title: HCT116 FOXD2-FLAG rep1

city: Seoul

first: Tae-Young

last: Roh

address: 52 Ewhayeodae-gil, Seodaemun-gu

department: Life Sciences

country: South Korea

institute: Ewha Womans University

description: ATCC (CCL-247)

data_processing:
cutadapt-3.4 was used to detect and remove Illumina adapter sequence.
Bowtie2-2.3.4.1 aligned sequences to the Homo sapiens genome (UCSC hg38).
Picard tools removed duplicates with parameters "VALIDATION_STRINGENCY=LENIENT".
MACS2-2.2.7.1 was used for peak calling with parameters "--nomodel --shift -100 --extsize 200" and q-value < 0.01.
Genome_build: hg38
Supplementary_files_format_and_content: narrowPeak files were generated using MACS2; bigWig files were generated using genomeCoverageBed and bedGraphToBigWig.

source_name: Large intestine; Colon

growth_protocol: DMEM high glucose + 10% FBS + 100 units/ml penicillin + 100 μg/ml  streptomycin  with 5 μg/ml Puromycin selection

extract_protocol:
Cultured cells were collected by 0.25% Trypsin-EDTA (Gibco, 25200), then washed with DPBS.
Crosslinked 6.0 or 10.0 × 106 HCT116 cells for 7 min at 37 °C with 1% formaldehyde. We perforemd FOXD2-flag or 6xHis ChIP with sonicated chromatin in RIPA buffer (20 mM Tris-Cl pH 8.0, 2 mM EDTA, 50 mM NaCl, 1% NP-40, 0.01% SDS, and 0.5% sodium deoxycholate, 1mM PMSF and 1X protease inhibitor cocktail) with 4μg of antibody; MLL4/KMT2D antibody (Santa crz, sc-293217) or Anti-6X His tag® antibody [HIS.H8] (Abcam, ab18184) or Monoclonal ANTI-FLAG® M2 antibody (Sigma-Aldrich, F1804). For histone ChIP using MNase without crosslinking method, we resuspended 1.0 x 106 HCT116 cells in 50ul of nuclei isolation buffer (Sigma-Aldrich, NUC101) and incubated on ice for 10 min. We then proceeded to MNase digestion with final concentration 2 units/μl (NEB, M0247), pre-clearing and immunoprecipitated chromatin in ChIP buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 150 mM NaCl, 0.1% Triton X-100, 1x Protease inhibitor cocktail, and 1 mM PMSF) with 2μg of antibody; H3K4me3 (Abcam, ab8580) or H3K4me1 (Abcam, ab8895) or H3K27ac (Abcam, ab4729).

treatment_protocol: For stable cell lines, we treated pSin empty and pSin. FOXD2 full-length CDS lentivirus onto HCT116 cells. Transduced stable cells were selected by puromycin (5ug/mL) in culture medium.

value: Large intestine; Colon

tag: disease state

value: Carcinoma; Colorectal

tag: chip antibody

value: FLAG M2 (Sigma-Aldrich, F1804)


title: HCT116 6xHis/FLAG Input

status: Public on Apr 20 2023

type: SRA

state: --- Select One ---

description: ATCC (CCL-247)

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: tissue

tag: treatment


title: 6_3_gWAT

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

country: USA

institute: UCLA

description:
gWAT.counts.txt
gWAT.TPM.txt

library_source: transcriptomic

data_processing:
Quality inspection of raw RNA-Seq reads was performed with FastQC v0.11.9.
Counts and TPM values were obtained using kallisto v0.45 against the Ensembl mouse transcriptome (v97)
Assembly: mm10
Supplementary files format and content: tab-delimited files contain counts and TPM values

molecule: polyA RNA

organism: Mus musculus

source_name: gonadal white adipose tissue

extract_protocol:
Whole quadriceps, gonadal white adipose tissue, heart, brown adipose tissue, and a portion of  the liver were pulverized at the temperature of liquid nitrogen. Tissue was homogenized in Trizol  (Invitrogen, Carlsbad, CA, USA), RNA was isolated using the RNeasy Isolation Kit (Qiagen, Hilden,  Germany), and RNA concentration and quality were assessed (RIN > 7.0 used in downstream  applications)
Libraries were prepared using KAPA mRNA HyperPrep Kits and KAPA Dual Index Adapters (Roche, Basel, Switzerland) per manufacturer’s instructions. A total of 800-1000 ng of RNA was used for library preparation with settings 200-300 bp and 12 PCR cycles. The resultant libraries were tested for quality.

value: gonadal white adipose tissue

tag: Sex

value: female

tag: strain

value: BALB/cJ

tag: exercise group

value: Exercised


title: HCT116 FOXD2-FLAG rep2

description: ATCC (CCL-247)


title: Mm_LPBN_05-4X-1

city: Boston

first: Stefano

last: Nardone

state: MASSACHUSETTS

address: 3,blackfan circle

department: Endocrinology

institute: Beth Israel Deaconess Medical Center

description: snRNA-seq (DroNc-seq)

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads were demultiplexed to FASTQ format files using bcl2fastq (Illumina; version 2.20.0). Digital expression matrices (DGE) were generated using the Drop-Seq tools pipeline (https://github.com/broadinstitute/Drop-seq, version 2.4.0) as follows. Cell and UMI barcodes were extracted from read 1 and tagged onto read 2 --- barcodes with any base quality score <10 were filtered out. Subsequently, reads were trimmed at the 5′ end to remove any TSO sequence and at the 3′ end to remove poly(A) tails and/or (reverse complemented) barcodes and adapters. Tagged and trimmed reads were aligned with STAR (version 2.7.3) against the GRCm38 genome assembly using the GENCODE M20 primary assembly genomic annotation, pre-filtered to remove pseudogenes. Gene counts were obtained on a per-barcode basis by summarizing the unique read alignments across exons and introns, collapsing UMI barcodes at hamming distance 1.
Assembly: GRCm38 - mm10
Supplementary files format and content: Digital expression matrices (DGE)

source_name: dorsal pontine tegmentum

extract_protocol:
5-6 bilateral tissue dissections were placed in a dounce homogenizer with 1 mL cold (4C°) Lysis Buffer containing 10 mM trisHCl pH 8 (Sigma-Aldrich), 250 mM Sucrose (Sigma-Aldrich), 25 mM KCl, 5mM MgCl2 (Sigma-Aldrich), 0.1% Triton x100 (Sigma-Aldrich), 0.5% RNasin Plus RNase Inhibitor (Promega), 0.1 mM Dithiothreitol (DTT) (Sigma-Aldrich) in UltraPure™ DNase/RNase-Free Distilled Water (Thermo Fisher Scientific). After douncing for 20 times, the solution was filtered through a sterile 20 µm Cell Strainer (pluriSelect), collected in 1.5 mL DNA LoBind® Tubes (Eppendorf), and centrifuged for 10 min at 900 g (rcf) at 4 C. The "slow sedimenting" component (debris and membranes) was aspirated and discarded while the "fast sedimenting" component (nuclear fraction) was gently resuspended in a 1 mL of Working Solution containing 1X pH 7.4 RNase free PBS (Thermo Fisher Scientific), 0.01% Albumin Bovine Serum (BSA) (Sigma-Aldrich), 0.5% RNasin Plus RNase inhibitor (Promega) in UltraPure™ DNase/RNase-Free Distilled Water (Thermo Fisher Scientific). Nuclei were kept on ice while transferred to the BNORC Functional Genomics and Bioinformatics (FGB) Core for DroNc-seq assay.
DroNc-seq was performed as per Habib et al. 2017, with minor modifications. Briefly, nuclei stained with Hoechst 33342 (ThermoFisher, cat. R37605) were counted on a hemocytometer and diluted in NSB to ~250,000 nuclei/ml. Barcoded beads (Chemgenes, Cat # Macosko-2011-10) were size-selected using a 40 μm strainer, diluted to 350,000 per ml, and loaded onto 70 μm wide and 75 μm deep microfluidic device (Nanoshift). The nuclei and barcoded bead suspensions were loaded and run at 35 ml/hr each, along with carrier oil (BioRad Sciences, Cat # 186-4006) at 200 ul/min, to co-encapsulate single nuclei and beads in ~75 μm drops (vol. ~ 200 pl) at 4,500 drops/sec and double Poisson loading concentrations. The microfluidic emulsion was collected into 50 ml Falcon tubes for 10-25 min each and placed on ice 2h before droplet disruption. Individual 200µl reverse transcription (RT) reactions were performed on up to 90K beads. After further exonuclease digestion, aliquots of 800-5K beads were PCR amplified for 10 cycles, and PCR products were pooled in batches of 4 wells or 16 wells for library construction. Purified cDNA was quantified, and 550 pg of each sample was fragmented, tagged, and amplified in each Nextera reaction. Libraries were sequenced on the Illumina NextSeq500 using between 1.6–1.7 pM and 0.3 μM Read1CustSeqB (GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC) using a 20 × 8 × 60 read structure to a depth of 60,000 reads/nucleus.

value: dorsal pontine tegmentum

tag: region-based dissection

value: PB

tag: batch

tag: cell type

value: neuronal/ non-neuronal/ glial cells

tag: age

value: 8-10 weeks old

tag: diet

value: NCD

tag: schedule

value: ad libitum

value: male

tag: co2 treatment

value: neg


title: Mm_LPBN_05-1X-1

description: snRNA-seq (DroNc-seq)

value: pos


title: HCT116 FOXD2-6xHis rep2

description: ATCC (CCL-247)

value: 6X His tag [HIS.H8] (Abcam, ab18184)


title: 11B_M_1659

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region


title: 11B_M_1666


title: 11B_M_1660


title: 50_8_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: LP/J

value: Sedentary


title: Mm_LPBN_04-4A-1

description: snRNA-seq (DroNc-seq)


title: 11B_M_1658


title: HCT116 FOXD2 Histone Input

description: ATCC (CCL-247)

value: Large intestine; Colon

value: Carcinoma; Colorectal

value: pSin-FOXD2 epxressing vector


title: 11B_M_1663


title: 11B_M_1657


title: HCT116 FOXD2-6xHis rep1

description: ATCC (CCL-247)


title: HCT116 Control Histone Input

description: ATCC (CCL-247)

value: pSin-Pur-MCS-Puro epmty vector


title: 5_8_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: gonadal white adipose tissue

value: female

value: CBA/J


title: 11B_M_1656


title: Mm_LPBN_04-3B-1

description: snRNA-seq (DroNc-seq)

value: dorsal pontine tegmentum

value: PB

value: neuronal/ non-neuronal/ glial cells


title: 50_1_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: Exercised


title: 5_4_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: Mm_LPBN_04-3A-1

description: snRNA-seq (DroNc-seq)

value: 8-10 weeks old

value: NCD

value: ad libitum


title: HCT116 FOXD2 H3K27ac ChIP rep2

description: ATCC (CCL-247)

value: H3K27ac (Abcam, ab4729)


title: 11B_M_1655

value: male


title: 49_5_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: NZB/BlNJ

value: Sedentary


title: Mm_LPBN_05-2X-1

description: snRNA-seq (DroNc-seq)

value: pos


title: 49_2_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: Mm_LPBN_04-2B-1

description: snRNA-seq (DroNc-seq)

value: neg


title: Mm_LPBN_04-2A-1

description: snRNA-seq (DroNc-seq)


title: 11B_M_1654


title: 11B_M_1653


title: 48_7_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: BTBR T<+> tf/J


title: 48_1_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: gonadal white adipose tissue


title: HCT116 Control H3K27ac ChIP rep1

description: ATCC (CCL-247)

value: Large intestine; Colon

value: Carcinoma; Colorectal

value: pSin-Pur-MCS-Puro epmty vector


title: 11B_M_1652


title: HCT116 FOXD2 H3K4me1 ChIP rep2

description: ATCC (CCL-247)

value: pSin-FOXD2 epxressing vector

value: H3K4me1 (Abcam, ab8895)


title: Mm_LPBN_04-1A-1

description: snRNA-seq (DroNc-seq)

value: dorsal pontine tegmentum

value: PB

value: neuronal/ non-neuronal/ glial cells

value: female


title: Mm_LPBN_03-3C-1

description: snRNA-seq (DroNc-seq)

value: 8-10 weeks old

value: NCD

value: fasted


title: HCT116 FOXD2 H3K4me1 ChIP rep1

description: ATCC (CCL-247)


title: 11B_M_1651

value: male


title: Mm_LPBN_03-3B-1

description: snRNA-seq (DroNc-seq)


title: 47_5_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: NZW/LacJ

value: Sedentary


title: HCT116 Control H3K4me1 ChIP rep1

description: ATCC (CCL-247)


title: Mm_LPBN_03-3A-1

description: snRNA-seq (DroNc-seq)

value: neg


title: 11B_M_1648


title: stressed_rep3

city: Changsha

first: fang

last: zhou

address: 283 Tongzipo Road, Yuelu District,

country: China

institute: hunan cancer hospital

description: stressed nude mice ovarian tumor tissue.

data_processing:
The raw reads were processed by filtering out containing adapter, poly ’N’, low quality, smaller than 17nt reads by FASTQC to get clean reads. Mapping reads were obtained by mapping clean reads to reference genome of by BWA.
miRDeep2 was used to identify known mature miRNA based on miRBase21 (www.miRBase.org) and predict novel miRNA. Databases of Rfam12.1 (www.rfam.xfam.org) and pirnabank (www.pirnabank.ibab.ac.in) were used to identify rRNA, tRNA, snRNA, snoRNA and piRNA by BLAST. The miRNA expression was calculated by RPM (Reads Per Million) values (PRM=(number of reads mapping to miRNA/ number of reads in Clean data)×10^6 ).
The expression levels were normalized by RPM, RPM is equal to (number of reads mapping to miRNA/ number of reads in Clean data)×10^6. Differential expression between two sets of samples was calculated by the limma algorithm according to the criteria of |log2（Fold Change）|≥1 and P-value < 0.05.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *txt: Tab-delimited text files include FPKM values for each Sample.

molecule: total RNA

source_name: SKOV3 cells

extract_protocol:
Tumor tissue were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Ovarian adenocarcinoma

tag: condition

value: Stressed


title: 47_3_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: gonadal white adipose tissue

value: Exercised


title: 11B_M_1650


title: HCT116 FOXD2 H3K27ac ChIP rep1

description: ATCC (CCL-247)

value: Large intestine; Colon

tag: disease state

value: Carcinoma; Colorectal

value: pSin-FOXD2 epxressing vector

value: H3K27ac (Abcam, ab4729)


title: 46_5_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: NOD/ShiLtJ


title: stressed_rep1


title: stressed_rep2


title: 11B_M_1647


title: Mm_LPBN_03-2B-1

description: snRNA-seq (DroNc-seq)

value: dorsal pontine tegmentum

value: PB

value: neuronal/ non-neuronal/ glial cells


title: non-stressed_rep4

description: Non-stressed nude mice ovarian tumor tissue.

value: Non-stressed


title: 11B_M_1646

value: male


title: Mm_LPBN_03-2C-1

description: snRNA-seq (DroNc-seq)

value: 8-10 weeks old

value: NCD

value: fasted


title: Mm_LPBN_03-2A-1

description: snRNA-seq (DroNc-seq)

value: neg


title: 11B_M_1645


title: Mm_LPBN_03-1A-1

description: snRNA-seq (DroNc-seq)


title: non-stressed_rep3

value: Ovarian adenocarcinoma


title: non-stressed_rep2


title: 11B_M_1643


title: 44_1_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: gonadal white adipose tissue

value: female


title: Mm_LPBN_02-3B-1

description: snRNA-seq (DroNc-seq)

value: ad libitum


title: 11B_M_1642


title: non-stressed_rep1


title: 11B_M_1641


title: 45_6_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: Sedentary


title: 46_2_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: Exercised


title: 43_4_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: 11B_M_1640


title: RIO1, 3rd biological repeat

city: Trento

first: Peter

last: De Wulf

state: TN

address: via Sommarive, 9

department: Department of Cellular, Computational and Integrative Biology

country: Italy

institute: University of Trento

data_processing:
Reads from each sample were preprocessed by filtering for nucleotide quality (Q30 threshold), read length (minimum 36 nucleotides after trimming, no more than one N in a read), and removing sequencing adapters with Trimmomatic.
Filtered reads were then aligned to the sacCer3 genome (assembly R64) with STAR, using the alignIntronMin 4 -alignIntronMax 5000 -outSAMmultNmax 1 parameters.
Aligned reads were assigned to genes by using the --QuantMode GeneCounts option.
Centromere positions for each chromosome were obtained from the SGD database.
Reads mapping to the centromeres and to the pericentromeres (500nt upstream and downstream of the CEN regions) were extracted to BED files for each sample using the bedtools intersect command.
Assembly: sacCer3
Supplementary files format and content: the tab-delimited text file includes CPM values for each Sample

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown at 25°C in YPDA medium

extract_protocol:
Exponentially grown yeast cultures (OD600 = 0,8) were isolated from a 5 ml culture sample (3,000 rpm; 3 min, 4°C), washed with ice-cold AE buffer (50mM sodium acetate pH 5.2, 10mM EDTA pH 8.0), and stored at -80°C. Next, total RNA was extracted using phenol and chloroform. Residual genomic DNA was removed (1h, 37°C) with DNase I (New England Biolabs, Cat # M0303L).
All cytoplasmic and mitochondrial rRNA were removed from one µg of purified yeast RNA (see above) with the QIASeq FastSelect rRNA Yeast (Qiagen, Cat # 334215). RNA-Seq libraries were synthesized with NEBNext Ultra II Directional Library Prep Kit for Illumina (NEB, Cat # E7760S) using Unique Dual Index UMI Adaptors RNA Set 1 (NEB #7416).

treatment_protocol: 1 hour of 500 uM Auxin

tag: genotype

value: mock


title: Rio1 auxin-inducible depletion, 3rd  biological repeat

value: 500 uM Auxin


title: Mm_LPBN_02-2A-1

description: snRNA-seq (DroNc-seq)

value: dorsal pontine tegmentum


title: Mm_LPBN_02-2B-1

description: snRNA-seq (DroNc-seq)

value: PB


title: Mm_LPBN_03-1B-1

description: snRNA-seq (DroNc-seq)

value: neuronal/ non-neuronal/ glial cells


title: 42_5_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: 42_1_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: 45_4_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: Rio1 auxin-inducible depletion, 2nd biological repeat


title: RIO1, 2nd biological repeat


title: 11B_M_1644


title: 11B_M_1639


title: 44_5_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: Mm_LPBN_02-1B-1

description: snRNA-seq (DroNc-seq)


title: 41_5_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: Rio1 auxin-inducible depletion, 1st biological repeat


title: 11B_M_1638


title: Mm_LPBN_02-1A-1

description: snRNA-seq (DroNc-seq)


title: 41_1_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: Mm_LPBN_01-2C-1

description: snRNA-seq (DroNc-seq)


title: Mm_LPBN_02-3A-1

description: snRNA-seq (DroNc-seq)


title: RIO1, 1st biological repeat


title: 43_6_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: Mm_LPBN_01-2B-1

description: snRNA-seq (DroNc-seq)


title: 40_5_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: rep9x3_B

city: Rehovot

first: Naama

last: Barkai

state: --- Select a state ---

address: Herzl St 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

data_processing:
demultiplexing with bcl2fastq
filtering of adapter dimers using cutadapt
paired end alignment to S288C_R64 with bowtie2 (-p8 --local --very-sensitive --trim-to 30 --dovetail)
genome coverage with bedtools (-5 -fs 1 -d)
Assembly: GCA_000146045.2 (R64)
Supplementary files format and content: *.out.gz file contains zipped genome coverage for all 12,157,105 bases in the S. cerevisiae genome (Chr 1-16+mitochondria)
Library strategy: ChEC-seq

source_name: budding yeast culture at OD=4

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

extract_protocol:
Phenol chlorofrom extraction
One tube library construction based on Skeene et al. 2017 as described in Gera 2021

treatment_protocol: ChEC-Seq protocol as described in Zentner et al. 2015

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(rep9x3)-Mnase (kanMX)


title: 11B_M_1634

value: male


title: Mm_LPBN_01-2A-1

description: snRNA-seq (DroNc-seq)

value: 8-10 weeks old


title: 40_1_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: 4_8_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: AKR/J


title: Mm_LPBN_01-1C-1

description: snRNA-seq (DroNc-seq)

value: NCD


title: rep9x2_B

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(rep9x2)-Mnase (kanMX)


title: Mm_LPBN_01-1B-1

description: snRNA-seq (DroNc-seq)

value: neg


title: 11B_M_1636


title: 11B_M_1629


title: 11B_M_1631


title: rep9x2_A


title: rep9_B

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(rep9)-Mnase (kanMX)


title: 11B_M_1628


title: 39_5_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: gonadal white adipose tissue

value: female


title: 39_3_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: 11B_M_1637


title: cGAS KO neutrophils, LPS 2 hours 3

city: Worcester

first: Patipark

last: Kueanjinda

state: MA

address: 368 Plantation St

institute: University of Massachusetts Medical School

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp module in galaxy (default parameters).
Trimmed sequence reads were mapped to GRCm39/mm10 using RNA STAR module in galaxy (default parameters).
BAM files were converted to fastq formats using SamToFastq module prior to quantification using Kallisto in galaxy (default parameters).
Read count extraction and normalization were performed using R.
Assembly: GRCm39
Supplementary files format and content: comma-separated values file includes log2-transformed of library size-normalized TPM values for each sample

source_name: neutrophil

growth_protocol: Peritoneal neutrophils from cGAS knockout mice were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified incubator with 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted from neutrophils using  RNeasy mini kit (Qiagen).
Approximately 300 ng of the total RNAs from each sample was used to create individually indexed strand-specific RNA-Seq libraries by using QIAseq Stranded mRNA Library kits (QIAGEN). The reactions were subjected to fragmentation and cDNA synthesis. QIAseq Beads (QIAGEN) were used to separate the cDNAs from the reaction mix. Indexing adapters were ligated to the cDNAs, and subsequently all cDNA libraries were inspected for quality by using Agilent 2100 Bioanalyzer (Agilent) and quantified with DeNovix fluorometer (DeNovix). The indexed sequencing libraries were pooled in equimolar quantity and subjected to cluster generation and paired end 150 nucleotide read sequencing on Illumina HiSeq sequencer.

treatment_protocol: Activation of neutrophils was induced with 500 ng/mL of LPS (E.coli 026:B6 from Sigma) or media control for 2 hours.

value: neutrophil

value: cGAS knockout

value: LPS

tag: time

value: 2 hours


title: Mm_LPBN_01-1A-1

description: snRNA-seq (DroNc-seq)

tag: tissue

value: dorsal pontine tegmentum

value: ad libitum


title: cGAS KO neutrophils, LPS 2 hours 2

tag: treatment


title: rep9_A


title: 11B_M_1627

tag: Sex


title: rep8x3_B

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(rep8x3)-Mnase (kanMX)


title: 38_7_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

tag: strain

value: Sedentary


title: 38_3_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

tag: exercise group

value: Exercised


title: rep8x3_A


title: rep9x3_A

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(rep9x3)-Mnase (kanMX)


title: 11B_M_1625

value: male


title: 11B_M_1626


title: 11B_M_1632


title: cGAS KO neutrophils, untreated 3

value: media control


title: cGAS KO neutrophils, LPS 2 hours 1


title: 4_4_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: AKR/J


title: 37_2_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: 11B_M_1624


title: rep8x2_A

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(rep8x2)-Mnase (kanMX)


title: rep8x2_B


title: 11B_M_1623


title: cGAS KO neutrophils, untreated 1


title: cGAS KO neutrophils, untreated 2


title: 36_7_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: 11B_M_1622


title: rep8_A

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(rep8)-Mnase (kanMX)


title: 11B_M_1621


title: 36_4_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: gonadal white adipose tissue


title: rep8_B


title: CL, scRNAseq

city: Wuhan

first: Yu

last: Zhou

address: Donghu Road, No. 115, Wuchang District, Wuhan, Hubei Province, P.R. China.

institute: Medical Research Institute, Wuhan University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: mammary gland (macrophage-depleted)

extract_protocol:
The mammary glands were collected from CL treated and control mice (8 to 10-week-old) and washed with cold PBS, and the tissues were cut into small pieces (about 1mm2) and transferred into digest buffer (RPMI 1640+5%FBS+1%Penicillin/ Streptomycin+25 mM HEPES), 5mL per mouse, and digested for 2 hours, 100 rpm, at 37 °C with a good shaking for every 15 minutes. The well-digested tissues were centrifuged at 4 °C, 1000 rpm for 5 minutes, and incubated with RBC lysis for red blood cell removement, then digested the cells with 0.05% trypsin (with EDTA), for 5 minutes at 37 °C to get single cells, and 0.1 mg/ml DNase I was used to digest the free DNA for preventing cell aggregation. Then the cells were passed through a 70μm strainer, since then the mammary single cell suspension was successfully prepared.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs 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 apropiated 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.

value: mammary gland (macrophage-depleted)

tag: cell line

value: primary cell

value: mammary cells

value: 9-10 weeks old

value: clodronate liposome treatment


title: Ctrl, scRNAseq

description: 10x Genomics

source_name: mammary gland

value: mammary gland

value: control


title: 35_5_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: female


title: rep7x2_B

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(rep7x2)-Mnase (kanMX)


title: T8.shCTCF.KLRG1hi.D8.Sp2.RNA

first: Ananda

last: Goldrath

address: 9500 Gilman Drive

institute: UCSD

data_processing:
Aligned with STAR 2.5.4a to mouse genome
Gene-level quantification calculated by featureCounts
Raw reads counts table normalized by median of ratios method with DESeq2
Assembly: mm10
Supplementary files format and content: Tab-delimited text files of normalized counts

source_name: spleen

extract_protocol:
Ultra-low-input RNA Seq was performed on sort purified cells, polyadenylated mRNA was converted to cDNA
Illumina adapters were added and product was PCR amplified for sequencing

value: spleen

value: OT-I

value: Lm-OVA

value: Day 8


title: 35_1_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: Exercised


title: 37_5_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: Sedentary


title: rep7x2_A


title: 34_8_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: SJL/J


title: 11B_M_1618

value: male


title: 11B_M_1619


title: 34_1_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: gonadal white adipose tissue


title: rep7_B

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(rep7)-Mnase (kanMX)


title: T8.shCD19.InVitro2.RNA

value: anti-CD3+anti-CD28 and 100U/mL IL-2

value: Day 4


title: rep7_A


title: 33_7_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: 11B_M_1616


title: 11B_M_1617


title: T8.shCTCF.InVitro2.RNA


title: 11B_M_1620


title: rep6x3_A

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(rep6x3)-Mnase (kanMX)


title: 32_5_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: 11B_M_1615


title: T8.shCD19.KLRG1.hi.D8.Sp2.RNA


title: rep6x2_B

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(rep6x2)-Mnase (kanMX)


title: T8.shCD19.KLRG1.hi.D8.Sp1.RNA


title: T8.shCTCF.InVitro1.RNA


title: rep6x3_B


title: 32_1_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: 31_6_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: I/LnJ


title: 11B_M_1613


title: hepatocytes_96hpf_cavdra_expt2_rep3

first: Scott

last: Freeburg

address: 77 Ave Louis Pasteur, New Research Building #458

institute: Brigham and Women's Hospital

data_processing:
FASTQ files were mapped to GRCz11 using STAR (v2.5.3), and read counting was performed using HTSeq (v0.11.1). Read count normalization was performed using the R package DEseq2.
Assembly: GRCz11
Supplementary files format and content: .csv files containing ensembl ids, gene names, and raw read counts or normalized read counts for each experiment

organism: Danio rerio

source_name: hepatocytes (sorted)

growth_protocol: Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.

extract_protocol:
Hepatocytes were sorted into 75 uL Buffer RLT containing b-mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on-column DNase treatment.
cDNA synthesis and amplification were performed according to the Smart-seq2 protocol (https://doi.org/10.1038/nprot.2014.006). Library prep was performed with the Nextera XT DNA Library Preparation Kit (Illumina).

value: hepatocytes (sorted)

value: 96 hpf


title: 11B_M_1612


title: T8.shCTCF.KLRG1hi.D8.Sp1.RNA

value: spleen


title: rep6_B

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(rep6)-Mnase (kanMX)


title: rep6_A


title: 31_1_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: female


title: T8.shCD19.InVitro1.RNA

value: OT-I


title: 11B_M_1611


title: 30_6_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: hepatocytes_96hpf_cavdra_expt2_rep2


title: rep5x3_B

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(rep5x3)-Mnase (kanMX)


title: 33_4_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: Exercised


title: 11B_M_1610


title: 11B_M_1614


title: 30_4_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: rep5x3_A


title: hepatocytes_96hpf_cavdra_expt2_rep1


title: hepatocytes_96hpf_wt_expt2_rep4

value: wt


title: rep6x2_A


title: 3_5_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: A/J

value: Sedentary


title: hepatocytes_96hpf_wt_expt2_rep3


title: 11B_M_1607

value: male


title: rep5x2_B

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(rep5x2)-Mnase (kanMX)


title: 11B_M_1608


title: 11B_M_1606


title: 29_6_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: gonadal white adipose tissue


title: hepatocytes_96hpf_wt_expt2_rep2


title: rep5x2_A


title: 29_4_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: hepatocytes_96hpf_wt_expt2_rep1


title: 11B_M_1604


title: 11B_M_1605


title: 28_6_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: rep5_A

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(rep5)-Mnase (kanMX)


title: 11B_M_1602


title: VC Patient 917933 Source LN 3 [R1200.S0030]

city: Cambridge

first: Jonathan

middle: Morris

last: Urbach

state: Massachusetts

address: 400 Technology Sq Rm 851

institute: Ragon Institute of MGH, MIT and Harvard

description: Lymph node-derived CD8+ T cells, patient 917933, phenotype VC replicate 3

data_processing:
Illumina sequencing run was deemultiplexed using bcl2fastq veersion 2.19.1.403.
Reads were then mappeed to the hg38 transcriptome using the RSEM pipeline version 1.3.0 with bowtie aligner version 1.2.2. Read counts were calculated as expected counts, and rounded to integer values for analysis with DESeq2, or used without rounding in edgeR.
Differential expression analysis was performed using DESeq2 version 1.26.0 using a model including the following terms: "~ patient_ID + tissue + GenesExpCountGRE1 + align_rate + pctGC.R1"
Prior to differential expression analysis, genes were filtered to have at least 5 expected counts in at least 10% of samples.
Genome_build: GRCh38.p5
Supplementary_files_format_and_content: The expected counts matrix (R1015R1200.FILT.EC.tsv) includes counts for samples and genes listed by their respective ENSEMBL gene IDs and gene symbols, delimited by an underscore. R1015R1200.FILT.EC.LTMM.tsv contains the corresponding TMM-normalized log transformed counts. The GEO.metadata file is complete sample metadata including QC evaluations in tab-separated format. R1015R1200.LNvPB.rslt.tsv is the DESeq2 result set as tab-separated values.

source_name: CD8+ T cells

growth_protocol: Frozen PBMCs or LNMCs were rested overnight in RPMI + 10% FBS at 37C.

extract_protocol:
Replicate populations of 500-2,500 HIV-specific CD8+ T cells were FACS sorted into RLT Plus lysis buffer supplemented with 1% beta-mercaptoethanol and flash frozen at -80C for storage. Lysates were thawed on ice and RNA was isolated using AllPrep DNA/RNA Micro Kit (Qiagen Cat#80284) per manufacturer's protocol for isolation of total RNA including small RNAs.
Whole-transcriptome libraries were prepared using oligo-dT priming and SuperScript II (ThermoFisher Cat#18064022) reverse transcription as per standard SmartSeq2 protocols, then barcoded and pooled for Illumina 76bp paired-end sequencing on a NextSeq 550.

treatment_protocol: Cells were pretreated with 50 nM dasatinib to prevent activation-induced transcription and TCR downregulaiton, then stained with 4 nM HIV peptide-HLA tetramer, lineage and viability markers for isolation of HIV-specific CD8+ T cells by FACS.

value: lymph node

tag: phenotype

value: VC

tag: cd4+ count

value: Male

tag: cell count

tag: replicate

tag: ugps

tag: align rate

tag: percent gc, r1

tag: percent gc, r2


title: 28_2_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: VC Patient 917933 Source LN 2 [R1200.S0029]

description: Lymph node-derived CD8+ T cells, patient 917933, phenotype VC replicate 2


title: 27_5_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: SEA/GnJ


title: 11B_M_1598

tag: brain region

tag: age


title: VC Patient 917933 Source LN 1 [R1200.S0028]

description: Lymph node-derived CD8+ T cells, patient 917933, phenotype VC replicate 1


title: 11B_M_1599


title: 27_1_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: 11B_M_1597


title: 26_5_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: RIIIS/J


title: VC Patient 917933 Source PB 2 [R1200.S0026]

description: PBMC-derived CD8+ T cells, patient 917933, phenotype VC replicate 2

value: PBMC


title: rep4x3_A

tag: genotype

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(rep4x3)-Mnase (kanMX)


title: VC Patient 917933 Source PB 3 [R1200.S0027]

description: PBMC-derived CD8+ T cells, patient 917933, phenotype VC replicate 3

tag: tissue


title: rep4_B

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(rep4)-Mnase (kanMX)


title: 3_4_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: female


title: VC Patient 917933 Source PB 1 [R1200.S0025]

description: PBMC-derived CD8+ T cells, patient 917933, phenotype VC replicate 1


title: 11B_M_1596


title: rep5_B


title: 26_1_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: Exercised


title: rep4_A


title: 11B_M_1595


title: 25_8_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: VC Patient 847041 Source LN 3 [R1200.S0024]

description: Lymph node-derived CD8+ T cells, patient 847041, phenotype VC replicate 3

value: Female


title: rep4x3_B


title: rep3x3_B

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(rep3x3)-Mnase (kanMX)


title: VC Patient 847041 Source LN 2 [R1200.S0023]

description: Lymph node-derived CD8+ T cells, patient 847041, phenotype VC replicate 2


title: 11B_M_1594


title: 25_3_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: 11B_M_1593


title: rep4x2_B

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(rep4x2)-Mnase (kanMX)


title: rep3x3_A


title: 24_5_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: Sedentary


title: rep3x2_B

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(rep3x2)-Mnase (kanMX)


title: VC Patient 847041 Source LN 1 [R1200.S0022]

description: Lymph node-derived CD8+ T cells, patient 847041, phenotype VC replicate 1


title: rep4x2_A


title: 11B_M_1592

value: male


title: VC Patient 847041 Source PB 3 [R1200.S0021]

description: PBMC-derived CD8+ T cells, patient 847041, phenotype VC replicate 3


title: 24_2_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: gonadal white adipose tissue


title: VC Patient 847041 Source PB 2 [R1200.S0020]

description: PBMC-derived CD8+ T cells, patient 847041, phenotype VC replicate 2


title: 23_5_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: 11B_M_1590


title: 11B_M_1591


title: VC Patient 847041 Source PB 1 [R1200.S0019]

description: PBMC-derived CD8+ T cells, patient 847041, phenotype VC replicate 1


title: 23_1_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: rep2x3_A

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(rep2x3)-Mnase (kanMX)


title: VC Patient 588800 Source LN 3 [R1200.S0018]

description: Lymph node-derived CD8+ T cells, patient 588800, phenotype VC replicate 3

value: lymph node

value: VC


title: 11B_M_1589


title: 22_5_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: rep2x2_B

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(rep2x2)-Mnase (kanMX)


title: 22_1_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: rep2x2_A


title: 11B_M_1588


title: VC Patient 588800 Source LN 2 [R1200.S0017]

description: Lymph node-derived CD8+ T cells, patient 588800, phenotype VC replicate 2

value: Male


title: VC Patient 588800 Source LN 1 [R1200.S0016]

description: Lymph node-derived CD8+ T cells, patient 588800, phenotype VC replicate 1


title: 21_5_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: rep2_A

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(rep2)-Mnase (kanMX)


title: rep2_B


title: 21_2_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: 11B_M_1587


title: 11B_M_1586


title: rep3x2_A


title: 11B_M_1585


title: VC Patient 588800 Source PB 3 [R1200.S0015]

description: PBMC-derived CD8+ T cells, patient 588800, phenotype VC replicate 3

value: PBMC


title: 20_5_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: VC Patient 588800 Source PB 2 [R1200.S0014]

description: PBMC-derived CD8+ T cells, patient 588800, phenotype VC replicate 2


title: rep2x3_B


title: VC Patient 588800 Source PB 1 [R1200.S0013]

description: PBMC-derived CD8+ T cells, patient 588800, phenotype VC replicate 1


title: rep1x3_B

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(rep1x3)-Mnase (kanMX)


title: rep1x3_A


title: 20_3_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: female


title: rep1x2_B

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(rep1x2)-Mnase (kanMX)


title: 11B_M_1584


title: VC Patient 495326 Source LN 2 [R1200.S0011]

description: Lymph node-derived CD8+ T cells, patient 495326, phenotype VC replicate 2

value: Female


title: VC Patient 495326 Source LN 3 [R1200.S0012]

description: Lymph node-derived CD8+ T cells, patient 495326, phenotype VC replicate 3


title: 2_2_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: Exercised


title: VC Patient 495326 Source LN 1 [R1200.S0010]

description: Lymph node-derived CD8+ T cells, patient 495326, phenotype VC replicate 1


title: 19_7_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: rep1_B

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(rep1)-Mnase (kanMX)


title: 11B_M_1581


title: 2_6_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: Sedentary


title: rep1x2_A


title: 11B_M_1580


title: VC Patient 495326 Source PB 3 [R1200.S0009]

description: PBMC-derived CD8+ T cells, patient 495326, phenotype VC replicate 3


title: 18_7_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: 19_3_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: VC Patient 495326 Source PB 2 [R1200.S0008]

description: PBMC-derived CD8+ T cells, patient 495326, phenotype VC replicate 2


title: 11B_M_1578


title: rep1_A


title: 18_3_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: rep10x2_B

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(rep10x2)-Mnase (kanMX)


title: 11B_M_1579

value: male


title: rep10x2_A


title: 11B_M_1583


title: EC Patient 473516 Source LN 3 [R1200.S0006]

description: Lymph node-derived CD8+ T cells, patient 473516, phenotype EC replicate 3

value: EC


title: 17_8_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: gonadal white adipose tissue


title: VC Patient 495326 Source PB 1 [R1200.S0007]

description: PBMC-derived CD8+ T cells, patient 495326, phenotype VC replicate 1


title: 11B_M_1577


title: 11B_M_1582


title: rep0x2_B

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(rep0x2)-Mnase (kanMX)


title: 11B_M_1576


title: 17_4_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: EC Patient 473516 Source LN 2 [R1200.S0005]

description: Lymph node-derived CD8+ T cells, patient 473516, phenotype EC replicate 2

value: lymph node


title: 11B_M_1575


title: rep0x2_A


title: EC Patient 473516 Source LN 1 [R1200.S0004]

description: Lymph node-derived CD8+ T cells, patient 473516, phenotype EC replicate 1


title: EC Patient 473516 Source PB 3 [R1200.S0003]

description: PBMC-derived CD8+ T cells, patient 473516, phenotype EC replicate 3


title: rep0_B

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(rep0)-Mnase (kanMX)


title: 11B_M_1574


title: 16_8_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: 16_2_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: rep0_A


title: 11B_M_1573


title: 15_7_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: SM/J


title: 11B_M_1572


title: 11B_M_1571


title: EC Patient 843456 Source PB 3 [R1015.S0048]

description: PBMC-derived CD8+ T cells, patient 843456, phenotype EC replicate 3

value: Male


title: 15_2_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: charged_random_cluster_2_1

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(charged_random_cluster_2)-Mnase (kanMX)


title: 14_7_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: Y_nextto_N_3

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(Y_nextto_N)-Mnase (kanMX)


title: 14_1_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: female


title: EC Patient 843456 Source PB 1 [R1015.S0046]

description: PBMC-derived CD8+ T cells, patient 843456, phenotype EC replicate 1

value: PBMC


title: 11B_M_1569


title: Y_nextto_N_1


title: EC Patient 473516 Source PB 1 [R1200.S0001]

description: PBMC-derived CD8+ T cells, patient 473516, phenotype EC replicate 1


title: 11B_M_1570


title: T_nextto_N_6

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(T_nextto_N)-Mnase (kanMX)


title: 13_7_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: 11B_M_1568


title: EC Patient 843456 Source LN 3 [R1015.S0045]

description: Lymph node-derived CD8+ T cells, patient 843456, phenotype EC replicate 3


title: T_nextto_N_5


title: EC Patient 843456 Source LN 2 [R1015.S0044]

description: Lymph node-derived CD8+ T cells, patient 843456, phenotype EC replicate 2


title: EC Patient 473516 Source PB 2 [R1200.S0002]

description: PBMC-derived CD8+ T cells, patient 473516, phenotype EC replicate 2


title: 12_5_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: 11B_M_1566


title: 13_2_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: Exercised


title: 11B_M_1567


title: 12_3_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: EC Patient 843456 Source LN 1 [R1015.S0043]

description: Lymph node-derived CD8+ T cells, patient 843456, phenotype EC replicate 1


title: charged_random_cluster_2_2


title: 11B_M_1565


title: S_to_A_2

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(S_to_A)-Mnase (kanMX)


title: EC Patient 843456 Source PB 2 [R1015.S0047]

description: PBMC-derived CD8+ T cells, patient 843456, phenotype EC replicate 2


title: 11_6_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: Sedentary


title: EC Patient 642488 Source PB 2 [R1015.S0041]

description: PBMC-derived CD8+ T cells, patient 642488, phenotype EC replicate 2


title: 11B_M_1564


title: S_to_A_1


title: EC Patient 642488 Source PB 3 [R1015.S0042]

description: PBMC-derived CD8+ T cells, patient 642488, phenotype EC replicate 3


title: 11_2_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: S_shift_2

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(S_shift)-Mnase (kanMX)


title: 11B_M_1563

value: male


title: 10_7_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: S_nextto_N_2

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(S_nextto_N)-Mnase (kanMX)


title: 11B_M_1562


title: EC Patient 642488 Source LN 3 [R1015.S0039]

description: Lymph node-derived CD8+ T cells, patient 642488, phenotype EC replicate 3

value: EC


title: S_nextto_N_1


title: 10_1_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: gonadal white adipose tissue


title: EC Patient 642488 Source PB 1 [R1015.S0040]

description: PBMC-derived CD8+ T cells, patient 642488, phenotype EC replicate 1


title: T_nextto_N_2


title: 11B_M_1561


title: S_clustering_5_2

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(S_clustering_5)-Mnase (kanMX)


title: EC Patient 642488 Source LN 1 [R1015.S0037]

description: Lymph node-derived CD8+ T cells, patient 642488, phenotype EC replicate 1

value: lymph node


title: EC Patient 642488 Source LN 2 [R1015.S0038]

description: Lymph node-derived CD8+ T cells, patient 642488, phenotype EC replicate 2


title: 1_26_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt


title: ART Patient 310817 Source PB 3 [R1015.S0036]

description: PBMC-derived CD8+ T cells, patient 310817, phenotype ART replicate 3

value: ART


title: 11B_M_1559


title: ESN25-3

city: Shenzhen

first: Qing

last: Li

address: No 7,Pengfei Road,Dapeng District

institute: Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences,

description:
25bp length ramdom DNA fragment library
plasmid pool

data_processing:
Library strategy: MAE-seq
The raw data of fastq format were firstly trimmed by cutadapt (v1.16) to remove adapter （-a CTGTCTCTTATACACATCT -g AGATGTGTATAAGAGACAG ）
Low quality reads were filtered by fastx-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Only the sequences which the number of bases with a minimum Phred-score quality score of 20 accounted for more than 95% of the total would be saved
The remaining reads which have the same length (25bp） inserted were picked out and aligned to mm9 / hg19 reference genome using bowtie (version 1.2.2) and bwa (version 0.7.5a-r405), respectively.Uniquely mapping reads with up to two mismatches from either bowtie or bwa were kept. The genomic start and end coordinates of these reads were regarded as the genome position of enhancers.
Genome_build: mm9
Genome_build: hg19
Supplementary_files_format_and_content: txt files include the genome position of enhancers

source_name: Embryonic stem cell

growth_protocol: E14 ESCs cultures were inoculated into 100 mm ES medium (KO-DMEM(Gibco, 10829-018); 15%FBS(Gibco, 10099-141);0.2 mM GlutaMAX™ Supplement (Gibco, 35050061); 0.1 mM MEM nonessential amino acids (NEAA) (Gibco, 11140-122); 50 U/ml penicillin/50 μg/mL streptomycin(Gibco, 15140-122); 1 U/mL LIF (Chemicon, ESG-1106;0.1 mM 2-Mercaptoethanol (BME)(Gibco, 21985023); 0.16 mM Vitamin C(Sigma, A4034); 1 μM PD0325901; 3 μM CHIR-99021 (CT99021)). HEK293T Cell cultures were inoculated into 100 mm DMEM (ThermoFisher; Cat. No.10566024) containing 10% FBS (Gibco; Cat. No.10437028) and 1% Penicillin Streptomycin P/S (Sigma; Cat. No. P0781) at 37 ℃ cell incubator.

extract_protocol:
Plasmid library was extracted together with whole genome of positive cells
One-step PCR (72℃ for 3min, 98℃ for 30min; followed by 5-15 cycles of 98℃ for 15s, 60℃ for 30s, 72℃ for 3min; 72℃ for 5min). The product was recovered by 2% agarose gel electrophoresis for 35 min (120v, 130mA) and sent for high-throughput sequencing. sequence after one-step PCR amplification is 5’-AATGATACGGCGACCACCGAGATCTACACIIIIIIIITCGTCGGCAGCGTCAGATGTGTATAAGAGACAG-NNNNNN-CTGTCTCTTATACACATCTCCGAGCCCACGAGACIIIIIIIIATCTCGTATGCCGTCTTCTGCTTG-3’, IIIIIIII: Index 2 (i5), IIIIIIII: Index 1 (i7), -NNNNNN-: random sequence.

treatment_protocol: Transfection of plasmid libraries (4µg DNA/1x106 cells) was performed with cells at 70-80% confluence using Lipofectamine 3000 Transfection Reagent (Invitrogen, Cat. No. L3000075) or HD Transfection Reagent (FuGENE, Cat. No. E2311). Fluorescence cells were collected 48 hours after transfection.

tag: cell type

value: Embryo-derived stem cell

tag: passages

tag: reporter vector

value: pmx-mp-mcherry


title: 11B_M_1558

tag: strain

tag: Sex


title: S_clustering_20_1

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(S_clustering_20)-Mnase (kanMX)


title: ART Patient 310817 Source PB 2 [R1015.S0035]

description: PBMC-derived CD8+ T cells, patient 310817, phenotype ART replicate 2

tag: phenotype

value: Male


title: S_clustering_10_2

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(S_clustering_10)-Mnase (kanMX)


title: ST_deletion_B

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(ST_deletion)-Mnase (kanMX)


title: ESN25-1

tag: cell line


title: 11B_M_1556


title: ART Patient 310817 Source LN 3 [R1015.S0033]

description: Lymph node-derived CD8+ T cells, patient 310817, phenotype ART replicate 3

tag: cd4+ count

tag: cell count


title: ART Patient 310817 Source PB 1 [R1015.S0034]

description: PBMC-derived CD8+ T cells, patient 310817, phenotype ART replicate 1

value: PBMC

tag: replicate

tag: ugps


title: ST_deletion_A


title: R_nextto_N_6

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(R_nextto_N)-Mnase (kanMX)


title: 1_34_gWAT

description:
gWAT.counts.txt
gWAT.TPM.txt

value: female

tag: exercise group

value: Exercised


title: 11B_M_1554

value: male


title: 11B_M_1560


title: ART Patient 310817 Source LN 1 [R1015.S0031]

description: Lymph node-derived CD8+ T cells, patient 310817, phenotype ART replicate 1

tag: align rate

tag: percent gc, r1

tag: percent gc, r2


title: ART Patient 310817 Source LN 2 [R1015.S0032]

description: Lymph node-derived CD8+ T cells, patient 310817, phenotype ART replicate 2


title: R_nextto_N_4

tag: genotype


title: S_clustering_5_1


title: Q_nextto_N_2

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(Q_nextto_N)-Mnase (kanMX)


title: ESN25-2


title: TN25-2

source_name: Embryonic kidney cell

value: Embryo-derived kidney cell


title: Q_nextto_N_1


title: 11B_M_1551

tag: brain region

tag: age


title: TN25-3

tag: cell type

tag: passages


title: 11B_M_1557

tag: strain


title: TN25-1

tag: reporter vector


title: 11B_M_1550

tag: Sex


title: 11B_M_1552


title: Basal_Tnfa

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

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

tag: tissue

value: mammary gland

tag: cell line

value: primary cell

value: epithelial cell

value: WT

tag: treatment

value: cultured with Tnfa


title: P_to_A_B

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(P_to_A)-Mnase (kanMX)


title: 11B_M_1555


title: Basal_ctrl


title: PG_shift_6

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(PG_shift)-Mnase (kanMX)


title: 11B_M_1553


title: 11B_M_1548


title: 11B_M_1549


title: M2

value: co-cultured with M2


title: 11B_M_1547


title: ctrl


title: PG_shift_5


title: N_to_Y_2

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(N_to_Y)-Mnase (kanMX)


title: 11B_M_1546


title: LISC RNA rep1

data_processing:
Reads were mapped to the genome (Ensembl GRCm38 release100) using STAR-v2.7.2b with ENCODE option.
RSEM-v1.2.31 was used to calculate read counts and normalization.
Genome_build: mm10
Supplementary_files_format_and_content: tab separated RSEM results

source_name: Large intestine

growth_protocol: primary cell isolates from Lgr5-EGFP reporter mouse

extract_protocol:
TRIzol™ Reagent (invitrogen 15596026)
mRNA-seq libraries were generated using the NEBNext Ultra II Directional RNA Library Prep Kit (NEB, E7760S) for Illumina with mRNA Magnetic Isolation module (NEB, E7490S)

value: Large intestine


title: N_to_Y_1


title: N_to_S_2

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(N_to_S)-Mnase (kanMX)


title: P_to_A_A


title: 11B_M_1544


title: 11B_M_1542


title: N_to_S_1


title: SISC RNA rep1

source_name: Small intestine

value: Small intestine


title: SISC RNA rep2


title: ARH-77 KEAP1 KO 0.4 μM CDDO-2P-Im Rep 2

city: Cleveland

first: George

last: Luo

state: OH

address: 2103 Cornell Rd. Wolstein Research Bldg/Rm 3501

institute: Case Western Reserve University

data_processing:
Cutadapt was used to remove reads with contamination/low quality
HISAT2 was used to map reads to genome
StringTie used to assembled and estimate transcription levels
edgeR used to estimate expression levels
Assembly: tp://ftp.ensembl.org/pub/release-96/fasta/homo_sapiens/dna/
Supplementary files format and content: tab-delimited text files include FPKM values

growth_protocol: Cells were grown in RPMI1640 medium with 10% FBS with 1% pen/strep

extract_protocol:
Cells were extracted with Purelink RNA Mini Kit
Illumina’s TruSeq-stranded-mRNA sample preparation protocol

treatment_protocol: Cells were treated with 1% DMSO or CDDO-2P-Im dissolved in DMSO for 6 hours

value: B-Cell

value: KEAP1 KO

value: 0.4 μM CDDO-2P-Im


title: ARH-77 KEAP1 KO 0.4 μM CDDO-2P-Im Rep 3


title: LISC ATAC rep2

data_processing:
cutadapt-3.4 was used to detect and remove Illumina adapter sequence.
Bowtie2-2.3.4.1 aligned sequences to the Homo sapiens genome (UCSC mm10).
Picard tools removed duplicates with parameters "VALIDATION_STRINGENCY=LENIENT".
The reads were offset by +4 bases for the + strand and -5 bases for the - strand.
MACS2-2.2.7.1 was used for peak calling with parameters "--nomodel --shift -100 --extsize 200" and q-value < 0.01.
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak files were generated using MACS2; bigWig files were generated using genomeCoverageBed and bedGraphToBigWig.

extract_protocol:
ATAC lysis buffer (10mM Tris-HCT pH7.4, 10mM NaCl, and 3mM MgCl2 containing 0.1% NP40, 0.1% Tween-20, and 0.01% Triton-X 100)
We lysed 50,000 cells of interest with 50 μl lysis buffer (10 mM Tris-Cl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20 and 0.01% Triton X-100) and incubated them for 10 min on ice. Following centrifugation at 1,000g for 10 min at 4 °C, we resuspended nuclei pellets with 50 μl of transposition mix (25 μl 2× TD buffer (20 mM Tris-HCl pH 7.6, 10 mM MgCl2 and 20% dimethyl formamide in sterile water) and 2.5 μl transposase (100 nM final concentration), 16.5 μl PBS, 0.01% Triton X-100, 0.1% Tween-20 and 5 μl H2O) and incubated the mixture with shaking for 1 h at 55 °C in a thermomixer. We purified transposed DNA using DNA Clean and a Concentrator-5 Kit (Zymo Research) then amplified it using the NEBNext High-Fidelity 2× PCR Master Mix for 10 cycles. Subsequently, we then performed ATAC-seq using the Illumina NovaSeq600 dual indexed platform.


title: 11B_M_1541

value: male


title: 11B_M_1545


title: N_to_R_1

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(N_to_R)-Mnase (kanMX)


title: 11B_M_1540


title: LISC ATAC rep1


title: ARH-77 KEAP1 KO 0.1 μM CDDO-2P-Im Rep 3

value: 0.1 μM CDDO-2P-Im


title: N_to_Q_2

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(N_to_Q)-Mnase (kanMX)


title: 11B_M_1538


title: ARH-77 KEAP1 KO 0.1 μM CDDO-2P-Im Rep 2


title: 11B_M_1539


title: N_to_R_2


title: SISC ATAC rep2


title: 11B_M_1537


title: LISC RNA rep2


title: N_to_Q_1


title: SISC ATAC rep1


title: ARH-77 KEAP1 KO 0.4 μM CDDO-2P-Im Rep 1


title: ARH-77 KEAP1 KO Rep 2

value: DMSO


title: N_to_H_2

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(N_to_H)-Mnase (kanMX)


title: ARH-77 KEAP1 KO 0.1 μM CDDO-2P-Im Rep 1


title: Six1-KO rep2

city: Madrid

first: Ignacio

last: Palmero

state: Madrid

address: Arturo Duperier, 4.

country: Spain

institute: CSIC

description: otic vesicles from E10.5 Six1-/- mouse embryo

data_processing:
Image analysis, per-cycle basecalling and quality score assignment was performed with Illumina HiSeq Control Software.
Conversion of BCL files to FASTQ format was performed with the bcl2fastq Software (Illumina).
Reads were aligned, counted, and mapped using BlueBee’s STAR-aligner, HTSeq-count, and RSEQC.
Differential gene expression analysis was performed with DESeq2 within Bluebee (Lexogen QuantSeq DE)
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text file includes normalised counts for each sample.

source_name: otic vesicle E10.5

extract_protocol:
E10.5 mouse embryos were obtained and the otic vesicles were removed with dissection tweezers. Total RNA from pools of vesicles (3 pools with 6 vesicles each for each genotype) was obtained using the Rneasy Micro Kit (Qiagen). Residual DNA was removed using the Turbo DNA Free Kit (Thermofisher). 10-30 ng of total RNA were used per sample for library preparation.
Libraries were constructed using the QuantSeq 3' mRNA-Seq Library Prep Kit (Illumina), following the manufacturer's instructions.

tag: developmental stage

value: E10.5 mouse embryo

value: otic vesicle


title: ARH-77 KEAP1 KO Rep 3


title: Six1-KO rep3


title: ARH-77 KEAP1 KO Rep 1


title: 11B_M_1536


title: 11B_M_1534


title: N_to_G_3

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(N_to_G)-Mnase (kanMX)


title: 11B_M_1535


title: N_to_G_4


title: N_to_H_1


title: wt rep3

description: otic vesicles from E10.5 wild-type mouse embryo

value: wt


title: 11B_M_1533


title: wt rep1


title: wt rep2


title: ARH-77 WT DMSO Rep 2

value: WT


title: Six1-KO rep1


title: ARH-77 WT DMSO Rep 3


title: ARH-77 WT DMSO Rep 1


title: N_to_E_1

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(N_to_E)-Mnase (kanMX)


title: PDF 0.4 μM CDDO-2P-Im rep3

data_processing:
Cutadapt was used to remove reads with contamination/low quality
HISAT2 was used to map reads to genome
StringTie used to assembled and estimate transcription levels
edgeR used to estimate expression levels
Assembly: tp://ftp.ensembl.org/pub/release-96/fasta/homo_sapiens/dna/
Supplementary files format and content: Excel file includes FPKM and count values

source_name: PDF

growth_protocol: Cells were grown in low-serum fibroblast medium (ATCC).

value: PDF

value: Fibroblasts


title: 11B_M_1532


title: S27: HLF Axl KO Axl WT

city: Vienna

first: Wolfgang

last: Mikulits

address: Borschkegasse 8A

country: Austria

institute: Medical University of Vienna

data_processing:
Analyses were performed with the help of custom R (v. 4.0.0) scripts and RStudio.
Trimming of poly-As from the 3’-ends of the 76 bp long reads was performed by cutadapt (v. 1.12; with options -O 3 -e 0.10 -m 20 --max-n 2), retaining reads with at least 20 bp.
Alignments to the human reference genome GRCh38.p13 (GCA_000001405.28) and the corresponding Gencode gene annotation were done using STAR 2.7.3a, with up to 1000 hits, a maximum error rate of 5%, and counts per gene as output.
Assembly: human reference genome GRCh38.p13 (GCA_000001405.28)
Supplementary files format and content: dontain information about: "gene", "gene_id“, "baseMean" , "log2FoldChange", "lfcSE", "stat", "pvalue", "padj", "read counts sample_A_replicate#1", "read counts sample_A_replicate#2", "read counts sample_A_replicate#3", " read counts sample_B_replicate#1", " read counts sample_B_replicate#2", " read counts sample_B_replicate#3", "sample_A_,AVG", "sample_B_,AVG", "Gene,type", "Gene,name", "Synonym", "Description"

source_name: liver

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

extract_protocol:
Total RNA was isolated using the Monarch total RNA miniprep kit (New England Biolabs, Ipswich, Massachusetts, USA).
Library preparation and sequencing was performed by Lexogen (Greenland, New Hampshire, USA). In brief, quality controlled and quantified RNA was used to prepare a QuantSeq 3’ mRNA-seq (fwd) library suitable for Illumina sequencing, containing Unique Molecular Identifiers (UMIs).

treatment_protocol: Axl signaling was ensured by stimulation with 500ng/mL recombinant Gas6 for 24 hours.

value: liver

value: HLF

value: Hepatocellular carcinoma cell line

value: Axl KO re-expressing WT Axl

value: Axl stimulation with Gas6


title: 10H

type: genomic

city: Xi'an

first: huayu

last: Zhu

address: No. 28 Road

institute: Fourth

description: hypertrophic scar

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Infinium Methylation EPIC BeadChip (850k) using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: hypertrophic scar

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from normal skin and hypertrophic scar samples using Qiagen DNeasy Kit according to standard instructions

value: hypertrophic scar


title: 4N

description: normal skin

source_name: normal skin

value: normal skin


title: N_to_D_2

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(N_to_D)-Mnase (kanMX)


title: N_to_E_2


title: 11B_M_1531

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2

source_name: C57BL/6J Male P56 Mouse Brain

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

value: male


title: 8N

description: normal skin


title: 11B_M_1530


title: N_clustering_5_2

source_name: budding yeast culture at OD=4

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(N_clustering_5)-Mnase (kanMX)


title: 10N

description: normal skin


title: 4H

description: hypertrophic scar


title: PDF 0.4 μM CDDO-2P-Im rep2

value: 0.4 μM CDDO-2P-Im


title: S25: HLF Axl KO

value: Axl KO


title: PDF 0.1 μM CDDO-2P-Im rep3

value: 0.1 μM CDDO-2P-Im


title: 3N

description: normal skin


title: 11B_M_1529


title: N_to_D_1


title: 9H

description: hypertrophic scar


title: S7: HLF Axl KO Axl WT


title: 8H

description: hypertrophic scar


title: PDF 0.1 μM CDDO-2P-Im rep2

value: WT


title: 11B_M_1528


title: NS_swapped_2

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(NS_swapped)-Mnase (kanMX)


title: NS_swapped_1


title: N_clustering_5_1


title: 11B_M_1527


title: PDF 0.4 μM CDDO-2P-Im rep1

value: PDF


title: NQ_to_A_1

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(NQ_to_A)-Mnase (kanMX)


title: S15: HLF Axl KO

value: liver


title: 3H

description: hypertrophic scar


title: WT-AG-haESC-3

city: Shanghai

address: 320 Yueyang Road

department: institute of biochemistry and cell biology

institute: Chinese Academy of Science

data_processing:
The adapter sequences were removed from the 3’ end of the sequenced reads using the fastp program (version 0.20.1) with parameters “-l 15 --length_limit 40”
The remaining reads were mapped to the mouse genome (version GRCm38) using bowtie (version 1.2.1.1) first.
The mapped reads were mapped again to the mature miRNA sequences annotated in miRbase (version 21), allowing -2 or +2 nt to be templated by the corresponding genomic sequence at the 3’ end to determine the expression level of each miRNA.
The differential expression analysis of each miRNA were performed by R package DESeq2 (version 1.30.1).
The miRNAs with foldchange >1.414 and P-value <0.05 were defined as significant different expressed miRNAs.
Assembly: GRCm38
Supplementary files format and content: Matrix table with raw miRNA counts for every miRNA and every sample

source_name: AG-haESCs

extract_protocol:
Total RNA was extracted from E6.5 and E7.5 embryos and AG-haESCs by using miRNeasy Micro Kit (QIAGEN, Cat#217084) according to the manufacturer's instructions.
The preparation of CAS-seq cDNA library was mainly followed the published protocol (Yang. Q., et al., 2019, Nature Communications). The extracted RNA (100 pg) underwent the following steps to construct small RNA libraries: adapter ligation, first-strand cDNA synthesis, Cas9/sgRNA treatment, on-bead in vitro transcription, second RT and PCR amplification and gel purification. An Illumina NovaSeq 6000 System was used to sequence the small RNA libraries at the MingmaTechnologies Co., Ltd., China

value: ESCs

tag: tisuue

value: AG-haESCs


title: 11N

description: normal skin


title: S13: HLF Nickase

value: HLF

value: Hepatocellular carcinoma cell line

value: CRISPR control cell line (only transfected with enzyme but no sgRNAs)


title: 11B_M_1526


title: S5: HLF Axl KO

value: Axl stimulation with Gas6


title: S3: HLF Nickase


title: 11B_M_1525


title: S17: HLF Axl KO Axl WT

value: Axl KO re-expressing WT Axl


title: NQ_to_A_2

data_processing:
demultiplexing with bcl2fastq
filtering of adapter dimers using cutadapt
paired end alignment to S288C_R64 with bowtie2 (-p8 --local --very-sensitive --trim-to 30 --dovetail)
genome coverage with bedtools (-5 -fs 1 -d)
Assembly: GCA_000146045.2 (R64)
Supplementary files format and content: *.out.gz file contains zipped genome coverage for all 12,157,105 bases in the S. cerevisiae genome (Chr 1-16+mitochondria)
Library strategy: ChEC-seq


title: 11H

description: hypertrophic scar

value: hypertrophic scar


title: NQ_shift_1

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(NQ_shift)-Mnase (kanMX)


title: S21: HLF wt


title: 9N

description: normal skin

value: normal skin


title: PDF 0.1 μM CDDO-2P-Im rep1

value: Fibroblasts


title: PDF DMSO rep2

value: DMSO


title: NQ_shift_2


title: S23: HLF Nickase


title: S11: HLF wt

value: WT


title: WT-AG-haESC-2


title: NQ_deletion_B

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(NQ_deletion)-Mnase (kanMX)


title: PDF DMSO rep3

value: PDF


title: WT-AG-haESC-1


title: 408-AG-haESC-2


title: 408-AG-haESC-3


title: S1: HLF wt


title: 408-AG-haESC-1


title: OVCAR-8 0.8 μM CDDO-2P-Im rep1

growth_protocol: Cells were grown in DMEM medium with 10% FBS with 1% pen/strep

value: Ovarian

value: 0.8 uM CDDO-2P-Im


title: OVCAR-8 0.8 μM CDDO-2P-Im rep3


title: MSN2WT_6

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2-Mnase (kanMX)


title: PDF DMSO rep1


title: MCF10A, p53 -/-, 10uM Nutlin3a, Replicate 2

city: Boulder

first: Taylor

middle: K

last: Jones

state: CO

address: 3415 Colorado Ave

institute: University of Colorado Boulder

data_processing:
library strategy: PRO-seq
Mapping of PRO-seq data was performed using the NascentFlow Pipeline (DOI 10.17605/OSF.IO/NDHJ2)
Assembly: hg38
Supplementary files format and content: proseq_mumerge_bidirectional_RNA_counts.txt

source_name: MCF10A Cells

extract_protocol:
As previously described in (Levandowski, C. B.; Jones, T.; Gruca, M.; Ramamoorthy, S.; Dowell, R. D.; Taatjes, D. J, 2021), after treatment the cells were washed 3x with ice cold PBS, and then treated with 10 ml (per 15 cm plate) ice-cold lysis buffer (10 mM Tris–HCl pH 7.4, 2 mM MgCl2, 3 mM CaCl2, 0.5% NP-40, 10% glycerol, 1 mM DTT, 1x Protease Inhibitors (1mM Benzamidine (Sigma B6506-100G), 1mM Sodium Metabisulfite (Sigma 255556-100G), 0.25mM Phenylmethylsulfonyl Fluoride (American Bioanalytical AB01620), and 4U/mL SUPERase-In). Cells were centrifuged with a fixed-angle rotor at 1000xg for 15 min at 4◦C. Supernatant was removed and pellet was resuspended in 1.5 mL lysis buffer to a homogenous mixture by pipetting 20-30X before adding another 8.5 mL lysis buffer. Suspension was centrifuged with a fixed-angle rotor at 1000xg for 15 min at 4◦C. Supernatant was removed and pellet was resuspended in 1 mL of lysis buffer and transferred to a 1.7 mL pre-lubricated tube (Costar cat. No. 3207). Suspensions were then pelleted in a microcentrifuge at 1000xg for 5 min at 4◦C. Next, supernatant was removed and pellets were resuspended in 500 μL of freezing buffer (50 mM Tris pH 8.3, 40% glycerol, 5 mM MgCl2, 0.1 mM EDTA, 4U/ml SUPERase-In). Nuclei were centrifuged 2000xg for 2 min at 4◦C. Pellets were resuspended in 100 μL freezing buffer. To determine concentration, nuclei were counted from 1 μL of suspension and freezing buffer was added to generate 100 μL aliquots of 10x106 nuclei. Aliquots were flash frozen in liquid nitrogen and stored at −80◦C.
Nuclear run-on experiments were performed as described previously (Mahat, D. B., Kwak, H., Booth, G. T., Jonkers, I. H., Danko, C. G., Patel, R. K., et al. (2016). Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq). Nature Protocols, 11(8), 1455–1476. with the following modifications: the final concentration of non-biotinylated CTP was raised from 0.25 μM to 25 μM, a clean-up and size selection was performed using 1X AMPure XP beads (1:1 ratio) (Beckman) prior to test PCR and final PCR amplification, and the final library clean-up and size selection was accomplished using 1X AMPure XP beads (1:1 ratio) (Beckman).

treatment_protocol: Cells were treated simultaneously with 10μM Nutlin3a or 0.1% DMSO for 3 hour.

value: mammary gland; breast

value: epithelial

value: 10uM Nutlin3a

tag: molecule subtype

value: nascent RNA


title: OVCAR-8 0.4 μM CDDO-2P-Im rep3

value: 0.4 uM CDDO-2P-Im


title: MSN2WT_5

extract_protocol:
Phenol chlorofrom extraction
One tube library construction based on Skeene et al. 2017 as described in Gera 2021


title: Mir-6KO-AG-haESC-2

value: ESCs

value: AG-haESCs


title: MCF10A, p53 -/-, 10uM Nutlin3a, Replicate 1


title: OVCAR-8 0.4 μM CDDO-2P-Im rep2


title: MSN2WT_3


title: Mir-6KO-AG-haESC-1


title: OVCAR-8 0.4 μM CDDO-2P-Im rep1


title: MCF10A, p53 -/-, DMSO, Replicate 2


title: OVCAR-8 0.8 μM CDDO-2P-Im rep2


title: MSN2WT_2


title: O48-AG-haESC-3


title: NQ_deletion_A


title: OVCAR-8 DMSO rep3


title: MSN2WT_1


title: O48-AG-haESC-2


title: MCF10A, p53 -/-, DMSO, Replicate 1


title: OVCAR-8 DMSO rep2


title: Left_positive_right_negative_2

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(Left_positive_right_negative)-Mnase (kanMX)


title: O48-AG-haESC-1


title: Left_positive_right_negative_1


title: MCF10A, 10uM Nutlin3a, Replicate 1


title: DKO-SC-3

source_name: semi-cloned embryo

value: C57BL/6 male X F1 female

value: semi-cloned embryo


title: MCF10A, 10uM Nutlin3a, Replicate 2


title: MCF10A,  DMSO, Replicate 2


title: OVCAR-8 DMSO rep1

value: DMSO


title: SF8628 0.7 μM CDDO-2P-Im rep3

description:
FPKM.G2_700_3
SF8268-2P-FPKM.xlsx

data_processing:
Cutadapt was used to remove reads with contamination/low quality
HISAT2 was used to map reads to genome
StringTie used to assembled and estimate transcription levels
edgeR used to estimate expression levels
Assembly: tp://ftp.ensembl.org/pub/release-96/fasta/homo_sapiens/dna/
Supplementary files format and content: tab-delimited text files include RPKM values

value: DIPG

value: WT

value: 0.7 μM CDDO-2P-Im


title: SF8628 0.7 μM CDDO-2P-Im rep2

description:
FPKM.G2_700_2
SF8268-2P-FPKM.xlsx


title: L_to_A_1

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(L_to_A)-Mnase (kanMX)


title: MCF10A, DMSO, Replicate 1


title: DKO-SC-2


title: DKO-SC-1


title: L_to_A_2


title: SF8628 0.7 μM CDDO-2P-Im rep1

description:
FPKM.G2_700_1
SF8268-2P-FPKM.xlsx


title: Dnmt-TKO-SC-3


title: Dnmt-TKO-SC-2


title: LI_shift_6

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(LI_shift)-Mnase (kanMX)


title: SF8628 0.3 μM CDDO-2P-Im rep3

description:
FPKM.G1_300_3
SF8268-2P-FPKM.xlsx

value: 0.3 μM CDDO-2P-Im


title: SF8628 0.3 μM CDDO-2P-Im rep2

description:
FPKM.G1_300_2
SF8268-2P-FPKM.xlsx


title: Sample.86

city: Aurora

first: Sana

middle: D

last: Karam

address: 1665 Aurora Ct.

department: Radiation Oncology

institute: CU Denver Anschutz

data_processing:
Reads were aligned and counts generated using Biospyder TempoSeqr platform. Genes with <1 mean raw counts or <1 mean counts per million (CPM) were removed from the data set. Differential expression was calculated using the limma R package. The resulting fold change was used with the fgsea R package to perform gene set enrichment analysis for Hallmark and C2 Curated gene sets. Heat map displaying Z-score transformed gene expression was generated using the ComplexHeatmap R package (v1.20.0) and hierarchical clustering using Euclidean distance with complete linkage.
Supplementary files format and content: Excel, CPM

extract_protocol:
Tumor tissue collected from patients at time of initial biopsy and at time of surgery were used for RNA sequencing. A pathologist reviewed H&E stains of the tumor samples, and areas of tumor cellularity were identified and marked. Only the pathologist-marked areas of tumor cellularity were scraped and processed per BioSpyder kit instructions.
For the human RNA sequencing library preparation, lysates were made from scapes using BioSpyer FFPE lysis protocol, then diluted in 1:5 in 1X TempO-Seq Lysis Buffer, and processed through a TempO-Seq Human Full Transcriptome FFPE Assay 96 sample Kit(BioSpyder, Carlsbad, CA).

value: Tumor

tag: response

value: Unk

value: PDAC

tag: timepoint

value: Post

value: Neoadjuvant chemo, 30-33.6 Gy SBRT, pancreaticoduodenectomy and adjuvant chemotherapy


title: LIV_random3_B

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(LIV_random3)-Mnase (kanMX)


title: LI_shift_5


title: Dnmt-TKO-SC-1


title: Sample.80


title: Sample.87

value: Pre


title: SF8628 0.3 μM CDDO-2P-Im rep1

description:
FPKM.G1_300_1
SF8268-2P-FPKM.xlsx


title: LIV_random3_A


title: WT-SC-3


title: Sample.78


title: SF8628 DMSO rep3

description:
FPKM.Control_3
SF8268-2P-FPKM.xlsx


title: Sample.77


title: LIV_random2_B

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(LIV_random2)-Mnase (kanMX)


title: Sample.76

value: R


title: SF8628 DMSO rep2

description:
FPKM.Control_2
SF8268-2P-FPKM.xlsx


title: WT-SC-2

value: C57BL/6 male X F1 female

value: semi-cloned embryo


title: LIV_random2_A


title: WT-SC-1


title: Sample.74


title: SF8628 DMSO rep1

description:
FPKM.Control_1
SF8268-2P-FPKM.xlsx

value: DIPG

value: DMSO


title: Mir-6KO-Dnmt-TKO-SC-3


title: shPRRC2B polysome bio rep 3

city: Rochester

first: feng

last: jiang

state: New York

address: 601 Elmwood Ave box CVRI

department: Biochemistry and Biophysics

institute: University of Rochester

data_processing:
Raw reads were demultiplexed using bcl2fastq version 2.19.0.
Quality filtering and adapter removal were performed using Trimmomatic version 0.36
Processed/cleaned reads were then mapped to the Homo sapien reference genome (GRCh38, hg38) with Hisat version 2.1.0
The subread-2.0.1(57) package (featureCounts) was used to derive gene counts based on utilizing the gencode.v38 gene annotations
Normalizing raw counts and identifying significantly changed genes were performed by DESeq2 within an R-4.1.2 environment.
Assembly: GRCh38, hg38
Supplementary files format and content: comma-delimited table includes raw counts for each sample
Library strategy: Polysome-Seq

growth_protocol: Human HEK293T cells were propagated in Dulbecco's modified Eagle's medium (DMEM; Gibco) supplemented with 10% fetal bovine serum.

extract_protocol:
For total RNA extraction, cells were lysed by 1000 ml of Trizol (Qiagen), then mixed with 200 ml of chloroform.  The mixture was spun down at 16,000 g for 10 min. RNA was precipitated from the aqueous layer by adding two volumes of isopropanol and spinning down at 16,000 g for 10 min. The pellet was washed twice with 70% ethanol, left to dry, and resuspended in nuclease-free water. For ploysome-associated RNA extraction, 400 ml of each fraction was mixed with an equal amount of chloroform: phenol: isoamyl alcohol and 0.1 x of 3M sodium acetate (pH 5.2), then spun down at 16,000 g for 10 min. The upper aqueous layer was mixed with 3 volumes of 100% ethanol and 0.1 volume of 3M sodium acetate (pH 5.2) and left to incubate at -20°C overnight. The solution was then spun at maximum speed for 30 min to pellet the RNA, which was washed twice with 70% ethanol and resuspended in nuclease-free water.
RNA libraries for RNA-seq were prepared using NGS Library Prep Kit following manufacturer's protocols.

treatment_protocol: Human HEK293T cells were treated with a doxycycline (Dox)-inducible short hairpin RNA (shRNA) targeting PRRC2B (shPRRC2B) or a non-silencing control shRNA (shCtrl)

value: human embryonic kidney

value: PRRC2B knockdown

tag: fraction

value: polysome-associated RNA


title: Mir-6KO-Dnmt-TKO-SC-2


title: LIV_random1_B

tag: genotype

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(LIV_random1)-Mnase (kanMX)


title: Sample.73

value: Tumor


title: LIV_random1_A


title: shPRRC2B polysome bio rep 2


title: Sample.69

value: Unk


title: shPRRC2B polysome bio rep 1


title: LIV_deletion_A

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(LIV_deletion)-Mnase (kanMX)


title: LIV_deletion_B


title: shPRRC2B total bio rep 3

data_processing:
Raw reads were demultiplexed using bcl2fastq version 2.19.0.
Quality filtering and adapter removal were performed using Trimmomatic version 0.36
Processed/cleaned reads were then mapped to the Homo sapien reference genome (GRCh38, hg38) with Hisat version 2.1.0
The subread-2.0.1(57) package (featureCounts) was used to derive gene counts based on utilizing the gencode.v38 gene annotations
Normalizing raw counts and identifying significantly changed genes were performed by DESeq2 within an R-4.1.2 environment.
Assembly: GRCh38, hg38
Supplementary files format and content: comma-delimited table includes raw counts for each sample

value: total RNA


title: Mir-6KO-Dnmt-TKO-SC-1


title: Sample.67

value: PDAC

value: Neoadjuvant chemo, 30-33.6 Gy SBRT, pancreaticoduodenectomy and adjuvant chemotherapy


title: Control-SC-3


title: Sample.65

value: Pre


title: shPRRC2B total bio rep 2


title: LIV_cluster3_B

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(LIV_cluster3)-Mnase (kanMX)


title: Control-SC-1


title: LIV_cluster3_A


title: Sample.64

value: R

value: Post


title: LIV_cluster2_B

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(LIV_cluster2)-Mnase (kanMX)


title: LIV_cluster2_A


title: Sample.62


title: shCtrl polysome bio rep 3

value: control shRNA


title: E7.5-TKO-epi-2

source_name: embryo

value: C57BL/6 male X F1 female

value: embryo


title: E7.5-TKO-epi-3


title: Sample.70


title: shCtrl polysome bio rep 2

value: human embryonic kidney


title: E7.5-TKO-epi-1


title: LIV_cluster1_B

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(LIV_cluster1)-Mnase (kanMX)


title: Sample.61


title: LIV_cluster1_A


title: shCtrl polysome bio rep 1

value: polysome-associated RNA


title: Control-SC-2

value: semi-cloned embryo


title: E7.5-DKO-epi-4


title: shCtrl total bio rep 3


title: Sample.59

value: Tumor

value: NR


title: E7.5-DKO-epi-3


title: KR_to_A_2

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(KR_to_A)-Mnase (kanMX)


title: shPRRC2B total bio rep 1

value: PRRC2B knockdown

value: total RNA


title: KR_to_A_1


title: shCtrl total bio rep 2


title: Sample.63

value: PDAC

value: Pre

value: Neoadjuvant chemo, 30-33.6 Gy SBRT, pancreaticoduodenectomy and adjuvant chemotherapy


title: shCtrl total bio rep 1


title: E7.5-DKO-epi-2


title: Sample.58

value: R

value: Post


title: G_to_A_A

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(G_to_A)-Mnase (kanMX)


title: Sample.56


title: G_to_A_B


title: E7.5-KO-epi-4

value: C57BL/6 male X F1 female


title: Sample.55


title: FWY_to_A_6

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(FWY_to_A)-Mnase (kanMX)


title: E7.5-KO-epi-3

value: embryo


title: FWY_to_A_5


title: NRF2 SNU638

city: Guangzhou

first: Ziqing

last: Yang

address: 26th Yuancun Erheng Road, Tianhe District

department: Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor Disease

institute: Sun Yat-sen University

data_processing:
Basecalls were performed using fastp v0.23.0 for Novaseq output.
The raw data format is fastq, using fastp (https://github.com/OpenGene/fastp) software (parameters: step_qc: -l 50 -q 20 -u 50 --detect_adapter_for_pe)  including the raw data of IP and Input samples conduct quality control, including the removal of connectors, repetitive sequences and low-quality sequences, obtaining CleanData in fastq format; at the same time, using FastQC (https://github.com/s-andrews/FastQC) perform quality control analysis on raw data.
The Clean reads  were aligmented to the reference genome using bwa mem (version：0.7.17-r1188)
MACS2 was used for peak calling with the following parameters: macs2 callpeak -t -f BAMPE -g --keep-dup all -q 0.05 -B. Cut&Tag signal was converted to bigwig format for visualization using deepTools bamCoverage with the following parameters: --bs 5 --smoothLength 105 --normalizeUsing RPKM --scaleFactor 50.
Motif analysis was performed by using Homer software(version 4.11)
Assembly: hg38
Supplementary files format and content: bigWig
Supplementary files format and content: bed
Library strategy: CUT&Tag

source_name: cell line

growth_protocol: SNU638 cells were obtained from KCLB, and maintained at 37℃ and 5% CO2. Cells were maintained in Dulbecco modified Eagle medium media supplemented with 10% (v/v) fetal bovine serum (FBS).

extract_protocol:
Briefly，about 100000 cells were washed twice gently with wash buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1× Protease inhibitor cocktail). 10μL Concanavalin A coated magnetic beads  were added per sample and incubated at RT for 10min. Remove unbound supernatant and resuspended bead-bound cells with dig wash buffer (20mM HEPES pH 7.5; 150mM NaCl; 0.5mM Spermidine; 1× Protease inhibitor cocktail; 0.05% Digitonin; 2mM EDTA) and a 1:50 dilution of primary antibody incubated on a roating platform overnight at 4℃.  The primary antibody was removed using magnet stand. Sencondary antibody was diluted 1:100 in dig wash buffer and cells were incubated at RT for 60 min. cells were washed using the magnet stand 2-3 times in dig wash buffer . A 1:100 dilution of pA-Tn5 adapter complex was prepared in digmed buffer (0.01% Digitonin; 20mM HEPES pH 7.5; 300mM NaCl; 0.5mM Spermidine; 1× Protease inhibitor cocktail) and incubated with cells at RT for 1h. Cells were washed 2–3× for 5 min in 1 mL Dig-med buffer. Then cells were resuspended in tagmentation buffer (10mM MgCl2 in Dig-med Buffer) and incubated at 37 °C for 1 h. DNA was purified using phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation.
To amplify libraries, 20μL DNA was mixed with 2μL of a universal i5 and auniquely barcoded i7 primer. A volume of 25 μL PCR Master mix was added and mixed. The sample was placed in a Thermocycler with a heated lid using the following cycling conditions: 72 °C for 5 min (gap filling); 98 °C for 30 s; 14 cycles of 98 °C for 10 s and 63 °C for 30 s; final extension at 72 °C for 1 min and hold at 8 °C. Libraried clean-up was performed by beads. The size distribution of libraries was determined and libraries were mixed to achieve equal representation as desired aiming for a final concentration as recommended by the manufacturer. Sequencing was performed in the Illumina Novaseq 6000 using 150bp paired-end following the manufacturer’s instructions.

value: cell line

value: gastric cancer cell

tag: chip antibody

value: anti-NRF2, Cell Signaling Technology, 12721s


title: ACTL6A SNU638

value: anti-ACTL6A, Abcam, ab3882


title: E7.5-KO-epi-2


title: Sample.53

value: Tumor


title: Sample.60

value: NR


title: FWY_to_A_4


title: Sample.52


title: IgG SNU638

data_processing:
Basecalls were performed using fastp v0.23.0 for Novaseq output.
The raw data format is fastq, using fastp (https://github.com/OpenGene/fastp) software (parameters: step_qc: -l 50 -q 20 -u 50 --detect_adapter_for_pe)  including the raw data of IP and Input samples conduct quality control, including the removal of connectors, repetitive sequences and low-quality sequences, obtaining CleanData in fastq format; at the same time, using FastQC (https://github.com/s-andrews/FastQC) perform quality control analysis on raw data.
The Clean reads  were aligmented to the reference genome using bwa mem (version：0.7.17-r1188)
MACS2 was used for peak calling with the following parameters: macs2 callpeak -t -f BAMPE -g --keep-dup all -q 0.05 -B. Cut&Tag signal was converted to bigwig format for visualization using deepTools bamCoverage with the following parameters: --bs 5 --smoothLength 105 --normalizeUsing RPKM --scaleFactor 50.
Motif analysis was performed by using Homer software(version 4.11)
Assembly: hg38
Supplementary files format and content: bigWig
Supplementary files format and content: bed

value: gastric cancer cell line

value: IgG, Millipore cat.no. 12-370


title: Sample.51

value: PDAC


title: BRG1 SNU638

value: anti-BRG1, Proteintech, 21634-1-AP


title: Sample.50

value: Unk

value: Neoadjuvant chemo, 30-33.6 Gy SBRT, pancreaticoduodenectomy and adjuvant chemotherapy


title: E7.5-Con-epi-3


title: FWY_shift_5

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(FWY_shift)-Mnase (kanMX)


title: Retinal organoids, DD230, RUN4, HTO

city: Leiden

first: Hailiang

last: Mei

address: Einthovenweg 20

department: Sequencing Analysis Support Core

country: Netherlands

institute: Leiden University Medical Center

description:
10x Genomics
barcodes_pool4.tsv.gz
features_pool4.tsv.gz
matrix_pool4.mtx.gz

library_source: other

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger software (v6.0.1)
Assembly: GRCh38
Supplementary files format and content: Processed data file contains genes and HTO information per sample

molecule: protein

source_name: Retinal organoid

growth_protocol: CRB1 patient-derived hiPSCs were differentiated into retinal organoids using a previosuly reported differentiation protocol (Quinn et al, 2019; Zhong et al, 2014)

extract_protocol:
Retinal organoids were dissociated using an adapted protocol from the Papain Dissociation kit (Worthington, I-LK 03150). In short, single retinal organoids were selected and cut into small pieces to remove excess RPE or non-neural tissue as much as possible, and placed on a 48 well plate with 500µl dissociation solution (20 units/ml papain and 0.005% DNase). These were incubated for 30 minutes on a shaker in the incubator, then the organoids were triturated using a 1mL pipettor to dissociate the tissue. The plate was placed back for 15-20 minutes on the shaker in the incubator, then again triturated, this was repeated until a single cell suspension was obtained. 500µl albumin ovomucoid protease inhibitor solution was added to the single cell suspension, centrifuged at 300x g for 5min. Supernatant was removed, pellet resuspend in PBS and filtered through 40um cell strainer (Pluristrainer; SKU 43-10040-50). Filtered single cell suspension was centrifuged at 300x g for 5min at 4˚C and resuspend in 100µl staining buffer (2%BSA/0.01%Tween, PBS) with 10µl Fc Blocking reagent (FcX, BioLegend) for 10 minutes on ice. 0.5µg of unique Cell Hashing antibodies were added and incubated for 20 minutes on ice. Stained cells were washed 3 times with 1mL staining buffer; spin at 4 ˚C for 5 minutes at 350g. Stained single cell suspensions were counted for cell concentration and cell viability (TC20, Bio-rad). Typically, all single cell suspensions had a 70% or higher cell viability. Stained cells were pooled and re-count until desired concentration for single cell sequencing (cell viability at least 80%). Every sequencing round contained 14 hashed retinal organoid samples, the goal was to capture a total of approximately 30.000 cells per pool.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics)

treatment_protocol: Differentiation day 120 (DD120) retinal organoids were treated with AAV5.CMV.GFP, or with AAV5.CMV.hCRB1 + AAV5.CMV.GFP, or with AAV5.CMV.hCRB2 + AAV5.CMV.GFP and were analyzed at DD230.

value: Retinal organoid

tag: library type

value: HTO

tag: antibodies/tags

value: AAV.GFP, or AAV.GFP + AAV.hCRB1, or AAV.GFP + AAV.hCRB2


title: E7.5-Con-epi-2

value: C57BL/6 male X F1 female

value: embryo


title: Retinal organoids, DD230, RUN4

value: RNA


title: FWY_random3_B

address: Herzl St 234

institute: Weizmann Institute

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(FWY_random3)-Mnase (kanMX)


title: E7.5-DKO-epi-1


title: IgG SNU638, 2

value: cell line

tag: cell type

value: Millipore cat.no. 12-370


title: E7.5-Con-epi-1

tag: strain


title: Retinal organoids, DD230, RUN3, HTO

description:
10x Genomics
barcodes_pool3.tsv.gz
features_pool3.tsv.gz
matrix_pool3.mtx.gz


title: E7.5-TKO-exe-4


title: Sample.47

value: Tumor

value: NR

value: Pre


title: FWY_random2_B

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(FWY_random2)-Mnase (kanMX)


title: E7.5-TKO-exe-3


title: Retinal organoids, DD230,  RUN3


title: Sample.46

value: R

value: PDAC

value: Post


title: E7.5-KO-epi-1


title: E7.5-TKO-exe-2


title: FWY_random3_A


title: FWY_shift_6

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(FWY_shift)-Mnase (kanMX)


title: FWY_random2_A


title: FWY_deletion_B

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(FWY_deletion)-Mnase (kanMX)


title: E7.5-TKO-exe-1


title: Sample.45

value: Neoadjuvant chemo, 30-33.6 Gy SBRT, pancreaticoduodenectomy and adjuvant chemotherapy


title: Sample.49

value: Unk


title: Retinal organoids, DD230, RUN2

description:
10x Genomics
barcodes_pool2.tsv.gz
features_pool2.tsv.gz
matrix_pool2.mtx.gz

value: Retinal organoid

value: AAV.GFP, or AAV.GFP + AAV.hCRB1, or AAV.GFP + AAV.hCRB2


title: Retinal organoids, DD230, RUN1, HTO

description:
10x Genomics
barcodes_pool1.tsv.gz
features_pool1.tsv.gz
matrix_pool1.mtx.gz

value: HTO


title: E7.5-DKO-exe-4

value: C57BL/6 male X F1 female

value: embryo


title: Sample.43


title: Sample.42


title: Sample.48


title: FWY_cluster3_F

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(FWY_cluster3)-Mnase (kanMX)


title: Sample.41

value: Tumor


title: Macrophage, oxLDL and glucose induction, 2

first: Jie

last: Qi

state: Shaanxi

address: 256 West youyi Rd.

department: Second Department of Cardiovascular Medicine

institute: Shaanxi Provincial People's Hospital

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v4-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.
The raw reads were further processed with a bioinformatic pipeline tool, BMKCloud(www.biocloud.net) online platform.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Hisat2 tools soft were used to map with reference genome.
Assembly: GRCh38_release101
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: THP-1 cells was maintained in PRMI-1640 medium supplemented with 10% FBS (Gibco BRL, USA) in a cell culture incubator (5% CO2, 37℃).

extract_protocol:
Total RNA was extracted using the Total RNA Extraction Kit (TAKARA, JPN), 1 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the NEBNext UltraTM RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: THP-1 cells were induced into macrophages, and then underwent different treatments for 48 h.

value: monocyte

tag: pre-treatment

value: induced to macrophages by PMA, LPS plus IFN-gamma

value: oxLDL and glucose induction


title: Retinal organoids, DD230, RUN1

value: RNA


title: Retinal organoids, DD230, RUN2, HTO


title: FWY_cluster3_E

first: Naama

last: Barkai


title: Sample.40

value: PDAC


title: FWY_cluster3_B


title: FWY_cluster3_A


title: Sample.39

value: Pre


title: Sample.38

value: Post


title: E7.5-DKO-exe-1


title: E7.5-DKO-exe-2


title: Macrophage, oxLDL induction, 1

value: oxLDL induction