title: synovial tissue_21days_treat4

city: Changsha

first: Yuqi

last: Wen

address: Xiangya Road

institute: Xiangya Hospital Central South University

description: lncRNA expression data from CIA rats

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human lncRNA Arrays (4x44K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software package. The lncRNAs that at least half of samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses. Differentially expressed lncRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. The lncRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed lncRNAs were annotated  in detail with the lncRNA/miRNA interaction information. The lncRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed lncRNAs were annotated  in detail with the lncRNA/miRNA interaction information.

source_name: Synovial tissue, induced arthritis rats, 21days

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

growth_protocol: Under the same conditions (temperature 21±2℃, humidity 70%, light time 6:00-18:00, free food)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Synovial tissues from CIA and normal rats promptly frozen in liquid nitrogen.

value: Synovial tissue

tag: gender

value: Male

value: 7-8 weeks


title: WT_SPG_1

status: Public on Nov 16 2022

type: SRA

city: Hangzhou

first: Heng-yu

last: Fan

state: Zhejiang

address: Yuhangtang Road

country: China

institute: Life Sciences  Institute

library_source: transcriptomic

data_processing:
RNA-Seq was performed with biological replicates for all samples.
Raw reads were trimmed to 50 bp and mapped to the mouse genome (mm9) and ERCC spike-in sequences with Tophat v2.1.1.
Only uniquely mapped reads were subsequently assembled into transcripts guided by the reference annotation (UCSC gene models) with Cufflinks v2.2.1.
Raw counts were aquired by using htseq v0.11.2, and different expressional genes were analized by DEseq2 v=3.11.
Expression level  was further normalized with the ERCC spike-in.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include raw count values of all RNA-seq samples

molecule: polyA RNA

organism: Mus musculus

source_name: Spermatogonia

extract_protocol:
Spermatogenic cells were collected with Fluorescence activated Cell Sorting (FACS) and Spermatocytes were flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Sequencing libraries were constructed from 500 pg of amplified cDNA using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503) according to manufacturer’s instructions. Barcoded libraries were pooled and sequenced on the Illumina HiSeq X Ten platform with 150 bp paired-end reads

tag: strain

tag: tissue

value: spermatogonia

tag: genotype

value: Wildtype


title: DURA50.N12.D20.ASTRO.B1

type: genomic

city: London

first: Silvia

last: Marino

address: Blizard Institute, 4 Newark Street

country: United Kingdom

institute: Queen Mary University of London

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised using standard Illumina protocol

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

data_processing: Raw array data were first pre-processed using the ChAMP package in R to remove failed detections and probes with known design flaws, before normalisation using the SWAN algorithm

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Dura mater

label_protocol: Standard Illumina Protocol

growth_protocol: Differentiation was initiated on Day -1, by seeding dissociated iNSCs at 1.5x10^4 cells/cm^2 density on GelTrex-coated plates in Neural Expansion media. On Day 0 Neural Expansion media was changed to Astrocyte media (ScienCell: Cat. #1801) supplemented with 2% FBS, Astrocyte Growth Supplement (AGS) and penicillin/streptomycin solution, provided with the media. From Day 2 onwards, media was changed every 48 hours for 20 – 30 days. At 80-90% confluence, the cells were passaged back to the starting seeding density (1.5 x 10^4 cells/cm^2), or at an approximate ratio of 1:6. Cells were detached using Accutase, and always cultured in the same Astrocyte media on GelTrex.

extract_protocol: DNA was extracted using Norgen Biotek RNA/DNA/Protein Purification Plus Kit (Cat. #47700), which allows genomic DNA, total RNA, and protein to be isolated from a single sample.

tag: tissue type

value: Cell culture

tag: cell type

value: Induced astrocyte progenitor


title: scRNA IL5466-N703-N506

city: Stanford

first: Helen

last: Blau

address: 3200 CCSR

country: USA

institute: Stanford University

description: scRNA..musc.TPM

data_processing:
RNA sequences were aligned against the Mus musculus mm10 reference genome using the Spliced Transcripts Alignment to a Reference STAR software.
Assembly: mm10
Supplementary files format and content: TPM expression file

molecule: total RNA

source_name: Muscle stem cell

growth_protocol: Following isolation, we resuspended MuSCs in myogenic cell culture medium containing DMEM/F10 50:50, 20% FBS, 2.5 ng·ml−1  fibroblast growth factor-2 FGF-2, also known as bFGF and 1% penicillin–streptomycin. We seeded MuSC suspensions at a density of 500 cells per cm2 surface area. We maintained cell cultures at 37°C in 5% CO2 and changed medium every other day.

extract_protocol:
RNA was isolated using Qiagen RNAEasy Micro kit from 5,000 -10,000 cells and cDNA generated and amplified using NuGEN Ovation RNA-Seq System v2 kit.
Libraries were constructed from cDNA with the TruSEQ RNA Library Preparation Kit v2 Illumina and sequenced to 30–40 × 106 1 × 75-bp reads per sample on a HiSEQ 2500

treatment_protocol: untreated

value: Muscle cell

tag: age


title: s1.U2OS.ctr.na.00h.1

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: set 1, U2OS cell line, control, 00h hours, replicate 1

data_processing:
RNA-Seq data analysis was done with bowtie2 and rsem (ver. 1.2.3) using EBV genome version hg19
DESeq2 was used for differentail expression analysis
Assembly: hg19
Supplementary files format and content: Prosessed files contains the raw counts for all genes

source_name: U2OS cell line

extract_protocol:
RNA was extracted with Trizol (Invitrogen) for all RNA preparations, then subsequently cleaned and DNase treated using RNeasy columns (Qiagen)
Sequencing library preparation was then completed using the QuantSeq 3’-mRNA kit (Lexogen) to generate Illumina-compatible sequencing libraries according to the manufacturer’s instructions

tag: set

tag: cell line

tag: knockout

value: ctr

tag: clone

tag: time

tag: replicate


title: DURA31.N44B.D20.ASTRO.B1


title: scRNA IL5466-N703-N505

description: scRNA..musc.TPM


title: WT_PreL_2

source_name: preleptotene stage spermatocyte

value: spermatocyte


title: synovial tissue_21days_treat1

type: RNA

description: lncRNA expression data from CIA rats

organism: Rattus norvegicus


title: WT_PreL_4


title: scRNA IL5466-N703-N504

description: scRNA..musc.TPM


title: DURA44.N8.D20.ASTRO.B1


title: s1.U2OS.sgA.E2.00h.2

description: set 1, U2OS cell line, ADIRF-AS1 knockout clone E2, 00h hours, replicate 2

value: sgA


title: synovial tissue_21days_control4

description: lncRNA expression data from normal rats

source_name: Synovial tissue, normal rats, 21days


title: WT_PreL_1


title: DURA19.N8C.D20.ASTRO.B2


title: SW480 cells, CR#1, 6 hrs

city: Xiamen

first: yongyou

last: zhang

state: Fujian

address: Xiang'an South Road

institute: Xiamen University

data_processing:
Illumina Novaseq platform
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Illumina Novaseq platform (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to hg38 using Illumina Novaseq platform (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using Illumina Novaseq platform
Supplementary files format and content: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: SW480 cells were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each samples.

treatment_protocol: SW480 cells werecultured in the full medium (FM) or cystine-restriction medium (CR)

value: colon cancer cell

value: WT

tag: treatment

value: cystine-restriction medium for 6 hrs


title: synovial tissue_21days_control5

description: lncRNA expression data from normal rats


title: CORR-K2957fs_ Replicate 4 Day 5

city: Cambridge

first: Rob

last: Moccia

state: MA

address: 610 Main Street

department: Rare Disease Research Unit

institute: Pfizer Inc

data_processing:
Basecalls were performed with RTA v2.4.11
Libraries were demultiplexed using bcl2fastq
Quality of fastq files was assessed using FastQC (v0.11.8)
Reads were aligned to the human reference genome (hg38, Ensembl version 98) using STAR (v2.7.3a) with additional settings: --quantMode TranscriptomeSAM;  --alignIntronMin 20; --alignIntronMax 1000000; --alignSJoverhangMin 8; --alignSJDBoverhangMin 1; --alignMatesGapMax 1000000; --sjdbScore 1; --outFilterMultimapNmax 20; --outFilterMismatchNmax 1000; --outFilterMismatchNoverLmax 0.10
Estimated counts were obtained using Salmon (v0.14.2) in alignment-based mode with the --gcBias flag
Genome_build: hg38
Supplementary_files_format_and_content: Salmon quant.sf output containing estimates of counts, effective length, and TPM

source_name: iPSC-derived myoblast/myotube

growth_protocol: A patient fibroblast line carrying the DMD c.8868delC (p.K2957fs) mutation was obtained from the MRC Centre for Neuromuscular Diseases Biobank (REC reference 06/Q0406/33). For the use of these cells, we have appropriate ethics approval (REC reference 13/LO/1826; IRAS project ID: 141100). In addition, all patients or their legal guardians gave written informed consent for industrial collaboration. We used a six-factor based reprogramming protocol and a recently developed expanded potential stem cell medium (EPSCM) (Wilkinson et al. 2019; Yang et al. 2017) to generate DMD-K2957fs pluripotent stem cells (PSCs). The isogenic control PSCs (CORR-K2957fs) were generated by precisely correcting the DMD c.8868delC mutation in the DMD-K2957fs PSCs using CRISPR/Cas9-mediated genome editing technology. Myogenic progenitor cells (MPCs) were generated from the isogenic pair of DMD-K2957fs and CORR-K2957fs PSCs as described (Chal et al. 2016). To induce secondary myogenic differentiation, MPCs were cultured in growth medium (Promocell, C-23060) and then switched to N2 based differentiation medium as described (Chal et al. 2016).

extract_protocol:
Total RNA was extracted from at least 5x10^5 cells using RNeasy Plus Mini Kit (Qiagen, 74134) following the manufacturer’s instructions and eluted in 10 ul of DNase/RNase free water.
Illumina TruSeq Stranded


title: WT_LZ_3

source_name: Leptotene and zygotene stage spermatocyte


title: CORR-K2957fs_ Replicate 4Day 2


title: DURA52.N8.D20.ASTRO.B2


title: scRNA IL5466-N703-N502

description: scRNA..musc.TPM


title: WT_LZ_2


title: scRNA IL5466-N703-N507

description: scRNA..musc.TPM


title: SW480 cells, FM#2, 6 hrs

value: complete medium for 6 hrs


title: CORR-K2957fs_ Replicate 4 Day 0


title: scRNA IL5466-N703-N503

description: scRNA..musc.TPM


title: synovial tissue_21days_control3

description: lncRNA expression data from normal rats


title: Nat10_sKO_SPG_4


title: scRNA IL5466-N703-N501

description: scRNA..musc.TPM


title: synovial tissue_21days_treat5

description: lncRNA expression data from CIA rats


title: scRNA IL5466-N702-N508

description: scRNA..musc.TPM


title: Nat10_sKO_SPG_3


title: synovial tissue_21days_treat2

description: lncRNA expression data from CIA rats


title: CORR-K2957fs_ Replicate 3 Day 7


title: synovial tissue_21days_treat3

description: lncRNA expression data from CIA rats


title: MPWT2

city: Madrid

first: Mercedes

last: Ricote

address: Darwin 3

country: Spain

institute: CNB-CSIC

description: Wild-type

library_source: genomic

data_processing:
Reads from the same sample were concatenated and pre-processed with a pipeline that used Cutadapt v1.7 to remove adapters and  FastQC to perform quality controls after each step.
Processed reads were mapped to mm10 whole genome using Bowtie2 v4.1.2 with parameters -X 2000 –very-sensitive
Alignments were filtered using SAMtools (v0.1.18) view to retain only properly paired reads (-f 0x0002) with minimum mapping quality 30 (-q 30) not aligning to unlocalized contigs, unassembled contigs, the mitochondrial genome, and chromosomes X and Y.
ATAC-seq peaks were called using MACS2 v2.1.1 (Zhang et al., 2008) with parameters -nomodel -shift 100 -extsize 200 -keep-dup all -q 0.05
A consensus peak set of peaks detected in at least two samples was generated using function dba.counts from DiffBind R package v2.6.6 (Stark and Brown, 2011; Ross-Innes et al., 2012) and a differential accessibility analysis was performed using EdgeR v3.20.9 (Robinson MD et al, 2010).
Nearest gene annotation and motif discovery were performed using HOMER v4.10.3 (Heinz at al., 2010) package.
Assembly: mm10
Supplementary files format and content: ENCODE narrow peak files (extended bed format) including coordinates, score and qvalue for ATACseq PEAKS called for each sample using MACS2

source_name: bone marrow

growth_protocol: Lineage negative cells from pulled animals were pre-flow purified using the Mouse Hematopoietic Progenitor (Stem) Cell Enrichment Set - DM (BD Bioscience). Thereafter, LT-HSC and MPP were FACS sorted in PBS 1x, 0.5 mM EDTA and 2% FCS to obtain pure populations.

extract_protocol:
Sorted LT-HSCs and MPPs were tagmented using Tn5 (Illumina)
Libraries were prepared according to Buenrostro et al. (2015, Curr Protoc Mol Biol) with minor modifications. Briefly, nuclei DNA was tagmented and extracted. Then, a size selection (0.65x) was applied. Libraries were barcoded with Illumina sequencing indexes. Sequencing was performed on 2×50 HiSeq 3000 (Illumina) and with an average of 25 million paired-end reads per sample.

value: MPPs

value: Wild-type


title: MPWT1

description: Wild-type


title: synovial tissue_21days_control2

description: lncRNA expression data from normal rats

value: Synovial tissue


title: scRNA IL5466-N702-N507

description: scRNA..musc.TPM


title: synovial tissue_21days_control1

description: lncRNA expression data from normal rats

value: Male


title: Nat10_sKO_SPG_1


title: CORR-K2957fs_ Replicate 3 Day 5


title: scRNA IL5466-N702-N506

description: scRNA..musc.TPM


title: CORR-K2957fs_ Replicate 3 Day 2


title: scRNA IL5466-N702-N505

description: scRNA..musc.TPM


title: Nat10_sKO_PreL_3


title: MPKO1

description: RXRα/RXRβ-KO

value: RXRa/RXRb-KO


title: DC_54_95

city: Boston

first: Ze

last: Zhang

address: 375 Longwood Ave

department: Medical Oncology & Population Sciences

institute: Harvard Medical School

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylationEPIC Beadchip using standard Illumina protocol

data_processing: R studio

label: Cy5 and Cy3

source_name: isolated dendritic cell

extract_protocol: Genomic DNA was extracted and purified from samples according to standard instructions

tag: Sex

value: F

tag: arraytypes

value: IlluminaHumanMethylationEPIC

value: isolated dendritic cell


title: Nat10_sKO_PreL_2


title: CORR-K2957fs_ Replicate 3 Day 0


title: scRNA IL5466-N702-N504

description: scRNA..musc.TPM


title: LTWT3

description: Wild-type

value: LT-HSCs


title: DC_32_41

value: M


title: scRNA IL5466-N702-N503

description: scRNA..musc.TPM

value: Muscle cell


title: LTWT2

description: Wild-type


title: CORR-K2957fs_ Replicate 3 Day -1


title: CORR-K2957fs_ Replicate 2 Day 7


title: Nat10_sKO_LZ_3

value: spermatocyte


title: LTKO4

description: RXRα/RXRβ-KO


title: scRNA IL5466-N702-N502

description: scRNA..musc.TPM


title: Nat10_sKO_PreL_1


title: LTKO2

description: RXRα/RXRβ-KO


title: Nat10_sKO_LZ_2


title: CORR-K2957fs_ Replicate 2 Day 5


title: CORR-K2957fs_ Replicate 2 Day 2


title: DC_8_66


title: scRNA IL5466-N701-N508

description: scRNA..musc.TPM


title: CORR-K2957fs_ Replicate 2 Day 0


title: WT mice fed with high glycemic diet (HGD) and with sEHI treated water [HGD_sEHI_3]

city: Davis

first: Saivageethi

last: Nuthikattu

state: CA

address: 550 Hutchison Dr

department: Internal Medicine, Cardiovascular division

institute: University of California Davis

description: Gene expression data of hippocampus microvessels from Female WT mice fed with high glycemic diet (HGD) with sEHI treated water

hyb_protocol: Following fragmentation and labeling, 5.5 ug of sscDNA were hybridized for 16 hr at 45C on the Mouse Gene 2.0 ST Array using Affymetrix WT array hybridization protocol. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: Analyses of gene expression levels were performed with Transcriptome Analysis Console software version 4.0.2.

label: biotin

source_name: Female Mice brain hippocampus microvessels

label_protocol: 122 pg of total RNA was used to prepare cRNA according to Affymetrix's GeneChip® WT Pico Kit protocol. Biotinylated sscDNA (5.5 ug) were prepared from 20 ug of cRNA.

growth_protocol: Female mice were housed in single cages in a temperature- and humidity-controlled environment with a 12 h light/dark cycle.

extract_protocol: Total RNA was extracted from the laser-captured hippocampal brain microvessels from each of the four experimental groups using an Arcturus PicoPure™ RNA Isolation Kit according to the manufacturer’s instructions.

treatment_protocol: 20 week old wild type Female mice were fed a low glycemic diet (LGD), or a high glycemic diet (HGD) with/without the sEHI, trans-4-[4-(3-adamantan-1-yl-ureido)-cyclohexyloxy]-benzoic acid (t-AUCB), for 12 wks.

value: Female

value: hippocampus microvessels


title: scRNA IL5466-N701-N507

description: scRNA..musc.TPM


title: CORR-K2957fs_ Replicate 2 Day -1


title: DC_10_29


title: Tet2+f_Rep1_WGBS

city: Lewiston

first: Andrew

middle: John

last: Kennedy

state: ME

address: 5 Andrews Rd, Dana 322

department: Chemistry

institute: Bates College

description: Bisufite-treated DNA

data_processing:
Reads were QC’d by FastQC (v0.11.5)
filtered by quality (average quality score < 20), Illumina adapters removed, and sequencing primers trimmed using Trim_Galore! (v0.4.5)
The filtered and trimmed reads were then mapped to the mouse genome (mm10), deduplicated, and CpG methylation levels extracted using Bismark (v0.19.0)
Altered CpG methylation was determined by dividing the mouse genome into 870,336 windows, each containing 25 CpG sites. Differentially methylated regions (DMRs) were determined using the EdgeR (for/rev) algorithm available in the Seqmonk (v1.44.0) software package, where a significant difference for any manipulation (VP64, SID4X, and NFD) was determined by a FDR < 0.3 independently against both other groups
Genome_build: mm10
Supplementary_files_format_and_content: One tab-delimited text file includes percent CpG methylation values for each 25 CpG window

source_name: CA1 Hippocampus

extract_protocol:
DNA was extracted, RNase treated, and purified (DNeasy, Qiagen).
gDNA was bisulfite converted (Accel-NGS Methyl-Seq DNA Library, Swift) and sequenced (Hudson Alpha GSL) on the Illumina platform (HiSeq_X10, paired end, 150 bp, 500 million reads per sample).

value: CA1 Hippocampal Tissue


title: Tet2+f_Rep2_WGBS

description: Bisufite-treated DNA


title: DC_73_87


title: CORR-K2957fs_ Replicate 4 Day 7


title: Nat10_sKO_LZ_1


title: Tet2+f_Camk2aCre_Rep2_WGBS

description: Bisufite-treated DNA


title: scRNA IL5466-N702-N501

description: scRNA..musc.TPM


title: WT mice fed with high glycemic diet (HGD) and with sEHI treated water [HGD_sEHI_1]

value: high glycemic diet (HGD) with sEHI treated water


title: LTKO1

description: RXRα/RXRβ-KO


title: scRNA IL5466-N701-N506

description: scRNA..musc.TPM


title: Tet2+f_Camk2aCre_Rep1_WGBS

description: Bisufite-treated DNA


title: scRNA IL5466-N701-N505

description: scRNA..musc.TPM


title: WT mice fed with low glycemic diet (LGD) and with sEHI treated water [LGD_sEHI_3]

description: Gene expression data of hippocampus microvessels from Female WT mice fed with low glycemic diet (LGD) with sEHI treated water


title: scRNA IL5466-N701-N504

description: scRNA..musc.TPM


title: WT mice fed with low glycemic diet (LGD) and with sEHI treated water [LGD_sEHI_2]

value: low glycemic diet (LGD) with sEHI treated water


title: CORR-K2957fs_ Replicate 1 Day 5


title: CORR-K2957fs_ Replicate 1 Day 2


title: WT mice fed with high glycemic diet (HGD) and with sEHI treated water [HGD_sEHI_2]


title: scRNA IL5466-N701-N503

description: scRNA..musc.TPM


title: WT mice fed with low glycemic diet (LGD) and with sEHI treated water [LGD_sEHI_1]


title: CORR-K2957fs_ Replicate 1 Day 0


title: scRNA IL5466-N701-N502

description: scRNA..musc.TPM


title: CORR-K2957fs_ Replicate 1 Day -1


title: WT mice fed with high glycemic diet (HGD) [HGD_3]

description: Gene expression data of hippocampus microvessels from Female WT mice fed with high glycemic diet (HGD)

value: high glycemic diet (HGD)


title: scRNA IL5466-N701-N501

description: scRNA..musc.TPM


title: RNA_Sminus_rep1 [S10_rep1]

city: Tokyo

first: Naoyuki

last: Sotta

address: 1-1-1 Yayoi, Bunkyo-ku

department: Department of Applied Biological Chemistry

country: Japan

institute: Graduate School of Agricultural and Life Sciences, The University of Tokyo

data_processing:
Quality filtering performed using FASTX-Toolkit.
For Ribo-seq, PCR duplicates were removed using clumpify.sh in BBtools
Reads were mapped to Sorghum bicolor v3.1 reference sequences using Bowtie2 (genome) or STAR (transcript). For Ribo-seq, P-site signal counts in CDSs were obtained using riboWaltz package in R. For RNA-seq, read counts on transcripts were counted using bamsignals package in R.
Genome_build: Sorghum bicolor v3.1
Supplementary_files_format_and_content: Comma-separated values of P-site signal counts in CDSs (Ribo-seq) and read counts in transcripts (RNA-seq).

organism: Sorghum bicolor

source_name: RNA_Sminus_whole shoot

growth_protocol: Seeds were shaken in 0.05% Tween 20 three times (1 min each) and then rinsed five times with sterile distilled water. They were surface sterilized in 0.3% hydrogen peroxide at 28 °C for 6 h in the dark with occasional stirring and rinsed three times with sterile distilled water. They were incubated overnight in water at 28 °C in the dark, transferred to vermiculite soaked with distilled water, and germinated under 14-h light at 30 °C / 10-h dark at 25 °C for 5 days. Seedlings were transplanted into pots containing vermiculite and exposed to different S deficiency treatments for 8 days. As a control, ¼-strength Hoagland’s nutrient solution was used. Solutions containing 10 µM MgSO4 were made by mixing S500 solution and ¼-strength modified Hoagland’s nutrient solution containing MgCl2 instead of MgSO4 in the proportions of  1:49 (v/v).

extract_protocol:
A whole shoot (2 g) was frozen in liquid nitrogen and powdered in a Multi-beads Shocker (Yasui Kikai, Osaka, Japan). Approximately 100 mg of powder was used for RNA-seq library construction,  and the rest was used for Ribo-seq.
For Ribo-seq, the powder was homogenized  in ice-cold polysome extraction buffer [100 mM Tris·HCl (pH 8.0), 40 mM KCl, 20 mM MgCl2, 1 mM dithiothreitol, 100 µg/mL cycloheximide, 2% polyoxyethylene (10) tridecyl ether, 1% deoxycholic acid, 10 U/mL DNase I (Qiagen, Hilden, Germany)]  in a Dounce homogenizer and incubated on ice for 10 min. The homogenates were centrifuged for 30 min at 16,000× g and 4 °C in a JA25.50 rotor (Beckman Coulter,  CA, USA) to pellet insoluble cell debris. Each supernatant was layered on the top of a 1.75-M sucrose cushion [100 mM Tris·HCl (pH 8.0), 40 mM KCl, 20 mM MgCl2, 1 mM dithiothreitol, 100 µg/mL cycloheximide, 1.75 M sucrose] and centrifuged for 18 h at 170,000× g and 4 °C in a TY70 Ti  rotor (Beckman Coulter). The polysome pellet was resuspended in the same buffer without sucrose . The OD260 was determined with a NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific,  MA, USA); 1 OD260 unit of polysomes was digested with 20 units of Epicentre RNase I (Lucigen, WI, USA) in a 90-mL reaction mixture for 45 min at 25 °C,  and 10 mL of SUPERase-In RNase inhibitor (Thermo Fisher Scientific) was added. Monosomes were isolated on Illustra MicroSpin S-400 HR columns (GE Healthcare,  IL, USA). RNA was extracted and concentrated with an RNA Clean & Concentrator Kit (Zymo Research,  CA, USA). Concentrated RNA was separated by 7 M urea–12% PAGE in TBE buffer [89 mM Tris·HCl (pH 8.0), 89 mM boric acid, 2 mM EDTA]. Gel slices corresponding to the 26–34-nt region were excised, and a ribosome profiling library was prepared according to McGlincy and Ingolia 2017 with several modifications. To extract RNA or reverse transcription products, crushed gel pieces were resuspended in 45 mM ammonium acetate, 0.045% SDS. For rRNA depletion, a Ribo-Zero Plant Leaf Kit (Illumina,  CA, USA) was used in ¼-scale reactions.   For RNA-seq, total RNA was extracted from approximately 100 mg of frozen tissue powder of the whole shoot using Trizol Reagent (Thermo Fisher Scientific). DNA was depleted with a Turbo DNA-free Kit (Thermo Fisher Scientific), and RNA was purified with an RNA Clean and Concentrator Kit-5 (Zymo). Poly-(A) mRNA was enriched using a NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, MA, USA). A library for Illumina sequencing was constructed using a NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs).

tag: cultivar

value: sulfur deficiency

value: whole shoot


title: CORR-K2957fs_ Replicate 1 Day 7


title: RNA_Ctrl_rep3 [S500_rep3]

source_name: RNA_Ctrl_whole shoot

value: control


title: Bulk_old_rep3

description:
24mo3
musc.TPM


title: WT mice fed with high glycemic diet (HGD) [HGD_1]


title: RNA_Ctrl_rep2 [S500_rep2]


title: RNA_Sminus_rep3 [S10_rep3]


title: WT mice fed with low glycemic diet (LGD) [LGD_3]

description: Gene expression data of hippocampus microvessels from Female WT mice fed with low glycemic diet (LGD)

value: low glycemic diet (LGD)


title: Bulk_old_rep1

description:
24mo1
musc.TPM


title: RNA_Ctrl_rep1 [S500_rep1]


title: Ribo_Sminus_rep3 [S10_rep3]

data_processing:
library strategy: Ribo-seq
Quality filtering performed using FASTX-Toolkit.
For Ribo-seq, PCR duplicates were removed using clumpify.sh in BBtools
Reads were mapped to Sorghum bicolor v3.1 reference sequences using Bowtie2 (genome) or STAR (transcript). For Ribo-seq, P-site signal counts in CDSs were obtained using riboWaltz package in R. For RNA-seq, read counts on transcripts were counted using bamsignals package in R.
Genome_build: Sorghum bicolor v3.1
Supplementary_files_format_and_content: Comma-separated values of P-site signal counts in CDSs (Ribo-seq) and read counts in transcripts (RNA-seq).

source_name: Ribo_Sminus_whole shoot


title: Bulk_old_rep2

description:
24mo2
musc.TPM


title: WT mice fed with low glycemic diet (LGD) [LGD_2]


title: DMD-K2957fs Replicate 4 Day 5


title: DMD-K2957fs Replicate 4 Day 0


title: RNA_Sminus_rep2 [S10_rep2]


title: Bulk_middle_aged_rep2

description:
13mo
musc.TPM


title: WT mice fed with low glycemic diet (LGD) [LGD_1]


title: Ribo_Sminus_rep2 [S10_rep2]


title: DMD-K2957fs Replicate 4 Day -1


title: WT mice fed with high glycemic diet (HGD) [HGD_2]


title: Ribo_Sminus_rep1 [S10_rep1]


title: DMD-K2957fs Replicate 4 Day 7


title: Ribo_Ctrl_rep3 [S500_rep3]

source_name: Ribo_Ctrl_whole shoot


title: Bulk_young_rep3

description:
2mo3
musc.TPM


title: Bulk_young_rep2

description:
2mo2
musc.TPM


title: DMD-K2957fs Replicate 3 Day 5


title: DMD-K2957fs Replicate 4 Day 2


title: DMD-K2957fs Replicate 3 Day 2


title: DMD-K2957fs Replicate 3 Day 0


title: Ribo_Ctrl_rep1 [S500_rep1]


title: CORR-K2957fs_ Replicate 4 Day -1


title: Bulk_young_rep1

description:
2mo1
musc.TPM


title: Ribo_Ctrl_rep2 [S500_rep2]


title: 7_09PH_01CCUKY_Pooled_Input_mm10_i84

city: Lexington

first: Fan

last: Chen

state: Kentucky

address: 1095 V.A. Drive, HSRB 461

department: Toxicology and Cancer Biology

institute: University of Kentucky

data_processing:
The 75-nt single-end (SE75) sequence reads generated by Illumina sequencing (using NextSeq 500) are mapped to the genome using the BWA algorithm. Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. In addition, duplicate reads (“PCR duplicates”) are removed.
The tags are extended in silico (using Active Motif software) at their 3´-ends to a length of 200 bp. The genome is divided into 32-nt bins and the number of fragments in each bin is determined.
ChIP-seq reads were aligned to the mm10 genome assembly.
Peaks were called using SICER 1.1 (default cutoff is FDR 1e-10 with gap parameter of 600 bp). Peak filtering was performed by removing false ChIP-Seq peaks as defined within the ENCODE blacklist.
Standard normalization was performed for the EZH2 ChIP, and spike-in normalization of Drosophila chromatin was performed for the H3K27me3 ChIP.
Genome_build: mm10

source_name: Mouse lung tumor spheroids

growth_protocol: Murine 3D lung tumor spheroids were propagated in DMEM/F12 media containing 1x penicillin/streptomycin, 4mM L-glutamine, 10% fetal bovine serum, 10µg/mL Insulin, 1x Insulin/transferrin/selenium mixture, 12.5µg/mL bovine pituitary extract, 0.1µg/mL cholera toxin, 25 ng/mL mEGF and 25 ng/mL rmFGF2, mixed 1:1 with growth factor-reduced Matrigel, and pipetted into a 24-well 0.4 µm Transwell insert for 12 consecutive days.

extract_protocol:
Matrigel was dissolved by Dispase and the cell pellets were collected and fixed.
Library is constructed by Active Motif using standard Illumina protocols.

treatment_protocol: Murine in vitro 3D spheroids were treated with DMSO (vehicle) or EPZ-6438 5µM for 12 days.

tag: chip antibody


title: 6_09XA_01CCUKY_WT-EPZ-K27me3_H3K27me3_mm10_i93

value: Ezh2 wild-type


title: Bulk_middle_aged_rep1

description:
12mo
musc.TPM

tag: strain


title: DMD-K2957fs Replicate 3 Day 7


title: DMD-K2957fs Replicate 2 Day 7


title: 5_09X9_01CCUKY_Null-K27me3_H3K27me3_mm10_i92

value: Ezh2 null

value: DMSO


title: 4_09X8_01CCUKY_Het_H3K27me3_mm10_i91

value: Ezh2 heterozygous


title: DMD-K2957fs Replicate 2 Day 2


title: DMD-K2957fs Replicate 2 Day 5


title: 3_09X7_01CCUKY_WT_H3K27me3_mm10_i88


title: Erg Fli1 dKO Liver Ecs day 12 post tamoxifen administration 3

city: New

first: Sean

last: Houghton

state: NY

address: 1300 York Ave

institute: Weill Cornell Medicine

description: K2_51_KO_Liver_EC_S42_L004_R1_001.fastq.gz

data_processing:
FastQC (v0.11.5) to check FASTQ quality.
Skewer (v0.2.2) for adapter trimming
Minion from Kraken tool (reaper-13-100) for adapter diagnosis
STAR (v2.7.6a) for alignment and gene count quantification using --quantMode GeneCounts
Assembly: ensembl 90 GRCm38
Supplementary files format and content: counts.txt

source_name: in vivo liver

growth_protocol: cells were isolated from mouse liver

extract_protocol:
Mice were intravital injected with VE-cadherin antibody. Tissues were dissociated by Collagenase Dispase digestion and stained for CD45 and CD31. Endothelial cells were sorted as live (Dapi negative), CD45 negative, CD31 positive, VE-cadherin positive cels. Sorted endothelial cells were processed for RNA isolation using a Qiagen Mini Kit and RNA was sequenced.
RNA-seq libraries of polyadenylated RNA were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina) or TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: mice were treated with tamoxifen to induce gene deletion

value: endothelial cells

tag: time points

value: 12 days post tamoxifen

tag: tissue

value: in vivo liver

value: dKO


title: DMD-K2957fs Replicate 2 Day 0


title: 2_09X6_01CCUKY_Het_EZH2_mm10_i87

tag: genotype


title: Control Liver Ecs day 12 post tamoxifen administration 2

description: C2_47_Ctrl_Liver_EC_S41_L004_R1_001.fastq.gz

tag: cell type

value: Ctl


title: DMD-K2957fs Replicate 2 Day -1


title: DMD-K2957fs Replicate 3 Day -1


title: DM1_3

city: Shanghai

first: Min

last: Hu

state: Select a State or Province

address: 1800 Yuntai Road, Shanghai 200123, China

institute: Tongji University School of Medicine

data_processing:
salmon v1.6.0
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp v 0.23.2
Trimmed sequence reads were mapped to GRCh38.104 using salmon v1.6.0 (parameters: -w 12 -q 30 -z 4 -5 -3 -M 20 -W 4 -u 40 -P 20 -h)
Read count extraction and normalization were performed using DESeq2 v1.34
Assembly: GRCh38.104
Supplementary files format and content: Matrix text files include normalized count for each Sample

source_name: cell type

extract_protocol:
RNA was harvested using Total RNA Extractor (Trizol) .
RNA libraries for RNA-seq were prepared using Hieff NGSTM MaxUp Dual-mode mRNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: cell type

value: human skin fibroblast


title: 1_09X5_01CCUKY_WT_EZH2_mm10_i86


title: DMD-K2957fs Replicate 1 Day 5


title: DMD-K2957fs Replicate 1 Day 7


title: DM1_2


title: DMD-K2957fs Replicate 1 Day 2


title: HM_Ctrl

city: Okayama

first: Yuze

last: Wang

state: Okayama

address: Kitaku Shikada-cho 2 - 5 - 1

institute: Okayama University

description: HM

data_processing:
Raw read data were subjected to quality control using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
And sequence reads were trimmed using Trimmomatic (http://www.usadellab.org/cms/?page=trimmomatic).
Sequence reads were aligned to the murine transcriptome (mm10, Ensembl.org) with HISAT2 (http://daehwankimlab.github.io/hisat2/).
Raw counts and FPKM values were calculated with featureCounts (https://rnnh.github.io/bioinfo-notebook/docs/featureCounts.html).
Next step analysis was based on R script and its pakages.
Assembly: mm10
Supplementary files format and content: Supplementary_files_format_and_content.txt

source_name: Cultured cells in vitro

growth_protocol: The 4T1 murine breast TNBC cell line was acquired from American Type Culture Collection (Manassas, Virginia). All parent cells and 4T1 single clones were grown in RPMI 1640 medium (Sigma-Aldrich, St. Louis, Missouri), supplemented with 10% fetal bovine serum (Cytiva, Marlborough, Massachusetts), 100 U/mL of penicillin, and 100 g/mL of streptomycin (Sigma-Aldrich) at 37°C in humidified air with 5% CO2

extract_protocol:
The total RNA of cells was isolated using the High Pure RNA Isolation Kit (Roche Life Science).
The Genetic Analysis company (Rhelixa, Tokyo, Japan) performed whole-transcriptome sequencing (Bulk RNA-seq) utilizing the NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, Massachusetts) and NEBNext® UltraTMII Directional RNA Library Prep Kit (New England Biolabs, Ipswich, Massachusetts). After ribosomal RNA (rRNA) was depleted, conventional Illumina techniques were performed to generate sequencing libraries, which were then processed on an Illumina NovaSeq 6000 sequencing machine (150-bp paired-end reads, two samples per lane; Illumina, San Diego, California).

treatment_protocol: In six-well plates, 4T1-HM or 4T1-LM cells were grown for 48 h with or without 50 μmol/L of DFX.

value: Cultured cells in vitro

value: Clone 4T1-HM (derived From Single Cell)


title: Mouse_C3_2

first: Franck

last: Rapaport

address: 350 Water Street

department: PMCB

institute: Sanofi

data_processing:
Illumina adaptors were trimmed during the BCL to FastQ conversion.
All raw data was checked for quality using the “Raw Data QC Wizard” function within Array Studio.
Poor quality reads were filtered out using a Q score cutoff of 20
paired-end reads per sample were uniquely mapped to the B38 Mouse Reference Genome using the Ensembl.R100 Gene Model.
Raw counts were then converted to fragments per kilobase of transcript per million mapped reads (FPKM) using the “Report Gene/Transcript Counts” function in Array Studio.
Assembly: B38 Mouse Reference Genome using the Ensembl.R100 Gene Model
Supplementary files format and content: table of FPKM for every sample / transcript

source_name: Conjunctiva

extract_protocol:
RNA was extracted with the RNeasy Lipid Tissue Mini kit from Qiagen.
RNA libraries for RNA-seq were prepared using Illumina's Stranded mRNA Prep Ligation Kit following manufacturer's protocols.

value: Conjunctiva

value: BALC/c

value: WT

tag: skin sensitization

value: MC903 + OVA

tag: ab

tag: ocular challenge

value: OVA


title: HM_DFX50

tag: cell line

value: 50uM DFX dissolved in DMSO


title: LM_Ctrl

description: LM

value: Clone 4T1-LM (derived From Single Cell)

value: DMSO


title: LM_DFX50


title: Mouse_C5_2


title: Mouse_C4_2


title: HCMV-infected Kasumi-3 reactivation, replicate 2 [shortread]

city: Seoul

first: Hyeshik

last: Chang

state: South Korea

address: Building 203 Room 525, School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

data_processing:
Raw files are mapped using STAR (v2.7.0).
Gene counting was done with using subread featureCount.
Assembly: Genome_build: hg38, Human herpesvirus strain Toledo (GU937742.2)
Supplementary files format and content: tab-delimited text files include read count values for each sample

growth_protocol: HFF were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and penicillin (100 U/ml)-streptomycin (100 µg/ml). Kasumi-3 were maintained in RPMI supplemented with 20% FBS, penicillin-streptoycin, 100 µg/mL gentamicin. Cells were incubated at 37ºC under 5% CO2 atmosphere.

extract_protocol:
Total RNAs were extracted using TRIzol reagent and treated with recombinant DNAse 1 for 1h at 37ºC, followed by purification using NucleoSpin RNA Clean-up kit.
Library preparation for RNA-seq was performed using the TruSeq Stranded Total RNA LT Sample Prep Kit Gold (Illumina) according to the manufacturer’s instruction.

treatment_protocol: HFFs were incubated with virus in serum-free DMEM for 1h, washed twice with PBS, and incubated in complex media. For HCMV latent and reactivation infection, Kasumi-3 cells were incubated in X-VIVO 15 for 48h before infection. Cells were infected with HCMV MOI of 1 by incubation in X-VIVO 15 for 4h with rocking every 30 min, followed by spinfection at 1000xg for 30 min. After overnight incubation with virus, cells were treated with trypsin-EDTA to detach remaining viruses and then cushioned onto Ficoll-Pacque to collect live cells from debris and viruses. Cells over cushion were washed with PBS, incubated in X-VIVO 15. For reactivation assay, cells were treated with 20 mM PMA or DMSO for additional 2 days.

value: Lymphoblast

value: PMA for differentiation


title: nor2

city: WuHan

first: shuai

last: mei

address: 1095# Jiefang Ave

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 12.0 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: aorta

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany)

growth_protocol: ApoE-/- mice were exposed to the chronic intermittent hypoxia (CIH) system combined with Ang II administration to establish the OSA-AD model.

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit（Cat#217004，QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: the aorta tissues were from the model mice and were milled to be dissolved in the Trizol (takara)

value: aorta

value: ApoE-/-

value: normal saline


title: DM1_1

value: cell type


title: nor3


title: Mouse_C2_2


title: DMD-K2957fs Replicate 1 Day 0


title: HCMV-infected Kasumi-3 reactivation, replicate 1 [shortread]


title: MPKO2

description: RXRα/RXRβ-KO

value: MPPs

value: RXRa/RXRb-KO


title: Mouse_C1_2


title: Con_3

value: human skin fibroblast

value: Control


title: DMD-K2957fs Replicate 1 Day -1


title: AD1

value: chronic intermittent hypoxia (CIH) system combined with Ang II


title: Mouse_B5_2

value: Conjunctiva

value: BALC/c

value: WT

value: Isotype


title: HCMV-infected Kasumi-3 latency, replicate 1 [shortread]


title: nor1


title: HCMV-infected Kasumi-3 latency, replicate 2 [shortread]


title: Con_1


title: Con_2


title: Mouse_B4_2

value: MC903 + OVA

value: OVA


title: AD2


title: AD3


title: Mouse_B3_2


title: Mouse_B2_2


title: AP64 grown with 20mg/L CaCl2, 24h, replicate 3

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

institute: Center Algatech, Institute of Microbiology of the Czech Academy of Science

data_processing:
Sequencing was performed on the NovaSeq 6000 instrument (Illumina). The demultiplexed raw fastq-files were quality-controlled using the FASTQ-mcf suite (https://github.com/ExpressionAnalysis/ea-utils). Low quality bases (Phred-score < 30) and Illumina adaptors were clipped. Reads were mapped to the reference genome using bowtie2 (Langmead et al., 2012) with default parameters for single end reads. Ambiguously mapping reads were randomly distributed between all regions to which they could be assigned. The resulting sam-files were converted to indexed binary format and pile-up format using samtools (Li et al., 2009). The program featureCounts (Liao et al., 2014) was used to count the reads mapping to genes.
Assembly: GCF_000695095.2
Supplementary files format and content: tab-delimited text file contains reads per gene

organism: Gemmatimonas phototrophica

source_name: Gemmatimonas phototrophica AP64 (DSM 29774) in R2A

growth_protocol: Cultures were grown aerobically on an orbital shaker (150 rpm) at 25±1°C in the dark for 8-10 days.

extract_protocol:
Cells were harvested by centrifugation (8,000 × g for 3 min, 4°C). Pellets were resuspended in 1 ml PGTX extraction solution (Pinto et al., 2009) and immediately frozen in liquid nitrogen was added to each cell pellet until dissolved. Cells were transferred into 2 ml Eppendorf tubes and were immediately frozen in liquid nitrogen and stored at –70°C until extraction. RNA was extracted as described earlier (Kopejtka et al., 2020). The RNeasy kit (Qiagen, the Netherlands) was used for purification according to the manufacturer’s protocol. The first digestion of genomic DNA was performed on the column, using DNase I (Qiagen, the Netherlands) as described by the manufacturer. Total RNA was eluted in 88 μl RNase-free H2O, and the second DNase I digestion was made in solution, followed by a second RNeasy purification step, which included an additional washing step with 80% ethanol done before elution with 30 μl RNase-free water.
Libraries were generated according to Shishkin et al. (https://doi.org/10.1038/nmeth.3313) including rRNA removal with the RiboZero Kit (Illumina Inc., USA).

tag: amendment

value: C


title: SIRT1+IGF2BP2 double KD-rep1

city: Ithaca

first: Elena

last: Panizza

address: 930 Campus Rd

department: Molecular Medicine

institute: Cornell University

data_processing:
Illumina Casava software were used for basecalling.
Genomic mapping was performed using Fastq files aligned to the Genome Reference Consortium Human Build 38 patch release 13 (GRCh38.p13, 2019-02-28), using STAR aligner to generate gene counts for each transcript identified.
Gene counts were normalized using the DESeq2 function.
Relative transcript expression levels were determined by first adding “1” to each gene count value, and then calculating the ratio of the gene count values to the average of the control samples for a given gene.
Ratios were normalized to the median ratio value for each experimental condition before being log2-transformed.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Table reporting normalized gene counts for every gene and every sample

source_name: MDA-MB-231 Cells

growth_protocol: cells were cultured in Roswell Park Memorial Institute 1640 (RPMI-1640) medium supplemented with 10% fetal bovine serum (FBS). Cells stably expressing the indicated constructs were selected for, and maintained by, supplementing the growth medium with 2.0 µg/mL puromycin. All cell lines were maintained at 37°C with 5% CO2.

extract_protocol:
Cells were flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing according to Illumina's protocols accompanying with New England Biolabs's Ultra™ II RNA Library Prep kit (E7775S).

treatment_protocol: Lentiviruses were generated by transfecting HEK-293T cells with a sham-targeting (control) shRNA or indicated shRNAs. Cells were infected by treatment with the various viruses generated and Polybrene (8 ug/mL).

value: Breast

value: MDA-MB-231 Cells

value: SIRT1+IGF2BP2 double knockdown


title: SIRT1+IGF2BP2 double KD-rep2


title: SIRT1+IGF2BP2 double KD-rep3


title: UM164_1

city: Shenyang

first: Huizhe

last: Xu

address: 44 Xiaoheyan Road Dadong District

institute: Liaoning Cancer Hospital & Institute

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as  follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: LN229  cell lines were obtained from American Type Culture Collection (ATCC), cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 5%  fetal bovine serum (FBS) according to the instruction.The cells were incubated at 37ºC in a 5% CO2 incubator.

extract_protocol:
The samples of LN229 cells treated with UM-164 or vehicle were collected and frozen in liquid nitrogen. The total RNA was extracted using Trizol reagent and checked its integrity. The qualified RNA was used to construct cDNA libraries.
cDNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: LN229 cells were treated with 100 nM UM-164 or vehicle for 24 h.

value: glioma


title: UM164_2


title: IGF2BP2 KD-rep3

value: IGF2BP2 knockdown


title: CONTRL_2

value: vehicle


title: IGF2BP2 KD-rep2


title: CONTRL_1


title: Mouse_A5_2

value: PBS


title: AP64 grown with 20 mg/L MgCl2 + 2mg/L CaCl2, 24h, replicate 3

tag: time


title: AP64 grown with 20mg/L CaCl2, 24h, replicate 1

tag: replicate

value: A


title: SW480 cells, shCBS#1, 24 hrs

first: yongyou

last: zhang

address: Xiang'an South Road

data_processing:
Illumina Novaseq platform
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Illumina Novaseq platform (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to hg38 using Illumina Novaseq platform (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using Illumina Novaseq platform
Supplementary files format and content: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each samples.

value: colon cancer cell

value: shCBS

tag: treatment

value: cystine-restriction medium for 24 hrs


title: AP64 grown with 20mg/L CaCl2, 24h, replicate 2

value: B


title: Mouse_A3_2

value: Conjunctiva

value: BALC/c

value: WT


title: IGF2BP2 KD-rep1


title: SW480 cells, shCBS#2, 24 hrs


title: SIRT1 KD-rep3

value: Sirtuin 1 (SIRT1) knockdown


title: Mouse_A4_2

value: MC903 + OVA


title: AP64 grown with 2mg/L CaCl2, 24h, replicate 3

value: C


title: SIRT1 KD-rep1

value: Breast

value: MDA-MB-231 Cells


title: SIRT1 KD-rep2


title: AP64 grown with 20 mg/L MgCl2 + 2mg/L CaCl2, 24h, replicate 1


title: SW480 cells, CR#1, 24 hrs

value: shCtrl


title: SW480 cells, CR#2, 24 hrs


title: Mouse_A2_2


title: SW480 cells, FM#2, 24 hrs

value: complete medium for 24 hrs


title: AP64 grown with 2mg/L CaCl2, 24h, replicate 2


title: AP64 grown with 2mg/L CaCl2, 24h, replicate 1


title: Control-rep3

value: Untreated


title: Mouse_A1_2

value: PBS


title: Control-rep2


title: SW480 cells, FM#1, 24 hrs


title: Mouse_B1_2

value: Isotype

value: OVA


title: AP64 grown with 20mg/L CaCl2, 8h, replicate 3


title: AP64 grown with 20 mg/L MgCl2 + 2mg/L CaCl2, 24h, replicate 2


title: AP64 grown with 20mg/L CaCl2, 8h, replicate 2


title: SW480 FM#2

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
CUT&Tag reads were filtered by fastp v0.19.7, command line: fastp-g-q5-u50-n15-1150
CUT&Tag reads were aligned to the UCSC hg19 genome using bwa version 0.7.17.
Peaks were called using macs2 2.2.7.1
bigWig files were generated using the UCSC tools
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CUT&Tag

extract_protocol:
About 100,000 cells were used to construct the library. Then we followed the standard instructions of the Cut and  Tag Kit
Libraries were prepared using the Cut and Tag Kit (Vazyme TD#903) Kit Libraries were validated using the Agilent High Sensitivity DNA Kit. DNA was extracted with phenol-chloroform isoamyl alcohol. PCR mix and adapter (Vazyme TD # 202) were used for library amplification. The fragment library was purified with 1.2 times the volume of DNA magnetic beads (Vazyme #N411). The library length distribution was checked on Agilent 2100 Bioanalyzer

value: Colorectal Cancer Cell Line

value: full medium (FM)


title: AP64 grown with 20mg/L CaCl2, 8h, replicate 1

value: A


title: SW480 FM#1


title: Normal_5

city: Hangzhou

first: Lixia

address: 1 Bachelor Road

institute: Women's Hospital School of Medicine Zhejiang University

description: placenta-derived exosomes from normal pregnant women

source_name: placenta

extract_protocol:
Total RNA was extracted using a miRNeasy Kit.
Small RNA sequencing libraries were prepared using TruSeq Small RNA Sample Preparation Kits (RS-200-0012, Illumina, San Diego).

value: placenta

value: no treatment


title: Normal_6


title: MCM2_2A NPC total_RNA rep2

city: New York

first: zhiguo

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

data_processing:
mapped to the mouse (mm10) reference genome by STAR software
Read coverage in a bin of 1bp was calculated from filtered bam files by deepTools2 and then normalized with total filtered reads number into reads per million (RPM).
Gene expression levels were firstly calculated by featureCounts [47] to obtain read counts and then normalized with total mapped reads into reads per kilobase in per million reads (RPKM).
Assembly: mm10
Supplementary files format and content: bw, bigwig format, contains the read density at each genomic position

source_name: NPC

growth_protocol: Mouse ES cells were disaggregated and suspended in ES cell medium without LIF. EBs were formed using hanging drop method (300 cells per drop) on dish lids for 3 days. EBs were then collected and cultured in 10 cm low attachment Petri dish in ES cell culture medium without LIF, and the medium was changed every other day.

extract_protocol:
Total RNA was isolated from 1 × 106 cells using RNeasy Plus Mini kit (74136, Qiagen). RNA-seq libraries were prepared and deep sequenced in Columbia University Genome Center.
library construction using Illumina TruSeq

treatment_protocol: To generate pluripotency EGFP reporter mouse E14 WT and Mcm2-2A ES cell line, the lentivirus-based EGFP reporter vector PL-SIN-EOS-C(3+)-EGFP plasmid (Addgene) was used for infection. After selection, single cells were seeded and individual clones were then isolated, expanded and confirmed under fluorescence microscope.

value: NPC


title: SW480 CR#2

city: Xiamen

institute: Xiamen University

value: cystine-restriction medium (CR)


title: Normal_4


title: MCM2_2A NPC total_RNA rep1


title: Normal_3


title: AP64 grown with 20 mg/L MgCl2 + 2mg/L CaCl2, 8h, replicate 2

value: B


title: SW480 CR#1


title: WT NPC total_RNA rep2

value: WT


title: AP64 grown with 20 mg/L MgCl2 + 2mg/L CaCl2, 8h, replicate 1


title: Normal_2


title: day8, exhausted CD8+ T cells, donor 6

city: Hong Kong

first: Weixin

address: 21 Sassoon Road

country: Hong Kong

institute: The University of Hong Kong

description:
Tex_donor6
raw_counts_2nd

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore.
Trimed reads were mapped to UCSC human genome GRCh38/hg38 using STAR.
Gene counts were quantified by featureCounts.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw count values for each sample

source_name: peripheral blood

growth_protocol: Purified CD8+ T cells were maintained in T cell medium (RPMI 1640 medium supplemented with 10% FBS, 50M -mercapteoethanol, 1M HEPES, 1X non-essential amino acids (NEAA), 100mM sodium pyruvate, and 1% penicillin-streptomycin)

extract_protocol: High-quality total RNA was extracted using RNeasy Mini Kit (Qiagen)

treatment_protocol: CD8+T cells were then stimulated with anti-CD3/anti-CD28-coated microbeads (Dynabeads M-450 Epoxy, Invitrogen; bead to cell ratio of 1:1) in the presence of 10U/ml recombinant human IL-2 (PeproTech) in the medium. In these conditions, human universal Type I interferon (PBL Assay science) was added at 1000U/mL throughout the culture for the IFN-Is treatment group.

value: peripheral blood

value: CD8+ T cells

value: Ctrl


title: day8, exhausted CD8+ T cells, donor 7

description:
Tex_donor7
raw_counts_2nd


title: Normal_1


title: day8, exhausted CD8+ T cells, donor 5

description:
Tex_donor5
raw_counts_2nd


title: MCM2_2A mES total_RNA rep2

source_name: mES

value: mES


title: Control-rep1

value: Breast

value: MDA-MB-231 Cells

value: Untreated


title: WT NPC total_RNA rep1


title: GDM8

description: placenta-derived exosomes from GDM pregnant women


title: AP64 grown with 2mg/L CaCl2, 8h, replicate 2


title: day2, effector CD8+ T cells, IFN-Is treatment, donor 7

description:
Teff_IFN_donor7
raw_counts_2nd

value: IFN-Is treatment


title: AP64 grown with 2mg/L CaCl2, 8h, replicate 1


title: MCM2_2A mES total_RNA rep1


title: AP64 grown with 20 mg/L MgCl2 + 2mg/L CaCl2, 8h, replicate 3

value: C


title: GDM7


title: WT mES total_RNA rep2


title: day2, effector CD8+ T cells, IFN-Is treatment, donor 6

description:
Teff_IFN_donor6
raw_counts_2nd


title: AP64 grown with 20mg/L CaCl2, 2h, replicate 3


title: WT mES total_RNA rep1


title: day2, effector CD8+ T cells, IFN-Is treatment, donor 5

description:
Teff_IFN_donor5
raw_counts_2nd


title: GDM6


title: AP64 grown with 20mg/L CaCl2, 2h, replicate 2


title: AP64 grown with 2mg/L CaCl2, 8h, replicate 3


title: GDM5


title: Multipotent progenitors - RxRa CUT&RUN rep 2

city: Madrid

first: Mercedes

address: Darwin 3

institute: CNB-CSIC

description: CUT&RUN assay using RxRa antibody (Protein tech, Catalog. 21218-1-AP)

data_processing:
library strategy: CUT&RUN
Sequenced reads were trimmed for adaptor sequence and  bad quality segments using Trim Galore! v0.4.2 and cutadapt v1.9.1.
Trimmed reads are mapped to mouse genome mm10  using bowtie v2.3.4.1 with parameters : --dovetail --local --very-sensitive-local -I 10 -X 700 --no-unal --no-discordant --no-mixed --un-conc-gz
Aligned reads were stripped of duplicate reads with the program sambamba v0.6.8
Peaks were called using the program MACS v2.1.4 using narrow peak mode with the parameters : -g mm -q 0.1
Peaks are extended by 50bp on both sides
Assembly: mm10
Supplementary files format and content: peak text files in standard MACS2 output format for narrow peak mode (columns : chromosome,start,end,name,score,strand,signalValue,pValue,qValue,peak)

source_name: Bone marrow

growth_protocol: Hematopoietic stem cells (HSC: Lin-cKit+Sca1+CD48-CD150+) and multipotent progenitors (MPP: Lin-cKit+Sca1+CD150-) were sorted from the BM of Rxrabfl/fl (WT) mice (pooled, n=3/4) aged ~10 months old and 10,000 HSC and 50,000 MPP were used for each RXRa CUT&RUN assay.

extract_protocol:
Sorted and Bexarotene treated HSC and MPP were washed twice with wash buffer [20 mM HEPES; PH-7.5, 150mM NaCl, 0.5mM spermidine] containing protease inhibitor cocktail (Roche, Catalog. 11873580001). Cells were bound to Concanavalin A magnetic beads (Bangs Laboratories, Inc. Catalog. BP531) followed by permeabilization and antibody binding (RxRa antibody, Catalog. 21218-1-AP, Proteintech)  at 1:50 dilution in wash buffer containing 0.025% digitonin. Antibody bound cells were treated with pA-MNase (700 ng/mL) for 1h at 40C followed by targeted digestion in presence of CaCl2 at 00C for 30 min. The digestion reaction was stopped by adding STOP buffer containing 20 mM EDTA and 4mM EGTA.  The MNase digested DNA fragments were released at 370C, and extracted using QIAGEN MinElute Reaction Cleanup kits (Catalog. 28204).
The CUT&RUNseq libraries were prepared by using NEBNext Ultra II DNA library preparation kit for Illumina (Catalog. E7103S) and NEBNext multiplex Oligoes for Illumina (Catalog. E7335S). The libraries were run on Illumina sequencer NovaSeq6000 with paired end sequencing.

treatment_protocol: HSC and MPP sorted from Rxrabfl/fl (WT) mice were treated with Bexarotene (1 mM) for 1 h followed by downstream processing to isolate RXRa CUT&RUN DNA fragments.

value: MPP

value: VavCre+; WT


title: AP64 grown with 20mg/L CaCl2, 2h, replicate 1

value: A


title: GDM4

value: placenta

value: no treatment


title: day2, effector CD8+ T cells, donor 7

description:
Teff_donor7
raw_counts_2nd


title: GDM3


title: day2, effector CD8+ T cells, donor 6

description:
Teff_donor6
raw_counts_2nd


title: AP64 grown with 20 mg/L MgCl2 + 2mg/L CaCl2, 2h, replicate 3


title: AP64 grown with 20 mg/L MgCl2 + 2mg/L CaCl2, 2h, replicate 2


title: Multipotent progenitors - RxRa CUT&RUN rep 1


title: GDM2


title: day8, exhausted CD8+ T cells, IFN-Is treatment, donor 4

description:
Tex_IFN_rep4
raw_counts_1st


title: Hematopoietic stem cells_RxRa∆/∆;RxRb∆/∆- H3K27Ac

description: CUT&RUN assay for maping  H3K27Ac

data_processing:
library strategy: CUT&RUN
Sequenced reads were trimmed for adaptor sequence and  bad quality segments using cutadapt v1.7.1.
Trimmed reads are mapped to mouse genome mm10  using bowtie v2.2.5 with parameters : --local -I 10 -X 700 --no-mixed --no-discordant --very-sensitive
Peaks were called using the program MACS v3 using narrow peak mode with the parameters : -g mm -q 0.05
Assembly: mm10
Supplementary files format and content: Peak text files in standard MACS3 output format for narrowPeak mode (columns : chromosome,start,end,name,score,strand,signalValue,pValue,qValue,peak)

source_name: BM marrow

growth_protocol: Hematopoietic stem cells (HSC: Lin-cKit+Sca1+CD48-CD150+) were sorted from the the BM of Rxrabfl/fl (WT) and VaviCre+Rxrabfl/fl (RXRKO) mice (pooled, n=4/5) aged ~10 months old and 7,500 HSC were used for each CUT&RUN assay using H3K4me1, H3K4me3, and H3K27Ac antibodies.

extract_protocol:
Sorted HSCs (WT and RXRKO) were washed twice with wash buffer [20 mM HEPES; PH-7.5, 150mM NaCl, 0.5mM spermidine] containing protease inhibitor cocktail (Roche, Catalog. 11873580001). Cells were bound to Concanavalin A magnetic beads (Bangs Laboratories, Inc. Catalog. BP531) followed by permeabilization and antibody binding (H3K4me1 Ab, Cell signaling technologies, Catalog-5326; H3K4me3 Ab, Active motif, Catalog. 39060; H3K27me3, Active motif, Catalog. 39055; H3K27Ac, Active motif, Catalog. 39034)  at 1:50 dilution in wash buffer containing 0.025% digitonin. Antibody bound cells were treated with proteinA-MNase (700 ng/mL) for 1h at 40C followed by targeted digestion in presence of CaCl2 at 00C for 30 min. The digestion reaction was stopped by adding STOP buffer containing 20 mM EDTA and 4mM EGTA.  The MNase digested DNA fragments were released at 370C, and extracted using QIAGEN MinElute Reaction Cleanup kits (Catalog. 28204), and used for DNA library preparation.
The CUT&RUNseq libraries were prepared by using NEBNext Ultra II DNA library preparation kit for Illumina (Catalog. E7103S) and NEBNext multiplex Oligoes for Illumina (Catalog. E7335S). The libraries were run on Illumina sequencer NovaSeq6000 with paired end sequencing.

treatment_protocol: HSCs were processed to isolate specific histone marked CUT&RUN DNA fragments.

value: HSC


title: AP64 grown with 20 mg/L MgCl2 + 2mg/L CaCl2, 2h, replicate 1


title: day8, exhausted CD8+ T cells, IFN-Is treatment, donor 3

description:
Tex_IFN_rep3
raw_counts_1st


title: AP64 grown with 2mg/L CaCl2, 2h, replicate 3


title: Hematopoietic stem cells_WT- H3K27Ac

description: CUT&RUN assay for maping  H3K27Ac


title: day8, exhausted CD8+ T cells, IFN-Is treatment, donor 2

description:
Tex_IFN_rep2
raw_counts_1st


title: breast_treated_06

city: Basel

first: Chia-Huey

last: Ooi

address: Grenzacherstrasse 124

country: Switzerland

institute: F. Hoffmann-La Roche Ltd.

data_processing:
Base calling was performed with BCL to FASTQ file converter bcl2fastq2 version 2.20.0 (Illumina).
FASTQ files were quality checked with FastQC version 0.11.5. RNASeq paired-end reads were mapped onto the human genome (build hg38) with read aligner STAR version 2.5.2a using default mapping parameters.
Aligned reads were quality checked with MultiQC version 1.7.
Numbers of mapped reads for all RefSeq and/or Ensembl transcript variants of a gene were combined into a single value (i.e., count) assuming unstranded library by featureCounts version 1.5.2 and normalized as tpm (transcripts per million).
Assembly: hg38
Supplementary files format and content: raw counts
Supplementary files format and content: TPM (Transcripts Per Kilobase Million)

source_name: breast

extract_protocol:
RNA isolation from formalin-fixed paraffin-embedded tissue (FFPET) using the Qiagen AllPrep DNA/RNA FFPE kit.
Total RNA was subjected to library preparation using Illumina TruSeq RNA Access Library Preparation (recently renamed TruSeq RNA Exome, Illumina 20020189, 48 rxns) which is a hybridization-based assay to enrich for coding RNAs from total RNA sequencing libraries.

value: breast

value: treated

tag: disease

value: breast cancer


title: Hematopoietic stem cells_RxRa∆/∆;RxRb∆/∆- H3K4me3

last: Ricote

description: CUT&RUN assay for maping  H3K4me3


title: AP64 grown with 2mg/L CaCl2, 2h, replicate 2

value: B


title: Hematopoietic stem cells_WT- H3K4me3

description: CUT&RUN assay for maping  H3K4me3


title: AP64 grown with 2mg/L CaCl2, 2h, replicate 1


title: day8, exhausted CD8+ T cells, donor 4

description:
Tex_rep4
raw_counts_1st

value: peripheral blood

value: CD8+ T cells

value: Ctrl


title: AP64 grown with 2mg/L CaCl2, 0h, replicate 3


title: day8, exhausted CD8+ T cells, IFN-Is treatment, donor 1

description:
Tex_IFN_rep1
raw_counts_1st


title: day2, effector CD8+ T cells, donor 5

description:
Teff_donor5
raw_counts_2nd


title: soft tissue_baseline_26

source_name: soft tissue

value: soft tissue

value: baseline


title: day8, exhausted CD8+ T cells, donor 3

description:
Tex_rep3
raw_counts_1st


title: AP64 grown with 2mg/L CaCl2, 0h, replicate 2


title: day8, exhausted CD8+ T cells, donor 2

description:
Tex_rep2
raw_counts_1st


title: AP64 grown with 2mg/L CaCl2, 0h, replicate 1


title: Hematopoietic stem cells- RxRa CUT&RUN


title: Hematopoietic stem cells_RxRa∆/∆;RxRb∆/∆- H3K4me1-rep2

description: CUT&RUN assay for maping H3K4me1


title: Hematopoietic stem cells_WT- H3K4me1-rep2

description: CUT&RUN assay for maping H3K4me1


title: day8, exhausted CD8+ T cells, donor 1

description:
Tex_rep1
raw_counts_1st


title: Hematopoietic stem cells_WT- H3K4me1-rep1

description: CUT&RUN assay for maping H3K4me1


title: pleura_treated_14

source_name: pleura

value: pleura

value: thymoma and thymic carcinoma


title: lymph node_treated_22

source_name: lymph node

value: lymph node

value: merkel cell carcinoma


title: GDM1

last: Zhang


title: Cortisol

city: Rochester

first: Thanh Thanh

middle: Le

last: Nguyen

state: Minnesota

address: 200 1st St. SW

institute: Mayo Clinic

data_processing:
alignment with feather pipeline
call loops with MAPS pipeline
H3K27ac ChIPseq for GM12878 on ENCODE was used as anchors
Genome_build: hg19
Supplementary_files_format_and_content: arcplot files for HiC visualization

source_name: B lymphoblastoid cell line

growth_protocol: 5% charcoal stripped FBS RPMI 1640 for 48hrs

extract_protocol:
Arima Genomics-HiC+ Kit
Swift BiosciencesÒ Accel-NGSÒ 2S Plus DNA Library Kit
Hi-C plus H3K27ac ChIP (HiChIP)

treatment_protocol: Drug treatment for 8.5 hours

value: 100nM hydrocortisone, 8.5 hours

value: LCL CA61


title: breast_baseline_06


title: lymph node_baseline_22


title: soft tissue_treated_26


title: Vehicle

value: 0.1% EtOH


title: Healthy control blood rep6 (ADT)

city: Atlanta

first: Eliver

last: Ghosn

state: GA

address: 1760 Haygood Dr NE

department: School of medicine

institute: Emory University

description:
PHA1010_bl
PHA1010_bl_filtered_matrix.h5
PHA1010_bl_raw_matrix.h5

data_processing:
Library strategy: ADT-seq
Cell Ranger Software (v.5.0.0) was used to perform barcode processing and single-cell 5′ unique molecular identifier (UMI) counting. Reads from GEX and ADT libraries were processed simultaneously using “cellranger count”.
Genome_build: GRCh38
Supplementary_files_format_and_content: mtx files are the sparse matrices of the gene expression and surface-protein expression data.

molecule: protein

source_name: Healthy control blood

extract_protocol:
Blood was collected bedside via standarad venipuncture into EDTA (lavender top) or sodium heparin (green top) vacutainer tubes. Blood was maintainted and transferred to the laboratory at room temperature for processing. Plasma from whole blood was isolated via centrifugation at 400 x g for 10 min at 4˚C. Untouched circulating leukocytes were isolated using the EasySep™ RBC Depletion Reagent (StemCell Technologies; Cat. #18170). Endotractheal aspirates (ETA) were collected bedside and transported to the laboratory at room temperature where it was then placed at 4˚C for processing in BSL3 containment. ETA was mixed 1:1 with a 50mM EDTA solution (final concentration 25 mM EDTA) in custom RPMI-1640 media deficient in biotin, L-glutamine, phenol red, riboflavin, and sodium bicarbonate (defRPMI-1640), with 3% newborn calf serum (NBCS) and mechanically dissociated using a syringe to liberate leukocytes from mucins and other respiratory secretions. ETA cells underwent an additional mechanical dissociation step using 1-3 mL of a 10 mM EDTA in defRPMI-1640 + 3% NBCS and a P1000 pipettor. Cells were then washed with 10 mL defRPMI-1640 + 3% NBCS, passed through a 70 µm nylon strainer, and pelleted through a 2 mL 100% NBCS layer. Leukocytes from whole blood and ETA samples were incubated with oligo-conjugated Ig-A/D/G/M for 10 min at 4˚C followed by the addition of Human TruStain FcX™ (BioLegend; Cat #422302) and 10 min incubation at RT. Cells were then surface stained with oligo-conjugated monoclonal antibody panel (total 89 antibodies; Extended Data Table 5) for 30 min at 4˚C, followed by two washes in def-RPMI-1640/0.04% BSA. Cells were resuspended at a concentration of 1200-1500 cells/µL in def-RPMI-1640/0.04% BSA and passed through a 20 (blood) or 40 µm (ETA) cell strainer before loading onto a Chromium Controller (10X Genomics, Pleasanton, CA).
Gene expression (GEX) and antibody-derived tag (ADT) libraries were generated using the Chromium Single Cell 5′ Library & Gel Bead Kit v1.1 with feature barcoding following the manufacturer's instructions (https://support.10xgenomics.com/single-cell-vdj/index/doc/user-guide-chromium-single-cell-vdj-reagent-kits-user-guide-v11-chemistry-with-feature-barcoding-technology-for-cell-surface-protein).

tag: disease state

value: Healthy

value: Blood

tag: ethnicity

value: Black/African-American (AA)


title: lymph node_baseline_21

value: breast cancer


title: Hematopoietic stem cells_RxRa∆/∆;RxRb∆/∆- H3K4me1-rep1

description: CUT&RUN assay for maping H3K4me1

value: HSC


title: Healthy control blood rep5 (ADT)

description:
PHA1009_bl
PHA1009_bl_filtered_matrix.h5
PHA1009_bl_raw_matrix.h5


title: lymph node_treated_40

value: treated


title: lymph node_baseline_40


title: lymph node_treated_37


title: Healthy control blood rep4 (ADT)

description:
PHA1008_bl
PHA1008_bl_filtered_matrix.h5
PHA1008_bl_raw_matrix.h5


title: lymph node_baseline_37


title: lymph node_treated_35


title: Healthy control blood rep2 (ADT)

description:
PHA1006_bl
PHA1006_bl_filtered_matrix.h5
PHA1006_bl_raw_matrix.h5


title: Healthy control blood rep1 (ADT)

description:
PHA1005_bl
PHA1005_bl_filtered_matrix.h5
PHA1005_bl_raw_matrix.h5


title: COVID-19 TA rep4 (ADT)

description:
PHA0018_TA
PHA0018_TA_filtered_matrix.h5
PHA0018_TA_raw_matrix.h5
PHA0018TA_scvelo.counts.matrices.rds

source_name: COVID-19 TA

value: Lung (Endotracheal aspirate, ETA)


title: Healthy control blood rep3 (ADT)

description:
PHA1007_bl
PHA1007_bl_filtered_matrix.h5
PHA1007_bl_raw_matrix.h5


title: lymph node_baseline_35


title: COVID-19 blood rep4 (ADT)

description:
PHA0018_bl
PHA0018_bl_filtered_matrix.h5
PHA0018_bl_raw_matrix.h5

source_name: COVID-19 blood


title: lymph node_treated_21


title: pleura_baseline_14


title: lung_treated_25

source_name: lung

value: lung


title: COVID-19 TA rep3 (ADT)

description:
PHA0010_TA
PHA0010_TA_filtered_matrix.h5
PHA0010_TA_raw_matrix.h5


title: COVID-19 blood rep3 (ADT)

description:
PHA0010_bl
PHA0010_bl_filtered_matrix.h5
PHA0010_bl_raw_matrix.h5


title: lung_treated_23

value: non small cell lung cancer


title: Phenion® Full-Thickness Skin Model exposed to Bio-Alcamid® replicate 3

city: Maastricht

first: Danyel

last: Jennen

address: Universiteitssingel 40

department: Toxicogenomics

country: Netherlands

institute: Maastricht University

hyb_protocol: Individual samples were hybridized on Agilent SurePrint G3 Human GE v2 8x60K Microarrays (G4851B; design ID 039494)

scan_protocol: Microarrays were scanned immediately after washing on an Agilent Technologies G2505C DNA Microarray Scanner. Raw data on pixel intensities were extracted from the scanned images using Agilent Feature Extraction Software (version 10.7.3.1; Agilent Technologies, Amstelveen, Netherlands) with default parameters (Protocol: GE1_107_Sep09; Grid 039494_D_F_20120628)

data_processing: All arrays were checked for their quality using ArrayQC (https://github.com/BiGCAT-UM/arrayQC_Module/), a quality control pipeline in R (version 2.10.1; The R Foundation for Statistical Computing, Vienna, Austria). For each spot, the following steps were taken: local background correction, flagging of bad spots, controls and spots with too low intensity, log2 transfor-mation, and quantile normalization. Further preprocessing included the omission of flagged probes and merging of replicate probes based on median.

source_name: Phenion® Full-Thickness Skin Model

label_protocol: 0.2 ug RNA samples were labelled with Cyanine 3 (Cy3) following the Agilent one-color Quick-Amp labeling protocol (Agilent Technologies, Amstelveen, The Netherlands)

growth_protocol: The human Phenion® Full-Thickness Skin Model (Henkel AG & Co, Düsseldorf , Germany) was handled and cultured under sterile conditions, applicable to standard cell culture conditions. Upon arrival the tissues were contained in a 24-well plate containing a semi-solid transport medium and a plastic insert to prevent damage during transport. After arrival, the tissues were immediately removed from their transport plate according to the manufacturer’s instruction. In short, culture dishes were prepared in a manner that allowed the culture of each tissue separately. The Air lift (ALI)-cell culture medium, culture dishes, culture supports and filter papers were all provided with the tissues by the manufacturer. A 24 or 48 hour recovery period at standard cell culture conditions (37°C in a humidified atmosphere containing 5% CO2) was implemented after transfer, after which all culture medium was removed and replaced by fresh ALI-culture medium (37°C). Every tissue used in these experiments was of identical age at this point and could be cultured for at least another 10 days.

extract_protocol: After exposure, the skin tissues were collected and cut into 4 quarters. Two opposite pieces were used for RNA isolation whereas the other two pieces were stored at -80°C. The skin pieces for RNA isolation were submerged in 1 mL pre-chilled (4°C) QIAzol (Qiagen, Venlo, The Netherlands). A T10 basic ULTRA-TURRAX® (IKA, Staufen, Germany) was used to homogenate the tissue in about 30 seconds after which the solution was kept on ice until further processing (no longer than 15 minutes). Total RNA was isolated from the homogenates using the miRNeasy isolation kit (Qiagen, Venlo, The Netherlands) as instructed by the manufacturer. After isolation, RNA concentrations were measured on a NanoDrop spectrophotometer and the integrity was determined with a Bioanalyzer 2100 (Agilent Technologies, Amstelveen, The Netherlands). Only samples of good quality (clear 18S and 28S peaks and the RNA integrity number (RIN) >6) were used for hybridization. An average RIN >9 was measured. Extracted RNA was stored at -80°C until it was used as template for cDNA synthesis.

treatment_protocol: The 3D skin tissues were exposed to the fillers by injecting ~0.3 mL directly under the top lay-er in the epidermal layer using a cross-hatching technique. The cross-hatching pattern ensures an equal distribution of the fillers in the whole tissue model. The commercial fillers Perfectha® and Bio-Alcamid® were injected as provided. The RIVM preparations (#1 to #5) were diluted with PBS 1:1 in order to be able to inject them. Unexposed tissue was used as control. Exposures lasted for 24 hours at 37°C and were performed in triplicate. Each set of exposures was performed on a different date using a fresh batch of tissue models, all constructed from the same donor. Thus, for each exposure three biological replicates were made.

tag: cell model

value: Phenion® Full-Thickness Skin Model

value: exposed to Bio-Alcamid®


title: Phenion® Full-Thickness Skin Model exposed to experimental HA filler RIVM2 replicate 3

value: exposed to experimental HA filler RIVM2


title: Phenion® Full-Thickness Skin Model not exposed; Control replicate 3

description: Control for replicates of experiment 3

value: not exposed; Control


title: Phenion® Full-Thickness Skin Model exposed to experimental HA filler RIVM3 replicate 3

value: exposed to experimental HA filler RIVM3


title: Phenion® Full-Thickness Skin Model exposed to experimental HA filler RIVM4 replicate 3

value: exposed to experimental HA filler RIVM4


title: COVID-19 TA rep2 (ADT)

description:
PHA0008_TA
PHA0008_TA_filtered_matrix.h5
PHA0008_TA_raw_matrix.h5


title: Phenion® Full-Thickness Skin Model not exposed; Control technical replicate 1b

description: Control for replicates of experiment 1; same RNA use as Phenion_Control_1a, i.e. technical replicate


title: Phenion® Full-Thickness Skin Model exposed to experimental HA filler RIVM3 replicate 2


title: Phenion® Full-Thickness Skin Model not exposed; Control replicate 2

description: Control for replicates of experiment 2


title: lung_baseline_23

value: baseline


title: Phenion® Full-Thickness Skin Model exposed to experimental HA filler RIVM5 replicate 3

value: exposed to experimental HA filler RIVM5


title: Phenion® Full-Thickness Skin Model exposed to experimental HA filler RIVM2 replicate 2


title: Phenion® Full-Thickness Skin Model exposed to experimental HA filler RIVM4 replicate 2


title: lung_treated_20


title: Phenion® Full-Thickness Skin Model exposed to experimental HA filler RIVM1 replicate 3

value: exposed to experimental HA filler RIVM1


title: lung_baseline_20


title: Phenion® Full-Thickness Skin Model exposed to Bio-Alcamid® replicate 2


title: lung_treated_11

value: mesothelioma


title: COVID-19 blood rep2 (ADT)

description:
PHA0008_bl
PHA0008_bl_filtered_matrix.h5
PHA0008_bl_raw_matrix.h5

value: Blood

value: Black/African-American (AA)


title: COVID-19 blood rep1 (ADT)

description:
PHA0007_bl
PHA0007_bl_filtered_matrix.h5
PHA0007_bl_raw_matrix.h5


title: Healthy control blood rep6 (GEX)

data_processing:
Cell Ranger Software (v.5.0.0) was used to perform barcode processing and single-cell 5′ unique molecular identifier (UMI) counting. Reads from GEX and ADT libraries were processed simultaneously using “cellranger count”.
Genome_build: GRCh38
Supplementary_files_format_and_content: mtx files are the sparse matrices of the gene expression and surface-protein expression data.

value: Healthy


title: COVID-19 TA rep1 (ADT)

description:
PHA0007_TA
PHA0007_TA_filtered_matrix.h5
PHA0007_TA_raw_matrix.h5


title: Healthy control blood rep5 (GEX)


title: Healthy control blood rep4 (GEX)


title: liver_treated_19

source_name: liver

value: liver

value: treated


title: lung_baseline_25

value: lung


title: liver_treated_32

value: breast cancer


title: Healthy control blood rep2 (GEX)


title: liver_baseline_19

value: non small cell lung cancer


title: Healthy control blood rep3 (GEX)


title: liver_baseline_32


title: Phenion® Full-Thickness Skin Model exposed to experimental HA filler RIVM1 replicate 2

value: Phenion® Full-Thickness Skin Model


title: Phenion® Full-Thickness Skin Model exposed to experimental HA filler RIVM5 replicate 2


title: Phenion® Full-Thickness Skin Model not exposed; Control replicate 1a

description: Control for replicates of experiment 1; same RNA use as Phenion_Control_1b, i.e. technical replicate; after preprocessing not used for further analyses.


title: Healthy control blood rep1 (GEX)


title: Phenion® Full-Thickness Skin Model exposed to experimental HA filler RIVM3 replicate 1


title: liver_treated_13

value: renal cell canver


title: Phenion® Full-Thickness Skin Model exposed to experimental HA filler RIVM4 replicate 1


title: lung_baseline_11


title: Phenion® Full-Thickness Skin Model exposed to experimental HA filler RIVM2 replicate 1

value: exposed to experimental HA filler RIVM2


title: Phenion® Full-Thickness Skin Model exposed to experimental HA filler RIVM5 replicate 1


title: Phenion® Full-Thickness Skin Model exposed to experimental HA filler RIVM1 replicate 1


title: Testis

city: London

first: Yan

last: Liang

state: London

address: mile end road

department: SBBS

institute: Queen Mary Univerisity of London

data_processing:
RNA-seq:the reads were mapped to the transcriptome by using Kallisto ( 0.44.0)
RNA-seq: the gene expression profile was normalized from 13 developmental stages by DESeq2 package (1.34.0) in R (version 4.1.2).
Assembly: owenia fusiformis
Supplementary files format and content: RNA-seq:Owenia_annotation_v250920.1_filtered_mRNA.fasta is the filtered gene model we used for Kallisto mapping; Ofus_adult_tissues_DESeq2_matrix.txt is the output results from DESeq2 normalization

organism: Owenia fusiformis

source_name: Testis

growth_protocol: The Owenia fusiformis adults were kept in the artificial sea water with mud, fed with mix algae

extract_protocol:
RNA-seq: All the fresh samples were snapped freezed by liquid nitrogen, then extracted using the Monarch total RNA Miniprep Kit
RNA-seq: All the libraries were constructed by BGI, BGISEQ-500 platform

treatment_protocol: dissect with forcep

tag: developmental stage

value: adult

value: Testis

tag: Sex

value: male


title: COVID-19 TA rep4 (GEX)

tag: tissue

value: Lung (Endotracheal aspirate, ETA)


title: COVID-19 blood rep4 (GEX)


title: liver_baseline_13

value: baseline


title: liver_treated_04

value: gastric cancer


title: liver_baseline_04


title: Tail

source_name: Tail

value: Tail

value: female


title: COVID-19 TA rep3 (GEX)

value: Black/African-American (AA)


title: COVID-19 blood rep3 (GEX)

value: Blood


title: Retractor-muscle

source_name: Retractor-muscle

value: Retractor-muscle


title: bladder_treated_12

source_name: bladder

value: bladder

value: treated


title: COVID-19 TA rep2 (GEX)


title: Ovary

source_name: Ovary

value: Ovary


title: 2DCellLine-FOXP2-oe4

city: Lexington

first: Fan

last: Chen

address: 1095 V.A. Drive, HSRB 461

institute: University of Kentucky

data_processing:
Sequencing and base-calling were performed by University of Kentucky Genomics core and BGI (Beijing Genomics Institute), respectively.
Sequencing reads were trimmed and filtered using Trimmomatic (V0.39) to remove adapters and low quality reads. Reads from human and mouse samples were mapped to Ensembl GRCh38 and GRCm38 transcripts annotation (release 82), respectively, using RSEM (v1.3.2) and STAR (2.6.1d) with default settings.
Genome_build: GRCh38, GRCm38 release 82
Supplementary_files_format_and_content: tab-delimited text files including TPM, FPKM and expected_count for each gene

source_name: Human lung cancer

growth_protocol: Murine 2D lung tumor cells were propagated in 100-mm dishes with maintained in DMEM F-12 media with 10% fetal bovine serum, 1% Insulin-Transferrin-Selenium, 4mM L-glutamine and penicillin/streptomycin. Murine 3D lung tumor cells were propagated in DMEM/F12 media containing 1x penicillin/streptomycin, 4mM L-glutamine, 10% fetal bovine serum, 10µg/mL Insulin, 1x Insulin/transferrin/selenium mixture, 12.5µg/mL bovine pituitary extract, 0.1µg/mL cholera toxin, 25 ng/mL mEGF and 25 ng/mL rmFGF2, mixed 1:1 with growth factor-reduced Matrigel, and pipetted into a 24-well 0.4 µm Transwell insert. Human 2D cells H460, H2030 and BEAS2B were propagated in 100-mm dishes with maintained in RPMI-1640 media with 10% fetal bovine serum, 4mM L-glutamine and penicillin/streptomycin. Human 2D cells HBEC3KT were propagated in gelatin pre-coated 100-mm dishes with PneumaCult-Ex Basal media with 1X PneumaCult-Ex Supplement media, Hydrocortisone and penicillin/streptomycin.

extract_protocol:
RNA from treated cell lines was extracted using Absolutely RNA Microprep (2D cell and total tumor) or Nanoprep (sorted tumor and 3D spheroid) kits (Agilent).
RNA libraries were prepared for sequencing using BGI or TruSeq standard Illumina protocols or the Smart-SeqII low-input protocol (sorted tumors).

treatment_protocol: Murine in vivo allografts were treated with DMSO (vehicle) or 50mg/kg JQ1 i.p. for 10 consecutive days prior to harvest. Murine in vitro 3D spheroids and 2D cells were treated with DMSO (vehicle) or 25nM JQ1 for 10-12 days.

tag: model system

value: in vitro 2D cell

tag: genotype

value: FOXP2 over-expression

tag: donor mouse/cell line

tag: seq platform

value: BGI std/DNBSEQ


title: Head

source_name: Head

value: adult

value: Head


title: COVID-19 blood rep2 (GEX)


title: Phenion® Full-Thickness Skin Model exposed to Bio-Alcamid® replicate 1

value: Phenion® Full-Thickness Skin Model

value: exposed to Bio-Alcamid®


title: Head+Chaetae

source_name: Head+Chaetae

value: Head+Chaetae

value: male


title: bladder_baseline_12

value: baseline


title: COVID-19 blood rep1 (GEX)


title: 2DCellLine-pLenti6.3-EV4

value: FOXP2 wild-type


title: Gut

source_name: Gut

value: Gut

value: female


title: Phenion® Full-Thickness Skin Model not exposed; Control replicate 1b

tag: included in analysis?

value: yes

value: not exposed; Control


title: Phenion® Full-Thickness Skin Model exposed to Perfectha® SubSkin replicate 3

value: exposed to Perfectha® SubSkin


title: Phenion® Full-Thickness Skin Model exposed to Perfectha® Deep replicate 3

value: exposed to Perfectha® Deep


title: Phenion® Full-Thickness Skin Model exposed to Perfectha® Derm replicate 3

value: exposed to Perfectha® Derm


title: Phenion® Full-Thickness Skin Model not exposed; Control replicate 3a

description: Control for replicates of experiment 3; same RNA use as Phenion_Control_3b, i.e. technical replicate


title: Phenion® Full-Thickness Skin Model exposed to Perfectha® FineLines replicate 3

value: exposed to Perfectha® FineLines


title: Body-Wall

source_name: Body-Wall

value: Body-Wall


title: BRCT3

city: Pamplona

first: Esther

last: Larrea

state: Navarra

address: CIMA Avda. Pio XII 55

institute: Institute of Tropical Health of Universidad de Navarra

data_processing:
The quality of the samples was verified using FastQC v0.11.8 software.
FASTQ files were mapped to hg38 human assembly using STAR v2.6.1c with default parameters.
featureCounts v1.6.0 software and Gencode v31 release were used to obtain read counts at gene level considering only those reads aligned to exonic regions
Obtained gene counts were normalized using edgeR and voom function of limma
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include gene counts obtained with featureCounts for each sample.

source_name: human embryonic kidney

growth_protocol: The human cell line HEK293T was cultured in Dulbecco’s modified Eagle’s medium (DMEN) supplemented with 10% (v/v) heat-inactivated fetal bovine serum (FBS), 100 IU/ml  penicillin and 100 μg/ml streptomycin (all culture reagents from Gibco). Cells grew at 37°C in a humidified atmosphere containing 5% CO2

extract_protocol:
Total RNA from HEK293T lentivirus infected cells was extracted using the automated Maxwell system (Promega)
RNA samples were shipped on dry ice to Macrogen Company (Seoul, Korea) where they were processed and sequenced. The sequencing library from mRNA was prepared using TruSeq Stranded mRNA Library Preparation Kit (Illumina) and RNA-seq was carried out using NovaSeq6000 platform following a configuration of paired readings of 100 base pairs.

treatment_protocol: Human HEK293T cells were seeded in 6-well plate at 1.5 x 10e4 cells/well. After 24 hours, cells were transduced with a lentivirus coding the BRCT domain from L. major Pes protein. Control cells transduced with a lentivirus coding for luciferase protein was also performed. The transductions were carried out with 1 ml of previously generated viral supernatants in the presence of polybrene (10 μg/ml, Santa Cruz Biotechnology).

tag: cell line

value: infected with a lentivirus coding the BRCT domain from Pes protein of Leishmania major


title: BRCT2


title: Blood-vessel

source_name: Blood-vessel

value: adult

value: Blood-vessel


title: 2DCellLine-FOXP2-oe3

value: in vitro 2D cell

value: FOXP2 over-expression

value: BGI std/DNBSEQ


title: E.coli_ALE_2

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

institute: UNIST

data_processing:
The sequencing libraries were sequenced by Nextseq 550, NextSeq 500/550 High Output Kit v2.5 (024906).
Using bowtie software, the sequence reads were mapped onto the wild-type reference genome (NC_000913.2) with the maximum insert size option of 1500bp.
Fragments per kilobase of exon per million fragments (FPKM) and log2 fold change value were calculated by cufflinks.
All the datasets were visualized using Metascope and NimbleGen’s Signalmap software.
Assembly: reference genome(NC_000913.2)
Supplementary files format and content: tab-separated text file includes various values for each sample (The column name is shown on the first line). Q1 = WT, q2 = ALE.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: bacteria cells

growth_protocol: E. coli K-12 MG1655 WT and pfk_ALE-1 strain were harvested at the mid-log growth phase (OD600 ~0.5 for MG1655 and ALE-1 strain). Strains were grown aerobically at 37°C in M9 minimal media supplemented with 0.4% glucose.

extract_protocol:
Cell culture samples were harvested at the mid-log growth phase (OD600 ~0.5 for MG1655 and ALE-1 strain). The RNA was stabilized using by RNAprotect® Bacteria Reagent (Qiagen #76506) and total RNA was isolated using RNeasy® Plus Mini Kit (Qiagen #74134). Ribosomal RNA (rRNA) was removed from isolated RNA samples through riboPooL Probes (Pan-prokaryote) siTOOLS BIOTECH and Dynabeads™ MyOne™ Streptavidin C1(Invitrogen #65001). For purification of RNA samples, RNA clean & concentrator (zymoresearch R1013) was used.
RNA library was constructed from rRNA-depleted RNA using the KAPA stranded RNA-seq kit (Roche KK8400).

treatment_protocol: M9 minimal medium supplemented with 2 mM MgSO4, 0.1 mM CaCl2, and 0.4% glucose was used for growth media.

tag: strain

value: adaptive laboratory evolution (pfk_ALE-1 strain)

tag: growth phase

value: mid-exp phase

tag: medium

value: M9 glucose minimal


title: 2DCellLine-FOXP2-oe2

tag: treatment


title: Phenion® Full-Thickness Skin Model exposed to Perfectha® Deep replicate 2

value: Phenion® Full-Thickness Skin Model


title: BRCT1


title: COVID-19 TA rep1 (GEX)

source_name: COVID-19 TA

value: Lung (Endotracheal aspirate, ETA)

value: Black/African-American (AA)


title: 2DCellLine-pLenti6.3-EV2

value: FOXP2 wild-type


title: E.coli_ALE_1


title: 2DCellLine-FOXP2-oe1


title: Luc3

value: infected with a lentivirus coding the luciferase protein


title: E.coli_WT_2

value: Wild-type


title: 2DCellLine-pLenti6.3-EV1


title: 2DCellLine-pLenti6.3-EV3


title: E.coli_WT_1


title: Luc1


title: Phenion® Full-Thickness Skin Model not exposed; Control replicate 2a

description: Control for replicates of experiment 2; same RNA use as Phenion_Control_2b, i.e. technical replicate

value: yes

value: not exposed; Control


title: Phenion® Full-Thickness Skin Model exposed to Perfectha® FineLines replicate 2

value: exposed to Perfectha® FineLines


title: TCR-seq_C3

status: Public on Nov 15 2022

city: Epalinges

first: Ping-Chih

last: Ho

address: Ch. des Boveresses 155

institute: Ludwig Cancer Institute, UNIL

data_processing:
TCR repertoire analysis and clonotype identification was done by MiXCR
The diversity estimation was quantified by “immunarch” package in R
Assembly: Mouse TCR library
Library strategy: TCR_seq

source_name: Sorted T cells from Braf/Pten induciable melanoma tumor

growth_protocol: Braf/Pten mice were treated with 4-hydroxytamoxifen (4-HT) on the skin surface to induce tumor formation.

extract_protocol:
TILs were lysis by Lysis/Binding Buffer for mRNA purification.
Murine TCR beta-chain specific primer was used for amplification

treatment_protocol: Tumor bearing Braf/PTEN mice, two weeks after tumor induction, were treated with a gradually decreased dosage of anti-CD4 and anti-CD8 antibodies.

tag: cell type

value: Sorted CD45+ CD3+ CD8+ CD44+ tumor-infiltrating T cells

tag: tumor type

value: Braf/Pten inducible melanoma tumor

value: control


title: TCR-seq_TD2

source_name: Sorted T cells from Braf/Pten induciable melanoma tumor with disconued T cell depletion

value: T cell depletion


title: TCR-seq_TD1


title: TCR-seq_TD3


title: Phenion® Full-Thickness Skin Model exposed to Perfectha® SubSkin replicate 2

source_name: Phenion® Full-Thickness Skin Model

value: exposed to Perfectha® SubSkin


title: Phenion® Full-Thickness Skin Model exposed to Perfectha® SubSkin replicate 1


title: Luc2


title: Phenion® Full-Thickness Skin Model exposed to Perfectha® Derm replicate 2

value: exposed to Perfectha® Derm


title: LAX7R Input

city: San Francisco

first: Huimin

last: Geng

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

institute: UCSF

data_processing:
Counts: Raw image data were converted into base calls via the Illumina pipeline CASAVA version 1.8 with default parameters. All 51-bp-long paired-end reads were mapped to the reference human genome sequence, hg18, using BWA aligner (Li H. and Durbin R. (2009) Bioinformatics, 25:1754-60) with the default parameters. Only reads mapping uniquely to the genome with not more than 2 mismatches were retained for downstream analysis.
Peaks: Peak detection was performed with the ChIPseeqer program (Giannopoulou and Elemento, BMC Bioinformatics 2011, 12:277) and annotated to genes and/or promoters based on hg18 refseq genes downloaded from the UCSC Genome Browser
Assembly: human hg18 build
Supplementary files format and content: bigwig and bigbed formats

source_name: LAX7R ALL cell

growth_protocol: The human SEM and RCH-ACV ALL cell lines purchased from DSMZ (Braunschweig, Germany) and maintained in Roswell Park Memorial Institute medium (RPMI-1640, Invitrogen, CA) with 10% fetal bovine serum (FBS), 100 IU/ml penicillin and 100 μg/ml streptomycin. Primary human ALL samples ICN12 ICN13 and LAX7R were cultured on OP9 stroma in Minimum Essential Medium (MEMα, Life Technologies) with GlutaMAX containing 20% FBS, 100 IU ml−1 penicillin, 100 μg ml−1 streptomycin and 1mM sodium pyruvate at 37°C in a humidified incubator with 5% CO2. (reference: Geng et al. Cancer Cell  . 2015 Mar 9;27(3):409-25. doi: 10.1016/j.ccell.2015.02.003; Hurtz et al. Genes Dev . 2019 Sep 1;33(17-18):1265-1279. doi: 10.1101/gad.327593.119.).

extract_protocol:
ChIP protocol: ALL cells were fixed with 1% formaldehyde, lysed and sonicated to generate fragments less than 500bp. Sonicated lysates were incubated with antibodies overnight and after increasing stringency washes immunocomplexes were recovered and DNA was isolated.
Genomic DNA-fragment libraries were prepared using the Illumina ChIP-seq Library preparation Kit following the manufacture’s instructions (Illumina, CA). Briefly 10ng of purified ChIP DNA was end repaired by conversion of overhangs into phosphorylated blunt ends with the use of T4 DNA polymerase and E. coli DNA polymerase I Klenow fragment. Illumina single-end adapters were ligated to the ends of the DNA fragments. Ligation products were purified on a 2% agarose gel with a size selection of 200-300bp. Fifteen PCR cycles were performed with Illumina genomic DNA primers that anneal to the ends of the adapters. The purified PCR-amplified fragment libraries were quantified with the use of the PicoGreen dsDNA Quantitation Assay with the Qubit Fluorometer (Invitrogen, CA). The size range of libraries was validated on the Agilent Technologies 2100 Bioanalyzer with the High Sensitivity DNA Kit (Agilent, CA).

value: relapsed B-cell acute lymphomablastic leukemia with KRAS-G12V mutation

tag: chip antibody

tag: chip antibody host, amount, catalog number and provider

value: Rabbit,  2ug, 2729, Cell Signaling


title: Phenion® Full-Thickness Skin Model exposed to Perfectha® FineLines replicate 1

tag: cell model

value: Phenion® Full-Thickness Skin Model


title: TCR-seq_C2