title: PC3_2

description:
control
PC3_group_gene_fpkm.txt

value: DMSO


title: PC3_3

status: Public on Sep 12 2023

type: SRA

city: nan ning

first: 周

last: 青鸟

address: shaungyonglu street num 22

country: China

institute: Guangxi Medical University

description:
control
PC3_group_gene_fpkm.txt

library_source: transcriptomic

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: Prostate

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Prostate

tag: cell line

tag: cell type

value: Prostate cancer cells

tag: genotype

value: WT

tag: treatment


title: PC3_1

description:
control
PC3_group_gene_fpkm.txt


title: C. elegans whole oocytes Rep-2

city: Nice

first: Arnaud

last: Hubstenberger

address: 28 avenue Valrose

department: IBV

country: France

institute: Université Côte D'Azur

data_processing:
Demultiplexing was performed by bcl2fastq application, sequencing reads were checked for quality by FastQC and 4 bases of the 5’-end, and 1 base of the 3’-end were trimmed. Read mapping was then performed on a local Galaxy server.
Reads were aligned to the C. elegans genome (WBcel235.96) using HISAT2 v2.1.0. For the alignment, the following stranded revers-forward design parameters were used: function governing the maximum number of ambiguous characters was allowed, maximum mismatch penalty = 6, minimum mismatch penalty = 2, maximum soft clipping penalty = 2, minimum soft clipping penalty = 1, ambiguous read penalty = 1, read gap open penalty = 5, read gap extend penalty = 3, reference gap open penalty = 5, reference gap extend penalty = 3, penalty for canonical splice sites = 0, penalty for non-canonical splice sites = 12, minimum intron length = 20, maximum intron length = 140000
To estimate relative RNA abundance for each transcript species, FPKM (Fragments Per Kilobase Million) and TPM (Transcripts Per Kilobase Million) were computed with StringTie using default parameters.
Raw read counts were determined for each annotated gene by HTseq-count using default stranded parameters.
DESeq2 Bioconductor package was used to detect fold-change differences between groups taking into account internal normalization with correction for library size and RNA composition bias.
Assembly: WBcel235.96
Supplementary files format and content: Gene_abundances_StringTie (samples in columns, replicates numbered1-3)
Supplementary files format and content: Raw_reads_HTSeqCounts (samples in columns, replicates numbered1-3)

organism: Caenorhabditis elegans

source_name: germline

extract_protocol:
Total RNA was extracted using a miRNeasy FFPE kit (Qiagen) with adaptations: i) deparaffinization step was skipped, and ii) since sorted oocyte P-bodies were subcellular fractions, the separation of cell debris by centrifugation was omitted for these samples.  The subsequent steps followed the recommendations of the supplier. the process included DNase-I treatment and revers crosslink of fixed fractions.
Ten ng of total RNA were used. Briefly, paired-end RNA-seq libraries with barcodes were generated using SMARTer Stranded Total RNA-Seq Kit v2 - Pico (Takara). The quality and average size of the libraries were confirmed with Agilent High Sensitivity DNA Chips (Agilent 2100 BioAnalyser), and the concentration was measured with dsDNA HS Assay Kit (Invitrogen) using a Qubit 4.0. For RNA-seq, libraries were pooled in equimolar concentrations of 4 nM.

tag: strain -_flourescent_labelling

value: fog2; car1:GFP, pgl1:RFP

tag: Sex

value: female

tag: developmental stage

value: oocyte arrest

tag: time

value: Day 3

tag: selection

value: dissected

value: germline


title: C. elegans whole oocytes Rep-1


title: LNCaP_5_0_Era_2

description:
treatment
LNCaP_group_gene_fpkm.txt

value: LNCaP


title: LNCaP_1

description:
control
LNCaP_group_gene_fpkm.txt


title: LNCaP_2

description:
control
LNCaP_group_gene_fpkm.txt


title: LNCaP_5_0_Era_1

description:
treatment
LNCaP_group_gene_fpkm.txt


title: Do18, moDC, LPS-R848, 48h

city: Nantes

first: Mickael

last: Guilbaud

address: 22 Boulevard Bénoni Goullin

data_processing:
The bioinformatic analysis was performed using a Snakemake-based (v5.71) pipeline for 3' seq RNA profiling. The pipeline code can be found at https://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline
The fastq files were trimmed using cutadapt (v1.18)
The trimmed fastq files were aligned to the hg19 reference transcriptome using bwa (v0.7.17-r1188)
A UMI count matrix was generated using pysam
The expression matrix was filtered and processed in R (3.6.1 (2019-07-05) using DEseq2 (v1.26.0)
Assembly: hg19
Supplementary files format and content: A tab delimited file containing the normalized gene expression count matrix, which was obtained using DESeq2 (v1.26.0)

source_name: monocyte-derived dendritic cell

growth_protocol: Fresh or frozen monocytes were differentiated in moDCs for 7 days at 37°C in RPMI medium supplemented with 10% Fetal Bovine Serum (GE HealthCare), 1% Penicillin/Streptomycin (ThermoFisher Scientific), 100 ng/mL of rGM-CSF (15 uL), 20ng/mL of rIL-4 (3 uL) and 20 ml/mL) of Human Serum Albumin (1.5 mL)

extract_protocol:
Total RNA was obtained from lysis of cell using TRIzol® (ThermoFisher Scientific) and chloroform-based (Merck) extraction. Briefly, 1 mL of TRIzol was added right after thawing to the frozen cell pellet to avoid RNA degradation, then after homogenization, 200 µL of chloroform was added. After a centrifugation step at 12,000g at +4°C, the upper aqueous phase was collected and mixed with glycogen and isopropanol. After precipitation, washing and Nanodrop quantification (ThermoFisher Scientific), total RNA was then treated with RNAse-free DNAse I from TURBO DNA-freetM Kit (ThermoFischer Scientific) to eliminate DNA contamination.
3'seq-RNA Profiling protocol was performed according to  (Charpentier et al., 2021). The libraries were prepared from 10 ng of total RNA in 4µl. The mRNA poly(A) tails were then tagged with universal adapters, well-specific barcodes and unique molecular identifiers (UMIs) during template-switching reverse transcription. Barcoded cDNAs from multiple samples were then pooled, amplified and tagmented using a transposon-fragmentation approach which enriches for 3'ends of cDNA: 200ng of full-length cDNAs were used as input to the Nextera™ DNA Flex Library Prep kit (ref #20018704, Illumina) and Nextera™ DNA CD Indexes (24 Indexes, 24 Samples) (ref #20018707, Illumina) according to the manufacturer's protocol (Nextera DNA Flex Library Document, ref #1000000025416 v04, Illumina). The size of library was controlled on 2200 Tape Station Sytem (Agilent Technologies). A library of 350-800 bp length was run on a NovaSeq 6000 using NovaSeq 6000 SP Reagent Kit 100 cycles (ref #20027464, Illumina) with 17*-8-105* cycles read. *Illumina recommended to add an additional cycle to the reads when sequencing on the NovaSeq
3'seq RNA-seq

treatment_protocol: Monocytes-derived Dendritic Cells were infected by rAAV8 GFP at a multiplicity of infection (MOI) of 1e6 vector genome per cell or recombinant Adenovirus expressing the eGFP under the control of the CMV promoter at a MOI = 500 Infectious particles per cells. As controls, moDC were incubated with Lipoloysaccharide/Resiquimod (LPS/R848) - TLR4/TLR7/TLR8 activation cocktail (0.1 µg/mL of LPS and 1µg/mL of R848) or in medium for non-activated control (NA)

tag: donor

value: monocyte-derived dendritic cell

tag: timing


title: Do18, moDC,Adenovirus, 48h

value: Adenovirus


title: Do18, moDC, AAV8ss, 48h


title: Do18, moDC, non-activated, 48h

value: non-activated


title: Do15, moDC, AAV8ss, 48h


title: Do15, moDC, LPS-R848, 48h


title: Do14, moDC, AAV8ss, 24h


title: Do15, moDC, non-activated, 48h


title: Do14, moDC, AAV8ss, 48h


title: Do14, moDC, non-activated, 48h


title: Do14, moDC, LPS-R848, 48h


title: LNCaP_5_0_Era_3

description:
treatment
LNCaP_group_gene_fpkm.txt


title: Do13, moDC, AAV8ss, 48h


title: Do13, moDC, LPS-R848, 48h


title: Do13, moDC, AAV8ss, 24h


title: Do13, moDC, Adenovirus, 48h


title: LNCaP_3

description:
control
LNCaP_group_gene_fpkm.txt


title: Do12, moDC, AAV8ss, 24h


title: Do12, moDC, Adenovirus, 48h


title: Do12, moDC, AAV8ss, 48h


title: Do12, moDC, LPS-R848, 48h


title: Do11, moDC, AAV8ss, 48h


title: Do13, moDC, non-activated, 48h


title: Do12, moDC, non-activated, 48h


title: Do11, moDC, non-activated, 48h


title: Do11, moDC, Adenovirus, 48h


title: Do10, moDC, AAV8ss, 48h


title: Do11, moDC, LPS-R848, 48h


title: Do10, moDC, Adenovirus, 48h


title: Do9, moDC, AAV8ss, 48h


title: Do10, moDC, LPS-R848, 48h


title: Do9, moDC, Adenovirus, 48h


title: Do9, moDC, non-activated, 48h


title: Do9, moDC, LPS-R848, 48h


title: Do8, moDC, Adenovirus, 48h


title: Do8, moDC, AAV8ss, 48h


title: Do7, moDC, AAV8ss. 48h


title: Do5, moDC, AAV8ss, 48h


title: Do14, moDC, Adenovirus, 48h


title: Do5, moDC, Adenovirus, 48h


title: Do7, moDC, Adenovirus, 48h


title: Do7, moDC, LPS-R848, 48h


title: Do1, moDC, Adenovirus,48h


title: Do8, moDC, LPS-R848, 48h


title: Do7, moDC, non-activated, 48h


title: HDLECs treated with 500 nM dmPGE2, n=2

city: New York

first: Timothy

middle: Cragin

last: Wang

state: New York

address: 1130 Saint Nicholas Avenue, ICRC

country: USA

institute: Columbia University

data_processing:
Illumina RTA
We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.19) for converting BCL to fastq format, coupled with adaptor trimming.
We perform a pseudoalignment to a kallisto index created from transcriptomes (Ensembl v96, Human:GRCh38.p12) using kallisto (0.44.0).
Assembly: Ensembl v96, Human:GRCh38.p12
Supplementary files format and content: tab-delimited text files include estimated transcript count values for each Sample

source_name: foreskin

growth_protocol: Human dermal lymphatic endothelial cells (HDLEC) from juvenile foreskin were purchased from Promocell (C-12216) and cultured in Endothelial Cell Growth Media MV2 (Promocell C22121). Cells were maintained in a humidified incubator set to 37°C and 5% CO2.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 200 ng of total RNA was used for the construction of sequencing libraries.
Libraries were constructed using Illumina TruSeq  RNA Library Prep Kit v2 following manufacturer's instructions

treatment_protocol: For PGE2 stimulation experiments, 3x105 cells per well were plated in a 12-well plate and allowed to seed overnight. dmPGE2 was added to a concentration of 500 nM, or PBS was used as a vehicle. Cells were incubated for 6 hours then harvested.

value: foreskin

value: HDLEC

value: lymphatic endothelial

value: 501 nM 16,16-dimethyl prostaglandin E2


title: Do5, moDC, non-activated, 48h


title: HDLECs treated with 500 nM dmPGE2, n=3

value: 502 nM 16,16-dimethyl prostaglandin E2


title: Do1, moDC, AAV8ss, 48h


title: HDLECs treated with 500 nM dmPGE2, n=1

value: 500 nM 16,16-dimethyl prostaglandin E2


title: HDLECs treated with vehicle, n=4

value: WT

value: PBS (vehicle)


title: HDLECs treated with 500 nM dmPGE2, n=4

value: 503 nM 16,16-dimethyl prostaglandin E2


title: HDLECs treated with vehicle, n=2


title: HDLECs treated with vehicle, n=1


title: HDLECs treated with vehicle, n=3


title: Do10, moDC, non-activated, 48h


title: Do8, moDC, non-activated, 48h


title: VMH, HCP-HP-RMEI, 8

city: Armidale

first: David

middle: J

last: Innes

state: New South Wales

address: University of New England

department: School of Environmental and Rural Science

country: Australia

institute: University of New England

data_processing:
The 119 RNA-seq 100 bp FASTQ files were assessed by sequencing confidence and integrity using FASTQC (Andrews, n.d.), version 0.11.8. Reads were removed that failed to pass quality thresholds and trimmed of low quality bases (Sliding Window of 4 bases at minimum quality Q15, minimum length 36 bases, trim leading 3 bases, trim trailing 3 bases) using the trimmomatic tool (Bolger et al., 2014), version 0.36. Surviving reads were mapped using STAR (Dobin et al., 2012), version 2.6.0b, against the Ovis aries (Oar_v3.1) reference genome from Ensembl (Yates et al., 2019) release 100 (Ovis_aries.Oar_v3.1.dna.toplevel.fa). Gene reads were counted using the featureCounts tool (Liao et al., 2013) referenced to the Ensembl (Yates et al., 2019) 100 annotation file (Oar_v3.1.100.gtf). This produced count tables for downstream normalisation and determination of differentially expressed (DE) genes. The entire analysis was completed on the Australian Galaxy web platform (Afgan et al., 2018), using wrappers for the above-mentioned tools. Approximately 86% of the average 22.3 million reads per sample in the hypothalamus (ARC, LHA and VMH) were aligned to the ovine reference genome. Approximately 43% of these reads were annotated to one gene, resulting in 20 904 of 27 054 genes (77%) in the ovine reference genome with more than 10 reads across all samples.
Assembly: Oar_v3.1
Supplementary files format and content: counts_matrix_allsamples.txt  - a matrix with first column as Ensembl ID and subsequent columns as raw counts featureCounts (output from featureCounts).

organism: Ovis aries

source_name: Ventromedial Hypothalamus (VMH)

growth_protocol: The experiment was conducted at the Queensland Animal Science Precinct, The University of Queensland, Gatton, Qld, Australia between May and August 2019. Forty Merino wethers of approximately 7 months age were sourced from a commercial supplier (Armidale, NSW, Australia), selected for inclusion in the experiment, weighed, ranked and blocked on LW (23.7 ± 1.42 kg) and randomly allocated to adjacent individual pens and one of five nutritional treatments within each block, resulting in eight replicates (i.e. individual wether) per treatment. Wethers were offered barley straw and their allocated pellet in separate feeders at 0800 h each morning after feed residues from the previous day were collected. The allocations of barley straw and pellets for wethers allocated to the HCP-HP-RMEI treatment were calculated every 7 days as a proportion of LW and weighed into daily allocations for each wether. Each HCP-HP-RMEI wether was fed the HCP-HP pellet at an amount restricted to the same intake (g DM kg/LW) as the LCP-LP-UMEI wether within its experimental block. For all other treatments, approximately 10% daily pellet residue was targeted to ensure the allocation of pellets remained ad libitum. The experiment was conducted at the Queensland Animal Science Precinct, The University of Queensland, Gatton, Qld, Australia between May and August 2019. The experiment consisted of a 24-day pre-experimental period, a 7-day pre-treatment covariate period and a 63-day experimental period. Forty Merino wethers of approximately 7 months age were sourced from a commercial supplier (Armidale, NSW, Australia), selected for inclusion in the experiment, weighed, ranked and blocked on LW (23.7 ± 1.42 kg) and randomly allocated to adjacent individual pens and one of five nutritional treatments within each block, resulting in eight replicates (i.e. individual wether) per treatment. Wethers were offered barley straw and their allocated pellet in separate feeders at 0800 h each morning after feed residues from the previous day were collected. The allocations of barley straw and pellets for wethers allocated to the HCP-HP-RMEI treatment were calculated every 7 days as a proportion of LW and weighed into daily allocations for each wether. Each HCP-HP-RMEI wether was fed the HCP-HP pellet at an amount restricted to the same intake (g DM kg/LW) as the LCP-LP-UMEI wether within its experimental block. For all other treatments, approximately 10% daily pellet residue was targeted to ensure the allocation of pellets remained ad libitum. Wethers were euthanased at the end of the experiment over four consecutive days, with two blocks euthanased each day in sequential pen order. All wethers were fed their respective nutritional treatments until euthanasia. Feeding time was staggered the day before euthanasia so that wethers were all fed exactly 2 h before they were euthanased. Wethers were euthanased by a sodium pentobarbitone overdose administered via the jugular vein, followed by exsanguination.

extract_protocol:
Approximately 30 mg of tissue sample was homogenised in 1 mL of TRIzol® reagent (Life Technologies; Carlsbad, CA, USA) before centrifuging at 13,000 g for 10 min at 4°C. The supernatant was removed and mixed vigorously with 200 µL of chloroform and incubated at room temperature for 3 min prior to centrifugation at 13,000 g for 10 min at 4°C. Approximately 350 µL of aqueous phase was mixed by pipette with an equal volume of ultra-pure isopropanol. Samples were incubated at room temperature for 10 min before centrifugation at 13,000 g for 10 min at 4°C with the supernatant discarded. The RNA pellets were washed with 1 mL of 70% ultra-pure ethanol and centrifuged at 7,500 g for 5 min at 4°C. The supernatant was discarded and the pellet was air dried for 5 min before resuspension in 30 µL of nuclease free water. The RNA yield and presence of contaminants was estimated using a Nanodrop® One spectrophotometer (Thermo Scientific; Waltham, MA, USA) before proceeding with further purification. The RNA was then mixed with 70 µL of nuclease free water, 250 µL of 100% ethanol and 350 µL RLT buffer (prepared with β-mercaptoethanol) and transferred directly to a RNEasy column. The RNA was retained on the column and washed using 350 µL RW1 before adding 80 µL of DNase incubation mix to the column membrane. The DNase incubation mix was prepared following the manufacturer’s instructions (RNAse-Free DNase Set; Qiagen, Hilden, Germany). The RNEasy columns were sat at room temperature for 15 min before the second 350 µL RW1 wash and centrifugation at 10,000 g for 30 sec at room temperature. The columns were then washed with RPE (3 x 500 µL). The columns were centrifuged at 10,000 g for 30 sec at room temperature for each wash, with the last wash centrifuged for 2 min. The flow through was discarded each time using a pipette. After the final wash, the column was centrifuged at 13,000 g for 2 min at room temperature in a new collector tube to completely remove the wash reagents. The RNA was eluted in 30 µL of nuclease free water, incubated at room temperature for 10 min and centrifuged at 10,000 g for 1 min. The integrity of the extracted RNA was confirmed by electrophoresis through a 1.5% agarose gel at 70 V for 45 min and the yield and presence of contaminants was estimated using a Nanodrop® One spectrophotometer (Thermo Scientific; Waltham, MA, USA).
The sample preparation and sequencing for the RNA were completed by the Ramaciotti Centre for Genomics, University of NSW, Sydney, NSW, Australia. The complementary deoxyribonucleic acid (cDNA) libraries were prepared using Illumina’s TruSeq stranded mRNA sample preparation kit following the manufacturer’s protocol and the libraries were sequenced using an Illumina NovaSeq 6000 producing 100 base pair single end reads with a target sequencing depth of at least 20 million reads. Briefly, mRNA was purified and fragmented with divalent cations and heat followed by a first strand cDNA synthesis with random primers and a second strand cDNA synthesis step. The cDNA library preparation protocol includes the repair of DNA fragment ends, 3' Adenylation of DNA fragments, sequencing adapter ligation, amplification of library via polymerase chain reaction, and library verification.

treatment_protocol: The experiment involved five nutritional treatments, four of which had divergent CP and P content and were considered experimental satiety models. These treatments targeted high and low CP and P content that broadly represented diets consumed by ruminants in northern Australia under the following conditions: 1) Wet season with adequate P – ad libitum intake of a High CP, High P diet (110 g CP/kg DM, 2.5 g P/kg DM; HCP-HP-UMEI), 2) Wet season with deficient P – ad libitum intake of a High CP, Low P diet (110 g CP/kg DM, 0.5 g P/kg DM; HCP-LP-UMEI), 3) Dry season with adequate P – ad libitum intake of a Low CP, High P diet (50 g CP/kg DM, 2.5 g P/kg DM; LCP-HP-UMEI), 4) Dry season with deficient P – ad libitum intake of a Low CP, Low P diet (50 g CP/kg DM, 0.5 g P/kg DM; LCP-LP-UMEI). These diets were formulated to provide 9 MJ metabolisable energy (ME) per kg DM and were fed ad libitum (Unrestricted ME Intake; UMEI). The fifth nutritional treatment (HCP-HP-RMEI) was designed to represent an experimental hunger model, where wethers were fed the HCP-HP diet restricted to provide the equivalent ME intake of wethers allocated to the LCP-LP-UMEI treatment.   The experimental diets were pellets (8 mm diameter) containing varying proportions of barley straw (~56%), sugar (~24%), cassava starch (~11%), gluten, monocalcium phosphate (as Biofos; The Mosaic Company, Florida, USA), lime, urea, bicarbonate of soda, gypsum, potassium chloride, magnesium oxide and trace mineral mix to generate the intended nutrient contents. All wethers were offered 5 g barley straw (35 mm chop length) DM/kg LW per day for the first 14 days of the experimental period to maintain rumination and to prevent acidosis. For the remainder of the experiment all wethers were offered 2.5 g barley straw (35 mm chop length) DM/kg LW per day to maintain rumen function and salivation.

value: Ventromedial Hypothalamus (VMH)

value: HCP-HP-RMEI


title: VMH, HCP-LP-UMEI, 8

value: HCP-LP-UMEI


title: VMH, LCP-LP-UMEI, 8

value: LCP-LP-UMEI


title: VMH, LCP-HP-UMEI, 8

value: LCP-HP-UMEI


title: Do6, moDC, non-activated, 48h

value: monocyte-derived dendritic cell


title: VMH, HCP-HP-RMEI, 7


title: VMH, LCP-LP-UMEI, 6


title: VMH, HCP-LP-UMEI, 6


title: VMH, HCP-HP-RMEI, 6


title: VMH, LCP-HP-UMEI, 6


title: VMH, LCP-HP-UMEI, 7


title: CDKO1312_D4aggregate_scRNAseq

city: Los Angeles

first: Fei-Man

last: Hsu

state: California

address: 610 Charles E Young Dr S

department: MCDB

institute: UCLA

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Valid cells and UMIs were determined by UMI-tools to generate whitelist. Reads corresponding to valid barcodes were aligned to GRCh38 with STAR 2.7, and only uniquely mapped reads were kept for further analyses.  Count matrices were generated by featureCounts v2.0.1 from the Subread R package, with UMIs info further appended to the alignment .bam file.  Finally, the count matrix of all valid cells was generated with umi_tools count function.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
TET1 CTRL and CDKO hESCs were differentiated as described above into iMeLCs and D4 aggregates for 10X Genomics analysis.  hESCs, iMeLCs and D4 aggregates from all six lines (n= 18 samples total) were dissociated into single cells with 0.05% Trypsin-EDTA (GIBCO, 25300-054), strained with 40um cell strainer (Flacon, 352340), and washed 5 times with ice-cold DPBS with 0.04% BSA.  Cell suspensions with viability over 70% was then proceeded to 10X Genomics GEM formation and library prep.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: D4 aggregate

value: TET1 catalytic domain knockout


title: CDKO1105_D4aggregate_scRNAseq

description: 10X Genomics


title: VMH, LCP-LP-UMEI, 5


title: VMH, HCP-HP-RMEI, 4


title: VMH, HCP-HP-UMEI, 8

value: HCP-HP-UMEI


title: VMH, LCP-HP-UMEI, 5


title: VMH, LCP-LP-UMEI, 4


title: CDKO1102_D4aggregate_scRNAseq

description: 10X Genomics


title: VMH, HCP-HP-RMEI, 5


title: VMH, HCP-HP-UMEI, 7


title: VMH, HCP-HP-UMEI, 6


title: VMH, LCP-LP-UMEI, 7


title: VMH, HCP-HP-RMEI, 3


title: VMH, HCP-HP-UMEI, 5


title: VMH, HCP-LP-UMEI, 7


title: CDKO1312_iMeLC_scRNAseq

description: 10X Genomics

value: iMeLC


title: CDKO1105_iMeLC_scRNAseq

description: 10X Genomics


title: CDKO1102_iMeLC_scRNAseq

description: 10X Genomics


title: VMH, LCP-LP-UMEI, 3


title: VMH, HCP-HP-UMEI, 4


title: CDKO1312_hESC_scRNAseq

description: 10X Genomics

value: hESC


title: VMH, HCP-LP-UMEI, 5


title: VMH, HCP-LP-UMEI, 4


title: CDKO1105_hESC_scRNAseq

description: 10X Genomics


title: VMH, LCP-HP-UMEI, 4


title: CDKO1102_hESC_scRNAseq

description: 10X Genomics


title: VMH, LCP-LP-UMEI, 2


title: VMH, LCP-HP-UMEI, 3


title: CTRL1109_D4aggregate_scRNAseq

description: 10X Genomics

value: Control


title: CTRL1109_iMeLC_scRNAseq

description: 10X Genomics


title: CTRL1106_D4aggregate_scRNAseq

description: 10X Genomics


title: CTRL1109_hESC_scRNAseq

description: 10X Genomics


title: CTRL1106_iMeLC_scRNAseq

description: 10X Genomics


title: CTRL1101_iMeLC_scRNAseq

description: 10X Genomics


title: CTRL1101_D4aggregate_scRNAseq

description: 10X Genomics


title: VMH, HCP-LP-UMEI, 3


title: VMH, LCP-HP-UMEI, 2


title: VMH, HCP-HP-UMEI, 3


title: VMH, HCP-HP-RMEI, 2


title: VMH, HCP-HP-UMEI, 2


title: VMH, LCP-HP-UMEI, 1


title: VMH, HCP-HP-UMEI, 1


title: VMH, LCP-LP-UMEI, 1


title: VMH, HCP-HP-RMEI, 1


title: VMH, HCP-LP-UMEI, 2


title: CTRL1101_hESC_scRNAseq

description: 10X Genomics


title: VMH, HCP-LP-UMEI, 1


title: CDKO1105_iMeLC_bulkRNAseq

description: bulk RNAseq

data_processing:
FastQC was used to check the quality of the sequencing reads.  After adaptor trimming with Cutadapt, read pairs with length above 30bp were kept, and aligned to the human reference genome GRCh38 using star.  Differentially expressed genes were called using edgeR package.
Assembly: GRCh38
Supplementary files format and content: Tab-separated count files

extract_protocol:
TET1 CTRL and CDKO hESCs were differentiated as described above into iMeLCs for bulk RNAseq.  Sorted cells or cell pellets were lysed in 350μL of RLT buffer (QIAGEN), and total RNA was extracted with RNeasy micro kit (QIAGEN, 74004).
Libraries were constructed with SMARTer Stranded Total RNA Sample Prep Kit (Takara 634861) following the manufacturer’s instructions.


title: LHA, HCP-LP-UMEI, 8

source_name: Lateral Hypothalamus (LHA)

value: Lateral Hypothalamus (LHA)


title: CDKO1312_hESC_bulkRNAseq

description: bulk RNAseq


title: CDKO1105_hESC_bulkRNAseq

description: bulk RNAseq


title: CDKO1102_hESC_bulkRNAseq

description: bulk RNAseq


title: CTRL1106_iMeLC_bulkRNAseq

description: bulk RNAseq


title: CTRL1101_hESC_bulkRNAseq

description: bulk RNAseq


title: LHA, LCP-HP-UMEI, 7


title: CTRL1106_hESC_scRNAseq

description: 10X Genomics


title: LHA, LCP-LP-UMEI, 8


title: LHA, LCP-HP-UMEI, 8


title: CDKO1102_iMeLC_bulkRNAseq

description: bulk RNAseq


title: LHA, HCP-HP-UMEI, 8


title: HiC_Saline_rep2

city: Helsinki

first: Liang

address: Viikinkaari 5

country: Finland

institute: University of Helsinki

library_source: genomic

data_processing:
The DLO Hi-C tool (Hong et al., 2019) v0.30 was applied to removes redundancy and reducing noise, removes pair end tags (PETs) of self-ligation, re-ligation, and dangling pairs.
The hiclib package was applied to calculate the eigenvector decomposition of the 1 Mb
A publicly available script (matrix2insulation.pl) was used to detect the TAD boundaries with default parameters at resolutions of 40 kb
The juicer_tools_1.13.01’s HiCCUPS was applied for discovery locally enriched peaks with default parameters at resolutions of 5 kb,10 kb
The juicer_tools’s HiCCUPS Diff was applied for discovery differential loops at resolutions of 5 kb,10 kb
Genome_build: hg19
Supplementary_files_format_and_content: bed,bedpe

molecule: genomic DNA

organism: Macaca mulatta

source_name: Cortical neuron

extract_protocol:
The cross-linked cells were lysed in lysis buffer,fragmentation of the genome using restriction enzymes
Hi-C libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Four male rhesus monkeys (Macaca mulatta; 3-4-year old; weighing from 3.0 to 5.0 kg),  were randomly divided into saline group (n=2) and morphine group (n=2). Morphine was subcutaneously (s.c.) injected into the back legs of monkey three times daily (at 9:00, 14:00, and 21:00 o’clock) for 90 days continuously to produce dependence. The doses of morphine were gradually elevated as following paradigm: day 1-7:3 mg/kg, day 8-14:6 mg/kg, day 15-21:9 mg/kg, day 22-28:12 mg/kg, day 29-90:15 mg/kg. Monkeys in saline group was injected subcutaneously three times daily with same volume of 0.9% saline (0.5 mL/kg) as a control.

value: Adult cortical neuron purified from the cortex regio

value: male

tag: age

value: 3-4 years

value: treated with saline as a control


title: LHA, HCP-HP-UMEI, 7


title: U3118 cells, GBM, rep2 (RNAseq)

city: Umeå

first: Silvia

last: Remeseiro

state: Västerbotten

address: UNIVERSITETSTORGET 4

department: UCMM

country: Sweden

institute: Umeå University

description: countmatrix_HGCC_RNASeq.xlsx column 'U3118_2'

data_processing:
Sequence reads were mapped to hg38 using STAR (options: --outSAMtype BAM SortedByCoordinate --seedSearchStartLmax 12 --outFilterScoreMinOverLread 0.3 --alignSJoverhangMin 15 --outFilterMismatchNmax 33 --outFilterMatchNminOverLread 0 --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outSAMstrandField intronMotif --quantMode GeneCounts)
Read count extraction and normalization were performed using R package DeSEQ2
Assembly: hg38
Supplementary files format and content: Excel file includes raw counts

molecule: polyA RNA

growth_protocol:
Astrocytes were cultured in AGM, or Astrocyte Growth Medium (#CC-3186) in humidified atmosphere with 5% CO2 at 37C
GBM Cells were grown in Feed Medium, which is composed of DMEM/F12 Glutamax (GIBCO, Life Technologies) and Neurobasal medium (GIBCO) mixed in 1:1 ratio, containing 1X B27 (Invitrogen, Life Technologies), 1X N2 (Invitrogen, Life Technologies), 1% penicillin/streptomycin (Sigma-Aldrich)), and supplemented with the growth factors endothelial growth factor (EGF) (10 ng/ml) and fibroblast growth factor (FGF) (10 ng/ml) (PeproTech, EC Ltd).

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Poly(A) mRNA Magnetic Isolation module (E7490) and NEBNext Ultra II RNA Library Prep Kit for Illumina (E7770) with NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs, E6440S) following manufacturer's protocols.

value: GBM

tag: molecular subtype

value: proneural


title: U3121 cells, GBM, rep1 (RNAseq)

description: countmatrix_HGCC_RNASeq.xlsx column 'U3121_1'

value: mesenchymal


title: LHA, LCP-HP-UMEI, 6


title: LHA, HCP-LP-UMEI, 7

value: HCP-LP-UMEI


title: HiC_Saline_rep1


title: LHA, HCP-LP-UMEI, 6


title: LHA, HCP-HP-RMEI, 8

value: HCP-HP-RMEI


title: CTRL1109_hESC_bulkRNAseq

description: bulk RNAseq


title: CDKO1312_iMeLC_bulkRNAseq

description: bulk RNAseq


title: CTRL1106_hESC_bulkRNAseq

description: bulk RNAseq


title: CTRL1101_iMeLC_bulkRNAseq

description: bulk RNAseq


title: LHA, HCP-HP-RMEI, 7


title: LHA, HCP-HP-RMEI, 6


title: HiC_Morphine_rep3

value: treated with Morphine


title: U3085 cells, GBM, rep2 (RNAseq)

description: countmatrix_HGCC_RNASeq.xlsx column 'U3085_2'

value: neural


title: HiC_Morphine_rep2


title: U3086 cells, GBM, rep2 (RNAseq)

description: countmatrix_HGCC_RNASeq.xlsx column 'U3086_2'

value: classical


title: U3118 cells, GBM, rep1 (RNAseq)

description: countmatrix_HGCC_RNASeq.xlsx column 'U3118_1'


title: CTRL1109_iMeLC_bulkRNAseq

description: bulk RNAseq


title: LHA, HCP-HP-RMEI, 5


title: U3121 cells, GBM, rep2 (RNAseq)

description: countmatrix_HGCC_RNASeq.xlsx column 'U3121_2'


title: Do1, moDC, non-activated, 48h

value: monocyte-derived dendritic cell

value: non-activated


title: LHA, HCP-HP-UMEI, 6

value: HCP-HP-UMEI


title: U3073 cells, GBM, rep1 (RNAseq)

description: countmatrix_HGCC_RNASeq.xlsx column 'U3073_1'


title: U3085 cells, GBM, rep1 (RNAseq)

description: countmatrix_HGCC_RNASeq.xlsx column 'U3085_1'


title: Human Tenon's fibroblasts, 0.01% Adrenaline 3, Day1

city: London

first: Cynthia

last: Yu-Wai-Man

address: Westminster Bridge Road

country: United Kingdom

institute: King's College London

data_processing:
Run data were demultiplexed and converted to fastq files using Illumina’s BCL Convert Software v3.75.
The unique molecular index was moved to the read header for downstream analysis.
Fastq files were then aligned to the human genome UCSC hg38 using RNA-STAR 2.5.2b.
Aligned reads were then UMI deduplicated using Je-suite (1.2.1), and reads per transcript were counted by FeatureCounts in order to produce a digital output of gene expression.
Differential expression was estimated using the BioConductor package SARTools, a DESeq2 wrapper.
Assembly: UCSC hg38
Supplementary files format and content: tab-delimited text files

source_name: Human Tenon's fibroblasts

growth_protocol: Fibroblasts were cultured in complete media consisting of DMEM, 10% fetal calf serum, 100 U/mL streptomycin and 2 nM L-glutamine, and incubated at 37℃, 5% CO2 and 95% humidity.

extract_protocol:
RNA was extracted using a RNeasy mini kit (Qiagen, Crawley, UK).
For each sample, 500 ng of total RNA were processed using the KAPA mRNA HyperPrep Kit (Roche p/n KK8580).

treatment_protocol: HTFs were treated in triplicate wells with different concentrations of adrenaline (0%, 0.0005%, 0.01%) for 24 hours.

value: Human Tenon's fibroblasts

value: Conjunctival fibroblasts

value: WT

value: 0.01% adrenaline


title: LHA, LCP-LP-UMEI, 7

value: Lateral Hypothalamus (LHA)

value: LCP-LP-UMEI


title: U3078 cells, GBM, rep2 (RNAseq)

description: countmatrix_HGCC_RNASeq.xlsx column 'U3078_2'

value: GBM


title: HiC_Morphine_rep1

value: Adult cortical neuron purified from the cortex regio

value: male

value: 3-4 years


title: U3047 cells, GBM, rep1 (RNAseq)

description: countmatrix_HGCC_RNASeq.xlsx column 'U3047_1'

value: proneural


title: LHA, LCP-HP-UMEI, 5

value: LCP-HP-UMEI


title: U3042 cells, GBM, rep2 (RNAseq)

description: countmatrix_HGCC_RNASeq.xlsx column 'U3042_2'


title: LHA, LCP-LP-UMEI, 5


title: U3054 cells, GBM, rep2 (RNAseq)

description: countmatrix_HGCC_RNASeq.xlsx column 'U3054_2'

value: mesenchymal


title: U3086 cells, GBM, rep1 (RNAseq)

description: countmatrix_HGCC_RNASeq.xlsx column 'U3086_1'

value: classical


title: LHA, HCP-HP-UMEI, 5


title: U3047 cells, GBM, rep2 (RNAseq)

description: countmatrix_HGCC_RNASeq.xlsx column 'U3047_2'


title: Human Tenon's fibroblasts, 0.01% Adrenaline 2, Day1


title: U3073 cells, GBM, rep2 (RNAseq)

description: countmatrix_HGCC_RNASeq.xlsx column 'U3073_2'


title: Human Tenon's fibroblasts, 0.0005% Adrenaline 2, Day1

value: 0.0005% adrenaline


title: U3031 cells, GBM, rep2 (RNAseq)

description: countmatrix_HGCC_RNASeq.xlsx column 'U3031_2'


title: LHA, LCP-LP-UMEI, 6


title: Human Tenon's fibroblasts, 0.01% Adrenaline 1, Day1


title: U3042 cells, GBM, rep1 (RNAseq)

description: countmatrix_HGCC_RNASeq.xlsx column 'U3042_1'


title: Human Tenon's fibroblasts, Control 3, Day1

value: No treatment


title: Human Tenon's fibroblasts, 0.0005% Adrenaline 3, Day1


title: U3078 cells, GBM, rep1 (RNAseq)

description: countmatrix_HGCC_RNASeq.xlsx column 'U3078_1'


title: U3039 cells, GBM, rep2 (RNAseq)

description: countmatrix_HGCC_RNASeq.xlsx column 'U3039_2'


title: U3013 cells, GBM, rep2 (RNAseq)

description: countmatrix_HGCC_RNASeq.xlsx column 'U3013_2'


title: U3039 cells, GBM, rep1 (RNAseq)

description: countmatrix_HGCC_RNASeq.xlsx column 'U3039_1'


title: Human Tenon's fibroblasts, Control 2, Day1


title: LHA, LCP-LP-UMEI, 4


title: Human Tenon's fibroblasts, 0.0005% Adrenaline 1, Day1


title: Human Tenon's fibroblasts, Control 1, Day1


title: U3028 cells, GBM, rep2 (RNAseq)

description: countmatrix_HGCC_RNASeq.xlsx column 'U3028_2'


title: LHA, HCP-HP-RMEI, 4

value: HCP-HP-RMEI


title: LHA, LCP-HP-UMEI, 4


title: U3028 cells, GBM, rep1 (RNAseq)

description: countmatrix_HGCC_RNASeq.xlsx column 'U3028_1'


title: U3008 cells, GBM, rep1 (RNAseq)

description: countmatrix_HGCC_RNASeq.xlsx column 'U3008_1'

value: neural


title: U3054 cells, GBM, rep1 (RNAseq)

description: countmatrix_HGCC_RNASeq.xlsx column 'U3054_1'


title: LHA, HCP-HP-RMEI, 3


title: U3031 cells, GBM, rep1 (RNAseq)

description: countmatrix_HGCC_RNASeq.xlsx column 'U3031_1'


title: LHA, LCP-HP-UMEI, 3


title: U3013 cells, GBM, rep1 (RNAseq)

description: countmatrix_HGCC_RNASeq.xlsx column 'U3013_1'


title: LHA, LCP-LP-UMEI, 2


title: U3121, cells, GBM (HiChIP)

data_processing:
Raw reads were mapped   to hg38 human genome and valid interacting segments were obtained and assessed using HiC-Pro software v3.1.0. at default settings with LIGATION_SITES set as GATCGATC,GANTGATC,GANTANTC,GATCANTC
Valid loops were extracted identified using hichipper v.0.7.3.
Assembly: hg38
Supplementary files format and content: mango files
Library strategy: HiChIP-seq

extract_protocol:
About 9-15 million cells were cross linked at 1 percent formaldehyde for 15 minutes to acquire approximately 12-15 ug of input DNA for HiChIP for each 16 cell lines
HiChIP was performed using Arima-HiC+ Kit (P/N A101020) as per manufacturer’s guidelines with anti-H3K27me3: ab8580. The sequencing library was prepared using Accel-NGS 2S Plus DNA Library Kit (Cat#21024) and Indexing Kit (Cat# 26696) from Swift Biosciences
Quality of chromatin digestion and ligation, shearing and library was assessed by running sample aliquots on Bioanalyzer chips.


title: astrocytes cells, control, rep2 (RNAseq)

description: countmatrix_HGCC_RNASeq.xlsx column 'hAstro_2'

source_name: hAstro

value: hAstro

value: normal human astrocytes

value: normal


title: BOP27_ndh_A16F47-I1R1_1

city: Mumbai

first: Amitesh

last: Anand

state: Maharashtra

address: Homi Bhabha Road

department: DBS

country: India

institute: TIFR

data_processing:
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2
Maximum insert size of 1000 and two maximum mismatches after trimming 3 bp at the 3' ends.
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments packageintersection mode
The dispersion and differential expression level of each gene were estimated using DESeq2
Transcripts per Million (TPM) were calculated by DESeq2
Assembly: NC_000913.3
Supplementary files format and content: csv, TPM counts

organism: Escherichia coli

extract_protocol: RNA was isolated from mid-log phase culture of respective strains

tag: strain

value: e{delta}ndh-D


title: U3008 cells, GBM, rep2 (RNAseq)

description: countmatrix_HGCC_RNASeq.xlsx column 'U3008_2'


title: BOP27_ndh_A16F47-I1R1_2


title: U3085, cells, GBM (HiChIP)


title: U3009 cells, GBM, rep2 (RNAseq)

description: countmatrix_HGCC_RNASeq.xlsx column 'U3009_2'


title: U3086, cells, GBM (HiChIP)


title: astrocytes cells, control, rep1 (RNAseq)

description: countmatrix_HGCC_RNASeq.xlsx column 'hAstro_1'

value: WT


title: LHA, HCP-HP-RMEI, 2

value: Lateral Hypothalamus (LHA)


title: LHA, HCP-HP-UMEI, 4

value: HCP-HP-UMEI


title: U3118, cells, GBM (HiChIP)

value: GBM


title: LHA, LCP-LP-UMEI, 3

value: LCP-LP-UMEI


title: U3078, cells, GBM (HiChIP)


title: BOP27_ndh_A14F46-I1R1_2

value: e{delta}ndh-B


title: BOP27_ndh_A15F46-I1R1_2

value: e{delta}ndh-C


title: BOP27_ndh_A15F46-I1R1_1


title: U3009 cells, GBM, rep1 (RNAseq)

description: countmatrix_HGCC_RNASeq.xlsx column 'U3009_1'


title: U3039, cells, GBM (HiChIP)


title: U3028, cells, GBM (HiChIP)


title: U3073, cells, GBM (HiChIP)

value: mesenchymal


title: U3054, cells, GBM (HiChIP)


title: LHA, HCP-LP-UMEI, 5

value: HCP-LP-UMEI


title: U3042, cells, GBM (HiChIP)

value: classical


title: BOP27_ndh_A14F46-I1R1_1


title: LHA, HCP-HP-RMEI, 1


title: BOP27_ndh_A13F47-I1R1_2

value: e{delta}ndh-A


title: LHA, HCP-LP-UMEI, 4


title: U3031, cells, GBM (HiChIP)


title: BOP27_ndh_1

value: {delta}ndh


title: LHA, HCP-HP-UMEI, 3


title: astrocytes, cells, control (HiChIP)


title: U3013, cells, GBM (HiChIP)

value: proneural


title: BOP27_ndh_A13F47-I1R1_1


title: hAstro, cells, control (input for H3K4me3)

data_processing:
Raw reads were mapped to the human genome (hg38, Ensembl genome version 96, ensembl.org) using bowtie2 (options: -f BAMPE --threads 4 --very-sensitive).
Enriched peaks were called using MACS2 (options: -f BAMPE --broad -g hs -B -q 0.05).
For the input (-c) the analysis was done as follows: Astrocytes were paired with the Astrocyte-input, classical-subtype cell lines qith the classical-input, mesenchymal cell lines with mesenchymal-input and neural or proneural cell lines with Neural/Proneural-input.
Assembly: hg38
Supplementary files format and content: bed files (except for Input sample)

extract_protocol:
Approximately 3-6 million cells were cross-linked with 1% formaldehyde for 15 minutes
After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris) for 12 minutes, IP was done with 4ug of anti-H3K4me3: ab192985
About 10ng of immunoprecipitated DNA from H3K4me3/ H3K4me3-ChIP was used to prepare libraries using Accel-NGS 2S Plus DNA Library kit (Swift Biosciences- 21024) and 2S Set S1 Single Indexed Adapters (24-plex, Swift Biosciences- 26596)

value: hAstro

tag: chip antibody


title: U3009, cells, GBM (HiChIP)


title: U3008, cells, GBM (HiChIP)

value: neural


title: classical subtypes, cells, GBM (input for H3K4me3)


title: neural and proneural subtypes, cells, GBM (input for H3K4me3)

value: proneural and neural


title: mesenchymal subtypes, cells, GBM (input for H3K4me3)


title: LHA, HCP-HP-UMEI, 2


title: LHA, LCP-LP-UMEI, 1


title: 11110-ip-amp

city: Gainesville

first: Peter

last: Hansen

state: Florida

address: 2250 Shealy Drive

department: Department of Animal Sciences

institute: University of Florida

data_processing:
Cutadapt program  to trim off sequencing adaptors and low-quality bases with a quality phred-like score < 20 as well as reads < 65 bases.
Reads mapped individually to the reference sequences using the read mapper of the STAR package (v.2.7.9a)
The mapping results were processed with the HTSeq (High-Throughput Sequence Analysis in Python, v0.11.2), samtools, and scripts developed in-house at University of Florida ICBR
Assembly: Bos taurus (ARS-UCD1.3)
Supplementary files format and content: Txt data file includes gene ID in the first column followed by each sample. The expression data is in reads per million (RPM)

organism: Bos taurus

source_name: ampulla

extract_protocol:
Qiagen Rneasy Microkit with prior tissue homogenization using beads
NEBNext Ultra II Directional RNA Library Prep Kit

value: ampulla


title: 11110-UB

source_name: uterine body

value: uterine body


title: 11110-con-upUH

source_name: upper uterine horn

value: upper uterine horn


title: LHA, HCP-LP-UMEI, 3

value: Lateral Hypothalamus (LHA)


title: U3121, cells, GBM (H3K4me3.ChIPseq)

value: GBM


title: LHA, HCP-HP-UMEI, 1

value: HCP-HP-UMEI


title: 11110-ip-midUH

source_name: mid-uterine horn

value: mid-uterine horn


title: U3118, cells, GBM (H3K4me3.ChIPseq)


title: 11110-con-midUH


title: U3047, cells, GBM (H3K4me3.ChIPseq)


title: LHA, HCP-LP-UMEI, 1


title: U3086, cells, GBM (H3K4me3.ChIPseq)


title: U3085, cells, GBM (H3K4me3.ChIPseq)


title: U3042, cells, GBM (H3K4me3.ChIPseq)


title: LHA, HCP-LP-UMEI, 2


title: BOP27_ndh_2


title: 11070-UB


title: U3073, cells, GBM (H3K4me3.ChIPseq)


title: U3028, cells, GBM (H3K4me3.ChIPseq)


title: U3054, cells, GBM (H3K4me3.ChIPseq)


title: ARC, LCP-HP-UMEI, 8

source_name: Arcuate Nucleus (ARC)

value: Arcuate Nucleus (ARC)

value: LCP-HP-UMEI


title: 11110-con-amp


title: U3039, cells, GBM (H3K4me3.ChIPseq)


title: LHA, LCP-HP-UMEI, 2


title: LHA, LCP-HP-UMEI, 1


title: U3031, cells, GBM (H3K4me3.ChIPseq)

value: mesenchymal


title: U3078, cells, GBM (H3K4me3.ChIPseq)


title: ARC, HCP-HP-RMEI, 8

value: HCP-HP-RMEI


title: ARC, LCP-LP-UMEI, 8

value: LCP-LP-UMEI


title: 11070-ip-upUH


title: U3013, cells, GBM (H3K4me3.ChIPseq)


title: 11070-ip-midUH


title: neural and proneural subtypes, cells, GBM (input for H3K27Me3)

extract_protocol:
Approximately 3-6 million cells were cross-linked with 1% formaldehyde for 15 minutes
After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris) for 12 minutes, IP was done with 4ug of anti-H3K27Me3: ab8580
About 10ng of immunoprecipitated DNA from H3K27Me3/ H3K27Me3-ChIP was used to prepare libraries using NEBNext Ultra II DNA Library Prep Kit for Illumina, E7645L and NEBNext® Multiplex Oligos for Illumina® (96 Unique Dual Index Primer Pairs), E6440S.

value: input


title: U3009, cells, GBM (H3K4me3.ChIPseq)

value: classical


title: hAstro, cells, control (H3K4me3.ChIPseq)

value: hAstro

value: normal human astrocytes

value: WT

value: normal


title: classical subtypes, cells, GBM (input for H3K27Me3)


title: mesenchymal subtypes, cells, GBM (input for H3K27Me3)


title: ARC, LCP-LP-UMEI, 7


title: 11070-ip-amp

value: ampulla


title: U3121, cells, GBM (H3K27Me3.ChIPseq)


title: ARC, HCP-HP-UMEI, 8


title: 11070-con-midUH


title: 11070-con-amp


title: ARC, HCP-HP-RMEI, 7


title: U3078, cells, GBM (H3K27Me3.ChIPseq)


title: U3086, cells, GBM (H3K27Me3.ChIPseq)


title: U3118, cells, GBM (H3K27Me3.ChIPseq)

value: proneural


title: U3085, cells, GBM (H3K27Me3.ChIPseq)

value: neural


title: ARC, LCP-HP-UMEI, 7


title: 11033-UB

value: uterine body


title: U3073, cells, GBM (H3K27Me3.ChIPseq)

value: GBM


title: U3054, cells, GBM (H3K27Me3.ChIPseq)


title: ARC, LCP-LP-UMEI, 6


title: U3047, cells, GBM (H3K27Me3.ChIPseq)


title: 11033-ip-midUH

value: mid-uterine horn


title: ARC, LCP-HP-UMEI, 6

value: Arcuate Nucleus (ARC)


title: U3008, cells, GBM (H3K4me3.ChIPseq)


title: U3039, cells, GBM (H3K27Me3.ChIPseq)


title: 11033-ip-upUH

value: upper uterine horn


title: ARC, HCP-HP-UMEI, 7

value: HCP-HP-UMEI


title: 11033-ip-amp


title: astrocytes, cells, control (input for H3K27Me3)


title: 11070-con-upUH


title: U3031, cells, GBM (H3K27Me3.ChIPseq)

value: mesenchymal


title: U3028, cells, GBM (H3K27Me3.ChIPseq)


title: ARC, HCP-HP-RMEI, 6

value: HCP-HP-RMEI


title: U3013, cells, GBM (H3K27Me3.ChIPseq)


title: 11033-con-upUH


title: ARC, HCP-HP-UMEI, 6


title: ARC, LCP-LP-UMEI, 5

value: LCP-LP-UMEI


title: astrocytes, cells, control (H3K27Me3.ChIPseq)


title: U3009, cells, GBM (H3K27Me3.ChIPseq)

value: classical


title: mesenchymal subtypes, cells, GBM (input for H3K27Ac)

extract_protocol:
Approximately 3-6 million cells were cross-linked with 1% formaldehyde for 15 minutes
After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris) for 12 minutes, IP was done with 4ug of anti-H3K27Ac: ab4729
About 10ng of immunoprecipitated DNA from H3K27Ac/ H3K27me3-ChIP was used to prepare libraries using NEBNext Ultra II DNA Library Prep Kit for Illumina, E7645L and NEBNext® Multiplex Oligos for Illumina® (96 Unique Dual Index Primer Pairs), E6440S.


title: U3008, cells, GBM (H3K27Me3.ChIPseq)


title: ARC, HCP-HP-RMEI, 4


title: U3042, cells, GBM (H3K27Me3.ChIPseq)


title: 11033-con-amp


title: astrocytes, cells, control (input for H3K27Ac)

value: hAstro


title: neural and proneural subtypes, cells, GBM (input for H3K27Ac)

value: proneural and neural


title: U3121, cells, GBM (H3K27Ac.ChIPseq)


title: 10882-UB


title: U3118, cells, GBM (H3K27Ac.ChIPseq)


title: 10882-ip-upUH


title: ARC, HCP-HP-RMEI, 5


title: U3086, cells, GBM (H3K27Ac.ChIPseq)


title: ARC, HCP-HP-UMEI, 5


title: U3085, cells, GBM (H3K27Ac.ChIPseq)


title: ARC, LCP-LP-UMEI, 4


title: 10882-ip-midUH


title: U3078, cells, GBM (H3K27Ac.ChIPseq)


title: ARC, LCP-LP-UMEI, 3


title: ARC, HCP-HP-UMEI, 4


title: 10882-con-upUH


title: classical subtypes, cells, GBM (input for H3K27Ac)


title: 10882-con-midUH


title: ARC, HCP-HP-UMEI, 3


title: U3039, cells, GBM (H3K27Ac.ChIPseq)


title: U3031, cells, GBM (H3K27Ac.ChIPseq)


title: U3013, cells, GBM (H3K27Ac.ChIPseq)


title: 10882-con-amp


title: U3073, cells, GBM (H3K27Ac.ChIPseq)


title: astrocytes, cells, control (H3K27Ac.ChIPseq)

value: normal human astrocytes

value: WT


title: U3009, cells, GBM (H3K27Ac.ChIPseq)


title: 10882-ip-amp

value: ampulla


title: ARC, HCP-HP-RMEI, 3


title: U3008, cells, GBM (H3K27Ac.ChIPseq)


title: ARC, LCP-LP-UMEI, 2


title: ARC, LCP-HP-UMEI, 4

value: LCP-HP-UMEI


title: 11033-con-midUH


title: U3121, cells, GBM (ATACseq)

data_processing:
Then, the raw read files were trimmed with cutadapt to remove the Nextera sequence, 5’CTGTCTCTTATACACATCT3’ prior to map them to hg38 using bowtie2 (--threads 8 -k 2 --local --maxins 2000)
reads were filtered with samtools -view with flag -q 10, to remove all reads having a MAPQ lower than 10
peaks were called by MACS2, for broad peaks by keeping the flags -f BAMPE (for a valid paired-end aligned .bam file), --broad, -q 0.05 --shift 100 --extSize 200 against baseline.
Assembly: hg38
Supplementary files format and content: bed files

extract_protocol:
For ATAC-seq, an exact number of 50,000 cells for each of the 16 cell lines were used to tagment DNA using Illumina Tagment DNA TDE1 Enzyme and Buffer Kits (small) (Illumia #20034197).
Exactly 5uL of tagmented DNA from each line was amplified with NEBNext High-Fidelity 2x PCR Master Mix (New England Biolabs #M0541S). Custom oligos and adapters were designed and used for library amplification.
Fragmentation of the libraries were assessed by running Bioanalyzer High Sensitivity DNA Analysis (Agilent # 5067-4626) and were sent to be sequenced at Novogene.


title: U3118, cells, GBM (ATACseq)

value: proneural


title: ARC, LCP-HP-UMEI, 5


title: 10872-ip-midUH


title: 10872-ip-upUH


title: 10872-UB

value: uterine body


title: U3086, cells, GBM (ATACseq)

value: GBM


title: U3047, cells, GBM (H3K27Ac.ChIPseq)


title: ARC, HCP-LP-UMEI, 7

value: HCP-LP-UMEI


title: U3028, cells, GBM (H3K27Ac.ChIPseq)


title: ARC, HCP-LP-UMEI, 6

value: Arcuate Nucleus (ARC)


title: 10872-con-upUH

value: upper uterine horn


title: U3073, cells, GBM (ATACseq)


title: ARC, HCP-HP-RMEI, 2


title: 10872-con-midUH

value: mid-uterine horn


title: U3047, cells, GBM (ATACseq)


title: 10872-con-amp


title: U3054, cells, GBM (ATACseq)

value: mesenchymal


title: U3039, cells, GBM (ATACseq)


title: ARC, LCP-HP-UMEI, 3


title: U3028, cells, GBM (ATACseq)


title: U3042, cells, GBM (ATACseq)


title: VCR

city: Dalian

first: chang

middle: miao

last: wang

address: Lianhe Road

department: Τhe First Affiliated Hospital of Dalian Medical University

institute: Department of General Surgery

data_processing:
CLC Genomics Workbench y 11.0.1
Sequence reads were trimmed for adaptor sequencellow-auality sequence using CLC genomic benchwork parameter- Quality limit: 0.05)
Timmed seouerce reads were maped to rcM3m10 usio clc aeromic bechwork parameters-mismat cost 2 nserio cost 3 deon cost 3 lerat faciom: 08 simianty factior 08
Read count extraction and norma ization were performed using Cl C genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: mammary tissue

growth_protocol: The MCF7 cells were preserved in MEM supplemented with 10% FBS.

extract_protocol:
The RNA of both MCF7-WT and Vincristine/MCF7 cells was isolated using the TRIzol Reagent (ambion)
The RNA of both MCF7-WT and Vincristine/MCF7 cells was isolated using the TRIzol Reagent (ambion),Then the libraries were constructed through end-repair, A-tailing, adapter ligation.

treatment_protocol: In order to investigate the specific mechanism underlying the development of Vincristine resistance in breast cancer treatment, we constructed a Vincristine-resistant breast cancer cell line MCF7/VCR. Firstly, we treated MCF7 cells with different concentrations of VCR in a 96-well plate, using 1nM for 5 days, followed by 5nM, 10nM, 50nM, 100nM, 500nM, 1000nM, 5000nM, and 10000nM for 5 days each. Eventually, the surviving MCF7 cells were expanded and screened to obtain the Vincristine-resistant MCF7 cell line. The IC50 of wild-type and MCF7/VCR cells to Vincristine were measured using the CCK8 method, and were found to be 7.371 nM and 10574 nM, respectively

value: mammary tissue

value: Human breast carcinoma cells


title: WT_MCF7


title: U3031, cells, GBM (ATACseq)


title: U3013, cells, GBM (ATACseq)


title: U3008, cells, GBM (ATACseq)

value: neural


title: ARC, LCP-LP-UMEI, 1

value: LCP-LP-UMEI


title: ARC, HCP-HP-UMEI, 2

value: HCP-HP-UMEI


title: ARC, LCP-HP-UMEI, 2


title: U3009, cells, GBM (ATACseq)

value: classical


title: U3078, cells, GBM (ATACseq)


title: 10872-ip-amp


title: astrocytes, cells, control (ATACseq)

value: hAstro

value: normal human astrocytes

value: WT

value: normal


title: ARC, HCP-LP-UMEI, 5


title: K108986

city: Indianapolis

first: Natascia

last: Marino

state: IN

address: 980 W. Walnut St, R3-C238

department: Hematology/Oncology Division

institute: Indiana University School of Medicine

description: normal breast tissue core

data_processing:
The raw RNA-seq reads were cleaned using Trimmomatic version 0.36 (Bolger et al. 2014) setting the cutoff threshold for average base quality score at 20 over a window of 3 bases. Reads shorter than 20 bases post-trimming were excluded.
The cleaned reads were aligned to the human genome reference, GRCh38.p12 using STAR (version STAR_2.5.2b) (Dobin et al. 2013).
Individual gene expression was quantified by counting the number reads mapping to the exon regions of each of the annotated genes from gencode v.28 using featureCounts tool of subread package (version 2.0.0) (Liao et al. 2014). Those reads that mapped to antisense strand, or mapped to multiple regions on the genome or those reads that overlapped with multiple genes were excluded.

source_name: normal breast tissue core

growth_protocol: Breast tissue biospies are collected using a vacuum-assisted breast biopsy system (ATEC, Hologic) and fresh frozen whitin 10 min.

extract_protocol:
Total RNA was extracted using the Allprep DNA/RNA/miRNA Universal Kit (QIAGEN, Germantown, MD).
The concentration and quality of total RNA samples were first assessed using Agilent 2100 Bioanalyzer. Then cDNA library was prepared using the  KAPA RNA HyperPrep kit (Roche, Wilmington, MA)  on  a BiomeK Automated worstation (Beckman coulter, Indianapolis, IN)

value: normal breast tissue core

tag: gender

value: female

tag: bmi

tag: racial background

value: AFRNAMER

tag: tyrer-cuzick lifetime_risk_score


title: WT5, TCPOBOP, 24h, RNA-seq

city: Heraklion

first: Dimitrios

last: Botskaris

address: Nikolaou Plastira 100

country: Greece

institute: IMBB FORTH

data_processing:
To remove low-quality bases and adapter sequences from the raw FASTQ files, we employed Trimmomatic (version 0.39). The FASTQ files were mapped on the UCSC mm10 genome using hisat2 with default settings. We retained only the reads with a mapping quality score greater than 30 and removed blacklisted regions from our BAM files which are known to be susceptible to technical artifacts and spurious signals. The resulting BAM files were converted to bigwig files using deeptools (version 3.3.2). Before identifying peak regions and to account for variations in the number of sequencing reads between ChIP and CUT&Tag samples, we standardized the total read count for each sample by equally reducing reads proportionally based on the sample with the fewer reads. Peaks for ChIP-seq data were initially identified using MACS2 (version 2.2.7.1) with a stringent p-value cutoff of 1.00e-13. Additionally, for CUT&TAG data, peak calling was performed using SICER2.  Differential expression analysis of RNA-seq data performed with metaseqR2.
Assembly: mm10
Supplementary files format and content: bigwig, narrowpeak, output of metaseqR2, output of SICER2

organism: Mus musculus

source_name: Liver

growth_protocol: We used livers dissected from 45-50 days old mice

extract_protocol:
For RNA: Total RNAs were purified from liver tissues by brief homogenization in 10 volumes of Trizol reagent using Polytron device, followed by incubation at room temperature for 5 min and the addition of 0.2 volumes of chloroform and further incubation at room temperature for 3 minutes. The samples were centrifuged at 12000 g for 15 minutes at 40C and the aqueous phase was collected, precipitated by the addition of equal volume of isopropanol. After 10 minutes at room temperature, the RNA was collected by centrifugation at 12000g for 15 minutes. The pellet was resuspended in H2O and re-precipitated with ethanol. The RNA samples were further purified by digestion with 10 units of DNase-I for 10 min at 370C, followed by purification with phenol/chlorophorm extraction and ethanol precipitation. For ChIP: Livers were minced to small pieces and crosslinked with 1% formaldehyde for 10 min. After the addition of glycine at 0.125 M final concentration, the cross-linked cells were washed with a buffer containing 50 mM Hepes pH 7.9, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA and sequentially treated with a buffer containing 0.25% Triton-X100, 10 mM EDTA, 0.5 mM EGTA, 20 mM HEPES and a buffer containing 0.15M NaCl, 1 mM EDTA, 0.5 mM EGTA, 20 mM HEPES for 10 minutes each. The resulting crosslinked nuclei were resuspended in 10 volumes of 50 mM Hepes pH 7.9, 140 mM NaCl, 1 mM EDTA, 0.1% Na-deoxycholate, 0.5% Sarkosyl, and protease inhibitor cocktail (CompleteTM Roche), sonicated for 10 minutes in Covaris Sonicator instrument with maximum setting. After sonication, samples were supplemented with 0.5 volume of 50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA, 3% Triton X-100, 0.1% Sodium deoxycholate, and protease inhibitor cocktail, and centrifuged for 15 minutes at 20.000g. The soluble chromatin was incubated overnight with Dynabeads Protein G (Invitrogen), that were prebound by 5 mg of the primary antibodies recognizing H3K27ac-modified histones, CTCF and Smc3. The beads were washed twice with a buffer containing 50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS, 0.5 mM PMSF, 2 mg/ml aprotinin, once with the same buffer but containing 500 mM NaCl, once with a buffer containing 20 mM Tris, pH 8.0, 1 mM EDTA, 250 mM LiCl, 0.5 % NP-40, 0.5 % Na-deoxycholate, 0.5 mM PMSF, 2 mg/ml aprotinin and once with a buffer containing 10 mM Tris pH 8.0, 0.1 mM EDTA, 0.5 mM PMSF, 2 mg/ml aprotinin.  Immunoprecipitated chromatin was eluted from the beads and reverse crosslinked by overnight incubation in a buffer containing 50 mM Tris-HCl, pH 8.0, 1 mM EDTA, 1% SDS and 50 mM NaHCO3 at 65oC. The samples were then incubated with 20 mg/ml RNase-A for 30 minutes at 37oC, followed by incubation with 20 mg/ml Proteinase-K for 2 hours at 42oC. DNA was extracted by phenol/chlorophorm and precipitated with ethanol. For CUT&Tag and ATAC-seq: Hepatocyte nuclei were prepared as follows: liver tissue was minced into small pieces in 20 volumes of ice cold buffer containing 10 mM Tris pH 7.5, 2 mM MgCl2, 3 mM CaCl2 and protease inhibitor cocktail (CompleteTM EDTA-free, Roche), and homogenized by 10 strokes using Dounce device. The suspension was filtered through 100 m mesh strainer and centrifuged for 5 min. at 400g. The resulting pellet was resuspended in a buffer containing 10 mM Tris pH 7.5, 2 mM MgCl2, 3 mM CaCl2, 10% glycerol, 1% NP40 and protease inhibitor cocktail (CompleteTM EDTA-free, Roche). After incubation in ice for 3 min the nuclei were collected by centrifugation for 5 min at 400g, washed twice with PBS and used for downstream applications. CUT&Tag assays were performed as follows: 105 nuclei were resuspended in a buffer containing 20 mM HEPES–KOH, pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% Glycerol, 0.5 mM Spermidine, protease inhibitor cocktail (CompleteTM EDTA-free, Roche) and incubated for 10 min with Concanavalin A-conjugated magnetic beads (Epicypher) that were previously activated by repeated washings with a buffer containing 20 mM HEPES, pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2. The reactions were supplemented with 0.5 volume of a buffer containing 20 mM HEPES, pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, protease inhibitor cocktail, 0.01% Digitonin, 2 mM EDTA and 0.5 g of the anti-Lamin A/C or anti-H4K20Me3 or IgG negative control primary antibodies (see Reporting Summary). The samples were incubated overnight at 40C by gentle agitation. The beads were collected and supplemented with a buffer containing 20 mM HEPES, pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, protease inhibitor cocktail, 0.01% Digitonin and 0.5 g of anti-rabbit or anti-mouse secondary antibodies (Epicypher). After incubation for 30 min at room temperature, the beads were washed twice with the same buffer and resuspended in the same buffer containing 300 mM NaCl. Protein A/G-fused Tn5 transposase protein (CUTANA pA/G-Tn5, Epicypher) was added and the samples were incubated for 1 hour at room temperature followed by washing with a buffer containing 20 mM HEPES, pH 7.5, 300 mM NaCl, 0.5 mM Spermidine, protease inhibitor cocktail, 0.01% Digitonin. The beads were collected and resuspended in the above buffer containing 10 mM MgCl2, and incubated for 1 hour at room temperature. The beads were collected and washed once with 10 mM TAPS, pH 8.5, 0.2 mM EDTA. DNA was released from the beads by incubation in 10 mM TAPS, pH 8.5, 0.1% SDS for 1 hour at 580C. After quenching by the addition of 3 volumes of 0.67% Triton-X100, the samples were used for PCR reaction (15 cycles) using universal i5 primers and barcoded i7 primers. For ATAC-seq reactions we used the ATAC-seq kit from Active Motif. Tagmentation reactions using 105 nuclei, DNA purification and PCR amplifications using combinations of indexed i5 and i7 primers were performed according to the manufacturer’s instructions.
RNA-seq libraries were generated using NEBNext Ultra II RNA Library preparation kit from New England Biolabs using Poly-A selection. ChIp-seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit of New England Biolabs. CUT&Tag and ATAC-seq libraries corresponded to the above-described PCR reactions with i5 and i7 primers, which were cleaned-up by AMPure.

treatment_protocol: Mice were treated with intraperitoneal injection of TCPOBOP mitogen (3mg/kg) for 24 hours

tag: tissue

value: Liver

tag: cell type

value: Whole Liver

tag: genotype

value: TCPOBOP


title: U3085, cells, GBM (ATACseq)

tag: cell line

value: GBM


title: K109037

description: normal breast tissue core


title: K108720

description: normal breast tissue core


title: ARC, HCP-LP-UMEI, 4

value: Arcuate Nucleus (ARC)

tag: treatment

value: HCP-LP-UMEI


title: K108734

description: normal breast tissue core


title: K108881

description: normal breast tissue core


title: WT4, TCPOBOP, 24h, RNA-seq


title: K108195

description: normal breast tissue core


title: ARC, HCP-LP-UMEI, 3


title: WT3, TCPOBOP, 24h, RNA-seq


title: WT2, TCPOBOP, 24h, RNA-seq


title: K108099

description: normal breast tissue core


title: K108519

description: normal breast tissue core


title: WT1, TCPOBOP, 24h, RNA-seq


title: K107990

description: normal breast tissue core


title: K107975

description: normal breast tissue core


title: ARC, LCP-HP-UMEI, 1

value: LCP-HP-UMEI


title: WT5, untreated, RNA-seq

value: Untreated


title: ARC, HCP-LP-UMEI, 1


title: WT4, untreated, RNA-seq


title: WT3, untreated, RNA-seq


title: K107893

description: normal breast tissue core


title: K107564

description: normal breast tissue core


title: K107799

description: normal breast tissue core


title: K107656

description: normal breast tissue core


title: ARC, HCP-HP-UMEI, 1

value: HCP-HP-UMEI


title: K108820

description: normal breast tissue core

value: WHITE


title: K107562

description: normal breast tissue core


title: ARC, HCP-HP-RMEI, 1

value: HCP-HP-RMEI


title: K106788

description: normal breast tissue core


title: K107217

description: normal breast tissue core


title: J4-STD

city: Columbia

first: Sathesh

middle: K

last: Sivasankaran

state: MO

address: Bond Life Sciences Center Suite 106, 1201 Rollins Street

institute: University of Missouri

description:
J4-STD_S3
Spatial transcriptomics of Sus scrofa: 8 weeks old female jejunum collected at location of distal-most discrete Peyer's patch

data_processing:
Read were aligned using Cell Ranger v6.1.2 (single-cell) and Space Ranger v1.3.0 (spatial)
Assembly: Sus Scrofa 11.1
Annotation build: Sus Scrofa 11.1.97
Library strategy: Spatial Transcriptomics

organism: Sus scrofa

source_name: Jejunum

extract_protocol:
Single-cell RNA sequencing: Reagents were equilibrated and processes carried out at room temperature (RT) unless stated otherwise. ~2-inch-length tissue cross-sections were placed into 30 mL of 2 mM ethylenediaminetetraacetic acid (EDTA; Invitrogen AM9260G), 2 mM L-glutamine (Gibco 25-030), 0.5% bovine serum albumin (BSA; Sigma-Aldrich A9418) in Hank’s balanced salt solution (HBSS; Gibco 14175) for transport. Tissues were cut open, rinsed with phosphate-buffered saline (PBS), pH 7.2 (made in-house), the muscularis layer was removed, and ~1.5 g of tissue was incubated in 30 mL of 5 mM dithiothretol (Invitrogen 15508), 2% fetal calf serum (FCS; heat-inactivated; Gibco A38401) in HBSS for 20 min, 37C, 200 rpm. Tissues were washed in 20 mL of 10 mM HEPES (Fisher BioReagents BP299) in HBSS for 10 min, 37C, 200 rpm, followed by transfer into a C-tube (Miltenyi 130-093-237) containing 15 mL of 10 mM HEPES, 0.2U/mL Liberase TM (Roche 5401127001), 30 ug/mL DNase I (Sigma D5025) in HBSS. Mechanical dissociation was executed with a gentleMACs Octo Dissociator (Miltenyi 130-095-937) intestine C-tube protocol. C-tubes were incubated 45 min, 37C, 200 rpm, followed by another round of mechanical dissociation. 10 mL of 2 mM EDTA, 2 mM L-glutamine, 0.5% BSA in HBSS was added to C-tubes, and samples were filtered sequentially through non-woven surgical gauze sponges (Starryshine GZNW44), 100-micron nylon filters, and 40-micron nylon filters. Collected suspensions were centrifuged 5 min, 200 xg and resuspended in 2 mM L-glutamine, 2% FCS in HBSS. Density gradient centrifugation was performed to enrich for lymphocytes by overlaying cell suspensions onto Histopaque 1077 (Sigma-Aldrich) and centrifuging 30 min, 400 xg, 22C. Cell fractions were collected from the interphase layer and washed with 2 mM L-glutamine, 2% FCS in HBSS. Final cell suspensions were poured over 40-micron nylon filters.
Tissues were embedded in optimal cutting temperature (OCT) compound (Sakura 4583) and snap frozen in an isopentane bath cooled with liquid nitrogen. Tissues were stored at -80C. For cryosectioning, tissue blocks were equilibrated to -20C for 20 minutes. On a cryostat (Leica CM 1860), OCT blocks were cut and faced to an appropriate plane and size that included transverse profiles of Peyer’s patches, lamina propria, and epithelium. 10-micron tissue sections were adhered to VIsium slides (10X Genomics).
Single-cell RNA sequencing: A target of 10,000 isolated cells per sample were partitioned using the Chromium Single Cell 3’ v3 Chemistry (10X Genomics CG000183). Samples were sequenced using 2x100, paired-end sequencing on a HiSeq 3000 and NovaSeq SP flow cell (Illumina).
Spatial transcriptomics: Using optimized permeabilization parameters, libraries were created using the Visium Spatial Gene Expression Reagent Kit (10X Genomics PN-1000186), Visium Spatial Gene Expression Slide Kit (10X Genomics PN-1000185), and Library Construction Kit (10X Genomics PN-1000190) according to procedures in User Manual CG000239 (10X Genomics). Tissue bluing was omitted from the manufacturer’s protocol. Tissue images were digitally scanned without coverslips by an Aperio AT2 whole slide imager (Leica Biosystems) at 40X (0.25 um/pixel) magnification. Samples were sequenced on a NovaSeq SP flow cell (Illumina) with 2x100, paired-end sequencing.

value: Jejunum

tag: tissue dissection

value: Jejunum collected at location of distal-most discrete Peyer's patch

tag: breed

value: Mixed-breed

value: 8 weeks

value: Female


title: WT2, untreated, RNA-seq

value: WT


title: J3-STC

description:
J3-STC_S1
Spatial transcriptomics of Sus scrofa: 8 weeks old female jejunum collected at location of distal-most discrete Peyer's patch


title: K105781

description: normal breast tissue core

value: normal breast tissue core

value: female

value: AFRNAMER


title: K107505

description: normal breast tissue core


title: J2-STB

description:
J2-STB_S2
Spatial transcriptomics of Sus scrofa: 8 weeks old female jejunum collected at location of distal-most discrete Peyer's patch


title: ARC, HCP-LP-UMEI, 2

extract_protocol:
Approximately 30 mg of tissue sample was homogenised in 1 mL of TRIzol® reagent (Life Technologies; Carlsbad, CA, USA) before centrifuging at 13,000 g for 10 min at 4°C. The supernatant was removed and mixed vigorously with 200 µL of chloroform and incubated at room temperature for 3 min prior to centrifugation at 13,000 g for 10 min at 4°C. Approximately 350 µL of aqueous phase was mixed by pipette with an equal volume of ultra-pure isopropanol. Samples were incubated at room temperature for 10 min before centrifugation at 13,000 g for 10 min at 4°C with the supernatant discarded. The RNA pellets were washed with 1 mL of 70% ultra-pure ethanol and centrifuged at 7,500 g for 5 min at 4°C. The supernatant was discarded and the pellet was air dried for 5 min before resuspension in 30 µL of nuclease free water. The RNA yield and presence of contaminants was estimated using a Nanodrop® One spectrophotometer (Thermo Scientific; Waltham, MA, USA) before proceeding with further purification. The RNA was then mixed with 70 µL of nuclease free water, 250 µL of 100% ethanol and 350 µL RLT buffer (prepared with β-mercaptoethanol) and transferred directly to a RNEasy column. The RNA was retained on the column and washed using 350 µL RW1 before adding 80 µL of DNase incubation mix to the column membrane. The DNase incubation mix was prepared following the manufacturer’s instructions (RNAse-Free DNase Set; Qiagen, Hilden, Germany). The RNEasy columns were sat at room temperature for 15 min before the second 350 µL RW1 wash and centrifugation at 10,000 g for 30 sec at room temperature. The columns were then washed with RPE (3 x 500 µL). The columns were centrifuged at 10,000 g for 30 sec at room temperature for each wash, with the last wash centrifuged for 2 min. The flow through was discarded each time using a pipette. After the final wash, the column was centrifuged at 13,000 g for 2 min at room temperature in a new collector tube to completely remove the wash reagents. The RNA was eluted in 30 µL of nuclease free water, incubated at room temperature for 10 min and centrifuged at 10,000 g for 1 min. The integrity of the extracted RNA was confirmed by electrophoresis through a 1.5% agarose gel at 70 V for 45 min and the yield and presence of contaminants was estimated using a Nanodrop® One spectrophotometer (Thermo Scientific; Waltham, MA, USA).
The sample preparation and sequencing for the RNA were completed by the Ramaciotti Centre for Genomics, University of NSW, Sydney, NSW, Australia. The complementary deoxyribonucleic acid (cDNA) libraries were prepared using Illumina’s TruSeq stranded mRNA sample preparation kit following the manufacturer’s protocol and the libraries were sequenced using an Illumina NovaSeq 6000 producing 100 base pair single end reads with a target sequencing depth of at least 20 million reads. Briefly, mRNA was purified and fragmented with divalent cations and heat followed by a first strand cDNA synthesis with random primers and a second strand cDNA synthesis step. The cDNA library preparation protocol includes the repair of DNA fragment ends, 3' Adenylation of DNA fragments, sequencing adapter ligation, amplification of library via polymerase chain reaction, and library verification.


title: Setd8-LKO3, TCPOBOP, RNA-seq

value: Liver

value: Whole Liver

value: TCPOBOP


title: K105693

description: normal breast tissue core


title: Setd8-LKO4, TCPOBOP, RNA-seq


title: K105688

description: normal breast tissue core


title: WT1, untreated, RNA-seq


title: Setd8-LKO2, TCPOBOP, RNA-seq


title: K105770

description: normal breast tissue core


title: K105551

description: normal breast tissue core


title: Setd8-LKO1, TCPOBOP, RNA-seq


title: I3-STC

description:
I3-STC_S2
Spatial transcriptomics of Sus scrofa: 8 weeks old female distal ileum with Peyer's patches

source_name: Ileum

value: Ileum

value: Distal ileum with Peyer's patches


title: K105344

description: normal breast tissue core


title: K105583

description: normal breast tissue core


title: WT2, untreated, H4K20me3, Mouse liver nuclei, CUT&TAG-seq

data_processing:
To remove low-quality bases and adapter sequences from the raw FASTQ files, we employed Trimmomatic (version 0.39). The FASTQ files were mapped on the UCSC mm10 genome using hisat2 with default settings. We retained only the reads with a mapping quality score greater than 30 and removed blacklisted regions from our BAM files which are known to be susceptible to technical artifacts and spurious signals. The resulting BAM files were converted to bigwig files using deeptools (version 3.3.2). Before identifying peak regions and to account for variations in the number of sequencing reads between ChIP and CUT&Tag samples, we standardized the total read count for each sample by equally reducing reads proportionally based on the sample with the fewer reads. Peaks for ChIP-seq data were initially identified using MACS2 (version 2.2.7.1) with a stringent p-value cutoff of 1.00e-13. Additionally, for CUT&TAG data, peak calling was performed using SICER2.  Differential expression analysis of RNA-seq data performed with metaseqR2.
Assembly: mm10
Supplementary files format and content: bigwig, narrowpeak, output of metaseqR2, output of SICER2
Library strategy: CUT&Tag

value: Untreated


title: I4-STD

description:
I4-STD_S3
Spatial transcriptomics of Sus scrofa: 8 weeks old female distal ileum with Peyer's patches


title: K105323

description: normal breast tissue core


title: K105417

description: normal breast tissue core


title: J4_2

description:
J4_S12
scRNA-seq of Sus scrofa: 8 weeks old female jejunum collected at location of distal-most discrete Peyer's patch

data_processing:
Read were aligned using Cell Ranger v6.1.2 (single-cell) and Space Ranger v1.3.0 (spatial)
Assembly: Sus Scrofa 11.1
Annotation build: Sus Scrofa 11.1.97


title: I2-STB

description:
I2-STB_S1
Spatial transcriptomics of Sus scrofa: 8 weeks old female distal ileum with Peyer's patches


title: K106143

description: normal breast tissue core


title: K105544

description: normal breast tissue core


title: WT2, untreated, LaminA/C, Mouse liver nuclei, CUT&TAG-seq NGS-2148


title: K106165

description: normal breast tissue core


title: K105117

description: normal breast tissue core

value: WHITE


title: K104743

description: normal breast tissue core


title: WT1, untreated, LaminA/C, Mouse liver nuclei, CUT&TAG-seq NGS-2147


title: WT2, untreated, LaminA/C, Mouse liver nuclei, CUT&TAG-seq


title: K109137

description: normal breast tissue core


title: J2_2

description:
J2_S10
scRNA-seq of Sus scrofa: 8 weeks old female jejunum collected at location of distal-most discrete Peyer's patch


title: K104926

description: normal breast tissue core


title: I3_2

description:
I3_S8
scRNA-seq of Sus scrofa: 8 weeks old female distal ileum with Peyer's patches


title: I4_2

description:
I4_S9
scRNA-seq of Sus scrofa: 8 weeks old female distal ileum with Peyer's patches


title: K109086

description: normal breast tissue core


title: Setd8-LKO2, TCPOBOP 24h, H4K20me3, Mouse liver nuclei, CUT&TAG-seq


title: K109029

description: normal breast tissue core


title: WT1, untreated, H4K20me3, Mouse liver nuclei, CUT&TAG-seq


title: K105300

description: normal breast tissue core


title: K108907

description: normal breast tissue core


title: J3_2

description:
J3_S11
scRNA-seq of Sus scrofa: 8 weeks old female jejunum collected at location of distal-most discrete Peyer's patch


title: K108901

description: normal breast tissue core


title: Setd8-LKO4, TCPOBOP 24h, LaminA/C, Mouse liver nuclei, CUT&TAG-seq


title: Setd8-LKO1, TCPOBOP 24h, H4K20me3, Mouse liver nuclei, CUT&TAG-seq


title: K108845

description: normal breast tissue core


title: K108897

description: normal breast tissue core


title: K108843

description: normal breast tissue core


title: Setd8-LKO3, TCPOBOP 24h, LaminA/C, Mouse liver nuclei, CUT&TAG-seq


title: Setd8-LKO2, TCPOBOP 24h, LaminA/C, Mouse liver nuclei, CUT&TAG-seq


title: WT1, untreated, LaminA/C, Mouse liver nuclei, CUT&TAG-seq


title: K108797

description: normal breast tissue core


title: Setd8-LKO1, TCPOBOP 24h, LaminA/C, Mouse liver nuclei, CUT&TAG-seq


title: K109138

description: normal breast tissue core


title: K108733

description: normal breast tissue core


title: I2_2

description:
I2_S7
scRNA-seq of Sus scrofa: 8 weeks old female distal ileum with Peyer's patches


title: K108626

description: normal breast tissue core


title: K108435

description: normal breast tissue core


title: Aragene-0934

type: RNA

city: Sakai

first: Noriko

last: Inada

email: norikoinada@omu.ac.jp, norikoq@me.com

state: Osaka

address: Gakuen-cho 1-1, Naka-ku

department: Agriculture

country: Japan

institute: Osaka Metropolitan University

description: adf4 powdery mildew-infected 5 days post inoculation

hyb_protocol: Hybridization, washing, and staining procedures were performed on Fluidics Station 450 (Affymetrix) with GeneChip Hybridization, Wash, and Stain Kit (Thermo Fisher Scientific).

scan_protocol: GeneChips were scanned with GeneChip Scanner 3000 7G.

data_processing: Gene-level RMA sketch normalization was performed was performed using standard settings for GeneChip Gene 1.0 ST arrays on Expression Console Version 1.3 (Affymetrix). Microarray data were quantified using Transcriptome Analysis Console 4.0 (Thermo Fisher Scientific).

label: biotin

organism: Arabidopsis thaliana

source_name: adf4 G. orontii infected leaves at 5dpi

label_protocol: Terminal labeling Kit and Controls Kit (Thermo Fisher Scientific) following the manufacturer’s protocols.

growth_protocol: Arabidopsis seeds were suspended in autoclaved 0.1% agarose and incubated at 4°C for vernalization for more than 1 day (up to 2 weeks) before direct sowing on 1:3 metromix:vermiculite in plastic pots. Entire pots were covered with plastic wrap for 1 week after sowing to maintain humidity and to encourage germination. Plants were grown at 22°C in a growth chamber under a 16-h light:8-h dark photoperiod (LH-411PFD-S, NK Systems, Osaka, Japan).

extract_protocol: RNA was extracted from 4-week old mature leaves using TRIzol reagent (Life Technologies Japan, Tokyo, Japan) and purified with an RNeasy Micro kit (Qiagen) following the manufacturers’ instructions.

treatment_protocol: Golovinomyces orontii-infection was performed as in Inada et al., 2016 Plant Physiology 170, 1420-1434

value: mature rosette leaves


title: Aragene-0935


title: K108369

description: normal breast tissue core


title: K108463

description: normal breast tissue core


title: WTuntr1, input, ChIP-seq


title: K108373

description: normal breast tissue core


title: K108345

description: normal breast tissue core


title: WTuntr2, input, ChIP-seq


title: K108796

description: normal breast tissue core


title: K108100

description: normal breast tissue core


title: K107992

description: normal breast tissue core


title: Aragene-0930

description: ADF1-4Ri powdery mildew-infected 3 days post inoculation

source_name: ADF1-4Ri G. orontii infected leaves at 3dpi


title: WT2 untreated, SMC3, ChIP-seq


title: K107989

description: normal breast tissue core


title: Aragene-0932

description: Col-0 powdery mildew-infected 5 days post inoculation

source_name: Col-0 G. orontii infected leaves at 5dpi


title: K107985

description: normal breast tissue core


title: Aragene-0933


title: Aragene-0929

description: Col-0 powdery mildew-infected 3 days post inoculation

source_name: Col-0 G. orontii infected leaves at 3dpi


title: K107908

description: normal breast tissue core


title: Aragene-0931


title: Aragene-0928


title: K108441

description: normal breast tissue core


title: U3042, cells, GBM (H3K27Ac.ChIPseq)

value: GBM

value: classical


title: U3054, cells, GBM (H3K27Ac.ChIPseq)

value: mesenchymal


title: K107720

description: normal breast tissue core


title: K107711

description: normal breast tissue core

value: ASIAN,CHINESE


title: WT1 untreated, SMC3, ChIP-seq


title: WT3 untreated, SMC3, ChIP-seq


title: K107841

description: normal breast tissue core


title: WT4 untreated, CTCF, ChIP-seq


title: K108125

description: normal breast tissue core


title: Aragene-0924

description: adf4 uninfected 4 week old mature leaves

source_name: adf4 uninfected leaves


title: K107782

description: normal breast tissue core

value: ASIAN


title: Aragene-0926

description: ADF1-4Ri uninfected 4 week old mature leaves

source_name: ADF1-4Ri uninfected leaves


title: K107788

description: normal breast tissue core


title: K107961

description: normal breast tissue core


title: K107662

description: normal breast tissue core


title: WT3 untreated, CTCF, ChIP-seq

value: WT


title: Aragene-0927


title: K107784

description: normal breast tissue core

value: normal breast tissue core


title: WT2 untreated, CTCF, ChIP-seq


title: WT3, untreated, H3K27ac, ChIP-seq


title: K107756

description: normal breast tissue core

value: female


title: WT1 untreated, CTCF, ChIP-seq


title: Healthy cardiac fibroblasts_2

city: Sutia

first: Hidehiro

last: Suginobe

address: 2-2, Yamadaoka

department: Pediatrics

institute: Osaka University

data_processing:
An Illumina HiSeq 2500 platform in 75-base single-end mode was used for sequencing.
Illumina CASAVA 1.8.2 software was used for base calling.
Sequenced reads were mapped to the human reference genome sequence (hg19) using TopHat version 2.0.13 in combination with Bowtie2 version 2.2.3 and SAMtools version 0.1.19.
Fragments per kilobase of exon per million mapped fragments were calculated using Cuffnorm version 2.2.1.
Ingenuity Pathway Analysis was used to identify canonical pathways of differentially expressed genes.
Assembly: hg19
Supplementary files format and content: Excel file includes FPKM values for each Sample
Supplementary files format and content: csv file includes counts for each Sample

source_name: heart

growth_protocol: Incubated in Dulbecco's modified Eagle's medium (DMEM) with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin

extract_protocol:
RNA was extracted using NucleoSpin (Takara Bio) following the manufacturer’s procedure.
Library preparation was performed using the TruSeq stranded mRNA sample prep kit (Illumina).

value: heart

value: cardiac fibroblast

tag: disease state

value: healthy control


title: Healthy cardiac fibroblasts_3


title: K107651

description: normal breast tissue core


title: K107627

description: normal breast tissue core


title: K107621

description: normal breast tissue core


title: K107632

description: normal breast tissue core


title: Aragene-0923

description: Col-0 uninfected 4 week old mature leaves

source_name: Col-0 uninfected leaves


title: Aragene-0922


title: WT2, untreated, H3K27ac, ChIP-seq

value: Liver

value: Whole Liver


title: Setd8-LKO2,TCPOBOP, input, ChIP-seq

value: TCP


title: Dilated cardiomyopathy_4

value: pediatric DCM


title: Healthy cardiac fibroblasts_1


title: K107623

description: normal breast tissue core

value: WHITE


title: K107578

description: normal breast tissue core


title: K107585

description: normal breast tissue core


title: Dilated cardiomyopathy_3


title: K107580

description: normal breast tissue core


title: Setd8-LKO1, TCPOBOP,  input, ChIP-seq


title: Dilated cardiomyopathy_2


title: K107566

description: normal breast tissue core

value: AFRNAMER


title: Setd8-LKO2, TCPOBOP 24h, SMC3. ChIP-seq

value: TCPOBOP


title: K107600

description: normal breast tissue core


title: Aragene-0925

value: mature rosette leaves


title: Dilated cardiomyopathy_1

value: TNNT2 mutation


title: K107551

description: normal breast tissue core


title: WX1 cells, with 50 mg/L doxycycline addition,rep3

city: Beijing

first: Xiuli

last: Chen

state: Beijing

address: 9/5000  School of Environmental Science

institute: Peking University

data_processing:
Mapping reads to reference genome (Bowtie2)
rRNA contamination assessment (Blast)
Expression analysis (RSEM)
Differential expression analysis (DESeq2)
Assembly: NCBI accession number CP120709
Supplementary files format and content: Tab-delimited text file includes TPM values of each sample

organism: Chryseobacterium sp.

extract_protocol:
Total RNA was extracted from the collected cells using TRIzol® Reagent (Invitrogen) and further purified using DNase I (TaKara).
RNA-seq transcriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 2μg of total RNA.

value: with doxycycline


title: K107555

description: normal breast tissue core


title: Setd8-LKO1, TCPOBOP 24h, SMC3, ChIP-seq


title: WT1, untreated, H3K27ac, ChIP-seq

value: Untreated


title: K107178

description: normal breast tissue core


title: S134A-GR Dex 3

city: Minneapolis

first: Carol

last: Lange

state: MN

address: 2231 6th ST SE

department: Masonic Cancer Center

institute: University of Minnesota

data_processing:
Total RNA was extracted using the Qiagen RNAeasy kit. RNA quality and concentration were assessed by nanodrop. A TruSeq RNA kit was utilized to prepare and generate the mRNA libraries that were sequenced on the Illumina HiSeq2500 in a 75-base paired-end mode. Forty million reads were sequenced on average per sample.
Quality of raw RNA-seq sequences for each sample was assessed with FastQC. Trimmommatic(v0.33) was used to remove low quality bases and trim adapters. FastQC(v0.11.7) was used again on each filtered FASTQ files to generate a sequence quality plot.
Abundance of transcript was estimated with the featureCounts program in the SubRead package. DESeq2 (Version 1.22.2) was used to evaluate differential expression across groups and generate Principal Component Analysis (PCA) plots
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: MDA-MB-231 cell line

growth_protocol: MDA-MB-231 expressing either wt-GR or S134A-GR were serum starved in IMEM containing 1% DCC for 18 hrs.

treatment_protocol: Cells were treated with vehicle treatment or either 1 uM of Dex for 6 hrs.

value: Dex


title: K107185

description: normal breast tissue core

value: normal breast tissue core


title: Setd8-LKO1, TCPOBOP 24h, CTCF, ChIP-seq


title: K107626

description: normal breast tissue core

value: female

value: ~~OTHRACE


title: WX1 cells, with 50 mg/L doxycycline addition,rep2


title: S134A-GR Dex 2

extract_protocol:
Total RNA was extracted using the Qiagen RNAeasy kit. RNA quality and concentration were assessed by nanodrop.
A TruSeq RNA kit was utilized to prepare and generate the mRNA libraries that were sequenced on the Illumina HiSeq2500 in a 75-base paired-end mode. Forty million reads were sequenced on average per sample.


title: S134A-GR Dex 1


title: WX1 cells, with 50 mg/L doxycycline addition,rep1


title: WX1 cells, without doxycycline addition,rep3

value: without doxycycline


title: K107495

description: normal breast tissue core


title: Setd8-LKO2, TCPOBOP 24h, H3K27ac, ChIP-seq


title: K107200

description: normal breast tissue core


title: S134A-GR Veh 1

value: Veh


title: K107492

description: normal breast tissue core


title: S134A-GR Veh 3


title: WX1 cells, without doxycycline addition,rep1


title: WT3, untreated, Mouse liver nuclei, ATAC-seq

value: Liver

value: WT


title: S134A-GR Veh 2


title: K107291

description: normal breast tissue core


title: Setd8-LKO2, TCPOBOP 24h, CTCF, ChIP-seq

value: Whole Liver


title: WT-GR Dex 3

value: wt-GR


title: Setd8-LKO1, TCPOBOP 24h,  H3K27ac, ChIP-seq


title: K107279

description: normal breast tissue core

value: WHITE


title: WT-GR Dex 2


title: K107294

description: normal breast tissue core


title: WT2, untreated, Mouse liver nuclei, ATAC-seq


title: WT1, untreated, Mouse liver nuclei, ATAC-seq


title: Aged_15_mnth_mice_6_bulk_mRNAseq_hypothalamus

city: Bongmyeongdong

first: Mihye

last: Lee

state: Cheonan

address: 25, Bongjeong-ro, Dongnam-gu, Cheonan-si, 31151, Korea

department: Department of Integrated Biomedical Science

country: South Korea

institute: Soonchunhyang Institute of Medi-bio Science (SIMS)

data_processing:
From mRNA sequencing, low-quality raw sequence reads, reads with adapters, and reads with unknown bases were filtered by SOAPnuke software to yield clean reads.
Filtered clean reads were mapped into the reference mouse genome (mm10) using HISAT.
Novel genes predicted using StringTie and Cuffcompare to compare the reconstructed transcripts to the reference annotation and then used CPC tools to predict the novel transcripts.
Gene expression level for each sample was determined using the tools Bowtie2 and RSEM.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Aged male C57BL/6J mice

extract_protocol:
The total RNA of the samples was extracted with the Trizol (Invitrogen) reagent and used for construction of sequencing libraries.
The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification. We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library.

value: Hypothalamus

tag: Sex

value: male

value: 15 months


title: Aged_15_mnth_mice_5_bulk_mRNAseq_hypothalamus

tag: age


title: WT-GR Dex 1


title: K107218

description: normal breast tissue core


title: Young_2_mnth_mice_3_bulk_mRNAseq_hypothalamus

source_name: Young male C57BL/6J mice

value: 2 months


title: Setd8-LKO4, TCPOBOP 24h, Mouse liver nuclei, ATAC-seq

value: TCPOBOP


title: Setd8-LKO5, TCPOBOP 24h, Mouse liver nuclei, ATAC-seq


title: WT-GR Veh 3


title: Setd8-LKO3,TCPOBOP 24h , H3K27ac, ChIP-seq


title: Aged_15_mnth_mice_4_bulk_mRNAseq_hypothalamus


title: WX1 cells, without doxycycline addition,rep2


title: WT-GR Veh 2


title: K107252

description: normal breast tissue core


title: Setd8-LKO3, TCPOBOP 24h, Mouse liver nuclei, ATAC-seq


title: Young_2_mnth_mice_2_bulk_mRNAseq_hypothalamus


title: WT-GR Veh 1


title: Young_2_mnth_mice_1_bulk_mRNAseq_hypothalamus


title: K107269

description: normal breast tissue core


title: Aged_15_mnth_mice_6_bulk_mRNAseq_hippocampus

source_name: Aged male C57BL/6J  mice

value: Hippocampus


title: Aged_15_mnth_mice_5_bulk_mRNAseq_hippocampus


title: K107236

description: normal breast tissue core


title: K107250

description: normal breast tissue core


title: K107525

description: normal breast tissue core


title: Setd8-LKO1, TCPOBOP 24h, Mouse liver nuclei, ATAC-seq


title: AAS_41_Atopic asthmatic_acute_visit_L006

city: Nedlands

first: Anya

last: Jones

state: Western Australia

address: Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue

institute: Telethon Kids Institute, The University of Western Australia

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_41 sequenced on lane L006
AAS_41_C80BLANXX_ACAGTG_L006
Barcode: ACAGTG

data_processing:
The Illumina bcl2fastq 1.8.4 pipeline was used to generate the sequence data.
Raw sequencing reads were aligned to the reference genome (hg19) using Rsubread and summarised at the gene-level with featureCounts. Genes were annotated using the genome wide annotation for human org.Hs.eg.db.
Genome_build: hg19
Supplementary_files_format_and_content: AAS_raw_counts.txt file includes raw-gene level counts. Sample were sequenced across two lanes and need to be collapsed prior to further downstream analysis (AAS_raw_counts_collapsed.txt). For differential expression analysis, the raw counts were used.
Supplementary_files_format_and_content: AAS_VST_transformed_counts.txt file includes DESeq2 vst transformed counts and samples need to be collapsed prior to further downstream analysis (AAS_VST_transformed_counts_collapsed.txt). For network analysis, the vst transformed data was used.

source_name: AAS_41_Atopic asthmatic_acute_visit

extract_protocol:
Total RNA was extracted from viable PBMC employing TRizol (Ambion, Life Technologies) followed by RNeasy MinElute (Qiagen, Hilden, Germany). The integrity of the RNA was 9.5 ± 0.3 (mean ± SD), as assessed on the Bioanalyzer (Agilent Technologies, California, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: subjectid

tag: visit

value: AV

tag: age at visit (years)

value: Male

tag: hdm-specific ige

tag: total ige

tag: cat-specific ige

tag: rhinovirus positive at av (1=yes, 0=no, 9=not measured)

tag: pbmc processing day (1=sameday, 2=overnight)

value: PBMC


title: AAS_41_Atopic asthmatic_acute_visit_L007

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_41 sequenced on lane L007
AAS_41_C80BLANXX_ACAGTG_L007
Barcode: ACAGTG

tag: gender

tag: cell type


title: AAS_42_Atopic asthmatic_convalescent_visit_L006

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_42 sequenced on lane L006
AAS_42_C80BLANXX_GCCAAT_L006
Barcode: GCCAAT

value: CV


title: 10

city: IOWA CITY

first: Thomas

last: rutkowski

state: Iowa

address: 51 newton Rd

department: Anatomy and Cell Biology

institute: uiowa

data_processing:
reads mapping
cell clustering
Assembly: Mm10
Supplementary files format and content: mtx, Gene expression matrix
Supplementary files format and content: rds, cell clustering results

source_name: Primary mouse embryonic fibroblasts

growth_protocol: Cells were cultured in normal MEF media, containing 10%FBS, 1% L-Glutamine, NEAA, AA, sodium pyruvate and P&S

extract_protocol:
Cells were washed 2 times with PBS and tripsinized off the plate using 0.05% Trypsin-EDTA. Then cells were centrifuged down and resuspended in HBSS solution.
Library was performed following manufacture's protocol (10XGenomics single cells 3' v2)

treatment_protocol: Cells were treated with 10 nM thapsigargin and cultured for 16 hrs before harvest.

value: Primary mouse embryonic fibroblasts

value: 10 nM thapsigargin


title: K107255

description: normal breast tissue core

source_name: normal breast tissue core

tag: tissue

value: normal breast tissue core

value: female

tag: bmi

tag: racial background

tag: tyrer-cuzick lifetime_risk_score


title: Young_2_mnth_mice_3_bulk_mRNAseq_hippocampus

tag: strain


title: Aged_15_mnth_mice_4_bulk_mRNAseq_hippocampus

tag: Sex


title: AAS_38_Atopic asthmatic_convalescent_visit_L007

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_38 sequenced on lane L007
AAS_38_C80BLANXX_CGATGT_L007
Barcode: CGATGT


title: K107502

description: normal breast tissue core

tag: age

value: AFRNAMER


title: K107507

description: normal breast tissue core


title: Young_2_mnth_mice_2_bulk_mRNAseq_hippocampus