title: H3 K9me3 in tetR-clr4-OFF-14 generations wt cells

type: genomic

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

description: H3K9me3 ChIP wt tetR-clr4-OFF V3

hyb_protocol: Equal amounts of Cy5-labeled immunoprecipitated DNA and Cy3-labeled input DNA were mixed with human Cot1 DNA, blocking agent and hybridization buffer, and hybridized to Agilent high-density microarrays at 65˚C for 24 hours, 10 rpm. After hybridization, slides were processed according to Agilent protocol.

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing: Data were extracted using Agilent Feature Extraction Software (ChIP_1200_Jun14). Signal was normalized by combined rank consistency filtering with LOWES intensity normalization.

organism: Schizosaccharomyces pombe

source_name: log. growing cells

label_protocol: ChIP and input DNA was random-primed PCR amplified and conjugated with Cy5 (ChIP DNA) or Cy3 (input DNA).

growth_protocol: Standard conditions were used to produce exponentially growing cultures in minimal media (EMM) at 32˚C. Cells were pre-cultured for 20 generations in thiamine-free EMM and grown in media supplemented with 5-fluoroorotic acid (850 ug/ml) for 5 generations. Portion of mid-log phase cells was fixated with 3% paraformaldehyde and harvested for ChIP (tetR-clr4ON cells). Remaining cells were transferred into EMM media supplemented with 5ug/ml thiamine and 2.5ug/ml tetracycline and cultured for 14 generations. Mid-log phase cells were fixated with 3% paraformaldehyde and harvested.

extract_protocol: Fixed cells were lysed with glass-beads in Biospec Mini-Beadbeater 16, DNA was sheared by sonication to ~ 1,000 bp fragments, cleared by centrifugation at 3,000 g and immunoprecipitated with 2ug of Abcam H3K9me3 antibody (ab8898). Immunoprecipitated DNA was recovered by incubation with protein A slurry and the crosslink reversed at 65˚C.Input and immunoprecipitated DNA was treated with RNase A (5ug) and Protease K (40ug) and column purified by Qiaquick PCR purification (Qiagen).

treatment_protocol: Exponentially growing cells were fixed in 3% paraformaldehyde at 32˚C.

value: wild type

tag: molecule subtype

value: H3K9me3 immunoprecipitated DNA

value: Whole-cell extract DNA


title: Col-0, SIM 4D, Low light, replicate 2

status: Public on Sep 16 2024

type: SRA

city: Yokohama

first: Yu

last: Chen

address: 1-7-22 Suehirocho, Tsurumi-ku

country: Japan

institute: RIKEN

library_source: transcriptomic

data_processing:
Sequenced reads were mapped to the TAIR10 Arabidopsis genome by STAR 87 using the “--outFilterMultimapNmax 1 --alignIntronMax 10000 --alignMatesGapMax 10000” options.
After indexing by the samtools, mapped reads were further counted by bedtools multicov.
Differentially expressed genes (DEGs) are defined by edgeR package on R by comparing between different timepoints, light conditions and genotypes with the criteria |log2fold change (FC)| > log2(1.5) & false discovery rate (FDR) <= 0.05.
Assembly: TAIR10
Supplementary files format and content: raw_counts.txt is a tab-delimited file containing the read counts of each genes mapped to TAIR10 Arabidopsis genome in each sample.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: hypocotyls

growth_protocol: Arabidopsis seeds were surface-sterilized with 70 % (v/v) ethanol for 1 min and then 20 % (v/v) bleach for 5 min. Sterilized seeds were rinsed with autoclaved water 3 times before sowing onto the MS media supplied with 1 % sucrose and solidified by 0.6 % Gelzan. After 4 days of stratification at 4ºC under darkness, seeds were stimulated for germination at 22ºC under continuous high light (40 µmol/m2/s) for several hours before growing under continuous low light (2 µmol/m2/s). 7-day-old seedlings grown at 22ºC under continuous low light (2 µmol/m2/s) were used for hormone-induced shoot regeneration.

extract_protocol:
Hypocotyl explants were frozen with liquid nitrogen and ground with beads by a TissueLyser II (QIAGEN). RNA extraction with DNase digestion was performed by the RNeasy Plant Mini Kit (QIAGEN) following the default instructions.
Isolated RNA was then subjected for library preparation using the KAPA Stranded mRNA-Seq Kit (NIPPON Genetics) with NEB adaptors for Illumina (New England Biolabs) and AMPure XP beads (Beckman Coulter).

treatment_protocol: Briefly, the excised hypocotyl explants were initially cultured on CIM (Gamborg’s B5 vitamin medium supplied with 2 % glucose and solidified by 0.25 % Gelzan, together with 0.5 mg/L 2,4-Dichlorophenoxyacetic acid (2,4-D) and 0.1 mg/L kinetin) for 4 days to induce callus formation. These explants were subsequently transferred to SIM (Gamborg’s B5 vitamin medium supplied with 2 % glucose and solidified by 0.25 % Gelzan, together with 0.15 mg/L Indole-3-acetic acid (IAA) and 0.5 mg/L 2-Isopentenyladenine (2-iPA)) for 14 days to induce shoot regeneration.

tag: tissue

value: hypocotyls

tag: genotype

tag: treatment

value: SIM

tag: time

value: 4 days after SIM incubation


title: H3 K9me3 in tetR-clr4-ON clr3-CDx2 cells

country: USA

description: H3K9me3 ChIP clr3-CDx2 V3 tetR-clr4-ON V3

molecule: genomic DNA


title: H3 K9me3 in tetR-clr4-ON wt cells

description: H3K9me3 ChIP wt  tetR-clr4-ON V3


title: H3 K9me3 in tetR-clr4-OFF-14 generations  clr3-CDx2 cells

description: H3K9me3 ChIP clr3-CDx2 tetR-clr4-OFF V3


title: BA612 + AHLs R1

city: Columbus

first: Brian

last: Ahmer

state: OH

address: 776 Biomedical Research Tower, 460 W 12th Ave

department: Microbial Infection and Immunity

institute: The Ohio State University

description:
total RNA from sdiA mutant Typhimurium grown in LB with AHL
14028_transcript_count_matrix.csv

data_processing:
Quality (FastQC)
Trimming (Trimmomatic)
Mapping (Bowtie2)
Assembly (Stringtie)
Quantification and assignation (Stringtie)
Assembly: CP001363
Supplementary files format and content: txt file
Supplementary files format and content: raw transcript counts of each treatment group

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: late exponential phase

growth_protocol: Each strain was grown over-night in LB at 37C. Washed cells were diluted 1:100 in LB broth + AHLs. Plasmid containing strains were treated with arabinose. Cells were re-grown until late exponential phase at 37C, shaking.

extract_protocol:
Cell pellets were frozen at -80. Total RNA was extracted from cells using the Purelink RNA mini kit (Invitrogen). Residual DNA was removed by Dnase digestion
Construction was performed by OSU Shared genomics resources

tag: culture medium

value: LB Broth

tag: cell type

value: late exponential phase

value: AHL


title: BA612 + pVector + AHLs R2

description:
total RNA from sdiA mutant Typhimurium grown in LB with AHL with vector control
pJVR2_transcript_count_matrix.csv

value: sdiA::mTn3 + pBAD

value: AHL + arabinose


title: H3-T7 i in tetR-clr4-ON wt cells

growth_protocol: Standard conditions were used to produce exponentially growing cultures of cdc22-25 cells in minimal media at permissive temperature (26˚C). To assay histone turnover at heterochromatin domain assembled by tethered Clr4, tetO-ade6+ cells expressing TetR-Clr4 from thiamine repressible promoter were pre-cultured at 26˚C for 20 generations in thiamine-free minimal media (tetR-clr4-ON). After 20 generations cells were diluted to optical density (595nm) of 0.01 and cultured overnight at 26˚C. At optical density of 0.1 cells were arrested at G2/M phase by incubation at 36˚C for 4 hours. G2/M arrested cells were treated with 1uM b-estradiol for 2 hours to induce the Cre recombinase catalyzed genetic replacement of H3-HA tag by H3-T7 tag, and cells were fixated with 1% formaldehyde. Control cells (tetR-clr4-OFF) were subjected to the same cultivation protocol, but the media were supplemented with 5ug/ml thiamine and 2.5ug/ml tetracycline.

extract_protocol: Fixed cells were lysed with glass-beads in Biospec Mini-Beadbeater 16, DNA was sheared by sonication to ~ 1,000 bp fragments, cleared by centrifugation at 3,000 g and immunoprecipitated with 2ug of Abcam H3-T7 (Ab9138) antibody. Immunoprecipitated DNA was recovered by incubation with protein A slurry and the crosslink reversed at 65˚C. Input and immunoprecipitated DNA was treated with RNase A (5ug) and Protease K (40ug) and column purified by Qiaquick PCR purification (Qiagen).

treatment_protocol: Exponentially growing cells were fixed in 1% formaldehyde at 37˚C.

value: H3-T7 immunoprecipitated DNA


title: BA612 + AHLs R2


title: BA612 + AHLs R3


title: BA612 + pSdiA + AHLs R1

description:
total RNA from sdiA mutant Typhimurium grown in LB with AHL expressing sdiA on plasmid
pJVR2_transcript_count_matrix.csv

value: sdiA::mTn3 + pBAD-SdiA


title: BA612 + pSdiA + AHLs R3


title: H3-T7 i in tetR-clr4-ON clr3-CDx2 cells

value: H3T7 cdc25-22 clr3-CDx2


title: BA612 + pVector + AHLs R3


title: 14028 + AHLs R2

description:
total RNA from wild-type Typhimurium grown in LB with AHL
14028_transcript_count_matrix.csv

value: wild-type


title: 14028 + AHLs R1


title: H3-T7 in tetR-clr4-OFF clr3-CDx2 cells


title: BA612 + pVector + AHLs R1


title: H3-T7 in tetR-clr4-OFF wt cells


title: BA612 + pSdiA + AHLs R2


title: 14028 + AHLs R3


type: RNA

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

country: Germany

institute: University Heidelberg

description: Gene expression of WT after 2 h of high light biological rep 2

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 10, from SAS. Gene expression profiling was performed using arrays of Arabidopsis AraGene-1_0-st type from Affymetrix. A Custom CDF Version 22 with TAIR based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: Biotin

source_name: WT after 2 h of high light

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Arabidopsis thaliana ecotype Co-0 and gnat2 mutants (SALK_033944) were grown on soil under short-day conditions (8 h light, 120 µmol m-2s-1 photon flux density, 23 °C and 50 % humidity).

extract_protocol: The peqGOLD Total RNA kit (Peqlab) was used to extract RNA from 100 mg plant powder. A global transcriptome analysis was performed using the Affimetrix (High Wycombe) Arabidopsis Genechip (AraGene-1_0st-typ) as described in detail by Linster et al. (2015).

treatment_protocol: After 4.5 weeks, the plants were subjected to different light regimes interrupting the short-day light cycle. Two hours after the regular onset of light, the plants were treated with either high light illumination (HL, 1000 µmol m-2s-1) or darkness (D) for two hours. The control group (C) continued growth at 120 µmol m-2s-1.

tag: ecotype

value: WT

tag: treatment/timepoint

value: after 2 h of high light


description: Gene expression of WT after 2 h of high light biological rep 3


description: Gene expression of WT after 2 h of control conditions, biological rep 2

source_name: WT after 2 h of control conditions

value: after 2 h of control conditions


description: Gene expression of WT after 2 h of control conditions, biological rep 3


description: Gene expression of WT after 2 h of high light biological rep 4


title: CTNNB1_Q76_20wk

city: Cleveland

first: Luke

last: Bury

address: Adelbert Road 2109, BRB 743

department: Genetics and Genome Sciences

institute: Case Western Reserve University

library_source: transcriptomic single cell

data_processing:
Raw FASTQ files for each experiment were uploaded to the Cloud Analysis platform from 10X Genomics. Read alignment and feature barcode matrices were generated via Cell Ranger Count v6.1.2 (10X Genomics) using standard settings and 10,000 expected number of cells. For all experiments, a custom reference genome was utilized that included unique sequences for tdTomato, ZsGreen, 2A-Cre recombinase, and 2A-Dre recombinase. This reference genome was built following the standard Cell Ranger mkref v3.1.0 pipeline (10X Genomics, https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_mr). First, the GRCh38 primary genome assembly along with the comprehensive gene annotation for the primary assembly (v37) were downloaded from the GENCODE website and utilized as inputs to generate the base genome via Cell Ranger mkref. Custom FASTA and GTF files were generated for individual COR-LT system genes, which were then appended onto the base genome as described in the mkref tutorial (10X Genomics).
Complete gene sequences for tdTomato, ZsGreen, 2A-Cre recombinase, and 2A-Dre recombinase that were used to build this custom reference can be found at https://github.com/lbury3/cor_lt/. In general, sequences include the coding sequence for each gene and the 3’ UTR sequence up but not including the polyA sequence. In one exception, there was a portion of the 3’ UTR sequence that was not included for ZsGreen as it overlapped with the SV40 sequences used as the STOP signal in the reporter constructs. Experimental scRNA-seq data indicated that the upstream CAG promoter drove production of nascent transcripts containing as least a portion of the SV40 polyA sequence in most cells, irrespective of ZsGreen expression (data not shown). Thus, this sequence was excluded from the overall ZsGreen sequence. Removal of this 3’ sequence from the reference genome might lead to under-detection of ZsGreen in scRNA-seq data, as transcripts recovered via the 10X Chromium Next GEM Single Cell 3’ Reagent Kit are enriched in 3’ sequences.
Assembly: Custom reference utilizing GRCh38.v37 human genome assembly with addition of COR-LT system components
Supplementary files format and content: All processed data are the feature barcode matrices produced by Cell Ranger analysis (10x Genomics) in HDF5 format

molecule: polyA RNA

organism: Homo sapiens

source_name: Cortical organoid

extract_protocol:
Organoids were dissociated into single cells utilizing the Worthington Papain Dissociation System kit, following a previously described protocol (https://protocolexchange.researchsquare.com/article/pex-258/v1) with the following modifications. 2-8 organoids were used per cell line per experiment (Supplemental Table 15). Organoids from the same cell lines were dissociated together so that cells from all organoids of the same cell line were pooled for individual experiments. For 16 week control and 20 week ASD organoids, the organoids were removed from culture medium and washed once with PBS. A clean razor blade was then used to cut individual organoids into approximately four to six pieces. These organoid pieces were then washed 3x with PBS in an attempt to remove dead and/or stressed cells from the interior of the organoid. After the third wash, PBS was removed, papain/DNase solution was added, and the organoid pieces were cut into smaller pieces to start the dissociation process as described in (https://protocolexchange.researchsquare.com/article/pex-258/v1). Upon dissociation completion, cells were diluted in PBS with 0.04% BSA (Millipore Sigma) and kept on ice.
Immediately after dissociation was completed, single-cell RNA libraries were generated with the Chromium Next GEM Single Cell 3’ Reagent Kit, v3.1 (10X Genomics) following the manufacturer’s instructions. For each experiment, 10,000 cells were targeted for recovery.

value: Cortical organoid

tag: cell line

value: CTNNB1 WT/Q76* COR-LT

value: mixed

value: CTNNB1 WT/Q76*


title: CTNNB1_WT_10wk

value: CTNNB1 WT/WT COR-LT

value: CTNNB1 WT/WT


description: Gene expression of WT after 2 h of high light biological rep 1


title: CTNNB1_WT_20wk


title: CTNNB1_Q76_10wk


title: control_AP

value: control COR-LT

value: Control


description: Gene expression of gnat2 after 2 h of control conditions, biological rep 4

source_name: gnat2 after 2 h of control conditions


description: Gene expression of WT after 2 h of control conditions, biological rep 1


description: Gene expression of WT after 2 h of darkness, biological rep 4

source_name: WT after 2 h of darkness

value: after 2 h of darkness


description: Gene expression of WT after 2 h of darkness, biological rep 3


description: Gene expression of gnat2 after 2 h of control conditions, biological rep 3


description: Gene expression of WT after 2 h of darkness, biological rep 2


description: Gene expression of gnat2 after 2 h of high light biological rep 4

source_name: gnat2 after 2 h of high light


description: Gene expression of gnat2 after 2 h of control conditions, biological rep 2


description: Gene expression of gnat2 after 2 h of high light biological rep 2


description: Gene expression of gnat2 after 2 h of darkness, biological rep 3

source_name: gnat2 after 2 h of darkness


description: Gene expression of gnat2 after 2 h of high light biological rep 1


description: Gene expression of gnat2 after 2 h of control conditions, biological rep 1


description: Gene expression of gnat2 after 2 h of darkness, biological rep 2


title: control_rep2


description: Gene expression of gnat2 after 2 h of high light biological rep 3


description: Gene expression of WT after 2 h of darkness, biological rep 1


title: SKM G4S BBz biol rep 3

first: Taku

last: Kouro

state: Kanagawa

address: 2-3-2 Nakao, Asahi-ku

department: Division of Cancer Immunotherapy

institute: Kanagawa Cancer Center Research Institute

description: sample 15

data_processing:
Sequence reads were mapped to GRCh38 (GENCODE v42) using STAR (2.7.10b)
TPM were calculated using RSEM (v1.3.3)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values as matrix file

source_name: cultured PBMC

growth_protocol: PBMC was prepared using lymphoprep and stimulated with plate-coated anti-CD3 mAb and 100U/ml IL-2 in AIM-V medium supplemented with 10% AB serum.

extract_protocol:
On day 11, RNA was harvested using Rneasy mini kit (Qiagen). 1.1 ~ 4.1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing and Nextera XT DNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: Retrovirus supernatants for each CAR was obtained using Phoenix-Ampho packaging cell line and infected to activated PBMC using retronectin (Takara) following manufacturer's instruction.　On day 8, CAR positive cells were labelled with anti-G4S linker mAb-PE or anti-Whitlow/218 linker mAb-PE and sorted on FACSAriaII cell sorter, and kept culturing

value: cultured PBMC

value: T lymphocytes

value: CD3/IL-2 stimulation, retrovirus infection


title: SKM G4S 28z biol rep 3

description: sample 14


description: Gene expression of gnat2 after 2 h of darkness, biological rep 1


title: SKM W218 BBz biol rep 3

description: sample 13


title: control_rep1


title: SKM W218 28z biol rep 3

description: sample 12


title: SKM G4S 28z biol rep 2

description: sample 9


title: no CAR biol rep 3

description: sample 11

value: CD3/IL-2 stimulation


title: SKM G4S BBz biol rep 2

description: sample 10


title: SKM G4S BBz biol rep 1

description: sample 5


title: SKM W218 28z biol rep 2

description: sample 7


title: SKM G4S 28z biol rep 1

description: sample 4


title: SKM W218 BBz biol rep 2

description: sample 8


title: SKM W218 28z biol rep 1

description: sample 2


title: SKM W218 BBz biol rep 1

description: sample 3


title: no CAR biol rep 1

description: sample 1


title: no CAR biol rep 2

description: sample 6


title: oeSTUB1-2

city: Wuhan

first: Junsheng

state: Wuhan

address: Bao Feng Street

department: Department of Biliary-Pancreatic Surgery

country: China

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

data_processing:
Raw reads of fastq format were firstly processed using fastp (v 0.20.1) and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2 (v 2.1.0).
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count (v 0.11.2).
PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Differential expression analysis was performed using the DESeq2 (v 1.22.2). Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs). Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate the expression pattern of genes in different groups and samples.
Assembly: NCBI:GRCh38.p13
Supplementary files format and content: Processed_data_FPKM.txt contains the FPKM value of each sample (oeNC-1, oeNC-2, oeNC-3, oeSTUB1-1, oeSTUB1-2, oeSTUB1-3).

source_name: Cholangiocarcinoma

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: Cholangiocarcinoma

value: Cancer cell line

value: STUB1 overexpression

value: no


title: oeNC-1

value: negative control


title: oeSTUB1-1


title: oeSTUB1-3


title: Control empty vector transfected cells, JQ1 treated ,biol HCT116 rep1

first: Dinah

middle: S.

last: Singer

address: Building 10, Room 4B-17

department: Division of Cancer Biology

institute: National Cancer Institute

data_processing:
RNA-seq reads were aligned to human reference genome (hg38) with STAR aligner (2.7.8a). Raw read counts were obtained using htseq-count (0.11.4).
Assembly: hg38
Supplementary files format and content: tab-delimited text files including raw counts for each sample

growth_protocol: The HCT116 cells were grown in DMEM media (Gibco) supplemented with 10% fetal bovine serum at 37 °C with 7.5% CO2

extract_protocol:
RNA was isolated from empty vector and BRD4 transfected cells using the Micro RNeasy-Plus Kit (Qiagen)
Libraries were prepared using  the Illumina Illumina® Stranded mRNA Prep according to the manufacturers' instructions.

treatment_protocol: DMSO or JQ1 treated for 18 hrs

value: colorectal carcinoma

tag: transfection

value: Control empty vector


title: BRD4 transfected cells, JQ1 treated ,biol HCT116 rep2

value: Brd4 transfected


title: Control empty vector transfected cells, JQ1 treated ,biol HCT116 rep3


title: oeNC-2


title: BRD4 transfected cells, JQ1 treated ,biol HCT116 rep3


title: Control empty vector transfected cells, biol HCT116 rep3

value: DMSO


title: Untreated BRD4 transfected cells, biol HCT116 rep 3


title: BRD4 transfected cells, JQ1 treated ,biol HCT116 rep1


title: ThymoSphere (TS) week 9 CD3+ TCRγδ- FB5P

city: Ghent

first: Laurenz

last: De Cock

address: Corneel Heymanslaan 10

department: Department of Diagnostic Sciences

country: Belgium

institute: Ghent University

description:
BVK004_FB5P
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz

library_source: other

data_processing:
*library strategy: CITE-Seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing) and scTCR-seq
The Cell Ranger pipeline (10x Genomics, version 3.1.0) was used to perform sample demultiplexing and to generate FASTQ files for read 1, read 2 and the i7 sample index for the gene expression libraries. Read 2 of the gene expression libraries was mapped to the reference genome (GRCh38.99) using STAR
Quality control of the count matrices and doublet removal was performed using Scater (version 1.30.1) and scDblFinder (version 1.14.0).
Further processing, e.g. normalization, clustering and differential gene expression analysis was performed with Seurat (version 5.0.1).
The scTCR-seq data was analysed with the scRepertoire package version 2.0.0.
Assembly: GRCh38.99
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, filtered_contig_annotations.csv

molecule: protein

source_name: T cells

extract_protocol:
At week 9, multiple TS-containing inserts were harvested and pooled. Subsequently, the CD3+ TCRγδ- fraction was sorted. Following FACS, the cells were resuspended at an estimated final concentration of 3000 cells/µl and loaded onto a Chromium GemCode Single Cell Instrument (10x Genomics) to generate single-cell gel beads-in-emulsion (GEM) at the VIB Single Cell Core.
The scRNA/TCR libraries were prepared using the GemCode Single Cell 5’ Gel Bead and Library kit, NextGEM v2 version (10x Genomics) according to the manufacturer’s instructions.

value: T cells

tag: cell fraction

value: CD3+ TCRγδ-

tag: library type

value: ADT

tag: adt

value: 277 oligo-conjugated antibodies (TotalSeq-A, BioLegend) including 6 TotalSeq-A isotype controls (See supplementary file CITE-Seq_Cell_Surface_Protein_Antibody_Panel.xlsx)


title: ThymoSphere (TS) week 9 CD3+ TCRγδ- cDNA

value: mRNA


title: Untreated BRD4 transfected cells, biol HCT116 rep 2


title: Untreated BRD4 transfected cells, biol HCT116 rep 1


title: Control empty vector transfected cells, biol HCT116 rep1


title: MA1

city: Oxford

first: Tatjana

last: Sauka-Spengler

state: Oxfordshire

address: Radcliffe Department of Medicine

department: University of Oxford

country: United Kingdom

institute: MRC Weatherall Institute of Molecular Medicine

library_source: genomic

data_processing:
Fastq files were delivered and initially processed with Cellranger v7.1.0 resulting in 8,479 cells with 81,249 reads per cell.
Pooled libraries were demultiplexed into individual foetal samples using genetic demultiplexing. RNA was isolated using Qiagen RNeasy kit. Bulk RNA libraries were generated using the KAPA RNA Hyperprep with Riboerase and sequenced to a targeted depth of 50 million reads. Variant calling and genotyping was performed in accordance with the GATK RNAseq short variant discovery (SNPs + Indels) pipeline. Multiome samples were demultiplexed using Souporcell within Demuxafy v2.0.1.
Ambient RNA was detected and removed using Cellbender v0.3.0. Doublets were detected based on genotype using Souporcell and separately using scDblFinder both using Demuxafy v2.0.1. Libraries were clustered with the standard Seurat v4.9.9.9058 pipeline (resolution 1.0). Clusters were annotated manually using the FindAllMarkers function (logfc threshold 0.25, min pct 0.25).
Assembly: Human GRCh38 (GENCODE v32/Ensembl98)
Supplementary files format and content: fragments.tsv

source_name: Head

growth_protocol: Human foetal samples were obtained from donors in accordance with ethically approved study REC 96/085 (University of Cambridge and Cambridge University Hospitals NHS Foundation Trust). Samples were transferred under a Material Transfer Agreement and stored and processed in accordance with ethically approved study REC 22/PR/0630 (University of Oxford) on HTA-licensed premises (license number 12433).

extract_protocol:
Nuclei isolation was performed by sectioning 100um curls on a cryostat without delay and collected in a 1.5ml centrifuge tube cooled on dry ice. Nuclei were isolated using the Chromium 10X nuclei isolation kit (CG000505 Rev A). Nuclei quality and quantity were assessed visually and using a Countess cell counter prior to loading a Chromium Chip J. Remaining nuclei were stored in buffer RLT (Qiagen).
Libraries were generated in accordance with CG000338 Rev F Chromium Next GEM Single Cell Multiome ATAC + Gene Expression. Libraries were sequenced in accordance with 10X recommendations targeting 50,000 reads per nucleus.
Multiome - scRNAseq, scATACseq

treatment_protocol: Four foetal heads across three Carnegie Stages (CS16, CS18, CS18, CS19) were collected fresh and then immediately embedded in OCT prior to transfer on dry ice for storage.

value: Head

value: Primary human tissue

value: Nuclei

value: 10X Genomics Chromium Single Cell Multiome ATAC


title: Control empty vector transfected cells, biol HCT116 rep2


title: Multiplexing Capture (hiPSC derived cardiac fibroblasts)

city: Boston

first: Seong Won

last: Kim

state: MA

address: 77 Ave Louis Pasteur

department: Genetics

institute: Harvard Medical School

description: 10X Genomics

data_processing:
CellRanger software was used to demultiplex and align to the reference genome (hg38).
For the final gene expression profiles, CellBender was used to remove non-specific RNA expression, and solo and scrublet were used for doublet detection.
Assembly: hg38
Supplementary files format and content: Tab separated matrix file, barcodes file, and feature files.
Supplementary files format and content: List of demultiplexed CellRanger barcodes and Genotype assignment

growth_protocol: Human hiPSCs were differentiated using the method established by Zhang et al. (PMID 31288631) Briefly, Cardiac progenitor cells (CPCs) were generated using small molecule modulation of the Wnt signaling pathway in CDM media, identical to CM differentiation, using Wnt-C59 rather than IWR2 as described in the original protocol. On day 5 post differentiation, CPCs were dissociated using Accutase (Stem Cell Technologies) and split 1:12 in Matrigel-coated plates and Advanced DMEM containing 2µM retinoic acid and 5µM CHIR and 5µM RI. On Day 6, medium was refreshed to Advanced DMEM + 5µM CHIR and retinoic acid for two days. On Day 8, cells were recovered in Advanced DMEM. On Day 11-14, cells were cultured in Advanced DMEM plus 2µM SB431542 (Tocris). On Day 14, cells were split at a density of 10,000/cm2 into a Fibroblast Growth Medium 3 (Promocell) supplemented with 20ng/ml FGF2 (Peprotech) and 10µM SB431542 until Day 20. Differentiated cardiac fibroblasts were maintained in Fibroblast Growth Medium 3. After differentiation, hiPSC-CF were split and cultured atop 8kPa Cytosoft plates (Advanced Biomatrix) which had been coated with Matrigel for one hour at room temperature.

extract_protocol:
hiPSC-CFs were dissociated with TrypLE, centrifuged for 5 minutes at 300g, and the pellet was snap-frozen for snRNA-seq
Cell pellets were barcoded with 3' CellPlex Kit from 10X Genomics. After barcoding the cells, nuclei were extracted, washed, and pooled. Library was constructed according to the manufacturer's instruction for Chromium 3’ v3.1 dual index kit.

treatment_protocol: Passage 1 hiPSC-CFs were cultured for 5 days atop soft 8kPa substrate plates (Advanced Biomatrix) prior to extraction.

value: hiPSC derived cardiac fibroblasts


title: Pooled Gene Expression of hiPSC-CFs

description: 10X Genomics


title: ThymoSphere (TS) week 9 CD3+ TCRγδ- TCR

value: TCR


title: A549 cells, PNDacute3

city: Bern

first: Georgia

last: Konstantinidou

address: Inselspital, INO-F

country: Switzerland

institute: Institute of Pharmacology, University of Bern

data_processing:
The quality of the RNA-seq data was assessed using fastqc v.0.11.9 and RSeQC v.4.0.0.
The reads were mapped to the reference genome using HiSat2 v.2.2.1.
FeatureCounts v.2.0.1 was used to count the number of reads overlapping with each gene as specified in the genome annotation
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: A549 cells

extract_protocol:
For the RNA sequencing, total RNA was extracted using a PureLink RNA Kit (Invitrogen, 12183018A), including an on-column DNase treatment (Invitrogen, 12185-010) according to the manufacturer`s instructions.
Sequencing libraries were made with 1000 ng input RNA using an illumina TruSeq Stranded mRNA Library Prep kit (illumina, 20020595) in combination with TruSeq RNA UD Indexes (illumina, 20022371) according to illumina’s guidelines. The cDNA libraries were evaluated using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific, Q32854) and an Agilent Fragment Analyzer (Agilent) with a HS NGS Fragment Kit (Agilent, DNF-474), respectively. Equimolar-pooled cDNA libraries were sequenced paired-end using a shared illumina NovaSeq 6000 SP Reagent Kit (100 cycles; illumina, 20028401) on an illumina NovaSeq 6000 instrument. An average of 37 million reads were generated/library. The quality of the sequencing run was assessed using illumina Sequencing Analysis Viewer (illumina version 2.4.7) and all base call files were demultiplexed and converted into FASTQ files using illumina bcl2fastq conversion software v2.20. The quality control assessments, generation of libraries and sequencing was conducted by the Next Generation Sequencing Platform, University of Bern

value: A549 cells

value: lung cancer cells

value: PNDacute


title: 14M cKO, NP 2

city: Philadelphia

first: Shira

middle: N

last: Johnston

state: PA

address: 1025 Walnut St., Suite 511 College Bldg.

institute: Thomas Jefferson University

description: Gene expression data from 14-month-old HIF-2α cKO mouse nucleus pulposus tissue.

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

label: biotin

organism: Mus musculus

source_name: Nucleus pulposus from 14-month-old HIF-2α cKO mice

label_protocol: standard Affymetrix protocol

extract_protocol: none provided by the submitter

value: nucleus pulposus

value: FoxA2Cre; HIF-2αf/f (cKO)

tag: age


title: A549 cells, PNDacute2


title: 14M CT, NP 4

description: Gene expression data from 14-month-old control mouse nucleus pulposus tissue.

source_name: Nucleus pulposus from 14-month-old control mice

value: HIF-2αf/f (CT)


title: A549 cells, PND_R2


title: LBW/WD liver, female, biological rep4

city: London

first: Ousseynou

last: Sarr

state: United States

address: 1811 Creekside Street

department: Physiology & Pharmacology

country: Canada

institute: Western universitry

description: Gene expression data from young adult LBW offspring fed a Western diet

hyb_protocol: After fragmentation and labeling, 2.1 µg cDNA was hybridized onto Guinea Pig Gene 1.1 ST Array Plate (Thermo Fisher Scientific).

scan_protocol: GeneChips were scanned using the GeneTitan® Instrument (Thermo Fisher Scientific).

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC) (version 4.0, Life Technologies) using Affymetrix default analysis settings, Summarization Method as normalization method  and the Differential Expression analysis.

organism: Cavia porcellus

source_name: guinea pig liver at postnatal day 150

label_protocol: Sense-strand cDNA was synthesized from 100 ng of total RNA, and fragmentation and labeling were performed to produce ss-cDNA with the GeneChip® WT Terminal Labeling Kit according to manufacturer’s instructions (Thermo Fisher Scientific).

growth_protocol: Uterine artery ablation-induced low birth weight (LBW) and normal birth weight (NBW) male and female guinea pig offspring were fed a control diet (CD) or a Western diet (WD) from weaning until postnatal day 150.

extract_protocol: Extraction of total RNA in livers was performed using Trizol and the RNeasy Plus Universal Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: At postnatal day 150, offspring of each sex were fasted overnight, euthanized via CO2 inhalation in the morning (~ 10 am) of the following day and tissue collection conducted. The whole liver was removed and weighed immediately and the right lobe liver was frozen in liquid nitrogen and stored at −80 °C.

tag: gender

value: Female

value: Liver

tag: strain

value: Dunkin Hartley


title: 14M CT, NP 1


description: Gene expression of WT after 2 h of control conditions, biological rep 4

value: WT

value: after 2 h of control conditions


title: 14M cKO, NP 1


title: 14M cKO, NP 4


title: 14M cKO, NP 3


title: 14M CT, NP 2


title: 14M CT, NP 3


title: 6M CT, NP 3

description: Gene expression data from 6-month-old control mouse nucleus pulposus tissue.

source_name: Nucleus pulposus from 6-month-old control mice


title: LBW/WD liver, female, biological rep5


title: A549 cells, PND_R3


title: A549 cells, NT3

value: NT


title: A549 cells, NT2


title: 6M cKO, NP 4

description: Gene expression data from 6-month-old HIF-2α cKO mouse nucleus pulposus tissue.

source_name: Nucleus pulposus from 6-month-old HIF-2α cKO mice


title: 6M cKO, NP 2


title: LBW/WD liver, female, biological rep3


title: 6M CT, NP 1


title: LBW/WD liver, female, biological rep2


title: 6M cKO, NP 3


title: d2-1_Liver_Ctrl

city: Melbourne

first: Laura

last: Mackay

state: Victoria

address: 792 Elizabeth street

department: Microbiology and Immunology

country: Australia

institute: The Peter Doherty Institute for Infection and Immunity

description:
11_S11_L001_R1_001
Biological replicate 2

data_processing:
raw fastq files were processed using the RNAsik pipeline
Sequence reads were mapped to the Mus musculus genome (GRCm38/mm10) using STAR
Sequence reads mapping to Ensemble annotated genes were counted with featureCounts
Genes without Entrez Gene IDs were filtered, as were genes which failed to achieve a count above 10 in all samples in at least one biological group
Counts are TMM normalised.
Assembly: mm10 (NCBI build 38.1)
Supplementary files format and content: tab-delimited text files; rows represent Ensembl Gene Symbol, Colums represent Samples, counts are TMM normalised.

source_name: Liver

extract_protocol:
mRNA was isolated using the RNAeasy Micro kit (Qiagen) and was converted into cDNA using High Capacity cDNA Reverse Transcription Kit (Thermofisher)
Libraries were prepared using the SMART-seq HT Plus kit (Takara/Clontech) according to manufacturer’s instructions.

treatment_protocol: Congenically marked naïve P14 T cells were transferred into LCMV-infected mice. At >30 d p.i., mice were treated with DMSO or AGN194310 (RA antag.) every other day for 6 d and CD69+ P14 TRM cells were sorted from the liver and SI the following day

value: Day >30 LCMV

value: control


title: 6M cKO, NP 1


title: NBW/WD liver, female, biological rep1

description: Gene expression data from young adult NBW offspring fed a Western diet


title: d2-1_SI_RA antag

description:
6_S6_L001_R1_001
Biological replicate 3

source_name: Small intestine

value: Small intestine

value: AGN194310 (RA antag.)


title: A549 cells, PND_R1


title: p23098-s003_Mouse-3

status: Public on Sep 17 2024

city: Atlanta

first: Christian

last: Larsen

state: Georgia

address: 101 Woodruff Circle

department: Department of Surgery

institute: Emory University

description: VDJ TCR

data_processing:
VDJ TCR alignment and filtering for single-cell TCR sequencing samples were performed using Cell Ranger v3.1
VDJ TCR alignment and filtering for non-paired TCR sequencing samples were performed using MIXCR
Assembly: A genome build is generally not required for TCR sequencing, as it focuses on the rearranged TCR genes using V(D)J reference libraries
Supplementary files format and content: The processed data for single-cell TCR sequencing samples include filtered contig annotations, consensus annotations, clonotypes, and all contig annotations. For bulk TCR sequencing, the processed data contain clonotype information for both TCRα and TCRβ chains.
Library strategy: VDJ TCR

source_name: Lymph node

extract_protocol:
Cells were FACS sorted and used to generate single cell suspensions. Samples were loaded onto the 10X Genomics Chromium Controller according to manufacturer's protocol.
Library construction was performed using the Chromium Single Cell 5’ Library Construction Kit

tag: Sex

value: Lymph node

value: CD4 T cells

value: Skin-graft rejection


title: 6M CT, NP 4

tag: tissue


title: LBW/WD liver, female, biological rep1


title: LBW/CD liver, female, biological rep5

description: Gene expression data from young adult LBW offspring fed a control diet


title: 6M CT, NP 2

tag: genotype


title: LBW/CD liver, female, biological rep4


title: Naïve P14_02

description:
20_S20_L001_R1_001
Biological replicate 2

source_name: Spleen

value: Spleen

tag: treatment


title: d1-2_Liver_RA antag

description:
14_S14_L001_R1_001
Biological replicate 2


title: d2-1_Liver_RA antag

description:
15_S15_L001_R1_001
Biological replicate 3


title: Naïve P14_01

description:
19_S19_L001_R1_001
Biological replicate 1


title: A549 cells, XMD3

data_processing:
The quality of the RNA-seq data was assessed using fastqc v. 0.11.9 and RSeQC v. 4.0.0.
The reads were mapped to the reference genome using HiSat2 v. 2.2.1.
FeatureCounts v. 2.0.1 was used to count the number of reads overlapping with each gene as specified in the genome annotation
Assembly: hg38
Supplementary files format and content: tab-delimited text file include raw counts for each sample

value: A549 cells

value: lung cancer cells

value: XMD


title: d1-1_Liver_RA antag

description:
13_S13_L001_R1_001
Biological replicate 1


title: A549 cells, NT1


title: d1-2_SI_Ctrl

description:
2_S2_L001_R1_001
Biological replicate 2


title: d2-2_Liver_Ctrl

description:
12_S12_L001_R1_001
Biological replicate 3


title: NBW/WD liver, female, biological rep2

value: Female


title: A549 cells, COMBO3

value: COMBO


title: d1-2_SI_RA antag

description:
5_S5_L001_R1_001
Biological replicate 2


title: d1-1_SI_RA antag

description:
4_S4_L001_R1_001
Biological replicate 1


title: A549 cells, COMBO1


title: NBW/WD liver, female, biological rep3

value: Liver

value: Dunkin Hartley


title: 17_Naïve P14_01

description:
Biological replicate 1
17_S17_L001_R1_001

data_processing:
Files were aligned to Mus musculus genome (GRCm39/mm39) using STAR
Reads were mapped to Ensembl annotated genes (GRCm39 Ensembl release 105) and counted using featureCounts.  Counts were loaded into R with samples grouped by tissue and genotype status.
Genes were filtered using edgeR ‘filterByExpr’ with a ‘min.count’ of 10 and ‘min.total.count’ of 15.
Assembly: mm39 (GRCm39)
Supplementary files format and content: tab-delimited text files; rows represent gene ensmbl Symbol and the number of reads mapping to that gene.

treatment_protocol: Effector P14 T cells were transduced with either empty (Ctrl-RV) or dnRARα (dnRARα-RV) retroviruses. Transduced cells were co-transferred into LCMV infected recipient mice and isolated from the SI and liver for RNA sequencing 14 days post LCMV infection.

value: Day 14 LCMV


title: A549 cells, COMBO2


title: 16_d2-2_SI_dnRARa

description:
Biological replicate 4
16_S16_L001_R1_001

value: transduced with dnRARα (dnRARα-RV) retroviruses


title: 14_d2-2_Liver_dnRARa

description:
Biological replicate 4
14_S14_L001_R1_001


title: A549 cells, ROSCO2

value: ROSCO


title: 12_d2-1_SI_dnRARa

description:
Biological replicate 3
12_S12_L001_R1_001


title: d2-1_SI_Ctrl

description:
3_S3_L001_R1_001
Biological replicate 3

value: Day >30 LCMV

value: control


title: d1-1_Liver_Ctrl

description:
10_S10_L001_R1_001
Biological replicate 1


title: A549 cells, PNDacute1

value: PNDacute


title: LBW/CD liver, female, biological rep2


title: A549 cells, ROSCO1


title: 9_d2-1_Liver_Ctrl

description:
Biological replicate 3
9_S9_L001_R1_001

value: transduced with empty (Ctrl-RV) retroviruses


title: A549 cells, CTRL3

value: CTRL


title: d1-1_SI_Ctrl

description:
1_S1_L001_R1_001
Biological replicate 1

value: Small intestine


title: oeNC-3

value: Cholangiocarcinoma

value: Cancer cell line

value: negative control

value: no


title: A549 cells, XMD2

value: A549 cells

value: lung cancer cells

value: XMD


title: A549 cells, CTRL2


title: 18_Naïve P14_02

description:
Biological replicate 2
18_S18_L001_R1_001

value: Spleen


title: A549 cells, XMD1


title: LBW/CD liver, female, biological rep3

value: Female

value: Liver

value: Dunkin Hartley


title: 5_d1-2_Liver_Ctrl

description:
Biological replicate 2
5_S5_L001_R1_001

value: Day 14 LCMV


title: LBW/CD liver, female, biological rep1


title: A549 cells, ROSCO3

value: ROSCO


title: NBW/CD liver, female, biological rep5

description: Gene expression data from young adult NBW offspring fed a control diet


title: 13_d2-2_Liver_Ctrl

description:
Biological replicate 4
13_S13_L001_R1_001


title: 2_d1-1_Liver_dnRARa

description:
Biological replicate 1
2_S2_L001_R1_001

value: transduced with dnRARα (dnRARα-RV) retroviruses


title: 1_d1-1_Liver_Ctrl

description:
Biological replicate 1
1_S1_L001_R1_001

value: transduced with empty (Ctrl-RV) retroviruses


title: 3A-BRD4 transfected cells,anisomycin treated,  biol rep 1, input

description: TMAR1 input

data_processing:
ChIP-seq reads were aligned to human reference genome hg38 using Bowtie2-2.3.4.1. The duplicated reads were removed, and only uniquely mapped reads were used for peak identification. ChIP-seq peaks were called using MACS 3.0.0.
Assembly: hg38
Supplementary files format and content: bigWig, narrow peak (except for input samples)

source_name: cell line

growth_protocol: The DLD1 BRD4-IAA7 cells were grown in DMEM media (Gibco) supplemented with 10% fetal bovine serum at 37 °C with 7.5% CO2

extract_protocol:
Chromatin preparation and IP was performed using the SimpleChIP® Plus Enzymatic Chromatin IP Kit (Magnetic Beads) #9005 from Cell signaling Technology
ChIP-seq libraries were prepared using SWIFT_Accel-NGS 2S DNA Library Prep

treatment_protocol: DMSO or Anisomycin treated for 2 hrs

value: cell line

value: colorectal adenocarcinoma

tag: antibody

value: Anisomycin, Auxin


title: NBW/CD liver, female, biological rep4


title: WT infected with MA-SARS-CoV-2

first: Sara

last: Kass-Gergi

address: 3900 Spruce St

department: Medicine

institute: University of Pennsylvania

description: 10x Genomics Chromium Fixed RNA Profiling kit

data_processing:
After sequencing, initial data processing was performed using Cellranger (v7.2.0). Cellranger mkfastq was used to generate demultiplexed FASTQ files from the raw sequencing data. Next, Cellranger count was used to align sequencing reads to the mouse reference genome (GRCm38) and generate single-cell gene barcode matrices.
Assembly: mm10
Supplementary files format and content: Matrix files

source_name: lung

extract_protocol:
Given the requirements for ABSL-3 safety precautions, the tissue harvested from these mice needs to be fixed in paraformaldehyde for at least 24 hours prior to further handling. Logistically, the digestion of tissue into a single cell suspension prior to the required fixation step was impossible due to time and staff constraints. To facilitate these experiments, we adapted a novel technique originally developed for the analysis of fixed tissue for scRNA-seq, Tissue Fixation & Dissociation for Chromium Fixed RNA Profiling (10x Genomics, Protocol CG000553). Tissue was harvested in the ABSL-3 facility by trained personnel and minced into square millimeter sized pieces before being fixed for 24 hours at 4ºC. Samples dedicated to scRNA sequencing were fixed with Fix & Perm Buffer (10x Genomics, PN-2000517) as per manufacturer’s protocol while samples for flow cytometry were fixed in 4% PFA. Samples were then washed with PBS and the fixation reaction was quenched. scRNA samples were quenched with Quench Buffer (10x Genomics, PN-2000516) as per manufacturer’s protocol, while flow cytometry samples were quenched in solution of 50mM glycine dissolved in PBS. Tissue was then dissociated into a single cell suspension shaking vigorously at 37ºC for 1 hour in Dissociation Solution made with LiberaseTM TL (concentration 0.2mg/mL, Millipore Sigma, PN 5401020001) as per manufacturer’s protocol. Tissue was further triturated with a P1000 pipette tip 15-20 times before being filtered through a 40µM filter, which was then washed with PBS. The samples were quenched again with Quench Buffer and cells were then counted by hemocytometer before proceeding to scRNA sequencing or flow cytometry. Samples were stored at 4ºC for up to 1 week before use. Samples designated for scRNA sequencing were incubated in Quenching Buffer and Enhancer (10x Genomics, PN- 2000482) as per manufacturer’s protocol.
Single-cell sequencing libraries were created according to 10x Genomics Chromium Fixed RNA Profiling Reagents (10x Genomics, PN 1000414) and associated user protocol (User Guide CG000477 Rev D). After fixation, the samples were first hybridized using mouse specific whole transcriptome probe pairs. Cell counts were verified using a LogosBio Luna-FL automated cell counter(1.05e6 cells•mL-1and 2.8e6 cells•mL-1for sample 708L and 719L, respectively). The cells were pelletized and re-suspended in a hybridization mixture prepared using 10x Genomics Hyb Buffer B (PN 2000483) and Enhancer (PN 2000482) according to the protocol. Mouse specific WTA Probes BC001 (10x Genomics, PN 2000703) were then added to each sample at room temperature. The samples were incubated at 42°C in a Bio-Rad C1000 Touch Thermal Cycler for 16 hours.

value: lung

value: WT


title: NBW/CD liver, female, biological rep3


title: T1DM infected with MA-SARS-CoV-2

value: Streptozocin, MA-SARS-CoV-2


title: 3_d1-1_SI_Ctrl

description:
Biological replicate 1
3_S3_L001_R1_001

value: Small intestine


title: RNA-seq_aNS_WT_rep2

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC (Andrews S. 2010, FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q18 in a window of 5 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data). Only reads above 30 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl mouse genome version mm10 (ensemble release 101) using STAR 2.7.10a with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
The number of reads aligning to genes was counted with featureCounts 2.0.3 tool from the Subread package (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features). Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Differentially expressed genes were identified using DESeq2 version 1.36.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2). Only genes with a minimum fold change of +- 1.5 (log2 +-0.59), a maximum Benjamini-Hochberg corrected p-value of 0.05, and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed.
Assembly: mm10
Supplementary files format and content: library-size normalized counts

source_name: V-SVZ derived

growth_protocol: Adult neural stem-/progenitor cells were isolated from the lateral walls of the lateral ventricle and propagated in culture medium at 37°C, 5% CO2 in the presence of EGF and FGF2 to allow for the formation of free-floating neurospheres (Schramm and Schulte, 2014, Grebbin et al., 2016). Adult neurospheres (aNS) were passaged after four days and passage 1 (p1) cells were used for all experiments.

extract_protocol:
Total RNA was isolated by Rneasy Mini Kit (Qiagen). For exclusion of genomic DNA contamination, the samples were treated by on-column DNase digestion (DNase-Free DNase Set, Qiagen). Total RNA and library integrity were verified with LabChip Gx Touch 24 (Perkin Elmer).
1µg of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Takara Bio).

treatment_protocol: For transient knockdown (kd), siRNAs targeting the coding sequences of Pbx1 (Ambion, s71280), Tcf3 (Ambion, s74858), or Tcf4 (Ambion, s74830) were transfected into 1Mio p1 aNS cells per condition with Metafectene (Biontex) according to the manufacturer’s instructions. Validated non-targeting siRNAs were used as controls in all experiments (Ambion, AM4611). After 48h incubation at 37°C, cells were collected by centrifugation and used for  RNA-seq analysis.

value: V-SVZ derived

value: primary cells

value: aNS cells

value: C57Bl/6J WT


title: Control empty vector transfected cells, Anisomycin treated ,biol rep2, input

description: EVAR2 input


title: RNA-seq_aNS_Tcf4-kd_rep3

value: siRNA ɑ Tcf4 (Ambion, s74830)


title: RNA-seq_aNS_WT_rep1


title: 11_d2-1_SI_Ctrl

description:
Biological replicate 3
11_S11_L001_R1_001


title: 10_d2-1_Liver_dnRARa

description:
Biological replicate 3
10_S10_L001_R1_001

value: Liver


title: 8_d1-2_SI_dnRARa

description:
Biological replicate 2
8_S8_L001_R1_001

value: Day 14 LCMV


title: NBW/CD liver, female, biological rep2

value: Female

value: Dunkin Hartley


title: Control empty vector transfected cells, Anisomycin treated ,biol rep1, input

description: EVAR1 input


title: RNA-seq_aNS_Tcf4-kd_rep2


title: RNA-seq_aNS_Tcf4-kd_rep1


title: LBW/WD liver, male, biological rep5

description: Gene expression data from young adult LBW offspring fed a Western diet

value: Male


title: NBW/WD liver, male, biological rep3

description: Gene expression data from young adult NBW offspring fed a Western diet


title: NBW/CD liver, female, biological rep1


title: 3A-BRD4 transfected cells, biol rep 2, input

description: TMR2 input

value: cell line

value: DMSO, Auxin


title: RNA-seq_aNS_Tcf4-ctrl_rep2

value: crtl siRNA (Ambion, AM4611)


title: 6_d1-2_Liver_dnRARa

description:
Biological replicate 2
6_S6_L001_R1_001

value: transduced with dnRARα (dnRARα-RV) retroviruses


title: A549 cells, CTRL1

value: A549 cells

value: lung cancer cells

value: CTRL


title: NBW/WD liver, male, biological rep2


title: 4_d1-1_SI_dnRARa

description:
Biological replicate 1
4_S4_L001_R1_001

value: Small intestine


title: 7_d1-2_SI_Ctrl

description:
Biological replicate 2
7_S7_L001_R1_001

value: transduced with empty (Ctrl-RV) retroviruses


title: NBW/WD liver, male, biological rep1


title: LBW/WD liver, male, biological rep4


title: WT BRD4 transfected cells, Anisomycin treated ,biol rep2, input

description: WTAR2 input

value: colorectal adenocarcinoma

value: Anisomycin, Auxin


title: LBW/WD liver, male, biological rep3


title: RNA-seq_aNS_Tcf3-ctrl_rep3

value: V-SVZ derived

value: primary cells

value: aNS cells

value: C57Bl/6J WT


title: LBW/WD liver, male, biological rep2

value: Liver

value: Dunkin Hartley


title: WT BRD4 transfected cells, biol rep 2, input

description: WTR2 input

value: cell line


title: LBW/WD liver, male, biological rep1

value: Male


title: LBW/CD liver, male, biological rep4

description: Gene expression data from young adult LBW offspring fed a control diet


title: RNA-seq_aNS_Pbx1-kd_rep3

value: siRNA ɑ Pbx1 (Ambion, s71280)


title: WT BRD4 transfected cells, Anisomycin treated ,biol rep1, input

description: WTAR1 input


title: RNA-seq_aNS_Pbx1-kd_rep1


title: LBW/CD liver, male, biological rep2


title: NBW/WD liver, male, biological rep5


title: 3A-BRD4 transfected cells,anisomycin treated,  biol rep 1, ChIP

value: BRD4 (Active motif;#91301)


title: NBW/WD liver, male, biological rep4


title: RNA-seq_aNS_Tcf4-ctrl_rep1

value: crtl siRNA (Ambion, AM4611)


title: RNA-seq_aNS_Tcf4-ctrl_rep3


title: RNA-seq_aNS_Tcf3-kd_rep3

value: siRNA ɑ Tcf3 (Ambion, s74858)


title: LBW/CD liver, male, biological rep3


title: RNA-seq_aNS_Tcf3-kd_rep2


title: WT BRD4 transfected cells, Anisomycin treated ,biol rep2, ChIP


title: LBW/CD liver, male, biological rep1


title: RNA-seq_aNS_Tcf3-ctrl_rep1


title: Control empty vector transfected cells, biol rep2, input

description: EVR2 input

value: DMSO


title: 3A-BRD4 transfected cells, biol rep 1, input

description: TMR1 input

value: DMSO, Auxin


title: RNA-seq_aNS_Pbx1-kd_rep2


title: RNA-seq_aNS_Tcf3-kd_rep1


title: Control empty vector transfected cells, biol rep1, input

description: EVR1 input


title: LBW/CD liver, male, biological rep5


title: SCC25, p63 enhancer library, replicate 4, RNA

city: Albany

first: Morgan

middle: A

last: Sammons

state: NY

address: 1400 Washington Ave, Life Sciences 2075

department: Biological Sciences

institute: University at Albany - SUNY

description: PCR amplified cDNA (STARR-seq transcript)

data_processing:
Raw reads were counted by searching for exact match in the designed enhancer library pool sequences in the fastq file using a custom python script.
Assembly: Assembly: GRCh38
Supplementary files format and content: Comma-delimited, raw read counts for each enhancer variant sequence in plasmid DNA pool and STARRSeq RNA from each condition.
Library strategy: STARR-Seq

growth_protocol: All human mammary epithelial cell lines MCF-10A TP53+/+ and TP53-/- (Sigma-Millipre clls1049) were cultured in 1:1 Dulbecco’s Modified Eagle’s Medium: Ham’s F-12 (Gibco, #11330-032), supplemented with 5% Horse Serum, (Gibco, #16050-122), 20 ng/mL epidermal growth factor (Peprotech, #AF-100-15), 0.5 µg/mL hydrocortisone (Sigma, #H-0888), 100 ng/mL cholera toxin (Sigma, #C-8052), 10 µg/mL insulin (Sigma, #I-1882), and 1% penicillin-streptomycin (Gibco, #15240-062).A total of approximately 50 million cells were used for each experimental relicate.

extract_protocol:
Total RNA was extracted (Quick RNA, Zymo, #R1055). 30 µg per sample of poly-adenylated mRNA was isolated using oligo d(T) beads (NEB E7490L).
Resulting mRNA was split into 6 separate reactions and cDNA was synthesized using a gene-specific primer (SL1972) and MultiScribe Reverse Transcriptase (Invitrogen, 4311235) . Following cDNA synthesis, all cDNA samples were pooled and one junction-PCR reaction was performed with 16 cycles (SL1973, SL1974) and I5 and i7 primers from NEBNext Oligo Kit (E7600S) were used for Illumina barcoding with between 5 and 9 cycles. MPRA plasmid DNA pools were amplified with i5 and i7 primers as a control for oligo representation. All libraries were pooled and sequenced as single-end, 100bp on an Illumina NextSeq 2000 instrument at the University at Albany Center for Functional Genomics.

treatment_protocol: 10 µg of plasmid library were transfected per 5 mln cells via lipofection (Polyplus #101000046, #101000025). For MCF10A TAp63β inducible cell line and negative control (Gus) cell line, doxycycline was added at 500 ng/ml at the same time as transfection. Cells were harvested after 24h.

value: WT


title: WT BRD4 transfected cells, biol rep 1, input

description: WTR1 input

value: colorectal adenocarcinoma


title: seCLIP IP Etoposide CHD4

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

data_processing:
Fastq files were generated Illumina’s BaseSpace platform and overall sequencing quality was analyzed with the FastQC script.
For seCLIP-seq, reads were mapped to hg19 using STAR, and then normalized based on the read depth.
Assembly: hg19
Supplementary files format and content: bw = bigwig
Library strategy: seCLIP-seq

source_name: Bone Marrow

growth_protocol: Cells were grown in DMEM supplemented with 10% FCS and 1% penicillin/streptomycin

extract_protocol: seCLIP DNA was used for library preparation with NEBNext Ultra II Directional DNA Library Prep kit. The libraries were amplified with 12-16 PCR cycles depending on the input DNA. The concentration and size distribution of the libraries were determined on a Fragment Analyzer using the NGS Fragment High Sensitivity Analysis Kit (1-6,000 bp; Agilent Technologies). The libraries were sequenced on the NextSeq2000 Illumina platform for 75 cycles. Base calling was performed using Illumina’s BaseSpace platform

treatment_protocol: Treatment as indicated

value: Bone Marrow

value: osteosarcoma cell line

value: wt

value: Etoposide, 2h, 20uM


title: seCLIP IN Etoposide CHD4


title: RNA-seq_aNS_Tcf3-ctrl_rep2

value: V-SVZ derived

value: primary cells

value: aNS cells

value: C57Bl/6J WT


title: RNA-seq_aNS_Pbx1-ctrl_rep3


title: seCLIP IN Control CHD4


title: RNA-seq_aNS_Pbx1-ctrl_rep2


title: RNA-seq_aNS_Pbx1-ctrl_rep1


title: WT BRD4 transfected cells, Anisomycin treated ,biol rep1, ChIP

city: Bethesda

value: cell line

value: Anisomycin, Auxin


title: seCLIP IP Control CHD4


title: Control empty vector transfected cells, Anisomycin treated ,biol rep2, ChIP

value: BRD4 (Active motif;#91301)


title: BLISS_siNEAT1_Etoposide_rep1

description: BLISS seq

data_processing:
Base calling was perfomed using Illumina's FASTQ Generation software v1.0.0. Reads were demultiplexed according to sample-barcodes with UMI-tools v1.0.1. The barcodes used are as follows: A1: CATCACGC, A2: GTCGTTCC, A3: TGATGATC, A4: ACGACATC
Reads were aligned with Bowtie2 v2.3.4.1 to hg19 and filtered with bedtools intersect v2.26.0. Reads were counted for specific regions using the R package exomeCopy v1.18.0. Following deduplication and read normalization, bedgraph files were generated from the alignment files.
Assembly: hg19
Supplementary files format and content: For BLISS sequencing samples, processed files are in bedgraph format for visualization in a genome-browser.
Library strategy: BLISS-seq

growth_protocol: Cells were grown in DMEM supplemented with 10% FCS and 1% penicillin/streptomycin.

extract_protocol:
First, the DSBs in the genome were blunted, followed by adapter ligation to the break-sites. DNA was then purified and fragmented.
In vitro transcription was used to generate single-stranded RNA-fragments from the adapter-ligated DNA. A second adapter-ligation was then followed by reverse-transcription. Single-stranded cDNA was used as template for a PCR that also introduced Illumina sequencing-adapter sites and sample-specific indexes. Overall, libraries were prepared for sequencing using a modified NEBNext Small RNA library preperation protocol (following the main steps outlined in the paper "Yan et al., 2017, Nature Communications").

treatment_protocol: Treatment as indicated. Cells were either transfected with control siRNA or with siRNA targeting NEAT1 and harvested for analysis after 48 hours. Where indicated, cells were treated with etoposide for 2 hours.

value: siNEAT1 transfection, 48 h

value: Etoposide, 20 uM, 2 h


title: BLISS_siCtrl_Etoposide_rep2

description: BLISS seq

value: siCtrl transfection, 48 h


title: BLISS_siCtrl_rep2

description: BLISS seq


title: BLISS_siNEAT1_Etoposide_rep2

description: BLISS seq


title: 3A-BRD4 transfected cells, biol rep 1, ChIP

value: DMSO, Auxin


title: 3A-BRD4 transfected cells, biol rep 2, ChIP


title: NBW/CD liver, male, biological rep5

value: Male

value: Liver

value: Dunkin Hartley


title: BLISS_siCtrl_Etoposide_rep1

description: BLISS seq

value: Bone Marrow

value: osteosarcoma cell line


title: Control empty vector transfected cells, Anisomycin treated ,biol rep1, ChIP

value: colorectal adenocarcinoma


title: NBW/CD liver, male, biological rep2


title: NBW/CD liver, male, biological rep4


title: NBW/CD liver, male, biological rep3


title: BLISS_siCtrl_rep1

description: BLISS seq


title: WT BRD4 transfected cells, biol rep 2, ChIP


title: NBW/CD liver, male, biological rep1


title: KO-NLS, KO+Nuclear-IMPDH2, NoGuan, rep3

city: Barcelona

first: Sdelci

last: Lab

address: Dr. Aiguader 88

department: Genome Biology

country: Spain

institute: Centre for Genomic Regulation (CRG)

data_processing:
Trim-Galore (v. 0.6.10) for adapter removal
Salmon(v. 1.10.0) for Index creation with decoys
Salmon (v. 1.10.0) for alignment
Assembly: hg19
Supplementary files format and content: sf.gz contains salmon output for each sample
Supplementary files format and content: csv.gz contains salmon output for all samples

growth_protocol: MDA-MB-231 cells were cultured in DMEM media (Gibco; #11966025) supplemented with 10% Fetal Bovine Serum (FBS, Gibco; #10270106) and 1% penicillin/streptomycin (Gibco; #15140122) at 37ºC and 5% CO2

extract_protocol:
RNA was extracted using the PureLink RNA mini kit (Thermo Fisher Scientific; #12183018A),libraries were prepared from 500 ng of total RNA using the TruSeq stranded mRNA Library Prep (Illumina; #20020594)
Libraries were prepared using the TruSeq stranded mRNA Library Prep (ref. 20020595, Illumina) according to the manufacturer's protocol

treatment_protocol: When indicated (+G) cells were cultured in the presence of guanosine supplementation (400µM)

value: TNB

value: No-Treatment


title: KO-NES, KO+Cyt-IMPDH2, NoGuan, rep3


title: KO-NES, KO+Cyt-IMPDH2, NoGuan, rep2


title: temporo-occipital cortex, A+/Pwt/wt, female, mouse 329

city: Kuopio

first: Sami

last: Heikkinen

address: Yliopistonranta 1E

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

description: column name in the common processed data matrices: mVC_329

data_processing:
The 150-nucleotide pair-end RNA-seq reads were quality-controlled using FastQC (version 0.11.7).
Reads were trimmed with Trimmomatic (version 0.39) to remove Illumina sequencing adapters and poor quality read ends, using as essential settings: ILLUMINACLIP:2:30:10:2:true, SLIDINGWINDOW:4:10, LEADING:3, TRAILING:3, MINLEN:50.
Trimmed reads were aligned to the Gencode mouse transcriptome version M25 (for genome version GRCm38) using STAR (version 2.7.9a) with essential non-default settings: --seedSearchStartLmax 12, --alignSJoverhangMin 15, --outFilterMultimapNmax 100, --outFilterMismatchNmax 33, --outFilterMatchNminOverLread 0, --outFilterScoreMinOverLread 0.3, and --outFilterType BySJout.
The unstranded, uniquely mapping, gene-wise counts for primary alignments produced by STAR were collected in R (version 4.2.2 or 4.3.2) using Rsubread::featureCounts (version 2.12.0 or 2.12.3).
Assembly: GRCm38
Supplementary files format and content: raw.counts_...txt: raw counts from featureCounts
Supplementary files format and content: normalized.counts_...txt: vst-normalized counts for genes with at least 10 reads for 3 samples

source_name: temporo-occipital cortex

growth_protocol: APPswe/PS1dE9 transgenic mouse line (later simply APP/PS1 line) on C57Bl/6J background was used as a model for AD (Jankowsky et al., 2004). This mouse co-expresses in a single transgene a chimeric mouse/human APP695 harboring the Swedish K670M/N671L mutations (Mo/Hu APPswe) and human PS1 with the exon-9 deletion (PS1dE9) under mouse prion protein promoter. This line was crossbred with a PLCG2-P522R KI mouse line generated using CRISPR/Cas9 assisted gene editing in C57Bl/6J background as we have reported before (Takalo et al., 2020). Wildtype and APP/PS1 mice were used as controls. The mice were kept in an environment with constant temperature, 22 ± 1 oC, humidity 50 – 60 %, lights on 07:00-19:00, with food and water available ad libitum.

extract_protocol:
Mouse temporo-occipital cortex homogenate was homogenized in TRI Reagent (#T9424, Sigma-Aldrich) after which chloroform was added (one fifth of the volume of TRI Reagent) and the tubes were shaken vigorously. Mixtures were incubated at room temperature for 5 min and the phase separation was performed by centrifugation at 12000× g for 20 min at +4 oC. RNA was precipitated from the aqueous phase with 2-propanol by mixing and incubating at room temperature for 30 min. Samples were centrifuged at 12000× g for 25 min at +4 oC and the pellets were washed twice with 75 % ethanol. RNA pellets were air-dried and dissolved in RNAse-free H2O. Isolated mouse CD11b+ microglia were resuspended in DPBS and immediately mixed with lysis buffer of the High Pure RNA Isolation kit (#11828665001, Roche). RNA was extracted following the kit instructions and sent for sequencing to Novogene Europe (below).
Library preparation and RNA sequencing was conducted by Novogene (Cambridge, UK) and executed with an Illumina high-throughput sequencing platform. mRNA enrichment was performed with oligo(dT) bead pulldown, from where pulldown material was subjected to fragmentation, followed by reverse transcription, second strand synthesis, A-tailing, and sequencing adaptor ligation. The final amplified and size selected library comprised of 250–300 bp insert cDNA and paired-end 150 bp. Sequencing yielded reads for 20.2–31.34 and 29.4–49.9 million library fragments per CD11b+ mouse microglia, and mouse cortex, respectively.

treatment_protocol: Tissue and acutely isolated tissue resident cells, no treatments

value: temporo-occipital cortex

value: female

tag: genotype apde9

value: A+

tag: genotype plcg2_p522r

value: wt/wt


title: temporo-occipital cortex, A-/Pwt/wt, female, mouse 312

description: column name in the common processed data matrices: mVC_312

value: A-


title: KO-NES, KO+Cyt-IMPDH2, NoGuan, rep1

tag: cell type


title: KO-NLS, KO+Nuclear-IMPDH2, NoGuan, rep2


title: KO-NLS, KO+Nuclear-IMPDH2, NoGuan, rep1


title: WT BRD4 transfected cells, biol rep 1, ChIP

value: cell line

value: BRD4 (Active motif;#91301)


title: Control empty vector transfected cells, biol rep1, ChIP

value: DMSO


title: KO-WT, KO+IMPDH2, NoGuan, rep3


title: Control empty vector transfected cells, biol rep2, ChIP


title: 3A-BRD4 transfected cells,anisomycin treated,  biol rep 3

data_processing:
RNA-seq reads were aligned to human reference genome (hg38) with STAR aligner (2.7.8a). Raw read counts were obtained using htseq-count (0.11.4).
Assembly: hg38
Supplementary files format and content: tab-delimited text files including raw counts for each sample

source_name: human cell line

extract_protocol:
RNA was isolated from empty vector, WT BRD4 and 3A-BRD4 transfected cells using the Micro RNeasy-Plus Kit (Qiagen)
Libraries were prepared using  the Illumina Illumina® Stranded mRNA Prep according to the manufacturers' instructions.

value: human cell line

value: colorectal carcinoma

value: 3A-Brd4 transfected, anisomycin treated

value: Anisomycin


title: temporo-occipital cortex, A+/Pwt/wt, female, mouse 259

description: column name in the common processed data matrices: mVC_259


title: KO-WT, KO+IMPDH2, NoGuan, rep1


title: temporo-occipital cortex, A+/Pwt/wt, female, mouse 257

description: column name in the common processed data matrices: mVC_257


title: KO-WT, KO+IMPDH2, NoGuan, rep2


title: temporo-occipital cortex, A+/Pki/ki, female, mouse 222

description: column name in the common processed data matrices: mVC_222

value: ki/ki


title: KO+G, KO, Guan, rep2

value: Guanosine supplementation


title: KO+G, KO, Guan, rep1


title: 3A-BRD4 transfected cells,anisomycin treated,  biol rep 1


title: KO+G, KO, Guan, rep3


title: 3A-BRD4 transfected cells,anisomycin treated,  biol rep 2


title: temporo-occipital cortex, A+/Pki/ki, female, mouse 216

description: column name in the common processed data matrices: mVC_216


title: KO-G, KO, NoGuan, rep2


title: KO-G, KO, NoGuan, rep3


title: temporo-occipital cortex, A+/Pki/ki, female, mouse 203

description: column name in the common processed data matrices: mVC_203


title: KO-G, KO, NoGuan, rep1


title: WT BRD4 transfected cells, Anisomycin treated ,biol rep3

value: WT Brd4 transfected, anisomycin treated


title: temporo-occipital cortex, A+/Pki/ki, female, mouse 184

description: column name in the common processed data matrices: mVC_184


title: temporo-occipital cortex, A+/Pwt/wt, female, mouse 236

description: column name in the common processed data matrices: mVC_236


title: WT, Control, NoGuan, rep3

value: TNB

value: WT


title: WT BRD4 transfected cells, Anisomycin treated ,biol rep2


title: microglia, A-/wt/wt, male, mouse 94

description: column name in the common processed data matrices: MTa001_94_M_WT_b1

source_name: whole brain

value: whole brain

value: acutely isolated microglia

value: male


title: WT, Control, NoGuan, rep2

value: No-Treatment


title: WT BRD4 transfected cells, Anisomycin treated ,biol rep1


title: CnR STM2457+4-OHT CHD4

data_processing:
library strategy: Cut&Run-seq
Fastq files were generated Illumina’s BaseSpace platform and overall sequencing quality was analyzed with the FastQC script.
For Cut&Run-seq, reads were mapped to hg19 withBowtie2,  and then normalized based on the read depth.
Assembly: hg19
Supplementary files format and content: bedgraph

extract_protocol:
Cut&Run DNA
Cut&Run DNA was used for library preparation with NEBNext Ultra II Directional DNA Library Prep kit. The libraries were amplified with 12-16 PCR cycles depending on the input DNA. The concentration and size distribution of the libraries were determined on a Fragment Analyzer using the NGS Fragment High Sensitivity Analysis Kit (1-6,000 bp; Agilent Technologies). The libraries were sequenced on the NextSeq2000 Illumina platform for 75 cycles. Base calling was performed using Illumina’s BaseSpace platform

value: Bone Marrow

value: U2OS DIvA

value: osteosarcoma cell line

value: 4-OHT inducible AsiSI


title: Control empty vector transfected cells, Anisomycin treated ,biol rep3

value: human cell line

value: Control, anisomycin treated


title: microglia, A-/ki/ki, male, mouse 84

description: column name in the common processed data matrices: MTa001_84_M_KI_b1

value: A-


title: CnR 4-OHT CHD4

value: 4-OHT, 10µM 4h


title: CnR IgG

value: IgG


title: microglia, A-/ki/ki, male, mouse 139

description: column name in the common processed data matrices: MTa001_139_M_KI_b1

value: ki/ki


title: CnR H3K4me3


title: Control empty vector transfected cells, Anisomycin treated ,biol rep2

value: colorectal carcinoma

value: Anisomycin


title: seCLIP Etoposide IgG

data_processing:
library strategy: seCLIP-seq
Fastq files were generated Illumina’s BaseSpace platform and overall sequencing quality was analyzed with the FastQC script.
For seCLIP-seq, reads were mapped to hg19 using STAR, and then normalized based on the read depth.
Assembly: hg19
Supplementary files format and content: bigwig

extract_protocol:
seCLIP
seCLIP DNA was used for library preparation with NEBNext Ultra II Directional DNA Library Prep kit. The libraries were amplified with 12-16 PCR cycles depending on the input DNA. The concentration and size distribution of the libraries were determined on a Fragment Analyzer using the NGS Fragment High Sensitivity Analysis Kit (1-6,000 bp; Agilent Technologies). The libraries were sequenced on the NextSeq2000 Illumina platform for 75 cycles. Base calling was performed using Illumina’s BaseSpace platform

value: wt

value: Etoposide, 2h, 20µM


title: seCLIP Control IgG


title: Control empty vector transfected cells, Anisomycin treated ,biol rep1


title: microglia, A-/ki/ki, male, mouse 104

description: column name in the common processed data matrices: MTa001_104_M_KI_b1

value: whole brain

value: acutely isolated microglia


title: 3A-BRD4 transfected cells, biol rep 3

value: 3A-Brd4 transfected, untreated

value: DMSO


title: seCLIP Control METTL3

value: Bone Marrow


title: CHART DIvA+4-OHT-COs

data_processing:
library strategy: Capture hybridization analysis of RNA targets (CHART)-seq
Fastq files were generated Illumina’s BaseSpace platform and overall sequencing quality was analyzed with the FastQC script.
For CHART-seq, reads were mapped to hg19 withBowtie2,  and then normalized based on the read depth.
Assembly: hg19
Supplementary files format and content: bedgraph

extract_protocol:
CHART DNA
CHART DNA was used for library preparation with NEBNext Ultra II Directional DNA Library Prep kit. The libraries were amplified with 12-16 PCR cycles depending on the input DNA. The concentration and size distribution of the libraries were determined on a Fragment Analyzer using the NGS Fragment High Sensitivity Analysis Kit (1-6,000 bp; Agilent Technologies). The libraries were sequenced on the NextSeq2000 Illumina platform for 75 cycles. Base calling was performed using Illumina’s BaseSpace platform

value: U2OS DIvA

value: osteosarcoma cell line

tag: capturing oligos

value: no oligoes


title: microglia, A-/wt/wt, male, mouse 102

description: column name in the common processed data matrices: MTa001_102_M_WT_b1

value: male

value: wt/wt


title: CHART DIvA+STM2457+4-OHT-COs

tag: cell line

value: 4-OHT inducible AsiSI


title: 3A-BRD4 transfected cells, biol rep 2

value: human cell line


title: WT, Control, NoGuan, rep1

value: TNB

value: WT

value: No-Treatment


title: CHART DIvA+STM2457+4-OHT+COs

value: Pool, 100 nM


title: CHART DIvA+4-OHT+COs


title: microglia, A+/ki/ki, female, mouse 405

description: column name in the common processed data matrices: Mta002_405_F_KIxAPdE9_b2

value: female

value: A+

value: ki/ki


title: microglia, A+/ki/ki, female, mouse 394

description: column name in the common processed data matrices: Mta002_394_F_KIxAPdE9_b2

value: whole brain

value: acutely isolated microglia


title: CHART wt+4-OHT+COs

value: Bone Marrow

value: wt


title: microglia, A+/wt/wt, female, mouse 380

description: column name in the common processed data matrices: Mta002_380_F_APdE9_b2


title: WT BRD4 transfected cells, biol rep 1

value: colorectal carcinoma

value: WT Brd4 transfected, untreated

value: DMSO


title: seCLIP Etoposide METTL3

value: osteosarcoma cell line

value: Etoposide, 2h, 20µM


title: Control empty vector transfected cells, biol rep3

value: human cell line

value: Control, untreated


title: Anterior chicken embryo HH10 10X single-cel RNA-seq

description: 10X 3' single-cell RNA-seq

data_processing:
Single-cell RNA-seq data was demultiplexed using 10x Genomics Cell Ranger v7.1.0 mkfastq (Zheng et al., 2017), followed by alignment to the bGalGal1.mat.broiler.GRCg7b genome assembly with Ensembl 110 gene models and subsequent quantification using cellranger count
Assembly: bGalGal1.mat.broiler.GRCg7b genome assembly with Ensembl 110 gene models
Supplementary files format and content: Tab-separated values files and matrix files

organism: Gallus gallus

source_name: Primary chicken embryo tissue

growth_protocol: Chicken embryos were reared for approximately 48 hours to HH10

extract_protocol:
Cells were dissociated from dissect tissue using Dispase/Trypsin as previosuly published DOI: 10.1016/j.xpro.2021.100414
Libraries were generated in accordance with CG000315 Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index). Libraries were sequenced in accordance with 10X recommendations.
3' single-cell RNA-seq

treatment_protocol: Anterior regions of 10 embryos was manually dissected.

value: Primary chicken embryo tissue


title: microglia, A-/wt/wt, male, mouse 101

description: column name in the common processed data matrices: MTa001_101_M_WT_b1

value: male

value: A-

value: wt/wt


title: Control empty vector transfected cells, biol rep2


title: microglia, A+/ki/ki, female, mouse 335

description: column name in the common processed data matrices: Mta002_335_F_KIxAPdE9_b2

value: female

value: A+


title: 5-4-16M

city: Toronto

first: Michael

middle: D

last: Taylor

address: 686 Bay St

institute: The Hospital for Sick Children

description: processed_rnaseq_count_matrix_lazy_piggy_tumours.txt

data_processing:
Paired-end FASTQs were aligned to mm9 using STAR (2.5.4b). Gene-level raw counts were extracted from the ReadsPerGene outs.
Assembly: mm9
Supplementary files format and content: Gene x sample RNA count matrices.

extract_protocol:
RNA was extracted using the RNEasy Mini Kit (Invitrogen).
Libraries were generated using the TruSeq RNA Sample Preparation kit (Illumina).

value: TAM-


title: 5-30-16P

value: TAM+


title: 10-23-15


title: 3A-BRD4 transfected cells, biol rep 1

value: 3A-Brd4 transfected, untreated


title: microglia, A+/wt/wt, female, mouse 331

description: column name in the common processed data matrices: Mta002_331_F_APdE9_b2

value: whole brain

value: acutely isolated microglia


title: WT BRD4 transfected cells, biol rep 3

value: colorectal carcinoma

value: WT Brd4 transfected, untreated


title: WT BRD4 transfected cells, biol rep 2

value: DMSO


title: CHART wt+4-OHT-COs

value: Bone Marrow

value: osteosarcoma cell line

value: wt

value: no oligoes


title: microglia, A+/wt/wt, female, mouse 367

description: column name in the common processed data matrices: Mta002_367_F_APdE9_b2


title: 3-23-16M


title: 4-14-16M


title: Sample2

city: Shenyang

first: Bitian

last: Liu

state: Liaoning

address: No.36 Sanhao Street

institute: China Medical University

description: 10x Genomics

data_processing:
The sequencing platform is novaseq 6000. After the data is off the machine, RTA (real time analysis) is used to convert it into the original BCL file, and the version is v3.4.4; It is split by bcl2fastq (btq) software and converted into FQ, version v2.19. Fastp software is used for quality control, version 0.19.7, involving the parameter fastp-G-Q5-U50-N 15-L150.
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz
Supplementary files format and content: features.tsv.gz
Supplementary files format and content: matrix.mtx.gz

source_name: Cancerous prostate tissue

extract_protocol:
The cell suspension was loaded into Chromium microfluidic chips with 3’ (v2 or v3, depends on project) chemistry and barcoded with a 10×Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed
sequencing libraries constructed with reagents from a Chromium Single Cell 3’ v2(v2 or v3, depends on project) reagent kit (10X Genomics) according to the manufacturer’s instructions. Sequencing was performed with Illumina (HiSeq 2000 or NovaSeq , depends on project) according to the manufacturer’s instructions (Illumina).

value: Cancerous prostate tissue

value: Cells isolated from cancerous prostate


title: Control empty vector transfected cells, biol rep1

first: Dinah

last: Singer

address: Building 10, Room 4B-17

institute: National Cancer Institute

value: human cell line

value: Control, untreated


title: microglia, A-/wt/wt, female, mouse 245

description: column name in the common processed data matrices: MTa002_245_F_WT_b3

value: female

value: A-

value: wt/wt


title: microglia, A+/wt/wt, female, mouse 375

description: column name in the common processed data matrices: Mta002_375_F_APdE9_b2

value: A+


title: 4-14-16N

value: TAM+


title: 4-14-16Q

value: TAM-


title: Sample1

description: 10x Genomics


title: 3-9-16M


title: 5-20-16M


title: 5-31-16M


title: microglia, A+/ki/ki, female, mouse 244

description: column name in the common processed data matrices: Mta002_244_F_KIxAPdE9_b2

value: whole brain

value: acutely isolated microglia

value: ki/ki


title: KO-KAP1-E2-1h.

city: SAN DIEGO

first: Lishuan

last: Wang

state: California

address: 9500 Gilman Drive

institute: UCSD

data_processing:
cutadapt: -u 10 -U 10 -a AGATCGGAAGAG -A GATCGTCGGACT
Quality control: FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and TRIMMOMATIC (http://www.usadellab.org/cms/?page=trimmomatic) were used to inspect the quality of the sequencing reads, and to trim the sequencing adaptors, if necessary.
bowtie2: -q -5 10 --very-sensitive-local --no-unal -N 1 -p 24
makeTagDirectory: -format sam -keepAll -tbp 1 -checkGC -sspe -fragLength given
makeUCSCfile
Assembly: hg38
Supplementary files format and content: bigWig
Supplementary files format and content: BedGraph
Library strategy: PRO-seq

molecule: nuclear RNA

growth_protocol: MCF7 cells were maintained at 37°C and 5% CO2 in Dulbecco's modified Eagle's medium (DMEM, GIBCO/Invitrogen), supplemented with 10% fetal bovine serum (FBS, GIBCO/Invitrogen). For hormone treatments, cells were incubated at 37°C and 5% CO2 for at least 3 days in phenol red-free DMEM (GIBCO/Invitrogen) supplemented with 5% charcoal dextran-stripped FBS (GIBCO/Invitrogen).

extract_protocol:
The resultant nuclei were washed two more times with 10ml lysis buffer and finally resuspended in 100 μl of freezing buffer (50mM Tris-HCl pH8.3, 40% glycerol, 5mM MgCl2, 0.1mM EDTA). For the run-on assay, resuspended nuclei were mixed with an equal volume of reaction buffer (10mM Tris-HCl pH 8.0, 5mM MgCl2, 1mM DTT, 300mM KCl, 20 units of SUPERase-In, 1% sarkosyl, 250 μM A/GTP, 50 µM biotin-11-C/UTP (Perkin-Elmer) and incubated for 5 min at 30°C. The resultant nuclear-run-on RNA (NRO-RNA) was then extracted with TRIzol® LS reagent (Life Technologies, Cat# 10296-028) following manufacturer’s instructions. NRO-RNA was fragmented to ∼200-500nt by alkaline base hydrolysis on ice for 30 min and and neutralized by adding 1× volume of 1 M Tris-HCl pH 6.8, Excessive salt and residual NTPs were removed by using P-30 column (Bio-Rad, Cat# 732-6250), followed by treatment with DNase I (Promega Cat# M6101) and antarctic phosphatase (NEB Cat# M0289L). Fragmented nascent RNA was bound to 10 µl of MyOne Streptavidin C1 dynabeads (Invitrogen, Cat# 65001) following the manufacturer’s instructions. The beads were washed twice in high salt (2 M NaCl, 50 mM Tris-HCl pH 7.5, 0.5% Triton X-100, 0.5 mM EDTA), once in medium salt (1M NaCl, 5 mM Tris-HCl pH 7.5, 0.1% Triton X-100, 0.5 mM EDTA), and once in low salt (5 mM Tris-HCl pH 7.5, 0.1% Triton X-100).
NEBNext® Small RNA Library Prep kit (NEB, Cat# E7330)

treatment_protocol: 17-β-Estradiol (E2; Steraloids, Inc.) was added to a final concentration of 100 nM.

value: Human breast cancers


title: 3-4-15M


title: microglia, A-/wt/wt, female, mouse 243

description: column name in the common processed data matrices: Mta002_243_F_WT_b3


title: 4-7-15KWC


title: WT-E2-1h.


title: microglia, A-/wt/wt, female, mouse 242

description: column name in the common processed data matrices: MTa002_242_F_WT_b3


title: 6-17-16M


title: microglia, A-/wt/wt, female, mouse 236

description: column name in the common processed data matrices: Mta002_236_F_WT_b3


title: KO-KAP1-Veh-1h.


title: 6-2-16M


title: 7-12-16N


title: 7-8-16T


title: WT-Veh-1h.


title: 2-11-16P


title: 11-25-15N


title: shKAP1-E2-1h-rep2


title: microglia, A-/wt/wt, female, mouse 224

description: column name in the common processed data matrices: MTa002_224_F_WT_b3


title: 11-18-15M


title: microglia, A-/wt/wt, female, mouse 225

description: column name in the common processed data matrices: Mta002_225_F_WT_b3


title: 11-13-15M


title: 1-7-16S


title: microglia, A-/wt/wt, female, mouse 223

description: column name in the common processed data matrices: Mta002_223c_F_WT_b3


title: 1-21-16M


title: shKAP1-E2-1h-rep1


title: 15_d2-2_SI_Ctrl

description:
Biological replicate 4
15_S15_L001_R1_001

data_processing:
Files were aligned to Mus musculus genome (GRCm39/mm39) using STAR
Reads were mapped to Ensembl annotated genes (GRCm39 Ensembl release 105) and counted using featureCounts.  Counts were loaded into R with samples grouped by tissue and genotype status.
Genes were filtered using edgeR ‘filterByExpr’ with a ‘min.count’ of 10 and ‘min.total.count’ of 15.
Assembly: mm39 (GRCm39)
Supplementary files format and content: tab-delimited text files; rows represent gene ensmbl Symbol and the number of reads mapping to that gene.

extract_protocol:
mRNA was isolated using the RNAeasy Micro kit (Qiagen) and was converted into cDNA using High Capacity cDNA Reverse Transcription Kit (Thermofisher)
Libraries were prepared using the SMART-seq HT Plus kit (Takara/Clontech) according to manufacturer’s instructions.

value: Small intestine

value: transduced with empty (Ctrl-RV) retroviruses

value: Day 14 LCMV


title: 2-11-16M


title: OT-I_WT_02

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

description: Biological replicate 2

data_processing:
FASTQ files were output using standard Illumina protocols and software
1: Trimmed sequencing reads were aligned with bowtie2.
2: PCR duplicates were Identified with Picard toools
3: Accessibility peaks and bigwigs were generated using macs2.
Assembly: fastq reads were aligned using Bowtie2 to the Mus musculus reference genome (GRCm39/mm39)
Supplementary files format and content: bigwig files of each library

extract_protocol:
Frozen cells were thawed and washed once in cold PBS. 70,000-200,000 cells were lysed using the 10x single-cell ATAC lysis buffer and centrifuged for 10 min at 4ºC/500g. Transposition reaction was performed using Illumina Tagment DNA TDE1 Enzyme and Buffer Kits (FC-121-1030), using 12.5 µL 2x TD Buffer, 10.5 µL H2O, and 2 µL transposase per reaction, and incubated at 37ºC for 30min. TE Buffer was added to halt the transposition reaction, then the product was purified using Qiagen Minelute (28004). The elute underwent PCR using Phusion High-Fidelity PCR MasterMix (NEB, M0531S) as follows; 5 min of initial extension at 72ºC, followed by 16 cycles of PCR (98ºC/15s, 63ºC/30s, 72ºC/60s), followed by final extension (72ºC/3min). The resulting product was purified using AMPure XP Beads (A63881), eluted in 20 µL H2O, and quantified using a Quibit dsDNA HS Assay Kit (Invitrogen) and a High Sensitivity DNA chip run on a Bioanalyzer 2100 system.
The final product was sequenced on a NovaSeq. For each bulk ATAC-seq library, adapters were trimmed, and fastq reads were aligned using Bowtie2
OMNI ATAC-seq (Corces et al. 2017)

treatment_protocol: WT and Tbx21-/- OT-I T cells were isolated from the SI 8 d following LCMV-OVA infection. CD69+ OT-I T cells were sorted and cryopreserved in DMSO (10%).

value: OT-I

value: WT

value: d8 LCMV


title: 11-27-15M


title: Control empty vector transfected cells, JQ1 treated ,biol HCT116 rep2

extract_protocol:
RNA was isolated from empty vector and BRD4 transfected cells using the Micro RNeasy-Plus Kit (Qiagen)
Libraries were prepared using  the Illumina Illumina® Stranded mRNA Prep according to the manufacturers' instructions.

value: colorectal carcinoma

tag: transfection

value: Control empty vector


title: 2-12-16N


title: shNTC-E2-1h-rep1


title: OT-I_WT_01

description: Biological replicate 1


title: 4-5-17M


title: 3-15-17N


title: shNTC-Veh-1h-rep1


title: OT-I_TbetKO_02

description: Biological replicate 2


title: 1-5-17M


title: 3-10-17N


title: shKAP1-Veh-1h-rep1


title: OT-I_TbetKO_01

description: Biological replicate 1


title: 12-30-16P


title: WT-E2-1h-Rb-Igg-Rep1

data_processing:
cutadapt: -u 15 -U 15 -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -b -B
Quality control: FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and TRIMMOMATIC (http://www.usadellab.org/cms/?page=trimmomatic) were used to inspect the quality of the sequencing reads, and to trim the sequencing adaptors, if necessary.
bowtie2:  -q --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700
makeTagDirectory: -format sam -keepAll -tbp 1 -checkGC -sspe -fragLength given
makeUCSCfile
Assembly: hg38
Supplementary files format and content: bigWig
Supplementary files format and content: BedGraph
Library strategy: CUT&Tag

growth_protocol: MCF7 cells were maintained at 37°C and 5% CO2 in Dulbecco's modified Eagle's medium (DMEM, GIBCO/Invitrogen), supplemented with 10% fetal bovine serum (FBS, GIBCO/Invitrogen). For hormone treatments, cells were incubated at 37°C and 5% CO2 for at least 3 days in phenol red-free DMEM (GIBCO/Invitrogen) supplemented with 5% charcoal dextran-stripped FBS (GIBCO/Invitrogen). 17-β-Estradiol (E2; Steraloids, Inc.) was added to a final concentration of 100 nM.

extract_protocol:
CUT&Tag standard Protocol
PCR Ampfication

value: Rb-Igg(Millipore, 12-370)


title: 12-7-16M


title: Y_AU1855_sgControl

first: ZHUXUAN

last: LI

address: 417 E 68th St

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

data_processing:
FASTQ files of bulk-cell RNA-sequencing data were aligned to a custom GRCm38 / mm10 reference containing additional transgenes using STAR (version 2.7.5a). Read counts were generated using the Python package HTSeq-count (version 0.13.5). The generated sample-gene count matrices were analyzed using a combination of published packages and custom scripts. The specific analytical workflows employed are summarized below.
Assembly: mm10
Supplementary files format and content: txt file includes raw counts of each sample
Supplementary files format and content: txt file includes RPKM counts of each sample

source_name: lung adenocarcinoma

growth_protocol: Samples are all derived from primary tumors by cell sorting. No cell culture step is involved.

extract_protocol:
RNA extraction was performed using RNeasy Mini Kit (Qiagen, #217004) on the QIAcube Connect (Qiagen) according to the manufacturer’s protocol.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 2 ng total RNA with RNA integrity numbers ranging from 9.0 to 9.7 underwent amplification using the SMART-Seq v4 Ultra Low Input RNA Kit (Clonetech,  #63488), with 12 cycles of amplification. Subsequently, 10 ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems, #KK8504) using 8 cycles of PCR. Samples were barcoded and run on a NovaSeq 6000 in a PE100 run, using the NovaSeq 6000 S2 Reagent Kit (200 Cycles) (Illumina).

treatment_protocol: Tumors derived from aged (A_Mouse ID) and young (Y_Mouse ID) were subjected to CRISPR-Cas9 mediated gene knockout.

value: lung adenocarcinoma

value: Primary lung tumor cells

tag: group

value: young

value: sgControl


title: 7-19-16M

value: TAM+


city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

institute: University Heidelberg

description: Gene expression of gnat2 after 2 h of darkness, biological rep 4

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 10, from SAS. Gene expression profiling was performed using arrays of Arabidopsis AraGene-1_0-st type from Affymetrix. A Custom CDF Version 22 with TAIR based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: gnat2 after 2 h of darkness

growth_protocol: Arabidopsis thaliana ecotype Co-0 and gnat2 mutants (SALK_033944) were grown on soil under short-day conditions (8 h light, 120 µmol m-2s-1 photon flux density, 23 °C and 50 % humidity).

extract_protocol: The peqGOLD Total RNA kit (Peqlab) was used to extract RNA from 100 mg plant powder. A global transcriptome analysis was performed using the Affimetrix (High Wycombe) Arabidopsis Genechip (AraGene-1_0st-typ) as described in detail by Linster et al. (2015).

treatment_protocol: After 4.5 weeks, the plants were subjected to different light regimes interrupting the short-day light cycle. Two hours after the regular onset of light, the plants were treated with either high light illumination (HL, 1000 µmol m-2s-1) or darkness (D) for two hours. The control group (C) continued growth at 120 µmol m-2s-1.

tag: ecotype

tag: treatment/timepoint

value: after 2 h of darkness


title: shNTC-E2-1h-rep2


title: WT-Veh-1h-Rb-Igg-Rep1


title: 6-26-15N


title: Y_AT1429_sgNupr1.2


title: 10-7-16R

value: TAM-


title: WT-E2-1h-Ms-Igg-Rep1

value: Ms-Igg(Millipore, 06-371)

value: Human breast cancers


title: Y_AT1428_sgNupr1.2


title: WT-Veh-1h-Ms-Igg-Rep1


title: RNA-seq_aNS_WT_rep3

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC (Andrews S. 2010, FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q18 in a window of 5 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data). Only reads above 30 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl mouse genome version mm10 (ensemble release 101) using STAR 2.7.10a with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
The number of reads aligning to genes was counted with featureCounts 2.0.3 tool from the Subread package (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features). Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Differentially expressed genes were identified using DESeq2 version 1.36.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2). Only genes with a minimum fold change of +- 1.5 (log2 +-0.59), a maximum Benjamini-Hochberg corrected p-value of 0.05, and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed.
Assembly: mm10
Supplementary files format and content: library-size normalized counts

extract_protocol:
Total RNA was isolated by Rneasy Mini Kit (Qiagen). For exclusion of genomic DNA contamination, the samples were treated by on-column DNase digestion (DNase-Free DNase Set, Qiagen). Total RNA and library integrity were verified with LabChip Gx Touch 24 (Perkin Elmer).
1µg of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Takara Bio).

value: V-SVZ derived

value: primary cells

value: aNS cells

value: C57Bl/6J WT


title: Y_AT1426_sgNupr1.2


title: 9-22-16Q


title: 9-9-16Q


title: 9-22-16P


title: 12-5-16P


title: KO-KAP1-Veh-1h-DNAPKcs-Rep1

value: DNA-PKcs(Novus Bio, NB100-658)


title: 10-14-16M


title: Y_AT1422_sgNupr1.2


title: 11-30-16M


title: Y_AT1421_sgNupr1.2


title: 11-24-16S


title: KO-KAP1-E2-1h-DNAPKcs-Rep1


title: 11-17-16T


title: WT-E2-1h-DNAPKcs-Rep1


title: WT-Veh-1h-DNAPKcs-Rep1


title: Y_AS1714_sgNupr1.2


title: 10-31-16M


title: 12-22-16Q


title: 12-28-16U


title: 11-29-16M


title: Y_AS1712_sgControl


title: MCF7-E2-1h-H3K9me3-Rep1

value: H3K9me3(Abcam, ab8898)


title: MCF7-Veh-1h-H3K9me3-Rep1


title: 2-17-17Q


title: 2-8-16M


title: 1-24-17R


title: Y_AS1711_sgControl


title: Y_AS1710_sgControl


title: MCF7-E2-1h-H3K27me3-Rep1

value: H3K4me3(Active motif, 39157)


title: 1-23-17M


title: 2-3-17M


title: Y_AT1420_sgNupr1.2


title: 12-30-16Q


title: MCF7-Veh-1h-H3K27me3-Rep1


title: MCF7-E2-1h-H3K4me3-Rep1

value: H3K4me3(Active motif, 39060)


title: 1-20-17M


title: MCF7-Veh-1h-H3K4me3-Rep1


title: 1-24-17Q


title: 2-15-17Q


title: 11-4-16R


title: Y_AS1707_sgControl

value: lung adenocarcinoma


title: MCF7-E2-1h-H3K4me2-Rep1


title: 11-8-16M


title: Y_AS1698_sgControl

value: Primary lung tumor cells


title: 9-16-16P


title: 10-24-16N


title: Y_AS1700_sgNupr1.1

value: young


title: MCF7-Veh-1h-H3K4me2-Rep1