title: Patient 34 KGH301

tag: age at dx

tag: gender

value: no

value: skin

tag: extranodal sites > 1

tag: Stage

tag: chemotherapy

tag: # of cycles

tag: status

value: Alive

tag: bcl2 by halo

tag: ihc bcl2 high?1=yes,0=no

tag: ihc myc high?1=yes,0=no

value: GCB

value: Group B

tag: tissue


title: Caco-2, mock, 48h, replicate 3

status: Public on Nov 10 2022

type: SRA

city: Heidelberg

first: Lukas

last: Adam

address: Im Neuenheimer Feld 267

department: BioQuant

country: Germany

institute: Heidelberg University

library_source: transcriptomic

data_processing:
Read counts were processed using the Spliced Transcripts Alignment to a Reference (STAR) software (version STAR-2.6.0c)
First a combined index was created by concatenating both genome assemblies (combine .fa files, combine .gff files, run star with default setting and --sjdbOverhang 100)
Each sample was then mapped to the combined index using the STAR aligner (default setting, --outSAMtype BAM SortedByCoordinate; --quantMode GeneCounts)
Using the samtools software package (version samtools-1.11) each BAM file (sample) was then indexed and reads were split into host-genome and virus mapping reads (one host.bam file and virus.sam file for each sample)
Read counts were extracted for each sample and separately for virus and host genome using the featureCounts function (version v2.0.0) from the subread package. Reads were mapped to exons for the host genome and CDS for the virus genome
Assembly: GRCh38.p13, NC_045512.2
Supplementary files format and content: comma-separated value (csv) files include raw counts for each sample and gene. A csv file is given for all the reads/counts that map to the host genome and

molecule: total RNA

organism: Homo sapiens

extract_protocol:
RNA was extracted from infected or mock-treated Caco-2 cells at 0, 1, 2, 4, 7, 12, 24 and 48  hpi using the Qiagen RNAeasy plus extraction kit (Qiagen, Hilden, Germany).
For quantifying SARS-CoV-2 genome abundance in mock samples, cDNA was made using  iSCRIPT reverse transcriptase (BioRad, Hercules, CA, USA). q-RT-PCR was performed  using iTaq SYBR green (BioRad) as per manufacturer’s instructions, TBP was used as  housekeeping gene and for normalization (COV1 primers: for 5’-  GCCTCTTCTGTTCCTCATCAC-3’, rev 5’-AGACAGCATCACCGCCATTG-3’; TBP  primers: for 5’-CCACTCACAGACTCTCACAAC-3’, rev 5’-  CCACTCACAGACTCTCACAAC-3’; Eurofins, Luxemburg). RNA samples were stored at -  80°C. DNA libraries were prepared at GeneWiz Inc. (Leipzig, Germany) using the NEBnext  Ultra II RNA directional Kit (New England Biolabs GmbH, Frankfurt, Germany). Paired-end  sequencing of 2×150bp was performed at GeneWiz Inc. using an Illumina NovaSeq 6000  instrument (Illumina, San Diego CA, USA).

treatment_protocol: SARS-CoV-2 (strain BavPat1) was obtained from the European Virology Archive. The virus  was amplified in Vero E6 cells and collected at passage 3. Virus titers were determined by  TCID50 assay. Caco-2 cells were infected using an MOI values of 0.1, 1 or 5 virus particles  per cell. For RNA-seq experiments, an MOI of 5 was chosen. Medium was removed from  Caco-2 cells and virus was added to cells for 1 hour at 37°C. Virus was removed, cells were  washed once with PBS, and medium containing a tested inhibitor or empty medium was  added to the cells.

tag: cell line

tag: cell type

value: Human colorectal adenocarcinoma cells

tag: genotype

value: WT

tag: treatment

value: mock

tag: time point_(in_hours)


title: Patient 32 KGH299

type: RNA

city: Kingston

first: David

last: LeBrun

state: Ontario

address: 88 Stuart street

department: Pathology and Molecular Medicine

country: Canada

institute: Queen's University

description: NanoString codeset was used to enumerate transcripts from 58 KHSC samples. This codeset was designed to quantify expression of 135 genes, including the 92 TCF3 target genes, 35 genes implicated in myelodysplastic syndrome (MDS), and 8 “housekeeping” genes whose expression we expected to be relatively invariant from case to case

hyb_protocol: Transcripts were enumerated using the NanoString nCounter® system (NanoString Technologies, Seattle, WA)

scan_protocol: According to manufacturer's instructions

data_processing: Quality assessment and normalization were performed with NSolver Analysis Software (NanoString Technologies, Inc., v3.0) using geometric mean for background correction and positive control normalization. ARHGAP27, RB1, NRF1, BAALC and ZNF19 showed very low variability among samples and were used as reference genes for normalization. Expression according to probes associated with the same gene (2 probes each for SAMHD1 and EPB41L5) was averaged.

source_name: biopsy

label_protocol: 500 ng of total RNA from each sample was used to enumerate transcripts using the NanoString nCounter® system (NanoString Technologies, Seattle, WA)

extract_protocol: Total RNA was purified from 1 mm cores of FFPE tissue from representative areas of paraffin blocks using the Qiagen AllPrep FFPE kit

tag: diagnosis

value: DLBCL

value: M

tag: b symptoms?

tag: bulky disease?

tag: biopsy site

value: vertebra

tag: ipi score

tag: ecog >= 2

value: yes

tag: ldh > uln

value: R-CHOP

tag: response chenson

value: complete

tag: relapse?

value: nd

tag: myc fish

tag: bcl2 fish

tag: coo by lymph2cx

tag: classification

value: FFPE tissue


title: Patient 31 KGH298

tag: age at dx

tag: gender

value: F

value: left inguinal LN

tag: extranodal sites > 1

tag: Stage

tag: chemotherapy

tag: # of cycles

value: partial

tag: status

tag: bcl2 by halo

tag: ihc bcl2 high?1=yes,0=no

tag: ihc myc high?1=yes,0=no

value: Normal

value: ABC

value: Group A

tag: tissue


title: HCT116 cells, Short transposon with wild-type piggyBac replicate 1

city: Bethesda

first: Pavol

last: Genzor

state: MD

address: 6720A Rockledge Drive, Suite 100

department: ACESO

country: USA

institute: Henry M Jackson Foundation

data_processing:
To generate *_peaks.bed files: The reads were trimmed twice using cutadapt (v3.4), first to remove the seqeuncing adapters, and second time to remove TIR seqeunce. Trimmed reads were alligned to human genome (hg38) using Hisat aligner (v2.2.1.0) using standard settings. Generated bam files were loaded into R using custom function and paired-end reads converted into read fragments. To call peaks, read fragments were used to generate genomic coverage, and any region with at least five reads coverage was considered as a peak and was reported in the *peaks.bed files. For exact methods and custom code please visit related github fount at https://github.com/HaaseLab.
Assembly: GRCh38.p5.v24
Supplementary files format and content: Tab delimited text files in standard bed format with following colums: chromosome, start, end, peakID, peak_area_under_the_curve, strand, peak_maximum_height, peak_width, total_read_fragments_analyzed_in_sample

source_name: Large intestine, colon

extract_protocol:
RNA was extracted using RNaesy Mini Kit (Qiagen #74106).
Total RNA was reverse-transcribed to cDNA using M-MLV (Promega #M3681) and primer SMART-dT18VN (5`-AAGCAGTGGTATCAACGCAGAGTACGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN). Next, cDNA was amplified using different pairs of primers containing regions within specific tranpsoson used in this study (see suplemental information) and primer Smart (5`-AAGCAGTGGTATCAACGCAGAGT). Amplified cDNA was purified using PCR gel purification column (Macherey-Nagel #740609) and 500 ng of purified cDNA was was fragmented and tagged using Illumina DNA Prep (Illumina #20060060). Tagged DNA was PCR amplified (Read1-TnME: 5`-ACACTCTTTCCCTACACGACGCTCTTCCGATCTAGATGTGTATAAGAGACA*G; Read2 primer was specific to transposase species, see suplemental information) and amplicons from 100-500 bp were size selected on 2% agarose gel. Dual index primers (NEB #E7780S) for seqeuncing were added by amplifying tagmented libraries usign Q5 Polymerase (NEB #M0544S) following the NEBnext protocol (NEB #E7645S - Section 4.1). The PCR products were purified using AMPure XP beads (Beckman Coulter #A63881) using 0.9x bead volume. The quality of final library was verified using TapeStation.
See the publication 10.1016/j.cell.2020.06.037 for detailed methods to construct library from self-reporting transposons (SRTs).

treatment_protocol: Cells transfected with different self-reporting transposon construct were grown in presence of 3 µg/ml puromycin for two weeks.

value: Large intestine, colon

tag: cell line

tag: cell type

value: colorectal carcinoma

tag: genotype

tag: transfection

value: transfected with self-reporting transposon (SRT)

tag: treatment


title: Caco-2, mock, 48h, replicate 2

value: Human colorectal adenocarcinoma cells

value: WT

value: mock

tag: time point_(in_hours)


title: Patient 29 KGH295

tag: diagnosis

value: DLBCL

tag: age at dx

value: M

tag: b symptoms?

value: no

tag: bulky disease?

tag: biopsy site

value: left neck LN

tag: ipi score

tag: ecog >= 2

tag: ldh > uln

tag: response chenson

tag: relapse?

value: Dead

tag: myc fish

value: Translocated

tag: bcl2 fish

value: CNI

tag: coo by lymph2cx

value: GCB

tag: classification


title: Caco-2, mock, 48h, replicate 1

tag: cell line

tag: cell type

tag: genotype


title: Caco-2, mock, 12h, replicate 2

tag: treatment

tag: time point_(in_hours)


title: Caco-2, mock, 12h, replicate 1


title: HCT116 cells, Short transposon with hyperactive piggyBac replicate 1

tag: tissue

tag: transfection


title: Caco-2, mock, 4h, replicate 3


title: Patient 30 KGH296

tag: diagnosis

tag: age at dx

tag: gender

value: F

tag: b symptoms?

tag: bulky disease?

tag: biopsy site

value: left scalene region

tag: extranodal sites > 1

tag: Stage

tag: chemotherapy

value: R-CHOP

tag: # of cycles

value: partial

tag: status

value: Alive

tag: bcl2 by halo

tag: ihc bcl2 high?1=yes,0=no

tag: ihc myc high?1=yes,0=no

value: nd

value: Group B

value: FFPE tissue


title: Caco-2, mock, 4h, replicate 2

tag: cell line

tag: cell type

value: Human colorectal adenocarcinoma cells

tag: genotype

value: WT

tag: treatment

value: mock

tag: time point_(in_hours)


title: Caco-2, mock,12h, replicate 3


title: Patient 28 KGH294

tag: diagnosis

value: DLBCL

tag: age at dx

tag: gender

value: M

value: no

value: left posterior triangle LN

tag: ipi score

tag: ecog >= 2

tag: ldh > uln

value: yes

tag: response chenson

tag: relapse?

tag: myc fish

tag: bcl2 fish

tag: coo by lymph2cx

tag: classification

tag: tissue


title: Caco-2, mock, 4h, replicate 1

tag: cell line

tag: cell type


title: Patient 26 KGH291

tag: b symptoms?

tag: bulky disease?

tag: biopsy site

value: right inguinal LN

tag: extranodal sites > 1

tag: Stage

tag: chemotherapy

tag: # of cycles

value: complete

tag: status

tag: bcl2 by halo

tag: ihc bcl2 high?1=yes,0=no

tag: ihc myc high?1=yes,0=no

value: CNI

value: Unclassified

value: Group A


title: Patient 25 KGH289

tag: diagnosis

tag: age at dx

tag: gender

value: F

value: left neck

tag: ipi score

tag: ecog >= 2

tag: ldh > uln

value: R-CHOP

tag: response chenson

value: partial

tag: relapse?

value: Alive

tag: myc fish

value: Normal

tag: bcl2 fish

value: GCB


title: Caco-2, infected, 48h, replicate 3

tag: cell line

tag: cell type

value: Human colorectal adenocarcinoma cells

tag: genotype

value: WT

tag: treatment

value: infected

tag: time point_(in_hours)


title: Patient 24 KGH287

value: DLBCL

tag: b symptoms?

value: no

tag: bulky disease?

tag: biopsy site

value: small bowel mesentery mass

tag: extranodal sites > 1

tag: Stage

tag: chemotherapy

tag: # of cycles

tag: status

tag: bcl2 by halo

tag: ihc bcl2 high?1=yes,0=no

value: nd

tag: coo by lymph2cx

tag: classification

value: Group B

tag: tissue

value: FFPE tissue


title: Patient 23 KGH286

tag: diagnosis

tag: age at dx

tag: gender

value: mesenteric LN

tag: ipi score

tag: ecog >= 2

tag: ldh > uln

value: yes

tag: response chenson

value: stable disease

tag: relapse?

value: Dead

tag: ihc myc high?1=yes,0=no

tag: myc fish

value: CNI

tag: bcl2 fish

value: Unclassified

value: Group A


title: Patient 22 KGH285

value: F

tag: b symptoms?

tag: bulky disease?

tag: biopsy site

value: bone

tag: extranodal sites > 1

tag: Stage

tag: chemotherapy

value: R-CHOP

tag: # of cycles

value: partial

tag: status

value: Alive

value: ABC


title: Patient 21 KGH282

tag: diagnosis

value: DLBCL

tag: age at dx

tag: gender

value: left axillary LN excision

value: no

tag: bcl2 by halo

tag: ihc bcl2 high?1=yes,0=no

value: Normal

value: Translocated

tag: coo by lymph2cx

value: GCB

tag: classification

tag: tissue


title: Mting2-1 rep 3

city: Auckland

first: Joanna

last: Putterill

state: Auckland

address: 3A Symonds Street

department: School of Biological Sciences

country: New Zealand

institute: The University of Auckland

library_source: genomic

data_processing:
Two biological replicates from each genotype were analyzed further. ChIP Sequencing datasets were aligned against the Medicago truncatula genome (Mt4.0) using Bowtie2 with default parameters. Only uniquely mapped reads were retained (Picard toolkit (https://broadinstitute.github.io/picard/faq.html) running MarkDuplicates with REMOVE_DUPLICATES=true).
The mapped reads were filtered based on mapping quality using samtools (-q 30).
ChIP binding peaks were called by MACS2. Only peaks detected by MACS2 and present in all two biological replicates of wild type R108 and Mting2-1 mutant were kept (using bedtools intersect (Quinlan et al., 2010)). Peaks were defined as specific when there are no peaks detected in the same region between the wild type R108 and the Mting2-1 mutant.
The RPKM and the heatmap for the ChIP-Seq datasets were computed using deepTools2.
Genome_build: MedtrA17_4.0 (Mt4.0v2_GenesCDSSeq_20140818_1100.fasta)
Supplementary_files_format_and_content: bigWig file containing H3K4me3 ChIP peaks for wild type R108 (K4_2.f. and K4_3.f.) and Mting2-1 mutant (K4_n7_2.f. and K4_n7_3.f.).

molecule: genomic DNA

organism: Medicago truncatula

source_name: whole aerial tissue

growth_protocol: Seeds from wild type R108 and Mting2-1 mutant plants were scarified, sterilized in chlorine for 45 minutes and germinated overnight at 15°C in the dark with gentle shaking. Germinated seeds were then transferred to ½ strength SH9 media with half strength sucrose in tubs and vernalized at 4°C for 3 weeks and then grown in LD conditions (16 h light/8 h dark) in growth cabinets for 2 weeks.

extract_protocol:
Chromatin was extracted and sonicated for 10 cycles (30s on, 30s off) using the Bioruptor® Pico sonication device (Diagenode, USA) to obtain the size range of 200–500 bp. Protein A magnetic beads were washed once and resuspended in ChIP Dilution Buffer. The chromatin was pre-cleared with protein A magnetic beads and then incubated overnight with monoclonal anti-H3K4me3 antibody, magnetic bead suspension, and ChIP Dilution Buffer with rotation at 4°C. The beads were collected using a magnetic rack, washed, reverse crosslinked and DNA was purified using phenol-chloroform extraction method. The quality and quantity of the ChIP DNA were checked by Bioanalyzer.
Total of 6 ChIP-Seq libraries (3 biological replicates from wild type R108 and 3 from Mting2-1 mutant) were constructed using the NEBNext ChIP-Seq Library Prep Kit for Illumina (NEB, USA). Sequencing was done in an Illumina platform (NovaSeq 6000, 150 bp paired-end) aimed to generate 20 million PE reads.

treatment_protocol: One gram of whole aerial tissues were harvested from 14-17 days old plants at 4 h after dawn (ZT4). One gram makes one biological replicate and three biological replicates were harvested from each genotype. All samples were fixed and crosslinked with formaldehyde under vacuum for 15 minutes. Crosslinking was stopped by glycine (0.125 M) and tissues were snap-frozen and ground into fine powder in liquid N2.

tag: genotype

value: Mting2-1 mutant

tag: treatment

value: vernalised long day

tag: age

value: 14-17 days old


title: Caco-2, infected, 24h, replicate 3

tag: cell line

tag: cell type

value: Human colorectal adenocarcinoma cells

value: WT

value: infected

tag: time point_(in_hours)


title: Mting2-1 rep 2


title: Patient 20 KGH281

value: M

tag: b symptoms?

value: yes

tag: bulky disease?

tag: biopsy site

value: left neck LN

tag: ipi score

tag: ecog >= 2

tag: ldh > uln

tag: extranodal sites > 1

tag: Stage

tag: chemotherapy

tag: response chenson

value: complete

tag: relapse?

tag: ihc myc high?1=yes,0=no

tag: myc fish

value: nd

tag: bcl2 fish

value: Group B

value: FFPE tissue


title: Mting2-1 rep 1

tag: genotype

tag: treatment

tag: age


title: Patient 27 KGH293

tag: diagnosis

value: DLBCL

tag: age at dx

tag: gender

value: F

tag: b symptoms?

value: no

value: bone

value: R-CHOP

tag: # of cycles

tag: status

value: Dead

tag: bcl2 by halo

tag: ihc bcl2 high?1=yes,0=no

tag: coo by lymph2cx

tag: classification

tag: tissue


title: Caco-2, infected, 48h, replicate 1

tag: cell line

tag: cell type

tag: time point_(in_hours)


title: Patient 19 KGH280

tag: bulky disease?

tag: biopsy site

value: left femur

tag: ipi score

tag: ecog >= 2

tag: ldh > uln

tag: extranodal sites > 1

tag: Stage

tag: chemotherapy

tag: response chenson

tag: relapse?

value: Alive

tag: ihc myc high?1=yes,0=no

tag: myc fish

value: Normal

tag: bcl2 fish

value: GCB


title: WT rep 2

tag: genotype

value: wild type R108

tag: treatment

value: vernalised long day

tag: age

value: 14-17 days old


title: WT rep 1


title: Patient 18 KGH279

tag: diagnosis

tag: age at dx

tag: gender

value: M

tag: b symptoms?

value: yes

value: left axillary LN excision

tag: # of cycles

value: complete

tag: status

tag: bcl2 by halo

tag: ihc bcl2 high?1=yes,0=no

value: CNI

tag: coo by lymph2cx

value: Unclassified

tag: classification

value: Group A

tag: tissue


title: WT rep 3


title: Caco-2, infected, 48h, replicate 2

tag: cell line

tag: cell type

value: Human colorectal adenocarcinoma cells

value: WT

value: infected

tag: time point_(in_hours)


title: Mting2-1 leaves rep 3

data_processing:
The quality of the sequenced raw reads was assessed using FastQC (v0.11.7), with reports combined using MultiQC (v1.7).
Residual adaptors and low-quality sequences from the reads were removed using BBDuk tool in the BBTools suite (v37.54). Reads were trimmed from the 3’ end where quality dropped below a PHRED score of 20 and any remaining reads under 36bp in length were also excluded.
Trimmed reads were mapped to the Mt4.0v2 transcriptome using Salmon (v0.8.2). The resulting count tables, in which abundance is measured as Transcripts per Million (TPM), were then imported into R using the tximport package (v1.12.0).
Normalisation, differential expression analysis and visualisation were performed using DESeq2 (v1.24.0). Differentially expressed transcripts were filtered-out using a cut-off of adjusted p-value ≤ 0.05 and log2fold-change ≥ 1.
Enrichment analyses were performed in R using the goseq package (v1.36.0).
Genome_build: MedtrA17_4.0 (Mt4.0v2_GenesCDSSeq_20140818_1100.fasta)
Supplementary_files_format_and_content: All files are in tab-delimited text file format containing matrix table of TPM values for each gene and each sample.

source_name: leaves

growth_protocol: Seeds were scarified, sterilised in chlorine solution for 15 minutes, and germinated overnight at 15°C in gently shaking tubes of water and dark conditions for 24 hours.Germinated seeds from wild type R108 and Mting2-1 mutant plants were transferred to ½ strength SH9 media with half strength sucrose in tubs and vernalized at 4 °C for 3 weeks and then grown in LD conditions (16 h light/8 h dark) in growth cabinets.

extract_protocol:
Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen, Germany) following the manufacturer's instructions. The quantity and quality of RNA samples were checked using the Bioanalyzer 2100 (Agilent Technologies, USA)
The 12 RNA-Seq libraries were prepared using the TruSeq Stranded mRNA kit (Illumina, USA) following standard protocol, by Macrogen

treatment_protocol: Trifoliate leaves or shoot apices were harvested from 13–15-day-old plants at 4 h after dawn (ZT4) and snap-frozen and ground to powder in liquid nitrogen. Three biological replicates per tissue type for each genotype were harvested.

value: leaves

tag: genotype

value: Mting2-1 mutant

value: 13 - 15 day old plants


title: Mting2-1 leaves rep 2

tag: treatment


title: Patient 17 KGH277

value: DLBCL

value: F

value: no

tag: bulky disease?

tag: biopsy site

value: right axillary LN

tag: ipi score

tag: ecog >= 2

tag: ldh > uln

tag: extranodal sites > 1

tag: Stage

tag: chemotherapy

value: R-CHOP

tag: response chenson

tag: relapse?

value: Dead

tag: ihc myc high?1=yes,0=no

tag: myc fish

tag: bcl2 fish

value: Normal

value: GCB

value: Group B

value: FFPE tissue


title: Caco-2, infected, 24h, replicate 2

tag: cell line

tag: cell type


title: Caco-2, infected, 12h, replicate 2

tag: genotype

tag: time point_(in_hours)


title: Patient 16 KGH276

tag: diagnosis

tag: age at dx

tag: gender

tag: b symptoms?

tag: bulky disease?

value: thyroidectomy

tag: # of cycles

value: complete

tag: status

value: Alive

tag: bcl2 by halo

tag: ihc bcl2 high?1=yes,0=no

tag: coo by lymph2cx

tag: classification

tag: tissue


title: WT leaves rep 3

value: wild type R108

tag: treatment

value: vernalised long day

tag: age


title: WT leaves rep 1

value: leaves


title: WT leaves rep 2

value: 13 - 15 day old plants


title: Caco-2, infected, 12h, replicate 1

tag: cell line

tag: cell type

value: Human colorectal adenocarcinoma cells

value: WT

value: infected


title: Mting2-1 apex rep 3

source_name: shoot apex

value: shoot apex

tag: genotype

value: Mting2-1 mutant


title: Patient 15 KGH275

tag: diagnosis

value: DLBCL

value: F

value: yes

tag: biopsy site

value: small bowel mesentery

tag: ipi score

tag: ecog >= 2

value: no

tag: ldh > uln

tag: extranodal sites > 1

tag: Stage

tag: chemotherapy

value: R-CHOP

tag: response chenson

value: partial

tag: relapse?

tag: ihc myc high?1=yes,0=no

tag: myc fish

value: CNI

tag: bcl2 fish

value: Translocated


title: Mting2-1 apex rep 2

tag: tissue

tag: treatment

value: vernalised long day

tag: age


title: Caco-2, infected, 7h, replicate 3

tag: cell line

tag: cell type

tag: genotype

tag: time point_(in_hours)


title: WT apex rep 3

value: wild type R108


title: Mting2-1 apex rep 1

value: 13 - 15 day old plants


title: Patient 13 KGH272

tag: diagnosis

tag: age at dx

tag: gender

value: M

tag: b symptoms?

tag: bulky disease?

tag: biopsy site

value: right neck LN

tag: ipi score

tag: ecog >= 2

tag: # of cycles

tag: status

value: Dead

tag: bcl2 by halo

tag: ihc bcl2 high?1=yes,0=no

value: Normal

tag: coo by lymph2cx

value: Unclassified

tag: classification

value: Group A

value: FFPE tissue


title: Caco-2, infected, 7h, replicate 2

tag: cell line

tag: cell type

value: Human colorectal adenocarcinoma cells

value: WT

tag: treatment

value: infected


title: Caco-2, infected, 12h, replicate 3

tag: genotype

tag: time point_(in_hours)


title: Caco-2, infected, 24h, replicate 1


title: Patient 12 KGH271

tag: diagnosis

value: DLBCL

tag: age at dx

tag: gender

value: no

value: mediastinum

tag: ldh > uln

value: yes

tag: extranodal sites > 1

tag: Stage

tag: chemotherapy

value: R-CHOP

tag: response chenson

tag: relapse?

tag: ihc myc high?1=yes,0=no

tag: myc fish

tag: bcl2 fish

value: GCB

tag: tissue


title: Caco-2, infected, 7h, replicate 1

tag: cell line

tag: cell type


title: WT apex rep 2

value: shoot apex

tag: genotype

value: wild type R108

tag: treatment

value: vernalised long day

tag: age

value: 13 - 15 day old plants


title: Caco-2, infected, 4h, replicate 3

tag: time point_(in_hours)


title: Mting2-1 leaves rep 1

value: leaves

value: Mting2-1 mutant


title: WT apex rep 1


title: SH_mut3_081121

city: Philadelphia

first: Brian

middle: C.

last: Capell

state: PA

address: 421 Curie Boulevard Biomedical Research Building 1020 Biomedical Research Building 1020

department: Dermatology

institute: University of Pennsylvania

data_processing:
Aligned using RNA STAR under default settings
Differential expression analysis was performed via DESeq2
Assembly: Mus musculus GRCm38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

molecule: polyA RNA

organism: Mus musculus

source_name: basal epidermal cells

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (QIAGEN)
RNA-seqNEBNext Poly(A) mRNA magnetic isolation module, followed by NEBNext Ultra Directional RNA library prep kit for Illumina

value: basal epidermal cells

value: p63CreER; Piezo1fl/fl ; R26-mTmG (Piezo1 cKO)

value: tamoxifen injections (3x, 20ug/dose)


title: SH_mut2_081121


title: Caco-2, infected, 4h, replicate 2

value: Human colorectal adenocarcinoma cells

value: WT


title: SH_ctrl1_081121

value: vehicle


title: SH_mut1_081121


title: SH_ctrl3_081121


title: Patient 14 KGH274

tag: diagnosis

value: DLBCL

tag: age at dx

tag: gender

value: F

tag: b symptoms?

tag: bulky disease?

tag: biopsy site

value: left neck LN

tag: ipi score

tag: ecog >= 2

value: no

tag: # of cycles

value: partial

tag: status

value: Dead

tag: bcl2 by halo

tag: ihc bcl2 high?1=yes,0=no

value: nd

tag: coo by lymph2cx

tag: classification

value: Group B

value: FFPE tissue


title: Patient 11 KGH270

value: M

value: yes

value: left thigh mass

tag: ldh > uln

tag: extranodal sites > 1

tag: Stage

tag: chemotherapy

value: R-CHOP

tag: response chenson

value: complete

tag: relapse?

value: Alive

tag: ihc myc high?1=yes,0=no

tag: myc fish

value: CNI

tag: bcl2 fish

value: Translocated

value: GCB

tag: tissue


title: Caco-2, infected, 4h, replicate 1

tag: cell line

tag: cell type

value: Human colorectal adenocarcinoma cells

tag: genotype

value: WT

tag: treatment

value: infected

tag: time point_(in_hours)


title: Patient 8 KGH262

tag: diagnosis

value: DLBCL

tag: age at dx

tag: gender

tag: b symptoms?

value: no

tag: bulky disease?

tag: biopsy site

value: left orbit

tag: ipi score

tag: ecog >= 2

value: R-CEOP

tag: # of cycles

tag: status

tag: bcl2 by halo

tag: ihc bcl2 high?1=yes,0=no

tag: coo by lymph2cx

value: ABC

value: Group A


title: Patient 10 KGH268

value: F

value: yes

value: right neck LN

tag: ldh > uln

tag: extranodal sites > 1

tag: Stage

tag: chemotherapy

tag: response chenson

tag: relapse?

tag: ihc myc high?1=yes,0=no

tag: myc fish

value: Normal

tag: bcl2 fish

tag: classification

value: Group B

tag: tissue

value: FFPE tissue


title: Sorted primary corpus Sox2-Tomato Sox2 positive_2

city: Tokyo

first: Ruslan

last: Deviatiiarov

address: Hongo 2-1-1, Bunkyo-ku

department: Intractable Disease Research Center

country: Japan

institute: Juntendo University

description: 20180510_13_2_111517_Sox2_Tomato_corpus_Sox2_low

data_processing:
Illumina NS500 Paired-End 75bp (PE75)
Reads were mapped to mouse mm9 reference genome using the STAR aligner. Read counts for individual transcripts from ENSEMBL annotation were obtained using HTSeq and further normalized using DESeq2. CPM values were calculated using EdgeR.
Assembly: mm9
Supplementary files format and content: Sox2 Lgr5 RNAseq counts, differential expression analysis, and number of cells per sample in .xlsx tables

growth_protocol: Cells were isolated and sorted based on the protocols descibed in the accompanying study

extract_protocol:
RNA extraction was performed using NEB RNeasy isilation kit according to the protocol
Low Input mRNA Library (Clontech SMARTer) v4

value: primary corpus

tag: cell marker

value: Sox2 positive

tag: genotype


title: Sorted primary corpus Sox2-Tomato Sox2 positive_3


title: Sorted primary corpus Sox2-Tomato Sox2 positive_1

description: 20180510_11_1_110717_Sox2_Tomato_corpus_Sox2_low


title: Patient 7 KGH260

tag: diagnosis

tag: age at dx

tag: gender

tag: b symptoms?

tag: bulky disease?

tag: biopsy site

value: nasopharynx

tag: ipi score

tag: ecog >= 2

value: R-CHOP

tag: # of cycles

value: partial

tag: status

value: Dead

value: Unclassified


title: Caco-2, infected, 2h, replicate 2

tag: cell line

tag: cell type

value: Human colorectal adenocarcinoma cells

value: WT

tag: treatment

value: infected

tag: time point_(in_hours)


title: Sorted primary corpus Sox2-Tomato Sox2 negative_2

description: 20180510_12_2_111517_Sox2_Tomato_corpus_Sox2_negative

tag: tissue

value: Sox2 negative


title: Caco-2, infected, 2h, replicate 1


title: Patient 6 KGH259

value: DLBCL

value: M

value: groin LN

value: no

tag: ldh > uln

tag: extranodal sites > 1

tag: Stage

tag: chemotherapy

tag: response chenson

value: complete

tag: relapse?

value: Alive

tag: bcl2 by halo

tag: ihc bcl2 high?1=yes,0=no

tag: ihc myc high?1=yes,0=no

tag: myc fish

value: CNI

tag: bcl2 fish

tag: coo by lymph2cx

value: ABC

tag: classification

value: Group A


title: Sorted primary corpus Sox2-Tomato Sox2 negative_1

description: 20180510_10_1_110717_Sox2_Tomato_corpus_Sox2_negative

value: primary corpus

tag: cell marker

tag: genotype


title: Sorted primary antrum Sox2-Tomato Sox2 high_3

description: 20180510_9_3_112017_Sox2_Tomato_pylorus_Sox2_high

value: primary antrum

value: Sox2 high


title: SH_ctrl2_081121

tag: cell type

value: basal epidermal cells

value: p63CreER; Piezo1fl/fl ; R26-mTmG (Piezo1 cKO)

tag: treatment

value: vehicle


title: Sorted primary antrum Sox2-Tomato Sox2 high_2

description: 20180510_6_2_92017_Sox2_Tomato_pylorus_Sox2_high

tag: tissue

value: WT


title: Sorted primary antrum Sox2-Tomato Sox2 high_1

description: 20180510_3_1_81417_Sox2_Tomato_pylorus_Sox2_high


title: Sorted primary antrum Sox2-Tomato Sox2 low_3

description: 20180510_8_3_112017_Sox2_Tomato_pylorus_Sox2_low

value: Sox2 low


title: Patient 5 KGH258

tag: diagnosis

value: DLBCL

tag: age at dx

tag: gender

value: F

tag: b symptoms?

value: yes

tag: bulky disease?

tag: biopsy site

value: skin

tag: ipi score

tag: ecog >= 2

tag: ldh > uln

tag: extranodal sites > 1

value: R-CHOP

tag: # of cycles

tag: status

value: Translocated

value: GCB

value: FFPE tissue


title: Caco-2, infected, 1h, replicate 2

tag: cell line

value: Human colorectal adenocarcinoma cells

value: infected

tag: time point_(in_hours)


title: Caco-2, infected, 1h, replicate 3

tag: cell type

tag: genotype


title: Caco-2, infected, 2h, replicate 3

tag: treatment


title: Patient 4 KGH257

tag: diagnosis

value: no

value: LN

tag: Stage

tag: chemotherapy

tag: response chenson

value: complete

tag: relapse?

value: Dead

tag: bcl2 by halo

tag: ihc bcl2 high?1=yes,0=no

tag: ihc myc high?1=yes,0=no

tag: myc fish

value: Normal

tag: bcl2 fish

tag: coo by lymph2cx

value: ABC

tag: classification

value: Group A

tag: tissue


title: Sorted primary antrum Sox2-Tomato Sox2 low_2

description: 20180510_5_2_92017_Sox2_Tomato_pylorus_Sox2_low

value: primary antrum

tag: cell marker

value: Sox2 low

value: WT


title: Sorted primary antrum Sox2-Tomato Sox2 negative_3

description: 20180510_7_3_112017_Sox2_Tomato_pylorus_Sox2_negative

value: Sox2 negative


title: Sorted primary antrum Sox2-Tomato Sox2 low_1

description: 20180510_2_1_81417_Sox2_Tomato_pylorus_Sox2_low


title: Caco-2, infected, 1h, replicate 1

tag: cell line

tag: cell type

tag: time point_(in_hours)


title: Caco-2, infected, 0h, replicate 3

tag: genotype

tag: treatment


title: Sorted primary antrum Sox2-Tomato Sox2 negative_2

description: 20180510_4_2_92017_Sox2_Tomato_pylorus_Sox2_negative


title: Caco-2, infected, 0h, replicate 2


title: Patient 2 KGH255

tag: diagnosis

value: DLBCL

tag: age at dx

tag: gender

value: M

tag: b symptoms?

value: yes

tag: bulky disease?

tag: biopsy site

value: left neck

tag: ipi score

tag: ecog >= 2

tag: ldh > uln

tag: extranodal sites > 1

tag: Stage

tag: chemotherapy

value: R-CHOP

tag: # of cycles

tag: status

value: Alive

value: CNI


title: Sorted primary corpus Sox2-Tomato Sox2 negative_3

description: 14_3_120417_Sox2_Tomato_corpus_Sox2_negative

tag: tissue

value: primary corpus

tag: cell marker


title: Sorted primary antrum Sox2-Tomato Sox2 negative_1

description: 20180510_1_1_81417_Sox2_Tomato_pylorus_Sox2_negative

tag: genotype


title: Sorted primary corpus Lgr5-DTR-GFP EpCAM high Lgr5 positive_3

description: 30_3_40218_Lgr5-DTR-GFP_corpus_EpCam_high_GFP_pos

value: high Lgr5 positive


title: Patient 1 KGH254

tag: diagnosis

value: F

value: no

value: bladder

tag: response chenson

value: complete

tag: relapse?

value: Dead

tag: bcl2 by halo

tag: ihc bcl2 high?1=yes,0=no

tag: ihc myc high?1=yes,0=no

tag: myc fish

value: Translocated

tag: bcl2 fish

tag: coo by lymph2cx

value: GCB

tag: classification

value: Group B

value: FFPE tissue


title: Caco-2, infected, 0h, replicate 1

tag: cell line

tag: cell type

value: Human colorectal adenocarcinoma cells

value: WT

tag: treatment

value: infected

tag: time point_(in_hours)


title: Sorted primary corpus Lgr5-DTR-GFP EpCAM high Lgr5 positive_2

description: 27_2_30518_Lgr5-DTR-GFP_corpus_EpCam_high_GFP_pos

tag: tissue


title: Sorted primary corpus Lgr5-DTR-GFP EpCAM high Lgr5 positive_1

description: 24_1_22118_Lgr5-DTR-GFP_corpus_EpCam_high_GFP_pos

tag: cell marker


title: Sorted primary corpus Lgr5-DTR-GFP EpCAM low Lgr5 positive_3

description: 29_3_40218_Lgr5-DTR-GFP_corpus_EpCam_low_GFP_pos

value: low Lgr5 positive

tag: genotype


title: Lcones06

first: Juan

last: Angueyra

address: 35 Convent Drive

department: Unit of Retinal Neurophysiology

institute: National Eye Institute

description: Sample is pool of 20 fluorescent cells derived from a single retina

data_processing:
Illumina software used for base calling and demultiplexing
Sequences for primers and adapters removed using Trimmomatic (Trimmomatic-0.36 - phred33 /adapters/TruSeq2-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:70)
Reads aligned to zebrafish genome (Danio rerio.GRCz11) using HiSat2 (hisat2 -p 8 --rna-strandness FR)
Transcript assembly and counts derived using StringTie
Differential gene expression analysis using DESeq2
Genome_build: Danio rerio.GRCz11
Supplementary_files_format_and_content: Comma-separated values files include FPKM values for each Sample
Comma-separated values files include DESeq2-analysis results comparing Rods vs. Cones
GTF files after trimming, alignment to genome and transcript assembly
RDS Seurat v03 file including count data for all samples

organism: Danio rerio

source_name: Dissociated adult photoreceptors

extract_protocol:
Pools of 20 photoreceptors of a single subtype, identified by their fluorescence, were manually collected and total RNA was obtained and amplified using the SMART-seq v4 ultra-low input RNA kit for sequencing (Takara #634897).
cDNA libraries were constructed using the Low Input Library Prep Kit v2 (Takara #634899).

treatment_protocol: After euthanasia, retinas from adult zebrafish were collected. Dissociated photoreceptors were obtained after enzymatic treatment with papain, gentle mechanic trituration and filtering.

tag: transgenic line

value: L cones

tag: age

value: Adult


title: Sorted primary corpus Lgr5-DTR-GFP EpCAM low Lgr5 positive_1

description: 23_1_22118_Lgr5-DTR-GFP_corpus_EpCam_low_GFP_pos

value: primary corpus


title: PC3_R3

city: Shanghai

first: Xinan

last: Chen

state: Shanghai

address: Wulumuqi road 12#

department: urology department

country: China

institute: Huashan Hospital

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: Hg18
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

growth_protocol: PC3 and DU145 were maintained with dulbecco's modified eagle's medium (Gibco, USA) supplemented with 10% fetal bovine serum (FBS; Gibco, USA);All cells were cultured in a humidified incubator with 5% CO2, 100 units/mL penicillin, and 100 mg/mL streptomycin.

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: prostate cancer cell

value: Docetaxel Resistance


title: Sorted primary corpus Lgr5-DTR-GFP EpCAM low Lgr5 positive_2

description: 26_2_30518_Lgr5-DTR-GFP_corpus_EpCam_low_GFP_pos


title: Sorted primary corpus Lgr5-DTR-GFP Lgr5 negative_2

description: 25_2_30518_Lgr5-DTR-GFP_corpus_Lgr5_negative

value: Lgr5 negative


title: Sorted primary corpus Lgr5-DTR-GFP Lgr5 negative_3

description: 28_3_40218_Lgr5-DTR-GFP_corpus_Lgr5_negative


title: PC3_R1


title: PC3_R2


title: Patient 3 KGH256

description: NanoString codeset was used to enumerate transcripts from 58 KHSC samples. This codeset was designed to quantify expression of 135 genes, including the 92 TCF3 target genes, 35 genes implicated in myelodysplastic syndrome (MDS), and 8 “housekeeping” genes whose expression we expected to be relatively invariant from case to case

tag: diagnosis

value: DLBCL

tag: age at dx

tag: gender

value: F

tag: b symptoms?

value: no

tag: bulky disease?

tag: biopsy site

value: left cervical LN

tag: ipi score

tag: ecog >= 2

tag: ldh > uln

value: yes

tag: extranodal sites > 1

tag: Stage

tag: chemotherapy

value: R-CHOP

tag: # of cycles

tag: response chenson

tag: relapse?

tag: status

value: CNI

value: ABC

value: Group A


title: Sorted primary corpus Lgr5-DTR-GFP Lgr5 negative_1

description: 20180515_22_1_22118_Lgr5-DTR-GFP_corpus_Lgr5_negative

tag: tissue

tag: cell marker

tag: genotype

value: WT


title: Sorted primary antrum Lgr5-DTR-GFP Lgr5 positive_3

description: 21_3_22018_Lgr5-DTR-GFP_pylorus_Lgr5_positive

value: primary antrum

value: Lgr5 positive


title: Lcones03

tag: transgenic line

tag: cell type

value: L cones

tag: age

value: Adult


title: Lcones01


title: Sorted primary antrum Lgr5-DTR-GFP Lgr5 positive_1

description: 17_1_83117_Lgr5-DTR-GFP_pylorus_Lgr5_positive


title: Sorted primary antrum Lgr5-DTR-GFP Lgr5 positive_2

description: 19_2_111417_Lgr5-DTR-GFP_pylorus_Lgr5_positive


title: PC3_NC2

tag: cell line

value: prostate cancer cell

tag: treatment

value: control


title: Sorted primary antrum Lgr5-DTR-GFP Lgr5 negative_2

description: 18_2_111417_Lgr5-DTR-GFP_pylorus_Lgr5_negative

value: Lgr5 negative


title: Mcones07

value: M cones


title: Sorted primary antrum Lgr5-DTR-GFP Lgr5 negative_3

description: 20_3_22018_Lgr5-DTR-GFP_pylorus_Lgr5_negative


title: PC3_NC1


title: Sorted primary antrum Lgr5-DTR-GFP Lgr5 negative_1

description: 16_1_83117_Lgr5-DTR-GFP_pylorus_Lgr5_negative


title: Lcones05


title: DU145_R3

value: Docetaxel Resistance


title: Mcones06


title: Lcones04


title: Lcones02


title: PC3_NC3


title: DU145_R2


title: Mcones04


title: DU145_R1


title: Mcones03


title: DU145_NC3


title: H3K9me3 ChIP WD8 rep1

city: Charlottesville

first: Irina

last: Bochkis

state: VA

address: 1340 Jefferson Park Ave

department: Pharmacology

institute: University of Virginia

description: ChIP-Seq

data_processing:
Reads were aligned to the mouse genome (mm10; NCBI Build 38) and human genome (hg19; NCBI build 37) using BWA v0.7.12 (Li and Durbin, 2009). Duplicate reads were removed using Picard v 1.134 (http://picard.sourceforge.net). Reads (phred score ≥ 30) that aligned uniquely were used for subsequent analysis.
Data from two murine biological replicates were merged for Foxa2 and lamin B1 ChIP-Seq comparison (2 ND, 2 WD8, 2 WD12).. LADs in mouse Lamin B1 ChIP-Seq were determined by SICER (Xu et al., 2014)(mm10 as species, window size 10,000 bp, gap size 10,000 bp, FDR 10%).  PeakSeq (Rozowsky et al., 2009) was used to identify Foxa2 bound peaks against input controls (FDR 5%, q-value<1.05E-2;)
Data from three human patients were merged for Foxa2 and Lamin B1 binding (3 normal and 3 NAFLD). Epic peak caller (https://github.com/daler/epic), (Xu et al., 2014), was used to determine Lamin B1 associated domains in human patients  (hg19 as species window size of 10kb, gap size of 3, FDR 5%).   PeakSeq (Rozowsky et al., 2009) was used to identify Foxa2 bound peaks against input controls ( FDR 5%, q-value<0.07).
RNA-Seq reads were aligned using STAR (Dobin et al., 2013) to mouse genome build mm10. Expression levels were calculated using RSEM (Li and Dewey, 2011). Differential expression analysis of RNA-seq (p-value <0.05) was performed in R using EdgeR package (Robinson et al., 2010) with a Benjamini-Hochberg FDR of 5%. Four replicates were sequenced for normal diet at each time point and WD8, 3 replicates for WD12.
Assembly: mm10; hg19

source_name: Liver

extract_protocol:
Snap-frozen  liver (100 mg) from mice on normal and Western diet (8 weeks and 12 weeks) or  from normal and NAFLD patients  was used to prepare chromatin. Foxa2‐specific rabbit antiserum (Seven Hills Bioreagents, WRAB‐1,200) and and rabbit antibody to lamin B1 (Abcam, Ab16048)  were used for immunoprecipitation.
Libraries were prepared according to Illumina's instructions. Briefly, DNAs were blunted with a combination of T4 DNA polymerase, Klenow polymerase, and T4 PNK, then a single 3′-end “A” base was added using Klenow exo (3′-to-5′ exo minus). multiplex adapters were then ligated to the ends of the modified DNA. After adapter ligation DNA was PCR amplified with Broad custom primers for 16 cycles and library fragments of ~280 bp (~150-bp insert plus ~130-bp adaptor and PCR primer sequences) were isolated using Pippin Prep agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. All libraries were sequenced on Illumina NextSeq 500 and Illumina NextS3eq2000.

treatment_protocol: Mice were fed Western diet (WD, 42% kcal from fat and containing 0.1% cholesterol; Harlan TD.88137) with ad libitum consumption of glucose and fructose (SW, 23.1 g/L d-fructose +18.9 g/L d-glucose)

value: liver

value: 4 months

tag: diet

value: Western, 8 wks

tag: chip antibody


title: H3K9me3 ChIP WD12 rep1

description: ChIP-Seq

value: 5 months

value: Western, 12 wks


title: H3K9me3 ChIP ND8 rep2

description: ChIP-Seq

value: Normal, 8 wks


title: H3K9me3 ChIP WD8 rep2

description: ChIP-Seq


title: H3K9me3 ChIP ND12 rep1

description: ChIP-Seq

value: Normal, 12 wks


title: Mcones02


title: Mcones01


title: DU145_NC2


title: H3K9me3 ChIP WD12 rep2

description: ChIP-Seq

value: WT


title: DU145_NC1


title: ChIP input mouse rep3

data_processing:
Reads were aligned to the mouse genome (mm10; NCBI Build 38) and human genome (hg19; NCBI build 37) using BWA v0.7.12 (Li and Durbin, 2009). Duplicate reads were removed using Picard v 1.134 (http://picard.sourceforge.net). Reads (phred score ≥ 30) that aligned uniquely were used for subsequent analysis.
Data from two murine biological replicates were merged for Foxa2 and lamin B1 ChIP-Seq comparison (2 ND, 2 WD8, 2 WD12). LADs in mouse Lamin B1 ChIP-Seq were determined by SICER (Xu et al., 2014) (mm10 as species, window size 10,000 bp, gap size 10,000 bp, FDR 10%). PeakSeq (Rozowsky et al., 2009) was used to identify Foxa2 bound peaks against input controls (FDR 5%, q-value<1.05E-2;).
Data from three human patients were merged for Foxa2 and Lamin B1 binding (3 normal and 3 NAFLD). Epic peak caller (https://github.com/daler/epic), (Xu et al., 2014), was used to determine Lamin B1 associated domains in human patients (hg19 as species window size of 10kb, gap size of 3, FDR 5%). PeakSeq (Rozowsky et al., 2009) was used to identify Foxa2 bound peaks against input controls (FDR 5%, q-value<0.07).
RNA-Seq reads were aligned using STAR (Dobin et al., 2013) to mouse genome build mm10. Expression levels were calculated using RSEM (Li and Dewey, 2011). Differential expression analysis of RNA-seq (p-value <0.05) was performed in R using EdgeR package (Robinson et al., 2010) with a Benjamini-Hochberg FDR of 5%. Four replicates were sequenced for normal diet at each time point and WD8, 3 replicates for WD12.
Genome_build: mm10 (GRCm38); hg19 (GRCh37)
Supplementary_files_format_and_content: bed files with domain regions called by SICER with following columns: chromosome, start coordinate, end coordinate, p-value.
Supplementary_files_format_and_content: bed files with domain regions called by Epic with following columns: chromosome, start coordinate, end coordinate, p-value.
Supplementary_files_format_and_content: bed files with peak calls from PeakSeq with the following columns: chromosome, start coordinate, end coordinate, q-value.
Supplementary_files_format_and_content: RNA_Seq_WD8.txt: Tab-delimited text file with logFC and logCPM.
Supplementary_files_format_and_content: RNA_Seq_WD12.txt: Tab-delimited text file with logFC and logCPM.
Supplementary_files_format_and_content: Foxa2_ND.bed: bed file with peak coordinates.
Supplementary_files_format_and_content: Foxa2_WD8.bed: bed file with peak coordinates.
Supplementary_files_format_and_content: Foxa2_WD12.bed: bed file with peak coordinates.
Supplementary_files_format_and_content: LaminB1_ND.bed: bed file with domain coordinates.
Supplementary_files_format_and_content: LaminB1_WD8.bed: bed file with domain coordinates.
Supplementary_files_format_and_content: LaminB1_WD12.bed: bed file with domain coordinates.
Supplementary_files_format_and_content: Foxa2_normal_patients.bed: bed file with peak coordinates.
Supplementary_files_format_and_content: Foxa2_NAFLD_patients.bed: bed file with peak coordinates.
Supplementary_files_format_and_content: LaminB1_normal_patients.bed: bed file with domain coordinates.
Supplementary_files_format_and_content: LaminB1_NAFLD_patients.bed: bed file with domain coordinates.

extract_protocol:
[RNA-Seq] Liver RNA was isolated from mice on control and Western diet (8 weeks and 12 weeks). Quality of RNA samples was analyzed using Agilent RNA 6000 Nano Kit (Bioanalyzer, Agilent Technologies). Samples with RIN scores above 9.5 were used in library preparation. 1 µg of total RNA was used to isolate mRNA (NebNext Poly(A) mRNA Magnetic Isolation Module).
[RNA-Seq] Libraries of resulting mRNA were prepared using NebNext Ultra II RNA library preparation kit. All samples were sequenced on Illumina NextSeq 500.
[ChIP-Seq] Snap-frozen liver (100 mg) from mice on normal and Western diet (8 weeks and 12 weeks) or from normal and NAFLD patients was used to prepare chromatin. Foxa2‐specific rabbit antiserum (Seven Hills Bioreagents, WRAB‐1,200) and rabbit antibody to lamin B1 (Abcam, Ab16048) were used for immunoprecipitation.
[ChIP-Seq] Libraries were prepared according to Illumina's instructions. Briefly, DNAs were blunted with a combination of T4 DNA polymerase, Klenow polymerase, and T4 PNK, then a single 3′-end “A” base was added using Klenow exo (3′-to-5′ exo minus). Multiplex adapters were then ligated to the ends of the modified DNA. After adapter ligation DNA was PCR amplified with Broad custom primers for 16 cycles and library fragments of ~280 bp (~150-bp insert plus ~130-bp adaptor and PCR primer sequences) were isolated using Pippin Prep agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. All libraries were sequenced on Illumina NextSeq 500.

treatment_protocol:
[RNA-Seq] Mice were fed Western diet (WD, 42% kcal from fat and containing 0.1% cholesterol; Harlan TD.88137) with ad libitum consumption of glucose and fructose (SW, 23.1 g/L d-fructose +18.9 g/L d-glucose).
[ChIP-Seq] Mice were fed Western diet (WD, 42% kcal from fat and containing 0.1% cholesterol; Harlan TD.88137) with ad libitum consumption of glucose and fructose (SW, 23.1 g/L d-fructose +18.9 g/L d-glucose).


title: Scones06

value: S cones


title: ChIP input mouse rep2


title: ChIP input mouse rep1


title: Scones05


title: H3K9me3 ChIP ND12 rep2

description: ChIP-Seq


title: Mcones05


title: Lamin B1 ChIP WD12 rep1

value: Lamin B1


title: Lamin B1 ChIP WD12 rep2


title: EA9R_Medulla

city: Gothenburg

first: Rasmus

last: Ågren

address: Pepparredsleden 1

country: Sweden

institute: AstraZeneca

data_processing:
Read quality for all libraries was accessed using FastQC (v0.11.7), Qualimap  (v2.2.2c) and  samtools stats (v1.9). QC metrics for Qualimap were based on a STAR (v2.7.2b) alignment against the human genome (GRCh38,  Ensembl  v100). Sequencing adapters were trimmed using NGmerge (v0.3). A human transcriptome index consisting of cDNA and ncRNA entries from Ensembl (v100) was generated and reads were mapped to the index using Salmon (v1.1.0).
Assembly: GRCh38

source_name: Kidney Medulla

extract_protocol:
Total RNA was extracted using Agencourt RNAdvance Tissue kit including DNase treatment for 15 min at 37 ̊C (Ambion DNaseI, ThermoFisher) on an automated Biomek i7 Hybrid system (Beckman Coulter).
KAPA RNA HyperPrep Kit with RiboErase (Roche) with 450ng of input RNA, 5min fragmentation at 95  ̊C, and 9 PCR cycles performed on a Tecan Fluent 1080 system (Tecan).

value: Kidney Medulla

tag: Sex

value: Male

tag: donor

tag: side

value: Right

tag: disease state

value: No AKI

tag: egfr

tag: bmi

tag: tissue weight_(mg)

tag: sampled date


title: EA9R_Cortex

source_name: Kidney Cortex

tag: tissue

value: Kidney Cortex


title: Lamin B1 ChIP WD8 rep1

tag: genotype


title: Scones04

tag: transgenic line

value: Adult


title: EA8L_Medulla

value: Left


title: H3K9me3 ChIP ND8 rep1

description: ChIP-Seq

value: liver


title: Lamin B1 ChIP ND12 rep1

value: Normal


title: EA8L_Cortex


title: Scones03

tag: cell type


title: Lamin B1 ChIP ND8 rep1

tag: age

value: 4 months


title: Scones02


title: Foxa2 ChIP WD12 rep2

value: 5 months


title: EA7L_Medulla

value: AKI


title: Foxa2 ChIP WD12 rep1

value: Western, 12 wks


title: Foxa2 ChIP WD8 rep2

value: Western, 8 wks


title: Foxa2 ChIP WD8 rep1

value: WT


title: Scones01

value: S cones


title: Lamin B1 ChIP WD8 rep2

value: Lamin B1


title: Foxa2 ChIP ND rep2


title: UVcones05

value: UV cones


title: EA6R_Medulla

value: Kidney Medulla

value: Male


title: UVcones04


title: RNA Seq WD12 rep3


title: Foxa2 ChIP ND rep1


title: RNA Seq WD12 rep2


title: Lamin B1 ChIP ND12 rep2


title: RNA Seq WD12 rep1


title: UVcones03


title: RNA Seq ND12 rep4

value: Normal, 12 wks


title: Lamin B1 ChIP ND8 rep2


title: EA6R_Cortex

value: Kidney Cortex

value: Right

value: No AKI


title: RNA Seq ND12 rep3

value: liver


title: EA5R_Cortex

value: Female


title: UVcones02

value: Adult


title: UVcones01


title: EA4R_Medulla


title: RNA Seq WD8 rep4

value: 5 months


title: Rods06

value: Rods


title: RNA Seq WD8 rep3

value: 4 months


title: EA4R_Cortex


title: RNA Seq WD8 rep1

value: Western, 8 wks


title: RNA Seq ND12 rep2

value: WT


title: Rods05


title: RNA Seq WD8 rep2


title: RNA Seq ND12 rep1


title: EA4L_Medulla

value: Left


title: EA4L_Cortex


title: Rods04


title: EA7L_Cortex

value: AKI


title: RNA Seq ND8 rep4

value: Normal, 8 wks


title: RNA Seq ND8 rep3


title: RNA Seq ND8 rep1


title: Rods03


title: RNA Seq ND8 rep2


title: EA5R_Medulla

value: Kidney Medulla


title: EA3R_Medulla

value: Male


title: THP-1_UF146-2 (RNA-seq)

first: Jiaying

last: Zhang

address: 320 Yue Yang Road

department: CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health

institute: Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences

description: THP-1 UF146 treated

data_processing:
Clean sequenced reads were alignmented to hg19 by bowtie2(2.2.9) with parameters: -N 1; alignmented SAM files were handled using samtools(1.7); peaks were called by macs2(2.1.1.20160309) callpeaks algorithm with default set; BigWig files were generated by deeptols(3.1.2) bamCoverage algorithm with paprameter --normalizeUsing BPM.(ChIP-seq)
Clean sequenced reads were alignmented to hg38  by HISAT2 (2.0.5) with default parameters; alignmented SAM files were handled using samtools(1.7); aligned reads were extracted by Htseq(0.9.1) with default parameters; FPKM were calculated by R script on its defination, differential genes were generated by R package Deseq2(1.22.2).(RNA-seq)
Raw reads were filtered by trimmomatic with parameter: SLIDINGWINDOW:4:15, LEADING:3, TRAILING:3, ILLIMINACLIP:adaper.fa:2:30:7:1:true, HEADCROP:10; clean sequenced reads were alignmented to hg19 by bismark(0.19.0) with parameters: deduplicated alignments were removed by deduplicate_bismark(bismark 0.19.0); coverage files were extracted by bismark_methylation_extractor(bismark 0.19.0); DMR regions were generated by R package DSS(2.26.0). (Bisulfite-Seq)
Genome_build: hg19 & hg38
Supplementary_files_format_and_content: FPKM were calculated by R script on its defination.  BigWig files were generated by deeptols(3.1.2) bamCoverage algorithm with paprameter --normalizeUsing BPM.

source_name: Cell line

growth_protocol: Kasumi-1 and THP-1 cells were cultured in RPMI1640 medium containing 10% FBS.

extract_protocol:
Fluorescence activated Cell Sorting
(For ChIP-seq): Library preparation was according to the manufacture’s guidelines (KAPA Biosystems KK8503) and sequencing procedures were carried out according to Illumina protocols with minor modifications (Illumina, San Diego).  (For RNA-seq): Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.  (For Bisulfite-Seq): A total amount of 5.2 microgram genomic DNA spiked with 26 ng lambda DNA were fragmented by sonication to 200-300bp with Covaris S220, followed by end repair and adenylation. Cytosine-methylated barcodes were ligated to sonicated DNA as per manufacturer’s instructions. Then these DNA fragments were treated twice with bisulfite using EZ DNA Methylation-GoldTM Kit (Zymo Research), before the resulting single-strand DNA fragments were PCR.

treatment_protocol: Kasumi-1 and THP-1 cells were transduced with UHRF1 shRNA and then AML cells were selected by puromycine for 48h,finally these AML cells were subjected to RNA-seq analysis and WGBS. Kasumi-1 and THP-1 cells were treated with UHRF1 inhibitor UF146 for 24h and these cells were subjected to RNA-seq analysis.

value: Blood cell

value: AML patient cell

tag: cell line

tag: agent


title: Rods02


title: THP-1_UF146-1 (RNA-seq)

description: THP-1 UF146 treated


title: EA3R_Cortex

value: Kidney Cortex

value: Right


title: Rods01


title: THP-1_DMSO-1 (RNA-seq)

description: THP-1 DMSO treated

value: DMSO


title: EA2R_Medulla

value: Female


title: THP-1_shUHRF1-2 (RNA-seq)

description: THP-1 shUHRF1 transduced

tag: shRNA


title: THP-1_shUHRF1-1 (RNA-seq)

description: THP-1 shUHRF1 transduced

tag: chip antibody


title: THP-1_shCtrl-2 (RNA-seq)

description: THP-1 scramble transduced

value: shCtrl


title: EA2R_Cortex

tag: Sex


title: subcutaneous white adipose resident eosinophils m2771

city: UNSW Sydney

first: Kate

last: Quinlan

state: NSW

address: Room 3102, Level 3, Biosciences South Building (E26)

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: UNSW Sydney

data_processing:
Raw fastq files were trimmed to remove any adapters using TrimGalore v0.6.4 (no quality trimming was performed, -q 0, -s 3, default parameters).
Fastq files were then quantified using Salmon v1.6.0 in mapping-based mode using a full decoy-aware GENCODE vM25 transcriptome.
Quantification files were then processed using tximport v1.18.0 to obtain gene-level counts. Any genes which did not contain at least 10 counts in at least 3 samples were filtered out before further processing.
Differential gene expression analysis was performed using DESeq2 v1.30.1. The mouse ID was included in the design matrix to account for any unwanted biological variation.
Assembly: mm10
Supplementary files format and content: sf - plain-text, tab separated file with header generated after quantification by salmon

source_name: subcutaneous white adipose

growth_protocol: Male FVB/NJ mice were fed a chow diet and cells harvested at 20 weeks of age

extract_protocol:
Peripheral blood was collected by cardiac puncture, subjected to red blood cell lysis. Adipose tissue was digested at 37C for 45 min with 1 mg/mL collagenase type II to isolate the stromal vascular fraction (SVF). The SVF was pelleted by centrifugation and then subjected to red blood cell lysis. Blood and adipose SVF cells were pre-blocked with Fc Block then stained with CD45-biotin/streptavidin-BV711, CD11b-FITC, F4/80-PECy7, and Siglec-F-BV421, prior to FACS sorting. TOPRO3 was used as a viability dye. Eosinophils were sorted using a BD FACS Aria III and defined as CD45+ CD11b+ SiglecF+ live cells. Cells were sorted into FACS buffer containing SUPERase-In RNase Inhibitor then carried forward for RNA isolation. RNA was extracted from sorted eosinophils using the Single Cell RNA Purification Kit (Norgen).
RNA quality was assessed using a Bioanalyzer Pico chip (Agilent) and cDNA libraries prepared using SMARTer Stranded Total RNA-Seq Kit v2 Pico Input Mammalian (ClonTech/Takara Bio).

treatment_protocol: Untreated (wild-type male FVB/NJ mice on a chow diet with no treatment were used)

tag: strain

value: FVB/NJ

value: eosinophils

value: subcutaneous white adipose

tag: mouse id


title: Kasumi-1_shUHRF1-1 (RNA-seq)

description: Kasumi-1 shUHRF1 transduced


title: subcutaneous white adipose resident eosinophils m2668


title: THP-1_shCtrl-1 (RNA-seq)

description: THP-1 scramble transduced


title: Kasumi-1_shUHRF1-2 (RNA-seq)

description: Kasumi-1 shUHRF1 transduced


title: subcutaneous white adipose resident eosinophils m2807


title: Kasumi-1_shCtrl-1 (RNA-seq)

description: Kasumi-1 scramble transduced


title: subcutaneous white adipose resident eosinophils m2846


title: EA20R_Medulla

tag: donor

tag: side

tag: disease state

value: No AKI


title: EA2L_Cortex

tag: egfr

tag: bmi

tag: tissue weight_(mg)


title: gonadal white adipose resident eosinophils m2668

source_name: gonadal white adipose

tag: tissue

value: gonadal white adipose


title: THP-1_DMSO-2 (RNA-seq)

description: THP-1 DMSO treated


title: Kasumi-1_shCtrl-2 (RNA-seq)

description: Kasumi-1 scramble transduced


title: THP-1 _IgG (CUT-TAG)

description: Endogenous

data_processing:
Library strategy: CUT&TAG
Clean sequenced reads were alignmented to hg19 by bowtie2(2.2.9) with parameters: -N 1; alignmented SAM files were handled using samtools(1.7); peaks were called by macs2(2.1.1.20160309) callpeaks algorithm with default set; BigWig files were generated by deeptols(3.1.2) bamCoverage algorithm with paprameter --normalizeUsing BPM.(ChIP-seq)
Clean sequenced reads were alignmented to hg38  by HISAT2 (2.0.5) with default parameters; alignmented SAM files were handled using samtools(1.7); aligned reads were extracted by Htseq(0.9.1) with default parameters; FPKM were calculated by R script on its defination, differential genes were generated by R package Deseq2(1.22.2).(RNA-seq)
Raw reads were filtered by trimmomatic with parameter: SLIDINGWINDOW:4:15, LEADING:3, TRAILING:3, ILLIMINACLIP:adaper.fa:2:30:7:1:true, HEADCROP:10; clean sequenced reads were alignmented to hg19 by bismark(0.19.0) with parameters: deduplicated alignments were removed by deduplicate_bismark(bismark 0.19.0); coverage files were extracted by bismark_methylation_extractor(bismark 0.19.0); DMR regions were generated by R package DSS(2.26.0). (Bisulfite-Seq)
Genome_build: hg19 & hg38
Supplementary_files_format_and_content: FPKM were calculated by R script on its defination.  BigWig files were generated by deeptols(3.1.2) bamCoverage algorithm with paprameter --normalizeUsing BPM.


title: THP-1 _UHRF1 (CUT-TAG)

description: Endogenous


title: THP-1 _SAP30 (CUT-TAG)

description: Endogenous


title: Kasumi-1 _UHRF1 (CUT-TAG)

description: Endogenous


title: gonadal white adipose resident eosinophils m2683


title: EA18R_Medulla

tag: sampled date


title: EA20R_Cortex


title: 786-M1A replicate 3

city: Liverpool

first: Marco

last: Sciacovelli

state: Select State

address: Ashton Street, Sherrington Building

country: United Kingdom

institute: University of Liverpool

data_processing:
Rsubread package version 2.10.5
Sequence reads were mapped to the Homo Sapiens GRCh38 primary assembly genome with Rsubread default parameters
Counts were extracted using the featureCounts function of Rsubread with default parameters
Assembly: GRCh38 primary assembly
Supplementary files format and content: CSV, counts

source_name: kidney

growth_protocol: All cells were cultured in full Plasmax medium in humidified atmosphere with 5% CO2 at 37C; cells grown stably in Plasmax.

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen)
RNA-seq sample libraries were prepared using TruSeq Stranded mRNA (Illumina) following the manufacturer’s description

value: kidney

tag: cell type

value: clear cell renal cell carcinoma

tag: phenotype

value: metastatic derivative of 786-O


title: 786-M1A replicate 1

tag: cell line


title: 786-M1A replicate 2


title: 786-O replicate 3

value: parental


title: EA18R_Cortex

tag: age


title: gonadal white adipose resident eosinophils m2807

value: Male


title: 786-O replicate 2


title: EA18L_Medulla

value: Kidney Medulla

value: Left


title: gonadal white adipose resident eosinophils m2846


title: EA2L_Medulla

value: AKI


title: 786-O replicate 1


title: blood eosinophils m2668

source_name: blood

value: blood


title: HK2 replicate 3

value: proximal tubuli cells


title: EA16L_Medulla

value: Female


title: HK2 replicate 1


title: LaminB1 ChIP human NAFLD Mild rep1

description: ChIP-Seq

value: liver

value: Mild NAFLD


title: LaminB1 ChIP human NAFLD Mild rep3

description: ChIP-Seq


title: EA18L_Cortex

value: Kidney Cortex


title: LaminB1 ChIP human NAFLD Mild rep2

description: ChIP-Seq


title: EA16R_Cortex

value: Right


title: Foxa2 ChIP human NAFLD Mild rep1

description: ChIP-Seq


title: blood eosinophils m2683

value: FVB/NJ

value: eosinophils


title: Foxa2 ChIP human NAFLD Mild rep2

description: ChIP-Seq


title: blood eosinophils m2807


title: EA16R_Medulla


title: Y641-FBR3

city: Lucknow

first: Dipak

last: Datta

address: B.S. 10/1, Sector-10, Jankipuram Extension Sitapur Road

department: Cancer Biology

country: India

institute: CSIR- CDRI

data_processing:
BCL to Fastq conversion by bcl2fastq 2.19.0.316
The sequence data quality was checked using FastQC v0.11.9 and MultiQC v1.9 software. The data was checked for base call quality distribution, % bases above Q20, Q30, %GC, and sequencing adapter contamination. All the samples passed QC threshold (Q20>95%).
The sequence data was processed using fastp v0.20.1 to remove adapter sequences, low quality reads, filtering reads shorther than 50 bp.
The QC passed reads were mapped onto indexed Mus musculus genome (GRCm39) using STAR v2 aligner.
Gene expression values were obtained as read counts using ensembl annotation file Mus musculus genome (GRCm39) and featureCounts v2.0.1 software.
Assembly: Assembly(GCF_000001635.27;GRCm39)
Supplementary files format and content: Raw reads counts in excel format
Supplementary files format and content: Expression counts in excel format

extract_protocol:
The RNA extraction was performed using TRIzol method.
Library was prepared using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina.

value: epithelial

tag: genotype

value: Y641 mutated


title: EA16L_Cortex


title: blood eosinophils m2771


title: Foxa2 ChIP human NAFLD Mild rep3

description: ChIP-Seq

tag: chip antibody


title: Kasumi-1 cells, shLYL1, 542

city: Beijing

first: Qian

address: Qinghuayuan Stress

institute: Tsinghua University

data_processing:
Adapters and low quality reads were trimmed with fastp v0.20.1 with parameter "-q 20"
Trimmed sequence reads were mapped to hg19 using Hisat2 v2.2.0 with default parameters.
Aligned reads stored in SAM format were manipulated to generate bam files using  SAMtools v1.7 with parameter "-Sb -q 20"
FeatureCounts v2.0.1 was applied to calculate the counts per gene under default parameters.
Differentially expressed genes were identified with FDR < 0.1 and fold change > 2 using R package DESeq2 v1.26.0.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include counts per gene for each Sample

growth_protocol: RPMI 1640 medium, 10% fetal bovine serum, 1% penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Total RNA was extracted from Kasumi-1 cells with TRIZOL reagent (Invitrogen)
RNA libraries for RNA-seq were prepared using standard Illumina protocols.

treatment_protocol: Kasumi-1 cells were infected with shRNA expressing lentiviruses. After 48 h of transduction, puromycin (1 μg/mL) was added into medium for another 48 h to select shRNA expressing cells.

value: Human acute myeloblastic leukemia

tag: treatment

value: LYL1 shRNA 542

tag: time

value: Day 4


title: EA15L_Medulla

value: Kidney Medulla

tag: Sex

value: Male


title: Kasumi-1 cells, shLYL1, 540

value: LYL1 shRNA 540


title: Y641-FBR2


title: CONTROLBR3

value: WT


title: Kasumi-1 cells, shLYL1, 538

value: LYL1 shRNA 538


title: Kasumi-1 cells, shAE, 3

value: AE shRNA 3


title: Kasumi-1 cells, shAE, 2

value: AE shRNA 2


title: HK2 replicate 2

value: kidney

value: proximal tubuli cells

value: parental


title: EA14R_Medulla

tag: donor

value: Right

value: No AKI


title: Y641-FBR1

value: epithelial


title: EA14R_Cortex

value: Kidney Cortex

tag: side


title: CONTROLBR2


title: Kasumi-1 cells, shControl, 2

value: Human acute myeloblastic leukemia

value: control shRNA


title: Kasumi-1 cells, shControl, 3

value: Day 4


title: Kasumi-1 cells, shControl, 1


title: CONTROLBR1


title: EA13R_Medulla

value: Kidney Medulla

tag: disease state

value: AKI


title: Donor 6, CD13+CD24+CD133+ kidney cells

city: Nijmegen

first: Martijn

last: Broek

address: Geert Grooteplein 24, route 846

department: Molecular Biology

country: Netherlands

institute: Radboud university - RIMLS Science

description: Column name in processed data file: PTECvsSTC-STC-6-17243

data_processing:
Reads were trimmed, using TrimGalore! v0.4.5
Reads were mapped to a human reference genome (GRCh38.95, Ensembl) with Star v2.6.0a.
MultiQC was used to combine results and perform quality checks.
Counts were produced with HTSeq v0.11.0
Assembly: GRCh38.95, Ensembl
Supplementary files format and content: counts per sample.txt is a .txt file containing the counts for each gene (rows) per sample (column). Per sample described above, the column name is indicated under description.

source_name: Human nephrectomy single cell suspension

extract_protocol:
Human renal cortex tissue from the unaffected pole of kidneys after tumor nephrectomy was cut into small pieces (≤1mm) and incubated in incubation medium consisting of DMEM/F12 (Gibco/Thermo Fisher Scientific, Breda, the Netherlands) supplemented with 200 U/mL collagenase IV (Thermo Fisher Scientific), 2 U/mL dispase II (Sigma-Aldrich, Zwijndrecht, the Netherlands) and 50 U/mL DNAse I (Sigma-Aldrich, Zwijndrecht, the Netherlands) for 15 minutes at 37 ˚C. This was pressed through a 150 µm sieve using the plunger of a syringe and washed with incubation medium. After this, the tissue solution was incubated again for 10 minutes in the incubation medium at 37 ˚C. This solution was rinsed through a 70 µm and a 32 µm sieve and washed using physiological NaCl solution. The flow-through was collected and centrifuged for 5 minutes at 1500 rcf, supernatant was removed and pellet was resuspended in NaCl solution. Pellet was resuspended in 1 ml PBS containing 1% BSA (v/v, Sigma-Aldrich) and antibodies against CD133, CD24 and CD13. Antibody incubation was performed for 1 hour at 4 ˚C in the dark. Pellet was washed three times with PBS and centrifuged at 1500xg for 5 minutes, supernatant was removed and pellet resuspended in PBS. This cell suspension was rinsed through a cell strainer (70 µm) and collected in a FACS tube for cell sorting. Cell sorting was performed to isolate PTECs and STCs for RNA sequencing using BD FACSAria instrument and software (BD Bioscience, Vianen, the Netherlands). PTECs were detected based on CD13 (PECy5) positive staining and sorted. STCs were detected based on CD13 (PECy5) positive staining and additional labeling of CD24 (FITC) and CD133 (PE). For bulk RNA sequencing (100,000 cells per sample), cells were collected in eppendorf tubes in PBS and RNA isolation was performed. Total RNA was used as input for bulk RNA sequencing
Total RNA was used for library preparation using the RNA HyperPrep Kit with RiboErase (KAPA Biosystems, Wilmington, MA). A fragmentation step was carried out for 6.5 min and NextFlex DNA barcodes (Bioo Scientific, Austin, TX) were used for adapter ligation. Libraries were amplified using 15 amplification cycles. Library concentration was measured using the dsDNA Fluorescence Quantification Assays (DeNovix, Wilmington, DE), and library size was determined using the BioAnalyzer High Sensitivity DNA Kit (Agilent, Amstelveen, the Netherlands). Sequencing was performed using an Illumina NextSeq 500, and 50-bp paired-end reads were generated.

tag: individual

value: Donor 6

value: Scattered tubular cells


title: Donor 4, CD13+CD24+CD133+ kidney cells

description: Column name in processed data file: PTECvsSTC-STC-4-16825

value: Donor 4


title: Donor 7, CD13+CD24+CD133+ kidney cells

description: Column name in processed data file: PTECvsSTC-STC-7-17245

value: Donor 7


title: EA13R_Cortex

value: Male

tag: egfr

tag: bmi


title: Donor 5, CD13+CD24+CD133+ kidney cells

description: Column name in processed data file: PTECvsSTC-STC-5-16827

value: Donor 5

tag: tissue

value: kidney


title: EA15L_Cortex

value: Left

tag: tissue weight_(mg)

tag: sampled date


title: EA12R_Medulla

value: Female

value: Right


title: Donor 3, CD13+CD24+CD133+ kidney cells

description: Column name in processed data file: PTECvsSTC-STC-3-16823

value: Donor 3

tag: cell type


title: Donor 1, CD13+CD24+CD133+ kidney cells

description: Column name in processed data file: PTECvsSTC-STC-1-16819

value: Donor 1


title: Donor 2, CD13+CD24+CD133+ kidney cells

description: Column name in processed data file: PTECvsSTC-STC-2-16821

value: Donor 2


title: C57BL/6J mouse heart, Sham, S2

city: Dresden

first: Erik

last: Klapproth

address: Fiedlerstraße 42

department: Institute of Pharmacology and Toxicology

institute: Technische Universität Dresden

data_processing:
bcl2fastq2 2.20.0
Alignment of the reads to the mus musculus reference (mm10) was done with GSNAP (v2020-12-16) and Ensembl gene annotation version 98 was used to detect splice sites (gsnap.sse42 -d mm10 --gunzip -A sam -t 12 --use-sarray=1 --input-buffer-size=500000 --output-buffer-size=500000 -B 5 -n 1 -m 0.6 -s EnsemblGene-98.ss.mm10.iit)
The uniquely aligned fragments were counted with featureCounts (v2.0.1) [3] and the same Ensembl annotation (featureCounts -a EnsemblGene-98.mm10.TR.gtf -s 2 -p -Q 1 -T 8)
Assembly: mm10
Supplementary files format and content: Tab separated file from featureCounts. The rows are genes and the columns provide gene information and list of samples. Each cell is the number of fragments per gene per sample

source_name: healthy tissue

extract_protocol:
miRNeasy Kit + on-column DNase digestion
mRNA was isolated from 300 ng total RNA by poly-dT enrichment using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) according to the manufacturer’s instructions. Samples were then directly subjected to the workflow for strand-specific RNA-Seq library preparation (Ultra II Directional RNA Library Prep, NEB). For ligation custom adapters were used (Adapter-Oligo 1: 5'-ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT-3', Adapter-Oligo 2: 5'-P-GAT CGG AAG AGC ACA CGT CTG AAC TCC AGT CAC-3'). After ligation, adapters were depleted by an XP bead purification (Beckman Coulter) adding the beads solution in a ratio of 1:0.9. Dual indexing was done during the following PCR enrichment (12 cycles, 65°C) using custom amplification primers carrying the same sequence for i7 and i5 index (Primer 1: AAT GAT ACG GCG ACC ACC GAG ATC TAC AC NNNNNNNN ACA TCT TTC CCT ACA CGA CGC TCT TCC GAT CT, Primer 2: CAA GCA GAA GAC GGC ATA CGA GAT NNNNNNNN GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC T). After 2x XP bead purification step (1:0.9), libraries were quantified using the Fragment Analyzer (Agilent). For Illumina flowcell production, libraries were equimolarly pooled and sequenced with 100 bp paired-end on an Illumina NovaSeq 6000, averaging 32 million fragments per library.

value: healthy tissue

tag: strain

value: female

value: 8 weeks

value: DMSO


title: C57BL/6J mouse heart, Sham, S3

tag: age


title: C57BL/6J mouse heart, Sham, S1


title: Donor 7, CD13+CD24-CD133- kidney cells

description: Column name in processed data file: PTECvsSTC-PTEC-7-17244

value: Proximal tubule epithelial cells


title: EA12L_Medulla

value: Kidney Medulla

value: AKI


title: EA12R_Cortex

value: Kidney Cortex


title: C57BL/6J mouse heart, DMSO, A129

source_name: infarct border zone

value: infarct border zone

value: Infarction, DMSO


title: Donor 6, CD13+CD24-CD133- kidney cells

description: Column name in processed data file: PTECvsSTC-PTEC-6-17242

value: Donor 6

value: kidney


title: Kasumi-1 cells, shAE, 1

tag: cell line

value: Human acute myeloblastic leukemia

value: AE shRNA 1

value: Day 4


title: Donor 5, CD13+CD24-CD133- kidney cells

description: Column name in processed data file: PTECvsSTC-PTEC-5-16826

value: Donor 5


title: C57BL/6J mouse heart, DMSO, A128


title: EA12L_Cortex

value: Female

value: Left


title: C57BL/6J mouse heart, DMSO, A127

value: female


title: Donor 4, CD13+CD24-CD133- kidney cells

description: Column name in processed data file: PTECvsSTC-PTEC-4-16824

value: Donor 4


title: EA11R_Medulla

value: Male

value: Right

value: No AKI


title: Donor 2, CD13+CD24-CD133- kidney cells

description: Column name in processed data file: PTECvsSTC-PTEC-2-16820

value: Donor 2

value: Proximal tubule epithelial cells


title: EA11R_Cortex

value: Kidney Cortex


title: Donor 1, CD13+CD24-CD133- kidney cells

description: Column name in processed data file: PTECvsSTC-PTEC-1-16818

value: Donor 1


title: C57BL/6J mouse heart, A10i, A120

value: infarct border zone

value: 8 weeks

value: Infarction, GI254023X 100mg/kg


title: C57BL/6J mouse heart, A10i, A117


title: C57BL/6J mouse heart, A10i, A119


title: C57BL/6J mouse heart, A10i, A116


title: Parental control for NEAT1 knockdown, replicate 3

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

data_processing:
Paired end reads of 76 bases were sequenced on a NextSeq 500 in mid-output mode. Data was demultiplexed with bcl2fastq2 v2.20.
Data was aligned to the hg38 genome from UCSC using STAR 2.7.3a with annotations from Ensembl 102, with the following parameters (including end to end alignments): --outSAMprimaryFlag OneBestScore --outFilterMultimapNmax 20 --outFilterMismatchNoverLmax 0.1 --outFilterType BySJout --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --readFilesCommand zcat --limitBAMsortRAM 60000000000 --quantMode TranscriptomeSAM GeneCounts --alignEndsType EndToEnd
Downstream analysis was done in R 4.0.0 with edger 3.30.3
Assembly: hg38
Supplementary files format and content: raw gene counts generated by STAR for each sample

source_name: HEK293FRT cells

extract_protocol:
RNA was extracted using Qiagen RNA extraction Kit, followed manufacturers instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: siRNA transfection for 72 hours

tag: genotype

value: Control


title: Parental control for NEAT1 knockdown, replicate 2


title: Parental control for NEAT1 knockdown, replicate 1


title: EA11L_Medulla

value: Kidney Medulla


title: RNAi knockdown of NEAT1, replicate 3


title: Wild type control for ARID kd, replicate 1

value: Parental


title: C57BL/6J mouse heart, DMSO, A105

tag: treatment

value: Infarction, DMSO


title: RNAi knockdown of NEAT1, replicate 2


title: Wild type control for ARID kd, replicate 3


title: RNAi knockdown of NEAT1, replicate 1


title: Wild type control for ARID kd, replicate 2


title: 87-AO6_E2-Input-Rep2

city: Leuven

first: Peihua

last: Zhao

address: Herestraat 49

country: Belgium

institute: KU Leuven

data_processing:
Paired-end fastq files were aligned to human genome hg38 using STAR
Peak calling was performed by ‘callpeak’ function in the Model-based Analysis of ChIP-Seq (MACS2 2.1.2). Peaks overlapping with the ENCODE blacklist regions were removed.
The genome-wide normalized signal coverage track was generated using MACS2 SPMR peak calling, followed by MACS2 ‘bdgcmp’ with parameter -m FE to calculate fold-enrichment score.
The output BedGraph file was converted to bigWig format by bdg2bw
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: MCF7 cells were maintained in DMEM/F12 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching, chromatin was prepared using SimpleChIP Enzymatic Chromatin Kit from cell signaling.
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit.

treatment_protocol: Cells were cultured under full media for 24 hrs, or starved in charcoal-stripped serum containing media for 72hrs and then stimulated with DMSO or 10nM estradiol for 45 mins.

value: ER+ breast cancer cell line


title: B16-OVA, aPD-1 + TBK1i, Replicate 4

city: Cambridge

first: Seth

middle: Allen

last: Anderson

state: MA

address: 75 Ames Street

department: Cancer Program

institute: Broad Institute of MIT and Harvard

library_source: transcriptomic single cell

data_processing:
Cellranger v3.0.1 mkfastq command to convert bcl files to fastq files and to demultiplex fastq files
Cellranger v3.0.1 count command to generate raw and filtered count matrices
10X Genomics 3'v2 chemistry; 2x NovaSeq SP flow cells with 2 lanes e/a; raw fastqs from each separate flow cell and lane are included, but included processed files are concatonated across replicate flow cells
Assembly: Assembly: mm10
Supplementary files format and content: Tab-separated values (.tsv.), matrix files (.mtx), hierarchical data file (.h5), and fastq (.fastq)

source_name: melanoma subcutaneous tumor

growth_protocol: 1E6 B16-OVA cells were resuspended in sterile Ca- and Mg-free PBS (Gibco), mixed 1:1 by volume with Matrigel (Corning) and subcutaneously injected into the flank on day 0.

extract_protocol:
Tumors were dissected on day 14 post-inoculation and disassociated using the Miltenyi Mouse Tumor Dissociation Kit and gentleMACS Octo-Dissociator (Miltenyi) using the m-TKD-1 program. After filtering through a 70-μm filter, live cells were isolated using a density gradient with Lympholyte-M separation media (Cedarlane Labs) per the manufacturer’s specifications. CD45+ tumor-infiltrating immune cells were enriched by positive selection with MicroBeads (Miltenyi) and magnetic separator (Miltenyi).
Four representative samples from each of the Control (Vehicle/IgG-treated), aPD-1 (Vehicle/anti-PD-1-treated), TBK1i (TBK1i/IgG-treated), and αPD-1 + TBK1i (TBK1i/anti-PD-1) groups were selected and droplet-based isolation of single cells was performed with the Chromium Controller (10X Genomics) according to the manufacturer’s specifications. Subsequent generation of 3′ sequencing libraries was performed per manufacturer’s instructions (10X Genomics). Libraries were prepared utilizing Chromium Next GEM Single Cell Reagent Kits 3′v2 chemistry (10X Genomics). Characterization of the sequencing library was performed with TapeStation (Agilent) and Qubit (ThermoFisher) instruments.

treatment_protocol: Mice were randomized into four groups of 10 using the stratified method via Study Log program based on tumor size. Randomization and treatment initiated on Day 1; mean TV at the start of dosing of 110.05 mm3. Vehicle (0.5% hydroxypropyl methylcellulose K100LV / 0.4% Tween 80 / 99.1% 0.05N hydrochloric acid) or TBK1i (Compound 1, Gilead Sciences; 40 mg/kg)14 was administered by oral gavage daily (Days 1-18) and isotype control IgG or anti–PD-1 (10 mg/kg) was administered three times weekly for a total of six doses. Investigators were not blinded to treatment groups.

value: melanoma subcutaneous tumor

value: CD45+ immune cells

value: aPD-1 + TBK1i


title: B16-OVA, aPD-1 + TBK1i, Replicate 3


title: ARID1A knockdown, replicate 2


title: ARID1B knockdown, replicate 3


title: EA11L_Cortex

value: Male

value: Left


title: Donor 3, CD13+CD24-CD133- kidney cells

description: Column name in processed data file: PTECvsSTC-PTEC-3-16822

value: Donor 3

value: kidney


title: ChIP input human rep3

value: liver

tag: chip antibody


title: ARID1A knockdown, replicate 1


title: ARID1A knockdown, replicate 3


title: 88-AO8_E2-Input-Rep2


title: ARID1B knockdown, replicate 1


title: ChIP input human rep1


title: 86-AO5_E2-Input-Rep2


title: B16-OVA, aPD-1 + TBK1i, Replicate 2


title: Lamin B1 ChIP human NAFLD Severe rep3

value: NAFLD

value: Lamin B1


title: 84-AO8_EDM-Input-Rep2


title: B16-OVA, aPD-1 + TBK1i, Replicate 1


title: ChIP input human rep2


title: B16-OVA, Isotype IgG + TBK1i, Replicate 4

value: Isotype IgG + TBK1i


title: 83-AO6_EDM-Input-Rep2


title: 85-AO3_E2-Input-Rep2

value: sgNT


title: IRF2_CUtnTAG

city: Toronto

first: David

last: Brooks

address: 610, University Ave

institute: Princess Margaret Cancer Centre

description: anti-CD3/ani-CD28 in vitro activated

data_processing:
For AB-Seq experiment, fastq files were generated using bcl2fastq2 v2.20. Read counts were generated from fastq files using the BD Rhapsody? WTA Analysis Pipeline, available on SevenBridges server, run with default parameters.
For scATAC-Seq experiments, to generated fastq files, we ran Illumina RTA v3.4.4 and we used bcl2fastq 2.20 to convert bcl to fastq files with default parameters, see https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/using/bcl2fastq-direct. For cell ranger analyses, cellranger-atac/2.0.0 count was used with the reference refdata-cellranger-arc-mm10-2020-A-2.0.0 downloaded from the 10x website. We set the chemistry parameter to --chemistry=ARC-v1, since we analysed the scATAC-Seq data of the multiomics data.
For CUT&TAG experiment, samples were aligned to the mm10 genome using bowtie v2.4.1 with the following parameters: ?--local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700? and preprocessed using samtools v1.10. A bedgraph file was generated by scaling the reads by a scaling factor defined as 1000000/number_of_aligned_reads. Regions overlapping the ENCODE mm10 blacklist regions were removed. Peaks were called using SEACR v1.3 with a signal_threshold of 1 and run in `stringent` and `norm` mode.
Assembly: GRCm38
Supplementary files format and content: For each AB-Seq sample an h5Seurat object contains: raw counts, normalized counts, clustering data, pca and umap data
Supplementary files format and content: For each scATAC-Seq sample a tar file containing:  a fragement and an index file from alignment and a metadata csv file
Supplementary files format and content: For each CUT&TAG experiment, a tar file containing: peaks in 'stringent' and 'norm' mode as called using SEACR v1.4 on blacklist filtered and normalized data

source_name: Spleen and lymph node

growth_protocol: 2x105 MC38 tumor cells were injected subcutaneously (s.c.) into one hind leg of each mouse. Tumors harvested on day 12 after implantation.

extract_protocol:
For AB-Seq experiment, Tumors were cut into small fragments and digested in RPMI media containing collagenase I, FBS, DnaseI in a gentleMACS dissociator. Tumor ells were filtered and subjected to red blood cell lysis. CD45+ tumor immune cells were FACSorted and the sorted cells  were labelled with sample multi-plexing antibodies and AbSeq Ab-Oligos (antibody-oligonucleotides) using the BD Mouse Immune Single-Cell Multiplexing Kit. For ATAC-Seq experiment, Tumors were cut into small fragments and digested in RPMI media containing collagenase I, FBS, DnaseI in a gentleMACS dissociator. Tumor cells were filtered and subjected to red blood cell lysis. CD8+ tumor immune cells were isolated using autoMACS Pro Separator (Miltenyi Biotec), washed and treated with DNase I, and nuclei isolated according to the 10x Genomics nuclei isolation for single cell ATAC sequencing protocol. For CUT&Tag, naïve CD8+ T cells were isolated from the spleens and lymph nodes of C57BL/6 by negative selection (Stem Cell Technologies). Isolated CD8+ T cells were activated for 3 days using 5ug/mL plate-bound anti-CD3 (16-0031-86 Invitrogen) and 2ug/mL soluble anti-CD28 (16-0281-86 Invitrogen) antibodies in 10% RPMI complete media containing 100U/ml rhIL2 (200-02 PeproTech). Nuclei were isolated and CUT&Tag performed using the protocol from Epicypher (EpiCypher® CUTANA? Direct-to-PCR CUT&Tag Protocol v1.6 Revised: 11.04.2021). Prior to sequencing, samples were normalized based on their DNA concentrations and pooled.
For AB-Seq experiment, Whole transcriptome Analysis (WTA), AbSeq and Sample Tag libraries were constructed using the BD Rhapsody? WTA Amplification Kit from cDNA encoded on beads after cell capture on the BD Rhapsody? Single-Cell Analysis System, using the manufacturer's recommended protocol.. For ATAC-Seq experiment, ATAC libraries were prepared following the 10x Genomics sequencing workflow and protocol. For CUT&Tag library preparetion was performed using the protocol from Epicypher (EpiCypher® CUTANA? Direct-to-PCR CUT&Tag Protocol v1.6 Revised: 11.04.2021).

treatment_protocol: For CUT&Tag: Isolated CD8+ T cells were activated for 3 days using 5ug/mL plate-bound anti-CD3 and 2ug/mL soluble anti-CD28.

value: Spleen and lymph node

value: CD8 T cells

value: WT CD8 T cells

tag: antibody


title: Lamin B1 ChIP human NAFLD Severe rep1


title: 81-AO3_EDM-Input-Rep2


title: dbf4_aaHH_rep2 (ChIP-seq)

city: Los Angeles

first: Meghan

middle: V

last: Petrie

state: CA

address: 1050 Childs Way

institute: University of Southern California

data_processing:
Barcode-splitting: Sequenced reads were first processed using ea-utils which de-multiplexes the reads based on the specified barcode sequences.
Alignment: The raw sequencing reads were then aligned to the indexed genome from Saccharomyces Genome Database using bowtie2.
Data-cleaning: Filterred reads that were mapped to more than one region in the genome using samtools view. Reads were sorted by coordinates of the reference genome using samtools sort. PCR duplicates were removed using samtools rmdup
Binning: sequencing reads were binned over 50bp bins across the genome using coverageBed.
Assembly: S228C
Supplementary files format and content: binned.bed files

organism: Saccharomyces cerevisiae

growth_protocol: ~100 mL of cells were grown per sample to OD ~ 0.5 in YEPD at 23 °C

extract_protocol:
Cells were resuspend in 500 μL ChIP lysis buffer and disrupted by bead-beating with FastPrep. Followed by PCI extraction and ethanol precipitaion.
Samples were end-labeled using KAPA Hyper prep kit with unique barcoded adapters that are compatible with the subsequent library-amplification and sequencing primers for the Illumina sequencing platform.

treatment_protocol: Cells were arrested with α-factor (~5 nM ) and incubated for ~3 h at 23 °C. Chrmatin was cross-linked with formaldehyde solution (1 % final concentration)

value: alpha-factor

value: anti-FLAG M2 (Sigma F1804)


title: B16-OVA, Isotype IgG + TBK1i, Replicate 3

value: melanoma subcutaneous tumor


title: 79-AO6_E2-ER-Rep2

value: ER+ breast cancer cell line

value: ER (Millipore, #06-935)


title: IgG_CUtnTAG

description: anti-CD3/ani-CD28 in vitro activated

value: IgG


title: B16-OVA, Isotype IgG + TBK1i, Replicate 2

value: CD45+ immune cells


title: Lamin B1 ChIP human normal rep2

value: Normal control


title: dbf4_aaHH_rep1 (ChIP-seq)


title: 82-AO5_EDM-Input-Rep2


title: B16-OVA, aPD-1 + Vehicle, Replicate 2

value: aPD-1 + Vehicle


title: 77-AO3_E2-ER-Rep2


title: Lamin B1 ChIP human normal rep1

value: liver


title: Dbf4_G1-rep1 (ChIP-seq)


title: B16-OVA, aPD-1 + Vehicle, Replicate 3


title: Foxa2 ChIP human NAFLD Severe rep3

value: NAFLD


title: 80-AO8_E2-ER-Rep2


title: Sample 40_fkh1∆dbf4-Zn*2_rep2

description: BrdU-IP sequencing

data_processing:
library strategy: BrdU-IP-seq
Barcode-splitting: Sequenced reads were first processed using ea-utils which de-multiplexes the reads based on the specified barcode sequences.
Alignment: The raw sequencing reads were then aligned to the indexed genome from Saccharomyces Genome Database using bowtie2.
Data-cleaning: Filterred reads that were mapped to more than one region in the genome using samtools view. Reads were sorted by coordinates of the reference genome using samtools sort. PCR duplicates were removed using samtools rmdup
Binning: sequencing reads were binned over 50bp bins across the genome using coverageBed.
Assembly: S228C
Supplementary files format and content: binned.bed files

source_name: Yeast cells

growth_protocol: 10–20 mL of cells were grown per sample to OD ~ 0.5 in YEPD at 23 °C

extract_protocol:
Cells were resuspend in 500 μL genomic lysis buffer and disrupted by bead-beating with FastPrep. Followed by PCI extractracion and ethanol precipitaion.
Samples were end-labeled using KAPA Hyper prep kit with unique barcoded adapters that are compatible with the subsequent library-amplification and sequencing primers for the Illumina sequencing platform.

treatment_protocol: Cells were arrested with α-factor (~5 nM ) and incubated for ~4 h at 23 °C then released in fresh YEPD containing 400 μg/mL BrdU, 200 μg/mL Pronase and 200 mM hydroxyurea. Harvested cells after 60min of incubation.

value: Non

value: fkh1{delta}dbf4-Zn*2 (H680C)

value: hydroxyurea


title: Lamin B1 ChIP human normal rep3

value: Lamin B1


title: B16-OVA, Isotype IgG + TBK1i, Replicate 1

value: Isotype IgG + TBK1i


title: 78-AO5_E2-ER-Rep2


title: Sample 39_fkh1∆dbf4-Zn*2_rep1

description: BrdU-IP sequencing


title: Lamin B1 ChIP human NAFLD Severe rep2


title: B16-OVA, Isotype IgG + Vehicle, Replicate 3

value: Isotype IgG + Vehicle


title: Sample 37_fkh1∆dbf4-Zn*1_rep1

description: BrdU-IP sequencing

value: fkh1{delta}dbf4-Zn*1 (C661A C664A)


title: 76-AO8_EDM-ER-Rep2


title: B16-OVA, aPD-1 + Vehicle, Replicate 4


title: B16-OVA, aPD-1 + Vehicle, Replicate 1


title: Dbf4_G1-rep2 (ChIP-seq)

value: alpha-factor

value: anti-FLAG M2 (Sigma F1804)


title: 72-AO8_E2-Input-Rep1

value: ER+ breast cancer cell line


title: Foxa2 ChIP human NAFLD Severe rep2


title: Foxa2 ChIP human normal rep2


title: B16-OVA, Isotype IgG + Vehicle, Replicate 2

value: melanoma subcutaneous tumor


title: 71-AO6_E2-Input-Rep1


title: 70-AO5_E2-Input-Rep1


title: Foxa2 ChIP human normal rep1


title: 75-AO6_EDM-ER-Rep2

value: ER (Millipore, #06-935)


title: Sample 18_fkh1∆dbf4-Zn*1_rep2

description: BrdU-IP sequencing

value: anti-BrdU


title: CD34+ cells from MDS patient #14, transduced with DDIT3 shRNA#2, differentiated for 7 days

city: Dublin

first: Marina

last: Ainciburu

state: Dublin

address: Foster Avenue

department: Bioinformatics

country: Ireland

institute: NIBRT

data_processing:
Samples were demultiplexed with Bcl2fastq (v2.20)
Reads were aligned to the human genome using STAR (v2.6)
Quantification was performed with the R package Rsubread (v1.32.4)
Subsequent analysis was carried out using the R/Bioconductor package DeSeq2
Genome_build: hg38
Supplementary_files_format_and_content: Raw counts matrix (genes x samples) as csv file

source_name: CD34+ differentiated ex vivo

extract_protocol:
FACS sorted infected cells were collected at the indicated times
3' RNA sequencing libraries were prepared using the MARS-seq protocol adapted for bulk RNA-seq, with minor modifications

value: Bone marrow

tag: condition

value: MDS cells, DDIT3 knockdown

tag: initial facs gating prior to cell culture

tag: plasmid used for trasduction of cells

value: pSIH1-H1-copGFP-DDIT3 shRNA#2

tag: time of ex vivo cell expansion

value: 2 days

tag: time of ex vivo erythroid differentiation

value: 7 days

tag: facs gating prior to rna-seq

value: GFP+


title: B16-OVA, Isotype IgG + Vehicle, Replicate 4

tag: tissue

value: CD45+ immune cells


title: Tumor CD8-IRF2cWT

source_name: MC38 tumor

value: MC38 tumor

value: MC38 tumor infiltrating CD8 T cells

value: IRF2 sufficient