title: KID_S_rep3

city: London

first: Ming Yang

last: Lee

address: 30 Guilford St.

department: Immunobiology

institute: UCL Great Ormond Street Institute of Child Health

data_processing:
Data were demultiplexed and converted to fastq files using bcl2fastq Conversion (v2.19, Illumina).
Fastq files were then pre-processed to remove adapter contamination and poor-quality base calls (Q20 or below) using a 5’ to 3’ sliding window approach.
The remaining read data were mapped to the hg38 reference genome using the gapped aligner, RNA-STAR (v2.5b).
Read data were counted per transcript using FeatureCounts (v1.4.6p5).
Normalization, modelling and differential expression analysis were carried out using the SARTools package (v1.3.2, BioConductor). All reference genomes and annotation were obtained from the Illumina iGenomes repository.
Differentially expressed genes were determined using a threshold of p-adj < 0.05 and |log2 fold change| ≥ 1 (Speranza et al., 2017).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include read counts for each Sample

source_name: KID syndrome patient-derived keratinocytes

growth_protocol: Cells were maintained in DMEM/Ham’s F12 medium (1:3) supplemented with 10% FBS, 0.4 μg/ml hydrocortisone, 10 ng/ml, epidermal growth factor, 5 µg/ml insulin, 5 μg/ml transferrin, 100 pM choleratoxin, 20 pM liothyronine, 100 IU/ml penicillin and 100 µg/ml streptomycin, and cultured at 37°C in humidified 10% CO2.

extract_protocol:
24 hrs post-transfection, total RNA was extracted from cultured keratinocytes using TRIzol reagent (Thermo Fisher Scientific). 500 ng of total RNA was used for the construction of sequencing libraries.
cDNA libraries were prepared using the KAPA mRNA HyperPrep Kit (KAPA Biosystems) according to manufacturers' instructions. The libraries were sequenced with a 43-bp paired-end run using a Illumina NextSeq 500 instrument.

treatment_protocol: Cells were transiently transfected, or not transfected, with siRNA S7 in triplicate at a concentration of 50 nM. Transient transfection using Lipofectamine RNAiMAX (Thermo Fisher Scientific).

tag: diagnosis

value: Keratinocytes

tag: genotype

tag: sirna s7 treatment

value: No


title: Med1313lfl_NChIP_H3K27me3_TAM_rep1

status: Public on May 23 2022

type: SRA

city: Oxford

first: Emilia

last: Dimitrova

address: South Parks Road

department: Biochemistry

country: United Kingdom

institute: University of Oxford

description: MED1313Lfl_K27me3_TAM_mm10_spikeinnormalised_MERGED.MACS2.bw

library_source: genomic

data_processing:
For cChIP-seq, Bowtie2 was used to align paired-end reads to the concatenated mouse and spike-in genome sequences (mm10+dm6 for native cChIP-seq for histone modifications; mm10+hg19 for cross-linked cChIP-seq) with the “--no-mixed” and “--no-discordant” options. Non-uniquely mapping reads were discarded, and PCR duplicates were removed with Sambamba.
For visualization of cChIP-seq, the data were internally calibrated using dm6 or hg19 spike-in as described previously (Fursova et al. 2019). Briefly, uniquely aligned mm10 reads were randomly subsampled based on the total number of spike-in (dm6 or hg19) reads in each sample. To account for variations in the spike-in cell mixing, we used the ratio of spike-in/mouse total read counts in the corresponding Input samples to correct the subsampling factors. After normalisation, read coverages across genomic regions of interest were compared for individual biological replicates using multiBamSummary and plotCorrelation from deepTools. For each experimental condition, biological replicates correlated well (Pearson correlation coefficient > 0.9) and were merged for downstream analysis.
Genome_build: mm10; dm6; hg19
Supplementary_files_format_and_content: bigWig files showing the genome coverage for merged spike-in normalised biological replicates were generated using the pileup function from MACS2.

molecule: genomic DNA

organism:
Drosophila melanogaster
Mus musculus

source_name: Mouse embryonic stem cells with Drosophila SG4 cells spike-in, tamoxifen treated, Med13/13l flfl, H3K27me3 ChIP-seq

growth_protocol: Mouse embryonic stem cells were grown on gelatin-coated plates at 37°C and 5% CO2, in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 15% fetal bovine serum (Labtech), 2 mM L-glutamine (Life Technologies), 1x penicillin-streptomycin solution (Life Technologies), 1x non-essential amino acids (Life Technologies), 0.5 mM beta-mercaptoethanol (Life Technologies), and 10 ng/mL leukemia inhibitory factor. HEK293T celles were grown in EC-10 medium (DMEM supplemented with 10% fetal bovine serum (Labtech), 2 mM L-glutamine (Life Technologies), 1x penicillin-streptomycin solution (Life Technologies), 1x non-essential amino acids (Life Technologies), 0.4 mM beta-mercaptoethanol (Life Technologies), and 10 ng/mL leukemia inhibitory factor). Drosophila S2 (SG4) cells were grown adhesively at 25°C in Schneider’s Drosophila Medium (Life Technologies), supplemented with 1x penicillin-streptomycin solution (Life Technologies) and 10% heat-inactivated fetal bovine serum (Labtech).

extract_protocol:
For cross-linked ChIP, 50x10^6 ES cells were fixed for 45min with with 2mM DSG (ThermoFisher scientific) in PBS and 12.5 min with 1% formaldehyde (methanol-free, ThermoFisher scientific). Reactions were quenched by the addition of glycine to a final concentration of 125 µM and the fixed cells were washed in ice-cold 1xPBS and snap frozen in liquid nitrogen. 50x10^6 HEK293T cells were fixed as above, snap frozen in 2x106 aliquots, and stored at -80°C until further use. For calibrated ChIPseq, 2x10^6 HEK293T cells were resuspended in 1ml ice-cold lysis buffer (50mM HEPES pH 7.9, 140mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton X-100) and added to 50x10^6 fixed ESCs, resuspended in 9ml lysis buffer. The cell suspension was incubated for 10 min at 4°C. The released nuclei were then washed (10mM Tris-HCl pH 8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA) for 10 min at 4°C. The chromatin pellet was resuspended in 1mL of ice-cold sonication buffer (10mM Tris-HCl pH 8, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na deoxycholate, 0.5% N-lauroylsarcosine) and sonicated for 25 min using a BioRuptor Pico sonicator (Diagenode), shearing genomic DNA to produce fragments between 300bp and 1kb. Following sonication, Triton X-100 was added to a final concentration of 1%. Two hundred and fifty µg chromatin diluted 10-fold in ChIP dilution buffer (1% Triton-X100, 1mM EDTA, 20mM Tris-HCl (pH 8.0), 150mM NaCl) was used per IP. Three reactions were set up per condition to allow for maximal DNA recovery suitable for library preparation. Chromatin was precleared with protein A Dynabeads blocked with 0.2 mg/ml BSA and 50 µg/ml yeast tRNA and incubated with the respective antibodies overnight at 4°C. Antibody-bound chromatin was purified using blocked protein A Dynabeads for 3 hours at 4°C. ChIP washes were performed as described in Farcas et al 2012. ChIP DNA was eluted in ChIP elution buffer (1% SDS, 100mM NaHCO3) and reversed cross-linked overnight at 65°C with 200mM NaCl and RNase A (Sigma). The reverse cross-linked samples were treated with 20 μg/ml Proteinase K and purified using ChIP DNA Clean and Concentrator kit (Zymo research). The three reactions per condition were pooled at this stage. For each sample, corresponding Input DNA was also reverse cross-linked and purified. The efficiency of the ChIP experiments was confirmed by quantitative PCR. Prior to library preparation, 5-10ng ChIP material was diluted to 50ul in TLE buffer (10mM Tris-HCl pH8.0, 0.1mM EDTA) and sonicated with Bioruptor Pico sonicator for 17 min (30 sec on/off). The antibodies used for ChIPseq experiments were rabbit polyclonal anti-CDK8 (A302-500A, Bethyl laboratories, 2.5μl), rabbit monoclonal anti-RING1B (5694, Cell signaling, 3 μl), rabbit polyclonal anti-PCGF2 (sc-10744, Santa Cruz, 3ul), rabbit monoclonal anti-T7-Tag (D9E1X) (13246, Cell signaling, 3ul). The antibodies used for ChIP-qPCR for TetO targeting experiments were rabbit polyclonal anti-FS2 (produced in house, 59, 3ul), polyclonal anti-MED12 (A300-774A, Bethyl laboratories, 3ul), polyclonal anti-MED1 (A300-793A, Bethyl laboratories, 3ul), polyclonal anti-CCNC (A301-989A, Bethyl laboratories, 3ul). For native ChIP, 50x10^6 ESCs were mixed with 20x10^6 SG4 Drosophila cells and washed with 1x PBS prior to chromatin isolation. Nuclei were released in ice cold lysis buffer (10mM Tris-HCl pH 8.0, 10mM NaCl, 3mM MgCl2, 0.1% NP40), washed and resuspended in 1ml ice cold digestion buffer (10mM Tris-HCl pH 8.0, 10mM NaCl, 3mM MgCl2, 0.1% NP40, 0.25M sucrose, 3mM CaCl2, 1x cOmplete protease inhibitor cocktail (Roche)). Chromatin was digested with 200mM MNase (ThermoFisher scientific) for 5 min at 37°C and the reaction was stopped by the addition of 4mM EDTA pH 8.0. The samples were centrifuged at 1500g for 5 min at 4°C, the supernatant (S1) was retained. The remaining pellet was incubated with 300μl of nucleosome release buffer (10mM Tris-HCl pH 7.5, 10mM NaCl, 0.2mM EDTA, 1x protease inhibitor cocktail (Roche)) at 4°C for 1 h, passed five times through a 27G needle using a 1mL syringe, and spun at 1500g for 5 min at 4°C. The second supernatant (S2) was collected and combined with corresponding S1 sample from above. Digestion to mostly mononucleosomes was confirmed on a 1.5% agarose gel. The prepared native chromatin was aliquot, snap frozen in liquid nitrogen and stored at -80°C until further use. ChIPs were performed as described in Fursova et al 2019, using 5ul of H3K27me3 antibody prepared in-house.
cChIP-seq libraries for both ChIP and Input samples were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina, following manufacturer’s guidelines. Samples were indexed using NEBNext Multiplex Oligos. The average size and concentration of all libraries were analysed using the 2100 Bioanalyzer High Sensitivity DNA Kit (Agilent) followed by qPCR quantification using SensiMix SYBR (Bioline, UK) and KAPA Illumina DNA standards (Roche). Libraries were sequenced as 40 bp paired-end reads in biological triplicate or quadruplicate on Illumina NextSeq 500 platform.

treatment_protocol: Med13/13lfl/fl ERT2-Cre ESCs were treated with 800nM 4-hydroxytamoxifen (Sigma) for 96 hours. Pcgf4-/-/Pcgf2fl/fl ERT2-Cre ESCs were treated with 800nM 4-hydroxytamoxifen (Sigma) for 72 hours. For RA differentiation, ESCs were treated with 1µM retinoic acid (Sigma-Aldrich) for 48h.

tag: cell line

value: Med13;Med13l flfl

tag: strain

tag: treatment

value: tamoxifen

tag: treatment time

tag: additional treatment

tag: additional treatment time

tag: replicate

tag: spike-in reference organism

value: Drosophila melanogster

tag: spike-in cell line

tag: type of chip

value: native

tag: ChIP

tag: antibody

value: rabbit polyclonal anti-H3K27me3, in-house


title: H35_MYC+BCL2+BCL6+

city: Singapore

first: Michal

middle: Marek

last: Hoppe

address: 14 Medical Dr

department: Cancer Science Institute of Singapore

country: Singapore

institute: National University of Singapore

description:
primary tonsil B-cells with MYC, BCL2, BCL6 overexpression
H35

library_source: transcriptomic

data_processing:
Raw read counts are provided by HTSeq-count 0.13.5
Mapping is using STAR
Gene expression quantification is based on featureCounts
raw files were processed via the publicly available portal: https://csibioinfo.nus.edu.sg/
Assembly: hg38
Supplementary files format and content: raw counts

molecule: total RNA

organism: Homo sapiens

source_name: B-cells primary tonsil tissue

growth_protocol: Fresh, tonsil tissue was sourced from the Addenbrooke’s ENT Department, Cambridge with written informed consent of the patient/parent/guardian and processed directly to preserve viability. Ethical approval for the use of human tissue was granted by the Health Research Authority Cambridgeshire Research Ethics Committee (REC no. 07/MRE05/44). GC B cells were purified using the human B cell negative selection isolation Kit II (MACS, Miltenyi Biotec) as per the manufacturer’s instructions. The protocol was modified to include negative selection antibodies IgD-BIOT (IADB6; SouthernBiotech 9030- 08, 1:100) and CD44-BIOT (F10-44-2; SouthernBiotech 9400-08, 1:100) to remove naïve and memory B cells. Cells were stained for CD38 (HB7; BioLegend #12- 0388-42, 1:500), CD20 (2H7; BioLegend #17-0209-41, 1:500), CD19 (HIB19; BioLegend #302223, 1:500), and CD10 (97C5; MiltenyiBiotec, 130-093-450, 1:500) to confirm enrichment of GC B cells. B cell genomic DNA was screened for EBV status using a quantitative real-time PCR (qPCR) assay and cells from EBV-positive patients were discarded. GC B cells were plated onto irradiated YK6-CD40lg-IL21 and split every 2–3 days. Fresh YK6-CD40lg-IL21 cells (irradiated 30 Gy) were added with each split. Primary human GC B cells were cultured in Advanced Roswell Park Memorial Institute medium (Advanced RPMI-1640, Invitrogen, Carlsbad, CA) with GlutaMAX containing 20% FBS, 100 IU/ml penicillin, and 100 µg/ml streptomycin and kept at 37 °C in a humidified incubator (5% CO2 and 95% atmosphere). For more details see Caeser et al. 2019 Nat Commun.

extract_protocol:
TRIzol extraction
250~300 bp insert cDNA library (Eukaryotic mRNA)

treatment_protocol: MYC, BCL2, BCL6 were cloned into MSCV-based vectors using synthetic double-stranded DNA and Gibson Assembly. For overexpression of multiple human genes, CDS sequences were cloned into the MSCV-IRES-huDC2 vector (kind gift of Dr Martin Turner, the Babraham Institute, UK) with the t2A peptides linking genes, such as BCL6-t2A-BCL2, or MYC-t2A-BCL2. Retroviral packaging plasmids pHIT60 (kind gift of Dr. Louis Staudt, National Cancer Institute, USA) and GaLV WT were used as follows: 1 μg pHIT60 (gag-pol), 1 μg GaLV WT (envelope), and 4 μg of a retroviral construct was used to transfect each 10 cm2 dish of HEK-293T, after mixing with 1 ml of Opti-MEM media (Invitrogen) and 18 μl of TransIT-293 (Mirus). The packaging line Lenti-X 293T Cell Line (Clontech Laboratories) was used for all transfections. After 36–48 h, the virus supernatant was filtered through a 0.45 μM filter. If needed, media was replenished and harvested again at 16 h later. For retroviral/lentiviral transduction, 1–2 × 106 target cells were resuspended with viral supernatant and infected by centrifugation (1500 × g, 90 min at 32 °C) with the addition of 10 μg/ml Polybrene (INSIGHT Biotechnology) and 25 μM HEPES (ThermoFisher) in 12- or 24-well plates. Viral supernatant was replaced with fresh media immediately after centrifugation for retroviral infection. Cells were maintained at 37 °C with 5% CO2 for 2–4 days before analyzing by FACS.

tag: tissue

value: primary tonsil

tag: cell type

value: B cells

tag: overexpression


title: Med1313lfl_NChIP_Input_UNT_rep1

description: input for H3K27me3 ChIPs in Med13:Med13lflfl

source_name: Mouse embryonic stem cells with Drosophila SG4 cells spike-in, untreated control, Med13/13l flfl, input

value: untreated


title: Med1313lfl_NChIP_H3K27me3_UNT_rep2

description: MED1313Lfl_K27me3_UNT_mm10_spikeinnormalised_MERGED.MACS2.bw

source_name: Mouse embryonic stem cells with Drosophila SG4 cells spike-in, untreated control, Med13/13l flfl, H3K27me3 ChIP-seq


title: Med1313lfl_NChIP_H3K27me3_UNT_rep1


title: Med1313lfl_NChIP_H3K27me3_TAM_rep3


title: Med1313lfl_NChIP_H3K27me3_UNT_rep3


title: Med1313lfl_NChIP_H3K27me3_TAM_rep2


title: KID_S_rep2

tag: diagnosis

tag: genotype


title: H34_MYC+BCL2+BCL6+

description:
primary tonsil B-cells with MYC, BCL2, BCL6 overexpression
H34


title: KID_S_rep1

tag: sirna s7 treatment


title: H33_MYC+BCL2+BCL6+

description:
primary tonsil B-cells with MYC, BCL2, BCL6 overexpression
H33


title: H29_MYC+BCL2+BCL6+

description:
primary tonsil B-cells with MYC, BCL2, BCL6 overexpression
H29


title: KID_U_rep3

value: Yes


title: KID_U_rep2


title: H27_MYC+BCL2+

description:
primary tonsil B-cells with MYC, BCL2 overexpression
H27


title: H26_MYC+BCL2+

description:
primary tonsil B-cells with MYC, BCL2 overexpression
H26


title: KID_U_rep1


title: H24_MYC+BCL2+

description:
primary tonsil B-cells with MYC, BCL2 overexpression
H24


title: P03-S, scRNAseq

city: changsha

first: Xiaofeng

last: Chen

state: Hunan

address: No.139 Renmin road, Furong district

country: China

institute: second xiangya hospital, central south university

description:
Md5 for processed file:
83307c5f9b07d76053a7cd724535af89

library_source: transcriptomic single cell

data_processing:
Celescope was used to base-calling, alignment, filtering and generation of normalized abundance measurements.
Read 1: contains the 24bp GEXSCOPE barcode and the 12bp UMI (bases 25-36). Read 2 contains the cDNA information.
Assembly: GRCh38
Supplementary files format and content: matrix files

source_name: lung adenocarcinoma

extract_protocol:
Focal areas of solid and GG components were identified by tissue appearance and compute tomography (CT) at the same time. Different components were macrodissected and stored at 4 ℃ GEXSCOPETM Tissue Preservation Solution. Then, we washed samples for 3 times with Hanks Balanced Salt Solution (HBSS) and minced them into 1–2 mm-thick pieces, 2 ml GEXSCOPETM Tissue Dissociation Solution (Singleron Biotechnologies) was added to each sample and allowed for digestion at 37 ℃ for 15 minutes to dissociate the tissue into single cells. Then, we filtrate the samples using 40-μm sterile strainers, followed by centrifuging at 1,000 rpm for 5 minutes. After the centrifugation, the precipitation was resuspended in 1 ml phosphate-buffered saline (PBS; HyClone, Marlborough, United States). Subsequently, 2 ml GEXSCOPETM Red Blood Cell Lysis Buﬀer (Singleron Biotechnologies) was added into the cell suspension and incubated at 25°C for 10 minutes to remove red blood cells. After that, the mixture was centrifuged at 500 × g for 5 minutes, followed by re-suspending the precipitation with PBS.
We used GEXSCOPETM Single Cell RNA Library Kit Tissue (Singleron Biotechnologies) to barcode single cells, capture mRNA from isolated single cells, and generate cDNA libraries for scRNA-seq. Then, individual libraries were diluted to 4 ng/μl, and pooled for sequencing on a HiSeq X platform (Illumina, San Diego, USA) with 150 bp paired-end reads.

value: lung adenocarcinoma

tag: tissue component

value: solid

tag: age

tag: Stage

value: treatment naive before surgery

tag: Sex

value: female


title: P03-GG, scRNAseq

description:
Md5 for processed file:
2701716bee2ccd668abf1afe6c75bb56

value: ground-glass like

tag: treatment


title: P01-S, scRNAseq

description:
Md5 for processed file:
dfa613be0815d4c97e3c978f84d8e208


title: Hela cells, si-U1A, biol rep2

city: San Sebastian

first: Lorea

last: Blazquez

address: Dr Begiristain

country: Spain

institute: Biogipuzkoa Health Research Institute

data_processing:
the quality of the samples was verified using FastQC software
the alignment of reads to the human genome (hg19) was performed using Bowtie2
gene expression quantification using read counts of exonic gene regions was carried out; the gene annotation reference was Gencode v19
differential expression statistical analysis was performed using R/Bioconductor
Assembly: hg19
Supplementary files format and content: 20151203_Up151013_e4X_m1_db-20151203_Up151013.exp_norm.bed contains bed files with read counts
Supplementary files format and content: QuantSeq_data_processed.xlsx contains mapped genes with logFC and statistics

source_name: HeLa

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

extract_protocol:
Magnetic bead-based RNA isolation (Maxwell RNA simply cells)
Libraries were prepared using QuantSeq 3' mRNA-Seq Library Prep Kit REV for Illumina from Lexogen

treatment_protocol: siRNAs against a non-targeting control or SNRPA gene

tag: cell line

value: HeLa

value: siRNA against SNRPA gene


title: Hela cells, si-U1A, biol rep3


title: Hela cells, si-Control, biol rep3

value: siRNA against a non-targeting sequence


title: Hela cells, si-U1A, biol rep1


title: P02-S, scRNAseq

description:
Md5 for processed file:
e8d14821b80cf1ccccf8d8c41c3bffee


title: Hela cells, si-Control, biol rep2


title: P02-GG, scRNAseq

description:
Md5 for processed file:
ec9341855cfec9e8b638bfab2b7caf3c


title: P01-GG, scRNAseq

description:
Md5 for processed file:
edd4cd7fb8b6793af70b40cc1df0fc08


title: Hela cells, si-Control, biol rep1


title: MOCK-OUT-6HPI-C

city: Bellaterra

first: Jose

last: Salguero Linares

state: Barcelona

address: Carrer de la Vall Moronta s/n

institute: Centre for Research in Agricultural Genomics

data_processing:
Base-calling protocol: RTA2.7.3 bcl2fastQV2.17.1.14
“FastQC” and “TrimGalore!” software was used for raw Illumina reads quality control analysis and  trimming  of  reads  containing  adaptor-   or  vector-derived  sequences, respectively
rRNA was detected and removed using “SortMeRNA 2.1b” software
Cleaned reads together with the transcriptome of Arabidopsis thaliana (as of 30 August 2018), including ncRNA, were used to quantify gene expression at transcript level using the software “Salmon v0.11.3”
Raw counts aggregated by gene were obtained using “tximport v1.14.2” and the result was used as input to “DESeq2”. Then, genes adding up to less than 10 counts across all 60 samples were removed.
Counts were normalized using size factors calculated by DESeq2.
Genome_build: EnsemblPlants cDNA file Arabidopsis_thaliana.TAIR10.cdna.all.fa.gz as of 30 August 2018
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: Leaf

growth_protocol: 7 days on MS sucrose 1% sucrose : 16h light / 22°C, 3 weeks in short day condition : 9h light / 22°C

extract_protocol:
NucleoSpin RNA Macherey-Nagel
PolyA-mRNA

treatment_protocol: Arabidopsis Col-0 leaves were infiltrated locally with Pto DC3000 (avrRpm1) (5*107cfu/mL) or mock in a spatio-temporal manner. The infiltrated cells (IN zone) were harvested in parallel with the immediately adjacent uninfected cells (OUT zone). Samples were taken at 0,1,2,4,6 post-inoculation in three biological replicates.

tag: ecotype

value: Leaf

value: Mock

tag: area

value: Area surrounding the infiltration zone (OUT)

tag: time

value: 6 hours post-infiltration

tag: biological replicate

value: C


title: MOCK-OUT-6HPI-A

value: A


title: MOCK-OUT-6HPI-B

value: B


title: wild type, mature leaves,1

city: Potsdam-Golm

first: Joerg

last: Fettke

state: Brandenburg

address: Karl-Liebknechtstr. 24/25, Building 20

country: Germany

institute: University of Potsdam

data_processing:
Original image data file is transformed to sequenced reads by CASAVA base recognition (Base Calling). Raw reads filtering is as follows: (1) Remove reads containing adapters; (2) Remove reads containing N > 10% (N represents base that could not be determined); (3) Remove low quality reads: The Qscore (Quality value) of over 50% bases of the read is <= 5.
Clean reads were mapped to the reference genome or the transcriptome with HISAT2.
The RNA-seq reads were assembled according to the reference genomes using Rockhopper(R. McClure, et al, 2013)
Gene expression level of different samples represented by FPKM, quantified by software FeatureCounts.
Assembly: ensemblplants_arabidopsis_thaliana_tair10_gca_000001735_1
Supplementary files format and content: txt file include FPKM values for each Sample

source_name: cells from Mature leaves and petioles

extract_protocol:
RNA was harvested using Trizol protocol (Invitrogen, US) . 1 ug of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations

value: cells from Mature leaves and petioles

value: Mature leaves and petioles from Col-0

value: Retard Period (5weeks after germination)


title: MOCK-OUT-4HPI-C

value: 4 hours post-infiltration


title: wild type, young leaves,2

source_name: cells from young leaves and petioles

value: cells from young leaves and petioles

value: young leaves and petioles from wild type Col-0


title: MOCK-OUT-4HPI-B


title: Astrocytes, D1, Rep2, P10, Bulk (204237150069_R06C01)

type: genomic

city: New Haven

first: Albert

middle: T

last: Higgins-Chen

state: CT

address: 60 Temple St

country: USA

institute: Yale University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

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

data_processing: minfi package in R

label: Cy3 and Cy5

label_protocol: Standard Illumina Protocol

growth_protocol: Cells were seeded at 8,000 cells/cm2 with appropriate growth media and supplements (complete astrocyte medium, containing amino acids, vitamins, hormones, trace minerals, 2% fetal bovine serum and 1% PEN/STREP in HEPES pH 7.4 bicarbonate buffer, ScienCell #1801) to promote cell adhesion and growth. Of note, Poly-L-Lysine was not required for adequate cell adhesion. Cells were grown under normoxic conditions (20% O2, 5% CO2) at 37°C.

extract_protocol: genomic DNA was extracted using the Qiagen DNAeasy Blood and Tissue Kit (69504). Samples were treated with proteinase K and RNAse A and eluted with 200 µl elution buffer. Following final elution, DNA was verified using nanodrop (Thermo Scientific). Spin concentration was used as necessary with low DNA content samples. Prior to library preparation, a Qubit fluorometer (Thermo Scientific) was used to quantify the extracted genomic DNA.

treatment_protocol: Cells were exhaustively passaged and split a total of 10 times (9-15 cumulative population doublings, depending on replicate). Cells were split when they reached approximately 90% confluence or when static growth was achieved. Cells were counted using the Invitrogen countess and cell counting chamber slide with trypan blue. β-gal activity (C12FDG) was measured using flow cytometry or confocal microscopy at each passage to confirm exhaustive replication was achieved.

value: Astrocytes

tag: code

tag: name

tag: replicate

tag: cpd

tag: days

tag: passage

value: Bulk

tag: donor

tag: purification

tag: shipping

tag: female


title: Astrocytes, D1, Rep2, P6, Bulk (204237140139_R04C01)

tag: cell type


title: Astrocytes, D1, Rep3, P8, Bulk (204237140139_R07C01)

description:
Astrocytes_D1_Rep3_P8_Bulk
Samples taken at passages 2 through 10 (total n = 27 samples) and DNA extracted.


title: Astrocytes, D1, Rep3, P2, Bulk (204237150069_R07C01)


title: MOCK-OUT-4HPI-A

tag: tissue

tag: treatment


title: Astrocytes, D1, Rep3, P10, Bulk (204237150069_R04C01)

description:
Astrocytes_D1_Rep3_P10_Bulk
Samples taken at passages 2 through 10 (total n = 27 samples) and DNA extracted.


title: Astrocytes, D1, Rep0, P2, Bulk (204237150069_R03C01)


title: Astrocytes, D1, Rep3, P2, Bulk (204237150069_R05C01)


title: Astrocytes, D1, Rep2, P10, Bulk (204237150069_R08C01)


title: Astrocytes, D2, Rep4, P4, Bulk (204237140120_R08C01)


title: Astrocytes, D1, Rep3, P6, Low gal (204237140139_R08C01)

description: Astrocytes_D1_Rep3_P6_Low gal

source_name: Astrocytes_D1_Rep3_P6_Low gal

value: Low gal


title: Astrocytes, D1, Rep1, P6, Bulk (204237140139_R01C01)


title: Astrocytes, D2, Rep4, P10, Sen (204237140067_R07C01)

value: Sen


title: Astrocytes, D1, Rep3, P2, Bulk (204237140139_R06C01)

description:
Astrocytes_D1_Rep3_P2_Bulk
Samples taken at passages 2 through 10 (total n = 27 samples) and DNA extracted.


title: Astrocytes, D1, Rep1, P6, High gal (204237150069_R01C01)

description: Astrocytes_D1_Rep1_P6_High gal

source_name: Astrocytes_D1_Rep1_P6_High gal

value: High gal


title: Astrocytes, D1, Rep1, P8, Bulk (204237140120_R02C01)

description:
Astrocytes_D1_Rep1_P8_Bulk
Samples taken at passages 2 through 10 (total n = 27 samples) and DNA extracted.


title: PDX_2017_94

city: Cambridge

first: Gabriela

last: Alexe

state: MA

address: 415 Main St.

department: Computational Biology and Bioinformatics

institute: Broad Institute

description: PDX_2017_94 parental

data_processing:
Quality control tests for unmapped sequences were performed based on the FastQC v.0.11.5 software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The spiked-in human reads were mapped to the GRCh37/hg19 human genome using STAR v2.7.3  with standard parameters  --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --outSAMattributes NH HI NM MD AS XS --outReadsUnmapped Fastx --outSAMstrandField intronMotif --quantMode TranscriptomeSAM GeneCounts --quantTranscriptomeBan IndelSoftclipSingleend.
The ERCC92 Mix1 Spike-in sequences were mapped using STAR v2.7.3 according to the standard ThermoFisher protocol https://www.thermofisher.com/order/catalog/product/4456740#/4456740.
Gene level reads were summarized by using the featureCounts v1.6.3 method implemented in the Subread v2.0.0 package (http://subread.sourceforge.net) ref FeatureCounts. The technical quality metrics of the spiked-in mapped reads   were investigated using the standard methods   implemented  in the  erccdashboard package. Additional quality control tests for the mapped reads and for replicate reproducibility were performed using SARTools v1.7.3.
Gene counts were normalized and used to quantify differential  genes between the experimental and control conditions using the DESeq2 v1.24.0 method implemented in Bioconductor v3.9. Genes with at least 10 reads across at least 3 samples were annotated  as "expressed".
Differentiability for the expressed genes  was assessed with DESeq2 based on the robust shrunken log2 fold change scores  and  the approximate posterior estimation for GLM coefficients  method for effect size. The cutoffs for differentially expressed genes were |fold change expression|>1.5 and adjusted p-value < 0.10.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Tab-delimited text file include gene level counts values for each sample.

source_name: PDX cells from AML patient with complex karyotype

extract_protocol:
MV4-11 and PDX 16-01 IRF2BP2 degrader vs. DMSO:  these experiments were performed in three technical replicates for each time point and condition. ERCC RNA spike-in mix was added to all samples following the manufacturer’s instructions (ThermoFischer, 4456740).  RNA was extracted from cells with the RNeasy Kit and on-column DNA digestion (Qiagen).
PDX AML parental: these experiments were performed in a single replicate. RNA was extracted from cells with the RNeasy Kit and on-column DNA digestion (Qiagen), except for PDX 2017-63 and PDX 2017-94 for which RNA was extracted using the mirVana miRNA Isolation Kit (Thermo Fisher, Grand Island, NY) with the total RNA extraction protocol.
MV4-11 and PDX 16-01 IRF2BP2 degrader vs. DMSO:   PolyA mRNA was isolated and libraries were prepared using the TruSeq Stranded mRNA Kit (Illumina) according to the manufacturer’s protocol. All samples were sequenced on a Illumina NovaSeq 6000 instrument with paired-end 150 bp reads to a depth of 40-60 million reads per sample.
PDX AML parental (except PDX 2017-63 and PDX 2017-94):  PolyA mRNA was isolated and libraries were prepared using the TruSeq Stranded mRNA Kit (Illumina) according to the manufacturer’s protocol. All samples were sequenced on a Illumina NovaSeq 6000 instrument with paired-end 150 bp reads to a depth of 40-60 million reads per sample.
PDX 2017-63 and PDX 2017-94 parental: NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA) was used for poly(A) RNA purification with 50 uL total RNA as input. SMARTer Apollo NGS library prep system (Takara, Mountain View, CA) was used for automated poly(A) RNA isolation. The library for RNA-Seq was prepared by using NEBNext Ultra II Directional RNA Library Prep kit (New England BioLabs, Ipswich, MA). Libraries at the final concentration of 15 pM were clustered onto a single read (SR) flow cell v3 using Illumina TruSeq SR Cluster kit v3 and sequenced to 51 bp using TruSeq SBS kit v3 on Illumina HiSeq system.

value: untreated

tag: disease state

value: Acute Myeloid Leukemia


title: MOCK-OUT-2HPI-B

tag: ecotype

value: Leaf

value: Mock

tag: area

value: Area surrounding the infiltration zone (OUT)

value: 2 hours post-infiltration


title: PDX_2017_63

description: PDX_2017_63 parental

source_name: PDX cells from refractory AML patient

value: PDX cells from refractory AML patient


title: Astrocytes, D1, Rep1, P10, High gal (204237140067_R08C01)

description: Astrocytes_D1_Rep1_P10_High gal

source_name: Astrocytes_D1_Rep1_P10_High gal


title: Astrocytes, D1, Rep2, P2, Bulk (204237150069_R02C01)

description:
Astrocytes_D1_Rep2_P2_Bulk
Samples taken at passages 2 through 10 (total n = 27 samples) and DNA extracted.


title: Astrocytes, D1, Rep1, P6, Sen (204237140139_R05C01)


title: Astrocytes, D1, Rep3, P10, Bulk (204237140139_R03C01)


title: Astrocytes, D1, Rep1, P3, Bulk (204237140120_R04C01)

description:
Astrocytes_D1_Rep1_P3_Bulk
Samples taken at passages 2 through 10 (total n = 27 samples) and DNA extracted.


title: Astrocytes, D1, Rep1, P7, Bulk (204237140120_R05C01)

description:
Astrocytes_D1_Rep1_P7_Bulk
Samples taken at passages 2 through 10 (total n = 27 samples) and DNA extracted.


title: bulk RNA seq of human nasal epithelial tissue rep2

city: Cleveland

first: Ann

last: Harris

state: Ohio

address: 2109 Adelbert Rd Building

department: Genetics and Genome Sciences

institute: Case Western Reserve University

description:
WT HNE rep2
RNA-seq

data_processing:
Bulk RNA-seq mapped to the hg19 human genome with STAR 2.6 (https://github.com/alexdobin/STAR)
Aligned reads were assigned to genomic features with featureCounts version 1.6.3 in the Subread package (http://subread.sourceforge.net/) to estimate expression levels for each transcript.
Differential gene expression was analyzed using EdgeR 3.14 (https://bioconductor.org/packages/release/bioc/html/edgeR.html)
Genome_build: hg19 genome v1.0
Supplementary_files_format_and_content: EdgeR output: Matrix of counts per million (CPM) of each gene for each tissue.

source_name: human nasal epithelial tissue

growth_protocol: Primary human airway epithelial cells from nasal brushings were expanded at 37 °C on irradiated 3T3 murine fibroblast feeder cells with growth media (F-12/DMEM [3:1] supplemented with 5% heat-inactivated FBS, 25 ng/mL hydrocortisone, 1 mg/mL insulin, 12.5 ng/mL EGF, 8.6 ng/mL cholera toxin, and 24 μg/mL Adenine) with ROCK inhibitor (RI, Y27632 at 16 μg/mL), antibiotics (50 µg/mL gentamicin, 0.25 µg/mL amphotericin B, 100 U/ml Penicillin, and 100 μg /ml Streptomycin), and cryopreserved upon initial passaging (P1). For ALI culture NHE cell stocks (P1) were expanded on collagen-coated culture dishes in AW#2 medium (F12/DMEM [1:1], supplemented with 2% Ultroser G, penicillin/streptomycin, gentamicin, and fungizone). Harvested cells were seeded (P2) onto collagen-coated 12 mm inserts (Costar 3801) in AW#2 with RI at 4 × 105 cells per insert. Media was replaced with AW #2 without RI 24 hours after seeding and cultures expanded for 3-4 days until confluent, when apical media was removed for mucociliary differentiation. Basolateral medium was exchanged for fresh AW#2 medium every other day. After six weeks, the ALI cultures were differentiated into polarized epithelia. Primary bronchial epithelial cells were Passage 1 (P1) obtained from the University of North Carolina at Chapel Hill. Cells were grown on collagen-coated plastic in bronchial epithelial growth medium (Lonza). Passage 2 primary HBE cells were used for air-liquid interface (ALI) cultures.

extract_protocol:
Confluent HNE cells were harvested for RNA extraction using TRIzol. RNA quality was confirmed by Nanodrop measurement of OD 260/280 and 260/230 ratios and stored at -80oC under ethanol. 1ug RNA was used for RNA-seq library preparation.
Bulk RNA-seq libraries were prepared using the TruSeq RNA Sample Preparation Kit v2 (Low-Throughput protocol, Illumina).

value: healthy donor


title: Astrocytes, D1, Rep0, P1, Bulk (204237140120_R03C01)


title: MOCK-OUT-2HPI-A

tag: time

tag: biological replicate

value: A


title: Astrocytes, D2, Rep4, P5, Bulk (204237140120_R06C01)

tag: code

tag: name


title: MOCK-OUT-1HPI-C

value: 1 hours post-infiltration

value: C


title: MOCK-OUT-2HPI-C


title: bulk RNA seq of human nasal epithelial tissue rep1

description:
WT HNE rep1
RNA-seq


title: Astrocytes, D1, Rep1, P6, Bulk (204237140139_R02C01)

description:
Astrocytes_D1_Rep1_P6_Bulk
Samples taken at passages 2 through 10 (total n = 27 samples) and DNA extracted.

tag: replicate

tag: cpd


title: Astrocytes, D1, Rep3, P6, Sen (204237140120_R07C01)

tag: days

tag: passage


title: MOCK-OUT-1HPI-B

value: B


title: MOCK-OUT-1HPI-A


title: Astrocytes, D1, Rep1, P5, Bulk (204237140120_R01C01)

description:
Astrocytes_D1_Rep1_P5_Bulk
Samples taken at passages 2 through 10 (total n = 27 samples) and DNA extracted.

value: Astrocytes

tag: donor

tag: purification


title: Astrocytes, D1, Rep3, P5, Bulk (204237140067_R05C01)

description:
Astrocytes_D1_Rep3_P5_Bulk
Samples taken at passages 2 through 10 (total n = 27 samples) and DNA extracted.

value: Bulk

tag: shipping

tag: female


title: control-ILC3-LI-3

city: Gainesville

first: Liang

last: Zhou

state: FL

address: 2015 SW 16th Ave

department: IDI

institute: University of Florida

data_processing:
Sequenced reads were mapped and raw count values quantified with STAR (v2.7.4a) to the Mus musculus genome (GRCm38/mm10 assembly) and filtered for uniquely mapped reads. Quantitated mRNA expression levels, FPKM aligned reads, were calculated based on exon regions using RSEM (v1.2.25).
Assembly: mm10
Supplementary files format and content: text file of raw counts for all samples

organism: Mus musculus

source_name: Large intestine ILC3

extract_protocol:
RNA was extracted using RNAeasy Micro Kit, followed by cDNA generation with SMART-Seq® HT Kit (TaKaRa).
Sequencing libraries were generated with Nextera® XT DNA Library Preparation Kit (Illumina), and sequenced on an Illumina HiSeq 2500 instrument.

treatment_protocol: ILC3 cells (Lin–CD90hiCD45lo) were sorted from the LI of uninfected and Salmonella-infected WT mice

tag: tissue

value: Large intestine

tag: cell type

tag: strain

tag: genotype

value: WT

tag: infection

value: uninfected


title: MOCK-OUT-0HPI-C

tag: ecotype

tag: treatment

tag: area

tag: time

value: 0 hours post-infiltration


title: control-ILC3-LI-2


title: Astrocytes, D1, Rep2, P10, Bulk (204237140067_R06C01)

description:
Astrocytes_D1_Rep2_P10_Bulk
Samples taken at passages 2 through 10 (total n = 27 samples) and DNA extracted.

tag: code

tag: name

tag: replicate


title: control-ILC3-LI-1


title: MOCK-OUT-0HPI-B

tag: biological replicate


title: SL1344-ILC3-LI-3

value: S. typhimurium (SL1344)


title: SL1344-ILC3-LI-2


title: MOCK-IN-6HPI-C

value: Leaf

value: Infiltrated area (IN)

value: 6 hours post-infiltration


title: Astrocytes, D1, Rep2, P3, Bulk (204237140067_R03C01)

description:
Astrocytes_D1_Rep2_P3_Bulk
Samples taken at passages 2 through 10 (total n = 27 samples) and DNA extracted.

tag: cpd

tag: days

tag: passage

tag: donor


title: SL1344-ILC3-LI-1

tag: tissue


title: Astrocytes, D1, Rep3, P6, High gal (204237140067_R04C01)

description: Astrocytes_D1_Rep3_P6_High gal

source_name: Astrocytes_D1_Rep3_P6_High gal

tag: cell type

value: High gal

tag: purification

tag: shipping

tag: female


title: MOCK-OUT-0HPI-A

tag: ecotype

value: Mock

value: Area surrounding the infiltration zone (OUT)


title: MOCK-IN-6HPI-B

tag: treatment


title: MOCK-IN-6HPI-A

tag: area

value: A


title: MOCK-IN-4HPI-C

tag: time

value: 4 hours post-infiltration


title: Astrocytes, D1, Rep1, P2, Bulk (204237140067_R02C01)

description:
Astrocytes_D1_Rep1_P2_Bulk
Samples taken at passages 2 through 10 (total n = 27 samples) and DNA extracted.

tag: code


title: MOCK-IN-4HPI-B


title: Astrocytes, D1, Rep2, P10, Sen (204237140059_R07C01)

tag: name

value: Sen


title: MOCK-IN-4HPI-A


title: Astrocytes, D1, Rep3, P6, Bulk (204237140067_R01C01)

description:
Astrocytes_D1_Rep3_P6_Bulk
Samples taken at passages 2 through 10 (total n = 27 samples) and DNA extracted.

tag: replicate


title: Astrocytes, D1, Rep2, P4, Bulk (204237140059_R03C01)

description:
Astrocytes_D1_Rep2_P4_Bulk
Samples taken at passages 2 through 10 (total n = 27 samples) and DNA extracted.


title: Astrocytes, D1, Rep1, P9, Bulk (204237140059_R08C01)

description:
Astrocytes_D1_Rep1_P9_Bulk
Samples taken at passages 2 through 10 (total n = 27 samples) and DNA extracted.


title: Astrocytes, D2, Rep4, P8, Bulk (204228990115_R08C01)


title: Astrocytes, D1, Rep3, P7, Bulk (204228990115_R03C01)

description:
Astrocytes_D1_Rep3_P7_Bulk
Samples taken at passages 2 through 10 (total n = 27 samples) and DNA extracted.


title: Selex-DllScr-24mer-R1

city: New York

first: Siqian

last: Feng

state: New York

address: 625 W. 130th Street

institute: Columbia University

data_processing:
Library strategy: Selex-seq
For ChIP-seq and ATAC-seq, mapping was done against dm3 with the “Map with Bowtie for Illumina” tool on usegalaxy.org, and only uniquely mapped reads were kept.
ChIP-seq peak calling was performed using the galaxy version of MACS2 (“MACS2 callpeak” on usegalaxy.org), with the following setting: --nomodel –extsize 200, and all other parameters were default
ATAC-seq peak calling was also performed with the galaxy version of MACS2, with the following setting: --nomodel –extsize 200 - -shift -100.
For RNA-seq, the cutadaptor tool on usegalaxy.eu was used to trim reads and remove reads shorter than 100bp. The filtered reads were then mapped to the genome build dm6 using the RNA STAR tool with the following parameters: --sjdbOverhang 149. The featurecount tool was used to obtain the transcript count tables.
Selex-seq data were processed using the NRLB algorithm
When analysing the Selex-seq raw data, the algorithm we used took the R0 and R1 data, and output the motifs enriched in the R1 data. This is somewhat similar to de novo motif search. The algorithm didn't output any intermediate quantitative data, and the motif logos were the only data it generated.
Genome_build: dm3 for ChIP-seq and ATAC-seq, dm6 for RNA-seq
Supplementary_files_format_and_content: bigwig (ChIP-seq and ATAC-seq) and count table (RNA-seq)

organism: synthetic construct

source_name: synthetic DNA

growth_protocol: Drosophila larvae were grown on standard cornmeal or molasses food at 25°C.

extract_protocol:
R0 DNA was from the Klenow product of the original synthetic random library, and R1 DNA was purified bound DNA fraction from the gel-free Selex experiments.
Selex-seq libraries were prepared by PCR amplification, followed by column purification

tag: genotype

tag: chip antibody

tag: genome build


title: Astrocytes, D2, Rep4, P6, Bulk (204228990115_R06C01)

tag: cpd

tag: days

tag: passage


title: Astrocytes, D2, Rep4, P9, Bulk (204237140059_R04C01)

tag: cell type

tag: donor


title: Astrocytes, D1, Rep2, P7, Bulk (204237140059_R01C01)

description:
Astrocytes_D1_Rep2_P7_Bulk
Samples taken at passages 2 through 10 (total n = 27 samples) and DNA extracted.

tag: purification

tag: shipping


title: MOCK-IN-2HPI-C

tag: ecotype

tag: tissue

value: 2 hours post-infiltration

tag: biological replicate

value: C


title: Astrocytes, D1, Rep3, P4, Bulk (204228990115_R07C01)

description:
Astrocytes_D1_Rep3_P4_Bulk
Samples taken at passages 2 through 10 (total n = 27 samples) and DNA extracted.

value: Astrocytes

value: Bulk

tag: female


title: Astrocytes, D2, Rep4, P10, Low gal (204228990087_R04C01)

description: Astrocytes_D2_Rep4_P10_Low gal

source_name: Astrocytes_D2_Rep4_P10_Low gal

tag: code

value: Low gal


title: Astrocytes, D2, Rep4, P4, Bulk (204237140059_R02C01)

tag: name


title: Astrocytes, D1, Rep2, P9, Bulk (204237140059_R06C01)

description:
Astrocytes_D1_Rep2_P9_Bulk
Samples taken at passages 2 through 10 (total n = 27 samples) and DNA extracted.

tag: replicate


title: Astrocytes, D1, Rep0, P2, High gal (204228990115_R04C01)

description: Astrocytes_D1_Rep0_P2_High gal

source_name: Astrocytes_D1_Rep0_P2_High gal


title: Astrocytes, D1, Rep1, P10, Low gal (204228990115_R01C01)

description: Astrocytes_D1_Rep1_P10_Low gal

source_name: Astrocytes_D1_Rep1_P10_Low gal


title: MOCK-IN-2HPI-B

tag: treatment

tag: area

tag: time

value: B


title: Selex-24mer-R0

tag: genotype

tag: chip antibody

tag: genome build


title: MOCK-IN-2HPI-A


title: Selex-ExdScr-24mer-R1


title: Selex-Scr-16mer-R1


title: Selex-16mer-R0


title: Astrocytes, D1, Rep2, P10, Low gal (204228990087_R03C01)

description: Astrocytes_D1_Rep2_P10_Low gal

source_name: Astrocytes_D1_Rep2_P10_Low gal

tag: cell type

tag: cpd

tag: days

tag: passage


title: MOCK-IN-1HPI-C

tag: ecotype

value: 1 hours post-infiltration


title: Astrocytes, D1, Rep2, P5, Bulk (204228990087_R05C01)

description:
Astrocytes_D1_Rep2_P5_Bulk
Samples taken at passages 2 through 10 (total n = 27 samples) and DNA extracted.

tag: donor

tag: purification

tag: shipping


title: shGPR81_glucose_4

city: Copenhagen

first: Jiayi

last: Yao

state: Copenhangen

address: Ole Maaløes Vej 5

country: Denmark

institute: University of Copenhagen

data_processing:
GRCh38 transcriptome and genome reference file were concatenated for Salmon indexing
Sequenced reads were quantified to transcipt level using Salmon v1.1.0 (Patro, R., Duggal, G., Love, M. et al. Nat Methods 14, 417–419 (2017)) with parameter --validateMappings
The quantification result was summarized to gene-level by GRCh38.p13 comprehensive gene annotation
Assembly: GRCh38.p13 transcriptome and genome
Supplementary files format and content: tab-delimited text file include CPM values for every gene and every sample

source_name: breast cancer

growth_protocol: DMEM with 5 mM glucose or 20 mM lactate

extract_protocol:
RNA was extracted using RNeasy Micro Kit (Qiagen)
RNA libraries for RNA-seq were prepared using DNBSEQ stranded mRNA library protocol.

treatment_protocol: 72 h treatment, in 2D cell culture plates

tag: tissue

value: breast cancer

tag: cell line

tag: genotype/variation

value: GPR81 knockdown

tag: gender

value: female

value: 5 mM glucose 72 h


title: shGPR81_glucose_3

tag: treatment


title: Astrocytes, D2, Rep4, P7, Bulk (204221250087_R07C01)

tag: code

tag: name

tag: replicate

tag: female


title: shGPR81_glucose_2


title: Astrocytes, D1, Rep1, P6, Low gal (204221250087_R08C01)

description: Astrocytes_D1_Rep1_P6_Low gal

source_name: Astrocytes_D1_Rep1_P6_Low gal

tag: cell type


title: Astrocytes, D2, Rep4, P6, Bulk (204228990087_R02C01)

tag: cpd


title: pLKO.1_glucose_4

value: pLKO.1 empty plasmid


title: MOCK-IN-0HPI-C

source_name: Leaf

value: Leaf

value: Mock

tag: area

value: Infiltrated area (IN)

tag: time

value: 0 hours post-infiltration

tag: biological replicate


title: Astrocytes, D2, Rep4, P10, Bulk (204228990115_R02C01)

tag: days

tag: passage

tag: donor


title: shGPR81_glucose_1

tag: tissue


title: pLKO.1_glucose_3

tag: cell line


title: pLKO.1_glucose_2

tag: genotype/variation


title: pLKO.1_glucose_1

tag: gender


title: Selex-Dll-16mer-R1

tag: genotype

tag: chip antibody

tag: genome build


title: shGPR81_lactate_3

tag: treatment

value: 20 mM lactate 72 h


title: Astrocytes, D2, Rep4, P3, Bulk (204228990087_R01C01)

tag: code

tag: name

tag: replicate

tag: purification

tag: shipping

tag: female


title: MOCK-IN-0HPI-B

tag: ecotype

tag: area

tag: time

tag: biological replicate


title: Astrocytes, D1, Rep0, P2, Low gal (204228990087_R06C01)

description: Astrocytes_D1_Rep0_P2_Low gal

source_name: Astrocytes_D1_Rep0_P2_Low gal

tag: cell type

tag: cpd

tag: days

tag: passage

tag: donor


title: shGPR81_lactate_4

tag: tissue

tag: cell line

tag: genotype/variation

tag: gender


title: Astrocytes, D1, Rep2, P8, Bulk (204228990087_R07C01)

description:
Astrocytes_D1_Rep2_P8_Bulk
Samples taken at passages 2 through 10 (total n = 27 samples) and DNA extracted.

tag: code

tag: name

tag: replicate


title: shGPR81_lactate_1

tag: treatment


title: MOCK-IN-0HPI-A

tag: ecotype

value: A


title: shGPR81_lactate_2


title: Astrocytes, D1, Rep3, P3, Bulk (204228990115_R05C01)

description:
Astrocytes_D1_Rep3_P3_Bulk
Samples taken at passages 2 through 10 (total n = 27 samples) and DNA extracted.

tag: purification

tag: shipping

tag: female


title: Astrocytes, D1, Rep1, P10, Bulk (204228990087_R08C01)

description:
Astrocytes_D1_Rep1_P10_Bulk
Samples taken at passages 2 through 10 (total n = 27 samples) and DNA extracted.

tag: cell type


title: avrRpm1-OUT-6HPI-C

value: Pto AvrRpm1

tag: area

value: Area surrounding the infiltration zone (OUT)

tag: time

value: 6 hours post-infiltration

tag: biological replicate

value: C


title: pLKO.1_lactate_3


title: pLKO.1_lactate_4


title: avrRpm1-OUT-6HPI-B

value: B


title: pLKO.1_lactate_2


title: Astrocytes, D1, Rep3, P9, Bulk (204221250087_R04C01)

description:
Astrocytes_D1_Rep3_P9_Bulk
Samples taken at passages 2 through 10 (total n = 27 samples) and DNA extracted.

value: Astrocytes

tag: cpd

tag: days

tag: passage

value: Bulk

tag: donor


title: ATAC-seq-T3-rep2

data_processing:
For ChIP-seq and ATAC-seq, mapping was done against dm3 with the “Map with Bowtie for Illumina” tool on usegalaxy.org, and only uniquely mapped reads were kept.
ChIP-seq peak calling was performed using the galaxy version of MACS2 (“MACS2 callpeak” on usegalaxy.org), with the following setting: --nomodel –extsize 200, and all other parameters were default
ATAC-seq peak calling was also performed with the galaxy version of MACS2, with the following setting: --nomodel –extsize 200 - -shift -100.
For RNA-seq, the cutadaptor tool on usegalaxy.eu was used to trim reads and remove reads shorter than 100bp. The filtered reads were then mapped to the genome build dm6 using the RNA STAR tool with the following parameters: --sjdbOverhang 149. The featurecount tool was used to obtain the transcript count tables.
Selex-seq data were processed using the NRLB algorithm
When analysing the Selex-seq raw data, the algorithm we used took the R0 and R1 data, and output the motifs enriched in the R1 data. This is somewhat similar to de novo motif search. The algorithm didn't output any intermediate quantitative data, and the motif logos were the only data it generated.
Genome_build: dm3 for ChIP-seq and ATAC-seq, dm6 for RNA-seq
Supplementary_files_format_and_content: bigwig (ChIP-seq and ATAC-seq) and count table (RNA-seq)

organism: Drosophila melanogaster

source_name: T3 leg imaginal discs, wandering larvae

extract_protocol:
Nuclei were isolated from freshly dissected leg discs, and Tn5 mediated transposition reactions were performed. Total DNA was then purified using NEB minElute PCR purification kit after the transposition reactions.
ATAC-seq libraries were generated by PCR amplification of the ATAC-seq DNA, followed by size selection

tag: genotype

value: isogenic 3xFLAG-Scr

tag: chip antibody

tag: genome build


title: avrRpm1-OUT-4HPI-C

tag: tissue

value: 4 hours post-infiltration


title: ATAC-seq-T3-rep1


title: ATAC-seq-T2-rep2

source_name: T2 leg imaginal discs, wandering larvae


title: pLKO.1_lactate_1

value: breast cancer

tag: cell line

tag: genotype/variation

tag: gender

value: female

tag: treatment


title: avrRpm1-OUT-4HPI-B

tag: ecotype

value: Leaf


title: ATAC-seq-T2-rep1


title: avrRpm1-OUT-6HPI-A


title: avrRpm1-OUT-4HPI-A


title: ATAC-seq-T1-rep1

source_name: T1 leg imaginal discs, wandering larvae


title: RNA-seq-T3-rep2

extract_protocol:
Total RNA was extracted from freshly dissected tissues using NEB RNeasy mini kit. The RNA samples were treated with DNaseI, and were cleaned up with NEB RNeasy kit.
RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB E7760S)

value: isogenic w1118 (BL5905)


title: MOCK-IN-1HPI-B

value: Mock

value: Infiltrated area (IN)

value: 1 hours post-infiltration


title: RNA-seq-T3-rep3


title: RNA-seq-T2-rep3


title: avrRpm1-OUT-2HPI-B

value: 2 hours post-infiltration


title: ATAC-seq-T1-rep2


title: avrRpm1-OUT-2HPI-A

value: Pto AvrRpm1

value: A


title: Astrocytes, D1, Rep2, P10, High gal (204221250087_R05C01)

description: Astrocytes_D1_Rep2_P10_High gal

source_name: Astrocytes_D1_Rep2_P10_High gal

tag: cell type

tag: code

tag: name

tag: replicate

value: High gal

tag: purification

tag: shipping

tag: female


title: RNA-seq-T2-rep2


title: RNA-seq-T2-rep1


title: Astrocytes, D1, Rep1, P4, Bulk (204221250087_R06C01)

description:
Astrocytes_D1_Rep1_P4_Bulk
Samples taken at passages 2 through 10 (total n = 27 samples) and DNA extracted.

tag: cpd

tag: days

tag: passage

tag: donor


title: avrRpm1-OUT-2HPI-C

tag: tissue

tag: area

value: Area surrounding the infiltration zone (OUT)

tag: time

tag: biological replicate

value: C


title: RNA-seq-T1-rep3

tag: genotype

tag: chip antibody

tag: genome build


title: MOCK-IN-1HPI-A

tag: ecotype

tag: treatment


title: RNA-seq-T1-rep2


title: RNA-seq-T1-rep1


title: input-Dll-T3-rep2

extract_protocol:
Tissues were crosslinked with 1% formaldehyde for 10 minutes at RT, and were sonicated. DNA was purified from input and ChIP samples.
ChIP-seq libraries were constructed using illumina TruSeq ChIP Library Preparation Kit


title: avrRpm1-OUT-1HPI-B

value: B


title: ChIP-Dll-T3-rep2

value: Guinea pig anti-Dll


title: input-Dll-T1-rep2


title: avrRpm1-OUT-1HPI-C


title: avrRpm1-OUT-1HPI-A


title: avrRpm1-OUT-0HPI-C

value: 0 hours post-infiltration


title: Cortical motor neurons, tdTomato_3 (sample27)

city: Los Angeles

first: Yuyan

last: Cheng

state: CA

address: 695 Charles E Young Dr S Rm 2305

department: Neurology

institute: UCLA

description:
SeqCov.PC1: -8.480370884
SeqCov.PC2: 11.46068586

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR
Transcript abundance values were obtained from Salmon and gene-level count matrices were generated by tximport
Gene counts were normalized using geometric mean (GEO) in DESeq2 package and log2 transformed. Removal of unwanted variation (RUV) was used to remove batch effects and genes with no counts in over 50% of the samples were removed.
Differential gene expression by limma voom was performed on normalized gene counts, using batch effects and the first two PCAs of aligning and sequencing as covariates.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes gene abundance for each sample, log fold changes and p-values from differential gene expression analysis

extract_protocol:
RNA from FACS-sorted neurons of the sensorimotor cortex (~1000 cells) was isolated with the NucleoSpin RNA XS kit (CloneTech) according to the manufacturerâs protocol.
RNA-seq libraries for cortical motor neurons were prepared with the QuantSeq 3âmRNA-Seq library prep kit FWD for Illumina (Lexogen) following the manufacturerâs instructions

tag: strain

value: SCI

value: RESTcKO

tag: time_recovered (days)

tag: Sex

value: F

tag: cell type

tag: batch


title: ChIP-Dll-T3-rep1


title: ChIP-Dll-T1-rep2


title: input-Dll-T3-rep1


title: RNA-seq-T3-rep1


title: input-Dll-T1-rep1


title: avrRpm1-OUT-0HPI-B

value: Leaf


title: Astrocytes, D2, Rep4, P10, High gal (204221250087_R03C01)

description: Astrocytes_D2_Rep4_P10_High gal

source_name: Astrocytes_D2_Rep4_P10_High gal

value: Astrocytes

tag: code

tag: name

tag: replicate

tag: cpd

tag: days

tag: purification

tag: shipping

tag: female


title: Cortical motor neurons, tdTomato_1 (sample25)

description:
SeqCov.PC1: 9.881966367
SeqCov.PC2: 7.210205488

tag: genotype

value: M


title: ChIP-Dll-T1-rep1

value: isogenic w1118 (BL5905)

tag: chip antibody

tag: genome build


title: Cortical motor neurons, tdTomato_0 (sample23)

description:
SeqCov.PC1: 10.45364964
SeqCov.PC2: 2.949373226

tag: treatment

value: Sham


title: Cortical motor neurons, tdTomato_7 (sample26)

description:
SeqCov.PC1: -5.804447069
SeqCov.PC2: 3.004595821

tag: strain


title: IHCC4-1

city: Guangzhou

first: zhiwu

last: jiang

address: 190 Kai Yuan Avenue, Science Park

institute: GIBH

description: rawCountsHCC.csv

data_processing:
Sequenced reads were trimmed for adaptor sequence and masked for a low complexity or low-quality sequence. The number of raw reads mapped to genes was calculated by RSEM (rsem-1.2.4), and the sample results were put together and normalized by EDAseq (1.99.1).
Genome_build: not provided
Supplementary_files_format_and_content: rawCountsHCC.csv: Comma-separated text file

source_name: HCC

growth_protocol: Primary human hepatocytes from five different donors were purchased from Bioreclamation IVT.

extract_protocol:
mRNA from primary PHH or iHCC was prepared according to the TruSeqTM RNA Sample Preparation Guide.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: tissue

value: liver

value: HCC


title: avrRpm1-IN-6HPI-C

tag: ecotype

value: Pto AvrRpm1

tag: area

value: Infiltrated area (IN)

tag: time

value: 6 hours post-infiltration

tag: biological replicate


title: Cortical motor neurons, GFP_3 (sample22)

description:
SeqCov.PC1: 8.352288798
SeqCov.PC2: 0.549299504

value: WT

tag: time_recovered (days)

tag: Sex

tag: cell type

tag: batch


title: IHCC3-3

description: rawCountsHCC.csv


title: Astrocytes, D1, Rep3, P6, Bulk (204221250087_R02C01)

tag: code

tag: name

tag: replicate

tag: cpd

tag: days

tag: passage

value: Bulk

tag: donor

tag: purification


title: avrRpm1-IN-6HPI-B

tag: tissue

tag: treatment

value: B


title: IHCC3-2

description: rawCountsHCC.csv


title: Cortical motor neurons, tdTomato_3 (sample20)

description:
SeqCov.PC1: 1.442843673
SeqCov.PC2: -4.115070842

tag: strain

tag: genotype


title: avrRpm1-IN-6HPI-A

tag: ecotype

tag: area

tag: time

tag: biological replicate

value: A


title: TM-466/7

city: Foshan

first: Dan

address: Shiwan Street, Chancheng District, Foshan City

institute: Center, First People's  Hospital of Foshan

description: This multiplexed sample includes the following samples: Peripheral blood sample from patient 1, 2, 3; Kidney tissue from patient 2 and 3, Urine sample from patients 1 and 2.

data_processing:
Raw files obtained by sequencing with Illumina high-throughput sequencers
The original file is an image file, and after base calling and Bcl2Fastq transformation, the original sequenced sequence (sequenced reads) in FASTQ (fq for short) format can be obtained
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: PBMC, kidney, urine

extract_protocol:
Cells from tissues, peripheral blood, and urine samples of patients with nephropathy were collected, and single-cell whole transcriptome sequencing libraries were constructed using R Hapsody reverse transcription kit and BD R Hapsody whole transcriptome amplification kit of BD platform
RNA libraries were prepared for sequencing using standard BD RhapsodyTM Single cell 3’ whole transcriptome amplification (WTA) with sample multiplexing kit (SMK) protocol

value: multiplexed sample:PBMC, kidney and urine


title: Cortical motor neurons, tdTomato_1 (sample19)

description:
SeqCov.PC1: 0.662853016
SeqCov.PC2: -3.910408328

value: SCI

value: RESTcKO

tag: time_recovered (days)

tag: Sex

tag: cell type

tag: batch


title: IHCC3-1

description: rawCountsHCC.csv


title: TM-464/5

description: This sample is not multiplexed and contains data for Kidney tissue sample from patient 1

source_name: Kidney tissue

value: Kidney


title: avrRpm1-IN-4HPI-C

value: Leaf

value: 4 hours post-infiltration

value: C


title: TM-468/9

description: This multiplexed sample includes the following samples: Peripheral blood sample from patient 4; Kidney tissue from patient 4, Urine sample from patient 3 and 4.


title: IHCC2-3

description: rawCountsHCC.csv


title: IHCC2-2

description: rawCountsHCC.csv


title: J-gammal cells, NC-2

city: Suzhou

first: Fang

last: Fang

state: Jiangsu

address: 92 Zhongnan street

institute: Children’s Hospital of Soochow University

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

source_name: J-gammal sample with no treatment

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

tag: cell line

value: J-gammal


title: avrRpm1-IN-4HPI-A


title: IHCC5-1

description: rawCountsHCC.csv

value: liver


title: avrRpm1-IN-4HPI-B


title: IHCC2-1

description: rawCountsHCC.csv

value: HCC


title: avrRpm1-IN-2HPI-C

value: Pto AvrRpm1

value: 2 hours post-infiltration


title: Astrocytes, D1, Rep2, P6, Bulk (204221250087_R01C01)

description:
Astrocytes_D1_Rep2_P6_Bulk
Samples taken at passages 2 through 10 (total n = 27 samples) and DNA extracted.

value: Astrocytes

tag: code

tag: name

tag: replicate

tag: cpd

tag: days

tag: shipping

tag: female


title: IHCC1-4

description: rawCountsHCC.csv

tag: tissue


title: Cortical motor neurons, GFP_3 (sample16)

description:
SeqCov.PC1: 1.337566444
SeqCov.PC2: -3.723605161

tag: strain

tag: treatment

tag: genotype

value: WT

value: M


title: J-gammal cells, sh-FYB1-2

source_name: J-gammal sample with FYB1 knockdown

value: FYB1 knockdown


title: J-gammal cells, sh-FYB1-1


title: PDX_17_14

description: PDX_17_14 parental

source_name: PDX cells from AML patient with MLL-PTD/MLL-AF10 fusion

value: PDX cells from AML patient with MLL-AF9 fusion

value: untreated

tag: disease state

value: Acute Myeloid Leukemia


title: Cortical motor neurons, tdTomato_3 (sample15)

description:
SeqCov.PC1: -2.017302201
SeqCov.PC2: -9.306353923

value: SCI

value: RESTcKO

tag: time_recovered (days)

value: F


title: Cortical motor neurons, GFP_0 (sample17)

description:
SeqCov.PC1: -10.84849323
SeqCov.PC2: -0.688548851

value: Sham

tag: Sex


title: avrRpm1-IN-2HPI-B

tag: ecotype

value: Leaf

tag: area

value: Infiltrated area (IN)

tag: time

tag: biological replicate

value: B


title: PDX_16_01

description: PDX_16_01 parental

source_name: PDX cells from AML patient with CALM-AF10 fusion

tag: cell type


title: avrRpm1-IN-2HPI-A

value: A


title: Cortical motor neurons, tdTomato_0 (sample18)

description:
SeqCov.PC1: 15.68995855
SeqCov.PC2: 4.730655026

tag: batch


title: IHCC1-2

description: rawCountsHCC.csv

value: liver

value: HCC


title: Cortical motor neurons, tdTomato_7 (sample13)

description:
SeqCov.PC1: 7.171499193
SeqCov.PC2: 0.165005878


title: IHCC1-1

description: rawCountsHCC.csv


title: PDX_CPCT_0027

description: PDX_CPCT_0027 parental

source_name: PDX cells from AML patient with CBFA2T3-GLIS2 fusion


title: J-gammal cells, NC-1

tag: cell line

value: J-gammal


title: Cortical motor neurons, GFP_1 (sample11)

description:
SeqCov.PC1: -12.32936729
SeqCov.PC2: 7.644721487

value: WT


title: PHH5

description: rawCountsHCC.csv

source_name: hepatocytes

value: hepatocytes


title: PHH4

description: rawCountsHCC.csv


title: PDX_DFAM_93240

description: PDX_DFAM_93240 parental

source_name: PDX cells from AML patient with inv(16) CBFB-MYH11


title: Cortical motor neurons, GFP_0 (sample10)

description:
SeqCov.PC1: 0.635497635
SeqCov.PC2: -2.494743434


title: PDX_CPCT_0007

description: PDX_CPCT_0007 parental

source_name: PDX cells from AML patient with MLL-PICALM rearrangement


title: IHCC1-3

description: rawCountsHCC.csv


title: PDX_CBAM_68552

description: PDX_CBAM_68552 parental

source_name: PDX cells from AML patient with MLL-AF6 fusion


title: avrRpm1-IN-0HPI-B

source_name: Leaf

value: Pto AvrRpm1

value: 0 hours post-infiltration


title: Cortical motor neurons, tdTomato_3 (sample9)

description:
SeqCov.PC1: -1.227403404
SeqCov.PC2: -4.85594583


title: PHH3

description: rawCountsHCC.csv


title: Cortical motor neurons, GFP_0 (sample14)

description:
SeqCov.PC1: -1.235078197
SeqCov.PC2: -4.611823589


title: JE_RNA_PDX1601_dTAG13_06h_R2

description: PDX1601 treated with dTAG-13 IRF2BP2 degrader for 6h

value: PDX cells from AML patient with CALM-AF10 fusion

value: dTAG-13 IRF2BP2 degrader for 6h


title: JE_RNA_PDX1601_dTAG13_06h_R3

value: Acute Myeloid Leukemia


title: avrRpm1-IN-0HPI-C

value: C


title: PHH2

description: rawCountsHCC.csv


title: Cortical motor neurons, GFP_7 (sample12)

description:
SeqCov.PC1: 10.42114137
SeqCov.PC2: 1.394553046

value: SCI

value: F


title: avrRpm1-OUT-0HPI-A

value: Leaf

value: Area surrounding the infiltration zone (OUT)


title: Cortical motor neurons, GFP_7 (sample7)

description:
SeqCov.PC1: -4.188590228
SeqCov.PC2: -0.881913185


title: PHH1

description: rawCountsHCC.csv


title: avrRpm1-IN-1HPI-B

value: Infiltrated area (IN)

value: 1 hours post-infiltration

value: B


title: JE_RNA_PDX1601_dTAG13_06h_R1


title: avrRpm1-IN-0HPI-A

value: A


title: avrRpm1-IN-1HPI-C


title: avrRpm1-IN-1HPI-A


title: Day0-WT3-mono

city: Seoul

first: Myung Jun

last: Kim

state: Jongno-gu

address: 103 Daehak-ro

department: College of Medicine

country: South Korea

institute: Seoul National University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: colon

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: colon

value: primary

value: Monocytes and Immature Macrophages

value: wild type


title: JE_RNA_PDX1601_DMSO_06h_R3

description: PDX1601 treated with DMSO for 6h

value: DMSO for 6h


title: Cortical motor neurons, tdTomato_0 (sample6)

description:
SeqCov.PC1: -2.618728267
SeqCov.PC2: -6.305041365

value: Sham

value: RESTcKO

value: M


title: 10a-sgUTX_rep2

first: SIQIN

last: ZHOU

address: 14 Medical Drive

institute: Cancer Science Institute of Singapore

description: MCF10A with sgRNA targeting UTX replicate

data_processing:
RNA-seq aligned to hg19 genome and UCSC reference transcript using STAR (version 2.4.0).
Expression analysis performed by Featurecounts (version 1.5.0).
Bigwig generated after normalization.
Genome_build: Hg19
Supplementary_files_format_and_content: Bigwig

source_name: mammary gland; breast epithelial

growth_protocol: MCF10A cells were purchased from American Type Culture Collection (ATCC). MCF10A cells were cultured in DMEM/F12 medium supplemented with 10% donor horse serum, 20ng/ml EGF, 0.5 mg/ml hydrocortisone, 100 ng/ml cholera toxin, 10 mg/ml insulin and 10% Pen/Strep. Cells were maintained in 37 °C in a humidified incubator with 5% CO2 supplement.

extract_protocol:
Total RNAs from MCF10A cells were isolated and purified using RNeasy mini extraction kit (74106, Qiagen).
After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA (for eukaryotes) or by removing rRNAs from the total RNA (for prokaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. The suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. At last, the library could be sequenced using Illumina HiSeqTM4000 or other sequencer when necessary.

treatment_protocol: CRISPR plasmids containing single-guide RNA (sgRNA) were generated following previously described protocol using plasmid lentiCRISPR V2. Lentiviral particles were obtained using third generation transfer plasmids, including pRSV-Rev, pMDLg/pRRE and pMD2.G with HEK293FT cells. After viral infection, MCF10A cells were subjected to puromycin selection for 7 days.

value: non-tumorigenic epithelial cell line

tag: genotype/variation

value: sgRNA targeting UTX

tag: passages


title: Day0-WT3-MO

value: Mature Macrophages


title: Cortical motor neurons, GFP_3 (sample5)

description:
SeqCov.PC1: 9.777261305
SeqCov.PC2: 2.796024332

value: SCI

value: WT

value: F


title: 10a-sgUTX_rep1

description: MCF10A with sgRNA targeting UTX


title: 10a-control_rep2

description: MCF10A with non-targeted control sgRNA replicate

value: non-targeted control sgRNA


title: JE_RNA_PDX1601_DMSO_06h_R2

description: PDX1601 treated with DMSO for 6h

value: PDX cells from AML patient with CALM-AF10 fusion

value: Acute Myeloid Leukemia


title: Day0-WT1-MO

value: colon


title: Cortical motor neurons, GFP_7 (sample4)

description:
SeqCov.PC1: -2.599763207
SeqCov.PC2: -6.53285773


title: 10a-control_rep1

description: MCF10A with non-targeted control sgRNA


title: Cortical motor neurons, GFP_1 (sample8)

description:
SeqCov.PC1: -3.48212047
SeqCov.PC2: -6.282960131


title: Cortical motor neurons, GFP_0 (sample3)

description:
SeqCov.PC1: -6.550179581
SeqCov.PC2: -1.578274058


title: PDX1714_Input_P0

description: Input on parental PDX 17-14 cells

data_processing:
Quality control tests for unmapped sequences were performed based on the FastQC v.0.11.5 software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The H3K27ac ChIP-Seq sequences were spiked-in with Drosophila Melanogaster based on the Active Motif kit protocol. The human ChIP-Seq sequences for IRF2BP2, H3K27ac, H3K4me3 and H3K4me1 antibodies were aligned to the GRCh37/hg19 genome and the Drosophila Melanogaster sequences were aligned to the dm6 genome using bowtie2-2.3.5  with the standard options.
PCR duplicates were removed with the Picard v2.18.2 MarkDuplicates tool (https://broadinstitute.github.io/picard/). The Active Motif Spike-in Normalization protocol (https://www.activemotif.com/catalog/1091/chip-normalization)  was applied to the H3K27ac samples by multiplying the human tag counts with the normalization factors derived from the uniquely mapped Drosophila reads as ratios between the sample with the lowest dm6 counts vs. the dm6 counts for that sample.
The mapped reads were normalized in units of Reads Per Kilobase per Million (RPKM or rpm/bp) and coverage tracks for the RPKM signal were created as bigwig files for bins of size 20 base pairs by using the bamCoverage tool available in deepTools v2.5.3.  Peak calling was performed against input control using the model-based MACS2 v2.1.1.20160309 software, with the cut-off FDR ≤ 0.01.  Area under Curve (AUC) RPKM normalized signal across genomic regions was computed with the bwtool software ref bwtool. Peaks with low area under curve coverage (< 300 RPKM)  were disregarded and the ENCODE black-listed regions for hg19 (available at https://www.encodeproject.org/annotations/ENCSR636HFF/) were removed from each set of peak regions. Quality control tests for the mapped reads were performed by using the ChIPQC library available from Bioconductor v3.9.
The ChIP-Seq IRF2BP2 data was produced for three different IRF2BP2 antibodies (r1: Abcam_ab114997, r2: Bethyl_A303-189A-T, r3: Bethyl_A303-190A).  The pairwise correlations between IRF2BP2 replicates were estimated based on the multiBamSummary function available from the deepTools v2.5.3  and visualized on correlation heatmaps and PCA plots. The IRF2BP2 replicates were found significantly correlated (Spearman R > 0.90) and they were merged into a single IRF2BP2 ChIP-Seq sample. The  IRF2BP2 binding sites was identified for the merged data (macs2, FDR ≤ 0.01).
The peaks were annotated with the closest hg19 genes by using the annotatePeaks function implemented in the Homer v4.11 platform  and the GREAT annotation platform.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Bigwig files for normalized coverage signal in units of reads per million mapped reads per bp (rpm/bp).  Coverage was computed for  bins of size 20 base pairs by using the bamCoverage module available in deepTools v2.5.3.  The Active Motif Spike-in Normalization protocol was  applied by multiplying the human tag counts with the normalization factors derived from the uniquely mapped Drosophila reads as ratios between the sample with the lowest dm6 counts vs. the dm6 counts for that sample.

source_name: PDX 17-34 cells from AML patient with MLL-PTD/MLL-AF10 fusion

extract_protocol:
25 million (for histone marks) to 100 million AML cells (for IRF2BP2) per condition were crosslinked with 1% formaldehyde in cell culture media for 10 minutes and then quenched with 0.125 mM glycine. Cells were lysed in Nuclei EZ Isolation buffer (Sigma EZ Prep Nuclear Isolation Kit, Cat No. NUC-101) supplemented with protease inhibitor. Chromatin was sheared using a Covaris instrument. Subsequently, 0.5% of the lysate was removed as the input control. The remaining lysate was incubated with 30 ul (for histone marks) or 100 ul (for IRF2BP2) of protein G dynabeads (Thermofisher) and 5 ug of H3K27Ac: ab4729 abcam,  H3K4me1: ab8895, H3K4me3: ab8580,  or 10 ug of IRF2BP2 antibody (r1: abcam_ab114997, r2: Bethyl_A303-189A-T, r3: Bethyl_A303-190A) and HA (Cell Signaling Technology_3724S),  at 4 degrees C overnight (antibodies and beads were incubated together for 30 minutes at 4 degrees C prior to the addition of cell lysate).
The precipitated lysate was then washed sequentially in two washes of each of the following buffers: ice cold low salt buffer (20 mM Tris-HCl pH 8.1, 150 mM NaCl, 2 nM EDTA, 1% Triton-X100, 0.1% SDS), high salt buffer (20 mM Tris-HCl pH 8.1, 2 mM EDTA, 500 mM NaCl, 1% Triton-X100, 0.1% SDS), LiCl buffer (10 mM Tris-HCl pH 8.1, 0.25 M LiCl, 1 mM EDTA, 1% desoxycholic acid, 1% IGEPAL CA-630) and TE buffer (10 mM Tris-HCl ph8.1, 1 mM EDTA). Samples were eluted in elution buffer (1x TE pH 7.4, 1% SDS, 150 mM NaCl, 5 mM DTT). RNase A, proteinase K, and 0.2 M NaCl was added to the elution buffer and samples were incubated at 65 degrees Celsius for at least four hours to reverse cross-linking. DNA was purified using AMPure XP beads (Agencourt). ChIP-seq libraries were prepared using Swift S2 Acel reagents on a Beckman Coulter Biomek i7 liquid handling platform from approximately 1ng of DNA according to manufacturer’s protocol and 14 cycles of PCR amplification. Finished sequencing libraries were quantified by Qubit fluorometer and Agilent TapeStation 2200. Library pooling and indexing was evaluated with shallow sequencing on an Illumina MiSeq.

treatment_protocol: H3K27Ac: ab4729 abcam, H3K4me1: ab8895, H3K4me3: ab8580, IRF2BP2 (r1: abcam_ab114997, r2: Bethyl_A303-189A-T, r3: Bethyl_A303-190A), HA (Cell Signaling Technology_3724S)

value: untreated


title: Cortical motor neurons, tdTomato_7 (sample2)

description:
SeqCov.PC1: -5.864126786
SeqCov.PC2: 2.781891479


title: PDX1714_H3K27ac_P0

description: H3K27ac on parental  PDX 17-14 cells


title: Cortical motor neurons, GFP_1 (sample1)

description:
SeqCov.PC1: -8.580555178
SeqCov.PC2: 10.60053528


title: Soleus Female rep 1

city: Lowell

first: Matthew

last: Gage

state: Massachusetts

address: 265 Riverside St

department: Chemistry

institute: University of Massachusetts Lowell

data_processing:
BCL files were demultiplexed using bcl2fastq, and adapters were trimmed using trimmomatic 0.32 based on the FastQC results.
The preprocessed short reads were aligned to the Mus Musculus GRCm38.p4 reference genome annotation using the Eli-Meyers alignment pipeline (Meyers July 2018 v2.0)
Assembly: GRCm38.p4
Supplementary files format and content: .tab

source_name: Soleus

extract_protocol:
Total RNA was extracted from Soleus and TA muscles using Qiagen fibrous tissue total RNA extraction mini kit. 10ng of total RNA from the extracted samples were used in the Tag-Seq library preparation.
Takara SMART-Seq Stranded protocol for Illumina sequencing platforms was used for cDNA library preparation.  libraries with concentration > 3ng/  ul and fragment size between 300-450 were sequenced using an Illumina 500 sequencer.

value: Soleus

value: Wild type

value: Female


title: TA Female rep 1

source_name: Tibialis Anterior

value: Tibialis Anterior


title: TA Female rep 2


title: JE_RNA_PDX1601_DMSO_06h_R1

description: PDX1601 treated with DMSO for 6h

value: DMSO for 6h


title: TA Male rep 3

value: Male


title: PDX1714_Input_dTAG.IRF2BP2

description: Input on PDX 17-14 IRF2BP2-HA cells


title: PDX1714_HA_dTAG.IRF2BP2

description: HA on PDX 17-14 IRF2BP2-HA cells


title: PDX1601_Input_P0

description: Input on parental PDX 16-01 cells

source_name: PDX 16-01 cells from AML patient with CALM-AF10 fusion


title: Soleus Male rep 3


title: Med1313lfl_TAM_CBX7_rep2

city: Oxford

first: Emilia

last: Dimitrova

address: South Parks Road

institute: University of Oxford

data_processing:
For cChIP-seq, Bowtie2 was used to align paired-end reads to the concatenated mouse and spike-in genome sequences (mm10+dm6 for native cChIP-seq for histone modifications; mm10+hg19 for cross-linked cChIP-seq) with the “--no-mixed” and “--no-discordant” options. Non-uniquely mapping reads were discarded, and PCR duplicates were removed with Sambamba.
For visualization of cChIP-seq, the data were internally calibrated using dm6 or hg19 spike-in as described previously (Fursova et al. 2019). Briefly, uniquely aligned mm10 reads were randomly subsampled based on the total number of spike-in (dm6 or hg19) reads in each sample. To account for variations in the spike-in cell mixing, we used the ratio of spike-in/mouse total read counts in the corresponding Input samples to correct the subsampling factors. After normalisation, read coverages across genomic regions of interest were compared for individual biological replicates using multiBamSummary and plotCorrelation from deepTools. For each experimental condition, biological replicates correlated well (Pearson correlation coefficient > 0.9) and were merged for downstream analysis.
Assembly: mm10; hg19
Supplementary files format and content: bigWig files showing the genome coverage for merged spike-in normalised biological replicates were generated using the pileup function from MACS2.

organism:
Homo sapiens
Mus musculus

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, tamoxifen treated, Med13/13l fl/fl CBX7 ChIP-seq

extract_protocol:
For cross-linked ChIP, 50x10^6 ES cells were fixed for 45min with with 2mM DSG (ThermoFisher scientific) in PBS and 12.5 min with 1% formaldehyde (methanol-free, ThermoFisher scientific). Reactions were quenched by the addition of glycine to a final concentration of 125 µM and the fixed cells were washed in ice-cold 1xPBS and snap frozen in liquid nitrogen. 50x10^6 HEK293T cells were fixed as above, snap frozen in 2x106 aliquots, and stored at -80°C until further use. For calibrated ChIPseq, 2x10^6 HEK293T cells were resuspended in 1ml ice-cold lysis buffer (50mM HEPES pH 7.9, 140mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton X-100) and added to 50x10^6 fixed ESCs, resuspended in 9ml lysis buffer. The cell suspension was incubated for 10 min at 4°C. The released nuclei were then washed (10mM Tris-HCl pH 8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA) for 10 min at 4°C. The chromatin pellet was resuspended in 1mL of ice-cold sonication buffer (10mM Tris-HCl pH 8, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na deoxycholate, 0.5% N-lauroylsarcosine) and sonicated for 25 min using a BioRuptor Pico sonicator (Diagenode), shearing genomic DNA to produce fragments between 300bp and 1kb. Following sonication, Triton X-100 was added to a final concentration of 1%. Two hundred and fifty µg chromatin diluted 10-fold in ChIP dilution buffer (1% Triton-X100, 1mM EDTA, 20mM Tris-HCl (pH 8.0), 150mM NaCl) was used per IP. Three reactions were set up per condition to allow for maximal DNA recovery suitable for library preparation. Chromatin was precleared with protein A Dynabeads blocked with 0.2 mg/ml BSA and 50 µg/ml yeast tRNA and incubated with the respective antibodies overnight at 4°C. Antibody-bound chromatin was purified using blocked protein A Dynabeads for 3 hours at 4°C. ChIP washes were performed as described in Farcas et al 2012. ChIP DNA was eluted in ChIP elution buffer (1% SDS, 100mM NaHCO3) and reversed cross-linked overnight at 65°C with 200mM NaCl and RNase A (Sigma). The reverse cross-linked samples were treated with 20 μg/ml Proteinase K and purified using ChIP DNA Clean and Concentrator kit (Zymo research). The three reactions per condition were pooled at this stage. For each sample, corresponding Input DNA was also reverse cross-linked and purified. The efficiency of the ChIP experiments was confirmed by quantitative PCR. Prior to library preparation, 5-10ng ChIP material was diluted to 50ul in TLE buffer (10mM Tris-HCl pH8.0, 0.1mM EDTA) and sonicated with Bioruptor Pico sonicator for 17 min (30 sec on/off). The antibodies used for ChIPseq experiments were rabbit polyclonal anti-CDK8 (A302-500A, Bethyl laboratories, 2.5μl), rabbit monoclonal anti-RING1B (5694, Cell signaling, 3 μl), rabbit polyclonal anti-PCGF2 (sc-10744, Santa Cruz, 3ul), rabbit monoclonal anti-T7-Tag (D9E1X) (13246, Cell signaling, 3ul). The antibodies used for ChIP-qPCR for TetO targeting experiments were rabbit polyclonal anti-FS2 (produced in house, 59, 3ul), polyclonal anti-MED12 (A300-774A, Bethyl laboratories, 3ul), polyclonal anti-MED1 (A300-793A, Bethyl laboratories, 3ul), polyclonal anti-CCNC (A301-989A, Bethyl laboratories, 3ul). For native ChIP, 50x10^6 ESCs were mixed with 20x10^6 SG4 Drosophila cells and washed with 1x PBS prior to chromatin isolation. Nuclei were released in ice cold lysis buffer (10mM Tris-HCl pH 8.0, 10mM NaCl, 3mM MgCl2, 0.1% NP40), washed and resuspended in 1ml ice cold digestion buffer (10mM Tris-HCl pH 8.0, 10mM NaCl, 3mM MgCl2, 0.1% NP40, 0.25M sucrose, 3mM CaCl2, 1x cOmplete protease inhibitor cocktail (Roche)). Chromatin was digested with 200mM MNase (ThermoFisher scientific) for 5 min at 37°C and the reaction was stopped by the addition of 4mM EDTA pH 8.0. The samples were centrifuged at 1500g for 5 min at 4°C, the supernatant (S1) was retained. The remaining pellet was incubated with 300μl of nucleosome release buffer (10mM Tris-HCl pH 7.5, 10mM NaCl, 0.2mM EDTA, 1x protease inhibitor cocktail (Roche)) at 4°C for 1 h, passed five times through a 27G needle using a 1mL syringe, and spun at 1500g for 5 min at 4°C. The second supernatant (S2) was collected and combined with corresponding S1 sample from above. Digestion to mostly mononucleosomes was confirmed on a 1.5% agarose gel. The prepared native chromatin was aliquot, snap frozen in liquid nitrogen and stored at -80°C until further use. ChIPs were performed as described in Fursova et al 2019, using 5ul of H3K27me3 antibody prepared in-house.
cChIP-seq libraries for both ChIP and Input samples were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina, following manufacturer’s guidelines. Samples were indexed using NEBNext Multiplex Oligos. The average size and concentration of all libraries were analysed using the 2100 Bioanalyzer High Sensitivity DNA Kit (Agilent) followed by qPCR quantification using SensiMix SYBR (Bioline, UK) and KAPA Illumina DNA standards (Roche). Libraries were sequenced as 40 bp paired-end reads in biological triplicate or quadruplicate on Illumina NextSeq 500 platform.

value: Med13;Med13l flfl

value: tamoxifen

tag: treatment time

tag: additional treatment

tag: additional treatment time

tag: replicate

tag: spike-in reference organism

value: Homo sapiens

tag: spike-in cell line

tag: type of chip

value: cross-linked

tag: ChIP

tag: antibody

value: rabbit polyclonal anti-CBX7 (ab21873, abcam)


title: Med1313lfl_TAM_CBX7_rep1

tag: strain

tag: treatment


title: Med1313lfl_TAM_CBX7_rep3


title: PDX1601_H3K27ac_P0

description: H3K27ac on parental PDX 16-01 cells

tag: disease state


title: Med1313lfl_UNT_CBX7_rep3

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, untreated control, Med13/13l fl/fl CBX7 ChIP-seq


title: Soleus Female rep 2

tag: tissue

tag: genotype

tag: Sex


title: TA Male rep 2


title: Soleus Male rep 2


title: PDX1601_IRF2BP2HA_Input

description: Input on PDX 16-01 IRF2BP2-HA cells

tag: cell type


title: PDX1601_IRF2BP2HA_HA

description: HA on PDX 16-01 IRF2BP2-HA cells


title: Med1313lfl_UNT_CBX7_rep2

tag: cell line


title: TA Male rep 1


title: THP1_Input_P0

description: Input on parental THP1 cells

source_name: THP1 cell line


title: Soleus Male rep 1


title: fhy3 mutant_Red light_40 h_rep1

type: RNA

city: Egham

first: Paul

last: Devlin

state: Surrey

address: Egham Hill

department: Biological Sciences

institute: Department of Biological Sciences, Royal Holloway University of London

description:
fhy3-4_40_hrs_Rc
Gene expression data from fhy3 mutant plants after 40 h in constant red light.

hyb_protocol: Biotin Labelled cRNA using Affymetrix GeneChip Hybridization, Wash and Stain Kit, according to guidelines set out by Affymetrix, Santa Clara, CA.

scan_protocol: Scanned according to guidelines set out by Affymetrix, Santa Clara, CA.

data_processing: Raw data from the microarrays was normalized at probe-level using MAS5 algorithm.

label: biotin

source_name: Arabidopsis whole seedlings fhy3 mutant 40 h in red light

label_protocol: Labelled using protocol described in manual Affymetrix GeneChip Expression Analysis Technical Manual, One-Cycle target labelling.

growth_protocol: Seeds were sterilised in 30% bleach, 0.02% Triton X-100, sown on Murashige and Skoog (MS) medium containing 2% sucrose, then stratified for 3 days in darkness at 4 oC. Following stratification, seeds were germinated and grown in 12 h white light/12 h dark cycles for 7 days prior to treatment conditions. White light for this consisted of equally mixed red light (660nm, 60 micromol m-2 s-1), blue light (450nm, 60 micromol m-2 s-1) provided by LEDs within Fytoscope FS80-RGBIR Minicabinets (Photon Systems International, Brno, Czech Republic). Seedlings were maintained at 21 oC.

extract_protocol: Qiagen RNeasy kit protocol.

treatment_protocol: Seedlings were transferred to constant red light (660nm, 120 micromol m-2 s-1) LEDs within Fytoscope FS80-RGBIR Minicabinets (Photon Systems International, Brno, Czech Republic).

value: ~100 whole seedlings

tag: time in red light


title: fhy3 mutant_Red light_24 h_rep1

description:
fhy3-4_24hrs _Rc
Gene expression data from fhy3 mutant plants after 24 h in constant red light.

source_name: Arabidopsis whole seedlings fhy3 mutant 24 h in red light


title: fhy3 mutant_Red light_32 h_rep1

description:
fhy3-4_32hrs_Rc
Gene expression data from fhy3 mutant plants after 32 h in constant red light.

source_name: Arabidopsis whole seedlings fhy3 mutant 32 h in red light


title: Pcgf4-/-Pcgf2fl_Input_TAM_rep3

description: input for CDK8 ChIPs in Pcgf4-/-Pcgf2 flfl

data_processing:
For cChIP-seq, Bowtie2 was used to align paired-end reads to the concatenated mouse and spike-in genome sequences (mm10+dm6 for native cChIP-seq for histone modifications; mm10+hg19 for cross-linked cChIP-seq) with the “--no-mixed” and “--no-discordant” options. Non-uniquely mapping reads were discarded, and PCR duplicates were removed with Sambamba.
For visualization of cChIP-seq, the data were internally calibrated using dm6 or hg19 spike-in as described previously (Fursova et al. 2019). Briefly, uniquely aligned mm10 reads were randomly subsampled based on the total number of spike-in (dm6 or hg19) reads in each sample. To account for variations in the spike-in cell mixing, we used the ratio of spike-in/mouse total read counts in the corresponding Input samples to correct the subsampling factors. After normalisation, read coverages across genomic regions of interest were compared for individual biological replicates using multiBamSummary and plotCorrelation from deepTools. For each experimental condition, biological replicates correlated well (Pearson correlation coefficient > 0.9) and were merged for downstream analysis.
Genome_build: mm10; dm6; hg19
Supplementary_files_format_and_content: bigWig files showing the genome coverage for merged spike-in normalised biological replicates were generated using the pileup function from MACS2.

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, tamoxifen treated,Pcgf4-/-Pcgf2 fl/fl, Input

value: Pcgf4-/-Pcgf2 flfl

tag: treatment time

tag: additional treatment

value: rabbit polyclonal anti-CDK8 (A302-500A, Bethyl laboratories)


title: Med1313lfl_UNT_CBX7_rep1

tag: additional treatment time

tag: replicate


title: Pcgf4-/-Pcgf2fl_Input_TAM_rep2

tag: spike-in reference organism

tag: spike-in cell line


title: AG CD45+ cells from female mice

city: Saint-Petersburg

first: Maria

last: Firulyova

address: Kronverksky Pr. 49

department: Department of Computer Technologies

country: Russia

institute: Information Technologies, Mechanics, and Optics University

description: 10x Genomics

data_processing:
quality control, Cell Ranger Single Cell Software Suite (v4.0.0)
sample de-multiplexing, Cell Ranger Single Cell Software Suite (v4.0.0)
barcode processing, Cell Ranger Single Cell Software Suite (v4.0.0)
single-cell 3′ gene counting , Cell Ranger Single Cell Software Suite (v4.0.0)
alignment, Cell Ranger Single Cell Software Suite (v4.0.0)
Assembly: mm10-2020-A
Supplementary files format and content: Filtered matrix of gene by cell expression, file with barcodes and file with expressed genes.

source_name: Adrenal glands

growth_protocol: All mice were bred and housed in specific pathogen-free conditions maintained by animal facilities in either the Mediterranean Center of Molecular Medicine (INSERM U1065, Université Côte d’Azur), facilitie were maintained at ambient temperature of ~20-23 °C, with 12/12-hour light/dark cycle and food available ad libitum

extract_protocol:
Tissues were harvested and washed in PBS. Adipose depots surrounding the adrenal glands were carefully removed before shredding the tissue with scissors. Then the samples were incubated for 30 minutes at 37°C in PBS containing 300 µg/mL Liberase and 100 µg/mL DNAse I. The resulting suspension was homogenized using a syringe and a 20G needle, passed through a 100 µm sieve and centrifuged at 400g for 5 minutes. Cells were then resuspended in FACS buffer (PBS containing 0,3 mM EDTA and 0,06% BSA), stained for 30 minutes at 4°C in the dark and then washed. Viabilty dye (DAPI) were applied and cells stain using CD45 antibody. CD45+ alive cells were purified using a BD FACS Aria III cell sorter. then cells were loaded on a Chromium Controller (10x Genomics) with a target output of 5000 cells per sample. Reverse transcription, cDNA synthesis/amplification and library preparation were performed according to the 10x Genomics protocol (Chromium™ Single Cell 3′ Reagent Kit, v3.1 Chemistry).
scRNA libraries were sequenced on an Illumina NextSeq 500/550 High Output flowcell: the forward read had a length of 28 bases that included the cell barcode and the UMI; the reverse read had a length of 55 bases that contained the cDNA insert.   Alignment, barcode assignment and UMI counting with Cell Ranger v4.0.0 was used to perform sample demultiplexing, barcode processing and single-cell 3ʹ counting. Cell Ranger’s mkfastq function was used to demultiplex raw base call files from the HiSeq4000 sequencer into sample specific FASTQ files.  Barcodes in both samples that were considered to represent noise and low-quality cells were filtered out using knee-inflection approach available in DropletUtils package (version 1.4.3). For analysis, Seurat package (version 3.1.0) was used, genes which express in less than 2 cells and cells which have non-zero counts in less than 200 genes were additionally filtered from both barcode expression matrices, and the result matrices were used as analysis inputs (Butler et al., 2018). The fraction of mitochondrial genes was calculated for every cell, and cells with a mitochondrial fraction >1.2% were filtered out. After all filtering procedures, 3,636 cells were left in the scRNA-seq data of the female sample, and 2,240 cells were left in scRNA-seq of the male sample.   Both samples were normalized using SCTransform function with mitochondrial content as variable to regress out in a second non-regularized linear regression (Hafemeister and Satija, 2019). For integration purpose, variable features across the samples were selected by SelectIntegrationFeatures function with the number of features equal to 2000. Then the object was prepared for integration (PrepSCTIntegration function), the anchors were found (FindIntegrationAnchors function) and the samples were merged into the whole object (IntegrateData function) (Stuart et al., 2019). The dimensionality of the object was reduced by principal component analysis (PCA), and the first 20 principal components (PCs) were used further to obtain uniform manifold approximation and projection (UMAP) dimensionality reduction by RunUMAP function. Graph-based clustering was run using FindNeighbors and FindClusters with a resolution of 1.0 and the first 20 PCs as input, and the 21 clusters were identified. Differential expression analysis was implemented using MAST package.  During manual cluster annotation using canonical gene markers, a cluster corresponding to doublets of NK cells and macrophages was identified and excluded from the main figures. We provide this suggestion using DoubletFinder package (version 2.0.3) using doubletFinder_v3 function (with parameters PCs = 10, pN = 0.25, pK = 0.005) for each sample separately (Figure S2A) (McGinnis et al., 2019).  For visualization purposes, the custom labels were assigned to several clusters by merging several clusters for simplification (e.g., clusters 1, 6, 20 were merged as T cells, clusters 2, 12 were merged as B cells and clusters 0, 3, 19 were merged as NK cells). The gene signature heatmap was drawn using the scaled data slot of the integrated assay.  For trajectory analysis, clusters assigned as monocytes and macrophages were used, and infer_trajectory function from the dyno package (version 0.1.2) was used with the available slingshot singularity container (version 1.0.3) (Saelens et al., 2019; Street et al., 2018). In order to exclude the technical bias across the samples, the data slot from the integrated assay was used as an input expression for trajectory inference. Monocytes cluster was used as a root cluster in terms of given priors to slingshot algorithm. Trajectory visualization was implemented after dimensionality reduction by UMAP using dimred_umap function.

value: CD45+ cells

value: Adrenal glands

tag: age

value: 7 week -old


title: Wild type_Red light_32 h_rep1

description:
No-0_32hrs_Rc
Gene expression data from wild type plants after 32 h in constant red light.

source_name: Arabidopsis whole seedlings wild type 32 h in red light

value: wild type No-0


title: THP1_H3K27ac_P0

description: H3K27ac on parental THP1 cells

value: untreated

value: Acute Myeloid Leukemia


title: THP1_IRF2BP2HA_Input

description: Input on on THP1 IRF2BP2-HA cells


title: AG CD45+ cells from male mice

description: 10x Genomics


title: Wild type_Red light_48 h_rep1

description:
No-0_48hrs_Rc
Gene expression data from wild type plants after 48 h in constant red light.

source_name: Arabidopsis whole seedlings wild type 48 h in red light


title: THP1_IRF2BP2HA_HA

description: HA on THP1 IRF2BP2-HA cells


title: fhy3 mutant_Red light_48 h_rep1

description:
fhy3-4_48hrs_Rc
Gene expression data from fhy3 mutant plants after 48 h in constant red light.

source_name: Arabidopsis whole seedlings fhy3 mutant 48 h in red light


title: Pcgf4-/-Pcgf2fl_Input_TAM_rep1

tag: type of chip

tag: ChIP

tag: antibody


title: Wild type_Red light_24 h_rep1

description:
No-0_24hrs _Rc
Gene expression data from wild type plants after 24 h in constant red light.

source_name: Arabidopsis whole seedlings wild type 24 h in red light


title: Pcgf4-/-Pcgf2fl_Input_UNT_rep3

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, untreated control,Pcgf4-/-Pcgf2 fl/fl, Input

tag: strain

tag: treatment


title: Wild type_Red light_40 h_rep1

description:
No-0_40hrs_Rc
Gene expression data from wild type plants after 40 h in constant red light.

source_name: Arabidopsis whole seedlings wild type 40 h in red light

tag: tissue

tag: genotype


title: single cell RNA seq of human nasal epithelial tissue 5

description: single-cell RNA-seq

data_processing:
Single cell RNA-seq matrices were generated using Cell Ranger 3.1.0
Genome_build: hg19 genome v1.0
Supplementary_files_format_and_content: 10X genomics CellRanger output: UMI count expression values for each gene (rows) in each cell (columns)

source_name: human nasal epithelial tissue

extract_protocol:
A total of 2500–3000 cells were used for scRNA-seq using the 10X Genomics Chromium system.
Single cell libraries were prepared using the Chromium Single Cell 3ʹ Library kit

treatment_protocol: The cultures were first digested with 0.25% trypsin and 1 mM EDTA at 37°C for 5 min, and then further digested to single cells using Accutase at 37°C for 10 min.

tag: disease

value: cystic fibrosis