title: SCAR_410_H3K27me3_Pola1Series_T0_r2

description:
EdU-labelled genomic DNA
SCAR_410_H3K27me3_Pola1Series_T0_r2.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: SCAR_410_H3K27me3_Pola1Series_T0_r1

status: Public on Feb 06 2023

type: SRA

city: Copenhagen

first: Anja

last: Groth

address: Blegdamsvej 3B

country: Denmark

institute: Novo Nordisk Foundation Center for Protein Research

description:
EdU-labelled genomic DNA
SCAR_410_H3K27me3_Pola1Series_T0_r1.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed

library_source: genomic

data_processing:
adapters and low quality reads were filtered with TrimGalore (v0.0.6)
reads were mapped to the genome with bowtie2 (v2.4.2) and uniquely mapped peaks kept using samtools (v1.12)
duplicate reads were removed with picard (version 2.26.10)
bam files were split into forward and reverse strands according to the SAM flag, using samtools view (version 1.5) -F 20 and -f 16, respectively
For each strand the SCAR normalized signal (CPM) was computed in 1kb bins and smoothed in a uniform blur considering the neighboring 30 bins on each side. For each 1kb window, the signal from its corresponding SCAR input was subtracted and negative values were set to zero
Assembly: mm10
Supplementary files format and content: SCAR-seq Partition scores in bigwig format
Library strategy: SCAR-Seq

molecule: genomic DNA

organism: Mus musculus

source_name: Embryonic stem cells

growth_protocol: ESCs were grown on gelatin-coated dishes in serum+LIF conditions at 37 °C with 5 % CO2. DMEM was supplied with fetal bovine serum (15 %), home-made LIF, non-essential amino acids, penicillin/streptomycin and beta-mercaptoethanol. Cells were passaged using Trypsin-EDTA or TrypLE.

extract_protocol: After the appropriate treatment, cells were collected by scraping and nuclei were isolated. Chromatin was digested with MNase. Sequentially, mononucleosomal fragments were immunoprecipitated, purified fragments were biotinylated, libraries were prepared, EdU-biotin fragments were pulled-down and sequenced.

treatment_protocol: Cells were incubated in EdU media (f.c. 10 µm)  for 10 min and then either collected (T0) or cultured for indicated maturation intervals (T30; T3; T8) in media without EdU before collection. If treated with DMSO or Indole-3-acetic acid (IAA), cells were incubated for 1h50 with 500uM IAA or DMSO prior to incubation with EdU for 10 min and then either collected (T0) or cultured for indicated timed in media without EdU but continuously with IAA or DMSO

tag: cell line

tag: strain

tag: genotype

value: wildtype


title: SCAR_442_strandedInput_MCM2Series_T30_r3

description: EdU-labelled genomic DNA


title: Patient P02 Non-lesional skin sample taken at visit V02

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

library_source: transcriptomic

data_processing:
10x genomics V3.0.2 cellranger mkfastq
10x genomics V3.0.2 cellranger count
10x genomics V3.0.2 cellranger aggr
custom Python notebook used to convert the matrix from cellranger into csv format (without additional processing), generate QC metrics and metadata files (see project repository)
Genome_build: GRCh38
Supplementary_files_format_and_content: SC_GEO_raw_counts.csv.gz is a comma-separated, gzipped file containing a Cells (rows) x Genes (columns) raw counts matrix (includes header and row names)
Supplementary_files_format_and_content: SC_GEO_cells.csv.gz is a comma-separated text file containing single cell metadata: sample of origin, quality metrics, QC pass/fail flag
Supplementary_files_format_and_content: SC_GEO_genes.csv.gz is a comma-separated text file containing genes names and ESEMBL gene IDs

molecule: polyA RNA

organism: Homo sapiens

source_name: Healthy skin cell suspension

extract_protocol:
6mm punch-biopsies were taken from affected skin as well as skin presenting no signs of inflammation before treatment. Sarcoidosis has been histologically and clinically confirmed by trained dermatologists. Fresh biopsies were digested according to a collagenase IV skin digestion protocol (M. C. Brüggen et al, blood 2014) to generate single-cell suspensions. Single cell suspensions obtained from non-lesional and lesional skin were next incubated with commercially available DNA-labeled antibodies (TotalSeq-A, Biolegend) together with an antibody against CD45 and a cell viability dye at 4 °C for 30 min. Following incubation, cell suspensions were washed three times with PBS containing BSA. After the final wash, cell suspensions were resuspended in PBS containing BSA and a viability dye for discrimination between live and dead cells. Next, 10,000 viable CD45+ and 10,000 viable CD45- cells were sort-purified from non-lesional and lesional skin and those four cell fractions were kept separately on ice and pooled together before being processed as a single sample.
Single-cell libraries were generated using the Chromium Controller and NEXT GEM Single Cell 3′ Reagent Kit v3 or v3.1 (10x Genomics) according to the manufacturer’s protocol.
The sequencing-ready scRNA-seq libraries were sequenced by the Biomedical Sequencing Facility at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, using the Illumina HiSeq 3000/4000 or the Illumina Novaseq platform (P12_V06, P13_V06) and the 75 bp paired-end configuration.

tag: batch

tag: patient

tag: visit

tag: tissue

value: Non-lesional skin


title: SCAR_438_strandedInput_MCM2Series_T30_r2

description: EdU-labelled genomic DNA


title: HSC and wild type macrophages, transwell

city: Boston

first: Waihay

middle: J

last: Wong

state: MA

address: 360 Longwood Ave

department: Medical Oncology

country: USA

institute: Dana-Farber Cancer Institute

data_processing:
Sequence reads were filtered to remove reads containing adapters, greater than 10% undetermined bases, or greated than 50% of bases with Q score less than or equal to 5.
Trimmed sequence reads were pseudo-aligned using Salmon (version 1.2.1). Salmon index and decoys were generated using GRCm38/mm10 assembly.
Supplementary files format and content: mm10
Supplementary files format and content: Quantification files for each sample.

molecule: total RNA

source_name: liver

growth_protocol: Spleens and livers from wild type or Tet2KO mice were harvested at 8 weeks for enzymatic and physical dissociation. B and T lymphocytes were isolated using antibody coated magnetic beads.  Hepatic macrophages and hepatic stellate cells were isolated using density gradient centrifugation.

extract_protocol:
RNA was isolated using Rneasy mini plus kit (Qiagen).
1.0-1.3 ug of total RNA was used for the construction of sequencing libraries.
cDNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit following manufacturer's protocols.
Pooled libraries were sequenced using Illumina NextSeq 550.

treatment_protocol: Purified cells were grown in monocultures overnight before directly co-cultured at 1:1 cell ratio. Hepatic macrophages were additionally grown in transwell inserts. After 48 hours, adherent cells were washed and harvested for analysis.

value: liver

tag: cell type

value: hepatic stellate cells

value: WT

tag: treatment

value: Co-culture in transwell with wild type hepatic macrophages


title: HSC and Tet2KO macrophages

value: Co-culture with Tet2KO macrophages


title: HSC and wild type T cells

value: Co-culture with wild type T cells


title: HSC and Tet2KO macrophages, transwell

value: Co-culture in transwell with Tet2KO hepatic macrophages


title: HSC and Tet2KO T cells

value: Co-culture with Tet2KO T cells


title: SCAR_438_strandedInput_MCM2Series_T30_r1

description: EdU-labelled genomic DNA


title: HSC and Tet2KO B cells

value: Co-culture with Tet2KO B cells


title: SCAR_410_strandedInput_MCM2Series_T30_r2

description: EdU-labelled genomic DNA


title: SCAR_410_strandedInput_MCM2Series_T30_r3

description: EdU-labelled genomic DNA


title: HSC only, rep4

value: Monoculture


title: SCAR_438_H2AK119ub_MCM2Series_T30_r2

description:
EdU-labelled genomic DNA
SCAR_438_H2AK119ub_MCM2Series_T30_r2.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: SCAR_410_strandedInput_MCM2Series_T30_r1

description: EdU-labelled genomic DNA


title: HSC only, rep2


title: SCAR_438_H2AK119ub_MCM2Series_T30_r1

description:
EdU-labelled genomic DNA
SCAR_438_H2AK119ub_MCM2Series_T30_r1.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: HSC and wild type B cells

value: Co-culture with wild type B cells


title: SCAR_442_H2AK119ub_MCM2Series_T30_r3

description:
EdU-labelled genomic DNA
SCAR_442_H2AK119ub_MCM2Series_T30_r3.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: HSC only, rep1


title: xSCAR_551_H2AZ_T0_r2_A+B

data_processing:
adapters and low quality reads were filtered with TrimGalore (v0.0.6)
reads were mapped to the genome with bowtie2 (v2.4.2) and uniquely mapped peaks kept using samtools (v1.12)
duplicate reads were removed with picard (version 2.26.10)
bam files were split into forward and reverse strands according to the SAM flag, using samtools view (version 1.5) -F 20 and -f 16, respectively
For each strand the SCAR normalized signal (CPM) was computed in 1kb bins and smoothed in a uniform blur considering the neighboring 30 bins on each side. For each 1kb window, the signal from its corresponding SCAR input was subtracted and negative values were set to zero
Assembly: mm10
Supplementary files format and content: SCAR-seq Partition scores in bed format
Library strategy: SCAR-seq

extract_protocol:
For SCAR samples: After the appropriate treatment, cells were collected by scraping and nuclei were isolated. Chromatin was digested with MNase. Sequentially, mononucleosomal fragments were immunoprecipitated, purified fragments were biotinylated, libraries were prepared, EdU-biotin fragments were pulled-down and sequenced. For xSCAR samples (H2A.Z, H4K20me0 when indicated, JARID2): cells were crosslinked for 10min with 1% formaldehyde, quenched, nuclei extracted and sonicated using Covaris. Sequentially, fragments were immunoprecipitated, purified, fragments were converted to libraries, biotinylated and EdU-biotin fragments were pulled-down and sequenced.
OTHER

treatment_protocol: Cells were incubated in EdU media (f.c. 10 µm)  for 10 min (JARID2 xSCAR and Input datasets: 30min) and then either collected (T0) or cultured for indicated maturation intervals (T30; T3; T8) in media without EdU before collection. If treated with DMSO or Indole-3-acetic acid (IAA), cells were incubated for 1h50 with 500uM IAA or DMSO prior to incubation with EdU for 10 min and then either collected (T0) or cultured for indicated timed in media without EdU but continuously with IAA or DMSO

value: EdU-labelled genomic DNA


title: SCAR_410_H2AK119ub_MCM2Series_T30_r2

description:
EdU-labelled genomic DNA
SCAR_410_H2AK119ub_MCM2Series_T30_r2.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: SCAR_410_H2AK119ub_MCM2Series_T30_r1

description:
EdU-labelled genomic DNA
SCAR_410_H2AK119ub_MCM2Series_T30_r1.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: SCAR_442_strandedInput_MCM2Series_T0_r3

description: EdU-labelled genomic DNA


title: HSC only, rep3


title: icSHAPE-SINE DMSO Nuc biol rep 2

city: Yokohama

first: Harshita

last: Sharma

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Division of Genomic Medicine

country: Japan

institute: RIKEN Center for Integrative Medical Sciences

description: in-vivo_icSHAPE_SINE_Nuc_ReactivityScores.txt

data_processing:
Standard icSHAPE bioinformatics pipeline was used (PMID:26766114). In case of SINEB2 whole cell libraries, the sequence data from two Illumina HiSeq runs were merged together for each replicate to ensure sufficient sequencing depth.
After PCR duplicates removal and adapter (13 nt from 5ʹ end) trimming, sequencing reads were mapped to human transcriptome (GRCh38) and custom EGFP and SINEUP transcripts index using Bowtie2. In case of SINEUP, the mapping was focused on the region starting from 1 bp upstream of the SINE element till 88 bp downstream of it (to encompass all the reads with in SINE region of SINEUP). Following the icSHAPE pipeline, RT stops were calculated and normalized, and subsequently enrichment reactivity scores were calculated for each base by subtracting the background signal (DMSO data).
Assembly: hg38 + custom sequences for SINEUP RNAs
Supplementary files format and content: Valid enrichment reactivity score for each base of SINE RNA elements. Format: Each base position is represented by a different row. Columns 1-4 correspond to transcript name, base position in SINE RNA element (used for RT stop calculation), valid enrichment reactivity score for each base (bases with null values were not detected by icSHAPE), and base sequence respectively.
Library strategy: icSHAPE

molecule: nuclear RNA

growth_protocol: HEK293T/17 cells were grown in 6-well culture dish in DMEM (1×) + GlutaMAX-1 supplemented with 10% fetal bovine serum and 1% penicillin streptomycin solution at 37°C, 5% CO2.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) and digested with DNaseI to remove DNA contamination. For subcellular fractionation, the method described by Pandya-Jones and Black (2009) (PMID: 19656867), and for the extraction of nuclear fraction, protocol from Brugiolo et al. (2017) (PMID: 28977534) were followed. The fractionated RNA was further purified by RNeasy Mini Kit (Qiagen) and treated with DNaseI. Purified Total, cytoplasmi and nuclear RNA were ribo-depleted and used for icSHAPE library construction.
icSHAPE library preparation protocol was followed (PMID:26766114). Briefly, ribo-depleted RNA was biotin-clicked, fragmented and end-repaired. Next, RNA was 3' end ligated followed by cDNA synthesis and circularization. Final library was PCR amplified.

treatment_protocol: Various SINEUP-GFP constructs were co-transfected with pEGFP-C2 in each well of 6-well plate. 24 h post-transfection, all the wells pooled together and cells were treated with either NAI-N3 or DMSO following the icSHAPE protocol (PMID:26766114).

value: Human embryonic kidney

tag: transfection

value: pEGFP-C2 and SINE

value: DMSO (mock)


title: icSHAPE-SINE NAI Nuc biol rep 2


title: icSHAPE-SINE DMSO Nuc biol rep 1


title: HSC and wild type macrophages

value: Co-culture with wild type hepatic macrophages


title: SCAR_410_H2AK119ub_MCM2Series_T30_r3

description:
EdU-labelled genomic DNA
SCAR_410_H2AK119ub_MCM2Series_T30_r3.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed

value: wildtype


title: SCAR_438_strandedInput_MCM2Series_T0_r2

description: EdU-labelled genomic DNA


title: icSHAPE-SINE NAI Nuc biol rep 1


title: icSHAPE-SINE DMSO Cyto biol rep 2

description: in-vivo_icSHAPE_SINE_Cyto_ReactivityScores.txt

molecule: cytoplasmic RNA


title: SCAR_438_strandedInput_MCM2Series_T0_r1

description: EdU-labelled genomic DNA


title: icSHAPE-SINE NAI Cyto biol rep 2


title: icSHAPE-FRAM Whole Cell DMSO biol rep 2

description: in-vivo_icSHAPE_FRAM_WholeCell_ReactivityScores.txt

value: pEGFP-C2 and FRAM


title: icSHAPE-SINE NAI Cyto biol rep 1


title: SCAR_410_strandedInput_MCM2Series_T0_r1

description: EdU-labelled genomic DNA


title: SCAR_410_H4K20me0_MCM2Series_T0_r3

description:
EdU-labelled genomic DNA
SCAR_410_H4K20me0_MCM2Series_T0_r3.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: SCAR_410_H4K20me0_MCM2Series_T0_r2

description:
EdU-labelled genomic DNA
SCAR_410_H4K20me0_MCM2Series_T0_r2.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: icSHAPE-FRAM Whole Cell NAI-N3 biol rep 1


title: icSHAPE-FRAM Whole Cell DMSO biol rep 1


title: icSHAPE-SINEB2 Whole Cell DMSO biol rep 2

description: in-vivo_icSHAPE_SINEB2_WholeCell_ReactivityScores.txt

value: pEGFP-C2 and SINEB2


title: icSHAPE-SINEB2 Whole Cell DMSO biol rep 1


title: SCAR_442_H2AK119ub_MCM2Series_T0_r3

description:
EdU-labelled genomic DNA
SCAR_442_H2AK119ub_MCM2Series_T0_r3.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: SCAR_438_H2AK119ub_MCM2Series_T0_r1

description:
EdU-labelled genomic DNA
SCAR_438_H2AK119ub_MCM2Series_T0_r1.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: SCAR_410_H2AK119ub_MCM2Series_T0_r3

description:
EdU-labelled genomic DNA
SCAR_410_H2AK119ub_MCM2Series_T0_r3.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: icSHAPE-SINEB2 Whole Cell NAI-N3 biol rep 2


title: SCAR_410_H2AK119ub_MCM2Series_T0_r1

description:
EdU-labelled genomic DNA
SCAR_410_H2AK119ub_MCM2Series_T0_r1.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: icSHAPE-SINEB2 Whole Cell NAI-N3 biol rep 1


title: PARIS2-SINEUP-GFP_SINEB2 Whole Cell biol rep 1

data_processing:
To check the SINEUP regions interacting with ribosomal RNAs, the PARIS2 analysis strategy was used as described by Zhang et al (2021) (https://github.com/minjiezhang-usc/PARIS2). The 3ʹ end adapters were removed by Trimmomatic v0.39 and sequencing reads were split according to the sample barcodes using splitFastq script from icSHAPE pipeline (Flynn et al 2016). PCR duplicates were removed using readCollapse script from icSHAPE pipeline (Flynn et al 2016) followed by removal of 5ʹ header using Trimmomatic v0.39.
The reads were mapped to a custom genome generated by adding SINEUP-GFP (SINEB2), miniSINEUP-GFP FRAM, and sense EGFP genes as separate chromosomes to the hg38 masked genome (Zhang et al 2021), containing single copy of multicopy genes such as rRNA. Mapping was done by STAR v2.7.10a following the parameters described in PARIS2 paper (Zhang et al 2021).
To extract SINEUP-rRNA chimeras, firstly the reads mapping to rRNA were extracted by samtools same as in PARIS2 analysis strategy and then rRNA chimeric reads where one of the arms of chimera is mapping to SINEUPs were extracted by grep command. The extracted file was sorted by samtools and visualized on IGV (v2.11.1).
Assembly: hg38 + custom sequences for SINEUP RNAs
Supplementary files format and content: Annotation of SINEUP-rRNA chimeric reads. Columns 1-5 correspond to read ID, chimera arm 1 transcript ID with start and end positions and strand direction of the mapped read, annotation of chimera arm 1 mapped read, chimera arm 2 transcript ID with start and end positions and strand direction of the mapped read, annotation of chimera arm 2 mapped read respectively.

extract_protocol:
Total RNA was extracted by TNA extraction method described by Zhang et al. (2021) (PMID: 33879794).
PARIS2 library construction protocol by Zhang et al. (2021) (PMID: 33879794) was used with some optimization.
RNA-Seq (PARIS2)

treatment_protocol: HEK293T/17 cells were transfected with pEGFP-C2 and SINEUP-GFP (SINEB2) or miniSINEUP-GFP FRAM plasmids in 6-well plates. 24h post-transfection, cells were treated with 1 mg/mL Amotosalen at 37°C for 30 min and then irradiated by 365 nm UV light on ice for 30 min to crosslink.

value: EGFP and SINEUP-GFP_SINEB2

value: Amotosalen crosslinked


title: SCAR_552_strandedInput_Pole4Series_T0_r2

description: EdU-labelled genomic DNA


title: PARIS2-SINEUP-GFP_SINEB2 Whole Cell biol rep 2


title: PARIS2-FRAM Whole Cell biol rep 2

value: EGFP and FRAM


title: SCAR_410_strandedInput_MCM2Series_T0_r2

description: EdU-labelled genomic DNA


title: icSHAPE-SINE DMSO Cyto biol rep 1


title: SCAR_410_H4K20me0_MCM2Series_T0_r1

description:
EdU-labelled genomic DNA
SCAR_410_H4K20me0_MCM2Series_T0_r1.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: PARIS2-FRAM Whole Cell biol rep 1


title: PRAISE-WT-rRNA-untreated

city: Beijing

first: Jiang

last: Zhe

state: Beijing

address: No. 5 Yiheyuan Road, Haidian District

department: School of Life Sciences

country: China

institute: Peking University

data_processing:
trimiming using cutadapt
mapping using HISAT2 and then tailored alignment
remove multiple mapping
converting bam into bw using bamCoverage
Assembly: hg38
Supplementary files format and content: bw files including mapping result data

growth_protocol: HEK293T were cultured in DMEM medium (Corning) supplemented with 10% (v/v) FBS (Gibco), 1% GlutaMAX (Gibco) and 0.5% penicillin/streptomycin (Gibco) at 37 °C with 5% CO2.

extract_protocol:
Total RNA was extracted with TRIzol (Invitrogen) followed by isopropanol precipitation, according to the manufacturer’s instructions. For PolyA+ RNA isolation, size selection was first performed using MEGAclear Transcription Clean-Up Kit (Ambion) to deplete small RNA, and RNA was subsequently purified with two sequential rounds of polyA tail purification using oligo (dT)25 Dynabeads (Invitrogen). Small RNA fractions were collected from the flow-through of MEGAclear Transcription Clean-Up Kit.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols. tRNA libraries for RNA-seq were prepared using eCLIP library construction method.

value: WT

value: untreated

tag: fraction

value: rRNA


title: PRAISE-WT-rRNA_rep2

value: PRAISE


title: PRAISE-WT-tRNA_rep2

value: tRNA


title: PRAISE-WT-tRNA-untreated


title: icSHAPE-FRAM Whole Cell NAI-N3 biol rep 2


title: SCAR_438_H2AK119ub_MCM2Series_T0_r2

description:
EdU-labelled genomic DNA
SCAR_438_H2AK119ub_MCM2Series_T0_r2.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: PRAISE-WT-tRNA_rep1


title: PRAISE-DKC1NC-untreated_rep1

value: DKC1 shcontrol

value: mRNA


title: SCAR_551_strandedInput_Pole4Series_T0_r1

description: EdU-labelled genomic DNA


title: SCAR_410_strandedInput_Pole4Series_T0_r2

description: EdU-labelled genomic DNA


title: PRAISE-DKC1NC_rep2


title: SCAR_410_H2AK119ub_MCM2Series_T0_r2

description:
EdU-labelled genomic DNA
SCAR_410_H2AK119ub_MCM2Series_T0_r2.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: Vehicle replicate 4 (miRNA-seq)

city: St Louis

first: Jie

last: Shen

state: MO

address: 425 S. Euclid Ave

institute: Washington University in St Louis

data_processing:
RNA-Seq reads were trimmed by cutadapt first, then trimmed read were aligned against mouse genome (mm10) using STAR v2.4.2a. Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread: featureCount (5) with mouse GENCODE gene annotation (M15).
All gene-level transcript counts were then imported into DESeq2, and normalization method was used to adjust for differences in library size

source_name: femoral head

growth_protocol: Following digestion, articular chondrocytes were harvested and cultured in high-glucose DMEM (Thermo Fisher Scientific, #10569010) supplemented with 10% fetal bovine serum (Gibco, #10437) and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was extracted using E.Z.N.A. Total RNA kit (Bio-Tek, R6834) with DNase 1 following the manufacturer’s instructions.
Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina HiSeq4000 at the Genome Technology Access Center of Washington University in St. Louis.

treatment_protocol: Primary articular chondrocytes were seeded at a density of 50 x 104 cells/well in 12-well plates and treated with vehicle or 1 ng/ml IL-1β (R&D Systems, #201-LB-005) for 24 hours.

value: articular chondrocytes

value: Vehicle


title: Vehicle replicate 2 (miRNA-seq)


title: SCAR_552_strandedInput_Pole4Series_T0_r1

description: EdU-labelled genomic DNA


title: PRAISE-DKC1NC_rep1


title: SCAR_410_strandedInput_Pole4Series_T0_r1

description: EdU-labelled genomic DNA


title: PRAISE-DKC1KD-untreated_rep1

value: DKC1 stable knockdown


title: PRAISE-DKC1KD_rep2


title: PRAISE-DKC1KD_rep1


title: Vehicle replicate 1 (miRNA-seq)


title: IL-1𝝱 replicate 4 (miRNA-seq)


title: PRAISE-WT-KAPA-untreated


title: SCAR_551_strandedInput_Pole4Series_T0_r2

description: EdU-labelled genomic DNA


title: SCAR_552_H2AK119ub_Pole4Series_T0_r1

description:
EdU-labelled genomic DNA
SCAR_552_H2AK119ub_Pole4Series_T0_r1.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: Vehicle replicate 3 (miRNA-seq)


title: IL-1𝝱 replicate 3 (miRNA-seq)


title: PRAISE-WT-KAPA_rep1

extract_protocol:
Total RNA was extracted with TRIzol (Invitrogen) followed by isopropanol precipitation, according to the manufacturer’s instructions. For PolyA+ RNA isolation, size selection was first performed using MEGAclear Transcription Clean-Up Kit (Ambion) to deplete small RNA, and RNA was subsequently purified with two sequential rounds of polyA tail purification using oligo (dT)25 Dynabeads (Invitrogen).
RNA libraries for RNA-seq were prepared using KAPA Stranded mRNA-Seq Kit following manufacturer's protocols.


title: PRAISE-WT-KAPA_rep2


title: SCAR_551_H2AK119ub_Pole4Series_T0_r2

description:
EdU-labelled genomic DNA
SCAR_551_H2AK119ub_Pole4Series_T0_r2.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: IL-1𝝱 replicate 2 (miRNA-seq)


title: SCAR_551_H2AK119ub_Pole4Series_T0_r1

description:
EdU-labelled genomic DNA
SCAR_551_H2AK119ub_Pole4Series_T0_r1.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: IL-1𝝱 replicate 1 (miRNA-seq)


title: SCAR_410_H2AK119ub_Pole4Series_T0_r2

description:
EdU-labelled genomic DNA
SCAR_410_H2AK119ub_Pole4Series_T0_r2.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: Vehicle replicate 4 (RNA-seq)

extract_protocol:
Total RNA was extracted using E.Z.N.A. Total RNA kit (Omega Bio-Tek, R6834) with DNase 1 following the manufacturer’s instructions.
Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina HiSeq4000 at the Genome Technology Access Center of Washington University in St. Louis.


title: SCAR_410_H2AK119ub_Pole4Series_T0_r1

description:
EdU-labelled genomic DNA
SCAR_410_H2AK119ub_Pole4Series_T0_r1.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: ChOR_T0_clickedInputs_IAAdTAG_EdU_r3

description: EdU-labelled genomic DNA

data_processing:
adapters and low quality reads were filtered with TrimGalore (v0.0.6)
reads were mapped to the genome with bowtie2 (v2.4.2) and uniquely mapped peaks kept using samtools (v1.12)
duplicate reads were removed with picard (version 2.26.10)
bam files were read into Seqmonk (v1.47.1) with MAPQ>20, ignoring duplicates, and reads extended by 250bp. Samples were normalized based on Drosphila spike-In abundance and corresponding ClickedInputs. Replicates were merged, exported as bedgraphs and converted to bigwig using UCSC BedGraphtoBigWig
Assembly: mm10
Assembly: dm6
Supplementary files format and content: bigwig files for merged replicates (RRPM-adjusted)  for the mouse genome
Library strategy: ChOR-seq

extract_protocol: After the appropriate treatment, cells were washed with cold PBS, crosslinked for 5min with 1% Formaldehyde at room temperature and subsequently quenched with 0.1M Glycin (final concentration) for 5min before harvesting. Then, nuclei were isolated and sonicated using the Covaris Chromatin Shearing Kit. ChIP-Immunoprecipation of chromatin was done using antibodies according to the manufacturers recommendation with EdU-labelled Drosophila S2 chromatin serving as Spike-In control and, where the epitope of the antibody does not recognize the Drosophila homolog (i.e. H2A.Z) , H2AV antibodies to immunoprecipitate Spike-In chromatin as well. Purified fragments were biotinylated, libraries prepared, EdU-biotinylated fragments pulled down using Streptavidin and sequenced

treatment_protocol: Cells were incubated in EdU media (f.c. 10 µm)  for 10 min and then either collected (T0) or cultured for indicated maturation intervals (T15-T480, in minutes) in media without EdU before collection. If treated with DMSO (volume equivalent), Triptolide (10uM), Indole-3-acetic acid (500uM) and/or dTAG-13 (1uM), cells were incubated for indicated times in the description and then  collected.

value: Ring1B-mAID BAP1dTAG Ring1AKO

value: Indole-3-acetic (IAA) 500uM, dTAG-13 (1uM) for 80min


title: SCAR_552_H2AK119ub_Pole4Series_T0_r2

description:
EdU-labelled genomic DNA
SCAR_552_H2AK119ub_Pole4Series_T0_r2.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: urine_TESEN_22

city: Brussel

first: Ellen

last: Goossens

address: Pleinlaan 2

country: Belgium

institute: Vrije Universiteit Brussel

data_processing:
bcl2fastq2-v2.19.1.403
miarma v 1.7.5
Assembly: hg19
Supplementary files format and content: fastq files

source_name: non-cell sample

extract_protocol:
miRNA extraction from seminal plasma was performed using the Qiagen RNeasy Mini Kit (74104; Qiagen, Antwerp, Belgium). The samples were thawed and resuspended. First, 500 µL Trizol was added to 400 µL seminal plasma and incubated for 5 minutes at RT. Next, 150 µL chloroform (102445; Merck) was added and the samples incubated for 3 minutes at RT. The sample was centrifuged at 11,900g for 15 minutes at 4°C. The aqueous phase was transferred into a new tube and one volume of 70% ethanol was added. Up to 700 µL of the sample was transferred to a RNeasy spin column in a 2 mL-collection tube and centrifuged for 15 seconds at >8000g at 4°C. The flow-through was discarded and the previous step was repeated until the whole sample was transferred to the spin column. Then, 700 µL buffer RWT was added to the spin column and centrifuged (15 seconds; >8000 x g ; 4°C), after which the flow-through was discarded. A total of 500 µL RPE buffer was added in the same manner. Next, 500 µL 80% ethanol was added and the sample was centrifuged for 2 minutes at >8,000g at 4°C. The collection tube with flow-through was discarded and a new 2 mL-collection tube was placed under the spin column. This was centrifuged with open lid at full speed for 5 minutes. Finally, the column was placed on a 1.5 mL-collection tube, 20 µL RNase-free water was added and the sample was centrifuged for 1 minute at >8000g at 4°C to elute the RNA.   miRNA extraction from the urine samples was performed using the Norgen Urine miRNA Purification Kit (29000; Norgen Biotek Corp., Thorold, Canada), according to the manufacturer’s instructions with a minor adaptation to the protocol (usage of 50 µL elution solution A instead of 20 µL).
Sequencing libraries were generated from 50 ng RNA input material using the SMARTer smRNA-Seq Kit for Illumina (Takara) according the instructions of the manufacturer. Size selection of final libraries was done using AMPure Xp beads. After library quality and fragmentation control on fragment analyzer (Agilent) samples were pooled and sequenced on a Novaseq 6000 platform (Illumina) using paired end sequencing (100*8*8*100).

tag: sample type

value: urine

tag: spermatozoa

value: no

value: non-cell sample


title: urine_TESEN_20


title: urine_TESEN_21


title: urine_TESEP_1

value: yes


title: urine_TESEP_3


title: urine_TESEP_2


title: urine_TESEN_18


title: urine_TESEN_19


title: Vehicle replicate 3 (RNA-seq)


title: urine_TESEN_23


title: Vehicle replicate 2 (RNA-seq)


title: Vehicle replicate 1 (RNA-seq)


title: urine_TESEN_16


title: ChOR_T0_clickedInputs_IAAdTAG_EdU_r2

description: EdU-labelled genomic DNA


title: urine_TESEN_17


title: urine_TESEN_15


title: ChOR_T0_clickedInputs_IAAdTAG_EdU_r1

description: EdU-labelled genomic DNA


title: urine_TESEN_13


title: IL-1𝝱 replicate 4 (RNA-seq)


title: ChOR_T0_clickedInputs_DMSO_EdU_r3

description: EdU-labelled genomic DNA

value: DMSO


title: urine_TESEN_14


title: urine_TESEN_12


title: IL-1𝝱 replicate 3 (RNA-seq)


title: ChOR_T0_clickedInputs_DMSO_EdU_r2

description: EdU-labelled genomic DNA


title: IL-1𝝱 replicate 2 (RNA-seq)


title: urine_TESEN_10


title: IL-1𝝱 replicate 1 (RNA-seq)


title: urine_TESEN_8


title: ChOR_totalChIP_IAAdTAG_EdU_r3

description:
ChIP-purified genomic DNA
ChOR_totalChIP_H2Aub_IAAdTAG_RRPM_MEAN.bw


title: ChOR_T0_clickedInputs_DMSO_EdU_r1

description: EdU-labelled genomic DNA


title: urine_TESEN_9


title: urine_TESEN_6


title: urine_TESEN_3


title: urine_TESEN_5


title: urine_TESEN_4


title: urine_TESEN_2


title: SSC Cxcr41013/1013 Replicate 2

city: Paris

first: Zeina

last: Abou Nader

address: 1 AVENUE CLAUDE VELLEFAUX

country: France

institute: Institut de Recherche Saint Louis- Hopital Saint Louis

data_processing:
Reads were processed using the FastQC program in order to remove adapter and low-quality sequences (reads shorter than 50 bp were removed)
Reads were aligned to the mm10 build of the Mus musculus genome using STAR tool
Gene expression quantification was obtained using read counting software Htseq81. Read counts normalization and differential analysis were performed using the DESeq2 package by applying the Benjamini-Hochberg FDR correction for comparison between samples.
Assembly: mm10

source_name: Bone

extract_protocol:
Total RNA was isolated using RNeasy Micro Kit (Qiagen).
cDNAs were generated from 400 to 1,000 pg of total RNA using Clontech SMART-Seq v4 Ultra Low Input RNA kit for Sequencing. 600 pg of pre-amplified cDNAs were used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit.

value: Bone

value: Skeletal Stromal/Stem Cells (SSC)


title: urine_TESEN_7


title: SSC  Cxcr4+/1013 Replicate 3


title: urine_TESEN_1


title: ChOR_totalChIP_IAAdTAG_EdU_r1


title: semen_TESEP_9

value: seminal plasma


title: SSC  Cxcr4+/1013 Replicate 2


title: semen_TESEP_8


title: semen_TESEP_7


title: urine_TESEN_11


title: ChOR_totalChIP_DMSO_EdU_r3

description:
ChIP-purified genomic DNA
ChOR_totalChIP_DMSO_H2Aub_RRPM_MEAN.bw


title: SSC  Cxcr4+/1013 Replicate 1


title: semen_TESEP_6


title: ChOR_totalChIP_DMSO_EdU_r2


title: ChOR_totalChIP_DMSO_EdU_r1


title: ChOR_totalChIP_IAAdTAG_EdU_r2


title: SSC Cxcr41013/1013 Replicate 1


title: ChOR_T0_IAAdTAG_noEdU_r3

description: noEdU-labelled (control) genomic DNA


title: SSC  Cxcr4+/+ Replicate 3


title: SSC  Cxcr4+/+ Replicate 2


title: semen_TESEP_4


title: semen_TESEP_1


title: semen_TESEN_29


title: ChOR_T0_IAAdTAG_noEdU_r1

description: noEdU-labelled (control) genomic DNA


title: ChOR_T0_IAAdTAG_EdU_r3

description:
EdU-labelled genomic DNA
ChOR_T0_IAAdTAG_H2Aub_RRPM_MEAN.bw


title: SSC  Cxcr4+/+ Replicate 1


title: semen_TESEN_27


title: semen_TESEN_28


title: semen_TESEN_24


title: semen_TESEN_25


title: semen_TESEN_26


title: OPC  Cxcr41013/1013 Replicate 1

value: OsteoProgenitor Cells  (OPC)


title: OPC  Cxcr41013/1013 Replicate 3


title: OPC  Cxcr41013/1013 Replicate 2


title: ChOR_T0_IAAdTAG_EdU_r2


title: semen_TESEP_5


title: semen_TESEN_23


title: OPC  Cxcr4+/1013 Replicate 3


title: ChOR_T0_DMSO_noEdU_r3

description: noEdU-labelled (control) genomic DNA


title: semen_TESEP_2


title: semen_TESEN_22


title: semen_TESEN_21


title: semen_TESEP_3


title: semen_TESEN_20


title: OPC  Cxcr4+/1013 Replicate 2


title: ChOR_T0_IAAdTAG_noEdU_r2

description: noEdU-labelled (control) genomic DNA


title: semen_TESEN_18


title: semen_TESEN_19


title: ChOR_T0_DMSO_noEdU_r2

description: noEdU-labelled (control) genomic DNA


title: ChOR_T0_DMSO_noEdU_r1

description: noEdU-labelled (control) genomic DNA


title: OPC  Cxcr4+/+ Replicate 3


title: OPC  Cxcr4+/1013 Replicate 1


title: semen_TESEN_16


title: ChOR_T0_IAAdTAG_EdU_r1


title: semen_TESEN_13


title: semen_TESEN_12


title: OPC  Cxcr4+/+ Replicate 1


title: ChOR_T0_DMSO_EdU_r3

description:
EdU-labelled genomic DNA
ChOR_T0_DMSO_H2Aub_RRPM_MEAN.bw


title: ChOR_T0_DMSO_EdU_r2


title: B6_24M_LG3

city: Houston

first: Cintia

middle: S.

last: de Paiva

state: TX

address: 6565 Fannin Street NC505G

department: Ophthalmology

institute: Baylor College of Medicine

description: Ad libitum

data_processing:
Data was analyzed by ROSALIND® (https://rosalind.bio/), with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA).
Reads were trimmed using cutadapt
Quality scores were assessed using FastQC
Reads were aligned to the Mus musculus genome build GRCm38 using STAR
Individual sample reads were quantified using HTseq
Reads were normalized via Relative Log Expression (RLE) using DESeq2 R library
Read Distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step using RSeQC
DEseq2 was also used to calculate fold changes and p-values and perform optional covariate correction. Clustering of genes for the final heatmap of differentially expressed genes was done using the PAM (Partitioning Around Medoids) method using the fpc R library
Assembly: Mus musculus genome build GRCm38
Supplementary files format and content: Raw Count matrix are provided in .txt file
Supplementary files format and content: Normalized Count matrix are provided in .txt file

source_name: Lacrimal Gland

growth_protocol: Mice were fed ad libitum and kept under a 12-hour light/12-hour dark cycle

extract_protocol:
Lacrimal glands were lysed into a tube containing RNA lysis buffer (Qiagen, Valencia, CA,USA). Total RNA was extracted using a QIAGEN RNeasy Plus Micro RNA isolation kit according to the manufacturer's instructions. The concentration and purity of RNA were assessed using a NanoDrop 1000 (ThermoFisher Scientific, Waltham, MA, USA).
RNA-Seq was performed by the Beijing Genomics Institute (BGI) using the BGISEQ500RS to generate 100 bp paired-end reads.

value: Lacrimal Gland

tag: age

value: 24 Months

tag: Sex

value: Female


title: semen_TESEN_15


title: semen_TESEN_17


title: semen_TESEN_14


title: OPC  Cxcr4+/+ Replicate 2


title: ChOR_T0_DMSO_EdU_r1


title: semen_TESEN_11


title: ChOR_panH3_T0_rep1

description: EdU-labelled genomic DNA

value: wildtype


title: ChOR_panH2A_T0_rep1

description: EdU-labelled genomic DNA


title: LXRα-/- HFD, replicate4

city: Guangzhou

first: Lan

last: Tang

state: Guangdong

address: 1838  Guangzhou North Ave,

department: School of Pharmaceutical Science

institute: Southern Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

value: LXR knockdown

value: high-fat diet

tag: time

value: week 24


title: B6_24M_LG1

description: Ad libitum


title: B6_24M_LG2

description: Ad libitum


title: LXRα-/- HFD, replicate3


title: semen_TESEN_9


title: semen_TESEN_10


title: B6_12M_LG3

description: Ad libitum

value: 12 Months


title: ChOR_T720_clickedInput_H3K27me3_r2

description: EdU-labelled genomic DNA


title: LXRα-/- HFD, replicate2


title: B6_12M_LG2

description: Ad libitum


title: semen_TESEN_8

value: no


title: B6_12M_LG1

description: Ad libitum


title: ChOR_T480_clickedInput_H3K27me3_r2

description: EdU-labelled genomic DNA


title: LXRα-/- HFD, replicate1


title: LXRα-/- HFD, replicate5


title: B6_8W_LG3

description: Ad libitum

value: 2 Months


title: semen_TESEN_6

value: non-cell sample


title: semen_TESEN_7


title: LXRα-/- Chow, replicate5

value: chow diet


title: semen_TESEN_5


title: ChOR_T180_clickedInput_H3K27me3_r2

description: EdU-labelled genomic DNA


title: ChOR_T720_clickedInput_H3K27me3_r1

description: EdU-labelled genomic DNA

value: wildtype (untreated)

value: DMSO


title: B6_8W_LG1

description: Ad libitum


title: semen_TESEN_4

value: seminal plasma


title: ChOR_T180_clickedInput_H3K27me3_r1

description: EdU-labelled genomic DNA


title: LXRα-/- Chow, replicate3


title: semen_TESEN_3


title: LXRα-/- Chow, replicate2


title: LXRα-/- Chow, replicate1


title: semen_TESEN_2


title: ChOR_T0_clickedInput_H3K27me3_r2

description: EdU-labelled genomic DNA


title: ChOR_T0_clickedInput_H3K27me3_r1

description: EdU-labelled genomic DNA


title: WT HFD, replicate5

value: WT


title: semen_TESEN_1


title: WT HFD, replicate4


title: LXRα-/- Chow, replicate4


title: GFP, rep2

city: Hangzhou

first: Chengyong

address: 268 Kaiquan Rd.

department: Institute of Translational medicine

institute: Zhejiang University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2).
Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20% and  base ('N' base) ratio is more than 5%.
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set.
The expression level of gene was calculated by RSEM (v1.2.12)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM and raw count values for each Sample

source_name: cortex

extract_protocol:
RNA was extracted using Trizol.
RNA libraries for RNA-seq were prepared by BGI standard protocol.

value: cortex

value: AAV-GFP


title: ChOR_T720_H3K27me3_r2

description:
EdU-labelled genomic DNA
ChOR_T720_H3K27me3_RRPM_MEAN.bw


title: ChOR_T480_clickedInput_H3K27me3_r1

description: EdU-labelled genomic DNA


title: WT HFD, replicate3


title: GA, rep2

value: AAV-GFP-GA


title: GA, rep3


title: ChOR_T720_H3K27me3_r1


title: GFP, rep1


title: GFP, rep3


title: HEK293, Bioreactor3, 72h

city: Morrisville

first: Cheng-Han

last: Chung

address: 7030 Kit Creek Rd

institute: Pfizer Inc.

data_processing:
kallisto version 0.44.0
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
All three trimmed paired-end sequencing techinical replicates for each sample were mapped to GRCh38.101 using Kallisto.
Assembly: GRCh38_ncbi_rna.101.fna.gz
Supplementary files format and content: tab-delimited text files include TPM (transcript per million) values for each Sample

extract_protocol:
total RNA extraction
mRNA enrichment followed by dA-Tailing for polyA selection

value: Embryonic kidney

tag: bioreactor

value: Plasmid transfection

value: 72hr post transfection


title: HEK293, Bioreactor3, 48h

tag: cell line

value: 48hr post transfection


title: ChOR_T480_H3K27me3_r2

description:
EdU-labelled genomic DNA
ChOR_T480_H3K27me3_RRPM_MEAN.bw

tag: strain

value: wildtype


title: B6_8W_LG2

description: Ad libitum

value: Lacrimal Gland

value: Female


title: HEK293, Bioreactor3, 36h

value: 36hr post transfection


title: GA, rep1

tag: genotype


title: WT HFD, replicate1

value: liver

value: high-fat diet

value: week 24


title: ChOR_T480_H3K27me3_r1

value: wildtype (untreated)

value: DMSO


title: ChOR_T180_H3K27me3_r2

description:
EdU-labelled genomic DNA
ChOR_T180_H3K27me3_RRPM_MEAN.bw


title: wing-disc, sup, H3.3Adelta, rep2

city: Chapel Hill

first: Gregory

last: Matera

state: North Carolina

address: Genome Science Building

institute: University of North Carolina at Chapel Hill

description: U9_H33A_S2-H3-3Adelta_3LW_wing_CnR_K27me3_rep2_sup_AGTTCAGG-CCAACAGA_S41

data_processing:
CUT&RUN data were processed as in https://github.com/mckaylabunc/cutNrun-pipeline with minor modifications.
Reads were aligned with Bowtie2 (v2.3.4.1) to the DM6 reference genome.
Duplicate reads were marked with Picard (v2.2.4) and removed using SAMtools (v1.10).
Bam files were sorted using SAMtools (v1.10) and then converted to bed files using BEDTools (v2.26).
Additional bed files containing the coordinates of only the fragments with lengths 20-120 bases (short fragments) and 150-700 bases (large fragments) were also created.
Bed files were converted to BigWig files using wigToBigWig(ucsctools/v320)
BigWig files were RPGC (reads per genome coverage) normalized, and further transformed by z-normalization.
Peak calling was performed by MACS2 (v2.1.2) with the use of an IgG control file.
Assembly: DM6
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

organism: Drosophila melanogaster

source_name: wing-disc

extract_protocol:
We performed CUT&RUN in wing disc tissue as described in K. Ahmad (2018) modified from P. J. Skene, et al. (2018). For each replicate, twenty WL3 imaginal wing discs along with two wing discs of D.yakuba were used per replicate. For the H3K27me3 experiment, aH3K27(CST#9733,1:100) and protein AG-MNase (1:100, UNC core) were used. For the H3.3 experiment, aH3.3 (H3F33B, Abnova #H00003021-M01, 1:100) and protein A-MNase from the Henikoff lab were used.
The Thruplex DNA-seq kit was used for the library preparation. The manufacturer’s protocol was followed until the amplification step. After the addition of indexes, 16-21 cycles of 98C, 20s; 67C, 10s were run. DNA library purification was done using AMPure XP beads. Libraries were sequenced on an Illumina NextSeqP2.

value: wing-disc

tag: developmental stage

tag: antibody

value: sup


title: HEK293, Bioreactor3, 24h

value: 24hr post transfection


title: HEK293, Bioreactor3, 12h

value: 12hr post transfection


title: WT Chow，replicate4

value: WT

value: chow diet


title: ChOR_T180_H3K27me3_r1


title: wing-disc, pellet, H3.3Adelta, rep1

description: U8_H33A_P1-H3-3Adelta_3LW_wing_CnR_K27me3_rep1_pel_TGGATCGA-GTGCGATA_S35

value: pellet


title: HEK293, Bioreactor3, 06h

value: Embryonic kidney

value: Plasmid transfection

value: 6hr post transfection


title: ChOR_T0_H3K27me3_r2

description:
EdU-labelled genomic DNA
ChOR_T0_H3K27me3_RRPM_MEAN.bw

value: wildtype


title: wing-disc, pellet, H3.3BK36R, rep3

description: U6_H33B_P3-H3-3BK36R_3LW_wing_CnR_K27me3_rep3_pel_GCTTGTCA-GAACATAC_S33


title: HEK293, Bioreactor3, 00h

value: 0hr post transfection


title: WT Chow，replicate3

value: liver


title: wing-disc, sup, H3.3Adelta, rep1

description: U7_H33A_S1-H3-3Adelta_3LW_wing_CnR_K27me3_rep1_sup_CAAGCTAG-ACATAGCG_S34


title: ChOR_T0_H3K27me3_r1


title: WT Chow，replicate1


title: WT Chow，replicate2


title: ChOR_T480_clickedInput_H2AZ_r2

description: EdU-labelled genomic DNA


title: wing-disc, pellet, H3.3BK36R, rep2

description: U4_H33B_P2-H3-3BK36R_3LW_wing_CnR_K27me3_rep2_pel_AAGTCCAA-TATGAGTA_S31


title: HEK293, Bioreactor3, 03h

value: 3hr post transfection


title: ChOR_T480_clickedInput_H2AZ_r1

description: EdU-labelled genomic DNA


title: wing-disc, sup, H3.3BK36R, rep3

description: U5_H33B_S3-H3-3BK36R_3LW_wing_CnR_K27me3_rep3_sup_ATCCACTG-AGGTGCGT_S32


title: HEK293, Bioreactor2, 48h

value: 48hr post transfection


title: HEK293, Bioreactor2, 72h

value: 72hr post transfection


title: WT HFD, replicate2

value: high-fat diet

value: week 24


title: wing-disc, sup, H3.3BK36R, rep1

description: U3_H33B_S1-H3-3BK36R_3LW_wing_CnR_K27me3_rep1_sup_GGACTTGG-CGCAGACG_S30

value: wing-disc

value: sup


title: WT Chow，replicate5


title: ChOR_T180_clickedInput_H2AZ_r2

description: EdU-labelled genomic DNA


title: Il 33 mt 5

city: San Francisco

first: Johan

last: Siewiera

address: 513 Parnassus Avenue

institute: UCSF

data_processing:
Reads were aligned to the mouse genome using the Splice-aware STAR aligner STAR_2.7.2b
Raw counts were determined using STAR_2.7.2b
Reads uniquely mapped to known mRNAs were used to identify genes with differential expression (praw<0,05) using DESeq2 R package v1.24. Three analyses were performed to compared each tissue layer to their counterparts.
Genome_build: Ensembl Mouse GRCm38.96
Supplementary_files_format_and_content: xlsx tables of raw counts

source_name: Homogenized whole tissue mesometrial triangle

extract_protocol:
Implantation site from gestation day 18.5 were dissected to separate decidua, myometrium and mesometrial triangle. Each layer was washed in cold PBS and homogenized in TRIzol. RNA was subsequently purified by phenol chloroform extraction.
RNA libraries were prepared according to Illumona's instructions, using Nugen Universal Plus mRNA

value: Mesometrial triangle


title: Il 33 mt 4


title: wing-disc, pellet, H3.3BK36R, rep1

description: U2_H33B_P1-H3-3BK36R_3LW_wing_CnR_K27me3_rep1_pel_TTATAACC-GATATCGA_S24


title: HEK293, Bioreactor2, 24h

value: 24hr post transfection


title: HEK293, Bioreactor2, 36h

value: 36hr post transfection


title: ChOR_T180_clickedInput_H2AZ_r1

description: EdU-labelled genomic DNA


title: ChOR_T120_clickedInput_H2AZ_r2

description: EdU-labelled genomic DNA


title: Il 33 mt 3


title: HEK293, Bioreactor2, 12h

value: 12hr post transfection


title: Il 33 mt 2


title: wing-disc, pellet, H3.2K36R, rep3

description: U24_H32_P3-H3-2K36R_3LW_wing_CnR_K27me3_rep3_pel_ATGAGGCC-GTTAATTG_S29

value: pellet


title: Il 33 mt 1


title: ChOR_T120_clickedInput_H2AZ_r1

description: EdU-labelled genomic DNA


title: wing-disc, sup, H3.2K36R, rep3

description: U23_H32_S3-H3-2K36R_3LW_wing_CnR_K27me3_rep3_sup_GCAGAATT-ACCGGCCA_S28


title: Il33 myo 5

source_name: Homogenized whole tissue myometrium

value: Myometrium


title: HEK293, Bioreactor2, 06h

value: Embryonic kidney

value: Plasmid transfection

value: 6hr post transfection


title: wing-disc, sup, H3.2K36R, rep2

description: U21_H32_P2-H3-2K36R_3LW_wing_CnR_K27me3_rep2_sup_GGTACCTT-AAGACGTC_S26


title: Il33 myo 4


title: ChOR_T60_clickedInput_H2AZ_r1

description: EdU-labelled genomic DNA

value: wildtype


title: HEK293, Bioreactor2, 03h

value: 3hr post transfection


title: ChOR_T30_clickedInput_H2AZ_r2

description: EdU-labelled genomic DNA


title: Il33 myo 3


title: wing-disc, pellet, H3.2K36R, rep1

description: U20_H32_P1-H3-2K36R_3LW_wing_CnR_K27me3_rep1_pel_GCACGGAC-GTCTCGCA_S25


title: ChOR_T30_clickedInput_H2AZ_r1

description: EdU-labelled genomic DNA


title: wing-disc, sup, H3.3BK36R, rep2

description: U1_H33B_S2-H3-3BK36R_3LW_wing_CnR_K27me3_rep2_sup_CCGCGGTT-AGCGCTAG_S13


title: Il33 myo 2


title: HEK293, Bioreactor1, 72h


title: ChOR_T15_clickedInput_H2AZ_r2

description: EdU-labelled genomic DNA


title: Il33 myo 1

source_name: Homogenized whole tissue decidua


title: HEK293, Bioreactor1, 36h


title: HEK293, Bioreactor1, 48h

value: 48hr post transfection


title: wing-disc, pellet, HWT, rep3

description: U18_Hwt_P3-Hwt_3LW_wing_CnR_K27me3_rep3_pel_CGGCGTGA-GCGCCTGT_S22

value: HWT


title: ChOR_T15_clickedInput_H2AZ_r1

description: EdU-labelled genomic DNA


title: ChOR_T60_clickedInput_H2AZ_r2

description: EdU-labelled genomic DNA


title: wing-disc, pellet, H3.2K36R, rep2

description: U22_H32_P2-H3-2K36R_3LW_wing_CnR_K27me3_rep2_pel_AACGTTCC-GGAGTACT_S27


title: Il33 dec 4

value: Decidua


title: wing-disc, sup, HWT, rep3

description: U17_Hwt_S3-Hwt_3LW_wing_CnR_K27me3_rep3_sup_TAATACAG-ATATTCAC_S21


title: ChOR_T0_clickedInput_H2AZ_r2

description: EdU-labelled genomic DNA


title: Il33 dec 3


title: HEK293, Bioreactor2, 00h

value: 0hr post transfection


title: HEK293, Bioreactor1, 12h


title: ChOR_T0_clickedInput_H2AZ_r1

description: EdU-labelled genomic DNA


title: HEK293, Bioreactor1, 06h


title: Il33 dec 2


title: wing-disc, pellet, HWT, rep2

description: U16_Hwt_P2-Hwt_3LW_wing_CnR_K27me3_rep2_pel_AATCCGGA-CTACAGTT_S20

value: wing-disc


title: ChOR_noEdU_H2AZ_r2

description: noEdU-labelled (control) genomic DNA


title: wing-disc, sup, HWT, rep2

description: U15_Hwt_S2-Hwt_3LW_wing_CnR_K27me3_rep2_sup_GGCTTAAG-TCGTGACC_S19

value: sup


title: HEK293, Bioreactor1, 03h


title: wing-disc, sup, H3.2K36R, rep1

description: U19_H32_S1-H3-2K36R_3LW_wing_CnR_K27me3_rep1_sup_ATGTAAGT-ACTCTATG_S23


title: Il33 dec 1


title: B6 mt 5

value: B6 control

value: Mesometrial triangle


title: wing-disc, pellet, HWT, rep1

description: U14_Hwt_P1-Hwt_3LW_wing_CnR_K27me3_rep1_pel_TTGGACTC-GGAAGCAG_S18


title: HEK293, Bioreactor1, 00h


title: ChOR_noEdU_H2AZ_r1

description: noEdU-labelled (control) genomic DNA


title: wing-disc, sup, HWT, rep1

description: U13_Hwt_S1-Hwt_3LW_wing_CnR_K27me3_rep1_sup_CCAAGTCT-AAGGATGA_S17


title: B6 mt 4


title: HEK293, Bioreactor1, 24h

value: 24hr post transfection


title: ChOR_T480_H2AZ_r2

description:
EdU-labelled genomic DNA
ChOR_T480_H2AZ_RRPM_MEAN.bw


title: ChOR_T480_H2AZ_r1


title: wing-disc, pellet, H3.3Adelta, rep3

description: U12_H33A_P3-H3-3Adelta_3LW_wing_CnR_K27me3_rep3_pel_CTCTCGTC-TATAACCT_S16


title: B6 mt 3


title: Hsap-4

city: Oxford

first: Thomas

middle: Lewin

last: Lewin

state: Oxfordshire

address: 11a Mansfield Road

department: Department of Biology

country: United Kingdom

institute: Thomas Lewin

data_processing:
FastQC version 0.11.8 and MultiQC version 1.8 were used for quality control, and reads (150 bp paired-end) were subjected to filtering to remove adapter-containing reads, low-quality reads (Qscore < 5), and reads with > 10% Ns (undetermined bases).
Pseudoalignment to the human transcriptome from genome build GRCh38.p14 (RefSeq annotation) was performed with Kallisto version 0.48.0 (Bray et al. 2016)
Gene-level transcript abundance estimates were created using tximport version 1.20.0 (Soneson et al. 2016), and then differential expression analysis completed in DESeq2 version 1.32.0 (Love et al. 2014)
Assembly: GRCh38.p14
Supplementary files format and content: Excel Files: transcripts per million (TPM) for each gene in each sample.

source_name: Stemnovate #SV-HF21-17-500

growth_protocol: Primary human dermal fibroblasts (HDFs) (Stemnovate #SV-HF21-17-500) were maintained in HDF medium at 37°C with 5% CO2 and passaged at approximately 70% confluency every 3-4 days. HDF medium consists of Dulbecco’s modified Eagle medium (Gibco #41965039) with 10% heat-inactivated fetal bovine serum (Gibco #10500064) and 1% penicillin-streptomycin (Gibco #15140122). Testing for mycoplasma (Sigma Aldrich #MP0035) revealed no contamination.

extract_protocol:
At 48 h post-transfection, RNA was extracted using an RNeasy Plus Micro kit (Qiagen #74034), and integrity tested using an Agilent 2100 Bioanalyzer.
poly(A)- enrichment performed by Novogene (https://www.novogene.com/us-en/services/research-services/transcriptome-sequencing/mrna-sequencing/)

treatment_protocol: Codon-optimised sequences of Homo sapiens and Callithrix jacchus LEUTX with a GGGGSGGGGS linker and C-terminal V5 tag were cloned into a pcDNA3.1 mammalian expression vector. For transfection, 65000 cells per well were seeded into 6-well plates. After 16 hours (h), medium was replaced with 2 mL antibiotic-free HDF medium. For each biological replicate, 108 μL Opti-MEM (Gibco #31985-062) was combined with 9.6 μL FUGENE 6 (Promega #E2691) and incubated for 5 minutes, then 2.4 μL of 1 μg/μL appropriate expression construct added before another 15-minute incubation. To each well, 120 μL of this mixture was added, and cells kept at 37°C with 5% CO2. After 24 h, transfection medium was removed and replaced with 2 mL HDF medium with 800 μg/mL G418 selective antibiotic (Gibco #10131-035).

value: Stemnovate #SV-HF21-17-500

value: Human dermal fibroblast

value: Homo sapiens LEUTX


title: Cjac-4

value: Callithrix jacchus LEUTX


title: ChOR_T180_H2AZ_r1

description:
EdU-labelled genomic DNA
ChOR_T180_H2AZ_RRPM_MEAN.bw


title: Hsap-2


title: wing-disc, pellet, H3.3Adelta, rep2

description: U10_H33A_P2-H3-3Adelta_3LW_wing_CnR_K27me3_rep2_pel_GACCTGAA-TTGGTGAG_S14

value: pellet


title: ChOR_T180_H2AZ_r2


title: B6 mt 1


title: wing-disc, sup, H3.3Adelta, rep3

description: U11_H33A_S3-H3-3Adelta_3LW_wing_CnR_K27me3_rep3_sup_TCTCTACT-CGCGGTTC_S15


title: siRAS rep 3 (RAS knockdown)

city: Tampere

first: Reetta

last: Nätkin

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Health Technology, Prostate Cancer Research Center

country: Finland

institute: Tampere University and Tays Cancer Center

data_processing:
Reads were trimmed with TrimGalore! v0.6.4._dev with the parameters: -- quality 20 --gzip -fastqc
Trimmed reads were aligned with STAR v2.5.3a with the parameters: --quantMode TranscriptomeSAM -- outSAMtype BAM SortedByCoordinate --chimOutType WithinBAM –twopassMode Basic --readFilesCommand zcat --genomeLoad NoSharedMemory -- outReadsUnmapped FastX ---bamRemoveDuplicatesType UniqueIdentical -- seedSearchStartLmax 25 --outFilterMismatchNoverReadLmax 25 -- outFilterMismatchNoverReadLmax 0.04 --winAnchorMultimapNmax 100. Ensembl Homo Sapiens GRCh38 v95 sequence and annotations were used as reference for the alignment.
Gene counts produced with STAR were then assembled into a read count matrix using R v4.1.0
Assembly: hg38
Supplementary files format and content: unnormalized gene read counts produced with STAR (.xlsx)

source_name: Uterus; Cervix

growth_protocol: Supplemented DMEM.

extract_protocol:
RNA was isolated using Qiagen AllPrep DNA/RNA/Protein Mini Kit.
Library preparation was done according to Illumina TruSeq® Stranded mRNA Sample Preparation Guide (part # 15031047)

treatment_protocol: Transfections were done utilizing RNAiMAX transfection reagent, according to manufacturers instructions.

value: Uterus; Cervix

value: HeLa

value: Epithelial cells

value: siRNA (RAS) transfected sample


title: ChOR_T120_H2AZ_r2

description:
EdU-labelled genomic DNA
ChOR_T120_H2AZ_RRPM_MEAN.bw

value: wildtype


title: B6 myo 4

value: Myometrium


title: Cjac-3


title: B6 myo 5


title: ChOR_T120_H2AZ_r1


title: Cjac-2


title: siRAS rep 2 (RAS knockdown)


title: Hsap-3


title: siRAS rep 1 (RAS knockdown)


title: ChOR_T60_H2AZ_r2

description:
EdU-labelled genomic DNA
ChOR_T60_H2AZ_RRPM_MEAN.bw


title: siCtrl for RAS rep 3 (Control knockdown)

value: siRNA (control) transfected sample


title: ESC, lentivirus-vector, 1 μM P4 + 0.25 mM db-cAMP

city: Shenzhen

first: Weijie

last: Zhao

address: Zhenyuan Road

institute: Reproductive Medicine Center, The Seventh Affiliated Hospital, Sun Yat-sen University

data_processing:
Sequencing adapters were removed from paired-end reads using Trimmomatic v0.39
Reads were aligned to the reference genome with bowtie2 v2.2.5
Peak callings were performed by macs2 v2.2.6
Assembly: human GRCh38
Supplementary files format and content: narrowPeak, peaks called by macs2 v2.2.6

source_name: Endometrium

extract_protocol:
Cells were dissociated by trypsin-EDTA digestion and lysed in hypotonic buffer. Nuclei were collected for library construction.
ATAC-seq libraries were prepared using a Chromatin Profile Kit (N248, Novoprotein). Nuclei were subjected to tagmentation for 30 mins at 37 ℃ with Transposome Mix. DNA fragments were cleaned up and amplified with AmpliMix for 9-12 cycles. Libraries were purified for sequencing.

value: Endometrium

value: stromal cells

value: WT

value: Lentivirus-vector, 1 microM P4 + 0.25 mM db-cAMP


title: B6 myo 3

value: B6 control


title: ESC, lentivirus-CIP2A, 1 μM P4 + 0.25 mM db-cAMP

value: Lentivirus-CIP2A, 1 micorM P4 + 0.25 mM db-cAMP


title: ChOR_T60_H2AZ_r1

city: Copenhagen

first: Anja

address: Blegdamsvej 3B


title: siCtrl for RAS rep 2 (Control knockdown)


title: ESC, lentivirus-vector, DMSO

value: Lentivirus-vector, DMSO


title: B6 dec 5

value: Decidua


title: ChOR_T15_H2AZ_r2

description:
EdU-labelled genomic DNA
ChOR_T15_H2AZ_RRPM_MEAN.bw


title: siPP2A rep 3 (PP2A-A knockdown)

value: siRNA (PP2A) transfected sample


title: ChOR_T30_H2AZ_r1

description:
EdU-labelled genomic DNA
ChOR_T30_H2AZ_RRPM_MEAN.bw


title: B6 dec 4


title: siPP2A rep 2 (PP2A-A knockdown)


title: ChOR_T15_H2AZ_r1


title: RNA-Seq_MCF7_si-circPVT1-1_rep2

city: Xiamen

first: Guosheng

last: Hu

state: Fujian

address: Xiang'an South Road, Xiang'an District

department: School of Pharmaceutical Sciences

institute: xiamen University

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the hg19 genome assembly using Tophat version 2.1.1.
Assembly: hg19

source_name: Human breast cancer MCF7 cells

growth_protocol: MCF7 cells were cultured in DMEM medium supplemented with 10% FBS.

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol. DNase I in column digestion was included to ensure the RNA quality.
RNA library preparation was performed by using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (E7420L). Paired-end sequencing was performed with Illumina HiSeq platform at RiboBio Co., Ltd. or Amogene Biotech Co., Ltd.

treatment_protocol: MCF7 cells transfected with control siRNA (siCTL) or two independent siRNAs specifically targeting circPVT1 (si-circPVT1-1 and si-circPVT1-2)

value: siRNA, si-circPVT1-1


title: siPP2A rep 1 (PP2A-A knockdown)

value: Uterus; Cervix


title: RNA-Seq_MCF7_siCTL_rep2

value: siRNA, siCTL


title: ChOR_T0_H2AZ_r2

last: Groth

institute: Novo Nordisk Foundation Center for Protein Research

description:
EdU-labelled genomic DNA
ChOR_T0_H2AZ_RRPM_MEAN.bw


title: B6 myo 2


title: B6 myo 1


title: ChOR_T30_H2AZ_r2


title: B6 dec 1


title: siCtrl rep 3 (Control knockdown)

value: HeLa

value: Epithelial cells


title: RNA-Seq_MCF7_si-circPVT1-1_rep1


title: RNA-Seq_MCF7_siCTL_rep1


title: ChOR_T0_H2AZ_r1

value: wildtype


title: siCtrl rep 2 (Control knockdown)


title: siCtrl for RAS rep 1 (Control knockdown)


title: Control.38_smRNA

city: Rochester

first: Nagaswaroop

last: Kengunte Nagaraj

state: Minnesota

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

data_processing:
Base calling was performed with the Illumina bcl2fastq
The paired end reads were aligned by Bowtie aligner
Assembly: hg19
Supplementary files format and content: tab-delimited text files include Raw counts and CPM values for each microRNA per sample

source_name: Adipose

growth_protocol: MSC were cultured in standard conditions (37 °C with 5% CO2) in advanced minimum essential medium supplemented with 5% platelet lysate in T-75 flasks, then washed extensively with phosphate-buffered saline and replenished with serum-free advanced minimum essential medium for 36 hours.

extract_protocol:
After serum-starvation, MSC was centrifuged at 400 x g for 5 minutes at 20°C to pellet cells and supernatant was aliquoted off.
Small RNA libraries were prepared from 250 ng of total RNA according to manufacturer’s instructions
NEBNext Multiplex Small RNA Kit

value: Adipose

value: Mesenchymal Stem Cells

tag: disease state

value: Control


title: ChOR_T480_clickedInput_H2A_H2Bub_r2

description: EdU-labelled genomic DNA

source_name: Embryonic stem cells


title: B6 dec 3

tag: tissue


title: siCtrl rep 1 (Control knockdown)

tag: cell type

value: siRNA (control) transfected sample


title: Control.35_smRNA


title: PRAISE-WT-Takara-second-biological-repeats-untreated_rep2

extract_protocol:
Total RNA was extracted with TRIzol (Life technologies) followed by isopropanol precipitation, according to the manufacturer’s instructions (Invitrogen).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: treatment

value: untreated


title: B6 dec 2


title: ChOR_T480_clickedInput_H2A_H2Bub_r1

description: EdU-labelled genomic DNA


title: P60 bio rep 2

city: Baltimore

first: Loyal

last: Goff

state: MD

address: 733 N Broadway

institute: Johns Hopkins University

data_processing:
FASTQ sequence files were processed following a Kallisto Bustools workflow compatible with downstream RNA velocity calculations [kallisto == 0.46.1, bustools == 0.39.3] (Bray et al., 2016). References required for pseudo-alignment of transcripts were obtained using the get_velocity_files() functionality of BUSpaRSE (https://github.com/BUStools/BUSpaRse), with “L=98” for 10X Genomics v3.0 sequencing chemistry. Reads were pseudo-aligned to an index built from Ensembl 97 transcriptome annotation (Gencode vM22; GRCm38).
Barcodes within a Hamming distance of one to known 10X Genomics v3.0  barcodes were corrected. Reads were classified as “spliced” or “unspliced” by their complement to the target list of intronic sequences and exonic sequences, respectively, and subsequently quantified separately into expression count matrices. Spliced counts are used for all analyses.
scRNA-seq count matrices were analyzed using Monocle3. 35,657 high-quality cells were identified as meeting a 600 UMI minimum threshold with a mitochondrial read ratio of less than 20%; droplets that did not meet these criteria were excluded from the analysis. Mitochondrial counts were determined as the sum of reads mapping to 37 genes annotated to the mitochondrial genome. All genes with non-zero expression were included for downstream analysis.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Raw counts after pseudoalignment are submitted as a .mtx file
Supplementary files format and content: Cell and gene metadata are submitted as comma deliminated .csv files

source_name: LMMP

extract_protocol:
A laparotomy was performed, and the ileum was removed and lavaged with PBS containing penicillin-streptomycin (PS; Invitrogen), then cut into 1-cm-long segments and placed over a sterile plastic rod. A super-ficial longitudinal incision was made along the serosal surface and the LM-MP was peeled off from the underlying tissue using a wet sterile cotton swab (Kulkarni et al., 2017) and placed in Opti-MEM medium (Invitrogen) containing Pen-Strep (Invitrogen). The tissues were then dissociated in Digestion Buffer containing 1 mg/ml Liberase (Sigma-Aldrich) in OptiMEM. Tissues from mouse 1 were dissociated in the Digestion buffer containing Liberase TH and tissues from mouse 2 were dissociated in the Digestion buffer containing Liberase TL. Dissociation was performed at 37°C for 30 minutes on a rotary shaker, after which the cells were centrifuged at 200g for 7 minutes, and the pellet was resuspended in ice cold ster-ile PBS. The cell suspension was passed through a 40 µm cell sieve and the resulting filtered cell suspension was again centrifuged at 200g for 7 minutes. This process of cell centrifugation and filtration was repeated two more times, after which the cells were resuspended in 1 ml ice cold sterile PBS. The repeated steps of serial cell washes and filtration removed clumps and debris and the viability of the resulting cell suspension was estimated to be >90% using Trypan Blue dye test. The cells were then processed through 10X Genomics Chromium V3.0 system according to the manufacturer’s suggested workflow. The processing was done at the GRCF Core Facility at the Johns Hopkins University.
10x Genomics Chromium v3.0 3' gene expression assay

treatment_protocol: Mice were anesthetized with isoflurane and sacrificed by cervical dislocation.

value: LMMP

value: WT


title: RNA-Seq_MCF7_si-circPVT1-2_rep2

value: siRNA, si-circPVT1-2


title: PRAISE-WT-Takara-second-biological-repeats-untreated_rep1

city: Beijing

first: Jiang

address: No. 5 Yiheyuan Road, Haidian District

institute: Peking University

data_processing:
trimiming using cutadapt
mapping using HISAT2 and then tailored alignment
remove multiple mapping
converting bam into bw using bamCoverage
Assembly: hg38
Supplementary files format and content: bw files including mapping result data


title: ChOR_T180_clickedInput_H2A_H2Bub_r2

description: EdU-labelled genomic DNA


title: Control.30_smRNA


title: Control.31_smRNA


title: RNA-Seq_MCF7_si-circPVT1-2_rep1


title: ChOR_T180_clickedInput_H2A_H2Bub_r1

description: EdU-labelled genomic DNA


title: P60 bio rep 1


title: P20 bio rep 2


title: DKD.21_smRNA

value: DKD, Diabetic Nephropathy


title: ChOR_T120_clickedInput_H2A_H2Bub_r2

description: EdU-labelled genomic DNA


title: P20 bio rep 1


title: PRAISE-WT-Takara-second-biological-repeats_rep1

value: PRAISE


title: DKD.20_smRNA


title: DKD.19_smRNA


title: PRAISE-IVT-untreated

library_source: other

molecule: other

extract_protocol:
Total RNA was extracted with TRIzol (Life technologies) followed by isopropanol precipitation, according to the manufacturer’s instructions (Invitrogen).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
Illumina PE150


title: ChOR_T120_clickedInput_H2A_H2Bub_r1

description: EdU-labelled genomic DNA

extract_protocol: After the appropriate treatment, cells were washed with cold PBS, crosslinked for 5min with 1% Formaldehyde at room temperature and subsequently quenched with 0.1M Glycin (final concentration) for 5min before harvesting. Then, nuclei were isolated and sonicated using the Covaris Chromatin Shearing Kit. ChIP-Immunoprecipation of chromatin was done using antibodies according to the manufacturers recommendation with EdU-labelled Drosophila S2 chromatin serving as Spike-In control and, where the epitope of the antibody does not recognize the Drosophila homolog (i.e. H2A.Z) , H2AV antibodies to immunoprecipitate Spike-In chromatin as well. Purified fragments were biotinylated, libraries prepared, EdU-biotinylated fragments pulled down using Streptavidin and sequenced


title: ChOR_T60_clickedInput_H2AK119ub_r2

description: EdU-labelled genomic DNA


title: P10 bio rep 2


title: P10 bio rep 1


title: PRAISE-IVT_rep2


title: PRAISE-WT-Takara-second-biological-repeats_rep2


title: PRAISE-IVT_rep1


title: ChOR_T60_clickedInput_H2AK119ub_r1

description: EdU-labelled genomic DNA


title: ChOR_T60_clickedInput_H2BK120ub_r1

description: EdU-labelled genomic DNA


title: DKD.16_smRNA


title: PRAISE-WT-untreated_rep2


title: DKD.17_mRNA


title: DKD.15_smRNA


title: KO_1_lungs

city: Augusta

first: Kebin

last: Liu

state: GA

address: 1410 Laney Walker Blvd

department: Biochemistry and Molecular Biology

institute: Augusta University

data_processing:
Mapping: STAR v2.5 mismatch =2
Quantification: HTSeq v0.6.1 -m union
Genome_build: Mus Musculus(GRCm38/mm10)
Supplementary_files_format_and_content: Tab-delim txt; raw counts

source_name: Tumor-bearing Lung

extract_protocol:
Lungs were mechanically homogenized and RNA was extracted using Direct-zol RNA microprep kit according to manufacturer’s instructions (Zymo Research, Irvine CA)
cDNA

tag: cell line injected

value: 4T1.PD-L1 KO

value: Balb/c


title: PRAISE-WT-untreated_rep1

last: Zhe


title: ChOR_T30_clickedInput_H2AK119ub_r2

description: EdU-labelled genomic DNA

data_processing:
adapters and low quality reads were filtered with TrimGalore (v0.0.6)
reads were mapped to the genome with bowtie2 (v2.4.2) and uniquely mapped peaks kept using samtools (v1.12)
duplicate reads were removed with picard (version 2.26.10)
bam files were read into Seqmonk (v1.47.1) with MAPQ>20, ignoring duplicates, and reads extended by 250bp. Samples were normalized based on Drosphila spike-In abundance and corresponding ClickedInputs. Replicates were merged, exported as bedgraphs and converted to bigwig using UCSC BedGraphtoBigWig
Assembly: mm10
Assembly: dm6
Supplementary files format and content: bigwig files for merged replicates (RRPM-adjusted)  for the mouse genome
Library strategy: ChOR-seq


title: KO_3_lungs


title: PRAISE-WT_rep2


title: ChOR_T30_clickedInput_H2BK120ub_r1

description: EdU-labelled genomic DNA


title: DKD.14_smRNA


title: ChOR_T30_clickedInput_H2AK119ub_r1

description: EdU-labelled genomic DNA


title: DKD.13_smRNA


title: WT_3_lungs


title: WT_2_lungs


title: PRAISE-WT_rep1


title: ChOR_T15_clickedInput_H2A_H2Bub_r2

description: EdU-labelled genomic DNA


title: DKD.12_smRNA


title: PRAISE-TRUB1KO-untreated_rep2


title: WT_1_lungs


title: ChOR_T15_clickedInput_H2A_H2Bub_r1

description: EdU-labelled genomic DNA


title: PRAISE-TRUB1KO-untreated_rep1


title: DKD.11_smRNA


title: KO_2_lungs


title: aCD40-treated, replicate 4, mRNA+ADT

city: Boston

first: Nicolas

middle: Alejandro

last: Gort-Freitas

address: 200 Longwood Ave

department: Systems Biology

institute: Harvard Medical School

data_processing:
Sequencing and basecalling was carried out on NovaSeqSP.
Raw FASTQ files were processed by Cell Ranger 6.0.1 using mm10-2020 as a reference. Count matrices for transcripts, captured antibodies, and multiplexing tags were simultaneously generated using cellranger multi with default parameters.
Single cell data filtering and normalization: Cells expressing >5% mitochondrial transcripts or fewer than 300 total transcripts were excluded as low quality cells. Cells with transcript numbers above the 99th percentile within each experiment were considered potential doublets and excluded.
Assembly: mm10-2020
Supplementary files format and content: Raw counts (tsv.gz): library identity, barcode, and raw counts for all cells included in each pool
Supplementary files format and content: Library barcodes and metadata: library identity, barcode, and associated metadata for all cells across all libraries

source_name: Lung tumor

growth_protocol: KP tumors were induced in C57BL6/J mice, and allowed to grow for 31 days before treating, or not, with aCD40.

extract_protocol:
Two days after the anti-CD40 treatment time point, mice were sacrificed and lungs and tumor nodules were isolated for generating single cell suspensions. Tissues were enzymatically digested, passed through a cell strainer, and cells were stained for CD11b and labeled with 7AAD; CD11b+ cells were sorted using a BD FACSAria sorter. TotalSeq single cell RNA sequencing was performed.
Cells were then stained with a combination of DNA-tagged TotalSeq-A antibodies and Hashtag antibodies, stained with a fluorochrome-labelled CD11b antibody for sorting, and labelled with 7AAD to identify live cells. 7AAD-CD11b+ cells were sorted, using a BD FACSAria sorter, into PBS (no Ca or Mg) with 0.04% BSA, at a concentration of 1000-1500 cells/μL. After this, cells were processed with Chromium Next GEM Single Cell 3’ Kit v3.1, 4 rxns (PN-1000269) before loading on a Chromium Next GEM Chip G Single Cell Kit, 16 rxns (PN-1000127). In collaboration with the Single Cell Core Facility at Harvard Medical School, standard steps were followed for library preparation, quality control and amplification. Sequencing was performed in collaboration with the Biopolymers Facility at Harvard Medical School, using the NovaSeqSP platform (1,600,000,000 reads, 20k reads/cell).

treatment_protocol: Tumor-bearing mice were injected intraperitoneally with 5 mg / kg agonist anti-CD40 monoclonal antibody, or left untreated

value: Lung tumor

tag: tag

tag: antibodies

value: Anti-Ly6C/TotalSeq-A0013 ; Anti-SiglecF/TotalSeq-A0431 ; Anti-CD14/TotalSeq-A0424 ; Anti-CXCR4/TotalSeq-A0444 ; Anti-CXCR2/TotalSeq-C0909 ; Anti-Csf1r/TotalSeq-A0105 ; Anti-PD-L1/TotalSeq-A0190 ; Anti-MHCII/TotalSeq-A0117 ; Anti-ICAM-2/TotalSeq-A0104 ; Anti-ICAM-1/TotalSeq-A0074 ; Anti-CD38/TotalSeq-A0557 ; Anti-CD11a/TotalSeq-A0595 ; Anti-CD62L/TotalSeq-A0112 ; Anti-CD103/TotalSeq-A0201 ; Anti-CD86/TotalSeq-A0200 ; Anti-F480/TotalSeq-A0114 ; Anti-CD49d/TotalSeq-A0078 ; Anti-cKit/TotalSeq-A0012 ; Anti-Ly6G/TotalSeq-A0015 ; Anti-CD19/TotalSeq-A0093


title: DKD.10_smRNA


title: ChOR_T0TPL_clickedInput_H2BK120ub_r2

description: EdU-labelled genomic DNA

value: Triptolide (10uM) for 10min


title: ChOR_T0TPL_clickedInput_H2BK120ub_r1

description: EdU-labelled genomic DNA


title: PRAISE-TRUB1KO_rep1


title: ChOR_T0_clickedInput_H2BK120ub_r2

description: EdU-labelled genomic DNA


title: DKD.9_smRNA


title: aCD40-treated, replicate 2, mRNA+ADT


title: aCD40-treated, replicate 3, mRNA+ADT


title: PRAISE-PUS7KO-untreated_rep2


title: aCD40-treated, replicate 1, mRNA+ADT


title: DKD.8_smRNA


title: PRAISE-PUS7KO-untreated_rep1


title: DKD.7_smRNA


title: PRAISE-PUS7KO_rep2


title: ChOR_T0_clickedInput_H2AK119ub_r2

description: EdU-labelled genomic DNA


title: KP19 tumor bearing, replicate 4, mRNA

value: KP19 tumor bearing


title: ChOR_T0_clickedInput_H2AK119ub_r1

description: EdU-labelled genomic DNA

value: wildtype


title: PRAISE-TRUB1KO_rep2


title: DKD.5_smRNA

value: Adipose


title: KP19 tumor bearing, replicate 3, mRNA+ADT


title: ChOR_T0TPL_H2BK120ub_r2

description:
EdU-labelled genomic DNA
ChOR_T0TPL_H2BK120ub_RRPM_MEAN.bw


title: PRAISE-PUS1KO-untreated_rep2


title: DKD.4_smRNA

value: Mesenchymal Stem Cells


title: KP19 tumor bearing, replicate 1, mRNA+ADT


title: DKD.3_smRNA


title: ChOR_T0TPL_H2BK120ub_r1


title: ChOR_T0_clickedInput_H2BK120ub_r1

description: EdU-labelled genomic DNA


title: PRAISE-PUS1KO_rep2


title: ChOR_noEdU_H2BK120ub_r2

description: noEdU-labelled (control) genomic DNA


title: DKD.2_smRNA


title: Healthy, replicate 1, mRNA+ADT

source_name: Lung

value: Lung

value: Healthy


title: PRAISE-PUS1KO_rep1


title: DKD.1_smRNA


title: ChOR_noEdU_H2BK120ub_r1

description: noEdU-labelled (control) genomic DNA


title: DKD.6_smRNA


title: KO rep1

city: Busan

first: Haeseung

last: Lee

address: 63 Beon-gil 2, Busandaehag-ro, Geumjeong-gu

department: College of Pharmacy

country: South Korea

institute: Pusan National University

data_processing:
Quality check and adapter trimming of RNA-seq data were conducted using FastQC and TrimGalore (https://www.bioinformatics.babraham.ac.uk/), respectively.
The cleaned reads were mapped to mouse genome assembly GRCm38 via the STAR aligner (v2.7.3a).
Transcript abundance per gene such as expected read count or Transcripts Per Million (TPM) was quantified by RSEM (v1.3.3) with mouse gene annotation GRCm38.86.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include Expected counts, FPKM, and TPM values for each Sample

source_name: Follicular helper T cells from LCMV-infected Nr1h2-/- mice

growth_protocol: Follicular helper T cells (CD3ε+ CD4+ PD-1+ CXCR5+) were flow-sorted from spleens of LCMV-infected wild type and Nr1h2-/- mice on day 8

extract_protocol:
Total RNA was isolated from cells according to theh manufacturer's instructions (mirVana miRNA Isolation Kit)
mrna sequencing libraries were prepared according to the manufacturer’s instructions (Illumina Truseq stranded mRNA library prep kit).
mRNA was purified and fragmented from total RNA (1ug) using poly-T oligo-attached magnetic beads using two rounds of purification. Cleaved RNA Fragments primed with random hexamers were reverse transcribed into first strand cDNA using reverse transcriptase, random primers, dUTP in place of dTTP. (The incorporation of dUTP quenches the second strand during amplification, because the polymerase does not incorporate past this nucleotide.) These cDNA fragments then had the addition of a single ‘A’ base and subsequent ligation of the adapter. The products were purified and enriched with PCR to create the final strand specific cDNA library. The quality of the amplified libraries was verified by capillary electrophoresis (Bioanalyzer, Agilent).

value: spleens

value: primary cell

value: Follicular helper T cells

value: Nr1h2 Knockout

value: Nr1h2-/- mice


title: ChOR_T480_H2BK120ub_r2

description:
EdU-labelled genomic DNA
ChOR_T480_H2BK120ub_RRPM_MEAN.bw


title: Control.45

data_processing:
Base calling was performed with the Illumina bcl2fastq
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by STAR-2.5.2b aligner
Gene counts were generated using Subread featureCounts (http://subread.sourceforge.net/)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include Raw counts and RPKM values for each gene per sample

extract_protocol:
After serum-starvation, MSC was centrifuged at 400 x g for 5 minutes at 20 °C to pellet cells and supernatant was aliquoted off.
RNA libraries were prepared using 200 ng of total RNA according to the manufacturer’s instructions.
TruSeq Stranded mRNA Sample Prep Kit v2

value: Control


title: WT rep1

source_name: Follicular helper T cells from LCMV-infected wilid-type mice

value: WT

value: wild-type mice


title: PRAISE-PUS7KO_rep1

value: PRAISE


title: KP19 tumor bearing, replicate 2, mRNA

value: Lung tumor


title: Ribo-ITP-100cell-3

city: Austin

first: Can

last: Cenik

address: Moffett Molecular Biology Building 2.122 2500 Speedway

department: Molecular Biosciences

institute: The University of Texas at Austin

description:
RNA from Ribosome Protected Footprint
human-itp_v4.ribo

data_processing:
Library strategy: Ribo-ITP
For ribosome profiling experiments (conventional ribosome profiling and Ribo-ITP), 5’ adapters are of the form  NNNNNNNNNNNNXXXX where Ns correspond to the UMIs and Xs correspond to the nucleotides to be discarded. The sequence of the 3’ adapters is AAAAAAAAAACAAAAAAAAAA.   5’ adapter sequence “ATTGCGCAATG” was clipped from the first read in the pair using cutadapt version 1.18. Clipped reads shorter than 8 nucleotides were removed using: “cutadapt -j 4 --trimmed-only -m 8  -g ATTGCGCAATG”. We then extracted the next 8 nucleotides corresponding to the UMIs from the first read in the pair and appended them to the headers (of FASTQ files) of both read pairs using UMI-tools with the following parameters: “umi_tools extract --bc-pattern NNNNNNNN”.  After UMI extraction, we used the second read in the pair (40 nt) for all subsequent analyses.   After filtering out reads aligning to a reference of ribosomal and tRNAs, the remaining reads were aligned to a transcriptome reference where SNPs were masked with Ns (see the next section for details); thereafter, we retained only the alignments with mapping quality greater than 2. We then collapsed reads that align to the same transcript using their respective UMIs: “umi_tools dedup --per-contig --per-gene”. For each transcript, we counted the number of reads aligning to the coding sequence. We used bowtie2 for all alignments and samtools 56 version 1.11 for processing BAM files.   We extracted the first 12 nucleotides from the 5’ end of the reads using UMI-tools version 1.1.1 with the following parameters: “umi_tools extract -p "^(?P<umi_1>.{12})(?P<discard_1>.{4}).+$" --extract-method=regex ”.  The four nucleotides downstream of the UMIs are discarded as they are incorporated during the reverse transcription step. Conventional ribosome profiling samples did not include UMIs.   Next we clipped the 3’ adapter AAAAAAAAAACAAAAAAAAAA, from the Ribo-ITP data, using cutadapt version 1.18 with the parameters “-a AAAAAAAAAACAAAAAAAAAA --overlap=4 --trimmed-only”. For conventional ribosome profiling data, we removed the poly-A tails and the first three nucleotides of the reads using “cutadapt -u 3 -a AAAAAAAAAA --overlap=4 --trimmed-only”.  After UMI extraction and adapter trimming, reads were aligned to ribosomal and transfer RNAs using Bowtie2 version 2.3.4.3. The unaligned reads were mapped to a manually-curated transcriptome. We retained alignments with mapping quality greater than 2 followed by deduplication using UMI-tools when applicable. In deduplication of external libraries without UMIs, a set of reads with the same length that are mapped to an identical nucleotide position are collapsed into a single read. As the last step, .ribo files are created using RiboPy version 0.0.1. All subsequent analyses used ribosome footprints that were 29-35 nucleotides in length.   For analyses involving nucleotide resolution data, we determined the A-site offset for each ribosome footprint length using translation stop site metagene plots. Specifically, for each read length, we identified the highest peak upstream of the translation stop site and used the distance to the annotated stop site as the offset.
For RNA-Seq experiments, 5’ adapter sequence “ATTGCGCAATG” was clipped from the first read in the pair using cutadapt version 1.18. Clipped reads shorter than 8 nucleotides were removed using: “cutadapt -j 4 --trimmed-only -m 8  -g ATTGCGCAATG”. We then extracted the next 8 nucleotides corresponding to the UMIs from the first read in the pair and appended them to the headers (of FASTQ files) of both read pairs using UMI-tools with the following parameters: “umi_tools extract --bc-pattern NNNNNNNN”.  After UMI extraction, we used the second read in the pair (40 nt) for all subsequent analyses. After filtering out reads aligning to a reference of ribosomal and tRNAs, the remaining reads were aligned to a transcriptome reference where SNPs were masked with Ns (see the next section for details); thereafter, we retained only the alignments with mapping quality greater than 2. We then collapsed reads that align to the same transcript using their respective UMIs: “umi_tools dedup --per-contig --per-gene”. For each transcript, we counted the number of reads aligning to the coding sequence. We used bowtie2 for all alignments and samtools version 1.11 for processing BAM files.
Supplementary_files_format_and_content: .ribo files contain ribosome occupancy at nucleotide resolution for lengths from 21 to 40. See https://ribopy.readthedocs.io/en/latest/ribo_file_format.html for a detailed description of the ribo format. Number of reads mapping to CDS are given in the csv file cds_counts.csv.gz.

growth_protocol: Human K562 cells were grown in RPMI 1640 medium (Gibco) supplemented with 10% fetal bovine serum (Gibco) and 1% Pen-Strep (Gibco) and incubated at 37 °C with 5% CO2 to a density of ~2.5 x 105 cells per mL. Cells were regularly tested for Mycoplasma contamination. The authentication of K562 cell line was validated using STR profiling from ATCC.

extract_protocol:
For 100-cell ribosome profiling experiments, K562 cells were pelleted, washed twice with PBS, and diluted to 100 cells in 5 µL of cold lysis buffer containing cycloheximide. MNase stock (2,000 gel units/ µL, NEB) was diluted 1:50 and 1 µL of the dilution was added to the samples. Digestion was performed for 30 minutes at 37°C in a thermal cycler with a heated lid. 1 µL EGTA was added to a final concentration of 10 mM in order to inhibit further digestion. Samples were placed on ice until processing through Ribo-ITP. Three replicates each were prepared for conventional ribosome profiling and Ribo-ITP.
For 100-cell human K562 cells and all mouse samples, Ribo-ITP outputs were immediately processed through the D-Plex Small RNA-seq Kit (Diagenode C05030001) with minor modifications as detailed here. The dephosphorylation reaction was supplemented with 0.5 µL T4 PNK (NEB) and the reaction was incubated for 25 minutes. For reverse transcription, the template switching oligo (TSO) was diluted 1:2 in nuclease-free water. All 100-cell human samples and three of the MII-stage oocytes were processed using the single index (SI) module; while the other mouse samples were processed using the unique dual index (UDI) module. Half of the cDNA was amplified for 17 PCR cycles and a 1:4 dilution of the resulting library was assessed by Agilent Bioanalyzer High Sensitivity DNA kit. The concentrations of the target peaks were used to pool samples with approximately equimolar representation. AMPure XP bead cleanup (1.8x) was performed followed by size-selection using 3% agarose, dye-free gel cassettes with internal standards (Sage Science BDQ3010) on the BluePippin platform. Tight parameter settings of 173-207 bp range were used for samples prepared with the SDI module. Tight parameter settings of 183-217 bp range were used for samples prepared with the UDI module. Samples were sequenced on a Illumina NovaSeq 6000.

treatment_protocol: No treatment


title: Control.44


title: ChOR_T480_H2BK120ub_r1


title: Healthy, replicate 2, mRNA+ADT

value: Anti-Ly6C/TotalSeq-A0013 ; Anti-SiglecF/TotalSeq-A0431 ; Anti-CD14/TotalSeq-A0424 ; Anti-CXCR4/TotalSeq-A0444 ; Anti-CXCR2/TotalSeq-C0909 ; Anti-Csf1r/TotalSeq-A0105 ; Anti-PD-L1/TotalSeq-A0190 ; Anti-MHCII/TotalSeq-A0117 ; Anti-ICAM-2/TotalSeq-A0104 ; Anti-ICAM-1/TotalSeq-A0074 ; Anti-CD38/TotalSeq-A0557 ; Anti-CD11a/TotalSeq-A0595 ; Anti-CD62L/TotalSeq-A0112 ; Anti-CD103/TotalSeq-A0201 ; Anti-CD86/TotalSeq-A0200 ; Anti-F480/TotalSeq-A0114 ; Anti-CD49d/TotalSeq-A0078 ; Anti-cKit/TotalSeq-A0012 ; Anti-Ly6G/TotalSeq-A0015 ; Anti-CD19/TotalSeq-A0093


title: ChOR_T180_H2BK120ub_r2

description:
EdU-labelled genomic DNA
ChOR_T180_H2BK120ub_RRPM_MEAN.bw


title: Control.43


title: CD8+T cells, PP2Cm KO biol rep 2

city: Shanghai

first: Chengcheng

last: Yao

address: 280 South Chongqing Road, Shanghai, China

institute: Shanghai Jiaotong University School of Medicine

data_processing:
The libraries were multiplexed and sequenced on Illumina Nextseq500 (75bp paired-end reads).
Raw FASTQ files from RNA-seq sequencing were aligned to the GRCm38 reference genome using Kallisto (https:// pachterlab.github.io/kallisto/)
remove transcripts with low counts
use the FPKM normalization method
Assembly: GRCm38
Supplementary files format and content: Excel file contains the FPKM value for each Sample

source_name: spleen

extract_protocol:
Total RNA was extracted using AllPrep DNA/RNA/miRNA Universal Kit (QIAGEN).
mRNA was further purified by using Dynabeads mRNA DIRECT Micro kit (Invitrogen) and subjected to library preparation using KAPA Stranded RNA-Seq Library Preparation Kit (KAPA).

treatment_protocol: Purified wild-type (WT) and PP2Cm-/-CD8+ T cells were stimulated with anti-CD3/CD28 beads for 24 h.

value: spleen

value: CD8+ T cells

value: PP2Cm KO

value: activated by anti-CD3/28 for 24 hours


title: CD8+T cells, PP2Cm KO biol rep 1


title: Ribo-ITP-100cell-2


title: PRAISE-PUS1KO-untreated_rep1

value: untreated


title: Ribo-ITP-100cell-1


title: Conventional-Ribo-10Mcell-3

data_processing:
Library strategy: ribosome profiling
For ribosome profiling experiments (conventional ribosome profiling and Ribo-ITP), 5’ adapters are of the form  NNNNNNNNNNNNXXXX where Ns correspond to the UMIs and Xs correspond to the nucleotides to be discarded. The sequence of the 3’ adapters is AAAAAAAAAACAAAAAAAAAA.   5’ adapter sequence “ATTGCGCAATG” was clipped from the first read in the pair using cutadapt version 1.18. Clipped reads shorter than 8 nucleotides were removed using: “cutadapt -j 4 --trimmed-only -m 8  -g ATTGCGCAATG”. We then extracted the next 8 nucleotides corresponding to the UMIs from the first read in the pair and appended them to the headers (of FASTQ files) of both read pairs using UMI-tools with the following parameters: “umi_tools extract --bc-pattern NNNNNNNN”.  After UMI extraction, we used the second read in the pair (40 nt) for all subsequent analyses.   After filtering out reads aligning to a reference of ribosomal and tRNAs, the remaining reads were aligned to a transcriptome reference where SNPs were masked with Ns (see the next section for details); thereafter, we retained only the alignments with mapping quality greater than 2. We then collapsed reads that align to the same transcript using their respective UMIs: “umi_tools dedup --per-contig --per-gene”. For each transcript, we counted the number of reads aligning to the coding sequence. We used bowtie2 for all alignments and samtools 56 version 1.11 for processing BAM files.   We extracted the first 12 nucleotides from the 5’ end of the reads using UMI-tools version 1.1.1 with the following parameters: “umi_tools extract -p "^(?P<umi_1>.{12})(?P<discard_1>.{4}).+$" --extract-method=regex ”.  The four nucleotides downstream of the UMIs are discarded as they are incorporated during the reverse transcription step. Conventional ribosome profiling samples did not include UMIs.   Next we clipped the 3’ adapter AAAAAAAAAACAAAAAAAAAA, from the Ribo-ITP data, using cutadapt version 1.18 with the parameters “-a AAAAAAAAAACAAAAAAAAAA --overlap=4 --trimmed-only”. For conventional ribosome profiling data, we removed the poly-A tails and the first three nucleotides of the reads using “cutadapt -u 3 -a AAAAAAAAAA --overlap=4 --trimmed-only”.  After UMI extraction and adapter trimming, reads were aligned to ribosomal and transfer RNAs using Bowtie2 version 2.3.4.3. The unaligned reads were mapped to a manually-curated transcriptome. We retained alignments with mapping quality greater than 2 followed by deduplication using UMI-tools when applicable. In deduplication of external libraries without UMIs, a set of reads with the same length that are mapped to an identical nucleotide position are collapsed into a single read. As the last step, .ribo files are created using RiboPy version 0.0.1. All subsequent analyses used ribosome footprints that were 29-35 nucleotides in length.   For analyses involving nucleotide resolution data, we determined the A-site offset for each ribosome footprint length using translation stop site metagene plots. Specifically, for each read length, we identified the highest peak upstream of the translation stop site and used the distance to the annotated stop site as the offset.
For RNA-Seq experiments, 5’ adapter sequence “ATTGCGCAATG” was clipped from the first read in the pair using cutadapt version 1.18. Clipped reads shorter than 8 nucleotides were removed using: “cutadapt -j 4 --trimmed-only -m 8  -g ATTGCGCAATG”. We then extracted the next 8 nucleotides corresponding to the UMIs from the first read in the pair and appended them to the headers (of FASTQ files) of both read pairs using UMI-tools with the following parameters: “umi_tools extract --bc-pattern NNNNNNNN”.  After UMI extraction, we used the second read in the pair (40 nt) for all subsequent analyses. After filtering out reads aligning to a reference of ribosomal and tRNAs, the remaining reads were aligned to a transcriptome reference where SNPs were masked with Ns (see the next section for details); thereafter, we retained only the alignments with mapping quality greater than 2. We then collapsed reads that align to the same transcript using their respective UMIs: “umi_tools dedup --per-contig --per-gene”. For each transcript, we counted the number of reads aligning to the coding sequence. We used bowtie2 for all alignments and samtools version 1.11 for processing BAM files.
Supplementary_files_format_and_content: .ribo files contain ribosome occupancy at nucleotide resolution for lengths from 21 to 40. See https://ribopy.readthedocs.io/en/latest/ribo_file_format.html for a detailed description of the ribo format. Number of reads mapping to CDS are given in the csv file cds_counts.csv.gz.

extract_protocol:
Approximately 10M K562 cells were pelleted, washed twice with PBS, and immediately flash-frozen in liquid nitrogen. Cells were lysed in 400 µL of cold lysis buffer (Supplementary Table 4) for 10 minutes on ice and pipetted to homogenize. The lysates were clarified by centrifugation at 1,300 x g for 10 minutes at 4 °C. Clarified supernatants were digested with 5 µL MNase (NEB M0247S) and incubated for 30 minutes at 37 °C. Digestions were stopped with 20 mM ribonucleoside vanadyl complex (NEB: S1402S). The samples were then loaded onto 20%- 50% sucrose gradients and ultracentrifuged in a SW41 Ti swinging-bucket rotor (Beckman 331362) at 38,000 rpm for 2.5 h at 4 °C. The samples were fractionated using a Biocomp gradient fractionator. RNA was extracted from the monosome fractions with the miRNeasy Micro kit (Qiagen). One third of the eluate was electrophoresed through a 15% TBE-Urea polyacrylamide gel. The ribosome footprints of ~17-35 nt were gel extracted using the crush-and-soak method as described. Final sample resuspension after ethanol precipitation was in 18 µL of nuclease-free water. The purified RNA was dephosphorylated with 1 µL of T4 polynucleotide kinase (NEB) in 1x T4 PNK buffer for 1 h at 37 °C. Dephosphorylated ribosome footprints were then ethanol precipitated (300 mM Sodium acetate, 2.5 volumes of ethanol, and 1.5 µL of GlycoBlue) overnight at -20 °C. Precipitated RNA was eluted in 10 µL nuclease-free water. The RNA was normalized to 350 ng in 6 µL of nuclease-free water before library preparation.
Conventional ribosome footprint libraries following monosome isolation (i.e. 350 ng RNA samples in 6 µL nuclease-free water) were generated using the Clontech SMARTer smRNA-Seq kit using 8 PCR cycles (Takara Bio). 30 µL of the PCR reaction was purified with AMPure XP beads (Beckman Coulter A63880) according to the manufacturer's instructions and eluted with 30 µL of nuclease-free water. The final size selection was performed with the BluePippin system (Sage Science) using 3% dye-free agarose cassettes (Sage Science BDQ3010).


title: CD8+T cells, WT biol rep 2


title: Control.42

value: Adipose

value: Mesenchymal Stem Cells


title: Conventional-Ribo-10Mcell-2


title: ChOR_T180_H2BK120ub_r1

value: wildtype


title: Control.41


title: ChOR_T120_H2BK120ub_r1

description:
EdU-labelled genomic DNA
ChOR_T120_H2BK120ub_RRPM_MEAN.bw


title: Control.38


title: CD8+T cells, WT biol rep 1


title: Conventional-Ribo-10Mcell-1