title: Hi-C MCF-7 -E2 replicate 1

description:
MCF-7 wild type cells treated with ICI 182,780, biological replicate 1
processed data file:
abcpw-0000.bw
tadpw-0000.bw
tadbb-0000.bed.gz

data_processing:
library strategy: in situ Hi-C
Basecalls were performed using Illumina RTA 1.18.64, and fastq files were then generated using Illumina bcl2fastq v2.17.1.14
Each 50-bp read from each pair was aligned, independently of its mate, to the hg18 reference genome using bowtie2 version 2.3.0 with the following parameters: --end-to-end --very-sensitive -L 30 --score-min L,-0.6,-0.2 --mp 6,2. Reads aligned to unique genomic locations were retained for subsequent analysis. Reads aligned to more than one location were discarded. Reads that could not be aligned were split at putative ligation junctions and the resulting parts were re-submitted to bowtie2 for alignment. If one or more parts were uniquely aligned, they were retained for subsequent analysis, otherwise a final attempt to align the read in question was carried out by applying the iterative mapping procedure of Imakaev et al (Imakaev 2012). Specifically, the read was iteratively trimmed in increments of 5 bases at its 3ʹ end and then submitted to bowtie2 at each iteration until a unique or multiple alignment was found. If the alignment was unique, the read was retained for subsequent analysis, otherwise it was discarded. To improved the yield of aligned reads, we carried out this iterative alignment procedure also by trimming the 5ʹ end of the read in question. Next, the reads and read parts that were uniquely aligned were combined into pairs based on the original unaligned read pair from which the aligned reads or parts were derived. Uniquely aligned reads or parts lacking a uniquely aligned mate were discarded because they cannot be used to count contacts. Uniquely aligned read pairs were sorted by genomic location of the upstream read and then by genomic location of the downstream read. Any aligned read pairs with genomic locations and strand orientations identical to those of another aligned pair were discarded as likely PCR artifacts. The remaining aligned pairs were then pooled from two different biological replicates for each treatment (-E2 and +E2), without removing duplicate pairs. The pooled pairs pairs were filtered to remove dangling ends and self-ligation products, as described by Jin F et al (Jin 2013). In particular, based on histograms of inter-read separation for each type of read pair, we found it adequate to discard both “samestrand” and “outward” pairs having inter-read separation less than 1 kb.
The retained pairs of aligned reads were used to construct a matrix of binned contact counts for each chromosome. Each pair of reads aligned to the same chromosome was used to increment the integer value at row i and column j, as well as row j and column i, of a matrix of contact counts for that chromosome, where i = floor(u/b) and j = floor(d/b), b is the genomic bin size, and u and d > u are the genomic locations of the midpoints of the restriction fragments overlapping the upstream and downstream reads in the pair, respectively. Contact count matrices were constructed using genomic bins of sizes of 20 kb, to identify contact domain boundaries, 250 kb, to generate A/B compartment profiles, and 500 kb, to generate heat maps representing low-resolution intra-chromosomal contacts. To omit genomic regions with excessively low numbers of mapped reads, matrix rows and columns having too many zero entries were discarded. The minimum number of non-zero entries required to retain a row was half of the median number of non-zero entries in all rows. Binned contact count matrices for each chromosome were individually un-biased using the iterative correction method of Imakaev et al. (Imakaev 2012). To obtain local mean and standard deviation of contact counts as functions of genomic inter-locus distance, we calculated mean and standard deviation along the upper diagonals of each un-biased contact count matrix. For each bin of the contact count matrix corresponding to the interaction between loci i and j, we calculated the z-score z(i,j) = [C(i,j) − m(d(i,j))] / s(d(i,j)), where C(i,j) is the un-biased contact count for the bin in question, d(i,j) is the genomic distance between loci i and j, and m(d(i,j)) and s(d(i,j)) are the local mean and standard deviation of un-biased contact counts for inter-locus distance d(i,j). A sliding window of 20 Mb was used to calculate m(d(i,j)) and s(d(i,j)).
To obtain profiles of A/B compartments over each chromosome, we applied a previously described procedure (Imakaev 2012, Barutcu 2015) with minor modifications. Specifically, the matrix of z-scores with bins of size 250 kb was edited by zeroing out the main diagonal as well as the diagonals immediately above and below the main diagonal. A Pearson correlation matrix was then calculated from the edited matrix of z-scores. The resulting correlation matrix was subjected to principal component analysis by first calculating the covariance matrix and then obtaining the eigenvector with the largest eigenvalue from such covariance matrix. The sign of this eigenvector was adjusted to yield a positive sign for the covariance between that eigenvector and a vector containing the GC content fractions in genomic bins matching those in the eigenvector. After this sign adjustment, positive eigenvector components correspond to A-compartment regions whereas negative components correspond to B-compartment regions.
To determine locations and intensities of boundaries between contact domains, we applied a method based on the calculation of  “insulation score” (Crane 2015). The insulation score was obtained by summing contact counts within a square region of side 25 bins, while sliding such region along the diagonal of the un-biased contact count matrix with bins of size 20 kb. The resulting sums were divided by their average value over the chromosome of interest. To identify boundaries of contact domains we applied a numerical procedure for finding local minima. Specifically, the derivative of the insulation score was estimated from the slope of a linear fit over a sliding window of 7 bins. Next, the zero-crossings of the estimated derivative as a function of bin index were used to identify local minima and local maxima of the insulation score. To omit weak or spurious boundaries, at each local minimum we calculated the peak-to-peak value as the larger of the two differences between the insulation score at the local minimum and the insulation scores at the preceding and following local maxima. A domain boundary was called if the corresponding local minimum had a peak-to-peak value greater than 25% of the median peak-to-peak value observed over the chromosome of interest.
Genome_build: hg18
Supplementary_files_format_and_content: bigWig and BED formats are defined by the UCSC Genome Browser.

source_name: Hi-C MCF-7 -E2

extract_protocol:
Hi-C, samples were fixed for 10 minutes with 1% formaldehyde. Fixation was stopped by adding Glycine (0.125M). Samples were frozen at -80 degee Celcius till used. In situ Hi-C was essentially performed as described(Rao et al., 2014). Briefly, for each experiment, 2 x 10E6 cells, fixed for 10 minutes with 1 % formaldehyde/PBS and washed twice with PBS, permeabilized for 7 minutes at 62°C in a PCR cycler with 200 µl lysis buffer (0.5% SDS, 50 mM Tris-HCl pH=7.5, 10 mM NaCl, 1mM EDTA, and 1X protease inhibitors solution (Roche)) and pelleted at 2500x g for 5 minutes. Supernatant was removed and nuclei were resuspended in 25 µl 10% Triton X-100, 25 µl NEB 2 buffer, 195 µl water, and rotated for 15’ at 37°C. Chromatin was digested overnight at 37°C after adding 0.5 µl 1 M DTT and 4 µl 25 U/µl Mbo I and rotated at 8 RPM. MboI was inactivated by incubation at 62°C for 20 minutes. Nuclei were centrifuged for 5 minutes at 500 x g and 200 µl supernatant was discarded. Overhangs were filled in by adding 32 μL water, 5 μl of 10X NEBuffer2, 0.35 μl of 10 mM dATP, 0.35 μl of 10 mM dTTP, 0.35 μl of 10 mM dGTP, 7.5 μl 0.4 mM Biotin-14-dCTP (Invitrogen), 4 μl 10% Triton X-100, and 5 μl of 5 U/μl Klenow enzyme (Enzymatics) and rotating for 40 minutes at room temperature. The reaction was stopped by adding 2.5 µl 0.5 M EDTA. DNA was ligated under rotation overnight at 16°C in a total volume of 400 µl ligase mix  containing 40ul 10x T4 DNA ligase buffer (Enzymatics), 36 µl 10 % Triton X-100, 5 µl 100x BSA (10 mg/ml), 1 µl (1200 U) T4 DNA ligase (Enzymatics). The reaction was terminated by adding 20 µl 0.5 M EDTA. Samples were digested for 15 minutes at 42°C with 1 µl 10 µg/µl RNase A. 33 μl of 5 M sodium chloride and 55 µl of 10% SDS were added and reverse crosslinked for 4 h at 65°C. Protein was digested with 10 μl of 20 mg/ml proteinase K (Life Technologies), incubated
at 55°C for 120 minutes, shaking at 800 RPM, then 65°C for 90 minutes. DNA was extracted once with 600 µl phenol/chloroform/isoamylalcohol (25:24:1) Tris-buffered to pH 8.0 and once with 300 µl CHCl3, and precipitated overnight at -20°C with 1.5 µl 20 mg/ml glycogen and 1412 µl 100% ethanol overnight. DNA was pelleted for 20 minutes at 16000x g, 4°C and washed once with 1 ml 80% ethanol for 5 minutes, 8000x g, 4°C. Pellets were dissolved in 131 µl TT (0.05% Tween 20/10 mM Tris pH=8) each. DNA was sheared with 300 bp Covaris protocol in snap cap tube in a Covaris E220 at 10 % duty cycle, intensity 140 W, 200 cycles/burst for 80” total time. Large DNA fragments (>400 bp) were depleted with 5 µl Speedbeads and 6.45% PEG8000/2.5 M NaCl. Supernatant was transferred to fresh tubes and small DNA fragments were collected with 9.5% PEG8000 by adding an additional 60 µl PEG8000/2.5 M NaCl and 3 µl Speedbeads. DNA was eluted in 50ul TT for 5 minutes. DNA was captured with 50 µl 2x B&W buffer containing 0.2 % Tween 20 and 15 µl T1 Dynabeads (Invitrogen, washed twice with 1x B&W buffer (10 mM Tris-HCl pH 7.5, 01 mM EDTA, 2 M NaCl, then suspended in 51 µl 2x B&W buffer containing 0.2% Tween 20), rotating for 30 minutes at room temperature. Beads were washed once with 500 µl each of 1x B&W/0.1 % Triton-X100, once with TET (0.05% Tween 20/TE).
Hi-C library bound to beads were resuspend in 100 µl end repair mix (KAPA Library Preparation for Illumina) Incubated for 30 minutes at 20°C. Reaction was stopped by adding 2.5 µl 0.5 M EDTA. Beads were collected and washed twice with 150 µl 1x B&W/0.1% Triton-X100, once with 180 µl TET. Beads were resuspend in 50 ul A-tailing reaction mix (KAPA Library Preparation for Illumina), incubated 30 minutes at 30°C. Reaction was stopped by adding 1.5 µl 0.5 M EDTA. Beads were collected and washed twice with 150 µl 1x B&W/0.1% Triton-X100, once with 180 µl TET. Sequencing adapters were ligated to the bead-bound DNA in 100 µl 1x rapid ligation buffer (Enzymatics) containing 0.1% Tween 20,  2ul 1:20 Truseq adapters (Illumina), 1 µl (3000 U) T4 DNA ligase (Enzymatics) for 20 minutes at room temperature. The reaction was stopped with 5 µl 0.5 M EDTA, beads washed twice with 1x B&W, twice with 0.1% Tween 20/TE, then resuspended in 30 µl 0.033% Tween20/LoTE, (TE diluted 1:4 with water). Libraries were PCR-amplified using the 10 µl of the bead suspension as template for 10 cycles using KAPA HiFi, size-selected to 225-425 bp insert size using speedbeads PEG8000/2.5 M NaCl solutions, and paired-end sequenced on an Illumina HiSeq 2500.

treatment_protocol: MCF7 cells  grown in phenol red free DMEM and charcoal stripped FBS were treated with estrogen for 60 before collecting the samples for ChIP-Seq. Control samples were treated with ICI 182,780, or ER alpha agonist


title: Hi-C MCF-7 +E2 replicate 1

status: Public on Feb 10 2019

type: SRA

city: San Diego

first: Qi

last: Ma

address: 9500 Gilman Dr,

country: USA

institute: UCSD

description:
MCF-7 wild type cells treated with estrogen, biological replicate 1
processed data file:
abcpw-0001.bw
tadpw-0001.bw
tadbb-0001.bed.gz

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: Hi-C MCF-7 +E2

growth_protocol: MCF7, estrogen receptor alpha positive breast cancer cells were cultured in DMEM and 10%FBS under standard condition

tag: cell line

tag: cell type

value: Human breast cancer cells

tag: genotype/variation

value: wild type

tag: treated with

value: estrogen; Treatement


title: Hi-C MCF-7 +E2 replicate 2

description:
MCF-7 wild type cells treated with estrogen, biological replicate 2
processed data file:
abcpw-0001.bw
tadpw-0001.bw
tadbb-0001.bed.gz


title: 0hr_rep1(RNAseq)

status: Public on Feb 11 2019

city: Nashville

first: Scott

last: Hiebert

state: TN

address: Vanderbilt University, 2220 pierce Avenue, 512 PRB

department: Biochemistry

institute: Vanderbilt University

library_source: transcriptomic

data_processing:
Base calling, filtering and demultiplexing was done by Illumina CASAVA 1.8.2 with default settings
Raw reads were trimmed to remove adapters and low quality reads using Trimmomatic (version0.32) with parameters IllUMINACLIP:adapter.txt:2:30:7TRAILING:15
Reverse complement of trimmed reads were generated using fastx_reverse_complement (version 0.0.13) with default settings.
For resequenced samples, the sequencing reads from DMSO_1hr and THZ1_1hr were pooled from both the runs and merged them for the dowstream PROseq analysis
The reverse complement sequences were then aligned to human genome hg19 using bowtie2 (version 2.2.4) with default settings.
RNSeq raw reads were aligned to hg19 using TopHat (version 2.0.10) with default settings
Genome_build: hg19
Supplementary_files_format_and_content: For PROseq genome coverage was normalized and calculated for each strand separately and reported in bedGraph format. For RNAseq a DIFF file with gene expression information is reported containing gene names, chromosomal coordinates, log2 transformed values of fold change along with test statistic.

molecule: total RNA

source_name: t(8;21)-containing acute myeloid leukemia cell line

growth_protocol: RPMI 1640 supplimented with 10% Fetal Plex and 2mM L-Glutamine

extract_protocol:
Nuclei were isolated by dounce homogenization of treated cells in isotonic buffer containing 0.1% triton-X 100. Nuclear run-on assay was performed with ATP,UTP,GTP and biotin-11-CTP. Nuclei were lyzed in Trizol and nuclear RNA was extracted and fragmented and biotinylated RNA was purified with streptavidin magnetic beads, followed by 3' adapter ligation, 5' repair and adapter ligation, RT and PCR amplification.
PROseq

value: Kasumi-1 cells

tag: treatment

value: Untreated


title: Hi-C MCF-7 -E2 replicate 2

description:
MCF-7 wild type cells treated with ICI 182,780, biological replicate 2
processed data file:
abcpw-0000.bw
tadpw-0000.bw
tadbb-0000.bed.gz

value: ICI 182,780, an estrogen receptor alpha antagonist; Control


title: ATAC-Seq plus Estrogen

description: MCF7 Wild Type cells treated with Estrogen

data_processing:
Basecalls performed using CASAVA version 1.4
ATAC-Seq reads were aligned to the hg19 genome assembly using Bowtie version 2.0.1.
The bigwig files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.

source_name: ATAC-Seq plus Estrogen

extract_protocol:
MCF7 cells after treatment were trypsinized and washed in PBS. 50,000 cells per sample were used for downstream assay.
ATAC-seq was performed as previously described (Buenrostro et al., 2015). Transposition reaction was performed at 37oC for 30 min using Nextera DNA Library Preparation Kit (Illumina Cat No. 15028212) in 50μl volume (2.5 μl Transposae enzyme, 25 μl 2X TD buffer and 22.5 μl nuclease-free water). The reaction mixture was immediately purified using MinElute PCR purification Kit (Qiagen, Cat No. 28006) and eluted in 10 μl nuclease-free water. The tagmented DNA was then PCR amplified using KAPA Real-Time Library Amplification Kit (Kapa Biosystems, Cat No. KK2701) in a 50 μl reaction (10 μl tagmented DNA, 2.5 μl25 μM PCR primer 1, 2.5 μl 25 μM barcoded PCR primer 2, 25 μl KAPA HiFi HotStart ReadyMix, 10 μl nuclease-free water), using the following program (One cycle at 72oC: 5 min, 98oC: 30sec; 8-12 cycles at 98oC: 10 sec, 63oC: 30 sec and 72oC: 1min). PCR standards, supplied in the kit, were included in separate wells and the reaction was stopped between standard 2 and 3.  The reaction mixture was subjected to size selection (to select fragments ranging 150-800bp) using 1.6 volume of Agencourt AMPure XP magnetic beads (Beckman Coulter, Cat No. A63880), washed once with 80% ethanol, air-dried and eluted in 15 μl of nuclease-free water. The resulting ATAC-seq library was quantified using Qubit Flurometer (Thermo Fisher) and the quality was analyzed by resolving 1 μl on Tapestation (Agilent). Ten nmol of the library was sequenced on HiSeq 4000 sequencer (Illumina). DATA was mapped to hg18 using Bowtie2 with standard settings. Tag directories were created after removing the reads mapped to the mitochondrial chromosome. ATAC-seq peaks were identified using HOMER.

treatment_protocol: MCF7 cells  grown in phenol red free DMEM and charcoal stripped FBS were treated with estrogen for 60 before collecting the samples for ATAC-Seq. Control samples were treated with ICI 182,780, and ER alpha antagonist

value: MCF7 WT obtained by clonal selection after transfecting with Cas9 vector


title: 4C-seq MCF7Cells minus Estrogen

description: MCF7 Wild Type cells treated with ICI 182,780

data_processing:
library strategy: 4C-seq
Basecalls performed using CASAVA version 1.4
4C-seq reads were aligned to the hg18 genome assembly using Bowtie version 2.0.1.
The bigwig files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.

source_name: MCF7_4C-Seq minus Estrogen

extract_protocol:
4C-seq, samples were fixed for 10 minutes with 1% formaldehyde. Fixation was stopped by adding Glycine (0.125M). Samples were frozen at -80 degee Celcius till used
The protocol of 4C-seq largely followed a published protocol (Stadhouders et al., 2013) with following modifications. Briefly, 10 million cells were cross-linked with 1% formaldehyde for 10 min and nuclei were extracted. Nuclei were resuspended in restriction enzyme buffer and incubated with 0.3 % SDS for 1h at 37’c and further incubated with 2% Triton X-100 for 1h. 400U of DpnII restriction enzyme was added and incubated overnight. Restriction enzyme was heat inactivated at 650C for 20 min. Ligation of DNA regions in close physical proximity was performed using 1000U of T4 DNA ligase (NEB) for overnight. After de-crosslinking, the second digestion and ligation was performed using restriction enzyme NlaIII and T4 DNA ligase. 4C-seq libraries were amplified using PCR with the first primer designed on each viewpoint and the second primer designed beside the NlaIII site. Both primers contained illumina sequencing adaptors and barcode. 4C libraries were sequenced on the Illumina Hi-Seq 2500 using single-read 100-cycle runs.

treatment_protocol: MCF7 cells  grown in phenol red free DMEM and charcoal stripped FBS were treated with estrogen for 60 before collecting the samples for 4C. Control samples were treated with ICI 182,780, and ER alpha antagonist


title: Control_RNA-seq_rep1

status: Public on Feb 08 2019

city: Houston

first: Kunal

last: Rai

state: TX

address: 1801 East Rd

department: Genomic Medicine

institute: MD Anderson Cancer Center

data_processing:
Raw fastq reads for all RNA-seq experiments were aligned to the hg19 reference genome using TopHat version 2.0.14 with a Bowtie2 version 2.2.3 index based on UCSC annotations using the following criteria: -G -g 1 -r 150 --mate-std-dev 50 --library-type fr-unstranded.
Raw counts were obtained by assigning reads at the gene level across the UCSC hg19 reference genome using featureCounts in the Rsubread package. DESeq2 was employed for normalization and identification of DEGs between UBR7-shRNA and Control samples.
deepTools version 2.4.0 was used to generate bigWig files by scaling the bam files to RPKM. Scaled bigWig files were then converted to bedGraph files using the bigWigToBedGraph tool.
Genome_build: hg19
Supplementary_files_format_and_content: Excel files containing normalized counts for all genes and DEGs identified using DESeq2. bigWig files of Forward and Reverse strand for Control and UBR7-shRNA samples

source_name: MCF10A Cell Line

growth_protocol: MCF10A cells were maintained in DMEM / Ham’s F12 supplemented with 5% horse serum (Gibco), EGF, insulin, hydrocortisone, cholera toxin (Sigma) and 1% antibiotic-antimycotic.

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Mini Kit and quantified using a Bioanalyzer 1000.
Libraries for Illumina sequencing were generated using the TruSeq RNA Library Prep Kit according to manufacturers instructions.

treatment_protocol: shRNA plasmids for UBR7 with pLKO.1-puro backbone (Sigma Aldrich) were screened for efficient knock-down.Two out seven shRNAs were selected for subsequent experiments. Four micrograms of shRNA and packaging vectors were transfected and cells were selected using puromycin (10 μg / ml) (Sigma) for 3 days.

value: Human mammary epithelial cell line


title: UBR7-shRNA-H3K27me3_ChIP-seq

data_processing:
Raw fastq reads for all ChIP-seq experiments were processed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and aligned to the hg19 reference genome using Bowtie version 1.1.2 with the following criteria: -n 1 -m 1 --best --strata. These criteria preserved only the best reads that uniquely mapped to the genome with 1 or fewer mismatches. Duplicate reads were marked using SAMBLASTER before compression to BAM files. To directly compare Control and UBR7-shRNA ChIP-seq samples, uniquely mapped reads for each mark were normalized by total reads per condition, sorted and indexed using samtools version 0.1.19
Genome_build: hg19
Supplementary_files_format_and_content: Model based analysis of ChIP-seq (MACS) version 1.4.2 peak calling algorithm with a p-value threshold of 1e-7 to identify H2BK120ub enrichment over “input” background
Supplementary_files_format_and_content: deepTools version 1.5.11 was used to generate bigWig files by scaling the bam files to reads per kilobase per million (RPKM). Scaled bigWig files were then converted to bedGraph files using the bigWigToBedGraph tool.

extract_protocol:
Histone-DNA complexes were isolated using antibodies described from Control and UBR7-shRNA sonicated nuclei.
Libraries for Illumina sequencing were generated following the New England BioLabs NEBNext Ultra DNA Library Prep Kit protocol. A total of 10x cycles were used during PCR amplification for the generation of all ChIP-seq libraries. Amplified ChIP DNA was purified using double-sided AMPure XP to retain fragments ~200 to 500bp and quantified using the Qubit 2000 and Bioanalyzer 1000 before multiplexing.

treatment_protocol: shRNA plasmids for UBR7 with pLKO.1-puro backbone (Sigma Aldrich) were screened for efficient knock-down.Two out seven shRNAs were selected for subsequent experiments. Four micrograms of shRNA and packaging vectors were transfected as described previously (ref). Cells were selected using puromycin (10 μg / ml) (Sigma) for 3days.

tag: chip-antibody

value: H3K27me3 Abcam ab6002


title: Control_RNA-seq_rep3


title: UBR7-shRNA_RNA-seq_rep1


title: UBR7-shRNA_RNA-seq_rep2


title: Control_RNA-seq_rep2


title: UBR7-shRNA_RNA-seq_rep3


title: UBR7-shRNA-H3K4me3_ChIP-seq

value: H3K4me3 Abcam/Millipore ab


title: GRO-MCF7_2,5-Hexanediol and Vehicle

description:
Treated with 2,5-Hexanediol and Vehicle
Gro-seq in MCF7 Cells Treated with 2,5-Hexanediol and Vehicle

data_processing:
library strategy: GRO-seq
Basecalls performed using CASAVA version 1.4
Gro-seq reads were aligned to the hg18 genome assembly using Bowtie version 2.0.1.
The bigwig files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.
Genome_build: hg18

source_name: Gro-Seq minus Estrogen

extract_protocol:
MCF7 cells after treatment were incubated in swellinig ice-cold buffer (10mM Tris-Cl pH7.5, 2mM MgCl2, 3mM CaCl2) for 5min. Cells were lysed in lysis buffer (swelling buffer with 0.5% IGEPAL and 10% glycerol). The resultant nuclei were washed once again with 10 ml lysis buffer and then re-suspended in 100μl of freezing buffer (50mM Tris-Cl pH 8.3, 40% glycerol, 5mM MgCl2, 0.1mM EDTA).
GRO-seq experiments were performed as previously reported (Li et al., 2013). Briefly, MCF7 cells were swollen in swelling buffer (10mM Tris-Cl pH7.5, 2mM MgCl2, 3mM CaCl2) for 5 min on ice and then lysed in lysis buffer (swelling buffer with 0.5% IGEPAL and 10% glycerol), before being re-suspended in 100µl of freezing buffer (50mM Tris-Cl pH8.3, 40% glycerol, 5mM MgCl2, 0.1mM EDTA). For the run-on assay, re-suspended nuclei were mixed with an equal volume of reaction buffer (10mM Tris-Cl pH 8.0, 5mM MgCl2, 1mM DTT, 300mM KCl, 20 units of Superase.In, 1% sarkosyl, 500µM ATP, GTP, and Br-UTP, 2µM CTP) and incubated for 5 min at 300C. The nuclear-run-on RNA (NRO-RNA) was then extracted with TRIzol LS reagent (Invitogen) following manufacturer’s instructions. After base hydrolysis on ice for 40min and followed by treatment with DNase I and antarctic phosphatase, the Br-UTP labeled NRO-RNA was purified by an anti-BrdU argarose beads (Santa Cruz Biotech) in binding buffer (0.5XSSPE, 1mM EDTA, 0.05% tween) for 3hr at 4°C while rotating. Then T4 PNK (NEB) was used to repair the end of NRO-RNA. Subsequently, cDNA synthesis was performed as reported(9,33) with few modifications. The RNA fragments were subjected to poly-A tailing reaction by poly-A polymerase (NEB) for 30 min at 37°C. Reverse transcription was then performed using superscript III (Invitrogen) with oNTI223 primer. The cDNA products were separated on a 10% polyacrylamide TBE-urea gel with right product (~100-500bp) being excised and recovered by gel extraction. After that, the first-strand cDNA was circularized by CircLigase (Epicentre) and re-linearized by Ape1 (NEB). Re-linearized single strand cDNA were separated by TBE gel and the products of desired size was excised (~120-320bp) for gel extraction. Finally, cDNA template was amplified by PCR using the Phusion High-Fidelity enzyme (NEB) with primers oNTI200 and oNTI201 for deep sequencing.

treatment_protocol: MCF7 cells  grown in phenol red free DMEM and charcoal stripped FBS. For eRNA knockdown, cells were transfected with LNA targeting specific enhancer RNA and after 24 hours were treated with estrogen for 60 before collecting the samples for ChIP-Seq. Control samples were treated with ICI 182,780, and ER alpha antagonist

value: 2, 5-Hexanediol and Vehicle

tag: molecule subtype

value: Nascent RNA


title: GRO-MCF7_1,6-Hexanediol and Vehicle

description:
Treated with 1,6-Hexanediol and Vehicle
Gro-seq in MCF7 Cells Treated with 1,6-Hexanediol and Vehicle (Ethyl Alcohol)

value: 1, 6-Hexanediol and Vehicle (Ethyl Alcohol)


title: 4C-seq MCF7Cells plus Estrogen

source_name: MCF7_4C-Seq plus Estrogen


title: THZ1_15min_rep2(PROseq)

value: 400nM THZ1-15min


title: UBR7-shRNA-H3K4me1_ChIP-seq

value: H3K4me1 Abcam ab8895


title: Control-H3K27me3_ChIP-seq


title: UBR7-shRNA-H3K79me2_ChIP-seq

value: H3K79me2 Abcam ab3594


title: UBR7-shRNA-H3K9me3_ChIP-seq

value: H3K9me3 Abcam ab8898


title: UBR7-shRNA-H2BK120ub_ChIP-seq

value: H2BK120ub Millipore 17-650


title: Control-H3K4me3_ChIP-seq


title: UBR7-shRNA-H3K27ac_ChIP-seq

value: H3K27ac Abcam ab4729


title: Control-H3K4me1_ChIP-seq


title: Control-H3K27ac_ChIP-seq


title: Control-H2BK120ub_ChIP-seq


title: WT2_RNASeq

city: Nanjing City

first: Xingyin

last: Liu

state: Jiangsu Province

address: Long Mian Street No.1

country: China

institute: Nanjing Medical University

data_processing:
After the sequencing platform generated the sequencing images, the pixel-level raw data collection, image analysis, and base calling were performed by Illumina's Real Time Analysis (RTA) software on a Dell PC attached to the HiSeq2500 sequencer.
The base call files (*.BCL) were converted to qseq files by the Illumina's BCL Converter, and the qseq files were subsequently converted to FASTQ files for downstream analysis.
The RNA-Seq reads from the FASTQ files were mapped to the Drosophila reference genome (dm5) using SOAP (Short Oligonucleotide Analysis Package) (Li et al., 2009).
The output files in BAM (binary alignment/map) format were analyzed by Cufflinks to estimate the transcript abundance and the presence of putative novel mRNA isoforms.
The transcript expression level was shown as with using TPM (Transcripts Per Kilobase Million)(Li et al., 2010). Exon splicing analysis were performed with using the DExSeq Bioconductor package by controlling false discovery rate(FDR) at 0.1(10%)(Anders et al., 2012).
Genome_build: dm5
Supplementary_files_format_and_content: Raw data were normalized abuandance using DESeq.

organism: Drosophila melanogaster

source_name: Female whole animal

growth_protocol: Flies were reared and maintained at 25°C, 50% relative humidity and a 12-hour light/dark cycle.

extract_protocol:
Total RNA was extracted from two separate samples of 30 dissected intestine tissues from w1118 and kdm510424/k6801 (3-5 days old) using TRIZOL (Life science) and cleaned up using DNA-free kit (Ambion).
RNA concentrations were quantified using a NanoDrop Spectrophotometer and sample integrity was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc). Only samples with RIN values above 8.0 were used for experiments.

tag: tissue

value: intestine

tag: age

value: 3-5 days

tag: strain

tag: Sex

value: female


title: UBR7-shRNA-Input_ChIP-seq

value: none (input)


title: WT1_RNASeq


title: KD1_RNASeq


title: KD2_RNASeq


title: dxo1-2_small_RNA_rep3

city: Warsaw

first: Michal

last: Krzyszton

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics, Polish Academy of Sciences

description: Illumina HiSeq

data_processing:
RNA-seq: mapping with hisat2
RNA-seq: expression estimation with HTseq-count and DESeq2
miRNA-seq: quality filtering and trimming, adapter removal
miRNA-seq: mapping with bowtie
miRNA-seq: expression estimation with HTseq-count and DESeq2
Genome_build: TAIR10
Supplementary_files_format_and_content: RNA-seq: bigwig files were generated using bedtools genomecov and bedGraphToBigWig; Scores represent reads normalized to 1e7 reads
Supplementary_files_format_and_content: miRNA-seq: bigwig files were generated using bedtools genomecov and bedGraphToBigWig; Scores represent reads normalized to 1e7 reads

organism: Arabidopsis thaliana

growth_protocol: Seeds were stratified for 2 days at 4ºC and grown on soil under a 16 h light/8 h dark (long-day) conditions.

extract_protocol:
trizol
BGI
Total plant RNA was isolated from 3-week-old plants grown using Trizol reagent (Sigma) according to manufacturer’s instructions.

value: 21 day old seedlings


title: C57Bl/6 SryHi Male Popliteal Lymph Nodes

status: Public on Feb 07 2019

city: Riverside

first: R

last: Dill

state: CA

address: 900 University Ave.

institute: University of California, Riverside

description: RNA - Ribosomal RNA depleted

data_processing:
Samtools vs 1.4 Create bam files
HSAT2 vs 2.4 Map reads to the mouse genome
Cufflinks vs 2.2.1 Assemble transcriptomes from RNA-Seq data and quantify expression.
Cuffdiff  Determine differentially expressed transcripts
Genome_build: UCSC-mm10
Supplementary_files_format_and_content: Excel File Cuffdiff output for comparisons included in sheets

organism: Mus musculus

source_name: popliteal lymph nodes

growth_protocol: Mice aged to 5 months

extract_protocol:
Whole tissues were homogenized and RNA was extracted by Trizol-Chloroform phase separation. RNA was then purified and concentrated using Qiagen Rneasy Mini columns
The same amount of total RNA for each sample was used to prepare libraries using the Kapa Biosystems Stranded library preparation kit with Riboerase. Libraries were labeled with barcodes from a New England Biosciences kit. After library preparation, samples were assessed for quantity and quality by bioanalyzer. Equal amounts of each library were multiplexed and submitted to the facility at University of California, San Francisco, Parnassas, CA for sequencing by Rapid paired end 2x50 on the Hiseq2500. Sequencing was per Illumina (San Diego, CA) protocol in rapid run mode.

treatment_protocol: No treatment

value: Four Core Genotype Model

tag: gondal sex

value: Male

value: 5 months


title: dxo1-2_small_RNA_rep1

description: Illumina HiSeq


title: Control-H3K79me2_ChIP-seq

value: Human mammary epithelial cell line


title: C57Bl/6 Wild-Type Female Popliteal Lymph Nodes

description: RNA - Ribosomal RNA depleted

value: wildtype

value: Female


title: EPO Treated Mouse Cell 35

city: Osaka

first: Shinya

last: Tanaka

state: Osaka

address: 2nd Fl. IFReC Research Building, Osaka University 3-1 Yamadaoka, Suita

department: Immunology Frontier Research Center

country: Japan

institute: Osaka University

description:
48_SCP6_C94-37557703
EPO-treated cell 35
RefSeq_mm9_expr_rpkm.txt

data_processing:
Illumina BaseSpace Informatics Suite was used for basecalling and demultiplexing.
Raw sequence reads were aligned to the mouse genome (NCBI build 37.2) using TopHat v2.0.9.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each cell

source_name: Murine marrow

extract_protocol:
single-cell isolation protocol: Individual cells were isolated for mRNA sequencing using the C1 Single-Cell Auto Prep System (Fluidigm).
imageing protocol:  Each cell isolation chamber was imaged at 20X (Leica DMI 6000) with bright-field illumination and fluorescent channels. The Ter119 antibody was labeled with PCP-Cy5.5 and imaged using a 488/705 nm (excitation/emission) fluorescence filter cube.
Cells were lysed, their mRNA reversely transcribed into cDNA, and the cDNA amplifed using the SMART-Seq whole-transcriptome amplification method on the C1 System according to the manufacturer's instructions.
The cDNA libraries were collected from the C1 and prepared for sequencing using a Nextera XT DNA Sample preparation kit (Illumina).

tag: genotype

value: EPO treated wild type mouse

value: erythroblast

tag: normalized ter119

tag: class


title: EPO Treated Mouse Cell 31

description:
44_SCP6_C32-37563698
EPO-treated cell 31
RefSeq_mm9_expr_rpkm.txt


title: EPO Treated Mouse Cell 25

description:
37_SCP7_C45-37561719
EPO-treated cell 25
RefSeq_mm9_expr_rpkm.txt


title: EPO Treated Mouse Cell 26

description:
39_SCP7_C92-37559710
EPO-treated cell 26
RefSeq_mm9_expr_rpkm.txt


title: EPO Treated Mouse Cell 29

description:
42_SCP6_C27-37557696
EPO-treated cell 29
RefSeq_mm9_expr_rpkm.txt


title: EPO Treated Mouse Cell 27

description:
40_SCP7_C46-37549838
EPO-treated cell 27
RefSeq_mm9_expr_rpkm.txt


title: EPO Treated Mouse Cell 24

description:
36_SCP7_C44-37549837
EPO-treated cell 24
RefSeq_mm9_expr_rpkm.txt


title: EPO Treated Mouse Cell 21

description:
31_SCP7_C87-37557724
EPO-treated cell 21
RefSeq_mm9_expr_rpkm.txt


title: EPO Treated Mouse Cell 20

description:
30_SCP7_C39-37550867
EPO-treated cell 20
RefSeq_mm9_expr_rpkm.txt


title: EPO Treated Mouse Cell 19

description:
28_SCP7_C37-37564694
EPO-treated cell 19
RefSeq_mm9_expr_rpkm.txt


title: EPO Treated Mouse Cell 22

description:
32_SCP7_C40-37558681
EPO-treated cell 22
RefSeq_mm9_expr_rpkm.txt


title: EPO Treated Mouse Cell 18

description:
27_SCP7_C82-37562709
EPO-treated cell 18
RefSeq_mm9_expr_rpkm.txt


title: EPO Treated Mouse Cell 17

description:
26_SCP7_C36-37562701
EPO-treated cell 17
RefSeq_mm9_expr_rpkm.txt


title: EPO Treated Mouse Cell 16

description:
24_SCP7_C80-37559708
EPO-treated cell 16
RefSeq_mm9_expr_rpkm.txt


title: EPO Treated Mouse Cell 28

description:
41_SCP6_C22-37557694
EPO-treated cell 28
RefSeq_mm9_expr_rpkm.txt


title: EPO Treated Mouse Cell 13

description:
18_SCP7_C75-37549844
EPO-treated cell 13
RefSeq_mm9_expr_rpkm.txt


title: C57Bl/6 Wild-Type Male Popliteal Lymph Nodes

description: RNA - Ribosomal RNA depleted


title: EPO Treated Mouse Cell 11

description:
16_SCP7_C25-37558678
EPO-treated cell 11
RefSeq_mm9_expr_rpkm.txt


title: EPO Treated Mouse Cell 14

description:
20_SCP7_C78-37561723
EPO-treated cell 14
RefSeq_mm9_expr_rpkm.txt


title: EPO Treated Mouse Cell 12

description:
17_SCP7_C26-37559702
EPO-treated cell 12
RefSeq_mm9_expr_rpkm.txt


title: EPO Treated Mouse Cell 09

description:
14_SCP7_C22-37557713
EPO-treated cell 09
RefSeq_mm9_expr_rpkm.txt


title: EPO Treated Mouse Cell 10

description:
15_SCP7_C71-37549843
EPO-treated cell 10
RefSeq_mm9_expr_rpkm.txt


title: EPO Treated Mouse Cell 08

description:
12_SCP7_C24-37560698
EPO-treated cell 08
RefSeq_mm9_expr_rpkm.txt


title: dxo1-2_small_RNA_rep2

description: Illumina HiSeq


title: EPO Treated Mouse Cell 06

description:
10_SCP7_C21-37549830
EPO-treated cell 06
RefSeq_mm9_expr_rpkm.txt


title: EPO Treated Mouse Cell 05

description:
09_SCP7_C66-37558685
EPO-treated cell 05
RefSeq_mm9_expr_rpkm.txt


title: EPO Treated Mouse Cell 07

description:
11_SCP7_C20-37560695
EPO-treated cell 07
RefSeq_mm9_expr_rpkm.txt


title: EPO Treated Mouse Cell 23

description:
35_SCP7_C43-37562702
EPO-treated cell 23
RefSeq_mm9_expr_rpkm.txt


title: EPO Treated Mouse Cell 03

description:
05_SCP7_C10-37564687
EPO-treated cell 03
RefSeq_mm9_expr_rpkm.txt


title: EPO Treated Mouse Cell 01

description:
01_SCP7_C03-37550853
EPO-treated cell 01
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 46

description:
SCP3-WT-E12
wild-type cell 46
RefSeq_mm9_expr_rpkm.txt

value: wild type


title: Wild Type Cell 47

description:
SCP3-WT-F12
wild-type cell 47
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 45

description:
SCP3-WT-C12
wild-type cell 45
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 43

description:
SCP3-WT-D11
wild-type cell 43
RefSeq_mm9_expr_rpkm.txt


title: EPO Treated Mouse Cell 15

description:
21_SCP7_C77-37564703
EPO-treated cell 15
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 48

description:
SCP3-WT-B9
wild-type cell 48
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 44

description:
SCP3-WT-E11
wild-type cell 44
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 42

description:
SCP3-WT-C11
wild-type cell 42
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 41

description:
SCP3-WT-E10
wild-type cell 41
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 39

description:
SCP3-WT-C10
wild-type cell 39
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 40

description:
SCP3-WT-D10
wild-type cell 40
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 37

description:
SCP3-WT-A10
wild-type cell 37
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 38

description:
SCP3-WT-B10
wild-type cell 38
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 36

description:
SCP3-WT-H9
wild-type cell 36
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 34

description:
SCP3-WT-G12
wild-type cell 34
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 35

description:
SCP3-WT-H8
wild-type cell 35
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 31

description:
SCP3-WT-B8
wild-type cell 31
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 32

description:
SCP3-WT-C8
wild-type cell 32
RefSeq_mm9_expr_rpkm.txt


title: EPO Treated Mouse Cell 04

description:
08_SCP7_C64-37549842
EPO-treated cell 04
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 30

description:
SCP3-WT-A8
wild-type cell 30
RefSeq_mm9_expr_rpkm.txt


title: EPO Treated Mouse Cell 02

description:
04_SCP7_C09-37557708
EPO-treated cell 02
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 28

description:
SCP3-WT-E7
wild-type cell 28
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 26

description:
SCP3-WT-B7
wild-type cell 26
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 25

description:
SCP3-WT-A7
wild-type cell 25
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 27

description:
SCP3-WT-D7
wild-type cell 27
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 23

description:
SCP3-WT-E6
wild-type cell 23
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 24

description:
SCP3-WT-H6
wild-type cell 24
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 22

description:
SCP3-WT-D6
wild-type cell 22
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 18

description:
SCP3-WT-F5
wild-type cell 18
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 19

description:
SCP3-WT-A6
wild-type cell 19
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 21

description:
SCP3-WT-C6
wild-type cell 21
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 16

description:
SCP3-WT-C5
wild-type cell 16
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 13

description:
SCP3-WT-E4
wild-type cell 13
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 33

description:
SCP3-WT-E8
wild-type cell 33
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 10

description:
SCP3-WT-E3
wild-type cell 10
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 14

description:
SCP3-WT-F4
wild-type cell 14
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 09

description:
SCP3-WT-D3
wild-type cell 09
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 29

description:
SCP3-WT-F7
wild-type cell 29
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 17

description:
SCP3-WT-D5
wild-type cell 17
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 08

description:
SCP3-WT-C3
wild-type cell 08
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 11

description:
SCP3-WT-H3
wild-type cell 11
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 12

description:
SCP3-WT-D4
wild-type cell 12
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 15

description:
SCP3-WT-A5
wild-type cell 15
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 05

description:
SCP3-WT-C2
wild-type cell 05
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 04

description:
SCP3-WT-B2
wild-type cell 04
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 07

description:
SCP3-WT-B3
wild-type cell 07
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 03

description:
SCP3-WT-G1
wild-type cell 03
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 06

description:
SCP3-WT-F2
wild-type cell 06
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 48

description:
SCP2-KO-B1
Flvcr-deleted cell 48
RefSeq_mm9_expr_rpkm.txt

value: Flvcr deleted


title: Wild Type Cell 01

description:
SCP3-WT-B1
wild-type cell 01
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 47

description:
SCP2-KO-F1
Flvcr-deleted cell 47
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 02

description:
SCP3-WT-D1
wild-type cell 02
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 45

description:
SCP2-KO-F12
Flvcr-deleted cell 45
RefSeq_mm9_expr_rpkm.txt


title: Wild Type Cell 20

description:
SCP3-WT-B6
wild-type cell 20
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 43

description:
SCP2-KO-C12
Flvcr-deleted cell 43
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 41

description:
SCP2-KO-F11
Flvcr-deleted cell 41
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 42

description:
SCP2-KO-H11
Flvcr-deleted cell 42
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 40

description:
SCP2-KO-E11
Flvcr-deleted cell 40
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 39

description:
SCP2-KO-D11
Flvcr-deleted cell 39
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 37

description:
SCP2-KO-A11
Flvcr-deleted cell 37
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 38

description:
SCP2-KO-C11
Flvcr-deleted cell 38
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 33

description:
SCP2-KO-G9
Flvcr-deleted cell 33
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 34

description:
SCP2-KO-H9
Flvcr-deleted cell 34
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 25

description:
SCP2-KO-G7
Flvcr-deleted cell 25
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 27

description:
SCP2-KO-F8
Flvcr-deleted cell 27
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 35

description:
SCP2-KO-B10
Flvcr-deleted cell 35
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 36

description:
SCP2-KO-D10
Flvcr-deleted cell 36
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 24

description:
SCP2-KO-C7
Flvcr-deleted cell 24
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 26

description:
SCP2-KO-D8
Flvcr-deleted cell 26
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 31

description:
SCP2-KO-C9
Flvcr-deleted cell 31
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 29

description:
SCP2-KO-A9
Flvcr-deleted cell 29
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 30

description:
SCP2-KO-B9
Flvcr-deleted cell 30
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 32

description:
SCP2-KO-F9
Flvcr-deleted cell 32
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 28

description:
SCP2-KO-H8
Flvcr-deleted cell 28
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 46

description:
SCP2-KO-H12
Flvcr-deleted cell 46
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 23

description:
SCP2-KO-A7
Flvcr-deleted cell 23
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 21

description:
SCP2-KO-B6
Flvcr-deleted cell 21
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 44

description:
SCP2-KO-D12
Flvcr-deleted cell 44
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 19

description:
SCP2-KO-G5
Flvcr-deleted cell 19
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 20

description:
SCP2-KO-H5
Flvcr-deleted cell 20
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 16

description:
SCP2-KO-C5
Flvcr-deleted cell 16
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 17

description:
SCP2-KO-D5
Flvcr-deleted cell 17
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 18

description:
SCP2-KO-F5
Flvcr-deleted cell 18
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 22

description:
SCP2-KO-G6
Flvcr-deleted cell 22
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 15

description:
SCP2-KO-B5
Flvcr-deleted cell 15
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 12

description:
SCP2-KO-D4
Flvcr-deleted cell 12
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 14

description:
SCP2-KO-A5
Flvcr-deleted cell 14
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 11

description:
SCP2-KO-C4
Flvcr-deleted cell 11
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 10

description:
SCP2-KO-F3
Flvcr-deleted cell 10
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 09

description:
SCP2-KO-C3
Flvcr-deleted cell 09
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 08

description:
SCP2-KO-B3
Flvcr-deleted cell 08
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 07

description:
SCP2-KO-A3
Flvcr-deleted cell 07
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 06

description:
SCP2-KO-G2
Flvcr-deleted cell 06
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 04

description:
SCP2-KO-E2
Flvcr-deleted cell 04
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 03

description:
SCP2-KO-B2
Flvcr-deleted cell 03
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 02

description:
SCP2-KO-A2
Flvcr-deleted cell 02
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 05

description:
SCP2-KO-F2
Flvcr-deleted cell 05
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 01

description:
SCP2-KO-E1
Flvcr-deleted cell 01
RefSeq_mm9_expr_rpkm.txt


title: Flvcr Deleted Cell 13

description:
SCP2-KO-G4
Flvcr-deleted cell 13
RefSeq_mm9_expr_rpkm.txt


title: Young Rep1

status: Public on Feb 06 2019

city: Glasgow

first: Neil

middle: A

last: Robertson

state: Scotland

address: Switchback Road

department: Beatson Institute for Cancer Research

country: United Kingdom

institute: University of Glasgow

description: RNA sequencing of young (3 month) mice

data_processing:
Basecalls performed in phred64 (solexa1.3-quals).
Sequenced reads were mapped to mm9 whole genome using Tophat with default settings
FPKM matrix was derived using Cufflinks suite using default settings
Differential expression quantified using DESeq2 (Bioconductor) following non-normalised read counting with Htseq (intersection-nonempty)
Genome_build: mm9
Supplementary_files_format_and_content: Summary files describe the results of DESeq2 differential expression analysis for core comparisons as well as FPKM matrix for all replicate created using Cufflinks suite.

source_name: Cardiomyocytes

growth_protocol: Inbred C57Bl6J mice were ordered from Janvier lab and sacrificed at 3 and 20 months.

extract_protocol:
Qiagen RNA extraction kit.
Samples were sequenced in house on a single flow cell on the illumina NextSeq

treatment_protocol: Animals were anesthetized and hearts were removed and placed on the Langendorff setup. Myocytes were first obtained by enzymatic digestion and sedimentation and further purified using the EasySep™ Mouse Biotin Positive Selection Kit which allowed removal of CD31, SCA1 and CD45 positive cells. Purity of adult cardiomyocyte culture was confirmed by immunofluorescent staining against CD31, SCA1, CD45 and alpha-actinin. RNA from purified adult cardiomyocytes was extracted using Qiagen RNA extraction kit.

value: 3 months


title: Input from Senescent Fibroblasts, Replicate #5

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

description:
PD78.Input.R5
processed data file:
S-input.bigWig

data_processing:
Pooling: for each sample, replicates from two independent sequencing runs were pooled together to yield an average of 79 million reads per sample.
Alignment: reads were mapped to the reference human genome assembly GRCh37 (hg19) using Bowtie2, allowing up to 1 mismatch in the seed alignment.
Quality Control: aligned tags were processed by SAMtools to remove low quality alignments (a minimum mapping quality of 10), duplicate reads, reads mapped to mitochondria and reads mapped to ENCODE blacklisted genomic regions.
Track Generation: genome-wide tag density was computed using BEDtools and UCSC command line utilities to generate tracks for visualization, for which purpose the visualization tracks were normalized to 10 million reads per sample. Tracks were subtracted by deepTools, to generate tracks of histone modification ChIP minus H3- or H4-ChIP then minus the difference between IgG-ChIP and the input control (corresponding to the differential analysis approach).
Genome_build: hg19
Supplementary_files_format_and_content: BigWigs are UCSC Genome Browser tracks, the generation of which is described above.

source_name: Input from Senescent Fibroblasts

growth_protocol: IMR90 cells (ATCC CCL-186) were obtained from Coriell Institute for Medical Research, Camden, NJ, and grown in standard tissue culture medium (DMEM with 10% FBS and 1% penicillin/streptomycin; Invitrogen) at 3% oxygen.

extract_protocol:
ChIP was performed as described in Shah et al., Genes & Development 2013 from ~12e6 cells. Briefly, cross-linked cells were lysed and the chromatin was sheared using a Covaris Ultrasonicator to achieve an average size of <500 bp. 2ug of sonicated chromatin (estimated by DNA concentration) was used per immunoprecipitation reaction, and 10% of the amount was saved as input. Immunoprecipitation was performed using protein A Dynabeads (Thermo Fisher).
1ng of DNA from immunoprecipitation and input was used to prepare libraries using the NEBNext Ultra II kit (New England Biolabs). The libraries were checked for quality and quantity by Bioanalyzer (Agilent) and qPCR (Kapa Biosystems) respectively. Multiplexed libraries were sequenced on a single lane of the NextSeq 500 platform (Illumina).

treatment_protocol: Cells were replicatively passaged until growth ceased. For each passage, cells were washed with PBS, trypsinized at 37 °C for 5 minutes, and plated on fresh 10 cm plates at 0.5-1e6/plate or fresh 15cm plates at 1-2e6/plate. p16 expression and β-gal were tested to confirm senescence. Additionally, senescent cells were maintained in dishes for 2 weeks to ensure growth termination.

value: Lung Fibroblasts

tag: population doubling

tag: senescence induction

value: Replicative Senescence

tag: target

tag: chip antibody


title: IgG ChIP-seq from Senescent Fibroblasts, Replicate #6

description:
PD76.IgG.R6
processed data file:
S-IgG.bigWig

source_name: IgG ChIP-seq from Senescent Fibroblasts

tag: cell line

tag: cell type

value: IgG


title: Young Rep2

description: RNA sequencing of young (3 month) mice


title: Old Rep3

description: RNA sequencing of old (20 month) mice

value: 20 months


title: IgG ChIP-seq from Proliferating Fibroblasts, Replicate #6

description:
PD25.IgG.R6
processed data file:
P-IgG.bigWig


title: Young Rep4

description: RNA sequencing of young (3 month) mice


title: Old Rep5

description: RNA sequencing of old (20 month) mice


title: Old Rep2

description: RNA sequencing of old (20 month) mice


title: Input from Senescent Fibroblasts, Replicate #6

description:
PD76.Input.R6
processed data file:
S-input.bigWig


title: Young Rep3

description: RNA sequencing of young (3 month) mice


title: Input from Proliferating Fibroblasts, Replicate #6

description:
PD25.Input.R6
processed data file:
P-input.bigWig

source_name: Input from Proliferating Fibroblasts


title: Young Rep5

description: RNA sequencing of young (3 month) mice


title: IgG ChIP-seq from Senescent Fibroblasts, Replicate #5

description:
PD78.IgG.R5
processed data file:
S-IgG.bigWig


title: Old Rep1

description: RNA sequencing of old (20 month) mice


title: p300 ChIP-seq from Proliferating Fibroblasts, Replicate #2

description:
PD25.p300.R2
processed data file:
P-p300.bigWig

value: Santa Cruz Biotechnology sc-585X, RRID:AB_2616339


title: p300 ChIP-seq from Proliferating Fibroblasts, Replicate #1

description:
PD30.p300.R1
processed data file:
P-p300.bigWig


title: p300 ChIP-seq from Senescent Fibroblasts, Replicate #2

description:
PD76.p300.R2
processed data file:
S-p300.bigWig


title: Old Rep4

description: RNA sequencing of old (20 month) mice


title: p300 ChIP-seq from Senescent Fibroblasts, Replicate #1

description:
PD78.p300.R1
processed data file:
S-p300.bigWig


title: CBP ChIP-seq from Senescent Fibroblasts, Replicate #1

description:
PD78.CBP.R1
processed data file:
S-CBP.bigWig

source_name: CBP ChIP-seq from Senescent Fibroblasts

value: CBP

value: Cell Signaling Technology 7389, RRID:AB_10949313


title: CBP ChIP-seq from Senescent Fibroblasts, Replicate #2

description:
PD76.CBP.R2
processed data file:
S-CBP.bigWig


title: Input from Proliferating Fibroblasts, Replicate #5

description:
PD30.Input.R5
processed data file:
P-input.bigWig


title: CBP ChIP-seq from Proliferating Fibroblasts, Replicate #1

description:
PD30.CBP.R1
processed data file:
P-CBP.bigWig


title: H3K27ac ChIP-seq from Senescent Fibroblasts (IR Senescence), Replicate #1

value: Irradiation


title: H3K4me1 ChIP-seq from Senescent Fibroblasts (IR Senescence), Replicate #2

value: Abcam ab8895


title: H3K4me1 ChIP-seq from Senescent Fibroblasts (IR Senescence), Replicate #1


title: IgG ChIP-seq from Senescent Fibroblasts (IR Senescence), Replicate #1


title: IgG ChIP-seq from Proliferating Fibroblasts, Replicate #5

description:
PD30.IgG.R5
processed data file:
P-IgG.bigWig


title: Input from Senescent Fibroblasts (IR Senescence), Replicate #2


title: IgG ChIP-seq from Senescent Fibroblasts (IR Senescence), Replicate #2


title: H4K5ac ChIP-seq from Senescent Fibroblasts, Replicate #1

description:
PD79.H4K5ac.R1
processed data file:
S2-H4K5ac.bigWig

value: EMD Millipore 07-327, RRID:AB_310523


title: H3 ChIP-seq from Senescent Fibroblasts (IR Senescence), Replicate #1

value: Abcam ab1791, RRID:AB_310523


title: H4K5ac ChIP-seq from Proliferating Fibroblasts, Replicate #2

description:
PD29.H4K5ac.R2
processed data file:
P1-H4K5ac.bigWig


title: H3K122ac ChIP-seq from Senescent Fibroblasts, Replicate #2

description:
PD78.H3K122ac.R2
processed data file:
S2-H3K122ac.bigWig


title: H4K5ac ChIP-seq from Senescent Fibroblasts, Replicate #2

description:
PD78.H4K5ac.R2
processed data file:
S2-H4K5ac.bigWig


title: H3 ChIP-seq from Senescent Fibroblasts (IR Senescence), Replicate #2


title: H3K122ac ChIP-seq from Proliferating Fibroblasts, Replicate #2

description:
PD29.H3K122ac.R2
processed data file:
P1-H3K122ac.bigWig


title: H3K27ac ChIP-seq from Senescent Fibroblasts, Replicate #1

description:
PD78.H3K27ac.R1
processed data file:
S1-H3K27ac.bigWig


title: H3K27ac ChIP-seq from Senescent Fibroblasts (IR Senescence), Replicate #2


title: H3K27ac ChIP-seq from Proliferating Fibroblasts, Replicate #2

description:
PD31.H3K27ac.R2
processed data file:
P2-H3K27ac.bigWig


title: H4K5ac ChIP-seq from Proliferating Fibroblasts, Replicate #1

description:
PD30.H4K5ac.R1
processed data file:
P1-H4K5ac.bigWig


title: Input from Senescent Fibroblasts (IR Senescence), Replicate #1


title: H3K27ac ChIP-seq from Proliferating Fibroblasts, Replicate #1

description:
PD36.H3K27ac.R1
processed data file:
P2-H3K27ac.bigWig


title: CBP ChIP-seq from Proliferating Fibroblasts, Replicate #2

description:
PD25.CBP.R2
processed data file:
P-CBP.bigWig


title: H3K122ac ChIP-seq from Proliferating Fibroblasts, Replicate #1

description:
PD30.H3K122ac.R1
processed data file:
P1-H3K122ac.bigWig


title: H3K23ac ChIP-seq from Senescent Fibroblasts, Replicate #2

description:
PD78.H3K23ac.R2
processed data file:
S2-H3K23ac.bigWig

value: EMD Millipore 07-355, RRID:AB_310546


title: H3K18ac ChIP-seq from Senescent Fibroblasts, Replicate #2

description:
PD78.H3K18ac.R2
processed data file:
S2-H3K18ac.bigWig

value: Active Motif 39755, RRID:AB_2714186


title: H3K18ac ChIP-seq from Senescent Fibroblasts, Replicate #1

description:
PD79.H3K18ac.R1
processed data file:
S2-H3K18ac.bigWig


title: H3K23ac ChIP-seq from Proliferating Fibroblasts, Replicate #2

description:
PD29.H3K23ac.R2
processed data file:
P1-H3K23ac.bigWig


title: H3K18ac ChIP-seq from Proliferating Fibroblasts, Replicate #2

description:
PD29.H3K18ac.R2
processed data file:
P1-H3K18ac.bigWig


title: H3K23ac ChIP-seq from Proliferating Fibroblasts, Replicate #1

description:
PD30.H3K23ac.R1
processed data file:
P1-H3K23ac.bigWig


title: H3K23ac ChIP-seq from Senescent Fibroblasts, Replicate #1

description:
PD79.H3K23ac.R1
processed data file:
S2-H3K23ac.bigWig


title: H3K18ac ChIP-seq from Proliferating Fibroblasts, Replicate #1

description:
PD30.H3K18ac.R1
processed data file:
P1-H3K18ac.bigWig


title: H3K122ac ChIP-seq from Senescent Fibroblasts, Replicate #1

description:
PD79.H3K122ac.R1
processed data file:
S2-H3K122ac.bigWig


title: H3K4me1 ChIP-seq from Proliferating Fibroblasts, Replicate #1

description:
PD36.H3K4me1.R1
processed data file:
P2-H3K4me1.bigWig


title: H3K4me1 ChIP-seq from Proliferating Fibroblasts, Replicate #2

description:
PD31.H3K4me1.R2
processed data file:
P2-H3K4me1.bigWig


title: H3K4me1 ChIP-seq from Senescent Fibroblasts, Replicate #2

description:
PD75.H3K4me1.R2
processed data file:
S1-H3K4me1.bigWig


title: H3K4me1 ChIP-seq from Senescent Fibroblasts, Replicate #1

description:
PD78.H3K4me1.R1
processed data file:
S1-H3K4me1.bigWig


title: IgG ChIP-seq from Senescent Fibroblasts, Replicate #4

description:
PD75.IgG.R4
processed data file:
S1-input.bigWig


title: IgG ChIP-seq from Senescent Fibroblasts, Replicate #3

description:
PD78.IgG.R3
processed data file:
S2-input.bigWig


title: H3K27ac ChIP-seq from Senescent Fibroblasts, Replicate #2

description:
PD75.H3K27ac.R2
processed data file:
S1-H3K27ac.bigWig


title: IgG ChIP-seq from Senescent Fibroblasts, Replicate #2

description:
PD78.IgG.R2
processed data file:
S1-input.bigWig


title: IgG ChIP-seq from Senescent Fibroblasts, Replicate #1

description:
PD79.IgG.R1
processed data file:
S2-input.bigWig


title: IgG ChIP-seq from Proliferating Fibroblasts, Replicate #3

description:
PD29.IgG.R3
processed data file:
P1-IgG.bigWig


title: IgG ChIP-seq from Proliferating Fibroblasts, Replicate #2

description:
PD36.IgG.R2
processed data file:
P2-IgG.bigWig


title: IgG ChIP-seq from Proliferating Fibroblasts, Replicate #4

description:
PD31.IgG.R4
processed data file:
P2-IgG.bigWig


title: Input from Senescent Fibroblasts, Replicate #3

description:
PD78.Input.R3
processed data file:
S2-input.bigWig


title: Input from Senescent Fibroblasts, Replicate #4

description:
PD75.Input.R4
processed data file:
S1-input.bigWig


title: IgG ChIP-seq from Proliferating Fibroblasts, Replicate #1

description:
PD30.IgG.R1
processed data file:
P1-IgG.bigWig


title: Input from Senescent Fibroblasts, Replicate #1

description:
PD79.Input.R1
processed data file:
S2-input.bigWig


title: Input from Proliferating Fibroblasts, Replicate #1

description:
PD30.Input.R1
processed data file:
P1-input.bigWig


title: Input from Proliferating Fibroblasts, Replicate #2

description:
PD36.Input.R2
processed data file:
P2-input.bigWig


title: Input from Proliferating Fibroblasts, Replicate #3

description:
PD29.Input.R3
processed data file:
P1-input.bigWig


title: Input from Proliferating Fibroblasts, Replicate #4

description:
PD31.Input.R4
processed data file:
P2-input.bigWig


title: H4 ChIP-seq from Proliferating Fibroblasts, Replicate #2

description:
PD36.H4.R2
processed data file:
P2-H4.bigWig

value: Abcam ab7311, RRID:AB_305837


title: H4 ChIP-seq from Proliferating Fibroblasts, Replicate #1

description:
PD30.H4.R1
processed data file:
P1-H4.bigWig


title: H4 ChIP-seq from Proliferating Fibroblasts, Replicate #3

description:
PD29.H4.R3
processed data file:
P1-H4.bigWig


title: H4 ChIP-seq from Proliferating Fibroblasts, Replicate #4

description:
PD31.H4.R4
processed data file:
P2-H4.bigWig


title: H3 ChIP-seq from Senescent Fibroblasts, Replicate #2

description:
PD78.H3.R2
processed data file:
S1-H3.bigWig

source_name: H3 ChIP-seq from Senescent Fibroblasts


title: H3 ChIP-seq from Senescent Fibroblasts, Replicate #4

description:
PD75.H3.R4
processed data file:
S1-H3.bigWig


title: H4 ChIP-seq from Senescent Fibroblasts, Replicate #4

description:
PD75.H4.R4
processed data file:
S1-H4.bigWig

source_name: H4 ChIP-seq from Senescent Fibroblasts


title: H3 ChIP-seq from Senescent Fibroblasts, Replicate #3

description:
PD78.H3.R3
processed data file:
S2-H3.bigWig


title: H3 ChIP-seq from Senescent Fibroblasts, Replicate #1

description:
PD79.H3.R1
processed data file:
S2-H3.bigWig


title: H3 ChIP-seq from Proliferating Fibroblasts, Replicate #4

description:
PD31.H3.R4
processed data file:
P2-H3.bigWig


title: H4 ChIP-seq from Senescent Fibroblasts, Replicate #1

description:
PD79.H4.R1
processed data file:
S2-H4.bigWig


title: H3 ChIP-seq from Proliferating Fibroblasts, Replicate #3

description:
PD29.H3.R3
processed data file:
P1-H3.bigWig


title: H3 ChIP-seq from Proliferating Fibroblasts, Replicate #2

description:
PD36.H3.R2
processed data file:
P2-H3.bigWig


title: H3 ChIP-seq from Proliferating Fibroblasts, Replicate #1

description:
PD30.H3.R1
processed data file:
P1-H3.bigWig


title: H4 ChIP-seq from Senescent Fibroblasts, Replicate #3

description:
PD78.H4.R3
processed data file:
S2-H4.bigWig


title: Input from Senescent Fibroblasts, Replicate #2

description:
PD78.Input.R2
processed data file:
S1-input.bigWig


title: PD60 Paired Pool 7

data_processing:
Trimming: hairpin tags were trimmed to remove the first 6 bases and all bases after the 27th, producing the hairpin-complementary region and removing the excision site.
Alignment: trimmed tags were then aligned using bowtie v1.0.1 to a custom index of hairpin sequences and control sequences (parameters --best).
Summary: aligned sequence tags were merged across pools and per-hairpin tag counts at each time point were tallied.
Genome_build: Hairpins.fa
Supplementary_files_format_and_content: Tags per Hairpin.txt describes the number of tags per hairpin at each five population doublings in the time course, from PD40 (proliferating control) to PD60 (replicative senescence). Hairpins.fa is the index of small hairpin sequences to which the data were aligned.

extract_protocol:
Genomic DNA was isolated at PD40, 45, 50, 55 and 60 using phenol chloroform and isopropanol precipitation.
Genomic DNA from reference and senescent samples was extracted, PCR amplified around the hairpin region, digested with XhoI to generate half hairpins and processed using the NEBNext Ultra kit (New England Biolabs) kit.

treatment_protocol: See methods for a description of how viral pools were prepared. Pools of lentiviruses were used to infect proliferating IMR90 cells at MOI = 0.3 and then cells were replicatively passaged until growth ceased. For each passage, cells were washed with PBS, trypsinized at 37 °C for 5 minutes, and plated on fresh 10 cm plates at 0.5-1e6/plate or fresh 15cm plates at 1-2e6/plate. p16 expression and β-gal were tested to confirm senescence. Additionally, senescent cells were maintained in dishes for 2 weeks to ensure growth termination.

tag: pool


title: PD60 Paired Pool 8


title: PD60 Paired Pool 2


title: PD60 Paired Pool 10


title: PD60 Paired Pool 5


title: PD60 Paired Pool 3


title: PD60 Paired Pool 4


title: PD60 Paired Pool 1


title: PD60 Paired Pool 6


title: PRO-seq from Senescent Fibroblasts

data_processing:
library strategy: precision run-on sequencing (PRO-seq)
Strategy: PRO-Seq tags were processed and aligned using ProSeqMapper (Danko lab, https://github.com/Danko-Lab/tutorials/blob/master/PRO-seq.md) with default parameters and a BWA index. Details of the pipeline are given in subsequent steps.
Quality control: reads not passing Illumina QC were removed.
Trimming: adapters were trimmed using CutAdapt.
Alignment: tags were aligned with BWA (default parameters) and aligned tags were converted to BAM files.
Track Generation: bigWigs were created for tag pile-ups aligned to the plus and minus reference strand using BEDtools' bamToBed and genomeCoverageBed and UCSC Genome Browser's bedGraphToBigWig.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files describe tags per million distributed along the plus or minus reference strand of the human genome for each sample.

source_name: IMR90 Lung Fibroblasts

extract_protocol:
PRO-seq was performed as described previously (Mahat et al., Nature Methods 2016). Briefly, ~12e6 trypsinized cells were permeabilized and stored in storage buffer (10mM Tris-HCl pH 8.0, 25% glycerol, 5mM MgCl2, 0.1mM EDTA, 5mM DTT) at -80°C until use. The permeabilized cells were then resuspended in 1X nuclear run-on reaction mix containing biotin-11-rCTP and unlabeled rATP, rGTP and rUTP for 3 minutes at 37°C. RNA was extracted, fragmented and subjected to biotin enrichment.
The enriched nascent RNA population was then ligated to a 3’ adapter sequence and subjected to a second round of biotin enrichment. The 5’ ends of the RNA were decapped, phosphorylated, ligated to 5’ adapter and subjected to a third biotin enrichment. The RNA was then reverse transcribed and PCR amplified with appropriate index primers. The libraries were purified by extraction from an 8% polyacrylamide gel, quantified by Bioanalyzer (Agilent) and qPCR (Kapa Biosystems). The PRO-seq run was performed on the NextSeq 500 platform (Illumina).

tag: cell status

value: replicative senescent


title: PRO-seq from Proliferating Fibroblasts

value: proliferating (control)


title: PD55 Paired Pool 10


title: PD55 Paired Pool 6


title: PD55 Paired Pool 8


title: PD55 Paired Pool 5


title: PD50 Paired Pool 10


title: PD55 Paired Pool 1


title: PD55 Paired Pool 2


title: PD60 Paired Pool 9


title: PD55 Paired Pool 4


title: PD55 Paired Pool 3


title: PD50 Paired Pool 9


title: PD50 Paired Pool 7


title: PD50 Paired Pool 6


title: PD50 Paired Pool 8


title: PD50 Paired Pool 4


title: PD50 Paired Pool 5


title: PD50 Paired Pool 3


title: PD55 Paired Pool 9


title: PD55 Paired Pool 7


title: PD50 Paired Pool 2


title: PD45 Paired Pool 10


title: PD50 Paired Pool 1


title: PD45 Paired Pool 8


title: PD45 Paired Pool 7


title: PD45 Paired Pool 5


title: PD45 Paired Pool 3


title: PD45 Paired Pool 4


title: PD45 Paired Pool 9


title: PD45 Paired Pool 2


title: PD45 Paired Pool 6


title: H4 ChIP-seq from Senescent Fibroblasts, Replicate #2

description:
PD78.H4.R2
processed data file:
S1-H4.bigWig


title: PD40 Paired Pool 6


title: PD40 Paired Pool 7


title: PD40 Paired Pool 8


title: PD40 Paired Pool 9


title: PD40 Paired Pool 2


title: PD40 Paired Pool 1


title: PD40 Paired Pool 3


title: PD40 Paired Pool 4


title: PD40 Paired Pool 5


title: Patient5-T1-Normal

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

data_processing:
Read preprocessing: Four fastq-files per sample (suffix L001, L002, L003, L004) were generated as the NextSeq has 4 lanes. Low quality ends and adapter sequences were trimmed off from the Illumina reads with FastX 0.0.14 and Cutadapt 1.7.1 (HannonLab, 2010; Martin, 2011). Subsequently, small reads (length < 35 bp), polyA-reads (more than 90 % of the bases equal A), ambiguous reads (containing N), low-quality reads (more than 50 % of the bases < Q25) and artifact reads (all but three bases in the read equal one base type) were filtered using using FastX 0.0.14 and ShortRead 1.24.0 (Morgan et al, 2009). With Bowtie2 2.2.4 we identified and removed reads that align to phix_illumina (Langmead & Salzberg, 2012).
Mapping: The preprocessed reads were aligned with STAR aligner v2.4.1d to the reference genome of Homo sapiens (GRCh37.73) (Dobin et al, 2013).  Default STAR aligner parameter settings were used, except for ‘outSAMprimaryFlag=OneBestScore’, twopassMode=Basic’, ‘alignIntronMin=50‘, ‘alignIntronMax=500,000’, ‘outSAMtype=BAM SortedByCoordinate’. Using Samtools 1.1, reads with a mapping quality smaller than 20 were removed from the alignments (Li et al, 2009). Alignments from the four lanes were merged per sample.
Counting: The number of reads in the alignments that overlap with gene features were counted with featureCounts 1.4.6 (Liao et al, 2014). Following parameters were chosen: -Q 0 –s 2 –t exon –g gene_id.
Differential expression analysis: We removed genes for which all samples had less than 1 count-per-million. The counts were further corrected within samples for GC-content and between samples using full quantile normalization, as implemented in the EDASeq package from Bioconductor (Risso et al, 2011). With the EdgeR 3.8.6 package of Bioconductor, a negative binomial generalized linear model (GLM) was fitted against the normalized counts (Robinson et al, 2007). We did not use the normalized counts directly, but worked with offsets. Differential expression was tested for with a GLM likelihood ratio test, also implemented in the EdgeR package. The resulting p-values were corrected for multiple testing with Benjamini-Hochberg to control the false discovery rate (Benjamini  & Hochberg, 1995).
Genome_build: GRCh37
Supplementary_files_format_and_content: RawCounts.xlsx contains the values after counting (integer numbers). The first column contains Ensembl gene IDs.

source_name: purified CD14+ monocytes from ACLF patient, in vitro cultured in the presence of pool of normal human serum

growth_protocol: CD14 + cells were cultured in RPMI medium supplemented with 20% of a pool of normal human serum obtained from healthy blood donors

extract_protocol:
Rneasy kit (Qiagen)
Per sample, an amount of 100 ng of total RNA was used as input. Using the Illumina TruSeq® Stranded mRNA Sample Prep Kit (protocol 15031047 Rev E October 2013) poly-A containing mRNA molecules were purified from the total RNA input using poly-T oligo-attached magnetic beads. In a reverse transcription reaction using random primers, RNA was converted into first strand cDNA and subsequently converted into double-stranded cDNA in a second strand cDNA synthesis reaction using DNA PolymeraseI and RNAse H. The cDNA fragments were extended with a single ‘A’ base to the 3’ ends of the blunt-ended cDNA fragments after which multiple indexing adapters were ligated introducing different barcodes for each sample. Finally, enrichment PCR was carried out to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. Sequence-libraries of each sample were equimolarly pooled and sequenced on an Illumina NextSeq 500 instrument (High Output, 75 bp, Single Reads, v2) at the VIB Nucleomics core (www.nucleomics.be).

tag: disease

value: acute-on-chronic liver failure (ACLF)

tag: gender

value: female

value: purified CD14+ monocytes

tag: treatment


title: Patient5-T1-ACLF

source_name: purified CD14+ monocytes from ACLF patient, in vitro cultured in the presence of pool of ACLF serum

growth_protocol: CD14 + cells were cultured in RPMI medium supplemented with20% of a pool of human serum obtained from 4 patients in ACLF-stadium 2

tag: age


title: Patient5-T0

source_name: purified CD14+ monocytes from ACLF patient, immediately after isolation

growth_protocol: Immediately after cell isolation

value: no treatment, immediately after isolation


title: BMDM EPSKO HiChIRP lincRNA-EPS biological replicate 2

city: Stanford

first: Howard

middle: Y

last: Chang

address: 269 Campus Drive

institute: Stanford University

description:
Negative control long-range DNA contact
BMDM_EPSKO_HiChIRP_EPS.hic

data_processing:
Library strategy: HiChIRP
Sequencing reads were aligned and paired, filtered for long-range contacts, and removed of duplicates using the HiC-Pro pipeline (PMID: 26619908)
Filtered reads were converted to a .hic file for visualization with Juicebox (PMID: 25497547)
Genome_build: hg19,mm10
Supplementary_files_format_and_content: validPairs output from the HiC-Pro pipeline. Aligned, filtered, and unique long-range contacts to call loops with.
Supplementary_files_format_and_content: HiC output from the Juicebox Tools pipeline. Matrix file to visualize long-range interactions with Juicebox.
Supplementary_files_format_and_content: Bam files were read into R through rsamtools and converted to a 250bp bin coverage object exported by rtracklayer.

source_name: Bone-marrow derived macrophages

growth_protocol: Grown in DMEM with 15% FBS and supplemented with L929

extract_protocol:
Knockout negative control of RNA enrichment of 3C library
Nextera

treatment_protocol: Crosslinked with 1% glutaraldehyde

value: Primary macrophage cells

value: male


title: PD45 Paired Pool 1

value: Lung Fibroblasts


title: BMDM EPSKO HiChIRP lincRNA-EPS biological replicate 1


title: Patient4-T1-Normal

value: in vitro cultured in the presence of pool of normal human serum


title: mES HiChIRP lacZ biological replicate 2

description:
Negative control long-range DNA contact
mES_HiChIRP_lacZ.hic

source_name: v6.5 embryonic stem cell line

growth_protocol: Grown on gelatin-coated plates with KO DMEM supplemented with LIF

extract_protocol:
LacZ negative control of RNA enrichment of 3C library
Nextera

value: ES cell


title: Patient4-T1-ACLF

value: in vitro cultured in the presence of pool of ACLF serum


title: Patient4-T0


title: mES HiChIRP lacZ biological replicate 1


title: PD40 Paired Pool 10


title: Patient3-T1-Normal


title: Patient3-T0


title: Patient3-T1-ACLF


title: WT3

city: New Haven

first: Hong

last: Li

state: CT

address: 333 Cedar Street

department: Neuroscience

institute: Yale University

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw reads were filtered to exclude adapters, low quality reads and  reads containing N (if more than 10%). Obtained clean reads in each sample were more than 96%.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Indexes of the reference genome were built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9. Bowtie uses a BWT(Burrows-Wheeler Transformer) algorithm for mapping reads to the genome and Tophat can generate a database of splice junctions based on the gene model annotation file and thus achieve a better mapping result than other non-splice mapping tools.
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. RPKM, Reads Per Kilobase of exon model per Million mapped reads, 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 (Mortazavi et al., 2008
(For DESeq with biological replicates) Differential expression analysis between two conditions/groups (three biological replicates per condition) was performed using the DESeq R package (1.10.1). DESeq 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(FDR). Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed.
Genome_build: mm10
Supplementary_files_format_and_content: text files include fpkm values or read counts for each sample

source_name: Dorsal telencephalon

extract_protocol:
Brains was removed from newborn pups. Dorsal telencephalons were dissected out and snap frozen on dry ice. Total RNA were extracted with QIAGEN RNeasy plus mini kit (CAT#:74134). The quality and concentration of RNA samples were measured with Agilen 2100 Bioanalyzer and Qubit 2.0 Fluorometer.
Libraries were constructed with NEBnext Ultra RNA library prep kit from Illumina.

tag: strain

tag: tissue

value: Dorsal telencephalon

tag: developmental stage

value: Newborn (P0)

value: wildtype


title: KO3

tag: genotype

value: TCF4 knockout


title: Hets3

value: TCF4 heterozygote


title: KO1


title: Patient2-T1-ACLF


title: Patient2-T0


title: Patient1-T1-ACLF


title: Hets2


title: KO2


title: Patient1-T0


title: Hets1


title: HeLa TERCKO HiChIRP TERC biological replicate 1

description:
Negative control long-range DNA contact
HeLa_TERCKO_HiChIRP_TERC.hic

source_name: HeLa cell line

growth_protocol: Grown in DMEM with 15% FBS

value: HeLa


title: Control4-T1-Normal

source_name: purified CD14+ monocytes from healthy human, in vitro cultured in the presence of pool of normal human serum

value: healthy


title: Control4-T0

source_name: purified CD14+ monocytes from healthy human, immediately after isolation


title: Control3-T0


title: Control3-T1-ACLF

source_name: purified CD14+ monocytes from healthy human, in vitro cultured in the presence of pool of ACLF serum


title: HeLa TERCKO HiChIRP TERC biological replicate 2


title: Control2-T1-Normal


title: WT2


title: Control2-T0


title: Control3-T1-Normal


title: Control1-T1-Normal


title: Control1-T1-ACLF


title: WT1


title: Control2-T1-ACLF


title: Control1-T0


title: Patient2-T1-Normal

value: acute-on-chronic liver failure (ACLF)


title: Patient1-T1-Normal


title: CR3L_PBMC_rep13

city: Freiburg

first: Gianni

last: Monaco

address: Breisacher Straße

country: Germany

institute: Freiburg Medical Center

description:
cell_number (facs): 5000000
total_rna_yield (ng): 2628.48
CR3L_PBMC

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
Genome_build: GENCODE 26
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample

molecule: polyA RNA

source_name: PBMCs

extract_protocol:
RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.

value: PBMCs

tag: disease status

value: F


title: 9JD4_PBMC_rep1

description:
cell_number (facs): 2000000
total_rna_yield (ng): 744.096
9JD4_PBMC


title: G4YW_PBMC_rep3

description:
cell_number (facs): 2000000
total_rna_yield (ng): 842.916
G4YW_PBMC


title: 36TS_PBMC_rep12

description:
cell_number (facs): 1000000
total_rna_yield (ng): 514.356
36TS_PBMC

value: M


title: 4DUY_PBMC_rep11

description:
cell_number (facs): 2000000
total_rna_yield (ng): 961.884
4DUY_PBMC


title: G4YW_Basophils_rep3

description:
cell_number (facs): 158470
total_rna_yield (ng): 13.464
G4YW_Basophils

source_name: Low-density basophils

value: Low-density basophils


title: DZQV_PBMC_rep4

description:
cell_number (facs): 2000000
total_rna_yield (ng): 284.268
DZQV_PBMC


title: G4YW_pDC_rep3

description:
cell_number (facs): 97851
total_rna_yield (ng): 158.352
G4YW_pDC

source_name: Plasmacytoid dendritic cells

value: Plasmacytoid dendritic cells


title: G4YW_Neutrophils_rep3

description:
cell_number (facs): 273969
total_rna_yield (ng): 5.448
G4YW_Neutrophils

source_name: Low-density neutrophils

value: Low-density neutrophils


title: Control4-T1-ACLF

value: male

value: purified CD14+ monocytes


title: G4YW_NC_mono_rep3

description:
cell_number (facs): 300203
total_rna_yield (ng): 135.048
G4YW_NC_mono

source_name: Non classical monocytes

value: Non classical monocytes


title: G4YW_I_mono_rep3

description:
cell_number (facs): 177839
total_rna_yield (ng): 141.216
G4YW_I_mono

source_name: Intermediate monocytes

value: Intermediate monocytes


title: G4YW_Plasmablasts_rep3

description:
cell_number (facs): 93153
total_rna_yield (ng): 107.928
G4YW_Plasmablasts

source_name: Plasmablasts

value: Plasmablasts


title: G4YW_B_SM_rep3

description:
cell_number (facs): 675060
total_rna_yield (ng): 670.464
G4YW_B_SM

source_name: Switched memory B cells

value: Switched memory B cells


title: G4YW_C_mono_rep3

description:
cell_number (facs): 300000
total_rna_yield (ng): 296.136
G4YW_C_mono

source_name: Classical monocytes

value: Classical monocytes


title: G4YW_mDC_rep3

description:
cell_number (facs): 299149
total_rna_yield (ng): 462.696
G4YW_mDC

source_name: Myeloid dendritic cells

value: Myeloid dendritic cells


title: G4YW_B_Ex_rep3

description:
cell_number (facs): 124143
total_rna_yield (ng): 44.496
G4YW_B_Ex

source_name: Exhausted B cells

value: Exhausted B cells


title: G4YW_NK_rep3

description:
cell_number (facs): 300000
total_rna_yield (ng): 90.936
G4YW_NK

source_name: Natural killer cells

value: Natural killer cells

value: healthy


title: G4YW_B_naive_rep3

description:
cell_number (facs): 1240800
total_rna_yield (ng): 619.272
G4YW_B_naive

source_name: Naive B cells

value: Naive B cells


title: G4YW_CD4_naive_rep3

description:
cell_number (facs): 450000
total_rna_yield (ng): 150.12
G4YW_CD4_naive

source_name: Naive CD4 T cells

value: Naive CD4 T cells

value: F


title: G4YW_Th2_rep3

description:
cell_number (facs): 366973
total_rna_yield (ng): 120.072
G4YW_Th2

source_name: Th2 cells

value: Th2 cells


title: G4YW_Th1/Th17_rep3

description:
cell_number (facs): 431351
total_rna_yield (ng): 175.272
G4YW_Th1/Th17

source_name: Th1/Th17 cells

value: Th1/Th17 cells


title: G4YW_Th1_rep3

description:
cell_number (facs): 450000
total_rna_yield (ng): 166.104
G4YW_Th1

source_name: Th1 cells

value: Th1 cells


title: G4YW_Treg_rep3

description:
cell_number (facs): 450000
total_rna_yield (ng): 168.6
G4YW_Treg

source_name: T regulatory cells

value: T regulatory cells


title: G4YW_TFH_rep3

description:
cell_number (facs): 648648
total_rna_yield (ng): 416.76
G4YW_TFH

source_name: Follicular helper T cells

value: Follicular helper T cells


title: G4YW_Th17_rep3

description:
cell_number (facs): 450000
total_rna_yield (ng): 194.268
G4YW_Th17

source_name: Th17 cells

value: Th17 cells


title: G4YW_Progenitor_rep3

description:
cell_number (facs): 24676
total_rna_yield (ng): 4.296
G4YW_Progenitor

source_name: Progenitor cells

value: Progenitor cells


title: 925L_PBMC_rep2

description:
cell_number (facs): 2000000
total_rna_yield (ng): 894.9
925L_PBMC

source_name: PBMCs

value: PBMCs

value: M


title: G4YW_VD2+_rep3

description:
cell_number (facs): 399400
total_rna_yield (ng): 304.332
G4YW_VD2+

source_name: Vd2 gd T cells

value: Vd2 gd T cells


title: G4YW_MAIT_rep3

description:
cell_number (facs): 300000
total_rna_yield (ng): 206.772
G4YW_MAIT

source_name: MAIT cells

value: MAIT cells


title: G4YW_CD8_TE_rep3

description:
cell_number (facs): 329051
total_rna_yield (ng): 131.496
G4YW_CD8_TE

source_name: Terminal effector CD8 T cells

value: Terminal effector CD8 T cells


title: FLWA_PBMC_rep10

description:
cell_number (facs): 2000000
total_rna_yield (ng): 3681.588
FLWA_PBMC


title: 453W_PBMC_rep5

description:
cell_number (facs): 1000000
total_rna_yield (ng): 559.32
453W_PBMC


title: 684C_PBMC_rep6

description:
cell_number (facs): 1000000
total_rna_yield (ng): 530.076
684C_PBMC


title: FY2H_PBMC_rep8

description:
cell_number (facs): 2000000
total_rna_yield (ng): 4728
FY2H_PBMC


title: G4YW_CD8_CM_rep3

description:
cell_number (facs): 232579
total_rna_yield (ng): 151.032
G4YW_CD8_CM

source_name: Central memory CD8 T cell

value: Central memory CD8 T cell


title: 9JD4_Basophils_rep1

description:
cell_number (facs): 300000
total_rna_yield (ng): 8.292
9JD4_Basophils

source_name: Low-density basophils

value: Low-density basophils

value: healthy


title: G4YW_CD8_naive_rep3

description:
cell_number (facs): 300000
total_rna_yield (ng): 99.768
G4YW_CD8_naive

source_name: Naive CD8 T cells

value: Naive CD8 T cells


title: 9JD4_NK_rep1

description:
cell_number (facs): 300000
total_rna_yield (ng): 90.216
9JD4_NK

source_name: Natural killer cells

value: Natural killer cells

value: F


title: G4YW_CD8_EM_rep3

description:
cell_number (facs): 391537
total_rna_yield (ng): 279.036
G4YW_CD8_EM

source_name: Effector memory CD8 T cells

value: Effector memory CD8 T cells


title: 9JD4_C_mono_rep1

description:
cell_number (facs): 300000
total_rna_yield (ng): 258.78
9JD4_C_mono

source_name: Classical monocytes

value: Classical monocytes


title: 9JD4_I_mono_rep1

description:
cell_number (facs): 172399
total_rna_yield (ng): 169.416
9JD4_I_mono

source_name: Intermediate monocytes

value: Intermediate monocytes


title: 9JD4_mDC_rep1

description:
cell_number (facs): 272295
total_rna_yield (ng): 295.98
9JD4_mDC

source_name: Myeloid dendritic cells

value: Myeloid dendritic cells


title: 9JD4_Neutrophils_rep1

description:
cell_number (facs): 287632
total_rna_yield (ng): 3.504
9JD4_Neutrophils

source_name: Low-density neutrophils

value: Low-density neutrophils


title: G4YW_B_NSM_rep3

description:
cell_number (facs): 275047
total_rna_yield (ng): 90.984
G4YW_B_NSM

source_name: Non-switched memory B cells

value: Non-switched memory B cells


title: 9JD4_NC_mono_rep1

description:
cell_number (facs): 195224
total_rna_yield (ng): 128.328
9JD4_NC_mono

source_name: Non classical monocytes

value: Non classical monocytes


title: 9JD4_pDC_rep1

description:
cell_number (facs): 247703
total_rna_yield (ng): 416.952
9JD4_pDC

source_name: Plasmacytoid dendritic cells

value: Plasmacytoid dendritic cells


title: 9JD4_B_NSM_rep1

description:
cell_number (facs): 317742
total_rna_yield (ng): 117.432
9JD4_B_NSM


title: 9JD4_Plasmablasts_rep1

description:
cell_number (facs): 61729
total_rna_yield (ng): 76.2
9JD4_Plasmablasts

source_name: Plasmablasts

value: Plasmablasts


title: 9JD4_B_naive_rep1

description:
cell_number (facs): 1499746
total_rna_yield (ng): 705.012
9JD4_B_naive

source_name: Naive B cells

value: Naive B cells


title: 9JD4_B_SM_rep1

description:
cell_number (facs): 557031
total_rna_yield (ng): 370.896
9JD4_B_SM

source_name: Switched memory B cells

value: Switched memory B cells


title: 9JD4_CD4_naive_rep1

description:
cell_number (facs): 450000
total_rna_yield (ng): 193.992
9JD4_CD4_naive

source_name: Naive CD4 T cells

value: Naive CD4 T cells


title: CZJE_PBMC_rep7

description:
cell_number (facs): 1000000
total_rna_yield (ng): 560.292
CZJE_PBMC

source_name: PBMCs

value: PBMCs

value: M


title: 9JD4_Th2_rep1

description:
cell_number (facs): 299584
total_rna_yield (ng): 111.06
9JD4_Th2

source_name: Th2 cells

value: Th2 cells

value: healthy


title: 9JD4_Th17_rep1

description:
cell_number (facs): 431738
total_rna_yield (ng): 261.564
9JD4_Th17

source_name: Th17 cells

value: Th17 cells

value: F


title: 9JD4_Treg_rep1

description:
cell_number (facs): 582455
total_rna_yield (ng): 295.668
9JD4_Treg

source_name: T regulatory cells

value: T regulatory cells


title: CYFZ_PBMC_rep9

description:
cell_number (facs): 2000000
total_rna_yield (ng): 3140.412
CYFZ_PBMC


title: 9JD4_Th1/Th17_rep1

description:
cell_number (facs): 450000
total_rna_yield (ng): 356.544
9JD4_Th1/Th17

source_name: Th1/Th17 cells

value: Th1/Th17 cells


title: 9JD4_TFH_rep1

description:
cell_number (facs): 716271
total_rna_yield (ng): 383.016
9JD4_TFH

source_name: Follicular helper T cells

value: Follicular helper T cells


title: 9JD4_VD2-_rep1

description:
cell_number (facs): 769746
total_rna_yield (ng): 414.984
9JD4_VD2-

source_name: Non-Vd2 gd T cells

value: Non-Vd2 gd T cells


title: 9JD4_MAIT_rep1

description:
cell_number (facs): 625000
total_rna_yield (ng): 633.516
9JD4_MAIT

source_name: MAIT cells

value: MAIT cells


title: G4YW_VD2-_rep3

description:
cell_number (facs): 300939
total_rna_yield (ng): 139.332
G4YW_VD2-


title: 9JD4_CD8_CM_rep1

description:
cell_number (facs): 351567
total_rna_yield (ng): 363.48
9JD4_CD8_CM

source_name: Central memory CD8 T cell

value: Central memory CD8 T cell


title: 9JD4_VD2+_rep1

description:
cell_number (facs): 464891
total_rna_yield (ng): 409.236
9JD4_VD2+

source_name: Vd2 gd T cells

value: Vd2 gd T cells


title: 925L_Basophils_rep2

description:
cell_number (facs): 300000
total_rna_yield (ng): 16.98
925L_Basophils

source_name: Low-density basophils

value: Low-density basophils


title: 9JD4_CD8_TE_rep1

description:
cell_number (facs): 625000
total_rna_yield (ng): 439.32
9JD4_CD8_TE

source_name: Terminal effector CD8 T cells

value: Terminal effector CD8 T cells


title: 9JD4_CD8_naive_rep1

description:
cell_number (facs): 625000
total_rna_yield (ng): 715.032
9JD4_CD8_naive

source_name: Naive CD8 T cells

value: Naive CD8 T cells


title: 9JD4_CD8_EM_rep1

description:
cell_number (facs): 625744
total_rna_yield (ng): 409.908
9JD4_CD8_EM

source_name: Effector memory CD8 T cells

value: Effector memory CD8 T cells


title: 925L_Neutrophils_rep2

description:
cell_number (facs): 217968
total_rna_yield (ng): 10.416
925L_Neutrophils

source_name: Low-density neutrophils

value: Low-density neutrophils


title: 925L_NK_rep2

description:
cell_number (facs): 300000
total_rna_yield (ng): 106.392
925L_NK

source_name: Natural killer cells

value: Natural killer cells

value: M


title: 925L_pDC_rep2

description:
cell_number (facs): 35453
total_rna_yield (ng): 40.176
925L_pDC

source_name: Plasmacytoid dendritic cells

value: Plasmacytoid dendritic cells

value: healthy


title: 9JD4_Progenitor_rep1

description:
cell_number (facs): 22930
total_rna_yield (ng): 7.548
9JD4_Progenitor

source_name: Progenitor cells

value: Progenitor cells

value: F


title: 9JD4_B_Ex_rep1

description:
cell_number (facs): 122804
total_rna_yield (ng): 30.18
9JD4_B_Ex

source_name: Exhausted B cells

value: Exhausted B cells


title: 925L_I_mono_rep2

description:
cell_number (facs): 216933
total_rna_yield (ng): 114.672
925L_I_mono

source_name: Intermediate monocytes

value: Intermediate monocytes


title: 925L_mDC_rep2

description:
cell_number (facs): 229213
total_rna_yield (ng): 363.624
925L_mDC

source_name: Myeloid dendritic cells

value: Myeloid dendritic cells


title: 925L_C_mono_rep2

description:
cell_number (facs): 300000
total_rna_yield (ng): 160.908
925L_C_mono

source_name: Classical monocytes

value: Classical monocytes


title: 9JD4_CD4_TE_rep1

description:
cell_number (facs): 114066
total_rna_yield (ng): 18.984
9JD4_CD4_TE

source_name: Terminal effector CD4 T cells

value: Terminal effector CD4 T cells


title: 925L_B_SM_rep2

description:
cell_number (facs): 564388
total_rna_yield (ng): 249.9
925L_B_SM

source_name: Switched memory B cells

value: Switched memory B cells


title: 925L_NC_mono_rep2

description:
cell_number (facs): 231932
total_rna_yield (ng): 153.492
925L_NC_mono

source_name: Non classical monocytes

value: Non classical monocytes


title: 925L_Plasmablasts_rep2

description:
cell_number (facs): 14264
total_rna_yield (ng): 10.788
925L_Plasmablasts

source_name: Plasmablasts

value: Plasmablasts


title: 925L_B_Ex_rep2

description:
cell_number (facs): 52906
total_rna_yield (ng): 7.752
925L_B_Ex


title: 9JD4_Th1_rep1

description:
cell_number (facs): 788747
total_rna_yield (ng): 408.648
9JD4_Th1

source_name: Th1 cells

value: Th1 cells


title: 925L_Progenitor_rep2

description:
cell_number (facs): 19215
total_rna_yield (ng): 4.656
925L_Progenitor


title: 925L_CD4_TE_rep2

description:
cell_number (facs): 183582
total_rna_yield (ng): 31.836
925L_CD4_TE


title: 925L_B_NSM_rep2

description:
cell_number (facs): 399587
total_rna_yield (ng): 123.852
925L_B_NSM

source_name: Non-switched memory B cells

value: Non-switched memory B cells


title: 925L_CD4_naive_rep2

description:
cell_number (facs): 370000
total_rna_yield (ng): 118.992
925L_CD4_naive

source_name: Naive CD4 T cells

value: Naive CD4 T cells


title: 925L_Th2_rep2

description:
cell_number (facs): 400198
total_rna_yield (ng): 255.192
925L_Th2

source_name: Th2 cells

value: Th2 cells


title: 925L_Th1/Th17_rep2

description:
cell_number (facs): 387451
total_rna_yield (ng): 203.832
925L_Th1/Th17

source_name: Th1/Th17 cells

value: Th1/Th17 cells

value: M


title: 925L_Th17_rep2

description:
cell_number (facs): 290254
total_rna_yield (ng): 165.576
925L_Th17

source_name: Th17 cells

value: Th17 cells

value: healthy


title: 925L_Th1_rep2

description:
cell_number (facs): 444395
total_rna_yield (ng): 214.788
925L_Th1


title: 925L_Treg_rep2

description:
cell_number (facs): 312007
total_rna_yield (ng): 93.456
925L_Treg

source_name: T regulatory cells

value: T regulatory cells


title: 925L_CD8_TE_rep2

description:
cell_number (facs): 400000
total_rna_yield (ng): 138.384
925L_CD8_TE

source_name: Terminal effector CD8 T cells

value: Terminal effector CD8 T cells


title: 925L_TFH_rep2

description:
cell_number (facs): 400000
total_rna_yield (ng): 161.46
925L_TFH

source_name: Follicular helper T cells

value: Follicular helper T cells


title: 925L_VD2+_rep2

description:
cell_number (facs): 400000
total_rna_yield (ng): 331.068
925L_VD2+

source_name: Vd2 gd T cells

value: Vd2 gd T cells


title: 925L_VD2-_rep2

description:
cell_number (facs): 295074
total_rna_yield (ng): 122.46
925L_VD2-

source_name: Non-Vd2 gd T cells

value: Non-Vd2 gd T cells


title: 925L_MAIT_rep2

description:
cell_number (facs): 387411
total_rna_yield (ng): 298.884
925L_MAIT

source_name: MAIT cells

value: MAIT cells


title: 925L_CD8_EM_rep2

description:
cell_number (facs): 400000
total_rna_yield (ng): 159.144
925L_CD8_EM

source_name: Effector memory CD8 T cells

value: Effector memory CD8 T cells


title: 925L_CD8_CM_rep2

description:
cell_number (facs): 400000
total_rna_yield (ng): 232.92
925L_CD8_CM

source_name: Central memory CD8 T cell

value: Central memory CD8 T cell


title: DZQV_mDC_rep4

description:
cell_number (facs): 236429
total_rna_yield (ng): 226.632
DZQV_mDC

source_name: Myeloid dendritic cells

value: Myeloid dendritic cells


title: DZQV_NC_mono_rep4

description:
cell_number (facs): 234326
total_rna_yield (ng): 120.108
DZQV_NC_mono

source_name: Non classical monocytes

value: Non classical monocytes


title: DZQV_Basophils_rep4

description:
cell_number (facs): 300000
total_rna_yield (ng): 8.496
DZQV_Basophils

source_name: Low-density basophils

value: Low-density basophils


title: 925L_CD8_naive_rep2

description:
cell_number (facs): 400000
total_rna_yield (ng): 211.392
925L_CD8_naive

source_name: Naive CD8 T cells

value: Naive CD8 T cells


title: DZQV_NK_rep4

description:
cell_number (facs): 300000
total_rna_yield (ng): 104.58
DZQV_NK

source_name: Natural killer cells

value: Natural killer cells


title: DZQV_I_mono_rep4

description:
cell_number (facs): 230847
total_rna_yield (ng): 326.124
DZQV_I_mono

source_name: Intermediate monocytes

value: Intermediate monocytes


title: DZQV_C_mono_rep4

description:
cell_number (facs): 300000
total_rna_yield (ng): 187.476
DZQV_C_mono

source_name: Classical monocytes

value: Classical monocytes

value: M


title: 925L_B_naive_rep2

description:
cell_number (facs): 2250000
total_rna_yield (ng): 784.5
925L_B_naive

source_name: Naive B cells

value: Naive B cells

value: healthy


title: DZQV_B_Ex_rep4

description:
cell_number (facs): 149548
total_rna_yield (ng): 29.112
DZQV_B_Ex

source_name: Exhausted B cells

value: Exhausted B cells


title: DZQV_Plasmablasts_rep4

description:
cell_number (facs): 291240
total_rna_yield (ng): 755.112
DZQV_Plasmablasts

source_name: Plasmablasts

value: Plasmablasts


title: DZQV_B_SM_rep4

description:
cell_number (facs): 450000
total_rna_yield (ng): 176.736
DZQV_B_SM

source_name: Switched memory B cells

value: Switched memory B cells


title: DZQV_B_NSM_rep4

description:
cell_number (facs): 450000
total_rna_yield (ng): 171.612
DZQV_B_NSM

source_name: Non-switched memory B cells

value: Non-switched memory B cells


title: DZQV_CD4_naive_rep4

description:
cell_number (facs): 450000
total_rna_yield (ng): 58.056
DZQV_CD4_naive

source_name: Naive CD4 T cells

value: Naive CD4 T cells


title: DZQV_Th2_rep4

description:
cell_number (facs): 82465
total_rna_yield (ng): 8.016
DZQV_Th2

source_name: Th2 cells

value: Th2 cells


title: DZQV_Progenitor_rep4

description:
cell_number (facs): 74692
total_rna_yield (ng): 15.024
DZQV_Progenitor

source_name: Progenitor cells

value: Progenitor cells