title: WT_PSK_30min_Replicate

city: Bangalore

first: Shivaprasad

last: Padubidri V.

address: UAS-GKVK Campus

country: India

institute: National Centre for Biological Sciences - TIFR

data_processing:
Adapter was removed and low quality bases were trimmed from sequenced reads using Trimmomatic.
The processed reads were aligned to the rice genome using HISAT2.
Gene expressions were calculated using CuffLinks (v2.2.1) as mentioned in Cole Trapnell et al, 2012.
Assembly: Oryza sativa japonica nipponbare genome – IRGSP1
Supplementary files format and content: Text delimited files including FPKM for each sample.

organism: Oryza sativa

source_name: Six-week-old leaf strips

growth_protocol: The plants were grown in green house with natural day-night cycles with temperature maintained around 28 degrees celsius.

extract_protocol:
Total RNA was isolated from leaves using TRIzol method.
Libraries were prepared for sequencing using standard Novaseq protocols. The kit used is NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads (Catalog no-E7765L) and the adapter sequences are Read 1- AGATCGGAAGAGCACACGTCTGAACTCCAGTCA and for read 2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT

treatment_protocol: For PSK treatment, 2 cm leaf strips were maintained overnight in sterile water to wash away residual wound signals. Peptides were dissolved in water and treatment was given in six well plates.

value: Six-week-old leaf strips

tag: subspecies, cultivar

value: Genotype:Rice, Indica, Pusa Basmati 1 (PB1)

value: WT

value: PSK


title: A305

status: Public on Jun 26 2024

type: RNA

city: Stirling

first: James

last: Timmons

address: Bridge of Allan

country: United Kingdom

institute: Augur Precision Medicine LTD

description: human skeletal muscle

hyb_protocol: Standard

scan_protocol: Standard

data_processing:
CEL files were GC correct and then processed using IRON (default settings) using custom CDFs and then an SD filter applied to focus on signals above background. The full length transcript probe-set based data are provided along with the custom CDF.
Array probes were aligned to genome reference Grch38 and transcriptome reference gencode43 and a probe-level CDF was created.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: PRE

label_protocol: Affymetrix WT kit

extract_protocol: Trizol

tag: tissue

value: vastus lateralis

tag: treatment group and time

value: PRE

tag: age

value: young adult


title: A353

description: human skeletal muscle

source_name: POST

value: POST


title: WT_PSK_30min

type: SRA

library_source: transcriptomic

tag: genotype

tag: treatment

tag: time


title: BrainCell_Enhancer-ProB12_MouseID-616739_Cell-26

city: Seattle

first: John

middle: Kenneth

last: Mich

state: WA

address: 615 Westlake Ave N

country: USA

institute: Allen Institute for Brain Science

library_source: transcriptomic single cell

data_processing:
Base-calling using standard Illumina software.
Alignment with STAR (https://github.com/alexdobin/STAR)
Transformed by counts per million.
Assembly: mm10
Supplementary files format and content: Processed data in counts per million (CPM) format.

molecule: polyA RNA

organism: Mus musculus

source_name: VISp

extract_protocol:
Single SYFP2-expressing cells from mouse brain were flow sorted into individual tubes in SMARTerv4 collection buffer.
SMARTerv4

value: VISp


title: A287

description: human skeletal muscle

value: middle aged adult


title: A299

description: human skeletal muscle


title: BrainCell_Enhancer-ProB12_MouseID-616739_Cell-25


title: BrainCell_Enhancer-ProB12_MouseID-616739_Cell-24


title: IMR-90, Sen, input

city: Kumamoto

first: Mitsuyoshi

last: Nakao

address: 2-2-1 Honjo, Chuo-ku

department: Institute of Molecular Embryology and Genetics

country: Japan

institute: Kumamoto University

library_source: genomic

data_processing:
Basecalls and conversion to FASTQ files were performed using BaseSpace Onsite (Illumina)
The sequenced reads were mapped to the human reference genome (hg19) using Bowtie2 version 2.3.4.1.
Uniquely mapped reads were extracted using samtools version 1.9. PCR duplicates and repeat regions (defined by hg19.RepeatMasker.20130422) were filtered outusing samtools version 1.9. and bedtools version 2.17.0.
BigWig files normalized by counts per million (CPM) are generated using bamCoverage 3.1.1.
BedGraph (.bdg) files normalized by the appropriate input sample for the ChIP sample are created using the "peakcall" function of macs2 version 2.1.1.
Assembly: hg19
Supplementary files format and content: BigWig files for input samples.
Supplementary files format and content: BedGraph (.bdg) files normalized by the appropriate input sample for the ChIP sample.

molecule: genomic DNA

growth_protocol: IMR-90 ER:Ras cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 200 mM L-glutamine, 1 mM sodium pyruvate, 10% (v/v) heat-inactivated fetal bovine serum (FBS), and penicillin/streptomycin.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at room temperature. Following cell lysis, cells were treated with 10 U of Micrococcal nuclease per 1 × 10^6 nuclei at 37℃ for 20 min and then sonicated by Picoruptor (Diagenode) for 2 min. Chromatin fragments were incubated at 4℃ overnight with the appropriate antibodies, followed by a pull-down assay using M-280 sheep anti-rabbit IgG (Thermo Fisher Scientific). After decrosslinking, the DNA was purified using a QIAquick PCR Purification Kit (Qiagen).
The ChIP-seq library was prepared using a NEBNext Ultra DNA Library Prep Kit and sequenced using the Illumina NextSeq 500/550 system (Illumina), according to the manufacturer’s protocol.

treatment_protocol: To induce oncogene-induced senescence, IMR-90 ER:Ras cells were treated with 100 nM 4-Hydroxytamoxifen (4-OHT) for 6 days.Transfection of siRNA was performed using RNAiMAX (Invitrogen).

tag: cell line

tag: cell type

value: senescent fibroblast

tag: chip antibody

value: siCtrl, 100 nM 4OHT for 6 days


title: A275

description: human skeletal muscle


title: WT_PSK_4hr_Replicate


title: WT_PSK_4hr


title: IMR-90, Sen-siACLY, input

value: siACLY, 100 nM 4OHT for 6 days


title: WT_PSK_2hr_Replicate


title: IMR-90, Pro, H3K27Ac ChIP

value: proliferative fibroblast

value: anti-H3K27Ac (abcam, ab4729)


title: BrainCell_Enhancer-ProB12_MouseID-616739_Cell-23


title: WT_PSK_2hr


title: IMR-90, Pro, input


title: ECFC_P26

city: Milan

first: Edoardo

last: Pedrini

state: Lombardy

address: Via Olgettina 60

department: Division of Neuroscience

country: Italy

institute: Hospital San Raffaele

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: refdata-gex-GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files, gzipped

source_name: endothelial progenitor cells

growth_protocol: human ECFCs were grown in ECM-2 media supplemented with 10% FBS

extract_protocol:
Cells were detached with trypsin, washed in DPBS, passed through a 40 µm strainer and cell suspension of 1000 cells/µl was prepared and loaded onto the microfluidic chip using the 10x Genomics v2 kit
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriately sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: ECFCs were cultured for 9 passages (proliferating), 19 passages (mid passage), and 26 passages (senescent). Passage 8 cells were grown and kept confluent for 4 days (quiescent)

value: endothelial progenitor cells

tag: replicate

value: ECFC

tag: passage

value: old


title: IMR-90, Sen, H3K27Ac ChIP


title: WT_PSK_0min_Replicate

value: Six-week-old leaf strips

value: Genotype:Rice, Indica, Pusa Basmati 1 (PB1)


title: A551

description: human skeletal muscle


title: BrainCell_Enhancer-ProB12_MouseID-616739_Cell-22


title: BrainCell_Enhancer-ProB12_MouseID-616739_Cell-21


title: ECFC_P19

description: 10X Genomics

value: mid


title: WT_PSK_0min

value: WT

value: PSK


title: A203

description: human skeletal muscle

value: vastus lateralis

value: young adult


title: BrainCell_Enhancer-ProB12_MouseID-616739_Cell-20

value: VISp


title: hiPSC1_d11_replica2_plate2

city: Nijmegen

first: Jo Huiqing

last: Zhou

address: Geert Grooteplein 26/28

country: Netherlands

institute: Radboud University

description:
hiPSC1_d11_replica2_plate2
scRNA_barcodes_384.tab

data_processing:
For the matrix files, preprocessing of reads was done automatically with workflow tool seq2science v0.9.2 using the scrna-seq workflow, Single-end reads were trimmed with fastp v0.20.1 with default options. Genome assembly GRCh38.p13 was downloaded with genomepy 0.12.0. The genome and gene annotations was extended with custom regions. Reads were aligned and transformed to bus format with kb-python v0.26.4, a python wrapper for kallisto and bustools.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include gene count values for each plate, for each sample a .mtx matrix file with the reads, a .genes.txt file with the genes corresponding the the matrix file, and a .barcodes.txt file containing the barcodes linked to the matrix file

growth_protocol: Corneal differentiation of hPSCs was performed with a previously established protocol  (Hongisto et al., 2017, 2018). Briefly, hPSCs cultured in Essential 8™ Flex medium (ThermoFisher) on recombinant laminin 521 (L521; Biolamina) were induced towards the surface ectoderm in a 4-day suspension culture, which involved the formation of embryoid bodies with 5 µM Blebbistatin overnight, followed by one day supplementation with bFGF (50 ng/ml) and SB-505124 (10 μM) and two-day supplementation with BMP4 (25 ng/ml).  Adherent differentiation from D4 onwards was carried out in CnT-30 medium (CELLnTEC) on Collagen IV (Col IV; Sigma, 5.0 µg/cm2) and L521 (0.5 µg/cm2) combination matrix

extract_protocol:
A single-cell suspension was made using trypsin. After which cells were filtered using a 40uM filter to remove cell clumps. Cells were stained with 7-AAD.
Live cells were selected for and FACs-sorted onto 384-well plates containing primers with unique molecular identifiers, according to the SORT-Seq protocol.  Plates were spun down (1200 × g, 1 min, 4 °C) and ERCC spike‐in mix (1:50,000) was dispensed by a Nanodrop into each well. 150 nl of the Reverse Transcription (RT) mix was similarly dispensed into each well. Thermal cycling conditions were set at 4 °C 5 min; 25 °C 10 min; 42 °C 1 h; 70 °C 10 min. Each plate their library was pooled together and the cDNA was purified using AmpureXP beads. Overnight In vitro transcription was carried out at 16 °C, with the lid set at 70 °C. An exonuclease digestion step was performed thereafter for 20 min at 37 °C, followed by fragmentation of the RNA samples. After a beads cleanup, the samples were subjected to library RT and amplification to tag the RNA molecules with specific and unique sample indexes, followed by a final beads cleanup (1:0.8, reaction mix: beads), and the sample cDNA libraries were eluted with DNAse free water. Libraries were quantified using the KAPPA quantification kit following manufacturers protocol after which the plates were sequenced on the Illumina NextSeq 500 for 25 million reads per plate.

value: differentiating hiPSC


title: ECFC_P09

description: 10X Genomics

value: young


title: BrainCell_Enhancer-ProB12_MouseID-616739_Cell-19


title: ECFC_P08

description: 10X Genomics

value: quiescent


title: A194

description: human skeletal muscle

value: POST


title: KO_PSK_30min_Replicate

value: KO


title: KO_PSK_30min


title: BrainCell_Enhancer-ProB12_MouseID-616739_Cell-18


title: Follicle small, Patient 2, 19

city: Tallinn

first: Ilmatar

last: Rooda

address: Akadeemia tee 15

department: Chemistry and Biotechnology

country: Estonia

institute: Tallinn University of Technology

description: H2Patient 2secondary

data_processing:
Raw FASTQ files were quality-filtered with Trimmomatic v 0.39  with the options of SLIDINGWINDOW:2:20. Adapter sequences (3´adapter AACTGTAGGCACCATCAAT and 5´ adapter GTTCAGAGTTCTACAGTCCGACGATC) were removed and reads below 17 nucleotides in length were discarded and the remaining filtered and trimmed reads were counted and mapped to the primary assembly of human genome GRCh38 using miRDeep2 with standard settings to obtain miRNA sequences from small RNA data.
Count tables from individual samples were merged using edgeR package v3.36.0  and the formed count matrix was used as input for DESeq2 v.1.34.0  in R version 4.1.1 for differential gene expression analysis between groups with standard options.
Human genome GRCh38 retrieved from Gencode
csv file, count matrix

source_name: ovary

extract_protocol:
Cryopreserved cortex tissue tubes were thawed by placing tubes into 37°C water bath for ~1 min. Tissue pieces were transferred into thawing media solutions with 10mg/ml HSA (Vitrolife) and decreasing sucrose concentrations (media I, II and III). All incubation steps were 10min. Thawed cortex tissue pieces were mechanically and enzymatically dissociated using McIIwain Tissue Chopper and digestion media containing McCoy’s (Thermo Fisher Scientific) medium with 1mg/mL HSA (Vitrolife), 1x GlutaMAX (Thermo Fisher Scientific), 1x Insulin-Transferrin solution (Thermo Fisher Scientific), 40μg/mL Liberase (Sigma-Aldrich), 0.4mg/mL Collagenase IV (Thermo Fisher Scientific), and 0.2mg/ml DNase I (BioRad). The chopped pieces were then incubated in a digestion medium containing Neutral Red (50mg/mL, Sigma-Aldrich) in +37°C shaking for 30–50min and the digestion was stopped using termination medium containing McCoy’s with 10% HSA (Thermo Fisher Scientific and Vitrolife). The proportion of viable (red) follicles of all follicles was evaluated under a stereomicroscope (Leica S9D) and only viable follicles were picked. Individual follicles were photographed under the microscope before they were lysed in 4ul of lysis buffer containing 0.2% Tween 20 (Merck), 2U/ul RNase inhibitor (Invitrogen) in RNase-free water (Invitrogen) and stored at -80°C until library preparation.
Starting amount of small RNA in library preparation was 2µl of follicle cells lysate.
Small RNA libraries were prepared with QIAseq miRNA Library Kit (QIAGEN) according to the manufacturer’s protocol. Final libraries were separated and excised from 5% TBE gels (Bio-Rad) after staining with 1X SYBR Gold stain (Thermo Fisher Scientific). Gel pieces containing the small RNA libraries were crushed with pellet pestles (Fisher Scientific). 300µl RNase free water (Thermo Fisher Scientific) was added to the gel debris and rotated for 2h at room temperature (RT) to elute miRNA libraries. Eluate and gel debris were transferred to the Spin X centrifuge tube filter (Merck) and centrifuged 2min at 16 000g. Thereafter 2µl glycogen (Thermo Scientific), 30µl 3M NaOAc (Thermo Fisher Scientific), 1µl 0.1x Pellet Paint (Merck) and 975µl of cold 100% ethanol (Naxo) were added to the eluate, and centrifuged for 20min at 20 000g at 4°C. Pellet was washed with 500µl of 70% ethanol and centrifuged for 2min at 20 000g. The final libraries were resuspended in 7µl of resuspension buffer (PerkinElmer). The size of libraries was estimated with Agilent DNA High Sensitivity chips on the Agilent 2100 Bioanalyzer system (Agilent Technologies). Library concentrations were measured using Qubit High Sensitivity Assay kit (Thermo Fisher Scientific) before pooling in equimolar amounts. Single-end sequencing of 75bp with single index (6bp) length was performed on NextSeq 500 platform with NextSeq HIGH75 kit or NextSeq MID150 kit (Illumina).

value: ovary

value: secondary


title: A176

description: human skeletal muscle


title: A164

description: human skeletal muscle

value: PRE


title: A239

description: human skeletal muscle


title: KO_PSK_4hr_Replicate


title: A146

description: human skeletal muscle


title: A143

description: human skeletal muscle


title: Follicle small, Patient 1, 16

description: H2Patient 1secondary


title: Follicle small, Patient 2, 18

description: H1Patient 2primary

value: primary


title: KO_PSK_4hr

value: Six-week-old leaf strips


title: BrainCell_Enhancer-ProB12_MouseID-616739_Cell-16


title: BrainCell_Enhancer-ProB12_MouseID-616739_Cell-17


title: KO_PSK_2hr_Replicate

value: Genotype:Rice, Indica, Pusa Basmati 1 (PB1)


title: Follicle small, Patient 1, 15

description: H1Patient 1intermediate

value: intermediate


title: BrainCell_Enhancer-ProB12_MouseID-616739_Cell-15


title: A140

description: human skeletal muscle


title: Follicle small, Patient 2, 17

description: G2Patient 2secondary


title: KO_PSK_0min_Replicate


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-30


title: KO_PSK_2hr


title: Follicle small, Patient 2, 16

description: G1Patient 2intermediate


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-29


title: A137

description: human skeletal muscle

value: middle aged adult


title: KO_PSK_0min

value: PSK


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-28


title: MP1_subset26_pool1_S1

city: Rehovot

first: Naama

last: Barkai

address: Herztel 234

department: Molecular genetics

country: Israel

institute: Weizmann institute of science

library_source: other

data_processing:
demultiplexing with bcl2fastq
forward primer removal using 'cutadapt'
sample demultiplexing using adapter removal
count number of read for each library variant
generate csv files
Assembly: GCA_000146045.2 (R64)
Supplementary files format and content: csv. Each file contains data for of all timepoint and repeats for TF a given library in a given experiment
Library strategy: Massively Parallel Binding Assay (Amplicon based PCR)

molecule: other

organism: Saccharomyces cerevisiae

growth_protocol: Overnight cultures from fresh colonies were diluted (>1:10000) and grown to OD4 in SC medium with glucose

extract_protocol:
In this method we extract plasmid DNA from yeast, serving as a template for by a PCR reaction which is the first step of the library preparation protocol. Plasmid DNA was extracted using the MasterPure Yeast DNA Purification Kit (Lucigen Corporation, MPY80200), with some modifications. Briefly, 300 ul of lysis buffer supplemented with RNase A (as recommended) were added to each sample. Following 15 minutes of incubation in 65 C, cells were moved into LoBind microcentrifuge tubes (Eppendorf®, 022431021) containing 0.5mm Zirconium Oxide beads (ZrOB05, Next Advance) and blended using the Bullet Blender 24 (Next Advance) for a single cycle of 3 minutes in level 8. Samples were cooled over ice and lysates were moved to 1.5 ml tubes, vortexed, and supplemented with 300 ul MPC buffer. Samples were vortexed vigorously and centrifuged for 10 minutes (17,000g). Supernatant was moved to 1.5 ml tubes containing 500 ul isopropanol. Samples were vortexed vigorously and DNA was precipitated (10 minutes, 17,000g). Isopropanol was removed, and pellets were washed in 70% EtOH, then air dried and finally resuspended in TE buffer.
Following DNA extraction, samples were 1.5 X SPRI (AMPure XP, A63881) cleaned and resuspended in 30 ul elution buffer (10mM Tris-HCl, pH 8) and then diluted 1:20. 1 ul was used as a template for PCR reaction for amplifying noncleaved variants and sample barcoding (28 cycles) using the Phusion® High-Fidelity PCR Master Mix (NEB, M0531L). Samples were verified using gel electrophoresis, and 0.5 reversed-SPRI cleaned. DNA concentrations were measured using Qubit™ Flex Fluorometer (Invitrogen), and samples were normalized to equal amounts, then pooled together. 1 ng was taken as a template for a PCR reaction using KAPA HiFi HotStart ReadyMix (Roche, KK2602) for adding iIlumina indices and machine adapters. Samples were 1X SPRI cleaned, then concentrations and library quality were validated using Qubit and tape station (Agilent).

treatment_protocol: Massively Parallel Binding Assay (MPBA), a novel method allowing parallel measurement of transcription factor (TF) binding to thousands of DNA sequence-variants within cells. In this project we apply it to quantify binding of dozens of TFs to libraries of mutated regulatory regions, systematically screening all motif combinations. In brief, we integrate a library of DNA variants into a designed plasmid and transform it into cells carrying an endogenous TF of interest fused to a Micrococcal Nuclease (MNase), which allows triggering the cleavage of TF-bound DNA upon a short calcium pulse. Next, after growing the culture to the desired condition, those cells are subjected to a short calcium pulse, triggering the cleavage of TF-bound plasmids. Following this step, variants are PCR amplified, thereby capturing only the non-cleaved (unbound) sequences. Then, the frequency of each variant is defined using high-throughput sequencing and compared to untreated culture.

tag: strain


title: Follicle small, Patient 1, 13

description: G1Patient 1intermediate


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-27


title: Follicle small, Patient 2, 15

description: F2Patient 2primary


title: A116

description: human skeletal muscle

value: vastus lateralis


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-26


title: A98

description: human skeletal muscle

value: young adult


title: Follicle small, Patient 1, 12

description: F2Patient 1secondary


title: H2452 DPT,48h,rep 4

city: Shanghai

first: Cheng

last: Zhong

state: Shanghai

address: Yishan road 600, Xuhui District, Shanghai, China

department: Department of Respiratory Medicine

country: China

institute: Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University

data_processing:
fastp (version 0.18.0).
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
RNAs differential expression analysis was performed by DESeq2 software between two different groups. The genes/transcripts with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change≥1 were considered differentially expressed genes.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files includes FPKM values and count for each sample to standardize.

growth_protocol: H2452 cells were maintained in 1640 medium supplemented with 10% fetal bovine serum(FBS) and 100 U/mL penicillin/streptomycin at 37°C, 5% CO2, and appropriate humidity.

extract_protocol:
Total RNA from DPT(20nM) or DMSO(control) treated H2452 cells was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads.
Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB#7530,New England Biolabs, Ipswich, MA, USA).

treatment_protocol: H2452 cells were treated with DPT(20nM) or DMSO(no more than 0.01%，sigma) for 48h.

value: Pleural Biphasic Mesothelioma

value: wt

value: DPT


title: BrainCell_Enhancer-ProB12_MouseID-616739_Cell-14

value: VISp


title: A107

description: human skeletal muscle


title: MP1_subset4_pool1_S1


title: Follicle small, Patient 1, 14

description: G2Patient 1secondary


title: A68

description: human skeletal muscle

value: POST


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-25


title: A92

description: human skeletal muscle


title: Follicle small, Patient 2, 14

description: F1Patient 2intermediate


title: A53

description: human skeletal muscle


title: H2452 DPT,48h,rep 1


title: MP1_subset7_pool1_S6


title: H2452 DPT,48h,rep 2


title: MP1_subset26_pool4_S4


title: MP1_subset10_pool1_S5


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-23


title: MP1_subset10_pool2_S6


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-24


title: A11

description: human skeletal muscle


title: H2452 DPT,48h,rep 3


title: Follicle small, Patient 2, 13

description: E2Patient 2primary


title: A8

description: human skeletal muscle


title: MP1_subset6_pool1_S4


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-22


title: H2452 DMSO,48h,rep 4

value: DMSO


title: Follicle small, Patient 1, 11

description: F1Patient 1primary

value: ovary


title: A5

description: human skeletal muscle


title: Follicle small, Patient 1, 10

description: E2Patient 1secondary

value: secondary


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-21


title: MP1_subset15_pool1_S7


title: MP1_subset9_pool1_S3


title: Follicle small, Patient 2, 12

description: E1Patient 2secondary


title: H2452 DMSO,48h,rep 2


title: H2452 DMSO,48h,rep 1


title: MP1_subset26_pool6_S6


title: Follicle small, Patient 1, 9

description: E1Patient 1secondary


title: Follicle small, Patient 2, 11

description: D2Patient 2primary


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-20


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-18


title: MP1_subset26_pool5_S5


title: MP1_subset6_pool2_S5


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-17


title: Follicle small, Patient 2, 10

description: D1Patient 2intermediate


title: BrainCell_Enhancer-ProB12_MouseID-616739_Cell-31


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-16


title: Follicle small, Patient 1, 7

description: D1Patient 1primary


title: Old subject serum treatment, replicate A, CT 58

city: Philadelphia

first: Antonijo

last: Mrčela

state: Pennsylvania

address: 3400 Civic Center Boulevard

department: Institute for Translational Medicine and Therapeutics

institute: University of Pennsylvania

data_processing:
Raw RNA-seq reads were aligned to the GRCh38 build of the human genome by STAR version 2.7.10a.
Data were normalized and quantified at both gene and exon-intron level, using a downsampling strategy implemented in PORT (Pipeline Of RNA-seq Transformations, available athttps://github.com/itmat/Normalization), version 0.8.5f-beta_hotfix1. Both STAR and PORT were provided with gene models from release 106 of the Ensembl annotation.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes PORT normalized counts for each sample.

source_name: Foreskin

growth_protocol: BJ-5TA BMAL1-dLuc-GFP cells in 24-well plates (~confluent) were washed (2x) with DPBS and given serum free media (DMEM with Penn Strep) for 24hrs.

extract_protocol:
Upon sample collection wells were place on ice and rinsed with cold DPBS and then put in cold RLT buffer with 2-Mercaptoethanol (10uL/mL). Samples were frozen at -80 overnight and sent to Admera for RNA extraction and sequencing. Total RNA was extracted with RNeay mini kit (Qiagen).
Isolated RNA sample quality was assessed by High Sensitivity RNA Tapestation (Agilent Technologies Inc., California, USA) and quantified by Qubit 2.0 RNA HS assay (ThermoFisher, Massachusetts, USA). Paramagnetic beads coupled with oligo d(T)25 are combined with total RNA to isolate poly(A)+ transcripts based on NEBNext® Poly(A) mRNA Magnetic Isolation Module manual (New England BioLabs Inc., Massachusetts, USA). Prior to first strand synthesis, samples are randomly primed (5 ́ d(N6) 3 ́ [N=A,C,G,T]) and fragmented based on manufacturer’s recommendations. The first strand is synthesized with the Protoscript II Reverse Transcriptase with a longer extension period, approximately 40 minutes at 42°C. All remaining steps for library construction were used according to the NEBNext® UltraTM II Non-Directional RNA Library Prep Kit for Illumina® (New England BioLabs Inc., Massachusetts, USA). Final libraries quantity was assessed by Qubit 2.0 (ThermoFisher, Massachusetts, USA) and quality was assessed by TapeStation D1000 ScreenTape (Agilent Technologies Inc., California, USA). Final library size was about 430bp with an insert size of about 300bp. Illumina® 8-nt dual-indices were used. Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® NovaSeq S4 Illumina, California, USA) with a read length configuration of 150 PE for 40 M PE reads per sample (20 M in each direction).

treatment_protocol: After 24hrs cells were given media with human serum (DMEM, Penn Strep, 10% human serum). Serum starvation was staggered every 12 hours over two days to allow for samples to be collected on the same day.

value: Foreskin

value: Fibroblast

value: Old serum

tag: subject

value: Old subject


title: Old subject serum treatment, replicate B, CT 58


title: Old subject serum treatment, replicate B, CT 56


title: H2452 DMSO,48h,rep 3


title: MP1_subset26_pool2_S2


title: Old subject serum treatment, replicate A, CT 56


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-15


title: Follicle small, Patient 2, 9

description: C3Patient 2secondary


title: Old subject serum treatment, replicate B, CT 54


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-19


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-14


title: Old subject serum treatment, replicate A, CT 54


title: MP1_subset5_pool1_S3


title: Follicle small, Patient 2, 8

description: C2Patient 2primordial

value: primordial


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-13


title: Follicle small, Patient 1, 6

description: C2Patient 1primary

value: primary


title: MP1_subset14_pool1_S4


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-12


title: MP1_subset8_pool2_S2


title: Follicle small, Patient 2, 7

description: C1Patient 2secondary


title: Follicle small, Patient 1, 8

description: D2Patient 1primary


title: Old subject serum treatment, replicate A, CT 52


title: MP1_subset13_pool3_S3


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-11


title: Old subject serum treatment, replicate B, CT 52


title: MP1_subset26_pool3_S3


title: Follicle small, Patient 1, 5

description: C1Patient 1secondary


title: Old subject serum treatment, replicate B, CT 50


title: Follicle small, Patient 2, 5

description: B2Patient 2primordial


title: MP1_subset13_pool1_S1


title: BrainCell_Enhancer-eHGT_390m_MouseID-616740_Cell-33


title: Old subject serum treatment, replicate A, CT 50


title: Follicle small, Patient 2, 6

description: B3Patient 2secondary


title: BrainCell_Enhancer-eHGT_390m_MouseID-616740_Cell-32


title: MP1_subset15_pool3_S9


title: MP1_subset13_pool2_S2


title: Old subject serum treatment, replicate B, CT 48


title: BrainCell_Enhancer-eHGT_390m_MouseID-616740_Cell-31


title: Follicle small, Patient 1, 4

description: B2Patient 1intermediate

value: intermediate


title: MP1_subset17_pool2_S9


title: Old subject serum treatment, replicate B, CT 46


title: Follicle small, Patient 2, 4

description: B1Patient 2primary


title: BrainCell_Enhancer-eHGT_390m_MouseID-616740_Cell-29


title: MP1_subset15_pool2_S8


title: Old subject serum treatment, replicate A, CT 46


title: Old subject serum treatment, replicate A, CT 48


title: MP1_subset17_pool1_S8


title: BrainCell_Enhancer-eHGT_390m_MouseID-616740_Cell-30


title: Follicle small, Patient 2, 3

description: A3Patient 2secondary


title: MP1_subset9_pool2_S4


title: BrainCell_Enhancer-eHGT_390m_MouseID-616740_Cell-27


title: Old subject serum treatment, replicate B, CT 44


title: Follicle small, Patient 2, 2

description: A2Patient 2secondary


title: Old subject serum treatment, replicate A, CT 44


title: BrainCell_Enhancer-eHGT_390m_MouseID-616740_Cell-26


title: Old subject serum treatment, replicate B, CT 42


title: Follicle small, Patient 1, 2

description: A2Patient 1primary


title: MP1_subset14_pool3_S6


title: Old subject serum treatment, replicate A, CT 42


title: Follicle small, Patient 2, 1

description: A1Patient 2primordial


title: BrainCell_Enhancer-eHGT_390m_MouseID-616740_Cell-25


title: Follicle small, Patient 1, 3

description: B1Patient 1primordial


title: MP1_subset14_pool2_S5


title: BrainCell_Enhancer-eHGT_390m_MouseID-616740_Cell-22


title: Follicle, half, Patient 2, 19

description: H2_2Patient 2secondary

data_processing:
Raw FASTQ files were quality filtered with Trimmomatic v 0.39 with the options of SLIDINGWINDOW:2:20. Reads below 36 nucleotides in length were discarded and all adapters sequences provided by Illumina were removed from the sequences. The remaining reads were aligned to the primary assembly of human genome GRCh38 retrieved from Gencode using STAR aligner v.2.7.1 with standard settings. Annotation of reads to genes was performed with htseq-count algorithm ( HTSeq v 0.11.2, Python v 3.6.4) by using the primary assembly annotation .gtf file v35 from Gencode. The intersection-nonempty option was used in htseq-count for annotating reads that overlap with multiple features.
The count files produced by htseq-counts were merged using edgeR package v3.36.0, and the formed count matrix was used as input for DeSeq2 v.1.34.0 in R version 4.1.1 for differential gene expression analysis between groups with standard options.
Human genome GRCh38 retrieved from Gencode and assembly annotation .gtf file v35 from Gencode
csv file, count matrix

extract_protocol:
Cryopreserved cortex tissue tubes were thawed by placing tubes into 37°C water bath for ~1 min. Tissue pieces were transferred into thawing media solutions with 10mg/ml HSA (Vitrolife) and decreasing sucrose concentrations (media I, II and III). All incubation steps were 10min. Thawed cortex tissue pieces were mechanically and enzymatically dissociated using McIIwain Tissue Chopper and digestion media containing McCoy’s (Thermo Fisher Scientific) medium with 1mg/mL HSA (Vitrolife), 1x GlutaMAX (Thermo Fisher Scientific), 1x Insulin-Transferrin solution (Thermo Fisher Scientific), 40μg/mL Liberase (Sigma-Aldrich), 0.4mg/mL Collagenase IV (Thermo Fisher Scientific), and 0.2mg/ml DNase I (BioRad). The chopped pieces were then incubated in a digestion medium containing Neutral Red (50mg/mL, Sigma-Aldrich) in +37°C shaking for 30–50min and the digestion was stopped using termination medium containing McCoy’s with 10% HSA (Thermo Fisher Scientific and Vitrolife). The proportion of viable (red) follicles of all follicles was evaluated under a stereomicroscope (Leica S9D) and only viable follicles were picked. Individual follicles were photographed under the microscope before they were lysed in 4ul of lysis buffer containing 0.2% Tween 20 (Merck), 2U/ul RNase inhibitor (Invitrogen) in RNase-free water (Invitrogen) and stored at -80°C until library preparation.
Starting amount of RNA in library preparation was 2µl of follicle cells lysate. Before removing 2µl of cell lysate from tube follicles were lysed at 72°C for three minutes.
Full-length RNA libraries were prepared according to the Smart-seq2 protocol  with small modifications as follows.  To the cell lysate placed on a 96-well plate (Eppendorf) 2µl lysis buffer together with 1µl 10mM dNTP mix and 1µl freshly diluted 10 µM Oligo-dT30VN (Metabion) were added. In reverse transcription reaction, RNase-free (Invitrogen) water volume was 0.59 µl to reach reaction volume of 6 µl which then was added to the 4µl cell lysate to obtain 10µl reaction volume. cDNA preamplification included 5.5µl 5x Phusion GC buffer and 0.55µl Phusion enzyme (2U/µl) (Thermo Fisher Scientific), 0.825µl DMSO (AppliChem), 0.55µl 10 mM dNTP mix and 0.275µl freshly diluted 10 µM ISPCR (Metabion) primer in 8.8µl RNase-free water (Invitrogen). PCR products were purified using AMPure XP beads (Beckman Coulter) in 1:0.9 ratio. DNA concentrations and DNA profile were measured Qubit HS DNA assay (Invitrogen) and Agilent HS DNA assay (Agilent Technologies), respectively. Tagmentation reaction was carried out by using Illumina Nextera XT DNA preparation kit (Illumina). Tagmentation reaction included 2µl ATM and 4µl TD buffer. To the tagmentation reaction 1ng of cDNA was added with final volume of 10µl.  Amplification of adapter-ligated fragments was carried out using 6µl Nextera PCR Master Mix, 2µl i5 primer, and 2µl i7 primer (both from TAG Copenhagen) using 12 cycles to amplify the DNA. Amplification reaction was purified using AMPure XP beads in 1:0.9 ratio. Final DNA library was quality controlled using Qubit HS DNA assay (Invitrogen) and Agilent HS DNA kit (Agilent Technologies). Libraries were sequenced in equimolar amounts using Single-end 76 bp with dual index (8 bp) sequencing on NextSeq 500 platform with NextSeq HIGH75 kit (Illumina).


title: Old subject serum treatment, replicate B, CT 40


title: Old subject serum treatment, replicate B, CT 38


title: BrainCell_Enhancer-eHGT_390m_MouseID-616740_Cell-28


title: Follicle, half, Patient 1, 16

description: H2_1Patient 1secondary


title: BrainCell_Enhancer-eHGT_390m_MouseID-616740_Cell-23


title: Follicle small, Patient 1, 1

description: A1Patient 1primordial


title: BrainCell_Enhancer-eHGT_390m_MouseID-616740_Cell-21


title: BrainCell_Enhancer-eHGT_390m_MouseID-616740_Cell-24


title: BrainCell_Enhancer-eHGT_390m_MouseID-616740_Cell-20


title: Old subject serum treatment, replicate A, CT 38


title: 23R-95 to 97, sort 3

first: David

last: Baker

address: Molecular Engineering and Sciences, Box 351655

institute: University of Washington

data_processing:
Read aligned (software developed in-house)
Counts determined for unmutated sequence and all single-position mutants (scripts developed in-house)
Enrichment ratios calculated based on counts in naïve library and sorted population
Assembly: 23R-1: MESEKYLRELVKKYYEGKLSVQEAVEEVRKYARKKGLEAWMLTWMFMELVKRYI
Assembly: 23R-2: NLWQIFYQLSTILKRTGDPTAKKLLKALAEALKKGDEKALKELAKKATKYIRS
Assembly: 17-1: TWHIDVLAPPEVVKTAASQAGAEVHKAPGDWWRITTDDETAVDIVELILFIAGYQFHISSS
Assembly: 17-2: EPREEEAEKYIKRANGDYDLAELLAFLDGNAEIASAIVEYKER
Assembly: 17-3: TWHIDVKADPSIVKAAASAAGAEVHKLPGDKWRITVDDETAVDIVELILFIWGVEFHISSS
Assembly: 23R-49: NLWQIFYQLSTILKRTGDPTAKKLLKALAEALKKGDEKALKELAKKATKYIRS
Assembly: 23R-64: MEPEKYLRELCKKYYEGKLSQQEAVEEIRKYARKKGLEAWKLVWYFMQCVKRDI
Assembly: 23R-95: CKVKCGPVEFQAQMNWMCFYWRWRYC
Assembly: 23R-96: CKVKCGPVEFQATARWMCFYWWWKYC
Assembly: 23R-97: CRVCMNNFCVDAQMCWMAFYLLNKYN
Supplementary files format and content: The processed data file in Excel format (.xlsx) contains enrichment ratios per variant per selection pool normalized to the enrichment ratio of the unmutated sequence.

growth_protocol: Please see our corresponding publication for the yeast protocols for growth and induction of protein expression.

extract_protocol:
Yeast were lysed with 125 U/ml Zymolase at 37 ºC for 5 h, and DNA was harvested (Zymoprep kit from Zymo Research). Genomic DNA was digested with 2 U/µl Exonuclease I and 0.25 U/µl Lambda exonuclease (New England Biolabs) for 90 min at 30 ºC, and plasmid DNA purified with a QIAquick kit (Qiagen).
In some instances, gene sequences were diversified by overlapping PCR for site-directed mutagenesis libaries as described in Procko et al. J Mol Bio 2013. In other instances, gene sequences were commercially synthesized. Genes were prepared with 5’ and 3’ overhangs >20 bp to enable homologous recombination with the plasmid backbone (pETCON) for yeast expression and surface display via fusion to Aga2p.
DNA amplicon sequencing

treatment_protocol: Please see our corresponding publication for library treatments prior to FACS selection


title: 23R-95 to 97, sort 4


title: 23R-95 to 97, sort 5


title: Follicle, half, Patient 2, 18

description: H1_2Patient 2primary


title: 23R-95 to 97, sort 6


title: MP1_subset4_pool2_S2


title: Old subject serum treatment, replicate B, CT 36


title: Old subject serum treatment, replicate A, CT 40


title: 23R-95 to 97, sort 2


title: BrainCell_Enhancer-eHGT_390m_MouseID-616740_Cell-19


title: Follicle, half, Patient 2, 17

description: G2_2Patient 2secondary


title: BrainCell_Enhancer-eHGT_390m_MouseID-616740_Cell-18


title: 23R-95 to 97, sort 1


title: Follicle, half, Patient 1, 14

description: G2_1Patient 1secondary


title: Old subject serum treatment, replicate B, CT 34


title: 23R-95 to 97, naïve


title: Old subject serum treatment, replicate A, CT 36


title: Follicle, half, Patient 1, 15

description: H1_1Patient 1intermediate


title: BrainCell_Enhancer-eHGT_390m_MouseID-616740_Cell-16


title: Old subject serum treatment, replicate B, CT 32


title: Follicle, half, Patient 1, 13

description: G1_1Patient 1intermediate


title: Follicle, half, Patient 2, 16

description: G1_2Patient 2intermediate


title: Old subject serum treatment, replicate A, CT 34


title: BrainCell_Enhancer-eHGT_390m_MouseID-616740_Cell-17


title: Follicle, half, Patient 1, 12

description: F2_1Patient 1secondary


title: Old subject serum treatment, replicate A, CT 32


title: Old subject serum treatment, replicate B, CT 30


title: 23R-64, sort 1 affinity


title: BrainCell_Enhancer-eHGT_390m_MouseID-616740_Cell-15


title: 23R-64, sort 2 specificity


title: Follicle, half, Patient 2, 14

description: F1_2Patient 2intermediate


title: 23R-64, sort 1 specificity


title: Old subject serum treatment, replicate A, CT 30


title: BrainCell_Enhancer-eHGT_390m_MouseID-616740_Cell-13


title: 23R-64, naïve


title: Follicle, half, Patient 1, 11

description: F1_1Patient 1primary


title: BrainCell_Enhancer-eHGT_390m_MouseID-616740_Cell-12


title: Old subject serum treatment, replicate B, CT 28


title: 23R-49, sort 2 specificity


title: BrainCell_Enhancer-eHGT_390m_MouseID-616740_Cell-11


title: Follicle, half, Patient 2, 13

description: E2_2Patient 2primary


title: 23R-64, sort 2 affinity


title: Follicle, half, Patient 2, 15

description: F2_2Patient 2primary


title: 23R-49, sort 2 affinity


title: BrainCell_Enhancer-eHGT_390m_MouseID-616740_Cell-10


title: Old subject serum treatment, replicate A, CT 28


title: BrainCell_Enhancer-eHGT_390m_MouseID-616740_Cell-14


title: BrainCell_Enhancer-eHGT_390m_MouseID-616740_Cell-9


title: Old subject serum treatment, replicate B, CT 26


title: 23R-49, sort 1 specificity


title: Old subject serum treatment, replicate A, CT 26


title: 23R-49, sort 1 affinity


title: Follicle, half, Patient 2, 12

description: E1_2Patient 2secondary


title: Follicle, half, Patient 1, 10

description: E2_1Patient 1secondary


title: Follicle, half, Patient 1, 9

description: E1_1Patient 1secondary


title: 23R-49, naïve


title: Old subject serum treatment, replicate A, CT 24


title: BrainCell_Enhancer-eHGT_390m_MouseID-616740_Cell-7


title: 17-3, sort 2


title: BrainCell_Enhancer-eHGT_390m_MouseID-616740_Cell-6


title: Follicle, half, Patient 2, 11

description: D2_2Patient 2primary


title: Old subject serum treatment, replicate B, CT 22


title: Follicle, half, Patient 1, 8

description: D2_1Patient 1primary


title: 17-3, sort 1


title: BrainCell_Enhancer-eHGT_373m_MouseID-616737_Cell-13


title: 17-3, naïve


title: Old subject serum treatment, replicate B, CT 20


title: 17-2, sort 2 200 nM


title: BrainCell_Enhancer-ProB12_MouseID-616739_Cell-12


title: Old subject serum treatment, replicate A, CT 22


title: Follicle, half, Patient 2, 9

description: C3_2Patient 2secondary


title: BrainCell_Enhancer-ProB12_MouseID-616739_Cell-13


title: Old subject serum treatment, replicate A, CT 20


title: Follicle, half, Patient 1, 7

description: D1_1Patient 1primary


title: Old subject serum treatment, replicate B, CT 24


title: BrainCell_Enhancer-ProB12_MouseID-616739_Cell-11


title: BrainCell_Enhancer-eHGT_390m_MouseID-616740_Cell-8


title: Old subject serum treatment, replicate B, CT 18


title: 17-2, sort 2 100 nM


title: Follicle, half, Patient 2, 8

description: C2_2Patient 2primordial


title: 17-2, sort 1 200 nM


title: 17-2, sort 1 100 nM


title: BrainCell_Enhancer-ProB12_MouseID-616739_Cell-10


title: Follicle, half, Patient 2, 10

description: D1_2Patient 2intermediate


title: Follicle, half, Patient 2, 7

description: C1_2Patient 2secondary


title: BrainCell_Enhancer-ProB12_MouseID-616739_Cell-9


title: 17-2, naïve


title: Old subject serum treatment, replicate B, CT 16


title: Follicle, half, Patient 1, 5

description: C1_1Patient 1secondary


title: Old subject serum treatment, replicate A, CT 18


title: Follicle, half, Patient 1, 6

description: C2_1Patient 1primary


title: Old subject serum treatment, replicate A, CT 16


title: 17-1, sort 2


title: BrainCell_Enhancer-ProB12_MouseID-616739_Cell-8


title: BrainCell_Enhancer-ProB12_MouseID-616739_Cell-7


title: Old subject serum treatment, replicate B, CT 14


title: Follicle, half, Patient 2, 6

description: B3_2Patient 2secondary


title: BrainCell_Enhancer-ProB12_MouseID-616739_Cell-6


title: 17-1, sort 1


title: Follicle, half, Patient 2, 5

description: B2_2Patient 2primordial


title: Old subject serum treatment, replicate A, CT 14


title: 17-1, naïve


title: BrainCell_Enhancer-ProB12_MouseID-616739_Cell-5


title: Follicle, half, Patient 1, 4

description: B2_1Patient 1intermediate


title: BrainCell_Enhancer-ProB12_MouseID-616739_Cell-4


title: WT_Wound_12h_Replicate

data_processing:
Adapter was removed and low quality bases were trimmed from sequenced reads using Trimmomatic and rRNA sequences were removed using Sortmerna.
The processed reads were aligned to the rice genome using HISAT2.
Gene expressions were calculated using CuffLinks (v2.2.1) as mentioned in Cole Trapnell et al, 2012.
Assembly: Oryza sativa japonica nipponbare genome – IRGSP1
Supplementary files format and content: Text delimited files including FPKM for each sample.

source_name: Six-week-old leaf

extract_protocol:
Total RNA was isolated from leaves using TRIzol method.
Libraries were prepared for sequencing using standard Illumina protocols. The kit used is NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads (Catalog no-E7765L) and the adapter sequences are Read 1- AGATCGGAAGAGCACACGTCTGAACTCCAGTCA and for read 2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT

treatment_protocol: For PEP treatment, 2 cm leaf strips were maintained overnight in sterile water to wash away residual wound signals. Peptides were dissolved in water and treatment was given in six well plates. For wounding, leaves were punched at the edges at 2 cm interval and corresponding unwounded samples were used as controls.

value: Genotype:Rice, Indica, Pusa Basmati 1 (PB1)

tag: genotype (wt or transgenics)

value: Wild type (PB1)

value: Wound


title: Old subject serum treatment, replicate B, CT 12


title: BrainCell_Enhancer-ProB12_MouseID-616739_Cell-2


title: Young subject serum treatment, replicate A, CT 58

value: Young serum

value: Young subject


title: Young subject serum treatment, replicate B, CT 58


title: Follicle, half, Patient 2, 3

description: A3_2Patient 2secondary


title: Follicle, half, Patient 1, 3

description: B1_1Patient 1primordial


title: WT


title: WT_Replicate


title: WT_Wound_12h


title: BrainCell_Enhancer-ProB12_MouseID-616739_Cell-1

value: VISp


title: Follicle, half, Patient 2, 2

description: A2_2Patient 2secondary


title: Wound_30min_Replicate


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-10


title: Young subject serum treatment, replicate A, CT 56


title: Follicle, half, Patient 1, 2

description: A2_1Patient 1primary


title: Young subject serum treatment, replicate B, CT 56


title: Wound_30min


title: Follicle, half, Patient 2, 1

description: A1_2Patient 2primordial


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-9


title: Young subject serum treatment, replicate B, CT 54


title: Young subject serum treatment, replicate A, CT 54


title: Old subject serum treatment, replicate A, CT 12


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-8


title: Follicle, half, Patient 2, 4

description: B1_2Patient 2primary


title: Follicle, half, Patient 1, 1

description: A1_1Patient 1primordial


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-7


title: Wound_15min


title: BrainCell_Enhancer-ProB12_MouseID-616739_Cell-3


title: Young subject serum treatment, replicate B, CT 52


title: Follicle, full, Patient 12, 8

extract_protocol:
Cryopreserved cortex tissue tubes were thawed by placing tubes into 37°C water bath for ~1 min. Tissue pieces were transferred into thawing media solutions with 10mg/ml HSA (Vitrolife) and decreasing sucrose concentrations (media I, II and III). All incubation steps were 10min. Thawed cortex tissue pieces were mechanically and enzymatically dissociated using McIIwain Tissue Chopper and digestion media containing McCoy’s (Thermo Fisher Scientific) medium with 1mg/mL HSA (Vitrolife), 1x GlutaMAX (Thermo Fisher Scientific), 1x Insulin-Transferrin solution (Thermo Fisher Scientific), 40μg/mL Liberase (Sigma-Aldrich), 0.4mg/mL Collagenase IV (Thermo Fisher Scientific), and 0.2mg/ml DNase I (BioRad). The chopped pieces were then incubated in a digestion medium containing Neutral Red (50mg/mL, Sigma-Aldrich) in +37°C shaking for 30–50min and the digestion was stopped using termination medium containing McCoy’s with 10% HSA (Thermo Fisher Scientific and Vitrolife). The proportion of viable (red) follicles of all follicles was evaluated under a stereomicroscope (Leica S9D) and only viable follicles were picked. Individual follicles were photographed under the microscope before they were lysed in 4ul of lysis buffer containing 0.2% Tween 20 (Merck), 2U/ul RNase inhibitor (Invitrogen) in RNase-free water (Invitrogen) and stored at -80°C until library preparation.
Starting amount of RNA in library preparation was 4µl of follicle cells lysate. Before removing 4µl of cell lysate from tube follicles were lysed at 72°C for three minutes.
Full-length RNA libraries were prepared according to the Smart-seq2 protocol  with small modifications as follows.  To the cell lysate placed on a 96-well plate (Eppendorf) 2µl lysis buffer together with 1µl 10mM dNTP mix and 1µl freshly diluted 10 µM Oligo-dT30VN (Metabion) were added. In reverse transcription reaction, RNase-free (Invitrogen) water volume was 0.59 µl to reach reaction volume of 6 µl which then was added to the 4µl cell lysate to obtain 10µl reaction volume. cDNA preamplification included 5.5µl 5x Phusion GC buffer and 0.55µl Phusion enzyme (2U/µl) (Thermo Fisher Scientific), 0.825µl DMSO (AppliChem), 0.55µl 10 mM dNTP mix and 0.275µl freshly diluted 10 µM ISPCR (Metabion) primer in 8.8µl RNase-free water (Invitrogen). PCR products were purified using AMPure XP beads (Beckman Coulter) in 1:0.9 ratio. DNA concentrations and DNA profile were measured Qubit HS DNA assay (Invitrogen) and Agilent HS DNA assay (Agilent Technologies), respectively. Tagmentation reaction was carried out by using Illumina Nextera XT DNA preparation kit (Illumina). Tagmentation reaction included 2µl ATM and 4µl TD buffer. To the tagmentation reaction 1ng of cDNA was added with final volume of 10µl.  Amplification of adapter-ligated fragments was carried out using 6µl Nextera PCR Master Mix, 2µl i5 primer, and 2µl i7 primer (both from TAG Copenhagen) using 12 cycles to amplify the DNA. Amplification reaction was purified using AMPure XP beads in 1:0.9 ratio. Final DNA library was quality controlled using Qubit HS DNA assay (Invitrogen) and Agilent HS DNA kit (Agilent Technologies). Libraries were sequenced in equimolar amounts using Single-end 76 bp with dual index (8 bp) sequencing on NextSeq 500 platform with NextSeq HIGH75 kit (Illumina).


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-6


title: Wound_2h


title: Follicle, full, Patient 12, 7


title: Young subject serum treatment, replicate B, CT 50


title: Young subject serum treatment, replicate A, CT 52


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-5


title: Follicle, full, Patient 12, 6


title: Wound_0min_Replicate


title: Young subject serum treatment, replicate A, CT 50


title: BrainCell_Enhancer-eHGT_390m_MouseID-616740_Cell-4


title: Wound_15min_Replicate


title: Follicle, full, Patient 12, 5


title: Young subject serum treatment, replicate B, CT 48


title: Wound_0min


title: Follicle, full, Patient 12, 4


title: BrainCell_Enhancer-eHGT_390m_MouseID-616740_Cell-3


title: Follicle, full, Patient 12, 2


title: BrainCell_Enhancer-eHGT_390m_MouseID-616740_Cell-2


title: Unwounded_15min


title: BrainCell_Enhancer-eHGT_373m_MouseID-616737_Cell-12


title: Young subject serum treatment, replicate B, CT 46


title: Young subject serum treatment, replicate A, CT 48


title: Unwounded_0min_Replicate


title: Follicle, full, Patient 12, 24


title: Young subject serum treatment, replicate A, CT 46


title: Unwounded_0min


title: BrainCell_Enhancer-eHGT_390m_MouseID-616740_Cell-5


title: Wound_2h_Replicate


title: Follicle, full, Patient 12, 23


title: BrainCell_Enhancer-eHGT_373m_MouseID-616737_Cell-10


title: BrainCell_Enhancer-eHGT_373m_MouseID-616737_Cell-11


title: Young subject serum treatment, replicate B, CT 44


title: RLK_OE_Wound_12h_Replicate

value: Overexpression of RLK1 gene in PB1 background


title: Follicle, full, Patient 12, 22


title: RLK_OE_Wound_12h


title: BrainCell_Enhancer-eHGT_373m_MouseID-616737_Cell-9


title: Follicle, full, Patient 12, 21


title: RLK_OE_Replicate


title: Young subject serum treatment, replicate B, CT 42


title: Unwounded_15min_Replicate


title: BrainCell_Enhancer-eHGT_373m_MouseID-616737_Cell-8


title: Follicle, full, Patient 12, 20


title: RLK_OE


title: Young subject serum treatment, replicate A, CT 42


title: BrainCell_Enhancer-eHGT_373m_MouseID-616737_Cell-7


title: Follicle, full, Patient 12, 1


title: Young subject serum treatment, replicate B, CT 40


title: rlk1_KO_Wound_12h_Replicate

value: Knock-out of RLK1 gene in PB1 background


title: Follicle, full, Patient 12, 19

value: ovary


title: rlk1_KO_Wound_12h


title: Young subject serum treatment, replicate A, CT 40


title: Young subject serum treatment, replicate A, CT 44


title: BrainCell_Enhancer-eHGT_373m_MouseID-616737_Cell-6


title: BrainCell_Enhancer-eHGT_373m_MouseID-616737_Cell-5


title: rlk1_KO_Celldeath_Replicate


title: Young subject serum treatment, replicate B, CT 38


title: BrainCell_Enhancer-eHGT_373m_MouseID-616737_Cell-4


title: Follicle, full, Patient 12, 18


title: Young subject serum treatment, replicate A, CT 38


title: BrainCell_Enhancer-eHGT_373m_MouseID-616737_Cell-2


title: Young subject serum treatment, replicate A, CT 36


title: BrainCell_Enhancer-eHGT_381h_MouseID-615516_Cell-38

source_name: MB/HB

value: MB/HB


title: rlk1_KO


title: Follicle, full, Patient 12, 3


title: Follicle, full, Patient 12, 17


title: Follicle, full, Patient 12, 12

value: secondary


title: Young subject serum treatment, replicate B, CT 34

value: Foreskin

value: Fibroblast


title: Pep3_30min_Replicate

value: OsPep3 peptide treatment


title: Follicle, full, Patient 12, 11


title: BrainCell_Enhancer-eHGT_381h_MouseID-615516_Cell-37


title: BrainCell_Enhancer-eHGT_381h_MouseID-615516_Cell-36


title: Young subject serum treatment, replicate A, CT 34


title: Follicle, full, Patient 12, 10


title: Pep3_30min


title: Follicle, full, Patient 12, 15


title: BrainCell_Enhancer-eHGT_373m_MouseID-616737_Cell-3


title: BrainCell_Enhancer-eHGT_381h_MouseID-615516_Cell-34


title: Pep3_2h


title: Young subject serum treatment, replicate A, CT 32


title: rlk1_KO_Replicate


title: Young subject serum treatment, replicate B, CT 32


title: rlk1_KO_Celldeath


title: Pep3_2h_Replicate


title: Young subject serum treatment, replicate B, CT 36


title: Follicle, full, Patient 11, 9


title: Follicle, full, Patient 11, 8


title: BrainCell_Enhancer-eHGT_381h_MouseID-615516_Cell-32


title: Follicle, full, Patient 11, 7


title: Young subject serum treatment, replicate B, CT 30


title: Pep3_0min_Replicate


title: Follicle, full, Patient 11, 5


title: Young subject serum treatment, replicate A, CT 30


title: Follicle, full, Patient 12, 14


title: Young subject serum treatment, replicate A, CT 28


title: BrainCell_Enhancer-eHGT_381h_MouseID-615516_Cell-33


title: Pep2_30min_Replicate

value: OsPep2 peptide treatment


title: Pep3_0min


title: BrainCell_Enhancer-eHGT_381h_MouseID-615516_Cell-31


title: BrainCell_Enhancer-eHGT_381h_MouseID-615516_Cell-30


title: Pep2_30min


title: Follicle, full, Patient 11, 3


title: Young subject serum treatment, replicate A, CT 26


title: Follicle, full, Patient 11, 4


title: BrainCell_Enhancer-eHGT_381h_MouseID-615516_Cell-28


title: Pep2_2h_Replicate


title: Follicle, full, Patient 11, 2


title: BrainCell_Enhancer-eHGT_381h_MouseID-615516_Cell-35


title: Young subject serum treatment, replicate B, CT 26


title: Pep2_0min_Replicate


title: BrainCell_Enhancer-eHGT_381h_MouseID-615516_Cell-27


title: Pep2_2h


title: Young subject serum treatment, replicate B, CT 24


title: Follicle, full, Patient 11, 1


title: Follicle, full, Patient 11, 6


title: Young subject serum treatment, replicate B, CT 28


title: Pep2_0min


title: Young subject serum treatment, replicate A, CT 24


title: BrainCell_Enhancer-eHGT_381h_MouseID-615516_Cell-25


title: Young subject serum treatment, replicate A, CT 22


title: BrainCell_Enhancer-eHGT_381h_MouseID-615516_Cell-29


title: Follicle, full, Patient 11, 15


title: Follicle, full, Patient 11, 14


title: Mock_30min_Replicate

value: Mock for peptide (PEPs) treatment


title: Mock_30min


title: Young subject serum treatment, replicate B, CT 20


title: Mock_2h_Replicate


title: BrainCell_Enhancer-eHGT_381h_MouseID-615516_Cell-23


title: Follicle, full, Patient 11, 13

value: intermediate


title: BrainCell_Enhancer-eHGT_381h_MouseID-615516_Cell-22


title: Young subject serum treatment, replicate A, CT 20


title: Young subject serum treatment, replicate B, CT 22


title: Follicle, full, Patient 11, 12


title: Mock_2h

value: Genotype:Rice, Indica, Pusa Basmati 1 (PB1)


title: BrainCell_Enhancer-eHGT_381h_MouseID-615516_Cell-21


title: Young subject serum treatment, replicate A, CT 18


title: Follicle, full, Patient 11, 11


title: BrainCell_Enhancer-eHGT_381h_MouseID-615516_Cell-20


title: Mock_0min

value: Wild type (PB1)


title: Young subject serum treatment, replicate B, CT 18


title: Mock_0min_Replicate


title: Follicle, full, Patient 11, 10


title: Young subject serum treatment, replicate B, CT 16


title: Follicle, full, Patient 11, 16


title: BrainCell_Enhancer-eHGT_381h_MouseID-615516_Cell-26


title: BrainCell_Enhancer-eHGT_381h_MouseID-615516_Cell-24


title: BrainCell_Enhancer-eHGT_381h_MouseID-615516_Cell-19


title: Follicle, full, Patient 10, 6

value: primordial


title: Young subject serum treatment, replicate A, CT 16

value: Young serum


title: Young subject serum treatment, replicate B, CT 14

value: Young subject


title: BrainCell_Enhancer-eHGT_381h_MouseID-615516_Cell-18


title: Young subject serum treatment, replicate A, CT 14


title: BrainCell_Enhancer-eHGT_381h_MouseID-615516_Cell-17


title: AGS cells, WT_3

city: Fuzhou

first: Songyi

last: Liu

address: No. 20 Chazhong Road

institute: the First Affiliated Hospital, Fujian Medical University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Hisat2 v2.0.5 was used for alignment to reference genome
Read count extraction and normalization were performed using featureCounts v1.5.0-p3
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Gastric cancer tissue

growth_protocol: Human gastric cancer, AGS cells were maintained in DMEM/F12 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
RNA was isolated using TRI Reagent (Invitrogen). Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Gastric cancer tissue

value: AGS

value: Gastric cancer cells

value: WT


title: AGS cells, WT_1


title: AGS cells, siSRSF_3

value: SRSF2 knockdown


title: AGS cells, WT_2


title: Treated for SCH772984 until resistant, replicate 2

city: Durham

first: Charles

middle: A

last: Gersbach

state: North Carolina

address: 101 science drive rm 2323

institute: Duke University

description: genomic DNA bound to H3K27 from MIA PaCa-2 cells resistant to ERK inhibition, replicate 2

data_processing:
Sequences for TruSeq Illumina adapters were removed from the raw reads using Trimmomatic v0.32 (Bolger et al., 2014).
Single-end reads were mapped using Bowtie (v1.0.0 PMID: 19261174) against hg38 genome with flags -v 2 -X 2000 --best --strata -m 1.
Duplicates were removed using Picard MarkDuplicates v1.130
Low mappability or blacklisted regions identified by the ENCODE project (Consortium, 2012) were filtered out from the final BAM files
Using the sequenced input controls, binding regions were identified using the callpeak function in MACS2 v2.1.0.20151222 (Zhang et al., 2008).
Signal files were generated with deeptools bamCoverage (v3.0.1 PMID:24799436) ignoring duplicates, extending reads 200bp and converting the read counts to RPKMs.
Assembly: GRCh38
Supplementary files format and content: BED6+4 files containing peak locations together with peak summit, p-value, and q-value (.narrowPeak files) called peaks were generated using MACS2 narrowPeak.
Supplementary files format and content: Counts per Million (CPM) input control subtracted signal files (bigWig files)

source_name: pancreatic

growth_protocol: MIA PaCa-2 cells were grown in DMEM/F12, 10% FBS, and 1% penicillin/streptomycin.  Cells were authenticated using Promega PowerPlex 18D kit or were purchased within 6 months from Duke CCF.

extract_protocol:
Cells were cross-linked using 1% formaldehyde followed by 2.5M glycine and washed with ice-cold PBS.  Cross-linked cells were then scraped in RIPA buffer and snap-frozen.  Extracts were resuspended in RIPA buffer (20 mM Tris-HCl [pH 8], 500 mM NaCl, 1 mM EDTA, 1% Triton X-100 and 0.1% SDS) and the protease inhibitor cocktail ((1mM DTT, and the protease inhibitor cocktail 0.25 mM phenylmethylsulfonyl fluoride (PMSF), 1 mM sodium metabisulfite, 0.012 TIU/mL aprotinin, 1 mM benzamidine and 1 mM dithiothreitol (DTT)). Chromatin was sheared at 4°C in a BioRuptor using the high setting alternating between 30 seconds on and 30 seconds off cycles for a total of 10 minutes.  25mL of Protein A Dynabeads beads (Invitrogen, #10001D) was used per 100µg chromatin (~15 million nuclei). Beads were incubated in blocking solution (PBS, 0.5% BSA) then 6 mg of H3K27ac antibody (Active Motif: 39133) was conjugated to beads in blocking solution, nutating at 4oC for 4 hours. Conjugated beads were washed 1x block solution and 1x IP buffer (15 mM Tris-HCl [pH 8], 150 mM NaCl, 1 mM EDTA, 1% Triton X-100 and the protease inhibitor cocktail). Sheared chromatin was added (100µg chromatin (~15 million nuclei)) to conjugated beads in IP buffer and then nutating at 4oC for at least 12 hours. Bound chromatin was washed 3x with IP buffer, 3x with RIPA buffer (20 mM Tris-HCl [pH 8], 500 mM NaCl, 1 mM EDTA, 1% Triton X-100 and 0.1% SDS), 2x with LiCl buffer (20 mM Tris-HCl [pH 8], 500 mM LiCl, 1 mM EDTA, 1% sodium deoxycholate and 1% NP-40) and 2x with TE Salt buffer (10 mM Tris-HCl [pH 8], 50 mM NaCl, 1 mM EDTA). Sample was eluted from beads with PK buffer (10 mM Tris-HCl [pH 8], 1 mM EDTA and 1% SDS) containing 100 mg of Proteinase K (New England BioLabs: P81075) incubated at 50oC, with shaking, for 1-hour then at 65oC for 1-hour. Eluted DNA was transferred to a new tube and incubated at 65ºC for 12 hours to reverse crosslinking. DNA was then purified by phenol chloroform extraction using Light-5PRIME Phase Lock Tubes (Quanta Bio: 2302820) based on the manufacturer’s instructions.
ChIP-seq libraries were prepared using the KAPA Hyper Prep Kit (KAPA Biosystems: KK8502)

treatment_protocol: MIA PaCa-2 cells were grown in 15cm2 plates in either ERK-inhibitor (SCH772984 1 µM) or DMSO (1:1,000) in biologic replicate.  For the one-week samples, 560,000 and 110,000 cells were plated in the SCH772984 and DMSO conditions, respectively, to achieve 70% confluence at one week.  For the terminally resistant cells, cells were plated at a density of 250,000 cells in 10 cm plates.  The following day, 1 µM SCH772984 was added. Cells were then split at weekly time points and replated at a density of 50,000.  Lines were generally considered resistant when the growth rate exceeded 50% of that of its parental, treatment-naïve derivative, and terminal resistance was defined once there was no interval increase in growth rate over a two-week period.  Then this cell population was plated at 110,000 cells per 15cm2 plate in biologic replicate and treated for one additional week with SCH772984.

value: pancreatic

value: MIA PaCa-2

value: epithelial cells

value: homozygous G12C KRAS-mutant

tag: antibody

value: H3K27ac (antibody from Active Motif:39133)


title: Young subject serum treatment, replicate B, CT 12

value: Foreskin

value: Fibroblast


title: AGS cells, siSRSF_2


title: Treated for SCH772984 until resistant, replicate 2 input

description: genomic input DNA  from MIA PaCa-2 cells resistant to ERK inhibition, replicate 2 input


title: Young subject serum treatment, replicate A, CT 12


title: BrainCell_Enhancer-eHGT_381h_MouseID-615516_Cell-16

value: MB/HB


title: AGS cells, siSRSF_1


title: BrainCell_Enhancer-eHGT_381h_MouseID-615516_Cell-15


title: Treated for SCH772984 until resistant, replicate 1 input

description: genomic input DNA from MIA PaCa-2 cells resistant to ERK inhibition, replicate 1  input


title: Treated for SCH772984 until resistant, replicate 1

description: genomic DNA bound to H3K27 from MIA PaCa-2 cells resistant to ERK inhibition, replicate 1


title: ko-rep-2+nac

city: tianjin

first: nannan

last: zhao

state: --- Select a state ---

address: nankai

institute: nankai university

data_processing:
The quality control with the software FastQC v0.11.9
Clean reads were aligned to the human hg38 genome with the hisat2 software
The normalized counts were calculated with featurecounts
Assembly: hg38
Supplementary files format and content: counts

source_name: ES

extract_protocol:
cells were flash frozen on dry ice, and RNA was harvested using RNA kit(QIAGEN,74134). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ES

value: human ES cells

value: UBQLN1 KO

value: NAC


title: Old subject D serum treatment, CT 58

value: Old serum

value: Old subject D


title: BrainCell_Enhancer-eHGT_381h_MouseID-615516_Cell-13


title: Treated with %0.01 DMSO, replicate 2 input

description: genomic input DNA from MIA PaCa-2 cells treated with %0.01 DMSO, replicate 2 input


title: BrainCell_Enhancer-eHGT_381h_MouseID-615516_Cell-12


title: Old subject C serum treatment, CT 58

value: Old subject C


title: ko-rep-1+nac


title: Follicle, full, Patient 10, 3

value: ovary

value: intermediate


title: Old subject B serum treatment, CT 58

value: Old subject B


title: wt-rep-2+nac

value: WT


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-4

value: VISp


title: Treated with %0.01 DMSO, replicate 1 input

description: genomic input DNA from MIA PaCa-2 cells treated with %0.01 DMSO, replicate 1 input

value: pancreatic

value: MIA PaCa-2

value: epithelial cells

value: homozygous G12C KRAS-mutant


title: Old subject A serum treatment, CT 58

value: Foreskin

value: Fibroblast

value: Old subject A


title: wt-rep-1+nac

value: ES

value: human ES cells


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-3


title: Treated with %0.01 DMSO, replicate 1

description: genomic DNA bound to H3K27 from MIA PaCa-2 cells treated with %0.01 DMSO, replicate 1

value: H3K27ac (antibody from Active Motif:39133)


title: BrainCell_Enhancer-eHGT_381h_MouseID-615516_Cell-14

value: MB/HB


title: Old subject D serum treatment, CT 56

value: Old serum

value: Old subject D


title: Treated for SCH772984 for 1 week, replicate 2 input

description: genomic input DNA from MIA PaCa-2 cells treated with ERK inhibitor for 1 week, replicate 2 input


title: WT-rep-2-low_O2


title: ko-rep-2-low_O2

value: UBQLN1 KO


title: BrainCell_Enhancer-eHGT_381h_MouseID-615516_Cell-9


title: Treated for SCH772984 for 1 week, replicate 1 input

description: genomic input DNA from MIA PaCa-2 cells treated with ERK inhibitor for 1 week, replicate 1 input


title: BrainCell_Enhancer-eHGT_381h_MouseID-615516_Cell-10


title: Treated for SCH772984 for 1 week, replicate 2

description: genomic DNA bound to H3K27 from MIA PaCa-2 cells treated with ERK inhibitor for 1 week, replicate 2


title: Old subject C serum treatment, CT 56

value: Old subject C


title: ko-rep-1-low_O2


title: Old subject A serum treatment, CT 56


title: Old subject B serum treatment, CT 56

value: Old subject B


title: BrainCell_Enhancer-eHGT_381h_MouseID-615516_Cell-11


title: WT-rep-1-low_O2

value: WT


title: Treated for SCH772984 for 1 week, replicate 1

description: genomic DNA bound to H3K27 from MIA PaCa-2 cells treated with ERK inhibitor for 1 week, replicate 1

value: pancreatic


title: Old subject D serum treatment, CT 54


title: Treated with %0.01 DMSO, replicate 2

description: genomic DNA bound to H3K27 from MIA PaCa-2 cells treated with %0.01 DMSO, replicate 2

value: MIA PaCa-2


title: ko-rep-2-Normal_O2

value: non


title: BrainCell_Enhancer-eHGT_381h_MouseID-615516_Cell-7


title: B cells, Control-KO, 3

city: Boston

first: Rui

last: Guo

state: Massachusetts

address: 150 Harrison Ave.

department: School of Medicine

institute: Tufts University

description:
Control_KO_3
BCAT1_KO_read.xlsx

data_processing:
Adaptor-trimmed Illumina reads for each individual library were mapped back to the human GRCh37.83 transcriptome assembly using STAR v2.5.2b
featureCounts v1.5.1 was used to estimate the number of reads mapped to each contig. Only transcripts with at least 5 cumulative mapping counts were used in this analysis.
DESeq2 v1.14.1 was used to evaluate gene differential expression (DE)
Each DE analysis was composed of a pairwise comparison between experimental group and the control group. Differentially expressed genes were identified after a correction for false discovery rate (FDR 0.05).
Assembly: GRCh37.83
Supplementary files format and content: Separate Excel speadsheets are provided for normalized counts of genes

source_name: Human naïve B cells

growth_protocol: Human primary B cells were cultured in GIBCO RPMI 1650 medium (Life Technologies) with 10% FBS and 10 mM HEPES in a humidified chamber at 37 degrees Celcius with 5% CO2.

extract_protocol:
Total RNAs were subsequently isolated using PureLink RNA Mini Kit (Thermo Fisher Scientific) following the manufacturer’s manual. An in-column DNA digestion step was included to remove any residual genomic DNA contamination
To construct RNA-seq libraries, 500 ng total RNA was used for polyA mRNA-selection using NEBNext Poly(A) mRNA Magnetic Isolation Module (#E7490, New England Biolabs, Inc.  Ipswich, MA), followed by library construction via NEBNext Ultra RNA Library Prep Kit for Illumina (#E7530, New England Biolabs, Inc., Ipswich, MA).

treatment_protocol: Primary human B-cells were isolated by negative selection using RosetteSep Human B-cell Enrichment and EasySep Human B-cell enrichment kits (Stem Cell Technologies), according to the manufacturers’ protocols. B-cell purity was confirmed by FACS analysis of plasma membrane CD19 positivity. Cells were then cultured with RPMI 1640 with 10% FCS. 7×10^6 B-cells were used for each stimulation condition. Stimulants were added at the following concentrations: CD40L 50ng/ml (Enzo Life Sciences), CpG 0.5μM (IDT), IL4 (R&D systems) 20ng/ml and aIgM at 1ug/ml. Cells were treated in cultured in the absence of stimulation or stimulated by, CD40L only, CpG only, IL4 only, aIgM only, CD40L+CpG, CD40L+IL4, CpG+ aIgM, CD40L+ aIgM, and CD40L+ aIgM+IL4. Cells were treated for 24 hours. For each experiment, cells from 3 donors were isolated and treated separately. To create a RNP complex for knocking out BCAT1 in human primary-B-cells, a mixture of 2.2 μL crRNA, 2.2 μL tracrRNA, and 5.6 μL duplex buffer was heated to 95°C for 5 minutes and then cooled to room temperature. The crRNA-tracrRNA complex was then combined with 0.6 μL of caspase 9 to assemble the RNP complex, which was incubated for 20 minutes at room temperature. The RNP complex was mixed with washed human primary-B-cells suspended in buffer T, then electroporated using parameters of 1700V, 20ms width, and 1 pulse. Finally, the cells were added to prewarmed media. To enhance the knock-out efficiency, a 1:1 mixture of two BCAT1 crRNA-tracrRNA-Cas9 RNP complexes was electroporated simultaneously.

value: Primary B cells

value: electroporated with control crRNA/tracrRNA/Caspase9 RNP and stimulated with anti-IgM IgG and CpG

value: control KO


title: BrainCell_Enhancer-eHGT_385m_MouseID-615515_Cell-32

value: VISp


title: ko-rep-1-Normal_O2

value: ES


title: Old subject C serum treatment, CT 54

value: Foreskin

value: Fibroblast


title: BrainCell_Enhancer-eHGT_381h_MouseID-615516_Cell-8

value: MB/HB


title: Old subject B serum treatment, CT 54

value: Old serum


title: Old subject A serum treatment, CT 54

value: Old subject A


title: WT-rep-2-Normal_O2

value: human ES cells


title: WT-rep-1-Normal_O2


title: B cells, BCAT1-KO, 3

description:
BCAT1_KO_3
BCAT1_KO_read.xlsx

value: electroporated with BCAT1 crRNA/tracrRNA/Caspase9 RNP and stimulated with anti-IgM IgG and CpG

value: BCAT1 KO


title: BrainCell_Enhancer-eHGT_385m_MouseID-615515_Cell-30


title: BrainCell_Enhancer-eHGT_385m_MouseID-615515_Cell-29


title: Old subject D serum treatment, CT 52

value: Old subject D


title: Old subject C serum treatment, CT 52

value: Old subject C


title: B cells, BCAT1-KO, 2

description:
BCAT1_KO_2
BCAT1_KO_read.xlsx


title: Old subject B serum treatment, CT 52

value: Old subject B


title: B cells, BCAT1-KO, 1

description:
BCAT1_KO_1
BCAT1_KO_read.xlsx


title: Modern human AHR, 100 nM kynurenic acid, 4h, biol rep 5

city: Leipzig

first: Svante

last: Paabo

address: Deutscher Platz 6

department: Department of Evolutionary Genetics

country: Germany

institute: Max-Planck-Institute for Evolutionary Anthropology

data_processing:
Illumina’s Bustard was used for base calling and adapters were trimmed using leeHom (Renaud et al. 2014)
Reads were aligned to the human reference (GRCh37.87) using tophat2 (v2.0.14) using default parameters (Kim et al. 2013)
Aligned reads were assigned to protein coding genes using the featureCounts software (Liao et al. 2014)
Assembly: GRCh37.87
Supplementary files format and content: csv file includes raw read count values for each sample, ENSEMBL IDs, HUGO gene names and gene length

growth_protocol: Cells were grown on Matrigel matrix (Corning, 35248) coated dishes in mTeSR1 medium (StemCell Technologies, 85850) supplemented with MycoZap Plus-CL (Lonza, VZA-2012)

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 300 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Collibri Stranded RNA Library Prep Kit for Illumina Systems with Human/Mouse/Rat rRNA Depletion Kit (Thermo Fisher Scientific) following manufacturer's protocols.

treatment_protocol: Cells were treated with the indicated ligand concentration (in 0.05% DMSO) or 0.05% DMSO for four 4 h prior to cell lysis

value: embryonic stem cells

value: modern human AHR (V381)

value: 100 nM kynurenic acid


title: Modern human AHR, 100 nM kynurenic acid, 4h, biol rep 6


title: BrainCell_Enhancer-eHGT_385m_MouseID-615515_Cell-27

extract_protocol:
Single SYFP2-expressing cells from mouse brain were flow sorted into individual tubes in SMARTerv4 collection buffer.
SMARTerv4


title: BrainCell_Enhancer-eHGT_385m_MouseID-615515_Cell-28


title: B cells, CD40L_IgM_IL4_3

description: BCAT1_10 condition RNAseq_read.xlsx

value: Primary B cells

value: stimulated by CD40L,anti-IgM IgG, and IL-4


title: Old subject A serum treatment, CT 52


title: Modern human AHR, 100 nM kynurenic acid, 4h, biol rep 3


title: B cells, Control-KO, 2

description:
Control_KO_2
BCAT1_KO_read.xlsx

value: electroporated with control crRNA/tracrRNA/Caspase9 RNP and stimulated with anti-IgM IgG and CpG

value: control KO


title: BrainCell_Enhancer-eHGT_385m_MouseID-615515_Cell-26

value: VISp


title: Old subject D serum treatment, CT 50

value: Foreskin

value: Fibroblast


title: Modern human AHR, 100 nM kynurenic acid, 4h, biol rep 2


title: B cells, CD40L_IgM_IL4_2

description: BCAT1_10 condition RNAseq_read.xlsx


title: BrainCell_Enhancer-eHGT_385m_MouseID-615515_Cell-31


title: BrainCell_Enhancer-eHGT_385m_MouseID-615515_Cell-25


title: B cells, CD40L_IgM_IL4_1

description: BCAT1_10 condition RNAseq_read.xlsx


title: Old subject C serum treatment, CT 50

value: Old serum


title: Modern human AHR, 100 nM kynurenic acid, 4h, biol rep 1


title: Old subject B serum treatment, CT 50


title: BrainCell_Enhancer-eHGT_385m_MouseID-615515_Cell-24


title: B cells, Control-KO, 1

description:
Control_KO_1
BCAT1_KO_read.xlsx


title: B cells, CD40L_CpG_3

description: BCAT1_10 condition RNAseq_read.xlsx

value: stimulated by CD40L and CpG


title: BrainCell_Enhancer-eHGT_385m_MouseID-615515_Cell-22


title: Modern human AHR, 10 nM indirubin, 4h, biol rep 5

value: 10 nM indirubin


title: B cells, CD40L_CpG_2

description: BCAT1_10 condition RNAseq_read.xlsx


title: BrainCell_Enhancer-eHGT_385m_MouseID-615515_Cell-23


title: Modern human AHR, 100 nM kynurenic acid, 4h, biol rep 4


title: Old subject D serum treatment, CT 48


title: Old subject A serum treatment, CT 50

value: Old subject A


title: BrainCell_Enhancer-eHGT_381h_MouseID-615516_Cell-6

value: MB/HB


title: Modern human AHR, 10 nM indirubin, 4h, biol rep 4


title: Modern human AHR, 10 nM indirubin, 4h, biol rep 3


title: B cells, IgM_CpG_2

description: BCAT1_10 condition RNAseq_read.xlsx

value: stimulated by anti-IgM IgG and CpG


title: BrainCell_Enhancer-eHGT_381h_MouseID-615516_Cell-5


title: B cells, IgM_CpG_3

description: BCAT1_10 condition RNAseq_read.xlsx


title: Old subject C serum treatment, CT 48

value: Old subject C


title: Old subject B serum treatment, CT 48

value: Old subject B


title: Modern human AHR, 10 nM indirubin, 4h, biol rep 2

value: embryonic stem cells

value: modern human AHR (V381)


title: B cells, IgM_CpG_1

description: BCAT1_10 condition RNAseq_read.xlsx

value: Primary B cells


title: BrainCell_Enhancer-eHGT_381h_MouseID-615516_Cell-4


title: BrainCell_Enhancer-eHGT_381h_MouseID-615516_Cell-3


title: Old subject A serum treatment, CT 48


title: B cells, CD40L_IL4_3

description: BCAT1_10 condition RNAseq_read.xlsx

value: stimulated by CD40L+IL-4


title: Modern human AHR, 10 nM indirubin, 4h, biol rep 1


title: Modern human AHR, 10 nM indirubin, 4h, biol rep 6


title: Old subject D serum treatment, CT 46

value: Old subject D


title: B cells, CD40L_CpG_1

description: BCAT1_10 condition RNAseq_read.xlsx


title: Modern human AHR, 0.05% DMSO, 4h, biol rep 6


title: Old subject C serum treatment, CT 46


title: B cells, CD40L_IL4_2

description: BCAT1_10 condition RNAseq_read.xlsx


title: BrainCell_Enhancer-eHGT_381h_MouseID-615516_Cell-2


title: Modern human AHR, 0.05% DMSO, 4h, biol rep 5


title: B cells, CD40L_IL4_1

description: BCAT1_10 condition RNAseq_read.xlsx


title: Old subject B serum treatment, CT 46


title: Modern human AHR, 0.05% DMSO, 4h, biol rep 4


title: Modern human AHR, 0.05% DMSO, 4h, biol rep 3


title: Old subject A serum treatment, CT 46


title: BrainCell_Enhancer-eHGT_374m_MouseID-614201_Cell-37


title: B cells, CD40L_IgM_2

description: BCAT1_10 condition RNAseq_read.xlsx

value: stimulated by CD40L and anti-IgM IgG


title: BrainCell_Enhancer-eHGT_381h_MouseID-615516_Cell-1


title: B cells, CD40L_IgM_3

description: BCAT1_10 condition RNAseq_read.xlsx


title: Old subject D serum treatment, CT 44


title: Modern human AHR, 0.05% DMSO, 4h, biol rep 2


title: Old subject C serum treatment, CT 44


title: B cells, CD40L_IgM_1

description: BCAT1_10 condition RNAseq_read.xlsx


title: BrainCell_Enhancer-eHGT_374m_MouseID-614201_Cell-35

value: VISp


title: Modern human AHR, 0.05% DMSO, 4h, biol rep 1


title: BrainCell_Enhancer-eHGT_374m_MouseID-614201_Cell-36


title: B cells, IL4_3

description: BCAT1_10 condition RNAseq_read.xlsx

value: stimulated by IL-4


title: Old subject B serum treatment, CT 44

value: Foreskin

value: Fibroblast


title: BrainCell_Enhancer-eHGT_374m_MouseID-614201_Cell-33


title: Modern human AHR, 5 µM CH-223191, 4h, biol rep 6


title: B cells, IL4_2

description: BCAT1_10 condition RNAseq_read.xlsx


title: BrainCell_Enhancer-eHGT_374m_MouseID-614201_Cell-34


title: BrainCell_Enhancer-eHGT_374m_MouseID-614201_Cell-32


title: B cells, IL4_1

description: BCAT1_10 condition RNAseq_read.xlsx


title: Old subject A serum treatment, CT 44

value: Old serum


title: Modern human AHR, 5 µM CH-223191, 4h, biol rep 5


title: Old subject D serum treatment, CT 42


title: Modern human AHR, 5 µM CH-223191, 4h, biol rep 4


title: BrainCell_Enhancer-eHGT_374m_MouseID-614201_Cell-31


title: Old subject C serum treatment, CT 42


title: Modern human AHR, 5 µM CH-223191, 4h, biol rep 3


title: Old subject B serum treatment, CT 42


title: BrainCell_Enhancer-eHGT_374m_MouseID-614201_Cell-29


title: Old subject A serum treatment, CT 42


title: Modern human AHR, 5 µM CH-223191, 4h, biol rep 1


title: B cells, CD40L_2

description: BCAT1_10 condition RNAseq_read.xlsx

value: stimulated by CD40L


title: B cells, CD40L_1

description: BCAT1_10 condition RNAseq_read.xlsx


title: Modern human AHR, 5 µM CH-223191, 4h, biol rep 2


title: BrainCell_Enhancer-eHGT_374m_MouseID-614201_Cell-28


title: B cells, CpG_2

description: BCAT1_10 condition RNAseq_read.xlsx

value: stimulated by CpG


title: Old subject C serum treatment, CT 40


title: BrainCell_Enhancer-eHGT_374m_MouseID-614201_Cell-27


title: B cells, CpG_3

description: BCAT1_10 condition RNAseq_read.xlsx


title: Modern human AHR, 50 nM benzo(a)pyrene, 4h, biol rep 6

value: 50 nM benzo(a)pyrene


title: B cells, CpG_1

description: BCAT1_10 condition RNAseq_read.xlsx


title: Old subject B serum treatment, CT 40


title: BrainCell_Enhancer-eHGT_374m_MouseID-614201_Cell-26


title: BrainCell_Enhancer-eHGT_374m_MouseID-614201_Cell-24


title: B cells, CD40L_3

description: BCAT1_10 condition RNAseq_read.xlsx


title: Modern human AHR, 50 nM benzo(a)pyrene, 4h, biol rep 3


title: Modern human AHR, 50 nM benzo(a)pyrene, 4h, biol rep 4


title: BrainCell_Enhancer-eHGT_374m_MouseID-614201_Cell-25


title: Old subject A serum treatment, CT 40

value: Old subject A


title: B cells, IgM_2

description: BCAT1_10 condition RNAseq_read.xlsx

value: stimulated by anti-IgM IgG


title: BrainCell_Enhancer-eHGT_374m_MouseID-614201_Cell-30


title: Modern human AHR, 50 nM benzo(a)pyrene, 4h, biol rep 2


title: BrainCell_Enhancer-eHGT_374m_MouseID-614201_Cell-23


title: Old subject D serum treatment, CT 40


title: Old subject C serum treatment, CT 38

value: Old subject C


title: B cells, IgM_1

description: BCAT1_10 condition RNAseq_read.xlsx


title: Modern human AHR, 50 nM benzo(a)pyrene, 4h, biol rep 1

value: embryonic stem cells


title: BrainCell_Enhancer-eHGT_374m_MouseID-614201_Cell-22


title: Modern human AHR, 50 nM benzo(a)pyrene, 4h, biol rep 5

value: modern human AHR (V381)


title: Old subject B serum treatment, CT 38

value: Old subject B


title: Ancestralized AHR, 100 nM kynurenic acid, 4h, biol rep 6

value: ancestralized AHR (A381)

value: 100 nM kynurenic acid


title: B cells, unstimulated_3

description: BCAT1_10 condition RNAseq_read.xlsx

value: Primary B cells

value: Mock stimulated


title: BrainCell_Enhancer-eHGT_374m_MouseID-614201_Cell-21

value: VISp


title: Old subject A serum treatment, CT 38

value: Foreskin


title: Ancestralized AHR, 100 nM kynurenic acid, 4h, biol rep 5


title: B cells, unstimulated_2

description: BCAT1_10 condition RNAseq_read.xlsx


title: B cells, unstimulated_1

description: BCAT1_10 condition RNAseq_read.xlsx


title: B cells, IgM_3

description: BCAT1_10 condition RNAseq_read.xlsx


title: Old subject D serum treatment, CT 36

value: Fibroblast

value: Old subject D


title: BrainCell_Enhancer-eHGT_380h_MouseID-614200_Cell-34


title: BrainCell_Enhancer-eHGT_374m_MouseID-614201_Cell-20


title: Ancestralized AHR, 100 nM kynurenic acid, 4h, biol rep 4


title: Old subject D serum treatment, CT 38

value: Old serum


title: Ancestralized AHR, 100 nM kynurenic acid, 4h, biol rep 3


title: Old subject C serum treatment, CT 36


title: EndoC-βH3 cells, Senescent cells, H3K9me3 4

city: Jerusalem

first: Milan

last: Patra

address: Hadassah Ein Kerem

department: Faculty of Medicine, Department of Developmental Biology and Cancer Research

institute: The Hebrew University of Jerusalem

description: processed data table contains bigwig files for each sample.

data_processing:
The library was demultiplexed using bcl2fastq program. The reads were aligned to human genome hg38 using Bowtie, and were sorted and indexed using Samtools.
Peak calling was done by using HOMER for H3K4me3 and SICER for H3K27me3, and H3K9me3. The differential binding of H3K4me3 was analyzed using DESeq2.
The bigwig files are generated using Deeptools.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: MINT(Multiplexed indexed T7 ChIP-seq)

growth_protocol: EndoC-βH3 cells are maintained in DMEM low glucose (1 g/L) supplemented with 2% fatty acid free BSA , 10 mM nicotinamide, 5.5 µg/mL  human transferrin, 6.7 ng/mL sodium selenite, 50 µM β-mercaptoethanol, 100 U/mL penicillin and 100 µg/mL streptomycin.

extract_protocol:
Genome wide chromatin profiles were generated using 500,000 cells per sample and MINT (Multiplexed indexed T7 ChIP-seq) v2 protocol.
Cells were lysed and digested with MNase separately to yield fragments of 1-5 nucleosomes. DNA fragment ends were ligated to adaptors having sample barcodes (#index 1). Barcoded DNA fragments from each sample were pooled and splited for separate ChIP reactions with antibodies.  After antibody pull down,  the purified DNA was linearly amplified and barcoded (#index 2, antibody brcode) to get the MINT-ChIP library. The library was sequenced by using Illumina NextSeq 500 instrument as paired-end.

treatment_protocol: Senescence induction of EndoC-βH3 cells was performed routinely by treatment with 1 mM 4-hydroxy tamoxifen (4-OHT) for 3 weeks.

value: H3K9me3 (Abcam, #ab8898)

value: pancreatic beta cells

value: WT

value: Senescence induction


title: Ancestralized AHR, 100 nM kynurenic acid, 4h, biol rep 2


title: Old subject B serum treatment, CT 36


title: BrainCell_Enhancer-eHGT_380h_MouseID-614200_Cell-32

data_processing:
Base-calling using standard Illumina software.
Alignment with STAR (https://github.com/alexdobin/STAR)
Transformed by counts per million.
Assembly: mm10
Supplementary files format and content: Processed data in counts per million (CPM) format.


title: EndoC-βH3 cells, Senescent cells, H3K9me3 2


title: Ancestralized AHR, 100 nM kynurenic acid, 4h, biol rep 1


title: EndoC-βH3 cells, Senescent cells, H3K9me3 1


title: BrainCell_Enhancer-eHGT_380h_MouseID-614200_Cell-31


title: Old subject D serum treatment, CT 34


title: Ancestralized AHR, 10 nM indirubin, 4h, biol rep 6

value: 10 nM indirubin


title: EndoC-βH3 cells, Non senescent cells, H3K9me3 4

value: control


title: Old subject C serum treatment, CT 34

value: Old subject C


title: BrainCell_Enhancer-eHGT_380h_MouseID-614200_Cell-30


title: EndoC-βH3 cells, Non senescent cells, H3K9me3 3


title: Old subject B serum treatment, CT 34

value: Old subject B


title: Ancestralized AHR, 10 nM indirubin, 4h, biol rep 5

value: embryonic stem cells

value: ancestralized AHR (A381)


title: BrainCell_Enhancer-eHGT_380h_MouseID-614200_Cell-28


title: BrainCell_Enhancer-eHGT_380h_MouseID-614200_Cell-29


title: Ancestralized AHR, 10 nM indirubin, 4h, biol rep 4


title: Old subject A serum treatment, CT 34

value: Old subject A


title: BrainCell_Enhancer-eHGT_380h_MouseID-614200_Cell-27


title: Old subject D serum treatment, CT 32


title: EndoC-βH3 cells, Non senescent cells, H3K9me3 1


title: EndoC-βH3 cells, Non senescent cells, H3K9me3 2


title: Ancestralized AHR, 10 nM indirubin, 4h, biol rep 2


title: Ancestralized AHR, 10 nM indirubin, 4h, biol rep 3


title: BrainCell_Enhancer-eHGT_380h_MouseID-614200_Cell-33


title: Old subject A serum treatment, CT 36


title: BrainCell_Enhancer-eHGT_380h_MouseID-614200_Cell-26


title: BrainCell_Enhancer-eHGT_380h_MouseID-614200_Cell-25


title: EndoC-βH3 cells, Senescent cells, H3K4me3 4

description:
processed data table contains bigwig files for each sample. The differential H3K4me3 binding was analyszed by using DESeq2.
H3K4me3_DESeq2.bed.gz

value: H3K4me3 (Abcam, #ab8580)


title: Ancestralized AHR, 10 nM indirubin, 4h, biol rep 1


title: Old subject C serum treatment, CT 32


title: Old subject B serum treatment, CT 32


title: BrainCell_Enhancer-eHGT_380h_MouseID-614200_Cell-24

value: VISp


title: Ancestralized AHR, 0.05% DMSO, 4h, biol rep 6


title: Old subject A serum treatment, CT 32

value: Foreskin


title: BrainCell_Enhancer-eHGT_380h_MouseID-614200_Cell-23


title: EndoC-βH3 cells, Senescent cells, H3K4me3 1


title: Young subject D serum treatment, CT 58

value: Fibroblast

value: Young serum

value: Young subject D


title: Ancestralized AHR, 0.05% DMSO, 4h, biol rep 4


title: Young subject C serum treatment, CT 58

value: Young subject C


title: EndoC-βH3 cells, Non senescent cells, H3K4me3 4

value: pancreatic beta cells


title: Ancestralized AHR, 0.05% DMSO, 4h, biol rep 2


title: BrainCell_Enhancer-eHGT_380h_MouseID-614200_Cell-21


title: EndoC-βH3 cells, Senescent cells, H3K4me3 3

value: WT


title: EndoC-βH3 cells, Non senescent cells, H3K4me3 2


title: EndoC-βH3 cells, Non senescent cells, H3K4me3 1


title: Ancestralized AHR, 5 µM CH-223191, 4h, biol rep 6


title: EndoC-βH3 cells, Non senescent cells, H3K4me3 3


title: BrainCell_Enhancer-eHGT_385m_MouseID-615515_Cell-21


title: Young subject B serum treatment, CT 58

value: Young subject B


title: BrainCell_Enhancer-eHGT_380h_MouseID-614200_Cell-20


title: Young subject C serum treatment, CT 56


title: BrainCell_Enhancer-eHGT_380h_MouseID-614200_Cell-19


title: Young subject D serum treatment, CT 56


title: Ancestralized AHR, 0.05% DMSO, 4h, biol rep 1


title: EndoC-βH3 cells, Senescent cells, H3K9me3 3

value: H3K9me3 (Abcam, #ab8898)

value: Senescence induction


title: Ancestralized AHR, 0.05% DMSO, 4h, biol rep 3


title: EndoC-βH3 cells, Senescent cells, H3K27me3 4


title: EndoC-βH3 cells, Senescent cells, H3K4me3 2


title: Young subject A serum treatment, CT 56

value: Young subject A


title: BrainCell_Enhancer-eHGT_385m_MouseID-615515_Cell-18


title: BrainCell_Enhancer-eHGT_385m_MouseID-615515_Cell-20


title: Ancestralized AHR, 0.05% DMSO, 4h, biol rep 5


title: EndoC-βH3 cells, Senescent cells, H3K27me3 3


title: EndoC-βH3 cells, Senescent cells, H3K27me3 1


title: Young subject D serum treatment, CT 54


title: BrainCell_Enhancer-eHGT_380h_MouseID-614200_Cell-22


title: Young subject B serum treatment, CT 56


title: EndoC-βH3 cells, Non senescent cells, H3K27me3 4

value: control


title: Ancestralized AHR, 5 µM CH-223191, 4h, biol rep 4

value: embryonic stem cells


title: BrainCell_Enhancer-eHGT_385m_MouseID-615515_Cell-19


title: BrainCell_Enhancer-eHGT_385m_MouseID-615515_Cell-15


title: Ancestralized AHR, 5 µM CH-223191, 4h, biol rep 1

value: ancestralized AHR (A381)


title: Young subject C serum treatment, CT 54


title: EndoC-βH3 cells, Non senescent cells, H3K27me3 3


title: EndoC-βH3 cells, Senescent cells, H3K27me3 2


title: EndoC-βH3 cells, Non senescent cells, H3K27me3 2


title: Young subject A serum treatment, CT 58


title: BrainCell_Enhancer-eHGT_385m_MouseID-615515_Cell-17


title: BrainCell_Enhancer-eHGT_385m_MouseID-615515_Cell-16


title: Ancestralized AHR, 50 nM benzo(a)pyrene, 4h, biol rep 6

value: 50 nM benzo(a)pyrene


title: BrainCell_Enhancer-eHGT_385m_MouseID-615515_Cell-14


title: Ancestralized AHR, 5 µM CH-223191, 4h, biol rep 5


title: Young subject B serum treatment, CT 54


title: Ancestralized AHR, 5 µM CH-223191, 4h, biol rep 2


title: Ancestralized AHR, 5 µM CH-223191, 4h, biol rep 3


title: Young subject C serum treatment, CT 52


title: Young subject A serum treatment, CT 54


title: Ancestralized AHR, 50 nM benzo(a)pyrene, 4h, biol rep 2


title: Young subject B serum treatment, CT 52


title: EndoC-βH3 cells, Senescent cells, Input of Rb 2

data_processing:
The library was demultiplexed using bcl2fastq program. The reads were aligned to human genome hg38 using Bowtie, and were sorted and indexed using Samtools.
Peak calling was done by using MACS2 for CTCF, Rb and HOMER for H3K27ac, H3K4me1, respectively. The differential binding of H3K27ac, and CTCF between non-senescent and senescent cells were analyzed using DESeq2.
The bigwig files are generated using Deeptools.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Five million cells per sample were fixed with 1% formaldehyde, followed by quenching and cell lysis. Chromatin was sonicated using diagenode bioruptor, calibrated to yeild 200-700 bp framents.
ChIP-seq libraries were generated using the KAPA Hyper Prep kit (Roche).


title: EndoC-βH3 cells, Non senescent cells, H3K27me3 1


title: BrainCell_Enhancer-eHGT_385m_MouseID-615515_Cell-11


title: Ancestralized AHR, 50 nM benzo(a)pyrene, 4h, biol rep 4


title: Ancestralized AHR, 50 nM benzo(a)pyrene, 4h, biol rep 5


title: BrainCell_Enhancer-eHGT_385m_MouseID-615515_Cell-12


title: EndoC-βH3 cells, Non senescent cells, Input of Rb 1


title: EndoC-βH3 cells, Senescent cells, Input of Rb 1


title: Young subject D serum treatment, CT 52


title: EndoC-βH3 cells, Senescent cells, Rb 2

description:
processed data table contains bigwig files for each sample.
Rb_Sen_specific.bed.gz


title: Young subject A serum treatment, CT 52


title: Young subject C serum treatment, CT 50


title: Ancestralized AHR, 50 nM benzo(a)pyrene, 4h, biol rep 1


title: EndoC-βH3 cells, Senescent cells B3

description: processed data table contains normalized expression and DESeq2 output

data_processing:
The raw files were filterd and trimmed using Cutadapt. Reads were aligned to human genome (HSA GRCh38) and counted using Salmon v0.13.1.
DESeq2  R package was used to get differentially expressed genes between Non-senescence and Senescent beta cells
Assembly: GRh38

extract_protocol:
Total RNA was extracted and isolated using TRI reagent (Sigma) and RNA isolation kit (Zymo Research).
Libraries for expression profile were prepared using standard CEL-Seq protocol.


title: BrainCell_Enhancer-eHGT_385m_MouseID-615515_Cell-10


title: EndoC-βH3 cells, Senescent cells B4


title: EndoC-βH3 cells, Non senescent cells, Input of Rb 2


title: BrainCell_Enhancer-eHGT_385m_MouseID-615515_Cell-13


title: BrainCell_Enhancer-eHGT_385m_MouseID-615515_Cell-9


title: EndoC-βH3 cells, Senescent cells, Rb 1


title: BrainCell_Enhancer-eHGT_385m_MouseID-615515_Cell-8


title: Young subject A serum treatment, CT 50


title: BrainCell_Enhancer-eHGT_385m_MouseID-615515_Cell-7


title: Young subject B serum treatment, CT 50


title: EndoC-βH3 cells, Senescent cells B2


title: Ancestralized AHR, 50 nM benzo(a)pyrene, 4h, biol rep 3


title: BrainCell_Enhancer-eHGT_385m_MouseID-615515_Cell-5


title: EndoC-βH3 cells, Non senescent cells, Rb 2


title: EndoC-βH3 cells, Senescent cells B1


title: EndoC-βH3 cells, Non senescent cells, Rb 1


title: Young subject D serum treatment, CT 50


title: BrainCell_Enhancer-eHGT_385m_MouseID-615515_Cell-6


title: Young subject D serum treatment, CT 48


title: EndoC-βH3 cells, Senescent cells A2


title: BrainCell_Enhancer-eHGT_385m_MouseID-615515_Cell-4


title: Young subject C serum treatment, CT 48


title: EndoC-βH3 cells, Senescent cells, Input of CTCF 3


title: Young subject A serum treatment, CT 48


title: EndoC-βH3 cells, Senescent cells A1


title: EndoC-βH3 cells, Non senescent cells B3


title: Young subject B serum treatment, CT 48


title: EndoC-βH3 cells, Senescent cells, Input of CTCF 2


title: BrainCell_Enhancer-eHGT_374m_MouseID-614201_Cell-19


title: EndoC-βH3 cells, Non senescent cells B4


title: BrainCell_Enhancer-eHGT_385m_MouseID-615515_Cell-3


title: EndoC-βH3 cells, Senescent cells, Input of CTCF 1


title: BrainCell_Enhancer-eHGT_385m_MouseID-615515_Cell-2


title: EndoC-βH3 cells, Non senescent cells B2


title: Young subject C serum treatment, CT 46


title: EndoC-βH3 cells, Non senescent cells B1


title: Young subject D serum treatment, CT 46


title: Young subject B serum treatment, CT 46


title: EndoC-βH3 cells, Non senescent cells, Input of CTCF 1


title: BrainCell_Enhancer-eHGT_374m_MouseID-614201_Cell-18


title: EndoC-βH3 cells, Senescent cells, CTCF 3

description:
processed data table contains bigwig files for each sample. Differential CTCF binding by usin DESeq2 is given.
CTCF_DESeq2.bed.gz


title: EndoC-βH3 cells, Non senescent cells A2


title: BrainCell_Enhancer-eHGT_374m_MouseID-614201_Cell-16


title: Young subject A serum treatment, CT 46


title: EndoC-βH3 cells, Non senescent cells A1


title: Young subject D serum treatment, CT 44