
Liver Fnip2T/T (YFN 659)
RNA958


title: A549 cells, sh-TAF15-2

city: Suzhou

first: Zhiyue

last: Su

address: 199 Ren'ai Road

country: China

institute: Soochow University

data_processing:
Sequencing was carried out using a 2x150bp paired-end (PE) configuration; image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument.
The raw data was treated using Cutadapt (V1.9.1) to filter out technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20 and then generate the high quality clean data.
Clean data were aligned to reference genome via software Hisat2 (v2.0.1).
HTSeq (v0.6.1) was used to estimate gene  expression levels from the pair-end clean data.
Assembly: Homo_sapiens.GRCh37.91
Supplementary files format and content: Tab-delimited text files include RPKM values for each Sample.

growth_protocol: A549 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) at 37 °C in a 5% CO2 humidified incubator.

extract_protocol:
Total RNA of each sample was extracted using TRIzol Reagent (Invitrogen). Total RNA of each sample was quantified and qualified by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), NanoDrop (Thermo Fisher Scientific Inc.) and 1% agrose gel. 1 μg total RNA with RIN value above 6.5 was used for following library preparation.
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol. The poly(A) mRNA isolation was performed using Poly(A) mRNA Magnetic Isolation Module or rRNA removal Kit. The mRNA fragmentation and priming was performed using First Strand Synthesis Reaction Buffer and Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified doublestranded cDNA by beads was then treated with End Prep Enzyme Mix to repair both ends and add a dAtailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptorligated DNA was then performed using beads, and fragments of ~420 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 13 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using beads, validated using an Qsep100 (Bioptic，Taiwan， China), and quantified by Qubit3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).Then libraries with different indices were multiplexed and loaded on an Illumina HiSeq instrument according to manufacturer’s instructions (Illumina, San Diego, CA, USA).

value: lung adenocarcinoma cell line

value: TAF15 knockdown


title: A549 cells, sh-TAF15-3


title: Day 6 differentiating adipocytes H3K27ac ChIP seq DKO3


title: A549 cells, sh-TAF15-1


title: gut tissue from patient IMM2

value: celiac

value: F

value: Positive


title: Liver Fnip2T/T (YFN 659) 2

description:
Liver Fnip2T/T (YFN 659)
RNA958


title: WT_2DG_2


title: Day 6 differentiating adipocytes H3K27ac ChIP seq DKO2

value: Hmgn1-/- and Hmgn2-/-


title: Liver Fnip2T/T (YFN 659) 1

description:
Liver Fnip2T/T (YFN 659)
RNA958


title: A549 cells, sh-NC-3


title: Day 6 differentiating adipocytes H3K27ac ChIP seq DKO1


title: A549 cells, sh-NC-2


title: Brown-like adipocytes H3K27ac ChIP seq WT2

value: Wild type


title: Liver Fnip2T/T (YFN 658) 4

description:
Liver Fnip2T/T (YFN 658)
RNA957


title: Day 6 differentiating adipocytes H3K27ac ChIP seq WT3


title: Liver Fnip2T/T (YFN 658) 3

description:
Liver Fnip2T/T (YFN 658)
RNA957


title: A549 cells, sh-NC-1


title: A549 cells, TIF1γ-3

value: TIF1gamma over-expression


title: Liver Fnip2T/T (YFN 658) 1

description:
Liver Fnip2T/T (YFN 658)
RNA957


title: Day 6 differentiating adipocytes H3K27ac ChIP seq WT2


title: Liver Fnip2T/T (YFN 657) 3

description:
Liver Fnip2T/T (YFN 657)
RNA956


title: Liver Fnip2T/T (YFN 657) 4

description:
Liver Fnip2T/T (YFN 657)
RNA956


title: Liver Fnip2T/T (YFN 657) 2

description:
Liver Fnip2T/T (YFN 657)
RNA956


title: A549 cells, Vector-3


title: Day 3 differentiating adipocytes H3K27ac ChIP seq DKO3


title: A549 cells, Vector-2


title: A549 cells, TIF1γ-1


title: Day 6 differentiating adipocytes H3K27ac ChIP seq WT1


title: Day 3 differentiating adipocytes H3K27ac ChIP seq DKO2


title: A549 cells, TIF1γ-2


title: Day 3 differentiating adipocytes H3K27ac ChIP seq DKO1


title: A549 cells, Vector-1


title: Liver Fnip2C/C (YFN 639) 3

description:
Liver Fnip2C/C (YFN 639)
RNA955


title: Day 3 differentiating adipocytes H3K27ac ChIP seq WT1


title: Liver Fnip2C/C (YFN 639) 4

description:
Liver Fnip2C/C (YFN 639)
RNA955


title: Liver Fnip2T/T (YFN 657) 1

description:
Liver Fnip2T/T (YFN 657)
RNA956


title: Day 3 differentiating adipocytes H3K27ac ChIP seq WT3


title: Day 3 differentiating adipocytes H3K27ac ChIP seq WT2


title: R71M4_CCGTCC_L008

city: Los Angeles

first: Minhyung

last: Kim

state: CA

address: 8700 Beverly Blvd

department: Urology

institute: Cedars-Sinai Medical Center

description: xenograft tumor generated by DDR1 overexpressed T24 human bladder cancer cell line

data_processing:
The quality of the RNA-seq data was checked using FastQC (version 0.11.9). Adaptor trimming was conducted using Trim Galore (version 0.6.4). Reads were aligned to the Human Genome (GRCh38) using STAR (version 2.7.5) and gene expression was quantified using RSEM (version 1.3.1).
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with TMM normalized gene expression for every gene and every sample.

source_name: xenograft bladder cancer

extract_protocol:
Tumors were mechanically disassociated with a homogenizer (Omni International) and then passed through a QIAshredder (Qiagen), gDNA eliminator columns (Qiagen), and RNeasy Plus Mini Kit, as per the manufacturer’s instructions, for RNA extraction.
Library preparation and sequencing were performed by Novogene. Quality and quantity of RNA were analyzed using NanoDrop, agarose gel electrophoresis, and Agilent 2100. mRNA was purified fromtotal RNA using poly-T oligo-attached magnetic beads. mRNA was first fragmented randomly by fragmentation buffer, followed by NEB library preparation (New England Biolabs). First-strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H−), with second-strand cDNA synthesized using DNA polymerase I and RNase H. Double-stranded cDNA was purified using AMPure XP beads (Beckman Coulter). Exonuclease was used to eliminate overhangs on the double-stranded cDNA. 3′ ends were adenylated, and NEBNext adaptors were ligated in preparation for hybridization. Library fragments were purified with AMPure XP system (Beckman Coulter). Sequencingwas performed byNovogene on an Illumina platform paired-end 150 bp with 20 million reads per sample.

value: T24 human bladder cancer cell line

tag: condition

value: DDR1 over expression


title: Liver Fnip2C/C (YFN 639) 2

description:
Liver Fnip2C/C (YFN 639)
RNA955


title: Liver Fnip2T/T (YFN 658) 2

description:
Liver Fnip2T/T (YFN 658)
RNA957


title: R71M2_CAGATC_L008


title: R71M1_TGACCA_L008


title: Liver Fnip2C/C (YFN 639) 1

description:
Liver Fnip2C/C (YFN 639)
RNA955


title: R70M1_CGATGT_L008


title: Preadipocytes H3K27ac ChIP seq DKO2


title: Liver Fnip2C/C (YFN 638) 4

description:
Liver Fnip2C/C (YFN 638)
RNA953


title: Preadipocytes H3K27ac ChIP seq DKO3


title: SAMPLE 21_SNU475-GSK_M

type: genomic

city: Grand Rapids

first: Peter

middle: A

last: Jones

state: MI

address: 333 Bostwick Ave NE

department: Center of Epigenetics

institute: Van Andel Research Institute

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

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

data_processing:
R package minfi
Normalized Average Beta (The intensities were corrected for background fluorescence and red-green dye-bias (35) using the ‘noob’ functionality in minfi. Beta (β) values were calculated as (M/(M+U)), in which M and U refer to the (pre-processed) mean methylated and unmethylated probe signal intensities, respectively. )
signal_intensities.txt contains Uunmethylated and methylated signal intensities

label_protocol: Standard Illumina Protocol

growth_protocol: SNU398, HepG2 and SNU475 cells were obtained form the American Type Culture Collection (ATCC; www.atcc.org). Each cell line was treated with daily doses of 100 nM 5-Aza-CdR (Sigma-Aldrich) at and/or of 500nM GSK-126 (Active Biochem, LTD, Hong Kong) for three days. SNU398 and HepG2 were harvested on day 14 after treatment, while SNU475 was harvested on day 21.

extract_protocol: Standard Illumina Protocol

treatment_protocol: Standard Illumina Protocol

tag: drug treatment

tag: enzyme treatment


title: Preadipocytes H3K27ac ChIP seq DKO1


title: Liver Fnip2C/C (YFN 638) 3

description:
Liver Fnip2C/C (YFN 638)
RNA953

tag: Sex


title: Preadipocytes H3K27ac ChIP seq WT3


title: R69_2M2_CTTGTA

description: xenograft tumor generated by T24 human bladder cancer cell line

value: control


title: Preadipocytes H3K27ac ChIP seq WT2


title: SAMPLE 24_SNU475-DAC_GSK_NM

value: No emzyme


title: Brown-like adipocytes H3K27ac ChIP seq WT1


title: SAMPLE 20_SNU475-DAC_NM

value: DAC


title: Preadipocytes H3K27ac ChIP seq WT1


title: SAMPLE 23_SNU475-DAC_GSK_M


title: Liver Fnip2T/T (YFN 608) 4

description:
Liver Fnip2T/T (YFN 608)
RNA950


title: R69_2M3_GTGAAA


title: Input  ChIPSeq

city: Clayton

first: Ron

last: Firestein

state: VIC

address: 21 Wright street

department: CCR

country: Australia

institute: Hudson Institute of Medical Research

data_processing:
Basecalls performed using BWA algorithm with default settings
ChIP-seq reads were aligned to the mouse genome (mm10) using the BWA algorithm.
The tags are extended in silico at their 3 ́- ends to a length of 200bp. To identify the density of fragments  along the genome, the genome is divided into 32-nt bins and the number of fragments in each bin is determined.
Peaks were callled using Model-based Analysis of ChIP-Seq (MACS) to identify significant enrichments in the ChIP/IP data file when compared to the Input data file.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files contains the density of fragments in every 32-nt bin of the genome.

source_name: small intestinal organoid

growth_protocol: Organoids were cultured in Matrigel (Corning® Matrigel® Matrix, phenol red-free, BDAA356231) in DMEM/F-12 (Thermo Fisher, 21041025) supplemented 2mM L-glutamine (Life technologies #25030081), 100 units/mL penicillin and 0.1% (w/v) streptomycin (Life technologies #15140122), 10mM HEPES (Thermo Fisher, 15630-080), 10% Noggin conditioned media (produced in house), 5% R-Spondin conditioned media), 1.25mM n-Acetylcysteine (Merck, A7250-5G), 1x N2 supplement (Thermo Fisher, 17502048), 1x B27 supplement (Thermo Fisher, 17504044) and 50ng/ml EGF (Lonza, AF-100-15-1000).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on a NexSeq 500 (100 bp, single end reads).

treatment_protocol: Organois were treated with 100nM 4-OHT or 0.001% EtOH as vehicle for 24h before the media was replaced. Organoids were collected seven days after treatment.

value: VillinCreERT2; Cdk8 fl/fl; Cdk19 ko/ko

tag: chip antibody

value: Input


title: SAMPLE 14_SNU398-GSK_NM


title: SAMPLE 17_SNU475-DPBS_M

value: DPBS


title: RNA-Seq-shRET-MCF7

city: Xiamen

first: Guosheng

last: Hu

state: Fujian

address: Xiang'an South Road, Xiang'an District

department: School of Pharmaceutical Sciences

institute: xiamen University

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the hg38 genome assembly using Tophat version 2.1.1.
Genome_build: hg38

source_name: Michigan Cancer Foundation-7 cells(MCF7 cells)

growth_protocol: MCF7 cells were cultured in DMEM medium supplemented with 10% FBS.

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit following the manufacturer’s protocol. DNase I in column digestion was included to ensure the RNA quality.
RNA library preparation was performed by using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (E7420L). Paired-end sequencing was performed with Illumina HiSeq platform.

treatment_protocol: MCF7 cells infected with lenti-viral control shRNA  or shRNA specifically targeting RET and maintained in  DMEM medium supplemented with 10% FBS.

value: shRET


title: Liver Fnip2T/T (YFN 608) 3

description:
Liver Fnip2T/T (YFN 608)
RNA950

value: Liver

value: Ad libitum acces to food and drink

value: Female


title: SAMPLE 22_SNU475-GSK_NM


title: SF3B1.K700K.Clone49

city: Charlestown

first: Timothy

last: Graubert

state: Massachusetts

address: 149, 13th Street, Navy Yard

department: Cancer Center

institute: Massachusetts General Hospital

data_processing:
fastp version 0.20.0 was invoked with default parameters to trim adapter reads
RSEM version 1.3.1 using Bowtie1 with parameters bowtie-v 2 --bowtie-m 100, --bowtie-chunkmbs 500, --calc-ci --output-genome-bam was invoked to align the reads to the transcriptome
Assembly: Homo_sapiens.GRCh37.87 was used as reference build
Supplementary files format and content: Tab delimited format evaluated for read count of genes from RSEM

growth_protocol: Clones were cultured in complete media (IMDM+10%FBS+1X Glutamax+1%Pen/Strep) at a density of 1 X 105 cells/ml with media changes every two days.

extract_protocol:
RNA was extracted from the cell lines using RNeasy kit (Qiagen) and treated with Turbo DNase (Ambion)
Poly(A)-selected, unstranded Illumina sequencing libraries were prepared with the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA). 150 million 150 bp paired-end reads per sample were sequenced using the NovaSeq 6000 (Illumina San Diego, CA).
Unstranded Paired End RNA-seq

value: Chronic Myelogenous Leukaemia

value: CRISPR targeted mutation


title: SF3B1.K700E.Clone87


title: RNA-Seq-shCTL-MCF7

value: shCTL


title: Liver Fnip2C/C (YFN 638) 1

description:
Liver Fnip2C/C (YFN 638)
RNA953


title: Liver Fnip2C/C (YFN 638) 2

description:
Liver Fnip2C/C (YFN 638)
RNA953


title: SAMPLE 12_SNU398-DAC_GSK_NM


title: SAMPLE 18_SNU475-DPBS_NM


title: R69M2_GCCAAT_L007


title: R68M2_ACAGTG_L007


title: SAMPLE 16_SNU398-DAC_NM


title: DKO-T Arid1a ChIPSeq

value: ARID1A; sc-32761 (Santa Cruz)


title: SAMPLE 15_SNU398-DAC_M


title: SF3B1.K700K.Clone389


title: Liver Fnip2T/T (YFN 608) 1

description:
Liver Fnip2T/T (YFN 608)
RNA950


title: Liver Fnip2T/T (YFN 608) 2

description:
Liver Fnip2T/T (YFN 608)
RNA950


title: Liver Fnip2T/T (YFN 607) 4

description:
Liver Fnip2T/T (YFN 607)
RNA949


title: P2KO-2

city: Ithaca

first: Jennifer

middle: K

last: Grenier

state: NY

address: 526 Campus Rd

department: Biomedical Sciences

institute: Cornell University

data_processing:
Illumina pipeline software was used for base calling.
Sequenced reads were trimmed for 3' adaptor sequence and low-quality sequence and filtered to remove reads < 50nt with TrimGalore/cutadapt.
Processed reads were mapped to the reference genome/transcriptome with STAR using --quantMode GeneCounts to generate raw counts per gene.
Raw counts were analyzed in R with DEseq2.
Genome_build: GRCm38 (Ensembl gene build)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: testis

growth_protocol: Mice were individually housed in an AAALAC certified facility, with 12 hours on/off light cycle, temperature control and food and water ad libitum

extract_protocol:
Total RNA extraction was performed using TRI reagent (Molecular Research Center, Inc. OH) according to the manufacturer’s protocol. The RNA concentration and purity were measured by Nanodrop and Qubit (Thermo Scientific, USA).
Directional RNA-seq libraries were prepared from 1 ug total RNA using the NEBNext Directional Ultra II RNA Library Prep Kit for Illumina (New England Biolabs), with initial polyA+ isolation.

treatment_protocol: Testes were dissected from age-matched adult mice and snap-frozen immediately following euthanasia by CO2 inhalation.

value: Padi2 single KO


title: Liver Fnip2T/T (YFN 607) 3

description:
Liver Fnip2T/T (YFN 607)
RNA949


title: SF3B1.K700E.Clone410


title: DKO-E RNA Pol II ChIPSeq

value: EtOH

value: RNA pol II; 91151 ( Active motif)


title: SF3B1.K700E.Clone150


title: DKO-T MED12 ChIPSeq

value: MED12; A300-774A - M  (Bethyl Laboratories)


title: SAMPLE 10_SNU398-DPBS_NM

value: No emzyme


title: P2KO-1


title: P2P4DKO-2

value: Padi2/Padi4 double KO


title: SAMPLE 5_HepG2-GSK_M


title: SAMPLE 11_SNU398-DAC_GSK_M


title: SAMPLE 13_SNU398-GSK_M


title: DKO-T RNA Pol II ChIPSeq

value: VillinCreERT2; Cdk8 fl/fl; Cdk19 ko/ko


title: DKO-E MED12 ChIPSeq


title: Liver Fnip2T/T (YFN 607) 2

description:
Liver Fnip2T/T (YFN 607)
RNA949


title: S24_line_Senicapoc_Rep_2

city: Heidelberg

first: Frank

last: Winkler

address: Im Neuenheimer Feld 400

department: Neurology Clinic and National Center for Tumor Diseases

country: Germany

institute: University Hospital Heidelberg, Heidelberg

data_processing:
The RNA sequencing data was aligned against human genome GRCh38 by STAR  (v.2.5.3a)
The reads mapped to multiple loci were filtered
The gene counts were quantified against GENCODE annotation (v.32) by the featureCounts function from Subread (v.1.5.3) with default setting
Assembly: Human genome GRCh38
Supplementary files format and content: Tab-delimited text files include log2(FPKM) values for each Sample

extract_protocol:
RNA was harvested using Rneasy Mini kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded RNA Library Prep Kit following manufacturer's protocols.

value: Patient derived glioblastoma cell line

value: WT

value: Senicapoc

tag: time

value: Day 2


title: SAMPLE 9_SNU398-DPBS_M

value: DPBS


title: SAMPLE 19_SNU475-DAC_M

value: DAC


title: P2P4DKO-1


title: SF3B1.K700K.Clone154

value: Chronic Myelogenous Leukaemia


title: DKO-T MED1 ChIPSeq

value: MED1; A300-793A (Bethyl Laboratories)


title: WT-2

value: FVB/NJ


title: WT-1


title: S24_line_Semicapoc_Rep_1


title: Liver Fnip2T/T (YFN 607) 1

description:
Liver Fnip2T/T (YFN 607)
RNA949

value: Liver

value: Ad libitum acces to food and drink

value: Female


title: SAMPLE 7_HepG2-DAC_GSK_M


title: SAMPLE 1_HepG2-DPBS_M


title: S24_line_Control_Rep_1


title: S24_line_Control_Rep_2


title: DKO-E MED1 ChIPSeq

value: EtOH


title: lncRNA-Smad7-KIpA-2-CM3.3

city: Beijing

first: kong

last: xiaohui

state: Beijing

address: Zheng Yutong medical building

department: school of life science

data_processing:
Illumina HiSeq 2000 software used for basecalling
RNA-seq, ChIP-seq, and ChIRP-seq reads were trimmed using TrimGalore for adaptor sequence, and masked for low-complexity or low-quality sequence.
RNA-seq reads were mapped to mm10 whole genome using hisat2 version 2.1.0 with parameters, reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using  Cufflinks (version 2.2.1). ChIP-seq, and ChIRP-seq reads mapped to mm10 genome assembly using Bowtie2 version 2.3.3.
Peaks were called using MACS2 for ChIP-seq and ChIRP-seq.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files were generated from the bam files using the Coverage function in deepTools.

source_name: mouse embryonic stem cell

growth_protocol: mESCs were cultured on gelatin coated plates with 15% serum ESC culture medium. Cardiac progenitor cells (CM3.3) were induced from mESCs and cultured by hanging drops for 2 days, then cultured on bacterial plates in 15% serum-containing ESC culture medium withdrawal LIF for 1.3 days. WT and lncRNA-Smad7 KIpA (4x polyA knock-in) mESCs and cardiac progenitor cells (CM3.3) were harvested for RNA extraction.

extract_protocol:
Total RNA was extracted by commerical RNA extraction Kit. Lysates for ChIP and ChIRP assays were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody or antisense probes.
RNA libraries were prepared for sequencing using standard Illumina protocols, and the libraries were sequenced on Illumina HiSeqXten-PE150 following the manufacturer's protocols. For ChIP-seq and ChIRP DNA-seq, libraries were prepared according to Illumina's instructions and the libraries were sequenced on the Illumina HiSeq-PE150 following the manufacturer's protocols.

treatment_protocol: There is no other treatment for the mESCs. The cardiac progenitor cells were treated with activin A, hBMP4, L-Ascorbic Acid, and hVEGF from day 2 to day 3.3. WT and lncRNA-Smad7 KIpA cardiac progenitor cells (CM3.3) were cross-linked and harvested for H3K27me3 ChIP-seq. WT and lncRNA-Smad7 KO (knock-out) mESCs were cross-linked and harvested for lncRNA-Smad7 ChIRP-seq.

value: ES-derived cardiomyocyte progenitor cells

tag: chirp probe


title: Liver Fnip2C/C (YFN 592) 3

description:
Liver Fnip2C/C (YFN 592)
RNA948


title: DKO-T H3K27Ac ChIPSeq

value: H3K27Ac; 39133 (Active motif)


title: SAMPLE 8_HepG2-DAC_GSK_NM

tag: cell line

value: No emzyme


title: LM3, SI-NPL4, rep3

city: Hang Zhou

first: xingxing

last: gao

state: Zhejiang

address: qingchun road

institute: zhejiang university

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Supplementary files format and content: The txt file includes TPM values for each Sample

extract_protocol:
Total RNA of normal control and treated cells was isolated by TRIzol
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: cell type

value: hepatocellular carcinoma cell

value: si-NPL4 for 48h


title: SAMPLE 6_HepG2-GSK_NM


title: LM3, SI-NPL4, rep2

tag: genotype

value: WT


title: DKO-E H3K27Ac ChIPSeq

value: VillinCreERT2; Cdk8 fl/fl; Cdk19 ko/ko

tag: treatment


title: Liver Fnip2C/C (YFN 592) 1

description:
Liver Fnip2C/C (YFN 592)
RNA948


title: Pcgf1_-/-_scRNAseq

city: Yokohama-shi

first: Junichiro

last: Takano

state: Kanagawa-kwn

department: IMS

country: Japan

institute: RIKEN

data_processing:
MNase-Seq: Sequenced reads were aligned to mm9 using bowtie248 and all uniquely matching reads were retained, using the following parameters. -I 0 -X 300 --no-mixed --no-discordant --very-sensitive. The SAM files were converted to the BAM format using Samtools. The BAM files were converted to bigwig files by R package rtracklayer for visualization.
Single cell RNA-seq: Raw sequencing data for control and Pcgf1-KO LSKs in this study were converted to fastq format using cellranger mkfastq (10x Genomics, v3.0.0). These fastq files were aligned to the mm9 reference genome and quantified using cellranger count (10x Genomics, v.3.0.0).
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files described in the data processing step columns and count matrix

source_name: Bone marrow

growth_protocol: Culture with TSt4 stroma cells by IMDM supplemented with IL7, SCF,Fl3L

extract_protocol:
MNase-seq:One million cells were cross-linked by adding formaldehyde to 1% and incubated for 10 min at RT, quenched using 1 M glycine, and washed three times in PBS. Collected cells were lysed in 1 ml PBS + 0.5% Triton X-100 for 3 min on ice. Nuclei were pelleted and washed by MNase digestion buffer (10 mM Tris-HCl, pH 7.4, 15 mM NaCl, 60 mM KCl, 0.5 mM spermidine), spun down and resuspended in the same buffer. Ca2+ concentration was adjusted to 1mM with 1M CaCl2 and MNase was added to 10 U/ml. The reaction mixture was incubated at 37°C for 10 min and the reaction was stopped by adding 150 μL of stop buffer (20 mM EDTA, 20 mM EGTA, 0.4% SDS, 0.5 mg/ml proteinase K) and then incubated for overnight at 65°C. DNA was purified using a MinElute PCR purification Kit (28006; QIAGEN) and loaded to 1.5% Agarose Gel. Mononucleosomal bands were excised and purified by a gel extraction kit (28705; QIAGEN).
Fragmented DNAs fragmentd by MNase were subjected to library preparation by NEBNext UltraⅡ DNA library preparation kit for Illumina(E7645; New England Biolabs). Preparation of scRNA-seq library: FACS sorted LSKs (control and Pcgf1-KO) were subjected to preparation of individually barcoded single-cell RNA-Seq libraries using the Chromium instrument and the Single Cell 3′ Reagent kit following the manufacturer’s instructions (10X Genomics).

tag: strain

value: LSK

value: Pcgf1 -/-

tag: antibody


title: WT-CM3.3


title: Liver Fnip2C/C (YFN 591) 4

description:
Liver Fnip2C/C (YFN 591)
RNA947


title: SAMPLE 2_HepG2-DPBS_NM

value: DPBS


title: lncRNA-Smad7-KIpA-2-ES-1

value: mouse embryonic stem cell


title: Pcgf1_f/f_scRNAseq

value: Pcgf1 fl/fl


title: Pcgf1_-/-_LSK_MNaseSeq_2


title: Liver Fnip2C/C (YFN 591) 3

description:
Liver Fnip2C/C (YFN 591)
RNA947


title: LM3, SI-NC, rep2

value: si-NC for 48h


title: Liver Fnip2C/C (YFN 591) 2

description:
Liver Fnip2C/C (YFN 591)
RNA947

value: Liver


title: SAMPLE 3_HepG2-DAC_M

value: DAC


title: LM3, SI-NC, rep3


title: DKO-E Arid1a ChIPSeq

value: ARID1A; sc-32761 (Santa Cruz)


title: LM3, SI-NPL4, rep1


title: Liver Fnip2C/C (YFN 591) 1

description:
Liver Fnip2C/C (YFN 591)
RNA947

value: Ad libitum acces to food and drink

value: Female


title: lncRNA-Smad7-KIpA-1-ES-1


title: Pcgf1_-/-_LSK_MNaseSeq_1


title: lncRNA-Smad7-KIpA-1-CM3.3

value: ES-derived cardiomyocyte progenitor cells


title: LM3, SI-NC, rep1


title: lncRNA-Smad7-KIpA-1-ES-2


title: lncRNA-Smad7-KIpA-2-ES-2


title: WT-ES-2


title: Liver Fnip2C/C (YFN 590) 4

description:
Liver Fnip2C/C (YFN 590)
RNA946


title: LM3, DSF, rep3

value: DSF/Cu for 24h


title: WT-ES-1


title: Pcgf1_f/f_LSK_MNaseSeq_1


title: Liver Fnip2C/C (YFN 590) 3

description:
Liver Fnip2C/C (YFN 590)
RNA946


title: LM3, DSF, rep2

value: hepatocellular carcinoma cell


title: LM3, DSF, rep1


title: Liver Fnip2C/C (YFN 590) 2

description:
Liver Fnip2C/C (YFN 590)
RNA946


title: Liver Fnip2C/C (YFN 590) 1

description:
Liver Fnip2C/C (YFN 590)
RNA946


title: LSK_Pcgf1_-/-_RING1B_1

data_processing:
For ChIP-seq without spike-in genome, reads were aligned to mm9 using bowtie2(Langmead et al., 2012). ChIP-seq experiments which contained a spike-in genome were aligned against concatenated genome of mm9 and dm3 using bowtie2 and resulting SAM files were then split such that reads aligning to mouse and drosophilia were placed in separate files. The SAM files were converted to the BAM format using Samtools, version 1.6.0 (Li et al., 2009). The PCR duplicates were removed by Picardtools (http://broadinstitute.Github.io/picard).
he BAM files were converted to bigwig files by deepTools2 (Ramirez et al. 2016) for visualization. For comparison across ChIP-seq samples without spike-in genome, the bigwig files were normalized to reads per million mapped sequence reads (RPKM). For ChIP-seq with spike-in genome, RPKM were further normalized according to normalization factors calculated as 1 over the number of reads (per million) mapping to drosophilia as previously reported(Orland et al., 2016).
Genome_build: mm9 or concateenated genomes of Mm9 and dm3
Supplementary_files_format_and_content: bigwig files described in the data processing step columns

extract_protocol:
ChIP for FLAG, RING1B, SUZ12, H3K27me3 and H3K27ac were performed as described previously (Isono et al., 2013). Cultured IdHP cells were cross-linked with 1% formaldehyde/PBS for 10 min at room temperature. Chromatin was sheared and used for each immunoprecipitation with indicated antibodies. ChIP for H2AK119ub was performed as described before (Mochizuki-Kashio et al., 2015). Cultured IdHP cells were cross-linked with 0.5% formaldehyde/PBS for 2 min at 37℃. Chromatin was sheared and used for each immunoprecipitation.
ChIP products and fragmented DNAs fragmentd by MNase were subjected to library preparation by NEBNext UltraⅡ DNA library preparation kit for Illumina(E7645; New England Biolabs).

value: LSK (Lin-, cKIt+, sca1+) cells

tag: passage

value: 8-10 weeks

value: anti RING1B (in house)


title: Pcgf1_f/f_LSK_MNaseSeq_2

value: LSK


title: MC3T3-E1 C3G group2

city: Shenyang

first: Lin

last: Chen

state: Liaoning

address: 146 North Huanghe St

department: School of Public Health

institute: Shenyang Medical College

description: Sample B2

data_processing:
Basecalls performed using Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.1.0)software
The transcript abundances for each sample was estimated with StringTie（1.3.3）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.10.0)
The mRNA reads were aligned to reference genome using STAR(2.5.2b)
Genome_build: hg19
Supplementary_files_format_and_content: The Fastq format file contains the sequence of reads and the sequencing quality of base.

source_name: MC3T3-E1 cells

growth_protocol: MC3T3-E1 cells, obtained from Cell Bank of the Chinese Academy of Science (Shanghai, China), were cultured in alpha-minimum essential media (α-MEM, Hyclone, UT, America) supplemented with 10% fetal bovine serum (FBS, Hyclone, UT, America) and 1% penicillin/streptomycin (Hyclone, UT, America). Cells were grown at 37°C in the 5% CO2 incubator. The cell culture medium was changed every 3 days.

extract_protocol:
RNA was harvested using Trizol reagent. The RNA library was constructed with KAPA Stranded RNA-seq Library Prep Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MC3T3-E1 cells were divided into 2 groups, including the control group and 100μm/l C3G group.

value: Murine pre-osteoblast

tag: passages


title: MC3T3-E1 C3G group3

description: Sample B3


title: MC3T3-E1 C3G group1

description: Sample B1


title: LSK_Pcgf1_f/f_RING1B_2


title: WAT Fnip2C/C (YFN 638) 4

description:
WAT Fnip2C/C (YFN 638)
RNA1014

source_name: Visceral white adipose tissue

tag: tissue

value: Visceral white adipose tissue


title: LSK_Pcgf1_f/f_RING1B_1


title: LM3, DMSO, rep1

value: WT

value: DMSO for 24h


title: LM3, DMSO, rep3


title: LM3, DMSO, rep2


title: LSK_Pcgf1_-/-_H3K27me3_spike_in_2

value: Pcgf1 -/-

value: H3K27me3 (Merk Millipore, 07-449)


title: LSK_Pcgf1_-/-_RING1B_2


title: WAT Fnip2C/C (YFN 638) 3

description:
WAT Fnip2C/C (YFN 638)
RNA1014

tag: feeding state


title: SAMPLE 4_HepG2-DAC_NM

value: DAC

value: No emzyme


title: MC3T3-E1 control group2

description: Sample A2


title: WAT Fnip2C/C (YFN 638) 2

description:
WAT Fnip2C/C (YFN 638)
RNA1014

value: Ad libitum acces to food and drink


title: MC3T3-E1 control group3

description: Sample A3


title: MS_8

city: New Haven

first: Hiromitsu

last: Asashima

state: CT

address: 300George St

institute: Yele School of Medicine

data_processing:
low quality ends (less than phred score=30) and short read length (minimum length=30) was trimmed using PRINSEQ++(version1.2).
Trimmed reads were aligned to the hg38 genome reference using STAR(v2.7.1), and subsequently RSEM (RNA-Seq by Expectation-Maximization) was used to count reads mapping to the genes from Ensembl release 93.
For remove unwanted variation, the top 5000 genes as ranked by edgeR p-values were set as a “in-silico empirical” negative controls and RUVSeq was performed
Read count normalization were performed using DESeq2CLC genomic benchwork
Supplementary files format and content: hg38
Supplementary files format and content: Three Matrix tables with raw gene counts for every gene and every sample

source_name: blood

growth_protocol: CD20+CD27+ B cells were stimulated under RPMI 1640 medium with 10% FBS

extract_protocol:
RNAs were isolated using RNeasy Plus Micro Kit (QIAGEN)
cDNAs were generated using the SMART-Seq v4 Ultra Low Input RNA Kit for sequencing (Takara/Clontech) and barcoded libraries were generated by the Nextera XT DNA Library Preparation kit (Illumina)

treatment_protocol: B cells were treated with CD40L (0.1 ug/ml) ± each cytokine for 2 days

tag: disease state

value: Multiple Sclerosis

value: blood

value: memory B cells

tag: subject

value: Multiple Sclerosis Patients_8


title: WAT Fnip2C/C (YFN 638) 1

description:
WAT Fnip2C/C (YFN 638)
RNA1014

value: Female


title: LSK_Pcgf1_-/-_H3K27me3_spike_in_1

value: LSK (Lin-, cKIt+, sca1+) cells

value: 8-10 weeks


title: MS_7

value: Multiple Sclerosis Patients_7


title: Small RNA-Seq. of Rattus norvegicus: striatum in METH self-administered rat 4

city: Daegu

first: Taekwon

last: Son

address: 61, Cheomdan-ro, Dong-gu

department: Korea Brain Bank

country: South Korea

institute: Korea Brain Research Institute

data_processing:
Sequence reads of the 8 independent samples were trimmed for both PCR and sequencing adapters with Cutadapt (version 1.18).
Trimmed reads were aligned to the rn6 rat reference genome using STAR (version 2.7.0e).
Read counts were generated using featureCounts function from the Subread package (version 1.6.4).
Assembly: rn6
Supplementary files format and content: Tab-delimited text file include raw counts per miRNA per sample.

organism: Rattus norvegicus

source_name: striatum

extract_protocol:
Total RNA was extracted using TRIzol® reagent (Invitrogen). 5 ~ 40 nucleotides of small RNA fraction were collected and gel-eluted from 3% agarose gel electrophoresis.
Small RNA sequencing libraries were prepared according to the manufacturer’s protocol (BGISEQ-500 Small RNA UMI Library Construction Protocol).

value: striatum

value: methamphetamine


title: LSK_Pcgf1_f/f_H3K27me3_spike_in_2

value: Pcgf1 fl/fl


title: WAT Fnip2T/T (YFN 658) 4

description:
WAT Fnip2T/T (YFN 658)
RNA1013

value: Visceral white adipose tissue


title: MC3T3-E1 control group1

description: Sample A1

value: Murine pre-osteoblast


title: LSK_Pcgf1_f/f_H3K27me3_spike_in_1

value: H3K27me3 (Merk Millipore, 07-449)


title: Small RNA-Seq. of Rattus norvegicus: striatum in METH self-administered rat 3

value: WT


title: WAT Fnip2T/T (YFN 658) 3

description:
WAT Fnip2T/T (YFN 658)
RNA1013


title: Small RNA-Seq. of Rattus norvegicus: striatum in METH self-administered rat 2


title: WAT Fnip2T/T (YFN 658) 1

description:
WAT Fnip2T/T (YFN 658)
RNA1013


title: Pcgf1_-/-_H2A.Z_1

value: Hemtopoietic progenitor cells (IdHPs)

value: Pcgf1 -/-

value: anti H2A.Z- ChIP Grade (abcam, ab4174)


title: WAT Fnip2T/T (YFN 658) 2

description:
WAT Fnip2T/T (YFN 658)
RNA1013

value: Ad libitum acces to food and drink


title: MS_6

value: Multiple Sclerosis

value: blood

value: memory B cells

value: Multiple Sclerosis Patients_6


title: Pcgf1_-/-_H2A.Z_2


title: HD_8

value: Healthy

value: Healthy Donor_8


title: Small RNA-Seq. of Rattus norvegicus: striatum in METH self-administered rat 1

value: striatum


title: Pcgf1_f/f_H2A.Z_2


title: HD_7

value: Healthy Donor_7


title: Small RNA-Seq. of Rattus norvegicus: striatum in SA self-administered rat 4

value: saline


title: WAT Fnip2C/C (YFN 599) 4

description:
WAT Fnip2C/C (YFN 599)
RNA1012

value: Visceral white adipose tissue

value: Female


title: HD_6

value: Healthy Donor_6


title: Small RNA-Seq. of Rattus norvegicus: striatum in SA self-administered rat 3

value: WT


title: Pcgf1_f/f_H2A.Z_1

value: Hemtopoietic progenitor cells (IdHPs)

value: Pcgf1 fl/fl


title: Liver Fnip2C/C (YFN 592) 4

description:
Liver Fnip2C/C (YFN 592)
RNA948

value: Liver


title: Small RNA-Seq. of Rattus norvegicus: striatum in SA self-administered rat 2


title: WAT Fnip2C/C (YFN 599) 2

description:
WAT Fnip2C/C (YFN 599)
RNA1012

value: Ad libitum acces to food and drink


title: Pcgf1_f/f_Pol2_2

value: Anti-RNA polymerase II CTD repeat YSPTSPS  [8WG16] - ChIP Grade (abcam, ab817)


title: HD_9

value: blood

value: Healthy Donor_9


title: WAT Fnip2C/C (YFN 599) 3

description:
WAT Fnip2C/C (YFN 599)
RNA1012


title: Pcgf1_f/f_Pol2_1


title: WAT Fnip2C/C (YFN 599) 1

description:
WAT Fnip2C/C (YFN 599)
RNA1012


title: NSD2_2

city: Dallas

first: Genevieve

last: Konopka

state: Texas

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: University of Texas Southwestern Medical Center

data_processing:
Barcode correction, alignment are performed using umitools and STAR aligner
Reads counted per gene (featureCounts) and gene-cell matrix was constructed (umi-tools)
Ambient RNA contamination removed (CellBender)
Cells were annotated using known cell type markers
Assembly: Human: GRCh38, Mouse: GRCm38
Supplementary files format and content: processed expression matrix: RDS files that contain seurat objects with or without CellBender step
Supplementary files format and content: Intronic read ratios per cell type: Text file, one row per cell barcode
Supplementary files format and content: processed expression matrix of only OPC: RDS files that contain seurat objects (with CellBender) that contain OPC clustering information

source_name: Post-mortem brain, Brodmann Area 23

extract_protocol:
Nuclei for snRNA-seq were isolated from human BA23 brain tissue. Debris was removed with a density gradient centrifugation using the Nuclei PURE 2M Sucrose Cushion Solution and Nuclei PURE Sucrose Cushion Buffer from Nuclei PURE Prep Isolation Kit (#NUC201-1KT, Sigma Aldrich).
Droplet-based single-nuclei RNA-seq libraries were prepared using the Chromium Single Cell 3? v3.1 (1000121, 10x Genomics) according to the manufacturer?s protocol81. Libraries were sequenced using an Illumina NovaSeq 6000.^SAMPLE = GSM6428210
Nuclei for snRNA-seq were isolated from human BA23 brain tissue. Debris was removed with a density gradient centrifugation using the Nuclei PURE 2M Sucrose Cushion Solution and Nuclei PURE Sucrose Cushion Buffer from Nuclei PURE Prep Isolation Kit (#NUC201-1KT, Sigma Aldrich).
Droplet-based single-nuclei RNA-seq libraries were prepared using the Chromium Single Cell 3? v3.1 (1000121, 10x Genomics) according to the manufacturer?s protocol81. Libraries were sequenced using an Illumina NovaSeq 6000.^SAMPLE = GSM6428210

value: M

tag: age


title: NSD2_3

extract_protocol:
Nuclei for snRNA-seq were isolated from human BA23 brain tissue. Debris was removed with a density gradient centrifugation using the Nuclei PURE 2M Sucrose Cushion Solution and Nuclei PURE Sucrose Cushion Buffer from Nuclei PURE Prep Isolation Kit (#NUC201-1KT, Sigma Aldrich).
Droplet-based single-nuclei RNA-seq libraries were prepared using the Chromium Single Cell 3? v3.1 (1000121, 10x Genomics) according to the manufacturer?s protocol81. Libraries were sequenced using an Illumina NovaSeq 6000.^SAMPLE = GSM6428210

tag: Sex


title: Pcgf1_-/-_H3K27me3_spike_in_1

value: Pcgf1 -/-

value: H3K27me3 (Merk Millipore, 07-449)


title: Pcgf1_-/-_PHC2_1

value: anti PHC2 (in house)


title: Pcgf1_f/f_H3K27me3_spike_in_2


title: Pcgf1_f/f_H3K27me3_spike_in_1


title: Pcgf1_f/f_PHC2_1


title: Pcgf1_f/f_PHC2_2


title: WAT Fnip2T/T (YFN 657) 1

description:
WAT Fnip2T/T (YFN 657)
RNA1011

data_processing:
RNA-seq processing:
Eightysix-base-pair single-end reads were preprocessed to remove possible traces of rRNA, adapters and polyA tails. The resulting reads were analysed with the nextpresso pipeline as follows: sequencing quality was checked with FastQC v0.11.9 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were aligned to the mouse genome (GRCm39) with Hisat2. SAMtools v1.12 was used to convert Hisat2 SAM output files to their corresponding sorted BAM files. The Gencode vM26 gene annotation was used to get read counts with HTSeq. Read count normalization and differential expression was performed with DESeq2, after removing all genes where the sum of raw counts was < 10 across all the samples. Finally, those genes that had an adjusted p-value below 0.05 FDR were selected. GSEAPreranked was used to perform gene set enrichment analysis for the selected gene signatures on a pre-ranked gene list, setting 1000 gene set permutations. Only those gene sets with significant enrichment levels (FDR q-value < 0.25) were considered.
Assembly: GRCm39
Supplementary files format and content: Normalized counts obtained with DESeq2

extract_protocol:
RNA was extracted using RNeasy Mini kit (QIAGEN)
Total RNA samples (250 ng for liver samples and 500 ng for adipose tissue samples) were converted into cDNA sequencing libraries with the "QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 015). Briefly, library generation is initiated by reverse transcription with oligodT priming, followed by a random-primed second strand synthesis. Primers from both steps contain Illumina-compatible sequences. Libraries were completed by PCR and sequenced on an Illumina NextSeq 550 (with v2.5 reagent kits) by following manufacturer's protocols. This library preparation kit generates directional libraries stranded in the sense orientation, the read1 (the only read in single read format) has the sense orientation.
Quantseq 3’UTR


title: MOLM-13 cells, Vehicle (DMSO) + RPMI, replicate 1

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

data_processing:
Illumina adapters were removed and reads <50bp after trimming were discarded
Reads were aligned and quantified using STAR (2.6.0a) to the Ensembl mouse transcriptome (hg38.p12, release 96)
Lowly abundant genes were removed as those <1 mean raw count or <1 mean count per million (CPM) across the dataset
Differential gene expression was calculated using the voom function in limma
Assembly: hg38
Supplementary files format and content: Text file containing STAR gene count values

growth_protocol: MOLM-13 cells were maintained in RPMI supplemented with 10% FBS with antibiotics

extract_protocol:
RNA was isolated using Rneasy Plus Mini Kit (Qiagen)
Poly-A-selected total RNA library construction was performed using Universal Plus mRNA-seq with NuQuant (Tecan)

treatment_protocol: MOLM-13 cells were treated with 3nM AC220(quizartinib) for 15 hours either in RPMI or hBMSC-CM

value: AML cells

value: Vehicle (DMSO)

tag: medium

value: RPMI


title: WAT Fnip2T/T (YFN 657) 3

city: Madrid

first: Osvaldo

last: Graña

description:
WAT Fnip2T/T (YFN 657)
RNA1011

value: Visceral white adipose tissue

value: Female


title: MOLM-13 cells, Vehicle (DMSO) + RPMI, replicate 3

value: WT


title: WAT Fnip2T/T (YFN 657) 2

description:
WAT Fnip2T/T (YFN 657)
RNA1011


title: MOLM-13 cells, Vehicle (DMSO) + RPMI, replicate 2


title: Small RNA-Seq. of Rattus norvegicus: striatum in SA self-administered rat 1

value: striatum

value: saline


title: Pcgf1_-/-_H3K27me3_2

value: Hemtopoietic progenitor cells (IdHPs)


title: WAT Fnip2C/C (YFN 593) 4

description:
WAT Fnip2C/C (YFN 593)
RNA1010

value: Ad libitum acces to food and drink


title: NSD2_4

value: F


title: WAT Fnip2C/C (YFN 593) 3

description:
WAT Fnip2C/C (YFN 593)
RNA1010


title: MOLM-13 cells, AC220 (quizartinib) + RPMI, replicate 3

value: 3nM AC220 (quizartinib)


title: Pcgf1_-/-_H3K27me3_1


title: MOLM-13 cells, AC220 (quizartinib) + RPMI, replicate 2


title: RNA-seq_LMPP_Pcgf1_-/-_2

description:
20191202LMPP_CPM.txt
DK18007_49_09

data_processing:
RNA-seq reads were aligned to the mouse reference genome (mm9) using Tophat (v2.0.13; https://ccb.jhu.edu/software/tophat/index.shtml).
Transcript levels (counts) were summarized per gene using Rsubread (Liao et al., 2013). Count per million (CPM) were calculated using edgeR (Robinson et al., 2010).
Genome_build: mm9
Supplementary_files_format_and_content: text file. CPM for whole genes in each samples,

extract_protocol:
Total RNA was extracted by RNeasy (74106; QIAGEN) following the manufacture’s protocol.
Poly(A) mRNA was isolated from total RNA by NEBNext poly(A) mRNA magnetic isolation module (E7490; New England Biolabs), and then library was prepared by NEBNext Ultra RNA library preparation kit for Illumina(E7530; New England Biolabs).

value: Hemtopoietic progenitor cells (LMPP)


title: WAT Fnip2T/T (YFN 657) 4

description:
WAT Fnip2T/T (YFN 657)
RNA1011


title: Pcgf1_-/-_PHC2_2


title: Pcgf1_-/-_H3K27me3_spike_in_2


title: Pcgf1_f/f_H3K27me3_2

description:
Pcgf1_f/f_H3K27me3_2
peak file = H3K27me3_Peaks.txt

value: Pcgf1 fl/fl


title: RNA-seq_LMPP_Pcgf1_-/-_1

description:
20191202LMPP_CPM.txt
DK18007_49_07

value: Pcgf1 -/-


title: RNA-seq_LMPP_Pcgf1_fl/fl_1

description:
20191202LMPP_CPM.txt
DK18007_49_05


title: MOLM-13 cells, AC220 (quizartinib) + RPMI, replicate 1


title: 24h_no_bc_2DG_rep3

city: Rehovot

first: Roi

last: Avraham

address: Herzl St 234

institute: Weizmann Institute of Science

data_processing:
Fastq reads were demultiplex to their respective sample by using fastq-multx (version 1.3.1) and aligned to a composite genome of S.Tm 14028S and mouse (mm10) using STAR (version 2.5.3a).
For the host, read counts were calculated using STAR. For S.Tm read counts, R2 reads were calculated by HTSeq.
Data of each organism was normalized to a library size factor. Factors were calculated by dividing the total number of reads from each sample to the median of the total number of reads across all samples.
Data was transformed to log2 scale. Host minimal expression threshold was set to 4.5 and bacteria minimal expression threshold was set to 2.
Genome_build: composite genome of S.Tm 14028S and mouse (mm10)
Supplementary_files_format_and_content: tab-delimited text files include normalized number of reads (log2 scale) for each sample

source_name: BMDMs

growth_protocol: Bone marrow was extracted from 6-8 week old female C57BL/6 mice as previously described (Falk et al., 1988). In brief, 6-8 week old female C57BL/6 mice were euthanized and femurs and tibias were harvested. Bone marrow was flushed from the cells, resuspended in DMEM, and plated in non-tissue culture treated dishes in DMEM media containing 5% sodium pyruvate, 20% fetal bovine serum, and 25 ng/ml recombinant mouse M-CSF. Cells were harvested at day 6 after bone marrow isolation and were frozen untill use. All bone marrows extractions were performed in accordance with the Institutional Animal Care and Use Committee at the Weizmann Institute. (IACUC Approval number 27410516-3)

extract_protocol:
Gentle bead beating was done using OmniLyse (disposable cell disruptors) to break the bacterial cell envelope without harming the macrophage RNA. miRNeasy kit (QIAGEN) was used for further RNA extraction
RNAtag-seq cDNA libraries for simultaneous detection of host and intracellular bacterial transcripts was done as previously described in Avraham et al (2016) (Avraham et al., 2016). In brief, samples contain murine RNA transcripts (uninfected controls) or a mix of bacterial and murine RNA transcripts (infected) were barcoded by ligation with RNA adaptors and pooled together. Murine rRNA was depleted using the RiboZero Gold (Human/Mouse/Rat) kit (Illumina) according to the manufacturer’s guidelines. Strand-specific cDNA libraries were prepared and sequenced as Paired-end (R1: 30, R2: 50) using Nextseq machine and 75 high throughput kit with total coverage of ~1.1B reads and a mean of ~19.5M reads per library, ranges from ~4.5M to ~45.5M. For each condition, biological triplicates were analyzed

treatment_protocol: 800,000 cells/well of BMDM cells were plated in non-tissue culture treated 6 well plates supplemented with DMEM with 20% FBS and 25ng/ml rmM-CSF. Infected BMDMs samples were infected with WT or the ∆manZ mutant strains harboring a GFP expressing plasmid (pFPV25.1; Addgene) at MOI of 10:1. In the 2-DG treated samples, 2-DG (Sigma D8375-5G) in a concentration of 1mM was supplemented to the media containing 15 μg/ml gentamicin after the wash of the uninternalized bacteria. Uninfected samples were treated under the same conditions.                                                                                20,000 cells per sample of uninfected controls or infected (GFP positive) cells were sorted under continuous cooling to 4°C by a BD FACS Aria III into a low bind eppendorfs contained 700μl QIAzol Lysis reagent, over a time curse of 0.5h, 6h and 24h post-infection.

tag: bacteria status

value: no bacteria

tag: 2-dg status

value: with 2-DG

tag: time post-infection (hours)

tag: replicate


title: WAT Fnip2C/C (YFN 593) 1

address: C/ Melchor Fernández Almagro, 3

institute: CNIO

description:
WAT Fnip2C/C (YFN 593)
RNA1010

tag: genotype


title: Pcgf1_f/f_H3K27me3_1

description:
Pcgf1_f/f_H3K27me3_1
peak file = H3K27me3_Peaks.txt

tag: cell type

value: H3K27me3 (Merk Millipore, 07-449)


title: WAT Fnip2T/T (YFN 609) 4

description:
WAT Fnip2T/T (YFN 609)
RNA1009


title: Pcgf1_f/f_H3K27ac_2

tag: strain

value: Anti-acetyl-Histone H3(Lys27) (Merk Millipore, 07-360)


title: RNA-seq_LMPP_Pcgf1_fl/fl_2

description:
20191202LMPP_CPM.txt
DK18007_49_08


title: 24h_no_bc_2DG_rep2


title: MOLM-13 cells, Vehicle (DMSO) + hBMSC-CM, replicate 1

tag: cell line

value: AML cells

tag: treatment

value: Vehicle (DMSO)

value: hBMSC-CM


title: WAT Fnip2T/T (YFN 609) 3

description:
WAT Fnip2T/T (YFN 609)
RNA1009

value: Visceral white adipose tissue

value: Female


title: WAT Fnip2T/T (YFN 609) 2

description:
WAT Fnip2T/T (YFN 609)
RNA1009


title: Pcgf1_-/-_SUZ12_2

tag: passage

tag: antibody

value: anti SUZ12(D39F6) (Cell Signaling #3737)


title: 24h_no_bc_2DG_rep1


title: Pcgf1_f/f_SUZ12_2

value: Hemtopoietic progenitor cells (IdHPs)


title: 24h_no_bc_no_2DG_rep2

value: without 2-DG


title: WAT Fnip2C/C (YFN 593) 2

description:
WAT Fnip2C/C (YFN 593)
RNA1010

tag: tissue

tag: feeding state

value: Ad libitum acces to food and drink


title: Pcgf1_-/-_SUZ12_1


title: MOLM-13 cells, AC220 (quizartinib) + hBMSC-CM, replicate 1

value: WT

value: 3nM AC220 (quizartinib)


title: WAT Fnip2T/T (YFN 608) 4

description:
WAT Fnip2T/T (YFN 608)
RNA1007


title: Pcgf1_f/f_H3K27ac_1

value: Pcgf1 fl/fl


title: WAT Fnip2T/T (YFN 608) 3

description:
WAT Fnip2T/T (YFN 608)
RNA1007


title: Pcgf1_f/f_SUZ12_1


title: MOLM-13 cells, Vehicle (DMSO) + hBMSC-CM, replicate 2


title: 24h_no_bc_no_2DG_rep3


title: MOLM-13 cells, AC220 (quizartinib) + hBMSC-CM, replicate 3


title: WAT Fnip2T/T (YFN 608) 2

description:
WAT Fnip2T/T (YFN 608)
RNA1007


title: input MOLM-13 cells, Vehicle + RPMI, replicate 3

treatment_protocol: MOLM-13 cells were treated with 3nM AC220(quizartinib) and/or 10nM Everolimus for 12 hours either in RPMI or hBMSC-CM

value: RPMI

tag: rna fraction

value: input RNAs


title: Ring1A/B_-/-_RING1B

value: Ring1A/B -/-

value: anti RING1B (in house)


title: input MOLM-13 cells, Vehicle + RPMI, replicate 2


title: 6h_no_bc_2DG_rep3

value: no bacteria

value: with 2-DG


title: 6h_no_bc_2DG_rep2


title: MOLM-13 cells, AC220 (quizartinib) + hBMSC-CM, replicate 2

value: AML cells


title: Pcgf1_-/-_RING1B_2

value: Pcgf1 -/-


title: WAT Fnip2T/T (YFN 608) 1

description:
WAT Fnip2T/T (YFN 608)
RNA1007

value: Visceral white adipose tissue


title: HD_5

tag: disease state

value: Healthy

value: blood

tag: time

value: memory B cells

tag: subject

value: Healthy Donor_5


title: input MOLM-13 cells, Vehicle + RPMI, replicate 1

value: Vehicle (DMSO)

tag: medium


title: 6h_no_bc_2DG_rep1

tag: bacteria status

tag: 2-dg status


title: heavy polysomes MOLM-13 cells, Vehicle + RPMI, replicate 3

value: WT

value: enriched in heavy polysomes


title: 6h_no_bc_no_2DG_rep3

value: without 2-DG

tag: time post-infection (hours)

tag: replicate


title: WAT Fnip2T/T (YFN 607) 4

description:
WAT Fnip2T/T (YFN 607)
RNA1005

tag: genotype

value: Ad libitum acces to food and drink

tag: Sex

value: Female


title: Pcgf1_-/-_RING1B_1

tag: strain

tag: cell type

value: Hemtopoietic progenitor cells (IdHPs)


title: Liver Fnip2C/C (YFN 592) 2

description:
Liver Fnip2C/C (YFN 592)
RNA948

value: Liver


title: Pcgf1_f/f_RING1B_2

description:
Pcgf1_f/f_RING1B_2
peak file = Ring1b_Peak.broadPeak

tag: passage

value: Pcgf1 fl/fl

value: anti RING1B (in house)


title: heavy polysomes MOLM-13 cells, Vehicle + RPMI, replicate 2

tag: cell line

value: AML cells

tag: treatment

value: RPMI


title: WAT Fnip2T/T (YFN 607) 3

description:
WAT Fnip2T/T (YFN 607)
RNA1005

tag: tissue

value: Visceral white adipose tissue

tag: feeding state


title: 24h_no_bc_no_2DG_rep1

value: no bacteria


title: 6h_no_bc_no_2DG_rep2


title: Pcgf1_f/f_RING1B_1

description:
Pcgf1_f/f_RING1B_1
peak file = Ring1b_Peak.broadPeak

tag: antibody


title: WAT Fnip2T/T (YFN 607) 2

description:
WAT Fnip2T/T (YFN 607)
RNA1005


title: 6h_no_bc_no_2DG_rep1


title: WAT Fnip2T/T (YFN 607) 1

description:
WAT Fnip2T/T (YFN 607)
RNA1005


title: FLAG_PCGF1_2

description:
FLAG_PCGF1_2
peak file = Pcgf1_Peak.broadPeak

value: Pcgf1 -/- + FLAG-PCGF1

value: anti m2_FLAG(Sigma-Aldrich , F3165)


title: input MOLM-13 cells, combo (AC220+everolimus) + RPMI, replicate 3

value: 3nM AC220+10nM Everolimus

tag: rna fraction

value: input RNAs


title: input MOLM-13 cells, combo (AC220+everolimus) + RPMI, replicate 2

value: WT


title: WAT Fnip2C/C (YFN 590) 4

description:
WAT Fnip2C/C (YFN 590)
RNA1004


title: 0.5h_no_bc_2DG_rep3

value: with 2-DG


title: FLAG_PCGF1_1

description:
FLAG_PCGF1_1
peak file = Pcgf1_Peak.broadPeak


title: input MOLM-13 cells, combo (AC220+everolimus) + RPMI, replicate 1


title: NC_for_Pcgf1

value: Pcgf1 -/- + NC


title: 0.5h_no_bc_2DG_rep1


title: WAT Fnip2C/C (YFN 590) 2

description:
WAT Fnip2C/C (YFN 590)
RNA1004

value: Ad libitum acces to food and drink


title: 0.5h_no_bc_2DG_rep2


title: Pcgf1_-/-_input 2

description: Pcgf1_-/-_input 2

value: Pcgf1 -/-


title: WAT Fnip2C/C (YFN 590) 3

description:
WAT Fnip2C/C (YFN 590)
RNA1004

value: Female


title: heavy polysomes MOLM-13 cells, combo (AC220+everolimus) + RPMI, replicate 3

value: enriched in heavy polysomes


title: 0.5h_no_bc_no_2DG_rep3

value: without 2-DG


title: heavy polysomes MOLM-13 cells, Vehicle + RPMI, replicate 1

value: Vehicle (DMSO)


title: WAT Fnip2C/C (YFN 590) 1

description:
WAT Fnip2C/C (YFN 590)
RNA1004


title: Pcgf1_-/-_input 1

description: Pcgf1_-/-_input 1

value: Hemtopoietic progenitor cells (IdHPs)


title: heavy polysomes MOLM-13 cells, combo (AC220+everolimus) + RPMI, replicate 2

value: AML cells

value: RPMI


title: heavy polysomes MOLM-13 cells, combo (AC220+everolimus) + RPMI, replicate 1


title: 0.5h_no_bc_no_2DG_rep1

value: no bacteria


title: Pcgf1_f/f_input_1

value: Pcgf1 fl/fl


title: 0.5h_no_bc_no_2DG_rep2


title: input MOLM-13 cells, AC220 (quizartinib) + RPMI, replicate 3

value: 3nM AC220 (quizartinib)


title: MOLM-13 cells, Vehicle (DMSO) + hBMSC-CM, replicate 3

value: hBMSC-CM


title: Day12_KO3_MEF

city: Bethesda

first: Michael

last: Bustin

address: Building 37, Room 3122

institute: NIH

data_processing:
Basecalling was performed using RTA version 2.4.11
Demultiplexing and FASTQ generation was performed using bcl2fastq (version 2.17) allowing 1 mismatch.
Trimming of adapters and low-quality bases was performed using CutAdapt (v.1.18).
Mapping to the mouse genome (mm10) was performed using STAR 2.7.0f
Gene-level expression quantificiation was performed using RSEM (version 1.3.0).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited raw counts matrix

molecule: polyA RNA

source_name: Embryo

growth_protocol: Preadipocytes were isolated from inguinal white adipose tissue of WT and DKO mice and cultured on collagen coated plates. MEF were isolated from WT and DKO mouse embryo and cultured on tissue culture plates.

extract_protocol:
For RNA seq, cells were scrapped in  trizol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Proliferating preadipocytes and MEF were replated and grown until confluency. Two days after reaching confulency,  Preadipocytes were treated to differentiate into adipocytes using differentiation media (Insulin (0.5 μg/ml), dexamethasone (5 μM), IBMX (0.5 mM), T3 (1 nM), Rosiglitazone (1 μM)) for 4 days and maintained in maintenance medium (Insulin (0.5 μg/ml), T3 (1 nM)) for 4 days. MEFs were differentiated into adipocytes with differentiation medium (Insulin (0.5 μg/ml), dexamethasone (5 μM), IBMX (0.5 mM), T3 (1 nM), Rosiglitazone (1 μM)) for 8 days and then with maintenance medium (Insulin (0.5 μg/ml), T3 (1 nM)) for 4 days.

value: Hmgn1-/- and Hmgn2-/-

value: adipocytes


title: Day12_KO2_MEF


title: Day12_KO1_MEF


title: Day12_WT3_MEF

value: Wild type


title: RNA-seq_Pcgf1_fl/fl_2

description:
Pcgf1CPM.txt
S08482


title: ACH-2 + 10ug Fentanyl - replicate 2

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: University of Cincinnati, 160 Panzeca Way

institute: University of Cincinnati

description: ACH-2 + 10ug Fentanyl - replicate 2

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq
fastq seqences were aligned to hg19 using bowtie
differential expression analysis was performed using edgeR
Assembly: hg19
Supplementary files format and content: tab delimited raw counts with genes in rows and samples in columns

source_name: ACH-2 + 10ug Fentanyl - replicate 2

growth_protocol: Cells were maintained in RPMI 1640 medium supplemented with 10% heat inactivated FBS, 100 U/mL penicillin, and 100 μg/mL streptomycin at 37°C and 5% CO2.

extract_protocol:
Total RNA of fentanyl-treated and untreated ACH-2 cells was isolated using the commercially available miRNA Isolation Kit (miVana; Applied Biosystems; Carlsbad, CA) according to the manufacturer's protocol.  A NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific; Waltham, MA) was used to determine total RNA concentration and purity.  A 2100 Bioanalyzer (Agilent; Santa Clara, CA) and agarose electrophoresis were used to assess RNA integrity.
NEBNext small RNA sample library preparation kit (NEB; Ipswich, MA) was used to prepare the library with a modified approach for precise miRNA library size selection that allowed the kit to process low input and low-quality RNA with higher library recovery and miRNA read alignment.  After 15 cycles of PCR with 100 ng total RNA as input, the libraries with unique indices were pooled, column cleaned, and combined with a custom-designed DNA ladder containing 135 and 146 base pairs (bp) purified PCR amplicon.  This size range corresponds to a 16-27 nt insert miRNA library that covers all miRNAs.  Agarose gel electrophoresis and gel excision were carried out.  The library pool ranging from 135 to 146 bp, including the DNA marker, was gel purified and quantified using the NEBNext Library Quant kit (NEB) in the QuantStudio 5 Real-Time PCR System (Thermo Fisher Scientific; Waltham, MA).  The first round of sequencing was performed using an Illumina Nextseq 550 sequencer to generate a few million reads to measure the relative concentration of each library.  For the final data analysis, the capacity of each library was adjusted to generate the predicted number of equal reads from each sample.

treatment_protocol: Cells were treated with 10ug of fentanyl for 24 hours

value: ACH-2, T lymphocyte cell line

value: 10ug Fentanyl

value: Peripheral blood


title: Day12_WT2_MEF


title: heavy polysomes MOLM-13 cells, AC220 (quizartinib) + RPMI, replicate 3

value: WT


title: ACH-2  No drug control - replicate 1

description: ACH-2  No drug control - replicate 1

source_name: ACH-2  No drug control - replicate 1

value: No drug control


title: RNA-seq_Pcgf1_-/-_1

description:
Pcgf1CPM.txt
S08481

value: Pcgf1 -/-


title: heavy polysomes MOLM-13 cells, AC220 (quizartinib) + RPMI, replicate 2

value: enriched in heavy polysomes


title: ACH-2  No drug control - replicate 2

description: ACH-2  No drug control - replicate 1


title: RNA-seq_Pcgf1_fl/fl_1

description:
Pcgf1CPM.txt
S08480

value: Hemtopoietic progenitor cells (IdHPs)


title: Day12_WT1_MEF


title: Pcgf1_f/f_input_2


title: input MOLM-13 cells, AC220 (quizartinib) + RPMI, replicate 1

value: AML cells

value: input RNAs


title: sh-circPRKAA1-3

city: Hefei

first: Qidong

last: Li

state: Anhui

address: 443 Huangshan Road, Shushan district

institute: Lianxin Liu Lab

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg18
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: HepG2 mesenchymal cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: HepG2 cells were infected with sh-ctrl and sh-circPRKAA1 lentivirus

value: Liver

value: epithelial

tag: shRNA

value: circPRKAA3 KD


title: sh-circPRKAA1-2

value: circPRKAA2 KD


title: RNA-seq_Pcgf1_-/-_2

description:
Pcgf1CPM.txt
S08483


title: input MOLM-13 cells, Vehicle + hBMSC-CM, replicate 3

value: Vehicle (DMSO)

tag: medium

value: hBMSC-CM


title: sh-circPRKAA1-1

value: circPRKAA1 KD


title: heavy polysomes MOLM-13 cells, AC220 (quizartinib) + RPMI, replicate 1

value: 3nM AC220 (quizartinib)

value: RPMI


title: PTECs VHL-KO;SETD2-KO 3

city: Shanghai

first: ChangWei

last: Liu

address: No. 1954 Huashan Road, Xuhui District

institute: Shanghai Jiaotong University

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
Count counting
Assembly: GRCm38
Supplementary files format and content: TXT file contain counts for each sample

source_name: primary cell

extract_protocol:
Total RNA was extracted from cell by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: primary cell

value: PTECs


title: Day8_KO2_MEF

state: MD

value: Hmgn1-/- and Hmgn2-/-

value: differentiating MEF


title: PTECs VHL-KO;SETD2-KO 2


title: Day8_KO1_MEF


title: input MOLM-13 cells, AC220 (quizartinib) + RPMI, replicate 2

value: WT


title: ACH-2 + 10ug Fentanyl - replicate 1

description: ACH-2 + 10ug Fentanyl - replicate 1

source_name: ACH-2 + 10ug Fentanyl - replicate 1

value: ACH-2, T lymphocyte cell line

value: 10ug Fentanyl

value: Peripheral blood


title: PTECs VHL-KO 4

value: VHL-KO


title: sh-ctrl-3

source_name: Liver

value: Liver

value: epithelial

value: ctrl


title: PTECs VHL-KO 2


title: heavy polysomes MOLM-13 cells, Vehicle + hBMSC-CM, replicate 3

value: AML cells

value: Vehicle (DMSO)

value: enriched in heavy polysomes


title: sh-ctrl-1


title: Day8_KO3_MEF


title: PTECs VHL-KO;SETD2-KO 4


title: sh-ctrl-2


title: heavy polysomes MOLM-13 cells, Vehicle + hBMSC-CM, replicate 2

value: hBMSC-CM


title: PTECs VHL-KO 1


title: Day4_KO3_MEF


title: heavy polysomes MOLM-13 cells, Vehicle + hBMSC-CM, replicate 1


title: MOI-5_R6

city: San Francisco

first: Warner

middle: C.

last: Greene

address: 1650 Owens St

institute: Gladstone institute ,UCSF

data_processing:
The raw sequencing reads were processed through the nf-core's nextflow RNAseq pipeline v3.0.
The reads quality was assessed and were trimmed using Trim Galore
The reads were aligned to the human genome GRCh37 using the STAR aligner  and the transcripts were quantified in Transcripts Per Million (TPM) units using Salmon. The transcript in TPM units was converted to gene-level counts using the tximport
The resulting count matrix was loaded in R, genes with at least 5 reads, and at least two replicate samples were used in the analyses for differential expression using edgeR v 3.36.0. The read counts were normalized using the TMM method as implemented in the calcNormFactors function and assessed for differential expression using the glmQLFit and glmQLFTest functions. Up and down-regulated genes were inferred using the DESeq2 v1.3.4 Bioconductor package. The size factors and dispersion estimates were performed using the DESeq function. Up-regulated genes then were identified using the results function setting the arguments lfcThreshold = log2(1.5) and altHypothesis = "greater" and similarly down-regulated genes were identified using the same lfcThreshold and setting the altHypothesis = "less".
Assembly: GRCh37
Supplementary files format and content: Salmon_abundances

source_name: SARS-CoV-2-astrocytes MOI=5

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Astrocytes were infected by SARS-CoV-2 at MOI=1 or MOI=5 for 4 days.

value: brain

value: astrocytes

tag: infected with

value: SARS-CoV-2 MOI=5


title: MOI-5_R5


title: input MOLM-13 cells, everolimus + hBMSC-CM, replicate 3

value: 10nM Everolimus

value: input RNAs


title: MOI-5_R4


title: Day4_KO2_MEF

value: Hmgn1-/- and Hmgn2-/-

value: differentiating MEF


title: input MOLM-13 cells, Vehicle + hBMSC-CM, replicate 2

value: WT


title: Day4_KO1_MEF


title: input MOLM-13 cells, everolimus + hBMSC-CM, replicate 2


title: Day8_WT3_MEF

value: Wild type


title: YbKO_2

city: Harbin

first: Zheng

state: Heilongjiang

address: 92 Xidazhijie  Harbin Institute of Technology

institute: Harbin Institute of Technology

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. 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 N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the mouse reference genome (GRCm38/mm10) using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining  differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. padj<=0.05 and |log2(foldchange)| >= 0 were set as the threshold for significantly differential expression.
Assembly: mouse reference genome (GRCm38/mm10)
Supplementary files format and content: Processed_data_files.txt: Tab-delimited text file includes FPKM of each gene.

source_name: Pancreatic islets

extract_protocol:
Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany) from pancreatic islets of Ythdc1flox/flox and Ythdc1-βKO mice at 7 weeks old. Three independent biological replicates for each group were used for RNA-seq.
mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.
After the library is qualified, the different libraries are pooling according to the effective concentration and the target amount of data off the machine, then being sequenced by the Illumina NovaSeq 6000. The end reading of 150bp pairing is generated. The basic principle of sequencing is to synthesize and sequence at the same time (Sequencing by Synthesis). Four fluorescent labeled dNTP, DNA polymerase and splice primers were added to the sequenced flowcell and amplified. When the sequence cluster extends the complementary chain, each dNTP labeled by fluorescence can release the corresponding fluorescence. The sequencer captures the fluorescence signal and converts the optical signal into the sequencing peak by computer software, so as to obtain the sequence information of the fragment to be tested.

value: Pancreatic islets

tag: age

value: 7 weeks


title: YbKO_3


title: MOI-5_R3

state: CA


title: input MOLM-13 cells, Vehicle + hBMSC-CM, replicate 1


title: YFF_3


title: Day8_WT1_MEF


title: input MOLM-13 cells, everolimus + hBMSC-CM, replicate 1


title: Day8_WT2_MEF


title: heavy polysomes MOLM-13 cells, everolimus + hBMSC-CM, replicate 3


title: MOI-5_R2


title: Day4_WT2_MEF


title: MOI-5_R1


title: YFF_1


title: heavy polysomes MOLM-13 cells, everolimus + hBMSC-CM, replicate 2


title: MOI1_R6

source_name: SARS-CoV-2-astrocytes MOI=1

value: SARS-CoV-2 MOI=1


title: Day4_WT1_MEF


title: SKMEL palbo 3

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

institute: IRB Barcelona

data_processing:
Reads were aligned to the mus musculus reference genome version mm10 using STAR (v2.5.2) with default parameters. SAM files were converted to BAM and sorted using Sambamba (v0.7.1)
Count matrices were generated using The Rsubread R package with the ENSEMBL Mus_musculus.GRCm38.97 custom annotation
Assembly: mm10
Supplementary files format and content: Raw count matrix in tab-delimited format

growth_protocol: Cells were grown in DMEM supplemented with 10% FBS and antibiotics.

extract_protocol:
Total RNA was extracted using Qiagen Rneasy Mini Kit (Cat #74106) according to manufacturer's instructions.
RNA libraries were prepared for sequencing using the kits NEBNext® Poly(A) mRNA Magnetic Isolation Module (Cat# E7490) and NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (Cat#E7760), following manufacturer´s instructions and 9 cycles of library amplification

treatment_protocol: Cells were treated with 1μM palboilicb (PD-0332991) dissolved in water for 7 days prior to harvest. Control cells were untreated. Media, including drug, was changed every third day. Replicates were grown and harvested separately.

value: melanoma cell

value: palbo

tag: sample id


title: YbKO_1


title: Day0_KO3_MEF

value: MEF


title: input MOLM-13 cells, combo (AC220+everolimus) + hBMSC-CM, replicate 3

value: AML cells

value: 3nM AC220+10nM Everolimus


title: SKMEL ctrl 3

value: Ctrl


title: Day0_KO2_MEF


title: MOI1_R5

value: brain

value: astrocytes


title: heavy polysomes MOLM-13 cells, everolimus + hBMSC-CM, replicate 1

value: 10nM Everolimus

value: hBMSC-CM

value: enriched in heavy polysomes


title: SKMEL palbo 2


title: Day4_WT3_MEF

value: differentiating MEF


title: Day0_KO1_MEF

value: Hmgn1-/- and Hmgn2-/-


title: input MOLM-13 cells, combo (AC220+everolimus) + hBMSC-CM, replicate 1

value: WT

value: input RNAs


title: SKMEL ctrl 2


title: MOI1_R3


title: Day0_WT3_MEF

value: Wild type


title: input MOLM-13 cells, combo (AC220+everolimus) + hBMSC-CM, replicate 2


title: YFF_2

value: Pancreatic islets

value: 7 weeks


title: MOI1_R2

value: SARS-CoV-2 MOI=1


title: Day0_WT2_MEF

value: MEF


title: Day0_WT1_MEF


title: MOI1_R1


title: heavy polysomes MOLM-13 cells, combo (AC220+everolimus) + hBMSC-CM, replicate 3

value: AML cells


title: heavy polysomes MOLM-13 cells, combo (AC220+everolimus) + hBMSC-CM, replicate 2

value: 3nM AC220+10nM Everolimus


title: SKMEL ctrl 1

value: melanoma cell

value: Ctrl


title: SKMEL palbo 1

value: palbo


title: WAT Fnip2T/T (YFN 609) 1

state: Comunidad de Madrid

description:
WAT Fnip2T/T (YFN 609)
RNA1009

value: Visceral white adipose tissue

value: Ad libitum acces to food and drink

value: Female


title: heavy polysomes MOLM-13 cells, combo (AC220+everolimus) + hBMSC-CM, replicate 1

value: hBMSC-CM

value: enriched in heavy polysomes


title: Mock_R6

source_name: Mock-astrocytes

value: brain

value: astrocytes

value: mock


title: Pcgf1_-/-_JARID2_2

data_processing:
For ChIP-seq without spike-in genome, reads were aligned to mm9 using bowtie2(Langmead et al., 2012). ChIP-seq experiments which contained a spike-in genome were aligned against concatenated genome of mm9 and dm3 using bowtie2 and resulting SAM files were then split such that reads aligning to mouse and drosophilia were placed in separate files. The SAM files were converted to the BAM format using Samtools, version 1.6.0 (Li et al., 2009). The PCR duplicates were removed by Picardtools (http://broadinstitute.Github.io/picard).
The BAM files were converted to bigwig files by deepTools2 (Ramirez et al. 2016) for visualization. For comparison across ChIP-seq samples without spike-in genome, the bigwig files were normalized to reads per million mapped sequence reads (RPKM). For ChIP-seq with spike-in genome, RPKM were further normalized according to normalization factors calculated as 1 over the number of reads (per million) mapping to drosophilia as previously reported(Orland et al., 2016).
Assembly: mm9 or concateenated genomes of Mm9 and dm3
Supplementary files format and content: bigwig files described in the data processing step columns

source_name: Bone marrow

extract_protocol: ChIP for TY1, RING1B, SUZ12, H3K27me3 and H3K27ac were performed as described previously (Isono et al., 2013). Cultured IdHP cells were cross-linked with 1% formaldehyde/PBS for 10 min at room temperature. Chromatin was sheared and used for each immunoprecipitation with indicated antibodies. ChIP for H2AK119ub was performed as described before (Mochizuki-Kashio et al., 2015). Cultured IdHP cells were cross-linked with 0.5% formaldehyde/PBS for 2 min at 37℃. Chromatin was sheared and used for each immunoprecipitation. MNase-seq:One million cells were cross-linked by adding formaldehyde to 1% and incubated for 10 min at RT, quenched using 1 M glycine, and washed three times in PBS. Collected cells were lysed in 1 ml PBS + 0.5% Triton X-100 for 3 min on ice. Nuclei were pelleted and washed by MNase digestion buffer (10 mM Tris-HCl, pH 7.4, 15 mM NaCl, 60 mM KCl, 0.5 mM spermidine), spun down and resuspended in the same buffer. Ca2+ concentration was adjusted to 1mM with 1M CaCl2 and MNase was added to 10 U/ml. The reaction mixture was incubated at 37°C for 10 min and the reaction was stopped by adding 150 μL of stop buffer (20 mM EDTA, 20 mM EGTA, 0.4% SDS, 0.5 mg/ml proteinase K) and then incubated for overnight at 65°C. DNA was purified using a MinElute PCR purification Kit (28006; QIAGEN) and loaded to 1.5% Agarose Gel. Mononucleosomal bands were excised and purified by a gel extraction kit (28705; QIAGEN).

value: Hemtopoietic progenitor cells

value: Pcgf1 -/-

value: anti JARID2(D6M9X) (Cell Signaling, #13594)


title: MOI1_R4

value: SARS-CoV-2 MOI=1


title: Day9_KO3_PRE

source_name: Inguinal white adipose tissue

value: Hmgn1-/- and Hmgn2-/-

value: brown-like adipocytes


title: Mock_R5


title: Day9_KO2_PRE


title: Pcgf1_-/-_JARID2_1


title: input MOLM-13 cells, AC220 (quizartinib) + hBMSC-CM, replicate 3

value: AML cells

value: WT

value: 3nM AC220 (quizartinib)

value: input RNAs


title: Mock_R4


title: Day9_KO1_PRE


title: Pcgf1_f/f_JARID2_2

value: Pcgf1 fl/fl


title: input MOLM-13 cells, AC220 (quizartinib) + hBMSC-CM, replicate 2


title: Mock_R3


title: Day9_WT3_PRE

value: Wild type


title: Pcgf1_f/f_JARID2_1


title: Ring1a -/- 1b -/- H2AK119ub 2

description: Ring1a -/- 1b -/- H2AK119ub 2

value: anti Ubiquityl-Histone H2A (Lys119) (Cell Signaling, #8240)


title: Mock_R2


title: input MOLM-13 cells, AC220 (quizartinib) + hBMSC-CM, replicate 1

value: hBMSC-CM


title: heavy polysomes MOLM-13 cells, AC220 (quizartinib) + hBMSC-CM, replicate 3

value: enriched in heavy polysomes


title: Mock_R1

value: brain

value: astrocytes


title: Day9_WT1_PRE


title: Ring1a -/- 1b -/- H2AK119ub 1

description: Ring1a -/- 1b -/- H2AK119ub 1

value: Hemtopoietic progenitor cells


title: heavy polysomes MOLM-13 cells, AC220 (quizartinib) + hBMSC-CM, replicate 2


title: Day9_WT2_PRE


title: Pcgf1_-/-_H2AK119ub_2 [FC00472]

value: Pcgf1 -/-


title: HK/siBCL6 cells RNA-seq.rep2

city: China

first: Yanan

address: 500 Dongchuan Road, Minhang District, Shanghai, China

department: School of Life Sciences

institute: East China Normal University

description:
K2
Gene-FPKM-expression of A B K

data_processing:
Quality control; Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC  content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome; We selected Hisat2 as the mapping tool; Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level; featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for  the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: GRCh38(HPNE, HK and HK siBCL6 cells) and mm9 (MEF1, MEF1/KRAS G12D, MEF2/KRAS G12D and MEF2/KRAS G12D/siBCL6 cells)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Normal human pancreatic duct cells

extract_protocol:
Cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) 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: Normal human pancreatic duct cells

value: HK cells treated with siBCL6


title: Pcgf1_-/-_H2AK119ub_1 [FC00472]


title: Day6_KO3_PRE

value: Hmgn1-/- and Hmgn2-/-

value: differentiating  preadipocytes


title: Day6_KO1_PRE


title: HK/siBCL6 cells RNA-seq.rep3

description:
K3
Gene-FPKM-expression of A B K


title: Pcgf1_f/f_H2AK119ub_2 [FC00472]


title: HK/siBCL6 cells RNA-seq.rep1

description:
K1
Gene-FPKM-expression of A B K


title: primary AML cells isolated from spleen of mice treated with Vehicle, replicate 3

source_name: Spleen

treatment_protocol: NRG-S mice engrafted with primary FLT3-ITD+ AML were treated with either vehicle or 2.5mg/kg quizartinib for 16 hours

value: Spleen

value: primary AML

value: Vehicle


title: Day6_KO2_PRE


title: primary AML cells isolated from spleen of mice treated with Vehicle, replicate 2


title: HK cells RNA-seq.rep3

description:
B3
Gene-FPKM-expression of A B K

value: HPNE cells stably expressed KRAS G12V


title: Pcgf1_f/f_H2AK119ub_1 [FC00472]

value: Pcgf1 fl/fl


title: Day6_WT3_PRE

value: Wild type


title: Pcgf1_-/-_KDM2B_2

value: anti KDM2B (in house)


title: primary AML cells isolated from spleen of mice treated with Vehicle, replicate 1


title: primary AML cells isolated from spleen of mice treated with AC220 (quizartinib), replicate 3

value: Quizartinib


title: primary AML cells isolated from spleen of mice treated with AC220 (quizartinib), replicate 2


title: HK cells RNA-seq.rep1

description:
B1
Gene-FPKM-expression of A B K


title: Day6_WT2_PRE


title: Day6_WT1_PRE


title: Pcgf1_-/-_KDM2B_1


title: heavy polysomes MOLM-13 cells, AC220 (quizartinib) + hBMSC-CM, replicate 1

value: AML cells

value: WT

value: 3nM AC220 (quizartinib)

value: hBMSC-CM

value: enriched in heavy polysomes


title: Pcgf1_f/f_KDM2B_2

value: Hemtopoietic progenitor cells


title: primary AML cells isolated from spleen of mice treated with AC220 (quizartinib), replicate 1


title: HPNE cells RNA-seq.rep3

description:
A3
Gene-FPKM-expression of A B K

value: Normal human pancreatic duct cells

value: untreated


title: Pcgf1_f/f_KDM2B_1


title: HPNE cells RNA-seq.rep2

description:
A2
Gene-FPKM-expression of A B K


title: HPNE cells RNA-seq.rep1

description:
A1
Gene-FPKM-expression of A B K


title: Day3_KO3_PRE

value: Hmgn1-/- and Hmgn2-/-

value: differentiating  preadipocytes


title: BRD4-E2-MCF7

city: Xiamen

first: Guosheng

last: Hu

state: Fujian

address: Xiang'an South Road, Xiang'an District

institute: xiamen University

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the hg19 genome assembly using Bowtie version 2.2.1.
The bigwig files were generated by using Homer v4.7, in which the total tags are normalized to 1.00e+07.
Genome_build: hg19

source_name: Michigan Cancer Foundation-7 cells(MCF-7 cells)

extract_protocol:
Cells were fixed with disuccinimidyl glutarate (DSG) (2 mM) (Proteochem) for 45 mins at RT, washed twice with PBS and then double-fixed with 1% formaldehyde for another 10 mins at RT. Fixation was stopped by adding glycine (0.125 M) and incubated for 5 mins at RT, followed by washing with PBS twice. Chromatin DNA was sheared to 300~500 bp average in size through sonication. The resultant protein was immunoprecipitated with anti-BRD4 antibody overnight at 4 °C, followed by incubation with protein G magnetic beads (Bio-Rad) for an additional 4 hrs. After washing and elution, the protein-DNA complex was reversed by heating at 65 °C overnight. Immunoprecipitated DNA was purified by using QIAquick spin columns and subjected to high throughput sequencing.
The libraries were constructed following Illumina’s Chip-Seq Sample prep kit. Briefly, Chip DNA was end-blunted and added with an ‘A’ base so the adaptors from Illumina with a ‘T’ can ligate on the ends. Then 200–400 bp fragments are gel-isolated and purified. The library was amplified by 18 cycles of PCR.

treatment_protocol: MCF7 cells  transfected with control siRNA or siRNA specifically targeting BRD4 and maintained in phenol red free DMEM (stripping medium) supplemented with 5% charcoal-treated FBS for three days, followed by treatemnt of either 10-7 M 17-β-estrodial or ethanol for 1 hr.

tag: chip antibody


title: Day3_KO2_PRE

tag: genotype


title: primary AML cells isolated from bone marrow of mice treated with Vehicle, replicate 1

value: Bone marrow

value: primary AML


title: Day3_WT3_PRE


title: BRD4-CTL-MCF7

value: CTL


title: HK cells RNA-seq.rep2

description:
B2
Gene-FPKM-expression of A B K

value: HPNE cells stably expressed KRAS G12V


title: Day3_KO1_PRE


title: B6CBAF1/J RNA-seq_Ring1A_-/-_Ring1B_-/-_3

city: Yokohama-shi

first: Junichiro

institute: RIKEN

data_processing:
RNA-seq reads were aligned to the mouse reference genome (mm9) using Tophat (v2.0.13; https://ccb.jhu.edu/software/tophat/index.shtml).
Transcript levels (counts) were summarized per gene using Rsubread (Liao et al., 2013). Count per million (CPM) were calculated using edgeR (Robinson et al., 2010).
Assembly: mm9
Supplementary files format and content: bigwig files normalized using RPKM in each samples,

value: Hemtopoietic progenitor cells (LMPP)

value: Ring1A/B -/-


title: primary AML cells isolated from bone marrow of mice treated with Vehicle, replicate 2

value: Vehicle


title: B6CBAF1/J RNA-seq_Ring1A_-/-_Ring1B_-/-_2


title: B6CBAF1/J RNA-seq_Ring1A_-/-_Ring1B_-/-_1


title: Day3_WT2_PRE

value: Wild type


title: primary AML cells isolated from bone marrow of mice treated with AC220 (quizartinib), replicate 3

value: Quizartinib